From 889c86057cdf95a89320fe6336308c55014be5e6 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 9 Aug 2024 10:53:05 -0700 Subject: [PATCH 01/96] WIP --- web/templates/grdi/export.js | 131 +++++++++++++++++++++++++++++++++++ 1 file changed, 131 insertions(+) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 525925e6..521e0abe 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -104,4 +104,135 @@ export default { return outputMatrix; }, }, + + BioSample: { + fileType: 'xls', + status: 'published', + method: function (dh) { + // Create an export table with template's headers (2nd row) and remaining rows of data + const ExportHeaders = new Map([ + ['sample_name', []], // * + +WORK IN PROGRESS + +sample_title +bioproject_accession +*strain +isolate_name_alias +culture_collection +reference_material +*organism +*collected_by +*collection_date +cult_isol_date +*geo_loc_name +*isolation_source +*source_type +samp_collect_device +*purpose_of_sampling +project_name +ifsac_category +lat_lon +serotype +serovar +sequenced_by +description +host +host_sex +host_age +host_disease +host_subject_id +animal_env +host_tissue_sampled +host_body_product +host_variety +host_animal_breed +upstream_intervention +host_am +host_group_size +host_housing +food_origin +intended_consumer +spec_intended_cons +food_source +food_processing_method +food_preserv_proc +food_prod +label_claims +food_product_type +food_industry_code +food_industry_class +food_additive +food_contact_surf +food_contain_wrap +food_pack_medium +food_pack_integrity +food_quality_date +food_prod_synonym +facility_type +building_setting +coll_site_geo_feat +food_type_processed +location_in_facility +env_monitoring_zone +indoor_surf +indoor_surf_subpart +surf_material +material_condition +surface_orientation +surf_temp +biocide_used +animal_intrusion +env_broad_scale +env_local_scale +env_medium +plant_growth_med +plant_water_method +rel_location +soil_type +farm_water_source +fertilizer_admin +food_clean_proc +sanitizer_used_postharvest +farm_equip +extr_weather_event +mechanical_damage +] + + ); + + +EXAMPLE +environmental_siteXenv_local_scale = "Agricultural Field [ENVO:00000114], Alluvial fan [ENVO:00000314], Artificial wetland [ENVO:03501406], Breeding ground [ENVO:03501441], Creek [ENVO:03501405], Farm [ENVO:00000078], Beef farm [ENVO:03501443], Breeder farm [ENVO:03501384], Dairy farm [ENVO:03501416], Feedlot [ENVO:01000627], Beef cattle feedlot [ENVO:03501444], Fish farm [ENVO:00000294], Research farm [ENVO:03501417], Freshwater environment [ENVO:01000306], Hatchery [ENVO:01001873], Poultry hatchery [ENVO:01001874], Lake [ENVO:00000020], Manure lagoon (Anaerobic lagoon) [ENVO:03501423], Manure pit [ENVO:01001872], Marine environment [ENVO:01000320], Benthic zone [ENVO:03501440], Pelagic zone [ENVO:00000208], Park [ENVO:00000562], Pond [ENVO:00000033], Reservoir [ENVO:00000025], Irrigation reservoir [ENVO:00000450], River [ENVO:00000022], Roost (bird) [ENVO:03501439], Rural area [ENVO:01000772], Slough [ENVO:03501438], Stream [ENVO:00000023], Tributary [ENVO:00000495], Water surface [ENVO:01001191], Woodland area [ENVO:00000109]".split(",") + + + const sourceFields = dh.getFields(dh.table); + const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + // Fills in the above mapping (or just set manually above) + dh.getHeaderMap(ExportHeaders, sourceFields, 'BIOSAMPLE'); + + // Copy headers to 1st row of new export table + const outputMatrix = [[...ExportHeaders.keys()]]; + + for (const inputRow of dh.getTrimmedData(dh.hot)) { + const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { + // Otherwise apply source (many to one) to target field transform: + const value = dh.getMappedField( + headerName, + inputRow, + sources, + sourceFields, + sourceFieldNameMap, + ':', + 'BIOSAMPLE' + ); + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + + return outputMatrix; + } + } }; From 6adba6373f930e1d77f5b98d34b1f1cccafa09f2 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 12 Aug 2024 13:56:05 -0700 Subject: [PATCH 02/96] WIP --- web/templates/grdi/export.js | 190 +- web/templates/grdi/schema.json | 17981 +++++++++++++++++++++++--- web/templates/grdi/schema.yaml | 2576 ++-- web/templates/grdi/schema_enums.tsv | 3039 ++--- web/templates/grdi/schema_slots.tsv | 1585 ++- 5 files changed, 20168 insertions(+), 5203 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 521e0abe..3b9363e6 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -73,6 +73,7 @@ export default { // ['gene_name_2', []], // ['diagnostic_PCR_CT_value_2', []], // ['description',[]], + // TODO there are additional fields now; what order? ]); const sourceFields = dh.getFields(dh.table); @@ -105,111 +106,106 @@ export default { }, }, - BioSample: { + // TODO I see other refs to NCBI_BioSample in project; good name? + NCBI_BioSample_Enterics: { fileType: 'xls', status: 'published', method: function (dh) { - // Create an export table with template's headers (2nd row) and remaining rows of data const ExportHeaders = new Map([ - ['sample_name', []], // * - -WORK IN PROGRESS - -sample_title -bioproject_accession -*strain -isolate_name_alias -culture_collection -reference_material -*organism -*collected_by -*collection_date -cult_isol_date -*geo_loc_name -*isolation_source -*source_type -samp_collect_device -*purpose_of_sampling -project_name -ifsac_category -lat_lon -serotype -serovar -sequenced_by -description -host -host_sex -host_age -host_disease -host_subject_id -animal_env -host_tissue_sampled -host_body_product -host_variety -host_animal_breed -upstream_intervention -host_am -host_group_size -host_housing -food_origin -intended_consumer -spec_intended_cons -food_source -food_processing_method -food_preserv_proc -food_prod -label_claims -food_product_type -food_industry_code -food_industry_class -food_additive -food_contact_surf -food_contain_wrap -food_pack_medium -food_pack_integrity -food_quality_date -food_prod_synonym -facility_type -building_setting -coll_site_geo_feat -food_type_processed -location_in_facility -env_monitoring_zone -indoor_surf -indoor_surf_subpart -surf_material -material_condition -surface_orientation -surf_temp -biocide_used -animal_intrusion -env_broad_scale -env_local_scale -env_medium -plant_growth_med -plant_water_method -rel_location -soil_type -farm_water_source -fertilizer_admin -food_clean_proc -sanitizer_used_postharvest -farm_equip -extr_weather_event -mechanical_damage -] - - ); - - -EXAMPLE -environmental_siteXenv_local_scale = "Agricultural Field [ENVO:00000114], Alluvial fan [ENVO:00000314], Artificial wetland [ENVO:03501406], Breeding ground [ENVO:03501441], Creek [ENVO:03501405], Farm [ENVO:00000078], Beef farm [ENVO:03501443], Breeder farm [ENVO:03501384], Dairy farm [ENVO:03501416], Feedlot [ENVO:01000627], Beef cattle feedlot [ENVO:03501444], Fish farm [ENVO:00000294], Research farm [ENVO:03501417], Freshwater environment [ENVO:01000306], Hatchery [ENVO:01001873], Poultry hatchery [ENVO:01001874], Lake [ENVO:00000020], Manure lagoon (Anaerobic lagoon) [ENVO:03501423], Manure pit [ENVO:01001872], Marine environment [ENVO:01000320], Benthic zone [ENVO:03501440], Pelagic zone [ENVO:00000208], Park [ENVO:00000562], Pond [ENVO:00000033], Reservoir [ENVO:00000025], Irrigation reservoir [ENVO:00000450], River [ENVO:00000022], Roost (bird) [ENVO:03501439], Rural area [ENVO:01000772], Slough [ENVO:03501438], Stream [ENVO:00000023], Tributary [ENVO:00000495], Water surface [ENVO:01001191], Woodland area [ENVO:00000109]".split(",") + ['*sample_name', []], + ['sample_title', []], + ['bioproject_accession', []], + ['*strain', []], + ['isolate_name_alias', []], + ['culture_collection', []], + ['reference_material', []], + ['*organism', []], + ['*collected_by', []], + ['*collection_date', []], + ['cult_isol_date', []], + ['*geo_loc_name', []], + ['*isolation_source', []], + ['*source_type', []], + ['samp_collect_device', []], + ['*purpose_of_sampling', []], + ['project_name', []], + ['ifsac_category', []], + ['lat_lon', []], + ['serotype', []], + ['serovar', []], + ['sequenced_by', []], + ['description', []], + ['host', []], + ['host_sex', []], + ['host_age', []], + ['host_disease', []], + ['host_subject_id', []], + ['animal_env', []], + ['host_tissue_sampled', []], + ['host_body_product', []], + ['host_variety', []], + ['host_animal_breed', []], + ['upstream_intervention', []], + ['host_am', []], + ['host_group_size', []], + ['host_housing', []], + ['food_origin', []], + ['intended_consumer', []], + ['spec_intended_cons', []], + ['food_source', []], + ['food_processing_method', []], + ['food_preserv_proc', []], + ['food_prod', []], + ['label_claims', []], + ['food_product_type', []], + ['food_industry_code', []], + ['food_industry_class', []], + ['food_additive', []], + ['food_contact_surf', []], + ['food_contain_wrap', []], + ['food_pack_medium', []], + ['food_pack_integrity', []], + ['food_quality_date', []], + ['food_prod_synonym', []], + ['facility_type', []], + ['building_setting', []], + ['coll_site_geo_feat', []], + ['food_type_processed', []], + ['location_in_facility', []], + ['env_monitoring_zone', []], + ['indoor_surf', []], + ['indoor_surf_subpart', []], + ['surf_material', []], + ['material_condition', []], + ['surface_orientation', []], + ['surf_temp', []], + ['biocide_used', []], + ['animal_intrusion', []], + ['env_broad_scale', []], + ['env_local_scale', []], + ['env_medium', []], + ['plant_growth_med', []], + ['plant_water_method', []], + ['rel_location', []], + ['soil_type', []], + ['farm_water_source', []], + ['fertilizer_admin', []], + ['food_clean_proc', []], + ['sanitizer_used_postharvest', []], + ['farm_equip', []], + ['extr_weather_event', []], + ['mechanical_damage', []] + ]); +// +// +// EXAMPLE +// environmental_siteXenv_local_scale = "Agricultural Field [ENVO:00000114], Alluvial fan [ENVO:00000314], Artificial wetland [ENVO:03501406], Breeding ground [ENVO:03501441], Creek [ENVO:03501405], Farm [ENVO:00000078], Beef farm [ENVO:03501443], Breeder farm [ENVO:03501384], Dairy farm [ENVO:03501416], Feedlot [ENVO:01000627], Beef cattle feedlot [ENVO:03501444], Fish farm [ENVO:00000294], Research farm [ENVO:03501417], Freshwater environment [ENVO:01000306], Hatchery [ENVO:01001873], Poultry hatchery [ENVO:01001874], Lake [ENVO:00000020], Manure lagoon (Anaerobic lagoon) [ENVO:03501423], Manure pit [ENVO:01001872], Marine environment [ENVO:01000320], Benthic zone [ENVO:03501440], Pelagic zone [ENVO:00000208], Park [ENVO:00000562], Pond [ENVO:00000033], Reservoir [ENVO:00000025], Irrigation reservoir [ENVO:00000450], River [ENVO:00000022], Roost (bird) [ENVO:03501439], Rural area [ENVO:01000772], Slough [ENVO:03501438], Stream [ENVO:00000023], Tributary [ENVO:00000495], Water surface [ENVO:01001191], Woodland area [ENVO:00000109]".split(",") const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); // Fills in the above mapping (or just set manually above) - dh.getHeaderMap(ExportHeaders, sourceFields, 'BIOSAMPLE'); + dh.getHeaderMap(ExportHeaders, sourceFields, 'NCBI_BIOSAMPLE_Enterics'); // Copy headers to 1st row of new export table const outputMatrix = [[...ExportHeaders.keys()]]; @@ -225,7 +221,7 @@ environmental_siteXenv_local_scale = "Agricultural Field [ENVO:00000114], Alluvi sourceFields, sourceFieldNameMap, ':', - 'BIOSAMPLE' + 'NCBI_BIOSAMPLE_Enterics' ); outputRow.push(value); } diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index c5582c71..0ae25eff 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -296,8 +296,8 @@ } }, "enums": { - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", "description": "", "title": "null value menu", "from_schema": "https://example.com/GRDI", @@ -306,7 +306,10 @@ "text": "Not Applicable [GENEPIO:0001619]" }, "Missing [GENEPIO:0001618]": { - "text": "Missing [GENEPIO:0001618]" + "text": "Missing [GENEPIO:0001618]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:missing" + ] }, "Not Collected [GENEPIO:0001620]": { "text": "Not Collected [GENEPIO:0001620]" @@ -319,8 +322,8 @@ } } }, - "sample_collected_by menu": { - "name": "sample_collected_by menu", + "SampleCollectedByMenu": { + "name": "SampleCollectedByMenu", "description": "", "title": "sample_collected_by menu", "from_schema": "https://example.com/GRDI", @@ -348,8 +351,8 @@ } } }, - "purpose_of_sampling menu": { - "name": "purpose_of_sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", "description": "", "title": "purpose_of_sampling menu", "from_schema": "https://example.com/GRDI", @@ -383,8 +386,8 @@ } } }, - "presampling_activity menu": { - "name": "presampling_activity menu", + "PresamplingActivityMenu": { + "name": "PresamplingActivityMenu", "description": "", "title": "presampling_activity menu", "from_schema": "https://example.com/GRDI", @@ -437,8 +440,8 @@ } } }, - "experimental_specimen_role_type menu": { - "name": "experimental_specimen_role_type menu", + "ExperimentalSpecimenRoleTypeMenu": { + "name": "ExperimentalSpecimenRoleTypeMenu", "description": "", "title": "experimental_specimen_role_type menu", "from_schema": "https://example.com/GRDI", @@ -457,8 +460,8 @@ } } }, - "specimen_processing menu": { - "name": "specimen_processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", "description": "", "title": "specimen_processing menu", "from_schema": "https://example.com/GRDI", @@ -477,8 +480,8 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", "description": "", "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/GRDI", @@ -1298,8 +1301,8 @@ } } }, - "geo_loc_name (state/province/region) menu": { - "name": "geo_loc_name (state/province/region) menu", + "GeoLocNameStateProvinceRegionMenu": { + "name": "GeoLocNameStateProvinceRegionMenu", "description": "", "title": "geo_loc_name (state/province/region) menu", "from_schema": "https://example.com/GRDI", @@ -1373,8 +1376,8 @@ } } }, - "sample_collection_date_precision menu": { - "name": "sample_collection_date_precision menu", + "SampleCollectionDatePrecisionMenu": { + "name": "SampleCollectionDatePrecisionMenu", "description": "", "title": "sample_collection_date_precision menu", "from_schema": "https://example.com/GRDI", @@ -1390,8 +1393,8 @@ } } }, - "environmental_site menu": { - "name": "environmental_site menu", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", "description": "", "title": "environmental_site menu", "from_schema": "https://example.com/GRDI", @@ -1636,8 +1639,8 @@ } } }, - "water_depth_units menu": { - "name": "water_depth_units menu", + "WaterDepthUnitsMenu": { + "name": "WaterDepthUnitsMenu", "description": "", "title": "water_depth_units menu", "from_schema": "https://example.com/GRDI", @@ -1659,8 +1662,8 @@ } } }, - "sediment_depth_units menu": { - "name": "sediment_depth_units menu", + "SedimentDepthUnitsMenu": { + "name": "SedimentDepthUnitsMenu", "description": "", "title": "sediment_depth_units menu", "from_schema": "https://example.com/GRDI", @@ -1682,8 +1685,8 @@ } } }, - "air_temperature_units menu": { - "name": "air_temperature_units menu", + "AirTemperatureUnitsMenu": { + "name": "AirTemperatureUnitsMenu", "description": "", "title": "air_temperature_units menu", "from_schema": "https://example.com/GRDI", @@ -1696,8 +1699,8 @@ } } }, - "water_temperature_units menu": { - "name": "water_temperature_units menu", + "WaterTemperatureUnitsMenu": { + "name": "WaterTemperatureUnitsMenu", "description": "", "title": "water_temperature_units menu", "from_schema": "https://example.com/GRDI", @@ -1710,8 +1713,8 @@ } } }, - "available_data_types menu": { - "name": "available_data_types menu", + "AvailableDataTypesMenu": { + "name": "AvailableDataTypesMenu", "description": "", "title": "available_data_types menu", "from_schema": "https://example.com/GRDI", @@ -1907,8 +1910,8 @@ } } }, - "weather_type menu": { - "name": "weather_type menu", + "WeatherTypeMenu": { + "name": "WeatherTypeMenu", "description": "", "title": "weather_type menu", "from_schema": "https://example.com/GRDI", @@ -1940,8 +1943,8 @@ } } }, - "animal_or_plant_population menu": { - "name": "animal_or_plant_population menu", + "AnimalOrPlantPopulationMenu": { + "name": "AnimalOrPlantPopulationMenu", "description": "", "title": "animal_or_plant_population menu", "from_schema": "https://example.com/GRDI", @@ -2012,8 +2015,8 @@ } } }, - "environmental_material menu": { - "name": "environmental_material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", "description": "", "title": "environmental_material menu", "from_schema": "https://example.com/GRDI", @@ -2229,8 +2232,8 @@ } } }, - "anatomical_material menu": { - "name": "anatomical_material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", "description": "", "title": "anatomical_material menu", "from_schema": "https://example.com/GRDI", @@ -2258,8 +2261,8 @@ } } }, - "body_product menu": { - "name": "body_product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", "description": "", "title": "body_product menu", "from_schema": "https://example.com/GRDI", @@ -2310,8 +2313,8 @@ } } }, - "anatomical_part menu": { - "name": "anatomical_part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", "description": "", "title": "anatomical_part menu", "from_schema": "https://example.com/GRDI", @@ -2643,8 +2646,8 @@ } } }, - "anatomical_region menu": { - "name": "anatomical_region menu", + "AnatomicalRegionMenu": { + "name": "AnatomicalRegionMenu", "description": "", "title": "anatomical_region menu", "from_schema": "https://example.com/GRDI", @@ -2660,8 +2663,8 @@ } } }, - "food_product menu": { - "name": "food_product menu", + "PriorSarsCov2InfectionMenu": { + "name": "PriorSarsCov2InfectionMenu", "description": "", "title": "food_product menu", "from_schema": "https://example.com/GRDI", @@ -3131,8 +3134,8 @@ "text": "Mussel [FOODON:03411223]", "is_a": "Shellfish [FOODON:03411433]" }, - "Oyster FOODON:03411224]": { - "text": "Oyster FOODON:03411224]", + "Oyster [FOODON:03411224]": { + "text": "Oyster [FOODON:03411224]", "is_a": "Shellfish [FOODON:03411433]" }, "Shrimp [FOODON:03301673]": { @@ -3572,8 +3575,8 @@ } } }, - "food_product_properties menu": { - "name": "food_product_properties menu", + "FoodProductPropertiesMenu": { + "name": "FoodProductPropertiesMenu", "description": "", "title": "food_product_properties menu", "from_schema": "https://example.com/GRDI", @@ -3648,16 +3651,13 @@ "Meat (with skin) [FOODON:02010111]": { "text": "Meat (with skin) [FOODON:02010111]" }, - "Ready-to-eat (RTE) [FOODON:03316636]": { - "text": "Ready-to-eat (RTE) [FOODON:03316636]" - }, "Soft [PATO:0000387]": { "text": "Soft [PATO:0000387]" } } }, - "label_claim menu": { - "name": "label_claim menu", + "LabelClaimMenu": { + "name": "LabelClaimMenu", "description": "", "title": "label_claim menu", "from_schema": "https://example.com/GRDI", @@ -3676,11 +3676,14 @@ }, "Pasture raised [FOODON:03601065]": { "text": "Pasture raised [FOODON:03601065]" + }, + "Ready-to-eat (RTE) [FOODON:03316636]": { + "text": "Ready-to-eat (RTE) [FOODON:03316636]" } } }, - "animal_source_of_food menu": { - "name": "animal_source_of_food menu", + "AnimalSourceOfFoodMenu": { + "name": "AnimalSourceOfFoodMenu", "description": "", "title": "animal_source_of_food menu", "from_schema": "https://example.com/GRDI", @@ -3729,8 +3732,8 @@ } } }, - "food_product_production_stream menu": { - "name": "food_product_production_stream menu", + "FoodProductProductionStreamMenu": { + "name": "FoodProductProductionStreamMenu", "description": "", "title": "food_product_production_stream menu", "from_schema": "https://example.com/GRDI", @@ -3762,8 +3765,8 @@ } } }, - "collection_device menu": { - "name": "collection_device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", "description": "", "title": "collection_device menu", "from_schema": "https://example.com/GRDI", @@ -3842,8 +3845,8 @@ } } }, - "collection_method menu": { - "name": "collection_method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", "description": "", "title": "collection_method menu", "from_schema": "https://example.com/GRDI", @@ -3902,8 +3905,8 @@ } } }, - "sample_volume_measurement_unit menu": { - "name": "sample_volume_measurement_unit menu", + "SampleVolumeMeasurementUnitMenu": { + "name": "SampleVolumeMeasurementUnitMenu", "description": "", "title": "sample_volume_measurement_unit menu", "from_schema": "https://example.com/GRDI", @@ -3919,8 +3922,8 @@ } } }, - "residual_sample_status menu": { - "name": "residual_sample_status menu", + "ResidualSampleStatusMenu": { + "name": "ResidualSampleStatusMenu", "description": "", "title": "residual_sample_status menu", "from_schema": "https://example.com/GRDI", @@ -3936,8 +3939,8 @@ } } }, - "sample_storage_duration_unit menu": { - "name": "sample_storage_duration_unit menu", + "SampleStorageDurationUnitMenu": { + "name": "SampleStorageDurationUnitMenu", "description": "", "title": "sample_storage_duration_unit menu", "from_schema": "https://example.com/GRDI", @@ -3965,8 +3968,8 @@ } } }, - "nucelic_acid_storage_duration_unit menu": { - "name": "nucelic_acid_storage_duration_unit menu", + "NucelicAcidStorageDurationUnitMenu": { + "name": "NucelicAcidStorageDurationUnitMenu", "description": "", "title": "nucelic_acid_storage_duration_unit menu", "from_schema": "https://example.com/GRDI", @@ -3994,8 +3997,8 @@ } } }, - "food_packaging menu": { - "name": "food_packaging menu", + "FoodPackagingMenu": { + "name": "FoodPackagingMenu", "description": "", "title": "food_packaging menu", "from_schema": "https://example.com/GRDI", @@ -4036,8 +4039,8 @@ } } }, - "host (common name) menu": { - "name": "host (common name) menu", + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", "description": "", "title": "host (common name) menu", "from_schema": "https://example.com/GRDI", @@ -4168,8 +4171,8 @@ } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", "description": "", "title": "host (scientific name) menu", "from_schema": "https://example.com/GRDI", @@ -4239,8 +4242,8 @@ } } }, - "host (food production name) menu": { - "name": "host (food production name) menu", + "HostFoodProductionNameMenu": { + "name": "HostFoodProductionNameMenu", "description": "", "title": "host (food production name) menu", "from_schema": "https://example.com/GRDI", @@ -4440,8 +4443,8 @@ } } }, - "host_age_bin menu": { - "name": "host_age_bin menu", + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", "description": "", "title": "host_age_bin menu", "from_schema": "https://example.com/GRDI", @@ -4466,8 +4469,8 @@ } } }, - "isolated_by menu": { - "name": "isolated_by menu", + "IsolatedByMenu": { + "name": "IsolatedByMenu", "description": "", "title": "isolated_by menu", "from_schema": "https://example.com/GRDI", @@ -4492,8 +4495,8 @@ } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", "description": "", "title": "organism menu", "from_schema": "https://example.com/GRDI", @@ -4969,8 +4972,8 @@ } } }, - "taxonomic_identification_process menu": { - "name": "taxonomic_identification_process menu", + "TaxonomicIdentificationProcessMenu": { + "name": "TaxonomicIdentificationProcessMenu", "description": "", "title": "taxonomic_identification_process menu", "from_schema": "https://example.com/GRDI", @@ -4992,8 +4995,8 @@ } } }, - "sequenced_by menu": { - "name": "sequenced_by menu", + "SequencedByMenu": { + "name": "SequencedByMenu", "description": "", "title": "sequenced_by menu", "from_schema": "https://example.com/GRDI", @@ -5021,8 +5024,8 @@ } } }, - "purpose_of_sequencing menu": { - "name": "purpose_of_sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", "description": "", "title": "purpose_of_sequencing menu", "from_schema": "https://example.com/GRDI", @@ -5060,8 +5063,8 @@ } } }, - "sequencing_platform menu": { - "name": "sequencing_platform menu", + "SequencingPlatformMenu": { + "name": "SequencingPlatformMenu", "description": "", "title": "sequencing_platform menu", "from_schema": "https://example.com/GRDI", @@ -5086,8 +5089,8 @@ } } }, - "sequencing_instrument menu": { - "name": "sequencing_instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", "description": "", "title": "sequencing_instrument menu", "from_schema": "https://example.com/GRDI", @@ -5280,8 +5283,8 @@ } } }, - "sequencing_assay_type menu": { - "name": "sequencing_assay_type menu", + "SequencingAssayTypeMenu": { + "name": "SequencingAssayTypeMenu", "description": "", "title": "sequencing_assay_type menu", "from_schema": "https://example.com/GRDI", @@ -5305,8 +5308,8 @@ } } }, - "genomic_target_enrichment_method menu": { - "name": "genomic_target_enrichment_method menu", + "GenomicTargetEnrichmentMethodMenu": { + "name": "GenomicTargetEnrichmentMethodMenu", "description": "", "title": "genomic_target_enrichment_method menu", "from_schema": "https://example.com/GRDI", @@ -5319,8 +5322,8 @@ } } }, - "sequence_submitted_by menu": { - "name": "sequence_submitted_by menu", + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", "description": "", "title": "sequence_submitted_by menu", "from_schema": "https://example.com/GRDI", @@ -5348,8 +5351,8 @@ } } }, - "quality_control_determination menu": { - "name": "quality_control_determination menu", + "QualityControlDeterminationMenu": { + "name": "QualityControlDeterminationMenu", "description": "", "title": "quality_control_determination menu", "from_schema": "https://example.com/GRDI", @@ -5374,8 +5377,8 @@ } } }, - "quality _control_issues menu": { - "name": "quality _control_issues menu", + "QualityControlIssuesMenu": { + "name": "QualityControlIssuesMenu", "description": "", "title": "quality _control_issues menu", "from_schema": "https://example.com/GRDI", @@ -5406,8 +5409,8 @@ } } }, - "attribute_package menu": { - "name": "attribute_package menu", + "AttributePackageMenu": { + "name": "AttributePackageMenu", "description": "", "title": "attribute_package menu", "from_schema": "https://example.com/GRDI", @@ -5417,15 +5420,7 @@ }, "Pathogen.env [GENEPIO:0100581]": { "text": "Pathogen.env [GENEPIO:0100581]" - } - } - }, - "experimental_intervention menu": { - "name": "experimental_intervention menu", - "description": "", - "title": "experimental_intervention menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { + }, "Addition of substances to food/water [GENEPIO:0100536]": { "text": "Addition of substances to food/water [GENEPIO:0100536]" }, @@ -5464,8 +5459,8 @@ } } }, - "AMR_testing_by menu": { - "name": "AMR_testing_by menu", + "AMRTestingByMenu": { + "name": "AMRTestingByMenu", "description": "", "title": "AMR_testing_by menu", "from_schema": "https://example.com/GRDI", @@ -5490,8 +5485,8 @@ } } }, - "antimicrobial_phenotype menu": { - "name": "antimicrobial_phenotype menu", + "AntimicrobialPhenotypeMenu": { + "name": "AntimicrobialPhenotypeMenu", "description": "", "title": "antimicrobial_phenotype menu", "from_schema": "https://example.com/GRDI", @@ -5521,8 +5516,8 @@ } } }, - "antimicrobial_measurement_units menu": { - "name": "antimicrobial_measurement_units menu", + "AntimicrobialMeasurementUnitsMenu": { + "name": "AntimicrobialMeasurementUnitsMenu", "description": "", "title": "antimicrobial_measurement_units menu", "from_schema": "https://example.com/GRDI", @@ -5538,8 +5533,8 @@ } } }, - "antimicrobial_measurement_sign menu": { - "name": "antimicrobial_measurement_sign menu", + "AntimicrobialMeasurementSignMenu": { + "name": "AntimicrobialMeasurementSignMenu", "description": "", "title": "antimicrobial_measurement_sign menu", "from_schema": "https://example.com/GRDI", @@ -5561,29 +5556,35 @@ } } }, - "antimicrobial_laboratory_typing_method menu": { - "name": "antimicrobial_laboratory_typing_method menu", + "AntimicrobialLaboratoryTypingMethodMenu": { + "name": "AntimicrobialLaboratoryTypingMethodMenu", "description": "", "title": "antimicrobial_laboratory_typing_method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "Agar diffusion [NCIT:85595]": { - "text": "Agar diffusion [NCIT:85595]" + "text": "Agar diffusion [NCIT:85595]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:disk%20diffusion" + ] }, "Antimicrobial gradient (E-test) [NCIT:85596]": { "text": "Antimicrobial gradient (E-test) [NCIT:85596]", "is_a": "Agar diffusion [NCIT:85595]" }, "Agar dilution [ARO:3004411]": { - "text": "Agar dilution [ARO:3004411]" + "text": "Agar dilution [ARO:3004411]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:agar%20dilution" + ] }, "Broth dilution [ARO:3004397]": { "text": "Broth dilution [ARO:3004397]" } } }, - "antimicrobial_laboratory_typing_platform menu": { - "name": "antimicrobial_laboratory_typing_platform menu", + "AntimicrobialLaboratoryTypingPlatformMenu": { + "name": "AntimicrobialLaboratoryTypingPlatformMenu", "description": "", "title": "antimicrobial_laboratory_typing_platform menu", "from_schema": "https://example.com/GRDI", @@ -5592,81 +5593,138 @@ "text": "BIOMIC Microbiology System [ARO:3007569]" }, "Microscan [ARO:3004400]": { - "text": "Microscan [ARO:3004400]" + "text": "Microscan [ARO:3004400]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Microscan" + ] }, "Phoenix [ARO:3004401]": { - "text": "Phoenix [ARO:3004401]" + "text": "Phoenix [ARO:3004401]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Phoenix" + ] }, "Sensititre [ARO:3004402]": { - "text": "Sensititre [ARO:3004402]" + "text": "Sensititre [ARO:3004402]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Sensititre" + ] }, "Vitek System [ARO:3004403]": { - "text": "Vitek System [ARO:3004403]" + "text": "Vitek System [ARO:3004403]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Vitek" + ] } } }, - "antimicrobial_vendor_name menu": { - "name": "antimicrobial_vendor_name menu", + "AntimicrobialVendorNameMenu": { + "name": "AntimicrobialVendorNameMenu", "description": "", "title": "antimicrobial_vendor_name menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "Becton Dickinson [ARO:3004405]": { - "text": "Becton Dickinson [ARO:3004405]" + "text": "Becton Dickinson [ARO:3004405]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Becton%20Dickinson" + ] }, "bioMérieux [ARO:3004406]": { - "text": "bioMérieux [ARO:3004406]" + "text": "bioMérieux [ARO:3004406]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Biom%C3%A9rieux" + ] }, "Omron [ARO:3004408]": { "text": "Omron [ARO:3004408]" }, "Siemens [ARO:3004407]": { - "text": "Siemens [ARO:3004407]" + "text": "Siemens [ARO:3004407]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Siemens" + ] }, "Trek [ARO:3004409]": { - "text": "Trek [ARO:3004409]" + "text": "Trek [ARO:3004409]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Trek" + ] } } }, - "antimicrobial_testing_standard menu": { - "name": "antimicrobial_testing_standard menu", + "AntimicrobialTestingStandardMenu": { + "name": "AntimicrobialTestingStandardMenu", "description": "", "title": "antimicrobial_testing_standard menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]": { - "text": "British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]" + "text": "British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:BSAC" + ] }, "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]": { - "text": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + "text": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:CLSI" + ] }, "Deutsches Institut für Normung (DIN) [ARO:3004367]": { - "text": "Deutsches Institut für Normung (DIN) [ARO:3004367]" + "text": "Deutsches Institut für Normung (DIN) [ARO:3004367]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:DIN" + ] }, "European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]": { - "text": "European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]" + "text": "European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:EUCAST" + ] }, "National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]": { - "text": "National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]" + "text": "National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:NARMS" + ] }, "National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]": { - "text": "National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]" + "text": "National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:NCCLS" + ] }, "Société Française de Microbiologie (SFM) [ARO:3004369]": { - "text": "Société Française de Microbiologie (SFM) [ARO:3004369]" + "text": "Société Française de Microbiologie (SFM) [ARO:3004369]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:SFM" + ] }, "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]": { - "text": "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]" + "text": "Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:SIR" + ] }, "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]": { - "text": "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]" + "text": "Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:WRG" + ] } } + }, + "AntimicrobialResistanceTestDrugMenu": { + "name": "AntimicrobialResistanceTestDrugMenu", + "description": "", + "title": "Antimicrobial Resistance Test Drug Menu", + "from_schema": "https://example.com/GRDI" } }, "slots": { - "sample_collector_sample_ID": { - "name": "sample_collector_sample_ID", + "sample_collector_sample_id": { + "name": "sample_collector_sample_id", "description": "The user-defined name for the sample.", "title": "sample_collector_sample_ID", "comments": [ @@ -5679,9 +5737,14 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:sample_name" + "BIOSAMPLE:sample_name", + "NCBI_BIOSAMPLE_Enterics:%2Asample_name", + "NCBI_ANTIBIOGRAM:%2Asample_name" ], "slot_uri": "GENEPIO:0001123", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -5692,12 +5755,12 @@ } ] }, - "alternative_sample_ID": { - "name": "alternative_sample_ID", + "alternative_sample_id": { + "name": "alternative_sample_id", "description": "An alternative sample_ID assigned to the sample by another organization.", "title": "alternative_sample_ID", "comments": [ - "\"Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.\"" + "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { @@ -5709,6 +5772,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100427", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "required": true }, @@ -5726,9 +5792,13 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:collected_by" + "BIOSAMPLE:collected_by", + "NCBI_BIOSAMPLE_Enterics:%2Acollected_by" ], "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -5753,6 +5823,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100428", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_collection_project_name": { @@ -5768,7 +5841,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:project_name" + ], "slot_uri": "GENEPIO:0100429", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_plan_name": { @@ -5785,11 +5864,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100430", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sample_plan_ID": { - "name": "sample_plan_ID", + "sample_plan_id": { + "name": "sample_plan_id", "description": "The identifier of the study design for a surveillance project.", "title": "sample_plan_ID", "comments": [ @@ -5802,6 +5884,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100431", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -5819,6 +5904,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100432", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_collector_contact_email": { @@ -5835,6 +5923,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -5859,9 +5950,13 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:purpose_of_sampling" + "BIOSAMPLE:purpose_of_sampling", + "NCBI_BIOSAMPLE_Enterics:%2Apurpose_of_sampling" ], "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -5885,7 +5980,14 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_am", + "NCBI_BIOSAMPLE_Enterics:fertilizer_admin" + ], "slot_uri": "GENEPIO:0100433", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "presampling_activity menu" @@ -5909,6 +6011,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100434", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "experimental_protocol_field": { @@ -5925,6 +6030,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101029", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "experimental_specimen_role_type": { @@ -5941,6 +6049,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100921", + "domain_of": [ + "GRDI" + ], "range": "experimental_specimen_role_type menu" }, "specimen_processing": { @@ -5957,6 +6068,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100435", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "specimen_processing menu" @@ -5966,8 +6080,8 @@ } ] }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", "title": "nucleic acid extraction method", "comments": [ @@ -5980,10 +6094,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100939", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "description": "The kit used to extract genomic material from a sample", "title": "nucleic acid extraction kit", "comments": [ @@ -5996,10 +6113,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100772", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo_loc_name (country)", "comments": [ @@ -6013,9 +6133,13 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:geo_loc_name", - "BIOSAMPLE:geo_loc_name%20%28country%29" + "BIOSAMPLE:geo_loc_name%20%28country%29", + "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" ], "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -6026,8 +6150,8 @@ } ] }, - "geo_loc_name (state/province/region)": { - "name": "geo_loc_name (state/province/region)", + "geo_loc_name_state_province_region": { + "name": "geo_loc_name_state_province_region", "description": "The state/province/territory of origin of the sample.", "title": "geo_loc_name (state/province/region)", "comments": [ @@ -6041,9 +6165,13 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:geo_loc_name", - "BIOSAMPLE:geo_loc_name%20%28state/province/region%29" + "BIOSAMPLE:geo_loc_name%20%28state/province/region%29", + "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" ], "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -6054,8 +6182,8 @@ } ] }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name (site)", "comments": [ @@ -6072,10 +6200,13 @@ "BIOSAMPLE:geo_loc_name%20%28site%29" ], "slot_uri": "GENEPIO:0100436", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "food_product_origin_geo_loc_name (country)": { - "name": "food_product_origin_geo_loc_name (country)", + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", "description": "The country of origin of a food product.", "title": "food_product_origin_geo_loc_name (country)", "comments": [ @@ -6087,7 +6218,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_origin" + ], "slot_uri": "GENEPIO:0100437", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "geo_loc_name (country) menu" @@ -6097,8 +6234,8 @@ } ] }, - "host_origin_geo_loc_name (country)": { - "name": "host_origin_geo_loc_name (country)", + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", "description": "The country of origin of the host.", "title": "host_origin_geo_loc_name (country)", "comments": [ @@ -6111,6 +6248,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100438", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "geo_loc_name (country) menu" @@ -6120,8 +6260,8 @@ } ] }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", "comments": [ @@ -6133,11 +6273,17 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:lat_lon" + ], "slot_uri": "GENEPIO:0100309", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", "comments": [ @@ -6149,7 +6295,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:lat_lon" + ], "slot_uri": "GENEPIO:0100310", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_collection_date": { @@ -6166,9 +6318,13 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:sample%20collection%20date" + "BIOSAMPLE:sample%20collection%20date", + "NCBI_BIOSAMPLE_Enterics:%2Acollection_date" ], "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "GRDI" + ], "range": "date", "required": true }, @@ -6186,6 +6342,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001177", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -6210,6 +6369,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "GRDI" + ], "range": "date" }, "original_sample_description": { @@ -6226,6 +6388,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100439", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "environmental_site": { @@ -6243,11 +6408,19 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:environmental_site" + "BIOSAMPLE:environmental_site", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:animal_env", + "NCBI_BIOSAMPLE_Enterics:host_housing", + "NCBI_BIOSAMPLE_Enterics:env_local_scale", + "NCBI_BIOSAMPLE_Enterics:facility_type" ], "slot_uri": "GENEPIO:0001232", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "environmental_site menu" @@ -6281,11 +6454,15 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:environmental_material" + "BIOSAMPLE:environmental_material", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" ], "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "environmental_material menu" @@ -6312,8 +6489,11 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101197", - "multivalued": true, - "range": "WhitespaceMinimizedString" + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString", + "multivalued": true }, "animal_or_plant_population": { "name": "animal_or_plant_population", @@ -6329,8 +6509,11 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100443", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "animal_or_plant_population menu" @@ -6358,11 +6541,16 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:anatomical_material" + "BIOSAMPLE:anatomical_material", + "NCBI_BIOSAMPLE_Enterics:host_tissue_sampled", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" ], "slot_uri": "GENEPIO:0001211", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "anatomical_material menu" @@ -6390,11 +6578,16 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:body_product" + "BIOSAMPLE:body_product", + "NCBI_BIOSAMPLE_Enterics:host_body_product", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" ], "slot_uri": "GENEPIO:0001216", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "body_product menu" @@ -6419,11 +6612,15 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:anatomical_part" + "BIOSAMPLE:anatomical_part", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" ], "slot_uri": "GENEPIO:0001214", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "anatomical_part menu" @@ -6447,8 +6644,11 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100700", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "anatomical_region menu" @@ -6482,8 +6682,11 @@ "BIOSAMPLE:food_product" ], "slot_uri": "GENEPIO:0100444", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "food_product menu" @@ -6511,11 +6714,17 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product_properties" + "BIOSAMPLE:food_product_properties", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:food_processing_method", + "NCBI_BIOSAMPLE_Enterics:food_preserv_proc" ], "slot_uri": "GENEPIO:0100445", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "food_product_properties menu" @@ -6538,7 +6747,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:label_claims" + ], "slot_uri": "FOODON:03602001", + "domain_of": [ + "GRDI" + ], "multivalued": true, "any_of": [ { @@ -6562,9 +6777,15 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_source" + ], "slot_uri": "GENEPIO:0100446", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "animal_source_of_food menu" @@ -6587,7 +6808,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_prod" + ], "slot_uri": "GENEPIO:0100699", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "food_product_production_stream menu" @@ -6612,11 +6839,15 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_packaging" + "BIOSAMPLE:food_packaging", + "NCBI_BIOSAMPLE_Enterics:food_contain_wrap" ], "slot_uri": "GENEPIO:0100447", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "food_packaging menu" @@ -6639,7 +6870,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_quality_date" + ], "slot_uri": "GENEPIO:0100615", + "domain_of": [ + "GRDI" + ], "range": "date" }, "food_packaging_date": { @@ -6656,6 +6893,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100616", + "domain_of": [ + "GRDI" + ], "range": "date" }, "collection_device": { @@ -6673,9 +6913,14 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:collection_device" + "BIOSAMPLE:collection_device", + "NCBI_BIOSAMPLE_Enterics:samp_collect_device", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" ], "slot_uri": "GENEPIO:0001234", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -6701,9 +6946,13 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:collection_method" + "BIOSAMPLE:collection_method", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" ], "slot_uri": "GENEPIO:0001241", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -6728,6 +6977,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100768", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_volume_measurement_unit": { @@ -6744,6 +6996,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100769", + "domain_of": [ + "GRDI" + ], "range": "sample_volume_measurement_unit menu" }, "residual_sample_status": { @@ -6760,6 +7015,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101090", + "domain_of": [ + "GRDI" + ], "range": "residual_sample_status menu" }, "sample_storage_method": { @@ -6776,6 +7034,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100448", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_storage_medium": { @@ -6792,6 +7053,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100449", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_storage_duration_value": { @@ -6808,6 +7072,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101014", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sample_storage_duration_unit": { @@ -6824,6 +7091,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101015", + "domain_of": [ + "GRDI" + ], "range": "sample_storage_duration_unit menu" }, "nucleic_acid_storage_duration_value": { @@ -6840,6 +7110,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101085", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nucleic_acid_storage_duration_unit": { @@ -6856,6 +7129,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101086", + "domain_of": [ + "GRDI" + ], "range": "nucleic_acid_storage_duration_unit menu" }, "available_data_types": { @@ -6872,6 +7148,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100690", + "domain_of": [ + "GRDI" + ], "multivalued": true, "any_of": [ { @@ -6896,6 +7175,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101023", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "water_depth": { @@ -6912,6 +7194,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100440", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "water_depth_units": { @@ -6928,6 +7213,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101025", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "water_depth_units menu" @@ -6951,6 +7239,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100697", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sediment_depth_units": { @@ -6967,6 +7258,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101026", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "sediment_depth_units menu" @@ -6990,6 +7284,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100441", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "air_temperature_units": { @@ -7006,6 +7303,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101027", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "air_temperature_units menu" @@ -7029,6 +7329,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100698", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "water_temperature_units": { @@ -7045,6 +7348,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101028", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "water_temperature_units menu" @@ -7068,6 +7374,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100442", + "domain_of": [ + "GRDI" + ], "multivalued": true, "any_of": [ { @@ -7078,8 +7387,8 @@ } ] }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", "comments": [ @@ -7094,7 +7403,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host" + ], "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -7105,8 +7420,8 @@ } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", "comments": [ @@ -7122,9 +7437,14 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:host" + "BIOSAMPLE:host", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:host" ], "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -7135,8 +7455,8 @@ } ] }, - "host (ecotype)": { - "name": "host (ecotype)", + "host_ecotype": { + "name": "host_ecotype", "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", "title": "host (ecotype)", "comments": [ @@ -7148,11 +7468,17 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_variety" + ], "slot_uri": "GENEPIO:0100450", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "host (breed)": { - "name": "host (breed)", + "host_breed": { + "name": "host_breed", "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", "title": "host (breed)", "comments": [ @@ -7165,13 +7491,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:host_disease" + "BIOSAMPLE:host_disease", + "NCBI_BIOSAMPLE_Enterics:host_animal_breed" ], "slot_uri": "GENEPIO:0100451", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "host (food production name)": { - "name": "host (food production name)", + "host_food_production_name": { + "name": "host_food_production_name", "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", "title": "host (food production name)", "comments": [ @@ -7183,7 +7513,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host" + ], "slot_uri": "GENEPIO:0100452", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "host (food production name) menu" @@ -7201,7 +7537,13 @@ "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_age" + ], "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "host_age_bin menu" @@ -7224,7 +7566,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_disease" + ], "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "microbiological_method": { @@ -7241,6 +7589,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100454", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -7257,11 +7608,17 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:strain" + ], "slot_uri": "GENEPIO:0100455", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "isolate_ID": { - "name": "isolate_ID", + "isolate_id": { + "name": "isolate_id", "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", "title": "isolate_ID", "comments": [ @@ -7273,7 +7630,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:strain" + ], "slot_uri": "GENEPIO:0100456", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -7284,12 +7647,12 @@ } ] }, - "alternative_isolate_ID": { - "name": "alternative_isolate_ID", + "alternative_isolate_id": { + "name": "alternative_isolate_id", "description": "An alternative isolate_ID assigned to the isolate by another organization.", "title": "alternative_isolate_ID", "comments": [ - "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple alternative isolate IDs can be provided, separated by semi-colons." + "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons." ], "examples": [ { @@ -7300,12 +7663,18 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:isolate_name_alias" + ], "slot_uri": "GENEPIO:0100457", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "progeny_isolate_ID": { - "name": "progeny_isolate_ID", + "progeny_isolate_id": { + "name": "progeny_isolate_id", "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", "title": "progeny_isolate_ID", "comments": [ @@ -7318,10 +7687,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100458", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "IRIDA_isolate_ID": { - "name": "IRIDA_isolate_ID", + "irida_isolate_id": { + "name": "irida_isolate_id", "description": "The identifier of the isolate in the IRIDA platform.", "title": "IRIDA_isolate_ID", "comments": [ @@ -7334,6 +7706,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100459", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -7344,8 +7719,8 @@ } ] }, - "IRIDA_project_ID": { - "name": "IRIDA_project_ID", + "irida_project_id": { + "name": "irida_project_id", "description": "The identifier of the Project in the iRIDA platform.", "title": "IRIDA_project_ID", "comments": [ @@ -7358,6 +7733,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100460", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -7382,6 +7760,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100461", + "domain_of": [ + "GRDI" + ], "range": "isolated_by menu" }, "isolated_by_laboratory_name": { @@ -7398,6 +7779,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100462", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "isolated_by_contact_name": { @@ -7414,6 +7798,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100463", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "isolated_by_contact_email": { @@ -7430,6 +7817,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100464", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "isolation_date": { @@ -7445,7 +7835,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:cult_isol_date" + ], "slot_uri": "GENEPIO:0100465", + "domain_of": [ + "GRDI" + ], "range": "date" }, "isolate_received_date": { @@ -7462,6 +7858,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100466", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "organism": { @@ -7478,11 +7877,15 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:organism" + "BIOSAMPLE:organism", + "NCBI_BIOSAMPLE_Enterics:%2Aorganism" ], "slot_uri": "GENEPIO:0001191", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "required": true, + "multivalued": true, "any_of": [ { "range": "organism menu" @@ -7506,6 +7909,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100583", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -7530,6 +7936,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100584", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "serovar": { @@ -7545,7 +7954,13 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:serovar" + ], "slot_uri": "GENEPIO:0100467", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -7563,6 +7978,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100468", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -7580,10 +7998,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100469", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "library_ID": { - "name": "library_ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library_ID", "comments": [ @@ -7596,6 +8017,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sequenced_by": { @@ -7612,9 +8036,13 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:sequenced_by" + "BIOSAMPLE:sequenced_by", + "NCBI_BIOSAMPLE_Enterics:sequenced_by" ], "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -7639,6 +8067,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100470", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sequenced_by_contact_name": { @@ -7655,6 +8086,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -7679,6 +8113,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100422", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -7706,8 +8143,11 @@ "BIOSAMPLE:purpose_of_sequencing" ], "slot_uri": "GENEPIO:0001445", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "required": true, + "multivalued": true, "any_of": [ { "range": "purpose_of_sequencing menu" @@ -7731,6 +8171,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100472", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sequencing_platform": { @@ -7747,6 +8190,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100473", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "sequencing_platform menu" @@ -7770,6 +8216,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001452", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "sequencing_instrument menu" @@ -7793,6 +8242,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100997", + "domain_of": [ + "GRDI" + ], "range": "sequencing_assay_type menu" }, "library_preparation_kit": { @@ -7809,10 +8261,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "DNA fragment length": { - "name": "DNA fragment length", + "dna_fragment_length": { + "name": "dna_fragment_length", "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", "title": "DNA fragment length", "comments": [ @@ -7825,10 +8280,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100843", + "domain_of": [ + "GRDI" + ], "range": "Integer" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method", "comments": [ @@ -7841,10 +8299,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100966", + "domain_of": [ + "GRDI" + ], "range": "genomic_target_enrichment_method menu" }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method details", "comments": [ @@ -7857,10 +8318,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100967", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", "comments": [ @@ -7873,10 +8337,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", "comments": [ @@ -7889,10 +8356,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "GRDI" + ], "range": "Integer" }, - "sequencing flow cell version": { - "name": "sequencing flow cell version", + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", "description": "The version number of the flow cell used for generating sequence data.", "title": "sequencing flow cell version", "comments": [ @@ -7905,6 +8375,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101102", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sequencing_protocol": { @@ -7921,6 +8394,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "r1_fastq_filename": { @@ -7937,6 +8413,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001476", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "r2_fastq_filename": { @@ -7953,6 +8432,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001477", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "fast5_filename": { @@ -7969,6 +8451,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001480", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "assembly_filename": { @@ -7985,10 +8470,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001461", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quality control method name": { - "name": "quality control method name", + "quality_control_method_name": { + "name": "quality_control_method_name", "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method name", "comments": [ @@ -8001,10 +8489,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100557", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_version": { + "name": "quality_control_method_version", "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method version", "comments": [ @@ -8017,10 +8508,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100558", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_determination": { + "name": "quality_control_determination", "description": "The determination of a quality control assessment.", "title": "quality control determination", "comments": [ @@ -8033,6 +8527,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100559", + "domain_of": [ + "GRDI" + ], "multivalued": true, "any_of": [ { @@ -8043,8 +8540,8 @@ } ] }, - "quality control issues": { - "name": "quality control issues", + "quality_control_issues": { + "name": "quality_control_issues", "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", "title": "quality control issues", "comments": [ @@ -8057,6 +8554,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100560", + "domain_of": [ + "GRDI" + ], "multivalued": true, "any_of": [ { @@ -8067,8 +8567,8 @@ } ] }, - "quality control details": { - "name": "quality control details", + "quality_control_details": { + "name": "quality_control_details", "description": "The details surrounding a low quality determination in a quality control assessment.", "title": "quality control details", "comments": [ @@ -8081,10 +8581,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100561", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "comments": [ @@ -8097,6 +8600,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -8107,8 +8613,8 @@ } ] }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "comments": [ @@ -8121,6 +8627,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -8131,8 +8640,8 @@ } ] }, - "sequence assembly software name": { - "name": "sequence assembly software name", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", "description": "The name of the software used to assemble a sequence.", "title": "sequence assembly software name", "comments": [ @@ -8145,6 +8654,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100825", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "WhitespaceMinimizedString" @@ -8154,8 +8666,8 @@ } ] }, - "sequence assembly software version": { - "name": "sequence assembly software version", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", "description": "The version of the software used to assemble a sequence.", "title": "sequence assembly software version", "comments": [ @@ -8168,6 +8680,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100826", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "WhitespaceMinimizedString" @@ -8177,8 +8692,8 @@ } ] }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of the software used to generate the consensus sequence.", "title": "consensus sequence software name", "comments": [ @@ -8191,6 +8706,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "WhitespaceMinimizedString" @@ -8200,8 +8718,8 @@ } ] }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "comments": [ @@ -8214,6 +8732,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "WhitespaceMinimizedString" @@ -8223,8 +8744,8 @@ } ] }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", "comments": [ @@ -8237,10 +8758,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", "comments": [ @@ -8253,10 +8777,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", "comments": [ @@ -8269,10 +8796,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "genome completeness": { - "name": "genome completeness", + "genome_completeness": { + "name": "genome_completeness", "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", "title": "genome completeness", "comments": [ @@ -8285,10 +8815,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100844", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", "comments": [ @@ -8301,10 +8834,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "number of total reads": { - "name": "number of total reads", + "number_of_total_reads": { + "name": "number_of_total_reads", "description": "The total number of non-unique reads generated by the sequencing process.", "title": "number of total reads", "comments": [ @@ -8317,10 +8853,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100827", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "number of unique reads": { - "name": "number of unique reads", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "description": "The number of unique reads generated by the sequencing process.", "title": "number of unique reads", "comments": [ @@ -8333,10 +8872,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100828", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", "title": "minimum post-trimming read length", "comments": [ @@ -8349,10 +8891,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100829", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "number of contigs": { - "name": "number of contigs", + "number_of_contigs": { + "name": "number_of_contigs", "description": "The number of contigs (contiguous sequences) in a sequence assembly.", "title": "number of contigs", "comments": [ @@ -8365,10 +8910,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100937", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", "title": "percent Ns across total genome length", "comments": [ @@ -8381,10 +8929,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100830", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", "title": "Ns per 100 kbp", "comments": [ @@ -8397,10 +8948,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "N50": { - "name": "N50", + "n50": { + "name": "n50", "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", "title": "N50", "comments": [ @@ -8413,10 +8967,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100938", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "percent read contamination": { - "name": "percent read contamination", + "percent_read_contamination_": { + "name": "percent_read_contamination_", "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", "title": "percent read contamination", "comments": [ @@ -8429,10 +8986,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100845", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "sequence assembly length": { - "name": "sequence assembly length", + "sequence_assembly_length": { + "name": "sequence_assembly_length", "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", "title": "sequence assembly length", "comments": [ @@ -8445,10 +9005,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100846", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "The length of the genome defined by the most common nucleotides at each position.", "title": "consensus genome length", "comments": [ @@ -8461,10 +9024,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "GRDI" + ], "range": "integer" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", "comments": [ @@ -8477,10 +9043,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "deduplication method": { - "name": "deduplication method", + "deduplication_method": { + "name": "deduplication_method", "description": "The method used to remove duplicated reads in a sequence read dataset.", "title": "deduplication method", "comments": [ @@ -8493,10 +9062,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100831", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "comments": [ @@ -8509,10 +9081,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "read mapping software name": { - "name": "read mapping software name", + "read_mapping_software_name": { + "name": "read_mapping_software_name", "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software name", "comments": [ @@ -8525,10 +9100,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100832", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "read mapping software version": { - "name": "read mapping software version", + "read_mapping_software_version": { + "name": "read_mapping_software_version", "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software version", "comments": [ @@ -8541,10 +9119,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100833", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", "description": "The name of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database name", "comments": [ @@ -8557,10 +9138,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100834", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", "description": "The version of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database version", "comments": [ @@ -8573,10 +9157,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100835", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", "description": "The filename of the report containing the results of a taxonomic analysis.", "title": "taxonomic analysis report filename", "comments": [ @@ -8589,10 +9176,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101074", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", "comments": [ @@ -8605,10 +9195,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101075", + "domain_of": [ + "GRDI" + ], "range": "date" }, - "read mapping criteria": { - "name": "read mapping criteria", + "read_mapping_criteria": { + "name": "read_mapping_criteria", "description": "A description of the criteria used to map reads to a reference sequence.", "title": "read mapping criteria", "comments": [ @@ -8621,6 +9214,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100836", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sequence_submitted_by": { @@ -8637,6 +9233,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "sequence_submitted_by menu" @@ -8660,6 +9259,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100474", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sequence_submitted_by_contact_email": { @@ -8676,10 +9278,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "publication_ID": { - "name": "publication_ID", + "publication_id": { + "name": "publication_id", "description": "The identifier for a publication.", "title": "publication_ID", "comments": [ @@ -8692,6 +9297,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100475", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "attribute_package": { @@ -8708,6 +9316,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100476", + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "attribute_package menu" @@ -8731,9 +9342,13 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "BIOSAMPLE:bioproject_accession" + "BIOSAMPLE:bioproject_accession", + "NCBI_BIOSAMPLE_Enterics:bioproject_accession" ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "biosample_accession": { @@ -8749,11 +9364,17 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "ENA_ANTIBIOGRAM:bioSample_ID" + ], "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "SRA_accession": { - "name": "SRA_accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA_accession", "comments": [ @@ -8766,10 +9387,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001142", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "GenBank_accession": { - "name": "GenBank_accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", "title": "GenBank_accession", "comments": [ @@ -8782,6 +9406,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001145", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "prevalence_metrics": { @@ -8798,6 +9425,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100480", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -8815,6 +9445,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100481", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -8832,6 +9465,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100482", + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -8855,9 +9491,15 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:upstream_intervention" + ], "slot_uri": "GENEPIO:0100483", - "multivalued": true, + "domain_of": [ + "GRDI" + ], "recommended": true, + "multivalued": true, "any_of": [ { "range": "experimental_intervention menu" @@ -8881,11 +9523,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100484", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR_testing_by": { - "name": "AMR_testing_by", + "amr_testing_by": { + "name": "amr_testing_by", "description": "The name of the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by", "comments": [ @@ -8898,6 +9543,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100511", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -8908,8 +9556,8 @@ } ] }, - "AMR_testing_by_laboratory_name": { - "name": "AMR_testing_by_laboratory_name", + "amr_testing_by_laboratory_name": { + "name": "amr_testing_by_laboratory_name", "description": "The name of the lab within the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by_laboratory_name", "comments": [ @@ -8922,10 +9570,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100512", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "AMR_testing_by_contact_name": { - "name": "AMR_testing_by_contact_name", + "amr_testing_by_contact_name": { + "name": "amr_testing_by_contact_name", "description": "The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by_contact_name", "comments": [ @@ -8938,6 +9589,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100513", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -8948,8 +9602,8 @@ } ] }, - "AMR_testing_by_contact_email": { - "name": "AMR_testing_by_contact_email", + "amr_testing_by_contact_email": { + "name": "amr_testing_by_contact_email", "description": "The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by_contact_email", "comments": [ @@ -8962,6 +9616,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100514", + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -8972,8 +9629,8 @@ } ] }, - "AMR_testing_date": { - "name": "AMR_testing_date", + "amr_testing_date": { + "name": "amr_testing_date", "description": "The date the antimicrobial resistance testing was performed.", "title": "AMR_testing_date", "comments": [ @@ -8986,6 +9643,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100515", + "domain_of": [ + "GRDI" + ], "range": "date" }, "amikacin_resistance_phenotype": { @@ -9001,6 +9661,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9024,6 +9690,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9047,6 +9719,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9070,6 +9748,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9093,6 +9777,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -9115,6 +9805,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -9137,6 +9833,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "amikacin_vendor_name": { @@ -9152,6 +9851,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name" @@ -9174,6 +9879,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9197,6 +9908,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "amikacin_testing_standard_details": { @@ -9215,6 +9929,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "amikacin_susceptible_breakpoint": { @@ -9230,6 +9947,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "amikacin_intermediate_breakpoint": { @@ -9242,6 +9962,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "amikacin_resistant_breakpoint": { @@ -9257,10 +9980,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_resistance_phenotype": { - "name": "amoxicillin-clavulanic_acid_resistance_phenotype", + "amoxicillinclavulanic_acid_resistance_phenotype": { + "name": "amoxicillinclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "amoxicillin-clavulanic_acid_resistance_phenotype", "comments": [ @@ -9272,6 +9998,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9282,8 +10014,8 @@ } ] }, - "amoxicillin-clavulanic_acid_measurement": { - "name": "amoxicillin-clavulanic_acid_measurement", + "amoxicillinclavulanic_acid_measurement": { + "name": "amoxicillinclavulanic_acid_measurement", "description": "The measured value of amoxicillin-clavulanic acid resistance.", "title": "amoxicillin-clavulanic_acid_measurement", "comments": [ @@ -9295,6 +10027,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9305,8 +10043,8 @@ } ] }, - "amoxicillin-clavulanic_acid_measurement_units": { - "name": "amoxicillin-clavulanic_acid_measurement_units", + "amoxicillinclavulanic_acid_measurement_units": { + "name": "amoxicillinclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "amoxicillin-clavulanic_acid_measurement_units", "comments": [ @@ -9318,6 +10056,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9328,8 +10072,8 @@ } ] }, - "amoxicillin-clavulanic_acid_measurement_sign": { - "name": "amoxicillin-clavulanic_acid_measurement_sign", + "amoxicillinclavulanic_acid_measurement_sign": { + "name": "amoxicillinclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "amoxicillin-clavulanic_acid_measurement_sign", "comments": [ @@ -9341,6 +10085,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9351,8 +10101,8 @@ } ] }, - "amoxicillin-clavulanic_acid_laboratory_typing_method": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_method", + "amoxicillinclavulanic_acid_laboratory_typing_method": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "amoxicillin-clavulanic_acid_laboratory_typing_method", "comments": [ @@ -9364,6 +10114,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -9373,8 +10129,8 @@ } ] }, - "amoxicillin-clavulanic_acid_laboratory_typing_platform": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_platform", + "amoxicillinclavulanic_acid_laboratory_typing_platform": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform", "comments": [ @@ -9386,6 +10142,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -9395,8 +10157,8 @@ } ] }, - "amoxicillin-clavulanic_acid_laboratory_typing_platform_version": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", + "amoxicillinclavulanic_acid_laboratory_typing_platform_version": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", "comments": [ @@ -9408,10 +10170,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_vendor_name": { - "name": "amoxicillin-clavulanic_acid_vendor_name", + "amoxicillinclavulanic_acid_vendor_name": { + "name": "amoxicillinclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "amoxicillin-clavulanic_acid_vendor_name", "comments": [ @@ -9423,6 +10188,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -9432,8 +10203,8 @@ } ] }, - "amoxicillin-clavulanic_acid_testing_standard": { - "name": "amoxicillin-clavulanic_acid_testing_standard", + "amoxicillinclavulanic_acid_testing_standard": { + "name": "amoxicillinclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "amoxicillin-clavulanic_acid_testing_standard", "comments": [ @@ -9445,6 +10216,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9455,8 +10232,8 @@ } ] }, - "amoxicillin-clavulanic_acid_testing_standard_version": { - "name": "amoxicillin-clavulanic_acid_testing_standard_version", + "amoxicillinclavulanic_acid_testing_standard_version": { + "name": "amoxicillinclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "amoxicillin-clavulanic_acid_testing_standard_version", "comments": [ @@ -9468,10 +10245,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_testing_standard_details": { - "name": "amoxicillin-clavulanic_acid_testing_standard_details", + "amoxicillinclavulanic_acid_testing_standard_details": { + "name": "amoxicillinclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "amoxicillin-clavulanic_acid_testing_standard_details", "comments": [ @@ -9486,10 +10266,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_susceptible_breakpoint": { - "name": "amoxicillin-clavulanic_acid_susceptible_breakpoint", + "amoxicillinclavulanic_acid_susceptible_breakpoint": { + "name": "amoxicillinclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "amoxicillin-clavulanic_acid_susceptible_breakpoint", "comments": [ @@ -9501,10 +10284,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_intermediate_breakpoint": { - "name": "amoxicillin-clavulanic_acid_intermediate_breakpoint", + "amoxicillinclavulanic_acid_intermediate_breakpoint": { + "name": "amoxicillinclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "amoxicillin-clavulanic_acid_intermediate_breakpoint", "examples": [ @@ -9513,10 +10299,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_resistant_breakpoint": { - "name": "amoxicillin-clavulanic_acid_resistant_breakpoint", + "amoxicillinclavulanic_acid_resistant_breakpoint": { + "name": "amoxicillinclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "amoxicillin-clavulanic_acid_resistant_breakpoint", "comments": [ @@ -9528,6 +10317,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ampicillin_resistance_phenotype": { @@ -9543,6 +10335,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9566,6 +10364,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9589,6 +10393,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9612,6 +10422,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9635,6 +10451,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -9657,6 +10479,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -9679,6 +10507,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ampicillin_vendor_name": { @@ -9694,6 +10525,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -9716,6 +10553,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9739,6 +10582,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ampicillin_testing_standard_details": { @@ -9757,6 +10603,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ampicillin_susceptible_breakpoint": { @@ -9772,6 +10621,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ampicillin_intermediate_breakpoint": { @@ -9784,6 +10636,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ampicillin_resistant_breakpoint": { @@ -9799,6 +10654,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "azithromycin_resistance_phenotype": { @@ -9814,6 +10672,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -9837,6 +10701,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9860,6 +10730,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9883,6 +10759,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -9906,6 +10788,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -9928,6 +10816,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -9950,6 +10844,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "azithromycin_vendor_name": { @@ -9965,6 +10862,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -9987,6 +10890,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10010,6 +10919,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "azithromycin_testing_standard_details": { @@ -10028,6 +10940,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "azithromycin_susceptible_breakpoint": { @@ -10043,6 +10958,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "azithromycin_intermediate_breakpoint": { @@ -10055,6 +10973,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "azithromycin_resistant_breakpoint": { @@ -10070,6 +10991,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefazolin_resistance_phenotype": { @@ -10085,6 +11009,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10108,6 +11038,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10131,6 +11067,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10154,6 +11096,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10177,6 +11125,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -10199,6 +11153,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -10221,6 +11181,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefazolin_vendor_name": { @@ -10236,6 +11199,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -10258,6 +11227,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10281,6 +11256,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefazolin_testing_standard_details": { @@ -10299,6 +11277,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefazolin_susceptible_breakpoint": { @@ -10314,6 +11295,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefazolin_intermediate_breakpoint": { @@ -10326,6 +11310,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefazolin_resistant_breakpoint": { @@ -10341,6 +11328,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefepime_resistance_phenotype": { @@ -10356,6 +11346,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10379,6 +11375,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10402,6 +11404,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10425,6 +11433,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10448,6 +11462,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -10470,6 +11490,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -10492,6 +11518,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefepime_vendor_name": { @@ -10507,6 +11536,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -10529,6 +11564,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10552,6 +11593,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefepime_testing_standard_details": { @@ -10570,6 +11614,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefepime_susceptible_breakpoint": { @@ -10585,6 +11632,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefepime_intermediate_breakpoint": { @@ -10597,6 +11647,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefepime_resistant_breakpoint": { @@ -10612,6 +11665,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefotaxime_resistance_phenotype": { @@ -10627,6 +11683,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10650,6 +11712,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10673,6 +11741,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10696,6 +11770,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10719,6 +11799,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -10741,6 +11827,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -10763,6 +11855,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefotaxime_vendor_name": { @@ -10778,6 +11873,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -10800,6 +11901,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10823,6 +11930,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefotaxime_testing_standard_details": { @@ -10841,6 +11951,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefotaxime_susceptible_breakpoint": { @@ -10856,6 +11969,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefotaxime_intermediate_breakpoint": { @@ -10868,6 +11984,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefotaxime_resistant_breakpoint": { @@ -10883,10 +12002,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_resistance_phenotype": { - "name": "cefotaxime-clavulanic_acid_resistance_phenotype", + "cefotaximeclavulanic_acid_resistance_phenotype": { + "name": "cefotaximeclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefotaxime-clavulanic_acid_resistance_phenotype", "comments": [ @@ -10898,6 +12020,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -10908,8 +12036,8 @@ } ] }, - "cefotaxime-clavulanic_acid_measurement": { - "name": "cefotaxime-clavulanic_acid_measurement", + "cefotaximeclavulanic_acid_measurement": { + "name": "cefotaximeclavulanic_acid_measurement", "description": "The measured value of cefotaxime-clavulanic acid resistance.", "title": "cefotaxime-clavulanic_acid_measurement", "comments": [ @@ -10921,6 +12049,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10931,8 +12065,8 @@ } ] }, - "cefotaxime-clavulanic_acid_measurement_units": { - "name": "cefotaxime-clavulanic_acid_measurement_units", + "cefotaximeclavulanic_acid_measurement_units": { + "name": "cefotaximeclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefotaxime-clavulanic_acid_measurement_units", "comments": [ @@ -10944,6 +12078,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10954,8 +12094,8 @@ } ] }, - "cefotaxime-clavulanic_acid_measurement_sign": { - "name": "cefotaxime-clavulanic_acid_measurement_sign", + "cefotaximeclavulanic_acid_measurement_sign": { + "name": "cefotaximeclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefotaxime-clavulanic_acid_measurement_sign", "comments": [ @@ -10967,6 +12107,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -10977,8 +12123,8 @@ } ] }, - "cefotaxime-clavulanic_acid_laboratory_typing_method": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_method", + "cefotaximeclavulanic_acid_laboratory_typing_method": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefotaxime-clavulanic_acid_laboratory_typing_method", "comments": [ @@ -10990,6 +12136,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -10999,8 +12151,8 @@ } ] }, - "cefotaxime-clavulanic_acid_laboratory_typing_platform": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_platform", + "cefotaximeclavulanic_acid_laboratory_typing_platform": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform", "comments": [ @@ -11012,6 +12164,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -11021,8 +12179,8 @@ } ] }, - "cefotaxime-clavulanic_acid_laboratory_typing_platform_version": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", + "cefotaximeclavulanic_acid_laboratory_typing_platform_version": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", "comments": [ @@ -11034,10 +12192,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_vendor_name": { - "name": "cefotaxime-clavulanic_acid_vendor_name", + "cefotaximeclavulanic_acid_vendor_name": { + "name": "cefotaximeclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefotaxime-clavulanic_acid_vendor_name", "comments": [ @@ -11049,6 +12210,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -11058,8 +12225,8 @@ } ] }, - "cefotaxime-clavulanic_acid_testing_standard": { - "name": "cefotaxime-clavulanic_acid_testing_standard", + "cefotaximeclavulanic_acid_testing_standard": { + "name": "cefotaximeclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefotaxime-clavulanic_acid_testing_standard", "comments": [ @@ -11071,6 +12238,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11081,8 +12254,8 @@ } ] }, - "cefotaxime-clavulanic_acid_testing_standard_version": { - "name": "cefotaxime-clavulanic_acid_testing_standard_version", + "cefotaximeclavulanic_acid_testing_standard_version": { + "name": "cefotaximeclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefotaxime-clavulanic_acid_testing_standard_version", "comments": [ @@ -11094,10 +12267,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_testing_standard_details": { - "name": "cefotaxime-clavulanic_acid_testing_standard_details", + "cefotaximeclavulanic_acid_testing_standard_details": { + "name": "cefotaximeclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefotaxime-clavulanic_acid_testing_standard_details", "comments": [ @@ -11112,10 +12288,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_susceptible_breakpoint": { - "name": "cefotaxime-clavulanic_acid_susceptible_breakpoint", + "cefotaximeclavulanic_acid_susceptible_breakpoint": { + "name": "cefotaximeclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefotaxime-clavulanic_acid_susceptible_breakpoint", "comments": [ @@ -11127,10 +12306,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_intermediate_breakpoint": { - "name": "cefotaxime-clavulanic_acid_intermediate_breakpoint", + "cefotaximeclavulanic_acid_intermediate_breakpoint": { + "name": "cefotaximeclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefotaxime-clavulanic_acid_intermediate_breakpoint", "examples": [ @@ -11139,10 +12321,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_resistant_breakpoint": { - "name": "cefotaxime-clavulanic_acid_resistant_breakpoint", + "cefotaximeclavulanic_acid_resistant_breakpoint": { + "name": "cefotaximeclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefotaxime-clavulanic_acid_resistant_breakpoint", "comments": [ @@ -11154,6 +12339,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefoxitin_resistance_phenotype": { @@ -11169,6 +12357,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11192,6 +12386,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11215,6 +12415,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11238,6 +12444,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11261,6 +12473,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -11283,6 +12501,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -11305,6 +12529,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefoxitin_vendor_name": { @@ -11320,6 +12547,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -11342,6 +12575,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11365,6 +12604,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefoxitin_testing_standard_details": { @@ -11383,6 +12625,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefoxitin_susceptible_breakpoint": { @@ -11398,6 +12643,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefoxitin_intermediate_breakpoint": { @@ -11410,6 +12658,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefoxitin_resistant_breakpoint": { @@ -11425,6 +12676,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefpodoxime_resistance_phenotype": { @@ -11440,6 +12694,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11463,6 +12723,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11486,6 +12752,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11509,6 +12781,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11532,6 +12810,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -11554,6 +12838,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -11576,6 +12866,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefpodoxime_vendor_name": { @@ -11591,6 +12884,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -11613,6 +12912,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11636,6 +12941,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefpodoxime_testing_standard_details": { @@ -11654,6 +12962,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefpodoxime_susceptible_breakpoint": { @@ -11669,6 +12980,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefpodoxime_intermediate_breakpoint": { @@ -11681,6 +12995,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cefpodoxime_resistant_breakpoint": { @@ -11696,6 +13013,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftazidime_resistance_phenotype": { @@ -11711,6 +13031,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11734,6 +13060,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11757,6 +13089,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11780,6 +13118,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -11803,6 +13147,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -11825,6 +13175,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -11847,6 +13203,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftazidime_vendor_name": { @@ -11862,6 +13221,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -11884,6 +13249,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11907,6 +13278,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftazidime_testing_standard_details": { @@ -11925,6 +13299,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftazidime_susceptible_breakpoint": { @@ -11940,6 +13317,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftazidime_intermediate_breakpoint": { @@ -11952,6 +13332,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftazidime_resistant_breakpoint": { @@ -11967,10 +13350,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_resistance_phenotype": { - "name": "ceftazidime-clavulanic_acid_resistance_phenotype", + "ceftazidimeclavulanic_acid_resistance_phenotype": { + "name": "ceftazidimeclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ceftazidime-clavulanic_acid_resistance_phenotype", "comments": [ @@ -11982,6 +13368,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -11992,8 +13384,8 @@ } ] }, - "ceftazidime-clavulanic_acid_measurement": { - "name": "ceftazidime-clavulanic_acid_measurement", + "ceftazidimeclavulanic_acid_measurement": { + "name": "ceftazidimeclavulanic_acid_measurement", "description": "The measured value of ceftazidime-clavulanic acid resistance.", "title": "ceftazidime-clavulanic_acid_measurement", "comments": [ @@ -12005,6 +13397,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12015,8 +13413,8 @@ } ] }, - "ceftazidime-clavulanic_acid_measurement_units": { - "name": "ceftazidime-clavulanic_acid_measurement_units", + "ceftazidimeclavulanic_acid_measurement_units": { + "name": "ceftazidimeclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ceftazidime-clavulanic_acid_measurement_units", "comments": [ @@ -12028,6 +13426,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12038,8 +13442,8 @@ } ] }, - "ceftazidime-clavulanic_acid_measurement_sign": { - "name": "ceftazidime-clavulanic_acid_measurement_sign", + "ceftazidimeclavulanic_acid_measurement_sign": { + "name": "ceftazidimeclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ceftazidime-clavulanic_acid_measurement_sign", "comments": [ @@ -12051,6 +13455,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12061,8 +13471,8 @@ } ] }, - "ceftazidime-clavulanic_acid_laboratory_typing_method": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_method", + "ceftazidimeclavulanic_acid_laboratory_typing_method": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ceftazidime-clavulanic_acid_laboratory_typing_method", "comments": [ @@ -12074,6 +13484,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -12083,8 +13499,8 @@ } ] }, - "ceftazidime-clavulanic_acid_laboratory_typing_platform": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_platform", + "ceftazidimeclavulanic_acid_laboratory_typing_platform": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform", "comments": [ @@ -12096,6 +13512,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -12105,8 +13527,8 @@ } ] }, - "ceftazidime-clavulanic_acid_laboratory_typing_platform_version": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", + "ceftazidimeclavulanic_acid_laboratory_typing_platform_version": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", "comments": [ @@ -12118,10 +13540,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_vendor_name": { - "name": "ceftazidime-clavulanic_acid_vendor_name", + "ceftazidimeclavulanic_acid_vendor_name": { + "name": "ceftazidimeclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ceftazidime-clavulanic_acid_vendor_name", "comments": [ @@ -12133,6 +13558,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -12142,8 +13573,8 @@ } ] }, - "ceftazidime-clavulanic_acid_testing_standard": { - "name": "ceftazidime-clavulanic_acid_testing_standard", + "ceftazidimeclavulanic_acid_testing_standard": { + "name": "ceftazidimeclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ceftazidime-clavulanic_acid_testing_standard", "comments": [ @@ -12155,6 +13586,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12165,8 +13602,8 @@ } ] }, - "ceftazidime-clavulanic_acid_testing_standard_version": { - "name": "ceftazidime-clavulanic_acid_testing_standard_version", + "ceftazidimeclavulanic_acid_testing_standard_version": { + "name": "ceftazidimeclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ceftazidime-clavulanic_acid_testing_standard_version", "comments": [ @@ -12178,10 +13615,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_testing_standard_details": { - "name": "ceftazidime-clavulanic_acid_testing_standard_details", + "ceftazidimeclavulanic_acid_testing_standard_details": { + "name": "ceftazidimeclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ceftazidime-clavulanic_acid_testing_standard_details", "comments": [ @@ -12196,10 +13636,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_susceptible_breakpoint": { - "name": "ceftazidime-clavulanic_acid_susceptible_breakpoint", + "ceftazidimeclavulanic_acid_susceptible_breakpoint": { + "name": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ceftazidime-clavulanic_acid_susceptible_breakpoint", "comments": [ @@ -12211,10 +13654,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_intermediate_breakpoint": { - "name": "ceftazidime-clavulanic_acid_intermediate_breakpoint", + "ceftazidimeclavulanic_acid_intermediate_breakpoint": { + "name": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ceftazidime-clavulanic_acid_intermediate_breakpoint", "examples": [ @@ -12223,10 +13669,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_resistant_breakpoint": { - "name": "ceftazidime-clavulanic_acid_resistant_breakpoint", + "ceftazidimeclavulanic_acid_resistant_breakpoint": { + "name": "ceftazidimeclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ceftazidime-clavulanic_acid_resistant_breakpoint", "comments": [ @@ -12238,6 +13687,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftiofur_resistance_phenotype": { @@ -12253,6 +13705,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12276,6 +13734,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12299,6 +13763,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12322,6 +13792,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12345,6 +13821,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -12367,6 +13849,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -12389,6 +13877,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftiofur_vendor_name": { @@ -12404,6 +13895,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -12426,6 +13923,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12449,6 +13952,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftiofur_testing_standard_details": { @@ -12467,6 +13973,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftiofur_susceptible_breakpoint": { @@ -12482,6 +13991,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftiofur_intermediate_breakpoint": { @@ -12494,6 +14006,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftiofur_resistant_breakpoint": { @@ -12509,6 +14024,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftriaxone_resistance_phenotype": { @@ -12524,6 +14042,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12547,6 +14071,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12570,6 +14100,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12593,6 +14129,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12616,6 +14158,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -12638,6 +14186,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -12660,6 +14214,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftriaxone_vendor_name": { @@ -12675,6 +14232,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -12697,6 +14260,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12720,6 +14289,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftriaxone_testing_standard_details": { @@ -12738,6 +14310,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftriaxone_susceptible_breakpoint": { @@ -12753,6 +14328,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftriaxone_intermediate_breakpoint": { @@ -12765,6 +14343,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ceftriaxone_resistant_breakpoint": { @@ -12780,6 +14361,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cephalothin_resistance_phenotype": { @@ -12795,6 +14379,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12818,6 +14408,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12841,6 +14437,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12864,6 +14466,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -12887,6 +14495,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -12909,6 +14523,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -12931,6 +14551,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cephalothin_vendor_name": { @@ -12946,6 +14569,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -12968,6 +14597,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -12991,6 +14626,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cephalothin_testing_standard_details": { @@ -13009,6 +14647,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cephalothin_susceptible_breakpoint": { @@ -13024,6 +14665,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cephalothin_intermediate_breakpoint": { @@ -13036,6 +14680,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "cephalothin_resistant_breakpoint": { @@ -13051,6 +14698,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "chloramphenicol_resistance_phenotype": { @@ -13066,6 +14716,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13089,6 +14745,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13112,6 +14774,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13135,6 +14803,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13158,6 +14832,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -13180,6 +14860,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -13202,6 +14888,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "chloramphenicol_vendor_name": { @@ -13217,6 +14906,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -13239,6 +14934,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13262,6 +14963,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "chloramphenicol_testing_standard_details": { @@ -13280,6 +14984,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "chloramphenicol_susceptible_breakpoint": { @@ -13295,6 +15002,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "chloramphenicol_intermediate_breakpoint": { @@ -13307,6 +15017,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "chloramphenicol_resistant_breakpoint": { @@ -13322,6 +15035,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ciprofloxacin_resistance_phenotype": { @@ -13337,6 +15053,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13360,6 +15082,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13383,6 +15111,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13406,6 +15140,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13429,6 +15169,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -13451,6 +15197,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -13473,6 +15225,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ciprofloxacin_vendor_name": { @@ -13488,6 +15243,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -13510,6 +15271,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13533,6 +15300,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ciprofloxacin_testing_standard_details": { @@ -13551,6 +15321,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ciprofloxacin_susceptible_breakpoint": { @@ -13566,6 +15339,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ciprofloxacin_intermediate_breakpoint": { @@ -13578,6 +15354,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "ciprofloxacin_resistant_breakpoint": { @@ -13593,6 +15372,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "clindamycin_resistance_phenotype": { @@ -13608,6 +15390,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13631,6 +15419,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13654,6 +15448,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13677,6 +15477,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13700,6 +15506,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -13722,6 +15534,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -13744,6 +15562,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "clindamycin_vendor_name": { @@ -13759,6 +15580,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -13781,6 +15608,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13804,6 +15637,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "clindamycin_testing_standard_details": { @@ -13822,6 +15658,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "clindamycin_susceptible_breakpoint": { @@ -13837,6 +15676,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "clindamycin_intermediate_breakpoint": { @@ -13849,6 +15691,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "clindamycin_resistant_breakpoint": { @@ -13864,6 +15709,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "doxycycline_resistance_phenotype": { @@ -13879,6 +15727,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -13902,6 +15756,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13925,6 +15785,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13948,6 +15814,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -13971,6 +15843,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -13993,6 +15871,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -14015,6 +15899,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "doxycycline_vendor_name": { @@ -14030,6 +15917,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -14052,6 +15945,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14075,6 +15974,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "doxycycline_testing_standard_details": { @@ -14093,6 +15995,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "doxycycline_susceptible_breakpoint": { @@ -14108,6 +16013,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "doxycycline_intermediate_breakpoint": { @@ -14120,6 +16028,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "doxycycline_resistant_breakpoint": { @@ -14135,6 +16046,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "enrofloxacin_resistance_phenotype": { @@ -14150,6 +16064,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14173,6 +16093,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14196,6 +16122,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14219,6 +16151,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14242,6 +16180,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -14264,6 +16208,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -14286,6 +16236,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "enrofloxacin_vendor_name": { @@ -14301,6 +16254,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -14323,6 +16282,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14346,6 +16311,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "enrofloxacin_testing_standard_details": { @@ -14364,6 +16332,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "enrofloxacin_susceptible_breakpoint": { @@ -14379,6 +16350,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "enrofloxacin_intermediate_breakpoint": { @@ -14391,6 +16365,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "enrofloxacin_resistant_breakpoint": { @@ -14406,6 +16383,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "erythromycin_resistance_phenotype": { @@ -14421,6 +16401,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14444,6 +16430,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14467,6 +16459,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14490,6 +16488,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14513,6 +16517,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -14535,6 +16545,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -14557,6 +16573,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "erythromycin_vendor_name": { @@ -14572,6 +16591,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -14594,6 +16619,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14617,6 +16648,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "erythromycin_testing_standard_details": { @@ -14635,6 +16669,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "erythromycin_susceptible_breakpoint": { @@ -14650,6 +16687,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "erythromycin_intermediate_breakpoint": { @@ -14662,6 +16702,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "erythromycin_resistant_breakpoint": { @@ -14677,6 +16720,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "florfenicol_resistance_phenotype": { @@ -14692,6 +16738,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14715,6 +16767,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14738,6 +16796,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14761,6 +16825,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -14784,6 +16854,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -14806,6 +16882,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -14828,6 +16910,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "florfenicol_vendor_name": { @@ -14843,6 +16928,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -14865,6 +16956,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14888,6 +16985,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "florfenicol_testing_standard_details": { @@ -14906,6 +17006,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "florfenicol_susceptible_breakpoint": { @@ -14921,6 +17024,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "florfenicol_intermediate_breakpoint": { @@ -14933,6 +17039,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "florfenicol_resistant_breakpoint": { @@ -14948,6 +17057,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "gentamicin_resistance_phenotype": { @@ -14963,6 +17075,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -14986,6 +17104,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15009,6 +17133,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15032,6 +17162,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15055,6 +17191,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -15077,6 +17219,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -15099,6 +17247,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "gentamicin_vendor_name": { @@ -15114,6 +17265,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -15136,6 +17293,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15159,6 +17322,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "gentamicin_testing_standard_details": { @@ -15177,6 +17343,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "gentamicin_susceptible_breakpoint": { @@ -15192,6 +17361,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "gentamicin_intermediate_breakpoint": { @@ -15204,6 +17376,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "gentamicin_resistant_breakpoint": { @@ -15219,6 +17394,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "imipenem_resistance_phenotype": { @@ -15234,6 +17412,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15257,6 +17441,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15280,6 +17470,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15303,6 +17499,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15326,6 +17528,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -15348,6 +17556,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -15370,6 +17584,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "imipenem_vendor_name": { @@ -15385,6 +17602,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -15407,6 +17630,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15430,6 +17659,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "imipenem_testing_standard_details": { @@ -15448,6 +17680,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "imipenem_susceptible_breakpoint": { @@ -15463,6 +17698,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "imipenem_intermediate_breakpoint": { @@ -15475,6 +17713,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "imipenem_resistant_breakpoint": { @@ -15490,6 +17731,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "kanamycin_resistance_phenotype": { @@ -15505,6 +17749,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15528,6 +17778,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15551,6 +17807,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15574,6 +17836,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15597,6 +17865,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -15619,6 +17893,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -15641,6 +17921,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "kanamycin_vendor_name": { @@ -15656,6 +17939,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -15678,6 +17967,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15701,6 +17996,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "kanamycin_testing_standard_details": { @@ -15719,6 +18017,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "kanamycin_susceptible_breakpoint": { @@ -15734,6 +18035,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "kanamycin_intermediate_breakpoint": { @@ -15746,6 +18050,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "kanamycin_resistant_breakpoint": { @@ -15761,6 +18068,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "levofloxacin_resistance_phenotype": { @@ -15776,6 +18086,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15799,6 +18115,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15822,6 +18144,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15845,6 +18173,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -15868,6 +18202,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -15890,6 +18230,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -15912,6 +18258,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "levofloxacin_vendor_name": { @@ -15927,6 +18276,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -15949,6 +18304,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -15972,6 +18333,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "levofloxacin_testing_standard_details": { @@ -15990,6 +18354,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "levofloxacin_susceptible_breakpoint": { @@ -16005,6 +18372,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "levofloxacin_intermediate_breakpoint": { @@ -16017,6 +18387,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "levofloxacin_resistant_breakpoint": { @@ -16032,6 +18405,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "linezolid_resistance_phenotype": { @@ -16047,6 +18423,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16070,6 +18452,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16093,6 +18481,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16116,6 +18510,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16139,6 +18539,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -16161,6 +18567,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -16183,6 +18595,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "linezolid_vendor_name": { @@ -16198,6 +18613,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -16220,6 +18641,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16243,6 +18670,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "linezolid_testing_standard_details": { @@ -16261,6 +18691,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "linezolid_susceptible_breakpoint": { @@ -16276,6 +18709,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "linezolid_intermediate_breakpoint": { @@ -16288,6 +18724,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "linezolid_resistant_breakpoint": { @@ -16303,6 +18742,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "meropenem_resistance_phenotype": { @@ -16318,6 +18760,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16341,6 +18789,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16364,6 +18818,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16387,6 +18847,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16410,6 +18876,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -16432,6 +18904,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -16454,6 +18932,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "meropenem_vendor_name": { @@ -16469,6 +18950,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -16491,6 +18978,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16514,6 +19007,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "meropenem_testing_standard_details": { @@ -16532,6 +19028,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "meropenem_susceptible_breakpoint": { @@ -16547,6 +19046,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "meropenem_intermediate_breakpoint": { @@ -16559,6 +19061,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "meropenem_resistant_breakpoint": { @@ -16574,6 +19079,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nalidixic_acid_resistance_phenotype": { @@ -16589,6 +19097,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16612,6 +19126,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16635,6 +19155,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16658,6 +19184,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16681,6 +19213,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -16703,6 +19241,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -16725,6 +19269,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nalidixic_acid_vendor_name": { @@ -16740,6 +19287,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -16762,6 +19315,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16785,6 +19344,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nalidixic_acid_testing_standard_details": { @@ -16803,6 +19365,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nalidixic_acid_susceptible_breakpoint": { @@ -16818,6 +19383,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nalidixic_acid_intermediate_breakpoint": { @@ -16830,6 +19398,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nalidixic_acid_resistant_breakpoint": { @@ -16845,6 +19416,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nitrofurantoin_resistance_phenotype": { @@ -16860,6 +19434,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -16883,6 +19463,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16906,6 +19492,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16929,6 +19521,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -16952,6 +19550,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -16974,6 +19578,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -16996,6 +19606,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nitrofurantoin_vendor_name": { @@ -17011,6 +19624,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -17033,6 +19652,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17056,6 +19681,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nitrofurantoin_testing_standard_details": { @@ -17074,6 +19702,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nitrofurantoin_susceptible_breakpoint": { @@ -17089,6 +19720,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nitrofurantoin_intermediate_breakpoint": { @@ -17101,6 +19735,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "nitrofurantoin_resistant_breakpoint": { @@ -17116,6 +19753,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "norfloxacin_resistance_phenotype": { @@ -17131,6 +19771,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17154,6 +19800,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17177,6 +19829,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17200,6 +19858,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17223,6 +19887,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -17245,6 +19915,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -17267,6 +19943,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "norfloxacin_vendor_name": { @@ -17282,6 +19961,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -17304,6 +19989,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17327,6 +20018,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "norfloxacin_testing_standard_details": { @@ -17345,6 +20039,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "norfloxacin_susceptible_breakpoint": { @@ -17360,6 +20057,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "norfloxacin_intermediate_breakpoint": { @@ -17372,6 +20072,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "norfloxacin_resistant_breakpoint": { @@ -17387,10 +20090,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_resistance_phenotype": { - "name": "oxolinic-acid_resistance_phenotype", + "oxolinicacid_resistance_phenotype": { + "name": "oxolinicacid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "oxolinic-acid_resistance_phenotype", "comments": [ @@ -17402,6 +20108,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17412,8 +20124,8 @@ } ] }, - "oxolinic-acid_measurement": { - "name": "oxolinic-acid_measurement", + "oxolinicacid_measurement": { + "name": "oxolinicacid_measurement", "description": "The measured value of oxolinic-acid resistance.", "title": "oxolinic-acid_measurement", "comments": [ @@ -17425,6 +20137,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17435,8 +20153,8 @@ } ] }, - "oxolinic-acid_measurement_units": { - "name": "oxolinic-acid_measurement_units", + "oxolinicacid_measurement_units": { + "name": "oxolinicacid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "oxolinic-acid_measurement_units", "comments": [ @@ -17448,6 +20166,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17458,8 +20182,8 @@ } ] }, - "oxolinic-acid_measurement_sign": { - "name": "oxolinic-acid_measurement_sign", + "oxolinicacid_measurement_sign": { + "name": "oxolinicacid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "oxolinic-acid_measurement_sign", "comments": [ @@ -17471,6 +20195,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17481,8 +20211,8 @@ } ] }, - "oxolinic-acid_laboratory_typing_method": { - "name": "oxolinic-acid_laboratory_typing_method", + "oxolinicacid_laboratory_typing_method": { + "name": "oxolinicacid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "oxolinic-acid_laboratory_typing_method", "comments": [ @@ -17494,6 +20224,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -17503,8 +20239,8 @@ } ] }, - "oxolinic-acid_laboratory_typing_platform": { - "name": "oxolinic-acid_laboratory_typing_platform", + "oxolinicacid_laboratory_typing_platform": { + "name": "oxolinicacid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "oxolinic-acid_laboratory_typing_platform", "comments": [ @@ -17516,6 +20252,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -17525,8 +20267,8 @@ } ] }, - "oxolinic-acid_laboratory_typing_platform_version": { - "name": "oxolinic-acid_laboratory_typing_platform_version", + "oxolinicacid_laboratory_typing_platform_version": { + "name": "oxolinicacid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "oxolinic-acid_laboratory_typing_platform_version", "comments": [ @@ -17538,10 +20280,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_vendor_name": { - "name": "oxolinic-acid_vendor_name", + "oxolinicacid_vendor_name": { + "name": "oxolinicacid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "oxolinic-acid_vendor_name", "comments": [ @@ -17553,6 +20298,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -17562,8 +20313,8 @@ } ] }, - "oxolinic-acid_testing_standard": { - "name": "oxolinic-acid_testing_standard", + "oxolinicacid_testing_standard": { + "name": "oxolinicacid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "oxolinic-acid_testing_standard", "comments": [ @@ -17575,6 +20326,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17585,8 +20342,8 @@ } ] }, - "oxolinic-acid_testing_standard_version": { - "name": "oxolinic-acid_testing_standard_version", + "oxolinicacid_testing_standard_version": { + "name": "oxolinicacid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "oxolinic-acid_testing_standard_version", "comments": [ @@ -17598,10 +20355,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_testing_standard_details": { - "name": "oxolinic-acid_testing_standard_details", + "oxolinicacid_testing_standard_details": { + "name": "oxolinicacid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "oxolinic-acid_testing_standard_details", "comments": [ @@ -17616,10 +20376,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_susceptible_breakpoint": { - "name": "oxolinic-acid_susceptible_breakpoint", + "oxolinicacid_susceptible_breakpoint": { + "name": "oxolinicacid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "oxolinic-acid_susceptible_breakpoint", "comments": [ @@ -17631,10 +20394,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_intermediate_breakpoint": { - "name": "oxolinic-acid_intermediate_breakpoint", + "oxolinicacid_intermediate_breakpoint": { + "name": "oxolinicacid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "oxolinic-acid_intermediate_breakpoint", "examples": [ @@ -17643,10 +20409,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_resistant_breakpoint": { - "name": "oxolinic-acid_resistant_breakpoint", + "oxolinicacid_resistant_breakpoint": { + "name": "oxolinicacid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "oxolinic-acid_resistant_breakpoint", "comments": [ @@ -17658,6 +20427,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "oxytetracycline_resistance_phenotype": { @@ -17673,6 +20445,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17696,6 +20474,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17719,6 +20503,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17742,6 +20532,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17765,6 +20561,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -17787,6 +20589,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -17809,6 +20617,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "oxytetracycline_vendor_name": { @@ -17824,6 +20635,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -17846,6 +20663,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17869,6 +20692,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "oxytetracycline_testing_standard_details": { @@ -17887,6 +20713,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "oxytetracycline_susceptible_breakpoint": { @@ -17902,6 +20731,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "oxytetracycline_intermediate_breakpoint": { @@ -17914,6 +20746,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "oxytetracycline_resistant_breakpoint": { @@ -17929,6 +20764,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "piperacillin_resistance_phenotype": { @@ -17944,6 +20782,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -17967,6 +20811,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -17990,6 +20840,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18013,6 +20869,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18036,6 +20898,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -18058,6 +20926,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -18080,6 +20954,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "piperacillin_vendor_name": { @@ -18095,6 +20972,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -18117,6 +21000,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18140,6 +21029,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "piperacillin_testing_standard_details": { @@ -18158,6 +21050,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "piperacillin_susceptible_breakpoint": { @@ -18173,6 +21068,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "piperacillin_intermediate_breakpoint": { @@ -18185,6 +21083,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "piperacillin_resistant_breakpoint": { @@ -18200,10 +21101,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_resistance_phenotype": { - "name": "piperacillin-tazobactam_resistance_phenotype", + "piperacillintazobactam_resistance_phenotype": { + "name": "piperacillintazobactam_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "piperacillin-tazobactam_resistance_phenotype", "comments": [ @@ -18215,6 +21119,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18225,8 +21135,8 @@ } ] }, - "piperacillin-tazobactam_measurement": { - "name": "piperacillin-tazobactam_measurement", + "piperacillintazobactam_measurement": { + "name": "piperacillintazobactam_measurement", "description": "The measured value of piperacillin-tazobactam resistance.", "title": "piperacillin-tazobactam_measurement", "comments": [ @@ -18238,6 +21148,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18248,8 +21164,8 @@ } ] }, - "piperacillin-tazobactam_measurement_units": { - "name": "piperacillin-tazobactam_measurement_units", + "piperacillintazobactam_measurement_units": { + "name": "piperacillintazobactam_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "piperacillin-tazobactam_measurement_units", "comments": [ @@ -18261,6 +21177,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18271,8 +21193,8 @@ } ] }, - "piperacillin-tazobactam_measurement_sign": { - "name": "piperacillin-tazobactam_measurement_sign", + "piperacillintazobactam_measurement_sign": { + "name": "piperacillintazobactam_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "piperacillin-tazobactam_measurement_sign", "comments": [ @@ -18284,6 +21206,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18294,8 +21222,8 @@ } ] }, - "piperacillin-tazobactam_laboratory_typing_method": { - "name": "piperacillin-tazobactam_laboratory_typing_method", + "piperacillintazobactam_laboratory_typing_method": { + "name": "piperacillintazobactam_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "piperacillin-tazobactam_laboratory_typing_method", "comments": [ @@ -18307,6 +21235,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -18316,8 +21250,8 @@ } ] }, - "piperacillin-tazobactam_laboratory_typing_platform": { - "name": "piperacillin-tazobactam_laboratory_typing_platform", + "piperacillintazobactam_laboratory_typing_platform": { + "name": "piperacillintazobactam_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "piperacillin-tazobactam_laboratory_typing_platform", "comments": [ @@ -18329,6 +21263,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -18338,8 +21278,8 @@ } ] }, - "piperacillin-tazobactam_laboratory_typing_platform_version": { - "name": "piperacillin-tazobactam_laboratory_typing_platform_version", + "piperacillintazobactam_laboratory_typing_platform_version": { + "name": "piperacillintazobactam_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "piperacillin-tazobactam_laboratory_typing_platform_version", "comments": [ @@ -18351,10 +21291,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_vendor_name": { - "name": "piperacillin-tazobactam_vendor_name", + "piperacillintazobactam_vendor_name": { + "name": "piperacillintazobactam_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "piperacillin-tazobactam_vendor_name", "comments": [ @@ -18366,6 +21309,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -18375,8 +21324,8 @@ } ] }, - "piperacillin-tazobactam_testing_standard": { - "name": "piperacillin-tazobactam_testing_standard", + "piperacillintazobactam_testing_standard": { + "name": "piperacillintazobactam_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "piperacillin-tazobactam_testing_standard", "comments": [ @@ -18388,6 +21337,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18398,8 +21353,8 @@ } ] }, - "piperacillin-tazobactam_testing_standard_version": { - "name": "piperacillin-tazobactam_testing_standard_version", + "piperacillintazobactam_testing_standard_version": { + "name": "piperacillintazobactam_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "piperacillin-tazobactam_testing_standard_version", "comments": [ @@ -18411,10 +21366,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_testing_standard_details": { - "name": "piperacillin-tazobactam_testing_standard_details", + "piperacillintazobactam_testing_standard_details": { + "name": "piperacillintazobactam_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "piperacillin-tazobactam_testing_standard_details", "comments": [ @@ -18429,10 +21387,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_susceptible_breakpoint": { - "name": "piperacillin-tazobactam_susceptible_breakpoint", + "piperacillintazobactam_susceptible_breakpoint": { + "name": "piperacillintazobactam_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "piperacillin-tazobactam_susceptible_breakpoint", "comments": [ @@ -18444,10 +21405,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_intermediate_breakpoint": { - "name": "piperacillin-tazobactam_intermediate_breakpoint", + "piperacillintazobactam_intermediate_breakpoint": { + "name": "piperacillintazobactam_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "piperacillin-tazobactam_intermediate_breakpoint", "examples": [ @@ -18456,10 +21420,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_resistant_breakpoint": { - "name": "piperacillin-tazobactam_resistant_breakpoint", + "piperacillintazobactam_resistant_breakpoint": { + "name": "piperacillintazobactam_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "piperacillin-tazobactam_resistant_breakpoint", "comments": [ @@ -18471,10 +21438,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "polymyxin-b_resistance_phenotype": { - "name": "polymyxin-b_resistance_phenotype", + "polymyxinb_resistance_phenotype": { + "name": "polymyxinb_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "polymyxin-b_resistance_phenotype", "comments": [ @@ -18486,6 +21456,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18496,8 +21472,8 @@ } ] }, - "polymyxin-b_measurement": { - "name": "polymyxin-b_measurement", + "polymyxinb_measurement": { + "name": "polymyxinb_measurement", "description": "The measured value of polymyxin B resistance.", "title": "polymyxin-b_measurement", "comments": [ @@ -18509,6 +21485,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18519,8 +21501,8 @@ } ] }, - "polymyxin-b_measurement_units": { - "name": "polymyxin-b_measurement_units", + "polymyxinb_measurement_units": { + "name": "polymyxinb_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "polymyxin-b_measurement_units", "comments": [ @@ -18532,6 +21514,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18542,8 +21530,8 @@ } ] }, - "polymyxin-b_measurement_sign": { - "name": "polymyxin-b_measurement_sign", + "polymyxinb_measurement_sign": { + "name": "polymyxinb_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "polymyxin-b_measurement_sign", "comments": [ @@ -18555,6 +21543,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18565,8 +21559,8 @@ } ] }, - "polymyxin-b_laboratory_typing_method": { - "name": "polymyxin-b_laboratory_typing_method", + "polymyxinb_laboratory_typing_method": { + "name": "polymyxinb_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "polymyxin-b_laboratory_typing_method", "comments": [ @@ -18578,6 +21572,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -18587,8 +21587,8 @@ } ] }, - "polymyxin-b_laboratory_typing_platform": { - "name": "polymyxin-b_laboratory_typing_platform", + "polymyxinb_laboratory_typing_platform": { + "name": "polymyxinb_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "polymyxin-b_laboratory_typing_platform", "comments": [ @@ -18600,6 +21600,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -18609,8 +21615,8 @@ } ] }, - "polymyxin-b_laboratory_typing_platform_version": { - "name": "polymyxin-b_laboratory_typing_platform_version", + "polymyxinb_laboratory_typing_platform_version": { + "name": "polymyxinb_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "polymyxin-b_laboratory_typing_platform_version", "comments": [ @@ -18622,10 +21628,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "polymyxin-b_vendor_name": { - "name": "polymyxin-b_vendor_name", + "polymyxinb_vendor_name": { + "name": "polymyxinb_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "polymyxin-b_vendor_name", "comments": [ @@ -18637,6 +21646,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -18646,8 +21661,8 @@ } ] }, - "polymyxin-b_testing_standard": { - "name": "polymyxin-b_testing_standard", + "polymyxinb_testing_standard": { + "name": "polymyxinb_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "polymyxin-b_testing_standard", "comments": [ @@ -18659,6 +21674,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18669,8 +21690,8 @@ } ] }, - "polymyxin-b_testing_standard_version": { - "name": "polymyxin-b_testing_standard_version", + "polymyxinb_testing_standard_version": { + "name": "polymyxinb_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "polymyxin-b_testing_standard_version", "comments": [ @@ -18682,10 +21703,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "polymyxin-b_testing_standard_details": { - "name": "polymyxin-b_testing_standard_details", + "polymyxinb_testing_standard_details": { + "name": "polymyxinb_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "polymyxin-b_testing_standard_details", "comments": [ @@ -18700,10 +21724,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "polymyxin-b_susceptible_breakpoint": { - "name": "polymyxin-b_susceptible_breakpoint", + "polymyxinb_susceptible_breakpoint": { + "name": "polymyxinb_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "polymyxin-b_susceptible_breakpoint", "comments": [ @@ -18715,10 +21742,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "polymyxin-b_intermediate_breakpoint": { - "name": "polymyxin-b_intermediate_breakpoint", + "polymyxinb_intermediate_breakpoint": { + "name": "polymyxinb_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "polymyxin-b_intermediate_breakpoint", "examples": [ @@ -18727,10 +21757,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "polymyxin-b_resistant_breakpoint": { - "name": "polymyxin-b_resistant_breakpoint", + "polymyxinb_resistant_breakpoint": { + "name": "polymyxinb_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "polymyxin-b_resistant_breakpoint", "comments": [ @@ -18742,10 +21775,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_resistance_phenotype": { - "name": "quinupristin-dalfopristin_resistance_phenotype", + "quinupristindalfopristin_resistance_phenotype": { + "name": "quinupristindalfopristin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "quinupristin-dalfopristin_resistance_phenotype", "comments": [ @@ -18757,6 +21793,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18767,8 +21809,8 @@ } ] }, - "quinupristin-dalfopristin_measurement": { - "name": "quinupristin-dalfopristin_measurement", + "quinupristindalfopristin_measurement": { + "name": "quinupristindalfopristin_measurement", "description": "The measured value of quinupristin-dalfopristin resistance.", "title": "quinupristin-dalfopristin_measurement", "comments": [ @@ -18780,6 +21822,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18790,8 +21838,8 @@ } ] }, - "quinupristin-dalfopristin_measurement_units": { - "name": "quinupristin-dalfopristin_measurement_units", + "quinupristindalfopristin_measurement_units": { + "name": "quinupristindalfopristin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "quinupristin-dalfopristin_measurement_units", "comments": [ @@ -18803,6 +21851,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18813,8 +21867,8 @@ } ] }, - "quinupristin-dalfopristin_measurement_sign": { - "name": "quinupristin-dalfopristin_measurement_sign", + "quinupristindalfopristin_measurement_sign": { + "name": "quinupristindalfopristin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "quinupristin-dalfopristin_measurement_sign", "comments": [ @@ -18826,6 +21880,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -18836,8 +21896,8 @@ } ] }, - "quinupristin-dalfopristin_laboratory_typing_method": { - "name": "quinupristin-dalfopristin_laboratory_typing_method", + "quinupristindalfopristin_laboratory_typing_method": { + "name": "quinupristindalfopristin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "quinupristin-dalfopristin_laboratory_typing_method", "comments": [ @@ -18849,6 +21909,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -18858,8 +21924,8 @@ } ] }, - "quinupristin-dalfopristin_laboratory_typing_platform": { - "name": "quinupristin-dalfopristin_laboratory_typing_platform", + "quinupristindalfopristin_laboratory_typing_platform": { + "name": "quinupristindalfopristin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "quinupristin-dalfopristin_laboratory_typing_platform", "comments": [ @@ -18871,6 +21937,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -18880,8 +21952,8 @@ } ] }, - "quinupristin-dalfopristin_laboratory_typing_platform_version": { - "name": "quinupristin-dalfopristin_laboratory_typing_platform_version", + "quinupristindalfopristin_laboratory_typing_platform_version": { + "name": "quinupristindalfopristin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "quinupristin-dalfopristin_laboratory_typing_platform_version", "comments": [ @@ -18893,10 +21965,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_vendor_name": { - "name": "quinupristin-dalfopristin_vendor_name", + "quinupristindalfopristin_vendor_name": { + "name": "quinupristindalfopristin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "quinupristin-dalfopristin_vendor_name", "comments": [ @@ -18908,6 +21983,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -18917,8 +21998,8 @@ } ] }, - "quinupristin-dalfopristin_testing_standard": { - "name": "quinupristin-dalfopristin_testing_standard", + "quinupristindalfopristin_testing_standard": { + "name": "quinupristindalfopristin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "quinupristin-dalfopristin_testing_standard", "comments": [ @@ -18930,6 +22011,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -18940,8 +22027,8 @@ } ] }, - "quinupristin-dalfopristin_testing_standard_version": { - "name": "quinupristin-dalfopristin_testing_standard_version", + "quinupristindalfopristin_testing_standard_version": { + "name": "quinupristindalfopristin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "quinupristin-dalfopristin_testing_standard_version", "comments": [ @@ -18953,10 +22040,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_testing_standard_details": { - "name": "quinupristin-dalfopristin_testing_standard_details", + "quinupristindalfopristin_testing_standard_details": { + "name": "quinupristindalfopristin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "quinupristin-dalfopristin_testing_standard_details", "comments": [ @@ -18971,10 +22061,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_susceptible_breakpoint": { - "name": "quinupristin-dalfopristin_susceptible_breakpoint", + "quinupristindalfopristin_susceptible_breakpoint": { + "name": "quinupristindalfopristin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "quinupristin-dalfopristin_susceptible_breakpoint", "comments": [ @@ -18986,10 +22079,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_intermediate_breakpoint": { - "name": "quinupristin-dalfopristin_intermediate_breakpoint", + "quinupristindalfopristin_intermediate_breakpoint": { + "name": "quinupristindalfopristin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "quinupristin-dalfopristin_intermediate_breakpoint", "examples": [ @@ -18998,10 +22094,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_resistant_breakpoint": { - "name": "quinupristin-dalfopristin_resistant_breakpoint", + "quinupristindalfopristin_resistant_breakpoint": { + "name": "quinupristindalfopristin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "quinupristin-dalfopristin_resistant_breakpoint", "comments": [ @@ -19013,6 +22112,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "streptomycin_resistance_phenotype": { @@ -19028,6 +22130,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19051,6 +22159,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19074,6 +22188,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19097,6 +22217,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19120,6 +22246,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -19142,6 +22274,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -19164,6 +22302,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "streptomycin_vendor_name": { @@ -19179,6 +22320,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -19201,6 +22348,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19224,6 +22377,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "streptomycin_testing_standard_details": { @@ -19242,6 +22398,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "streptomycin_susceptible_breakpoint": { @@ -19257,6 +22416,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "streptomycin_intermediate_breakpoint": { @@ -19269,6 +22431,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "streptomycin_resistant_breakpoint": { @@ -19284,6 +22449,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sulfisoxazole_resistance_phenotype": { @@ -19299,6 +22467,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19322,6 +22496,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19345,6 +22525,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19368,6 +22554,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19391,6 +22583,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -19413,6 +22611,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -19435,6 +22639,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sulfisoxazole_vendor_name": { @@ -19450,6 +22657,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -19472,6 +22685,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19495,6 +22714,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sulfisoxazole_testing_standard_details": { @@ -19513,6 +22735,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sulfisoxazole_susceptible_breakpoint": { @@ -19528,6 +22753,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sulfisoxazole_intermediate_breakpoint": { @@ -19540,6 +22768,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "sulfisoxazole_resistant_breakpoint": { @@ -19555,6 +22786,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "telithromycin_resistance_phenotype": { @@ -19570,6 +22804,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19593,6 +22833,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19616,6 +22862,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19639,6 +22891,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19662,6 +22920,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -19684,6 +22948,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -19706,6 +22976,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "telithromycin_vendor_name": { @@ -19721,6 +22994,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -19743,6 +23022,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19766,6 +23051,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "telithromycin_testing_standard_details": { @@ -19784,6 +23072,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "telithromycin_susceptible_breakpoint": { @@ -19799,6 +23090,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "telithromycin_intermediate_breakpoint": { @@ -19811,6 +23105,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "telithromycin_resistant_breakpoint": { @@ -19826,6 +23123,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tetracycline_resistance_phenotype": { @@ -19841,6 +23141,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -19864,6 +23170,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19887,6 +23199,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19910,6 +23228,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -19933,6 +23257,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -19955,6 +23285,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -19977,6 +23313,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tetracycline_vendor_name": { @@ -19992,6 +23331,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -20014,6 +23359,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -20037,6 +23388,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tetracycline_testing_standard_details": { @@ -20055,6 +23409,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tetracycline_susceptible_breakpoint": { @@ -20070,6 +23427,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tetracycline_intermediate_breakpoint": { @@ -20082,6 +23442,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tetracycline_resistant_breakpoint": { @@ -20097,6 +23460,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tigecycline_resistance_phenotype": { @@ -20112,6 +23478,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -20135,6 +23507,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -20158,6 +23536,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -20181,6 +23565,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -20204,6 +23594,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -20226,6 +23622,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -20248,6 +23650,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tigecycline_vendor_name": { @@ -20263,6 +23668,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -20285,6 +23696,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -20308,6 +23725,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tigecycline_testing_standard_details": { @@ -20326,6 +23746,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tigecycline_susceptible_breakpoint": { @@ -20341,6 +23764,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tigecycline_intermediate_breakpoint": { @@ -20353,6 +23779,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "tigecycline_resistant_breakpoint": { @@ -20368,10 +23797,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_resistance_phenotype": { - "name": "trimethoprim-sulfamethoxazole_resistance_phenotype", + "trimethoprimsulfamethoxazole_resistance_phenotype": { + "name": "trimethoprimsulfamethoxazole_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "trimethoprim-sulfamethoxazole_resistance_phenotype", "comments": [ @@ -20383,6 +23815,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -20393,8 +23831,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_measurement": { - "name": "trimethoprim-sulfamethoxazole_measurement", + "trimethoprimsulfamethoxazole_measurement": { + "name": "trimethoprimsulfamethoxazole_measurement", "description": "The measured value of trimethoprim-sulfamethoxazole resistance.", "title": "trimethoprim-sulfamethoxazole_measurement", "comments": [ @@ -20406,6 +23844,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -20416,8 +23860,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_measurement_units": { - "name": "trimethoprim-sulfamethoxazole_measurement_units", + "trimethoprimsulfamethoxazole_measurement_units": { + "name": "trimethoprimsulfamethoxazole_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "trimethoprim-sulfamethoxazole_measurement_units", "comments": [ @@ -20429,6 +23873,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -20439,8 +23889,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_measurement_sign": { - "name": "trimethoprim-sulfamethoxazole_measurement_sign", + "trimethoprimsulfamethoxazole_measurement_sign": { + "name": "trimethoprimsulfamethoxazole_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "trimethoprim-sulfamethoxazole_measurement_sign", "comments": [ @@ -20452,6 +23902,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], + "domain_of": [ + "GRDI" + ], "required": true, "any_of": [ { @@ -20462,8 +23918,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_laboratory_typing_method": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_method", + "trimethoprimsulfamethoxazole_laboratory_typing_method": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "trimethoprim-sulfamethoxazole_laboratory_typing_method", "comments": [ @@ -20475,6 +23931,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_method menu" @@ -20484,8 +23946,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_laboratory_typing_platform": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", + "trimethoprimsulfamethoxazole_laboratory_typing_platform": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", "comments": [ @@ -20497,6 +23959,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_laboratory_typing_platform menu" @@ -20506,8 +23974,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", + "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", "comments": [ @@ -20519,10 +23987,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_vendor_name": { - "name": "trimethoprim-sulfamethoxazole_vendor_name", + "trimethoprimsulfamethoxazole_vendor_name": { + "name": "trimethoprimsulfamethoxazole_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "trimethoprim-sulfamethoxazole_vendor_name", "comments": [ @@ -20534,6 +24005,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], + "domain_of": [ + "GRDI" + ], "any_of": [ { "range": "antimicrobial_vendor_name menu" @@ -20543,8 +24020,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_testing_standard": { - "name": "trimethoprim-sulfamethoxazole_testing_standard", + "trimethoprimsulfamethoxazole_testing_standard": { + "name": "trimethoprimsulfamethoxazole_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "trimethoprim-sulfamethoxazole_testing_standard", "comments": [ @@ -20556,6 +24033,12 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], + "domain_of": [ + "GRDI" + ], "recommended": true, "any_of": [ { @@ -20566,8 +24049,8 @@ } ] }, - "trimethoprim-sulfamethoxazole_testing_standard_version": { - "name": "trimethoprim-sulfamethoxazole_testing_standard_version", + "trimethoprimsulfamethoxazole_testing_standard_version": { + "name": "trimethoprimsulfamethoxazole_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "trimethoprim-sulfamethoxazole_testing_standard_version", "comments": [ @@ -20579,10 +24062,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_testing_standard_details": { - "name": "trimethoprim-sulfamethoxazole_testing_standard_details", + "trimethoprimsulfamethoxazole_testing_standard_details": { + "name": "trimethoprimsulfamethoxazole_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "trimethoprim-sulfamethoxazole_testing_standard_details", "comments": [ @@ -20597,10 +24083,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_susceptible_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", + "trimethoprimsulfamethoxazole_susceptible_breakpoint": { + "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", "comments": [ @@ -20612,10 +24101,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_intermediate_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", + "trimethoprimsulfamethoxazole_intermediate_breakpoint": { + "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", "examples": [ @@ -20624,10 +24116,13 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_resistant_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_resistant_breakpoint", + "trimethoprimsulfamethoxazole_resistant_breakpoint": { + "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "trimethoprim-sulfamethoxazole_resistant_breakpoint", "comments": [ @@ -20639,6 +24134,9 @@ } ], "from_schema": "https://example.com/GRDI", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString" }, "authors": { @@ -20655,11 +24153,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "GRDI" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", "comments": [ @@ -20672,6 +24173,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "GRDI" + ], "range": "Provenance" } }, @@ -20687,13 +24191,13 @@ "from_schema": "https://example.com/GRDI", "is_a": "dh_interface", "slot_usage": { - "sample_collector_sample_ID": { - "name": "sample_collector_sample_ID", + "sample_collector_sample_id": { + "name": "sample_collector_sample_id", "rank": 1, "slot_group": "Sample collection and processing" }, - "alternative_sample_ID": { - "name": "alternative_sample_ID", + "alternative_sample_id": { + "name": "alternative_sample_id", "rank": 2, "slot_group": "Sample collection and processing" }, @@ -20717,8 +24221,8 @@ "rank": 6, "slot_group": "Sample collection and processing" }, - "sample_plan_ID": { - "name": "sample_plan_ID", + "sample_plan_id": { + "name": "sample_plan_id", "rank": 7, "slot_group": "Sample collection and processing" }, @@ -20762,48 +24266,48 @@ "rank": 15, "slot_group": "Sample collection and processing" }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "rank": 16, "slot_group": "Sample collection and processing" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 18, "slot_group": "Sample collection and processing" }, - "geo_loc_name (state/province/region)": { - "name": "geo_loc_name (state/province/region)", + "geo_loc_name_state_province_region": { + "name": "geo_loc_name_state_province_region", "rank": 19, "slot_group": "Sample collection and processing" }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 20, "slot_group": "Sample collection and processing" }, - "food_product_origin_geo_loc_name (country)": { - "name": "food_product_origin_geo_loc_name (country)", + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", "rank": 21, "slot_group": "Sample collection and processing" }, - "host_origin_geo_loc_name (country)": { - "name": "host_origin_geo_loc_name (country)", + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", "rank": 22, "slot_group": "Sample collection and processing" }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "rank": 23, "slot_group": "Sample collection and processing" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "rank": 24, "slot_group": "Sample collection and processing" }, @@ -21017,28 +24521,28 @@ "rank": 66, "slot_group": "Environmental conditions and measurements" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "rank": 67, "slot_group": "Host information" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 68, "slot_group": "Host information" }, - "host (ecotype)": { - "name": "host (ecotype)", + "host_ecotype": { + "name": "host_ecotype", "rank": 69, "slot_group": "Host information" }, - "host (breed)": { - "name": "host (breed)", + "host_breed": { + "name": "host_breed", "rank": 70, "slot_group": "Host information" }, - "host (food production name)": { - "name": "host (food production name)", + "host_food_production_name": { + "name": "host_food_production_name", "rank": 71, "slot_group": "Host information" }, @@ -21062,28 +24566,28 @@ "rank": 75, "slot_group": "Strain and isolation information" }, - "isolate_ID": { - "name": "isolate_ID", + "isolate_id": { + "name": "isolate_id", "rank": 76, "slot_group": "Strain and isolation information" }, - "alternative_isolate_ID": { - "name": "alternative_isolate_ID", + "alternative_isolate_id": { + "name": "alternative_isolate_id", "rank": 77, "slot_group": "Strain and isolation information" }, - "progeny_isolate_ID": { - "name": "progeny_isolate_ID", + "progeny_isolate_id": { + "name": "progeny_isolate_id", "rank": 78, "slot_group": "Strain and isolation information" }, - "IRIDA_isolate_ID": { - "name": "IRIDA_isolate_ID", + "irida_isolate_id": { + "name": "irida_isolate_id", "rank": 79, "slot_group": "Strain and isolation information" }, - "IRIDA_project_ID": { - "name": "IRIDA_project_ID", + "irida_project_id": { + "name": "irida_project_id", "rank": 80, "slot_group": "Strain and isolation information" }, @@ -21147,8 +24651,8 @@ "rank": 92, "slot_group": "Strain and isolation information" }, - "library_ID": { - "name": "library_ID", + "library_id": { + "name": "library_id", "rank": 93, "slot_group": "Sequence information" }, @@ -21202,33 +24706,33 @@ "rank": 103, "slot_group": "Sequence information" }, - "DNA fragment length": { - "name": "DNA fragment length", + "dna_fragment_length": { + "name": "dna_fragment_length", "rank": 104, "slot_group": "Sequence information" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", "rank": 105, "slot_group": "Sequence information" }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", "rank": 106, "slot_group": "Sequence information" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 107, "slot_group": "Sequence information" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "rank": 108, "slot_group": "Sequence information" }, - "sequencing flow cell version": { - "name": "sequencing flow cell version", + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", "rank": 109, "slot_group": "Sequence information" }, @@ -21257,183 +24761,183 @@ "rank": 114, "slot_group": "Sequence information" }, - "quality control method name": { - "name": "quality control method name", + "quality_control_method_name": { + "name": "quality_control_method_name", "rank": 115, "slot_group": "Bioinformatics and QC metrics" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_version": { + "name": "quality_control_method_version", "rank": 116, "slot_group": "Bioinformatics and QC metrics" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_determination": { + "name": "quality_control_determination", "rank": 117, "slot_group": "Bioinformatics and QC metrics" }, - "quality control issues": { - "name": "quality control issues", + "quality_control_issues": { + "name": "quality_control_issues", "rank": 118, "slot_group": "Bioinformatics and QC metrics" }, - "quality control details": { - "name": "quality control details", + "quality_control_details": { + "name": "quality_control_details", "rank": 119, "slot_group": "Bioinformatics and QC metrics" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 120, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "rank": 121, "slot_group": "Bioinformatics and QC metrics" }, - "sequence assembly software name": { - "name": "sequence assembly software name", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", "rank": 122, "slot_group": "Bioinformatics and QC metrics" }, - "sequence assembly software version": { - "name": "sequence assembly software version", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", "rank": 123, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 124, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 125, "slot_group": "Bioinformatics and QC metrics" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 126, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 127, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 128, "slot_group": "Bioinformatics and QC metrics" }, - "genome completeness": { - "name": "genome completeness", + "genome_completeness": { + "name": "genome_completeness", "rank": 129, "slot_group": "Bioinformatics and QC metrics" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 130, "slot_group": "Bioinformatics and QC metrics" }, - "number of total reads": { - "name": "number of total reads", + "number_of_total_reads": { + "name": "number_of_total_reads", "rank": 131, "slot_group": "Bioinformatics and QC metrics" }, - "number of unique reads": { - "name": "number of unique reads", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "rank": 132, "slot_group": "Bioinformatics and QC metrics" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "rank": 133, "slot_group": "Bioinformatics and QC metrics" }, - "number of contigs": { - "name": "number of contigs", + "number_of_contigs": { + "name": "number_of_contigs", "rank": 134, "slot_group": "Bioinformatics and QC metrics" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "rank": 135, "slot_group": "Bioinformatics and QC metrics" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "rank": 136, "slot_group": "Bioinformatics and QC metrics" }, - "N50": { - "name": "N50", + "n50": { + "name": "n50", "rank": 137, "slot_group": "Bioinformatics and QC metrics" }, - "percent read contamination": { - "name": "percent read contamination", + "percent_read_contamination_": { + "name": "percent_read_contamination_", "rank": 138, "slot_group": "Bioinformatics and QC metrics" }, - "sequence assembly length": { - "name": "sequence assembly length", + "sequence_assembly_length": { + "name": "sequence_assembly_length", "rank": 139, "slot_group": "Bioinformatics and QC metrics" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "rank": 140, "slot_group": "Bioinformatics and QC metrics" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 141, "slot_group": "Bioinformatics and QC metrics" }, - "deduplication method": { - "name": "deduplication method", + "deduplication_method": { + "name": "deduplication_method", "rank": 142, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 143, "slot_group": "Bioinformatics and QC metrics" }, - "read mapping software name": { - "name": "read mapping software name", + "read_mapping_software_name": { + "name": "read_mapping_software_name", "rank": 144, "slot_group": "Taxonomic identification information" }, - "read mapping software version": { - "name": "read mapping software version", + "read_mapping_software_version": { + "name": "read_mapping_software_version", "rank": 145, "slot_group": "Taxonomic identification information" }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", "rank": 146, "slot_group": "Taxonomic identification information" }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", "rank": 147, "slot_group": "Taxonomic identification information" }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", "rank": 148, "slot_group": "Taxonomic identification information" }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", "rank": 149, "slot_group": "Taxonomic identification information" }, - "read mapping criteria": { - "name": "read mapping criteria", + "read_mapping_criteria": { + "name": "read_mapping_criteria", "rank": 150, "slot_group": "Taxonomic identification information" }, @@ -21452,8 +24956,8 @@ "rank": 153, "slot_group": "Public repository information" }, - "publication_ID": { - "name": "publication_ID", + "publication_id": { + "name": "publication_id", "rank": 154, "slot_group": "Public repository information" }, @@ -21472,13 +24976,13 @@ "rank": 157, "slot_group": "Public repository information" }, - "SRA_accession": { - "name": "SRA_accession", + "sra_accession": { + "name": "sra_accession", "rank": 158, "slot_group": "Public repository information" }, - "GenBank_accession": { - "name": "GenBank_accession", + "genbank_accession": { + "name": "genbank_accession", "rank": 159, "slot_group": "Public repository information" }, @@ -21507,28 +25011,28 @@ "rank": 164, "slot_group": "Risk assessment information" }, - "AMR_testing_by": { - "name": "AMR_testing_by", + "amr_testing_by": { + "name": "amr_testing_by", "rank": 165, "slot_group": "Antimicrobial resistance" }, - "AMR_testing_by_laboratory_name": { - "name": "AMR_testing_by_laboratory_name", + "amr_testing_by_laboratory_name": { + "name": "amr_testing_by_laboratory_name", "rank": 166, "slot_group": "Antimicrobial resistance" }, - "AMR_testing_by_contact_name": { - "name": "AMR_testing_by_contact_name", + "amr_testing_by_contact_name": { + "name": "amr_testing_by_contact_name", "rank": 167, "slot_group": "Antimicrobial resistance" }, - "AMR_testing_by_contact_email": { - "name": "AMR_testing_by_contact_email", + "amr_testing_by_contact_email": { + "name": "amr_testing_by_contact_email", "rank": 168, "slot_group": "Antimicrobial resistance" }, - "AMR_testing_date": { - "name": "AMR_testing_date", + "amr_testing_date": { + "name": "amr_testing_date", "rank": 169, "slot_group": "Antimicrobial resistance" }, @@ -21602,73 +25106,73 @@ "rank": 183, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_resistance_phenotype": { - "name": "amoxicillin-clavulanic_acid_resistance_phenotype", + "amoxicillinclavulanic_acid_resistance_phenotype": { + "name": "amoxicillinclavulanic_acid_resistance_phenotype", "rank": 184, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_measurement": { - "name": "amoxicillin-clavulanic_acid_measurement", + "amoxicillinclavulanic_acid_measurement": { + "name": "amoxicillinclavulanic_acid_measurement", "rank": 185, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_measurement_units": { - "name": "amoxicillin-clavulanic_acid_measurement_units", + "amoxicillinclavulanic_acid_measurement_units": { + "name": "amoxicillinclavulanic_acid_measurement_units", "rank": 186, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_measurement_sign": { - "name": "amoxicillin-clavulanic_acid_measurement_sign", + "amoxicillinclavulanic_acid_measurement_sign": { + "name": "amoxicillinclavulanic_acid_measurement_sign", "rank": 187, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_laboratory_typing_method": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_method", + "amoxicillinclavulanic_acid_laboratory_typing_method": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_method", "rank": 188, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_laboratory_typing_platform": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_platform", + "amoxicillinclavulanic_acid_laboratory_typing_platform": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform", "rank": 189, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_laboratory_typing_platform_version": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", + "amoxicillinclavulanic_acid_laboratory_typing_platform_version": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", "rank": 190, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_vendor_name": { - "name": "amoxicillin-clavulanic_acid_vendor_name", + "amoxicillinclavulanic_acid_vendor_name": { + "name": "amoxicillinclavulanic_acid_vendor_name", "rank": 191, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_testing_standard": { - "name": "amoxicillin-clavulanic_acid_testing_standard", + "amoxicillinclavulanic_acid_testing_standard": { + "name": "amoxicillinclavulanic_acid_testing_standard", "rank": 192, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_testing_standard_version": { - "name": "amoxicillin-clavulanic_acid_testing_standard_version", + "amoxicillinclavulanic_acid_testing_standard_version": { + "name": "amoxicillinclavulanic_acid_testing_standard_version", "rank": 193, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_testing_standard_details": { - "name": "amoxicillin-clavulanic_acid_testing_standard_details", + "amoxicillinclavulanic_acid_testing_standard_details": { + "name": "amoxicillinclavulanic_acid_testing_standard_details", "rank": 194, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_susceptible_breakpoint": { - "name": "amoxicillin-clavulanic_acid_susceptible_breakpoint", + "amoxicillinclavulanic_acid_susceptible_breakpoint": { + "name": "amoxicillinclavulanic_acid_susceptible_breakpoint", "rank": 195, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_intermediate_breakpoint": { - "name": "amoxicillin-clavulanic_acid_intermediate_breakpoint", + "amoxicillinclavulanic_acid_intermediate_breakpoint": { + "name": "amoxicillinclavulanic_acid_intermediate_breakpoint", "rank": 196, "slot_group": "Antimicrobial resistance" }, - "amoxicillin-clavulanic_acid_resistant_breakpoint": { - "name": "amoxicillin-clavulanic_acid_resistant_breakpoint", + "amoxicillinclavulanic_acid_resistant_breakpoint": { + "name": "amoxicillinclavulanic_acid_resistant_breakpoint", "rank": 197, "slot_group": "Antimicrobial resistance" }, @@ -22022,73 +25526,73 @@ "rank": 267, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_resistance_phenotype": { - "name": "cefotaxime-clavulanic_acid_resistance_phenotype", + "cefotaximeclavulanic_acid_resistance_phenotype": { + "name": "cefotaximeclavulanic_acid_resistance_phenotype", "rank": 268, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_measurement": { - "name": "cefotaxime-clavulanic_acid_measurement", + "cefotaximeclavulanic_acid_measurement": { + "name": "cefotaximeclavulanic_acid_measurement", "rank": 269, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_measurement_units": { - "name": "cefotaxime-clavulanic_acid_measurement_units", + "cefotaximeclavulanic_acid_measurement_units": { + "name": "cefotaximeclavulanic_acid_measurement_units", "rank": 270, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_measurement_sign": { - "name": "cefotaxime-clavulanic_acid_measurement_sign", + "cefotaximeclavulanic_acid_measurement_sign": { + "name": "cefotaximeclavulanic_acid_measurement_sign", "rank": 271, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_laboratory_typing_method": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_method", + "cefotaximeclavulanic_acid_laboratory_typing_method": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_method", "rank": 272, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_laboratory_typing_platform": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_platform", + "cefotaximeclavulanic_acid_laboratory_typing_platform": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform", "rank": 273, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_laboratory_typing_platform_version": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", + "cefotaximeclavulanic_acid_laboratory_typing_platform_version": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "rank": 274, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_vendor_name": { - "name": "cefotaxime-clavulanic_acid_vendor_name", + "cefotaximeclavulanic_acid_vendor_name": { + "name": "cefotaximeclavulanic_acid_vendor_name", "rank": 275, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_testing_standard": { - "name": "cefotaxime-clavulanic_acid_testing_standard", + "cefotaximeclavulanic_acid_testing_standard": { + "name": "cefotaximeclavulanic_acid_testing_standard", "rank": 276, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_testing_standard_version": { - "name": "cefotaxime-clavulanic_acid_testing_standard_version", + "cefotaximeclavulanic_acid_testing_standard_version": { + "name": "cefotaximeclavulanic_acid_testing_standard_version", "rank": 277, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_testing_standard_details": { - "name": "cefotaxime-clavulanic_acid_testing_standard_details", + "cefotaximeclavulanic_acid_testing_standard_details": { + "name": "cefotaximeclavulanic_acid_testing_standard_details", "rank": 278, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_susceptible_breakpoint": { - "name": "cefotaxime-clavulanic_acid_susceptible_breakpoint", + "cefotaximeclavulanic_acid_susceptible_breakpoint": { + "name": "cefotaximeclavulanic_acid_susceptible_breakpoint", "rank": 279, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_intermediate_breakpoint": { - "name": "cefotaxime-clavulanic_acid_intermediate_breakpoint", + "cefotaximeclavulanic_acid_intermediate_breakpoint": { + "name": "cefotaximeclavulanic_acid_intermediate_breakpoint", "rank": 280, "slot_group": "Antimicrobial resistance" }, - "cefotaxime-clavulanic_acid_resistant_breakpoint": { - "name": "cefotaxime-clavulanic_acid_resistant_breakpoint", + "cefotaximeclavulanic_acid_resistant_breakpoint": { + "name": "cefotaximeclavulanic_acid_resistant_breakpoint", "rank": 281, "slot_group": "Antimicrobial resistance" }, @@ -22302,73 +25806,73 @@ "rank": 323, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_resistance_phenotype": { - "name": "ceftazidime-clavulanic_acid_resistance_phenotype", + "ceftazidimeclavulanic_acid_resistance_phenotype": { + "name": "ceftazidimeclavulanic_acid_resistance_phenotype", "rank": 324, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_measurement": { - "name": "ceftazidime-clavulanic_acid_measurement", + "ceftazidimeclavulanic_acid_measurement": { + "name": "ceftazidimeclavulanic_acid_measurement", "rank": 325, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_measurement_units": { - "name": "ceftazidime-clavulanic_acid_measurement_units", + "ceftazidimeclavulanic_acid_measurement_units": { + "name": "ceftazidimeclavulanic_acid_measurement_units", "rank": 326, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_measurement_sign": { - "name": "ceftazidime-clavulanic_acid_measurement_sign", + "ceftazidimeclavulanic_acid_measurement_sign": { + "name": "ceftazidimeclavulanic_acid_measurement_sign", "rank": 327, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_laboratory_typing_method": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_method", + "ceftazidimeclavulanic_acid_laboratory_typing_method": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_method", "rank": 328, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_laboratory_typing_platform": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_platform", + "ceftazidimeclavulanic_acid_laboratory_typing_platform": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "rank": 329, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_laboratory_typing_platform_version": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", + "ceftazidimeclavulanic_acid_laboratory_typing_platform_version": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "rank": 330, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_vendor_name": { - "name": "ceftazidime-clavulanic_acid_vendor_name", + "ceftazidimeclavulanic_acid_vendor_name": { + "name": "ceftazidimeclavulanic_acid_vendor_name", "rank": 331, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_testing_standard": { - "name": "ceftazidime-clavulanic_acid_testing_standard", + "ceftazidimeclavulanic_acid_testing_standard": { + "name": "ceftazidimeclavulanic_acid_testing_standard", "rank": 332, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_testing_standard_version": { - "name": "ceftazidime-clavulanic_acid_testing_standard_version", + "ceftazidimeclavulanic_acid_testing_standard_version": { + "name": "ceftazidimeclavulanic_acid_testing_standard_version", "rank": 333, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_testing_standard_details": { - "name": "ceftazidime-clavulanic_acid_testing_standard_details", + "ceftazidimeclavulanic_acid_testing_standard_details": { + "name": "ceftazidimeclavulanic_acid_testing_standard_details", "rank": 334, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_susceptible_breakpoint": { - "name": "ceftazidime-clavulanic_acid_susceptible_breakpoint", + "ceftazidimeclavulanic_acid_susceptible_breakpoint": { + "name": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "rank": 335, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_intermediate_breakpoint": { - "name": "ceftazidime-clavulanic_acid_intermediate_breakpoint", + "ceftazidimeclavulanic_acid_intermediate_breakpoint": { + "name": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "rank": 336, "slot_group": "Antimicrobial resistance" }, - "ceftazidime-clavulanic_acid_resistant_breakpoint": { - "name": "ceftazidime-clavulanic_acid_resistant_breakpoint", + "ceftazidimeclavulanic_acid_resistant_breakpoint": { + "name": "ceftazidimeclavulanic_acid_resistant_breakpoint", "rank": 337, "slot_group": "Antimicrobial resistance" }, @@ -23702,73 +27206,73 @@ "rank": 603, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_resistance_phenotype": { - "name": "oxolinic-acid_resistance_phenotype", + "oxolinicacid_resistance_phenotype": { + "name": "oxolinicacid_resistance_phenotype", "rank": 604, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_measurement": { - "name": "oxolinic-acid_measurement", + "oxolinicacid_measurement": { + "name": "oxolinicacid_measurement", "rank": 605, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_measurement_units": { - "name": "oxolinic-acid_measurement_units", + "oxolinicacid_measurement_units": { + "name": "oxolinicacid_measurement_units", "rank": 606, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_measurement_sign": { - "name": "oxolinic-acid_measurement_sign", + "oxolinicacid_measurement_sign": { + "name": "oxolinicacid_measurement_sign", "rank": 607, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_laboratory_typing_method": { - "name": "oxolinic-acid_laboratory_typing_method", + "oxolinicacid_laboratory_typing_method": { + "name": "oxolinicacid_laboratory_typing_method", "rank": 608, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_laboratory_typing_platform": { - "name": "oxolinic-acid_laboratory_typing_platform", + "oxolinicacid_laboratory_typing_platform": { + "name": "oxolinicacid_laboratory_typing_platform", "rank": 609, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_laboratory_typing_platform_version": { - "name": "oxolinic-acid_laboratory_typing_platform_version", + "oxolinicacid_laboratory_typing_platform_version": { + "name": "oxolinicacid_laboratory_typing_platform_version", "rank": 610, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_vendor_name": { - "name": "oxolinic-acid_vendor_name", + "oxolinicacid_vendor_name": { + "name": "oxolinicacid_vendor_name", "rank": 611, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_testing_standard": { - "name": "oxolinic-acid_testing_standard", + "oxolinicacid_testing_standard": { + "name": "oxolinicacid_testing_standard", "rank": 612, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_testing_standard_version": { - "name": "oxolinic-acid_testing_standard_version", + "oxolinicacid_testing_standard_version": { + "name": "oxolinicacid_testing_standard_version", "rank": 613, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_testing_standard_details": { - "name": "oxolinic-acid_testing_standard_details", + "oxolinicacid_testing_standard_details": { + "name": "oxolinicacid_testing_standard_details", "rank": 614, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_susceptible_breakpoint": { - "name": "oxolinic-acid_susceptible_breakpoint", + "oxolinicacid_susceptible_breakpoint": { + "name": "oxolinicacid_susceptible_breakpoint", "rank": 615, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_intermediate_breakpoint": { - "name": "oxolinic-acid_intermediate_breakpoint", + "oxolinicacid_intermediate_breakpoint": { + "name": "oxolinicacid_intermediate_breakpoint", "rank": 616, "slot_group": "Antimicrobial resistance" }, - "oxolinic-acid_resistant_breakpoint": { - "name": "oxolinic-acid_resistant_breakpoint", + "oxolinicacid_resistant_breakpoint": { + "name": "oxolinicacid_resistant_breakpoint", "rank": 617, "slot_group": "Antimicrobial resistance" }, @@ -23912,213 +27416,213 @@ "rank": 645, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_resistance_phenotype": { - "name": "piperacillin-tazobactam_resistance_phenotype", + "piperacillintazobactam_resistance_phenotype": { + "name": "piperacillintazobactam_resistance_phenotype", "rank": 646, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_measurement": { - "name": "piperacillin-tazobactam_measurement", + "piperacillintazobactam_measurement": { + "name": "piperacillintazobactam_measurement", "rank": 647, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_measurement_units": { - "name": "piperacillin-tazobactam_measurement_units", + "piperacillintazobactam_measurement_units": { + "name": "piperacillintazobactam_measurement_units", "rank": 648, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_measurement_sign": { - "name": "piperacillin-tazobactam_measurement_sign", + "piperacillintazobactam_measurement_sign": { + "name": "piperacillintazobactam_measurement_sign", "rank": 649, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_laboratory_typing_method": { - "name": "piperacillin-tazobactam_laboratory_typing_method", + "piperacillintazobactam_laboratory_typing_method": { + "name": "piperacillintazobactam_laboratory_typing_method", "rank": 650, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_laboratory_typing_platform": { - "name": "piperacillin-tazobactam_laboratory_typing_platform", + "piperacillintazobactam_laboratory_typing_platform": { + "name": "piperacillintazobactam_laboratory_typing_platform", "rank": 651, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_laboratory_typing_platform_version": { - "name": "piperacillin-tazobactam_laboratory_typing_platform_version", + "piperacillintazobactam_laboratory_typing_platform_version": { + "name": "piperacillintazobactam_laboratory_typing_platform_version", "rank": 652, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_vendor_name": { - "name": "piperacillin-tazobactam_vendor_name", + "piperacillintazobactam_vendor_name": { + "name": "piperacillintazobactam_vendor_name", "rank": 653, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_testing_standard": { - "name": "piperacillin-tazobactam_testing_standard", + "piperacillintazobactam_testing_standard": { + "name": "piperacillintazobactam_testing_standard", "rank": 654, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_testing_standard_version": { - "name": "piperacillin-tazobactam_testing_standard_version", + "piperacillintazobactam_testing_standard_version": { + "name": "piperacillintazobactam_testing_standard_version", "rank": 655, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_testing_standard_details": { - "name": "piperacillin-tazobactam_testing_standard_details", + "piperacillintazobactam_testing_standard_details": { + "name": "piperacillintazobactam_testing_standard_details", "rank": 656, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_susceptible_breakpoint": { - "name": "piperacillin-tazobactam_susceptible_breakpoint", + "piperacillintazobactam_susceptible_breakpoint": { + "name": "piperacillintazobactam_susceptible_breakpoint", "rank": 657, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_intermediate_breakpoint": { - "name": "piperacillin-tazobactam_intermediate_breakpoint", + "piperacillintazobactam_intermediate_breakpoint": { + "name": "piperacillintazobactam_intermediate_breakpoint", "rank": 658, "slot_group": "Antimicrobial resistance" }, - "piperacillin-tazobactam_resistant_breakpoint": { - "name": "piperacillin-tazobactam_resistant_breakpoint", + "piperacillintazobactam_resistant_breakpoint": { + "name": "piperacillintazobactam_resistant_breakpoint", "rank": 659, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_resistance_phenotype": { - "name": "polymyxin-b_resistance_phenotype", + "polymyxinb_resistance_phenotype": { + "name": "polymyxinb_resistance_phenotype", "rank": 660, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_measurement": { - "name": "polymyxin-b_measurement", + "polymyxinb_measurement": { + "name": "polymyxinb_measurement", "rank": 661, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_measurement_units": { - "name": "polymyxin-b_measurement_units", + "polymyxinb_measurement_units": { + "name": "polymyxinb_measurement_units", "rank": 662, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_measurement_sign": { - "name": "polymyxin-b_measurement_sign", + "polymyxinb_measurement_sign": { + "name": "polymyxinb_measurement_sign", "rank": 663, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_laboratory_typing_method": { - "name": "polymyxin-b_laboratory_typing_method", + "polymyxinb_laboratory_typing_method": { + "name": "polymyxinb_laboratory_typing_method", "rank": 664, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_laboratory_typing_platform": { - "name": "polymyxin-b_laboratory_typing_platform", + "polymyxinb_laboratory_typing_platform": { + "name": "polymyxinb_laboratory_typing_platform", "rank": 665, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_laboratory_typing_platform_version": { - "name": "polymyxin-b_laboratory_typing_platform_version", + "polymyxinb_laboratory_typing_platform_version": { + "name": "polymyxinb_laboratory_typing_platform_version", "rank": 666, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_vendor_name": { - "name": "polymyxin-b_vendor_name", + "polymyxinb_vendor_name": { + "name": "polymyxinb_vendor_name", "rank": 667, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_testing_standard": { - "name": "polymyxin-b_testing_standard", + "polymyxinb_testing_standard": { + "name": "polymyxinb_testing_standard", "rank": 668, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_testing_standard_version": { - "name": "polymyxin-b_testing_standard_version", + "polymyxinb_testing_standard_version": { + "name": "polymyxinb_testing_standard_version", "rank": 669, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_testing_standard_details": { - "name": "polymyxin-b_testing_standard_details", + "polymyxinb_testing_standard_details": { + "name": "polymyxinb_testing_standard_details", "rank": 670, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_susceptible_breakpoint": { - "name": "polymyxin-b_susceptible_breakpoint", + "polymyxinb_susceptible_breakpoint": { + "name": "polymyxinb_susceptible_breakpoint", "rank": 671, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_intermediate_breakpoint": { - "name": "polymyxin-b_intermediate_breakpoint", + "polymyxinb_intermediate_breakpoint": { + "name": "polymyxinb_intermediate_breakpoint", "rank": 672, "slot_group": "Antimicrobial resistance" }, - "polymyxin-b_resistant_breakpoint": { - "name": "polymyxin-b_resistant_breakpoint", + "polymyxinb_resistant_breakpoint": { + "name": "polymyxinb_resistant_breakpoint", "rank": 673, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_resistance_phenotype": { - "name": "quinupristin-dalfopristin_resistance_phenotype", + "quinupristindalfopristin_resistance_phenotype": { + "name": "quinupristindalfopristin_resistance_phenotype", "rank": 674, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_measurement": { - "name": "quinupristin-dalfopristin_measurement", + "quinupristindalfopristin_measurement": { + "name": "quinupristindalfopristin_measurement", "rank": 675, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_measurement_units": { - "name": "quinupristin-dalfopristin_measurement_units", + "quinupristindalfopristin_measurement_units": { + "name": "quinupristindalfopristin_measurement_units", "rank": 676, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_measurement_sign": { - "name": "quinupristin-dalfopristin_measurement_sign", + "quinupristindalfopristin_measurement_sign": { + "name": "quinupristindalfopristin_measurement_sign", "rank": 677, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_laboratory_typing_method": { - "name": "quinupristin-dalfopristin_laboratory_typing_method", + "quinupristindalfopristin_laboratory_typing_method": { + "name": "quinupristindalfopristin_laboratory_typing_method", "rank": 678, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_laboratory_typing_platform": { - "name": "quinupristin-dalfopristin_laboratory_typing_platform", + "quinupristindalfopristin_laboratory_typing_platform": { + "name": "quinupristindalfopristin_laboratory_typing_platform", "rank": 679, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_laboratory_typing_platform_version": { - "name": "quinupristin-dalfopristin_laboratory_typing_platform_version", + "quinupristindalfopristin_laboratory_typing_platform_version": { + "name": "quinupristindalfopristin_laboratory_typing_platform_version", "rank": 680, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_vendor_name": { - "name": "quinupristin-dalfopristin_vendor_name", + "quinupristindalfopristin_vendor_name": { + "name": "quinupristindalfopristin_vendor_name", "rank": 681, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_testing_standard": { - "name": "quinupristin-dalfopristin_testing_standard", + "quinupristindalfopristin_testing_standard": { + "name": "quinupristindalfopristin_testing_standard", "rank": 682, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_testing_standard_version": { - "name": "quinupristin-dalfopristin_testing_standard_version", + "quinupristindalfopristin_testing_standard_version": { + "name": "quinupristindalfopristin_testing_standard_version", "rank": 683, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_testing_standard_details": { - "name": "quinupristin-dalfopristin_testing_standard_details", + "quinupristindalfopristin_testing_standard_details": { + "name": "quinupristindalfopristin_testing_standard_details", "rank": 684, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_susceptible_breakpoint": { - "name": "quinupristin-dalfopristin_susceptible_breakpoint", + "quinupristindalfopristin_susceptible_breakpoint": { + "name": "quinupristindalfopristin_susceptible_breakpoint", "rank": 685, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_intermediate_breakpoint": { - "name": "quinupristin-dalfopristin_intermediate_breakpoint", + "quinupristindalfopristin_intermediate_breakpoint": { + "name": "quinupristindalfopristin_intermediate_breakpoint", "rank": 686, "slot_group": "Antimicrobial resistance" }, - "quinupristin-dalfopristin_resistant_breakpoint": { - "name": "quinupristin-dalfopristin_resistant_breakpoint", + "quinupristindalfopristin_resistant_breakpoint": { + "name": "quinupristindalfopristin_resistant_breakpoint", "rank": 687, "slot_group": "Antimicrobial resistance" }, @@ -24472,73 +27976,73 @@ "rank": 757, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_resistance_phenotype": { - "name": "trimethoprim-sulfamethoxazole_resistance_phenotype", + "trimethoprimsulfamethoxazole_resistance_phenotype": { + "name": "trimethoprimsulfamethoxazole_resistance_phenotype", "rank": 758, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_measurement": { - "name": "trimethoprim-sulfamethoxazole_measurement", + "trimethoprimsulfamethoxazole_measurement": { + "name": "trimethoprimsulfamethoxazole_measurement", "rank": 759, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_measurement_units": { - "name": "trimethoprim-sulfamethoxazole_measurement_units", + "trimethoprimsulfamethoxazole_measurement_units": { + "name": "trimethoprimsulfamethoxazole_measurement_units", "rank": 760, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_measurement_sign": { - "name": "trimethoprim-sulfamethoxazole_measurement_sign", + "trimethoprimsulfamethoxazole_measurement_sign": { + "name": "trimethoprimsulfamethoxazole_measurement_sign", "rank": 761, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_laboratory_typing_method": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_method", + "trimethoprimsulfamethoxazole_laboratory_typing_method": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", "rank": 762, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_laboratory_typing_platform": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", + "trimethoprimsulfamethoxazole_laboratory_typing_platform": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", "rank": 763, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", + "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", "rank": 764, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_vendor_name": { - "name": "trimethoprim-sulfamethoxazole_vendor_name", + "trimethoprimsulfamethoxazole_vendor_name": { + "name": "trimethoprimsulfamethoxazole_vendor_name", "rank": 765, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_testing_standard": { - "name": "trimethoprim-sulfamethoxazole_testing_standard", + "trimethoprimsulfamethoxazole_testing_standard": { + "name": "trimethoprimsulfamethoxazole_testing_standard", "rank": 766, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_testing_standard_version": { - "name": "trimethoprim-sulfamethoxazole_testing_standard_version", + "trimethoprimsulfamethoxazole_testing_standard_version": { + "name": "trimethoprimsulfamethoxazole_testing_standard_version", "rank": 767, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_testing_standard_details": { - "name": "trimethoprim-sulfamethoxazole_testing_standard_details", + "trimethoprimsulfamethoxazole_testing_standard_details": { + "name": "trimethoprimsulfamethoxazole_testing_standard_details", "rank": 768, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_susceptible_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", + "trimethoprimsulfamethoxazole_susceptible_breakpoint": { + "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", "rank": 769, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_intermediate_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", + "trimethoprimsulfamethoxazole_intermediate_breakpoint": { + "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", "rank": 770, "slot_group": "Antimicrobial resistance" }, - "trimethoprim-sulfamethoxazole_resistant_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_resistant_breakpoint", + "trimethoprimsulfamethoxazole_resistant_breakpoint": { + "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", "rank": 771, "slot_group": "Antimicrobial resistance" }, @@ -24547,36 +28051,68 @@ "rank": 772, "slot_group": "Contributor acknowledgement" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 773, "slot_group": "Contributor acknowledgement" } }, "attributes": { - "sample_collector_sample_ID": { - "name": "sample_collector_sample_ID", + "sample_collector_sample_id": { + "name": "sample_collector_sample_id", "description": "The user-defined name for the sample.", "title": "sample_collector_sample_ID", + "comments": [ + "The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "ABCD123" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:sample_name", + "NCBI_BIOSAMPLE_Enterics:%2Asample_name", + "NCBI_ANTIBIOGRAM:%2Asample_name" + ], "rank": 1, "slot_uri": "GENEPIO:0001123", - "alias": "sample_collector_sample_ID", + "alias": "sample_collector_sample_id", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true - }, - "alternative_sample_ID": { - "name": "alternative_sample_ID", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "alternative_sample_id": { + "name": "alternative_sample_id", "description": "An alternative sample_ID assigned to the sample by another organization.", "title": "alternative_sample_ID", + "comments": [ + "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "ABCD1234[PHAC]" + }, + { + "value": "12345rev[CFIA]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 2, "slot_uri": "GENEPIO:0100427", - "alias": "alternative_sample_ID", + "alias": "alternative_sample_id", "owner": "GRDI", "domain_of": [ "GRDI" @@ -24589,7 +28125,19 @@ "name": "sample_collected_by", "description": "The name of the agency, organization or institution with which the sample collector is affiliated.", "title": "sample_collected_by", + "comments": [ + "Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:collected_by", + "NCBI_BIOSAMPLE_Enterics:%2Acollected_by" + ], "rank": 3, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", @@ -24598,12 +28146,28 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "sample_collected_by menu" + }, + { + "range": "null value menu" + } + ] }, "sample_collected_by_laboratory_name": { "name": "sample_collected_by_laboratory_name", "description": "The specific laboratory affiliation of the sample collector.", "title": "sample_collected_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", "rank": 4, "slot_uri": "GENEPIO:0100428", @@ -24619,7 +28183,18 @@ "name": "sample_collection_project_name", "description": "The name of the project/initiative/program for which the sample was collected.", "title": "sample_collection_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Watershed Project (HA-120)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:project_name" + ], "rank": 5, "slot_uri": "GENEPIO:0100429", "alias": "sample_collection_project_name", @@ -24634,6 +28209,14 @@ "name": "sample_plan_name", "description": "The name of the study design for a surveillance project.", "title": "sample_plan_name", + "comments": [ + "Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "National Microbiological Baseline Study in Broiler Chicken" + } + ], "from_schema": "https://example.com/GRDI", "rank": 6, "slot_uri": "GENEPIO:0100430", @@ -24646,14 +28229,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "sample_plan_ID": { - "name": "sample_plan_ID", + "sample_plan_id": { + "name": "sample_plan_id", "description": "The identifier of the study design for a surveillance project.", "title": "sample_plan_ID", + "comments": [ + "Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2001_M205" + } + ], "from_schema": "https://example.com/GRDI", "rank": 7, "slot_uri": "GENEPIO:0100431", - "alias": "sample_plan_ID", + "alias": "sample_plan_id", "owner": "GRDI", "domain_of": [ "GRDI" @@ -24666,6 +28257,14 @@ "name": "sample_collector_contact_name", "description": "The name or job title of the contact responsible for follow-up regarding the sample.", "title": "sample_collector_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", "rank": 8, "slot_uri": "GENEPIO:0100432", @@ -24681,6 +28280,14 @@ "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample_collector_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "johnnyblogs@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", "rank": 9, "slot_uri": "GENEPIO:0001156", @@ -24690,13 +28297,33 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "purpose_of_sampling": { "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Surveillance [GENEPIO:0100004]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:purpose_of_sampling", + "NCBI_BIOSAMPLE_Enterics:%2Apurpose_of_sampling" + ], "rank": 10, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", @@ -24705,13 +28332,33 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] }, "presampling_activity": { "name": "presampling_activity", "description": "The experimental activities or variables that affected the sample collected.", "title": "presampling_activity", + "comments": [ + "If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Antimicrobial pre-treatment [GENEPIO:0100537]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_am", + "NCBI_BIOSAMPLE_Enterics:fertilizer_admin" + ], "rank": 11, "slot_uri": "GENEPIO:0100433", "alias": "presampling_activity", @@ -24719,12 +28366,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] }, "presampling_activity_details": { "name": "presampling_activity_details", "description": "The details of the experimental activities or variables that affected the sample collected.", "title": "presampling_activity_details", + "comments": [ + "Briefly describe the experimental details using free text." + ], + "examples": [ + { + "value": "Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter." + } + ], "from_schema": "https://example.com/GRDI", "rank": 12, "slot_uri": "GENEPIO:0100434", @@ -24740,6 +28403,14 @@ "name": "experimental_protocol_field", "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", "title": "experimental_protocol_field", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "examples": [ + { + "value": "OneHealth2024_protocol" + } + ], "from_schema": "https://example.com/GRDI", "rank": 13, "slot_uri": "GENEPIO:0101029", @@ -24755,6 +28426,14 @@ "name": "experimental_specimen_role_type", "description": "The type of role that the sample represents in the experiment.", "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control [GENEPIO:0101018]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 14, "slot_uri": "GENEPIO:0100921", @@ -24770,6 +28449,14 @@ "name": "specimen_processing", "description": "The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.", "title": "specimen_processing", + "comments": [ + "Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Samples pooled [OBI:0600016]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 15, "slot_uri": "GENEPIO:0100435", @@ -24778,12 +28465,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" - }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", "title": "nucleic acid extraction method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and Salmonella (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], "from_schema": "https://example.com/GRDI", "rank": 16, "slot_uri": "GENEPIO:0100939", @@ -24795,10 +28498,18 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "description": "The kit used to extract genomic material from a sample", "title": "nucleic acid extraction kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 17, "slot_uri": "GENEPIO:0100772", @@ -24810,44 +28521,98 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo_loc_name (country)", + "comments": [ + "Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value." + ], + "examples": [ + { + "value": "Canada [GAZ:00002560]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:geo_loc_name", + "BIOSAMPLE:geo_loc_name%20%28country%29", + "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" + ], "rank": 18, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "alias": "geo_loc_name_country", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true - }, - "geo_loc_name (state/province/region)": { - "name": "geo_loc_name (state/province/region)", + "required": true, + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_region": { + "name": "geo_loc_name_state_province_region", "description": "The state/province/territory of origin of the sample.", "title": "geo_loc_name (state/province/region)", + "comments": [ + "Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value." + ], + "examples": [ + { + "value": "British Columbia [GAZ:00002562]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:geo_loc_name", + "BIOSAMPLE:geo_loc_name%20%28state/province/region%29", + "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" + ], "rank": 19, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/region)", + "alias": "geo_loc_name_state_province_region", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true - }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", + "required": true, + "any_of": [ + { + "range": "geo_loc_name (state/province/region) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name (site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:geo_loc_name", + "BIOSAMPLE:geo_loc_name%20%28site%29" + ], "rank": 20, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_(site)", + "alias": "geo_loc_name_site", "owner": "GRDI", "domain_of": [ "GRDI" @@ -24855,39 +28620,85 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "food_product_origin_geo_loc_name (country)": { - "name": "food_product_origin_geo_loc_name (country)", + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", "description": "The country of origin of a food product.", "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_origin" + ], "rank": 21, "slot_uri": "GENEPIO:0100437", - "alias": "food_product_origin_geo_loc_name_(country)", + "alias": "food_product_origin_geo_loc_name_country", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" - }, - "host_origin_geo_loc_name (country)": { - "name": "host_origin_geo_loc_name (country)", + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", "description": "The country of origin of the host.", "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 22, "slot_uri": "GENEPIO:0100438", - "alias": "host_origin_geo_loc_name_(country)", + "alias": "host_origin_geo_loc_name_country", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" - }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", + "comments": [ + "If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "38.98 N" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:lat_lon" + ], "rank": 23, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", @@ -24898,11 +28709,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", + "comments": [ + "If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "77.11 W" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:lat_lon" + ], "rank": 24, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", @@ -24917,7 +28739,19 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample_collection_date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2020-10-30" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:sample%20collection%20date", + "NCBI_BIOSAMPLE_Enterics:%2Acollection_date" + ], "rank": 25, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", @@ -24933,6 +28767,14 @@ "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample_collection_date_precision", + "comments": [ + "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + ], + "examples": [ + { + "value": "day [UO:0000033]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 26, "slot_uri": "GENEPIO:0001177", @@ -24942,12 +28784,28 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "sample_collection_date_precision menu" + }, + { + "range": "null value menu" + } + ] }, "sample_received_date": { "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample_received_date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2020-11-15" + } + ], "from_schema": "https://example.com/GRDI", "rank": 27, "slot_uri": "GENEPIO:0001179", @@ -24963,6 +28821,14 @@ "name": "original_sample_description", "description": "The original sample description provided by the sample collector.", "title": "original_sample_description", + "comments": [ + "Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications." + ], + "examples": [ + { + "value": "RTE Prosciutto from deli" + } + ], "from_schema": "https://example.com/GRDI", "rank": 28, "slot_uri": "GENEPIO:0100439", @@ -24978,198 +28844,468 @@ "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_site", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:animal_env", + "NCBI_BIOSAMPLE_Enterics:host_housing", + "NCBI_BIOSAMPLE_Enterics:env_local_scale", + "NCBI_BIOSAMPLE_Enterics:facility_type" + ], "rank": 29, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] }, "environmental_material": { "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", "title": "environmental_material", - "from_schema": "https://example.com/GRDI", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_material", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + ], "rank": 30, "slot_uri": "GENEPIO:0001223", - "multivalued": true, "alias": "environmental_material", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] }, "environmental_material_constituent": { "name": "environmental_material_constituent", "description": "The material constituents that comprise an environmental material e.g. lead, plastic, paper.", "title": "environmental_material_constituent", + "comments": [ + "If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "lead" + }, + { + "value": "plastic" + } + ], "from_schema": "https://example.com/GRDI", "rank": 31, "slot_uri": "GENEPIO:0101197", - "multivalued": true, "alias": "environmental_material_constituent", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "range": "WhitespaceMinimizedString", + "multivalued": true }, "animal_or_plant_population": { "name": "animal_or_plant_population", "description": "The type of animal or plant population inhabiting an area.", "title": "animal_or_plant_population", + "comments": [ + "This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Turkey [NCBITaxon:9103]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 32, "slot_uri": "GENEPIO:0100443", - "multivalued": true, "alias": "animal_or_plant_population", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "animal_or_plant_population menu" + }, + { + "range": "null value menu" + } + ] }, "anatomical_material": { "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "NCBI_BIOSAMPLE_Enterics:host_tissue_sampled", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + ], "rank": 33, "slot_uri": "GENEPIO:0001211", - "multivalued": true, "alias": "anatomical_material", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] }, "body_product": { "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "NCBI_BIOSAMPLE_Enterics:host_body_product", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + ], "rank": 34, "slot_uri": "GENEPIO:0001216", - "multivalued": true, "alias": "body_product", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] }, "anatomical_part": { "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + ], "rank": 35, "slot_uri": "GENEPIO:0001214", - "multivalued": true, "alias": "anatomical_part", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] }, "anatomical_region": { "name": "anatomical_region", "description": "A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.", "title": "anatomical_region", + "comments": [ + "This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist." + ], + "examples": [ + { + "value": "Dorso-lateral region [BSPO:0000080]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 36, "slot_uri": "GENEPIO:0100700", - "multivalued": true, "alias": "anatomical_region", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_region menu" + }, + { + "range": "null value menu" + } + ] }, "food_product": { "name": "food_product", "description": "A material consumed and digested for nutritional value or enjoyment.", "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:food_product" + ], "rank": 37, "slot_uri": "GENEPIO:0100444", - "multivalued": true, "alias": "food_product", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] }, "food_product_properties": { "name": "food_product_properties", "description": "Any characteristic of the food product pertaining to its state, processing, or implications for consumers.", "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:food_product_properties", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:food_processing_method", + "NCBI_BIOSAMPLE_Enterics:food_preserv_proc" + ], "rank": 38, "slot_uri": "GENEPIO:0100445", - "multivalued": true, "alias": "food_product_properties", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] }, "label_claim": { "name": "label_claim", "description": "The claim made by the label that relates to food processing, allergen information etc.", "title": "label_claim", + "comments": [ + "Provide any characteristic of the food product, as described on the label only." + ], + "examples": [ + { + "value": "Antibiotic free [FOODON:03601063]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:label_claims" + ], "rank": 39, "slot_uri": "FOODON:03602001", - "multivalued": true, "alias": "label_claim", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "label_claim menu" + }, + { + "range": "null value menu" + } + ] }, "animal_source_of_food": { "name": "animal_source_of_food", "description": "The animal from which the food product was derived.", "title": "animal_source_of_food", + "comments": [ + "Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma." + ], + "examples": [ + { + "value": "Chicken [NCBITaxon:9031]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_source" + ], "rank": 40, "slot_uri": "GENEPIO:0100446", - "multivalued": true, "alias": "animal_source_of_food", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "animal_source_of_food menu" + }, + { + "range": "null value menu" + } + ] }, "food_product_production_stream": { "name": "food_product_production_stream", "description": "A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity.", "title": "food_product_production_stream", + "comments": [ + "Provide the name of the agricultural production stream from the picklist." + ], + "examples": [ + { + "value": "Beef cattle production stream [FOODON:03000452]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_prod" + ], "rank": 41, "slot_uri": "GENEPIO:0100699", "alias": "food_product_production_stream", @@ -25177,29 +29313,69 @@ "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "food_product_production_stream menu" + }, + { + "range": "null value menu" + } + ] }, "food_packaging": { "name": "food_packaging", "description": "The type of packaging used to contain a food product.", "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:food_packaging", + "NCBI_BIOSAMPLE_Enterics:food_contain_wrap" + ], "rank": 42, "slot_uri": "GENEPIO:0100447", - "multivalued": true, "alias": "food_packaging", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] }, "food_quality_date": { "name": "food_quality_date", "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:food_quality_date" + ], "rank": 43, "slot_uri": "GENEPIO:0100615", "alias": "food_quality_date", @@ -25214,6 +29390,14 @@ "name": "food_packaging_date", "description": "A food product's packaging date as marked by a food manufacturer or retailer.", "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], "from_schema": "https://example.com/GRDI", "rank": 44, "slot_uri": "GENEPIO:0100616", @@ -25229,7 +29413,21 @@ "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "NCBI_BIOSAMPLE_Enterics:samp_collect_device", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + ], "rank": 45, "slot_uri": "GENEPIO:0001234", "alias": "collection_device", @@ -25238,13 +29436,34 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] }, "collection_method": { "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + ], "rank": 46, "slot_uri": "GENEPIO:0001241", "alias": "collection_method", @@ -25253,12 +29472,28 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] }, "sample_volume_measurement_value": { "name": "sample_volume_measurement_value", "description": "The numerical value of the volume measurement of the sample collected.", "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 47, "slot_uri": "GENEPIO:0100768", @@ -25274,6 +29509,14 @@ "name": "sample_volume_measurement_unit", "description": "The units of the volume measurement of the sample collected.", "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 48, "slot_uri": "GENEPIO:0100769", @@ -25289,6 +29532,14 @@ "name": "residual_sample_status", "description": "The status of the residual sample (whether any sample remains after its original use).", "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 49, "slot_uri": "GENEPIO:0101090", @@ -25304,6 +29555,14 @@ "name": "sample_storage_method", "description": "A specification of the way that a specimen is or was stored.", "title": "sample_storage_method", + "comments": [ + "Provide a description of how the sample was stored." + ], + "examples": [ + { + "value": "packed on ice during transport" + } + ], "from_schema": "https://example.com/GRDI", "rank": 50, "slot_uri": "GENEPIO:0100448", @@ -25319,6 +29578,14 @@ "name": "sample_storage_medium", "description": "The material or matrix in which a sample is stored.", "title": "sample_storage_medium", + "comments": [ + "Provide a description of the medium in which the sample was stored." + ], + "examples": [ + { + "value": "PBS + 20% glycerol" + } + ], "from_schema": "https://example.com/GRDI", "rank": 51, "slot_uri": "GENEPIO:0100449", @@ -25334,6 +29601,14 @@ "name": "sample_storage_duration_value", "description": "The numerical value of the time measurement during which a sample is in storage.", "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 52, "slot_uri": "GENEPIO:0101014", @@ -25349,6 +29624,14 @@ "name": "sample_storage_duration_unit", "description": "The units of a measured sample storage duration.", "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day [UO:0000033]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 53, "slot_uri": "GENEPIO:0101015", @@ -25364,6 +29647,14 @@ "name": "nucleic_acid_storage_duration_value", "description": "The numerical value of the time measurement during which the extracted nucleic acid is in storage.", "title": "nucleic_acid_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 54, "slot_uri": "GENEPIO:0101085", @@ -25379,6 +29670,14 @@ "name": "nucleic_acid_storage_duration_unit", "description": "The units of a measured extracted nucleic acid storage duration.", "title": "nucleic_acid_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Year [UO:0000036]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 55, "slot_uri": "GENEPIO:0101086", @@ -25394,21 +29693,45 @@ "name": "available_data_types", "description": "The type of data that is available, that may or may not require permission to access.", "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 56, "slot_uri": "GENEPIO:0100690", - "multivalued": true, "alias": "available_data_types", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] }, "available_data_type_details": { "name": "available_data_type_details", "description": "Detailed information regarding other available data types.", "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], "from_schema": "https://example.com/GRDI", "rank": 57, "slot_uri": "GENEPIO:0101023", @@ -25424,6 +29747,14 @@ "name": "water_depth", "description": "The depth of some water.", "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 58, "slot_uri": "GENEPIO:0100440", @@ -25439,6 +29770,14 @@ "name": "water_depth_units", "description": "The units of measurement for water depth.", "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 59, "slot_uri": "GENEPIO:0101025", @@ -25447,12 +29786,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] }, "sediment_depth": { "name": "sediment_depth", "description": "The depth of some sediment.", "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 60, "slot_uri": "GENEPIO:0100697", @@ -25468,6 +29823,14 @@ "name": "sediment_depth_units", "description": "The units of measurement for sediment depth.", "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 61, "slot_uri": "GENEPIO:0101026", @@ -25476,12 +29839,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] }, "air_temperature": { "name": "air_temperature", "description": "The temperature of some air.", "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], "from_schema": "https://example.com/GRDI", "rank": 62, "slot_uri": "GENEPIO:0100441", @@ -25497,6 +29876,14 @@ "name": "air_temperature_units", "description": "The units of measurement for air temperature.", "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 63, "slot_uri": "GENEPIO:0101027", @@ -25505,12 +29892,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] }, "water_temperature": { "name": "water_temperature", "description": "The temperature of some water.", "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", "rank": 64, "slot_uri": "GENEPIO:0100698", @@ -25526,6 +29929,14 @@ "name": "water_temperature_units", "description": "The units of measurement for water temperature.", "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 65, "slot_uri": "GENEPIO:0101028", @@ -25534,61 +29945,142 @@ "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value menu" + } + ] }, "weather_type": { "name": "weather_type", "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", "title": "weather_type", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 66, "slot_uri": "GENEPIO:0100442", - "multivalued": true, "alias": "weather_type", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Environmental conditions and measurements" - }, - "host (common name)": { - "name": "host (common name)", + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "weather_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host" + ], "rank": 67, "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", + "alias": "host_common_name", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Host information", - "recommended": true - }, - "host (scientific name)": { - "name": "host (scientific name)", + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:host", + "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:host" + ], "rank": 68, "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", + "alias": "host_scientific_name", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Host information", - "recommended": true - }, - "host (ecotype)": { - "name": "host (ecotype)", + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", "title": "host (ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_variety" + ], "rank": 69, "slot_uri": "GENEPIO:0100450", - "alias": "host_(ecotype)", + "alias": "host_ecotype", "owner": "GRDI", "domain_of": [ "GRDI" @@ -25596,14 +30088,26 @@ "slot_group": "Host information", "range": "WhitespaceMinimizedString" }, - "host (breed)": { - "name": "host (breed)", + "host_breed": { + "name": "host_breed", "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", "title": "host (breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:host_disease", + "NCBI_BIOSAMPLE_Enterics:host_animal_breed" + ], "rank": 70, "slot_uri": "GENEPIO:0100451", - "alias": "host_(breed)", + "alias": "host_breed", "owner": "GRDI", "domain_of": [ "GRDI" @@ -25611,25 +30115,50 @@ "slot_group": "Host information", "range": "WhitespaceMinimizedString" }, - "host (food production name)": { - "name": "host (food production name)", + "host_food_production_name": { + "name": "host_food_production_name", "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", "title": "host (food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host" + ], "rank": 71, "slot_uri": "GENEPIO:0100452", - "alias": "host_(food_production_name)", + "alias": "host_food_production_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Host information" + "slot_group": "Host information", + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] }, "host_age_bin": { "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_age" + ], "rank": 72, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", @@ -25637,13 +30166,32 @@ "domain_of": [ "GRDI" ], - "slot_group": "Host information" + "slot_group": "Host information", + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] }, "host_disease": { "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:host_disease" + ], "rank": 73, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", @@ -25658,6 +30206,14 @@ "name": "microbiological_method", "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", "title": "microbiological_method", + "comments": [ + "Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure." + ], + "examples": [ + { + "value": "MFHPB-30" + } + ], "from_schema": "https://example.com/GRDI", "rank": 74, "slot_uri": "GENEPIO:0100454", @@ -25674,7 +30230,18 @@ "name": "strain", "description": "The strain identifier.", "title": "strain", + "comments": [ + "If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier." + ], + "examples": [ + { + "value": "K12" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:strain" + ], "rank": 75, "slot_uri": "GENEPIO:0100455", "alias": "strain", @@ -25685,29 +30252,62 @@ "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "isolate_ID": { - "name": "isolate_ID", + "isolate_id": { + "name": "isolate_id", "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", "title": "isolate_ID", + "comments": [ + "Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field." + ], + "examples": [ + { + "value": "SA20131043" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:strain" + ], "rank": 76, "slot_uri": "GENEPIO:0100456", - "alias": "isolate_ID", + "alias": "isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Strain and isolation information", - "required": true - }, - "alternative_isolate_ID": { - "name": "alternative_isolate_ID", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "alternative_isolate_id": { + "name": "alternative_isolate_id", "description": "An alternative isolate_ID assigned to the isolate by another organization.", "title": "alternative_isolate_ID", + "comments": [ + "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons." + ], + "examples": [ + { + "value": "GHIF3456[PHAC]" + }, + { + "value": "QWICK222[CFIA]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:isolate_name_alias" + ], "rank": 77, "slot_uri": "GENEPIO:0100457", - "alias": "alternative_isolate_ID", + "alias": "alternative_isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" @@ -25716,14 +30316,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "progeny_isolate_ID": { - "name": "progeny_isolate_ID", + "progeny_isolate_id": { + "name": "progeny_isolate_id", "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", "title": "progeny_isolate_ID", + "comments": [ + "If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID." + ], + "examples": [ + { + "value": "SUB_ON_1526" + } + ], "from_schema": "https://example.com/GRDI", "rank": 78, "slot_uri": "GENEPIO:0100458", - "alias": "progeny_isolate_ID", + "alias": "progeny_isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" @@ -25731,40 +30339,80 @@ "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "IRIDA_isolate_ID": { - "name": "IRIDA_isolate_ID", + "irida_isolate_id": { + "name": "irida_isolate_id", "description": "The identifier of the isolate in the IRIDA platform.", "title": "IRIDA_isolate_ID", + "comments": [ + "Provide the \"sample ID\" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices." + ], + "examples": [ + { + "value": "GRDI_LL_12345" + } + ], "from_schema": "https://example.com/GRDI", "rank": 79, "slot_uri": "GENEPIO:0100459", - "alias": "IRIDA_isolate_ID", + "alias": "irida_isolate_id", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Strain and isolation information", - "required": true - }, - "IRIDA_project_ID": { - "name": "IRIDA_project_ID", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "irida_project_id": { + "name": "irida_project_id", "description": "The identifier of the Project in the iRIDA platform.", "title": "IRIDA_project_ID", + "comments": [ + "Provide the IRIDA \"project ID\"." + ], + "examples": [ + { + "value": "666" + } + ], "from_schema": "https://example.com/GRDI", "rank": 80, "slot_uri": "GENEPIO:0100460", - "alias": "IRIDA_project_ID", + "alias": "irida_project_id", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Strain and isolation information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "isolated_by": { "name": "isolated_by", "description": "The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.", "title": "isolated_by", + "comments": [ + "Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 81, "slot_uri": "GENEPIO:0100461", @@ -25780,6 +30428,14 @@ "name": "isolated_by_laboratory_name", "description": "The specific laboratory affiliation of the individual who performed the isolation procedure.", "title": "isolated_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", "rank": 82, "slot_uri": "GENEPIO:0100462", @@ -25795,6 +30451,14 @@ "name": "isolated_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the isolate.", "title": "isolated_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", "rank": 83, "slot_uri": "GENEPIO:0100463", @@ -25810,6 +30474,14 @@ "name": "isolated_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the isolate.", "title": "isolated_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", "rank": 84, "slot_uri": "GENEPIO:0100464", @@ -25825,7 +30497,18 @@ "name": "isolation_date", "description": "The date on which the isolate was isolated from a sample.", "title": "isolation_date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2020-10-30" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:cult_isol_date" + ], "rank": 85, "slot_uri": "GENEPIO:0100465", "alias": "isolation_date", @@ -25840,6 +30523,14 @@ "name": "isolate_received_date", "description": "The date on which the isolate was received by the laboratory.", "title": "isolate_received_date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2020-11-15" + } + ], "from_schema": "https://example.com/GRDI", "rank": 86, "slot_uri": "GENEPIO:0100466", @@ -25855,22 +30546,50 @@ "name": "organism", "description": "Taxonomic name of the organism.", "title": "organism", + "comments": [ + "Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used." + ], + "examples": [ + { + "value": "Salmonella enterica subsp. enterica [NCBITaxon:59201]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:organism", + "NCBI_BIOSAMPLE_Enterics:%2Aorganism" + ], "rank": 87, "slot_uri": "GENEPIO:0001191", - "multivalued": true, "alias": "organism", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Strain and isolation information", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", "description": "The type of planned process by which an organismal entity is associated with a taxon or taxa.", "title": "taxonomic_identification_process", + "comments": [ + "Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "PCR assay [OBI:0002740]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 88, "slot_uri": "GENEPIO:0100583", @@ -25880,12 +30599,28 @@ "GRDI" ], "slot_group": "Strain and isolation information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "taxonomic_identification_process menu" + }, + { + "range": "null value menu" + } + ] }, "taxonomic_identification_process_details": { "name": "taxonomic_identification_process_details", "description": "The details of the process used to determine the taxonomic identification of an organism.", "title": "taxonomic_identification_process_details", + "comments": [ + "Briefly describe the taxonomic identififcation method details using free text." + ], + "examples": [ + { + "value": "Biolog instrument" + } + ], "from_schema": "https://example.com/GRDI", "rank": 89, "slot_uri": "GENEPIO:0100584", @@ -25901,7 +30636,18 @@ "name": "serovar", "description": "The serovar of the organism.", "title": "serovar", + "comments": [ + "Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR." + ], + "examples": [ + { + "value": "Heidelberg" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:serovar" + ], "rank": 90, "slot_uri": "GENEPIO:0100467", "alias": "serovar", @@ -25917,6 +30663,14 @@ "name": "serotyping_method", "description": "The method used to determine the serovar.", "title": "serotyping_method", + "comments": [ + "If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software." + ], + "examples": [ + { + "value": "SISTR 1.0.1" + } + ], "from_schema": "https://example.com/GRDI", "rank": 91, "slot_uri": "GENEPIO:0100468", @@ -25933,6 +30687,14 @@ "name": "phagetype", "description": "The phagetype of the organism.", "title": "phagetype", + "comments": [ + "Provide if known. If unknown, put “missing”." + ], + "examples": [ + { + "value": "47" + } + ], "from_schema": "https://example.com/GRDI", "rank": 92, "slot_uri": "GENEPIO:0100469", @@ -25944,14 +30706,22 @@ "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "library_ID": { - "name": "library_ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], "from_schema": "https://example.com/GRDI", "rank": 93, "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", + "alias": "library_id", "owner": "GRDI", "domain_of": [ "GRDI" @@ -25963,7 +30733,19 @@ "name": "sequenced_by", "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:sequenced_by", + "NCBI_BIOSAMPLE_Enterics:sequenced_by" + ], "rank": 94, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", @@ -25972,12 +30754,28 @@ "GRDI" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "sequenced_by menu" + }, + { + "range": "null value menu" + } + ] }, "sequenced_by_laboratory_name": { "name": "sequenced_by_laboratory_name", "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", "rank": 95, "slot_uri": "GENEPIO:0100470", @@ -25993,6 +30791,14 @@ "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", "rank": 96, "slot_uri": "GENEPIO:0100471", @@ -26002,12 +30808,28 @@ "GRDI" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", "rank": 97, "slot_uri": "GENEPIO:0100422", @@ -26017,28 +30839,63 @@ "GRDI" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "purpose_of_sequencing": { "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", + "comments": [ + "Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Research [GENEPIO:0100003]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:purpose_of_sequencing" + ], "rank": 98, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Sequence information", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] }, "sequencing_project_name": { "name": "sequencing_project_name", "description": "The name of the project/initiative/program for which sequencing was performed.", "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 99, "slot_uri": "GENEPIO:0100472", @@ -26054,6 +30911,14 @@ "name": "sequencing_platform", "description": "The platform technology used to perform the sequencing.", "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 100, "slot_uri": "GENEPIO:0100473", @@ -26062,12 +30927,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Sequence information" + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "sequencing_instrument": { "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 101, "slot_uri": "GENEPIO:0001452", @@ -26076,12 +30957,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Sequence information" + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] }, "sequencing_assay_type": { "name": "sequencing_assay_type", "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 102, "slot_uri": "GENEPIO:0100997", @@ -26097,6 +30994,14 @@ "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/GRDI", "rank": 103, "slot_uri": "GENEPIO:0001450", @@ -26108,14 +31013,22 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "DNA fragment length": { - "name": "DNA fragment length", + "dna_fragment_length": { + "name": "dna_fragment_length", "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", "title": "DNA fragment length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], "from_schema": "https://example.com/GRDI", "rank": 104, "slot_uri": "GENEPIO:0100843", - "alias": "DNA_fragment_length", + "alias": "dna_fragment_length", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26123,10 +31036,18 @@ "slot_group": "Sequence information", "range": "Integer" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 105, "slot_uri": "GENEPIO:0100966", @@ -26138,10 +31059,18 @@ "slot_group": "Sequence information", "range": "genomic_target_enrichment_method menu" }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], "from_schema": "https://example.com/GRDI", "rank": 106, "slot_uri": "GENEPIO:0100967", @@ -26153,10 +31082,18 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 107, "slot_uri": "GENEPIO:0001456", @@ -26168,10 +31105,18 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], "from_schema": "https://example.com/GRDI", "rank": 108, "slot_uri": "GENEPIO:0001449", @@ -26183,10 +31128,18 @@ "slot_group": "Sequence information", "range": "Integer" }, - "sequencing flow cell version": { - "name": "sequencing flow cell version", + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", "description": "The version number of the flow cell used for generating sequence data.", "title": "sequencing flow cell version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], "from_schema": "https://example.com/GRDI", "rank": 109, "slot_uri": "GENEPIO:0101102", @@ -26202,6 +31155,14 @@ "name": "sequencing_protocol", "description": "The protocol or method used for sequencing.", "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], "from_schema": "https://example.com/GRDI", "rank": 110, "slot_uri": "GENEPIO:0001454", @@ -26217,6 +31178,14 @@ "name": "r1_fastq_filename", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], "from_schema": "https://example.com/GRDI", "rank": 111, "slot_uri": "GENEPIO:0001476", @@ -26232,6 +31201,14 @@ "name": "r2_fastq_filename", "description": "The user-specified filename of the r2 FASTQ file.", "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], "from_schema": "https://example.com/GRDI", "rank": 112, "slot_uri": "GENEPIO:0001477", @@ -26247,6 +31224,14 @@ "name": "fast5_filename", "description": "The user-specified filename of the FAST5 file.", "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 113, "slot_uri": "GENEPIO:0001480", @@ -26262,6 +31247,14 @@ "name": "assembly_filename", "description": "The user-defined filename of the FASTA file.", "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], "from_schema": "https://example.com/GRDI", "rank": 114, "slot_uri": "GENEPIO:0001461", @@ -26273,10 +31266,18 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "quality control method name": { - "name": "quality control method name", + "quality_control_method_name": { + "name": "quality_control_method_name", "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], "from_schema": "https://example.com/GRDI", "rank": 115, "slot_uri": "GENEPIO:0100557", @@ -26288,10 +31289,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_version": { + "name": "quality_control_method_version", "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 116, "slot_uri": "GENEPIO:0100558", @@ -26303,40 +31312,80 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_determination": { + "name": "quality_control_determination", "description": "The determination of a quality control assessment.", "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], "from_schema": "https://example.com/GRDI", "rank": 117, "slot_uri": "GENEPIO:0100559", - "multivalued": true, "alias": "quality_control_determination", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics" - }, - "quality control issues": { - "name": "quality control issues", + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], "from_schema": "https://example.com/GRDI", "rank": 118, "slot_uri": "GENEPIO:0100560", - "multivalued": true, "alias": "quality_control_issues", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics" - }, - "quality control details": { - "name": "quality control details", + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", "description": "The details surrounding a low quality determination in a quality control assessment.", "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], "from_schema": "https://example.com/GRDI", "rank": 119, "slot_uri": "GENEPIO:0100561", @@ -26348,10 +31397,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 120, "slot_uri": "GENEPIO:0001458", @@ -26361,12 +31418,28 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true - }, - "dehosting method": { - "name": "dehosting method", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/GRDI", "rank": 121, "slot_uri": "GENEPIO:0001459", @@ -26376,12 +31449,28 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true - }, - "sequence assembly software name": { - "name": "sequence assembly software name", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", "description": "The name of the software used to assemble a sequence.", "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], "from_schema": "https://example.com/GRDI", "rank": 122, "slot_uri": "GENEPIO:0100825", @@ -26390,12 +31479,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics" - }, - "sequence assembly software version": { - "name": "sequence assembly software version", + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", "description": "The version of the software used to assemble a sequence.", "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 123, "slot_uri": "GENEPIO:0100826", @@ -26404,12 +31509,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of the software used to generate the consensus sequence.", "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], "from_schema": "https://example.com/GRDI", "rank": 124, "slot_uri": "GENEPIO:0001463", @@ -26418,12 +31539,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 125, "slot_uri": "GENEPIO:0001469", @@ -26432,12 +31569,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Bioinformatics and QC metrics" - }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], "from_schema": "https://example.com/GRDI", "rank": 126, "slot_uri": "GENEPIO:0001472", @@ -26449,10 +31602,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], "from_schema": "https://example.com/GRDI", "rank": 127, "slot_uri": "GENEPIO:0001474", @@ -26464,10 +31625,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 128, "slot_uri": "GENEPIO:0001475", @@ -26479,10 +31648,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "genome completeness": { - "name": "genome completeness", + "genome_completeness": { + "name": "genome_completeness", "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], "from_schema": "https://example.com/GRDI", "rank": 129, "slot_uri": "GENEPIO:0100844", @@ -26494,10 +31671,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], "from_schema": "https://example.com/GRDI", "rank": 130, "slot_uri": "GENEPIO:0001482", @@ -26509,10 +31694,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of total reads": { - "name": "number of total reads", + "number_of_total_reads": { + "name": "number_of_total_reads", "description": "The total number of non-unique reads generated by the sequencing process.", "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], "from_schema": "https://example.com/GRDI", "rank": 131, "slot_uri": "GENEPIO:0100827", @@ -26524,10 +31717,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of unique reads": { - "name": "number of unique reads", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "description": "The number of unique reads generated by the sequencing process.", "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], "from_schema": "https://example.com/GRDI", "rank": 132, "slot_uri": "GENEPIO:0100828", @@ -26539,14 +31740,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", "rank": 133, "slot_uri": "GENEPIO:0100829", - "alias": "minimum_post_trimming_read_length", + "alias": "minimum_posttrimming_read_length", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26554,10 +31763,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of contigs": { - "name": "number of contigs", + "number_of_contigs": { + "name": "number_of_contigs", "description": "The number of contigs (contiguous sequences) in a sequence assembly.", "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", "rank": 134, "slot_uri": "GENEPIO:0100937", @@ -26569,14 +31786,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 135, "slot_uri": "GENEPIO:0100830", - "alias": "percent_Ns_across_total_genome_length", + "alias": "percent_ns_across_total_genome_length", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26584,14 +31809,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], "from_schema": "https://example.com/GRDI", "rank": 136, "slot_uri": "GENEPIO:0001484", - "alias": "Ns_per_100_kbp", + "alias": "ns_per_100_kbp", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26599,14 +31832,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "N50": { - "name": "N50", + "n50": { + "name": "n50", "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", "rank": 137, "slot_uri": "GENEPIO:0100938", - "alias": "N50", + "alias": "n50", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26614,14 +31855,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "percent read contamination": { - "name": "percent read contamination", + "percent_read_contamination_": { + "name": "percent_read_contamination_", "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 138, "slot_uri": "GENEPIO:0100845", - "alias": "percent_read_contamination", + "alias": "percent_read_contamination_", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26629,10 +31878,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "sequence assembly length": { - "name": "sequence assembly length", + "sequence_assembly_length": { + "name": "sequence_assembly_length", "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], "from_schema": "https://example.com/GRDI", "rank": 139, "slot_uri": "GENEPIO:0100846", @@ -26644,10 +31901,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "The length of the genome defined by the most common nucleotides at each position.", "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], "from_schema": "https://example.com/GRDI", "rank": 140, "slot_uri": "GENEPIO:0001483", @@ -26659,10 +31924,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 141, "slot_uri": "GENEPIO:0001485", @@ -26674,10 +31947,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "deduplication method": { - "name": "deduplication method", + "deduplication_method": { + "name": "deduplication_method", "description": "The method used to remove duplicated reads in a sequence read dataset.", "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 142, "slot_uri": "GENEPIO:0100831", @@ -26689,10 +31970,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/GRDI", "rank": 143, "slot_uri": "GENEPIO:0001489", @@ -26704,10 +31993,18 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "read mapping software name": { - "name": "read mapping software name", + "read_mapping_software_name": { + "name": "read_mapping_software_name", "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], "from_schema": "https://example.com/GRDI", "rank": 144, "slot_uri": "GENEPIO:0100832", @@ -26719,10 +32016,18 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "read mapping software version": { - "name": "read mapping software version", + "read_mapping_software_version": { + "name": "read_mapping_software_version", "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], "from_schema": "https://example.com/GRDI", "rank": 145, "slot_uri": "GENEPIO:0100833", @@ -26734,10 +32039,18 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", "description": "The name of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], "from_schema": "https://example.com/GRDI", "rank": 146, "slot_uri": "GENEPIO:0100834", @@ -26749,10 +32062,18 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", "description": "The version of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 147, "slot_uri": "GENEPIO:0100835", @@ -26764,10 +32085,18 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", "description": "The filename of the report containing the results of a taxonomic analysis.", "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], "from_schema": "https://example.com/GRDI", "rank": 148, "slot_uri": "GENEPIO:0101074", @@ -26779,10 +32108,18 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], "from_schema": "https://example.com/GRDI", "rank": 149, "slot_uri": "GENEPIO:0101075", @@ -26794,10 +32131,18 @@ "slot_group": "Taxonomic identification information", "range": "date" }, - "read mapping criteria": { - "name": "read mapping criteria", + "read_mapping_criteria": { + "name": "read_mapping_criteria", "description": "A description of the criteria used to map reads to a reference sequence.", "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], "from_schema": "https://example.com/GRDI", "rank": 150, "slot_uri": "GENEPIO:0100836", @@ -26813,6 +32158,14 @@ "name": "sequence_submitted_by", "description": "The name of the agency that submitted the sequence to a database.", "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Environment and Climate Change Canada (ECCC) [GENEPIO:0100555]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 151, "slot_uri": "GENEPIO:0001159", @@ -26821,12 +32174,28 @@ "domain_of": [ "GRDI" ], - "slot_group": "Public repository information" + "slot_group": "Public repository information", + "any_of": [ + { + "range": "sequence_submitted_by menu" + }, + { + "range": "null value menu" + } + ] }, "sequence_submitted_by_contact_name": { "name": "sequence_submitted_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database.", "title": "sequence_submitted_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", "rank": 152, "slot_uri": "GENEPIO:0100474", @@ -26842,6 +32211,14 @@ "name": "sequence_submitted_by_contact_email", "description": "The email address of the agency responsible for submission of the sequence.", "title": "sequence_submitted_by_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", "rank": 153, "slot_uri": "GENEPIO:0001165", @@ -26853,14 +32230,22 @@ "slot_group": "Public repository information", "range": "WhitespaceMinimizedString" }, - "publication_ID": { - "name": "publication_ID", + "publication_id": { + "name": "publication_id", "description": "The identifier for a publication.", "title": "publication_ID", + "comments": [ + "If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable." + ], + "examples": [ + { + "value": "PMID: 33205991" + } + ], "from_schema": "https://example.com/GRDI", "rank": 154, "slot_uri": "GENEPIO:0100475", - "alias": "publication_ID", + "alias": "publication_id", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26872,6 +32257,14 @@ "name": "attribute_package", "description": "The attribute package used to structure metadata in an INSDC BioSample.", "title": "attribute_package", + "comments": [ + "If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”." + ], + "examples": [ + { + "value": "Pathogen.env [GENEPIO:0100581]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 155, "slot_uri": "GENEPIO:0100476", @@ -26880,13 +32273,33 @@ "domain_of": [ "GRDI" ], - "slot_group": "Public repository information" + "slot_group": "Public repository information", + "any_of": [ + { + "range": "attribute_package menu" + }, + { + "range": "null value menu" + } + ] }, "bioproject_accession": { "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject_accession", + "comments": [ + "Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects." + ], + "examples": [ + { + "value": "PRJNA12345" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "BIOSAMPLE:bioproject_accession", + "NCBI_BIOSAMPLE_Enterics:bioproject_accession" + ], "rank": 156, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", @@ -26901,7 +32314,18 @@ "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "ENA_ANTIBIOGRAM:bioSample_ID" + ], "rank": 157, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", @@ -26912,14 +32336,22 @@ "slot_group": "Public repository information", "range": "WhitespaceMinimizedString" }, - "SRA_accession": { - "name": "SRA_accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA_accession", + "comments": [ + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], "from_schema": "https://example.com/GRDI", "rank": 158, "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "alias": "sra_accession", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26927,14 +32359,22 @@ "slot_group": "Public repository information", "range": "WhitespaceMinimizedString" }, - "GenBank_accession": { - "name": "GenBank_accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", "title": "GenBank_accession", + "comments": [ + "Store the accession returned from a GenBank/ENA/DDBJ submission." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 159, "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", + "alias": "genbank_accession", "owner": "GRDI", "domain_of": [ "GRDI" @@ -26946,6 +32386,14 @@ "name": "prevalence_metrics", "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], "from_schema": "https://example.com/GRDI", "rank": 160, "slot_uri": "GENEPIO:0100480", @@ -26962,6 +32410,14 @@ "name": "prevalence_metrics_details", "description": "The details pertaining to the prevalence metrics from a surveillance project.", "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], "from_schema": "https://example.com/GRDI", "rank": 161, "slot_uri": "GENEPIO:0100481", @@ -26978,6 +32434,14 @@ "name": "stage_of_production", "description": "The stage of food production.", "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 162, "slot_uri": "GENEPIO:0100482", @@ -26987,29 +32451,64 @@ "GRDI" ], "slot_group": "Risk assessment information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] }, "experimental_intervention": { "name": "experimental_intervention", "description": "The category of the experimental intervention applied in the food production system.", "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_Enterics:upstream_intervention" + ], "rank": 163, "slot_uri": "GENEPIO:0100483", - "multivalued": true, "alias": "experimental_intervention", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Risk assessment information", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] }, "experiment_intervention_details": { "name": "experiment_intervention_details", "description": "The details of the experimental intervention applied in the food production system.", "title": "experiment_intervention_details", - "from_schema": "https://example.com/GRDI", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/GRDI", "rank": 164, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", @@ -27021,29 +32520,53 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR_testing_by": { - "name": "AMR_testing_by", + "amr_testing_by": { + "name": "amr_testing_by", "description": "The name of the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 165, "slot_uri": "GENEPIO:0100511", - "alias": "AMR_testing_by", + "alias": "amr_testing_by", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "AMR_testing_by menu" + }, + { + "range": "null value menu" + } + ] }, - "AMR_testing_by_laboratory_name": { - "name": "AMR_testing_by_laboratory_name", + "amr_testing_by_laboratory_name": { + "name": "amr_testing_by_laboratory_name", "description": "The name of the lab within the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", "rank": 166, "slot_uri": "GENEPIO:0100512", - "alias": "AMR_testing_by_laboratory_name", + "alias": "amr_testing_by_laboratory_name", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27051,44 +32574,84 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "AMR_testing_by_contact_name": { - "name": "AMR_testing_by_contact_name", + "amr_testing_by_contact_name": { + "name": "amr_testing_by_contact_name", "description": "The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", "rank": 167, "slot_uri": "GENEPIO:0100513", - "alias": "AMR_testing_by_contact_name", + "alias": "amr_testing_by_contact_name", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "AMR_testing_by_contact_email": { - "name": "AMR_testing_by_contact_email", + "amr_testing_by_contact_email": { + "name": "amr_testing_by_contact_email", "description": "The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing.", "title": "AMR_testing_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "johnnyblogs@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", "rank": 168, "slot_uri": "GENEPIO:0100514", - "alias": "AMR_testing_by_contact_email", + "alias": "amr_testing_by_contact_email", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "AMR_testing_date": { - "name": "AMR_testing_date", + "amr_testing_date": { + "name": "amr_testing_date", "description": "The date the antimicrobial resistance testing was performed.", "title": "AMR_testing_date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2022-04-03" + } + ], "from_schema": "https://example.com/GRDI", "rank": 169, "slot_uri": "GENEPIO:0100515", - "alias": "AMR_testing_date", + "alias": "amr_testing_date", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27100,7 +32663,18 @@ "name": "amikacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "amikacin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 170, "alias": "amikacin_resistance_phenotype", "owner": "GRDI", @@ -27108,13 +32682,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "amikacin_measurement": { "name": "amikacin_measurement", "description": "The measured value of amikacin resistance.", "title": "amikacin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 171, "alias": "amikacin_measurement", "owner": "GRDI", @@ -27122,13 +32715,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "amikacin_measurement_units": { "name": "amikacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "amikacin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 172, "alias": "amikacin_measurement_units", "owner": "GRDI", @@ -27136,13 +32748,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "amikacin_measurement_sign": { "name": "amikacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "amikacin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 173, "alias": "amikacin_measurement_sign", "owner": "GRDI", @@ -27150,38 +32781,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "amikacin_laboratory_typing_method": { "name": "amikacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "amikacin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 174, "alias": "amikacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "amikacin_laboratory_typing_platform": { "name": "amikacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "amikacin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 175, "alias": "amikacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "amikacin_laboratory_typing_platform_version": { "name": "amikacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "amikacin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 176, "alias": "amikacin_laboratory_typing_platform_version", @@ -27196,20 +32881,50 @@ "name": "amikacin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "amikacin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 177, "alias": "amikacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name" + }, + { + "range": "null value menu" + } + ] }, "amikacin_testing_standard": { "name": "amikacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "amikacin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 178, "alias": "amikacin_testing_standard", "owner": "GRDI", @@ -27217,12 +32932,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "amikacin_testing_standard_version": { "name": "amikacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "amikacin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 179, "alias": "amikacin_testing_standard_version", @@ -27237,6 +32968,17 @@ "name": "amikacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "amikacin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 180, "alias": "amikacin_testing_standard_details", @@ -27251,6 +32993,14 @@ "name": "amikacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "amikacin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 181, "alias": "amikacin_susceptible_breakpoint", @@ -27265,6 +33015,11 @@ "name": "amikacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "amikacin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 182, "alias": "amikacin_intermediate_breakpoint", @@ -27279,6 +33034,14 @@ "name": "amikacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "amikacin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 183, "alias": "amikacin_resistant_breakpoint", @@ -27289,95 +33052,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_resistance_phenotype": { - "name": "amoxicillin-clavulanic_acid_resistance_phenotype", + "amoxicillinclavulanic_acid_resistance_phenotype": { + "name": "amoxicillinclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "amoxicillin-clavulanic_acid_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 184, - "alias": "amoxicillin_clavulanic_acid_resistance_phenotype", + "alias": "amoxicillinclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_measurement": { - "name": "amoxicillin-clavulanic_acid_measurement", + "amoxicillinclavulanic_acid_measurement": { + "name": "amoxicillinclavulanic_acid_measurement", "description": "The measured value of amoxicillin-clavulanic acid resistance.", "title": "amoxicillin-clavulanic_acid_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 185, - "alias": "amoxicillin_clavulanic_acid_measurement", + "alias": "amoxicillinclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_measurement_units": { - "name": "amoxicillin-clavulanic_acid_measurement_units", + "amoxicillinclavulanic_acid_measurement_units": { + "name": "amoxicillinclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "amoxicillin-clavulanic_acid_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 186, - "alias": "amoxicillin_clavulanic_acid_measurement_units", + "alias": "amoxicillinclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_measurement_sign": { - "name": "amoxicillin-clavulanic_acid_measurement_sign", + "amoxicillinclavulanic_acid_measurement_sign": { + "name": "amoxicillinclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "amoxicillin-clavulanic_acid_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 187, - "alias": "amoxicillin_clavulanic_acid_measurement_sign", + "alias": "amoxicillinclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_laboratory_typing_method": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_method", + "amoxicillinclavulanic_acid_laboratory_typing_method": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "amoxicillin-clavulanic_acid_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 188, - "alias": "amoxicillin_clavulanic_acid_laboratory_typing_method", + "alias": "amoxicillinclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_laboratory_typing_platform": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_platform", + "amoxicillinclavulanic_acid_laboratory_typing_platform": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 189, - "alias": "amoxicillin_clavulanic_acid_laboratory_typing_platform", + "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_laboratory_typing_platform_version": { - "name": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", + "amoxicillinclavulanic_acid_laboratory_typing_platform_version": { + "name": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "amoxicillin-clavulanic_acid_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 190, - "alias": "amoxicillin_clavulanic_acid_laboratory_typing_platform_version", + "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27385,40 +33270,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_vendor_name": { - "name": "amoxicillin-clavulanic_acid_vendor_name", + "amoxicillinclavulanic_acid_vendor_name": { + "name": "amoxicillinclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "amoxicillin-clavulanic_acid_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 191, - "alias": "amoxicillin_clavulanic_acid_vendor_name", + "alias": "amoxicillinclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_testing_standard": { - "name": "amoxicillin-clavulanic_acid_testing_standard", + "amoxicillinclavulanic_acid_testing_standard": { + "name": "amoxicillinclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "amoxicillin-clavulanic_acid_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 192, - "alias": "amoxicillin_clavulanic_acid_testing_standard", + "alias": "amoxicillinclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "amoxicillin-clavulanic_acid_testing_standard_version": { - "name": "amoxicillin-clavulanic_acid_testing_standard_version", + "amoxicillinclavulanic_acid_testing_standard_version": { + "name": "amoxicillinclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "amoxicillin-clavulanic_acid_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 193, - "alias": "amoxicillin_clavulanic_acid_testing_standard_version", + "alias": "amoxicillinclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27426,13 +33357,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_testing_standard_details": { - "name": "amoxicillin-clavulanic_acid_testing_standard_details", + "amoxicillinclavulanic_acid_testing_standard_details": { + "name": "amoxicillinclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "amoxicillin-clavulanic_acid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 194, - "alias": "amoxicillin_clavulanic_acid_testing_standard_details", + "alias": "amoxicillinclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27440,13 +33382,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_susceptible_breakpoint": { - "name": "amoxicillin-clavulanic_acid_susceptible_breakpoint", + "amoxicillinclavulanic_acid_susceptible_breakpoint": { + "name": "amoxicillinclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "amoxicillin-clavulanic_acid_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 195, - "alias": "amoxicillin_clavulanic_acid_susceptible_breakpoint", + "alias": "amoxicillinclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27454,13 +33404,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_intermediate_breakpoint": { - "name": "amoxicillin-clavulanic_acid_intermediate_breakpoint", + "amoxicillinclavulanic_acid_intermediate_breakpoint": { + "name": "amoxicillinclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "amoxicillin-clavulanic_acid_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 196, - "alias": "amoxicillin_clavulanic_acid_intermediate_breakpoint", + "alias": "amoxicillinclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27468,13 +33423,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "amoxicillin-clavulanic_acid_resistant_breakpoint": { - "name": "amoxicillin-clavulanic_acid_resistant_breakpoint", + "amoxicillinclavulanic_acid_resistant_breakpoint": { + "name": "amoxicillinclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "amoxicillin-clavulanic_acid_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 197, - "alias": "amoxicillin_clavulanic_acid_resistant_breakpoint", + "alias": "amoxicillinclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -27486,7 +33449,18 @@ "name": "ampicillin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ampicillin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 198, "alias": "ampicillin_resistance_phenotype", "owner": "GRDI", @@ -27494,13 +33468,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_measurement": { "name": "ampicillin_measurement", "description": "The measured value of ampicillin resistance.", "title": "ampicillin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 199, "alias": "ampicillin_measurement", "owner": "GRDI", @@ -27508,13 +33501,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_measurement_units": { "name": "ampicillin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ampicillin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 200, "alias": "ampicillin_measurement_units", "owner": "GRDI", @@ -27522,13 +33534,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_measurement_sign": { "name": "ampicillin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ampicillin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 201, "alias": "ampicillin_measurement_sign", "owner": "GRDI", @@ -27536,38 +33567,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_laboratory_typing_method": { "name": "ampicillin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ampicillin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 202, "alias": "ampicillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_laboratory_typing_platform": { "name": "ampicillin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ampicillin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 203, "alias": "ampicillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_laboratory_typing_platform_version": { "name": "ampicillin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ampicillin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 204, "alias": "ampicillin_laboratory_typing_platform_version", @@ -27582,20 +33667,50 @@ "name": "ampicillin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ampicillin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 205, "alias": "ampicillin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_testing_standard": { "name": "ampicillin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ampicillin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 206, "alias": "ampicillin_testing_standard", "owner": "GRDI", @@ -27603,12 +33718,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "ampicillin_testing_standard_version": { "name": "ampicillin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ampicillin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 207, "alias": "ampicillin_testing_standard_version", @@ -27623,6 +33754,17 @@ "name": "ampicillin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ampicillin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 208, "alias": "ampicillin_testing_standard_details", @@ -27637,6 +33779,14 @@ "name": "ampicillin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ampicillin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 209, "alias": "ampicillin_susceptible_breakpoint", @@ -27651,6 +33801,11 @@ "name": "ampicillin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ampicillin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 210, "alias": "ampicillin_intermediate_breakpoint", @@ -27665,6 +33820,14 @@ "name": "ampicillin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ampicillin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 211, "alias": "ampicillin_resistant_breakpoint", @@ -27679,7 +33842,18 @@ "name": "azithromycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "azithromycin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 212, "alias": "azithromycin_resistance_phenotype", "owner": "GRDI", @@ -27687,13 +33861,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_measurement": { "name": "azithromycin_measurement", "description": "The measured value of azithromycin resistance.", "title": "azithromycin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 213, "alias": "azithromycin_measurement", "owner": "GRDI", @@ -27701,13 +33894,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_measurement_units": { "name": "azithromycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "azithromycin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 214, "alias": "azithromycin_measurement_units", "owner": "GRDI", @@ -27715,13 +33927,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_measurement_sign": { "name": "azithromycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "azithromycin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 215, "alias": "azithromycin_measurement_sign", "owner": "GRDI", @@ -27729,38 +33960,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_laboratory_typing_method": { "name": "azithromycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "azithromycin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 216, "alias": "azithromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_laboratory_typing_platform": { "name": "azithromycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "azithromycin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 217, "alias": "azithromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_laboratory_typing_platform_version": { "name": "azithromycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "azithromycin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 218, "alias": "azithromycin_laboratory_typing_platform_version", @@ -27775,20 +34060,50 @@ "name": "azithromycin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "azithromycin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 219, "alias": "azithromycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_testing_standard": { "name": "azithromycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "azithromycin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 220, "alias": "azithromycin_testing_standard", "owner": "GRDI", @@ -27796,12 +34111,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "azithromycin_testing_standard_version": { "name": "azithromycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "azithromycin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 221, "alias": "azithromycin_testing_standard_version", @@ -27816,6 +34147,17 @@ "name": "azithromycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "azithromycin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 222, "alias": "azithromycin_testing_standard_details", @@ -27830,6 +34172,14 @@ "name": "azithromycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "azithromycin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 223, "alias": "azithromycin_susceptible_breakpoint", @@ -27844,6 +34194,11 @@ "name": "azithromycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "azithromycin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 224, "alias": "azithromycin_intermediate_breakpoint", @@ -27858,6 +34213,14 @@ "name": "azithromycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "azithromycin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 225, "alias": "azithromycin_resistant_breakpoint", @@ -27872,7 +34235,18 @@ "name": "cefazolin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefazolin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 226, "alias": "cefazolin_resistance_phenotype", "owner": "GRDI", @@ -27880,13 +34254,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_measurement": { "name": "cefazolin_measurement", "description": "The measured value of cefazolin resistance.", "title": "cefazolin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 227, "alias": "cefazolin_measurement", "owner": "GRDI", @@ -27894,13 +34287,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_measurement_units": { "name": "cefazolin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefazolin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 228, "alias": "cefazolin_measurement_units", "owner": "GRDI", @@ -27908,13 +34320,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_measurement_sign": { "name": "cefazolin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefazolin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 229, "alias": "cefazolin_measurement_sign", "owner": "GRDI", @@ -27922,38 +34353,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_laboratory_typing_method": { "name": "cefazolin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefazolin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 230, "alias": "cefazolin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_laboratory_typing_platform": { "name": "cefazolin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefazolin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 231, "alias": "cefazolin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_laboratory_typing_platform_version": { "name": "cefazolin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefazolin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 232, "alias": "cefazolin_laboratory_typing_platform_version", @@ -27968,20 +34453,50 @@ "name": "cefazolin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefazolin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 233, "alias": "cefazolin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_testing_standard": { "name": "cefazolin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefazolin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 234, "alias": "cefazolin_testing_standard", "owner": "GRDI", @@ -27989,12 +34504,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "cefazolin_testing_standard_version": { "name": "cefazolin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefazolin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 235, "alias": "cefazolin_testing_standard_version", @@ -28009,6 +34540,17 @@ "name": "cefazolin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefazolin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 236, "alias": "cefazolin_testing_standard_details", @@ -28023,6 +34565,14 @@ "name": "cefazolin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefazolin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 237, "alias": "cefazolin_susceptible_breakpoint", @@ -28037,6 +34587,11 @@ "name": "cefazolin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefazolin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 238, "alias": "cefazolin_intermediate_breakpoint", @@ -28051,6 +34606,14 @@ "name": "cefazolin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefazolin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 239, "alias": "cefazolin_resistant_breakpoint", @@ -28065,7 +34628,18 @@ "name": "cefepime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefepime_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 240, "alias": "cefepime_resistance_phenotype", "owner": "GRDI", @@ -28073,13 +34647,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_measurement": { "name": "cefepime_measurement", "description": "The measured value of cefepime resistance.", "title": "cefepime_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 241, "alias": "cefepime_measurement", "owner": "GRDI", @@ -28087,13 +34680,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "cefepime_measurement_units": { "name": "cefepime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefepime_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 242, "alias": "cefepime_measurement_units", "owner": "GRDI", @@ -28101,13 +34713,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_measurement_sign": { "name": "cefepime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefepime_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 243, "alias": "cefepime_measurement_sign", "owner": "GRDI", @@ -28115,38 +34746,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_laboratory_typing_method": { "name": "cefepime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefepime_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 244, "alias": "cefepime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_laboratory_typing_platform": { "name": "cefepime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefepime_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 245, "alias": "cefepime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_laboratory_typing_platform_version": { "name": "cefepime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefepime_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 246, "alias": "cefepime_laboratory_typing_platform_version", @@ -28161,20 +34846,50 @@ "name": "cefepime_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefepime_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 247, "alias": "cefepime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_testing_standard": { "name": "cefepime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefepime_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 248, "alias": "cefepime_testing_standard", "owner": "GRDI", @@ -28182,12 +34897,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "cefepime_testing_standard_version": { "name": "cefepime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefepime_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 249, "alias": "cefepime_testing_standard_version", @@ -28202,6 +34933,17 @@ "name": "cefepime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefepime_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 250, "alias": "cefepime_testing_standard_details", @@ -28216,6 +34958,14 @@ "name": "cefepime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefepime_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 251, "alias": "cefepime_susceptible_breakpoint", @@ -28230,6 +34980,11 @@ "name": "cefepime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefepime_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 252, "alias": "cefepime_intermediate_breakpoint", @@ -28244,6 +34999,14 @@ "name": "cefepime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefepime_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 253, "alias": "cefepime_resistant_breakpoint", @@ -28258,7 +35021,18 @@ "name": "cefotaxime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefotaxime_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 254, "alias": "cefotaxime_resistance_phenotype", "owner": "GRDI", @@ -28266,13 +35040,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_measurement": { "name": "cefotaxime_measurement", "description": "The measured value of cefotaxime resistance.", "title": "cefotaxime_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 255, "alias": "cefotaxime_measurement", "owner": "GRDI", @@ -28280,13 +35073,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_measurement_units": { "name": "cefotaxime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefotaxime_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 256, "alias": "cefotaxime_measurement_units", "owner": "GRDI", @@ -28294,13 +35106,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_measurement_sign": { "name": "cefotaxime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefotaxime_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 257, "alias": "cefotaxime_measurement_sign", "owner": "GRDI", @@ -28308,38 +35139,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_laboratory_typing_method": { "name": "cefotaxime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefotaxime_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 258, "alias": "cefotaxime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_laboratory_typing_platform": { "name": "cefotaxime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefotaxime_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 259, "alias": "cefotaxime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_laboratory_typing_platform_version": { "name": "cefotaxime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefotaxime_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 260, "alias": "cefotaxime_laboratory_typing_platform_version", @@ -28354,20 +35239,50 @@ "name": "cefotaxime_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefotaxime_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 261, "alias": "cefotaxime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_testing_standard": { "name": "cefotaxime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefotaxime_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 262, "alias": "cefotaxime_testing_standard", "owner": "GRDI", @@ -28375,12 +35290,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "cefotaxime_testing_standard_version": { "name": "cefotaxime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefotaxime_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 263, "alias": "cefotaxime_testing_standard_version", @@ -28395,6 +35326,17 @@ "name": "cefotaxime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefotaxime_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 264, "alias": "cefotaxime_testing_standard_details", @@ -28409,6 +35351,14 @@ "name": "cefotaxime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefotaxime_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 265, "alias": "cefotaxime_susceptible_breakpoint", @@ -28423,6 +35373,11 @@ "name": "cefotaxime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefotaxime_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 266, "alias": "cefotaxime_intermediate_breakpoint", @@ -28437,6 +35392,14 @@ "name": "cefotaxime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefotaxime_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 267, "alias": "cefotaxime_resistant_breakpoint", @@ -28447,95 +35410,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_resistance_phenotype": { - "name": "cefotaxime-clavulanic_acid_resistance_phenotype", + "cefotaximeclavulanic_acid_resistance_phenotype": { + "name": "cefotaximeclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefotaxime-clavulanic_acid_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 268, - "alias": "cefotaxime_clavulanic_acid_resistance_phenotype", + "alias": "cefotaximeclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_measurement": { - "name": "cefotaxime-clavulanic_acid_measurement", + "cefotaximeclavulanic_acid_measurement": { + "name": "cefotaximeclavulanic_acid_measurement", "description": "The measured value of cefotaxime-clavulanic acid resistance.", "title": "cefotaxime-clavulanic_acid_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 269, - "alias": "cefotaxime_clavulanic_acid_measurement", + "alias": "cefotaximeclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_measurement_units": { - "name": "cefotaxime-clavulanic_acid_measurement_units", + "cefotaximeclavulanic_acid_measurement_units": { + "name": "cefotaximeclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefotaxime-clavulanic_acid_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 270, - "alias": "cefotaxime_clavulanic_acid_measurement_units", + "alias": "cefotaximeclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_measurement_sign": { - "name": "cefotaxime-clavulanic_acid_measurement_sign", + "cefotaximeclavulanic_acid_measurement_sign": { + "name": "cefotaximeclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefotaxime-clavulanic_acid_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 271, - "alias": "cefotaxime_clavulanic_acid_measurement_sign", + "alias": "cefotaximeclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_laboratory_typing_method": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_method", + "cefotaximeclavulanic_acid_laboratory_typing_method": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefotaxime-clavulanic_acid_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 272, - "alias": "cefotaxime_clavulanic_acid_laboratory_typing_method", + "alias": "cefotaximeclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_laboratory_typing_platform": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_platform", + "cefotaximeclavulanic_acid_laboratory_typing_platform": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 273, - "alias": "cefotaxime_clavulanic_acid_laboratory_typing_platform", + "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_laboratory_typing_platform_version": { - "name": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", + "cefotaximeclavulanic_acid_laboratory_typing_platform_version": { + "name": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefotaxime-clavulanic_acid_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 274, - "alias": "cefotaxime_clavulanic_acid_laboratory_typing_platform_version", + "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28543,40 +35628,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_vendor_name": { - "name": "cefotaxime-clavulanic_acid_vendor_name", + "cefotaximeclavulanic_acid_vendor_name": { + "name": "cefotaximeclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefotaxime-clavulanic_acid_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 275, - "alias": "cefotaxime_clavulanic_acid_vendor_name", + "alias": "cefotaximeclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_testing_standard": { - "name": "cefotaxime-clavulanic_acid_testing_standard", + "cefotaximeclavulanic_acid_testing_standard": { + "name": "cefotaximeclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefotaxime-clavulanic_acid_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 276, - "alias": "cefotaxime_clavulanic_acid_testing_standard", + "alias": "cefotaximeclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "cefotaxime-clavulanic_acid_testing_standard_version": { - "name": "cefotaxime-clavulanic_acid_testing_standard_version", + "cefotaximeclavulanic_acid_testing_standard_version": { + "name": "cefotaximeclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefotaxime-clavulanic_acid_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 277, - "alias": "cefotaxime_clavulanic_acid_testing_standard_version", + "alias": "cefotaximeclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28584,13 +35715,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_testing_standard_details": { - "name": "cefotaxime-clavulanic_acid_testing_standard_details", + "cefotaximeclavulanic_acid_testing_standard_details": { + "name": "cefotaximeclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefotaxime-clavulanic_acid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 278, - "alias": "cefotaxime_clavulanic_acid_testing_standard_details", + "alias": "cefotaximeclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28598,13 +35740,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_susceptible_breakpoint": { - "name": "cefotaxime-clavulanic_acid_susceptible_breakpoint", + "cefotaximeclavulanic_acid_susceptible_breakpoint": { + "name": "cefotaximeclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefotaxime-clavulanic_acid_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 279, - "alias": "cefotaxime_clavulanic_acid_susceptible_breakpoint", + "alias": "cefotaximeclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28612,13 +35762,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_intermediate_breakpoint": { - "name": "cefotaxime-clavulanic_acid_intermediate_breakpoint", + "cefotaximeclavulanic_acid_intermediate_breakpoint": { + "name": "cefotaximeclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefotaxime-clavulanic_acid_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 280, - "alias": "cefotaxime_clavulanic_acid_intermediate_breakpoint", + "alias": "cefotaximeclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28626,13 +35781,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "cefotaxime-clavulanic_acid_resistant_breakpoint": { - "name": "cefotaxime-clavulanic_acid_resistant_breakpoint", + "cefotaximeclavulanic_acid_resistant_breakpoint": { + "name": "cefotaximeclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefotaxime-clavulanic_acid_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 281, - "alias": "cefotaxime_clavulanic_acid_resistant_breakpoint", + "alias": "cefotaximeclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -28644,7 +35807,18 @@ "name": "cefoxitin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefoxitin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 282, "alias": "cefoxitin_resistance_phenotype", "owner": "GRDI", @@ -28652,13 +35826,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_measurement": { "name": "cefoxitin_measurement", "description": "The measured value of cefoxitin resistance.", "title": "cefoxitin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 283, "alias": "cefoxitin_measurement", "owner": "GRDI", @@ -28666,13 +35859,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_measurement_units": { "name": "cefoxitin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefoxitin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 284, "alias": "cefoxitin_measurement_units", "owner": "GRDI", @@ -28680,13 +35892,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_measurement_sign": { "name": "cefoxitin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefoxitin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 285, "alias": "cefoxitin_measurement_sign", "owner": "GRDI", @@ -28694,38 +35925,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_laboratory_typing_method": { "name": "cefoxitin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefoxitin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 286, "alias": "cefoxitin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_laboratory_typing_platform": { "name": "cefoxitin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefoxitin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 287, "alias": "cefoxitin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_laboratory_typing_platform_version": { "name": "cefoxitin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefoxitin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 288, "alias": "cefoxitin_laboratory_typing_platform_version", @@ -28740,20 +36025,50 @@ "name": "cefoxitin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefoxitin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 289, "alias": "cefoxitin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_testing_standard": { "name": "cefoxitin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefoxitin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 290, "alias": "cefoxitin_testing_standard", "owner": "GRDI", @@ -28761,12 +36076,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "cefoxitin_testing_standard_version": { "name": "cefoxitin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefoxitin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 291, "alias": "cefoxitin_testing_standard_version", @@ -28781,6 +36112,17 @@ "name": "cefoxitin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefoxitin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 292, "alias": "cefoxitin_testing_standard_details", @@ -28795,6 +36137,14 @@ "name": "cefoxitin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefoxitin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 293, "alias": "cefoxitin_susceptible_breakpoint", @@ -28809,6 +36159,11 @@ "name": "cefoxitin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefoxitin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 294, "alias": "cefoxitin_intermediate_breakpoint", @@ -28823,6 +36178,14 @@ "name": "cefoxitin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefoxitin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 295, "alias": "cefoxitin_resistant_breakpoint", @@ -28837,7 +36200,18 @@ "name": "cefpodoxime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cefpodoxime_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 296, "alias": "cefpodoxime_resistance_phenotype", "owner": "GRDI", @@ -28845,13 +36219,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_measurement": { "name": "cefpodoxime_measurement", "description": "The measured value of cefpodoxime resistance.", "title": "cefpodoxime_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 297, "alias": "cefpodoxime_measurement", "owner": "GRDI", @@ -28859,13 +36252,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_measurement_units": { "name": "cefpodoxime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cefpodoxime_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 298, "alias": "cefpodoxime_measurement_units", "owner": "GRDI", @@ -28873,13 +36285,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_measurement_sign": { "name": "cefpodoxime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cefpodoxime_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 299, "alias": "cefpodoxime_measurement_sign", "owner": "GRDI", @@ -28887,38 +36318,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_laboratory_typing_method": { "name": "cefpodoxime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cefpodoxime_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 300, "alias": "cefpodoxime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_laboratory_typing_platform": { "name": "cefpodoxime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cefpodoxime_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 301, "alias": "cefpodoxime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_laboratory_typing_platform_version": { "name": "cefpodoxime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cefpodoxime_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 302, "alias": "cefpodoxime_laboratory_typing_platform_version", @@ -28933,20 +36418,50 @@ "name": "cefpodoxime_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cefpodoxime_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 303, "alias": "cefpodoxime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_testing_standard": { "name": "cefpodoxime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cefpodoxime_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 304, "alias": "cefpodoxime_testing_standard", "owner": "GRDI", @@ -28954,12 +36469,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "cefpodoxime_testing_standard_version": { "name": "cefpodoxime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cefpodoxime_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 305, "alias": "cefpodoxime_testing_standard_version", @@ -28974,6 +36505,17 @@ "name": "cefpodoxime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cefpodoxime_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 306, "alias": "cefpodoxime_testing_standard_details", @@ -28988,6 +36530,14 @@ "name": "cefpodoxime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cefpodoxime_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 307, "alias": "cefpodoxime_susceptible_breakpoint", @@ -29002,6 +36552,11 @@ "name": "cefpodoxime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cefpodoxime_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 308, "alias": "cefpodoxime_intermediate_breakpoint", @@ -29016,6 +36571,14 @@ "name": "cefpodoxime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cefpodoxime_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 309, "alias": "cefpodoxime_resistant_breakpoint", @@ -29030,7 +36593,18 @@ "name": "ceftazidime_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ceftazidime_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 310, "alias": "ceftazidime_resistance_phenotype", "owner": "GRDI", @@ -29038,13 +36612,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_measurement": { "name": "ceftazidime_measurement", "description": "The measured value of ceftazidime resistance.", "title": "ceftazidime_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 311, "alias": "ceftazidime_measurement", "owner": "GRDI", @@ -29052,13 +36645,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_measurement_units": { "name": "ceftazidime_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ceftazidime_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 312, "alias": "ceftazidime_measurement_units", "owner": "GRDI", @@ -29066,13 +36678,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_measurement_sign": { "name": "ceftazidime_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ceftazidime_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 313, "alias": "ceftazidime_measurement_sign", "owner": "GRDI", @@ -29080,38 +36711,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_laboratory_typing_method": { "name": "ceftazidime_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ceftazidime_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 314, "alias": "ceftazidime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_laboratory_typing_platform": { "name": "ceftazidime_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ceftazidime_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 315, "alias": "ceftazidime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_laboratory_typing_platform_version": { "name": "ceftazidime_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ceftazidime_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 316, "alias": "ceftazidime_laboratory_typing_platform_version", @@ -29126,20 +36811,50 @@ "name": "ceftazidime_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ceftazidime_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 317, "alias": "ceftazidime_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_testing_standard": { "name": "ceftazidime_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ceftazidime_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 318, "alias": "ceftazidime_testing_standard", "owner": "GRDI", @@ -29147,12 +36862,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "ceftazidime_testing_standard_version": { "name": "ceftazidime_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ceftazidime_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 319, "alias": "ceftazidime_testing_standard_version", @@ -29167,6 +36898,17 @@ "name": "ceftazidime_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ceftazidime_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 320, "alias": "ceftazidime_testing_standard_details", @@ -29181,6 +36923,14 @@ "name": "ceftazidime_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ceftazidime_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 321, "alias": "ceftazidime_susceptible_breakpoint", @@ -29195,6 +36945,11 @@ "name": "ceftazidime_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ceftazidime_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 322, "alias": "ceftazidime_intermediate_breakpoint", @@ -29209,6 +36964,14 @@ "name": "ceftazidime_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ceftazidime_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 323, "alias": "ceftazidime_resistant_breakpoint", @@ -29219,95 +36982,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_resistance_phenotype": { - "name": "ceftazidime-clavulanic_acid_resistance_phenotype", + "ceftazidimeclavulanic_acid_resistance_phenotype": { + "name": "ceftazidimeclavulanic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ceftazidime-clavulanic_acid_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 324, - "alias": "ceftazidime_clavulanic_acid_resistance_phenotype", + "alias": "ceftazidimeclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_measurement": { - "name": "ceftazidime-clavulanic_acid_measurement", + "ceftazidimeclavulanic_acid_measurement": { + "name": "ceftazidimeclavulanic_acid_measurement", "description": "The measured value of ceftazidime-clavulanic acid resistance.", "title": "ceftazidime-clavulanic_acid_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 325, - "alias": "ceftazidime_clavulanic_acid_measurement", + "alias": "ceftazidimeclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_measurement_units": { - "name": "ceftazidime-clavulanic_acid_measurement_units", + "ceftazidimeclavulanic_acid_measurement_units": { + "name": "ceftazidimeclavulanic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ceftazidime-clavulanic_acid_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 326, - "alias": "ceftazidime_clavulanic_acid_measurement_units", + "alias": "ceftazidimeclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_measurement_sign": { - "name": "ceftazidime-clavulanic_acid_measurement_sign", + "ceftazidimeclavulanic_acid_measurement_sign": { + "name": "ceftazidimeclavulanic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ceftazidime-clavulanic_acid_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 327, - "alias": "ceftazidime_clavulanic_acid_measurement_sign", + "alias": "ceftazidimeclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_laboratory_typing_method": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_method", + "ceftazidimeclavulanic_acid_laboratory_typing_method": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ceftazidime-clavulanic_acid_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 328, - "alias": "ceftazidime_clavulanic_acid_laboratory_typing_method", + "alias": "ceftazidimeclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_laboratory_typing_platform": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_platform", + "ceftazidimeclavulanic_acid_laboratory_typing_platform": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 329, - "alias": "ceftazidime_clavulanic_acid_laboratory_typing_platform", + "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_laboratory_typing_platform_version": { - "name": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", + "ceftazidimeclavulanic_acid_laboratory_typing_platform_version": { + "name": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ceftazidime-clavulanic_acid_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 330, - "alias": "ceftazidime_clavulanic_acid_laboratory_typing_platform_version", + "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29315,40 +37200,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_vendor_name": { - "name": "ceftazidime-clavulanic_acid_vendor_name", + "ceftazidimeclavulanic_acid_vendor_name": { + "name": "ceftazidimeclavulanic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ceftazidime-clavulanic_acid_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 331, - "alias": "ceftazidime_clavulanic_acid_vendor_name", + "alias": "ceftazidimeclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_testing_standard": { - "name": "ceftazidime-clavulanic_acid_testing_standard", + "ceftazidimeclavulanic_acid_testing_standard": { + "name": "ceftazidimeclavulanic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ceftazidime-clavulanic_acid_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 332, - "alias": "ceftazidime_clavulanic_acid_testing_standard", + "alias": "ceftazidimeclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "ceftazidime-clavulanic_acid_testing_standard_version": { - "name": "ceftazidime-clavulanic_acid_testing_standard_version", + "ceftazidimeclavulanic_acid_testing_standard_version": { + "name": "ceftazidimeclavulanic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ceftazidime-clavulanic_acid_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 333, - "alias": "ceftazidime_clavulanic_acid_testing_standard_version", + "alias": "ceftazidimeclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29356,13 +37287,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_testing_standard_details": { - "name": "ceftazidime-clavulanic_acid_testing_standard_details", + "ceftazidimeclavulanic_acid_testing_standard_details": { + "name": "ceftazidimeclavulanic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ceftazidime-clavulanic_acid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 334, - "alias": "ceftazidime_clavulanic_acid_testing_standard_details", + "alias": "ceftazidimeclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29370,13 +37312,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_susceptible_breakpoint": { - "name": "ceftazidime-clavulanic_acid_susceptible_breakpoint", + "ceftazidimeclavulanic_acid_susceptible_breakpoint": { + "name": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ceftazidime-clavulanic_acid_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 335, - "alias": "ceftazidime_clavulanic_acid_susceptible_breakpoint", + "alias": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29384,13 +37334,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_intermediate_breakpoint": { - "name": "ceftazidime-clavulanic_acid_intermediate_breakpoint", + "ceftazidimeclavulanic_acid_intermediate_breakpoint": { + "name": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ceftazidime-clavulanic_acid_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 336, - "alias": "ceftazidime_clavulanic_acid_intermediate_breakpoint", + "alias": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29398,13 +37353,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "ceftazidime-clavulanic_acid_resistant_breakpoint": { - "name": "ceftazidime-clavulanic_acid_resistant_breakpoint", + "ceftazidimeclavulanic_acid_resistant_breakpoint": { + "name": "ceftazidimeclavulanic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ceftazidime-clavulanic_acid_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 337, - "alias": "ceftazidime_clavulanic_acid_resistant_breakpoint", + "alias": "ceftazidimeclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -29416,7 +37379,18 @@ "name": "ceftiofur_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ceftiofur_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 338, "alias": "ceftiofur_resistance_phenotype", "owner": "GRDI", @@ -29424,13 +37398,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_measurement": { "name": "ceftiofur_measurement", "description": "The measured value of ceftiofur resistance.", "title": "ceftiofur_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 339, "alias": "ceftiofur_measurement", "owner": "GRDI", @@ -29438,13 +37431,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_measurement_units": { "name": "ceftiofur_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ceftiofur_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 340, "alias": "ceftiofur_measurement_units", "owner": "GRDI", @@ -29452,13 +37464,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_measurement_sign": { "name": "ceftiofur_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ceftiofur_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 341, "alias": "ceftiofur_measurement_sign", "owner": "GRDI", @@ -29466,38 +37497,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_laboratory_typing_method": { "name": "ceftiofur_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ceftiofur_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 342, "alias": "ceftiofur_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_laboratory_typing_platform": { "name": "ceftiofur_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ceftiofur_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 343, "alias": "ceftiofur_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_laboratory_typing_platform_version": { "name": "ceftiofur_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ceftiofur_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 344, "alias": "ceftiofur_laboratory_typing_platform_version", @@ -29512,20 +37597,50 @@ "name": "ceftiofur_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ceftiofur_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 345, "alias": "ceftiofur_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_testing_standard": { "name": "ceftiofur_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ceftiofur_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 346, "alias": "ceftiofur_testing_standard", "owner": "GRDI", @@ -29533,12 +37648,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "ceftiofur_testing_standard_version": { "name": "ceftiofur_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ceftiofur_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 347, "alias": "ceftiofur_testing_standard_version", @@ -29553,6 +37684,17 @@ "name": "ceftiofur_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ceftiofur_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 348, "alias": "ceftiofur_testing_standard_details", @@ -29567,6 +37709,14 @@ "name": "ceftiofur_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ceftiofur_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 349, "alias": "ceftiofur_susceptible_breakpoint", @@ -29581,6 +37731,11 @@ "name": "ceftiofur_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ceftiofur_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 350, "alias": "ceftiofur_intermediate_breakpoint", @@ -29595,6 +37750,14 @@ "name": "ceftiofur_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ceftiofur_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 351, "alias": "ceftiofur_resistant_breakpoint", @@ -29609,7 +37772,18 @@ "name": "ceftriaxone_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ceftriaxone_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 352, "alias": "ceftriaxone_resistance_phenotype", "owner": "GRDI", @@ -29617,13 +37791,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_measurement": { "name": "ceftriaxone_measurement", "description": "The measured value of ceftriaxone resistance.", "title": "ceftriaxone_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 353, "alias": "ceftriaxone_measurement", "owner": "GRDI", @@ -29631,13 +37824,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_measurement_units": { "name": "ceftriaxone_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ceftriaxone_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 354, "alias": "ceftriaxone_measurement_units", "owner": "GRDI", @@ -29645,13 +37857,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_measurement_sign": { "name": "ceftriaxone_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ceftriaxone_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 355, "alias": "ceftriaxone_measurement_sign", "owner": "GRDI", @@ -29659,38 +37890,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_laboratory_typing_method": { "name": "ceftriaxone_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ceftriaxone_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 356, "alias": "ceftriaxone_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_laboratory_typing_platform": { "name": "ceftriaxone_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ceftriaxone_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 357, "alias": "ceftriaxone_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_laboratory_typing_platform_version": { "name": "ceftriaxone_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ceftriaxone_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 358, "alias": "ceftriaxone_laboratory_typing_platform_version", @@ -29705,20 +37990,50 @@ "name": "ceftriaxone_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ceftriaxone_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 359, "alias": "ceftriaxone_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_testing_standard": { "name": "ceftriaxone_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ceftriaxone_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 360, "alias": "ceftriaxone_testing_standard", "owner": "GRDI", @@ -29726,12 +38041,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "ceftriaxone_testing_standard_version": { "name": "ceftriaxone_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ceftriaxone_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 361, "alias": "ceftriaxone_testing_standard_version", @@ -29746,6 +38077,17 @@ "name": "ceftriaxone_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ceftriaxone_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 362, "alias": "ceftriaxone_testing_standard_details", @@ -29760,6 +38102,14 @@ "name": "ceftriaxone_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ceftriaxone_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 363, "alias": "ceftriaxone_susceptible_breakpoint", @@ -29774,6 +38124,11 @@ "name": "ceftriaxone_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ceftriaxone_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 364, "alias": "ceftriaxone_intermediate_breakpoint", @@ -29788,6 +38143,14 @@ "name": "ceftriaxone_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ceftriaxone_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 365, "alias": "ceftriaxone_resistant_breakpoint", @@ -29802,7 +38165,18 @@ "name": "cephalothin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "cephalothin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 366, "alias": "cephalothin_resistance_phenotype", "owner": "GRDI", @@ -29810,13 +38184,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_measurement": { "name": "cephalothin_measurement", "description": "The measured value of cephalothin resistance.", "title": "cephalothin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 367, "alias": "cephalothin_measurement", "owner": "GRDI", @@ -29824,13 +38217,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_measurement_units": { "name": "cephalothin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "cephalothin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 368, "alias": "cephalothin_measurement_units", "owner": "GRDI", @@ -29838,13 +38250,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_measurement_sign": { "name": "cephalothin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "cephalothin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 369, "alias": "cephalothin_measurement_sign", "owner": "GRDI", @@ -29852,38 +38283,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_laboratory_typing_method": { "name": "cephalothin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "cephalothin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 370, "alias": "cephalothin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_laboratory_typing_platform": { "name": "cephalothin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "cephalothin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 371, "alias": "cephalothin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_laboratory_typing_platform_version": { "name": "cephalothin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "cephalothin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 372, "alias": "cephalothin_laboratory_typing_platform_version", @@ -29898,20 +38383,50 @@ "name": "cephalothin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "cephalothin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 373, "alias": "cephalothin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_testing_standard": { "name": "cephalothin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "cephalothin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 374, "alias": "cephalothin_testing_standard", "owner": "GRDI", @@ -29919,12 +38434,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "cephalothin_testing_standard_version": { "name": "cephalothin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "cephalothin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 375, "alias": "cephalothin_testing_standard_version", @@ -29939,6 +38470,17 @@ "name": "cephalothin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "cephalothin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 376, "alias": "cephalothin_testing_standard_details", @@ -29953,6 +38495,14 @@ "name": "cephalothin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "cephalothin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 377, "alias": "cephalothin_susceptible_breakpoint", @@ -29967,6 +38517,11 @@ "name": "cephalothin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "cephalothin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 378, "alias": "cephalothin_intermediate_breakpoint", @@ -29981,6 +38536,14 @@ "name": "cephalothin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "cephalothin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 379, "alias": "cephalothin_resistant_breakpoint", @@ -29995,7 +38558,18 @@ "name": "chloramphenicol_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "chloramphenicol_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 380, "alias": "chloramphenicol_resistance_phenotype", "owner": "GRDI", @@ -30003,13 +38577,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_measurement": { "name": "chloramphenicol_measurement", "description": "The measured value of chloramphenicol resistance.", "title": "chloramphenicol_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 381, "alias": "chloramphenicol_measurement", "owner": "GRDI", @@ -30017,13 +38610,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_measurement_units": { "name": "chloramphenicol_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "chloramphenicol_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 382, "alias": "chloramphenicol_measurement_units", "owner": "GRDI", @@ -30031,13 +38643,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_measurement_sign": { "name": "chloramphenicol_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "chloramphenicol_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 383, "alias": "chloramphenicol_measurement_sign", "owner": "GRDI", @@ -30045,38 +38676,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_laboratory_typing_method": { "name": "chloramphenicol_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "chloramphenicol_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 384, "alias": "chloramphenicol_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_laboratory_typing_platform": { "name": "chloramphenicol_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "chloramphenicol_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 385, "alias": "chloramphenicol_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_laboratory_typing_platform_version": { "name": "chloramphenicol_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "chloramphenicol_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 386, "alias": "chloramphenicol_laboratory_typing_platform_version", @@ -30091,20 +38776,50 @@ "name": "chloramphenicol_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "chloramphenicol_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 387, "alias": "chloramphenicol_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_testing_standard": { "name": "chloramphenicol_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "chloramphenicol_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 388, "alias": "chloramphenicol_testing_standard", "owner": "GRDI", @@ -30112,12 +38827,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "chloramphenicol_testing_standard_version": { "name": "chloramphenicol_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "chloramphenicol_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 389, "alias": "chloramphenicol_testing_standard_version", @@ -30132,6 +38863,17 @@ "name": "chloramphenicol_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "chloramphenicol_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 390, "alias": "chloramphenicol_testing_standard_details", @@ -30146,6 +38888,14 @@ "name": "chloramphenicol_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "chloramphenicol_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 391, "alias": "chloramphenicol_susceptible_breakpoint", @@ -30160,6 +38910,11 @@ "name": "chloramphenicol_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "chloramphenicol_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 392, "alias": "chloramphenicol_intermediate_breakpoint", @@ -30174,6 +38929,14 @@ "name": "chloramphenicol_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "chloramphenicol_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 393, "alias": "chloramphenicol_resistant_breakpoint", @@ -30188,7 +38951,18 @@ "name": "ciprofloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "ciprofloxacin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 394, "alias": "ciprofloxacin_resistance_phenotype", "owner": "GRDI", @@ -30196,13 +38970,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_measurement": { "name": "ciprofloxacin_measurement", "description": "The measured value of ciprofloxacin resistance.", "title": "ciprofloxacin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 395, "alias": "ciprofloxacin_measurement", "owner": "GRDI", @@ -30210,13 +39003,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_measurement_units": { "name": "ciprofloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "ciprofloxacin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 396, "alias": "ciprofloxacin_measurement_units", "owner": "GRDI", @@ -30224,13 +39036,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_measurement_sign": { "name": "ciprofloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "ciprofloxacin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 397, "alias": "ciprofloxacin_measurement_sign", "owner": "GRDI", @@ -30238,38 +39069,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_laboratory_typing_method": { "name": "ciprofloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "ciprofloxacin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 398, "alias": "ciprofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_laboratory_typing_platform": { "name": "ciprofloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "ciprofloxacin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 399, "alias": "ciprofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_laboratory_typing_platform_version": { "name": "ciprofloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "ciprofloxacin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 400, "alias": "ciprofloxacin_laboratory_typing_platform_version", @@ -30284,20 +39169,50 @@ "name": "ciprofloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "ciprofloxacin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 401, "alias": "ciprofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_testing_standard": { "name": "ciprofloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "ciprofloxacin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 402, "alias": "ciprofloxacin_testing_standard", "owner": "GRDI", @@ -30305,12 +39220,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "ciprofloxacin_testing_standard_version": { "name": "ciprofloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "ciprofloxacin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 403, "alias": "ciprofloxacin_testing_standard_version", @@ -30325,6 +39256,17 @@ "name": "ciprofloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "ciprofloxacin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 404, "alias": "ciprofloxacin_testing_standard_details", @@ -30339,6 +39281,14 @@ "name": "ciprofloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "ciprofloxacin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 405, "alias": "ciprofloxacin_susceptible_breakpoint", @@ -30353,6 +39303,11 @@ "name": "ciprofloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "ciprofloxacin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 406, "alias": "ciprofloxacin_intermediate_breakpoint", @@ -30367,6 +39322,14 @@ "name": "ciprofloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "ciprofloxacin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 407, "alias": "ciprofloxacin_resistant_breakpoint", @@ -30381,7 +39344,18 @@ "name": "clindamycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "clindamycin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 408, "alias": "clindamycin_resistance_phenotype", "owner": "GRDI", @@ -30389,13 +39363,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_measurement": { "name": "clindamycin_measurement", "description": "The measured value of clindamycin resistance.", "title": "clindamycin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 409, "alias": "clindamycin_measurement", "owner": "GRDI", @@ -30403,13 +39396,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_measurement_units": { "name": "clindamycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "clindamycin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 410, "alias": "clindamycin_measurement_units", "owner": "GRDI", @@ -30417,13 +39429,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_measurement_sign": { "name": "clindamycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "clindamycin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 411, "alias": "clindamycin_measurement_sign", "owner": "GRDI", @@ -30431,38 +39462,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_laboratory_typing_method": { "name": "clindamycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "clindamycin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 412, "alias": "clindamycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_laboratory_typing_platform": { "name": "clindamycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "clindamycin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 413, "alias": "clindamycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_laboratory_typing_platform_version": { "name": "clindamycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "clindamycin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 414, "alias": "clindamycin_laboratory_typing_platform_version", @@ -30477,20 +39562,50 @@ "name": "clindamycin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "clindamycin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 415, "alias": "clindamycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_testing_standard": { "name": "clindamycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "clindamycin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 416, "alias": "clindamycin_testing_standard", "owner": "GRDI", @@ -30498,12 +39613,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "clindamycin_testing_standard_version": { "name": "clindamycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "clindamycin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 417, "alias": "clindamycin_testing_standard_version", @@ -30518,6 +39649,17 @@ "name": "clindamycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "clindamycin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 418, "alias": "clindamycin_testing_standard_details", @@ -30532,6 +39674,14 @@ "name": "clindamycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "clindamycin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 419, "alias": "clindamycin_susceptible_breakpoint", @@ -30546,6 +39696,11 @@ "name": "clindamycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "clindamycin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 420, "alias": "clindamycin_intermediate_breakpoint", @@ -30560,6 +39715,14 @@ "name": "clindamycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "clindamycin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 421, "alias": "clindamycin_resistant_breakpoint", @@ -30574,7 +39737,18 @@ "name": "doxycycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "doxycycline_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 422, "alias": "doxycycline_resistance_phenotype", "owner": "GRDI", @@ -30582,13 +39756,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_measurement": { "name": "doxycycline_measurement", "description": "The measured value of doxycycline resistance.", "title": "doxycycline_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 423, "alias": "doxycycline_measurement", "owner": "GRDI", @@ -30596,13 +39789,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_measurement_units": { "name": "doxycycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "doxycycline_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 424, "alias": "doxycycline_measurement_units", "owner": "GRDI", @@ -30610,13 +39822,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_measurement_sign": { "name": "doxycycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "doxycycline_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 425, "alias": "doxycycline_measurement_sign", "owner": "GRDI", @@ -30624,38 +39855,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_laboratory_typing_method": { "name": "doxycycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "doxycycline_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 426, "alias": "doxycycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_laboratory_typing_platform": { "name": "doxycycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "doxycycline_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 427, "alias": "doxycycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_laboratory_typing_platform_version": { "name": "doxycycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "doxycycline_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 428, "alias": "doxycycline_laboratory_typing_platform_version", @@ -30670,20 +39955,50 @@ "name": "doxycycline_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "doxycycline_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 429, "alias": "doxycycline_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_testing_standard": { "name": "doxycycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "doxycycline_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 430, "alias": "doxycycline_testing_standard", "owner": "GRDI", @@ -30691,12 +40006,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "doxycycline_testing_standard_version": { "name": "doxycycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "doxycycline_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 431, "alias": "doxycycline_testing_standard_version", @@ -30711,6 +40042,17 @@ "name": "doxycycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "doxycycline_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 432, "alias": "doxycycline_testing_standard_details", @@ -30725,6 +40067,14 @@ "name": "doxycycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "doxycycline_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 433, "alias": "doxycycline_susceptible_breakpoint", @@ -30739,6 +40089,11 @@ "name": "doxycycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "doxycycline_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 434, "alias": "doxycycline_intermediate_breakpoint", @@ -30753,6 +40108,14 @@ "name": "doxycycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "doxycycline_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 435, "alias": "doxycycline_resistant_breakpoint", @@ -30767,7 +40130,18 @@ "name": "enrofloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "enrofloxacin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 436, "alias": "enrofloxacin_resistance_phenotype", "owner": "GRDI", @@ -30775,13 +40149,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_measurement": { "name": "enrofloxacin_measurement", "description": "The measured value of enrofloxacin resistance.", "title": "enrofloxacin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 437, "alias": "enrofloxacin_measurement", "owner": "GRDI", @@ -30789,13 +40182,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_measurement_units": { "name": "enrofloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "enrofloxacin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 438, "alias": "enrofloxacin_measurement_units", "owner": "GRDI", @@ -30803,13 +40215,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_measurement_sign": { "name": "enrofloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "enrofloxacin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 439, "alias": "enrofloxacin_measurement_sign", "owner": "GRDI", @@ -30817,38 +40248,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_laboratory_typing_method": { "name": "enrofloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "enrofloxacin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 440, "alias": "enrofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_laboratory_typing_platform": { "name": "enrofloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "enrofloxacin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 441, "alias": "enrofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_laboratory_typing_platform_version": { "name": "enrofloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "enrofloxacin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 442, "alias": "enrofloxacin_laboratory_typing_platform_version", @@ -30863,20 +40348,50 @@ "name": "enrofloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "enrofloxacin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 443, "alias": "enrofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_testing_standard": { "name": "enrofloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "enrofloxacin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 444, "alias": "enrofloxacin_testing_standard", "owner": "GRDI", @@ -30884,12 +40399,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "enrofloxacin_testing_standard_version": { "name": "enrofloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "enrofloxacin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 445, "alias": "enrofloxacin_testing_standard_version", @@ -30904,6 +40435,17 @@ "name": "enrofloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "enrofloxacin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 446, "alias": "enrofloxacin_testing_standard_details", @@ -30918,6 +40460,14 @@ "name": "enrofloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "enrofloxacin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 447, "alias": "enrofloxacin_susceptible_breakpoint", @@ -30932,6 +40482,11 @@ "name": "enrofloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "enrofloxacin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 448, "alias": "enrofloxacin_intermediate_breakpoint", @@ -30946,6 +40501,14 @@ "name": "enrofloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "enrofloxacin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 449, "alias": "enrofloxacin_resistant_breakpoint", @@ -30960,7 +40523,18 @@ "name": "erythromycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "erythromycin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 450, "alias": "erythromycin_resistance_phenotype", "owner": "GRDI", @@ -30968,13 +40542,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_measurement": { "name": "erythromycin_measurement", "description": "The measured value of erythromycin resistance.", "title": "erythromycin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 451, "alias": "erythromycin_measurement", "owner": "GRDI", @@ -30982,13 +40575,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_measurement_units": { "name": "erythromycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "erythromycin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 452, "alias": "erythromycin_measurement_units", "owner": "GRDI", @@ -30996,13 +40608,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_measurement_sign": { "name": "erythromycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "erythromycin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 453, "alias": "erythromycin_measurement_sign", "owner": "GRDI", @@ -31010,38 +40641,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_laboratory_typing_method": { "name": "erythromycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "erythromycin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 454, "alias": "erythromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_laboratory_typing_platform": { "name": "erythromycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "erythromycin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 455, "alias": "erythromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_laboratory_typing_platform_version": { "name": "erythromycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "erythromycin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 456, "alias": "erythromycin_laboratory_typing_platform_version", @@ -31056,20 +40741,50 @@ "name": "erythromycin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "erythromycin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 457, "alias": "erythromycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_testing_standard": { "name": "erythromycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "erythromycin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 458, "alias": "erythromycin_testing_standard", "owner": "GRDI", @@ -31077,12 +40792,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "erythromycin_testing_standard_version": { "name": "erythromycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "erythromycin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 459, "alias": "erythromycin_testing_standard_version", @@ -31097,6 +40828,17 @@ "name": "erythromycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "erythromycin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 460, "alias": "erythromycin_testing_standard_details", @@ -31111,6 +40853,14 @@ "name": "erythromycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "erythromycin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 461, "alias": "erythromycin_susceptible_breakpoint", @@ -31125,6 +40875,11 @@ "name": "erythromycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "erythromycin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 462, "alias": "erythromycin_intermediate_breakpoint", @@ -31139,6 +40894,14 @@ "name": "erythromycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "erythromycin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 463, "alias": "erythromycin_resistant_breakpoint", @@ -31153,7 +40916,18 @@ "name": "florfenicol_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "florfenicol_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 464, "alias": "florfenicol_resistance_phenotype", "owner": "GRDI", @@ -31161,13 +40935,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_measurement": { "name": "florfenicol_measurement", "description": "The measured value of florfenicol resistance.", "title": "florfenicol_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 465, "alias": "florfenicol_measurement", "owner": "GRDI", @@ -31175,13 +40968,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_measurement_units": { "name": "florfenicol_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "florfenicol_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 466, "alias": "florfenicol_measurement_units", "owner": "GRDI", @@ -31189,13 +41001,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_measurement_sign": { "name": "florfenicol_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "florfenicol_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 467, "alias": "florfenicol_measurement_sign", "owner": "GRDI", @@ -31203,38 +41034,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_laboratory_typing_method": { "name": "florfenicol_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "florfenicol_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 468, "alias": "florfenicol_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_laboratory_typing_platform": { "name": "florfenicol_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "florfenicol_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 469, "alias": "florfenicol_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_laboratory_typing_platform_version": { "name": "florfenicol_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "florfenicol_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 470, "alias": "florfenicol_laboratory_typing_platform_version", @@ -31249,20 +41134,50 @@ "name": "florfenicol_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "florfenicol_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 471, "alias": "florfenicol_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_testing_standard": { "name": "florfenicol_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "florfenicol_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 472, "alias": "florfenicol_testing_standard", "owner": "GRDI", @@ -31270,12 +41185,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "florfenicol_testing_standard_version": { "name": "florfenicol_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "florfenicol_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 473, "alias": "florfenicol_testing_standard_version", @@ -31290,6 +41221,17 @@ "name": "florfenicol_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "florfenicol_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 474, "alias": "florfenicol_testing_standard_details", @@ -31304,7 +41246,15 @@ "name": "florfenicol_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "florfenicol_susceptible_breakpoint", - "from_schema": "https://example.com/GRDI", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], + "from_schema": "https://example.com/GRDI", "rank": 475, "alias": "florfenicol_susceptible_breakpoint", "owner": "GRDI", @@ -31318,6 +41268,11 @@ "name": "florfenicol_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "florfenicol_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 476, "alias": "florfenicol_intermediate_breakpoint", @@ -31332,6 +41287,14 @@ "name": "florfenicol_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "florfenicol_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 477, "alias": "florfenicol_resistant_breakpoint", @@ -31346,7 +41309,18 @@ "name": "gentamicin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "gentamicin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 478, "alias": "gentamicin_resistance_phenotype", "owner": "GRDI", @@ -31354,13 +41328,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_measurement": { "name": "gentamicin_measurement", "description": "The measured value of gentamicin resistance.", "title": "gentamicin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 479, "alias": "gentamicin_measurement", "owner": "GRDI", @@ -31368,13 +41361,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_measurement_units": { "name": "gentamicin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "gentamicin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 480, "alias": "gentamicin_measurement_units", "owner": "GRDI", @@ -31382,13 +41394,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_measurement_sign": { "name": "gentamicin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "gentamicin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 481, "alias": "gentamicin_measurement_sign", "owner": "GRDI", @@ -31396,38 +41427,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_laboratory_typing_method": { "name": "gentamicin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "gentamicin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 482, "alias": "gentamicin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_laboratory_typing_platform": { "name": "gentamicin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "gentamicin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 483, "alias": "gentamicin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_laboratory_typing_platform_version": { "name": "gentamicin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "gentamicin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 484, "alias": "gentamicin_laboratory_typing_platform_version", @@ -31442,20 +41527,50 @@ "name": "gentamicin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "gentamicin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 485, "alias": "gentamicin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_testing_standard": { "name": "gentamicin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "gentamicin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 486, "alias": "gentamicin_testing_standard", "owner": "GRDI", @@ -31463,12 +41578,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "gentamicin_testing_standard_version": { "name": "gentamicin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "gentamicin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 487, "alias": "gentamicin_testing_standard_version", @@ -31483,6 +41614,17 @@ "name": "gentamicin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "gentamicin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 488, "alias": "gentamicin_testing_standard_details", @@ -31497,6 +41639,14 @@ "name": "gentamicin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "gentamicin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 489, "alias": "gentamicin_susceptible_breakpoint", @@ -31511,6 +41661,11 @@ "name": "gentamicin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "gentamicin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 490, "alias": "gentamicin_intermediate_breakpoint", @@ -31525,6 +41680,14 @@ "name": "gentamicin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "gentamicin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 491, "alias": "gentamicin_resistant_breakpoint", @@ -31539,7 +41702,18 @@ "name": "imipenem_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "imipenem_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 492, "alias": "imipenem_resistance_phenotype", "owner": "GRDI", @@ -31547,13 +41721,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_measurement": { "name": "imipenem_measurement", "description": "The measured value of imipenem resistance.", "title": "imipenem_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 493, "alias": "imipenem_measurement", "owner": "GRDI", @@ -31561,13 +41754,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "imipenem_measurement_units": { "name": "imipenem_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "imipenem_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 494, "alias": "imipenem_measurement_units", "owner": "GRDI", @@ -31575,13 +41787,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_measurement_sign": { "name": "imipenem_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "imipenem_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 495, "alias": "imipenem_measurement_sign", "owner": "GRDI", @@ -31589,38 +41820,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_laboratory_typing_method": { "name": "imipenem_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "imipenem_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 496, "alias": "imipenem_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_laboratory_typing_platform": { "name": "imipenem_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "imipenem_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 497, "alias": "imipenem_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_laboratory_typing_platform_version": { "name": "imipenem_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "imipenem_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 498, "alias": "imipenem_laboratory_typing_platform_version", @@ -31635,20 +41920,50 @@ "name": "imipenem_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "imipenem_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 499, "alias": "imipenem_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_testing_standard": { "name": "imipenem_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "imipenem_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 500, "alias": "imipenem_testing_standard", "owner": "GRDI", @@ -31656,12 +41971,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "imipenem_testing_standard_version": { "name": "imipenem_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "imipenem_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 501, "alias": "imipenem_testing_standard_version", @@ -31676,6 +42007,17 @@ "name": "imipenem_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "imipenem_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 502, "alias": "imipenem_testing_standard_details", @@ -31690,6 +42032,14 @@ "name": "imipenem_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "imipenem_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 503, "alias": "imipenem_susceptible_breakpoint", @@ -31704,6 +42054,11 @@ "name": "imipenem_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "imipenem_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 504, "alias": "imipenem_intermediate_breakpoint", @@ -31718,6 +42073,14 @@ "name": "imipenem_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "imipenem_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 505, "alias": "imipenem_resistant_breakpoint", @@ -31732,7 +42095,18 @@ "name": "kanamycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "kanamycin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 506, "alias": "kanamycin_resistance_phenotype", "owner": "GRDI", @@ -31740,13 +42114,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_measurement": { "name": "kanamycin_measurement", "description": "The measured value of kanamycin resistance.", "title": "kanamycin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 507, "alias": "kanamycin_measurement", "owner": "GRDI", @@ -31754,13 +42147,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_measurement_units": { "name": "kanamycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "kanamycin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 508, "alias": "kanamycin_measurement_units", "owner": "GRDI", @@ -31768,13 +42180,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_measurement_sign": { "name": "kanamycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "kanamycin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 509, "alias": "kanamycin_measurement_sign", "owner": "GRDI", @@ -31782,38 +42213,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_laboratory_typing_method": { "name": "kanamycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "kanamycin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 510, "alias": "kanamycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_laboratory_typing_platform": { "name": "kanamycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "kanamycin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 511, "alias": "kanamycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_laboratory_typing_platform_version": { "name": "kanamycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "kanamycin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 512, "alias": "kanamycin_laboratory_typing_platform_version", @@ -31828,20 +42313,50 @@ "name": "kanamycin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "kanamycin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 513, "alias": "kanamycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_testing_standard": { "name": "kanamycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "kanamycin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 514, "alias": "kanamycin_testing_standard", "owner": "GRDI", @@ -31849,12 +42364,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "kanamycin_testing_standard_version": { "name": "kanamycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "kanamycin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 515, "alias": "kanamycin_testing_standard_version", @@ -31869,6 +42400,17 @@ "name": "kanamycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "kanamycin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 516, "alias": "kanamycin_testing_standard_details", @@ -31883,6 +42425,14 @@ "name": "kanamycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "kanamycin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 517, "alias": "kanamycin_susceptible_breakpoint", @@ -31897,6 +42447,11 @@ "name": "kanamycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "kanamycin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 518, "alias": "kanamycin_intermediate_breakpoint", @@ -31911,6 +42466,14 @@ "name": "kanamycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "kanamycin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 519, "alias": "kanamycin_resistant_breakpoint", @@ -31925,7 +42488,18 @@ "name": "levofloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "levofloxacin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 520, "alias": "levofloxacin_resistance_phenotype", "owner": "GRDI", @@ -31933,13 +42507,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_measurement": { "name": "levofloxacin_measurement", "description": "The measured value of levofloxacin resistance.", "title": "levofloxacin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 521, "alias": "levofloxacin_measurement", "owner": "GRDI", @@ -31947,13 +42540,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_measurement_units": { "name": "levofloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "levofloxacin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 522, "alias": "levofloxacin_measurement_units", "owner": "GRDI", @@ -31961,13 +42573,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_measurement_sign": { "name": "levofloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "levofloxacin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 523, "alias": "levofloxacin_measurement_sign", "owner": "GRDI", @@ -31975,38 +42606,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_laboratory_typing_method": { "name": "levofloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "levofloxacin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 524, "alias": "levofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_laboratory_typing_platform": { "name": "levofloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "levofloxacin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 525, "alias": "levofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_laboratory_typing_platform_version": { "name": "levofloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "levofloxacin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 526, "alias": "levofloxacin_laboratory_typing_platform_version", @@ -32021,20 +42706,50 @@ "name": "levofloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "levofloxacin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 527, "alias": "levofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_testing_standard": { "name": "levofloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "levofloxacin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 528, "alias": "levofloxacin_testing_standard", "owner": "GRDI", @@ -32042,12 +42757,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "levofloxacin_testing_standard_version": { "name": "levofloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "levofloxacin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 529, "alias": "levofloxacin_testing_standard_version", @@ -32062,6 +42793,17 @@ "name": "levofloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "levofloxacin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 530, "alias": "levofloxacin_testing_standard_details", @@ -32076,6 +42818,14 @@ "name": "levofloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "levofloxacin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 531, "alias": "levofloxacin_susceptible_breakpoint", @@ -32090,6 +42840,11 @@ "name": "levofloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "levofloxacin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 532, "alias": "levofloxacin_intermediate_breakpoint", @@ -32104,6 +42859,14 @@ "name": "levofloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "levofloxacin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 533, "alias": "levofloxacin_resistant_breakpoint", @@ -32118,7 +42881,18 @@ "name": "linezolid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "linezolid_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 534, "alias": "linezolid_resistance_phenotype", "owner": "GRDI", @@ -32126,13 +42900,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_measurement": { "name": "linezolid_measurement", "description": "The measured value of linezolid resistance.", "title": "linezolid_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 535, "alias": "linezolid_measurement", "owner": "GRDI", @@ -32140,13 +42933,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "linezolid_measurement_units": { "name": "linezolid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "linezolid_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 536, "alias": "linezolid_measurement_units", "owner": "GRDI", @@ -32154,13 +42966,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_measurement_sign": { "name": "linezolid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "linezolid_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 537, "alias": "linezolid_measurement_sign", "owner": "GRDI", @@ -32168,38 +42999,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_laboratory_typing_method": { "name": "linezolid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "linezolid_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 538, "alias": "linezolid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_laboratory_typing_platform": { "name": "linezolid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "linezolid_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 539, "alias": "linezolid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_laboratory_typing_platform_version": { "name": "linezolid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "linezolid_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 540, "alias": "linezolid_laboratory_typing_platform_version", @@ -32214,20 +43099,50 @@ "name": "linezolid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "linezolid_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 541, "alias": "linezolid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_testing_standard": { "name": "linezolid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "linezolid_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 542, "alias": "linezolid_testing_standard", "owner": "GRDI", @@ -32235,12 +43150,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "linezolid_testing_standard_version": { "name": "linezolid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "linezolid_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 543, "alias": "linezolid_testing_standard_version", @@ -32255,6 +43186,17 @@ "name": "linezolid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "linezolid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 544, "alias": "linezolid_testing_standard_details", @@ -32269,6 +43211,14 @@ "name": "linezolid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "linezolid_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 545, "alias": "linezolid_susceptible_breakpoint", @@ -32283,6 +43233,11 @@ "name": "linezolid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "linezolid_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 546, "alias": "linezolid_intermediate_breakpoint", @@ -32297,6 +43252,14 @@ "name": "linezolid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "linezolid_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 547, "alias": "linezolid_resistant_breakpoint", @@ -32311,7 +43274,18 @@ "name": "meropenem_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "meropenem_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 548, "alias": "meropenem_resistance_phenotype", "owner": "GRDI", @@ -32319,13 +43293,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_measurement": { "name": "meropenem_measurement", "description": "The measured value of meropenem resistance.", "title": "meropenem_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 549, "alias": "meropenem_measurement", "owner": "GRDI", @@ -32333,13 +43326,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "meropenem_measurement_units": { "name": "meropenem_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "meropenem_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 550, "alias": "meropenem_measurement_units", "owner": "GRDI", @@ -32347,13 +43359,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_measurement_sign": { "name": "meropenem_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "meropenem_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 551, "alias": "meropenem_measurement_sign", "owner": "GRDI", @@ -32361,38 +43392,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_laboratory_typing_method": { "name": "meropenem_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "meropenem_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 552, "alias": "meropenem_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_laboratory_typing_platform": { "name": "meropenem_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "meropenem_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 553, "alias": "meropenem_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_laboratory_typing_platform_version": { "name": "meropenem_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "meropenem_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 554, "alias": "meropenem_laboratory_typing_platform_version", @@ -32407,20 +43492,50 @@ "name": "meropenem_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "meropenem_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 555, "alias": "meropenem_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_testing_standard": { "name": "meropenem_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "meropenem_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 556, "alias": "meropenem_testing_standard", "owner": "GRDI", @@ -32428,12 +43543,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "meropenem_testing_standard_version": { "name": "meropenem_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "meropenem_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 557, "alias": "meropenem_testing_standard_version", @@ -32448,6 +43579,17 @@ "name": "meropenem_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "meropenem_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 558, "alias": "meropenem_testing_standard_details", @@ -32462,6 +43604,14 @@ "name": "meropenem_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "meropenem_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 559, "alias": "meropenem_susceptible_breakpoint", @@ -32476,6 +43626,11 @@ "name": "meropenem_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "meropenem_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 560, "alias": "meropenem_intermediate_breakpoint", @@ -32490,6 +43645,14 @@ "name": "meropenem_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "meropenem_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 561, "alias": "meropenem_resistant_breakpoint", @@ -32504,7 +43667,18 @@ "name": "nalidixic_acid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "nalidixic_acid_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 562, "alias": "nalidixic_acid_resistance_phenotype", "owner": "GRDI", @@ -32512,13 +43686,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_measurement": { "name": "nalidixic_acid_measurement", "description": "The measured value of nalidixic-acid resistance.", "title": "nalidixic_acid_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 563, "alias": "nalidixic_acid_measurement", "owner": "GRDI", @@ -32526,13 +43719,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_measurement_units": { "name": "nalidixic_acid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "nalidixic_acid_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 564, "alias": "nalidixic_acid_measurement_units", "owner": "GRDI", @@ -32540,13 +43752,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_measurement_sign": { "name": "nalidixic_acid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "nalidixic_acid_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 565, "alias": "nalidixic_acid_measurement_sign", "owner": "GRDI", @@ -32554,38 +43785,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_laboratory_typing_method": { "name": "nalidixic_acid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "nalidixic_acid_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 566, "alias": "nalidixic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_laboratory_typing_platform": { "name": "nalidixic_acid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "nalidixic_acid_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 567, "alias": "nalidixic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_laboratory_typing_platform_version": { "name": "nalidixic_acid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "nalidixic_acid_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 568, "alias": "nalidixic_acid_laboratory_typing_platform_version", @@ -32600,20 +43885,50 @@ "name": "nalidixic_acid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "nalidixic_acid_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 569, "alias": "nalidixic_acid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_testing_standard": { "name": "nalidixic_acid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "nalidixic_acid_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 570, "alias": "nalidixic_acid_testing_standard", "owner": "GRDI", @@ -32621,12 +43936,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "nalidixic_acid_testing_standard_version": { "name": "nalidixic_acid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "nalidixic_acid_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 571, "alias": "nalidixic_acid_testing_standard_version", @@ -32641,6 +43972,17 @@ "name": "nalidixic_acid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "nalidixic_acid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 572, "alias": "nalidixic_acid_testing_standard_details", @@ -32655,6 +43997,14 @@ "name": "nalidixic_acid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "nalidixic_acid_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 573, "alias": "nalidixic_acid_susceptible_breakpoint", @@ -32669,6 +44019,11 @@ "name": "nalidixic_acid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "nalidixic_acid_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 574, "alias": "nalidixic_acid_intermediate_breakpoint", @@ -32683,6 +44038,14 @@ "name": "nalidixic_acid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "nalidixic_acid_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 575, "alias": "nalidixic_acid_resistant_breakpoint", @@ -32697,7 +44060,18 @@ "name": "nitrofurantoin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "nitrofurantoin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 576, "alias": "nitrofurantoin_resistance_phenotype", "owner": "GRDI", @@ -32705,13 +44079,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_measurement": { "name": "nitrofurantoin_measurement", "description": "The measured value of nitrofurantoin resistance.", "title": "nitrofurantoin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 577, "alias": "nitrofurantoin_measurement", "owner": "GRDI", @@ -32719,13 +44112,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_measurement_units": { "name": "nitrofurantoin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "nitrofurantoin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 578, "alias": "nitrofurantoin_measurement_units", "owner": "GRDI", @@ -32733,13 +44145,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_measurement_sign": { "name": "nitrofurantoin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "nitrofurantoin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 579, "alias": "nitrofurantoin_measurement_sign", "owner": "GRDI", @@ -32747,38 +44178,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_laboratory_typing_method": { "name": "nitrofurantoin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "nitrofurantoin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 580, "alias": "nitrofurantoin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_laboratory_typing_platform": { "name": "nitrofurantoin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "nitrofurantoin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 581, "alias": "nitrofurantoin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_laboratory_typing_platform_version": { "name": "nitrofurantoin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "nitrofurantoin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 582, "alias": "nitrofurantoin_laboratory_typing_platform_version", @@ -32793,20 +44278,50 @@ "name": "nitrofurantoin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "nitrofurantoin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 583, "alias": "nitrofurantoin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_testing_standard": { "name": "nitrofurantoin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "nitrofurantoin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 584, "alias": "nitrofurantoin_testing_standard", "owner": "GRDI", @@ -32814,12 +44329,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "nitrofurantoin_testing_standard_version": { "name": "nitrofurantoin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "nitrofurantoin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 585, "alias": "nitrofurantoin_testing_standard_version", @@ -32834,6 +44365,17 @@ "name": "nitrofurantoin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "nitrofurantoin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 586, "alias": "nitrofurantoin_testing_standard_details", @@ -32848,6 +44390,14 @@ "name": "nitrofurantoin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "nitrofurantoin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 587, "alias": "nitrofurantoin_susceptible_breakpoint", @@ -32862,6 +44412,11 @@ "name": "nitrofurantoin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "nitrofurantoin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 588, "alias": "nitrofurantoin_intermediate_breakpoint", @@ -32876,6 +44431,14 @@ "name": "nitrofurantoin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "nitrofurantoin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 589, "alias": "nitrofurantoin_resistant_breakpoint", @@ -32890,7 +44453,18 @@ "name": "norfloxacin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "norfloxacin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 590, "alias": "norfloxacin_resistance_phenotype", "owner": "GRDI", @@ -32898,13 +44472,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_measurement": { "name": "norfloxacin_measurement", "description": "The measured value of norfloxacin resistance.", "title": "norfloxacin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 591, "alias": "norfloxacin_measurement", "owner": "GRDI", @@ -32912,13 +44505,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_measurement_units": { "name": "norfloxacin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "norfloxacin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 592, "alias": "norfloxacin_measurement_units", "owner": "GRDI", @@ -32926,13 +44538,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_measurement_sign": { "name": "norfloxacin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "norfloxacin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 593, "alias": "norfloxacin_measurement_sign", "owner": "GRDI", @@ -32940,38 +44571,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_laboratory_typing_method": { "name": "norfloxacin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "norfloxacin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 594, "alias": "norfloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_laboratory_typing_platform": { "name": "norfloxacin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "norfloxacin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 595, "alias": "norfloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_laboratory_typing_platform_version": { "name": "norfloxacin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "norfloxacin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 596, "alias": "norfloxacin_laboratory_typing_platform_version", @@ -32986,20 +44671,50 @@ "name": "norfloxacin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "norfloxacin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 597, "alias": "norfloxacin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_testing_standard": { "name": "norfloxacin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "norfloxacin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 598, "alias": "norfloxacin_testing_standard", "owner": "GRDI", @@ -33007,12 +44722,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "norfloxacin_testing_standard_version": { "name": "norfloxacin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "norfloxacin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 599, "alias": "norfloxacin_testing_standard_version", @@ -33027,6 +44758,17 @@ "name": "norfloxacin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "norfloxacin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 600, "alias": "norfloxacin_testing_standard_details", @@ -33041,6 +44783,14 @@ "name": "norfloxacin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "norfloxacin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 601, "alias": "norfloxacin_susceptible_breakpoint", @@ -33055,6 +44805,11 @@ "name": "norfloxacin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "norfloxacin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 602, "alias": "norfloxacin_intermediate_breakpoint", @@ -33069,6 +44824,14 @@ "name": "norfloxacin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "norfloxacin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 603, "alias": "norfloxacin_resistant_breakpoint", @@ -33079,95 +44842,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_resistance_phenotype": { - "name": "oxolinic-acid_resistance_phenotype", + "oxolinicacid_resistance_phenotype": { + "name": "oxolinicacid_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "oxolinic-acid_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 604, - "alias": "oxolinic_acid_resistance_phenotype", + "alias": "oxolinicacid_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_measurement": { - "name": "oxolinic-acid_measurement", + "oxolinicacid_measurement": { + "name": "oxolinicacid_measurement", "description": "The measured value of oxolinic-acid resistance.", "title": "oxolinic-acid_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 605, - "alias": "oxolinic_acid_measurement", + "alias": "oxolinicacid_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_measurement_units": { - "name": "oxolinic-acid_measurement_units", + "oxolinicacid_measurement_units": { + "name": "oxolinicacid_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "oxolinic-acid_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 606, - "alias": "oxolinic_acid_measurement_units", + "alias": "oxolinicacid_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_measurement_sign": { - "name": "oxolinic-acid_measurement_sign", + "oxolinicacid_measurement_sign": { + "name": "oxolinicacid_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "oxolinic-acid_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 607, - "alias": "oxolinic_acid_measurement_sign", + "alias": "oxolinicacid_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_laboratory_typing_method": { - "name": "oxolinic-acid_laboratory_typing_method", + "oxolinicacid_laboratory_typing_method": { + "name": "oxolinicacid_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "oxolinic-acid_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 608, - "alias": "oxolinic_acid_laboratory_typing_method", + "alias": "oxolinicacid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_laboratory_typing_platform": { - "name": "oxolinic-acid_laboratory_typing_platform", + "oxolinicacid_laboratory_typing_platform": { + "name": "oxolinicacid_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "oxolinic-acid_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 609, - "alias": "oxolinic_acid_laboratory_typing_platform", + "alias": "oxolinicacid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_laboratory_typing_platform_version": { - "name": "oxolinic-acid_laboratory_typing_platform_version", + "oxolinicacid_laboratory_typing_platform_version": { + "name": "oxolinicacid_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "oxolinic-acid_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 610, - "alias": "oxolinic_acid_laboratory_typing_platform_version", + "alias": "oxolinicacid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33175,40 +45060,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_vendor_name": { - "name": "oxolinic-acid_vendor_name", + "oxolinicacid_vendor_name": { + "name": "oxolinicacid_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "oxolinic-acid_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 611, - "alias": "oxolinic_acid_vendor_name", + "alias": "oxolinicacid_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_testing_standard": { - "name": "oxolinic-acid_testing_standard", + "oxolinicacid_testing_standard": { + "name": "oxolinicacid_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "oxolinic-acid_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 612, - "alias": "oxolinic_acid_testing_standard", + "alias": "oxolinicacid_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "oxolinic-acid_testing_standard_version": { - "name": "oxolinic-acid_testing_standard_version", + "oxolinicacid_testing_standard_version": { + "name": "oxolinicacid_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "oxolinic-acid_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 613, - "alias": "oxolinic_acid_testing_standard_version", + "alias": "oxolinicacid_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33216,13 +45147,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_testing_standard_details": { - "name": "oxolinic-acid_testing_standard_details", + "oxolinicacid_testing_standard_details": { + "name": "oxolinicacid_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "oxolinic-acid_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 614, - "alias": "oxolinic_acid_testing_standard_details", + "alias": "oxolinicacid_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33230,13 +45172,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_susceptible_breakpoint": { - "name": "oxolinic-acid_susceptible_breakpoint", + "oxolinicacid_susceptible_breakpoint": { + "name": "oxolinicacid_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "oxolinic-acid_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 615, - "alias": "oxolinic_acid_susceptible_breakpoint", + "alias": "oxolinicacid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33244,13 +45194,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_intermediate_breakpoint": { - "name": "oxolinic-acid_intermediate_breakpoint", + "oxolinicacid_intermediate_breakpoint": { + "name": "oxolinicacid_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "oxolinic-acid_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 616, - "alias": "oxolinic_acid_intermediate_breakpoint", + "alias": "oxolinicacid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33258,13 +45213,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "oxolinic-acid_resistant_breakpoint": { - "name": "oxolinic-acid_resistant_breakpoint", + "oxolinicacid_resistant_breakpoint": { + "name": "oxolinicacid_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "oxolinic-acid_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 617, - "alias": "oxolinic_acid_resistant_breakpoint", + "alias": "oxolinicacid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33276,7 +45239,18 @@ "name": "oxytetracycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "oxytetracycline_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 618, "alias": "oxytetracycline_resistance_phenotype", "owner": "GRDI", @@ -33284,13 +45258,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_measurement": { "name": "oxytetracycline_measurement", "description": "The measured value of oxytetracycline resistance.", "title": "oxytetracycline_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 619, "alias": "oxytetracycline_measurement", "owner": "GRDI", @@ -33298,13 +45291,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_measurement_units": { "name": "oxytetracycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "oxytetracycline_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 620, "alias": "oxytetracycline_measurement_units", "owner": "GRDI", @@ -33312,13 +45324,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_measurement_sign": { "name": "oxytetracycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "oxytetracycline_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 621, "alias": "oxytetracycline_measurement_sign", "owner": "GRDI", @@ -33326,38 +45357,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_laboratory_typing_method": { "name": "oxytetracycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "oxytetracycline_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 622, "alias": "oxytetracycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_laboratory_typing_platform": { "name": "oxytetracycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "oxytetracycline_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 623, "alias": "oxytetracycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_laboratory_typing_platform_version": { "name": "oxytetracycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "oxytetracycline_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 624, "alias": "oxytetracycline_laboratory_typing_platform_version", @@ -33372,20 +45457,50 @@ "name": "oxytetracycline_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "oxytetracycline_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 625, "alias": "oxytetracycline_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_testing_standard": { "name": "oxytetracycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "oxytetracycline_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 626, "alias": "oxytetracycline_testing_standard", "owner": "GRDI", @@ -33393,12 +45508,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "oxytetracycline_testing_standard_version": { "name": "oxytetracycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "oxytetracycline_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 627, "alias": "oxytetracycline_testing_standard_version", @@ -33413,6 +45544,17 @@ "name": "oxytetracycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "oxytetracycline_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 628, "alias": "oxytetracycline_testing_standard_details", @@ -33427,6 +45569,14 @@ "name": "oxytetracycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "oxytetracycline_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 629, "alias": "oxytetracycline_susceptible_breakpoint", @@ -33441,6 +45591,11 @@ "name": "oxytetracycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "oxytetracycline_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 630, "alias": "oxytetracycline_intermediate_breakpoint", @@ -33455,6 +45610,14 @@ "name": "oxytetracycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "oxytetracycline_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 631, "alias": "oxytetracycline_resistant_breakpoint", @@ -33469,7 +45632,18 @@ "name": "piperacillin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "piperacillin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 632, "alias": "piperacillin_resistance_phenotype", "owner": "GRDI", @@ -33477,13 +45651,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_measurement": { "name": "piperacillin_measurement", "description": "The measured value of piperacillin resistance.", "title": "piperacillin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 633, "alias": "piperacillin_measurement", "owner": "GRDI", @@ -33491,13 +45684,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_measurement_units": { "name": "piperacillin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "piperacillin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 634, "alias": "piperacillin_measurement_units", "owner": "GRDI", @@ -33505,13 +45717,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_measurement_sign": { "name": "piperacillin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "piperacillin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 635, "alias": "piperacillin_measurement_sign", "owner": "GRDI", @@ -33519,38 +45750,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_laboratory_typing_method": { "name": "piperacillin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "piperacillin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 636, "alias": "piperacillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_laboratory_typing_platform": { "name": "piperacillin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "piperacillin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 637, "alias": "piperacillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_laboratory_typing_platform_version": { "name": "piperacillin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "piperacillin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 638, "alias": "piperacillin_laboratory_typing_platform_version", @@ -33565,20 +45850,50 @@ "name": "piperacillin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "piperacillin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 639, "alias": "piperacillin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_testing_standard": { "name": "piperacillin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "piperacillin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 640, "alias": "piperacillin_testing_standard", "owner": "GRDI", @@ -33586,12 +45901,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "piperacillin_testing_standard_version": { "name": "piperacillin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "piperacillin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 641, "alias": "piperacillin_testing_standard_version", @@ -33606,6 +45937,17 @@ "name": "piperacillin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "piperacillin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 642, "alias": "piperacillin_testing_standard_details", @@ -33620,6 +45962,14 @@ "name": "piperacillin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "piperacillin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 643, "alias": "piperacillin_susceptible_breakpoint", @@ -33634,6 +45984,11 @@ "name": "piperacillin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "piperacillin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 644, "alias": "piperacillin_intermediate_breakpoint", @@ -33648,6 +46003,14 @@ "name": "piperacillin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "piperacillin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 645, "alias": "piperacillin_resistant_breakpoint", @@ -33658,95 +46021,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_resistance_phenotype": { - "name": "piperacillin-tazobactam_resistance_phenotype", + "piperacillintazobactam_resistance_phenotype": { + "name": "piperacillintazobactam_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "piperacillin-tazobactam_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 646, - "alias": "piperacillin_tazobactam_resistance_phenotype", + "alias": "piperacillintazobactam_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_measurement": { - "name": "piperacillin-tazobactam_measurement", + "piperacillintazobactam_measurement": { + "name": "piperacillintazobactam_measurement", "description": "The measured value of piperacillin-tazobactam resistance.", "title": "piperacillin-tazobactam_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 647, - "alias": "piperacillin_tazobactam_measurement", + "alias": "piperacillintazobactam_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_measurement_units": { - "name": "piperacillin-tazobactam_measurement_units", + "piperacillintazobactam_measurement_units": { + "name": "piperacillintazobactam_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "piperacillin-tazobactam_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 648, - "alias": "piperacillin_tazobactam_measurement_units", + "alias": "piperacillintazobactam_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_measurement_sign": { - "name": "piperacillin-tazobactam_measurement_sign", + "piperacillintazobactam_measurement_sign": { + "name": "piperacillintazobactam_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "piperacillin-tazobactam_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 649, - "alias": "piperacillin_tazobactam_measurement_sign", + "alias": "piperacillintazobactam_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_laboratory_typing_method": { - "name": "piperacillin-tazobactam_laboratory_typing_method", + "piperacillintazobactam_laboratory_typing_method": { + "name": "piperacillintazobactam_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "piperacillin-tazobactam_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 650, - "alias": "piperacillin_tazobactam_laboratory_typing_method", + "alias": "piperacillintazobactam_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_laboratory_typing_platform": { - "name": "piperacillin-tazobactam_laboratory_typing_platform", + "piperacillintazobactam_laboratory_typing_platform": { + "name": "piperacillintazobactam_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "piperacillin-tazobactam_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 651, - "alias": "piperacillin_tazobactam_laboratory_typing_platform", + "alias": "piperacillintazobactam_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_laboratory_typing_platform_version": { - "name": "piperacillin-tazobactam_laboratory_typing_platform_version", + "piperacillintazobactam_laboratory_typing_platform_version": { + "name": "piperacillintazobactam_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "piperacillin-tazobactam_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 652, - "alias": "piperacillin_tazobactam_laboratory_typing_platform_version", + "alias": "piperacillintazobactam_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33754,40 +46239,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_vendor_name": { - "name": "piperacillin-tazobactam_vendor_name", + "piperacillintazobactam_vendor_name": { + "name": "piperacillintazobactam_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "piperacillin-tazobactam_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 653, - "alias": "piperacillin_tazobactam_vendor_name", + "alias": "piperacillintazobactam_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_testing_standard": { - "name": "piperacillin-tazobactam_testing_standard", + "piperacillintazobactam_testing_standard": { + "name": "piperacillintazobactam_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "piperacillin-tazobactam_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 654, - "alias": "piperacillin_tazobactam_testing_standard", + "alias": "piperacillintazobactam_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "piperacillin-tazobactam_testing_standard_version": { - "name": "piperacillin-tazobactam_testing_standard_version", + "piperacillintazobactam_testing_standard_version": { + "name": "piperacillintazobactam_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "piperacillin-tazobactam_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 655, - "alias": "piperacillin_tazobactam_testing_standard_version", + "alias": "piperacillintazobactam_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33795,13 +46326,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_testing_standard_details": { - "name": "piperacillin-tazobactam_testing_standard_details", + "piperacillintazobactam_testing_standard_details": { + "name": "piperacillintazobactam_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "piperacillin-tazobactam_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 656, - "alias": "piperacillin_tazobactam_testing_standard_details", + "alias": "piperacillintazobactam_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33809,13 +46351,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_susceptible_breakpoint": { - "name": "piperacillin-tazobactam_susceptible_breakpoint", + "piperacillintazobactam_susceptible_breakpoint": { + "name": "piperacillintazobactam_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "piperacillin-tazobactam_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 657, - "alias": "piperacillin_tazobactam_susceptible_breakpoint", + "alias": "piperacillintazobactam_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33823,13 +46373,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_intermediate_breakpoint": { - "name": "piperacillin-tazobactam_intermediate_breakpoint", + "piperacillintazobactam_intermediate_breakpoint": { + "name": "piperacillintazobactam_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "piperacillin-tazobactam_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 658, - "alias": "piperacillin_tazobactam_intermediate_breakpoint", + "alias": "piperacillintazobactam_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33837,13 +46392,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "piperacillin-tazobactam_resistant_breakpoint": { - "name": "piperacillin-tazobactam_resistant_breakpoint", + "piperacillintazobactam_resistant_breakpoint": { + "name": "piperacillintazobactam_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "piperacillin-tazobactam_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 659, - "alias": "piperacillin_tazobactam_resistant_breakpoint", + "alias": "piperacillintazobactam_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33851,95 +46414,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "polymyxin-b_resistance_phenotype": { - "name": "polymyxin-b_resistance_phenotype", + "polymyxinb_resistance_phenotype": { + "name": "polymyxinb_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "polymyxin-b_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 660, - "alias": "polymyxin_b_resistance_phenotype", + "alias": "polymyxinb_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_measurement": { - "name": "polymyxin-b_measurement", + "polymyxinb_measurement": { + "name": "polymyxinb_measurement", "description": "The measured value of polymyxin B resistance.", "title": "polymyxin-b_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 661, - "alias": "polymyxin_b_measurement", + "alias": "polymyxinb_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_measurement_units": { - "name": "polymyxin-b_measurement_units", + "polymyxinb_measurement_units": { + "name": "polymyxinb_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "polymyxin-b_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 662, - "alias": "polymyxin_b_measurement_units", + "alias": "polymyxinb_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_measurement_sign": { - "name": "polymyxin-b_measurement_sign", + "polymyxinb_measurement_sign": { + "name": "polymyxinb_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "polymyxin-b_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 663, - "alias": "polymyxin_b_measurement_sign", + "alias": "polymyxinb_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_laboratory_typing_method": { - "name": "polymyxin-b_laboratory_typing_method", + "polymyxinb_laboratory_typing_method": { + "name": "polymyxinb_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "polymyxin-b_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 664, - "alias": "polymyxin_b_laboratory_typing_method", + "alias": "polymyxinb_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_laboratory_typing_platform": { - "name": "polymyxin-b_laboratory_typing_platform", + "polymyxinb_laboratory_typing_platform": { + "name": "polymyxinb_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "polymyxin-b_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 665, - "alias": "polymyxin_b_laboratory_typing_platform", + "alias": "polymyxinb_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_laboratory_typing_platform_version": { - "name": "polymyxin-b_laboratory_typing_platform_version", + "polymyxinb_laboratory_typing_platform_version": { + "name": "polymyxinb_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "polymyxin-b_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 666, - "alias": "polymyxin_b_laboratory_typing_platform_version", + "alias": "polymyxinb_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33947,40 +46632,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "polymyxin-b_vendor_name": { - "name": "polymyxin-b_vendor_name", + "polymyxinb_vendor_name": { + "name": "polymyxinb_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "polymyxin-b_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 667, - "alias": "polymyxin_b_vendor_name", + "alias": "polymyxinb_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_testing_standard": { - "name": "polymyxin-b_testing_standard", + "polymyxinb_testing_standard": { + "name": "polymyxinb_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "polymyxin-b_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 668, - "alias": "polymyxin_b_testing_standard", + "alias": "polymyxinb_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "polymyxin-b_testing_standard_version": { - "name": "polymyxin-b_testing_standard_version", + "polymyxinb_testing_standard_version": { + "name": "polymyxinb_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "polymyxin-b_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 669, - "alias": "polymyxin_b_testing_standard_version", + "alias": "polymyxinb_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -33988,13 +46719,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "polymyxin-b_testing_standard_details": { - "name": "polymyxin-b_testing_standard_details", + "polymyxinb_testing_standard_details": { + "name": "polymyxinb_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "polymyxin-b_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 670, - "alias": "polymyxin_b_testing_standard_details", + "alias": "polymyxinb_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34002,13 +46744,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "polymyxin-b_susceptible_breakpoint": { - "name": "polymyxin-b_susceptible_breakpoint", + "polymyxinb_susceptible_breakpoint": { + "name": "polymyxinb_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "polymyxin-b_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 671, - "alias": "polymyxin_b_susceptible_breakpoint", + "alias": "polymyxinb_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34016,13 +46766,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "polymyxin-b_intermediate_breakpoint": { - "name": "polymyxin-b_intermediate_breakpoint", + "polymyxinb_intermediate_breakpoint": { + "name": "polymyxinb_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "polymyxin-b_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 672, - "alias": "polymyxin_b_intermediate_breakpoint", + "alias": "polymyxinb_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34030,13 +46785,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "polymyxin-b_resistant_breakpoint": { - "name": "polymyxin-b_resistant_breakpoint", + "polymyxinb_resistant_breakpoint": { + "name": "polymyxinb_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "polymyxin-b_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 673, - "alias": "polymyxin_b_resistant_breakpoint", + "alias": "polymyxinb_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34044,95 +46807,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_resistance_phenotype": { - "name": "quinupristin-dalfopristin_resistance_phenotype", + "quinupristindalfopristin_resistance_phenotype": { + "name": "quinupristindalfopristin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "quinupristin-dalfopristin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 674, - "alias": "quinupristin_dalfopristin_resistance_phenotype", + "alias": "quinupristindalfopristin_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_measurement": { - "name": "quinupristin-dalfopristin_measurement", + "quinupristindalfopristin_measurement": { + "name": "quinupristindalfopristin_measurement", "description": "The measured value of quinupristin-dalfopristin resistance.", "title": "quinupristin-dalfopristin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 675, - "alias": "quinupristin_dalfopristin_measurement", + "alias": "quinupristindalfopristin_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_measurement_units": { - "name": "quinupristin-dalfopristin_measurement_units", + "quinupristindalfopristin_measurement_units": { + "name": "quinupristindalfopristin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "quinupristin-dalfopristin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 676, - "alias": "quinupristin_dalfopristin_measurement_units", + "alias": "quinupristindalfopristin_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_measurement_sign": { - "name": "quinupristin-dalfopristin_measurement_sign", + "quinupristindalfopristin_measurement_sign": { + "name": "quinupristindalfopristin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "quinupristin-dalfopristin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 677, - "alias": "quinupristin_dalfopristin_measurement_sign", + "alias": "quinupristindalfopristin_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_laboratory_typing_method": { - "name": "quinupristin-dalfopristin_laboratory_typing_method", + "quinupristindalfopristin_laboratory_typing_method": { + "name": "quinupristindalfopristin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "quinupristin-dalfopristin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 678, - "alias": "quinupristin_dalfopristin_laboratory_typing_method", + "alias": "quinupristindalfopristin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_laboratory_typing_platform": { - "name": "quinupristin-dalfopristin_laboratory_typing_platform", + "quinupristindalfopristin_laboratory_typing_platform": { + "name": "quinupristindalfopristin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "quinupristin-dalfopristin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 679, - "alias": "quinupristin_dalfopristin_laboratory_typing_platform", + "alias": "quinupristindalfopristin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_laboratory_typing_platform_version": { - "name": "quinupristin-dalfopristin_laboratory_typing_platform_version", + "quinupristindalfopristin_laboratory_typing_platform_version": { + "name": "quinupristindalfopristin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "quinupristin-dalfopristin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 680, - "alias": "quinupristin_dalfopristin_laboratory_typing_platform_version", + "alias": "quinupristindalfopristin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34140,40 +47025,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_vendor_name": { - "name": "quinupristin-dalfopristin_vendor_name", + "quinupristindalfopristin_vendor_name": { + "name": "quinupristindalfopristin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "quinupristin-dalfopristin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 681, - "alias": "quinupristin_dalfopristin_vendor_name", + "alias": "quinupristindalfopristin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_testing_standard": { - "name": "quinupristin-dalfopristin_testing_standard", + "quinupristindalfopristin_testing_standard": { + "name": "quinupristindalfopristin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "quinupristin-dalfopristin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 682, - "alias": "quinupristin_dalfopristin_testing_standard", + "alias": "quinupristindalfopristin_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "quinupristin-dalfopristin_testing_standard_version": { - "name": "quinupristin-dalfopristin_testing_standard_version", + "quinupristindalfopristin_testing_standard_version": { + "name": "quinupristindalfopristin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "quinupristin-dalfopristin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 683, - "alias": "quinupristin_dalfopristin_testing_standard_version", + "alias": "quinupristindalfopristin_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34181,13 +47112,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_testing_standard_details": { - "name": "quinupristin-dalfopristin_testing_standard_details", + "quinupristindalfopristin_testing_standard_details": { + "name": "quinupristindalfopristin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "quinupristin-dalfopristin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 684, - "alias": "quinupristin_dalfopristin_testing_standard_details", + "alias": "quinupristindalfopristin_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34195,13 +47137,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_susceptible_breakpoint": { - "name": "quinupristin-dalfopristin_susceptible_breakpoint", + "quinupristindalfopristin_susceptible_breakpoint": { + "name": "quinupristindalfopristin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "quinupristin-dalfopristin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 685, - "alias": "quinupristin_dalfopristin_susceptible_breakpoint", + "alias": "quinupristindalfopristin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34209,13 +47159,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_intermediate_breakpoint": { - "name": "quinupristin-dalfopristin_intermediate_breakpoint", + "quinupristindalfopristin_intermediate_breakpoint": { + "name": "quinupristindalfopristin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "quinupristin-dalfopristin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 686, - "alias": "quinupristin_dalfopristin_intermediate_breakpoint", + "alias": "quinupristindalfopristin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34223,13 +47178,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "quinupristin-dalfopristin_resistant_breakpoint": { - "name": "quinupristin-dalfopristin_resistant_breakpoint", + "quinupristindalfopristin_resistant_breakpoint": { + "name": "quinupristindalfopristin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "quinupristin-dalfopristin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 687, - "alias": "quinupristin_dalfopristin_resistant_breakpoint", + "alias": "quinupristindalfopristin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -34241,7 +47204,18 @@ "name": "streptomycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "streptomycin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 688, "alias": "streptomycin_resistance_phenotype", "owner": "GRDI", @@ -34249,13 +47223,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_measurement": { "name": "streptomycin_measurement", "description": "The measured value of streptomycin resistance.", "title": "streptomycin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 689, "alias": "streptomycin_measurement", "owner": "GRDI", @@ -34263,13 +47256,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_measurement_units": { "name": "streptomycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "streptomycin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 690, "alias": "streptomycin_measurement_units", "owner": "GRDI", @@ -34277,13 +47289,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_measurement_sign": { "name": "streptomycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "streptomycin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 691, "alias": "streptomycin_measurement_sign", "owner": "GRDI", @@ -34291,38 +47322,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_laboratory_typing_method": { "name": "streptomycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "streptomycin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 692, "alias": "streptomycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_laboratory_typing_platform": { "name": "streptomycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "streptomycin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 693, "alias": "streptomycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_laboratory_typing_platform_version": { "name": "streptomycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "streptomycin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 694, "alias": "streptomycin_laboratory_typing_platform_version", @@ -34337,20 +47422,50 @@ "name": "streptomycin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "streptomycin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 695, "alias": "streptomycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_testing_standard": { "name": "streptomycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "streptomycin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 696, "alias": "streptomycin_testing_standard", "owner": "GRDI", @@ -34358,12 +47473,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "streptomycin_testing_standard_version": { "name": "streptomycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "streptomycin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 697, "alias": "streptomycin_testing_standard_version", @@ -34378,6 +47509,17 @@ "name": "streptomycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "streptomycin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 698, "alias": "streptomycin_testing_standard_details", @@ -34392,6 +47534,14 @@ "name": "streptomycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "streptomycin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 699, "alias": "streptomycin_susceptible_breakpoint", @@ -34406,6 +47556,11 @@ "name": "streptomycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "streptomycin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 700, "alias": "streptomycin_intermediate_breakpoint", @@ -34420,6 +47575,14 @@ "name": "streptomycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "streptomycin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 701, "alias": "streptomycin_resistant_breakpoint", @@ -34434,7 +47597,18 @@ "name": "sulfisoxazole_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "sulfisoxazole_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 702, "alias": "sulfisoxazole_resistance_phenotype", "owner": "GRDI", @@ -34442,13 +47616,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_measurement": { "name": "sulfisoxazole_measurement", "description": "The measured value of sulfisoxazole resistance.", "title": "sulfisoxazole_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 703, "alias": "sulfisoxazole_measurement", "owner": "GRDI", @@ -34456,13 +47649,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_measurement_units": { "name": "sulfisoxazole_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "sulfisoxazole_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 704, "alias": "sulfisoxazole_measurement_units", "owner": "GRDI", @@ -34470,13 +47682,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_measurement_sign": { "name": "sulfisoxazole_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "sulfisoxazole_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 705, "alias": "sulfisoxazole_measurement_sign", "owner": "GRDI", @@ -34484,38 +47715,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_laboratory_typing_method": { "name": "sulfisoxazole_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "sulfisoxazole_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 706, "alias": "sulfisoxazole_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_laboratory_typing_platform": { "name": "sulfisoxazole_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "sulfisoxazole_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 707, "alias": "sulfisoxazole_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_laboratory_typing_platform_version": { "name": "sulfisoxazole_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "sulfisoxazole_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 708, "alias": "sulfisoxazole_laboratory_typing_platform_version", @@ -34530,20 +47815,50 @@ "name": "sulfisoxazole_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "sulfisoxazole_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 709, "alias": "sulfisoxazole_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_testing_standard": { "name": "sulfisoxazole_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "sulfisoxazole_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 710, "alias": "sulfisoxazole_testing_standard", "owner": "GRDI", @@ -34551,12 +47866,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "sulfisoxazole_testing_standard_version": { "name": "sulfisoxazole_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "sulfisoxazole_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 711, "alias": "sulfisoxazole_testing_standard_version", @@ -34571,6 +47902,17 @@ "name": "sulfisoxazole_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "sulfisoxazole_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 712, "alias": "sulfisoxazole_testing_standard_details", @@ -34585,6 +47927,14 @@ "name": "sulfisoxazole_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "sulfisoxazole_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 713, "alias": "sulfisoxazole_susceptible_breakpoint", @@ -34599,6 +47949,11 @@ "name": "sulfisoxazole_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "sulfisoxazole_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 714, "alias": "sulfisoxazole_intermediate_breakpoint", @@ -34613,6 +47968,14 @@ "name": "sulfisoxazole_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "sulfisoxazole_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 715, "alias": "sulfisoxazole_resistant_breakpoint", @@ -34627,7 +47990,18 @@ "name": "telithromycin_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "telithromycin_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 716, "alias": "telithromycin_resistance_phenotype", "owner": "GRDI", @@ -34635,13 +48009,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_measurement": { "name": "telithromycin_measurement", "description": "The measured value of telithromycin resistance.", "title": "telithromycin_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 717, "alias": "telithromycin_measurement", "owner": "GRDI", @@ -34649,13 +48042,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_measurement_units": { "name": "telithromycin_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "telithromycin_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 718, "alias": "telithromycin_measurement_units", "owner": "GRDI", @@ -34663,13 +48075,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_measurement_sign": { "name": "telithromycin_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "telithromycin_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 719, "alias": "telithromycin_measurement_sign", "owner": "GRDI", @@ -34677,38 +48108,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_laboratory_typing_method": { "name": "telithromycin_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "telithromycin_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 720, "alias": "telithromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_laboratory_typing_platform": { "name": "telithromycin_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "telithromycin_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 721, "alias": "telithromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_laboratory_typing_platform_version": { "name": "telithromycin_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "telithromycin_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 722, "alias": "telithromycin_laboratory_typing_platform_version", @@ -34723,20 +48208,50 @@ "name": "telithromycin_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "telithromycin_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 723, "alias": "telithromycin_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_testing_standard": { "name": "telithromycin_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "telithromycin_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 724, "alias": "telithromycin_testing_standard", "owner": "GRDI", @@ -34744,12 +48259,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "telithromycin_testing_standard_version": { "name": "telithromycin_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "telithromycin_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 725, "alias": "telithromycin_testing_standard_version", @@ -34764,6 +48295,17 @@ "name": "telithromycin_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "telithromycin_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 726, "alias": "telithromycin_testing_standard_details", @@ -34778,6 +48320,14 @@ "name": "telithromycin_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "telithromycin_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 727, "alias": "telithromycin_susceptible_breakpoint", @@ -34792,6 +48342,11 @@ "name": "telithromycin_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "telithromycin_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 728, "alias": "telithromycin_intermediate_breakpoint", @@ -34806,6 +48361,14 @@ "name": "telithromycin_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "telithromycin_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 729, "alias": "telithromycin_resistant_breakpoint", @@ -34820,7 +48383,18 @@ "name": "tetracycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "tetracycline_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 730, "alias": "tetracycline_resistance_phenotype", "owner": "GRDI", @@ -34828,13 +48402,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_measurement": { "name": "tetracycline_measurement", "description": "The measured value of tetracycline resistance.", "title": "tetracycline_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 731, "alias": "tetracycline_measurement", "owner": "GRDI", @@ -34842,13 +48435,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_measurement_units": { "name": "tetracycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "tetracycline_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 732, "alias": "tetracycline_measurement_units", "owner": "GRDI", @@ -34856,13 +48468,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_measurement_sign": { "name": "tetracycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "tetracycline_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 733, "alias": "tetracycline_measurement_sign", "owner": "GRDI", @@ -34870,38 +48501,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_laboratory_typing_method": { "name": "tetracycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "tetracycline_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 734, "alias": "tetracycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_laboratory_typing_platform": { "name": "tetracycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "tetracycline_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 735, "alias": "tetracycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_laboratory_typing_platform_version": { "name": "tetracycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "tetracycline_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 736, "alias": "tetracycline_laboratory_typing_platform_version", @@ -34916,20 +48601,50 @@ "name": "tetracycline_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "tetracycline_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 737, "alias": "tetracycline_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_testing_standard": { "name": "tetracycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "tetracycline_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 738, "alias": "tetracycline_testing_standard", "owner": "GRDI", @@ -34937,12 +48652,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "tetracycline_testing_standard_version": { "name": "tetracycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "tetracycline_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 739, "alias": "tetracycline_testing_standard_version", @@ -34957,6 +48688,17 @@ "name": "tetracycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "tetracycline_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 740, "alias": "tetracycline_testing_standard_details", @@ -34971,6 +48713,14 @@ "name": "tetracycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "tetracycline_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 741, "alias": "tetracycline_susceptible_breakpoint", @@ -34985,6 +48735,11 @@ "name": "tetracycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "tetracycline_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 742, "alias": "tetracycline_intermediate_breakpoint", @@ -34999,6 +48754,14 @@ "name": "tetracycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "tetracycline_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 743, "alias": "tetracycline_resistant_breakpoint", @@ -35013,7 +48776,18 @@ "name": "tigecycline_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "tigecycline_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 744, "alias": "tigecycline_resistance_phenotype", "owner": "GRDI", @@ -35021,13 +48795,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_measurement": { "name": "tigecycline_measurement", "description": "The measured value of tigecycline resistance.", "title": "tigecycline_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 745, "alias": "tigecycline_measurement", "owner": "GRDI", @@ -35035,13 +48828,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_measurement_units": { "name": "tigecycline_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "tigecycline_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 746, "alias": "tigecycline_measurement_units", "owner": "GRDI", @@ -35049,13 +48861,32 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_measurement_sign": { "name": "tigecycline_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "tigecycline_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 747, "alias": "tigecycline_measurement_sign", "owner": "GRDI", @@ -35063,38 +48894,92 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_laboratory_typing_method": { "name": "tigecycline_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "tigecycline_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 748, "alias": "tigecycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_laboratory_typing_platform": { "name": "tigecycline_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "tigecycline_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 749, "alias": "tigecycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_laboratory_typing_platform_version": { "name": "tigecycline_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "tigecycline_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 750, "alias": "tigecycline_laboratory_typing_platform_version", @@ -35109,20 +48994,50 @@ "name": "tigecycline_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "tigecycline_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 751, "alias": "tigecycline_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_testing_standard": { "name": "tigecycline_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "tigecycline_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 752, "alias": "tigecycline_testing_standard", "owner": "GRDI", @@ -35130,12 +49045,28 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, "tigecycline_testing_standard_version": { "name": "tigecycline_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "tigecycline_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 753, "alias": "tigecycline_testing_standard_version", @@ -35150,6 +49081,17 @@ "name": "tigecycline_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "tigecycline_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 754, "alias": "tigecycline_testing_standard_details", @@ -35164,6 +49106,14 @@ "name": "tigecycline_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "tigecycline_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 755, "alias": "tigecycline_susceptible_breakpoint", @@ -35178,6 +49128,11 @@ "name": "tigecycline_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "tigecycline_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 756, "alias": "tigecycline_intermediate_breakpoint", @@ -35192,6 +49147,14 @@ "name": "tigecycline_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "tigecycline_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 757, "alias": "tigecycline_resistant_breakpoint", @@ -35202,95 +49165,217 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_resistance_phenotype": { - "name": "trimethoprim-sulfamethoxazole_resistance_phenotype", + "trimethoprimsulfamethoxazole_resistance_phenotype": { + "name": "trimethoprimsulfamethoxazole_resistance_phenotype", "description": "The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic", "title": "trimethoprim-sulfamethoxazole_resistance_phenotype", + "comments": [ + "Select a phenotype from the pick list provided." + ], + "examples": [ + { + "value": "Susceptible antimicrobial phenotype [ARO:3004302]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + ], "rank": 758, - "alias": "trimethoprim_sulfamethoxazole_resistance_phenotype", + "alias": "trimethoprimsulfamethoxazole_resistance_phenotype", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_phenotype menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_measurement": { - "name": "trimethoprim-sulfamethoxazole_measurement", + "trimethoprimsulfamethoxazole_measurement": { + "name": "trimethoprimsulfamethoxazole_measurement", "description": "The measured value of trimethoprim-sulfamethoxazole resistance.", "title": "trimethoprim-sulfamethoxazole_measurement", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals)." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement" + ], "rank": 759, - "alias": "trimethoprim_sulfamethoxazole_measurement", + "alias": "trimethoprimsulfamethoxazole_measurement", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_measurement_units": { - "name": "trimethoprim-sulfamethoxazole_measurement_units", + "trimethoprimsulfamethoxazole_measurement_units": { + "name": "trimethoprimsulfamethoxazole_measurement_units", "description": "The units of the antimicrobial resistance measurement.", "title": "trimethoprim-sulfamethoxazole_measurement_units", + "comments": [ + "Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary." + ], + "examples": [ + { + "value": "ug/mL [UO:0000274]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + ], "rank": 760, - "alias": "trimethoprim_sulfamethoxazole_measurement_units", + "alias": "trimethoprimsulfamethoxazole_measurement_units", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_units menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_measurement_sign": { - "name": "trimethoprim-sulfamethoxazole_measurement_sign", + "trimethoprimsulfamethoxazole_measurement_sign": { + "name": "trimethoprimsulfamethoxazole_measurement_sign", "description": "The qualifier associated with the antimicrobial resistance measurement", "title": "trimethoprim-sulfamethoxazole_measurement_sign", + "comments": [ + "Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary." + ], + "examples": [ + { + "value": "greater than (>) [GENEPIO:0001006]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + ], "rank": 761, - "alias": "trimethoprim_sulfamethoxazole_measurement_sign", + "alias": "trimethoprimsulfamethoxazole_measurement_sign", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "required": true + "required": true, + "any_of": [ + { + "range": "antimicrobial_measurement_sign menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_laboratory_typing_method": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_method", + "trimethoprimsulfamethoxazole_laboratory_typing_method": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", "description": "The general method used for antimicrobial susceptibility testing.", "title": "trimethoprim-sulfamethoxazole_laboratory_typing_method", + "comments": [ + "Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary." + ], + "examples": [ + { + "value": "Broth dilution [ARO:3004397]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + ], "rank": 762, - "alias": "trimethoprim_sulfamethoxazole_laboratory_typing_method", + "alias": "trimethoprimsulfamethoxazole_laboratory_typing_method", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_method menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_laboratory_typing_platform": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", + "trimethoprimsulfamethoxazole_laboratory_typing_platform": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", "description": "The brand/platform used for antimicrobial susceptibility testing.", "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform", + "comments": [ + "Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary." + ], + "examples": [ + { + "value": "Sensitire [ARO:3004402]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:laboratory_typing_platform" + ], "rank": 763, - "alias": "trimethoprim_sulfamethoxazole_laboratory_typing_platform", + "alias": "trimethoprimsulfamethoxazole_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_laboratory_typing_platform menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version": { - "name": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", + "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { + "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", "description": "The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing.", "title": "trimethoprim-sulfamethoxazole_laboratory_typing_platform_version", + "comments": [ + "Include any additional information about the antimicrobial susceptibility test such as the drug panel details." + ], + "examples": [ + { + "value": "CMV3AGNF" + } + ], "from_schema": "https://example.com/GRDI", "rank": 764, - "alias": "trimethoprim_sulfamethoxazole_laboratory_typing_platform_version", + "alias": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35298,40 +49383,86 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_vendor_name": { - "name": "trimethoprim-sulfamethoxazole_vendor_name", + "trimethoprimsulfamethoxazole_vendor_name": { + "name": "trimethoprimsulfamethoxazole_vendor_name", "description": "The name of the vendor of the testing platform used.", "title": "trimethoprim-sulfamethoxazole_vendor_name", + "comments": [ + "Provide the full name of the company (avoid abbreviations)." + ], + "examples": [ + { + "value": "Sensititre" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:vendor" + ], "rank": 765, - "alias": "trimethoprim_sulfamethoxazole_vendor_name", + "alias": "trimethoprimsulfamethoxazole_vendor_name", "owner": "GRDI", "domain_of": [ "GRDI" ], - "slot_group": "Antimicrobial resistance" + "slot_group": "Antimicrobial resistance", + "any_of": [ + { + "range": "antimicrobial_vendor_name menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_testing_standard": { - "name": "trimethoprim-sulfamethoxazole_testing_standard", + "trimethoprimsulfamethoxazole_testing_standard": { + "name": "trimethoprimsulfamethoxazole_testing_standard", "description": "The testing standard used for determination of resistance phenotype", "title": "trimethoprim-sulfamethoxazole_testing_standard", + "comments": [ + "Select a testing standard from the pick list provided." + ], + "examples": [ + { + "value": "Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%2Atesting_standard" + ], "rank": 766, - "alias": "trimethoprim_sulfamethoxazole_testing_standard", + "alias": "trimethoprimsulfamethoxazole_testing_standard", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Antimicrobial resistance", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "antimicrobial_testing_standard menu" + }, + { + "range": "null value menu" + } + ] }, - "trimethoprim-sulfamethoxazole_testing_standard_version": { - "name": "trimethoprim-sulfamethoxazole_testing_standard_version", + "trimethoprimsulfamethoxazole_testing_standard_version": { + "name": "trimethoprimsulfamethoxazole_testing_standard_version", "description": "The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used.", "title": "trimethoprim-sulfamethoxazole_testing_standard_version", + "comments": [ + "If applicable, include a version number for the testing standard used." + ], + "examples": [ + { + "value": "M100" + } + ], "from_schema": "https://example.com/GRDI", "rank": 767, - "alias": "trimethoprim_sulfamethoxazole_testing_standard_version", + "alias": "trimethoprimsulfamethoxazole_testing_standard_version", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35339,13 +49470,24 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_testing_standard_details": { - "name": "trimethoprim-sulfamethoxazole_testing_standard_details", + "trimethoprimsulfamethoxazole_testing_standard_details": { + "name": "trimethoprimsulfamethoxazole_testing_standard_details", "description": "Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype", "title": "trimethoprim-sulfamethoxazole_testing_standard_details", + "comments": [ + "This information may include the year or location where the testing standard was published. If not applicable, leave blank." + ], + "examples": [ + { + "value": "27th ed. Wayne, PA: Clinical and Laboratory Standards Institute" + }, + { + "value": "2017." + } + ], "from_schema": "https://example.com/GRDI", "rank": 768, - "alias": "trimethoprim_sulfamethoxazole_testing_standard_details", + "alias": "trimethoprimsulfamethoxazole_testing_standard_details", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35353,13 +49495,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_susceptible_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", + "trimethoprimsulfamethoxazole_susceptible_breakpoint": { + "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", "description": "The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial.", "title": "trimethoprim-sulfamethoxazole_susceptible_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", "rank": 769, - "alias": "trimethoprim_sulfamethoxazole_susceptible_breakpoint", + "alias": "trimethoprimsulfamethoxazole_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35367,13 +49517,18 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_intermediate_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", + "trimethoprimsulfamethoxazole_intermediate_breakpoint": { + "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", "description": "The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial.", "title": "trimethoprim-sulfamethoxazole_intermediate_breakpoint", + "examples": [ + { + "value": "16" + } + ], "from_schema": "https://example.com/GRDI", "rank": 770, - "alias": "trimethoprim_sulfamethoxazole_intermediate_breakpoint", + "alias": "trimethoprimsulfamethoxazole_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35381,13 +49536,21 @@ "slot_group": "Antimicrobial resistance", "range": "WhitespaceMinimizedString" }, - "trimethoprim-sulfamethoxazole_resistant_breakpoint": { - "name": "trimethoprim-sulfamethoxazole_resistant_breakpoint", + "trimethoprimsulfamethoxazole_resistant_breakpoint": { + "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", "description": "The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial.", "title": "trimethoprim-sulfamethoxazole_resistant_breakpoint", + "comments": [ + "This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied." + ], + "examples": [ + { + "value": "32" + } + ], "from_schema": "https://example.com/GRDI", "rank": 771, - "alias": "trimethoprim_sulfamethoxazole_resistant_breakpoint", + "alias": "trimethoprimsulfamethoxazole_resistant_breakpoint", "owner": "GRDI", "domain_of": [ "GRDI" @@ -35399,6 +49562,14 @@ "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/GRDI", "rank": 772, "slot_uri": "GENEPIO:0001517", @@ -35411,14 +49582,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, GRDI v1.0.0" + } + ], "from_schema": "https://example.com/GRDI", "rank": 773, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "alias": "dataharmonizer_provenance", "owner": "GRDI", "domain_of": [ "GRDI" diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index e14df577..6a5be7fe 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -17,13 +17,13 @@ classes: description: Specification for GRDI virus biosample data gathering is_a: dh_interface slots: - - sample_collector_sample_ID - - alternative_sample_ID + - sample_collector_sample_id + - alternative_sample_id - sample_collected_by - sample_collected_by_laboratory_name - sample_collection_project_name - sample_plan_name - - sample_plan_ID + - sample_plan_id - sample_collector_contact_name - sample_collector_contact_email - purpose_of_sampling @@ -32,15 +32,15 @@ classes: - experimental_protocol_field - experimental_specimen_role_type - specimen_processing - - nucleic acid extraction method - - nucleic acid extraction kit - - geo_loc_name (country) - - geo_loc_name (state/province/region) - - geo_loc_name (site) - - food_product_origin_geo_loc_name (country) - - host_origin_geo_loc_name (country) - - geo_loc latitude - - geo_loc longitude + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - geo_loc_name_country + - geo_loc_name_state_province_region + - geo_loc_name_site + - food_product_origin_geo_loc_name_country + - host_origin_geo_loc_name_country + - geo_loc_latitude + - geo_loc_longitude - sample_collection_date - sample_collection_date_precision - sample_received_date @@ -83,20 +83,20 @@ classes: - water_temperature - water_temperature_units - weather_type - - host (common name) - - host (scientific name) - - host (ecotype) - - host (breed) - - host (food production name) + - host_common_name + - host_scientific_name + - host_ecotype + - host_breed + - host_food_production_name - host_age_bin - host_disease - microbiological_method - strain - - isolate_ID - - alternative_isolate_ID - - progeny_isolate_ID - - IRIDA_isolate_ID - - IRIDA_project_ID + - isolate_id + - alternative_isolate_id + - progeny_isolate_id + - irida_isolate_id + - irida_project_id - isolated_by - isolated_by_laboratory_name - isolated_by_contact_name @@ -109,7 +109,7 @@ classes: - serovar - serotyping_method - phagetype - - library_ID + - library_id - sequenced_by - sequenced_by_laboratory_name - sequenced_by_contact_name @@ -120,72 +120,72 @@ classes: - sequencing_instrument - sequencing_assay_type - library_preparation_kit - - DNA fragment length - - genomic target enrichment method - - genomic target enrichment method details - - amplicon pcr primer scheme - - amplicon size - - sequencing flow cell version + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version - sequencing_protocol - r1_fastq_filename - r2_fastq_filename - fast5_filename - assembly_filename - - quality control method name - - quality control method version - - quality control determination - - quality control issues - - quality control details - - raw sequence data processing method - - dehosting method - - sequence assembly software name - - sequence assembly software version - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - genome completeness - - number of base pairs sequenced - - number of total reads - - number of unique reads - - minimum post-trimming read length - - number of contigs - - percent Ns across total genome length - - Ns per 100 kbp - - N50 - - percent read contamination - - sequence assembly length - - consensus genome length - - reference genome accession - - deduplication method - - bioinformatics protocol - - read mapping software name - - read mapping software version - - taxonomic reference database name - - taxonomic reference database version - - taxonomic analysis report filename - - taxonomic analysis date - - read mapping criteria + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria - sequence_submitted_by - sequence_submitted_by_contact_name - sequence_submitted_by_contact_email - - publication_ID + - publication_id - attribute_package - bioproject_accession - biosample_accession - - SRA_accession - - GenBank_accession + - sra_accession + - genbank_accession - prevalence_metrics - prevalence_metrics_details - stage_of_production - experimental_intervention - experiment_intervention_details - - AMR_testing_by - - AMR_testing_by_laboratory_name - - AMR_testing_by_contact_name - - AMR_testing_by_contact_email - - AMR_testing_date + - amr_testing_by + - amr_testing_by_laboratory_name + - amr_testing_by_contact_name + - amr_testing_by_contact_email + - amr_testing_date - amikacin_resistance_phenotype - amikacin_measurement - amikacin_measurement_units @@ -200,20 +200,20 @@ classes: - amikacin_susceptible_breakpoint - amikacin_intermediate_breakpoint - amikacin_resistant_breakpoint - - amoxicillin-clavulanic_acid_resistance_phenotype - - amoxicillin-clavulanic_acid_measurement - - amoxicillin-clavulanic_acid_measurement_units - - amoxicillin-clavulanic_acid_measurement_sign - - amoxicillin-clavulanic_acid_laboratory_typing_method - - amoxicillin-clavulanic_acid_laboratory_typing_platform - - amoxicillin-clavulanic_acid_laboratory_typing_platform_version - - amoxicillin-clavulanic_acid_vendor_name - - amoxicillin-clavulanic_acid_testing_standard - - amoxicillin-clavulanic_acid_testing_standard_version - - amoxicillin-clavulanic_acid_testing_standard_details - - amoxicillin-clavulanic_acid_susceptible_breakpoint - - amoxicillin-clavulanic_acid_intermediate_breakpoint - - amoxicillin-clavulanic_acid_resistant_breakpoint + - amoxicillinclavulanic_acid_resistance_phenotype + - amoxicillinclavulanic_acid_measurement + - amoxicillinclavulanic_acid_measurement_units + - amoxicillinclavulanic_acid_measurement_sign + - amoxicillinclavulanic_acid_laboratory_typing_method + - amoxicillinclavulanic_acid_laboratory_typing_platform + - amoxicillinclavulanic_acid_laboratory_typing_platform_version + - amoxicillinclavulanic_acid_vendor_name + - amoxicillinclavulanic_acid_testing_standard + - amoxicillinclavulanic_acid_testing_standard_version + - amoxicillinclavulanic_acid_testing_standard_details + - amoxicillinclavulanic_acid_susceptible_breakpoint + - amoxicillinclavulanic_acid_intermediate_breakpoint + - amoxicillinclavulanic_acid_resistant_breakpoint - ampicillin_resistance_phenotype - ampicillin_measurement - ampicillin_measurement_units @@ -284,20 +284,20 @@ classes: - cefotaxime_susceptible_breakpoint - cefotaxime_intermediate_breakpoint - cefotaxime_resistant_breakpoint - - cefotaxime-clavulanic_acid_resistance_phenotype - - cefotaxime-clavulanic_acid_measurement - - cefotaxime-clavulanic_acid_measurement_units - - cefotaxime-clavulanic_acid_measurement_sign - - cefotaxime-clavulanic_acid_laboratory_typing_method - - cefotaxime-clavulanic_acid_laboratory_typing_platform - - cefotaxime-clavulanic_acid_laboratory_typing_platform_version - - cefotaxime-clavulanic_acid_vendor_name - - cefotaxime-clavulanic_acid_testing_standard - - cefotaxime-clavulanic_acid_testing_standard_version - - cefotaxime-clavulanic_acid_testing_standard_details - - cefotaxime-clavulanic_acid_susceptible_breakpoint - - cefotaxime-clavulanic_acid_intermediate_breakpoint - - cefotaxime-clavulanic_acid_resistant_breakpoint + - cefotaximeclavulanic_acid_resistance_phenotype + - cefotaximeclavulanic_acid_measurement + - cefotaximeclavulanic_acid_measurement_units + - cefotaximeclavulanic_acid_measurement_sign + - cefotaximeclavulanic_acid_laboratory_typing_method + - cefotaximeclavulanic_acid_laboratory_typing_platform + - cefotaximeclavulanic_acid_laboratory_typing_platform_version + - cefotaximeclavulanic_acid_vendor_name + - cefotaximeclavulanic_acid_testing_standard + - cefotaximeclavulanic_acid_testing_standard_version + - cefotaximeclavulanic_acid_testing_standard_details + - cefotaximeclavulanic_acid_susceptible_breakpoint + - cefotaximeclavulanic_acid_intermediate_breakpoint + - cefotaximeclavulanic_acid_resistant_breakpoint - cefoxitin_resistance_phenotype - cefoxitin_measurement - cefoxitin_measurement_units @@ -340,20 +340,20 @@ classes: - ceftazidime_susceptible_breakpoint - ceftazidime_intermediate_breakpoint - ceftazidime_resistant_breakpoint - - ceftazidime-clavulanic_acid_resistance_phenotype - - ceftazidime-clavulanic_acid_measurement - - ceftazidime-clavulanic_acid_measurement_units - - ceftazidime-clavulanic_acid_measurement_sign - - ceftazidime-clavulanic_acid_laboratory_typing_method - - ceftazidime-clavulanic_acid_laboratory_typing_platform - - ceftazidime-clavulanic_acid_laboratory_typing_platform_version - - ceftazidime-clavulanic_acid_vendor_name - - ceftazidime-clavulanic_acid_testing_standard - - ceftazidime-clavulanic_acid_testing_standard_version - - ceftazidime-clavulanic_acid_testing_standard_details - - ceftazidime-clavulanic_acid_susceptible_breakpoint - - ceftazidime-clavulanic_acid_intermediate_breakpoint - - ceftazidime-clavulanic_acid_resistant_breakpoint + - ceftazidimeclavulanic_acid_resistance_phenotype + - ceftazidimeclavulanic_acid_measurement + - ceftazidimeclavulanic_acid_measurement_units + - ceftazidimeclavulanic_acid_measurement_sign + - ceftazidimeclavulanic_acid_laboratory_typing_method + - ceftazidimeclavulanic_acid_laboratory_typing_platform + - ceftazidimeclavulanic_acid_laboratory_typing_platform_version + - ceftazidimeclavulanic_acid_vendor_name + - ceftazidimeclavulanic_acid_testing_standard + - ceftazidimeclavulanic_acid_testing_standard_version + - ceftazidimeclavulanic_acid_testing_standard_details + - ceftazidimeclavulanic_acid_susceptible_breakpoint + - ceftazidimeclavulanic_acid_intermediate_breakpoint + - ceftazidimeclavulanic_acid_resistant_breakpoint - ceftiofur_resistance_phenotype - ceftiofur_measurement - ceftiofur_measurement_units @@ -620,20 +620,20 @@ classes: - norfloxacin_susceptible_breakpoint - norfloxacin_intermediate_breakpoint - norfloxacin_resistant_breakpoint - - oxolinic-acid_resistance_phenotype - - oxolinic-acid_measurement - - oxolinic-acid_measurement_units - - oxolinic-acid_measurement_sign - - oxolinic-acid_laboratory_typing_method - - oxolinic-acid_laboratory_typing_platform - - oxolinic-acid_laboratory_typing_platform_version - - oxolinic-acid_vendor_name - - oxolinic-acid_testing_standard - - oxolinic-acid_testing_standard_version - - oxolinic-acid_testing_standard_details - - oxolinic-acid_susceptible_breakpoint - - oxolinic-acid_intermediate_breakpoint - - oxolinic-acid_resistant_breakpoint + - oxolinicacid_resistance_phenotype + - oxolinicacid_measurement + - oxolinicacid_measurement_units + - oxolinicacid_measurement_sign + - oxolinicacid_laboratory_typing_method + - oxolinicacid_laboratory_typing_platform + - oxolinicacid_laboratory_typing_platform_version + - oxolinicacid_vendor_name + - oxolinicacid_testing_standard + - oxolinicacid_testing_standard_version + - oxolinicacid_testing_standard_details + - oxolinicacid_susceptible_breakpoint + - oxolinicacid_intermediate_breakpoint + - oxolinicacid_resistant_breakpoint - oxytetracycline_resistance_phenotype - oxytetracycline_measurement - oxytetracycline_measurement_units @@ -662,48 +662,48 @@ classes: - piperacillin_susceptible_breakpoint - piperacillin_intermediate_breakpoint - piperacillin_resistant_breakpoint - - piperacillin-tazobactam_resistance_phenotype - - piperacillin-tazobactam_measurement - - piperacillin-tazobactam_measurement_units - - piperacillin-tazobactam_measurement_sign - - piperacillin-tazobactam_laboratory_typing_method - - piperacillin-tazobactam_laboratory_typing_platform - - piperacillin-tazobactam_laboratory_typing_platform_version - - piperacillin-tazobactam_vendor_name - - piperacillin-tazobactam_testing_standard - - piperacillin-tazobactam_testing_standard_version - - piperacillin-tazobactam_testing_standard_details - - piperacillin-tazobactam_susceptible_breakpoint - - piperacillin-tazobactam_intermediate_breakpoint - - piperacillin-tazobactam_resistant_breakpoint - - polymyxin-b_resistance_phenotype - - polymyxin-b_measurement - - polymyxin-b_measurement_units - - polymyxin-b_measurement_sign - - polymyxin-b_laboratory_typing_method - - polymyxin-b_laboratory_typing_platform - - polymyxin-b_laboratory_typing_platform_version - - polymyxin-b_vendor_name - - polymyxin-b_testing_standard - - polymyxin-b_testing_standard_version - - polymyxin-b_testing_standard_details - - polymyxin-b_susceptible_breakpoint - - polymyxin-b_intermediate_breakpoint - - polymyxin-b_resistant_breakpoint - - quinupristin-dalfopristin_resistance_phenotype - - quinupristin-dalfopristin_measurement - - quinupristin-dalfopristin_measurement_units - - quinupristin-dalfopristin_measurement_sign - - quinupristin-dalfopristin_laboratory_typing_method - - quinupristin-dalfopristin_laboratory_typing_platform - - quinupristin-dalfopristin_laboratory_typing_platform_version - - quinupristin-dalfopristin_vendor_name - - quinupristin-dalfopristin_testing_standard - - quinupristin-dalfopristin_testing_standard_version - - quinupristin-dalfopristin_testing_standard_details - - quinupristin-dalfopristin_susceptible_breakpoint - - quinupristin-dalfopristin_intermediate_breakpoint - - quinupristin-dalfopristin_resistant_breakpoint + - piperacillintazobactam_resistance_phenotype + - piperacillintazobactam_measurement + - piperacillintazobactam_measurement_units + - piperacillintazobactam_measurement_sign + - piperacillintazobactam_laboratory_typing_method + - piperacillintazobactam_laboratory_typing_platform + - piperacillintazobactam_laboratory_typing_platform_version + - piperacillintazobactam_vendor_name + - piperacillintazobactam_testing_standard + - piperacillintazobactam_testing_standard_version + - piperacillintazobactam_testing_standard_details + - piperacillintazobactam_susceptible_breakpoint + - piperacillintazobactam_intermediate_breakpoint + - piperacillintazobactam_resistant_breakpoint + - polymyxinb_resistance_phenotype + - polymyxinb_measurement + - polymyxinb_measurement_units + - polymyxinb_measurement_sign + - polymyxinb_laboratory_typing_method + - polymyxinb_laboratory_typing_platform + - polymyxinb_laboratory_typing_platform_version + - polymyxinb_vendor_name + - polymyxinb_testing_standard + - polymyxinb_testing_standard_version + - polymyxinb_testing_standard_details + - polymyxinb_susceptible_breakpoint + - polymyxinb_intermediate_breakpoint + - polymyxinb_resistant_breakpoint + - quinupristindalfopristin_resistance_phenotype + - quinupristindalfopristin_measurement + - quinupristindalfopristin_measurement_units + - quinupristindalfopristin_measurement_sign + - quinupristindalfopristin_laboratory_typing_method + - quinupristindalfopristin_laboratory_typing_platform + - quinupristindalfopristin_laboratory_typing_platform_version + - quinupristindalfopristin_vendor_name + - quinupristindalfopristin_testing_standard + - quinupristindalfopristin_testing_standard_version + - quinupristindalfopristin_testing_standard_details + - quinupristindalfopristin_susceptible_breakpoint + - quinupristindalfopristin_intermediate_breakpoint + - quinupristindalfopristin_resistant_breakpoint - streptomycin_resistance_phenotype - streptomycin_measurement - streptomycin_measurement_units @@ -774,27 +774,27 @@ classes: - tigecycline_susceptible_breakpoint - tigecycline_intermediate_breakpoint - tigecycline_resistant_breakpoint - - trimethoprim-sulfamethoxazole_resistance_phenotype - - trimethoprim-sulfamethoxazole_measurement - - trimethoprim-sulfamethoxazole_measurement_units - - trimethoprim-sulfamethoxazole_measurement_sign - - trimethoprim-sulfamethoxazole_laboratory_typing_method - - trimethoprim-sulfamethoxazole_laboratory_typing_platform - - trimethoprim-sulfamethoxazole_laboratory_typing_platform_version - - trimethoprim-sulfamethoxazole_vendor_name - - trimethoprim-sulfamethoxazole_testing_standard - - trimethoprim-sulfamethoxazole_testing_standard_version - - trimethoprim-sulfamethoxazole_testing_standard_details - - trimethoprim-sulfamethoxazole_susceptible_breakpoint - - trimethoprim-sulfamethoxazole_intermediate_breakpoint - - trimethoprim-sulfamethoxazole_resistant_breakpoint + - trimethoprimsulfamethoxazole_resistance_phenotype + - trimethoprimsulfamethoxazole_measurement + - trimethoprimsulfamethoxazole_measurement_units + - trimethoprimsulfamethoxazole_measurement_sign + - trimethoprimsulfamethoxazole_laboratory_typing_method + - trimethoprimsulfamethoxazole_laboratory_typing_platform + - trimethoprimsulfamethoxazole_laboratory_typing_platform_version + - trimethoprimsulfamethoxazole_vendor_name + - trimethoprimsulfamethoxazole_testing_standard + - trimethoprimsulfamethoxazole_testing_standard_version + - trimethoprimsulfamethoxazole_testing_standard_details + - trimethoprimsulfamethoxazole_susceptible_breakpoint + - trimethoprimsulfamethoxazole_intermediate_breakpoint + - trimethoprimsulfamethoxazole_resistant_breakpoint - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - sample_collector_sample_ID: + sample_collector_sample_id: rank: 1 slot_group: Sample collection and processing - alternative_sample_ID: + alternative_sample_id: rank: 2 slot_group: Sample collection and processing sample_collected_by: @@ -809,7 +809,7 @@ classes: sample_plan_name: rank: 6 slot_group: Sample collection and processing - sample_plan_ID: + sample_plan_id: rank: 7 slot_group: Sample collection and processing sample_collector_contact_name: @@ -836,31 +836,31 @@ classes: specimen_processing: rank: 15 slot_group: Sample collection and processing - nucleic acid extraction method: + nucleic_acid_extraction_method: rank: 16 slot_group: Sample collection and processing - nucleic acid extraction kit: + nucleic_acid_extraction_kit: rank: 17 slot_group: Sample collection and processing - geo_loc_name (country): + geo_loc_name_country: rank: 18 slot_group: Sample collection and processing - geo_loc_name (state/province/region): + geo_loc_name_state_province_region: rank: 19 slot_group: Sample collection and processing - geo_loc_name (site): + geo_loc_name_site: rank: 20 slot_group: Sample collection and processing - food_product_origin_geo_loc_name (country): + food_product_origin_geo_loc_name_country: rank: 21 slot_group: Sample collection and processing - host_origin_geo_loc_name (country): + host_origin_geo_loc_name_country: rank: 22 slot_group: Sample collection and processing - geo_loc latitude: + geo_loc_latitude: rank: 23 slot_group: Sample collection and processing - geo_loc longitude: + geo_loc_longitude: rank: 24 slot_group: Sample collection and processing sample_collection_date: @@ -989,19 +989,19 @@ classes: weather_type: rank: 66 slot_group: Environmental conditions and measurements - host (common name): + host_common_name: rank: 67 slot_group: Host information - host (scientific name): + host_scientific_name: rank: 68 slot_group: Host information - host (ecotype): + host_ecotype: rank: 69 slot_group: Host information - host (breed): + host_breed: rank: 70 slot_group: Host information - host (food production name): + host_food_production_name: rank: 71 slot_group: Host information host_age_bin: @@ -1016,19 +1016,19 @@ classes: strain: rank: 75 slot_group: Strain and isolation information - isolate_ID: + isolate_id: rank: 76 slot_group: Strain and isolation information - alternative_isolate_ID: + alternative_isolate_id: rank: 77 slot_group: Strain and isolation information - progeny_isolate_ID: + progeny_isolate_id: rank: 78 slot_group: Strain and isolation information - IRIDA_isolate_ID: + irida_isolate_id: rank: 79 slot_group: Strain and isolation information - IRIDA_project_ID: + irida_project_id: rank: 80 slot_group: Strain and isolation information isolated_by: @@ -1067,7 +1067,7 @@ classes: phagetype: rank: 92 slot_group: Strain and isolation information - library_ID: + library_id: rank: 93 slot_group: Sequence information sequenced_by: @@ -1100,22 +1100,22 @@ classes: library_preparation_kit: rank: 103 slot_group: Sequence information - DNA fragment length: + dna_fragment_length: rank: 104 slot_group: Sequence information - genomic target enrichment method: + genomic_target_enrichment_method: rank: 105 slot_group: Sequence information - genomic target enrichment method details: + genomic_target_enrichment_method_details: rank: 106 slot_group: Sequence information - amplicon pcr primer scheme: + amplicon_pcr_primer_scheme: rank: 107 slot_group: Sequence information - amplicon size: + amplicon_size: rank: 108 slot_group: Sequence information - sequencing flow cell version: + sequencing_flow_cell_version: rank: 109 slot_group: Sequence information sequencing_protocol: @@ -1133,112 +1133,112 @@ classes: assembly_filename: rank: 114 slot_group: Sequence information - quality control method name: + quality_control_method_name: rank: 115 slot_group: Bioinformatics and QC metrics - quality control method version: + quality_control_method_version: rank: 116 slot_group: Bioinformatics and QC metrics - quality control determination: + quality_control_determination: rank: 117 slot_group: Bioinformatics and QC metrics - quality control issues: + quality_control_issues: rank: 118 slot_group: Bioinformatics and QC metrics - quality control details: + quality_control_details: rank: 119 slot_group: Bioinformatics and QC metrics - raw sequence data processing method: + raw_sequence_data_processing_method: rank: 120 slot_group: Bioinformatics and QC metrics - dehosting method: + dehosting_method: rank: 121 slot_group: Bioinformatics and QC metrics - sequence assembly software name: + sequence_assembly_software_name: rank: 122 slot_group: Bioinformatics and QC metrics - sequence assembly software version: + sequence_assembly_software_version: rank: 123 slot_group: Bioinformatics and QC metrics - consensus sequence software name: + consensus_sequence_software_name: rank: 124 slot_group: Bioinformatics and QC metrics - consensus sequence software version: + consensus_sequence_software_version: rank: 125 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + breadth_of_coverage_value: rank: 126 slot_group: Bioinformatics and QC metrics - depth of coverage value: + depth_of_coverage_value: rank: 127 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + depth_of_coverage_threshold: rank: 128 slot_group: Bioinformatics and QC metrics - genome completeness: + genome_completeness: rank: 129 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + number_of_base_pairs_sequenced: rank: 130 slot_group: Bioinformatics and QC metrics - number of total reads: + number_of_total_reads: rank: 131 slot_group: Bioinformatics and QC metrics - number of unique reads: + number_of_unique_reads: rank: 132 slot_group: Bioinformatics and QC metrics - minimum post-trimming read length: + minimum_posttrimming_read_length: rank: 133 slot_group: Bioinformatics and QC metrics - number of contigs: + number_of_contigs: rank: 134 slot_group: Bioinformatics and QC metrics - percent Ns across total genome length: + percent_ns_across_total_genome_length: rank: 135 slot_group: Bioinformatics and QC metrics - Ns per 100 kbp: + ns_per_100_kbp: rank: 136 slot_group: Bioinformatics and QC metrics - N50: + n50: rank: 137 slot_group: Bioinformatics and QC metrics - percent read contamination: + percent_read_contamination_: rank: 138 slot_group: Bioinformatics and QC metrics - sequence assembly length: + sequence_assembly_length: rank: 139 slot_group: Bioinformatics and QC metrics - consensus genome length: + consensus_genome_length: rank: 140 slot_group: Bioinformatics and QC metrics - reference genome accession: + reference_genome_accession: rank: 141 slot_group: Bioinformatics and QC metrics - deduplication method: + deduplication_method: rank: 142 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + bioinformatics_protocol: rank: 143 slot_group: Bioinformatics and QC metrics - read mapping software name: + read_mapping_software_name: rank: 144 slot_group: Taxonomic identification information - read mapping software version: + read_mapping_software_version: rank: 145 slot_group: Taxonomic identification information - taxonomic reference database name: + taxonomic_reference_database_name: rank: 146 slot_group: Taxonomic identification information - taxonomic reference database version: + taxonomic_reference_database_version: rank: 147 slot_group: Taxonomic identification information - taxonomic analysis report filename: + taxonomic_analysis_report_filename: rank: 148 slot_group: Taxonomic identification information - taxonomic analysis date: + taxonomic_analysis_date: rank: 149 slot_group: Taxonomic identification information - read mapping criteria: + read_mapping_criteria: rank: 150 slot_group: Taxonomic identification information sequence_submitted_by: @@ -1250,7 +1250,7 @@ classes: sequence_submitted_by_contact_email: rank: 153 slot_group: Public repository information - publication_ID: + publication_id: rank: 154 slot_group: Public repository information attribute_package: @@ -1262,10 +1262,10 @@ classes: biosample_accession: rank: 157 slot_group: Public repository information - SRA_accession: + sra_accession: rank: 158 slot_group: Public repository information - GenBank_accession: + genbank_accession: rank: 159 slot_group: Public repository information prevalence_metrics: @@ -1283,19 +1283,19 @@ classes: experiment_intervention_details: rank: 164 slot_group: Risk assessment information - AMR_testing_by: + amr_testing_by: rank: 165 slot_group: Antimicrobial resistance - AMR_testing_by_laboratory_name: + amr_testing_by_laboratory_name: rank: 166 slot_group: Antimicrobial resistance - AMR_testing_by_contact_name: + amr_testing_by_contact_name: rank: 167 slot_group: Antimicrobial resistance - AMR_testing_by_contact_email: + amr_testing_by_contact_email: rank: 168 slot_group: Antimicrobial resistance - AMR_testing_date: + amr_testing_date: rank: 169 slot_group: Antimicrobial resistance amikacin_resistance_phenotype: @@ -1340,46 +1340,46 @@ classes: amikacin_resistant_breakpoint: rank: 183 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_resistance_phenotype: + amoxicillinclavulanic_acid_resistance_phenotype: rank: 184 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_measurement: + amoxicillinclavulanic_acid_measurement: rank: 185 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_measurement_units: + amoxicillinclavulanic_acid_measurement_units: rank: 186 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_measurement_sign: + amoxicillinclavulanic_acid_measurement_sign: rank: 187 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_laboratory_typing_method: + amoxicillinclavulanic_acid_laboratory_typing_method: rank: 188 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_laboratory_typing_platform: + amoxicillinclavulanic_acid_laboratory_typing_platform: rank: 189 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_laboratory_typing_platform_version: + amoxicillinclavulanic_acid_laboratory_typing_platform_version: rank: 190 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_vendor_name: + amoxicillinclavulanic_acid_vendor_name: rank: 191 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_testing_standard: + amoxicillinclavulanic_acid_testing_standard: rank: 192 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_testing_standard_version: + amoxicillinclavulanic_acid_testing_standard_version: rank: 193 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_testing_standard_details: + amoxicillinclavulanic_acid_testing_standard_details: rank: 194 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_susceptible_breakpoint: + amoxicillinclavulanic_acid_susceptible_breakpoint: rank: 195 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_intermediate_breakpoint: + amoxicillinclavulanic_acid_intermediate_breakpoint: rank: 196 slot_group: Antimicrobial resistance - amoxicillin-clavulanic_acid_resistant_breakpoint: + amoxicillinclavulanic_acid_resistant_breakpoint: rank: 197 slot_group: Antimicrobial resistance ampicillin_resistance_phenotype: @@ -1592,46 +1592,46 @@ classes: cefotaxime_resistant_breakpoint: rank: 267 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_resistance_phenotype: + cefotaximeclavulanic_acid_resistance_phenotype: rank: 268 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_measurement: + cefotaximeclavulanic_acid_measurement: rank: 269 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_measurement_units: + cefotaximeclavulanic_acid_measurement_units: rank: 270 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_measurement_sign: + cefotaximeclavulanic_acid_measurement_sign: rank: 271 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_laboratory_typing_method: + cefotaximeclavulanic_acid_laboratory_typing_method: rank: 272 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_laboratory_typing_platform: + cefotaximeclavulanic_acid_laboratory_typing_platform: rank: 273 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_laboratory_typing_platform_version: + cefotaximeclavulanic_acid_laboratory_typing_platform_version: rank: 274 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_vendor_name: + cefotaximeclavulanic_acid_vendor_name: rank: 275 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_testing_standard: + cefotaximeclavulanic_acid_testing_standard: rank: 276 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_testing_standard_version: + cefotaximeclavulanic_acid_testing_standard_version: rank: 277 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_testing_standard_details: + cefotaximeclavulanic_acid_testing_standard_details: rank: 278 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_susceptible_breakpoint: + cefotaximeclavulanic_acid_susceptible_breakpoint: rank: 279 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_intermediate_breakpoint: + cefotaximeclavulanic_acid_intermediate_breakpoint: rank: 280 slot_group: Antimicrobial resistance - cefotaxime-clavulanic_acid_resistant_breakpoint: + cefotaximeclavulanic_acid_resistant_breakpoint: rank: 281 slot_group: Antimicrobial resistance cefoxitin_resistance_phenotype: @@ -1760,46 +1760,46 @@ classes: ceftazidime_resistant_breakpoint: rank: 323 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_resistance_phenotype: + ceftazidimeclavulanic_acid_resistance_phenotype: rank: 324 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_measurement: + ceftazidimeclavulanic_acid_measurement: rank: 325 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_measurement_units: + ceftazidimeclavulanic_acid_measurement_units: rank: 326 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_measurement_sign: + ceftazidimeclavulanic_acid_measurement_sign: rank: 327 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_laboratory_typing_method: + ceftazidimeclavulanic_acid_laboratory_typing_method: rank: 328 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_laboratory_typing_platform: + ceftazidimeclavulanic_acid_laboratory_typing_platform: rank: 329 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_laboratory_typing_platform_version: + ceftazidimeclavulanic_acid_laboratory_typing_platform_version: rank: 330 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_vendor_name: + ceftazidimeclavulanic_acid_vendor_name: rank: 331 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_testing_standard: + ceftazidimeclavulanic_acid_testing_standard: rank: 332 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_testing_standard_version: + ceftazidimeclavulanic_acid_testing_standard_version: rank: 333 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_testing_standard_details: + ceftazidimeclavulanic_acid_testing_standard_details: rank: 334 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_susceptible_breakpoint: + ceftazidimeclavulanic_acid_susceptible_breakpoint: rank: 335 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_intermediate_breakpoint: + ceftazidimeclavulanic_acid_intermediate_breakpoint: rank: 336 slot_group: Antimicrobial resistance - ceftazidime-clavulanic_acid_resistant_breakpoint: + ceftazidimeclavulanic_acid_resistant_breakpoint: rank: 337 slot_group: Antimicrobial resistance ceftiofur_resistance_phenotype: @@ -2600,46 +2600,46 @@ classes: norfloxacin_resistant_breakpoint: rank: 603 slot_group: Antimicrobial resistance - oxolinic-acid_resistance_phenotype: + oxolinicacid_resistance_phenotype: rank: 604 slot_group: Antimicrobial resistance - oxolinic-acid_measurement: + oxolinicacid_measurement: rank: 605 slot_group: Antimicrobial resistance - oxolinic-acid_measurement_units: + oxolinicacid_measurement_units: rank: 606 slot_group: Antimicrobial resistance - oxolinic-acid_measurement_sign: + oxolinicacid_measurement_sign: rank: 607 slot_group: Antimicrobial resistance - oxolinic-acid_laboratory_typing_method: + oxolinicacid_laboratory_typing_method: rank: 608 slot_group: Antimicrobial resistance - oxolinic-acid_laboratory_typing_platform: + oxolinicacid_laboratory_typing_platform: rank: 609 slot_group: Antimicrobial resistance - oxolinic-acid_laboratory_typing_platform_version: + oxolinicacid_laboratory_typing_platform_version: rank: 610 slot_group: Antimicrobial resistance - oxolinic-acid_vendor_name: + oxolinicacid_vendor_name: rank: 611 slot_group: Antimicrobial resistance - oxolinic-acid_testing_standard: + oxolinicacid_testing_standard: rank: 612 slot_group: Antimicrobial resistance - oxolinic-acid_testing_standard_version: + oxolinicacid_testing_standard_version: rank: 613 slot_group: Antimicrobial resistance - oxolinic-acid_testing_standard_details: + oxolinicacid_testing_standard_details: rank: 614 slot_group: Antimicrobial resistance - oxolinic-acid_susceptible_breakpoint: + oxolinicacid_susceptible_breakpoint: rank: 615 slot_group: Antimicrobial resistance - oxolinic-acid_intermediate_breakpoint: + oxolinicacid_intermediate_breakpoint: rank: 616 slot_group: Antimicrobial resistance - oxolinic-acid_resistant_breakpoint: + oxolinicacid_resistant_breakpoint: rank: 617 slot_group: Antimicrobial resistance oxytetracycline_resistance_phenotype: @@ -2726,130 +2726,130 @@ classes: piperacillin_resistant_breakpoint: rank: 645 slot_group: Antimicrobial resistance - piperacillin-tazobactam_resistance_phenotype: + piperacillintazobactam_resistance_phenotype: rank: 646 slot_group: Antimicrobial resistance - piperacillin-tazobactam_measurement: + piperacillintazobactam_measurement: rank: 647 slot_group: Antimicrobial resistance - piperacillin-tazobactam_measurement_units: + piperacillintazobactam_measurement_units: rank: 648 slot_group: Antimicrobial resistance - piperacillin-tazobactam_measurement_sign: + piperacillintazobactam_measurement_sign: rank: 649 slot_group: Antimicrobial resistance - piperacillin-tazobactam_laboratory_typing_method: + piperacillintazobactam_laboratory_typing_method: rank: 650 slot_group: Antimicrobial resistance - piperacillin-tazobactam_laboratory_typing_platform: + piperacillintazobactam_laboratory_typing_platform: rank: 651 slot_group: Antimicrobial resistance - piperacillin-tazobactam_laboratory_typing_platform_version: + piperacillintazobactam_laboratory_typing_platform_version: rank: 652 slot_group: Antimicrobial resistance - piperacillin-tazobactam_vendor_name: + piperacillintazobactam_vendor_name: rank: 653 slot_group: Antimicrobial resistance - piperacillin-tazobactam_testing_standard: + piperacillintazobactam_testing_standard: rank: 654 slot_group: Antimicrobial resistance - piperacillin-tazobactam_testing_standard_version: + piperacillintazobactam_testing_standard_version: rank: 655 slot_group: Antimicrobial resistance - piperacillin-tazobactam_testing_standard_details: + piperacillintazobactam_testing_standard_details: rank: 656 slot_group: Antimicrobial resistance - piperacillin-tazobactam_susceptible_breakpoint: + piperacillintazobactam_susceptible_breakpoint: rank: 657 slot_group: Antimicrobial resistance - piperacillin-tazobactam_intermediate_breakpoint: + piperacillintazobactam_intermediate_breakpoint: rank: 658 slot_group: Antimicrobial resistance - piperacillin-tazobactam_resistant_breakpoint: + piperacillintazobactam_resistant_breakpoint: rank: 659 slot_group: Antimicrobial resistance - polymyxin-b_resistance_phenotype: + polymyxinb_resistance_phenotype: rank: 660 slot_group: Antimicrobial resistance - polymyxin-b_measurement: + polymyxinb_measurement: rank: 661 slot_group: Antimicrobial resistance - polymyxin-b_measurement_units: + polymyxinb_measurement_units: rank: 662 slot_group: Antimicrobial resistance - polymyxin-b_measurement_sign: + polymyxinb_measurement_sign: rank: 663 slot_group: Antimicrobial resistance - polymyxin-b_laboratory_typing_method: + polymyxinb_laboratory_typing_method: rank: 664 slot_group: Antimicrobial resistance - polymyxin-b_laboratory_typing_platform: + polymyxinb_laboratory_typing_platform: rank: 665 slot_group: Antimicrobial resistance - polymyxin-b_laboratory_typing_platform_version: + polymyxinb_laboratory_typing_platform_version: rank: 666 slot_group: Antimicrobial resistance - polymyxin-b_vendor_name: + polymyxinb_vendor_name: rank: 667 slot_group: Antimicrobial resistance - polymyxin-b_testing_standard: + polymyxinb_testing_standard: rank: 668 slot_group: Antimicrobial resistance - polymyxin-b_testing_standard_version: + polymyxinb_testing_standard_version: rank: 669 slot_group: Antimicrobial resistance - polymyxin-b_testing_standard_details: + polymyxinb_testing_standard_details: rank: 670 slot_group: Antimicrobial resistance - polymyxin-b_susceptible_breakpoint: + polymyxinb_susceptible_breakpoint: rank: 671 slot_group: Antimicrobial resistance - polymyxin-b_intermediate_breakpoint: + polymyxinb_intermediate_breakpoint: rank: 672 slot_group: Antimicrobial resistance - polymyxin-b_resistant_breakpoint: + polymyxinb_resistant_breakpoint: rank: 673 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_resistance_phenotype: + quinupristindalfopristin_resistance_phenotype: rank: 674 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_measurement: + quinupristindalfopristin_measurement: rank: 675 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_measurement_units: + quinupristindalfopristin_measurement_units: rank: 676 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_measurement_sign: + quinupristindalfopristin_measurement_sign: rank: 677 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_laboratory_typing_method: + quinupristindalfopristin_laboratory_typing_method: rank: 678 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_laboratory_typing_platform: + quinupristindalfopristin_laboratory_typing_platform: rank: 679 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_laboratory_typing_platform_version: + quinupristindalfopristin_laboratory_typing_platform_version: rank: 680 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_vendor_name: + quinupristindalfopristin_vendor_name: rank: 681 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_testing_standard: + quinupristindalfopristin_testing_standard: rank: 682 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_testing_standard_version: + quinupristindalfopristin_testing_standard_version: rank: 683 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_testing_standard_details: + quinupristindalfopristin_testing_standard_details: rank: 684 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_susceptible_breakpoint: + quinupristindalfopristin_susceptible_breakpoint: rank: 685 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_intermediate_breakpoint: + quinupristindalfopristin_intermediate_breakpoint: rank: 686 slot_group: Antimicrobial resistance - quinupristin-dalfopristin_resistant_breakpoint: + quinupristindalfopristin_resistant_breakpoint: rank: 687 slot_group: Antimicrobial resistance streptomycin_resistance_phenotype: @@ -3062,57 +3062,57 @@ classes: tigecycline_resistant_breakpoint: rank: 757 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_resistance_phenotype: + trimethoprimsulfamethoxazole_resistance_phenotype: rank: 758 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_measurement: + trimethoprimsulfamethoxazole_measurement: rank: 759 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_measurement_units: + trimethoprimsulfamethoxazole_measurement_units: rank: 760 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_measurement_sign: + trimethoprimsulfamethoxazole_measurement_sign: rank: 761 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_laboratory_typing_method: + trimethoprimsulfamethoxazole_laboratory_typing_method: rank: 762 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_laboratory_typing_platform: + trimethoprimsulfamethoxazole_laboratory_typing_platform: rank: 763 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_laboratory_typing_platform_version: + trimethoprimsulfamethoxazole_laboratory_typing_platform_version: rank: 764 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_vendor_name: + trimethoprimsulfamethoxazole_vendor_name: rank: 765 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_testing_standard: + trimethoprimsulfamethoxazole_testing_standard: rank: 766 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_testing_standard_version: + trimethoprimsulfamethoxazole_testing_standard_version: rank: 767 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_testing_standard_details: + trimethoprimsulfamethoxazole_testing_standard_details: rank: 768 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_susceptible_breakpoint: + trimethoprimsulfamethoxazole_susceptible_breakpoint: rank: 769 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_intermediate_breakpoint: + trimethoprimsulfamethoxazole_intermediate_breakpoint: rank: 770 slot_group: Antimicrobial resistance - trimethoprim-sulfamethoxazole_resistant_breakpoint: + trimethoprimsulfamethoxazole_resistant_breakpoint: rank: 771 slot_group: Antimicrobial resistance authors: rank: 772 slot_group: Contributor acknowledgement - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 773 slot_group: Contributor acknowledgement slots: - sample_collector_sample_ID: - name: sample_collector_sample_ID + sample_collector_sample_id: + name: sample_collector_sample_id title: sample_collector_sample_ID description: The user-defined name for the sample. comments: The sample_ID should represent the identifier assigned to the sample @@ -3128,21 +3128,23 @@ slots: - value: ABCD123 exact_mappings: - BIOSAMPLE:sample_name - alternative_sample_ID: - name: alternative_sample_ID + - NCBI_BIOSAMPLE_Enterics:%2Asample_name + - NCBI_ANTIBIOGRAM:%2Asample_name + alternative_sample_id: + name: alternative_sample_id title: alternative_sample_ID description: An alternative sample_ID assigned to the sample by another organization. - comments: "\"Alternative identifiers assigned to the sample should be tracked\ - \ along with original IDs to establish chain of custody. Alternative sample\ - \ IDs should be provided in the in a prescribed format which consists of the\ - \ ID followed by square brackets (no space in between the ID and bracket) containing\ - \ the short form of ID provider\u2019s agency name i.e. ID[short organization\ - \ code]. Agency short forms include the following:\nPublic Health Agency of\ - \ Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food\ - \ Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change\ - \ Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and\ - \ separated by semi-colons. If the information is unknown or cannot be provided,\ - \ leave blank or provide a null value.\"" + comments: "Alternative identifiers assigned to the sample should be tracked along\ + \ with original IDs to establish chain of custody. Alternative sample IDs should\ + \ be provided in the in a prescribed format which consists of the ID followed\ + \ by square brackets (no space in between the ID and bracket) containing the\ + \ short form of ID provider\u2019s agency name i.e. ID[short organization code].\ + \ Agency short forms include the following: Public Health Agency of Canada:\ + \ PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada:\ + \ AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada:\ + \ ECCC Health Canada: HC Multiple identifiers can be provided and separated\ + \ by semi-colons. If the information is unknown or cannot be provided, leave\ + \ blank or provide a null value." slot_uri: GENEPIO:0100427 range: WhitespaceMinimizedString required: true @@ -3166,6 +3168,7 @@ slots: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] exact_mappings: - BIOSAMPLE:collected_by + - NCBI_BIOSAMPLE_Enterics:%2Acollected_by sample_collected_by_laboratory_name: name: sample_collected_by_laboratory_name title: sample_collected_by_laboratory_name @@ -3188,6 +3191,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Watershed Project (HA-120) + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:project_name sample_plan_name: name: sample_plan_name title: sample_plan_name @@ -3200,8 +3205,8 @@ slots: recommended: true examples: - value: National Microbiological Baseline Study in Broiler Chicken - sample_plan_ID: - name: sample_plan_ID + sample_plan_id: + name: sample_plan_id title: sample_plan_ID description: The identifier of the study design for a surveillance project. comments: Provide the identifier of the sample plan used for sample collection. @@ -3262,6 +3267,7 @@ slots: - value: Surveillance [GENEPIO:0100004] exact_mappings: - BIOSAMPLE:purpose_of_sampling + - NCBI_BIOSAMPLE_Enterics:%2Apurpose_of_sampling presampling_activity: name: presampling_activity title: presampling_activity @@ -3278,6 +3284,9 @@ slots: - range: null value menu examples: - value: Antimicrobial pre-treatment [GENEPIO:0100537] + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:host_am + - NCBI_BIOSAMPLE_Enterics:fertilizer_admin presampling_activity_details: name: presampling_activity_details title: presampling_activity_details @@ -3328,8 +3337,8 @@ slots: - range: null value menu examples: - value: Samples pooled [OBI:0600016] - nucleic acid extraction method: - name: nucleic acid extraction method + nucleic_acid_extraction_method: + name: nucleic_acid_extraction_method title: nucleic acid extraction method description: The process used to extract genomic material from a sample. comments: Briefly describe the extraction method used. @@ -3338,8 +3347,8 @@ slots: examples: - value: Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 - nucleic acid extraction kit: - name: nucleic acid extraction kit + nucleic_acid_extraction_kit: + name: nucleic_acid_extraction_kit title: nucleic acid extraction kit description: The kit used to extract genomic material from a sample comments: Provide the name of the genomic extraction kit used. @@ -3347,8 +3356,8 @@ slots: range: WhitespaceMinimizedString examples: - value: QIAamp PowerFecal Pro DNA Kit - geo_loc_name (country): - name: geo_loc_name (country) + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc_name (country) description: The country of origin of the sample. comments: Provide the name of the country where the sample was collected. Use @@ -3364,8 +3373,9 @@ slots: exact_mappings: - BIOSAMPLE:geo_loc_name - BIOSAMPLE:geo_loc_name%20%28country%29 - geo_loc_name (state/province/region): - name: geo_loc_name (state/province/region) + - NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name + geo_loc_name_state_province_region: + name: geo_loc_name_state_province_region title: geo_loc_name (state/province/region) description: The state/province/territory of origin of the sample. comments: Provide the name of the province/state/region where the sample was collected. If @@ -3380,8 +3390,9 @@ slots: exact_mappings: - BIOSAMPLE:geo_loc_name - BIOSAMPLE:geo_loc_name%20%28state/province/region%29 - geo_loc_name (site): - name: geo_loc_name (site) + - NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name + geo_loc_name_site: + name: geo_loc_name_site title: geo_loc_name (site) description: The name of a specific geographical location e.g. Credit River (rather than river). @@ -3394,8 +3405,8 @@ slots: exact_mappings: - BIOSAMPLE:geo_loc_name - BIOSAMPLE:geo_loc_name%20%28site%29 - food_product_origin_geo_loc_name (country): - name: food_product_origin_geo_loc_name (country) + food_product_origin_geo_loc_name_country: + name: food_product_origin_geo_loc_name_country title: food_product_origin_geo_loc_name (country) description: The country of origin of a food product. comments: If a food product was sampled and the food product was manufactured @@ -3408,8 +3419,10 @@ slots: - range: null value menu examples: - value: United States of America [GAZ:00002459] - host_origin_geo_loc_name (country): - name: host_origin_geo_loc_name (country) + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:food_origin + host_origin_geo_loc_name_country: + name: host_origin_geo_loc_name_country title: host_origin_geo_loc_name (country) description: The country of origin of the host. comments: If a sample is from a human or animal host that originated from outside @@ -3422,8 +3435,8 @@ slots: - range: null value menu examples: - value: South Africa [GAZ:00001094] - geo_loc latitude: - name: geo_loc latitude + geo_loc_latitude: + name: geo_loc_latitude title: geo_loc latitude description: The latitude coordinates of the geographical location of sample collection. comments: If known, provide the degrees latitude. Do NOT simply provide latitude @@ -3435,8 +3448,10 @@ slots: range: WhitespaceMinimizedString examples: - value: 38.98 N - geo_loc longitude: - name: geo_loc longitude + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:lat_lon + geo_loc_longitude: + name: geo_loc_longitude title: geo_loc longitude description: The longitude coordinates of the geographical location of sample collection. @@ -3449,6 +3464,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 77.11 W + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:lat_lon sample_collection_date: name: sample_collection_date title: sample_collection_date @@ -3462,6 +3479,7 @@ slots: - value: '2020-10-30' exact_mappings: - BIOSAMPLE:sample%20collection%20date + - NCBI_BIOSAMPLE_Enterics:%2Acollection_date sample_collection_date_precision: name: sample_collection_date_precision title: sample_collection_date_precision @@ -3517,6 +3535,11 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_site + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:animal_env + - NCBI_BIOSAMPLE_Enterics:host_housing + - NCBI_BIOSAMPLE_Enterics:env_local_scale + - NCBI_BIOSAMPLE_Enterics:facility_type environmental_material: name: environmental_material title: environmental_material @@ -3539,6 +3562,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_material + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source environmental_material_constituent: name: environmental_material_constituent title: environmental_material_constituent @@ -3590,6 +3614,8 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_material + - NCBI_BIOSAMPLE_Enterics:host_tissue_sampled + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source body_product: name: body_product title: body_product @@ -3611,6 +3637,8 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:body_product + - NCBI_BIOSAMPLE_Enterics:host_body_product + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source anatomical_part: name: anatomical_part title: anatomical_part @@ -3629,6 +3657,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_part + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source anatomical_region: name: anatomical_region title: anatomical_region @@ -3685,6 +3714,9 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:food_product_properties + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:food_processing_method + - NCBI_BIOSAMPLE_Enterics:food_preserv_proc label_claim: name: label_claim title: label_claim @@ -3699,6 +3731,8 @@ slots: multivalued: true examples: - value: Antibiotic free [FOODON:03601063] + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:label_claims animal_source_of_food: name: animal_source_of_food title: animal_source_of_food @@ -3713,6 +3747,8 @@ slots: recommended: true examples: - value: Chicken [NCBITaxon:9031] + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:food_source food_product_production_stream: name: food_product_production_stream title: food_product_production_stream @@ -3726,6 +3762,8 @@ slots: - range: null value menu examples: - value: Beef cattle production stream [FOODON:03000452] + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:food_prod food_packaging: name: food_packaging title: food_packaging @@ -3742,6 +3780,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:food_packaging + - NCBI_BIOSAMPLE_Enterics:food_contain_wrap food_quality_date: name: food_quality_date title: food_quality_date @@ -3754,6 +3793,8 @@ slots: range: date examples: - value: '2020-05-25' + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:food_quality_date food_packaging_date: name: food_packaging_date title: food_packaging_date @@ -3783,6 +3824,8 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_device + - NCBI_BIOSAMPLE_Enterics:samp_collect_device + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source collection_method: name: collection_method title: collection_method @@ -3800,6 +3843,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source sample_volume_measurement_value: name: sample_volume_measurement_value title: sample_volume_measurement_value @@ -4009,8 +4053,8 @@ slots: multivalued: true examples: - value: Rain [ENVO:01001564] - host (common name): - name: host (common name) + host_common_name: + name: host_common_name title: host (common name) description: The commonly used name of the host. comments: If the sample is directly from a host, either a common or scientific @@ -4024,8 +4068,10 @@ slots: examples: - value: Cow [NCBITaxon:9913] - value: Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] - host (scientific name): - name: host (scientific name) + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:host + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. comments: If the sample is directly from a host, either a common or scientific @@ -4041,8 +4087,10 @@ slots: - value: Homo sapiens [NCBITaxon:9103] exact_mappings: - BIOSAMPLE:host - host (ecotype): - name: host (ecotype) + - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:host + host_ecotype: + name: host_ecotype title: host (ecotype) description: The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. @@ -4051,8 +4099,10 @@ slots: range: WhitespaceMinimizedString examples: - value: Sea ecotype - host (breed): - name: host (breed) + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:host_variety + host_breed: + name: host_breed title: host (breed) description: A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that @@ -4065,8 +4115,9 @@ slots: - value: Holstein exact_mappings: - BIOSAMPLE:host_disease - host (food production name): - name: host (food production name) + - NCBI_BIOSAMPLE_Enterics:host_animal_breed + host_food_production_name: + name: host_food_production_name title: host (food production name) description: The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. @@ -4077,6 +4128,8 @@ slots: - range: null value menu examples: - value: Calf [FOODON:03411349] + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:host host_age_bin: name: host_age_bin title: host_age_bin @@ -4087,6 +4140,8 @@ slots: any_of: - range: host_age_bin menu - range: null value menu + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:host_age host_disease: name: host_disease title: host_disease @@ -4099,6 +4154,8 @@ slots: range: WhitespaceMinimizedString examples: - value: mastitis, gastroenteritis + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:host_disease microbiological_method: name: microbiological_method title: microbiological_method @@ -4122,8 +4179,10 @@ slots: range: WhitespaceMinimizedString examples: - value: K12 - isolate_ID: - name: isolate_ID + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:strain + isolate_id: + name: isolate_id title: isolate_ID description: The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. @@ -4139,18 +4198,20 @@ slots: required: true examples: - value: SA20131043 - alternative_isolate_ID: - name: alternative_isolate_ID + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:strain + alternative_isolate_id: + name: alternative_isolate_id title: alternative_isolate_ID description: An alternative isolate_ID assigned to the isolate by another organization. comments: "Alternative isolate IDs should be provided in the in a prescribed format\ \ which consists of the ID followed by square brackets (no space in between\ \ the ID and bracket) containing the short form of ID provider\u2019s agency\ - \ name i.e. ID[short organization code]. Agency short forms include the following:\n\ - Public Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\n\ - Agriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment\ - \ and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly\ - \ formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple\ + \ name i.e. ID[short organization code]. Agency short forms include the following:\ + \ Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA\ + \ Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment\ + \ and Climate Change Canada: ECCC Health Canada: HC An example of a properly\ + \ formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple\ \ alternative isolate IDs can be provided, separated by semi-colons." slot_uri: GENEPIO:0100457 range: WhitespaceMinimizedString @@ -4158,8 +4219,10 @@ slots: examples: - value: GHIF3456[PHAC] - value: QWICK222[CFIA] - progeny_isolate_ID: - name: progeny_isolate_ID + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:isolate_name_alias + progeny_isolate_id: + name: progeny_isolate_id title: progeny_isolate_ID description: The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. @@ -4169,8 +4232,8 @@ slots: range: WhitespaceMinimizedString examples: - value: SUB_ON_1526 - IRIDA_isolate_ID: - name: IRIDA_isolate_ID + irida_isolate_id: + name: irida_isolate_id title: IRIDA_isolate_ID description: The identifier of the isolate in the IRIDA platform. comments: Provide the "sample ID" used to track information linked to the isolate @@ -4185,8 +4248,8 @@ slots: required: true examples: - value: GRDI_LL_12345 - IRIDA_project_ID: - name: IRIDA_project_ID + irida_project_id: + name: irida_project_id title: IRIDA_project_ID description: The identifier of the Project in the iRIDA platform. comments: Provide the IRIDA "project ID". @@ -4258,6 +4321,8 @@ slots: range: date examples: - value: '2020-10-30' + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:cult_isol_date isolate_received_date: name: isolate_received_date title: isolate_received_date @@ -4289,6 +4354,7 @@ slots: - value: Salmonella enterica subsp. enterica [NCBITaxon:59201] exact_mappings: - BIOSAMPLE:organism + - NCBI_BIOSAMPLE_Enterics:%2Aorganism taxonomic_identification_process: name: taxonomic_identification_process title: taxonomic_identification_process @@ -4326,6 +4392,8 @@ slots: recommended: true examples: - value: Heidelberg + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:serovar serotyping_method: name: serotyping_method title: serotyping_method @@ -4347,8 +4415,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '47' - library_ID: - name: library_ID + library_id: + name: library_id title: library_ID description: The user-specified identifier for the library prepared for sequencing. comments: Every "library ID" from a single submitter must be unique. It can have @@ -4375,6 +4443,7 @@ slots: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] exact_mappings: - BIOSAMPLE:sequenced_by + - NCBI_BIOSAMPLE_Enterics:sequenced_by sequenced_by_laboratory_name: name: sequenced_by_laboratory_name title: sequenced_by_laboratory_name @@ -4498,8 +4567,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Nextera XT - DNA fragment length: - name: DNA fragment length + dna_fragment_length: + name: dna_fragment_length title: DNA fragment length description: The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. @@ -4508,8 +4577,8 @@ slots: range: Integer examples: - value: '400' - genomic target enrichment method: - name: genomic target enrichment method + genomic_target_enrichment_method: + name: genomic_target_enrichment_method title: genomic target enrichment method description: The molecular technique used to selectively capture and amplify specific regions of interest from a genome. @@ -4518,8 +4587,8 @@ slots: range: genomic_target_enrichment_method menu examples: - value: Hybrid selection method (bait-capture) [GENEPIO:0001950] - genomic target enrichment method details: - name: genomic target enrichment method details + genomic_target_enrichment_method_details: + name: genomic_target_enrichment_method_details title: genomic target enrichment method details description: Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a @@ -4532,8 +4601,8 @@ slots: examples: - value: 'enrichment was done using Twist''s respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel' - amplicon pcr primer scheme: - name: amplicon pcr primer scheme + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme title: amplicon pcr primer scheme description: The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. @@ -4543,8 +4612,8 @@ slots: range: WhitespaceMinimizedString examples: - value: artic v3 - amplicon size: - name: amplicon size + amplicon_size: + name: amplicon_size title: amplicon size description: The length of the amplicon generated by PCR amplification. comments: Provide the amplicon size expressed in base pairs. @@ -4552,8 +4621,8 @@ slots: range: Integer examples: - value: '300' - sequencing flow cell version: - name: sequencing flow cell version + sequencing_flow_cell_version: + name: sequencing_flow_cell_version title: sequencing flow cell version description: The version number of the flow cell used for generating sequence data. @@ -4611,8 +4680,8 @@ slots: range: WhitespaceMinimizedString examples: - value: pathogenassembly123.fasta - quality control method name: - name: quality control method name + quality_control_method_name: + name: quality_control_method_name title: quality control method name description: The name of the method used to assess whether a sequence passed a predetermined quality control threshold. @@ -4625,8 +4694,8 @@ slots: range: WhitespaceMinimizedString examples: - value: ncov-tools - quality control method version: - name: quality control method version + quality_control_method_version: + name: quality_control_method_version title: quality control method version description: The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. @@ -4639,8 +4708,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 1.2.3 - quality control determination: - name: quality control determination + quality_control_determination: + name: quality_control_determination title: quality control determination description: The determination of a quality control assessment. comments: Select a value from the pick list provided. If a desired value is missing, @@ -4653,8 +4722,8 @@ slots: multivalued: true examples: - value: sequence failed quality control - quality control issues: - name: quality control issues + quality_control_issues: + name: quality_control_issues title: quality control issues description: The reason contributing to, or causing, a low quality determination in a quality control assessment. @@ -4668,8 +4737,8 @@ slots: multivalued: true examples: - value: low average genome coverage - quality control details: - name: quality control details + quality_control_details: + name: quality_control_details title: quality control details description: The details surrounding a low quality determination in a quality control assessment. @@ -4678,8 +4747,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CT value of 39. Low viral load. Low DNA concentration after amplification. - raw sequence data processing method: - name: raw sequence data processing method + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method description: The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. @@ -4694,8 +4763,8 @@ slots: recommended: true examples: - value: Porechop 0.2.3 - dehosting method: - name: dehosting method + dehosting_method: + name: dehosting_method title: dehosting method description: The method used to remove host reads from the pathogen sequence. comments: Provide the name and version number of the software used to remove host @@ -4707,8 +4776,8 @@ slots: recommended: true examples: - value: Nanostripper - sequence assembly software name: - name: sequence assembly software name + sequence_assembly_software_name: + name: sequence_assembly_software_name title: sequence assembly software name description: The name of the software used to assemble a sequence. comments: Provide the name of the software used to assemble the sequence. @@ -4718,8 +4787,8 @@ slots: - range: null value menu examples: - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet - sequence assembly software version: - name: sequence assembly software version + sequence_assembly_software_version: + name: sequence_assembly_software_version title: sequence assembly software version description: The version of the software used to assemble a sequence. comments: Provide the version of the software used to assemble the sequence. @@ -4729,8 +4798,8 @@ slots: - range: null value menu examples: - value: 3.15.5 - consensus sequence software name: - name: consensus sequence software name + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name description: The name of the software used to generate the consensus sequence. comments: Provide the name of the software used to generate the consensus sequence. @@ -4740,8 +4809,8 @@ slots: - range: null value menu examples: - value: iVar - consensus sequence software version: - name: consensus sequence software version + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version description: The version of the software used to generate the consensus sequence. comments: Provide the version of the software used to generate the consensus sequence. @@ -4751,8 +4820,8 @@ slots: - range: null value menu examples: - value: '1.3' - breadth of coverage value: - name: breadth of coverage value + breadth_of_coverage_value: + name: breadth_of_coverage_value title: breadth of coverage value description: The percentage of the reference genome covered by the sequenced data, to a prescribed depth. @@ -4761,8 +4830,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '95' - depth of coverage value: - name: depth of coverage value + depth_of_coverage_value: + name: depth_of_coverage_value title: depth of coverage value description: The average number of reads representing a given nucleotide in the reconstructed sequence. @@ -4771,8 +4840,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '400' - depth of coverage threshold: - name: depth of coverage threshold + depth_of_coverage_threshold: + name: depth_of_coverage_threshold title: depth of coverage threshold description: The threshold used as a cut-off for the depth of coverage. comments: Provide the threshold fold coverage. @@ -4780,8 +4849,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '100' - genome completeness: - name: genome completeness + genome_completeness: + name: genome_completeness title: genome completeness description: The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. @@ -4790,8 +4859,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '85' - number of base pairs sequenced: - name: number of base pairs sequenced + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced title: number of base pairs sequenced description: The number of total base pairs generated by the sequencing process. comments: Provide a numerical value (no need to include units). @@ -4799,8 +4868,8 @@ slots: range: integer examples: - value: '387566' - number of total reads: - name: number of total reads + number_of_total_reads: + name: number_of_total_reads title: number of total reads description: The total number of non-unique reads generated by the sequencing process. @@ -4809,8 +4878,8 @@ slots: range: integer examples: - value: '423867' - number of unique reads: - name: number of unique reads + number_of_unique_reads: + name: number_of_unique_reads title: number of unique reads description: The number of unique reads generated by the sequencing process. comments: Provide a numerical value (no need to include units). @@ -4818,8 +4887,8 @@ slots: range: integer examples: - value: '248236' - minimum post-trimming read length: - name: minimum post-trimming read length + minimum_posttrimming_read_length: + name: minimum_posttrimming_read_length title: minimum post-trimming read length description: The threshold used as a cut-off for the minimum length of a read after trimming. @@ -4828,8 +4897,8 @@ slots: range: integer examples: - value: '150' - number of contigs: - name: number of contigs + number_of_contigs: + name: number_of_contigs title: number of contigs description: The number of contigs (contiguous sequences) in a sequence assembly. comments: Provide a numerical value. @@ -4837,8 +4906,8 @@ slots: range: integer examples: - value: '10' - percent Ns across total genome length: - name: percent Ns across total genome length + percent_ns_across_total_genome_length: + name: percent_ns_across_total_genome_length title: percent Ns across total genome length description: The percentage of the assembly that consists of ambiguous bases (Ns). comments: Provide a numerical value (no need to include units). @@ -4846,8 +4915,8 @@ slots: range: integer examples: - value: '2' - Ns per 100 kbp: - name: Ns per 100 kbp + ns_per_100_kbp: + name: ns_per_100_kbp title: Ns per 100 kbp description: The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). @@ -4856,8 +4925,8 @@ slots: range: integer examples: - value: '342' - N50: - name: N50 + n50: + name: n50 title: N50 description: The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. @@ -4866,8 +4935,8 @@ slots: range: integer examples: - value: '150' - percent read contamination: - name: percent read contamination + percent_read_contamination_: + name: percent_read_contamination_ title: percent read contamination description: The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. @@ -4876,8 +4945,8 @@ slots: range: integer examples: - value: '2' - sequence assembly length: - name: sequence assembly length + sequence_assembly_length: + name: sequence_assembly_length title: sequence assembly length description: The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. @@ -4886,8 +4955,8 @@ slots: range: integer examples: - value: '34272' - consensus genome length: - name: consensus genome length + consensus_genome_length: + name: consensus_genome_length title: consensus genome length description: The length of the genome defined by the most common nucleotides at each position. @@ -4896,8 +4965,8 @@ slots: range: integer examples: - value: '38677' - reference genome accession: - name: reference genome accession + reference_genome_accession: + name: reference_genome_accession title: reference genome accession description: A persistent, unique identifier of a genome database entry. comments: Provide the accession number of the reference genome. @@ -4905,8 +4974,8 @@ slots: range: WhitespaceMinimizedString examples: - value: NC_045512.2 - deduplication method: - name: deduplication method + deduplication_method: + name: deduplication_method title: deduplication method description: The method used to remove duplicated reads in a sequence read dataset. comments: Provide the deduplication software name followed by the version, or @@ -4915,8 +4984,8 @@ slots: range: WhitespaceMinimizedString examples: - value: DeDup 0.12.8 - bioinformatics protocol: - name: bioinformatics protocol + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Further details regarding the methods used to process raw data, and/or @@ -4927,8 +4996,8 @@ slots: range: WhitespaceMinimizedString examples: - value: https://github.com/phac-nml/ncov2019-artic-nf - read mapping software name: - name: read mapping software name + read_mapping_software_name: + name: read_mapping_software_name title: read mapping software name description: The name of the software used to map sequence reads to a reference genome or set of reference genes. @@ -4937,8 +5006,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Bowtie2, BWA-MEM, TopHat - read mapping software version: - name: read mapping software version + read_mapping_software_version: + name: read_mapping_software_version title: read mapping software version description: The version of the software used to map sequence reads to a reference genome or set of reference genes. @@ -4947,8 +5016,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 2.5.1 - taxonomic reference database name: - name: taxonomic reference database name + taxonomic_reference_database_name: + name: taxonomic_reference_database_name title: taxonomic reference database name description: The name of the taxonomic reference database used to identify the organism. @@ -4957,8 +5026,8 @@ slots: range: WhitespaceMinimizedString examples: - value: NCBITaxon - taxonomic reference database version: - name: taxonomic reference database version + taxonomic_reference_database_version: + name: taxonomic_reference_database_version title: taxonomic reference database version description: The version of the taxonomic reference database used to identify the organism. @@ -4967,8 +5036,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '1.3' - taxonomic analysis report filename: - name: taxonomic analysis report filename + taxonomic_analysis_report_filename: + name: taxonomic_analysis_report_filename title: taxonomic analysis report filename description: The filename of the report containing the results of a taxonomic analysis. @@ -4978,8 +5047,8 @@ slots: range: WhitespaceMinimizedString examples: - value: WWtax_report_Feb1_2024.doc - taxonomic analysis date: - name: taxonomic analysis date + taxonomic_analysis_date: + name: taxonomic_analysis_date title: taxonomic analysis date description: The date a taxonomic analysis was performed. comments: Providing the date that an analyis was performed can help provide context @@ -4989,8 +5058,8 @@ slots: range: date examples: - value: '2024-02-01' - read mapping criteria: - name: read mapping criteria + read_mapping_criteria: + name: read_mapping_criteria title: read mapping criteria description: A description of the criteria used to map reads to a reference sequence. comments: Provide a description of the read mapping criteria. @@ -5035,8 +5104,8 @@ slots: range: WhitespaceMinimizedString examples: - value: RespLab@lab.ca - publication_ID: - name: publication_ID + publication_id: + name: publication_id title: publication_ID description: The identifier for a publication. comments: If the isolate is associated with a published work which can provide @@ -5075,6 +5144,7 @@ slots: - value: PRJNA12345 exact_mappings: - BIOSAMPLE:bioproject_accession + - NCBI_BIOSAMPLE_Enterics:bioproject_accession biosample_accession: name: biosample_accession title: biosample_accession @@ -5085,8 +5155,10 @@ slots: range: WhitespaceMinimizedString examples: - value: SAMN14180202 - SRA_accession: - name: SRA_accession + exact_mappings: + - ENA_ANTIBIOGRAM:bioSample_ID + sra_accession: + name: sra_accession title: SRA_accession description: The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological @@ -5097,8 +5169,8 @@ slots: range: WhitespaceMinimizedString examples: - value: SRR11177792 - GenBank_accession: - name: GenBank_accession + genbank_accession: + name: genbank_accession title: GenBank_accession description: The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. @@ -5166,6 +5238,8 @@ slots: recommended: true examples: - value: Vaccination [NCIT:C15346] + exact_mappings: + - NCBI_BIOSAMPLE_Enterics:upstream_intervention experiment_intervention_details: name: experiment_intervention_details title: experiment_intervention_details @@ -5178,8 +5252,8 @@ slots: recommended: true examples: - value: 2% cranberry solution mixed in feed - AMR_testing_by: - name: AMR_testing_by + amr_testing_by: + name: amr_testing_by title: AMR_testing_by description: The name of the organization that performed the antimicrobial resistance testing. @@ -5193,8 +5267,8 @@ slots: required: true examples: - value: Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - AMR_testing_by_laboratory_name: - name: AMR_testing_by_laboratory_name + amr_testing_by_laboratory_name: + name: amr_testing_by_laboratory_name title: AMR_testing_by_laboratory_name description: The name of the lab within the organization that performed the antimicrobial resistance testing. @@ -5205,8 +5279,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Topp Lab - AMR_testing_by_contact_name: - name: AMR_testing_by_contact_name + amr_testing_by_contact_name: + name: amr_testing_by_contact_name title: AMR_testing_by_contact_name description: The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. @@ -5222,8 +5296,8 @@ slots: required: true examples: - value: Enterics Lab Manager - AMR_testing_by_contact_email: - name: AMR_testing_by_contact_email + amr_testing_by_contact_email: + name: amr_testing_by_contact_email title: AMR_testing_by_contact_email description: The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. @@ -5239,8 +5313,8 @@ slots: required: true examples: - value: johnnyblogs@lab.ca - AMR_testing_date: - name: AMR_testing_date + amr_testing_date: + name: amr_testing_date title: AMR_testing_date description: The date the antimicrobial resistance testing was performed. comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" @@ -5261,6 +5335,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype amikacin_measurement: name: amikacin_measurement title: amikacin_measurement @@ -5273,6 +5349,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement amikacin_measurement_units: name: amikacin_measurement_units title: amikacin_measurement_units @@ -5285,6 +5363,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units amikacin_measurement_sign: name: amikacin_measurement_sign title: amikacin_measurement_sign @@ -5297,6 +5377,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign amikacin_laboratory_typing_method: name: amikacin_laboratory_typing_method title: amikacin_laboratory_typing_method @@ -5308,6 +5390,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method amikacin_laboratory_typing_platform: name: amikacin_laboratory_typing_platform title: amikacin_laboratory_typing_platform @@ -5319,6 +5403,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform amikacin_laboratory_typing_platform_version: name: amikacin_laboratory_typing_platform_version title: amikacin_laboratory_typing_platform_version @@ -5339,6 +5425,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor amikacin_testing_standard: name: amikacin_testing_standard title: amikacin_testing_standard @@ -5350,6 +5438,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard amikacin_testing_standard_version: name: amikacin_testing_standard_version title: amikacin_testing_standard_version @@ -5400,8 +5490,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - amoxicillin-clavulanic_acid_resistance_phenotype: - name: amoxicillin-clavulanic_acid_resistance_phenotype + amoxicillinclavulanic_acid_resistance_phenotype: + name: amoxicillinclavulanic_acid_resistance_phenotype title: amoxicillin-clavulanic_acid_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -5412,8 +5502,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - amoxicillin-clavulanic_acid_measurement: - name: amoxicillin-clavulanic_acid_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + amoxicillinclavulanic_acid_measurement: + name: amoxicillinclavulanic_acid_measurement title: amoxicillin-clavulanic_acid_measurement description: The measured value of amoxicillin-clavulanic acid resistance. comments: This field should only contain a number (either an integer or a number @@ -5424,8 +5516,10 @@ slots: required: true examples: - value: '4' - amoxicillin-clavulanic_acid_measurement_units: - name: amoxicillin-clavulanic_acid_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + amoxicillinclavulanic_acid_measurement_units: + name: amoxicillinclavulanic_acid_measurement_units title: amoxicillin-clavulanic_acid_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -5436,8 +5530,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - amoxicillin-clavulanic_acid_measurement_sign: - name: amoxicillin-clavulanic_acid_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + amoxicillinclavulanic_acid_measurement_sign: + name: amoxicillinclavulanic_acid_measurement_sign title: amoxicillin-clavulanic_acid_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -5448,8 +5544,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - amoxicillin-clavulanic_acid_laboratory_typing_method: - name: amoxicillin-clavulanic_acid_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + amoxicillinclavulanic_acid_laboratory_typing_method: + name: amoxicillinclavulanic_acid_laboratory_typing_method title: amoxicillin-clavulanic_acid_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -5459,8 +5557,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - amoxicillin-clavulanic_acid_laboratory_typing_platform: - name: amoxicillin-clavulanic_acid_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + amoxicillinclavulanic_acid_laboratory_typing_platform: + name: amoxicillinclavulanic_acid_laboratory_typing_platform title: amoxicillin-clavulanic_acid_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -5470,8 +5570,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - amoxicillin-clavulanic_acid_laboratory_typing_platform_version: - name: amoxicillin-clavulanic_acid_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + amoxicillinclavulanic_acid_laboratory_typing_platform_version: + name: amoxicillinclavulanic_acid_laboratory_typing_platform_version title: amoxicillin-clavulanic_acid_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -5480,8 +5582,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - amoxicillin-clavulanic_acid_vendor_name: - name: amoxicillin-clavulanic_acid_vendor_name + amoxicillinclavulanic_acid_vendor_name: + name: amoxicillinclavulanic_acid_vendor_name title: amoxicillin-clavulanic_acid_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -5490,8 +5592,10 @@ slots: - range: null value menu examples: - value: Sensititre - amoxicillin-clavulanic_acid_testing_standard: - name: amoxicillin-clavulanic_acid_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + amoxicillinclavulanic_acid_testing_standard: + name: amoxicillinclavulanic_acid_testing_standard title: amoxicillin-clavulanic_acid_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -5501,8 +5605,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - amoxicillin-clavulanic_acid_testing_standard_version: - name: amoxicillin-clavulanic_acid_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + amoxicillinclavulanic_acid_testing_standard_version: + name: amoxicillinclavulanic_acid_testing_standard_version title: amoxicillin-clavulanic_acid_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -5511,8 +5617,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - amoxicillin-clavulanic_acid_testing_standard_details: - name: amoxicillin-clavulanic_acid_testing_standard_details + amoxicillinclavulanic_acid_testing_standard_details: + name: amoxicillinclavulanic_acid_testing_standard_details title: amoxicillin-clavulanic_acid_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -5522,8 +5628,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - amoxicillin-clavulanic_acid_susceptible_breakpoint: - name: amoxicillin-clavulanic_acid_susceptible_breakpoint + amoxicillinclavulanic_acid_susceptible_breakpoint: + name: amoxicillinclavulanic_acid_susceptible_breakpoint title: amoxicillin-clavulanic_acid_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -5532,8 +5638,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - amoxicillin-clavulanic_acid_intermediate_breakpoint: - name: amoxicillin-clavulanic_acid_intermediate_breakpoint + amoxicillinclavulanic_acid_intermediate_breakpoint: + name: amoxicillinclavulanic_acid_intermediate_breakpoint title: amoxicillin-clavulanic_acid_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -5541,8 +5647,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - amoxicillin-clavulanic_acid_resistant_breakpoint: - name: amoxicillin-clavulanic_acid_resistant_breakpoint + amoxicillinclavulanic_acid_resistant_breakpoint: + name: amoxicillinclavulanic_acid_resistant_breakpoint title: amoxicillin-clavulanic_acid_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -5563,6 +5669,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype ampicillin_measurement: name: ampicillin_measurement title: ampicillin_measurement @@ -5575,6 +5683,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement ampicillin_measurement_units: name: ampicillin_measurement_units title: ampicillin_measurement_units @@ -5587,6 +5697,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units ampicillin_measurement_sign: name: ampicillin_measurement_sign title: ampicillin_measurement_sign @@ -5599,6 +5711,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign ampicillin_laboratory_typing_method: name: ampicillin_laboratory_typing_method title: ampicillin_laboratory_typing_method @@ -5610,6 +5724,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method ampicillin_laboratory_typing_platform: name: ampicillin_laboratory_typing_platform title: ampicillin_laboratory_typing_platform @@ -5621,6 +5737,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform ampicillin_laboratory_typing_platform_version: name: ampicillin_laboratory_typing_platform_version title: ampicillin_laboratory_typing_platform_version @@ -5641,6 +5759,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor ampicillin_testing_standard: name: ampicillin_testing_standard title: ampicillin_testing_standard @@ -5652,6 +5772,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard ampicillin_testing_standard_version: name: ampicillin_testing_standard_version title: ampicillin_testing_standard_version @@ -5714,6 +5836,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype azithromycin_measurement: name: azithromycin_measurement title: azithromycin_measurement @@ -5726,6 +5850,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement azithromycin_measurement_units: name: azithromycin_measurement_units title: azithromycin_measurement_units @@ -5738,6 +5864,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units azithromycin_measurement_sign: name: azithromycin_measurement_sign title: azithromycin_measurement_sign @@ -5750,6 +5878,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign azithromycin_laboratory_typing_method: name: azithromycin_laboratory_typing_method title: azithromycin_laboratory_typing_method @@ -5761,6 +5891,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method azithromycin_laboratory_typing_platform: name: azithromycin_laboratory_typing_platform title: azithromycin_laboratory_typing_platform @@ -5772,6 +5904,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform azithromycin_laboratory_typing_platform_version: name: azithromycin_laboratory_typing_platform_version title: azithromycin_laboratory_typing_platform_version @@ -5792,6 +5926,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor azithromycin_testing_standard: name: azithromycin_testing_standard title: azithromycin_testing_standard @@ -5803,6 +5939,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard azithromycin_testing_standard_version: name: azithromycin_testing_standard_version title: azithromycin_testing_standard_version @@ -5865,6 +6003,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype cefazolin_measurement: name: cefazolin_measurement title: cefazolin_measurement @@ -5877,6 +6017,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement cefazolin_measurement_units: name: cefazolin_measurement_units title: cefazolin_measurement_units @@ -5889,6 +6031,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units cefazolin_measurement_sign: name: cefazolin_measurement_sign title: cefazolin_measurement_sign @@ -5901,6 +6045,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign cefazolin_laboratory_typing_method: name: cefazolin_laboratory_typing_method title: cefazolin_laboratory_typing_method @@ -5912,6 +6058,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method cefazolin_laboratory_typing_platform: name: cefazolin_laboratory_typing_platform title: cefazolin_laboratory_typing_platform @@ -5923,6 +6071,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform cefazolin_laboratory_typing_platform_version: name: cefazolin_laboratory_typing_platform_version title: cefazolin_laboratory_typing_platform_version @@ -5943,6 +6093,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor cefazolin_testing_standard: name: cefazolin_testing_standard title: cefazolin_testing_standard @@ -5954,6 +6106,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard cefazolin_testing_standard_version: name: cefazolin_testing_standard_version title: cefazolin_testing_standard_version @@ -6016,6 +6170,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype cefepime_measurement: name: cefepime_measurement title: cefepime_measurement @@ -6028,6 +6184,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement cefepime_measurement_units: name: cefepime_measurement_units title: cefepime_measurement_units @@ -6040,6 +6198,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units cefepime_measurement_sign: name: cefepime_measurement_sign title: cefepime_measurement_sign @@ -6052,6 +6212,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign cefepime_laboratory_typing_method: name: cefepime_laboratory_typing_method title: cefepime_laboratory_typing_method @@ -6063,6 +6225,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method cefepime_laboratory_typing_platform: name: cefepime_laboratory_typing_platform title: cefepime_laboratory_typing_platform @@ -6074,6 +6238,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform cefepime_laboratory_typing_platform_version: name: cefepime_laboratory_typing_platform_version title: cefepime_laboratory_typing_platform_version @@ -6094,6 +6260,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor cefepime_testing_standard: name: cefepime_testing_standard title: cefepime_testing_standard @@ -6105,6 +6273,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard cefepime_testing_standard_version: name: cefepime_testing_standard_version title: cefepime_testing_standard_version @@ -6167,6 +6337,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype cefotaxime_measurement: name: cefotaxime_measurement title: cefotaxime_measurement @@ -6179,6 +6351,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement cefotaxime_measurement_units: name: cefotaxime_measurement_units title: cefotaxime_measurement_units @@ -6191,6 +6365,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units cefotaxime_measurement_sign: name: cefotaxime_measurement_sign title: cefotaxime_measurement_sign @@ -6203,6 +6379,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign cefotaxime_laboratory_typing_method: name: cefotaxime_laboratory_typing_method title: cefotaxime_laboratory_typing_method @@ -6214,6 +6392,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method cefotaxime_laboratory_typing_platform: name: cefotaxime_laboratory_typing_platform title: cefotaxime_laboratory_typing_platform @@ -6225,6 +6405,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform cefotaxime_laboratory_typing_platform_version: name: cefotaxime_laboratory_typing_platform_version title: cefotaxime_laboratory_typing_platform_version @@ -6245,6 +6427,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor cefotaxime_testing_standard: name: cefotaxime_testing_standard title: cefotaxime_testing_standard @@ -6256,6 +6440,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard cefotaxime_testing_standard_version: name: cefotaxime_testing_standard_version title: cefotaxime_testing_standard_version @@ -6306,8 +6492,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - cefotaxime-clavulanic_acid_resistance_phenotype: - name: cefotaxime-clavulanic_acid_resistance_phenotype + cefotaximeclavulanic_acid_resistance_phenotype: + name: cefotaximeclavulanic_acid_resistance_phenotype title: cefotaxime-clavulanic_acid_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -6318,8 +6504,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - cefotaxime-clavulanic_acid_measurement: - name: cefotaxime-clavulanic_acid_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + cefotaximeclavulanic_acid_measurement: + name: cefotaximeclavulanic_acid_measurement title: cefotaxime-clavulanic_acid_measurement description: The measured value of cefotaxime-clavulanic acid resistance. comments: This field should only contain a number (either an integer or a number @@ -6330,8 +6518,10 @@ slots: required: true examples: - value: '4' - cefotaxime-clavulanic_acid_measurement_units: - name: cefotaxime-clavulanic_acid_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + cefotaximeclavulanic_acid_measurement_units: + name: cefotaximeclavulanic_acid_measurement_units title: cefotaxime-clavulanic_acid_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -6342,8 +6532,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - cefotaxime-clavulanic_acid_measurement_sign: - name: cefotaxime-clavulanic_acid_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + cefotaximeclavulanic_acid_measurement_sign: + name: cefotaximeclavulanic_acid_measurement_sign title: cefotaxime-clavulanic_acid_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -6354,8 +6546,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - cefotaxime-clavulanic_acid_laboratory_typing_method: - name: cefotaxime-clavulanic_acid_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + cefotaximeclavulanic_acid_laboratory_typing_method: + name: cefotaximeclavulanic_acid_laboratory_typing_method title: cefotaxime-clavulanic_acid_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -6365,8 +6559,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - cefotaxime-clavulanic_acid_laboratory_typing_platform: - name: cefotaxime-clavulanic_acid_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + cefotaximeclavulanic_acid_laboratory_typing_platform: + name: cefotaximeclavulanic_acid_laboratory_typing_platform title: cefotaxime-clavulanic_acid_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -6376,8 +6572,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - cefotaxime-clavulanic_acid_laboratory_typing_platform_version: - name: cefotaxime-clavulanic_acid_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + cefotaximeclavulanic_acid_laboratory_typing_platform_version: + name: cefotaximeclavulanic_acid_laboratory_typing_platform_version title: cefotaxime-clavulanic_acid_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -6386,8 +6584,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - cefotaxime-clavulanic_acid_vendor_name: - name: cefotaxime-clavulanic_acid_vendor_name + cefotaximeclavulanic_acid_vendor_name: + name: cefotaximeclavulanic_acid_vendor_name title: cefotaxime-clavulanic_acid_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -6396,8 +6594,10 @@ slots: - range: null value menu examples: - value: Sensititre - cefotaxime-clavulanic_acid_testing_standard: - name: cefotaxime-clavulanic_acid_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + cefotaximeclavulanic_acid_testing_standard: + name: cefotaximeclavulanic_acid_testing_standard title: cefotaxime-clavulanic_acid_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -6407,8 +6607,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - cefotaxime-clavulanic_acid_testing_standard_version: - name: cefotaxime-clavulanic_acid_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + cefotaximeclavulanic_acid_testing_standard_version: + name: cefotaximeclavulanic_acid_testing_standard_version title: cefotaxime-clavulanic_acid_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -6417,8 +6619,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - cefotaxime-clavulanic_acid_testing_standard_details: - name: cefotaxime-clavulanic_acid_testing_standard_details + cefotaximeclavulanic_acid_testing_standard_details: + name: cefotaximeclavulanic_acid_testing_standard_details title: cefotaxime-clavulanic_acid_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -6428,8 +6630,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - cefotaxime-clavulanic_acid_susceptible_breakpoint: - name: cefotaxime-clavulanic_acid_susceptible_breakpoint + cefotaximeclavulanic_acid_susceptible_breakpoint: + name: cefotaximeclavulanic_acid_susceptible_breakpoint title: cefotaxime-clavulanic_acid_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -6438,8 +6640,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - cefotaxime-clavulanic_acid_intermediate_breakpoint: - name: cefotaxime-clavulanic_acid_intermediate_breakpoint + cefotaximeclavulanic_acid_intermediate_breakpoint: + name: cefotaximeclavulanic_acid_intermediate_breakpoint title: cefotaxime-clavulanic_acid_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -6447,8 +6649,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - cefotaxime-clavulanic_acid_resistant_breakpoint: - name: cefotaxime-clavulanic_acid_resistant_breakpoint + cefotaximeclavulanic_acid_resistant_breakpoint: + name: cefotaximeclavulanic_acid_resistant_breakpoint title: cefotaxime-clavulanic_acid_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -6469,6 +6671,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype cefoxitin_measurement: name: cefoxitin_measurement title: cefoxitin_measurement @@ -6481,6 +6685,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement cefoxitin_measurement_units: name: cefoxitin_measurement_units title: cefoxitin_measurement_units @@ -6493,6 +6699,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units cefoxitin_measurement_sign: name: cefoxitin_measurement_sign title: cefoxitin_measurement_sign @@ -6505,6 +6713,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign cefoxitin_laboratory_typing_method: name: cefoxitin_laboratory_typing_method title: cefoxitin_laboratory_typing_method @@ -6516,6 +6726,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method cefoxitin_laboratory_typing_platform: name: cefoxitin_laboratory_typing_platform title: cefoxitin_laboratory_typing_platform @@ -6527,6 +6739,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform cefoxitin_laboratory_typing_platform_version: name: cefoxitin_laboratory_typing_platform_version title: cefoxitin_laboratory_typing_platform_version @@ -6547,6 +6761,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor cefoxitin_testing_standard: name: cefoxitin_testing_standard title: cefoxitin_testing_standard @@ -6558,6 +6774,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard cefoxitin_testing_standard_version: name: cefoxitin_testing_standard_version title: cefoxitin_testing_standard_version @@ -6620,6 +6838,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype cefpodoxime_measurement: name: cefpodoxime_measurement title: cefpodoxime_measurement @@ -6632,6 +6852,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement cefpodoxime_measurement_units: name: cefpodoxime_measurement_units title: cefpodoxime_measurement_units @@ -6644,6 +6866,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units cefpodoxime_measurement_sign: name: cefpodoxime_measurement_sign title: cefpodoxime_measurement_sign @@ -6656,6 +6880,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign cefpodoxime_laboratory_typing_method: name: cefpodoxime_laboratory_typing_method title: cefpodoxime_laboratory_typing_method @@ -6667,6 +6893,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method cefpodoxime_laboratory_typing_platform: name: cefpodoxime_laboratory_typing_platform title: cefpodoxime_laboratory_typing_platform @@ -6678,6 +6906,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform cefpodoxime_laboratory_typing_platform_version: name: cefpodoxime_laboratory_typing_platform_version title: cefpodoxime_laboratory_typing_platform_version @@ -6698,6 +6928,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor cefpodoxime_testing_standard: name: cefpodoxime_testing_standard title: cefpodoxime_testing_standard @@ -6709,6 +6941,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard cefpodoxime_testing_standard_version: name: cefpodoxime_testing_standard_version title: cefpodoxime_testing_standard_version @@ -6771,6 +7005,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype ceftazidime_measurement: name: ceftazidime_measurement title: ceftazidime_measurement @@ -6783,6 +7019,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement ceftazidime_measurement_units: name: ceftazidime_measurement_units title: ceftazidime_measurement_units @@ -6795,6 +7033,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units ceftazidime_measurement_sign: name: ceftazidime_measurement_sign title: ceftazidime_measurement_sign @@ -6807,6 +7047,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign ceftazidime_laboratory_typing_method: name: ceftazidime_laboratory_typing_method title: ceftazidime_laboratory_typing_method @@ -6818,6 +7060,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method ceftazidime_laboratory_typing_platform: name: ceftazidime_laboratory_typing_platform title: ceftazidime_laboratory_typing_platform @@ -6829,6 +7073,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform ceftazidime_laboratory_typing_platform_version: name: ceftazidime_laboratory_typing_platform_version title: ceftazidime_laboratory_typing_platform_version @@ -6849,6 +7095,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor ceftazidime_testing_standard: name: ceftazidime_testing_standard title: ceftazidime_testing_standard @@ -6860,6 +7108,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard ceftazidime_testing_standard_version: name: ceftazidime_testing_standard_version title: ceftazidime_testing_standard_version @@ -6910,8 +7160,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - ceftazidime-clavulanic_acid_resistance_phenotype: - name: ceftazidime-clavulanic_acid_resistance_phenotype + ceftazidimeclavulanic_acid_resistance_phenotype: + name: ceftazidimeclavulanic_acid_resistance_phenotype title: ceftazidime-clavulanic_acid_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -6922,8 +7172,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - ceftazidime-clavulanic_acid_measurement: - name: ceftazidime-clavulanic_acid_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + ceftazidimeclavulanic_acid_measurement: + name: ceftazidimeclavulanic_acid_measurement title: ceftazidime-clavulanic_acid_measurement description: The measured value of ceftazidime-clavulanic acid resistance. comments: This field should only contain a number (either an integer or a number @@ -6934,8 +7186,10 @@ slots: required: true examples: - value: '4' - ceftazidime-clavulanic_acid_measurement_units: - name: ceftazidime-clavulanic_acid_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + ceftazidimeclavulanic_acid_measurement_units: + name: ceftazidimeclavulanic_acid_measurement_units title: ceftazidime-clavulanic_acid_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -6946,8 +7200,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - ceftazidime-clavulanic_acid_measurement_sign: - name: ceftazidime-clavulanic_acid_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + ceftazidimeclavulanic_acid_measurement_sign: + name: ceftazidimeclavulanic_acid_measurement_sign title: ceftazidime-clavulanic_acid_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -6958,8 +7214,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - ceftazidime-clavulanic_acid_laboratory_typing_method: - name: ceftazidime-clavulanic_acid_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + ceftazidimeclavulanic_acid_laboratory_typing_method: + name: ceftazidimeclavulanic_acid_laboratory_typing_method title: ceftazidime-clavulanic_acid_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -6969,8 +7227,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - ceftazidime-clavulanic_acid_laboratory_typing_platform: - name: ceftazidime-clavulanic_acid_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + ceftazidimeclavulanic_acid_laboratory_typing_platform: + name: ceftazidimeclavulanic_acid_laboratory_typing_platform title: ceftazidime-clavulanic_acid_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -6980,8 +7240,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - ceftazidime-clavulanic_acid_laboratory_typing_platform_version: - name: ceftazidime-clavulanic_acid_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + ceftazidimeclavulanic_acid_laboratory_typing_platform_version: + name: ceftazidimeclavulanic_acid_laboratory_typing_platform_version title: ceftazidime-clavulanic_acid_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -6990,8 +7252,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - ceftazidime-clavulanic_acid_vendor_name: - name: ceftazidime-clavulanic_acid_vendor_name + ceftazidimeclavulanic_acid_vendor_name: + name: ceftazidimeclavulanic_acid_vendor_name title: ceftazidime-clavulanic_acid_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -7000,8 +7262,10 @@ slots: - range: null value menu examples: - value: Sensititre - ceftazidime-clavulanic_acid_testing_standard: - name: ceftazidime-clavulanic_acid_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + ceftazidimeclavulanic_acid_testing_standard: + name: ceftazidimeclavulanic_acid_testing_standard title: ceftazidime-clavulanic_acid_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -7011,8 +7275,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - ceftazidime-clavulanic_acid_testing_standard_version: - name: ceftazidime-clavulanic_acid_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + ceftazidimeclavulanic_acid_testing_standard_version: + name: ceftazidimeclavulanic_acid_testing_standard_version title: ceftazidime-clavulanic_acid_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -7021,8 +7287,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - ceftazidime-clavulanic_acid_testing_standard_details: - name: ceftazidime-clavulanic_acid_testing_standard_details + ceftazidimeclavulanic_acid_testing_standard_details: + name: ceftazidimeclavulanic_acid_testing_standard_details title: ceftazidime-clavulanic_acid_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -7032,8 +7298,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - ceftazidime-clavulanic_acid_susceptible_breakpoint: - name: ceftazidime-clavulanic_acid_susceptible_breakpoint + ceftazidimeclavulanic_acid_susceptible_breakpoint: + name: ceftazidimeclavulanic_acid_susceptible_breakpoint title: ceftazidime-clavulanic_acid_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -7042,8 +7308,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - ceftazidime-clavulanic_acid_intermediate_breakpoint: - name: ceftazidime-clavulanic_acid_intermediate_breakpoint + ceftazidimeclavulanic_acid_intermediate_breakpoint: + name: ceftazidimeclavulanic_acid_intermediate_breakpoint title: ceftazidime-clavulanic_acid_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -7051,8 +7317,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - ceftazidime-clavulanic_acid_resistant_breakpoint: - name: ceftazidime-clavulanic_acid_resistant_breakpoint + ceftazidimeclavulanic_acid_resistant_breakpoint: + name: ceftazidimeclavulanic_acid_resistant_breakpoint title: ceftazidime-clavulanic_acid_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -7073,6 +7339,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype ceftiofur_measurement: name: ceftiofur_measurement title: ceftiofur_measurement @@ -7085,6 +7353,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement ceftiofur_measurement_units: name: ceftiofur_measurement_units title: ceftiofur_measurement_units @@ -7097,6 +7367,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units ceftiofur_measurement_sign: name: ceftiofur_measurement_sign title: ceftiofur_measurement_sign @@ -7109,6 +7381,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign ceftiofur_laboratory_typing_method: name: ceftiofur_laboratory_typing_method title: ceftiofur_laboratory_typing_method @@ -7120,6 +7394,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method ceftiofur_laboratory_typing_platform: name: ceftiofur_laboratory_typing_platform title: ceftiofur_laboratory_typing_platform @@ -7131,6 +7407,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform ceftiofur_laboratory_typing_platform_version: name: ceftiofur_laboratory_typing_platform_version title: ceftiofur_laboratory_typing_platform_version @@ -7151,6 +7429,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor ceftiofur_testing_standard: name: ceftiofur_testing_standard title: ceftiofur_testing_standard @@ -7162,6 +7442,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard ceftiofur_testing_standard_version: name: ceftiofur_testing_standard_version title: ceftiofur_testing_standard_version @@ -7224,6 +7506,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype ceftriaxone_measurement: name: ceftriaxone_measurement title: ceftriaxone_measurement @@ -7236,6 +7520,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement ceftriaxone_measurement_units: name: ceftriaxone_measurement_units title: ceftriaxone_measurement_units @@ -7248,6 +7534,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units ceftriaxone_measurement_sign: name: ceftriaxone_measurement_sign title: ceftriaxone_measurement_sign @@ -7260,6 +7548,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign ceftriaxone_laboratory_typing_method: name: ceftriaxone_laboratory_typing_method title: ceftriaxone_laboratory_typing_method @@ -7271,6 +7561,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method ceftriaxone_laboratory_typing_platform: name: ceftriaxone_laboratory_typing_platform title: ceftriaxone_laboratory_typing_platform @@ -7282,6 +7574,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform ceftriaxone_laboratory_typing_platform_version: name: ceftriaxone_laboratory_typing_platform_version title: ceftriaxone_laboratory_typing_platform_version @@ -7302,6 +7596,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor ceftriaxone_testing_standard: name: ceftriaxone_testing_standard title: ceftriaxone_testing_standard @@ -7313,6 +7609,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard ceftriaxone_testing_standard_version: name: ceftriaxone_testing_standard_version title: ceftriaxone_testing_standard_version @@ -7375,6 +7673,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype cephalothin_measurement: name: cephalothin_measurement title: cephalothin_measurement @@ -7387,6 +7687,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement cephalothin_measurement_units: name: cephalothin_measurement_units title: cephalothin_measurement_units @@ -7399,6 +7701,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units cephalothin_measurement_sign: name: cephalothin_measurement_sign title: cephalothin_measurement_sign @@ -7411,6 +7715,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign cephalothin_laboratory_typing_method: name: cephalothin_laboratory_typing_method title: cephalothin_laboratory_typing_method @@ -7422,6 +7728,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method cephalothin_laboratory_typing_platform: name: cephalothin_laboratory_typing_platform title: cephalothin_laboratory_typing_platform @@ -7433,6 +7741,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform cephalothin_laboratory_typing_platform_version: name: cephalothin_laboratory_typing_platform_version title: cephalothin_laboratory_typing_platform_version @@ -7453,6 +7763,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor cephalothin_testing_standard: name: cephalothin_testing_standard title: cephalothin_testing_standard @@ -7464,6 +7776,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard cephalothin_testing_standard_version: name: cephalothin_testing_standard_version title: cephalothin_testing_standard_version @@ -7526,6 +7840,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype chloramphenicol_measurement: name: chloramphenicol_measurement title: chloramphenicol_measurement @@ -7538,6 +7854,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement chloramphenicol_measurement_units: name: chloramphenicol_measurement_units title: chloramphenicol_measurement_units @@ -7550,6 +7868,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units chloramphenicol_measurement_sign: name: chloramphenicol_measurement_sign title: chloramphenicol_measurement_sign @@ -7562,6 +7882,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign chloramphenicol_laboratory_typing_method: name: chloramphenicol_laboratory_typing_method title: chloramphenicol_laboratory_typing_method @@ -7573,6 +7895,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method chloramphenicol_laboratory_typing_platform: name: chloramphenicol_laboratory_typing_platform title: chloramphenicol_laboratory_typing_platform @@ -7584,6 +7908,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform chloramphenicol_laboratory_typing_platform_version: name: chloramphenicol_laboratory_typing_platform_version title: chloramphenicol_laboratory_typing_platform_version @@ -7604,6 +7930,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor chloramphenicol_testing_standard: name: chloramphenicol_testing_standard title: chloramphenicol_testing_standard @@ -7615,6 +7943,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard chloramphenicol_testing_standard_version: name: chloramphenicol_testing_standard_version title: chloramphenicol_testing_standard_version @@ -7677,6 +8007,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype ciprofloxacin_measurement: name: ciprofloxacin_measurement title: ciprofloxacin_measurement @@ -7689,6 +8021,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement ciprofloxacin_measurement_units: name: ciprofloxacin_measurement_units title: ciprofloxacin_measurement_units @@ -7701,6 +8035,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units ciprofloxacin_measurement_sign: name: ciprofloxacin_measurement_sign title: ciprofloxacin_measurement_sign @@ -7713,6 +8049,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign ciprofloxacin_laboratory_typing_method: name: ciprofloxacin_laboratory_typing_method title: ciprofloxacin_laboratory_typing_method @@ -7724,6 +8062,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method ciprofloxacin_laboratory_typing_platform: name: ciprofloxacin_laboratory_typing_platform title: ciprofloxacin_laboratory_typing_platform @@ -7735,6 +8075,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform ciprofloxacin_laboratory_typing_platform_version: name: ciprofloxacin_laboratory_typing_platform_version title: ciprofloxacin_laboratory_typing_platform_version @@ -7755,6 +8097,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor ciprofloxacin_testing_standard: name: ciprofloxacin_testing_standard title: ciprofloxacin_testing_standard @@ -7766,6 +8110,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard ciprofloxacin_testing_standard_version: name: ciprofloxacin_testing_standard_version title: ciprofloxacin_testing_standard_version @@ -7828,6 +8174,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype clindamycin_measurement: name: clindamycin_measurement title: clindamycin_measurement @@ -7840,6 +8188,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement clindamycin_measurement_units: name: clindamycin_measurement_units title: clindamycin_measurement_units @@ -7852,6 +8202,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units clindamycin_measurement_sign: name: clindamycin_measurement_sign title: clindamycin_measurement_sign @@ -7864,6 +8216,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign clindamycin_laboratory_typing_method: name: clindamycin_laboratory_typing_method title: clindamycin_laboratory_typing_method @@ -7875,6 +8229,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method clindamycin_laboratory_typing_platform: name: clindamycin_laboratory_typing_platform title: clindamycin_laboratory_typing_platform @@ -7886,6 +8242,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform clindamycin_laboratory_typing_platform_version: name: clindamycin_laboratory_typing_platform_version title: clindamycin_laboratory_typing_platform_version @@ -7906,6 +8264,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor clindamycin_testing_standard: name: clindamycin_testing_standard title: clindamycin_testing_standard @@ -7917,6 +8277,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard clindamycin_testing_standard_version: name: clindamycin_testing_standard_version title: clindamycin_testing_standard_version @@ -7979,6 +8341,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype doxycycline_measurement: name: doxycycline_measurement title: doxycycline_measurement @@ -7991,6 +8355,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement doxycycline_measurement_units: name: doxycycline_measurement_units title: doxycycline_measurement_units @@ -8003,6 +8369,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units doxycycline_measurement_sign: name: doxycycline_measurement_sign title: doxycycline_measurement_sign @@ -8015,6 +8383,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign doxycycline_laboratory_typing_method: name: doxycycline_laboratory_typing_method title: doxycycline_laboratory_typing_method @@ -8026,6 +8396,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method doxycycline_laboratory_typing_platform: name: doxycycline_laboratory_typing_platform title: doxycycline_laboratory_typing_platform @@ -8037,6 +8409,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform doxycycline_laboratory_typing_platform_version: name: doxycycline_laboratory_typing_platform_version title: doxycycline_laboratory_typing_platform_version @@ -8057,6 +8431,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor doxycycline_testing_standard: name: doxycycline_testing_standard title: doxycycline_testing_standard @@ -8068,6 +8444,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard doxycycline_testing_standard_version: name: doxycycline_testing_standard_version title: doxycycline_testing_standard_version @@ -8130,6 +8508,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype enrofloxacin_measurement: name: enrofloxacin_measurement title: enrofloxacin_measurement @@ -8142,6 +8522,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement enrofloxacin_measurement_units: name: enrofloxacin_measurement_units title: enrofloxacin_measurement_units @@ -8154,6 +8536,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units enrofloxacin_measurement_sign: name: enrofloxacin_measurement_sign title: enrofloxacin_measurement_sign @@ -8166,6 +8550,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign enrofloxacin_laboratory_typing_method: name: enrofloxacin_laboratory_typing_method title: enrofloxacin_laboratory_typing_method @@ -8177,6 +8563,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method enrofloxacin_laboratory_typing_platform: name: enrofloxacin_laboratory_typing_platform title: enrofloxacin_laboratory_typing_platform @@ -8188,6 +8576,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform enrofloxacin_laboratory_typing_platform_version: name: enrofloxacin_laboratory_typing_platform_version title: enrofloxacin_laboratory_typing_platform_version @@ -8208,6 +8598,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor enrofloxacin_testing_standard: name: enrofloxacin_testing_standard title: enrofloxacin_testing_standard @@ -8219,6 +8611,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard enrofloxacin_testing_standard_version: name: enrofloxacin_testing_standard_version title: enrofloxacin_testing_standard_version @@ -8281,6 +8675,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype erythromycin_measurement: name: erythromycin_measurement title: erythromycin_measurement @@ -8293,6 +8689,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement erythromycin_measurement_units: name: erythromycin_measurement_units title: erythromycin_measurement_units @@ -8305,6 +8703,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units erythromycin_measurement_sign: name: erythromycin_measurement_sign title: erythromycin_measurement_sign @@ -8317,6 +8717,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign erythromycin_laboratory_typing_method: name: erythromycin_laboratory_typing_method title: erythromycin_laboratory_typing_method @@ -8328,6 +8730,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method erythromycin_laboratory_typing_platform: name: erythromycin_laboratory_typing_platform title: erythromycin_laboratory_typing_platform @@ -8339,6 +8743,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform erythromycin_laboratory_typing_platform_version: name: erythromycin_laboratory_typing_platform_version title: erythromycin_laboratory_typing_platform_version @@ -8359,6 +8765,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor erythromycin_testing_standard: name: erythromycin_testing_standard title: erythromycin_testing_standard @@ -8370,6 +8778,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard erythromycin_testing_standard_version: name: erythromycin_testing_standard_version title: erythromycin_testing_standard_version @@ -8432,6 +8842,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype florfenicol_measurement: name: florfenicol_measurement title: florfenicol_measurement @@ -8444,6 +8856,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement florfenicol_measurement_units: name: florfenicol_measurement_units title: florfenicol_measurement_units @@ -8456,6 +8870,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units florfenicol_measurement_sign: name: florfenicol_measurement_sign title: florfenicol_measurement_sign @@ -8468,6 +8884,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign florfenicol_laboratory_typing_method: name: florfenicol_laboratory_typing_method title: florfenicol_laboratory_typing_method @@ -8479,6 +8897,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method florfenicol_laboratory_typing_platform: name: florfenicol_laboratory_typing_platform title: florfenicol_laboratory_typing_platform @@ -8490,6 +8910,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform florfenicol_laboratory_typing_platform_version: name: florfenicol_laboratory_typing_platform_version title: florfenicol_laboratory_typing_platform_version @@ -8510,6 +8932,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor florfenicol_testing_standard: name: florfenicol_testing_standard title: florfenicol_testing_standard @@ -8521,6 +8945,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard florfenicol_testing_standard_version: name: florfenicol_testing_standard_version title: florfenicol_testing_standard_version @@ -8583,6 +9009,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype gentamicin_measurement: name: gentamicin_measurement title: gentamicin_measurement @@ -8595,6 +9023,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement gentamicin_measurement_units: name: gentamicin_measurement_units title: gentamicin_measurement_units @@ -8607,6 +9037,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units gentamicin_measurement_sign: name: gentamicin_measurement_sign title: gentamicin_measurement_sign @@ -8619,6 +9051,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign gentamicin_laboratory_typing_method: name: gentamicin_laboratory_typing_method title: gentamicin_laboratory_typing_method @@ -8630,6 +9064,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method gentamicin_laboratory_typing_platform: name: gentamicin_laboratory_typing_platform title: gentamicin_laboratory_typing_platform @@ -8641,6 +9077,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform gentamicin_laboratory_typing_platform_version: name: gentamicin_laboratory_typing_platform_version title: gentamicin_laboratory_typing_platform_version @@ -8661,6 +9099,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor gentamicin_testing_standard: name: gentamicin_testing_standard title: gentamicin_testing_standard @@ -8672,6 +9112,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard gentamicin_testing_standard_version: name: gentamicin_testing_standard_version title: gentamicin_testing_standard_version @@ -8734,6 +9176,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype imipenem_measurement: name: imipenem_measurement title: imipenem_measurement @@ -8746,6 +9190,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement imipenem_measurement_units: name: imipenem_measurement_units title: imipenem_measurement_units @@ -8758,6 +9204,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units imipenem_measurement_sign: name: imipenem_measurement_sign title: imipenem_measurement_sign @@ -8770,6 +9218,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign imipenem_laboratory_typing_method: name: imipenem_laboratory_typing_method title: imipenem_laboratory_typing_method @@ -8781,6 +9231,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method imipenem_laboratory_typing_platform: name: imipenem_laboratory_typing_platform title: imipenem_laboratory_typing_platform @@ -8792,6 +9244,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform imipenem_laboratory_typing_platform_version: name: imipenem_laboratory_typing_platform_version title: imipenem_laboratory_typing_platform_version @@ -8812,6 +9266,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor imipenem_testing_standard: name: imipenem_testing_standard title: imipenem_testing_standard @@ -8823,6 +9279,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard imipenem_testing_standard_version: name: imipenem_testing_standard_version title: imipenem_testing_standard_version @@ -8885,6 +9343,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype kanamycin_measurement: name: kanamycin_measurement title: kanamycin_measurement @@ -8897,6 +9357,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement kanamycin_measurement_units: name: kanamycin_measurement_units title: kanamycin_measurement_units @@ -8909,6 +9371,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units kanamycin_measurement_sign: name: kanamycin_measurement_sign title: kanamycin_measurement_sign @@ -8921,6 +9385,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign kanamycin_laboratory_typing_method: name: kanamycin_laboratory_typing_method title: kanamycin_laboratory_typing_method @@ -8932,6 +9398,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method kanamycin_laboratory_typing_platform: name: kanamycin_laboratory_typing_platform title: kanamycin_laboratory_typing_platform @@ -8943,6 +9411,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform kanamycin_laboratory_typing_platform_version: name: kanamycin_laboratory_typing_platform_version title: kanamycin_laboratory_typing_platform_version @@ -8963,6 +9433,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor kanamycin_testing_standard: name: kanamycin_testing_standard title: kanamycin_testing_standard @@ -8974,6 +9446,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard kanamycin_testing_standard_version: name: kanamycin_testing_standard_version title: kanamycin_testing_standard_version @@ -9036,6 +9510,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype levofloxacin_measurement: name: levofloxacin_measurement title: levofloxacin_measurement @@ -9048,6 +9524,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement levofloxacin_measurement_units: name: levofloxacin_measurement_units title: levofloxacin_measurement_units @@ -9060,6 +9538,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units levofloxacin_measurement_sign: name: levofloxacin_measurement_sign title: levofloxacin_measurement_sign @@ -9072,6 +9552,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign levofloxacin_laboratory_typing_method: name: levofloxacin_laboratory_typing_method title: levofloxacin_laboratory_typing_method @@ -9083,6 +9565,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method levofloxacin_laboratory_typing_platform: name: levofloxacin_laboratory_typing_platform title: levofloxacin_laboratory_typing_platform @@ -9094,6 +9578,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform levofloxacin_laboratory_typing_platform_version: name: levofloxacin_laboratory_typing_platform_version title: levofloxacin_laboratory_typing_platform_version @@ -9114,6 +9600,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor levofloxacin_testing_standard: name: levofloxacin_testing_standard title: levofloxacin_testing_standard @@ -9125,6 +9613,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard levofloxacin_testing_standard_version: name: levofloxacin_testing_standard_version title: levofloxacin_testing_standard_version @@ -9187,6 +9677,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype linezolid_measurement: name: linezolid_measurement title: linezolid_measurement @@ -9199,6 +9691,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement linezolid_measurement_units: name: linezolid_measurement_units title: linezolid_measurement_units @@ -9211,6 +9705,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units linezolid_measurement_sign: name: linezolid_measurement_sign title: linezolid_measurement_sign @@ -9223,6 +9719,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign linezolid_laboratory_typing_method: name: linezolid_laboratory_typing_method title: linezolid_laboratory_typing_method @@ -9234,6 +9732,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method linezolid_laboratory_typing_platform: name: linezolid_laboratory_typing_platform title: linezolid_laboratory_typing_platform @@ -9245,6 +9745,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform linezolid_laboratory_typing_platform_version: name: linezolid_laboratory_typing_platform_version title: linezolid_laboratory_typing_platform_version @@ -9265,6 +9767,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor linezolid_testing_standard: name: linezolid_testing_standard title: linezolid_testing_standard @@ -9276,6 +9780,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard linezolid_testing_standard_version: name: linezolid_testing_standard_version title: linezolid_testing_standard_version @@ -9338,6 +9844,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype meropenem_measurement: name: meropenem_measurement title: meropenem_measurement @@ -9350,6 +9858,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement meropenem_measurement_units: name: meropenem_measurement_units title: meropenem_measurement_units @@ -9362,6 +9872,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units meropenem_measurement_sign: name: meropenem_measurement_sign title: meropenem_measurement_sign @@ -9374,6 +9886,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign meropenem_laboratory_typing_method: name: meropenem_laboratory_typing_method title: meropenem_laboratory_typing_method @@ -9385,6 +9899,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method meropenem_laboratory_typing_platform: name: meropenem_laboratory_typing_platform title: meropenem_laboratory_typing_platform @@ -9396,6 +9912,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform meropenem_laboratory_typing_platform_version: name: meropenem_laboratory_typing_platform_version title: meropenem_laboratory_typing_platform_version @@ -9416,6 +9934,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor meropenem_testing_standard: name: meropenem_testing_standard title: meropenem_testing_standard @@ -9427,6 +9947,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard meropenem_testing_standard_version: name: meropenem_testing_standard_version title: meropenem_testing_standard_version @@ -9489,6 +10011,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype nalidixic_acid_measurement: name: nalidixic_acid_measurement title: nalidixic_acid_measurement @@ -9501,6 +10025,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement nalidixic_acid_measurement_units: name: nalidixic_acid_measurement_units title: nalidixic_acid_measurement_units @@ -9513,6 +10039,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units nalidixic_acid_measurement_sign: name: nalidixic_acid_measurement_sign title: nalidixic_acid_measurement_sign @@ -9525,6 +10053,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign nalidixic_acid_laboratory_typing_method: name: nalidixic_acid_laboratory_typing_method title: nalidixic_acid_laboratory_typing_method @@ -9536,6 +10066,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method nalidixic_acid_laboratory_typing_platform: name: nalidixic_acid_laboratory_typing_platform title: nalidixic_acid_laboratory_typing_platform @@ -9547,6 +10079,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform nalidixic_acid_laboratory_typing_platform_version: name: nalidixic_acid_laboratory_typing_platform_version title: nalidixic_acid_laboratory_typing_platform_version @@ -9567,6 +10101,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor nalidixic_acid_testing_standard: name: nalidixic_acid_testing_standard title: nalidixic_acid_testing_standard @@ -9578,6 +10114,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard nalidixic_acid_testing_standard_version: name: nalidixic_acid_testing_standard_version title: nalidixic_acid_testing_standard_version @@ -9640,6 +10178,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype nitrofurantoin_measurement: name: nitrofurantoin_measurement title: nitrofurantoin_measurement @@ -9652,6 +10192,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement nitrofurantoin_measurement_units: name: nitrofurantoin_measurement_units title: nitrofurantoin_measurement_units @@ -9664,6 +10206,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units nitrofurantoin_measurement_sign: name: nitrofurantoin_measurement_sign title: nitrofurantoin_measurement_sign @@ -9676,6 +10220,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign nitrofurantoin_laboratory_typing_method: name: nitrofurantoin_laboratory_typing_method title: nitrofurantoin_laboratory_typing_method @@ -9687,6 +10233,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method nitrofurantoin_laboratory_typing_platform: name: nitrofurantoin_laboratory_typing_platform title: nitrofurantoin_laboratory_typing_platform @@ -9698,6 +10246,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform nitrofurantoin_laboratory_typing_platform_version: name: nitrofurantoin_laboratory_typing_platform_version title: nitrofurantoin_laboratory_typing_platform_version @@ -9718,6 +10268,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor nitrofurantoin_testing_standard: name: nitrofurantoin_testing_standard title: nitrofurantoin_testing_standard @@ -9729,6 +10281,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard nitrofurantoin_testing_standard_version: name: nitrofurantoin_testing_standard_version title: nitrofurantoin_testing_standard_version @@ -9791,6 +10345,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype norfloxacin_measurement: name: norfloxacin_measurement title: norfloxacin_measurement @@ -9803,6 +10359,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement norfloxacin_measurement_units: name: norfloxacin_measurement_units title: norfloxacin_measurement_units @@ -9815,6 +10373,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units norfloxacin_measurement_sign: name: norfloxacin_measurement_sign title: norfloxacin_measurement_sign @@ -9827,6 +10387,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign norfloxacin_laboratory_typing_method: name: norfloxacin_laboratory_typing_method title: norfloxacin_laboratory_typing_method @@ -9838,6 +10400,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method norfloxacin_laboratory_typing_platform: name: norfloxacin_laboratory_typing_platform title: norfloxacin_laboratory_typing_platform @@ -9849,6 +10413,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform norfloxacin_laboratory_typing_platform_version: name: norfloxacin_laboratory_typing_platform_version title: norfloxacin_laboratory_typing_platform_version @@ -9869,6 +10435,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor norfloxacin_testing_standard: name: norfloxacin_testing_standard title: norfloxacin_testing_standard @@ -9880,6 +10448,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard norfloxacin_testing_standard_version: name: norfloxacin_testing_standard_version title: norfloxacin_testing_standard_version @@ -9930,8 +10500,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - oxolinic-acid_resistance_phenotype: - name: oxolinic-acid_resistance_phenotype + oxolinicacid_resistance_phenotype: + name: oxolinicacid_resistance_phenotype title: oxolinic-acid_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -9942,8 +10512,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - oxolinic-acid_measurement: - name: oxolinic-acid_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + oxolinicacid_measurement: + name: oxolinicacid_measurement title: oxolinic-acid_measurement description: The measured value of oxolinic-acid resistance. comments: This field should only contain a number (either an integer or a number @@ -9954,8 +10526,10 @@ slots: required: true examples: - value: '4' - oxolinic-acid_measurement_units: - name: oxolinic-acid_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + oxolinicacid_measurement_units: + name: oxolinicacid_measurement_units title: oxolinic-acid_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -9966,8 +10540,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - oxolinic-acid_measurement_sign: - name: oxolinic-acid_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + oxolinicacid_measurement_sign: + name: oxolinicacid_measurement_sign title: oxolinic-acid_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -9978,8 +10554,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - oxolinic-acid_laboratory_typing_method: - name: oxolinic-acid_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + oxolinicacid_laboratory_typing_method: + name: oxolinicacid_laboratory_typing_method title: oxolinic-acid_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -9989,8 +10567,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - oxolinic-acid_laboratory_typing_platform: - name: oxolinic-acid_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + oxolinicacid_laboratory_typing_platform: + name: oxolinicacid_laboratory_typing_platform title: oxolinic-acid_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -10000,8 +10580,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - oxolinic-acid_laboratory_typing_platform_version: - name: oxolinic-acid_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + oxolinicacid_laboratory_typing_platform_version: + name: oxolinicacid_laboratory_typing_platform_version title: oxolinic-acid_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -10010,8 +10592,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - oxolinic-acid_vendor_name: - name: oxolinic-acid_vendor_name + oxolinicacid_vendor_name: + name: oxolinicacid_vendor_name title: oxolinic-acid_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -10020,8 +10602,10 @@ slots: - range: null value menu examples: - value: Sensititre - oxolinic-acid_testing_standard: - name: oxolinic-acid_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + oxolinicacid_testing_standard: + name: oxolinicacid_testing_standard title: oxolinic-acid_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -10031,8 +10615,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - oxolinic-acid_testing_standard_version: - name: oxolinic-acid_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + oxolinicacid_testing_standard_version: + name: oxolinicacid_testing_standard_version title: oxolinic-acid_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -10041,8 +10627,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - oxolinic-acid_testing_standard_details: - name: oxolinic-acid_testing_standard_details + oxolinicacid_testing_standard_details: + name: oxolinicacid_testing_standard_details title: oxolinic-acid_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -10052,8 +10638,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - oxolinic-acid_susceptible_breakpoint: - name: oxolinic-acid_susceptible_breakpoint + oxolinicacid_susceptible_breakpoint: + name: oxolinicacid_susceptible_breakpoint title: oxolinic-acid_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -10062,8 +10648,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - oxolinic-acid_intermediate_breakpoint: - name: oxolinic-acid_intermediate_breakpoint + oxolinicacid_intermediate_breakpoint: + name: oxolinicacid_intermediate_breakpoint title: oxolinic-acid_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -10071,8 +10657,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - oxolinic-acid_resistant_breakpoint: - name: oxolinic-acid_resistant_breakpoint + oxolinicacid_resistant_breakpoint: + name: oxolinicacid_resistant_breakpoint title: oxolinic-acid_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -10093,6 +10679,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype oxytetracycline_measurement: name: oxytetracycline_measurement title: oxytetracycline_measurement @@ -10105,6 +10693,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement oxytetracycline_measurement_units: name: oxytetracycline_measurement_units title: oxytetracycline_measurement_units @@ -10117,6 +10707,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units oxytetracycline_measurement_sign: name: oxytetracycline_measurement_sign title: oxytetracycline_measurement_sign @@ -10129,6 +10721,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign oxytetracycline_laboratory_typing_method: name: oxytetracycline_laboratory_typing_method title: oxytetracycline_laboratory_typing_method @@ -10140,6 +10734,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method oxytetracycline_laboratory_typing_platform: name: oxytetracycline_laboratory_typing_platform title: oxytetracycline_laboratory_typing_platform @@ -10151,6 +10747,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform oxytetracycline_laboratory_typing_platform_version: name: oxytetracycline_laboratory_typing_platform_version title: oxytetracycline_laboratory_typing_platform_version @@ -10171,6 +10769,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor oxytetracycline_testing_standard: name: oxytetracycline_testing_standard title: oxytetracycline_testing_standard @@ -10182,6 +10782,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard oxytetracycline_testing_standard_version: name: oxytetracycline_testing_standard_version title: oxytetracycline_testing_standard_version @@ -10244,6 +10846,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype piperacillin_measurement: name: piperacillin_measurement title: piperacillin_measurement @@ -10256,6 +10860,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement piperacillin_measurement_units: name: piperacillin_measurement_units title: piperacillin_measurement_units @@ -10268,6 +10874,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units piperacillin_measurement_sign: name: piperacillin_measurement_sign title: piperacillin_measurement_sign @@ -10280,6 +10888,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign piperacillin_laboratory_typing_method: name: piperacillin_laboratory_typing_method title: piperacillin_laboratory_typing_method @@ -10291,6 +10901,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method piperacillin_laboratory_typing_platform: name: piperacillin_laboratory_typing_platform title: piperacillin_laboratory_typing_platform @@ -10302,6 +10914,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform piperacillin_laboratory_typing_platform_version: name: piperacillin_laboratory_typing_platform_version title: piperacillin_laboratory_typing_platform_version @@ -10322,6 +10936,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor piperacillin_testing_standard: name: piperacillin_testing_standard title: piperacillin_testing_standard @@ -10333,6 +10949,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard piperacillin_testing_standard_version: name: piperacillin_testing_standard_version title: piperacillin_testing_standard_version @@ -10383,8 +11001,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - piperacillin-tazobactam_resistance_phenotype: - name: piperacillin-tazobactam_resistance_phenotype + piperacillintazobactam_resistance_phenotype: + name: piperacillintazobactam_resistance_phenotype title: piperacillin-tazobactam_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -10395,8 +11013,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - piperacillin-tazobactam_measurement: - name: piperacillin-tazobactam_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + piperacillintazobactam_measurement: + name: piperacillintazobactam_measurement title: piperacillin-tazobactam_measurement description: The measured value of piperacillin-tazobactam resistance. comments: This field should only contain a number (either an integer or a number @@ -10407,8 +11027,10 @@ slots: required: true examples: - value: '4' - piperacillin-tazobactam_measurement_units: - name: piperacillin-tazobactam_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + piperacillintazobactam_measurement_units: + name: piperacillintazobactam_measurement_units title: piperacillin-tazobactam_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -10419,8 +11041,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - piperacillin-tazobactam_measurement_sign: - name: piperacillin-tazobactam_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + piperacillintazobactam_measurement_sign: + name: piperacillintazobactam_measurement_sign title: piperacillin-tazobactam_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -10431,8 +11055,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - piperacillin-tazobactam_laboratory_typing_method: - name: piperacillin-tazobactam_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + piperacillintazobactam_laboratory_typing_method: + name: piperacillintazobactam_laboratory_typing_method title: piperacillin-tazobactam_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -10442,8 +11068,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - piperacillin-tazobactam_laboratory_typing_platform: - name: piperacillin-tazobactam_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + piperacillintazobactam_laboratory_typing_platform: + name: piperacillintazobactam_laboratory_typing_platform title: piperacillin-tazobactam_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -10453,8 +11081,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - piperacillin-tazobactam_laboratory_typing_platform_version: - name: piperacillin-tazobactam_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + piperacillintazobactam_laboratory_typing_platform_version: + name: piperacillintazobactam_laboratory_typing_platform_version title: piperacillin-tazobactam_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -10463,8 +11093,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - piperacillin-tazobactam_vendor_name: - name: piperacillin-tazobactam_vendor_name + piperacillintazobactam_vendor_name: + name: piperacillintazobactam_vendor_name title: piperacillin-tazobactam_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -10473,8 +11103,10 @@ slots: - range: null value menu examples: - value: Sensititre - piperacillin-tazobactam_testing_standard: - name: piperacillin-tazobactam_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + piperacillintazobactam_testing_standard: + name: piperacillintazobactam_testing_standard title: piperacillin-tazobactam_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -10484,8 +11116,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - piperacillin-tazobactam_testing_standard_version: - name: piperacillin-tazobactam_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + piperacillintazobactam_testing_standard_version: + name: piperacillintazobactam_testing_standard_version title: piperacillin-tazobactam_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -10494,8 +11128,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - piperacillin-tazobactam_testing_standard_details: - name: piperacillin-tazobactam_testing_standard_details + piperacillintazobactam_testing_standard_details: + name: piperacillintazobactam_testing_standard_details title: piperacillin-tazobactam_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -10505,8 +11139,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - piperacillin-tazobactam_susceptible_breakpoint: - name: piperacillin-tazobactam_susceptible_breakpoint + piperacillintazobactam_susceptible_breakpoint: + name: piperacillintazobactam_susceptible_breakpoint title: piperacillin-tazobactam_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -10515,8 +11149,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - piperacillin-tazobactam_intermediate_breakpoint: - name: piperacillin-tazobactam_intermediate_breakpoint + piperacillintazobactam_intermediate_breakpoint: + name: piperacillintazobactam_intermediate_breakpoint title: piperacillin-tazobactam_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -10524,8 +11158,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - piperacillin-tazobactam_resistant_breakpoint: - name: piperacillin-tazobactam_resistant_breakpoint + piperacillintazobactam_resistant_breakpoint: + name: piperacillintazobactam_resistant_breakpoint title: piperacillin-tazobactam_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -10534,8 +11168,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - polymyxin-b_resistance_phenotype: - name: polymyxin-b_resistance_phenotype + polymyxinb_resistance_phenotype: + name: polymyxinb_resistance_phenotype title: polymyxin-b_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -10546,8 +11180,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - polymyxin-b_measurement: - name: polymyxin-b_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + polymyxinb_measurement: + name: polymyxinb_measurement title: polymyxin-b_measurement description: The measured value of polymyxin B resistance. comments: This field should only contain a number (either an integer or a number @@ -10558,8 +11194,10 @@ slots: required: true examples: - value: '4' - polymyxin-b_measurement_units: - name: polymyxin-b_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + polymyxinb_measurement_units: + name: polymyxinb_measurement_units title: polymyxin-b_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -10570,8 +11208,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - polymyxin-b_measurement_sign: - name: polymyxin-b_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + polymyxinb_measurement_sign: + name: polymyxinb_measurement_sign title: polymyxin-b_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -10582,8 +11222,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - polymyxin-b_laboratory_typing_method: - name: polymyxin-b_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + polymyxinb_laboratory_typing_method: + name: polymyxinb_laboratory_typing_method title: polymyxin-b_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -10593,8 +11235,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - polymyxin-b_laboratory_typing_platform: - name: polymyxin-b_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + polymyxinb_laboratory_typing_platform: + name: polymyxinb_laboratory_typing_platform title: polymyxin-b_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -10604,8 +11248,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - polymyxin-b_laboratory_typing_platform_version: - name: polymyxin-b_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + polymyxinb_laboratory_typing_platform_version: + name: polymyxinb_laboratory_typing_platform_version title: polymyxin-b_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -10614,8 +11260,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - polymyxin-b_vendor_name: - name: polymyxin-b_vendor_name + polymyxinb_vendor_name: + name: polymyxinb_vendor_name title: polymyxin-b_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -10624,8 +11270,10 @@ slots: - range: null value menu examples: - value: Sensititre - polymyxin-b_testing_standard: - name: polymyxin-b_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + polymyxinb_testing_standard: + name: polymyxinb_testing_standard title: polymyxin-b_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -10635,8 +11283,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - polymyxin-b_testing_standard_version: - name: polymyxin-b_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + polymyxinb_testing_standard_version: + name: polymyxinb_testing_standard_version title: polymyxin-b_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -10645,8 +11295,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - polymyxin-b_testing_standard_details: - name: polymyxin-b_testing_standard_details + polymyxinb_testing_standard_details: + name: polymyxinb_testing_standard_details title: polymyxin-b_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -10656,8 +11306,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - polymyxin-b_susceptible_breakpoint: - name: polymyxin-b_susceptible_breakpoint + polymyxinb_susceptible_breakpoint: + name: polymyxinb_susceptible_breakpoint title: polymyxin-b_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -10666,8 +11316,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - polymyxin-b_intermediate_breakpoint: - name: polymyxin-b_intermediate_breakpoint + polymyxinb_intermediate_breakpoint: + name: polymyxinb_intermediate_breakpoint title: polymyxin-b_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -10675,8 +11325,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - polymyxin-b_resistant_breakpoint: - name: polymyxin-b_resistant_breakpoint + polymyxinb_resistant_breakpoint: + name: polymyxinb_resistant_breakpoint title: polymyxin-b_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -10685,8 +11335,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - quinupristin-dalfopristin_resistance_phenotype: - name: quinupristin-dalfopristin_resistance_phenotype + quinupristindalfopristin_resistance_phenotype: + name: quinupristindalfopristin_resistance_phenotype title: quinupristin-dalfopristin_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -10697,8 +11347,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - quinupristin-dalfopristin_measurement: - name: quinupristin-dalfopristin_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + quinupristindalfopristin_measurement: + name: quinupristindalfopristin_measurement title: quinupristin-dalfopristin_measurement description: The measured value of quinupristin-dalfopristin resistance. comments: This field should only contain a number (either an integer or a number @@ -10709,8 +11361,10 @@ slots: required: true examples: - value: '4' - quinupristin-dalfopristin_measurement_units: - name: quinupristin-dalfopristin_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + quinupristindalfopristin_measurement_units: + name: quinupristindalfopristin_measurement_units title: quinupristin-dalfopristin_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -10721,8 +11375,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - quinupristin-dalfopristin_measurement_sign: - name: quinupristin-dalfopristin_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + quinupristindalfopristin_measurement_sign: + name: quinupristindalfopristin_measurement_sign title: quinupristin-dalfopristin_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -10733,8 +11389,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - quinupristin-dalfopristin_laboratory_typing_method: - name: quinupristin-dalfopristin_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + quinupristindalfopristin_laboratory_typing_method: + name: quinupristindalfopristin_laboratory_typing_method title: quinupristin-dalfopristin_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -10744,8 +11402,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - quinupristin-dalfopristin_laboratory_typing_platform: - name: quinupristin-dalfopristin_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + quinupristindalfopristin_laboratory_typing_platform: + name: quinupristindalfopristin_laboratory_typing_platform title: quinupristin-dalfopristin_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -10755,8 +11415,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - quinupristin-dalfopristin_laboratory_typing_platform_version: - name: quinupristin-dalfopristin_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + quinupristindalfopristin_laboratory_typing_platform_version: + name: quinupristindalfopristin_laboratory_typing_platform_version title: quinupristin-dalfopristin_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -10765,8 +11427,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - quinupristin-dalfopristin_vendor_name: - name: quinupristin-dalfopristin_vendor_name + quinupristindalfopristin_vendor_name: + name: quinupristindalfopristin_vendor_name title: quinupristin-dalfopristin_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -10775,8 +11437,10 @@ slots: - range: null value menu examples: - value: Sensititre - quinupristin-dalfopristin_testing_standard: - name: quinupristin-dalfopristin_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + quinupristindalfopristin_testing_standard: + name: quinupristindalfopristin_testing_standard title: quinupristin-dalfopristin_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -10786,8 +11450,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - quinupristin-dalfopristin_testing_standard_version: - name: quinupristin-dalfopristin_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + quinupristindalfopristin_testing_standard_version: + name: quinupristindalfopristin_testing_standard_version title: quinupristin-dalfopristin_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -10796,8 +11462,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - quinupristin-dalfopristin_testing_standard_details: - name: quinupristin-dalfopristin_testing_standard_details + quinupristindalfopristin_testing_standard_details: + name: quinupristindalfopristin_testing_standard_details title: quinupristin-dalfopristin_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -10807,8 +11473,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - quinupristin-dalfopristin_susceptible_breakpoint: - name: quinupristin-dalfopristin_susceptible_breakpoint + quinupristindalfopristin_susceptible_breakpoint: + name: quinupristindalfopristin_susceptible_breakpoint title: quinupristin-dalfopristin_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -10817,8 +11483,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - quinupristin-dalfopristin_intermediate_breakpoint: - name: quinupristin-dalfopristin_intermediate_breakpoint + quinupristindalfopristin_intermediate_breakpoint: + name: quinupristindalfopristin_intermediate_breakpoint title: quinupristin-dalfopristin_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -10826,8 +11492,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - quinupristin-dalfopristin_resistant_breakpoint: - name: quinupristin-dalfopristin_resistant_breakpoint + quinupristindalfopristin_resistant_breakpoint: + name: quinupristindalfopristin_resistant_breakpoint title: quinupristin-dalfopristin_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -10848,6 +11514,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype streptomycin_measurement: name: streptomycin_measurement title: streptomycin_measurement @@ -10860,6 +11528,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement streptomycin_measurement_units: name: streptomycin_measurement_units title: streptomycin_measurement_units @@ -10872,6 +11542,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units streptomycin_measurement_sign: name: streptomycin_measurement_sign title: streptomycin_measurement_sign @@ -10884,6 +11556,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign streptomycin_laboratory_typing_method: name: streptomycin_laboratory_typing_method title: streptomycin_laboratory_typing_method @@ -10895,6 +11569,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method streptomycin_laboratory_typing_platform: name: streptomycin_laboratory_typing_platform title: streptomycin_laboratory_typing_platform @@ -10906,6 +11582,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform streptomycin_laboratory_typing_platform_version: name: streptomycin_laboratory_typing_platform_version title: streptomycin_laboratory_typing_platform_version @@ -10926,6 +11604,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor streptomycin_testing_standard: name: streptomycin_testing_standard title: streptomycin_testing_standard @@ -10937,6 +11617,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard streptomycin_testing_standard_version: name: streptomycin_testing_standard_version title: streptomycin_testing_standard_version @@ -10999,6 +11681,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype sulfisoxazole_measurement: name: sulfisoxazole_measurement title: sulfisoxazole_measurement @@ -11011,6 +11695,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement sulfisoxazole_measurement_units: name: sulfisoxazole_measurement_units title: sulfisoxazole_measurement_units @@ -11023,6 +11709,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units sulfisoxazole_measurement_sign: name: sulfisoxazole_measurement_sign title: sulfisoxazole_measurement_sign @@ -11035,6 +11723,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign sulfisoxazole_laboratory_typing_method: name: sulfisoxazole_laboratory_typing_method title: sulfisoxazole_laboratory_typing_method @@ -11046,6 +11736,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method sulfisoxazole_laboratory_typing_platform: name: sulfisoxazole_laboratory_typing_platform title: sulfisoxazole_laboratory_typing_platform @@ -11057,6 +11749,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform sulfisoxazole_laboratory_typing_platform_version: name: sulfisoxazole_laboratory_typing_platform_version title: sulfisoxazole_laboratory_typing_platform_version @@ -11077,6 +11771,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor sulfisoxazole_testing_standard: name: sulfisoxazole_testing_standard title: sulfisoxazole_testing_standard @@ -11088,6 +11784,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard sulfisoxazole_testing_standard_version: name: sulfisoxazole_testing_standard_version title: sulfisoxazole_testing_standard_version @@ -11150,6 +11848,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype telithromycin_measurement: name: telithromycin_measurement title: telithromycin_measurement @@ -11162,6 +11862,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement telithromycin_measurement_units: name: telithromycin_measurement_units title: telithromycin_measurement_units @@ -11174,6 +11876,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units telithromycin_measurement_sign: name: telithromycin_measurement_sign title: telithromycin_measurement_sign @@ -11186,6 +11890,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign telithromycin_laboratory_typing_method: name: telithromycin_laboratory_typing_method title: telithromycin_laboratory_typing_method @@ -11197,6 +11903,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method telithromycin_laboratory_typing_platform: name: telithromycin_laboratory_typing_platform title: telithromycin_laboratory_typing_platform @@ -11208,6 +11916,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform telithromycin_laboratory_typing_platform_version: name: telithromycin_laboratory_typing_platform_version title: telithromycin_laboratory_typing_platform_version @@ -11228,6 +11938,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor telithromycin_testing_standard: name: telithromycin_testing_standard title: telithromycin_testing_standard @@ -11239,6 +11951,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard telithromycin_testing_standard_version: name: telithromycin_testing_standard_version title: telithromycin_testing_standard_version @@ -11301,6 +12015,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype tetracycline_measurement: name: tetracycline_measurement title: tetracycline_measurement @@ -11313,6 +12029,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement tetracycline_measurement_units: name: tetracycline_measurement_units title: tetracycline_measurement_units @@ -11325,6 +12043,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units tetracycline_measurement_sign: name: tetracycline_measurement_sign title: tetracycline_measurement_sign @@ -11337,6 +12057,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign tetracycline_laboratory_typing_method: name: tetracycline_laboratory_typing_method title: tetracycline_laboratory_typing_method @@ -11348,6 +12070,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method tetracycline_laboratory_typing_platform: name: tetracycline_laboratory_typing_platform title: tetracycline_laboratory_typing_platform @@ -11359,6 +12083,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform tetracycline_laboratory_typing_platform_version: name: tetracycline_laboratory_typing_platform_version title: tetracycline_laboratory_typing_platform_version @@ -11379,6 +12105,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor tetracycline_testing_standard: name: tetracycline_testing_standard title: tetracycline_testing_standard @@ -11390,6 +12118,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard tetracycline_testing_standard_version: name: tetracycline_testing_standard_version title: tetracycline_testing_standard_version @@ -11452,6 +12182,8 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype tigecycline_measurement: name: tigecycline_measurement title: tigecycline_measurement @@ -11464,6 +12196,8 @@ slots: required: true examples: - value: '4' + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement tigecycline_measurement_units: name: tigecycline_measurement_units title: tigecycline_measurement_units @@ -11476,6 +12210,8 @@ slots: required: true examples: - value: ug/mL [UO:0000274] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units tigecycline_measurement_sign: name: tigecycline_measurement_sign title: tigecycline_measurement_sign @@ -11488,6 +12224,8 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign tigecycline_laboratory_typing_method: name: tigecycline_laboratory_typing_method title: tigecycline_laboratory_typing_method @@ -11499,6 +12237,8 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method tigecycline_laboratory_typing_platform: name: tigecycline_laboratory_typing_platform title: tigecycline_laboratory_typing_platform @@ -11510,6 +12250,8 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform tigecycline_laboratory_typing_platform_version: name: tigecycline_laboratory_typing_platform_version title: tigecycline_laboratory_typing_platform_version @@ -11530,6 +12272,8 @@ slots: - range: null value menu examples: - value: Sensititre + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor tigecycline_testing_standard: name: tigecycline_testing_standard title: tigecycline_testing_standard @@ -11541,6 +12285,8 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard tigecycline_testing_standard_version: name: tigecycline_testing_standard_version title: tigecycline_testing_standard_version @@ -11591,8 +12337,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '32' - trimethoprim-sulfamethoxazole_resistance_phenotype: - name: trimethoprim-sulfamethoxazole_resistance_phenotype + trimethoprimsulfamethoxazole_resistance_phenotype: + name: trimethoprimsulfamethoxazole_resistance_phenotype title: trimethoprim-sulfamethoxazole_resistance_phenotype description: The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic @@ -11603,8 +12349,10 @@ slots: recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] - trimethoprim-sulfamethoxazole_measurement: - name: trimethoprim-sulfamethoxazole_measurement + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + trimethoprimsulfamethoxazole_measurement: + name: trimethoprimsulfamethoxazole_measurement title: trimethoprim-sulfamethoxazole_measurement description: The measured value of trimethoprim-sulfamethoxazole resistance. comments: This field should only contain a number (either an integer or a number @@ -11615,8 +12363,10 @@ slots: required: true examples: - value: '4' - trimethoprim-sulfamethoxazole_measurement_units: - name: trimethoprim-sulfamethoxazole_measurement_units + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement + trimethoprimsulfamethoxazole_measurement_units: + name: trimethoprimsulfamethoxazole_measurement_units title: trimethoprim-sulfamethoxazole_measurement_units description: The units of the antimicrobial resistance measurement. comments: Select the units from the pick list provided. Use the Term Request System @@ -11627,8 +12377,10 @@ slots: required: true examples: - value: ug/mL [UO:0000274] - trimethoprim-sulfamethoxazole_measurement_sign: - name: trimethoprim-sulfamethoxazole_measurement_sign + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_units + trimethoprimsulfamethoxazole_measurement_sign: + name: trimethoprimsulfamethoxazole_measurement_sign title: trimethoprim-sulfamethoxazole_measurement_sign description: The qualifier associated with the antimicrobial resistance measurement comments: Select the comparator sign from the pick list provided. Use the Term @@ -11639,8 +12391,10 @@ slots: required: true examples: - value: greater than (>) [GENEPIO:0001006] - trimethoprim-sulfamethoxazole_laboratory_typing_method: - name: trimethoprim-sulfamethoxazole_laboratory_typing_method + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + trimethoprimsulfamethoxazole_laboratory_typing_method: + name: trimethoprimsulfamethoxazole_laboratory_typing_method title: trimethoprim-sulfamethoxazole_laboratory_typing_method description: The general method used for antimicrobial susceptibility testing. comments: Select a typing method from the pick list provided. Use the Term Request @@ -11650,8 +12404,10 @@ slots: - range: null value menu examples: - value: Broth dilution [ARO:3004397] - trimethoprim-sulfamethoxazole_laboratory_typing_platform: - name: trimethoprim-sulfamethoxazole_laboratory_typing_platform + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + trimethoprimsulfamethoxazole_laboratory_typing_platform: + name: trimethoprimsulfamethoxazole_laboratory_typing_platform title: trimethoprim-sulfamethoxazole_laboratory_typing_platform description: The brand/platform used for antimicrobial susceptibility testing. comments: Select a typing platform from the pick list provided. Use the Term Request @@ -11661,8 +12417,10 @@ slots: - range: null value menu examples: - value: Sensitire [ARO:3004402] - trimethoprim-sulfamethoxazole_laboratory_typing_platform_version: - name: trimethoprim-sulfamethoxazole_laboratory_typing_platform_version + exact_mappings: + - NCBI_ANTIBIOGRAM:laboratory_typing_platform + trimethoprimsulfamethoxazole_laboratory_typing_platform_version: + name: trimethoprimsulfamethoxazole_laboratory_typing_platform_version title: trimethoprim-sulfamethoxazole_laboratory_typing_platform_version description: The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. @@ -11671,8 +12429,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CMV3AGNF - trimethoprim-sulfamethoxazole_vendor_name: - name: trimethoprim-sulfamethoxazole_vendor_name + trimethoprimsulfamethoxazole_vendor_name: + name: trimethoprimsulfamethoxazole_vendor_name title: trimethoprim-sulfamethoxazole_vendor_name description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). @@ -11681,8 +12439,10 @@ slots: - range: null value menu examples: - value: Sensititre - trimethoprim-sulfamethoxazole_testing_standard: - name: trimethoprim-sulfamethoxazole_testing_standard + exact_mappings: + - NCBI_ANTIBIOGRAM:vendor + trimethoprimsulfamethoxazole_testing_standard: + name: trimethoprimsulfamethoxazole_testing_standard title: trimethoprim-sulfamethoxazole_testing_standard description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. @@ -11692,8 +12452,10 @@ slots: recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - trimethoprim-sulfamethoxazole_testing_standard_version: - name: trimethoprim-sulfamethoxazole_testing_standard_version + exact_mappings: + - NCBI_ANTIBIOGRAM:%2Atesting_standard + trimethoprimsulfamethoxazole_testing_standard_version: + name: trimethoprimsulfamethoxazole_testing_standard_version title: trimethoprim-sulfamethoxazole_testing_standard_version description: The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include @@ -11702,8 +12464,8 @@ slots: range: WhitespaceMinimizedString examples: - value: M100 - trimethoprim-sulfamethoxazole_testing_standard_details: - name: trimethoprim-sulfamethoxazole_testing_standard_details + trimethoprimsulfamethoxazole_testing_standard_details: + name: trimethoprimsulfamethoxazole_testing_standard_details title: trimethoprim-sulfamethoxazole_testing_standard_details description: Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype @@ -11713,8 +12475,8 @@ slots: examples: - value: '27th ed. Wayne, PA: Clinical and Laboratory Standards Institute' - value: '2017.' - trimethoprim-sulfamethoxazole_susceptible_breakpoint: - name: trimethoprim-sulfamethoxazole_susceptible_breakpoint + trimethoprimsulfamethoxazole_susceptible_breakpoint: + name: trimethoprimsulfamethoxazole_susceptible_breakpoint title: trimethoprim-sulfamethoxazole_susceptible_breakpoint description: "The maximum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Csensitive\u201D to this antimicrobial." @@ -11723,8 +12485,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - trimethoprim-sulfamethoxazole_intermediate_breakpoint: - name: trimethoprim-sulfamethoxazole_intermediate_breakpoint + trimethoprimsulfamethoxazole_intermediate_breakpoint: + name: trimethoprimsulfamethoxazole_intermediate_breakpoint title: trimethoprim-sulfamethoxazole_intermediate_breakpoint description: "The intermediate measurement(s), in the units specified in the \u201C\ AMR_measurement_units\u201D field, where a sample would be considered to have\ @@ -11732,8 +12494,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '16' - trimethoprim-sulfamethoxazole_resistant_breakpoint: - name: trimethoprim-sulfamethoxazole_resistant_breakpoint + trimethoprimsulfamethoxazole_resistant_breakpoint: + name: trimethoprimsulfamethoxazole_resistant_breakpoint title: trimethoprim-sulfamethoxazole_resistant_breakpoint description: "The minimum measurement, in the units specified in the \u201Cantibiotic_measurement_units\u201D\ \ field, for a sample to be considered \u201Cresistant\u201D to this antimicrobial." @@ -11754,8 +12516,8 @@ slots: recommended: true examples: - value: Tejinder Singh, Fei Hu, Joe Blogs - DataHarmonizer provenance: - name: DataHarmonizer provenance + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance description: The DataHarmonizer software and template version provenance. comments: The current software and template version information will be automatically @@ -11766,8 +12528,8 @@ slots: examples: - value: DataHarmonizer v1.4.3, GRDI v1.0.0 enums: - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu title: null value menu description: '' permissible_values: @@ -11775,14 +12537,16 @@ enums: text: Not Applicable [GENEPIO:0001619] Missing [GENEPIO:0001618]: text: Missing [GENEPIO:0001618] + exact_mappings: + - NCBI_ANTIBIOGRAM:missing Not Collected [GENEPIO:0001620]: text: Not Collected [GENEPIO:0001620] Not Provided [GENEPIO:0001668]: text: Not Provided [GENEPIO:0001668] Restricted Access [GENEPIO:0001810]: text: Restricted Access [GENEPIO:0001810] - sample_collected_by menu: - name: sample_collected_by menu + SampleCollectedByMenu: + name: SampleCollectedByMenu title: sample_collected_by menu description: '' permissible_values: @@ -11800,8 +12564,8 @@ enums: text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] University of Manitoba (UM) [GENEPIO:0004434]: text: University of Manitoba (UM) [GENEPIO:0004434] - purpose_of_sampling menu: - name: purpose_of_sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu title: purpose_of_sampling menu description: '' permissible_values: @@ -11824,8 +12588,8 @@ enums: is_a: Research [GENEPIO:0100003] Surveillance [GENEPIO:0100004]: text: Surveillance [GENEPIO:0100004] - presampling_activity menu: - name: presampling_activity menu + PresamplingActivityMenu: + name: PresamplingActivityMenu title: presampling_activity menu description: '' permissible_values: @@ -11860,8 +12624,8 @@ enums: text: Probiotic pre-treatment [GENEPIO:0100547] Vaccination [NCIT:C15346]: text: Vaccination [NCIT:C15346] - experimental_specimen_role_type menu: - name: experimental_specimen_role_type menu + ExperimentalSpecimenRoleTypeMenu: + name: ExperimentalSpecimenRoleTypeMenu title: experimental_specimen_role_type menu description: '' permissible_values: @@ -11873,8 +12637,8 @@ enums: text: Technical replicate [EFO:0002090] Biological replicate [EFO:0002091]: text: Biological replicate [EFO:0002091] - specimen_processing menu: - name: specimen_processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu title: specimen_processing menu description: '' permissible_values: @@ -11886,8 +12650,8 @@ enums: text: Technical replicate process [GENEPIO:0101021] Isolated from single source [OBI:0002079]: text: Isolated from single source [OBI:0002079] - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu title: geo_loc_name (country) menu description: '' permissible_values: @@ -12433,8 +13197,8 @@ enums: text: Zambia [GAZ:00001107] Zimbabwe [GAZ:00001106]: text: Zimbabwe [GAZ:00001106] - geo_loc_name (state/province/region) menu: - name: geo_loc_name (state/province/region) menu + GeoLocNameStateProvinceRegionMenu: + name: GeoLocNameStateProvinceRegionMenu title: geo_loc_name (state/province/region) menu description: '' permissible_values: @@ -12487,8 +13251,8 @@ enums: Saskatchewan [GAZ:00002564]: text: Saskatchewan [GAZ:00002564] is_a: Prairie region (Canada) [wikidata:Q1364746] - sample_collection_date_precision menu: - name: sample_collection_date_precision menu + SampleCollectionDatePrecisionMenu: + name: SampleCollectionDatePrecisionMenu title: sample_collection_date_precision menu description: '' permissible_values: @@ -12498,8 +13262,8 @@ enums: text: month [UO:0000035] day [UO:0000033]: text: day [UO:0000033] - environmental_site menu: - name: environmental_site menu + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu title: environmental_site menu description: '' permissible_values: @@ -12673,8 +13437,8 @@ enums: text: Woodland area [ENVO:00000109] Zoo [ENVO:00010625]: text: Zoo [ENVO:00010625] - water_depth_units menu: - name: water_depth_units menu + WaterDepthUnitsMenu: + name: WaterDepthUnitsMenu title: water_depth_units menu description: '' permissible_values: @@ -12688,8 +13452,8 @@ enums: text: inch (in) [UO:0010011] foot (ft) [UO:0010013]: text: foot (ft) [UO:0010013] - sediment_depth_units menu: - name: sediment_depth_units menu + SedimentDepthUnitsMenu: + name: SedimentDepthUnitsMenu title: sediment_depth_units menu description: '' permissible_values: @@ -12703,8 +13467,8 @@ enums: text: inch (in) [UO:0010011] foot (ft) [UO:0010013]: text: foot (ft) [UO:0010013] - air_temperature_units menu: - name: air_temperature_units menu + AirTemperatureUnitsMenu: + name: AirTemperatureUnitsMenu title: air_temperature_units menu description: '' permissible_values: @@ -12712,8 +13476,8 @@ enums: text: degree Fahrenheit (F) [UO:0000195] degree Celsius (C) [UO:0000027]: text: degree Celsius (C) [UO:0000027] - water_temperature_units menu: - name: water_temperature_units menu + WaterTemperatureUnitsMenu: + name: WaterTemperatureUnitsMenu title: water_temperature_units menu description: '' permissible_values: @@ -12721,8 +13485,8 @@ enums: text: degree Fahrenheit (F) [UO:0000195] degree Celsius (C) [UO:0000027]: text: degree Celsius (C) [UO:0000027] - available_data_types menu: - name: available_data_types menu + AvailableDataTypesMenu: + name: AvailableDataTypesMenu title: available_data_types menu description: '' permissible_values: @@ -12866,8 +13630,8 @@ enums: Turbidity measurement [GENEPIO:0100749]: text: Turbidity measurement [GENEPIO:0100749] is_a: Physical characterization [GENEPIO:0100742] - weather_type menu: - name: weather_type menu + WeatherTypeMenu: + name: WeatherTypeMenu title: weather_type menu description: '' permissible_values: @@ -12888,8 +13652,8 @@ enums: text: Storm [ENVO:01000876] Sunny/Clear [ENVO:03501421]: text: Sunny/Clear [ENVO:03501421] - animal_or_plant_population menu: - name: animal_or_plant_population menu + AnimalOrPlantPopulationMenu: + name: AnimalOrPlantPopulationMenu title: animal_or_plant_population menu description: '' permissible_values: @@ -12938,8 +13702,8 @@ enums: Seabird [FOODON:00004504]: text: Seabird [FOODON:00004504] is_a: Wild bird [FOODON:00004505] - environmental_material menu: - name: environmental_material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu title: environmental_material menu description: '' permissible_values: @@ -13092,8 +13856,8 @@ enums: Surface water [ENVO:00002042]: text: Surface water [ENVO:00002042] is_a: Water [CHEBI:15377] - anatomical_material menu: - name: anatomical_material menu + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu title: anatomical_material menu description: '' permissible_values: @@ -13112,8 +13876,8 @@ enums: is_a: Fluid [UBERON:0006314] Tissue [UBERON:0000479]: text: Tissue [UBERON:0000479] - body_product menu: - name: body_product menu + BodyProductMenu: + name: BodyProductMenu title: body_product menu description: '' permissible_values: @@ -13149,8 +13913,8 @@ enums: is_a: Milk [UBERON:0001913] Urine [UBERON:0001088]: text: Urine [UBERON:0001088] - anatomical_part menu: - name: anatomical_part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu title: anatomical_part menu description: '' permissible_values: @@ -13394,8 +14158,8 @@ enums: Fish vent [GENEPIO:0100902]: text: Fish vent [GENEPIO:0100902] is_a: Vent (anatomical) [UBERON:2000298] - anatomical_region menu: - name: anatomical_region menu + AnatomicalRegionMenu: + name: AnatomicalRegionMenu title: anatomical_region menu description: '' permissible_values: @@ -13405,8 +14169,8 @@ enums: text: Exterior anatomical region [BSPO:0000034] Interior anatomical region [BSPO:0000033]: text: Interior anatomical region [BSPO:0000033] - food_product menu: - name: food_product menu + PriorSarsCov2InfectionMenu: + name: PriorSarsCov2InfectionMenu title: food_product menu description: '' permissible_values: @@ -13756,8 +14520,8 @@ enums: Mussel [FOODON:03411223]: text: Mussel [FOODON:03411223] is_a: Shellfish [FOODON:03411433] - Oyster FOODON:03411224]: - text: Oyster FOODON:03411224] + Oyster [FOODON:03411224]: + text: Oyster [FOODON:03411224] is_a: Shellfish [FOODON:03411433] Shrimp [FOODON:03301673]: text: Shrimp [FOODON:03301673] @@ -14084,8 +14848,8 @@ enums: White peppercorn (whole or parts) [FOODON:03000251]: text: White peppercorn (whole or parts) [FOODON:03000251] is_a: Spice or herb [FOODON:00001242] - food_product_properties menu: - name: food_product_properties menu + FoodProductPropertiesMenu: + name: FoodProductPropertiesMenu title: food_product_properties menu description: '' permissible_values: @@ -14138,12 +14902,10 @@ enums: text: Meat (with bone) [FOODON:02010116] Meat (with skin) [FOODON:02010111]: text: Meat (with skin) [FOODON:02010111] - Ready-to-eat (RTE) [FOODON:03316636]: - text: Ready-to-eat (RTE) [FOODON:03316636] Soft [PATO:0000387]: text: Soft [PATO:0000387] - label_claim menu: - name: label_claim menu + LabelClaimMenu: + name: LabelClaimMenu title: label_claim menu description: '' permissible_values: @@ -14157,8 +14919,10 @@ enums: text: Organic food claim or use [FOODON:03510128] Pasture raised [FOODON:03601065]: text: Pasture raised [FOODON:03601065] - animal_source_of_food menu: - name: animal_source_of_food menu + Ready-to-eat (RTE) [FOODON:03316636]: + text: Ready-to-eat (RTE) [FOODON:03316636] + AnimalSourceOfFoodMenu: + name: AnimalSourceOfFoodMenu title: animal_source_of_food menu description: '' permissible_values: @@ -14192,8 +14956,8 @@ enums: Squid [FOODON:03411205]: text: Squid [FOODON:03411205] is_a: Shellfish [FOODON:03411433] - food_product_production_stream menu: - name: food_product_production_stream menu + FoodProductProductionStreamMenu: + name: FoodProductProductionStreamMenu title: food_product_production_stream menu description: '' permissible_values: @@ -14214,8 +14978,8 @@ enums: is_a: Meat production stream [FOODON:03000460] Milk production stream [FOODON:03000459]: text: Milk production stream [FOODON:03000459] - collection_device menu: - name: collection_device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu title: collection_device menu description: '' permissible_values: @@ -14270,8 +15034,8 @@ enums: Vacutainer [OBIB:0000032]: text: Vacutainer [OBIB:0000032] is_a: Vacuum device [GENEPIO:0002127] - collection_method menu: - name: collection_method menu + CollectionMethodMenu: + name: CollectionMethodMenu title: collection_method menu description: '' permissible_values: @@ -14311,8 +15075,8 @@ enums: text: Soil coring [GENEPIO:0100934] Weep fluid collection (pouring) [GENEPIO:0101003]: text: Weep fluid collection (pouring) [GENEPIO:0101003] - sample_volume_measurement_unit menu: - name: sample_volume_measurement_unit menu + SampleVolumeMeasurementUnitMenu: + name: SampleVolumeMeasurementUnitMenu title: sample_volume_measurement_unit menu description: '' permissible_values: @@ -14322,8 +15086,8 @@ enums: text: milliliter (mL) [UO:0000098] liter (L) [UO:0000099]: text: liter (L) [UO:0000099] - residual_sample_status menu: - name: residual_sample_status menu + ResidualSampleStatusMenu: + name: ResidualSampleStatusMenu title: residual_sample_status menu description: '' permissible_values: @@ -14333,8 +15097,8 @@ enums: text: No residual sample (sample all used) [GENEPIO:0101088] Residual sample status unkown [GENEPIO:0101089]: text: Residual sample status unkown [GENEPIO:0101089] - sample_storage_duration_unit menu: - name: sample_storage_duration_unit menu + SampleStorageDurationUnitMenu: + name: SampleStorageDurationUnitMenu title: sample_storage_duration_unit menu description: '' permissible_values: @@ -14352,8 +15116,8 @@ enums: text: Month [UO:0000035] Year [UO:0000036]: text: Year [UO:0000036] - nucelic_acid_storage_duration_unit menu: - name: nucelic_acid_storage_duration_unit menu + NucelicAcidStorageDurationUnitMenu: + name: NucelicAcidStorageDurationUnitMenu title: nucelic_acid_storage_duration_unit menu description: '' permissible_values: @@ -14371,8 +15135,8 @@ enums: text: Month [UO:0000035] Year [UO:0000036]: text: Year [UO:0000036] - food_packaging menu: - name: food_packaging menu + FoodPackagingMenu: + name: FoodPackagingMenu title: food_packaging menu description: '' permissible_values: @@ -14400,8 +15164,8 @@ enums: text: Paper container, untreated [FOODON:03490334] Plastic tray or pan [FOODON:03490126]: text: Plastic tray or pan [FOODON:03490126] - host (common name) menu: - name: host (common name) menu + HostCommonNameMenu: + name: HostCommonNameMenu title: host (common name) menu description: '' permissible_values: @@ -14497,8 +15261,8 @@ enums: Blue Mussel [NCBITaxon:6550]: text: Blue Mussel [NCBITaxon:6550] is_a: Shellfish [FOODON:03411433] - host (scientific name) menu: - name: host (scientific name) menu + HostScientificNameMenu: + name: HostScientificNameMenu title: host (scientific name) menu description: '' permissible_values: @@ -14544,8 +15308,8 @@ enums: text: Somateria mollissima [NCBITaxon:76058] Sus scrofa domesticus [NCBITaxon:9825]: text: Sus scrofa domesticus [NCBITaxon:9825] - host (food production name) menu: - name: host (food production name) menu + HostFoodProductionNameMenu: + name: HostFoodProductionNameMenu title: host (food production name) menu description: '' permissible_values: @@ -14692,8 +15456,8 @@ enums: Juvenile fish [FOODON_00004317]: text: Juvenile fish [FOODON_00004317] is_a: Fish [FOODON:03411222] - host_age_bin menu: - name: host_age_bin menu + HostAgeBinMenu: + name: HostAgeBinMenu title: host_age_bin menu description: '' permissible_values: @@ -14709,8 +15473,8 @@ enums: text: Third winter [GENEPIO:0100688] Third summer [GENEPIO:0100689]: text: Third summer [GENEPIO:0100689] - isolated_by menu: - name: isolated_by menu + IsolatedByMenu: + name: IsolatedByMenu title: isolated_by menu description: '' permissible_values: @@ -14726,8 +15490,8 @@ enums: text: Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]: text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu title: organism menu description: '' permissible_values: @@ -15075,8 +15839,8 @@ enums: Vibrio parahaemolyticus [NCBITaxon:670]: text: Vibrio parahaemolyticus [NCBITaxon:670] is_a: Vibrio [NCBITaxon:662] - taxonomic_identification_process menu: - name: taxonomic_identification_process menu + TaxonomicIdentificationProcessMenu: + name: TaxonomicIdentificationProcessMenu title: taxonomic_identification_process menu description: '' permissible_values: @@ -15091,8 +15855,8 @@ enums: Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099]: text: Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] - sequenced_by menu: - name: sequenced_by menu + SequencedByMenu: + name: SequencedByMenu title: sequenced_by menu description: '' permissible_values: @@ -15110,8 +15874,8 @@ enums: text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] McGill University [GENEPIO:0101103]: text: McGill University [GENEPIO:0101103] - purpose_of_sequencing menu: - name: purpose_of_sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu title: purpose_of_sequencing menu description: '' permissible_values: @@ -15137,8 +15901,8 @@ enums: is_a: Research [GENEPIO:0100003] Surveillance [GENEPIO:0100004]: text: Surveillance [GENEPIO:0100004] - sequencing_platform menu: - name: sequencing_platform menu + SequencingPlatformMenu: + name: SequencingPlatformMenu title: sequencing_platform menu description: '' permissible_values: @@ -15154,8 +15918,8 @@ enums: text: BGI Genomics [GENEPIO:0004324] MGI [GENEPIO:0004325]: text: MGI [GENEPIO:0004325] - sequencing_instrument menu: - name: sequencing_instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu title: sequencing_instrument menu description: '' permissible_values: @@ -15297,8 +16061,8 @@ enums: DNBSEQ-G50 [GENEPIO:0100150]: text: DNBSEQ-G50 [GENEPIO:0100150] is_a: DNBSEQ [GENEPIO:0100146] - sequencing_assay_type menu: - name: sequencing_assay_type menu + SequencingAssayTypeMenu: + name: SequencingAssayTypeMenu title: sequencing_assay_type menu description: '' permissible_values: @@ -15314,8 +16078,8 @@ enums: Whole virome sequencing assay [OBI:0002768]: text: Whole virome sequencing assay [OBI:0002768] is_a: Whole metagenome sequencing assay [OBI:0002623] - genomic_target_enrichment_method menu: - name: genomic_target_enrichment_method menu + GenomicTargetEnrichmentMethodMenu: + name: GenomicTargetEnrichmentMethodMenu title: genomic_target_enrichment_method menu description: '' permissible_values: @@ -15323,8 +16087,8 @@ enums: text: Hybrid selection method (bait-capture) [GENEPIO:0001950] rRNA depletion method [GENEPIO:0101020]: text: rRNA depletion method [GENEPIO:0101020] - sequence_submitted_by menu: - name: sequence_submitted_by menu + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu title: sequence_submitted_by menu description: '' permissible_values: @@ -15342,8 +16106,8 @@ enums: text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] McGill University [GENEPIO:0101103]: text: McGill University [GENEPIO:0101103] - quality_control_determination menu: - name: quality_control_determination menu + QualityControlDeterminationMenu: + name: QualityControlDeterminationMenu title: quality_control_determination menu description: '' permissible_values: @@ -15359,8 +16123,8 @@ enums: text: Sequence flagged for potential quality control issues [GENEPIO:0100566] Quality control not performed [GENEPIO:0100567]: text: Quality control not performed [GENEPIO:0100567] - quality _control_issues menu: - name: quality _control_issues menu + QualityControlIssuesMenu: + name: QualityControlIssuesMenu title: quality _control_issues menu description: '' permissible_values: @@ -15380,8 +16144,8 @@ enums: text: Low signal to noise ratio [GENEPIO:0100574] Low coverage of characteristic mutations [GENEPIO:0100575]: text: Low coverage of characteristic mutations [GENEPIO:0100575] - attribute_package menu: - name: attribute_package menu + AttributePackageMenu: + name: AttributePackageMenu title: attribute_package menu description: '' permissible_values: @@ -15389,11 +16153,6 @@ enums: text: Pathogen.cl [GENEPIO:0001835] Pathogen.env [GENEPIO:0100581]: text: Pathogen.env [GENEPIO:0100581] - experimental_intervention menu: - name: experimental_intervention menu - title: experimental_intervention menu - description: '' - permissible_values: Addition of substances to food/water [GENEPIO:0100536]: text: Addition of substances to food/water [GENEPIO:0100536] Antimicrobial pre-treatment [GENEPIO:0100537]: @@ -15418,8 +16177,8 @@ enums: text: Probiotic pre-treatment [GENEPIO:0100547] Vaccination [NCIT:C15346]: text: Vaccination [NCIT:C15346] - AMR_testing_by menu: - name: AMR_testing_by menu + AMRTestingByMenu: + name: AMRTestingByMenu title: AMR_testing_by menu description: '' permissible_values: @@ -15435,8 +16194,8 @@ enums: text: Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] Fisheries and Oceans Canada (DFO) [GENEPIO:0100556]: text: Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - antimicrobial_phenotype menu: - name: antimicrobial_phenotype menu + AntimicrobialPhenotypeMenu: + name: AntimicrobialPhenotypeMenu title: antimicrobial_phenotype menu description: '' permissible_values: @@ -15456,8 +16215,8 @@ enums: text: Susceptible antimicrobial phenotype [ARO:3004302] Susceptible dose dependent antimicrobial phenotype [ARO:3004304]: text: Susceptible dose dependent antimicrobial phenotype [ARO:3004304] - antimicrobial_measurement_units menu: - name: antimicrobial_measurement_units menu + AntimicrobialMeasurementUnitsMenu: + name: AntimicrobialMeasurementUnitsMenu title: antimicrobial_measurement_units menu description: '' permissible_values: @@ -15467,8 +16226,8 @@ enums: text: millimetre (mm) [UO:0000016] microgram per millilitre (ug/mL) [UO:0000274]: text: microgram per millilitre (ug/mL) [UO:0000274] - antimicrobial_measurement_sign menu: - name: antimicrobial_measurement_sign menu + AntimicrobialMeasurementSignMenu: + name: AntimicrobialMeasurementSignMenu title: antimicrobial_measurement_sign menu description: '' permissible_values: @@ -15482,22 +16241,26 @@ enums: text: greater than (>) [GENEPIO:0001006] greater than or equal to (>=) [GENEPIO:0001005]: text: greater than or equal to (>=) [GENEPIO:0001005] - antimicrobial_laboratory_typing_method menu: - name: antimicrobial_laboratory_typing_method menu + AntimicrobialLaboratoryTypingMethodMenu: + name: AntimicrobialLaboratoryTypingMethodMenu title: antimicrobial_laboratory_typing_method menu description: '' permissible_values: Agar diffusion [NCIT:85595]: text: Agar diffusion [NCIT:85595] + exact_mappings: + - NCBI_ANTIBIOGRAM:disk%20diffusion Antimicrobial gradient (E-test) [NCIT:85596]: text: Antimicrobial gradient (E-test) [NCIT:85596] is_a: Agar diffusion [NCIT:85595] Agar dilution [ARO:3004411]: text: Agar dilution [ARO:3004411] + exact_mappings: + - NCBI_ANTIBIOGRAM:agar%20dilution Broth dilution [ARO:3004397]: text: Broth dilution [ARO:3004397] - antimicrobial_laboratory_typing_platform menu: - name: antimicrobial_laboratory_typing_platform menu + AntimicrobialLaboratoryTypingPlatformMenu: + name: AntimicrobialLaboratoryTypingPlatformMenu title: antimicrobial_laboratory_typing_platform menu description: '' permissible_values: @@ -15505,51 +16268,90 @@ enums: text: BIOMIC Microbiology System [ARO:3007569] Microscan [ARO:3004400]: text: Microscan [ARO:3004400] + exact_mappings: + - NCBI_ANTIBIOGRAM:Microscan Phoenix [ARO:3004401]: text: Phoenix [ARO:3004401] + exact_mappings: + - NCBI_ANTIBIOGRAM:Phoenix Sensititre [ARO:3004402]: text: Sensititre [ARO:3004402] + exact_mappings: + - NCBI_ANTIBIOGRAM:Sensititre Vitek System [ARO:3004403]: text: Vitek System [ARO:3004403] - antimicrobial_vendor_name menu: - name: antimicrobial_vendor_name menu + exact_mappings: + - NCBI_ANTIBIOGRAM:Vitek + AntimicrobialVendorNameMenu: + name: AntimicrobialVendorNameMenu title: antimicrobial_vendor_name menu description: '' permissible_values: Becton Dickinson [ARO:3004405]: text: Becton Dickinson [ARO:3004405] + exact_mappings: + - NCBI_ANTIBIOGRAM:Becton%20Dickinson "bioM\xE9rieux [ARO:3004406]": text: "bioM\xE9rieux [ARO:3004406]" + exact_mappings: + - NCBI_ANTIBIOGRAM:Biom%C3%A9rieux Omron [ARO:3004408]: text: Omron [ARO:3004408] Siemens [ARO:3004407]: text: Siemens [ARO:3004407] + exact_mappings: + - NCBI_ANTIBIOGRAM:Siemens Trek [ARO:3004409]: text: Trek [ARO:3004409] - antimicrobial_testing_standard menu: - name: antimicrobial_testing_standard menu + exact_mappings: + - NCBI_ANTIBIOGRAM:Trek + AntimicrobialTestingStandardMenu: + name: AntimicrobialTestingStandardMenu title: antimicrobial_testing_standard menu description: '' permissible_values: British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]: text: British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] + exact_mappings: + - NCBI_ANTIBIOGRAM:BSAC Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]: text: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] + exact_mappings: + - NCBI_ANTIBIOGRAM:CLSI "Deutsches Institut f\xFCr Normung (DIN) [ARO:3004367]": text: "Deutsches Institut f\xFCr Normung (DIN) [ARO:3004367]" + exact_mappings: + - NCBI_ANTIBIOGRAM:DIN European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]: text: European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] + exact_mappings: + - NCBI_ANTIBIOGRAM:EUCAST National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]: text: National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] + exact_mappings: + - NCBI_ANTIBIOGRAM:NARMS National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]: text: National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] + exact_mappings: + - NCBI_ANTIBIOGRAM:NCCLS "Soci\xE9t\xE9 Fran\xE7aise de Microbiologie (SFM) [ARO:3004369]": text: "Soci\xE9t\xE9 Fran\xE7aise de Microbiologie (SFM) [ARO:3004369]" + exact_mappings: + - NCBI_ANTIBIOGRAM:SFM Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]: text: Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] + exact_mappings: + - NCBI_ANTIBIOGRAM:SIR Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]: text: Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] + exact_mappings: + - NCBI_ANTIBIOGRAM:WRG + AntimicrobialResistanceTestDrugMenu: + name: AntimicrobialResistanceTestDrugMenu + title: Antimicrobial Resistance Test Drug Menu + description: '' + permissible_values: {} types: WhitespaceMinimizedString: name: WhitespaceMinimizedString diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index a136bfd5..1c04f806 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -1,1518 +1,1521 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description - -null value menu Not Applicable [GENEPIO:0001619] - Missing [GENEPIO:0001618] - Not Collected [GENEPIO:0001620] - Not Provided [GENEPIO:0001668] - Restricted Access [GENEPIO:0001810] - -sample_collected_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - University of Manitoba (UM) [GENEPIO:0004434] - - -purpose_of_sampling menu Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549] - Field experiment [GENEPIO:0100550] - Survey study [GENEPIO:0100582] - Surveillance [GENEPIO:0100004] - - -presampling_activity menu Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538] - Certified humane animal husbandry practices [GENEPIO:0100894] - Certified organic farming practices [GENEPIO:0100539] - Conventional farming practices [GENEPIO:0100895] - Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543] - Genetic mutation [GENEPIO:0100544[ - Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346] - -experimental_specimen_role_type menu Positive experimental control [GENEPIO:0101018] - Negative experimental control [GENEPIO:0101019] - Technical replicate [EFO:0002090] - Biological replicate [EFO:0002091] - - -specimen_processing menu Biological replicate process [GENEPIO:0101022] - Samples pooled [OBI:0600016] - Technical replicate process [GENEPIO:0101021] - Isolated from single source [OBI:0002079] - - -geo_loc_name (country) menu Afghanistan [GAZ:00006882] - Albania [GAZ:00002953] - Algeria [GAZ:00000563] - American Samoa [GAZ:00003957] - Andorra [GAZ:00002948] - Angola [GAZ:00001095] - Anguilla [GAZ:00009159] - Antarctica [GAZ:00000462] - Antigua and Barbuda [GAZ:00006883] - Argentina [GAZ:00002928] - Armenia [GAZ:00004094] - Aruba [GAZ:00004025] - Ashmore and Cartier Islands [GAZ:00005901] - Australia [GAZ:00000463] - Austria [GAZ:00002942] - Azerbaijan [GAZ:00004941] - Bahamas [GAZ:00002733] - Bahrain [GAZ:00005281] - Baker Island [GAZ:00007117] - Bangladesh [GAZ:00003750] - Barbados [GAZ:00001251] - Bassas da India [GAZ:00005810] - Belarus [GAZ:00006886] - Belgium [GAZ:00002938] - Belize [GAZ:00002934] - Benin [GAZ:00000904] - Bermuda [GAZ:00001264] - Bhutan [GAZ:00003920] - Bolivia [GAZ:00002511] - Borneo [GAZ:00025355] - Bosnia and Herzegovina [GAZ:00006887] - Botswana [GAZ:00001097] - Bouvet Island [GAZ:00001453] - Brazil [GAZ:00002828] - British Virgin Islands [GAZ:00003961] - Brunei [GAZ:00003901] - Bulgaria [GAZ:00002950] - Burkina Faso [GAZ:00000905] - Burundi [GAZ:00001090] - Cambodia [GAZ:00006888] - Cameroon [GAZ:00001093] - Canada [GAZ:00002560] - Cape Verde [GAZ:00001227] - Cayman Islands [GAZ:00003986] - Central African Republic [GAZ:00001089] - Chad [GAZ:00000586] - Chile [GAZ:00002825] - China [GAZ:00002845] - Christmas Island [GAZ:00005915] - Clipperton Island [GAZ:00005838] - Cocos Islands [GAZ:00009721] - Colombia [GAZ:00002929] - Comoros [GAZ:00005820] - Cook Islands [GAZ:00053798] - Coral Sea Islands [GAZ:00005917] - Costa Rica [GAZ:00002901] - Cote d'Ivoire [GAZ:00000906] - Croatia [GAZ:00002719] - Cuba [GAZ:00003762] - Curacao [GAZ:00012582] - Cyprus [GAZ:00004006] - Czech Republic [GAZ:00002954] - Democratic Republic of the Congo [GAZ:00001086] - Denmark [GAZ:00005852] - Djibouti [GAZ:00000582] - Dominica [GAZ:00006890] - Dominican Republic [GAZ:00003952] - Ecuador [GAZ:00002912] - Egypt [GAZ:00003934] - El Salvador [GAZ:00002935] - Equatorial Guinea [GAZ:00001091] - Eritrea [GAZ:00000581] - Estonia [GAZ:00002959] - Eswatini [GAZ:00001099] - Ethiopia [GAZ:00000567] - Europa Island [GAZ:00005811] - Falkland Islands (Islas Malvinas) [GAZ:00001412] - Faroe Islands [GAZ:00059206] - Fiji [GAZ:00006891] - Finland [GAZ:00002937] - France [GAZ:00003940] - French Guiana [GAZ:00002516] - French Polynesia [GAZ:00002918] - French Southern and Antarctic Lands [GAZ:00003753] - Gabon [GAZ:00001092] - Gambia [GAZ:00000907] - Gaza Strip [GAZ:00009571] - Georgia [GAZ:00004942] - Germany [GAZ:00002646] - Ghana [GAZ:00000908] - Gibraltar [GAZ:00003987] - Glorioso Islands [GAZ:00005808] - Greece [GAZ:00002945] - Greenland [GAZ:00001507] - Grenada [GAZ:02000573] - Guadeloupe [GAZ:00067142] - Guam [GAZ:00003706] - Guatemala [GAZ:00002936] - Guernsey [GAZ:00001550] - Guinea [GAZ:00000909] - Guinea-Bissau [GAZ:00000910] - Guyana [GAZ:00002522] - Haiti [GAZ:00003953] - Heard Island and McDonald Islands [GAZ:00009718] - Honduras [GAZ:00002894] - Hong Kong [GAZ:00003203] - Howland Island [GAZ:00007120] - Hungary [GAZ:00002952] - Iceland [GAZ:00000843] - India [GAZ:00002839] - Indonesia [GAZ:00003727] - Iran [GAZ:00004474] - Iraq [GAZ:00004483] - Ireland [GAZ:00002943] - Isle of Man [GAZ:00052477] - Israel [GAZ:00002476] - Italy [GAZ:00002650] - Jamaica [GAZ:00003781] - Jan Mayen [GAZ:00005853] - Japan [GAZ:00002747] - Jarvis Island [GAZ:00007118] - Jersey [GAZ:00001551] - Johnston Atoll [GAZ:00007114] - Jordan [GAZ:00002473] - Juan de Nova Island [GAZ:00005809] - Kazakhstan [GAZ:00004999] - Kenya [GAZ:00001101] - Kerguelen Archipelago [GAZ:00005682] - Kingman Reef [GAZ:00007116] - Kiribati [GAZ:00006894] - Kosovo [GAZ:00011337] - Kuwait [GAZ:00005285] - Kyrgyzstan [GAZ:00006893] - Laos [GAZ:00006889] - Latvia [GAZ:00002958] - Lebanon [GAZ:00002478] - Lesotho [GAZ:00001098] - Liberia [GAZ:00000911] - Libya [GAZ:00000566] - Liechtenstein [GAZ:00003858] - Line Islands [GAZ:00007144] - Lithuania [GAZ:00002960] - Luxembourg [GAZ:00002947] - Macau [GAZ:00003202] - Madagascar [GAZ:00001108] - Malawi [GAZ:00001105] - Malaysia [GAZ:00003902] - Maldives [GAZ:00006924] - Mali [GAZ:00000584] - Malta [GAZ:00004017] - Marshall Islands [GAZ:00007161] - Martinique [GAZ:00067143] - Mauritania [GAZ:00000583] - Mauritius [GAZ:00003745] - Mayotte [GAZ:00003943] - Mexico [GAZ:00002852] - Micronesia [GAZ:00005862] - Midway Islands [GAZ:00007112] - Moldova [GAZ:00003897] - Monaco [GAZ:00003857] - Mongolia [GAZ:00008744] - Montenegro [GAZ:00006898] - Montserrat [GAZ:00003988] - Morocco [GAZ:00000565] - Mozambique [GAZ:00001100] - Myanmar [GAZ:00006899] - Namibia [GAZ:00001096] - Nauru [GAZ:00006900] - Navassa Island [GAZ:00007119] - Nepal [GAZ:00004399] - Netherlands [GAZ:00002946] - New Caledonia [GAZ:00005206] - New Zealand [GAZ:00000469] - Nicaragua [GAZ:00002978] - Niger [GAZ:00000585] - Nigeria [GAZ:00000912] - Niue [GAZ:00006902] - Norfolk Island [GAZ:00005908] - North Korea [GAZ:00002801] - North Macedonia [GAZ:00006895] - North Sea [GAZ:00002284] - Northern Mariana Islands [GAZ:00003958] - Norway [GAZ:00002699] - Oman [GAZ:00005283] - Pakistan [GAZ:00005246] - Palau [GAZ:00006905] - Panama [GAZ:00002892] - Papua New Guinea [GAZ:00003922] - Paracel Islands [GAZ:00010832] - Paraguay [GAZ:00002933] - Peru [GAZ:00002932] - Philippines [GAZ:00004525] - Pitcairn Islands [GAZ:00005867] - Poland [GAZ:00002939] - Portugal [GAZ:00004126] - Puerto Rico [GAZ:00006935] - Qatar [GAZ:00005286] - Republic of the Congo [GAZ:00001088] - Reunion [GAZ:00003945] - Romania [GAZ:00002951] - Ross Sea [GAZ:00023304] - Russia [GAZ:00002721] - Rwanda [GAZ:00001087] - Saint Helena [GAZ:00000849] - Saint Kitts and Nevis [GAZ:00006906] - Saint Lucia [GAZ:00006909] - Saint Pierre and Miquelon [GAZ:00003942] - Saint Martin [GAZ:00005841] - Saint Vincent and the Grenadines [GAZ:02000565] - Samoa [GAZ:00006910] - San Marino [GAZ:00003102] - Sao Tome and Principe [GAZ:00006927] - Saudi Arabia [GAZ:00005279] - Senegal [GAZ:00000913] - Serbia [GAZ:00002957] - Seychelles [GAZ:00006922] - Sierra Leone [GAZ:00000914] - Singapore [GAZ:00003923] - Sint Maarten [GAZ:00012579] - Slovakia [GAZ:00002956] - Slovenia [GAZ:00002955] - Solomon Islands [GAZ:00005275] - Somalia [GAZ:00001104] - South Africa [GAZ:00001094] - South Georgia and the South Sandwich Islands [GAZ:00003990] - South Korea [GAZ:00002802] - South Sudan [GAZ:00233439] - Spain [GAZ:00003936] - Spratly Islands [GAZ:00010831] - Sri Lanka [GAZ:00003924] - State of Palestine [GAZ:00002475] - Sudan [GAZ:00000560] - Suriname [GAZ:00002525] - Svalbard [GAZ:00005396] - Swaziland [GAZ:00001099] - Sweden [GAZ:00002729] - Switzerland [GAZ:00002941] - Syria [GAZ:00002474] - Taiwan [GAZ:00005341] - Tajikistan [GAZ:00006912] - Tanzania [GAZ:00001103] - Thailand [GAZ:00003744] - Timor-Leste [GAZ:00006913] - Togo [GAZ:00000915] - Tokelau [GAZ:00260188] - Tonga [GAZ:00006916] - Trinidad and Tobago [GAZ:00003767] - Tromelin Island [GAZ:00005812] - Tunisia [GAZ:00000562] - Turkey [GAZ:00000558] - Turkmenistan [GAZ:00005018] - Turks and Caicos Islands [GAZ:00003955] - Tuvalu [GAZ:00009715] - United States of America [GAZ:00002459] - Uganda [GAZ:00001102] - Ukraine [GAZ:00002724] - United Arab Emirates [GAZ:00005282] - United Kingdom [GAZ:00002637] - Uruguay [GAZ:00002930] - Uzbekistan [GAZ:00004979] - Vanuatu [GAZ:00006918] - Venezuela [GAZ:00002931] - Viet Nam [GAZ:00003756] - Virgin Islands [GAZ:00003959] - Wake Island [GAZ:00007111] - Wallis and Futuna [GAZ:00007191] - West Bank [GAZ:00009572] - Western Sahara [GAZ:00000564] - Yemen [GAZ:00005284] - Zambia [GAZ:00001107] - Zimbabwe [GAZ:00001106] - - -geo_loc_name (state/province/region) menu Atlantic region (Canada) [wikidata:Q246972] - New Brunswick [GAZ:00002570] - Newfoundland & Labrador [GAZ:00002567] - Nova Scotia [GAZ:00002565] - Prince Edward Island [GAZ:00002572] - Central region (Canada) [wikidata:Q1048064] - Ontario [GAZ:00002563] - Quebec [GAZ:00002569] - Northern region (Canada) [wikidata:Q764146] - Northwest Territories [GAZ:00002575] - Nunuvut [GAZ:00002574] - Yukon [GAZ:00002576] - Pacific region (Canada) [wikidata:Q122953299] - British Columbia [GAZ:00002562] - Prairie region (Canada) [wikidata:Q1364746] - Alberta [GAZ:00002566] - Manitoba [GAZ:00002571] - Saskatchewan [GAZ:00002564] - - -sample_collection_date_precision menu year [UO:0000036] - month [UO:0000035] - day [UO:0000033] - - -environmental_site menu Abattoir [ENVO:01000925] - Agricultural Field [ENVO:00000114] - Alluvial fan [ENVO:00000314] - Animal cage [ENVO:01000922] - Aquarium [ENVO:00002196] - Artificial wetland [ENVO:03501406] - Breeding ground [ENVO:03501441] - Building [ENVO:00000073] - Barn [ENVO:03501257] - Breeder barn [ENVO:03501383] - Broiler barn [ENVO:03501386] - Sheep barn [ENVO:03501385] - Biodome [ENVO:03501397] - Cottage [ENVO:03501393] - Dairy [ENVO:00003862] - Hospital [ENVO:00002173] - Laboratory facility [ENVO:01001406] - Pigsty [ENVO:03501413] - Building part (organizational term) - Air intake [ENVO:03501380] - Animal pen [ENVO:03501387] - Building floor [ENVO:01000486] - Building wall [ENVO:01000465] - Countertop [ENVO:03501404] - Shelf [ENVO:03501403] - Stall [EOL:0001903] - Window sill [ENVO:03501381] - Creek [ENVO:03501405] - Farm [ENVO:00000078] - Beef farm [ENVO:03501443] - Breeder farm [ENVO:03501384] - Dairy farm [ENVO:03501416] - Feedlot [ENVO:01000627] - Beef cattle feedlot [ENVO:03501444] - Fish farm [ENVO:00000294] - Research farm [ENVO:03501417] - Central Experimental Farm [GAZ:00004603] Central Experimental Farm - Freshwater environment [ENVO:01000306] - Hatchery [ENVO:01001873] - Poultry hatchery [ENVO:01001874] - Lake [ENVO:00000020] - Manure digester facility [ENVO:03501422] - Manure lagoon (Anaerobic lagoon) [ENVO:03501423] - Manure pit [ENVO:01001872] - Marine environment [ENVO:01000320] - Benthic zone [ENVO:03501440] - Pelagic zone [ENVO:00000208] - Park [ENVO:00000562] - Pond [ENVO:00000033] - Reservoir [ENVO:00000025] - Irrigation reservoir [ENVO:00000450] - Retail environment [ENVO:01001448] - Shop [ENVO:00002221] - Butcher shop [ENVO:03501396] - Pet store [ENVO:03501395] - Supermarket [ENVO:01000984] - River [ENVO:00000022] - Roost (bird) [ENVO:03501439] - Rural area [ENVO:01000772] - Slough [ENVO:03501438] - Stream [ENVO:00000023] - Trailer [ENVO:03501394] - Tributary [ENVO:00000495] - Truck [ENVO:01000602] - Urban area [ENVO:03501437] - Water surface [ENVO:01001191] - Woodland area [ENVO:00000109] - Zoo [ENVO:00010625] - - -water_depth_units menu centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - kilometer (km) [UO:0010066] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - - -sediment_depth_units menu centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - kilometer (km) [UO:0010066] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - - -air_temperature_units menu degree Fahrenheit (F) [UO:0000195] - degree Celsius (C) [UO:0000027] - - -water_temperature_units menu degree Fahrenheit (F) [UO:0000195] - degree Celsius (C) [UO:0000027] - - -available_data_types menu Documentation [GENEPIO:0100702] - Experimental parameters documentation [GENEPIO:0100703] - Feed history [GENEPIO:0100704] - Land use information [GENEPIO:0100705] - Therapeutic administration history [GENEPIO:0100706] - Chemical characterization [GENEPIO:0100707] - pH measurement [GENEPIO:0100708] - Dissolved oxygen measurement [GENEPIO:0100709] - Nitrate measurement [GENEPIO:0100710] - Nitrite measurement [GENEPIO:0100711] - Phosphorous measurement [GENEPIO:0100712] - Salinity measurement [GENEPIO:0100713] - Microbiological characterization [GENEPIO:0100714] - Microbiological identification [GENEPIO:0100715] - Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] - Microbiological identification (bioMérieux API) [GENEPIO:0100717] - Microbiological identification (Biolog) [GENEPIO:0100718] - Microbiological identification (FAME) [GENEPIO:0100719] - Microbiological identification (Sensititre) [GENEPIO:0100720] - Microbiological identification (ViTek) [GENEPIO:0100721] - Phage type [GENEPIO:0100722] - Serotype [GENEPIO:0100723] - Phenotypic microbiological characterization [GENEPIO:0100724] - AMR phenotypic testing [GENEPIO:0100725] - Biolog phenotype microarray [GENEPIO:0100726] - Microbiological quantification [GENEPIO:0100727] - Colony count [GENEPIO:0100728] - Total coliform count [GENEPIO:0100729] - Total fecal coliform count [GENEPIO:0100730] - Infectivity assay [GENEPIO:0100731] - ELISA toxin binding [GENEPIO:0100732] - Molecular characterization [GENEPIO:0100733] - 16S rRNA Sanger sequencing [GENEPIO:0100734] - Metagenomic sequencing [GENEPIO:0101024] - PCR marker detection [GENEPIO:0100735] - BOX PCR fingerprint [GENEPIO:0100736] - ERIC PCR fingerprint [GENEPIO:0100737] - Plasmid type [GENEPIO:0100738] - Ribotype [GENEPIO:0100739] - Molecular quantification [GENEPIO:0100740] - qPCR marker organism quantification [GENEPIO:0100741] - Physical characterization [GENEPIO:0100742] - Conductivity measurement [GENEPIO:0100743] - Mollusc shell measurement [GENEPIO:0100744] - Mollusc shell length [GENEPIO:0100745] - Matter compostion [GENEPIO:0100746] - Dry matter composition [GENEPIO:0100747] - Organic matter composition [GENEPIO:0100748] - Turbidity measurement [GENEPIO:0100749] - - -weather_type menu Cloudy/Overcast [ENVO:03501418] - Partially cloudy [ENVO:03501419] - Drizzle [ENVO:03501420] - Fog [ENVO:01000844] - Rain [ENVO:01001564] - Snow [ENVO:01000406] - Storm [ENVO:01000876] - Sunny/Clear [ENVO:03501421] - - -animal_or_plant_population menu Algae [FOODON:03411301] - Algal bloom [ENVO:2000004] - Cattle [NCBITaxon:9913] - Beef cattle [FOODON:00004413] - Dairy cattle [FOODON:00002505] - Chicken [NCBITaxon:9031] - Crop [AGRO:00000325] - Fish [FOODON:03411222] - Pig [NCBITaxon:9823] - Poultry [FOODON:00004298] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Crustacean [FOODON:03411374] - Mollusc [FOODON:03412112] - Tropical fish [FOODON:00004283] - Turkey [NCBITaxon:9103] - Wildlife [FOODON:00004503] - Wild bird [FOODON:00004505] - Seabird [FOODON:00004504] - - - -environmental_material menu Air [ENVO:00002005] - Alluvium [ENVO:01001202] - Animal feeding equipment [AGRO:00000675] - Animal feeder [AGRO:00000679] - Animal drinker [AGRO:00000680] - Feed pan [AGRO:00000676] - Watering bowl [AGRO:00000677] - Animal transportation equipment [AGRO:00000671] - Dead haul trailer [GENEPIO:0100896] - Dead haul truck [AGRO:00000673] - Live haul trailer [GENEPIO:0100897] - Live haul truck [AGRO:00000674] - Belt [NCIT:C49844] - Biosolids [ENVO:00002059] - Boot [GSSO:012935] - Boot cover [OBI:0002806] - Broom [ENVO:03501431] - Bulk tank [ENVO:03501379] - Chick box [AGRO:00000678] - Chick pad [AGRO:00000672] - Cleaning equipment [ENVO:03501430] - Compost [ENVO:00002170] - Contaminated water [ENVO:00002186] - Fecal slurry [ENVO:03501436] - Fluid from meat rinse [GENEPIO:0004323] - Effluent [ENVO:03501407] - Influent [ENVO:03501442] - Surface runoff [ENVO:03501408] - Poultry plucking water [AGRO_00000693] - Wastewater [ENVO:00002001] - Weep fluid [AGRO_00000692] - Crate [ENVO:03501372] - Dumpster [ENVO:03501400] - Dust [ENVO:00002008] - Egg belt [AGRO:00000670] - Fan [NCIT:C49947] - Freezer [ENVO:03501415] - Freezer handle [ENVO:03501414] - Manure [ENVO:00003031] - Animal manure [AGRO:00000079] - Pig manure [AGRO:00000080] - Manure digester equipment [ENVO:03501424] - Nest [ENVO:03501432] - Bird's nest [ENVO:00005805] - Permafrost [ENVO:00000134] - Plucking belt [AGRO:00000669] - Poultry fluff [UBERON:0008291] - Poultry litter [AGRO:00000080] - Sediment [ENVO:00002007] - Soil [ENVO:00001998] - Agricultural soil [ENVO:00002259] - Forest soil [ENVO:00002261] - Straw [ENVO:00003869] - Canola straw [FOODON:00004430] - Oat straw [FOODON:03309878] - Barley straw [FOODON:00004559] - Water [CHEBI:15377] - Drinking water [ENVO:00003064] - Groundwater [ENVO:01001004] - Surface water [ENVO:00002042] - - -anatomical_material menu Blood [UBERON:0000178] - Fluid [UBERON:0006314] - Fluid (cerebrospinal (CSF)) [UBERON:0001359] - Fluid (amniotic) [UBERON:0000173] - Saliva [UBERON:0001836] - Tissue [UBERON:0000479] - - -body_product menu Digestive tract substance [GENEPIO:0100898] - Caecal content [GENEPIO:0100899] - Intestinal content [GENEPIO:0100900] - Stomach content [GENEPIO:0100901] - Feces [UBERON:0001988] - Fecal composite [GENEPIO:0004512] - Feces (fresh) [GENEPIO:0004513] - Feces (environmental) [GENEPIO:0004514] - Meconium [UBERON:0007109] - Milk [UBERON:0001913] - Colostrum [UBERON:0001914] - Urine [UBERON:0001088] - - -anatomical_part menu Carcass [UBERON:0008979] - Swine carcass [FOODON:03311719] - Digestive system [UBERON:0001007] - Caecum [UBERON:0001153] - Colon [UBERON:0001155] - Digestive gland [UBERON:0006925] - Foregut [UBERON:0001041] - Gall bladder [UBERON:0002110] - Gastrointestinal system mucosa [UBERON:0004786] - Gizzard [UBERON:0005052] - Hindgut [UBERON:0001046] - Intestine [UBERON:0000160] - Small intestine [UBERON:0002108] - Duodenum [UBERON:0002114] - Ileum [UBERON:0002116] - Jejunum [UBERON:0002115] - Stomach [UBERON:0000945] - Abomasum [UBERON:0007358] - Rumen [UBERON:0007365] - Excretory system (organizational term) - Anus [UBERON:0001245] - Anal gland [UBERON:0011253] - Cloaca [UBERON:0000162] - Liver [UBERON:0002107] - Kidney [UBERON:0002113] - Rectum [UBERON:0001052] - Spleen [UBERON:0002106] - Urinary bladder [UBERON:0001255] - Foot [UBERON:0002387] - Head [UBERON:0000033] - Brain [UBERON:0000955] - Ear [UBERON:0001690] - Eye [UBERON:0000970] - Mouth [UBERON:0000165] - Nose [UBERON:0000004] - Nasal turbinal [UBERON:0035612] - Nasopharynx (NP) [UBERON:0001728] - Pair of nares [UBERON:0002109] - Paranasal sinus [UBERON:0001825] - Snout [UBERON:0006333] - Lymphatic system [UBERON:0006558] - Lymph node [UBERON:0000029] - Mesenteric lymph node [UBERON:0002509] - Mantle (bird) [GENEPIO:0100927] - Neck [UBERON:0000974] - Esophagus [UBERON:0001043] - Trachea [UBERON:0003126] - Nerve [UBERON:0001021] - Spinal cord [UBERON:0002240] - Organs or organ parts [GENEPIO:0001117] - Organ [UBERON:0000062] - Muscle organ [UBERON:0001630] - Skin of body [UBERON:0002097] - Reproductive system [UBERON:0000990] - Embryo [UBERON:0000922] - Fetus [UBERON:0000323] - Ovary [UBERON:0000992] - Oviduct [UBERON:0000993] - Placenta [UBERON:0001987] - Testis [UBERON:0000473] - Udder [UBERON:0013216] - Uterus [UBERON:0000995] - Vagina [UBERON:0000996] - Yolk sac [UBERON:0001040] - Respiratory system [UBERON:0001004] - Air sac [UBERON:0009060] - Lung [UBERON:0002048] - Pleura [UBERON:0000977] - Respiratory system mucosa [UBERON:0004785] - Skeletal system [UBERON:0001434] - Skeletal joint [UBERON:0000982] - Bone element [UBERON:0001474] - Thoracic segment of trunk [UBERON:0000915] - Abdomen [UBERON:0000916] - Muscle of abdomen [UBERON:0002378] - Peritoneum [UBERON:0002358] - Vascular system [UBERON:0007798] - Blood vessel [UBERON:0001981] - Bursa of Fabricius [UBERON:0003903] - Gill [UBERON:0002535] - Heart [UBERON:0000948] - Lung [UBERON:0002048] - Pericardium [UBERON:0002407] - Vent (anatomical) [UBERON:2000298] - Bird vent [UBERON:0012464] - Fish vent [GENEPIO:0100902] - - -anatomical_region menu Dorso-lateral region [BSPO:0000080] - Exterior anatomical region [BSPO:0000034] - Interior anatomical region [BSPO:0000033] - - -food_product menu Animal feed [ENVO:02000047] - Blood meal [FOODON:00001564] - Bone meal [ENVO:02000054] - Brassica carinata meal [FOODON:00004310] - Canola meal [FOODON:00002694] - Compound feed premix [FOODON:00004323] - Compound feed premix (medicated) [FOODON:00004324] - Feather meal [FOODON:00003927] - Fish meal [FOODON:03301620] - Lay ration [FOODON:00004286] - Meat and bone meal [FOODON:00002738] - Meat meal [FOODON:00004282] - Pet food [FOODON:00002682] - Soybean meal [FOODON:03302757] - Animal feed ingredient [FOODON:00004322] - Dairy food product [FOODON:00001256] - Cheese block (whole or parts) [FOODON:03000287] - Cow skim milk (powdered) [FOODON:03310016] - Milk [UBERON:0001913] - Dietary supplement [FOODON:03401298] - Egg or egg component [FOODON:03420194] - Balut [FOODON:03302184] - Egg yolk [UBERON:0007378] - Poultry egg [FOODON:03000414] - Hen egg (whole) [FOODON:03316061] - Poultry egg (whole, shell on) [FOODON:03000415] - Food mixture [FOODON:00004130] - Food product analog (food subsitute) [FOODON:00001871] - Milk substitute [FOODON:03305408] - Meat (whole or parts) [FOODON:03317170] - Cutlet [FOODON:00003001] - Filet [FOODON:03530144] - Liver (whole, raw) [FOODON:03309772] - Meat trim [FOODON:03309475] - Rib (meat cut) [FOODON:03530023] - Rib chop [FOODON:00004290] - Shoulder (meat cut) [FOODON:03530043] - Grains, cereals, and bakery product (organizational term) - Bread loaf (whole or parts) [FOODON:03000288] - Breakfast cereal [FOODON:03311075] - Bulk grain [FOODON:03309390] - Oat grain [FOODON:00003429] - Legume food product [FOODON:00001264] - Chickpea (whole) [FOODON:03306811] - Hummus [FOODON:00003049] - Soybean (whole or parts) [FOODON:03000245] - Meat, poultry and fish (organizational term) - Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, boneless) [FOODON:0001282] - Beef (ground, extra lean) [FOODON:02000426] - Beef (ground, lean) [FOODON:02000425] - Beef (ground, medium) [FOODON:02000427] - Beef (ground, regular) [FOODON:02000428] - Beef (ground, sirloin) [FOODON:02000429] - Beef hamburger (dish) [FOODON:00002737] - Beef shoulder [FOODON:02000069] - Beef shoulder chop [FOODON:03000387] - Beef sirloin chop [FOODON:03000389] - Beef stew chunk [FOODON:00004288] - Beef tenderloin [FOODON:00003302] - Beef (pieces) [FOODON:02000412] - Brisket [FOODON:03530020] - Chicken breast [FOODON:00002703] - Chicken breast (back off) [FOODON:03000385] - Chicken breast (skinless) [FOODON:02020231] - Chicken breast (with skin) [FOODON:02020233] - Chicken breast (skinless, boneless) [FOODON:02020235] - Chicken breast cutlet [FOODON:00004308] - Chicken drumstick [FOODON:00002716] - Chicken drumstick (skinless) [FOODON:02020237] - Chicken drumstick(with skin) [FOODON:02020239] - Chicken meat [FOODON:00001040] - Chicken meat (ground) [FOODON:02020311] - Chicken meat (ground or minced, lean) [FOODON:03000392] - Chicken meat (ground or minced, extra lean) [FOODON:03000396] - Chicken meat (ground or minced, medium) [FOODON:03000400] - Chicken meat (ground or minced, regular) [FOODON:03000404] - Chicken meat (ground or minced, boneless) [FOODON:03000410] - Chicken nugget [FOODON:00002672] - Chicken thigh [FOODON:02020219] - Chicken thigh (skinless) [FOODON:00003331] - Chicken thigh (skinless, with bone) [FOODON:02020227] - Chicken thigh (skinless, boneless) [FOODON:02020228] - Chicken upper thigh [FOODON:03000381] - Chicken upper thigh (with skin) [FOODON:03000383] - Chicken thigh (with skin) [FOODON:00003330] - Chicken thigh (with skin, with bone) [FOODON_00003363] - Chicken wing [FOODON:00002674] - Fish food product [FOODON:00001248] - Fish steak [FOODON:00002986] - Ham food product [FOODON:00002502] - Head cheese [FOODON:03315658] - Lamb [FOODON:03411669] - Meat strip [FOODON:00004285] - Mutton [FOODON:00002912] - Pork chop [FOODON:00001049] - pork meat (ground) [FOODON:02021718] - Pork meat (ground or minced, boneless) [FOODON:03000413] - Pork meat (ground or minced, extra lean) [FOODON:03000399] - Pork meat (ground or minced, lean) [FOODON:03000395] - Pork meat (ground or minced, medium) [FOODON:03000403] - Pork meat (ground or minced, regular) [FOODON:03000407] - Pork meat (ground or minced, Sirloin) [FOODON:03000409] - Pork shoulder [FOODON:02000322] - Pork shoulder chop [FOODON:03000388] - Pork sirloin chop [FOODON:02000300] - Pork steak [FOODON:02021757] - Pork tenderloin [FOODON:02000306] - Poultry meat [FOODON:03315883] - Leg (poultry meat cut) [FOODON:03530159] - Poultry drumstick [FOODON:00003469] - Neck (poultry meat cut) [FOODON:03530294] - Thigh (poultry meat cut) [FOODON:03530160] - Wing (poultry meat cut) [FOODON:03530157] - Sausage (whole) [FOODON:03315904] - Pepperoni [FOODON:03311003] - Salami [FOODON:03312067] - Shellfish [FOODON:03411433] - Mussel [FOODON:03411223] - Oyster FOODON:03411224] - Shrimp [FOODON:03301673] - Scallop [FOODON:02020805] - Squid [FOODON:03411205] - Turkey breast [FOODON:00002690] - Turkey breast (back off) [FOODON:03000386] - Turkey breast (skinless) [FOODON:02020495] - Turkey breast (skinless, boneless) [FOODON:02020499] - Turkey breast (with skin) [FOODON:02020497] - Turkey drumstick [FOODON:02020477] - Turkey drumstick (skinless) [FOODON:02020501] - Turkey drumstick (with skin) [FOODON:02020503] - Turkey meat [FOODON:00001286] - Turkey meat (ground) [FOODON:02020577] - Turkey meat (ground or minced, lean) [FOODON:03000393] - Turkey meat (ground or minced, extra lean) [FOODON:03000397] - Turkey meat (ground or minced, medium) [FOODON:03000401] - Turkey meat (ground or minced, regular) [FOODON:03000405] - Turkey meat (ground or minced, boneless) [FOODON:03000411] - Turkey thigh [FOODON:00003325] - Turkey thigh (skinless) [FOODON:00003329] - Turkey thigh (skinless, boneless) [FOODON:02020491] - Turkey thigh (with skin) [FOODON:00003328] - Turkey upper thigh [FOODON:03000382] - Turkey upper thigh (with skin) [FOODON:03000384] - Turkey wing [FOODON:02020478] - Veal [FOODON:00003083] - Formula fed veal [FOODON:000039111] - Grain-fed veal [FOODON:00004280] - Microbial food product [FOODON:00001145] - Yeast [FOODON:03411345] - Nuts and seed products - Almond (whole or parts) [FOODON:03000218] - Almond (whole) [FOODON:00003523] - Barley seed [FOODON:00003394] - Canola seed [FOODON:00004560] - Chia seed powder [FOODON:00003925] - Chia seed (whole or parts) [FOODON:03000241] - Flaxseed powder [FOODON:00004276] - Hazelnut [FOODON:00002933] - Nut (whole or part) [FOODON:03306632] - Peanut butter [FOODON:03306867] - Sesame seed [FOODON:03310306] - Tahini [FOODON:00003855] - Walnut (whole or parts) [FOODON:03316466] - Prepared food product [FOODON:00001180] - Condiment [FOODON:03315708] - Confectionery food product [FOODON:00001149] - Snack food [FOODON:03315013] - Produce [FOODON:03305145] - Apple (whole or parts) [FOODON:03310788] - Apple (whole) [FOODON:00002473] - Arugula greens bunch [FOODON:00003643] - Avocado [FOODON:00003600] - Cantaloupe (whole or parts) [FOODON:03000243] - Chilli pepper [FOODON:00003744] - Coconut (whole or parts) [FOODON:03309861] - Coconut meat [FOODON:00003856] - Corn cob (whole or parts) [FOODON:03310791] - Cucumber (whole or parts) [FOODON:03000229] - Fruit [PO:0009001] - Goji berry [FOODON:00004360] - Greens (raw) [FOODON:03310765] - Kale leaf (whole or parts) [FOODON:03000236] - Karela (bitter melon) [FOODON:00004367] - Lettuce head (whole or parts) [FOODON:03000239] - Mango (whole or parts) [FOODON:03000217] - Mushroom (fruitbody) [FOODON:00003528] - Papaya (whole or parts) [FOODON:03000228] - Pattypan squash (whole or parts) [FOODON:03000232] - Peach [FOODON:00002485] - Pepper (whole or parts) [FOODON:03000249] - Potato [FOODON:03315354] - Salad [FOODON:03316042] - Scallion (whole or parts) [FOODON:03000250] - Spinach (whole or parts) [FOODON:03000221] - Sprout [FOODON:03420183] - Germinated or sprouted seed [FOODON:03420102] - Alfalfa sprout [FOODON:00002670] - Bean sprout [FOODON:00002576] - Chia sprout [FOODON:03000180] - Mixed sprouts [FOODON:03000182] - Mung bean sprout [FOODON:03301446] - Tomato (whole or pieces) [FOODON:00002318] - Vegetable (whole or parts) [FOODON:03315308] - Spice or herb [FOODON:00001242] - Basil (whole or parts) [FOODON:03000233] - Black pepper (whole or parts) [FOODON:03000242] - Cardamom (whole or parts) [FOODON:03000246] - Chive leaf (whole or parts) [FOODON:03000240] - Coriander powder [FOODON:00004274] - Coriander seed (whole or parts) [FOODON:03000224] - Cumin powder [FOODON:00004275] - Cumin seed (whole) [FOODON:00003396] - Black cumin seed (whole or parts) [FOODON:03000247] - Curry leaf (whole or parts) [FOODON:03000225] - Curry powder [FOODON:03301842] - Dill spice [FOODON:00004307] - Fennel (whole or parts) [FOODON:03000244] - Garlic powder [FOODON:03301844] - Ginger root (whole or parts) [FOODON:03000220] - Mint leaf (whole or parts) [FOODON:03000238] - Oregano (whole or parts) [FOODON:03000226] - Paprika (ground) [FOODON:03301223] - Parsley leaf (whole or parts) [FOODON:03000231] - Pepper (ground) [FOODON:03301526] - Rasam powder [FOODON:00004277] - Sage [FOODON:03301560] - Turmeric (ground) [FOODON:03310841] - Spice [FOODON:03303380] - White peppercorn (whole or parts) [FOODON:03000251] - - -food_product_properties menu Food (canned) [FOODON:00002418] - Food (cooked) [FOODON:00001181] - Food (cut) [FOODON:00004291] - Food (chopped) [FOODON:00002777] - Food (chunks) [FOODON:00004555] - Food (cubed) [FOODON:00004278] - Food (diced) [FOODON:00004549] - Food (grated) [FOODON:00004552] - Food (sliced) [FOODON:00002455] - Food (shredded) [FOODON:00004553] - Food (dried) [FOODON:03307539] - Food (fresh) [FOODON:00002457] - Food (frozen) [FOODON:03302148] - Food (pulped) [FOODON:00004554] - Food (raw) [FOODON:03311126] - Food (unseasoned) [FOODON:00004287] - Italian-style food product [FOODON:00004321] - Meat (boneless) [FOODON:00003467] - Meat (skinless) [FOODON:00003468] - Meat (with bone) [FOODON:02010116] - Meat (with skin) [FOODON:02010111] - Ready-to-eat (RTE) [FOODON:03316636] - Soft [PATO:0000387] - - - -label_claim menu Antibiotic free [FOODON:03601063] - Cage free [FOODON:03601064] - Hormone free [FOODON:03601062] - Organic food claim or use [FOODON:03510128] - Pasture raised [FOODON:03601065] - - - -animal_source_of_food menu Cow [NCBITaxon:9913] - Fish [FOODON:03411222] - Pig [NCBITaxon:9823] - Poultry or game bird [FOODON:03411563] - Chicken [NCBITaxon:9031] - Turkey [NCBITaxon:9103] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Mussel [FOODON:03411223] - Scallop [NCBITaxon:6566] - Shrimp [FOODON:03411237] - Squid [FOODON:03411205] - - -food_product_production_stream menu Beef cattle production stream [FOODON:03000452] - Broiler chicken production stream [FOODON:03000455] - Dairy cattle production stream [FOODON:03000453] - Egg production stream [FOODON:03000458] - Layer chicken production stream [FOODON:03000456] - Meat production stream [FOODON:03000460] - Veal meat production stream [FOODON:03000461] - Milk production stream [FOODON:03000459] - - -collection_device menu Auger (earth auger) [AGRO:00000405] - Box corer [GENEPIO:0100928] - Container [OBI:0000967] - Bag [GSSO:008558] - Whirlpak sampling bag [GENEPIO:0002122] - Bottle [FOODON:03490214] - Vial [OBI:0000522] - Culture plate [GENEPIO:0004318] - Petri dish [NCIT:C96141] - Filter [GENEPIO:0100103] - PONAR grab sampler [GENEPIO:0100929] - Scoop [GENEPIO:0002125] - Soil sample probe [GENEPIO:0100930] - Spatula [NCIT:C149941] - Sponge [OBI:0002819] - Swab [GENEPIO:0100027] - Drag swab [OBI:0002822] - Surface wipe [OBI:0002824] - Tube [GENEPIO:0101196] - Vacuum device [GENEPIO:0002127] - Vacutainer [OBIB:0000032] - - -collection_method menu Aspiration [HP:0002835] - Biopsy [OBI:0002650] - Fecal grab [GENEPIO:0004326] - Filtration [OBI:0302885] - Air filtration [GENEPIO:0100031] - Water filtration [GENEPIO:0100931] - Lavage [OBI:0600044] - Bronchoalveolar lavage [GENEPIO:0100032] - Gastric lavage [GENEPIO:0100033] - Necropsy [MMO:0000344] - Phlebotomy [NCIT:C28221] - Rinsing for specimen collection [GENEPIO_0002116] - Scooping [GENEPIO:0100932] - Sediment collection [GENEPIO:0100933] - Soil coring [GENEPIO:0100934] - Weep fluid collection (pouring) [GENEPIO:0101003] - -sample_volume_measurement_unit menu microliter (uL) [UO:0000101] - milliliter (mL) [UO:0000098] - liter (L) [UO:0000099] - -residual_sample_status menu Residual sample remaining (some sample left) [GENEPIO:0101087] - No residual sample (sample all used) [GENEPIO:0101088] - Residual sample status unkown [GENEPIO:0101089] - -sample_storage_duration_unit menu Second [UO:0000010] - Minute [UO:0000031] - Hour [UO:0000032] - Day [UO:0000033] - Week [UO:0000034] - Month [UO:0000035] - Year [UO:0000036] - -nucelic_acid_storage_duration_unit menu Second [UO:0000010] - Minute [UO:0000031] - Hour [UO:0000032] - Day [UO:0000033] - Week [UO:0000034] - Month [UO:0000035] - Year [UO:0000036] - -food_packaging menu Bag, sack or pouch [FOODON:03490197] - Paper bag, sack or pouch [FOODON:03490120] - Plastic bag, sack or pouch [FOODON:03490166] - Plastic shrink wrap [FOODON:03490137] - Plastic wrapper [FOODON:03490128] - Bottle or jar [FOODON:03490203] - Can (container) [FOODON:03490204] - Paper container, treated [FOODON:03490330] - Paper container, untreated [FOODON:03490334] - Plastic tray or pan [FOODON:03490126] - - -host (common name) menu Bird [NCBITaxon:8782] - Chicken [NCBITaxon:9031] - Seabird [FOODON:00004504] - Cormorant [NCBITaxon:9206] - Double Crested Cormorant [NCBITaxon:56069] - Crane [NCBITaxon:9109] - Whooping Crane [NCBITaxon:9117] - Gull (Seagull) [NCBITaxon:8911] - Glaucous-winged Gull [NCBITaxon:119606] - Great Black-backed Gull [NCBITaxon:8912] - Herring Gull [NCBITaxon:35669] - Ring-billed Gull [NCBITaxon:126683] - Eider [NCBITaxon:50366] - Common Eider [NCBITaxon:76058] - Turkey [NCBITaxon:9103] - Fish [FOODON:03411222] - Rainbow Trout [NCBITaxon:8022] - Sablefish [NCBITaxon:229290] - Salmon [FOODON:00003473] - Atlantic Salmon [NCBITaxon:8030] - Chinook salmon [NCBITaxon:74940] - Coho Salmon [NCBITaxon:8019] - Mammal [FOODON:03411134] - Companion animal [FOODON:03000300] - Cow [NCBITaxon:9913] - Human [NCBITaxon:9606] - Pig [NCBITaxon:9823] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Atlantic Lobster [NCBITaxon:6706] - Atlantic Oyster [NCBITaxon:6565] - Blue Mussel [NCBITaxon:6550] - - -host (scientific name) menu Anoplopoma fimbria [NCBITaxon:229290] - Bos taurus [NCBITaxon:9913] - Crassostrea virginica [NCBITaxon:6565] - Gallus gallus [NCBITaxon:9031] - Grus americana [NCBITaxon:9117] - Homarus americanus [NCBITaxon:6706] - Homo sapiens [NCBITaxon:9606] - Larus argentatus [NCBITaxon:35669] - Larus delawarensis [NCBITaxon:126683] - Larus glaucescens [NCBITaxon:119606] - Larus marinus [NCBITaxon:8912] - Meleagris gallopavo [NCBITaxon:9103] - Mytilus edulis [NCBITaxon:6550] - Oncorhynchus kisutch [NCBITaxon:8019] - Oncorhynchus mykiss [NCBITaxon:8022] - Oncorhynchus tshawytscha [NCBITaxon:74940] - Ovis aries [NCBITaxon:9940] - Phalacrocorax auritus [NCBITaxon:56069] - Salmo salar [NCBITaxon:8030] - Somateria mollissima [NCBITaxon:76058] - Sus scrofa domesticus [NCBITaxon:9825] - - -host (food production name) menu Cow (by age/production stage) (organizational term) - Calf [FOODON:03411349] - Dry cow [FOODON:00004411] - Feeder cow [FOODON:00004292] - Finisher cow [FOODON:00004293] - Milker cow [FOODON:03411201] - Stocker cow [FOODON:00004294] - Weanling cow [FOODON:00004295] - Cow (by sex/reproductive stage) (organizational term) - Bull [FOODON:00000015] - Cow [NCBITaxon:9913] - Freemartin [FOODON:00004296] - Heifer [FOODON:00002518] - Steer [FOODON:00002531] - Pig (by age/production stage) (organizational term) - Finisher pig [FOODON:00003371] - Grower pig [FOODON:00003370] - Nursing pig [FOODON:00004297 ] - Pig [NCBITaxon:9823] - Piglet [FOODON:00003952] - Weanling (weaner) pig [FOODON:00003373] - Pig (by sex/reproductive stage) (organizational term) - Barrow [FOODON:03411280] - Boar [FOODON:03412248] - Gilt [FOODON:00003369] - Sow [FOODON:00003333] - Poultry or game bird [FOODON:03411563] - Broiler or fryer chicken [FOODON:03411198] - Capon [FOODON:03411711] - Chick [FOODON:00004299] - Chicken [NCBITaxon:9031] - Egg [UBERON:0007379] - Hatchling [FOODON:00004300] - Hen [FOODON:00003282] - Layer chicken [FOODON:00004301] - Layer turkey [FOODON:00004302] - Poult [FOODON:00002962] - Pullet [FOODON:00004303] - Rooster [FOODON:03411714] - Tom (Gobbler) [FOODON:00004304 ] - Turkey [NCBITaxon:9103] - Sheep [NCBITaxon:9940] - Ram [FOODON:00004305] - Wether sheep [FOODON:00004306] - Ewe [FOODON:03412610] - Lamb [FOODON:03411669] - Fish [FOODON:03411222] - Fish egg [FOODON_00004319] - Fry (fish) [FOODON_00004318] - Juvenile fish [FOODON_00004317] - - -host_age_bin menu First winter [GENEPIO:0100684] - First summer [GENEPIO:0100685] - Second winter [GENEPIO:0100686] - Second summer [GENEPIO:0100687] - Third winter [GENEPIO:0100688] - Third summer [GENEPIO:0100689] - - -isolated_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - - -organism menu Acinetobacter [NCBITaxon:469] - Acinetobacter baumannii [NCBITaxon:470] - Acinetobacter bereziniae [NCBITaxon:106648] - Acinetobacter ursingii [NCBITaxon:108980] - Aeromonas [NCBITaxon:642] - Aeromonas allosaccharophila [NCBITaxon:656] - Aeromonas hydrophila [NCBITaxon:644] - Aeromonas rivipollensis [NCBITaxon:948519] - Aeromonas salmonicida [NCBITaxon:645] - Campylobacter [NCBITaxon:194] - Campylobacter coli [NCBITaxon:195] - Campylobacter jejuni [NCBITaxon:197] - Campylobacter lari [NCBITaxon:201] - Citrobacter [NCBITaxon:544] - Citrobacter braakii [NCBITaxon:57706] - Citrobacter freundii [NCBITaxon:546] - Citrobacter gillenii [NCBITaxon:67828] - Clostridioides [NCBITaxon:1870884] - Clostridioides difficile [NCBITaxon:1496] - Clostridium [NCBITaxon:1485] - Clostridium perfringens [NCBITaxon:1502] - Clostridium sporogenes [NCBITaxon:1509] - Comamonas [NCBITaxon:283] - Comamonas aquatica [NCBITaxon:225991] - Enterobacter [NCBITaxon:547] - Enterobacter asburiae [NCBITaxon:61645] - Enterobacter cancerogenus [NCBITaxon:69218] - Enterobacter cloacae [NCBITaxon:550] - Enterobacter hormaechei [NCBITaxon:158836] - Enterobacter kobei [NCBITaxon:208224] - Enterobacter roggenkampii [NCBITaxon:1812935] - Enterobacter sp. [NCBITaxon:42895] - Lelliottia amnigena [NCBITaxon:61646] - Pluralibacter gergoviae [NCBITaxon:61647] - Enterococcus [NCBITaxon:1350] - Enterococcus asini [NCBITaxon:57732] - Enterococcus avium [NCBITaxon:33945] - Enterococcus caccae [NCBITaxon:317735] - Enterococcus canis [NCBITaxon:214095] - Enterococcus casseliflavus [NCBITaxon:37734] - Enterococcus cecorum [NCBITaxon:44008] - Enterococcus dispar [NCBITaxon:44009] - Enterococcus durans [NCBITaxon:53345] - Enterococcus faecium [NCBITaxon:1352] - Enterococcus faecalis [NCBITaxon:1351] - Enterococcus gallinarum [NCBITaxon:1353] - Enterococcus hirae [NCBITaxon:1354] - Enterococcus malodoratus [NCBITaxon:71451] - Enterococcus mundtii [NCBITaxon:53346] - Enterococcus ratti [NCBITaxon:150033] - Enterococcus saccharolyticus [NCBITaxon:41997] - Enterococcus thailandicus [NCBITaxon:417368] - Enterococcus villorum [NCBITaxon:112904] - Escherichia [NCBITaxon:561] - Escherichia coli [NCBITaxon:562] - Escherichia fergusonii [NCBITaxon:564] - Exiguobacterium [NCBITaxon:33986] - Exiguobacterium oxidotolerans [NCBITaxon:223958] - Exiguobacterium sp. [NCBITaxon:44751] - Klebsiella [NCBITaxon:570] - Klebsiella aerogenes [NCBITaxon:548] - Klebsiella michiganensis [NCBITaxon:1134687] - Klebsiella oxytoca [NCBITaxon:571] - Klebsiella pneumoniae [NCBITaxon:573] - Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] - Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] - Kluyvera [NCBITaxon:579] - Kluyvera intermedia [NCBITaxon:61648] - Kosakonia [NCBITaxon:1330547] - Kosakonia cowanii [NCBITaxon:208223] - Leclercia [NCBITaxon:83654] - Leclercia adecarboxylata [NCBITaxon:83655] - Listeria [NCBITaxon:1637] - Listeria monocytogenes [NCBITaxon:1639] - Ochrobactrum [NCBITaxon:528] - Ochrobactrum sp. [NCBITaxon:42190] - Pantoea [NCBITaxon:53335] - Pantoea ananatis [NCBITaxon:553] - Pantoea sp. [NCBITaxon:69393] - Photobacterium [NCBITaxon:657] - Photobacterium indicum[NCBITaxon:81447] - Photobacterium sp. [NCBITaxon:660] - Providencia [NCBITaxon:586] - Providencia rettgeri [NCBITaxon:587] - Pseudoalteromonas [NCBITaxon:53246] - Pseudoalteromonas tetraodonis [NCBITaxon:43659] - Pseudomonas [NCBITaxon:286] - Pseudomonas aeruginosa [NCBITaxon:287] - Pseudomonas fluorescens [NCBITaxon:294] - Pseudomonas soli [NCBITaxon:1306993] - Pseudomonas sp. [NCBITaxon:306] - Psychrobacter [NCBITaxon:497] - Psychrobacter faecalis [NCBITaxon:180588] - Psychrobacter nivimaris [NCBITaxon:281738] - Psychrobacter sp. [NCBITaxon:56811] - Rahnella [NCBITaxon:34037] - Rahnella aquatilis [NCBITaxon:34038] - Rahnella sp. [NCBITaxon:1873497] - Raoultella [NCBITaxon:160674] - Raoultella ornithinolytica [NCBITaxon:54291] - Raoultella planticola [NCBITaxon:575] - Salmonella enterica [NCBITaxon:28901] - Salmonella enterica subsp. enterica [NCBITaxon:59201] - Salmonella enterica subsp. arizonae [NCBITaxon:59203] - Serratia [NCBITaxon:613] - Shewanella [NCBITaxon:22] - Shewanella pealeana [NCBITaxon:70864] - Shewanella putrefaciens [NCBITaxon:24] - Shewanella oncorhynchi [NCBITaxon:2726434] - Shewanella sp. [NCBITaxon:50422] - Staphylococcus [NCBITaxon:1279] - Staphylococcus aureus [NCBITaxon:1280] - Streptococcus [NCBITaxon:1301] - Streptococcus alactolyticus [NCBITaxon:29389] - Streptococcus bovis [NCBITaxon:1335] - Streptococcus equinus [NCBITaxon:1335] - Streptococcus gallolyticus [NCBITaxon:315405] - Streptococcus infantarius [NCBITaxon:102684] - Streptococcus lutetiensis [NCBITaxon:150055] - Streptococcus macedonicus [NCBITaxon:59310] - Streptococcus pasteurianus [NCBITaxon:197614] - Streptococcus suis [NCBITaxon:1307] - Vibrio [NCBITaxon:662] - Vibrio cholerae [NCBITaxon:666] - Vibrio parahaemolyticus [NCBITaxon:670] - -taxonomic_identification_process menu Whole genome sequencing assay [OBI:0002117] - 16S ribosomal gene sequencing assay [OBI:0002763] - PCR assay [OBI:0002740] - Comparative phenotypic assessment [OBI:0001546] - Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] - - -sequenced_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - McGill University [GENEPIO:0101103] - - -purpose_of_sequencing menu Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549] - Field experiment [GENEPIO:0100550] - Protocol testing experiment [GENEPIO:0100024] - Survey study [GENEPIO:0100582] - Surveillance [GENEPIO:0100004] - - -sequencing_platform menu Illumina [GENEPIO:0001923] - Pacific Biosciences [GENEPIO:0001927] - Ion Torrent [GENEPIO:0002683] - Oxford Nanopore Technologies [OBI:0002755] - BGI Genomics [GENEPIO:0004324] - MGI [GENEPIO:0004325] - - -sequencing_instrument menu Illumina [GENEPIO:0100105] - Illumina Genome Analyzer [GENEPIO:0100106] - Illumina Genome Analyzer II [OBI:0000703] - Illumina Genome Analyzer IIx [OBI:0002000] - Illumina HiScanSQ [GENEPIO:0100109] - Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq X [GENEPIO:0100111] - Illumina HiSeq X Five [GENEPIO:0100112] - Illumina HiSeq X Ten [GENEPIO:0100113] - Illumina HiSeq 1000 [OBI:0002022] - Illumina HiSeq 1500 [GENEPIO:0100115] - Illumina HiSeq 2000 [OBI:0002001] - Illumina HiSeq 2500 [OBI:0002002] - Illumina HiSeq 3000 [OBI:0002048] - Illumina HiSeq 4000 [OBI:0002049] - Illumina iSeq [GENEPIO:0100120] - Illumina iSeq 100 [GENEPIO:0100121] - Illumina NovaSeq [GENEPIO:0100122] - Illumina NovaSeq 6000 [GENEPIO:0100123] - Illumina MiniSeq [GENEPIO:0100124] - Illumina MiSeq [OBI:0002003] - Illumina NextSeq [GENEPIO:0100126] - Illumina NextSeq 500 [OBI:0002021] - Illumina NextSeq 550 [GENEPIO:0100128] - Illumina NextSeq 2000 [GENEPIO:0100129] - Illumina NextSeq 1000 [GENEPIO:0004432] - PacBio [GENEPIO:0100130] - PacBio RS [GENEPIO:0100131] - PacBio RS II [OBI:0002012] - PacBio Sequel [GENEPIO:0100133] - PacBio Sequel II [GENEPIO:0100134] - Ion Torrent [GENEPIO:0100135] - Ion Torrent PGM [GENEPIO:0100136] - Ion Torrent Proton [GENEPIO:0100137] - Ion Torrent S5 XL [GENEPIO:0100138] - Ion Torrent S5 [GENEPIO:0100139] - Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore Flongle [GENEPIO:0004433] - Oxford Nanopore GridION [GENEPIO:0100141] - Oxford Nanopore MinION [GENEPIO:0100142] - Oxford Nanopore PromethION [GENEPIO:0100143] - BGISEQ [GENEPIO:0100144] - BGISEQ-500 [GENEPIO:0100145] - DNBSEQ [GENEPIO:0100146] - DNBSEQ-T7 [GENEPIO:0100147] - DNBSEQ-G400 [GENEPIO:0100148] - DNBSEQ-G400 FAST [GENEPIO:0100149] - DNBSEQ-G50 [GENEPIO:0100150] - - -sequencing_assay_type menu Amplicon sequencing assay [OBI:0002767] - 16S ribosomal gene sequencing assay [OBI:0002763] - Whole genome sequencing assay [OBI:0002117] - Whole metagenome sequencing assay [OBI:0002623] - Whole virome sequencing assay [OBI:0002768] - -genomic_target_enrichment_method menu Hybrid selection method (bait-capture) [GENEPIO:0001950] - rRNA depletion method [GENEPIO:0101020] - - -sequence_submitted_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - McGill University [GENEPIO:0101103] - -quality_control_determination menu No quality control issues identified [GENEPIO:0100562] - Sequence passed quality control [GENEPIO:0100563] - Sequence failed quality control [GENEPIO:0100564] - Minor quality control issues identified [GENEPIO:0100565] - Sequence flagged for potential quality control issues [GENEPIO:0100566] - Quality control not performed [GENEPIO:0100567] - -quality _control_issues menu Low quality sequence [GENEPIO:0100568] - Sequence contaminated [GENEPIO:0100569] - Low average genome coverage [GENEPIO:0100570] - Low percent genome captured [GENEPIO:0100571] - Read lengths shorter than expected [GENEPIO:0100572] - Sequence amplification artifacts [GENEPIO:0100573] - Low signal to noise ratio [GENEPIO:0100574] - Low coverage of characteristic mutations [GENEPIO:0100575] - - -attribute_package menu Pathogen.cl [GENEPIO:0001835] - Pathogen.env [GENEPIO:0100581] - - -experimental_intervention menu Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538] - Certified organic farming practices [GENEPIO:0100539] - Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543] - Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346] - - -AMR_testing_by menu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - - -antimicrobial_phenotype menu Antibiotic resistance not defined [GENEPIO:0002040] - Intermediate antimicrobial phenotype [ARO:3004300] - Indeterminate antimicrobial phenotype [GENEPIO:0100585] - Nonsusceptible antimicrobial phenotype [ARO:3004303] - Resistant antimicrobial phenotype [ARO:3004301] - Susceptible antimicrobial phenotype [ARO:3004302] - Susceptible dose dependent antimicrobial phenotype [ARO:3004304] - - -antimicrobial_measurement_units menu milligram per litre (mg/L) [UO:0000273] - millimetre (mm) [UO:0000016] - microgram per millilitre (ug/mL) [UO:0000274] - - -antimicrobial_measurement_sign menu less than (<) [GENEPIO:0001002] - less than or equal to (<=) [GENEPIO:0001003] - equal to (==) [GENEPIO:0001004] - greater than (>) [GENEPIO:0001006] - greater than or equal to (>=) [GENEPIO:0001005] - - -antimicrobial_laboratory_typing_method menu Agar diffusion [NCIT:85595] - Antimicrobial gradient (E-test) [NCIT:85596] - Agar dilution [ARO:3004411] - Broth dilution [ARO:3004397] - - -antimicrobial_laboratory_typing_platform menu BIOMIC Microbiology System [ARO:3007569] - Microscan [ARO:3004400] - Phoenix [ARO:3004401] - Sensititre [ARO:3004402] - Vitek System [ARO:3004403] - - -antimicrobial_vendor_name menu Becton Dickinson [ARO:3004405] - bioMérieux [ARO:3004406] - Omron [ARO:3004408] - Siemens [ARO:3004407] - Trek [ARO:3004409] - - -antimicrobial_testing_standard menu British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] - Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Deutsches Institut für Normung (DIN) [ARO:3004367] - European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] - National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] - National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] - Société Française de Microbiologie (SFM) [ARO:3004369] - Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] - Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM + +null value menu NullValueMenu Not Applicable [GENEPIO:0001619] + Missing [GENEPIO:0001618] missing + Not Collected [GENEPIO:0001620] + Not Provided [GENEPIO:0001668] + Restricted Access [GENEPIO:0001810] + +sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + University of Manitoba (UM) [GENEPIO:0004434] + + +purpose_of_sampling menu PurposeOfSamplingMenu Cluster/Outbreak investigation [GENEPIO:0100001] + Diagnostic testing [GENEPIO:0100002] + Environmental testing [GENEPIO:0100548] + Research [GENEPIO:0100003] + Clinical trial [GENEPIO:0100549] + Field experiment [GENEPIO:0100550] + Survey study [GENEPIO:0100582] + Surveillance [GENEPIO:0100004] + + +presampling_activity menu PresamplingActivityMenu Addition of substances to food/water [GENEPIO:0100536] + Antimicrobial pre-treatment [GENEPIO:0100537] + Certified animal husbandry practices [GENEPIO:0100538] + Certified humane animal husbandry practices [GENEPIO:0100894] + Certified organic farming practices [GENEPIO:0100539] + Conventional farming practices [GENEPIO:0100895] + Change in storage conditions [GENEPIO:0100540] + Cleaning/disinfection [GENEPIO:0100541] + Extended downtime between activities [GENEPIO:0100542] + Fertilizer pre-treatment [GENEPIO:0100543] + Genetic mutation [GENEPIO:0100544[ + Logistic slaughter [GENEPIO:0100545] + Microbial pre-treatment [GENEPIO:0100546] + Probiotic pre-treatment [GENEPIO:0100547] + Vaccination [NCIT:C15346] + +experimental_specimen_role_type menu ExperimentalSpecimenRoleTypeMenu Positive experimental control [GENEPIO:0101018] + Negative experimental control [GENEPIO:0101019] + Technical replicate [EFO:0002090] + Biological replicate [EFO:0002091] + + +specimen_processing menu SpecimenProcessingMenu Biological replicate process [GENEPIO:0101022] + Samples pooled [OBI:0600016] + Technical replicate process [GENEPIO:0101021] + Isolated from single source [OBI:0002079] + + +geo_loc_name (country) menu GeoLocNameCountryMenu Afghanistan [GAZ:00006882] + Albania [GAZ:00002953] + Algeria [GAZ:00000563] + American Samoa [GAZ:00003957] + Andorra [GAZ:00002948] + Angola [GAZ:00001095] + Anguilla [GAZ:00009159] + Antarctica [GAZ:00000462] + Antigua and Barbuda [GAZ:00006883] + Argentina [GAZ:00002928] + Armenia [GAZ:00004094] + Aruba [GAZ:00004025] + Ashmore and Cartier Islands [GAZ:00005901] + Australia [GAZ:00000463] + Austria [GAZ:00002942] + Azerbaijan [GAZ:00004941] + Bahamas [GAZ:00002733] + Bahrain [GAZ:00005281] + Baker Island [GAZ:00007117] + Bangladesh [GAZ:00003750] + Barbados [GAZ:00001251] + Bassas da India [GAZ:00005810] + Belarus [GAZ:00006886] + Belgium [GAZ:00002938] + Belize [GAZ:00002934] + Benin [GAZ:00000904] + Bermuda [GAZ:00001264] + Bhutan [GAZ:00003920] + Bolivia [GAZ:00002511] + Borneo [GAZ:00025355] + Bosnia and Herzegovina [GAZ:00006887] + Botswana [GAZ:00001097] + Bouvet Island [GAZ:00001453] + Brazil [GAZ:00002828] + British Virgin Islands [GAZ:00003961] + Brunei [GAZ:00003901] + Bulgaria [GAZ:00002950] + Burkina Faso [GAZ:00000905] + Burundi [GAZ:00001090] + Cambodia [GAZ:00006888] + Cameroon [GAZ:00001093] + Canada [GAZ:00002560] + Cape Verde [GAZ:00001227] + Cayman Islands [GAZ:00003986] + Central African Republic [GAZ:00001089] + Chad [GAZ:00000586] + Chile [GAZ:00002825] + China [GAZ:00002845] + Christmas Island [GAZ:00005915] + Clipperton Island [GAZ:00005838] + Cocos Islands [GAZ:00009721] + Colombia [GAZ:00002929] + Comoros [GAZ:00005820] + Cook Islands [GAZ:00053798] + Coral Sea Islands [GAZ:00005917] + Costa Rica [GAZ:00002901] + Cote d'Ivoire [GAZ:00000906] + Croatia [GAZ:00002719] + Cuba [GAZ:00003762] + Curacao [GAZ:00012582] + Cyprus [GAZ:00004006] + Czech Republic [GAZ:00002954] + Democratic Republic of the Congo [GAZ:00001086] + Denmark [GAZ:00005852] + Djibouti [GAZ:00000582] + Dominica [GAZ:00006890] + Dominican Republic [GAZ:00003952] + Ecuador [GAZ:00002912] + Egypt [GAZ:00003934] + El Salvador [GAZ:00002935] + Equatorial Guinea [GAZ:00001091] + Eritrea [GAZ:00000581] + Estonia [GAZ:00002959] + Eswatini [GAZ:00001099] + Ethiopia [GAZ:00000567] + Europa Island [GAZ:00005811] + Falkland Islands (Islas Malvinas) [GAZ:00001412] + Faroe Islands [GAZ:00059206] + Fiji [GAZ:00006891] + Finland [GAZ:00002937] + France [GAZ:00003940] + French Guiana [GAZ:00002516] + French Polynesia [GAZ:00002918] + French Southern and Antarctic Lands [GAZ:00003753] + Gabon [GAZ:00001092] + Gambia [GAZ:00000907] + Gaza Strip [GAZ:00009571] + Georgia [GAZ:00004942] + Germany [GAZ:00002646] + Ghana [GAZ:00000908] + Gibraltar [GAZ:00003987] + Glorioso Islands [GAZ:00005808] + Greece [GAZ:00002945] + Greenland [GAZ:00001507] + Grenada [GAZ:02000573] + Guadeloupe [GAZ:00067142] + Guam [GAZ:00003706] + Guatemala [GAZ:00002936] + Guernsey [GAZ:00001550] + Guinea [GAZ:00000909] + Guinea-Bissau [GAZ:00000910] + Guyana [GAZ:00002522] + Haiti [GAZ:00003953] + Heard Island and McDonald Islands [GAZ:00009718] + Honduras [GAZ:00002894] + Hong Kong [GAZ:00003203] + Howland Island [GAZ:00007120] + Hungary [GAZ:00002952] + Iceland [GAZ:00000843] + India [GAZ:00002839] + Indonesia [GAZ:00003727] + Iran [GAZ:00004474] + Iraq [GAZ:00004483] + Ireland [GAZ:00002943] + Isle of Man [GAZ:00052477] + Israel [GAZ:00002476] + Italy [GAZ:00002650] + Jamaica [GAZ:00003781] + Jan Mayen [GAZ:00005853] + Japan [GAZ:00002747] + Jarvis Island [GAZ:00007118] + Jersey [GAZ:00001551] + Johnston Atoll [GAZ:00007114] + Jordan [GAZ:00002473] + Juan de Nova Island [GAZ:00005809] + Kazakhstan [GAZ:00004999] + Kenya [GAZ:00001101] + Kerguelen Archipelago [GAZ:00005682] + Kingman Reef [GAZ:00007116] + Kiribati [GAZ:00006894] + Kosovo [GAZ:00011337] + Kuwait [GAZ:00005285] + Kyrgyzstan [GAZ:00006893] + Laos [GAZ:00006889] + Latvia [GAZ:00002958] + Lebanon [GAZ:00002478] + Lesotho [GAZ:00001098] + Liberia [GAZ:00000911] + Libya [GAZ:00000566] + Liechtenstein [GAZ:00003858] + Line Islands [GAZ:00007144] + Lithuania [GAZ:00002960] + Luxembourg [GAZ:00002947] + Macau [GAZ:00003202] + Madagascar [GAZ:00001108] + Malawi [GAZ:00001105] + Malaysia [GAZ:00003902] + Maldives [GAZ:00006924] + Mali [GAZ:00000584] + Malta [GAZ:00004017] + Marshall Islands [GAZ:00007161] + Martinique [GAZ:00067143] + Mauritania [GAZ:00000583] + Mauritius [GAZ:00003745] + Mayotte [GAZ:00003943] + Mexico [GAZ:00002852] + Micronesia [GAZ:00005862] + Midway Islands [GAZ:00007112] + Moldova [GAZ:00003897] + Monaco [GAZ:00003857] + Mongolia [GAZ:00008744] + Montenegro [GAZ:00006898] + Montserrat [GAZ:00003988] + Morocco [GAZ:00000565] + Mozambique [GAZ:00001100] + Myanmar [GAZ:00006899] + Namibia [GAZ:00001096] + Nauru [GAZ:00006900] + Navassa Island [GAZ:00007119] + Nepal [GAZ:00004399] + Netherlands [GAZ:00002946] + New Caledonia [GAZ:00005206] + New Zealand [GAZ:00000469] + Nicaragua [GAZ:00002978] + Niger [GAZ:00000585] + Nigeria [GAZ:00000912] + Niue [GAZ:00006902] + Norfolk Island [GAZ:00005908] + North Korea [GAZ:00002801] + North Macedonia [GAZ:00006895] + North Sea [GAZ:00002284] + Northern Mariana Islands [GAZ:00003958] + Norway [GAZ:00002699] + Oman [GAZ:00005283] + Pakistan [GAZ:00005246] + Palau [GAZ:00006905] + Panama [GAZ:00002892] + Papua New Guinea [GAZ:00003922] + Paracel Islands [GAZ:00010832] + Paraguay [GAZ:00002933] + Peru [GAZ:00002932] + Philippines [GAZ:00004525] + Pitcairn Islands [GAZ:00005867] + Poland [GAZ:00002939] + Portugal [GAZ:00004126] + Puerto Rico [GAZ:00006935] + Qatar [GAZ:00005286] + Republic of the Congo [GAZ:00001088] + Reunion [GAZ:00003945] + Romania [GAZ:00002951] + Ross Sea [GAZ:00023304] + Russia [GAZ:00002721] + Rwanda [GAZ:00001087] + Saint Helena [GAZ:00000849] + Saint Kitts and Nevis [GAZ:00006906] + Saint Lucia [GAZ:00006909] + Saint Pierre and Miquelon [GAZ:00003942] + Saint Martin [GAZ:00005841] + Saint Vincent and the Grenadines [GAZ:02000565] + Samoa [GAZ:00006910] + San Marino [GAZ:00003102] + Sao Tome and Principe [GAZ:00006927] + Saudi Arabia [GAZ:00005279] + Senegal [GAZ:00000913] + Serbia [GAZ:00002957] + Seychelles [GAZ:00006922] + Sierra Leone [GAZ:00000914] + Singapore [GAZ:00003923] + Sint Maarten [GAZ:00012579] + Slovakia [GAZ:00002956] + Slovenia [GAZ:00002955] + Solomon Islands [GAZ:00005275] + Somalia [GAZ:00001104] + South Africa [GAZ:00001094] + South Georgia and the South Sandwich Islands [GAZ:00003990] + South Korea [GAZ:00002802] + South Sudan [GAZ:00233439] + Spain [GAZ:00003936] + Spratly Islands [GAZ:00010831] + Sri Lanka [GAZ:00003924] + State of Palestine [GAZ:00002475] + Sudan [GAZ:00000560] + Suriname [GAZ:00002525] + Svalbard [GAZ:00005396] + Swaziland [GAZ:00001099] + Sweden [GAZ:00002729] + Switzerland [GAZ:00002941] + Syria [GAZ:00002474] + Taiwan [GAZ:00005341] + Tajikistan [GAZ:00006912] + Tanzania [GAZ:00001103] + Thailand [GAZ:00003744] + Timor-Leste [GAZ:00006913] + Togo [GAZ:00000915] + Tokelau [GAZ:00260188] + Tonga [GAZ:00006916] + Trinidad and Tobago [GAZ:00003767] + Tromelin Island [GAZ:00005812] + Tunisia [GAZ:00000562] + Turkey [GAZ:00000558] + Turkmenistan [GAZ:00005018] + Turks and Caicos Islands [GAZ:00003955] + Tuvalu [GAZ:00009715] + United States of America [GAZ:00002459] + Uganda [GAZ:00001102] + Ukraine [GAZ:00002724] + United Arab Emirates [GAZ:00005282] + United Kingdom [GAZ:00002637] + Uruguay [GAZ:00002930] + Uzbekistan [GAZ:00004979] + Vanuatu [GAZ:00006918] + Venezuela [GAZ:00002931] + Viet Nam [GAZ:00003756] + Virgin Islands [GAZ:00003959] + Wake Island [GAZ:00007111] + Wallis and Futuna [GAZ:00007191] + West Bank [GAZ:00009572] + Western Sahara [GAZ:00000564] + Yemen [GAZ:00005284] + Zambia [GAZ:00001107] + Zimbabwe [GAZ:00001106] + + +geo_loc_name (state/province/region) menu GeoLocNameStateProvinceRegionMenu Atlantic region (Canada) [wikidata:Q246972] + New Brunswick [GAZ:00002570] + Newfoundland & Labrador [GAZ:00002567] + Nova Scotia [GAZ:00002565] + Prince Edward Island [GAZ:00002572] + Central region (Canada) [wikidata:Q1048064] + Ontario [GAZ:00002563] + Quebec [GAZ:00002569] + Northern region (Canada) [wikidata:Q764146] + Northwest Territories [GAZ:00002575] + Nunuvut [GAZ:00002574] + Yukon [GAZ:00002576] + Pacific region (Canada) [wikidata:Q122953299] + British Columbia [GAZ:00002562] + Prairie region (Canada) [wikidata:Q1364746] + Alberta [GAZ:00002566] + Manitoba [GAZ:00002571] + Saskatchewan [GAZ:00002564] + + +sample_collection_date_precision menu SampleCollectionDatePrecisionMenu year [UO:0000036] + month [UO:0000035] + day [UO:0000033] + + +environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] + Agricultural Field [ENVO:00000114] + Alluvial fan [ENVO:00000314] + Animal cage [ENVO:01000922] + Aquarium [ENVO:00002196] + Artificial wetland [ENVO:03501406] + Breeding ground [ENVO:03501441] + Building [ENVO:00000073] + Barn [ENVO:03501257] + Breeder barn [ENVO:03501383] + Broiler barn [ENVO:03501386] + Sheep barn [ENVO:03501385] + Biodome [ENVO:03501397] + Cottage [ENVO:03501393] + Dairy [ENVO:00003862] + Hospital [ENVO:00002173] + Laboratory facility [ENVO:01001406] + Pigsty [ENVO:03501413] + Building part (organizational term) + Air intake [ENVO:03501380] + Animal pen [ENVO:03501387] + Building floor [ENVO:01000486] + Building wall [ENVO:01000465] + Countertop [ENVO:03501404] + Shelf [ENVO:03501403] + Stall [EOL:0001903] + Window sill [ENVO:03501381] + Creek [ENVO:03501405] + Farm [ENVO:00000078] + Beef farm [ENVO:03501443] + Breeder farm [ENVO:03501384] + Dairy farm [ENVO:03501416] + Feedlot [ENVO:01000627] + Beef cattle feedlot [ENVO:03501444] + Fish farm [ENVO:00000294] + Research farm [ENVO:03501417] + Central Experimental Farm [GAZ:00004603] Central Experimental Farm + Freshwater environment [ENVO:01000306] + Hatchery [ENVO:01001873] + Poultry hatchery [ENVO:01001874] + Lake [ENVO:00000020] + Manure digester facility [ENVO:03501422] + Manure lagoon (Anaerobic lagoon) [ENVO:03501423] + Manure pit [ENVO:01001872] + Marine environment [ENVO:01000320] + Benthic zone [ENVO:03501440] + Pelagic zone [ENVO:00000208] + Park [ENVO:00000562] + Pond [ENVO:00000033] + Reservoir [ENVO:00000025] + Irrigation reservoir [ENVO:00000450] + Retail environment [ENVO:01001448] + Shop [ENVO:00002221] + Butcher shop [ENVO:03501396] + Pet store [ENVO:03501395] + Supermarket [ENVO:01000984] + River [ENVO:00000022] + Roost (bird) [ENVO:03501439] + Rural area [ENVO:01000772] + Slough [ENVO:03501438] + Stream [ENVO:00000023] + Trailer [ENVO:03501394] + Tributary [ENVO:00000495] + Truck [ENVO:01000602] + Urban area [ENVO:03501437] + Water surface [ENVO:01001191] + Woodland area [ENVO:00000109] + Zoo [ENVO:00010625] + + +water_depth_units menu WaterDepthUnitsMenu centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + kilometer (km) [UO:0010066] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + + +sediment_depth_units menu SedimentDepthUnitsMenu centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + kilometer (km) [UO:0010066] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + + +air_temperature_units menu AirTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] + degree Celsius (C) [UO:0000027] + + +water_temperature_units menu WaterTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] + degree Celsius (C) [UO:0000027] + + +available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702] + Experimental parameters documentation [GENEPIO:0100703] + Feed history [GENEPIO:0100704] + Land use information [GENEPIO:0100705] + Therapeutic administration history [GENEPIO:0100706] + Chemical characterization [GENEPIO:0100707] + pH measurement [GENEPIO:0100708] + Dissolved oxygen measurement [GENEPIO:0100709] + Nitrate measurement [GENEPIO:0100710] + Nitrite measurement [GENEPIO:0100711] + Phosphorous measurement [GENEPIO:0100712] + Salinity measurement [GENEPIO:0100713] + Microbiological characterization [GENEPIO:0100714] + Microbiological identification [GENEPIO:0100715] + Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] + Microbiological identification (bioMérieux API) [GENEPIO:0100717] + Microbiological identification (Biolog) [GENEPIO:0100718] + Microbiological identification (FAME) [GENEPIO:0100719] + Microbiological identification (Sensititre) [GENEPIO:0100720] + Microbiological identification (ViTek) [GENEPIO:0100721] + Phage type [GENEPIO:0100722] + Serotype [GENEPIO:0100723] + Phenotypic microbiological characterization [GENEPIO:0100724] + AMR phenotypic testing [GENEPIO:0100725] + Biolog phenotype microarray [GENEPIO:0100726] + Microbiological quantification [GENEPIO:0100727] + Colony count [GENEPIO:0100728] + Total coliform count [GENEPIO:0100729] + Total fecal coliform count [GENEPIO:0100730] + Infectivity assay [GENEPIO:0100731] + ELISA toxin binding [GENEPIO:0100732] + Molecular characterization [GENEPIO:0100733] + 16S rRNA Sanger sequencing [GENEPIO:0100734] + Metagenomic sequencing [GENEPIO:0101024] + PCR marker detection [GENEPIO:0100735] + BOX PCR fingerprint [GENEPIO:0100736] + ERIC PCR fingerprint [GENEPIO:0100737] + Plasmid type [GENEPIO:0100738] + Ribotype [GENEPIO:0100739] + Molecular quantification [GENEPIO:0100740] + qPCR marker organism quantification [GENEPIO:0100741] + Physical characterization [GENEPIO:0100742] + Conductivity measurement [GENEPIO:0100743] + Mollusc shell measurement [GENEPIO:0100744] + Mollusc shell length [GENEPIO:0100745] + Matter compostion [GENEPIO:0100746] + Dry matter composition [GENEPIO:0100747] + Organic matter composition [GENEPIO:0100748] + Turbidity measurement [GENEPIO:0100749] + + +weather_type menu WeatherTypeMenu Cloudy/Overcast [ENVO:03501418] + Partially cloudy [ENVO:03501419] + Drizzle [ENVO:03501420] + Fog [ENVO:01000844] + Rain [ENVO:01001564] + Snow [ENVO:01000406] + Storm [ENVO:01000876] + Sunny/Clear [ENVO:03501421] + + +animal_or_plant_population menu AnimalOrPlantPopulationMenu Algae [FOODON:03411301] + Algal bloom [ENVO:2000004] + Cattle [NCBITaxon:9913] + Beef cattle [FOODON:00004413] + Dairy cattle [FOODON:00002505] + Chicken [NCBITaxon:9031] + Crop [AGRO:00000325] + Fish [FOODON:03411222] + Pig [NCBITaxon:9823] + Poultry [FOODON:00004298] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Crustacean [FOODON:03411374] + Mollusc [FOODON:03412112] + Tropical fish [FOODON:00004283] + Turkey [NCBITaxon:9103] + Wildlife [FOODON:00004503] + Wild bird [FOODON:00004505] + Seabird [FOODON:00004504] + + + +environmental_material menu EnvironmentalMaterialMenu Air [ENVO:00002005] + Alluvium [ENVO:01001202] + Animal feeding equipment [AGRO:00000675] + Animal feeder [AGRO:00000679] + Animal drinker [AGRO:00000680] + Feed pan [AGRO:00000676] + Watering bowl [AGRO:00000677] + Animal transportation equipment [AGRO:00000671] + Dead haul trailer [GENEPIO:0100896] + Dead haul truck [AGRO:00000673] + Live haul trailer [GENEPIO:0100897] + Live haul truck [AGRO:00000674] + Belt [NCIT:C49844] + Biosolids [ENVO:00002059] + Boot [GSSO:012935] + Boot cover [OBI:0002806] + Broom [ENVO:03501431] + Bulk tank [ENVO:03501379] + Chick box [AGRO:00000678] + Chick pad [AGRO:00000672] + Cleaning equipment [ENVO:03501430] + Compost [ENVO:00002170] + Contaminated water [ENVO:00002186] + Fecal slurry [ENVO:03501436] + Fluid from meat rinse [GENEPIO:0004323] + Effluent [ENVO:03501407] + Influent [ENVO:03501442] + Surface runoff [ENVO:03501408] + Poultry plucking water [AGRO_00000693] + Wastewater [ENVO:00002001] + Weep fluid [AGRO_00000692] + Crate [ENVO:03501372] + Dumpster [ENVO:03501400] + Dust [ENVO:00002008] + Egg belt [AGRO:00000670] + Fan [NCIT:C49947] + Freezer [ENVO:03501415] + Freezer handle [ENVO:03501414] + Manure [ENVO:00003031] + Animal manure [AGRO:00000079] + Pig manure [AGRO:00000080] + Manure digester equipment [ENVO:03501424] + Nest [ENVO:03501432] + Bird's nest [ENVO:00005805] + Permafrost [ENVO:00000134] + Plucking belt [AGRO:00000669] + Poultry fluff [UBERON:0008291] + Poultry litter [AGRO:00000080] + Sediment [ENVO:00002007] + Soil [ENVO:00001998] + Agricultural soil [ENVO:00002259] + Forest soil [ENVO:00002261] + Straw [ENVO:00003869] + Canola straw [FOODON:00004430] + Oat straw [FOODON:03309878] + Barley straw [FOODON:00004559] + Water [CHEBI:15377] + Drinking water [ENVO:00003064] + Groundwater [ENVO:01001004] + Surface water [ENVO:00002042] + + +anatomical_material menu AnatomicalMaterialMenu Blood [UBERON:0000178] + Fluid [UBERON:0006314] + Fluid (cerebrospinal (CSF)) [UBERON:0001359] + Fluid (amniotic) [UBERON:0000173] + Saliva [UBERON:0001836] + Tissue [UBERON:0000479] + + +body_product menu BodyProductMenu Digestive tract substance [GENEPIO:0100898] + Caecal content [GENEPIO:0100899] + Intestinal content [GENEPIO:0100900] + Stomach content [GENEPIO:0100901] + Feces [UBERON:0001988] + Fecal composite [GENEPIO:0004512] + Feces (fresh) [GENEPIO:0004513] + Feces (environmental) [GENEPIO:0004514] + Meconium [UBERON:0007109] + Milk [UBERON:0001913] + Colostrum [UBERON:0001914] + Urine [UBERON:0001088] + + +anatomical_part menu AnatomicalPartMenu Carcass [UBERON:0008979] + Swine carcass [FOODON:03311719] + Digestive system [UBERON:0001007] + Caecum [UBERON:0001153] + Colon [UBERON:0001155] + Digestive gland [UBERON:0006925] + Foregut [UBERON:0001041] + Gall bladder [UBERON:0002110] + Gastrointestinal system mucosa [UBERON:0004786] + Gizzard [UBERON:0005052] + Hindgut [UBERON:0001046] + Intestine [UBERON:0000160] + Small intestine [UBERON:0002108] + Duodenum [UBERON:0002114] + Ileum [UBERON:0002116] + Jejunum [UBERON:0002115] + Stomach [UBERON:0000945] + Abomasum [UBERON:0007358] + Rumen [UBERON:0007365] + Excretory system (organizational term) + Anus [UBERON:0001245] + Anal gland [UBERON:0011253] + Cloaca [UBERON:0000162] + Liver [UBERON:0002107] + Kidney [UBERON:0002113] + Rectum [UBERON:0001052] + Spleen [UBERON:0002106] + Urinary bladder [UBERON:0001255] + Foot [UBERON:0002387] + Head [UBERON:0000033] + Brain [UBERON:0000955] + Ear [UBERON:0001690] + Eye [UBERON:0000970] + Mouth [UBERON:0000165] + Nose [UBERON:0000004] + Nasal turbinal [UBERON:0035612] + Nasopharynx (NP) [UBERON:0001728] + Pair of nares [UBERON:0002109] + Paranasal sinus [UBERON:0001825] + Snout [UBERON:0006333] + Lymphatic system [UBERON:0006558] + Lymph node [UBERON:0000029] + Mesenteric lymph node [UBERON:0002509] + Mantle (bird) [GENEPIO:0100927] + Neck [UBERON:0000974] + Esophagus [UBERON:0001043] + Trachea [UBERON:0003126] + Nerve [UBERON:0001021] + Spinal cord [UBERON:0002240] + Organs or organ parts [GENEPIO:0001117] + Organ [UBERON:0000062] + Muscle organ [UBERON:0001630] + Skin of body [UBERON:0002097] + Reproductive system [UBERON:0000990] + Embryo [UBERON:0000922] + Fetus [UBERON:0000323] + Ovary [UBERON:0000992] + Oviduct [UBERON:0000993] + Placenta [UBERON:0001987] + Testis [UBERON:0000473] + Udder [UBERON:0013216] + Uterus [UBERON:0000995] + Vagina [UBERON:0000996] + Yolk sac [UBERON:0001040] + Respiratory system [UBERON:0001004] + Air sac [UBERON:0009060] + Lung [UBERON:0002048] + Pleura [UBERON:0000977] + Respiratory system mucosa [UBERON:0004785] + Skeletal system [UBERON:0001434] + Skeletal joint [UBERON:0000982] + Bone element [UBERON:0001474] + Thoracic segment of trunk [UBERON:0000915] + Abdomen [UBERON:0000916] + Muscle of abdomen [UBERON:0002378] + Peritoneum [UBERON:0002358] + Vascular system [UBERON:0007798] + Blood vessel [UBERON:0001981] + Bursa of Fabricius [UBERON:0003903] + Gill [UBERON:0002535] + Heart [UBERON:0000948] + Lung [UBERON:0002048] + Pericardium [UBERON:0002407] + Vent (anatomical) [UBERON:2000298] + Bird vent [UBERON:0012464] + Fish vent [GENEPIO:0100902] + + +anatomical_region menu AnatomicalRegionMenu Dorso-lateral region [BSPO:0000080] + Exterior anatomical region [BSPO:0000034] + Interior anatomical region [BSPO:0000033] + + +food_product menu PriorSarsCov2InfectionMenu Animal feed [ENVO:02000047] + Blood meal [FOODON:00001564] + Bone meal [ENVO:02000054] + Brassica carinata meal [FOODON:00004310] + Canola meal [FOODON:00002694] + Compound feed premix [FOODON:00004323] + Compound feed premix (medicated) [FOODON:00004324] + Feather meal [FOODON:00003927] + Fish meal [FOODON:03301620] + Lay ration [FOODON:00004286] + Meat and bone meal [FOODON:00002738] + Meat meal [FOODON:00004282] + Pet food [FOODON:00002682] + Soybean meal [FOODON:03302757] + Animal feed ingredient [FOODON:00004322] + Dairy food product [FOODON:00001256] + Cheese block (whole or parts) [FOODON:03000287] + Cow skim milk (powdered) [FOODON:03310016] + Milk [UBERON:0001913] + Dietary supplement [FOODON:03401298] + Egg or egg component [FOODON:03420194] + Balut [FOODON:03302184] + Egg yolk [UBERON:0007378] + Poultry egg [FOODON:03000414] + Hen egg (whole) [FOODON:03316061] + Poultry egg (whole, shell on) [FOODON:03000415] + Food mixture [FOODON:00004130] + Food product analog (food subsitute) [FOODON:00001871] + Milk substitute [FOODON:03305408] + Meat (whole or parts) [FOODON:03317170] + Cutlet [FOODON:00003001] + Filet [FOODON:03530144] + Liver (whole, raw) [FOODON:03309772] + Meat trim [FOODON:03309475] + Rib (meat cut) [FOODON:03530023] + Rib chop [FOODON:00004290] + Shoulder (meat cut) [FOODON:03530043] + Grains, cereals, and bakery product (organizational term) + Bread loaf (whole or parts) [FOODON:03000288] + Breakfast cereal [FOODON:03311075] + Bulk grain [FOODON:03309390] + Oat grain [FOODON:00003429] + Legume food product [FOODON:00001264] + Chickpea (whole) [FOODON:03306811] + Hummus [FOODON:00003049] + Soybean (whole or parts) [FOODON:03000245] + Meat, poultry and fish (organizational term) + Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, boneless) [FOODON:0001282] + Beef (ground, extra lean) [FOODON:02000426] + Beef (ground, lean) [FOODON:02000425] + Beef (ground, medium) [FOODON:02000427] + Beef (ground, regular) [FOODON:02000428] + Beef (ground, sirloin) [FOODON:02000429] + Beef hamburger (dish) [FOODON:00002737] + Beef shoulder [FOODON:02000069] + Beef shoulder chop [FOODON:03000387] + Beef sirloin chop [FOODON:03000389] + Beef stew chunk [FOODON:00004288] + Beef tenderloin [FOODON:00003302] + Beef (pieces) [FOODON:02000412] + Brisket [FOODON:03530020] + Chicken breast [FOODON:00002703] + Chicken breast (back off) [FOODON:03000385] + Chicken breast (skinless) [FOODON:02020231] + Chicken breast (with skin) [FOODON:02020233] + Chicken breast (skinless, boneless) [FOODON:02020235] + Chicken breast cutlet [FOODON:00004308] + Chicken drumstick [FOODON:00002716] + Chicken drumstick (skinless) [FOODON:02020237] + Chicken drumstick(with skin) [FOODON:02020239] + Chicken meat [FOODON:00001040] + Chicken meat (ground) [FOODON:02020311] + Chicken meat (ground or minced, lean) [FOODON:03000392] + Chicken meat (ground or minced, extra lean) [FOODON:03000396] + Chicken meat (ground or minced, medium) [FOODON:03000400] + Chicken meat (ground or minced, regular) [FOODON:03000404] + Chicken meat (ground or minced, boneless) [FOODON:03000410] + Chicken nugget [FOODON:00002672] + Chicken thigh [FOODON:02020219] + Chicken thigh (skinless) [FOODON:00003331] + Chicken thigh (skinless, with bone) [FOODON:02020227] + Chicken thigh (skinless, boneless) [FOODON:02020228] + Chicken upper thigh [FOODON:03000381] + Chicken upper thigh (with skin) [FOODON:03000383] + Chicken thigh (with skin) [FOODON:00003330] + Chicken thigh (with skin, with bone) [FOODON_00003363] + Chicken wing [FOODON:00002674] + Fish food product [FOODON:00001248] + Fish steak [FOODON:00002986] + Ham food product [FOODON:00002502] + Head cheese [FOODON:03315658] + Lamb [FOODON:03411669] + Meat strip [FOODON:00004285] + Mutton [FOODON:00002912] + Pork chop [FOODON:00001049] + pork meat (ground) [FOODON:02021718] + Pork meat (ground or minced, boneless) [FOODON:03000413] + Pork meat (ground or minced, extra lean) [FOODON:03000399] + Pork meat (ground or minced, lean) [FOODON:03000395] + Pork meat (ground or minced, medium) [FOODON:03000403] + Pork meat (ground or minced, regular) [FOODON:03000407] + Pork meat (ground or minced, Sirloin) [FOODON:03000409] + Pork shoulder [FOODON:02000322] + Pork shoulder chop [FOODON:03000388] + Pork sirloin chop [FOODON:02000300] + Pork steak [FOODON:02021757] + Pork tenderloin [FOODON:02000306] + Poultry meat [FOODON:03315883] + Leg (poultry meat cut) [FOODON:03530159] + Poultry drumstick [FOODON:00003469] + Neck (poultry meat cut) [FOODON:03530294] + Thigh (poultry meat cut) [FOODON:03530160] + Wing (poultry meat cut) [FOODON:03530157] + Sausage (whole) [FOODON:03315904] + Pepperoni [FOODON:03311003] + Salami [FOODON:03312067] + Shellfish [FOODON:03411433] + Mussel [FOODON:03411223] + Oyster [FOODON:03411224] + Shrimp [FOODON:03301673] + Scallop [FOODON:02020805] + Squid [FOODON:03411205] + Turkey breast [FOODON:00002690] + Turkey breast (back off) [FOODON:03000386] + Turkey breast (skinless) [FOODON:02020495] + Turkey breast (skinless, boneless) [FOODON:02020499] + Turkey breast (with skin) [FOODON:02020497] + Turkey drumstick [FOODON:02020477] + Turkey drumstick (skinless) [FOODON:02020501] + Turkey drumstick (with skin) [FOODON:02020503] + Turkey meat [FOODON:00001286] + Turkey meat (ground) [FOODON:02020577] + Turkey meat (ground or minced, lean) [FOODON:03000393] + Turkey meat (ground or minced, extra lean) [FOODON:03000397] + Turkey meat (ground or minced, medium) [FOODON:03000401] + Turkey meat (ground or minced, regular) [FOODON:03000405] + Turkey meat (ground or minced, boneless) [FOODON:03000411] + Turkey thigh [FOODON:00003325] + Turkey thigh (skinless) [FOODON:00003329] + Turkey thigh (skinless, boneless) [FOODON:02020491] + Turkey thigh (with skin) [FOODON:00003328] + Turkey upper thigh [FOODON:03000382] + Turkey upper thigh (with skin) [FOODON:03000384] + Turkey wing [FOODON:02020478] + Veal [FOODON:00003083] + Formula fed veal [FOODON:000039111] + Grain-fed veal [FOODON:00004280] + Microbial food product [FOODON:00001145] + Yeast [FOODON:03411345] + Nuts and seed products + Almond (whole or parts) [FOODON:03000218] + Almond (whole) [FOODON:00003523] + Barley seed [FOODON:00003394] + Canola seed [FOODON:00004560] + Chia seed powder [FOODON:00003925] + Chia seed (whole or parts) [FOODON:03000241] + Flaxseed powder [FOODON:00004276] + Hazelnut [FOODON:00002933] + Nut (whole or part) [FOODON:03306632] + Peanut butter [FOODON:03306867] + Sesame seed [FOODON:03310306] + Tahini [FOODON:00003855] + Walnut (whole or parts) [FOODON:03316466] + Prepared food product [FOODON:00001180] + Condiment [FOODON:03315708] + Confectionery food product [FOODON:00001149] + Snack food [FOODON:03315013] + Produce [FOODON:03305145] + Apple (whole or parts) [FOODON:03310788] + Apple (whole) [FOODON:00002473] + Arugula greens bunch [FOODON:00003643] + Avocado [FOODON:00003600] + Cantaloupe (whole or parts) [FOODON:03000243] + Chilli pepper [FOODON:00003744] + Coconut (whole or parts) [FOODON:03309861] + Coconut meat [FOODON:00003856] + Corn cob (whole or parts) [FOODON:03310791] + Cucumber (whole or parts) [FOODON:03000229] + Fruit [PO:0009001] + Goji berry [FOODON:00004360] + Greens (raw) [FOODON:03310765] + Kale leaf (whole or parts) [FOODON:03000236] + Karela (bitter melon) [FOODON:00004367] + Lettuce head (whole or parts) [FOODON:03000239] + Mango (whole or parts) [FOODON:03000217] + Mushroom (fruitbody) [FOODON:00003528] + Papaya (whole or parts) [FOODON:03000228] + Pattypan squash (whole or parts) [FOODON:03000232] + Peach [FOODON:00002485] + Pepper (whole or parts) [FOODON:03000249] + Potato [FOODON:03315354] + Salad [FOODON:03316042] + Scallion (whole or parts) [FOODON:03000250] + Spinach (whole or parts) [FOODON:03000221] + Sprout [FOODON:03420183] + Germinated or sprouted seed [FOODON:03420102] + Alfalfa sprout [FOODON:00002670] + Bean sprout [FOODON:00002576] + Chia sprout [FOODON:03000180] + Mixed sprouts [FOODON:03000182] + Mung bean sprout [FOODON:03301446] + Tomato (whole or pieces) [FOODON:00002318] + Vegetable (whole or parts) [FOODON:03315308] + Spice or herb [FOODON:00001242] + Basil (whole or parts) [FOODON:03000233] + Black pepper (whole or parts) [FOODON:03000242] + Cardamom (whole or parts) [FOODON:03000246] + Chive leaf (whole or parts) [FOODON:03000240] + Coriander powder [FOODON:00004274] + Coriander seed (whole or parts) [FOODON:03000224] + Cumin powder [FOODON:00004275] + Cumin seed (whole) [FOODON:00003396] + Black cumin seed (whole or parts) [FOODON:03000247] + Curry leaf (whole or parts) [FOODON:03000225] + Curry powder [FOODON:03301842] + Dill spice [FOODON:00004307] + Fennel (whole or parts) [FOODON:03000244] + Garlic powder [FOODON:03301844] + Ginger root (whole or parts) [FOODON:03000220] + Mint leaf (whole or parts) [FOODON:03000238] + Oregano (whole or parts) [FOODON:03000226] + Paprika (ground) [FOODON:03301223] + Parsley leaf (whole or parts) [FOODON:03000231] + Pepper (ground) [FOODON:03301526] + Rasam powder [FOODON:00004277] + Sage [FOODON:03301560] + Turmeric (ground) [FOODON:03310841] + Spice [FOODON:03303380] + White peppercorn (whole or parts) [FOODON:03000251] + + +food_product_properties menu FoodProductPropertiesMenu Food (canned) [FOODON:00002418] + Food (cooked) [FOODON:00001181] + Food (cut) [FOODON:00004291] + Food (chopped) [FOODON:00002777] + Food (chunks) [FOODON:00004555] + Food (cubed) [FOODON:00004278] + Food (diced) [FOODON:00004549] + Food (grated) [FOODON:00004552] + Food (sliced) [FOODON:00002455] + Food (shredded) [FOODON:00004553] + Food (dried) [FOODON:03307539] + Food (fresh) [FOODON:00002457] + Food (frozen) [FOODON:03302148] + Food (pulped) [FOODON:00004554] + Food (raw) [FOODON:03311126] + Food (unseasoned) [FOODON:00004287] + Italian-style food product [FOODON:00004321] + Meat (boneless) [FOODON:00003467] + Meat (skinless) [FOODON:00003468] + Meat (with bone) [FOODON:02010116] + Meat (with skin) [FOODON:02010111] + Soft [PATO:0000387] + + + + +label_claim menu LabelClaimMenu Antibiotic free [FOODON:03601063] + Cage free [FOODON:03601064] + Hormone free [FOODON:03601062] + Organic food claim or use [FOODON:03510128] + Pasture raised [FOODON:03601065] + Ready-to-eat (RTE) [FOODON:03316636] + + +animal_source_of_food menu AnimalSourceOfFoodMenu Cow [NCBITaxon:9913] + Fish [FOODON:03411222] + Pig [NCBITaxon:9823] + Poultry or game bird [FOODON:03411563] + Chicken [NCBITaxon:9031] + Turkey [NCBITaxon:9103] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Mussel [FOODON:03411223] + Scallop [NCBITaxon:6566] + Shrimp [FOODON:03411237] + Squid [FOODON:03411205] + + +food_product_production_stream menu FoodProductProductionStreamMenu Beef cattle production stream [FOODON:03000452] + Broiler chicken production stream [FOODON:03000455] + Dairy cattle production stream [FOODON:03000453] + Egg production stream [FOODON:03000458] + Layer chicken production stream [FOODON:03000456] + Meat production stream [FOODON:03000460] + Veal meat production stream [FOODON:03000461] + Milk production stream [FOODON:03000459] + + +collection_device menu CollectionDeviceMenu Auger (earth auger) [AGRO:00000405] + Box corer [GENEPIO:0100928] + Container [OBI:0000967] + Bag [GSSO:008558] + Whirlpak sampling bag [GENEPIO:0002122] + Bottle [FOODON:03490214] + Vial [OBI:0000522] + Culture plate [GENEPIO:0004318] + Petri dish [NCIT:C96141] + Filter [GENEPIO:0100103] + PONAR grab sampler [GENEPIO:0100929] + Scoop [GENEPIO:0002125] + Soil sample probe [GENEPIO:0100930] + Spatula [NCIT:C149941] + Sponge [OBI:0002819] + Swab [GENEPIO:0100027] + Drag swab [OBI:0002822] + Surface wipe [OBI:0002824] + Tube [GENEPIO:0101196] + Vacuum device [GENEPIO:0002127] + Vacutainer [OBIB:0000032] + + +collection_method menu CollectionMethodMenu Aspiration [HP:0002835] + Biopsy [OBI:0002650] + Fecal grab [GENEPIO:0004326] + Filtration [OBI:0302885] + Air filtration [GENEPIO:0100031] + Water filtration [GENEPIO:0100931] + Lavage [OBI:0600044] + Bronchoalveolar lavage [GENEPIO:0100032] + Gastric lavage [GENEPIO:0100033] + Necropsy [MMO:0000344] + Phlebotomy [NCIT:C28221] + Rinsing for specimen collection [GENEPIO_0002116] + Scooping [GENEPIO:0100932] + Sediment collection [GENEPIO:0100933] + Soil coring [GENEPIO:0100934] + Weep fluid collection (pouring) [GENEPIO:0101003] + +sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu microliter (uL) [UO:0000101] + milliliter (mL) [UO:0000098] + liter (L) [UO:0000099] + +residual_sample_status menu ResidualSampleStatusMenu Residual sample remaining (some sample left) [GENEPIO:0101087] + No residual sample (sample all used) [GENEPIO:0101088] + Residual sample status unkown [GENEPIO:0101089] + +sample_storage_duration_unit menu SampleStorageDurationUnitMenu Second [UO:0000010] + Minute [UO:0000031] + Hour [UO:0000032] + Day [UO:0000033] + Week [UO:0000034] + Month [UO:0000035] + Year [UO:0000036] + +nucelic_acid_storage_duration_unit menu NucelicAcidStorageDurationUnitMenu Second [UO:0000010] + Minute [UO:0000031] + Hour [UO:0000032] + Day [UO:0000033] + Week [UO:0000034] + Month [UO:0000035] + Year [UO:0000036] + +food_packaging menu FoodPackagingMenu Bag, sack or pouch [FOODON:03490197] + Paper bag, sack or pouch [FOODON:03490120] + Plastic bag, sack or pouch [FOODON:03490166] + Plastic shrink wrap [FOODON:03490137] + Plastic wrapper [FOODON:03490128] + Bottle or jar [FOODON:03490203] + Can (container) [FOODON:03490204] + Paper container, treated [FOODON:03490330] + Paper container, untreated [FOODON:03490334] + Plastic tray or pan [FOODON:03490126] + + +host (common name) menu HostCommonNameMenu Bird [NCBITaxon:8782] + Chicken [NCBITaxon:9031] + Seabird [FOODON:00004504] + Cormorant [NCBITaxon:9206] + Double Crested Cormorant [NCBITaxon:56069] + Crane [NCBITaxon:9109] + Whooping Crane [NCBITaxon:9117] + Gull (Seagull) [NCBITaxon:8911] + Glaucous-winged Gull [NCBITaxon:119606] + Great Black-backed Gull [NCBITaxon:8912] + Herring Gull [NCBITaxon:35669] + Ring-billed Gull [NCBITaxon:126683] + Eider [NCBITaxon:50366] + Common Eider [NCBITaxon:76058] + Turkey [NCBITaxon:9103] + Fish [FOODON:03411222] + Rainbow Trout [NCBITaxon:8022] + Sablefish [NCBITaxon:229290] + Salmon [FOODON:00003473] + Atlantic Salmon [NCBITaxon:8030] + Chinook salmon [NCBITaxon:74940] + Coho Salmon [NCBITaxon:8019] + Mammal [FOODON:03411134] + Companion animal [FOODON:03000300] + Cow [NCBITaxon:9913] + Human [NCBITaxon:9606] + Pig [NCBITaxon:9823] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Atlantic Lobster [NCBITaxon:6706] + Atlantic Oyster [NCBITaxon:6565] + Blue Mussel [NCBITaxon:6550] + + +host (scientific name) menu HostScientificNameMenu Anoplopoma fimbria [NCBITaxon:229290] + Bos taurus [NCBITaxon:9913] + Crassostrea virginica [NCBITaxon:6565] + Gallus gallus [NCBITaxon:9031] + Grus americana [NCBITaxon:9117] + Homarus americanus [NCBITaxon:6706] + Homo sapiens [NCBITaxon:9606] + Larus argentatus [NCBITaxon:35669] + Larus delawarensis [NCBITaxon:126683] + Larus glaucescens [NCBITaxon:119606] + Larus marinus [NCBITaxon:8912] + Meleagris gallopavo [NCBITaxon:9103] + Mytilus edulis [NCBITaxon:6550] + Oncorhynchus kisutch [NCBITaxon:8019] + Oncorhynchus mykiss [NCBITaxon:8022] + Oncorhynchus tshawytscha [NCBITaxon:74940] + Ovis aries [NCBITaxon:9940] + Phalacrocorax auritus [NCBITaxon:56069] + Salmo salar [NCBITaxon:8030] + Somateria mollissima [NCBITaxon:76058] + Sus scrofa domesticus [NCBITaxon:9825] + + +host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) + Calf [FOODON:03411349] + Dry cow [FOODON:00004411] + Feeder cow [FOODON:00004292] + Finisher cow [FOODON:00004293] + Milker cow [FOODON:03411201] + Stocker cow [FOODON:00004294] + Weanling cow [FOODON:00004295] + Cow (by sex/reproductive stage) (organizational term) + Bull [FOODON:00000015] + Cow [NCBITaxon:9913] + Freemartin [FOODON:00004296] + Heifer [FOODON:00002518] + Steer [FOODON:00002531] + Pig (by age/production stage) (organizational term) + Finisher pig [FOODON:00003371] + Grower pig [FOODON:00003370] + Nursing pig [FOODON:00004297 ] + Pig [NCBITaxon:9823] + Piglet [FOODON:00003952] + Weanling (weaner) pig [FOODON:00003373] + Pig (by sex/reproductive stage) (organizational term) + Barrow [FOODON:03411280] + Boar [FOODON:03412248] + Gilt [FOODON:00003369] + Sow [FOODON:00003333] + Poultry or game bird [FOODON:03411563] + Broiler or fryer chicken [FOODON:03411198] + Capon [FOODON:03411711] + Chick [FOODON:00004299] + Chicken [NCBITaxon:9031] + Egg [UBERON:0007379] + Hatchling [FOODON:00004300] + Hen [FOODON:00003282] + Layer chicken [FOODON:00004301] + Layer turkey [FOODON:00004302] + Poult [FOODON:00002962] + Pullet [FOODON:00004303] + Rooster [FOODON:03411714] + Tom (Gobbler) [FOODON:00004304 ] + Turkey [NCBITaxon:9103] + Sheep [NCBITaxon:9940] + Ram [FOODON:00004305] + Wether sheep [FOODON:00004306] + Ewe [FOODON:03412610] + Lamb [FOODON:03411669] + Fish [FOODON:03411222] + Fish egg [FOODON_00004319] + Fry (fish) [FOODON_00004318] + Juvenile fish [FOODON_00004317] + + +host_age_bin menu HostAgeBinMenu First winter [GENEPIO:0100684] + First summer [GENEPIO:0100685] + Second winter [GENEPIO:0100686] + Second summer [GENEPIO:0100687] + Third winter [GENEPIO:0100688] + Third summer [GENEPIO:0100689] + + +isolated_by menu IsolatedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + + +organism menu OrganismMenu Acinetobacter [NCBITaxon:469] + Acinetobacter baumannii [NCBITaxon:470] + Acinetobacter bereziniae [NCBITaxon:106648] + Acinetobacter ursingii [NCBITaxon:108980] + Aeromonas [NCBITaxon:642] + Aeromonas allosaccharophila [NCBITaxon:656] + Aeromonas hydrophila [NCBITaxon:644] + Aeromonas rivipollensis [NCBITaxon:948519] + Aeromonas salmonicida [NCBITaxon:645] + Campylobacter [NCBITaxon:194] + Campylobacter coli [NCBITaxon:195] + Campylobacter jejuni [NCBITaxon:197] + Campylobacter lari [NCBITaxon:201] + Citrobacter [NCBITaxon:544] + Citrobacter braakii [NCBITaxon:57706] + Citrobacter freundii [NCBITaxon:546] + Citrobacter gillenii [NCBITaxon:67828] + Clostridioides [NCBITaxon:1870884] + Clostridioides difficile [NCBITaxon:1496] + Clostridium [NCBITaxon:1485] + Clostridium perfringens [NCBITaxon:1502] + Clostridium sporogenes [NCBITaxon:1509] + Comamonas [NCBITaxon:283] + Comamonas aquatica [NCBITaxon:225991] + Enterobacter [NCBITaxon:547] + Enterobacter asburiae [NCBITaxon:61645] + Enterobacter cancerogenus [NCBITaxon:69218] + Enterobacter cloacae [NCBITaxon:550] + Enterobacter hormaechei [NCBITaxon:158836] + Enterobacter kobei [NCBITaxon:208224] + Enterobacter roggenkampii [NCBITaxon:1812935] + Enterobacter sp. [NCBITaxon:42895] + Lelliottia amnigena [NCBITaxon:61646] + Pluralibacter gergoviae [NCBITaxon:61647] + Enterococcus [NCBITaxon:1350] + Enterococcus asini [NCBITaxon:57732] + Enterococcus avium [NCBITaxon:33945] + Enterococcus caccae [NCBITaxon:317735] + Enterococcus canis [NCBITaxon:214095] + Enterococcus casseliflavus [NCBITaxon:37734] + Enterococcus cecorum [NCBITaxon:44008] + Enterococcus dispar [NCBITaxon:44009] + Enterococcus durans [NCBITaxon:53345] + Enterococcus faecium [NCBITaxon:1352] + Enterococcus faecalis [NCBITaxon:1351] + Enterococcus gallinarum [NCBITaxon:1353] + Enterococcus hirae [NCBITaxon:1354] + Enterococcus malodoratus [NCBITaxon:71451] + Enterococcus mundtii [NCBITaxon:53346] + Enterococcus ratti [NCBITaxon:150033] + Enterococcus saccharolyticus [NCBITaxon:41997] + Enterococcus thailandicus [NCBITaxon:417368] + Enterococcus villorum [NCBITaxon:112904] + Escherichia [NCBITaxon:561] + Escherichia coli [NCBITaxon:562] + Escherichia fergusonii [NCBITaxon:564] + Exiguobacterium [NCBITaxon:33986] + Exiguobacterium oxidotolerans [NCBITaxon:223958] + Exiguobacterium sp. [NCBITaxon:44751] + Klebsiella [NCBITaxon:570] + Klebsiella aerogenes [NCBITaxon:548] + Klebsiella michiganensis [NCBITaxon:1134687] + Klebsiella oxytoca [NCBITaxon:571] + Klebsiella pneumoniae [NCBITaxon:573] + Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] + Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] + Kluyvera [NCBITaxon:579] + Kluyvera intermedia [NCBITaxon:61648] + Kosakonia [NCBITaxon:1330547] + Kosakonia cowanii [NCBITaxon:208223] + Leclercia [NCBITaxon:83654] + Leclercia adecarboxylata [NCBITaxon:83655] + Listeria [NCBITaxon:1637] + Listeria monocytogenes [NCBITaxon:1639] + Ochrobactrum [NCBITaxon:528] + Ochrobactrum sp. [NCBITaxon:42190] + Pantoea [NCBITaxon:53335] + Pantoea ananatis [NCBITaxon:553] + Pantoea sp. [NCBITaxon:69393] + Photobacterium [NCBITaxon:657] + Photobacterium indicum[NCBITaxon:81447] + Photobacterium sp. [NCBITaxon:660] + Providencia [NCBITaxon:586] + Providencia rettgeri [NCBITaxon:587] + Pseudoalteromonas [NCBITaxon:53246] + Pseudoalteromonas tetraodonis [NCBITaxon:43659] + Pseudomonas [NCBITaxon:286] + Pseudomonas aeruginosa [NCBITaxon:287] + Pseudomonas fluorescens [NCBITaxon:294] + Pseudomonas soli [NCBITaxon:1306993] + Pseudomonas sp. [NCBITaxon:306] + Psychrobacter [NCBITaxon:497] + Psychrobacter faecalis [NCBITaxon:180588] + Psychrobacter nivimaris [NCBITaxon:281738] + Psychrobacter sp. [NCBITaxon:56811] + Rahnella [NCBITaxon:34037] + Rahnella aquatilis [NCBITaxon:34038] + Rahnella sp. [NCBITaxon:1873497] + Raoultella [NCBITaxon:160674] + Raoultella ornithinolytica [NCBITaxon:54291] + Raoultella planticola [NCBITaxon:575] + Salmonella enterica [NCBITaxon:28901] + Salmonella enterica subsp. enterica [NCBITaxon:59201] + Salmonella enterica subsp. arizonae [NCBITaxon:59203] + Serratia [NCBITaxon:613] + Shewanella [NCBITaxon:22] + Shewanella pealeana [NCBITaxon:70864] + Shewanella putrefaciens [NCBITaxon:24] + Shewanella oncorhynchi [NCBITaxon:2726434] + Shewanella sp. [NCBITaxon:50422] + Staphylococcus [NCBITaxon:1279] + Staphylococcus aureus [NCBITaxon:1280] + Streptococcus [NCBITaxon:1301] + Streptococcus alactolyticus [NCBITaxon:29389] + Streptococcus bovis [NCBITaxon:1335] + Streptococcus equinus [NCBITaxon:1335] + Streptococcus gallolyticus [NCBITaxon:315405] + Streptococcus infantarius [NCBITaxon:102684] + Streptococcus lutetiensis [NCBITaxon:150055] + Streptococcus macedonicus [NCBITaxon:59310] + Streptococcus pasteurianus [NCBITaxon:197614] + Streptococcus suis [NCBITaxon:1307] + Vibrio [NCBITaxon:662] + Vibrio cholerae [NCBITaxon:666] + Vibrio parahaemolyticus [NCBITaxon:670] + +taxonomic_identification_process menu TaxonomicIdentificationProcessMenu Whole genome sequencing assay [OBI:0002117] + 16S ribosomal gene sequencing assay [OBI:0002763] + PCR assay [OBI:0002740] + Comparative phenotypic assessment [OBI:0001546] + Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] + + +sequenced_by menu SequencedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + McGill University [GENEPIO:0101103] + + +purpose_of_sequencing menu PurposeOfSequencingMenu Cluster/Outbreak investigation [GENEPIO:0100001] + Diagnostic testing [GENEPIO:0100002] + Environmental testing [GENEPIO:0100548] + Research [GENEPIO:0100003] + Clinical trial [GENEPIO:0100549] + Field experiment [GENEPIO:0100550] + Protocol testing experiment [GENEPIO:0100024] + Survey study [GENEPIO:0100582] + Surveillance [GENEPIO:0100004] + + +sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] + Pacific Biosciences [GENEPIO:0001927] + Ion Torrent [GENEPIO:0002683] + Oxford Nanopore Technologies [OBI:0002755] + BGI Genomics [GENEPIO:0004324] + MGI [GENEPIO:0004325] + + +sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] + Illumina Genome Analyzer [GENEPIO:0100106] + Illumina Genome Analyzer II [OBI:0000703] + Illumina Genome Analyzer IIx [OBI:0002000] + Illumina HiScanSQ [GENEPIO:0100109] + Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X [GENEPIO:0100111] + Illumina HiSeq X Five [GENEPIO:0100112] + Illumina HiSeq X Ten [GENEPIO:0100113] + Illumina HiSeq 1000 [OBI:0002022] + Illumina HiSeq 1500 [GENEPIO:0100115] + Illumina HiSeq 2000 [OBI:0002001] + Illumina HiSeq 2500 [OBI:0002002] + Illumina HiSeq 3000 [OBI:0002048] + Illumina HiSeq 4000 [OBI:0002049] + Illumina iSeq [GENEPIO:0100120] + Illumina iSeq 100 [GENEPIO:0100121] + Illumina NovaSeq [GENEPIO:0100122] + Illumina NovaSeq 6000 [GENEPIO:0100123] + Illumina MiniSeq [GENEPIO:0100124] + Illumina MiSeq [OBI:0002003] + Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 500 [OBI:0002021] + Illumina NextSeq 550 [GENEPIO:0100128] + Illumina NextSeq 2000 [GENEPIO:0100129] + Illumina NextSeq 1000 [GENEPIO:0004432] + PacBio [GENEPIO:0100130] + PacBio RS [GENEPIO:0100131] + PacBio RS II [OBI:0002012] + PacBio Sequel [GENEPIO:0100133] + PacBio Sequel II [GENEPIO:0100134] + Ion Torrent [GENEPIO:0100135] + Ion Torrent PGM [GENEPIO:0100136] + Ion Torrent Proton [GENEPIO:0100137] + Ion Torrent S5 XL [GENEPIO:0100138] + Ion Torrent S5 [GENEPIO:0100139] + Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore Flongle [GENEPIO:0004433] + Oxford Nanopore GridION [GENEPIO:0100141] + Oxford Nanopore MinION [GENEPIO:0100142] + Oxford Nanopore PromethION [GENEPIO:0100143] + BGISEQ [GENEPIO:0100144] + BGISEQ-500 [GENEPIO:0100145] + DNBSEQ [GENEPIO:0100146] + DNBSEQ-T7 [GENEPIO:0100147] + DNBSEQ-G400 [GENEPIO:0100148] + DNBSEQ-G400 FAST [GENEPIO:0100149] + DNBSEQ-G50 [GENEPIO:0100150] + + +sequencing_assay_type menu SequencingAssayTypeMenu Amplicon sequencing assay [OBI:0002767] + 16S ribosomal gene sequencing assay [OBI:0002763] + Whole genome sequencing assay [OBI:0002117] + Whole metagenome sequencing assay [OBI:0002623] + Whole virome sequencing assay [OBI:0002768] + +genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu Hybrid selection method (bait-capture) [GENEPIO:0001950] + rRNA depletion method [GENEPIO:0101020] + + +sequence_submitted_by menu SequenceSubmittedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + McGill University [GENEPIO:0101103] + +quality_control_determination menu QualityControlDeterminationMenu No quality control issues identified [GENEPIO:0100562] + Sequence passed quality control [GENEPIO:0100563] + Sequence failed quality control [GENEPIO:0100564] + Minor quality control issues identified [GENEPIO:0100565] + Sequence flagged for potential quality control issues [GENEPIO:0100566] + Quality control not performed [GENEPIO:0100567] + +quality _control_issues menu QualityControlIssuesMenu Low quality sequence [GENEPIO:0100568] + Sequence contaminated [GENEPIO:0100569] + Low average genome coverage [GENEPIO:0100570] + Low percent genome captured [GENEPIO:0100571] + Read lengths shorter than expected [GENEPIO:0100572] + Sequence amplification artifacts [GENEPIO:0100573] + Low signal to noise ratio [GENEPIO:0100574] + Low coverage of characteristic mutations [GENEPIO:0100575] + + +attribute_package menu AttributePackageMenu Pathogen.cl [GENEPIO:0001835] + Pathogen.env [GENEPIO:0100581] + + +experimental_intervention menu PriorSarsCov2InfectionMenu Addition of substances to food/water [GENEPIO:0100536] + Antimicrobial pre-treatment [GENEPIO:0100537] + Certified animal husbandry practices [GENEPIO:0100538] + Certified organic farming practices [GENEPIO:0100539] + Change in storage conditions [GENEPIO:0100540] + Cleaning/disinfection [GENEPIO:0100541] + Extended downtime between activities [GENEPIO:0100542] + Fertilizer pre-treatment [GENEPIO:0100543] + Logistic slaughter [GENEPIO:0100545] + Microbial pre-treatment [GENEPIO:0100546] + Probiotic pre-treatment [GENEPIO:0100547] + Vaccination [NCIT:C15346] + + +AMR_testing_by menu AMRTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + + +antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] + Intermediate antimicrobial phenotype [ARO:3004300] + Indeterminate antimicrobial phenotype [GENEPIO:0100585] + Nonsusceptible antimicrobial phenotype [ARO:3004303] + Resistant antimicrobial phenotype [ARO:3004301] + Susceptible antimicrobial phenotype [ARO:3004302] + Susceptible dose dependent antimicrobial phenotype [ARO:3004304] + + +antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] + millimetre (mm) [UO:0000016] + microgram per millilitre (ug/mL) [UO:0000274] + + +antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] + less than or equal to (<=) [GENEPIO:0001003] + equal to (==) [GENEPIO:0001004] + greater than (>) [GENEPIO:0001006] + greater than or equal to (>=) [GENEPIO:0001005] + + +antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion + Antimicrobial gradient (E-test) [NCIT:85596] + Agar dilution [ARO:3004411] agar dilution + Broth dilution [ARO:3004397] + + +antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] + Microscan [ARO:3004400] Microscan + Phoenix [ARO:3004401] Phoenix + Sensititre [ARO:3004402] Sensititre + Vitek System [ARO:3004403] Vitek + + +antimicrobial_vendor_name menu AntimicrobialVendorNameMenu Becton Dickinson [ARO:3004405] Becton Dickinson + bioMérieux [ARO:3004406] Biomérieux + Omron [ARO:3004408] + Siemens [ARO:3004407] Siemens + Trek [ARO:3004409] Trek + + +antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] BSAC + Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] CLSI + Deutsches Institut für Normung (DIN) [ARO:3004367] DIN + European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] EUCAST + National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] NARMS + National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] NCCLS + Société Française de Microbiologie (SFM) [ARO:3004369] SFM + Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] SIR + Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG + + +Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu \ No newline at end of file diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index f67e0019..0534117c 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -1,800 +1,785 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE -GRDI GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID WhitespaceMinimizedString null value menu TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name - Sample collection and processing GENEPIO:0100427 alternative_sample_ID WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. """Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: -Public Health Agency of Canada: PHAC -Canadian Food Inspection Agency: CFIA -Agriculture and Agri-Food Canada: AAFC -Fisheries and Oceans Canada: DFO -Environment and Climate Change Canada: ECCC -Health Canada: HC -Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.""" ABCD1234[PHAC]; 12345rev[CFIA] - Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by menu null value menu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by - Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sample collection and processing GENEPIO:0100429 sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) - Sample collection and processing GENEPIO:0100430 sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken - Sample collection and processing GENEPIO:0100431 sample_plan_ID WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 - Sample collection and processing GENEPIO:0100432 sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sample collection and processing GENEPIO:0001156 sample_collector_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling menu null value menu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity menu null value menu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] - Sample collection and processing GENEPIO:0100434 presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. - Sample collection and processing GENEPIO:0101029 experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol - Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type menu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] - Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing menu null value menu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] - Sample collection and processing GENEPIO:0100939 nucleic acid extraction method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 - Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) menu null value menu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name (state/province/region) menu null value menu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) - Sample collection and processing GENEPIO:0100436 geo_loc_name (site) WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) - Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) geo_loc_name (country) menu null value menu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] - Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) geo_loc_name (country) menu null value menu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] - Sample collection and processing GENEPIO:0100309 geo_loc latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N - Sample collection and processing GENEPIO:0100310 geo_loc longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W - Sample collection and processing GENEPIO:0001174 sample_collection_date date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date - Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] - Sample collection and processing GENEPIO:0001179 sample_received_date date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Sample collection and processing GENEPIO:0100439 original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli - Sample collection and processing GENEPIO:0001232 environmental_site environmental_site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site - Sample collection and processing GENEPIO:0001223 environmental_material environmental_material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material - Sample collection and processing GENEPIO:0101197 environmental_material_constituent WhitespaceMinimizedString TRUE The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic - Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population menu null value menu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] - Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material - Sample collection and processing GENEPIO:0001216 body_product body_product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product - Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part - Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region menu null value menu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] - Sample collection and processing GENEPIO:0100444 food_product food_product menu null value menu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product - Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties menu null value menu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties - Sample collection and processing FOODON:03602001 label_claim label_claim menu null value menu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] - Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food menu null value menu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] - Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream menu null value menu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] - Sample collection and processing GENEPIO:0100447 food_packaging food_packaging menu null value menu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging - Sample collection and processing GENEPIO:0100615 food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 - Sample collection and processing GENEPIO:0100616 food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 - Sample collection and processing GENEPIO:0001234 collection_device collection_device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device - Sample collection and processing GENEPIO:0001241 collection_method collection_method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method - Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 - Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit menu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] - Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status menu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] - Sample collection and processing GENEPIO:0100448 sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport - Sample collection and processing GENEPIO:0100449 sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol - Sample collection and processing GENEPIO:0101014 sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit menu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] - Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit menu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] - Sample collection and processing GENEPIO:0100690 available_data_types available_data_types menu null value menu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] - Sample collection and processing GENEPIO:0101023 available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria - Environmental conditions and measurements - Environmental conditions and measurements GENEPIO:0100440 water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 - Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units menu null value menu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100697 sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 - Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units menu null value menu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100441 air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 - Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units menu null value menu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100698 water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 - Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units menu null value menu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] - GENEPIO:0001268 Host information - Host information GENEPIO:0001386 host (common name) host (common name) menu null value menu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] - Host information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host - Host information GENEPIO:0100450 host (ecotype) WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype - Host information GENEPIO:0100451 host (breed) WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease - Host information GENEPIO:0100452 host (food production name) host (food production name) menu null value menu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] - Host information GENEPIO:0001394 host_age_bin host_age_bin menu null value menu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. - Host information GENEPIO:0001391 host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis - GENEPIO:0100453 Strain and isolation information - Strain and isolation information GENEPIO:0100454 microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 - Strain and isolation information GENEPIO:0100455 strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 - Strain and isolation information GENEPIO:0100456 isolate_ID WhitespaceMinimizedString null value menu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 - Strain and isolation information GENEPIO:0100457 alternative_isolate_ID WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: -Public Health Agency of Canada: PHAC -Canadian Food Inspection Agency: CFIA -Agriculture and Agri-Food Canada: AAFC -Fisheries and Oceans Canada: DFO -Environment and Climate Change Canada: ECCC -Health Canada: HC -An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] -Multiple alternative isolate IDs can be provided, separated by semi-colons." GHIF3456[PHAC]; QWICK222[CFIA] - Strain and isolation information GENEPIO:0100458 progeny_isolate_ID WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 - Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID WhitespaceMinimizedString null value menu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 - Strain and isolation information GENEPIO:0100460 IRIDA_project_ID WhitespaceMinimizedString null value menu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 - Strain and isolation information GENEPIO:0100461 isolated_by isolated_by menu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Strain and isolation information GENEPIO:0100463 isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Strain and isolation information GENEPIO:0100464 isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Strain and isolation information GENEPIO:0100465 isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 - Strain and isolation information GENEPIO:0100466 isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Strain and isolation information GENEPIO:0001191 organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism - Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process menu null value menu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] - Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument - Strain and isolation information GENEPIO:0100467 serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg - Strain and isolation information GENEPIO:0100468 serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 - Strain and isolation information GENEPIO:0100469 phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 - GENEPIO:0001441 Sequence information - Sequence information GENEPIO:0001448 library_ID WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 - Sequence information GENEPIO:0100416 sequenced_by sequenced_by menu null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by - Sequence information GENEPIO:0100470 sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sequence information GENEPIO:0100471 sequenced_by_contact_name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sequence information GENEPIO:0100422 sequenced_by_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing - Sequence information GENEPIO:0100472 sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) - Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] - Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] - Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] - Sequence information GENEPIO:0001450 library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequence information GENEPIO:0100843 DNA fragment length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 - Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method menu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] - Sequence information GENEPIO:0100967 genomic target enrichment method details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel - Sequence information GENEPIO:0001456 amplicon pcr primer scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 - Sequence information GENEPIO:0001449 amplicon size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 - Sequence information GENEPIO:0101102 sequencing flow cell version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 - Sequence information GENEPIO:0001454 sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no - Sequence information GENEPIO:0001476 r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Sequence information GENEPIO:0001477 r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Sequence information GENEPIO:0001480 fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 - Sequence information GENEPIO:0001461 assembly_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0100557 quality control method name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools - Bioinformatics and QC metrics GENEPIO:0100558 quality control method version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control - Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage - Bioinformatics and QC metrics GENEPIO:0100561 quality control details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper - Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet - Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 - Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 - Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 - Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 - Bioinformatics and QC metrics GENEPIO:0100844 genome completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 - Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics GENEPIO:0100827 number of total reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 - Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 - Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 - Bioinformatics and QC metrics GENEPIO:0100937 number of contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 - Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 - Bioinformatics and QC metrics GENEPIO:0100938 N50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 - Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 - Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 - Bioinformatics and QC metrics GENEPIO:0100831 deduplication method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf - GENEPIO:0101082 Taxonomic identification information - Taxonomic identification information GENEPIO:0100832 read mapping software name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat - Taxonomic identification information GENEPIO:0100833 read mapping software version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 - Taxonomic identification information GENEPIO:0100834 taxonomic reference database name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon - Taxonomic identification information GENEPIO:0100835 taxonomic reference database version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 - Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc - Taxonomic identification information GENEPIO:0101075 taxonomic analysis date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 - Taxonomic identification information GENEPIO:0100836 read mapping criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 - GENEPIO:0100477 Public repository information - Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by menu null value menu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca - Public repository information GENEPIO:0100475 publication_ID WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 - Public repository information GENEPIO:0100476 attribute_package attribute_package menu null value menu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] - Public repository information GENEPIO:0001136 bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession - Public repository information GENEPIO:0001139 biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 - Public repository information GENEPIO:0001142 SRA_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 - Public repository information GENEPIO:0001145 GenBank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 - GENEPIO:0100478 Risk assessment information - Risk assessment information GENEPIO:0100480 prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples - Risk assessment information GENEPIO:0100481 prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. - Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production menu null value menu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] - Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention menu null value menu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] - Risk assessment information GENEPIO:0100484 experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed - GENEPIO:0100479 Antimicrobial resistance - Antimicrobial resistance GENEPIO:0100511 AMR_testing_by AMR_testing_by menu null value menu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name WhitespaceMinimizedString null value menu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email WhitespaceMinimizedString null value menu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Antimicrobial resistance GENEPIO:0100515 AMR_testing_date date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 - Antimicrobial resistance amikacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance amikacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance amikacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance amikacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance amikacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance amikacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amikacin_vendor_name antimicrobial_vendor_name null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance amikacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ampicillin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance ampicillin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance ampicillin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance ampicillin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance ampicillin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance ampicillin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ampicillin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance ampicillin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance azithromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance azithromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance azithromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance azithromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance azithromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance azithromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance azithromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance azithromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefazolin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cefazolin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cefazolin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cefazolin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cefazolin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cefazolin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefazolin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cefazolin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefepime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cefepime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cefepime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cefepime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cefepime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cefepime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefepime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cefepime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cefotaxime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cefotaxime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cefotaxime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cefotaxime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cefotaxime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cefotaxime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefoxitin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cefoxitin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cefoxitin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cefoxitin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cefoxitin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cefoxitin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefoxitin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cefoxitin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefpodoxime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cefpodoxime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cefpodoxime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cefpodoxime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cefpodoxime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cefpodoxime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefpodoxime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cefpodoxime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance ceftazidime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance ceftazidime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance ceftazidime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance ceftazidime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance ceftazidime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance ceftazidime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftiofur_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance ceftiofur_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance ceftiofur_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance ceftiofur_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance ceftiofur_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance ceftiofur_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftiofur_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance ceftiofur_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftriaxone_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance ceftriaxone_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance ceftriaxone_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance ceftriaxone_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance ceftriaxone_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance ceftriaxone_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftriaxone_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance ceftriaxone_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cephalothin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance cephalothin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance cephalothin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance cephalothin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance cephalothin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance cephalothin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cephalothin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance cephalothin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance chloramphenicol_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance chloramphenicol_measurement WhitespaceMinimizedString null value menu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance chloramphenicol_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance chloramphenicol_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance chloramphenicol_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance chloramphenicol_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance chloramphenicol_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance chloramphenicol_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ciprofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance ciprofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance ciprofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance ciprofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance ciprofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ciprofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance ciprofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance clindamycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance clindamycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance clindamycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance clindamycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance clindamycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance clindamycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance clindamycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance clindamycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance doxycycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance doxycycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance doxycycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance doxycycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance doxycycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance doxycycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance doxycycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance doxycycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance enrofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance enrofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance enrofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance enrofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance enrofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance enrofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance enrofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance enrofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance erythromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance erythromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance erythromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance erythromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance erythromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance erythromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance erythromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance erythromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance florfenicol_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance florfenicol_measurement WhitespaceMinimizedString null value menu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance florfenicol_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance florfenicol_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance florfenicol_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance florfenicol_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance florfenicol_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance florfenicol_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance gentamicin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance gentamicin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance gentamicin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance gentamicin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance gentamicin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance gentamicin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance gentamicin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance gentamicin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance imipenem_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance imipenem_measurement WhitespaceMinimizedString null value menu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance imipenem_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance imipenem_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance imipenem_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance imipenem_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance imipenem_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance imipenem_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance kanamycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance kanamycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance kanamycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance kanamycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance kanamycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance kanamycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance kanamycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance kanamycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance levofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance levofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance levofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance levofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance levofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance levofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance levofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance levofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance linezolid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance linezolid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance linezolid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance linezolid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance linezolid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance linezolid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance linezolid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance linezolid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance meropenem_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance meropenem_measurement WhitespaceMinimizedString null value menu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance meropenem_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance meropenem_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance meropenem_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance meropenem_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance meropenem_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance meropenem_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nalidixic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance nalidixic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance nalidixic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance nalidixic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance nalidixic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nalidixic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance nalidixic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nitrofurantoin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance nitrofurantoin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance nitrofurantoin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance nitrofurantoin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance nitrofurantoin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nitrofurantoin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance nitrofurantoin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance norfloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance norfloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance norfloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance norfloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance norfloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance norfloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance norfloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance norfloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxolinic-acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance oxolinic-acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance oxolinic-acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance oxolinic-acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance oxolinic-acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxolinic-acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance oxolinic-acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance oxolinic-acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxolinic-acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxolinic-acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxolinic-acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxolinic-acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxytetracycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance oxytetracycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance oxytetracycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance oxytetracycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance oxytetracycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance oxytetracycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxytetracycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance oxytetracycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance piperacillin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance piperacillin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance piperacillin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance piperacillin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance piperacillin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance piperacillin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance piperacillin-tazobactam_measurement WhitespaceMinimizedString null value menu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance piperacillin-tazobactam_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance piperacillin-tazobactam_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin-tazobactam_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance piperacillin-tazobactam_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance piperacillin-tazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin-tazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance polymyxin-b_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance polymyxin-b_measurement WhitespaceMinimizedString null value menu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance polymyxin-b_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance polymyxin-b_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance polymyxin-b_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance polymyxin-b_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance polymyxin-b_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance polymyxin-b_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance polymyxin-b_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance polymyxin-b_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance polymyxin-b_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance polymyxin-b_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance polymyxin-b_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance quinupristin-dalfopristin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance quinupristin-dalfopristin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance quinupristin-dalfopristin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance quinupristin-dalfopristin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance quinupristin-dalfopristin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance streptomycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance streptomycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance streptomycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance streptomycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance streptomycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance streptomycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance streptomycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance streptomycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance sulfisoxazole_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance sulfisoxazole_measurement WhitespaceMinimizedString null value menu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance sulfisoxazole_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance sulfisoxazole_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance sulfisoxazole_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance sulfisoxazole_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance sulfisoxazole_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance telithromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance telithromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance telithromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance telithromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance telithromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance telithromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance telithromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance telithromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tetracycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance tetracycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance tetracycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance tetracycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance tetracycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance tetracycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tetracycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance tetracycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tigecycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance tigecycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance tigecycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance tigecycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance tigecycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance tigecycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tigecycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance tigecycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement WhitespaceMinimizedString null value menu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM +GRDI GENEPIO:0001150 Sample collection and processing + Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString null value menu TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name *sample_name *sample_name + Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." ABCD1234[PHAC]; 12345rev[CFIA] + Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by sample_collected_by menu null value menu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by *collected_by + Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name + Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken + Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 + Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling purpose_of_sampling menu null value menu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling *purpose_of_sampling + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity presampling_activity menu null value menu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] host_am;fertilizer_admin + Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. + Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol + Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type experimental_specimen_role_type menu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] + Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing specimen_processing menu null value menu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] + Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 + Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country geo_loc_name (country) menu null value menu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) *geo_loc_name + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region geo_loc_name (state/province/region) menu null value menu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) *geo_loc_name + Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) + Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin + Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] + Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon + Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon + Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date *collection_date + Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision sample_collection_date_precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] + Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli + Sample collection and processing GENEPIO:0001232 environmental_site environmental_site environmental_site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site *isolation_source;animal_env;host_housing;env_local_scale;facility_type + Sample collection and processing GENEPIO:0001223 environmental_material environmental_material environmental_material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material *isolation_source + Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString TRUE The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic + Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population animal_or_plant_population menu null value menu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] + Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material anatomical_material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;*isolation_source + Sample collection and processing GENEPIO:0001216 body_product body_product body_product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;*isolation_source + Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part anatomical_part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part *isolation_source + Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region anatomical_region menu null value menu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] + Sample collection and processing GENEPIO:0100444 food_product food_product food_product menu null value menu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product + Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties food_product_properties menu null value menu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties *isolation_source;food_processing_method;food_preserv_proc + Sample collection and processing FOODON:03602001 label_claim label_claim label_claim menu null value menu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims + Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food animal_source_of_food menu null value menu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source + Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream food_product_production_stream menu null value menu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod + Sample collection and processing GENEPIO:0100447 food_packaging food_packaging food_packaging menu null value menu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap + Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date + Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 + Sample collection and processing GENEPIO:0001234 collection_device collection_device collection_device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;*isolation_source + Sample collection and processing GENEPIO:0001241 collection_method collection_method collection_method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method *isolation_source + Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 + Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit sample_volume_measurement_unit menu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] + Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status residual_sample_status menu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] + Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport + Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol + Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit sample_storage_duration_unit menu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] + Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit menu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] + Sample collection and processing GENEPIO:0100690 available_data_types available_data_types available_data_types menu null value menu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] + Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria + Environmental conditions and measurements + Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 + Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units water_depth_units menu null value menu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 + Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units sediment_depth_units menu null value menu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 + Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units air_temperature_units menu null value menu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 + Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units water_temperature_units menu null value menu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type weather_type menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] + GENEPIO:0001268 Host information host_information + Host information GENEPIO:0001386 host (common name) host_common_name host (common name) menu null value menu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host + Host information GENEPIO:0001387 host (scientific name) host_scientific_name host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host *isolation_source;host + Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety + Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed + Host information GENEPIO:0100452 host (food production name) host_food_production_name host (food production name) menu null value menu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host + Host information GENEPIO:0001394 host_age_bin host_age_bin host_age_bin menu null value menu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease + GENEPIO:0100453 Strain and isolation information strain_and_isolation_information + Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString null value menu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain + Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias + Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 + Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString null value menu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 + Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString null value menu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 + Strain and isolation information GENEPIO:0100461 isolated_by isolated_by isolated_by menu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Strain and isolation information GENEPIO:0100465 isolation_date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date + Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Strain and isolation information GENEPIO:0001191 organism organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism *organism + Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process taxonomic_identification_process menu null value menu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] + Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument + Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar + Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 + Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 + GENEPIO:0001441 Sequence information sequence_information + Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 + Sequence information GENEPIO:0100416 sequenced_by sequenced_by sequenced_by menu null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by + Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing purpose_of_sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing + Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) + Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] + Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] + Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] + Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 + Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method genomic_target_enrichment_method menu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] + Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel + Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 + Sequence information GENEPIO:0001449 amplicon size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 + Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 + Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no + Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz + Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz + Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 + Sequence information GENEPIO:0001461 assembly_filename assembly_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta + GENEPIO:0001457 Bioinformatics and QC metrics + Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools + Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 + Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination quality_control_determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control + Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues quality_control_issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage + Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper + Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet + Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 + Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 + Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 + Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 + Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 + Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 + Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 + Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 + Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 + Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 + Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 + Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 + Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 + Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf + GENEPIO:0101082 Taxonomic identification information + Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat + Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 + Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon + Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 + Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc + Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 + Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 + GENEPIO:0100477 Public repository information public_repository_information + Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by sequence_submitted_by menu null value menu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca + Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 + Public repository information GENEPIO:0100476 attribute_package attribute_package attribute_package menu null value menu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] + Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession + Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID + Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 + Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 + GENEPIO:0100478 Risk assessment information risk_assessment_information + Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples + Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. + Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production stage_of_production menu null value menu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] + Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention experimental_intervention menu null value menu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention + Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed + GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance + Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AMR_testing_by menu null value menu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString null value menu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString null value menu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 + Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name antimicrobial_vendor_name null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString null value menu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString null value menu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString null value menu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString null value menu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString null value menu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString null value menu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString null value menu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString null value menu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + GENEPIO:0001516 Contributor acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file From 7de55ae96e9246a6e14e8ba5065cab6f48a72d86 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 12 Aug 2024 14:02:08 -0700 Subject: [PATCH 03/96] Finish non-conditional exports --- web/templates/grdi/schema.json | 8 ++++---- web/templates/grdi/schema.yaml | 4 ++-- web/templates/grdi/schema_slots.tsv | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index 0ae25eff..bc093528 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -7609,7 +7609,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" + "NCBI_BIOSAMPLE_Enterics:%2Astrain" ], "slot_uri": "GENEPIO:0100455", "domain_of": [ @@ -7631,7 +7631,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" + "NCBI_BIOSAMPLE_Enterics:%2Astrain" ], "slot_uri": "GENEPIO:0100456", "domain_of": [ @@ -30240,7 +30240,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" + "NCBI_BIOSAMPLE_Enterics:%2Astrain" ], "rank": 75, "slot_uri": "GENEPIO:0100455", @@ -30266,7 +30266,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" + "NCBI_BIOSAMPLE_Enterics:%2Astrain" ], "rank": 76, "slot_uri": "GENEPIO:0100456", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 6a5be7fe..13c32a94 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -4180,7 +4180,7 @@ slots: examples: - value: K12 exact_mappings: - - NCBI_BIOSAMPLE_Enterics:strain + - NCBI_BIOSAMPLE_Enterics:%2Astrain isolate_id: name: isolate_id title: isolate_ID @@ -4199,7 +4199,7 @@ slots: examples: - value: SA20131043 exact_mappings: - - NCBI_BIOSAMPLE_Enterics:strain + - NCBI_BIOSAMPLE_Enterics:%2Astrain alternative_isolate_id: name: alternative_isolate_id title: alternative_isolate_ID diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 0534117c..1585747c 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -77,8 +77,8 @@ GRDI GENEPIO:0001150 Sample collection and processing Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease GENEPIO:0100453 Strain and isolation information strain_and_isolation_information Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 - Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain - Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString null value menu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 *strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString null value menu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 *strain Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString null value menu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 From c7ce36d2c53c123a02c0d8f5c6a93074e7daaa9f Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Wed, 14 Aug 2024 14:37:20 -0700 Subject: [PATCH 04/96] Start implementing if then conds --- lib/DataHarmonizer.js | 22 ++++++++++++++++++++++ web/templates/grdi/export.js | 31 +++++++++++++++++++++---------- 2 files changed, 43 insertions(+), 10 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 357acf8b..4e69b289 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1762,6 +1762,28 @@ class DataHarmonizer { return mappedCell.join(delimiter); } + /** + * TODO is there any need for additional complexities in getMappedField? + * i.e., transforming field + * @param headerNameToCheck + * @param valToMatch + * @param headerNameToOutput + * @param inputRow + * @param sourceFieldNameMap + * @return TODO + */ + getIfThenField( + headerNameToCheck, + valToMatch, + headerNameToOutput, + inputRow, + sourceFieldNameMap + ) { + const valToCheck = inputRow[sourceFieldNameMap[headerNameToCheck]]; + const valToOutput = inputRow[sourceFieldNameMap[headerNameToOutput]]; + return valToCheck === valToMatch ? valToOutput : ''; + } + /** * Some enumeration values get mapped over to export format values. * diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 3b9363e6..f4f47c09 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -213,16 +213,27 @@ export default { for (const inputRow of dh.getTrimmedData(dh.hot)) { const outputRow = []; for (const [headerName, sources] of ExportHeaders) { - // Otherwise apply source (many to one) to target field transform: - const value = dh.getMappedField( - headerName, - inputRow, - sources, - sourceFields, - sourceFieldNameMap, - ':', - 'NCBI_BIOSAMPLE_Enterics' - ); + let value; + if (headerName == 'fertilizer_admin') { + value = dh.getIfThenField( + 'presampling_activity', + 'Fertilizer pre-treatment [GENEPIO:0100543]', + 'presampling_activity_details', + inputRow, + sourceFieldNameMap + ); + } else { + // Otherwise apply source (many to one) to target field transform: + value = dh.getMappedField( + headerName, + inputRow, + sources, + sourceFields, + sourceFieldNameMap, + ':', + 'NCBI_BIOSAMPLE_Enterics' + ); + } outputRow.push(value); } outputMatrix.push(outputRow); From 46caca54c0403d7336192f8e4893911b0fa7e08b Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 15 Aug 2024 10:35:13 -0700 Subject: [PATCH 05/96] wip --- web/templates/grdi/export.js | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index f4f47c09..a177d47e 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -214,7 +214,9 @@ export default { const outputRow = []; for (const [headerName, sources] of ExportHeaders) { let value; - if (headerName == 'fertilizer_admin') { + // TODO some of these seem like they are supposed to have picklists, + // but do not? + if (headerName === 'fertilizer_admin') { value = dh.getIfThenField( 'presampling_activity', 'Fertilizer pre-treatment [GENEPIO:0100543]', @@ -222,6 +224,14 @@ export default { inputRow, sourceFieldNameMap ); + } else if (headerName === 'host_am') { + value = dh.getIfThenField( + 'presampling_activity', + 'Antimicrobial pre-treatment [GENEPIO:0100537]', + 'presampling_activity_details', + inputRow, + sourceFieldNameMap + ); } else { // Otherwise apply source (many to one) to target field transform: value = dh.getMappedField( From 30b224db83279bc275485079ca3df86e8226fbf6 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 15 Aug 2024 14:48:23 -0700 Subject: [PATCH 06/96] Update grdi schemas --- web/templates/grdi/schema.json | 8123 +++++++++++++++------------ web/templates/grdi/schema.yaml | 3957 +++++++------ web/templates/grdi/schema_enums.tsv | 57 +- web/templates/grdi/schema_slots.tsv | 880 +-- 4 files changed, 7098 insertions(+), 5919 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index bc093528..64aaffdb 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -437,6 +437,35 @@ }, "Vaccination [NCIT:C15346]": { "text": "Vaccination [NCIT:C15346]" + }, + "Wastewater treatment process [ENVO:06105300]": { + "text": "Wastewater treatment process [ENVO:06105300]", + "description": "A recycling process during which wastewater is treated." + }, + "Wastewater filtration [GENEPIO:0100881]": { + "text": "Wastewater filtration [GENEPIO:0100881]", + "description": "A wastewater treatment process which removes solid particles from wastewater by means of filtration.", + "is_a": "Wastewater treatment process [ENVO:06105300]" + }, + "Wastewater grit removal [GENEPIO:0100882]": { + "text": "Wastewater grit removal [GENEPIO:0100882]", + "description": "A wastewater treatment process which removes sand, silt, and grit from wastewater.", + "is_a": "Wastewater treatment process [ENVO:06105300]" + }, + "Wastewater microbial treatment [GENEPIO:0100883]": { + "text": "Wastewater microbial treatment [GENEPIO:0100883]", + "description": "A wastewater treatment process in which microbes are used to degrade the biological material in wastewater.", + "is_a": "Wastewater treatment process [ENVO:06105300]" + }, + "Wastewater primary sedimentation [GENEPIO:0100884]": { + "text": "Wastewater primary sedimentation [GENEPIO:0100884]", + "description": "A wastewater treatment process which removes solids and large particles from influent through gravitational force.", + "is_a": "Wastewater treatment process [ENVO:06105300]" + }, + "Wastewater secondary sedimentation [GENEPIO:0100885]": { + "text": "Wastewater secondary sedimentation [GENEPIO:0100885]", + "description": "A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force.", + "is_a": "Wastewater treatment process [ENVO:06105300]" } } }, @@ -1501,6 +1530,20 @@ "Creek [ENVO:03501405]": { "text": "Creek [ENVO:03501405]" }, + "Ditch [ENVO:00000037]": { + "text": "Ditch [ENVO:00000037]", + "description": "A small, human-made channel which has been dug for draining or irrigating the land." + }, + "Drainage ditch [ENVO:00000140]": { + "text": "Drainage ditch [ENVO:00000140]", + "description": "A ditch that collects water from the surrounding land.", + "is_a": "Ditch [ENVO:00000037]" + }, + "Irrigation ditch [ENVO:00000139]": { + "text": "Irrigation ditch [ENVO:00000139]", + "description": "A ditch that supplies water to surrounding land.", + "is_a": "Ditch [ENVO:00000037]" + }, "Farm [ENVO:00000078]": { "text": "Farm [ENVO:00000078]" }, @@ -1572,6 +1615,9 @@ "Park [ENVO:00000562]": { "text": "Park [ENVO:00000562]" }, + "Plumbing drain [ENVO:01000924 ]": { + "text": "Plumbing drain [ENVO:01000924 ]" + }, "Pond [ENVO:00000033]": { "text": "Pond [ENVO:00000033]" }, @@ -1628,6 +1674,10 @@ "Urban area [ENVO:03501437]": { "text": "Urban area [ENVO:03501437]" }, + "Wastewater treatment plant [ENVO:00002272]": { + "text": "Wastewater treatment plant [ENVO:00002272]", + "description": "A plant in which wastewater is treated." + }, "Water surface [ENVO:01001191]": { "text": "Water surface [ENVO:01001191]" }, @@ -1910,10 +1960,10 @@ } } }, - "WeatherTypeMenu": { - "name": "WeatherTypeMenu", + "SamplingWeatherConditionsMenu": { + "name": "SamplingWeatherConditionsMenu", "description": "", - "title": "weather_type menu", + "title": "sampling_weather_conditions menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "Cloudy/Overcast [ENVO:03501418]": { @@ -5719,7 +5769,138 @@ "name": "AntimicrobialResistanceTestDrugMenu", "description": "", "title": "Antimicrobial Resistance Test Drug Menu", - "from_schema": "https://example.com/GRDI" + "from_schema": "https://example.com/GRDI", + "permissible_values": { + "amikacin": { + "text": "amikacin" + }, + "amoxicillin-clavulanic_acid": { + "text": "amoxicillin-clavulanic_acid" + }, + "ampicillin": { + "text": "ampicillin" + }, + "azithromycin": { + "text": "azithromycin" + }, + "cefazolin": { + "text": "cefazolin" + }, + "cefepime": { + "text": "cefepime" + }, + "cefotaxime": { + "text": "cefotaxime" + }, + "cefotaxime-clavulanic_acid": { + "text": "cefotaxime-clavulanic_acid" + }, + "cefoxitin": { + "text": "cefoxitin" + }, + "cefpodoxime": { + "text": "cefpodoxime" + }, + "ceftazidime": { + "text": "ceftazidime" + }, + "ceftazidime-clavulanic_acid": { + "text": "ceftazidime-clavulanic_acid" + }, + "ceftiofur": { + "text": "ceftiofur" + }, + "ceftriaxone": { + "text": "ceftriaxone" + }, + "cephalothin": { + "text": "cephalothin" + }, + "chloramphenicol": { + "text": "chloramphenicol" + }, + "ciprofloxacin": { + "text": "ciprofloxacin" + }, + "clindamycin": { + "text": "clindamycin" + }, + "doxycycline": { + "text": "doxycycline" + }, + "enrofloxacin": { + "text": "enrofloxacin" + }, + "erythromycin": { + "text": "erythromycin" + }, + "florfenicol": { + "text": "florfenicol" + }, + "gentamicin": { + "text": "gentamicin" + }, + "imipenem": { + "text": "imipenem" + }, + "kanamycin": { + "text": "kanamycin" + }, + "levofloxacin": { + "text": "levofloxacin" + }, + "linezolid": { + "text": "linezolid" + }, + "meropenem": { + "text": "meropenem" + }, + "nalidixic_acid": { + "text": "nalidixic_acid" + }, + "nitrofurantoin": { + "text": "nitrofurantoin" + }, + "norfloxacin": { + "text": "norfloxacin" + }, + "oxolinic-acid": { + "text": "oxolinic-acid" + }, + "oxytetracycline": { + "text": "oxytetracycline" + }, + "piperacillin": { + "text": "piperacillin" + }, + "piperacillin-tazobactam": { + "text": "piperacillin-tazobactam" + }, + "polymyxin-b": { + "text": "polymyxin-b" + }, + "quinupristin-dalfopristin": { + "text": "quinupristin-dalfopristin" + }, + "streptomycin": { + "text": "streptomycin" + }, + "sulfisoxazole": { + "text": "sulfisoxazole" + }, + "telithromycin": { + "text": "telithromycin" + }, + "tetracycline": { + "text": "tetracycline" + }, + "tigecycline": { + "text": "tigecycline" + }, + "trimethoprim-sulfamethoxazole": { + "text": "trimethoprim-sulfamethoxazole" + } + } } }, "slots": { @@ -5738,10 +5919,11 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:sample_name", - "NCBI_BIOSAMPLE_Enterics:%2Asample_name", - "NCBI_ANTIBIOGRAM:%2Asample_name" + "NCBI_BIOSAMPLE_Enterics:sample_name", + "NCBI_ANTIBIOGRAM:sample_name" ], "slot_uri": "GENEPIO:0001123", + "identifier": true, "domain_of": [ "GRDI" ], @@ -5751,7 +5933,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -5793,7 +5975,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:collected_by", - "NCBI_BIOSAMPLE_Enterics:%2Acollected_by" + "NCBI_BIOSAMPLE_Enterics:collected_by" ], "slot_uri": "GENEPIO:0001153", "domain_of": [ @@ -5802,10 +5984,10 @@ "required": true, "any_of": [ { - "range": "sample_collected_by menu" + "range": "SampleCollectedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -5932,7 +6114,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -5951,7 +6133,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:purpose_of_sampling", - "NCBI_BIOSAMPLE_Enterics:%2Apurpose_of_sampling" + "NCBI_BIOSAMPLE_Enterics:purpose_of_sampling" ], "slot_uri": "GENEPIO:0001198", "domain_of": [ @@ -5960,10 +6142,10 @@ "required": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -5990,10 +6172,10 @@ ], "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6052,7 +6234,7 @@ "domain_of": [ "GRDI" ], - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, "specimen_processing": { "name": "specimen_processing", @@ -6073,13 +6255,32 @@ ], "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", @@ -6134,7 +6335,7 @@ "exact_mappings": [ "BIOSAMPLE:geo_loc_name", "BIOSAMPLE:geo_loc_name%20%28country%29", - "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" + "NCBI_BIOSAMPLE_Enterics:geo_loc_name" ], "slot_uri": "GENEPIO:0001181", "domain_of": [ @@ -6143,10 +6344,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6166,7 +6367,7 @@ "exact_mappings": [ "BIOSAMPLE:geo_loc_name", "BIOSAMPLE:geo_loc_name%20%28state/province/region%29", - "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" + "NCBI_BIOSAMPLE_Enterics:geo_loc_name" ], "slot_uri": "GENEPIO:0001185", "domain_of": [ @@ -6175,10 +6376,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name (state/province/region) menu" + "range": "GeoLocNameStateProvinceRegionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6227,10 +6428,10 @@ ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6253,10 +6454,10 @@ ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6319,13 +6520,13 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:sample%20collection%20date", - "NCBI_BIOSAMPLE_Enterics:%2Acollection_date" + "NCBI_BIOSAMPLE_Enterics:collection_date" ], "slot_uri": "GENEPIO:0001174", "domain_of": [ "GRDI" ], - "range": "date", + "range": "Date", "required": true }, "sample_collection_date_precision": { @@ -6348,10 +6549,197 @@ "required": true, "any_of": [ { - "range": "sample_collection_date_precision menu" + "range": "SampleCollectionDatePrecisionMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101071", + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "Date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample_processing_date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100763", + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "Date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101072", + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "Time" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101073", + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "Time" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100765", + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "SampleCollectionTimeOfDayMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "1900-01-03" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100766", + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100767", + "domain_of": [ + "GRDI" + ], + "recommended": true, + "any_of": [ + { + "range": "SampleCollectionDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6372,7 +6760,7 @@ "domain_of": [ "GRDI" ], - "range": "date" + "range": "Date" }, "original_sample_description": { "name": "original_sample_description", @@ -6409,7 +6797,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_site", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:isolation_source", "NCBI_BIOSAMPLE_Enterics:animal_env", "NCBI_BIOSAMPLE_Enterics:host_housing", "NCBI_BIOSAMPLE_Enterics:env_local_scale", @@ -6423,10 +6811,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6455,7 +6843,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_material", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0001223", "domain_of": [ @@ -6465,10 +6853,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6492,8 +6880,7 @@ "domain_of": [ "GRDI" ], - "range": "WhitespaceMinimizedString", - "multivalued": true + "range": "WhitespaceMinimizedString" }, "animal_or_plant_population": { "name": "animal_or_plant_population", @@ -6516,10 +6903,10 @@ "multivalued": true, "any_of": [ { - "range": "animal_or_plant_population menu" + "range": "AnimalOrPlantPopulationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6543,7 +6930,7 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_material", "NCBI_BIOSAMPLE_Enterics:host_tissue_sampled", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0001211", "domain_of": [ @@ -6553,10 +6940,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6580,7 +6967,7 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:body_product", "NCBI_BIOSAMPLE_Enterics:host_body_product", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0001216", "domain_of": [ @@ -6590,10 +6977,10 @@ "multivalued": true, "any_of": [ { - "range": "body_product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6613,7 +7000,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_part", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0001214", "domain_of": [ @@ -6623,10 +7010,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6651,10 +7038,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_region menu" + "range": "AnatomicalRegionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6689,10 +7076,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product menu" + "range": "FoodProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6715,7 +7102,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:food_product_properties", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:isolation_source", "NCBI_BIOSAMPLE_Enterics:food_processing_method", "NCBI_BIOSAMPLE_Enterics:food_preserv_proc" ], @@ -6727,10 +7114,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product_properties menu" + "range": "FoodProductPropertiesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6757,10 +7144,10 @@ "multivalued": true, "any_of": [ { - "range": "label_claim menu" + "range": "LabelClaimMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6788,10 +7175,10 @@ "multivalued": true, "any_of": [ { - "range": "animal_source_of_food menu" + "range": "AnimalSourceOfFoodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6817,10 +7204,10 @@ ], "any_of": [ { - "range": "food_product_production_stream menu" + "range": "FoodProductProductionStreamMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6850,10 +7237,10 @@ "multivalued": true, "any_of": [ { - "range": "food_packaging menu" + "range": "FoodPackagingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6877,7 +7264,7 @@ "domain_of": [ "GRDI" ], - "range": "date" + "range": "Date" }, "food_packaging_date": { "name": "food_packaging_date", @@ -6896,7 +7283,7 @@ "domain_of": [ "GRDI" ], - "range": "date" + "range": "Date" }, "collection_device": { "name": "collection_device", @@ -6915,7 +7302,7 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_device", "NCBI_BIOSAMPLE_Enterics:samp_collect_device", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0001234", "domain_of": [ @@ -6924,10 +7311,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6947,7 +7334,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_method", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0001241", "domain_of": [ @@ -6956,10 +7343,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6999,7 +7386,7 @@ "domain_of": [ "GRDI" ], - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -7018,7 +7405,7 @@ "domain_of": [ "GRDI" ], - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "sample_storage_method": { "name": "sample_storage_method", @@ -7094,7 +7481,7 @@ "domain_of": [ "GRDI" ], - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, "nucleic_acid_storage_duration_value": { "name": "nucleic_acid_storage_duration_value", @@ -7132,7 +7519,7 @@ "domain_of": [ "GRDI" ], - "range": "nucleic_acid_storage_duration_unit menu" + "range": "NucleicAcidStorageDurationUnitMenu" }, "available_data_types": { "name": "available_data_types", @@ -7154,10 +7541,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7218,10 +7605,10 @@ ], "any_of": [ { - "range": "water_depth_units menu" + "range": "WaterDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7263,10 +7650,10 @@ ], "any_of": [ { - "range": "sediment_depth_units menu" + "range": "SedimentDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7308,10 +7695,10 @@ ], "any_of": [ { - "range": "air_temperature_units menu" + "range": "AirTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7353,40 +7740,96 @@ ], "any_of": [ { - "range": "water_temperature_units menu" + "range": "WaterTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "weather_type": { - "name": "weather_type", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "title": "sampling_weather_conditions", "comments": [ "Provide the weather conditions at the time of sample collection." ], - "examples": [ + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100779", + "domain_of": [ + "GRDI" + ], + "multivalued": true, + "any_of": [ + { + "range": "SamplingWeatherConditionsMenu" + }, { - "value": "Rain [ENVO:01001564]" + "range": "NullValueMenu" } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "title": "presampling_weather_conditions", + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100780", + "domain_of": [ + "GRDI" ], + "any_of": [ + { + "range": "PresamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "title": "precipitation_measurement_value", "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100442", + "slot_uri": "GENEPIO:0100911", + "domain_of": [ + "GRDI" + ], + "any_of": [ + { + "range": "Whitespaceminimizedstring" + }, + { + "range": "NullValueMenu" + } + ] + }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "title": "precipitation_measurement_unit", + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100912", "domain_of": [ "GRDI" ], - "multivalued": true, "any_of": [ { - "range": "weather_type menu" + "range": "PrecipitationMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "title": "precipitation_measurement_method", + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100913", + "domain_of": [ + "GRDI" + ], + "range": "WhitespaceMinimizedString" + }, "host_common_name": { "name": "host_common_name", "description": "The commonly used name of the host.", @@ -7413,10 +7856,10 @@ "recommended": true, "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7438,7 +7881,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:host", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:isolation_source", "NCBI_BIOSAMPLE_Enterics:host" ], "slot_uri": "GENEPIO:0001387", @@ -7448,10 +7891,10 @@ "recommended": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7522,10 +7965,10 @@ ], "any_of": [ { - "range": "host (food production name) menu" + "range": "HostFoodProductionNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7546,10 +7989,10 @@ ], "any_of": [ { - "range": "host_age_bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7609,7 +8052,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:%2Astrain" + "NCBI_BIOSAMPLE_Enterics:strain" ], "slot_uri": "GENEPIO:0100455", "domain_of": [ @@ -7631,7 +8074,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:%2Astrain" + "NCBI_BIOSAMPLE_Enterics:strain" ], "slot_uri": "GENEPIO:0100456", "domain_of": [ @@ -7643,7 +8086,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7715,7 +8158,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7742,7 +8185,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7763,7 +8206,7 @@ "domain_of": [ "GRDI" ], - "range": "isolated_by menu" + "range": "IsolatedByMenu" }, "isolated_by_laboratory_name": { "name": "isolated_by_laboratory_name", @@ -7842,7 +8285,7 @@ "domain_of": [ "GRDI" ], - "range": "date" + "range": "Date" }, "isolate_received_date": { "name": "isolate_received_date", @@ -7878,7 +8321,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:organism", - "NCBI_BIOSAMPLE_Enterics:%2Aorganism" + "NCBI_BIOSAMPLE_Enterics:organism" ], "slot_uri": "GENEPIO:0001191", "domain_of": [ @@ -7888,10 +8331,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7915,10 +8358,10 @@ "recommended": true, "any_of": [ { - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8046,10 +8489,10 @@ "required": true, "any_of": [ { - "range": "sequenced_by menu" + "range": "SequencedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8095,7 +8538,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8122,7 +8565,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8150,10 +8593,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8195,10 +8638,10 @@ ], "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8221,10 +8664,10 @@ ], "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8245,7 +8688,7 @@ "domain_of": [ "GRDI" ], - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "library_preparation_kit": { "name": "library_preparation_kit", @@ -8302,7 +8745,7 @@ "domain_of": [ "GRDI" ], - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -8533,10 +8976,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8560,10 +9003,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8609,7 +9052,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8636,7 +9079,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8662,7 +9105,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8688,7 +9131,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8714,7 +9157,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8740,7 +9183,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8837,7 +9280,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "number_of_total_reads": { "name": "number_of_total_reads", @@ -8856,7 +9299,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "number_of_unique_reads": { "name": "number_of_unique_reads", @@ -8875,7 +9318,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", @@ -8894,7 +9337,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "number_of_contigs": { "name": "number_of_contigs", @@ -8913,7 +9356,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", @@ -8932,7 +9375,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", @@ -8951,7 +9394,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "n50": { "name": "n50", @@ -8970,7 +9413,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "percent_read_contamination_": { "name": "percent_read_contamination_", @@ -8989,7 +9432,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "sequence_assembly_length": { "name": "sequence_assembly_length", @@ -9008,7 +9451,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "consensus_genome_length": { "name": "consensus_genome_length", @@ -9027,7 +9470,7 @@ "domain_of": [ "GRDI" ], - "range": "integer" + "range": "Integer" }, "reference_genome_accession": { "name": "reference_genome_accession", @@ -9198,7 +9641,7 @@ "domain_of": [ "GRDI" ], - "range": "date" + "range": "Date" }, "read_mapping_criteria": { "name": "read_mapping_criteria", @@ -9238,10 +9681,10 @@ ], "any_of": [ { - "range": "sequence_submitted_by menu" + "range": "SequenceSubmittedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9321,10 +9764,10 @@ ], "any_of": [ { - "range": "attribute_package menu" + "range": "AttributePackageMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9471,10 +9914,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9502,10 +9945,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9549,10 +9992,10 @@ "required": true, "any_of": [ { - "range": "AMR_testing_by menu" + "range": "AmrTestingByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9598,7 +10041,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9625,7 +10068,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9646,7 +10089,7 @@ "domain_of": [ "GRDI" ], - "range": "date" + "range": "Date" }, "amikacin_resistance_phenotype": { "name": "amikacin_resistance_phenotype", @@ -9662,7 +10105,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -9670,10 +10113,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9691,7 +10134,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -9702,7 +10145,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9720,7 +10163,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -9728,10 +10171,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9749,7 +10192,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -9757,10 +10200,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9778,17 +10221,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9813,10 +10256,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9859,10 +10302,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name" + "range": "AntimicrobialVendorName" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9880,7 +10323,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -9888,10 +10331,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9999,7 +10442,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -10007,10 +10450,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10028,7 +10471,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -10039,7 +10482,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10057,7 +10500,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -10065,10 +10508,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10086,7 +10529,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -10094,10 +10537,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10115,17 +10558,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10150,10 +10593,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10196,10 +10639,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10217,7 +10660,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -10225,10 +10668,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10336,7 +10779,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -10344,10 +10787,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10365,7 +10808,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -10376,7 +10819,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10394,7 +10837,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -10402,10 +10845,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10423,7 +10866,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -10431,10 +10874,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10452,17 +10895,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10487,10 +10930,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10533,10 +10976,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10554,7 +10997,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -10562,10 +11005,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10673,7 +11116,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -10681,10 +11124,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10702,7 +11145,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -10713,7 +11156,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10731,7 +11174,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -10739,10 +11182,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10760,7 +11203,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -10768,10 +11211,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10789,17 +11232,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10824,10 +11267,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10870,10 +11313,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10891,7 +11334,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -10899,10 +11342,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11010,7 +11453,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -11018,10 +11461,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11039,7 +11482,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -11050,7 +11493,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11068,7 +11511,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -11076,10 +11519,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11097,7 +11540,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -11105,10 +11548,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11126,17 +11569,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11161,10 +11604,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11207,10 +11650,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11228,7 +11671,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -11236,10 +11679,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11347,7 +11790,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -11355,10 +11798,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11376,7 +11819,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -11387,7 +11830,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11405,7 +11848,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -11413,10 +11856,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11434,7 +11877,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -11442,10 +11885,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11463,17 +11906,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11498,10 +11941,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11544,10 +11987,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11565,7 +12008,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -11573,10 +12016,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11684,7 +12127,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -11692,10 +12135,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11713,7 +12156,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -11724,7 +12167,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11742,7 +12185,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -11750,10 +12193,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11771,7 +12214,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -11779,10 +12222,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11800,17 +12243,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11835,10 +12278,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11881,10 +12324,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11902,7 +12345,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -11910,10 +12353,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12021,7 +12464,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -12029,10 +12472,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12050,7 +12493,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -12061,7 +12504,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12079,7 +12522,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -12087,10 +12530,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12108,7 +12551,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -12116,10 +12559,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12137,17 +12580,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12172,10 +12615,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12218,10 +12661,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12239,7 +12682,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -12247,10 +12690,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12358,7 +12801,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -12366,10 +12809,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12387,7 +12830,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -12398,7 +12841,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12416,7 +12859,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -12424,10 +12867,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12445,7 +12888,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -12453,10 +12896,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12474,17 +12917,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12509,10 +12952,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12555,10 +12998,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12576,7 +13019,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -12584,10 +13027,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12695,7 +13138,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -12703,10 +13146,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12724,7 +13167,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -12735,7 +13178,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12753,7 +13196,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -12761,10 +13204,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12782,7 +13225,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -12790,10 +13233,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12811,17 +13254,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12846,10 +13289,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12892,10 +13335,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12913,7 +13356,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -12921,10 +13364,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13032,7 +13475,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -13040,10 +13483,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13061,7 +13504,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -13072,7 +13515,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13090,7 +13533,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -13098,10 +13541,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13119,7 +13562,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -13127,10 +13570,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13148,17 +13591,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13183,10 +13626,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13229,10 +13672,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13250,7 +13693,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -13258,10 +13701,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13369,7 +13812,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -13377,10 +13820,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13398,7 +13841,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -13409,7 +13852,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13427,7 +13870,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -13435,10 +13878,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13456,7 +13899,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -13464,10 +13907,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13485,17 +13928,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13520,10 +13963,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13566,10 +14009,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13587,7 +14030,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -13595,10 +14038,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13706,7 +14149,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -13714,10 +14157,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13735,7 +14178,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -13746,7 +14189,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13764,7 +14207,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -13772,10 +14215,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13793,7 +14236,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -13801,10 +14244,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13822,17 +14265,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13857,10 +14300,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13903,10 +14346,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13924,7 +14367,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -13932,10 +14375,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14043,7 +14486,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -14051,10 +14494,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14072,7 +14515,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -14083,7 +14526,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14101,7 +14544,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -14109,10 +14552,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14130,7 +14573,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -14138,10 +14581,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14159,17 +14602,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14194,10 +14637,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14240,10 +14683,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14261,7 +14704,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -14269,10 +14712,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14380,7 +14823,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -14388,10 +14831,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14409,7 +14852,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -14420,7 +14863,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14438,7 +14881,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -14446,10 +14889,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14467,7 +14910,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -14475,10 +14918,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14496,17 +14939,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14531,10 +14974,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14577,10 +15020,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14598,7 +15041,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -14606,10 +15049,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14717,7 +15160,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -14725,10 +15168,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14746,7 +15189,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -14757,7 +15200,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14775,7 +15218,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -14783,10 +15226,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14804,7 +15247,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -14812,10 +15255,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14833,17 +15276,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14868,10 +15311,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14914,10 +15357,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14935,7 +15378,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -14943,10 +15386,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15054,7 +15497,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -15062,10 +15505,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15083,7 +15526,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -15094,7 +15537,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15112,7 +15555,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -15120,10 +15563,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15141,7 +15584,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -15149,10 +15592,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15170,17 +15613,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15205,10 +15648,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15251,10 +15694,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15272,7 +15715,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -15280,10 +15723,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15391,7 +15834,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -15399,10 +15842,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15420,7 +15863,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -15431,7 +15874,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15449,7 +15892,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -15457,10 +15900,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15478,7 +15921,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -15486,10 +15929,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15507,17 +15950,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15542,10 +15985,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15588,10 +16031,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15609,7 +16052,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -15617,10 +16060,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15728,7 +16171,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -15736,10 +16179,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15757,7 +16200,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -15768,7 +16211,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15786,7 +16229,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -15794,10 +16237,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15815,7 +16258,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -15823,10 +16266,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15844,17 +16287,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15879,10 +16322,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15925,10 +16368,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -15946,7 +16389,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -15954,10 +16397,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16065,7 +16508,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -16073,10 +16516,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16094,7 +16537,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -16105,7 +16548,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16123,7 +16566,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -16131,10 +16574,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16152,7 +16595,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -16160,10 +16603,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16181,17 +16624,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16216,10 +16659,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16262,10 +16705,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16283,7 +16726,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -16291,10 +16734,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16402,7 +16845,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -16410,10 +16853,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16431,7 +16874,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -16442,7 +16885,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16460,7 +16903,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -16468,10 +16911,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16489,7 +16932,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -16497,10 +16940,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16518,17 +16961,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16553,10 +16996,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16599,10 +17042,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16620,7 +17063,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -16628,10 +17071,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16739,7 +17182,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -16747,10 +17190,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16768,7 +17211,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -16779,7 +17222,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16797,7 +17240,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -16805,10 +17248,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16826,7 +17269,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -16834,10 +17277,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16855,17 +17298,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16890,10 +17333,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16936,10 +17379,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16957,7 +17400,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -16965,10 +17408,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17076,7 +17519,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -17084,10 +17527,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17105,7 +17548,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -17116,7 +17559,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17134,7 +17577,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -17142,10 +17585,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17163,7 +17606,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -17171,10 +17614,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17192,17 +17635,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17227,10 +17670,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17273,10 +17716,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17294,7 +17737,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -17302,10 +17745,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17413,7 +17856,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -17421,10 +17864,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17442,7 +17885,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -17453,7 +17896,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17471,7 +17914,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -17479,10 +17922,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17500,7 +17943,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -17508,10 +17951,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17529,17 +17972,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17564,10 +18007,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17610,10 +18053,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17631,7 +18074,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -17639,10 +18082,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17750,7 +18193,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -17758,10 +18201,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17779,7 +18222,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -17790,7 +18233,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17808,7 +18251,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -17816,10 +18259,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17837,7 +18280,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -17845,10 +18288,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17866,17 +18309,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17901,10 +18344,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17947,10 +18390,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17968,7 +18411,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -17976,10 +18419,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18087,7 +18530,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -18095,10 +18538,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18116,7 +18559,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -18127,7 +18570,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18145,7 +18588,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -18153,10 +18596,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18174,7 +18617,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -18182,10 +18625,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18203,17 +18646,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18238,10 +18681,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18284,10 +18727,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18305,7 +18748,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -18313,10 +18756,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18424,7 +18867,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -18432,10 +18875,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18453,7 +18896,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -18464,7 +18907,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18482,7 +18925,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -18490,10 +18933,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18511,7 +18954,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -18519,10 +18962,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18540,17 +18983,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18575,10 +19018,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18621,10 +19064,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18642,7 +19085,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -18650,10 +19093,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18761,7 +19204,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -18769,10 +19212,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18790,7 +19233,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -18801,7 +19244,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18819,7 +19262,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -18827,10 +19270,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18848,7 +19291,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -18856,10 +19299,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18877,17 +19320,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18912,10 +19355,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18958,10 +19401,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18979,7 +19422,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -18987,10 +19430,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19098,7 +19541,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -19106,10 +19549,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19127,7 +19570,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -19138,7 +19581,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19156,7 +19599,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -19164,10 +19607,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19185,7 +19628,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -19193,10 +19636,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19214,17 +19657,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19249,10 +19692,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19295,10 +19738,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19316,7 +19759,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -19324,10 +19767,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19435,7 +19878,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -19443,10 +19886,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19464,7 +19907,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -19475,7 +19918,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19493,7 +19936,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -19501,10 +19944,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19522,7 +19965,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -19530,10 +19973,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19551,17 +19994,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19586,10 +20029,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19632,10 +20075,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19653,7 +20096,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -19661,10 +20104,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19772,7 +20215,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -19780,10 +20223,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19801,7 +20244,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -19812,7 +20255,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19830,7 +20273,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -19838,10 +20281,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19859,7 +20302,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -19867,10 +20310,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19888,17 +20331,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19923,10 +20366,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19969,10 +20412,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19990,7 +20433,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -19998,10 +20441,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20109,7 +20552,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -20117,10 +20560,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20138,7 +20581,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -20149,7 +20592,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20167,7 +20610,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -20175,10 +20618,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20196,7 +20639,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -20204,10 +20647,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20225,17 +20668,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20260,10 +20703,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20306,10 +20749,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20327,7 +20770,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -20335,10 +20778,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20446,7 +20889,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -20454,10 +20897,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20475,7 +20918,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -20486,7 +20929,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20504,7 +20947,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -20512,10 +20955,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20533,7 +20976,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -20541,10 +20984,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20562,17 +21005,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20597,10 +21040,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20643,10 +21086,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20664,7 +21107,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -20672,10 +21115,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20783,7 +21226,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -20791,10 +21234,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20812,7 +21255,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -20823,7 +21266,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20841,7 +21284,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -20849,10 +21292,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20870,7 +21313,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -20878,10 +21321,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20899,17 +21342,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20934,10 +21377,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20980,10 +21423,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21001,7 +21444,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -21009,10 +21452,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21120,7 +21563,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -21128,10 +21571,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21149,7 +21592,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -21160,7 +21603,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21178,7 +21621,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -21186,10 +21629,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21207,7 +21650,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -21215,10 +21658,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21236,17 +21679,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21271,10 +21714,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21317,10 +21760,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21338,7 +21781,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -21346,10 +21789,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21457,7 +21900,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -21465,10 +21908,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21486,7 +21929,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -21497,7 +21940,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21515,7 +21958,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -21523,10 +21966,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21544,7 +21987,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -21552,10 +21995,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21573,17 +22016,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21608,10 +22051,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21654,10 +22097,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21675,7 +22118,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -21683,10 +22126,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21794,7 +22237,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -21802,10 +22245,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21823,7 +22266,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -21834,7 +22277,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21852,7 +22295,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -21860,10 +22303,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21881,7 +22324,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -21889,10 +22332,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21910,17 +22353,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21945,10 +22388,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21991,10 +22434,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22012,7 +22455,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -22020,10 +22463,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22131,7 +22574,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -22139,10 +22582,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22160,7 +22603,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -22171,7 +22614,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22189,7 +22632,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -22197,10 +22640,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22218,7 +22661,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -22226,10 +22669,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22247,17 +22690,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22282,10 +22725,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22328,10 +22771,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22349,7 +22792,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -22357,10 +22800,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22468,7 +22911,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -22476,10 +22919,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22497,7 +22940,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -22508,7 +22951,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22526,7 +22969,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -22534,10 +22977,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22555,7 +22998,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -22563,10 +23006,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22584,17 +23027,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22619,10 +23062,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22665,10 +23108,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22686,7 +23129,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -22694,10 +23137,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22805,7 +23248,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -22813,10 +23256,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22834,7 +23277,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -22845,7 +23288,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22863,7 +23306,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -22871,10 +23314,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22892,7 +23335,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -22900,10 +23343,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22921,17 +23364,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22956,10 +23399,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23002,10 +23445,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23023,7 +23466,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -23031,10 +23474,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23142,7 +23585,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -23150,10 +23593,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23171,7 +23614,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -23182,7 +23625,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23200,7 +23643,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -23208,10 +23651,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23229,7 +23672,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -23237,10 +23680,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23258,17 +23701,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23293,10 +23736,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23339,10 +23782,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23360,7 +23803,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -23368,10 +23811,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23479,7 +23922,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -23487,10 +23930,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23508,7 +23951,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -23519,7 +23962,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23537,7 +23980,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -23545,10 +23988,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23566,7 +24009,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -23574,10 +24017,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23595,17 +24038,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23630,10 +24073,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23676,10 +24119,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23697,7 +24140,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -23705,10 +24148,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23816,7 +24259,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], "domain_of": [ "GRDI" @@ -23824,10 +24267,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23845,7 +24288,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], "domain_of": [ "GRDI" @@ -23856,7 +24299,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23874,7 +24317,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], "domain_of": [ "GRDI" @@ -23882,10 +24325,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23903,7 +24346,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], "domain_of": [ "GRDI" @@ -23911,10 +24354,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23932,17 +24375,17 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], "domain_of": [ "GRDI" ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23967,10 +24410,10 @@ ], "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24013,10 +24456,10 @@ ], "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24034,7 +24477,7 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], "domain_of": [ "GRDI" @@ -24042,10 +24485,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24266,3794 +24709,3854 @@ "rank": 15, "slot_group": "Sample collection and processing" }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 16, + "slot_group": "Sample collection and processing" + }, "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", - "rank": 16, + "rank": 17, "slot_group": "Sample collection and processing" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", - "rank": 17, + "rank": 18, "slot_group": "Sample collection and processing" }, "geo_loc_name_country": { "name": "geo_loc_name_country", - "rank": 18, + "rank": 19, "slot_group": "Sample collection and processing" }, "geo_loc_name_state_province_region": { "name": "geo_loc_name_state_province_region", - "rank": 19, + "rank": 20, "slot_group": "Sample collection and processing" }, "geo_loc_name_site": { "name": "geo_loc_name_site", - "rank": 20, + "rank": 21, "slot_group": "Sample collection and processing" }, "food_product_origin_geo_loc_name_country": { "name": "food_product_origin_geo_loc_name_country", - "rank": 21, + "rank": 22, "slot_group": "Sample collection and processing" }, "host_origin_geo_loc_name_country": { "name": "host_origin_geo_loc_name_country", - "rank": 22, + "rank": 23, "slot_group": "Sample collection and processing" }, "geo_loc_latitude": { "name": "geo_loc_latitude", - "rank": 23, + "rank": 24, "slot_group": "Sample collection and processing" }, "geo_loc_longitude": { "name": "geo_loc_longitude", - "rank": 24, + "rank": 25, "slot_group": "Sample collection and processing" }, "sample_collection_date": { "name": "sample_collection_date", - "rank": 25, + "rank": 26, "slot_group": "Sample collection and processing" }, "sample_collection_date_precision": { "name": "sample_collection_date_precision", - "rank": 26, + "rank": 27, + "slot_group": "Sample collection and processing" + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "rank": 28, + "slot_group": "Sample collection and processing" + }, + "sample_processing_date": { + "name": "sample_processing_date", + "rank": 29, + "slot_group": "Sample collection and processing" + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "rank": 30, + "slot_group": "Sample collection and processing" + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "rank": 31, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "rank": 32, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "rank": 33, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "rank": 34, "slot_group": "Sample collection and processing" }, "sample_received_date": { "name": "sample_received_date", - "rank": 27, + "rank": 35, "slot_group": "Sample collection and processing" }, "original_sample_description": { "name": "original_sample_description", - "rank": 28, + "rank": 36, "slot_group": "Sample collection and processing" }, "environmental_site": { "name": "environmental_site", - "rank": 29, + "rank": 37, "slot_group": "Sample collection and processing" }, "environmental_material": { "name": "environmental_material", - "rank": 30, + "rank": 38, "slot_group": "Sample collection and processing" }, "environmental_material_constituent": { "name": "environmental_material_constituent", - "rank": 31, + "rank": 39, "slot_group": "Sample collection and processing" }, "animal_or_plant_population": { "name": "animal_or_plant_population", - "rank": 32, + "rank": 40, "slot_group": "Sample collection and processing" }, "anatomical_material": { "name": "anatomical_material", - "rank": 33, + "rank": 41, "slot_group": "Sample collection and processing" }, "body_product": { "name": "body_product", - "rank": 34, + "rank": 42, "slot_group": "Sample collection and processing" }, "anatomical_part": { "name": "anatomical_part", - "rank": 35, + "rank": 43, "slot_group": "Sample collection and processing" }, "anatomical_region": { "name": "anatomical_region", - "rank": 36, + "rank": 44, "slot_group": "Sample collection and processing" }, "food_product": { "name": "food_product", - "rank": 37, + "rank": 45, "slot_group": "Sample collection and processing" }, "food_product_properties": { "name": "food_product_properties", - "rank": 38, + "rank": 46, "slot_group": "Sample collection and processing" }, "label_claim": { "name": "label_claim", - "rank": 39, + "rank": 47, "slot_group": "Sample collection and processing" }, "animal_source_of_food": { "name": "animal_source_of_food", - "rank": 40, + "rank": 48, "slot_group": "Sample collection and processing" }, "food_product_production_stream": { "name": "food_product_production_stream", - "rank": 41, + "rank": 49, "slot_group": "Sample collection and processing" }, "food_packaging": { "name": "food_packaging", - "rank": 42, + "rank": 50, "slot_group": "Sample collection and processing" }, "food_quality_date": { "name": "food_quality_date", - "rank": 43, + "rank": 51, "slot_group": "Sample collection and processing" }, "food_packaging_date": { "name": "food_packaging_date", - "rank": 44, + "rank": 52, "slot_group": "Sample collection and processing" }, "collection_device": { "name": "collection_device", - "rank": 45, + "rank": 53, "slot_group": "Sample collection and processing" }, "collection_method": { "name": "collection_method", - "rank": 46, + "rank": 54, "slot_group": "Sample collection and processing" }, "sample_volume_measurement_value": { "name": "sample_volume_measurement_value", - "rank": 47, + "rank": 55, "slot_group": "Sample collection and processing" }, "sample_volume_measurement_unit": { "name": "sample_volume_measurement_unit", - "rank": 48, + "rank": 56, "slot_group": "Sample collection and processing" }, "residual_sample_status": { "name": "residual_sample_status", - "rank": 49, + "rank": 57, "slot_group": "Sample collection and processing" }, "sample_storage_method": { "name": "sample_storage_method", - "rank": 50, + "rank": 58, "slot_group": "Sample collection and processing" }, "sample_storage_medium": { "name": "sample_storage_medium", - "rank": 51, + "rank": 59, "slot_group": "Sample collection and processing" }, "sample_storage_duration_value": { "name": "sample_storage_duration_value", - "rank": 52, + "rank": 60, "slot_group": "Sample collection and processing" }, "sample_storage_duration_unit": { "name": "sample_storage_duration_unit", - "rank": 53, + "rank": 61, "slot_group": "Sample collection and processing" }, "nucleic_acid_storage_duration_value": { "name": "nucleic_acid_storage_duration_value", - "rank": 54, + "rank": 62, "slot_group": "Sample collection and processing" }, "nucleic_acid_storage_duration_unit": { "name": "nucleic_acid_storage_duration_unit", - "rank": 55, + "rank": 63, "slot_group": "Sample collection and processing" }, "available_data_types": { "name": "available_data_types", - "rank": 56, + "rank": 64, "slot_group": "Sample collection and processing" }, "available_data_type_details": { "name": "available_data_type_details", - "rank": 57, + "rank": 65, "slot_group": "Sample collection and processing" }, "water_depth": { "name": "water_depth", - "rank": 58, + "rank": 66, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 59, + "rank": 67, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 60, + "rank": 68, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 61, + "rank": 69, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 62, + "rank": 70, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 63, + "rank": 71, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 64, + "rank": 72, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 65, + "rank": 73, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 66, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "rank": 74, + "slot_group": "Environmental conditions and measurements" + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "rank": 75, + "slot_group": "Environmental conditions and measurements" + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 76, + "slot_group": "Environmental conditions and measurements" + }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "rank": 77, + "slot_group": "Environmental conditions and measurements" + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "rank": 78, "slot_group": "Environmental conditions and measurements" }, "host_common_name": { "name": "host_common_name", - "rank": 67, + "rank": 79, "slot_group": "Host information" }, "host_scientific_name": { "name": "host_scientific_name", - "rank": 68, + "rank": 80, "slot_group": "Host information" }, "host_ecotype": { "name": "host_ecotype", - "rank": 69, + "rank": 81, "slot_group": "Host information" }, "host_breed": { "name": "host_breed", - "rank": 70, + "rank": 82, "slot_group": "Host information" }, "host_food_production_name": { "name": "host_food_production_name", - "rank": 71, + "rank": 83, "slot_group": "Host information" }, "host_age_bin": { "name": "host_age_bin", - "rank": 72, + "rank": 84, "slot_group": "Host information" }, "host_disease": { "name": "host_disease", - "rank": 73, + "rank": 85, "slot_group": "Host information" }, "microbiological_method": { "name": "microbiological_method", - "rank": 74, + "rank": 86, "slot_group": "Strain and isolation information" }, "strain": { "name": "strain", - "rank": 75, + "rank": 87, "slot_group": "Strain and isolation information" }, "isolate_id": { "name": "isolate_id", - "rank": 76, + "rank": 88, "slot_group": "Strain and isolation information" }, "alternative_isolate_id": { "name": "alternative_isolate_id", - "rank": 77, + "rank": 89, "slot_group": "Strain and isolation information" }, "progeny_isolate_id": { "name": "progeny_isolate_id", - "rank": 78, + "rank": 90, "slot_group": "Strain and isolation information" }, "irida_isolate_id": { "name": "irida_isolate_id", - "rank": 79, + "rank": 91, "slot_group": "Strain and isolation information" }, "irida_project_id": { "name": "irida_project_id", - "rank": 80, + "rank": 92, "slot_group": "Strain and isolation information" }, "isolated_by": { "name": "isolated_by", - "rank": 81, + "rank": 93, "slot_group": "Strain and isolation information" }, "isolated_by_laboratory_name": { "name": "isolated_by_laboratory_name", - "rank": 82, + "rank": 94, "slot_group": "Strain and isolation information" }, "isolated_by_contact_name": { "name": "isolated_by_contact_name", - "rank": 83, + "rank": 95, "slot_group": "Strain and isolation information" }, "isolated_by_contact_email": { "name": "isolated_by_contact_email", - "rank": 84, + "rank": 96, "slot_group": "Strain and isolation information" }, "isolation_date": { "name": "isolation_date", - "rank": 85, + "rank": 97, "slot_group": "Strain and isolation information" }, "isolate_received_date": { "name": "isolate_received_date", - "rank": 86, + "rank": 98, "slot_group": "Strain and isolation information" }, "organism": { "name": "organism", - "rank": 87, + "rank": 99, "slot_group": "Strain and isolation information" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", - "rank": 88, + "rank": 100, "slot_group": "Strain and isolation information" }, "taxonomic_identification_process_details": { "name": "taxonomic_identification_process_details", - "rank": 89, + "rank": 101, "slot_group": "Strain and isolation information" }, "serovar": { "name": "serovar", - "rank": 90, + "rank": 102, "slot_group": "Strain and isolation information" }, "serotyping_method": { "name": "serotyping_method", - "rank": 91, + "rank": 103, "slot_group": "Strain and isolation information" }, "phagetype": { "name": "phagetype", - 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"rank": 667, + "rank": 679, "slot_group": "Antimicrobial resistance" }, "polymyxinb_testing_standard": { "name": "polymyxinb_testing_standard", - "rank": 668, + "rank": 680, "slot_group": "Antimicrobial resistance" }, "polymyxinb_testing_standard_version": { "name": "polymyxinb_testing_standard_version", - "rank": 669, + "rank": 681, "slot_group": "Antimicrobial resistance" }, "polymyxinb_testing_standard_details": { "name": "polymyxinb_testing_standard_details", - "rank": 670, + "rank": 682, "slot_group": "Antimicrobial resistance" }, "polymyxinb_susceptible_breakpoint": { "name": "polymyxinb_susceptible_breakpoint", - "rank": 671, + "rank": 683, "slot_group": "Antimicrobial resistance" }, "polymyxinb_intermediate_breakpoint": { "name": "polymyxinb_intermediate_breakpoint", - "rank": 672, + "rank": 684, "slot_group": "Antimicrobial resistance" }, "polymyxinb_resistant_breakpoint": { "name": "polymyxinb_resistant_breakpoint", - "rank": 673, + "rank": 685, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_resistance_phenotype": { "name": "quinupristindalfopristin_resistance_phenotype", - "rank": 674, + "rank": 686, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_measurement": { "name": "quinupristindalfopristin_measurement", - "rank": 675, + "rank": 687, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_measurement_units": { "name": "quinupristindalfopristin_measurement_units", - "rank": 676, + "rank": 688, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_measurement_sign": { "name": "quinupristindalfopristin_measurement_sign", - "rank": 677, + "rank": 689, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_laboratory_typing_method": { "name": "quinupristindalfopristin_laboratory_typing_method", - "rank": 678, + "rank": 690, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_laboratory_typing_platform": { "name": "quinupristindalfopristin_laboratory_typing_platform", - "rank": 679, + "rank": 691, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_laboratory_typing_platform_version": { "name": "quinupristindalfopristin_laboratory_typing_platform_version", - "rank": 680, + "rank": 692, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_vendor_name": { "name": "quinupristindalfopristin_vendor_name", - "rank": 681, + "rank": 693, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_testing_standard": { "name": "quinupristindalfopristin_testing_standard", - "rank": 682, + "rank": 694, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_testing_standard_version": { "name": "quinupristindalfopristin_testing_standard_version", - "rank": 683, + "rank": 695, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_testing_standard_details": { "name": "quinupristindalfopristin_testing_standard_details", - "rank": 684, + "rank": 696, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_susceptible_breakpoint": { "name": "quinupristindalfopristin_susceptible_breakpoint", - "rank": 685, + "rank": 697, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_intermediate_breakpoint": { "name": "quinupristindalfopristin_intermediate_breakpoint", - "rank": 686, + "rank": 698, "slot_group": "Antimicrobial resistance" }, "quinupristindalfopristin_resistant_breakpoint": { "name": "quinupristindalfopristin_resistant_breakpoint", - "rank": 687, + "rank": 699, "slot_group": "Antimicrobial resistance" }, "streptomycin_resistance_phenotype": { "name": "streptomycin_resistance_phenotype", - "rank": 688, + "rank": 700, "slot_group": "Antimicrobial resistance" }, "streptomycin_measurement": { "name": "streptomycin_measurement", - "rank": 689, + "rank": 701, "slot_group": "Antimicrobial resistance" }, "streptomycin_measurement_units": { "name": "streptomycin_measurement_units", - "rank": 690, + "rank": 702, "slot_group": "Antimicrobial resistance" }, "streptomycin_measurement_sign": { "name": "streptomycin_measurement_sign", - "rank": 691, + "rank": 703, "slot_group": "Antimicrobial resistance" }, "streptomycin_laboratory_typing_method": { "name": "streptomycin_laboratory_typing_method", - "rank": 692, + "rank": 704, "slot_group": "Antimicrobial resistance" }, "streptomycin_laboratory_typing_platform": { "name": "streptomycin_laboratory_typing_platform", - "rank": 693, + "rank": 705, "slot_group": "Antimicrobial resistance" }, "streptomycin_laboratory_typing_platform_version": { "name": "streptomycin_laboratory_typing_platform_version", - "rank": 694, + "rank": 706, "slot_group": "Antimicrobial resistance" }, "streptomycin_vendor_name": { "name": "streptomycin_vendor_name", - "rank": 695, + "rank": 707, "slot_group": "Antimicrobial resistance" }, "streptomycin_testing_standard": { "name": "streptomycin_testing_standard", - "rank": 696, + "rank": 708, "slot_group": "Antimicrobial resistance" }, "streptomycin_testing_standard_version": { "name": "streptomycin_testing_standard_version", - "rank": 697, + "rank": 709, "slot_group": "Antimicrobial resistance" }, "streptomycin_testing_standard_details": { "name": "streptomycin_testing_standard_details", - "rank": 698, + "rank": 710, "slot_group": "Antimicrobial resistance" }, "streptomycin_susceptible_breakpoint": { "name": "streptomycin_susceptible_breakpoint", - "rank": 699, + "rank": 711, "slot_group": "Antimicrobial resistance" }, "streptomycin_intermediate_breakpoint": { "name": "streptomycin_intermediate_breakpoint", - "rank": 700, + "rank": 712, "slot_group": "Antimicrobial resistance" }, "streptomycin_resistant_breakpoint": { "name": "streptomycin_resistant_breakpoint", - "rank": 701, + "rank": 713, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_resistance_phenotype": { "name": "sulfisoxazole_resistance_phenotype", - "rank": 702, + "rank": 714, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_measurement": { "name": "sulfisoxazole_measurement", - "rank": 703, + "rank": 715, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_measurement_units": { "name": "sulfisoxazole_measurement_units", - "rank": 704, + "rank": 716, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_measurement_sign": { "name": "sulfisoxazole_measurement_sign", - "rank": 705, + "rank": 717, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_laboratory_typing_method": { "name": "sulfisoxazole_laboratory_typing_method", - "rank": 706, + "rank": 718, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_laboratory_typing_platform": { "name": "sulfisoxazole_laboratory_typing_platform", - "rank": 707, + "rank": 719, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_laboratory_typing_platform_version": { "name": "sulfisoxazole_laboratory_typing_platform_version", - "rank": 708, + "rank": 720, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_vendor_name": { "name": "sulfisoxazole_vendor_name", - "rank": 709, + "rank": 721, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_testing_standard": { "name": "sulfisoxazole_testing_standard", - "rank": 710, + "rank": 722, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_testing_standard_version": { "name": "sulfisoxazole_testing_standard_version", - "rank": 711, + "rank": 723, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_testing_standard_details": { "name": "sulfisoxazole_testing_standard_details", - "rank": 712, + "rank": 724, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_susceptible_breakpoint": { "name": "sulfisoxazole_susceptible_breakpoint", - "rank": 713, + "rank": 725, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_intermediate_breakpoint": { "name": "sulfisoxazole_intermediate_breakpoint", - "rank": 714, + "rank": 726, "slot_group": "Antimicrobial resistance" }, "sulfisoxazole_resistant_breakpoint": { "name": "sulfisoxazole_resistant_breakpoint", - "rank": 715, + "rank": 727, "slot_group": "Antimicrobial resistance" }, "telithromycin_resistance_phenotype": { "name": "telithromycin_resistance_phenotype", - "rank": 716, + "rank": 728, "slot_group": "Antimicrobial resistance" }, "telithromycin_measurement": { "name": "telithromycin_measurement", - "rank": 717, + "rank": 729, "slot_group": "Antimicrobial resistance" }, "telithromycin_measurement_units": { "name": "telithromycin_measurement_units", - "rank": 718, + "rank": 730, "slot_group": "Antimicrobial resistance" }, "telithromycin_measurement_sign": { "name": "telithromycin_measurement_sign", - "rank": 719, + "rank": 731, "slot_group": "Antimicrobial resistance" }, "telithromycin_laboratory_typing_method": { "name": "telithromycin_laboratory_typing_method", - "rank": 720, + "rank": 732, "slot_group": "Antimicrobial resistance" }, "telithromycin_laboratory_typing_platform": { "name": "telithromycin_laboratory_typing_platform", - "rank": 721, + "rank": 733, "slot_group": "Antimicrobial resistance" }, "telithromycin_laboratory_typing_platform_version": { "name": "telithromycin_laboratory_typing_platform_version", - "rank": 722, + "rank": 734, "slot_group": "Antimicrobial resistance" }, "telithromycin_vendor_name": { "name": "telithromycin_vendor_name", - "rank": 723, + "rank": 735, "slot_group": "Antimicrobial resistance" }, "telithromycin_testing_standard": { "name": "telithromycin_testing_standard", - "rank": 724, + "rank": 736, "slot_group": "Antimicrobial resistance" }, "telithromycin_testing_standard_version": { "name": "telithromycin_testing_standard_version", - "rank": 725, + "rank": 737, "slot_group": "Antimicrobial resistance" }, "telithromycin_testing_standard_details": { "name": "telithromycin_testing_standard_details", - "rank": 726, + "rank": 738, "slot_group": "Antimicrobial resistance" }, "telithromycin_susceptible_breakpoint": { "name": "telithromycin_susceptible_breakpoint", - "rank": 727, + "rank": 739, "slot_group": "Antimicrobial resistance" }, "telithromycin_intermediate_breakpoint": { "name": "telithromycin_intermediate_breakpoint", - "rank": 728, + "rank": 740, "slot_group": "Antimicrobial resistance" }, "telithromycin_resistant_breakpoint": { "name": "telithromycin_resistant_breakpoint", - "rank": 729, + "rank": 741, "slot_group": "Antimicrobial resistance" }, "tetracycline_resistance_phenotype": { "name": "tetracycline_resistance_phenotype", - "rank": 730, + "rank": 742, "slot_group": "Antimicrobial resistance" }, "tetracycline_measurement": { "name": "tetracycline_measurement", - "rank": 731, + "rank": 743, "slot_group": "Antimicrobial resistance" }, "tetracycline_measurement_units": { "name": "tetracycline_measurement_units", - "rank": 732, + "rank": 744, "slot_group": "Antimicrobial resistance" }, "tetracycline_measurement_sign": { "name": "tetracycline_measurement_sign", - "rank": 733, + "rank": 745, "slot_group": "Antimicrobial resistance" }, "tetracycline_laboratory_typing_method": { "name": "tetracycline_laboratory_typing_method", - "rank": 734, + "rank": 746, "slot_group": "Antimicrobial resistance" }, "tetracycline_laboratory_typing_platform": { "name": "tetracycline_laboratory_typing_platform", - "rank": 735, + "rank": 747, "slot_group": "Antimicrobial resistance" }, "tetracycline_laboratory_typing_platform_version": { "name": "tetracycline_laboratory_typing_platform_version", - "rank": 736, + "rank": 748, "slot_group": "Antimicrobial resistance" }, "tetracycline_vendor_name": { "name": "tetracycline_vendor_name", - "rank": 737, + "rank": 749, "slot_group": "Antimicrobial resistance" }, "tetracycline_testing_standard": { "name": "tetracycline_testing_standard", - "rank": 738, + "rank": 750, "slot_group": "Antimicrobial resistance" }, "tetracycline_testing_standard_version": { "name": "tetracycline_testing_standard_version", - "rank": 739, + "rank": 751, "slot_group": "Antimicrobial resistance" }, "tetracycline_testing_standard_details": { "name": "tetracycline_testing_standard_details", - "rank": 740, + "rank": 752, "slot_group": "Antimicrobial resistance" }, "tetracycline_susceptible_breakpoint": { "name": "tetracycline_susceptible_breakpoint", - "rank": 741, + "rank": 753, "slot_group": "Antimicrobial resistance" }, "tetracycline_intermediate_breakpoint": { "name": "tetracycline_intermediate_breakpoint", - "rank": 742, + "rank": 754, "slot_group": "Antimicrobial resistance" }, "tetracycline_resistant_breakpoint": { "name": "tetracycline_resistant_breakpoint", - "rank": 743, + "rank": 755, "slot_group": "Antimicrobial resistance" }, "tigecycline_resistance_phenotype": { "name": "tigecycline_resistance_phenotype", - "rank": 744, + "rank": 756, "slot_group": "Antimicrobial resistance" }, "tigecycline_measurement": { "name": "tigecycline_measurement", - "rank": 745, + "rank": 757, "slot_group": "Antimicrobial resistance" }, "tigecycline_measurement_units": { "name": "tigecycline_measurement_units", - "rank": 746, + "rank": 758, "slot_group": "Antimicrobial resistance" }, "tigecycline_measurement_sign": { "name": "tigecycline_measurement_sign", - "rank": 747, + "rank": 759, "slot_group": "Antimicrobial resistance" }, "tigecycline_laboratory_typing_method": { "name": "tigecycline_laboratory_typing_method", - "rank": 748, + "rank": 760, "slot_group": "Antimicrobial resistance" }, "tigecycline_laboratory_typing_platform": { "name": "tigecycline_laboratory_typing_platform", - "rank": 749, + "rank": 761, "slot_group": "Antimicrobial resistance" }, "tigecycline_laboratory_typing_platform_version": { "name": "tigecycline_laboratory_typing_platform_version", - "rank": 750, + "rank": 762, "slot_group": "Antimicrobial resistance" }, "tigecycline_vendor_name": { "name": "tigecycline_vendor_name", - "rank": 751, + "rank": 763, "slot_group": "Antimicrobial resistance" }, "tigecycline_testing_standard": { "name": "tigecycline_testing_standard", - "rank": 752, + "rank": 764, "slot_group": "Antimicrobial resistance" }, "tigecycline_testing_standard_version": { "name": "tigecycline_testing_standard_version", - "rank": 753, + "rank": 765, "slot_group": "Antimicrobial resistance" }, "tigecycline_testing_standard_details": { "name": "tigecycline_testing_standard_details", - "rank": 754, + "rank": 766, "slot_group": "Antimicrobial resistance" }, "tigecycline_susceptible_breakpoint": { "name": "tigecycline_susceptible_breakpoint", - "rank": 755, + "rank": 767, "slot_group": "Antimicrobial resistance" }, "tigecycline_intermediate_breakpoint": { "name": "tigecycline_intermediate_breakpoint", - "rank": 756, + "rank": 768, "slot_group": "Antimicrobial resistance" }, "tigecycline_resistant_breakpoint": { "name": "tigecycline_resistant_breakpoint", - "rank": 757, + "rank": 769, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_resistance_phenotype": { "name": "trimethoprimsulfamethoxazole_resistance_phenotype", - "rank": 758, + "rank": 770, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_measurement": { "name": "trimethoprimsulfamethoxazole_measurement", - "rank": 759, + "rank": 771, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_measurement_units": { "name": "trimethoprimsulfamethoxazole_measurement_units", - "rank": 760, + "rank": 772, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_measurement_sign": { "name": "trimethoprimsulfamethoxazole_measurement_sign", - "rank": 761, + "rank": 773, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_laboratory_typing_method": { "name": "trimethoprimsulfamethoxazole_laboratory_typing_method", - "rank": 762, + "rank": 774, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_laboratory_typing_platform": { "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform", - "rank": 763, + "rank": 775, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_laboratory_typing_platform_version": { "name": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", - "rank": 764, + "rank": 776, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_vendor_name": { "name": "trimethoprimsulfamethoxazole_vendor_name", - "rank": 765, + "rank": 777, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_testing_standard": { "name": "trimethoprimsulfamethoxazole_testing_standard", - "rank": 766, + "rank": 778, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_testing_standard_version": { "name": "trimethoprimsulfamethoxazole_testing_standard_version", - "rank": 767, + "rank": 779, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_testing_standard_details": { "name": "trimethoprimsulfamethoxazole_testing_standard_details", - "rank": 768, + "rank": 780, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_susceptible_breakpoint": { "name": "trimethoprimsulfamethoxazole_susceptible_breakpoint", - "rank": 769, + "rank": 781, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_intermediate_breakpoint": { "name": "trimethoprimsulfamethoxazole_intermediate_breakpoint", - "rank": 770, + "rank": 782, "slot_group": "Antimicrobial resistance" }, "trimethoprimsulfamethoxazole_resistant_breakpoint": { "name": "trimethoprimsulfamethoxazole_resistant_breakpoint", - "rank": 771, + "rank": 783, "slot_group": "Antimicrobial resistance" }, "authors": { "name": "authors", - "rank": 772, + "rank": 784, "slot_group": "Contributor acknowledgement" }, "dataharmonizer_provenance": { "name": "dataharmonizer_provenance", - "rank": 773, + "rank": 785, "slot_group": "Contributor acknowledgement" } }, @@ -28073,11 +28576,12 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:sample_name", - "NCBI_BIOSAMPLE_Enterics:%2Asample_name", - "NCBI_ANTIBIOGRAM:%2Asample_name" + "NCBI_BIOSAMPLE_Enterics:sample_name", + "NCBI_ANTIBIOGRAM:sample_name" ], "rank": 1, "slot_uri": "GENEPIO:0001123", + "identifier": true, "alias": "sample_collector_sample_id", "owner": "GRDI", "domain_of": [ @@ -28090,7 +28594,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28136,7 +28640,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:collected_by", - "NCBI_BIOSAMPLE_Enterics:%2Acollected_by" + "NCBI_BIOSAMPLE_Enterics:collected_by" ], "rank": 3, "slot_uri": "GENEPIO:0001153", @@ -28149,10 +28653,10 @@ "required": true, "any_of": [ { - "range": "sample_collected_by menu" + "range": "SampleCollectedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28303,7 +28807,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28322,7 +28826,7 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:purpose_of_sampling", - "NCBI_BIOSAMPLE_Enterics:%2Apurpose_of_sampling" + "NCBI_BIOSAMPLE_Enterics:purpose_of_sampling" ], "rank": 10, "slot_uri": "GENEPIO:0001198", @@ -28335,10 +28839,10 @@ "required": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28369,10 +28873,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28443,7 +28947,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, "specimen_processing": { "name": "specimen_processing", @@ -28468,13 +28972,36 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 16, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", @@ -28488,7 +29015,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 16, + "rank": 17, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "GRDI", @@ -28511,7 +29038,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 17, + "rank": 18, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "GRDI", @@ -28537,9 +29064,9 @@ "exact_mappings": [ "BIOSAMPLE:geo_loc_name", "BIOSAMPLE:geo_loc_name%20%28country%29", - "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" + "NCBI_BIOSAMPLE_Enterics:geo_loc_name" ], - "rank": 18, + "rank": 19, "slot_uri": "GENEPIO:0001181", "alias": "geo_loc_name_country", "owner": "GRDI", @@ -28550,10 +29077,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28573,9 +29100,9 @@ "exact_mappings": [ "BIOSAMPLE:geo_loc_name", "BIOSAMPLE:geo_loc_name%20%28state/province/region%29", - "NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name" + "NCBI_BIOSAMPLE_Enterics:geo_loc_name" ], - "rank": 19, + "rank": 20, "slot_uri": "GENEPIO:0001185", "alias": "geo_loc_name_state_province_region", "owner": "GRDI", @@ -28586,10 +29113,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name (state/province/region) menu" + "range": "GeoLocNameStateProvinceRegionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28610,7 +29137,7 @@ "BIOSAMPLE:geo_loc_name", "BIOSAMPLE:geo_loc_name%20%28site%29" ], - "rank": 20, + "rank": 21, "slot_uri": "GENEPIO:0100436", "alias": "geo_loc_name_site", "owner": "GRDI", @@ -28636,7 +29163,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:food_origin" ], - "rank": 21, + "rank": 22, "slot_uri": "GENEPIO:0100437", "alias": "food_product_origin_geo_loc_name_country", "owner": "GRDI", @@ -28646,10 +29173,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28666,7 +29193,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 22, + "rank": 23, "slot_uri": "GENEPIO:0100438", "alias": "host_origin_geo_loc_name_country", "owner": "GRDI", @@ -28676,10 +29203,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28699,7 +29226,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:lat_lon" ], - "rank": 23, + "rank": 24, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", "owner": "GRDI", @@ -28725,7 +29252,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:lat_lon" ], - "rank": 24, + "rank": 25, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", "owner": "GRDI", @@ -28750,9 +29277,9 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:sample%20collection%20date", - "NCBI_BIOSAMPLE_Enterics:%2Acollection_date" + "NCBI_BIOSAMPLE_Enterics:collection_date" ], - "rank": 25, + "rank": 26, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", "owner": "GRDI", @@ -28760,7 +29287,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "date", + "range": "Date", "required": true }, "sample_collection_date_precision": { @@ -28776,7 +29303,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 26, + "rank": 27, "slot_uri": "GENEPIO:0001177", "alias": "sample_collection_date_precision", "owner": "GRDI", @@ -28787,10 +29314,225 @@ "required": true, "any_of": [ { - "range": "sample_collection_date_precision menu" + "range": "SampleCollectionDatePrecisionMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "Date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample_processing_date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 29, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "Date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 30, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "Time" }, { - "range": "null value menu" + "range": "NullValueMenu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 31, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "Time" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 32, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleCollectionTimeOfDayMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "1900-01-03" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 33, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 34, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "SampleCollectionDurationUnitMenu" + }, + { + "range": "NullValueMenu" } ] }, @@ -28807,7 +29549,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 27, + "rank": 35, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "GRDI", @@ -28815,7 +29557,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "date" + "range": "Date" }, "original_sample_description": { "name": "original_sample_description", @@ -28830,7 +29572,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 28, + "rank": 36, "slot_uri": "GENEPIO:0100439", "alias": "original_sample_description", "owner": "GRDI", @@ -28856,13 +29598,13 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_site", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:isolation_source", "NCBI_BIOSAMPLE_Enterics:animal_env", "NCBI_BIOSAMPLE_Enterics:host_housing", "NCBI_BIOSAMPLE_Enterics:env_local_scale", "NCBI_BIOSAMPLE_Enterics:facility_type" ], - "rank": 29, + "rank": 37, "slot_uri": "GENEPIO:0001232", "alias": "environmental_site", "owner": "GRDI", @@ -28874,10 +29616,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28906,9 +29648,9 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_material", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 30, + "rank": 38, "slot_uri": "GENEPIO:0001223", "alias": "environmental_material", "owner": "GRDI", @@ -28920,10 +29662,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28943,7 +29685,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 31, + "rank": 39, "slot_uri": "GENEPIO:0101197", "alias": "environmental_material_constituent", "owner": "GRDI", @@ -28951,8 +29693,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "multivalued": true + "range": "WhitespaceMinimizedString" }, "animal_or_plant_population": { "name": "animal_or_plant_population", @@ -28967,7 +29708,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 32, + "rank": 40, "slot_uri": "GENEPIO:0100443", "alias": "animal_or_plant_population", "owner": "GRDI", @@ -28979,10 +29720,10 @@ "multivalued": true, "any_of": [ { - "range": "animal_or_plant_population menu" + "range": "AnimalOrPlantPopulationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29006,9 +29747,9 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_material", "NCBI_BIOSAMPLE_Enterics:host_tissue_sampled", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 33, + "rank": 41, "slot_uri": "GENEPIO:0001211", "alias": "anatomical_material", "owner": "GRDI", @@ -29020,10 +29761,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29047,9 +29788,9 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:body_product", "NCBI_BIOSAMPLE_Enterics:host_body_product", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 34, + "rank": 42, "slot_uri": "GENEPIO:0001216", "alias": "body_product", "owner": "GRDI", @@ -29061,10 +29802,10 @@ "multivalued": true, "any_of": [ { - "range": "body_product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29084,9 +29825,9 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_part", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 35, + "rank": 43, "slot_uri": "GENEPIO:0001214", "alias": "anatomical_part", "owner": "GRDI", @@ -29098,10 +29839,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29118,7 +29859,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 36, + "rank": 44, "slot_uri": "GENEPIO:0100700", "alias": "anatomical_region", "owner": "GRDI", @@ -29130,10 +29871,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_region menu" + "range": "AnatomicalRegionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29160,7 +29901,7 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:food_product" ], - "rank": 37, + "rank": 45, "slot_uri": "GENEPIO:0100444", "alias": "food_product", "owner": "GRDI", @@ -29172,10 +29913,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product menu" + "range": "FoodProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29198,11 +29939,11 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:food_product_properties", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:isolation_source", "NCBI_BIOSAMPLE_Enterics:food_processing_method", "NCBI_BIOSAMPLE_Enterics:food_preserv_proc" ], - "rank": 38, + "rank": 46, "slot_uri": "GENEPIO:0100445", "alias": "food_product_properties", "owner": "GRDI", @@ -29214,10 +29955,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product_properties menu" + "range": "FoodProductPropertiesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29237,7 +29978,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:label_claims" ], - "rank": 39, + "rank": 47, "slot_uri": "FOODON:03602001", "alias": "label_claim", "owner": "GRDI", @@ -29248,10 +29989,10 @@ "multivalued": true, "any_of": [ { - "range": "label_claim menu" + "range": "LabelClaimMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29271,7 +30012,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:food_source" ], - "rank": 40, + "rank": 48, "slot_uri": "GENEPIO:0100446", "alias": "animal_source_of_food", "owner": "GRDI", @@ -29283,10 +30024,10 @@ "multivalued": true, "any_of": [ { - "range": "animal_source_of_food menu" + "range": "AnimalSourceOfFoodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29306,7 +30047,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:food_prod" ], - "rank": 41, + "rank": 49, "slot_uri": "GENEPIO:0100699", "alias": "food_product_production_stream", "owner": "GRDI", @@ -29316,10 +30057,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "food_product_production_stream menu" + "range": "FoodProductProductionStreamMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29341,7 +30082,7 @@ "BIOSAMPLE:food_packaging", "NCBI_BIOSAMPLE_Enterics:food_contain_wrap" ], - "rank": 42, + "rank": 50, "slot_uri": "GENEPIO:0100447", "alias": "food_packaging", "owner": "GRDI", @@ -29353,10 +30094,10 @@ "multivalued": true, "any_of": [ { - "range": "food_packaging menu" + "range": "FoodPackagingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29376,7 +30117,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:food_quality_date" ], - "rank": 43, + "rank": 51, "slot_uri": "GENEPIO:0100615", "alias": "food_quality_date", "owner": "GRDI", @@ -29384,7 +30125,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "date" + "range": "Date" }, "food_packaging_date": { "name": "food_packaging_date", @@ -29399,7 +30140,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 44, + "rank": 52, "slot_uri": "GENEPIO:0100616", "alias": "food_packaging_date", "owner": "GRDI", @@ -29407,7 +30148,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "date" + "range": "Date" }, "collection_device": { "name": "collection_device", @@ -29426,9 +30167,9 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_device", "NCBI_BIOSAMPLE_Enterics:samp_collect_device", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 45, + "rank": 53, "slot_uri": "GENEPIO:0001234", "alias": "collection_device", "owner": "GRDI", @@ -29439,10 +30180,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29462,9 +30203,9 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_method", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], - "rank": 46, + "rank": 54, "slot_uri": "GENEPIO:0001241", "alias": "collection_method", "owner": "GRDI", @@ -29475,10 +30216,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29495,7 +30236,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 47, + "rank": 55, "slot_uri": "GENEPIO:0100768", "alias": "sample_volume_measurement_value", "owner": "GRDI", @@ -29518,7 +30259,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 48, + "rank": 56, "slot_uri": "GENEPIO:0100769", "alias": "sample_volume_measurement_unit", "owner": "GRDI", @@ -29526,7 +30267,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -29541,7 +30282,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 49, + "rank": 57, "slot_uri": "GENEPIO:0101090", "alias": "residual_sample_status", "owner": "GRDI", @@ -29549,7 +30290,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "sample_storage_method": { "name": "sample_storage_method", @@ -29564,7 +30305,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 50, + "rank": 58, "slot_uri": "GENEPIO:0100448", "alias": "sample_storage_method", "owner": "GRDI", @@ -29587,7 +30328,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 51, + "rank": 59, "slot_uri": "GENEPIO:0100449", "alias": "sample_storage_medium", "owner": "GRDI", @@ -29610,7 +30351,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 52, + "rank": 60, "slot_uri": "GENEPIO:0101014", "alias": "sample_storage_duration_value", "owner": "GRDI", @@ -29633,7 +30374,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 53, + "rank": 61, "slot_uri": "GENEPIO:0101015", "alias": "sample_storage_duration_unit", "owner": "GRDI", @@ -29641,7 +30382,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, "nucleic_acid_storage_duration_value": { "name": "nucleic_acid_storage_duration_value", @@ -29656,7 +30397,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 54, + "rank": 62, "slot_uri": "GENEPIO:0101085", "alias": "nucleic_acid_storage_duration_value", "owner": "GRDI", @@ -29679,7 +30420,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 55, + "rank": 63, "slot_uri": "GENEPIO:0101086", "alias": "nucleic_acid_storage_duration_unit", "owner": "GRDI", @@ -29687,7 +30428,7 @@ "GRDI" ], "slot_group": "Sample collection and processing", - "range": "nucleic_acid_storage_duration_unit menu" + "range": "NucleicAcidStorageDurationUnitMenu" }, "available_data_types": { "name": "available_data_types", @@ -29702,7 +30443,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 56, + "rank": 64, "slot_uri": "GENEPIO:0100690", "alias": "available_data_types", "owner": "GRDI", @@ -29713,10 +30454,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29733,7 +30474,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 57, + "rank": 65, "slot_uri": "GENEPIO:0101023", "alias": "available_data_type_details", "owner": "GRDI", @@ -29756,7 +30497,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 58, + "rank": 66, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "GRDI", @@ -29779,7 +30520,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 59, + "rank": 67, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "GRDI", @@ -29789,10 +30530,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_depth_units menu" + "range": "WaterDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29809,7 +30550,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 60, + "rank": 68, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "GRDI", @@ -29832,7 +30573,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 61, + "rank": 69, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "GRDI", @@ -29842,10 +30583,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sediment_depth_units menu" + "range": "SedimentDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29862,7 +30603,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 62, + "rank": 70, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "GRDI", @@ -29885,7 +30626,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 63, + "rank": 71, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "GRDI", @@ -29895,10 +30636,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "air_temperature_units menu" + "range": "AirTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29915,7 +30656,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 64, + "rank": 72, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "GRDI", @@ -29938,7 +30679,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 65, + "rank": 73, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "GRDI", @@ -29948,44 +30689,116 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_temperature_units menu" + "range": "WaterTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "weather_type": { - "name": "weather_type", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "title": "sampling_weather_conditions", "comments": [ "Provide the weather conditions at the time of sample collection." ], - "examples": [ + "from_schema": "https://example.com/GRDI", + "rank": 74, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "SamplingWeatherConditionsMenu" + }, { - "value": "Rain [ENVO:01001564]" + "range": "NullValueMenu" } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "title": "presampling_weather_conditions", + "from_schema": "https://example.com/GRDI", + "rank": 75, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "GRDI", + "domain_of": [ + "GRDI" ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "PresamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "title": "precipitation_measurement_value", "from_schema": "https://example.com/GRDI", - "rank": 66, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 76, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "GRDI", "domain_of": [ "GRDI" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, "any_of": [ { - "range": "weather_type menu" + "range": "Whitespaceminimizedstring" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "title": "precipitation_measurement_unit", + "from_schema": "https://example.com/GRDI", + "rank": 77, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "PrecipitationMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "title": "precipitation_measurement_method", + "from_schema": "https://example.com/GRDI", + "rank": 78, + "slot_uri": "GENEPIO:0100913", + "alias": "precipitation_measurement_method", + "owner": "GRDI", + "domain_of": [ + "GRDI" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, "host_common_name": { "name": "host_common_name", "description": "The commonly used name of the host.", @@ -30005,7 +30818,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:host" ], - "rank": 67, + "rank": 79, "slot_uri": "GENEPIO:0001386", "alias": "host_common_name", "owner": "GRDI", @@ -30016,10 +30829,10 @@ "recommended": true, "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30041,10 +30854,10 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:host", - "NCBI_BIOSAMPLE_Enterics:%2Aisolation_source", + "NCBI_BIOSAMPLE_Enterics:isolation_source", "NCBI_BIOSAMPLE_Enterics:host" ], - "rank": 68, + "rank": 80, "slot_uri": "GENEPIO:0001387", "alias": "host_scientific_name", "owner": "GRDI", @@ -30055,10 +30868,10 @@ "recommended": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30078,7 +30891,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:host_variety" ], - "rank": 69, + "rank": 81, "slot_uri": "GENEPIO:0100450", "alias": "host_ecotype", "owner": "GRDI", @@ -30105,7 +30918,7 @@ "BIOSAMPLE:host_disease", "NCBI_BIOSAMPLE_Enterics:host_animal_breed" ], - "rank": 70, + "rank": 82, "slot_uri": "GENEPIO:0100451", "alias": "host_breed", "owner": "GRDI", @@ -30131,7 +30944,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:host" ], - "rank": 71, + "rank": 83, "slot_uri": "GENEPIO:0100452", "alias": "host_food_production_name", "owner": "GRDI", @@ -30141,10 +30954,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host (food production name) menu" + "range": "HostFoodProductionNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30159,7 +30972,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:host_age" ], - "rank": 72, + "rank": 84, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", "owner": "GRDI", @@ -30169,10 +30982,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host_age_bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30192,7 +31005,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:host_disease" ], - "rank": 73, + "rank": 85, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", "owner": "GRDI", @@ -30215,7 +31028,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 74, + "rank": 86, "slot_uri": "GENEPIO:0100454", "alias": "microbiological_method", "owner": "GRDI", @@ -30240,9 +31053,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:%2Astrain" + "NCBI_BIOSAMPLE_Enterics:strain" ], - "rank": 75, + "rank": 87, "slot_uri": "GENEPIO:0100455", "alias": "strain", "owner": "GRDI", @@ -30266,9 +31079,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:%2Astrain" + "NCBI_BIOSAMPLE_Enterics:strain" ], - "rank": 76, + "rank": 88, "slot_uri": "GENEPIO:0100456", "alias": "isolate_id", "owner": "GRDI", @@ -30282,7 +31095,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30305,7 +31118,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:isolate_name_alias" ], - "rank": 77, + "rank": 89, "slot_uri": "GENEPIO:0100457", "alias": "alternative_isolate_id", "owner": "GRDI", @@ -30329,7 +31142,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 78, + "rank": 90, "slot_uri": "GENEPIO:0100458", "alias": "progeny_isolate_id", "owner": "GRDI", @@ -30352,7 +31165,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 79, + "rank": 91, "slot_uri": "GENEPIO:0100459", "alias": "irida_isolate_id", "owner": "GRDI", @@ -30366,7 +31179,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30383,7 +31196,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 80, + "rank": 92, "slot_uri": "GENEPIO:0100460", "alias": "irida_project_id", "owner": "GRDI", @@ -30397,7 +31210,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30414,7 +31227,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 81, + "rank": 93, "slot_uri": "GENEPIO:0100461", "alias": "isolated_by", "owner": "GRDI", @@ -30422,7 +31235,7 @@ "GRDI" ], "slot_group": "Strain and isolation information", - "range": "isolated_by menu" + "range": "IsolatedByMenu" }, "isolated_by_laboratory_name": { "name": "isolated_by_laboratory_name", @@ -30437,7 +31250,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 82, + "rank": 94, "slot_uri": "GENEPIO:0100462", "alias": "isolated_by_laboratory_name", "owner": "GRDI", @@ -30460,7 +31273,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 83, + "rank": 95, "slot_uri": "GENEPIO:0100463", "alias": "isolated_by_contact_name", "owner": "GRDI", @@ -30483,7 +31296,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 84, + "rank": 96, "slot_uri": "GENEPIO:0100464", "alias": "isolated_by_contact_email", "owner": "GRDI", @@ -30509,7 +31322,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:cult_isol_date" ], - "rank": 85, + "rank": 97, "slot_uri": "GENEPIO:0100465", "alias": "isolation_date", "owner": "GRDI", @@ -30517,7 +31330,7 @@ "GRDI" ], "slot_group": "Strain and isolation information", - "range": "date" + "range": "Date" }, "isolate_received_date": { "name": "isolate_received_date", @@ -30532,7 +31345,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 86, + "rank": 98, "slot_uri": "GENEPIO:0100466", "alias": "isolate_received_date", "owner": "GRDI", @@ -30557,9 +31370,9 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:organism", - "NCBI_BIOSAMPLE_Enterics:%2Aorganism" + "NCBI_BIOSAMPLE_Enterics:organism" ], - "rank": 87, + "rank": 99, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "GRDI", @@ -30571,10 +31384,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30591,7 +31404,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 88, + "rank": 100, "slot_uri": "GENEPIO:0100583", "alias": "taxonomic_identification_process", "owner": "GRDI", @@ -30602,10 +31415,10 @@ "recommended": true, "any_of": [ { - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30622,7 +31435,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 89, + "rank": 101, "slot_uri": "GENEPIO:0100584", "alias": "taxonomic_identification_process_details", "owner": "GRDI", @@ -30648,7 +31461,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:serovar" ], - "rank": 90, + "rank": 102, "slot_uri": "GENEPIO:0100467", "alias": "serovar", "owner": "GRDI", @@ -30672,7 +31485,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 91, + "rank": 103, "slot_uri": "GENEPIO:0100468", "alias": "serotyping_method", "owner": "GRDI", @@ -30696,7 +31509,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 92, + "rank": 104, "slot_uri": "GENEPIO:0100469", "alias": "phagetype", "owner": "GRDI", @@ -30719,7 +31532,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 93, + "rank": 105, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "GRDI", @@ -30746,7 +31559,7 @@ "BIOSAMPLE:sequenced_by", "NCBI_BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 94, + "rank": 106, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "GRDI", @@ -30757,10 +31570,10 @@ "required": true, "any_of": [ { - "range": "sequenced_by menu" + "range": "SequencedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30777,7 +31590,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 95, + "rank": 107, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "GRDI", @@ -30800,7 +31613,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 96, + "rank": 108, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "GRDI", @@ -30814,7 +31627,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30831,7 +31644,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 97, + "rank": 109, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "GRDI", @@ -30845,7 +31658,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30865,7 +31678,7 @@ "exact_mappings": [ "BIOSAMPLE:purpose_of_sequencing" ], - "rank": 98, + "rank": 110, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing", "owner": "GRDI", @@ -30877,10 +31690,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30897,7 +31710,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 99, + "rank": 111, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "GRDI", @@ -30920,7 +31733,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 100, + "rank": 112, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "GRDI", @@ -30930,10 +31743,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30950,7 +31763,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 101, + "rank": 113, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "GRDI", @@ -30960,10 +31773,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30980,7 +31793,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 102, + "rank": 114, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "GRDI", @@ -30988,7 +31801,7 @@ "GRDI" ], "slot_group": "Sequence information", - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "library_preparation_kit": { "name": "library_preparation_kit", @@ -31003,7 +31816,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 103, + "rank": 115, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "GRDI", @@ -31026,7 +31839,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 104, + "rank": 116, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "GRDI", @@ -31049,7 +31862,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 105, + "rank": 117, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "GRDI", @@ -31057,7 +31870,7 @@ "GRDI" ], "slot_group": "Sequence information", - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -31072,7 +31885,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 106, + "rank": 118, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "GRDI", @@ -31095,7 +31908,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 107, + "rank": 119, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "GRDI", @@ -31118,7 +31931,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 108, + "rank": 120, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "GRDI", @@ -31141,7 +31954,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 109, + "rank": 121, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "GRDI", @@ -31164,7 +31977,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 110, + "rank": 122, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "GRDI", @@ -31187,7 +32000,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 111, + "rank": 123, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "GRDI", @@ -31210,7 +32023,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 112, + "rank": 124, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "GRDI", @@ -31233,7 +32046,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 113, + "rank": 125, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "GRDI", @@ -31256,7 +32069,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 114, + "rank": 126, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "GRDI", @@ -31279,7 +32092,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 115, + "rank": 127, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "GRDI", @@ -31302,7 +32115,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 116, + "rank": 128, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "GRDI", @@ -31325,7 +32138,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 117, + "rank": 129, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "GRDI", @@ -31336,10 +32149,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31356,7 +32169,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 118, + "rank": 130, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "GRDI", @@ -31367,10 +32180,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31387,7 +32200,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 119, + "rank": 131, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "GRDI", @@ -31410,7 +32223,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 120, + "rank": 132, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "GRDI", @@ -31424,7 +32237,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31441,7 +32254,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 121, + "rank": 133, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "GRDI", @@ -31455,7 +32268,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31472,7 +32285,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 122, + "rank": 134, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "GRDI", @@ -31485,7 +32298,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31502,7 +32315,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 123, + "rank": 135, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "GRDI", @@ -31515,7 +32328,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31532,7 +32345,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 124, + "rank": 136, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "GRDI", @@ -31545,7 +32358,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31562,7 +32375,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 125, + "rank": 137, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "GRDI", @@ -31575,7 +32388,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31592,7 +32405,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 126, + "rank": 138, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "GRDI", @@ -31615,7 +32428,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 127, + "rank": 139, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "GRDI", @@ -31638,7 +32451,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 128, + "rank": 140, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "GRDI", @@ -31661,7 +32474,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 129, + "rank": 141, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "GRDI", @@ -31684,7 +32497,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 130, + "rank": 142, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "GRDI", @@ -31692,7 +32505,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "number_of_total_reads": { "name": "number_of_total_reads", @@ -31707,7 +32520,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 131, + "rank": 143, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "GRDI", @@ -31715,7 +32528,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "number_of_unique_reads": { "name": "number_of_unique_reads", @@ -31730,7 +32543,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 132, + "rank": 144, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "GRDI", @@ -31738,7 +32551,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", @@ -31753,7 +32566,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 133, + "rank": 145, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "GRDI", @@ -31761,7 +32574,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "number_of_contigs": { "name": "number_of_contigs", @@ -31776,7 +32589,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 134, + "rank": 146, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "GRDI", @@ -31784,7 +32597,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", @@ -31799,7 +32612,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 135, + "rank": 147, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "GRDI", @@ -31807,7 +32620,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", @@ -31822,7 +32635,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 136, + "rank": 148, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "GRDI", @@ -31830,7 +32643,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "n50": { "name": "n50", @@ -31845,7 +32658,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 137, + "rank": 149, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "GRDI", @@ -31853,7 +32666,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "percent_read_contamination_": { "name": "percent_read_contamination_", @@ -31868,7 +32681,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 138, + "rank": 150, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "GRDI", @@ -31876,7 +32689,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "sequence_assembly_length": { "name": "sequence_assembly_length", @@ -31891,7 +32704,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 139, + "rank": 151, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "GRDI", @@ -31899,7 +32712,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "consensus_genome_length": { "name": "consensus_genome_length", @@ -31914,7 +32727,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 140, + "rank": 152, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "GRDI", @@ -31922,7 +32735,7 @@ "GRDI" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "range": "Integer" }, "reference_genome_accession": { "name": "reference_genome_accession", @@ -31937,7 +32750,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 141, + "rank": 153, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "GRDI", @@ -31960,7 +32773,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 142, + "rank": 154, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "GRDI", @@ -31983,7 +32796,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 143, + "rank": 155, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "GRDI", @@ -32006,7 +32819,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 144, + "rank": 156, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "GRDI", @@ -32029,7 +32842,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 145, + "rank": 157, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "GRDI", @@ -32052,7 +32865,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 146, + "rank": 158, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "GRDI", @@ -32075,7 +32888,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 147, + "rank": 159, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "GRDI", @@ -32098,7 +32911,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 148, + "rank": 160, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "GRDI", @@ -32121,7 +32934,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 149, + "rank": 161, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "GRDI", @@ -32129,7 +32942,7 @@ "GRDI" ], "slot_group": "Taxonomic identification information", - "range": "date" + "range": "Date" }, "read_mapping_criteria": { "name": "read_mapping_criteria", @@ -32144,7 +32957,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 150, + "rank": 162, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "GRDI", @@ -32167,7 +32980,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 151, + "rank": 163, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "GRDI", @@ -32177,10 +32990,10 @@ "slot_group": "Public repository information", "any_of": [ { - "range": "sequence_submitted_by menu" + "range": "SequenceSubmittedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32197,7 +33010,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 152, + "rank": 164, "slot_uri": "GENEPIO:0100474", "alias": "sequence_submitted_by_contact_name", "owner": "GRDI", @@ -32220,7 +33033,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 153, + "rank": 165, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitted_by_contact_email", "owner": "GRDI", @@ -32243,7 +33056,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 154, + "rank": 166, "slot_uri": "GENEPIO:0100475", "alias": "publication_id", "owner": "GRDI", @@ -32266,7 +33079,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 155, + "rank": 167, "slot_uri": "GENEPIO:0100476", "alias": "attribute_package", "owner": "GRDI", @@ -32276,10 +33089,10 @@ "slot_group": "Public repository information", "any_of": [ { - "range": "attribute_package menu" + "range": "AttributePackageMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32300,7 +33113,7 @@ "BIOSAMPLE:bioproject_accession", "NCBI_BIOSAMPLE_Enterics:bioproject_accession" ], - "rank": 156, + "rank": 168, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", "owner": "GRDI", @@ -32326,7 +33139,7 @@ "exact_mappings": [ "ENA_ANTIBIOGRAM:bioSample_ID" ], - "rank": 157, + "rank": 169, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", "owner": "GRDI", @@ -32349,7 +33162,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 158, + "rank": 170, "slot_uri": "GENEPIO:0001142", "alias": "sra_accession", "owner": "GRDI", @@ -32372,7 +33185,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 159, + "rank": 171, "slot_uri": "GENEPIO:0001145", "alias": "genbank_accession", "owner": "GRDI", @@ -32395,7 +33208,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 160, + "rank": 172, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "GRDI", @@ -32419,7 +33232,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 161, + "rank": 173, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "GRDI", @@ -32443,7 +33256,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 162, + "rank": 174, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "GRDI", @@ -32454,10 +33267,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32477,7 +33290,7 @@ "exact_mappings": [ "NCBI_BIOSAMPLE_Enterics:upstream_intervention" ], - "rank": 163, + "rank": 175, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "GRDI", @@ -32489,10 +33302,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32509,7 +33322,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 164, + "rank": 176, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "GRDI", @@ -32533,7 +33346,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 165, + "rank": 177, "slot_uri": "GENEPIO:0100511", "alias": "amr_testing_by", "owner": "GRDI", @@ -32544,10 +33357,10 @@ "required": true, "any_of": [ { - "range": "AMR_testing_by menu" + "range": "AmrTestingByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32564,7 +33377,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 166, + "rank": 178, "slot_uri": "GENEPIO:0100512", "alias": "amr_testing_by_laboratory_name", "owner": "GRDI", @@ -32587,7 +33400,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 167, + "rank": 179, "slot_uri": "GENEPIO:0100513", "alias": "amr_testing_by_contact_name", "owner": "GRDI", @@ -32601,7 +33414,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32618,7 +33431,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 168, + "rank": 180, "slot_uri": "GENEPIO:0100514", "alias": "amr_testing_by_contact_email", "owner": "GRDI", @@ -32632,7 +33445,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32649,7 +33462,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 169, + "rank": 181, "slot_uri": "GENEPIO:0100515", "alias": "amr_testing_date", "owner": "GRDI", @@ -32657,7 +33470,7 @@ "GRDI" ], "slot_group": "Antimicrobial resistance", - "range": "date" + "range": "Date" }, "amikacin_resistance_phenotype": { "name": "amikacin_resistance_phenotype", @@ -32673,9 +33486,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 170, + "rank": 182, "alias": "amikacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -32685,10 +33498,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32706,9 +33519,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 171, + "rank": 183, "alias": "amikacin_measurement", "owner": "GRDI", "domain_of": [ @@ -32721,7 +33534,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32739,9 +33552,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 172, + "rank": 184, "alias": "amikacin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -32751,10 +33564,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32772,9 +33585,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 173, + "rank": 185, "alias": "amikacin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -32784,10 +33597,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32805,9 +33618,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 174, + "rank": 186, "alias": "amikacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -32816,10 +33629,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32839,7 +33652,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 175, + "rank": 187, "alias": "amikacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -32848,10 +33661,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32868,7 +33681,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 176, + "rank": 188, "alias": "amikacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -32893,7 +33706,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 177, + "rank": 189, "alias": "amikacin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -32902,10 +33715,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name" + "range": "AntimicrobialVendorName" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32923,9 +33736,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 178, + "rank": 190, "alias": "amikacin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -32935,10 +33748,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32955,7 +33768,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 179, + "rank": 191, "alias": "amikacin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -32980,7 +33793,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 180, + "rank": 192, "alias": "amikacin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -33002,7 +33815,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 181, + "rank": 193, "alias": "amikacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33021,7 +33834,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 182, + "rank": 194, "alias": "amikacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33043,7 +33856,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 183, + "rank": 195, "alias": "amikacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33066,9 +33879,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 184, + "rank": 196, "alias": "amoxicillinclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -33078,10 +33891,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33099,9 +33912,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 185, + "rank": 197, "alias": "amoxicillinclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ @@ -33114,7 +33927,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33132,9 +33945,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 186, + "rank": 198, "alias": "amoxicillinclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ @@ -33144,10 +33957,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33165,9 +33978,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 187, + "rank": 199, "alias": "amoxicillinclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -33177,10 +33990,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33198,9 +34011,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 188, + "rank": 200, "alias": "amoxicillinclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -33209,10 +34022,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33232,7 +34045,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 189, + "rank": 201, "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -33241,10 +34054,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33261,7 +34074,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 190, + "rank": 202, "alias": "amoxicillinclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -33286,7 +34099,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 191, + "rank": 203, "alias": "amoxicillinclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ @@ -33295,10 +34108,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33316,9 +34129,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 192, + "rank": 204, "alias": "amoxicillinclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ @@ -33328,10 +34141,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33348,7 +34161,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 193, + "rank": 205, "alias": "amoxicillinclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -33373,7 +34186,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 194, + "rank": 206, "alias": "amoxicillinclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -33395,7 +34208,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 195, + "rank": 207, "alias": "amoxicillinclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33414,7 +34227,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 196, + "rank": 208, "alias": "amoxicillinclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33436,7 +34249,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 197, + "rank": 209, "alias": "amoxicillinclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33459,9 +34272,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 198, + "rank": 210, "alias": "ampicillin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -33471,10 +34284,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33492,9 +34305,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 199, + "rank": 211, "alias": "ampicillin_measurement", "owner": "GRDI", "domain_of": [ @@ -33507,7 +34320,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33525,9 +34338,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 200, + "rank": 212, "alias": "ampicillin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -33537,10 +34350,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33558,9 +34371,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 201, + "rank": 213, "alias": "ampicillin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -33570,10 +34383,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33591,9 +34404,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 202, + "rank": 214, "alias": "ampicillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -33602,10 +34415,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33625,7 +34438,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 203, + "rank": 215, "alias": "ampicillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -33634,10 +34447,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33654,7 +34467,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 204, + "rank": 216, "alias": "ampicillin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -33679,7 +34492,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 205, + "rank": 217, "alias": "ampicillin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -33688,10 +34501,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33709,9 +34522,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 206, + "rank": 218, "alias": "ampicillin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -33721,10 +34534,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33741,7 +34554,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 207, + "rank": 219, "alias": "ampicillin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -33766,7 +34579,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 208, + "rank": 220, "alias": "ampicillin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -33788,7 +34601,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 209, + "rank": 221, "alias": "ampicillin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33807,7 +34620,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 210, + "rank": 222, "alias": "ampicillin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33829,7 +34642,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 211, + "rank": 223, "alias": "ampicillin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -33852,9 +34665,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 212, + "rank": 224, "alias": "azithromycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -33864,10 +34677,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33885,9 +34698,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 213, + "rank": 225, "alias": "azithromycin_measurement", "owner": "GRDI", "domain_of": [ @@ -33900,7 +34713,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33918,9 +34731,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 214, + "rank": 226, "alias": "azithromycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -33930,10 +34743,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33951,9 +34764,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 215, + "rank": 227, "alias": "azithromycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -33963,10 +34776,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33984,9 +34797,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 216, + "rank": 228, "alias": "azithromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -33995,10 +34808,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34018,7 +34831,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 217, + "rank": 229, "alias": "azithromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -34027,10 +34840,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34047,7 +34860,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 218, + "rank": 230, "alias": "azithromycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -34072,7 +34885,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 219, + "rank": 231, "alias": "azithromycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -34081,10 +34894,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34102,9 +34915,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 220, + "rank": 232, "alias": "azithromycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -34114,10 +34927,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34134,7 +34947,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 221, + "rank": 233, "alias": "azithromycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -34159,7 +34972,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 222, + "rank": 234, "alias": "azithromycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -34181,7 +34994,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 223, + "rank": 235, "alias": "azithromycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34200,7 +35013,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 224, + "rank": 236, "alias": "azithromycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34222,7 +35035,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 225, + "rank": 237, "alias": "azithromycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34245,9 +35058,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 226, + "rank": 238, "alias": "cefazolin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -34257,10 +35070,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34278,9 +35091,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 227, + "rank": 239, "alias": "cefazolin_measurement", "owner": "GRDI", "domain_of": [ @@ -34293,7 +35106,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34311,9 +35124,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 228, + "rank": 240, "alias": "cefazolin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -34323,10 +35136,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34344,9 +35157,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 229, + "rank": 241, "alias": "cefazolin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -34356,10 +35169,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34377,9 +35190,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 230, + "rank": 242, "alias": "cefazolin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -34388,10 +35201,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34411,7 +35224,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 231, + "rank": 243, "alias": "cefazolin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -34420,10 +35233,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34440,7 +35253,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 232, + "rank": 244, "alias": "cefazolin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -34465,7 +35278,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 233, + "rank": 245, "alias": "cefazolin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -34474,10 +35287,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34495,9 +35308,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 234, + "rank": 246, "alias": "cefazolin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -34507,10 +35320,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34527,7 +35340,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 235, + "rank": 247, "alias": "cefazolin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -34552,7 +35365,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 236, + "rank": 248, "alias": "cefazolin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -34574,7 +35387,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 237, + "rank": 249, "alias": "cefazolin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34593,7 +35406,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 238, + "rank": 250, "alias": "cefazolin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34615,7 +35428,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 239, + "rank": 251, "alias": "cefazolin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34638,9 +35451,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 240, + "rank": 252, "alias": "cefepime_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -34650,10 +35463,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34671,9 +35484,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 241, + "rank": 253, "alias": "cefepime_measurement", "owner": "GRDI", "domain_of": [ @@ -34686,7 +35499,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34704,9 +35517,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 242, + "rank": 254, "alias": "cefepime_measurement_units", "owner": "GRDI", "domain_of": [ @@ -34716,10 +35529,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34737,9 +35550,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 243, + "rank": 255, "alias": "cefepime_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -34749,10 +35562,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34770,9 +35583,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 244, + "rank": 256, "alias": "cefepime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -34781,10 +35594,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34804,7 +35617,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 245, + "rank": 257, "alias": "cefepime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -34813,10 +35626,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34833,7 +35646,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 246, + "rank": 258, "alias": "cefepime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -34858,7 +35671,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 247, + "rank": 259, "alias": "cefepime_vendor_name", "owner": "GRDI", "domain_of": [ @@ -34867,10 +35680,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34888,9 +35701,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 248, + "rank": 260, "alias": "cefepime_testing_standard", "owner": "GRDI", "domain_of": [ @@ -34900,10 +35713,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34920,7 +35733,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 249, + "rank": 261, "alias": "cefepime_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -34945,7 +35758,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 250, + "rank": 262, "alias": "cefepime_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -34967,7 +35780,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 251, + "rank": 263, "alias": "cefepime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -34986,7 +35799,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 252, + "rank": 264, "alias": "cefepime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35008,7 +35821,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 253, + "rank": 265, "alias": "cefepime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35031,9 +35844,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 254, + "rank": 266, "alias": "cefotaxime_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -35043,10 +35856,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35064,9 +35877,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 255, + "rank": 267, "alias": "cefotaxime_measurement", "owner": "GRDI", "domain_of": [ @@ -35079,7 +35892,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35097,9 +35910,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 256, + "rank": 268, "alias": "cefotaxime_measurement_units", "owner": "GRDI", "domain_of": [ @@ -35109,10 +35922,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35130,9 +35943,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 257, + "rank": 269, "alias": "cefotaxime_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -35142,10 +35955,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35163,9 +35976,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 258, + "rank": 270, "alias": "cefotaxime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -35174,10 +35987,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35197,7 +36010,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 259, + "rank": 271, "alias": "cefotaxime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -35206,10 +36019,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35226,7 +36039,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 260, + "rank": 272, "alias": "cefotaxime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -35251,7 +36064,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 261, + "rank": 273, "alias": "cefotaxime_vendor_name", "owner": "GRDI", "domain_of": [ @@ -35260,10 +36073,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35281,9 +36094,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 262, + "rank": 274, "alias": "cefotaxime_testing_standard", "owner": "GRDI", "domain_of": [ @@ -35293,10 +36106,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35313,7 +36126,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 263, + "rank": 275, "alias": "cefotaxime_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -35338,7 +36151,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 264, + "rank": 276, "alias": "cefotaxime_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -35360,7 +36173,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 265, + "rank": 277, "alias": "cefotaxime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35379,7 +36192,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 266, + "rank": 278, "alias": "cefotaxime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35401,7 +36214,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 267, + "rank": 279, "alias": "cefotaxime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35424,9 +36237,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 268, + "rank": 280, "alias": "cefotaximeclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -35436,10 +36249,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35457,9 +36270,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 269, + "rank": 281, "alias": "cefotaximeclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ @@ -35472,7 +36285,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35490,9 +36303,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 270, + "rank": 282, "alias": "cefotaximeclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ @@ -35502,10 +36315,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35523,9 +36336,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 271, + "rank": 283, "alias": "cefotaximeclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -35535,10 +36348,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35556,9 +36369,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 272, + "rank": 284, "alias": "cefotaximeclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -35567,10 +36380,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35590,7 +36403,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 273, + "rank": 285, "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -35599,10 +36412,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35619,7 +36432,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 274, + "rank": 286, "alias": "cefotaximeclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -35644,7 +36457,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 275, + "rank": 287, "alias": "cefotaximeclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ @@ -35653,10 +36466,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35674,9 +36487,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 276, + "rank": 288, "alias": "cefotaximeclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ @@ -35686,10 +36499,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35706,7 +36519,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 277, + "rank": 289, "alias": "cefotaximeclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -35731,7 +36544,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 278, + "rank": 290, "alias": "cefotaximeclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -35753,7 +36566,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 279, + "rank": 291, "alias": "cefotaximeclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35772,7 +36585,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 280, + "rank": 292, "alias": "cefotaximeclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35794,7 +36607,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 281, + "rank": 293, "alias": "cefotaximeclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -35817,9 +36630,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 282, + "rank": 294, "alias": "cefoxitin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -35829,10 +36642,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35850,9 +36663,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 283, + "rank": 295, "alias": "cefoxitin_measurement", "owner": "GRDI", "domain_of": [ @@ -35865,7 +36678,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35883,9 +36696,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 284, + "rank": 296, "alias": "cefoxitin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -35895,10 +36708,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35916,9 +36729,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 285, + "rank": 297, "alias": "cefoxitin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -35928,10 +36741,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35949,9 +36762,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 286, + "rank": 298, "alias": "cefoxitin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -35960,10 +36773,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35983,7 +36796,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 287, + "rank": 299, "alias": "cefoxitin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -35992,10 +36805,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36012,7 +36825,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 288, + "rank": 300, "alias": "cefoxitin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -36037,7 +36850,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 289, + "rank": 301, "alias": "cefoxitin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -36046,10 +36859,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36067,9 +36880,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 290, + "rank": 302, "alias": "cefoxitin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -36079,10 +36892,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36099,7 +36912,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 291, + "rank": 303, "alias": "cefoxitin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -36124,7 +36937,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 292, + "rank": 304, "alias": "cefoxitin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -36146,7 +36959,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 293, + "rank": 305, "alias": "cefoxitin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36165,7 +36978,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 294, + "rank": 306, "alias": "cefoxitin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36187,7 +37000,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 295, + "rank": 307, "alias": "cefoxitin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36210,9 +37023,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 296, + "rank": 308, "alias": "cefpodoxime_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -36222,10 +37035,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36243,9 +37056,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 297, + "rank": 309, "alias": "cefpodoxime_measurement", "owner": "GRDI", "domain_of": [ @@ -36258,7 +37071,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36276,9 +37089,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 298, + "rank": 310, "alias": "cefpodoxime_measurement_units", "owner": "GRDI", "domain_of": [ @@ -36288,10 +37101,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36309,9 +37122,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 299, + "rank": 311, "alias": "cefpodoxime_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -36321,10 +37134,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36342,9 +37155,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 300, + "rank": 312, "alias": "cefpodoxime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -36353,10 +37166,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36376,7 +37189,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 301, + "rank": 313, "alias": "cefpodoxime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -36385,10 +37198,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36405,7 +37218,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 302, + "rank": 314, "alias": "cefpodoxime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -36430,7 +37243,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 303, + "rank": 315, "alias": "cefpodoxime_vendor_name", "owner": "GRDI", "domain_of": [ @@ -36439,10 +37252,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36460,9 +37273,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 304, + "rank": 316, "alias": "cefpodoxime_testing_standard", "owner": "GRDI", "domain_of": [ @@ -36472,10 +37285,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36492,7 +37305,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 305, + "rank": 317, "alias": "cefpodoxime_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -36517,7 +37330,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 306, + "rank": 318, "alias": "cefpodoxime_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -36539,7 +37352,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 307, + "rank": 319, "alias": "cefpodoxime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36558,7 +37371,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 308, + "rank": 320, "alias": "cefpodoxime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36580,7 +37393,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 309, + "rank": 321, "alias": "cefpodoxime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36603,9 +37416,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 310, + "rank": 322, "alias": "ceftazidime_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -36615,10 +37428,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36636,9 +37449,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 311, + "rank": 323, "alias": "ceftazidime_measurement", "owner": "GRDI", "domain_of": [ @@ -36651,7 +37464,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36669,9 +37482,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 312, + "rank": 324, "alias": "ceftazidime_measurement_units", "owner": "GRDI", "domain_of": [ @@ -36681,10 +37494,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36702,9 +37515,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 313, + "rank": 325, "alias": "ceftazidime_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -36714,10 +37527,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36735,9 +37548,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 314, + "rank": 326, "alias": "ceftazidime_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -36746,10 +37559,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36769,7 +37582,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 315, + "rank": 327, "alias": "ceftazidime_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -36778,10 +37591,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36798,7 +37611,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 316, + "rank": 328, "alias": "ceftazidime_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -36823,7 +37636,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 317, + "rank": 329, "alias": "ceftazidime_vendor_name", "owner": "GRDI", "domain_of": [ @@ -36832,10 +37645,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36853,9 +37666,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 318, + "rank": 330, "alias": "ceftazidime_testing_standard", "owner": "GRDI", "domain_of": [ @@ -36865,10 +37678,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -36885,7 +37698,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 319, + "rank": 331, "alias": "ceftazidime_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -36910,7 +37723,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 320, + "rank": 332, "alias": "ceftazidime_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -36932,7 +37745,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 321, + "rank": 333, "alias": "ceftazidime_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36951,7 +37764,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 322, + "rank": 334, "alias": "ceftazidime_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36973,7 +37786,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 323, + "rank": 335, "alias": "ceftazidime_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -36996,9 +37809,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 324, + "rank": 336, "alias": "ceftazidimeclavulanic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -37008,10 +37821,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37029,9 +37842,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 325, + "rank": 337, "alias": "ceftazidimeclavulanic_acid_measurement", "owner": "GRDI", "domain_of": [ @@ -37044,7 +37857,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37062,9 +37875,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 326, + "rank": 338, "alias": "ceftazidimeclavulanic_acid_measurement_units", "owner": "GRDI", "domain_of": [ @@ -37074,10 +37887,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37095,9 +37908,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 327, + "rank": 339, "alias": "ceftazidimeclavulanic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -37107,10 +37920,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37128,9 +37941,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 328, + "rank": 340, "alias": "ceftazidimeclavulanic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -37139,10 +37952,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37162,7 +37975,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 329, + "rank": 341, "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -37171,10 +37984,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37191,7 +38004,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 330, + "rank": 342, "alias": "ceftazidimeclavulanic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -37216,7 +38029,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 331, + "rank": 343, "alias": "ceftazidimeclavulanic_acid_vendor_name", "owner": "GRDI", "domain_of": [ @@ -37225,10 +38038,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37246,9 +38059,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 332, + "rank": 344, "alias": "ceftazidimeclavulanic_acid_testing_standard", "owner": "GRDI", "domain_of": [ @@ -37258,10 +38071,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37278,7 +38091,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 333, + "rank": 345, "alias": "ceftazidimeclavulanic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -37303,7 +38116,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 334, + "rank": 346, "alias": "ceftazidimeclavulanic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -37325,7 +38138,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 335, + "rank": 347, "alias": "ceftazidimeclavulanic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -37344,7 +38157,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 336, + "rank": 348, "alias": "ceftazidimeclavulanic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -37366,7 +38179,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 337, + "rank": 349, "alias": "ceftazidimeclavulanic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -37389,9 +38202,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 338, + "rank": 350, "alias": "ceftiofur_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -37401,10 +38214,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37422,9 +38235,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 339, + "rank": 351, "alias": "ceftiofur_measurement", "owner": "GRDI", "domain_of": [ @@ -37437,7 +38250,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37455,9 +38268,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 340, + "rank": 352, "alias": "ceftiofur_measurement_units", "owner": "GRDI", "domain_of": [ @@ -37467,10 +38280,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37488,9 +38301,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 341, + "rank": 353, "alias": "ceftiofur_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -37500,10 +38313,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37521,9 +38334,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 342, + "rank": 354, "alias": "ceftiofur_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -37532,10 +38345,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37555,7 +38368,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 343, + "rank": 355, "alias": "ceftiofur_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -37564,10 +38377,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37584,7 +38397,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 344, + "rank": 356, "alias": "ceftiofur_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -37609,7 +38422,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 345, + "rank": 357, "alias": "ceftiofur_vendor_name", "owner": "GRDI", "domain_of": [ @@ -37618,10 +38431,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37639,9 +38452,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 346, + "rank": 358, "alias": "ceftiofur_testing_standard", "owner": "GRDI", "domain_of": [ @@ -37651,10 +38464,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37671,7 +38484,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 347, + "rank": 359, "alias": "ceftiofur_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -37696,7 +38509,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 348, + "rank": 360, "alias": "ceftiofur_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -37718,7 +38531,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 349, + "rank": 361, "alias": "ceftiofur_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -37737,7 +38550,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 350, + "rank": 362, "alias": "ceftiofur_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -37759,7 +38572,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 351, + "rank": 363, "alias": "ceftiofur_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -37782,9 +38595,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 352, + "rank": 364, "alias": "ceftriaxone_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -37794,10 +38607,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37815,9 +38628,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 353, + "rank": 365, "alias": "ceftriaxone_measurement", "owner": "GRDI", "domain_of": [ @@ -37830,7 +38643,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37848,9 +38661,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 354, + "rank": 366, "alias": "ceftriaxone_measurement_units", "owner": "GRDI", "domain_of": [ @@ -37860,10 +38673,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37881,9 +38694,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 355, + "rank": 367, "alias": "ceftriaxone_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -37893,10 +38706,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37914,9 +38727,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 356, + "rank": 368, "alias": "ceftriaxone_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -37925,10 +38738,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37948,7 +38761,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 357, + "rank": 369, "alias": "ceftriaxone_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -37957,10 +38770,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37977,7 +38790,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 358, + "rank": 370, "alias": "ceftriaxone_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -38002,7 +38815,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 359, + "rank": 371, "alias": "ceftriaxone_vendor_name", "owner": "GRDI", "domain_of": [ @@ -38011,10 +38824,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38032,9 +38845,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 360, + "rank": 372, "alias": "ceftriaxone_testing_standard", "owner": "GRDI", "domain_of": [ @@ -38044,10 +38857,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38064,7 +38877,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 361, + "rank": 373, "alias": "ceftriaxone_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -38089,7 +38902,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 362, + "rank": 374, "alias": "ceftriaxone_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -38111,7 +38924,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 363, + "rank": 375, "alias": "ceftriaxone_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38130,7 +38943,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 364, + "rank": 376, "alias": "ceftriaxone_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38152,7 +38965,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 365, + "rank": 377, "alias": "ceftriaxone_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38175,9 +38988,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 366, + "rank": 378, "alias": "cephalothin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -38187,10 +39000,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38208,9 +39021,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 367, + "rank": 379, "alias": "cephalothin_measurement", "owner": "GRDI", "domain_of": [ @@ -38223,7 +39036,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38241,9 +39054,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 368, + "rank": 380, "alias": "cephalothin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -38253,10 +39066,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38274,9 +39087,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 369, + "rank": 381, "alias": "cephalothin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -38286,10 +39099,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38307,9 +39120,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 370, + "rank": 382, "alias": "cephalothin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -38318,10 +39131,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38341,7 +39154,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 371, + "rank": 383, "alias": "cephalothin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -38350,10 +39163,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38370,7 +39183,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 372, + "rank": 384, "alias": "cephalothin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -38395,7 +39208,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 373, + "rank": 385, "alias": "cephalothin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -38404,10 +39217,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38425,9 +39238,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 374, + "rank": 386, "alias": "cephalothin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -38437,10 +39250,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38457,7 +39270,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 375, + "rank": 387, "alias": "cephalothin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -38482,7 +39295,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 376, + "rank": 388, "alias": "cephalothin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -38504,7 +39317,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 377, + "rank": 389, "alias": "cephalothin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38523,7 +39336,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 378, + "rank": 390, "alias": "cephalothin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38545,7 +39358,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 379, + "rank": 391, "alias": "cephalothin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38568,9 +39381,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 380, + "rank": 392, "alias": "chloramphenicol_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -38580,10 +39393,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38601,9 +39414,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 381, + "rank": 393, "alias": "chloramphenicol_measurement", "owner": "GRDI", "domain_of": [ @@ -38616,7 +39429,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38634,9 +39447,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 382, + "rank": 394, "alias": "chloramphenicol_measurement_units", "owner": "GRDI", "domain_of": [ @@ -38646,10 +39459,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38667,9 +39480,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 383, + "rank": 395, "alias": "chloramphenicol_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -38679,10 +39492,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38700,9 +39513,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 384, + "rank": 396, "alias": "chloramphenicol_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -38711,10 +39524,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38734,7 +39547,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 385, + "rank": 397, "alias": "chloramphenicol_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -38743,10 +39556,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38763,7 +39576,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 386, + "rank": 398, "alias": "chloramphenicol_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -38788,7 +39601,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 387, + "rank": 399, "alias": "chloramphenicol_vendor_name", "owner": "GRDI", "domain_of": [ @@ -38797,10 +39610,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38818,9 +39631,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 388, + "rank": 400, "alias": "chloramphenicol_testing_standard", "owner": "GRDI", "domain_of": [ @@ -38830,10 +39643,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38850,7 +39663,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 389, + "rank": 401, "alias": "chloramphenicol_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -38875,7 +39688,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 390, + "rank": 402, "alias": "chloramphenicol_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -38897,7 +39710,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 391, + "rank": 403, "alias": "chloramphenicol_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38916,7 +39729,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 392, + "rank": 404, "alias": "chloramphenicol_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38938,7 +39751,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 393, + "rank": 405, "alias": "chloramphenicol_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -38961,9 +39774,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 394, + "rank": 406, "alias": "ciprofloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -38973,10 +39786,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38994,9 +39807,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 395, + "rank": 407, "alias": "ciprofloxacin_measurement", "owner": "GRDI", "domain_of": [ @@ -39009,7 +39822,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39027,9 +39840,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 396, + "rank": 408, "alias": "ciprofloxacin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -39039,10 +39852,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39060,9 +39873,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 397, + "rank": 409, "alias": "ciprofloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -39072,10 +39885,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39093,9 +39906,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 398, + "rank": 410, "alias": "ciprofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -39104,10 +39917,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39127,7 +39940,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 399, + "rank": 411, "alias": "ciprofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -39136,10 +39949,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39156,7 +39969,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 400, + "rank": 412, "alias": "ciprofloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -39181,7 +39994,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 401, + "rank": 413, "alias": "ciprofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -39190,10 +40003,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39211,9 +40024,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 402, + "rank": 414, "alias": "ciprofloxacin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -39223,10 +40036,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39243,7 +40056,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 403, + "rank": 415, "alias": "ciprofloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -39268,7 +40081,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 404, + "rank": 416, "alias": "ciprofloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -39290,7 +40103,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 405, + "rank": 417, "alias": "ciprofloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -39309,7 +40122,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 406, + "rank": 418, "alias": "ciprofloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -39331,7 +40144,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 407, + "rank": 419, "alias": "ciprofloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -39354,9 +40167,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 408, + "rank": 420, "alias": "clindamycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -39366,10 +40179,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39387,9 +40200,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 409, + "rank": 421, "alias": "clindamycin_measurement", "owner": "GRDI", "domain_of": [ @@ -39402,7 +40215,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39420,9 +40233,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 410, + "rank": 422, "alias": "clindamycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -39432,10 +40245,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39453,9 +40266,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 411, + "rank": 423, "alias": "clindamycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -39465,10 +40278,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39486,9 +40299,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 412, + "rank": 424, "alias": "clindamycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -39497,10 +40310,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39520,7 +40333,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 413, + "rank": 425, "alias": "clindamycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -39529,10 +40342,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39549,7 +40362,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 414, + "rank": 426, "alias": "clindamycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -39574,7 +40387,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 415, + "rank": 427, "alias": "clindamycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -39583,10 +40396,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39604,9 +40417,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 416, + "rank": 428, "alias": "clindamycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -39616,10 +40429,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39636,7 +40449,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 417, + "rank": 429, "alias": "clindamycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -39661,7 +40474,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 418, + "rank": 430, "alias": "clindamycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -39683,7 +40496,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 419, + "rank": 431, "alias": "clindamycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -39702,7 +40515,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 420, + "rank": 432, "alias": "clindamycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -39724,7 +40537,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 421, + "rank": 433, "alias": "clindamycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -39747,9 +40560,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 422, + "rank": 434, "alias": "doxycycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -39759,10 +40572,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39780,9 +40593,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 423, + "rank": 435, "alias": "doxycycline_measurement", "owner": "GRDI", "domain_of": [ @@ -39795,7 +40608,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39813,9 +40626,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 424, + "rank": 436, "alias": "doxycycline_measurement_units", "owner": "GRDI", "domain_of": [ @@ -39825,10 +40638,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39846,9 +40659,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 425, + "rank": 437, "alias": "doxycycline_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -39858,10 +40671,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39879,9 +40692,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 426, + "rank": 438, "alias": "doxycycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -39890,10 +40703,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39913,7 +40726,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 427, + "rank": 439, "alias": "doxycycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -39922,10 +40735,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39942,7 +40755,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 428, + "rank": 440, "alias": "doxycycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -39967,7 +40780,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 429, + "rank": 441, "alias": "doxycycline_vendor_name", "owner": "GRDI", "domain_of": [ @@ -39976,10 +40789,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39997,9 +40810,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 430, + "rank": 442, "alias": "doxycycline_testing_standard", "owner": "GRDI", "domain_of": [ @@ -40009,10 +40822,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40029,7 +40842,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 431, + "rank": 443, "alias": "doxycycline_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -40054,7 +40867,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 432, + "rank": 444, "alias": "doxycycline_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -40076,7 +40889,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 433, + "rank": 445, "alias": "doxycycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40095,7 +40908,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 434, + "rank": 446, "alias": "doxycycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40117,7 +40930,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 435, + "rank": 447, "alias": "doxycycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40140,9 +40953,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 436, + "rank": 448, "alias": "enrofloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -40152,10 +40965,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40173,9 +40986,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 437, + "rank": 449, "alias": "enrofloxacin_measurement", "owner": "GRDI", "domain_of": [ @@ -40188,7 +41001,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40206,9 +41019,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 438, + "rank": 450, "alias": "enrofloxacin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -40218,10 +41031,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40239,9 +41052,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 439, + "rank": 451, "alias": "enrofloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -40251,10 +41064,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40272,9 +41085,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 440, + "rank": 452, "alias": "enrofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -40283,10 +41096,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40306,7 +41119,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 441, + "rank": 453, "alias": "enrofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -40315,10 +41128,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40335,7 +41148,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 442, + "rank": 454, "alias": "enrofloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -40360,7 +41173,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 443, + "rank": 455, "alias": "enrofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -40369,10 +41182,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40390,9 +41203,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 444, + "rank": 456, "alias": "enrofloxacin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -40402,10 +41215,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40422,7 +41235,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 445, + "rank": 457, "alias": "enrofloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -40447,7 +41260,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 446, + "rank": 458, "alias": "enrofloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -40469,7 +41282,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 447, + "rank": 459, "alias": "enrofloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40488,7 +41301,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 448, + "rank": 460, "alias": "enrofloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40510,7 +41323,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 449, + "rank": 461, "alias": "enrofloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40533,9 +41346,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 450, + "rank": 462, "alias": "erythromycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -40545,10 +41358,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40566,9 +41379,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 451, + "rank": 463, "alias": "erythromycin_measurement", "owner": "GRDI", "domain_of": [ @@ -40581,7 +41394,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40599,9 +41412,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 452, + "rank": 464, "alias": "erythromycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -40611,10 +41424,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40632,9 +41445,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 453, + "rank": 465, "alias": "erythromycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -40644,10 +41457,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40665,9 +41478,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 454, + "rank": 466, "alias": "erythromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -40676,10 +41489,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40699,7 +41512,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 455, + "rank": 467, "alias": "erythromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -40708,10 +41521,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40728,7 +41541,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 456, + "rank": 468, "alias": "erythromycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -40753,7 +41566,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 457, + "rank": 469, "alias": "erythromycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -40762,10 +41575,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40783,9 +41596,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 458, + "rank": 470, "alias": "erythromycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -40795,10 +41608,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40815,7 +41628,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 459, + "rank": 471, "alias": "erythromycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -40840,7 +41653,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 460, + "rank": 472, "alias": "erythromycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -40862,7 +41675,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 461, + "rank": 473, "alias": "erythromycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40881,7 +41694,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 462, + "rank": 474, "alias": "erythromycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40903,7 +41716,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 463, + "rank": 475, "alias": "erythromycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -40926,9 +41739,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 464, + "rank": 476, "alias": "florfenicol_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -40938,10 +41751,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40959,9 +41772,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 465, + "rank": 477, "alias": "florfenicol_measurement", "owner": "GRDI", "domain_of": [ @@ -40974,7 +41787,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40992,9 +41805,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 466, + "rank": 478, "alias": "florfenicol_measurement_units", "owner": "GRDI", "domain_of": [ @@ -41004,10 +41817,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41025,9 +41838,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 467, + "rank": 479, "alias": "florfenicol_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -41037,10 +41850,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41058,9 +41871,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 468, + "rank": 480, "alias": "florfenicol_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -41069,10 +41882,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41092,7 +41905,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 469, + "rank": 481, "alias": "florfenicol_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -41101,10 +41914,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41121,7 +41934,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 470, + "rank": 482, "alias": "florfenicol_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -41146,7 +41959,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 471, + "rank": 483, "alias": "florfenicol_vendor_name", "owner": "GRDI", "domain_of": [ @@ -41155,10 +41968,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41176,9 +41989,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 472, + "rank": 484, "alias": "florfenicol_testing_standard", "owner": "GRDI", "domain_of": [ @@ -41188,10 +42001,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41208,7 +42021,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 473, + "rank": 485, "alias": "florfenicol_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -41233,7 +42046,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 474, + "rank": 486, "alias": "florfenicol_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -41255,7 +42068,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 475, + "rank": 487, "alias": "florfenicol_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -41274,7 +42087,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 476, + "rank": 488, "alias": "florfenicol_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -41296,7 +42109,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 477, + "rank": 489, "alias": "florfenicol_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -41319,9 +42132,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 478, + "rank": 490, "alias": "gentamicin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -41331,10 +42144,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41352,9 +42165,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 479, + "rank": 491, "alias": "gentamicin_measurement", "owner": "GRDI", "domain_of": [ @@ -41367,7 +42180,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41385,9 +42198,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 480, + "rank": 492, "alias": "gentamicin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -41397,10 +42210,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41418,9 +42231,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 481, + "rank": 493, "alias": "gentamicin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -41430,10 +42243,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41451,9 +42264,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 482, + "rank": 494, "alias": "gentamicin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -41462,10 +42275,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41485,7 +42298,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 483, + "rank": 495, "alias": "gentamicin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -41494,10 +42307,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41514,7 +42327,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 484, + "rank": 496, "alias": "gentamicin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -41539,7 +42352,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 485, + "rank": 497, "alias": "gentamicin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -41548,10 +42361,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41569,9 +42382,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 486, + "rank": 498, "alias": "gentamicin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -41581,10 +42394,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41601,7 +42414,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 487, + "rank": 499, "alias": "gentamicin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -41626,7 +42439,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 488, + "rank": 500, "alias": "gentamicin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -41648,7 +42461,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 489, + "rank": 501, "alias": "gentamicin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -41667,7 +42480,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 490, + "rank": 502, "alias": "gentamicin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -41689,7 +42502,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 491, + "rank": 503, "alias": "gentamicin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -41712,9 +42525,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 492, + "rank": 504, "alias": "imipenem_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -41724,10 +42537,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41745,9 +42558,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 493, + "rank": 505, "alias": "imipenem_measurement", "owner": "GRDI", "domain_of": [ @@ -41760,7 +42573,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41778,9 +42591,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 494, + "rank": 506, "alias": "imipenem_measurement_units", "owner": "GRDI", "domain_of": [ @@ -41790,10 +42603,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41811,9 +42624,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 495, + "rank": 507, "alias": "imipenem_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -41823,10 +42636,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41844,9 +42657,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 496, + "rank": 508, "alias": "imipenem_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -41855,10 +42668,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41878,7 +42691,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 497, + "rank": 509, "alias": "imipenem_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -41887,10 +42700,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41907,7 +42720,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 498, + "rank": 510, "alias": "imipenem_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -41932,7 +42745,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 499, + "rank": 511, "alias": "imipenem_vendor_name", "owner": "GRDI", "domain_of": [ @@ -41941,10 +42754,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41962,9 +42775,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 500, + "rank": 512, "alias": "imipenem_testing_standard", "owner": "GRDI", "domain_of": [ @@ -41974,10 +42787,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41994,7 +42807,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 501, + "rank": 513, "alias": "imipenem_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -42019,7 +42832,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 502, + "rank": 514, "alias": "imipenem_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -42041,7 +42854,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 503, + "rank": 515, "alias": "imipenem_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42060,7 +42873,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 504, + "rank": 516, "alias": "imipenem_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42082,7 +42895,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 505, + "rank": 517, "alias": "imipenem_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42105,9 +42918,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 506, + "rank": 518, "alias": "kanamycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -42117,10 +42930,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42138,9 +42951,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 507, + "rank": 519, "alias": "kanamycin_measurement", "owner": "GRDI", "domain_of": [ @@ -42153,7 +42966,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42171,9 +42984,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 508, + "rank": 520, "alias": "kanamycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -42183,10 +42996,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42204,9 +43017,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 509, + "rank": 521, "alias": "kanamycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -42216,10 +43029,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42237,9 +43050,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 510, + "rank": 522, "alias": "kanamycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -42248,10 +43061,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42271,7 +43084,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 511, + "rank": 523, "alias": "kanamycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -42280,10 +43093,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42300,7 +43113,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 512, + "rank": 524, "alias": "kanamycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -42325,7 +43138,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 513, + "rank": 525, "alias": "kanamycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -42334,10 +43147,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42355,9 +43168,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 514, + "rank": 526, "alias": "kanamycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -42367,10 +43180,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42387,7 +43200,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 515, + "rank": 527, "alias": "kanamycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -42412,7 +43225,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 516, + "rank": 528, "alias": "kanamycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -42434,7 +43247,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 517, + "rank": 529, "alias": "kanamycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42453,7 +43266,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 518, + "rank": 530, "alias": "kanamycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42475,7 +43288,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 519, + "rank": 531, "alias": "kanamycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42498,9 +43311,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 520, + "rank": 532, "alias": "levofloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -42510,10 +43323,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42531,9 +43344,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 521, + "rank": 533, "alias": "levofloxacin_measurement", "owner": "GRDI", "domain_of": [ @@ -42546,7 +43359,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42564,9 +43377,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 522, + "rank": 534, "alias": "levofloxacin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -42576,10 +43389,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42597,9 +43410,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 523, + "rank": 535, "alias": "levofloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -42609,10 +43422,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42630,9 +43443,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 524, + "rank": 536, "alias": "levofloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -42641,10 +43454,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42664,7 +43477,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 525, + "rank": 537, "alias": "levofloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -42673,10 +43486,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42693,7 +43506,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 526, + "rank": 538, "alias": "levofloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -42718,7 +43531,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 527, + "rank": 539, "alias": "levofloxacin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -42727,10 +43540,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42748,9 +43561,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 528, + "rank": 540, "alias": "levofloxacin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -42760,10 +43573,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42780,7 +43593,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 529, + "rank": 541, "alias": "levofloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -42805,7 +43618,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 530, + "rank": 542, "alias": "levofloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -42827,7 +43640,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 531, + "rank": 543, "alias": "levofloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42846,7 +43659,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 532, + "rank": 544, "alias": "levofloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42868,7 +43681,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 533, + "rank": 545, "alias": "levofloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -42891,9 +43704,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 534, + "rank": 546, "alias": "linezolid_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -42903,10 +43716,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42924,9 +43737,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 535, + "rank": 547, "alias": "linezolid_measurement", "owner": "GRDI", "domain_of": [ @@ -42939,7 +43752,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42957,9 +43770,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 536, + "rank": 548, "alias": "linezolid_measurement_units", "owner": "GRDI", "domain_of": [ @@ -42969,10 +43782,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42990,9 +43803,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 537, + "rank": 549, "alias": "linezolid_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -43002,10 +43815,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43023,9 +43836,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 538, + "rank": 550, "alias": "linezolid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -43034,10 +43847,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43057,7 +43870,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 539, + "rank": 551, "alias": "linezolid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -43066,10 +43879,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43086,7 +43899,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 540, + "rank": 552, "alias": "linezolid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -43111,7 +43924,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 541, + "rank": 553, "alias": "linezolid_vendor_name", "owner": "GRDI", "domain_of": [ @@ -43120,10 +43933,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43141,9 +43954,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 542, + "rank": 554, "alias": "linezolid_testing_standard", "owner": "GRDI", "domain_of": [ @@ -43153,10 +43966,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43173,7 +43986,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 543, + "rank": 555, "alias": "linezolid_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -43198,7 +44011,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 544, + "rank": 556, "alias": "linezolid_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -43220,7 +44033,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 545, + "rank": 557, "alias": "linezolid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -43239,7 +44052,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 546, + "rank": 558, "alias": "linezolid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -43261,7 +44074,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 547, + "rank": 559, "alias": "linezolid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -43284,9 +44097,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 548, + "rank": 560, "alias": "meropenem_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -43296,10 +44109,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43317,9 +44130,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 549, + "rank": 561, "alias": "meropenem_measurement", "owner": "GRDI", "domain_of": [ @@ -43332,7 +44145,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43350,9 +44163,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 550, + "rank": 562, "alias": "meropenem_measurement_units", "owner": "GRDI", "domain_of": [ @@ -43362,10 +44175,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43383,9 +44196,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 551, + "rank": 563, "alias": "meropenem_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -43395,10 +44208,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43416,9 +44229,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 552, + "rank": 564, "alias": "meropenem_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -43427,10 +44240,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43450,7 +44263,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 553, + "rank": 565, "alias": "meropenem_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -43459,10 +44272,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43479,7 +44292,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 554, + "rank": 566, "alias": "meropenem_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -43504,7 +44317,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 555, + "rank": 567, "alias": "meropenem_vendor_name", "owner": "GRDI", "domain_of": [ @@ -43513,10 +44326,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43534,9 +44347,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 556, + "rank": 568, "alias": "meropenem_testing_standard", "owner": "GRDI", "domain_of": [ @@ -43546,10 +44359,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43566,7 +44379,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 557, + "rank": 569, "alias": "meropenem_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -43591,7 +44404,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 558, + "rank": 570, "alias": "meropenem_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -43613,7 +44426,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 559, + "rank": 571, "alias": "meropenem_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -43632,7 +44445,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 560, + "rank": 572, "alias": "meropenem_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -43654,7 +44467,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 561, + "rank": 573, "alias": "meropenem_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -43677,9 +44490,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 562, + "rank": 574, "alias": "nalidixic_acid_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -43689,10 +44502,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43710,9 +44523,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 563, + "rank": 575, "alias": "nalidixic_acid_measurement", "owner": "GRDI", "domain_of": [ @@ -43725,7 +44538,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43743,9 +44556,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 564, + "rank": 576, "alias": "nalidixic_acid_measurement_units", "owner": "GRDI", "domain_of": [ @@ -43755,10 +44568,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43776,9 +44589,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 565, + "rank": 577, "alias": "nalidixic_acid_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -43788,10 +44601,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43809,9 +44622,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 566, + "rank": 578, "alias": "nalidixic_acid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -43820,10 +44633,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43843,7 +44656,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 567, + "rank": 579, "alias": "nalidixic_acid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -43852,10 +44665,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43872,7 +44685,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 568, + "rank": 580, "alias": "nalidixic_acid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -43897,7 +44710,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 569, + "rank": 581, "alias": "nalidixic_acid_vendor_name", "owner": "GRDI", "domain_of": [ @@ -43906,10 +44719,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43927,9 +44740,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 570, + "rank": 582, "alias": "nalidixic_acid_testing_standard", "owner": "GRDI", "domain_of": [ @@ -43939,10 +44752,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43959,7 +44772,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 571, + "rank": 583, "alias": "nalidixic_acid_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -43984,7 +44797,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 572, + "rank": 584, "alias": "nalidixic_acid_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -44006,7 +44819,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 573, + "rank": 585, "alias": "nalidixic_acid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44025,7 +44838,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 574, + "rank": 586, "alias": "nalidixic_acid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44047,7 +44860,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 575, + "rank": 587, "alias": "nalidixic_acid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44070,9 +44883,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 576, + "rank": 588, "alias": "nitrofurantoin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -44082,10 +44895,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44103,9 +44916,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 577, + "rank": 589, "alias": "nitrofurantoin_measurement", "owner": "GRDI", "domain_of": [ @@ -44118,7 +44931,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44136,9 +44949,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 578, + "rank": 590, "alias": "nitrofurantoin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -44148,10 +44961,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44169,9 +44982,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 579, + "rank": 591, "alias": "nitrofurantoin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -44181,10 +44994,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44202,9 +45015,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 580, + "rank": 592, "alias": "nitrofurantoin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -44213,10 +45026,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44236,7 +45049,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 581, + "rank": 593, "alias": "nitrofurantoin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -44245,10 +45058,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44265,7 +45078,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 582, + "rank": 594, "alias": "nitrofurantoin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -44290,7 +45103,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 583, + "rank": 595, "alias": "nitrofurantoin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -44299,10 +45112,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44320,9 +45133,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 584, + "rank": 596, "alias": "nitrofurantoin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -44332,10 +45145,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44352,7 +45165,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 585, + "rank": 597, "alias": "nitrofurantoin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -44377,7 +45190,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 586, + "rank": 598, "alias": "nitrofurantoin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -44399,7 +45212,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 587, + "rank": 599, "alias": "nitrofurantoin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44418,7 +45231,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 588, + "rank": 600, "alias": "nitrofurantoin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44440,7 +45253,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 589, + "rank": 601, "alias": "nitrofurantoin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44463,9 +45276,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 590, + "rank": 602, "alias": "norfloxacin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -44475,10 +45288,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44496,9 +45309,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 591, + "rank": 603, "alias": "norfloxacin_measurement", "owner": "GRDI", "domain_of": [ @@ -44511,7 +45324,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44529,9 +45342,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 592, + "rank": 604, "alias": "norfloxacin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -44541,10 +45354,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44562,9 +45375,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 593, + "rank": 605, "alias": "norfloxacin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -44574,10 +45387,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44595,9 +45408,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 594, + "rank": 606, "alias": "norfloxacin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -44606,10 +45419,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44629,7 +45442,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 595, + "rank": 607, "alias": "norfloxacin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -44638,10 +45451,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44658,7 +45471,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 596, + "rank": 608, "alias": "norfloxacin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -44683,7 +45496,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 597, + "rank": 609, "alias": "norfloxacin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -44692,10 +45505,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44713,9 +45526,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 598, + "rank": 610, "alias": "norfloxacin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -44725,10 +45538,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44745,7 +45558,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 599, + "rank": 611, "alias": "norfloxacin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -44770,7 +45583,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 600, + "rank": 612, "alias": "norfloxacin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -44792,7 +45605,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 601, + "rank": 613, "alias": "norfloxacin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44811,7 +45624,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 602, + "rank": 614, "alias": "norfloxacin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44833,7 +45646,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 603, + "rank": 615, "alias": "norfloxacin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -44856,9 +45669,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 604, + "rank": 616, "alias": "oxolinicacid_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -44868,10 +45681,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44889,9 +45702,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 605, + "rank": 617, "alias": "oxolinicacid_measurement", "owner": "GRDI", "domain_of": [ @@ -44904,7 +45717,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44922,9 +45735,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 606, + "rank": 618, "alias": "oxolinicacid_measurement_units", "owner": "GRDI", "domain_of": [ @@ -44934,10 +45747,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44955,9 +45768,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 607, + "rank": 619, "alias": "oxolinicacid_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -44967,10 +45780,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44988,9 +45801,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 608, + "rank": 620, "alias": "oxolinicacid_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -44999,10 +45812,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45022,7 +45835,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 609, + "rank": 621, "alias": "oxolinicacid_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -45031,10 +45844,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45051,7 +45864,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 610, + "rank": 622, "alias": "oxolinicacid_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -45076,7 +45889,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 611, + "rank": 623, "alias": "oxolinicacid_vendor_name", "owner": "GRDI", "domain_of": [ @@ -45085,10 +45898,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45106,9 +45919,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 612, + "rank": 624, "alias": "oxolinicacid_testing_standard", "owner": "GRDI", "domain_of": [ @@ -45118,10 +45931,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45138,7 +45951,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 613, + "rank": 625, "alias": "oxolinicacid_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -45163,7 +45976,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 614, + "rank": 626, "alias": "oxolinicacid_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -45185,7 +45998,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 615, + "rank": 627, "alias": "oxolinicacid_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45204,7 +46017,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 616, + "rank": 628, "alias": "oxolinicacid_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45226,7 +46039,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 617, + "rank": 629, "alias": "oxolinicacid_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45249,9 +46062,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 618, + "rank": 630, "alias": "oxytetracycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -45261,10 +46074,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45282,9 +46095,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 619, + "rank": 631, "alias": "oxytetracycline_measurement", "owner": "GRDI", "domain_of": [ @@ -45297,7 +46110,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45315,9 +46128,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 620, + "rank": 632, "alias": "oxytetracycline_measurement_units", "owner": "GRDI", "domain_of": [ @@ -45327,10 +46140,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45348,9 +46161,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 621, + "rank": 633, "alias": "oxytetracycline_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -45360,10 +46173,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45381,9 +46194,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 622, + "rank": 634, "alias": "oxytetracycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -45392,10 +46205,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45415,7 +46228,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 623, + "rank": 635, "alias": "oxytetracycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -45424,10 +46237,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45444,7 +46257,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 624, + "rank": 636, "alias": "oxytetracycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -45469,7 +46282,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 625, + "rank": 637, "alias": "oxytetracycline_vendor_name", "owner": "GRDI", "domain_of": [ @@ -45478,10 +46291,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45499,9 +46312,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 626, + "rank": 638, "alias": "oxytetracycline_testing_standard", "owner": "GRDI", "domain_of": [ @@ -45511,10 +46324,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45531,7 +46344,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 627, + "rank": 639, "alias": "oxytetracycline_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -45556,7 +46369,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 628, + "rank": 640, "alias": "oxytetracycline_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -45578,7 +46391,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 629, + "rank": 641, "alias": "oxytetracycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45597,7 +46410,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 630, + "rank": 642, "alias": "oxytetracycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45619,7 +46432,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 631, + "rank": 643, "alias": "oxytetracycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45642,9 +46455,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 632, + "rank": 644, "alias": "piperacillin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -45654,10 +46467,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45675,9 +46488,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 633, + "rank": 645, "alias": "piperacillin_measurement", "owner": "GRDI", "domain_of": [ @@ -45690,7 +46503,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45708,9 +46521,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 634, + "rank": 646, "alias": "piperacillin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -45720,10 +46533,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45741,9 +46554,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 635, + "rank": 647, "alias": "piperacillin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -45753,10 +46566,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45774,9 +46587,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 636, + "rank": 648, "alias": "piperacillin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -45785,10 +46598,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45808,7 +46621,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 637, + "rank": 649, "alias": "piperacillin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -45817,10 +46630,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45837,7 +46650,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 638, + "rank": 650, "alias": "piperacillin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -45862,7 +46675,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 639, + "rank": 651, "alias": "piperacillin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -45871,10 +46684,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45892,9 +46705,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 640, + "rank": 652, "alias": "piperacillin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -45904,10 +46717,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45924,7 +46737,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 641, + "rank": 653, "alias": "piperacillin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -45949,7 +46762,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 642, + "rank": 654, "alias": "piperacillin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -45971,7 +46784,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 643, + "rank": 655, "alias": "piperacillin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -45990,7 +46803,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 644, + "rank": 656, "alias": "piperacillin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46012,7 +46825,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 645, + "rank": 657, "alias": "piperacillin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46035,9 +46848,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 646, + "rank": 658, "alias": "piperacillintazobactam_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -46047,10 +46860,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46068,9 +46881,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 647, + "rank": 659, "alias": "piperacillintazobactam_measurement", "owner": "GRDI", "domain_of": [ @@ -46083,7 +46896,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46101,9 +46914,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 648, + "rank": 660, "alias": "piperacillintazobactam_measurement_units", "owner": "GRDI", "domain_of": [ @@ -46113,10 +46926,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46134,9 +46947,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 649, + "rank": 661, "alias": "piperacillintazobactam_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -46146,10 +46959,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46167,9 +46980,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 650, + "rank": 662, "alias": "piperacillintazobactam_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -46178,10 +46991,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46201,7 +47014,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 651, + "rank": 663, "alias": "piperacillintazobactam_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -46210,10 +47023,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46230,7 +47043,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 652, + "rank": 664, "alias": "piperacillintazobactam_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -46255,7 +47068,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 653, + "rank": 665, "alias": "piperacillintazobactam_vendor_name", "owner": "GRDI", "domain_of": [ @@ -46264,10 +47077,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46285,9 +47098,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 654, + "rank": 666, "alias": "piperacillintazobactam_testing_standard", "owner": "GRDI", "domain_of": [ @@ -46297,10 +47110,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46317,7 +47130,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 655, + "rank": 667, "alias": "piperacillintazobactam_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -46342,7 +47155,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 656, + "rank": 668, "alias": "piperacillintazobactam_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -46364,7 +47177,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 657, + "rank": 669, "alias": "piperacillintazobactam_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46383,7 +47196,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 658, + "rank": 670, "alias": "piperacillintazobactam_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46405,7 +47218,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 659, + "rank": 671, "alias": "piperacillintazobactam_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46428,9 +47241,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 660, + "rank": 672, "alias": "polymyxinb_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -46440,10 +47253,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46461,9 +47274,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 661, + "rank": 673, "alias": "polymyxinb_measurement", "owner": "GRDI", "domain_of": [ @@ -46476,7 +47289,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46494,9 +47307,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 662, + "rank": 674, "alias": "polymyxinb_measurement_units", "owner": "GRDI", "domain_of": [ @@ -46506,10 +47319,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46527,9 +47340,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 663, + "rank": 675, "alias": "polymyxinb_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -46539,10 +47352,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46560,9 +47373,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 664, + "rank": 676, "alias": "polymyxinb_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -46571,10 +47384,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46594,7 +47407,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 665, + "rank": 677, "alias": "polymyxinb_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -46603,10 +47416,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46623,7 +47436,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 666, + "rank": 678, "alias": "polymyxinb_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -46648,7 +47461,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 667, + "rank": 679, "alias": "polymyxinb_vendor_name", "owner": "GRDI", "domain_of": [ @@ -46657,10 +47470,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46678,9 +47491,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 668, + "rank": 680, "alias": "polymyxinb_testing_standard", "owner": "GRDI", "domain_of": [ @@ -46690,10 +47503,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46710,7 +47523,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 669, + "rank": 681, "alias": "polymyxinb_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -46735,7 +47548,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 670, + "rank": 682, "alias": "polymyxinb_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -46757,7 +47570,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 671, + "rank": 683, "alias": "polymyxinb_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46776,7 +47589,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 672, + "rank": 684, "alias": "polymyxinb_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46798,7 +47611,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 673, + "rank": 685, "alias": "polymyxinb_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -46821,9 +47634,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 674, + "rank": 686, "alias": "quinupristindalfopristin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -46833,10 +47646,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46854,9 +47667,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 675, + "rank": 687, "alias": "quinupristindalfopristin_measurement", "owner": "GRDI", "domain_of": [ @@ -46869,7 +47682,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46887,9 +47700,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 676, + "rank": 688, "alias": "quinupristindalfopristin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -46899,10 +47712,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46920,9 +47733,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 677, + "rank": 689, "alias": "quinupristindalfopristin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -46932,10 +47745,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46953,9 +47766,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 678, + "rank": 690, "alias": "quinupristindalfopristin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -46964,10 +47777,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46987,7 +47800,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 679, + "rank": 691, "alias": "quinupristindalfopristin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -46996,10 +47809,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47016,7 +47829,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 680, + "rank": 692, "alias": "quinupristindalfopristin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -47041,7 +47854,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 681, + "rank": 693, "alias": "quinupristindalfopristin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -47050,10 +47863,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47071,9 +47884,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 682, + "rank": 694, "alias": "quinupristindalfopristin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -47083,10 +47896,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47103,7 +47916,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 683, + "rank": 695, "alias": "quinupristindalfopristin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -47128,7 +47941,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 684, + "rank": 696, "alias": "quinupristindalfopristin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -47150,7 +47963,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 685, + "rank": 697, "alias": "quinupristindalfopristin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47169,7 +47982,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 686, + "rank": 698, "alias": "quinupristindalfopristin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47191,7 +48004,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 687, + "rank": 699, "alias": "quinupristindalfopristin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47214,9 +48027,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 688, + "rank": 700, "alias": "streptomycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -47226,10 +48039,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47247,9 +48060,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 689, + "rank": 701, "alias": "streptomycin_measurement", "owner": "GRDI", "domain_of": [ @@ -47262,7 +48075,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47280,9 +48093,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 690, + "rank": 702, "alias": "streptomycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -47292,10 +48105,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47313,9 +48126,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 691, + "rank": 703, "alias": "streptomycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -47325,10 +48138,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47346,9 +48159,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 692, + "rank": 704, "alias": "streptomycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -47357,10 +48170,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47380,7 +48193,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 693, + "rank": 705, "alias": "streptomycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -47389,10 +48202,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47409,7 +48222,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 694, + "rank": 706, "alias": "streptomycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -47434,7 +48247,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 695, + "rank": 707, "alias": "streptomycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -47443,10 +48256,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47464,9 +48277,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 696, + "rank": 708, "alias": "streptomycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -47476,10 +48289,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47496,7 +48309,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 697, + "rank": 709, "alias": "streptomycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -47521,7 +48334,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 698, + "rank": 710, "alias": "streptomycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -47543,7 +48356,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 699, + "rank": 711, "alias": "streptomycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47562,7 +48375,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 700, + "rank": 712, "alias": "streptomycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47584,7 +48397,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 701, + "rank": 713, "alias": "streptomycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47607,9 +48420,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 702, + "rank": 714, "alias": "sulfisoxazole_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -47619,10 +48432,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47640,9 +48453,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 703, + "rank": 715, "alias": "sulfisoxazole_measurement", "owner": "GRDI", "domain_of": [ @@ -47655,7 +48468,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47673,9 +48486,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 704, + "rank": 716, "alias": "sulfisoxazole_measurement_units", "owner": "GRDI", "domain_of": [ @@ -47685,10 +48498,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47706,9 +48519,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 705, + "rank": 717, "alias": "sulfisoxazole_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -47718,10 +48531,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47739,9 +48552,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 706, + "rank": 718, "alias": "sulfisoxazole_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -47750,10 +48563,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47773,7 +48586,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 707, + "rank": 719, "alias": "sulfisoxazole_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -47782,10 +48595,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47802,7 +48615,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 708, + "rank": 720, "alias": "sulfisoxazole_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -47827,7 +48640,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 709, + "rank": 721, "alias": "sulfisoxazole_vendor_name", "owner": "GRDI", "domain_of": [ @@ -47836,10 +48649,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47857,9 +48670,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 710, + "rank": 722, "alias": "sulfisoxazole_testing_standard", "owner": "GRDI", "domain_of": [ @@ -47869,10 +48682,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47889,7 +48702,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 711, + "rank": 723, "alias": "sulfisoxazole_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -47914,7 +48727,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 712, + "rank": 724, "alias": "sulfisoxazole_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -47936,7 +48749,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 713, + "rank": 725, "alias": "sulfisoxazole_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47955,7 +48768,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 714, + "rank": 726, "alias": "sulfisoxazole_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -47977,7 +48790,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 715, + "rank": 727, "alias": "sulfisoxazole_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48000,9 +48813,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 716, + "rank": 728, "alias": "telithromycin_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -48012,10 +48825,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48033,9 +48846,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 717, + "rank": 729, "alias": "telithromycin_measurement", "owner": "GRDI", "domain_of": [ @@ -48048,7 +48861,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48066,9 +48879,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 718, + "rank": 730, "alias": "telithromycin_measurement_units", "owner": "GRDI", "domain_of": [ @@ -48078,10 +48891,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48099,9 +48912,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 719, + "rank": 731, "alias": "telithromycin_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -48111,10 +48924,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48132,9 +48945,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 720, + "rank": 732, "alias": "telithromycin_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -48143,10 +48956,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48166,7 +48979,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 721, + "rank": 733, "alias": "telithromycin_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -48175,10 +48988,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48195,7 +49008,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 722, + "rank": 734, "alias": "telithromycin_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -48220,7 +49033,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 723, + "rank": 735, "alias": "telithromycin_vendor_name", "owner": "GRDI", "domain_of": [ @@ -48229,10 +49042,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48250,9 +49063,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 724, + "rank": 736, "alias": "telithromycin_testing_standard", "owner": "GRDI", "domain_of": [ @@ -48262,10 +49075,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48282,7 +49095,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 725, + "rank": 737, "alias": "telithromycin_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -48307,7 +49120,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 726, + "rank": 738, "alias": "telithromycin_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -48329,7 +49142,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 727, + "rank": 739, "alias": "telithromycin_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48348,7 +49161,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 728, + "rank": 740, "alias": "telithromycin_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48370,7 +49183,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 729, + "rank": 741, "alias": "telithromycin_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48393,9 +49206,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 730, + "rank": 742, "alias": "tetracycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -48405,10 +49218,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48426,9 +49239,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 731, + "rank": 743, "alias": "tetracycline_measurement", "owner": "GRDI", "domain_of": [ @@ -48441,7 +49254,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48459,9 +49272,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 732, + "rank": 744, "alias": "tetracycline_measurement_units", "owner": "GRDI", "domain_of": [ @@ -48471,10 +49284,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48492,9 +49305,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 733, + "rank": 745, "alias": "tetracycline_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -48504,10 +49317,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48525,9 +49338,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 734, + "rank": 746, "alias": "tetracycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -48536,10 +49349,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48559,7 +49372,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 735, + "rank": 747, "alias": "tetracycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -48568,10 +49381,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48588,7 +49401,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 736, + "rank": 748, "alias": "tetracycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -48613,7 +49426,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 737, + "rank": 749, "alias": "tetracycline_vendor_name", "owner": "GRDI", "domain_of": [ @@ -48622,10 +49435,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48643,9 +49456,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 738, + "rank": 750, "alias": "tetracycline_testing_standard", "owner": "GRDI", "domain_of": [ @@ -48655,10 +49468,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48675,7 +49488,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 739, + "rank": 751, "alias": "tetracycline_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -48700,7 +49513,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 740, + "rank": 752, "alias": "tetracycline_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -48722,7 +49535,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 741, + "rank": 753, "alias": "tetracycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48741,7 +49554,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 742, + "rank": 754, "alias": "tetracycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48763,7 +49576,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 743, + "rank": 755, "alias": "tetracycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -48786,9 +49599,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 744, + "rank": 756, "alias": "tigecycline_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -48798,10 +49611,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48819,9 +49632,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 745, + "rank": 757, "alias": "tigecycline_measurement", "owner": "GRDI", "domain_of": [ @@ -48834,7 +49647,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48852,9 +49665,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 746, + "rank": 758, "alias": "tigecycline_measurement_units", "owner": "GRDI", "domain_of": [ @@ -48864,10 +49677,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48885,9 +49698,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 747, + "rank": 759, "alias": "tigecycline_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -48897,10 +49710,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48918,9 +49731,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 748, + "rank": 760, "alias": "tigecycline_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -48929,10 +49742,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48952,7 +49765,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 749, + "rank": 761, "alias": "tigecycline_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -48961,10 +49774,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48981,7 +49794,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 750, + "rank": 762, "alias": "tigecycline_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -49006,7 +49819,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 751, + "rank": 763, "alias": "tigecycline_vendor_name", "owner": "GRDI", "domain_of": [ @@ -49015,10 +49828,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49036,9 +49849,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 752, + "rank": 764, "alias": "tigecycline_testing_standard", "owner": "GRDI", "domain_of": [ @@ -49048,10 +49861,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49068,7 +49881,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 753, + "rank": 765, "alias": "tigecycline_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -49093,7 +49906,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 754, + "rank": 766, "alias": "tigecycline_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -49115,7 +49928,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 755, + "rank": 767, "alias": "tigecycline_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49134,7 +49947,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 756, + "rank": 768, "alias": "tigecycline_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49156,7 +49969,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 757, + "rank": 769, "alias": "tigecycline_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49179,9 +49992,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Aresistance_phenotype" + "NCBI_ANTIBIOGRAM:resistance_phenotype" ], - "rank": 758, + "rank": 770, "alias": "trimethoprimsulfamethoxazole_resistance_phenotype", "owner": "GRDI", "domain_of": [ @@ -49191,10 +50004,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_phenotype menu" + "range": "AntimicrobialPhenotypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49212,9 +50025,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement" + "NCBI_ANTIBIOGRAM:measurement" ], - "rank": 759, + "rank": 771, "alias": "trimethoprimsulfamethoxazole_measurement", "owner": "GRDI", "domain_of": [ @@ -49227,7 +50040,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49245,9 +50058,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_units" + "NCBI_ANTIBIOGRAM:measurement_units" ], - "rank": 760, + "rank": 772, "alias": "trimethoprimsulfamethoxazole_measurement_units", "owner": "GRDI", "domain_of": [ @@ -49257,10 +50070,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_units menu" + "range": "AntimicrobialMeasurementUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49278,9 +50091,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Ameasurement_sign" + "NCBI_ANTIBIOGRAM:measurement_sign" ], - "rank": 761, + "rank": 773, "alias": "trimethoprimsulfamethoxazole_measurement_sign", "owner": "GRDI", "domain_of": [ @@ -49290,10 +50103,10 @@ "required": true, "any_of": [ { - "range": "antimicrobial_measurement_sign menu" + "range": "AntimicrobialMeasurementSignMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49311,9 +50124,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method" + "NCBI_ANTIBIOGRAM:laboratory_typing_method" ], - "rank": 762, + "rank": 774, "alias": "trimethoprimsulfamethoxazole_laboratory_typing_method", "owner": "GRDI", "domain_of": [ @@ -49322,10 +50135,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_method menu" + "range": "AntimicrobialLaboratoryTypingMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49345,7 +50158,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:laboratory_typing_platform" ], - "rank": 763, + "rank": 775, "alias": "trimethoprimsulfamethoxazole_laboratory_typing_platform", "owner": "GRDI", "domain_of": [ @@ -49354,10 +50167,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_laboratory_typing_platform menu" + "range": "AntimicrobialLaboratoryTypingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49374,7 +50187,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 764, + "rank": 776, "alias": "trimethoprimsulfamethoxazole_laboratory_typing_platform_version", "owner": "GRDI", "domain_of": [ @@ -49399,7 +50212,7 @@ "exact_mappings": [ "NCBI_ANTIBIOGRAM:vendor" ], - "rank": 765, + "rank": 777, "alias": "trimethoprimsulfamethoxazole_vendor_name", "owner": "GRDI", "domain_of": [ @@ -49408,10 +50221,10 @@ "slot_group": "Antimicrobial resistance", "any_of": [ { - "range": "antimicrobial_vendor_name menu" + "range": "AntimicrobialVendorNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49429,9 +50242,9 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:%2Atesting_standard" + "NCBI_ANTIBIOGRAM:testing_standard" ], - "rank": 766, + "rank": 778, "alias": "trimethoprimsulfamethoxazole_testing_standard", "owner": "GRDI", "domain_of": [ @@ -49441,10 +50254,10 @@ "recommended": true, "any_of": [ { - "range": "antimicrobial_testing_standard menu" + "range": "AntimicrobialTestingStandardMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49461,7 +50274,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 767, + "rank": 779, "alias": "trimethoprimsulfamethoxazole_testing_standard_version", "owner": "GRDI", "domain_of": [ @@ -49486,7 +50299,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 768, + "rank": 780, "alias": "trimethoprimsulfamethoxazole_testing_standard_details", "owner": "GRDI", "domain_of": [ @@ -49508,7 +50321,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 769, + "rank": 781, "alias": "trimethoprimsulfamethoxazole_susceptible_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49527,7 +50340,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 770, + "rank": 782, "alias": "trimethoprimsulfamethoxazole_intermediate_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49549,7 +50362,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 771, + "rank": 783, "alias": "trimethoprimsulfamethoxazole_resistant_breakpoint", "owner": "GRDI", "domain_of": [ @@ -49571,7 +50384,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 772, + "rank": 784, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "GRDI", @@ -49595,7 +50408,7 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 773, + "rank": 785, "slot_uri": "GENEPIO:0001518", "alias": "dataharmonizer_provenance", "owner": "GRDI", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 13c32a94..00f09e23 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -32,6 +32,7 @@ classes: - experimental_protocol_field - experimental_specimen_role_type - specimen_processing + - specimen_processing_details - nucleic_acid_extraction_method - nucleic_acid_extraction_kit - geo_loc_name_country @@ -43,6 +44,13 @@ classes: - geo_loc_longitude - sample_collection_date - sample_collection_date_precision + - sample_collection_end_date + - sample_processing_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit - sample_received_date - original_sample_description - environmental_site @@ -82,7 +90,11 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - precipitation_measurement_unit + - precipitation_measurement_method - host_common_name - host_scientific_name - host_ecotype @@ -836,2279 +848,2315 @@ classes: specimen_processing: rank: 15 slot_group: Sample collection and processing - nucleic_acid_extraction_method: + specimen_processing_details: rank: 16 slot_group: Sample collection and processing - nucleic_acid_extraction_kit: + nucleic_acid_extraction_method: rank: 17 slot_group: Sample collection and processing - geo_loc_name_country: + nucleic_acid_extraction_kit: rank: 18 slot_group: Sample collection and processing - geo_loc_name_state_province_region: + geo_loc_name_country: rank: 19 slot_group: Sample collection and processing - geo_loc_name_site: + geo_loc_name_state_province_region: rank: 20 slot_group: Sample collection and processing - food_product_origin_geo_loc_name_country: + geo_loc_name_site: rank: 21 slot_group: Sample collection and processing - host_origin_geo_loc_name_country: + food_product_origin_geo_loc_name_country: rank: 22 slot_group: Sample collection and processing - geo_loc_latitude: + host_origin_geo_loc_name_country: rank: 23 slot_group: Sample collection and processing - geo_loc_longitude: + geo_loc_latitude: rank: 24 slot_group: Sample collection and processing - sample_collection_date: + geo_loc_longitude: rank: 25 slot_group: Sample collection and processing - sample_collection_date_precision: + sample_collection_date: rank: 26 slot_group: Sample collection and processing - sample_received_date: + sample_collection_date_precision: rank: 27 slot_group: Sample collection and processing - original_sample_description: + sample_collection_end_date: rank: 28 slot_group: Sample collection and processing - environmental_site: + sample_processing_date: rank: 29 slot_group: Sample collection and processing - environmental_material: + sample_collection_start_time: rank: 30 slot_group: Sample collection and processing - environmental_material_constituent: + sample_collection_end_time: rank: 31 slot_group: Sample collection and processing - animal_or_plant_population: + sample_collection_time_of_day: rank: 32 slot_group: Sample collection and processing - anatomical_material: + sample_collection_time_duration_value: rank: 33 slot_group: Sample collection and processing - body_product: + sample_collection_time_duration_unit: rank: 34 slot_group: Sample collection and processing - anatomical_part: + sample_received_date: rank: 35 slot_group: Sample collection and processing - anatomical_region: + original_sample_description: rank: 36 slot_group: Sample collection and processing - food_product: + environmental_site: rank: 37 slot_group: Sample collection and processing - food_product_properties: + environmental_material: rank: 38 slot_group: Sample collection and processing - label_claim: + environmental_material_constituent: rank: 39 slot_group: Sample collection and processing - animal_source_of_food: + animal_or_plant_population: rank: 40 slot_group: Sample collection and processing - food_product_production_stream: + anatomical_material: rank: 41 slot_group: Sample collection and processing - food_packaging: + body_product: rank: 42 slot_group: Sample collection and processing - food_quality_date: + anatomical_part: rank: 43 slot_group: Sample collection and processing - food_packaging_date: + anatomical_region: rank: 44 slot_group: Sample collection and processing - collection_device: + food_product: rank: 45 slot_group: Sample collection and processing - collection_method: + food_product_properties: rank: 46 slot_group: Sample collection and processing - sample_volume_measurement_value: + label_claim: rank: 47 slot_group: Sample collection and processing - sample_volume_measurement_unit: + animal_source_of_food: rank: 48 slot_group: Sample collection and processing - residual_sample_status: + food_product_production_stream: rank: 49 slot_group: Sample collection and processing - sample_storage_method: + food_packaging: rank: 50 slot_group: Sample collection and processing - sample_storage_medium: + food_quality_date: rank: 51 slot_group: Sample collection and processing - sample_storage_duration_value: + food_packaging_date: rank: 52 slot_group: Sample collection and processing - sample_storage_duration_unit: + collection_device: rank: 53 slot_group: Sample collection and processing - nucleic_acid_storage_duration_value: + collection_method: rank: 54 slot_group: Sample collection and processing - nucleic_acid_storage_duration_unit: + sample_volume_measurement_value: rank: 55 slot_group: Sample collection and processing - available_data_types: + sample_volume_measurement_unit: rank: 56 slot_group: Sample collection and processing - available_data_type_details: + residual_sample_status: rank: 57 slot_group: Sample collection and processing - water_depth: + sample_storage_method: rank: 58 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 59 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 60 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 61 + slot_group: Sample collection and processing + nucleic_acid_storage_duration_value: + rank: 62 + slot_group: Sample collection and processing + nucleic_acid_storage_duration_unit: + rank: 63 + slot_group: Sample collection and processing + available_data_types: + rank: 64 + slot_group: Sample collection and processing + available_data_type_details: + rank: 65 + slot_group: Sample collection and processing + water_depth: + rank: 66 slot_group: Environmental conditions and measurements water_depth_units: - rank: 59 + rank: 67 slot_group: Environmental conditions and measurements sediment_depth: - rank: 60 + rank: 68 slot_group: Environmental conditions and measurements sediment_depth_units: - rank: 61 + rank: 69 slot_group: Environmental conditions and measurements air_temperature: - rank: 62 + rank: 70 slot_group: Environmental conditions and measurements air_temperature_units: - rank: 63 + rank: 71 slot_group: Environmental conditions and measurements water_temperature: - rank: 64 + rank: 72 slot_group: Environmental conditions and measurements water_temperature_units: - rank: 65 + rank: 73 slot_group: Environmental conditions and measurements - weather_type: - rank: 66 + sampling_weather_conditions: + rank: 74 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 75 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 76 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 77 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 78 slot_group: Environmental conditions and measurements host_common_name: - rank: 67 + rank: 79 slot_group: Host information host_scientific_name: - rank: 68 + rank: 80 slot_group: Host information host_ecotype: - rank: 69 + rank: 81 slot_group: Host information host_breed: - rank: 70 + rank: 82 slot_group: Host information host_food_production_name: - rank: 71 + rank: 83 slot_group: Host information host_age_bin: - rank: 72 + rank: 84 slot_group: Host information host_disease: - rank: 73 + rank: 85 slot_group: Host information microbiological_method: - rank: 74 + rank: 86 slot_group: Strain and isolation information strain: - rank: 75 + rank: 87 slot_group: Strain and isolation information isolate_id: - rank: 76 + rank: 88 slot_group: Strain and isolation information alternative_isolate_id: - rank: 77 + rank: 89 slot_group: Strain and isolation information progeny_isolate_id: - rank: 78 + rank: 90 slot_group: Strain and isolation information irida_isolate_id: - rank: 79 + rank: 91 slot_group: Strain and isolation information irida_project_id: - rank: 80 + rank: 92 slot_group: Strain and isolation information isolated_by: - rank: 81 + rank: 93 slot_group: Strain and isolation information isolated_by_laboratory_name: - rank: 82 + rank: 94 slot_group: Strain and isolation information isolated_by_contact_name: - rank: 83 + rank: 95 slot_group: Strain and isolation information isolated_by_contact_email: - rank: 84 + rank: 96 slot_group: Strain and isolation information isolation_date: - rank: 85 + rank: 97 slot_group: Strain and isolation information isolate_received_date: - rank: 86 + rank: 98 slot_group: Strain and isolation information organism: - rank: 87 + rank: 99 slot_group: Strain and isolation information taxonomic_identification_process: - rank: 88 + rank: 100 slot_group: Strain and isolation information taxonomic_identification_process_details: - rank: 89 + rank: 101 slot_group: Strain and isolation information serovar: - rank: 90 + rank: 102 slot_group: Strain and isolation information serotyping_method: - rank: 91 + rank: 103 slot_group: Strain and isolation information phagetype: - rank: 92 + rank: 104 slot_group: Strain and isolation information library_id: - rank: 93 + rank: 105 slot_group: Sequence information sequenced_by: - rank: 94 + rank: 106 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 95 + rank: 107 slot_group: Sequence information sequenced_by_contact_name: - rank: 96 + rank: 108 slot_group: Sequence information sequenced_by_contact_email: - rank: 97 + rank: 109 slot_group: Sequence information purpose_of_sequencing: - rank: 98 + rank: 110 slot_group: Sequence information sequencing_project_name: - rank: 99 + rank: 111 slot_group: Sequence information sequencing_platform: - rank: 100 + rank: 112 slot_group: Sequence information sequencing_instrument: - rank: 101 + rank: 113 slot_group: Sequence information sequencing_assay_type: - rank: 102 + rank: 114 slot_group: Sequence information library_preparation_kit: - rank: 103 + rank: 115 slot_group: Sequence information dna_fragment_length: - rank: 104 + rank: 116 slot_group: Sequence information genomic_target_enrichment_method: - rank: 105 + rank: 117 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 106 + rank: 118 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 107 + rank: 119 slot_group: Sequence information amplicon_size: - rank: 108 + rank: 120 slot_group: Sequence information sequencing_flow_cell_version: - rank: 109 + rank: 121 slot_group: Sequence information sequencing_protocol: - rank: 110 + rank: 122 slot_group: Sequence information r1_fastq_filename: - rank: 111 + rank: 123 slot_group: Sequence information r2_fastq_filename: - rank: 112 + rank: 124 slot_group: Sequence information fast5_filename: - rank: 113 + rank: 125 slot_group: Sequence information assembly_filename: - rank: 114 + rank: 126 slot_group: Sequence information quality_control_method_name: - rank: 115 + rank: 127 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 116 + rank: 128 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 117 + rank: 129 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 118 + rank: 130 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 119 + rank: 131 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 120 + rank: 132 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 121 + rank: 133 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 122 + rank: 134 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 123 + rank: 135 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 124 + rank: 136 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 125 + rank: 137 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 126 + rank: 138 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 127 + rank: 139 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 128 + rank: 140 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 129 + rank: 141 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 130 + rank: 142 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 131 + rank: 143 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 132 + rank: 144 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 133 + rank: 145 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 134 + rank: 146 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 135 + rank: 147 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 136 + rank: 148 slot_group: Bioinformatics and QC metrics n50: - rank: 137 + rank: 149 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 138 + rank: 150 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 139 + rank: 151 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 140 + rank: 152 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 141 + rank: 153 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 142 + rank: 154 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 143 + rank: 155 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 144 + rank: 156 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 145 + rank: 157 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 146 + rank: 158 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 147 + rank: 159 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 148 + rank: 160 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 149 + rank: 161 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 150 + rank: 162 slot_group: Taxonomic identification information sequence_submitted_by: - rank: 151 + rank: 163 slot_group: Public repository information sequence_submitted_by_contact_name: - rank: 152 + rank: 164 slot_group: Public repository information sequence_submitted_by_contact_email: - rank: 153 + rank: 165 slot_group: Public repository information publication_id: - rank: 154 + rank: 166 slot_group: Public repository information attribute_package: - rank: 155 + rank: 167 slot_group: Public repository information bioproject_accession: - rank: 156 + rank: 168 slot_group: Public repository information biosample_accession: - rank: 157 + rank: 169 slot_group: Public repository information sra_accession: - rank: 158 + rank: 170 slot_group: Public repository information genbank_accession: - rank: 159 + rank: 171 slot_group: Public repository information prevalence_metrics: - rank: 160 + rank: 172 slot_group: Risk assessment information prevalence_metrics_details: - rank: 161 + rank: 173 slot_group: Risk assessment information stage_of_production: - rank: 162 + rank: 174 slot_group: Risk assessment information experimental_intervention: - rank: 163 + rank: 175 slot_group: Risk assessment information experiment_intervention_details: - rank: 164 + rank: 176 slot_group: Risk assessment information amr_testing_by: - rank: 165 + rank: 177 slot_group: Antimicrobial resistance amr_testing_by_laboratory_name: - rank: 166 + rank: 178 slot_group: Antimicrobial resistance amr_testing_by_contact_name: - rank: 167 + rank: 179 slot_group: Antimicrobial resistance amr_testing_by_contact_email: - rank: 168 + rank: 180 slot_group: Antimicrobial resistance amr_testing_date: - rank: 169 + rank: 181 slot_group: Antimicrobial resistance amikacin_resistance_phenotype: - rank: 170 + rank: 182 slot_group: Antimicrobial resistance amikacin_measurement: - rank: 171 + rank: 183 slot_group: Antimicrobial resistance amikacin_measurement_units: - rank: 172 + rank: 184 slot_group: Antimicrobial resistance amikacin_measurement_sign: - rank: 173 + rank: 185 slot_group: Antimicrobial resistance amikacin_laboratory_typing_method: - rank: 174 + rank: 186 slot_group: Antimicrobial resistance amikacin_laboratory_typing_platform: - rank: 175 + rank: 187 slot_group: Antimicrobial resistance amikacin_laboratory_typing_platform_version: - rank: 176 + rank: 188 slot_group: Antimicrobial resistance amikacin_vendor_name: - rank: 177 + rank: 189 slot_group: Antimicrobial resistance amikacin_testing_standard: - rank: 178 + rank: 190 slot_group: Antimicrobial resistance amikacin_testing_standard_version: - rank: 179 + rank: 191 slot_group: Antimicrobial resistance amikacin_testing_standard_details: - rank: 180 + rank: 192 slot_group: Antimicrobial resistance amikacin_susceptible_breakpoint: - rank: 181 + rank: 193 slot_group: Antimicrobial resistance amikacin_intermediate_breakpoint: - rank: 182 + rank: 194 slot_group: Antimicrobial resistance amikacin_resistant_breakpoint: - rank: 183 + rank: 195 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_resistance_phenotype: - rank: 184 + rank: 196 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_measurement: - rank: 185 + rank: 197 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_measurement_units: - rank: 186 + rank: 198 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_measurement_sign: - rank: 187 + rank: 199 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_laboratory_typing_method: - rank: 188 + rank: 200 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_laboratory_typing_platform: - rank: 189 + rank: 201 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_laboratory_typing_platform_version: - rank: 190 + rank: 202 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_vendor_name: - rank: 191 + rank: 203 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_testing_standard: - rank: 192 + rank: 204 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_testing_standard_version: - rank: 193 + rank: 205 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_testing_standard_details: - rank: 194 + rank: 206 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_susceptible_breakpoint: - rank: 195 + rank: 207 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_intermediate_breakpoint: - rank: 196 + rank: 208 slot_group: Antimicrobial resistance amoxicillinclavulanic_acid_resistant_breakpoint: - rank: 197 + rank: 209 slot_group: Antimicrobial resistance ampicillin_resistance_phenotype: - rank: 198 + rank: 210 slot_group: Antimicrobial resistance ampicillin_measurement: - rank: 199 + rank: 211 slot_group: Antimicrobial resistance ampicillin_measurement_units: - rank: 200 + rank: 212 slot_group: Antimicrobial resistance ampicillin_measurement_sign: - rank: 201 + rank: 213 slot_group: Antimicrobial resistance ampicillin_laboratory_typing_method: - rank: 202 + rank: 214 slot_group: Antimicrobial resistance ampicillin_laboratory_typing_platform: - rank: 203 + rank: 215 slot_group: Antimicrobial resistance ampicillin_laboratory_typing_platform_version: - rank: 204 + rank: 216 slot_group: Antimicrobial resistance ampicillin_vendor_name: - rank: 205 + rank: 217 slot_group: Antimicrobial resistance ampicillin_testing_standard: - rank: 206 + rank: 218 slot_group: Antimicrobial resistance ampicillin_testing_standard_version: - rank: 207 + rank: 219 slot_group: Antimicrobial resistance ampicillin_testing_standard_details: - rank: 208 + rank: 220 slot_group: Antimicrobial resistance ampicillin_susceptible_breakpoint: - rank: 209 + rank: 221 slot_group: Antimicrobial resistance ampicillin_intermediate_breakpoint: - rank: 210 + rank: 222 slot_group: Antimicrobial resistance ampicillin_resistant_breakpoint: - rank: 211 + rank: 223 slot_group: Antimicrobial resistance azithromycin_resistance_phenotype: - rank: 212 + rank: 224 slot_group: Antimicrobial resistance azithromycin_measurement: - rank: 213 + rank: 225 slot_group: Antimicrobial resistance azithromycin_measurement_units: - rank: 214 + rank: 226 slot_group: Antimicrobial resistance azithromycin_measurement_sign: - rank: 215 + rank: 227 slot_group: Antimicrobial resistance azithromycin_laboratory_typing_method: - rank: 216 + rank: 228 slot_group: Antimicrobial resistance azithromycin_laboratory_typing_platform: - rank: 217 + rank: 229 slot_group: Antimicrobial resistance azithromycin_laboratory_typing_platform_version: - rank: 218 + rank: 230 slot_group: Antimicrobial resistance azithromycin_vendor_name: - rank: 219 + rank: 231 slot_group: Antimicrobial resistance azithromycin_testing_standard: - rank: 220 + rank: 232 slot_group: Antimicrobial resistance azithromycin_testing_standard_version: - rank: 221 + rank: 233 slot_group: Antimicrobial resistance azithromycin_testing_standard_details: - rank: 222 + rank: 234 slot_group: Antimicrobial resistance azithromycin_susceptible_breakpoint: - rank: 223 + rank: 235 slot_group: Antimicrobial resistance azithromycin_intermediate_breakpoint: - rank: 224 + rank: 236 slot_group: Antimicrobial resistance azithromycin_resistant_breakpoint: - rank: 225 + rank: 237 slot_group: Antimicrobial resistance cefazolin_resistance_phenotype: - rank: 226 + rank: 238 slot_group: Antimicrobial resistance cefazolin_measurement: - rank: 227 + rank: 239 slot_group: Antimicrobial resistance cefazolin_measurement_units: - rank: 228 + rank: 240 slot_group: Antimicrobial resistance cefazolin_measurement_sign: - rank: 229 + rank: 241 slot_group: Antimicrobial resistance cefazolin_laboratory_typing_method: - rank: 230 + rank: 242 slot_group: Antimicrobial resistance cefazolin_laboratory_typing_platform: - rank: 231 + rank: 243 slot_group: Antimicrobial resistance cefazolin_laboratory_typing_platform_version: - rank: 232 + rank: 244 slot_group: Antimicrobial resistance cefazolin_vendor_name: - rank: 233 + rank: 245 slot_group: Antimicrobial resistance cefazolin_testing_standard: - rank: 234 + rank: 246 slot_group: Antimicrobial resistance cefazolin_testing_standard_version: - rank: 235 + rank: 247 slot_group: Antimicrobial resistance cefazolin_testing_standard_details: - rank: 236 + rank: 248 slot_group: Antimicrobial resistance cefazolin_susceptible_breakpoint: - rank: 237 + rank: 249 slot_group: Antimicrobial resistance cefazolin_intermediate_breakpoint: - rank: 238 + rank: 250 slot_group: Antimicrobial resistance cefazolin_resistant_breakpoint: - rank: 239 + rank: 251 slot_group: Antimicrobial resistance cefepime_resistance_phenotype: - rank: 240 + rank: 252 slot_group: Antimicrobial resistance cefepime_measurement: - rank: 241 + rank: 253 slot_group: Antimicrobial resistance cefepime_measurement_units: - rank: 242 + rank: 254 slot_group: Antimicrobial resistance cefepime_measurement_sign: - rank: 243 + rank: 255 slot_group: Antimicrobial resistance cefepime_laboratory_typing_method: - rank: 244 + rank: 256 slot_group: Antimicrobial resistance cefepime_laboratory_typing_platform: - rank: 245 + rank: 257 slot_group: Antimicrobial resistance cefepime_laboratory_typing_platform_version: - rank: 246 + rank: 258 slot_group: Antimicrobial resistance cefepime_vendor_name: - rank: 247 + rank: 259 slot_group: Antimicrobial resistance cefepime_testing_standard: - rank: 248 + rank: 260 slot_group: Antimicrobial resistance cefepime_testing_standard_version: - rank: 249 + rank: 261 slot_group: Antimicrobial resistance cefepime_testing_standard_details: - rank: 250 + rank: 262 slot_group: Antimicrobial resistance cefepime_susceptible_breakpoint: - rank: 251 + rank: 263 slot_group: Antimicrobial resistance cefepime_intermediate_breakpoint: - rank: 252 + rank: 264 slot_group: Antimicrobial resistance cefepime_resistant_breakpoint: - rank: 253 + rank: 265 slot_group: Antimicrobial resistance cefotaxime_resistance_phenotype: - rank: 254 + rank: 266 slot_group: Antimicrobial resistance cefotaxime_measurement: - rank: 255 + rank: 267 slot_group: Antimicrobial resistance cefotaxime_measurement_units: - rank: 256 + rank: 268 slot_group: Antimicrobial resistance cefotaxime_measurement_sign: - rank: 257 + rank: 269 slot_group: Antimicrobial resistance cefotaxime_laboratory_typing_method: - rank: 258 + rank: 270 slot_group: Antimicrobial resistance cefotaxime_laboratory_typing_platform: - rank: 259 + rank: 271 slot_group: Antimicrobial resistance cefotaxime_laboratory_typing_platform_version: - rank: 260 + rank: 272 slot_group: Antimicrobial resistance cefotaxime_vendor_name: - rank: 261 + rank: 273 slot_group: Antimicrobial resistance cefotaxime_testing_standard: - rank: 262 + rank: 274 slot_group: Antimicrobial resistance cefotaxime_testing_standard_version: - rank: 263 + rank: 275 slot_group: Antimicrobial resistance cefotaxime_testing_standard_details: - rank: 264 + rank: 276 slot_group: Antimicrobial resistance cefotaxime_susceptible_breakpoint: - rank: 265 + rank: 277 slot_group: Antimicrobial resistance cefotaxime_intermediate_breakpoint: - rank: 266 + rank: 278 slot_group: Antimicrobial resistance cefotaxime_resistant_breakpoint: - rank: 267 + rank: 279 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_resistance_phenotype: - rank: 268 + rank: 280 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_measurement: - rank: 269 + rank: 281 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_measurement_units: - rank: 270 + rank: 282 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_measurement_sign: - rank: 271 + rank: 283 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_laboratory_typing_method: - rank: 272 + rank: 284 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_laboratory_typing_platform: - rank: 273 + rank: 285 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_laboratory_typing_platform_version: - rank: 274 + rank: 286 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_vendor_name: - rank: 275 + rank: 287 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_testing_standard: - rank: 276 + rank: 288 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_testing_standard_version: - rank: 277 + rank: 289 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_testing_standard_details: - rank: 278 + rank: 290 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_susceptible_breakpoint: - rank: 279 + rank: 291 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_intermediate_breakpoint: - rank: 280 + rank: 292 slot_group: Antimicrobial resistance cefotaximeclavulanic_acid_resistant_breakpoint: - rank: 281 + rank: 293 slot_group: Antimicrobial resistance cefoxitin_resistance_phenotype: - rank: 282 + rank: 294 slot_group: Antimicrobial resistance cefoxitin_measurement: - rank: 283 + rank: 295 slot_group: Antimicrobial resistance cefoxitin_measurement_units: - rank: 284 + rank: 296 slot_group: Antimicrobial resistance cefoxitin_measurement_sign: - rank: 285 + rank: 297 slot_group: Antimicrobial resistance cefoxitin_laboratory_typing_method: - rank: 286 + rank: 298 slot_group: Antimicrobial resistance cefoxitin_laboratory_typing_platform: - rank: 287 + rank: 299 slot_group: Antimicrobial resistance cefoxitin_laboratory_typing_platform_version: - rank: 288 + rank: 300 slot_group: Antimicrobial resistance cefoxitin_vendor_name: - rank: 289 + rank: 301 slot_group: Antimicrobial resistance cefoxitin_testing_standard: - rank: 290 + rank: 302 slot_group: Antimicrobial resistance cefoxitin_testing_standard_version: - rank: 291 + rank: 303 slot_group: Antimicrobial resistance cefoxitin_testing_standard_details: - rank: 292 + rank: 304 slot_group: Antimicrobial resistance cefoxitin_susceptible_breakpoint: - rank: 293 + rank: 305 slot_group: Antimicrobial resistance cefoxitin_intermediate_breakpoint: - rank: 294 + rank: 306 slot_group: Antimicrobial resistance cefoxitin_resistant_breakpoint: - rank: 295 + rank: 307 slot_group: Antimicrobial resistance cefpodoxime_resistance_phenotype: - rank: 296 + rank: 308 slot_group: Antimicrobial resistance cefpodoxime_measurement: - rank: 297 + rank: 309 slot_group: Antimicrobial resistance cefpodoxime_measurement_units: - rank: 298 + rank: 310 slot_group: Antimicrobial resistance cefpodoxime_measurement_sign: - rank: 299 + rank: 311 slot_group: Antimicrobial resistance cefpodoxime_laboratory_typing_method: - rank: 300 + rank: 312 slot_group: Antimicrobial resistance cefpodoxime_laboratory_typing_platform: - rank: 301 + rank: 313 slot_group: Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version: - rank: 302 + rank: 314 slot_group: Antimicrobial resistance cefpodoxime_vendor_name: - rank: 303 + rank: 315 slot_group: Antimicrobial resistance cefpodoxime_testing_standard: - rank: 304 + rank: 316 slot_group: Antimicrobial resistance cefpodoxime_testing_standard_version: - rank: 305 + rank: 317 slot_group: Antimicrobial resistance cefpodoxime_testing_standard_details: - rank: 306 + rank: 318 slot_group: Antimicrobial resistance cefpodoxime_susceptible_breakpoint: - rank: 307 + rank: 319 slot_group: Antimicrobial resistance cefpodoxime_intermediate_breakpoint: - rank: 308 + rank: 320 slot_group: Antimicrobial resistance cefpodoxime_resistant_breakpoint: - rank: 309 + rank: 321 slot_group: Antimicrobial resistance ceftazidime_resistance_phenotype: - rank: 310 + rank: 322 slot_group: Antimicrobial resistance ceftazidime_measurement: - rank: 311 + rank: 323 slot_group: Antimicrobial resistance ceftazidime_measurement_units: - rank: 312 + rank: 324 slot_group: Antimicrobial resistance ceftazidime_measurement_sign: - rank: 313 + rank: 325 slot_group: Antimicrobial resistance ceftazidime_laboratory_typing_method: - rank: 314 + rank: 326 slot_group: Antimicrobial resistance ceftazidime_laboratory_typing_platform: - rank: 315 + rank: 327 slot_group: Antimicrobial resistance ceftazidime_laboratory_typing_platform_version: - rank: 316 + rank: 328 slot_group: Antimicrobial resistance ceftazidime_vendor_name: - rank: 317 + rank: 329 slot_group: Antimicrobial resistance ceftazidime_testing_standard: - rank: 318 + rank: 330 slot_group: Antimicrobial resistance ceftazidime_testing_standard_version: - rank: 319 + rank: 331 slot_group: Antimicrobial resistance ceftazidime_testing_standard_details: - rank: 320 + rank: 332 slot_group: Antimicrobial resistance ceftazidime_susceptible_breakpoint: - rank: 321 + rank: 333 slot_group: Antimicrobial resistance ceftazidime_intermediate_breakpoint: - rank: 322 + rank: 334 slot_group: Antimicrobial resistance ceftazidime_resistant_breakpoint: - rank: 323 + rank: 335 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_resistance_phenotype: - rank: 324 + rank: 336 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_measurement: - rank: 325 + rank: 337 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_measurement_units: - rank: 326 + rank: 338 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_measurement_sign: - rank: 327 + rank: 339 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_laboratory_typing_method: - rank: 328 + rank: 340 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_laboratory_typing_platform: - rank: 329 + rank: 341 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_laboratory_typing_platform_version: - rank: 330 + rank: 342 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_vendor_name: - rank: 331 + rank: 343 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_testing_standard: - rank: 332 + rank: 344 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_testing_standard_version: - rank: 333 + rank: 345 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_testing_standard_details: - rank: 334 + rank: 346 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_susceptible_breakpoint: - rank: 335 + rank: 347 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_intermediate_breakpoint: - rank: 336 + rank: 348 slot_group: Antimicrobial resistance ceftazidimeclavulanic_acid_resistant_breakpoint: - rank: 337 + rank: 349 slot_group: Antimicrobial resistance ceftiofur_resistance_phenotype: - rank: 338 + rank: 350 slot_group: Antimicrobial resistance ceftiofur_measurement: - rank: 339 + rank: 351 slot_group: Antimicrobial resistance ceftiofur_measurement_units: - rank: 340 + rank: 352 slot_group: Antimicrobial resistance ceftiofur_measurement_sign: - rank: 341 + rank: 353 slot_group: Antimicrobial resistance ceftiofur_laboratory_typing_method: - rank: 342 + rank: 354 slot_group: Antimicrobial resistance ceftiofur_laboratory_typing_platform: - rank: 343 + rank: 355 slot_group: Antimicrobial resistance ceftiofur_laboratory_typing_platform_version: - rank: 344 + rank: 356 slot_group: Antimicrobial resistance ceftiofur_vendor_name: - rank: 345 + rank: 357 slot_group: Antimicrobial resistance ceftiofur_testing_standard: - rank: 346 + rank: 358 slot_group: Antimicrobial resistance ceftiofur_testing_standard_version: - rank: 347 + rank: 359 slot_group: Antimicrobial resistance ceftiofur_testing_standard_details: - rank: 348 + rank: 360 slot_group: Antimicrobial resistance ceftiofur_susceptible_breakpoint: - rank: 349 + rank: 361 slot_group: Antimicrobial resistance ceftiofur_intermediate_breakpoint: - rank: 350 + rank: 362 slot_group: Antimicrobial resistance ceftiofur_resistant_breakpoint: - rank: 351 + rank: 363 slot_group: Antimicrobial resistance ceftriaxone_resistance_phenotype: - rank: 352 + rank: 364 slot_group: Antimicrobial resistance ceftriaxone_measurement: - rank: 353 + rank: 365 slot_group: Antimicrobial resistance ceftriaxone_measurement_units: - rank: 354 + rank: 366 slot_group: Antimicrobial resistance ceftriaxone_measurement_sign: - rank: 355 + rank: 367 slot_group: Antimicrobial resistance ceftriaxone_laboratory_typing_method: - rank: 356 + rank: 368 slot_group: Antimicrobial resistance ceftriaxone_laboratory_typing_platform: - rank: 357 + rank: 369 slot_group: Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version: - rank: 358 + rank: 370 slot_group: Antimicrobial resistance ceftriaxone_vendor_name: - rank: 359 + rank: 371 slot_group: Antimicrobial resistance ceftriaxone_testing_standard: - rank: 360 + rank: 372 slot_group: Antimicrobial resistance ceftriaxone_testing_standard_version: - rank: 361 + rank: 373 slot_group: Antimicrobial resistance ceftriaxone_testing_standard_details: - rank: 362 + rank: 374 slot_group: Antimicrobial resistance ceftriaxone_susceptible_breakpoint: - rank: 363 + rank: 375 slot_group: Antimicrobial resistance ceftriaxone_intermediate_breakpoint: - rank: 364 + rank: 376 slot_group: Antimicrobial resistance ceftriaxone_resistant_breakpoint: - rank: 365 + rank: 377 slot_group: Antimicrobial resistance cephalothin_resistance_phenotype: - rank: 366 + rank: 378 slot_group: Antimicrobial resistance cephalothin_measurement: - rank: 367 + rank: 379 slot_group: Antimicrobial resistance cephalothin_measurement_units: - rank: 368 + rank: 380 slot_group: Antimicrobial resistance cephalothin_measurement_sign: - rank: 369 + rank: 381 slot_group: Antimicrobial resistance cephalothin_laboratory_typing_method: - rank: 370 + rank: 382 slot_group: Antimicrobial resistance cephalothin_laboratory_typing_platform: - rank: 371 + rank: 383 slot_group: Antimicrobial resistance cephalothin_laboratory_typing_platform_version: - rank: 372 + rank: 384 slot_group: Antimicrobial resistance cephalothin_vendor_name: - rank: 373 + rank: 385 slot_group: Antimicrobial resistance cephalothin_testing_standard: - rank: 374 + rank: 386 slot_group: Antimicrobial resistance cephalothin_testing_standard_version: - rank: 375 + rank: 387 slot_group: Antimicrobial resistance cephalothin_testing_standard_details: - rank: 376 + rank: 388 slot_group: Antimicrobial resistance cephalothin_susceptible_breakpoint: - rank: 377 + rank: 389 slot_group: Antimicrobial resistance cephalothin_intermediate_breakpoint: - rank: 378 + rank: 390 slot_group: Antimicrobial resistance cephalothin_resistant_breakpoint: - rank: 379 + rank: 391 slot_group: Antimicrobial resistance chloramphenicol_resistance_phenotype: - rank: 380 + rank: 392 slot_group: Antimicrobial resistance chloramphenicol_measurement: - rank: 381 + rank: 393 slot_group: Antimicrobial resistance chloramphenicol_measurement_units: - rank: 382 + rank: 394 slot_group: Antimicrobial resistance chloramphenicol_measurement_sign: - rank: 383 + rank: 395 slot_group: Antimicrobial resistance chloramphenicol_laboratory_typing_method: - rank: 384 + rank: 396 slot_group: Antimicrobial resistance chloramphenicol_laboratory_typing_platform: - rank: 385 + rank: 397 slot_group: Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version: - rank: 386 + rank: 398 slot_group: Antimicrobial resistance chloramphenicol_vendor_name: - rank: 387 + rank: 399 slot_group: Antimicrobial resistance chloramphenicol_testing_standard: - rank: 388 + rank: 400 slot_group: Antimicrobial resistance chloramphenicol_testing_standard_version: - rank: 389 + rank: 401 slot_group: Antimicrobial resistance chloramphenicol_testing_standard_details: - rank: 390 + rank: 402 slot_group: Antimicrobial resistance chloramphenicol_susceptible_breakpoint: - rank: 391 + rank: 403 slot_group: Antimicrobial resistance chloramphenicol_intermediate_breakpoint: - rank: 392 + rank: 404 slot_group: Antimicrobial resistance chloramphenicol_resistant_breakpoint: - rank: 393 + rank: 405 slot_group: Antimicrobial resistance ciprofloxacin_resistance_phenotype: - rank: 394 + rank: 406 slot_group: Antimicrobial resistance ciprofloxacin_measurement: - rank: 395 + rank: 407 slot_group: Antimicrobial resistance ciprofloxacin_measurement_units: - rank: 396 + rank: 408 slot_group: Antimicrobial resistance ciprofloxacin_measurement_sign: - rank: 397 + rank: 409 slot_group: Antimicrobial resistance ciprofloxacin_laboratory_typing_method: - rank: 398 + rank: 410 slot_group: Antimicrobial resistance ciprofloxacin_laboratory_typing_platform: - rank: 399 + rank: 411 slot_group: Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version: - rank: 400 + rank: 412 slot_group: Antimicrobial resistance ciprofloxacin_vendor_name: - rank: 401 + rank: 413 slot_group: Antimicrobial resistance ciprofloxacin_testing_standard: - rank: 402 + rank: 414 slot_group: Antimicrobial resistance ciprofloxacin_testing_standard_version: - rank: 403 + rank: 415 slot_group: Antimicrobial resistance ciprofloxacin_testing_standard_details: - rank: 404 + rank: 416 slot_group: Antimicrobial resistance ciprofloxacin_susceptible_breakpoint: - rank: 405 + rank: 417 slot_group: Antimicrobial resistance ciprofloxacin_intermediate_breakpoint: - rank: 406 + rank: 418 slot_group: Antimicrobial resistance ciprofloxacin_resistant_breakpoint: - rank: 407 + rank: 419 slot_group: Antimicrobial resistance clindamycin_resistance_phenotype: - rank: 408 + rank: 420 slot_group: Antimicrobial resistance clindamycin_measurement: - rank: 409 + rank: 421 slot_group: Antimicrobial resistance clindamycin_measurement_units: - rank: 410 + rank: 422 slot_group: Antimicrobial resistance clindamycin_measurement_sign: - rank: 411 + rank: 423 slot_group: Antimicrobial resistance clindamycin_laboratory_typing_method: - rank: 412 + rank: 424 slot_group: Antimicrobial resistance clindamycin_laboratory_typing_platform: - rank: 413 + rank: 425 slot_group: Antimicrobial resistance clindamycin_laboratory_typing_platform_version: - rank: 414 + rank: 426 slot_group: Antimicrobial resistance clindamycin_vendor_name: - rank: 415 + rank: 427 slot_group: Antimicrobial resistance clindamycin_testing_standard: - rank: 416 + rank: 428 slot_group: Antimicrobial resistance clindamycin_testing_standard_version: - rank: 417 + rank: 429 slot_group: Antimicrobial resistance clindamycin_testing_standard_details: - rank: 418 + rank: 430 slot_group: Antimicrobial resistance clindamycin_susceptible_breakpoint: - rank: 419 + rank: 431 slot_group: Antimicrobial resistance clindamycin_intermediate_breakpoint: - rank: 420 + rank: 432 slot_group: Antimicrobial resistance clindamycin_resistant_breakpoint: - rank: 421 + rank: 433 slot_group: Antimicrobial resistance doxycycline_resistance_phenotype: - rank: 422 + rank: 434 slot_group: Antimicrobial resistance doxycycline_measurement: - rank: 423 + rank: 435 slot_group: Antimicrobial resistance doxycycline_measurement_units: - rank: 424 + rank: 436 slot_group: Antimicrobial resistance doxycycline_measurement_sign: - rank: 425 + rank: 437 slot_group: Antimicrobial resistance doxycycline_laboratory_typing_method: - rank: 426 + rank: 438 slot_group: Antimicrobial resistance doxycycline_laboratory_typing_platform: - rank: 427 + rank: 439 slot_group: Antimicrobial resistance doxycycline_laboratory_typing_platform_version: - rank: 428 + rank: 440 slot_group: Antimicrobial resistance doxycycline_vendor_name: - rank: 429 + rank: 441 slot_group: Antimicrobial resistance doxycycline_testing_standard: - rank: 430 + rank: 442 slot_group: Antimicrobial resistance doxycycline_testing_standard_version: - rank: 431 + rank: 443 slot_group: Antimicrobial resistance doxycycline_testing_standard_details: - rank: 432 + rank: 444 slot_group: Antimicrobial resistance doxycycline_susceptible_breakpoint: - rank: 433 + rank: 445 slot_group: Antimicrobial resistance doxycycline_intermediate_breakpoint: - rank: 434 + rank: 446 slot_group: Antimicrobial resistance doxycycline_resistant_breakpoint: - rank: 435 + rank: 447 slot_group: Antimicrobial resistance enrofloxacin_resistance_phenotype: - rank: 436 + rank: 448 slot_group: Antimicrobial resistance enrofloxacin_measurement: - rank: 437 + rank: 449 slot_group: Antimicrobial resistance enrofloxacin_measurement_units: - rank: 438 + rank: 450 slot_group: Antimicrobial resistance enrofloxacin_measurement_sign: - rank: 439 + rank: 451 slot_group: Antimicrobial resistance enrofloxacin_laboratory_typing_method: - rank: 440 + rank: 452 slot_group: Antimicrobial resistance enrofloxacin_laboratory_typing_platform: - rank: 441 + rank: 453 slot_group: Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version: - rank: 442 + rank: 454 slot_group: Antimicrobial resistance enrofloxacin_vendor_name: - rank: 443 + rank: 455 slot_group: Antimicrobial resistance enrofloxacin_testing_standard: - rank: 444 + rank: 456 slot_group: Antimicrobial resistance enrofloxacin_testing_standard_version: - rank: 445 + rank: 457 slot_group: Antimicrobial resistance enrofloxacin_testing_standard_details: - rank: 446 + rank: 458 slot_group: Antimicrobial resistance enrofloxacin_susceptible_breakpoint: - rank: 447 + rank: 459 slot_group: Antimicrobial resistance enrofloxacin_intermediate_breakpoint: - rank: 448 + rank: 460 slot_group: Antimicrobial resistance enrofloxacin_resistant_breakpoint: - rank: 449 + rank: 461 slot_group: Antimicrobial resistance erythromycin_resistance_phenotype: - rank: 450 + rank: 462 slot_group: Antimicrobial resistance erythromycin_measurement: - rank: 451 + rank: 463 slot_group: Antimicrobial resistance erythromycin_measurement_units: - rank: 452 + rank: 464 slot_group: Antimicrobial resistance erythromycin_measurement_sign: - rank: 453 + rank: 465 slot_group: Antimicrobial resistance erythromycin_laboratory_typing_method: - rank: 454 + rank: 466 slot_group: Antimicrobial resistance erythromycin_laboratory_typing_platform: - rank: 455 + rank: 467 slot_group: Antimicrobial resistance erythromycin_laboratory_typing_platform_version: - rank: 456 + rank: 468 slot_group: Antimicrobial resistance erythromycin_vendor_name: - rank: 457 + rank: 469 slot_group: Antimicrobial resistance erythromycin_testing_standard: - rank: 458 + rank: 470 slot_group: Antimicrobial resistance erythromycin_testing_standard_version: - rank: 459 + rank: 471 slot_group: Antimicrobial resistance erythromycin_testing_standard_details: - rank: 460 + rank: 472 slot_group: Antimicrobial resistance erythromycin_susceptible_breakpoint: - rank: 461 + rank: 473 slot_group: Antimicrobial resistance erythromycin_intermediate_breakpoint: - rank: 462 + rank: 474 slot_group: Antimicrobial resistance erythromycin_resistant_breakpoint: - rank: 463 + rank: 475 slot_group: Antimicrobial resistance florfenicol_resistance_phenotype: - rank: 464 + rank: 476 slot_group: Antimicrobial resistance florfenicol_measurement: - rank: 465 + rank: 477 slot_group: Antimicrobial resistance florfenicol_measurement_units: - rank: 466 + rank: 478 slot_group: Antimicrobial resistance florfenicol_measurement_sign: - rank: 467 + rank: 479 slot_group: Antimicrobial resistance florfenicol_laboratory_typing_method: - rank: 468 + rank: 480 slot_group: Antimicrobial resistance florfenicol_laboratory_typing_platform: - rank: 469 + rank: 481 slot_group: Antimicrobial resistance florfenicol_laboratory_typing_platform_version: - rank: 470 + rank: 482 slot_group: Antimicrobial resistance florfenicol_vendor_name: - rank: 471 + rank: 483 slot_group: Antimicrobial resistance florfenicol_testing_standard: - rank: 472 + rank: 484 slot_group: Antimicrobial resistance florfenicol_testing_standard_version: - rank: 473 + rank: 485 slot_group: Antimicrobial resistance florfenicol_testing_standard_details: - rank: 474 + rank: 486 slot_group: Antimicrobial resistance florfenicol_susceptible_breakpoint: - rank: 475 + rank: 487 slot_group: Antimicrobial resistance florfenicol_intermediate_breakpoint: - rank: 476 + rank: 488 slot_group: Antimicrobial resistance florfenicol_resistant_breakpoint: - rank: 477 + rank: 489 slot_group: Antimicrobial resistance gentamicin_resistance_phenotype: - rank: 478 + rank: 490 slot_group: Antimicrobial resistance gentamicin_measurement: - rank: 479 + rank: 491 slot_group: Antimicrobial resistance gentamicin_measurement_units: - rank: 480 + rank: 492 slot_group: Antimicrobial resistance gentamicin_measurement_sign: - rank: 481 + rank: 493 slot_group: Antimicrobial resistance gentamicin_laboratory_typing_method: - rank: 482 + rank: 494 slot_group: Antimicrobial resistance gentamicin_laboratory_typing_platform: - rank: 483 + rank: 495 slot_group: Antimicrobial resistance gentamicin_laboratory_typing_platform_version: - rank: 484 + rank: 496 slot_group: Antimicrobial resistance gentamicin_vendor_name: - rank: 485 + rank: 497 slot_group: Antimicrobial resistance gentamicin_testing_standard: - rank: 486 + rank: 498 slot_group: Antimicrobial resistance gentamicin_testing_standard_version: - rank: 487 + rank: 499 slot_group: Antimicrobial resistance gentamicin_testing_standard_details: - rank: 488 + rank: 500 slot_group: Antimicrobial resistance gentamicin_susceptible_breakpoint: - rank: 489 + rank: 501 slot_group: Antimicrobial resistance gentamicin_intermediate_breakpoint: - rank: 490 + rank: 502 slot_group: Antimicrobial resistance gentamicin_resistant_breakpoint: - rank: 491 + rank: 503 slot_group: Antimicrobial resistance imipenem_resistance_phenotype: - rank: 492 + rank: 504 slot_group: Antimicrobial resistance imipenem_measurement: - rank: 493 + rank: 505 slot_group: Antimicrobial resistance imipenem_measurement_units: - rank: 494 + rank: 506 slot_group: Antimicrobial resistance imipenem_measurement_sign: - rank: 495 + rank: 507 slot_group: Antimicrobial resistance imipenem_laboratory_typing_method: - rank: 496 + rank: 508 slot_group: Antimicrobial resistance imipenem_laboratory_typing_platform: - rank: 497 + rank: 509 slot_group: Antimicrobial resistance imipenem_laboratory_typing_platform_version: - rank: 498 + rank: 510 slot_group: Antimicrobial resistance imipenem_vendor_name: - rank: 499 + rank: 511 slot_group: Antimicrobial resistance imipenem_testing_standard: - rank: 500 + rank: 512 slot_group: Antimicrobial resistance imipenem_testing_standard_version: - rank: 501 + rank: 513 slot_group: Antimicrobial resistance imipenem_testing_standard_details: - rank: 502 + rank: 514 slot_group: Antimicrobial resistance imipenem_susceptible_breakpoint: - rank: 503 + rank: 515 slot_group: Antimicrobial resistance imipenem_intermediate_breakpoint: - rank: 504 + rank: 516 slot_group: Antimicrobial resistance imipenem_resistant_breakpoint: - rank: 505 + rank: 517 slot_group: Antimicrobial resistance kanamycin_resistance_phenotype: - rank: 506 + rank: 518 slot_group: Antimicrobial resistance kanamycin_measurement: - rank: 507 + rank: 519 slot_group: Antimicrobial resistance kanamycin_measurement_units: - rank: 508 + rank: 520 slot_group: Antimicrobial resistance kanamycin_measurement_sign: - rank: 509 + rank: 521 slot_group: Antimicrobial resistance kanamycin_laboratory_typing_method: - rank: 510 + rank: 522 slot_group: Antimicrobial resistance kanamycin_laboratory_typing_platform: - rank: 511 + rank: 523 slot_group: Antimicrobial resistance kanamycin_laboratory_typing_platform_version: - rank: 512 + rank: 524 slot_group: Antimicrobial resistance kanamycin_vendor_name: - rank: 513 + rank: 525 slot_group: Antimicrobial resistance kanamycin_testing_standard: - rank: 514 + rank: 526 slot_group: Antimicrobial resistance kanamycin_testing_standard_version: - rank: 515 + rank: 527 slot_group: Antimicrobial resistance kanamycin_testing_standard_details: - rank: 516 + rank: 528 slot_group: Antimicrobial resistance kanamycin_susceptible_breakpoint: - rank: 517 + rank: 529 slot_group: Antimicrobial resistance kanamycin_intermediate_breakpoint: - rank: 518 + rank: 530 slot_group: Antimicrobial resistance kanamycin_resistant_breakpoint: - rank: 519 + rank: 531 slot_group: Antimicrobial resistance levofloxacin_resistance_phenotype: - rank: 520 + rank: 532 slot_group: Antimicrobial resistance levofloxacin_measurement: - rank: 521 + rank: 533 slot_group: Antimicrobial resistance levofloxacin_measurement_units: - rank: 522 + rank: 534 slot_group: Antimicrobial resistance levofloxacin_measurement_sign: - rank: 523 + rank: 535 slot_group: Antimicrobial resistance levofloxacin_laboratory_typing_method: - rank: 524 + rank: 536 slot_group: Antimicrobial resistance levofloxacin_laboratory_typing_platform: - rank: 525 + rank: 537 slot_group: Antimicrobial resistance levofloxacin_laboratory_typing_platform_version: - rank: 526 + rank: 538 slot_group: Antimicrobial resistance levofloxacin_vendor_name: - rank: 527 + rank: 539 slot_group: Antimicrobial resistance levofloxacin_testing_standard: - rank: 528 + rank: 540 slot_group: Antimicrobial resistance levofloxacin_testing_standard_version: - rank: 529 + rank: 541 slot_group: Antimicrobial resistance levofloxacin_testing_standard_details: - rank: 530 + rank: 542 slot_group: Antimicrobial resistance levofloxacin_susceptible_breakpoint: - rank: 531 + rank: 543 slot_group: Antimicrobial resistance levofloxacin_intermediate_breakpoint: - rank: 532 + rank: 544 slot_group: Antimicrobial resistance levofloxacin_resistant_breakpoint: - rank: 533 + rank: 545 slot_group: Antimicrobial resistance linezolid_resistance_phenotype: - rank: 534 + rank: 546 slot_group: Antimicrobial resistance linezolid_measurement: - rank: 535 + rank: 547 slot_group: Antimicrobial resistance linezolid_measurement_units: - rank: 536 + rank: 548 slot_group: Antimicrobial resistance linezolid_measurement_sign: - rank: 537 + rank: 549 slot_group: Antimicrobial resistance linezolid_laboratory_typing_method: - rank: 538 + rank: 550 slot_group: Antimicrobial resistance linezolid_laboratory_typing_platform: - rank: 539 + rank: 551 slot_group: Antimicrobial resistance linezolid_laboratory_typing_platform_version: - rank: 540 + rank: 552 slot_group: Antimicrobial resistance linezolid_vendor_name: - rank: 541 + rank: 553 slot_group: Antimicrobial resistance linezolid_testing_standard: - rank: 542 + rank: 554 slot_group: Antimicrobial resistance linezolid_testing_standard_version: - rank: 543 + rank: 555 slot_group: Antimicrobial resistance linezolid_testing_standard_details: - rank: 544 + rank: 556 slot_group: Antimicrobial resistance linezolid_susceptible_breakpoint: - rank: 545 + rank: 557 slot_group: Antimicrobial resistance linezolid_intermediate_breakpoint: - rank: 546 + rank: 558 slot_group: Antimicrobial resistance linezolid_resistant_breakpoint: - rank: 547 + rank: 559 slot_group: Antimicrobial resistance meropenem_resistance_phenotype: - rank: 548 + rank: 560 slot_group: Antimicrobial resistance meropenem_measurement: - rank: 549 + rank: 561 slot_group: Antimicrobial resistance meropenem_measurement_units: - rank: 550 + rank: 562 slot_group: Antimicrobial resistance meropenem_measurement_sign: - rank: 551 + rank: 563 slot_group: Antimicrobial resistance meropenem_laboratory_typing_method: - rank: 552 + rank: 564 slot_group: Antimicrobial resistance meropenem_laboratory_typing_platform: - rank: 553 + rank: 565 slot_group: Antimicrobial resistance meropenem_laboratory_typing_platform_version: - rank: 554 + rank: 566 slot_group: Antimicrobial resistance meropenem_vendor_name: - rank: 555 + rank: 567 slot_group: Antimicrobial resistance meropenem_testing_standard: - rank: 556 + rank: 568 slot_group: Antimicrobial resistance meropenem_testing_standard_version: - rank: 557 + rank: 569 slot_group: Antimicrobial resistance meropenem_testing_standard_details: - rank: 558 + rank: 570 slot_group: Antimicrobial resistance meropenem_susceptible_breakpoint: - rank: 559 + rank: 571 slot_group: Antimicrobial resistance meropenem_intermediate_breakpoint: - rank: 560 + rank: 572 slot_group: Antimicrobial resistance meropenem_resistant_breakpoint: - rank: 561 + rank: 573 slot_group: Antimicrobial resistance nalidixic_acid_resistance_phenotype: - rank: 562 + rank: 574 slot_group: Antimicrobial resistance nalidixic_acid_measurement: - rank: 563 + rank: 575 slot_group: Antimicrobial resistance nalidixic_acid_measurement_units: - rank: 564 + rank: 576 slot_group: Antimicrobial resistance nalidixic_acid_measurement_sign: - rank: 565 + rank: 577 slot_group: Antimicrobial resistance nalidixic_acid_laboratory_typing_method: - rank: 566 + rank: 578 slot_group: Antimicrobial resistance nalidixic_acid_laboratory_typing_platform: - rank: 567 + rank: 579 slot_group: Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version: - rank: 568 + rank: 580 slot_group: Antimicrobial resistance nalidixic_acid_vendor_name: - rank: 569 + rank: 581 slot_group: Antimicrobial resistance nalidixic_acid_testing_standard: - rank: 570 + rank: 582 slot_group: Antimicrobial resistance nalidixic_acid_testing_standard_version: - rank: 571 + rank: 583 slot_group: Antimicrobial resistance nalidixic_acid_testing_standard_details: - rank: 572 + rank: 584 slot_group: Antimicrobial resistance nalidixic_acid_susceptible_breakpoint: - rank: 573 + rank: 585 slot_group: Antimicrobial resistance nalidixic_acid_intermediate_breakpoint: - rank: 574 + rank: 586 slot_group: Antimicrobial resistance nalidixic_acid_resistant_breakpoint: - rank: 575 + rank: 587 slot_group: Antimicrobial resistance nitrofurantoin_resistance_phenotype: - rank: 576 + rank: 588 slot_group: Antimicrobial resistance nitrofurantoin_measurement: - rank: 577 + rank: 589 slot_group: Antimicrobial resistance nitrofurantoin_measurement_units: - rank: 578 + rank: 590 slot_group: Antimicrobial resistance nitrofurantoin_measurement_sign: - rank: 579 + rank: 591 slot_group: Antimicrobial resistance nitrofurantoin_laboratory_typing_method: - rank: 580 + rank: 592 slot_group: Antimicrobial resistance nitrofurantoin_laboratory_typing_platform: - rank: 581 + rank: 593 slot_group: Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version: - rank: 582 + rank: 594 slot_group: Antimicrobial resistance nitrofurantoin_vendor_name: - rank: 583 + rank: 595 slot_group: Antimicrobial resistance nitrofurantoin_testing_standard: - rank: 584 + rank: 596 slot_group: Antimicrobial resistance nitrofurantoin_testing_standard_version: - rank: 585 + rank: 597 slot_group: Antimicrobial resistance nitrofurantoin_testing_standard_details: - rank: 586 + rank: 598 slot_group: Antimicrobial resistance nitrofurantoin_susceptible_breakpoint: - rank: 587 + rank: 599 slot_group: Antimicrobial resistance nitrofurantoin_intermediate_breakpoint: - rank: 588 + rank: 600 slot_group: Antimicrobial resistance nitrofurantoin_resistant_breakpoint: - rank: 589 + rank: 601 slot_group: Antimicrobial resistance norfloxacin_resistance_phenotype: - rank: 590 + rank: 602 slot_group: Antimicrobial resistance norfloxacin_measurement: - rank: 591 + rank: 603 slot_group: Antimicrobial resistance norfloxacin_measurement_units: - rank: 592 + rank: 604 slot_group: Antimicrobial resistance norfloxacin_measurement_sign: - rank: 593 + rank: 605 slot_group: Antimicrobial resistance norfloxacin_laboratory_typing_method: - rank: 594 + rank: 606 slot_group: Antimicrobial resistance norfloxacin_laboratory_typing_platform: - rank: 595 + rank: 607 slot_group: Antimicrobial resistance norfloxacin_laboratory_typing_platform_version: - rank: 596 + rank: 608 slot_group: Antimicrobial resistance norfloxacin_vendor_name: - rank: 597 + rank: 609 slot_group: Antimicrobial resistance norfloxacin_testing_standard: - rank: 598 + rank: 610 slot_group: Antimicrobial resistance norfloxacin_testing_standard_version: - rank: 599 + rank: 611 slot_group: Antimicrobial resistance norfloxacin_testing_standard_details: - rank: 600 + rank: 612 slot_group: Antimicrobial resistance norfloxacin_susceptible_breakpoint: - rank: 601 + rank: 613 slot_group: Antimicrobial resistance norfloxacin_intermediate_breakpoint: - rank: 602 + rank: 614 slot_group: Antimicrobial resistance norfloxacin_resistant_breakpoint: - rank: 603 + rank: 615 slot_group: Antimicrobial resistance oxolinicacid_resistance_phenotype: - rank: 604 + rank: 616 slot_group: Antimicrobial resistance oxolinicacid_measurement: - rank: 605 + rank: 617 slot_group: Antimicrobial resistance oxolinicacid_measurement_units: - rank: 606 + rank: 618 slot_group: Antimicrobial resistance oxolinicacid_measurement_sign: - rank: 607 + rank: 619 slot_group: Antimicrobial resistance oxolinicacid_laboratory_typing_method: - rank: 608 + rank: 620 slot_group: Antimicrobial resistance oxolinicacid_laboratory_typing_platform: - rank: 609 + rank: 621 slot_group: Antimicrobial resistance oxolinicacid_laboratory_typing_platform_version: - rank: 610 + rank: 622 slot_group: Antimicrobial resistance oxolinicacid_vendor_name: - rank: 611 + rank: 623 slot_group: Antimicrobial resistance oxolinicacid_testing_standard: - rank: 612 + rank: 624 slot_group: Antimicrobial resistance oxolinicacid_testing_standard_version: - rank: 613 + rank: 625 slot_group: Antimicrobial resistance oxolinicacid_testing_standard_details: - rank: 614 + rank: 626 slot_group: Antimicrobial resistance oxolinicacid_susceptible_breakpoint: - rank: 615 + rank: 627 slot_group: Antimicrobial resistance oxolinicacid_intermediate_breakpoint: - rank: 616 + rank: 628 slot_group: Antimicrobial resistance oxolinicacid_resistant_breakpoint: - rank: 617 + rank: 629 slot_group: Antimicrobial resistance oxytetracycline_resistance_phenotype: - rank: 618 + rank: 630 slot_group: Antimicrobial resistance oxytetracycline_measurement: - rank: 619 + rank: 631 slot_group: Antimicrobial resistance oxytetracycline_measurement_units: - rank: 620 + rank: 632 slot_group: Antimicrobial resistance oxytetracycline_measurement_sign: - rank: 621 + rank: 633 slot_group: Antimicrobial resistance oxytetracycline_laboratory_typing_method: - rank: 622 + rank: 634 slot_group: Antimicrobial resistance oxytetracycline_laboratory_typing_platform: - rank: 623 + rank: 635 slot_group: Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version: - rank: 624 + rank: 636 slot_group: Antimicrobial resistance oxytetracycline_vendor_name: - rank: 625 + rank: 637 slot_group: Antimicrobial resistance oxytetracycline_testing_standard: - rank: 626 + rank: 638 slot_group: Antimicrobial resistance oxytetracycline_testing_standard_version: - rank: 627 + rank: 639 slot_group: Antimicrobial resistance oxytetracycline_testing_standard_details: - rank: 628 + rank: 640 slot_group: Antimicrobial resistance oxytetracycline_susceptible_breakpoint: - rank: 629 + rank: 641 slot_group: Antimicrobial resistance oxytetracycline_intermediate_breakpoint: - rank: 630 + rank: 642 slot_group: Antimicrobial resistance oxytetracycline_resistant_breakpoint: - rank: 631 + rank: 643 slot_group: Antimicrobial resistance piperacillin_resistance_phenotype: - rank: 632 + rank: 644 slot_group: Antimicrobial resistance piperacillin_measurement: - rank: 633 + rank: 645 slot_group: Antimicrobial resistance piperacillin_measurement_units: - rank: 634 + rank: 646 slot_group: Antimicrobial resistance piperacillin_measurement_sign: - rank: 635 + rank: 647 slot_group: Antimicrobial resistance piperacillin_laboratory_typing_method: - rank: 636 + rank: 648 slot_group: Antimicrobial resistance piperacillin_laboratory_typing_platform: - rank: 637 + rank: 649 slot_group: Antimicrobial resistance piperacillin_laboratory_typing_platform_version: - rank: 638 + rank: 650 slot_group: Antimicrobial resistance piperacillin_vendor_name: - rank: 639 + rank: 651 slot_group: Antimicrobial resistance piperacillin_testing_standard: - rank: 640 + rank: 652 slot_group: Antimicrobial resistance piperacillin_testing_standard_version: - rank: 641 + rank: 653 slot_group: Antimicrobial resistance piperacillin_testing_standard_details: - rank: 642 + rank: 654 slot_group: Antimicrobial resistance piperacillin_susceptible_breakpoint: - rank: 643 + rank: 655 slot_group: Antimicrobial resistance piperacillin_intermediate_breakpoint: - rank: 644 + rank: 656 slot_group: Antimicrobial resistance piperacillin_resistant_breakpoint: - rank: 645 + rank: 657 slot_group: Antimicrobial resistance piperacillintazobactam_resistance_phenotype: - rank: 646 + rank: 658 slot_group: Antimicrobial resistance piperacillintazobactam_measurement: - rank: 647 + rank: 659 slot_group: Antimicrobial resistance piperacillintazobactam_measurement_units: - rank: 648 + rank: 660 slot_group: Antimicrobial resistance piperacillintazobactam_measurement_sign: - rank: 649 + rank: 661 slot_group: Antimicrobial resistance piperacillintazobactam_laboratory_typing_method: - rank: 650 + rank: 662 slot_group: Antimicrobial resistance piperacillintazobactam_laboratory_typing_platform: - rank: 651 + rank: 663 slot_group: Antimicrobial resistance piperacillintazobactam_laboratory_typing_platform_version: - rank: 652 + rank: 664 slot_group: Antimicrobial resistance piperacillintazobactam_vendor_name: - rank: 653 + rank: 665 slot_group: Antimicrobial resistance piperacillintazobactam_testing_standard: - rank: 654 + rank: 666 slot_group: Antimicrobial resistance piperacillintazobactam_testing_standard_version: - rank: 655 + rank: 667 slot_group: Antimicrobial resistance piperacillintazobactam_testing_standard_details: - rank: 656 + rank: 668 slot_group: Antimicrobial resistance piperacillintazobactam_susceptible_breakpoint: - rank: 657 + rank: 669 slot_group: Antimicrobial resistance piperacillintazobactam_intermediate_breakpoint: - rank: 658 + rank: 670 slot_group: Antimicrobial resistance piperacillintazobactam_resistant_breakpoint: - rank: 659 + rank: 671 slot_group: Antimicrobial resistance polymyxinb_resistance_phenotype: - rank: 660 + rank: 672 slot_group: Antimicrobial resistance polymyxinb_measurement: - rank: 661 + rank: 673 slot_group: Antimicrobial resistance polymyxinb_measurement_units: - rank: 662 + rank: 674 slot_group: Antimicrobial resistance polymyxinb_measurement_sign: - rank: 663 + rank: 675 slot_group: Antimicrobial resistance polymyxinb_laboratory_typing_method: - rank: 664 + rank: 676 slot_group: Antimicrobial resistance polymyxinb_laboratory_typing_platform: - rank: 665 + rank: 677 slot_group: Antimicrobial resistance polymyxinb_laboratory_typing_platform_version: - rank: 666 + rank: 678 slot_group: Antimicrobial resistance polymyxinb_vendor_name: - rank: 667 + rank: 679 slot_group: Antimicrobial resistance polymyxinb_testing_standard: - rank: 668 + rank: 680 slot_group: Antimicrobial resistance polymyxinb_testing_standard_version: - rank: 669 + rank: 681 slot_group: Antimicrobial resistance polymyxinb_testing_standard_details: - rank: 670 + rank: 682 slot_group: Antimicrobial resistance polymyxinb_susceptible_breakpoint: - rank: 671 + rank: 683 slot_group: Antimicrobial resistance polymyxinb_intermediate_breakpoint: - rank: 672 + rank: 684 slot_group: Antimicrobial resistance polymyxinb_resistant_breakpoint: - rank: 673 + rank: 685 slot_group: Antimicrobial resistance quinupristindalfopristin_resistance_phenotype: - rank: 674 + rank: 686 slot_group: Antimicrobial resistance quinupristindalfopristin_measurement: - rank: 675 + rank: 687 slot_group: Antimicrobial resistance quinupristindalfopristin_measurement_units: - rank: 676 + rank: 688 slot_group: Antimicrobial resistance quinupristindalfopristin_measurement_sign: - rank: 677 + rank: 689 slot_group: Antimicrobial resistance quinupristindalfopristin_laboratory_typing_method: - rank: 678 + rank: 690 slot_group: Antimicrobial resistance quinupristindalfopristin_laboratory_typing_platform: - rank: 679 + rank: 691 slot_group: Antimicrobial resistance quinupristindalfopristin_laboratory_typing_platform_version: - rank: 680 + rank: 692 slot_group: Antimicrobial resistance quinupristindalfopristin_vendor_name: - rank: 681 + rank: 693 slot_group: Antimicrobial resistance quinupristindalfopristin_testing_standard: - rank: 682 + rank: 694 slot_group: Antimicrobial resistance quinupristindalfopristin_testing_standard_version: - rank: 683 + rank: 695 slot_group: Antimicrobial resistance quinupristindalfopristin_testing_standard_details: - rank: 684 + rank: 696 slot_group: Antimicrobial resistance quinupristindalfopristin_susceptible_breakpoint: - rank: 685 + rank: 697 slot_group: Antimicrobial resistance quinupristindalfopristin_intermediate_breakpoint: - rank: 686 + rank: 698 slot_group: Antimicrobial resistance quinupristindalfopristin_resistant_breakpoint: - rank: 687 + rank: 699 slot_group: Antimicrobial resistance streptomycin_resistance_phenotype: - rank: 688 + rank: 700 slot_group: Antimicrobial resistance streptomycin_measurement: - rank: 689 + rank: 701 slot_group: Antimicrobial resistance streptomycin_measurement_units: - rank: 690 + rank: 702 slot_group: Antimicrobial resistance streptomycin_measurement_sign: - rank: 691 + rank: 703 slot_group: Antimicrobial resistance streptomycin_laboratory_typing_method: - rank: 692 + rank: 704 slot_group: Antimicrobial resistance streptomycin_laboratory_typing_platform: - rank: 693 + rank: 705 slot_group: Antimicrobial resistance streptomycin_laboratory_typing_platform_version: - rank: 694 + rank: 706 slot_group: Antimicrobial resistance streptomycin_vendor_name: - rank: 695 + rank: 707 slot_group: Antimicrobial resistance streptomycin_testing_standard: - rank: 696 + rank: 708 slot_group: Antimicrobial resistance streptomycin_testing_standard_version: - rank: 697 + rank: 709 slot_group: Antimicrobial resistance streptomycin_testing_standard_details: - rank: 698 + rank: 710 slot_group: Antimicrobial resistance streptomycin_susceptible_breakpoint: - rank: 699 + rank: 711 slot_group: Antimicrobial resistance streptomycin_intermediate_breakpoint: - rank: 700 + rank: 712 slot_group: Antimicrobial resistance streptomycin_resistant_breakpoint: - rank: 701 + rank: 713 slot_group: Antimicrobial resistance sulfisoxazole_resistance_phenotype: - rank: 702 + rank: 714 slot_group: Antimicrobial resistance sulfisoxazole_measurement: - rank: 703 + rank: 715 slot_group: Antimicrobial resistance sulfisoxazole_measurement_units: - rank: 704 + rank: 716 slot_group: Antimicrobial resistance sulfisoxazole_measurement_sign: - rank: 705 + rank: 717 slot_group: Antimicrobial resistance sulfisoxazole_laboratory_typing_method: - rank: 706 + rank: 718 slot_group: Antimicrobial resistance sulfisoxazole_laboratory_typing_platform: - rank: 707 + rank: 719 slot_group: Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version: - rank: 708 + rank: 720 slot_group: Antimicrobial resistance sulfisoxazole_vendor_name: - rank: 709 + rank: 721 slot_group: Antimicrobial resistance sulfisoxazole_testing_standard: - rank: 710 + rank: 722 slot_group: Antimicrobial resistance sulfisoxazole_testing_standard_version: - rank: 711 + rank: 723 slot_group: Antimicrobial resistance sulfisoxazole_testing_standard_details: - rank: 712 + rank: 724 slot_group: Antimicrobial resistance sulfisoxazole_susceptible_breakpoint: - rank: 713 + rank: 725 slot_group: Antimicrobial resistance sulfisoxazole_intermediate_breakpoint: - rank: 714 + rank: 726 slot_group: Antimicrobial resistance sulfisoxazole_resistant_breakpoint: - rank: 715 + rank: 727 slot_group: Antimicrobial resistance telithromycin_resistance_phenotype: - rank: 716 + rank: 728 slot_group: Antimicrobial resistance telithromycin_measurement: - rank: 717 + rank: 729 slot_group: Antimicrobial resistance telithromycin_measurement_units: - rank: 718 + rank: 730 slot_group: Antimicrobial resistance telithromycin_measurement_sign: - rank: 719 + rank: 731 slot_group: Antimicrobial resistance telithromycin_laboratory_typing_method: - rank: 720 + rank: 732 slot_group: Antimicrobial resistance telithromycin_laboratory_typing_platform: - rank: 721 + rank: 733 slot_group: Antimicrobial resistance telithromycin_laboratory_typing_platform_version: - rank: 722 + rank: 734 slot_group: Antimicrobial resistance telithromycin_vendor_name: - rank: 723 + rank: 735 slot_group: Antimicrobial resistance telithromycin_testing_standard: - rank: 724 + rank: 736 slot_group: Antimicrobial resistance telithromycin_testing_standard_version: - rank: 725 + rank: 737 slot_group: Antimicrobial resistance telithromycin_testing_standard_details: - rank: 726 + rank: 738 slot_group: Antimicrobial resistance telithromycin_susceptible_breakpoint: - rank: 727 + rank: 739 slot_group: Antimicrobial resistance telithromycin_intermediate_breakpoint: - rank: 728 + rank: 740 slot_group: Antimicrobial resistance telithromycin_resistant_breakpoint: - rank: 729 + rank: 741 slot_group: Antimicrobial resistance tetracycline_resistance_phenotype: - rank: 730 + rank: 742 slot_group: Antimicrobial resistance tetracycline_measurement: - rank: 731 + rank: 743 slot_group: Antimicrobial resistance tetracycline_measurement_units: - rank: 732 + rank: 744 slot_group: Antimicrobial resistance tetracycline_measurement_sign: - rank: 733 + rank: 745 slot_group: Antimicrobial resistance tetracycline_laboratory_typing_method: - rank: 734 + rank: 746 slot_group: Antimicrobial resistance tetracycline_laboratory_typing_platform: - rank: 735 + rank: 747 slot_group: Antimicrobial resistance tetracycline_laboratory_typing_platform_version: - rank: 736 + rank: 748 slot_group: Antimicrobial resistance tetracycline_vendor_name: - rank: 737 + rank: 749 slot_group: Antimicrobial resistance tetracycline_testing_standard: - rank: 738 + rank: 750 slot_group: Antimicrobial resistance tetracycline_testing_standard_version: - rank: 739 + rank: 751 slot_group: Antimicrobial resistance tetracycline_testing_standard_details: - rank: 740 + rank: 752 slot_group: Antimicrobial resistance tetracycline_susceptible_breakpoint: - rank: 741 + rank: 753 slot_group: Antimicrobial resistance tetracycline_intermediate_breakpoint: - rank: 742 + rank: 754 slot_group: Antimicrobial resistance tetracycline_resistant_breakpoint: - rank: 743 + rank: 755 slot_group: Antimicrobial resistance tigecycline_resistance_phenotype: - rank: 744 + rank: 756 slot_group: Antimicrobial resistance tigecycline_measurement: - rank: 745 + rank: 757 slot_group: Antimicrobial resistance tigecycline_measurement_units: - rank: 746 + rank: 758 slot_group: Antimicrobial resistance tigecycline_measurement_sign: - rank: 747 + rank: 759 slot_group: Antimicrobial resistance tigecycline_laboratory_typing_method: - rank: 748 + rank: 760 slot_group: Antimicrobial resistance tigecycline_laboratory_typing_platform: - rank: 749 + rank: 761 slot_group: Antimicrobial resistance tigecycline_laboratory_typing_platform_version: - rank: 750 + rank: 762 slot_group: Antimicrobial resistance tigecycline_vendor_name: - rank: 751 + rank: 763 slot_group: Antimicrobial resistance tigecycline_testing_standard: - rank: 752 + rank: 764 slot_group: Antimicrobial resistance tigecycline_testing_standard_version: - rank: 753 + rank: 765 slot_group: Antimicrobial resistance tigecycline_testing_standard_details: - rank: 754 + rank: 766 slot_group: Antimicrobial resistance tigecycline_susceptible_breakpoint: - rank: 755 + rank: 767 slot_group: Antimicrobial resistance tigecycline_intermediate_breakpoint: - rank: 756 + rank: 768 slot_group: Antimicrobial resistance tigecycline_resistant_breakpoint: - rank: 757 + rank: 769 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_resistance_phenotype: - rank: 758 + rank: 770 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_measurement: - rank: 759 + rank: 771 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_measurement_units: - rank: 760 + rank: 772 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_measurement_sign: - rank: 761 + rank: 773 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_laboratory_typing_method: - rank: 762 + rank: 774 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_laboratory_typing_platform: - rank: 763 + rank: 775 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_laboratory_typing_platform_version: - rank: 764 + rank: 776 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_vendor_name: - rank: 765 + rank: 777 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_testing_standard: - rank: 766 + rank: 778 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_testing_standard_version: - rank: 767 + rank: 779 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_testing_standard_details: - rank: 768 + rank: 780 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_susceptible_breakpoint: - rank: 769 + rank: 781 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_intermediate_breakpoint: - rank: 770 + rank: 782 slot_group: Antimicrobial resistance trimethoprimsulfamethoxazole_resistant_breakpoint: - rank: 771 + rank: 783 slot_group: Antimicrobial resistance authors: - rank: 772 + rank: 784 slot_group: Contributor acknowledgement dataharmonizer_provenance: - rank: 773 + rank: 785 slot_group: Contributor acknowledgement slots: sample_collector_sample_id: @@ -3120,16 +3168,17 @@ slots: the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0001123 + identifier: true any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: ABCD123 exact_mappings: - BIOSAMPLE:sample_name - - NCBI_BIOSAMPLE_Enterics:%2Asample_name - - NCBI_ANTIBIOGRAM:%2Asample_name + - NCBI_BIOSAMPLE_Enterics:sample_name + - NCBI_ANTIBIOGRAM:sample_name alternative_sample_id: name: alternative_sample_id title: alternative_sample_ID @@ -3161,14 +3210,14 @@ slots: be provided, leave blank or provide a null value. slot_uri: GENEPIO:0001153 any_of: - - range: sample_collected_by menu - - range: null value menu + - range: SampleCollectedByMenu + - range: NullValueMenu required: true examples: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] exact_mappings: - BIOSAMPLE:collected_by - - NCBI_BIOSAMPLE_Enterics:%2Acollected_by + - NCBI_BIOSAMPLE_Enterics:collected_by sample_collected_by_laboratory_name: name: sample_collected_by_laboratory_name title: sample_collected_by_laboratory_name @@ -3244,7 +3293,7 @@ slots: slot_uri: GENEPIO:0001156 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: johnnyblogs@lab.ca @@ -3260,14 +3309,14 @@ slots: of sequencing" field. slot_uri: GENEPIO:0001198 any_of: - - range: purpose_of_sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu required: true examples: - value: Surveillance [GENEPIO:0100004] exact_mappings: - BIOSAMPLE:purpose_of_sampling - - NCBI_BIOSAMPLE_Enterics:%2Apurpose_of_sampling + - NCBI_BIOSAMPLE_Enterics:purpose_of_sampling presampling_activity: name: presampling_activity title: presampling_activity @@ -3280,8 +3329,8 @@ slots: value. slot_uri: GENEPIO:0100433 any_of: - - range: presampling_activity menu - - range: null value menu + - range: PresamplingActivityMenu + - range: NullValueMenu examples: - value: Antimicrobial pre-treatment [GENEPIO:0100537] exact_mappings: @@ -3320,7 +3369,7 @@ slots: or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". slot_uri: GENEPIO:0100921 - range: experimental_specimen_role_type menu + range: ExperimentalSpecimenRoleTypeMenu examples: - value: Positive experimental control [GENEPIO:0101018] specimen_processing: @@ -3333,10 +3382,21 @@ slots: leave blank or provide a null value. slot_uri: GENEPIO:0100435 any_of: - - range: specimen_processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu examples: - value: Samples pooled [OBI:0600016] + specimen_processing_details: + name: specimen_processing_details + title: specimen_processing_details + description: The details of the processing applied to the sample during or after + receiving the sample. + comments: Briefly describe the processes applied to the sample. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString + examples: + - value: 25 samples were pooled and further prepared as a single sample during + library prep. nucleic_acid_extraction_method: name: nucleic_acid_extraction_method title: nucleic acid extraction method @@ -3365,15 +3425,15 @@ slots: is unknown or cannot be provided, provide a null value. slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true examples: - value: Canada [GAZ:00002560] exact_mappings: - BIOSAMPLE:geo_loc_name - BIOSAMPLE:geo_loc_name%20%28country%29 - - NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name + - NCBI_BIOSAMPLE_Enterics:geo_loc_name geo_loc_name_state_province_region: name: geo_loc_name_state_province_region title: geo_loc_name (state/province/region) @@ -3382,15 +3442,15 @@ slots: the information is unknown or cannot be provided, provide a null value. slot_uri: GENEPIO:0001185 any_of: - - range: geo_loc_name (state/province/region) menu - - range: null value menu + - range: GeoLocNameStateProvinceRegionMenu + - range: NullValueMenu required: true examples: - value: British Columbia [GAZ:00002562] exact_mappings: - BIOSAMPLE:geo_loc_name - BIOSAMPLE:geo_loc_name%20%28state/province/region%29 - - NCBI_BIOSAMPLE_Enterics:%2Ageo_loc_name + - NCBI_BIOSAMPLE_Enterics:geo_loc_name geo_loc_name_site: name: geo_loc_name_site title: geo_loc_name (site) @@ -3415,8 +3475,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100437 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: United States of America [GAZ:00002459] exact_mappings: @@ -3431,8 +3491,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100438 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: South Africa [GAZ:00001094] geo_loc_latitude: @@ -3473,13 +3533,13 @@ slots: comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". slot_uri: GENEPIO:0001174 - range: date + range: Date required: true examples: - value: '2020-10-30' exact_mappings: - BIOSAMPLE:sample%20collection%20date - - NCBI_BIOSAMPLE_Enterics:%2Acollection_date + - NCBI_BIOSAMPLE_Enterics:collection_date sample_collection_date_precision: name: sample_collection_date_precision title: sample_collection_date_precision @@ -3490,11 +3550,98 @@ slots: "month" for "YYYY-MM", or "year" for "YYYY". slot_uri: GENEPIO:0001177 any_of: - - range: sample_collection_date_precision menu - - range: null value menu + - range: SampleCollectionDatePrecisionMenu + - range: NullValueMenu required: true examples: - value: day [UO:0000033] + sample_collection_end_date: + name: sample_collection_end_date + title: sample_collection_end_date + description: The date on which sample collection ended for a continuous sample. + comments: Provide the date that sample collection ended in ISO 8601 format i.e. + YYYY-MM-DD + slot_uri: GENEPIO:0101071 + any_of: + - range: Date + - range: NullValueMenu + recommended: true + examples: + - value: '2020-03-18' + sample_processing_date: + name: sample_processing_date + title: sample_processing_date + description: The date on which the sample was processed. + comments: Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". + The sample may be collected and processed (e.g. filtered, extraction) on the + same day, or on different dates. + slot_uri: GENEPIO:0100763 + any_of: + - range: Date + - range: NullValueMenu + examples: + - value: '2020-03-16' + sample_collection_start_time: + name: sample_collection_start_time + title: sample_collection_start_time + description: The time at which sample collection began. + comments: Provide this time in ISO 8601 24hr format, in your local time. + slot_uri: GENEPIO:0101072 + any_of: + - range: Time + - range: NullValueMenu + recommended: true + examples: + - value: 17:15 PST + sample_collection_end_time: + name: sample_collection_end_time + title: sample_collection_end_time + description: The time at which sample collection ended. + comments: Provide this time in ISO 8601 24hr format, in your local time. + slot_uri: GENEPIO:0101073 + any_of: + - range: Time + - range: NullValueMenu + recommended: true + examples: + - value: 19:15 PST + sample_collection_time_of_day: + name: sample_collection_time_of_day + title: sample_collection_time_of_day + description: The descriptive time of day during which the sample was collected. + comments: If known, select a value from the pick list. The time of sample processing + matters especially for grab samples, as fecal concentration in wastewater fluctuates + over the course of the day. + slot_uri: GENEPIO:0100765 + any_of: + - range: SampleCollectionTimeOfDayMenu + - range: NullValueMenu + examples: + - value: Morning + sample_collection_time_duration_value: + name: sample_collection_time_duration_value + title: sample_collection_time_duration_value + description: The amount of time over which the sample was collected. + comments: Provide the numerical value of time. + slot_uri: GENEPIO:0100766 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + recommended: true + examples: + - value: '1900-01-03' + sample_collection_time_duration_unit: + name: sample_collection_time_duration_unit + title: sample_collection_time_duration_unit + description: The units of the time duration measurement of sample collection. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0100767 + any_of: + - range: SampleCollectionDurationUnitMenu + - range: NullValueMenu + recommended: true + examples: + - value: Hour sample_received_date: name: sample_received_date title: sample_received_date @@ -3502,7 +3649,7 @@ slots: comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". slot_uri: GENEPIO:0001179 - range: date + range: Date examples: - value: '2020-11-15' original_sample_description: @@ -3526,8 +3673,8 @@ slots: separated by a semi-colon. slot_uri: GENEPIO:0001232 any_of: - - range: environmental_site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3535,7 +3682,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_site - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source - NCBI_BIOSAMPLE_Enterics:animal_env - NCBI_BIOSAMPLE_Enterics:host_housing - NCBI_BIOSAMPLE_Enterics:env_local_scale @@ -3550,8 +3697,8 @@ slots: separated by a semi-colon. slot_uri: GENEPIO:0001223 any_of: - - range: environmental_material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3562,7 +3709,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_material - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source environmental_material_constituent: name: environmental_material_constituent title: environmental_material_constituent @@ -3572,7 +3719,6 @@ slots: material. Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0101197 range: WhitespaceMinimizedString - multivalued: true examples: - value: lead - value: plastic @@ -3588,8 +3734,8 @@ slots: If not applicable, leave blank.' slot_uri: GENEPIO:0100443 any_of: - - range: animal_or_plant_population menu - - range: null value menu + - range: AnimalOrPlantPopulationMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3604,8 +3750,8 @@ slots: the picklist provided. Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001211 any_of: - - range: anatomical_material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3615,7 +3761,7 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_material - NCBI_BIOSAMPLE_Enterics:host_tissue_sampled - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source body_product: name: body_product title: body_product @@ -3627,8 +3773,8 @@ slots: can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001216 any_of: - - range: body_product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3638,7 +3784,7 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:body_product - NCBI_BIOSAMPLE_Enterics:host_body_product - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source anatomical_part: name: anatomical_part title: anatomical_part @@ -3648,8 +3794,8 @@ slots: the picklist provided. Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001214 any_of: - - range: anatomical_part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3657,7 +3803,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_part - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source anatomical_region: name: anatomical_region title: anatomical_region @@ -3667,8 +3813,8 @@ slots: part e.g. dorso-lateral region vs back. Select a term from the picklist. slot_uri: GENEPIO:0100700 any_of: - - range: anatomical_region menu - - range: null value menu + - range: AnatomicalRegionMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3682,8 +3828,8 @@ slots: Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0100444 any_of: - - range: food_product menu - - range: null value menu + - range: FoodProductMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3704,8 +3850,8 @@ slots: canned), and any information about a label claim (e.g. organic, fat-free). slot_uri: GENEPIO:0100445 any_of: - - range: food_product_properties menu - - range: null value menu + - range: FoodProductPropertiesMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3714,7 +3860,7 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:food_product_properties - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source - NCBI_BIOSAMPLE_Enterics:food_processing_method - NCBI_BIOSAMPLE_Enterics:food_preserv_proc label_claim: @@ -3726,8 +3872,8 @@ slots: label only. slot_uri: FOODON:03602001 any_of: - - range: label_claim menu - - range: null value menu + - range: LabelClaimMenu + - range: NullValueMenu multivalued: true examples: - value: Antibiotic free [FOODON:03601063] @@ -3741,8 +3887,8 @@ slots: Multiple entries can be provided, separated by a comma. slot_uri: GENEPIO:0100446 any_of: - - range: animal_source_of_food menu - - range: null value menu + - range: AnimalSourceOfFoodMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3758,8 +3904,8 @@ slots: comments: Provide the name of the agricultural production stream from the picklist. slot_uri: GENEPIO:0100699 any_of: - - range: food_product_production_stream menu - - range: null value menu + - range: FoodProductProductionStreamMenu + - range: NullValueMenu examples: - value: Beef cattle production stream [FOODON:03000452] exact_mappings: @@ -3771,8 +3917,8 @@ slots: comments: If known, provide information regarding how the food product was packaged. slot_uri: GENEPIO:0100447 any_of: - - range: food_packaging menu - - range: null value menu + - range: FoodPackagingMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3790,7 +3936,7 @@ slots: best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. slot_uri: GENEPIO:0100615 - range: date + range: Date examples: - value: '2020-05-25' exact_mappings: @@ -3804,7 +3950,7 @@ slots: Before date or other food quality date. If the date is known, leave blank or provide a null value. slot_uri: GENEPIO:0100616 - range: date + range: Date examples: - value: '2020-05-25' collection_device: @@ -3816,8 +3962,8 @@ slots: Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001234 any_of: - - range: collection_device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu recommended: true examples: - value: Drag swab [OBI:0002822] @@ -3825,7 +3971,7 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_device - NCBI_BIOSAMPLE_Enterics:samp_collect_device - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source collection_method: name: collection_method title: collection_method @@ -3835,15 +3981,15 @@ slots: separated by a semi-colon. slot_uri: GENEPIO:0001241 any_of: - - range: collection_method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu recommended: true examples: - value: Rinsing for specimen collection [GENEPIO_0002116] exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source sample_volume_measurement_value: name: sample_volume_measurement_value title: sample_volume_measurement_value @@ -3859,7 +4005,7 @@ slots: description: The units of the volume measurement of the sample collected. comments: Provide the units from the pick list. slot_uri: GENEPIO:0100769 - range: sample_volume_measurement_unit menu + range: SampleVolumeMeasurementUnitMenu examples: - value: milliliter (mL) [UO:0000098] residual_sample_status: @@ -3871,7 +4017,7 @@ slots: used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". slot_uri: GENEPIO:0101090 - range: residual_sample_status menu + range: ResidualSampleStatusMenu examples: - value: No residual sample (sample all used) [GENEPIO:0101088] sample_storage_method: @@ -3908,7 +4054,7 @@ slots: description: The units of a measured sample storage duration. comments: Provide the units from the pick list. slot_uri: GENEPIO:0101015 - range: sample_storage_duration_unit menu + range: SampleStorageDurationUnitMenu examples: - value: Day [UO:0000033] nucleic_acid_storage_duration_value: @@ -3927,7 +4073,7 @@ slots: description: The units of a measured extracted nucleic acid storage duration. comments: Provide the units from the pick list. slot_uri: GENEPIO:0101086 - range: nucleic_acid_storage_duration_unit menu + range: NucleicAcidStorageDurationUnitMenu examples: - value: Year [UO:0000036] available_data_types: @@ -3942,8 +4088,8 @@ slots: data provider for more information. slot_uri: GENEPIO:0100690 any_of: - - range: available_data_types menu - - range: null value menu + - range: AvailableDataTypesMenu + - range: NullValueMenu multivalued: true examples: - value: Total coliform count [GENEPIO:0100729] @@ -3974,8 +4120,8 @@ slots: comments: Provide the units of measurement for which the depth was recorded. slot_uri: GENEPIO:0101025 any_of: - - range: water_depth_units menu - - range: null value menu + - range: WaterDepthUnitsMenu + - range: NullValueMenu examples: - value: meter (m) [UO:0000008] sediment_depth: @@ -3994,8 +4140,8 @@ slots: comments: Provide the units of measurement for which the depth was recorded. slot_uri: GENEPIO:0101026 any_of: - - range: sediment_depth_units menu - - range: null value menu + - range: SedimentDepthUnitsMenu + - range: NullValueMenu examples: - value: meter (m) [UO:0000008] air_temperature: @@ -4015,8 +4161,8 @@ slots: comments: Provide the units of measurement for which the temperature was recorded. slot_uri: GENEPIO:0101027 any_of: - - range: air_temperature_units menu - - range: null value menu + - range: AirTemperatureUnitsMenu + - range: NullValueMenu examples: - value: degree Celsius (C) [UO:0000027] water_temperature: @@ -4036,23 +4182,47 @@ slots: comments: Provide the units of measurement for which the temperature was recorded. slot_uri: GENEPIO:0101028 any_of: - - range: water_temperature_units menu - - range: null value menu + - range: WaterTemperatureUnitsMenu + - range: NullValueMenu examples: - value: degree Celsius (C) [UO:0000027] - weather_type: - name: weather_type - title: weather_type + sampling_weather_conditions: + name: sampling_weather_conditions + title: sampling_weather_conditions description: The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. comments: Provide the weather conditions at the time of sample collection. - slot_uri: GENEPIO:0100442 + slot_uri: GENEPIO:0100779 any_of: - - range: weather_type menu - - range: null value menu + - range: SamplingWeatherConditionsMenu + - range: NullValueMenu multivalued: true - examples: - - value: Rain [ENVO:01001564] + presampling_weather_conditions: + name: presampling_weather_conditions + title: presampling_weather_conditions + slot_uri: GENEPIO:0100780 + any_of: + - range: PresamplingWeatherConditionsMenu + - range: NullValueMenu + precipitation_measurement_value: + name: precipitation_measurement_value + title: precipitation_measurement_value + slot_uri: GENEPIO:0100911 + any_of: + - range: Whitespaceminimizedstring + - range: NullValueMenu + precipitation_measurement_unit: + name: precipitation_measurement_unit + title: precipitation_measurement_unit + slot_uri: GENEPIO:0100912 + any_of: + - range: PrecipitationMeasurementUnitMenu + - range: NullValueMenu + precipitation_measurement_method: + name: precipitation_measurement_method + title: precipitation_measurement_method + slot_uri: GENEPIO:0100913 + range: WhitespaceMinimizedString host_common_name: name: host_common_name title: host (common name) @@ -4062,8 +4232,8 @@ slots: provide the common name. slot_uri: GENEPIO:0001386 any_of: - - range: host (common name) menu - - range: null value menu + - range: HostCommonNameMenu + - range: NullValueMenu recommended: true examples: - value: Cow [NCBITaxon:9913] @@ -4079,15 +4249,15 @@ slots: select the scientific name from the picklist provided. slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu + - range: HostScientificNameMenu + - range: NullValueMenu recommended: true examples: - value: Bos taurus [NCBITaxon:9913] - value: Homo sapiens [NCBITaxon:9103] exact_mappings: - BIOSAMPLE:host - - NCBI_BIOSAMPLE_Enterics:%2Aisolation_source + - NCBI_BIOSAMPLE_Enterics:isolation_source - NCBI_BIOSAMPLE_Enterics:host host_ecotype: name: host_ecotype @@ -4124,8 +4294,8 @@ slots: comments: Select the host's food production name from the pick list. slot_uri: GENEPIO:0100452 any_of: - - range: host (food production name) menu - - range: null value menu + - range: HostFoodProductionNameMenu + - range: NullValueMenu examples: - value: Calf [FOODON:03411349] exact_mappings: @@ -4138,8 +4308,8 @@ slots: the template. If not available, provide a null value or leave blank. slot_uri: GENEPIO:0001394 any_of: - - range: host_age_bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu exact_mappings: - NCBI_BIOSAMPLE_Enterics:host_age host_disease: @@ -4180,7 +4350,7 @@ slots: examples: - value: K12 exact_mappings: - - NCBI_BIOSAMPLE_Enterics:%2Astrain + - NCBI_BIOSAMPLE_Enterics:strain isolate_id: name: isolate_id title: isolate_ID @@ -4194,12 +4364,12 @@ slots: slot_uri: GENEPIO:0100456 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: SA20131043 exact_mappings: - - NCBI_BIOSAMPLE_Enterics:%2Astrain + - NCBI_BIOSAMPLE_Enterics:strain alternative_isolate_id: name: alternative_isolate_id title: alternative_isolate_ID @@ -4244,7 +4414,7 @@ slots: slot_uri: GENEPIO:0100459 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: GRDI_LL_12345 @@ -4256,7 +4426,7 @@ slots: slot_uri: GENEPIO:0100460 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '666' @@ -4269,7 +4439,7 @@ slots: the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100461 - range: isolated_by menu + range: IsolatedByMenu examples: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] isolated_by_laboratory_name: @@ -4318,7 +4488,7 @@ slots: comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". slot_uri: GENEPIO:0100465 - range: date + range: Date examples: - value: '2020-10-30' exact_mappings: @@ -4346,15 +4516,15 @@ slots: mapping software and reference database(s) used.' slot_uri: GENEPIO:0001191 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu multivalued: true required: true examples: - value: Salmonella enterica subsp. enterica [NCBITaxon:59201] exact_mappings: - BIOSAMPLE:organism - - NCBI_BIOSAMPLE_Enterics:%2Aorganism + - NCBI_BIOSAMPLE_Enterics:organism taxonomic_identification_process: name: taxonomic_identification_process title: taxonomic_identification_process @@ -4365,8 +4535,8 @@ slots: is unknown or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100583 any_of: - - range: taxonomic_identification_process menu - - range: null value menu + - range: TaxonomicIdentificationProcessMenu + - range: NullValueMenu recommended: true examples: - value: PCR assay [OBI:0002740] @@ -4436,8 +4606,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100416 any_of: - - range: sequenced_by menu - - range: null value menu + - range: SequencedByMenu + - range: NullValueMenu required: true examples: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -4469,7 +4639,7 @@ slots: slot_uri: GENEPIO:0100471 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Enterics Lab Manager @@ -4486,7 +4656,7 @@ slots: slot_uri: GENEPIO:0100422 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: enterics@lab.ca @@ -4500,8 +4670,8 @@ slots: provided, leave blank or provide a null value.' slot_uri: GENEPIO:0001445 any_of: - - range: purpose_of_sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -4528,8 +4698,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100473 any_of: - - range: sequencing_platform menu - - range: null value menu + - range: SequencingPlatformMenu + - range: NullValueMenu examples: - value: Illumina [GENEPIO:0001923] sequencing_instrument: @@ -4541,8 +4711,8 @@ slots: blank or provide a null value. slot_uri: GENEPIO:0001452 any_of: - - range: sequencing_instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu examples: - value: Illumina HiSeq 2500 [GENEPIO:0100117] sequencing_assay_type: @@ -4554,7 +4724,7 @@ slots: used in your study. If unsure refer to the protocol documentation, or provide a null value.' slot_uri: GENEPIO:0100997 - range: sequencing_assay_type menu + range: SequencingAssayTypeMenu examples: - value: whole genome sequencing assay [OBI:0002117] library_preparation_kit: @@ -4584,7 +4754,7 @@ slots: regions of interest from a genome. comments: Provide the name of the enrichment method slot_uri: GENEPIO:0100966 - range: genomic_target_enrichment_method menu + range: GenomicTargetEnrichmentMethodMenu examples: - value: Hybrid selection method (bait-capture) [GENEPIO:0001950] genomic_target_enrichment_method_details: @@ -4717,8 +4887,8 @@ slots: New Term Request form. slot_uri: GENEPIO:0100559 any_of: - - range: quality_control_determination menu - - range: null value menu + - range: QualityControlDeterminationMenu + - range: NullValueMenu multivalued: true examples: - value: sequence failed quality control @@ -4732,8 +4902,8 @@ slots: New Term Request form. slot_uri: GENEPIO:0100560 any_of: - - range: quality_control_issues menu - - range: null value menu + - range: QualityControlIssuesMenu + - range: NullValueMenu multivalued: true examples: - value: low average genome coverage @@ -4759,7 +4929,7 @@ slots: slot_uri: GENEPIO:0001458 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Porechop 0.2.3 @@ -4772,7 +4942,7 @@ slots: slot_uri: GENEPIO:0001459 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Nanostripper @@ -4784,7 +4954,7 @@ slots: slot_uri: GENEPIO:0100825 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet sequence_assembly_software_version: @@ -4795,7 +4965,7 @@ slots: slot_uri: GENEPIO:0100826 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: 3.15.5 consensus_sequence_software_name: @@ -4806,7 +4976,7 @@ slots: slot_uri: GENEPIO:0001463 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: iVar consensus_sequence_software_version: @@ -4817,7 +4987,7 @@ slots: slot_uri: GENEPIO:0001469 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: '1.3' breadth_of_coverage_value: @@ -4865,7 +5035,7 @@ slots: description: The number of total base pairs generated by the sequencing process. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001482 - range: integer + range: Integer examples: - value: '387566' number_of_total_reads: @@ -4875,7 +5045,7 @@ slots: process. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0100827 - range: integer + range: Integer examples: - value: '423867' number_of_unique_reads: @@ -4884,7 +5054,7 @@ slots: description: The number of unique reads generated by the sequencing process. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0100828 - range: integer + range: Integer examples: - value: '248236' minimum_posttrimming_read_length: @@ -4894,7 +5064,7 @@ slots: after trimming. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0100829 - range: integer + range: Integer examples: - value: '150' number_of_contigs: @@ -4903,7 +5073,7 @@ slots: description: The number of contigs (contiguous sequences) in a sequence assembly. comments: Provide a numerical value. slot_uri: GENEPIO:0100937 - range: integer + range: Integer examples: - value: '10' percent_ns_across_total_genome_length: @@ -4912,7 +5082,7 @@ slots: description: The percentage of the assembly that consists of ambiguous bases (Ns). comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0100830 - range: integer + range: Integer examples: - value: '2' ns_per_100_kbp: @@ -4922,7 +5092,7 @@ slots: (kbp). comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001484 - range: integer + range: Integer examples: - value: '342' n50: @@ -4932,7 +5102,7 @@ slots: represents at least 50% of the nucleotides in a set of sequences. comments: Provide the N50 value in Mb. slot_uri: GENEPIO:0100938 - range: integer + range: Integer examples: - value: '150' percent_read_contamination_: @@ -4942,7 +5112,7 @@ slots: (not belonging to the target organism) in a sequence dataset. comments: Provide the percent contamination value (no need to include units). slot_uri: GENEPIO:0100845 - range: integer + range: Integer examples: - value: '2' sequence_assembly_length: @@ -4952,7 +5122,7 @@ slots: or by reference-based mapping. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0100846 - range: integer + range: Integer examples: - value: '34272' consensus_genome_length: @@ -4962,7 +5132,7 @@ slots: each position. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001483 - range: integer + range: Integer examples: - value: '38677' reference_genome_accession: @@ -5055,7 +5225,7 @@ slots: for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". slot_uri: GENEPIO:0101075 - range: date + range: Date examples: - value: '2024-02-01' read_mapping_criteria: @@ -5076,8 +5246,8 @@ slots: than sequencing data, please put the "National Microbiology Laboratory (NML)". slot_uri: GENEPIO:0001159 any_of: - - range: sequence_submitted_by menu - - range: null value menu + - range: SequenceSubmittedByMenu + - range: NullValueMenu examples: - value: Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] sequence_submitted_by_contact_name: @@ -5124,8 +5294,8 @@ slots: \ facility, farm, water source, manure etc, put \u201CPathogen.env\u201D." slot_uri: GENEPIO:0100476 any_of: - - range: attribute_package menu - - range: null value menu + - range: AttributePackageMenu + - range: NullValueMenu examples: - value: Pathogen.env [GENEPIO:0100581] bioproject_accession: @@ -5217,8 +5387,8 @@ slots: comments: Provide the stage of food production as free text. slot_uri: GENEPIO:0100482 any_of: - - range: stage_of_production menu - - range: null value menu + - range: StageOfProductionMenu + - range: NullValueMenu recommended: true examples: - value: Abattoir [ENVO:01000925] @@ -5232,8 +5402,8 @@ slots: the intervention category from the pick list provided. slot_uri: GENEPIO:0100483 any_of: - - range: experimental_intervention menu - - range: null value menu + - range: ExperimentalInterventionMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -5262,8 +5432,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100511 any_of: - - range: AMR_testing_by menu - - range: null value menu + - range: AmrTestingByMenu + - range: NullValueMenu required: true examples: - value: Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] @@ -5292,7 +5462,7 @@ slots: slot_uri: GENEPIO:0100513 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Enterics Lab Manager @@ -5309,7 +5479,7 @@ slots: slot_uri: GENEPIO:0100514 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: johnnyblogs@lab.ca @@ -5320,7 +5490,7 @@ slots: comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". slot_uri: GENEPIO:0100515 - range: date + range: Date examples: - value: '2022-04-03' amikacin_resistance_phenotype: @@ -5330,13 +5500,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype amikacin_measurement: name: amikacin_measurement title: amikacin_measurement @@ -5345,12 +5515,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement amikacin_measurement_units: name: amikacin_measurement_units title: amikacin_measurement_units @@ -5358,13 +5528,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units amikacin_measurement_sign: name: amikacin_measurement_sign title: amikacin_measurement_sign @@ -5372,13 +5542,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign amikacin_laboratory_typing_method: name: amikacin_laboratory_typing_method title: amikacin_laboratory_typing_method @@ -5386,12 +5556,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method amikacin_laboratory_typing_platform: name: amikacin_laboratory_typing_platform title: amikacin_laboratory_typing_platform @@ -5399,8 +5569,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -5421,8 +5591,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name - - range: null value menu + - range: AntimicrobialVendorName + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -5433,13 +5603,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard amikacin_testing_standard_version: name: amikacin_testing_standard_version title: amikacin_testing_standard_version @@ -5497,13 +5667,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype amoxicillinclavulanic_acid_measurement: name: amoxicillinclavulanic_acid_measurement title: amoxicillin-clavulanic_acid_measurement @@ -5512,12 +5682,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement amoxicillinclavulanic_acid_measurement_units: name: amoxicillinclavulanic_acid_measurement_units title: amoxicillin-clavulanic_acid_measurement_units @@ -5525,13 +5695,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units amoxicillinclavulanic_acid_measurement_sign: name: amoxicillinclavulanic_acid_measurement_sign title: amoxicillin-clavulanic_acid_measurement_sign @@ -5539,13 +5709,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign amoxicillinclavulanic_acid_laboratory_typing_method: name: amoxicillinclavulanic_acid_laboratory_typing_method title: amoxicillin-clavulanic_acid_laboratory_typing_method @@ -5553,12 +5723,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_platform: name: amoxicillinclavulanic_acid_laboratory_typing_platform title: amoxicillin-clavulanic_acid_laboratory_typing_platform @@ -5566,8 +5736,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -5588,8 +5758,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -5600,13 +5770,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard amoxicillinclavulanic_acid_testing_standard_version: name: amoxicillinclavulanic_acid_testing_standard_version title: amoxicillin-clavulanic_acid_testing_standard_version @@ -5664,13 +5834,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype ampicillin_measurement: name: ampicillin_measurement title: ampicillin_measurement @@ -5679,12 +5849,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement ampicillin_measurement_units: name: ampicillin_measurement_units title: ampicillin_measurement_units @@ -5692,13 +5862,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units ampicillin_measurement_sign: name: ampicillin_measurement_sign title: ampicillin_measurement_sign @@ -5706,13 +5876,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign ampicillin_laboratory_typing_method: name: ampicillin_laboratory_typing_method title: ampicillin_laboratory_typing_method @@ -5720,12 +5890,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method ampicillin_laboratory_typing_platform: name: ampicillin_laboratory_typing_platform title: ampicillin_laboratory_typing_platform @@ -5733,8 +5903,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -5755,8 +5925,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -5767,13 +5937,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard ampicillin_testing_standard_version: name: ampicillin_testing_standard_version title: ampicillin_testing_standard_version @@ -5831,13 +6001,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype azithromycin_measurement: name: azithromycin_measurement title: azithromycin_measurement @@ -5846,12 +6016,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement azithromycin_measurement_units: name: azithromycin_measurement_units title: azithromycin_measurement_units @@ -5859,13 +6029,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units azithromycin_measurement_sign: name: azithromycin_measurement_sign title: azithromycin_measurement_sign @@ -5873,13 +6043,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign azithromycin_laboratory_typing_method: name: azithromycin_laboratory_typing_method title: azithromycin_laboratory_typing_method @@ -5887,12 +6057,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method azithromycin_laboratory_typing_platform: name: azithromycin_laboratory_typing_platform title: azithromycin_laboratory_typing_platform @@ -5900,8 +6070,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -5922,8 +6092,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -5934,13 +6104,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard azithromycin_testing_standard_version: name: azithromycin_testing_standard_version title: azithromycin_testing_standard_version @@ -5998,13 +6168,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cefazolin_measurement: name: cefazolin_measurement title: cefazolin_measurement @@ -6013,12 +6183,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cefazolin_measurement_units: name: cefazolin_measurement_units title: cefazolin_measurement_units @@ -6026,13 +6196,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cefazolin_measurement_sign: name: cefazolin_measurement_sign title: cefazolin_measurement_sign @@ -6040,13 +6210,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cefazolin_laboratory_typing_method: name: cefazolin_laboratory_typing_method title: cefazolin_laboratory_typing_method @@ -6054,12 +6224,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cefazolin_laboratory_typing_platform: name: cefazolin_laboratory_typing_platform title: cefazolin_laboratory_typing_platform @@ -6067,8 +6237,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -6089,8 +6259,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -6101,13 +6271,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cefazolin_testing_standard_version: name: cefazolin_testing_standard_version title: cefazolin_testing_standard_version @@ -6165,13 +6335,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cefepime_measurement: name: cefepime_measurement title: cefepime_measurement @@ -6180,12 +6350,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cefepime_measurement_units: name: cefepime_measurement_units title: cefepime_measurement_units @@ -6193,13 +6363,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cefepime_measurement_sign: name: cefepime_measurement_sign title: cefepime_measurement_sign @@ -6207,13 +6377,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cefepime_laboratory_typing_method: name: cefepime_laboratory_typing_method title: cefepime_laboratory_typing_method @@ -6221,12 +6391,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cefepime_laboratory_typing_platform: name: cefepime_laboratory_typing_platform title: cefepime_laboratory_typing_platform @@ -6234,8 +6404,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -6256,8 +6426,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -6268,13 +6438,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cefepime_testing_standard_version: name: cefepime_testing_standard_version title: cefepime_testing_standard_version @@ -6332,13 +6502,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cefotaxime_measurement: name: cefotaxime_measurement title: cefotaxime_measurement @@ -6347,12 +6517,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cefotaxime_measurement_units: name: cefotaxime_measurement_units title: cefotaxime_measurement_units @@ -6360,13 +6530,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cefotaxime_measurement_sign: name: cefotaxime_measurement_sign title: cefotaxime_measurement_sign @@ -6374,13 +6544,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cefotaxime_laboratory_typing_method: name: cefotaxime_laboratory_typing_method title: cefotaxime_laboratory_typing_method @@ -6388,12 +6558,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cefotaxime_laboratory_typing_platform: name: cefotaxime_laboratory_typing_platform title: cefotaxime_laboratory_typing_platform @@ -6401,8 +6571,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -6423,8 +6593,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -6435,13 +6605,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cefotaxime_testing_standard_version: name: cefotaxime_testing_standard_version title: cefotaxime_testing_standard_version @@ -6499,13 +6669,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cefotaximeclavulanic_acid_measurement: name: cefotaximeclavulanic_acid_measurement title: cefotaxime-clavulanic_acid_measurement @@ -6514,12 +6684,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cefotaximeclavulanic_acid_measurement_units: name: cefotaximeclavulanic_acid_measurement_units title: cefotaxime-clavulanic_acid_measurement_units @@ -6527,13 +6697,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cefotaximeclavulanic_acid_measurement_sign: name: cefotaximeclavulanic_acid_measurement_sign title: cefotaxime-clavulanic_acid_measurement_sign @@ -6541,13 +6711,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cefotaximeclavulanic_acid_laboratory_typing_method: name: cefotaximeclavulanic_acid_laboratory_typing_method title: cefotaxime-clavulanic_acid_laboratory_typing_method @@ -6555,12 +6725,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_platform: name: cefotaximeclavulanic_acid_laboratory_typing_platform title: cefotaxime-clavulanic_acid_laboratory_typing_platform @@ -6568,8 +6738,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -6590,8 +6760,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -6602,13 +6772,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cefotaximeclavulanic_acid_testing_standard_version: name: cefotaximeclavulanic_acid_testing_standard_version title: cefotaxime-clavulanic_acid_testing_standard_version @@ -6666,13 +6836,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cefoxitin_measurement: name: cefoxitin_measurement title: cefoxitin_measurement @@ -6681,12 +6851,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cefoxitin_measurement_units: name: cefoxitin_measurement_units title: cefoxitin_measurement_units @@ -6694,13 +6864,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cefoxitin_measurement_sign: name: cefoxitin_measurement_sign title: cefoxitin_measurement_sign @@ -6708,13 +6878,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cefoxitin_laboratory_typing_method: name: cefoxitin_laboratory_typing_method title: cefoxitin_laboratory_typing_method @@ -6722,12 +6892,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cefoxitin_laboratory_typing_platform: name: cefoxitin_laboratory_typing_platform title: cefoxitin_laboratory_typing_platform @@ -6735,8 +6905,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -6757,8 +6927,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -6769,13 +6939,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cefoxitin_testing_standard_version: name: cefoxitin_testing_standard_version title: cefoxitin_testing_standard_version @@ -6833,13 +7003,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cefpodoxime_measurement: name: cefpodoxime_measurement title: cefpodoxime_measurement @@ -6848,12 +7018,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cefpodoxime_measurement_units: name: cefpodoxime_measurement_units title: cefpodoxime_measurement_units @@ -6861,13 +7031,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cefpodoxime_measurement_sign: name: cefpodoxime_measurement_sign title: cefpodoxime_measurement_sign @@ -6875,13 +7045,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cefpodoxime_laboratory_typing_method: name: cefpodoxime_laboratory_typing_method title: cefpodoxime_laboratory_typing_method @@ -6889,12 +7059,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cefpodoxime_laboratory_typing_platform: name: cefpodoxime_laboratory_typing_platform title: cefpodoxime_laboratory_typing_platform @@ -6902,8 +7072,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -6924,8 +7094,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -6936,13 +7106,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cefpodoxime_testing_standard_version: name: cefpodoxime_testing_standard_version title: cefpodoxime_testing_standard_version @@ -7000,13 +7170,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype ceftazidime_measurement: name: ceftazidime_measurement title: ceftazidime_measurement @@ -7015,12 +7185,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement ceftazidime_measurement_units: name: ceftazidime_measurement_units title: ceftazidime_measurement_units @@ -7028,13 +7198,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units ceftazidime_measurement_sign: name: ceftazidime_measurement_sign title: ceftazidime_measurement_sign @@ -7042,13 +7212,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign ceftazidime_laboratory_typing_method: name: ceftazidime_laboratory_typing_method title: ceftazidime_laboratory_typing_method @@ -7056,12 +7226,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method ceftazidime_laboratory_typing_platform: name: ceftazidime_laboratory_typing_platform title: ceftazidime_laboratory_typing_platform @@ -7069,8 +7239,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -7091,8 +7261,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -7103,13 +7273,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard ceftazidime_testing_standard_version: name: ceftazidime_testing_standard_version title: ceftazidime_testing_standard_version @@ -7167,13 +7337,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype ceftazidimeclavulanic_acid_measurement: name: ceftazidimeclavulanic_acid_measurement title: ceftazidime-clavulanic_acid_measurement @@ -7182,12 +7352,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement ceftazidimeclavulanic_acid_measurement_units: name: ceftazidimeclavulanic_acid_measurement_units title: ceftazidime-clavulanic_acid_measurement_units @@ -7195,13 +7365,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units ceftazidimeclavulanic_acid_measurement_sign: name: ceftazidimeclavulanic_acid_measurement_sign title: ceftazidime-clavulanic_acid_measurement_sign @@ -7209,13 +7379,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign ceftazidimeclavulanic_acid_laboratory_typing_method: name: ceftazidimeclavulanic_acid_laboratory_typing_method title: ceftazidime-clavulanic_acid_laboratory_typing_method @@ -7223,12 +7393,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_platform: name: ceftazidimeclavulanic_acid_laboratory_typing_platform title: ceftazidime-clavulanic_acid_laboratory_typing_platform @@ -7236,8 +7406,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -7258,8 +7428,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -7270,13 +7440,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard ceftazidimeclavulanic_acid_testing_standard_version: name: ceftazidimeclavulanic_acid_testing_standard_version title: ceftazidime-clavulanic_acid_testing_standard_version @@ -7334,13 +7504,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype ceftiofur_measurement: name: ceftiofur_measurement title: ceftiofur_measurement @@ -7349,12 +7519,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement ceftiofur_measurement_units: name: ceftiofur_measurement_units title: ceftiofur_measurement_units @@ -7362,13 +7532,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units ceftiofur_measurement_sign: name: ceftiofur_measurement_sign title: ceftiofur_measurement_sign @@ -7376,13 +7546,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign ceftiofur_laboratory_typing_method: name: ceftiofur_laboratory_typing_method title: ceftiofur_laboratory_typing_method @@ -7390,12 +7560,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method ceftiofur_laboratory_typing_platform: name: ceftiofur_laboratory_typing_platform title: ceftiofur_laboratory_typing_platform @@ -7403,8 +7573,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -7425,8 +7595,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -7437,13 +7607,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard ceftiofur_testing_standard_version: name: ceftiofur_testing_standard_version title: ceftiofur_testing_standard_version @@ -7501,13 +7671,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype ceftriaxone_measurement: name: ceftriaxone_measurement title: ceftriaxone_measurement @@ -7516,12 +7686,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement ceftriaxone_measurement_units: name: ceftriaxone_measurement_units title: ceftriaxone_measurement_units @@ -7529,13 +7699,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units ceftriaxone_measurement_sign: name: ceftriaxone_measurement_sign title: ceftriaxone_measurement_sign @@ -7543,13 +7713,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign ceftriaxone_laboratory_typing_method: name: ceftriaxone_laboratory_typing_method title: ceftriaxone_laboratory_typing_method @@ -7557,12 +7727,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method ceftriaxone_laboratory_typing_platform: name: ceftriaxone_laboratory_typing_platform title: ceftriaxone_laboratory_typing_platform @@ -7570,8 +7740,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -7592,8 +7762,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -7604,13 +7774,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard ceftriaxone_testing_standard_version: name: ceftriaxone_testing_standard_version title: ceftriaxone_testing_standard_version @@ -7668,13 +7838,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype cephalothin_measurement: name: cephalothin_measurement title: cephalothin_measurement @@ -7683,12 +7853,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement cephalothin_measurement_units: name: cephalothin_measurement_units title: cephalothin_measurement_units @@ -7696,13 +7866,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units cephalothin_measurement_sign: name: cephalothin_measurement_sign title: cephalothin_measurement_sign @@ -7710,13 +7880,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign cephalothin_laboratory_typing_method: name: cephalothin_laboratory_typing_method title: cephalothin_laboratory_typing_method @@ -7724,12 +7894,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method cephalothin_laboratory_typing_platform: name: cephalothin_laboratory_typing_platform title: cephalothin_laboratory_typing_platform @@ -7737,8 +7907,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -7759,8 +7929,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -7771,13 +7941,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard cephalothin_testing_standard_version: name: cephalothin_testing_standard_version title: cephalothin_testing_standard_version @@ -7835,13 +8005,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype chloramphenicol_measurement: name: chloramphenicol_measurement title: chloramphenicol_measurement @@ -7850,12 +8020,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement chloramphenicol_measurement_units: name: chloramphenicol_measurement_units title: chloramphenicol_measurement_units @@ -7863,13 +8033,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units chloramphenicol_measurement_sign: name: chloramphenicol_measurement_sign title: chloramphenicol_measurement_sign @@ -7877,13 +8047,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign chloramphenicol_laboratory_typing_method: name: chloramphenicol_laboratory_typing_method title: chloramphenicol_laboratory_typing_method @@ -7891,12 +8061,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method chloramphenicol_laboratory_typing_platform: name: chloramphenicol_laboratory_typing_platform title: chloramphenicol_laboratory_typing_platform @@ -7904,8 +8074,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -7926,8 +8096,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -7938,13 +8108,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard chloramphenicol_testing_standard_version: name: chloramphenicol_testing_standard_version title: chloramphenicol_testing_standard_version @@ -8002,13 +8172,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype ciprofloxacin_measurement: name: ciprofloxacin_measurement title: ciprofloxacin_measurement @@ -8017,12 +8187,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement ciprofloxacin_measurement_units: name: ciprofloxacin_measurement_units title: ciprofloxacin_measurement_units @@ -8030,13 +8200,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units ciprofloxacin_measurement_sign: name: ciprofloxacin_measurement_sign title: ciprofloxacin_measurement_sign @@ -8044,13 +8214,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign ciprofloxacin_laboratory_typing_method: name: ciprofloxacin_laboratory_typing_method title: ciprofloxacin_laboratory_typing_method @@ -8058,12 +8228,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method ciprofloxacin_laboratory_typing_platform: name: ciprofloxacin_laboratory_typing_platform title: ciprofloxacin_laboratory_typing_platform @@ -8071,8 +8241,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -8093,8 +8263,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -8105,13 +8275,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard ciprofloxacin_testing_standard_version: name: ciprofloxacin_testing_standard_version title: ciprofloxacin_testing_standard_version @@ -8169,13 +8339,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype clindamycin_measurement: name: clindamycin_measurement title: clindamycin_measurement @@ -8184,12 +8354,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement clindamycin_measurement_units: name: clindamycin_measurement_units title: clindamycin_measurement_units @@ -8197,13 +8367,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units clindamycin_measurement_sign: name: clindamycin_measurement_sign title: clindamycin_measurement_sign @@ -8211,13 +8381,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign clindamycin_laboratory_typing_method: name: clindamycin_laboratory_typing_method title: clindamycin_laboratory_typing_method @@ -8225,12 +8395,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method clindamycin_laboratory_typing_platform: name: clindamycin_laboratory_typing_platform title: clindamycin_laboratory_typing_platform @@ -8238,8 +8408,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -8260,8 +8430,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -8272,13 +8442,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard clindamycin_testing_standard_version: name: clindamycin_testing_standard_version title: clindamycin_testing_standard_version @@ -8336,13 +8506,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype doxycycline_measurement: name: doxycycline_measurement title: doxycycline_measurement @@ -8351,12 +8521,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement doxycycline_measurement_units: name: doxycycline_measurement_units title: doxycycline_measurement_units @@ -8364,13 +8534,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units doxycycline_measurement_sign: name: doxycycline_measurement_sign title: doxycycline_measurement_sign @@ -8378,13 +8548,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign doxycycline_laboratory_typing_method: name: doxycycline_laboratory_typing_method title: doxycycline_laboratory_typing_method @@ -8392,12 +8562,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method doxycycline_laboratory_typing_platform: name: doxycycline_laboratory_typing_platform title: doxycycline_laboratory_typing_platform @@ -8405,8 +8575,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -8427,8 +8597,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -8439,13 +8609,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard doxycycline_testing_standard_version: name: doxycycline_testing_standard_version title: doxycycline_testing_standard_version @@ -8503,13 +8673,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype enrofloxacin_measurement: name: enrofloxacin_measurement title: enrofloxacin_measurement @@ -8518,12 +8688,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement enrofloxacin_measurement_units: name: enrofloxacin_measurement_units title: enrofloxacin_measurement_units @@ -8531,13 +8701,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units enrofloxacin_measurement_sign: name: enrofloxacin_measurement_sign title: enrofloxacin_measurement_sign @@ -8545,13 +8715,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign enrofloxacin_laboratory_typing_method: name: enrofloxacin_laboratory_typing_method title: enrofloxacin_laboratory_typing_method @@ -8559,12 +8729,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method enrofloxacin_laboratory_typing_platform: name: enrofloxacin_laboratory_typing_platform title: enrofloxacin_laboratory_typing_platform @@ -8572,8 +8742,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -8594,8 +8764,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -8606,13 +8776,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard enrofloxacin_testing_standard_version: name: enrofloxacin_testing_standard_version title: enrofloxacin_testing_standard_version @@ -8670,13 +8840,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype erythromycin_measurement: name: erythromycin_measurement title: erythromycin_measurement @@ -8685,12 +8855,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement erythromycin_measurement_units: name: erythromycin_measurement_units title: erythromycin_measurement_units @@ -8698,13 +8868,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units erythromycin_measurement_sign: name: erythromycin_measurement_sign title: erythromycin_measurement_sign @@ -8712,13 +8882,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign erythromycin_laboratory_typing_method: name: erythromycin_laboratory_typing_method title: erythromycin_laboratory_typing_method @@ -8726,12 +8896,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method erythromycin_laboratory_typing_platform: name: erythromycin_laboratory_typing_platform title: erythromycin_laboratory_typing_platform @@ -8739,8 +8909,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -8761,8 +8931,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -8773,13 +8943,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard erythromycin_testing_standard_version: name: erythromycin_testing_standard_version title: erythromycin_testing_standard_version @@ -8837,13 +9007,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype florfenicol_measurement: name: florfenicol_measurement title: florfenicol_measurement @@ -8852,12 +9022,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement florfenicol_measurement_units: name: florfenicol_measurement_units title: florfenicol_measurement_units @@ -8865,13 +9035,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units florfenicol_measurement_sign: name: florfenicol_measurement_sign title: florfenicol_measurement_sign @@ -8879,13 +9049,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign florfenicol_laboratory_typing_method: name: florfenicol_laboratory_typing_method title: florfenicol_laboratory_typing_method @@ -8893,12 +9063,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method florfenicol_laboratory_typing_platform: name: florfenicol_laboratory_typing_platform title: florfenicol_laboratory_typing_platform @@ -8906,8 +9076,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -8928,8 +9098,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -8940,13 +9110,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard florfenicol_testing_standard_version: name: florfenicol_testing_standard_version title: florfenicol_testing_standard_version @@ -9004,13 +9174,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype gentamicin_measurement: name: gentamicin_measurement title: gentamicin_measurement @@ -9019,12 +9189,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement gentamicin_measurement_units: name: gentamicin_measurement_units title: gentamicin_measurement_units @@ -9032,13 +9202,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units gentamicin_measurement_sign: name: gentamicin_measurement_sign title: gentamicin_measurement_sign @@ -9046,13 +9216,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign gentamicin_laboratory_typing_method: name: gentamicin_laboratory_typing_method title: gentamicin_laboratory_typing_method @@ -9060,12 +9230,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method gentamicin_laboratory_typing_platform: name: gentamicin_laboratory_typing_platform title: gentamicin_laboratory_typing_platform @@ -9073,8 +9243,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -9095,8 +9265,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -9107,13 +9277,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard gentamicin_testing_standard_version: name: gentamicin_testing_standard_version title: gentamicin_testing_standard_version @@ -9171,13 +9341,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype imipenem_measurement: name: imipenem_measurement title: imipenem_measurement @@ -9186,12 +9356,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement imipenem_measurement_units: name: imipenem_measurement_units title: imipenem_measurement_units @@ -9199,13 +9369,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units imipenem_measurement_sign: name: imipenem_measurement_sign title: imipenem_measurement_sign @@ -9213,13 +9383,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign imipenem_laboratory_typing_method: name: imipenem_laboratory_typing_method title: imipenem_laboratory_typing_method @@ -9227,12 +9397,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method imipenem_laboratory_typing_platform: name: imipenem_laboratory_typing_platform title: imipenem_laboratory_typing_platform @@ -9240,8 +9410,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -9262,8 +9432,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -9274,13 +9444,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard imipenem_testing_standard_version: name: imipenem_testing_standard_version title: imipenem_testing_standard_version @@ -9338,13 +9508,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype kanamycin_measurement: name: kanamycin_measurement title: kanamycin_measurement @@ -9353,12 +9523,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement kanamycin_measurement_units: name: kanamycin_measurement_units title: kanamycin_measurement_units @@ -9366,13 +9536,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units kanamycin_measurement_sign: name: kanamycin_measurement_sign title: kanamycin_measurement_sign @@ -9380,13 +9550,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign kanamycin_laboratory_typing_method: name: kanamycin_laboratory_typing_method title: kanamycin_laboratory_typing_method @@ -9394,12 +9564,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method kanamycin_laboratory_typing_platform: name: kanamycin_laboratory_typing_platform title: kanamycin_laboratory_typing_platform @@ -9407,8 +9577,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -9429,8 +9599,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -9441,13 +9611,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard kanamycin_testing_standard_version: name: kanamycin_testing_standard_version title: kanamycin_testing_standard_version @@ -9505,13 +9675,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype levofloxacin_measurement: name: levofloxacin_measurement title: levofloxacin_measurement @@ -9520,12 +9690,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement levofloxacin_measurement_units: name: levofloxacin_measurement_units title: levofloxacin_measurement_units @@ -9533,13 +9703,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units levofloxacin_measurement_sign: name: levofloxacin_measurement_sign title: levofloxacin_measurement_sign @@ -9547,13 +9717,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign levofloxacin_laboratory_typing_method: name: levofloxacin_laboratory_typing_method title: levofloxacin_laboratory_typing_method @@ -9561,12 +9731,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method levofloxacin_laboratory_typing_platform: name: levofloxacin_laboratory_typing_platform title: levofloxacin_laboratory_typing_platform @@ -9574,8 +9744,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -9596,8 +9766,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -9608,13 +9778,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard levofloxacin_testing_standard_version: name: levofloxacin_testing_standard_version title: levofloxacin_testing_standard_version @@ -9672,13 +9842,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype linezolid_measurement: name: linezolid_measurement title: linezolid_measurement @@ -9687,12 +9857,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement linezolid_measurement_units: name: linezolid_measurement_units title: linezolid_measurement_units @@ -9700,13 +9870,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units linezolid_measurement_sign: name: linezolid_measurement_sign title: linezolid_measurement_sign @@ -9714,13 +9884,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign linezolid_laboratory_typing_method: name: linezolid_laboratory_typing_method title: linezolid_laboratory_typing_method @@ -9728,12 +9898,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method linezolid_laboratory_typing_platform: name: linezolid_laboratory_typing_platform title: linezolid_laboratory_typing_platform @@ -9741,8 +9911,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -9763,8 +9933,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -9775,13 +9945,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard linezolid_testing_standard_version: name: linezolid_testing_standard_version title: linezolid_testing_standard_version @@ -9839,13 +10009,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype meropenem_measurement: name: meropenem_measurement title: meropenem_measurement @@ -9854,12 +10024,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement meropenem_measurement_units: name: meropenem_measurement_units title: meropenem_measurement_units @@ -9867,13 +10037,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units meropenem_measurement_sign: name: meropenem_measurement_sign title: meropenem_measurement_sign @@ -9881,13 +10051,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign meropenem_laboratory_typing_method: name: meropenem_laboratory_typing_method title: meropenem_laboratory_typing_method @@ -9895,12 +10065,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method meropenem_laboratory_typing_platform: name: meropenem_laboratory_typing_platform title: meropenem_laboratory_typing_platform @@ -9908,8 +10078,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -9930,8 +10100,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -9942,13 +10112,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard meropenem_testing_standard_version: name: meropenem_testing_standard_version title: meropenem_testing_standard_version @@ -10006,13 +10176,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype nalidixic_acid_measurement: name: nalidixic_acid_measurement title: nalidixic_acid_measurement @@ -10021,12 +10191,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement nalidixic_acid_measurement_units: name: nalidixic_acid_measurement_units title: nalidixic_acid_measurement_units @@ -10034,13 +10204,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units nalidixic_acid_measurement_sign: name: nalidixic_acid_measurement_sign title: nalidixic_acid_measurement_sign @@ -10048,13 +10218,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign nalidixic_acid_laboratory_typing_method: name: nalidixic_acid_laboratory_typing_method title: nalidixic_acid_laboratory_typing_method @@ -10062,12 +10232,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method nalidixic_acid_laboratory_typing_platform: name: nalidixic_acid_laboratory_typing_platform title: nalidixic_acid_laboratory_typing_platform @@ -10075,8 +10245,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -10097,8 +10267,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -10109,13 +10279,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard nalidixic_acid_testing_standard_version: name: nalidixic_acid_testing_standard_version title: nalidixic_acid_testing_standard_version @@ -10173,13 +10343,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype nitrofurantoin_measurement: name: nitrofurantoin_measurement title: nitrofurantoin_measurement @@ -10188,12 +10358,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement nitrofurantoin_measurement_units: name: nitrofurantoin_measurement_units title: nitrofurantoin_measurement_units @@ -10201,13 +10371,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units nitrofurantoin_measurement_sign: name: nitrofurantoin_measurement_sign title: nitrofurantoin_measurement_sign @@ -10215,13 +10385,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign nitrofurantoin_laboratory_typing_method: name: nitrofurantoin_laboratory_typing_method title: nitrofurantoin_laboratory_typing_method @@ -10229,12 +10399,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method nitrofurantoin_laboratory_typing_platform: name: nitrofurantoin_laboratory_typing_platform title: nitrofurantoin_laboratory_typing_platform @@ -10242,8 +10412,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -10264,8 +10434,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -10276,13 +10446,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard nitrofurantoin_testing_standard_version: name: nitrofurantoin_testing_standard_version title: nitrofurantoin_testing_standard_version @@ -10340,13 +10510,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype norfloxacin_measurement: name: norfloxacin_measurement title: norfloxacin_measurement @@ -10355,12 +10525,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement norfloxacin_measurement_units: name: norfloxacin_measurement_units title: norfloxacin_measurement_units @@ -10368,13 +10538,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units norfloxacin_measurement_sign: name: norfloxacin_measurement_sign title: norfloxacin_measurement_sign @@ -10382,13 +10552,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign norfloxacin_laboratory_typing_method: name: norfloxacin_laboratory_typing_method title: norfloxacin_laboratory_typing_method @@ -10396,12 +10566,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method norfloxacin_laboratory_typing_platform: name: norfloxacin_laboratory_typing_platform title: norfloxacin_laboratory_typing_platform @@ -10409,8 +10579,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -10431,8 +10601,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -10443,13 +10613,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard norfloxacin_testing_standard_version: name: norfloxacin_testing_standard_version title: norfloxacin_testing_standard_version @@ -10507,13 +10677,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype oxolinicacid_measurement: name: oxolinicacid_measurement title: oxolinic-acid_measurement @@ -10522,12 +10692,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement oxolinicacid_measurement_units: name: oxolinicacid_measurement_units title: oxolinic-acid_measurement_units @@ -10535,13 +10705,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units oxolinicacid_measurement_sign: name: oxolinicacid_measurement_sign title: oxolinic-acid_measurement_sign @@ -10549,13 +10719,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign oxolinicacid_laboratory_typing_method: name: oxolinicacid_laboratory_typing_method title: oxolinic-acid_laboratory_typing_method @@ -10563,12 +10733,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method oxolinicacid_laboratory_typing_platform: name: oxolinicacid_laboratory_typing_platform title: oxolinic-acid_laboratory_typing_platform @@ -10576,8 +10746,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -10598,8 +10768,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -10610,13 +10780,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard oxolinicacid_testing_standard_version: name: oxolinicacid_testing_standard_version title: oxolinic-acid_testing_standard_version @@ -10674,13 +10844,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype oxytetracycline_measurement: name: oxytetracycline_measurement title: oxytetracycline_measurement @@ -10689,12 +10859,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement oxytetracycline_measurement_units: name: oxytetracycline_measurement_units title: oxytetracycline_measurement_units @@ -10702,13 +10872,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units oxytetracycline_measurement_sign: name: oxytetracycline_measurement_sign title: oxytetracycline_measurement_sign @@ -10716,13 +10886,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign oxytetracycline_laboratory_typing_method: name: oxytetracycline_laboratory_typing_method title: oxytetracycline_laboratory_typing_method @@ -10730,12 +10900,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method oxytetracycline_laboratory_typing_platform: name: oxytetracycline_laboratory_typing_platform title: oxytetracycline_laboratory_typing_platform @@ -10743,8 +10913,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -10765,8 +10935,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -10777,13 +10947,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard oxytetracycline_testing_standard_version: name: oxytetracycline_testing_standard_version title: oxytetracycline_testing_standard_version @@ -10841,13 +11011,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype piperacillin_measurement: name: piperacillin_measurement title: piperacillin_measurement @@ -10856,12 +11026,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement piperacillin_measurement_units: name: piperacillin_measurement_units title: piperacillin_measurement_units @@ -10869,13 +11039,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units piperacillin_measurement_sign: name: piperacillin_measurement_sign title: piperacillin_measurement_sign @@ -10883,13 +11053,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign piperacillin_laboratory_typing_method: name: piperacillin_laboratory_typing_method title: piperacillin_laboratory_typing_method @@ -10897,12 +11067,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method piperacillin_laboratory_typing_platform: name: piperacillin_laboratory_typing_platform title: piperacillin_laboratory_typing_platform @@ -10910,8 +11080,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -10932,8 +11102,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -10944,13 +11114,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard piperacillin_testing_standard_version: name: piperacillin_testing_standard_version title: piperacillin_testing_standard_version @@ -11008,13 +11178,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype piperacillintazobactam_measurement: name: piperacillintazobactam_measurement title: piperacillin-tazobactam_measurement @@ -11023,12 +11193,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement piperacillintazobactam_measurement_units: name: piperacillintazobactam_measurement_units title: piperacillin-tazobactam_measurement_units @@ -11036,13 +11206,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units piperacillintazobactam_measurement_sign: name: piperacillintazobactam_measurement_sign title: piperacillin-tazobactam_measurement_sign @@ -11050,13 +11220,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign piperacillintazobactam_laboratory_typing_method: name: piperacillintazobactam_laboratory_typing_method title: piperacillin-tazobactam_laboratory_typing_method @@ -11064,12 +11234,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method piperacillintazobactam_laboratory_typing_platform: name: piperacillintazobactam_laboratory_typing_platform title: piperacillin-tazobactam_laboratory_typing_platform @@ -11077,8 +11247,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -11099,8 +11269,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -11111,13 +11281,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard piperacillintazobactam_testing_standard_version: name: piperacillintazobactam_testing_standard_version title: piperacillin-tazobactam_testing_standard_version @@ -11175,13 +11345,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype polymyxinb_measurement: name: polymyxinb_measurement title: polymyxin-b_measurement @@ -11190,12 +11360,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement polymyxinb_measurement_units: name: polymyxinb_measurement_units title: polymyxin-b_measurement_units @@ -11203,13 +11373,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units polymyxinb_measurement_sign: name: polymyxinb_measurement_sign title: polymyxin-b_measurement_sign @@ -11217,13 +11387,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign polymyxinb_laboratory_typing_method: name: polymyxinb_laboratory_typing_method title: polymyxin-b_laboratory_typing_method @@ -11231,12 +11401,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method polymyxinb_laboratory_typing_platform: name: polymyxinb_laboratory_typing_platform title: polymyxin-b_laboratory_typing_platform @@ -11244,8 +11414,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -11266,8 +11436,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -11278,13 +11448,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard polymyxinb_testing_standard_version: name: polymyxinb_testing_standard_version title: polymyxin-b_testing_standard_version @@ -11342,13 +11512,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype quinupristindalfopristin_measurement: name: quinupristindalfopristin_measurement title: quinupristin-dalfopristin_measurement @@ -11357,12 +11527,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement quinupristindalfopristin_measurement_units: name: quinupristindalfopristin_measurement_units title: quinupristin-dalfopristin_measurement_units @@ -11370,13 +11540,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units quinupristindalfopristin_measurement_sign: name: quinupristindalfopristin_measurement_sign title: quinupristin-dalfopristin_measurement_sign @@ -11384,13 +11554,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign quinupristindalfopristin_laboratory_typing_method: name: quinupristindalfopristin_laboratory_typing_method title: quinupristin-dalfopristin_laboratory_typing_method @@ -11398,12 +11568,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method quinupristindalfopristin_laboratory_typing_platform: name: quinupristindalfopristin_laboratory_typing_platform title: quinupristin-dalfopristin_laboratory_typing_platform @@ -11411,8 +11581,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -11433,8 +11603,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -11445,13 +11615,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard quinupristindalfopristin_testing_standard_version: name: quinupristindalfopristin_testing_standard_version title: quinupristin-dalfopristin_testing_standard_version @@ -11509,13 +11679,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype streptomycin_measurement: name: streptomycin_measurement title: streptomycin_measurement @@ -11524,12 +11694,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement streptomycin_measurement_units: name: streptomycin_measurement_units title: streptomycin_measurement_units @@ -11537,13 +11707,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units streptomycin_measurement_sign: name: streptomycin_measurement_sign title: streptomycin_measurement_sign @@ -11551,13 +11721,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign streptomycin_laboratory_typing_method: name: streptomycin_laboratory_typing_method title: streptomycin_laboratory_typing_method @@ -11565,12 +11735,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method streptomycin_laboratory_typing_platform: name: streptomycin_laboratory_typing_platform title: streptomycin_laboratory_typing_platform @@ -11578,8 +11748,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -11600,8 +11770,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -11612,13 +11782,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard streptomycin_testing_standard_version: name: streptomycin_testing_standard_version title: streptomycin_testing_standard_version @@ -11676,13 +11846,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype sulfisoxazole_measurement: name: sulfisoxazole_measurement title: sulfisoxazole_measurement @@ -11691,12 +11861,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement sulfisoxazole_measurement_units: name: sulfisoxazole_measurement_units title: sulfisoxazole_measurement_units @@ -11704,13 +11874,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units sulfisoxazole_measurement_sign: name: sulfisoxazole_measurement_sign title: sulfisoxazole_measurement_sign @@ -11718,13 +11888,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign sulfisoxazole_laboratory_typing_method: name: sulfisoxazole_laboratory_typing_method title: sulfisoxazole_laboratory_typing_method @@ -11732,12 +11902,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method sulfisoxazole_laboratory_typing_platform: name: sulfisoxazole_laboratory_typing_platform title: sulfisoxazole_laboratory_typing_platform @@ -11745,8 +11915,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -11767,8 +11937,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -11779,13 +11949,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard sulfisoxazole_testing_standard_version: name: sulfisoxazole_testing_standard_version title: sulfisoxazole_testing_standard_version @@ -11843,13 +12013,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype telithromycin_measurement: name: telithromycin_measurement title: telithromycin_measurement @@ -11858,12 +12028,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement telithromycin_measurement_units: name: telithromycin_measurement_units title: telithromycin_measurement_units @@ -11871,13 +12041,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units telithromycin_measurement_sign: name: telithromycin_measurement_sign title: telithromycin_measurement_sign @@ -11885,13 +12055,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign telithromycin_laboratory_typing_method: name: telithromycin_laboratory_typing_method title: telithromycin_laboratory_typing_method @@ -11899,12 +12069,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method telithromycin_laboratory_typing_platform: name: telithromycin_laboratory_typing_platform title: telithromycin_laboratory_typing_platform @@ -11912,8 +12082,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -11934,8 +12104,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -11946,13 +12116,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard telithromycin_testing_standard_version: name: telithromycin_testing_standard_version title: telithromycin_testing_standard_version @@ -12010,13 +12180,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype tetracycline_measurement: name: tetracycline_measurement title: tetracycline_measurement @@ -12025,12 +12195,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement tetracycline_measurement_units: name: tetracycline_measurement_units title: tetracycline_measurement_units @@ -12038,13 +12208,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units tetracycline_measurement_sign: name: tetracycline_measurement_sign title: tetracycline_measurement_sign @@ -12052,13 +12222,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign tetracycline_laboratory_typing_method: name: tetracycline_laboratory_typing_method title: tetracycline_laboratory_typing_method @@ -12066,12 +12236,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method tetracycline_laboratory_typing_platform: name: tetracycline_laboratory_typing_platform title: tetracycline_laboratory_typing_platform @@ -12079,8 +12249,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -12101,8 +12271,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -12113,13 +12283,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard tetracycline_testing_standard_version: name: tetracycline_testing_standard_version title: tetracycline_testing_standard_version @@ -12177,13 +12347,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype tigecycline_measurement: name: tigecycline_measurement title: tigecycline_measurement @@ -12192,12 +12362,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement tigecycline_measurement_units: name: tigecycline_measurement_units title: tigecycline_measurement_units @@ -12205,13 +12375,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units tigecycline_measurement_sign: name: tigecycline_measurement_sign title: tigecycline_measurement_sign @@ -12219,13 +12389,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign tigecycline_laboratory_typing_method: name: tigecycline_laboratory_typing_method title: tigecycline_laboratory_typing_method @@ -12233,12 +12403,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method tigecycline_laboratory_typing_platform: name: tigecycline_laboratory_typing_platform title: tigecycline_laboratory_typing_platform @@ -12246,8 +12416,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -12268,8 +12438,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -12280,13 +12450,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard tigecycline_testing_standard_version: name: tigecycline_testing_standard_version title: tigecycline_testing_standard_version @@ -12344,13 +12514,13 @@ slots: susceptibility measurement and testing standard for this antibiotic comments: Select a phenotype from the pick list provided. any_of: - - range: antimicrobial_phenotype menu - - range: null value menu + - range: AntimicrobialPhenotypeMenu + - range: NullValueMenu recommended: true examples: - value: Susceptible antimicrobial phenotype [ARO:3004302] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Aresistance_phenotype + - NCBI_ANTIBIOGRAM:resistance_phenotype trimethoprimsulfamethoxazole_measurement: name: trimethoprimsulfamethoxazole_measurement title: trimethoprim-sulfamethoxazole_measurement @@ -12359,12 +12529,12 @@ slots: with decimals). any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: '4' exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement + - NCBI_ANTIBIOGRAM:measurement trimethoprimsulfamethoxazole_measurement_units: name: trimethoprimsulfamethoxazole_measurement_units title: trimethoprim-sulfamethoxazole_measurement_units @@ -12372,13 +12542,13 @@ slots: comments: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. any_of: - - range: antimicrobial_measurement_units menu - - range: null value menu + - range: AntimicrobialMeasurementUnitsMenu + - range: NullValueMenu required: true examples: - value: ug/mL [UO:0000274] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_units + - NCBI_ANTIBIOGRAM:measurement_units trimethoprimsulfamethoxazole_measurement_sign: name: trimethoprimsulfamethoxazole_measurement_sign title: trimethoprim-sulfamethoxazole_measurement_sign @@ -12386,13 +12556,13 @@ slots: comments: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. any_of: - - range: antimicrobial_measurement_sign menu - - range: null value menu + - range: AntimicrobialMeasurementSignMenu + - range: NullValueMenu required: true examples: - value: greater than (>) [GENEPIO:0001006] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Ameasurement_sign + - NCBI_ANTIBIOGRAM:measurement_sign trimethoprimsulfamethoxazole_laboratory_typing_method: name: trimethoprimsulfamethoxazole_laboratory_typing_method title: trimethoprim-sulfamethoxazole_laboratory_typing_method @@ -12400,12 +12570,12 @@ slots: comments: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. any_of: - - range: antimicrobial_laboratory_typing_method menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingMethodMenu + - range: NullValueMenu examples: - value: Broth dilution [ARO:3004397] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Alaboratory_typing_method + - NCBI_ANTIBIOGRAM:laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_platform: name: trimethoprimsulfamethoxazole_laboratory_typing_platform title: trimethoprim-sulfamethoxazole_laboratory_typing_platform @@ -12413,8 +12583,8 @@ slots: comments: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. any_of: - - range: antimicrobial_laboratory_typing_platform menu - - range: null value menu + - range: AntimicrobialLaboratoryTypingPlatformMenu + - range: NullValueMenu examples: - value: Sensitire [ARO:3004402] exact_mappings: @@ -12435,8 +12605,8 @@ slots: description: The name of the vendor of the testing platform used. comments: Provide the full name of the company (avoid abbreviations). any_of: - - range: antimicrobial_vendor_name menu - - range: null value menu + - range: AntimicrobialVendorNameMenu + - range: NullValueMenu examples: - value: Sensititre exact_mappings: @@ -12447,13 +12617,13 @@ slots: description: The testing standard used for determination of resistance phenotype comments: Select a testing standard from the pick list provided. any_of: - - range: antimicrobial_testing_standard menu - - range: null value menu + - range: AntimicrobialTestingStandardMenu + - range: NullValueMenu recommended: true examples: - value: Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] exact_mappings: - - NCBI_ANTIBIOGRAM:%2Atesting_standard + - NCBI_ANTIBIOGRAM:testing_standard trimethoprimsulfamethoxazole_testing_standard_version: name: trimethoprimsulfamethoxazole_testing_standard_version title: trimethoprim-sulfamethoxazole_testing_standard_version @@ -12624,6 +12794,34 @@ enums: text: Probiotic pre-treatment [GENEPIO:0100547] Vaccination [NCIT:C15346]: text: Vaccination [NCIT:C15346] + Wastewater treatment process [ENVO:06105300]: + text: Wastewater treatment process [ENVO:06105300] + description: A recycling process during which wastewater is treated. + Wastewater filtration [GENEPIO:0100881]: + text: Wastewater filtration [GENEPIO:0100881] + description: A wastewater treatment process which removes solid particles + from wastewater by means of filtration. + is_a: Wastewater treatment process [ENVO:06105300] + Wastewater grit removal [GENEPIO:0100882]: + text: Wastewater grit removal [GENEPIO:0100882] + description: A wastewater treatment process which removes sand, silt, and + grit from wastewater. + is_a: Wastewater treatment process [ENVO:06105300] + Wastewater microbial treatment [GENEPIO:0100883]: + text: Wastewater microbial treatment [GENEPIO:0100883] + description: A wastewater treatment process in which microbes are used to + degrade the biological material in wastewater. + is_a: Wastewater treatment process [ENVO:06105300] + Wastewater primary sedimentation [GENEPIO:0100884]: + text: Wastewater primary sedimentation [GENEPIO:0100884] + description: A wastewater treatment process which removes solids and large + particles from influent through gravitational force. + is_a: Wastewater treatment process [ENVO:06105300] + Wastewater secondary sedimentation [GENEPIO:0100885]: + text: Wastewater secondary sedimentation [GENEPIO:0100885] + description: A wastewater treatment process which removes biomass produced + in aeration from influent through gravitational force. + is_a: Wastewater treatment process [ENVO:06105300] ExperimentalSpecimenRoleTypeMenu: name: ExperimentalSpecimenRoleTypeMenu title: experimental_specimen_role_type menu @@ -13341,6 +13539,18 @@ enums: is_a: Building part (organizational term) Creek [ENVO:03501405]: text: Creek [ENVO:03501405] + Ditch [ENVO:00000037]: + text: Ditch [ENVO:00000037] + description: A small, human-made channel which has been dug for draining or + irrigating the land. + Drainage ditch [ENVO:00000140]: + text: Drainage ditch [ENVO:00000140] + description: A ditch that collects water from the surrounding land. + is_a: Ditch [ENVO:00000037] + Irrigation ditch [ENVO:00000139]: + text: Irrigation ditch [ENVO:00000139] + description: A ditch that supplies water to surrounding land. + is_a: Ditch [ENVO:00000037] Farm [ENVO:00000078]: text: Farm [ENVO:00000078] Beef farm [ENVO:03501443]: @@ -13392,6 +13602,8 @@ enums: is_a: Marine environment [ENVO:01000320] Park [ENVO:00000562]: text: Park [ENVO:00000562] + Plumbing drain [ENVO:01000924 ]: + text: Plumbing drain [ENVO:01000924 ] Pond [ENVO:00000033]: text: Pond [ENVO:00000033] Reservoir [ENVO:00000025]: @@ -13431,6 +13643,9 @@ enums: text: Truck [ENVO:01000602] Urban area [ENVO:03501437]: text: Urban area [ENVO:03501437] + Wastewater treatment plant [ENVO:00002272]: + text: Wastewater treatment plant [ENVO:00002272] + description: A plant in which wastewater is treated. Water surface [ENVO:01001191]: text: Water surface [ENVO:01001191] Woodland area [ENVO:00000109]: @@ -13630,9 +13845,9 @@ enums: Turbidity measurement [GENEPIO:0100749]: text: Turbidity measurement [GENEPIO:0100749] is_a: Physical characterization [GENEPIO:0100742] - WeatherTypeMenu: - name: WeatherTypeMenu - title: weather_type menu + SamplingWeatherConditionsMenu: + name: SamplingWeatherConditionsMenu + title: sampling_weather_conditions menu description: '' permissible_values: Cloudy/Overcast [ENVO:03501418]: @@ -16351,7 +16566,93 @@ enums: name: AntimicrobialResistanceTestDrugMenu title: Antimicrobial Resistance Test Drug Menu description: '' - permissible_values: {} + permissible_values: + amikacin: + text: amikacin + amoxicillin-clavulanic_acid: + text: amoxicillin-clavulanic_acid + ampicillin: + text: ampicillin + azithromycin: + text: azithromycin + cefazolin: + text: cefazolin + cefepime: + text: cefepime + cefotaxime: + text: cefotaxime + cefotaxime-clavulanic_acid: + text: cefotaxime-clavulanic_acid + cefoxitin: + text: cefoxitin + cefpodoxime: + text: cefpodoxime + ceftazidime: + text: ceftazidime + ceftazidime-clavulanic_acid: + text: ceftazidime-clavulanic_acid + ceftiofur: + text: ceftiofur + ceftriaxone: + text: ceftriaxone + cephalothin: + text: cephalothin + chloramphenicol: + text: chloramphenicol + ciprofloxacin: + text: ciprofloxacin + clindamycin: + text: clindamycin + doxycycline: + text: doxycycline + enrofloxacin: + text: enrofloxacin + erythromycin: + text: erythromycin + florfenicol: + text: florfenicol + gentamicin: + text: gentamicin + imipenem: + text: imipenem + kanamycin: + text: kanamycin + levofloxacin: + text: levofloxacin + linezolid: + text: linezolid + meropenem: + text: meropenem + nalidixic_acid: + text: nalidixic_acid + nitrofurantoin: + text: nitrofurantoin + norfloxacin: + text: norfloxacin + oxolinic-acid: + text: oxolinic-acid + oxytetracycline: + text: oxytetracycline + piperacillin: + text: piperacillin + piperacillin-tazobactam: + text: piperacillin-tazobactam + polymyxin-b: + text: polymyxin-b + quinupristin-dalfopristin: + text: quinupristin-dalfopristin + streptomycin: + text: streptomycin + sulfisoxazole: + text: sulfisoxazole + telithromycin: + text: telithromycin + tetracycline: + text: tetracycline + tigecycline: + text: tigecycline + trimethoprim-sulfamethoxazole: + text: trimethoprim-sulfamethoxazole types: WhitespaceMinimizedString: name: WhitespaceMinimizedString diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 1c04f806..61d37bd0 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -40,6 +40,12 @@ presampling_activity menu PresamplingActivityMenu Addition of substances to foo Microbial pre-treatment [GENEPIO:0100546] Probiotic pre-treatment [GENEPIO:0100547] Vaccination [NCIT:C15346] + Wastewater treatment process [ENVO:06105300] A recycling process during which wastewater is treated. + Wastewater filtration [GENEPIO:0100881] A wastewater treatment process which removes solid particles from wastewater by means of filtration. + Wastewater grit removal [GENEPIO:0100882] A wastewater treatment process which removes sand, silt, and grit from wastewater. + Wastewater microbial treatment [GENEPIO:0100883] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. + Wastewater primary sedimentation [GENEPIO:0100884] A wastewater treatment process which removes solids and large particles from influent through gravitational force. + Wastewater secondary sedimentation [GENEPIO:0100885] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. experimental_specimen_role_type menu ExperimentalSpecimenRoleTypeMenu Positive experimental control [GENEPIO:0101018] Negative experimental control [GENEPIO:0101019] @@ -379,6 +385,9 @@ environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] Stall [EOL:0001903] Window sill [ENVO:03501381] Creek [ENVO:03501405] + Ditch [ENVO:00000037] A small, human-made channel which has been dug for draining or irrigating the land. + Drainage ditch [ENVO:00000140] A ditch that collects water from the surrounding land. + Irrigation ditch [ENVO:00000139] A ditch that supplies water to surrounding land. Farm [ENVO:00000078] Beef farm [ENVO:03501443] Breeder farm [ENVO:03501384] @@ -399,6 +408,7 @@ environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] Benthic zone [ENVO:03501440] Pelagic zone [ENVO:00000208] Park [ENVO:00000562] + Plumbing drain [ENVO:01000924 ] Pond [ENVO:00000033] Reservoir [ENVO:00000025] Irrigation reservoir [ENVO:00000450] @@ -416,6 +426,7 @@ environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] Tributary [ENVO:00000495] Truck [ENVO:01000602] Urban area [ENVO:03501437] + Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. Water surface [ENVO:01001191] Woodland area [ENVO:00000109] Zoo [ENVO:00010625] @@ -494,7 +505,7 @@ available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702 Turbidity measurement [GENEPIO:0100749] -weather_type menu WeatherTypeMenu Cloudy/Overcast [ENVO:03501418] +sampling_weather_conditions menu SamplingWeatherConditionsMenu Cloudy/Overcast [ENVO:03501418] Partially cloudy [ENVO:03501419] Drizzle [ENVO:03501420] Fog [ENVO:01000844] @@ -1518,4 +1529,46 @@ antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British So Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG -Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu \ No newline at end of file +Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin + amoxicillin-clavulanic_acid + ampicillin + azithromycin + cefazolin + cefepime + cefotaxime + cefotaxime-clavulanic_acid + cefoxitin + cefpodoxime + ceftazidime + ceftazidime-clavulanic_acid + ceftiofur + ceftriaxone + cephalothin + chloramphenicol + ciprofloxacin + clindamycin + doxycycline + enrofloxacin + erythromycin + florfenicol + gentamicin + imipenem + kanamycin + levofloxacin + linezolid + meropenem + nalidixic_acid + nitrofurantoin + norfloxacin + oxolinic-acid + oxytetracycline + piperacillin + piperacillin-tazobactam + polymyxin-b + quinupristin-dalfopristin + streptomycin + sulfisoxazole + telithromycin + tetracycline + tigecycline + trimethoprim-sulfamethoxazole \ No newline at end of file diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 1585747c..0b5920d3 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -1,114 +1,126 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM GRDI GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString null value menu TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name *sample_name *sample_name + Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." ABCD1234[PHAC]; 12345rev[CFIA] - Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by sample_collected_by menu null value menu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by *collected_by + Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling purpose_of_sampling menu null value menu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling *purpose_of_sampling - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity presampling_activity menu null value menu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] host_am;fertilizer_admin + Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] host_am;fertilizer_admin Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol - Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type experimental_specimen_role_type menu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] - Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing specimen_processing menu null value menu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] + Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] + Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] + Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country geo_loc_name (country) menu null value menu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) *geo_loc_name - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region geo_loc_name (state/province/region) menu null value menu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) *geo_loc_name + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) - Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin - Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] + Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin + Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon - Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date *collection_date - Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision sample_collection_date_precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] - Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date Date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date + Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] + Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date Date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 + Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date Date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 + Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time Time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST + Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time Time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST + Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning + Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 + Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour + Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date Date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli - Sample collection and processing GENEPIO:0001232 environmental_site environmental_site environmental_site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site *isolation_source;animal_env;host_housing;env_local_scale;facility_type - Sample collection and processing GENEPIO:0001223 environmental_material environmental_material environmental_material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material *isolation_source - Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString TRUE The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic - Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population animal_or_plant_population menu null value menu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] - Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material anatomical_material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;*isolation_source - Sample collection and processing GENEPIO:0001216 body_product body_product body_product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;*isolation_source - Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part anatomical_part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part *isolation_source - Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region anatomical_region menu null value menu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] - Sample collection and processing GENEPIO:0100444 food_product food_product food_product menu null value menu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product - Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties food_product_properties menu null value menu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties *isolation_source;food_processing_method;food_preserv_proc - Sample collection and processing FOODON:03602001 label_claim label_claim label_claim menu null value menu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims - Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food animal_source_of_food menu null value menu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source - Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream food_product_production_stream menu null value menu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod - Sample collection and processing GENEPIO:0100447 food_packaging food_packaging food_packaging menu null value menu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap - Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date - Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 - Sample collection and processing GENEPIO:0001234 collection_device collection_device collection_device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;*isolation_source - Sample collection and processing GENEPIO:0001241 collection_method collection_method collection_method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method *isolation_source + Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env;host_housing;env_local_scale;facility_type + Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source + Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic + Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] + Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source + Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source + Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source + Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] + Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product + Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source;food_processing_method;food_preserv_proc + Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims + Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source + Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod + Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap + Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date Date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date + Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date Date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 + Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source + Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 - Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit sample_volume_measurement_unit menu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] - Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status residual_sample_status menu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] + Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] + Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit sample_storage_duration_unit menu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] + Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit menu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] - Sample collection and processing GENEPIO:0100690 available_data_types available_data_types available_data_types menu null value menu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] + Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] + Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria Environmental conditions and measurements Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 - Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units water_depth_units menu null value menu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 - Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units sediment_depth_units menu null value menu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 - Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units air_temperature_units menu null value menu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 - Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units water_temperature_units menu null value menu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type weather_type menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. + Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu + Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu + Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu + Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString GENEPIO:0001268 Host information host_information - Host information GENEPIO:0001386 host (common name) host_common_name host (common name) menu null value menu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host - Host information GENEPIO:0001387 host (scientific name) host_scientific_name host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host *isolation_source;host + Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host + Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed - Host information GENEPIO:0100452 host (food production name) host_food_production_name host (food production name) menu null value menu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host - Host information GENEPIO:0001394 host_age_bin host_age_bin host_age_bin menu null value menu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host + Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease GENEPIO:0100453 Strain and isolation information strain_and_isolation_information Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 - Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 *strain - Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString null value menu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 *strain + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 - Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString null value menu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 - Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString null value menu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 - Strain and isolation information GENEPIO:0100461 isolated_by isolated_by isolated_by menu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 + Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 + Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Strain and isolation information GENEPIO:0100465 isolation_date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date + Strain and isolation information GENEPIO:0100465 isolation_date isolation_date Date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Strain and isolation information GENEPIO:0001191 organism organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism *organism - Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process taxonomic_identification_process menu null value menu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] + Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism + Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 GENEPIO:0001441 Sequence information sequence_information Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 - Sequence information GENEPIO:0100416 sequenced_by sequenced_by sequenced_by menu null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by + Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing purpose_of_sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing + Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) - Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] - Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] - Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] + Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] + Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] + Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 - Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method genomic_target_enrichment_method menu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] + Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 Sequence information GENEPIO:0001449 amplicon size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 @@ -121,30 +133,30 @@ GRDI GENEPIO:0001150 Sample collection and processing GENEPIO:0001457 Bioinformatics and QC metrics Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination quality_control_determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control - Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues quality_control_issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage + Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control + Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper - Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet - Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper + Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet + Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 - Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 - Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 - Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 - Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 - Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 - Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 - Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 - Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 + Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 + Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 + Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 + Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 + Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 + Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ Integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 + Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length Integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf @@ -154,14 +166,14 @@ GRDI GENEPIO:0001150 Sample collection and processing Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc - Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 + Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date Date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 GENEPIO:0100477 Public repository information public_repository_information - Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by sequence_submitted_by menu null value menu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 - Public repository information GENEPIO:0100476 attribute_package attribute_package attribute_package menu null value menu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] + Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 @@ -169,612 +181,612 @@ GRDI GENEPIO:0001150 Sample collection and processing GENEPIO:0100478 Risk assessment information risk_assessment_information Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. - Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production stage_of_production menu null value menu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] - Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention experimental_intervention menu null value menu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention + Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] + Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance - Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AMR_testing_by menu null value menu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString null value menu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString null value menu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 - Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date Date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 + Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name antimicrobial_vendor_name null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString null value menu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString null value menu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString null value menu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString null value menu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString null value menu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString null value menu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString null value menu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString null value menu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString null value menu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString null value menu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype antimicrobial_phenotype menu null value menu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] *resistance_phenotype - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString null value menu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 *measurement - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units antimicrobial_measurement_units menu null value menu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] *measurement_units - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign antimicrobial_measurement_sign menu null value menu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] *measurement_sign - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method antimicrobial_laboratory_typing_method menu null value menu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] *laboratory_typing_method - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform antimicrobial_laboratory_typing_platform menu null value menu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name antimicrobial_vendor_name menu null value menu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard antimicrobial_testing_standard menu null value menu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] *testing_standard + Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 From c5325b4e5be0a66013480dfb52c6d2034367b9ef Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 19 Aug 2024 12:02:12 -0700 Subject: [PATCH 07/96] Begin matched vals fields --- lib/DataHarmonizer.js | 22 ++++++++++++++++++++++ web/templates/grdi/export.js | 22 ++++++++++++++++++++++ 2 files changed, 44 insertions(+) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 4e69b289..85920daa 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1784,6 +1784,28 @@ class DataHarmonizer { return valToCheck === valToMatch ? valToOutput : ''; } + /** + * TODO + * @param headerNameToCheck + * @param matchedValsSet + * @param inputRow + * @param sourceFieldNameMap + * @return {string} + */ + getMatchedValsField( + headerNameToCheck, + matchedValsSet, + inputRow, + sourceFieldNameMap) { + const valsToCheckStr = inputRow[sourceFieldNameMap[headerNameToCheck]]; + if (!valsToCheckStr) return ''; + + const valsToCheckArray = valsToCheckStr.split('; '); + const valsToOutputArray = + valsToCheckArray.filter((e) => matchedValsSet.has(e)); + return valsToOutputArray.join('; '); + } + /** * Some enumeration values get mapped over to export format values. * diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index a177d47e..68b7fa38 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -232,6 +232,28 @@ export default { inputRow, sourceFieldNameMap ); + } else if (headerName === 'host_housing') { + const matchedValsSet = new Set([ + 'Animal cage [ENVO:01000922]', + 'Aquarium [ENVO:00002196]', + 'Building [ENVO:00000073]', + 'Barn [ENVO:03501257]', + 'Breeder barn [ENVO:03501383]', + 'Broiler barn [ENVO:03501386]', + 'Sheep barn [ENVO:03501385]', + 'Pigsty [ENVO:03501413]', + 'Animal pen [ENVO:03501387]', + 'Stall [EOL:0001903]', + 'Poultry hatchery [ENVO:01001874]', + 'Roost (bird) [ENVO:03501439]', + 'Crate [ENVO:03501372]' + ]) + value = dh.getMatchedValsField( + 'environmental_site', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) } else { // Otherwise apply source (many to one) to target field transform: value = dh.getMappedField( From 0164921db2c6ddc8379554a6a08525a908a3dce3 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 19 Aug 2024 13:12:57 -0700 Subject: [PATCH 08/96] Prettier --- lib/DataHarmonizer.js | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 85920daa..2714f187 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1796,13 +1796,15 @@ class DataHarmonizer { headerNameToCheck, matchedValsSet, inputRow, - sourceFieldNameMap) { + sourceFieldNameMap + ) { const valsToCheckStr = inputRow[sourceFieldNameMap[headerNameToCheck]]; if (!valsToCheckStr) return ''; const valsToCheckArray = valsToCheckStr.split('; '); - const valsToOutputArray = - valsToCheckArray.filter((e) => matchedValsSet.has(e)); + const valsToOutputArray = valsToCheckArray.filter((e) => + matchedValsSet.has(e) + ); return valsToOutputArray.join('; '); } From 70309a6027dd4ba434cf5bab96fc6a7d33ad7b9a Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 19 Aug 2024 13:28:54 -0700 Subject: [PATCH 09/96] Finish implementing matched val fields * Needs testing --- web/templates/grdi/export.js | 202 +++++++++++++++++++++++++++++++++++ 1 file changed, 202 insertions(+) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 68b7fa38..1c26e87f 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -254,6 +254,208 @@ export default { inputRow, sourceFieldNameMap ) + } else if (headerName === 'env_local_scale') { + const matchedValsSet = new Set([ + 'Agricultural Field [ENVO:00000114]', + 'Alluvial fan [ENVO:00000314]', + 'Artificial wetland [ENVO:03501406]', + 'Breeding ground [ENVO:03501441]', + 'Creek [ENVO:03501405]', + 'Farm [ENVO:00000078]', + 'Beef farm [ENVO:03501443]', + 'Breeder farm [ENVO:03501384]', + 'Dairy farm [ENVO:03501416]', + 'Feedlot [ENVO:01000627]', + 'Beef cattle feedlot [ENVO:03501444]', + 'Fish farm [ENVO:00000294]', + 'Research farm [ENVO:03501417]', + 'Freshwater environment [ENVO:01000306]', + 'Hatchery [ENVO:01001873]', + 'Poultry hatchery [ENVO:01001874]', + 'Lake [ENVO:00000020]', + 'Manure lagoon (Anaerobic lagoon) [ENVO:03501423]', + 'Manure pit [ENVO:01001872]', + 'Marine environment [ENVO:01000320]', + 'Benthic zone [ENVO:03501440]', + 'Pelagic zone [ENVO:00000208]', + 'Park [ENVO:00000562]', + 'Pond [ENVO:00000033]', + 'Reservoir [ENVO:00000025]', + 'Irrigation reservoir [ENVO:00000450]', + 'River [ENVO:00000022]', + 'Roost (bird) [ENVO:03501439]', + 'Rural area [ENVO:01000772]', + 'Slough [ENVO:03501438]', + 'Stream [ENVO:00000023]', + 'Tributary [ENVO:00000495]', + 'Water surface [ENVO:01001191]', + 'Woodland area [ENVO:00000109]' + ]) + value = dh.getMatchedValsField( + 'environmental_site', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) + } else if (headerName === 'facility_type') { + const matchedValsSet = new Set([ + 'Abattoir [ENVO:01000925]', + 'Dairy [ENVO:00003862]', + 'Farm [ENVO:00000078]', + 'Hatchery [ENVO:01001873]', + 'Retail environment [ENVO:01001448]', + 'Shop [ENVO:00002221]', + 'Butcher shop [ENVO:03501396]', + 'Supermarket [ENVO:01000984]', + 'Manure digester facility [ENVO:03501422]' + ]) + value = dh.getMatchedValsField( + 'environmental_site', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) + } else if (headerName === 'coll_site_geo_feat') { + const matchedValsSet = new Set([ + 'Animal transportation equipment [AGRO:00000671]', + 'Dead haul trailer [GENEPIO:0100896]', + 'Dead haul truck [AGRO:00000673]', + 'Live haul trailer [GENEPIO:0100897]', + 'Live haul truck [AGRO:00000674]', + 'Bulk tank [ENVO:03501379]', + 'Animal feeding equipment [AGRO:00000675]', + 'Animal feeder [AGRO:00000679]', + 'Animal drinker [AGRO:00000680]', + 'Feed pan [AGRO:00000676]', + 'Watering bowl [AGRO:00000677]', + '"Belt [NCIT:C49844]', + 'Boot [GSSO:012935]', + 'Boot cover [OBI:0002806]', + 'Broom [ENVO:03501431]', + 'Bulk tank [ENVO:03501379]', + 'Chick box [AGRO:00000678]', + 'Chick pad [AGRO:00000672]', + 'Cleaning equipment [ENVO:03501430]', + 'Dumpster [ENVO:03501400]', + 'Egg belt [AGRO:00000670]', + 'Fan [NCIT:C49947]', + 'Freezer [ENVO:03501415]', + 'Freezer handle [ENVO:03501414]', + 'Plucking belt [AGRO:00000669]' + ]) + value = dh.getMatchedValsField( + 'environmental_material', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) + } else if (headerName === 'env_medium') { + const matchedValsSet = new Set([ + 'Air [ENVO:00002005]', + 'Alluvium [ENVO:01001202]', + 'Animal feeding equipment [AGRO:00000675]', + 'Animal feeder [AGRO:00000679]', + 'Animal drinker [AGRO:00000680]', + 'Feed pan [AGRO:00000676]', + 'Watering bowl [AGRO:00000677]', + 'Animal transportation equipment [AGRO:00000671]', + 'Dead haul trailer [GENEPIO:0100896]', + 'Dead haul truck [AGRO:00000673]', + 'Live haul trailer [GENEPIO:0100897]', + 'Live haul truck [AGRO:00000674]', + 'Belt [NCIT:C49844]', + 'Biosolids [ENVO:00002059]', + 'Boot [GSSO:012935]', + 'Boot cover [OBI:0002806]', + 'Broom [ENVO:03501431]', + 'Bulk tank [ENVO:03501379]', + 'Chick box [AGRO:00000678]', + 'Chick pad [AGRO:00000672]', + 'Cleaning equipment [ENVO:03501430]', + 'Compost [ENVO:00002170]', + 'Contaminated water [ENVO:00002186]', + 'Fecal slurry [ENVO:03501436]', + 'Fluid from meat rinse [GENEPIO:0004323]', + 'Effluent [ENVO:03501407]', + 'Influent [ENVO:03501442]', + 'Surface runoff [ENVO:03501408]', + 'Poultry plucking water [AGRO_00000693]', + 'Wastewater [ENVO:00002001]', + 'Weep fluid [AGRO_00000692]', + 'Crate [ENVO:03501372]', + 'Dumpster [ENVO:03501400]', + 'Dust [ENVO:00002008]', + 'Egg belt [AGRO:00000670]', + 'Fan [NCIT:C49947]', + 'Freezer [ENVO:03501415]', + 'Freezer handle [ENVO:03501414]', + 'Manure [ENVO:00003031]', + 'Animal manure [AGRO:00000079]', + 'Pig manure [AGRO:00000080]', + 'Manure digester equipment [ENVO:03501424]', + 'Nest [ENVO:03501432]', + 'Bird\'s nest [ENVO:00005805]', + 'Permafrost [ENVO:00000134]', + 'Plucking belt [AGRO:00000669]', + 'Poultry fluff [UBERON:0008291]', + 'Poultry litter [AGRO:00000080]', + 'Sediment [ENVO:00002007]', + 'Soil [ENVO:00001998]', + 'Agricultural soil [ENVO:00002259]', + 'Forest soil [ENVO:00002261]', + 'Straw [ENVO:00003869]', + 'Canola straw [FOODON:00004430]', + 'Oat straw [FOODON:03309878]', + 'Barley straw [FOODON:00004559]', + 'Water [CHEBI:15377]', + 'Drinking water [ENVO:00003064]', + 'Groundwater [ENVO:01001004]', + 'Surface water [ENVO:00002042]' + ]) + value = dh.getMatchedValsField( + 'environmental_material', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) + } else if (headerName === 'food_processing_method') { + const matchedValsSet = new Set([ + 'Food (cooked) [FOODON:00001181]', + 'Food (cut) [FOODON:00004291]', + 'Food (chopped) [FOODON:00002777]', + 'Food (chunks) [FOODON:00004555]', + 'Food (cubed) [FOODON:00004278]', + 'Food (diced) [FOODON:00004549]', + 'Food (grated) [FOODON:00004552]', + 'Food (sliced) [FOODON:00002455]', + 'Food (shredded) [FOODON:00004553]', + 'Food (fresh) [FOODON:00002457]', + 'Food (pulped) [FOODON:00004554]', + 'Food (raw) [FOODON:03311126]', + 'Food (unseasoned) [FOODON:00004287]', + 'Meat (boneless) [FOODON:00003467]', + 'Meat (skinless) [FOODON:00003468]', + 'Meat (with bone) [FOODON:02010116]', + 'Meat (with skin) [FOODON:02010111]' + ]) + value = dh.getMatchedValsField( + 'food_product_properties', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) + } else if (headerName === 'food_preserv_proc') { + const matchedValsSet = new Set([ + 'Food (canned) [FOODON:00002418]', + 'Food (dried) [FOODON:03307539]', + 'Food (frozen) [FOODON:03302148]' + ]) + value = dh.getMatchedValsField( + 'food_product_properties', + matchedValsSet, + inputRow, + sourceFieldNameMap + ) } else { // Otherwise apply source (many to one) to target field transform: value = dh.getMappedField( From d487691d6b305e46e999a712b7b35f1952d22fb4 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 19 Aug 2024 14:49:03 -0700 Subject: [PATCH 10/96] Update schema --- web/templates/grdi/schema.json | 91 +++++++++++++++++++++++----------- web/templates/grdi/schema.yaml | 82 ++++++++++++++++++++---------- 2 files changed, 118 insertions(+), 55 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index 64aaffdb..6f68b9aa 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -1763,6 +1763,29 @@ } } }, + "PrecipitationMeasurementUnitMenu": { + "name": "PrecipitationMeasurementUnitMenu", + "description": "", + "title": "precipitation_measurement_unit menu", + "from_schema": "https://example.com/GRDI", + "permissible_values": { + "millimeter (mm) [UO:0000016]": { + "text": "millimeter (mm) [UO:0000016]" + }, + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]" + } + } + }, "AvailableDataTypesMenu": { "name": "AvailableDataTypesMenu", "description": "", @@ -2713,8 +2736,8 @@ } } }, - "PriorSarsCov2InfectionMenu": { - "name": "PriorSarsCov2InfectionMenu", + "FoodProductMenu": { + "name": "FoodProductMenu", "description": "", "title": "food_product menu", "from_schema": "https://example.com/GRDI", @@ -5148,8 +5171,8 @@ "Illumina [GENEPIO:0100105]": { "text": "Illumina [GENEPIO:0100105]" }, - "Illumina Genome Analyzer [GENEPIO:0100106]": { - "text": "Illumina Genome Analyzer [GENEPIO:0100106]", + "Illumina Genome Analyzer [OBI:0002128]": { + "text": "Illumina Genome Analyzer [OBI:0002128]", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina Genome Analyzer II [OBI:0000703]": { @@ -5176,16 +5199,16 @@ "text": "Illumina HiSeq X Five [GENEPIO:0100112]", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq X Ten [GENEPIO:0100113]": { - "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", + "Illumina HiSeq X Ten [OBI:0002129]": { + "text": "Illumina HiSeq X Ten [OBI:0002129]", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 1000 [OBI:0002022]": { "text": "Illumina HiSeq 1000 [OBI:0002022]", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 1500 [GENEPIO:0100115]": { - "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", + "Illumina HiSeq 1500 [OBI:0003386]": { + "text": "Illumina HiSeq 1500 [OBI:0003386]", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 2000 [OBI:0002001]": { @@ -5216,12 +5239,12 @@ "text": "Illumina NovaSeq [GENEPIO:0100122]", "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina NovaSeq 6000 [GENEPIO:0100123]": { - "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "Illumina NovaSeq 6000 [OBI:0002630]": { + "text": "Illumina NovaSeq 6000 [OBI:0002630]", "is_a": "Illumina NovaSeq [GENEPIO:0100122]" }, - "Illumina MiniSeq [GENEPIO:0100124]": { - "text": "Illumina MiniSeq [GENEPIO:0100124]", + "Illumina MiniSeq [OBI:0003114]": { + "text": "Illumina MiniSeq [OBI:0003114]", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina MiSeq [OBI:0002003]": { @@ -5240,12 +5263,12 @@ "text": "Illumina NextSeq 550 [GENEPIO:0100128]", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, - "Illumina NextSeq 2000 [GENEPIO:0100129]": { - "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", + "Illumina NextSeq 1000 [OBI:0003606]": { + "text": "Illumina NextSeq 1000 [OBI:0003606]", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, - "Illumina NextSeq 1000 [GENEPIO:0004432]": { - "text": "Illumina NextSeq 1000 [GENEPIO:0004432]", + "Illumina NextSeq 2000 [GENEPIO:0100129]": { + "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "PacBio [GENEPIO:0100130]": { @@ -5259,12 +5282,12 @@ "text": "PacBio RS II [OBI:0002012]", "is_a": "PacBio [GENEPIO:0100130]" }, - "PacBio Sequel [GENEPIO:0100133]": { - "text": "PacBio Sequel [GENEPIO:0100133]", + "PacBio Sequel [OBI:0002632]": { + "text": "PacBio Sequel [OBI:0002632]", "is_a": "PacBio [GENEPIO:0100130]" }, - "PacBio Sequel II [GENEPIO:0100134]": { - "text": "PacBio Sequel II [GENEPIO:0100134]", + "PacBio Sequel II [OBI:0002632]": { + "text": "PacBio Sequel II [OBI:0002632]", "is_a": "PacBio [GENEPIO:0100130]" }, "Ion Torrent [GENEPIO:0100135]": { @@ -5297,12 +5320,14 @@ "text": "Oxford Nanopore GridION [GENEPIO:0100141]", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore MinION [GENEPIO:0100142]": { - "text": "Oxford Nanopore MinION [GENEPIO:0100142]", + "Oxford Nanopore MinION [OBI:0002750]": { + "text": "Oxford Nanopore MinION [OBI:0002750]", + "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore PromethION [GENEPIO:0100143]": { - "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", + "Oxford Nanopore PromethION [OBI:0002752]": { + "text": "Oxford Nanopore PromethION [OBI:0002752]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, "BGISEQ [GENEPIO:0100144]": { @@ -5470,7 +5495,15 @@ }, "Pathogen.env [GENEPIO:0100581]": { "text": "Pathogen.env [GENEPIO:0100581]" - }, + } + } + }, + "ExperimentalInterventionMenu": { + "name": "ExperimentalInterventionMenu", + "description": "", + "title": "experimental_intervention menu", + "from_schema": "https://example.com/GRDI", + "permissible_values": { "Addition of substances to food/water [GENEPIO:0100536]": { "text": "Addition of substances to food/water [GENEPIO:0100536]" }, @@ -5509,8 +5542,8 @@ } } }, - "AMRTestingByMenu": { - "name": "AMRTestingByMenu", + "AmrTestingByMenu": { + "name": "AmrTestingByMenu", "description": "", "title": "AMR_testing_by menu", "from_schema": "https://example.com/GRDI", @@ -7779,7 +7812,7 @@ ], "any_of": [ { - "range": "PresamplingWeatherConditionsMenu" + "range": "SamplingWeatherConditionsMenu" }, { "range": "NullValueMenu" @@ -30736,7 +30769,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "PresamplingWeatherConditionsMenu" + "range": "SamplingWeatherConditionsMenu" }, { "range": "NullValueMenu" diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 00f09e23..428f8ab8 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -4202,7 +4202,7 @@ slots: title: presampling_weather_conditions slot_uri: GENEPIO:0100780 any_of: - - range: PresamplingWeatherConditionsMenu + - range: SamplingWeatherConditionsMenu - range: NullValueMenu precipitation_measurement_value: name: precipitation_measurement_value @@ -13700,6 +13700,21 @@ enums: text: degree Fahrenheit (F) [UO:0000195] degree Celsius (C) [UO:0000027]: text: degree Celsius (C) [UO:0000027] + PrecipitationMeasurementUnitMenu: + name: PrecipitationMeasurementUnitMenu + title: precipitation_measurement_unit menu + description: '' + permissible_values: + millimeter (mm) [UO:0000016]: + text: millimeter (mm) [UO:0000016] + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] AvailableDataTypesMenu: name: AvailableDataTypesMenu title: available_data_types menu @@ -14384,8 +14399,8 @@ enums: text: Exterior anatomical region [BSPO:0000034] Interior anatomical region [BSPO:0000033]: text: Interior anatomical region [BSPO:0000033] - PriorSarsCov2InfectionMenu: - name: PriorSarsCov2InfectionMenu + FoodProductMenu: + name: FoodProductMenu title: food_product menu description: '' permissible_values: @@ -16140,8 +16155,8 @@ enums: permissible_values: Illumina [GENEPIO:0100105]: text: Illumina [GENEPIO:0100105] - Illumina Genome Analyzer [GENEPIO:0100106]: - text: Illumina Genome Analyzer [GENEPIO:0100106] + Illumina Genome Analyzer [OBI:0002128]: + text: Illumina Genome Analyzer [OBI:0002128] is_a: Illumina [GENEPIO:0100105] Illumina Genome Analyzer II [OBI:0000703]: text: Illumina Genome Analyzer II [OBI:0000703] @@ -16161,14 +16176,14 @@ enums: Illumina HiSeq X Five [GENEPIO:0100112]: text: Illumina HiSeq X Five [GENEPIO:0100112] is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq X Ten [GENEPIO:0100113]: - text: Illumina HiSeq X Ten [GENEPIO:0100113] + Illumina HiSeq X Ten [OBI:0002129]: + text: Illumina HiSeq X Ten [OBI:0002129] is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 1000 [OBI:0002022]: text: Illumina HiSeq 1000 [OBI:0002022] is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 1500 [GENEPIO:0100115]: - text: Illumina HiSeq 1500 [GENEPIO:0100115] + Illumina HiSeq 1500 [OBI:0003386]: + text: Illumina HiSeq 1500 [OBI:0003386] is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 2000 [OBI:0002001]: text: Illumina HiSeq 2000 [OBI:0002001] @@ -16191,11 +16206,11 @@ enums: Illumina NovaSeq [GENEPIO:0100122]: text: Illumina NovaSeq [GENEPIO:0100122] is_a: Illumina [GENEPIO:0100105] - Illumina NovaSeq 6000 [GENEPIO:0100123]: - text: Illumina NovaSeq 6000 [GENEPIO:0100123] + Illumina NovaSeq 6000 [OBI:0002630]: + text: Illumina NovaSeq 6000 [OBI:0002630] is_a: Illumina NovaSeq [GENEPIO:0100122] - Illumina MiniSeq [GENEPIO:0100124]: - text: Illumina MiniSeq [GENEPIO:0100124] + Illumina MiniSeq [OBI:0003114]: + text: Illumina MiniSeq [OBI:0003114] is_a: Illumina [GENEPIO:0100105] Illumina MiSeq [OBI:0002003]: text: Illumina MiSeq [OBI:0002003] @@ -16209,12 +16224,12 @@ enums: Illumina NextSeq 550 [GENEPIO:0100128]: text: Illumina NextSeq 550 [GENEPIO:0100128] is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 1000 [OBI:0003606]: + text: Illumina NextSeq 1000 [OBI:0003606] + is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 2000 [GENEPIO:0100129]: text: Illumina NextSeq 2000 [GENEPIO:0100129] is_a: Illumina NextSeq [GENEPIO:0100126] - Illumina NextSeq 1000 [GENEPIO:0004432]: - text: Illumina NextSeq 1000 [GENEPIO:0004432] - is_a: Illumina NextSeq [GENEPIO:0100126] PacBio [GENEPIO:0100130]: text: PacBio [GENEPIO:0100130] PacBio RS [GENEPIO:0100131]: @@ -16223,11 +16238,11 @@ enums: PacBio RS II [OBI:0002012]: text: PacBio RS II [OBI:0002012] is_a: PacBio [GENEPIO:0100130] - PacBio Sequel [GENEPIO:0100133]: - text: PacBio Sequel [GENEPIO:0100133] + PacBio Sequel [OBI:0002632]: + text: PacBio Sequel [OBI:0002632] is_a: PacBio [GENEPIO:0100130] - PacBio Sequel II [GENEPIO:0100134]: - text: PacBio Sequel II [GENEPIO:0100134] + PacBio Sequel II [OBI:0002632]: + text: PacBio Sequel II [OBI:0002632] is_a: PacBio [GENEPIO:0100130] Ion Torrent [GENEPIO:0100135]: text: Ion Torrent [GENEPIO:0100135] @@ -16251,11 +16266,21 @@ enums: Oxford Nanopore GridION [GENEPIO:0100141]: text: Oxford Nanopore GridION [GENEPIO:0100141] is_a: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore MinION [GENEPIO:0100142]: - text: Oxford Nanopore MinION [GENEPIO:0100142] + Oxford Nanopore MinION [OBI:0002750]: + text: Oxford Nanopore MinION [OBI:0002750] + description: A portable DNA sequencer which is manufactured by the Oxford + Nanopore Technologies corporation, that uses consumable flow cells producing + up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time + results and utilizes nanopore technology with up to 512 nanopore channels + in the sensor array. is_a: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore PromethION [GENEPIO:0100143]: - text: Oxford Nanopore PromethION [GENEPIO:0100143] + Oxford Nanopore PromethION [OBI:0002752]: + text: Oxford Nanopore PromethION [OBI:0002752] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, capable of running up to 48 flow cells and producing up to + 7.6 Tb of data per run. The sequencer produces real-time results and utilizes + Nanopore technology, with each flow cell allowing up to 3,000 nanopores + to be sequencing simultaneously. is_a: Oxford Nanopore [GENEPIO:0100140] BGISEQ [GENEPIO:0100144]: text: BGISEQ [GENEPIO:0100144] @@ -16368,6 +16393,11 @@ enums: text: Pathogen.cl [GENEPIO:0001835] Pathogen.env [GENEPIO:0100581]: text: Pathogen.env [GENEPIO:0100581] + ExperimentalInterventionMenu: + name: ExperimentalInterventionMenu + title: experimental_intervention menu + description: '' + permissible_values: Addition of substances to food/water [GENEPIO:0100536]: text: Addition of substances to food/water [GENEPIO:0100536] Antimicrobial pre-treatment [GENEPIO:0100537]: @@ -16392,8 +16422,8 @@ enums: text: Probiotic pre-treatment [GENEPIO:0100547] Vaccination [NCIT:C15346]: text: Vaccination [NCIT:C15346] - AMRTestingByMenu: - name: AMRTestingByMenu + AmrTestingByMenu: + name: AmrTestingByMenu title: AMR_testing_by menu description: '' permissible_values: From 93b6b619488a831afb56145764e99d55b6b94bc2 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 19 Aug 2024 14:49:22 -0700 Subject: [PATCH 11/96] Update schema --- web/templates/grdi/schema_enums.tsv | 31 +++++++++++++++++------------ web/templates/grdi/schema_slots.tsv | 2 +- 2 files changed, 19 insertions(+), 14 deletions(-) diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 61d37bd0..991bea19 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -453,6 +453,11 @@ air_temperature_units menu AirTemperatureUnitsMenu degree Fahrenheit (F) [UO:00 water_temperature_units menu WaterTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] degree Celsius (C) [UO:0000027] +precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu millimeter (mm) [UO:0000016] + centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702] Experimental parameters documentation [GENEPIO:0100703] @@ -714,7 +719,7 @@ anatomical_region menu AnatomicalRegionMenu Dorso-lateral region [BSPO:0000080] Interior anatomical region [BSPO:0000033] -food_product menu PriorSarsCov2InfectionMenu Animal feed [ENVO:02000047] +food_product menu FoodProductMenu Animal feed [ENVO:02000047] Blood meal [FOODON:00001564] Bone meal [ENVO:02000054] Brassica carinata meal [FOODON:00004310] @@ -1367,16 +1372,16 @@ sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] - Illumina Genome Analyzer [GENEPIO:0100106] + Illumina Genome Analyzer [OBI:0002128] Illumina Genome Analyzer II [OBI:0000703] Illumina Genome Analyzer IIx [OBI:0002000] Illumina HiScanSQ [GENEPIO:0100109] Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq X [GENEPIO:0100111] Illumina HiSeq X Five [GENEPIO:0100112] - Illumina HiSeq X Ten [GENEPIO:0100113] + Illumina HiSeq X Ten [OBI:0002129] Illumina HiSeq 1000 [OBI:0002022] - Illumina HiSeq 1500 [GENEPIO:0100115] + Illumina HiSeq 1500 [OBI:0003386] Illumina HiSeq 2000 [OBI:0002001] Illumina HiSeq 2500 [OBI:0002002] Illumina HiSeq 3000 [OBI:0002048] @@ -1384,19 +1389,19 @@ sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] Illumina iSeq [GENEPIO:0100120] Illumina iSeq 100 [GENEPIO:0100121] Illumina NovaSeq [GENEPIO:0100122] - Illumina NovaSeq 6000 [GENEPIO:0100123] - Illumina MiniSeq [GENEPIO:0100124] + Illumina NovaSeq 6000 [OBI:0002630] + Illumina MiniSeq [OBI:0003114] Illumina MiSeq [OBI:0002003] Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 500 [OBI:0002021] Illumina NextSeq 550 [GENEPIO:0100128] + Illumina NextSeq 1000 [OBI:0003606] Illumina NextSeq 2000 [GENEPIO:0100129] - Illumina NextSeq 1000 [GENEPIO:0004432] PacBio [GENEPIO:0100130] PacBio RS [GENEPIO:0100131] PacBio RS II [OBI:0002012] - PacBio Sequel [GENEPIO:0100133] - PacBio Sequel II [GENEPIO:0100134] + PacBio Sequel [OBI:0002632] + PacBio Sequel II [OBI:0002632] Ion Torrent [GENEPIO:0100135] Ion Torrent PGM [GENEPIO:0100136] Ion Torrent Proton [GENEPIO:0100137] @@ -1405,8 +1410,8 @@ sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] Oxford Nanopore [GENEPIO:0100140] Oxford Nanopore Flongle [GENEPIO:0004433] Oxford Nanopore GridION [GENEPIO:0100141] - Oxford Nanopore MinION [GENEPIO:0100142] - Oxford Nanopore PromethION [GENEPIO:0100143] + Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. BGISEQ [GENEPIO:0100144] BGISEQ-500 [GENEPIO:0100145] DNBSEQ [GENEPIO:0100146] @@ -1455,7 +1460,7 @@ attribute_package menu AttributePackageMenu Pathogen.cl [GENEPIO:0001835] Pathogen.env [GENEPIO:0100581] -experimental_intervention menu PriorSarsCov2InfectionMenu Addition of substances to food/water [GENEPIO:0100536] +experimental_intervention menu ExperimentalInterventionMenu Addition of substances to food/water [GENEPIO:0100536] Antimicrobial pre-treatment [GENEPIO:0100537] Certified animal husbandry practices [GENEPIO:0100538] Certified organic farming practices [GENEPIO:0100539] @@ -1469,7 +1474,7 @@ experimental_intervention menu PriorSarsCov2InfectionMenu Addition of substance Vaccination [NCIT:C15346] -AMR_testing_by menu AMRTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] +AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] Health Canada (HC) [GENEPIO:0100554] diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 0b5920d3..6c1fa469 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -75,7 +75,7 @@ GRDI GENEPIO:0001150 Sample collection and processing Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. - Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu + Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString From 085b1a2b65a294a2d0f538fdaccc4c10acfad47a Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 19 Aug 2024 14:53:17 -0700 Subject: [PATCH 12/96] Complex if then else --- web/templates/grdi/export.js | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 1c26e87f..97d8b090 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -455,7 +455,24 @@ export default { matchedValsSet, inputRow, sourceFieldNameMap - ) + ); + } else if (headerName === '*source_type') { + const hostScientificName = + inputRow[sourceFieldNameMap['host_scientific_name']]; + const foodProduct = inputRow[sourceFieldNameMap['food_product']]; + const nullValsSet = new Set( + Object.keys( + dh.schema.enums.NullValueMenu.permissible_values + ).concat(['', null]) + ); + + if (hostScientificName === 'Homo sapiens [NCBITaxon:9606]') { + value = 'Human'; + } else if (nullValsSet.has(foodProduct)) { + value = 'Animal'; + } else { + value = 'Food'; + } } else { // Otherwise apply source (many to one) to target field transform: value = dh.getMappedField( From 3defcfb8443f6f6a7c2b0b130796ec401fb8ad76 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 20 Aug 2024 10:59:04 -0700 Subject: [PATCH 13/96] Cascading nulls case --- lib/DataHarmonizer.js | 22 ++++++++++++++++++++++ web/templates/grdi/export.js | 10 ++++++++++ 2 files changed, 32 insertions(+) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 2714f187..d820e2ac 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1808,6 +1808,28 @@ class DataHarmonizer { return valsToOutputArray.join('; '); } + /** + * TODO + * @param headerNamesToCheck + * @param inputRow + * @param sourceFieldNameMap + * @return {string} + */ + getFirstNonNullField( + headerNamesToCheck, + inputRow, + sourceFieldNameMap + ) { + const nullValsSet = new Set( + Object.keys(this.schema.enums.NullValueMenu.permissible_values) + .concat(['', null]) + ); + const valsToCheck = + headerNamesToCheck.map((e) => inputRow[sourceFieldNameMap[e]]); + const firstNonNullVal = valsToCheck.find((e) => !nullValsSet.has(e.trim())); + return firstNonNullVal ? firstNonNullVal : ''; + } + /** * Some enumeration values get mapped over to export format values. * diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 97d8b090..6e74c1df 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -473,6 +473,16 @@ export default { } else { value = 'Food'; } + } else if (headerName === 'host') { + value = dh.getFirstNonNullField( + [ + 'host_scientific_name', + 'host_common_name', + 'host_food_production_name' + ], + inputRow, + sourceFieldNameMap + ) } else { // Otherwise apply source (many to one) to target field transform: value = dh.getMappedField( From da5f483e2342a94fca18d96018aa8ee2382f8813 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 20 Aug 2024 11:18:36 -0700 Subject: [PATCH 14/96] Helpful TODO --- lib/DataHarmonizer.js | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index d820e2ac..84c3e4d3 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1826,6 +1826,7 @@ class DataHarmonizer { ); const valsToCheck = headerNamesToCheck.map((e) => inputRow[sourceFieldNameMap[e]]); + // TODO trim because copy pasting from excel == '\r\n'; wider issue? const firstNonNullVal = valsToCheck.find((e) => !nullValsSet.has(e.trim())); return firstNonNullVal ? firstNonNullVal : ''; } From 2c8005bb56dbebb085c46c8ca40bdbdcf595d5bc Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 20 Aug 2024 11:20:37 -0700 Subject: [PATCH 15/96] Prettier --- lib/DataHarmonizer.js | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 84c3e4d3..1ed0a5d0 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1815,17 +1815,16 @@ class DataHarmonizer { * @param sourceFieldNameMap * @return {string} */ - getFirstNonNullField( - headerNamesToCheck, - inputRow, - sourceFieldNameMap - ) { + getFirstNonNullField(headerNamesToCheck, inputRow, sourceFieldNameMap) { const nullValsSet = new Set( - Object.keys(this.schema.enums.NullValueMenu.permissible_values) - .concat(['', null]) + Object.keys(this.schema.enums.NullValueMenu.permissible_values).concat([ + '', + null, + ]) + ); + const valsToCheck = headerNamesToCheck.map( + (e) => inputRow[sourceFieldNameMap[e]] ); - const valsToCheck = - headerNamesToCheck.map((e) => inputRow[sourceFieldNameMap[e]]); // TODO trim because copy pasting from excel == '\r\n'; wider issue? const firstNonNullVal = valsToCheck.find((e) => !nullValsSet.has(e.trim())); return firstNonNullVal ? firstNonNullVal : ''; From 5843a34232f51b0fa320e5729777b385eae62328 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 22 Aug 2024 13:27:10 -0700 Subject: [PATCH 16/96] wip --- lib/DataHarmonizer.js | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 1ed0a5d0..39bc9a84 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1822,11 +1822,12 @@ class DataHarmonizer { null, ]) ); - const valsToCheck = headerNamesToCheck.map( - (e) => inputRow[sourceFieldNameMap[e]] - ); + const valsToCheck = headerNamesToCheck.map((headerName) => { + const valToCheck = inputRow[sourceFieldNameMap[headerName]]; // TODO trim because copy pasting from excel == '\r\n'; wider issue? - const firstNonNullVal = valsToCheck.find((e) => !nullValsSet.has(e.trim())); + return typeof valToCheck === 'string' ? valToCheck.trim() : valToCheck; + }); + const firstNonNullVal = valsToCheck.find((e) => !nullValsSet.has(e)); return firstNonNullVal ? firstNonNullVal : ''; } From 3093260f98fbe568fe04af68b843fb086cea8b7f Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 22 Aug 2024 13:29:25 -0700 Subject: [PATCH 17/96] Prettier --- lib/DataHarmonizer.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 39bc9a84..b34a1822 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1824,7 +1824,7 @@ class DataHarmonizer { ); const valsToCheck = headerNamesToCheck.map((headerName) => { const valToCheck = inputRow[sourceFieldNameMap[headerName]]; - // TODO trim because copy pasting from excel == '\r\n'; wider issue? + // TODO trim because copy pasting from excel == '\r\n'; wider issue? return typeof valToCheck === 'string' ? valToCheck.trim() : valToCheck; }); const firstNonNullVal = valsToCheck.find((e) => !nullValsSet.has(e)); From 59e17b2c5f43c471f6506f05e05e2a1182dee69c Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 22 Aug 2024 14:45:54 -0700 Subject: [PATCH 18/96] Finish implementation --- web/templates/grdi/export.js | 25 ++++++++++--------------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 6e74c1df..78a0b0de 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -112,22 +112,22 @@ export default { status: 'published', method: function (dh) { const ExportHeaders = new Map([ - ['*sample_name', []], + ['sample_name', []], ['sample_title', []], ['bioproject_accession', []], - ['*strain', []], + ['strain', []], ['isolate_name_alias', []], ['culture_collection', []], ['reference_material', []], - ['*organism', []], - ['*collected_by', []], - ['*collection_date', []], + ['organism', []], + ['collected_by', []], + ['collection_date', []], ['cult_isol_date', []], - ['*geo_loc_name', []], - ['*isolation_source', []], - ['*source_type', []], + ['geo_loc_name', []], + ['isolation_source', []], + ['source_type', []], ['samp_collect_device', []], - ['*purpose_of_sampling', []], + ['purpose_of_sampling', []], ['project_name', []], ['ifsac_category', []], ['lat_lon', []], @@ -196,11 +196,6 @@ export default { ['extr_weather_event', []], ['mechanical_damage', []] ]); -// -// -// EXAMPLE -// environmental_siteXenv_local_scale = "Agricultural Field [ENVO:00000114], Alluvial fan [ENVO:00000314], Artificial wetland [ENVO:03501406], Breeding ground [ENVO:03501441], Creek [ENVO:03501405], Farm [ENVO:00000078], Beef farm [ENVO:03501443], Breeder farm [ENVO:03501384], Dairy farm [ENVO:03501416], Feedlot [ENVO:01000627], Beef cattle feedlot [ENVO:03501444], Fish farm [ENVO:00000294], Research farm [ENVO:03501417], Freshwater environment [ENVO:01000306], Hatchery [ENVO:01001873], Poultry hatchery [ENVO:01001874], Lake [ENVO:00000020], Manure lagoon (Anaerobic lagoon) [ENVO:03501423], Manure pit [ENVO:01001872], Marine environment [ENVO:01000320], Benthic zone [ENVO:03501440], Pelagic zone [ENVO:00000208], Park [ENVO:00000562], Pond [ENVO:00000033], Reservoir [ENVO:00000025], Irrigation reservoir [ENVO:00000450], River [ENVO:00000022], Roost (bird) [ENVO:03501439], Rural area [ENVO:01000772], Slough [ENVO:03501438], Stream [ENVO:00000023], Tributary [ENVO:00000495], Water surface [ENVO:01001191], Woodland area [ENVO:00000109]".split(",") - const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); @@ -456,7 +451,7 @@ export default { inputRow, sourceFieldNameMap ); - } else if (headerName === '*source_type') { + } else if (headerName === 'source_type') { const hostScientificName = inputRow[sourceFieldNameMap['host_scientific_name']]; const foodProduct = inputRow[sourceFieldNameMap['food_product']]; From 9edbb4fe05db730a6960cc360d2719f020c9fa0b Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 22 Aug 2024 15:15:04 -0700 Subject: [PATCH 19/96] jsdoc --- lib/DataHarmonizer.js | 55 ++++++++++++++++++++++++++++++------------- 1 file changed, 38 insertions(+), 17 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index b34a1822..4c012c40 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1763,14 +1763,27 @@ class DataHarmonizer { } /** + * Given a table row, output a value based on the following conditional: + * ``` + * if (value in headerNameToCheck == valToMatch) { + * return value in headerNameToOutput; + * } else { + * return ""; + * } + * ``` * TODO is there any need for additional complexities in getMappedField? * i.e., transforming field - * @param headerNameToCheck - * @param valToMatch - * @param headerNameToOutput - * @param inputRow - * @param sourceFieldNameMap - * @return TODO + * @param {string} headerNameToCheck Field name of user-inputted vals to check + * against `valToMatch`. + * @param {string} valToMatch Value to match user-inputted vals against during + * conditional. + * @param {string} headerNameToOutput Field name of user-inputted vals to + * return if conditional is satisfied. + * @param {string[]} inputRow Table row. + * @param {Object} sourceFieldNameMap `getFieldNameMap` return + * val. + * @return {string} `valToMatch` if condition is satisfied; empty str + * otherwise. */ getIfThenField( headerNameToCheck, @@ -1785,12 +1798,17 @@ class DataHarmonizer { } /** - * TODO - * @param headerNameToCheck - * @param matchedValsSet - * @param inputRow - * @param sourceFieldNameMap - * @return {string} + * Given a table row, find the intersection of user-inputted values in + * `headerNameToCheck` and vals in `matchedValsSet`. + * @param {string} headerNameToCheck Field name of user-inputted vals to + * intersect against `matchedValsSet`. + * @param {Set} matchedValsSet Set of values that user-inputted vals + * are intersected against. + * @param {string[]} inputRow Table row. + * @param {Object} sourceFieldNameMap `getFieldNameMap` return + * val. + * @return {string} Intersection of user-inputted values in + * `headerNameToCheck` and vals in `matchedValsSet`. */ getMatchedValsField( headerNameToCheck, @@ -1809,11 +1827,14 @@ class DataHarmonizer { } /** - * TODO - * @param headerNamesToCheck - * @param inputRow - * @param sourceFieldNameMap - * @return {string} + * Given a table row, and an ordered collection of field names, return the + * first non-null field val. + * @param {string[]} headerNamesToCheck Field names of user-inputted vals to + * check for non-null vals, in 0-indexed order. + * @param {string[]} inputRow Table row. + * @param {Object} sourceFieldNameMap `getFieldNameMap` return + * val. + * @return {string} First non-null val in `headerNamesToCheck`. */ getFirstNonNullField(headerNamesToCheck, inputRow, sourceFieldNameMap) { const nullValsSet = new Set( From 1e5b58efa7cd2c0238b56f3fd828e190b59a6dab Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 22 Aug 2024 15:21:08 -0700 Subject: [PATCH 20/96] Stale TODO --- web/templates/grdi/export.js | 2 -- 1 file changed, 2 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 78a0b0de..01a200d2 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -209,8 +209,6 @@ export default { const outputRow = []; for (const [headerName, sources] of ExportHeaders) { let value; - // TODO some of these seem like they are supposed to have picklists, - // but do not? if (headerName === 'fertilizer_admin') { value = dh.getIfThenField( 'presampling_activity', From 298cbcd22eeda96e4d208eb30fd3693a23a01589 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Fri, 23 Aug 2024 14:13:49 -0700 Subject: [PATCH 21/96] Update schema --- web/templates/grdi/schema.json | 8 ++++++-- web/templates/grdi/schema.yaml | 2 ++ web/templates/grdi/schema_slots.tsv | 2 +- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index 6f68b9aa..7aac0bbf 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -7099,7 +7099,9 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product" + "BIOSAMPLE:food_product", + "NCBI_BIOSAMPLE_Enterics:isolation_source", + "NCBI_BIOSAMPLE_Enterics:food_product_type" ], "slot_uri": "GENEPIO:0100444", "domain_of": [ @@ -29932,7 +29934,9 @@ "from_schema": "https://example.com/GRDI", "exact_mappings": [ "BIOSAMPLE:isolation_source", - "BIOSAMPLE:food_product" + "BIOSAMPLE:food_product", + "NCBI_BIOSAMPLE_Enterics:isolation_source", + "NCBI_BIOSAMPLE_Enterics:food_product_type" ], "rank": 45, "slot_uri": "GENEPIO:0100444", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 428f8ab8..99b4cd89 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -3839,6 +3839,8 @@ slots: exact_mappings: - BIOSAMPLE:isolation_source - BIOSAMPLE:food_product + - NCBI_BIOSAMPLE_Enterics:isolation_source + - NCBI_BIOSAMPLE_Enterics:food_product_type food_product_properties: name: food_product_properties title: food_product_properties diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 6c1fa469..d97837eb 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -44,7 +44,7 @@ GRDI GENEPIO:0001150 Sample collection and processing Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] - Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product + Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source;food_processing_method;food_preserv_proc Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source From d94e5dfee96918384f3c306e30350a4e95b676da Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 29 Aug 2024 10:35:02 -0700 Subject: [PATCH 22/96] Update schema --- web/templates/grdi/schema.json | 123 ++++++++++++++------- web/templates/grdi/schema.yaml | 165 +++++++++++++++++++++++++--- web/templates/grdi/schema_enums.tsv | 95 ++++++++-------- web/templates/grdi/schema_slots.tsv | 8 +- 4 files changed, 282 insertions(+), 109 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index 7aac0bbf..d1a69987 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -2288,6 +2288,17 @@ "text": "Barley straw [FOODON:00004559]", "is_a": "Straw [ENVO:00003869]" }, + "Sludge [ENVO:00002044]": { + "text": "Sludge [ENVO:00002044]" + }, + "Primary sludge [ENVO:00002057]": { + "text": "Primary sludge [ENVO:00002057]", + "is_a": "Sludge [ENVO:00002044]" + }, + "Secondary sludge [ENVO:00002058]": { + "text": "Secondary sludge [ENVO:00002058]", + "is_a": "Sludge [ENVO:00002044]" + }, "Water [CHEBI:15377]": { "text": "Water [CHEBI:15377]" }, @@ -5164,160 +5175,199 @@ }, "SequencingInstrumentMenu": { "name": "SequencingInstrumentMenu", - "description": "", + "description": "A DNA sequencer manufactured by the Illumina corporation.", "title": "sequencing_instrument menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "Illumina [GENEPIO:0100105]": { - "text": "Illumina [GENEPIO:0100105]" + "text": "Illumina [GENEPIO:0100105]", + "description": "A DNA sequencer manufactured by the Illumina corporation." }, "Illumina Genome Analyzer [OBI:0002128]": { "text": "Illumina Genome Analyzer [OBI:0002128]", + "description": "A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina Genome Analyzer II [OBI:0000703]": { "text": "Illumina Genome Analyzer II [OBI:0000703]", + "description": "A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina Genome Analyzer IIx [OBI:0002000]": { "text": "Illumina Genome Analyzer IIx [OBI:0002000]", + "description": "An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina HiScanSQ [GENEPIO:0100109]": { "text": "Illumina HiScanSQ [GENEPIO:0100109]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an \"SQ Module\" to support microfluidics.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina HiSeq [GENEPIO:0100110]": { "text": "Illumina HiSeq [GENEPIO:0100110]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina HiSeq X [GENEPIO:0100111]": { "text": "Illumina HiSeq X [GENEPIO:0100111]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq X Five [GENEPIO:0100112]": { "text": "Illumina HiSeq X Five [GENEPIO:0100112]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq X Ten [OBI:0002129]": { "text": "Illumina HiSeq X Ten [OBI:0002129]", + "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 1000 [OBI:0002022]": { "text": "Illumina HiSeq 1000 [OBI:0002022]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 1500 [OBI:0003386]": { "text": "Illumina HiSeq 1500 [OBI:0003386]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 2000 [OBI:0002001]": { "text": "Illumina HiSeq 2000 [OBI:0002001]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 2500 [OBI:0002002]": { "text": "Illumina HiSeq 2500 [OBI:0002002]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 3000 [OBI:0002048]": { "text": "Illumina HiSeq 3000 [OBI:0002048]", + "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq 4000 [OBI:0002049]": { "text": "Illumina HiSeq 4000 [OBI:0002049]", + "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina iSeq [GENEPIO:0100120]": { "text": "Illumina iSeq [GENEPIO:0100120]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina iSeq 100 [GENEPIO:0100121]": { "text": "Illumina iSeq 100 [GENEPIO:0100121]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", "is_a": "Illumina iSeq [GENEPIO:0100120]" }, "Illumina NovaSeq [GENEPIO:0100122]": { "text": "Illumina NovaSeq [GENEPIO:0100122]", + "description": "A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina NovaSeq 6000 [OBI:0002630]": { "text": "Illumina NovaSeq 6000 [OBI:0002630]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", "is_a": "Illumina NovaSeq [GENEPIO:0100122]" }, "Illumina MiniSeq [OBI:0003114]": { "text": "Illumina MiniSeq [OBI:0003114]", + "description": "A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina MiSeq [OBI:0002003]": { "text": "Illumina MiSeq [OBI:0002003]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina NextSeq [GENEPIO:0100126]": { "text": "Illumina NextSeq [GENEPIO:0100126]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina NextSeq 500 [OBI:0002021]": { "text": "Illumina NextSeq 500 [OBI:0002021]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "Illumina NextSeq 550 [GENEPIO:0100128]": { "text": "Illumina NextSeq 550 [GENEPIO:0100128]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "Illumina NextSeq 1000 [OBI:0003606]": { "text": "Illumina NextSeq 1000 [OBI:0003606]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "Illumina NextSeq 2000 [GENEPIO:0100129]": { "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "PacBio [GENEPIO:0100130]": { - "text": "PacBio [GENEPIO:0100130]" + "text": "PacBio [GENEPIO:0100130]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation." }, "PacBio RS [GENEPIO:0100131]": { "text": "PacBio RS [GENEPIO:0100131]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", "is_a": "PacBio [GENEPIO:0100130]" }, "PacBio RS II [OBI:0002012]": { "text": "PacBio RS II [OBI:0002012]", + "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", "is_a": "PacBio [GENEPIO:0100130]" }, "PacBio Sequel [OBI:0002632]": { "text": "PacBio Sequel [OBI:0002632]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", "is_a": "PacBio [GENEPIO:0100130]" }, - "PacBio Sequel II [OBI:0002632]": { - "text": "PacBio Sequel II [OBI:0002632]", + "PacBio Sequel II [OBI:0002633]": { + "text": "PacBio Sequel II [OBI:0002633]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", "is_a": "PacBio [GENEPIO:0100130]" }, "Ion Torrent [GENEPIO:0100135]": { - "text": "Ion Torrent [GENEPIO:0100135]" + "text": "Ion Torrent [GENEPIO:0100135]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation." }, "Ion Torrent PGM [GENEPIO:0100136]": { "text": "Ion Torrent PGM [GENEPIO:0100136]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", "is_a": "Ion Torrent [GENEPIO:0100135]" }, "Ion Torrent Proton [GENEPIO:0100137]": { "text": "Ion Torrent Proton [GENEPIO:0100137]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", "is_a": "Ion Torrent [GENEPIO:0100135]" }, "Ion Torrent S5 XL [GENEPIO:0100138]": { "text": "Ion Torrent S5 XL [GENEPIO:0100138]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", "is_a": "Ion Torrent [GENEPIO:0100135]" }, "Ion Torrent S5 [GENEPIO:0100139]": { "text": "Ion Torrent S5 [GENEPIO:0100139]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", "is_a": "Ion Torrent [GENEPIO:0100135]" }, "Oxford Nanopore [GENEPIO:0100140]": { - "text": "Oxford Nanopore [GENEPIO:0100140]" + "text": "Oxford Nanopore [GENEPIO:0100140]", + "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation." }, "Oxford Nanopore Flongle [GENEPIO:0004433]": { "text": "Oxford Nanopore Flongle [GENEPIO:0004433]", + "description": "An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, "Oxford Nanopore GridION [GENEPIO:0100141]": { "text": "Oxford Nanopore GridION [GENEPIO:0100141]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, "Oxford Nanopore MinION [OBI:0002750]": { @@ -5331,29 +5381,36 @@ "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, "BGISEQ [GENEPIO:0100144]": { - "text": "BGISEQ [GENEPIO:0100144]" + "text": "BGISEQ [GENEPIO:0100144]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation." }, "BGISEQ-500 [GENEPIO:0100145]": { "text": "BGISEQ-500 [GENEPIO:0100145]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", "is_a": "BGISEQ [GENEPIO:0100144]" }, "DNBSEQ [GENEPIO:0100146]": { - "text": "DNBSEQ [GENEPIO:0100146]" + "text": "DNBSEQ [GENEPIO:0100146]", + "description": "A DNA sequencer manufactured by the MGI corporation." }, "DNBSEQ-T7 [GENEPIO:0100147]": { "text": "DNBSEQ-T7 [GENEPIO:0100147]", + "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day.", "is_a": "DNBSEQ [GENEPIO:0100146]" }, "DNBSEQ-G400 [GENEPIO:0100148]": { "text": "DNBSEQ-G400 [GENEPIO:0100148]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run.", "is_a": "DNBSEQ [GENEPIO:0100146]" }, "DNBSEQ-G400 FAST [GENEPIO:0100149]": { "text": "DNBSEQ-G400 FAST [GENEPIO:0100149]", + "description": "A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400.", "is_a": "DNBSEQ [GENEPIO:0100146]" }, "DNBSEQ-G50 [GENEPIO:0100150]": { "text": "DNBSEQ-G50 [GENEPIO:0100150]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", "is_a": "DNBSEQ [GENEPIO:0100146]" } } @@ -6195,10 +6252,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host_am", - "NCBI_BIOSAMPLE_Enterics:fertilizer_admin" - ], "slot_uri": "GENEPIO:0100433", "domain_of": [ "GRDI" @@ -6831,10 +6884,7 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_site", "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:animal_env", - "NCBI_BIOSAMPLE_Enterics:host_housing", - "NCBI_BIOSAMPLE_Enterics:env_local_scale", - "NCBI_BIOSAMPLE_Enterics:facility_type" + "NCBI_BIOSAMPLE_Enterics:animal_env" ], "slot_uri": "GENEPIO:0001232", "domain_of": [ @@ -7137,9 +7187,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:food_product_properties", - "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:food_processing_method", - "NCBI_BIOSAMPLE_Enterics:food_preserv_proc" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "slot_uri": "GENEPIO:0100445", "domain_of": [ @@ -8934,10 +8982,10 @@ ], "range": "WhitespaceMinimizedString" }, - "assembly_filename": { - "name": "assembly_filename", + "genome_sequence_filename": { + "name": "genome_sequence_filename", "description": "The user-defined filename of the FASTA file.", - "title": "assembly_filename", + "title": "genome sequence filename", "comments": [ "Provide the FASTA filename." ], @@ -8947,7 +8995,7 @@ } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001461", + "slot_uri": "GENEPIO:0101715", "domain_of": [ "GRDI" ], @@ -25294,8 +25342,8 @@ "rank": 125, "slot_group": "Sequence information" }, - "assembly_filename": { - "name": "assembly_filename", + "genome_sequence_filename": { + "name": "genome_sequence_filename", "rank": 126, "slot_group": "Sequence information" }, @@ -28894,10 +28942,6 @@ } ], "from_schema": "https://example.com/GRDI", - "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:host_am", - "NCBI_BIOSAMPLE_Enterics:fertilizer_admin" - ], "rank": 11, "slot_uri": "GENEPIO:0100433", "alias": "presampling_activity", @@ -29634,10 +29678,7 @@ "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_site", "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:animal_env", - "NCBI_BIOSAMPLE_Enterics:host_housing", - "NCBI_BIOSAMPLE_Enterics:env_local_scale", - "NCBI_BIOSAMPLE_Enterics:facility_type" + "NCBI_BIOSAMPLE_Enterics:animal_env" ], "rank": 37, "slot_uri": "GENEPIO:0001232", @@ -29976,9 +30017,7 @@ "exact_mappings": [ "BIOSAMPLE:isolation_source", "BIOSAMPLE:food_product_properties", - "NCBI_BIOSAMPLE_Enterics:isolation_source", - "NCBI_BIOSAMPLE_Enterics:food_processing_method", - "NCBI_BIOSAMPLE_Enterics:food_preserv_proc" + "NCBI_BIOSAMPLE_Enterics:isolation_source" ], "rank": 46, "slot_uri": "GENEPIO:0100445", @@ -32093,10 +32132,10 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "assembly_filename": { - "name": "assembly_filename", + "genome_sequence_filename": { + "name": "genome_sequence_filename", "description": "The user-defined filename of the FASTA file.", - "title": "assembly_filename", + "title": "genome sequence filename", "comments": [ "Provide the FASTA filename." ], @@ -32107,8 +32146,8 @@ ], "from_schema": "https://example.com/GRDI", "rank": 126, - "slot_uri": "GENEPIO:0001461", - "alias": "assembly_filename", + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_filename", "owner": "GRDI", "domain_of": [ "GRDI" diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 99b4cd89..8e1e4841 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -142,7 +142,7 @@ classes: - r1_fastq_filename - r2_fastq_filename - fast5_filename - - assembly_filename + - genome_sequence_filename - quality_control_method_name - quality_control_method_version - quality_control_determination @@ -1178,7 +1178,7 @@ classes: fast5_filename: rank: 125 slot_group: Sequence information - assembly_filename: + genome_sequence_filename: rank: 126 slot_group: Sequence information quality_control_method_name: @@ -3333,9 +3333,6 @@ slots: - range: NullValueMenu examples: - value: Antimicrobial pre-treatment [GENEPIO:0100537] - exact_mappings: - - NCBI_BIOSAMPLE_Enterics:host_am - - NCBI_BIOSAMPLE_Enterics:fertilizer_admin presampling_activity_details: name: presampling_activity_details title: presampling_activity_details @@ -3684,9 +3681,6 @@ slots: - BIOSAMPLE:environmental_site - NCBI_BIOSAMPLE_Enterics:isolation_source - NCBI_BIOSAMPLE_Enterics:animal_env - - NCBI_BIOSAMPLE_Enterics:host_housing - - NCBI_BIOSAMPLE_Enterics:env_local_scale - - NCBI_BIOSAMPLE_Enterics:facility_type environmental_material: name: environmental_material title: environmental_material @@ -3863,8 +3857,6 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:food_product_properties - NCBI_BIOSAMPLE_Enterics:isolation_source - - NCBI_BIOSAMPLE_Enterics:food_processing_method - - NCBI_BIOSAMPLE_Enterics:food_preserv_proc label_claim: name: label_claim title: label_claim @@ -4843,12 +4835,12 @@ slots: range: WhitespaceMinimizedString examples: - value: batch1a_sequences.fast5 - assembly_filename: - name: assembly_filename - title: assembly_filename + genome_sequence_filename: + name: genome_sequence_filename + title: genome sequence filename description: The user-defined filename of the FASTA file. comments: Provide the FASTA filename. - slot_uri: GENEPIO:0001461 + slot_uri: GENEPIO:0101715 range: WhitespaceMinimizedString examples: - value: pathogenassembly123.fasta @@ -14077,6 +14069,14 @@ enums: Barley straw [FOODON:00004559]: text: Barley straw [FOODON:00004559] is_a: Straw [ENVO:00003869] + Sludge [ENVO:00002044]: + text: Sludge [ENVO:00002044] + Primary sludge [ENVO:00002057]: + text: Primary sludge [ENVO:00002057] + is_a: Sludge [ENVO:00002044] + Secondary sludge [ENVO:00002058]: + text: Secondary sludge [ENVO:00002058] + is_a: Sludge [ENVO:00002044] Water [CHEBI:15377]: text: Water [CHEBI:15377] Drinking water [ENVO:00003064]: @@ -16153,120 +16153,238 @@ enums: SequencingInstrumentMenu: name: SequencingInstrumentMenu title: sequencing_instrument menu - description: '' + description: A DNA sequencer manufactured by the Illumina corporation. permissible_values: Illumina [GENEPIO:0100105]: text: Illumina [GENEPIO:0100105] + description: A DNA sequencer manufactured by the Illumina corporation. Illumina Genome Analyzer [OBI:0002128]: text: Illumina Genome Analyzer [OBI:0002128] + description: A DNA sequencer manufactured by Solexa as one of its first sequencer + lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data + in a single run. is_a: Illumina [GENEPIO:0100105] Illumina Genome Analyzer II [OBI:0000703]: text: Illumina Genome Analyzer II [OBI:0000703] + description: A DNA sequencer which is manufactured by Illumina (Solexa) corporation. + it support sequencing of single or paired end clone libraries relying on + sequencing by synthesis technology is_a: Illumina [GENEPIO:0100105] Illumina Genome Analyzer IIx [OBI:0002000]: text: Illumina Genome Analyzer IIx [OBI:0002000] + description: An Illumina Genome Analyzer II which is manufactured by the Illumina + corporation. It supports sequencing of single, long or short insert paired + end clone libraries relying on sequencing by synthesis technology. The Genome + Analyzer IIx is the most widely adopted next-generation sequencing platform + and proven and published across the broadest range of research applications. is_a: Illumina [GENEPIO:0100105] Illumina HiScanSQ [GENEPIO:0100109]: text: Illumina HiScanSQ [GENEPIO:0100109] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing + and microarray-based analyses as well as an "SQ Module" to support microfluidics. is_a: Illumina [GENEPIO:0100105] Illumina HiSeq [GENEPIO:0100110]: text: Illumina HiSeq [GENEPIO:0100110] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, enabling deep sequencing and high yield. is_a: Illumina [GENEPIO:0100105] Illumina HiSeq X [GENEPIO:0100111]: text: Illumina HiSeq X [GENEPIO:0100111] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that oenabled sufficent depth and coverage + to produce the first 30x human genome for $1000. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq X Five [GENEPIO:0100112]: text: Illumina HiSeq X Five [GENEPIO:0100112] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing + Systems. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq X Ten [OBI:0002129]: text: Illumina HiSeq X Ten [OBI:0002129] + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 1000 [OBI:0002022]: text: Illumina HiSeq 1000 [OBI:0002022] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 1500 [OBI:0003386]: text: Illumina HiSeq 1500 [OBI:0003386] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell. Built upon sequencing by synthesis technology, + the machine employs dual surface imaging and offers two high-output options + and one rapid-run option. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 2000 [OBI:0002001]: text: Illumina HiSeq 2000 [OBI:0002001] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 2500 [OBI:0002002]: text: Illumina HiSeq 2500 [OBI:0002002] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 3000 [OBI:0002048]: text: Illumina HiSeq 3000 [OBI:0002048] + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 4000 [OBI:0002049]: text: Illumina HiSeq 4000 [OBI:0002049] + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. is_a: Illumina HiSeq [GENEPIO:0100110] Illumina iSeq [GENEPIO:0100120]: text: Illumina iSeq [GENEPIO:0100120] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight. is_a: Illumina [GENEPIO:0100105] Illumina iSeq 100 [GENEPIO:0100121]: text: Illumina iSeq 100 [GENEPIO:0100121] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight and has an output capacity + between 144MB-1.2GB. is_a: Illumina iSeq [GENEPIO:0100120] Illumina NovaSeq [GENEPIO:0100122]: text: Illumina NovaSeq [GENEPIO:0100122] + description: A DNA sequencer manufactured by the Illunina corporation using + sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and + 20 billion reads in dual flow cell mode. is_a: Illumina [GENEPIO:0100105] Illumina NovaSeq 6000 [OBI:0002630]: text: Illumina NovaSeq 6000 [OBI:0002630] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). + The sequencer utilizes synthesis technology and patterned flow cells to + optimize throughput and even spacing of sequencing clusters. is_a: Illumina NovaSeq [GENEPIO:0100122] Illumina MiniSeq [OBI:0003114]: text: Illumina MiniSeq [OBI:0003114] + description: A small benchtop DNA sequencer which is manufactured by the Illumina + corporation with integrated cluster generation, sequencing and data analysis. + The sequencer accommodates various flow cell configurations and can produce + up to 25M single reads or 50M paired-end reads per run. is_a: Illumina [GENEPIO:0100105] Illumina MiSeq [OBI:0002003]: text: Illumina MiSeq [OBI:0002003] + description: A DNA sequencer which is manufactured by the Illumina corporation. + Built upon sequencing by synthesis technology, the machine provides an end-to-end + solution (cluster generation, amplification, sequencing, and data analysis) + in a single machine. is_a: Illumina [GENEPIO:0100105] Illumina NextSeq [GENEPIO:0100126]: text: Illumina NextSeq [GENEPIO:0100126] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. is_a: Illumina [GENEPIO:0100105] Illumina NextSeq 500 [OBI:0002021]: text: Illumina NextSeq 500 [OBI:0002021] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 550 [GENEPIO:0100128]: text: Illumina NextSeq 550 [GENEPIO:0100128] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. The 550 is an upgrade on the 500 model. is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 1000 [OBI:0003606]: text: Illumina NextSeq 1000 [OBI:0003606] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 + and P2 flow cells. is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 2000 [GENEPIO:0100129]: text: Illumina NextSeq 2000 [GENEPIO:0100129] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 30-360 Gb. is_a: Illumina NextSeq [GENEPIO:0100126] PacBio [GENEPIO:0100130]: text: PacBio [GENEPIO:0100130] + description: A DNA sequencer manufactured by the Pacific Biosciences corporation. PacBio RS [GENEPIO:0100131]: text: PacBio RS [GENEPIO:0100131] + description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ + \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ + \ The RS was the first model made by the company." is_a: PacBio [GENEPIO:0100130] PacBio RS II [OBI:0002012]: text: PacBio RS II [OBI:0002012] + description: A DNA sequencer which is manufactured by the Pacific Biosciences + corporation. Built upon single molecule real-time sequencing technology, + the machine is optimized for generation with long reads and high consensus + accuracy. is_a: PacBio [GENEPIO:0100130] PacBio Sequel [OBI:0002632]: text: PacBio Sequel [OBI:0002632] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation with long reads and high consensus + accuracy, and manufactured by the Pacific Biosciences corporation is_a: PacBio [GENEPIO:0100130] - PacBio Sequel II [OBI:0002632]: - text: PacBio Sequel II [OBI:0002632] + PacBio Sequel II [OBI:0002633]: + text: PacBio Sequel II [OBI:0002633] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation of highly accurate ("HiFi") long reads, + and which is manufactured by the Pacific Biosciences corporation. is_a: PacBio [GENEPIO:0100130] Ion Torrent [GENEPIO:0100135]: text: Ion Torrent [GENEPIO:0100135] + description: A DNA sequencer manufactured by the Ion Torrent corporation. Ion Torrent PGM [GENEPIO:0100136]: text: Ion Torrent PGM [GENEPIO:0100136] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of 300 + MB - 1GB. is_a: Ion Torrent [GENEPIO:0100135] Ion Torrent Proton [GENEPIO:0100137]: text: Ion Torrent Proton [GENEPIO:0100137] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of up to + 15 Gb. is_a: Ion Torrent [GENEPIO:0100135] Ion Torrent S5 XL [GENEPIO:0100138]: text: Ion Torrent S5 XL [GENEPIO:0100138] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material while producing data faster than the S5 model. is_a: Ion Torrent [GENEPIO:0100135] Ion Torrent S5 [GENEPIO:0100139]: text: Ion Torrent S5 [GENEPIO:0100139] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material. is_a: Ion Torrent [GENEPIO:0100135] Oxford Nanopore [GENEPIO:0100140]: text: Oxford Nanopore [GENEPIO:0100140] + description: A DNA sequencer manufactured by the Oxford Nanopore corporation. Oxford Nanopore Flongle [GENEPIO:0004433]: text: Oxford Nanopore Flongle [GENEPIO:0004433] + description: An adapter for MinION or GridION DNA sequencers manufactured + by the Oxford Nanopore corporation that enables sequencing on smaller, single-use + flow cells. is_a: Oxford Nanopore [GENEPIO:0100140] Oxford Nanopore GridION [GENEPIO:0100141]: text: Oxford Nanopore GridION [GENEPIO:0100141] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, that can run and analyze up to five individual flow cells producing + up to 150 Gb of data per run. The sequencer produces real-time results and + utilizes nanopore technology with the option of running the flow cells concurrently + or individual is_a: Oxford Nanopore [GENEPIO:0100140] Oxford Nanopore MinION [OBI:0002750]: text: Oxford Nanopore MinION [OBI:0002750] @@ -16286,22 +16404,35 @@ enums: is_a: Oxford Nanopore [GENEPIO:0100140] BGISEQ [GENEPIO:0100144]: text: BGISEQ [GENEPIO:0100144] + description: A DNA sequencer manufactured by the BGI Genomics corporation. BGISEQ-500 [GENEPIO:0100145]: text: BGISEQ-500 [GENEPIO:0100145] + description: A DNA sequencer manufactured by the BGI Genomics corporation + that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". is_a: BGISEQ [GENEPIO:0100144] DNBSEQ [GENEPIO:0100146]: text: DNBSEQ [GENEPIO:0100146] + description: A DNA sequencer manufactured by the MGI corporation. DNBSEQ-T7 [GENEPIO:0100147]: text: DNBSEQ-T7 [GENEPIO:0100147] + description: A high throughput DNA sequencer manufactured by the MGI corporation + with an output capacity of 1~6TB of data per day. is_a: DNBSEQ [GENEPIO:0100146] DNBSEQ-G400 [GENEPIO:0100148]: text: DNBSEQ-G400 [GENEPIO:0100148] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB~1440GB per run. is_a: DNBSEQ [GENEPIO:0100146] DNBSEQ-G400 FAST [GENEPIO:0100149]: text: DNBSEQ-G400 FAST [GENEPIO:0100149] + description: A DNA sequencer manufactured by the MGI corporation with an outout + capacity of 55GB~330GB per run, which enables faster sequencing than the + DNBSEQ-G400. is_a: DNBSEQ [GENEPIO:0100146] DNBSEQ-G50 [GENEPIO:0100150]: text: DNBSEQ-G50 [GENEPIO:0100150] + description: "A DNA sequencer manufactured by the MGI corporation with an\ + \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." is_a: DNBSEQ [GENEPIO:0100146] SequencingAssayTypeMenu: name: SequencingAssayTypeMenu diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 991bea19..97c6d38c 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -598,6 +598,9 @@ environmental_material menu EnvironmentalMaterialMenu Air [ENVO:00002005] Canola straw [FOODON:00004430] Oat straw [FOODON:03309878] Barley straw [FOODON:00004559] + Sludge [ENVO:00002044] + Primary sludge [ENVO:00002057] + Secondary sludge [ENVO:00002058] Water [CHEBI:15377] Drinking water [ENVO:00003064] Groundwater [ENVO:01001004] @@ -1371,54 +1374,54 @@ sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] MGI [GENEPIO:0004325] -sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] - Illumina Genome Analyzer [OBI:0002128] - Illumina Genome Analyzer II [OBI:0000703] - Illumina Genome Analyzer IIx [OBI:0002000] - Illumina HiScanSQ [GENEPIO:0100109] - Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq X [GENEPIO:0100111] - Illumina HiSeq X Five [GENEPIO:0100112] - Illumina HiSeq X Ten [OBI:0002129] - Illumina HiSeq 1000 [OBI:0002022] - Illumina HiSeq 1500 [OBI:0003386] - Illumina HiSeq 2000 [OBI:0002001] - Illumina HiSeq 2500 [OBI:0002002] - Illumina HiSeq 3000 [OBI:0002048] - Illumina HiSeq 4000 [OBI:0002049] - Illumina iSeq [GENEPIO:0100120] - Illumina iSeq 100 [GENEPIO:0100121] - Illumina NovaSeq [GENEPIO:0100122] - Illumina NovaSeq 6000 [OBI:0002630] - Illumina MiniSeq [OBI:0003114] - Illumina MiSeq [OBI:0002003] - Illumina NextSeq [GENEPIO:0100126] - Illumina NextSeq 500 [OBI:0002021] - Illumina NextSeq 550 [GENEPIO:0100128] - Illumina NextSeq 1000 [OBI:0003606] - Illumina NextSeq 2000 [GENEPIO:0100129] - PacBio [GENEPIO:0100130] - PacBio RS [GENEPIO:0100131] - PacBio RS II [OBI:0002012] - PacBio Sequel [OBI:0002632] - PacBio Sequel II [OBI:0002632] - Ion Torrent [GENEPIO:0100135] - Ion Torrent PGM [GENEPIO:0100136] - Ion Torrent Proton [GENEPIO:0100137] - Ion Torrent S5 XL [GENEPIO:0100138] - Ion Torrent S5 [GENEPIO:0100139] - Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore Flongle [GENEPIO:0004433] - Oxford Nanopore GridION [GENEPIO:0100141] +sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. + Illumina Genome Analyzer [OBI:0002128] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. + Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + Illumina HiSeq X Ten [OBI:0002129] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Illumina HiSeq 1500 [OBI:0003386] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. + Illumina NovaSeq 6000 [OBI:0002630] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + Illumina MiniSeq [OBI:0003114] A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + Illumina NextSeq 1000 [OBI:0003606] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + PacBio Sequel [OBI:0002632] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + PacBio Sequel II [OBI:0002633] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - BGISEQ [GENEPIO:0100144] - BGISEQ-500 [GENEPIO:0100145] - DNBSEQ [GENEPIO:0100146] - DNBSEQ-T7 [GENEPIO:0100147] - DNBSEQ-G400 [GENEPIO:0100148] - DNBSEQ-G400 FAST [GENEPIO:0100149] - DNBSEQ-G50 [GENEPIO:0100150] + BGISEQ [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + DNBSEQ [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. + DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. + DNBSEQ-G400 FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. + DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. sequencing_assay_type menu SequencingAssayTypeMenu Amplicon sequencing assay [OBI:0002767] diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index d97837eb..2a6ce49a 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -10,7 +10,7 @@ GRDI GENEPIO:0001150 Sample collection and processing Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] host_am;fertilizer_admin + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] @@ -36,7 +36,7 @@ GRDI GENEPIO:0001150 Sample collection and processing Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date Date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli - Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env;host_housing;env_local_scale;facility_type + Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] @@ -45,7 +45,7 @@ GRDI GENEPIO:0001150 Sample collection and processing Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type - Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source;food_processing_method;food_preserv_proc + Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod @@ -129,7 +129,7 @@ GRDI GENEPIO:0001150 Sample collection and processing Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 - Sequence information GENEPIO:0001461 assembly_filename assembly_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta + Sequence information GENEPIO:0101715 genome sequence filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta GENEPIO:0001457 Bioinformatics and QC metrics Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 From 3ddc6f2bdd1bf9bb3c5a884764eb40497ffc2491 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 5 Sep 2024 12:49:17 -0700 Subject: [PATCH 23/96] version bump Addition of dh-validate.py script. --- package.json | 2 +- script/dh-validate.py | 531 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 532 insertions(+), 1 deletion(-) create mode 100644 script/dh-validate.py diff --git a/package.json b/package.json index 7a0a2af3..5850c9f5 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "data-harmonizer", - "version": "1.6.9", + "version": "1.7.0", "description": "A standardized spreadsheet editor and validator that can be run offline and locally", "repository": "git@github.com:cidgoh/DataHarmonizer.git", "license": "MIT", diff --git a/script/dh-validate.py b/script/dh-validate.py new file mode 100644 index 00000000..61d0657a --- /dev/null +++ b/script/dh-validate.py @@ -0,0 +1,531 @@ +#!/opt/anaconda3/bin/python + +# dh-validate.py +# +# A script to validate DataHarmonizer data files according to a given schema +# and optionally Class, in the case of data files that don't identify which +# class their fields are from. Passes data file to linkml-validate. +# +# To prepare tsv/csv/xls/xlsx files for above validation, this script will +# remove header lines until it encounters a line with every cell containing +# text, which is assumed to be the field name header. (IN FUTURE this will +# be sniffed better). This includes removing section header line if any. +# Then a temporary file is created in yaml format, which adjusts number fields +# to be unquoted if linkml spec says its a number, and it is a valid number. +# As well, multivalued fields are split up into an array of separate values. +# cli linkml-validate is then applied to this temporary file. +# +# DataHarmonizer-generated data file with its section headers must be removed, +# +# +# Options: +# -s, --schema FILE Schema file to validate data against +# -C, --target-class TEXT +# -S, --index-slot TEXT top level slot. Required for CSV dumping/loading +# -V, --version Show the version and exit. +# +# > cd web/templates/[template folder]/ +# > python ../../../script/dh-validate.py +# +# Allowed data file types: '.tsv','.csv','.xls','.xlsx','.json','.yml','.yaml' +# Some formats (.json, .yml, .yaml) are evolving on DH side so not yet tested. +# +# dh-validate.py --schema schema.yaml test_data.csv +# dh-validate.py --schema schema.yaml --target-class "CanCOGeN Covid-19" some_data_file.csv +# +# Author: Damion Dooley +# + +from collections import OrderedDict +from decimal import Decimal +import csv +import re +from openpyxl import load_workbook # For .xlsx +import xlrd # for .xls // pip install xlrd +import yaml +import json +import pathlib +import os +from sys import exit +import argparse +from linkml_runtime.utils.schemaview import SchemaView +from linkml_runtime.dumpers.yaml_dumper import YAMLDumper +import subprocess + +# ISSUE TRYING TO IMPORT linkml, getting "error: no such option: --schema" when --schema provided to argparse; and "Input LinkML schema file not given" when not given that parameter! +""" +try: + from linkml.validator import validate +except Exception as inst: + print(type(inst)) # the exception type + print(inst.args) # arguments stored in .args + print(inst) # __str__ allows args to be printed directly, + # but may be overridden in exception subclasses +""" + +def init_parser(): + + parser = argparse.ArgumentParser( + prog='dh-validate', + description='A wrapper around linkml-validate for validating data files against a LinkML schema.', + epilog='For more information, see https://github.com/cidgoh/DataHarmonizer/') + + # FUTURE: In case of json, schema will be provided in data file url, and + # potentially can be looked up dynamically. + parser.add_argument("-s", "--schema", + dest="schema_path", + metavar="FILE", + default= os.getcwd() +"/schema.yaml", + help='A LinkML yaml schema to test given data file against. Default is "schema.yaml"'); + + parser.add_argument("-C", "--target-class", + dest="target_class", + metavar="TEXT", + required=False, + help="A schema class to test given data file against."); + + parser.add_argument("-S", "--index-slot", + dest="index_slot", + metavar="TEXT", + required=False, + help="A slot within target class which acts as an identifier or unique key. This is required for CSV dumping/loading. It is optional when this slot can be identified automatically as the only identifier or unique_key in the slot."); + + parser.add_argument('data_sources', + metavar='DATA_SOURCES', + #nargs='+', + help="One or more data files to validate using given schema."); + + """ parser.add_argument("-V", "--version", + dest="version", + default=False, + help="Return version # and then exit.", + ) + """ + + return parser.parse_args(); + + +# For a given schema, return the class that possibly fits data to be +# validated. Also return the "index_slot" or likely identifier or +# primary key slot, useful in converting tabular tsv / csv data. +# +# Currently tries to match inputted target_class if any. +# Alternately returns class if there is only one in schema. +# Future: could sniff data to see what matches best in case where +# there are multiple classes. + +def getTargetClass(SCHEMA, target_class, slot_key = None): + templates = {}; + for name, class_obj in SCHEMA.all_classes().items(): + # Generate schema's list of possible template classes: + if name == 'dh_interface': # Archaic class + continue; + templates[name] = class_obj; + + if target_class and not target_class in templates: + exit("The given validation target class [" + target_class + "] was not found in schema!"); + + # So far many DH schemas only have one class so only possibility is to validate against that: + if not target_class: + if len(templates) == 1: + target_class = next(iter(templates.keys())); + else: + # FUTURE: determine if one of the multiple classes is a good match for given data. + exit("No validation class was provided, and no default could be found!"); + + # Determined target_class at this point. + found = False; + template = SCHEMA.get_class(target_class); + for name in SCHEMA.class_slots(target_class): + slot = template['attributes'][name]; + if 'identifier' in slot and slot['identifier'] == True: + if slot_key: + if slot_key != name: + continue; # Continue search + else: + found = True; + break; + # Pick first eligable slot key if none provided on command line + else: + found = True; + slot_key = name; + + break; + + if not found: + exit("Target class [" + target_class + "] does not have an identifier or key slot!"); + + print ("index:", slot_key); + return (target_class, slot_key); + + +# A dictionary of all the sections that may appear on first line of a DH data file +def getSlotGroupTitleDict(SCHEMA, target_class): + + slot_group_titles = {}; + + template = SCHEMA.get_class(target_class); + for name in SCHEMA.class_slots(target_class): + slot = template['attributes'][name]; + #print("SLOT", slot); + if slot['slot_group'] and slot['slot_group'] > '': + slot_group_titles[slot['slot_group']] = True; + + return slot_group_titles; + + +def getSlotTitleToNameDict(SCHEMA, target_class): + slot_title_name_map = {}; + + template = SCHEMA.get_class(target_class); + for name in SCHEMA.class_slots(target_class): + slot = template['attributes'][name]; + slot_title_name_map[slot['title']] = name; + + return slot_title_name_map; + + +# Used to compose columns of new output file +# uses class.slots array to determine order, which should be same as +# order in slot_usage and its rank. FUTURE: ensure sort by slot_usage rank, +# if any. +def getSlotNameToTitleDict(SCHEMA, target_class): + slot_name_title_map = OrderedDict(); + + template = SCHEMA.get_class(target_class); + for name in SCHEMA.class_slots(target_class): + slot = template['attributes'][name]; + slot_name_title_map[name] = slot['title'] or None; + + return slot_name_title_map; + + +# LinkML validation doesn't care about order of fields, so we can add +# missing schema headers in appropriate columns (according to ordering) +# with empty values. This enables a "new" tabular data file to be saved. +# subsequent data columns have to be mapped over however. + +# Returns converted headers along with a report of mismatched headers which +# arise when old schema applied to newer data file or visa versa. +# In contrast to JSON, schema-version-appropriate tabular data should mention +# All columns/slots in SCHEMA +def getNormalizedHeaders(SCHEMA, target_class, row, slot_header_map, slot_title_map): + + report = OrderedDict(); + header_count = 0; + + # Data_row_map will always have a place for every place in row. + data_row_map = []; + ignored = OrderedDict(); + + for field in row: + if field in slot_header_map: # row already mentions slot name + data_row_map.append(field); + header_count +=1; + continue; + + if field in slot_title_map: # row mentions slot title, so translate. + data_row_map.append(slot_title_map[field]); + report[field] = 'Mapped "' + field + '" to ' + slot_title_map[field]; + header_count +=1; + continue; + + # Possibly old naming that doesn't match title but would match name, try: + # try_name = Lower(regexreplace(regexreplace(field,"[ /]","_"),"[-()]","")). + # ... + + else: + data_row_map.append(''); + ignored[field] = 'Ignored "' + field + '", not in schema.'; + + # TO DO: Determine how to handle rows with fewer or more unmatched columns. + if header_count < len(row): + exit ("Data file is missing fields: " + str(report)); + # FUTURE: allow shorter (empty tail) rows? NO. + # take out unused columns? + + report |= ignored; # Add ignored fields to end of report. + + return (tuple(data_row_map), report, header_count); + + +# A normalized data file has tsv/csv/xls/xlsx files converted to JSON format. +# (This does not handle .yaml, .yml, .json-ld since those are validated ok +# with data elements saved by LinkML slot name rather than title.) +# +# FUTURE: handle situation where for every section there is only one slot name/title +def getNormalizedDataFile(SCHEMA, target_class, data_source, temp_base): + + if not os.path.isfile(data_source): + exit("ERROR: Data file not found: " + data_source); + + # slot_group_titles = getSlotGroupTitleDict(SCHEMA, target_class); + slot_title_map = getSlotTitleToNameDict(SCHEMA, target_class); + slot_header_map = getSlotNameToTitleDict(SCHEMA, target_class); + file_path_obj = pathlib.Path(data_source); + target_class_CC = re.sub("[_ (/)-]","", target_class)# CamelCase version. + reader = None; + + if file_path_obj.suffix in ['.xls','.xlsx']: + file_mode = "rb" + else: + file_mode = "r" + + with open(data_source, file_mode) as data_handle: + + match file_path_obj.suffix: + + case '.yaml' | '.yml': + exit("ERROR: getNormalizedDataFile() does not process yaml/yml files."); + + # For CSV and TSV, if reader.fieldnames has empty labels, it means its + # not a header line, i.e. skipping "section" line or other stuff. + # (Don't even need to use "next(data_handle)") + # Here we find reader.fieldnames, AND move reader TO FIRST ROW OF DATA. + case '.csv' | '.tsv': + while True: + reader = csv.DictReader(data_handle, dialect = ('excel' if file_path_obj.suffix == ".csv" else 'excel-tab')); + # Empty fieldname indicates superfluous initial row. + if not '' in reader.fieldnames: + # Found row of full table cells. Additional test on cell text = slot name/title? + (header_row, report, header_count) = getNormalizedHeaders(SCHEMA, target_class, reader.fieldnames, slot_header_map, slot_title_map); + break; + + # Excell types can hold multiple tabs, each of which needs to be validated separately. + # Excel returns a tuple, one value position for each column. + case '.xlsx': + + workbook = load_workbook(data_source); + if target_class in workbook.sheetnames or target_class_CC in workbook.sheetnames: # e.g. ['Sheet1'], also note "sheet.title" + sheet = workbook.worksheets[workbook.sheetnames.index(target_class_CC)]; + else: + if len(workbook.sheetnames) > 1: + exit("ERROR: getNormalizedDataFile() cannot find " + target_class + " tab in excel spreadsheet tabs: " + str(workbook.sheetnames)); + else: + sheet = workbook.worksheets[0]; # pick the one and only tab/sheet. + + reader = sheet.iter_rows(values_only=True); + + for row in reader: + # Skip superfluous header liness: + if not '' in row: + # Found row with value in each cell, so likely header. + (header_row, report, header_count) = getNormalizedHeaders(SCHEMA, target_class, row, slot_header_map, slot_title_map); + break; + + # Aligning .xls with same output as .xlsx + case '.xls': + + workbook = xlrd.open_workbook(data_source); + sheets = workbook.nsheets; + sheetnames = workbook.sheet_names(); + if target_class in sheetnames: + sheet = workbook.sheet_by_index(sheetnames.index(target_class)); + else: + if sheets > 1: + exit("ERROR: getNormalizedDataFile() cannot find " + target_class + " tab in excel spreadsheet tabs: " + str(sheetnames)); + else: + sheet = workbook.sheet_by_index(0); + + # Returns array of values for given row + reader = iter(tuple([sheet.cell_value(rx, cx) for cx in range(sheet.ncols)]) for rx in range(sheet.nrows)); + + for row in reader: + # Skip superfluous header liness: + if not '' in row: + (header_row, report, header_count) = getNormalizedHeaders(SCHEMA, target_class, row, slot_header_map, slot_title_map); + break; + + case _: + exit("ERROR: Data file doesn't have compatible type ('tsv/csv/xls/xlsx/json/yml/yaml) :" + data_source); + + # Write both normalized TSV and JSON files: + + yaml = writeTmpFiles (SCHEMA, target_class, header_row, reader, temp_base); + + return (yaml, report); + + +def writeTmpFiles (SCHEMA, target_class, header_row, reader, temp_base): + # First row of DH tabular data may be slot_groups + # 2nd DH row likely has column/field/slot names which need adjustment + # (newline = '' prevents extra blank line) + data = []; + template = SCHEMA.get_class(target_class); + + with open(temp_base + '.tsv', 'w', newline='') as tsv_file: + + writer = csv.DictWriter(tsv_file, fieldnames = header_row, dialect='excel-tab'); + writer.writeheader(); + + # We are in the data rows now, which can be written to new file: + for row in reader: + + if type(row) is tuple: # xls/xlsx: for value in row: + row_data = {k: v for k, v in zip(header_row, row)} + + else: # tsv/csv Dict: e.g. row = {'first name': 'foo', ...}, wher keys have to be converted + row_data = {k: row[v] for k, v in zip(header_row, row)} + #print("ROW:",row_data) + + # Yaml only gets fields that have values, and as well transformation of some data types. + data.append(getLinkMLTransform(SCHEMA, template, row_data)); + writer.writerow(row_data); + + YAMLDumper().dump(data, temp_base + '.yaml'); + return data; + + +# Could be made more efficient by running vertical loop on columns of a given +# data type. +def getLinkMLTransform(SCHEMA, template, row_data): + + data = {}; + for key, val in row_data.items(): + if val: # Only return dict keys that have values. + slot = template['attributes'][key]; + output_val = val; + ranges = []; + + if slot['range']: + ranges = [slot['range']]; + else: + for range_type in ['any_of','exactly_one_of','none_of','all_of']: + if slot[range_type]: + # e.g. 'any_of': [AnonymousSlotExpression({'range': 'decimal'}), + # AnonymousSlotExpression({'range': 'NullValueMenu'})] + ranges = [binding.range for binding in slot[range_type]] + break; + + # ISSUE: If a slot is integer, decimal or date, but value is saved as + # a string in yaml file, linkml-validate throws error. Must adjust saved + # datatype + for slot_range in ranges: + match slot_range: + case 'integer': + if isInteger(val): + output_val = int(val); + case 'decimal'|'float': + if isDecimal(val): # Note .isdecimal() does NOT test for decimals. + if '.' in val: + output_val = float(val); + else: + output_val = int(val); + #case 'date': + case _: # Nothing to do, but error situation since all slots have ranges + #print (SCHEMA.get_enums(slot_range)) + pass + + if slot['multivalued'] == True: + output_val = [x.strip() for x in re.split(DELIMITERS, output_val)]; + data[key] = output_val; + + return data; + +def isDecimal(x): + try: + float(x); + return True + except ValueError: + return False + +def isInteger(x): + try: + int(x) + except ValueError: + return False + else: + return True + +############################################################################### + +warnings = []; +DELIMITERS = '[;|]'; # regex for delimiters in multivalued fields. + +args = init_parser(); + +if not os.path.isfile(args.schema_path): + exit("LinkML schema file not found: " + args.schema_path) + +with open(args.schema_path, "r") as schema_handle: + + # Using SchemaView() to generate inferred slot attributes + # like in schema.json generated by tabular_to_schema.py + # Converts schema as javascript object into LinkML schemaView object; + schema_obj = yaml.safe_load(schema_handle); + + if not "classes" in schema_obj or not "slots" in schema_obj: + exit("Given schema is missing classes or slots."); + + SCHEMA = SchemaView(yaml.dump(schema_obj, sort_keys=False)); + # Brings in any "imports:". This also includes built-in linkml:types + SCHEMA.merge_imports(); + + # Loop through each class and replace it with its induced version which + # includes attributes dictionary containing inferred slot definitions. + for name, class_obj in SCHEMA.all_classes().items(): + # Note classDef["@type"]: "ClassDefinition" is only in json output + if SCHEMA.class_slots(name): + new_obj = SCHEMA.induced_class(name); + SCHEMA.add_class(new_obj); + + (target_class, slot_key) = getTargetClass(SCHEMA, args.target_class); + # HAD TO Normalize target class : "CanCoGEN Covid-19" => "CanCOGeNCovid19" + + # Cycle through each data_source file to validate + for data_source in args.data_sources.split(): + + print ("VALIDATING: ", data_source); + + file_path_obj = pathlib.Path(data_source); + if file_path_obj.suffix in ['.json','.json-ld','.yaml','.yml']: + + # FUTURE: Handle slot name / title variations here too that be + # encountered when using a newer or older schema. + temp_file = data_source; + + else: + # Deal with section headers and column headers as titles + # Writes a temporary file with all fields renamed + temp_file = file_path_obj.stem + ".tmp"; + (yaml, report) = getNormalizedDataFile(SCHEMA, target_class, data_source, temp_file); + + #for item in report: + # print (report[item]); + + subprocess.run(["linkml-validate", "-s", args.schema_path, "-C", target_class, temp_file + '.yaml']); # input='foobar'.encode('utf-8') + + print ("File scan complete."); + +if len(warnings): + print ("\nWARNING: \n", "\n ".join(warnings)); + + +# SNIPETS: +# +#stderr=None; +#try: +# e.g. > linkml-convert -s schema.yaml -C CanCOGeNCovid19 --index-slot specimen_collector_sample_id -o validTestData_2-1-2.tmp.tsv.json validTestData_2-1-2.tmp.tsv +# ISSUE IS range="ANY_OF" slots may have content but if REQUIRED=True, ARE THROWING ERROR. +#run_state = subprocess.check_output(["linkml-convert", "-s", args.schema_path, "-C", target_class, "--index-slot", slot_key, "-o", temp_file + '.json', temp_file]) #, stderr=subprocess.STDOUT +""" +except BaseException as inst: + + print(type(inst)) # the exception type + print(inst.args) # arguments stored in .args + print(inst) # __str__ allows args to be printed directly, + # but may be overridden in exception subclasses + +finally: +""" + +""" +# A challenge trying to get linkml-validate working via python module. + +report = validate(data_handle, args.schema_path, "Person") # , "Person" +if not report.results: + print('The instance is valid!') +else: + for result in report.results: + print(result.message) +""" \ No newline at end of file From 185805428d41571bfb8b8856d788ac67c9666691 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 5 Sep 2024 13:50:12 -0700 Subject: [PATCH 24/96] Adding list of schema classes when one not found And relabling keys to match way linkml renables them in case of non standard names. But note linkml does not take () parentheses out, and does not change capitalization. --- script/dh-validate.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/script/dh-validate.py b/script/dh-validate.py index 61d0657a..65c4ea7b 100644 --- a/script/dh-validate.py +++ b/script/dh-validate.py @@ -123,7 +123,7 @@ def getTargetClass(SCHEMA, target_class, slot_key = None): templates[name] = class_obj; if target_class and not target_class in templates: - exit("The given validation target class [" + target_class + "] was not found in schema!"); + exit("The given validation target class [" + target_class + "] was not found in schema! Schema has: " + str([key for key in templates.keys()]) ); # So far many DH schemas only have one class so only possibility is to validate against that: if not target_class: @@ -418,6 +418,17 @@ def getLinkMLTransform(SCHEMA, template, row_data): if slot['multivalued'] == True: output_val = [x.strip() for x in re.split(DELIMITERS, output_val)]; + + # If key isn't in snake_case, then convert it to that, since + # linkml-validate insists on that: + # ISSUE: () preserved rather than eliminated + # ISSUE: diagnostic pcr Ct value 1 not transformed to diagnostic_pcr_ct_value_1 + # ISSUE: geo_loc_name_(state_province_territory) not transformed to geo_loc_name_(state_province_territory) + # ISSUE: NML submitted specimen type not transformed to nml_submitted_specimen_type + # ISSUE: specimen collector sample ID not transformed to specimen_collector_sample_id + + # This relabling of key helps + key = re.sub("[-]","",re.sub("[ /]","_", key)); #LinkML doesn't convert to lowercase data[key] = output_val; return data; From 654f11d861a8cd9231a5eb1a9549aedcd62d66c0 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 5 Sep 2024 14:18:29 -0700 Subject: [PATCH 25/96] Documentation + bug fix --- script/dh-validate.py | 35 ++++++++++++---- script/tabular_to_schema.py | 80 ++++++++++++++++++++----------------- 2 files changed, 71 insertions(+), 44 deletions(-) diff --git a/script/dh-validate.py b/script/dh-validate.py index 65c4ea7b..c732d04b 100644 --- a/script/dh-validate.py +++ b/script/dh-validate.py @@ -419,16 +419,35 @@ def getLinkMLTransform(SCHEMA, template, row_data): if slot['multivalued'] == True: output_val = [x.strip() for x in re.split(DELIMITERS, output_val)]; - # If key isn't in snake_case, then convert it to that, since - # linkml-validate insists on that: + # ISSUE: () preserved rather than eliminated # ISSUE: diagnostic pcr Ct value 1 not transformed to diagnostic_pcr_ct_value_1 - # ISSUE: geo_loc_name_(state_province_territory) not transformed to geo_loc_name_(state_province_territory) - # ISSUE: NML submitted specimen type not transformed to nml_submitted_specimen_type - # ISSUE: specimen collector sample ID not transformed to specimen_collector_sample_id - - # This relabling of key helps - key = re.sub("[-]","",re.sub("[ /]","_", key)); #LinkML doesn't convert to lowercase + # ISSUE: + + + # For validation, LinkML will transform both schema and slot labels into + # what it considers are standardized names, so we have to anticipate what + # new slot label will be via search and replace. Convert keys to + # **snake_case** since linkml-validate insists on that. However: + # - Forward slashes and parentheses are preserved though this is + # nonstandard, so: + # "geo_loc name (state/province/territory)" + # is changed to + # "geo_loc_name_(state/province/territory)" + # - Case is preserved though that is non-standard. So + # "specimen collector sample ID" + # is changed to + # "specimen_collector_sample_ID" + # + # - Validating caps CamelCase Enums is hard, e.g. if an Enum is named + # "geo_loc_name (state/province/territory) menu" + # LinkML will automatically rename this to + # "GeoLocName(state/province/territory)Menu" + # However, it doesn't update the name in slot range expressions! + # Hence these must be renamed in source schema. + + The GeoLocName(state/province/territory)Menu + key = re.sub("[-]","",re.sub("[ ]","_", key)); # Accepts ()/ in field name. data[key] = output_val; return data; diff --git a/script/tabular_to_schema.py b/script/tabular_to_schema.py index 40ef0b18..88235743 100644 --- a/script/tabular_to_schema.py +++ b/script/tabular_to_schema.py @@ -149,19 +149,37 @@ def set_range(slot, slot_range, slot_range_2): def set_min_max(slot, slot_minimum_value, slot_maximum_value): if slot_minimum_value > '': - if slot_minimum_value.isnumeric(): + if isInteger(slot_minimum_value): slot['minimum_value'] = int(slot_minimum_value); + elif isDecimal(slot_minimum_value): + slot['minimum_value'] = float(slot_minimum_value); else: slot['todos'] = ['>=' + slot_minimum_value]; if slot_maximum_value > '': - if slot_maximum_value.isnumeric(): + if isInteger(slot_maximum_value): slot['maximum_value'] = int(slot_maximum_value); + elif isDecimal(slot_maximum_value): + slot['maximum_value'] = float(slot_maximum_value); else: if slot['todos']: slot['todos'].append('<=' + slot_maximum_value); else: slot['todos'] = ['<=' + slot_maximum_value]; +def isDecimal(x): + try: + float(x); + return True + except ValueError: + return False + +def isInteger(x): + try: + int(x) + except ValueError: + return False + else: + return True def set_classes(schema_slot_path, schema, locale_schemas, export_format, warnings): @@ -356,9 +374,8 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings): reader = csv.DictReader(tsvfile, dialect='excel-tab'); enumerations = schema['enums']; - - name = ''; # running title for chunks of enumeration rows - menu_path = []; + name = ''; # running name for chunks of enumeration rows + choice_path = []; enum = {}; for row in reader: @@ -368,21 +385,18 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings): row[field] = row[field].strip(); # Each enumeration begins with a row that provides the name of the enum. - if row.get('title','') > '': + # subsequent rows may not have a name. + if row.get('name','') > '' or row.get('title','') > '': # Process default language title - + name = row.get('name'); title = row.get('title'); - name = row.get('name',''); - if name == '': name = title; - print ("name:", name) - - description = row.get('description',''); + if not name: # For enumerations that don't have separate name field + name = title; if not (name in enumerations): enum = { 'name': name, 'title': title, - 'description': description, 'permissible_values': {} }; enumerations[name] = enum; @@ -393,36 +407,29 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings): for lcode in locale_schemas.keys(): locale_schema = locale_schemas[lcode]; locale_schema['enums'][name] = { - 'name': name, # default (usu. english) name acts as key + 'name': name, # Acts as key 'permissible_values': {} }; # Provide translation title if available for this menu. locale_title = row.get('title_' + lcode, ''); if locale_title > '': - locale_schema['enums'][name]['title'] = row.get('title_' + lcode, title); - - # Provide translation description if available for this menu. - locale_description = row.get('description_' + lcode, ''); - if locale_description > '': - locale_schema['enums'][name]['description'] = locale_description; - + locale_schema['enums'][name]['title'] = locale_title; - # If there is a title (or name) of an emum at play - if name and name > '': + if name > '': # Text is label of a particular menu choice # Loop scans through columns until it gets a value for depth in range(1,6): menu_x = 'menu_' + str(depth); - choice_value = row.get(menu_x); + choice_text = row.get(menu_x); # Here there is a menu item to process - if choice_value > '': - del menu_path[depth-1:] # Menu path always points to parent + if choice_text > '': + del choice_path[depth-1:] # Menu path always points to parent description = row.get('description',''); meaning = row.get('meaning',''); - choice = {'text' : choice_value} + choice = {'text' : choice_text} if description > '': choice['description'] = description; if meaning > '': choice['meaning'] = meaning; @@ -430,21 +437,22 @@ def set_enums(enum_path, schema, locale_schemas, export_format, warnings): set_mappings(choice, row, export_format); # IMPLEMENTS FLAT LIST WITH IS_A HIERARCHY - if len(menu_path) > 0: - choice['is_a'] = menu_path[-1]; # Last item in path + if len(choice_path) > 0: + choice['is_a'] = choice_path[-1]; # Last item in path - enum['permissible_values'][choice_value] = choice - menu_path.append(choice_value) + enum['permissible_values'][choice_text] = choice; + choice_path.append(choice_text); for lcode in locale_schemas.keys(): translation = row.get(menu_x + '_' + lcode, ''); - if translation > '': + if translation > '' and translation != choice['text']: - local_choice = copy.deepcopy(choice); - del local_choice['text']; # in language variant files this isn't needed. - local_choice['title'] = translation; + local_choice = {'title': translation} + description = row.get(description + '_' + lcode, ''); + if description: + local_choice['description': description]; - locale_schemas[lcode]['enums'][name]['permissible_values'][choice_value] = local_choice; + locale_schemas[lcode]['enums'][name]['permissible_values'][choice_text] = local_choice; break; From 1890c40c29c521c4901221820ad1e8cb9e2b0846 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 6 Sep 2024 10:27:56 -0700 Subject: [PATCH 26/96] Update dh-validate.py --- script/dh-validate.py | 52 +++++++++++++++++++++---------------------- 1 file changed, 25 insertions(+), 27 deletions(-) diff --git a/script/dh-validate.py b/script/dh-validate.py index c732d04b..33d8d5b3 100644 --- a/script/dh-validate.py +++ b/script/dh-validate.py @@ -52,17 +52,6 @@ from linkml_runtime.dumpers.yaml_dumper import YAMLDumper import subprocess -# ISSUE TRYING TO IMPORT linkml, getting "error: no such option: --schema" when --schema provided to argparse; and "Input LinkML schema file not given" when not given that parameter! -""" -try: - from linkml.validator import validate -except Exception as inst: - print(type(inst)) # the exception type - print(inst.args) # arguments stored in .args - print(inst) # __str__ allows args to be printed directly, - # but may be overridden in exception subclasses -""" - def init_parser(): parser = argparse.ArgumentParser( @@ -530,15 +519,33 @@ def isInteger(x): if len(warnings): print ("\nWARNING: \n", "\n ".join(warnings)); - +""" # SNIPETS: -# -#stderr=None; -#try: +# A challenge trying to get linkml-validate working via python module. + +report = validate(data_handle, args.schema_path, "Person") # , "Person" +if not report.results: + print('The instance is valid!') +else: + for result in report.results: + print(result.message) + +# ISSUE TRYING TO IMPORT linkml, getting "error: no such option: --schema" when --schema provided to argparse; and "Input LinkML schema file not given" when not given that parameter! +try: + from linkml.validator import validate +except Exception as inst: + print(type(inst)) # the exception type + print(inst.args) # arguments stored in .args + print(inst) # __str__ allows args to be printed directly, + # but may be overridden in exception subclasses + + +stderr=None; +try: # e.g. > linkml-convert -s schema.yaml -C CanCOGeNCovid19 --index-slot specimen_collector_sample_id -o validTestData_2-1-2.tmp.tsv.json validTestData_2-1-2.tmp.tsv # ISSUE IS range="ANY_OF" slots may have content but if REQUIRED=True, ARE THROWING ERROR. -#run_state = subprocess.check_output(["linkml-convert", "-s", args.schema_path, "-C", target_class, "--index-slot", slot_key, "-o", temp_file + '.json', temp_file]) #, stderr=subprocess.STDOUT -""" + run_state = subprocess.check_output(["linkml-convert", "-s", args.schema_path, "-C", target_class, "--index-slot", slot_key, "-o", temp_file + '.json', temp_file]) #, stderr=subprocess.STDOUT + except BaseException as inst: print(type(inst)) # the exception type @@ -547,15 +554,6 @@ def isInteger(x): # but may be overridden in exception subclasses finally: -""" +... """ -# A challenge trying to get linkml-validate working via python module. - -report = validate(data_handle, args.schema_path, "Person") # , "Person" -if not report.results: - print('The instance is valid!') -else: - for result in report.results: - print(result.message) -""" \ No newline at end of file From af2edf74df972e0985a6d4bae28ba9253417598e Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 6 Sep 2024 10:31:42 -0700 Subject: [PATCH 27/96] fix extranious text --- script/dh-validate.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/script/dh-validate.py b/script/dh-validate.py index 33d8d5b3..d0da2df6 100644 --- a/script/dh-validate.py +++ b/script/dh-validate.py @@ -386,8 +386,8 @@ def getLinkMLTransform(SCHEMA, template, row_data): ranges = [binding.range for binding in slot[range_type]] break; - # ISSUE: If a slot is integer, decimal or date, but value is saved as - # a string in yaml file, linkml-validate throws error. Must adjust saved + # ISSUE: If a slot is integer or decimal but value is saved as a + # string in yaml file, linkml-validate throws error. Must adjust saved # datatype for slot_range in ranges: match slot_range: @@ -401,8 +401,7 @@ def getLinkMLTransform(SCHEMA, template, row_data): else: output_val = int(val); #case 'date': - case _: # Nothing to do, but error situation since all slots have ranges - #print (SCHEMA.get_enums(slot_range)) + case _: # Nothing to do pass if slot['multivalued'] == True: @@ -434,8 +433,7 @@ def getLinkMLTransform(SCHEMA, template, row_data): # "GeoLocName(state/province/territory)Menu" # However, it doesn't update the name in slot range expressions! # Hence these must be renamed in source schema. - - The GeoLocName(state/province/territory)Menu + key = re.sub("[-]","",re.sub("[ ]","_", key)); # Accepts ()/ in field name. data[key] = output_val; From 4b248a1ec5ba26717f1d15f28b9057de8375f37b Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 6 Sep 2024 10:39:09 -0700 Subject: [PATCH 28/96] Update dh-validate.py --- script/dh-validate.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/script/dh-validate.py b/script/dh-validate.py index d0da2df6..b8eed8f1 100644 --- a/script/dh-validate.py +++ b/script/dh-validate.py @@ -407,12 +407,6 @@ def getLinkMLTransform(SCHEMA, template, row_data): if slot['multivalued'] == True: output_val = [x.strip() for x in re.split(DELIMITERS, output_val)]; - - # ISSUE: () preserved rather than eliminated - # ISSUE: diagnostic pcr Ct value 1 not transformed to diagnostic_pcr_ct_value_1 - # ISSUE: - - # For validation, LinkML will transform both schema and slot labels into # what it considers are standardized names, so we have to anticipate what # new slot label will be via search and replace. Convert keys to From 007a6f16d8ad0bbbbab322e122fa0f0cc32c3a9a Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 23 Sep 2024 13:58:42 -0700 Subject: [PATCH 29/96] Update schema --- web/templates/grdi/schema.json | 4 +- web/templates/grdi/schema.yaml | 2 +- web/templates/grdi/schema_enums.tsv | 3164 +++++++++++++-------------- web/templates/grdi/schema_slots.tsv | 2 +- 4 files changed, 1586 insertions(+), 1586 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index d1a69987..799b8c7c 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -6010,7 +6010,7 @@ "exact_mappings": [ "BIOSAMPLE:sample_name", "NCBI_BIOSAMPLE_Enterics:sample_name", - "NCBI_ANTIBIOGRAM:sample_name" + "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" ], "slot_uri": "GENEPIO:0001123", "identifier": true, @@ -28660,7 +28660,7 @@ "exact_mappings": [ "BIOSAMPLE:sample_name", "NCBI_BIOSAMPLE_Enterics:sample_name", - "NCBI_ANTIBIOGRAM:sample_name" + "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" ], "rank": 1, "slot_uri": "GENEPIO:0001123", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 8e1e4841..e5d00ea8 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -3178,7 +3178,7 @@ slots: exact_mappings: - BIOSAMPLE:sample_name - NCBI_BIOSAMPLE_Enterics:sample_name - - NCBI_ANTIBIOGRAM:sample_name + - NCBI_ANTIBIOGRAM:sample_name/biosample_accession alternative_sample_id: name: alternative_sample_id title: alternative_sample_ID diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 97c6d38c..6e9e46cf 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -1,1582 +1,1582 @@ -title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM - -null value menu NullValueMenu Not Applicable [GENEPIO:0001619] - Missing [GENEPIO:0001618] missing - Not Collected [GENEPIO:0001620] - Not Provided [GENEPIO:0001668] - Restricted Access [GENEPIO:0001810] - -sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - University of Manitoba (UM) [GENEPIO:0004434] - - -purpose_of_sampling menu PurposeOfSamplingMenu Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549] - Field experiment [GENEPIO:0100550] - Survey study [GENEPIO:0100582] - Surveillance [GENEPIO:0100004] - - -presampling_activity menu PresamplingActivityMenu Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538] - Certified humane animal husbandry practices [GENEPIO:0100894] - Certified organic farming practices [GENEPIO:0100539] - Conventional farming practices [GENEPIO:0100895] - Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543] - Genetic mutation [GENEPIO:0100544[ - Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346] - Wastewater treatment process [ENVO:06105300] A recycling process during which wastewater is treated. - Wastewater filtration [GENEPIO:0100881] A wastewater treatment process which removes solid particles from wastewater by means of filtration. - Wastewater grit removal [GENEPIO:0100882] A wastewater treatment process which removes sand, silt, and grit from wastewater. - Wastewater microbial treatment [GENEPIO:0100883] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. - Wastewater primary sedimentation [GENEPIO:0100884] A wastewater treatment process which removes solids and large particles from influent through gravitational force. - Wastewater secondary sedimentation [GENEPIO:0100885] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. - -experimental_specimen_role_type menu ExperimentalSpecimenRoleTypeMenu Positive experimental control [GENEPIO:0101018] - Negative experimental control [GENEPIO:0101019] - Technical replicate [EFO:0002090] - Biological replicate [EFO:0002091] - - -specimen_processing menu SpecimenProcessingMenu Biological replicate process [GENEPIO:0101022] - Samples pooled [OBI:0600016] - Technical replicate process [GENEPIO:0101021] - Isolated from single source [OBI:0002079] - - -geo_loc_name (country) menu GeoLocNameCountryMenu Afghanistan [GAZ:00006882] - Albania [GAZ:00002953] - Algeria [GAZ:00000563] - American Samoa [GAZ:00003957] - Andorra [GAZ:00002948] - Angola [GAZ:00001095] - Anguilla [GAZ:00009159] - Antarctica [GAZ:00000462] - Antigua and Barbuda [GAZ:00006883] - Argentina [GAZ:00002928] - Armenia [GAZ:00004094] - Aruba [GAZ:00004025] - Ashmore and Cartier Islands [GAZ:00005901] - Australia [GAZ:00000463] - Austria [GAZ:00002942] - Azerbaijan [GAZ:00004941] - Bahamas [GAZ:00002733] - Bahrain [GAZ:00005281] - Baker Island [GAZ:00007117] - Bangladesh [GAZ:00003750] - Barbados [GAZ:00001251] - Bassas da India [GAZ:00005810] - Belarus [GAZ:00006886] - Belgium [GAZ:00002938] - Belize [GAZ:00002934] - Benin [GAZ:00000904] - Bermuda [GAZ:00001264] - Bhutan [GAZ:00003920] - Bolivia [GAZ:00002511] - Borneo [GAZ:00025355] - Bosnia and Herzegovina [GAZ:00006887] - Botswana [GAZ:00001097] - Bouvet Island [GAZ:00001453] - Brazil [GAZ:00002828] - British Virgin Islands [GAZ:00003961] - Brunei [GAZ:00003901] - Bulgaria [GAZ:00002950] - Burkina Faso [GAZ:00000905] - Burundi [GAZ:00001090] - Cambodia [GAZ:00006888] - Cameroon [GAZ:00001093] - Canada [GAZ:00002560] - Cape Verde [GAZ:00001227] - Cayman Islands [GAZ:00003986] - Central African Republic [GAZ:00001089] - Chad [GAZ:00000586] - Chile [GAZ:00002825] - China [GAZ:00002845] - Christmas Island [GAZ:00005915] - Clipperton Island [GAZ:00005838] - Cocos Islands [GAZ:00009721] - Colombia [GAZ:00002929] - Comoros [GAZ:00005820] - Cook Islands [GAZ:00053798] - Coral Sea Islands [GAZ:00005917] - Costa Rica [GAZ:00002901] - Cote d'Ivoire [GAZ:00000906] - Croatia [GAZ:00002719] - Cuba [GAZ:00003762] - Curacao [GAZ:00012582] - Cyprus [GAZ:00004006] - Czech Republic [GAZ:00002954] - Democratic Republic of the Congo [GAZ:00001086] - Denmark [GAZ:00005852] - Djibouti [GAZ:00000582] - Dominica [GAZ:00006890] - Dominican Republic [GAZ:00003952] - Ecuador [GAZ:00002912] - Egypt [GAZ:00003934] - El Salvador [GAZ:00002935] - Equatorial Guinea [GAZ:00001091] - Eritrea [GAZ:00000581] - Estonia [GAZ:00002959] - Eswatini [GAZ:00001099] - Ethiopia [GAZ:00000567] - Europa Island [GAZ:00005811] - Falkland Islands (Islas Malvinas) [GAZ:00001412] - Faroe Islands [GAZ:00059206] - Fiji [GAZ:00006891] - Finland [GAZ:00002937] - France [GAZ:00003940] - French Guiana [GAZ:00002516] - French Polynesia [GAZ:00002918] - French Southern and Antarctic Lands [GAZ:00003753] - Gabon [GAZ:00001092] - Gambia [GAZ:00000907] - Gaza Strip [GAZ:00009571] - Georgia [GAZ:00004942] - Germany [GAZ:00002646] - Ghana [GAZ:00000908] - Gibraltar [GAZ:00003987] - Glorioso Islands [GAZ:00005808] - Greece [GAZ:00002945] - Greenland [GAZ:00001507] - Grenada [GAZ:02000573] - Guadeloupe [GAZ:00067142] - Guam [GAZ:00003706] - Guatemala [GAZ:00002936] - Guernsey [GAZ:00001550] - Guinea [GAZ:00000909] - Guinea-Bissau [GAZ:00000910] - Guyana [GAZ:00002522] - Haiti [GAZ:00003953] - Heard Island and McDonald Islands [GAZ:00009718] - Honduras [GAZ:00002894] - Hong Kong [GAZ:00003203] - Howland Island [GAZ:00007120] - Hungary [GAZ:00002952] - Iceland [GAZ:00000843] - India [GAZ:00002839] - Indonesia [GAZ:00003727] - Iran [GAZ:00004474] - Iraq [GAZ:00004483] - Ireland [GAZ:00002943] - Isle of Man [GAZ:00052477] - Israel [GAZ:00002476] - Italy [GAZ:00002650] - Jamaica [GAZ:00003781] - Jan Mayen [GAZ:00005853] - Japan [GAZ:00002747] - Jarvis Island [GAZ:00007118] - Jersey [GAZ:00001551] - Johnston Atoll [GAZ:00007114] - Jordan [GAZ:00002473] - Juan de Nova Island [GAZ:00005809] - Kazakhstan [GAZ:00004999] - Kenya [GAZ:00001101] - Kerguelen Archipelago [GAZ:00005682] - Kingman Reef [GAZ:00007116] - Kiribati [GAZ:00006894] - Kosovo [GAZ:00011337] - Kuwait [GAZ:00005285] - Kyrgyzstan [GAZ:00006893] - Laos [GAZ:00006889] - Latvia [GAZ:00002958] - Lebanon [GAZ:00002478] - Lesotho [GAZ:00001098] - Liberia [GAZ:00000911] - Libya [GAZ:00000566] - Liechtenstein [GAZ:00003858] - Line Islands [GAZ:00007144] - Lithuania [GAZ:00002960] - Luxembourg [GAZ:00002947] - Macau [GAZ:00003202] - Madagascar [GAZ:00001108] - Malawi [GAZ:00001105] - Malaysia [GAZ:00003902] - Maldives [GAZ:00006924] - Mali [GAZ:00000584] - Malta [GAZ:00004017] - Marshall Islands [GAZ:00007161] - Martinique [GAZ:00067143] - Mauritania [GAZ:00000583] - Mauritius [GAZ:00003745] - Mayotte [GAZ:00003943] - Mexico [GAZ:00002852] - Micronesia [GAZ:00005862] - Midway Islands [GAZ:00007112] - Moldova [GAZ:00003897] - Monaco [GAZ:00003857] - Mongolia [GAZ:00008744] - Montenegro [GAZ:00006898] - Montserrat [GAZ:00003988] - Morocco [GAZ:00000565] - Mozambique [GAZ:00001100] - Myanmar [GAZ:00006899] - Namibia [GAZ:00001096] - Nauru [GAZ:00006900] - Navassa Island [GAZ:00007119] - Nepal [GAZ:00004399] - Netherlands [GAZ:00002946] - New Caledonia [GAZ:00005206] - New Zealand [GAZ:00000469] - Nicaragua [GAZ:00002978] - Niger [GAZ:00000585] - Nigeria [GAZ:00000912] - Niue [GAZ:00006902] - Norfolk Island [GAZ:00005908] - North Korea [GAZ:00002801] - North Macedonia [GAZ:00006895] - North Sea [GAZ:00002284] - Northern Mariana Islands [GAZ:00003958] - Norway [GAZ:00002699] - Oman [GAZ:00005283] - Pakistan [GAZ:00005246] - Palau [GAZ:00006905] - Panama [GAZ:00002892] - Papua New Guinea [GAZ:00003922] - Paracel Islands [GAZ:00010832] - Paraguay [GAZ:00002933] - Peru [GAZ:00002932] - Philippines [GAZ:00004525] - Pitcairn Islands [GAZ:00005867] - Poland [GAZ:00002939] - Portugal [GAZ:00004126] - Puerto Rico [GAZ:00006935] - Qatar [GAZ:00005286] - Republic of the Congo [GAZ:00001088] - Reunion [GAZ:00003945] - Romania [GAZ:00002951] - Ross Sea [GAZ:00023304] - Russia [GAZ:00002721] - Rwanda [GAZ:00001087] - Saint Helena [GAZ:00000849] - Saint Kitts and Nevis [GAZ:00006906] - Saint Lucia [GAZ:00006909] - Saint Pierre and Miquelon [GAZ:00003942] - Saint Martin [GAZ:00005841] - Saint Vincent and the Grenadines [GAZ:02000565] - Samoa [GAZ:00006910] - San Marino [GAZ:00003102] - Sao Tome and Principe [GAZ:00006927] - Saudi Arabia [GAZ:00005279] - Senegal [GAZ:00000913] - Serbia [GAZ:00002957] - Seychelles [GAZ:00006922] - Sierra Leone [GAZ:00000914] - Singapore [GAZ:00003923] - Sint Maarten [GAZ:00012579] - Slovakia [GAZ:00002956] - Slovenia [GAZ:00002955] - Solomon Islands [GAZ:00005275] - Somalia [GAZ:00001104] - South Africa [GAZ:00001094] - South Georgia and the South Sandwich Islands [GAZ:00003990] - South Korea [GAZ:00002802] - South Sudan [GAZ:00233439] - Spain [GAZ:00003936] - Spratly Islands [GAZ:00010831] - Sri Lanka [GAZ:00003924] - State of Palestine [GAZ:00002475] - Sudan [GAZ:00000560] - Suriname [GAZ:00002525] - Svalbard [GAZ:00005396] - Swaziland [GAZ:00001099] - Sweden [GAZ:00002729] - Switzerland [GAZ:00002941] - Syria [GAZ:00002474] - Taiwan [GAZ:00005341] - Tajikistan [GAZ:00006912] - Tanzania [GAZ:00001103] - Thailand [GAZ:00003744] - Timor-Leste [GAZ:00006913] - Togo [GAZ:00000915] - Tokelau [GAZ:00260188] - Tonga [GAZ:00006916] - Trinidad and Tobago [GAZ:00003767] - Tromelin Island [GAZ:00005812] - Tunisia [GAZ:00000562] - Turkey [GAZ:00000558] - Turkmenistan [GAZ:00005018] - Turks and Caicos Islands [GAZ:00003955] - Tuvalu [GAZ:00009715] - United States of America [GAZ:00002459] - Uganda [GAZ:00001102] - Ukraine [GAZ:00002724] - United Arab Emirates [GAZ:00005282] - United Kingdom [GAZ:00002637] - Uruguay [GAZ:00002930] - Uzbekistan [GAZ:00004979] - Vanuatu [GAZ:00006918] - Venezuela [GAZ:00002931] - Viet Nam [GAZ:00003756] - Virgin Islands [GAZ:00003959] - Wake Island [GAZ:00007111] - Wallis and Futuna [GAZ:00007191] - West Bank [GAZ:00009572] - Western Sahara [GAZ:00000564] - Yemen [GAZ:00005284] - Zambia [GAZ:00001107] - Zimbabwe [GAZ:00001106] - - -geo_loc_name (state/province/region) menu GeoLocNameStateProvinceRegionMenu Atlantic region (Canada) [wikidata:Q246972] - New Brunswick [GAZ:00002570] - Newfoundland & Labrador [GAZ:00002567] - Nova Scotia [GAZ:00002565] - Prince Edward Island [GAZ:00002572] - Central region (Canada) [wikidata:Q1048064] - Ontario [GAZ:00002563] - Quebec [GAZ:00002569] - Northern region (Canada) [wikidata:Q764146] - Northwest Territories [GAZ:00002575] - Nunuvut [GAZ:00002574] - Yukon [GAZ:00002576] - Pacific region (Canada) [wikidata:Q122953299] - British Columbia [GAZ:00002562] - Prairie region (Canada) [wikidata:Q1364746] - Alberta [GAZ:00002566] - Manitoba [GAZ:00002571] - Saskatchewan [GAZ:00002564] - - -sample_collection_date_precision menu SampleCollectionDatePrecisionMenu year [UO:0000036] - month [UO:0000035] - day [UO:0000033] - - -environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] - Agricultural Field [ENVO:00000114] - Alluvial fan [ENVO:00000314] - Animal cage [ENVO:01000922] - Aquarium [ENVO:00002196] - Artificial wetland [ENVO:03501406] - Breeding ground [ENVO:03501441] - Building [ENVO:00000073] - Barn [ENVO:03501257] - Breeder barn [ENVO:03501383] - Broiler barn [ENVO:03501386] - Sheep barn [ENVO:03501385] - Biodome [ENVO:03501397] - Cottage [ENVO:03501393] - Dairy [ENVO:00003862] - Hospital [ENVO:00002173] - Laboratory facility [ENVO:01001406] - Pigsty [ENVO:03501413] - Building part (organizational term) - Air intake [ENVO:03501380] - Animal pen [ENVO:03501387] - Building floor [ENVO:01000486] - Building wall [ENVO:01000465] - Countertop [ENVO:03501404] - Shelf [ENVO:03501403] - Stall [EOL:0001903] - Window sill [ENVO:03501381] - Creek [ENVO:03501405] - Ditch [ENVO:00000037] A small, human-made channel which has been dug for draining or irrigating the land. - Drainage ditch [ENVO:00000140] A ditch that collects water from the surrounding land. - Irrigation ditch [ENVO:00000139] A ditch that supplies water to surrounding land. - Farm [ENVO:00000078] - Beef farm [ENVO:03501443] - Breeder farm [ENVO:03501384] - Dairy farm [ENVO:03501416] - Feedlot [ENVO:01000627] - Beef cattle feedlot [ENVO:03501444] - Fish farm [ENVO:00000294] - Research farm [ENVO:03501417] - Central Experimental Farm [GAZ:00004603] Central Experimental Farm - Freshwater environment [ENVO:01000306] - Hatchery [ENVO:01001873] - Poultry hatchery [ENVO:01001874] - Lake [ENVO:00000020] - Manure digester facility [ENVO:03501422] - Manure lagoon (Anaerobic lagoon) [ENVO:03501423] - Manure pit [ENVO:01001872] - Marine environment [ENVO:01000320] - Benthic zone [ENVO:03501440] - Pelagic zone [ENVO:00000208] - Park [ENVO:00000562] - Plumbing drain [ENVO:01000924 ] - Pond [ENVO:00000033] - Reservoir [ENVO:00000025] - Irrigation reservoir [ENVO:00000450] - Retail environment [ENVO:01001448] - Shop [ENVO:00002221] - Butcher shop [ENVO:03501396] - Pet store [ENVO:03501395] - Supermarket [ENVO:01000984] - River [ENVO:00000022] - Roost (bird) [ENVO:03501439] - Rural area [ENVO:01000772] - Slough [ENVO:03501438] - Stream [ENVO:00000023] - Trailer [ENVO:03501394] - Tributary [ENVO:00000495] - Truck [ENVO:01000602] - Urban area [ENVO:03501437] - Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. - Water surface [ENVO:01001191] - Woodland area [ENVO:00000109] - Zoo [ENVO:00010625] - - -water_depth_units menu WaterDepthUnitsMenu centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - kilometer (km) [UO:0010066] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - - -sediment_depth_units menu SedimentDepthUnitsMenu centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - kilometer (km) [UO:0010066] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - - -air_temperature_units menu AirTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] - degree Celsius (C) [UO:0000027] - - -water_temperature_units menu WaterTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] - degree Celsius (C) [UO:0000027] - -precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu millimeter (mm) [UO:0000016] - centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - -available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702] - Experimental parameters documentation [GENEPIO:0100703] - Feed history [GENEPIO:0100704] - Land use information [GENEPIO:0100705] - Therapeutic administration history [GENEPIO:0100706] - Chemical characterization [GENEPIO:0100707] - pH measurement [GENEPIO:0100708] - Dissolved oxygen measurement [GENEPIO:0100709] - Nitrate measurement [GENEPIO:0100710] - Nitrite measurement [GENEPIO:0100711] - Phosphorous measurement [GENEPIO:0100712] - Salinity measurement [GENEPIO:0100713] - Microbiological characterization [GENEPIO:0100714] - Microbiological identification [GENEPIO:0100715] - Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] - Microbiological identification (bioMérieux API) [GENEPIO:0100717] - Microbiological identification (Biolog) [GENEPIO:0100718] - Microbiological identification (FAME) [GENEPIO:0100719] - Microbiological identification (Sensititre) [GENEPIO:0100720] - Microbiological identification (ViTek) [GENEPIO:0100721] - Phage type [GENEPIO:0100722] - Serotype [GENEPIO:0100723] - Phenotypic microbiological characterization [GENEPIO:0100724] - AMR phenotypic testing [GENEPIO:0100725] - Biolog phenotype microarray [GENEPIO:0100726] - Microbiological quantification [GENEPIO:0100727] - Colony count [GENEPIO:0100728] - Total coliform count [GENEPIO:0100729] - Total fecal coliform count [GENEPIO:0100730] - Infectivity assay [GENEPIO:0100731] - ELISA toxin binding [GENEPIO:0100732] - Molecular characterization [GENEPIO:0100733] - 16S rRNA Sanger sequencing [GENEPIO:0100734] - Metagenomic sequencing [GENEPIO:0101024] - PCR marker detection [GENEPIO:0100735] - BOX PCR fingerprint [GENEPIO:0100736] - ERIC PCR fingerprint [GENEPIO:0100737] - Plasmid type [GENEPIO:0100738] - Ribotype [GENEPIO:0100739] - Molecular quantification [GENEPIO:0100740] - qPCR marker organism quantification [GENEPIO:0100741] - Physical characterization [GENEPIO:0100742] - Conductivity measurement [GENEPIO:0100743] - Mollusc shell measurement [GENEPIO:0100744] - Mollusc shell length [GENEPIO:0100745] - Matter compostion [GENEPIO:0100746] - Dry matter composition [GENEPIO:0100747] - Organic matter composition [GENEPIO:0100748] - Turbidity measurement [GENEPIO:0100749] - - -sampling_weather_conditions menu SamplingWeatherConditionsMenu Cloudy/Overcast [ENVO:03501418] - Partially cloudy [ENVO:03501419] - Drizzle [ENVO:03501420] - Fog [ENVO:01000844] - Rain [ENVO:01001564] - Snow [ENVO:01000406] - Storm [ENVO:01000876] - Sunny/Clear [ENVO:03501421] - - -animal_or_plant_population menu AnimalOrPlantPopulationMenu Algae [FOODON:03411301] - Algal bloom [ENVO:2000004] - Cattle [NCBITaxon:9913] - Beef cattle [FOODON:00004413] - Dairy cattle [FOODON:00002505] - Chicken [NCBITaxon:9031] - Crop [AGRO:00000325] - Fish [FOODON:03411222] - Pig [NCBITaxon:9823] - Poultry [FOODON:00004298] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Crustacean [FOODON:03411374] - Mollusc [FOODON:03412112] - Tropical fish [FOODON:00004283] - Turkey [NCBITaxon:9103] - Wildlife [FOODON:00004503] - Wild bird [FOODON:00004505] - Seabird [FOODON:00004504] - - - -environmental_material menu EnvironmentalMaterialMenu Air [ENVO:00002005] - Alluvium [ENVO:01001202] - Animal feeding equipment [AGRO:00000675] - Animal feeder [AGRO:00000679] - Animal drinker [AGRO:00000680] - Feed pan [AGRO:00000676] - Watering bowl [AGRO:00000677] - Animal transportation equipment [AGRO:00000671] - Dead haul trailer [GENEPIO:0100896] - Dead haul truck [AGRO:00000673] - Live haul trailer [GENEPIO:0100897] - Live haul truck [AGRO:00000674] - Belt [NCIT:C49844] - Biosolids [ENVO:00002059] - Boot [GSSO:012935] - Boot cover [OBI:0002806] - Broom [ENVO:03501431] - Bulk tank [ENVO:03501379] - Chick box [AGRO:00000678] - Chick pad [AGRO:00000672] - Cleaning equipment [ENVO:03501430] - Compost [ENVO:00002170] - Contaminated water [ENVO:00002186] - Fecal slurry [ENVO:03501436] - Fluid from meat rinse [GENEPIO:0004323] - Effluent [ENVO:03501407] - Influent [ENVO:03501442] - Surface runoff [ENVO:03501408] - Poultry plucking water [AGRO_00000693] - Wastewater [ENVO:00002001] - Weep fluid [AGRO_00000692] - Crate [ENVO:03501372] - Dumpster [ENVO:03501400] - Dust [ENVO:00002008] - Egg belt [AGRO:00000670] - Fan [NCIT:C49947] - Freezer [ENVO:03501415] - Freezer handle [ENVO:03501414] - Manure [ENVO:00003031] - Animal manure [AGRO:00000079] - Pig manure [AGRO:00000080] - Manure digester equipment [ENVO:03501424] - Nest [ENVO:03501432] - Bird's nest [ENVO:00005805] - Permafrost [ENVO:00000134] - Plucking belt [AGRO:00000669] - Poultry fluff [UBERON:0008291] - Poultry litter [AGRO:00000080] - Sediment [ENVO:00002007] - Soil [ENVO:00001998] - Agricultural soil [ENVO:00002259] - Forest soil [ENVO:00002261] - Straw [ENVO:00003869] - Canola straw [FOODON:00004430] - Oat straw [FOODON:03309878] - Barley straw [FOODON:00004559] - Sludge [ENVO:00002044] - Primary sludge [ENVO:00002057] - Secondary sludge [ENVO:00002058] - Water [CHEBI:15377] - Drinking water [ENVO:00003064] - Groundwater [ENVO:01001004] - Surface water [ENVO:00002042] - - -anatomical_material menu AnatomicalMaterialMenu Blood [UBERON:0000178] - Fluid [UBERON:0006314] - Fluid (cerebrospinal (CSF)) [UBERON:0001359] - Fluid (amniotic) [UBERON:0000173] - Saliva [UBERON:0001836] - Tissue [UBERON:0000479] - - -body_product menu BodyProductMenu Digestive tract substance [GENEPIO:0100898] - Caecal content [GENEPIO:0100899] - Intestinal content [GENEPIO:0100900] - Stomach content [GENEPIO:0100901] - Feces [UBERON:0001988] - Fecal composite [GENEPIO:0004512] - Feces (fresh) [GENEPIO:0004513] - Feces (environmental) [GENEPIO:0004514] - Meconium [UBERON:0007109] - Milk [UBERON:0001913] - Colostrum [UBERON:0001914] - Urine [UBERON:0001088] - - -anatomical_part menu AnatomicalPartMenu Carcass [UBERON:0008979] - Swine carcass [FOODON:03311719] - Digestive system [UBERON:0001007] - Caecum [UBERON:0001153] - Colon [UBERON:0001155] - Digestive gland [UBERON:0006925] - Foregut [UBERON:0001041] - Gall bladder [UBERON:0002110] - Gastrointestinal system mucosa [UBERON:0004786] - Gizzard [UBERON:0005052] - Hindgut [UBERON:0001046] - Intestine [UBERON:0000160] - Small intestine [UBERON:0002108] - Duodenum [UBERON:0002114] - Ileum [UBERON:0002116] - Jejunum [UBERON:0002115] - Stomach [UBERON:0000945] - Abomasum [UBERON:0007358] - Rumen [UBERON:0007365] - Excretory system (organizational term) - Anus [UBERON:0001245] - Anal gland [UBERON:0011253] - Cloaca [UBERON:0000162] - Liver [UBERON:0002107] - Kidney [UBERON:0002113] - Rectum [UBERON:0001052] - Spleen [UBERON:0002106] - Urinary bladder [UBERON:0001255] - Foot [UBERON:0002387] - Head [UBERON:0000033] - Brain [UBERON:0000955] - Ear [UBERON:0001690] - Eye [UBERON:0000970] - Mouth [UBERON:0000165] - Nose [UBERON:0000004] - Nasal turbinal [UBERON:0035612] - Nasopharynx (NP) [UBERON:0001728] - Pair of nares [UBERON:0002109] - Paranasal sinus [UBERON:0001825] - Snout [UBERON:0006333] - Lymphatic system [UBERON:0006558] - Lymph node [UBERON:0000029] - Mesenteric lymph node [UBERON:0002509] - Mantle (bird) [GENEPIO:0100927] - Neck [UBERON:0000974] - Esophagus [UBERON:0001043] - Trachea [UBERON:0003126] - Nerve [UBERON:0001021] - Spinal cord [UBERON:0002240] - Organs or organ parts [GENEPIO:0001117] - Organ [UBERON:0000062] - Muscle organ [UBERON:0001630] - Skin of body [UBERON:0002097] - Reproductive system [UBERON:0000990] - Embryo [UBERON:0000922] - Fetus [UBERON:0000323] - Ovary [UBERON:0000992] - Oviduct [UBERON:0000993] - Placenta [UBERON:0001987] - Testis [UBERON:0000473] - Udder [UBERON:0013216] - Uterus [UBERON:0000995] - Vagina [UBERON:0000996] - Yolk sac [UBERON:0001040] - Respiratory system [UBERON:0001004] - Air sac [UBERON:0009060] - Lung [UBERON:0002048] - Pleura [UBERON:0000977] - Respiratory system mucosa [UBERON:0004785] - Skeletal system [UBERON:0001434] - Skeletal joint [UBERON:0000982] - Bone element [UBERON:0001474] - Thoracic segment of trunk [UBERON:0000915] - Abdomen [UBERON:0000916] - Muscle of abdomen [UBERON:0002378] - Peritoneum [UBERON:0002358] - Vascular system [UBERON:0007798] - Blood vessel [UBERON:0001981] - Bursa of Fabricius [UBERON:0003903] - Gill [UBERON:0002535] - Heart [UBERON:0000948] - Lung [UBERON:0002048] - Pericardium [UBERON:0002407] - Vent (anatomical) [UBERON:2000298] - Bird vent [UBERON:0012464] - Fish vent [GENEPIO:0100902] - - -anatomical_region menu AnatomicalRegionMenu Dorso-lateral region [BSPO:0000080] - Exterior anatomical region [BSPO:0000034] - Interior anatomical region [BSPO:0000033] - - -food_product menu FoodProductMenu Animal feed [ENVO:02000047] - Blood meal [FOODON:00001564] - Bone meal [ENVO:02000054] - Brassica carinata meal [FOODON:00004310] - Canola meal [FOODON:00002694] - Compound feed premix [FOODON:00004323] - Compound feed premix (medicated) [FOODON:00004324] - Feather meal [FOODON:00003927] - Fish meal [FOODON:03301620] - Lay ration [FOODON:00004286] - Meat and bone meal [FOODON:00002738] - Meat meal [FOODON:00004282] - Pet food [FOODON:00002682] - Soybean meal [FOODON:03302757] - Animal feed ingredient [FOODON:00004322] - Dairy food product [FOODON:00001256] - Cheese block (whole or parts) [FOODON:03000287] - Cow skim milk (powdered) [FOODON:03310016] - Milk [UBERON:0001913] - Dietary supplement [FOODON:03401298] - Egg or egg component [FOODON:03420194] - Balut [FOODON:03302184] - Egg yolk [UBERON:0007378] - Poultry egg [FOODON:03000414] - Hen egg (whole) [FOODON:03316061] - Poultry egg (whole, shell on) [FOODON:03000415] - Food mixture [FOODON:00004130] - Food product analog (food subsitute) [FOODON:00001871] - Milk substitute [FOODON:03305408] - Meat (whole or parts) [FOODON:03317170] - Cutlet [FOODON:00003001] - Filet [FOODON:03530144] - Liver (whole, raw) [FOODON:03309772] - Meat trim [FOODON:03309475] - Rib (meat cut) [FOODON:03530023] - Rib chop [FOODON:00004290] - Shoulder (meat cut) [FOODON:03530043] - Grains, cereals, and bakery product (organizational term) - Bread loaf (whole or parts) [FOODON:03000288] - Breakfast cereal [FOODON:03311075] - Bulk grain [FOODON:03309390] - Oat grain [FOODON:00003429] - Legume food product [FOODON:00001264] - Chickpea (whole) [FOODON:03306811] - Hummus [FOODON:00003049] - Soybean (whole or parts) [FOODON:03000245] - Meat, poultry and fish (organizational term) - Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, boneless) [FOODON:0001282] - Beef (ground, extra lean) [FOODON:02000426] - Beef (ground, lean) [FOODON:02000425] - Beef (ground, medium) [FOODON:02000427] - Beef (ground, regular) [FOODON:02000428] - Beef (ground, sirloin) [FOODON:02000429] - Beef hamburger (dish) [FOODON:00002737] - Beef shoulder [FOODON:02000069] - Beef shoulder chop [FOODON:03000387] - Beef sirloin chop [FOODON:03000389] - Beef stew chunk [FOODON:00004288] - Beef tenderloin [FOODON:00003302] - Beef (pieces) [FOODON:02000412] - Brisket [FOODON:03530020] - Chicken breast [FOODON:00002703] - Chicken breast (back off) [FOODON:03000385] - Chicken breast (skinless) [FOODON:02020231] - Chicken breast (with skin) [FOODON:02020233] - Chicken breast (skinless, boneless) [FOODON:02020235] - Chicken breast cutlet [FOODON:00004308] - Chicken drumstick [FOODON:00002716] - Chicken drumstick (skinless) [FOODON:02020237] - Chicken drumstick(with skin) [FOODON:02020239] - Chicken meat [FOODON:00001040] - Chicken meat (ground) [FOODON:02020311] - Chicken meat (ground or minced, lean) [FOODON:03000392] - Chicken meat (ground or minced, extra lean) [FOODON:03000396] - Chicken meat (ground or minced, medium) [FOODON:03000400] - Chicken meat (ground or minced, regular) [FOODON:03000404] - Chicken meat (ground or minced, boneless) [FOODON:03000410] - Chicken nugget [FOODON:00002672] - Chicken thigh [FOODON:02020219] - Chicken thigh (skinless) [FOODON:00003331] - Chicken thigh (skinless, with bone) [FOODON:02020227] - Chicken thigh (skinless, boneless) [FOODON:02020228] - Chicken upper thigh [FOODON:03000381] - Chicken upper thigh (with skin) [FOODON:03000383] - Chicken thigh (with skin) [FOODON:00003330] - Chicken thigh (with skin, with bone) [FOODON_00003363] - Chicken wing [FOODON:00002674] - Fish food product [FOODON:00001248] - Fish steak [FOODON:00002986] - Ham food product [FOODON:00002502] - Head cheese [FOODON:03315658] - Lamb [FOODON:03411669] - Meat strip [FOODON:00004285] - Mutton [FOODON:00002912] - Pork chop [FOODON:00001049] - pork meat (ground) [FOODON:02021718] - Pork meat (ground or minced, boneless) [FOODON:03000413] - Pork meat (ground or minced, extra lean) [FOODON:03000399] - Pork meat (ground or minced, lean) [FOODON:03000395] - Pork meat (ground or minced, medium) [FOODON:03000403] - Pork meat (ground or minced, regular) [FOODON:03000407] - Pork meat (ground or minced, Sirloin) [FOODON:03000409] - Pork shoulder [FOODON:02000322] - Pork shoulder chop [FOODON:03000388] - Pork sirloin chop [FOODON:02000300] - Pork steak [FOODON:02021757] - Pork tenderloin [FOODON:02000306] - Poultry meat [FOODON:03315883] - Leg (poultry meat cut) [FOODON:03530159] - Poultry drumstick [FOODON:00003469] - Neck (poultry meat cut) [FOODON:03530294] - Thigh (poultry meat cut) [FOODON:03530160] - Wing (poultry meat cut) [FOODON:03530157] - Sausage (whole) [FOODON:03315904] - Pepperoni [FOODON:03311003] - Salami [FOODON:03312067] - Shellfish [FOODON:03411433] - Mussel [FOODON:03411223] - Oyster [FOODON:03411224] - Shrimp [FOODON:03301673] - Scallop [FOODON:02020805] - Squid [FOODON:03411205] - Turkey breast [FOODON:00002690] - Turkey breast (back off) [FOODON:03000386] - Turkey breast (skinless) [FOODON:02020495] - Turkey breast (skinless, boneless) [FOODON:02020499] - Turkey breast (with skin) [FOODON:02020497] - Turkey drumstick [FOODON:02020477] - Turkey drumstick (skinless) [FOODON:02020501] - Turkey drumstick (with skin) [FOODON:02020503] - Turkey meat [FOODON:00001286] - Turkey meat (ground) [FOODON:02020577] - Turkey meat (ground or minced, lean) [FOODON:03000393] - Turkey meat (ground or minced, extra lean) [FOODON:03000397] - Turkey meat (ground or minced, medium) [FOODON:03000401] - Turkey meat (ground or minced, regular) [FOODON:03000405] - Turkey meat (ground or minced, boneless) [FOODON:03000411] - Turkey thigh [FOODON:00003325] - Turkey thigh (skinless) [FOODON:00003329] - Turkey thigh (skinless, boneless) [FOODON:02020491] - Turkey thigh (with skin) [FOODON:00003328] - Turkey upper thigh [FOODON:03000382] - Turkey upper thigh (with skin) [FOODON:03000384] - Turkey wing [FOODON:02020478] - Veal [FOODON:00003083] - Formula fed veal [FOODON:000039111] - Grain-fed veal [FOODON:00004280] - Microbial food product [FOODON:00001145] - Yeast [FOODON:03411345] - Nuts and seed products - Almond (whole or parts) [FOODON:03000218] - Almond (whole) [FOODON:00003523] - Barley seed [FOODON:00003394] - Canola seed [FOODON:00004560] - Chia seed powder [FOODON:00003925] - Chia seed (whole or parts) [FOODON:03000241] - Flaxseed powder [FOODON:00004276] - Hazelnut [FOODON:00002933] - Nut (whole or part) [FOODON:03306632] - Peanut butter [FOODON:03306867] - Sesame seed [FOODON:03310306] - Tahini [FOODON:00003855] - Walnut (whole or parts) [FOODON:03316466] - Prepared food product [FOODON:00001180] - Condiment [FOODON:03315708] - Confectionery food product [FOODON:00001149] - Snack food [FOODON:03315013] - Produce [FOODON:03305145] - Apple (whole or parts) [FOODON:03310788] - Apple (whole) [FOODON:00002473] - Arugula greens bunch [FOODON:00003643] - Avocado [FOODON:00003600] - Cantaloupe (whole or parts) [FOODON:03000243] - Chilli pepper [FOODON:00003744] - Coconut (whole or parts) [FOODON:03309861] - Coconut meat [FOODON:00003856] - Corn cob (whole or parts) [FOODON:03310791] - Cucumber (whole or parts) [FOODON:03000229] - Fruit [PO:0009001] - Goji berry [FOODON:00004360] - Greens (raw) [FOODON:03310765] - Kale leaf (whole or parts) [FOODON:03000236] - Karela (bitter melon) [FOODON:00004367] - Lettuce head (whole or parts) [FOODON:03000239] - Mango (whole or parts) [FOODON:03000217] - Mushroom (fruitbody) [FOODON:00003528] - Papaya (whole or parts) [FOODON:03000228] - Pattypan squash (whole or parts) [FOODON:03000232] - Peach [FOODON:00002485] - Pepper (whole or parts) [FOODON:03000249] - Potato [FOODON:03315354] - Salad [FOODON:03316042] - Scallion (whole or parts) [FOODON:03000250] - Spinach (whole or parts) [FOODON:03000221] - Sprout [FOODON:03420183] - Germinated or sprouted seed [FOODON:03420102] - Alfalfa sprout [FOODON:00002670] - Bean sprout [FOODON:00002576] - Chia sprout [FOODON:03000180] - Mixed sprouts [FOODON:03000182] - Mung bean sprout [FOODON:03301446] - Tomato (whole or pieces) [FOODON:00002318] - Vegetable (whole or parts) [FOODON:03315308] - Spice or herb [FOODON:00001242] - Basil (whole or parts) [FOODON:03000233] - Black pepper (whole or parts) [FOODON:03000242] - Cardamom (whole or parts) [FOODON:03000246] - Chive leaf (whole or parts) [FOODON:03000240] - Coriander powder [FOODON:00004274] - Coriander seed (whole or parts) [FOODON:03000224] - Cumin powder [FOODON:00004275] - Cumin seed (whole) [FOODON:00003396] - Black cumin seed (whole or parts) [FOODON:03000247] - Curry leaf (whole or parts) [FOODON:03000225] - Curry powder [FOODON:03301842] - Dill spice [FOODON:00004307] - Fennel (whole or parts) [FOODON:03000244] - Garlic powder [FOODON:03301844] - Ginger root (whole or parts) [FOODON:03000220] - Mint leaf (whole or parts) [FOODON:03000238] - Oregano (whole or parts) [FOODON:03000226] - Paprika (ground) [FOODON:03301223] - Parsley leaf (whole or parts) [FOODON:03000231] - Pepper (ground) [FOODON:03301526] - Rasam powder [FOODON:00004277] - Sage [FOODON:03301560] - Turmeric (ground) [FOODON:03310841] - Spice [FOODON:03303380] - White peppercorn (whole or parts) [FOODON:03000251] - - -food_product_properties menu FoodProductPropertiesMenu Food (canned) [FOODON:00002418] - Food (cooked) [FOODON:00001181] - Food (cut) [FOODON:00004291] - Food (chopped) [FOODON:00002777] - Food (chunks) [FOODON:00004555] - Food (cubed) [FOODON:00004278] - Food (diced) [FOODON:00004549] - Food (grated) [FOODON:00004552] - Food (sliced) [FOODON:00002455] - Food (shredded) [FOODON:00004553] - Food (dried) [FOODON:03307539] - Food (fresh) [FOODON:00002457] - Food (frozen) [FOODON:03302148] - Food (pulped) [FOODON:00004554] - Food (raw) [FOODON:03311126] - Food (unseasoned) [FOODON:00004287] - Italian-style food product [FOODON:00004321] - Meat (boneless) [FOODON:00003467] - Meat (skinless) [FOODON:00003468] - Meat (with bone) [FOODON:02010116] - Meat (with skin) [FOODON:02010111] - Soft [PATO:0000387] - - - - -label_claim menu LabelClaimMenu Antibiotic free [FOODON:03601063] - Cage free [FOODON:03601064] - Hormone free [FOODON:03601062] - Organic food claim or use [FOODON:03510128] - Pasture raised [FOODON:03601065] - Ready-to-eat (RTE) [FOODON:03316636] - - -animal_source_of_food menu AnimalSourceOfFoodMenu Cow [NCBITaxon:9913] - Fish [FOODON:03411222] - Pig [NCBITaxon:9823] - Poultry or game bird [FOODON:03411563] - Chicken [NCBITaxon:9031] - Turkey [NCBITaxon:9103] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Mussel [FOODON:03411223] - Scallop [NCBITaxon:6566] - Shrimp [FOODON:03411237] - Squid [FOODON:03411205] - - -food_product_production_stream menu FoodProductProductionStreamMenu Beef cattle production stream [FOODON:03000452] - Broiler chicken production stream [FOODON:03000455] - Dairy cattle production stream [FOODON:03000453] - Egg production stream [FOODON:03000458] - Layer chicken production stream [FOODON:03000456] - Meat production stream [FOODON:03000460] - Veal meat production stream [FOODON:03000461] - Milk production stream [FOODON:03000459] - - -collection_device menu CollectionDeviceMenu Auger (earth auger) [AGRO:00000405] - Box corer [GENEPIO:0100928] - Container [OBI:0000967] - Bag [GSSO:008558] - Whirlpak sampling bag [GENEPIO:0002122] - Bottle [FOODON:03490214] - Vial [OBI:0000522] - Culture plate [GENEPIO:0004318] - Petri dish [NCIT:C96141] - Filter [GENEPIO:0100103] - PONAR grab sampler [GENEPIO:0100929] - Scoop [GENEPIO:0002125] - Soil sample probe [GENEPIO:0100930] - Spatula [NCIT:C149941] - Sponge [OBI:0002819] - Swab [GENEPIO:0100027] - Drag swab [OBI:0002822] - Surface wipe [OBI:0002824] - Tube [GENEPIO:0101196] - Vacuum device [GENEPIO:0002127] - Vacutainer [OBIB:0000032] - - -collection_method menu CollectionMethodMenu Aspiration [HP:0002835] - Biopsy [OBI:0002650] - Fecal grab [GENEPIO:0004326] - Filtration [OBI:0302885] - Air filtration [GENEPIO:0100031] - Water filtration [GENEPIO:0100931] - Lavage [OBI:0600044] - Bronchoalveolar lavage [GENEPIO:0100032] - Gastric lavage [GENEPIO:0100033] - Necropsy [MMO:0000344] - Phlebotomy [NCIT:C28221] - Rinsing for specimen collection [GENEPIO_0002116] - Scooping [GENEPIO:0100932] - Sediment collection [GENEPIO:0100933] - Soil coring [GENEPIO:0100934] - Weep fluid collection (pouring) [GENEPIO:0101003] - -sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu microliter (uL) [UO:0000101] - milliliter (mL) [UO:0000098] - liter (L) [UO:0000099] - -residual_sample_status menu ResidualSampleStatusMenu Residual sample remaining (some sample left) [GENEPIO:0101087] - No residual sample (sample all used) [GENEPIO:0101088] - Residual sample status unkown [GENEPIO:0101089] - -sample_storage_duration_unit menu SampleStorageDurationUnitMenu Second [UO:0000010] - Minute [UO:0000031] - Hour [UO:0000032] - Day [UO:0000033] - Week [UO:0000034] - Month [UO:0000035] - Year [UO:0000036] - -nucelic_acid_storage_duration_unit menu NucelicAcidStorageDurationUnitMenu Second [UO:0000010] - Minute [UO:0000031] - Hour [UO:0000032] - Day [UO:0000033] - Week [UO:0000034] - Month [UO:0000035] - Year [UO:0000036] - -food_packaging menu FoodPackagingMenu Bag, sack or pouch [FOODON:03490197] - Paper bag, sack or pouch [FOODON:03490120] - Plastic bag, sack or pouch [FOODON:03490166] - Plastic shrink wrap [FOODON:03490137] - Plastic wrapper [FOODON:03490128] - Bottle or jar [FOODON:03490203] - Can (container) [FOODON:03490204] - Paper container, treated [FOODON:03490330] - Paper container, untreated [FOODON:03490334] - Plastic tray or pan [FOODON:03490126] - - -host (common name) menu HostCommonNameMenu Bird [NCBITaxon:8782] - Chicken [NCBITaxon:9031] - Seabird [FOODON:00004504] - Cormorant [NCBITaxon:9206] - Double Crested Cormorant [NCBITaxon:56069] - Crane [NCBITaxon:9109] - Whooping Crane [NCBITaxon:9117] - Gull (Seagull) [NCBITaxon:8911] - Glaucous-winged Gull [NCBITaxon:119606] - Great Black-backed Gull [NCBITaxon:8912] - Herring Gull [NCBITaxon:35669] - Ring-billed Gull [NCBITaxon:126683] - Eider [NCBITaxon:50366] - Common Eider [NCBITaxon:76058] - Turkey [NCBITaxon:9103] - Fish [FOODON:03411222] - Rainbow Trout [NCBITaxon:8022] - Sablefish [NCBITaxon:229290] - Salmon [FOODON:00003473] - Atlantic Salmon [NCBITaxon:8030] - Chinook salmon [NCBITaxon:74940] - Coho Salmon [NCBITaxon:8019] - Mammal [FOODON:03411134] - Companion animal [FOODON:03000300] - Cow [NCBITaxon:9913] - Human [NCBITaxon:9606] - Pig [NCBITaxon:9823] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Atlantic Lobster [NCBITaxon:6706] - Atlantic Oyster [NCBITaxon:6565] - Blue Mussel [NCBITaxon:6550] - - -host (scientific name) menu HostScientificNameMenu Anoplopoma fimbria [NCBITaxon:229290] - Bos taurus [NCBITaxon:9913] - Crassostrea virginica [NCBITaxon:6565] - Gallus gallus [NCBITaxon:9031] - Grus americana [NCBITaxon:9117] - Homarus americanus [NCBITaxon:6706] - Homo sapiens [NCBITaxon:9606] - Larus argentatus [NCBITaxon:35669] - Larus delawarensis [NCBITaxon:126683] - Larus glaucescens [NCBITaxon:119606] - Larus marinus [NCBITaxon:8912] - Meleagris gallopavo [NCBITaxon:9103] - Mytilus edulis [NCBITaxon:6550] - Oncorhynchus kisutch [NCBITaxon:8019] - Oncorhynchus mykiss [NCBITaxon:8022] - Oncorhynchus tshawytscha [NCBITaxon:74940] - Ovis aries [NCBITaxon:9940] - Phalacrocorax auritus [NCBITaxon:56069] - Salmo salar [NCBITaxon:8030] - Somateria mollissima [NCBITaxon:76058] - Sus scrofa domesticus [NCBITaxon:9825] - - -host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) - Calf [FOODON:03411349] - Dry cow [FOODON:00004411] - Feeder cow [FOODON:00004292] - Finisher cow [FOODON:00004293] - Milker cow [FOODON:03411201] - Stocker cow [FOODON:00004294] - Weanling cow [FOODON:00004295] - Cow (by sex/reproductive stage) (organizational term) - Bull [FOODON:00000015] - Cow [NCBITaxon:9913] - Freemartin [FOODON:00004296] - Heifer [FOODON:00002518] - Steer [FOODON:00002531] - Pig (by age/production stage) (organizational term) - Finisher pig [FOODON:00003371] - Grower pig [FOODON:00003370] - Nursing pig [FOODON:00004297 ] - Pig [NCBITaxon:9823] - Piglet [FOODON:00003952] - Weanling (weaner) pig [FOODON:00003373] - Pig (by sex/reproductive stage) (organizational term) - Barrow [FOODON:03411280] - Boar [FOODON:03412248] - Gilt [FOODON:00003369] - Sow [FOODON:00003333] - Poultry or game bird [FOODON:03411563] - Broiler or fryer chicken [FOODON:03411198] - Capon [FOODON:03411711] - Chick [FOODON:00004299] - Chicken [NCBITaxon:9031] - Egg [UBERON:0007379] - Hatchling [FOODON:00004300] - Hen [FOODON:00003282] - Layer chicken [FOODON:00004301] - Layer turkey [FOODON:00004302] - Poult [FOODON:00002962] - Pullet [FOODON:00004303] - Rooster [FOODON:03411714] - Tom (Gobbler) [FOODON:00004304 ] - Turkey [NCBITaxon:9103] - Sheep [NCBITaxon:9940] - Ram [FOODON:00004305] - Wether sheep [FOODON:00004306] - Ewe [FOODON:03412610] - Lamb [FOODON:03411669] - Fish [FOODON:03411222] - Fish egg [FOODON_00004319] - Fry (fish) [FOODON_00004318] - Juvenile fish [FOODON_00004317] - - -host_age_bin menu HostAgeBinMenu First winter [GENEPIO:0100684] - First summer [GENEPIO:0100685] - Second winter [GENEPIO:0100686] - Second summer [GENEPIO:0100687] - Third winter [GENEPIO:0100688] - Third summer [GENEPIO:0100689] - - -isolated_by menu IsolatedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - - -organism menu OrganismMenu Acinetobacter [NCBITaxon:469] - Acinetobacter baumannii [NCBITaxon:470] - Acinetobacter bereziniae [NCBITaxon:106648] - Acinetobacter ursingii [NCBITaxon:108980] - Aeromonas [NCBITaxon:642] - Aeromonas allosaccharophila [NCBITaxon:656] - Aeromonas hydrophila [NCBITaxon:644] - Aeromonas rivipollensis [NCBITaxon:948519] - Aeromonas salmonicida [NCBITaxon:645] - Campylobacter [NCBITaxon:194] - Campylobacter coli [NCBITaxon:195] - Campylobacter jejuni [NCBITaxon:197] - Campylobacter lari [NCBITaxon:201] - Citrobacter [NCBITaxon:544] - Citrobacter braakii [NCBITaxon:57706] - Citrobacter freundii [NCBITaxon:546] - Citrobacter gillenii [NCBITaxon:67828] - Clostridioides [NCBITaxon:1870884] - Clostridioides difficile [NCBITaxon:1496] - Clostridium [NCBITaxon:1485] - Clostridium perfringens [NCBITaxon:1502] - Clostridium sporogenes [NCBITaxon:1509] - Comamonas [NCBITaxon:283] - Comamonas aquatica [NCBITaxon:225991] - Enterobacter [NCBITaxon:547] - Enterobacter asburiae [NCBITaxon:61645] - Enterobacter cancerogenus [NCBITaxon:69218] - Enterobacter cloacae [NCBITaxon:550] - Enterobacter hormaechei [NCBITaxon:158836] - Enterobacter kobei [NCBITaxon:208224] - Enterobacter roggenkampii [NCBITaxon:1812935] - Enterobacter sp. [NCBITaxon:42895] - Lelliottia amnigena [NCBITaxon:61646] - Pluralibacter gergoviae [NCBITaxon:61647] - Enterococcus [NCBITaxon:1350] - Enterococcus asini [NCBITaxon:57732] - Enterococcus avium [NCBITaxon:33945] - Enterococcus caccae [NCBITaxon:317735] - Enterococcus canis [NCBITaxon:214095] - Enterococcus casseliflavus [NCBITaxon:37734] - Enterococcus cecorum [NCBITaxon:44008] - Enterococcus dispar [NCBITaxon:44009] - Enterococcus durans [NCBITaxon:53345] - Enterococcus faecium [NCBITaxon:1352] - Enterococcus faecalis [NCBITaxon:1351] - Enterococcus gallinarum [NCBITaxon:1353] - Enterococcus hirae [NCBITaxon:1354] - Enterococcus malodoratus [NCBITaxon:71451] - Enterococcus mundtii [NCBITaxon:53346] - Enterococcus ratti [NCBITaxon:150033] - Enterococcus saccharolyticus [NCBITaxon:41997] - Enterococcus thailandicus [NCBITaxon:417368] - Enterococcus villorum [NCBITaxon:112904] - Escherichia [NCBITaxon:561] - Escherichia coli [NCBITaxon:562] - Escherichia fergusonii [NCBITaxon:564] - Exiguobacterium [NCBITaxon:33986] - Exiguobacterium oxidotolerans [NCBITaxon:223958] - Exiguobacterium sp. [NCBITaxon:44751] - Klebsiella [NCBITaxon:570] - Klebsiella aerogenes [NCBITaxon:548] - Klebsiella michiganensis [NCBITaxon:1134687] - Klebsiella oxytoca [NCBITaxon:571] - Klebsiella pneumoniae [NCBITaxon:573] - Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] - Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] - Kluyvera [NCBITaxon:579] - Kluyvera intermedia [NCBITaxon:61648] - Kosakonia [NCBITaxon:1330547] - Kosakonia cowanii [NCBITaxon:208223] - Leclercia [NCBITaxon:83654] - Leclercia adecarboxylata [NCBITaxon:83655] - Listeria [NCBITaxon:1637] - Listeria monocytogenes [NCBITaxon:1639] - Ochrobactrum [NCBITaxon:528] - Ochrobactrum sp. [NCBITaxon:42190] - Pantoea [NCBITaxon:53335] - Pantoea ananatis [NCBITaxon:553] - Pantoea sp. [NCBITaxon:69393] - Photobacterium [NCBITaxon:657] - Photobacterium indicum[NCBITaxon:81447] - Photobacterium sp. [NCBITaxon:660] - Providencia [NCBITaxon:586] - Providencia rettgeri [NCBITaxon:587] - Pseudoalteromonas [NCBITaxon:53246] - Pseudoalteromonas tetraodonis [NCBITaxon:43659] - Pseudomonas [NCBITaxon:286] - Pseudomonas aeruginosa [NCBITaxon:287] - Pseudomonas fluorescens [NCBITaxon:294] - Pseudomonas soli [NCBITaxon:1306993] - Pseudomonas sp. [NCBITaxon:306] - Psychrobacter [NCBITaxon:497] - Psychrobacter faecalis [NCBITaxon:180588] - Psychrobacter nivimaris [NCBITaxon:281738] - Psychrobacter sp. [NCBITaxon:56811] - Rahnella [NCBITaxon:34037] - Rahnella aquatilis [NCBITaxon:34038] - Rahnella sp. [NCBITaxon:1873497] - Raoultella [NCBITaxon:160674] - Raoultella ornithinolytica [NCBITaxon:54291] - Raoultella planticola [NCBITaxon:575] - Salmonella enterica [NCBITaxon:28901] - Salmonella enterica subsp. enterica [NCBITaxon:59201] - Salmonella enterica subsp. arizonae [NCBITaxon:59203] - Serratia [NCBITaxon:613] - Shewanella [NCBITaxon:22] - Shewanella pealeana [NCBITaxon:70864] - Shewanella putrefaciens [NCBITaxon:24] - Shewanella oncorhynchi [NCBITaxon:2726434] - Shewanella sp. [NCBITaxon:50422] - Staphylococcus [NCBITaxon:1279] - Staphylococcus aureus [NCBITaxon:1280] - Streptococcus [NCBITaxon:1301] - Streptococcus alactolyticus [NCBITaxon:29389] - Streptococcus bovis [NCBITaxon:1335] - Streptococcus equinus [NCBITaxon:1335] - Streptococcus gallolyticus [NCBITaxon:315405] - Streptococcus infantarius [NCBITaxon:102684] - Streptococcus lutetiensis [NCBITaxon:150055] - Streptococcus macedonicus [NCBITaxon:59310] - Streptococcus pasteurianus [NCBITaxon:197614] - Streptococcus suis [NCBITaxon:1307] - Vibrio [NCBITaxon:662] - Vibrio cholerae [NCBITaxon:666] - Vibrio parahaemolyticus [NCBITaxon:670] - -taxonomic_identification_process menu TaxonomicIdentificationProcessMenu Whole genome sequencing assay [OBI:0002117] - 16S ribosomal gene sequencing assay [OBI:0002763] - PCR assay [OBI:0002740] - Comparative phenotypic assessment [OBI:0001546] - Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] - - -sequenced_by menu SequencedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - McGill University [GENEPIO:0101103] - - -purpose_of_sequencing menu PurposeOfSequencingMenu Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549] - Field experiment [GENEPIO:0100550] - Protocol testing experiment [GENEPIO:0100024] - Survey study [GENEPIO:0100582] - Surveillance [GENEPIO:0100004] - - -sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] - Pacific Biosciences [GENEPIO:0001927] - Ion Torrent [GENEPIO:0002683] - Oxford Nanopore Technologies [OBI:0002755] - BGI Genomics [GENEPIO:0004324] - MGI [GENEPIO:0004325] - - -sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. - Illumina Genome Analyzer [OBI:0002128] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. - Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology - Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. - Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. - Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. - Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. - Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. - Illumina HiSeq X Ten [OBI:0002129] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Illumina HiSeq 1500 [OBI:0003386] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. - Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. - Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. - Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. - Illumina NovaSeq 6000 [OBI:0002630] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - Illumina MiniSeq [OBI:0003114] A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. - Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. - Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. - Illumina NextSeq 1000 [OBI:0003606] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. - Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. - PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. - PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. - PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - PacBio Sequel [OBI:0002632] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - PacBio Sequel II [OBI:0002633] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. - Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. - Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. - Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. - Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. - Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. - Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. - Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. - Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual - Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - BGISEQ [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. - BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". - DNBSEQ [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. - DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. - DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. - DNBSEQ-G400 FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. - DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. - - -sequencing_assay_type menu SequencingAssayTypeMenu Amplicon sequencing assay [OBI:0002767] - 16S ribosomal gene sequencing assay [OBI:0002763] - Whole genome sequencing assay [OBI:0002117] - Whole metagenome sequencing assay [OBI:0002623] - Whole virome sequencing assay [OBI:0002768] - -genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu Hybrid selection method (bait-capture) [GENEPIO:0001950] - rRNA depletion method [GENEPIO:0101020] - - -sequence_submitted_by menu SequenceSubmittedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - McGill University [GENEPIO:0101103] - -quality_control_determination menu QualityControlDeterminationMenu No quality control issues identified [GENEPIO:0100562] - Sequence passed quality control [GENEPIO:0100563] - Sequence failed quality control [GENEPIO:0100564] - Minor quality control issues identified [GENEPIO:0100565] - Sequence flagged for potential quality control issues [GENEPIO:0100566] - Quality control not performed [GENEPIO:0100567] - -quality _control_issues menu QualityControlIssuesMenu Low quality sequence [GENEPIO:0100568] - Sequence contaminated [GENEPIO:0100569] - Low average genome coverage [GENEPIO:0100570] - Low percent genome captured [GENEPIO:0100571] - Read lengths shorter than expected [GENEPIO:0100572] - Sequence amplification artifacts [GENEPIO:0100573] - Low signal to noise ratio [GENEPIO:0100574] - Low coverage of characteristic mutations [GENEPIO:0100575] - - -attribute_package menu AttributePackageMenu Pathogen.cl [GENEPIO:0001835] - Pathogen.env [GENEPIO:0100581] - - -experimental_intervention menu ExperimentalInterventionMenu Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538] - Certified organic farming practices [GENEPIO:0100539] - Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543] - Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346] - - -AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - - -antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] - Intermediate antimicrobial phenotype [ARO:3004300] - Indeterminate antimicrobial phenotype [GENEPIO:0100585] - Nonsusceptible antimicrobial phenotype [ARO:3004303] - Resistant antimicrobial phenotype [ARO:3004301] - Susceptible antimicrobial phenotype [ARO:3004302] - Susceptible dose dependent antimicrobial phenotype [ARO:3004304] - - -antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] - millimetre (mm) [UO:0000016] - microgram per millilitre (ug/mL) [UO:0000274] - - -antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] - less than or equal to (<=) [GENEPIO:0001003] - equal to (==) [GENEPIO:0001004] - greater than (>) [GENEPIO:0001006] - greater than or equal to (>=) [GENEPIO:0001005] - - -antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion - Antimicrobial gradient (E-test) [NCIT:85596] - Agar dilution [ARO:3004411] agar dilution - Broth dilution [ARO:3004397] - - -antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] - Microscan [ARO:3004400] Microscan - Phoenix [ARO:3004401] Phoenix - Sensititre [ARO:3004402] Sensititre - Vitek System [ARO:3004403] Vitek - - -antimicrobial_vendor_name menu AntimicrobialVendorNameMenu Becton Dickinson [ARO:3004405] Becton Dickinson - bioMérieux [ARO:3004406] Biomérieux - Omron [ARO:3004408] - Siemens [ARO:3004407] Siemens - Trek [ARO:3004409] Trek - - -antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] BSAC - Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] CLSI - Deutsches Institut für Normung (DIN) [ARO:3004367] DIN - European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] EUCAST - National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] NARMS - National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] NCCLS - Société Française de Microbiologie (SFM) [ARO:3004369] SFM - Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] SIR - Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG - - -Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin - amoxicillin-clavulanic_acid - ampicillin - azithromycin - cefazolin - cefepime - cefotaxime - cefotaxime-clavulanic_acid - cefoxitin - cefpodoxime - ceftazidime - ceftazidime-clavulanic_acid - ceftiofur - ceftriaxone - cephalothin - chloramphenicol - ciprofloxacin - clindamycin - doxycycline - enrofloxacin - erythromycin - florfenicol - gentamicin - imipenem - kanamycin - levofloxacin - linezolid - meropenem - nalidixic_acid - nitrofurantoin - norfloxacin - oxolinic-acid - oxytetracycline - piperacillin - piperacillin-tazobactam - polymyxin-b - quinupristin-dalfopristin - streptomycin - sulfisoxazole - telithromycin - tetracycline - tigecycline - trimethoprim-sulfamethoxazole \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM Template + +null value menu NullValueMenu Not Applicable [GENEPIO:0001619] + Missing [GENEPIO:0001618] missing + Not Collected [GENEPIO:0001620] + Not Provided [GENEPIO:0001668] + Restricted Access [GENEPIO:0001810] + +sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + University of Manitoba (UM) [GENEPIO:0004434] + + +purpose_of_sampling menu PurposeOfSamplingMenu Cluster/Outbreak investigation [GENEPIO:0100001] + Diagnostic testing [GENEPIO:0100002] + Environmental testing [GENEPIO:0100548] + Research [GENEPIO:0100003] + Clinical trial [GENEPIO:0100549] + Field experiment [GENEPIO:0100550] + Survey study [GENEPIO:0100582] + Surveillance [GENEPIO:0100004] + + +presampling_activity menu PresamplingActivityMenu Addition of substances to food/water [GENEPIO:0100536] + Antimicrobial pre-treatment [GENEPIO:0100537] + Certified animal husbandry practices [GENEPIO:0100538] + Certified humane animal husbandry practices [GENEPIO:0100894] + Certified organic farming practices [GENEPIO:0100539] + Conventional farming practices [GENEPIO:0100895] + Change in storage conditions [GENEPIO:0100540] + Cleaning/disinfection [GENEPIO:0100541] + Extended downtime between activities [GENEPIO:0100542] + Fertilizer pre-treatment [GENEPIO:0100543] + Genetic mutation [GENEPIO:0100544[ + Logistic slaughter [GENEPIO:0100545] + Microbial pre-treatment [GENEPIO:0100546] + Probiotic pre-treatment [GENEPIO:0100547] + Vaccination [NCIT:C15346] + Wastewater treatment process [ENVO:06105300] A recycling process during which wastewater is treated. + Wastewater filtration [GENEPIO:0100881] A wastewater treatment process which removes solid particles from wastewater by means of filtration. + Wastewater grit removal [GENEPIO:0100882] A wastewater treatment process which removes sand, silt, and grit from wastewater. + Wastewater microbial treatment [GENEPIO:0100883] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. + Wastewater primary sedimentation [GENEPIO:0100884] A wastewater treatment process which removes solids and large particles from influent through gravitational force. + Wastewater secondary sedimentation [GENEPIO:0100885] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. + +experimental_specimen_role_type menu ExperimentalSpecimenRoleTypeMenu Positive experimental control [GENEPIO:0101018] + Negative experimental control [GENEPIO:0101019] + Technical replicate [EFO:0002090] + Biological replicate [EFO:0002091] + + +specimen_processing menu SpecimenProcessingMenu Biological replicate process [GENEPIO:0101022] + Samples pooled [OBI:0600016] + Technical replicate process [GENEPIO:0101021] + Isolated from single source [OBI:0002079] + + +geo_loc_name (country) menu GeoLocNameCountryMenu Afghanistan [GAZ:00006882] + Albania [GAZ:00002953] + Algeria [GAZ:00000563] + American Samoa [GAZ:00003957] + Andorra [GAZ:00002948] + Angola [GAZ:00001095] + Anguilla [GAZ:00009159] + Antarctica [GAZ:00000462] + Antigua and Barbuda [GAZ:00006883] + Argentina [GAZ:00002928] + Armenia [GAZ:00004094] + Aruba [GAZ:00004025] + Ashmore and Cartier Islands [GAZ:00005901] + Australia [GAZ:00000463] + Austria [GAZ:00002942] + Azerbaijan [GAZ:00004941] + Bahamas [GAZ:00002733] + Bahrain [GAZ:00005281] + Baker Island [GAZ:00007117] + Bangladesh [GAZ:00003750] + Barbados [GAZ:00001251] + Bassas da India [GAZ:00005810] + Belarus [GAZ:00006886] + Belgium [GAZ:00002938] + Belize [GAZ:00002934] + Benin [GAZ:00000904] + Bermuda [GAZ:00001264] + Bhutan [GAZ:00003920] + Bolivia [GAZ:00002511] + Borneo [GAZ:00025355] + Bosnia and Herzegovina [GAZ:00006887] + Botswana [GAZ:00001097] + Bouvet Island [GAZ:00001453] + Brazil [GAZ:00002828] + British Virgin Islands [GAZ:00003961] + Brunei [GAZ:00003901] + Bulgaria [GAZ:00002950] + Burkina Faso [GAZ:00000905] + Burundi [GAZ:00001090] + Cambodia [GAZ:00006888] + Cameroon [GAZ:00001093] + Canada [GAZ:00002560] + Cape Verde [GAZ:00001227] + Cayman Islands [GAZ:00003986] + Central African Republic [GAZ:00001089] + Chad [GAZ:00000586] + Chile [GAZ:00002825] + China [GAZ:00002845] + Christmas Island [GAZ:00005915] + Clipperton Island [GAZ:00005838] + Cocos Islands [GAZ:00009721] + Colombia [GAZ:00002929] + Comoros [GAZ:00005820] + Cook Islands [GAZ:00053798] + Coral Sea Islands [GAZ:00005917] + Costa Rica [GAZ:00002901] + Cote d'Ivoire [GAZ:00000906] + Croatia [GAZ:00002719] + Cuba [GAZ:00003762] + Curacao [GAZ:00012582] + Cyprus [GAZ:00004006] + Czech Republic [GAZ:00002954] + Democratic Republic of the Congo [GAZ:00001086] + Denmark [GAZ:00005852] + Djibouti [GAZ:00000582] + Dominica [GAZ:00006890] + Dominican Republic [GAZ:00003952] + Ecuador [GAZ:00002912] + Egypt [GAZ:00003934] + El Salvador [GAZ:00002935] + Equatorial Guinea [GAZ:00001091] + Eritrea [GAZ:00000581] + Estonia [GAZ:00002959] + Eswatini [GAZ:00001099] + Ethiopia [GAZ:00000567] + Europa Island [GAZ:00005811] + Falkland Islands (Islas Malvinas) [GAZ:00001412] + Faroe Islands [GAZ:00059206] + Fiji [GAZ:00006891] + Finland [GAZ:00002937] + France [GAZ:00003940] + French Guiana [GAZ:00002516] + French Polynesia [GAZ:00002918] + French Southern and Antarctic Lands [GAZ:00003753] + Gabon [GAZ:00001092] + Gambia [GAZ:00000907] + Gaza Strip [GAZ:00009571] + Georgia [GAZ:00004942] + Germany [GAZ:00002646] + Ghana [GAZ:00000908] + Gibraltar [GAZ:00003987] + Glorioso Islands [GAZ:00005808] + Greece [GAZ:00002945] + Greenland [GAZ:00001507] + Grenada [GAZ:02000573] + Guadeloupe [GAZ:00067142] + Guam [GAZ:00003706] + Guatemala [GAZ:00002936] + Guernsey [GAZ:00001550] + Guinea [GAZ:00000909] + Guinea-Bissau [GAZ:00000910] + Guyana [GAZ:00002522] + Haiti [GAZ:00003953] + Heard Island and McDonald Islands [GAZ:00009718] + Honduras [GAZ:00002894] + Hong Kong [GAZ:00003203] + Howland Island [GAZ:00007120] + Hungary [GAZ:00002952] + Iceland [GAZ:00000843] + India [GAZ:00002839] + Indonesia [GAZ:00003727] + Iran [GAZ:00004474] + Iraq [GAZ:00004483] + Ireland [GAZ:00002943] + Isle of Man [GAZ:00052477] + Israel [GAZ:00002476] + Italy [GAZ:00002650] + Jamaica [GAZ:00003781] + Jan Mayen [GAZ:00005853] + Japan [GAZ:00002747] + Jarvis Island [GAZ:00007118] + Jersey [GAZ:00001551] + Johnston Atoll [GAZ:00007114] + Jordan [GAZ:00002473] + Juan de Nova Island [GAZ:00005809] + Kazakhstan [GAZ:00004999] + Kenya [GAZ:00001101] + Kerguelen Archipelago [GAZ:00005682] + Kingman Reef [GAZ:00007116] + Kiribati [GAZ:00006894] + Kosovo [GAZ:00011337] + Kuwait [GAZ:00005285] + Kyrgyzstan [GAZ:00006893] + Laos [GAZ:00006889] + Latvia [GAZ:00002958] + Lebanon [GAZ:00002478] + Lesotho [GAZ:00001098] + Liberia [GAZ:00000911] + Libya [GAZ:00000566] + Liechtenstein [GAZ:00003858] + Line Islands [GAZ:00007144] + Lithuania [GAZ:00002960] + Luxembourg [GAZ:00002947] + Macau [GAZ:00003202] + Madagascar [GAZ:00001108] + Malawi [GAZ:00001105] + Malaysia [GAZ:00003902] + Maldives [GAZ:00006924] + Mali [GAZ:00000584] + Malta [GAZ:00004017] + Marshall Islands [GAZ:00007161] + Martinique [GAZ:00067143] + Mauritania [GAZ:00000583] + Mauritius [GAZ:00003745] + Mayotte [GAZ:00003943] + Mexico [GAZ:00002852] + Micronesia [GAZ:00005862] + Midway Islands [GAZ:00007112] + Moldova [GAZ:00003897] + Monaco [GAZ:00003857] + Mongolia [GAZ:00008744] + Montenegro [GAZ:00006898] + Montserrat [GAZ:00003988] + Morocco [GAZ:00000565] + Mozambique [GAZ:00001100] + Myanmar [GAZ:00006899] + Namibia [GAZ:00001096] + Nauru [GAZ:00006900] + Navassa Island [GAZ:00007119] + Nepal [GAZ:00004399] + Netherlands [GAZ:00002946] + New Caledonia [GAZ:00005206] + New Zealand [GAZ:00000469] + Nicaragua [GAZ:00002978] + Niger [GAZ:00000585] + Nigeria [GAZ:00000912] + Niue [GAZ:00006902] + Norfolk Island [GAZ:00005908] + North Korea [GAZ:00002801] + North Macedonia [GAZ:00006895] + North Sea [GAZ:00002284] + Northern Mariana Islands [GAZ:00003958] + Norway [GAZ:00002699] + Oman [GAZ:00005283] + Pakistan [GAZ:00005246] + Palau [GAZ:00006905] + Panama [GAZ:00002892] + Papua New Guinea [GAZ:00003922] + Paracel Islands [GAZ:00010832] + Paraguay [GAZ:00002933] + Peru [GAZ:00002932] + Philippines [GAZ:00004525] + Pitcairn Islands [GAZ:00005867] + Poland [GAZ:00002939] + Portugal [GAZ:00004126] + Puerto Rico [GAZ:00006935] + Qatar [GAZ:00005286] + Republic of the Congo [GAZ:00001088] + Reunion [GAZ:00003945] + Romania [GAZ:00002951] + Ross Sea [GAZ:00023304] + Russia [GAZ:00002721] + Rwanda [GAZ:00001087] + Saint Helena [GAZ:00000849] + Saint Kitts and Nevis [GAZ:00006906] + Saint Lucia [GAZ:00006909] + Saint Pierre and Miquelon [GAZ:00003942] + Saint Martin [GAZ:00005841] + Saint Vincent and the Grenadines [GAZ:02000565] + Samoa [GAZ:00006910] + San Marino [GAZ:00003102] + Sao Tome and Principe [GAZ:00006927] + Saudi Arabia [GAZ:00005279] + Senegal [GAZ:00000913] + Serbia [GAZ:00002957] + Seychelles [GAZ:00006922] + Sierra Leone [GAZ:00000914] + Singapore [GAZ:00003923] + Sint Maarten [GAZ:00012579] + Slovakia [GAZ:00002956] + Slovenia [GAZ:00002955] + Solomon Islands [GAZ:00005275] + Somalia [GAZ:00001104] + South Africa [GAZ:00001094] + South Georgia and the South Sandwich Islands [GAZ:00003990] + South Korea [GAZ:00002802] + South Sudan [GAZ:00233439] + Spain [GAZ:00003936] + Spratly Islands [GAZ:00010831] + Sri Lanka [GAZ:00003924] + State of Palestine [GAZ:00002475] + Sudan [GAZ:00000560] + Suriname [GAZ:00002525] + Svalbard [GAZ:00005396] + Swaziland [GAZ:00001099] + Sweden [GAZ:00002729] + Switzerland [GAZ:00002941] + Syria [GAZ:00002474] + Taiwan [GAZ:00005341] + Tajikistan [GAZ:00006912] + Tanzania [GAZ:00001103] + Thailand [GAZ:00003744] + Timor-Leste [GAZ:00006913] + Togo [GAZ:00000915] + Tokelau [GAZ:00260188] + Tonga [GAZ:00006916] + Trinidad and Tobago [GAZ:00003767] + Tromelin Island [GAZ:00005812] + Tunisia [GAZ:00000562] + Turkey [GAZ:00000558] + Turkmenistan [GAZ:00005018] + Turks and Caicos Islands [GAZ:00003955] + Tuvalu [GAZ:00009715] + United States of America [GAZ:00002459] + Uganda [GAZ:00001102] + Ukraine [GAZ:00002724] + United Arab Emirates [GAZ:00005282] + United Kingdom [GAZ:00002637] + Uruguay [GAZ:00002930] + Uzbekistan [GAZ:00004979] + Vanuatu [GAZ:00006918] + Venezuela [GAZ:00002931] + Viet Nam [GAZ:00003756] + Virgin Islands [GAZ:00003959] + Wake Island [GAZ:00007111] + Wallis and Futuna [GAZ:00007191] + West Bank [GAZ:00009572] + Western Sahara [GAZ:00000564] + Yemen [GAZ:00005284] + Zambia [GAZ:00001107] + Zimbabwe [GAZ:00001106] + + +geo_loc_name (state/province/region) menu GeoLocNameStateProvinceRegionMenu Atlantic region (Canada) [wikidata:Q246972] + New Brunswick [GAZ:00002570] + Newfoundland & Labrador [GAZ:00002567] + Nova Scotia [GAZ:00002565] + Prince Edward Island [GAZ:00002572] + Central region (Canada) [wikidata:Q1048064] + Ontario [GAZ:00002563] + Quebec [GAZ:00002569] + Northern region (Canada) [wikidata:Q764146] + Northwest Territories [GAZ:00002575] + Nunuvut [GAZ:00002574] + Yukon [GAZ:00002576] + Pacific region (Canada) [wikidata:Q122953299] + British Columbia [GAZ:00002562] + Prairie region (Canada) [wikidata:Q1364746] + Alberta [GAZ:00002566] + Manitoba [GAZ:00002571] + Saskatchewan [GAZ:00002564] + + +sample_collection_date_precision menu SampleCollectionDatePrecisionMenu year [UO:0000036] + month [UO:0000035] + day [UO:0000033] + + +environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] + Agricultural Field [ENVO:00000114] + Alluvial fan [ENVO:00000314] + Animal cage [ENVO:01000922] + Aquarium [ENVO:00002196] + Artificial wetland [ENVO:03501406] + Breeding ground [ENVO:03501441] + Building [ENVO:00000073] + Barn [ENVO:03501257] + Breeder barn [ENVO:03501383] + Broiler barn [ENVO:03501386] + Sheep barn [ENVO:03501385] + Biodome [ENVO:03501397] + Cottage [ENVO:03501393] + Dairy [ENVO:00003862] + Hospital [ENVO:00002173] + Laboratory facility [ENVO:01001406] + Pigsty [ENVO:03501413] + Building part (organizational term) + Air intake [ENVO:03501380] + Animal pen [ENVO:03501387] + Building floor [ENVO:01000486] + Building wall [ENVO:01000465] + Countertop [ENVO:03501404] + Shelf [ENVO:03501403] + Stall [EOL:0001903] + Window sill [ENVO:03501381] + Creek [ENVO:03501405] + Ditch [ENVO:00000037] A small, human-made channel which has been dug for draining or irrigating the land. + Drainage ditch [ENVO:00000140] A ditch that collects water from the surrounding land. + Irrigation ditch [ENVO:00000139] A ditch that supplies water to surrounding land. + Farm [ENVO:00000078] + Beef farm [ENVO:03501443] + Breeder farm [ENVO:03501384] + Dairy farm [ENVO:03501416] + Feedlot [ENVO:01000627] + Beef cattle feedlot [ENVO:03501444] + Fish farm [ENVO:00000294] + Research farm [ENVO:03501417] + Central Experimental Farm [GAZ:00004603] Central Experimental Farm + Freshwater environment [ENVO:01000306] + Hatchery [ENVO:01001873] + Poultry hatchery [ENVO:01001874] + Lake [ENVO:00000020] + Manure digester facility [ENVO:03501422] + Manure lagoon (Anaerobic lagoon) [ENVO:03501423] + Manure pit [ENVO:01001872] + Marine environment [ENVO:01000320] + Benthic zone [ENVO:03501440] + Pelagic zone [ENVO:00000208] + Park [ENVO:00000562] + Plumbing drain [ENVO:01000924 ] + Pond [ENVO:00000033] + Reservoir [ENVO:00000025] + Irrigation reservoir [ENVO:00000450] + Retail environment [ENVO:01001448] + Shop [ENVO:00002221] + Butcher shop [ENVO:03501396] + Pet store [ENVO:03501395] + Supermarket [ENVO:01000984] + River [ENVO:00000022] + Roost (bird) [ENVO:03501439] + Rural area [ENVO:01000772] + Slough [ENVO:03501438] + Stream [ENVO:00000023] + Trailer [ENVO:03501394] + Tributary [ENVO:00000495] + Truck [ENVO:01000602] + Urban area [ENVO:03501437] + Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. + Water surface [ENVO:01001191] + Woodland area [ENVO:00000109] + Zoo [ENVO:00010625] + + +water_depth_units menu WaterDepthUnitsMenu centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + kilometer (km) [UO:0010066] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + + +sediment_depth_units menu SedimentDepthUnitsMenu centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + kilometer (km) [UO:0010066] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + + +air_temperature_units menu AirTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] + degree Celsius (C) [UO:0000027] + + +water_temperature_units menu WaterTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] + degree Celsius (C) [UO:0000027] + +precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu millimeter (mm) [UO:0000016] + centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + +available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702] + Experimental parameters documentation [GENEPIO:0100703] + Feed history [GENEPIO:0100704] + Land use information [GENEPIO:0100705] + Therapeutic administration history [GENEPIO:0100706] + Chemical characterization [GENEPIO:0100707] + pH measurement [GENEPIO:0100708] + Dissolved oxygen measurement [GENEPIO:0100709] + Nitrate measurement [GENEPIO:0100710] + Nitrite measurement [GENEPIO:0100711] + Phosphorous measurement [GENEPIO:0100712] + Salinity measurement [GENEPIO:0100713] + Microbiological characterization [GENEPIO:0100714] + Microbiological identification [GENEPIO:0100715] + Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] + Microbiological identification (bioMérieux API) [GENEPIO:0100717] + Microbiological identification (Biolog) [GENEPIO:0100718] + Microbiological identification (FAME) [GENEPIO:0100719] + Microbiological identification (Sensititre) [GENEPIO:0100720] + Microbiological identification (ViTek) [GENEPIO:0100721] + Phage type [GENEPIO:0100722] + Serotype [GENEPIO:0100723] + Phenotypic microbiological characterization [GENEPIO:0100724] + AMR phenotypic testing [GENEPIO:0100725] + Biolog phenotype microarray [GENEPIO:0100726] + Microbiological quantification [GENEPIO:0100727] + Colony count [GENEPIO:0100728] + Total coliform count [GENEPIO:0100729] + Total fecal coliform count [GENEPIO:0100730] + Infectivity assay [GENEPIO:0100731] + ELISA toxin binding [GENEPIO:0100732] + Molecular characterization [GENEPIO:0100733] + 16S rRNA Sanger sequencing [GENEPIO:0100734] + Metagenomic sequencing [GENEPIO:0101024] + PCR marker detection [GENEPIO:0100735] + BOX PCR fingerprint [GENEPIO:0100736] + ERIC PCR fingerprint [GENEPIO:0100737] + Plasmid type [GENEPIO:0100738] + Ribotype [GENEPIO:0100739] + Molecular quantification [GENEPIO:0100740] + qPCR marker organism quantification [GENEPIO:0100741] + Physical characterization [GENEPIO:0100742] + Conductivity measurement [GENEPIO:0100743] + Mollusc shell measurement [GENEPIO:0100744] + Mollusc shell length [GENEPIO:0100745] + Matter compostion [GENEPIO:0100746] + Dry matter composition [GENEPIO:0100747] + Organic matter composition [GENEPIO:0100748] + Turbidity measurement [GENEPIO:0100749] + + +sampling_weather_conditions menu SamplingWeatherConditionsMenu Cloudy/Overcast [ENVO:03501418] + Partially cloudy [ENVO:03501419] + Drizzle [ENVO:03501420] + Fog [ENVO:01000844] + Rain [ENVO:01001564] + Snow [ENVO:01000406] + Storm [ENVO:01000876] + Sunny/Clear [ENVO:03501421] + + +animal_or_plant_population menu AnimalOrPlantPopulationMenu Algae [FOODON:03411301] + Algal bloom [ENVO:2000004] + Cattle [NCBITaxon:9913] + Beef cattle [FOODON:00004413] + Dairy cattle [FOODON:00002505] + Chicken [NCBITaxon:9031] + Crop [AGRO:00000325] + Fish [FOODON:03411222] + Pig [NCBITaxon:9823] + Poultry [FOODON:00004298] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Crustacean [FOODON:03411374] + Mollusc [FOODON:03412112] + Tropical fish [FOODON:00004283] + Turkey [NCBITaxon:9103] + Wildlife [FOODON:00004503] + Wild bird [FOODON:00004505] + Seabird [FOODON:00004504] + + + +environmental_material menu EnvironmentalMaterialMenu Air [ENVO:00002005] + Alluvium [ENVO:01001202] + Animal feeding equipment [AGRO:00000675] + Animal feeder [AGRO:00000679] + Animal drinker [AGRO:00000680] + Feed pan [AGRO:00000676] + Watering bowl [AGRO:00000677] + Animal transportation equipment [AGRO:00000671] + Dead haul trailer [GENEPIO:0100896] + Dead haul truck [AGRO:00000673] + Live haul trailer [GENEPIO:0100897] + Live haul truck [AGRO:00000674] + Belt [NCIT:C49844] + Biosolids [ENVO:00002059] + Boot [GSSO:012935] + Boot cover [OBI:0002806] + Broom [ENVO:03501431] + Bulk tank [ENVO:03501379] + Chick box [AGRO:00000678] + Chick pad [AGRO:00000672] + Cleaning equipment [ENVO:03501430] + Compost [ENVO:00002170] + Contaminated water [ENVO:00002186] + Fecal slurry [ENVO:03501436] + Fluid from meat rinse [GENEPIO:0004323] + Effluent [ENVO:03501407] + Influent [ENVO:03501442] + Surface runoff [ENVO:03501408] + Poultry plucking water [AGRO_00000693] + Wastewater [ENVO:00002001] + Weep fluid [AGRO_00000692] + Crate [ENVO:03501372] + Dumpster [ENVO:03501400] + Dust [ENVO:00002008] + Egg belt [AGRO:00000670] + Fan [NCIT:C49947] + Freezer [ENVO:03501415] + Freezer handle [ENVO:03501414] + Manure [ENVO:00003031] + Animal manure [AGRO:00000079] + Pig manure [AGRO:00000080] + Manure digester equipment [ENVO:03501424] + Nest [ENVO:03501432] + Bird's nest [ENVO:00005805] + Permafrost [ENVO:00000134] + Plucking belt [AGRO:00000669] + Poultry fluff [UBERON:0008291] + Poultry litter [AGRO:00000080] + Sediment [ENVO:00002007] + Soil [ENVO:00001998] + Agricultural soil [ENVO:00002259] + Forest soil [ENVO:00002261] + Straw [ENVO:00003869] + Canola straw [FOODON:00004430] + Oat straw [FOODON:03309878] + Barley straw [FOODON:00004559] + Sludge [ENVO:00002044] + Primary sludge [ENVO:00002057] + Secondary sludge [ENVO:00002058] + Water [CHEBI:15377] + Drinking water [ENVO:00003064] + Groundwater [ENVO:01001004] + Surface water [ENVO:00002042] + + +anatomical_material menu AnatomicalMaterialMenu Blood [UBERON:0000178] + Fluid [UBERON:0006314] + Fluid (cerebrospinal (CSF)) [UBERON:0001359] + Fluid (amniotic) [UBERON:0000173] + Saliva [UBERON:0001836] + Tissue [UBERON:0000479] + + +body_product menu BodyProductMenu Digestive tract substance [GENEPIO:0100898] + Caecal content [GENEPIO:0100899] + Intestinal content [GENEPIO:0100900] + Stomach content [GENEPIO:0100901] + Feces [UBERON:0001988] + Fecal composite [GENEPIO:0004512] + Feces (fresh) [GENEPIO:0004513] + Feces (environmental) [GENEPIO:0004514] + Meconium [UBERON:0007109] + Milk [UBERON:0001913] + Colostrum [UBERON:0001914] + Urine [UBERON:0001088] + + +anatomical_part menu AnatomicalPartMenu Carcass [UBERON:0008979] + Swine carcass [FOODON:03311719] + Digestive system [UBERON:0001007] + Caecum [UBERON:0001153] + Colon [UBERON:0001155] + Digestive gland [UBERON:0006925] + Foregut [UBERON:0001041] + Gall bladder [UBERON:0002110] + Gastrointestinal system mucosa [UBERON:0004786] + Gizzard [UBERON:0005052] + Hindgut [UBERON:0001046] + Intestine [UBERON:0000160] + Small intestine [UBERON:0002108] + Duodenum [UBERON:0002114] + Ileum [UBERON:0002116] + Jejunum [UBERON:0002115] + Stomach [UBERON:0000945] + Abomasum [UBERON:0007358] + Rumen [UBERON:0007365] + Excretory system (organizational term) + Anus [UBERON:0001245] + Anal gland [UBERON:0011253] + Cloaca [UBERON:0000162] + Liver [UBERON:0002107] + Kidney [UBERON:0002113] + Rectum [UBERON:0001052] + Spleen [UBERON:0002106] + Urinary bladder [UBERON:0001255] + Foot [UBERON:0002387] + Head [UBERON:0000033] + Brain [UBERON:0000955] + Ear [UBERON:0001690] + Eye [UBERON:0000970] + Mouth [UBERON:0000165] + Nose [UBERON:0000004] + Nasal turbinal [UBERON:0035612] + Nasopharynx (NP) [UBERON:0001728] + Pair of nares [UBERON:0002109] + Paranasal sinus [UBERON:0001825] + Snout [UBERON:0006333] + Lymphatic system [UBERON:0006558] + Lymph node [UBERON:0000029] + Mesenteric lymph node [UBERON:0002509] + Mantle (bird) [GENEPIO:0100927] + Neck [UBERON:0000974] + Esophagus [UBERON:0001043] + Trachea [UBERON:0003126] + Nerve [UBERON:0001021] + Spinal cord [UBERON:0002240] + Organs or organ parts [GENEPIO:0001117] + Organ [UBERON:0000062] + Muscle organ [UBERON:0001630] + Skin of body [UBERON:0002097] + Reproductive system [UBERON:0000990] + Embryo [UBERON:0000922] + Fetus [UBERON:0000323] + Ovary [UBERON:0000992] + Oviduct [UBERON:0000993] + Placenta [UBERON:0001987] + Testis [UBERON:0000473] + Udder [UBERON:0013216] + Uterus [UBERON:0000995] + Vagina [UBERON:0000996] + Yolk sac [UBERON:0001040] + Respiratory system [UBERON:0001004] + Air sac [UBERON:0009060] + Lung [UBERON:0002048] + Pleura [UBERON:0000977] + Respiratory system mucosa [UBERON:0004785] + Skeletal system [UBERON:0001434] + Skeletal joint [UBERON:0000982] + Bone element [UBERON:0001474] + Thoracic segment of trunk [UBERON:0000915] + Abdomen [UBERON:0000916] + Muscle of abdomen [UBERON:0002378] + Peritoneum [UBERON:0002358] + Vascular system [UBERON:0007798] + Blood vessel [UBERON:0001981] + Bursa of Fabricius [UBERON:0003903] + Gill [UBERON:0002535] + Heart [UBERON:0000948] + Lung [UBERON:0002048] + Pericardium [UBERON:0002407] + Vent (anatomical) [UBERON:2000298] + Bird vent [UBERON:0012464] + Fish vent [GENEPIO:0100902] + + +anatomical_region menu AnatomicalRegionMenu Dorso-lateral region [BSPO:0000080] + Exterior anatomical region [BSPO:0000034] + Interior anatomical region [BSPO:0000033] + + +food_product menu FoodProductMenu Animal feed [ENVO:02000047] + Blood meal [FOODON:00001564] + Bone meal [ENVO:02000054] + Brassica carinata meal [FOODON:00004310] + Canola meal [FOODON:00002694] + Compound feed premix [FOODON:00004323] + Compound feed premix (medicated) [FOODON:00004324] + Feather meal [FOODON:00003927] + Fish meal [FOODON:03301620] + Lay ration [FOODON:00004286] + Meat and bone meal [FOODON:00002738] + Meat meal [FOODON:00004282] + Pet food [FOODON:00002682] + Soybean meal [FOODON:03302757] + Animal feed ingredient [FOODON:00004322] + Dairy food product [FOODON:00001256] + Cheese block (whole or parts) [FOODON:03000287] + Cow skim milk (powdered) [FOODON:03310016] + Milk [UBERON:0001913] + Dietary supplement [FOODON:03401298] + Egg or egg component [FOODON:03420194] + Balut [FOODON:03302184] + Egg yolk [UBERON:0007378] + Poultry egg [FOODON:03000414] + Hen egg (whole) [FOODON:03316061] + Poultry egg (whole, shell on) [FOODON:03000415] + Food mixture [FOODON:00004130] + Food product analog (food subsitute) [FOODON:00001871] + Milk substitute [FOODON:03305408] + Meat (whole or parts) [FOODON:03317170] + Cutlet [FOODON:00003001] + Filet [FOODON:03530144] + Liver (whole, raw) [FOODON:03309772] + Meat trim [FOODON:03309475] + Rib (meat cut) [FOODON:03530023] + Rib chop [FOODON:00004290] + Shoulder (meat cut) [FOODON:03530043] + Grains, cereals, and bakery product (organizational term) + Bread loaf (whole or parts) [FOODON:03000288] + Breakfast cereal [FOODON:03311075] + Bulk grain [FOODON:03309390] + Oat grain [FOODON:00003429] + Legume food product [FOODON:00001264] + Chickpea (whole) [FOODON:03306811] + Hummus [FOODON:00003049] + Soybean (whole or parts) [FOODON:03000245] + Meat, poultry and fish (organizational term) + Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, boneless) [FOODON:0001282] + Beef (ground, extra lean) [FOODON:02000426] + Beef (ground, lean) [FOODON:02000425] + Beef (ground, medium) [FOODON:02000427] + Beef (ground, regular) [FOODON:02000428] + Beef (ground, sirloin) [FOODON:02000429] + Beef hamburger (dish) [FOODON:00002737] + Beef shoulder [FOODON:02000069] + Beef shoulder chop [FOODON:03000387] + Beef sirloin chop [FOODON:03000389] + Beef stew chunk [FOODON:00004288] + Beef tenderloin [FOODON:00003302] + Beef (pieces) [FOODON:02000412] + Brisket [FOODON:03530020] + Chicken breast [FOODON:00002703] + Chicken breast (back off) [FOODON:03000385] + Chicken breast (skinless) [FOODON:02020231] + Chicken breast (with skin) [FOODON:02020233] + Chicken breast (skinless, boneless) [FOODON:02020235] + Chicken breast cutlet [FOODON:00004308] + Chicken drumstick [FOODON:00002716] + Chicken drumstick (skinless) [FOODON:02020237] + Chicken drumstick(with skin) [FOODON:02020239] + Chicken meat [FOODON:00001040] + Chicken meat (ground) [FOODON:02020311] + Chicken meat (ground or minced, lean) [FOODON:03000392] + Chicken meat (ground or minced, extra lean) [FOODON:03000396] + Chicken meat (ground or minced, medium) [FOODON:03000400] + Chicken meat (ground or minced, regular) [FOODON:03000404] + Chicken meat (ground or minced, boneless) [FOODON:03000410] + Chicken nugget [FOODON:00002672] + Chicken thigh [FOODON:02020219] + Chicken thigh (skinless) [FOODON:00003331] + Chicken thigh (skinless, with bone) [FOODON:02020227] + Chicken thigh (skinless, boneless) [FOODON:02020228] + Chicken upper thigh [FOODON:03000381] + Chicken upper thigh (with skin) [FOODON:03000383] + Chicken thigh (with skin) [FOODON:00003330] + Chicken thigh (with skin, with bone) [FOODON_00003363] + Chicken wing [FOODON:00002674] + Fish food product [FOODON:00001248] + Fish steak [FOODON:00002986] + Ham food product [FOODON:00002502] + Head cheese [FOODON:03315658] + Lamb [FOODON:03411669] + Meat strip [FOODON:00004285] + Mutton [FOODON:00002912] + Pork chop [FOODON:00001049] + pork meat (ground) [FOODON:02021718] + Pork meat (ground or minced, boneless) [FOODON:03000413] + Pork meat (ground or minced, extra lean) [FOODON:03000399] + Pork meat (ground or minced, lean) [FOODON:03000395] + Pork meat (ground or minced, medium) [FOODON:03000403] + Pork meat (ground or minced, regular) [FOODON:03000407] + Pork meat (ground or minced, Sirloin) [FOODON:03000409] + Pork shoulder [FOODON:02000322] + Pork shoulder chop [FOODON:03000388] + Pork sirloin chop [FOODON:02000300] + Pork steak [FOODON:02021757] + Pork tenderloin [FOODON:02000306] + Poultry meat [FOODON:03315883] + Leg (poultry meat cut) [FOODON:03530159] + Poultry drumstick [FOODON:00003469] + Neck (poultry meat cut) [FOODON:03530294] + Thigh (poultry meat cut) [FOODON:03530160] + Wing (poultry meat cut) [FOODON:03530157] + Sausage (whole) [FOODON:03315904] + Pepperoni [FOODON:03311003] + Salami [FOODON:03312067] + Shellfish [FOODON:03411433] + Mussel [FOODON:03411223] + Oyster [FOODON:03411224] + Shrimp [FOODON:03301673] + Scallop [FOODON:02020805] + Squid [FOODON:03411205] + Turkey breast [FOODON:00002690] + Turkey breast (back off) [FOODON:03000386] + Turkey breast (skinless) [FOODON:02020495] + Turkey breast (skinless, boneless) [FOODON:02020499] + Turkey breast (with skin) [FOODON:02020497] + Turkey drumstick [FOODON:02020477] + Turkey drumstick (skinless) [FOODON:02020501] + Turkey drumstick (with skin) [FOODON:02020503] + Turkey meat [FOODON:00001286] + Turkey meat (ground) [FOODON:02020577] + Turkey meat (ground or minced, lean) [FOODON:03000393] + Turkey meat (ground or minced, extra lean) [FOODON:03000397] + Turkey meat (ground or minced, medium) [FOODON:03000401] + Turkey meat (ground or minced, regular) [FOODON:03000405] + Turkey meat (ground or minced, boneless) [FOODON:03000411] + Turkey thigh [FOODON:00003325] + Turkey thigh (skinless) [FOODON:00003329] + Turkey thigh (skinless, boneless) [FOODON:02020491] + Turkey thigh (with skin) [FOODON:00003328] + Turkey upper thigh [FOODON:03000382] + Turkey upper thigh (with skin) [FOODON:03000384] + Turkey wing [FOODON:02020478] + Veal [FOODON:00003083] + Formula fed veal [FOODON:000039111] + Grain-fed veal [FOODON:00004280] + Microbial food product [FOODON:00001145] + Yeast [FOODON:03411345] + Nuts and seed products + Almond (whole or parts) [FOODON:03000218] + Almond (whole) [FOODON:00003523] + Barley seed [FOODON:00003394] + Canola seed [FOODON:00004560] + Chia seed powder [FOODON:00003925] + Chia seed (whole or parts) [FOODON:03000241] + Flaxseed powder [FOODON:00004276] + Hazelnut [FOODON:00002933] + Nut (whole or part) [FOODON:03306632] + Peanut butter [FOODON:03306867] + Sesame seed [FOODON:03310306] + Tahini [FOODON:00003855] + Walnut (whole or parts) [FOODON:03316466] + Prepared food product [FOODON:00001180] + Condiment [FOODON:03315708] + Confectionery food product [FOODON:00001149] + Snack food [FOODON:03315013] + Produce [FOODON:03305145] + Apple (whole or parts) [FOODON:03310788] + Apple (whole) [FOODON:00002473] + Arugula greens bunch [FOODON:00003643] + Avocado [FOODON:00003600] + Cantaloupe (whole or parts) [FOODON:03000243] + Chilli pepper [FOODON:00003744] + Coconut (whole or parts) [FOODON:03309861] + Coconut meat [FOODON:00003856] + Corn cob (whole or parts) [FOODON:03310791] + Cucumber (whole or parts) [FOODON:03000229] + Fruit [PO:0009001] + Goji berry [FOODON:00004360] + Greens (raw) [FOODON:03310765] + Kale leaf (whole or parts) [FOODON:03000236] + Karela (bitter melon) [FOODON:00004367] + Lettuce head (whole or parts) [FOODON:03000239] + Mango (whole or parts) [FOODON:03000217] + Mushroom (fruitbody) [FOODON:00003528] + Papaya (whole or parts) [FOODON:03000228] + Pattypan squash (whole or parts) [FOODON:03000232] + Peach [FOODON:00002485] + Pepper (whole or parts) [FOODON:03000249] + Potato [FOODON:03315354] + Salad [FOODON:03316042] + Scallion (whole or parts) [FOODON:03000250] + Spinach (whole or parts) [FOODON:03000221] + Sprout [FOODON:03420183] + Germinated or sprouted seed [FOODON:03420102] + Alfalfa sprout [FOODON:00002670] + Bean sprout [FOODON:00002576] + Chia sprout [FOODON:03000180] + Mixed sprouts [FOODON:03000182] + Mung bean sprout [FOODON:03301446] + Tomato (whole or pieces) [FOODON:00002318] + Vegetable (whole or parts) [FOODON:03315308] + Spice or herb [FOODON:00001242] + Basil (whole or parts) [FOODON:03000233] + Black pepper (whole or parts) [FOODON:03000242] + Cardamom (whole or parts) [FOODON:03000246] + Chive leaf (whole or parts) [FOODON:03000240] + Coriander powder [FOODON:00004274] + Coriander seed (whole or parts) [FOODON:03000224] + Cumin powder [FOODON:00004275] + Cumin seed (whole) [FOODON:00003396] + Black cumin seed (whole or parts) [FOODON:03000247] + Curry leaf (whole or parts) [FOODON:03000225] + Curry powder [FOODON:03301842] + Dill spice [FOODON:00004307] + Fennel (whole or parts) [FOODON:03000244] + Garlic powder [FOODON:03301844] + Ginger root (whole or parts) [FOODON:03000220] + Mint leaf (whole or parts) [FOODON:03000238] + Oregano (whole or parts) [FOODON:03000226] + Paprika (ground) [FOODON:03301223] + Parsley leaf (whole or parts) [FOODON:03000231] + Pepper (ground) [FOODON:03301526] + Rasam powder [FOODON:00004277] + Sage [FOODON:03301560] + Turmeric (ground) [FOODON:03310841] + Spice [FOODON:03303380] + White peppercorn (whole or parts) [FOODON:03000251] + + +food_product_properties menu FoodProductPropertiesMenu Food (canned) [FOODON:00002418] + Food (cooked) [FOODON:00001181] + Food (cut) [FOODON:00004291] + Food (chopped) [FOODON:00002777] + Food (chunks) [FOODON:00004555] + Food (cubed) [FOODON:00004278] + Food (diced) [FOODON:00004549] + Food (grated) [FOODON:00004552] + Food (sliced) [FOODON:00002455] + Food (shredded) [FOODON:00004553] + Food (dried) [FOODON:03307539] + Food (fresh) [FOODON:00002457] + Food (frozen) [FOODON:03302148] + Food (pulped) [FOODON:00004554] + Food (raw) [FOODON:03311126] + Food (unseasoned) [FOODON:00004287] + Italian-style food product [FOODON:00004321] + Meat (boneless) [FOODON:00003467] + Meat (skinless) [FOODON:00003468] + Meat (with bone) [FOODON:02010116] + Meat (with skin) [FOODON:02010111] + Soft [PATO:0000387] + + + + +label_claim menu LabelClaimMenu Antibiotic free [FOODON:03601063] + Cage free [FOODON:03601064] + Hormone free [FOODON:03601062] + Organic food claim or use [FOODON:03510128] + Pasture raised [FOODON:03601065] + Ready-to-eat (RTE) [FOODON:03316636] + + +animal_source_of_food menu AnimalSourceOfFoodMenu Cow [NCBITaxon:9913] + Fish [FOODON:03411222] + Pig [NCBITaxon:9823] + Poultry or game bird [FOODON:03411563] + Chicken [NCBITaxon:9031] + Turkey [NCBITaxon:9103] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Mussel [FOODON:03411223] + Scallop [NCBITaxon:6566] + Shrimp [FOODON:03411237] + Squid [FOODON:03411205] + + +food_product_production_stream menu FoodProductProductionStreamMenu Beef cattle production stream [FOODON:03000452] + Broiler chicken production stream [FOODON:03000455] + Dairy cattle production stream [FOODON:03000453] + Egg production stream [FOODON:03000458] + Layer chicken production stream [FOODON:03000456] + Meat production stream [FOODON:03000460] + Veal meat production stream [FOODON:03000461] + Milk production stream [FOODON:03000459] + + +collection_device menu CollectionDeviceMenu Auger (earth auger) [AGRO:00000405] + Box corer [GENEPIO:0100928] + Container [OBI:0000967] + Bag [GSSO:008558] + Whirlpak sampling bag [GENEPIO:0002122] + Bottle [FOODON:03490214] + Vial [OBI:0000522] + Culture plate [GENEPIO:0004318] + Petri dish [NCIT:C96141] + Filter [GENEPIO:0100103] + PONAR grab sampler [GENEPIO:0100929] + Scoop [GENEPIO:0002125] + Soil sample probe [GENEPIO:0100930] + Spatula [NCIT:C149941] + Sponge [OBI:0002819] + Swab [GENEPIO:0100027] + Drag swab [OBI:0002822] + Surface wipe [OBI:0002824] + Tube [GENEPIO:0101196] + Vacuum device [GENEPIO:0002127] + Vacutainer [OBIB:0000032] + + +collection_method menu CollectionMethodMenu Aspiration [HP:0002835] + Biopsy [OBI:0002650] + Fecal grab [GENEPIO:0004326] + Filtration [OBI:0302885] + Air filtration [GENEPIO:0100031] + Water filtration [GENEPIO:0100931] + Lavage [OBI:0600044] + Bronchoalveolar lavage [GENEPIO:0100032] + Gastric lavage [GENEPIO:0100033] + Necropsy [MMO:0000344] + Phlebotomy [NCIT:C28221] + Rinsing for specimen collection [GENEPIO_0002116] + Scooping [GENEPIO:0100932] + Sediment collection [GENEPIO:0100933] + Soil coring [GENEPIO:0100934] + Weep fluid collection (pouring) [GENEPIO:0101003] + +sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu microliter (uL) [UO:0000101] + milliliter (mL) [UO:0000098] + liter (L) [UO:0000099] + +residual_sample_status menu ResidualSampleStatusMenu Residual sample remaining (some sample left) [GENEPIO:0101087] + No residual sample (sample all used) [GENEPIO:0101088] + Residual sample status unkown [GENEPIO:0101089] + +sample_storage_duration_unit menu SampleStorageDurationUnitMenu Second [UO:0000010] + Minute [UO:0000031] + Hour [UO:0000032] + Day [UO:0000033] + Week [UO:0000034] + Month [UO:0000035] + Year [UO:0000036] + +nucelic_acid_storage_duration_unit menu NucelicAcidStorageDurationUnitMenu Second [UO:0000010] + Minute [UO:0000031] + Hour [UO:0000032] + Day [UO:0000033] + Week [UO:0000034] + Month [UO:0000035] + Year [UO:0000036] + +food_packaging menu FoodPackagingMenu Bag, sack or pouch [FOODON:03490197] + Paper bag, sack or pouch [FOODON:03490120] + Plastic bag, sack or pouch [FOODON:03490166] + Plastic shrink wrap [FOODON:03490137] + Plastic wrapper [FOODON:03490128] + Bottle or jar [FOODON:03490203] + Can (container) [FOODON:03490204] + Paper container, treated [FOODON:03490330] + Paper container, untreated [FOODON:03490334] + Plastic tray or pan [FOODON:03490126] + + +host (common name) menu HostCommonNameMenu Bird [NCBITaxon:8782] + Chicken [NCBITaxon:9031] + Seabird [FOODON:00004504] + Cormorant [NCBITaxon:9206] + Double Crested Cormorant [NCBITaxon:56069] + Crane [NCBITaxon:9109] + Whooping Crane [NCBITaxon:9117] + Gull (Seagull) [NCBITaxon:8911] + Glaucous-winged Gull [NCBITaxon:119606] + Great Black-backed Gull [NCBITaxon:8912] + Herring Gull [NCBITaxon:35669] + Ring-billed Gull [NCBITaxon:126683] + Eider [NCBITaxon:50366] + Common Eider [NCBITaxon:76058] + Turkey [NCBITaxon:9103] + Fish [FOODON:03411222] + Rainbow Trout [NCBITaxon:8022] + Sablefish [NCBITaxon:229290] + Salmon [FOODON:00003473] + Atlantic Salmon [NCBITaxon:8030] + Chinook salmon [NCBITaxon:74940] + Coho Salmon [NCBITaxon:8019] + Mammal [FOODON:03411134] + Companion animal [FOODON:03000300] + Cow [NCBITaxon:9913] + Human [NCBITaxon:9606] + Pig [NCBITaxon:9823] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Atlantic Lobster [NCBITaxon:6706] + Atlantic Oyster [NCBITaxon:6565] + Blue Mussel [NCBITaxon:6550] + + +host (scientific name) menu HostScientificNameMenu Anoplopoma fimbria [NCBITaxon:229290] + Bos taurus [NCBITaxon:9913] + Crassostrea virginica [NCBITaxon:6565] + Gallus gallus [NCBITaxon:9031] + Grus americana [NCBITaxon:9117] + Homarus americanus [NCBITaxon:6706] + Homo sapiens [NCBITaxon:9606] + Larus argentatus [NCBITaxon:35669] + Larus delawarensis [NCBITaxon:126683] + Larus glaucescens [NCBITaxon:119606] + Larus marinus [NCBITaxon:8912] + Meleagris gallopavo [NCBITaxon:9103] + Mytilus edulis [NCBITaxon:6550] + Oncorhynchus kisutch [NCBITaxon:8019] + Oncorhynchus mykiss [NCBITaxon:8022] + Oncorhynchus tshawytscha [NCBITaxon:74940] + Ovis aries [NCBITaxon:9940] + Phalacrocorax auritus [NCBITaxon:56069] + Salmo salar [NCBITaxon:8030] + Somateria mollissima [NCBITaxon:76058] + Sus scrofa domesticus [NCBITaxon:9825] + + +host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) + Calf [FOODON:03411349] + Dry cow [FOODON:00004411] + Feeder cow [FOODON:00004292] + Finisher cow [FOODON:00004293] + Milker cow [FOODON:03411201] + Stocker cow [FOODON:00004294] + Weanling cow [FOODON:00004295] + Cow (by sex/reproductive stage) (organizational term) + Bull [FOODON:00000015] + Cow [NCBITaxon:9913] + Freemartin [FOODON:00004296] + Heifer [FOODON:00002518] + Steer [FOODON:00002531] + Pig (by age/production stage) (organizational term) + Finisher pig [FOODON:00003371] + Grower pig [FOODON:00003370] + Nursing pig [FOODON:00004297 ] + Pig [NCBITaxon:9823] + Piglet [FOODON:00003952] + Weanling (weaner) pig [FOODON:00003373] + Pig (by sex/reproductive stage) (organizational term) + Barrow [FOODON:03411280] + Boar [FOODON:03412248] + Gilt [FOODON:00003369] + Sow [FOODON:00003333] + Poultry or game bird [FOODON:03411563] + Broiler or fryer chicken [FOODON:03411198] + Capon [FOODON:03411711] + Chick [FOODON:00004299] + Chicken [NCBITaxon:9031] + Egg [UBERON:0007379] + Hatchling [FOODON:00004300] + Hen [FOODON:00003282] + Layer chicken [FOODON:00004301] + Layer turkey [FOODON:00004302] + Poult [FOODON:00002962] + Pullet [FOODON:00004303] + Rooster [FOODON:03411714] + Tom (Gobbler) [FOODON:00004304 ] + Turkey [NCBITaxon:9103] + Sheep [NCBITaxon:9940] + Ram [FOODON:00004305] + Wether sheep [FOODON:00004306] + Ewe [FOODON:03412610] + Lamb [FOODON:03411669] + Fish [FOODON:03411222] + Fish egg [FOODON_00004319] + Fry (fish) [FOODON_00004318] + Juvenile fish [FOODON_00004317] + + +host_age_bin menu HostAgeBinMenu First winter [GENEPIO:0100684] + First summer [GENEPIO:0100685] + Second winter [GENEPIO:0100686] + Second summer [GENEPIO:0100687] + Third winter [GENEPIO:0100688] + Third summer [GENEPIO:0100689] + + +isolated_by menu IsolatedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + + +organism menu OrganismMenu Acinetobacter [NCBITaxon:469] + Acinetobacter baumannii [NCBITaxon:470] + Acinetobacter bereziniae [NCBITaxon:106648] + Acinetobacter ursingii [NCBITaxon:108980] + Aeromonas [NCBITaxon:642] + Aeromonas allosaccharophila [NCBITaxon:656] + Aeromonas hydrophila [NCBITaxon:644] + Aeromonas rivipollensis [NCBITaxon:948519] + Aeromonas salmonicida [NCBITaxon:645] + Campylobacter [NCBITaxon:194] + Campylobacter coli [NCBITaxon:195] + Campylobacter jejuni [NCBITaxon:197] + Campylobacter lari [NCBITaxon:201] + Citrobacter [NCBITaxon:544] + Citrobacter braakii [NCBITaxon:57706] + Citrobacter freundii [NCBITaxon:546] + Citrobacter gillenii [NCBITaxon:67828] + Clostridioides [NCBITaxon:1870884] + Clostridioides difficile [NCBITaxon:1496] + Clostridium [NCBITaxon:1485] + Clostridium perfringens [NCBITaxon:1502] + Clostridium sporogenes [NCBITaxon:1509] + Comamonas [NCBITaxon:283] + Comamonas aquatica [NCBITaxon:225991] + Enterobacter [NCBITaxon:547] + Enterobacter asburiae [NCBITaxon:61645] + Enterobacter cancerogenus [NCBITaxon:69218] + Enterobacter cloacae [NCBITaxon:550] + Enterobacter hormaechei [NCBITaxon:158836] + Enterobacter kobei [NCBITaxon:208224] + Enterobacter roggenkampii [NCBITaxon:1812935] + Enterobacter sp. [NCBITaxon:42895] + Lelliottia amnigena [NCBITaxon:61646] + Pluralibacter gergoviae [NCBITaxon:61647] + Enterococcus [NCBITaxon:1350] + Enterococcus asini [NCBITaxon:57732] + Enterococcus avium [NCBITaxon:33945] + Enterococcus caccae [NCBITaxon:317735] + Enterococcus canis [NCBITaxon:214095] + Enterococcus casseliflavus [NCBITaxon:37734] + Enterococcus cecorum [NCBITaxon:44008] + Enterococcus dispar [NCBITaxon:44009] + Enterococcus durans [NCBITaxon:53345] + Enterococcus faecium [NCBITaxon:1352] + Enterococcus faecalis [NCBITaxon:1351] + Enterococcus gallinarum [NCBITaxon:1353] + Enterococcus hirae [NCBITaxon:1354] + Enterococcus malodoratus [NCBITaxon:71451] + Enterococcus mundtii [NCBITaxon:53346] + Enterococcus ratti [NCBITaxon:150033] + Enterococcus saccharolyticus [NCBITaxon:41997] + Enterococcus thailandicus [NCBITaxon:417368] + Enterococcus villorum [NCBITaxon:112904] + Escherichia [NCBITaxon:561] + Escherichia coli [NCBITaxon:562] + Escherichia fergusonii [NCBITaxon:564] + Exiguobacterium [NCBITaxon:33986] + Exiguobacterium oxidotolerans [NCBITaxon:223958] + Exiguobacterium sp. [NCBITaxon:44751] + Klebsiella [NCBITaxon:570] + Klebsiella aerogenes [NCBITaxon:548] + Klebsiella michiganensis [NCBITaxon:1134687] + Klebsiella oxytoca [NCBITaxon:571] + Klebsiella pneumoniae [NCBITaxon:573] + Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] + Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] + Kluyvera [NCBITaxon:579] + Kluyvera intermedia [NCBITaxon:61648] + Kosakonia [NCBITaxon:1330547] + Kosakonia cowanii [NCBITaxon:208223] + Leclercia [NCBITaxon:83654] + Leclercia adecarboxylata [NCBITaxon:83655] + Listeria [NCBITaxon:1637] + Listeria monocytogenes [NCBITaxon:1639] + Ochrobactrum [NCBITaxon:528] + Ochrobactrum sp. [NCBITaxon:42190] + Pantoea [NCBITaxon:53335] + Pantoea ananatis [NCBITaxon:553] + Pantoea sp. [NCBITaxon:69393] + Photobacterium [NCBITaxon:657] + Photobacterium indicum[NCBITaxon:81447] + Photobacterium sp. [NCBITaxon:660] + Providencia [NCBITaxon:586] + Providencia rettgeri [NCBITaxon:587] + Pseudoalteromonas [NCBITaxon:53246] + Pseudoalteromonas tetraodonis [NCBITaxon:43659] + Pseudomonas [NCBITaxon:286] + Pseudomonas aeruginosa [NCBITaxon:287] + Pseudomonas fluorescens [NCBITaxon:294] + Pseudomonas soli [NCBITaxon:1306993] + Pseudomonas sp. [NCBITaxon:306] + Psychrobacter [NCBITaxon:497] + Psychrobacter faecalis [NCBITaxon:180588] + Psychrobacter nivimaris [NCBITaxon:281738] + Psychrobacter sp. [NCBITaxon:56811] + Rahnella [NCBITaxon:34037] + Rahnella aquatilis [NCBITaxon:34038] + Rahnella sp. [NCBITaxon:1873497] + Raoultella [NCBITaxon:160674] + Raoultella ornithinolytica [NCBITaxon:54291] + Raoultella planticola [NCBITaxon:575] + Salmonella enterica [NCBITaxon:28901] + Salmonella enterica subsp. enterica [NCBITaxon:59201] + Salmonella enterica subsp. arizonae [NCBITaxon:59203] + Serratia [NCBITaxon:613] + Shewanella [NCBITaxon:22] + Shewanella pealeana [NCBITaxon:70864] + Shewanella putrefaciens [NCBITaxon:24] + Shewanella oncorhynchi [NCBITaxon:2726434] + Shewanella sp. [NCBITaxon:50422] + Staphylococcus [NCBITaxon:1279] + Staphylococcus aureus [NCBITaxon:1280] + Streptococcus [NCBITaxon:1301] + Streptococcus alactolyticus [NCBITaxon:29389] + Streptococcus bovis [NCBITaxon:1335] + Streptococcus equinus [NCBITaxon:1335] + Streptococcus gallolyticus [NCBITaxon:315405] + Streptococcus infantarius [NCBITaxon:102684] + Streptococcus lutetiensis [NCBITaxon:150055] + Streptococcus macedonicus [NCBITaxon:59310] + Streptococcus pasteurianus [NCBITaxon:197614] + Streptococcus suis [NCBITaxon:1307] + Vibrio [NCBITaxon:662] + Vibrio cholerae [NCBITaxon:666] + Vibrio parahaemolyticus [NCBITaxon:670] + +taxonomic_identification_process menu TaxonomicIdentificationProcessMenu Whole genome sequencing assay [OBI:0002117] + 16S ribosomal gene sequencing assay [OBI:0002763] + PCR assay [OBI:0002740] + Comparative phenotypic assessment [OBI:0001546] + Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] + + +sequenced_by menu SequencedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + McGill University [GENEPIO:0101103] + + +purpose_of_sequencing menu PurposeOfSequencingMenu Cluster/Outbreak investigation [GENEPIO:0100001] + Diagnostic testing [GENEPIO:0100002] + Environmental testing [GENEPIO:0100548] + Research [GENEPIO:0100003] + Clinical trial [GENEPIO:0100549] + Field experiment [GENEPIO:0100550] + Protocol testing experiment [GENEPIO:0100024] + Survey study [GENEPIO:0100582] + Surveillance [GENEPIO:0100004] + + +sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] + Pacific Biosciences [GENEPIO:0001927] + Ion Torrent [GENEPIO:0002683] + Oxford Nanopore Technologies [OBI:0002755] + BGI Genomics [GENEPIO:0004324] + MGI [GENEPIO:0004325] + + +sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. + Illumina Genome Analyzer [OBI:0002128] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. + Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + Illumina HiSeq X Ten [OBI:0002129] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Illumina HiSeq 1500 [OBI:0003386] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. + Illumina NovaSeq 6000 [OBI:0002630] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + Illumina MiniSeq [OBI:0003114] A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + Illumina NextSeq 1000 [OBI:0003606] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + PacBio Sequel [OBI:0002632] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + PacBio Sequel II [OBI:0002633] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + BGISEQ [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + DNBSEQ [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. + DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. + DNBSEQ-G400 FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. + DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + + +sequencing_assay_type menu SequencingAssayTypeMenu Amplicon sequencing assay [OBI:0002767] + 16S ribosomal gene sequencing assay [OBI:0002763] + Whole genome sequencing assay [OBI:0002117] + Whole metagenome sequencing assay [OBI:0002623] + Whole virome sequencing assay [OBI:0002768] + +genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu Hybrid selection method (bait-capture) [GENEPIO:0001950] + rRNA depletion method [GENEPIO:0101020] + + +sequence_submitted_by menu SequenceSubmittedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + McGill University [GENEPIO:0101103] + +quality_control_determination menu QualityControlDeterminationMenu No quality control issues identified [GENEPIO:0100562] + Sequence passed quality control [GENEPIO:0100563] + Sequence failed quality control [GENEPIO:0100564] + Minor quality control issues identified [GENEPIO:0100565] + Sequence flagged for potential quality control issues [GENEPIO:0100566] + Quality control not performed [GENEPIO:0100567] + +quality _control_issues menu QualityControlIssuesMenu Low quality sequence [GENEPIO:0100568] + Sequence contaminated [GENEPIO:0100569] + Low average genome coverage [GENEPIO:0100570] + Low percent genome captured [GENEPIO:0100571] + Read lengths shorter than expected [GENEPIO:0100572] + Sequence amplification artifacts [GENEPIO:0100573] + Low signal to noise ratio [GENEPIO:0100574] + Low coverage of characteristic mutations [GENEPIO:0100575] + + +attribute_package menu AttributePackageMenu Pathogen.cl [GENEPIO:0001835] + Pathogen.env [GENEPIO:0100581] + + +experimental_intervention menu ExperimentalInterventionMenu Addition of substances to food/water [GENEPIO:0100536] + Antimicrobial pre-treatment [GENEPIO:0100537] + Certified animal husbandry practices [GENEPIO:0100538] + Certified organic farming practices [GENEPIO:0100539] + Change in storage conditions [GENEPIO:0100540] + Cleaning/disinfection [GENEPIO:0100541] + Extended downtime between activities [GENEPIO:0100542] + Fertilizer pre-treatment [GENEPIO:0100543] + Logistic slaughter [GENEPIO:0100545] + Microbial pre-treatment [GENEPIO:0100546] + Probiotic pre-treatment [GENEPIO:0100547] + Vaccination [NCIT:C15346] + + +AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + + +antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] + Intermediate antimicrobial phenotype [ARO:3004300] + Indeterminate antimicrobial phenotype [GENEPIO:0100585] + Nonsusceptible antimicrobial phenotype [ARO:3004303] + Resistant antimicrobial phenotype [ARO:3004301] + Susceptible antimicrobial phenotype [ARO:3004302] + Susceptible dose dependent antimicrobial phenotype [ARO:3004304] + + +antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] + millimetre (mm) [UO:0000016] + microgram per millilitre (ug/mL) [UO:0000274] + + +antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] + less than or equal to (<=) [GENEPIO:0001003] + equal to (==) [GENEPIO:0001004] + greater than (>) [GENEPIO:0001006] + greater than or equal to (>=) [GENEPIO:0001005] + + +antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion + Antimicrobial gradient (E-test) [NCIT:85596] + Agar dilution [ARO:3004411] agar dilution + Broth dilution [ARO:3004397] + + +antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] + Microscan [ARO:3004400] Microscan + Phoenix [ARO:3004401] Phoenix + Sensititre [ARO:3004402] Sensititre + Vitek System [ARO:3004403] Vitek + + +antimicrobial_vendor_name menu AntimicrobialVendorNameMenu Becton Dickinson [ARO:3004405] Becton Dickinson + bioMérieux [ARO:3004406] Biomérieux + Omron [ARO:3004408] + Siemens [ARO:3004407] Siemens + Trek [ARO:3004409] Trek + + +antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] BSAC + Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] CLSI + Deutsches Institut für Normung (DIN) [ARO:3004367] DIN + European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] EUCAST + National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] NARMS + National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] NCCLS + Société Française de Microbiologie (SFM) [ARO:3004369] SFM + Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] SIR + Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG + + +Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin + amoxicillin-clavulanic_acid + ampicillin + azithromycin + cefazolin + cefepime + cefotaxime + cefotaxime-clavulanic_acid + cefoxitin + cefpodoxime + ceftazidime + ceftazidime-clavulanic_acid + ceftiofur + ceftriaxone + cephalothin + chloramphenicol + ciprofloxacin + clindamycin + doxycycline + enrofloxacin + erythromycin + florfenicol + gentamicin + imipenem + kanamycin + levofloxacin + linezolid + meropenem + nalidixic_acid + nitrofurantoin + norfloxacin + oxolinic-acid + oxytetracycline + piperacillin + piperacillin-tazobactam + polymyxin-b + quinupristin-dalfopristin + streptomycin + sulfisoxazole + telithromycin + tetracycline + tigecycline + trimethoprim-sulfamethoxazole \ No newline at end of file diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 2a6ce49a..81b94ecc 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -1,6 +1,6 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM GRDI GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name + Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." ABCD1234[PHAC]; 12345rev[CFIA] Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab From afabb5b52460f7f268f4e869537f22e9d74f99dc Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Mon, 23 Sep 2024 13:59:49 -0700 Subject: [PATCH 30/96] wip --- web/templates/grdi/export.js | 113 +++++++++++++++++++++++++++++++++++ 1 file changed, 113 insertions(+) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 01a200d2..5b45c597 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -493,6 +493,119 @@ export default { outputMatrix.push(outputRow); } + return outputMatrix; + } + }, + + NCBI_Antibiogram: { + fileType: 'xls', + status: 'published', + method: function (dh) { + const ExportHeaders = new Map([ + ['sample_name/biosample_accession', []], + ['antibiotic', []], + ['resistance_phenotype', []], + ['measurement_sign', []], + ['measurement', []], + ['measurement_units', []], + ['laboratory_typing_method', []], + ['laboratory_typing_platform', []], + ['vendor', []], + ['laboratory_typing_method_version_or_reagent', []], + ['testing_standard', []] + ]); + const longHeadersObj = { + 'antibiotic': [], + 'resistance_phenotype': [], + 'measurement_sign': [], + 'measurement': [], + 'measurement_units': [], + 'laboratory_typing_method': [], + 'laboratory_typing_platform': [], + 'vendor': [], + 'laboratory_typing_method_version_or_reagent': [], + 'testing_standard': [] + }; + const antibiotics = [ + 'amikacin', + 'amoxicillin-clavulanic_acid', + 'ampicillin', + 'azithromycin', + 'cefazolin', + 'cefepime', + 'cefotaxime', + 'cefotaxime-clavulanic_acid', + 'cefoxitin', + 'cefpodoxime', + 'ceftazidime', + 'ceftazidime-clavulanic_acid', + 'ceftiofur', + 'ceftriaxone', + 'cephalothin', + 'chloramphenicol', + 'ciprofloxacin', + 'clindamycin', + 'doxycycline', + 'enrofloxacin', + 'erythromycin', + 'florfenicol', + 'gentamicin', + 'imipenem', + 'kanamycin', + 'levofloxacin', + 'linezolid', + 'meropenem', + 'nalidixic', + 'nitrofurantoin', + 'norfloxacin', + 'oxolinic-acid', + 'oxytetracycline', + 'piperacillin', + 'piperacillin-tazobactam', + 'polymyxin-b', + 'quinupristin-dalfopristin', + 'streptomycin', + 'sulfisoxazole', + 'telithromycin', + 'tetracycline', + 'tigecycline', + 'trimethoprim-sulfamethoxazole' + ]; + for (let longHeader in longHeadersObj) { + if (longHeader === 'antibiotic') continue; + longHeadersObj[longHeader] = antibiotics.map((e) => { + return e.concat('_', longHeader); + }); + } + + const sourceFields = dh.getFields(dh.table); + const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + // Fills in the above mapping (or just set manually above) + dh.getHeaderMap(ExportHeaders, sourceFields, 'NCBI_ANTIBIOGRAM'); + + // Copy headers to 1st row of new export table + const outputMatrix = [[...ExportHeaders.keys()]]; + + for (const inputRow of dh.getTrimmedData(dh.hot)) { + const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { + let value; + if (headerName in longHeadersObj) { + value = dh.getMappedField( + headerName, + inputRow, + sources, + sourceFields, + sourceFieldNameMap, + ':', + 'NCBI_ANTIBIOGRAM' + ); + } + outputRow.push(value); + } + outputMatrix.push(outputRow); + } + return outputMatrix; } } From f60812048e46deaad46fcbda48d738e817e2923d Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 24 Sep 2024 11:19:31 -0700 Subject: [PATCH 31/96] wip --- web/templates/grdi/export.js | 69 ++++++++++++++++++------------------ 1 file changed, 35 insertions(+), 34 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 5b45c597..559a9387 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -514,19 +514,7 @@ export default { ['laboratory_typing_method_version_or_reagent', []], ['testing_standard', []] ]); - const longHeadersObj = { - 'antibiotic': [], - 'resistance_phenotype': [], - 'measurement_sign': [], - 'measurement': [], - 'measurement_units': [], - 'laboratory_typing_method': [], - 'laboratory_typing_platform': [], - 'vendor': [], - 'laboratory_typing_method_version_or_reagent': [], - 'testing_standard': [] - }; - const antibiotics = [ + const antibioticsArr = [ 'amikacin', 'amoxicillin-clavulanic_acid', 'ampicillin', @@ -571,12 +559,7 @@ export default { 'tigecycline', 'trimethoprim-sulfamethoxazole' ]; - for (let longHeader in longHeadersObj) { - if (longHeader === 'antibiotic') continue; - longHeadersObj[longHeader] = antibiotics.map((e) => { - return e.concat('_', longHeader); - }); - } + const longHeadersArr = Array.from(ExportHeaders.keys()).slice(2); const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); @@ -587,23 +570,41 @@ export default { const outputMatrix = [[...ExportHeaders.keys()]]; for (const inputRow of dh.getTrimmedData(dh.hot)) { - const outputRow = []; - for (const [headerName, sources] of ExportHeaders) { - let value; - if (headerName in longHeadersObj) { - value = dh.getMappedField( - headerName, - inputRow, - sources, - sourceFields, - sourceFieldNameMap, - ':', - 'NCBI_ANTIBIOGRAM' - ); + const outputRow = Array(ExportHeaders.size); + outputRow[0] = dh.getMappedField( + 'sample_name/biosample_accession', + inputRow, + ExportHeaders.get('sample_name/biosample_accession'), + sourceFields, + sourceFieldNameMap, + ':', + 'NCBI_ANTIBIOGRAM' + ); + // TODO do not export row if above val is empty? + + // Wide to long logic + const oldOutputMatrixLen = outputMatrix.length; + for (const antibiotic of antibioticsArr) { + const longRow = [...outputRow]; + let atLeastOneWideVal = false; + for (const [i, longHeader] of longHeadersArr.entries()) { + const antibioticHeader = antibiotic.concat('_', longHeader); + const wideVal = + inputRow[sourceFieldNameMap[antibioticHeader]]; + if (wideVal) { + atLeastOneWideVal = true; + longRow[i+2] = wideVal; + } + } + if (atLeastOneWideVal) { + longRow[1] = antibiotic; + outputMatrix.push(longRow); } - outputRow.push(value); } - outputMatrix.push(outputRow); + // Ensures a row is still added if no antibiotic info is present + if (oldOutputMatrixLen === outputMatrix.length) { + outputMatrix.push(outputRow); + } } return outputMatrix; From 83d0fa048a270ee1a80e4121bac859fe4f68695c Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 24 Sep 2024 11:38:13 -0700 Subject: [PATCH 32/96] wip --- web/templates/grdi/export.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 559a9387..e5957729 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -588,9 +588,10 @@ export default { const longRow = [...outputRow]; let atLeastOneWideVal = false; for (const [i, longHeader] of longHeadersArr.entries()) { - const antibioticHeader = antibiotic.concat('_', longHeader); + let wideHeader = antibiotic.concat('_', longHeader); + if (longHeader === 'vendor') wideHeader += '_name'; const wideVal = - inputRow[sourceFieldNameMap[antibioticHeader]]; + inputRow[sourceFieldNameMap[wideHeader]]; if (wideVal) { atLeastOneWideVal = true; longRow[i+2] = wideVal; From bbc0774f85997fedc3d0bc297a2795d8625e2988 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 24 Sep 2024 12:14:10 -0700 Subject: [PATCH 33/96] wip --- web/templates/grdi/export.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index e5957729..6220eba0 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -571,7 +571,7 @@ export default { for (const inputRow of dh.getTrimmedData(dh.hot)) { const outputRow = Array(ExportHeaders.size); - outputRow[0] = dh.getMappedField( + const primaryKey = dh.getMappedField( 'sample_name/biosample_accession', inputRow, ExportHeaders.get('sample_name/biosample_accession'), @@ -580,7 +580,8 @@ export default { ':', 'NCBI_ANTIBIOGRAM' ); - // TODO do not export row if above val is empty? + if (!primaryKey) continue; + outputRow[0] = primaryKey; // Wide to long logic const oldOutputMatrixLen = outputMatrix.length; From 69615b33d8e2c8520bacb7f9eccd05a5bdcad908 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Wed, 25 Sep 2024 13:42:58 -0700 Subject: [PATCH 34/96] Parse isolate and sample ids as primary * Also update schema --- web/templates/grdi/export.js | 10 +++------- web/templates/grdi/schema.json | 6 ++++-- web/templates/grdi/schema.yaml | 1 + web/templates/grdi/schema_slots.tsv | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 6220eba0..3e1b1013 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -571,14 +571,10 @@ export default { for (const inputRow of dh.getTrimmedData(dh.hot)) { const outputRow = Array(ExportHeaders.size); - const primaryKey = dh.getMappedField( - 'sample_name/biosample_accession', + const primaryKey = dh.getFirstNonNullField( + ['isolate_id', 'sample_collector_sample_id'], inputRow, - ExportHeaders.get('sample_name/biosample_accession'), - sourceFields, - sourceFieldNameMap, - ':', - 'NCBI_ANTIBIOGRAM' + sourceFieldNameMap ); if (!primaryKey) continue; outputRow[0] = primaryKey; diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index 799b8c7c..bd8d9356 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -8157,7 +8157,8 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" + "NCBI_BIOSAMPLE_Enterics:strain", + "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" ], "slot_uri": "GENEPIO:0100456", "domain_of": [ @@ -31155,7 +31156,8 @@ ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "NCBI_BIOSAMPLE_Enterics:strain" + "NCBI_BIOSAMPLE_Enterics:strain", + "NCBI_ANTIBIOGRAM:sample_name/biosample_accession" ], "rank": 88, "slot_uri": "GENEPIO:0100456", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index e5d00ea8..148e2714 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -4364,6 +4364,7 @@ slots: - value: SA20131043 exact_mappings: - NCBI_BIOSAMPLE_Enterics:strain + - NCBI_ANTIBIOGRAM:sample_name/biosample_accession alternative_isolate_id: name: alternative_isolate_id title: alternative_isolate_ID diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index 81b94ecc..c8a3ddff 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -90,7 +90,7 @@ GRDI GENEPIO:0001150 Sample collection and processing GENEPIO:0100453 Strain and isolation information strain_and_isolation_information Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain - Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 From 5d9e452f4943c124ea0f4879a8121866e26d9092 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Wed, 25 Sep 2024 14:21:14 -0700 Subject: [PATCH 35/96] Implement transformation of GRDI vals to NCBI --- web/templates/grdi/export.js | 73 +++++++++++++++++++++++++++++++++++- 1 file changed, 72 insertions(+), 1 deletion(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 3e1b1013..af1349ad 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -560,6 +560,72 @@ export default { 'trimethoprim-sulfamethoxazole' ]; const longHeadersArr = Array.from(ExportHeaders.keys()).slice(2); + const GRDItoNCBIObj = { + 'resistance_phenotype': { + 'Resistant antimicrobial phenotype [ARO:3004301]': + 'resistant', + 'Susceptible antimicrobial phenotype [ARO:3004302]': + 'susceptible', + 'Intermediate antimicrobial phenotype [ARO:3004300]': + 'intermediate', + 'Nonsusceptible antimicrobial phenotype [ARO:3004303]': + 'nonsusceptible', + 'Antibiotic resistance not defined [GENEPIO:0002040]': + 'not defined', + 'Susceptible dose dependent antimicrobial phenotype [ARO:3004304]': + 'susceptible-dose dependent' + }, + 'measurement_sign': { + 'less than (<) [GENEPIO:0001002]': '<', + 'less than or equal to (<=) [GENEPIO:0001003]': '<=', + 'equal to (==) [GENEPIO:0001004]': '==', + 'greater than (>) [GENEPIO:0001006]': '>', + 'greater than or equal to (>=) [GENEPIO:0001005]': '>=' + }, + 'measurement_units': { + 'milligram per litre (mg/L) [UO:0000273]': 'mg/L', + 'millimetre (mm) [UO:0000016]': 'mm' + }, + 'laboratory_typing_method': { + 'Agar dilution [ARO:3004411]': 'agar dilution', + 'Agar diffusion [NCIT:85595]': 'disk diffusion', + 'Missing [GENEPIO:0001618]': 'missing' + }, + 'laboratory_typing_platform': { + 'Microscan [ARO:3004400]': 'Microscan', + 'Phoenix [ARO:3004401]': 'Phoenix', + 'Sensititre [ARO:3004402]': 'Sensititre', + 'Vitek System [ARO:3004403]': 'Vitek' + }, + 'vendor': { + 'Becton Dickinson [ARO:3004405]': 'Becton Dickinson', + 'bioMérieux [ARO:3004406]': 'Biomérieux', + 'Siemens [ARO:3004407]': 'Siemens', + 'Trek [ARO:3004409]': 'Trek' + }, + 'testing_standard': { + 'British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]': + 'BSAC', + 'Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]': + 'CLSI', + 'Deutsches Institut für Normung (DIN) [ARO:3004367]': + 'DIN', + 'European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]': + 'EUCAST', + 'National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]': + 'NARMS', + 'National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]': + 'NCCLS', + 'Société Française de Microbiologie (SFM) [ARO:3004369]': + 'SFM', + 'Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]': + 'SIR', + 'Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]': + 'WRG', + 'Missing [GENEPIO:0001618]': + 'missing' + } + } const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); @@ -587,10 +653,15 @@ export default { for (const [i, longHeader] of longHeadersArr.entries()) { let wideHeader = antibiotic.concat('_', longHeader); if (longHeader === 'vendor') wideHeader += '_name'; - const wideVal = + let wideVal = inputRow[sourceFieldNameMap[wideHeader]]; if (wideVal) { atLeastOneWideVal = true; + if (longHeader in GRDItoNCBIObj) { + if (wideVal in GRDItoNCBIObj[longHeader]) { + wideVal = GRDItoNCBIObj[longHeader][wideVal]; + } + } longRow[i+2] = wideVal; } } From a73a74afd8802e9f1ebca145dc2cb247799528dc Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Fri, 27 Sep 2024 13:57:24 -0700 Subject: [PATCH 36/96] - and _ handling --- web/templates/grdi/export.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index af1349ad..adf5b1dd 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -654,7 +654,7 @@ export default { let wideHeader = antibiotic.concat('_', longHeader); if (longHeader === 'vendor') wideHeader += '_name'; let wideVal = - inputRow[sourceFieldNameMap[wideHeader]]; + inputRow[sourceFieldNameMap[wideHeader.replaceAll('-', '')]]; if (wideVal) { atLeastOneWideVal = true; if (longHeader in GRDItoNCBIObj) { @@ -666,7 +666,7 @@ export default { } } if (atLeastOneWideVal) { - longRow[1] = antibiotic; + longRow[1] = antibiotic.replaceAll('_', ' '); outputMatrix.push(longRow); } } From 6d82f5f2f9316ae5779ed1f22eba590086408816 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Thu, 3 Oct 2024 13:07:50 -0700 Subject: [PATCH 37/96] Use getMappedField * Need to update enums --- web/templates/grdi/export.js | 139 ++++++++++++++++++----------------- 1 file changed, 73 insertions(+), 66 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index adf5b1dd..3b79fd3c 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -561,70 +561,70 @@ export default { ]; const longHeadersArr = Array.from(ExportHeaders.keys()).slice(2); const GRDItoNCBIObj = { - 'resistance_phenotype': { - 'Resistant antimicrobial phenotype [ARO:3004301]': - 'resistant', - 'Susceptible antimicrobial phenotype [ARO:3004302]': - 'susceptible', - 'Intermediate antimicrobial phenotype [ARO:3004300]': - 'intermediate', - 'Nonsusceptible antimicrobial phenotype [ARO:3004303]': - 'nonsusceptible', - 'Antibiotic resistance not defined [GENEPIO:0002040]': - 'not defined', - 'Susceptible dose dependent antimicrobial phenotype [ARO:3004304]': - 'susceptible-dose dependent' - }, - 'measurement_sign': { - 'less than (<) [GENEPIO:0001002]': '<', - 'less than or equal to (<=) [GENEPIO:0001003]': '<=', - 'equal to (==) [GENEPIO:0001004]': '==', - 'greater than (>) [GENEPIO:0001006]': '>', - 'greater than or equal to (>=) [GENEPIO:0001005]': '>=' - }, - 'measurement_units': { - 'milligram per litre (mg/L) [UO:0000273]': 'mg/L', - 'millimetre (mm) [UO:0000016]': 'mm' - }, - 'laboratory_typing_method': { - 'Agar dilution [ARO:3004411]': 'agar dilution', - 'Agar diffusion [NCIT:85595]': 'disk diffusion', - 'Missing [GENEPIO:0001618]': 'missing' - }, - 'laboratory_typing_platform': { - 'Microscan [ARO:3004400]': 'Microscan', - 'Phoenix [ARO:3004401]': 'Phoenix', - 'Sensititre [ARO:3004402]': 'Sensititre', - 'Vitek System [ARO:3004403]': 'Vitek' - }, - 'vendor': { - 'Becton Dickinson [ARO:3004405]': 'Becton Dickinson', - 'bioMérieux [ARO:3004406]': 'Biomérieux', - 'Siemens [ARO:3004407]': 'Siemens', - 'Trek [ARO:3004409]': 'Trek' - }, - 'testing_standard': { - 'British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]': - 'BSAC', - 'Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]': - 'CLSI', - 'Deutsches Institut für Normung (DIN) [ARO:3004367]': - 'DIN', - 'European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]': - 'EUCAST', - 'National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]': - 'NARMS', - 'National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]': - 'NCCLS', - 'Société Française de Microbiologie (SFM) [ARO:3004369]': - 'SFM', - 'Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]': - 'SIR', - 'Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]': - 'WRG', - 'Missing [GENEPIO:0001618]': - 'missing' - } + // 'resistance_phenotype': { + // 'Resistant antimicrobial phenotype [ARO:3004301]': + // 'resistant', + // 'Susceptible antimicrobial phenotype [ARO:3004302]': + // 'susceptible', + // 'Intermediate antimicrobial phenotype [ARO:3004300]': + // 'intermediate', + // 'Nonsusceptible antimicrobial phenotype [ARO:3004303]': + // 'nonsusceptible', + // 'Antibiotic resistance not defined [GENEPIO:0002040]': + // 'not defined', + // 'Susceptible dose dependent antimicrobial phenotype [ARO:3004304]': + // 'susceptible-dose dependent' + // }, + // 'measurement_sign': { + // 'less than (<) [GENEPIO:0001002]': '<', + // 'less than or equal to (<=) [GENEPIO:0001003]': '<=', + // 'equal to (==) [GENEPIO:0001004]': '==', + // 'greater than (>) [GENEPIO:0001006]': '>', + // 'greater than or equal to (>=) [GENEPIO:0001005]': '>=' + // }, + // 'measurement_units': { + // 'milligram per litre (mg/L) [UO:0000273]': 'mg/L', + // 'millimetre (mm) [UO:0000016]': 'mm' + // }, + // 'laboratory_typing_method': { + // 'Agar dilution [ARO:3004411]': 'agar dilution', + // 'Agar diffusion [NCIT:85595]': 'disk diffusion', + // 'Missing [GENEPIO:0001618]': 'missing' + // }, + // 'laboratory_typing_platform': { + // 'Microscan [ARO:3004400]': 'Microscan', + // 'Phoenix [ARO:3004401]': 'Phoenix', + // 'Sensititre [ARO:3004402]': 'Sensititre', + // 'Vitek System [ARO:3004403]': 'Vitek' + // }, + // 'vendor': { + // 'Becton Dickinson [ARO:3004405]': 'Becton Dickinson', + // 'bioMérieux [ARO:3004406]': 'Biomérieux', + // 'Siemens [ARO:3004407]': 'Siemens', + // 'Trek [ARO:3004409]': 'Trek' + // }, + // 'testing_standard': { + // 'British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]': + // 'BSAC', + // 'Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]': + // 'CLSI', + // 'Deutsches Institut für Normung (DIN) [ARO:3004367]': + // 'DIN', + // 'European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]': + // 'EUCAST', + // 'National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]': + // 'NARMS', + // 'National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]': + // 'NCCLS', + // 'Société Française de Microbiologie (SFM) [ARO:3004369]': + // 'SFM', + // 'Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]': + // 'SIR', + // 'Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]': + // 'WRG', + // 'Missing [GENEPIO:0001618]': + // 'missing' + // } } const sourceFields = dh.getFields(dh.table); @@ -653,8 +653,15 @@ export default { for (const [i, longHeader] of longHeadersArr.entries()) { let wideHeader = antibiotic.concat('_', longHeader); if (longHeader === 'vendor') wideHeader += '_name'; - let wideVal = - inputRow[sourceFieldNameMap[wideHeader.replaceAll('-', '')]]; + let wideVal = dh.getMappedField( + longHeader, + inputRow, + [wideHeader.replaceAll('-', '')], + sourceFields, + sourceFieldNameMap, + ':', + 'NCBI_ANTIBIOGRAM' + ); if (wideVal) { atLeastOneWideVal = true; if (longHeader in GRDItoNCBIObj) { From 695a76a0c1a77d17aeea0aa66f3b4d1f8ef7bf54 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 3 Oct 2024 15:25:34 -0700 Subject: [PATCH 38/96] Update dh-validate.py linkml installation requirement. --- script/dh-validate.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/script/dh-validate.py b/script/dh-validate.py index b8eed8f1..3bf37998 100644 --- a/script/dh-validate.py +++ b/script/dh-validate.py @@ -4,7 +4,8 @@ # # A script to validate DataHarmonizer data files according to a given schema # and optionally Class, in the case of data files that don't identify which -# class their fields are from. Passes data file to linkml-validate. +# class their fields are from. Passes data file to linkml-validate. For this +# reason, the script only works with LinkML installed. # # To prepare tsv/csv/xls/xlsx files for above validation, this script will # remove header lines until it encounters a line with every cell containing From 28a42af581dfe70fb39a1e4544820a4a318f45f2 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 3 Oct 2024 15:46:46 -0700 Subject: [PATCH 39/96] translated file --- web/translations/translations.json | 350 +++++++++++++++++++++++++++++ 1 file changed, 350 insertions(+) create mode 100644 web/translations/translations.json diff --git a/web/translations/translations.json b/web/translations/translations.json new file mode 100644 index 00000000..b014576f --- /dev/null +++ b/web/translations/translations.json @@ -0,0 +1,350 @@ +{ + "file-menu-button": { + "en": "File", + "fr": "Fichier" + }, + "select-template-modal-button": { + "en": "Select Template", + "fr": "Sélectionner un modèle" + }, + "upload-template-dropdown-item": { + "en": "Upload Template", + "fr": "Télécharger le modèle" + }, + "new-dropdown-item": { + "en": "New", + "fr": "Nouveau" + }, + "open-dropdown-item": { + "en": "Open", + "fr": "Ouvrir" + }, + "save-as-dropdown-item": { + "en": "Save As...", + "fr": "Enregistrer sous..." + }, + "export-to-dropdown-item": { + "en": "Export To...", + "fr": "Exporter vers..." + }, + + "settings-menu-button": { + "en": "Settings", + "fr": "Paramètres" + }, + "show-all-cols-dropdown-item": { + "en": "Show all columns", + "fr": "Afficher toutes les colonnes" + }, + "show-required-cols-dropdown-item": { + "en": "Show required columns", + "fr": "Afficher les colonnes requises" + }, + "show-recommended-cols-dropdown-item": { + "en": "Show required + recommended columns", + "fr": "Afficher les colonnes obligatoires + recommandées" + }, + "show-all-rows-dropdown-item": { + "en": "Show all rows", + "fr": "Afficher toutes les lignes" + }, + "show-valid-rows-dropdown-item": { + "en": "Show valid rows", + "fr": "Afficher les lignes valides" + }, + "show-invalid-rows-dropdown-item": { + "en": "Show invalid rows", + "fr": "Afficher les lignes invalides" + }, + "show-section-menu": { + "en": "Show section:", + "fr": "Afficher la section:" + }, + "jump-to-dropdown-item": { + "en": "Jump to...", + "fr": "Aller à..." + }, + "fill-dropdown-item": { + "en": "Fill column...", + "fr": "Remplir la colonne..." + }, + "validate-btn": { + "en": "Validate", + "fr": "Valider" + }, + + "help-menu-button": { + "en": "Help", + "fr": "Aide" + }, + "getting-started-modal-menu": { + "en": "Getting Started", + "fr": "Pour commencer" + }, + "help_reference": { + "en": "Reference Guide", + "fr": "Guide de référence" + }, + "help_sop": { + "en": "SOP", + "fr": "PON" + }, + "help_release": { + "en": "Get Latest Release", + "fr": "Obtenir la dernière version" + }, + "help_contact": { + "en": "Contact Us", + "fr": "Contactez-nous" + }, + + "template_label": { + "en": "Template", + "fr": "Modèle" + }, + "language_label": { + "en": "Language", + "fr": "Langue" + }, + "translation_label": { + "en": "Language", + "fr": "Langue" + }, + "loaded_file_label": { + "en": "Loaded file", + "fr": "Fichier téléchargé" + }, + "add-row": { + "en": "Add", + "fr": "Ajouter" + }, + "add-row-text": { + "en": "more rows at the bottom", + "fr": "plus de lignes en bas" + }, + "template-cancel": { + "en": "Cancel", + "fr": "Annuler" + }, + "template-save": { + "en": "Save", + "fr": "Enregistrer" + }, + "template-continue": { + "en": "Continue", + "fr": "Continuer" + }, + "template-ok": { + "en": "Ok", + "fr": "Ok" + }, + "no-error-button": { + "en": "No Errors", + "fr": "Aucune erreur" + }, + "next-error-button": { + "en": "Next Error", + "fr": "Erreur suivante" + }, + "change-template": { + "en": "Change Template", + "fr": "Modifier le modèle" + }, + "view-template-draft-prompt": { + "en": "View draft templates", + "fr": "Afficher les ébauches de modèles" + }, + "select-template-load": { + "en": "Open", + "fr": "Ouvrir" + }, + "clear-data-prompt": { + "en": "Clear existing data?", + "fr": "Effacer les données existantes?" + }, + "clear-data-confirm-btn": { + "en": "Clear", + "fr": "Effacer" + }, + "save-as-warning": { + "en": "You have invalid cells. Continue saving?", + "fr": "Vous avez des cellules invalides. Continuer à enregistrer?" + }, + + "save-as-json-use-index": { + "en": "Save as object with index key", + "fr": "Enregistrer comme objet avec clé d’indexation" + }, + "save-as-json-use-index-key": { + "en": "Name", + "fr": "Nom" + }, + + "export-to-invalid-warning": { + "en": "You have invalid cells. Continue exporting?", + "fr": "Vous avez des cellules invalides. Continuer l'exportation?" + }, + + "export-to-confirm-btn": { + "en": "Export", + "fr": "Exporter" + }, + + "jump-to-input-prompt": { + "en": "Jump to...", + "fr": "Aller à..." + }, + + "fill-column-input-prompt": { + "en": "Fill cells in column ...", + "fr": "Remplir les cellules dans la colonne..." + }, + "fill-column-input-part2": { + "en": "with value", + "fr": "avec valeur" + }, + "fill-column-help": { + "en": "Utilisez cette fonctionnalité pour remplir toutes les cellules d'une colonne avec une valeur donnée. Cela ne remplira pas les lignes vides de la feuille de calcul (comme cela se produit lors du collage d'une valeur dans la cellule d'en-tête d'une colonne).", + "fr": "" + }, + "template-help-title": { + "en": "Are you ready to harmonize your contextual data?", + "fr": "Êtes-vous prêt à harmoniser vos données contextuelles?" + }, + "template-contact-blurb": { + "en": "", + "fr": "" + }, + "dataharmonizer-contact-blurb": { + "en": "If you have questions about the DataHarmonizer application, or want to notify us of bugs or potential improvements, contact us by either posting an issue at https://github.com/cidgoh/DataHarmonizer/issues or emailing us at emma_griffiths@sfu.ca", + "fr": "Si vous avez des questions sur l’application DataHarmonizer, ou si vous souhaitez nous informer de bogues ou d’améliorations potentielles, communiquez avec nous en publiant un problème sur https://github.com/Public-Health-Bioinformatics/DataHarmonizer/issues ou en nous envoyant un courriel à l’adresse emma_griffiths@sfu.ca" + }, + "help-sidebar__column": { + "en": "Column", + "fr": "Colonne" + }, + "help-sidebar__description": { + "en": "Description", + "fr": "Description" + }, + "help-sidebar__examples": { + "en": "Examples", + "fr": "Exemples" + }, + "help-sidebar__guidance": { + "en": "Guidance", + "fr": "Conseils" + }, + "help-sidebar__menus": { + "en": "Menus", + "fr": "Menus" + }, + "reference_guide_title": { + "en": "Reference Guide for", + "fr": "Guide de référence pour" + }, + "reference_guide_msg_pattern_regex": { + "en": "Pattern as regular expression:", + "fr": "Motif en tant qu'expression régulière :" + }, + "reference_guide_msg_pattern_hint": { + "en": "Pattern hint:", + "fr": "Indice du motif :" + }, + "reference_guide_msg_value_comparison": { + "en": "Value should be", + "fr": "La valeur doit être" + }, + "reference_guide_msg_value_comparison_btwn_1": { + "en": "between", + "fr": "entre" + }, + "reference_guide_msg_value_comparison_btwn_2": { + "en": "and", + "fr": "et" + }, + "reference_guide_msg_value_comparison_btwn_3": { + "en": "(inclusive).", + "fr": "(inclus)." + }, + "reference_guide_msg_value_comparison_gte": { + "en": "greater than or equal to", + "fr": "supérieure ou égale à" + }, + "reference_guide_msg_value_comparison_lte": { + "en": "less than or equal to", + "fr": "inférieure ou égale à" + }, + "reference_guide_msg_unique_record": { + "en": "Each record must have a unique value for this field.", + "fr": "Chaque enregistrement doit avoir une valeur unique pour ce champ." + }, + "reference_guide_msg_more_than_one_selection": { + "en": "More than one selection is allowed.", + "fr": "Plus d'une sélection est autorisée." + }, + "carousel-caption-text-0": { + "en": "The DataHarmonizer contextual data collection template\nand validator application enables users to enter data as\nin an excel spreadsheet - type and pick values from\ndropdowns, copy/paste, add rows, etc. You can edit the cells\nmanually, or upload .xlsx, .xls, .tsv, .csv and .json\nfiles via **File** > **Open**.", + "fr": "Le modèle de collecte de données contextuelles et l’application de validation DataHarmonizer permettent aux utilisateurs d’entrer des données comme dans une feuille de calcul Excel - taper et choisir des valeurs dans des menus déroulants, copier/coller, ajouter des lignes, etc. Vous pouvez modifier les cellules manuellement, ou télécharger des fichiers .xlsx, .xls, .tsv, .csv et .json dans **Fichier** > **Ouvrir**." + }, + "carousel-caption-text-1": { + "en": "The default template loaded is the \"CanCOGeN Covid-19\"\ntemplate. To change the spreadsheet template, select the\nwhite text box to the right of “Template”, it always\ncontains the name of the template currently active, or\nnavigated to “File” followed by “Change Template”. An\nin-app window will appear that allows you to select from\nthe available templates in the drop-down menu. After\nselecting the desired template, click **Open** to activate\nthe template.", + "fr": "Le modèle par défaut téléchargé est le modèle « CanCOGeN Covid-19 ». Pour changer le modèle de feuille de calcul, sélectionnez la zone de texte blanche à droite de « Modèle », qui contient toujours le nom du modèle actuellement actif, ou naviguez vers « Fichier », puis « Changer de modèle ». Une fenêtre dans l’application apparaîtra, vous permettant de sélectionner parmi les modèles disponibles dans le menu déroulant. Après avoir sélectionné le modèle souhaité, cliquez sur **Ouvrir** pour activer le modèle." + }, + "carousel-caption-text-2": { + "en": "Fields are colour-coded; required fields (minimal\nmetadata) are yellow, strongly recommended fields are\npurple, optional fields are white/gray.\n\nYou can toggle between all, the required fields, and the\nrequired + recommended fields by going to “Settings” and\nselecting “Show required columns”, etc.", + "fr": "Les champs sont codés par couleur; les champs obligatoires (métadonnées minimales) sont en jaune, les champs fortement recommandés sont en violet, les champs optionnels sont en blanc/gris. \n\nVous pouvez basculer entre tous les champs, les champs obligatoires et les champs obligatoires + recommandés en allant dans « Paramètres » et en sélectionnant « Afficher les colonnes obligatoires », etc." + }, + "carousel-caption-text-3": { + "en": "Double click on field headers to see the definition of\nthe field, guidance on filling in the field, and\nexamples of how data might look structured according\nto the constraints of the validator.", + "fr": "Double-cliquez sur les en-têtes de champ pour voir la définition du champ, des conseils pour remplir le champ et des exemples de la manière dont les données pourraient être structurées selon les contraintes du validateur." + }, + "carousel-caption-text-4": { + "en": "Picklists of controlled vocabulary are available for\nmany fields. There are dropdown menus for some, and\nmulti-select options for others (e.g. Signs and\nSymptoms). You can also see the list of terms in\nmulti-select columns by clicking once in the\nmulti-select box.", + "fr": "Des listes de choix de vocabulaire contrôlé sont disponibles pour de nombreux champs. Il y a des menus déroulants pour certains, et des options multisélection pour d’autres (par exemple, les signes et symptômes). Vous pouvez également voir la liste des termes dans les colonnes multisélection en cliquant une fois dans la case multisélection." + }, + "carousel-caption-text-5": { + "en": "When you’re done entering your data, you can validate\nvalues by clicking on “Validate”. Errors and missing\ninformation in required fields will be coloured light\nred and dark red, respectively.\n\nYou can navigate to and between errors by clicking the\n“Next Error” button that appears when errors are\npresent. After resolving these errors, revalidate to\nsee if any remain. If there are no more errors the “Next\nError” button will change to “No Errors” and fade away.", + "fr": "Lorsque vous avez terminé de saisir vos données, vous pouvez valider les valeurs en cliquant sur « Valider ». Les erreurs et les informations manquantes dans les champs obligatoires seront respectivement colorées en rouge clair et rouge foncé.\n\nVous pouvez naviguer vers et entre les erreurs en cliquant sur le bouton « Erreur suivante » qui s’affiche lorsque des erreurs sont présentes. Après avoir résolu ces erreurs, revalidez pour voir s’il en reste. S’il n’y a plus d’erreurs, le bouton « Erreur suivante » se transformera en « Pas d’erreurs » et s’estompera." + }, + "carousel-caption-text-6": { + "en": "To facilitate editing data post-validation, you can\nchange your view to only “Show valid rows” or only\n“Show invalid rows” by selecting these options under the\n“Settings” menu. You can select “Show all rows” to return\nto the original view.", + "fr": "Pour faciliter la modification des données après validation, vous pouvez changer votre vue pour ne montrer que les « lignes valides » ou les « lignes invalides » en sélectionnant ces options dans le menu « Paramètres ». Vous pouvez sélectionner « Afficher toutes les lignes » pour revenir à la vue originale" + }, + "carousel-caption-text-7": { + "en": "You can quickly navigate to a section of fields by\nselecting “Settings” and then selecting one of the\noptions listed under “Show section:”.", + "fr": "Vous pouvez naviguer rapidement vers une section de champs en sélectionnant « Paramètres », puis en sélectionnant l’une des options énumérées sous « Afficher la section : »" + }, + "carousel-caption-text-8": { + "en": "You can quickly navigate to a column by selecting\n“Settings” > “Jump to…”. An in-app window will appear,\nselect the desired column header from the drop-down list\nor begin typing its name to narrow down the list options.\nSelecting the column header from the drop down list will\nimmediately relocate you to that column on the spreadsheet.", + "fr": "Vous pouvez rapidement naviguer vers une colonne en sélectionnant « Paramètres » > « Aller à… ». Une fenêtre dans l’application s’affichera, sélectionnez l’en-tête de colonne souhaitée dans la liste déroulante ou commencez à taper son nom pour affiner les options de la liste. Sélectionner l’en-tête de colonne dans la liste déroulante vous repositionnera immédiatement à cette colonne dans la feuille de calcul." + }, + "carousel-caption-text-9": { + "en": "You can also automatically fill a column with a specified\nvalue, but only in rows with corresponding values in the\nfirst “sample ID” column. To use this feature select\n“Settings” > “Fill column...\". Select the desired column\nheader from the drop-down list or begin typing its name to\nnarrow down the list options, then specify the value to\nfill with and click “Ok” to apply.", + "fr": "Vous pouvez également remplir automatiquement une colonne avec une valeur spécifiée, mais seulement dans les lignes avec des valeurs correspondantes dans la première colonne « ID de l’échantillon ». Pour utiliser cette fonctionnalité, sélectionnez « Paramètres » > « Remplir la colonne... ». Sélectionnez l’en-tête de colonne souhaitée dans la liste déroulante ou commencez à taper son nom pour affiner les options de la liste, puis spécifiez la valeur à remplir et cliquez sur « Ok » pour l’appliquer." + }, + "carousel-caption-text-10": { + "en": "When you’ve entered and validated your data, you can\nsave it as a .xlsx, .xls, .tsv, .csv, or .json format\nfile, by clicking on “File” followed by “Save as”.\nYou can also format your data for IRIDA upload (you will\nneed to perform the upload yourself), or use your entered\ndata to create a GISAID submission form (you will need to\nadd additional information, and perform the upload\nyourself), by clicking on \"File\" followed by \"Export\nto\".", + "fr": "Lorsque vous avez saisi et validé vos données, vous pouvez les enregistrer au format .xlsx, .xls, .tsv, .csv ou .json, en cliquant sur « Fichier », puis sur « Enregistrer sous ». Vous pouvez également formater vos données pour le téléchargement IRIDA (vous devrez effectuer le téléchargement vous-même), ou utiliser vos données saisies pour créer un formulaire de soumission GISAID (vous devrez ajouter des renseignements supplémentaires et effectuer le téléchargement vous-même), en cliquant sur « Fichier », puis sur « Exporter vers »." + }, + "carousel-caption-text-11": { + "en": "If your template uses the DataHarmonizer provenance field,\nprovenance information will automatically be added upon\n“Validation” for all rows containing data. Provenance\ninformation includes the DataHarmonizer application version\nnumber, and the template schema version number (if\navailable).", + "fr": "Si votre modèle utilise le champ de provenance DataHarmonizer, les renseignements de provenance seront automatiquement ajoutés lors de la « validation » pour toutes les lignes contenant des données. Ces renseignements incluent le numéro de version de l’application DataHarmonizer et le numéro de version du schéma du modèle (si disponible)" + }, + "carousel-caption-text-12": { + "en": "You can find more information about a template under\nthe “Help” button. “Reference Guide” includes additional\ninformation about fields and the “SOP” (short for Standard\nOperating Procedure) contains additional information about\ncurating data. For a reference guide that includes picklist\nvalues, please contact us.", + "fr": "Vous pouvez trouver plus de renseignements sur un modèle sous le bouton « Aide ». Le « Guide de référence » inclut des renseignements supplémentaires sur les champs et la « PON » (abréviation de procédure d’opération normalisée) contient des renseignements supplémentaires sur la conservation des données. Pour un guide de référence incluant les valeurs des listes de choix, veuillez communiquer avec nous." + }, + "carousel-caption-text-13": { + "en": "Make sure you are using the latest version of the\nDataHarmonizer (and your template). You can check your\ncurrent Data Harmonizer Template version by looking at\nthe bottom of the “Settings” menu. To update your application\nand/or template, open the “Help” menu and select “Get latest\nrelease”.\n\nIf you have questions, or require assistance,\ncontact emma_griffiths@sfu.ca.", + "fr": "Assurez-vous d’utiliser la dernière version de DataHarmonizer (et de votre modèle). Vous pouvez vérifier votre version actuelle du modèle DataHarmonizer en regardant au bas du menu « Paramètres ». Pour mettre à jour votre application ou votre modèle, ouvrez le menu « Aide » et sélectionnez « Obtenir la dernière version ». \n\nSi vous avez des questions ou avez besoin d’assistance, envoyez un courriel à l’adresse emma_griffiths@sfu.ca." + }, + "help-sidebar__title": { + "en": "Column Help", + "fr": "Aide avec la colonne" + }, + "help-sidebar__placeholder": { + "en": "Select a cell to get help for that column.", + "fr": "Sélectionnez une cellule pour obtenir de l’aide avec cette colonne." + } +} From ae5a9d3dd62c56e9a1563ccb0e495dfc72ea1900 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Fri, 4 Oct 2024 13:07:43 -0700 Subject: [PATCH 40/96] Update schema * Remove obsolete mapping obj --- web/templates/grdi/export.js | 71 ------- web/templates/grdi/schema.json | 310 ++++++++++++++++++++++------ web/templates/grdi/schema.yaml | 124 +++++++++++ web/templates/grdi/schema_enums.tsv | 124 +++++------ 4 files changed, 434 insertions(+), 195 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 3b79fd3c..9c649283 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -560,72 +560,6 @@ export default { 'trimethoprim-sulfamethoxazole' ]; const longHeadersArr = Array.from(ExportHeaders.keys()).slice(2); - const GRDItoNCBIObj = { - // 'resistance_phenotype': { - // 'Resistant antimicrobial phenotype [ARO:3004301]': - // 'resistant', - // 'Susceptible antimicrobial phenotype [ARO:3004302]': - // 'susceptible', - // 'Intermediate antimicrobial phenotype [ARO:3004300]': - // 'intermediate', - // 'Nonsusceptible antimicrobial phenotype [ARO:3004303]': - // 'nonsusceptible', - // 'Antibiotic resistance not defined [GENEPIO:0002040]': - // 'not defined', - // 'Susceptible dose dependent antimicrobial phenotype [ARO:3004304]': - // 'susceptible-dose dependent' - // }, - // 'measurement_sign': { - // 'less than (<) [GENEPIO:0001002]': '<', - // 'less than or equal to (<=) [GENEPIO:0001003]': '<=', - // 'equal to (==) [GENEPIO:0001004]': '==', - // 'greater than (>) [GENEPIO:0001006]': '>', - // 'greater than or equal to (>=) [GENEPIO:0001005]': '>=' - // }, - // 'measurement_units': { - // 'milligram per litre (mg/L) [UO:0000273]': 'mg/L', - // 'millimetre (mm) [UO:0000016]': 'mm' - // }, - // 'laboratory_typing_method': { - // 'Agar dilution [ARO:3004411]': 'agar dilution', - // 'Agar diffusion [NCIT:85595]': 'disk diffusion', - // 'Missing [GENEPIO:0001618]': 'missing' - // }, - // 'laboratory_typing_platform': { - // 'Microscan [ARO:3004400]': 'Microscan', - // 'Phoenix [ARO:3004401]': 'Phoenix', - // 'Sensititre [ARO:3004402]': 'Sensititre', - // 'Vitek System [ARO:3004403]': 'Vitek' - // }, - // 'vendor': { - // 'Becton Dickinson [ARO:3004405]': 'Becton Dickinson', - // 'bioMérieux [ARO:3004406]': 'Biomérieux', - // 'Siemens [ARO:3004407]': 'Siemens', - // 'Trek [ARO:3004409]': 'Trek' - // }, - // 'testing_standard': { - // 'British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]': - // 'BSAC', - // 'Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366]': - // 'CLSI', - // 'Deutsches Institut für Normung (DIN) [ARO:3004367]': - // 'DIN', - // 'European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368]': - // 'EUCAST', - // 'National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195]': - // 'NARMS', - // 'National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193]': - // 'NCCLS', - // 'Société Française de Microbiologie (SFM) [ARO:3004369]': - // 'SFM', - // 'Swedish Reference Group for Antibiotics (SIR) [ARO:3007397]': - // 'SIR', - // 'Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398]': - // 'WRG', - // 'Missing [GENEPIO:0001618]': - // 'missing' - // } - } const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); @@ -664,11 +598,6 @@ export default { ); if (wideVal) { atLeastOneWideVal = true; - if (longHeader in GRDItoNCBIObj) { - if (wideVal in GRDItoNCBIObj[longHeader]) { - wideVal = GRDItoNCBIObj[longHeader][wideVal]; - } - } longRow[i+2] = wideVal; } } diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index bd8d9356..ca80b359 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -303,7 +303,10 @@ "from_schema": "https://example.com/GRDI", "permissible_values": { "Not Applicable [GENEPIO:0001619]": { - "text": "Not Applicable [GENEPIO:0001619]" + "text": "Not Applicable [GENEPIO:0001619]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Not%20applicable" + ] }, "Missing [GENEPIO:0001618]": { "text": "Missing [GENEPIO:0001618]", @@ -312,13 +315,22 @@ ] }, "Not Collected [GENEPIO:0001620]": { - "text": "Not Collected [GENEPIO:0001620]" + "text": "Not Collected [GENEPIO:0001620]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Not%20collected" + ] }, "Not Provided [GENEPIO:0001668]": { - "text": "Not Provided [GENEPIO:0001668]" + "text": "Not Provided [GENEPIO:0001668]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Not%20provided" + ] }, "Restricted Access [GENEPIO:0001810]": { - "text": "Restricted Access [GENEPIO:0001810]" + "text": "Restricted Access [GENEPIO:0001810]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Restricted%20access" + ] } } }, @@ -5632,27 +5644,48 @@ "from_schema": "https://example.com/GRDI", "permissible_values": { "Antibiotic resistance not defined [GENEPIO:0002040]": { - "text": "Antibiotic resistance not defined [GENEPIO:0002040]" + "text": "Antibiotic resistance not defined [GENEPIO:0002040]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:not%20defined" + ] }, "Intermediate antimicrobial phenotype [ARO:3004300]": { "text": "Intermediate antimicrobial phenotype [ARO:3004300]", - "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]" + "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:not%20defined" + ] }, "Indeterminate antimicrobial phenotype [GENEPIO:0100585]": { "text": "Indeterminate antimicrobial phenotype [GENEPIO:0100585]", - "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]" + "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:not%20defined" + ] }, "Nonsusceptible antimicrobial phenotype [ARO:3004303]": { - "text": "Nonsusceptible antimicrobial phenotype [ARO:3004303]" + "text": "Nonsusceptible antimicrobial phenotype [ARO:3004303]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:nonsusceptible" + ] }, "Resistant antimicrobial phenotype [ARO:3004301]": { - "text": "Resistant antimicrobial phenotype [ARO:3004301]" + "text": "Resistant antimicrobial phenotype [ARO:3004301]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:resistant" + ] }, "Susceptible antimicrobial phenotype [ARO:3004302]": { - "text": "Susceptible antimicrobial phenotype [ARO:3004302]" + "text": "Susceptible antimicrobial phenotype [ARO:3004302]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:susceptible" + ] }, "Susceptible dose dependent antimicrobial phenotype [ARO:3004304]": { - "text": "Susceptible dose dependent antimicrobial phenotype [ARO:3004304]" + "text": "Susceptible dose dependent antimicrobial phenotype [ARO:3004304]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:susceptible-dose%20dependent" + ] } } }, @@ -5663,10 +5696,16 @@ "from_schema": "https://example.com/GRDI", "permissible_values": { "milligram per litre (mg/L) [UO:0000273]": { - "text": "milligram per litre (mg/L) [UO:0000273]" + "text": "milligram per litre (mg/L) [UO:0000273]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:mg/L" + ] }, "millimetre (mm) [UO:0000016]": { - "text": "millimetre (mm) [UO:0000016]" + "text": "millimetre (mm) [UO:0000016]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:mm" + ] }, "microgram per millilitre (ug/mL) [UO:0000274]": { "text": "microgram per millilitre (ug/mL) [UO:0000274]" @@ -5680,19 +5719,34 @@ "from_schema": "https://example.com/GRDI", "permissible_values": { "less than (<) [GENEPIO:0001002]": { - "text": "less than (<) [GENEPIO:0001002]" + "text": "less than (<) [GENEPIO:0001002]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%3C" + ] }, "less than or equal to (<=) [GENEPIO:0001003]": { - "text": "less than or equal to (<=) [GENEPIO:0001003]" + "text": "less than or equal to (<=) [GENEPIO:0001003]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%3C%3D" + ] }, "equal to (==) [GENEPIO:0001004]": { - "text": "equal to (==) [GENEPIO:0001004]" + "text": "equal to (==) [GENEPIO:0001004]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%3D%3D" + ] }, "greater than (>) [GENEPIO:0001006]": { - "text": "greater than (>) [GENEPIO:0001006]" + "text": "greater than (>) [GENEPIO:0001006]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%3E" + ] }, "greater than or equal to (>=) [GENEPIO:0001005]": { - "text": "greater than or equal to (>=) [GENEPIO:0001005]" + "text": "greater than or equal to (>=) [GENEPIO:0001005]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:%3E%3D" + ] } } }, @@ -5710,7 +5764,10 @@ }, "Antimicrobial gradient (E-test) [NCIT:85596]": { "text": "Antimicrobial gradient (E-test) [NCIT:85596]", - "is_a": "Agar diffusion [NCIT:85595]" + "is_a": "Agar diffusion [NCIT:85595]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:disk%20diffusion" + ] }, "Agar dilution [ARO:3004411]": { "text": "Agar dilution [ARO:3004411]", @@ -5862,133 +5919,262 @@ "from_schema": "https://example.com/GRDI", "permissible_values": { "amikacin": { - "text": "amikacin" + "text": "amikacin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:amikacin" + ] }, "amoxicillin-clavulanic_acid": { - "text": "amoxicillin-clavulanic_acid" + "text": "amoxicillin-clavulanic_acid", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:amoxicillin-clavulanic%20acid" + ] }, "ampicillin": { - "text": "ampicillin" + "text": "ampicillin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:ampicillin" + ] }, "azithromycin": { - "text": "azithromycin" + "text": "azithromycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:azithromycin" + ] }, "cefazolin": { - "text": "cefazolin" + "text": "cefazolin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cefazolin" + ] }, "cefepime": { - "text": "cefepime" + "text": "cefepime", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cefepime" + ] }, "cefotaxime": { - "text": "cefotaxime" + "text": "cefotaxime", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cefotaxime" + ] }, "cefotaxime-clavulanic_acid": { - "text": "cefotaxime-clavulanic_acid" + "text": "cefotaxime-clavulanic_acid", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cefotaxime-clavulanic%20acid" + ] }, "cefoxitin": { - "text": "cefoxitin" + "text": "cefoxitin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cefoxitin" + ] }, "cefpodoxime": { - "text": "cefpodoxime" + "text": "cefpodoxime", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cefpodoxime" + ] }, "ceftazidime": { - "text": "ceftazidime" + "text": "ceftazidime", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:ceftazidime" + ] }, "ceftazidime-clavulanic_acid": { - "text": "ceftazidime-clavulanic_acid" + "text": "ceftazidime-clavulanic_acid", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:ceftazidime-clavulanic%20acid" + ] }, "ceftiofur": { - "text": "ceftiofur" + "text": "ceftiofur", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:ceftiofur" + ] }, "ceftriaxone": { - "text": "ceftriaxone" + "text": "ceftriaxone", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:ceftriaxone" + ] }, "cephalothin": { - "text": "cephalothin" + "text": "cephalothin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:cephalothin" + ] }, "chloramphenicol": { - "text": "chloramphenicol" + "text": "chloramphenicol", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:chloramphenicol" + ] }, "ciprofloxacin": { - "text": "ciprofloxacin" + "text": "ciprofloxacin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:ciprofloxacin" + ] }, "clindamycin": { - "text": "clindamycin" + "text": "clindamycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:clindamycin" + ] }, "doxycycline": { - "text": "doxycycline" + "text": "doxycycline", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:doxycycline" + ] }, "enrofloxacin": { - "text": "enrofloxacin" + "text": "enrofloxacin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:enrofloxacin" + ] }, "erythromycin": { - "text": "erythromycin" + "text": "erythromycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:erythromycin" + ] }, "florfenicol": { - "text": "florfenicol" + "text": "florfenicol", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:florfenicol" + ] }, "gentamicin": { - "text": "gentamicin" + "text": "gentamicin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:gentamicin" + ] }, "imipenem": { - "text": "imipenem" + "text": "imipenem", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:imipenem" + ] }, "kanamycin": { - "text": "kanamycin" + "text": "kanamycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:kanamycin" + ] }, "levofloxacin": { - "text": "levofloxacin" + "text": "levofloxacin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:levofloxacin" + ] }, "linezolid": { - "text": "linezolid" + "text": "linezolid", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:linezolid" + ] }, "meropenem": { - "text": "meropenem" + "text": "meropenem", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:meropenem" + ] }, "nalidixic_acid": { - "text": "nalidixic_acid" + "text": "nalidixic_acid", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:nalidixic%20acid" + ] }, "nitrofurantoin": { - "text": "nitrofurantoin" + "text": "nitrofurantoin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:nitrofurantoin" + ] }, "norfloxacin": { - "text": "norfloxacin" + "text": "norfloxacin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:norfloxacin" + ] }, "oxolinic-acid": { - "text": "oxolinic-acid" + "text": "oxolinic-acid", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:oxolinic-acid" + ] }, "oxytetracycline": { - "text": "oxytetracycline" + "text": "oxytetracycline", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:oxytetracycline" + ] }, "piperacillin": { - "text": "piperacillin" + "text": "piperacillin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:piperacillin" + ] }, "piperacillin-tazobactam": { - "text": "piperacillin-tazobactam" + "text": "piperacillin-tazobactam", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:piperacillin-tazobactam" + ] }, "polymyxin-b": { - "text": "polymyxin-b" + "text": "polymyxin-b", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:polymyxin-b" + ] }, "quinupristin-dalfopristin": { - "text": "quinupristin-dalfopristin" + "text": "quinupristin-dalfopristin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:quinupristin-dalfopristin" + ] }, "streptomycin": { - "text": "streptomycin" + "text": "streptomycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:streptomycin" + ] }, "sulfisoxazole": { - "text": "sulfisoxazole" + "text": "sulfisoxazole", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:sulfisoxazole" + ] }, "telithromycin": { - "text": "telithromycin" + "text": "telithromycin", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:telithromycin" + ] }, "tetracycline": { - "text": "tetracycline" + "text": "tetracycline", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:tetracycline" + ] }, "tigecycline": { - "text": "tigecycline" + "text": "tigecycline", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:tigecycline" + ] }, "trimethoprim-sulfamethoxazole": { - "text": "trimethoprim-sulfamethoxazole" + "text": "trimethoprim-sulfamethoxazole", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:trimethoprim-sulfamethoxazole" + ] } } } diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 148e2714..0bb6a741 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -12700,16 +12700,24 @@ enums: permissible_values: Not Applicable [GENEPIO:0001619]: text: Not Applicable [GENEPIO:0001619] + exact_mappings: + - NCBI_ANTIBIOGRAM:Not%20applicable Missing [GENEPIO:0001618]: text: Missing [GENEPIO:0001618] exact_mappings: - NCBI_ANTIBIOGRAM:missing Not Collected [GENEPIO:0001620]: text: Not Collected [GENEPIO:0001620] + exact_mappings: + - NCBI_ANTIBIOGRAM:Not%20collected Not Provided [GENEPIO:0001668]: text: Not Provided [GENEPIO:0001668] + exact_mappings: + - NCBI_ANTIBIOGRAM:Not%20provided Restricted Access [GENEPIO:0001810]: text: Restricted Access [GENEPIO:0001810] + exact_mappings: + - NCBI_ANTIBIOGRAM:Restricted%20access SampleCollectedByMenu: name: SampleCollectedByMenu title: sample_collected_by menu @@ -16580,20 +16588,34 @@ enums: permissible_values: Antibiotic resistance not defined [GENEPIO:0002040]: text: Antibiotic resistance not defined [GENEPIO:0002040] + exact_mappings: + - NCBI_ANTIBIOGRAM:not%20defined Intermediate antimicrobial phenotype [ARO:3004300]: text: Intermediate antimicrobial phenotype [ARO:3004300] + exact_mappings: + - NCBI_ANTIBIOGRAM:not%20defined is_a: Antibiotic resistance not defined [GENEPIO:0002040] Indeterminate antimicrobial phenotype [GENEPIO:0100585]: text: Indeterminate antimicrobial phenotype [GENEPIO:0100585] + exact_mappings: + - NCBI_ANTIBIOGRAM:not%20defined is_a: Antibiotic resistance not defined [GENEPIO:0002040] Nonsusceptible antimicrobial phenotype [ARO:3004303]: text: Nonsusceptible antimicrobial phenotype [ARO:3004303] + exact_mappings: + - NCBI_ANTIBIOGRAM:nonsusceptible Resistant antimicrobial phenotype [ARO:3004301]: text: Resistant antimicrobial phenotype [ARO:3004301] + exact_mappings: + - NCBI_ANTIBIOGRAM:resistant Susceptible antimicrobial phenotype [ARO:3004302]: text: Susceptible antimicrobial phenotype [ARO:3004302] + exact_mappings: + - NCBI_ANTIBIOGRAM:susceptible Susceptible dose dependent antimicrobial phenotype [ARO:3004304]: text: Susceptible dose dependent antimicrobial phenotype [ARO:3004304] + exact_mappings: + - NCBI_ANTIBIOGRAM:susceptible-dose%20dependent AntimicrobialMeasurementUnitsMenu: name: AntimicrobialMeasurementUnitsMenu title: antimicrobial_measurement_units menu @@ -16601,8 +16623,12 @@ enums: permissible_values: milligram per litre (mg/L) [UO:0000273]: text: milligram per litre (mg/L) [UO:0000273] + exact_mappings: + - NCBI_ANTIBIOGRAM:mg/L millimetre (mm) [UO:0000016]: text: millimetre (mm) [UO:0000016] + exact_mappings: + - NCBI_ANTIBIOGRAM:mm microgram per millilitre (ug/mL) [UO:0000274]: text: microgram per millilitre (ug/mL) [UO:0000274] AntimicrobialMeasurementSignMenu: @@ -16612,14 +16638,24 @@ enums: permissible_values: less than (<) [GENEPIO:0001002]: text: less than (<) [GENEPIO:0001002] + exact_mappings: + - NCBI_ANTIBIOGRAM:%3C less than or equal to (<=) [GENEPIO:0001003]: text: less than or equal to (<=) [GENEPIO:0001003] + exact_mappings: + - NCBI_ANTIBIOGRAM:%3C%3D equal to (==) [GENEPIO:0001004]: text: equal to (==) [GENEPIO:0001004] + exact_mappings: + - NCBI_ANTIBIOGRAM:%3D%3D greater than (>) [GENEPIO:0001006]: text: greater than (>) [GENEPIO:0001006] + exact_mappings: + - NCBI_ANTIBIOGRAM:%3E greater than or equal to (>=) [GENEPIO:0001005]: text: greater than or equal to (>=) [GENEPIO:0001005] + exact_mappings: + - NCBI_ANTIBIOGRAM:%3E%3D AntimicrobialLaboratoryTypingMethodMenu: name: AntimicrobialLaboratoryTypingMethodMenu title: antimicrobial_laboratory_typing_method menu @@ -16631,6 +16667,8 @@ enums: - NCBI_ANTIBIOGRAM:disk%20diffusion Antimicrobial gradient (E-test) [NCIT:85596]: text: Antimicrobial gradient (E-test) [NCIT:85596] + exact_mappings: + - NCBI_ANTIBIOGRAM:disk%20diffusion is_a: Agar diffusion [NCIT:85595] Agar dilution [ARO:3004411]: text: Agar dilution [ARO:3004411] @@ -16733,90 +16771,176 @@ enums: permissible_values: amikacin: text: amikacin + exact_mappings: + - NCBI_ANTIBIOGRAM:amikacin amoxicillin-clavulanic_acid: text: amoxicillin-clavulanic_acid + exact_mappings: + - NCBI_ANTIBIOGRAM:amoxicillin-clavulanic%20acid ampicillin: text: ampicillin + exact_mappings: + - NCBI_ANTIBIOGRAM:ampicillin azithromycin: text: azithromycin + exact_mappings: + - NCBI_ANTIBIOGRAM:azithromycin cefazolin: text: cefazolin + exact_mappings: + - NCBI_ANTIBIOGRAM:cefazolin cefepime: text: cefepime + exact_mappings: + - NCBI_ANTIBIOGRAM:cefepime cefotaxime: text: cefotaxime + exact_mappings: + - NCBI_ANTIBIOGRAM:cefotaxime cefotaxime-clavulanic_acid: text: cefotaxime-clavulanic_acid + exact_mappings: + - NCBI_ANTIBIOGRAM:cefotaxime-clavulanic%20acid cefoxitin: text: cefoxitin + exact_mappings: + - NCBI_ANTIBIOGRAM:cefoxitin cefpodoxime: text: cefpodoxime + exact_mappings: + - NCBI_ANTIBIOGRAM:cefpodoxime ceftazidime: text: ceftazidime + exact_mappings: + - NCBI_ANTIBIOGRAM:ceftazidime ceftazidime-clavulanic_acid: text: ceftazidime-clavulanic_acid + exact_mappings: + - NCBI_ANTIBIOGRAM:ceftazidime-clavulanic%20acid ceftiofur: text: ceftiofur + exact_mappings: + - NCBI_ANTIBIOGRAM:ceftiofur ceftriaxone: text: ceftriaxone + exact_mappings: + - NCBI_ANTIBIOGRAM:ceftriaxone cephalothin: text: cephalothin + exact_mappings: + - NCBI_ANTIBIOGRAM:cephalothin chloramphenicol: text: chloramphenicol + exact_mappings: + - NCBI_ANTIBIOGRAM:chloramphenicol ciprofloxacin: text: ciprofloxacin + exact_mappings: + - NCBI_ANTIBIOGRAM:ciprofloxacin clindamycin: text: clindamycin + exact_mappings: + - NCBI_ANTIBIOGRAM:clindamycin doxycycline: text: doxycycline + exact_mappings: + - NCBI_ANTIBIOGRAM:doxycycline enrofloxacin: text: enrofloxacin + exact_mappings: + - NCBI_ANTIBIOGRAM:enrofloxacin erythromycin: text: erythromycin + exact_mappings: + - NCBI_ANTIBIOGRAM:erythromycin florfenicol: text: florfenicol + exact_mappings: + - NCBI_ANTIBIOGRAM:florfenicol gentamicin: text: gentamicin + exact_mappings: + - NCBI_ANTIBIOGRAM:gentamicin imipenem: text: imipenem + exact_mappings: + - NCBI_ANTIBIOGRAM:imipenem kanamycin: text: kanamycin + exact_mappings: + - NCBI_ANTIBIOGRAM:kanamycin levofloxacin: text: levofloxacin + exact_mappings: + - NCBI_ANTIBIOGRAM:levofloxacin linezolid: text: linezolid + exact_mappings: + - NCBI_ANTIBIOGRAM:linezolid meropenem: text: meropenem + exact_mappings: + - NCBI_ANTIBIOGRAM:meropenem nalidixic_acid: text: nalidixic_acid + exact_mappings: + - NCBI_ANTIBIOGRAM:nalidixic%20acid nitrofurantoin: text: nitrofurantoin + exact_mappings: + - NCBI_ANTIBIOGRAM:nitrofurantoin norfloxacin: text: norfloxacin + exact_mappings: + - NCBI_ANTIBIOGRAM:norfloxacin oxolinic-acid: text: oxolinic-acid + exact_mappings: + - NCBI_ANTIBIOGRAM:oxolinic-acid oxytetracycline: text: oxytetracycline + exact_mappings: + - NCBI_ANTIBIOGRAM:oxytetracycline piperacillin: text: piperacillin + exact_mappings: + - NCBI_ANTIBIOGRAM:piperacillin piperacillin-tazobactam: text: piperacillin-tazobactam + exact_mappings: + - NCBI_ANTIBIOGRAM:piperacillin-tazobactam polymyxin-b: text: polymyxin-b + exact_mappings: + - NCBI_ANTIBIOGRAM:polymyxin-b quinupristin-dalfopristin: text: quinupristin-dalfopristin + exact_mappings: + - NCBI_ANTIBIOGRAM:quinupristin-dalfopristin streptomycin: text: streptomycin + exact_mappings: + - NCBI_ANTIBIOGRAM:streptomycin sulfisoxazole: text: sulfisoxazole + exact_mappings: + - NCBI_ANTIBIOGRAM:sulfisoxazole telithromycin: text: telithromycin + exact_mappings: + - NCBI_ANTIBIOGRAM:telithromycin tetracycline: text: tetracycline + exact_mappings: + - NCBI_ANTIBIOGRAM:tetracycline tigecycline: text: tigecycline + exact_mappings: + - NCBI_ANTIBIOGRAM:tigecycline trimethoprim-sulfamethoxazole: text: trimethoprim-sulfamethoxazole + exact_mappings: + - NCBI_ANTIBIOGRAM:trimethoprim-sulfamethoxazole types: WhitespaceMinimizedString: name: WhitespaceMinimizedString diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 6e9e46cf..2e032c89 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -1,10 +1,10 @@ title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM Template -null value menu NullValueMenu Not Applicable [GENEPIO:0001619] +null value menu NullValueMenu Not Applicable [GENEPIO:0001619] Not applicable Missing [GENEPIO:0001618] missing - Not Collected [GENEPIO:0001620] - Not Provided [GENEPIO:0001668] - Restricted Access [GENEPIO:0001810] + Not Collected [GENEPIO:0001620] Not collected + Not Provided [GENEPIO:0001668] Not provided + Restricted Access [GENEPIO:0001810] Restricted access sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] @@ -1485,29 +1485,29 @@ AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GEN Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] -antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] - Intermediate antimicrobial phenotype [ARO:3004300] - Indeterminate antimicrobial phenotype [GENEPIO:0100585] - Nonsusceptible antimicrobial phenotype [ARO:3004303] - Resistant antimicrobial phenotype [ARO:3004301] - Susceptible antimicrobial phenotype [ARO:3004302] - Susceptible dose dependent antimicrobial phenotype [ARO:3004304] +antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] not defined + Intermediate antimicrobial phenotype [ARO:3004300] not defined + Indeterminate antimicrobial phenotype [GENEPIO:0100585] not defined + Nonsusceptible antimicrobial phenotype [ARO:3004303] nonsusceptible + Resistant antimicrobial phenotype [ARO:3004301] resistant + Susceptible antimicrobial phenotype [ARO:3004302] susceptible + Susceptible dose dependent antimicrobial phenotype [ARO:3004304] susceptible-dose dependent -antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] - millimetre (mm) [UO:0000016] +antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] mg/L + millimetre (mm) [UO:0000016] mm microgram per millilitre (ug/mL) [UO:0000274] -antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] - less than or equal to (<=) [GENEPIO:0001003] - equal to (==) [GENEPIO:0001004] - greater than (>) [GENEPIO:0001006] - greater than or equal to (>=) [GENEPIO:0001005] +antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] < + less than or equal to (<=) [GENEPIO:0001003] <= + equal to (==) [GENEPIO:0001004] == + greater than (>) [GENEPIO:0001006] > + greater than or equal to (>=) [GENEPIO:0001005] >= antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion - Antimicrobial gradient (E-test) [NCIT:85596] + Antimicrobial gradient (E-test) [NCIT:85596] disk diffusion Agar dilution [ARO:3004411] agar dilution Broth dilution [ARO:3004397] @@ -1537,46 +1537,46 @@ antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British So Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG -Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin - amoxicillin-clavulanic_acid - ampicillin - azithromycin - cefazolin - cefepime - cefotaxime - cefotaxime-clavulanic_acid - cefoxitin - cefpodoxime - ceftazidime - ceftazidime-clavulanic_acid - ceftiofur - ceftriaxone - cephalothin - chloramphenicol - ciprofloxacin - clindamycin - doxycycline - enrofloxacin - erythromycin - florfenicol - gentamicin - imipenem - kanamycin - levofloxacin - linezolid - meropenem - nalidixic_acid - nitrofurantoin - norfloxacin - oxolinic-acid - oxytetracycline - piperacillin - piperacillin-tazobactam - polymyxin-b - quinupristin-dalfopristin - streptomycin - sulfisoxazole - telithromycin - tetracycline - tigecycline - trimethoprim-sulfamethoxazole \ No newline at end of file +Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin amikacin + amoxicillin-clavulanic_acid amoxicillin-clavulanic acid + ampicillin ampicillin + azithromycin azithromycin + cefazolin cefazolin + cefepime cefepime + cefotaxime cefotaxime + cefotaxime-clavulanic_acid cefotaxime-clavulanic acid + cefoxitin cefoxitin + cefpodoxime cefpodoxime + ceftazidime ceftazidime + ceftazidime-clavulanic_acid ceftazidime-clavulanic acid + ceftiofur ceftiofur + ceftriaxone ceftriaxone + cephalothin cephalothin + chloramphenicol chloramphenicol + ciprofloxacin ciprofloxacin + clindamycin clindamycin + doxycycline doxycycline + enrofloxacin enrofloxacin + erythromycin erythromycin + florfenicol florfenicol + gentamicin gentamicin + imipenem imipenem + kanamycin kanamycin + levofloxacin levofloxacin + linezolid linezolid + meropenem meropenem + nalidixic_acid nalidixic acid + nitrofurantoin nitrofurantoin + norfloxacin norfloxacin + oxolinic-acid oxolinic-acid + oxytetracycline oxytetracycline + piperacillin piperacillin + piperacillin-tazobactam piperacillin-tazobactam + polymyxin-b polymyxin-b + quinupristin-dalfopristin quinupristin-dalfopristin + streptomycin streptomycin + sulfisoxazole sulfisoxazole + telithromycin telithromycin + tetracycline tetracycline + tigecycline tigecycline + trimethoprim-sulfamethoxazole trimethoprim-sulfamethoxazole \ No newline at end of file From 02963fff183e9b4895490f43456fdd47d1540469 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Fri, 4 Oct 2024 13:29:08 -0700 Subject: [PATCH 41/96] Use shared string table when exporting xls * Removes cell cap of 255 chars --- lib/utils/files.js | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/utils/files.js b/lib/utils/files.js index 1b46283a..f431ce88 100644 --- a/lib/utils/files.js +++ b/lib/utils/files.js @@ -62,7 +62,11 @@ export function exportFile(matrix, baseName, ext) { writeFile(workbook, `${baseName}.xlsx`); break; case 'xls': - writeFile(workbook, `${baseName}.xls`); + writeFile(workbook, `${baseName}.xls`, { + bookType: 'biff8', + type: 'file', + bookSST: true, + }); break; case 'tsv': writeFile(workbook, `${baseName}.tsv`, { From 36a5e7182f24945530f9098e9279f14474a79db6 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Fri, 4 Oct 2024 15:17:06 -0700 Subject: [PATCH 42/96] Update schemas --- web/templates/grdi/schema.json | 24 +++++++++++++++--------- web/templates/grdi/schema.yaml | 12 ++++++++---- web/templates/grdi/schema_enums.tsv | 12 ++++++------ 3 files changed, 29 insertions(+), 19 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index ca80b359..caa37dda 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -5653,14 +5653,14 @@ "text": "Intermediate antimicrobial phenotype [ARO:3004300]", "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:not%20defined" + "NCBI_ANTIBIOGRAM:intermediate" ] }, "Indeterminate antimicrobial phenotype [GENEPIO:0100585]": { "text": "Indeterminate antimicrobial phenotype [GENEPIO:0100585]", "is_a": "Antibiotic resistance not defined [GENEPIO:0002040]", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:not%20defined" + "NCBI_ANTIBIOGRAM:indeterminate" ] }, "Nonsusceptible antimicrobial phenotype [ARO:3004303]": { @@ -5764,10 +5764,7 @@ }, "Antimicrobial gradient (E-test) [NCIT:85596]": { "text": "Antimicrobial gradient (E-test) [NCIT:85596]", - "is_a": "Agar diffusion [NCIT:85595]", - "exact_mappings": [ - "NCBI_ANTIBIOGRAM:disk%20diffusion" - ] + "is_a": "Agar diffusion [NCIT:85595]" }, "Agar dilution [ARO:3004411]": { "text": "Agar dilution [ARO:3004411]", @@ -5776,7 +5773,10 @@ ] }, "Broth dilution [ARO:3004397]": { - "text": "Broth dilution [ARO:3004397]" + "text": "Broth dilution [ARO:3004397]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:broth%20dilution" + ] } } }, @@ -5787,7 +5787,10 @@ "from_schema": "https://example.com/GRDI", "permissible_values": { "BIOMIC Microbiology System [ARO:3007569]": { - "text": "BIOMIC Microbiology System [ARO:3007569]" + "text": "BIOMIC Microbiology System [ARO:3007569]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:BIOMIC" + ] }, "Microscan [ARO:3004400]": { "text": "Microscan [ARO:3004400]", @@ -5834,7 +5837,10 @@ ] }, "Omron [ARO:3004408]": { - "text": "Omron [ARO:3004408]" + "text": "Omron [ARO:3004408]", + "exact_mappings": [ + "NCBI_ANTIBIOGRAM:Omron" + ] }, "Siemens [ARO:3004407]": { "text": "Siemens [ARO:3004407]", diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 0bb6a741..96fd8cf0 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -16593,12 +16593,12 @@ enums: Intermediate antimicrobial phenotype [ARO:3004300]: text: Intermediate antimicrobial phenotype [ARO:3004300] exact_mappings: - - NCBI_ANTIBIOGRAM:not%20defined + - NCBI_ANTIBIOGRAM:intermediate is_a: Antibiotic resistance not defined [GENEPIO:0002040] Indeterminate antimicrobial phenotype [GENEPIO:0100585]: text: Indeterminate antimicrobial phenotype [GENEPIO:0100585] exact_mappings: - - NCBI_ANTIBIOGRAM:not%20defined + - NCBI_ANTIBIOGRAM:indeterminate is_a: Antibiotic resistance not defined [GENEPIO:0002040] Nonsusceptible antimicrobial phenotype [ARO:3004303]: text: Nonsusceptible antimicrobial phenotype [ARO:3004303] @@ -16667,8 +16667,6 @@ enums: - NCBI_ANTIBIOGRAM:disk%20diffusion Antimicrobial gradient (E-test) [NCIT:85596]: text: Antimicrobial gradient (E-test) [NCIT:85596] - exact_mappings: - - NCBI_ANTIBIOGRAM:disk%20diffusion is_a: Agar diffusion [NCIT:85595] Agar dilution [ARO:3004411]: text: Agar dilution [ARO:3004411] @@ -16676,6 +16674,8 @@ enums: - NCBI_ANTIBIOGRAM:agar%20dilution Broth dilution [ARO:3004397]: text: Broth dilution [ARO:3004397] + exact_mappings: + - NCBI_ANTIBIOGRAM:broth%20dilution AntimicrobialLaboratoryTypingPlatformMenu: name: AntimicrobialLaboratoryTypingPlatformMenu title: antimicrobial_laboratory_typing_platform menu @@ -16683,6 +16683,8 @@ enums: permissible_values: BIOMIC Microbiology System [ARO:3007569]: text: BIOMIC Microbiology System [ARO:3007569] + exact_mappings: + - NCBI_ANTIBIOGRAM:BIOMIC Microscan [ARO:3004400]: text: Microscan [ARO:3004400] exact_mappings: @@ -16714,6 +16716,8 @@ enums: - NCBI_ANTIBIOGRAM:Biom%C3%A9rieux Omron [ARO:3004408]: text: Omron [ARO:3004408] + exact_mappings: + - NCBI_ANTIBIOGRAM:Omron Siemens [ARO:3004407]: text: Siemens [ARO:3004407] exact_mappings: diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index 2e032c89..ab2335ec 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -1486,8 +1486,8 @@ AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GEN antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] not defined - Intermediate antimicrobial phenotype [ARO:3004300] not defined - Indeterminate antimicrobial phenotype [GENEPIO:0100585] not defined + Intermediate antimicrobial phenotype [ARO:3004300] intermediate + Indeterminate antimicrobial phenotype [GENEPIO:0100585] indeterminate Nonsusceptible antimicrobial phenotype [ARO:3004303] nonsusceptible Resistant antimicrobial phenotype [ARO:3004301] resistant Susceptible antimicrobial phenotype [ARO:3004302] susceptible @@ -1507,12 +1507,12 @@ antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion - Antimicrobial gradient (E-test) [NCIT:85596] disk diffusion + Antimicrobial gradient (E-test) [NCIT:85596] Agar dilution [ARO:3004411] agar dilution - Broth dilution [ARO:3004397] + Broth dilution [ARO:3004397] broth dilution -antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] +antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] BIOMIC Microscan [ARO:3004400] Microscan Phoenix [ARO:3004401] Phoenix Sensititre [ARO:3004402] Sensititre @@ -1521,7 +1521,7 @@ antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatf antimicrobial_vendor_name menu AntimicrobialVendorNameMenu Becton Dickinson [ARO:3004405] Becton Dickinson bioMérieux [ARO:3004406] Biomérieux - Omron [ARO:3004408] + Omron [ARO:3004408] Omron Siemens [ARO:3004407] Siemens Trek [ARO:3004409] Trek From 5637377eff11fb865462891feed00ef4c61197a0 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 8 Oct 2024 08:26:30 -0700 Subject: [PATCH 43/96] Enable slot usage to be added to rather than overwritten But commenting out gen-sqltables attribute generation for now as it adds tables for each enumeration. --- script/tabular_to_schema.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/script/tabular_to_schema.py b/script/tabular_to_schema.py index 88235743..ef589801 100644 --- a/script/tabular_to_schema.py +++ b/script/tabular_to_schema.py @@ -48,6 +48,7 @@ from functools import reduce from linkml_runtime.utils.schemaview import SchemaView from linkml_runtime.dumpers.json_dumper import JSONDumper +import subprocess def init_parser(): @@ -85,7 +86,10 @@ def set_class_slot(schema_class, slot, slot_group): schema_class['slots'].append(slot_name); #### Now initialize slot_usage requirements - schema_class['slot_usage'][slot_name] = {'rank': len(schema_class['slots'])}; + if not (slot_name in schema_class['slot_usage']): + schema_class['slot_usage'][slot_name] = {'rank': len(schema_class['slots'])}; + else: + schema_class['slot_usage'][slot_name]['rank'] = len(schema_class['slots']); if slot_group > '': schema_class['slot_usage'][slot_name]['slot_group'] = slot_group; @@ -466,6 +470,16 @@ def write_schema(schema): with open(w_filename_base + '.yaml', 'w') as output_handle: yaml.dump(schema, output_handle, sort_keys=False) + #with open("temp.yaml", 'w') as output_handle: + #yaml.dump(schema, output_handle, sort_keys=False) + + # Add primary key / foreign key relational annotations. SQL table + # definition output is hidden but could be put in an optional output. + #subprocess.run(["gen-sqltables", "--no-metadata", "--relmodel-output", w_filename_base + '.yaml', "temp.yaml"],capture_output=True); + # Read in schema that is now endowed with relationship annotations: + #with open(w_filename_base + '.yaml', "r") as schema_handle: + # schema = yaml.safe_load(schema_handle); + # Now create schema.json which browser app can read directly. Replaces each # class with its induced version. This shifts each slot's content into an # attributes: {} dictionary object. From 0ca3a32fc409f9d4f838608a039f0e009276d634 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 8 Oct 2024 14:05:23 -0700 Subject: [PATCH 44/96] Remove stale TODOs --- web/templates/grdi/export.js | 2 -- 1 file changed, 2 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 9c649283..61a36119 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -73,7 +73,6 @@ export default { // ['gene_name_2', []], // ['diagnostic_PCR_CT_value_2', []], // ['description',[]], - // TODO there are additional fields now; what order? ]); const sourceFields = dh.getFields(dh.table); @@ -106,7 +105,6 @@ export default { }, }, - // TODO I see other refs to NCBI_BioSample in project; good name? NCBI_BioSample_Enterics: { fileType: 'xls', status: 'published', From 82b0b35ecf4b1933515e9302386720dc35bb6dc6 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 8 Oct 2024 14:35:18 -0700 Subject: [PATCH 45/96] Declare matched vals sets once --- web/templates/grdi/export.js | 366 ++++++++++++++++++----------------- 1 file changed, 184 insertions(+), 182 deletions(-) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index 61a36119..afeef473 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -194,6 +194,183 @@ export default { ['extr_weather_event', []], ['mechanical_damage', []] ]); + const matchedValSets = { + 'host_housing': new Set([ + 'Animal cage [ENVO:01000922]', + 'Aquarium [ENVO:00002196]', + 'Building [ENVO:00000073]', + 'Barn [ENVO:03501257]', + 'Breeder barn [ENVO:03501383]', + 'Broiler barn [ENVO:03501386]', + 'Sheep barn [ENVO:03501385]', + 'Pigsty [ENVO:03501413]', + 'Animal pen [ENVO:03501387]', + 'Stall [EOL:0001903]', + 'Poultry hatchery [ENVO:01001874]', + 'Roost (bird) [ENVO:03501439]', + 'Crate [ENVO:03501372]' + ]), + 'env_local_scale': new Set([ + 'Agricultural Field [ENVO:00000114]', + 'Alluvial fan [ENVO:00000314]', + 'Artificial wetland [ENVO:03501406]', + 'Breeding ground [ENVO:03501441]', + 'Creek [ENVO:03501405]', + 'Farm [ENVO:00000078]', + 'Beef farm [ENVO:03501443]', + 'Breeder farm [ENVO:03501384]', + 'Dairy farm [ENVO:03501416]', + 'Feedlot [ENVO:01000627]', + 'Beef cattle feedlot [ENVO:03501444]', + 'Fish farm [ENVO:00000294]', + 'Research farm [ENVO:03501417]', + 'Freshwater environment [ENVO:01000306]', + 'Hatchery [ENVO:01001873]', + 'Poultry hatchery [ENVO:01001874]', + 'Lake [ENVO:00000020]', + 'Manure lagoon (Anaerobic lagoon) [ENVO:03501423]', + 'Manure pit [ENVO:01001872]', + 'Marine environment [ENVO:01000320]', + 'Benthic zone [ENVO:03501440]', + 'Pelagic zone [ENVO:00000208]', + 'Park [ENVO:00000562]', + 'Pond [ENVO:00000033]', + 'Reservoir [ENVO:00000025]', + 'Irrigation reservoir [ENVO:00000450]', + 'River [ENVO:00000022]', + 'Roost (bird) [ENVO:03501439]', + 'Rural area [ENVO:01000772]', + 'Slough [ENVO:03501438]', + 'Stream [ENVO:00000023]', + 'Tributary [ENVO:00000495]', + 'Water surface [ENVO:01001191]', + 'Woodland area [ENVO:00000109]' + ]), + 'facility_type': new Set([ + 'Abattoir [ENVO:01000925]', + 'Dairy [ENVO:00003862]', + 'Farm [ENVO:00000078]', + 'Hatchery [ENVO:01001873]', + 'Retail environment [ENVO:01001448]', + 'Shop [ENVO:00002221]', + 'Butcher shop [ENVO:03501396]', + 'Supermarket [ENVO:01000984]', + 'Manure digester facility [ENVO:03501422]' + ]), + 'coll_site_geo_feat': new Set([ + 'Animal transportation equipment [AGRO:00000671]', + 'Dead haul trailer [GENEPIO:0100896]', + 'Dead haul truck [AGRO:00000673]', + 'Live haul trailer [GENEPIO:0100897]', + 'Live haul truck [AGRO:00000674]', + 'Bulk tank [ENVO:03501379]', + 'Animal feeding equipment [AGRO:00000675]', + 'Animal feeder [AGRO:00000679]', + 'Animal drinker [AGRO:00000680]', + 'Feed pan [AGRO:00000676]', + 'Watering bowl [AGRO:00000677]', + '"Belt [NCIT:C49844]', + 'Boot [GSSO:012935]', + 'Boot cover [OBI:0002806]', + 'Broom [ENVO:03501431]', + 'Bulk tank [ENVO:03501379]', + 'Chick box [AGRO:00000678]', + 'Chick pad [AGRO:00000672]', + 'Cleaning equipment [ENVO:03501430]', + 'Dumpster [ENVO:03501400]', + 'Egg belt [AGRO:00000670]', + 'Fan [NCIT:C49947]', + 'Freezer [ENVO:03501415]', + 'Freezer handle [ENVO:03501414]', + 'Plucking belt [AGRO:00000669]' + ]), + 'env_medium': new Set([ + 'Air [ENVO:00002005]', + 'Alluvium [ENVO:01001202]', + 'Animal feeding equipment [AGRO:00000675]', + 'Animal feeder [AGRO:00000679]', + 'Animal drinker [AGRO:00000680]', + 'Feed pan [AGRO:00000676]', + 'Watering bowl [AGRO:00000677]', + 'Animal transportation equipment [AGRO:00000671]', + 'Dead haul trailer [GENEPIO:0100896]', + 'Dead haul truck [AGRO:00000673]', + 'Live haul trailer [GENEPIO:0100897]', + 'Live haul truck [AGRO:00000674]', + 'Belt [NCIT:C49844]', + 'Biosolids [ENVO:00002059]', + 'Boot [GSSO:012935]', + 'Boot cover [OBI:0002806]', + 'Broom [ENVO:03501431]', + 'Bulk tank [ENVO:03501379]', + 'Chick box [AGRO:00000678]', + 'Chick pad [AGRO:00000672]', + 'Cleaning equipment [ENVO:03501430]', + 'Compost [ENVO:00002170]', + 'Contaminated water [ENVO:00002186]', + 'Fecal slurry [ENVO:03501436]', + 'Fluid from meat rinse [GENEPIO:0004323]', + 'Effluent [ENVO:03501407]', + 'Influent [ENVO:03501442]', + 'Surface runoff [ENVO:03501408]', + 'Poultry plucking water [AGRO_00000693]', + 'Wastewater [ENVO:00002001]', + 'Weep fluid [AGRO_00000692]', + 'Crate [ENVO:03501372]', + 'Dumpster [ENVO:03501400]', + 'Dust [ENVO:00002008]', + 'Egg belt [AGRO:00000670]', + 'Fan [NCIT:C49947]', + 'Freezer [ENVO:03501415]', + 'Freezer handle [ENVO:03501414]', + 'Manure [ENVO:00003031]', + 'Animal manure [AGRO:00000079]', + 'Pig manure [AGRO:00000080]', + 'Manure digester equipment [ENVO:03501424]', + 'Nest [ENVO:03501432]', + 'Bird\'s nest [ENVO:00005805]', + 'Permafrost [ENVO:00000134]', + 'Plucking belt [AGRO:00000669]', + 'Poultry fluff [UBERON:0008291]', + 'Poultry litter [AGRO:00000080]', + 'Sediment [ENVO:00002007]', + 'Soil [ENVO:00001998]', + 'Agricultural soil [ENVO:00002259]', + 'Forest soil [ENVO:00002261]', + 'Straw [ENVO:00003869]', + 'Canola straw [FOODON:00004430]', + 'Oat straw [FOODON:03309878]', + 'Barley straw [FOODON:00004559]', + 'Water [CHEBI:15377]', + 'Drinking water [ENVO:00003064]', + 'Groundwater [ENVO:01001004]', + 'Surface water [ENVO:00002042]' + ]), + 'food_processing_method': new Set([ + 'Food (cooked) [FOODON:00001181]', + 'Food (cut) [FOODON:00004291]', + 'Food (chopped) [FOODON:00002777]', + 'Food (chunks) [FOODON:00004555]', + 'Food (cubed) [FOODON:00004278]', + 'Food (diced) [FOODON:00004549]', + 'Food (grated) [FOODON:00004552]', + 'Food (sliced) [FOODON:00002455]', + 'Food (shredded) [FOODON:00004553]', + 'Food (fresh) [FOODON:00002457]', + 'Food (pulped) [FOODON:00004554]', + 'Food (raw) [FOODON:03311126]', + 'Food (unseasoned) [FOODON:00004287]', + 'Meat (boneless) [FOODON:00003467]', + 'Meat (skinless) [FOODON:00003468]', + 'Meat (with bone) [FOODON:02010116]', + 'Meat (with skin) [FOODON:02010111]' + ]), + 'food_preserv_proc': new Set([ + 'Food (canned) [FOODON:00002418]', + 'Food (dried) [FOODON:03307539]', + 'Food (frozen) [FOODON:03302148]' + ]), + }; const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); @@ -224,226 +401,51 @@ export default { sourceFieldNameMap ); } else if (headerName === 'host_housing') { - const matchedValsSet = new Set([ - 'Animal cage [ENVO:01000922]', - 'Aquarium [ENVO:00002196]', - 'Building [ENVO:00000073]', - 'Barn [ENVO:03501257]', - 'Breeder barn [ENVO:03501383]', - 'Broiler barn [ENVO:03501386]', - 'Sheep barn [ENVO:03501385]', - 'Pigsty [ENVO:03501413]', - 'Animal pen [ENVO:03501387]', - 'Stall [EOL:0001903]', - 'Poultry hatchery [ENVO:01001874]', - 'Roost (bird) [ENVO:03501439]', - 'Crate [ENVO:03501372]' - ]) value = dh.getMatchedValsField( 'environmental_site', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ) } else if (headerName === 'env_local_scale') { - const matchedValsSet = new Set([ - 'Agricultural Field [ENVO:00000114]', - 'Alluvial fan [ENVO:00000314]', - 'Artificial wetland [ENVO:03501406]', - 'Breeding ground [ENVO:03501441]', - 'Creek [ENVO:03501405]', - 'Farm [ENVO:00000078]', - 'Beef farm [ENVO:03501443]', - 'Breeder farm [ENVO:03501384]', - 'Dairy farm [ENVO:03501416]', - 'Feedlot [ENVO:01000627]', - 'Beef cattle feedlot [ENVO:03501444]', - 'Fish farm [ENVO:00000294]', - 'Research farm [ENVO:03501417]', - 'Freshwater environment [ENVO:01000306]', - 'Hatchery [ENVO:01001873]', - 'Poultry hatchery [ENVO:01001874]', - 'Lake [ENVO:00000020]', - 'Manure lagoon (Anaerobic lagoon) [ENVO:03501423]', - 'Manure pit [ENVO:01001872]', - 'Marine environment [ENVO:01000320]', - 'Benthic zone [ENVO:03501440]', - 'Pelagic zone [ENVO:00000208]', - 'Park [ENVO:00000562]', - 'Pond [ENVO:00000033]', - 'Reservoir [ENVO:00000025]', - 'Irrigation reservoir [ENVO:00000450]', - 'River [ENVO:00000022]', - 'Roost (bird) [ENVO:03501439]', - 'Rural area [ENVO:01000772]', - 'Slough [ENVO:03501438]', - 'Stream [ENVO:00000023]', - 'Tributary [ENVO:00000495]', - 'Water surface [ENVO:01001191]', - 'Woodland area [ENVO:00000109]' - ]) value = dh.getMatchedValsField( 'environmental_site', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ) } else if (headerName === 'facility_type') { - const matchedValsSet = new Set([ - 'Abattoir [ENVO:01000925]', - 'Dairy [ENVO:00003862]', - 'Farm [ENVO:00000078]', - 'Hatchery [ENVO:01001873]', - 'Retail environment [ENVO:01001448]', - 'Shop [ENVO:00002221]', - 'Butcher shop [ENVO:03501396]', - 'Supermarket [ENVO:01000984]', - 'Manure digester facility [ENVO:03501422]' - ]) value = dh.getMatchedValsField( 'environmental_site', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ) } else if (headerName === 'coll_site_geo_feat') { - const matchedValsSet = new Set([ - 'Animal transportation equipment [AGRO:00000671]', - 'Dead haul trailer [GENEPIO:0100896]', - 'Dead haul truck [AGRO:00000673]', - 'Live haul trailer [GENEPIO:0100897]', - 'Live haul truck [AGRO:00000674]', - 'Bulk tank [ENVO:03501379]', - 'Animal feeding equipment [AGRO:00000675]', - 'Animal feeder [AGRO:00000679]', - 'Animal drinker [AGRO:00000680]', - 'Feed pan [AGRO:00000676]', - 'Watering bowl [AGRO:00000677]', - '"Belt [NCIT:C49844]', - 'Boot [GSSO:012935]', - 'Boot cover [OBI:0002806]', - 'Broom [ENVO:03501431]', - 'Bulk tank [ENVO:03501379]', - 'Chick box [AGRO:00000678]', - 'Chick pad [AGRO:00000672]', - 'Cleaning equipment [ENVO:03501430]', - 'Dumpster [ENVO:03501400]', - 'Egg belt [AGRO:00000670]', - 'Fan [NCIT:C49947]', - 'Freezer [ENVO:03501415]', - 'Freezer handle [ENVO:03501414]', - 'Plucking belt [AGRO:00000669]' - ]) value = dh.getMatchedValsField( 'environmental_material', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ) } else if (headerName === 'env_medium') { - const matchedValsSet = new Set([ - 'Air [ENVO:00002005]', - 'Alluvium [ENVO:01001202]', - 'Animal feeding equipment [AGRO:00000675]', - 'Animal feeder [AGRO:00000679]', - 'Animal drinker [AGRO:00000680]', - 'Feed pan [AGRO:00000676]', - 'Watering bowl [AGRO:00000677]', - 'Animal transportation equipment [AGRO:00000671]', - 'Dead haul trailer [GENEPIO:0100896]', - 'Dead haul truck [AGRO:00000673]', - 'Live haul trailer [GENEPIO:0100897]', - 'Live haul truck [AGRO:00000674]', - 'Belt [NCIT:C49844]', - 'Biosolids [ENVO:00002059]', - 'Boot [GSSO:012935]', - 'Boot cover [OBI:0002806]', - 'Broom [ENVO:03501431]', - 'Bulk tank [ENVO:03501379]', - 'Chick box [AGRO:00000678]', - 'Chick pad [AGRO:00000672]', - 'Cleaning equipment [ENVO:03501430]', - 'Compost [ENVO:00002170]', - 'Contaminated water [ENVO:00002186]', - 'Fecal slurry [ENVO:03501436]', - 'Fluid from meat rinse [GENEPIO:0004323]', - 'Effluent [ENVO:03501407]', - 'Influent [ENVO:03501442]', - 'Surface runoff [ENVO:03501408]', - 'Poultry plucking water [AGRO_00000693]', - 'Wastewater [ENVO:00002001]', - 'Weep fluid [AGRO_00000692]', - 'Crate [ENVO:03501372]', - 'Dumpster [ENVO:03501400]', - 'Dust [ENVO:00002008]', - 'Egg belt [AGRO:00000670]', - 'Fan [NCIT:C49947]', - 'Freezer [ENVO:03501415]', - 'Freezer handle [ENVO:03501414]', - 'Manure [ENVO:00003031]', - 'Animal manure [AGRO:00000079]', - 'Pig manure [AGRO:00000080]', - 'Manure digester equipment [ENVO:03501424]', - 'Nest [ENVO:03501432]', - 'Bird\'s nest [ENVO:00005805]', - 'Permafrost [ENVO:00000134]', - 'Plucking belt [AGRO:00000669]', - 'Poultry fluff [UBERON:0008291]', - 'Poultry litter [AGRO:00000080]', - 'Sediment [ENVO:00002007]', - 'Soil [ENVO:00001998]', - 'Agricultural soil [ENVO:00002259]', - 'Forest soil [ENVO:00002261]', - 'Straw [ENVO:00003869]', - 'Canola straw [FOODON:00004430]', - 'Oat straw [FOODON:03309878]', - 'Barley straw [FOODON:00004559]', - 'Water [CHEBI:15377]', - 'Drinking water [ENVO:00003064]', - 'Groundwater [ENVO:01001004]', - 'Surface water [ENVO:00002042]' - ]) value = dh.getMatchedValsField( 'environmental_material', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ) } else if (headerName === 'food_processing_method') { - const matchedValsSet = new Set([ - 'Food (cooked) [FOODON:00001181]', - 'Food (cut) [FOODON:00004291]', - 'Food (chopped) [FOODON:00002777]', - 'Food (chunks) [FOODON:00004555]', - 'Food (cubed) [FOODON:00004278]', - 'Food (diced) [FOODON:00004549]', - 'Food (grated) [FOODON:00004552]', - 'Food (sliced) [FOODON:00002455]', - 'Food (shredded) [FOODON:00004553]', - 'Food (fresh) [FOODON:00002457]', - 'Food (pulped) [FOODON:00004554]', - 'Food (raw) [FOODON:03311126]', - 'Food (unseasoned) [FOODON:00004287]', - 'Meat (boneless) [FOODON:00003467]', - 'Meat (skinless) [FOODON:00003468]', - 'Meat (with bone) [FOODON:02010116]', - 'Meat (with skin) [FOODON:02010111]' - ]) value = dh.getMatchedValsField( 'food_product_properties', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ) } else if (headerName === 'food_preserv_proc') { - const matchedValsSet = new Set([ - 'Food (canned) [FOODON:00002418]', - 'Food (dried) [FOODON:03307539]', - 'Food (frozen) [FOODON:03302148]' - ]) value = dh.getMatchedValsField( 'food_product_properties', - matchedValsSet, + matchedValSets[headerName], inputRow, sourceFieldNameMap ); From b2ac5a7571d919886fdfdb28532062b85c16b7d9 Mon Sep 17 00:00:00 2001 From: Ivan S Gill Date: Tue, 8 Oct 2024 14:36:37 -0700 Subject: [PATCH 46/96] Comment --- web/templates/grdi/export.js | 1 + 1 file changed, 1 insertion(+) diff --git a/web/templates/grdi/export.js b/web/templates/grdi/export.js index afeef473..e5753530 100644 --- a/web/templates/grdi/export.js +++ b/web/templates/grdi/export.js @@ -586,6 +586,7 @@ export default { let atLeastOneWideVal = false; for (const [i, longHeader] of longHeadersArr.entries()) { let wideHeader = antibiotic.concat('_', longHeader); + // Vendor is the only header =/= imported header suffix if (longHeader === 'vendor') wideHeader += '_name'; let wideVal = dh.getMappedField( longHeader, From 1a51858f9e9f5b597d745d2c90cdd9e489862f86 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 8 Oct 2024 23:17:25 -0700 Subject: [PATCH 47/96] fix for export target --- web/templates/mpox/export.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/templates/mpox/export.js b/web/templates/mpox/export.js index 4f3ed335..4dafaaf4 100644 --- a/web/templates/mpox/export.js +++ b/web/templates/mpox/export.js @@ -237,7 +237,7 @@ export default { 'NML LIMS': { fileType: 'csv', - pertains_to: ['Monkeypox'], + pertains_to: ['Mpox'], status: 'published', method: function (dh) { // A full export table field list enables ordering of these fields in export From bc3c784905dbb5d161538d7bd75de2fc071729d6 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 8 Oct 2024 23:27:08 -0700 Subject: [PATCH 48/96] Mpox update --- web/templates/mpox/schema.json | 20867 ++++++++++++++++++-------- web/templates/mpox/schema.yaml | 10217 +++++++++++-- web/templates/mpox/schema_core.yaml | 10 +- web/templates/mpox/schema_enums.tsv | 3395 +++-- web/templates/mpox/schema_slots.tsv | 422 +- 5 files changed, 25644 insertions(+), 9267 deletions(-) diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 64d5e467..64044c3a 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -2,7 +2,7 @@ "name": "Mpox", "description": "", "id": "https://example.com/mpox", - "version": "5.3.3", + "version": "7.5.5", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -296,1771 +296,2273 @@ } }, "enums": { - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "null value menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Not Applicable": { "text": "Not Applicable", + "description": "A categorical choice recorded when a datum does not apply to a given context.", "meaning": "GENEPIO:0001619" }, "Missing": { "text": "Missing", + "description": "A categorical choice recorded when a datum is not included for an unknown reason.", "meaning": "GENEPIO:0001618" }, "Not Collected": { "text": "Not Collected", + "description": "A categorical choice recorded when a datum was not measured or collected.", "meaning": "GENEPIO:0001620" }, "Not Provided": { "text": "Not Provided", + "description": "A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage.", "meaning": "GENEPIO:0001668" }, "Restricted Access": { "text": "Restricted Access", + "description": "A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns.", "meaning": "GENEPIO:0001810" } } }, - "geo_loc_name (state/province/territory) menu": { - "name": "geo_loc_name (state/province/territory) menu", + "GeoLocNameStateProvinceTerritoryMenu": { + "name": "GeoLocNameStateProvinceTerritoryMenu", + "title": "geo_loc_name (state/province/territory) menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Alberta": { "text": "Alberta", + "description": "One of Canada's prairie provinces. It became a province on 1905-09-01. Alberta is located in western Canada, bounded by the provinces of British Columbia to the west and Saskatchewan to the east, Northwest Territories to the north, and by the State of Montana to the south. Statistics Canada divides the province of Alberta into nineteen census divisions, each with one or more municipal governments overseeing county municipalities, improvement districts, special areas, specialized municipalities, municipal districts, regional municipalities, cities, towns, villages, summer villages, Indian settlements, and Indian reserves. Census divisions are not a unit of local government in Alberta.", "meaning": "GAZ:00002566" }, "British Columbia": { "text": "British Columbia", + "description": "The westernmost of Canada's provinces. British Columbia is bordered by the Pacific Ocean on the west, by the American State of Alaska on the northwest, and to the north by the Yukon and the Northwest Territories, on the east by the province of Alberta, and on the south by the States of Washington, Idaho, and Montana. The current southern border of British Columbia was established by the 1846 Oregon Treaty, although its history is tied with lands as far south as the California border. British Columbia's rugged coastline stretches for more than 27,000 km, and includes deep, mountainous fjords and about 6,000 islands, most of which are uninhabited. British Columbia is carved into 27 regional districts. These regional districts are federations of member municipalities and electoral areas. The unincorporated area of the regional district is carved into electoral areas.", "meaning": "GAZ:00002562" }, "Manitoba": { "text": "Manitoba", + "description": "One of Canada's 10 provinces. Manitoba is located at the longitudinal centre of Canada, although it is considered to be part of Western Canada. It borders Saskatchewan to the west, Ontario to the east, Nunavut and Hudson Bay to the north, and the American states of North Dakota and Minnesota to the south. Statistics Canada divides the province of Manitoba into 23 census divisions. Census divisions are not a unit of local government in Manitoba.", "meaning": "GAZ:00002571" }, "New Brunswick": { "text": "New Brunswick", + "description": "One of Canada's three Maritime provinces. New Brunswick is bounded on the north by Quebec's Gaspe Peninsula and by Chaleur Bay. Along the east coast, the Gulf of Saint Lawrence and Northumberland Strait form the boundaries. In the south-east corner of the province, the narrow Isthmus of Chignecto connects New Brunswick to the Nova Scotia peninsula. The south of the province is bounded by the Bay of Fundy, which has the highest tides in the world with a rise of 16 m. To the west, the province borders the American State of Maine. New Brunswick is divided into 15 counties, which no longer have administrative roles except in the court system. The counties are divided into parishes.", "meaning": "GAZ:00002570" }, "Newfoundland and Labrador": { "text": "Newfoundland and Labrador", + "description": "A province of Canada, the tenth and latest to join the Confederation. Geographically, the province consists of the island of Newfoundland and the mainland Labrador, on Canada's Atlantic coast.", "meaning": "GAZ:00002567" }, "Northwest Territories": { "text": "Northwest Territories", + "description": "A territory of Canada. Located in northern Canada, it borders Canada's two other territories, Yukon to the west and Nunavut to the east, and three provinces: British Columbia to the southwest, Alberta to the south, and Saskatchewan to the southeast. The present-day territory was created in 1870-06, when the Hudson's Bay Company transferred Rupert's Land and North-Western Territory to the government of Canada.", "meaning": "GAZ:00002575" }, "Nova Scotia": { "text": "Nova Scotia", + "description": "A Canadian province located on Canada's southeastern coast. The province's mainland is the Nova Scotia peninsula surrounded by the Atlantic Ocean, including numerous bays and estuaries. No where in Nova Scotia is more than 67 km from the ocean. Cape Breton Island, a large island to the northeast of the Nova Scotia mainland, is also part of the province, as is Sable Island.", "meaning": "GAZ:00002565" }, "Nunavut": { "text": "Nunavut", + "description": "The largest and newest territory of Canada; it was separated officially from the Northwest Territories on 1999-04-01. The Territory covers about 1.9 million km2 of land and water in Northern Canada including part of the mainland, most of the Arctic Archipelago, and all of the islands in Hudson Bay, James Bay, and Ungava Bay (including the Belcher Islands) which belonged to the Northwest Territories. Nunavut has land borders with the Northwest Territories on several islands as well as the mainland, a border with Manitoba to the south of the Nunavut mainland, and a tiny land border with Newfoundland and Labrador on Killiniq Island. It also shares aquatic borders with the provinces of Quebec, Ontario and Manitoba and with Greenland.", "meaning": "GAZ:00002574" }, "Ontario": { "text": "Ontario", + "description": "A province located in the central part of Canada. Ontario is bordered by the provinces of Manitoba to the west, Quebec to the east, and the States of Michigan, New York, and Minnesota. Most of Ontario's borders with the United States are natural, starting at the Lake of the Woods and continuing through the four Great Lakes: Superior, Huron (which includes Georgian Bay), Erie, and Ontario (for which the province is named), then along the Saint Lawrence River near Cornwall. Ontario is the only Canadian Province that borders the Great Lakes. There are three different types of census divisions: single-tier municipalities, upper-tier municipalities (which can be regional municipalities or counties) and districts.", "meaning": "GAZ:00002563" }, "Prince Edward Island": { "text": "Prince Edward Island", + "description": "A Canadian province consisting of an island of the same name. It is divided into 3 counties.", "meaning": "GAZ:00002572" }, "Quebec": { "text": "Quebec", + "description": "A province in the central part of Canada. Quebec is Canada's largest province by area and its second-largest administrative division; only the territory of Nunavut is larger. It is bordered to the west by the province of Ontario, James Bay and Hudson Bay, to the north by Hudson Strait and Ungava Bay, to the east by the Gulf of Saint Lawrence and the provinces of Newfoundland and Labrador and New Brunswick. It is bordered on the south by the American states of Maine, New Hampshire, Vermont, and New York. It also shares maritime borders with the Territory of Nunavut, the Province of Prince Edward Island and the Province of Nova Scotia.", "meaning": "GAZ:00002569" }, "Saskatchewan": { "text": "Saskatchewan", + "description": "A prairie province in Canada. Saskatchewan is bounded on the west by Alberta, on the north by the Northwest Territories, on the east by Manitoba, and on the south by the States of Montana and North Dakota. It is divided into 18 census divisions according to Statistics Canada.", "meaning": "GAZ:00002564" }, "Yukon": { "text": "Yukon", + "description": "The westernmost of Canada's three territories. The territory is the approximate shape of a right triangle, bordering the American State of Alaska to the west, the Northwest Territories to the east and British Columbia to the south. Its northern coast is on the Beaufort Sea. Its ragged eastern boundary mostly follows the divide between the Yukon Basin and the Mackenzie River drainage basin to the east in the Mackenzie mountains. Its capital is Whitehorse.", "meaning": "GAZ:00002576" } } }, - "sample collection date precision menu": { - "name": "sample collection date precision menu", + "SampleCollectionDatePrecisionMenu": { + "name": "SampleCollectionDatePrecisionMenu", + "title": "sample collection date precision menu", "from_schema": "https://example.com/mpox", "permissible_values": { "year": { "text": "year", + "description": "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.", "meaning": "UO:0000036" }, "month": { "text": "month", + "description": "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.", "meaning": "UO:0000035" }, "day": { "text": "day", + "description": "A time unit which is equal to 24 hours.", "meaning": "UO:0000033" } } }, - "NML submitted specimen type menu": { - "name": "NML submitted specimen type menu", + "NmlSubmittedSpecimenTypeMenu": { + "name": "NmlSubmittedSpecimenTypeMenu", + "title": "NML submitted specimen type menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Bodily fluid": { "text": "Bodily fluid", + "description": "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", "meaning": "UBERON:0006314" }, "DNA": { "text": "DNA", + "description": "The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.", "meaning": "OBI:0001051" }, "Nucleic acid": { "text": "Nucleic acid", + "description": "An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.", "meaning": "OBI:0001010" }, "RNA": { "text": "RNA", + "description": "An extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.", "meaning": "OBI:0000880" }, "Swab": { "text": "Swab", + "description": "A device which is a soft, absorbent material mounted on one or both ends of a stick.", "meaning": "OBI:0002600" }, "Tissue": { "text": "Tissue", + "description": "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", "meaning": "UBERON:0000479" }, "Not Applicable": { "text": "Not Applicable", + "description": "A categorical choice recorded when a datum does not apply to a given context.", "meaning": "GENEPIO:0001619" } } }, - "Related specimen relationship type menu": { - "name": "Related specimen relationship type menu", + "RelatedSpecimenRelationshipTypeMenu": { + "name": "RelatedSpecimenRelationshipTypeMenu", + "title": "Related specimen relationship type menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Acute": { "text": "Acute", + "description": "Sudden appearance of disease manifestations over a short period of time. The word acute is applied to different time scales depending on the disease or manifestation and does not have an exact definition in minutes, hours, or days.", "meaning": "HP:0011009" }, "Convalescent": { - "text": "Convalescent" + "text": "Convalescent", + "description": "A specimen collected from an individual during the recovery phase following the resolution of acute symptoms of a disease, often used to assess immune response or recovery progression." }, "Familial": { - "text": "Familial" + "text": "Familial", + "description": "A specimen obtained from a relative of an individual, often used in studies examining genetic or hereditary factors, or familial transmission of conditions." }, "Follow-up": { "text": "Follow-up", + "description": "The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done.", "meaning": "EFO:0009642" }, "Reinfection testing": { "text": "Reinfection testing", + "description": "A specimen collected to determine if an individual has been re-exposed to and reinfected by a pathogen after an initial infection and recovery.", "is_a": "Follow-up" }, "Previously Submitted": { - "text": "Previously Submitted" + "text": "Previously Submitted", + "description": "A specimen that has been previously provided or used in a study or testing but is being considered for re-analysis or additional testing." }, "Sequencing/bioinformatics methods development/validation": { - "text": "Sequencing/bioinformatics methods development/validation" + "text": "Sequencing/bioinformatics methods development/validation", + "description": "A specimen used specifically for the purpose of developing, testing, or validating sequencing or bioinformatics methodologies." }, "Specimen sampling methods testing": { - "text": "Specimen sampling methods testing" + "text": "Specimen sampling methods testing", + "description": "A specimen used to test, refine, or validate methods and techniques for collecting and processing samples." } } }, - "anatomical material menu": { - "name": "anatomical material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical material menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Blood": { "text": "Blood", + "description": "A fluid that is composed of blood plasma and erythrocytes.", "meaning": "UBERON:0000178" }, "Blood clot": { "text": "Blood clot", + "description": "Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis).", "meaning": "UBERON:0010210", "is_a": "Blood" }, "Blood serum": { "text": "Blood serum", + "description": "The portion of blood plasma that excludes clotting factors.", "meaning": "UBERON:0001977", "is_a": "Blood" }, "Blood plasma": { "text": "Blood plasma", + "description": "The liquid component of blood, in which erythrocytes are suspended.", "meaning": "UBERON:0001969", "is_a": "Blood" }, "Whole blood": { "text": "Whole blood", + "description": "Blood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant.", "meaning": "NCIT:C41067", "is_a": "Blood" }, "Fluid": { "text": "Fluid", + "description": "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", "meaning": "UBERON:0006314" }, "Saliva": { "text": "Saliva", + "description": "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.", "meaning": "UBERON:0001836", "is_a": "Fluid" }, "Fluid (cerebrospinal (CSF))": { "text": "Fluid (cerebrospinal (CSF))", + "description": "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.", "meaning": "UBERON:0001359", "is_a": "Fluid" }, "Fluid (pericardial)": { "text": "Fluid (pericardial)", + "description": "Transudate contained in the pericardial cavity.", "meaning": "UBERON:0002409", "is_a": "Fluid" }, "Fluid (pleural)": { "text": "Fluid (pleural)", + "description": "Transudate contained in the pleural cavity.", "meaning": "UBERON:0001087", "is_a": "Fluid" }, "Fluid (vaginal)": { "text": "Fluid (vaginal)", + "description": "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands", "meaning": "UBERON:0036243", "is_a": "Fluid" }, "Fluid (amniotic)": { "text": "Fluid (amniotic)", + "description": "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion.", "meaning": "UBERON:0000173", "is_a": "Fluid" }, "Lesion": { "text": "Lesion", + "description": "A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part.", "meaning": "NCIT:C3824" }, "Lesion (Macule)": { "text": "Lesion (Macule)", + "description": "A flat lesion characterized by change in the skin color.", "meaning": "NCIT:C43278", "is_a": "Lesion" }, "Lesion (Papule)": { "text": "Lesion (Papule)", + "description": "A small (less than 5-10 mm) elevation of skin that is non-suppurative.", "meaning": "NCIT:C39690", "is_a": "Lesion" }, "Lesion (Pustule)": { "text": "Lesion (Pustule)", + "description": "A circumscribed and elevated skin lesion filled with purulent material.", "meaning": "NCIT:C78582", "is_a": "Lesion" }, "Lesion (Scab)": { "text": "Lesion (Scab)", + "description": "A dry, rough, crust-like lesion that forms over a wound or ulcer as part of the natural healing process. It consists of dried blood, serum, and cellular debris.", "meaning": "GENEPIO:0100490", "is_a": "Lesion" }, "Lesion (Vesicle)": { "text": "Lesion (Vesicle)", + "description": "A small, fluid-filled elevation on the skin. Vesicles are often clear or slightly cloudy and can be a sign of various skin conditions or infections.", "meaning": "GENEPIO:0100491", "is_a": "Lesion" }, "Rash": { "text": "Rash", + "description": "A skin and integumentary tissue symptom that is characterized by an eruption on the body typically with little or no elevation above the surface.", "meaning": "SYMP:0000487" }, "Ulcer": { "text": "Ulcer", + "description": "A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue.", "meaning": "NCIT:C3426" }, "Tissue": { "text": "Tissue", + "description": "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", "meaning": "UBERON:0000479" }, "Wound tissue (injury)": { "text": "Wound tissue (injury)", + "description": "Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.", "meaning": "NCIT:C3671", "is_a": "Tissue" } } }, - "anatomical material international menu": { - "name": "anatomical material international menu", + "AnatomicalMaterialInternationalMenu": { + "name": "AnatomicalMaterialInternationalMenu", + "title": "anatomical material international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Blood [UBERON:0000178]": { "text": "Blood [UBERON:0000178]", + "description": "A fluid that is composed of blood plasma and erythrocytes.", "meaning": "UBERON:0000178" }, "Blood clot [UBERON:0010210]": { "text": "Blood clot [UBERON:0010210]", + "description": "Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis).", "meaning": "UBERON:0010210", "is_a": "Blood [UBERON:0000178]" }, "Blood serum [UBERON:0001977]": { "text": "Blood serum [UBERON:0001977]", + "description": "The portion of blood plasma that excludes clotting factors.", "meaning": "UBERON:0001977", "is_a": "Blood [UBERON:0000178]" }, "Blood plasma [UBERON:0001969]": { "text": "Blood plasma [UBERON:0001969]", + "description": "The liquid component of blood, in which erythrocytes are suspended.", "meaning": "UBERON:0001969", "is_a": "Blood [UBERON:0000178]" }, "Whole blood [NCIT:C41067]": { "text": "Whole blood [NCIT:C41067]", + "description": "Blood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant.", "meaning": "NCIT:C41067", "is_a": "Blood [UBERON:0000178]" }, "Fluid [UBERON:0006314]": { "text": "Fluid [UBERON:0006314]", + "description": "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", "meaning": "UBERON:0006314" }, "Saliva [UBERON:0001836]": { "text": "Saliva [UBERON:0001836]", + "description": "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.", "meaning": "UBERON:0001836", "is_a": "Fluid [UBERON:0006314]" }, "Fluid (cerebrospinal (CSF)) [UBERON:0001359]": { "text": "Fluid (cerebrospinal (CSF)) [UBERON:0001359]", + "description": "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.", "meaning": "UBERON:0001359", "is_a": "Fluid [UBERON:0006314]" }, "Fluid (pericardial) [UBERON:0002409]": { "text": "Fluid (pericardial) [UBERON:0002409]", + "description": "Transudate contained in the pericardial cavity.", "meaning": "UBERON:0002409", "is_a": "Fluid [UBERON:0006314]" }, "Fluid (pleural) [UBERON:0001087]": { "text": "Fluid (pleural) [UBERON:0001087]", + "description": "Transudate contained in the pleural cavity.", "meaning": "UBERON:0001087", "is_a": "Fluid [UBERON:0006314]" }, "Fluid (vaginal) [UBERON:0036243]": { "text": "Fluid (vaginal) [UBERON:0036243]", + "description": "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands", "meaning": "UBERON:0036243", "is_a": "Fluid [UBERON:0006314]" }, "Fluid (amniotic) [UBERON:0000173]": { "text": "Fluid (amniotic) [UBERON:0000173]", + "description": "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion.", "meaning": "UBERON:0000173", "is_a": "Fluid [UBERON:0006314]" }, "Lesion [NCIT:C3824]": { "text": "Lesion [NCIT:C3824]", + "description": "A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part.", "meaning": "NCIT:C3824" }, "Lesion (Macule) [NCIT:C43278]": { "text": "Lesion (Macule) [NCIT:C43278]", + "description": "A flat lesion characterized by change in the skin color.", "meaning": "NCIT:C43278", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Papule) [NCIT:C39690]": { "text": "Lesion (Papule) [NCIT:C39690]", + "description": "A small (less than 5-10 mm) elevation of skin that is non-suppurative.", "meaning": "NCIT:C39690", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Pustule) [NCIT:C78582]": { "text": "Lesion (Pustule) [NCIT:C78582]", + "description": "A circumscribed and elevated skin lesion filled with purulent material.", "meaning": "NCIT:C78582", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Scab) [GENEPIO:0100490]": { "text": "Lesion (Scab) [GENEPIO:0100490]", + "description": "A dry, rough, crust-like lesion that forms over a wound or ulcer as part of the natural healing process. It consists of dried blood, serum, and cellular debris.", "meaning": "GENEPIO:0100490", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Vesicle) [GENEPIO:0100491]": { "text": "Lesion (Vesicle) [GENEPIO:0100491]", + "description": "A small, fluid-filled elevation on the skin. Vesicles are often clear or slightly cloudy and can be a sign of various skin conditions or infections.", "meaning": "GENEPIO:0100491", "is_a": "Lesion [NCIT:C3824]" }, "Rash [SYMP:0000487]": { "text": "Rash [SYMP:0000487]", + "description": "A skin and integumentary tissue symptom that is characterized by an eruption on the body typically with little or no elevation above the surface.", "meaning": "SYMP:0000487" }, "Ulcer [NCIT:C3426]": { "text": "Ulcer [NCIT:C3426]", + "description": "A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue.", "meaning": "NCIT:C3426" }, "Tissue [UBERON:0000479]": { "text": "Tissue [UBERON:0000479]", + "description": "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", "meaning": "UBERON:0000479" }, "Wound tissue (injury) [NCIT:C3671]": { "text": "Wound tissue (injury) [NCIT:C3671]", + "description": "Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.", "meaning": "NCIT:C3671", "is_a": "Tissue [UBERON:0000479]" } } }, - "anatomical part menu": { - "name": "anatomical part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical part menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Anus": { "text": "Anus", + "description": "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.", "meaning": "UBERON:0001245" }, "Perianal skin": { "text": "Perianal skin", + "description": "A zone of skin that is part of the area surrounding the anus.", "meaning": "UBERON:0012336", "is_a": "Anus" }, "Arm": { "text": "Arm", + "description": "The part of the forelimb extending from the shoulder to the autopod.", "meaning": "UBERON:0001460" }, "Arm (forearm)": { "text": "Arm (forearm)", + "description": "The structure on the upper limb, between the elbow and the wrist.", "meaning": "NCIT:C32628", "is_a": "Arm" }, "Elbow": { "text": "Elbow", + "description": "The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa.", "meaning": "UBERON:0001461", "is_a": "Arm" }, "Back": { "text": "Back", + "description": "The rear surface of the human body from the shoulders to the hips.", "meaning": "FMA:14181" }, "Buttock": { "text": "Buttock", + "description": "A zone of soft tissue located on the posterior of the lateral side of the pelvic region corresponding to the gluteal muscles.", "meaning": "UBERON:0013691" }, "Cervix": { "text": "Cervix", + "description": "Lower, narrow portion of the uterus where it joins with the top end of the vagina.", "meaning": "UBERON:0000002" }, "Chest": { "text": "Chest", + "description": "Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper", "meaning": "UBERON:0001443" }, "Foot": { "text": "Foot", + "description": "The terminal part of the vertebrate leg upon which an individual stands. 2: An invertebrate organ of locomotion or attachment; especially: a ventral muscular surface or process of a mollusk.", "meaning": "BTO:0000476" }, "Genital area": { "text": "Genital area", + "description": "The area where the upper thigh meets the trunk. More precisely, the fold or depression marking the juncture of the lower abdomen and the inner part of the thigh.", "meaning": "BTO:0003358" }, "Penis": { "text": "Penis", + "description": "An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.", "meaning": "UBERON:0000989", "is_a": "Genital area" }, "Glans (tip of penis)": { "text": "Glans (tip of penis)", + "description": "The bulbous structure at the distal end of the human penis", "meaning": "UBERON:0035651", "is_a": "Penis" }, "Prepuce of penis (foreskin)": { "text": "Prepuce of penis (foreskin)", + "description": "A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect.", "meaning": "UBERON:0001332", "is_a": "Penis" }, "Perineum": { "text": "Perineum", + "description": "The space between the anus and scrotum in the male human, or between the anus and the vulva in the female human.", "meaning": "UBERON:0002356", "is_a": "Genital area" }, "Scrotum": { "text": "Scrotum", + "description": "The external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus.", "meaning": "UBERON:0001300", "is_a": "Genital area" }, "Vagina": { "text": "Vagina", + "description": "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles", "meaning": "UBERON:0000996", "is_a": "Genital area" }, "Gland": { "text": "Gland", + "description": "An organ that functions as a secretory or excretory organ.", "meaning": "UBERON:0002530" }, "Hand": { "text": "Hand", + "description": "The terminal part of the vertebrate forelimb when modified, as in humans, as a grasping organ.", "meaning": "BTO:0004668" }, "Finger": { "text": "Finger", + "description": "Subdivision of the hand demarcated from the hand proper by the skin crease in line with the distal edge of finger webs. Examples: thumb, right middle finger, left little finger.", "meaning": "FMA:9666", "is_a": "Hand" }, "Hand (palm)": { "text": "Hand (palm)", + "description": "The inner surface of the hand between the wrist and fingers.", "meaning": "FMA:24920", "is_a": "Hand" }, "Head": { "text": "Head", + "description": "The head is the anterior-most division of the body.", "meaning": "UBERON:0000033" }, "Buccal mucosa": { "text": "Buccal mucosa", + "description": "The inner lining of the cheeks and lips.", "meaning": "UBERON:0006956", "is_a": "Head" }, "Cheek": { "text": "Cheek", + "description": "A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.", "meaning": "UBERON:0001567", "is_a": "Head" }, "Ear": { "text": "Ear", + "description": "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.", "meaning": "UBERON:0001690", "is_a": "Head" }, "Preauricular region": { "text": "Preauricular region", + "description": "Of or pertaining to the area in front of the auricle of the ear.", "meaning": "NCIT:C103848", "is_a": "Ear" }, "Eye": { "text": "Eye", + "description": "An organ that detects light.", "meaning": "UBERON:0000970", "is_a": "Head" }, "Face": { "text": "Face", + "description": "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).", "meaning": "UBERON:0001456", "is_a": "Head" }, "Forehead": { "text": "Forehead", + "description": "The part of the face above the eyes. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond", "meaning": "UBERON:0008200", "is_a": "Head" }, "Lip": { "text": "Lip", + "description": "One of the two fleshy folds which surround the opening of the mouth.", "meaning": "UBERON:0001833", "is_a": "Head" }, "Jaw": { "text": "Jaw", + "description": "A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.", "meaning": "UBERON:0011595", "is_a": "Head" }, "Tongue": { "text": "Tongue", + "description": "A muscular organ in the floor of the mouth.", "meaning": "UBERON:0001723", "is_a": "Head" }, "Hypogastrium (suprapubic region)": { "text": "Hypogastrium (suprapubic region)", + "description": "The hypogastrium (or hypogastric region, or pubic region) is an area of the human abdomen located below the navel.", "meaning": "UBERON:0013203" }, "Leg": { "text": "Leg", + "description": "The portion of the hindlimb that contains both the stylopod and zeugopod.", "meaning": "UBERON:0000978" }, "Ankle": { "text": "Ankle", + "description": "A zone of skin that is part of an ankle", "meaning": "UBERON:0001512", "is_a": "Leg" }, "Knee": { "text": "Knee", + "description": "A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.", "meaning": "UBERON:0001465", "is_a": "Leg" }, "Thigh": { "text": "Thigh", + "description": "The part of the hindlimb between pelvis and the knee, corresponding to the femur.", "meaning": "UBERON:0000376", "is_a": "Leg" }, "Lower body": { "text": "Lower body", + "description": "The part of the body that includes the leg, ankle, and foot.", "meaning": "GENEPIO:0100492" }, "Nasal Cavity": { "text": "Nasal Cavity", + "description": "An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.", "meaning": "UBERON:0001707" }, "Anterior Nares": { "text": "Anterior Nares", + "description": "The external part of the nose containing the lower nostrils.", "meaning": "UBERON:2001427", "is_a": "Nasal Cavity" }, "Inferior Nasal Turbinate": { "text": "Inferior Nasal Turbinate", + "description": "The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.", "meaning": "UBERON:0005921", "is_a": "Nasal Cavity" }, "Middle Nasal Turbinate": { "text": "Middle Nasal Turbinate", + "description": "A turbinal located on the maxilla bone.", "meaning": "UBERON:0005922", "is_a": "Nasal Cavity" }, "Neck": { "text": "Neck", + "description": "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.", "meaning": "UBERON:0000974" }, "Pharynx (throat)": { "text": "Pharynx (throat)", - "meaning": "UBERON:0000341", + "description": "The pharynx is the part of the digestive system immediately posterior to the mouth.", + "meaning": "UBERON:0006562", "is_a": "Neck" }, "Nasopharynx (NP)": { "text": "Nasopharynx (NP)", + "description": "The section of the pharynx that lies above the soft palate.", "meaning": "UBERON:0001728", "is_a": "Pharynx (throat)" }, "Oropharynx (OP)": { "text": "Oropharynx (OP)", + "description": "The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.", "meaning": "UBERON:0001729", "is_a": "Pharynx (throat)" }, "Trachea": { "text": "Trachea", + "description": "The trachea is the portion of the airway that attaches to the bronchi as it branches.", "meaning": "UBERON:0003126", "is_a": "Neck" }, "Rectum": { "text": "Rectum", + "description": "The terminal portion of the intestinal tube, terminating with the anus.", "meaning": "UBERON:0001052" }, "Shoulder": { "text": "Shoulder", + "description": "A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).", "meaning": "UBERON:0001467" }, "Skin": { "text": "Skin", + "description": "The outer epithelial layer of the skin that is superficial to the dermis.", "meaning": "UBERON:0001003" } } }, - "anatomical part international menu": { - "name": "anatomical part international menu", + "AnatomicalPartInternationalMenu": { + "name": "AnatomicalPartInternationalMenu", + "title": "anatomical part international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Anus [UBERON:0001245]": { "text": "Anus [UBERON:0001245]", + "description": "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.", "meaning": "UBERON:0001245" }, "Perianal skin [UBERON:0012336]": { "text": "Perianal skin [UBERON:0012336]", + "description": "A zone of skin that is part of the area surrounding the anus.", "meaning": "UBERON:0012336", "is_a": "Anus [UBERON:0001245]" }, "Arm [UBERON:0001460]": { "text": "Arm [UBERON:0001460]", + "description": "The part of the forelimb extending from the shoulder to the autopod.", "meaning": "UBERON:0001460" }, "Arm (forearm) [NCIT:C32628]": { "text": "Arm (forearm) [NCIT:C32628]", + "description": "The structure on the upper limb, between the elbow and the wrist.", "meaning": "NCIT:C32628", "is_a": "Arm [UBERON:0001460]" }, "Elbow [UBERON:0001461]": { "text": "Elbow [UBERON:0001461]", + "description": "The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa.", "meaning": "UBERON:0001461", "is_a": "Arm [UBERON:0001460]" }, "Back [FMA:14181]": { "text": "Back [FMA:14181]", + "description": "The rear surface of the human body from the shoulders to the hips.", "meaning": "FMA:14181" }, "Buttock [UBERON:0013691]": { "text": "Buttock [UBERON:0013691]", + "description": "A zone of soft tissue located on the posterior of the lateral side of the pelvic region corresponding to the gluteal muscles.", "meaning": "UBERON:0013691" }, "Cervix [UBERON:0000002]": { "text": "Cervix [UBERON:0000002]", + "description": "Lower, narrow portion of the uterus where it joins with the top end of the vagina.", "meaning": "UBERON:0000002" }, "Chest [UBERON:0001443]": { "text": "Chest [UBERON:0001443]", + "description": "Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper", "meaning": "UBERON:0001443" }, "Foot [BTO:0000476]": { "text": "Foot [BTO:0000476]", + "description": "The terminal part of the vertebrate leg upon which an individual stands.", "meaning": "BTO:0000476" }, "Genital area [BTO:0003358]": { "text": "Genital area [BTO:0003358]", + "description": "The area where the upper thigh meets the trunk. More precisely, the fold or depression marking the juncture of the lower abdomen and the inner part of the thigh.", "meaning": "BTO:0003358" }, "Penis [UBERON:0000989]": { "text": "Penis [UBERON:0000989]", + "description": "An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.", "meaning": "UBERON:0000989", "is_a": "Genital area [BTO:0003358]" }, "Glans (tip of penis) [UBERON:0035651]": { "text": "Glans (tip of penis) [UBERON:0035651]", + "description": "The bulbous structure at the distal end of the human penis", "meaning": "UBERON:0035651", "is_a": "Penis [UBERON:0000989]" }, "Prepuce of penis (foreskin)": { "text": "Prepuce of penis (foreskin)", + "description": "A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect.", "meaning": "UBERON:0001332", "is_a": "Penis [UBERON:0000989]" }, "Perineum [UBERON:0002356]": { "text": "Perineum [UBERON:0002356]", + "description": "The space between the anus and scrotum in the male human, or between the anus and the vulva in the female human.", "meaning": "UBERON:0002356", "is_a": "Genital area [BTO:0003358]" }, "Scrotum [UBERON:0001300]": { "text": "Scrotum [UBERON:0001300]", + "description": "The external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus.", "meaning": "UBERON:0001300", "is_a": "Genital area [BTO:0003358]" }, "Vagina [UBERON:0000996]": { "text": "Vagina [UBERON:0000996]", + "description": "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles", "meaning": "UBERON:0000996", "is_a": "Genital area [BTO:0003358]" }, "Gland [UBERON:0002530]": { "text": "Gland [UBERON:0002530]", + "description": "An organ that functions as a secretory or excretory organ.", "meaning": "UBERON:0002530" }, "Hand [BTO:0004668]": { "text": "Hand [BTO:0004668]", + "description": "The terminal part of the vertebrate forelimb when modified, as in humans, as a grasping organ.", "meaning": "BTO:0004668" }, "Finger [FMA:9666]": { "text": "Finger [FMA:9666]", + "description": "Subdivision of the hand demarcated from the hand proper by the skin crease in line with the distal edge of finger webs. Examples: thumb, right middle finger, left little finger.", "meaning": "FMA:9666", "is_a": "Hand [BTO:0004668]" }, "Hand (palm) [FMA:24920]": { "text": "Hand (palm) [FMA:24920]", + "description": "The inner surface of the hand between the wrist and fingers.", "meaning": "FMA:24920", "is_a": "Hand [BTO:0004668]" }, "Head [UBERON:0000033]": { "text": "Head [UBERON:0000033]", + "description": "The head is the anterior-most division of the body.", "meaning": "UBERON:0000033" }, "Buccal mucosa [UBERON:0006956]": { "text": "Buccal mucosa [UBERON:0006956]", + "description": "The inner lining of the cheeks and lips.", "meaning": "UBERON:0006956", "is_a": "Head [UBERON:0000033]" }, "Cheek [UBERON:0001567]": { "text": "Cheek [UBERON:0001567]", + "description": "A fleshy subdivision of one side of the face bounded by an eye, ear and the nose.", "meaning": "UBERON:0001567", "is_a": "Head [UBERON:0000033]" }, "Ear [UBERON:0001690]": { "text": "Ear [UBERON:0001690]", + "description": "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.", "meaning": "UBERON:0001690", "is_a": "Head [UBERON:0000033]" }, "Preauricular region [NCIT:C103848]": { "text": "Preauricular region [NCIT:C103848]", + "description": "Of or pertaining to the area in front of the auricle of the ear.", "meaning": "NCIT:C103848", "is_a": "Ear [UBERON:0001690]" }, "Eye [UBERON:0000970]": { "text": "Eye [UBERON:0000970]", + "description": "An organ that detects light.", "meaning": "UBERON:0000970", "is_a": "Head [UBERON:0000033]" }, "Face [UBERON:0001456]": { "text": "Face [UBERON:0001456]", + "description": "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).", "meaning": "UBERON:0001456", "is_a": "Head [UBERON:0000033]" }, "Forehead [UBERON:0008200]": { "text": "Forehead [UBERON:0008200]", + "description": "The part of the face above the eyes. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond", "meaning": "UBERON:0008200", "is_a": "Head [UBERON:0000033]" }, "Lip [UBERON:0001833]": { "text": "Lip [UBERON:0001833]", + "description": "One of the two fleshy folds which surround the opening of the mouth.", "meaning": "UBERON:0001833", "is_a": "Head [UBERON:0000033]" }, "Jaw [UBERON:0011595]": { "text": "Jaw [UBERON:0011595]", + "description": "A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.", "meaning": "UBERON:0011595", "is_a": "Head [UBERON:0000033]" }, "Tongue [UBERON:0001723]": { "text": "Tongue [UBERON:0001723]", + "description": "A muscular organ in the floor of the mouth.", "meaning": "UBERON:0001723", "is_a": "Head [UBERON:0000033]" }, "Hypogastrium (suprapubic region) [UBERON:0013203]": { "text": "Hypogastrium (suprapubic region) [UBERON:0013203]", + "description": "The hypogastrium (or hypogastric region, or pubic region) is an area of the human abdomen located below the navel.", "meaning": "UBERON:0013203" }, "Leg [UBERON:0000978]": { "text": "Leg [UBERON:0000978]", + "description": "The portion of the hindlimb that contains both the stylopod and zeugopod.", "meaning": "UBERON:0000978" }, "Ankle [UBERON:0001512]": { "text": "Ankle [UBERON:0001512]", + "description": "A zone of skin that is part of an ankle", "meaning": "UBERON:0001512", "is_a": "Leg [UBERON:0000978]" }, "Knee [UBERON:0001465]": { "text": "Knee [UBERON:0001465]", + "description": "A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod.", "meaning": "UBERON:0001465", "is_a": "Leg [UBERON:0000978]" }, "Thigh [UBERON:0000376]": { "text": "Thigh [UBERON:0000376]", + "description": "The part of the hindlimb between pelvis and the knee, corresponding to the femur.", "meaning": "UBERON:0000376", "is_a": "Leg [UBERON:0000978]" }, "Lower body [GENEPIO:0100492]": { "text": "Lower body [GENEPIO:0100492]", + "description": "The part of the body that includes the leg, ankle, and foot.", "meaning": "GENEPIO:0100492" }, "Nasal Cavity [UBERON:0001707]": { "text": "Nasal Cavity [UBERON:0001707]", + "description": "An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.", "meaning": "UBERON:0001707" }, "Anterior Nares [UBERON:2001427]": { "text": "Anterior Nares [UBERON:2001427]", + "description": "The external part of the nose containing the lower nostrils.", "meaning": "UBERON:2001427", "is_a": "Nasal Cavity [UBERON:0001707]" }, "Inferior Nasal Turbinate [UBERON:0005921]": { "text": "Inferior Nasal Turbinate [UBERON:0005921]", + "description": "The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha.", "meaning": "UBERON:0005921", "is_a": "Nasal Cavity [UBERON:0001707]" }, "Middle Nasal Turbinate [UBERON:0005922]": { "text": "Middle Nasal Turbinate [UBERON:0005922]", + "description": "A turbinal located on the maxilla bone.", "meaning": "UBERON:0005922", "is_a": "Nasal Cavity [UBERON:0001707]" }, "Neck [UBERON:0000974]": { "text": "Neck [UBERON:0000974]", + "description": "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.", "meaning": "UBERON:0000974" }, - "Pharynx (throat) [UBERON:0000341]": { - "text": "Pharynx (throat) [UBERON:0000341]", - "meaning": "UBERON:0000341", + "Pharynx (throat) [UBERON:0006562]": { + "text": "Pharynx (throat) [UBERON:0006562]", + "description": "A zone of skin that is part of an ankle", + "meaning": "UBERON:0006562", "is_a": "Neck [UBERON:0000974]" }, "Nasopharynx (NP) [UBERON:0001728]": { "text": "Nasopharynx (NP) [UBERON:0001728]", + "description": "The section of the pharynx that lies above the soft palate.", "meaning": "UBERON:0001728", - "is_a": "Pharynx (throat) [UBERON:0000341]" + "is_a": "Pharynx (throat) [UBERON:0006562]" }, "Oropharynx (OP) [UBERON:0001729]": { "text": "Oropharynx (OP) [UBERON:0001729]", + "description": "The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis.", "meaning": "UBERON:0001729", - "is_a": "Pharynx (throat) [UBERON:0000341]" + "is_a": "Pharynx (throat) [UBERON:0006562]" }, "Trachea [UBERON:0003126]": { "text": "Trachea [UBERON:0003126]", + "description": "The trachea is the portion of the airway that attaches to the bronchi as it branches.", "meaning": "UBERON:0003126", "is_a": "Neck [UBERON:0000974]" }, "Rectum [UBERON:0001052]": { "text": "Rectum [UBERON:0001052]", + "description": "The terminal portion of the intestinal tube, terminating with the anus.", "meaning": "UBERON:0001052" }, "Shoulder [UBERON:0001467]": { "text": "Shoulder [UBERON:0001467]", + "description": "A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle).", "meaning": "UBERON:0001467" }, "Skin [UBERON:0001003]": { "text": "Skin [UBERON:0001003]", + "description": "The outer epithelial layer of the skin that is superficial to the dermis.", "meaning": "UBERON:0001003" } } }, - "body product menu": { - "name": "body product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body product menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Breast Milk": { "text": "Breast Milk", + "description": "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.", "meaning": "UBERON:0001913" }, "Feces": { "text": "Feces", + "description": "Portion of semisolid bodily waste discharged through the anus.", "meaning": "UBERON:0001988" }, "Fluid (discharge)": { "text": "Fluid (discharge)", + "description": "A fluid that comes out of the body.", "meaning": "SYMP:0000651" }, "Pus": { "text": "Pus", + "description": "A bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections.", "meaning": "UBERON:0000177", "is_a": "Fluid (discharge)" }, "Fluid (seminal)": { "text": "Fluid (seminal)", + "description": "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended.", "meaning": "UBERON:0006530" }, "Mucus": { "text": "Mucus", + "description": "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.", "meaning": "UBERON:0000912" }, "Sputum": { "text": "Sputum", + "description": "Matter ejected from the lungs, bronchi, and trachea, through the mouth.", "meaning": "UBERON:0007311", "is_a": "Mucus" }, "Sweat": { "text": "Sweat", + "description": "Secretion produced by a sweat gland.", "meaning": "UBERON:0001089" }, "Tear": { "text": "Tear", + "description": "Aqueous substance secreted by the lacrimal gland.", "meaning": "UBERON:0001827" }, "Urine": { "text": "Urine", + "description": "Excretion that is the output of a kidney.", "meaning": "UBERON:0001088" } } }, - "body product international menu": { - "name": "body product international menu", + "BodyProductInternationalMenu": { + "name": "BodyProductInternationalMenu", + "title": "body product international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Breast Milk [UBERON:0001913]": { "text": "Breast Milk [UBERON:0001913]", + "description": "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.", "meaning": "UBERON:0001913" }, "Feces [UBERON:0001988]": { "text": "Feces [UBERON:0001988]", + "description": "Portion of semisolid bodily waste discharged through the anus.", "meaning": "UBERON:0001988" }, "Fluid (discharge) [SYMP:0000651]": { "text": "Fluid (discharge) [SYMP:0000651]", + "description": "A fluid that comes out of the body.", "meaning": "SYMP:0000651" }, "Pus [UBERON:0000177]": { "text": "Pus [UBERON:0000177]", + "description": "A bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections.", "meaning": "UBERON:0000177", "is_a": "Fluid (discharge) [SYMP:0000651]" }, "Fluid (seminal) [UBERON:0006530]": { "text": "Fluid (seminal) [UBERON:0006530]", + "description": "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended.", "meaning": "UBERON:0006530" }, "Mucus [UBERON:0000912]": { "text": "Mucus [UBERON:0000912]", + "description": "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.", "meaning": "UBERON:0000912" }, "Sputum [UBERON:0007311]": { "text": "Sputum [UBERON:0007311]", + "description": "Matter ejected from the lungs, bronchi, and trachea, through the mouth.", "meaning": "UBERON:0007311", "is_a": "Mucus [UBERON:0000912]" }, "Sweat [UBERON:0001089]": { "text": "Sweat [UBERON:0001089]", + "description": "Secretion produced by a sweat gland.", "meaning": "UBERON:0001089" }, "Tear [UBERON:0001827]": { "text": "Tear [UBERON:0001827]", + "description": "Aqueous substance secreted by the lacrimal gland.", "meaning": "UBERON:0001827" }, "Urine [UBERON:0001088]": { "text": "Urine [UBERON:0001088]", + "description": "Excretion that is the output of a kidney.", "meaning": "UBERON:0001088" } } }, - "environmental material international menu": { - "name": "environmental material international menu", + "EnvironmentalMaterialInternationalMenu": { + "name": "EnvironmentalMaterialInternationalMenu", + "title": "environmental material international menu", "from_schema": "https://example.com/mpox", "permissible_values": { - "Animal carcass": { - "text": "Animal carcass" - }, - "Bedding (Bed linen)": { - "text": "Bedding (Bed linen)", + "Animal carcass [FOODON:02010020]": { + "text": "Animal carcass [FOODON:02010020]", + "description": "A carcass of an animal that includes all anatomical parts. This includes a carcass with all organs and skin.", + "meaning": "FOODON:02010020" + }, + "Bedding (Bed linen) [GSSO:005304]": { + "text": "Bedding (Bed linen) [GSSO:005304]", + "description": "Bedding is the removable and washable portion of a human sleeping environment.", "meaning": "GSSO:005304" }, - "Clothing": { - "text": "Clothing", + "Clothing [GSSO:003405]": { + "text": "Clothing [GSSO:003405]", + "description": "Fabric or other material used to cover the body.", "meaning": "GSSO:003405" }, "Drinkware": { - "text": "Drinkware" + "text": "Drinkware", + "description": "Utensils with an open top that are used to hold liquids for consumption." + }, + "Cup [ENVO:03501330]": { + "text": "Cup [ENVO:03501330]", + "description": "A utensil which is a hand-sized container with an open top. A cup may be used to hold liquids for pouring or drinking, or to store solids for pouring.", + "meaning": "ENVO:03501330", + "is_a": "Drinkware" }, "Tableware": { - "text": "Tableware" + "text": "Tableware", + "description": "Items used in setting a table and serving food and beverages. This includes various utensils, plates, bowls, cups, glasses, and serving dishes designed for dining and drinking." }, "Dish": { "text": "Dish", + "description": "A flat, typically round or oval item used for holding or serving food. It can also refer to a specific type of plate, often used to describe the container itself, such as a \"plate dish\" which is used for placing and serving individual portions of food.", "is_a": "Tableware" }, - "Utensil": { - "text": "Utensil", + "Eating utensil [ENVO:03501353]": { + "text": "Eating utensil [ENVO:03501353]", + "description": "A utensil used for consuming food.", + "meaning": "ENVO:03501353", "is_a": "Tableware" + }, + "Wastewater": { + "text": "Wastewater", + "description": "Water that has been adversely affected in quality by anthropogenic influence.", + "meaning": "ENVO:00002001" } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Amniocentesis": { "text": "Amniocentesis", + "description": "A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus.", "meaning": "NCIT:C52009" }, "Aspiration": { "text": "Aspiration", + "description": "Inspiration of a foreign object into the airway.", "meaning": "NCIT:C15631" }, "Suprapubic Aspiration": { "text": "Suprapubic Aspiration", + "description": "An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample.", "meaning": "GENEPIO:0100028", "is_a": "Aspiration" }, "Tracheal aspiration": { "text": "Tracheal aspiration", + "description": "An aspiration process which collects tracheal secretions.", "meaning": "GENEPIO:0100029", "is_a": "Aspiration" }, "Vacuum Aspiration": { "text": "Vacuum Aspiration", + "description": "An aspiration process which uses a vacuum source to remove a sample.", "meaning": "GENEPIO:0100030", "is_a": "Aspiration" }, "Biopsy": { "text": "Biopsy", + "description": "A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.", "meaning": "OBI:0002650" }, "Needle Biopsy": { "text": "Needle Biopsy", + "description": "A biopsy that uses a hollow needle to extract cells.", "meaning": "OBI:0002651", "is_a": "Biopsy" }, "Filtration": { "text": "Filtration", + "description": "Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device", "meaning": "OBI:0302885" }, "Air filtration": { "text": "Air filtration", + "description": "A filtration process which removes solid particulates from the air via an air filtration device.", "meaning": "GENEPIO:0100031", "is_a": "Filtration" }, "Lavage": { "text": "Lavage", + "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid", "meaning": "OBI:0600044" }, "Bronchoalveolar lavage (BAL)": { "text": "Bronchoalveolar lavage (BAL)", + "description": "The collection of bronchoalveolar lavage fluid (BAL) from the lungs.", "meaning": "GENEPIO:0100032", "is_a": "Lavage" }, "Gastric Lavage": { "text": "Gastric Lavage", + "description": "The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach.", "meaning": "GENEPIO:0100033", "is_a": "Lavage" }, "Lumbar Puncture": { "text": "Lumbar Puncture", + "description": "An invasive procedure in which a hollow needle is introduced through an intervertebral space in the lower back to access the subarachnoid space in order to sample cerebrospinal fluid or to administer medication.", "meaning": "NCIT:C15327" }, "Necropsy": { "text": "Necropsy", + "description": "A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease.", "meaning": "MMO:0000344" }, "Phlebotomy": { "text": "Phlebotomy", + "description": "The collection of blood from a vein, most commonly via needle venipuncture.", "meaning": "NCIT:C28221" }, "Rinsing": { "text": "Rinsing", + "description": "The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.", "meaning": "GENEPIO:0002116" }, "Saline gargle (mouth rinse and gargle)": { "text": "Saline gargle (mouth rinse and gargle)", + "description": "A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device.", "meaning": "GENEPIO:0100034", "is_a": "Rinsing" }, "Scraping": { "text": "Scraping", + "description": "A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device.", "meaning": "GENEPIO:0100035" }, "Swabbing": { "text": "Swabbing", + "description": "The process of collecting specimen material using a swab collection device.", "meaning": "GENEPIO:0002117" }, "Finger Prick": { "text": "Finger Prick", + "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.", "meaning": "GENEPIO:0100036", "is_a": "Swabbing" }, "Thoracentesis (chest tap)": { "text": "Thoracentesis (chest tap)", + "description": "The removal of excess fluid via needle puncture from the thoracic cavity.", "meaning": "NCIT:C15392" } } }, - "collection method international menu": { - "name": "collection method international menu", + "CollectionMethodInternationalMenu": { + "name": "CollectionMethodInternationalMenu", + "title": "collection method international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Amniocentesis [NCIT:C52009]": { "text": "Amniocentesis [NCIT:C52009]", + "description": "A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus.", "meaning": "NCIT:C52009" }, "Aspiration [NCIT:C15631]": { "text": "Aspiration [NCIT:C15631]", + "description": "Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue.", "meaning": "NCIT:C15631" }, "Suprapubic Aspiration [GENEPIO:0100028]": { "text": "Suprapubic Aspiration [GENEPIO:0100028]", + "description": "An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample.", "meaning": "GENEPIO:0100028", "is_a": "Aspiration [NCIT:C15631]" }, "Tracheal aspiration [GENEPIO:0100029]": { "text": "Tracheal aspiration [GENEPIO:0100029]", + "description": "An aspiration process which collects tracheal secretions.", "meaning": "GENEPIO:0100029", "is_a": "Aspiration [NCIT:C15631]" }, "Vacuum Aspiration [GENEPIO:0100030]": { "text": "Vacuum Aspiration [GENEPIO:0100030]", + "description": "An aspiration process which uses a vacuum source to remove a sample.", "meaning": "GENEPIO:0100030", "is_a": "Aspiration [NCIT:C15631]" }, "Biopsy [OBI:0002650]": { "text": "Biopsy [OBI:0002650]", + "description": "A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.", "meaning": "OBI:0002650" }, "Needle Biopsy [OBI:0002651]": { "text": "Needle Biopsy [OBI:0002651]", + "description": "A biopsy that uses a hollow needle to extract cells.", "meaning": "OBI:0002651", "is_a": "Biopsy [OBI:0002650]" }, "Filtration [OBI:0302885]": { "text": "Filtration [OBI:0302885]", + "description": "Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device.", "meaning": "OBI:0302885" }, "Air filtration [GENEPIO:0100031]": { "text": "Air filtration [GENEPIO:0100031]", + "description": "A filtration process which removes solid particulates from the air via an air filtration device.", "meaning": "GENEPIO:0100031", "is_a": "Filtration [OBI:0302885]" }, "Lavage [OBI:0600044]": { "text": "Lavage [OBI:0600044]", + "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid.", "meaning": "OBI:0600044" }, "Bronchoalveolar lavage (BAL) [GENEPIO:0100032]": { "text": "Bronchoalveolar lavage (BAL) [GENEPIO:0100032]", + "description": "The collection of bronchoalveolar lavage fluid (BAL) from the lungs.", "meaning": "GENEPIO:0100032", "is_a": "Lavage [OBI:0600044]" }, "Gastric Lavage [GENEPIO:0100033]": { "text": "Gastric Lavage [GENEPIO:0100033]", + "description": "The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach.", "meaning": "GENEPIO:0100033", "is_a": "Lavage [OBI:0600044]" }, "Lumbar Puncture [NCIT:C15327]": { "text": "Lumbar Puncture [NCIT:C15327]", + "description": "An invasive procedure in which a hollow needle is introduced through an intervertebral space in the lower back to access the subarachnoid space in order to sample cerebrospinal fluid or to administer medication.", "meaning": "NCIT:C15327" }, "Necropsy [MMO:0000344]": { "text": "Necropsy [MMO:0000344]", + "description": "A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease.", "meaning": "MMO:0000344" }, "Phlebotomy [NCIT:C28221]": { "text": "Phlebotomy [NCIT:C28221]", + "description": "The collection of blood from a vein, most commonly via needle venipuncture.", "meaning": "NCIT:C28221" }, "Rinsing [GENEPIO:0002116]": { "text": "Rinsing [GENEPIO:0002116]", + "description": "The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.", "meaning": "GENEPIO:0002116" }, "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]": { "text": "Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]", + "description": "A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device.", "meaning": "GENEPIO:0100034", "is_a": "Rinsing [GENEPIO:0002116]" }, "Scraping [GENEPIO:0100035]": { "text": "Scraping [GENEPIO:0100035]", + "description": "A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device.", "meaning": "GENEPIO:0100035" }, "Swabbing [GENEPIO:0002117]": { "text": "Swabbing [GENEPIO:0002117]", + "description": "The process of collecting specimen material using a swab collection device.", "meaning": "GENEPIO:0002117" }, "Finger Prick [GENEPIO:0100036]": { "text": "Finger Prick [GENEPIO:0100036]", + "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.", "meaning": "GENEPIO:0100036", "is_a": "Swabbing [GENEPIO:0002117]" }, "Thoracentesis (chest tap) [NCIT:C15392]": { "text": "Thoracentesis (chest tap) [NCIT:C15392]", + "description": "The removal of excess fluid via needle puncture from the thoracic cavity.", "meaning": "NCIT:C15392" } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Blood Collection Tube": { "text": "Blood Collection Tube", + "description": "A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection", "meaning": "OBI:0002859" }, "Bronchoscope": { "text": "Bronchoscope", + "description": "A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung.", "meaning": "OBI:0002826" }, "Collection Container": { "text": "Collection Container", + "description": "A container with the function of containing a specimen.", "meaning": "OBI:0002088" }, "Collection Cup": { "text": "Collection Cup", + "description": "A device which is used to collect liquid samples.", "meaning": "GENEPIO:0100026" }, "Filter": { "text": "Filter", + "description": "A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass.", "meaning": "GENEPIO:0100103" }, "Needle": { "text": "Needle", + "description": "A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.", "meaning": "OBI:0000436" }, "Serum Collection Tube": { "text": "Serum Collection Tube", + "description": "A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum.", "meaning": "OBI:0002860" }, "Sputum Collection Tube": { "text": "Sputum Collection Tube", + "description": "A specimen collection tube which is designed for collecting sputum.", "meaning": "OBI:0002861" }, "Suction Catheter": { "text": "Suction Catheter", + "description": "A catheter which is used to remove mucus and other secretions from the body.", "meaning": "OBI:0002831" }, "Swab": { "text": "Swab", + "description": "A device which is a soft, absorbent material mounted on one or both ends of a stick.", "meaning": "GENEPIO:0100027" }, "Dry swab": { "text": "Dry swab", + "description": "A swab device that consists of soft, absorbent material mounted on one or both ends of a stick, designed to collect samples without the presence of a liquid or preservative medium.", "meaning": "GENEPIO:0100493", "is_a": "Swab" }, "Urine Collection Tube": { "text": "Urine Collection Tube", + "description": "A specimen container which is designed for holding urine.", "meaning": "OBI:0002862" }, "Universal Transport Medium (UTM)": { "text": "Universal Transport Medium (UTM)", + "description": "A sterile, balanced medium designed to preserve and transport clinical specimens, such as viruses, bacteria, and mycoplasma, ensuring the viability of the sample for subsequent analysis or culture.", "meaning": "GENEPIO:0100509" }, "Virus Transport Medium": { "text": "Virus Transport Medium", + "description": "A medium designed to promote longevity of a viral sample. FROM Corona19", "meaning": "OBI:0002866" } } }, - "collection device international menu": { - "name": "collection device international menu", + "CollectionDeviceInternationalMenu": { + "name": "CollectionDeviceInternationalMenu", + "title": "collection device international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Blood Collection Tube [OBI:0002859]": { "text": "Blood Collection Tube [OBI:0002859]", + "description": "A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection", "meaning": "OBI:0002859" }, "Bronchoscope [OBI:0002826]": { "text": "Bronchoscope [OBI:0002826]", + "description": "A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung.", "meaning": "OBI:0002826" }, "Collection Container [OBI:0002088]": { "text": "Collection Container [OBI:0002088]", + "description": "A container with the function of containing a specimen.", "meaning": "OBI:0002088" }, "Collection Cup [GENEPIO:0100026]": { "text": "Collection Cup [GENEPIO:0100026]", + "description": "A device which is used to collect liquid samples.", "meaning": "GENEPIO:0100026" }, "Filter [GENEPIO:0100103]": { "text": "Filter [GENEPIO:0100103]", + "description": "A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass.", "meaning": "GENEPIO:0100103" }, "Needle [OBI:0000436]": { "text": "Needle [OBI:0000436]", + "description": "A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.", "meaning": "OBI:0000436" }, "Serum Collection Tube [OBI:0002860]": { "text": "Serum Collection Tube [OBI:0002860]", + "description": "A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum.", "meaning": "OBI:0002860" }, "Sputum Collection Tube [OBI:0002861]": { "text": "Sputum Collection Tube [OBI:0002861]", + "description": "A specimen collection tube which is designed for collecting sputum.", "meaning": "OBI:0002861" }, "Suction Catheter [OBI:0002831]": { "text": "Suction Catheter [OBI:0002831]", + "description": "A catheter which is used to remove mucus and other secretions from the body.", "meaning": "OBI:0002831" }, "Swab [GENEPIO:0100027]": { "text": "Swab [GENEPIO:0100027]", + "description": "A device which is a soft, absorbent material mounted on one or both ends of a stick.", "meaning": "GENEPIO:0100027" }, "Dry swab [GENEPIO:0100493]": { "text": "Dry swab [GENEPIO:0100493]", + "description": "A swab device that consists of soft, absorbent material mounted on one or both ends of a stick, designed to collect samples without the presence of a liquid or preservative medium.", "meaning": "GENEPIO:0100493", "is_a": "Swab [GENEPIO:0100027]" }, "Urine Collection Tube [OBI:0002862]": { "text": "Urine Collection Tube [OBI:0002862]", + "description": "A specimen container which is designed for holding urine.", "meaning": "OBI:0002862" }, "Universal Transport Medium (UTM) [GENEPIO:0100509]": { "text": "Universal Transport Medium (UTM) [GENEPIO:0100509]", + "description": "A sterile, balanced medium designed to preserve and transport clinical specimens, such as viruses, bacteria, and mycoplasma, ensuring the viability of the sample for subsequent analysis or culture.", "meaning": "GENEPIO:0100509" }, "Virus Transport Medium [OBI:0002866]": { "text": "Virus Transport Medium [OBI:0002866]", + "description": "A medium designed to promote longevity of a viral sample. FROM Corona19", "meaning": "OBI:0002866" } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Virus passage": { "text": "Virus passage", + "description": "The process of growing a virus in serial iterations.", "meaning": "GENEPIO:0100039" }, - "RNA re-extraction (post RT-PCR)": { - "text": "RNA re-extraction (post RT-PCR)", - "meaning": "GENEPIO:0100040" - }, "Specimens pooled": { "text": "Specimens pooled", + "description": "Physical combination of several instances of like material.", "meaning": "OBI:0600016" } } }, - "specimen processing international menu": { - "name": "specimen processing international menu", + "SpecimenProcessingInternationalMenu": { + "name": "SpecimenProcessingInternationalMenu", + "title": "specimen processing international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Virus passage [GENEPIO:0100039]": { "text": "Virus passage [GENEPIO:0100039]", + "description": "The process of growing a virus in serial iterations.", "meaning": "GENEPIO:0100039" }, - "RNA re-extraction (post RT-PCR) [GENEPIO:0100040]": { - "text": "RNA re-extraction (post RT-PCR) [GENEPIO:0100040]", - "meaning": "GENEPIO:0100040" - }, "Specimens pooled [OBI:0600016]": { "text": "Specimens pooled [OBI:0600016]", + "description": "Physical combination of several instances of like material.", "meaning": "OBI:0600016" } } }, - "host (common name) menu": { - "name": "host (common name) menu", + "ExperimentalSpecimenRoleTypeMenu": { + "name": "ExperimentalSpecimenRoleTypeMenu", + "title": "experimental specimen role type menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Positive experimental control": { + "text": "Positive experimental control", + "description": "A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment.", + "meaning": "GENEPIO:0101018" + }, + "Negative experimental control": { + "text": "Negative experimental control", + "description": "A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment", + "meaning": "GENEPIO:0101019" + }, + "Technical replicate": { + "text": "Technical replicate", + "description": "A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.", + "meaning": "EFO:0002090" + }, + "Biological replicate": { + "text": "Biological replicate", + "description": "A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples.", + "meaning": "EFO:0002091" + } + } + }, + "ExperimentalSpecimenRoleTypeInternationalMenu": { + "name": "ExperimentalSpecimenRoleTypeInternationalMenu", + "title": "experimental specimen role type international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Positive experimental control [GENEPIO:0101018]": { + "text": "Positive experimental control [GENEPIO:0101018]", + "description": "A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment.", + "meaning": "GENEPIO:0101018" + }, + "Negative experimental control [GENEPIO:0101019]": { + "text": "Negative experimental control [GENEPIO:0101019]", + "description": "A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment", + "meaning": "GENEPIO:0101019" + }, + "Technical replicate [EFO:0002090]": { + "text": "Technical replicate [EFO:0002090]", + "description": "A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.", + "meaning": "EFO:0002090" + }, + "Biological replicate [EFO:0002091]": { + "text": "Biological replicate [EFO:0002091]", + "description": "A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples.", + "meaning": "EFO:0002091" + } + } + }, + "LineageCladeNameInternationalMenu": { + "name": "LineageCladeNameInternationalMenu", + "title": "lineage/clade name international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Mpox virus clade I [GENEPIO:0102029]": { + "text": "Mpox virus clade I [GENEPIO:0102029]", + "description": "An Mpox virus clade with at least 99% similarity to the West African/USA-derived Mpox strain.", + "meaning": "GENEPIO:0102029" + }, + "Mpox virus clade Ia [GENEPIO:0102030]": { + "text": "Mpox virus clade Ia [GENEPIO:0102030]", + "description": "An Mpox virus that clusters in phylogenetic trees within the Ia clade.", + "meaning": "GENEPIO:0102030", + "is_a": "Mpox virus clade I [GENEPIO:0102029]" + }, + "Mpox virus clade Ib [GENEPIO:0102031]": { + "text": "Mpox virus clade Ib [GENEPIO:0102031]", + "description": "An Mpox virus that clusters in phylogenetic trees within the Ib clade.", + "meaning": "GENEPIO:0102031", + "is_a": "Mpox virus clade I [GENEPIO:0102029]" + }, + "Mpox virus clade II [GENEPIO:0102032]": { + "text": "Mpox virus clade II [GENEPIO:0102032]", + "description": "An Mpox virus clade with at least 99% similarity to the Congo Basin-derived Mpox strain.", + "meaning": "GENEPIO:0102032" + }, + "Mpox virus clade IIa [GENEPIO:0102033]": { + "text": "Mpox virus clade IIa [GENEPIO:0102033]", + "description": "An Mpox virus that clusters in phylogenetic trees within the IIa clade.", + "meaning": "GENEPIO:0102033", + "is_a": "Mpox virus clade II [GENEPIO:0102032]" + }, + "Mpox virus clade IIb [GENEPIO:0102034]": { + "text": "Mpox virus clade IIb [GENEPIO:0102034]", + "description": "An Mpox virus that clusters in phylogenetic trees within the IIb clade.", + "meaning": "GENEPIO:0102034", + "is_a": "Mpox virus clade II [GENEPIO:0102032]" + }, + "Mpox virus lineage B.1": { + "text": "Mpox virus lineage B.1", + "is_a": "Mpox virus clade IIb [GENEPIO:0102034]" + }, + "Mpox virus lineage A": { + "text": "Mpox virus lineage A", + "is_a": "Mpox virus clade IIb [GENEPIO:0102034]" + } + } + }, + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Human": { "text": "Human", + "description": "A bipedal primate mammal of the species Homo sapiens.", "meaning": "NCBITaxon:9606" } } }, - "host (common name) international menu": { - "name": "host (common name) international menu", + "HostCommonNameInternationalMenu": { + "name": "HostCommonNameInternationalMenu", + "title": "host (common name) international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Human [NCBITaxon:9606]": { "text": "Human [NCBITaxon:9606]", + "description": "A bipedal primate mammal of the species Homo sapiens.", "meaning": "NCBITaxon:9606" }, - "Rodent": { - "text": "Rodent", + "Rodent [NCBITaxon:9989]": { + "text": "Rodent [NCBITaxon:9989]", + "description": "A mammal of the order Rodentia which are characterized by a single pair of continuously growing incisors in each of the upper and lower jaws.", "meaning": "NCBITaxon:9989" }, - "Mouse": { - "text": "Mouse", + "Mouse [NCBITaxon:10090]": { + "text": "Mouse [NCBITaxon:10090]", + "description": "A small rodent that typically has a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate.", "meaning": "NCBITaxon:10090", - "is_a": "Rodent" + "is_a": "Rodent [NCBITaxon:9989]" }, - "Prairie Dog": { - "text": "Prairie Dog", - "is_a": "Rodent" + "Prairie Dog [NCBITaxon:45478]": { + "text": "Prairie Dog [NCBITaxon:45478]", + "description": "A herbivorous burrowing ground squirrels native to the grasslands of North America.", + "meaning": "NCBITaxon:45478", + "is_a": "Rodent [NCBITaxon:9989]" }, - "Rat": { - "text": "Rat", + "Rat [NCBITaxon:10116]": { + "text": "Rat [NCBITaxon:10116]", + "description": "A medium sized rodent that typically is long tailed.", "meaning": "NCBITaxon:10116", - "is_a": "Rodent" + "is_a": "Rodent [NCBITaxon:9989]" }, - "Squirrel": { - "text": "Squirrel", + "Squirrel [FOODON:03411389]": { + "text": "Squirrel [FOODON:03411389]", + "description": "A small to medium-sized rodent belonging to the family Sciuridae, characterized by a bushy tail, sharp claws, and strong hind legs, commonly found in trees, but some species live on the ground", "meaning": "FOODON:03411389", - "is_a": "Rodent" + "is_a": "Rodent [NCBITaxon:9989]" } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Homo sapiens": { "text": "Homo sapiens", + "description": "A type of primate characterized by bipedalism and large, complex brain.", "meaning": "NCBITaxon:9606" } } }, - "host (scientific name) international menu": { - "name": "host (scientific name) international menu", + "HostScientificNameInternationalMenu": { + "name": "HostScientificNameInternationalMenu", + "title": "host (scientific name) international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Homo sapiens [NCBITaxon:9606]": { "text": "Homo sapiens [NCBITaxon:9606]", + "description": "A bipedal primate mammal of the species Homo sapiens.", "meaning": "NCBITaxon:9606" } } }, - "host health state menu": { - "name": "host health state menu", + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "host health state menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Asymptomatic": { "text": "Asymptomatic", + "description": "Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.", "meaning": "NCIT:C3833" }, "Deceased": { "text": "Deceased", + "description": "The cessation of life.", "meaning": "NCIT:C28554" }, "Healthy": { "text": "Healthy", + "description": "Having no significant health-related issues.", "meaning": "NCIT:C115935" }, "Recovered": { "text": "Recovered", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", "meaning": "NCIT:C49498" }, "Symptomatic": { "text": "Symptomatic", + "description": "Exhibiting the symptoms of a particular disease.", "meaning": "NCIT:C25269" } } }, - "host health state international menu": { - "name": "host health state international menu", + "HostHealthStateInternationalMenu": { + "name": "HostHealthStateInternationalMenu", + "title": "host health state international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Asymptomatic [NCIT:C3833]": { "text": "Asymptomatic [NCIT:C3833]", + "description": "Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.", "meaning": "NCIT:C3833" }, "Deceased [NCIT:C28554]": { "text": "Deceased [NCIT:C28554]", + "description": "The cessation of life.", "meaning": "NCIT:C28554" }, "Healthy [NCIT:C115935]": { "text": "Healthy [NCIT:C115935]", + "description": "Having no significant health-related issues.", "meaning": "NCIT:C115935" }, "Recovered [NCIT:C49498]": { "text": "Recovered [NCIT:C49498]", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", "meaning": "NCIT:C49498" }, "Symptomatic [NCIT:C25269]": { "text": "Symptomatic [NCIT:C25269]", + "description": "Exhibiting the symptoms of a particular disease.", "meaning": "NCIT:C25269" } } }, - "host health status details menu": { - "name": "host health status details menu", + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "host health status details menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Hospitalized": { "text": "Hospitalized", + "description": "The condition of being treated as a patient in a hospital.", "meaning": "NCIT:C25179" }, "Hospitalized (Non-ICU)": { "text": "Hospitalized (Non-ICU)", + "description": "The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU).", "meaning": "GENEPIO:0100045", "is_a": "Hospitalized" }, "Hospitalized (ICU)": { "text": "Hospitalized (ICU)", + "description": "The condition of being treated as a patient in a hospital intensive care unit (ICU).", "meaning": "GENEPIO:0100046", "is_a": "Hospitalized" }, "Medically Isolated": { "text": "Medically Isolated", + "description": "Separation of people with a contagious disease from population to reduce the spread of the disease.", "meaning": "GENEPIO:0100047" }, "Medically Isolated (Negative Pressure)": { "text": "Medically Isolated (Negative Pressure)", + "description": "Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter.", "meaning": "GENEPIO:0100048", "is_a": "Medically Isolated" }, "Self-quarantining": { "text": "Self-quarantining", + "description": "A method used by an individual to be kept apart in seclusion from others for a period of time in an attempt to minimize the risk of transmission of an infectious disease.", "meaning": "NCIT:C173768" } } }, - "host health status details international menu": { - "name": "host health status details international menu", + "HostHealthStatusDetailsInternationalMenu": { + "name": "HostHealthStatusDetailsInternationalMenu", + "title": "host health status details international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Hospitalized [NCIT:C25179]": { "text": "Hospitalized [NCIT:C25179]", + "description": "The condition of being treated as a patient in a hospital.", "meaning": "NCIT:C25179" }, "Hospitalized (Non-ICU) [GENEPIO:0100045]": { "text": "Hospitalized (Non-ICU) [GENEPIO:0100045]", + "description": "The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU).", "meaning": "GENEPIO:0100045", "is_a": "Hospitalized [NCIT:C25179]" }, "Hospitalized (ICU) [GENEPIO:0100046]": { "text": "Hospitalized (ICU) [GENEPIO:0100046]", + "description": "The condition of being treated as a patient in a hospital intensive care unit (ICU).", "meaning": "GENEPIO:0100046", "is_a": "Hospitalized [NCIT:C25179]" }, "Medically Isolated [GENEPIO:0100047]": { "text": "Medically Isolated [GENEPIO:0100047]", + "description": "Separation of people with a contagious disease from population to reduce the spread of the disease.", "meaning": "GENEPIO:0100047" }, "Medically Isolated (Negative Pressure) [GENEPIO:0100048]": { "text": "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", + "description": "Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter.", "meaning": "GENEPIO:0100048", "is_a": "Medically Isolated [GENEPIO:0100047]" }, "Self-quarantining [NCIT:C173768]": { "text": "Self-quarantining [NCIT:C173768]", + "description": "A method used by an individual to be kept apart in seclusion from others for a period of time in an attempt to minimize the risk of transmission of an infectious disease.", "meaning": "NCIT:C173768" } } }, - "host health outcome menu": { - "name": "host health outcome menu", + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "host health outcome menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Deceased": { "text": "Deceased", + "description": "The cessation of life.", "meaning": "NCIT:C28554" }, "Deteriorating": { "text": "Deteriorating", + "description": "Advancing in extent or severity.", "meaning": "NCIT:C25254" }, "Recovered": { "text": "Recovered", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", "meaning": "NCIT:C49498" }, "Stable": { "text": "Stable", + "description": "Subject to little fluctuation; showing little if any change.", "meaning": "NCIT:C30103" } } }, - "host health outcome international menu": { - "name": "host health outcome international menu", + "HostHealthOutcomeInternationalMenu": { + "name": "HostHealthOutcomeInternationalMenu", + "title": "host health outcome international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Deceased [NCIT:C28554]": { "text": "Deceased [NCIT:C28554]", + "description": "The cessation of life.", "meaning": "NCIT:C28554" }, "Deteriorating [NCIT:C25254]": { "text": "Deteriorating [NCIT:C25254]", + "description": "Advancing in extent or severity.", "meaning": "NCIT:C25254" }, "Recovered [NCIT:C49498]": { "text": "Recovered [NCIT:C49498]", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", "meaning": "NCIT:C49498" }, "Stable [NCIT:C30103]": { "text": "Stable [NCIT:C30103]", + "description": "Subject to little fluctuation; showing little if any change.", "meaning": "NCIT:C30103" } } }, - "host age unit menu": { - "name": "host age unit menu", + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host age unit menu", "from_schema": "https://example.com/mpox", "permissible_values": { "month": { "text": "month", + "description": "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.", "meaning": "UO:0000035" }, "year": { "text": "year", + "description": "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.", "meaning": "UO:0000036" } } }, - "host age unit international menu": { - "name": "host age unit international menu", + "HostAgeUnitInternationalMenu": { + "name": "HostAgeUnitInternationalMenu", + "title": "host age unit international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "month [UO:0000035]": { "text": "month [UO:0000035]", + "description": "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.", "meaning": "UO:0000035" }, "year [UO:0000036]": { "text": "year [UO:0000036]", + "description": "A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days.", "meaning": "UO:0000036" } } }, - "host age bin menu": { - "name": "host age bin menu", + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host age bin menu", "from_schema": "https://example.com/mpox", "permissible_values": { "0 - 9": { "text": "0 - 9", + "description": "An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive).", "meaning": "GENEPIO:0100049" }, "10 - 19": { "text": "10 - 19", + "description": "An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive).", "meaning": "GENEPIO:0100050" }, "20 - 29": { "text": "20 - 29", + "description": "An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive).", "meaning": "GENEPIO:0100051" }, "30 - 39": { "text": "30 - 39", + "description": "An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive).", "meaning": "GENEPIO:0100052" }, "40 - 49": { "text": "40 - 49", + "description": "An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive).", "meaning": "GENEPIO:0100053" }, "50 - 59": { "text": "50 - 59", + "description": "An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive).", "meaning": "GENEPIO:0100054" }, "60 - 69": { "text": "60 - 69", + "description": "An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive).", "meaning": "GENEPIO:0100055" }, "70 - 79": { "text": "70 - 79", + "description": "An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive).", "meaning": "GENEPIO:0100056" }, "80 - 89": { "text": "80 - 89", + "description": "An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive).", "meaning": "GENEPIO:0100057" }, "90 - 99": { "text": "90 - 99", + "description": "An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive).", "meaning": "GENEPIO:0100058" }, "100+": { "text": "100+", + "description": "An age group that stratifies the age of a case to be greater than or equal to 100 years old.", "meaning": "GENEPIO:0100059" } } }, - "host age bin international menu": { - "name": "host age bin international menu", + "HostAgeBinInternationalMenu": { + "name": "HostAgeBinInternationalMenu", + "title": "host age bin international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "0 - 9 [GENEPIO:0100049]": { "text": "0 - 9 [GENEPIO:0100049]", + "description": "An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive).", "meaning": "GENEPIO:0100049" }, "10 - 19 [GENEPIO:0100050]": { "text": "10 - 19 [GENEPIO:0100050]", + "description": "An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive).", "meaning": "GENEPIO:0100050" }, "20 - 29 [GENEPIO:0100051]": { "text": "20 - 29 [GENEPIO:0100051]", + "description": "An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive).", "meaning": "GENEPIO:0100051" }, "30 - 39 [GENEPIO:0100052]": { "text": "30 - 39 [GENEPIO:0100052]", + "description": "An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive).", "meaning": "GENEPIO:0100052" }, "40 - 49 [GENEPIO:0100053]": { "text": "40 - 49 [GENEPIO:0100053]", + "description": "An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive).", "meaning": "GENEPIO:0100053" }, "50 - 59 [GENEPIO:0100054]": { "text": "50 - 59 [GENEPIO:0100054]", + "description": "An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive).", "meaning": "GENEPIO:0100054" }, "60 - 69 [GENEPIO:0100055]": { "text": "60 - 69 [GENEPIO:0100055]", + "description": "An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive).", "meaning": "GENEPIO:0100055" }, "70 - 79 [GENEPIO:0100056]": { "text": "70 - 79 [GENEPIO:0100056]", + "description": "An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive).", "meaning": "GENEPIO:0100056" }, "80 - 89 [GENEPIO:0100057]": { "text": "80 - 89 [GENEPIO:0100057]", + "description": "An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive).", "meaning": "GENEPIO:0100057" }, "90 - 99 [GENEPIO:0100058]": { "text": "90 - 99 [GENEPIO:0100058]", + "description": "An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive).", "meaning": "GENEPIO:0100058" }, "100+ [GENEPIO:0100059]": { "text": "100+ [GENEPIO:0100059]", + "description": "An age group that stratifies the age of a case to be greater than or equal to 100 years old.", "meaning": "GENEPIO:0100059" } } }, - "host gender menu": { - "name": "host gender menu", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host gender menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Female": { "text": "Female", + "description": "An individual who reports belonging to the cultural gender role distinction of female.", "meaning": "NCIT:C46110" }, "Male": { "text": "Male", + "description": "An individual who reports belonging to the cultural gender role distinction of male.", "meaning": "NCIT:C46109" }, "Non-binary gender": { "text": "Non-binary gender", + "description": "Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female.", "meaning": "GSSO:000132" }, "Transgender (assigned male at birth)": { "text": "Transgender (assigned male at birth)", + "description": "Having a feminine gender (identity) which is different from the sex one was assigned at birth.", "meaning": "GSSO:004004" }, "Transgender (assigned female at birth)": { "text": "Transgender (assigned female at birth)", + "description": "Having a masculine gender (identity) which is different from the sex one was assigned at birth.", "meaning": "GSSO:004005" }, "Undeclared": { "text": "Undeclared", + "description": "A categorical choice recorded when an individual being interviewed is unable or chooses not to provide a datum.", "meaning": "NCIT:C110959" } } }, - "host gender international menu": { - "name": "host gender international menu", + "HostGenderInternationalMenu": { + "name": "HostGenderInternationalMenu", + "title": "host gender international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Female [NCIT:C46110]": { "text": "Female [NCIT:C46110]", + "description": "An individual who reports belonging to the cultural gender role distinction of female.", "meaning": "NCIT:C46110" }, "Male [NCIT:C46109]": { "text": "Male [NCIT:C46109]", + "description": "An individual who reports belonging to the cultural gender role distinction of male.", "meaning": "NCIT:C46109" }, "Non-binary gender [GSSO:000132]": { "text": "Non-binary gender [GSSO:000132]", + "description": "Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female.", "meaning": "GSSO:000132" }, "Transgender (assigned male at birth) [GSSO:004004]": { "text": "Transgender (assigned male at birth) [GSSO:004004]", + "description": "Having a feminine gender (identity) which is different from the sex one was assigned at birth.", "meaning": "GSSO:004004" }, "Transgender (assigned female at birth) [GSSO:004005]": { "text": "Transgender (assigned female at birth) [GSSO:004005]", + "description": "Having a masculine gender (identity) which is different from the sex one was assigned at birth.", "meaning": "GSSO:004005" }, "Undeclared [NCIT:C110959]": { "text": "Undeclared [NCIT:C110959]", + "description": "A categorical choice recorded when an individual being interviewed is unable or chooses not to provide a datum.", "meaning": "NCIT:C110959" } } }, - "signs and symptoms menu": { - "name": "signs and symptoms menu", + "SignsAndSymptomsMenu": { + "name": "SignsAndSymptomsMenu", + "title": "signs and symptoms menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Chills (sudden cold sensation)": { @@ -2095,30 +2597,36 @@ }, "Lesion": { "text": "Lesion", + "description": "A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part.", "meaning": "NCIT:C3824" }, "Lesion (Macule)": { "text": "Lesion (Macule)", + "description": "A flat lesion characterized by change in the skin color.", "meaning": "NCIT:C43278", "is_a": "Lesion" }, "Lesion (Papule)": { "text": "Lesion (Papule)", + "description": "A small (less than 5-10 mm) elevation of skin that is non-suppurative.", "meaning": "NCIT:C39690", "is_a": "Lesion" }, "Lesion (Pustule)": { "text": "Lesion (Pustule)", + "description": "A circumscribed and elevated skin lesion filled with purulent material.", "meaning": "NCIT:C78582", "is_a": "Lesion" }, "Lesion (Scab)": { "text": "Lesion (Scab)", + "description": "Dried purulent material on the skin from a skin lesion.", "meaning": "GENEPIO:0100490", "is_a": "Lesion" }, "Lesion (Vesicle)": { "text": "Lesion (Vesicle)", + "description": "Small, inflamed, pus-filled, blister-like sores (lesions) on the skin surface.", "meaning": "GENEPIO:0100491", "is_a": "Lesion" }, @@ -2129,6 +2637,7 @@ }, "Back pain": { "text": "Back pain", + "description": "An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.", "meaning": "HP:0003418", "is_a": "Myalgia (muscle pain)" }, @@ -2149,6 +2658,7 @@ }, "Sweating": { "text": "Sweating", + "description": "A watery secretion by the sweat glands that is primarily composed of salt, urea and minerals.", "meaning": "NCIT:C36172" }, "Swollen Lymph Nodes": { @@ -2158,6 +2668,7 @@ }, "Ulcer": { "text": "Ulcer", + "description": "A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue.", "meaning": "NCIT:C3426" }, "Vomiting (throwing up)": { @@ -2167,8 +2678,9 @@ } } }, - "signs and symptoms international menu": { - "name": "signs and symptoms international menu", + "SignsAndSymptomsInternationalMenu": { + "name": "SignsAndSymptomsInternationalMenu", + "title": "signs and symptoms international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Chills (sudden cold sensation) [HP:0025143]": { @@ -2203,30 +2715,36 @@ }, "Lesion [NCIT:C3824]": { "text": "Lesion [NCIT:C3824]", + "description": "A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part.", "meaning": "NCIT:C3824" }, "Lesion (Macule) [NCIT:C43278]": { "text": "Lesion (Macule) [NCIT:C43278]", + "description": "A flat lesion characterized by change in the skin color.", "meaning": "NCIT:C43278", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Papule) [NCIT:C39690]": { "text": "Lesion (Papule) [NCIT:C39690]", + "description": "A small (less than 5-10 mm) elevation of skin that is non-suppurative.", "meaning": "NCIT:C39690", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Pustule) [NCIT:C78582]": { "text": "Lesion (Pustule) [NCIT:C78582]", + "description": "A circumscribed and elevated skin lesion filled with purulent material.", "meaning": "NCIT:C78582", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Scab) [GENEPIO:0100490]": { "text": "Lesion (Scab) [GENEPIO:0100490]", + "description": "Dried purulent material on the skin from a skin lesion.", "meaning": "GENEPIO:0100490", "is_a": "Lesion [NCIT:C3824]" }, "Lesion (Vesicle) [GENEPIO:0100491]": { "text": "Lesion (Vesicle) [GENEPIO:0100491]", + "description": "Small, inflamed, pus-filled, blister-like sores (lesions) on the skin surface.", "meaning": "GENEPIO:0100491", "is_a": "Lesion [NCIT:C3824]" }, @@ -2237,6 +2755,7 @@ }, "Back pain [HP:0003418]": { "text": "Back pain [HP:0003418]", + "description": "An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back.", "meaning": "HP:0003418", "is_a": "Myalgia (muscle pain) [HP:0003326]" }, @@ -2257,6 +2776,7 @@ }, "Sweating [NCIT:C36172]": { "text": "Sweating [NCIT:C36172]", + "description": "A watery secretion by the sweat glands that is primarily composed of salt, urea and minerals.", "meaning": "NCIT:C36172" }, "Swollen Lymph Nodes [HP:0002716]": { @@ -2266,6 +2786,7 @@ }, "Ulcer [NCIT:C3426]": { "text": "Ulcer [NCIT:C3426]", + "description": "A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue.", "meaning": "NCIT:C3426" }, "Vomiting (throwing up) [HP:0002013]": { @@ -2275,386 +2796,474 @@ } } }, - "pre-existing conditions and risk factors menu": { - "name": "pre-existing conditions and risk factors menu", + "PreExistingConditionsAndRiskFactorsMenu": { + "name": "PreExistingConditionsAndRiskFactorsMenu", + "title": "pre-existing conditions and risk factors menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Cancer": { "text": "Cancer", + "description": "A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.", "meaning": "MONDO:0004992" }, "Diabetes mellitus (diabetes)": { "text": "Diabetes mellitus (diabetes)", + "description": "A group of abnormalities characterized by hyperglycemia and glucose intolerance.", "meaning": "HP:0000819" }, "Type I diabetes mellitus (T1D)": { "text": "Type I diabetes mellitus (T1D)", + "description": "A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin.", "meaning": "HP:0100651", "is_a": "Diabetes mellitus (diabetes)" }, "Type II diabetes mellitus (T2D)": { "text": "Type II diabetes mellitus (T2D)", + "description": "A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.", "meaning": "HP:0005978", "is_a": "Diabetes mellitus (diabetes)" }, "Immunocompromised": { "text": "Immunocompromised", + "description": "A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions.", "meaning": "NCIT:C14139" }, "Infectious disorder": { "text": "Infectious disorder", + "description": "A disorder resulting from the presence and activity of a microbial, viral, fungal, or parasitic agent. It can be transmitted by direct or indirect contact.", "meaning": "NCIT:C26726" }, "Chancroid (Haemophilus ducreyi)": { "text": "Chancroid (Haemophilus ducreyi)", + "description": "A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers.", "meaning": "DOID:13778", "is_a": "Infectious disorder" }, "Chlamydia": { "text": "Chlamydia", + "description": "A commensal bacterial infectious disease that is caused by Chlamydia trachomatis.", "meaning": "DOID:11263", "is_a": "Infectious disorder" }, "Gonorrhea": { "text": "Gonorrhea", + "description": "A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods.", "meaning": "DOID:7551", "is_a": "Infectious disorder" }, "Herpes Simplex Virus infection (HSV)": { "text": "Herpes Simplex Virus infection (HSV)", + "description": "An infection that is caused by herpes simplex virus.", "meaning": "NCIT:C155871", "is_a": "Infectious disorder" }, "Human immunodeficiency virus (HIV)": { "text": "Human immunodeficiency virus (HIV)", + "description": "An infection caused by the human immunodeficiency virus.", "meaning": "MONDO:0005109", "is_a": "Infectious disorder" }, "Acquired immunodeficiency syndrome (AIDS)": { "text": "Acquired immunodeficiency syndrome (AIDS)", + "description": "A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes.", "meaning": "MONDO:0012268", "is_a": "Human immunodeficiency virus (HIV)" }, "Human papilloma virus infection (HPV)": { "text": "Human papilloma virus infection (HPV)", + "description": "An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth.", "meaning": "MONDO:0005161", "is_a": "Infectious disorder" }, "Lymphogranuloma venereum": { "text": "Lymphogranuloma venereum", + "description": "A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis.", "meaning": "DOID:13819", "is_a": "Infectious disorder" }, "Mycoplsma genitalium": { "text": "Mycoplsma genitalium", + "description": "A sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans.", "meaning": "NCBITaxon:2097", "is_a": "Infectious disorder" }, "Syphilis": { "text": "Syphilis", + "description": "A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years.", "meaning": "DOID:4166", "is_a": "Infectious disorder" }, "Trichomoniasis": { "text": "Trichomoniasis", + "description": "A parasitic protozoa infectious disease that is caused by singled-celled protozoan parasites Trichomonas vaginalis or Trichomonas tenax, which infect the urogenital tract and mouth respectively.", "meaning": "DOID:1947", "is_a": "Infectious disorder" }, "Lupus": { "text": "Lupus", + "description": "An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus.", "meaning": "MONDO:0004670" }, "Pregnancy": { "text": "Pregnancy", + "description": "The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.", "meaning": "NCIT:C25742" }, "Prior therapy": { "text": "Prior therapy", + "description": "Prior action or administration of therapeutic agents that produced an effect that is intended to alter or stop a pathologic process.", "meaning": "NCIT:C16124" }, "Cancer treatment": { "text": "Cancer treatment", + "description": "Any intervention for management of a malignant neoplasm.", "meaning": "NCIT:C16212", "is_a": "Prior therapy" }, "Chemotherapy": { "text": "Chemotherapy", + "description": "The use of synthetic or naturally-occurring chemicals for the treatment of diseases.", "meaning": "NCIT:C15632", "is_a": "Cancer treatment" }, "HIV and Antiretroviral therapy (ART)": { "text": "HIV and Antiretroviral therapy (ART)", + "description": "Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles.", "meaning": "NCIT:C16118", "is_a": "Prior therapy" }, "Steroid": { "text": "Steroid", + "description": "Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.", "meaning": "CHEBI:35341", "is_a": "Prior therapy" }, "Transplant": { "text": "Transplant", + "description": "An individual receiving a transplant.", "meaning": "NCIT:C159659" } } }, - "pre-existing conditions and risk factors international menu": { - "name": "pre-existing conditions and risk factors international menu", + "PreExistingConditionsAndRiskFactorsInternationalMenu": { + "name": "PreExistingConditionsAndRiskFactorsInternationalMenu", + "title": "pre-existing conditions and risk factors international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Cancer [MONDO:0004992]": { "text": "Cancer [MONDO:0004992]", + "description": "A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.", "meaning": "MONDO:0004992" }, "Diabetes mellitus (diabetes) [HP:0000819]": { "text": "Diabetes mellitus (diabetes) [HP:0000819]", + "description": "A group of abnormalities characterized by hyperglycemia and glucose intolerance.", "meaning": "HP:0000819" }, "Type I diabetes mellitus (T1D) [HP:0100651]": { "text": "Type I diabetes mellitus (T1D) [HP:0100651]", + "description": "A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin.", "meaning": "HP:0100651", "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" }, "Type II diabetes mellitus (T2D) [HP:0005978]": { "text": "Type II diabetes mellitus (T2D) [HP:0005978]", + "description": "A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.", "meaning": "HP:0005978", "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" }, "Immunocompromised [NCIT:C14139]": { "text": "Immunocompromised [NCIT:C14139]", + "description": "A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions.", "meaning": "NCIT:C14139" }, "Infectious disorder [NCIT:C26726]": { "text": "Infectious disorder [NCIT:C26726]", + "description": "A disorder resulting from the presence and activity of a microbial, viral, fungal, or parasitic agent. It can be transmitted by direct or indirect contact.", "meaning": "NCIT:C26726" }, "Chancroid (Haemophilus ducreyi) [DOID:13778]": { "text": "Chancroid (Haemophilus ducreyi) [DOID:13778]", + "description": "A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers.", "meaning": "DOID:13778", "is_a": "Infectious disorder [NCIT:C26726]" }, "Chlamydia [DOID:11263]": { "text": "Chlamydia [DOID:11263]", + "description": "A commensal bacterial infectious disease that is caused by Chlamydia trachomatis.", "meaning": "DOID:11263", "is_a": "Infectious disorder [NCIT:C26726]" }, "Gonorrhea [DOID:7551]": { "text": "Gonorrhea [DOID:7551]", + "description": "A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods.", "meaning": "DOID:7551", "is_a": "Infectious disorder [NCIT:C26726]" }, "Herpes Simplex Virus infection (HSV) [NCIT:C155871]": { "text": "Herpes Simplex Virus infection (HSV) [NCIT:C155871]", + "description": "An infection that is caused by herpes simplex virus.", "meaning": "NCIT:C155871", "is_a": "Infectious disorder [NCIT:C26726]" }, "Human immunodeficiency virus (HIV) [MONDO:0005109]": { "text": "Human immunodeficiency virus (HIV) [MONDO:0005109]", + "description": "An infection caused by the human immunodeficiency virus.", "meaning": "MONDO:0005109", "is_a": "Infectious disorder [NCIT:C26726]" }, "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]": { "text": "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]", + "description": "A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes.", "meaning": "MONDO:0012268", "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" }, "Human papilloma virus infection (HPV) [MONDO:0005161]": { "text": "Human papilloma virus infection (HPV) [MONDO:0005161]", + "description": "An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth.", "meaning": "MONDO:0005161", "is_a": "Infectious disorder [NCIT:C26726]" }, "Lymphogranuloma venereum [DOID:13819]": { "text": "Lymphogranuloma venereum [DOID:13819]", + "description": "A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis.", "meaning": "DOID:13819", "is_a": "Infectious disorder [NCIT:C26726]" }, "Mycoplsma genitalium [NCBITaxon:2097]": { "text": "Mycoplsma genitalium [NCBITaxon:2097]", + "description": "A sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans.", "meaning": "NCBITaxon:2097", "is_a": "Infectious disorder [NCIT:C26726]" }, "Syphilis [DOID:4166]": { "text": "Syphilis [DOID:4166]", + "description": "A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years.", "meaning": "DOID:4166", "is_a": "Infectious disorder [NCIT:C26726]" }, "Trichomoniasis [DOID:1947]": { "text": "Trichomoniasis [DOID:1947]", + "description": "A parasitic protozoa infectious disease that is caused by singled-celled protozoan parasites Trichomonas vaginalis or Trichomonas tenax, which infect the urogenital tract and mouth respectively.", "meaning": "DOID:1947", "is_a": "Infectious disorder [NCIT:C26726]" }, "Lupus [MONDO:0004670]": { "text": "Lupus [MONDO:0004670]", + "description": "An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus.", "meaning": "MONDO:0004670" }, "Pregnancy [NCIT:C25742]": { "text": "Pregnancy [NCIT:C25742]", + "description": "The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.", "meaning": "NCIT:C25742" }, "Prior therapy [NCIT:C16124]": { "text": "Prior therapy [NCIT:C16124]", + "description": "Prior action or administration of therapeutic agents that produced an effect that is intended to alter or stop a pathologic process.", "meaning": "NCIT:C16124" }, "Cancer treatment [NCIT:C16212]": { "text": "Cancer treatment [NCIT:C16212]", + "description": "Any intervention for management of a malignant neoplasm.", "meaning": "NCIT:C16212", "is_a": "Prior therapy [NCIT:C16124]" }, "Chemotherapy [NCIT:C15632]": { "text": "Chemotherapy [NCIT:C15632]", + "description": "The use of synthetic or naturally-occurring chemicals for the treatment of diseases.", "meaning": "NCIT:C15632", "is_a": "Cancer treatment [NCIT:C16212]" }, "HIV and Antiretroviral therapy (ART) [NCIT:C16118]": { "text": "HIV and Antiretroviral therapy (ART) [NCIT:C16118]", + "description": "Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles.", "meaning": "NCIT:C16118", "is_a": "Prior therapy [NCIT:C16124]" }, "Steroid [CHEBI:35341]": { "text": "Steroid [CHEBI:35341]", + "description": "Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.", "meaning": "CHEBI:35341", "is_a": "Prior therapy [NCIT:C16124]" }, "Transplant [NCIT:C159659]": { "text": "Transplant [NCIT:C159659]", + "description": "An individual receiving a transplant.", "meaning": "NCIT:C159659" } } }, - "complications menu": { - "name": "complications menu", + "ComplicationsMenu": { + "name": "ComplicationsMenu", + "title": "complications menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Bronchopneumonia": { "text": "Bronchopneumonia", + "description": "Acute inflammation of the walls of the terminal bronchioles that spreads into the peribronchial alveoli and alveolar ducts. It results in the creation of foci of consolidation, which are surrounded by normal parenchyma. It affects one or more lobes, and is frequently bilateral and basal. It is usually caused by bacteria (e.g., Staphylococcus, Streptococcus, Haemophilus influenzae). Signs and symptoms include fever, cough with production of brown-red sputum, dyspnea, and chest pain.", "meaning": "MONDO:0005682" }, "Corneal infection": { "text": "Corneal infection", + "description": "A viral or bacterial infectious process affecting the cornea. Symptoms include pain and redness in the eye, photophobia and eye watering.", "meaning": "MONDO:0023865" }, "Delayed wound healing (lesion healing)": { "text": "Delayed wound healing (lesion healing)", + "description": "Longer time requirement for the ability to self-repair and close wounds than normal", "meaning": "MP:0002908" }, "Encephalitis": { "text": "Encephalitis", + "description": "A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms.", "meaning": "DOID:9588" }, "Myocarditis": { "text": "Myocarditis", + "description": "An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle.", "meaning": "DOID:820" }, "Secondary infection": { "text": "Secondary infection", + "description": "An infection bearing the secondary infection role.", "meaning": "IDO:0000567" }, "Sepsis": { "text": "Sepsis", + "description": "Systemic inflammatory response to infection.", "meaning": "HP:0100806" } } }, - "complications international menu": { - "name": "complications international menu", + "ComplicationsInternationalMenu": { + "name": "ComplicationsInternationalMenu", + "title": "complications international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Bronchopneumonia [MONDO:0005682]": { "text": "Bronchopneumonia [MONDO:0005682]", + "description": "Acute inflammation of the walls of the terminal bronchioles that spreads into the peribronchial alveoli and alveolar ducts. It results in the creation of foci of consolidation, which are surrounded by normal parenchyma. It affects one or more lobes, and is frequently bilateral and basal. It is usually caused by bacteria (e.g., Staphylococcus, Streptococcus, Haemophilus influenzae). Signs and symptoms include fever, cough with production of brown-red sputum, dyspnea, and chest pain.", "meaning": "MONDO:0005682" }, "Corneal infection [MONDO:0023865]": { "text": "Corneal infection [MONDO:0023865]", + "description": "A viral or bacterial infectious process affecting the cornea. Symptoms include pain and redness in the eye, photophobia and eye watering.", "meaning": "MONDO:0023865" }, "Delayed wound healing (lesion healing) [MP:0002908]": { "text": "Delayed wound healing (lesion healing) [MP:0002908]", + "description": "Longer time requirement for the ability to self-repair and close wounds than normal", "meaning": "MP:0002908" }, "Encephalitis [DOID:9588]": { "text": "Encephalitis [DOID:9588]", + "description": "A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms.", "meaning": "DOID:9588" }, "Myocarditis [DOID:820]": { "text": "Myocarditis [DOID:820]", + "description": "An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle.", "meaning": "DOID:820" }, "Secondary infection [IDO:0000567]": { "text": "Secondary infection [IDO:0000567]", + "description": "An infection bearing the secondary infection role.", "meaning": "IDO:0000567" }, "Sepsis [HP:0100806]": { "text": "Sepsis [HP:0100806]", + "description": "Systemic inflammatory response to infection.", "meaning": "HP:0100806" } } }, - "host vaccination status menu": { - "name": "host vaccination status menu", + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "host vaccination status menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Fully Vaccinated": { "text": "Fully Vaccinated", + "description": "Completed a full series of an authorized vaccine according to the regional health institutional guidance.", "meaning": "GENEPIO:0100100" }, "Not Vaccinated": { "text": "Not Vaccinated", + "description": "Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance.", "meaning": "GENEPIO:0100102" } } }, - "host vaccination status international menu": { - "name": "host vaccination status international menu", + "HostVaccinationStatusInternationalMenu": { + "name": "HostVaccinationStatusInternationalMenu", + "title": "host vaccination status international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Fully Vaccinated [GENEPIO:0100100]": { "text": "Fully Vaccinated [GENEPIO:0100100]", + "description": "Completed a full series of an authorized vaccine according to the regional health institutional guidance.", "meaning": "GENEPIO:0100100" }, + "Partially Vaccinated [GENEPIO:0100101]": { + "text": "Partially Vaccinated [GENEPIO:0100101]", + "description": "Initiated but not yet completed the full series of an authorized vaccine according to the regional health institutional guidance.", + "meaning": "GENEPIO:0100101" + }, "Not Vaccinated [GENEPIO:0100102]": { "text": "Not Vaccinated [GENEPIO:0100102]", + "description": "Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance.", "meaning": "GENEPIO:0100102" } } }, - "exposure event menu": { - "name": "exposure event menu", + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "exposure event menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Mass Gathering": { "text": "Mass Gathering", + "description": "A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held.", "meaning": "GENEPIO:0100237" }, "Convention (conference)": { "text": "Convention (conference)", + "description": "A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom.", "meaning": "GENEPIO:0100238" }, "Agricultural Event": { "text": "Agricultural Event", + "description": "A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry.", "meaning": "GENEPIO:0100240", "is_a": "Convention (conference)" }, "Social Gathering": { "text": "Social Gathering", + "description": "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially.", "meaning": "PCO:0000033" }, "Community Event": { "text": "Community Event", + "description": "A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area.", "meaning": "PCO:0000034", "is_a": "Social Gathering" }, "Party": { "text": "Party", + "description": "A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose.", "meaning": "PCO:0000035", "is_a": "Social Gathering" }, "Other exposure event": { - "text": "Other exposure event" + "text": "Other exposure event", + "description": "An event or situation not classified under other specific exposure types, in which an individual may be exposed to conditions or factors that could impact health or safety. This term encompasses a wide range of gatherings, activities, or circumstances that do not fit into predefined exposure categories." } } }, - "exposure event international menu": { - "name": "exposure event international menu", + "ExposureEventInternationalMenu": { + "name": "ExposureEventInternationalMenu", + "title": "exposure event international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Mass Gathering [GENEPIO:0100237]": { @@ -2696,1870 +3305,2549 @@ } } }, - "exposure contact level menu": { - "name": "exposure contact level menu", + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "exposure contact level menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Contact with animal": { "text": "Contact with animal", + "description": "A type of contact in which an individual comes into contact with an animal, either directly or indirectly, which could include physical interaction or exposure to animal bodily fluids, feces, or other contaminated materials.", "meaning": "GENEPIO:0100494" }, "Contact with rodent": { "text": "Contact with rodent", + "description": "A type of contact in which an individual comes into contact with a rodent, either directly or indirectly, such as through handling, exposure to rodent droppings, urine, or nests, which could potentially lead to the transmission of rodent-borne diseases.", "meaning": "GENEPIO:0100495", "is_a": "Contact with animal" }, "Contact with fomite": { "text": "Contact with fomite", + "description": "A type of contact in which an individual comes into contact with an inanimate object or surface that has been contaminated with pathogens, such as doorknobs, countertops, or medical equipment, which can transfer infectious agents to the individual.", "meaning": "GENEPIO:0100496" }, "Contact with infected individual": { "text": "Contact with infected individual", + "description": "A type of contact in which an individual comes in contact with an infected person, either directly or indirectly.", "meaning": "GENEPIO:0100357" }, "Direct (human-to-human contact)": { "text": "Direct (human-to-human contact)", + "description": "Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.", "meaning": "TRANS:0000001", "is_a": "Contact with infected individual" }, "Mother-to-child transmission": { "text": "Mother-to-child transmission", + "description": "A direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth.", "meaning": "TRANS:0000006", "is_a": "Direct (human-to-human contact)" }, "Sexual transmission": { "text": "Sexual transmission", + "description": "Passage or transfer, as of a disease, from a donor individual to a recipient during or as a result of sexual activity.", "meaning": "NCIT:C19085", "is_a": "Direct (human-to-human contact)" }, "Indirect contact": { "text": "Indirect contact", + "description": "A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces.", "meaning": "GENEPIO:0100246", "is_a": "Contact with infected individual" }, "Close contact (face-to-face contact)": { "text": "Close contact (face-to-face contact)", + "description": "A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time.", "meaning": "GENEPIO:0100247", "is_a": "Indirect contact" }, "Casual contact": { "text": "Casual contact", + "description": "A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission.", "meaning": "GENEPIO:0100248", "is_a": "Indirect contact" }, "Workplace associated transmission": { "text": "Workplace associated transmission", + "description": "A type of transmission where an individual acquires an infection or disease as a result of exposure in their workplace environment. This can include direct contact with infected individuals, exposure to contaminated materials or surfaces, or other workplace-specific risk factors.", "meaning": "GENEPIO:0100497" }, "Healthcare associated transmission": { "text": "Healthcare associated transmission", + "description": "A type of transmission where an individual acquires an infection or disease as a result of exposure within a healthcare setting. This includes transmission through direct contact with patients, contaminated medical equipment, or surfaces within healthcare facilities, such as hospitals or clinics.", "meaning": "GENEPIO:0100498", "is_a": "Workplace associated transmission" }, "Laboratory associated transmission": { "text": "Laboratory associated transmission", + "description": "A type of transmission where an individual acquires an infection or disease as a result of exposure within a laboratory setting. This includes contact with infectious agents, contaminated equipment, or laboratory surfaces, as well as potential aerosol exposure or spills of hazardous substances.", "meaning": "GENEPIO:0100499", "is_a": "Workplace associated transmission" } } }, - "exposure contact level international menu": { - "name": "exposure contact level international menu", + "ExposureContactLevelInternationalMenu": { + "name": "ExposureContactLevelInternationalMenu", + "title": "exposure contact level international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Contact with animal [GENEPIO:0100494]": { "text": "Contact with animal [GENEPIO:0100494]", + "description": "A type of contact in which an individual comes into contact with an animal, either directly or indirectly, which could include physical interaction or exposure to animal bodily fluids, feces, or other contaminated materials.", "meaning": "GENEPIO:0100494" }, "Contact with rodent [GENEPIO:0100495]": { "text": "Contact with rodent [GENEPIO:0100495]", + "description": "A type of contact in which an individual comes into contact with a rodent, either directly or indirectly, such as through handling, exposure to rodent droppings, urine, or nests, which could potentially lead to the transmission of rodent-borne diseases.", "meaning": "GENEPIO:0100495", "is_a": "Contact with animal [GENEPIO:0100494]" }, "Contact with fomite [GENEPIO:0100496]": { "text": "Contact with fomite [GENEPIO:0100496]", + "description": "A type of contact in which an individual comes into contact with an inanimate object or surface that has been contaminated with pathogens, such as doorknobs, countertops, or medical equipment, which can transfer infectious agents to the individual.", "meaning": "GENEPIO:0100496" }, "Contact with infected individual [GENEPIO:0100357]": { "text": "Contact with infected individual [GENEPIO:0100357]", + "description": "A type of contact in which an individual comes in contact with an infected person, either directly or indirectly.", "meaning": "GENEPIO:0100357" }, "Direct (human-to-human contact) [TRANS:0000001]": { "text": "Direct (human-to-human contact) [TRANS:0000001]", + "description": "Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.", "meaning": "TRANS:0000001", "is_a": "Contact with infected individual [GENEPIO:0100357]" }, "Mother-to-child transmission [TRANS:0000006]": { "text": "Mother-to-child transmission [TRANS:0000006]", + "description": "A direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth.", "meaning": "TRANS:0000006", "is_a": "Direct (human-to-human contact) [TRANS:0000001]" }, "Sexual transmission [NCIT:C19085]": { "text": "Sexual transmission [NCIT:C19085]", + "description": "Passage or transfer, as of a disease, from a donor individual to a recipient during or as a result of sexual activity.", "meaning": "NCIT:C19085", "is_a": "Direct (human-to-human contact) [TRANS:0000001]" }, "Indirect contact [GENEPIO:0100246]": { "text": "Indirect contact [GENEPIO:0100246]", + "description": "A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces.", "meaning": "GENEPIO:0100246", "is_a": "Contact with infected individual [GENEPIO:0100357]" }, "Close contact (face-to-face contact) [GENEPIO:0100247]": { "text": "Close contact (face-to-face contact) [GENEPIO:0100247]", + "description": "A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time.", "meaning": "GENEPIO:0100247", "is_a": "Indirect contact [GENEPIO:0100246]" }, "Casual contact [GENEPIO:0100248]": { "text": "Casual contact [GENEPIO:0100248]", + "description": "A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission.", "meaning": "GENEPIO:0100248", "is_a": "Indirect contact [GENEPIO:0100246]" }, "Workplace associated transmission [GENEPIO:0100497]": { "text": "Workplace associated transmission [GENEPIO:0100497]", + "description": "A type of transmission where an individual acquires an infection or disease as a result of exposure in their workplace environment. This can include direct contact with infected individuals, exposure to contaminated materials or surfaces, or other workplace-specific risk factors.", "meaning": "GENEPIO:0100497" }, "Healthcare associated transmission [GENEPIO:0100498]": { "text": "Healthcare associated transmission [GENEPIO:0100498]", + "description": "A type of transmission where an individual acquires an infection or disease as a result of exposure within a healthcare setting. This includes transmission through direct contact with patients, contaminated medical equipment, or surfaces within healthcare facilities, such as hospitals or clinics.", "meaning": "GENEPIO:0100498", "is_a": "Workplace associated transmission [GENEPIO:0100497]" }, "Laboratory associated transmission [GENEPIO:0100499]": { "text": "Laboratory associated transmission [GENEPIO:0100499]", + "description": "A type of transmission where an individual acquires an infection or disease as a result of exposure within a laboratory setting. This includes contact with infectious agents, contaminated equipment, or laboratory surfaces, as well as potential aerosol exposure or spills of hazardous substances.", "meaning": "GENEPIO:0100499", "is_a": "Workplace associated transmission [GENEPIO:0100497]" } } }, - "host role menu": { - "name": "host role menu", + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "host role menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Attendee": { "text": "Attendee", + "description": "A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place.", "meaning": "GENEPIO:0100249" }, "Student": { "text": "Student", + "description": "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.", "meaning": "OMRSE:00000058", "is_a": "Attendee" }, "Patient": { "text": "Patient", + "description": "A patient role that inheres in a human being.", "meaning": "OMRSE:00000030" }, "Inpatient": { "text": "Inpatient", + "description": "A patient who is residing in the hospital where he is being treated.", "meaning": "NCIT:C25182", "is_a": "Patient" }, "Outpatient": { "text": "Outpatient", + "description": "A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay.", "meaning": "NCIT:C28293", "is_a": "Patient" }, "Passenger": { "text": "Passenger", + "description": "A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination.", "meaning": "GENEPIO:0100250" }, "Resident": { "text": "Resident", + "description": "A role inhering in a person that is realized when the bearer maintains residency in a given place.", "meaning": "GENEPIO:0100251" }, "Visitor": { "text": "Visitor", + "description": "A role inhering in a person that is realized when the bearer pays a visit to a specific place or event.", "meaning": "GENEPIO:0100252" }, "Volunteer": { "text": "Volunteer", + "description": "A role inhering in a person that is realized when the bearer enters into any service of their own free will.", "meaning": "GENEPIO:0100253" }, "Work": { "text": "Work", + "description": "A role inhering in a person that is realized when the bearer performs labor for a living.", "meaning": "GENEPIO:0100254" }, "Administrator": { "text": "Administrator", + "description": "A role inhering in a person that is realized when the bearer is engaged in administration or administrative work.", "meaning": "GENEPIO:0100255", "is_a": "Work" }, "First Responder": { "text": "First Responder", + "description": "A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance.", "meaning": "GENEPIO:0100256", "is_a": "Work" }, "Housekeeper": { "text": "Housekeeper", + "description": "A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff.", "meaning": "GENEPIO:0100260", "is_a": "Work" }, "Kitchen Worker": { "text": "Kitchen Worker", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen.", "meaning": "GENEPIO:0100261", "is_a": "Work" }, "Healthcare Worker": { "text": "Healthcare Worker", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting.", "meaning": "GENEPIO:0100334", "is_a": "Work" }, "Community Healthcare Worker": { "text": "Community Healthcare Worker", + "description": "A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home.", "meaning": "GENEPIO:0100420", "is_a": "Healthcare Worker" }, "Laboratory Worker": { "text": "Laboratory Worker", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory.", "meaning": "GENEPIO:0100262", "is_a": "Healthcare Worker" }, "Nurse": { "text": "Nurse", + "description": "A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.", "meaning": "OMRSE:00000014", "is_a": "Healthcare Worker" }, "Personal Care Aid": { "text": "Personal Care Aid", + "description": "A role inhering in a person that is realized when the bearer works to help another person complete their daily activities.", "meaning": "GENEPIO:0100263", "is_a": "Healthcare Worker" }, "Pharmacist": { "text": "Pharmacist", + "description": "A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility.", "meaning": "GENEPIO:0100264", "is_a": "Healthcare Worker" }, "Physician": { "text": "Physician", + "description": "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.", "meaning": "OMRSE:00000013", "is_a": "Healthcare Worker" }, "Rotational Worker": { "text": "Rotational Worker", + "description": "A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live.", "meaning": "GENEPIO:0100354", "is_a": "Work" }, "Seasonal Worker": { "text": "Seasonal Worker", + "description": "A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas.", "meaning": "GENEPIO:0100355", "is_a": "Work" }, "Sex Worker": { "text": "Sex Worker", + "description": "A person who supplies sex work (some form of sexual services) in exchange for compensation. This term is promoted along with the idea that what has previously been termed prostitution should be recognized as work on equal terms with that of conventional jobs, with the legal implications this has. It is sometimes regarded as a less offensive alternative to prostitute, although \"sex worker\" has a much broader meaning.", "meaning": "GSSO:005831", "is_a": "Work" }, "Veterinarian": { "text": "Veterinarian", + "description": "A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine.", "meaning": "GENEPIO:0100265", "is_a": "Work" }, "Social role": { "text": "Social role", + "description": "A social role inhering in a human being.", "meaning": "OMRSE:00000001" }, "Acquaintance of case": { "text": "Acquaintance of case", + "description": "A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person.", "meaning": "GENEPIO:0100266", "is_a": "Social role" }, "Relative of case": { "text": "Relative of case", + "description": "A role inhering in a person that is realized when the bearer is a relative of the case.", "meaning": "GENEPIO:0100267", "is_a": "Social role" }, "Child of case": { "text": "Child of case", + "description": "A role inhering in a person that is realized when the bearer is a person younger than the age of majority.", "meaning": "GENEPIO:0100268", "is_a": "Relative of case" }, "Parent of case": { "text": "Parent of case", + "description": "A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species.", "meaning": "GENEPIO:0100269", "is_a": "Relative of case" }, "Father of case": { "text": "Father of case", + "description": "A role inhering in a person that is realized when the bearer is the male parent of a child.", "meaning": "GENEPIO:0100270", "is_a": "Parent of case" }, "Mother of case": { "text": "Mother of case", + "description": "A role inhering in a person that is realized when the bearer is the female parent of a child.", "meaning": "GENEPIO:0100271", "is_a": "Parent of case" }, "Sexual partner of case": { "text": "Sexual partner of case", + "description": "A role inhering in a person that is realized when the bearer is a sexual partner of the case.", "meaning": "GENEPIO:0100500", "is_a": "Social role" }, "Spouse of case": { "text": "Spouse of case", + "description": "A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage.", "meaning": "GENEPIO:0100272", "is_a": "Social role" }, "Other Host Role": { - "text": "Other Host Role" + "text": "Other Host Role", + "description": "A role undertaken by a host that is not categorized under specific predefined host roles." } } }, - "host role international menu": { - "name": "host role international menu", + "HostRoleInternationalMenu": { + "name": "HostRoleInternationalMenu", + "title": "host role international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Attendee [GENEPIO:0100249]": { "text": "Attendee [GENEPIO:0100249]", + "description": "A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place.", "meaning": "GENEPIO:0100249" }, "Student [OMRSE:00000058]": { "text": "Student [OMRSE:00000058]", + "description": "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.", "meaning": "OMRSE:00000058", "is_a": "Attendee [GENEPIO:0100249]" }, "Patient [OMRSE:00000030]": { "text": "Patient [OMRSE:00000030]", + "description": "A patient role that inheres in a human being.", "meaning": "OMRSE:00000030" }, "Inpatient [NCIT:C25182]": { "text": "Inpatient [NCIT:C25182]", + "description": "A patient who is residing in the hospital where he is being treated.", "meaning": "NCIT:C25182", "is_a": "Patient [OMRSE:00000030]" }, "Outpatient [NCIT:C28293]": { "text": "Outpatient [NCIT:C28293]", + "description": "A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay.", "meaning": "NCIT:C28293", "is_a": "Patient [OMRSE:00000030]" }, "Passenger [GENEPIO:0100250]": { "text": "Passenger [GENEPIO:0100250]", + "description": "A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination.", "meaning": "GENEPIO:0100250" }, "Resident [GENEPIO:0100251]": { "text": "Resident [GENEPIO:0100251]", + "description": "A role inhering in a person that is realized when the bearer maintains residency in a given place.", "meaning": "GENEPIO:0100251" }, "Visitor [GENEPIO:0100252]": { "text": "Visitor [GENEPIO:0100252]", + "description": "A role inhering in a person that is realized when the bearer pays a visit to a specific place or event.", "meaning": "GENEPIO:0100252" }, "Volunteer [GENEPIO:0100253]": { "text": "Volunteer [GENEPIO:0100253]", + "description": "A role inhering in a person that is realized when the bearer enters into any service of their own free will.", "meaning": "GENEPIO:0100253" }, "Work [GENEPIO:0100254]": { "text": "Work [GENEPIO:0100254]", + "description": "A role inhering in a person that is realized when the bearer performs labor for a living.", "meaning": "GENEPIO:0100254" }, "Administrator [GENEPIO:0100255]": { "text": "Administrator [GENEPIO:0100255]", + "description": "A role inhering in a person that is realized when the bearer is engaged in administration or administrative work.", "meaning": "GENEPIO:0100255", "is_a": "Work [GENEPIO:0100254]" }, "First Responder [GENEPIO:0100256]": { "text": "First Responder [GENEPIO:0100256]", + "description": "A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance.", "meaning": "GENEPIO:0100256", "is_a": "Work [GENEPIO:0100254]" }, "Housekeeper [GENEPIO:0100260]": { "text": "Housekeeper [GENEPIO:0100260]", + "description": "A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff.", "meaning": "GENEPIO:0100260", "is_a": "Work [GENEPIO:0100254]" }, "Kitchen Worker [GENEPIO:0100261]": { "text": "Kitchen Worker [GENEPIO:0100261]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen.", "meaning": "GENEPIO:0100261", "is_a": "Work [GENEPIO:0100254]" }, "Healthcare Worker [GENEPIO:0100334]": { "text": "Healthcare Worker [GENEPIO:0100334]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting.", "meaning": "GENEPIO:0100334", "is_a": "Work [GENEPIO:0100254]" }, "Community Healthcare Worker [GENEPIO:0100420]": { "text": "Community Healthcare Worker [GENEPIO:0100420]", + "description": "A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home.", "meaning": "GENEPIO:0100420", "is_a": "Healthcare Worker [GENEPIO:0100334]" }, "Laboratory Worker [GENEPIO:0100262]": { "text": "Laboratory Worker [GENEPIO:0100262]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory.", "meaning": "GENEPIO:0100262", "is_a": "Healthcare Worker [GENEPIO:0100334]" }, "Nurse [OMRSE:00000014]": { "text": "Nurse [OMRSE:00000014]", + "description": "A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.", "meaning": "OMRSE:00000014", "is_a": "Healthcare Worker [GENEPIO:0100334]" }, "Personal Care Aid [GENEPIO:0100263]": { "text": "Personal Care Aid [GENEPIO:0100263]", + "description": "A role inhering in a person that is realized when the bearer works to help another person complete their daily activities.", "meaning": "GENEPIO:0100263", "is_a": "Healthcare Worker [GENEPIO:0100334]" }, "Pharmacist [GENEPIO:0100264]": { "text": "Pharmacist [GENEPIO:0100264]", + "description": "A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility.", "meaning": "GENEPIO:0100264", "is_a": "Healthcare Worker [GENEPIO:0100334]" }, "Physician [OMRSE:00000013]": { "text": "Physician [OMRSE:00000013]", + "description": "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.", "meaning": "OMRSE:00000013", "is_a": "Healthcare Worker [GENEPIO:0100334]" }, "Rotational Worker [GENEPIO:0100354]": { "text": "Rotational Worker [GENEPIO:0100354]", + "description": "A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live.", "meaning": "GENEPIO:0100354", "is_a": "Work [GENEPIO:0100254]" }, "Seasonal Worker [GENEPIO:0100355]": { "text": "Seasonal Worker [GENEPIO:0100355]", + "description": "A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas.", "meaning": "GENEPIO:0100355", "is_a": "Work [GENEPIO:0100254]" }, "Sex Worker [GSSO:005831]": { "text": "Sex Worker [GSSO:005831]", + "description": "A person who supplies sex work (some form of sexual services) in exchange for compensation. This term is promoted along with the idea that what has previously been termed prostitution should be recognized as work on equal terms with that of conventional jobs, with the legal implications this has. It is sometimes regarded as a less offensive alternative to prostitute, although \"sex worker\" has a much broader meaning.", "meaning": "GSSO:005831", "is_a": "Work [GENEPIO:0100254]" }, "Veterinarian [GENEPIO:0100265]": { "text": "Veterinarian [GENEPIO:0100265]", + "description": "A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine.", "meaning": "GENEPIO:0100265", "is_a": "Work [GENEPIO:0100254]" }, "Social role [OMRSE:00000001]": { "text": "Social role [OMRSE:00000001]", + "description": "A social role inhering in a human being.", "meaning": "OMRSE:00000001" }, "Acquaintance of case [GENEPIO:0100266]": { "text": "Acquaintance of case [GENEPIO:0100266]", + "description": "A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person.", "meaning": "GENEPIO:0100266", "is_a": "Social role [OMRSE:00000001]" }, "Relative of case [GENEPIO:0100267]": { "text": "Relative of case [GENEPIO:0100267]", + "description": "A role inhering in a person that is realized when the bearer is a relative of the case.", "meaning": "GENEPIO:0100267", "is_a": "Social role [OMRSE:00000001]" }, "Child of case [GENEPIO:0100268]": { "text": "Child of case [GENEPIO:0100268]", + "description": "A role inhering in a person that is realized when the bearer is a person younger than the age of majority.", "meaning": "GENEPIO:0100268", "is_a": "Relative of case [GENEPIO:0100267]" }, "Parent of case [GENEPIO:0100269]": { "text": "Parent of case [GENEPIO:0100269]", + "description": "A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species.", "meaning": "GENEPIO:0100269", "is_a": "Relative of case [GENEPIO:0100267]" }, "Father of case [GENEPIO:0100270]": { "text": "Father of case [GENEPIO:0100270]", + "description": "A role inhering in a person that is realized when the bearer is the male parent of a child.", "meaning": "GENEPIO:0100270", "is_a": "Parent of case [GENEPIO:0100269]" }, "Mother of case [GENEPIO:0100271]": { "text": "Mother of case [GENEPIO:0100271]", + "description": "A role inhering in a person that is realized when the bearer is the female parent of a child.", "meaning": "GENEPIO:0100271", "is_a": "Parent of case [GENEPIO:0100269]" }, "Sexual partner of case [GENEPIO:0100500]": { "text": "Sexual partner of case [GENEPIO:0100500]", + "description": "A role inhering in a person that is realized when the bearer is a sexual partner of the case.", "meaning": "GENEPIO:0100500", "is_a": "Social role [OMRSE:00000001]" }, "Spouse of case [GENEPIO:0100272]": { "text": "Spouse of case [GENEPIO:0100272]", + "description": "A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage.", "meaning": "GENEPIO:0100272", "is_a": "Social role [OMRSE:00000001]" }, "Other Host Role": { - "text": "Other Host Role" + "text": "Other Host Role", + "description": "A role undertaken by a host that is not categorized under specific predefined host roles." } } }, - "exposure setting menu": { - "name": "exposure setting menu", + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "exposure setting menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Human Exposure": { "text": "Human Exposure", + "description": "A history of exposure to Homo sapiens.", "meaning": "ECTO:3000005" }, "Contact with Known Monkeypox Case": { "text": "Contact with Known Monkeypox Case", + "description": "A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox.", "meaning": "GENEPIO:0100501", "is_a": "Human Exposure" }, "Contact with Patient": { "text": "Contact with Patient", + "description": "A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100185", "is_a": "Human Exposure" }, "Contact with Probable Monkeypox Case": { "text": "Contact with Probable Monkeypox Case", + "description": "A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox.", "meaning": "GENEPIO:0100502", "is_a": "Human Exposure" }, "Contact with Person who Recently Travelled": { "text": "Contact with Person who Recently Travelled", + "description": "A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100189", "is_a": "Human Exposure" }, "Occupational, Residency or Patronage Exposure": { "text": "Occupational, Residency or Patronage Exposure", + "description": "A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100190" }, "Abbatoir": { "text": "Abbatoir", + "description": "A exposure event involving the interaction of an exposure receptor to abattoir.", "meaning": "ECTO:1000033", "is_a": "Occupational, Residency or Patronage Exposure" }, "Animal Rescue": { "text": "Animal Rescue", + "description": "A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100191", "is_a": "Occupational, Residency or Patronage Exposure" }, "Bar (pub)": { "text": "Bar (pub)", + "description": "A process occurring within or in the vicinity of a bar or pub environment that exposes the recipient organism to a material entity", "meaning": "GENEPIO:0100503", "is_a": "Occupational, Residency or Patronage Exposure" }, "Childcare": { "text": "Childcare", + "description": "A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100192", "is_a": "Occupational, Residency or Patronage Exposure" }, "Daycare": { "text": "Daycare", + "description": "A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100193", "is_a": "Childcare" }, "Nursery": { "text": "Nursery", + "description": "A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100194", "is_a": "Childcare" }, "Community Service Centre": { "text": "Community Service Centre", + "description": "A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100195", "is_a": "Occupational, Residency or Patronage Exposure" }, "Correctional Facility": { "text": "Correctional Facility", + "description": "A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100196", "is_a": "Occupational, Residency or Patronage Exposure" }, "Dormitory": { "text": "Dormitory", + "description": "A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100197", "is_a": "Occupational, Residency or Patronage Exposure" }, "Farm": { "text": "Farm", + "description": "A exposure event involving the interaction of an exposure receptor to farm", "meaning": "ECTO:1000034", "is_a": "Occupational, Residency or Patronage Exposure" }, "First Nations Reserve": { "text": "First Nations Reserve", + "description": "A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100198", "is_a": "Occupational, Residency or Patronage Exposure" }, "Funeral Home": { "text": "Funeral Home", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100199", "is_a": "Occupational, Residency or Patronage Exposure" }, "Group Home": { "text": "Group Home", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100200", "is_a": "Occupational, Residency or Patronage Exposure" }, "Healthcare Setting": { "text": "Healthcare Setting", + "description": "A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100201", "is_a": "Occupational, Residency or Patronage Exposure" }, "Ambulance": { "text": "Ambulance", + "description": "A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100202", "is_a": "Healthcare Setting" }, "Acute Care Facility": { "text": "Acute Care Facility", + "description": "A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100203", "is_a": "Healthcare Setting" }, "Clinic": { "text": "Clinic", + "description": "A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100204", "is_a": "Healthcare Setting" }, "Community Healthcare (At-Home) Setting": { "text": "Community Healthcare (At-Home) Setting", + "description": "A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home.", "meaning": "GENEPIO:0100415", "is_a": "Healthcare Setting" }, "Community Health Centre": { "text": "Community Health Centre", + "description": "A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100205", "is_a": "Healthcare Setting" }, "Hospital": { "text": "Hospital", + "description": "A exposure event involving the interaction of an exposure receptor to hospital.", "meaning": "ECTO:1000035", "is_a": "Healthcare Setting" }, "Emergency Department": { "text": "Emergency Department", + "description": "A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100206", "is_a": "Hospital" }, "ICU": { "text": "ICU", + "description": "A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100207", "is_a": "Hospital" }, "Ward": { "text": "Ward", + "description": "A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100208", "is_a": "Hospital" }, "Laboratory": { "text": "Laboratory", + "description": "A exposure event involving the interaction of an exposure receptor to laboratory facility.", "meaning": "ECTO:1000036", "is_a": "Healthcare Setting" }, "Long-Term Care Facility": { "text": "Long-Term Care Facility", + "description": "A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100209", "is_a": "Healthcare Setting" }, "Pharmacy": { "text": "Pharmacy", + "description": "A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100210", "is_a": "Healthcare Setting" }, "Physician's Office": { "text": "Physician's Office", + "description": "A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100211", "is_a": "Healthcare Setting" }, "Household": { "text": "Household", + "description": "A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100212", "is_a": "Occupational, Residency or Patronage Exposure" }, "Insecure Housing (Homeless)": { "text": "Insecure Housing (Homeless)", + "description": "A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing.", "meaning": "GENEPIO:0100213", "is_a": "Occupational, Residency or Patronage Exposure" }, "Occupational Exposure": { "text": "Occupational Exposure", + "description": "A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100214", "is_a": "Occupational, Residency or Patronage Exposure" }, "Worksite": { "text": "Worksite", + "description": "A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100215", "is_a": "Occupational Exposure" }, "Office": { "text": "Office", + "description": "A exposure event involving the interaction of an exposure receptor to office.", "meaning": "ECTO:1000037", "is_a": "Worksite" }, "Outdoors": { "text": "Outdoors", + "description": "A process occuring outdoors that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100216", "is_a": "Occupational, Residency or Patronage Exposure" }, "Camp/camping": { "text": "Camp/camping", + "description": "A exposure event involving the interaction of an exposure receptor to campground.", "meaning": "ECTO:5000009", "is_a": "Outdoors" }, "Hiking Trail": { "text": "Hiking Trail", + "description": "A process that exposes the recipient organism to a material entity as a consequence of hiking.", "meaning": "GENEPIO:0100217", "is_a": "Outdoors" }, "Hunting Ground": { "text": "Hunting Ground", + "description": "An exposure event involving hunting behavior", "meaning": "ECTO:6000030", "is_a": "Outdoors" }, "Ski Resort": { "text": "Ski Resort", + "description": "A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100218", "is_a": "Outdoors" }, "Petting zoo": { "text": "Petting zoo", + "description": "A exposure event involving the interaction of an exposure receptor to petting zoo.", "meaning": "ECTO:5000008", "is_a": "Occupational, Residency or Patronage Exposure" }, "Place of Worship": { "text": "Place of Worship", + "description": "A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100220", "is_a": "Occupational, Residency or Patronage Exposure" }, "Church": { "text": "Church", + "description": "A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100221", "is_a": "Place of Worship" }, "Mosque": { "text": "Mosque", + "description": "A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100222", "is_a": "Place of Worship" }, "Temple": { "text": "Temple", + "description": "A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100223", "is_a": "Place of Worship" }, "Restaurant": { "text": "Restaurant", + "description": "A exposure event involving the interaction of an exposure receptor to restaurant.", "meaning": "ECTO:1000040", "is_a": "Occupational, Residency or Patronage Exposure" }, "Retail Store": { "text": "Retail Store", + "description": "A exposure event involving the interaction of an exposure receptor to shop.", "meaning": "ECTO:1000041", "is_a": "Occupational, Residency or Patronage Exposure" }, "School": { "text": "School", + "description": "A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100224", "is_a": "Occupational, Residency or Patronage Exposure" }, "Temporary Residence": { "text": "Temporary Residence", + "description": "A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100225", "is_a": "Occupational, Residency or Patronage Exposure" }, "Homeless Shelter": { "text": "Homeless Shelter", + "description": "A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100226", "is_a": "Temporary Residence" }, "Hotel": { "text": "Hotel", + "description": "A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100227", "is_a": "Temporary Residence" }, "Veterinary Care Clinic": { "text": "Veterinary Care Clinic", + "description": "A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100228", "is_a": "Occupational, Residency or Patronage Exposure" }, "Travel Exposure": { "text": "Travel Exposure", + "description": "A process occuring as a result of travel that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100229" }, "Travelled on a Cruise Ship": { "text": "Travelled on a Cruise Ship", + "description": "A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100230", "is_a": "Travel Exposure" }, "Travelled on a Plane": { "text": "Travelled on a Plane", + "description": "A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100231", "is_a": "Travel Exposure" }, "Travelled on Ground Transport": { "text": "Travelled on Ground Transport", + "description": "A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100232", "is_a": "Travel Exposure" }, "Other Exposure Setting": { "text": "Other Exposure Setting", + "description": "A process occuring that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100235" } } }, - "exposure setting international menu": { - "name": "exposure setting international menu", + "ExposureSettingInternationalMenu": { + "name": "ExposureSettingInternationalMenu", + "title": "exposure setting international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Human Exposure [ECTO:3000005]": { "text": "Human Exposure [ECTO:3000005]", + "description": "A history of exposure to Homo sapiens.", "meaning": "ECTO:3000005" }, "Contact with Known Monkeypox Case [GENEPIO:0100501]": { "text": "Contact with Known Monkeypox Case [GENEPIO:0100501]", + "description": "A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox.", "meaning": "GENEPIO:0100501", "is_a": "Human Exposure [ECTO:3000005]" }, "Contact with Patient [GENEPIO:0100185]": { "text": "Contact with Patient [GENEPIO:0100185]", + "description": "A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100185", "is_a": "Human Exposure [ECTO:3000005]" }, "Contact with Probable Monkeypox Case [GENEPIO:0100502]": { "text": "Contact with Probable Monkeypox Case [GENEPIO:0100502]", + "description": "A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox.", "meaning": "GENEPIO:0100502", "is_a": "Human Exposure [ECTO:3000005]" }, "Contact with Person who Recently Travelled [GENEPIO:0100189]": { "text": "Contact with Person who Recently Travelled [GENEPIO:0100189]", + "description": "A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100189", "is_a": "Human Exposure [ECTO:3000005]" }, "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]": { "text": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]", + "description": "A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100190" }, "Abbatoir [ECTO:1000033]": { "text": "Abbatoir [ECTO:1000033]", + "description": "A exposure event involving the interaction of an exposure receptor to abattoir.", "meaning": "ECTO:1000033", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Animal Rescue [GENEPIO:0100191]": { "text": "Animal Rescue [GENEPIO:0100191]", + "description": "A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100191", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Bar (pub) [GENEPIO:0100503]": { "text": "Bar (pub) [GENEPIO:0100503]", + "description": "A process occurring within or in the vicinity of a bar or pub environment that exposes the recipient organism to a material entity", "meaning": "GENEPIO:0100503", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Childcare [GENEPIO:0100192]": { "text": "Childcare [GENEPIO:0100192]", + "description": "A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100192", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Daycare [GENEPIO:0100193]": { "text": "Daycare [GENEPIO:0100193]", + "description": "A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100193", "is_a": "Childcare [GENEPIO:0100192]" }, "Nursery [GENEPIO:0100194]": { "text": "Nursery [GENEPIO:0100194]", + "description": "A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100194", "is_a": "Childcare [GENEPIO:0100192]" }, "Community Service Centre [GENEPIO:0100195]": { "text": "Community Service Centre [GENEPIO:0100195]", + "description": "A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100195", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Correctional Facility [GENEPIO:0100196]": { "text": "Correctional Facility [GENEPIO:0100196]", + "description": "A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100196", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Dormitory [GENEPIO:0100197]": { "text": "Dormitory [GENEPIO:0100197]", + "description": "A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100197", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Farm [ECTO:1000034]": { "text": "Farm [ECTO:1000034]", + "description": "A exposure event involving the interaction of an exposure receptor to farm", "meaning": "ECTO:1000034", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "First Nations Reserve [GENEPIO:0100198]": { "text": "First Nations Reserve [GENEPIO:0100198]", + "description": "A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100198", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Funeral Home [GENEPIO:0100199]": { "text": "Funeral Home [GENEPIO:0100199]", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100199", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Group Home [GENEPIO:0100200]": { "text": "Group Home [GENEPIO:0100200]", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100200", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Healthcare Setting [GENEPIO:0100201]": { "text": "Healthcare Setting [GENEPIO:0100201]", + "description": "A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100201", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Ambulance [GENEPIO:0100202]": { "text": "Ambulance [GENEPIO:0100202]", + "description": "A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100202", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Acute Care Facility [GENEPIO:0100203]": { "text": "Acute Care Facility [GENEPIO:0100203]", + "description": "A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100203", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Clinic [GENEPIO:0100204]": { "text": "Clinic [GENEPIO:0100204]", + "description": "A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100204", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Community Healthcare (At-Home) Setting [GENEPIO:0100415]": { "text": "Community Healthcare (At-Home) Setting [GENEPIO:0100415]", + "description": "A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home.", "meaning": "GENEPIO:0100415", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Community Health Centre [GENEPIO:0100205]": { "text": "Community Health Centre [GENEPIO:0100205]", + "description": "A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100205", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Hospital [ECTO:1000035]": { "text": "Hospital [ECTO:1000035]", + "description": "A exposure event involving the interaction of an exposure receptor to hospital.", "meaning": "ECTO:1000035", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Emergency Department [GENEPIO:0100206]": { "text": "Emergency Department [GENEPIO:0100206]", + "description": "A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100206", "is_a": "Hospital [ECTO:1000035]" }, "ICU [GENEPIO:0100207]": { "text": "ICU [GENEPIO:0100207]", + "description": "A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100207", "is_a": "Hospital [ECTO:1000035]" }, "Ward [GENEPIO:0100208]": { "text": "Ward [GENEPIO:0100208]", + "description": "A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100208", "is_a": "Hospital [ECTO:1000035]" }, "Laboratory [ECTO:1000036]": { "text": "Laboratory [ECTO:1000036]", + "description": "A exposure event involving the interaction of an exposure receptor to laboratory facility.", "meaning": "ECTO:1000036", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Long-Term Care Facility [GENEPIO:0100209]": { "text": "Long-Term Care Facility [GENEPIO:0100209]", + "description": "A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100209", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Pharmacy [GENEPIO:0100210]": { "text": "Pharmacy [GENEPIO:0100210]", + "description": "A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100210", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Physician's Office [GENEPIO:0100211]": { "text": "Physician's Office [GENEPIO:0100211]", + "description": "A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100211", "is_a": "Healthcare Setting [GENEPIO:0100201]" }, "Household [GENEPIO:0100212]": { "text": "Household [GENEPIO:0100212]", + "description": "A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100212", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Insecure Housing (Homeless) [GENEPIO:0100213]": { "text": "Insecure Housing (Homeless) [GENEPIO:0100213]", + "description": "A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing.", "meaning": "GENEPIO:0100213", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Occupational Exposure [GENEPIO:0100214]": { "text": "Occupational Exposure [GENEPIO:0100214]", + "description": "A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100214", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Worksite [GENEPIO:0100215]": { "text": "Worksite [GENEPIO:0100215]", + "description": "A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100215", "is_a": "Occupational Exposure [GENEPIO:0100214]" }, "Office [ECTO:1000037]": { "text": "Office [ECTO:1000037]", + "description": "A exposure event involving the interaction of an exposure receptor to office.", "meaning": "ECTO:1000037", "is_a": "Worksite [GENEPIO:0100215]" }, "Outdoors [GENEPIO:0100216]": { "text": "Outdoors [GENEPIO:0100216]", + "description": "A process occuring outdoors that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100216", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Camp/camping [ECTO:5000009]": { "text": "Camp/camping [ECTO:5000009]", + "description": "A exposure event involving the interaction of an exposure receptor to campground.", "meaning": "ECTO:5000009", "is_a": "Outdoors [GENEPIO:0100216]" }, "Hiking Trail [GENEPIO:0100217]": { "text": "Hiking Trail [GENEPIO:0100217]", + "description": "A process that exposes the recipient organism to a material entity as a consequence of hiking.", "meaning": "GENEPIO:0100217", "is_a": "Outdoors [GENEPIO:0100216]" }, "Hunting Ground [ECTO:6000030]": { "text": "Hunting Ground [ECTO:6000030]", + "description": "An exposure event involving hunting behavior", "meaning": "ECTO:6000030", "is_a": "Outdoors [GENEPIO:0100216]" }, "Ski Resort [GENEPIO:0100218]": { "text": "Ski Resort [GENEPIO:0100218]", + "description": "A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100218", "is_a": "Outdoors [GENEPIO:0100216]" }, "Petting zoo [ECTO:5000008]": { "text": "Petting zoo [ECTO:5000008]", + "description": "A exposure event involving the interaction of an exposure receptor to petting zoo.", "meaning": "ECTO:5000008", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Place of Worship [GENEPIO:0100220]": { "text": "Place of Worship [GENEPIO:0100220]", + "description": "A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100220", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Church [GENEPIO:0100221]": { "text": "Church [GENEPIO:0100221]", + "description": "A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100221", "is_a": "Place of Worship [GENEPIO:0100220]" }, "Mosque [GENEPIO:0100222]": { "text": "Mosque [GENEPIO:0100222]", + "description": "A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100222", "is_a": "Place of Worship [GENEPIO:0100220]" }, "Temple [GENEPIO:0100223]": { "text": "Temple [GENEPIO:0100223]", + "description": "A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100223", "is_a": "Place of Worship [GENEPIO:0100220]" }, "Restaurant [ECTO:1000040]": { "text": "Restaurant [ECTO:1000040]", + "description": "A exposure event involving the interaction of an exposure receptor to restaurant.", "meaning": "ECTO:1000040", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Retail Store [ECTO:1000041]": { "text": "Retail Store [ECTO:1000041]", + "description": "A exposure event involving the interaction of an exposure receptor to shop.", "meaning": "ECTO:1000041", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "School [GENEPIO:0100224]": { "text": "School [GENEPIO:0100224]", + "description": "A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100224", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Temporary Residence [GENEPIO:0100225]": { "text": "Temporary Residence [GENEPIO:0100225]", + "description": "A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100225", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Homeless Shelter [GENEPIO:0100226]": { "text": "Homeless Shelter [GENEPIO:0100226]", + "description": "A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100226", "is_a": "Temporary Residence [GENEPIO:0100225]" }, "Hotel [GENEPIO:0100227]": { "text": "Hotel [GENEPIO:0100227]", + "description": "A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100227", "is_a": "Temporary Residence [GENEPIO:0100225]" }, "Veterinary Care Clinic [GENEPIO:0100228]": { "text": "Veterinary Care Clinic [GENEPIO:0100228]", + "description": "A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100228", "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" }, "Travel Exposure [GENEPIO:0100229]": { "text": "Travel Exposure [GENEPIO:0100229]", + "description": "A process occuring as a result of travel that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100229" }, "Travelled on a Cruise Ship [GENEPIO:0100230]": { "text": "Travelled on a Cruise Ship [GENEPIO:0100230]", + "description": "A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100230", "is_a": "Travel Exposure [GENEPIO:0100229]" }, "Travelled on a Plane [GENEPIO:0100231]": { "text": "Travelled on a Plane [GENEPIO:0100231]", + "description": "A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100231", "is_a": "Travel Exposure [GENEPIO:0100229]" }, "Travelled on Ground Transport [GENEPIO:0100232]": { "text": "Travelled on Ground Transport [GENEPIO:0100232]", + "description": "A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100232", "is_a": "Travel Exposure [GENEPIO:0100229]" }, "Other Exposure Setting [GENEPIO:0100235]": { "text": "Other Exposure Setting [GENEPIO:0100235]", + "description": "A process occuring that exposes the recipient organism to a material entity.", "meaning": "GENEPIO:0100235" } } }, - "prior Mpox infection menu": { - "name": "prior Mpox infection menu", + "PriorMpoxInfectionMenu": { + "name": "PriorMpoxInfectionMenu", + "title": "prior Mpox infection menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Prior infection": { "text": "Prior infection", + "description": "Antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100037" }, "No prior infection": { "text": "No prior infection", + "description": "An absence of antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100233" } } }, - "prior Mpox infection international menu": { - "name": "prior Mpox infection international menu", + "PriorMpoxInfectionInternationalMenu": { + "name": "PriorMpoxInfectionInternationalMenu", + "title": "prior Mpox infection international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Prior infection [GENEPIO:0100037]": { "text": "Prior infection [GENEPIO:0100037]", + "description": "Antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100037" }, "No prior infection [GENEPIO:0100233]": { "text": "No prior infection [GENEPIO:0100233]", + "description": "An absence of antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100233" } } }, - "prior Mpox antiviral treatment menu": { - "name": "prior Mpox antiviral treatment menu", + "PriorMpoxAntiviralTreatmentMenu": { + "name": "PriorMpoxAntiviralTreatmentMenu", + "title": "prior Mpox antiviral treatment menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Prior antiviral treatment": { "text": "Prior antiviral treatment", + "description": "Antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100037" }, "No prior antiviral treatment": { "text": "No prior antiviral treatment", + "description": "An absence of antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100233" } } }, - "prior Mpox antiviral treatment international menu": { - "name": "prior Mpox antiviral treatment international menu", + "PriorMpoxAntiviralTreatmentInternationalMenu": { + "name": "PriorMpoxAntiviralTreatmentInternationalMenu", + "title": "prior Mpox antiviral treatment international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Prior antiviral treatment [GENEPIO:0100037]": { "text": "Prior antiviral treatment [GENEPIO:0100037]", + "description": "Antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100037" }, "No prior antiviral treatment [GENEPIO:0100233]": { "text": "No prior antiviral treatment [GENEPIO:0100233]", + "description": "An absence of antiviral treatment administered prior to the current regimen or test.", "meaning": "GENEPIO:0100233" } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Mpox virus": { "text": "Mpox virus", + "description": "A zoonotic virus belonging to the Orthopoxvirus genus and closely related to the variola, cowpox, and vaccinia viruses. MPV is oval, with a lipoprotein outer membrane.", "meaning": "NCBITaxon:10244" } } }, - "organism international menu": { - "name": "organism international menu", + "OrganismInternationalMenu": { + "name": "OrganismInternationalMenu", + "title": "organism international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Mpox virus [NCBITaxon:10244]": { "text": "Mpox virus [NCBITaxon:10244]", + "description": "A zoonotic virus belonging to the Orthopoxvirus genus and closely related to the variola, cowpox, and vaccinia viruses. MPV is oval, with a lipoprotein outer membrane.", "meaning": "NCBITaxon:10244" } } }, - "host disease menu": { - "name": "host disease menu", + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host disease menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Mpox": { "text": "Mpox", + "description": "An infection that is caused by an Orthopoxvirus, which is transmitted by primates or rodents, and which is characterized by a prodromal syndrome of fever, chills, headache, myalgia, and lymphedema; initial symptoms are followed by a generalized papular rash that typically progresses from vesiculation through crusting over the course of two weeks.", "meaning": "MONDO:0002594" } } }, - "host disease international menu": { - "name": "host disease international menu", + "HostDiseaseInternationalMenu": { + "name": "HostDiseaseInternationalMenu", + "title": "host disease international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Mpox [MONDO:0002594]": { "text": "Mpox [MONDO:0002594]", + "description": "An infection that is caused by an Orthopoxvirus, which is transmitted by primates or rodents, and which is characterized by a prodromal syndrome of fever, chills, headache, myalgia, and lymphedema; initial symptoms are followed by a generalized papular rash that typically progresses from vesiculation through crusting over the course of two weeks.", "meaning": "MONDO:0002594" } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Cluster/Outbreak investigation": { "text": "Cluster/Outbreak investigation", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", "meaning": "GENEPIO:0100001" }, "Diagnostic testing": { "text": "Diagnostic testing", + "description": "A sampling strategy in which individuals are sampled in the context of diagnostic testing.", "meaning": "GENEPIO:0100002" }, "Research": { "text": "Research", + "description": "A sampling strategy in which individuals are sampled in order to perform research.", "meaning": "GENEPIO:0100003" }, "Surveillance": { "text": "Surveillance", + "description": "A sampling strategy in which individuals are sampled for surveillance investigations.", "meaning": "GENEPIO:0100004" } } }, - "purpose of sampling international menu": { - "name": "purpose of sampling international menu", + "PurposeOfSamplingInternationalMenu": { + "name": "PurposeOfSamplingInternationalMenu", + "title": "purpose of sampling international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Cluster/Outbreak investigation [GENEPIO:0100001]": { "text": "Cluster/Outbreak investigation [GENEPIO:0100001]", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", "meaning": "GENEPIO:0100001" }, "Diagnostic testing [GENEPIO:0100002]": { "text": "Diagnostic testing [GENEPIO:0100002]", + "description": "A sampling strategy in which individuals are sampled in the context of diagnostic testing.", "meaning": "GENEPIO:0100002" }, "Research [GENEPIO:0100003]": { "text": "Research [GENEPIO:0100003]", + "description": "A sampling strategy in which individuals are sampled in order to perform research.", "meaning": "GENEPIO:0100003" }, "Surveillance [GENEPIO:0100004]": { "text": "Surveillance [GENEPIO:0100004]", + "description": "A sampling strategy in which individuals are sampled for surveillance investigations.", "meaning": "GENEPIO:0100004" } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose of sequencing menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Baseline surveillance (random sampling)": { "text": "Baseline surveillance (random sampling)", + "description": "A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.", "meaning": "GENEPIO:0100005" }, "Targeted surveillance (non-random sampling)": { "text": "Targeted surveillance (non-random sampling)", + "description": "A surveillance sampling strategy in which an aspired outcome is explicity stated.", "meaning": "GENEPIO:0100006" }, "Priority surveillance project": { "text": "Priority surveillance project", + "description": "A targeted surveillance strategy which is considered important and/or urgent.", "meaning": "GENEPIO:0100007", "is_a": "Targeted surveillance (non-random sampling)" }, "Longitudinal surveillance (repeat sampling of individuals)": { "text": "Longitudinal surveillance (repeat sampling of individuals)", + "description": "A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time.", "meaning": "GENEPIO:0100009", "is_a": "Priority surveillance project" }, "Re-infection surveillance": { "text": "Re-infection surveillance", + "description": "A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time.", "meaning": "GENEPIO:0100010", "is_a": "Priority surveillance project" }, "Vaccine escape surveillance": { "text": "Vaccine escape surveillance", + "description": "A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest.", "meaning": "GENEPIO:0100011", "is_a": "Priority surveillance project" }, "Travel-associated surveillance": { "text": "Travel-associated surveillance", + "description": "A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms.", "meaning": "GENEPIO:0100012", "is_a": "Priority surveillance project" }, "Domestic travel surveillance": { "text": "Domestic travel surveillance", + "description": "A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms.", "meaning": "GENEPIO:0100013", "is_a": "Travel-associated surveillance" }, "Interstate/ interprovincial travel surveillance": { "text": "Interstate/ interprovincial travel surveillance", + "description": "A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation.", "meaning": "GENEPIO:0100275", "is_a": "Domestic travel surveillance" }, "Intra-state/ intra-provincial travel surveillance": { "text": "Intra-state/ intra-provincial travel surveillance", + "description": "A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation.", "meaning": "GENEPIO:0100276", "is_a": "Domestic travel surveillance" }, "International travel surveillance": { "text": "International travel surveillance", + "description": "A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms.", "meaning": "GENEPIO:0100014", "is_a": "Travel-associated surveillance" }, "Cluster/Outbreak investigation": { "text": "Cluster/Outbreak investigation", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", "meaning": "GENEPIO:0100019" }, "Multi-jurisdictional outbreak investigation": { "text": "Multi-jurisdictional outbreak investigation", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions.", "meaning": "GENEPIO:0100020", "is_a": "Cluster/Outbreak investigation" }, "Intra-jurisdictional outbreak investigation": { "text": "Intra-jurisdictional outbreak investigation", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction.", "meaning": "GENEPIO:0100021", "is_a": "Cluster/Outbreak investigation" }, "Research": { "text": "Research", + "description": "A sampling strategy in which individuals are sampled in order to perform research.", "meaning": "GENEPIO:0100022" }, "Viral passage experiment": { "text": "Viral passage experiment", + "description": "A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment.", "meaning": "GENEPIO:0100023", "is_a": "Research" }, "Protocol testing experiment": { "text": "Protocol testing experiment", + "description": "A research sampling strategy in which individuals are sampled in order to perform a protocol testing experiment.", "meaning": "GENEPIO:0100024", "is_a": "Research" }, "Retrospective sequencing": { "text": "Retrospective sequencing", + "description": "A sampling strategy in which stored samples from past events are sequenced.", "meaning": "GENEPIO:0100356" } } }, - "purpose of sequencing international menu": { - "name": "purpose of sequencing international menu", + "PurposeOfSequencingInternationalMenu": { + "name": "PurposeOfSequencingInternationalMenu", + "title": "purpose of sequencing international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Baseline surveillance (random sampling) [GENEPIO:0100005]": { "text": "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "description": "A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.", "meaning": "GENEPIO:0100005" }, "Targeted surveillance (non-random sampling) [GENEPIO:0100006]": { "text": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "description": "A surveillance sampling strategy in which an aspired outcome is explicity stated.", "meaning": "GENEPIO:0100006" }, "Priority surveillance project [GENEPIO:0100007]": { "text": "Priority surveillance project [GENEPIO:0100007]", + "description": "A targeted surveillance strategy which is considered important and/or urgent.", "meaning": "GENEPIO:0100007", "is_a": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]" }, "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]": { "text": "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "description": "A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time.", "meaning": "GENEPIO:0100009", "is_a": "Priority surveillance project [GENEPIO:0100007]" }, "Re-infection surveillance [GENEPIO:0100010]": { "text": "Re-infection surveillance [GENEPIO:0100010]", + "description": "A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time.", "meaning": "GENEPIO:0100010", "is_a": "Priority surveillance project [GENEPIO:0100007]" }, "Vaccine escape surveillance [GENEPIO:0100011]": { "text": "Vaccine escape surveillance [GENEPIO:0100011]", + "description": "A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest.", "meaning": "GENEPIO:0100011", "is_a": "Priority surveillance project [GENEPIO:0100007]" }, "Travel-associated surveillance [GENEPIO:0100012]": { "text": "Travel-associated surveillance [GENEPIO:0100012]", + "description": "A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms.", "meaning": "GENEPIO:0100012", "is_a": "Priority surveillance project [GENEPIO:0100007]" }, "Domestic travel surveillance [GENEPIO:0100013]": { "text": "Domestic travel surveillance [GENEPIO:0100013]", + "description": "A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms.", "meaning": "GENEPIO:0100013", "is_a": "Travel-associated surveillance [GENEPIO:0100012]" }, "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]": { "text": "Interstate/ interprovincial travel surveillance [GENEPIO:0100275]", + "description": "A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation.", "meaning": "GENEPIO:0100275", "is_a": "Domestic travel surveillance [GENEPIO:0100013]" }, "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]": { "text": "Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]", + "description": "A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation.", "meaning": "GENEPIO:0100276", "is_a": "Domestic travel surveillance [GENEPIO:0100013]" }, "International travel surveillance [GENEPIO:0100014]": { "text": "International travel surveillance [GENEPIO:0100014]", + "description": "A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms.", "meaning": "GENEPIO:0100014", "is_a": "Travel-associated surveillance [GENEPIO:0100012]" }, "Cluster/Outbreak investigation [GENEPIO:0100019]": { "text": "Cluster/Outbreak investigation [GENEPIO:0100019]", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", "meaning": "GENEPIO:0100019" }, "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]": { "text": "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions.", "meaning": "GENEPIO:0100020", "is_a": "Cluster/Outbreak investigation [GENEPIO:0100019]" }, "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]": { "text": "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction.", "meaning": "GENEPIO:0100021", "is_a": "Cluster/Outbreak investigation [GENEPIO:0100019]" }, "Research [GENEPIO:0100022]": { "text": "Research [GENEPIO:0100022]", + "description": "A sampling strategy in which individuals are sampled in order to perform research.", "meaning": "GENEPIO:0100022" }, "Viral passage experiment [GENEPIO:0100023]": { "text": "Viral passage experiment [GENEPIO:0100023]", + "description": "A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment.", "meaning": "GENEPIO:0100023", "is_a": "Research [GENEPIO:0100022]" }, "Protocol testing experiment [GENEPIO:0100024]": { "text": "Protocol testing experiment [GENEPIO:0100024]", + "description": "A research sampling strategy in which individuals are sampled in order to perform a protocol testing experiment.", "meaning": "GENEPIO:0100024", "is_a": "Research [GENEPIO:0100022]" }, "Retrospective sequencing [GENEPIO:0100356]": { "text": "Retrospective sequencing [GENEPIO:0100356]", + "description": "A sampling strategy in which stored samples from past events are sequenced.", "meaning": "GENEPIO:0100356" } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingAssayTypeMenu": { + "name": "SequencingAssayTypeMenu", + "title": "sequencing assay type menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Amplicon sequencing assay": { + "text": "Amplicon sequencing assay", + "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", + "meaning": "OBI:0002767" + }, + "16S ribosomal gene sequencing assay": { + "text": "16S ribosomal gene sequencing assay", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community.", + "meaning": "OBI:0002763", + "is_a": "Amplicon sequencing assay" + }, + "Whole genome sequencing assay": { + "text": "Whole genome sequencing assay", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", + "meaning": "OBI:0002117" + }, + "Whole metagenome sequencing assay": { + "text": "Whole metagenome sequencing assay", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", + "meaning": "OBI:0002623" + }, + "Whole virome sequencing assay": { + "text": "Whole virome sequencing assay", + "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", + "meaning": "OBI:0002768", + "is_a": "Whole metagenome sequencing assay" + } + } + }, + "SequencingAssayTypeInternationalMenu": { + "name": "SequencingAssayTypeInternationalMenu", + "title": "sequencing assay type international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Amplicon sequencing assay [OBI:0002767]": { + "text": "Amplicon sequencing assay [OBI:0002767]", + "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", + "meaning": "OBI:0002767" + }, + "16S ribosomal gene sequencing assay [OBI:0002763]": { + "text": "16S ribosomal gene sequencing assay [OBI:0002763]", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community.", + "meaning": "OBI:0002763", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "Whole genome sequencing assay [OBI:0002117]": { + "text": "Whole genome sequencing assay [OBI:0002117]", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", + "meaning": "OBI:0002117" + }, + "Whole metagenome sequencing assay [OBI:0002623]": { + "text": "Whole metagenome sequencing assay [OBI:0002623]", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", + "meaning": "OBI:0002623" + }, + "Whole virome sequencing assay [OBI:0002768]": { + "text": "Whole virome sequencing assay [OBI:0002768]", + "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", + "meaning": "OBI:0002768", + "is_a": "Whole metagenome sequencing assay [OBI:0002623]" + } + } + }, + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Illumina": { "text": "Illumina", + "description": "A DNA sequencer manufactured by the Illumina corporation.", "meaning": "GENEPIO:0100105" }, "Illumina Genome Analyzer": { "text": "Illumina 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It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", + "meaning": "OBI:0002000", "is_a": "Illumina Genome Analyzer" }, "Illumina HiScanSQ": { "text": "Illumina HiScanSQ", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an \"SQ Module\" to support microfluidics.", "meaning": "GENEPIO:0100109", "is_a": "Illumina" }, "Illumina HiSeq": { "text": "Illumina HiSeq", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.", "meaning": "GENEPIO:0100110", "is_a": "Illumina" }, "Illumina HiSeq X": { "text": "Illumina HiSeq X", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000.", "meaning": "GENEPIO:0100111", "is_a": "Illumina HiSeq" }, "Illumina HiSeq X Five": { "text": "Illumina HiSeq X Five", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", "meaning": "GENEPIO:0100112", "is_a": "Illumina HiSeq X" }, "Illumina HiSeq X Ten": { "text": "Illumina HiSeq X Ten", - "meaning": "GENEPIO:0100113", + "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", + "meaning": "OBI:0002129", "is_a": "Illumina HiSeq X" }, "Illumina HiSeq 1000": { "text": "Illumina HiSeq 1000", - "meaning": "GENEPIO:0100114", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. 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Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", + "meaning": "OBI:0002001", "is_a": "Illumina HiSeq" }, "Illumina HiSeq 2500": { "text": "Illumina HiSeq 2500", - "meaning": "GENEPIO:0100117", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", + "meaning": "OBI:0002002", "is_a": "Illumina HiSeq" }, "Illumina HiSeq 3000": { "text": "Illumina HiSeq 3000", - "meaning": "GENEPIO:0100118", + "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", + "meaning": "OBI:0002048", "is_a": "Illumina HiSeq" }, "Illumina HiSeq 4000": { "text": "Illumina HiSeq 4000", - "meaning": "GENEPIO:0100119", + "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", + "meaning": "OBI:0002049", "is_a": "Illumina HiSeq" }, "Illumina iSeq": { "text": "Illumina iSeq", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", "meaning": "GENEPIO:0100120", "is_a": "Illumina" }, "Illumina iSeq 100": { "text": "Illumina iSeq 100", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", "meaning": "GENEPIO:0100121", "is_a": "Illumina iSeq" }, "Illumina NovaSeq": { "text": "Illumina NovaSeq", + "description": "A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode.", "meaning": "GENEPIO:0100122", "is_a": "Illumina" }, "Illumina NovaSeq 6000": { "text": "Illumina NovaSeq 6000", - "meaning": "GENEPIO:0100123", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", + "meaning": "OBI:0002630", "is_a": "Illumina NovaSeq" }, "Illumina MiniSeq": { "text": "Illumina MiniSeq", - "meaning": "GENEPIO:0100124", + "description": "A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.", + "meaning": "OBI:0003114", "is_a": "Illumina" }, "Illumina MiSeq": { "text": "Illumina MiSeq", - "meaning": "GENEPIO:0100125", + "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", + "meaning": "OBI:0002003", "is_a": "Illumina" }, "Illumina NextSeq": { "text": "Illumina NextSeq", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", "meaning": "GENEPIO:0100126", "is_a": "Illumina" }, "Illumina NextSeq 500": { "text": "Illumina NextSeq 500", - "meaning": "GENEPIO:0100127", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002021", "is_a": "Illumina NextSeq" }, "Illumina NextSeq 550": { "text": "Illumina NextSeq 550", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", "meaning": "GENEPIO:0100128", "is_a": "Illumina NextSeq" }, + "Illumina NextSeq 1000": { + "text": "Illumina NextSeq 1000", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", + "meaning": "OBI:0003606", + "is_a": "Illumina NextSeq" + }, "Illumina NextSeq 2000": { "text": "Illumina NextSeq 2000", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", "meaning": "GENEPIO:0100129", "is_a": "Illumina NextSeq" }, "Pacific Biosciences": { "text": "Pacific Biosciences", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation.", "meaning": "GENEPIO:0100130" }, "PacBio RS": { "text": "PacBio RS", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", "meaning": "GENEPIO:0100131", "is_a": "Pacific Biosciences" }, "PacBio RS II": { "text": "PacBio RS II", - "meaning": "GENEPIO:0100132", + "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", + "meaning": "OBI:0002012", "is_a": "Pacific Biosciences" }, "PacBio Sequel": { "text": "PacBio Sequel", - "meaning": "GENEPIO:0100133", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", + "meaning": "OBI:0002632", "is_a": "Pacific Biosciences" }, "PacBio Sequel II": { "text": "PacBio Sequel II", - "meaning": "GENEPIO:0100134", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", + "meaning": "OBI:0002633", "is_a": "Pacific Biosciences" }, "Ion Torrent": { "text": "Ion Torrent", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation.", "meaning": "GENEPIO:0100135" }, "Ion Torrent PGM": { "text": "Ion Torrent PGM", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", "meaning": "GENEPIO:0100136", "is_a": "Ion Torrent" }, "Ion Torrent Proton": { "text": "Ion Torrent Proton", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", "meaning": "GENEPIO:0100137", "is_a": "Ion Torrent" }, "Ion Torrent S5 XL": { "text": "Ion Torrent S5 XL", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", "meaning": "GENEPIO:0100138", "is_a": "Ion Torrent" }, "Ion Torrent S5": { "text": "Ion Torrent S5", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", "meaning": "GENEPIO:0100139", "is_a": "Ion Torrent" }, "Oxford Nanopore": { "text": "Oxford Nanopore", + "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation.", "meaning": "GENEPIO:0100140" }, + "Oxford Nanopore Flongle": { + "text": "Oxford Nanopore Flongle", + "description": "An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.", + "meaning": "GENEPIO:0004433", + "is_a": "Oxford Nanopore" + }, "Oxford Nanopore GridION": { "text": "Oxford Nanopore GridION", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", "meaning": "GENEPIO:0100141", "is_a": "Oxford Nanopore" }, "Oxford Nanopore MinION": { "text": "Oxford Nanopore MinION", - "meaning": "GENEPIO:0100142", + "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", + "meaning": "OBI:0002750", "is_a": "Oxford Nanopore" }, "Oxford Nanopore PromethION": { "text": "Oxford Nanopore PromethION", - "meaning": "GENEPIO:0100143", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", + "meaning": "OBI:0002752", "is_a": "Oxford Nanopore" }, "BGI Genomics": { "text": "BGI Genomics", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation.", "meaning": "GENEPIO:0100144" }, "BGI Genomics BGISEQ-500": { "text": "BGI Genomics BGISEQ-500", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", "meaning": "GENEPIO:0100145", "is_a": "BGI Genomics" }, "MGI": { "text": "MGI", + "description": "A DNA sequencer manufactured by the MGI corporation.", "meaning": "GENEPIO:0100146" }, "MGI DNBSEQ-T7": { "text": "MGI DNBSEQ-T7", + "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day.", "meaning": "GENEPIO:0100147", "is_a": "MGI" }, "MGI DNBSEQ-G400": { "text": "MGI DNBSEQ-G400", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run.", "meaning": "GENEPIO:0100148", "is_a": "MGI" }, "MGI DNBSEQ-G400 FAST": { "text": "MGI DNBSEQ-G400 FAST", + "description": "A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400.", "meaning": "GENEPIO:0100149", "is_a": "MGI" }, "MGI DNBSEQ-G50": { "text": "MGI DNBSEQ-G50", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", "meaning": "GENEPIO:0100150", "is_a": "MGI" } } }, - "sequencing instrument international menu": { - "name": "sequencing instrument international menu", + "SequencingInstrumentInternationalMenu": { + "name": "SequencingInstrumentInternationalMenu", + "title": "sequencing instrument international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Illumina [GENEPIO:0100105]": { "text": "Illumina [GENEPIO:0100105]", + "description": "A DNA sequencer manufactured by the Illumina corporation.", "meaning": "GENEPIO:0100105" }, - "Illumina Genome Analyzer [GENEPIO:0100106]": { - "text": "Illumina Genome Analyzer [GENEPIO:0100106]", - "meaning": "GENEPIO:0100106", + "Illumina Genome Analyzer [OBI:0002128]": { + "text": "Illumina Genome Analyzer [OBI:0002128]", + "description": "A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.", + "meaning": "OBI:0002128", "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina Genome Analyzer II [GENEPIO:0100107]": { - "text": "Illumina Genome Analyzer II [GENEPIO:0100107]", - "meaning": "GENEPIO:0100107", - "is_a": "Illumina Genome Analyzer [GENEPIO:0100106]" + "Illumina Genome Analyzer II [OBI:0000703]": { + "text": "Illumina Genome Analyzer II [OBI:0000703]", + "description": "A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology", + "meaning": "OBI:0000703", + "is_a": "Illumina Genome Analyzer [OBI:0002128]" }, - "Illumina Genome Analyzer IIx [GENEPIO:0100108]": { - "text": "Illumina Genome Analyzer IIx [GENEPIO:0100108]", - "meaning": "GENEPIO:0100108", - "is_a": "Illumina Genome Analyzer [GENEPIO:0100106]" + "Illumina Genome Analyzer IIx [OBI:0002000]": { + "text": "Illumina Genome Analyzer IIx [OBI:0002000]", + "description": "An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", + "meaning": "OBI:0002000", + "is_a": "Illumina Genome Analyzer [OBI:0002128]" }, "Illumina HiScanSQ [GENEPIO:0100109]": { "text": "Illumina HiScanSQ [GENEPIO:0100109]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an \"SQ Module\" to support microfluidics.", "meaning": "GENEPIO:0100109", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina HiSeq [GENEPIO:0100110]": { "text": "Illumina HiSeq [GENEPIO:0100110]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.", "meaning": "GENEPIO:0100110", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina HiSeq X [GENEPIO:0100111]": { "text": "Illumina HiSeq X [GENEPIO:0100111]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000.", "meaning": "GENEPIO:0100111", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina HiSeq X Five [GENEPIO:0100112]": { "text": "Illumina HiSeq X Five [GENEPIO:0100112]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", "meaning": "GENEPIO:0100112", "is_a": "Illumina HiSeq X [GENEPIO:0100111]" }, - "Illumina HiSeq X Ten [GENEPIO:0100113]": { - "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", - "meaning": "GENEPIO:0100113", + "Illumina HiSeq X Ten [OBI:0002129]": { + "text": "Illumina HiSeq X Ten [OBI:0002129]", + "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", + "meaning": "OBI:0002129", "is_a": "Illumina HiSeq X [GENEPIO:0100111]" }, - "Illumina HiSeq 1000 [GENEPIO:0100114]": { - "text": "Illumina HiSeq 1000 [GENEPIO:0100114]", - "meaning": "GENEPIO:0100114", + "Illumina HiSeq 1000 [OBI:0002022]": { + "text": "Illumina HiSeq 1000 [OBI:0002022]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002022", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 1500 [GENEPIO:0100115]": { - "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", - "meaning": "GENEPIO:0100115", + "Illumina HiSeq 1500 [OBI:0003386]": { + "text": "Illumina HiSeq 1500 [OBI:0003386]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option.", + "meaning": "OBI:0003386", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 2000 [GENEPIO:0100116]": { - "text": "Illumina HiSeq 2000 [GENEPIO:0100116]", - "meaning": "GENEPIO:0100116", + "Illumina HiSeq 2000 [OBI:0002001]": { + "text": "Illumina HiSeq 2000 [OBI:0002001]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", + "meaning": "OBI:0002001", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 2500 [GENEPIO:0100117]": { - "text": "Illumina HiSeq 2500 [GENEPIO:0100117]", - "meaning": "GENEPIO:0100117", + "Illumina HiSeq 2500 [OBI:0002002]": { + "text": "Illumina HiSeq 2500 [OBI:0002002]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", + "meaning": "OBI:0002002", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 3000 [GENEPIO:0100118]": { - "text": "Illumina HiSeq 3000 [GENEPIO:0100118]", - "meaning": "GENEPIO:0100118", + "Illumina HiSeq 3000 [OBI:0002048]": { + "text": "Illumina HiSeq 3000 [OBI:0002048]", + "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", + "meaning": "OBI:0002048", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 4000 [GENEPIO:0100119]": { - "text": "Illumina HiSeq 4000 [GENEPIO:0100119]", - "meaning": "GENEPIO:0100119", + "Illumina HiSeq 4000 [OBI:0002049]": { + "text": "Illumina HiSeq 4000 [OBI:0002049]", + "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", + "meaning": "OBI:0002049", "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, "Illumina iSeq [GENEPIO:0100120]": { "text": "Illumina iSeq [GENEPIO:0100120]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", "meaning": "GENEPIO:0100120", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina iSeq 100 [GENEPIO:0100121]": { "text": "Illumina iSeq 100 [GENEPIO:0100121]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", "meaning": "GENEPIO:0100121", "is_a": "Illumina iSeq [GENEPIO:0100120]" }, "Illumina NovaSeq [GENEPIO:0100122]": { "text": "Illumina NovaSeq [GENEPIO:0100122]", + "description": "A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode.", "meaning": "GENEPIO:0100122", "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina NovaSeq 6000 [GENEPIO:0100123]": { - "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", - "meaning": "GENEPIO:0100123", + "Illumina NovaSeq 6000 [OBI:0002630]": { + "text": "Illumina NovaSeq 6000 [OBI:0002630]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", + "meaning": "OBI:0002630", "is_a": "Illumina NovaSeq [GENEPIO:0100122]" }, - "Illumina MiniSeq [GENEPIO:0100124]": { - "text": "Illumina MiniSeq [GENEPIO:0100124]", - "meaning": "GENEPIO:0100124", + "Illumina MiniSeq [OBI:0003114]": { + "text": "Illumina MiniSeq [OBI:0003114]", + "description": "A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run.", + "meaning": "OBI:0003114", "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina MiSeq [GENEPIO:0100125]": { - "text": "Illumina MiSeq [GENEPIO:0100125]", - "meaning": "GENEPIO:0100125", + "Illumina MiSeq [OBI:0002003]": { + "text": "Illumina MiSeq [OBI:0002003]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", + "meaning": "OBI:0002003", "is_a": "Illumina [GENEPIO:0100105]" }, "Illumina NextSeq [GENEPIO:0100126]": { "text": "Illumina NextSeq [GENEPIO:0100126]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", "meaning": "GENEPIO:0100126", "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina NextSeq 500 [GENEPIO:0100127]": { - "text": "Illumina NextSeq 500 [GENEPIO:0100127]", - "meaning": "GENEPIO:0100127", + "Illumina NextSeq 500 [OBI:0002021]": { + "text": "Illumina NextSeq 500 [OBI:0002021]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002021", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "Illumina NextSeq 550 [GENEPIO:0100128]": { "text": "Illumina NextSeq 550 [GENEPIO:0100128]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", "meaning": "GENEPIO:0100128", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, + "Illumina NextSeq 1000 [OBI:0003606]": { + "text": "Illumina NextSeq 1000 [OBI:0003606]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", + "meaning": "OBI:0003606", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, "Illumina NextSeq 2000 [GENEPIO:0100129]": { "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", "meaning": "GENEPIO:0100129", "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, "Pacific Biosciences [GENEPIO:0100130]": { "text": "Pacific Biosciences [GENEPIO:0100130]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation.", "meaning": "GENEPIO:0100130" }, "PacBio RS [GENEPIO:0100131]": { "text": "PacBio RS [GENEPIO:0100131]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", "meaning": "GENEPIO:0100131", "is_a": "Pacific Biosciences [GENEPIO:0100130]" }, - "PacBio RS II [GENEPIO:0100132]": { - "text": "PacBio RS II [GENEPIO:0100132]", - "meaning": "GENEPIO:0100132", + "PacBio RS II [OBI:0002012]": { + "text": "PacBio RS II [OBI:0002012]", + "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", + "meaning": "OBI:0002012", "is_a": "Pacific Biosciences [GENEPIO:0100130]" }, - "PacBio Sequel [GENEPIO:0100133]": { - "text": "PacBio Sequel [GENEPIO:0100133]", - "meaning": "GENEPIO:0100133", + "PacBio Sequel [OBI:0002632]": { + "text": "PacBio Sequel [OBI:0002632]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", + "meaning": "OBI:0002632", "is_a": "Pacific Biosciences [GENEPIO:0100130]" }, - "PacBio Sequel II [GENEPIO:0100134]": { - "text": "PacBio Sequel II [GENEPIO:0100134]", - "meaning": "GENEPIO:0100134", + "PacBio Sequel II [OBI:0002633]": { + "text": "PacBio Sequel II [OBI:0002633]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", + "meaning": "OBI:0002633", "is_a": "Pacific Biosciences [GENEPIO:0100130]" }, "Ion Torrent [GENEPIO:0100135": { "text": "Ion Torrent [GENEPIO:0100135", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation.", "meaning": "GENEPIO:0100135" }, - "Ion Torrent PGM [GENEPIO:0100136": { - "text": "Ion Torrent PGM [GENEPIO:0100136", + "Ion Torrent PGM [GENEPIO:0100136]": { + "text": "Ion Torrent PGM [GENEPIO:0100136]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", "meaning": "GENEPIO:0100136", "is_a": "Ion Torrent [GENEPIO:0100135" }, "Ion Torrent Proton [GENEPIO:0100137]": { "text": "Ion Torrent Proton [GENEPIO:0100137]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", "meaning": "GENEPIO:0100137", "is_a": "Ion Torrent [GENEPIO:0100135" }, "Ion Torrent S5 XL [GENEPIO:0100138]": { "text": "Ion Torrent S5 XL [GENEPIO:0100138]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", "meaning": "GENEPIO:0100138", "is_a": "Ion Torrent [GENEPIO:0100135" }, "Ion Torrent S5 [GENEPIO:0100139]": { "text": "Ion Torrent S5 [GENEPIO:0100139]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", "meaning": "GENEPIO:0100139", "is_a": "Ion Torrent [GENEPIO:0100135" }, "Oxford Nanopore [GENEPIO:0100140]": { "text": "Oxford Nanopore [GENEPIO:0100140]", + "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation.", "meaning": "GENEPIO:0100140" }, - "Oxford Nanopore GridION [GENEPIO:0100141": { - "text": "Oxford Nanopore GridION [GENEPIO:0100141", + "Oxford Nanopore Flongle [GENEPIO:0004433]": { + "text": "Oxford Nanopore Flongle [GENEPIO:0004433]", + "description": "An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.", + "meaning": "GENEPIO:0004433", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore GridION [GENEPIO:0100141]": { + "text": "Oxford Nanopore GridION [GENEPIO:0100141]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", "meaning": "GENEPIO:0100141", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore MinION [GENEPIO:0100142]": { - "text": "Oxford Nanopore MinION [GENEPIO:0100142]", - "meaning": "GENEPIO:0100142", + "Oxford Nanopore MinION [OBI:0002750]": { + "text": "Oxford Nanopore MinION [OBI:0002750]", + "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", + "meaning": "OBI:0002750", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore PromethION [GENEPIO:0100143]": { - "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", - "meaning": "GENEPIO:0100143", + "Oxford Nanopore PromethION [OBI:0002752]": { + "text": "Oxford Nanopore PromethION [OBI:0002752]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", + "meaning": "OBI:0002752", "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, "BGI Genomics [GENEPIO:0100144]": { "text": "BGI Genomics [GENEPIO:0100144]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation.", "meaning": "GENEPIO:0100144" }, "BGI Genomics BGISEQ-500 [GENEPIO:0100145]": { "text": "BGI Genomics BGISEQ-500 [GENEPIO:0100145]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", "meaning": "GENEPIO:0100145", "is_a": "BGI Genomics [GENEPIO:0100144]" }, "MGI [GENEPIO:0100146]": { "text": "MGI [GENEPIO:0100146]", + "description": "A DNA sequencer manufactured by the MGI corporation.", "meaning": "GENEPIO:0100146" }, "MGI DNBSEQ-T7 [GENEPIO:0100147]": { "text": "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day.", "meaning": "GENEPIO:0100147", "is_a": "MGI [GENEPIO:0100146]" }, "MGI DNBSEQ-G400 [GENEPIO:0100148]": { "text": "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run.", "meaning": "GENEPIO:0100148", "is_a": "MGI [GENEPIO:0100146]" }, "MGI DNBSEQ-G400 FAST [GENEPIO:0100149]": { "text": "MGI DNBSEQ-G400 FAST [GENEPIO:0100149]", + "description": "A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400.", "meaning": "GENEPIO:0100149", "is_a": "MGI [GENEPIO:0100146]" }, "MGI DNBSEQ-G50 [GENEPIO:0100150]": { "text": "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", "meaning": "GENEPIO:0100150", "is_a": "MGI [GENEPIO:0100146]" } } }, - "sequence submitted by menu": { - "name": "sequence submitted by menu", + "GenomicTargetEnrichmentMethodMenu": { + "name": "GenomicTargetEnrichmentMethodMenu", + "title": "genomic target enrichment method menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Hybridization capture": { + "text": "Hybridization capture", + "description": "Selection by hybridization in array or solution.", + "meaning": "GENEPIO:0001950" + }, + "rRNA depletion method": { + "text": "rRNA depletion method", + "description": "Removal of background RNA for the purposes of enriching the genomic target.", + "meaning": "GENEPIO:0101020" + } + } + }, + "GenomicTargetEnrichmentMethodInternationalMenu": { + "name": "GenomicTargetEnrichmentMethodInternationalMenu", + "title": "genomic target enrichment method international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Hybridization capture [GENEPIO:0001950]": { + "text": "Hybridization capture [GENEPIO:0001950]", + "description": "Selection by hybridization in array or solution.", + "meaning": "GENEPIO:0001950" + }, + "rRNA depletion method [GENEPIO:0101020]": { + "text": "rRNA depletion method [GENEPIO:0101020]", + "description": "Removal of background RNA for the purposes of enriching the genomic target.", + "meaning": "GENEPIO:0101020" + } + } + }, + "QualityControlDeterminationMenu": { + "name": "QualityControlDeterminationMenu", + "title": "quality control determination menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "No quality control issues identified": { + "text": "No quality control issues identified", + "description": "A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected.", + "meaning": "GENEPIO:0100562" + }, + "Sequence passed quality control": { + "text": "Sequence passed quality control", + "description": "A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", + "meaning": "GENEPIO:0100563" + }, + "Sequence failed quality control": { + "text": "Sequence failed quality control", + "description": "A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", + "meaning": "GENEPIO:0100564" + }, + "Minor quality control issues identified": { + "text": "Minor quality control issues identified", + "description": "A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", + "meaning": "GENEPIO:0100565" + }, + "Sequence flagged for potential quality control issues": { + "text": "Sequence flagged for potential quality control issues", + "description": "A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", + "meaning": "GENEPIO:0100566" + }, + "Quality control not performed": { + "text": "Quality control not performed", + "description": "A data item which is a statement confirming that quality control processes have not been carried out.", + "meaning": "GENEPIO:0100567" + } + } + }, + "QualityControlDeterminationInternationalMenu": { + "name": "QualityControlDeterminationInternationalMenu", + "title": "quality control determination international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "No quality control issues identified [GENEPIO:0100562]": { + "text": "No quality control issues identified [GENEPIO:0100562]", + "description": "A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected.", + "meaning": "GENEPIO:0100562" + }, + "Sequence passed quality control [GENEPIO:0100563]": { + "text": "Sequence passed quality control [GENEPIO:0100563]", + "description": "A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", + "meaning": "GENEPIO:0100563" + }, + "Sequence failed quality control [GENEPIO:0100564]": { + "text": "Sequence failed quality control [GENEPIO:0100564]", + "description": "A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", + "meaning": "GENEPIO:0100564" + }, + "Minor quality control issues identified [GENEPIO:0100565]": { + "text": "Minor quality control issues identified [GENEPIO:0100565]", + "description": "A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", + "meaning": "GENEPIO:0100565" + }, + "Sequence flagged for potential quality control issues [GENEPIO:0100566]": { + "text": "Sequence flagged for potential quality control issues [GENEPIO:0100566]", + "description": "A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", + "meaning": "GENEPIO:0100566" + }, + "Quality control not performed [GENEPIO:0100567]": { + "text": "Quality control not performed [GENEPIO:0100567]", + "description": "A data item which is a statement confirming that quality control processes have not been carried out.", + "meaning": "GENEPIO:0100567" + } + } + }, + "QualityControlIssuesMenu": { + "name": "QualityControlIssuesMenu", + "title": "quality control issues menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Low quality sequence": { + "text": "Low quality sequence", + "description": "A data item that describes sequence data that does not meet quality control thresholds.", + "meaning": "GENEPIO:0100568" + }, + "Sequence contaminated": { + "text": "Sequence contaminated", + "description": "A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", + "meaning": "GENEPIO:0100569" + }, + "Low average genome coverage": { + "text": "Low average genome coverage", + "description": "A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", + "meaning": "GENEPIO:0100570" + }, + "Low percent genome captured": { + "text": "Low percent genome captured", + "description": "A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", + "meaning": "GENEPIO:0100571" + }, + "Read lengths shorter than expected": { + "text": "Read lengths shorter than expected", + "description": "A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", + "meaning": "GENEPIO:0100572" + }, + "Sequence amplification artifacts": { + "text": "Sequence amplification artifacts", + "description": "A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", + "meaning": "GENEPIO:0100573" + }, + "Low signal to noise ratio": { + "text": "Low signal to noise ratio", + "description": "A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", + "meaning": "GENEPIO:0100574" + }, + "Low coverage of characteristic mutations": { + "text": "Low coverage of characteristic mutations", + "description": "A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", + "meaning": "GENEPIO:0100575" + } + } + }, + "QualityControlIssuesInternationalMenu": { + "name": "QualityControlIssuesInternationalMenu", + "title": "quality control issues international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "Low quality sequence [GENEPIO:0100568]": { + "text": "Low quality sequence [GENEPIO:0100568]", + "description": "A data item that describes sequence data that does not meet quality control thresholds.", + "meaning": "GENEPIO:0100568" + }, + "Sequence contaminated [GENEPIO:0100569]": { + "text": "Sequence contaminated [GENEPIO:0100569]", + "description": "A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", + "meaning": "GENEPIO:0100569" + }, + "Low average genome coverage [GENEPIO:0100570]": { + "text": "Low average genome coverage [GENEPIO:0100570]", + "description": "A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", + "meaning": "GENEPIO:0100570" + }, + "Low percent genome captured [GENEPIO:0100571]": { + "text": "Low percent genome captured [GENEPIO:0100571]", + "description": "A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", + "meaning": "GENEPIO:0100571" + }, + "Read lengths shorter than expected [GENEPIO:0100572]": { + "text": "Read lengths shorter than expected [GENEPIO:0100572]", + "description": "A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", + "meaning": "GENEPIO:0100572" + }, + "Sequence amplification artifacts [GENEPIO:0100573]": { + "text": "Sequence amplification artifacts [GENEPIO:0100573]", + "description": "A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", + "meaning": "GENEPIO:0100573" + }, + "Low signal to noise ratio [GENEPIO:0100574]": { + "text": "Low signal to noise ratio [GENEPIO:0100574]", + "description": "A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", + "meaning": "GENEPIO:0100574" + }, + "Low coverage of characteristic mutations [GENEPIO:0100575]": { + "text": "Low coverage of characteristic mutations [GENEPIO:0100575]", + "description": "A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", + "meaning": "GENEPIO:0100575" + } + } + }, + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", + "title": "sequence submitted by menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -4601,7 +5889,8 @@ "text": "Manitoba Cadham Provincial Laboratory" }, "McGill University": { - "text": "McGill University" + "text": "McGill University", + "description": "McGill University is an English-language public research university located in Montreal, Quebec, Canada." }, "McMaster University": { "text": "McMaster University" @@ -4641,8 +5930,9 @@ } } }, - "sequenced by menu": { - "name": "sequenced by menu", + "SequencedByMenu": { + "name": "SequencedByMenu", + "title": "sequenced by menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -4684,7 +5974,8 @@ "text": "Manitoba Cadham Provincial Laboratory" }, "McGill University": { - "text": "McGill University" + "text": "McGill University", + "description": "McGill University is an English-language public research university located in Montreal, Quebec, Canada." }, "McMaster University": { "text": "McMaster University" @@ -4724,8 +6015,9 @@ } } }, - "sample collected by menu": { - "name": "sample collected by menu", + "SampleCollectedByMenu": { + "name": "SampleCollectedByMenu", + "title": "sample collected by menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -4831,8 +6123,9 @@ } } }, - "gene name menu": { - "name": "gene name menu", + "GeneNameMenu": { + "name": "GeneNameMenu", + "title": "gene name menu", "from_schema": "https://example.com/mpox", "permissible_values": { "MPX (orf B6R)": { @@ -4860,2190 +6153,3601 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeneSymbolInternationalMenu": { + "name": "GeneSymbolInternationalMenu", + "title": "gene symbol international menu", + "from_schema": "https://example.com/mpox", + "permissible_values": { + "opg001 gene (MPOX)": { + "text": "opg001 gene (MPOX)", + "description": "A gene that encodes the Chemokine binding protein (MPOX).", + "meaning": "GENEPIO:0101382" + }, + "opg002 gene (MPOX)": { + "text": "opg002 gene (MPOX)", + "description": "A gene that encodes the Crm-B secreted TNF-alpha-receptor-like protein (MPOX).", + "meaning": "GENEPIO:0101383" + }, + "opg003 gene (MPOX)": { + "text": "opg003 gene (MPOX)", + "description": "A gene that encodes the Ankyrin repeat protein (25) (MPOX).", + "meaning": "GENEPIO:0101384" + }, + "opg015 gene (MPOX)": { + "text": "opg015 gene (MPOX)", + "description": "A gene that encodes the Ankyrin repeat protein (39) (MPOX).", + "meaning": "GENEPIO:0101385" + }, + "opg019 gene (MPOX)": { + "text": "opg019 gene (MPOX)", + "description": "A gene that encodes the EGF-like domain protein (MPOX).", + "meaning": "GENEPIO:0101386" + }, + "opg021 gene (MPOX)": { + "text": "opg021 gene (MPOX)", + "description": "A gene that encodes the Zinc finger-like protein (2) (MPOX).", + "meaning": "GENEPIO:0101387" + }, + "opg022 gene (MPOX)": { + "text": "opg022 gene (MPOX)", + "description": "A gene that encodes the Interleukin-18-binding protein (MPOX).", + "meaning": "GENEPIO:0101388" + }, + "opg023 gene (MPOX)": { + "text": "opg023 gene (MPOX)", + "description": "A gene that encodes the Ankyrin repeat protein (2) (MPOX).", + "meaning": "GENEPIO:0101389" + }, + "opg024 gene (MPOX)": { + "text": "opg024 gene (MPOX)", + "description": "A gene that encodes the retroviral pseudoprotease-like protein (MPOX).", + "meaning": "GENEPIO:0101390" + }, + "opg025 gene (MPOX)": { + "text": "opg025 gene (MPOX)", + "description": "A gene that encodes the Ankyrin repeat protein (14) (MPOX).", + "meaning": "GENEPIO:0101391" + }, + "opg027 gene (MPOX)": { + "text": "opg027 gene (MPOX)", + "description": "A gene that encodes the Host range protein (MPOX).", + "meaning": "GENEPIO:0101392" + }, + "opg029 gene (MPOX)": { + "text": "opg029 gene (MPOX)", + "description": "A gene that encodes the Bcl-2-like protein (MPOX).", + "meaning": "GENEPIO:0101393" + }, + "opg030 gene (MPOX)": { + "text": "opg030 gene (MPOX)", + "description": "A gene that encodes the Kelch-like protein (1) (MPOX).", + "meaning": "GENEPIO:0101394" + }, + "opg031 gene (MPOX)": { + "text": "opg031 gene (MPOX)", + "description": "A gene that encodes the C4L/C10L-like family protein (MPOX).", + "meaning": "GENEPIO:0101395" + }, + "opg034 gene (MPOX)": { + "text": "opg034 gene (MPOX)", + "description": "A gene that encodes the Bcl-2-like protein (MPOX).", + "meaning": "GENEPIO:0101396" + }, + "opg035 gene (MPOX)": { + "text": "opg035 gene (MPOX)", + "description": "A gene that encodes the Bcl-2-like protein (MPOX).", + "meaning": "GENEPIO:0101397" + }, + "opg037 gene (MPOX)": { + "text": "opg037 gene (MPOX)", + "description": "A gene that encodes the Ankyrin-like protein (1) (MPOX).", + "meaning": "GENEPIO:0101399" + }, + "opg038 gene (MPOX)": { + "text": "opg038 gene (MPOX)", + "description": "A gene that encodes the NFkB inhibitor protein (MPOX).", + "meaning": "GENEPIO:0101400" + }, + "opg039 gene (MPOX)": { + "text": "opg039 gene (MPOX)", + "description": "A gene that encodes the Ankyrin-like protein (3) (MPOX).", + "meaning": "GENEPIO:0101401" + }, + "opg040 gene (MPOX)": { + "text": "opg040 gene (MPOX)", + "description": "A gene that encodes the Serpin protein (MPOX).", + "meaning": "GENEPIO:0101402" + }, + "opg042 gene (MPOX)": { + "text": "opg042 gene (MPOX)", + "description": "A gene that encodes the Phospholipase-D-like protein (MPOX).", + "meaning": "GENEPIO:0101403" + }, + "opg043 gene (MPOX)": { + "text": "opg043 gene (MPOX)", + "description": "A gene that encodes the Putative monoglyceride lipase protein (MPOX).", + "meaning": "GENEPIO:0101404" + }, + "opg045 gene (MPOX)": { + "text": "opg045 gene (MPOX)", + "description": "A gene that encodes the Caspase-9 inhibitor protein (MPOX).", + "meaning": "GENEPIO:0101406" + }, + "opg046 gene (MPOX)": { + "text": "opg046 gene (MPOX)", + "description": "A gene that encodes the dUTPase protein (MPOX).", + "meaning": "GENEPIO:0101407" + }, + "opg047 gene (MPOX)": { + "text": "opg047 gene (MPOX)", + "description": "A gene that encodes the Kelch-like protein (2) (MPOX).", + "meaning": "GENEPIO:0101408" + }, + "opg048 gene (MPOX)": { + "text": "opg048 gene (MPOX)", + "description": "A gene that encodes the Ribonucleotide reductase small subunit protein (MPOX).", + "meaning": "GENEPIO:0101409" + }, + "opg049 gene (MPOX)": { + "text": "opg049 gene (MPOX)", + "description": "A gene that encodes the Telomere-binding protein I6 (1) (MPOX).", + "meaning": "GENEPIO:0101410" + }, + "opg050 gene (MPOX)": { + "text": "opg050 gene (MPOX)", + "description": "A gene that encodes the CPXV053 protein (MPOX).", + "meaning": "GENEPIO:0101411" + }, + "opg051 gene (MPOX)": { + "text": "opg051 gene (MPOX)", + "description": "A gene that encodes the CPXV054 protein (MPOX).", + "meaning": "GENEPIO:0101412" + }, + "opg052 gene (MPOX)": { + "text": "opg052 gene (MPOX)", + "description": "A gene that encodes the Cytoplasmic protein (MPOX).", + "meaning": "GENEPIO:0101413" + }, + "opg053 gene (MPOX)": { + "text": "opg053 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein L1R (MPOX).", + "meaning": "GENEPIO:0101414" + }, + "opg054 gene (MPOX)": { + "text": "opg054 gene (MPOX)", + "description": "A gene that encodes the Serine/threonine-protein kinase (MPOX).", + "meaning": "GENEPIO:0101415" + }, + "opg055 gene (MPOX)": { + "text": "opg055 gene (MPOX)", + "description": "A gene that encodes the Protein F11 protein (MPOX).", + "meaning": "GENEPIO:0101416" + }, + "opg056 gene (MPOX)": { + "text": "opg056 gene (MPOX)", + "description": "A gene that encodes the EEV maturation protein (MPOX).", + "meaning": "GENEPIO:0101417" + }, + "opg057 gene (MPOX)": { + "text": "opg057 gene (MPOX)", + "description": "A gene that encodes the Palmytilated EEV membrane protein (MPOX).", + "meaning": "GENEPIO:0101418" + }, + "opg058 gene (MPOX)": { + "text": "opg058 gene (MPOX)", + "description": "A gene that encodes the Protein F14 (1) protein (MPOX).", + "meaning": "GENEPIO:0101419" + }, + "opg059 gene (MPOX)": { + "text": "opg059 gene (MPOX)", + "description": "A gene that encodes the Cytochrome C oxidase protein (MPOX).", + "meaning": "GENEPIO:0101420" + }, + "opg060 gene (MPOX)": { + "text": "opg060 gene (MPOX)", + "description": "A gene that encodes the Protein F15 protein (MPOX).", + "meaning": "GENEPIO:0101421" + }, + "opg061 gene (MPOX)": { + "text": "opg061 gene (MPOX)", + "description": "A gene that encodes the Protein F16 (1) protein (MPOX).", + "meaning": "GENEPIO:0101422" + }, + "opg062 gene (MPOX)": { + "text": "opg062 gene (MPOX)", + "description": "A gene that encodes the DNA-binding phosphoprotein (1) (MPOX).", + "meaning": "GENEPIO:0101423" + }, + "opg063 gene (MPOX)": { + "text": "opg063 gene (MPOX)", + "description": "A gene that encodes the Poly(A) polymerase catalytic subunit (3) protein (MPOX).", + "meaning": "GENEPIO:0101424" + }, + "opg064 gene (MPOX)": { + "text": "opg064 gene (MPOX)", + "description": "A gene that encodes the Iev morphogenesis protein (MPOX).", + "meaning": "GENEPIO:0101425" + }, + "opg065 gene (MPOX)": { + "text": "opg065 gene (MPOX)", + "description": "A gene that encodes the Double-stranded RNA binding protein (MPOX).", + "meaning": "GENEPIO:0101426" + }, + "opg066 gene (MPOX)": { + "text": "opg066 gene (MPOX)", + "description": "A gene that encodes the DNA-directed RNA polymerase 30 kDa polypeptide protein (MPOX).", + "meaning": "GENEPIO:0101427" + }, + "opg068 gene (MPOX)": { + "text": "opg068 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein E6 (MPOX).", + "meaning": "GENEPIO:0101428" + }, + "opg069 gene (MPOX)": { + "text": "opg069 gene (MPOX)", + "description": "A gene that encodes the Myristoylated protein E7 (MPOX).", + "meaning": "GENEPIO:0101429" + }, + "opg070 gene (MPOX)": { + "text": "opg070 gene (MPOX)", + "description": "A gene that encodes the Membrane protein E8 (MPOX).", + "meaning": "GENEPIO:0101430" + }, + "opg071 gene (MPOX)": { + "text": "opg071 gene (MPOX)", + "description": "A gene that encodes the DNA polymerase (2) protein (MPOX).", + "meaning": "GENEPIO:0101431" + }, + "opg072 gene (MPOX)": { + "text": "opg072 gene (MPOX)", + "description": "A gene that encodes the Sulfhydryl oxidase protein (MPOX).", + "meaning": "GENEPIO:0101432" + }, + "opg073 gene (MPOX)": { + "text": "opg073 gene (MPOX)", + "description": "A gene that encodes the Virion core protein E11 (MPOX).", + "meaning": "GENEPIO:0101433" + }, + "opg074 gene (MPOX)": { + "text": "opg074 gene (MPOX)", + "description": "A gene that encodes the Iev morphogenesis protein (MPOX).", + "meaning": "GENEPIO:0101434" + }, + "opg075 gene (MPOX)": { + "text": "opg075 gene (MPOX)", + "description": "A gene that encodes the Glutaredoxin-1 protein (MPOX).", + "meaning": "GENEPIO:0101435" + }, + "opg077 gene (MPOX)": { + "text": "opg077 gene (MPOX)", + "description": "A gene that encodes the Telomere-binding protein I1 (MPOX).", + "meaning": "GENEPIO:0101437" + }, + "opg078 gene (MPOX)": { + "text": "opg078 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein I2 (MPOX).", + "meaning": "GENEPIO:0101438" + }, + "opg079 gene (MPOX)": { + "text": "opg079 gene (MPOX)", + "description": "A gene that encodes the DNA-binding phosphoprotein (2) (MPOX).", + "meaning": "GENEPIO:0101439" + }, + "opg080 gene (MPOX)": { + "text": "opg080 gene (MPOX)", + "description": "A gene that encodes the Ribonucleoside-diphosphate reductase (2) protein (MPOX).", + "meaning": "GENEPIO:0101440" + }, + "opg081 gene (MPOX)": { + "text": "opg081 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein I5 (MPOX).", + "meaning": "GENEPIO:0101441" + }, + "opg082 gene (MPOX)": { + "text": "opg082 gene (MPOX)", + "description": "A gene that encodes the Telomere-binding protein (MPOX).", + "meaning": "GENEPIO:0101442" + }, + "opg083 gene (MPOX)": { + "text": "opg083 gene (MPOX)", + "description": "A gene that encodes the Viral core cysteine proteinase (MPOX).", + "meaning": "GENEPIO:0101443" + }, + "opg084 gene (MPOX)": { + "text": "opg084 gene (MPOX)", + "description": "A gene that encodes the RNA helicase NPH-II (2) protein (MPOX).", + "meaning": "GENEPIO:0101444" + }, + "opg085 gene (MPOX)": { + "text": "opg085 gene (MPOX)", + "description": "A gene that encodes the Metalloendopeptidase protein (MPOX).", + "meaning": "GENEPIO:0101445" + }, + "opg086 gene (MPOX)": { + "text": "opg086 gene (MPOX)", + "description": "A gene that encodes the Entry/fusion complex component protein (MPOX).", + "meaning": "GENEPIO:0101446" + }, + "opg087 gene (MPOX)": { + "text": "opg087 gene (MPOX)", + "description": "A gene that encodes the Late transcription elongation factor protein (MPOX).", + "meaning": "GENEPIO:0101447" + }, + "opg088 gene (MPOX)": { + "text": "opg088 gene (MPOX)", + "description": "A gene that encodes the Glutaredoxin-2 protein (MPOX).", + "meaning": "GENEPIO:0101448" + }, + "opg089 gene (MPOX)": { + "text": "opg089 gene (MPOX)", + "description": "A gene that encodes the FEN1-like nuclease protein (MPOX).", + "meaning": "GENEPIO:0101449" + }, + "opg090 gene (MPOX)": { + "text": "opg090 gene (MPOX)", + "description": "A gene that encodes the DNA-directed RNA polymerase 7 kDa subunit protein (MPOX).", + "meaning": "GENEPIO:0101450" + }, + "opg091 gene (MPOX)": { + "text": "opg091 gene (MPOX)", + "description": "A gene that encodes the Nlpc/p60 superfamily protein (MPOX).", + "meaning": "GENEPIO:0101451" + }, + "opg092 gene (MPOX)": { + "text": "opg092 gene (MPOX)", + "description": "A gene that encodes the Assembly protein G7 (MPOX).", + "meaning": "GENEPIO:0101452" + }, + "opg093 gene (MPOX)": { + "text": "opg093 gene (MPOX)", + "description": "A gene that encodes the Late transcription factor VLTF-1 protein (MPOX).", + "meaning": "GENEPIO:0101453" + }, + "opg094 gene (MPOX)": { + "text": "opg094 gene (MPOX)", + "description": "A gene that encodes the Myristylated protein (MPOX).", + "meaning": "GENEPIO:0101454" + }, + "opg095 gene (MPOX)": { + "text": "opg095 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein L1R (MPOX).", + "meaning": "GENEPIO:0101455" + }, + "opg096 gene (MPOX)": { + "text": "opg096 gene (MPOX)", + "description": "A gene that encodes the Crescent membrane and immature virion formation protein (MPOX).", + "meaning": "GENEPIO:0101456" + }, + "opg097 gene (MPOX)": { + "text": "opg097 gene (MPOX)", + "description": "A gene that encodes the Internal virion L3/FP4 protein (MPOX).", + "meaning": "GENEPIO:0101457" + }, + "opg098 gene (MPOX)": { + "text": "opg098 gene (MPOX)", + "description": "A gene that encodes the Nucleic acid binding protein VP8/L4R (MPOX).", + "meaning": "GENEPIO:0101458" + }, + "opg099 gene (MPOX)": { + "text": "opg099 gene (MPOX)", + "description": "A gene that encodes the Membrane protein CL5 (MPOX).", + "meaning": "GENEPIO:0101459" + }, + "opg100 gene (MPOX)": { + "text": "opg100 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein J1 (MPOX).", + "meaning": "GENEPIO:0101460" + }, + "opg101 gene (MPOX)": { + "text": "opg101 gene (MPOX)", + "description": "A gene that encodes the Thymidine kinase protein (MPOX).", + "meaning": "GENEPIO:0101461" + }, + "opg102 gene (MPOX)": { + "text": "opg102 gene (MPOX)", + "description": "A gene that encodes the Cap-specific mRNA protein (MPOX).", + "meaning": "GENEPIO:0101462" + }, + "opg103 gene (MPOX)": { + "text": "opg103 gene (MPOX)", + "description": "A gene that encodes the DNA-directed RNA polymerase subunit protein (MPOX).", + "meaning": "GENEPIO:0101463" + }, + "opg104 gene (MPOX)": { + "text": "opg104 gene (MPOX)", + "description": "A gene that encodes the Myristylated protein (MPOX).", + "meaning": "GENEPIO:0101464" + }, + "opg105 gene (MPOX)": { + "text": "opg105 gene (MPOX)", + "description": "A gene that encodes the DNA-dependent RNA polymerase subunit rpo147 protein (MPOX).", + "meaning": "GENEPIO:0101465" + }, + "opg106 gene (MPOX)": { + "text": "opg106 gene (MPOX)", + "description": "A gene that encodes the Tyr/ser protein phosphatase (MPOX).", + "meaning": "GENEPIO:0101466" + }, + "opg107 gene (MPOX)": { + "text": "opg107 gene (MPOX)", + "description": "A gene that encodes the Entry-fusion complex essential component protein (MPOX).", + "meaning": "GENEPIO:0101467" + }, + "opg108 gene (MPOX)": { + "text": "opg108 gene (MPOX)", + "description": "A gene that encodes the IMV heparin binding surface protein (MPOX).", + "meaning": "GENEPIO:0101468" + }, + "opg109 gene (MPOX)": { + "text": "opg109 gene (MPOX)", + "description": "A gene that encodes the RNA polymerase-associated transcription-specificity factor RAP94 protein (MPOX).", + "meaning": "GENEPIO:0101469" + }, + "opg110 gene (MPOX)": { + "text": "opg110 gene (MPOX)", + "description": "A gene that encodes the Late transcription factor VLTF-4 (1) protein (MPOX).", + "meaning": "GENEPIO:0101470" + }, + "opg111 gene (MPOX)": { + "text": "opg111 gene (MPOX)", + "description": "A gene that encodes the DNA topoisomerase type I protein (MPOX).", + "meaning": "GENEPIO:0101471" + }, + "opg112 gene (MPOX)": { + "text": "opg112 gene (MPOX)", + "description": "A gene that encodes the Late protein H7 (MPOX).", + "meaning": "GENEPIO:0101472" + }, + "opg113 gene (MPOX)": { + "text": "opg113 gene (MPOX)", + "description": "A gene that encodes the mRNA capping enzyme large subunit protein (MPOX).", + "meaning": "GENEPIO:0101473" + }, + "opg114 gene (MPOX)": { + "text": "opg114 gene (MPOX)", + "description": "A gene that encodes the Virion protein D2 (MPOX).", + "meaning": "GENEPIO:0101474" + }, + "opg115 gene (MPOX)": { + "text": "opg115 gene (MPOX)", + "description": "A gene that encodes the Virion core protein D3 (MPOX).", + "meaning": "GENEPIO:0101475" + }, + "opg116 gene (MPOX)": { + "text": "opg116 gene (MPOX)", + "description": "A gene that encodes the Uracil DNA glycosylase superfamily protein (MPOX).", + "meaning": "GENEPIO:0101476" + }, + "opg117 gene (MPOX)": { + "text": "opg117 gene (MPOX)", + "description": "A gene that encodes the NTPase (1) protein (MPOX).", + "meaning": "GENEPIO:0101477" + }, + "opg118 gene (MPOX)": { + "text": "opg118 gene (MPOX)", + "description": "A gene that encodes the Early transcription factor 70 kDa subunit protein (MPOX).", + "meaning": "GENEPIO:0101478" + }, + "opg119 gene (MPOX)": { + "text": "opg119 gene (MPOX)", + "description": "A gene that encodes the RNA polymerase subunit RPO18 protein (MPOX).", + "meaning": "GENEPIO:0101479" + }, + "opg120 gene (MPOX)": { + "text": "opg120 gene (MPOX)", + "description": "A gene that encodes the Carbonic anhydrase protein (MPOX).", + "meaning": "GENEPIO:0101480" + }, + "opg121 gene (MPOX)": { + "text": "opg121 gene (MPOX)", + "description": "A gene that encodes the NUDIX domain protein (MPOX).", + "meaning": "GENEPIO:0101481" + }, + "opg122 gene (MPOX)": { + "text": "opg122 gene (MPOX)", + "description": "A gene that encodes the MutT motif protein (MPOX).", + "meaning": "GENEPIO:0101482" + }, + "opg123 gene (MPOX)": { + "text": "opg123 gene (MPOX)", + "description": "A gene that encodes the Nucleoside triphosphatase I protein (MPOX).", + "meaning": "GENEPIO:0101483" + }, + "opg124 gene (MPOX)": { + "text": "opg124 gene (MPOX)", + "description": "A gene that encodes the mRNA capping enzyme small subunit protein (MPOX).", + "meaning": "GENEPIO:0101484" + }, + "opg125 gene (MPOX)": { + "text": "opg125 gene (MPOX)", + "description": "A gene that encodes the Rifampicin resistance protein (MPOX).", + "meaning": "GENEPIO:0101485" + }, + "opg126 gene (MPOX)": { + "text": "opg126 gene (MPOX)", + "description": "A gene that encodes the Late transcription factor VLTF-2 (2) protein (MPOX).", + "meaning": "GENEPIO:0101486" + }, + "opg127 gene (MPOX)": { + "text": "opg127 gene (MPOX)", + "description": "A gene that encodes the Late transcription factor VLTF-3 (1) protein (MPOX).", + "meaning": "GENEPIO:0101487" + }, + "opg128 gene (MPOX)": { + "text": "opg128 gene (MPOX)", + "description": "A gene that encodes the S-S bond formation pathway protein (MPOX).", + "meaning": "GENEPIO:0101488" + }, + "opg129 gene (MPOX)": { + "text": "opg129 gene (MPOX)", + "description": "A gene that encodes the Virion core protein P4b (MPOX).", + "meaning": "GENEPIO:0101489" + }, + "opg130 gene (MPOX)": { + "text": "opg130 gene (MPOX)", + "description": "A gene that encodes the A5L protein-like (MPOX).", + "meaning": "GENEPIO:0101490" + }, + "opg131 gene (MPOX)": { + "text": "opg131 gene (MPOX)", + "description": "A gene that encodes the DNA-directed RNA polymerase 19 kDa subunit protein (MPOX).", + "meaning": "GENEPIO:0101491" + }, + "opg132 gene (MPOX)": { + "text": "opg132 gene (MPOX)", + "description": "A gene that encodes the Virion morphogenesis protein (MPOX).", + "meaning": "GENEPIO:0101492" + }, + "opg133 gene (MPOX)": { + "text": "opg133 gene (MPOX)", + "description": "A gene that encodes the Early transcription factor 82 kDa subunit protein (MPOX).", + "meaning": "GENEPIO:0101493" + }, + "opg134 gene (MPOX)": { + "text": "opg134 gene (MPOX)", + "description": "A gene that encodes the Intermediate transcription factor VITF-3 (1) protein (MPOX).", + "meaning": "GENEPIO:0101494" + }, + "opg135 gene (MPOX)": { + "text": "opg135 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein A9 (MPOX).", + "meaning": "GENEPIO:0101495" + }, + "opg136 gene (MPOX)": { + "text": "opg136 gene (MPOX)", + "description": "A gene that encodes the Virion core protein P4a (MPOX).", + "meaning": "GENEPIO:0101496" + }, + "opg137 gene (MPOX)": { + "text": "opg137 gene (MPOX)", + "description": "A gene that encodes the Viral membrane formation protein (MPOX).", + "meaning": "GENEPIO:0101497" + }, + "opg138 gene (MPOX)": { + "text": "opg138 gene (MPOX)", + "description": "A gene that encodes the A12 protein (MPOX).", + "meaning": "GENEPIO:0101498" + }, + "opg139 gene (MPOX)": { + "text": "opg139 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein A13L (MPOX).", + "meaning": "GENEPIO:0101499" + }, + "opg140 gene (MPOX)": { + "text": "opg140 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein A14 (MPOX).", + "meaning": "GENEPIO:0101500" + }, + "opg141 gene (MPOX)": { + "text": "opg141 gene (MPOX)", + "description": "A gene that encodes the DUF1029 domain protein (MPOX).", + "meaning": "GENEPIO:0101501" + }, + "opg142 gene (MPOX)": { + "text": "opg142 gene (MPOX)", + "description": "A gene that encodes the Core protein A15 (MPOX).", + "meaning": "GENEPIO:0101502" + }, + "opg143 gene (MPOX)": { + "text": "opg143 gene (MPOX)", + "description": "A gene that encodes the Myristylated protein (MPOX).", + "meaning": "GENEPIO:0101503" + }, + "opg144 gene (MPOX)": { + "text": "opg144 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein P21 (MPOX).", + "meaning": "GENEPIO:0101504" + }, + "opg145 gene (MPOX)": { + "text": "opg145 gene (MPOX)", + "description": "A gene that encodes the DNA helicase protein (MPOX).", + "meaning": "GENEPIO:0101505" + }, + "opg146 gene (MPOX)": { + "text": "opg146 gene (MPOX)", + "description": "A gene that encodes the Zinc finger-like protein (1) (MPOX).", + "meaning": "GENEPIO:0101506" + }, + "opg147 gene (MPOX)": { + "text": "opg147 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein A21 (MPOX).", + "meaning": "GENEPIO:0101507" + }, + "opg148 gene (MPOX)": { + "text": "opg148 gene (MPOX)", + "description": "A gene that encodes the DNA polymerase processivity factor protein (MPOX).", + "meaning": "GENEPIO:0101508" + }, + "opg149 gene (MPOX)": { + "text": "opg149 gene (MPOX)", + "description": "A gene that encodes the Holliday junction resolvase protein (MPOX).", + "meaning": "GENEPIO:0101509" + }, + "opg150 gene (MPOX)": { + "text": "opg150 gene (MPOX)", + "description": "A gene that encodes the Intermediate transcription factor VITF-3 (2) protein (MPOX).", + "meaning": "GENEPIO:0101510" + }, + "opg151 gene (MPOX)": { + "text": "opg151 gene (MPOX)", + "description": "A gene that encodes the DNA-dependent RNA polymerase subunit rpo132 protein (MPOX).", + "meaning": "GENEPIO:0101511" + }, + "opg153 gene (MPOX)": { + "text": "opg153 gene (MPOX)", + "description": "A gene that encodes the Orthopoxvirus A26L/A30L protein (MPOX).", + "meaning": "GENEPIO:0101512" + }, + "opg154 gene (MPOX)": { + "text": "opg154 gene (MPOX)", + "description": "A gene that encodes the IMV surface fusion protein (MPOX).", + "meaning": "GENEPIO:0101513" + }, + "opg155 gene (MPOX)": { + "text": "opg155 gene (MPOX)", + "description": "A gene that encodes the Envelope protein A28 homolog (MPOX).", + "meaning": "GENEPIO:0101514" + }, + "opg156 gene (MPOX)": { + "text": "opg156 gene (MPOX)", + "description": "A gene that encodes the DNA-directed RNA polymerase 35 kDa subunit protein (MPOX).", + "meaning": "GENEPIO:0101515" + }, + "opg157 gene (MPOX)": { + "text": "opg157 gene (MPOX)", + "description": "A gene that encodes the IMV membrane protein A30 (MPOX).", + "meaning": "GENEPIO:0101516" + }, + "opg158 gene (MPOX)": { + "text": "opg158 gene (MPOX)", + "description": "A gene that encodes the A32.5L protein (MPOX).", + "meaning": "GENEPIO:0101517" + }, + "opg159 gene (MPOX)": { + "text": "opg159 gene (MPOX)", + "description": "A gene that encodes the CPXV166 protein (MPOX).", + "meaning": "GENEPIO:0101518" + }, + "opg160 gene (MPOX)": { + "text": "opg160 gene (MPOX)", + "description": "A gene that encodes the ATPase A32 protein (MPOX).", + "meaning": "GENEPIO:0101519" + }, + "opg161 gene (MPOX)": { + "text": "opg161 gene (MPOX)", + "description": "A gene that encodes the EEV glycoprotein (1) (MPOX).", + "meaning": "GENEPIO:0101520" + }, + "opg162 gene (MPOX)": { + "text": "opg162 gene (MPOX)", + "description": "A gene that encodes the EEV glycoprotein (2) (MPOX).", + "meaning": "GENEPIO:0101521" + }, + "opg163 gene (MPOX)": { + "text": "opg163 gene (MPOX)", + "description": "A gene that encodes the MHC class II antigen presentation inhibitor protein (MPOX).", + "meaning": "GENEPIO:0101522" + }, + "opg164 gene (MPOX)": { + "text": "opg164 gene (MPOX)", + "description": "A gene that encodes the IEV transmembrane phosphoprotein (MPOX).", + "meaning": "GENEPIO:0101523" + }, + "opg165 gene (MPOX)": { + "text": "opg165 gene (MPOX)", + "description": "A gene that encodes the CPXV173 protein (MPOX).", + "meaning": "GENEPIO:0101524" + }, + "opg166 gene (MPOX)": { + "text": "opg166 gene (MPOX)", + "description": "A gene that encodes the hypothetical protein (MPOX).", + "meaning": "GENEPIO:0101525" + }, + "opg167 gene (MPOX)": { + "text": "opg167 gene (MPOX)", + "description": "A gene that encodes the CD47-like protein (MPOX).", + "meaning": "GENEPIO:0101526" + }, + "opg170 gene (MPOX)": { + "text": "opg170 gene (MPOX)", + "description": "A gene that encodes the Chemokine binding protein (MPOX).", + "meaning": "GENEPIO:0101527" + }, + "opg171 gene (MPOX)": { + "text": "opg171 gene (MPOX)", + "description": "A gene that encodes the Profilin domain protein (MPOX).", + "meaning": "GENEPIO:0101528" + }, + "opg172 gene (MPOX)": { + "text": "opg172 gene (MPOX)", + "description": "A gene that encodes the Type-I membrane glycoprotein (MPOX).", + "meaning": "GENEPIO:0101529" + }, + "opg173 gene (MPOX)": { + "text": "opg173 gene (MPOX)", + "description": "A gene that encodes the MPXVgp154 protein (MPOX).", + "meaning": "GENEPIO:0101530" + }, + "opg174 gene (MPOX)": { + "text": "opg174 gene (MPOX)", + "description": "A gene that encodes the Hydroxysteroid dehydrogenase protein (MPOX).", + "meaning": "GENEPIO:0101531" + }, + "opg175 gene (MPOX)": { + "text": "opg175 gene (MPOX)", + "description": "A gene that encodes the Copper/zinc superoxide dismutase protein (MPOX).", + "meaning": "GENEPIO:0101532" + }, + "opg176 gene (MPOX)": { + "text": "opg176 gene (MPOX)", + "description": "A gene that encodes the Bcl-2-like protein (MPOX).", + "meaning": "GENEPIO:0101533" + }, + "opg178 gene (MPOX)": { + "text": "opg178 gene (MPOX)", + "description": "A gene that encodes the Thymidylate kinase protein (MPOX).", + "meaning": "GENEPIO:0101534" + }, + "opg180 gene (MPOX)": { + "text": "opg180 gene (MPOX)", + "description": "A gene that encodes the DNA ligase (2) protein (MPOX).", + "meaning": "GENEPIO:0101535" + }, + "opg181 gene (MPOX)": { + "text": "opg181 gene (MPOX)", + "description": "A gene that encodes the M137R protein (MPOX).", + "meaning": "GENEPIO:0101536" + }, + "opg185 gene (MPOX)": { + "text": "opg185 gene (MPOX)", + "description": "A gene that encodes the Hemagglutinin protein (MPOX).", + "meaning": "GENEPIO:0101537" + }, + "opg187 gene (MPOX)": { + "text": "opg187 gene (MPOX)", + "description": "A gene that encodes the Ser/thr kinase protein (MPOX).", + "meaning": "GENEPIO:0101538" + }, + "opg188 gene (MPOX)": { + "text": "opg188 gene (MPOX)", + "description": "A gene that encodes the Schlafen (1) protein (MPOX).", + "meaning": "GENEPIO:0101539" + }, + "opg189 gene (MPOX)": { + "text": "opg189 gene (MPOX)", + "description": "A gene that encodes the Ankyrin repeat protein (25) (MPOX).", + "meaning": "GENEPIO:0101540" + }, + "opg190 gene (MPOX)": { + "text": "opg190 gene (MPOX)", + "description": "A gene that encodes the EEV type-I membrane glycoprotein (MPOX).", + "meaning": "GENEPIO:0101541" + }, + "opg191 gene (MPOX)": { + "text": "opg191 gene (MPOX)", + "description": "A gene that encodes the Ankyrin-like protein (46) (MPOX).", + "meaning": "GENEPIO:0101542" + }, + "opg192 gene (MPOX)": { + "text": "opg192 gene (MPOX)", + "description": "A gene that encodes the Virulence protein (MPOX).", + "meaning": "GENEPIO:0101543" + }, + "opg193 gene (MPOX)": { + "text": "opg193 gene (MPOX)", + "description": "A gene that encodes the Soluble interferon-gamma receptor-like protein (MPOX).", + "meaning": "GENEPIO:0101544" + }, + "opg195 gene (MPOX)": { + "text": "opg195 gene (MPOX)", + "description": "A gene that encodes the Intracellular viral protein (MPOX).", + "meaning": "GENEPIO:0101545" + }, + "opg197 gene (MPOX)": { + "text": "opg197 gene (MPOX)", + "description": "A gene that encodes the CPXV205 protein (MPOX).", + "meaning": "GENEPIO:0101546" + }, + "opg198 gene (MPOX)": { + "text": "opg198 gene (MPOX)", + "description": "A gene that encodes the Ser/thr kinase protein (MPOX).", + "meaning": "GENEPIO:0101547" + }, + "opg199 gene (MPOX)": { + "text": "opg199 gene (MPOX)", + "description": "A gene that encodes the Serpin protein (MPOX).", + "meaning": "GENEPIO:0101548" + }, + "opg200 gene (MPOX)": { + "text": "opg200 gene (MPOX)", + "description": "A gene that encodes the Bcl-2-like protein (MPOX).", + "meaning": "GENEPIO:0101549" + }, + "opg204 gene (MPOX)": { + "text": "opg204 gene (MPOX)", + "description": "A gene that encodes the IFN-alpha/beta-receptor-like secreted glycoprotein (MPOX).", + "meaning": "GENEPIO:0101550" + }, + "opg205 gene (MPOX)": { + "text": "opg205 gene (MPOX)", + "description": "A gene that encodes the Ankyrin repeat protein (44) (MPOX).", + "meaning": "GENEPIO:0101551" + }, + "opg208 gene (MPOX)": { + "text": "opg208 gene (MPOX)", + "description": "A gene that encodes the Serpin protein (MPOX).", + "meaning": "GENEPIO:0101552" + }, + "opg209 gene (MPOX)": { + "text": "opg209 gene (MPOX)", + "description": "A gene that encodes the Virulence protein (MPOX).", + "meaning": "GENEPIO:0101553" + }, + "opg210 gene (MPOX)": { + "text": "opg210 gene (MPOX)", + "description": "A gene that encodes the B22R family protein (MPOX).", + "meaning": "GENEPIO:0101554" + }, + "opg005 gene (MPOX)": { + "text": "opg005 gene (MPOX)", + "description": "A gene that encodes the Bcl-2-like protein (MPOX).", + "meaning": "GENEPIO:0101555" + }, + "opg016 gene (MPOX)": { + "text": "opg016 gene (MPOX)", + "description": "A gene that encodes the Brix domain protein (MPOX).", + "meaning": "GENEPIO:0101556" + } + } + }, + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Afghanistan": { "text": "Afghanistan", + "description": "A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ]", "meaning": "GAZ:00006882" }, "Albania": { "text": "Albania", + "description": "A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ]", "meaning": "GAZ:00002953" }, "Algeria": { "text": "Algeria", + "description": "A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ]", "meaning": "GAZ:00000563" }, "American Samoa": { "text": "American Samoa", + "description": "An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ]", "meaning": "GAZ:00003957" }, "Andorra": { "text": "Andorra", + "description": "A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]", "meaning": "GAZ:00002948" }, "Angola": { "text": "Angola", + "description": "A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ]", "meaning": "GAZ:00001095" }, "Anguilla": { "text": "Anguilla", + "description": "A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ]", "meaning": "GAZ:00009159" }, "Antarctica": { "text": "Antarctica", + "description": "The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ]", "meaning": "GAZ:00000462" }, "Antigua and Barbuda": { "text": "Antigua and Barbuda", + "description": "An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ]", "meaning": "GAZ:00006883" }, "Argentina": { "text": "Argentina", + "description": "A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ]", "meaning": "GAZ:00002928" }, "Armenia": { "text": "Armenia", + "description": "A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ]", "meaning": "GAZ:00004094" }, "Aruba": { "text": "Aruba", + "description": "An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ]", "meaning": "GAZ:00004025" }, "Ashmore and Cartier Islands": { "text": "Ashmore and Cartier Islands", + "description": "A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ]", "meaning": "GAZ:00005901" }, "Australia": { "text": "Australia", + "description": "A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories.", "meaning": "GAZ:00000463" }, "Austria": { "text": "Austria", + "description": "A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities.", "meaning": "GAZ:00002942" }, "Azerbaijan": { "text": "Azerbaijan", + "description": "A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika).", "meaning": "GAZ:00004941" }, "Bahamas": { "text": "Bahamas", + "description": "A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government.", "meaning": "GAZ:00002733" }, "Bahrain": { "text": "Bahrain", + "description": "A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates.", "meaning": "GAZ:00005281" }, "Baker Island": { "text": "Baker Island", + "description": "An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US.", "meaning": "GAZ:00007117" }, "Bangladesh": { "text": "Bangladesh", + "description": "A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana (\"police stations\").", "meaning": "GAZ:00003750" }, "Barbados": { "text": "Barbados", + "description": "An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown.", "meaning": "GAZ:00001251" }, "Bassas da India": { "text": "Bassas da India", + "description": "A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below.", "meaning": "GAZ:00005810" }, "Belarus": { "text": "Belarus", + "description": "A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital.", "meaning": "GAZ:00006886" }, "Belgium": { "text": "Belgium", + "description": "A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977).", "meaning": "GAZ:00002938" }, "Belize": { "text": "Belize", + "description": "A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies.", "meaning": "GAZ:00002934" }, "Benin": { "text": "Benin", + "description": "A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes.", "meaning": "GAZ:00000904" }, "Bermuda": { "text": "Bermuda", + "description": "A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands.", "meaning": "GAZ:00001264" }, "Bhutan": { "text": "Bhutan", + "description": "A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog.", "meaning": "GAZ:00003920" }, "Bolivia": { "text": "Bolivia", + "description": "A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios).", "meaning": "GAZ:00002511" }, "Borneo": { "text": "Borneo", + "description": "An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres.", "meaning": "GAZ:00025355" }, "Bosnia and Herzegovina": { "text": "Bosnia and Herzegovina", + "description": "A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina.", "meaning": "GAZ:00006887" }, "Botswana": { "text": "Botswana", + "description": "A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts.", "meaning": "GAZ:00001097" }, "Bouvet Island": { "text": "Bouvet Island", + "description": "A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended.", "meaning": "GAZ:00001453" }, "Brazil": { "text": "Brazil", + "description": "A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South.", "meaning": "GAZ:00002828" }, "British Virgin Islands": { "text": "British Virgin Islands", + "description": "A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited.", "meaning": "GAZ:00003961" }, "Brunei": { "text": "Brunei", + "description": "A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages).", "meaning": "GAZ:00003901" }, "Bulgaria": { "text": "Bulgaria", + "description": "A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities.", "meaning": "GAZ:00002950" }, "Burkina Faso": { "text": "Burkina Faso", + "description": "A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes).", "meaning": "GAZ:00000905" }, "Burundi": { "text": "Burundi", + "description": "A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines.", "meaning": "GAZ:00001090" }, "Cambodia": { "text": "Cambodia", + "description": "A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand.", "meaning": "GAZ:00006888" }, "Cameroon": { "text": "Cameroon", + "description": "A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts.", "meaning": "GAZ:00001093" }, "Canada": { "text": "Canada", + "description": "A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada.", "meaning": "GAZ:00002560" }, "Cape Verde": { "text": "Cape Verde", + "description": "A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias).", "meaning": "GAZ:00001227" }, "Cayman Islands": { "text": "Cayman Islands", + "description": "A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts.", "meaning": "GAZ:00003986" }, "Central African Republic": { "text": "Central African Republic", + "description": "A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures).", "meaning": "GAZ:00001089" }, "Chad": { "text": "Chad", + "description": "A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change.", "meaning": "GAZ:00000586" }, "Chile": { "text": "Chile", + "description": "A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10.", "meaning": "GAZ:00002825" }, "China": { "text": "China", + "description": "A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.", "meaning": "GAZ:00002845" }, "Christmas Island": { "text": "Christmas Island", + "description": "An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain.", "meaning": "GAZ:00005915" }, "Clipperton Island": { "text": "Clipperton Island", + "description": "A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica.", "meaning": "GAZ:00005838" }, "Cocos Islands": { "text": "Cocos Islands", + "description": "Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group.", "meaning": "GAZ:00009721" }, "Colombia": { "text": "Colombia", + "description": "A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities.", "meaning": "GAZ:00002929" }, "Comoros": { "text": "Comoros", + "description": "An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique.", "meaning": "GAZ:00005820" }, "Cook Islands": { "text": "Cook Islands", + "description": "A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean.", "meaning": "GAZ:00053798" }, "Coral Sea Islands": { "text": "Coral Sea Islands", + "description": "A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups.", "meaning": "GAZ:00005917" }, "Costa Rica": { "text": "Costa Rica", + "description": "A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons.", "meaning": "GAZ:00002901" }, "Cote d'Ivoire": { "text": "Cote d'Ivoire", + "description": "A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments.", "meaning": "GAZ:00000906" }, "Croatia": { "text": "Croatia", + "description": "A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district.", "meaning": "GAZ:00002719" }, "Cuba": { "text": "Cuba", + "description": "A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba.", "meaning": "GAZ:00003762" }, "Curacao": { "text": "Curacao", + "description": "One of five island areas of the Netherlands Antilles.", "meaning": "GAZ:00012582" }, "Cyprus": { "text": "Cyprus", + "description": "The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west.", "meaning": "GAZ:00004006" }, "Czech Republic": { "text": "Czech Republic", + "description": "A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named \"Little Districts\" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices.", "meaning": "GAZ:00002954" }, "Democratic Republic of the Congo": { "text": "Democratic Republic of the Congo", + "description": "A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones.", "meaning": "GAZ:00001086" }, "Denmark": { "text": "Denmark", + "description": "That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago.", "meaning": "GAZ:00005852" }, "Djibouti": { "text": "Djibouti", + "description": "A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts.", "meaning": "GAZ:00000582" }, "Dominica": { "text": "Dominica", + "description": "An island nation in the Caribbean Sea. Dominica is divided into ten parishes.", "meaning": "GAZ:00006890" }, "Dominican Republic": { "text": "Dominican Republic", + "description": "A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio).", "meaning": "GAZ:00003952" }, "Ecuador": { "text": "Ecuador", + "description": "A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias).", "meaning": "GAZ:00002912" }, "Egypt": { "text": "Egypt", + "description": "A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes).", "meaning": "GAZ:00003934" }, "El Salvador": { "text": "El Salvador", + "description": "A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios).", "meaning": "GAZ:00002935" }, "Equatorial Guinea": { "text": "Equatorial Guinea", + "description": "A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts.", "meaning": "GAZ:00001091" }, "Eritrea": { "text": "Eritrea", + "description": "A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts (\"sub-zobas\").", "meaning": "GAZ:00000581" }, "Estonia": { "text": "Estonia", + "description": "A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities.", "meaning": "GAZ:00002959" }, "Eswatini": { "text": "Eswatini", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", "meaning": "GAZ:00001099" }, "Ethiopia": { "text": "Ethiopia", + "description": "A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas.", "meaning": "GAZ:00000567" }, "Europa Island": { "text": "Europa Island", + "description": "A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique.", "meaning": "GAZ:00005811" }, "Falkland Islands (Islas Malvinas)": { "text": "Falkland Islands (Islas Malvinas)", + "description": "An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands.", "meaning": "GAZ:00001412" }, "Faroe Islands": { "text": "Faroe Islands", + "description": "An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie.", "meaning": "GAZ:00059206" }, "Fiji": { "text": "Fiji", + "description": "An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population.", "meaning": "GAZ:00006891" }, "Finland": { "text": "Finland", + "description": "A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta).", "meaning": "GAZ:00002937" }, "France": { "text": "France", + "description": "A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments.", "meaning": "GAZ:00003940" }, "French Guiana": { "text": "French Guiana", + "description": "An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes.", "meaning": "GAZ:00002516" }, "French Polynesia": { "text": "French Polynesia", + "description": "A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives).", "meaning": "GAZ:00002918" }, "French Southern and Antarctic Lands": { "text": "French Southern and Antarctic Lands", + "description": "The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts.", "meaning": "GAZ:00003753" }, "Gabon": { "text": "Gabon", + "description": "A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments.", "meaning": "GAZ:00001092" }, "Gambia": { "text": "Gambia", + "description": "A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts.", "meaning": "GAZ:00000907" }, "Gaza Strip": { "text": "Gaza Strip", + "description": "A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine.", "meaning": "GAZ:00009571" }, "Georgia": { "text": "Georgia", + "description": "A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni).", "meaning": "GAZ:00004942" }, "Germany": { "text": "Germany", + "description": "A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte).", "meaning": "GAZ:00002646" }, "Ghana": { "text": "Ghana", + "description": "A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts.", "meaning": "GAZ:00000908" }, "Gibraltar": { "text": "Gibraltar", + "description": "A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north.", "meaning": "GAZ:00003987" }, "Glorioso Islands": { "text": "Glorioso Islands", + "description": "A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar.", "meaning": "GAZ:00005808" }, "Greece": { "text": "Greece", + "description": "A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia.", "meaning": "GAZ:00002945" }, "Greenland": { "text": "Greenland", + "description": "A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago.", "meaning": "GAZ:00001507" }, "Grenada": { "text": "Grenada", + "description": "An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020.", "meaning": "GAZ:02000573" }, "Guadeloupe": { "text": "Guadeloupe", + "description": "An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica.", "meaning": "GAZ:00067142" }, "Guam": { "text": "Guam", + "description": "An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia.", "meaning": "GAZ:00003706" }, "Guatemala": { "text": "Guatemala", + "description": "A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios).", "meaning": "GAZ:00002936" }, "Guernsey": { "text": "Guernsey", + "description": "A British Crown Dependency in the English Channel off the coast of Normandy.", "meaning": "GAZ:00001550" }, "Guinea": { "text": "Guinea", + "description": "A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip.", "meaning": "GAZ:00000909" }, "Guinea-Bissau": { "text": "Guinea-Bissau", + "description": "A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea.", "meaning": "GAZ:00000910" }, "Guyana": { "text": "Guyana", + "description": "A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils.", "meaning": "GAZ:00002522" }, "Haiti": { "text": "Haiti", + "description": "A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions.", "meaning": "GAZ:00003953" }, "Heard Island and McDonald Islands": { "text": "Heard Island and McDonald Islands", + "description": "An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica.", "meaning": "GAZ:00009718" }, "Honduras": { "text": "Honduras", + "description": "A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan.", "meaning": "GAZ:00002894" }, "Hong Kong": { "text": "Hong Kong", + "description": "A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997.", "meaning": "GAZ:00003203" }, "Howland Island": { "text": "Howland Island", + "description": "An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands.", "meaning": "GAZ:00007120" }, "Hungary": { "text": "Hungary", + "description": "A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary.", "meaning": "GAZ:00002952" }, "Iceland": { "text": "Iceland", + "description": "A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland.", "meaning": "GAZ:00000843" }, "India": { "text": "India", + "description": "A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages.", "meaning": "GAZ:00002839" }, "Indonesia": { "text": "Indonesia", + "description": "An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan).", "meaning": "GAZ:00003727" }, "Iran": { "text": "Iran", + "description": "A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan).", "meaning": "GAZ:00004474" }, "Iraq": { "text": "Iraq", + "description": "A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts).", "meaning": "GAZ:00004483" }, "Ireland": { "text": "Ireland", + "description": "A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 \"county-level\" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a \"city council\"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties.", "meaning": "GAZ:00002943" }, "Isle of Man": { "text": "Isle of Man", + "description": "A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations.", "meaning": "GAZ:00052477" }, "Israel": { "text": "Israel", + "description": "A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions.", "meaning": "GAZ:00002476" }, "Italy": { "text": "Italy", + "description": "A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni).", "meaning": "GAZ:00002650" }, "Jamaica": { "text": "Jamaica", + "description": "A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance.", "meaning": "GAZ:00003781" }, "Jan Mayen": { "text": "Jan Mayen", + "description": "A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.", "meaning": "GAZ:00005853" }, "Japan": { "text": "Japan", + "description": "An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.", "meaning": "GAZ:00002747" }, "Jarvis Island": { "text": "Jarvis Island", + "description": "An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount.", "meaning": "GAZ:00007118" }, "Jersey": { "text": "Jersey", + "description": "A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq.", "meaning": "GAZ:00001551" }, "Johnston Atoll": { "text": "Johnston Atoll", + "description": "A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount.", "meaning": "GAZ:00007114" }, "Jordan": { "text": "Jordan", + "description": "A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias.", "meaning": "GAZ:00002473" }, "Juan de Nova Island": { "text": "Juan de Nova Island", + "description": "A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique.", "meaning": "GAZ:00005809" }, "Kazakhstan": { "text": "Kazakhstan", + "description": "A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions.", "meaning": "GAZ:00004999" }, "Kenya": { "text": "Kenya", + "description": "A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province.", "meaning": "GAZ:00001101" }, "Kerguelen Archipelago": { "text": "Kerguelen Archipelago", + "description": "A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap.", "meaning": "GAZ:00005682" }, "Kingman Reef": { "text": "Kingman Reef", + "description": "A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount.", "meaning": "GAZ:00007116" }, "Kiribati": { "text": "Kiribati", + "description": "An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea).", "meaning": "GAZ:00006894" }, "Kosovo": { "text": "Kosovo", + "description": "A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija.", "meaning": "GAZ:00011337" }, "Kuwait": { "text": "Kuwait", + "description": "A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah).", "meaning": "GAZ:00005285" }, "Kyrgyzstan": { "text": "Kyrgyzstan", + "description": "A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions).", "meaning": "GAZ:00006893" }, "Laos": { "text": "Laos", + "description": "A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang).", "meaning": "GAZ:00006889" }, "Latvia": { "text": "Latvia", + "description": "A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions.", "meaning": "GAZ:00002958" }, "Lebanon": { "text": "Lebanon", + "description": "A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa).", "meaning": "GAZ:00002478" }, "Lesotho": { "text": "Lesotho", + "description": "A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils.", "meaning": "GAZ:00001098" }, "Liberia": { "text": "Liberia", + "description": "A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean.", "meaning": "GAZ:00000911" }, "Libya": { "text": "Libya", + "description": "A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s.", "meaning": "GAZ:00000566" }, "Liechtenstein": { "text": "Liechtenstein", + "description": "A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county).", "meaning": "GAZ:00003858" }, "Line Islands": { "text": "Line Islands", + "description": "A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands.", "meaning": "GAZ:00007144" }, "Lithuania": { "text": "Lithuania", + "description": "A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos).", "meaning": "GAZ:00002960" }, "Luxembourg": { "text": "Luxembourg", + "description": "A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest.", "meaning": "GAZ:00002947" }, "Macau": { "text": "Macau", + "description": "One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China.", "meaning": "GAZ:00003202" }, "Madagascar": { "text": "Madagascar", + "description": "An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany.", "meaning": "GAZ:00001108" }, "Malawi": { "text": "Malawi", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", "meaning": "GAZ:00001105" }, "Malaysia": { "text": "Malaysia", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", "meaning": "GAZ:00003902" }, "Maldives": { "text": "Maldives", + "description": "An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2.", "meaning": "GAZ:00006924" }, "Mali": { "text": "Mali", + "description": "A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements.", "meaning": "GAZ:00000584" }, "Malta": { "text": "Malta", + "description": "A Southern European country and consists of an archipelago situated centrally in the Mediterranean.", "meaning": "GAZ:00004017" }, "Marshall Islands": { "text": "Marshall Islands", + "description": "An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning \"sunrise\" and \"sunset\" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated.", "meaning": "GAZ:00007161" }, "Martinique": { "text": "Martinique", + "description": "An island and an overseas department/region and single territorial collectivity of France.", "meaning": "GAZ:00067143" }, "Mauritania": { "text": "Mauritania", + "description": "A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements).", "meaning": "GAZ:00000583" }, "Mauritius": { "text": "Mauritius", + "description": "An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands.", "meaning": "GAZ:00003745" }, "Mayotte": { "text": "Mayotte", + "description": "An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two.", "meaning": "GAZ:00003943" }, "Mexico": { "text": "Mexico", + "description": "A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City.", "meaning": "GAZ:00002852" }, "Micronesia": { "text": "Micronesia", + "description": "A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east.", "meaning": "GAZ:00005862" }, "Midway Islands": { "text": "Midway Islands", + "description": "A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior.", "meaning": "GAZ:00007112" }, "Moldova": { "text": "Moldova", + "description": "A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic.", "meaning": "GAZ:00003897" }, "Monaco": { "text": "Monaco", + "description": "A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards.", "meaning": "GAZ:00003857" }, "Mongolia": { "text": "Mongolia", + "description": "A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status.", "meaning": "GAZ:00008744" }, "Montenegro": { "text": "Montenegro", + "description": "A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality.", "meaning": "GAZ:00006898" }, "Montserrat": { "text": "Montserrat", + "description": "A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes.", "meaning": "GAZ:00003988" }, "Morocco": { "text": "Morocco", + "description": "A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of \"Saguia el-Hamra\" and \"Rio de Oro\" is disputed.", "meaning": "GAZ:00000565" }, "Mozambique": { "text": "Mozambique", + "description": "A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in \"Postos Administrativos\" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration.", "meaning": "GAZ:00001100" }, "Myanmar": { "text": "Myanmar", + "description": "A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages.", "meaning": "GAZ:00006899" }, "Namibia": { "text": "Namibia", + "description": "A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies.", "meaning": "GAZ:00001096" }, "Nauru": { "text": "Nauru", + "description": "An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies.", "meaning": "GAZ:00006900" }, "Navassa Island": { "text": "Navassa Island", + "description": "A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti.", "meaning": "GAZ:00007119" }, "Nepal": { "text": "Nepal", + "description": "A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the \"Chicken's Neck\". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions.", "meaning": "GAZ:00004399" }, "Netherlands": { "text": "Netherlands", + "description": "The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007).", "meaning": "GAZ:00002946" }, "New Caledonia": { "text": "New Caledonia", + "description": "A \"sui generis collectivity\" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes.", "meaning": "GAZ:00005206" }, "New Zealand": { "text": "New Zealand", + "description": "A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands.", "meaning": "GAZ:00000469" }, "Nicaragua": { "text": "Nicaragua", + "description": "A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya.", "meaning": "GAZ:00002978" }, "Niger": { "text": "Niger", + "description": "A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes.", "meaning": "GAZ:00000585" }, "Nigeria": { "text": "Nigeria", + "description": "A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs).", "meaning": "GAZ:00000912" }, "Niue": { "text": "Niue", + "description": "An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state.", "meaning": "GAZ:00006902" }, "Norfolk Island": { "text": "Norfolk Island", + "description": "A Territory of Australia that includes Norfolk Island and neighboring islands.", "meaning": "GAZ:00005908" }, "North Korea": { "text": "North Korea", + "description": "A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia.", "meaning": "GAZ:00002801" }, "North Macedonia": { "text": "North Macedonia", + "description": "A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts.", "meaning": "GAZ:00006895" }, "North Sea": { "text": "North Sea", + "description": "A sea situated between the eastern coasts of the British Isles and the western coast of Europe.", "meaning": "GAZ:00002284" }, "Northern Mariana Islands": { "text": "Northern Mariana Islands", + "description": "A group of 15 islands about three-quarters of the way from Hawaii to the Philippines.", "meaning": "GAZ:00003958" }, "Norway": { "text": "Norway", + "description": "A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom.", "meaning": "GAZ:00002699" }, "Oman": { "text": "Oman", + "description": "A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat).", "meaning": "GAZ:00005283" }, "Pakistan": { "text": "Pakistan", + "description": "A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan.", "meaning": "GAZ:00005246" }, "Palau": { "text": "Palau", + "description": "A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines.", "meaning": "GAZ:00006905" }, "Panama": { "text": "Panama", + "description": "The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports.", "meaning": "GAZ:00002892" }, "Papua New Guinea": { "text": "Papua New Guinea", + "description": "A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia).", "meaning": "GAZ:00003922" }, "Paracel Islands": { "text": "Paracel Islands", + "description": "A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines.", "meaning": "GAZ:00010832" }, "Paraguay": { "text": "Paraguay", + "description": "A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts.", "meaning": "GAZ:00002933" }, "Peru": { "text": "Peru", + "description": "A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao.", "meaning": "GAZ:00002932" }, "Philippines": { "text": "Philippines", + "description": "An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays.", "meaning": "GAZ:00004525" }, "Pitcairn Islands": { "text": "Pitcairn Islands", + "description": "A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia.", "meaning": "GAZ:00005867" }, "Poland": { "text": "Poland", + "description": "A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas.", "meaning": "GAZ:00002939" }, "Portugal": { "text": "Portugal", + "description": "That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands.", "meaning": "GAZ:00004126" }, "Puerto Rico": { "text": "Puerto Rico", + "description": "A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States).", "meaning": "GAZ:00006935" }, "Qatar": { "text": "Qatar", + "description": "An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts).", "meaning": "GAZ:00005286" }, "Republic of the Congo": { "text": "Republic of the Congo", + "description": "A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts.", "meaning": "GAZ:00001088" }, "Reunion": { "text": "Reunion", + "description": "An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island.", "meaning": "GAZ:00003945" }, "Romania": { "text": "Romania", + "description": "A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities).", "meaning": "GAZ:00002951" }, "Ross Sea": { "text": "Ross Sea", + "description": "A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW.", "meaning": "GAZ:00023304" }, "Russia": { "text": "Russia", + "description": "A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts.", "meaning": "GAZ:00002721" }, "Rwanda": { "text": "Rwanda", + "description": "A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge).", "meaning": "GAZ:00001087" }, "Saint Helena": { "text": "Saint Helena", + "description": "An island of volcanic origin and a British overseas territory in the South Atlantic Ocean.", "meaning": "GAZ:00000849" }, "Saint Kitts and Nevis": { "text": "Saint Kitts and Nevis", + "description": "A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis.", "meaning": "GAZ:00006906" }, "Saint Lucia": { "text": "Saint Lucia", + "description": "An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean.", "meaning": "GAZ:00006909" }, "Saint Pierre and Miquelon": { "text": "Saint Pierre and Miquelon", + "description": "An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985.", "meaning": "GAZ:00003942" }, "Saint Martin": { "text": "Saint Martin", + "description": "An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe.", "meaning": "GAZ:00005841" }, "Saint Vincent and the Grenadines": { "text": "Saint Vincent and the Grenadines", + "description": "An island nation in the Lesser Antilles chain of the Caribbean Sea.", "meaning": "GAZ:02000565" }, "Samoa": { "text": "Samoa", + "description": "A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts).", "meaning": "GAZ:00006910" }, "San Marino": { "text": "San Marino", + "description": "A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello).", "meaning": "GAZ:00003102" }, "Sao Tome and Principe": { "text": "Sao Tome and Principe", + "description": "An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29).", "meaning": "GAZ:00006927" }, "Saudi Arabia": { "text": "Saudi Arabia", + "description": "A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates.", "meaning": "GAZ:00005279" }, "Senegal": { "text": "Senegal", + "description": "A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales.", "meaning": "GAZ:00000913" }, "Serbia": { "text": "Serbia", + "description": "A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities).", "meaning": "GAZ:00002957" }, "Seychelles": { "text": "Seychelles", + "description": "An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands.", "meaning": "GAZ:00006922" }, "Sierra Leone": { "text": "Sierra Leone", + "description": "A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts.", "meaning": "GAZ:00000914" }, "Singapore": { "text": "Singapore", + "description": "An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role.", "meaning": "GAZ:00003923" }, "Sint Maarten": { "text": "Sint Maarten", + "description": "One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten.", "meaning": "GAZ:00012579" }, "Slovakia": { "text": "Slovakia", + "description": "A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts.", "meaning": "GAZ:00002956" }, "Slovenia": { "text": "Slovenia", + "description": "A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status.", "meaning": "GAZ:00002955" }, "Solomon Islands": { "text": "Solomon Islands", + "description": "A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal.", "meaning": "GAZ:00005275" }, "Somalia": { "text": "Somalia", + "description": "A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir.", "meaning": "GAZ:00001104" }, "South Africa": { "text": "South Africa", + "description": "A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities.", "meaning": "GAZ:00001094" }, "South Georgia and the South Sandwich Islands": { "text": "South Georgia and the South Sandwich Islands", + "description": "A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE.", "meaning": "GAZ:00003990" }, "South Korea": { "text": "South Korea", + "description": "A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri).", "meaning": "GAZ:00002802" }, "South Sudan": { "text": "South Sudan", + "description": "A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel.", "meaning": "GAZ:00233439" }, "Spain": { "text": "Spain", + "description": "That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal.", "meaning": "GAZ:00000591" }, "Spratly Islands": { "text": "Spratly Islands", + "description": "A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines.", "meaning": "GAZ:00010831" }, "Sri Lanka": { "text": "Sri Lanka", + "description": "An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats.", "meaning": "GAZ:00003924" }, "State of Palestine": { "text": "State of Palestine", + "description": "The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates.", "meaning": "GAZ:00002475" }, "Sudan": { "text": "Sudan", + "description": "A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts.", "meaning": "GAZ:00000560" }, "Suriname": { "text": "Suriname", + "description": "A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten.", "meaning": "GAZ:00002525" }, "Svalbard": { "text": "Svalbard", + "description": "An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole.", "meaning": "GAZ:00005396" }, "Swaziland": { "text": "Swaziland", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", "meaning": "GAZ:00001099" }, "Sweden": { "text": "Sweden", + "description": "A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004.", "meaning": "GAZ:00002729" }, "Switzerland": { "text": "Switzerland", + "description": "A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy.", "meaning": "GAZ:00002941" }, "Syria": { "text": "Syria", + "description": "A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia).", "meaning": "GAZ:00002474" }, "Taiwan": { "text": "Taiwan", + "description": "A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities.", "meaning": "GAZ:00005341" }, "Tajikistan": { "text": "Tajikistan", + "description": "A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion).", "meaning": "GAZ:00006912" }, "Tanzania": { "text": "Tanzania", + "description": "A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities).", "meaning": "GAZ:00001103" }, "Thailand": { "text": "Thailand", + "description": "A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province.", "meaning": "GAZ:00003744" }, "Timor-Leste": { "text": "Timor-Leste", + "description": "A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets.", "meaning": "GAZ:00006913" }, "Togo": { "text": "Togo", + "description": "A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located.", "meaning": "GAZ:00000915" }, "Tokelau": { "text": "Tokelau", + "description": "A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi).", "meaning": "GAZ:00260188" }, "Tonga": { "text": "Tonga", + "description": "A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean.", "meaning": "GAZ:00006916" }, "Trinidad and Tobago": { "text": "Trinidad and Tobago", + "description": "An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands.", "meaning": "GAZ:00003767" }, "Tromelin Island": { "text": "Tromelin Island", + "description": "A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point.", "meaning": "GAZ:00005812" }, "Tunisia": { "text": "Tunisia", + "description": "A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 \"delegations\" or \"districts\" (mutamadiyat), and further subdivided into municipalities (shaykhats).", "meaning": "GAZ:00000562" }, "Turkey": { "text": "Turkey", + "description": "A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts.", "meaning": "GAZ:00000558" }, "Turkmenistan": { "text": "Turkmenistan", + "description": "A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city.", "meaning": "GAZ:00005018" }, "Turks and Caicos Islands": { "text": "Turks and Caicos Islands", + "description": "A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands.", "meaning": "GAZ:00003955" }, "Tuvalu": { "text": "Tuvalu", + "description": "A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia.", "meaning": "GAZ:00009715" }, "United States of America": { "text": "United States of America", + "description": "A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into \"census areas\"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a \"charter township\", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.", "meaning": "GAZ:00002459" }, "Uganda": { "text": "Uganda", + "description": "A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.", "meaning": "GAZ:00001102" }, "Ukraine": { "text": "Ukraine", + "description": "A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units.", "meaning": "GAZ:00002724" }, "United Arab Emirates": { "text": "United Arab Emirates", + "description": "A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain.", "meaning": "GAZ:00005282" }, "United Kingdom": { "text": "United Kingdom", + "description": "A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.", "meaning": "GAZ:00002637" }, "Uruguay": { "text": "Uruguay", + "description": "A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento).", "meaning": "GAZ:00002930" }, "Uzbekistan": { "text": "Uzbekistan", + "description": "A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar).", "meaning": "GAZ:00004979" }, "Vanuatu": { "text": "Vanuatu", + "description": "An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji.", "meaning": "GAZ:00006918" }, "Venezuela": { "text": "Venezuela", + "description": "A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias).", "meaning": "GAZ:00002931" }, "Viet Nam": { "text": "Viet Nam", + "description": "The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia.", "meaning": "GAZ:00003756" }, "Virgin Islands": { "text": "Virgin Islands", + "description": "A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts.", "meaning": "GAZ:00003959" }, "Wake Island": { "text": "Wake Island", + "description": "A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east).", "meaning": "GAZ:00007111" }, "Wallis and Futuna": { "text": "Wallis and Futuna", + "description": "A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets.", "meaning": "GAZ:00007191" }, "West Bank": { "text": "West Bank", + "description": "A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian \"islands\" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is \"pipelined\".", "meaning": "GAZ:00009572" }, "Western Sahara": { "text": "Western Sahara", + "description": "A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions.", "meaning": "GAZ:00000564" }, "Yemen": { "text": "Yemen", + "description": "A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001).", "meaning": "GAZ:00005284" }, "Zambia": { "text": "Zambia", + "description": "A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts.", "meaning": "GAZ:00001107" }, "Zimbabwe": { "text": "Zimbabwe", + "description": "A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities.", "meaning": "GAZ:00001106" } } }, - "geo_loc_name (country) international menu": { - "name": "geo_loc_name (country) international menu", + "GeoLocNameCountryInternationalMenu": { + "name": "GeoLocNameCountryInternationalMenu", + "title": "geo_loc_name (country) international menu", "from_schema": "https://example.com/mpox", "permissible_values": { "Afghanistan [GAZ:00006882]": { "text": "Afghanistan [GAZ:00006882]", + "description": "A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ]", "meaning": "GAZ:00006882" }, "Albania [GAZ:00002953]": { "text": "Albania [GAZ:00002953]", + "description": "A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ]", "meaning": "GAZ:00002953" }, "Algeria [GAZ:00000563]": { "text": "Algeria [GAZ:00000563]", + "description": "A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ]", "meaning": "GAZ:00000563" }, "American Samoa [GAZ:00003957]": { "text": "American Samoa [GAZ:00003957]", + "description": "An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ]", "meaning": "GAZ:00003957" }, "Andorra [GAZ:00002948]": { "text": "Andorra [GAZ:00002948]", + "description": "A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]", "meaning": "GAZ:00002948" }, "Angola [GAZ:00001095]": { "text": "Angola [GAZ:00001095]", + "description": "A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ]", "meaning": "GAZ:00001095" }, "Anguilla [GAZ:00009159]": { "text": "Anguilla [GAZ:00009159]", + "description": "A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ]", "meaning": "GAZ:00009159" }, "Antarctica [GAZ:00000462]": { "text": "Antarctica [GAZ:00000462]", + "description": "The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ]", "meaning": "GAZ:00000462" }, "Antigua and Barbuda [GAZ:00006883]": { "text": "Antigua and Barbuda [GAZ:00006883]", + "description": "An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ]", "meaning": "GAZ:00006883" }, "Argentina [GAZ:00002928]": { "text": "Argentina [GAZ:00002928]", + "description": "A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ]", "meaning": "GAZ:00002928" }, "Armenia [GAZ:00004094]": { "text": "Armenia [GAZ:00004094]", + "description": "A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ]", "meaning": "GAZ:00004094" }, "Aruba [GAZ:00004025]": { "text": "Aruba [GAZ:00004025]", + "description": "An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ]", "meaning": "GAZ:00004025" }, "Ashmore and Cartier Islands [GAZ:00005901]": { "text": "Ashmore and Cartier Islands [GAZ:00005901]", + "description": "A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ]", "meaning": "GAZ:00005901" }, "Australia [GAZ:00000463]": { "text": "Australia [GAZ:00000463]", + "description": "A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories.", "meaning": "GAZ:00000463" }, "Austria [GAZ:00002942]": { "text": "Austria [GAZ:00002942]", + "description": "A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities.", "meaning": "GAZ:00002942" }, "Azerbaijan [GAZ:00004941]": { "text": "Azerbaijan [GAZ:00004941]", + "description": "A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika).", "meaning": "GAZ:00004941" }, "Bahamas [GAZ:00002733]": { "text": "Bahamas [GAZ:00002733]", + "description": "A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government.", "meaning": "GAZ:00002733" }, "Bahrain [GAZ:00005281]": { "text": "Bahrain [GAZ:00005281]", + "description": "A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates.", "meaning": "GAZ:00005281" }, "Baker Island [GAZ:00007117]": { "text": "Baker Island [GAZ:00007117]", + "description": "An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US.", "meaning": "GAZ:00007117" }, "Bangladesh [GAZ:00003750]": { "text": "Bangladesh [GAZ:00003750]", + "description": "A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana (\"police stations\").", "meaning": "GAZ:00003750" }, "Barbados [GAZ:00001251]": { "text": "Barbados [GAZ:00001251]", + "description": "An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown.", "meaning": "GAZ:00001251" }, "Bassas da India [GAZ:00005810]": { "text": "Bassas da India [GAZ:00005810]", + "description": "A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below.", "meaning": "GAZ:00005810" }, "Belarus [GAZ:00006886]": { "text": "Belarus [GAZ:00006886]", + "description": "A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital.", "meaning": "GAZ:00006886" }, "Belgium [GAZ:00002938]": { "text": "Belgium [GAZ:00002938]", + "description": "A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977).", "meaning": "GAZ:00002938" }, "Belize [GAZ:00002934]": { "text": "Belize [GAZ:00002934]", + "description": "A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies.", "meaning": "GAZ:00002934" }, "Benin [GAZ:00000904]": { "text": "Benin [GAZ:00000904]", + "description": "A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes.", "meaning": "GAZ:00000904" }, "Bermuda [GAZ:00001264]": { "text": "Bermuda [GAZ:00001264]", + "description": "A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands.", "meaning": "GAZ:00001264" }, "Bhutan [GAZ:00003920]": { "text": "Bhutan [GAZ:00003920]", + "description": "A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog.", "meaning": "GAZ:00003920" }, "Bolivia [GAZ:00002511]": { "text": "Bolivia [GAZ:00002511]", + "description": "A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios).", "meaning": "GAZ:00002511" }, "Borneo [GAZ:00025355]": { "text": "Borneo [GAZ:00025355]", + "description": "An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres.", "meaning": "GAZ:00025355" }, "Bosnia and Herzegovina [GAZ:00006887]": { "text": "Bosnia and Herzegovina [GAZ:00006887]", + "description": "A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina.", "meaning": "GAZ:00006887" }, "Botswana [GAZ:00001097]": { "text": "Botswana [GAZ:00001097]", + "description": "A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts.", "meaning": "GAZ:00001097" }, "Bouvet Island [GAZ:00001453]": { "text": "Bouvet Island [GAZ:00001453]", + "description": "A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended.", "meaning": "GAZ:00001453" }, "Brazil [GAZ:00002828]": { "text": "Brazil [GAZ:00002828]", + "description": "A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South.", "meaning": "GAZ:00002828" }, "British Virgin Islands [GAZ:00003961]": { "text": "British Virgin Islands [GAZ:00003961]", + "description": "A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited.", "meaning": "GAZ:00003961" }, "Brunei [GAZ:00003901]": { "text": "Brunei [GAZ:00003901]", + "description": "A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages).", "meaning": "GAZ:00003901" }, "Bulgaria [GAZ:00002950]": { "text": "Bulgaria [GAZ:00002950]", + "description": "A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities.", "meaning": "GAZ:00002950" }, "Burkina Faso [GAZ:00000905]": { "text": "Burkina Faso [GAZ:00000905]", + "description": "A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes).", "meaning": "GAZ:00000905" }, "Burundi [GAZ:00001090]": { "text": "Burundi [GAZ:00001090]", + "description": "A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines.", "meaning": "GAZ:00001090" }, "Cambodia [GAZ:00006888]": { "text": "Cambodia [GAZ:00006888]", + "description": "A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand.", "meaning": "GAZ:00006888" }, "Cameroon [GAZ:00001093]": { "text": "Cameroon [GAZ:00001093]", + "description": "A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts.", "meaning": "GAZ:00001093" }, "Canada [GAZ:00002560]": { "text": "Canada [GAZ:00002560]", + "description": "A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada.", "meaning": "GAZ:00002560" }, "Cape Verde [GAZ:00001227]": { "text": "Cape Verde [GAZ:00001227]", + "description": "A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias).", "meaning": "GAZ:00001227" }, "Cayman Islands [GAZ:00003986]": { "text": "Cayman Islands [GAZ:00003986]", + "description": "A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts.", "meaning": "GAZ:00003986" }, "Central African Republic [GAZ:00001089]": { "text": "Central African Republic [GAZ:00001089]", + "description": "A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures).", "meaning": "GAZ:00001089" }, "Chad [GAZ:00000586]": { "text": "Chad [GAZ:00000586]", + "description": "A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change.", "meaning": "GAZ:00000586" }, "Chile [GAZ:00002825]": { "text": "Chile [GAZ:00002825]", + "description": "A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10.", "meaning": "GAZ:00002825" }, "China [GAZ:00002845]": { "text": "China [GAZ:00002845]", + "description": "A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.", "meaning": "GAZ:00002845" }, "Christmas Island [GAZ:00005915]": { "text": "Christmas Island [GAZ:00005915]", + "description": "An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain.", "meaning": "GAZ:00005915" }, "Clipperton Island [GAZ:00005838]": { "text": "Clipperton Island [GAZ:00005838]", + "description": "A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica.", "meaning": "GAZ:00005838" }, "Cocos Islands [GAZ:00009721]": { "text": "Cocos Islands [GAZ:00009721]", + "description": "Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group.", "meaning": "GAZ:00009721" }, "Colombia [GAZ:00002929]": { "text": "Colombia [GAZ:00002929]", + "description": "A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities.", "meaning": "GAZ:00002929" }, "Comoros [GAZ:00005820]": { "text": "Comoros [GAZ:00005820]", + "description": "An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique.", "meaning": "GAZ:00005820" }, "Cook Islands [GAZ:00053798]": { "text": "Cook Islands [GAZ:00053798]", + "description": "A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean.", "meaning": "GAZ:00053798" }, "Coral Sea Islands [GAZ:00005917]": { "text": "Coral Sea Islands [GAZ:00005917]", + "description": "A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups.", "meaning": "GAZ:00005917" }, "Costa Rica [GAZ:00002901]": { "text": "Costa Rica [GAZ:00002901]", + "description": "A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons.", "meaning": "GAZ:00002901" }, "Cote d'Ivoire [GAZ:00000906]": { "text": "Cote d'Ivoire [GAZ:00000906]", + "description": "A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments.", "meaning": "GAZ:00000906" }, "Croatia [GAZ:00002719]": { "text": "Croatia [GAZ:00002719]", + "description": "A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district.", "meaning": "GAZ:00002719" }, "Cuba [GAZ:00003762]": { "text": "Cuba [GAZ:00003762]", + "description": "A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba.", "meaning": "GAZ:00003762" }, "Curacao [GAZ:00012582]": { "text": "Curacao [GAZ:00012582]", + "description": "One of five island areas of the Netherlands Antilles.", "meaning": "GAZ:00012582" }, "Cyprus [GAZ:00004006]": { "text": "Cyprus [GAZ:00004006]", + "description": "The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west.", "meaning": "GAZ:00004006" }, "Czech Republic [GAZ:00002954]": { "text": "Czech Republic [GAZ:00002954]", + "description": "A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named \"Little Districts\" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices.", "meaning": "GAZ:00002954" }, "Democratic Republic of the Congo [GAZ:00001086]": { "text": "Democratic Republic of the Congo [GAZ:00001086]", + "description": "A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones.", "meaning": "GAZ:00001086" }, "Denmark [GAZ:00005852]": { "text": "Denmark [GAZ:00005852]", + "description": "That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago.", "meaning": "GAZ:00005852" }, "Djibouti [GAZ:00000582]": { "text": "Djibouti [GAZ:00000582]", + "description": "A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts.", "meaning": "GAZ:00000582" }, "Dominica [GAZ:00006890]": { "text": "Dominica [GAZ:00006890]", + "description": "An island nation in the Caribbean Sea. Dominica is divided into ten parishes.", "meaning": "GAZ:00006890" }, "Dominican Republic [GAZ:00003952]": { "text": "Dominican Republic [GAZ:00003952]", + "description": "A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio).", "meaning": "GAZ:00003952" }, "Ecuador [GAZ:00002912]": { "text": "Ecuador [GAZ:00002912]", + "description": "A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias).", "meaning": "GAZ:00002912" }, "Egypt [GAZ:00003934]": { "text": "Egypt [GAZ:00003934]", + "description": "A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes).", "meaning": "GAZ:00003934" }, "El Salvador [GAZ:00002935]": { "text": "El Salvador [GAZ:00002935]", + "description": "A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios).", "meaning": "GAZ:00002935" }, "Equatorial Guinea [GAZ:00001091]": { "text": "Equatorial Guinea [GAZ:00001091]", + "description": "A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts.", "meaning": "GAZ:00001091" }, "Eritrea [GAZ:00000581]": { "text": "Eritrea [GAZ:00000581]", + "description": "A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts (\"sub-zobas\").", "meaning": "GAZ:00000581" }, "Estonia [GAZ:00002959]": { "text": "Estonia [GAZ:00002959]", + "description": "A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities.", "meaning": "GAZ:00002959" }, "Eswatini [GAZ:00001099]": { "text": "Eswatini [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", "meaning": "GAZ:00001099" }, "Ethiopia [GAZ:00000567]": { "text": "Ethiopia [GAZ:00000567]", + "description": "A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas.", "meaning": "GAZ:00000567" }, "Europa Island [GAZ:00005811]": { "text": "Europa Island [GAZ:00005811]", + "description": "A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique.", "meaning": "GAZ:00005811" }, "Falkland Islands (Islas Malvinas) [GAZ:00001412]": { "text": "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "description": "An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands.", "meaning": "GAZ:00001412" }, "Faroe Islands [GAZ:00059206]": { "text": "Faroe Islands [GAZ:00059206]", + "description": "An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie.", "meaning": "GAZ:00059206" }, "Fiji [GAZ:00006891]": { "text": "Fiji [GAZ:00006891]", + "description": "An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population.", "meaning": "GAZ:00006891" }, "Finland [GAZ:00002937]": { "text": "Finland [GAZ:00002937]", + "description": "A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta).", "meaning": "GAZ:00002937" }, "France [GAZ:00003940]": { "text": "France [GAZ:00003940]", + "description": "A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments.", "meaning": "GAZ:00003940" }, "French Guiana [GAZ:00002516]": { "text": "French Guiana [GAZ:00002516]", + "description": "An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes.", "meaning": "GAZ:00002516" }, "French Polynesia [GAZ:00002918]": { "text": "French Polynesia [GAZ:00002918]", + "description": "A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives).", "meaning": "GAZ:00002918" }, "French Southern and Antarctic Lands [GAZ:00003753]": { "text": "French Southern and Antarctic Lands [GAZ:00003753]", + "description": "The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts.", "meaning": "GAZ:00003753" }, "Gabon [GAZ:00001092]": { "text": "Gabon [GAZ:00001092]", + "description": "A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments.", "meaning": "GAZ:00001092" }, "Gambia [GAZ:00000907]": { "text": "Gambia [GAZ:00000907]", + "description": "A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts.", "meaning": "GAZ:00000907" }, "Gaza Strip [GAZ:00009571]": { "text": "Gaza Strip [GAZ:00009571]", + "description": "A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine.", "meaning": "GAZ:00009571" }, "Georgia [GAZ:00004942]": { "text": "Georgia [GAZ:00004942]", + "description": "A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni).", "meaning": "GAZ:00004942" }, "Germany [GAZ:00002646]": { "text": "Germany [GAZ:00002646]", + "description": "A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte).", "meaning": "GAZ:00002646" }, "Ghana [GAZ:00000908]": { "text": "Ghana [GAZ:00000908]", + "description": "A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts.", "meaning": "GAZ:00000908" }, "Gibraltar [GAZ:00003987]": { "text": "Gibraltar [GAZ:00003987]", + "description": "A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north.", "meaning": "GAZ:00003987" }, "Glorioso Islands [GAZ:00005808]": { "text": "Glorioso Islands [GAZ:00005808]", + "description": "A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar.", "meaning": "GAZ:00005808" }, "Greece [GAZ:00002945]": { "text": "Greece [GAZ:00002945]", + "description": "A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia.", "meaning": "GAZ:00002945" }, "Greenland [GAZ:00001507]": { "text": "Greenland [GAZ:00001507]", + "description": "A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago.", "meaning": "GAZ:00001507" }, "Grenada [GAZ:02000573]": { "text": "Grenada [GAZ:02000573]", + "description": "An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020.", "meaning": "GAZ:02000573" }, "Guadeloupe [GAZ:00067142]": { "text": "Guadeloupe [GAZ:00067142]", + "description": "An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica.", "meaning": "GAZ:00067142" }, "Guam [GAZ:00003706]": { "text": "Guam [GAZ:00003706]", + "description": "An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia.", "meaning": "GAZ:00003706" }, "Guatemala [GAZ:00002936]": { "text": "Guatemala [GAZ:00002936]", + "description": "A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios).", "meaning": "GAZ:00002936" }, "Guernsey [GAZ:00001550]": { "text": "Guernsey [GAZ:00001550]", + "description": "A British Crown Dependency in the English Channel off the coast of Normandy.", "meaning": "GAZ:00001550" }, "Guinea [GAZ:00000909]": { "text": "Guinea [GAZ:00000909]", + "description": "A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip.", "meaning": "GAZ:00000909" }, "Guinea-Bissau [GAZ:00000910]": { "text": "Guinea-Bissau [GAZ:00000910]", + "description": "A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea.", "meaning": "GAZ:00000910" }, "Guyana [GAZ:00002522]": { "text": "Guyana [GAZ:00002522]", + "description": "A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils.", "meaning": "GAZ:00002522" }, "Haiti [GAZ:00003953]": { "text": "Haiti [GAZ:00003953]", + "description": "A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions.", "meaning": "GAZ:00003953" }, "Heard Island and McDonald Islands [GAZ:00009718]": { "text": "Heard Island and McDonald Islands [GAZ:00009718]", + "description": "An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica.", "meaning": "GAZ:00009718" }, "Honduras [GAZ:00002894]": { "text": "Honduras [GAZ:00002894]", + "description": "A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan.", "meaning": "GAZ:00002894" }, "Hong Kong [GAZ:00003203]": { "text": "Hong Kong [GAZ:00003203]", + "description": "A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997.", "meaning": "GAZ:00003203" }, "Howland Island [GAZ:00007120]": { "text": "Howland Island [GAZ:00007120]", + "description": "An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands.", "meaning": "GAZ:00007120" }, "Hungary [GAZ:00002952]": { "text": "Hungary [GAZ:00002952]", + "description": "A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary.", "meaning": "GAZ:00002952" }, "Iceland [GAZ:00000843]": { "text": "Iceland [GAZ:00000843]", + "description": "A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland.", "meaning": "GAZ:00000843" }, "India [GAZ:00002839]": { "text": "India [GAZ:00002839]", + "description": "A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages.", "meaning": "GAZ:00002839" }, "Indonesia [GAZ:00003727]": { "text": "Indonesia [GAZ:00003727]", + "description": "An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan).", "meaning": "GAZ:00003727" }, "Iran [GAZ:00004474]": { "text": "Iran [GAZ:00004474]", + "description": "A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan).", "meaning": "GAZ:00004474" }, "Iraq [GAZ:00004483]": { "text": "Iraq [GAZ:00004483]", + "description": "A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts).", "meaning": "GAZ:00004483" }, "Ireland [GAZ:00002943]": { "text": "Ireland [GAZ:00002943]", + "description": "A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 \"county-level\" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a \"city council\"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties.", "meaning": "GAZ:00002943" }, "Isle of Man [GAZ:00052477]": { "text": "Isle of Man [GAZ:00052477]", + "description": "A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations.", "meaning": "GAZ:00052477" }, "Israel [GAZ:00002476]": { "text": "Israel [GAZ:00002476]", + "description": "A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions.", "meaning": "GAZ:00002476" }, "Italy [GAZ:00002650]": { "text": "Italy [GAZ:00002650]", + "description": "A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni).", "meaning": "GAZ:00002650" }, "Jamaica [GAZ:00003781]": { "text": "Jamaica [GAZ:00003781]", + "description": "A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance.", "meaning": "GAZ:00003781" }, "Jan Mayen [GAZ:00005853]": { "text": "Jan Mayen [GAZ:00005853]", + "description": "A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.", "meaning": "GAZ:00005853" }, "Japan [GAZ:00002747]": { "text": "Japan [GAZ:00002747]", + "description": "An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.", "meaning": "GAZ:00002747" }, "Jarvis Island [GAZ:00007118]": { "text": "Jarvis Island [GAZ:00007118]", + "description": "An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount.", "meaning": "GAZ:00007118" }, "Jersey [GAZ:00001551]": { "text": "Jersey [GAZ:00001551]", + "description": "A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq.", "meaning": "GAZ:00001551" }, "Johnston Atoll [GAZ:00007114]": { "text": "Johnston Atoll [GAZ:00007114]", + "description": "A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount.", "meaning": "GAZ:00007114" }, "Jordan [GAZ:00002473]": { "text": "Jordan [GAZ:00002473]", + "description": "A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias.", "meaning": "GAZ:00002473" }, "Juan de Nova Island [GAZ:00005809]": { "text": "Juan de Nova Island [GAZ:00005809]", + "description": "A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique.", "meaning": "GAZ:00005809" }, "Kazakhstan [GAZ:00004999]": { "text": "Kazakhstan [GAZ:00004999]", + "description": "A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions.", "meaning": "GAZ:00004999" }, "Kenya [GAZ:00001101]": { "text": "Kenya [GAZ:00001101]", + "description": "A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province.", "meaning": "GAZ:00001101" }, "Kerguelen Archipelago [GAZ:00005682]": { "text": "Kerguelen Archipelago [GAZ:00005682]", + "description": "A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap.", "meaning": "GAZ:00005682" }, "Kingman Reef [GAZ:00007116]": { "text": "Kingman Reef [GAZ:00007116]", + "description": "A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount.", "meaning": "GAZ:00007116" }, "Kiribati [GAZ:00006894]": { "text": "Kiribati [GAZ:00006894]", + "description": "An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea).", "meaning": "GAZ:00006894" }, "Kosovo [GAZ:00011337]": { "text": "Kosovo [GAZ:00011337]", + "description": "A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija.", "meaning": "GAZ:00011337" }, "Kuwait [GAZ:00005285]": { "text": "Kuwait [GAZ:00005285]", + "description": "A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah).", "meaning": "GAZ:00005285" }, "Kyrgyzstan [GAZ:00006893]": { "text": "Kyrgyzstan [GAZ:00006893]", + "description": "A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions).", "meaning": "GAZ:00006893" }, "Laos [GAZ:00006889]": { "text": "Laos [GAZ:00006889]", + "description": "A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang).", "meaning": "GAZ:00006889" }, "Latvia [GAZ:00002958]": { "text": "Latvia [GAZ:00002958]", + "description": "A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions.", "meaning": "GAZ:00002958" }, "Lebanon [GAZ:00002478]": { "text": "Lebanon [GAZ:00002478]", + "description": "A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa).", "meaning": "GAZ:00002478" }, "Lesotho [GAZ:00001098]": { "text": "Lesotho [GAZ:00001098]", + "description": "A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils.", "meaning": "GAZ:00001098" }, "Liberia [GAZ:00000911]": { "text": "Liberia [GAZ:00000911]", + "description": "A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean.", "meaning": "GAZ:00000911" }, "Libya [GAZ:00000566]": { "text": "Libya [GAZ:00000566]", + "description": "A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s.", "meaning": "GAZ:00000566" }, "Liechtenstein [GAZ:00003858]": { "text": "Liechtenstein [GAZ:00003858]", + "description": "A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county).", "meaning": "GAZ:00003858" }, "Line Islands [GAZ:00007144]": { "text": "Line Islands [GAZ:00007144]", + "description": "A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands.", "meaning": "GAZ:00007144" }, "Lithuania [GAZ:00002960]": { "text": "Lithuania [GAZ:00002960]", + "description": "A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos).", "meaning": "GAZ:00002960" }, "Luxembourg [GAZ:00002947]": { "text": "Luxembourg [GAZ:00002947]", + "description": "A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest.", "meaning": "GAZ:00002947" }, "Macau [GAZ:00003202]": { "text": "Macau [GAZ:00003202]", + "description": "One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China.", "meaning": "GAZ:00003202" }, "Madagascar [GAZ:00001108]": { "text": "Madagascar [GAZ:00001108]", + "description": "An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany.", "meaning": "GAZ:00001108" }, "Malawi [GAZ:00001105]": { "text": "Malawi [GAZ:00001105]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", "meaning": "GAZ:00001105" }, "Malaysia [GAZ:00003902]": { "text": "Malaysia [GAZ:00003902]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", "meaning": "GAZ:00003902" }, "Maldives [GAZ:00006924]": { "text": "Maldives [GAZ:00006924]", + "description": "An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2.", "meaning": "GAZ:00006924" }, "Mali [GAZ:00000584]": { "text": "Mali [GAZ:00000584]", + "description": "A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements.", "meaning": "GAZ:00000584" }, "Malta [GAZ:00004017]": { "text": "Malta [GAZ:00004017]", + "description": "A Southern European country and consists of an archipelago situated centrally in the Mediterranean.", "meaning": "GAZ:00004017" }, "Marshall Islands [GAZ:00007161]": { "text": "Marshall Islands [GAZ:00007161]", + "description": "An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning \"sunrise\" and \"sunset\" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated.", "meaning": "GAZ:00007161" }, "Martinique [GAZ:00067143]": { "text": "Martinique [GAZ:00067143]", + "description": "An island and an overseas department/region and single territorial collectivity of France.", "meaning": "GAZ:00067143" }, "Mauritania [GAZ:00000583]": { "text": "Mauritania [GAZ:00000583]", + "description": "A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements).", "meaning": "GAZ:00000583" }, "Mauritius [GAZ:00003745]": { "text": "Mauritius [GAZ:00003745]", + "description": "An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands.", "meaning": "GAZ:00003745" }, "Mayotte [GAZ:00003943]": { "text": "Mayotte [GAZ:00003943]", + "description": "An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two.", "meaning": "GAZ:00003943" }, "Mexico [GAZ:00002852]": { "text": "Mexico [GAZ:00002852]", + "description": "A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City.", "meaning": "GAZ:00002852" }, "Micronesia [GAZ:00005862]": { "text": "Micronesia [GAZ:00005862]", + "description": "A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east.", "meaning": "GAZ:00005862" }, "Midway Islands [GAZ:00007112]": { "text": "Midway Islands [GAZ:00007112]", + "description": "A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior.", "meaning": "GAZ:00007112" }, "Moldova [GAZ:00003897]": { "text": "Moldova [GAZ:00003897]", + "description": "A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic.", "meaning": "GAZ:00003897" }, "Monaco [GAZ:00003857]": { "text": "Monaco [GAZ:00003857]", + "description": "A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards.", "meaning": "GAZ:00003857" }, "Mongolia [GAZ:00008744]": { "text": "Mongolia [GAZ:00008744]", + "description": "A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status.", "meaning": "GAZ:00008744" }, "Montenegro [GAZ:00006898]": { "text": "Montenegro [GAZ:00006898]", + "description": "A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality.", "meaning": "GAZ:00006898" }, "Montserrat [GAZ:00003988]": { "text": "Montserrat [GAZ:00003988]", + "description": "A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes.", "meaning": "GAZ:00003988" }, "Morocco [GAZ:00000565]": { "text": "Morocco [GAZ:00000565]", + "description": "A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of \"Saguia el-Hamra\" and \"Rio de Oro\" is disputed.", "meaning": "GAZ:00000565" }, "Mozambique [GAZ:00001100]": { "text": "Mozambique [GAZ:00001100]", + "description": "A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in \"Postos Administrativos\" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration.", "meaning": "GAZ:00001100" }, "Myanmar [GAZ:00006899]": { "text": "Myanmar [GAZ:00006899]", + "description": "A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages.", "meaning": "GAZ:00006899" }, "Namibia [GAZ:00001096]": { "text": "Namibia [GAZ:00001096]", + "description": "A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies.", "meaning": "GAZ:00001096" }, "Nauru [GAZ:00006900]": { "text": "Nauru [GAZ:00006900]", + "description": "An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies.", "meaning": "GAZ:00006900" }, "Navassa Island [GAZ:00007119]": { "text": "Navassa Island [GAZ:00007119]", + "description": "A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti.", "meaning": "GAZ:00007119" }, "Nepal [GAZ:00004399]": { "text": "Nepal [GAZ:00004399]", + "description": "A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the \"Chicken's Neck\". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions.", "meaning": "GAZ:00004399" }, "Netherlands [GAZ:00002946]": { "text": "Netherlands [GAZ:00002946]", + "description": "The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007).", "meaning": "GAZ:00002946" }, "New Caledonia [GAZ:00005206]": { "text": "New Caledonia [GAZ:00005206]", + "description": "A \"sui generis collectivity\" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes.", "meaning": "GAZ:00005206" }, "New Zealand [GAZ:00000469]": { "text": "New Zealand [GAZ:00000469]", + "description": "A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands.", "meaning": "GAZ:00000469" }, "Nicaragua [GAZ:00002978]": { "text": "Nicaragua [GAZ:00002978]", + "description": "A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya.", "meaning": "GAZ:00002978" }, "Niger [GAZ:00000585]": { "text": "Niger [GAZ:00000585]", + "description": "A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes.", "meaning": "GAZ:00000585" }, "Nigeria [GAZ:00000912]": { "text": "Nigeria [GAZ:00000912]", + "description": "A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs).", "meaning": "GAZ:00000912" }, "Niue [GAZ:00006902]": { "text": "Niue [GAZ:00006902]", + "description": "An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state.", "meaning": "GAZ:00006902" }, "Norfolk Island [GAZ:00005908]": { "text": "Norfolk Island [GAZ:00005908]", + "description": "A Territory of Australia that includes Norfolk Island and neighboring islands.", "meaning": "GAZ:00005908" }, "North Korea [GAZ:00002801]": { "text": "North Korea [GAZ:00002801]", + "description": "A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia.", "meaning": "GAZ:00002801" }, "North Macedonia [GAZ:00006895]": { "text": "North Macedonia [GAZ:00006895]", + "description": "A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts.", "meaning": "GAZ:00006895" }, "North Sea [GAZ:00002284]": { "text": "North Sea [GAZ:00002284]", + "description": "A sea situated between the eastern coasts of the British Isles and the western coast of Europe.", "meaning": "GAZ:00002284" }, "Northern Mariana Islands [GAZ:00003958]": { "text": "Northern Mariana Islands [GAZ:00003958]", + "description": "A group of 15 islands about three-quarters of the way from Hawaii to the Philippines.", "meaning": "GAZ:00003958" }, "Norway [GAZ:00002699]": { "text": "Norway [GAZ:00002699]", + "description": "A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom.", "meaning": "GAZ:00002699" }, "Oman [GAZ:00005283]": { "text": "Oman [GAZ:00005283]", + "description": "A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat).", "meaning": "GAZ:00005283" }, "Pakistan [GAZ:00005246]": { "text": "Pakistan [GAZ:00005246]", + "description": "A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan.", "meaning": "GAZ:00005246" }, "Palau [GAZ:00006905]": { "text": "Palau [GAZ:00006905]", + "description": "A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines.", "meaning": "GAZ:00006905" }, "Panama [GAZ:00002892]": { "text": "Panama [GAZ:00002892]", + "description": "The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports.", "meaning": "GAZ:00002892" }, "Papua New Guinea [GAZ:00003922]": { "text": "Papua New Guinea [GAZ:00003922]", + "description": "A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia).", "meaning": "GAZ:00003922" }, "Paracel Islands [GAZ:00010832]": { "text": "Paracel Islands [GAZ:00010832]", + "description": "A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines.", "meaning": "GAZ:00010832" }, "Paraguay [GAZ:00002933]": { "text": "Paraguay [GAZ:00002933]", + "description": "A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts.", "meaning": "GAZ:00002933" }, "Peru [GAZ:00002932]": { "text": "Peru [GAZ:00002932]", + "description": "A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao.", "meaning": "GAZ:00002932" }, "Philippines [GAZ:00004525]": { "text": "Philippines [GAZ:00004525]", + "description": "An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays.", "meaning": "GAZ:00004525" }, "Pitcairn Islands [GAZ:00005867]": { "text": "Pitcairn Islands [GAZ:00005867]", + "description": "A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia.", "meaning": "GAZ:00005867" }, "Poland [GAZ:00002939]": { "text": "Poland [GAZ:00002939]", + "description": "A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas.", "meaning": "GAZ:00002939" }, "Portugal [GAZ:00004126]": { "text": "Portugal [GAZ:00004126]", + "description": "That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands.", "meaning": "GAZ:00004126" }, "Puerto Rico [GAZ:00006935]": { "text": "Puerto Rico [GAZ:00006935]", + "description": "A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States).", "meaning": "GAZ:00006935" }, "Qatar [GAZ:00005286]": { "text": "Qatar [GAZ:00005286]", + "description": "An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts).", "meaning": "GAZ:00005286" }, "Republic of the Congo [GAZ:00001088]": { "text": "Republic of the Congo [GAZ:00001088]", + "description": "A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts.", "meaning": "GAZ:00001088" }, "Reunion [GAZ:00003945]": { "text": "Reunion [GAZ:00003945]", + "description": "An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island.", "meaning": "GAZ:00003945" }, "Romania [GAZ:00002951]": { "text": "Romania [GAZ:00002951]", + "description": "A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities).", "meaning": "GAZ:00002951" }, "Ross Sea [GAZ:00023304]": { "text": "Ross Sea [GAZ:00023304]", + "description": "A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW.", "meaning": "GAZ:00023304" }, "Russia [GAZ:00002721]": { "text": "Russia [GAZ:00002721]", + "description": "A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts.", "meaning": "GAZ:00002721" }, "Rwanda [GAZ:00001087]": { "text": "Rwanda [GAZ:00001087]", + "description": "A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge).", "meaning": "GAZ:00001087" }, "Saint Helena [GAZ:00000849]": { "text": "Saint Helena [GAZ:00000849]", + "description": "An island of volcanic origin and a British overseas territory in the South Atlantic Ocean.", "meaning": "GAZ:00000849" }, "Saint Kitts and Nevis [GAZ:00006906]": { "text": "Saint Kitts and Nevis [GAZ:00006906]", + "description": "A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis.", "meaning": "GAZ:00006906" }, "Saint Lucia [GAZ:00006909]": { "text": "Saint Lucia [GAZ:00006909]", + "description": "An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean.", "meaning": "GAZ:00006909" }, "Saint Pierre and Miquelon [GAZ:00003942]": { "text": "Saint Pierre and Miquelon [GAZ:00003942]", + "description": "An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985.", "meaning": "GAZ:00003942" }, "Saint Martin [GAZ:00005841]": { "text": "Saint Martin [GAZ:00005841]", + "description": "An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe.", "meaning": "GAZ:00005841" }, "Saint Vincent and the Grenadines [GAZ:02000565]": { "text": "Saint Vincent and the Grenadines [GAZ:02000565]", + "description": "An island nation in the Lesser Antilles chain of the Caribbean Sea.", "meaning": "GAZ:02000565" }, "Samoa [GAZ:00006910]": { "text": "Samoa [GAZ:00006910]", + "description": "A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts).", "meaning": "GAZ:00006910" }, "San Marino [GAZ:00003102]": { "text": "San Marino [GAZ:00003102]", + "description": "A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello).", "meaning": "GAZ:00003102" }, "Sao Tome and Principe [GAZ:00006927]": { "text": "Sao Tome and Principe [GAZ:00006927]", + "description": "An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29).", "meaning": "GAZ:00006927" }, "Saudi Arabia [GAZ:00005279]": { "text": "Saudi Arabia [GAZ:00005279]", + "description": "A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates.", "meaning": "GAZ:00005279" }, "Senegal [GAZ:00000913]": { "text": "Senegal [GAZ:00000913]", + "description": "A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales.", "meaning": "GAZ:00000913" }, "Serbia [GAZ:00002957]": { "text": "Serbia [GAZ:00002957]", + "description": "A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities).", "meaning": "GAZ:00002957" }, "Seychelles [GAZ:00006922]": { "text": "Seychelles [GAZ:00006922]", + "description": "An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands.", "meaning": "GAZ:00006922" }, "Sierra Leone [GAZ:00000914]": { "text": "Sierra Leone [GAZ:00000914]", + "description": "A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts.", "meaning": "GAZ:00000914" }, "Singapore [GAZ:00003923]": { "text": "Singapore [GAZ:00003923]", + "description": "An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role.", "meaning": "GAZ:00003923" }, "Sint Maarten [GAZ:00012579]": { "text": "Sint Maarten [GAZ:00012579]", + "description": "One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten.", "meaning": "GAZ:00012579" }, "Slovakia [GAZ:00002956]": { "text": "Slovakia [GAZ:00002956]", + "description": "A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts.", "meaning": "GAZ:00002956" }, "Slovenia [GAZ:00002955]": { "text": "Slovenia [GAZ:00002955]", + "description": "A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status.", "meaning": "GAZ:00002955" }, "Solomon Islands [GAZ:00005275]": { "text": "Solomon Islands [GAZ:00005275]", + "description": "A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal.", "meaning": "GAZ:00005275" }, "Somalia [GAZ:00001104]": { "text": "Somalia [GAZ:00001104]", + "description": "A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir.", "meaning": "GAZ:00001104" }, "South Africa [GAZ:00001094]": { "text": "South Africa [GAZ:00001094]", + "description": "A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities.", "meaning": "GAZ:00001094" }, "South Georgia and the South Sandwich Islands [GAZ:00003990]": { "text": "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "description": "A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE.", "meaning": "GAZ:00003990" }, "South Korea [GAZ:00002802]": { "text": "South Korea [GAZ:00002802]", + "description": "A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri).", "meaning": "GAZ:00002802" }, "South Sudan [GAZ:00233439]": { "text": "South Sudan [GAZ:00233439]", + "description": "A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel.", "meaning": "GAZ:00233439" }, "Spain [GAZ:00003936]": { "text": "Spain [GAZ:00003936]", + "description": "That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal.", "meaning": "GAZ:00003936" }, "Spratly Islands [GAZ:00010831]": { "text": "Spratly Islands [GAZ:00010831]", + "description": "A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines.", "meaning": "GAZ:00010831" }, "Sri Lanka [GAZ:00003924]": { "text": "Sri Lanka [GAZ:00003924]", + "description": "An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats.", "meaning": "GAZ:00003924" }, "State of Palestine [GAZ:00002475]": { "text": "State of Palestine [GAZ:00002475]", + "description": "The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates.", "meaning": "GAZ:00002475" }, "Sudan [GAZ:00000560]": { "text": "Sudan [GAZ:00000560]", + "description": "A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts.", "meaning": "GAZ:00000560" }, "Suriname [GAZ:00002525]": { "text": "Suriname [GAZ:00002525]", + "description": "A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten.", "meaning": "GAZ:00002525" }, "Svalbard [GAZ:00005396]": { "text": "Svalbard [GAZ:00005396]", + "description": "An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole.", "meaning": "GAZ:00005396" }, "Swaziland [GAZ:00001099]": { "text": "Swaziland [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", "meaning": "GAZ:00001099" }, "Sweden [GAZ:00002729]": { "text": "Sweden [GAZ:00002729]", + "description": "A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004.", "meaning": "GAZ:00002729" }, "Switzerland [GAZ:00002941]": { "text": "Switzerland [GAZ:00002941]", + "description": "A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy.", "meaning": "GAZ:00002941" }, "Syria [GAZ:00002474]": { "text": "Syria [GAZ:00002474]", + "description": "A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia).", "meaning": "GAZ:00002474" }, "Taiwan [GAZ:00005341]": { "text": "Taiwan [GAZ:00005341]", + "description": "A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities.", "meaning": "GAZ:00005341" }, "Tajikistan [GAZ:00006912]": { "text": "Tajikistan [GAZ:00006912]", + "description": "A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion).", "meaning": "GAZ:00006912" }, "Tanzania [GAZ:00001103]": { "text": "Tanzania [GAZ:00001103]", + "description": "A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities).", "meaning": "GAZ:00001103" }, "Thailand [GAZ:00003744]": { "text": "Thailand [GAZ:00003744]", + "description": "A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province.", "meaning": "GAZ:00003744" }, "Timor-Leste [GAZ:00006913]": { "text": "Timor-Leste [GAZ:00006913]", + "description": "A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets.", "meaning": "GAZ:00006913" }, "Togo [GAZ:00000915]": { "text": "Togo [GAZ:00000915]", + "description": "A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located.", "meaning": "GAZ:00000915" }, "Tokelau [GAZ:00260188]": { "text": "Tokelau [GAZ:00260188]", + "description": "A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi).", "meaning": "GAZ:00260188" }, "Tonga [GAZ:00006916]": { "text": "Tonga [GAZ:00006916]", + "description": "A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean.", "meaning": "GAZ:00006916" }, "Trinidad and Tobago [GAZ:00003767]": { "text": "Trinidad and Tobago [GAZ:00003767]", + "description": "An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands.", "meaning": "GAZ:00003767" }, "Tromelin Island [GAZ:00005812]": { "text": "Tromelin Island [GAZ:00005812]", + "description": "A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point.", "meaning": "GAZ:00005812" }, "Tunisia [GAZ:00000562]": { "text": "Tunisia [GAZ:00000562]", + "description": "A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 \"delegations\" or \"districts\" (mutamadiyat), and further subdivided into municipalities (shaykhats).", "meaning": "GAZ:00000562" }, "Turkey [GAZ:00000558]": { "text": "Turkey [GAZ:00000558]", + "description": "A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts.", "meaning": "GAZ:00000558" }, "Turkmenistan [GAZ:00005018]": { "text": "Turkmenistan [GAZ:00005018]", + "description": "A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city.", "meaning": "GAZ:00005018" }, "Turks and Caicos Islands [GAZ:00003955]": { "text": "Turks and Caicos Islands [GAZ:00003955]", + "description": "A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands.", "meaning": "GAZ:00003955" }, "Tuvalu [GAZ:00009715]": { "text": "Tuvalu [GAZ:00009715]", + "description": "A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia.", "meaning": "GAZ:00009715" }, "United States of America [GAZ:00002459]": { "text": "United States of America [GAZ:00002459]", + "description": "A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into \"census areas\"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a \"charter township\", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.", "meaning": "GAZ:00002459" }, "Uganda [GAZ:00001102]": { "text": "Uganda [GAZ:00001102]", + "description": "A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.", "meaning": "GAZ:00001102" }, "Ukraine [GAZ:00002724]": { "text": "Ukraine [GAZ:00002724]", + "description": "A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units.", "meaning": "GAZ:00002724" }, "United Arab Emirates [GAZ:00005282]": { "text": "United Arab Emirates [GAZ:00005282]", + "description": "A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain.", "meaning": "GAZ:00005282" }, "United Kingdom [GAZ:00002637]": { "text": "United Kingdom [GAZ:00002637]", + "description": "A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.", "meaning": "GAZ:00002637" }, "Uruguay [GAZ:00002930]": { "text": "Uruguay [GAZ:00002930]", + "description": "A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento).", "meaning": "GAZ:00002930" }, "Uzbekistan [GAZ:00004979]": { "text": "Uzbekistan [GAZ:00004979]", + "description": "A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar).", "meaning": "GAZ:00004979" }, "Vanuatu [GAZ:00006918]": { "text": "Vanuatu [GAZ:00006918]", + "description": "An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji.", "meaning": "GAZ:00006918" }, "Venezuela [GAZ:00002931]": { "text": "Venezuela [GAZ:00002931]", + "description": "A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias).", "meaning": "GAZ:00002931" }, "Viet Nam [GAZ:00003756]": { "text": "Viet Nam [GAZ:00003756]", + "description": "The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia.", "meaning": "GAZ:00003756" }, "Virgin Islands [GAZ:00003959]": { "text": "Virgin Islands [GAZ:00003959]", + "description": "A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts.", "meaning": "GAZ:00003959" }, "Wake Island [GAZ:00007111]": { "text": "Wake Island [GAZ:00007111]", + "description": "A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east).", "meaning": "GAZ:00007111" }, "Wallis and Futuna [GAZ:00007191]": { "text": "Wallis and Futuna [GAZ:00007191]", + "description": "A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets.", "meaning": "GAZ:00007191" }, "West Bank [GAZ:00009572]": { "text": "West Bank [GAZ:00009572]", + "description": "A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian \"islands\" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is \"pipelined\".", "meaning": "GAZ:00009572" }, "Western Sahara [GAZ:00000564]": { "text": "Western Sahara [GAZ:00000564]", + "description": "A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions.", "meaning": "GAZ:00000564" }, "Yemen [GAZ:00005284]": { "text": "Yemen [GAZ:00005284]", + "description": "A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001).", "meaning": "GAZ:00005284" }, "Zambia [GAZ:00001107]": { "text": "Zambia [GAZ:00001107]", + "description": "A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts.", "meaning": "GAZ:00001107" }, "Zimbabwe [GAZ:00001106]": { "text": "Zimbabwe [GAZ:00001106]", + "description": "A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities.", "meaning": "GAZ:00001106" } } } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -7064,11 +9768,15 @@ ], "slot_uri": "GENEPIO:0001123", "identifier": true, + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", "comments": [ @@ -7087,17 +9795,20 @@ "BIOSAMPLE:host_subject_ID" ], "slot_uri": "GENEPIO:0001128", + "domain_of": [ + "Mpox" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", "comments": [ @@ -7113,10 +9824,14 @@ "NML_LIMS:PH_CASE_ID" ], "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", "comments": [ @@ -7132,6 +9847,10 @@ "NML_LIMS:SUBMISSIONS%20-%20BioProject%20Accession" ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -7139,8 +9858,8 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", "comments": [ @@ -7156,6 +9875,10 @@ "NML_LIMS:SUBMISSIONS%20-%20BioSample%20Accession" ], "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -7163,56 +9886,68 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", "comments": [ - "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR." + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." ], "examples": [ { - "value": "SRR11177792" + "value": "SRR123456, ERR123456, DRR123456, CRR123456" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:SUBMISSIONS%20-%20SRA%20Accession" + "CNPHI:SRA%20Accession", + "NML_LIMS:PH_SRA_ACCESSION" + ], + "slot_uri": "GENEPIO:0101203", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001142", "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", - "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank accession", + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", "comments": [ - "Store the accession returned from a GenBank submission (viral genome assembly)." + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." ], "examples": [ { - "value": "MN908947.3" + "value": "LZ986655.1" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:SUBMISSIONS%20-%20GenBank%20Accession" + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" + ], + "slot_uri": "GENEPIO:0101204", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001145", "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "description": "Identifier of the specific isolate.", "title": "GISAID virus name", "comments": [ @@ -7229,10 +9964,13 @@ "BIOSAMPLE:GISAID_virus_name" ], "slot_uri": "GENEPIO:0100282", + "domain_of": [ + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "comments": [ @@ -7251,6 +9989,10 @@ "VirusSeq_Portal:GISAID%20accession" ], "slot_uri": "GENEPIO:0001147", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -7258,8 +10000,8 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", "comments": [ @@ -7272,10 +10014,14 @@ ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "comments": [ @@ -7291,11 +10037,15 @@ "NML_LIMS:sample%20collector%20contact%20email" ], "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "comments": [ @@ -7312,119 +10062,14 @@ "NML_LIMS:sample%20collector%20contact%20address" ], "slot_uri": "GENEPIO:0001158", - "range": "WhitespaceMinimizedString" - }, - "sequenced by": { - "name": "sequenced by", - "description": "The name of the agency that generated the sequence.", - "title": "sequenced by", - "comments": [ - "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." - ], - "examples": [ - { - "value": "Public Health Ontario (PHO)" - } - ], - "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0100416", - "required": true - }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced by contact email", - "comments": [ - "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" - ], - "examples": [ - { - "value": "RespLab@lab.ca" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:sequenced%20by%20contact%20email" - ], - "slot_uri": "GENEPIO:0100422", - "range": "WhitespaceMinimizedString" - }, - "sequenced by contact address": { - "name": "sequenced by contact address", - "description": "The mailing address of the agency submitting the sequence.", - "title": "sequenced by contact address", - "comments": [ - "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" - ], - "examples": [ - { - "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:sequenced%20by%20contact%20address" - ], - "slot_uri": "GENEPIO:0100423", - "range": "WhitespaceMinimizedString" - }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "The name of the agency that submitted the sequence to a database.", - "title": "sequence submitted by", - "comments": [ - "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." - ], - "examples": [ - { - "value": "Public Health Ontario (PHO)" - } - ], - "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001159", - "required": true - }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "description": "The email address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact email", - "comments": [ - "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "examples": [ - { - "value": "RespLab@lab.ca" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:sequence%20submitter%20contact%20email" - ], - "slot_uri": "GENEPIO:0001165", - "range": "WhitespaceMinimizedString" - }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "description": "The mailing address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact address", - "comments": [ - "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" - ], - "examples": [ - { - "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Address", - "NML_LIMS:sequence%20submitter%20contact%20address" - ], - "slot_uri": "GENEPIO:0001167", "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", "todos": [ @@ -7448,18 +10093,22 @@ "VirusSeq_Portal:sample%20collection%20date" ], "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", "comments": [ @@ -7476,18 +10125,21 @@ "NML_LIMS:HC_TEXT2" ], "slot_uri": "GENEPIO:0001177", + "domain_of": [ + "Mpox" + ], "required": true, "any_of": [ { - "range": "sample collection date precision menu" + "range": "SampleCollectionDatePrecisionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", "todos": [ @@ -7507,17 +10159,21 @@ "NML_LIMS:sample%20received%20date" ], "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", "comments": [ @@ -7532,10 +10188,14 @@ "VirusSeq_Portal:geo_loc_name%20%28country%29" ], "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The state/province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", "examples": [ @@ -7551,10 +10211,14 @@ "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" ], "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", "comments": [ @@ -7570,10 +10234,13 @@ "BIOSAMPLE:lat_lon" ], "slot_uri": "GENEPIO:0100309", + "domain_of": [ + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", "comments": [ @@ -7589,6 +10256,9 @@ "BIOSAMPLE:lat_lon" ], "slot_uri": "GENEPIO:0100310", + "domain_of": [ + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, "organism": { @@ -7603,6 +10273,10 @@ "VirusSeq_Portal:organism" ], "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true }, "isolate": { @@ -7610,18 +10284,22 @@ "description": "Identifier of the specific isolate.", "title": "isolate", "from_schema": "https://example.com/mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", "comments": [ @@ -7635,10 +10313,14 @@ "VirusSeq_Portal:purpose%20of%20sampling" ], "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "comments": [ @@ -7657,18 +10339,22 @@ "VirusSeq_Portal:purpose%20of%20sampling%20details" ], "slot_uri": "GENEPIO:0001200", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", "comments": [ @@ -7685,11 +10371,14 @@ "NML_LIMS:PH_SPECIMEN_TYPE" ], "slot_uri": "GENEPIO:0001204", - "range": "NML submitted specimen type menu", + "domain_of": [ + "Mpox" + ], + "range": "NmlSubmittedSpecimenTypeMenu", "required": true }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", "title": "Related specimen relationship type", "comments": [ @@ -7707,17 +10396,20 @@ "NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE" ], "slot_uri": "GENEPIO:0001209", + "domain_of": [ + "Mpox" + ], "any_of": [ { - "range": "Related specimen relationship type menu" + "range": "RelatedSpecimenRelationshipTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", "comments": [ @@ -7733,10 +10425,14 @@ "VirusSeq_Portal:anatomical%20material" ], "slot_uri": "GENEPIO:0001211", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", "comments": [ @@ -7752,10 +10448,14 @@ "VirusSeq_Portal:anatomical%20part" ], "slot_uri": "GENEPIO:0001214", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", "comments": [ @@ -7771,10 +10471,14 @@ "VirusSeq_Portal:body%20product" ], "slot_uri": "GENEPIO:0001216", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", "comments": [ @@ -7792,19 +10496,22 @@ "BIOSAMPLE:environmental_material" ], "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "domain_of": [ + "MpoxInternational" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "environmental material international menu" + "range": "EnvironmentalMaterialInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", "comments": [ @@ -7820,10 +10527,14 @@ "VirusSeq_Portal:collection%20device" ], "slot_uri": "GENEPIO:0001234", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", "comments": [ @@ -7839,10 +10550,14 @@ "VirusSeq_Portal:collection%20method" ], "slot_uri": "GENEPIO:0001241", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -7850,10 +10565,14 @@ ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001253", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -7869,72 +10588,218 @@ "NML_LIMS:specimen%20processing%20details" ], "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "host (common name)": { - "name": "host (common name)", - "description": "The commonly used name of the host.", - "title": "host (common name)", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental specimen role type", "comments": [ - "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human." + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100921", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "multivalued": true + }, + "experimental_control_details": { + "name": "experimental_control_details", + "description": "The details regarding the experimental control contained in the sample.", + "title": "experimental control details", + "comments": [ + "Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor." ], "examples": [ { - "value": "Human" + "value": "Human coronavirus 229E (HCoV-229E) spiked in sample as process control" } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001386" + "slot_uri": "GENEPIO:0100922", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "lineage/clade name": { + "name": "lineage/clade name", + "description": "The name of the lineage or clade.", + "title": "lineage/clade name", "comments": [ - "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + "Provide the lineage/clade name." + ], + "examples": [ + { + "value": "B.1.1.7" + } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Host", - "NML_LIMS:host%20%28scientific%20name%29", - "BIOSAMPLE:host", - "VirusSeq_Portal:host%20%28scientific%20name%29" + "NML_LIMS:PH_LINEAGE_CLADE_NAME" ], - "slot_uri": "GENEPIO:0001387", - "required": true - }, - "host health state": { - "name": "host health state", - "description": "Health status of the host at the time of sample collection.", - "title": "host health state", - "comments": [ - "If known, select a value from the pick list." + "slot_uri": "GENEPIO:0001500", + "domain_of": [ + "MpoxInternational" ], - "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001388" + "any_of": [ + { + "range": "LineageCladeNameINternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health status details": { - "name": "host health status details", - "description": "Further details pertaining to the health or disease status of the host at time of collection.", - "title": "host health status details", + "lineage/clade analysis software name": { + "name": "lineage/clade analysis software name", + "description": "The name of the software used to determine the lineage/clade.", + "title": "lineage/clade analysis software name", "comments": [ - "If known, select a descriptor from the pick list provided in the template." + "Provide the name of the software used to determine the lineage/clade." + ], + "examples": [ + { + "value": "Pangolin" + } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001389" - }, - "host health outcome": { - "name": "host health outcome", + "exact_mappings": [ + "NML_LIMS:PH_LINEAGE_CLADE_SOFTWARE" + ], + "slot_uri": "GENEPIO:0001501", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "lineage/clade analysis software version": { + "name": "lineage/clade analysis software version", + "description": "The version of the software used to determine the lineage/clade.", + "title": "lineage/clade analysis software version", + "comments": [ + "Provide the version of the software used ot determine the lineage/clade." + ], + "examples": [ + { + "value": "2.1.10" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_LINEAGE_CLADE_VERSION" + ], + "slot_uri": "GENEPIO:0001502", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human." + ], + "examples": [ + { + "value": "Human" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host%20%28scientific%20name%29", + "BIOSAMPLE:host", + "VirusSeq_Portal:host%20%28scientific%20name%29" + ], + "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "required": true + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host health state", + "comments": [ + "If known, select a value from the pick list." + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001388", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host health status details", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", "comments": [ "If known, select a value from the pick list." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001389" + "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", "from_schema": "https://example.com/mpox", @@ -7945,10 +10810,14 @@ "VirusSeq_Portal:host%20disease" ], "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "required": true }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to.", "title": "host subject ID", "comments": [ @@ -7964,10 +10833,13 @@ "BIOSAMPLE:host_subject_id" ], "slot_uri": "GENEPIO:0001398", + "domain_of": [ + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", "comments": [ @@ -7980,39 +10852,51 @@ ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001392", - "minimum_value": "0", - "maximum_value": "130", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "minimum_value": 0, + "maximum_value": 130, "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The units used to measure the host's age.", "title": "host age unit", "comments": [ "If known, provide the age units used to measure the host's age from the pick list." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001393" + "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "The age category of the host at the time of sampling.", "title": "host age bin", "comments": [ "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001394" + "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", "comments": [ @@ -8020,24 +10904,32 @@ ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001395", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "structured_pattern": { "syntax": "{Title_Case}", "interpolated": true, "partial_match": false } }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "description": "The country of residence of the host.", "title": "host residence geo_loc name (country)", "comments": [ "Select the country name from pick list provided in the template." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001396" + "slot_uri": "GENEPIO:0001396", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", "description": "The state/province/territory of residence of the host.", "title": "host residence geo_loc name (state/province/territory)", "comments": [ @@ -8053,17 +10945,20 @@ "NML_LIMS:PH_HOST_PROVINCE" ], "slot_uri": "GENEPIO:0001397", + "domain_of": [ + "Mpox" + ], "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "GeoLocNameStateProvinceTerritoryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", "todos": [ @@ -8083,17 +10978,21 @@ "NML_LIMS:HC_ONSET_DATE" ], "slot_uri": "GENEPIO:0001399", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", "title": "signs and symptoms", "comments": [ @@ -8101,10 +11000,14 @@ ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001400", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", "title": "pre-existing conditions and risk factors", "comments": [ @@ -8115,6 +11018,10 @@ "NML_LIMS:pre-existing%20conditions%20and%20risk%20factors" ], "slot_uri": "GENEPIO:0001401", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, "complications": { @@ -8126,10 +11033,14 @@ ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001402", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "antiviral therapy": { - "name": "antiviral therapy", + "antiviral_therapy": { + "name": "antiviral_therapy", "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", "title": "antiviral therapy", "comments": [ @@ -8148,10 +11059,14 @@ "NML_LIMS:antiviral%20therapy" ], "slot_uri": "GENEPIO:0100580", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", "comments": [ @@ -8161,10 +11076,14 @@ "exact_mappings": [ "NML_LIMS:PH_VACCINATION_HISTORY" ], - "slot_uri": "GENEPIO:0001404" + "slot_uri": "GENEPIO:0001404", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "description": "The number of doses of the vaccine recived by the host.", "title": "number of vaccine doses received", "comments": [ @@ -8180,10 +11099,14 @@ "NML_LIMS:number%20of%20vaccine%20doses%20received" ], "slot_uri": "GENEPIO:0001406", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "integer" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", "title": "vaccination dose 1 vaccine name", "comments": [ @@ -8199,17 +11122,21 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100313", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", "todos": [ @@ -8229,17 +11156,21 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100314", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", "comments": [ @@ -8258,20 +11189,28 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100321", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "description": "The country where the host was likely exposed to the causative agent of the illness.", "title": "location of exposure geo_loc name (country)", "comments": [ "Select the country name from the pick list provided in the template." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001410" + "slot_uri": "GENEPIO:0001410", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "description": "The name of the city that was the destination of most recent travel.", "title": "destination of most recent travel (city)", "comments": [ @@ -8287,27 +11226,39 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001411", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "description": "The name of the state/province/territory that was the destination of most recent travel.", "title": "destination of most recent travel (state/province/territory)", "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001412" + "slot_uri": "GENEPIO:0001412", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "description": "The name of the country that was the destination of most recent travel.", "title": "destination of most recent travel (country)", "comments": [ "Select the country name from the pick list provided in the template." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001413" + "slot_uri": "GENEPIO:0001413", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", "title": "most recent travel departure date", "comments": [ @@ -8323,17 +11274,21 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001414", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", "title": "most recent travel return date", "comments": [ @@ -8349,17 +11304,21 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001415", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "description": "Travel history in last six months.", "title": "travel history", "comments": [ @@ -8381,10 +11340,14 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001416", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", "comments": [ @@ -8396,10 +11359,14 @@ "CNPHI:Exposure%20Event", "NML_LIMS:PH_EXPOSURE" ], - "slot_uri": "GENEPIO:0001417" + "slot_uri": "GENEPIO:0001417", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", "comments": [ @@ -8409,10 +11376,14 @@ "exact_mappings": [ "NML_LIMS:exposure%20contact%20level" ], - "slot_uri": "GENEPIO:0001418" + "slot_uri": "GENEPIO:0001418", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", "comments": [ @@ -8423,10 +11394,14 @@ "NML_LIMS:PH_HOST_ROLE" ], "slot_uri": "GENEPIO:0001419", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", "comments": [ @@ -8437,10 +11412,14 @@ "NML_LIMS:PH_EXPOSURE" ], "slot_uri": "GENEPIO:0001428", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", "comments": [ @@ -8456,20 +11435,28 @@ "NML_LIMS:PH_EXPOSURE_DETAILS" ], "slot_uri": "GENEPIO:0001431", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "prior Mpox infection": { - "name": "prior Mpox infection", + "prior_mpox_infection": { + "name": "prior_mpox_infection", "description": "The absence or presence of a prior Mpox infection.", "title": "prior Mpox infection", "comments": [ "If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0100532" + "slot_uri": "GENEPIO:0100532", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "prior Mpox infection date": { - "name": "prior Mpox infection date", + "prior_mpox_infection_date": { + "name": "prior_mpox_infection_date", "description": "The date of diagnosis of the prior Mpox infection.", "title": "prior Mpox infection date", "comments": [ @@ -8485,27 +11472,35 @@ "NML_LIMS:prior%20Monkeypox%20infection%20date" ], "slot_uri": "GENEPIO:0100533", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior Mpox antiviral treatment": { - "name": "prior Mpox antiviral treatment", + "prior_mpox_antiviral_treatment": { + "name": "prior_mpox_antiviral_treatment", "description": "The absence or presence of antiviral treatment for a prior Mpox infection.", "title": "prior Mpox antiviral treatment", "comments": [ "If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list." ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0100534" + "slot_uri": "GENEPIO:0100534", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] }, - "prior antiviral treatment during prior Mpox infection": { - "name": "prior antiviral treatment during prior Mpox infection", + "prior_antiviral_treatment_during_prior_mpox_infection": { + "name": "prior_antiviral_treatment_during_prior_mpox_infection", "description": "Antiviral treatment for any infection during the prior Mpox infection period.", "title": "prior antiviral treatment during prior Mpox infection", "comments": [ @@ -8521,4775 +11516,9826 @@ "NML_LIMS:prior%20antiviral%20treatment%20during%20Monkeypox%20infection" ], "slot_uri": "GENEPIO:0100535", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "purpose of sequencing": { - "name": "purpose of sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose of sequencing", + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing project name", "comments": [ - "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "MPOX-1356" + } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Sampling%20Strategy", - "CNPHI:Reason%20for%20Sequencing", - "NML_LIMS:PH_REASON_FOR_SEQUENCING", - "BIOSAMPLE:purpose_of_sequencing", - "VirusSeq_Portal:purpose%20of%20sequencing" + "slot_uri": "GENEPIO:0100472", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency that generated the sequence.", + "title": "sequenced by", + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001445", - "multivalued": true, "required": true }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "description": "The description of why the sample was sequenced providing specific details.", - "title": "purpose of sequencing details", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", "comments": [ - "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual." + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "Outbreak in MSM community" + "value": "Topp Lab" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", - "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", - "VirusSeq_Portal:purpose%20of%20sequencing%20details" + "slot_uri": "GENEPIO:0100470", + "domain_of": [ + "Mpox" ], - "slot_uri": "GENEPIO:0001446", - "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", - "description": "The date the sample was sequenced.", - "title": "sequencing date", - "todos": [ - ">={sample collection date}" - ], + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact name", "comments": [ - "ISO 8601 standard \"YYYY-MM-DD\"." + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." ], "examples": [ { - "value": "2020-06-22" + "value": "Joe Bloggs, Enterics Lab Manager" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_SEQUENCING_DATE" + "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001447", + "required": true, "any_of": [ { - "range": "date" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "library ID": { - "name": "library ID", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library ID", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact email", "comments": [ - "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" ], "examples": [ { - "value": "XYZ_123345" + "value": "RespLab@lab.ca" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:library%20ID" + "NML_LIMS:sequenced%20by%20contact%20email" ], - "slot_uri": "GENEPIO:0001448", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_uri": "GENEPIO:0100422", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "amplicon size": { - "name": "amplicon size", - "description": "The length of the amplicon generated by PCR amplification.", - "title": "amplicon size", + "sequenced_by_contact_address": { + "name": "sequenced_by_contact_address", + "description": "The mailing address of the agency submitting the sequence.", + "title": "sequenced by contact address", "comments": [ - "Provide the amplicon size, including the units." + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" ], "examples": [ { - "value": "300bp" + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:amplicon%20size" + "NML_LIMS:sequenced%20by%20contact%20address" + ], + "slot_uri": "GENEPIO:0100423", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001449", "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "title": "library preparation kit", + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence submitted by", "comments": [ - "Provide the name of the library preparation kit used." + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." ], "examples": [ { - "value": "Nextera XT" + "value": "Public Health Ontario (PHO)" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_LIBRARY_PREP_KIT" - ], - "slot_uri": "GENEPIO:0001450", - "range": "WhitespaceMinimizedString" - }, - "sequencing instrument": { - "name": "sequencing instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing instrument", - "comments": [ - "Select a sequencing instrument from the picklist provided in the template." - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Sequencing%20technology", - "CNPHI:Sequencing%20Instrument", - "NML_LIMS:PH_SEQUENCING_INSTRUMENT", - "VirusSeq_Portal:sequencing%20instrument" + "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001452", - "multivalued": true, "required": true }, - "sequencing protocol": { - "name": "sequencing protocol", - "description": "The protocol used to generate the sequence.", - "title": "sequencing protocol", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the agency responsible for submission of the sequence.", + "title": "sequence submitter contact email", "comments": [ - "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" ], "examples": [ { - "value": "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + "value": "RespLab@lab.ca" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_TESTING_PROTOCOL", - "VirusSeq_Portal:sequencing%20protocol" + "NML_LIMS:sequence%20submitter%20contact%20email" + ], + "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001454", "range": "WhitespaceMinimizedString" }, - "sequencing kit number": { - "name": "sequencing kit number", - "description": "The manufacturer's kit number.", - "title": "sequencing kit number", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", + "description": "The mailing address of the agency responsible for submission of the sequence.", + "title": "sequence submitter contact address", "comments": [ - "Alphanumeric value." + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" ], "examples": [ { - "value": "AB456XYZ789" + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:sequencing%20kit%20number" + "GISAID:Address", + "NML_LIMS:sequence%20submitter%20contact%20address" + ], + "slot_uri": "GENEPIO:0001167", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001455", "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "title": "amplicon pcr primer scheme", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "The reason that the sample was sequenced.", + "title": "purpose of sequencing", "comments": [ - "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." - ], - "examples": [ - { - "value": "MPXV Sunrise 3.1" - } + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:amplicon%20pcr%20primer%20scheme" - ], - "slot_uri": "GENEPIO:0001456", - "range": "WhitespaceMinimizedString" + "GISAID:Sampling%20Strategy", + "CNPHI:Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING", + "BIOSAMPLE:purpose_of_sequencing", + "VirusSeq_Portal:purpose%20of%20sequencing" + ], + "slot_uri": "GENEPIO:0001445", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "required": true, + "multivalued": true }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "title": "raw sequence data processing method", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose of sequencing details", "comments": [ - "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual." ], "examples": [ { - "value": "Porechop 0.2.3" + "value": "Outbreak in MSM community" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_RAW_SEQUENCE_METHOD", - "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", + "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], - "slot_uri": "GENEPIO:0001458", - "range": "WhitespaceMinimizedString" + "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "dehosting method": { - "name": "dehosting method", - "description": "The method used to remove host reads from the pathogen sequence.", - "title": "dehosting method", + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], "comments": [ - "Provide the name and version number of the software used to remove host reads." + "ISO 8601 standard \"YYYY-MM-DD\"." ], "examples": [ { - "value": "Nanostripper" + "value": "2020-06-22" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_DEHOSTING_METHOD", - "VirusSeq_Portal:dehosting%20method" + "NML_LIMS:PH_SEQUENCING_DATE" ], - "slot_uri": "GENEPIO:0001459", - "range": "WhitespaceMinimizedString" + "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "The name of the consensus sequence.", - "title": "consensus sequence name", + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", "comments": [ - "Provide the name and version number of the consensus sequence." + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." ], "examples": [ { - "value": "mpxvassembly3" + "value": "XYZ_123345" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:consensus%20sequence%20name" + "NML_LIMS:library%20ID" ], - "slot_uri": "GENEPIO:0001460", - "range": "WhitespaceMinimizedString" + "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "recommended": true }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "The name of the consensus sequence file.", - "title": "consensus sequence filename", + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library preparation kit", "comments": [ - "Provide the name and version number of the consensus sequence FASTA file." + "Provide the name of the library preparation kit used." ], "examples": [ { - "value": "mpxvassembly.fasta" + "value": "Nextera XT" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:consensus%20sequence%20filename" + "NML_LIMS:PH_LIBRARY_PREP_KIT" + ], + "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001461", "range": "WhitespaceMinimizedString" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "The filepath of the consensus sequence file.", - "title": "consensus sequence filepath", + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing assay type", "comments": [ - "Provide the filepath of the consensus sequence FASTA file." + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." ], - "examples": [ - { - "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" - } + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100997", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:consensus%20sequence%20filepath" + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", + "NML_LIMS:PH_SEQUENCING_INSTRUMENT", + "VirusSeq_Portal:sequencing%20instrument" ], - "slot_uri": "GENEPIO:0001462", - "range": "WhitespaceMinimizedString" + "slot_uri": "GENEPIO:0001452", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "required": true, + "multivalued": true }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "The name of software used to generate the consensus sequence.", - "title": "consensus sequence software name", + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing flow cell version", "comments": [ - "Provide the name of the software used to generate the consensus sequence." + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." ], "examples": [ { - "value": "iVar" + "value": "R.9.4.1" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Assembly%20method", - "CNPHI:consensus%20sequence", - "NML_LIMS:PH_CONSENSUS_SEQUENCE", - "VirusSeq_Portal:consensus%20sequence%20software%20name" + "slot_uri": "GENEPIO:0101102", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001463", - "range": "WhitespaceMinimizedString", - "required": true + "range": "WhitespaceMinimizedString" }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "The version of the software used to generate the consensus sequence.", - "title": "consensus sequence software version", + "sequencing_protocol__": { + "name": "sequencing_protocol__", + "description": "The protocol used to generate the sequence.", + "title": "sequencing protocol", "comments": [ - "Provide the version of the software used to generate the consensus sequence." + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" ], "examples": [ { - "value": "1.3" + "value": "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Assembly%20method", - "CNPHI:consensus%20sequence", - "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", - "VirusSeq_Portal:consensus%20sequence%20software%20version" + "NML_LIMS:PH_TESTING_PROTOCOL", + "VirusSeq_Portal:sequencing%20protocol" ], - "slot_uri": "GENEPIO:0001469", - "range": "WhitespaceMinimizedString", - "required": true + "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth of coverage value", + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "description": "The manufacturer's kit number.", + "title": "sequencing kit number", "comments": [ - "Provide value as a percent." + "Alphanumeric value." ], "examples": [ { - "value": "95%" + "value": "AB456XYZ789" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:breadth%20of%20coverage%20value", - "VirusSeq_Portal:breadth%20of%20coverage%20value" + "NML_LIMS:sequencing%20kit%20number" + ], + "slot_uri": "GENEPIO:0001455", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001472", "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA fragment length", "comments": [ - "Provide value as a fold of coverage." + "Provide the fragment length in base pairs (do not include the units)." ], "examples": [ { - "value": "400x" + "value": "400" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Depth%20of%20coverage", - "NML_LIMS:depth%20of%20coverage%20value", - "VirusSeq_Portal:depth%20of%20coverage%20value" + "slot_uri": "GENEPIO:0100843", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001474", "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth of coverage threshold", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method", "comments": [ - "Provide the threshold fold coverage." + "Provide the name of the enrichment method" ], "examples": [ { - "value": "100x" + "value": "hybrid selection method" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:depth%20of%20coverage%20threshold" + "slot_uri": "GENEPIO:0100966", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001475", - "range": "WhitespaceMinimizedString" + "recommended": true, + "multivalued": true }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1 fastq filename", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method details", "comments": [ - "Provide the r1 FASTQ filename. This information aids in data management." + "Provide details that are applicable to the method you used." ], "examples": [ { - "value": "ABC123_S1_L001_R1_001.fastq.gz" + "value": "enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit." } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001476", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_uri": "GENEPIO:0100967", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2 fastq filename", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", "comments": [ - "Provide the r2 FASTQ filename. This information aids in data management." + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." ], "examples": [ { - "value": "ABC123_S1_L001_R2_001.fastq.gz" + "value": "MPXV Sunrise 3.1" } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001477", - "range": "WhitespaceMinimizedString", - "recommended": true + "exact_mappings": [ + "NML_LIMS:amplicon%20pcr%20primer%20scheme" + ], + "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "The location of the r1 FASTQ file within a user's file system.", - "title": "r1 fastq filepath", + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", "comments": [ - "Provide the filepath for the r1 FASTQ file. This information aids in data management." + "Provide the amplicon size expressed in base pairs." ], "examples": [ { - "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" + "value": "300bp" } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001478", - "range": "WhitespaceMinimizedString" + "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "integer" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "The location of the r2 FASTQ file within a user's file system.", - "title": "r2 fastq filepath", + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", "comments": [ - "Provide the filepath for the r2 FASTQ file. This information aids in data management." + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." ], "examples": [ { - "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" + "value": "ncov-tools" } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001479", + "slot_uri": "GENEPIO:0100557", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "fast5 filename": { - "name": "fast5 filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5 filename", + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", "comments": [ - "Provide the FAST5 filename. This information aids in data management." + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." ], "examples": [ { - "value": "mpxv123seq.fast5" + "value": "1.2.3" } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001480", + "slot_uri": "GENEPIO:0100558", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "The location of the FAST5 file within a user's file system.", - "title": "fast5 filepath", + "quality_control_determination": { + "name": "quality_control_determination", + "title": "quality control determination", + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100559", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "title": "quality control issues", + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100560", + "domain_of": [ + "Mpox", + "MpoxInternational" + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", "comments": [ - "Provide the filepath for the FAST5 file. This information aids in data management." + "Provide notes or details regarding QC results using free text." ], "examples": [ { - "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." } ], "from_schema": "https://example.com/mpox", - "slot_uri": "GENEPIO:0001481", + "slot_uri": "GENEPIO:0100561", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "The number of total base pairs generated by the sequencing process.", - "title": "number of base pairs sequenced", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" ], "examples": [ { - "value": "2639019" + "value": "Porechop 0.2.3" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:number%20of%20base%20pairs%20sequenced" + "NML_LIMS:PH_RAW_SEQUENCE_METHOD", + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" ], - "slot_uri": "GENEPIO:0001482", - "range": "integer", - "minimum_value": "0" + "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Size of the reconstructed genome described as the number of base pairs.", - "title": "consensus genome length", + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the name and version number of the software used to remove host reads." ], "examples": [ { - "value": "197063" + "value": "Nanostripper" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:consensus%20genome%20length" - ], - "slot_uri": "GENEPIO:0001483", - "range": "integer", - "minimum_value": "0" + "NML_LIMS:PH_DEHOSTING_METHOD", + "VirusSeq_Portal:dehosting%20method" + ], + "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "reference genome accession": { - "name": "reference genome accession", - "description": "A persistent, unique identifier of a genome database entry.", - "title": "reference genome accession", + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", "comments": [ - "Provide the accession number of the reference genome." + "Provide the deduplication software name followed by the version, or a link to a tool or method." ], "examples": [ { - "value": "NC_063383.1" + "value": "DeDup 0.12.8" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:reference%20genome%20accession" + "slot_uri": "GENEPIO:0100831", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001485", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "A description of the overall bioinformatics strategy used.", - "title": "bioinformatics protocol", + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "description": "The name of the consensus sequence.", + "title": "consensus sequence name", "comments": [ - "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + "Provide the name and version number of the consensus sequence." ], "examples": [ { - "value": "https://github.com/phac-nml/monkeypox-nf" + "value": "mpxvassembly3" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "CNPHI:Bioinformatics%20Protocol", - "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", - "VirusSeq_Portal:bioinformatics%20protocol" + "NML_LIMS:consensus%20sequence%20name" + ], + "slot_uri": "GENEPIO:0001460", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001489", "range": "WhitespaceMinimizedString" }, - "gene name 1": { - "name": "gene name 1", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 1", + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], "examples": [ { - "value": "MPX (orf B6R)" + "value": "mpxvassembly.fasta" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "CNPHI:Gene%20Target%201", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", - "BIOSAMPLE:gene_name_1", - "VirusSeq_Portal:gene%20name" + "NML_LIMS:consensus%20sequence%20filename" ], - "slot_uri": "GENEPIO:0001507" + "slot_uri": "GENEPIO:0101715", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 1", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", "comments": [ - "Provide the CT value of the sample from the diagnostic RT-PCR test." + "Provide the filepath of the genome sequence FASTA file." ], "examples": [ { - "value": "21" + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "CNPHI:Gene%20Target%201%20CT%20Value", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", - "BIOSAMPLE:diagnostic_PCR_CT_value_1", - "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" - ], - "slot_uri": "GENEPIO:0001509", - "any_of": [ - { - "range": "decimal" - }, - { - "range": "null value menu" - } - ] - }, - "gene name 2": { - "name": "gene name 2", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 2", - "examples": [ - { - "value": "OVP (orf 17L)" - } + "NML_LIMS:consensus%20sequence%20filepath" ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Gene%20Target%202", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", - "BIOSAMPLE:gene_name_2" + "slot_uri": "GENEPIO:0101716", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001510" + "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 2", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of software used to generate the consensus sequence.", + "title": "consensus sequence software name", "comments": [ - "Provide the CT value of the sample from the second diagnostic RT-PCR test." + "Provide the name of the software used to generate the consensus sequence." ], "examples": [ { - "value": "36" + "value": "iVar" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "CNPHI:Gene%20Target%202%20CT%20Value", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", - "BIOSAMPLE:diagnostic_PCR_CT_value_2" + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" ], - "slot_uri": "GENEPIO:0001512", - "any_of": [ - { - "range": "decimal" - }, - { - "range": "null value menu" - } - ] + "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "required": true }, - "gene name 3": { - "name": "gene name 3", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 3", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], "examples": [ { - "value": "OPHA (orf B2R)" + "value": "1.3" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "CNPHI:Gene%20Target%203", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233", - "BIOSAMPLE:gene_name_3" + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" ], - "slot_uri": "GENEPIO:0001513" + "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "required": true }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 3", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", "comments": [ - "Provide the CT value of the sample from the second diagnostic RT-PCR test." + "Provide the name of the software used to assemble the sequence." ], "examples": [ { - "value": "19" + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Gene%20Target%203%20CT%20Value", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value", - "BIOSAMPLE:diagnostic_PCR_CT_value_3" + "slot_uri": "GENEPIO:0100825", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001515", + "required": true, "any_of": [ { - "range": "decimal" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "gene name 4": { - "name": "gene name 4", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 4", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "Provide the version of the software used to assemble the sequence." ], "examples": [ { - "value": "G2R_G (TNFR)" + "value": "3.15.5" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Gene%20Target%204", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234", - "BIOSAMPLE:gene_name_4" + "slot_uri": "GENEPIO:0100826", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0100576", + "required": true, "any_of": [ { - "range": "gene name menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 4": { - "name": "diagnostic pcr Ct value 4", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 4", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", "comments": [ - "Provide the CT value of the sample from the second diagnostic RT-PCR test." + "Provide the r1 FASTQ filename. This information aids in data management." ], "examples": [ { - "value": "27" + "value": "ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Gene%20Target%204%20CT%20Value", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234%20CT%20Value", - "BIOSAMPLE:diagnostic_PCR_CT_value_4" + "slot_uri": "GENEPIO:0001476", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0100577", - "any_of": [ - { - "range": "decimal" - }, - { - "range": "null value menu" - } - ] + "range": "WhitespaceMinimizedString", + "recommended": true }, - "gene name 5": { - "name": "gene name 5", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 5", + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "Provide the r2 FASTQ filename. This information aids in data management." ], "examples": [ { - "value": "RNAse P" + "value": "ABC123_S1_L001_R2_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Gene%20Target%205", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235", - "BIOSAMPLE:gene_name_5" + "slot_uri": "GENEPIO:0001477", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0100578", - "any_of": [ - { - "range": "gene name menu" - }, - { - "range": "null value menu" - } - ] + "range": "WhitespaceMinimizedString", + "recommended": true }, - "diagnostic pcr Ct value 5": { - "name": "diagnostic pcr Ct value 5", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 5", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", "comments": [ - "Provide the CT value of the sample from the second diagnostic RT-PCR test." + "Provide the filepath for the r1 FASTQ file. This information aids in data management." ], "examples": [ { - "value": "30" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Gene%20Target%205%20CT%20Value", - "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235%20CT%20Value", - "BIOSAMPLE:diagnostic_PCR_CT_value_5" + "slot_uri": "GENEPIO:0001478", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0100579", - "any_of": [ - { - "range": "decimal" - }, + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", + "comments": [ + "Provide the filepath for the r2 FASTQ file. This information aids in data management." + ], + "examples": [ { - "range": "null value menu" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" } - ] + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001479", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", "comments": [ - "Include the first and last names of all individuals that should be attributed, separated by a comma." + "Provide the FAST5 filename. This information aids in data management." ], "examples": [ { - "value": "Tejinder Singh, Fei Hu, Joe Blogs" + "value": "mpxv123seq.fast5" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Authors", - "CNPHI:Authors", - "NML_LIMS:PH_SEQUENCING_AUTHORS" + "slot_uri": "GENEPIO:0001480", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001517", - "range": "WhitespaceMinimizedString", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", + "fast5_filepath": { + "name": "fast5_filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", "comments": [ - "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + "Provide the filepath for the FAST5 file. This information aids in data management." ], "examples": [ { - "value": "DataHarmonizer v1.4.3, Mpox v3.3.1" + "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "CNPHI:Additional%20Comments", - "NML_LIMS:HC_COMMENTS" + "slot_uri": "GENEPIO:0001481", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "slot_uri": "GENEPIO:0001518", - "range": "Provenance" - } - }, - "classes": { - "dh_interface": { - "name": "dh_interface", - "description": "A DataHarmonizer interface", - "from_schema": "https://example.com/mpox" + "range": "WhitespaceMinimizedString" }, - "Mpox": { - "name": "Mpox", - "annotations": { - "version": { - "tag": "version", - "value": "4.3.3" + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" } - }, - "description": "Canadian specification for Mpox clinical virus biosample data gathering", + ], "from_schema": "https://example.com/mpox", - "see_also": [ - "templates/mpox/SOP_Mpox.pdf" + "slot_uri": "GENEPIO:0100827", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "is_a": "dh_interface", - "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "rank": 1, - "slot_group": "Database Identifiers" + "range": "Integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100828", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100829", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400x" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Depth%20of%20coverage", + "NML_LIMS:depth%20of%20coverage%20value", + "VirusSeq_Portal:depth%20of%20coverage%20value" + ], + "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100x" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:depth%20of%20coverage%20threshold" + ], + "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2639019" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:number%20of%20base%20pairs%20sequenced" + ], + "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "integer", + "minimum_value": 0 + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "Size of the reconstructed genome described as the number of base pairs.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "197063" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:consensus%20genome%20length" + ], + "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "integer", + "minimum_value": 0 + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100846", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100937", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100844", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100938", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100830", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_063383.1" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:reference%20genome%20accession" + ], + "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/monkeypox-nf" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Bioinformatics%20Protocol", + "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", + "VirusSeq_Portal:bioinformatics%20protocol" + ], + "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100832", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100833", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100834", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100835", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "MPXV_report123.doc" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0101074", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0101075", + "domain_of": [ + "MpoxInternational" + ], + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0100836", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "assay_target_name_1": { + "name": "assay_target_name_1", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 1", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "examples": [ + { + "value": "MPX (orf B6R)" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0101206", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_details_1": { + "name": "assay_target_details_1", + "description": "Describe any details of the assay target.", + "title": "assay target details 1", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0102045", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "gene_name_1": { + "name": "gene_name_1", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 1", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "examples": [ + { + "value": "MPX (orf B6R)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", + "BIOSAMPLE:gene_name_1", + "VirusSeq_Portal:gene%20name" + ], + "slot_uri": "GENEPIO:0001507", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "gene_symbol_1": { + "name": "gene_symbol_1", + "description": "The gene symbol used in the diagnostic RT-PCR test.", + "title": "gene symbol 1", + "comments": [ + "Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name." + ], + "examples": [ + { + "value": "opg190 gene (MPOX)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", + "BIOSAMPLE:gene_name_1", + "VirusSeq_Portal:gene%20name" + ], + "slot_uri": "GENEPIO:0102041", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "GeneSymbolInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "title": "diagnostic pcr protocol 1", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "B6R (Li et al., 2006)" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001508", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 1", + "comments": [ + "Provide the CT value of the sample from the diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "21" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%201%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_1", + "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" + ], + "slot_uri": "GENEPIO:0001509", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_name_2": { + "name": "assay_target_name_2", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 2", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "examples": [ + { + "value": "OVP (orf 17L)" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0102038", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_details_2": { + "name": "assay_target_details_2", + "description": "Describe any details of the assay target.", + "title": "assay target details 2", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0102046", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "gene_name_2": { + "name": "gene_name_2", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 2", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "examples": [ + { + "value": "OVP (orf 17L)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", + "BIOSAMPLE:gene_name_2" + ], + "slot_uri": "GENEPIO:0001510", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "gene_symbol_2": { + "name": "gene_symbol_2", + "description": "The gene symbol used in the diagnostic RT-PCR test.", + "title": "gene symbol 2", + "comments": [ + "Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name." + ], + "examples": [ + { + "value": "opg002 gene (MPOX)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", + "BIOSAMPLE:gene_name_2" + ], + "slot_uri": "GENEPIO:0102042", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "GeneSymbolInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "title": "diagnostic pcr protocol 2", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G)." + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001511", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 2", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "36" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%202%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_2" + ], + "slot_uri": "GENEPIO:0001512", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_name_3": { + "name": "assay_target_name_3", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 3", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "examples": [ + { + "value": "OPHA (orf B2R)" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0102039", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_details_3": { + "name": "assay_target_details_3", + "description": "Describe any details of the assay target.", + "title": "assay target details 3", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0102047", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "gene_name_3": { + "name": "gene_name_3", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 3", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "examples": [ + { + "value": "OPHA (orf B2R)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233", + "BIOSAMPLE:gene_name_3" + ], + "slot_uri": "GENEPIO:0001513", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "gene_symbol_3": { + "name": "gene_symbol_3", + "description": "The gene symbol used in the diagnostic RT-PCR test.", + "title": "gene symbol 3", + "comments": [ + "Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name." + ], + "examples": [ + { + "value": "opg188 gene (MPOX)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233", + "BIOSAMPLE:gene_name_3" + ], + "slot_uri": "GENEPIO:0102043", + "domain_of": [ + "MpoxInternational" + ], + "any_of": [ + { + "range": "GeneSymbolInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "title": "diagnostic pcr protocol 3", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "G2R_G (Li et al., 2010) assay" + } + ], + "from_schema": "https://example.com/mpox", + "slot_uri": "GENEPIO:0001514", + "domain_of": [ + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 3", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "19" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%203%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_3" + ], + "slot_uri": "GENEPIO:0001515", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] + }, + "gene_name_4": { + "name": "gene_name_4", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 4", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "examples": [ + { + "value": "G2R_G (TNFR)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%204", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234", + "BIOSAMPLE:gene_name_4" + ], + "slot_uri": "GENEPIO:0100576", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_pcr_ct_value_4": { + "name": "diagnostic_pcr_ct_value_4", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 4", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "27" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%204%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_4" + ], + "slot_uri": "GENEPIO:0100577", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] + }, + "gene_name_5": { + "name": "gene_name_5", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 5", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "examples": [ + { + "value": "RNAse P" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%205", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235", + "BIOSAMPLE:gene_name_5" + ], + "slot_uri": "GENEPIO:0100578", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_pcr_ct_value_5": { + "name": "diagnostic_pcr_ct_value_5", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 5", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "30" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%205%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_5" + ], + "slot_uri": "GENEPIO:0100579", + "domain_of": [ + "Mpox" + ], + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] + }, + "authors": { + "name": "authors", + "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", + "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Authors", + "CNPHI:Authors", + "NML_LIMS:PH_SEQUENCING_AUTHORS" + ], + "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "The DataHarmonizer software and template version provenance.", + "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, Mpox v3.3.1" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Additional%20Comments", + "NML_LIMS:HC_COMMENTS" + ], + "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "range": "Provenance" + } + }, + "classes": { + "dh_interface": { + "name": "dh_interface", + "description": "A DataHarmonizer interface", + "from_schema": "https://example.com/mpox" + }, + "Mpox": { + "name": "Mpox", + "annotations": { + "version": { + "tag": "version", + "value": "6.5.5" + } + }, + "description": "Canadian specification for Mpox clinical virus biosample data gathering", + "from_schema": "https://example.com/mpox", + "see_also": [ + "templates/mpox/SOP_Mpox.pdf" + ], + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database Identifiers" + }, + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", + "rank": 2, + "slot_group": "Database Identifiers" + }, + "case_id": { + "name": "case_id", + "rank": 3, + "slot_group": "Database Identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 4, + "slot_group": "Database Identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 5, + "slot_group": "Database Identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "gisaid_accession": { + "name": "gisaid_accession", + "rank": 8, + "slot_group": "Database Identifiers" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "exact_mappings": [ + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", + "NML_LIMS:CUSTOMER", + "BIOSAMPLE:collected_by", + "VirusSeq_Portal:sample%20collected%20by" + ], + "rank": 9, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleCollectedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "sample_received_date": { + "name": "sample_received_date", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "examples": [ + { + "value": "Canada" + } + ], + "rank": 15, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." + ], + "rank": 16, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "organism": { + "name": "organism", + "comments": [ + "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." + ], + "examples": [ + { + "value": "Mpox virus" + } + ], + "rank": 17, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "OrganismMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "isolate": { + "name": "isolate", + "comments": [ + "Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put \"UN\" for \"Unknown\"." + ], + "examples": [ + { + "value": "hMpxV/Canada/UN-NML-12345/2022" + } + ], + "exact_mappings": [ + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Virus%20Name", + "BIOSAMPLE:isolate", + "BIOSAMPLE:GISAID_virus_name", + "VirusSeq_Portal:isolate", + "VirusSeq_Portal:fasta%20header%20name" + ], + "rank": 18, + "slot_uri": "GENEPIO:0001195", + "slot_group": "Sample collection and processing" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "examples": [ + { + "value": "Diagnostic testing" + } + ], + "rank": 19, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", + "rank": 20, + "slot_group": "Sample collection and processing" + }, + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", + "rank": 21, + "slot_group": "Sample collection and processing" + }, + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", + "rank": 22, + "slot_group": "Sample collection and processing" + }, + "anatomical_material": { + "name": "anatomical_material", + "examples": [ + { + "value": "Lesion (Pustule)" + } + ], + "rank": 23, + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "examples": [ + { + "value": "Genital area" + } + ], + "rank": 24, + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "body_product": { + "name": "body_product", + "examples": [ + { + "value": "Pus" + } + ], + "rank": 25, + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "examples": [ + { + "value": "Swab" + } + ], + "rank": 26, + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "examples": [ + { + "value": "Biopsy" + } + ], + "rank": 27, + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "examples": [ + { + "value": "Specimens pooled" + } + ], + "exact_mappings": [ + "NML_LIMS:specimen%20processing" + ], + "rank": 28, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 29, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "examples": [ + { + "value": "Positive experimental control" + } + ], + "rank": 30, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "ExperimentalSpecimenRoleTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "experimental_control_details": { + "name": "experimental_control_details", + "rank": 31, + "slot_group": "Sample collection and processing" + }, + "host_common_name": { + "name": "host_common_name", + "exact_mappings": [ + "NML_LIMS:PH_ANIMAL_TYPE" + ], + "rank": 32, + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostCommonNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "examples": [ + { + "value": "Homo sapiens" + } + ], + "rank": 33, + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "examples": [ + { + "value": "Asymptomatic" + } + ], + "exact_mappings": [ + "GISAID:Patient%20status", + "NML_LIMS:PH_HOST_HEALTH", + "BIOSAMPLE:host_health_state" + ], + "rank": 34, + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStateMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "examples": [ + { + "value": "Hospitalized" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_DETAILS" + ], + "rank": 35, + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStatusDetailsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "examples": [ + { + "value": "Recovered" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_OUTCOME", + "BIOSAMPLE:host_health_outcome" + ], + "rank": 36, + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthOutcomeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "comments": [ + "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + ], + "examples": [ + { + "value": "Mpox" + } + ], + "rank": 37, + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_age": { + "name": "host_age", + "exact_mappings": [ + "GISAID:Patient%20age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age" + ], + "rank": 38, + "slot_group": "Host Information", + "required": true + }, + "host_age_unit": { + "name": "host_age_unit", + "examples": [ + { + "value": "year" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_AGE_UNIT", + "BIOSAMPLE:host_age_unit" + ], + "rank": 39, + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostAgeUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "examples": [ + { + "value": "50 - 59" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_AGE_GROUP", + "BIOSAMPLE:host_age_bin" + ], + "rank": 40, + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_gender": { + "name": "host_gender", + "examples": [ + { + "value": "Male" + } + ], + "exact_mappings": [ + "GISAID:Gender", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex" + ], + "rank": 41, + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostGenderMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", + "examples": [ + { + "value": "Canada" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_HOST_COUNTRY" + ], + "rank": 42, + "slot_group": "Host Information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", + "rank": 43, + "slot_group": "Host Information" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "rank": 44, + "slot_group": "Host Information" + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "examples": [ + { + "value": "Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain)" + } + ], + "exact_mappings": [ + "NML_LIMS:HC_SYMPTOMS" + ], + "rank": 45, + "slot_group": "Host Information", + "any_of": [ + { + "range": "SignsAndSymptomsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "rank": 46, + "slot_group": "Host Information", + "any_of": [ + { + "range": "PreExistingConditionsAndRiskFactorsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "complications": { + "name": "complications", + "examples": [ + { + "value": "Delayed wound healing (lesion healing)" + } + ], + "exact_mappings": [ + "NML_LIMS:complications" + ], + "rank": 47, + "slot_group": "Host Information", + "any_of": [ + { + "range": "ComplicationsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "antiviral_therapy": { + "name": "antiviral_therapy", + "rank": 48, + "slot_group": "Host Information" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "examples": [ + { + "value": "Not Vaccinated" + } + ], + "rank": 49, + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "HostVaccinationStatusMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "rank": 50, + "slot_group": "Host vaccination information" + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "rank": 51, + "slot_group": "Host vaccination information" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "rank": 52, + "slot_group": "Host vaccination information" + }, + "vaccination_history": { + "name": "vaccination_history", + "rank": 53, + "slot_group": "Host vaccination information" + }, + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", + "examples": [ + { + "value": "Canada" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_COUNTRY" + ], + "rank": 54, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", + "rank": 55, + "slot_group": "Host exposure information" + }, + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", + "comments": [ + "Select the province name from the pick list provided in the template." + ], + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 56, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", + "examples": [ + { + "value": "Canada" + } + ], + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 57, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", + "rank": 58, + "slot_group": "Host exposure information" + }, + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", + "rank": 59, + "slot_group": "Host exposure information" + }, + "travel_history": { + "name": "travel_history", + "rank": 60, + "slot_group": "Host exposure information" + }, + "exposure_event": { + "name": "exposure_event", + "examples": [ + { + "value": "Party" + } + ], + "rank": 61, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureEventMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "examples": [ + { + "value": "Contact with infected individual" + } + ], + "rank": 62, + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureContactLevelMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_role": { + "name": "host_role", + "examples": [ + { + "value": "Acquaintance of case" + } + ], + "rank": 63, + "slot_group": "Host exposure information", + "range": "HostRoleMenu" + }, + "exposure_setting": { + "name": "exposure_setting", + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "rank": 64, + "slot_group": "Host exposure information", + "range": "ExposureSettingMenu" + }, + "exposure_details": { + "name": "exposure_details", + "rank": 65, + "slot_group": "Host exposure information" + }, + "prior_mpox_infection": { + "name": "prior_mpox_infection", + "examples": [ + { + "value": "Prior infection" + } + ], + "exact_mappings": [ + "NML_LIMS:prior%20Monkeypox%20infection" + ], + "rank": 66, + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorMonkeypoxInfectionMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "prior_mpox_infection_date": { + "name": "prior_mpox_infection_date", + "rank": 67, + "slot_group": "Host reinfection information" + }, + "prior_mpox_antiviral_treatment": { + "name": "prior_mpox_antiviral_treatment", + "examples": [ + { + "value": "Prior antiviral treatment" + } + ], + "exact_mappings": [ + "NML_LIMS:prior%20Monkeypox%20antiviral%20treatment" + ], + "rank": 68, + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorMonkeypoxAntiviralTreatmentMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "prior_antiviral_treatment_during_prior_mpox_infection": { + "name": "prior_antiviral_treatment_during_prior_mpox_infection", + "rank": 69, + "slot_group": "Host reinfection information" + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "rank": 70, + "slot_group": "Sequence information" + }, + "sequenced_by": { + "name": "sequenced_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by" + ], + "rank": 71, + "slot_group": "Sequencing", + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "rank": 72, + "slot_group": "Sequence information" + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "rank": 73, + "slot_group": "Sequencing" + }, + "sequenced_by_contact_address": { + "name": "sequenced_by_contact_address", + "rank": 74, + "slot_group": "Sequencing" + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", + "NML_LIMS:PH_SEQUENCE_SUBMITTER", + "BIOSAMPLE:sequence_submitted_by", + 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attributed to individuals self-identifying as “female”" + }, + { + "value": "Domestic travel surveillance", + "description": "For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options" + }, + { + "value": "International travel surveillance" + }, + { + "value": "Travel-associated surveillance" + }, + { + "value": "Cluster/Outbreak investigation", + "description": "For specimens targeted for sequencing as part of an outbreak investigation, please select" + }, + { + "value": "Baseline surveillance (random sampling).", + "description": "In all other cases use" + } + ], + "rank": 78, + "slot_group": "Sequencing", + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "rank": 79, + "slot_group": "Sequencing" + }, + "sequencing_date": { + "name": "sequencing_date", + "rank": 80, + "slot_group": "Sequencing", + "required": true + }, + "library_id": { + "name": "library_id", + "rank": 81, + "slot_group": "Sequencing" + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "rank": 82, + "slot_group": "Sequencing" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "examples": [ + { + "value": "whole genome sequencing assay" + } + ], + "rank": 83, + "slot_group": "Sequence information", + "range": "SequencingAssayTypeMenu" + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], + "rank": 84, + "slot_group": "Sequencing", + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "rank": 85, + "slot_group": "Sequence information" + }, + "sequencing_protocol__": { + "name": "sequencing_protocol__", + "rank": 86, + "slot_group": "Sequencing" + }, + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "rank": 87, + "slot_group": "Sequencing" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "rank": 88, + "slot_group": "Sequencing" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "rank": 89, + "slot_group": "Sequencing", + "any_of": [ + { + "range": "GenomicTargetEnrichmentMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "rank": 90, + "slot_group": "Sequencing" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "rank": 91, + "slot_group": "Sequencing" + }, + "amplicon_size": { + "name": "amplicon_size", + "rank": 92, + "slot_group": "Sequencing" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "rank": 93, + "slot_group": "Bioinformatics and QC 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If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "rank": 95, + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlDeterminationMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "rank": 96, + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlIssuesMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "rank": 97, + "slot_group": "Bioinformatics and QC metrics" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "rank": 98, + "slot_group": "Bioinformatics and QC metrics", + "required": true + }, + "dehosting_method": { + "name": "dehosting_method", + "rank": 99, + "slot_group": "Bioinformatics and QC metrics", + "required": true + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 100, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "rank": 101, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "rank": 102, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "rank": 103, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "rank": 104, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "rank": 105, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "rank": 106, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "rank": 107, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "rank": 108, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "rank": 109, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "rank": 110, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "rank": 111, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5_filename": { + "name": "fast5_filename", + "rank": 112, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5_filepath": { + "name": "fast5_filepath", + "rank": 113, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "rank": 114, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "rank": 115, + "slot_group": "Bioinformatics and QC metrics" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "rank": 116, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "rank": 117, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "rank": 118, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "rank": 119, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "rank": 120, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "rank": 121, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "rank": 122, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_completeness": { + "name": "genome_completeness", + "rank": 123, + "slot_group": "Bioinformatics and QC metrics" + }, + "n50": { + "name": "n50", + "rank": 124, + "slot_group": "Bioinformatics and QC metrics" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "rank": 125, + "slot_group": "Bioinformatics and QC metrics" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "rank": 126, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "rank": 127, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 128, + "slot_group": "Bioinformatics and QC metrics", + "required": true + }, + "gene_name_1": { + "name": "gene_name_1", + "rank": 129, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_pcr_ct_value_1": { + "name": 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"diagnostic_pcr_ct_value_5", + "rank": 138, + "slot_group": "Pathogen diagnostic testing" + }, + "authors": { + "name": "authors", + "rank": 139, + "slot_group": "Contributor acknowledgement" + }, + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "rank": 140, + "slot_group": "Contributor acknowledgement" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "prov_mpox_1234" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", + "NML_LIMS:TEXT_ID", + "BIOSAMPLE:sample_name", + "VirusSeq_Portal:specimen%20collector%20sample%20ID" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", + "description": "The primary ID of a related specimen previously submitted to the repository.", + "title": "Related specimen primary ID", + "comments": [ + "Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system." + ], + "examples": [ + { + "value": "SR20-12345" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_PRIMARY_ID", + "BIOSAMPLE:host_subject_ID" + ], + "rank": 2, + "slot_uri": "GENEPIO:0001128", + "alias": "related_specimen_primary_id", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], + "slot_group": "Database Identifiers", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_CASE_ID" + ], + "rank": 3, + "slot_uri": "GENEPIO:0100281", + "alias": "case_id", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "title": "bioproject accession", + "comments": [ + "Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects." + ], + "examples": [ + { + "value": "PRJNA12345" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS%20-%20BioProject%20Accession" + ], + "rank": 4, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "title": "biosample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS%20-%20BioSample%20Accession" + ], + "rank": 5, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "SRR123456, ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:SRA%20Accession", + "NML_LIMS:PH_SRA_ACCESSION" + ], + "rank": 6, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" + ], + "rank": 7, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "gisaid_accession": { + "name": "gisaid_accession", + "description": "The GISAID accession number assigned to the sequence.", + "title": "GISAID accession", + "comments": [ + "Store the accession returned from the GISAID submission." + ], + "examples": [ + { + "value": "EPI_ISL_436489" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession", + "BIOSAMPLE:GISAID_accession", + "VirusSeq_Portal:GISAID%20accession" + ], + "rank": 8, + "slot_uri": "GENEPIO:0001147", + "alias": "gisaid_accession", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the agency that collected the original sample.", + "title": "sample collected by", + "comments": [ + "The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)." + ], + "examples": [ + { + "value": "BC Centre for Disease Control" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", + "NML_LIMS:CUSTOMER", + "BIOSAMPLE:collected_by", + "VirusSeq_Portal:sample%20collected%20by" + ], + "rank": 9, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "SampleCollectedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:sample%20collector%20contact%20email" + ], + "rank": 10, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", + "description": "The mailing address of the agency submitting the sample.", + "title": "sample collector contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ + { + "value": "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Address", + "NML_LIMS:sample%20collector%20contact%20address" + ], + "rank": 11, + "slot_uri": "GENEPIO:0001158", + "alias": "sample_collector_contact_address", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected.", + "title": "sample collection date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add \"jitter\" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", + "NML_LIMS:HC_COLLECT_DATE", + "BIOSAMPLE:collection_date", + "VirusSeq_Portal:sample%20collection%20date" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", + "description": "The precision to which the \"sample collection date\" was provided.", + "title": "sample collection date precision", + "comments": [ + "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + ], + "examples": [ + { + "value": "year" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Precision%20of%20date%20collected", + "NML_LIMS:HC_TEXT2" + ], + "rank": 13, + "slot_uri": "GENEPIO:0001177", + "alias": "sample_collection_date_precision", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "SampleCollectionDatePrecisionMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:sample%20received%20date" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country where the sample was collected.", + "title": "geo_loc_name (country)", + "comments": [ + "Provide the country name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Location", + "CNPHI:Patient%20Country", + "NML_LIMS:HC_COUNTRY", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28country%29" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory where the sample was collected.", + "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Patient%20Province", + "NML_LIMS:HC_PROVINCE", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" + ], + "rank": 16, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." + ], + "examples": [ + { + "value": "Mpox virus" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Pathogen", + "NML_LIMS:HC_CURRENT_ID", + "BIOSAMPLE:organism", + "VirusSeq_Portal:organism" + ], + "rank": 17, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "OrganismMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "isolate": { + "name": "isolate", + "description": "Identifier of the specific isolate.", + "title": "isolate", + "comments": [ + "Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put \"UN\" for \"Unknown\"." + ], + "examples": [ + { + "value": "hMpxV/Canada/UN-NML-12345/2022" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Virus%20Name", + "BIOSAMPLE:isolate", + "BIOSAMPLE:GISAID_virus_name", + "VirusSeq_Portal:isolate", + "VirusSeq_Portal:fasta%20header%20name" + ], + "rank": 18, + "slot_uri": "GENEPIO:0001195", + "alias": "isolate", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose of sampling", + "comments": [ + "As all samples are taken for diagnostic purposes, \"Diagnostic Testing\" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Diagnostic testing" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sampling", + "NML_LIMS:HC_SAMPLE_CATEGORY", + "BIOSAMPLE:purpose_of_sampling", + "VirusSeq_Portal:purpose%20of%20sampling" + ], + "rank": 19, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", + "description": "The description of why the sample was collected, providing specific details.", + "title": "purpose of sampling details", + "comments": [ + "Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value." + ], + "examples": [ + { + "value": "Symptomology and history suggested Monkeypox diagnosis." + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", + "NML_LIMS:PH_SAMPLING_DETAILS", + "BIOSAMPLE:description", + "VirusSeq_Portal:purpose%20of%20sampling%20details" + ], + "rank": 20, + "slot_uri": "GENEPIO:0001200", + "alias": "purpose_of_sampling_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", + "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", + "title": "NML submitted specimen type", + "comments": [ + "This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”." + ], + "examples": [ + { + "value": "Nucleic Acid" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Specimen%20Type", + "NML_LIMS:PH_SPECIMEN_TYPE" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001204", + "alias": "nml_submitted_specimen_type", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], + "slot_group": "Sample collection and processing", + "range": "NmlSubmittedSpecimenTypeMenu", + "required": true + }, + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", + "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", + "title": "Related specimen relationship type", + "comments": [ + "Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system." + ], + "examples": [ + { + "value": "Previously Submitted" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE" + ], + "rank": 22, + "slot_uri": "GENEPIO:0001209", + "alias": "related_specimen_relationship_type", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "RelatedSpecimenRelationshipTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Lesion (Pustule)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", + "NML_LIMS:PH_ISOLATION_SITE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "VirusSeq_Portal:anatomical%20material" + ], + "rank": 23, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Genital area" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", + "NML_LIMS:PH_ISOLATION_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "VirusSeq_Portal:anatomical%20part" + ], + "rank": 24, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Pus" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", + "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "VirusSeq_Portal:body%20product" + ], + "rank": 25, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection device", + "comments": [ + "Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Swab" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", + "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "VirusSeq_Portal:collection%20device" + ], + "rank": 26, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", + "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Biopsy" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", + "NML_LIMS:COLLECTION_METHOD", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "VirusSeq_Portal:collection%20method" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen processing", + "comments": [ + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." + ], + "examples": [ + { + "value": "Specimens pooled" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:specimen%20processing" + ], + "rank": 28, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", + "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample." + ], + "examples": [ + { + "value": "5 swabs from different body sites were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:specimen%20processing%20details" + ], + "rank": 29, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental specimen role type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 30, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "ExperimentalSpecimenRoleTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "experimental_control_details": { + "name": "experimental_control_details", + "description": "The details regarding the experimental control contained in the sample.", + "title": "experimental control details", + "comments": [ + "Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor." + ], + "examples": [ + { + "value": "Human coronavirus 229E (HCoV-229E) spiked in sample as process control" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 31, + "slot_uri": "GENEPIO:0100922", + "alias": "experimental_control_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human." + ], + "examples": [ + { + "value": "Human" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_ANIMAL_TYPE" + ], + "rank": 32, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostCommonNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], + "examples": [ + { + "value": "Homo sapiens" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host%20%28scientific%20name%29", + "BIOSAMPLE:host", + "VirusSeq_Portal:host%20%28scientific%20name%29" + ], + "rank": 33, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host health state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Patient%20status", + "NML_LIMS:PH_HOST_HEALTH", + "BIOSAMPLE:host_health_state" + ], + "rank": 34, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStateMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host health status details", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Hospitalized" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_DETAILS" + ], + "rank": 35, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStatusDetailsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host health outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_OUTCOME", + "BIOSAMPLE:host_health_outcome" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_outcome", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthOutcomeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host disease", + "comments": [ + "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + ], + "examples": [ + { + "value": "Mpox" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Host%20Disease", + "NML_LIMS:PH_HOST_DISEASE", + "BIOSAMPLE:host_disease", + "VirusSeq_Portal:host%20disease" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Patient%20age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, + "minimum_value": 0, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host age unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_AGE_UNIT", + "BIOSAMPLE:host_age_unit" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostAgeUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "The age category of the host at the time of sampling.", + "title": "host age bin", + "comments": [ + "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative." + ], + "examples": [ + { + "value": "50 - 59" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_AGE_GROUP", + "BIOSAMPLE:host_age_bin" + ], + "rank": 40, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_gender": { + "name": "host_gender", + "description": "The gender of the host at the time of sample collection.", + "title": "host gender", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Male" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Gender", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex" + ], + "rank": 41, + "slot_uri": "GENEPIO:0001395", + "alias": "host_gender", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, + "structured_pattern": { + "syntax": "{Title_Case}", + "interpolated": true, + "partial_match": false + }, + "any_of": [ + { + "range": "HostGenderMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", + "description": "The country of residence of the host.", + "title": "host residence geo_loc name (country)", + "comments": [ + "Select the country name from pick list provided in the template." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_HOST_COUNTRY" + ], + "rank": 42, + "slot_uri": "GENEPIO:0001396", + "alias": "host_residence_geo_loc_name_country", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", + "description": "The state/province/territory of residence of the host.", + "title": "host residence geo_loc name (state/province/territory)", + "comments": [ + "Select the province/territory name from pick list provided in the template." + ], + "examples": [ + { + "value": "Quebec" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_HOST_PROVINCE" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001397", + "alias": "host_residence_geo_loc_name_state_province_territory", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom onset date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-05-25" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:HC_ONSET_DATE" + ], + "rank": 44, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs and symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:HC_SYMPTOMS" + ], + "rank": 45, + "slot_uri": "GENEPIO:0001400", + "alias": "signs_and_symptoms", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "SignsAndSymptomsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing conditions and risk factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:pre-existing%20conditions%20and%20risk%20factors" + ], + "rank": 46, + "slot_uri": "GENEPIO:0001401", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "PreExistingConditionsAndRiskFactorsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Delayed wound healing (lesion healing)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:complications" + ], + "rank": 47, + "slot_uri": "GENEPIO:0001402", + "alias": "complications", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "ComplicationsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "antiviral_therapy": { + "name": "antiviral_therapy", + "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", + "title": "antiviral therapy", + "comments": [ + "Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information." + ], + "examples": [ + { + "value": "Tecovirimat used to treat current Monkeypox infection" + }, + { + "value": "AZT administered for concurrent HIV infection" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:antiviral%20therapy" + ], + "rank": 48, + "slot_uri": "GENEPIO:0100580", + "alias": "antiviral_therapy", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host vaccination status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Not Vaccinated" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], + "rank": 49, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "HostVaccinationStatusMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number of vaccine doses received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "1" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:number%20of%20vaccine%20doses%20received" + ], + "rank": 50, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host vaccination information", + "range": "integer" + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination dose 1 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose." + ], + "examples": [ + { + "value": "IMVAMUNE (Bavarian Nordic)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], + "rank": 51, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination dose 1 vaccination date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-06-01" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], + "rank": 52, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "IMVAMUNE (Bavarian Nordic)" + }, + { + "value": "2022-06-01" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], + "rank": 53, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", + "description": "The country where the host was likely exposed to the causative agent of the illness.", + "title": "location of exposure geo_loc name (country)", + "comments": [ + "Select the country name from the pick list provided in the template." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_COUNTRY" + ], + "rank": 54, + "slot_uri": "GENEPIO:0001410", + "alias": "location_of_exposure_geo_loc_name_country", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", + "description": "The name of the city that was the destination of most recent travel.", + "title": "destination of most recent travel (city)", + "comments": [ + "Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "New York City" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 55, + "slot_uri": "GENEPIO:0001411", + "alias": "destination_of_most_recent_travel_city", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", + "description": "The name of the state/province/territory that was the destination of most recent travel.", + "title": "destination of most recent travel (state/province/territory)", + "comments": [ + "Select the province name from the pick list provided in the template." + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 56, + "slot_uri": "GENEPIO:0001412", + "alias": "destination_of_most_recent_travel_state_province_territory", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", + "description": "The name of the country that was the destination of most recent travel.", + "title": "destination of most recent travel (country)", + "comments": [ + "Select the country name from the pick list provided in the template." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 57, + "slot_uri": "GENEPIO:0001413", + "alias": "destination_of_most_recent_travel_country", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", + "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", + "title": "most recent travel departure date", + "comments": [ + "Provide the travel departure date." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 58, + "slot_uri": "GENEPIO:0001414", + "alias": "most_recent_travel_departure_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", + "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", + "title": "most recent travel return date", + "comments": [ + "Provide the travel return date." + ], + "examples": [ + { + "value": "2020-04-26" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 59, + "slot_uri": "GENEPIO:0001415", + "alias": "most_recent_travel_return_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "travel_history": { + "name": "travel_history", + "description": "Travel history in last six months.", + "title": "travel history", + "comments": [ + "Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first." + ], + "examples": [ + { + "value": "Canada, Vancouver" + }, + { + "value": "USA, Seattle" + }, + { + "value": "Italy, Milan" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 60, + "slot_uri": "GENEPIO:0001416", + "alias": "travel_history", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team." + ], + "examples": [ + { + "value": "Party" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 61, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureEventMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select exposure contact level from the pick-list." + ], + "examples": [ + { + "value": "Contact with infected individual" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "rank": 62, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureContactLevelMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team." + ], + "examples": [ + { + "value": "Acquaintance of case" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "rank": 63, + "slot_uri": "GENEPIO:0001419", + "alias": "host_role", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "range": "HostRoleMenu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 64, + "slot_uri": "GENEPIO:0001428", + "alias": "exposure_setting", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "range": "ExposureSettingMenu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Large party, many contacts" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "rank": 65, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "prior_mpox_infection": { + "name": "prior_mpox_infection", + "description": "The absence or presence of a prior Mpox infection.", + "title": "prior Mpox infection", + "comments": [ + "If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list." + ], + "examples": [ + { + "value": "Prior infection" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:prior%20Monkeypox%20infection" + ], + "rank": 66, + "slot_uri": "GENEPIO:0100532", + "alias": "prior_mpox_infection", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorMonkeypoxInfectionMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "prior_mpox_infection_date": { + "name": "prior_mpox_infection_date", + "description": "The date of diagnosis of the prior Mpox infection.", + "title": "prior Mpox infection date", + "comments": [ + "Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-06-20" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:prior%20Monkeypox%20infection%20date" + ], + "rank": 67, + "slot_uri": "GENEPIO:0100533", + "alias": "prior_mpox_infection_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "prior_mpox_antiviral_treatment": { + "name": "prior_mpox_antiviral_treatment", + "description": "The absence or presence of antiviral treatment for a prior Mpox infection.", + "title": "prior Mpox antiviral treatment", + "comments": [ + "If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list." + ], + "examples": [ + { + "value": "Prior antiviral treatment" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:prior%20Monkeypox%20antiviral%20treatment" + ], + "rank": 68, + "slot_uri": "GENEPIO:0100534", + "alias": "prior_mpox_antiviral_treatment", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorMonkeypoxAntiviralTreatmentMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "prior_antiviral_treatment_during_prior_mpox_infection": { + "name": "prior_antiviral_treatment_during_prior_mpox_infection", + "description": "Antiviral treatment for any infection during the prior Mpox infection period.", + "title": "prior antiviral treatment during prior Mpox infection", + "comments": [ + "Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information." + ], + "examples": [ + { + "value": "AZT was administered for HIV infection during the prior Mpox infection." + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:prior%20antiviral%20treatment%20during%20Monkeypox%20infection" + ], + "rank": 69, + "slot_uri": "GENEPIO:0100535", + "alias": "prior_antiviral_treatment_during_prior_mpox_infection", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host reinfection information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing project name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "MPOX-1356" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 70, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency that generated the sequence.", + "title": "sequenced by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by" + ], + "rank": 71, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 72, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:sequenced%20by%20contact%20email" + ], + "rank": 73, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_address": { + "name": "sequenced_by_contact_address", + "description": "The mailing address of the agency submitting the sequence.", + "title": "sequenced by contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ + { + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:sequenced%20by%20contact%20address" + ], + "rank": 74, + "slot_uri": "GENEPIO:0100423", + "alias": "sequenced_by_contact_address", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", + "NML_LIMS:PH_SEQUENCE_SUBMITTER", + "BIOSAMPLE:sequence_submitted_by", + "VirusSeq_Portal:sequence%20submitted%20by" + ], + "rank": 75, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the agency responsible for submission of the sequence.", + "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:sequence%20submitter%20contact%20email" + ], + "rank": 76, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", - "rank": 2, - "slot_group": "Database Identifiers" + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", + "description": "The mailing address of the agency responsible for submission of the sequence.", + "title": "sequence submitter contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ + { + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Address", + "NML_LIMS:sequence%20submitter%20contact%20address" + ], + "rank": 77, + "slot_uri": "GENEPIO:0001167", + "alias": "sequence_submitter_contact_address", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", - "rank": 3, - "slot_group": "Database Identifiers" + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "The reason that the sample was sequenced.", + "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Specimens attributed to individuals with no known intimate contacts to positive cases", + "description": "Select \"Targeted surveillance (non-random sampling)\" if the specimen fits any of the following criteria" + }, + { + "value": "Specimens attributed to youth/minors <18 yrs." + }, + { + "value": "Specimens attributed to vulnerable persons living in transient shelters or congregant settings" + }, + { + "value": "Specimens attributed to individuals self-identifying as “female”" + }, + { + "value": "Domestic travel surveillance", + "description": "For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options" + }, + { + "value": "International travel surveillance" + }, + { + "value": "Travel-associated surveillance" + }, + { + "value": "Cluster/Outbreak investigation", + "description": "For specimens targeted for sequencing as part of an outbreak investigation, please select" + }, + { + "value": "Baseline surveillance (random sampling).", + "description": "In all other cases use" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Sampling%20Strategy", + "CNPHI:Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING", + "BIOSAMPLE:purpose_of_sequencing", + "VirusSeq_Portal:purpose%20of%20sequencing" + ], + "rank": 78, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "bioproject accession": { - "name": "bioproject accession", - "rank": 4, - "slot_group": "Database Identifiers" + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual." + ], + "examples": [ + { + "value": "Outbreak in MSM community" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", + "VirusSeq_Portal:purpose%20of%20sequencing%20details" + ], + "rank": 79, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "biosample accession": { - "name": "biosample accession", - "rank": 5, - "slot_group": "Database Identifiers" + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_DATE" + ], + "rank": 80, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "SRA accession": { - "name": "SRA accession", - "rank": 6, - "slot_group": "Database Identifiers" + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:library%20ID" + ], + "rank": 81, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "GenBank accession": { - "name": "GenBank accession", - "rank": 7, - "slot_group": "Database Identifiers" + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_LIBRARY_PREP_KIT" + ], + "rank": 82, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "GISAID accession": { - "name": "GISAID accession", - "rank": 8, - "slot_group": "Database Identifiers" + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing assay type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 83, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequence information", + "range": "SequencingAssayTypeMenu" }, - "sample collected by": { - "name": "sample collected by", + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Originating%20lab", - "CNPHI:Lab%20Name", - "NML_LIMS:CUSTOMER", - "BIOSAMPLE:collected_by", - "VirusSeq_Portal:sample%20collected%20by" + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", + "NML_LIMS:PH_SEQUENCING_INSTRUMENT", + "VirusSeq_Portal:sequencing%20instrument" ], - "rank": 9, - "slot_group": "Sample collection and processing", + "rank": 84, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "required": true, + "multivalued": true, "any_of": [ { - "range": "sample collected by menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", - "rank": 10, - "slot_group": "Sample collection and processing" + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing flow cell version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 85, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "sample collector contact address": { - "name": "sample collector contact address", - "rank": 11, - "slot_group": "Sample collection and processing" + "sequencing_protocol__": { + "name": "sequencing_protocol__", + "description": "The protocol used to generate the sequence.", + "title": "sequencing protocol", + "comments": [ + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + ], + "examples": [ + { + "value": "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_TESTING_PROTOCOL", + "VirusSeq_Portal:sequencing%20protocol" + ], + "rank": 86, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol__", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "sequenced by": { - "name": "sequenced by", - "exact_mappings": [ - "NML_LIMS:PH_SEQUENCING_CENTRE", - "BIOSAMPLE:sequenced_by" + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "description": "The manufacturer's kit number.", + "title": "sequencing kit number", + "comments": [ + "Alphanumeric value." ], - "rank": 12, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "sequence submitted by menu" - }, + "examples": [ { - "range": "null value menu" + "value": "AB456XYZ789" } - ] - }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "rank": 13, - "slot_group": "Sample collection and processing" - }, - "sequenced by contact address": { - "name": "sequenced by contact address", - "rank": 14, - "slot_group": "Sample collection and processing" - }, - "sequence submitted by": { - "name": "sequence submitted by", + ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Submitting%20lab", - "CNPHI:Sequencing%20Centre", - "NML_LIMS:PH_SEQUENCE_SUBMITTER", - "BIOSAMPLE:sequence_submitted_by", - "VirusSeq_Portal:sequence%20submitted%20by" + "NML_LIMS:sequencing%20kit%20number" ], - "rank": 15, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "sequence submitted by menu" - }, + "rank": 87, + "slot_uri": "GENEPIO:0001455", + "alias": "sequencing_kit_number", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA fragment length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ { - "range": "null value menu" + "value": "400" } - ] - }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "rank": 16, - "slot_group": "Sample collection and processing" - }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "rank": 17, - "slot_group": "Sample collection and processing" - }, - "sample collection date": { - "name": "sample collection date", - "rank": 18, - "slot_group": "Sample collection and processing" - }, - "sample collection date precision": { - "name": "sample collection date precision", - "rank": 19, - "slot_group": "Sample collection and processing" - }, - "sample received date": { - "name": "sample received date", - "rank": 20, - "slot_group": "Sample collection and processing" + ], + "from_schema": "https://example.com/mpox", + "rank": 88, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method", + "comments": [ + "Provide the name of the enrichment method" + ], "examples": [ { - "value": "Canada" + "value": "hybrid selection method" } ], - "rank": 21, - "slot_group": "Sample collection and processing", + "from_schema": "https://example.com/mpox", + "rank": 89, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method details", "comments": [ - "Provide the province/territory name from the controlled vocabulary provided." + "Provide details that are applicable to the method you used." ], - "rank": 22, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "geo_loc_name (state/province/territory) menu" - }, + "examples": [ { - "range": "null value menu" + "value": "enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit." } - ] + ], + "from_schema": "https://example.com/mpox", + "rank": 90, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "organism": { - "name": "organism", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", "comments": [ - "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." ], "examples": [ { - "value": "Mpox virus" + "value": "MPXV Sunrise 3.1" } ], - "rank": 23, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "organism menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:amplicon%20pcr%20primer%20scheme" + ], + "rank": 91, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "isolate": { - "name": "isolate", + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", "comments": [ - "Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put \"UN\" for \"Unknown\"." + "Provide the amplicon size expressed in base pairs." ], "examples": [ { - "value": "hMpxV/Canada/UN-NML-12345/2022" + "value": "300bp" } ], - "exact_mappings": [ - "GISAID:Virus%20name", - "CNPHI:GISAID%20Virus%20Name", - "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Virus%20Name", - "BIOSAMPLE:isolate", - "BIOSAMPLE:GISAID_virus_name", - "VirusSeq_Portal:isolate", - "VirusSeq_Portal:fasta%20header%20name" + "from_schema": "https://example.com/mpox", + "rank": 92, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 24, - "slot_uri": "GENEPIO:0001195", - "slot_group": "Sample collection and processing" + "slot_group": "Sequencing", + "range": "integer" }, - "purpose of sampling": { - "name": "purpose of sampling", + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], "examples": [ { - "value": "Diagnostic testing" + "value": "ncov-tools" } ], - "rank": 25, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "purpose of sampling menu" - }, + "from_schema": "https://example.com/mpox", + "rank": 93, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ { - "range": "null value menu" + "value": "1.2.3" } - ] - }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "rank": 26, - "slot_group": "Sample collection and processing" - }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", - "rank": 27, - "slot_group": "Sample collection and processing" - }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", - "rank": 28, - "slot_group": "Sample collection and processing" + ], + "from_schema": "https://example.com/mpox", + "rank": 94, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "anatomical material": { - "name": "anatomical material", + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], "examples": [ { - "value": "Lesion (Pustule)" + "value": "sequence failed quality control" } ], - "rank": 29, - "slot_group": "Sample collection and processing", - "required": true, + "from_schema": "https://example.com/mpox", + "rank": 95, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, "any_of": [ { - "range": "anatomical material menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], "examples": [ { - "value": "Genital area" + "value": "low average genome coverage" } ], - "rank": 30, - "slot_group": "Sample collection and processing", - "required": true, + "from_schema": "https://example.com/mpox", + "rank": 96, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, "any_of": [ { - "range": "anatomical part menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], "examples": [ { - "value": "Pus" + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." } ], - "rank": 31, - "slot_group": "Sample collection and processing", - "required": true, - "any_of": [ - { - "range": "body product menu" - }, + "from_schema": "https://example.com/mpox", + "rank": 97, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ { - "range": "null value menu" + "value": "Porechop 0.2.3" } - ] + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_RAW_SEQUENCE_METHOD", + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" + ], + "rank": 98, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "required": true }, - "collection device": { - "name": "collection device", + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], "examples": [ { - "value": "Swab" + "value": "Nanostripper" } ], - "rank": 32, - "slot_group": "Sample collection and processing", - "required": true, - "any_of": [ - { - "range": "collection device menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_DEHOSTING_METHOD", + "VirusSeq_Portal:dehosting%20method" + ], + "rank": 99, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "required": true }, - "collection method": { - "name": "collection method", + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], "examples": [ { - "value": "Biopsy" + "value": "DeDup 0.12.8" } ], - "rank": 33, - "slot_group": "Sample collection and processing", - "required": true, - "any_of": [ - { - "range": "collection method menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/mpox", + "rank": 100, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "description": "The name of the consensus sequence.", + "title": "consensus sequence name", + "comments": [ + "Provide the name and version number of the consensus sequence." + ], "examples": [ { - "value": "Specimens pooled" + "value": "mpxvassembly3" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:specimen%20processing" + "NML_LIMS:consensus%20sequence%20name" ], - "rank": 34, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "specimen processing menu" - }, - { - "range": "null value menu" - } - ] - }, - "specimen processing details": { - "name": "specimen processing details", - "rank": 35, - "slot_group": "Sample collection and processing" + "rank": 101, + "slot_uri": "GENEPIO:0001460", + "alias": "consensus_sequence_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "host (common name)": { - "name": "host (common name)", - "exact_mappings": [ - "NML_LIMS:PH_ANIMAL_TYPE" + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." ], - "rank": 36, - "slot_group": "Host Information", - "any_of": [ - { - "range": "host (common name) menu" - }, + "examples": [ { - "range": "null value menu" + "value": "mpxvassembly.fasta" } - ] + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filename" + ], + "rank": 102, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "host (scientific name)": { - "name": "host (scientific name)", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", + "comments": [ + "Provide the filepath of the genome sequence FASTA file." + ], "examples": [ { - "value": "Homo sapiens" + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" } ], - "rank": 37, - "slot_group": "Host Information", - "any_of": [ - { - "range": "host (scientific name) menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filepath" + ], + "rank": 103, + "slot_uri": "GENEPIO:0101716", + "alias": "genome_sequence_file_path", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "host health state": { - "name": "host health state", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], "examples": [ { - "value": "Asymptomatic" + "value": "iVar" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Patient%20status", - "NML_LIMS:PH_HOST_HEALTH", - "BIOSAMPLE:host_health_state" + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" ], - "rank": 38, - "slot_group": "Host Information", - "any_of": [ - { - "range": "host health state menu" - }, - { - "range": "null value menu" - } - ] + "rank": 104, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "required": true }, - "host health status details": { - "name": "host health status details", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], "examples": [ { - "value": "Hospitalized" + "value": "1.3" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_HOST_HEALTH_DETAILS" + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" ], - "rank": 39, - "slot_group": "Host Information", - "any_of": [ - { - "range": "host health status details menu" - }, - { - "range": "null value menu" - } - ] + "rank": 105, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "required": true }, - "host health outcome": { - "name": "host health outcome", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], "examples": [ { - "value": "Recovered" + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" } ], - "exact_mappings": [ - "NML_LIMS:PH_HOST_HEALTH_OUTCOME", - "BIOSAMPLE:host_health_outcome" + "from_schema": "https://example.com/mpox", + "rank": 106, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 40, - "slot_group": "Host Information", + "slot_group": "Bioinformatics and QC metrics", + "required": true, "any_of": [ { - "range": "host health outcome menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", "comments": [ - "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + "Provide the version of the software used to assemble the sequence." ], "examples": [ { - "value": "Mpox" + "value": "3.15.5" } ], - "rank": 41, - "slot_group": "Host Information", + "from_schema": "https://example.com/mpox", + "rank": 107, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "required": true, "any_of": [ { - "range": "host disease menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age": { - "name": "host age", - "exact_mappings": [ - "GISAID:Patient%20age", - "NML_LIMS:PH_AGE", - "BIOSAMPLE:host_age" + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", + "comments": [ + "Provide the r1 FASTQ filename. This information aids in data management." ], - "rank": 42, - "slot_group": "Host Information", - "required": true - }, - "host age unit": { - "name": "host age unit", "examples": [ { - "value": "year" + "value": "ABC123_S1_L001_R1_001.fastq.gz" } ], - "exact_mappings": [ - "NML_LIMS:PH_AGE_UNIT", - "BIOSAMPLE:host_age_unit" + "from_schema": "https://example.com/mpox", + "rank": 108, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename________", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 43, - "slot_group": "Host Information", - "required": true, - "any_of": [ - { - "range": "host age unit menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", + "comments": [ + "Provide the r2 FASTQ filename. This information aids in data management." + ], + "examples": [ { - "range": "null value menu" + "value": "ABC123_S1_L001_R2_001.fastq.gz" } - ] + ], + "from_schema": "https://example.com/mpox", + "rank": 109, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "host age bin": { - "name": "host age bin", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", + "comments": [ + "Provide the filepath for the r1 FASTQ file. This information aids in data management." + ], "examples": [ { - "value": "50 - 59" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" } ], - "exact_mappings": [ - "NML_LIMS:PH_AGE_GROUP", - "BIOSAMPLE:host_age_bin" + "from_schema": "https://example.com/mpox", + "rank": 110, + "slot_uri": "GENEPIO:0001478", + "alias": "r1_fastq_filepath", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 44, - "slot_group": "Host Information", - "required": true, - "any_of": [ - { - "range": "host age bin menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "host gender": { - "name": "host gender", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", + "comments": [ + "Provide the filepath for the r2 FASTQ file. This information aids in data management." + ], "examples": [ { - "value": "Male" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" } ], - "exact_mappings": [ - "GISAID:Gender", - "NML_LIMS:VD_SEX", - "BIOSAMPLE:host_sex" + "from_schema": "https://example.com/mpox", + "rank": 111, + "slot_uri": "GENEPIO:0001479", + "alias": "r2_fastq_filepath", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 45, - "slot_group": "Host Information", - "required": true, - "any_of": [ - { - "range": "host gender menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", + "comments": [ + "Provide the FAST5 filename. This information aids in data management." + ], "examples": [ { - "value": "Canada" + "value": "mpxv123seq.fast5" } ], - "exact_mappings": [ - "NML_LIMS:PH_HOST_COUNTRY" + "from_schema": "https://example.com/mpox", + "rank": 112, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 46, - "slot_group": "Host Information", - "any_of": [ - { - "range": "geo_loc_name (country) menu" - }, - { - "range": "null value menu" - } - ] - }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", - "rank": 47, - "slot_group": "Host Information" - }, - "symptom onset date": { - "name": "symptom onset date", - "rank": 48, - "slot_group": "Host Information" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "signs and symptoms": { - "name": "signs and symptoms", + "fast5_filepath": { + "name": "fast5_filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", + "comments": [ + "Provide the filepath for the FAST5 file. This information aids in data management." + ], "examples": [ { - "value": "Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain)" + "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" } ], - "exact_mappings": [ - "NML_LIMS:HC_SYMPTOMS" + "from_schema": "https://example.com/mpox", + "rank": 113, + "slot_uri": "GENEPIO:0001481", + "alias": "fast5_filepath", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 49, - "slot_group": "Host Information", - "any_of": [ - { - "range": "signs and symptoms menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "rank": 50, - "slot_group": "Host Information", - "any_of": [ - { - "range": "pre-existing conditions and risk factors menu" - }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ { - "range": "null value menu" + "value": "423867" } - ] + ], + "from_schema": "https://example.com/mpox", + "rank": 114, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "complications": { - "name": "complications", + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Delayed wound healing (lesion healing)" + "value": "248236" } ], - "exact_mappings": [ - "NML_LIMS:complications" + "from_schema": "https://example.com/mpox", + "rank": 115, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 51, - "slot_group": "Host Information", - "any_of": [ - { - "range": "complications menu" - }, - { - "range": "null value menu" - } - ] - }, - "antiviral therapy": { - "name": "antiviral therapy", - "rank": 52, - "slot_group": "Host Information" + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "host vaccination status": { - "name": "host vaccination status", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Not Vaccinated" + "value": "150" } ], - "rank": 53, - "slot_group": "Host vaccination information", - "any_of": [ - { - "range": "host vaccination status menu" - }, - { - "range": "null value menu" - } - ] - }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", - "rank": 54, - "slot_group": "Host vaccination information" - }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", - "rank": 55, - "slot_group": "Host vaccination information" - }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", - "rank": 56, - "slot_group": "Host vaccination information" - }, - "vaccination history": { - "name": "vaccination history", - "rank": 57, - "slot_group": "Host vaccination information" + "from_schema": "https://example.com/mpox", + "rank": 116, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], "examples": [ { - "value": "Canada" + "value": "400x" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_EXPOSURE_COUNTRY" + "GISAID:Depth%20of%20coverage", + "NML_LIMS:depth%20of%20coverage%20value", + "VirusSeq_Portal:depth%20of%20coverage%20value" ], - "rank": 58, - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "geo_loc_name (country) menu" - }, - { - "range": "null value menu" - } - ] - }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", - "rank": 59, - "slot_group": "Host exposure information" + "rank": 117, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", "comments": [ - "Select the province name from the pick list provided in the template." - ], - "exact_mappings": [ - "NML_LIMS:PH_TRAVEL" + "Provide the threshold fold coverage." ], - "rank": 60, - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "geo_loc_name (state/province/territory) menu" - }, + "examples": [ { - "range": "null value menu" + "value": "100x" } - ] + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:depth%20of%20coverage%20threshold" + ], + "rank": 118, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Canada" + "value": "2639019" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_TRAVEL" + "NML_LIMS:number%20of%20base%20pairs%20sequenced" ], - "rank": 61, - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "geo_loc_name (country) menu" - }, - { - "range": "null value menu" - } - ] - }, - "most recent travel departure date": { - "name": "most recent travel departure date", - "rank": 62, - "slot_group": "Host exposure information" - }, - "most recent travel return date": { - "name": "most recent travel return date", - "rank": 63, - "slot_group": "Host exposure information" - }, - "travel history": { - "name": "travel history", - "rank": 64, - "slot_group": "Host exposure information" + "rank": 119, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer", + "minimum_value": 0 }, - "exposure event": { - "name": "exposure event", + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "Size of the reconstructed genome described as the number of base pairs.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Party" + "value": "197063" } ], - "rank": 65, - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "exposure event menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:consensus%20genome%20length" + ], + "rank": 120, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer", + "minimum_value": 0 }, - "exposure contact level": { - "name": "exposure contact level", + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Contact with infected individual" + "value": "34272" } ], - "rank": 66, - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "exposure contact level menu" - }, - { - "range": "null value menu" - } - ] + "from_schema": "https://example.com/mpox", + "rank": 121, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "host role": { - "name": "host role", + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], "examples": [ { - "value": "Acquaintance of case" + "value": "10" } ], - "rank": 67, - "slot_group": "Host exposure information", - "range": "host role menu" + "from_schema": "https://example.com/mpox", + "rank": 122, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "exposure setting": { - "name": "exposure setting", + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], "examples": [ { - "value": "Healthcare Setting" + "value": "85" } ], - "rank": 68, - "slot_group": "Host exposure information", - "range": "exposure setting menu" - }, - "exposure details": { - "name": "exposure details", - "rank": 69, - "slot_group": "Host exposure information" + "from_schema": "https://example.com/mpox", + "rank": 123, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "prior Mpox infection": { - "name": "prior Mpox infection", + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], "examples": [ { - "value": "Prior infection" + "value": "150" } ], - "exact_mappings": [ - "NML_LIMS:prior%20Monkeypox%20infection" + "from_schema": "https://example.com/mpox", + "rank": 124, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 70, - "slot_group": "Host reinfection information", - "any_of": [ - { - "range": "prior Monkeypox infection menu" - }, - { - "range": "null value menu" - } - ] - }, - "prior Mpox infection date": { - "name": "prior Mpox infection date", - "rank": 71, - "slot_group": "Host reinfection information" + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "prior Mpox antiviral treatment": { - "name": "prior Mpox antiviral treatment", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Prior antiviral treatment" + "value": "2" } ], - "exact_mappings": [ - "NML_LIMS:prior%20Monkeypox%20antiviral%20treatment" + "from_schema": "https://example.com/mpox", + "rank": 125, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 72, - "slot_group": "Host reinfection information", - "any_of": [ - { - "range": "prior Monkeypox antiviral treatment menu" - }, - { - "range": "null value menu" - } - ] - }, - "prior antiviral treatment during prior Mpox infection": { - "name": "prior antiviral treatment during prior Mpox infection", - "rank": 73, - "slot_group": "Host reinfection information" + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Specimens attributed to individuals with no known intimate contacts to positive cases", - "description": "Select \"Targeted surveillance (non-random sampling)\" if the specimen fits any of the following criteria" - }, - { - "value": "Specimens attributed to youth/minors <18 yrs." - }, - { - "value": "Specimens attributed to vulnerable persons living in transient shelters or congregant settings" - }, - { - "value": "Specimens attributed to individuals self-identifying as “female”" - }, - { - "value": "Domestic travel surveillance", - "description": "For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options" - }, - { - "value": "International travel surveillance" - }, - { - "value": "Travel-associated surveillance" - }, - { - "value": "Cluster/Outbreak investigation", - "description": "For specimens targeted for sequencing as part of an outbreak investigation, please select" - }, - { - "value": "Baseline surveillance (random sampling).", - "description": "In all other cases use" + "value": "342" } ], - "rank": 74, - "slot_group": "Sequencing", - "any_of": [ - { - "range": "purpose of sequencing menu" - }, - { - "range": "null value menu" - } - ] - }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "rank": 75, - "slot_group": "Sequencing" - }, - "sequencing date": { - "name": "sequencing date", - "rank": 76, - "slot_group": "Sequencing", - "required": true - }, - "library ID": { - "name": "library ID", - "rank": 77, - "slot_group": "Sequencing" - }, - "amplicon size": { - "name": "amplicon size", - "rank": 78, - "slot_group": "Sequencing" - }, - "library preparation kit": { - "name": "library preparation kit", - "rank": 79, - "slot_group": "Sequencing" + "from_schema": "https://example.com/mpox", + "rank": 126, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "sequencing instrument": { - "name": "sequencing instrument", + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], "examples": [ { - "value": "Oxford Nanopore MinION" + "value": "NC_063383.1" } ], - "rank": 80, - "slot_group": "Sequencing", - "any_of": [ - { - "range": "sequencing instrument menu" - }, - { - "range": "null value menu" - } - ] - }, - "sequencing protocol": { - "name": "sequencing protocol", - "rank": 81, - "slot_group": "Sequencing" - }, - "sequencing kit number": { - "name": "sequencing kit number", - "rank": 82, - "slot_group": "Sequencing" - }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "rank": 83, - "slot_group": "Sequencing" - }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "rank": 84, - "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "dehosting method": { - "name": "dehosting method", - "rank": 85, - "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "consensus sequence name": { - "name": "consensus sequence name", - "rank": 86, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "rank": 87, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "rank": 88, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "rank": 89, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "rank": 90, - "slot_group": "Bioinformatics and QC metrics" - }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "rank": 91, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth of coverage value": { - "name": "depth of coverage value", - "rank": 92, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "rank": 93, - "slot_group": "Bioinformatics and QC metrics" - }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "rank": 94, - "slot_group": "Bioinformatics and QC metrics" - }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "rank": 95, - "slot_group": "Bioinformatics and QC metrics" - }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "rank": 96, - "slot_group": "Bioinformatics and QC metrics" - }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "rank": 97, - "slot_group": "Bioinformatics and QC metrics" - }, - "fast5 filename": { - "name": "fast5 filename", - "rank": 98, - "slot_group": "Bioinformatics and QC metrics" - }, - "fast5 filepath": { - "name": "fast5 filepath", - "rank": 99, - "slot_group": "Bioinformatics and QC metrics" - }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "rank": 100, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus genome length": { - "name": "consensus genome length", - "rank": 101, - "slot_group": "Bioinformatics and QC metrics" - }, - "reference genome accession": { - "name": "reference genome accession", - "rank": 102, - "slot_group": "Bioinformatics and QC metrics" + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:reference%20genome%20accession" + ], + "rank": 127, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "rank": 103, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/monkeypox-nf" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Bioinformatics%20Protocol", + "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", + "VirusSeq_Portal:bioinformatics%20protocol" + ], + "rank": 128, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", "required": true }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 1", "comments": [ "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "rank": 104, + "examples": [ + { + "value": "MPX (orf B6R)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", + "BIOSAMPLE:gene_name_1", + "VirusSeq_Portal:gene%20name" + ], + "rank": 129, + "slot_uri": "GENEPIO:0001507", + "alias": "gene_name_1", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "rank": 105, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 2": { - "name": "gene name 2", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 1", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "Provide the CT value of the sample from the diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "21" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%201%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_1", + "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" + ], + "rank": 130, + "slot_uri": "GENEPIO:0001509", + "alias": "diagnostic_pcr_ct_value_1", + "owner": "Mpox", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 106, "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name menu" + "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "rank": 107, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 3": { - "name": "gene name 3", + "gene_name_2": { + "name": "gene_name_2", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 2", "comments": [ "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "rank": 108, + "examples": [ + { + "value": "OVP (orf 17L)" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", + "BIOSAMPLE:gene_name_2" + ], + "rank": 131, + "slot_uri": "GENEPIO:0001510", + "alias": "gene_name_2", + "owner": "Mpox", + "domain_of": [ + "Mpox" + ], "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "rank": 109, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 4": { - "name": "gene name 4", - "rank": 110, - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic pcr Ct value 4": { - "name": "diagnostic pcr Ct value 4", - "rank": 111, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 5": { - "name": "gene name 5", - "rank": 112, - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic pcr Ct value 5": { - "name": "diagnostic pcr Ct value 5", - "rank": 113, - "slot_group": "Pathogen diagnostic testing" - }, - "authors": { - "name": "authors", - "rank": 114, - "slot_group": "Contributor acknowledgement" - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 115, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "The user-defined name for the sample.", - "title": "specimen collector sample ID", - "from_schema": "https://example.com/mpox", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "specimen_collector_sample_ID", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 2", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "required": true - }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", - "description": "The primary ID of a related specimen previously submitted to the repository.", - "title": "Related specimen primary ID", - "from_schema": "https://example.com/mpox", - "rank": 2, - "slot_uri": "GENEPIO:0001128", - "alias": "Related_specimen_primary_ID", - "owner": "Mpox", - "domain_of": [ - "Mpox" + "examples": [ + { + "value": "36" + } ], - "slot_group": "Database Identifiers" - }, - "case ID": { - "name": "case ID", - "description": "The identifier used to specify an epidemiologically detected case of disease.", - "title": "case ID", "from_schema": "https://example.com/mpox", - "rank": 3, - "slot_uri": "GENEPIO:0100281", - "alias": "case_ID", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "exact_mappings": [ + "CNPHI:Gene%20Target%202%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_2" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString" - }, - "bioproject accession": { - "name": "bioproject accession", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "title": "bioproject accession", - "from_schema": "https://example.com/mpox", - "rank": 4, - "slot_uri": "GENEPIO:0001136", - "alias": "bioproject_accession", + "rank": 132, + "slot_uri": "GENEPIO:0001512", + "alias": "diagnostic_pcr_ct_value_2", "owner": "Mpox", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "biosample accession": { - "name": "biosample accession", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "title": "biosample accession", - "from_schema": "https://example.com/mpox", - "rank": 5, - "slot_uri": "GENEPIO:0001139", - "alias": "biosample_accession", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "gene_name_3": { + "name": "gene_name_3", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 3", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", - "from_schema": "https://example.com/mpox", - "rank": 6, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "examples": [ + { + "value": "OPHA (orf B2R)" + } ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "GenBank accession": { - "name": "GenBank accession", - "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank accession", "from_schema": "https://example.com/mpox", - "rank": 7, - "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "exact_mappings": [ + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233", + "BIOSAMPLE:gene_name_3" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The GISAID accession number assigned to the sequence.", - "title": "GISAID accession", - "from_schema": "https://example.com/mpox", - "rank": 8, - "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "rank": 133, + "slot_uri": "GENEPIO:0001513", + "alias": "gene_name_3", "owner": "Mpox", "domain_of": [ - "Mpox", - "Mpox_international" + "Mpox" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collected by": { - "name": "sample collected by", - "description": "The name of the agency that collected the original sample.", - "title": "sample collected by", - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Originating%20lab", - "CNPHI:Lab%20Name", - "NML_LIMS:CUSTOMER", - "BIOSAMPLE:collected_by", - "VirusSeq_Portal:sample%20collected%20by" + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 3", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "19" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Gene%20Target%203%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_3" ], - "rank": 9, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", + "rank": 134, + "slot_uri": "GENEPIO:0001515", + "alias": "diagnostic_pcr_ct_value_3", "owner": "Mpox", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "sample collected by menu" + "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "title": "sample collector contact email", - "from_schema": "https://example.com/mpox", - "rank": 10, - "slot_uri": "GENEPIO:0001156", - "alias": "sample_collector_contact_email", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "gene_name_4": { + "name": "gene_name_4", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 4", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "pattern": "^\\S+@\\S+\\.\\S+$" - }, - "sample collector contact address": { - "name": "sample collector contact address", - "description": "The mailing address of the agency submitting the sample.", - "title": "sample collector contact address", - "from_schema": "https://example.com/mpox", - "rank": 11, - "slot_uri": "GENEPIO:0001158", - "alias": "sample_collector_contact_address", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "examples": [ + { + "value": "G2R_G (TNFR)" + } ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sequenced by": { - "name": "sequenced by", - "description": "The name of the agency that generated the sequence.", - "title": "sequenced by", "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_SEQUENCING_CENTRE", - "BIOSAMPLE:sequenced_by" + "CNPHI:Gene%20Target%204", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234", + "BIOSAMPLE:gene_name_4" ], - "rank": 12, - "slot_uri": "GENEPIO:0100416", - "alias": "sequenced_by", + "rank": 135, + "slot_uri": "GENEPIO:0100576", + "alias": "gene_name_4", "owner": "Mpox", "domain_of": [ - "Mpox", - "Mpox_international" + "Mpox" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "sequence submitted by menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced by contact email", - "from_schema": "https://example.com/mpox", - "rank": 13, - "slot_uri": "GENEPIO:0100422", - "alias": "sequenced_by_contact_email", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "diagnostic_pcr_ct_value_4": { + "name": "diagnostic_pcr_ct_value_4", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 4", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "27" + } ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sequenced by contact address": { - "name": "sequenced by contact address", - "description": "The mailing address of the agency submitting the sequence.", - "title": "sequenced by contact address", "from_schema": "https://example.com/mpox", - "rank": 14, - "slot_uri": "GENEPIO:0100423", - "alias": "sequenced_by_contact_address", + "exact_mappings": [ + "CNPHI:Gene%20Target%204%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_4" + ], + "rank": 136, + "slot_uri": "GENEPIO:0100577", + "alias": "diagnostic_pcr_ct_value_4", "owner": "Mpox", "domain_of": [ - "Mpox", - "Mpox_international" + "Mpox" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "The name of the agency that submitted the sequence to a database.", - "title": "sequence submitted by", + "gene_name_5": { + "name": "gene_name_5", + "description": "The name of the gene used in the diagnostic RT-PCR test.", + "title": "gene name 5", + "comments": [ + "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + ], + "examples": [ + { + "value": "RNAse P" + } + ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Submitting%20lab", - "CNPHI:Sequencing%20Centre", - "NML_LIMS:PH_SEQUENCE_SUBMITTER", - "BIOSAMPLE:sequence_submitted_by", - "VirusSeq_Portal:sequence%20submitted%20by" + "CNPHI:Gene%20Target%205", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235", + "BIOSAMPLE:gene_name_5" ], - "rank": 15, - "slot_uri": "GENEPIO:0001159", - "alias": "sequence_submitted_by", + "rank": 137, + "slot_uri": "GENEPIO:0100578", + "alias": "gene_name_5", "owner": "Mpox", "domain_of": [ - "Mpox", - "Mpox_international" + "Mpox" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "sequence submitted by menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "description": "The email address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact email", + "diagnostic_pcr_ct_value_5": { + "name": "diagnostic_pcr_ct_value_5", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 5", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "30" + } + ], "from_schema": "https://example.com/mpox", - "rank": 16, - "slot_uri": "GENEPIO:0001165", - "alias": "sequence_submitter_contact_email", + "exact_mappings": [ + "CNPHI:Gene%20Target%205%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_5" + ], + "rank": 138, + "slot_uri": "GENEPIO:0100579", + "alias": "diagnostic_pcr_ct_value_5", "owner": "Mpox", "domain_of": [ - "Mpox", - "Mpox_international" + "Mpox" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "description": "The mailing address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact address", + "authors": { + "name": "authors", + "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", + "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/mpox", - "rank": 17, - "slot_uri": "GENEPIO:0001167", - "alias": "sequence_submitter_contact_address", + "exact_mappings": [ + "GISAID:Authors", + "CNPHI:Authors", + "NML_LIMS:PH_SEQUENCING_AUTHORS" + ], + "rank": 139, + "slot_uri": "GENEPIO:0001517", + "alias": "authors", "owner": "Mpox", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Contributor acknowledgement", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "sample collection date": { - "name": "sample collection date", - "description": "The date on which the sample was collected.", - "title": "sample collection date", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "The DataHarmonizer software and template version provenance.", + "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, Mpox v3.3.1" + } + ], "from_schema": "https://example.com/mpox", - "rank": 18, - "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", + "exact_mappings": [ + "CNPHI:Additional%20Comments", + "NML_LIMS:HC_COMMENTS" + ], + "rank": 140, + "slot_uri": "GENEPIO:0001518", + "alias": "dataharmonizer_provenance", "owner": "Mpox", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Contributor acknowledgement", + "range": "Provenance" + } + } + }, + "MpoxInternational": { + "name": "MpoxInternational", + "annotations": { + "version": { + "tag": "version", + "value": "7.5.5" + } + }, + "description": "International specification for Mpox clinical virus biosample data gathering", + "from_schema": "https://example.com/mpox", + "see_also": [ + "templates/mpox/SOP_Mpox_international.pdf" + ], + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database Identifiers" }, - "sample collection date precision": { - "name": "sample collection date precision", - "description": "The precision to which the \"sample collection date\" was provided.", - "title": "sample collection date precision", - "from_schema": "https://example.com/mpox", - "rank": 19, - "slot_uri": "GENEPIO:0001177", - "alias": "sample_collection_date_precision", - "owner": "Mpox", - "domain_of": [ - "Mpox" + "case_id": { + "name": "case_id", + "rank": 2, + "slot_group": "Database Identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 3, + "slot_group": "Database Identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 4, + "slot_group": "Database Identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 5, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "rank": 7, + "slot_group": "Database Identifiers" + }, + "gisaid_accession": { + "name": "gisaid_accession", + "rank": 8, + "slot_group": "Database Identifiers" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "exact_mappings": [ + "GISAID:Originating%20lab", + "BIOSAMPLE:collected_by" ], + "rank": 9, "slot_group": "Sample collection and processing", - "required": true + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "rank": 12, + "slot_group": "Sample collection and processing" }, - "sample received date": { - "name": "sample received date", - "description": "The date on which the sample was received.", - "title": "sample received date", - "from_schema": "https://example.com/mpox", - "rank": 20, - "slot_uri": "GENEPIO:0001179", - "alias": "sample_received_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "sample_received_date": { + "name": "sample_received_date", + "rank": 13, "slot_group": "Sample collection and processing" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "description": "The country where the sample was collected.", - "title": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "examples": [ { - "value": "Canada" + "value": "United States of America [GAZ:00002459]" } ], - "from_schema": "https://example.com/mpox", - "rank": 21, - "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 14, "slot_group": "Sample collection and processing", - "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", - "description": "The state/province/territory where the sample was collected.", - "title": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "comments": [ - "Provide the province/territory name from the controlled vocabulary provided." - ], - "from_schema": "https://example.com/mpox", - "rank": 22, - "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "Provide the state/province/territory name from the controlled vocabulary provided." ], + "rank": 15, "slot_group": "Sample collection and processing", - "required": true, "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "rank": 17, + "slot_group": "Sample collection and processing" + }, "organism": { "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", "comments": [ - "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." + "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." ], "examples": [ { - "value": "Mpox virus" + "value": "Mpox virus [NCBITaxon:10244]" } ], - "from_schema": "https://example.com/mpox", - "rank": 23, - "slot_uri": "GENEPIO:0001191", - "alias": "organism", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 18, "slot_group": "Sample collection and processing", - "required": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, "isolate": { "name": "isolate", - "description": "Identifier of the specific isolate.", - "title": "isolate", "comments": [ - "Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put \"UN\" for \"Unknown\"." + "This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the \"isolate\" name is propagated throughtout different databases. As such, structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"MpxV/host/country/sampleID/date\"." ], "examples": [ { - "value": "hMpxV/Canada/UN-NML-12345/2022" + "value": "MpxV/human/USA/CA-CDPH-001/2020" } ], - "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Virus%20name", - "CNPHI:GISAID%20Virus%20Name", - "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Virus%20Name", - "BIOSAMPLE:isolate", - "BIOSAMPLE:GISAID_virus_name", - "VirusSeq_Portal:isolate", - "VirusSeq_Portal:fasta%20header%20name" - ], - "rank": 24, - "slot_uri": "GENEPIO:0001195", - "alias": "isolate", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "BIOSAMPLE:isolate" ], - "slot_group": "Sample collection and processing", - "required": true + "rank": 19, + "slot_uri": "GENEPIO:0001644", + "slot_group": "Sample collection and processing" }, - "purpose of sampling": { - "name": "purpose of sampling", - "description": "The reason that the sample was collected.", - "title": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "examples": [ { - "value": "Diagnostic testing" + "value": "Diagnostic testing [GENEPIO:0100002]" } ], - "from_schema": "https://example.com/mpox", - "rank": 25, - "slot_uri": "GENEPIO:0001198", - "alias": "purpose_of_sampling", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 20, "slot_group": "Sample collection and processing", - "required": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "description": "The description of why the sample was collected, providing specific details.", - "title": "purpose of sampling details", - "from_schema": "https://example.com/mpox", - "rank": 26, - "slot_uri": "GENEPIO:0001200", - "alias": "purpose_of_sampling_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sample collection and processing", - "required": true + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", + "rank": 21, + "slot_group": "Sample collection and processing" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", - "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", - "title": "NML submitted specimen type", - "from_schema": "https://example.com/mpox", - "rank": 27, - "slot_uri": "GENEPIO:0001204", - "alias": "NML_submitted_specimen_type", - "owner": "Mpox", - "domain_of": [ - "Mpox" + "anatomical_material": { + "name": "anatomical_material", + "examples": [ + { + "value": "Lesion (Pustule) [NCIT:C78582]" + } ], + "rank": 22, "slot_group": "Sample collection and processing", - "range": "NML submitted specimen type menu", - "required": true - }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", - "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", - "title": "Related specimen relationship type", - "from_schema": "https://example.com/mpox", - "rank": 28, - "slot_uri": "GENEPIO:0001209", - "alias": "Related_specimen_relationship_type", - "owner": "Mpox", - "domain_of": [ - "Mpox" - ], - "slot_group": "Sample collection and processing" + "recommended": true, + "any_of": [ + { + "range": "AnatomicalMaterialInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "anatomical material": { - "name": "anatomical material", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "title": "anatomical material", + "anatomical_part": { + "name": "anatomical_part", "examples": [ { - "value": "Lesion (Pustule)" + "value": "Genital area [BTO:0003358]" } ], - "from_schema": "https://example.com/mpox", - "rank": 29, - "slot_uri": "GENEPIO:0001211", - "multivalued": true, - "alias": "anatomical_material", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 23, "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, "any_of": [ { - "range": "anatomical material menu" + "range": "AnatomicalPartInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", - "description": "An anatomical part of an organism e.g. oropharynx.", - "title": "anatomical part", + "body_product": { + "name": "body_product", "examples": [ { - "value": "Genital area" + "value": "Pus [UBERON:0000177]" } ], - "from_schema": "https://example.com/mpox", - "rank": 30, - "slot_uri": "GENEPIO:0001214", - "multivalued": true, - "alias": "anatomical_part", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 24, "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, "any_of": [ { - "range": "anatomical part menu" + "range": "BodyProductInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body product", + "environmental_material": { + "name": "environmental_material", + "rank": 25, + "slot_group": "Sample collection and processing" + }, + "collection_device": { + "name": "collection_device", "examples": [ { - "value": "Pus" + "value": "Swab [GENEPIO:0100027]" } ], - "from_schema": "https://example.com/mpox", - "rank": 31, - "slot_uri": "GENEPIO:0001216", - "multivalued": true, - "alias": "body_product", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 26, "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, "any_of": [ { - "range": "body product menu" + "range": "CollectionDeviceInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", - "description": "The instrument or container used to collect the sample e.g. swab.", - "title": "collection device", + "collection_method": { + "name": "collection_method", "examples": [ { - "value": "Swab" + "value": "Biopsy [OBI:0002650]" } ], - "from_schema": "https://example.com/mpox", - "rank": 32, - "slot_uri": "GENEPIO:0001234", - "multivalued": true, - "alias": "collection_device", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 27, "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionMethodInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", - "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", - "title": "collection method", + "specimen_processing": { + "name": "specimen_processing", "examples": [ { - "value": "Biopsy" + "value": "Specimens pooled [OBI:0600016]" } ], - "from_schema": "https://example.com/mpox", - "rank": 33, - "slot_uri": "GENEPIO:0001241", - "multivalued": true, - "alias": "collection_method", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 28, "slot_group": "Sample collection and processing", - "required": true, "any_of": [ { - "range": "collection method menu" + "range": "SpecimenProcessingInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing": { - "name": "specimen processing", - "description": "Any processing applied to the sample during or after receiving the sample.", - "title": "specimen processing", + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 29, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", "examples": [ { - "value": "Specimens pooled" + "value": "Positive experimental control [GENEPIO:0101018]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:specimen%20processing" - ], - "rank": 34, - "slot_uri": "GENEPIO:0001253", - "multivalued": true, - "alias": "specimen_processing", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 30, "slot_group": "Sample collection and processing", "any_of": [ { - "range": "specimen processing menu" + "range": "ExperimentalSpecimenRoleTypeInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", - "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", - "title": "specimen processing details", - "from_schema": "https://example.com/mpox", + "experimental_control_details": { + "name": "experimental_control_details", + "rank": 31, + "slot_group": "Sample collection and processing" + }, + "lineage/clade name": { + "name": "lineage/clade name", + "rank": 32, + "slot_group": "Lineage and Variant information" + }, + "lineage/clade analysis software name": { + "name": "lineage/clade analysis software name", + "rank": 33, + "slot_group": "Lineage and Variant information" + }, + "lineage/clade analysis software version": { + "name": "lineage/clade analysis software version", + "rank": 34, + "slot_group": "Lineage and Variant information" + }, + "host_common_name": { + "name": "host_common_name", "rank": 35, - "slot_uri": "GENEPIO:0100311", - "alias": "specimen_processing_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "host (common name)": { - "name": "host (common name)", - "description": "The commonly used name of the host.", - "title": "host (common name)", - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_ANIMAL_TYPE" - ], - "rank": 36, - "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information", "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "examples": [ { - "value": "Homo sapiens" + "value": "Homo sapiens [NCBITaxon:9606]" } ], - "from_schema": "https://example.com/mpox", - "rank": 37, - "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 36, "slot_group": "Host Information", - "required": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health state": { - "name": "host health state", - "description": "Health status of the host at the time of sample collection.", - "title": "host health state", + "host_health_state": { + "name": "host_health_state", "examples": [ { - "value": "Asymptomatic" + "value": "Asymptomatic [NCIT:C3833]" } ], - "from_schema": "https://example.com/mpox", "exact_mappings": [ "GISAID:Patient%20status", - "NML_LIMS:PH_HOST_HEALTH", "BIOSAMPLE:host_health_state" ], - "rank": 38, - "slot_uri": "GENEPIO:0001388", - "alias": "host_health_state", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 37, "slot_group": "Host Information", "any_of": [ { - "range": "host health state menu" + "range": "HostHealthStateInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health status details": { - "name": "host health status details", - "description": "Further details pertaining to the health or disease status of the host at time of collection.", - "title": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "examples": [ { - "value": "Hospitalized" + "value": "Hospitalized [NCIT:C25179]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_HOST_HEALTH_DETAILS" - ], - "rank": 39, - "slot_uri": "GENEPIO:0001389", - "alias": "host_health_status_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 38, "slot_group": "Host Information", "any_of": [ { - "range": "host health status details menu" + "range": "HostHealthStatusDetailsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health outcome": { - "name": "host health outcome", - "description": "Disease outcome in the host.", - "title": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "examples": [ { - "value": "Recovered" + "value": "Recovered [NCIT:C49498]" } ], - "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_HOST_HEALTH_OUTCOME", "BIOSAMPLE:host_health_outcome" ], - "rank": 40, - "slot_uri": "GENEPIO:0001389", - "alias": "host_health_outcome", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 39, "slot_group": "Host Information", "any_of": [ { - "range": "host health outcome menu" + "range": "HostHealthOutcomeInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", - "description": "The name of the disease experienced by the host.", - "title": "host disease", + "host_disease": { + "name": "host_disease", "comments": [ - "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." ], "examples": [ { - "value": "Mpox" + "value": "Mpox [MONDO:0002594]" } ], - "from_schema": "https://example.com/mpox", - "rank": 41, - "slot_uri": "GENEPIO:0001391", - "alias": "host_disease", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 40, "slot_group": "Host Information", - "required": true, "any_of": [ { - "range": "host disease menu" + "range": "HostDiseaseInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age": { - "name": "host age", - "description": "Age of host at the time of sampling.", - "title": "host age", - "from_schema": "https://example.com/mpox", + "host_subject_id": { + "name": "host_subject_id", + "rank": 41, + "slot_group": "Host Information" + }, + "host_age": { + "name": "host_age", "exact_mappings": [ "GISAID:Patient%20age", - "NML_LIMS:PH_AGE", "BIOSAMPLE:host_age" ], "rank": 42, - "slot_uri": "GENEPIO:0001392", - "alias": "host_age", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information", - "required": true, - "minimum_value": "0", - "maximum_value": "130" + "recommended": true }, - "host age unit": { - "name": "host age unit", - "description": "The units used to measure the host's age.", - "title": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "examples": [ { - "value": "year" + "value": "year [UO:0000036]" } ], - "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_AGE_UNIT", "BIOSAMPLE:host_age_unit" ], "rank": 43, - "slot_uri": "GENEPIO:0001393", - "alias": "host_age_unit", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information", - "required": true, + "recommended": true, "any_of": [ { - "range": "host age unit menu" + "range": "HostAgeUnitInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", - "description": "The age category of the host at the time of sampling.", - "title": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "examples": [ { - "value": "50 - 59" + "value": "50 - 59 [GENEPIO:0100054]" } ], - "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:PH_AGE_GROUP", "BIOSAMPLE:host_age_bin" ], "rank": 44, - "slot_uri": "GENEPIO:0001394", - "alias": "host_age_bin", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information", - "required": true, + "recommended": true, "any_of": [ { - "range": "host age bin menu" + "range": "HostAgeBinInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host gender": { - "name": "host gender", - "description": "The gender of the host at the time of sample collection.", - "title": "host gender", + "host_gender": { + "name": "host_gender", "examples": [ { - "value": "Male" + "value": "Male [NCIT:C46109]" } ], - "from_schema": "https://example.com/mpox", "exact_mappings": [ "GISAID:Gender", - "NML_LIMS:VD_SEX", "BIOSAMPLE:host_sex" ], "rank": 45, - "slot_uri": "GENEPIO:0001395", - "alias": "host_gender", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information", - "required": true, - "structured_pattern": { - "syntax": "{Title_Case}", - "interpolated": true, - "partial_match": false - }, + "recommended": true, "any_of": [ { - "range": "host gender menu" + "range": "HostGenderInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", - "description": "The country of residence of the host.", - "title": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "examples": [ { - "value": "Canada" + "value": "Canada [GAZ:00002560]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_HOST_COUNTRY" - ], "rank": 46, - "slot_uri": "GENEPIO:0001396", - "alias": "host_residence_geo_loc_name_(country)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", - "description": "The state/province/territory of residence of the host.", - "title": "host residence geo_loc name (state/province/territory)", - "from_schema": "https://example.com/mpox", + "symptom_onset_date": { + "name": "symptom_onset_date", "rank": 47, - "slot_uri": "GENEPIO:0001397", - "alias": "host_residence_geo_loc_name_(state/province/territory)", - "owner": "Mpox", - "domain_of": [ - "Mpox" - ], - "slot_group": "Host Information" - }, - "symptom onset date": { - "name": "symptom onset date", - "description": "The date on which the symptoms began or were first noted.", - "title": "symptom onset date", - "from_schema": "https://example.com/mpox", - "rank": 48, - "slot_uri": "GENEPIO:0001399", - "alias": "symptom_onset_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host Information" }, - "signs and symptoms": { - "name": "signs and symptoms", - "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", - "title": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "examples": [ { - "value": "Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain)" + "value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:HC_SYMPTOMS" - ], - "rank": 49, - "slot_uri": "GENEPIO:0001400", - "multivalued": true, - "alias": "signs_and_symptoms", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 48, "slot_group": "Host Information", "any_of": [ { - "range": "signs and symptoms menu" + "range": "SignsAndSymptomsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", - "title": "pre-existing conditions and risk factors", - "from_schema": "https://example.com/mpox", - "rank": 50, - "slot_uri": "GENEPIO:0001401", - "multivalued": true, - "alias": "pre_existing_conditions_and_risk_factors", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "rank": 49, "slot_group": "Host Information", "any_of": [ { - "range": "pre-existing conditions and risk factors menu" + "range": "PreExistingConditionsAndRiskFactorsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, "complications": { "name": "complications", - "description": "Patient medical complications that are believed to have occurred as a result of host disease.", - "title": "complications", "examples": [ { - "value": "Delayed wound healing (lesion healing)" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:complications" - ], - "rank": 51, - "slot_uri": "GENEPIO:0001402", - "multivalued": true, - "alias": "complications", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host Information", - "any_of": [ - { - "range": "complications menu" - }, - { - "range": "null value menu" - } - ] - }, - "antiviral therapy": { - "name": "antiviral therapy", - "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", - "title": "antiviral therapy", - "from_schema": "https://example.com/mpox", - "rank": 52, - "slot_uri": "GENEPIO:0100580", - "alias": "antiviral_therapy", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "value": "Delayed wound healing (lesion healing) [MP:0002908]" + } ], + "rank": 50, "slot_group": "Host Information", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "ComplicationsInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host vaccination status": { - "name": "host vaccination status", - "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", - "title": "host vaccination status", + "antiviral_therapy": { + "name": "antiviral_therapy", + "rank": 51, + "slot_group": "Host Information" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", "examples": [ { - "value": "Not Vaccinated" + "value": "Not Vaccinated [GENEPIO:0100102]" } ], - "from_schema": "https://example.com/mpox", - "rank": 53, - "slot_uri": "GENEPIO:0001404", - "alias": "host_vaccination_status", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 52, "slot_group": "Host vaccination information", "any_of": [ { - "range": "host vaccination status menu" + "range": "HostVaccinationStatusInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", - "description": "The number of doses of the vaccine recived by the host.", - "title": "number of vaccine doses received", - "from_schema": "https://example.com/mpox", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "rank": 53, + "slot_group": "Host vaccination information" + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "rank": 54, - "slot_uri": "GENEPIO:0001406", - "alias": "number_of_vaccine_doses_received", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host vaccination information", - "range": "integer" + "slot_group": "Host vaccination information" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", - "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", - "title": "vaccination dose 1 vaccine name", - "from_schema": "https://example.com/mpox", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "rank": 55, - "slot_uri": "GENEPIO:0100313", - "alias": "vaccination_dose_1_vaccine_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host vaccination information" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", - "description": "The date the first dose of a vaccine was administered.", - "title": "vaccination dose 1 vaccination date", - "from_schema": "https://example.com/mpox", + "vaccination_history": { + "name": "vaccination_history", "rank": 56, - "slot_uri": "GENEPIO:0100314", - "alias": "vaccination_dose_1_vaccination_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host vaccination information" }, - "vaccination history": { - "name": "vaccination history", - "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", - "title": "vaccination history", - "from_schema": "https://example.com/mpox", - "rank": 57, - "slot_uri": "GENEPIO:0100321", - "alias": "vaccination_history", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host vaccination information", - "range": "WhitespaceMinimizedString" - }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", - "description": "The country where the host was likely exposed to the causative agent of the illness.", - "title": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "examples": [ { - "value": "Canada" + "value": "Canada [GAZ:00002560]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_EXPOSURE_COUNTRY" - ], - "rank": 58, - "slot_uri": "GENEPIO:0001410", - "alias": "location_of_exposure_geo_loc_name_(country)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 57, "slot_group": "Host exposure information", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", - "description": "The name of the city that was the destination of most recent travel.", - "title": "destination of most recent travel (city)", - "from_schema": "https://example.com/mpox", - "rank": 59, - "slot_uri": "GENEPIO:0001411", - "alias": "destination_of_most_recent_travel_(city)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host exposure information", - "range": "WhitespaceMinimizedString" + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", + "rank": 58, + "slot_group": "Host exposure information" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", - "description": "The name of the state/province/territory that was the destination of most recent travel.", - "title": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "comments": [ - "Select the province name from the pick list provided in the template." - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_TRAVEL" - ], - "rank": 60, - "slot_uri": "GENEPIO:0001412", - "alias": "destination_of_most_recent_travel_(state/province/territory)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" ], - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "geo_loc_name (state/province/territory) menu" - }, + "examples": [ { - "range": "null value menu" + "value": "California" } - ] + ], + "rank": 59, + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", - "description": "The name of the country that was the destination of most recent travel.", - "title": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "examples": [ { - "value": "Canada" + "value": "United Kingdom [GAZ:00002637]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:PH_TRAVEL" - ], - "rank": 61, - "slot_uri": "GENEPIO:0001413", - "alias": "destination_of_most_recent_travel_(country)", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 60, "slot_group": "Host exposure information", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", - "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", - "title": "most recent travel departure date", - "from_schema": "https://example.com/mpox", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", + "rank": 61, + "slot_group": "Host exposure information" + }, + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "rank": 62, - "slot_uri": "GENEPIO:0001414", - "alias": "most_recent_travel_departure_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host exposure information" }, - "most recent travel return date": { - "name": "most recent travel return date", - "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", - "title": "most recent travel return date", - "from_schema": "https://example.com/mpox", + "travel_history": { + "name": "travel_history", "rank": 63, - "slot_uri": "GENEPIO:0001415", - "alias": "most_recent_travel_return_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], "slot_group": "Host exposure information" }, - "travel history": { - "name": "travel history", - "description": "Travel history in last six months.", - "title": "travel history", - "from_schema": "https://example.com/mpox", - "rank": 64, - "slot_uri": "GENEPIO:0001416", - "alias": "travel_history", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host exposure information", - "range": "WhitespaceMinimizedString" - }, - "exposure event": { - "name": "exposure event", - "description": "Event leading to exposure.", - "title": "exposure event", + "exposure_event": { + "name": "exposure_event", "examples": [ { - "value": "Party" + "value": "Party [PCO:0000035]" } ], - "from_schema": "https://example.com/mpox", - "rank": 65, - "slot_uri": "GENEPIO:0001417", - "alias": "exposure_event", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 64, "slot_group": "Host exposure information", "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure contact level": { - "name": "exposure contact level", - "description": "The exposure transmission contact type.", - "title": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "examples": [ { - "value": "Contact with infected individual" + "value": "Contact with infected individual [GENEPIO:0100357]" } ], - "from_schema": "https://example.com/mpox", - "rank": 66, - "slot_uri": "GENEPIO:0001418", - "alias": "exposure_contact_level", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 65, "slot_group": "Host exposure information", "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host role": { - "name": "host role", - "description": "The role of the host in relation to the exposure setting.", - "title": "host role", + "host_role": { + "name": "host_role", "examples": [ { - "value": "Acquaintance of case" + "value": "Acquaintance of case [GENEPIO:0100266]" } ], - "from_schema": "https://example.com/mpox", - "rank": 67, - "slot_uri": "GENEPIO:0001419", - "multivalued": true, - "alias": "host_role", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 66, "slot_group": "Host exposure information", - "range": "host role menu" + "range": "HostRoleInternationalMenu" }, - "exposure setting": { - "name": "exposure setting", - "description": "The setting leading to exposure.", - "title": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "examples": [ { - "value": "Healthcare Setting" + "value": "Healthcare Setting [GENEPIO:0100201]" } ], - "from_schema": "https://example.com/mpox", - "rank": 68, - "slot_uri": "GENEPIO:0001428", - "multivalued": true, - "alias": "exposure_setting", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 67, "slot_group": "Host exposure information", - "range": "exposure setting menu" + "range": "ExposureSettingInternationalMenu" }, - "exposure details": { - "name": "exposure details", - "description": "Additional host exposure information.", - "title": "exposure details", - "from_schema": "https://example.com/mpox", - "rank": 69, - "slot_uri": "GENEPIO:0001431", - "alias": "exposure_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host exposure information", - "range": "WhitespaceMinimizedString" + "exposure_details": { + "name": "exposure_details", + "rank": 68, + "slot_group": "Host exposure information" }, - "prior Mpox infection": { - "name": "prior Mpox infection", - "description": "The absence or presence of a prior Mpox infection.", - "title": "prior Mpox infection", + "prior_mpox_infection": { + "name": "prior_mpox_infection", "examples": [ - { - "value": "Prior infection" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:prior%20Monkeypox%20infection" - ], - "rank": 70, - "slot_uri": "GENEPIO:0100532", - "alias": "prior_Mpox_infection", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + { + "value": "Prior infection [GENEPIO:0100037]" + } ], + "rank": 69, "slot_group": "Host reinfection information", "any_of": [ { - "range": "prior Monkeypox infection menu" + "range": "PriorMonkeypoxInfectionInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior Mpox infection date": { - "name": "prior Mpox infection date", - "description": "The date of diagnosis of the prior Mpox infection.", - "title": "prior Mpox infection date", - "from_schema": "https://example.com/mpox", - "rank": 71, - "slot_uri": "GENEPIO:0100533", - "alias": "prior_Mpox_infection_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "prior_mpox_infection_date": { + "name": "prior_mpox_infection_date", + "rank": 70, "slot_group": "Host reinfection information" }, - "prior Mpox antiviral treatment": { - "name": "prior Mpox antiviral treatment", - "description": "The absence or presence of antiviral treatment for a prior Mpox infection.", - "title": "prior Mpox antiviral treatment", + "prior_mpox_antiviral_treatment": { + "name": "prior_mpox_antiviral_treatment", "examples": [ { - "value": "Prior antiviral treatment" + "value": "Prior antiviral treatment [GENEPIO:0100037]" } ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:prior%20Monkeypox%20antiviral%20treatment" - ], - "rank": 72, - "slot_uri": "GENEPIO:0100534", - "alias": "prior_Mpox_antiviral_treatment", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "rank": 71, "slot_group": "Host reinfection information", "any_of": [ { - "range": "prior Monkeypox antiviral treatment menu" + "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior antiviral treatment during prior Mpox infection": { - "name": "prior antiviral treatment during prior Mpox infection", - "description": "Antiviral treatment for any infection during the prior Mpox infection period.", - "title": "prior antiviral treatment during prior Mpox infection", - "from_schema": "https://example.com/mpox", + "prior_antiviral_treatment_during_prior_mpox_infection": { + "name": "prior_antiviral_treatment_during_prior_mpox_infection", + "rank": 72, + "slot_group": "Host reinfection information" + }, + "sequencing_project_name": { + "name": "sequencing_project_name", "rank": 73, - "slot_uri": "GENEPIO:0100535", - "alias": "prior_antiviral_treatment_during_prior_Mpox_infection", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Host reinfection information", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information" }, - "purpose of sequencing": { - "name": "purpose of sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose of sequencing", - "examples": [ - { - "value": "Specimens attributed to individuals with no known intimate contacts to positive cases", - "description": "Select \"Targeted surveillance (non-random sampling)\" if the specimen fits any of the following criteria" - }, + "sequenced_by": { + "name": "sequenced_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "exact_mappings": [ + "BIOSAMPLE:sequenced_by" + ], + "rank": 74, + "slot_group": "Sequencing", + "any_of": [ { - "value": "Specimens attributed to youth/minors <18 yrs." + "range": "WhitespaceMinimizedString" }, { - "value": "Specimens attributed to vulnerable persons living in transient shelters or congregant settings" - }, + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "rank": 75, + "slot_group": "Sequence information" + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "rank": 76, + "slot_group": "Sequencing" + }, + "sequenced_by_contact_address": { + "name": "sequenced_by_contact_address", + "rank": 77, + "slot_group": "Sequencing" + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "BIOSAMPLE:sequence_submitted_by" + ], + "rank": 78, + "slot_group": "Sequencing", + "any_of": [ { - "value": "Specimens attributed to individuals self-identifying as “female”" + "range": "WhitespaceMinimizedString" }, { - "value": "Domestic travel surveillance", - "description": "For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options" - }, + "range": "NullValueMenu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "rank": 79, + "slot_group": "Sequencing" + }, + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", + "rank": 80, + "slot_group": "Sequencing" + }, + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "examples": [ { - "value": "International travel surveillance" - }, + "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" + } + ], + "rank": 81, + "slot_group": "Sequencing", + "any_of": [ { - "value": "Travel-associated surveillance" + "range": "PurposeOfSequencingInternationalMenu" }, { - "value": "Cluster/Outbreak investigation", - "description": "For specimens targeted for sequencing as part of an outbreak investigation, please select" - }, + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "rank": 82, + "slot_group": "Sequencing" + }, + "sequencing_date": { + "name": "sequencing_date", + "rank": 83, + "slot_group": "Sequencing" + }, + "library_id": { + "name": "library_id", + "rank": 84, + "slot_group": "Sequencing" + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "rank": 85, + "slot_group": "Sequencing" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "examples": [ { - "value": "Baseline surveillance (random sampling).", - "description": "In all other cases use" + "value": "whole genome sequencing assay [OBI:0002117]" } ], - "from_schema": "https://example.com/mpox", - "rank": 74, - "slot_uri": "GENEPIO:0001445", - "multivalued": true, - "alias": "purpose_of_sequencing", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "rank": 86, + "slot_group": "Sequence information", + "range": "SequencingAssayTypeInternationalMenu" + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "examples": [ + { + "value": "Oxford Nanopore MinION [GENEPIO:0100142]" + } ], + "rank": 87, "slot_group": "Sequencing", - "required": true, "any_of": [ { - "range": "purpose of sequencing menu" + "range": "SequencingInstrumentInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "description": "The description of why the sample was sequenced providing specific details.", - "title": "purpose of sequencing details", - "from_schema": "https://example.com/mpox", - "rank": 75, - "slot_uri": "GENEPIO:0001446", - "alias": "purpose_of_sequencing_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "rank": 88, + "slot_group": "Sequence information" + }, + "sequencing_protocol__": { + "name": "sequencing_protocol__", + "rank": 89, + "slot_group": "Sequencing" + }, + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "rank": 90, + "slot_group": "Sequencing" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "rank": 91, + "slot_group": "Sequencing" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "rank": 92, "slot_group": "Sequencing", - "required": true + "any_of": [ + { + "range": "GenomicTargetEnrichmentMethodInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "rank": 93, + "slot_group": "Sequencing" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "rank": 94, + "slot_group": "Sequencing" + }, + "amplicon_size": { + "name": "amplicon_size", + "rank": 95, + "slot_group": "Sequencing" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "rank": 96, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "rank": 97, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "rank": 98, + "slot_group": "Bioinformatics and QC metrics", + "range": "QualityControlDeterminationInternationalMenu" + }, + "quality_control_issues": { + "name": "quality_control_issues", + "rank": 99, + "slot_group": "Bioinformatics and QC metrics", + "range": "QualityControlIssuesInternationalMenu" + }, + "quality_control_details": { + "name": "quality_control_details", + "rank": 100, + "slot_group": "Bioinformatics and QC metrics" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "rank": 101, + "slot_group": "Bioinformatics and QC metrics" + }, + "dehosting_method": { + "name": "dehosting_method", + "rank": 102, + "slot_group": "Bioinformatics and QC metrics" + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 103, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "rank": 104, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "rank": 105, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "rank": 106, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "rank": 107, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "rank": 108, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "rank": 109, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "rank": 110, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "rank": 111, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "rank": 112, + "slot_group": "Bioinformatics and QC metrics" + }, + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "rank": 113, + "slot_group": "Bioinformatics and QC metrics" + }, + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "rank": 114, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5_filename": { + "name": "fast5_filename", + "rank": 115, + "slot_group": "Bioinformatics and QC metrics" + }, + "fast5_filepath": { + "name": "fast5_filepath", + "rank": 116, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "rank": 117, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "rank": 118, + "slot_group": "Bioinformatics and QC metrics" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "rank": 119, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "rank": 120, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "rank": 121, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "rank": 122, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "rank": 123, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "rank": 124, + "slot_group": "Bioinformatics and QC metrics" }, - "sequencing date": { - "name": "sequencing date", - "description": "The date the sample was sequenced.", - "title": "sequencing date", - "from_schema": "https://example.com/mpox", - "rank": 76, - "slot_uri": "GENEPIO:0001447", - "alias": "sequencing_date", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "required": true + "number_of_contigs": { + "name": "number_of_contigs", + "rank": 125, + "slot_group": "Bioinformatics and QC metrics" }, - "library ID": { - "name": "library ID", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library ID", - "from_schema": "https://example.com/mpox", - "rank": 77, - "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString", - "recommended": true + "genome_completeness": { + "name": "genome_completeness", + "rank": 126, + "slot_group": "Bioinformatics and QC metrics" }, - "amplicon size": { - "name": "amplicon size", - "description": "The length of the amplicon generated by PCR amplification.", - "title": "amplicon size", - "from_schema": "https://example.com/mpox", - "rank": 78, - "slot_uri": "GENEPIO:0001449", - "alias": "amplicon_size", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "n50": { + "name": "n50", + "rank": 127, + "slot_group": "Bioinformatics and QC metrics" }, - "library preparation kit": { - "name": "library preparation kit", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "title": "library preparation kit", - "from_schema": "https://example.com/mpox", - "rank": 79, - "slot_uri": "GENEPIO:0001450", - "alias": "library_preparation_kit", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "rank": 128, + "slot_group": "Bioinformatics and QC metrics" }, - "sequencing instrument": { - "name": "sequencing instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing instrument", - "examples": [ - { - "value": "Oxford Nanopore MinION" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 80, - "slot_uri": "GENEPIO:0001452", - "multivalued": true, - "alias": "sequencing_instrument", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "required": true, - "any_of": [ - { - "range": "sequencing instrument menu" - }, - { - "range": "null value menu" - } - ] + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "rank": 129, + "slot_group": "Bioinformatics and QC metrics" }, - "sequencing protocol": { - "name": "sequencing protocol", - "description": "The protocol used to generate the sequence.", - "title": "sequencing protocol", - "from_schema": "https://example.com/mpox", - "rank": 81, - "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "reference_genome_accession": { + "name": "reference_genome_accession", + "rank": 130, + "slot_group": "Bioinformatics and QC metrics" }, - "sequencing kit number": { - "name": "sequencing kit number", - "description": "The manufacturer's kit number.", - "title": "sequencing kit number", - "from_schema": "https://example.com/mpox", - "rank": 82, - "slot_uri": "GENEPIO:0001455", - "alias": "sequencing_kit_number", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 131, + "slot_group": "Bioinformatics and QC metrics" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "title": "amplicon pcr primer scheme", - "from_schema": "https://example.com/mpox", - "rank": 83, - "slot_uri": "GENEPIO:0001456", - "alias": "amplicon_pcr_primer_scheme", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "rank": 132, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "rank": 133, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "rank": 134, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "rank": 135, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "rank": 136, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "rank": 137, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "rank": 138, + "slot_group": "Taxonomic identification information" + }, + "assay_target_name_1": { + "name": "assay_target_name_1", + "rank": 139, + "slot_group": "Pathogen diagnostic testing" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "title": "raw sequence data processing method", - "from_schema": "https://example.com/mpox", - "rank": 84, - "slot_uri": "GENEPIO:0001458", - "alias": "raw_sequence_data_processing_method", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "required": true + "assay_target_details_1": { + "name": "assay_target_details_1", + "rank": 140, + "slot_group": "Pathogen diagnostic testing" }, - "dehosting method": { - "name": "dehosting method", - "description": "The method used to remove host reads from the pathogen sequence.", - "title": "dehosting method", - "from_schema": "https://example.com/mpox", - "rank": 85, - "slot_uri": "GENEPIO:0001459", - "alias": "dehosting_method", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "required": true + "gene_symbol_1": { + "name": "gene_symbol_1", + "rank": 141, + "slot_group": "Pathogen diagnostic testing" }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "The name of the consensus sequence.", - "title": "consensus sequence name", - "from_schema": "https://example.com/mpox", - "rank": 86, - "slot_uri": "GENEPIO:0001460", - "alias": "consensus_sequence_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", + "rank": 142, + "slot_group": "Pathogen diagnostic testing" }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "The name of the consensus sequence file.", - "title": "consensus sequence filename", - "from_schema": "https://example.com/mpox", - "rank": 87, - "slot_uri": "GENEPIO:0001461", - "alias": "consensus_sequence_filename", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", + "rank": 143, + "slot_group": "Pathogen diagnostic testing" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "The filepath of the consensus sequence file.", - "title": "consensus sequence filepath", - "from_schema": "https://example.com/mpox", - "rank": 88, - "slot_uri": "GENEPIO:0001462", - "alias": "consensus_sequence_filepath", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "assay_target_name_2": { + "name": "assay_target_name_2", + "rank": 144, + "slot_group": "Pathogen diagnostic testing" }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "The name of software used to generate the consensus sequence.", - "title": "consensus sequence software name", - "from_schema": "https://example.com/mpox", - "rank": 89, - "slot_uri": "GENEPIO:0001463", - "alias": "consensus_sequence_software_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "required": true + "assay_target_details_2": { + "name": "assay_target_details_2", + "rank": 145, + "slot_group": "Pathogen diagnostic testing" }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "The version of the software used to generate the consensus sequence.", - "title": "consensus sequence software version", - "from_schema": "https://example.com/mpox", - "rank": 90, - "slot_uri": "GENEPIO:0001469", - "alias": "consensus_sequence_software_version", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "required": true + "gene_symbol_2": { + "name": "gene_symbol_2", + "rank": 146, + "slot_group": "Pathogen diagnostic testing" }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth of coverage value", - "from_schema": "https://example.com/mpox", - "rank": 91, - "slot_uri": "GENEPIO:0001472", - "alias": "breadth_of_coverage_value", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", + "rank": 147, + "slot_group": "Pathogen diagnostic testing" }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", - "from_schema": "https://example.com/mpox", - "rank": 92, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", + "rank": 148, + "slot_group": "Pathogen diagnostic testing" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth of coverage threshold", - "from_schema": "https://example.com/mpox", - "rank": 93, - "slot_uri": "GENEPIO:0001475", - "alias": "depth_of_coverage_threshold", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "assay_target_name_3": { + "name": "assay_target_name_3", + "rank": 149, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details_3": { + "name": "assay_target_details_3", + "rank": 150, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_3": { + "name": "gene_symbol_3", + "rank": 151, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", + "rank": 152, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", + "rank": 153, + "slot_group": "Pathogen diagnostic testing" + }, + "authors": { + "name": "authors", + "rank": 154, + "slot_group": "Contributor acknowledgement" + }, + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "rank": 155, + "slot_group": "Contributor acknowledgement" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1 fastq filename", - "from_schema": "https://example.com/mpox", - "rank": 94, - "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "examples": [ + { + "value": "prov_mpox_1234" + } ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2 fastq filename", "from_schema": "https://example.com/mpox", - "rank": 95, - "slot_uri": "GENEPIO:0001477", - "alias": "r2_fastq_filename", - "owner": "Mpox", + "exact_mappings": [ + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", + "NML_LIMS:TEXT_ID", + "BIOSAMPLE:sample_name", + "VirusSeq_Portal:specimen%20collector%20sample%20ID" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", - "recommended": true + "required": true }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "The location of the r1 FASTQ file within a user's file system.", - "title": "r1 fastq filepath", - "from_schema": "https://example.com/mpox", - "rank": 96, - "slot_uri": "GENEPIO:0001478", - "alias": "r1_fastq_filepath", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "The location of the r2 FASTQ file within a user's file system.", - "title": "r2 fastq filepath", - "from_schema": "https://example.com/mpox", - "rank": 97, - "slot_uri": "GENEPIO:0001479", - "alias": "r2_fastq_filepath", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "examples": [ + { + "value": "ABCD1234" + } ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "fast5 filename": { - "name": "fast5 filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5 filename", "from_schema": "https://example.com/mpox", - "rank": 98, - "slot_uri": "GENEPIO:0001480", - "alias": "fast5_filename", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "exact_mappings": [ + "NML_LIMS:PH_CASE_ID" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "The location of the FAST5 file within a user's file system.", - "title": "fast5 filepath", - "from_schema": "https://example.com/mpox", - "rank": 99, - "slot_uri": "GENEPIO:0001481", - "alias": "fast5_filepath", - "owner": "Mpox", + "rank": 2, + "slot_uri": "GENEPIO:0100281", + "alias": "case_id", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "The number of total base pairs generated by the sequencing process.", - "title": "number of base pairs sequenced", + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", + "title": "bioproject accession", + "comments": [ + "Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects." + ], + "examples": [ + { + "value": "PRJNA12345" + } + ], "from_schema": "https://example.com/mpox", - "rank": 100, - "slot_uri": "GENEPIO:0001482", - "alias": "number_of_base_pairs_sequenced", - "owner": "Mpox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS%20-%20BioProject%20Accession" + ], + "rank": 3, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer", - "minimum_value": "0" + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Size of the reconstructed genome described as the number of base pairs.", - "title": "consensus genome length", + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC archives.", + "title": "biosample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/mpox", - "rank": 101, - "slot_uri": "GENEPIO:0001483", - "alias": "consensus_genome_length", - "owner": "Mpox", + "exact_mappings": [ + "NML_LIMS:SUBMISSIONS%20-%20BioSample%20Accession" + ], + "rank": 4, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer", - "minimum_value": "0" + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } }, - "reference genome accession": { - "name": "reference genome accession", - "description": "A persistent, unique identifier of a genome database entry.", - "title": "reference genome accession", + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "SRR123456, ERR123456, DRR123456, CRR123456" + } + ], "from_schema": "https://example.com/mpox", - "rank": 102, - "slot_uri": "GENEPIO:0001485", - "alias": "reference_genome_accession", - "owner": "Mpox", + "exact_mappings": [ + "CNPHI:SRA%20Accession", + "NML_LIMS:PH_SRA_ACCESSION" + ], + "rank": 5, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "A description of the overall bioinformatics strategy used.", - "title": "bioinformatics protocol", + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], "from_schema": "https://example.com/mpox", - "rank": 103, - "slot_uri": "GENEPIO:0001489", - "alias": "bioinformatics_protocol", - "owner": "Mpox", + "exact_mappings": [ + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString", - "required": true + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } }, - "gene name 1": { - "name": "gene name 1", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 1", + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "description": "Identifier of the specific isolate.", + "title": "GISAID virus name", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put \"UN\" for \"Unknown\"." + ], + "examples": [ + { + "value": "hMpxV/Canada/UN-NML-12345/2022" + } ], "from_schema": "https://example.com/mpox", - "rank": 104, - "slot_uri": "GENEPIO:0001507", - "alias": "gene_name_1", - "owner": "Mpox", + "exact_mappings": [ + "GISAID:Virus%20name", + "BIOSAMPLE:GISAID_virus_name" + ], + "rank": 7, + "slot_uri": "GENEPIO:0100282", + "alias": "gisaid_virus_name", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing", - "any_of": [ - { - "range": "gene name menu" - }, + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString" + }, + "gisaid_accession": { + "name": "gisaid_accession", + "description": "The GISAID accession number assigned to the sequence.", + "title": "GISAID accession", + "comments": [ + "Store the accession returned from the GISAID submission." + ], + "examples": [ { - "range": "null value menu" + "value": "EPI_ISL_436489" } - ] - }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 1", + ], "from_schema": "https://example.com/mpox", - "rank": 105, - "slot_uri": "GENEPIO:0001509", - "alias": "diagnostic_pcr_Ct_value_1", - "owner": "Mpox", + "exact_mappings": [ + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession", + "BIOSAMPLE:GISAID_accession", + "VirusSeq_Portal:GISAID%20accession" + ], + "rank": 8, + "slot_uri": "GENEPIO:0001147", + "alias": "gisaid_accession", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } }, - "gene name 2": { - "name": "gene name 2", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 2", + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the agency that collected the original sample.", + "title": "sample collected by", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." + "The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)." + ], + "examples": [ + { + "value": "BC Centre for Disease Control" + } ], "from_schema": "https://example.com/mpox", - "rank": 106, - "slot_uri": "GENEPIO:0001510", - "alias": "gene_name_2", - "owner": "Mpox", + "exact_mappings": [ + "GISAID:Originating%20lab", + "BIOSAMPLE:collected_by" + ], + "rank": 9, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing", + "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "gene name menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 2", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/mpox", - "rank": 107, - "slot_uri": "GENEPIO:0001512", - "alias": "diagnostic_pcr_Ct_value_2", - "owner": "Mpox", + "exact_mappings": [ + "NML_LIMS:sample%20collector%20contact%20email" + ], + "rank": 10, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" }, - "gene name 3": { - "name": "gene name 3", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 3", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", + "description": "The mailing address of the agency submitting the sample.", + "title": "sample collector contact address", "comments": [ - "Select the name of the gene used for the diagnostic PCR from the standardized pick list." - ], - "from_schema": "https://example.com/mpox", - "rank": 108, - "slot_uri": "GENEPIO:0001513", - "alias": "gene_name_3", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" ], - "slot_group": "Pathogen diagnostic testing", - "any_of": [ - { - "range": "gene name menu" - }, + "examples": [ { - "range": "null value menu" + "value": "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" } - ] - }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 3", - "from_schema": "https://example.com/mpox", - "rank": 109, - "slot_uri": "GENEPIO:0001515", - "alias": "diagnostic_pcr_Ct_value_3", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" ], - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 4": { - "name": "gene name 4", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 4", "from_schema": "https://example.com/mpox", - "rank": 110, - "slot_uri": "GENEPIO:0100576", - "alias": "gene_name_4", - "owner": "Mpox", - "domain_of": [ - "Mpox" + "exact_mappings": [ + "GISAID:Address", + "NML_LIMS:sample%20collector%20contact%20address" ], - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic pcr Ct value 4": { - "name": "diagnostic pcr Ct value 4", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 4", - "from_schema": "https://example.com/mpox", - "rank": 111, - "slot_uri": "GENEPIO:0100577", - "alias": "diagnostic_pcr_Ct_value_4", - "owner": "Mpox", + "rank": 11, + "slot_uri": "GENEPIO:0001158", + "alias": "sample_collector_contact_address", + "owner": "MpoxInternational", "domain_of": [ - "Mpox" + "Mpox", + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "gene name 5": { - "name": "gene name 5", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 5", - "from_schema": "https://example.com/mpox", - "rank": 112, - "slot_uri": "GENEPIO:0100578", - "alias": "gene_name_5", - "owner": "Mpox", - "domain_of": [ - "Mpox" + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected.", + "title": "sample collection date", + "todos": [ + ">=2019-10-01", + "<={today}" ], - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic pcr Ct value 5": { - "name": "diagnostic pcr Ct value 5", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 5", - "from_schema": "https://example.com/mpox", - "rank": 113, - "slot_uri": "GENEPIO:0100579", - "alias": "diagnostic_pcr_Ct_value_5", - "owner": "Mpox", - "domain_of": [ - "Mpox" + "comments": [ + "Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add \"jitter\" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], - "slot_group": "Pathogen diagnostic testing" - }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", - "from_schema": "https://example.com/mpox", - "rank": 114, - "slot_uri": "GENEPIO:0001517", - "alias": "authors", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "Mpox_international" + "examples": [ + { + "value": "2020-03-16" + } ], - "slot_group": "Contributor acknowledgement", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", "from_schema": "https://example.com/mpox", - "rank": 115, - "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", - "owner": "Mpox", + "exact_mappings": [ + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", + "NML_LIMS:HC_COLLECT_DATE", + "BIOSAMPLE:collection_date", + "VirusSeq_Portal:sample%20collection%20date" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" - ], - "slot_group": "Contributor acknowledgement", - "range": "Provenance" - } - } - }, - "Mpox_international": { - "name": "Mpox_international", - "annotations": { - "version": { - "tag": "version", - "value": "5.3.3" - } - }, - "description": "International specification for Mpox clinical virus biosample data gathering", - "from_schema": "https://example.com/mpox", - "see_also": [ - "templates/mpox/SOP_Mpox_international.pdf" - ], - "is_a": "dh_interface", - "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "rank": 1, - "slot_group": "Database Identifiers" - }, - "case ID": { - "name": "case ID", - "rank": 2, - "slot_group": "Database Identifiers" - }, - "bioproject accession": { - "name": "bioproject accession", - "rank": 3, - "slot_group": "Database Identifiers" - }, - "biosample accession": { - "name": "biosample accession", - "rank": 4, - "slot_group": "Database Identifiers" - }, - "SRA accession": { - "name": "SRA accession", - "rank": 5, - "slot_group": "Database Identifiers" - }, - "GenBank accession": { - "name": "GenBank accession", - "rank": 6, - "slot_group": "Database Identifiers" - }, - "GISAID virus name": { - "name": "GISAID virus name", - "rank": 7, - "slot_group": "Database Identifiers" - }, - "GISAID accession": { - "name": "GISAID accession", - "rank": 8, - "slot_group": "Database Identifiers" - }, - "sample collected by": { - "name": "sample collected by", - "exact_mappings": [ - "GISAID:Originating%20lab", - "BIOSAMPLE:collected_by" + "MpoxInternational" ], - "rank": 9, "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", - "rank": 10, - "slot_group": "Sample collection and processing" - }, - "sample collector contact address": { - "name": "sample collector contact address", - "rank": 11, - "slot_group": "Sample collection and processing" - }, - "sequenced by": { - "name": "sequenced by", + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:sequenced_by" + "NML_LIMS:sample%20received%20date" + ], + "rank": 13, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 12, "slot_group": "Sample collection and processing", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "rank": 13, - "slot_group": "Sample collection and processing" - }, - "sequenced by contact address": { - "name": "sequenced by contact address", - "rank": 14, - "slot_group": "Sample collection and processing" - }, - "sequence submitted by": { - "name": "sequence submitted by", + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country where the sample was collected.", + "title": "geo_loc_name (country)", + "comments": [ + "Provide the country name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Submitting%20lab", - "BIOSAMPLE:sequence_submitted_by" + "GISAID:Location", + "CNPHI:Patient%20Country", + "NML_LIMS:HC_COUNTRY", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28country%29" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 15, "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "rank": 16, - "slot_group": "Sample collection and processing" - }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "rank": 17, - "slot_group": "Sample collection and processing" - }, - "sample collection date": { - "name": "sample collection date", - "rank": 18, - "slot_group": "Sample collection and processing" - }, - "sample received date": { - "name": "sample received date", - "rank": 19, - "slot_group": "Sample collection and processing" - }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory where the sample was collected.", + "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the controlled vocabulary provided." + ], "examples": [ { - "value": "United States of America [GAZ:00002459]" + "value": "Saskatchewan" } ], - "rank": 20, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Patient%20Province", + "NML_LIMS:HC_PROVINCE", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "geo_loc_name (country) international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc latitude", "comments": [ - "Provide the state/province/territory name from the controlled vocabulary provided." + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." ], - "rank": 21, - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, + "examples": [ { - "range": "null value menu" + "value": "38.98 N" } - ] - }, - "geo_loc latitude": { - "name": "geo_loc latitude", - "rank": 22, - "slot_group": "Sample collection and processing" + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "BIOSAMPLE:lat_lon" + ], + "rank": 16, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "geo_loc longitude": { - "name": "geo_loc longitude", - "rank": 23, - "slot_group": "Sample collection and processing" + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "BIOSAMPLE:lat_lon" + ], + "rank": 17, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, "organism": { "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", "comments": [ "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." ], @@ -13298,19 +21344,36 @@ "value": "Mpox virus [NCBITaxon:10244]" } ], - "rank": 24, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Pathogen", + "NML_LIMS:HC_CURRENT_ID", + "BIOSAMPLE:organism", + "VirusSeq_Portal:organism" + ], + "rank": 18, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "organism international menu" + "range": "OrganismInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, "isolate": { "name": "isolate", + "description": "Identifier of the specific isolate.", + "title": "isolate", "comments": [ "This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the \"isolate\" name is propagated throughtout different databases. As such, structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"MpxV/host/country/sampleID/date\"." ], @@ -13319,3125 +21382,3856 @@ "value": "MpxV/human/USA/CA-CDPH-001/2020" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ "BIOSAMPLE:isolate" ], - "rank": 25, + "rank": 19, "slot_uri": "GENEPIO:0001644", - "slot_group": "Sample collection and processing" - }, - "purpose of sampling": { - "name": "purpose of sampling", - "examples": [ - { - "value": "Diagnostic testing [GENEPIO:0100002]" - } + "alias": "isolate", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" ], - "rank": 26, "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { - "range": "purpose of sampling international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "rank": 27, - "slot_group": "Sample collection and processing" - }, - "anatomical material": { - "name": "anatomical material", + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose of sampling", + "comments": [ + "As all samples are taken for diagnostic purposes, \"Diagnostic Testing\" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], "examples": [ { - "value": "Lesion (Pustule) [NCIT:C78582]" + "value": "Diagnostic testing [GENEPIO:0100002]" } ], - "rank": 28, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sampling", + "NML_LIMS:HC_SAMPLE_CATEGORY", + "BIOSAMPLE:purpose_of_sampling", + "VirusSeq_Portal:purpose%20of%20sampling" + ], + "rank": 20, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", - "recommended": true, + "required": true, "any_of": [ { - "range": "anatomical material international menu" + "range": "PurposeOfSamplingInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", + "description": "The description of why the sample was collected, providing specific details.", + "title": "purpose of sampling details", + "comments": [ + "Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value." + ], "examples": [ { - "value": "Genital area [BTO:0003358]" + "value": "Symptomology and history suggested Monkeypox diagnosis." } ], - "rank": 29, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", + "NML_LIMS:PH_SAMPLING_DETAILS", + "BIOSAMPLE:description", + "VirusSeq_Portal:purpose%20of%20sampling%20details" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001200", + "alias": "purpose_of_sampling_details", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", - "recommended": true, + "required": true, "any_of": [ { - "range": "anatomical part international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], "examples": [ { - "value": "Pus [UBERON:0000177]" + "value": "Lesion (Pustule) [NCIT:C78582]" } ], - "rank": 30, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", + "NML_LIMS:PH_ISOLATION_SITE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "VirusSeq_Portal:anatomical%20material" + ], + "rank": 22, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", "recommended": true, + "multivalued": true, "any_of": [ { - "range": "body product international menu" + "range": "AnatomicalMaterialInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", - "rank": 31, - "slot_group": "Sample collection and processing" - }, - "collection device": { - "name": "collection device", + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], "examples": [ { - "value": "Swab [GENEPIO:0100027]" + "value": "Genital area [BTO:0003358]" } ], - "rank": 32, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", + "NML_LIMS:PH_ISOLATION_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "VirusSeq_Portal:anatomical%20part" + ], + "rank": 23, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", "recommended": true, + "multivalued": true, "any_of": [ { - "range": "collection device international menu" + "range": "AnatomicalPartInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], "examples": [ { - "value": "Biopsy [OBI:0002650]" + "value": "Pus [UBERON:0000177]" } ], - "rank": 33, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", + "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "VirusSeq_Portal:body%20product" + ], + "rank": 24, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Sample collection and processing", "recommended": true, + "multivalued": true, "any_of": [ { - "range": "collection method international menu" + "range": "BodyProductInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing": { - "name": "specimen processing", + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", + "title": "environmental material", + "comments": [ + "Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], "examples": [ { - "value": "Specimens pooled [OBI:0600016]" + "value": "Bed linen" } ], - "rank": 34, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_material" + ], + "rank": 25, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "specimen processing international menu" - }, - { - "range": "null value menu" - } - ] - }, - "specimen processing details": { - "name": "specimen processing details", - "rank": 35, - "slot_group": "Sample collection and processing" - }, - "host (common name)": { - "name": "host (common name)", - "rank": 36, - "slot_group": "Host Information", - "any_of": [ - { - "range": "host (common name) international menu" + "range": "EnvironmentalMaterialInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection device", + "comments": [ + "Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], "examples": [ { - "value": "Homo sapiens [NCBITaxon:9606]" + "value": "Swab [GENEPIO:0100027]" } ], - "rank": 37, - "slot_group": "Host Information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", + "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "VirusSeq_Portal:collection%20device" + ], + "rank": 26, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "host (scientific name) international menu" + "range": "CollectionDeviceInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health state": { - "name": "host health state", + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", + "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], "examples": [ { - "value": "Asymptomatic [NCIT:C3833]" + "value": "Biopsy [OBI:0002650]" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Patient%20status", - "BIOSAMPLE:host_health_state" + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", + "NML_LIMS:COLLECTION_METHOD", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "VirusSeq_Portal:collection%20method" ], - "rank": 38, - "slot_group": "Host Information", + "rank": 27, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "host health state international menu" + "range": "CollectionMethodInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health status details": { - "name": "host health status details", + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen processing", + "comments": [ + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." + ], "examples": [ { - "value": "Hospitalized [NCIT:C25179]" + "value": "Specimens pooled [OBI:0600016]" } ], - "rank": 39, - "slot_group": "Host Information", + "from_schema": "https://example.com/mpox", + "rank": 28, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, "any_of": [ { - "range": "host health status details international menu" + "range": "SpecimenProcessingInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health outcome": { - "name": "host health outcome", + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", + "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample." + ], "examples": [ { - "value": "Recovered [NCIT:C49498]" + "value": "5 swabs from different body sites were pooled and further prepared as a single sample during library prep." } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:host_health_outcome" + "NML_LIMS:specimen%20processing%20details" ], - "rank": 40, - "slot_group": "Host Information", - "any_of": [ - { - "range": "host health outcome international menu" - }, - { - "range": "null value menu" - } - ] + "rank": 29, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "host disease": { - "name": "host disease", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental specimen role type", "comments": [ - "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." ], "examples": [ { - "value": "Mpox [MONDO:0002594]" + "value": "Positive experimental control [GENEPIO:0101018]" } ], - "rank": 41, - "slot_group": "Host Information", + "from_schema": "https://example.com/mpox", + "rank": 30, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, "any_of": [ { - "range": "host disease international menu" + "range": "ExperimentalSpecimenRoleTypeInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host subject ID": { - "name": "host subject ID", - "rank": 42, - "slot_group": "Host Information" - }, - "host age": { - "name": "host age", - "exact_mappings": [ - "GISAID:Patient%20age", - "BIOSAMPLE:host_age" + "experimental_control_details": { + "name": "experimental_control_details", + "description": "The details regarding the experimental control contained in the sample.", + "title": "experimental control details", + "comments": [ + "Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor." ], - "rank": 43, - "slot_group": "Host Information", - "recommended": true + "examples": [ + { + "value": "Human coronavirus 229E (HCoV-229E) spiked in sample as process control" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 31, + "slot_uri": "GENEPIO:0100922", + "alias": "experimental_control_details", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "host age unit": { - "name": "host age unit", + "lineage/clade name": { + "name": "lineage/clade name", + "description": "The name of the lineage or clade.", + "title": "lineage/clade name", + "comments": [ + "Provide the lineage/clade name." + ], "examples": [ { - "value": "year [UO:0000036]" + "value": "B.1.1.7" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:host_age_unit" + "NML_LIMS:PH_LINEAGE_CLADE_NAME" ], - "rank": 44, - "slot_group": "Host Information", - "recommended": true, + "rank": 32, + "slot_uri": "GENEPIO:0001500", + "alias": "lineage/clade_name", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Lineage and Variant information", "any_of": [ { - "range": "host age unit international menu" + "range": "LineageCladeNameINternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", + "lineage/clade analysis software name": { + "name": "lineage/clade analysis software name", + "description": "The name of the software used to determine the lineage/clade.", + "title": "lineage/clade analysis software name", + "comments": [ + "Provide the name of the software used to determine the lineage/clade." + ], "examples": [ { - "value": "50 - 59 [GENEPIO:0100054]" + "value": "Pangolin" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:host_age_bin" + "NML_LIMS:PH_LINEAGE_CLADE_SOFTWARE" ], - "rank": 45, - "slot_group": "Host Information", - "recommended": true, + "rank": 33, + "slot_uri": "GENEPIO:0001501", + "alias": "lineage/clade_analysis_software_name", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Lineage and Variant information", "any_of": [ { - "range": "host age bin international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host gender": { - "name": "host gender", + "lineage/clade analysis software version": { + "name": "lineage/clade analysis software version", + "description": "The version of the software used to determine the lineage/clade.", + "title": "lineage/clade analysis software version", + "comments": [ + "Provide the version of the software used ot determine the lineage/clade." + ], "examples": [ { - "value": "Male [NCIT:C46109]" + "value": "2.1.10" } ], + "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Gender", - "BIOSAMPLE:host_sex" + "NML_LIMS:PH_LINEAGE_CLADE_VERSION" ], - "rank": 46, - "slot_group": "Host Information", - "recommended": true, + "rank": 34, + "slot_uri": "GENEPIO:0001502", + "alias": "lineage/clade_analysis_software_version", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Lineage and Variant information", "any_of": [ { - "range": "host gender international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human." + ], "examples": [ { - "value": "Canada [GAZ:00002560]" + "value": "Human" } ], - "rank": 47, + "from_schema": "https://example.com/mpox", + "rank": 35, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Host Information", "any_of": [ { - "range": "geo_loc_name (country) international menu" + "range": "HostCommonNameInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "symptom onset date": { - "name": "symptom onset date", - "rank": 48, - "slot_group": "Host Information" - }, - "signs and symptoms": { - "name": "signs and symptoms", + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], "examples": [ { - "value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]" + "value": "Homo sapiens [NCBITaxon:9606]" } ], - "rank": 49, + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host%20%28scientific%20name%29", + "BIOSAMPLE:host", + "VirusSeq_Portal:host%20%28scientific%20name%29" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Host Information", + "required": true, "any_of": [ { - "range": "signs and symptoms international menu" + "range": "HostScientificNameInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "rank": 50, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host health state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Patient%20status", + "BIOSAMPLE:host_health_state" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Host Information", "any_of": [ { - "range": "pre-existing conditions and risk factors international menu" + "range": "HostHealthStateInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "complications": { - "name": "complications", + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host health status details", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], "examples": [ { - "value": "Delayed wound healing (lesion healing) [MP:0002908]" + "value": "Hospitalized [NCIT:C25179]" } ], - "rank": 51, + "from_schema": "https://example.com/mpox", + "rank": 38, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], "slot_group": "Host Information", "any_of": [ { - "range": "complications international menu" + "range": "HostHealthStatusDetailsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "antiviral therapy": { - "name": "antiviral therapy", - "rank": 52, - "slot_group": "Host Information" - }, - "host vaccination status": { - "name": "host vaccination status", + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host health outcome", + "comments": [ + "If known, select a value from the pick list." + ], "examples": [ { - "value": "Not Vaccinated [GENEPIO:0100102]" + "value": "Recovered [NCIT:C49498]" } ], - "rank": 53, - "slot_group": "Host vaccination information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "BIOSAMPLE:host_health_outcome" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_outcome", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", "any_of": [ { - "range": "host vaccination status international menu" + "range": "HostHealthOutcomeInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", - "rank": 54, - "slot_group": "Host vaccination information" - }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", - "rank": 55, - "slot_group": "Host vaccination information" - }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", - "rank": 56, - "slot_group": "Host vaccination information" - }, - "vaccination history": { - "name": "vaccination history", - "rank": 57, - "slot_group": "Host vaccination information" - }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host disease", + "comments": [ + "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + ], "examples": [ { - "value": "Canada [GAZ:00002560]" + "value": "Mpox [MONDO:0002594]" } ], - "rank": 58, - "slot_group": "Host exposure information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "CNPHI:Host%20Disease", + "NML_LIMS:PH_HOST_DISEASE", + "BIOSAMPLE:host_disease", + "VirusSeq_Portal:host%20disease" + ], + "rank": 40, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "required": true, "any_of": [ { - "range": "geo_loc_name (country) international menu" + "range": "HostDiseaseInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", - "rank": 59, - "slot_group": "Host exposure information" - }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to.", + "title": "host subject ID", "comments": [ - "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + "This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information." ], "examples": [ { - "value": "California" + "value": "12345B-222" } ], - "rank": 60, - "slot_group": "Host exposure information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "BIOSAMPLE:host_subject_id" + ], + "rank": 41, + "slot_uri": "GENEPIO:0001398", + "alias": "host_subject_id", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], "examples": [ { - "value": "United Kingdom [GAZ:00002637]" + "value": "79" } ], - "rank": 61, - "slot_group": "Host exposure information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Patient%20age", + "BIOSAMPLE:host_age" + ], + "rank": 42, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "recommended": true, + "minimum_value": 0, + "maximum_value": 130, "any_of": [ { - "range": "geo_loc_name (country) international menu" + "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", - "rank": 62, - "slot_group": "Host exposure information" - }, - "most recent travel return date": { - "name": "most recent travel return date", - "rank": 63, - "slot_group": "Host exposure information" - }, - "travel history": { - "name": "travel history", - "rank": 64, - "slot_group": "Host exposure information" - }, - "exposure event": { - "name": "exposure event", + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host age unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], "examples": [ { - "value": "Party [PCO:0000035]" + "value": "year [UO:0000036]" } ], - "rank": 65, - "slot_group": "Host exposure information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "BIOSAMPLE:host_age_unit" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "recommended": true, "any_of": [ { - "range": "exposure event international menu" + "range": "HostAgeUnitInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure contact level": { - "name": "exposure contact level", + "host_age_bin": { + "name": "host_age_bin", + "description": "The age category of the host at the time of sampling.", + "title": "host age bin", + "comments": [ + "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative." + ], "examples": [ { - "value": "Contact with infected individual [GENEPIO:0100357]" + "value": "50 - 59 [GENEPIO:0100054]" } ], - "rank": 66, - "slot_group": "Host exposure information", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "BIOSAMPLE:host_age_bin" + ], + "rank": 44, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "recommended": true, "any_of": [ { - "range": "exposure contact level international menu" + "range": "HostAgeBinInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host role": { - "name": "host role", - "examples": [ - { - "value": "Acquaintance of case [GENEPIO:0100266]" - } + "host_gender": { + "name": "host_gender", + "description": "The gender of the host at the time of sample collection.", + "title": "host gender", + "comments": [ + "If known, select a value from the pick list." ], - "rank": 67, - "slot_group": "Host exposure information", - "range": "host role international menu" - }, - "exposure setting": { - "name": "exposure setting", "examples": [ { - "value": "Healthcare Setting [GENEPIO:0100201]" + "value": "Male [NCIT:C46109]" } ], - "rank": 68, - "slot_group": "Host exposure information", - "range": "exposure setting international menu" - }, - "exposure details": { - "name": "exposure details", - "rank": 69, - "slot_group": "Host exposure information" - }, - "prior Mpox infection": { - "name": "prior Mpox infection", - "examples": [ - { - "value": "Prior infection [GENEPIO:0100037]" - } + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Gender", + "BIOSAMPLE:host_sex" ], - "rank": 70, - "slot_group": "Host reinfection information", + "rank": 45, + "slot_uri": "GENEPIO:0001395", + "alias": "host_gender", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "recommended": true, + "structured_pattern": { + "syntax": "{Title_Case}", + "interpolated": true, + "partial_match": false + }, "any_of": [ { - "range": "prior Monkeypox infection international menu" + "range": "HostGenderInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior Mpox infection date": { - "name": "prior Mpox infection date", - "rank": 71, - "slot_group": "Host reinfection information" - }, - "prior Mpox antiviral treatment": { - "name": "prior Mpox antiviral treatment", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", + "description": "The country of residence of the host.", + "title": "host residence geo_loc name (country)", + "comments": [ + "Select the country name from pick list provided in the template." + ], "examples": [ { - "value": "Prior antiviral treatment [GENEPIO:0100037]" + "value": "Canada [GAZ:00002560]" } ], - "rank": 72, - "slot_group": "Host reinfection information", + "from_schema": "https://example.com/mpox", + "rank": 46, + "slot_uri": "GENEPIO:0001396", + "alias": "host_residence_geo_loc_name_country", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", "any_of": [ { - "range": "prior Monkeypox antiviral treatment international menu" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior antiviral treatment during prior Mpox infection": { - "name": "prior antiviral treatment during prior Mpox infection", - "rank": 73, - "slot_group": "Host reinfection information" - }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom onset date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], "examples": [ { - "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" + "value": "2022-05-25" } ], - "rank": 74, - "slot_group": "Sequencing", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:HC_ONSET_DATE" + ], + "rank": 47, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", "any_of": [ { - "range": "purpose of sequencing international menu" + "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "rank": 75, - "slot_group": "Sequencing" - }, - "sequencing date": { - "name": "sequencing date", - "rank": 76, - "slot_group": "Sequencing" - }, - "library ID": { - "name": "library ID", - "rank": 77, - "slot_group": "Sequencing" - }, - "amplicon size": { - "name": "amplicon size", - "rank": 78, - "slot_group": "Sequencing" - }, - "library preparation kit": { - "name": "library preparation kit", - "rank": 79, - "slot_group": "Sequencing" - }, - "sequencing instrument": { - "name": "sequencing instrument", + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs and symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], "examples": [ { - "value": "Oxford Nanopore MinION [GENEPIO:0100142]" + "value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]" } ], - "rank": 80, - "slot_group": "Sequencing", + "from_schema": "https://example.com/mpox", + "rank": 48, + "slot_uri": "GENEPIO:0001400", + "alias": "signs_and_symptoms", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "multivalued": true, "any_of": [ { - "range": "sequencing instrument international menu" + "range": "SignsAndSymptomsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing protocol": { - "name": "sequencing protocol", - "rank": 81, - "slot_group": "Sequencing" - }, - "sequencing kit number": { - "name": "sequencing kit number", - "rank": 82, - "slot_group": "Sequencing" - }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "rank": 83, - "slot_group": "Sequencing" - }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "rank": 84, - "slot_group": "Bioinformatics and QC metrics" - }, - "dehosting method": { - "name": "dehosting method", - "rank": 85, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence name": { - "name": "consensus sequence name", - "rank": 86, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "rank": 87, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "rank": 88, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "rank": 89, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "rank": 90, - "slot_group": "Bioinformatics and QC metrics" - }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "rank": 91, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth of coverage value": { - "name": "depth of coverage value", - "rank": 92, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "rank": 93, - "slot_group": "Bioinformatics and QC metrics" - }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "rank": 94, - "slot_group": "Bioinformatics and QC metrics" - }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "rank": 95, - "slot_group": "Bioinformatics and QC metrics" - }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "rank": 96, - "slot_group": "Bioinformatics and QC metrics" - }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "rank": 97, - "slot_group": "Bioinformatics and QC metrics" - }, - "fast5 filename": { - "name": "fast5 filename", - "rank": 98, - "slot_group": "Bioinformatics and QC metrics" - }, - "fast5 filepath": { - "name": "fast5 filepath", - "rank": 99, - "slot_group": "Bioinformatics and QC metrics" - }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "rank": 100, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus genome length": { - "name": "consensus genome length", - "rank": 101, - "slot_group": "Bioinformatics and QC metrics" - }, - "reference genome accession": { - "name": "reference genome accession", - "rank": 102, - "slot_group": "Bioinformatics and QC metrics" - }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "rank": 103, - "slot_group": "Bioinformatics and QC metrics" - }, - "gene name 1": { - "name": "gene name 1", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing conditions and risk factors", "comments": [ - "Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." ], - "rank": 104, - "slot_group": "Pathogen diagnostic testing", + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:pre-existing%20conditions%20and%20risk%20factors" + ], + "rank": 49, + "slot_uri": "GENEPIO:0001401", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "multivalued": true, "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "PreExistingConditionsAndRiskFactorsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Delayed wound healing (lesion healing) [MP:0002908]" } - ] - }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "rank": 105, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 2": { - "name": "gene name 2", - "comments": [ - "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" ], - "rank": 106, - "slot_group": "Pathogen diagnostic testing", + "from_schema": "https://example.com/mpox", + "rank": 50, + "slot_uri": "GENEPIO:0001402", + "alias": "complications", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host Information", + "multivalued": true, "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "ComplicationsInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "rank": 107, - "slot_group": "Pathogen diagnostic testing" - }, - "gene name 3": { - "name": "gene name 3", + "antiviral_therapy": { + "name": "antiviral_therapy", + "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", + "title": "antiviral therapy", "comments": [ - "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + "Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information." ], - "rank": 108, - "slot_group": "Pathogen diagnostic testing", - "any_of": [ + "examples": [ { - "range": "WhitespaceMinimizedString" + "value": "Tecovirimat used to treat current Monkeypox infection" }, { - "range": "null value menu" + "value": "AZT administered for concurrent HIV infection" } - ] - }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "rank": 109, - "slot_group": "Pathogen diagnostic testing" - }, - "authors": { - "name": "authors", - "rank": 110, - "slot_group": "Contributor acknowledgement" - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 111, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "The user-defined name for the sample.", - "title": "specimen collector sample ID", - "from_schema": "https://example.com/mpox", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "specimen_collector_sample_ID", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "required": true - }, - "case ID": { - "name": "case ID", - "description": "The identifier used to specify an epidemiologically detected case of disease.", - "title": "case ID", "from_schema": "https://example.com/mpox", - "rank": 2, - "slot_uri": "GENEPIO:0100281", - "alias": "case_ID", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:antiviral%20therapy" + ], + "rank": 51, + "slot_uri": "GENEPIO:0100580", + "alias": "antiviral_therapy", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Database Identifiers", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "bioproject accession": { - "name": "bioproject accession", - "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", - "title": "bioproject accession", - "from_schema": "https://example.com/mpox", - "rank": 3, - "slot_uri": "GENEPIO:0001136", - "alias": "bioproject_accession", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host vaccination status", + "comments": [ + "Select the vaccination status of the host from the pick list." ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "biosample accession": { - "name": "biosample accession", - "description": "The identifier assigned to a BioSample in INSDC archives.", - "title": "biosample accession", - "from_schema": "https://example.com/mpox", - "rank": 4, - "slot_uri": "GENEPIO:0001139", - "alias": "biosample_accession", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" + "examples": [ + { + "value": "Not Vaccinated [GENEPIO:0100102]" + } ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", "from_schema": "https://example.com/mpox", - "rank": 5, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "GenBank accession": { - "name": "GenBank accession", - "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", - "title": "GenBank accession", - "from_schema": "https://example.com/mpox", - "rank": 6, - "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", - "owner": "Mpox_international", + "rank": 52, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "HostVaccinationStatusInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "GISAID virus name": { - "name": "GISAID virus name", - "description": "Identifier of the specific isolate.", - "title": "GISAID virus name", - "from_schema": "https://example.com/mpox", - "rank": 7, - "slot_uri": "GENEPIO:0100282", - "alias": "GISAID_virus_name", - "owner": "Mpox_international", - "domain_of": [ - "Mpox_international" + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number of vaccine doses received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "1" + } ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString" - }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The GISAID accession number assigned to the sequence.", - "title": "GISAID accession", "from_schema": "https://example.com/mpox", - "rank": 8, - "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:number%20of%20vaccine%20doses%20received" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Database Identifiers", - "range": "WhitespaceMinimizedString", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Host vaccination information", + "range": "integer" }, - "sample collected by": { - "name": "sample collected by", - "description": "The name of the agency that collected the original sample.", - "title": "sample collected by", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination dose 1 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose." + ], + "examples": [ + { + "value": "IMVAMUNE (Bavarian Nordic)" + } + ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Originating%20lab", - "BIOSAMPLE:collected_by" + "NML_LIMS:PH_VACCINATION_HISTORY" ], - "rank": 9, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", - "owner": "Mpox_international", + "rank": 54, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host vaccination information", "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "title": "sample collector contact email", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination dose 1 vaccination date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-06-01" + } + ], "from_schema": "https://example.com/mpox", - "rank": 10, - "slot_uri": "GENEPIO:0001156", - "alias": "sample_collector_contact_email", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], + "rank": 55, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "pattern": "^\\S+@\\S+\\.\\S+$" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collector contact address": { - "name": "sample collector contact address", - "description": "The mailing address of the agency submitting the sample.", - "title": "sample collector contact address", + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "IMVAMUNE (Bavarian Nordic)" + }, + { + "value": "2022-06-01" + } + ], "from_schema": "https://example.com/mpox", - "rank": 11, - "slot_uri": "GENEPIO:0001158", - "alias": "sample_collector_contact_address", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], + "rank": 56, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "sequenced by": { - "name": "sequenced by", - "description": "The name of the agency that generated the sequence.", - "title": "sequenced by", - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "BIOSAMPLE:sequenced_by" + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", + "description": "The country where the host was likely exposed to the causative agent of the illness.", + "title": "location of exposure geo_loc name (country)", + "comments": [ + "Select the country name from the pick list provided in the template." + ], + "examples": [ + { + "value": "Canada [GAZ:00002560]" + } ], - "rank": 12, - "slot_uri": "GENEPIO:0100416", - "alias": "sequenced_by", - "owner": "Mpox_international", + "from_schema": "https://example.com/mpox", + "rank": 57, + "slot_uri": "GENEPIO:0001410", + "alias": "location_of_exposure_geo_loc_name_country", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced by contact email", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", + "description": "The name of the city that was the destination of most recent travel.", + "title": "destination of most recent travel (city)", + "comments": [ + "Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "New York City" + } + ], "from_schema": "https://example.com/mpox", - "rank": 13, - "slot_uri": "GENEPIO:0100422", - "alias": "sequenced_by_contact_email", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 58, + "slot_uri": "GENEPIO:0001411", + "alias": "destination_of_most_recent_travel_city", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "sequenced by contact address": { - "name": "sequenced by contact address", - "description": "The mailing address of the agency submitting the sequence.", - "title": "sequenced by contact address", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", + "description": "The name of the state/province/territory that was the destination of most recent travel.", + "title": "destination of most recent travel (state/province/territory)", + "comments": [ + "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "California" + } + ], "from_schema": "https://example.com/mpox", - "rank": 14, - "slot_uri": "GENEPIO:0100423", - "alias": "sequenced_by_contact_address", - "owner": "Mpox_international", + "rank": 59, + "slot_uri": "GENEPIO:0001412", + "alias": "destination_of_most_recent_travel_state_province_territory", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "The name of the agency that submitted the sequence to a database.", - "title": "sequence submitted by", - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Submitting%20lab", - "BIOSAMPLE:sequence_submitted_by" + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", + "description": "The name of the country that was the destination of most recent travel.", + "title": "destination of most recent travel (country)", + "comments": [ + "Select the country name from the pick list provided in the template." ], - "rank": 15, - "slot_uri": "GENEPIO:0001159", - "alias": "sequence_submitted_by", - "owner": "Mpox_international", + "examples": [ + { + "value": "United Kingdom [GAZ:00002637]" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 60, + "slot_uri": "GENEPIO:0001413", + "alias": "destination_of_most_recent_travel_country", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "GeoLocNameCountryInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "description": "The email address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact email", - "from_schema": "https://example.com/mpox", - "rank": 16, - "slot_uri": "GENEPIO:0001165", - "alias": "sequence_submitter_contact_email", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", + "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", + "title": "most recent travel departure date", + "comments": [ + "Provide the travel departure date." + ], + "examples": [ + { + "value": "2020-03-16" + } ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "description": "The mailing address of the agency responsible for submission of the sequence.", - "title": "sequence submitter contact address", "from_schema": "https://example.com/mpox", - "rank": 17, - "slot_uri": "GENEPIO:0001167", - "alias": "sequence_submitter_contact_address", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 61, + "slot_uri": "GENEPIO:0001414", + "alias": "most_recent_travel_departure_date", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", - "description": "The date on which the sample was collected.", - "title": "sample collection date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", + "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", + "title": "most recent travel return date", + "comments": [ + "Provide the travel return date." + ], + "examples": [ + { + "value": "2020-04-26" + } + ], "from_schema": "https://example.com/mpox", - "rank": 18, - "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 62, + "slot_uri": "GENEPIO:0001415", + "alias": "most_recent_travel_return_date", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", - "description": "The date on which the sample was received.", - "title": "sample received date", + "travel_history": { + "name": "travel_history", + "description": "Travel history in last six months.", + "title": "travel history", + "comments": [ + "Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first." + ], + "examples": [ + { + "value": "Canada, Vancouver" + }, + { + "value": "USA, Seattle" + }, + { + "value": "Italy, Milan" + } + ], "from_schema": "https://example.com/mpox", - "rank": 19, - "slot_uri": "GENEPIO:0001179", - "alias": "sample_received_date", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], + "rank": 63, + "slot_uri": "GENEPIO:0001416", + "alias": "travel_history", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing" + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "description": "The country where the sample was collected.", - "title": "geo_loc_name (country)", + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team." + ], "examples": [ { - "value": "United States of America [GAZ:00002459]" + "value": "Party [PCO:0000035]" } ], "from_schema": "https://example.com/mpox", - "rank": 20, - "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", - "owner": "Mpox_international", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 64, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "geo_loc_name (country) international menu" + "range": "ExposureEventInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", - "description": "The state/province/territory where the sample was collected.", - "title": "geo_loc_name (state/province/territory)", + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", "comments": [ - "Provide the state/province/territory name from the controlled vocabulary provided." + "Select exposure contact level from the pick-list." + ], + "examples": [ + { + "value": "Contact with infected individual [GENEPIO:0100357]" + } ], "from_schema": "https://example.com/mpox", - "rank": 21, - "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "rank": 65, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host exposure information", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "ExposureContactLevelInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc latitude": { - "name": "geo_loc latitude", - "description": "The latitude coordinates of the geographical location of sample collection.", - "title": "geo_loc latitude", + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team." + ], + "examples": [ + { + "value": "Acquaintance of case [GENEPIO:0100266]" + } + ], "from_schema": "https://example.com/mpox", - "rank": 22, - "slot_uri": "GENEPIO:0100309", - "alias": "geo_loc_latitude", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "rank": 66, + "slot_uri": "GENEPIO:0001419", + "alias": "host_role", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Host exposure information", + "range": "HostRoleInternationalMenu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team." + ], + "examples": [ + { + "value": "Healthcare Setting [GENEPIO:0100201]" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 67, + "slot_uri": "GENEPIO:0001428", + "alias": "exposure_setting", + "owner": "MpoxInternational", "domain_of": [ - "Mpox_international" + "Mpox", + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Host exposure information", + "range": "ExposureSettingInternationalMenu", + "multivalued": true }, - "geo_loc longitude": { - "name": "geo_loc longitude", - "description": "The longitude coordinates of the geographical location of sample collection.", - "title": "geo_loc longitude", + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Large party, many contacts" + } + ], "from_schema": "https://example.com/mpox", - "rank": 23, - "slot_uri": "GENEPIO:0100310", - "alias": "geo_loc_longitude", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "rank": 68, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "MpoxInternational", "domain_of": [ - "Mpox_international" + "Mpox", + "MpoxInternational" ], - "slot_group": "Sample collection and processing", + "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "organism": { - "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", + "prior_mpox_infection": { + "name": "prior_mpox_infection", + "description": "The absence or presence of a prior Mpox infection.", + "title": "prior Mpox infection", "comments": [ - "Use \"Mpox virus\". This value is provided in the template. Note: the Mpox virus was formerly referred to as the \"Monkeypox virus\" but the international nomenclature has changed (2022)." + "If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list." ], "examples": [ { - "value": "Mpox virus [NCBITaxon:10244]" + "value": "Prior infection [GENEPIO:0100037]" } ], "from_schema": "https://example.com/mpox", - "rank": 24, - "slot_uri": "GENEPIO:0001191", - "alias": "organism", - "owner": "Mpox_international", + "rank": 69, + "slot_uri": "GENEPIO:0100532", + "alias": "prior_mpox_infection", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host reinfection information", "any_of": [ { - "range": "organism international menu" + "range": "PriorMonkeypoxInfectionInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "isolate": { - "name": "isolate", - "description": "Identifier of the specific isolate.", - "title": "isolate", + "prior_mpox_infection_date": { + "name": "prior_mpox_infection_date", + "description": "The date of diagnosis of the prior Mpox infection.", + "title": "prior Mpox infection date", "comments": [ - "This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the \"isolate\" name is propagated throughtout different databases. As such, structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"MpxV/host/country/sampleID/date\"." + "Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format \"YYYY-MM-DD\"." ], "examples": [ { - "value": "MpxV/human/USA/CA-CDPH-001/2020" + "value": "2022-06-20" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:isolate" + "NML_LIMS:prior%20Monkeypox%20infection%20date" ], - "rank": 25, - "slot_uri": "GENEPIO:0001644", - "alias": "isolate", - "owner": "Mpox_international", + "rank": 70, + "slot_uri": "GENEPIO:0100533", + "alias": "prior_mpox_infection_date", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling": { - "name": "purpose of sampling", - "description": "The reason that the sample was collected.", - "title": "purpose of sampling", + "prior_mpox_antiviral_treatment": { + "name": "prior_mpox_antiviral_treatment", + "description": "The absence or presence of antiviral treatment for a prior Mpox infection.", + "title": "prior Mpox antiviral treatment", + "comments": [ + "If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list." + ], "examples": [ { - "value": "Diagnostic testing [GENEPIO:0100002]" + "value": "Prior antiviral treatment [GENEPIO:0100037]" } ], "from_schema": "https://example.com/mpox", - "rank": 26, - "slot_uri": "GENEPIO:0001198", - "alias": "purpose_of_sampling", - "owner": "Mpox_international", + "rank": 71, + "slot_uri": "GENEPIO:0100534", + "alias": "prior_mpox_antiviral_treatment", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true, + "slot_group": "Host reinfection information", "any_of": [ { - "range": "purpose of sampling international menu" + "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "description": "The description of why the sample was collected, providing specific details.", - "title": "purpose of sampling details", + "prior_antiviral_treatment_during_prior_mpox_infection": { + "name": "prior_antiviral_treatment_during_prior_mpox_infection", + "description": "Antiviral treatment for any infection during the prior Mpox infection period.", + "title": "prior antiviral treatment during prior Mpox infection", + "comments": [ + "Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information." + ], + "examples": [ + { + "value": "AZT was administered for HIV infection during the prior Mpox infection." + } + ], "from_schema": "https://example.com/mpox", - "rank": 27, - "slot_uri": "GENEPIO:0001200", - "alias": "purpose_of_sampling_details", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:prior%20antiviral%20treatment%20during%20Monkeypox%20infection" + ], + "rank": 72, + "slot_uri": "GENEPIO:0100535", + "alias": "prior_antiviral_treatment_during_prior_mpox_infection", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "required": true + "slot_group": "Host reinfection information", + "range": "WhitespaceMinimizedString" }, - "anatomical material": { - "name": "anatomical material", - "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", - "title": "anatomical material", + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing project name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], "examples": [ { - "value": "Lesion (Pustule) [NCIT:C78582]" + "value": "MPOX-1356" } ], "from_schema": "https://example.com/mpox", - "rank": 28, - "slot_uri": "GENEPIO:0001211", - "multivalued": true, - "alias": "anatomical_material", - "owner": "Mpox_international", + "rank": 73, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "any_of": [ - { - "range": "anatomical material international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "anatomical part": { - "name": "anatomical part", - "description": "An anatomical part of an organism e.g. oropharynx.", - "title": "anatomical part", + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency that generated the sequence.", + "title": "sequenced by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], "examples": [ { - "value": "Genital area [BTO:0003358]" + "value": "Public Health Ontario (PHO)" } ], "from_schema": "https://example.com/mpox", - "rank": 29, - "slot_uri": "GENEPIO:0001214", - "multivalued": true, - "alias": "anatomical_part", - "owner": "Mpox_international", + "exact_mappings": [ + "BIOSAMPLE:sequenced_by" + ], + "rank": 74, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Sequencing", + "required": true, "any_of": [ { - "range": "anatomical part international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", - "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", - "title": "body product", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], "examples": [ { - "value": "Pus [UBERON:0000177]" + "value": "Joe Bloggs, Enterics Lab Manager" } ], "from_schema": "https://example.com/mpox", - "rank": 30, - "slot_uri": "GENEPIO:0001216", - "multivalued": true, - "alias": "body_product", - "owner": "Mpox_international", + "rank": 75, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Sequence information", + "required": true, "any_of": [ { - "range": "body product international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", - "title": "environmental material", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/mpox", - "rank": 31, - "slot_uri": "GENEPIO:0001223", - "multivalued": true, - "alias": "environmental_material", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:sequenced%20by%20contact%20email" + ], + "rank": 76, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "MpoxInternational", "domain_of": [ - "Mpox_international" + "Mpox", + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "recommended": true + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "collection device": { - "name": "collection device", - "description": "The instrument or container used to collect the sample e.g. swab.", - "title": "collection device", + "sequenced_by_contact_address": { + "name": "sequenced_by_contact_address", + "description": "The mailing address of the agency submitting the sequence.", + "title": "sequenced by contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], "examples": [ { - "value": "Swab [GENEPIO:0100027]" + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" } ], "from_schema": "https://example.com/mpox", - "rank": 32, - "slot_uri": "GENEPIO:0001234", - "multivalued": true, - "alias": "collection_device", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:sequenced%20by%20contact%20address" + ], + "rank": 77, + "slot_uri": "GENEPIO:0100423", + "alias": "sequenced_by_contact_address", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "recommended": true, - "any_of": [ - { - "range": "collection device international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "collection method": { - "name": "collection method", - "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", - "title": "collection method", + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], "examples": [ { - "value": "Biopsy [OBI:0002650]" + "value": "Public Health Ontario (PHO)" } ], "from_schema": "https://example.com/mpox", - "rank": 33, - "slot_uri": "GENEPIO:0001241", - "multivalued": true, - "alias": "collection_method", - "owner": "Mpox_international", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "BIOSAMPLE:sequence_submitted_by" + ], + "rank": 78, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "recommended": true, + "slot_group": "Sequencing", + "required": true, "any_of": [ { - "range": "collection method international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing": { - "name": "specimen processing", - "description": "Any processing applied to the sample during or after receiving the sample.", - "title": "specimen processing", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the agency responsible for submission of the sequence.", + "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], "examples": [ { - "value": "Specimens pooled [OBI:0600016]" + "value": "RespLab@lab.ca" } ], "from_schema": "https://example.com/mpox", - "rank": 34, - "slot_uri": "GENEPIO:0001253", - "multivalued": true, - "alias": "specimen_processing", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:sequence%20submitter%20contact%20email" + ], + "rank": 79, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sample collection and processing", - "any_of": [ - { - "range": "specimen processing international menu" - }, + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", + "description": "The mailing address of the agency responsible for submission of the sequence.", + "title": "sequence submitter contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ { - "range": "null value menu" + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" } - ] - }, - "specimen processing details": { - "name": "specimen processing details", - "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", - "title": "specimen processing details", - "from_schema": "https://example.com/mpox", - "rank": 35, - "slot_uri": "GENEPIO:0100311", - "alias": "specimen_processing_details", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "host (common name)": { - "name": "host (common name)", - "description": "The commonly used name of the host.", - "title": "host (common name)", "from_schema": "https://example.com/mpox", - "rank": 36, - "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", - "owner": "Mpox_international", + "exact_mappings": [ + "GISAID:Address", + "NML_LIMS:sequence%20submitter%20contact%20address" + ], + "rank": 80, + "slot_uri": "GENEPIO:0001167", + "alias": "sequence_submitter_contact_address", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "any_of": [ - { - "range": "host (common name) international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "The taxonomic, or scientific name of the host.", - "title": "host (scientific name)", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "The reason that the sample was sequenced.", + "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], "examples": [ { - "value": "Homo sapiens [NCBITaxon:9606]" + "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" } ], "from_schema": "https://example.com/mpox", - "rank": 37, - "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", - "owner": "Mpox_international", + "exact_mappings": [ + "GISAID:Sampling%20Strategy", + "CNPHI:Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING", + "BIOSAMPLE:purpose_of_sequencing", + "VirusSeq_Portal:purpose%20of%20sequencing" + ], + "rank": 81, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", + "slot_group": "Sequencing", "required": true, + "multivalued": true, "any_of": [ { - "range": "host (scientific name) international menu" + "range": "PurposeOfSequencingInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health state": { - "name": "host health state", - "description": "Health status of the host at the time of sample collection.", - "title": "host health state", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual." + ], "examples": [ { - "value": "Asymptomatic [NCIT:C3833]" + "value": "Outbreak in MSM community" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Patient%20status", - "BIOSAMPLE:host_health_state" + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", + "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], - "rank": 38, - "slot_uri": "GENEPIO:0001388", - "alias": "host_health_state", - "owner": "Mpox_international", + "rank": 82, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", + "slot_group": "Sequencing", + "required": true, "any_of": [ { - "range": "host health state international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health status details": { - "name": "host health status details", - "description": "Further details pertaining to the health or disease status of the host at time of collection.", - "title": "host health status details", + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], "examples": [ { - "value": "Hospitalized [NCIT:C25179]" + "value": "2020-06-22" } ], "from_schema": "https://example.com/mpox", - "rank": 39, - "slot_uri": "GENEPIO:0001389", - "alias": "host_health_status_details", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_DATE" + ], + "rank": 83, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", + "slot_group": "Sequencing", "any_of": [ { - "range": "host health status details international menu" + "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health outcome": { - "name": "host health outcome", - "description": "Disease outcome in the host.", - "title": "host health outcome", + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], "examples": [ { - "value": "Recovered [NCIT:C49498]" + "value": "XYZ_123345" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:host_health_outcome" + "NML_LIMS:library%20ID" ], - "rank": 40, - "slot_uri": "GENEPIO:0001389", - "alias": "host_health_outcome", - "owner": "Mpox_international", + "rank": 84, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "any_of": [ - { - "range": "host health outcome international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "host disease": { - "name": "host disease", - "description": "The name of the disease experienced by the host.", - "title": "host disease", + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library preparation kit", "comments": [ - "Select \"Mpox\" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as \"Monkeypox\" but the international nomenclature has changed (2022)." + "Provide the name of the library preparation kit used." ], "examples": [ { - "value": "Mpox [MONDO:0002594]" + "value": "Nextera XT" } ], "from_schema": "https://example.com/mpox", - "rank": 41, - "slot_uri": "GENEPIO:0001391", - "alias": "host_disease", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_LIBRARY_PREP_KIT" + ], + "rank": 85, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "required": true, - "any_of": [ - { - "range": "host disease international menu" - }, + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing assay type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ { - "range": "null value menu" + "value": "whole genome sequencing assay [OBI:0002117]" } - ] - }, - "host subject ID": { - "name": "host subject ID", - "description": "A unique identifier by which each host can be referred to.", - "title": "host subject ID", - "from_schema": "https://example.com/mpox", - "rank": 42, - "slot_uri": "GENEPIO:0001398", - "alias": "host_subject_ID", - "owner": "Mpox_international", - "domain_of": [ - "Mpox_international" ], - "slot_group": "Host Information", - "range": "WhitespaceMinimizedString" - }, - "host age": { - "name": "host age", - "description": "Age of host at the time of sampling.", - "title": "host age", "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Patient%20age", - "BIOSAMPLE:host_age" - ], - "rank": 43, - "slot_uri": "GENEPIO:0001392", - "alias": "host_age", - "owner": "Mpox_international", + "rank": 86, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "recommended": true, - "minimum_value": "0", - "maximum_value": "130" + "slot_group": "Sequence information", + "range": "SequencingAssayTypeInternationalMenu" }, - "host age unit": { - "name": "host age unit", - "description": "The units used to measure the host's age.", - "title": "host age unit", + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." + ], "examples": [ { - "value": "year [UO:0000036]" + "value": "Oxford Nanopore MinION [GENEPIO:0100142]" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "BIOSAMPLE:host_age_unit" + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", + "NML_LIMS:PH_SEQUENCING_INSTRUMENT", + "VirusSeq_Portal:sequencing%20instrument" ], - "rank": 44, - "slot_uri": "GENEPIO:0001393", - "alias": "host_age_unit", - "owner": "Mpox_international", + "rank": 87, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "recommended": true, + "slot_group": "Sequencing", + "required": true, + "multivalued": true, "any_of": [ { - "range": "host age unit international menu" + "range": "SequencingInstrumentInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", - "description": "The age category of the host at the time of sampling.", - "title": "host age bin", + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing flow cell version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], "examples": [ { - "value": "50 - 59 [GENEPIO:0100054]" + "value": "R.9.4.1" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "BIOSAMPLE:host_age_bin" - ], - "rank": 45, - "slot_uri": "GENEPIO:0001394", - "alias": "host_age_bin", - "owner": "Mpox_international", + "rank": 88, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "recommended": true, - "any_of": [ - { - "range": "host age bin international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "host gender": { - "name": "host gender", - "description": "The gender of the host at the time of sample collection.", - "title": "host gender", + "sequencing_protocol__": { + "name": "sequencing_protocol__", + "description": "The protocol used to generate the sequence.", + "title": "sequencing protocol", + "comments": [ + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + ], "examples": [ { - "value": "Male [NCIT:C46109]" + "value": "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Gender", - "BIOSAMPLE:host_sex" + "NML_LIMS:PH_TESTING_PROTOCOL", + "VirusSeq_Portal:sequencing%20protocol" ], - "rank": 46, - "slot_uri": "GENEPIO:0001395", - "alias": "host_gender", - "owner": "Mpox_international", + "rank": 89, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol__", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "recommended": true, - "structured_pattern": { - "syntax": "{Title_Case}", - "interpolated": true, - "partial_match": false - }, - "any_of": [ - { - "range": "host gender international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", - "description": "The country of residence of the host.", - "title": "host residence geo_loc name (country)", + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "description": "The manufacturer's kit number.", + "title": "sequencing kit number", + "comments": [ + "Alphanumeric value." + ], "examples": [ { - "value": "Canada [GAZ:00002560]" + "value": "AB456XYZ789" } ], "from_schema": "https://example.com/mpox", - "rank": 47, - "slot_uri": "GENEPIO:0001396", - "alias": "host_residence_geo_loc_name_(country)", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:sequencing%20kit%20number" + ], + "rank": 90, + "slot_uri": "GENEPIO:0001455", + "alias": "sequencing_kit_number", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "any_of": [ - { - "range": "geo_loc_name (country) international menu" - }, + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA fragment length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ { - "range": "null value menu" + "value": "400" } - ] - }, - "symptom onset date": { - "name": "symptom onset date", - "description": "The date on which the symptoms began or were first noted.", - "title": "symptom onset date", + ], "from_schema": "https://example.com/mpox", - "rank": 48, - "slot_uri": "GENEPIO:0001399", - "alias": "symptom_onset_date", - "owner": "Mpox_international", + "rank": 91, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method", + "comments": [ + "Provide the name of the enrichment method" ], - "slot_group": "Host Information" - }, - "signs and symptoms": { - "name": "signs and symptoms", - "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", - "title": "signs and symptoms", "examples": [ { - "value": "Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326]" + "value": "hybrid selection method" } ], "from_schema": "https://example.com/mpox", - "rank": 49, - "slot_uri": "GENEPIO:0001400", - "multivalued": true, - "alias": "signs_and_symptoms", - "owner": "Mpox_international", + "rank": 92, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", + "slot_group": "Sequencing", + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "signs and symptoms international menu" + "range": "GenomicTargetEnrichmentMethodInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", - "title": "pre-existing conditions and risk factors", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method details", + "comments": [ + "Provide details that are applicable to the method you used." + ], + "examples": [ + { + "value": "enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit." + } + ], "from_schema": "https://example.com/mpox", - "rank": 50, - "slot_uri": "GENEPIO:0001401", - "multivalued": true, - "alias": "pre_existing_conditions_and_risk_factors", - "owner": "Mpox_international", + "rank": 93, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "any_of": [ - { - "range": "pre-existing conditions and risk factors international menu" - }, + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ { - "range": "null value menu" + "value": "MPXV Sunrise 3.1" } - ] + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:amplicon%20pcr%20primer%20scheme" + ], + "rank": 94, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "MpoxInternational", + "domain_of": [ + "Mpox", + "MpoxInternational" + ], + "slot_group": "Sequencing", + "range": "WhitespaceMinimizedString" }, - "complications": { - "name": "complications", - "description": "Patient medical complications that are believed to have occurred as a result of host disease.", - "title": "complications", + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], "examples": [ { - "value": "Delayed wound healing (lesion healing) [MP:0002908]" + "value": "300bp" } ], "from_schema": "https://example.com/mpox", - "rank": 51, - "slot_uri": "GENEPIO:0001402", - "multivalued": true, - "alias": "complications", - "owner": "Mpox_international", + "rank": 95, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", - "any_of": [ - { - "range": "complications international menu" - }, + "slot_group": "Sequencing", + "range": "integer" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ { - "range": "null value menu" + "value": "ncov-tools" } - ] - }, - "antiviral therapy": { - "name": "antiviral therapy", - "description": "Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function.", - "title": "antiviral therapy", + ], "from_schema": "https://example.com/mpox", - "rank": 52, - "slot_uri": "GENEPIO:0100580", - "alias": "antiviral_therapy", - "owner": "Mpox_international", + "rank": 96, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host Information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "host vaccination status": { - "name": "host vaccination status", - "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", - "title": "host vaccination status", + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], "examples": [ { - "value": "Not Vaccinated [GENEPIO:0100102]" + "value": "1.2.3" } ], "from_schema": "https://example.com/mpox", - "rank": 53, - "slot_uri": "GENEPIO:0001404", - "alias": "host_vaccination_status", - "owner": "Mpox_international", + "rank": 97, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host vaccination information", - "any_of": [ - { - "range": "host vaccination status international menu" - }, - { - "range": "null value menu" - } - ] + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", - "description": "The number of doses of the vaccine recived by the host.", - "title": "number of vaccine doses received", + "quality_control_determination": { + "name": "quality_control_determination", + "title": "quality control determination", "from_schema": "https://example.com/mpox", - "rank": 54, - "slot_uri": "GENEPIO:0001406", - "alias": "number_of_vaccine_doses_received", - "owner": "Mpox_international", + "rank": 98, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host vaccination information", - "range": "integer" + "slot_group": "Bioinformatics and QC metrics", + "range": "QualityControlDeterminationInternationalMenu" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", - "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", - "title": "vaccination dose 1 vaccine name", + "quality_control_issues": { + "name": "quality_control_issues", + "title": "quality control issues", "from_schema": "https://example.com/mpox", - "rank": 55, - "slot_uri": "GENEPIO:0100313", - "alias": "vaccination_dose_1_vaccine_name", - "owner": "Mpox_international", + "rank": 99, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host vaccination information" + "slot_group": "Bioinformatics and QC metrics", + "range": "QualityControlIssuesInternationalMenu" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", - "description": "The date the first dose of a vaccine was administered.", - "title": "vaccination dose 1 vaccination date", + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], "from_schema": "https://example.com/mpox", - "rank": 56, - "slot_uri": "GENEPIO:0100314", - "alias": "vaccination_dose_1_vaccination_date", - "owner": "Mpox_international", + "rank": 100, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host vaccination information" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "vaccination history": { - "name": "vaccination history", - "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", - "title": "vaccination history", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/mpox", - "rank": 57, - "slot_uri": "GENEPIO:0100321", - "alias": "vaccination_history", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_RAW_SEQUENCE_METHOD", + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" + ], + "rank": 101, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host vaccination information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", - "description": "The country where the host was likely exposed to the causative agent of the illness.", - "title": "location of exposure geo_loc name (country)", + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], "examples": [ { - "value": "Canada [GAZ:00002560]" + "value": "Nanostripper" } ], "from_schema": "https://example.com/mpox", - "rank": 58, - "slot_uri": "GENEPIO:0001410", - "alias": "location_of_exposure_geo_loc_name_(country)", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:PH_DEHOSTING_METHOD", + "VirusSeq_Portal:dehosting%20method" + ], + "rank": 102, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "geo_loc_name (country) international menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ { - "range": "null value menu" + "value": "DeDup 0.12.8" } - ] - }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", - "description": "The name of the city that was the destination of most recent travel.", - "title": "destination of most recent travel (city)", + ], "from_schema": "https://example.com/mpox", - "rank": 59, - "slot_uri": "GENEPIO:0001411", - "alias": "destination_of_most_recent_travel_(city)", - "owner": "Mpox_international", + "rank": 103, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", - "description": "The name of the state/province/territory that was the destination of most recent travel.", - "title": "destination of most recent travel (state/province/territory)", + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "description": "The name of the consensus sequence.", + "title": "consensus sequence name", "comments": [ - "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + "Provide the name and version number of the consensus sequence." ], "examples": [ { - "value": "California" + "value": "mpxvassembly3" } ], "from_schema": "https://example.com/mpox", - "rank": 60, - "slot_uri": "GENEPIO:0001412", - "alias": "destination_of_most_recent_travel_(state/province/territory)", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20name" + ], + "rank": 104, + "slot_uri": "GENEPIO:0001460", + "alias": "consensus_sequence_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", - "description": "The name of the country that was the destination of most recent travel.", - "title": "destination of most recent travel (country)", + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], "examples": [ { - "value": "United Kingdom [GAZ:00002637]" + "value": "mpxvassembly.fasta" } ], "from_schema": "https://example.com/mpox", - "rank": 61, - "slot_uri": "GENEPIO:0001413", - "alias": "destination_of_most_recent_travel_(country)", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filename" + ], + "rank": 105, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", - "any_of": [ - { - "range": "geo_loc_name (country) international menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", + "comments": [ + "Provide the filepath of the genome sequence FASTA file." + ], + "examples": [ { - "range": "null value menu" + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" } - ] - }, - "most recent travel departure date": { - "name": "most recent travel departure date", - "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", - "title": "most recent travel departure date", + ], "from_schema": "https://example.com/mpox", - "rank": 62, - "slot_uri": "GENEPIO:0001414", - "alias": "most_recent_travel_departure_date", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filepath" + ], + "rank": 106, + "slot_uri": "GENEPIO:0101716", + "alias": "genome_sequence_file_path", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "most recent travel return date": { - "name": "most recent travel return date", - "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", - "title": "most recent travel return date", - "from_schema": "https://example.com/mpox", - "rank": 63, - "slot_uri": "GENEPIO:0001415", - "alias": "most_recent_travel_return_date", - "owner": "Mpox_international", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" + ], + "rank": 107, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "required": true }, - "travel history": { - "name": "travel history", - "description": "Travel history in last six months.", - "title": "travel history", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/mpox", - "rank": 64, - "slot_uri": "GENEPIO:0001416", - "alias": "travel_history", - "owner": "Mpox_international", + "exact_mappings": [ + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" + ], + "rank": 108, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "required": true }, - "exposure event": { - "name": "exposure event", - "description": "Event leading to exposure.", - "title": "exposure event", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], "examples": [ { - "value": "Party [PCO:0000035]" + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" } ], "from_schema": "https://example.com/mpox", - "rank": 65, - "slot_uri": "GENEPIO:0001417", - "alias": "exposure_event", - "owner": "Mpox_international", + "rank": 109, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", + "slot_group": "Bioinformatics and QC metrics", + "required": true, "any_of": [ { - "range": "exposure event international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure contact level": { - "name": "exposure contact level", - "description": "The exposure transmission contact type.", - "title": "exposure contact level", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], "examples": [ { - "value": "Contact with infected individual [GENEPIO:0100357]" + "value": "3.15.5" } ], "from_schema": "https://example.com/mpox", - "rank": 66, - "slot_uri": "GENEPIO:0001418", - "alias": "exposure_contact_level", - "owner": "Mpox_international", + "rank": 110, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", + "slot_group": "Bioinformatics and QC metrics", + "required": true, "any_of": [ { - "range": "exposure contact level international menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host role": { - "name": "host role", - "description": "The role of the host in relation to the exposure setting.", - "title": "host role", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", + "comments": [ + "Provide the r1 FASTQ filename. This information aids in data management." + ], "examples": [ { - "value": "Acquaintance of case [GENEPIO:0100266]" + "value": "ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "rank": 67, - "slot_uri": "GENEPIO:0001419", - "multivalued": true, - "alias": "host_role", - "owner": "Mpox_international", + "rank": 111, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename________", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", - "range": "host role international menu" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "exposure setting": { - "name": "exposure setting", - "description": "The setting leading to exposure.", - "title": "exposure setting", + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", + "comments": [ + "Provide the r2 FASTQ filename. This information aids in data management." + ], "examples": [ { - "value": "Healthcare Setting [GENEPIO:0100201]" + "value": "ABC123_S1_L001_R2_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "rank": 68, - "slot_uri": "GENEPIO:0001428", - "multivalued": true, - "alias": "exposure_setting", - "owner": "Mpox_international", + "rank": 112, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host exposure information", - "range": "exposure setting international menu" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "exposure details": { - "name": "exposure details", - "description": "Additional host exposure information.", - "title": "exposure details", - "from_schema": "https://example.com/mpox", - "rank": 69, - "slot_uri": "GENEPIO:0001431", - "alias": "exposure_details", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", + "comments": [ + "Provide the filepath for the r1 FASTQ file. This information aids in data management." ], - "slot_group": "Host exposure information", - "range": "WhitespaceMinimizedString" - }, - "prior Mpox infection": { - "name": "prior Mpox infection", - "description": "The absence or presence of a prior Mpox infection.", - "title": "prior Mpox infection", "examples": [ { - "value": "Prior infection [GENEPIO:0100037]" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "rank": 70, - "slot_uri": "GENEPIO:0100532", - "alias": "prior_Mpox_infection", - "owner": "Mpox_international", + "rank": 113, + "slot_uri": "GENEPIO:0001478", + "alias": "r1_fastq_filepath", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host reinfection information", - "any_of": [ - { - "range": "prior Monkeypox infection international menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", + "comments": [ + "Provide the filepath for the r2 FASTQ file. This information aids in data management." + ], + "examples": [ { - "range": "null value menu" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" } - ] - }, - "prior Mpox infection date": { - "name": "prior Mpox infection date", - "description": "The date of diagnosis of the prior Mpox infection.", - "title": "prior Mpox infection date", + ], "from_schema": "https://example.com/mpox", - "rank": 71, - "slot_uri": "GENEPIO:0100533", - "alias": "prior_Mpox_infection_date", - "owner": "Mpox_international", + "rank": 114, + "slot_uri": "GENEPIO:0001479", + "alias": "r2_fastq_filepath", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host reinfection information" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "prior Mpox antiviral treatment": { - "name": "prior Mpox antiviral treatment", - "description": "The absence or presence of antiviral treatment for a prior Mpox infection.", - "title": "prior Mpox antiviral treatment", + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", + "comments": [ + "Provide the FAST5 filename. This information aids in data management." + ], "examples": [ { - "value": "Prior antiviral treatment [GENEPIO:0100037]" + "value": "mpxv123seq.fast5" } ], "from_schema": "https://example.com/mpox", - "rank": 72, - "slot_uri": "GENEPIO:0100534", - "alias": "prior_Mpox_antiviral_treatment", - "owner": "Mpox_international", + "rank": 115, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host reinfection information", - "any_of": [ - { - "range": "prior Monkeypox antiviral treatment international menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "fast5_filepath": { + "name": "fast5_filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", + "comments": [ + "Provide the filepath for the FAST5 file. This information aids in data management." + ], + "examples": [ { - "range": "null value menu" + "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" } - ] - }, - "prior antiviral treatment during prior Mpox infection": { - "name": "prior antiviral treatment during prior Mpox infection", - "description": "Antiviral treatment for any infection during the prior Mpox infection period.", - "title": "prior antiviral treatment during prior Mpox infection", + ], "from_schema": "https://example.com/mpox", - "rank": 73, - "slot_uri": "GENEPIO:0100535", - "alias": "prior_antiviral_treatment_during_prior_Mpox_infection", - "owner": "Mpox_international", + "rank": 116, + "slot_uri": "GENEPIO:0001481", + "alias": "fast5_filepath", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Host reinfection information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "purpose of sequencing": { - "name": "purpose of sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose of sequencing", + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" + "value": "423867" } ], "from_schema": "https://example.com/mpox", - "rank": 74, - "slot_uri": "GENEPIO:0001445", - "multivalued": true, - "alias": "purpose_of_sequencing", - "owner": "Mpox_international", + "rank": 117, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "required": true, - "any_of": [ - { - "range": "purpose of sequencing international menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ { - "range": "null value menu" + "value": "248236" } - ] - }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "description": "The description of why the sample was sequenced providing specific details.", - "title": "purpose of sequencing details", + ], "from_schema": "https://example.com/mpox", - "rank": 75, - "slot_uri": "GENEPIO:0001446", - "alias": "purpose_of_sequencing_details", - "owner": "Mpox_international", + "rank": 118, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "required": true + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "sequencing date": { - "name": "sequencing date", - "description": "The date the sample was sequenced.", - "title": "sequencing date", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/mpox", - "rank": 76, - "slot_uri": "GENEPIO:0001447", - "alias": "sequencing_date", - "owner": "Mpox_international", + "rank": 119, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing" + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "library ID": { - "name": "library ID", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library ID", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400x" + } + ], "from_schema": "https://example.com/mpox", - "rank": 77, - "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", - "owner": "Mpox_international", + "exact_mappings": [ + "GISAID:Depth%20of%20coverage", + "NML_LIMS:depth%20of%20coverage%20value", + "VirusSeq_Portal:depth%20of%20coverage%20value" + ], + "rank": 120, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "amplicon size": { - "name": "amplicon size", - "description": "The length of the amplicon generated by PCR amplification.", - "title": "amplicon size", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100x" + } + ], "from_schema": "https://example.com/mpox", - "rank": 78, - "slot_uri": "GENEPIO:0001449", - "alias": "amplicon_size", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:depth%20of%20coverage%20threshold" + ], + "rank": 121, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "title": "library preparation kit", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2639019" + } + ], "from_schema": "https://example.com/mpox", - "rank": 79, - "slot_uri": "GENEPIO:0001450", - "alias": "library_preparation_kit", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:number%20of%20base%20pairs%20sequenced" + ], + "rank": 122, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer", + "minimum_value": 0 }, - "sequencing instrument": { - "name": "sequencing instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing instrument", + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "Size of the reconstructed genome described as the number of base pairs.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "examples": [ { - "value": "Oxford Nanopore MinION [GENEPIO:0100142]" + "value": "197063" } ], "from_schema": "https://example.com/mpox", - "rank": 80, - "slot_uri": "GENEPIO:0001452", - "multivalued": true, - "alias": "sequencing_instrument", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:consensus%20genome%20length" + ], + "rank": 123, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "required": true, - "any_of": [ - { - "range": "sequencing instrument international menu" - }, + "slot_group": "Bioinformatics and QC metrics", + "range": "integer", + "minimum_value": 0 + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ { - "range": "null value menu" + "value": "34272" } - ] - }, - "sequencing protocol": { - "name": "sequencing protocol", - "description": "The protocol used to generate the sequence.", - "title": "sequencing protocol", + ], "from_schema": "https://example.com/mpox", - "rank": 81, - "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol", - "owner": "Mpox_international", + "rank": 124, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "sequencing kit number": { - "name": "sequencing kit number", - "description": "The manufacturer's kit number.", - "title": "sequencing kit number", + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/mpox", - "rank": 82, - "slot_uri": "GENEPIO:0001455", - "alias": "sequencing_kit_number", - "owner": "Mpox_international", + "rank": 125, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "Integer" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "title": "amplicon pcr primer scheme", + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], "from_schema": "https://example.com/mpox", - "rank": 83, - "slot_uri": "GENEPIO:0001456", - "alias": "amplicon_pcr_primer_scheme", - "owner": "Mpox_international", + "rank": 126, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Sequencing", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "title": "raw sequence data processing method", + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/mpox", - "rank": 84, - "slot_uri": "GENEPIO:0001458", - "alias": "raw_sequence_data_processing_method", - "owner": "Mpox_international", + "rank": 127, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "Integer" }, - "dehosting method": { - "name": "dehosting method", - "description": "The method used to remove host reads from the pathogen sequence.", - "title": "dehosting method", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/mpox", - "rank": 85, - "slot_uri": "GENEPIO:0001459", - "alias": "dehosting_method", - "owner": "Mpox_international", + "rank": 128, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "Integer" }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "The name of the consensus sequence.", - "title": "consensus sequence name", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], "from_schema": "https://example.com/mpox", - "rank": 86, - "slot_uri": "GENEPIO:0001460", - "alias": "consensus_sequence_name", - "owner": "Mpox_international", + "rank": 129, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "Integer" }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "The name of the consensus sequence file.", - "title": "consensus sequence filename", + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_063383.1" + } + ], "from_schema": "https://example.com/mpox", - "rank": 87, - "slot_uri": "GENEPIO:0001461", - "alias": "consensus_sequence_filename", - "owner": "Mpox_international", + "exact_mappings": [ + "NML_LIMS:reference%20genome%20accession" + ], + "rank": 130, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "The filepath of the consensus sequence file.", - "title": "consensus sequence filepath", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/monkeypox-nf" + } + ], "from_schema": "https://example.com/mpox", - "rank": 88, - "slot_uri": "GENEPIO:0001462", - "alias": "consensus_sequence_filepath", - "owner": "Mpox_international", + "exact_mappings": [ + "CNPHI:Bioinformatics%20Protocol", + "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", + "VirusSeq_Portal:bioinformatics%20protocol" + ], + "rank": 131, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "The name of software used to generate the consensus sequence.", - "title": "consensus sequence software name", + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], "from_schema": "https://example.com/mpox", - "rank": 89, - "slot_uri": "GENEPIO:0001463", - "alias": "consensus_sequence_software_name", - "owner": "Mpox_international", + "rank": 132, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString", - "required": true + "recommended": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "The version of the software used to generate the consensus sequence.", - "title": "consensus sequence software version", + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], "from_schema": "https://example.com/mpox", - "rank": 90, - "slot_uri": "GENEPIO:0001469", - "alias": "consensus_sequence_software_version", - "owner": "Mpox_international", + "rank": 133, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString", - "required": true + "recommended": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth of coverage value", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], "from_schema": "https://example.com/mpox", - "rank": 91, - "slot_uri": "GENEPIO:0001472", - "alias": "breadth_of_coverage_value", - "owner": "Mpox_international", + "rank": 134, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/mpox", - "rank": 92, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", - "owner": "Mpox_international", + "rank": 135, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth of coverage threshold", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "MPXV_report123.doc" + } + ], "from_schema": "https://example.com/mpox", - "rank": 93, - "slot_uri": "GENEPIO:0001475", - "alias": "depth_of_coverage_threshold", - "owner": "Mpox_international", + "rank": 136, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1 fastq filename", - "from_schema": "https://example.com/mpox", - "rank": 94, - "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename", - "owner": "Mpox_international", - "domain_of": [ - "Mpox", - "Mpox_international" + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2 fastq filename", "from_schema": "https://example.com/mpox", - "rank": 95, - "slot_uri": "GENEPIO:0001477", - "alias": "r2_fastq_filename", - "owner": "Mpox_international", + "rank": 137, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Taxonomic identification information", + "range": "date" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "The location of the r1 FASTQ file within a user's file system.", - "title": "r1 fastq filepath", + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], "from_schema": "https://example.com/mpox", - "rank": 96, - "slot_uri": "GENEPIO:0001478", - "alias": "r1_fastq_filepath", - "owner": "Mpox_international", + "rank": 138, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "The location of the r2 FASTQ file within a user's file system.", - "title": "r2 fastq filepath", + "assay_target_name_1": { + "name": "assay_target_name_1", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 1", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "examples": [ + { + "value": "MPX (orf B6R)" + } + ], "from_schema": "https://example.com/mpox", - "rank": 97, - "slot_uri": "GENEPIO:0001479", - "alias": "r2_fastq_filepath", - "owner": "Mpox_international", + "rank": 139, + "slot_uri": "GENEPIO:0101206", + "alias": "assay_target_name_1", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "fast5 filename": { - "name": "fast5 filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5 filename", + "assay_target_details_1": { + "name": "assay_target_details_1", + "description": "Describe any details of the assay target.", + "title": "assay target details 1", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/mpox", - "rank": 98, - "slot_uri": "GENEPIO:0001480", - "alias": "fast5_filename", - "owner": "Mpox_international", + "rank": 140, + "slot_uri": "GENEPIO:0102045", + "alias": "assay_target_details_1", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "The location of the FAST5 file within a user's file system.", - "title": "fast5 filepath", + "gene_symbol_1": { + "name": "gene_symbol_1", + "description": "The gene symbol used in the diagnostic RT-PCR test.", + "title": "gene symbol 1", + "comments": [ + "Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name." + ], + "examples": [ + { + "value": "opg190 gene (MPOX)" + } + ], "from_schema": "https://example.com/mpox", - "rank": 99, - "slot_uri": "GENEPIO:0001481", - "alias": "fast5_filepath", - "owner": "Mpox_international", + "exact_mappings": [ + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", + "BIOSAMPLE:gene_name_1", + "VirusSeq_Portal:gene%20name" + ], + "rank": 141, + "slot_uri": "GENEPIO:0102041", + "alias": "gene_symbol_1", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneSymbolInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "The number of total base pairs generated by the sequencing process.", - "title": "number of base pairs sequenced", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "title": "diagnostic pcr protocol 1", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "B6R (Li et al., 2006)" + } + ], "from_schema": "https://example.com/mpox", - "rank": 100, - "slot_uri": "GENEPIO:0001482", - "alias": "number_of_base_pairs_sequenced", - "owner": "Mpox_international", + "rank": 142, + "slot_uri": "GENEPIO:0001508", + "alias": "diagnostic_pcr_protocol_1", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer", - "minimum_value": "0" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Size of the reconstructed genome described as the number of base pairs.", - "title": "consensus genome length", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", + "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", + "title": "diagnostic pcr Ct value 1", + "comments": [ + "Provide the CT value of the sample from the diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "21" + } + ], "from_schema": "https://example.com/mpox", - "rank": 101, - "slot_uri": "GENEPIO:0001483", - "alias": "consensus_genome_length", - "owner": "Mpox_international", + "exact_mappings": [ + "CNPHI:Gene%20Target%201%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_1", + "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" + ], + "rank": 143, + "slot_uri": "GENEPIO:0001509", + "alias": "diagnostic_pcr_ct_value_1", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer", - "minimum_value": "0" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "reference genome accession": { - "name": "reference genome accession", - "description": "A persistent, unique identifier of a genome database entry.", - "title": "reference genome accession", + "assay_target_name_2": { + "name": "assay_target_name_2", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 2", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "examples": [ + { + "value": "OVP (orf 17L)" + } + ], "from_schema": "https://example.com/mpox", - "rank": 102, - "slot_uri": "GENEPIO:0001485", - "alias": "reference_genome_accession", - "owner": "Mpox_international", + "rank": 144, + "slot_uri": "GENEPIO:0102038", + "alias": "assay_target_name_2", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "A description of the overall bioinformatics strategy used.", - "title": "bioinformatics protocol", + "assay_target_details_2": { + "name": "assay_target_details_2", + "description": "Describe any details of the assay target.", + "title": "assay target details 2", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/mpox", - "rank": 103, - "slot_uri": "GENEPIO:0001489", - "alias": "bioinformatics_protocol", - "owner": "Mpox_international", + "rank": 145, + "slot_uri": "GENEPIO:0102046", + "alias": "assay_target_details_2", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "gene name 1": { - "name": "gene name 1", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 1", + "gene_symbol_2": { + "name": "gene_symbol_2", + "description": "The gene symbol used in the diagnostic RT-PCR test.", + "title": "gene symbol 2", "comments": [ - "Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + "Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name." + ], + "examples": [ + { + "value": "opg002 gene (MPOX)" + } ], "from_schema": "https://example.com/mpox", - "rank": 104, - "slot_uri": "GENEPIO:0001507", - "alias": "gene_name_1", - "owner": "Mpox_international", + "exact_mappings": [ + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", + "BIOSAMPLE:gene_name_2" + ], + "rank": 146, + "slot_uri": "GENEPIO:0102042", + "alias": "gene_symbol_2", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "GeneSymbolInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "title": "diagnostic pcr protocol 2", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G)." + } + ], + "from_schema": "https://example.com/mpox", + "rank": 147, + "slot_uri": "GENEPIO:0001511", + "alias": "diagnostic_pcr_protocol_2", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 1", + "title": "diagnostic pcr Ct value 2", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "36" + } + ], "from_schema": "https://example.com/mpox", - "rank": 105, - "slot_uri": "GENEPIO:0001509", - "alias": "diagnostic_pcr_Ct_value_1", - "owner": "Mpox_international", + "exact_mappings": [ + "CNPHI:Gene%20Target%202%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_2" + ], + "rank": 148, + "slot_uri": "GENEPIO:0001512", + "alias": "diagnostic_pcr_ct_value_2", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "gene name 2": { - "name": "gene name 2", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 2", + "assay_target_name_3": { + "name": "assay_target_name_3", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 3", "comments": [ - "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "examples": [ + { + "value": "OPHA (orf B2R)" + } ], "from_schema": "https://example.com/mpox", - "rank": 106, - "slot_uri": "GENEPIO:0001510", - "alias": "gene_name_2", - "owner": "Mpox_international", + "rank": 149, + "slot_uri": "GENEPIO:0102039", + "alias": "assay_target_name_3", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Pathogen diagnostic testing", "any_of": [ @@ -16445,95 +25239,176 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", - "title": "diagnostic pcr Ct value 2", + "assay_target_details_3": { + "name": "assay_target_details_3", + "description": "Describe any details of the assay target.", + "title": "assay target details 3", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/mpox", - "rank": 107, - "slot_uri": "GENEPIO:0001512", - "alias": "diagnostic_pcr_Ct_value_2", - "owner": "Mpox_international", + "rank": 150, + "slot_uri": "GENEPIO:0102047", + "alias": "assay_target_details_3", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "gene name 3": { - "name": "gene name 3", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name 3", + "gene_symbol_3": { + "name": "gene_symbol_3", + "description": "The gene symbol used in the diagnostic RT-PCR test.", + "title": "gene symbol 3", "comments": [ - "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + "Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name." + ], + "examples": [ + { + "value": "opg188 gene (MPOX)" + } ], "from_schema": "https://example.com/mpox", - "rank": 108, - "slot_uri": "GENEPIO:0001513", - "alias": "gene_name_3", - "owner": "Mpox_international", + "exact_mappings": [ + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233", + "BIOSAMPLE:gene_name_3" + ], + "rank": 151, + "slot_uri": "GENEPIO:0102043", + "alias": "gene_symbol_3", + "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "GeneSymbolInternationalMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", + "description": "The name and version number of the protocol used for diagnostic marker amplification.", + "title": "diagnostic pcr protocol 3", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "G2R_G (Li et al., 2010) assay" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 152, + "slot_uri": "GENEPIO:0001514", + "alias": "diagnostic_pcr_protocol_3", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "19" + } + ], "from_schema": "https://example.com/mpox", - "rank": 109, + "exact_mappings": [ + "CNPHI:Gene%20Target%203%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_3" + ], + "rank": 153, "slot_uri": "GENEPIO:0001515", - "alias": "diagnostic_pcr_Ct_value_3", - "owner": "Mpox_international", + "alias": "diagnostic_pcr_ct_value_3", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, "authors": { "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/mpox", - "rank": 110, + "exact_mappings": [ + "GISAID:Authors", + "CNPHI:Authors", + "NML_LIMS:PH_SEQUENCING_AUTHORS" + ], + "rank": 154, "slot_uri": "GENEPIO:0001517", "alias": "authors", - "owner": "Mpox_international", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Contributor acknowledgement", "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, Mpox v3.3.1" + } + ], "from_schema": "https://example.com/mpox", - "rank": 111, + "exact_mappings": [ + "CNPHI:Additional%20Comments", + "NML_LIMS:HC_COMMENTS" + ], + "rank": 155, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", - "owner": "Mpox_international", + "alias": "dataharmonizer_provenance", + "owner": "MpoxInternational", "domain_of": [ "Mpox", - "Mpox_international" + "MpoxInternational" ], "slot_group": "Contributor acknowledgement", "range": "Provenance" diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 672a02d7..4d3a318e 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -1,6 +1,6 @@ id: https://example.com/mpox name: Mpox -version: 5.3.3 +version: 7.5.5 description: '' imports: - linkml:types @@ -18,226 +18,218 @@ classes: is_a: dh_interface see_also: templates/mpox/SOP_Mpox.pdf annotations: - version: 4.3.3 + version: 6.5.5 slots: - - specimen collector sample ID - - Related specimen primary ID - - case ID - - bioproject accession - - biosample accession - - SRA accession - - GenBank accession - - GISAID accession - - sample collected by - - sample collector contact email - - sample collector contact address - - sequenced by - - sequenced by contact email - - sequenced by contact address - - sequence submitted by - - sequence submitter contact email - - sequence submitter contact address - - sample collection date - - sample collection date precision - - sample received date - - geo_loc_name (country) - - geo_loc_name (state/province/territory) + - specimen_collector_sample_id + - related_specimen_primary_id + - case_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - gisaid_accession + - sample_collected_by + - sample_collector_contact_email + - sample_collector_contact_address + - sample_collection_date + - sample_collection_date_precision + - sample_received_date + - geo_loc_name_country + - geo_loc_name_state_province_territory - organism - isolate - - purpose of sampling - - purpose of sampling details - - NML submitted specimen type - - Related specimen relationship type - - anatomical material - - anatomical part - - body product - - collection device - - collection method - - specimen processing - - specimen processing details - - host (common name) - - host (scientific name) - - host health state - - host health status details - - host health outcome - - host disease - - host age - - host age unit - - host age bin - - host gender - - host residence geo_loc name (country) - - host residence geo_loc name (state/province/territory) - - symptom onset date - - signs and symptoms - - pre-existing conditions and risk factors + - purpose_of_sampling + - purpose_of_sampling_details + - nml_submitted_specimen_type + - related_specimen_relationship_type + - anatomical_material + - anatomical_part + - body_product + - collection_device + - collection_method + - specimen_processing + - specimen_processing_details + - experimental_specimen_role_type + - experimental_control_details + - host_common_name + - host_scientific_name + - host_health_state + - host_health_status_details + - host_health_outcome + - host_disease + - host_age + - host_age_unit + - host_age_bin + - host_gender + - host_residence_geo_loc_name_country + - host_residence_geo_loc_name_state_province_territory + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors - complications - - antiviral therapy - - host vaccination status - - number of vaccine doses received - - vaccination dose 1 vaccine name - - vaccination dose 1 vaccination date - - vaccination history - - location of exposure geo_loc name (country) - - destination of most recent travel (city) - - destination of most recent travel (state/province/territory) - - destination of most recent travel (country) - - most recent travel departure date - - most recent travel return date - - travel history - - exposure event - - exposure contact level - - host role - - exposure setting - - exposure details - - prior Mpox infection - - prior Mpox infection date - - prior Mpox antiviral treatment - - prior antiviral treatment during prior Mpox infection - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library ID - - amplicon size - - library preparation kit - - sequencing instrument - - sequencing protocol - - sequencing kit number - - amplicon pcr primer scheme - - raw sequence data processing method - - dehosting method - - consensus sequence name - - consensus sequence filename - - consensus sequence filepath - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - r1 fastq filename - - r2 fastq filename - - r1 fastq filepath - - r2 fastq filepath - - fast5 filename - - fast5 filepath - - number of base pairs sequenced - - consensus genome length - - reference genome accession - - bioinformatics protocol - - gene name 1 - - diagnostic pcr Ct value 1 - - gene name 2 - - diagnostic pcr Ct value 2 - - gene name 3 - - diagnostic pcr Ct value 3 - - gene name 4 - - diagnostic pcr Ct value 4 - - gene name 5 - - diagnostic pcr Ct value 5 + - antiviral_therapy + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_history + - location_of_exposure_geo_loc_name_country + - destination_of_most_recent_travel_city + - destination_of_most_recent_travel_state_province_territory + - destination_of_most_recent_travel_country + - most_recent_travel_departure_date + - most_recent_travel_return_date + - travel_history + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - prior_mpox_infection + - prior_mpox_infection_date + - prior_mpox_antiviral_treatment + - prior_antiviral_treatment_during_prior_mpox_infection + - sequencing_project_name + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_email + - sequenced_by_contact_address + - sequence_submitted_by + - sequence_submitter_contact_email + - sequence_submitter_contact_address + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_id + - library_preparation_kit + - sequencing_assay_type + - sequencing_instrument + - sequencing_flow_cell_version + - sequencing_protocol__ + - sequencing_kit_number + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - deduplication_method + - consensus_sequence_name + - genome_sequence_file_name + - genome_sequence_file_path + - consensus_sequence_software_name + - consensus_sequence_software_version + - sequence_assembly_software_name + - sequence_assembly_software_version + - r1_fastq_filename________ + - r2_fastq_filename + - r1_fastq_filepath + - r2_fastq_filepath + - fast5_filename + - fast5_filepath + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - depth_of_coverage_value + - depth_of_coverage_threshold + - number_of_base_pairs_sequenced + - consensus_genome_length + - sequence_assembly_length + - number_of_contigs + - genome_completeness + - n50 + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - reference_genome_accession + - bioinformatics_protocol + - gene_name_1 + - diagnostic_pcr_ct_value_1 + - gene_name_2 + - diagnostic_pcr_ct_value_2 + - gene_name_3 + - diagnostic_pcr_ct_value_3 + - gene_name_4 + - diagnostic_pcr_ct_value_4 + - gene_name_5 + - diagnostic_pcr_ct_value_5 - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database Identifiers - Related specimen primary ID: + related_specimen_primary_id: rank: 2 slot_group: Database Identifiers - case ID: + case_id: rank: 3 slot_group: Database Identifiers - bioproject accession: + bioproject_accession: rank: 4 slot_group: Database Identifiers - biosample accession: + biosample_accession: rank: 5 slot_group: Database Identifiers - SRA accession: + insdc_sequence_read_accession: rank: 6 - slot_group: Database Identifiers - GenBank accession: + slot_group: Database identifiers + insdc_assembly_accession: rank: 7 - slot_group: Database Identifiers - GISAID accession: + slot_group: Database identifiers + gisaid_accession: rank: 8 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 9 slot_group: Sample collection and processing any_of: - - range: sample collected by menu - - range: null value menu + - range: SampleCollectedByMenu + - range: NullValueMenu exact_mappings: - GISAID:Originating%20lab - CNPHI:Lab%20Name - NML_LIMS:CUSTOMER - BIOSAMPLE:collected_by - VirusSeq_Portal:sample%20collected%20by - sample collector contact email: + sample_collector_contact_email: rank: 10 slot_group: Sample collection and processing - sample collector contact address: + sample_collector_contact_address: rank: 11 slot_group: Sample collection and processing - sequenced by: + sample_collection_date: rank: 12 slot_group: Sample collection and processing - any_of: - - range: sequence submitted by menu - - range: null value menu - exact_mappings: - - NML_LIMS:PH_SEQUENCING_CENTRE - - BIOSAMPLE:sequenced_by - sequenced by contact email: + sample_collection_date_precision: rank: 13 slot_group: Sample collection and processing - sequenced by contact address: + sample_received_date: rank: 14 slot_group: Sample collection and processing - sequence submitted by: + geo_loc_name_country: rank: 15 slot_group: Sample collection and processing - any_of: - - range: sequence submitted by menu - - range: null value menu - exact_mappings: - - GISAID:Submitting%20lab - - CNPHI:Sequencing%20Centre - - NML_LIMS:PH_SEQUENCE_SUBMITTER - - BIOSAMPLE:sequence_submitted_by - - VirusSeq_Portal:sequence%20submitted%20by - sequence submitter contact email: - rank: 16 - slot_group: Sample collection and processing - sequence submitter contact address: - rank: 17 - slot_group: Sample collection and processing - sample collection date: - rank: 18 - slot_group: Sample collection and processing - sample collection date precision: - rank: 19 - slot_group: Sample collection and processing - sample received date: - rank: 20 - slot_group: Sample collection and processing - geo_loc_name (country): - rank: 21 - slot_group: Sample collection and processing examples: - value: Canada any_of: - - range: geo_loc_name (country) menu - - range: null value menu - geo_loc_name (state/province/territory): - rank: 22 + - range: GeoLocNameCountryMenu + - range: NullValueMenu + geo_loc_name_state_province_territory: + rank: 16 slot_group: Sample collection and processing comments: Provide the province/territory name from the controlled vocabulary provided. any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu organism: - rank: 23 + rank: 17 slot_group: Sample collection and processing comments: 'Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the @@ -245,10 +237,10 @@ classes: examples: - value: Mpox virus any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu isolate: - rank: 24 + rank: 18 slot_group: Sample collection and processing slot_uri: GENEPIO:0001195 comments: "Provide the GISAID EpiPox virus name, which should be written in\ @@ -265,132 +257,143 @@ classes: - BIOSAMPLE:GISAID_virus_name - VirusSeq_Portal:isolate - VirusSeq_Portal:fasta%20header%20name - purpose of sampling: - rank: 25 + purpose_of_sampling: + rank: 19 slot_group: Sample collection and processing examples: - value: Diagnostic testing any_of: - - range: purpose of sampling menu - - range: null value menu - purpose of sampling details: - rank: 26 + - range: PurposeOfSamplingMenu + - range: NullValueMenu + purpose_of_sampling_details: + rank: 20 slot_group: Sample collection and processing - NML submitted specimen type: - rank: 27 + nml_submitted_specimen_type: + rank: 21 slot_group: Sample collection and processing - Related specimen relationship type: - rank: 28 + related_specimen_relationship_type: + rank: 22 slot_group: Sample collection and processing - anatomical material: - rank: 29 + anatomical_material: + rank: 23 slot_group: Sample collection and processing required: true examples: - value: Lesion (Pustule) any_of: - - range: anatomical material menu - - range: null value menu - anatomical part: - rank: 30 + - range: AnatomicalMaterialMenu + - range: NullValueMenu + anatomical_part: + rank: 24 slot_group: Sample collection and processing required: true examples: - value: Genital area any_of: - - range: anatomical part menu - - range: null value menu - body product: - rank: 31 + - range: AnatomicalPartMenu + - range: NullValueMenu + body_product: + rank: 25 slot_group: Sample collection and processing required: true examples: - value: Pus any_of: - - range: body product menu - - range: null value menu - collection device: - rank: 32 + - range: BodyProductMenu + - range: NullValueMenu + collection_device: + rank: 26 slot_group: Sample collection and processing required: true examples: - value: Swab any_of: - - range: collection device menu - - range: null value menu - collection method: - rank: 33 + - range: CollectionDeviceMenu + - range: NullValueMenu + collection_method: + rank: 27 slot_group: Sample collection and processing required: true examples: - value: Biopsy any_of: - - range: collection method menu - - range: null value menu - specimen processing: - rank: 34 + - range: CollectionMethodMenu + - range: NullValueMenu + specimen_processing: + rank: 28 slot_group: Sample collection and processing examples: - value: Specimens pooled any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:specimen%20processing - specimen processing details: - rank: 35 + specimen_processing_details: + rank: 29 slot_group: Sample collection and processing - host (common name): - rank: 36 + experimental_specimen_role_type: + rank: 30 + slot_group: Sample collection and processing + examples: + - value: Positive experimental control + any_of: + - range: ExperimentalSpecimenRoleTypeMenu + - range: NullValueMenu + experimental_control_details: + rank: 31 + slot_group: Sample collection and processing + host_common_name: + rank: 32 slot_group: Host Information any_of: - - range: host (common name) menu - - range: null value menu + - range: HostCommonNameMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_ANIMAL_TYPE - host (scientific name): - rank: 37 + host_scientific_name: + rank: 33 slot_group: Host Information examples: - value: Homo sapiens any_of: - - range: host (scientific name) menu - - range: null value menu - host health state: - rank: 38 + - range: HostScientificNameMenu + - range: NullValueMenu + host_health_state: + rank: 34 slot_group: Host Information examples: - value: Asymptomatic any_of: - - range: host health state menu - - range: null value menu + - range: HostHealthStateMenu + - range: NullValueMenu exact_mappings: - GISAID:Patient%20status - NML_LIMS:PH_HOST_HEALTH - BIOSAMPLE:host_health_state - host health status details: - rank: 39 + host_health_status_details: + rank: 35 slot_group: Host Information examples: - value: Hospitalized any_of: - - range: host health status details menu - - range: null value menu + - range: HostHealthStatusDetailsMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_HOST_HEALTH_DETAILS - host health outcome: - rank: 40 + host_health_outcome: + rank: 36 slot_group: Host Information examples: - value: Recovered any_of: - - range: host health outcome menu - - range: null value menu + - range: HostHealthOutcomeMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_HOST_HEALTH_OUTCOME - BIOSAMPLE:host_health_outcome - host disease: - rank: 41 + host_disease: + rank: 37 slot_group: Host Information comments: 'Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international @@ -398,219 +401,262 @@ classes: examples: - value: Mpox any_of: - - range: host disease menu - - range: null value menu - host age: - rank: 42 + - range: HostDiseaseMenu + - range: NullValueMenu + host_age: + rank: 38 slot_group: Host Information required: true exact_mappings: - GISAID:Patient%20age - NML_LIMS:PH_AGE - BIOSAMPLE:host_age - host age unit: - rank: 43 + host_age_unit: + rank: 39 slot_group: Host Information required: true examples: - value: year any_of: - - range: host age unit menu - - range: null value menu + - range: HostAgeUnitMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_AGE_UNIT - BIOSAMPLE:host_age_unit - host age bin: - rank: 44 + host_age_bin: + rank: 40 slot_group: Host Information required: true examples: - value: 50 - 59 any_of: - - range: host age bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_AGE_GROUP - BIOSAMPLE:host_age_bin - host gender: - rank: 45 + host_gender: + rank: 41 slot_group: Host Information required: true examples: - value: Male any_of: - - range: host gender menu - - range: null value menu + - range: HostGenderMenu + - range: NullValueMenu exact_mappings: - GISAID:Gender - NML_LIMS:VD_SEX - BIOSAMPLE:host_sex - host residence geo_loc name (country): - rank: 46 + host_residence_geo_loc_name_country: + rank: 42 slot_group: Host Information examples: - value: Canada any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_HOST_COUNTRY - host residence geo_loc name (state/province/territory): - rank: 47 + host_residence_geo_loc_name_state_province_territory: + rank: 43 slot_group: Host Information - symptom onset date: - rank: 48 + symptom_onset_date: + rank: 44 slot_group: Host Information - signs and symptoms: - rank: 49 + signs_and_symptoms: + rank: 45 slot_group: Host Information examples: - value: Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) any_of: - - range: signs and symptoms menu - - range: null value menu + - range: SignsAndSymptomsMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:HC_SYMPTOMS - pre-existing conditions and risk factors: - rank: 50 + preexisting_conditions_and_risk_factors: + rank: 46 slot_group: Host Information any_of: - - range: pre-existing conditions and risk factors menu - - range: null value menu + - range: PreExistingConditionsAndRiskFactorsMenu + - range: NullValueMenu complications: - rank: 51 + rank: 47 slot_group: Host Information examples: - value: Delayed wound healing (lesion healing) any_of: - - range: complications menu - - range: null value menu + - range: ComplicationsMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:complications - antiviral therapy: - rank: 52 + antiviral_therapy: + rank: 48 slot_group: Host Information - host vaccination status: - rank: 53 + host_vaccination_status: + rank: 49 slot_group: Host vaccination information examples: - value: Not Vaccinated any_of: - - range: host vaccination status menu - - range: null value menu - number of vaccine doses received: - rank: 54 + - range: HostVaccinationStatusMenu + - range: NullValueMenu + number_of_vaccine_doses_received: + rank: 50 slot_group: Host vaccination information - vaccination dose 1 vaccine name: - rank: 55 + vaccination_dose_1_vaccine_name: + rank: 51 slot_group: Host vaccination information - vaccination dose 1 vaccination date: - rank: 56 + vaccination_dose_1_vaccination_date: + rank: 52 slot_group: Host vaccination information - vaccination history: - rank: 57 + vaccination_history: + rank: 53 slot_group: Host vaccination information - location of exposure geo_loc name (country): - rank: 58 + location_of_exposure_geo_loc_name_country: + rank: 54 slot_group: Host exposure information examples: - value: Canada any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_EXPOSURE_COUNTRY - destination of most recent travel (city): - rank: 59 + destination_of_most_recent_travel_city: + rank: 55 slot_group: Host exposure information - destination of most recent travel (state/province/territory): - rank: 60 + destination_of_most_recent_travel_state_province_territory: + rank: 56 slot_group: Host exposure information comments: Select the province name from the pick list provided in the template. any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_TRAVEL - destination of most recent travel (country): - rank: 61 + destination_of_most_recent_travel_country: + rank: 57 slot_group: Host exposure information examples: - value: Canada any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:PH_TRAVEL - most recent travel departure date: - rank: 62 + most_recent_travel_departure_date: + rank: 58 slot_group: Host exposure information - most recent travel return date: - rank: 63 + most_recent_travel_return_date: + rank: 59 slot_group: Host exposure information - travel history: - rank: 64 + travel_history: + rank: 60 slot_group: Host exposure information - exposure event: - rank: 65 + exposure_event: + rank: 61 slot_group: Host exposure information examples: - value: Party any_of: - - range: exposure event menu - - range: null value menu - exposure contact level: - rank: 66 + - range: ExposureEventMenu + - range: NullValueMenu + exposure_contact_level: + rank: 62 slot_group: Host exposure information examples: - value: Contact with infected individual any_of: - - range: exposure contact level menu - - range: null value menu - host role: - rank: 67 + - range: ExposureContactLevelMenu + - range: NullValueMenu + host_role: + rank: 63 slot_group: Host exposure information - range: host role menu + range: HostRoleMenu examples: - value: Acquaintance of case - exposure setting: - rank: 68 + exposure_setting: + rank: 64 slot_group: Host exposure information - range: exposure setting menu + range: ExposureSettingMenu examples: - value: Healthcare Setting - exposure details: - rank: 69 + exposure_details: + rank: 65 slot_group: Host exposure information - prior Mpox infection: - rank: 70 + prior_mpox_infection: + rank: 66 slot_group: Host reinfection information examples: - value: Prior infection any_of: - - range: prior Monkeypox infection menu - - range: null value menu + - range: PriorMonkeypoxInfectionMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:prior%20Monkeypox%20infection - prior Mpox infection date: - rank: 71 + prior_mpox_infection_date: + rank: 67 slot_group: Host reinfection information - prior Mpox antiviral treatment: - rank: 72 + prior_mpox_antiviral_treatment: + rank: 68 slot_group: Host reinfection information examples: - value: Prior antiviral treatment any_of: - - range: prior Monkeypox antiviral treatment menu - - range: null value menu + - range: PriorMonkeypoxAntiviralTreatmentMenu + - range: NullValueMenu exact_mappings: - NML_LIMS:prior%20Monkeypox%20antiviral%20treatment - prior antiviral treatment during prior Mpox infection: - rank: 73 + prior_antiviral_treatment_during_prior_mpox_infection: + rank: 69 slot_group: Host reinfection information - purpose of sequencing: + sequencing_project_name: + rank: 70 + slot_group: Sequence information + sequenced_by: + rank: 71 + slot_group: Sequencing + comments: The name of the agency should be written out in full, (with minor + exceptions) and be consistent across multiple submissions. If submitting + specimens rather than sequencing data, please put the "National Microbiology + Laboratory (NML)". + any_of: + - range: SequenceSubmittedByMenu + - range: NullValueMenu + exact_mappings: + - NML_LIMS:PH_SEQUENCING_CENTRE + - BIOSAMPLE:sequenced_by + sequenced_by_laboratory_name: + rank: 72 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 73 + slot_group: Sequencing + sequenced_by_contact_address: rank: 74 slot_group: Sequencing + sequence_submitted_by: + rank: 75 + slot_group: Sequencing + any_of: + - range: SequenceSubmittedByMenu + - range: NullValueMenu + exact_mappings: + - GISAID:Submitting%20lab + - CNPHI:Sequencing%20Centre + - NML_LIMS:PH_SEQUENCE_SUBMITTER + - BIOSAMPLE:sequence_submitted_by + - VirusSeq_Portal:sequence%20submitted%20by + sequence_submitter_contact_email: + rank: 76 + slot_group: Sequencing + sequence_submitter_contact_address: + rank: 77 + slot_group: Sequencing + purpose_of_sequencing: + rank: 78 + slot_group: Sequencing examples: - description: Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria @@ -632,374 +678,464 @@ classes: - description: In all other cases use value: Baseline surveillance (random sampling). any_of: - - range: purpose of sequencing menu - - range: null value menu - purpose of sequencing details: - rank: 75 - slot_group: Sequencing - sequencing date: - rank: 76 - slot_group: Sequencing - required: true - library ID: - rank: 77 - slot_group: Sequencing - amplicon size: - rank: 78 - slot_group: Sequencing - library preparation kit: + - range: PurposeOfSequencingMenu + - range: NullValueMenu + purpose_of_sequencing_details: rank: 79 slot_group: Sequencing - sequencing instrument: + sequencing_date: rank: 80 slot_group: Sequencing - examples: - - value: Oxford Nanopore MinION - any_of: - - range: sequencing instrument menu - - range: null value menu - sequencing protocol: + required: true + library_id: rank: 81 slot_group: Sequencing - sequencing kit number: + library_preparation_kit: rank: 82 slot_group: Sequencing - amplicon pcr primer scheme: + sequencing_assay_type: rank: 83 - slot_group: Sequencing - raw sequence data processing method: + slot_group: Sequence information + range: SequencingAssayTypeMenu + examples: + - value: whole genome sequencing assay + sequencing_instrument: rank: 84 - slot_group: Bioinformatics and QC metrics - required: true - dehosting method: + slot_group: Sequencing + examples: + - value: Oxford Nanopore MinION + any_of: + - range: SequencingInstrumentMenu + - range: NullValueMenu + sequencing_flow_cell_version: rank: 85 - slot_group: Bioinformatics and QC metrics - required: true - consensus sequence name: + slot_group: Sequence information + sequencing_protocol__: rank: 86 - slot_group: Bioinformatics and QC metrics - consensus sequence filename: + slot_group: Sequencing + sequencing_kit_number: rank: 87 - slot_group: Bioinformatics and QC metrics - consensus sequence filepath: + slot_group: Sequencing + dna_fragment_length: rank: 88 - slot_group: Bioinformatics and QC metrics - consensus sequence software name: + slot_group: Sequencing + genomic_target_enrichment_method: rank: 89 - slot_group: Bioinformatics and QC metrics - consensus sequence software version: + slot_group: Sequencing + any_of: + - range: GenomicTargetEnrichmentMethodMenu + - range: NullValueMenu + genomic_target_enrichment_method_details: rank: 90 - slot_group: Bioinformatics and QC metrics - breadth of coverage value: + slot_group: Sequencing + amplicon_pcr_primer_scheme: rank: 91 - slot_group: Bioinformatics and QC metrics - depth of coverage value: + slot_group: Sequencing + amplicon_size: rank: 92 - slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + slot_group: Sequencing + quality_control_method_name: rank: 93 slot_group: Bioinformatics and QC metrics - r1 fastq filename: + quality_control_method_version: rank: 94 slot_group: Bioinformatics and QC metrics - r2 fastq filename: + quality_control_determination: rank: 95 slot_group: Bioinformatics and QC metrics - r1 fastq filepath: + multivalued: true + description: The determination of a quality control assessment. + comments: Select a value from the pick list provided. If a desired value is + missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker + using the New Term Request form. + examples: + - value: sequence failed quality control + any_of: + - range: QualityControlDeterminationMenu + - range: NullValueMenu + quality_control_issues: rank: 96 slot_group: Bioinformatics and QC metrics - r2 fastq filepath: + multivalued: true + description: The reason contributing to, or causing, a low quality determination + in a quality control assessment. + comments: Select a value from the pick list provided. If a desired value is + missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker + using the New Term Request form. + examples: + - value: low average genome coverage + any_of: + - range: QualityControlIssuesMenu + - range: NullValueMenu + quality_control_details: rank: 97 slot_group: Bioinformatics and QC metrics - fast5 filename: + raw_sequence_data_processing_method: rank: 98 slot_group: Bioinformatics and QC metrics - fast5 filepath: + required: true + dehosting_method: rank: 99 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + required: true + deduplication_method: rank: 100 slot_group: Bioinformatics and QC metrics - consensus genome length: + consensus_sequence_name: rank: 101 slot_group: Bioinformatics and QC metrics - reference genome accession: + genome_sequence_file_name: rank: 102 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + genome_sequence_file_path: rank: 103 slot_group: Bioinformatics and QC metrics - required: true - gene name 1: + consensus_sequence_software_name: rank: 104 - slot_group: Pathogen diagnostic testing - comments: Select the name of the gene used for the diagnostic PCR from the - standardized pick list. - any_of: - - range: gene name menu - - range: null value menu - diagnostic pcr Ct value 1: + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: rank: 105 - slot_group: Pathogen diagnostic testing - gene name 2: + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: rank: 106 - slot_group: Pathogen diagnostic testing - comments: Select the name of the gene used for the diagnostic PCR from the - standardized pick list. - any_of: - - range: gene name menu - - range: null value menu - diagnostic pcr Ct value 2: + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: rank: 107 - slot_group: Pathogen diagnostic testing - gene name 3: + slot_group: Bioinformatics and QC metrics + r1_fastq_filename________: rank: 108 - slot_group: Pathogen diagnostic testing - comments: Select the name of the gene used for the diagnostic PCR from the - standardized pick list. - any_of: - - range: gene name menu - - range: null value menu - diagnostic pcr Ct value 3: + slot_group: Bioinformatics and QC metrics + r2_fastq_filename: rank: 109 - slot_group: Pathogen diagnostic testing - gene name 4: + slot_group: Bioinformatics and QC metrics + r1_fastq_filepath: rank: 110 - slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 4: + slot_group: Bioinformatics and QC metrics + r2_fastq_filepath: rank: 111 - slot_group: Pathogen diagnostic testing - gene name 5: + slot_group: Bioinformatics and QC metrics + fast5_filename: rank: 112 - slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 5: + slot_group: Bioinformatics and QC metrics + fast5_filepath: rank: 113 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 114 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 115 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 116 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 117 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 118 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 119 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 120 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 121 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 122 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 123 + slot_group: Bioinformatics and QC metrics + n50: + rank: 124 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 125 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 126 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 127 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 128 + slot_group: Bioinformatics and QC metrics + required: true + gene_name_1: + rank: 129 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_1: + rank: 130 + slot_group: Pathogen diagnostic testing + gene_name_2: + rank: 131 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_2: + rank: 132 + slot_group: Pathogen diagnostic testing + gene_name_3: + rank: 133 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_3: + rank: 134 + slot_group: Pathogen diagnostic testing + gene_name_4: + rank: 135 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_4: + rank: 136 + slot_group: Pathogen diagnostic testing + gene_name_5: + rank: 137 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_5: + rank: 138 slot_group: Pathogen diagnostic testing authors: - rank: 114 + rank: 139 slot_group: Contributor acknowledgement - DataHarmonizer provenance: - rank: 115 + dataharmonizer_provenance: + rank: 140 slot_group: Contributor acknowledgement - Mpox_international: - name: Mpox_international + MpoxInternational: + name: MpoxInternational description: International specification for Mpox clinical virus biosample data gathering is_a: dh_interface see_also: templates/mpox/SOP_Mpox_international.pdf annotations: - version: 5.3.3 + version: 7.5.5 slots: - - specimen collector sample ID - - case ID - - bioproject accession - - biosample accession - - SRA accession - - GenBank accession - - GISAID virus name - - GISAID accession - - sample collected by - - sample collector contact email - - sample collector contact address - - sequenced by - - sequenced by contact email - - sequenced by contact address - - sequence submitted by - - sequence submitter contact email - - sequence submitter contact address - - sample collection date - - sample received date - - geo_loc_name (country) - - geo_loc_name (state/province/territory) - - geo_loc latitude - - geo_loc longitude + - specimen_collector_sample_id + - case_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - gisaid_virus_name + - gisaid_accession + - sample_collected_by + - sample_collector_contact_email + - sample_collector_contact_address + - sample_collection_date + - sample_received_date + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_latitude + - geo_loc_longitude - organism - isolate - - purpose of sampling - - purpose of sampling details - - anatomical material - - anatomical part - - body product - - environmental material - - collection device - - collection method - - specimen processing - - specimen processing details - - host (common name) - - host (scientific name) - - host health state - - host health status details - - host health outcome - - host disease - - host subject ID - - host age - - host age unit - - host age bin - - host gender - - host residence geo_loc name (country) - - symptom onset date - - signs and symptoms - - pre-existing conditions and risk factors + - purpose_of_sampling + - purpose_of_sampling_details + - anatomical_material + - anatomical_part + - body_product + - environmental_material + - collection_device + - collection_method + - specimen_processing + - specimen_processing_details + - experimental_specimen_role_type + - experimental_control_details + - lineage/clade name + - lineage/clade analysis software name + - lineage/clade analysis software version + - host_common_name + - host_scientific_name + - host_health_state + - host_health_status_details + - host_health_outcome + - host_disease + - host_subject_id + - host_age + - host_age_unit + - host_age_bin + - host_gender + - host_residence_geo_loc_name_country + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors - complications - - antiviral therapy - - host vaccination status - - number of vaccine doses received - - vaccination dose 1 vaccine name - - vaccination dose 1 vaccination date - - vaccination history - - location of exposure geo_loc name (country) - - destination of most recent travel (city) - - destination of most recent travel (state/province/territory) - - destination of most recent travel (country) - - most recent travel departure date - - most recent travel return date - - travel history - - exposure event - - exposure contact level - - host role - - exposure setting - - exposure details - - prior Mpox infection - - prior Mpox infection date - - prior Mpox antiviral treatment - - prior antiviral treatment during prior Mpox infection - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library ID - - amplicon size - - library preparation kit - - sequencing instrument - - sequencing protocol - - sequencing kit number - - amplicon pcr primer scheme - - raw sequence data processing method - - dehosting method - - consensus sequence name - - consensus sequence filename - - consensus sequence filepath - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - r1 fastq filename - - r2 fastq filename - - r1 fastq filepath - - r2 fastq filepath - - fast5 filename - - fast5 filepath - - number of base pairs sequenced - - consensus genome length - - reference genome accession - - bioinformatics protocol - - gene name 1 - - diagnostic pcr Ct value 1 - - gene name 2 - - diagnostic pcr Ct value 2 - - gene name 3 - - diagnostic pcr Ct value 3 + - antiviral_therapy + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_history + - location_of_exposure_geo_loc_name_country + - destination_of_most_recent_travel_city + - destination_of_most_recent_travel_state_province_territory + - destination_of_most_recent_travel_country + - most_recent_travel_departure_date + - most_recent_travel_return_date + - travel_history + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - prior_mpox_infection + - prior_mpox_infection_date + - prior_mpox_antiviral_treatment + - prior_antiviral_treatment_during_prior_mpox_infection + - sequencing_project_name + - sequenced_by + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequenced_by_contact_address + - sequence_submitted_by + - sequence_submitter_contact_email + - sequence_submitter_contact_address + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_id + - library_preparation_kit + - sequencing_assay_type + - sequencing_instrument + - sequencing_flow_cell_version + - sequencing_protocol__ + - sequencing_kit_number + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - deduplication_method + - consensus_sequence_name + - genome_sequence_file_name + - genome_sequence_file_path + - consensus_sequence_software_name + - consensus_sequence_software_version + - sequence_assembly_software_name + - sequence_assembly_software_version + - r1_fastq_filename________ + - r2_fastq_filename + - r1_fastq_filepath + - r2_fastq_filepath + - fast5_filename + - fast5_filepath + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - depth_of_coverage_value + - depth_of_coverage_threshold + - number_of_base_pairs_sequenced + - consensus_genome_length + - sequence_assembly_length + - number_of_contigs + - genome_completeness + - n50 + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - reference_genome_accession + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - assay_target_name_1 + - assay_target_details_1 + - gene_symbol_1 + - diagnostic_pcr_protocol_1 + - diagnostic_pcr_ct_value_1 + - assay_target_name_2 + - assay_target_details_2 + - gene_symbol_2 + - diagnostic_pcr_protocol_2 + - diagnostic_pcr_ct_value_2 + - assay_target_name_3 + - assay_target_details_3 + - gene_symbol_3 + - diagnostic_pcr_protocol_3 + - diagnostic_pcr_ct_value_3 - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database Identifiers - case ID: + case_id: rank: 2 slot_group: Database Identifiers - bioproject accession: + bioproject_accession: rank: 3 slot_group: Database Identifiers - biosample accession: + biosample_accession: rank: 4 slot_group: Database Identifiers - SRA accession: + insdc_sequence_read_accession: rank: 5 - slot_group: Database Identifiers - GenBank accession: + slot_group: Database identifiers + insdc_assembly_accession: rank: 6 - slot_group: Database Identifiers - GISAID virus name: + slot_group: Database identifiers + gisaid_virus_name: rank: 7 slot_group: Database Identifiers - GISAID accession: + gisaid_accession: rank: 8 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 9 slot_group: Sample collection and processing any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu exact_mappings: - GISAID:Originating%20lab - BIOSAMPLE:collected_by - sample collector contact email: + sample_collector_contact_email: rank: 10 slot_group: Sample collection and processing - sample collector contact address: + sample_collector_contact_address: rank: 11 slot_group: Sample collection and processing - sequenced by: + sample_collection_date: rank: 12 slot_group: Sample collection and processing - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - exact_mappings: - - BIOSAMPLE:sequenced_by - sequenced by contact email: + sample_received_date: rank: 13 slot_group: Sample collection and processing - sequenced by contact address: + geo_loc_name_country: rank: 14 slot_group: Sample collection and processing - sequence submitted by: - rank: 15 - slot_group: Sample collection and processing - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - exact_mappings: - - GISAID:Submitting%20lab - - BIOSAMPLE:sequence_submitted_by - sequence submitter contact email: - rank: 16 - slot_group: Sample collection and processing - sequence submitter contact address: - rank: 17 - slot_group: Sample collection and processing - sample collection date: - rank: 18 - slot_group: Sample collection and processing - sample received date: - rank: 19 - slot_group: Sample collection and processing - geo_loc_name (country): - rank: 20 - slot_group: Sample collection and processing examples: - value: United States of America [GAZ:00002459] any_of: - - range: geo_loc_name (country) international menu - - range: null value menu - geo_loc_name (state/province/territory): - rank: 21 + - range: GeoLocNameCountryInternationalMenu + - range: NullValueMenu + geo_loc_name_state_province_territory: + rank: 15 slot_group: Sample collection and processing comments: Provide the state/province/territory name from the controlled vocabulary provided. any_of: - range: WhitespaceMinimizedString - - range: null value menu - geo_loc latitude: - rank: 22 + - range: NullValueMenu + geo_loc_latitude: + rank: 16 slot_group: Sample collection and processing - geo_loc longitude: - rank: 23 + geo_loc_longitude: + rank: 17 slot_group: Sample collection and processing organism: - rank: 24 + rank: 18 slot_group: Sample collection and processing comments: 'Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the @@ -1007,10 +1143,10 @@ classes: examples: - value: Mpox virus [NCBITaxon:10244] any_of: - - range: organism international menu - - range: null value menu + - range: OrganismInternationalMenu + - range: NullValueMenu isolate: - rank: 25 + rank: 19 slot_group: Sample collection and processing slot_uri: GENEPIO:0001644 comments: 'This identifier should be an unique, indexed, alpha-numeric ID @@ -1021,121 +1157,141 @@ classes: - value: MpxV/human/USA/CA-CDPH-001/2020 exact_mappings: - BIOSAMPLE:isolate - purpose of sampling: - rank: 26 + purpose_of_sampling: + rank: 20 slot_group: Sample collection and processing examples: - value: Diagnostic testing [GENEPIO:0100002] any_of: - - range: purpose of sampling international menu - - range: null value menu - purpose of sampling details: - rank: 27 + - range: PurposeOfSamplingInternationalMenu + - range: NullValueMenu + purpose_of_sampling_details: + rank: 21 slot_group: Sample collection and processing - anatomical material: - rank: 28 + anatomical_material: + rank: 22 slot_group: Sample collection and processing recommended: true examples: - value: Lesion (Pustule) [NCIT:C78582] any_of: - - range: anatomical material international menu - - range: null value menu - anatomical part: - rank: 29 + - range: AnatomicalMaterialInternationalMenu + - range: NullValueMenu + anatomical_part: + rank: 23 slot_group: Sample collection and processing recommended: true examples: - value: Genital area [BTO:0003358] any_of: - - range: anatomical part international menu - - range: null value menu - body product: - rank: 30 + - range: AnatomicalPartInternationalMenu + - range: NullValueMenu + body_product: + rank: 24 slot_group: Sample collection and processing recommended: true examples: - value: Pus [UBERON:0000177] any_of: - - range: body product international menu - - range: null value menu - environmental material: - rank: 31 + - range: BodyProductInternationalMenu + - range: NullValueMenu + environmental_material: + rank: 25 slot_group: Sample collection and processing - collection device: - rank: 32 + collection_device: + rank: 26 slot_group: Sample collection and processing recommended: true examples: - value: Swab [GENEPIO:0100027] any_of: - - range: collection device international menu - - range: null value menu - collection method: - rank: 33 + - range: CollectionDeviceInternationalMenu + - range: NullValueMenu + collection_method: + rank: 27 slot_group: Sample collection and processing recommended: true examples: - value: Biopsy [OBI:0002650] any_of: - - range: collection method international menu - - range: null value menu - specimen processing: - rank: 34 + - range: CollectionMethodInternationalMenu + - range: NullValueMenu + specimen_processing: + rank: 28 slot_group: Sample collection and processing examples: - value: Specimens pooled [OBI:0600016] any_of: - - range: specimen processing international menu - - range: null value menu - specimen processing details: - rank: 35 + - range: SpecimenProcessingInternationalMenu + - range: NullValueMenu + specimen_processing_details: + rank: 29 slot_group: Sample collection and processing - host (common name): - rank: 36 + experimental_specimen_role_type: + rank: 30 + slot_group: Sample collection and processing + examples: + - value: Positive experimental control [GENEPIO:0101018] + any_of: + - range: ExperimentalSpecimenRoleTypeInternationalMenu + - range: NullValueMenu + experimental_control_details: + rank: 31 + slot_group: Sample collection and processing + lineage/clade name: + rank: 32 + slot_group: Lineage and Variant information + lineage/clade analysis software name: + rank: 33 + slot_group: Lineage and Variant information + lineage/clade analysis software version: + rank: 34 + slot_group: Lineage and Variant information + host_common_name: + rank: 35 slot_group: Host Information any_of: - - range: host (common name) international menu - - range: null value menu - host (scientific name): - rank: 37 + - range: HostCommonNameInternationalMenu + - range: NullValueMenu + host_scientific_name: + rank: 36 slot_group: Host Information examples: - value: Homo sapiens [NCBITaxon:9606] any_of: - - range: host (scientific name) international menu - - range: null value menu - host health state: - rank: 38 + - range: HostScientificNameInternationalMenu + - range: NullValueMenu + host_health_state: + rank: 37 slot_group: Host Information examples: - value: Asymptomatic [NCIT:C3833] any_of: - - range: host health state international menu - - range: null value menu + - range: HostHealthStateInternationalMenu + - range: NullValueMenu exact_mappings: - GISAID:Patient%20status - BIOSAMPLE:host_health_state - host health status details: - rank: 39 + host_health_status_details: + rank: 38 slot_group: Host Information examples: - value: Hospitalized [NCIT:C25179] any_of: - - range: host health status details international menu - - range: null value menu - host health outcome: - rank: 40 + - range: HostHealthStatusDetailsInternationalMenu + - range: NullValueMenu + host_health_outcome: + rank: 39 slot_group: Host Information examples: - value: Recovered [NCIT:C49498] any_of: - - range: host health outcome international menu - - range: null value menu + - range: HostHealthOutcomeInternationalMenu + - range: NullValueMenu exact_mappings: - BIOSAMPLE:host_health_outcome - host disease: - rank: 41 + host_disease: + rank: 40 slot_group: Host Information comments: 'Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international @@ -1143,122 +1299,122 @@ classes: examples: - value: Mpox [MONDO:0002594] any_of: - - range: host disease international menu - - range: null value menu - host subject ID: - rank: 42 + - range: HostDiseaseInternationalMenu + - range: NullValueMenu + host_subject_id: + rank: 41 slot_group: Host Information - host age: - rank: 43 + host_age: + rank: 42 slot_group: Host Information recommended: true exact_mappings: - GISAID:Patient%20age - BIOSAMPLE:host_age - host age unit: - rank: 44 + host_age_unit: + rank: 43 slot_group: Host Information recommended: true examples: - value: year [UO:0000036] any_of: - - range: host age unit international menu - - range: null value menu + - range: HostAgeUnitInternationalMenu + - range: NullValueMenu exact_mappings: - BIOSAMPLE:host_age_unit - host age bin: - rank: 45 + host_age_bin: + rank: 44 slot_group: Host Information recommended: true examples: - value: 50 - 59 [GENEPIO:0100054] any_of: - - range: host age bin international menu - - range: null value menu + - range: HostAgeBinInternationalMenu + - range: NullValueMenu exact_mappings: - BIOSAMPLE:host_age_bin - host gender: - rank: 46 + host_gender: + rank: 45 slot_group: Host Information recommended: true examples: - value: Male [NCIT:C46109] any_of: - - range: host gender international menu - - range: null value menu + - range: HostGenderInternationalMenu + - range: NullValueMenu exact_mappings: - GISAID:Gender - BIOSAMPLE:host_sex - host residence geo_loc name (country): - rank: 47 + host_residence_geo_loc_name_country: + rank: 46 slot_group: Host Information examples: - value: Canada [GAZ:00002560] any_of: - - range: geo_loc_name (country) international menu - - range: null value menu - symptom onset date: - rank: 48 + - range: GeoLocNameCountryInternationalMenu + - range: NullValueMenu + symptom_onset_date: + rank: 47 slot_group: Host Information - signs and symptoms: - rank: 49 + signs_and_symptoms: + rank: 48 slot_group: Host Information examples: - value: Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] any_of: - - range: signs and symptoms international menu - - range: null value menu - pre-existing conditions and risk factors: - rank: 50 + - range: SignsAndSymptomsInternationalMenu + - range: NullValueMenu + preexisting_conditions_and_risk_factors: + rank: 49 slot_group: Host Information any_of: - - range: pre-existing conditions and risk factors international menu - - range: null value menu + - range: PreExistingConditionsAndRiskFactorsInternationalMenu + - range: NullValueMenu complications: - rank: 51 + rank: 50 slot_group: Host Information examples: - value: Delayed wound healing (lesion healing) [MP:0002908] any_of: - - range: complications international menu - - range: null value menu - antiviral therapy: - rank: 52 + - range: ComplicationsInternationalMenu + - range: NullValueMenu + antiviral_therapy: + rank: 51 slot_group: Host Information - host vaccination status: - rank: 53 + host_vaccination_status: + rank: 52 slot_group: Host vaccination information examples: - value: Not Vaccinated [GENEPIO:0100102] any_of: - - range: host vaccination status international menu - - range: null value menu - number of vaccine doses received: + - range: HostVaccinationStatusInternationalMenu + - range: NullValueMenu + number_of_vaccine_doses_received: + rank: 53 + slot_group: Host vaccination information + vaccination_dose_1_vaccine_name: rank: 54 slot_group: Host vaccination information - vaccination dose 1 vaccine name: + vaccination_dose_1_vaccination_date: rank: 55 slot_group: Host vaccination information - vaccination dose 1 vaccination date: + vaccination_history: rank: 56 slot_group: Host vaccination information - vaccination history: + location_of_exposure_geo_loc_name_country: rank: 57 - slot_group: Host vaccination information - location of exposure geo_loc name (country): - rank: 58 slot_group: Host exposure information examples: - value: Canada [GAZ:00002560] any_of: - - range: geo_loc_name (country) international menu - - range: null value menu - destination of most recent travel (city): - rank: 59 + - range: GeoLocNameCountryInternationalMenu + - range: NullValueMenu + destination_of_most_recent_travel_city: + rank: 58 slot_group: Host exposure information - destination of most recent travel (state/province/territory): - rank: 60 + destination_of_most_recent_travel_state_province_territory: + rank: 59 slot_group: Host exposure information range: WhitespaceMinimizedString comments: 'Provide the name of the state/province/territory that the host @@ -1266,224 +1422,359 @@ classes: https://www.ebi.ac.uk/ols/ontologies/gaz' examples: - value: California - destination of most recent travel (country): - rank: 61 + destination_of_most_recent_travel_country: + rank: 60 slot_group: Host exposure information examples: - value: United Kingdom [GAZ:00002637] any_of: - - range: geo_loc_name (country) international menu - - range: null value menu - most recent travel departure date: + - range: GeoLocNameCountryInternationalMenu + - range: NullValueMenu + most_recent_travel_departure_date: + rank: 61 + slot_group: Host exposure information + most_recent_travel_return_date: rank: 62 slot_group: Host exposure information - most recent travel return date: + travel_history: rank: 63 slot_group: Host exposure information - travel history: + exposure_event: rank: 64 slot_group: Host exposure information - exposure event: - rank: 65 - slot_group: Host exposure information examples: - value: Party [PCO:0000035] any_of: - - range: exposure event international menu - - range: null value menu - exposure contact level: - rank: 66 + - range: ExposureEventInternationalMenu + - range: NullValueMenu + exposure_contact_level: + rank: 65 slot_group: Host exposure information examples: - value: Contact with infected individual [GENEPIO:0100357] any_of: - - range: exposure contact level international menu - - range: null value menu - host role: - rank: 67 + - range: ExposureContactLevelInternationalMenu + - range: NullValueMenu + host_role: + rank: 66 slot_group: Host exposure information - range: host role international menu + range: HostRoleInternationalMenu examples: - value: Acquaintance of case [GENEPIO:0100266] - exposure setting: - rank: 68 + exposure_setting: + rank: 67 slot_group: Host exposure information - range: exposure setting international menu + range: ExposureSettingInternationalMenu examples: - value: Healthcare Setting [GENEPIO:0100201] - exposure details: - rank: 69 + exposure_details: + rank: 68 slot_group: Host exposure information - prior Mpox infection: - rank: 70 + prior_mpox_infection: + rank: 69 slot_group: Host reinfection information examples: - value: Prior infection [GENEPIO:0100037] any_of: - - range: prior Monkeypox infection international menu - - range: null value menu - prior Mpox infection date: - rank: 71 + - range: PriorMonkeypoxInfectionInternationalMenu + - range: NullValueMenu + prior_mpox_infection_date: + rank: 70 slot_group: Host reinfection information - prior Mpox antiviral treatment: - rank: 72 + prior_mpox_antiviral_treatment: + rank: 71 slot_group: Host reinfection information examples: - value: Prior antiviral treatment [GENEPIO:0100037] any_of: - - range: prior Monkeypox antiviral treatment international menu - - range: null value menu - prior antiviral treatment during prior Mpox infection: - rank: 73 + - range: PriorMonkeypoxAntiviralTreatmentInternationalMenu + - range: NullValueMenu + prior_antiviral_treatment_during_prior_mpox_infection: + rank: 72 slot_group: Host reinfection information - purpose of sequencing: + sequencing_project_name: + rank: 73 + slot_group: Sequence information + sequenced_by: rank: 74 slot_group: Sequencing - examples: - - value: Baseline surveillance (random sampling) [GENEPIO:0100005] + comments: The name of the agency should be written out in full, (with minor + exceptions) and be consistent across multiple submissions. any_of: - - range: purpose of sequencing international menu - - range: null value menu - purpose of sequencing details: + - range: WhitespaceMinimizedString + - range: NullValueMenu + exact_mappings: + - BIOSAMPLE:sequenced_by + sequenced_by_contact_name: rank: 75 - slot_group: Sequencing - sequencing date: + slot_group: Sequence information + sequenced_by_contact_email: rank: 76 slot_group: Sequencing - library ID: + sequenced_by_contact_address: rank: 77 slot_group: Sequencing - amplicon size: + sequence_submitted_by: rank: 78 slot_group: Sequencing - library preparation kit: + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + exact_mappings: + - GISAID:Submitting%20lab + - BIOSAMPLE:sequence_submitted_by + sequence_submitter_contact_email: rank: 79 slot_group: Sequencing - sequencing instrument: + sequence_submitter_contact_address: rank: 80 slot_group: Sequencing - examples: - - value: Oxford Nanopore MinION [GENEPIO:0100142] - any_of: - - range: sequencing instrument international menu - - range: null value menu - sequencing protocol: + purpose_of_sequencing: rank: 81 slot_group: Sequencing - sequencing kit number: + examples: + - value: Baseline surveillance (random sampling) [GENEPIO:0100005] + any_of: + - range: PurposeOfSequencingInternationalMenu + - range: NullValueMenu + purpose_of_sequencing_details: rank: 82 slot_group: Sequencing - amplicon pcr primer scheme: + sequencing_date: rank: 83 slot_group: Sequencing - raw sequence data processing method: + library_id: rank: 84 - slot_group: Bioinformatics and QC metrics - dehosting method: + slot_group: Sequencing + library_preparation_kit: rank: 85 - slot_group: Bioinformatics and QC metrics - consensus sequence name: + slot_group: Sequencing + sequencing_assay_type: rank: 86 - slot_group: Bioinformatics and QC metrics - consensus sequence filename: + slot_group: Sequence information + range: SequencingAssayTypeInternationalMenu + examples: + - value: whole genome sequencing assay [OBI:0002117] + sequencing_instrument: rank: 87 - slot_group: Bioinformatics and QC metrics - consensus sequence filepath: + slot_group: Sequencing + examples: + - value: Oxford Nanopore MinION [GENEPIO:0100142] + any_of: + - range: SequencingInstrumentInternationalMenu + - range: NullValueMenu + sequencing_flow_cell_version: rank: 88 - slot_group: Bioinformatics and QC metrics - consensus sequence software name: + slot_group: Sequence information + sequencing_protocol__: rank: 89 - slot_group: Bioinformatics and QC metrics - consensus sequence software version: + slot_group: Sequencing + sequencing_kit_number: rank: 90 - slot_group: Bioinformatics and QC metrics - breadth of coverage value: + slot_group: Sequencing + dna_fragment_length: rank: 91 - slot_group: Bioinformatics and QC metrics - depth of coverage value: + slot_group: Sequencing + genomic_target_enrichment_method: rank: 92 - slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + slot_group: Sequencing + any_of: + - range: GenomicTargetEnrichmentMethodInternationalMenu + - range: NullValueMenu + genomic_target_enrichment_method_details: rank: 93 - slot_group: Bioinformatics and QC metrics - r1 fastq filename: + slot_group: Sequencing + amplicon_pcr_primer_scheme: rank: 94 - slot_group: Bioinformatics and QC metrics - r2 fastq filename: + slot_group: Sequencing + amplicon_size: rank: 95 - slot_group: Bioinformatics and QC metrics - r1 fastq filepath: + slot_group: Sequencing + quality_control_method_name: rank: 96 slot_group: Bioinformatics and QC metrics - r2 fastq filepath: + quality_control_method_version: rank: 97 slot_group: Bioinformatics and QC metrics - fast5 filename: + quality_control_determination: rank: 98 slot_group: Bioinformatics and QC metrics - fast5 filepath: + range: QualityControlDeterminationInternationalMenu + quality_control_issues: rank: 99 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + range: QualityControlIssuesInternationalMenu + quality_control_details: rank: 100 slot_group: Bioinformatics and QC metrics - consensus genome length: + raw_sequence_data_processing_method: rank: 101 slot_group: Bioinformatics and QC metrics - reference genome accession: + dehosting_method: rank: 102 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + deduplication_method: rank: 103 slot_group: Bioinformatics and QC metrics - gene name 1: + consensus_sequence_name: rank: 104 - slot_group: Pathogen diagnostic testing - comments: 'Provide the full name of the gene used in the test. The gene symbol - (short form of gene name) can also be provided. Standardized gene names - and symbols can be found in the Gene Ontology using this look-up service: - https://bit.ly/2Sq1LbI' - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - diagnostic pcr Ct value 1: + slot_group: Bioinformatics and QC metrics + genome_sequence_file_name: rank: 105 - slot_group: Pathogen diagnostic testing - gene name 2: + slot_group: Bioinformatics and QC metrics + genome_sequence_file_path: rank: 106 - slot_group: Pathogen diagnostic testing - comments: 'Provide the full name of another gene used in an RT-PCR test. The - gene symbol (short form of gene name) can also be provided. Standardized - gene names and symbols can be found in the Gene Ontology using this look-up - service: https://bit.ly/2Sq1LbI' - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - diagnostic pcr Ct value 2: + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: rank: 107 - slot_group: Pathogen diagnostic testing - gene name 3: + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: rank: 108 - slot_group: Pathogen diagnostic testing - comments: 'Provide the full name of another gene used in an RT-PCR test. The - gene symbol (short form of gene name) can also be provided. Standardized - gene names and symbols can be found in the Gene Ontology using this look-up - service: https://bit.ly/2Sq1LbI' - any_of: - - range: WhitespaceMinimizedString - - range: null value menu - diagnostic pcr Ct value 3: + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: rank: 109 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 110 + slot_group: Bioinformatics and QC metrics + r1_fastq_filename________: + rank: 111 + slot_group: Bioinformatics and QC metrics + r2_fastq_filename: + rank: 112 + slot_group: Bioinformatics and QC metrics + r1_fastq_filepath: + rank: 113 + slot_group: Bioinformatics and QC metrics + r2_fastq_filepath: + rank: 114 + slot_group: Bioinformatics and QC metrics + fast5_filename: + rank: 115 + slot_group: Bioinformatics and QC metrics + fast5_filepath: + rank: 116 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 117 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 118 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 119 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 120 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 121 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 122 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 123 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 124 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 125 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 126 + slot_group: Bioinformatics and QC metrics + n50: + rank: 127 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 128 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 129 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 130 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 131 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 132 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 133 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 134 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 135 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 136 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 137 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 138 + slot_group: Taxonomic identification information + assay_target_name_1: + rank: 139 + slot_group: Pathogen diagnostic testing + assay_target_details_1: + rank: 140 + slot_group: Pathogen diagnostic testing + gene_symbol_1: + rank: 141 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_protocol_1: + rank: 142 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_1: + rank: 143 + slot_group: Pathogen diagnostic testing + assay_target_name_2: + rank: 144 + slot_group: Pathogen diagnostic testing + assay_target_details_2: + rank: 145 + slot_group: Pathogen diagnostic testing + gene_symbol_2: + rank: 146 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_protocol_2: + rank: 147 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_2: + rank: 148 + slot_group: Pathogen diagnostic testing + assay_target_name_3: + rank: 149 + slot_group: Pathogen diagnostic testing + assay_target_details_3: + rank: 150 + slot_group: Pathogen diagnostic testing + gene_symbol_3: + rank: 151 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_protocol_3: + rank: 152 + slot_group: Pathogen diagnostic testing + diagnostic_pcr_ct_value_3: + rank: 153 slot_group: Pathogen diagnostic testing authors: - rank: 110 + rank: 154 slot_group: Contributor acknowledgement - DataHarmonizer provenance: - rank: 111 + dataharmonizer_provenance: + rank: 155 slot_group: Contributor acknowledgement slots: - specimen collector sample ID: - name: specimen collector sample ID + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. comments: Store the collector sample ID. If this number is considered identifiable @@ -1504,8 +1795,8 @@ slots: - NML_LIMS:TEXT_ID - BIOSAMPLE:sample_name - VirusSeq_Portal:specimen%20collector%20sample%20ID - Related specimen primary ID: - name: Related specimen primary ID + related_specimen_primary_id: + name: related_specimen_primary_id title: Related specimen primary ID description: The primary ID of a related specimen previously submitted to the repository. @@ -1515,7 +1806,7 @@ slots: slot_uri: GENEPIO:0001128 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: SR20-12345 exact_mappings: @@ -1523,8 +1814,8 @@ slots: - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_PRIMARY_ID - BIOSAMPLE:host_subject_ID - case ID: - name: case ID + case_id: + name: case_id title: case ID description: The identifier used to specify an epidemiologically detected case of disease. @@ -1537,8 +1828,8 @@ slots: - value: ABCD1234 exact_mappings: - NML_LIMS:PH_CASE_ID - bioproject accession: - name: bioproject accession + bioproject_accession: + name: bioproject_accession title: bioproject accession description: The INSDC accession number of the BioProject(s) to which the BioSample belongs. @@ -1557,8 +1848,8 @@ slots: - value: PRJNA12345 exact_mappings: - NML_LIMS:SUBMISSIONS%20-%20BioProject%20Accession - biosample accession: - name: biosample accession + biosample_accession: + name: biosample_accession title: biosample accession description: The identifier assigned to a BioSample in INSDC archives. comments: Store the accession returned from the BioSample submission. NCBI BioSamples @@ -1573,41 +1864,49 @@ slots: - value: SAMN14180202 exact_mappings: - NML_LIMS:SUBMISSIONS%20-%20BioSample%20Accession - SRA accession: - name: SRA accession - title: SRA accession - description: The Sequence Read Archive (SRA) identifier linking raw read data, - methodological metadata and quality control metrics submitted to the INSDC. - comments: Store the accession assigned to the submitted "run". NCBI-SRA accessions - start with SRR. - slot_uri: GENEPIO:0001142 + insdc_sequence_read_accession: + name: insdc_sequence_read_accession + title: INSDC sequence read accession + description: The identifier assigned to a sequence in one of the International + Nucleotide Sequence Database Collaboration (INSDC) repositories. + comments: Store the accession assigned to the submitted sequence. European Nucleotide + Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start + with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome + Sequence Archive (GSA) accessions start with CRR. + slot_uri: GENEPIO:0101203 range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true examples: - - value: SRR11177792 + - value: SRR123456, ERR123456, DRR123456, CRR123456 exact_mappings: - - NML_LIMS:SUBMISSIONS%20-%20SRA%20Accession - GenBank accession: - name: GenBank accession - title: GenBank accession - description: The GenBank identifier assigned to the sequence in the INSDC archives. - comments: Store the accession returned from a GenBank submission (viral genome - assembly). - slot_uri: GENEPIO:0001145 + - CNPHI:SRA%20Accession + - NML_LIMS:PH_SRA_ACCESSION + insdc_assembly_accession: + name: insdc_assembly_accession + title: INSDC assembly accession + description: The versioned identifier assigned to an assembly or consensus sequence + in one of the International Nucleotide Sequence Database Collaboration (INSDC) + repositories. + comments: Store the versioned accession assigned to the submitted sequence e.g. + the GenBank accession version. + slot_uri: GENEPIO:0101204 range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true examples: - - value: MN908947.3 + - value: LZ986655.1 exact_mappings: - - NML_LIMS:SUBMISSIONS%20-%20GenBank%20Accession - GISAID virus name: - name: GISAID virus name + - CNPHI:GenBank%20Accession + - NML_LIMS:GenBank%20accession + gisaid_virus_name: + name: gisaid_virus_name title: GISAID virus name description: Identifier of the specific isolate. comments: "Provide the GISAID EpiPox virus name, which should be written in the\ @@ -1621,8 +1920,8 @@ slots: exact_mappings: - GISAID:Virus%20name - BIOSAMPLE:GISAID_virus_name - GISAID accession: - name: GISAID accession + gisaid_accession: + name: gisaid_accession title: GISAID accession description: The GISAID accession number assigned to the sequence. comments: Store the accession returned from the GISAID submission. @@ -1639,8 +1938,8 @@ slots: - NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession - BIOSAMPLE:GISAID_accession - VirusSeq_Portal:GISAID%20accession - sample collected by: - name: sample collected by + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the agency that collected the original sample. comments: The name of the sample collector should be written out in full, (with @@ -1652,8 +1951,8 @@ slots: required: true examples: - value: BC Centre for Disease Control - sample collector contact email: - name: sample collector contact email + sample_collector_contact_email: + name: sample_collector_contact_email title: sample collector contact email description: The email address of the contact responsible for follow-up regarding the sample. @@ -1666,8 +1965,8 @@ slots: - value: RespLab@lab.ca exact_mappings: - NML_LIMS:sample%20collector%20contact%20email - sample collector contact address: - name: sample collector contact address + sample_collector_contact_address: + name: sample_collector_contact_address title: sample collector contact address description: The mailing address of the agency submitting the sample. comments: 'The mailing address should be in the format: Street number and name, @@ -1679,82 +1978,8 @@ slots: exact_mappings: - GISAID:Address - NML_LIMS:sample%20collector%20contact%20address - sequenced by: - name: sequenced by - title: sequenced by - description: The name of the agency that generated the sequence. - comments: The name of the agency should be written out in full, (with minor exceptions) - and be consistent across multiple submissions. If submitting specimens rather - than sequencing data, please put the "National Microbiology Laboratory (NML)". - slot_uri: GENEPIO:0100416 - required: true - examples: - - value: Public Health Ontario (PHO) - sequenced by contact email: - name: sequenced by contact email - title: sequenced by contact email - description: The email address of the contact responsible for follow-up regarding - the sequence. - comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, - or RespLab@lab.ca - slot_uri: GENEPIO:0100422 - range: WhitespaceMinimizedString - examples: - - value: RespLab@lab.ca - exact_mappings: - - NML_LIMS:sequenced%20by%20contact%20email - sequenced by contact address: - name: sequenced by contact address - title: sequenced by contact address - description: The mailing address of the agency submitting the sequence. - comments: 'The mailing address should be in the format: Street number and name, - City, Province/Territory, Postal Code, Country' - slot_uri: GENEPIO:0100423 - range: WhitespaceMinimizedString - examples: - - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada - exact_mappings: - - NML_LIMS:sequenced%20by%20contact%20address - sequence submitted by: - name: sequence submitted by - title: sequence submitted by - description: The name of the agency that submitted the sequence to a database. - comments: The name of the agency should be written out in full, (with minor exceptions) - and be consistent across multiple submissions. If submitting specimens rather - than sequencing data, please put the "National Microbiology Laboratory (NML)". - slot_uri: GENEPIO:0001159 - required: true - examples: - - value: Public Health Ontario (PHO) - sequence submitter contact email: - name: sequence submitter contact email - title: sequence submitter contact email - description: The email address of the agency responsible for submission of the - sequence. - comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, - or RespLab@lab.ca - slot_uri: GENEPIO:0001165 - range: WhitespaceMinimizedString - examples: - - value: RespLab@lab.ca - exact_mappings: - - NML_LIMS:sequence%20submitter%20contact%20email - sequence submitter contact address: - name: sequence submitter contact address - title: sequence submitter contact address - description: The mailing address of the agency responsible for submission of the - sequence. - comments: 'The mailing address should be in the format: Street number and name, - City, Province/Territory, Postal Code, Country' - slot_uri: GENEPIO:0001167 - range: WhitespaceMinimizedString - examples: - - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada - exact_mappings: - - GISAID:Address - - NML_LIMS:sequence%20submitter%20contact%20address - sample collection date: - name: sample collection date + sample_collection_date: + name: sample_collection_date title: sample collection date description: The date on which the sample was collected. comments: "Sample collection date is critical for surveillance and many types\ @@ -1766,7 +1991,7 @@ slots: slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} @@ -1779,8 +2004,8 @@ slots: - NML_LIMS:HC_COLLECT_DATE - BIOSAMPLE:collection_date - VirusSeq_Portal:sample%20collection%20date - sample collection date precision: - name: sample collection date precision + sample_collection_date_precision: + name: sample_collection_date_precision title: sample collection date precision description: The precision to which the "sample collection date" was provided. comments: Provide the precision of granularity to the "day", "month", or "year" @@ -1789,23 +2014,23 @@ slots: "month" for "YYYY-MM", or "year" for "YYYY". slot_uri: GENEPIO:0001177 any_of: - - range: sample collection date precision menu - - range: null value menu + - range: SampleCollectionDatePrecisionMenu + - range: NullValueMenu required: true examples: - value: year exact_mappings: - CNPHI:Precision%20of%20date%20collected - NML_LIMS:HC_TEXT2 - sample received date: - name: sample received date + sample_received_date: + name: sample_received_date title: sample received date description: The date on which the sample was received. comments: ISO 8601 standard "YYYY-MM-DD". slot_uri: GENEPIO:0001179 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} @@ -1813,8 +2038,8 @@ slots: - value: '2020-03-20' exact_mappings: - NML_LIMS:sample%20received%20date - geo_loc_name (country): - name: geo_loc_name (country) + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc_name (country) description: The country where the sample was collected. comments: Provide the country name from the controlled vocabulary provided. @@ -1826,8 +2051,8 @@ slots: - NML_LIMS:HC_COUNTRY - BIOSAMPLE:geo_loc_name - VirusSeq_Portal:geo_loc_name%20%28country%29 - geo_loc_name (state/province/territory): - name: geo_loc_name (state/province/territory) + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo_loc_name (state/province/territory) description: The state/province/territory where the sample was collected. slot_uri: GENEPIO:0001185 @@ -1839,8 +2064,8 @@ slots: - NML_LIMS:HC_PROVINCE - BIOSAMPLE:geo_loc_name - VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29 - geo_loc latitude: - name: geo_loc latitude + geo_loc_latitude: + name: geo_loc_latitude title: geo_loc latitude description: The latitude coordinates of the geographical location of sample collection. comments: Provide latitude coordinates if available. Do not use the centre of @@ -1853,8 +2078,8 @@ slots: - value: 38.98 N exact_mappings: - BIOSAMPLE:lat_lon - geo_loc longitude: - name: geo_loc longitude + geo_loc_longitude: + name: geo_loc_longitude title: geo_loc longitude description: The longitude coordinates of the geographical location of sample collection. @@ -1885,10 +2110,10 @@ slots: description: Identifier of the specific isolate. any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - purpose of sampling: - name: purpose of sampling + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: As all samples are taken for diagnostic purposes, "Diagnostic Testing" @@ -1902,8 +2127,8 @@ slots: - NML_LIMS:HC_SAMPLE_CATEGORY - BIOSAMPLE:purpose_of_sampling - VirusSeq_Portal:purpose%20of%20sampling - purpose of sampling details: - name: purpose of sampling details + purpose_of_sampling_details: + name: purpose_of_sampling_details title: purpose of sampling details description: The description of why the sample was collected, providing specific details. @@ -1914,7 +2139,7 @@ slots: slot_uri: GENEPIO:0001200 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Symptomology and history suggested Monkeypox diagnosis. @@ -1923,8 +2148,8 @@ slots: - NML_LIMS:PH_SAMPLING_DETAILS - BIOSAMPLE:description - VirusSeq_Portal:purpose%20of%20sampling%20details - NML submitted specimen type: - name: NML submitted specimen type + nml_submitted_specimen_type: + name: nml_submitted_specimen_type title: NML submitted specimen type description: The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. @@ -1933,15 +2158,15 @@ slots: \ being submitted rather than a specimen for testing, select \u201CNot Applicable\u201D\ ." slot_uri: GENEPIO:0001204 - range: NML submitted specimen type menu + range: NmlSubmittedSpecimenTypeMenu required: true examples: - value: Nucleic Acid exact_mappings: - CNPHI:Specimen%20Type - NML_LIMS:PH_SPECIMEN_TYPE - Related specimen relationship type: - name: Related specimen relationship type + related_specimen_relationship_type: + name: related_specimen_relationship_type title: Related specimen relationship type description: The relationship of the current specimen to the specimen/sample previously submitted to the repository. @@ -1950,16 +2175,16 @@ slots: samples can be linked and tracked in the system. slot_uri: GENEPIO:0001209 any_of: - - range: Related specimen relationship type menu - - range: null value menu + - range: RelatedSpecimenRelationshipTypeMenu + - range: NullValueMenu examples: - value: Previously Submitted exact_mappings: - CNPHI:Related%20Specimen%20ID - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE - anatomical material: - name: anatomical material + anatomical_material: + name: anatomical_material title: anatomical material description: A substance obtained from an anatomical part of an organism e.g. tissue, blood. @@ -1976,8 +2201,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_material - VirusSeq_Portal:anatomical%20material - anatomical part: - name: anatomical part + anatomical_part: + name: anatomical_part title: anatomical part description: An anatomical part of an organism e.g. oropharynx. comments: Provide a descriptor if an anatomical part was sampled. Use the picklist @@ -1993,8 +2218,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_part - VirusSeq_Portal:anatomical%20part - body product: - name: body product + body_product: + name: body_product title: body product description: A substance excreted/secreted from an organism e.g. feces, urine, sweat. @@ -2011,8 +2236,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:body_product - VirusSeq_Portal:body%20product - environmental material: - name: environmental material + environmental_material: + name: environmental_material title: environmental material description: A substance obtained from the natural or man-made environment e.g. soil, water, sewage. @@ -2022,8 +2247,8 @@ slots: a null value. slot_uri: GENEPIO:0001223 any_of: - - range: environmental material international menu - - range: null value menu + - range: EnvironmentalMaterialInternationalMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -2032,8 +2257,8 @@ slots: - GISAID:Specimen%20source - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_material - collection device: - name: collection device + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. swab. comments: Provide a descriptor if a device was used for sampling. Use the picklist @@ -2049,8 +2274,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_device - VirusSeq_Portal:collection%20device - collection method: - name: collection method + collection_method: + name: collection_method title: collection method description: The process used to collect the sample e.g. phlebotamy, necropsy. comments: Provide a descriptor if a collection method was used for sampling. Use @@ -2066,8 +2291,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method - VirusSeq_Portal:collection%20method - specimen processing: - name: specimen processing + specimen_processing: + name: specimen_processing title: specimen processing description: Any processing applied to the sample during or after receiving the sample. @@ -2077,8 +2302,8 @@ slots: pick list apply, put "not applicable". slot_uri: GENEPIO:0001253 multivalued: true - specimen processing details: - name: specimen processing details + specimen_processing_details: + name: specimen_processing_details title: specimen processing details description: Detailed information regarding the processing applied to a sample during or after receiving the sample. @@ -2091,8 +2316,69 @@ slots: a single sample during library prep. exact_mappings: - NML_LIMS:specimen%20processing%20details - host (common name): - name: host (common name) + experimental_specimen_role_type: + name: experimental_specimen_role_type + title: experimental specimen role type + description: The type of role that the sample represents in the experiment. + comments: Samples can play different types of roles in experiments. A sample under + study in one experiment may act as a control or be a replicate of another sample + in another experiment. This field is used to distinguish samples under study + from controls, replicates, etc. If the sample acted as an experimental control + or a replicate, select a role type from the picklist. If the sample was not + a control, leave blank or select "Not Applicable". + slot_uri: GENEPIO:0100921 + multivalued: true + experimental_control_details: + name: experimental_control_details + title: experimental control details + description: The details regarding the experimental control contained in the sample. + comments: Provide details regarding the nature of the reference strain used as + a control, or what is was used to monitor. + slot_uri: GENEPIO:0100922 + range: WhitespaceMinimizedString + examples: + - value: Human coronavirus 229E (HCoV-229E) spiked in sample as process control + lineage/clade name: + name: lineage/clade name + title: lineage/clade name + description: The name of the lineage or clade. + comments: Provide the lineage/clade name. + slot_uri: GENEPIO:0001500 + any_of: + - range: LineageCladeNameINternationalMenu + - range: NullValueMenu + examples: + - value: B.1.1.7 + exact_mappings: + - NML_LIMS:PH_LINEAGE_CLADE_NAME + lineage/clade analysis software name: + name: lineage/clade analysis software name + title: lineage/clade analysis software name + description: The name of the software used to determine the lineage/clade. + comments: Provide the name of the software used to determine the lineage/clade. + slot_uri: GENEPIO:0001501 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: Pangolin + exact_mappings: + - NML_LIMS:PH_LINEAGE_CLADE_SOFTWARE + lineage/clade analysis software version: + name: lineage/clade analysis software version + title: lineage/clade analysis software version + description: The version of the software used to determine the lineage/clade. + comments: Provide the version of the software used ot determine the lineage/clade. + slot_uri: GENEPIO:0001502 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: 2.1.10 + exact_mappings: + - NML_LIMS:PH_LINEAGE_CLADE_VERSION + host_common_name: + name: host_common_name title: host (common name) description: The commonly used name of the host. comments: Common name or scientific name are required if there was a host. Both @@ -2101,8 +2387,8 @@ slots: slot_uri: GENEPIO:0001386 examples: - value: Human - host (scientific name): - name: host (scientific name) + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. comments: Common name or scientific name are required if there was a host. Both @@ -2115,27 +2401,27 @@ slots: - NML_LIMS:host%20%28scientific%20name%29 - BIOSAMPLE:host - VirusSeq_Portal:host%20%28scientific%20name%29 - host health state: - name: host health state + host_health_state: + name: host_health_state title: host health state description: Health status of the host at the time of sample collection. comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001388 - host health status details: - name: host health status details + host_health_status_details: + name: host_health_status_details title: host health status details description: Further details pertaining to the health or disease status of the host at time of collection. comments: If known, select a descriptor from the pick list provided in the template. slot_uri: GENEPIO:0001389 - host health outcome: - name: host health outcome + host_health_outcome: + name: host_health_outcome title: host health outcome description: Disease outcome in the host. comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001389 - host disease: - name: host disease + host_disease: + name: host_disease title: host disease description: The name of the disease experienced by the host. slot_uri: GENEPIO:0001391 @@ -2145,8 +2431,8 @@ slots: - NML_LIMS:PH_HOST_DISEASE - BIOSAMPLE:host_disease - VirusSeq_Portal:host%20disease - host subject ID: - name: host subject ID + host_subject_id: + name: host_subject_id title: host subject ID description: A unique identifier by which each host can be referred to. comments: 'This identifier can be used to link samples from the same individual. @@ -2158,35 +2444,35 @@ slots: - value: 12345B-222 exact_mappings: - BIOSAMPLE:host_subject_id - host age: - name: host age + host_age: + name: host_age title: host age description: Age of host at the time of sampling. comments: If known, provide age. Age-binning is also acceptable. slot_uri: GENEPIO:0001392 any_of: - range: decimal - - range: null value menu - minimum_value: '0' - maximum_value: '130' + - range: NullValueMenu + minimum_value: 0 + maximum_value: 130 examples: - value: '79' - host age unit: - name: host age unit + host_age_unit: + name: host_age_unit title: host age unit description: The units used to measure the host's age. comments: If known, provide the age units used to measure the host's age from the pick list. slot_uri: GENEPIO:0001393 - host age bin: - name: host age bin + host_age_bin: + name: host_age_bin title: host age bin description: The age category of the host at the time of sampling. comments: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. slot_uri: GENEPIO:0001394 - host gender: - name: host gender + host_gender: + name: host_gender title: host gender description: The gender of the host at the time of sample collection. comments: If known, select a value from the pick list. @@ -2195,27 +2481,27 @@ slots: syntax: '{Title_Case}' partial_match: false interpolated: true - host residence geo_loc name (country): - name: host residence geo_loc name (country) + host_residence_geo_loc_name_country: + name: host_residence_geo_loc_name_country title: host residence geo_loc name (country) description: The country of residence of the host. comments: Select the country name from pick list provided in the template. slot_uri: GENEPIO:0001396 - host residence geo_loc name (state/province/territory): - name: host residence geo_loc name (state/province/territory) + host_residence_geo_loc_name_state_province_territory: + name: host_residence_geo_loc_name_state_province_territory title: host residence geo_loc name (state/province/territory) description: The state/province/territory of residence of the host. comments: Select the province/territory name from pick list provided in the template. slot_uri: GENEPIO:0001397 any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu examples: - value: Quebec exact_mappings: - NML_LIMS:PH_HOST_PROVINCE - symptom onset date: - name: symptom onset date + symptom_onset_date: + name: symptom_onset_date title: symptom onset date description: The date on which the symptoms began or were first noted. comments: If known, provide the symptom onset date in ISO 8601 standard format @@ -2223,7 +2509,7 @@ slots: slot_uri: GENEPIO:0001399 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} @@ -2231,16 +2517,16 @@ slots: - value: '2022-05-25' exact_mappings: - NML_LIMS:HC_ONSET_DATE - signs and symptoms: - name: signs and symptoms + signs_and_symptoms: + name: signs_and_symptoms title: signs and symptoms description: A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. comments: Select all of the symptoms experienced by the host from the pick list. slot_uri: GENEPIO:0001400 multivalued: true - pre-existing conditions and risk factors: - name: pre-existing conditions and risk factors + preexisting_conditions_and_risk_factors: + name: preexisting_conditions_and_risk_factors title: pre-existing conditions and risk factors description: 'Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection. @@ -2262,8 +2548,8 @@ slots: list. If the desired term is missing, contact the curation team. slot_uri: GENEPIO:0001402 multivalued: true - antiviral therapy: - name: antiviral therapy + antiviral_therapy: + name: antiviral_therapy title: antiviral therapy description: Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. @@ -2277,8 +2563,8 @@ slots: - value: AZT administered for concurrent HIV infection exact_mappings: - NML_LIMS:antiviral%20therapy - host vaccination status: - name: host vaccination status + host_vaccination_status: + name: host_vaccination_status title: host vaccination status description: The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). @@ -2286,8 +2572,8 @@ slots: slot_uri: GENEPIO:0001404 exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - number of vaccine doses received: - name: number of vaccine doses received + number_of_vaccine_doses_received: + name: number_of_vaccine_doses_received title: number of vaccine doses received description: The number of doses of the vaccine recived by the host. comments: Record how many doses of the vaccine the host has received. @@ -2297,8 +2583,8 @@ slots: - value: '1' exact_mappings: - NML_LIMS:number%20of%20vaccine%20doses%20received - vaccination dose 1 vaccine name: - name: vaccination dose 1 vaccine name + vaccination_dose_1_vaccine_name: + name: vaccination_dose_1_vaccine_name title: vaccination dose 1 vaccine name description: The name of the vaccine administered as the first dose of a vaccine regimen. @@ -2307,13 +2593,13 @@ slots: slot_uri: GENEPIO:0100313 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: IMVAMUNE (Bavarian Nordic) exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 1 vaccination date: - name: vaccination dose 1 vaccination date + vaccination_dose_1_vaccination_date: + name: vaccination_dose_1_vaccination_date title: vaccination dose 1 vaccination date description: The date the first dose of a vaccine was administered. comments: Provide the date the first dose of Smallpox vaccine was administered. @@ -2321,7 +2607,7 @@ slots: slot_uri: GENEPIO:0100314 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} @@ -2329,8 +2615,8 @@ slots: - value: '2022-06-01' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination history: - name: vaccination history + vaccination_history: + name: vaccination_history title: vaccination history description: A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. @@ -2344,15 +2630,15 @@ slots: - value: '2022-06-01' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - location of exposure geo_loc name (country): - name: location of exposure geo_loc name (country) + location_of_exposure_geo_loc_name_country: + name: location_of_exposure_geo_loc_name_country title: location of exposure geo_loc name (country) description: The country where the host was likely exposed to the causative agent of the illness. comments: Select the country name from the pick list provided in the template. slot_uri: GENEPIO:0001410 - destination of most recent travel (city): - name: destination of most recent travel (city) + destination_of_most_recent_travel_city: + name: destination_of_most_recent_travel_city title: destination of most recent travel (city) description: The name of the city that was the destination of most recent travel. comments: 'Provide the name of the city that the host travelled to. Use this look-up @@ -2363,20 +2649,20 @@ slots: - value: New York City exact_mappings: - NML_LIMS:PH_TRAVEL - destination of most recent travel (state/province/territory): - name: destination of most recent travel (state/province/territory) + destination_of_most_recent_travel_state_province_territory: + name: destination_of_most_recent_travel_state_province_territory title: destination of most recent travel (state/province/territory) description: The name of the state/province/territory that was the destination of most recent travel. slot_uri: GENEPIO:0001412 - destination of most recent travel (country): - name: destination of most recent travel (country) + destination_of_most_recent_travel_country: + name: destination_of_most_recent_travel_country title: destination of most recent travel (country) description: The name of the country that was the destination of most recent travel. comments: Select the country name from the pick list provided in the template. slot_uri: GENEPIO:0001413 - most recent travel departure date: - name: most recent travel departure date + most_recent_travel_departure_date: + name: most_recent_travel_departure_date title: most recent travel departure date description: The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. @@ -2384,13 +2670,13 @@ slots: slot_uri: GENEPIO:0001414 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-16' exact_mappings: - NML_LIMS:PH_TRAVEL - most recent travel return date: - name: most recent travel return date + most_recent_travel_return_date: + name: most_recent_travel_return_date title: most recent travel return date description: The date of a person's most recent return to some residence from a journey originating at that residence. @@ -2398,13 +2684,13 @@ slots: slot_uri: GENEPIO:0001415 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-04-26' exact_mappings: - NML_LIMS:PH_TRAVEL - travel history: - name: travel history + travel_history: + name: travel_history title: travel history description: Travel history in last six months. comments: Specify the countries (and more granular locations if known, separated @@ -2418,8 +2704,8 @@ slots: - value: Italy, Milan exact_mappings: - NML_LIMS:PH_TRAVEL - exposure event: - name: exposure event + exposure_event: + name: exposure_event title: exposure event description: Event leading to exposure. comments: Select an exposure event from the pick list provided in the template. @@ -2429,16 +2715,16 @@ slots: - GISAID:Additional%20location%20information - CNPHI:Exposure%20Event - NML_LIMS:PH_EXPOSURE - exposure contact level: - name: exposure contact level + exposure_contact_level: + name: exposure_contact_level title: exposure contact level description: The exposure transmission contact type. comments: Select exposure contact level from the pick-list. slot_uri: GENEPIO:0001418 exact_mappings: - NML_LIMS:exposure%20contact%20level - host role: - name: host role + host_role: + name: host_role title: host role description: The role of the host in relation to the exposure setting. comments: Select the host's personal role(s) from the pick list provided in the @@ -2448,8 +2734,8 @@ slots: multivalued: true exact_mappings: - NML_LIMS:PH_HOST_ROLE - exposure setting: - name: exposure setting + exposure_setting: + name: exposure_setting title: exposure setting description: The setting leading to exposure. comments: Select the host exposure setting(s) from the pick list provided in the @@ -2459,61 +2745,174 @@ slots: multivalued: true exact_mappings: - NML_LIMS:PH_EXPOSURE - exposure details: - name: exposure details + exposure_details: + name: exposure_details title: exposure details description: Additional host exposure information. comments: Free text description of the exposure. slot_uri: GENEPIO:0001431 range: WhitespaceMinimizedString examples: - - value: Large party, many contacts + - value: Large party, many contacts + exact_mappings: + - NML_LIMS:PH_EXPOSURE_DETAILS + prior_mpox_infection: + name: prior_mpox_infection + title: prior Mpox infection + description: The absence or presence of a prior Mpox infection. + comments: If known, provide information about whether the individual had a previous + Mpox infection. Select a value from the pick list. + slot_uri: GENEPIO:0100532 + prior_mpox_infection_date: + name: prior_mpox_infection_date + title: prior Mpox infection date + description: The date of diagnosis of the prior Mpox infection. + comments: Provide the date that the most recent prior infection was diagnosed. + Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0100533 + any_of: + - range: date + - range: NullValueMenu + examples: + - value: '2022-06-20' + exact_mappings: + - NML_LIMS:prior%20Monkeypox%20infection%20date + prior_mpox_antiviral_treatment: + name: prior_mpox_antiviral_treatment + title: prior Mpox antiviral treatment + description: The absence or presence of antiviral treatment for a prior Mpox infection. + comments: If known, provide information about whether the individual had a previous + Mpox antiviral treatment. Select a value from the pick list. + slot_uri: GENEPIO:0100534 + prior_antiviral_treatment_during_prior_mpox_infection: + name: prior_antiviral_treatment_during_prior_mpox_infection + title: prior antiviral treatment during prior Mpox infection + description: Antiviral treatment for any infection during the prior Mpox infection + period. + comments: Provide a description of any antiviral treatment administered for viral + infections (not including Mpox treatment) during the prior Mpox infection period. + This field is meant to capture concurrent treatment information. + slot_uri: GENEPIO:0100535 + range: WhitespaceMinimizedString + examples: + - value: AZT was administered for HIV infection during the prior Mpox infection. + exact_mappings: + - NML_LIMS:prior%20antiviral%20treatment%20during%20Monkeypox%20infection + sequencing_project_name: + name: sequencing_project_name + title: sequencing project name + description: The name of the project/initiative/program for which sequencing was + performed. + comments: Provide the name of the project and/or the project ID here. If the information + is unknown or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100472 + range: WhitespaceMinimizedString + examples: + - value: MPOX-1356 + sequenced_by: + name: sequenced_by + title: sequenced by + description: The name of the agency that generated the sequence. + slot_uri: GENEPIO:0100416 + required: true + examples: + - value: Public Health Ontario (PHO) + sequenced_by_laboratory_name: + name: sequenced_by_laboratory_name + title: sequenced by laboratory name + description: The specific laboratory affiliation of the responsible for sequencing + the isolate's genome. + comments: Provide the name of the specific laboratory that that performed the + sequencing in full (avoid abbreviations). If the information is unknown or cannot + be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100470 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: Topp Lab + sequenced_by_contact_name: + name: sequenced_by_contact_name + title: sequenced by contact name + description: The name or title of the contact responsible for follow-up regarding + the sequence. + comments: Provide the name of an individual or their job title. As personnel turnover + may render the contact's name obsolete, it is more prefereable to provide a + job title for ensuring accuracy of information and institutional memory. If + the information is unknown or cannot be provided, leave blank or provide a null + value. + slot_uri: GENEPIO:0100471 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + required: true + examples: + - value: Joe Bloggs, Enterics Lab Manager + sequenced_by_contact_email: + name: sequenced_by_contact_email + title: sequenced by contact email + description: The email address of the contact responsible for follow-up regarding + the sequence. + comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, + or RespLab@lab.ca + slot_uri: GENEPIO:0100422 + range: WhitespaceMinimizedString + examples: + - value: RespLab@lab.ca + exact_mappings: + - NML_LIMS:sequenced%20by%20contact%20email + sequenced_by_contact_address: + name: sequenced_by_contact_address + title: sequenced by contact address + description: The mailing address of the agency submitting the sequence. + comments: 'The mailing address should be in the format: Street number and name, + City, Province/Territory, Postal Code, Country' + slot_uri: GENEPIO:0100423 + range: WhitespaceMinimizedString + examples: + - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada exact_mappings: - - NML_LIMS:PH_EXPOSURE_DETAILS - prior Mpox infection: - name: prior Mpox infection - title: prior Mpox infection - description: The absence or presence of a prior Mpox infection. - comments: If known, provide information about whether the individual had a previous - Mpox infection. Select a value from the pick list. - slot_uri: GENEPIO:0100532 - prior Mpox infection date: - name: prior Mpox infection date - title: prior Mpox infection date - description: The date of diagnosis of the prior Mpox infection. - comments: Provide the date that the most recent prior infection was diagnosed. - Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". - slot_uri: GENEPIO:0100533 - any_of: - - range: date - - range: null value menu + - NML_LIMS:sequenced%20by%20contact%20address + sequence_submitted_by: + name: sequence_submitted_by + title: sequence submitted by + description: The name of the agency that submitted the sequence to a database. + comments: The name of the agency should be written out in full, (with minor exceptions) + and be consistent across multiple submissions. If submitting specimens rather + than sequencing data, please put the "National Microbiology Laboratory (NML)". + slot_uri: GENEPIO:0001159 + required: true examples: - - value: '2022-06-20' + - value: Public Health Ontario (PHO) + sequence_submitter_contact_email: + name: sequence_submitter_contact_email + title: sequence submitter contact email + description: The email address of the agency responsible for submission of the + sequence. + comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, + or RespLab@lab.ca + slot_uri: GENEPIO:0001165 + range: WhitespaceMinimizedString + examples: + - value: RespLab@lab.ca exact_mappings: - - NML_LIMS:prior%20Monkeypox%20infection%20date - prior Mpox antiviral treatment: - name: prior Mpox antiviral treatment - title: prior Mpox antiviral treatment - description: The absence or presence of antiviral treatment for a prior Mpox infection. - comments: If known, provide information about whether the individual had a previous - Mpox antiviral treatment. Select a value from the pick list. - slot_uri: GENEPIO:0100534 - prior antiviral treatment during prior Mpox infection: - name: prior antiviral treatment during prior Mpox infection - title: prior antiviral treatment during prior Mpox infection - description: Antiviral treatment for any infection during the prior Mpox infection - period. - comments: Provide a description of any antiviral treatment administered for viral - infections (not including Mpox treatment) during the prior Mpox infection period. - This field is meant to capture concurrent treatment information. - slot_uri: GENEPIO:0100535 + - NML_LIMS:sequence%20submitter%20contact%20email + sequence_submitter_contact_address: + name: sequence_submitter_contact_address + title: sequence submitter contact address + description: The mailing address of the agency responsible for submission of the + sequence. + comments: 'The mailing address should be in the format: Street number and name, + City, Province/Territory, Postal Code, Country' + slot_uri: GENEPIO:0001167 range: WhitespaceMinimizedString examples: - - value: AZT was administered for HIV infection during the prior Mpox infection. + - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada exact_mappings: - - NML_LIMS:prior%20antiviral%20treatment%20during%20Monkeypox%20infection - purpose of sequencing: - name: purpose of sequencing + - GISAID:Address + - NML_LIMS:sequence%20submitter%20contact%20address + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the @@ -2530,8 +2929,8 @@ slots: - NML_LIMS:PH_REASON_FOR_SEQUENCING - BIOSAMPLE:purpose_of_sequencing - VirusSeq_Portal:purpose%20of%20sequencing - purpose of sequencing details: - name: purpose of sequencing details + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details description: The description of why the sample was sequenced providing specific details. @@ -2543,7 +2942,7 @@ slots: slot_uri: GENEPIO:0001446 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Outbreak in MSM community @@ -2551,23 +2950,23 @@ slots: - CNPHI:Details%20on%20the%20Reason%20for%20Sequencing - NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS - VirusSeq_Portal:purpose%20of%20sequencing%20details - sequencing date: - name: sequencing date + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: ISO 8601 standard "YYYY-MM-DD". slot_uri: GENEPIO:0001447 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>={sample collection date}' examples: - value: '2020-06-22' exact_mappings: - NML_LIMS:PH_SEQUENCING_DATE - library ID: - name: library ID + library_id: + name: library_id title: library ID description: The user-specified identifier for the library prepared for sequencing. comments: The library name should be unique, and can be an autogenerated ID from @@ -2579,19 +2978,8 @@ slots: - value: XYZ_123345 exact_mappings: - NML_LIMS:library%20ID - amplicon size: - name: amplicon size - title: amplicon size - description: The length of the amplicon generated by PCR amplification. - comments: Provide the amplicon size, including the units. - slot_uri: GENEPIO:0001449 - range: WhitespaceMinimizedString - examples: - - value: 300bp - exact_mappings: - - NML_LIMS:amplicon%20size - library preparation kit: - name: library preparation kit + library_preparation_kit: + name: library_preparation_kit title: library preparation kit description: The name of the DNA library preparation kit used to generate the library being sequenced. @@ -2602,8 +2990,17 @@ slots: - value: Nextera XT exact_mappings: - NML_LIMS:PH_LIBRARY_PREP_KIT - sequencing instrument: - name: sequencing instrument + sequencing_assay_type: + name: sequencing_assay_type + title: sequencing assay type + description: The overarching sequencing methodology that was used to determine + the sequence of a biomaterial. + comments: 'Example Guidance: Provide the name of the DNA or RNA sequencing technology + used in your study. If unsure refer to the protocol documentation, or provide + a null value.' + slot_uri: GENEPIO:0100997 + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Select a sequencing instrument from the picklist provided in the template. @@ -2615,8 +3012,21 @@ slots: - CNPHI:Sequencing%20Instrument - NML_LIMS:PH_SEQUENCING_INSTRUMENT - VirusSeq_Portal:sequencing%20instrument - sequencing protocol: - name: sequencing protocol + sequencing_flow_cell_version: + name: sequencing_flow_cell_version + title: sequencing flow cell version + description: The version number of the flow cell used for generating sequence + data. + comments: Flow cells can vary in terms of design, chemistry, capacity, etc. The + version of the flow cell used to generate sequence data can affect sequence + quantity and quality. Record the version of the flow cell used to generate sequence + data. Do not include "version" or "v" in the version number. + slot_uri: GENEPIO:0101102 + range: WhitespaceMinimizedString + examples: + - value: R.9.4.1 + sequencing_protocol__: + name: sequencing_protocol__ title: sequencing protocol description: The protocol used to generate the sequence. comments: 'Provide a free text description of the methods and materials used to @@ -2633,8 +3043,8 @@ slots: exact_mappings: - NML_LIMS:PH_TESTING_PROTOCOL - VirusSeq_Portal:sequencing%20protocol - sequencing kit number: - name: sequencing kit number + sequencing_kit_number: + name: sequencing_kit_number title: sequencing kit number description: The manufacturer's kit number. comments: Alphanumeric value. @@ -2644,8 +3054,41 @@ slots: - value: AB456XYZ789 exact_mappings: - NML_LIMS:sequencing%20kit%20number - amplicon pcr primer scheme: - name: amplicon pcr primer scheme + dna_fragment_length: + name: dna_fragment_length + title: DNA fragment length + description: The length of the DNA fragment generated by mechanical shearing or + enzymatic digestion for the purposes of library preparation. + comments: Provide the fragment length in base pairs (do not include the units). + slot_uri: GENEPIO:0100843 + range: WhitespaceMinimizedString + examples: + - value: '400' + genomic_target_enrichment_method: + name: genomic_target_enrichment_method + title: genomic target enrichment method + description: The molecular technique used to selectively capture and amplify specific + regions of interest from a genome. + comments: Provide the name of the enrichment method + slot_uri: GENEPIO:0100966 + multivalued: true + recommended: true + examples: + - value: hybrid selection method + genomic_target_enrichment_method_details: + name: genomic_target_enrichment_method_details + title: genomic target enrichment method details + description: Details that provide additional context to the molecular technique + used to selectively capture and amplify specific regions of interest from a + genome. + comments: Provide details that are applicable to the method you used. + slot_uri: GENEPIO:0100967 + range: WhitespaceMinimizedString + examples: + - value: enrichment was done using Illumina Target Enrichment methodology with + the Illumina DNA Prep with enrichment kit. + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme title: amplicon pcr primer scheme description: The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. @@ -2657,8 +3100,63 @@ slots: - value: MPXV Sunrise 3.1 exact_mappings: - NML_LIMS:amplicon%20pcr%20primer%20scheme - raw sequence data processing method: - name: raw sequence data processing method + amplicon_size: + name: amplicon_size + title: amplicon size + description: The length of the amplicon generated by PCR amplification. + comments: Provide the amplicon size expressed in base pairs. + slot_uri: GENEPIO:0001449 + range: integer + examples: + - value: 300bp + quality_control_method_name: + name: quality_control_method_name + title: quality control method name + description: The name of the method used to assess whether a sequence passed a + predetermined quality control threshold. + comments: Providing the name of the method used for quality control is very important + for interpreting the rest of the QC information. Method names can be provided + as the name of a pipeline or a link to a GitHub repository. Multiple methods + should be listed and separated by a semi-colon. Do not include QC tags in other + fields if no method name is provided. + slot_uri: GENEPIO:0100557 + range: WhitespaceMinimizedString + examples: + - value: ncov-tools + quality_control_method_version: + name: quality_control_method_version + title: quality control method version + description: The version number of the method used to assess whether a sequence + passed a predetermined quality control threshold. + comments: Methods updates can make big differences to their outputs. Provide the + version of the method used for quality control. The version can be expressed + using whatever convention the developer implements (e.g. date, semantic versioning). + If multiple methods were used, record the version numbers in the same order + as the method names. Separate the version numbers using a semi-colon. + slot_uri: GENEPIO:0100558 + range: WhitespaceMinimizedString + examples: + - value: 1.2.3 + quality_control_determination: + name: quality_control_determination + title: quality control determination + slot_uri: GENEPIO:0100559 + quality_control_issues: + name: quality_control_issues + title: quality control issues + slot_uri: GENEPIO:0100560 + quality_control_details: + name: quality_control_details + title: quality control details + description: The details surrounding a low quality determination in a quality + control assessment. + comments: Provide notes or details regarding QC results using free text. + slot_uri: GENEPIO:0100561 + range: WhitespaceMinimizedString + examples: + - value: CT value of 39. Low viral load. Low DNA concentration after amplification. + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method description: The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. @@ -2671,8 +3169,8 @@ slots: exact_mappings: - NML_LIMS:PH_RAW_SEQUENCE_METHOD - VirusSeq_Portal:raw%20sequence%20data%20processing%20method - dehosting method: - name: dehosting method + dehosting_method: + name: dehosting_method title: dehosting method description: The method used to remove host reads from the pathogen sequence. comments: Provide the name and version number of the software used to remove host @@ -2684,8 +3182,18 @@ slots: exact_mappings: - NML_LIMS:PH_DEHOSTING_METHOD - VirusSeq_Portal:dehosting%20method - consensus sequence name: - name: consensus sequence name + deduplication_method: + name: deduplication_method + title: deduplication method + description: The method used to remove duplicated reads in a sequence read dataset. + comments: Provide the deduplication software name followed by the version, or + a link to a tool or method. + slot_uri: GENEPIO:0100831 + range: WhitespaceMinimizedString + examples: + - value: DeDup 0.12.8 + consensus_sequence_name: + name: consensus_sequence_name title: consensus sequence name description: The name of the consensus sequence. comments: Provide the name and version number of the consensus sequence. @@ -2695,31 +3203,32 @@ slots: - value: mpxvassembly3 exact_mappings: - NML_LIMS:consensus%20sequence%20name - consensus sequence filename: - name: consensus sequence filename - title: consensus sequence filename + genome_sequence_file_name: + name: genome_sequence_file_name + title: genome sequence file name description: The name of the consensus sequence file. - comments: Provide the name and version number of the consensus sequence FASTA - file. - slot_uri: GENEPIO:0001461 + comments: Provide the name and version number, with the file extension, of the + processed genome sequence file e.g. a consensus sequence FASTA file or a genome + assembly file. + slot_uri: GENEPIO:0101715 range: WhitespaceMinimizedString examples: - value: mpxvassembly.fasta exact_mappings: - NML_LIMS:consensus%20sequence%20filename - consensus sequence filepath: - name: consensus sequence filepath - title: consensus sequence filepath + genome_sequence_file_path: + name: genome_sequence_file_path + title: genome sequence file path description: The filepath of the consensus sequence file. - comments: Provide the filepath of the consensus sequence FASTA file. - slot_uri: GENEPIO:0001462 + comments: Provide the filepath of the genome sequence FASTA file. + slot_uri: GENEPIO:0101716 range: WhitespaceMinimizedString examples: - value: /User/Documents/ViralLab/Data/mpxvassembly.fasta exact_mappings: - NML_LIMS:consensus%20sequence%20filepath - consensus sequence software name: - name: consensus sequence software name + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name description: The name of software used to generate the consensus sequence. comments: Provide the name of the software used to generate the consensus sequence. @@ -2733,8 +3242,8 @@ slots: - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE - VirusSeq_Portal:consensus%20sequence%20software%20name - consensus sequence software version: - name: consensus sequence software version + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version description: The version of the software used to generate the consensus sequence. comments: Provide the version of the software used to generate the consensus sequence. @@ -2748,46 +3257,32 @@ slots: - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION - VirusSeq_Portal:consensus%20sequence%20software%20version - breadth of coverage value: - name: breadth of coverage value - title: breadth of coverage value - description: The percentage of the reference genome covered by the sequenced data, - to a prescribed depth. - comments: Provide value as a percent. - slot_uri: GENEPIO:0001472 - range: WhitespaceMinimizedString - examples: - - value: 95% - exact_mappings: - - NML_LIMS:breadth%20of%20coverage%20value - - VirusSeq_Portal:breadth%20of%20coverage%20value - depth of coverage value: - name: depth of coverage value - title: depth of coverage value - description: The average number of reads representing a given nucleotide in the - reconstructed sequence. - comments: Provide value as a fold of coverage. - slot_uri: GENEPIO:0001474 - range: WhitespaceMinimizedString + sequence_assembly_software_name: + name: sequence_assembly_software_name + title: sequence assembly software name + description: The name of the software used to assemble a sequence. + comments: Provide the name of the software used to assemble the sequence. + slot_uri: GENEPIO:0100825 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + required: true examples: - - value: 400x - exact_mappings: - - GISAID:Depth%20of%20coverage - - NML_LIMS:depth%20of%20coverage%20value - - VirusSeq_Portal:depth%20of%20coverage%20value - depth of coverage threshold: - name: depth of coverage threshold - title: depth of coverage threshold - description: The threshold used as a cut-off for the depth of coverage. - comments: Provide the threshold fold coverage. - slot_uri: GENEPIO:0001475 - range: WhitespaceMinimizedString + - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet + sequence_assembly_software_version: + name: sequence_assembly_software_version + title: sequence assembly software version + description: The version of the software used to assemble a sequence. + comments: Provide the version of the software used to assemble the sequence. + slot_uri: GENEPIO:0100826 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + required: true examples: - - value: 100x - exact_mappings: - - NML_LIMS:depth%20of%20coverage%20threshold - r1 fastq filename: - name: r1 fastq filename + - value: 3.15.5 + r1_fastq_filename________: + name: r1_fastq_filename________ title: r1 fastq filename description: The user-specified filename of the r1 FASTQ file. comments: Provide the r1 FASTQ filename. This information aids in data management. @@ -2796,8 +3291,8 @@ slots: recommended: true examples: - value: ABC123_S1_L001_R1_001.fastq.gz - r2 fastq filename: - name: r2 fastq filename + r2_fastq_filename: + name: r2_fastq_filename title: r2 fastq filename description: The user-specified filename of the r2 FASTQ file. comments: Provide the r2 FASTQ filename. This information aids in data management. @@ -2806,8 +3301,8 @@ slots: recommended: true examples: - value: ABC123_S1_L001_R2_001.fastq.gz - r1 fastq filepath: - name: r1 fastq filepath + r1_fastq_filepath: + name: r1_fastq_filepath title: r1 fastq filepath description: The location of the r1 FASTQ file within a user's file system. comments: Provide the filepath for the r1 FASTQ file. This information aids in @@ -2816,8 +3311,8 @@ slots: range: WhitespaceMinimizedString examples: - value: /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz - r2 fastq filepath: - name: r2 fastq filepath + r2_fastq_filepath: + name: r2_fastq_filepath title: r2 fastq filepath description: The location of the r2 FASTQ file within a user's file system. comments: Provide the filepath for the r2 FASTQ file. This information aids in @@ -2826,8 +3321,8 @@ slots: range: WhitespaceMinimizedString examples: - value: /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz - fast5 filename: - name: fast5 filename + fast5_filename: + name: fast5_filename title: fast5 filename description: The user-specified filename of the FAST5 file. comments: Provide the FAST5 filename. This information aids in data management. @@ -2835,8 +3330,8 @@ slots: range: WhitespaceMinimizedString examples: - value: mpxv123seq.fast5 - fast5 filepath: - name: fast5 filepath + fast5_filepath: + name: fast5_filepath title: fast5 filepath description: The location of the FAST5 file within a user's file system. comments: Provide the filepath for the FAST5 file. This information aids in data @@ -2845,33 +3340,145 @@ slots: range: WhitespaceMinimizedString examples: - value: /User/Documents/RespLab/Data/mpxv123seq.fast5 - number of base pairs sequenced: - name: number of base pairs sequenced + number_of_total_reads: + name: number_of_total_reads + title: number of total reads + description: The total number of non-unique reads generated by the sequencing + process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100827 + range: Integer + examples: + - value: '423867' + number_of_unique_reads: + name: number_of_unique_reads + title: number of unique reads + description: The number of unique reads generated by the sequencing process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100828 + range: Integer + examples: + - value: '248236' + minimum_posttrimming_read_length: + name: minimum_posttrimming_read_length + title: minimum post-trimming read length + description: The threshold used as a cut-off for the minimum length of a read + after trimming. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100829 + range: Integer + examples: + - value: '150' + depth_of_coverage_value: + name: depth_of_coverage_value + title: depth of coverage value + description: The average number of reads representing a given nucleotide in the + reconstructed sequence. + comments: Provide value as a fold of coverage. + slot_uri: GENEPIO:0001474 + range: WhitespaceMinimizedString + examples: + - value: 400x + exact_mappings: + - GISAID:Depth%20of%20coverage + - NML_LIMS:depth%20of%20coverage%20value + - VirusSeq_Portal:depth%20of%20coverage%20value + depth_of_coverage_threshold: + name: depth_of_coverage_threshold + title: depth of coverage threshold + description: The threshold used as a cut-off for the depth of coverage. + comments: Provide the threshold fold coverage. + slot_uri: GENEPIO:0001475 + range: WhitespaceMinimizedString + examples: + - value: 100x + exact_mappings: + - NML_LIMS:depth%20of%20coverage%20threshold + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced title: number of base pairs sequenced description: The number of total base pairs generated by the sequencing process. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001482 range: integer - minimum_value: '0' + minimum_value: 0 examples: - value: '2639019' exact_mappings: - NML_LIMS:number%20of%20base%20pairs%20sequenced - consensus genome length: - name: consensus genome length + consensus_genome_length: + name: consensus_genome_length title: consensus genome length description: Size of the reconstructed genome described as the number of base pairs. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001483 range: integer - minimum_value: '0' + minimum_value: 0 examples: - value: '197063' exact_mappings: - NML_LIMS:consensus%20genome%20length - reference genome accession: - name: reference genome accession + sequence_assembly_length: + name: sequence_assembly_length + title: sequence assembly length + description: The length of the genome generated by assembling reads using a scaffold + or by reference-based mapping. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100846 + range: Integer + examples: + - value: '34272' + number_of_contigs: + name: number_of_contigs + title: number of contigs + description: The number of contigs (contiguous sequences) in a sequence assembly. + comments: Provide a numerical value. + slot_uri: GENEPIO:0100937 + range: Integer + examples: + - value: '10' + genome_completeness: + name: genome_completeness + title: genome completeness + description: The percentage of expected genes identified in the genome being sequenced. + Missing genes indicate missing genomic regions (incompleteness) in the data. + comments: Provide the genome completeness as a percent (no need to include units). + slot_uri: GENEPIO:0100844 + range: WhitespaceMinimizedString + examples: + - value: '85' + n50: + name: n50 + title: N50 + description: The length of the shortest read that, together with other reads, + represents at least 50% of the nucleotides in a set of sequences. + comments: Provide the N50 value in Mb. + slot_uri: GENEPIO:0100938 + range: Integer + examples: + - value: '150' + percent_ns_across_total_genome_length: + name: percent_ns_across_total_genome_length + title: percent Ns across total genome length + description: The percentage of the assembly that consists of ambiguous bases (Ns). + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100830 + range: Integer + examples: + - value: '2' + ns_per_100_kbp: + name: ns_per_100_kbp + title: Ns per 100 kbp + description: The number of ambiguous bases (Ns) normalized per 100 kilobasepairs + (kbp). + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001484 + range: Integer + examples: + - value: '342' + reference_genome_accession: + name: reference_genome_accession title: reference genome accession description: A persistent, unique identifier of a genome database entry. comments: Provide the accession number of the reference genome. @@ -2881,8 +3488,8 @@ slots: - value: NC_063383.1 exact_mappings: - NML_LIMS:reference%20genome%20accession - bioinformatics protocol: - name: bioinformatics protocol + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Further details regarding the methods used to process raw data, and/or @@ -2897,11 +3504,113 @@ slots: - CNPHI:Bioinformatics%20Protocol - NML_LIMS:PH_BIOINFORMATICS_PROTOCOL - VirusSeq_Portal:bioinformatics%20protocol - gene name 1: - name: gene name 1 + read_mapping_software_name: + name: read_mapping_software_name + title: read mapping software name + description: The name of the software used to map sequence reads to a reference + genome or set of reference genes. + comments: Provide the name of the read mapping software. + slot_uri: GENEPIO:0100832 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Bowtie2, BWA-MEM, TopHat + read_mapping_software_version: + name: read_mapping_software_version + title: read mapping software version + description: The version of the software used to map sequence reads to a reference + genome or set of reference genes. + comments: Provide the version number of the read mapping software. + slot_uri: GENEPIO:0100833 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: 2.5.1 + taxonomic_reference_database_name: + name: taxonomic_reference_database_name + title: taxonomic reference database name + description: The name of the taxonomic reference database used to identify the + organism. + comments: Provide the name of the taxonomic reference database. + slot_uri: GENEPIO:0100834 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: NCBITaxon + taxonomic_reference_database_version: + name: taxonomic_reference_database_version + title: taxonomic reference database version + description: The version of the taxonomic reference database used to identify + the organism. + comments: Provide the version number of the taxonomic reference database. + slot_uri: GENEPIO:0100835 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: '1.3' + taxonomic_analysis_report_filename: + name: taxonomic_analysis_report_filename + title: taxonomic analysis report filename + description: The filename of the report containing the results of a taxonomic + analysis. + comments: Provide the filename of the report containing the results of the taxonomic + analysis. + slot_uri: GENEPIO:0101074 + range: WhitespaceMinimizedString + examples: + - value: MPXV_report123.doc + taxonomic_analysis_date: + name: taxonomic_analysis_date + title: taxonomic analysis date + description: The date a taxonomic analysis was performed. + comments: Providing the date that an analyis was performed can help provide context + for tool and reference database versions. Provide the date that the taxonomic + analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". + slot_uri: GENEPIO:0101075 + range: date + examples: + - value: '2024-02-01' + read_mapping_criteria: + name: read_mapping_criteria + title: read mapping criteria + description: A description of the criteria used to map reads to a reference sequence. + comments: Provide a description of the read mapping criteria. + slot_uri: GENEPIO:0100836 + range: WhitespaceMinimizedString + examples: + - value: Phred score >20 + assay_target_name_1: + name: assay_target_name_1 + title: assay target name 1 + description: The name of the assay target used in the diagnostic RT-PCR test. + comments: The specific genomic region, sequence, or variant targeted by the assay + in a diagnostic test. This may include parts of a gene, non-coding regions, + or other genetic elements that serve as a marker for detecting the presence + of a pathogen or other relevant entities. + slot_uri: GENEPIO:0101206 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: MPX (orf B6R) + assay_target_details_1: + name: assay_target_details_1 + title: assay target details 1 + description: Describe any details of the assay target. + comments: Provide details that are applicable to the assay used for the diagnostic + test. + slot_uri: GENEPIO:0102045 + range: WhitespaceMinimizedString + gene_name_1: + name: gene_name_1 title: gene name 1 description: The name of the gene used in the diagnostic RT-PCR test. + comments: Select the name of the gene used for the diagnostic PCR from the standardized + pick list. slot_uri: GENEPIO:0001507 + any_of: + - range: GeneNameMenu + - range: NullValueMenu examples: - value: MPX (orf B6R) exact_mappings: @@ -2909,15 +3618,45 @@ slots: - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231 - BIOSAMPLE:gene_name_1 - VirusSeq_Portal:gene%20name - diagnostic pcr Ct value 1: - name: diagnostic pcr Ct value 1 + gene_symbol_1: + name: gene_symbol_1 + title: gene symbol 1 + description: The gene symbol used in the diagnostic RT-PCR test. + comments: Select the abbreviated representation or standardized symbol of the + gene used in the diagnostic test from the pick list. The assay target or specific + primer region should be added to assay target name. + slot_uri: GENEPIO:0102041 + any_of: + - range: GeneSymbolInternationalMenu + - range: NullValueMenu + examples: + - value: opg190 gene (MPOX) + exact_mappings: + - CNPHI:Gene%20Target%201 + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231 + - BIOSAMPLE:gene_name_1 + - VirusSeq_Portal:gene%20name + diagnostic_pcr_protocol_1: + name: diagnostic_pcr_protocol_1 + title: diagnostic pcr protocol 1 + description: The name and version number of the protocol used for diagnostic marker + amplification. + comments: The name and version number of the protocol used for carrying out a + diagnostic PCR test. This information can be compared to sequence data for evaluation + of performance and quality control. + slot_uri: GENEPIO:0001508 + range: WhitespaceMinimizedString + examples: + - value: B6R (Li et al., 2006) + diagnostic_pcr_ct_value_1: + name: diagnostic_pcr_ct_value_1 title: diagnostic pcr Ct value 1 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the diagnostic RT-PCR test. slot_uri: GENEPIO:0001509 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '21' exact_mappings: @@ -2925,19 +3664,75 @@ slots: - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_1 - VirusSeq_Portal:diagnostic%20pcr%20Ct%20value - gene name 2: - name: gene name 2 + assay_target_name_2: + name: assay_target_name_2 + title: assay target name 2 + description: The name of the assay target used in the diagnostic RT-PCR test. + comments: The specific genomic region, sequence, or variant targeted by the assay + in a diagnostic test. This may include parts of a gene, non-coding regions, + or other genetic elements that serve as a marker for detecting the presence + of a pathogen or other relevant entities. + slot_uri: GENEPIO:0102038 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: OVP (orf 17L) + assay_target_details_2: + name: assay_target_details_2 + title: assay target details 2 + description: Describe any details of the assay target. + comments: Provide details that are applicable to the assay used for the diagnostic + test. + slot_uri: GENEPIO:0102046 + range: WhitespaceMinimizedString + gene_name_2: + name: gene_name_2 title: gene name 2 description: The name of the gene used in the diagnostic RT-PCR test. + comments: Select the name of the gene used for the diagnostic PCR from the standardized + pick list. slot_uri: GENEPIO:0001510 + any_of: + - range: GeneNameMenu + - range: NullValueMenu examples: - value: OVP (orf 17L) exact_mappings: - CNPHI:Gene%20Target%202 - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232 - BIOSAMPLE:gene_name_2 - diagnostic pcr Ct value 2: - name: diagnostic pcr Ct value 2 + gene_symbol_2: + name: gene_symbol_2 + title: gene symbol 2 + description: The gene symbol used in the diagnostic RT-PCR test. + comments: Select the abbreviated representation or standardized symbol of the + gene used in the diagnostic test from the pick list. The assay target or specific + primer region should be added to assay target name. + slot_uri: GENEPIO:0102042 + any_of: + - range: GeneSymbolInternationalMenu + - range: NullValueMenu + examples: + - value: opg002 gene (MPOX) + exact_mappings: + - CNPHI:Gene%20Target%202 + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232 + - BIOSAMPLE:gene_name_2 + diagnostic_pcr_protocol_2: + name: diagnostic_pcr_protocol_2 + title: diagnostic pcr protocol 2 + description: The name and version number of the protocol used for diagnostic marker + amplification. + comments: The name and version number of the protocol used for carrying out a + diagnostic PCR test. This information can be compared to sequence data for evaluation + of performance and quality control. + slot_uri: GENEPIO:0001511 + range: WhitespaceMinimizedString + examples: + - value: G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G). + diagnostic_pcr_ct_value_2: + name: diagnostic_pcr_ct_value_2 title: diagnostic pcr Ct value 2 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR @@ -2945,26 +3740,82 @@ slots: slot_uri: GENEPIO:0001512 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '36' exact_mappings: - CNPHI:Gene%20Target%202%20CT%20Value - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_2 - gene name 3: - name: gene name 3 + assay_target_name_3: + name: assay_target_name_3 + title: assay target name 3 + description: The name of the assay target used in the diagnostic RT-PCR test. + comments: The specific genomic region, sequence, or variant targeted by the assay + in a diagnostic test. This may include parts of a gene, non-coding regions, + or other genetic elements that serve as a marker for detecting the presence + of a pathogen or other relevant entities. + slot_uri: GENEPIO:0102039 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: OPHA (orf B2R) + assay_target_details_3: + name: assay_target_details_3 + title: assay target details 3 + description: Describe any details of the assay target. + comments: Provide details that are applicable to the assay used for the diagnostic + test. + slot_uri: GENEPIO:0102047 + range: WhitespaceMinimizedString + gene_name_3: + name: gene_name_3 title: gene name 3 description: The name of the gene used in the diagnostic RT-PCR test. + comments: Select the name of the gene used for the diagnostic PCR from the standardized + pick list. slot_uri: GENEPIO:0001513 + any_of: + - range: GeneNameMenu + - range: NullValueMenu examples: - value: OPHA (orf B2R) exact_mappings: - CNPHI:Gene%20Target%203 - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233 - BIOSAMPLE:gene_name_3 - diagnostic pcr Ct value 3: - name: diagnostic pcr Ct value 3 + gene_symbol_3: + name: gene_symbol_3 + title: gene symbol 3 + description: The gene symbol used in the diagnostic RT-PCR test. + comments: Select the abbreviated representation or standardized symbol of the + gene used in the diagnostic test from the pick list. The assay target or specific + primer region should be added to assay target name. + slot_uri: GENEPIO:0102043 + any_of: + - range: GeneSymbolInternationalMenu + - range: NullValueMenu + examples: + - value: opg188 gene (MPOX) + exact_mappings: + - CNPHI:Gene%20Target%203 + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233 + - BIOSAMPLE:gene_name_3 + diagnostic_pcr_protocol_3: + name: diagnostic_pcr_protocol_3 + title: diagnostic pcr protocol 3 + description: The name and version number of the protocol used for diagnostic marker + amplification. + comments: The name and version number of the protocol used for carrying out a + diagnostic PCR test. This information can be compared to sequence data for evaluation + of performance and quality control. + slot_uri: GENEPIO:0001514 + range: WhitespaceMinimizedString + examples: + - value: G2R_G (Li et al., 2010) assay + diagnostic_pcr_ct_value_3: + name: diagnostic_pcr_ct_value_3 title: diagnostic pcr Ct value 3 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR @@ -2972,31 +3823,31 @@ slots: slot_uri: GENEPIO:0001515 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '19' exact_mappings: - CNPHI:Gene%20Target%203%20CT%20Value - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_3 - gene name 4: - name: gene name 4 + gene_name_4: + name: gene_name_4 title: gene name 4 description: The name of the gene used in the diagnostic RT-PCR test. comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. slot_uri: GENEPIO:0100576 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu examples: - value: G2R_G (TNFR) exact_mappings: - CNPHI:Gene%20Target%204 - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234 - BIOSAMPLE:gene_name_4 - diagnostic pcr Ct value 4: - name: diagnostic pcr Ct value 4 + diagnostic_pcr_ct_value_4: + name: diagnostic_pcr_ct_value_4 title: diagnostic pcr Ct value 4 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR @@ -3004,31 +3855,31 @@ slots: slot_uri: GENEPIO:0100577 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '27' exact_mappings: - CNPHI:Gene%20Target%204%20CT%20Value - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_4 - gene name 5: - name: gene name 5 + gene_name_5: + name: gene_name_5 title: gene name 5 description: The name of the gene used in the diagnostic RT-PCR test. comments: Select the name of the gene used for the diagnostic PCR from the standardized pick list. slot_uri: GENEPIO:0100578 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu examples: - value: RNAse P exact_mappings: - CNPHI:Gene%20Target%205 - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235 - BIOSAMPLE:gene_name_5 - diagnostic pcr Ct value 5: - name: diagnostic pcr Ct value 5 + diagnostic_pcr_ct_value_5: + name: diagnostic_pcr_ct_value_5 title: diagnostic pcr Ct value 5 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR @@ -3036,7 +3887,7 @@ slots: slot_uri: GENEPIO:0100579 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '30' exact_mappings: @@ -3059,8 +3910,8 @@ slots: - GISAID:Authors - CNPHI:Authors - NML_LIMS:PH_SEQUENCING_AUTHORS - DataHarmonizer provenance: - name: DataHarmonizer provenance + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance description: The DataHarmonizer software and template version provenance. comments: The current software and template version information will be automatically @@ -3074,1309 +3925,2282 @@ slots: - CNPHI:Additional%20Comments - NML_LIMS:HC_COMMENTS enums: - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu + title: null value menu permissible_values: Not Applicable: text: Not Applicable + description: A categorical choice recorded when a datum does not apply to + a given context. meaning: GENEPIO:0001619 Missing: text: Missing + description: A categorical choice recorded when a datum is not included for + an unknown reason. meaning: GENEPIO:0001618 Not Collected: text: Not Collected + description: A categorical choice recorded when a datum was not measured or + collected. meaning: GENEPIO:0001620 Not Provided: text: Not Provided + description: A categorical choice recorded when a datum was collected but + is not currently provided in the information being shared. This value indicates + the information may be shared at the later stage. meaning: GENEPIO:0001668 Restricted Access: text: Restricted Access + description: A categorical choice recorded when a given datum is available + but not shared publicly because of information privacy concerns. meaning: GENEPIO:0001810 - geo_loc_name (state/province/territory) menu: - name: geo_loc_name (state/province/territory) menu + GeoLocNameStateProvinceTerritoryMenu: + name: GeoLocNameStateProvinceTerritoryMenu + title: geo_loc_name (state/province/territory) menu permissible_values: Alberta: text: Alberta + description: One of Canada's prairie provinces. It became a province on 1905-09-01. + Alberta is located in western Canada, bounded by the provinces of British + Columbia to the west and Saskatchewan to the east, Northwest Territories + to the north, and by the State of Montana to the south. Statistics Canada + divides the province of Alberta into nineteen census divisions, each with + one or more municipal governments overseeing county municipalities, improvement + districts, special areas, specialized municipalities, municipal districts, + regional municipalities, cities, towns, villages, summer villages, Indian + settlements, and Indian reserves. Census divisions are not a unit of local + government in Alberta. meaning: GAZ:00002566 British Columbia: text: British Columbia + description: The westernmost of Canada's provinces. British Columbia is bordered + by the Pacific Ocean on the west, by the American State of Alaska on the + northwest, and to the north by the Yukon and the Northwest Territories, + on the east by the province of Alberta, and on the south by the States of + Washington, Idaho, and Montana. The current southern border of British Columbia + was established by the 1846 Oregon Treaty, although its history is tied + with lands as far south as the California border. British Columbia's rugged + coastline stretches for more than 27,000 km, and includes deep, mountainous + fjords and about 6,000 islands, most of which are uninhabited. British Columbia + is carved into 27 regional districts. These regional districts are federations + of member municipalities and electoral areas. The unincorporated area of + the regional district is carved into electoral areas. meaning: GAZ:00002562 Manitoba: text: Manitoba + description: One of Canada's 10 provinces. Manitoba is located at the longitudinal + centre of Canada, although it is considered to be part of Western Canada. + It borders Saskatchewan to the west, Ontario to the east, Nunavut and Hudson + Bay to the north, and the American states of North Dakota and Minnesota + to the south. Statistics Canada divides the province of Manitoba into 23 + census divisions. Census divisions are not a unit of local government in + Manitoba. meaning: GAZ:00002571 New Brunswick: text: New Brunswick + description: One of Canada's three Maritime provinces. New Brunswick is bounded + on the north by Quebec's Gaspe Peninsula and by Chaleur Bay. Along the east + coast, the Gulf of Saint Lawrence and Northumberland Strait form the boundaries. + In the south-east corner of the province, the narrow Isthmus of Chignecto + connects New Brunswick to the Nova Scotia peninsula. The south of the province + is bounded by the Bay of Fundy, which has the highest tides in the world + with a rise of 16 m. To the west, the province borders the American State + of Maine. New Brunswick is divided into 15 counties, which no longer have + administrative roles except in the court system. The counties are divided + into parishes. meaning: GAZ:00002570 Newfoundland and Labrador: text: Newfoundland and Labrador + description: A province of Canada, the tenth and latest to join the Confederation. + Geographically, the province consists of the island of Newfoundland and + the mainland Labrador, on Canada's Atlantic coast. meaning: GAZ:00002567 Northwest Territories: text: Northwest Territories + description: 'A territory of Canada. Located in northern Canada, it borders + Canada''s two other territories, Yukon to the west and Nunavut to the east, + and three provinces: British Columbia to the southwest, Alberta to the south, + and Saskatchewan to the southeast. The present-day territory was created + in 1870-06, when the Hudson''s Bay Company transferred Rupert''s Land and + North-Western Territory to the government of Canada.' meaning: GAZ:00002575 Nova Scotia: text: Nova Scotia + description: A Canadian province located on Canada's southeastern coast. The + province's mainland is the Nova Scotia peninsula surrounded by the Atlantic + Ocean, including numerous bays and estuaries. No where in Nova Scotia is + more than 67 km from the ocean. Cape Breton Island, a large island to the + northeast of the Nova Scotia mainland, is also part of the province, as + is Sable Island. meaning: GAZ:00002565 Nunavut: text: Nunavut + description: The largest and newest territory of Canada; it was separated + officially from the Northwest Territories on 1999-04-01. The Territory covers + about 1.9 million km2 of land and water in Northern Canada including part + of the mainland, most of the Arctic Archipelago, and all of the islands + in Hudson Bay, James Bay, and Ungava Bay (including the Belcher Islands) + which belonged to the Northwest Territories. Nunavut has land borders with + the Northwest Territories on several islands as well as the mainland, a + border with Manitoba to the south of the Nunavut mainland, and a tiny land + border with Newfoundland and Labrador on Killiniq Island. It also shares + aquatic borders with the provinces of Quebec, Ontario and Manitoba and with + Greenland. meaning: GAZ:00002574 Ontario: text: Ontario + description: 'A province located in the central part of Canada. Ontario is + bordered by the provinces of Manitoba to the west, Quebec to the east, and + the States of Michigan, New York, and Minnesota. Most of Ontario''s borders + with the United States are natural, starting at the Lake of the Woods and + continuing through the four Great Lakes: Superior, Huron (which includes + Georgian Bay), Erie, and Ontario (for which the province is named), then + along the Saint Lawrence River near Cornwall. Ontario is the only Canadian + Province that borders the Great Lakes. There are three different types of + census divisions: single-tier municipalities, upper-tier municipalities + (which can be regional municipalities or counties) and districts.' meaning: GAZ:00002563 Prince Edward Island: text: Prince Edward Island + description: A Canadian province consisting of an island of the same name. + It is divided into 3 counties. meaning: GAZ:00002572 Quebec: text: Quebec + description: A province in the central part of Canada. Quebec is Canada's + largest province by area and its second-largest administrative division; + only the territory of Nunavut is larger. It is bordered to the west by the + province of Ontario, James Bay and Hudson Bay, to the north by Hudson Strait + and Ungava Bay, to the east by the Gulf of Saint Lawrence and the provinces + of Newfoundland and Labrador and New Brunswick. It is bordered on the south + by the American states of Maine, New Hampshire, Vermont, and New York. It + also shares maritime borders with the Territory of Nunavut, the Province + of Prince Edward Island and the Province of Nova Scotia. meaning: GAZ:00002569 Saskatchewan: text: Saskatchewan + description: A prairie province in Canada. Saskatchewan is bounded on the + west by Alberta, on the north by the Northwest Territories, on the east + by Manitoba, and on the south by the States of Montana and North Dakota. + It is divided into 18 census divisions according to Statistics Canada. meaning: GAZ:00002564 Yukon: text: Yukon + description: The westernmost of Canada's three territories. The territory + is the approximate shape of a right triangle, bordering the American State + of Alaska to the west, the Northwest Territories to the east and British + Columbia to the south. Its northern coast is on the Beaufort Sea. Its ragged + eastern boundary mostly follows the divide between the Yukon Basin and the + Mackenzie River drainage basin to the east in the Mackenzie mountains. Its + capital is Whitehorse. meaning: GAZ:00002576 - sample collection date precision menu: - name: sample collection date precision menu + SampleCollectionDatePrecisionMenu: + name: SampleCollectionDatePrecisionMenu + title: sample collection date precision menu permissible_values: year: text: year + description: A time unit which is equal to 12 months which in science is taken + to be equal to 365.25 days. meaning: UO:0000036 month: text: month + description: A time unit which is approximately equal to the length of time + of one of cycle of the moon's phases which in science is taken to be equal + to 30 days. meaning: UO:0000035 day: text: day + description: A time unit which is equal to 24 hours. meaning: UO:0000033 - NML submitted specimen type menu: - name: NML submitted specimen type menu + NmlSubmittedSpecimenTypeMenu: + name: NmlSubmittedSpecimenTypeMenu + title: NML submitted specimen type menu permissible_values: Bodily fluid: text: Bodily fluid + description: Liquid components of living organisms. includes fluids that are + excreted or secreted from the body as well as body water that normally is + not. meaning: UBERON:0006314 DNA: text: DNA + description: The output of an extraction process in which DNA molecules are + purified in order to exclude DNA from organellas. meaning: OBI:0001051 Nucleic acid: text: Nucleic acid + description: An extract that is the output of an extraction process in which + nucleic acid molecules are isolated from a specimen. meaning: OBI:0001010 RNA: text: RNA + description: An extract which is the output of an extraction process in which + RNA molecules are isolated from a specimen. meaning: OBI:0000880 Swab: text: Swab + description: A device which is a soft, absorbent material mounted on one or + both ends of a stick. meaning: OBI:0002600 Tissue: text: Tissue + description: Multicellular anatomical structure that consists of many cells + of one or a few types, arranged in an extracellular matrix such that their + long-range organisation is at least partly a repetition of their short-range + organisation. meaning: UBERON:0000479 Not Applicable: text: Not Applicable + description: A categorical choice recorded when a datum does not apply to + a given context. meaning: GENEPIO:0001619 - Related specimen relationship type menu: - name: Related specimen relationship type menu + RelatedSpecimenRelationshipTypeMenu: + name: RelatedSpecimenRelationshipTypeMenu + title: Related specimen relationship type menu permissible_values: Acute: text: Acute + description: Sudden appearance of disease manifestations over a short period + of time. The word acute is applied to different time scales depending on + the disease or manifestation and does not have an exact definition in minutes, + hours, or days. meaning: HP:0011009 Convalescent: text: Convalescent + description: A specimen collected from an individual during the recovery phase + following the resolution of acute symptoms of a disease, often used to assess + immune response or recovery progression. Familial: text: Familial + description: A specimen obtained from a relative of an individual, often used + in studies examining genetic or hereditary factors, or familial transmission + of conditions. Follow-up: text: Follow-up + description: The process by which information about the health status of an + individual is obtained after a study has officially closed; an activity + that continues something that has already begun or that repeats something + that has already been done. meaning: EFO:0009642 Reinfection testing: text: Reinfection testing + description: A specimen collected to determine if an individual has been re-exposed + to and reinfected by a pathogen after an initial infection and recovery. is_a: Follow-up Previously Submitted: text: Previously Submitted + description: A specimen that has been previously provided or used in a study + or testing but is being considered for re-analysis or additional testing. Sequencing/bioinformatics methods development/validation: text: Sequencing/bioinformatics methods development/validation + description: A specimen used specifically for the purpose of developing, testing, + or validating sequencing or bioinformatics methodologies. Specimen sampling methods testing: text: Specimen sampling methods testing - anatomical material menu: - name: anatomical material menu + description: A specimen used to test, refine, or validate methods and techniques + for collecting and processing samples. + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical material menu permissible_values: Blood: text: Blood + description: A fluid that is composed of blood plasma and erythrocytes. meaning: UBERON:0000178 Blood clot: text: Blood clot + description: Venous or arterial thrombosis (formation of blood clots) of spontaneous + nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). meaning: UBERON:0010210 is_a: Blood Blood serum: text: Blood serum + description: The portion of blood plasma that excludes clotting factors. meaning: UBERON:0001977 is_a: Blood Blood plasma: text: Blood plasma + description: The liquid component of blood, in which erythrocytes are suspended. meaning: UBERON:0001969 is_a: Blood Whole blood: text: Whole blood + description: Blood that has not been separated into its various components; + blood that has not been modified except for the addition of an anticoagulant. meaning: NCIT:C41067 is_a: Blood Fluid: text: Fluid + description: Liquid components of living organisms. includes fluids that are + excreted or secreted from the body as well as body water that normally is + not. meaning: UBERON:0006314 Saliva: text: Saliva + description: A fluid produced in the oral cavity by salivary glands, typically + used in predigestion, but also in other functions. meaning: UBERON:0001836 is_a: Fluid Fluid (cerebrospinal (CSF)): text: Fluid (cerebrospinal (CSF)) + description: A clear, colorless, bodily fluid, that occupies the subarachnoid + space and the ventricular system around and inside the brain and spinal + cord. meaning: UBERON:0001359 is_a: Fluid Fluid (pericardial): text: Fluid (pericardial) + description: Transudate contained in the pericardial cavity. meaning: UBERON:0002409 is_a: Fluid Fluid (pleural): text: Fluid (pleural) + description: Transudate contained in the pleural cavity. meaning: UBERON:0001087 is_a: Fluid Fluid (vaginal): text: Fluid (vaginal) + description: Fluid that lines the vaginal walls that consists of multiple + secretions that collect in the vagina from different glands meaning: UBERON:0036243 is_a: Fluid Fluid (amniotic): text: Fluid (amniotic) + description: Amniotic fluid is a bodily fluid consisting of watery liquid + surrounding and cushioning a growing fetus within the amnion. meaning: UBERON:0000173 is_a: Fluid Lesion: text: Lesion + description: A localized pathological or traumatic structural change, damage, + deformity, or discontinuity of tissue, organ, or body part. meaning: NCIT:C3824 Lesion (Macule): text: Lesion (Macule) + description: A flat lesion characterized by change in the skin color. meaning: NCIT:C43278 is_a: Lesion Lesion (Papule): text: Lesion (Papule) + description: A small (less than 5-10 mm) elevation of skin that is non-suppurative. meaning: NCIT:C39690 is_a: Lesion Lesion (Pustule): text: Lesion (Pustule) + description: A circumscribed and elevated skin lesion filled with purulent + material. meaning: NCIT:C78582 is_a: Lesion Lesion (Scab): text: Lesion (Scab) + description: A dry, rough, crust-like lesion that forms over a wound or ulcer + as part of the natural healing process. It consists of dried blood, serum, + and cellular debris. meaning: GENEPIO:0100490 is_a: Lesion Lesion (Vesicle): text: Lesion (Vesicle) + description: A small, fluid-filled elevation on the skin. Vesicles are often + clear or slightly cloudy and can be a sign of various skin conditions or + infections. meaning: GENEPIO:0100491 is_a: Lesion Rash: text: Rash + description: A skin and integumentary tissue symptom that is characterized + by an eruption on the body typically with little or no elevation above the + surface. meaning: SYMP:0000487 Ulcer: text: Ulcer + description: A circumscribed inflammatory and often suppurating lesion on + the skin or an internal mucous surface resulting in necrosis of tissue. meaning: NCIT:C3426 Tissue: text: Tissue + description: Multicellular anatomical structure that consists of many cells + of one or a few types, arranged in an extracellular matrix such that their + long-range organisation is at least partly a repetition of their short-range + organisation. meaning: UBERON:0000479 Wound tissue (injury): text: Wound tissue (injury) + description: Damage inflicted on the body as the direct or indirect result + of an external force, with or without disruption of structural continuity. meaning: NCIT:C3671 is_a: Tissue - anatomical material international menu: - name: anatomical material international menu + AnatomicalMaterialInternationalMenu: + name: AnatomicalMaterialInternationalMenu + title: anatomical material international menu permissible_values: Blood [UBERON:0000178]: text: Blood [UBERON:0000178] + description: A fluid that is composed of blood plasma and erythrocytes. meaning: UBERON:0000178 Blood clot [UBERON:0010210]: text: Blood clot [UBERON:0010210] + description: Venous or arterial thrombosis (formation of blood clots) of spontaneous + nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). meaning: UBERON:0010210 is_a: Blood [UBERON:0000178] Blood serum [UBERON:0001977]: text: Blood serum [UBERON:0001977] + description: The portion of blood plasma that excludes clotting factors. meaning: UBERON:0001977 is_a: Blood [UBERON:0000178] Blood plasma [UBERON:0001969]: text: Blood plasma [UBERON:0001969] + description: The liquid component of blood, in which erythrocytes are suspended. meaning: UBERON:0001969 is_a: Blood [UBERON:0000178] Whole blood [NCIT:C41067]: text: Whole blood [NCIT:C41067] + description: Blood that has not been separated into its various components; + blood that has not been modified except for the addition of an anticoagulant. meaning: NCIT:C41067 is_a: Blood [UBERON:0000178] Fluid [UBERON:0006314]: text: Fluid [UBERON:0006314] + description: Liquid components of living organisms. includes fluids that are + excreted or secreted from the body as well as body water that normally is + not. meaning: UBERON:0006314 Saliva [UBERON:0001836]: text: Saliva [UBERON:0001836] + description: A fluid produced in the oral cavity by salivary glands, typically + used in predigestion, but also in other functions. meaning: UBERON:0001836 is_a: Fluid [UBERON:0006314] Fluid (cerebrospinal (CSF)) [UBERON:0001359]: text: Fluid (cerebrospinal (CSF)) [UBERON:0001359] + description: A clear, colorless, bodily fluid, that occupies the subarachnoid + space and the ventricular system around and inside the brain and spinal + cord. meaning: UBERON:0001359 is_a: Fluid [UBERON:0006314] Fluid (pericardial) [UBERON:0002409]: text: Fluid (pericardial) [UBERON:0002409] + description: Transudate contained in the pericardial cavity. meaning: UBERON:0002409 is_a: Fluid [UBERON:0006314] Fluid (pleural) [UBERON:0001087]: text: Fluid (pleural) [UBERON:0001087] + description: Transudate contained in the pleural cavity. meaning: UBERON:0001087 is_a: Fluid [UBERON:0006314] Fluid (vaginal) [UBERON:0036243]: text: Fluid (vaginal) [UBERON:0036243] + description: Fluid that lines the vaginal walls that consists of multiple + secretions that collect in the vagina from different glands meaning: UBERON:0036243 is_a: Fluid [UBERON:0006314] Fluid (amniotic) [UBERON:0000173]: text: Fluid (amniotic) [UBERON:0000173] + description: Amniotic fluid is a bodily fluid consisting of watery liquid + surrounding and cushioning a growing fetus within the amnion. meaning: UBERON:0000173 is_a: Fluid [UBERON:0006314] Lesion [NCIT:C3824]: text: Lesion [NCIT:C3824] + description: A localized pathological or traumatic structural change, damage, + deformity, or discontinuity of tissue, organ, or body part. meaning: NCIT:C3824 Lesion (Macule) [NCIT:C43278]: text: Lesion (Macule) [NCIT:C43278] + description: A flat lesion characterized by change in the skin color. meaning: NCIT:C43278 is_a: Lesion [NCIT:C3824] Lesion (Papule) [NCIT:C39690]: text: Lesion (Papule) [NCIT:C39690] + description: A small (less than 5-10 mm) elevation of skin that is non-suppurative. meaning: NCIT:C39690 is_a: Lesion [NCIT:C3824] Lesion (Pustule) [NCIT:C78582]: text: Lesion (Pustule) [NCIT:C78582] + description: A circumscribed and elevated skin lesion filled with purulent + material. meaning: NCIT:C78582 is_a: Lesion [NCIT:C3824] Lesion (Scab) [GENEPIO:0100490]: text: Lesion (Scab) [GENEPIO:0100490] + description: A dry, rough, crust-like lesion that forms over a wound or ulcer + as part of the natural healing process. It consists of dried blood, serum, + and cellular debris. meaning: GENEPIO:0100490 is_a: Lesion [NCIT:C3824] Lesion (Vesicle) [GENEPIO:0100491]: text: Lesion (Vesicle) [GENEPIO:0100491] + description: A small, fluid-filled elevation on the skin. Vesicles are often + clear or slightly cloudy and can be a sign of various skin conditions or + infections. meaning: GENEPIO:0100491 is_a: Lesion [NCIT:C3824] Rash [SYMP:0000487]: text: Rash [SYMP:0000487] + description: A skin and integumentary tissue symptom that is characterized + by an eruption on the body typically with little or no elevation above the + surface. meaning: SYMP:0000487 Ulcer [NCIT:C3426]: text: Ulcer [NCIT:C3426] + description: A circumscribed inflammatory and often suppurating lesion on + the skin or an internal mucous surface resulting in necrosis of tissue. meaning: NCIT:C3426 Tissue [UBERON:0000479]: text: Tissue [UBERON:0000479] + description: Multicellular anatomical structure that consists of many cells + of one or a few types, arranged in an extracellular matrix such that their + long-range organisation is at least partly a repetition of their short-range + organisation. meaning: UBERON:0000479 Wound tissue (injury) [NCIT:C3671]: text: Wound tissue (injury) [NCIT:C3671] + description: Damage inflicted on the body as the direct or indirect result + of an external force, with or without disruption of structural continuity. meaning: NCIT:C3671 is_a: Tissue [UBERON:0000479] - anatomical part menu: - name: anatomical part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical part menu permissible_values: Anus: text: Anus + description: 'Orifice at the opposite end of an animal''s digestive tract + from the mouth. Its function is to expel feces, unwanted semi-solid matter + produced during digestion, which, depending on the type of animal, may be + one or more of: matter which the animal cannot digest, such as bones; food + material after all the nutrients have been extracted, for example cellulose + or lignin; ingested matter which would be toxic if it remained in the digestive + tract; and dead or excess gut bacteria and other endosymbionts.' meaning: UBERON:0001245 Perianal skin: text: Perianal skin + description: A zone of skin that is part of the area surrounding the anus. meaning: UBERON:0012336 is_a: Anus Arm: text: Arm + description: The part of the forelimb extending from the shoulder to the autopod. meaning: UBERON:0001460 Arm (forearm): text: Arm (forearm) + description: The structure on the upper limb, between the elbow and the wrist. meaning: NCIT:C32628 is_a: Arm Elbow: text: Elbow + description: 'The elbow is the region surrounding the elbow-joint-the ginglymus + or hinge joint in the middle of the arm. Three bones form the elbow joint: + the humerus of the upper arm, and the paired radius and ulna of the forearm. + The bony prominence at the very tip of the elbow is the olecranon process + of the ulna, and the inner aspect of the elbow is called the antecubital + fossa.' meaning: UBERON:0001461 is_a: Arm Back: text: Back + description: The rear surface of the human body from the shoulders to the + hips. meaning: FMA:14181 Buttock: text: Buttock + description: A zone of soft tissue located on the posterior of the lateral + side of the pelvic region corresponding to the gluteal muscles. meaning: UBERON:0013691 Cervix: text: Cervix + description: Lower, narrow portion of the uterus where it joins with the top + end of the vagina. meaning: UBERON:0000002 Chest: text: Chest + description: Subdivision of trunk proper, which is demarcated from the neck + by the plane of the superior thoracic aperture and from the abdomen internally + by the inferior surface of the diaphragm and externally by the costal margin + and associated with the thoracic vertebral column and ribcage and from the + back of the thorax by the external surface of the posterolateral part of + the rib cage, the anterior surface of the thoracic vertebral column and + the posterior axillary lines; together with the abdomen and the perineum, + it constitutes the trunk proper meaning: UBERON:0001443 Foot: text: Foot + description: 'The terminal part of the vertebrate leg upon which an individual + stands. 2: An invertebrate organ of locomotion or attachment; especially: + a ventral muscular surface or process of a mollusk.' meaning: BTO:0000476 Genital area: text: Genital area + description: The area where the upper thigh meets the trunk. More precisely, + the fold or depression marking the juncture of the lower abdomen and the + inner part of the thigh. meaning: BTO:0003358 Penis: text: Penis + description: An intromittent organ in certain biologically male organisms. + In placental mammals, this also serves as the organ of urination. meaning: UBERON:0000989 is_a: Genital area Glans (tip of penis): text: Glans (tip of penis) + description: The bulbous structure at the distal end of the human penis meaning: UBERON:0035651 is_a: Penis Prepuce of penis (foreskin): text: Prepuce of penis (foreskin) + description: A retractable double-layered fold of skin and mucous membrane + that covers the glans penis and protects the urinary meatus when the penis + is not erect. meaning: UBERON:0001332 is_a: Penis Perineum: text: Perineum + description: The space between the anus and scrotum in the male human, or + between the anus and the vulva in the female human. meaning: UBERON:0002356 is_a: Genital area Scrotum: text: Scrotum + description: The external sac of skin that encloses the testes. It is an extension + of the abdomen, and in placentals is located between the penis and anus. meaning: UBERON:0001300 is_a: Genital area Vagina: text: Vagina + description: A fibromuscular tubular tract leading from the uterus to the + exterior of the body in female placental mammals and marsupials, or to the + cloaca in female birds, monotremes, and some reptiles meaning: UBERON:0000996 is_a: Genital area Gland: text: Gland + description: An organ that functions as a secretory or excretory organ. meaning: UBERON:0002530 Hand: text: Hand + description: The terminal part of the vertebrate forelimb when modified, as + in humans, as a grasping organ. meaning: BTO:0004668 Finger: text: Finger + description: 'Subdivision of the hand demarcated from the hand proper by the + skin crease in line with the distal edge of finger webs. Examples: thumb, + right middle finger, left little finger.' meaning: FMA:9666 is_a: Hand Hand (palm): text: Hand (palm) + description: The inner surface of the hand between the wrist and fingers. meaning: FMA:24920 is_a: Hand Head: text: Head + description: The head is the anterior-most division of the body. meaning: UBERON:0000033 Buccal mucosa: text: Buccal mucosa + description: The inner lining of the cheeks and lips. meaning: UBERON:0006956 is_a: Head Cheek: text: Cheek + description: A fleshy subdivision of one side of the face bounded by an eye, + ear and the nose. meaning: UBERON:0001567 is_a: Head Ear: text: Ear + description: Sense organ in vertebrates that is specialized for the detection + of sound, and the maintenance of balance. Includes the outer ear and middle + ear, which collect and transmit sound waves; and the inner ear, which contains + the organs of balance and (except in fish) hearing. Also includes the pinna, + the visible part of the outer ear, present in some mammals. meaning: UBERON:0001690 is_a: Head Preauricular region: text: Preauricular region + description: Of or pertaining to the area in front of the auricle of the ear. meaning: NCIT:C103848 is_a: Ear Eye: text: Eye + description: An organ that detects light. meaning: UBERON:0000970 is_a: Head Face: text: Face + description: A subdivision of the head that has as parts the layers deep to + the surface of the anterior surface, including the mouth, eyes, and nose + (when present). In vertebrates, this includes the facial skeleton and structures + superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, + etc). meaning: UBERON:0001456 is_a: Head Forehead: text: Forehead + description: The part of the face above the eyes. In human anatomy, the forehead + is the fore part of the head. It is, formally, an area of the head bounded + by three features, two of the skull and one of the scalp. The top of the + forehead is marked by the hairline, the edge of the area where hair on the + scalp grows. The bottom of the forehead is marked by the supraorbital ridge, + the bone feature of the skull above the eyes. The two sides of the forehead + are marked by the temporal ridge, a bone feature that links the supraorbital + ridge to the coronal suture line and beyond meaning: UBERON:0008200 is_a: Head Lip: text: Lip + description: One of the two fleshy folds which surround the opening of the + mouth. meaning: UBERON:0001833 is_a: Head Jaw: text: Jaw + description: A subdivision of the head that corresponds to the jaw skeleton, + containing both soft tissue, skeleton and teeth (when present). The jaw + region is divided into upper and lower regions. meaning: UBERON:0011595 is_a: Head Tongue: text: Tongue + description: A muscular organ in the floor of the mouth. meaning: UBERON:0001723 is_a: Head Hypogastrium (suprapubic region): text: Hypogastrium (suprapubic region) + description: The hypogastrium (or hypogastric region, or pubic region) is + an area of the human abdomen located below the navel. meaning: UBERON:0013203 Leg: text: Leg + description: The portion of the hindlimb that contains both the stylopod and + zeugopod. meaning: UBERON:0000978 Ankle: text: Ankle + description: A zone of skin that is part of an ankle meaning: UBERON:0001512 is_a: Leg Knee: text: Knee + description: A segment of the hindlimb that corresponds to the joint connecting + a hindlimb stylopod and zeugopod. meaning: UBERON:0001465 is_a: Leg Thigh: text: Thigh + description: The part of the hindlimb between pelvis and the knee, corresponding + to the femur. meaning: UBERON:0000376 is_a: Leg Lower body: text: Lower body + description: The part of the body that includes the leg, ankle, and foot. meaning: GENEPIO:0100492 Nasal Cavity: text: Nasal Cavity + description: An anatomical cavity that is part of the olfactory apparatus. + This includes the space bounded anteriorly by the nares and posteriorly + by the choanae, when these structures are present. meaning: UBERON:0001707 Anterior Nares: text: Anterior Nares + description: The external part of the nose containing the lower nostrils. meaning: UBERON:2001427 is_a: Nasal Cavity Inferior Nasal Turbinate: text: Inferior Nasal Turbinate + description: The medial surface of the labyrinth of ethmoid consists of a + thin lamella, which descends from the under surface of the cribriform plate, + and ends below in a free, convoluted margin, the middle nasal concha. It + is rough, and marked above by numerous grooves, directed nearly vertically + downward from the cribriform plate; they lodge branches of the olfactory + nerves, which are distributed to the mucous membrane covering the superior + nasal concha. meaning: UBERON:0005921 is_a: Nasal Cavity Middle Nasal Turbinate: text: Middle Nasal Turbinate + description: A turbinal located on the maxilla bone. meaning: UBERON:0005922 is_a: Nasal Cavity Neck: text: Neck + description: An organism subdivision that extends from the head to the pectoral + girdle, encompassing the cervical vertebral column. meaning: UBERON:0000974 Pharynx (throat): text: Pharynx (throat) - meaning: UBERON:0000341 + description: The pharynx is the part of the digestive system immediately posterior + to the mouth. + meaning: UBERON:0006562 is_a: Neck Nasopharynx (NP): text: Nasopharynx (NP) + description: The section of the pharynx that lies above the soft palate. meaning: UBERON:0001728 is_a: Pharynx (throat) Oropharynx (OP): text: Oropharynx (OP) + description: The portion of the pharynx that lies between the soft palate + and the upper edge of the epiglottis. meaning: UBERON:0001729 is_a: Pharynx (throat) Trachea: text: Trachea + description: The trachea is the portion of the airway that attaches to the + bronchi as it branches. meaning: UBERON:0003126 is_a: Neck Rectum: text: Rectum + description: The terminal portion of the intestinal tube, terminating with + the anus. meaning: UBERON:0001052 Shoulder: text: Shoulder + description: A subdivision of the pectoral complex consisting of the structures + in the region of the shoulder joint (which connects the humerus, scapula + and clavicle). meaning: UBERON:0001467 Skin: text: Skin + description: The outer epithelial layer of the skin that is superficial to + the dermis. meaning: UBERON:0001003 - anatomical part international menu: - name: anatomical part international menu + AnatomicalPartInternationalMenu: + name: AnatomicalPartInternationalMenu + title: anatomical part international menu permissible_values: Anus [UBERON:0001245]: text: Anus [UBERON:0001245] + description: 'Orifice at the opposite end of an animal''s digestive tract + from the mouth. Its function is to expel feces, unwanted semi-solid matter + produced during digestion, which, depending on the type of animal, may be + one or more of: matter which the animal cannot digest, such as bones; food + material after all the nutrients have been extracted, for example cellulose + or lignin; ingested matter which would be toxic if it remained in the digestive + tract; and dead or excess gut bacteria and other endosymbionts.' meaning: UBERON:0001245 Perianal skin [UBERON:0012336]: text: Perianal skin [UBERON:0012336] + description: A zone of skin that is part of the area surrounding the anus. meaning: UBERON:0012336 is_a: Anus [UBERON:0001245] Arm [UBERON:0001460]: text: Arm [UBERON:0001460] + description: The part of the forelimb extending from the shoulder to the autopod. meaning: UBERON:0001460 Arm (forearm) [NCIT:C32628]: text: Arm (forearm) [NCIT:C32628] + description: The structure on the upper limb, between the elbow and the wrist. meaning: NCIT:C32628 is_a: Arm [UBERON:0001460] Elbow [UBERON:0001461]: text: Elbow [UBERON:0001461] + description: 'The elbow is the region surrounding the elbow-joint-the ginglymus + or hinge joint in the middle of the arm. Three bones form the elbow joint: + the humerus of the upper arm, and the paired radius and ulna of the forearm. + The bony prominence at the very tip of the elbow is the olecranon process + of the ulna, and the inner aspect of the elbow is called the antecubital + fossa.' meaning: UBERON:0001461 is_a: Arm [UBERON:0001460] Back [FMA:14181]: text: Back [FMA:14181] + description: The rear surface of the human body from the shoulders to the + hips. meaning: FMA:14181 Buttock [UBERON:0013691]: text: Buttock [UBERON:0013691] + description: A zone of soft tissue located on the posterior of the lateral + side of the pelvic region corresponding to the gluteal muscles. meaning: UBERON:0013691 Cervix [UBERON:0000002]: text: Cervix [UBERON:0000002] + description: Lower, narrow portion of the uterus where it joins with the top + end of the vagina. meaning: UBERON:0000002 Chest [UBERON:0001443]: text: Chest [UBERON:0001443] + description: Subdivision of trunk proper, which is demarcated from the neck + by the plane of the superior thoracic aperture and from the abdomen internally + by the inferior surface of the diaphragm and externally by the costal margin + and associated with the thoracic vertebral column and ribcage and from the + back of the thorax by the external surface of the posterolateral part of + the rib cage, the anterior surface of the thoracic vertebral column and + the posterior axillary lines; together with the abdomen and the perineum, + it constitutes the trunk proper meaning: UBERON:0001443 Foot [BTO:0000476]: text: Foot [BTO:0000476] + description: The terminal part of the vertebrate leg upon which an individual + stands. meaning: BTO:0000476 Genital area [BTO:0003358]: text: Genital area [BTO:0003358] + description: The area where the upper thigh meets the trunk. More precisely, + the fold or depression marking the juncture of the lower abdomen and the + inner part of the thigh. meaning: BTO:0003358 Penis [UBERON:0000989]: text: Penis [UBERON:0000989] + description: An intromittent organ in certain biologically male organisms. + In placental mammals, this also serves as the organ of urination. meaning: UBERON:0000989 is_a: Genital area [BTO:0003358] Glans (tip of penis) [UBERON:0035651]: text: Glans (tip of penis) [UBERON:0035651] + description: The bulbous structure at the distal end of the human penis meaning: UBERON:0035651 is_a: Penis [UBERON:0000989] Prepuce of penis (foreskin): text: Prepuce of penis (foreskin) + description: A retractable double-layered fold of skin and mucous membrane + that covers the glans penis and protects the urinary meatus when the penis + is not erect. meaning: UBERON:0001332 is_a: Penis [UBERON:0000989] Perineum [UBERON:0002356]: text: Perineum [UBERON:0002356] + description: The space between the anus and scrotum in the male human, or + between the anus and the vulva in the female human. meaning: UBERON:0002356 is_a: Genital area [BTO:0003358] Scrotum [UBERON:0001300]: text: Scrotum [UBERON:0001300] + description: The external sac of skin that encloses the testes. It is an extension + of the abdomen, and in placentals is located between the penis and anus. meaning: UBERON:0001300 is_a: Genital area [BTO:0003358] Vagina [UBERON:0000996]: text: Vagina [UBERON:0000996] + description: A fibromuscular tubular tract leading from the uterus to the + exterior of the body in female placental mammals and marsupials, or to the + cloaca in female birds, monotremes, and some reptiles meaning: UBERON:0000996 is_a: Genital area [BTO:0003358] Gland [UBERON:0002530]: text: Gland [UBERON:0002530] + description: An organ that functions as a secretory or excretory organ. meaning: UBERON:0002530 Hand [BTO:0004668]: text: Hand [BTO:0004668] + description: The terminal part of the vertebrate forelimb when modified, as + in humans, as a grasping organ. meaning: BTO:0004668 Finger [FMA:9666]: text: Finger [FMA:9666] + description: 'Subdivision of the hand demarcated from the hand proper by the + skin crease in line with the distal edge of finger webs. Examples: thumb, + right middle finger, left little finger.' meaning: FMA:9666 is_a: Hand [BTO:0004668] Hand (palm) [FMA:24920]: text: Hand (palm) [FMA:24920] + description: The inner surface of the hand between the wrist and fingers. meaning: FMA:24920 is_a: Hand [BTO:0004668] Head [UBERON:0000033]: text: Head [UBERON:0000033] + description: The head is the anterior-most division of the body. meaning: UBERON:0000033 Buccal mucosa [UBERON:0006956]: text: Buccal mucosa [UBERON:0006956] + description: The inner lining of the cheeks and lips. meaning: UBERON:0006956 is_a: Head [UBERON:0000033] Cheek [UBERON:0001567]: text: Cheek [UBERON:0001567] + description: A fleshy subdivision of one side of the face bounded by an eye, + ear and the nose. meaning: UBERON:0001567 is_a: Head [UBERON:0000033] Ear [UBERON:0001690]: text: Ear [UBERON:0001690] + description: Sense organ in vertebrates that is specialized for the detection + of sound, and the maintenance of balance. Includes the outer ear and middle + ear, which collect and transmit sound waves; and the inner ear, which contains + the organs of balance and (except in fish) hearing. Also includes the pinna, + the visible part of the outer ear, present in some mammals. meaning: UBERON:0001690 is_a: Head [UBERON:0000033] Preauricular region [NCIT:C103848]: text: Preauricular region [NCIT:C103848] + description: Of or pertaining to the area in front of the auricle of the ear. meaning: NCIT:C103848 is_a: Ear [UBERON:0001690] Eye [UBERON:0000970]: text: Eye [UBERON:0000970] + description: An organ that detects light. meaning: UBERON:0000970 is_a: Head [UBERON:0000033] Face [UBERON:0001456]: text: Face [UBERON:0001456] + description: A subdivision of the head that has as parts the layers deep to + the surface of the anterior surface, including the mouth, eyes, and nose + (when present). In vertebrates, this includes the facial skeleton and structures + superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, + etc). meaning: UBERON:0001456 is_a: Head [UBERON:0000033] Forehead [UBERON:0008200]: text: Forehead [UBERON:0008200] + description: The part of the face above the eyes. In human anatomy, the forehead + is the fore part of the head. It is, formally, an area of the head bounded + by three features, two of the skull and one of the scalp. The top of the + forehead is marked by the hairline, the edge of the area where hair on the + scalp grows. The bottom of the forehead is marked by the supraorbital ridge, + the bone feature of the skull above the eyes. The two sides of the forehead + are marked by the temporal ridge, a bone feature that links the supraorbital + ridge to the coronal suture line and beyond meaning: UBERON:0008200 is_a: Head [UBERON:0000033] Lip [UBERON:0001833]: text: Lip [UBERON:0001833] + description: One of the two fleshy folds which surround the opening of the + mouth. meaning: UBERON:0001833 is_a: Head [UBERON:0000033] Jaw [UBERON:0011595]: text: Jaw [UBERON:0011595] + description: A subdivision of the head that corresponds to the jaw skeleton, + containing both soft tissue, skeleton and teeth (when present). The jaw + region is divided into upper and lower regions. meaning: UBERON:0011595 is_a: Head [UBERON:0000033] Tongue [UBERON:0001723]: text: Tongue [UBERON:0001723] + description: A muscular organ in the floor of the mouth. meaning: UBERON:0001723 is_a: Head [UBERON:0000033] Hypogastrium (suprapubic region) [UBERON:0013203]: text: Hypogastrium (suprapubic region) [UBERON:0013203] + description: The hypogastrium (or hypogastric region, or pubic region) is + an area of the human abdomen located below the navel. meaning: UBERON:0013203 Leg [UBERON:0000978]: text: Leg [UBERON:0000978] + description: The portion of the hindlimb that contains both the stylopod and + zeugopod. meaning: UBERON:0000978 Ankle [UBERON:0001512]: text: Ankle [UBERON:0001512] + description: A zone of skin that is part of an ankle meaning: UBERON:0001512 is_a: Leg [UBERON:0000978] Knee [UBERON:0001465]: text: Knee [UBERON:0001465] + description: A segment of the hindlimb that corresponds to the joint connecting + a hindlimb stylopod and zeugopod. meaning: UBERON:0001465 is_a: Leg [UBERON:0000978] Thigh [UBERON:0000376]: text: Thigh [UBERON:0000376] + description: The part of the hindlimb between pelvis and the knee, corresponding + to the femur. meaning: UBERON:0000376 is_a: Leg [UBERON:0000978] Lower body [GENEPIO:0100492]: text: Lower body [GENEPIO:0100492] + description: The part of the body that includes the leg, ankle, and foot. meaning: GENEPIO:0100492 Nasal Cavity [UBERON:0001707]: text: Nasal Cavity [UBERON:0001707] + description: An anatomical cavity that is part of the olfactory apparatus. + This includes the space bounded anteriorly by the nares and posteriorly + by the choanae, when these structures are present. meaning: UBERON:0001707 Anterior Nares [UBERON:2001427]: text: Anterior Nares [UBERON:2001427] + description: The external part of the nose containing the lower nostrils. meaning: UBERON:2001427 is_a: Nasal Cavity [UBERON:0001707] Inferior Nasal Turbinate [UBERON:0005921]: text: Inferior Nasal Turbinate [UBERON:0005921] + description: The medial surface of the labyrinth of ethmoid consists of a + thin lamella, which descends from the under surface of the cribriform plate, + and ends below in a free, convoluted margin, the middle nasal concha. It + is rough, and marked above by numerous grooves, directed nearly vertically + downward from the cribriform plate; they lodge branches of the olfactory + nerves, which are distributed to the mucous membrane covering the superior + nasal concha. meaning: UBERON:0005921 is_a: Nasal Cavity [UBERON:0001707] Middle Nasal Turbinate [UBERON:0005922]: text: Middle Nasal Turbinate [UBERON:0005922] + description: A turbinal located on the maxilla bone. meaning: UBERON:0005922 is_a: Nasal Cavity [UBERON:0001707] Neck [UBERON:0000974]: text: Neck [UBERON:0000974] + description: An organism subdivision that extends from the head to the pectoral + girdle, encompassing the cervical vertebral column. meaning: UBERON:0000974 - Pharynx (throat) [UBERON:0000341]: - text: Pharynx (throat) [UBERON:0000341] - meaning: UBERON:0000341 + Pharynx (throat) [UBERON:0006562]: + text: Pharynx (throat) [UBERON:0006562] + description: A zone of skin that is part of an ankle + meaning: UBERON:0006562 is_a: Neck [UBERON:0000974] Nasopharynx (NP) [UBERON:0001728]: text: Nasopharynx (NP) [UBERON:0001728] + description: The section of the pharynx that lies above the soft palate. meaning: UBERON:0001728 - is_a: Pharynx (throat) [UBERON:0000341] + is_a: Pharynx (throat) [UBERON:0006562] Oropharynx (OP) [UBERON:0001729]: text: Oropharynx (OP) [UBERON:0001729] + description: The portion of the pharynx that lies between the soft palate + and the upper edge of the epiglottis. meaning: UBERON:0001729 - is_a: Pharynx (throat) [UBERON:0000341] + is_a: Pharynx (throat) [UBERON:0006562] Trachea [UBERON:0003126]: text: Trachea [UBERON:0003126] + description: The trachea is the portion of the airway that attaches to the + bronchi as it branches. meaning: UBERON:0003126 is_a: Neck [UBERON:0000974] Rectum [UBERON:0001052]: text: Rectum [UBERON:0001052] + description: The terminal portion of the intestinal tube, terminating with + the anus. meaning: UBERON:0001052 Shoulder [UBERON:0001467]: text: Shoulder [UBERON:0001467] + description: A subdivision of the pectoral complex consisting of the structures + in the region of the shoulder joint (which connects the humerus, scapula + and clavicle). meaning: UBERON:0001467 Skin [UBERON:0001003]: text: Skin [UBERON:0001003] + description: The outer epithelial layer of the skin that is superficial to + the dermis. meaning: UBERON:0001003 - body product menu: - name: body product menu + BodyProductMenu: + name: BodyProductMenu + title: body product menu permissible_values: Breast Milk: text: Breast Milk + description: An emulsion of fat globules within a fluid that is secreted by + the mammary gland during lactation. meaning: UBERON:0001913 Feces: text: Feces + description: Portion of semisolid bodily waste discharged through the anus. meaning: UBERON:0001988 Fluid (discharge): text: Fluid (discharge) + description: A fluid that comes out of the body. meaning: SYMP:0000651 Pus: text: Pus + description: A bodily fluid consisting of a whitish-yellow or yellow substance + produced during inflammatory responses of the body that can be found in + regions of pyogenic bacterial infections. meaning: UBERON:0000177 is_a: Fluid (discharge) Fluid (seminal): text: Fluid (seminal) + description: A substance formed from the secretion of one or more glands of + the male genital tract in which sperm cells are suspended. meaning: UBERON:0006530 Mucus: text: Mucus + description: Mucus is a bodily fluid consisting of a slippery secretion of + the lining of the mucous membranes in the body. It is a viscous colloid + containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus + is produced by goblet cells in the mucous membranes that cover the surfaces + of the membranes. It is made up of mucins and inorganic salts suspended + in water. meaning: UBERON:0000912 Sputum: text: Sputum + description: Matter ejected from the lungs, bronchi, and trachea, through + the mouth. meaning: UBERON:0007311 is_a: Mucus Sweat: text: Sweat + description: Secretion produced by a sweat gland. meaning: UBERON:0001089 Tear: text: Tear + description: Aqueous substance secreted by the lacrimal gland. meaning: UBERON:0001827 Urine: text: Urine + description: Excretion that is the output of a kidney. meaning: UBERON:0001088 - body product international menu: - name: body product international menu + BodyProductInternationalMenu: + name: BodyProductInternationalMenu + title: body product international menu permissible_values: Breast Milk [UBERON:0001913]: text: Breast Milk [UBERON:0001913] + description: An emulsion of fat globules within a fluid that is secreted by + the mammary gland during lactation. meaning: UBERON:0001913 Feces [UBERON:0001988]: text: Feces [UBERON:0001988] + description: Portion of semisolid bodily waste discharged through the anus. meaning: UBERON:0001988 Fluid (discharge) [SYMP:0000651]: text: Fluid (discharge) [SYMP:0000651] + description: A fluid that comes out of the body. meaning: SYMP:0000651 Pus [UBERON:0000177]: text: Pus [UBERON:0000177] + description: A bodily fluid consisting of a whitish-yellow or yellow substance + produced during inflammatory responses of the body that can be found in + regions of pyogenic bacterial infections. meaning: UBERON:0000177 is_a: Fluid (discharge) [SYMP:0000651] Fluid (seminal) [UBERON:0006530]: text: Fluid (seminal) [UBERON:0006530] + description: A substance formed from the secretion of one or more glands of + the male genital tract in which sperm cells are suspended. meaning: UBERON:0006530 Mucus [UBERON:0000912]: text: Mucus [UBERON:0000912] + description: Mucus is a bodily fluid consisting of a slippery secretion of + the lining of the mucous membranes in the body. It is a viscous colloid + containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus + is produced by goblet cells in the mucous membranes that cover the surfaces + of the membranes. It is made up of mucins and inorganic salts suspended + in water. meaning: UBERON:0000912 Sputum [UBERON:0007311]: text: Sputum [UBERON:0007311] + description: Matter ejected from the lungs, bronchi, and trachea, through + the mouth. meaning: UBERON:0007311 is_a: Mucus [UBERON:0000912] Sweat [UBERON:0001089]: text: Sweat [UBERON:0001089] + description: Secretion produced by a sweat gland. meaning: UBERON:0001089 Tear [UBERON:0001827]: text: Tear [UBERON:0001827] + description: Aqueous substance secreted by the lacrimal gland. meaning: UBERON:0001827 Urine [UBERON:0001088]: text: Urine [UBERON:0001088] + description: Excretion that is the output of a kidney. meaning: UBERON:0001088 - environmental material international menu: - name: environmental material international menu + EnvironmentalMaterialInternationalMenu: + name: EnvironmentalMaterialInternationalMenu + title: environmental material international menu permissible_values: - Animal carcass: - text: Animal carcass - Bedding (Bed linen): - text: Bedding (Bed linen) + Animal carcass [FOODON:02010020]: + text: Animal carcass [FOODON:02010020] + description: A carcass of an animal that includes all anatomical parts. This + includes a carcass with all organs and skin. + meaning: FOODON:02010020 + Bedding (Bed linen) [GSSO:005304]: + text: Bedding (Bed linen) [GSSO:005304] + description: Bedding is the removable and washable portion of a human sleeping + environment. meaning: GSSO:005304 - Clothing: - text: Clothing + Clothing [GSSO:003405]: + text: Clothing [GSSO:003405] + description: Fabric or other material used to cover the body. meaning: GSSO:003405 Drinkware: text: Drinkware + description: Utensils with an open top that are used to hold liquids for consumption. + Cup [ENVO:03501330]: + text: Cup [ENVO:03501330] + description: A utensil which is a hand-sized container with an open top. A + cup may be used to hold liquids for pouring or drinking, or to store solids + for pouring. + meaning: ENVO:03501330 + is_a: Drinkware Tableware: text: Tableware + description: Items used in setting a table and serving food and beverages. + This includes various utensils, plates, bowls, cups, glasses, and serving + dishes designed for dining and drinking. Dish: text: Dish + description: A flat, typically round or oval item used for holding or serving + food. It can also refer to a specific type of plate, often used to describe + the container itself, such as a "plate dish" which is used for placing and + serving individual portions of food. is_a: Tableware - Utensil: - text: Utensil + Eating utensil [ENVO:03501353]: + text: Eating utensil [ENVO:03501353] + description: A utensil used for consuming food. + meaning: ENVO:03501353 is_a: Tableware - collection method menu: - name: collection method menu + Wastewater: + text: Wastewater + description: Water that has been adversely affected in quality by anthropogenic + influence. + meaning: ENVO:00002001 + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: Amniocentesis: text: Amniocentesis + description: A prenatal diagnostic procedure in which a small sample of amniotic + fluid is removed from the uterus by a needle inserted into the abdomen. + This procedure is used to detect various genetic abnormalities in the fetus + and/or the sex of the fetus. meaning: NCIT:C52009 Aspiration: text: Aspiration + description: Inspiration of a foreign object into the airway. meaning: NCIT:C15631 Suprapubic Aspiration: text: Suprapubic Aspiration + description: An aspiration process which involves putting a needle through + the skin just above the pubic bone into the bladder to take a urine sample. meaning: GENEPIO:0100028 is_a: Aspiration Tracheal aspiration: text: Tracheal aspiration + description: An aspiration process which collects tracheal secretions. meaning: GENEPIO:0100029 is_a: Aspiration Vacuum Aspiration: text: Vacuum Aspiration + description: An aspiration process which uses a vacuum source to remove a + sample. meaning: GENEPIO:0100030 is_a: Aspiration Biopsy: text: Biopsy + description: A specimen collection that obtains a sample of tissue or cell + from a living multicellular organism body for diagnostic purposes by means + intended to be minimally invasive. meaning: OBI:0002650 Needle Biopsy: text: Needle Biopsy + description: A biopsy that uses a hollow needle to extract cells. meaning: OBI:0002651 is_a: Biopsy Filtration: text: Filtration + description: Filtration is a process which separates components suspended + in a fluid based on granularity properties relying on a filter device meaning: OBI:0302885 Air filtration: text: Air filtration + description: A filtration process which removes solid particulates from the + air via an air filtration device. meaning: GENEPIO:0100031 is_a: Filtration Lavage: text: Lavage + description: A protocol application to separate cells and/or cellular secretions + from an anatomical space by the introduction and removal of fluid meaning: OBI:0600044 Bronchoalveolar lavage (BAL): text: Bronchoalveolar lavage (BAL) + description: The collection of bronchoalveolar lavage fluid (BAL) from the + lungs. meaning: GENEPIO:0100032 is_a: Lavage Gastric Lavage: text: Gastric Lavage + description: The administration and evacuation of small volumes of liquid + through an orogastric tube to remove toxic substances within the stomach. meaning: GENEPIO:0100033 is_a: Lavage Lumbar Puncture: text: Lumbar Puncture + description: An invasive procedure in which a hollow needle is introduced + through an intervertebral space in the lower back to access the subarachnoid + space in order to sample cerebrospinal fluid or to administer medication. meaning: NCIT:C15327 Necropsy: text: Necropsy + description: A postmortem examination of the body of an animal to determine + the cause of death or the character and extent of changes produced by disease. meaning: MMO:0000344 Phlebotomy: text: Phlebotomy + description: The collection of blood from a vein, most commonly via needle + venipuncture. meaning: NCIT:C28221 Rinsing: text: Rinsing + description: The process of removal and collection of specimen material from + the surface of an entity by washing, or a similar application of fluids. meaning: GENEPIO:0002116 Saline gargle (mouth rinse and gargle): text: Saline gargle (mouth rinse and gargle) + description: A collecting specimen from organism process in which a salt water + solution is taken into the oral cavity, rinsed around, and gargled before + being deposited into an external collection device. meaning: GENEPIO:0100034 is_a: Rinsing Scraping: text: Scraping + description: A specimen collection process in which a sample is collected + by scraping a surface with a sterile sampling device. meaning: GENEPIO:0100035 Swabbing: text: Swabbing + description: The process of collecting specimen material using a swab collection + device. meaning: GENEPIO:0002117 Finger Prick: text: Finger Prick + description: A collecting specimen from organism process in which a skin site + free of surface arterial flow is pierced with a sterile lancet, after a + capillary blood droplet is formed a sample is captured in a capillary tupe. meaning: GENEPIO:0100036 is_a: Swabbing Thoracentesis (chest tap): text: Thoracentesis (chest tap) + description: The removal of excess fluid via needle puncture from the thoracic + cavity. meaning: NCIT:C15392 - collection method international menu: - name: collection method international menu + CollectionMethodInternationalMenu: + name: CollectionMethodInternationalMenu + title: collection method international menu permissible_values: Amniocentesis [NCIT:C52009]: text: Amniocentesis [NCIT:C52009] + description: A prenatal diagnostic procedure in which a small sample of amniotic + fluid is removed from the uterus by a needle inserted into the abdomen. + This procedure is used to detect various genetic abnormalities in the fetus + and/or the sex of the fetus. meaning: NCIT:C52009 Aspiration [NCIT:C15631]: text: Aspiration [NCIT:C15631] + description: Procedure using suction, usually with a thin needle and syringe, + to remove bodily fluid or tissue. meaning: NCIT:C15631 Suprapubic Aspiration [GENEPIO:0100028]: text: Suprapubic Aspiration [GENEPIO:0100028] + description: An aspiration process which involves putting a needle through + the skin just above the pubic bone into the bladder to take a urine sample. meaning: GENEPIO:0100028 is_a: Aspiration [NCIT:C15631] Tracheal aspiration [GENEPIO:0100029]: text: Tracheal aspiration [GENEPIO:0100029] + description: An aspiration process which collects tracheal secretions. meaning: GENEPIO:0100029 is_a: Aspiration [NCIT:C15631] Vacuum Aspiration [GENEPIO:0100030]: text: Vacuum Aspiration [GENEPIO:0100030] + description: An aspiration process which uses a vacuum source to remove a + sample. meaning: GENEPIO:0100030 is_a: Aspiration [NCIT:C15631] Biopsy [OBI:0002650]: text: Biopsy [OBI:0002650] + description: A specimen collection that obtains a sample of tissue or cell + from a living multicellular organism body for diagnostic purposes by means + intended to be minimally invasive. meaning: OBI:0002650 Needle Biopsy [OBI:0002651]: text: Needle Biopsy [OBI:0002651] + description: A biopsy that uses a hollow needle to extract cells. meaning: OBI:0002651 is_a: Biopsy [OBI:0002650] Filtration [OBI:0302885]: text: Filtration [OBI:0302885] + description: Filtration is a process which separates components suspended + in a fluid based on granularity properties relying on a filter device. meaning: OBI:0302885 Air filtration [GENEPIO:0100031]: text: Air filtration [GENEPIO:0100031] + description: A filtration process which removes solid particulates from the + air via an air filtration device. meaning: GENEPIO:0100031 is_a: Filtration [OBI:0302885] Lavage [OBI:0600044]: text: Lavage [OBI:0600044] + description: A protocol application to separate cells and/or cellular secretions + from an anatomical space by the introduction and removal of fluid. meaning: OBI:0600044 Bronchoalveolar lavage (BAL) [GENEPIO:0100032]: text: Bronchoalveolar lavage (BAL) [GENEPIO:0100032] + description: The collection of bronchoalveolar lavage fluid (BAL) from the + lungs. meaning: GENEPIO:0100032 is_a: Lavage [OBI:0600044] Gastric Lavage [GENEPIO:0100033]: text: Gastric Lavage [GENEPIO:0100033] + description: The administration and evacuation of small volumes of liquid + through an orogastric tube to remove toxic substances within the stomach. meaning: GENEPIO:0100033 is_a: Lavage [OBI:0600044] Lumbar Puncture [NCIT:C15327]: text: Lumbar Puncture [NCIT:C15327] + description: An invasive procedure in which a hollow needle is introduced + through an intervertebral space in the lower back to access the subarachnoid + space in order to sample cerebrospinal fluid or to administer medication. meaning: NCIT:C15327 Necropsy [MMO:0000344]: text: Necropsy [MMO:0000344] + description: A postmortem examination of the body of an animal to determine + the cause of death or the character and extent of changes produced by disease. meaning: MMO:0000344 Phlebotomy [NCIT:C28221]: text: Phlebotomy [NCIT:C28221] + description: The collection of blood from a vein, most commonly via needle + venipuncture. meaning: NCIT:C28221 Rinsing [GENEPIO:0002116]: text: Rinsing [GENEPIO:0002116] + description: The process of removal and collection of specimen material from + the surface of an entity by washing, or a similar application of fluids. meaning: GENEPIO:0002116 Saline gargle (mouth rinse and gargle) [GENEPIO:0100034]: text: Saline gargle (mouth rinse and gargle) [GENEPIO:0100034] + description: A collecting specimen from organism process in which a salt water + solution is taken into the oral cavity, rinsed around, and gargled before + being deposited into an external collection device. meaning: GENEPIO:0100034 is_a: Rinsing [GENEPIO:0002116] Scraping [GENEPIO:0100035]: text: Scraping [GENEPIO:0100035] + description: A specimen collection process in which a sample is collected + by scraping a surface with a sterile sampling device. meaning: GENEPIO:0100035 Swabbing [GENEPIO:0002117]: text: Swabbing [GENEPIO:0002117] + description: The process of collecting specimen material using a swab collection + device. meaning: GENEPIO:0002117 Finger Prick [GENEPIO:0100036]: text: Finger Prick [GENEPIO:0100036] + description: A collecting specimen from organism process in which a skin site + free of surface arterial flow is pierced with a sterile lancet, after a + capillary blood droplet is formed a sample is captured in a capillary tupe. meaning: GENEPIO:0100036 is_a: Swabbing [GENEPIO:0002117] Thoracentesis (chest tap) [NCIT:C15392]: text: Thoracentesis (chest tap) [NCIT:C15392] + description: The removal of excess fluid via needle puncture from the thoracic + cavity. meaning: NCIT:C15392 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: Blood Collection Tube: text: Blood Collection Tube + description: 'A specimen collection tube which is designed for the collection + of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection' meaning: OBI:0002859 Bronchoscope: text: Bronchoscope + description: A device which is a thin, tube-like instrument which includes + a light and a lens used to examine a lung. meaning: OBI:0002826 Collection Container: text: Collection Container + description: A container with the function of containing a specimen. meaning: OBI:0002088 Collection Cup: text: Collection Cup + description: A device which is used to collect liquid samples. meaning: GENEPIO:0100026 Filter: text: Filter + description: A manufactured product which separates solids from fluids by + adding a medium through which only a fluid can pass. meaning: GENEPIO:0100103 Needle: text: Needle + description: A needle is a sharp, hollow device used to penetrate tissue or + soft material. When attached to a syringe. it allows delivery of a specific + volume of liquid or gaseous mixture. meaning: OBI:0000436 Serum Collection Tube: text: Serum Collection Tube + description: A specimen collection tube which is designed for collecting whole + blood and enabling the separation of serum. meaning: OBI:0002860 Sputum Collection Tube: text: Sputum Collection Tube + description: A specimen collection tube which is designed for collecting sputum. meaning: OBI:0002861 Suction Catheter: text: Suction Catheter + description: A catheter which is used to remove mucus and other secretions + from the body. meaning: OBI:0002831 Swab: text: Swab + description: A device which is a soft, absorbent material mounted on one or + both ends of a stick. meaning: GENEPIO:0100027 Dry swab: text: Dry swab + description: A swab device that consists of soft, absorbent material mounted + on one or both ends of a stick, designed to collect samples without the + presence of a liquid or preservative medium. meaning: GENEPIO:0100493 is_a: Swab Urine Collection Tube: text: Urine Collection Tube + description: A specimen container which is designed for holding urine. meaning: OBI:0002862 Universal Transport Medium (UTM): text: Universal Transport Medium (UTM) + description: A sterile, balanced medium designed to preserve and transport + clinical specimens, such as viruses, bacteria, and mycoplasma, ensuring + the viability of the sample for subsequent analysis or culture. meaning: GENEPIO:0100509 Virus Transport Medium: text: Virus Transport Medium + description: A medium designed to promote longevity of a viral sample. FROM + Corona19 meaning: OBI:0002866 - collection device international menu: - name: collection device international menu + CollectionDeviceInternationalMenu: + name: CollectionDeviceInternationalMenu + title: collection device international menu permissible_values: Blood Collection Tube [OBI:0002859]: text: Blood Collection Tube [OBI:0002859] + description: 'A specimen collection tube which is designed for the collection + of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection' meaning: OBI:0002859 Bronchoscope [OBI:0002826]: text: Bronchoscope [OBI:0002826] + description: A device which is a thin, tube-like instrument which includes + a light and a lens used to examine a lung. meaning: OBI:0002826 Collection Container [OBI:0002088]: text: Collection Container [OBI:0002088] + description: A container with the function of containing a specimen. meaning: OBI:0002088 Collection Cup [GENEPIO:0100026]: text: Collection Cup [GENEPIO:0100026] + description: A device which is used to collect liquid samples. meaning: GENEPIO:0100026 Filter [GENEPIO:0100103]: text: Filter [GENEPIO:0100103] + description: A manufactured product which separates solids from fluids by + adding a medium through which only a fluid can pass. meaning: GENEPIO:0100103 Needle [OBI:0000436]: text: Needle [OBI:0000436] + description: A needle is a sharp, hollow device used to penetrate tissue or + soft material. When attached to a syringe. it allows delivery of a specific + volume of liquid or gaseous mixture. meaning: OBI:0000436 Serum Collection Tube [OBI:0002860]: text: Serum Collection Tube [OBI:0002860] + description: A specimen collection tube which is designed for collecting whole + blood and enabling the separation of serum. meaning: OBI:0002860 Sputum Collection Tube [OBI:0002861]: text: Sputum Collection Tube [OBI:0002861] + description: A specimen collection tube which is designed for collecting sputum. meaning: OBI:0002861 Suction Catheter [OBI:0002831]: text: Suction Catheter [OBI:0002831] + description: A catheter which is used to remove mucus and other secretions + from the body. meaning: OBI:0002831 Swab [GENEPIO:0100027]: text: Swab [GENEPIO:0100027] + description: A device which is a soft, absorbent material mounted on one or + both ends of a stick. meaning: GENEPIO:0100027 Dry swab [GENEPIO:0100493]: text: Dry swab [GENEPIO:0100493] + description: A swab device that consists of soft, absorbent material mounted + on one or both ends of a stick, designed to collect samples without the + presence of a liquid or preservative medium. meaning: GENEPIO:0100493 is_a: Swab [GENEPIO:0100027] Urine Collection Tube [OBI:0002862]: text: Urine Collection Tube [OBI:0002862] + description: A specimen container which is designed for holding urine. meaning: OBI:0002862 Universal Transport Medium (UTM) [GENEPIO:0100509]: text: Universal Transport Medium (UTM) [GENEPIO:0100509] + description: A sterile, balanced medium designed to preserve and transport + clinical specimens, such as viruses, bacteria, and mycoplasma, ensuring + the viability of the sample for subsequent analysis or culture. meaning: GENEPIO:0100509 Virus Transport Medium [OBI:0002866]: text: Virus Transport Medium [OBI:0002866] + description: A medium designed to promote longevity of a viral sample. FROM + Corona19 meaning: OBI:0002866 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Virus passage: text: Virus passage + description: The process of growing a virus in serial iterations. meaning: GENEPIO:0100039 - RNA re-extraction (post RT-PCR): - text: RNA re-extraction (post RT-PCR) - meaning: GENEPIO:0100040 Specimens pooled: text: Specimens pooled + description: Physical combination of several instances of like material. meaning: OBI:0600016 - specimen processing international menu: - name: specimen processing international menu + SpecimenProcessingInternationalMenu: + name: SpecimenProcessingInternationalMenu + title: specimen processing international menu permissible_values: Virus passage [GENEPIO:0100039]: text: Virus passage [GENEPIO:0100039] + description: The process of growing a virus in serial iterations. meaning: GENEPIO:0100039 - RNA re-extraction (post RT-PCR) [GENEPIO:0100040]: - text: RNA re-extraction (post RT-PCR) [GENEPIO:0100040] - meaning: GENEPIO:0100040 Specimens pooled [OBI:0600016]: text: Specimens pooled [OBI:0600016] + description: Physical combination of several instances of like material. meaning: OBI:0600016 - host (common name) menu: - name: host (common name) menu + ExperimentalSpecimenRoleTypeMenu: + name: ExperimentalSpecimenRoleTypeMenu + title: experimental specimen role type menu + permissible_values: + Positive experimental control: + text: Positive experimental control + description: A control specimen that is expected to yield a positive result, + to establish a reference baseline for an experiment. + meaning: GENEPIO:0101018 + Negative experimental control: + text: Negative experimental control + description: A control specimen that is expected to yield a negative result, + to establish a reference baseline for an experiment + meaning: GENEPIO:0101019 + Technical replicate: + text: Technical replicate + description: A technical replicate is a replicate role where the same BioSample + is use e.g. the same pool of RNA used to assess technical (as opposed to + biological) variation within an experiment. + meaning: EFO:0002090 + Biological replicate: + text: Biological replicate + description: A biological replicate is a replicate role that consists of independent + biological replicates made from different individual biosamples. + meaning: EFO:0002091 + ExperimentalSpecimenRoleTypeInternationalMenu: + name: ExperimentalSpecimenRoleTypeInternationalMenu + title: experimental specimen role type international menu + permissible_values: + Positive experimental control [GENEPIO:0101018]: + text: Positive experimental control [GENEPIO:0101018] + description: A control specimen that is expected to yield a positive result, + to establish a reference baseline for an experiment. + meaning: GENEPIO:0101018 + Negative experimental control [GENEPIO:0101019]: + text: Negative experimental control [GENEPIO:0101019] + description: A control specimen that is expected to yield a negative result, + to establish a reference baseline for an experiment + meaning: GENEPIO:0101019 + Technical replicate [EFO:0002090]: + text: Technical replicate [EFO:0002090] + description: A technical replicate is a replicate role where the same BioSample + is use e.g. the same pool of RNA used to assess technical (as opposed to + biological) variation within an experiment. + meaning: EFO:0002090 + Biological replicate [EFO:0002091]: + text: Biological replicate [EFO:0002091] + description: A biological replicate is a replicate role that consists of independent + biological replicates made from different individual biosamples. + meaning: EFO:0002091 + LineageCladeNameInternationalMenu: + name: LineageCladeNameInternationalMenu + title: lineage/clade name international menu + permissible_values: + Mpox virus clade I [GENEPIO:0102029]: + text: Mpox virus clade I [GENEPIO:0102029] + description: An Mpox virus clade with at least 99% similarity to the West + African/USA-derived Mpox strain. + meaning: GENEPIO:0102029 + Mpox virus clade Ia [GENEPIO:0102030]: + text: Mpox virus clade Ia [GENEPIO:0102030] + description: An Mpox virus that clusters in phylogenetic trees within the + Ia clade. + meaning: GENEPIO:0102030 + is_a: Mpox virus clade I [GENEPIO:0102029] + Mpox virus clade Ib [GENEPIO:0102031]: + text: Mpox virus clade Ib [GENEPIO:0102031] + description: An Mpox virus that clusters in phylogenetic trees within the + Ib clade. + meaning: GENEPIO:0102031 + is_a: Mpox virus clade I [GENEPIO:0102029] + Mpox virus clade II [GENEPIO:0102032]: + text: Mpox virus clade II [GENEPIO:0102032] + description: An Mpox virus clade with at least 99% similarity to the Congo + Basin-derived Mpox strain. + meaning: GENEPIO:0102032 + Mpox virus clade IIa [GENEPIO:0102033]: + text: Mpox virus clade IIa [GENEPIO:0102033] + description: An Mpox virus that clusters in phylogenetic trees within the + IIa clade. + meaning: GENEPIO:0102033 + is_a: Mpox virus clade II [GENEPIO:0102032] + Mpox virus clade IIb [GENEPIO:0102034]: + text: Mpox virus clade IIb [GENEPIO:0102034] + description: An Mpox virus that clusters in phylogenetic trees within the + IIb clade. + meaning: GENEPIO:0102034 + is_a: Mpox virus clade II [GENEPIO:0102032] + Mpox virus lineage B.1: + text: Mpox virus lineage B.1 + is_a: Mpox virus clade IIb [GENEPIO:0102034] + Mpox virus lineage A: + text: Mpox virus lineage A + is_a: Mpox virus clade IIb [GENEPIO:0102034] + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu permissible_values: Human: text: Human + description: A bipedal primate mammal of the species Homo sapiens. meaning: NCBITaxon:9606 - host (common name) international menu: - name: host (common name) international menu + HostCommonNameInternationalMenu: + name: HostCommonNameInternationalMenu + title: host (common name) international menu permissible_values: Human [NCBITaxon:9606]: text: Human [NCBITaxon:9606] + description: A bipedal primate mammal of the species Homo sapiens. meaning: NCBITaxon:9606 - Rodent: - text: Rodent + Rodent [NCBITaxon:9989]: + text: Rodent [NCBITaxon:9989] + description: A mammal of the order Rodentia which are characterized by a single + pair of continuously growing incisors in each of the upper and lower jaws. meaning: NCBITaxon:9989 - Mouse: - text: Mouse + Mouse [NCBITaxon:10090]: + text: Mouse [NCBITaxon:10090] + description: A small rodent that typically has a pointed snout, small rounded + ears, a body-length scaly tail, and a high breeding rate. meaning: NCBITaxon:10090 - is_a: Rodent - Prairie Dog: - text: Prairie Dog - is_a: Rodent - Rat: - text: Rat + is_a: Rodent [NCBITaxon:9989] + Prairie Dog [NCBITaxon:45478]: + text: Prairie Dog [NCBITaxon:45478] + description: A herbivorous burrowing ground squirrels native to the grasslands + of North America. + meaning: NCBITaxon:45478 + is_a: Rodent [NCBITaxon:9989] + Rat [NCBITaxon:10116]: + text: Rat [NCBITaxon:10116] + description: A medium sized rodent that typically is long tailed. meaning: NCBITaxon:10116 - is_a: Rodent - Squirrel: - text: Squirrel + is_a: Rodent [NCBITaxon:9989] + Squirrel [FOODON:03411389]: + text: Squirrel [FOODON:03411389] + description: A small to medium-sized rodent belonging to the family Sciuridae, + characterized by a bushy tail, sharp claws, and strong hind legs, commonly + found in trees, but some species live on the ground meaning: FOODON:03411389 - is_a: Rodent - host (scientific name) menu: - name: host (scientific name) menu + is_a: Rodent [NCBITaxon:9989] + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu permissible_values: Homo sapiens: text: Homo sapiens + description: A type of primate characterized by bipedalism and large, complex + brain. meaning: NCBITaxon:9606 - host (scientific name) international menu: - name: host (scientific name) international menu + HostScientificNameInternationalMenu: + name: HostScientificNameInternationalMenu + title: host (scientific name) international menu permissible_values: Homo sapiens [NCBITaxon:9606]: text: Homo sapiens [NCBITaxon:9606] + description: A bipedal primate mammal of the species Homo sapiens. meaning: NCBITaxon:9606 - host health state menu: - name: host health state menu + HostHealthStateMenu: + name: HostHealthStateMenu + title: host health state menu permissible_values: Asymptomatic: text: Asymptomatic + description: Without clinical signs or indications that raise the possibility + of a particular disorder or dysfunction. meaning: NCIT:C3833 Deceased: text: Deceased + description: The cessation of life. meaning: NCIT:C28554 Healthy: text: Healthy + description: Having no significant health-related issues. meaning: NCIT:C115935 Recovered: text: Recovered + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. meaning: NCIT:C49498 Symptomatic: text: Symptomatic + description: Exhibiting the symptoms of a particular disease. meaning: NCIT:C25269 - host health state international menu: - name: host health state international menu + HostHealthStateInternationalMenu: + name: HostHealthStateInternationalMenu + title: host health state international menu permissible_values: Asymptomatic [NCIT:C3833]: text: Asymptomatic [NCIT:C3833] + description: Without clinical signs or indications that raise the possibility + of a particular disorder or dysfunction. meaning: NCIT:C3833 Deceased [NCIT:C28554]: text: Deceased [NCIT:C28554] + description: The cessation of life. meaning: NCIT:C28554 Healthy [NCIT:C115935]: text: Healthy [NCIT:C115935] + description: Having no significant health-related issues. meaning: NCIT:C115935 Recovered [NCIT:C49498]: text: Recovered [NCIT:C49498] + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. meaning: NCIT:C49498 Symptomatic [NCIT:C25269]: text: Symptomatic [NCIT:C25269] + description: Exhibiting the symptoms of a particular disease. meaning: NCIT:C25269 - host health status details menu: - name: host health status details menu + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu + title: host health status details menu permissible_values: Hospitalized: text: Hospitalized + description: The condition of being treated as a patient in a hospital. meaning: NCIT:C25179 Hospitalized (Non-ICU): text: Hospitalized (Non-ICU) + description: The condition of being treated as a patient in a hospital without + admission to an intensive care unit (ICU). meaning: GENEPIO:0100045 is_a: Hospitalized Hospitalized (ICU): text: Hospitalized (ICU) + description: The condition of being treated as a patient in a hospital intensive + care unit (ICU). meaning: GENEPIO:0100046 is_a: Hospitalized Medically Isolated: text: Medically Isolated + description: Separation of people with a contagious disease from population + to reduce the spread of the disease. meaning: GENEPIO:0100047 Medically Isolated (Negative Pressure): text: Medically Isolated (Negative Pressure) + description: 'Medical isolation in a negative pressure environment: 6 to 12 + air exchanges per hour, and direct exhaust to the outside or through a high + efficiency particulate air filter.' meaning: GENEPIO:0100048 is_a: Medically Isolated Self-quarantining: text: Self-quarantining + description: A method used by an individual to be kept apart in seclusion + from others for a period of time in an attempt to minimize the risk of transmission + of an infectious disease. meaning: NCIT:C173768 - host health status details international menu: - name: host health status details international menu + HostHealthStatusDetailsInternationalMenu: + name: HostHealthStatusDetailsInternationalMenu + title: host health status details international menu permissible_values: Hospitalized [NCIT:C25179]: text: Hospitalized [NCIT:C25179] + description: The condition of being treated as a patient in a hospital. meaning: NCIT:C25179 Hospitalized (Non-ICU) [GENEPIO:0100045]: text: Hospitalized (Non-ICU) [GENEPIO:0100045] + description: The condition of being treated as a patient in a hospital without + admission to an intensive care unit (ICU). meaning: GENEPIO:0100045 is_a: Hospitalized [NCIT:C25179] Hospitalized (ICU) [GENEPIO:0100046]: text: Hospitalized (ICU) [GENEPIO:0100046] + description: The condition of being treated as a patient in a hospital intensive + care unit (ICU). meaning: GENEPIO:0100046 is_a: Hospitalized [NCIT:C25179] Medically Isolated [GENEPIO:0100047]: text: Medically Isolated [GENEPIO:0100047] + description: Separation of people with a contagious disease from population + to reduce the spread of the disease. meaning: GENEPIO:0100047 Medically Isolated (Negative Pressure) [GENEPIO:0100048]: text: Medically Isolated (Negative Pressure) [GENEPIO:0100048] + description: 'Medical isolation in a negative pressure environment: 6 to 12 + air exchanges per hour, and direct exhaust to the outside or through a high + efficiency particulate air filter.' meaning: GENEPIO:0100048 is_a: Medically Isolated [GENEPIO:0100047] Self-quarantining [NCIT:C173768]: text: Self-quarantining [NCIT:C173768] + description: A method used by an individual to be kept apart in seclusion + from others for a period of time in an attempt to minimize the risk of transmission + of an infectious disease. meaning: NCIT:C173768 - host health outcome menu: - name: host health outcome menu + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu + title: host health outcome menu permissible_values: Deceased: text: Deceased + description: The cessation of life. meaning: NCIT:C28554 Deteriorating: text: Deteriorating + description: Advancing in extent or severity. meaning: NCIT:C25254 Recovered: text: Recovered + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. meaning: NCIT:C49498 Stable: text: Stable + description: Subject to little fluctuation; showing little if any change. meaning: NCIT:C30103 - host health outcome international menu: - name: host health outcome international menu + HostHealthOutcomeInternationalMenu: + name: HostHealthOutcomeInternationalMenu + title: host health outcome international menu permissible_values: Deceased [NCIT:C28554]: text: Deceased [NCIT:C28554] + description: The cessation of life. meaning: NCIT:C28554 Deteriorating [NCIT:C25254]: text: Deteriorating [NCIT:C25254] + description: Advancing in extent or severity. meaning: NCIT:C25254 Recovered [NCIT:C49498]: text: Recovered [NCIT:C49498] + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. meaning: NCIT:C49498 Stable [NCIT:C30103]: text: Stable [NCIT:C30103] + description: Subject to little fluctuation; showing little if any change. meaning: NCIT:C30103 - host age unit menu: - name: host age unit menu + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host age unit menu permissible_values: month: text: month + description: A time unit which is approximately equal to the length of time + of one of cycle of the moon's phases which in science is taken to be equal + to 30 days. meaning: UO:0000035 year: text: year + description: A time unit which is equal to 12 months which in science is taken + to be equal to 365.25 days. meaning: UO:0000036 - host age unit international menu: - name: host age unit international menu + HostAgeUnitInternationalMenu: + name: HostAgeUnitInternationalMenu + title: host age unit international menu permissible_values: month [UO:0000035]: text: month [UO:0000035] + description: A time unit which is approximately equal to the length of time + of one of cycle of the moon's phases which in science is taken to be equal + to 30 days. meaning: UO:0000035 year [UO:0000036]: text: year [UO:0000036] + description: A time unit which is equal to 12 months which in science is taken + to be equal to 365.25 days. meaning: UO:0000036 - host age bin menu: - name: host age bin menu + HostAgeBinMenu: + name: HostAgeBinMenu + title: host age bin menu permissible_values: 0 - 9: text: 0 - 9 + description: An age group that stratifies the age of a case to be between + 0 to 9 years old (inclusive). meaning: GENEPIO:0100049 10 - 19: text: 10 - 19 + description: An age group that stratifies the age of a case to be between + 10 to 19 years old (inclusive). meaning: GENEPIO:0100050 20 - 29: text: 20 - 29 + description: An age group that stratifies the age of a case to be between + 20 to 29 years old (inclusive). meaning: GENEPIO:0100051 30 - 39: text: 30 - 39 + description: An age group that stratifies the age of a case to be between + 30 to 39 years old (inclusive). meaning: GENEPIO:0100052 40 - 49: text: 40 - 49 + description: An age group that stratifies the age of a case to be between + 40 to 49 years old (inclusive). meaning: GENEPIO:0100053 50 - 59: text: 50 - 59 + description: An age group that stratifies the age of a case to be between + 50 to 59 years old (inclusive). meaning: GENEPIO:0100054 60 - 69: text: 60 - 69 + description: An age group that stratifies the age of a case to be between + 60 to 69 years old (inclusive). meaning: GENEPIO:0100055 70 - 79: text: 70 - 79 + description: An age group that stratifies the age of a case to be between + 70 to 79 years old (inclusive). meaning: GENEPIO:0100056 80 - 89: text: 80 - 89 + description: An age group that stratifies the age of a case to be between + 80 to 89 years old (inclusive). meaning: GENEPIO:0100057 90 - 99: text: 90 - 99 + description: An age group that stratifies the age of a case to be between + 90 to 99 years old (inclusive). meaning: GENEPIO:0100058 100+: text: 100+ + description: An age group that stratifies the age of a case to be greater + than or equal to 100 years old. meaning: GENEPIO:0100059 - host age bin international menu: - name: host age bin international menu + HostAgeBinInternationalMenu: + name: HostAgeBinInternationalMenu + title: host age bin international menu permissible_values: 0 - 9 [GENEPIO:0100049]: text: 0 - 9 [GENEPIO:0100049] + description: An age group that stratifies the age of a case to be between + 0 to 9 years old (inclusive). meaning: GENEPIO:0100049 10 - 19 [GENEPIO:0100050]: text: 10 - 19 [GENEPIO:0100050] + description: An age group that stratifies the age of a case to be between + 10 to 19 years old (inclusive). meaning: GENEPIO:0100050 20 - 29 [GENEPIO:0100051]: text: 20 - 29 [GENEPIO:0100051] + description: An age group that stratifies the age of a case to be between + 20 to 29 years old (inclusive). meaning: GENEPIO:0100051 30 - 39 [GENEPIO:0100052]: text: 30 - 39 [GENEPIO:0100052] + description: An age group that stratifies the age of a case to be between + 30 to 39 years old (inclusive). meaning: GENEPIO:0100052 40 - 49 [GENEPIO:0100053]: text: 40 - 49 [GENEPIO:0100053] + description: An age group that stratifies the age of a case to be between + 40 to 49 years old (inclusive). meaning: GENEPIO:0100053 50 - 59 [GENEPIO:0100054]: text: 50 - 59 [GENEPIO:0100054] + description: An age group that stratifies the age of a case to be between + 50 to 59 years old (inclusive). meaning: GENEPIO:0100054 60 - 69 [GENEPIO:0100055]: text: 60 - 69 [GENEPIO:0100055] + description: An age group that stratifies the age of a case to be between + 60 to 69 years old (inclusive). meaning: GENEPIO:0100055 70 - 79 [GENEPIO:0100056]: text: 70 - 79 [GENEPIO:0100056] + description: An age group that stratifies the age of a case to be between + 70 to 79 years old (inclusive). meaning: GENEPIO:0100056 80 - 89 [GENEPIO:0100057]: text: 80 - 89 [GENEPIO:0100057] + description: An age group that stratifies the age of a case to be between + 80 to 89 years old (inclusive). meaning: GENEPIO:0100057 90 - 99 [GENEPIO:0100058]: text: 90 - 99 [GENEPIO:0100058] + description: An age group that stratifies the age of a case to be between + 90 to 99 years old (inclusive). meaning: GENEPIO:0100058 100+ [GENEPIO:0100059]: text: 100+ [GENEPIO:0100059] + description: An age group that stratifies the age of a case to be greater + than or equal to 100 years old. meaning: GENEPIO:0100059 - host gender menu: - name: host gender menu + HostGenderMenu: + name: HostGenderMenu + title: host gender menu permissible_values: Female: text: Female + description: An individual who reports belonging to the cultural gender role + distinction of female. meaning: NCIT:C46110 Male: text: Male + description: An individual who reports belonging to the cultural gender role + distinction of male. meaning: NCIT:C46109 Non-binary gender: text: Non-binary gender + description: Either, a specific gender identity which is not male or female; + or, more broadly, an umbrella term for gender identities not considered + male or female. meaning: GSSO:000132 Transgender (assigned male at birth): text: Transgender (assigned male at birth) + description: Having a feminine gender (identity) which is different from the + sex one was assigned at birth. meaning: GSSO:004004 Transgender (assigned female at birth): text: Transgender (assigned female at birth) + description: Having a masculine gender (identity) which is different from + the sex one was assigned at birth. meaning: GSSO:004005 Undeclared: text: Undeclared + description: A categorical choice recorded when an individual being interviewed + is unable or chooses not to provide a datum. meaning: NCIT:C110959 - host gender international menu: - name: host gender international menu + HostGenderInternationalMenu: + name: HostGenderInternationalMenu + title: host gender international menu permissible_values: Female [NCIT:C46110]: text: Female [NCIT:C46110] + description: An individual who reports belonging to the cultural gender role + distinction of female. meaning: NCIT:C46110 Male [NCIT:C46109]: text: Male [NCIT:C46109] + description: An individual who reports belonging to the cultural gender role + distinction of male. meaning: NCIT:C46109 Non-binary gender [GSSO:000132]: text: Non-binary gender [GSSO:000132] + description: Either, a specific gender identity which is not male or female; + or, more broadly, an umbrella term for gender identities not considered + male or female. meaning: GSSO:000132 Transgender (assigned male at birth) [GSSO:004004]: text: Transgender (assigned male at birth) [GSSO:004004] + description: Having a feminine gender (identity) which is different from the + sex one was assigned at birth. meaning: GSSO:004004 Transgender (assigned female at birth) [GSSO:004005]: text: Transgender (assigned female at birth) [GSSO:004005] + description: Having a masculine gender (identity) which is different from + the sex one was assigned at birth. meaning: GSSO:004005 Undeclared [NCIT:C110959]: text: Undeclared [NCIT:C110959] + description: A categorical choice recorded when an individual being interviewed + is unable or chooses not to provide a datum. meaning: NCIT:C110959 - signs and symptoms menu: - name: signs and symptoms menu + SignsAndSymptomsMenu: + name: SignsAndSymptomsMenu + title: signs and symptoms menu permissible_values: Chills (sudden cold sensation): text: Chills (sudden cold sensation) @@ -4407,25 +6231,34 @@ enums: meaning: HP:0002315 Lesion: text: Lesion + description: A localized pathological or traumatic structural change, damage, + deformity, or discontinuity of tissue, organ, or body part. meaning: NCIT:C3824 Lesion (Macule): text: Lesion (Macule) + description: A flat lesion characterized by change in the skin color. meaning: NCIT:C43278 is_a: Lesion Lesion (Papule): text: Lesion (Papule) + description: A small (less than 5-10 mm) elevation of skin that is non-suppurative. meaning: NCIT:C39690 is_a: Lesion Lesion (Pustule): text: Lesion (Pustule) + description: A circumscribed and elevated skin lesion filled with purulent + material. meaning: NCIT:C78582 is_a: Lesion Lesion (Scab): text: Lesion (Scab) + description: Dried purulent material on the skin from a skin lesion. meaning: GENEPIO:0100490 is_a: Lesion Lesion (Vesicle): text: Lesion (Vesicle) + description: Small, inflamed, pus-filled, blister-like sores (lesions) on + the skin surface. meaning: GENEPIO:0100491 is_a: Lesion Myalgia (muscle pain): @@ -4434,6 +6267,8 @@ enums: meaning: HP:0003326 Back pain: text: Back pain + description: An unpleasant sensation characterized by physical discomfort + (such as pricking, throbbing, or aching) localized to the back. meaning: HP:0003418 is_a: Myalgia (muscle pain) Nausea: @@ -4452,6 +6287,8 @@ enums: meaning: NCIT:C50747 Sweating: text: Sweating + description: A watery secretion by the sweat glands that is primarily composed + of salt, urea and minerals. meaning: NCIT:C36172 Swollen Lymph Nodes: text: Swollen Lymph Nodes @@ -4459,14 +6296,17 @@ enums: meaning: HP:0002716 Ulcer: text: Ulcer + description: A circumscribed inflammatory and often suppurating lesion on + the skin or an internal mucous surface resulting in necrosis of tissue. meaning: NCIT:C3426 Vomiting (throwing up): text: Vomiting (throwing up) description: Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. meaning: HP:0002013 - signs and symptoms international menu: - name: signs and symptoms international menu + SignsAndSymptomsInternationalMenu: + name: SignsAndSymptomsInternationalMenu + title: signs and symptoms international menu permissible_values: Chills (sudden cold sensation) [HP:0025143]: text: Chills (sudden cold sensation) [HP:0025143] @@ -4497,25 +6337,34 @@ enums: meaning: HP:0002315 Lesion [NCIT:C3824]: text: Lesion [NCIT:C3824] + description: A localized pathological or traumatic structural change, damage, + deformity, or discontinuity of tissue, organ, or body part. meaning: NCIT:C3824 Lesion (Macule) [NCIT:C43278]: text: Lesion (Macule) [NCIT:C43278] + description: A flat lesion characterized by change in the skin color. meaning: NCIT:C43278 is_a: Lesion [NCIT:C3824] Lesion (Papule) [NCIT:C39690]: text: Lesion (Papule) [NCIT:C39690] + description: A small (less than 5-10 mm) elevation of skin that is non-suppurative. meaning: NCIT:C39690 is_a: Lesion [NCIT:C3824] Lesion (Pustule) [NCIT:C78582]: text: Lesion (Pustule) [NCIT:C78582] + description: A circumscribed and elevated skin lesion filled with purulent + material. meaning: NCIT:C78582 is_a: Lesion [NCIT:C3824] Lesion (Scab) [GENEPIO:0100490]: text: Lesion (Scab) [GENEPIO:0100490] + description: Dried purulent material on the skin from a skin lesion. meaning: GENEPIO:0100490 is_a: Lesion [NCIT:C3824] Lesion (Vesicle) [GENEPIO:0100491]: text: Lesion (Vesicle) [GENEPIO:0100491] + description: Small, inflamed, pus-filled, blister-like sores (lesions) on + the skin surface. meaning: GENEPIO:0100491 is_a: Lesion [NCIT:C3824] Myalgia (muscle pain) [HP:0003326]: @@ -4524,6 +6373,8 @@ enums: meaning: HP:0003326 Back pain [HP:0003418]: text: Back pain [HP:0003418] + description: An unpleasant sensation characterized by physical discomfort + (such as pricking, throbbing, or aching) localized to the back. meaning: HP:0003418 is_a: Myalgia (muscle pain) [HP:0003326] Nausea [HP:0002018]: @@ -4542,6 +6393,8 @@ enums: meaning: NCIT:C50747 Sweating [NCIT:C36172]: text: Sweating [NCIT:C36172] + description: A watery secretion by the sweat glands that is primarily composed + of salt, urea and minerals. meaning: NCIT:C36172 Swollen Lymph Nodes [HP:0002716]: text: Swollen Lymph Nodes [HP:0002716] @@ -4549,296 +6402,539 @@ enums: meaning: HP:0002716 Ulcer [NCIT:C3426]: text: Ulcer [NCIT:C3426] + description: A circumscribed inflammatory and often suppurating lesion on + the skin or an internal mucous surface resulting in necrosis of tissue. meaning: NCIT:C3426 Vomiting (throwing up) [HP:0002013]: text: Vomiting (throwing up) [HP:0002013] description: Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. meaning: HP:0002013 - pre-existing conditions and risk factors menu: - name: pre-existing conditions and risk factors menu + PreExistingConditionsAndRiskFactorsMenu: + name: PreExistingConditionsAndRiskFactorsMenu + title: pre-existing conditions and risk factors menu permissible_values: Cancer: text: Cancer + description: A tumor composed of atypical neoplastic, often pleomorphic cells + that invade other tissues. Malignant neoplasms often metastasize to distant + anatomic sites and may recur after excision. The most common malignant neoplasms + are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and + non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. meaning: MONDO:0004992 Diabetes mellitus (diabetes): text: Diabetes mellitus (diabetes) + description: A group of abnormalities characterized by hyperglycemia and glucose + intolerance. meaning: HP:0000819 Type I diabetes mellitus (T1D): text: Type I diabetes mellitus (T1D) + description: A chronic condition in which the pancreas produces little or + no insulin. Type I diabetes mellitus is manifested by the sudden onset of + severe hyperglycemia with rapid progression to diabetic ketoacidosis unless + treated with insulin. meaning: HP:0100651 is_a: Diabetes mellitus (diabetes) Type II diabetes mellitus (T2D): text: Type II diabetes mellitus (T2D) + description: A type of diabetes mellitus initially characterized by insulin + resistance and hyperinsulinemia and subsequently by glucose interolerance + and hyperglycemia. meaning: HP:0005978 is_a: Diabetes mellitus (diabetes) Immunocompromised: text: Immunocompromised + description: A loss of any arm of immune functions, resulting in potential + or actual increase in infections. This state may be reached secondary to + specific genetic lesions, syndromes with unidentified or polygenic causes, + acquired deficits from other disease states, or as result of therapy for + other diseases or conditions. meaning: NCIT:C14139 Infectious disorder: text: Infectious disorder + description: A disorder resulting from the presence and activity of a microbial, + viral, fungal, or parasitic agent. It can be transmitted by direct or indirect + contact. meaning: NCIT:C26726 Chancroid (Haemophilus ducreyi): text: Chancroid (Haemophilus ducreyi) + description: A primary bacterial infectious disease that is a sexually transmitted + infection located in skin of the genitals, has_material_basis_in Haemophilus + ducreyi, which is transmitted by sexual contact. The infection has symptom + painful and soft ulcers. meaning: DOID:13778 is_a: Infectious disorder Chlamydia: text: Chlamydia + description: A commensal bacterial infectious disease that is caused by Chlamydia + trachomatis. meaning: DOID:11263 is_a: Infectious disorder Gonorrhea: text: Gonorrhea + description: A primary bacterial infectious disease that is a sexually transmitted + infection, located_in uterus, located_in fallopian tube, located_in urethra, + located_in mouth, located_in throat, located_in eye or located_in anus, + has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact + with the penis, vagina, mouth, or anus or transmitted_by congenitally from + mother to baby during delivery. The infection has_symptom burning sensation + during urination, has_symptom discharge from the penis, has_symptom increased + vaginal discharge, or has_symptom vaginal bleeding between periods. meaning: DOID:7551 is_a: Infectious disorder Herpes Simplex Virus infection (HSV): text: Herpes Simplex Virus infection (HSV) + description: An infection that is caused by herpes simplex virus. meaning: NCIT:C155871 is_a: Infectious disorder Human immunodeficiency virus (HIV): text: Human immunodeficiency virus (HIV) + description: An infection caused by the human immunodeficiency virus. meaning: MONDO:0005109 is_a: Infectious disorder Acquired immunodeficiency syndrome (AIDS): text: Acquired immunodeficiency syndrome (AIDS) + description: A syndrome resulting from the acquired deficiency of cellular + immunity caused by the human immunodeficiency virus (HIV). It is characterized + by the reduction of the Helper T-lymphocytes in the peripheral blood and + the lymph nodes. meaning: MONDO:0012268 is_a: Human immunodeficiency virus (HIV) Human papilloma virus infection (HPV): text: Human papilloma virus infection (HPV) + description: An infectious process caused by a human papillomavirus. This + infection can cause abnormal tissue growth. meaning: MONDO:0005161 is_a: Infectious disorder Lymphogranuloma venereum: text: Lymphogranuloma venereum + description: A commensal bacterial infectious disease that results_in infection + located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which + is transmitted_by sexual contact, and transmitted_by fomites. The infection + has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, + and has_symptom lymphangitis. meaning: DOID:13819 is_a: Infectious disorder Mycoplsma genitalium: text: Mycoplsma genitalium + description: A sexually transmitted, small and pathogenic bacterium that lives + on the mucous epithelial cells of the urinary and genital tracts in humans. meaning: NCBITaxon:2097 is_a: Infectious disorder Syphilis: text: Syphilis + description: A primary bacterial infectious disease that is a sexually transmitted + systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, + which is transmitted_by sexual contact, transmitted_by blood product transfusion, + transmitted_by congenital method from mother to fetus or transmitted_by + contact with infectious lesions. If left untreated, produces chancres, rashes, + and systemic lesions in a clinical course with three stages continued over + many years. meaning: DOID:4166 is_a: Infectious disorder Trichomoniasis: text: Trichomoniasis + description: A parasitic protozoa infectious disease that is caused by singled-celled + protozoan parasites Trichomonas vaginalis or Trichomonas tenax, which infect + the urogenital tract and mouth respectively. meaning: DOID:1947 is_a: Infectious disorder Lupus: text: Lupus + description: An autoimmune, connective tissue chronic inflammatory disorder + affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood + cells. It is more commonly seen in women than men. Variants include discoid + and systemic lupus erythematosus. meaning: MONDO:0004670 Pregnancy: text: Pregnancy + description: The state or condition of having a developing embryo or fetus + in the body (uterus), after union of an ovum and spermatozoon, during the + period from conception to birth. meaning: NCIT:C25742 Prior therapy: text: Prior therapy + description: Prior action or administration of therapeutic agents that produced + an effect that is intended to alter or stop a pathologic process. meaning: NCIT:C16124 Cancer treatment: text: Cancer treatment + description: Any intervention for management of a malignant neoplasm. meaning: NCIT:C16212 is_a: Prior therapy Chemotherapy: text: Chemotherapy + description: The use of synthetic or naturally-occurring chemicals for the + treatment of diseases. meaning: NCIT:C15632 is_a: Cancer treatment HIV and Antiretroviral therapy (ART): text: HIV and Antiretroviral therapy (ART) + description: Treatment of human immunodeficiency virus (HIV) infections with + medications that target the virus directly, limiting the ability of infected + cells to produce new HIV particles. meaning: NCIT:C16118 is_a: Prior therapy Steroid: text: Steroid + description: Any of naturally occurring compounds and synthetic analogues, + based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely + hydrogenated; there are usually methyl groups at C-10 and C-13, and often + an alkyl group at C-17. By extension, one or more bond scissions, ring expansions + and/or ring contractions of the skeleton may have occurred. Natural steroids + are derived biogenetically from squalene which is a triterpene. meaning: CHEBI:35341 is_a: Prior therapy Transplant: text: Transplant + description: An individual receiving a transplant. meaning: NCIT:C159659 - pre-existing conditions and risk factors international menu: - name: pre-existing conditions and risk factors international menu + PreExistingConditionsAndRiskFactorsInternationalMenu: + name: PreExistingConditionsAndRiskFactorsInternationalMenu + title: pre-existing conditions and risk factors international menu permissible_values: Cancer [MONDO:0004992]: text: Cancer [MONDO:0004992] + description: A tumor composed of atypical neoplastic, often pleomorphic cells + that invade other tissues. Malignant neoplasms often metastasize to distant + anatomic sites and may recur after excision. The most common malignant neoplasms + are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and + non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. meaning: MONDO:0004992 Diabetes mellitus (diabetes) [HP:0000819]: text: Diabetes mellitus (diabetes) [HP:0000819] + description: A group of abnormalities characterized by hyperglycemia and glucose + intolerance. meaning: HP:0000819 Type I diabetes mellitus (T1D) [HP:0100651]: text: Type I diabetes mellitus (T1D) [HP:0100651] + description: A chronic condition in which the pancreas produces little or + no insulin. Type I diabetes mellitus is manifested by the sudden onset of + severe hyperglycemia with rapid progression to diabetic ketoacidosis unless + treated with insulin. meaning: HP:0100651 is_a: Diabetes mellitus (diabetes) [HP:0000819] Type II diabetes mellitus (T2D) [HP:0005978]: text: Type II diabetes mellitus (T2D) [HP:0005978] + description: A type of diabetes mellitus initially characterized by insulin + resistance and hyperinsulinemia and subsequently by glucose interolerance + and hyperglycemia. meaning: HP:0005978 is_a: Diabetes mellitus (diabetes) [HP:0000819] Immunocompromised [NCIT:C14139]: text: Immunocompromised [NCIT:C14139] + description: A loss of any arm of immune functions, resulting in potential + or actual increase in infections. This state may be reached secondary to + specific genetic lesions, syndromes with unidentified or polygenic causes, + acquired deficits from other disease states, or as result of therapy for + other diseases or conditions. meaning: NCIT:C14139 Infectious disorder [NCIT:C26726]: text: Infectious disorder [NCIT:C26726] + description: A disorder resulting from the presence and activity of a microbial, + viral, fungal, or parasitic agent. It can be transmitted by direct or indirect + contact. meaning: NCIT:C26726 Chancroid (Haemophilus ducreyi) [DOID:13778]: text: Chancroid (Haemophilus ducreyi) [DOID:13778] + description: A primary bacterial infectious disease that is a sexually transmitted + infection located in skin of the genitals, has_material_basis_in Haemophilus + ducreyi, which is transmitted by sexual contact. The infection has symptom + painful and soft ulcers. meaning: DOID:13778 is_a: Infectious disorder [NCIT:C26726] Chlamydia [DOID:11263]: text: Chlamydia [DOID:11263] + description: A commensal bacterial infectious disease that is caused by Chlamydia + trachomatis. meaning: DOID:11263 is_a: Infectious disorder [NCIT:C26726] Gonorrhea [DOID:7551]: text: Gonorrhea [DOID:7551] + description: A primary bacterial infectious disease that is a sexually transmitted + infection, located_in uterus, located_in fallopian tube, located_in urethra, + located_in mouth, located_in throat, located_in eye or located_in anus, + has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact + with the penis, vagina, mouth, or anus or transmitted_by congenitally from + mother to baby during delivery. The infection has_symptom burning sensation + during urination, has_symptom discharge from the penis, has_symptom increased + vaginal discharge, or has_symptom vaginal bleeding between periods. meaning: DOID:7551 is_a: Infectious disorder [NCIT:C26726] Herpes Simplex Virus infection (HSV) [NCIT:C155871]: text: Herpes Simplex Virus infection (HSV) [NCIT:C155871] + description: An infection that is caused by herpes simplex virus. meaning: NCIT:C155871 is_a: Infectious disorder [NCIT:C26726] Human immunodeficiency virus (HIV) [MONDO:0005109]: text: Human immunodeficiency virus (HIV) [MONDO:0005109] + description: An infection caused by the human immunodeficiency virus. meaning: MONDO:0005109 is_a: Infectious disorder [NCIT:C26726] Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]: text: Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] + description: A syndrome resulting from the acquired deficiency of cellular + immunity caused by the human immunodeficiency virus (HIV). It is characterized + by the reduction of the Helper T-lymphocytes in the peripheral blood and + the lymph nodes. meaning: MONDO:0012268 is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] Human papilloma virus infection (HPV) [MONDO:0005161]: text: Human papilloma virus infection (HPV) [MONDO:0005161] + description: An infectious process caused by a human papillomavirus. This + infection can cause abnormal tissue growth. meaning: MONDO:0005161 is_a: Infectious disorder [NCIT:C26726] Lymphogranuloma venereum [DOID:13819]: text: Lymphogranuloma venereum [DOID:13819] + description: A commensal bacterial infectious disease that results_in infection + located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which + is transmitted_by sexual contact, and transmitted_by fomites. The infection + has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, + and has_symptom lymphangitis. meaning: DOID:13819 is_a: Infectious disorder [NCIT:C26726] Mycoplsma genitalium [NCBITaxon:2097]: text: Mycoplsma genitalium [NCBITaxon:2097] + description: A sexually transmitted, small and pathogenic bacterium that lives + on the mucous epithelial cells of the urinary and genital tracts in humans. meaning: NCBITaxon:2097 is_a: Infectious disorder [NCIT:C26726] Syphilis [DOID:4166]: text: Syphilis [DOID:4166] + description: A primary bacterial infectious disease that is a sexually transmitted + systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, + which is transmitted_by sexual contact, transmitted_by blood product transfusion, + transmitted_by congenital method from mother to fetus or transmitted_by + contact with infectious lesions. If left untreated, produces chancres, rashes, + and systemic lesions in a clinical course with three stages continued over + many years. meaning: DOID:4166 is_a: Infectious disorder [NCIT:C26726] Trichomoniasis [DOID:1947]: text: Trichomoniasis [DOID:1947] + description: A parasitic protozoa infectious disease that is caused by singled-celled + protozoan parasites Trichomonas vaginalis or Trichomonas tenax, which infect + the urogenital tract and mouth respectively. meaning: DOID:1947 is_a: Infectious disorder [NCIT:C26726] Lupus [MONDO:0004670]: text: Lupus [MONDO:0004670] + description: An autoimmune, connective tissue chronic inflammatory disorder + affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood + cells. It is more commonly seen in women than men. Variants include discoid + and systemic lupus erythematosus. meaning: MONDO:0004670 Pregnancy [NCIT:C25742]: text: Pregnancy [NCIT:C25742] + description: The state or condition of having a developing embryo or fetus + in the body (uterus), after union of an ovum and spermatozoon, during the + period from conception to birth. meaning: NCIT:C25742 Prior therapy [NCIT:C16124]: text: Prior therapy [NCIT:C16124] + description: Prior action or administration of therapeutic agents that produced + an effect that is intended to alter or stop a pathologic process. meaning: NCIT:C16124 Cancer treatment [NCIT:C16212]: text: Cancer treatment [NCIT:C16212] + description: Any intervention for management of a malignant neoplasm. meaning: NCIT:C16212 is_a: Prior therapy [NCIT:C16124] Chemotherapy [NCIT:C15632]: text: Chemotherapy [NCIT:C15632] + description: The use of synthetic or naturally-occurring chemicals for the + treatment of diseases. meaning: NCIT:C15632 is_a: Cancer treatment [NCIT:C16212] HIV and Antiretroviral therapy (ART) [NCIT:C16118]: text: HIV and Antiretroviral therapy (ART) [NCIT:C16118] + description: Treatment of human immunodeficiency virus (HIV) infections with + medications that target the virus directly, limiting the ability of infected + cells to produce new HIV particles. meaning: NCIT:C16118 is_a: Prior therapy [NCIT:C16124] Steroid [CHEBI:35341]: text: Steroid [CHEBI:35341] + description: Any of naturally occurring compounds and synthetic analogues, + based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely + hydrogenated; there are usually methyl groups at C-10 and C-13, and often + an alkyl group at C-17. By extension, one or more bond scissions, ring expansions + and/or ring contractions of the skeleton may have occurred. Natural steroids + are derived biogenetically from squalene which is a triterpene. meaning: CHEBI:35341 is_a: Prior therapy [NCIT:C16124] Transplant [NCIT:C159659]: text: Transplant [NCIT:C159659] + description: An individual receiving a transplant. meaning: NCIT:C159659 - complications menu: - name: complications menu + ComplicationsMenu: + name: ComplicationsMenu + title: complications menu permissible_values: Bronchopneumonia: text: Bronchopneumonia + description: Acute inflammation of the walls of the terminal bronchioles that + spreads into the peribronchial alveoli and alveolar ducts. It results in + the creation of foci of consolidation, which are surrounded by normal parenchyma. + It affects one or more lobes, and is frequently bilateral and basal. It + is usually caused by bacteria (e.g., Staphylococcus, Streptococcus, Haemophilus + influenzae). Signs and symptoms include fever, cough with production of + brown-red sputum, dyspnea, and chest pain. meaning: MONDO:0005682 Corneal infection: text: Corneal infection + description: A viral or bacterial infectious process affecting the cornea. + Symptoms include pain and redness in the eye, photophobia and eye watering. meaning: MONDO:0023865 Delayed wound healing (lesion healing): text: Delayed wound healing (lesion healing) + description: Longer time requirement for the ability to self-repair and close + wounds than normal meaning: MP:0002908 Encephalitis: text: Encephalitis + description: A brain disease that is characterized as an acute inflammation + of the brain with flu-like symptoms. meaning: DOID:9588 Myocarditis: text: Myocarditis + description: An extrinsic cardiomyopathy that is characterized as an inflammation + of the heart muscle. meaning: DOID:820 Secondary infection: text: Secondary infection + description: An infection bearing the secondary infection role. meaning: IDO:0000567 Sepsis: text: Sepsis + description: Systemic inflammatory response to infection. meaning: HP:0100806 - complications international menu: - name: complications international menu + ComplicationsInternationalMenu: + name: ComplicationsInternationalMenu + title: complications international menu permissible_values: Bronchopneumonia [MONDO:0005682]: text: Bronchopneumonia [MONDO:0005682] + description: Acute inflammation of the walls of the terminal bronchioles that + spreads into the peribronchial alveoli and alveolar ducts. It results in + the creation of foci of consolidation, which are surrounded by normal parenchyma. + It affects one or more lobes, and is frequently bilateral and basal. It + is usually caused by bacteria (e.g., Staphylococcus, Streptococcus, Haemophilus + influenzae). Signs and symptoms include fever, cough with production of + brown-red sputum, dyspnea, and chest pain. meaning: MONDO:0005682 Corneal infection [MONDO:0023865]: text: Corneal infection [MONDO:0023865] + description: A viral or bacterial infectious process affecting the cornea. + Symptoms include pain and redness in the eye, photophobia and eye watering. meaning: MONDO:0023865 Delayed wound healing (lesion healing) [MP:0002908]: text: Delayed wound healing (lesion healing) [MP:0002908] + description: Longer time requirement for the ability to self-repair and close + wounds than normal meaning: MP:0002908 Encephalitis [DOID:9588]: text: Encephalitis [DOID:9588] + description: A brain disease that is characterized as an acute inflammation + of the brain with flu-like symptoms. meaning: DOID:9588 Myocarditis [DOID:820]: text: Myocarditis [DOID:820] + description: An extrinsic cardiomyopathy that is characterized as an inflammation + of the heart muscle. meaning: DOID:820 Secondary infection [IDO:0000567]: text: Secondary infection [IDO:0000567] + description: An infection bearing the secondary infection role. meaning: IDO:0000567 Sepsis [HP:0100806]: text: Sepsis [HP:0100806] + description: Systemic inflammatory response to infection. meaning: HP:0100806 - host vaccination status menu: - name: host vaccination status menu + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu + title: host vaccination status menu permissible_values: Fully Vaccinated: text: Fully Vaccinated + description: Completed a full series of an authorized vaccine according to + the regional health institutional guidance. meaning: GENEPIO:0100100 Not Vaccinated: text: Not Vaccinated + description: Have not completed or initiated a vaccine series authorized and + administered according to the regional health institutional guidance. meaning: GENEPIO:0100102 - host vaccination status international menu: - name: host vaccination status international menu + HostVaccinationStatusInternationalMenu: + name: HostVaccinationStatusInternationalMenu + title: host vaccination status international menu permissible_values: Fully Vaccinated [GENEPIO:0100100]: text: Fully Vaccinated [GENEPIO:0100100] + description: Completed a full series of an authorized vaccine according to + the regional health institutional guidance. meaning: GENEPIO:0100100 + Partially Vaccinated [GENEPIO:0100101]: + text: Partially Vaccinated [GENEPIO:0100101] + description: Initiated but not yet completed the full series of an authorized + vaccine according to the regional health institutional guidance. + meaning: GENEPIO:0100101 Not Vaccinated [GENEPIO:0100102]: text: Not Vaccinated [GENEPIO:0100102] + description: Have not completed or initiated a vaccine series authorized and + administered according to the regional health institutional guidance. meaning: GENEPIO:0100102 - exposure event menu: - name: exposure event menu + ExposureEventMenu: + name: ExposureEventMenu + title: exposure event menu permissible_values: Mass Gathering: text: Mass Gathering + description: A gathering or event attended by a sufficient number of people + to strain the planning and response resources of the host community, state/province, + nation, or region where it is being held. meaning: GENEPIO:0100237 Convention (conference): text: Convention (conference) + description: A gathering of individuals who meet at an arranged place and + time in order to discuss or engage in some common interest. The most common + conventions are based upon industry, profession, and fandom. meaning: GENEPIO:0100238 Agricultural Event: text: Agricultural Event + description: A gathering exhibiting the equipment, animals, sports and recreation + associated with agriculture and animal husbandry. meaning: GENEPIO:0100240 is_a: Convention (conference) Social Gathering: text: Social Gathering + description: A type of social behavior in which a collection of humans intentionally + gathers together on a temporary basis to engage socially. meaning: PCO:0000033 Community Event: text: Community Event + description: A human social event in which humans living in the same area + or neighborhood gather to carry out activiites relevent to the people living + in the area. meaning: PCO:0000034 is_a: Social Gathering Party: text: Party + description: A human social gathering in which the intention is to have a + good time. Often the intention is to celebrate something like a birthday, + anniversary, or holiday, but there is not always a purpose. meaning: PCO:0000035 is_a: Social Gathering Other exposure event: text: Other exposure event - exposure event international menu: - name: exposure event international menu + description: An event or situation not classified under other specific exposure + types, in which an individual may be exposed to conditions or factors that + could impact health or safety. This term encompasses a wide range of gatherings, + activities, or circumstances that do not fit into predefined exposure categories. + ExposureEventInternationalMenu: + name: ExposureEventInternationalMenu + title: exposure event international menu permissible_values: Mass Gathering [GENEPIO:0100237]: text: Mass Gathering [GENEPIO:0100237] @@ -4880,1446 +6976,2683 @@ enums: Other exposure event: text: Other exposure event description: An exposure event not specified in the picklist. - exposure contact level menu: - name: exposure contact level menu + ExposureContactLevelMenu: + name: ExposureContactLevelMenu + title: exposure contact level menu permissible_values: Contact with animal: text: Contact with animal + description: A type of contact in which an individual comes into contact with + an animal, either directly or indirectly, which could include physical interaction + or exposure to animal bodily fluids, feces, or other contaminated materials. meaning: GENEPIO:0100494 Contact with rodent: text: Contact with rodent + description: A type of contact in which an individual comes into contact with + a rodent, either directly or indirectly, such as through handling, exposure + to rodent droppings, urine, or nests, which could potentially lead to the + transmission of rodent-borne diseases. meaning: GENEPIO:0100495 is_a: Contact with animal Contact with fomite: text: Contact with fomite + description: A type of contact in which an individual comes into contact with + an inanimate object or surface that has been contaminated with pathogens, + such as doorknobs, countertops, or medical equipment, which can transfer + infectious agents to the individual. meaning: GENEPIO:0100496 Contact with infected individual: text: Contact with infected individual + description: A type of contact in which an individual comes in contact with + an infected person, either directly or indirectly. meaning: GENEPIO:0100357 Direct (human-to-human contact): text: Direct (human-to-human contact) + description: Direct and essentially immediate transfer of infectious agents + to a receptive portal of entry through which human or animal infection may + take place. This may be by direct contact such as touching, kissing, biting, + or sexual intercourse or by the direct projection (droplet spread) of droplet + spray onto the conjunctiva or the mucous membranes of the eyes, nose, or + mouth. It may also be by direct exposure of susceptible tissue to an agent + in soil, compost, or decaying vegetable matter or by the bite of a rabid + animal. Transplacental transmission is another form of direct transmission. meaning: TRANS:0000001 is_a: Contact with infected individual Mother-to-child transmission: text: Mother-to-child transmission + description: A direct transmission process during which the pathogen is transmitted + directly from mother to child at or around the time of birth. meaning: TRANS:0000006 is_a: Direct (human-to-human contact) Sexual transmission: text: Sexual transmission + description: Passage or transfer, as of a disease, from a donor individual + to a recipient during or as a result of sexual activity. meaning: NCIT:C19085 is_a: Direct (human-to-human contact) Indirect contact: text: Indirect contact + description: A type of contact in which an individual does not come in direct + contact with a source of infection e.g. through airborne transmission, contact + with contaminated surfaces. meaning: GENEPIO:0100246 is_a: Contact with infected individual Close contact (face-to-face contact): text: Close contact (face-to-face contact) + description: A type of indirect contact where an individual sustains unprotected + exposure by being within 6 feet of an infected individual over a sustained + period of time. meaning: GENEPIO:0100247 is_a: Indirect contact Casual contact: text: Casual contact + description: A type of indirect contact where an individual may at the same + location at the same time as a positive case; however, they may have been + there only briefly, or it may have been a location that carries a lower + risk of transmission. meaning: GENEPIO:0100248 is_a: Indirect contact Workplace associated transmission: text: Workplace associated transmission + description: A type of transmission where an individual acquires an infection + or disease as a result of exposure in their workplace environment. This + can include direct contact with infected individuals, exposure to contaminated + materials or surfaces, or other workplace-specific risk factors. meaning: GENEPIO:0100497 Healthcare associated transmission: text: Healthcare associated transmission + description: A type of transmission where an individual acquires an infection + or disease as a result of exposure within a healthcare setting. This includes + transmission through direct contact with patients, contaminated medical + equipment, or surfaces within healthcare facilities, such as hospitals or + clinics. meaning: GENEPIO:0100498 is_a: Workplace associated transmission Laboratory associated transmission: text: Laboratory associated transmission + description: A type of transmission where an individual acquires an infection + or disease as a result of exposure within a laboratory setting. This includes + contact with infectious agents, contaminated equipment, or laboratory surfaces, + as well as potential aerosol exposure or spills of hazardous substances. meaning: GENEPIO:0100499 is_a: Workplace associated transmission - exposure contact level international menu: - name: exposure contact level international menu + ExposureContactLevelInternationalMenu: + name: ExposureContactLevelInternationalMenu + title: exposure contact level international menu permissible_values: Contact with animal [GENEPIO:0100494]: text: Contact with animal [GENEPIO:0100494] + description: A type of contact in which an individual comes into contact with + an animal, either directly or indirectly, which could include physical interaction + or exposure to animal bodily fluids, feces, or other contaminated materials. meaning: GENEPIO:0100494 Contact with rodent [GENEPIO:0100495]: text: Contact with rodent [GENEPIO:0100495] + description: A type of contact in which an individual comes into contact with + a rodent, either directly or indirectly, such as through handling, exposure + to rodent droppings, urine, or nests, which could potentially lead to the + transmission of rodent-borne diseases. meaning: GENEPIO:0100495 is_a: Contact with animal [GENEPIO:0100494] Contact with fomite [GENEPIO:0100496]: text: Contact with fomite [GENEPIO:0100496] + description: A type of contact in which an individual comes into contact with + an inanimate object or surface that has been contaminated with pathogens, + such as doorknobs, countertops, or medical equipment, which can transfer + infectious agents to the individual. meaning: GENEPIO:0100496 Contact with infected individual [GENEPIO:0100357]: text: Contact with infected individual [GENEPIO:0100357] + description: A type of contact in which an individual comes in contact with + an infected person, either directly or indirectly. meaning: GENEPIO:0100357 Direct (human-to-human contact) [TRANS:0000001]: text: Direct (human-to-human contact) [TRANS:0000001] + description: Direct and essentially immediate transfer of infectious agents + to a receptive portal of entry through which human or animal infection may + take place. This may be by direct contact such as touching, kissing, biting, + or sexual intercourse or by the direct projection (droplet spread) of droplet + spray onto the conjunctiva or the mucous membranes of the eyes, nose, or + mouth. It may also be by direct exposure of susceptible tissue to an agent + in soil, compost, or decaying vegetable matter or by the bite of a rabid + animal. Transplacental transmission is another form of direct transmission. meaning: TRANS:0000001 is_a: Contact with infected individual [GENEPIO:0100357] Mother-to-child transmission [TRANS:0000006]: text: Mother-to-child transmission [TRANS:0000006] + description: A direct transmission process during which the pathogen is transmitted + directly from mother to child at or around the time of birth. meaning: TRANS:0000006 is_a: Direct (human-to-human contact) [TRANS:0000001] Sexual transmission [NCIT:C19085]: text: Sexual transmission [NCIT:C19085] + description: Passage or transfer, as of a disease, from a donor individual + to a recipient during or as a result of sexual activity. meaning: NCIT:C19085 is_a: Direct (human-to-human contact) [TRANS:0000001] Indirect contact [GENEPIO:0100246]: text: Indirect contact [GENEPIO:0100246] + description: A type of contact in which an individual does not come in direct + contact with a source of infection e.g. through airborne transmission, contact + with contaminated surfaces. meaning: GENEPIO:0100246 is_a: Contact with infected individual [GENEPIO:0100357] Close contact (face-to-face contact) [GENEPIO:0100247]: text: Close contact (face-to-face contact) [GENEPIO:0100247] + description: A type of indirect contact where an individual sustains unprotected + exposure by being within 6 feet of an infected individual over a sustained + period of time. meaning: GENEPIO:0100247 is_a: Indirect contact [GENEPIO:0100246] Casual contact [GENEPIO:0100248]: text: Casual contact [GENEPIO:0100248] + description: A type of indirect contact where an individual may at the same + location at the same time as a positive case; however, they may have been + there only briefly, or it may have been a location that carries a lower + risk of transmission. meaning: GENEPIO:0100248 is_a: Indirect contact [GENEPIO:0100246] Workplace associated transmission [GENEPIO:0100497]: text: Workplace associated transmission [GENEPIO:0100497] + description: A type of transmission where an individual acquires an infection + or disease as a result of exposure in their workplace environment. This + can include direct contact with infected individuals, exposure to contaminated + materials or surfaces, or other workplace-specific risk factors. meaning: GENEPIO:0100497 Healthcare associated transmission [GENEPIO:0100498]: text: Healthcare associated transmission [GENEPIO:0100498] + description: A type of transmission where an individual acquires an infection + or disease as a result of exposure within a healthcare setting. This includes + transmission through direct contact with patients, contaminated medical + equipment, or surfaces within healthcare facilities, such as hospitals or + clinics. meaning: GENEPIO:0100498 is_a: Workplace associated transmission [GENEPIO:0100497] Laboratory associated transmission [GENEPIO:0100499]: text: Laboratory associated transmission [GENEPIO:0100499] + description: A type of transmission where an individual acquires an infection + or disease as a result of exposure within a laboratory setting. This includes + contact with infectious agents, contaminated equipment, or laboratory surfaces, + as well as potential aerosol exposure or spills of hazardous substances. meaning: GENEPIO:0100499 is_a: Workplace associated transmission [GENEPIO:0100497] - host role menu: - name: host role menu + HostRoleMenu: + name: HostRoleMenu + title: host role menu permissible_values: Attendee: text: Attendee + description: A role inhering in a person that is realized when the bearer + is present on a given occasion or at a given place. meaning: GENEPIO:0100249 Student: text: Student + description: A human social role that, if realized, is realized by the process + of formal education that the bearer undergoes. meaning: OMRSE:00000058 is_a: Attendee Patient: text: Patient + description: A patient role that inheres in a human being. meaning: OMRSE:00000030 Inpatient: text: Inpatient + description: A patient who is residing in the hospital where he is being treated. meaning: NCIT:C25182 is_a: Patient Outpatient: text: Outpatient + description: A patient who comes to a healthcare facility for diagnosis or + treatment but is not admitted for an overnight stay. meaning: NCIT:C28293 is_a: Patient Passenger: text: Passenger + description: A role inhering in a person that is realized when the bearer + travels in a vehicle but bears little to no responsibility for vehicle operation + nor arrival at its destination. meaning: GENEPIO:0100250 Resident: text: Resident + description: A role inhering in a person that is realized when the bearer + maintains residency in a given place. meaning: GENEPIO:0100251 Visitor: text: Visitor + description: A role inhering in a person that is realized when the bearer + pays a visit to a specific place or event. meaning: GENEPIO:0100252 Volunteer: text: Volunteer + description: A role inhering in a person that is realized when the bearer + enters into any service of their own free will. meaning: GENEPIO:0100253 Work: text: Work + description: A role inhering in a person that is realized when the bearer + performs labor for a living. meaning: GENEPIO:0100254 Administrator: text: Administrator + description: A role inhering in a person that is realized when the bearer + is engaged in administration or administrative work. meaning: GENEPIO:0100255 is_a: Work First Responder: text: First Responder + description: A role inhering in a person that is realized when the bearer + is among the first to arrive at the scene of an emergency and has specialized + training to provide assistance. meaning: GENEPIO:0100256 is_a: Work Housekeeper: text: Housekeeper + description: A role inhering in a person that is realized when the bearer + is an individual who performs cleaning duties and/or is responsible for + the supervision of cleaning staff. meaning: GENEPIO:0100260 is_a: Work Kitchen Worker: text: Kitchen Worker + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a kitchen. meaning: GENEPIO:0100261 is_a: Work Healthcare Worker: text: Healthcare Worker + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a healthcare setting. meaning: GENEPIO:0100334 is_a: Work Community Healthcare Worker: text: Community Healthcare Worker + description: A role inhering in a person that is realized when the bearer + a professional caregiver that provides health care or supportive care in + the individual home where the patient or client is living, as opposed to + care provided in group accommodations like clinics or nursing home. meaning: GENEPIO:0100420 is_a: Healthcare Worker Laboratory Worker: text: Laboratory Worker + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a laboratory. meaning: GENEPIO:0100262 is_a: Healthcare Worker Nurse: text: Nurse + description: A health care role borne by a human being and realized by the + care of individuals, families, and communities so they may attain, maintain, + or recover optimal health and quality of life. meaning: OMRSE:00000014 is_a: Healthcare Worker Personal Care Aid: text: Personal Care Aid + description: A role inhering in a person that is realized when the bearer + works to help another person complete their daily activities. meaning: GENEPIO:0100263 is_a: Healthcare Worker Pharmacist: text: Pharmacist + description: A role inhering in a person that is realized when the bearer + is a health professional who specializes in dispensing prescription drugs + at a healthcare facility. meaning: GENEPIO:0100264 is_a: Healthcare Worker Physician: text: Physician + description: A health care role borne by a human being and realized by promoting, + maintaining or restoring human health through the study, diagnosis, and + treatment of disease, injury and other physical and mental impairments. meaning: OMRSE:00000013 is_a: Healthcare Worker Rotational Worker: text: Rotational Worker + description: A role inhering in a person that is realized when the bearer + performs labor on a regular schedule, often requiring travel to geographic + locations other than where they live. meaning: GENEPIO:0100354 is_a: Work Seasonal Worker: text: Seasonal Worker + description: A role inhering in a person that is realized when the bearer + performs labor for a particular period of the year, such as harvest, or + Christmas. meaning: GENEPIO:0100355 is_a: Work Sex Worker: text: Sex Worker + description: A person who supplies sex work (some form of sexual services) + in exchange for compensation. This term is promoted along with the idea + that what has previously been termed prostitution should be recognized as + work on equal terms with that of conventional jobs, with the legal implications + this has. It is sometimes regarded as a less offensive alternative to prostitute, + although "sex worker" has a much broader meaning. meaning: GSSO:005831 is_a: Work Veterinarian: text: Veterinarian + description: A role inhering in a person that is realized when the bearer + is a professional who practices veterinary medicine. meaning: GENEPIO:0100265 is_a: Work Social role: text: Social role + description: A social role inhering in a human being. meaning: OMRSE:00000001 Acquaintance of case: text: Acquaintance of case + description: A role inhering in a person that is realized when the bearer + is in a state of being acquainted with a person. meaning: GENEPIO:0100266 is_a: Social role Relative of case: text: Relative of case + description: A role inhering in a person that is realized when the bearer + is a relative of the case. meaning: GENEPIO:0100267 is_a: Social role Child of case: text: Child of case + description: A role inhering in a person that is realized when the bearer + is a person younger than the age of majority. meaning: GENEPIO:0100268 is_a: Relative of case Parent of case: text: Parent of case + description: A role inhering in a person that is realized when the bearer + is a caregiver of the offspring of their own species. meaning: GENEPIO:0100269 is_a: Relative of case Father of case: text: Father of case + description: A role inhering in a person that is realized when the bearer + is the male parent of a child. meaning: GENEPIO:0100270 is_a: Parent of case Mother of case: text: Mother of case + description: A role inhering in a person that is realized when the bearer + is the female parent of a child. meaning: GENEPIO:0100271 is_a: Parent of case Sexual partner of case: text: Sexual partner of case + description: A role inhering in a person that is realized when the bearer + is a sexual partner of the case. meaning: GENEPIO:0100500 is_a: Social role Spouse of case: text: Spouse of case + description: A role inhering in a person that is realized when the bearer + is a significant other in a marriage, civil union, or common-law marriage. meaning: GENEPIO:0100272 is_a: Social role Other Host Role: text: Other Host Role - host role international menu: - name: host role international menu + description: A role undertaken by a host that is not categorized under specific + predefined host roles. + HostRoleInternationalMenu: + name: HostRoleInternationalMenu + title: host role international menu permissible_values: Attendee [GENEPIO:0100249]: text: Attendee [GENEPIO:0100249] + description: A role inhering in a person that is realized when the bearer + is present on a given occasion or at a given place. meaning: GENEPIO:0100249 Student [OMRSE:00000058]: text: Student [OMRSE:00000058] + description: A human social role that, if realized, is realized by the process + of formal education that the bearer undergoes. meaning: OMRSE:00000058 is_a: Attendee [GENEPIO:0100249] Patient [OMRSE:00000030]: text: Patient [OMRSE:00000030] + description: A patient role that inheres in a human being. meaning: OMRSE:00000030 Inpatient [NCIT:C25182]: text: Inpatient [NCIT:C25182] + description: A patient who is residing in the hospital where he is being treated. meaning: NCIT:C25182 is_a: Patient [OMRSE:00000030] Outpatient [NCIT:C28293]: text: Outpatient [NCIT:C28293] + description: A patient who comes to a healthcare facility for diagnosis or + treatment but is not admitted for an overnight stay. meaning: NCIT:C28293 is_a: Patient [OMRSE:00000030] Passenger [GENEPIO:0100250]: text: Passenger [GENEPIO:0100250] + description: A role inhering in a person that is realized when the bearer + travels in a vehicle but bears little to no responsibility for vehicle operation + nor arrival at its destination. meaning: GENEPIO:0100250 Resident [GENEPIO:0100251]: text: Resident [GENEPIO:0100251] + description: A role inhering in a person that is realized when the bearer + maintains residency in a given place. meaning: GENEPIO:0100251 Visitor [GENEPIO:0100252]: text: Visitor [GENEPIO:0100252] + description: A role inhering in a person that is realized when the bearer + pays a visit to a specific place or event. meaning: GENEPIO:0100252 Volunteer [GENEPIO:0100253]: text: Volunteer [GENEPIO:0100253] + description: A role inhering in a person that is realized when the bearer + enters into any service of their own free will. meaning: GENEPIO:0100253 Work [GENEPIO:0100254]: text: Work [GENEPIO:0100254] + description: A role inhering in a person that is realized when the bearer + performs labor for a living. meaning: GENEPIO:0100254 Administrator [GENEPIO:0100255]: text: Administrator [GENEPIO:0100255] + description: A role inhering in a person that is realized when the bearer + is engaged in administration or administrative work. meaning: GENEPIO:0100255 is_a: Work [GENEPIO:0100254] First Responder [GENEPIO:0100256]: text: First Responder [GENEPIO:0100256] + description: A role inhering in a person that is realized when the bearer + is among the first to arrive at the scene of an emergency and has specialized + training to provide assistance. meaning: GENEPIO:0100256 is_a: Work [GENEPIO:0100254] Housekeeper [GENEPIO:0100260]: text: Housekeeper [GENEPIO:0100260] + description: A role inhering in a person that is realized when the bearer + is an individual who performs cleaning duties and/or is responsible for + the supervision of cleaning staff. meaning: GENEPIO:0100260 is_a: Work [GENEPIO:0100254] Kitchen Worker [GENEPIO:0100261]: text: Kitchen Worker [GENEPIO:0100261] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a kitchen. meaning: GENEPIO:0100261 is_a: Work [GENEPIO:0100254] Healthcare Worker [GENEPIO:0100334]: text: Healthcare Worker [GENEPIO:0100334] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a healthcare setting. meaning: GENEPIO:0100334 is_a: Work [GENEPIO:0100254] Community Healthcare Worker [GENEPIO:0100420]: text: Community Healthcare Worker [GENEPIO:0100420] + description: A role inhering in a person that is realized when the bearer + a professional caregiver that provides health care or supportive care in + the individual home where the patient or client is living, as opposed to + care provided in group accommodations like clinics or nursing home. meaning: GENEPIO:0100420 is_a: Healthcare Worker [GENEPIO:0100334] Laboratory Worker [GENEPIO:0100262]: text: Laboratory Worker [GENEPIO:0100262] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a laboratory. meaning: GENEPIO:0100262 is_a: Healthcare Worker [GENEPIO:0100334] Nurse [OMRSE:00000014]: text: Nurse [OMRSE:00000014] + description: A health care role borne by a human being and realized by the + care of individuals, families, and communities so they may attain, maintain, + or recover optimal health and quality of life. meaning: OMRSE:00000014 is_a: Healthcare Worker [GENEPIO:0100334] Personal Care Aid [GENEPIO:0100263]: text: Personal Care Aid [GENEPIO:0100263] + description: A role inhering in a person that is realized when the bearer + works to help another person complete their daily activities. meaning: GENEPIO:0100263 is_a: Healthcare Worker [GENEPIO:0100334] Pharmacist [GENEPIO:0100264]: text: Pharmacist [GENEPIO:0100264] + description: A role inhering in a person that is realized when the bearer + is a health professional who specializes in dispensing prescription drugs + at a healthcare facility. meaning: GENEPIO:0100264 is_a: Healthcare Worker [GENEPIO:0100334] Physician [OMRSE:00000013]: text: Physician [OMRSE:00000013] + description: A health care role borne by a human being and realized by promoting, + maintaining or restoring human health through the study, diagnosis, and + treatment of disease, injury and other physical and mental impairments. meaning: OMRSE:00000013 is_a: Healthcare Worker [GENEPIO:0100334] Rotational Worker [GENEPIO:0100354]: text: Rotational Worker [GENEPIO:0100354] + description: A role inhering in a person that is realized when the bearer + performs labor on a regular schedule, often requiring travel to geographic + locations other than where they live. meaning: GENEPIO:0100354 is_a: Work [GENEPIO:0100254] Seasonal Worker [GENEPIO:0100355]: text: Seasonal Worker [GENEPIO:0100355] + description: A role inhering in a person that is realized when the bearer + performs labor for a particular period of the year, such as harvest, or + Christmas. meaning: GENEPIO:0100355 is_a: Work [GENEPIO:0100254] Sex Worker [GSSO:005831]: text: Sex Worker [GSSO:005831] + description: A person who supplies sex work (some form of sexual services) + in exchange for compensation. This term is promoted along with the idea + that what has previously been termed prostitution should be recognized as + work on equal terms with that of conventional jobs, with the legal implications + this has. It is sometimes regarded as a less offensive alternative to prostitute, + although "sex worker" has a much broader meaning. meaning: GSSO:005831 is_a: Work [GENEPIO:0100254] Veterinarian [GENEPIO:0100265]: text: Veterinarian [GENEPIO:0100265] + description: A role inhering in a person that is realized when the bearer + is a professional who practices veterinary medicine. meaning: GENEPIO:0100265 is_a: Work [GENEPIO:0100254] Social role [OMRSE:00000001]: text: Social role [OMRSE:00000001] + description: A social role inhering in a human being. meaning: OMRSE:00000001 Acquaintance of case [GENEPIO:0100266]: text: Acquaintance of case [GENEPIO:0100266] + description: A role inhering in a person that is realized when the bearer + is in a state of being acquainted with a person. meaning: GENEPIO:0100266 is_a: Social role [OMRSE:00000001] Relative of case [GENEPIO:0100267]: text: Relative of case [GENEPIO:0100267] + description: A role inhering in a person that is realized when the bearer + is a relative of the case. meaning: GENEPIO:0100267 is_a: Social role [OMRSE:00000001] Child of case [GENEPIO:0100268]: text: Child of case [GENEPIO:0100268] + description: A role inhering in a person that is realized when the bearer + is a person younger than the age of majority. meaning: GENEPIO:0100268 is_a: Relative of case [GENEPIO:0100267] Parent of case [GENEPIO:0100269]: text: Parent of case [GENEPIO:0100269] + description: A role inhering in a person that is realized when the bearer + is a caregiver of the offspring of their own species. meaning: GENEPIO:0100269 is_a: Relative of case [GENEPIO:0100267] Father of case [GENEPIO:0100270]: text: Father of case [GENEPIO:0100270] + description: A role inhering in a person that is realized when the bearer + is the male parent of a child. meaning: GENEPIO:0100270 is_a: Parent of case [GENEPIO:0100269] Mother of case [GENEPIO:0100271]: text: Mother of case [GENEPIO:0100271] + description: A role inhering in a person that is realized when the bearer + is the female parent of a child. meaning: GENEPIO:0100271 is_a: Parent of case [GENEPIO:0100269] Sexual partner of case [GENEPIO:0100500]: text: Sexual partner of case [GENEPIO:0100500] + description: A role inhering in a person that is realized when the bearer + is a sexual partner of the case. meaning: GENEPIO:0100500 is_a: Social role [OMRSE:00000001] Spouse of case [GENEPIO:0100272]: text: Spouse of case [GENEPIO:0100272] + description: A role inhering in a person that is realized when the bearer + is a significant other in a marriage, civil union, or common-law marriage. meaning: GENEPIO:0100272 is_a: Social role [OMRSE:00000001] Other Host Role: text: Other Host Role - exposure setting menu: - name: exposure setting menu + description: A role undertaken by a host that is not categorized under specific + predefined host roles. + ExposureSettingMenu: + name: ExposureSettingMenu + title: exposure setting menu permissible_values: Human Exposure: text: Human Exposure + description: A history of exposure to Homo sapiens. meaning: ECTO:3000005 Contact with Known Monkeypox Case: text: Contact with Known Monkeypox Case + description: A process occuring within or in the vicinity of a human with + a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox. meaning: GENEPIO:0100501 is_a: Human Exposure Contact with Patient: text: Contact with Patient + description: A process occuring within or in the vicinity of a human patient + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100185 is_a: Human Exposure Contact with Probable Monkeypox Case: text: Contact with Probable Monkeypox Case + description: A process occuring within or in the vicinity of a human with + a probable case of COVID-19 that exposes the recipient organism to Monkeypox. meaning: GENEPIO:0100502 is_a: Human Exposure Contact with Person who Recently Travelled: text: Contact with Person who Recently Travelled + description: A process occuring within or in the vicinity of a human, who + recently travelled, that exposes the recipient organism to a material entity. meaning: GENEPIO:0100189 is_a: Human Exposure Occupational, Residency or Patronage Exposure: text: Occupational, Residency or Patronage Exposure + description: A process occuring within or in the vicinity of a human residential + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100190 Abbatoir: text: Abbatoir + description: A exposure event involving the interaction of an exposure receptor + to abattoir. meaning: ECTO:1000033 is_a: Occupational, Residency or Patronage Exposure Animal Rescue: text: Animal Rescue + description: A process occuring within or in the vicinity of an animal rescue + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100191 is_a: Occupational, Residency or Patronage Exposure Bar (pub): text: Bar (pub) + description: A process occurring within or in the vicinity of a bar or pub + environment that exposes the recipient organism to a material entity meaning: GENEPIO:0100503 is_a: Occupational, Residency or Patronage Exposure Childcare: text: Childcare + description: A process occuring within or in the vicinity of a human childcare + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100192 is_a: Occupational, Residency or Patronage Exposure Daycare: text: Daycare + description: A process occuring within or in the vicinity of a human daycare + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100193 is_a: Childcare Nursery: text: Nursery + description: A process occuring within or in the vicinity of a human nursery + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100194 is_a: Childcare Community Service Centre: text: Community Service Centre + description: A process occuring within or in the vicinity of a community service + centre that exposes the recipient organism to a material entity. meaning: GENEPIO:0100195 is_a: Occupational, Residency or Patronage Exposure Correctional Facility: text: Correctional Facility + description: A process occuring within or in the vicinity of a correctional + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100196 is_a: Occupational, Residency or Patronage Exposure Dormitory: text: Dormitory + description: A process occuring within or in the vicinity of a dormitory that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100197 is_a: Occupational, Residency or Patronage Exposure Farm: text: Farm + description: A exposure event involving the interaction of an exposure receptor + to farm meaning: ECTO:1000034 is_a: Occupational, Residency or Patronage Exposure First Nations Reserve: text: First Nations Reserve + description: A process occuring within or in the vicinity of a first nations + reserve that exposes the recipient organism to a material entity. meaning: GENEPIO:0100198 is_a: Occupational, Residency or Patronage Exposure Funeral Home: text: Funeral Home + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100199 is_a: Occupational, Residency or Patronage Exposure Group Home: text: Group Home + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100200 is_a: Occupational, Residency or Patronage Exposure Healthcare Setting: text: Healthcare Setting + description: A process occuring within or in the vicinity of a healthcare + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100201 is_a: Occupational, Residency or Patronage Exposure Ambulance: text: Ambulance + description: A process occuring within or in the vicinity of an ambulance + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100202 is_a: Healthcare Setting Acute Care Facility: text: Acute Care Facility + description: A process occuring within or in the vicinity of an acute care + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100203 is_a: Healthcare Setting Clinic: text: Clinic + description: A process occuring within or in the vicinity of a medical clinic + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100204 is_a: Healthcare Setting Community Healthcare (At-Home) Setting: text: Community Healthcare (At-Home) Setting + description: A process occuring within or in the vicinty of a the individual + home where the patient or client is living and health care or supportive + care is being being delivered, as opposed to care provided in group accommodations + like clinics or nursing home. meaning: GENEPIO:0100415 is_a: Healthcare Setting Community Health Centre: text: Community Health Centre + description: A process occuring within or in the vicinity of a community health + centre that exposes the recipient organism to a material entity. meaning: GENEPIO:0100205 is_a: Healthcare Setting Hospital: text: Hospital + description: A exposure event involving the interaction of an exposure receptor + to hospital. meaning: ECTO:1000035 is_a: Healthcare Setting Emergency Department: text: Emergency Department + description: A process occuring within or in the vicinity of an emergency + department that exposes the recipient organism to a material entity. meaning: GENEPIO:0100206 is_a: Hospital ICU: text: ICU + description: A process occuring within or in the vicinity of an ICU that exposes + the recipient organism to a material entity. meaning: GENEPIO:0100207 is_a: Hospital Ward: text: Ward + description: A process occuring within or in the vicinity of a hospital ward + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100208 is_a: Hospital Laboratory: text: Laboratory + description: A exposure event involving the interaction of an exposure receptor + to laboratory facility. meaning: ECTO:1000036 is_a: Healthcare Setting Long-Term Care Facility: text: Long-Term Care Facility + description: A process occuring within or in the vicinity of a long-term care + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100209 is_a: Healthcare Setting Pharmacy: text: Pharmacy + description: A process occuring within or in the vicinity of a pharmacy that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100210 is_a: Healthcare Setting Physician's Office: text: Physician's Office + description: A process occuring within or in the vicinity of a physician's + office that exposes the recipient organism to a material entity. meaning: GENEPIO:0100211 is_a: Healthcare Setting Household: text: Household + description: A process occuring within or in the vicinity of a household that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100212 is_a: Occupational, Residency or Patronage Exposure Insecure Housing (Homeless): text: Insecure Housing (Homeless) + description: A process occuring that exposes the recipient organism to a material + entity as a consequence of said organism having insecure housing. meaning: GENEPIO:0100213 is_a: Occupational, Residency or Patronage Exposure Occupational Exposure: text: Occupational Exposure + description: A process occuring within or in the vicinity of a human occupational + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100214 is_a: Occupational, Residency or Patronage Exposure Worksite: text: Worksite + description: A process occuring within or in the vicinity of an office that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100215 is_a: Occupational Exposure Office: text: Office + description: A exposure event involving the interaction of an exposure receptor + to office. meaning: ECTO:1000037 is_a: Worksite Outdoors: text: Outdoors + description: A process occuring outdoors that exposes the recipient organism + to a material entity. meaning: GENEPIO:0100216 is_a: Occupational, Residency or Patronage Exposure Camp/camping: text: Camp/camping + description: A exposure event involving the interaction of an exposure receptor + to campground. meaning: ECTO:5000009 is_a: Outdoors Hiking Trail: text: Hiking Trail + description: A process that exposes the recipient organism to a material entity + as a consequence of hiking. meaning: GENEPIO:0100217 is_a: Outdoors Hunting Ground: text: Hunting Ground + description: An exposure event involving hunting behavior meaning: ECTO:6000030 is_a: Outdoors Ski Resort: text: Ski Resort + description: A process occuring within or in the vicinity of a ski resort + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100218 is_a: Outdoors Petting zoo: text: Petting zoo + description: A exposure event involving the interaction of an exposure receptor + to petting zoo. meaning: ECTO:5000008 is_a: Occupational, Residency or Patronage Exposure Place of Worship: text: Place of Worship + description: A process occuring within or in the vicinity of a place of worship + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100220 is_a: Occupational, Residency or Patronage Exposure Church: text: Church + description: A process occuring within or in the vicinity of a church that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100221 is_a: Place of Worship Mosque: text: Mosque + description: A process occuring within or in the vicinity of a mosque that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100222 is_a: Place of Worship Temple: text: Temple + description: A process occuring within or in the vicinity of a temple that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100223 is_a: Place of Worship Restaurant: text: Restaurant + description: A exposure event involving the interaction of an exposure receptor + to restaurant. meaning: ECTO:1000040 is_a: Occupational, Residency or Patronage Exposure Retail Store: text: Retail Store + description: A exposure event involving the interaction of an exposure receptor + to shop. meaning: ECTO:1000041 is_a: Occupational, Residency or Patronage Exposure School: text: School + description: A process occuring within or in the vicinity of a school that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100224 is_a: Occupational, Residency or Patronage Exposure Temporary Residence: text: Temporary Residence + description: A process occuring within or in the vicinity of a temporary residence + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100225 is_a: Occupational, Residency or Patronage Exposure Homeless Shelter: text: Homeless Shelter + description: A process occuring within or in the vicinity of a homeless shelter + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100226 is_a: Temporary Residence Hotel: text: Hotel + description: A process occuring within or in the vicinity of a hotel exposure + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100227 is_a: Temporary Residence Veterinary Care Clinic: text: Veterinary Care Clinic + description: A process occuring within or in the vicinity of a veterinary + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100228 is_a: Occupational, Residency or Patronage Exposure Travel Exposure: text: Travel Exposure + description: A process occuring as a result of travel that exposes the recipient + organism to a material entity. meaning: GENEPIO:0100229 Travelled on a Cruise Ship: text: Travelled on a Cruise Ship + description: A process occuring within or in the vicinity of a cruise ship + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100230 is_a: Travel Exposure Travelled on a Plane: text: Travelled on a Plane + description: A process occuring within or in the vicinity of an airplane that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100231 is_a: Travel Exposure Travelled on Ground Transport: text: Travelled on Ground Transport + description: A process occuring within or in the vicinity of ground transport + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100232 is_a: Travel Exposure Other Exposure Setting: text: Other Exposure Setting + description: A process occuring that exposes the recipient organism to a material + entity. meaning: GENEPIO:0100235 - exposure setting international menu: - name: exposure setting international menu + ExposureSettingInternationalMenu: + name: ExposureSettingInternationalMenu + title: exposure setting international menu permissible_values: Human Exposure [ECTO:3000005]: text: Human Exposure [ECTO:3000005] + description: A history of exposure to Homo sapiens. meaning: ECTO:3000005 Contact with Known Monkeypox Case [GENEPIO:0100501]: text: Contact with Known Monkeypox Case [GENEPIO:0100501] + description: A process occuring within or in the vicinity of a human with + a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox. meaning: GENEPIO:0100501 is_a: Human Exposure [ECTO:3000005] Contact with Patient [GENEPIO:0100185]: text: Contact with Patient [GENEPIO:0100185] + description: A process occuring within or in the vicinity of a human patient + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100185 is_a: Human Exposure [ECTO:3000005] Contact with Probable Monkeypox Case [GENEPIO:0100502]: text: Contact with Probable Monkeypox Case [GENEPIO:0100502] + description: A process occuring within or in the vicinity of a human with + a probable case of COVID-19 that exposes the recipient organism to Monkeypox. meaning: GENEPIO:0100502 is_a: Human Exposure [ECTO:3000005] Contact with Person who Recently Travelled [GENEPIO:0100189]: text: Contact with Person who Recently Travelled [GENEPIO:0100189] + description: A process occuring within or in the vicinity of a human, who + recently travelled, that exposes the recipient organism to a material entity. meaning: GENEPIO:0100189 is_a: Human Exposure [ECTO:3000005] Occupational, Residency or Patronage Exposure [GENEPIO:0100190]: text: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + description: A process occuring within or in the vicinity of a human residential + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100190 Abbatoir [ECTO:1000033]: text: Abbatoir [ECTO:1000033] + description: A exposure event involving the interaction of an exposure receptor + to abattoir. meaning: ECTO:1000033 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Animal Rescue [GENEPIO:0100191]: text: Animal Rescue [GENEPIO:0100191] + description: A process occuring within or in the vicinity of an animal rescue + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100191 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Bar (pub) [GENEPIO:0100503]: text: Bar (pub) [GENEPIO:0100503] + description: A process occurring within or in the vicinity of a bar or pub + environment that exposes the recipient organism to a material entity meaning: GENEPIO:0100503 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Childcare [GENEPIO:0100192]: text: Childcare [GENEPIO:0100192] + description: A process occuring within or in the vicinity of a human childcare + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100192 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Daycare [GENEPIO:0100193]: text: Daycare [GENEPIO:0100193] + description: A process occuring within or in the vicinity of a human daycare + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100193 is_a: Childcare [GENEPIO:0100192] Nursery [GENEPIO:0100194]: text: Nursery [GENEPIO:0100194] + description: A process occuring within or in the vicinity of a human nursery + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100194 is_a: Childcare [GENEPIO:0100192] Community Service Centre [GENEPIO:0100195]: text: Community Service Centre [GENEPIO:0100195] + description: A process occuring within or in the vicinity of a community service + centre that exposes the recipient organism to a material entity. meaning: GENEPIO:0100195 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Correctional Facility [GENEPIO:0100196]: text: Correctional Facility [GENEPIO:0100196] + description: A process occuring within or in the vicinity of a correctional + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100196 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Dormitory [GENEPIO:0100197]: text: Dormitory [GENEPIO:0100197] + description: A process occuring within or in the vicinity of a dormitory that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100197 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Farm [ECTO:1000034]: text: Farm [ECTO:1000034] + description: A exposure event involving the interaction of an exposure receptor + to farm meaning: ECTO:1000034 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] First Nations Reserve [GENEPIO:0100198]: text: First Nations Reserve [GENEPIO:0100198] + description: A process occuring within or in the vicinity of a first nations + reserve that exposes the recipient organism to a material entity. meaning: GENEPIO:0100198 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Funeral Home [GENEPIO:0100199]: text: Funeral Home [GENEPIO:0100199] + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100199 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Group Home [GENEPIO:0100200]: text: Group Home [GENEPIO:0100200] + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100200 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Healthcare Setting [GENEPIO:0100201]: text: Healthcare Setting [GENEPIO:0100201] + description: A process occuring within or in the vicinity of a healthcare + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100201 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Ambulance [GENEPIO:0100202]: text: Ambulance [GENEPIO:0100202] + description: A process occuring within or in the vicinity of an ambulance + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100202 is_a: Healthcare Setting [GENEPIO:0100201] Acute Care Facility [GENEPIO:0100203]: text: Acute Care Facility [GENEPIO:0100203] + description: A process occuring within or in the vicinity of an acute care + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100203 is_a: Healthcare Setting [GENEPIO:0100201] Clinic [GENEPIO:0100204]: text: Clinic [GENEPIO:0100204] + description: A process occuring within or in the vicinity of a medical clinic + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100204 is_a: Healthcare Setting [GENEPIO:0100201] Community Healthcare (At-Home) Setting [GENEPIO:0100415]: text: Community Healthcare (At-Home) Setting [GENEPIO:0100415] + description: A process occuring within or in the vicinty of a the individual + home where the patient or client is living and health care or supportive + care is being being delivered, as opposed to care provided in group accommodations + like clinics or nursing home. meaning: GENEPIO:0100415 is_a: Healthcare Setting [GENEPIO:0100201] Community Health Centre [GENEPIO:0100205]: text: Community Health Centre [GENEPIO:0100205] + description: A process occuring within or in the vicinity of a community health + centre that exposes the recipient organism to a material entity. meaning: GENEPIO:0100205 is_a: Healthcare Setting [GENEPIO:0100201] Hospital [ECTO:1000035]: text: Hospital [ECTO:1000035] + description: A exposure event involving the interaction of an exposure receptor + to hospital. meaning: ECTO:1000035 is_a: Healthcare Setting [GENEPIO:0100201] Emergency Department [GENEPIO:0100206]: text: Emergency Department [GENEPIO:0100206] + description: A process occuring within or in the vicinity of an emergency + department that exposes the recipient organism to a material entity. meaning: GENEPIO:0100206 is_a: Hospital [ECTO:1000035] ICU [GENEPIO:0100207]: text: ICU [GENEPIO:0100207] + description: A process occuring within or in the vicinity of an ICU that exposes + the recipient organism to a material entity. meaning: GENEPIO:0100207 is_a: Hospital [ECTO:1000035] Ward [GENEPIO:0100208]: text: Ward [GENEPIO:0100208] + description: A process occuring within or in the vicinity of a hospital ward + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100208 is_a: Hospital [ECTO:1000035] Laboratory [ECTO:1000036]: text: Laboratory [ECTO:1000036] + description: A exposure event involving the interaction of an exposure receptor + to laboratory facility. meaning: ECTO:1000036 is_a: Healthcare Setting [GENEPIO:0100201] Long-Term Care Facility [GENEPIO:0100209]: text: Long-Term Care Facility [GENEPIO:0100209] + description: A process occuring within or in the vicinity of a long-term care + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100209 is_a: Healthcare Setting [GENEPIO:0100201] Pharmacy [GENEPIO:0100210]: text: Pharmacy [GENEPIO:0100210] + description: A process occuring within or in the vicinity of a pharmacy that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100210 is_a: Healthcare Setting [GENEPIO:0100201] Physician's Office [GENEPIO:0100211]: text: Physician's Office [GENEPIO:0100211] + description: A process occuring within or in the vicinity of a physician's + office that exposes the recipient organism to a material entity. meaning: GENEPIO:0100211 is_a: Healthcare Setting [GENEPIO:0100201] Household [GENEPIO:0100212]: text: Household [GENEPIO:0100212] + description: A process occuring within or in the vicinity of a household that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100212 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Insecure Housing (Homeless) [GENEPIO:0100213]: text: Insecure Housing (Homeless) [GENEPIO:0100213] + description: A process occuring that exposes the recipient organism to a material + entity as a consequence of said organism having insecure housing. meaning: GENEPIO:0100213 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Occupational Exposure [GENEPIO:0100214]: text: Occupational Exposure [GENEPIO:0100214] + description: A process occuring within or in the vicinity of a human occupational + environment that exposes the recipient organism to a material entity. meaning: GENEPIO:0100214 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Worksite [GENEPIO:0100215]: text: Worksite [GENEPIO:0100215] + description: A process occuring within or in the vicinity of an office that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100215 is_a: Occupational Exposure [GENEPIO:0100214] Office [ECTO:1000037]: text: Office [ECTO:1000037] + description: A exposure event involving the interaction of an exposure receptor + to office. meaning: ECTO:1000037 is_a: Worksite [GENEPIO:0100215] Outdoors [GENEPIO:0100216]: text: Outdoors [GENEPIO:0100216] + description: A process occuring outdoors that exposes the recipient organism + to a material entity. meaning: GENEPIO:0100216 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Camp/camping [ECTO:5000009]: text: Camp/camping [ECTO:5000009] + description: A exposure event involving the interaction of an exposure receptor + to campground. meaning: ECTO:5000009 is_a: Outdoors [GENEPIO:0100216] Hiking Trail [GENEPIO:0100217]: text: Hiking Trail [GENEPIO:0100217] + description: A process that exposes the recipient organism to a material entity + as a consequence of hiking. meaning: GENEPIO:0100217 is_a: Outdoors [GENEPIO:0100216] Hunting Ground [ECTO:6000030]: text: Hunting Ground [ECTO:6000030] + description: An exposure event involving hunting behavior meaning: ECTO:6000030 is_a: Outdoors [GENEPIO:0100216] Ski Resort [GENEPIO:0100218]: text: Ski Resort [GENEPIO:0100218] + description: A process occuring within or in the vicinity of a ski resort + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100218 is_a: Outdoors [GENEPIO:0100216] Petting zoo [ECTO:5000008]: text: Petting zoo [ECTO:5000008] + description: A exposure event involving the interaction of an exposure receptor + to petting zoo. meaning: ECTO:5000008 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Place of Worship [GENEPIO:0100220]: text: Place of Worship [GENEPIO:0100220] + description: A process occuring within or in the vicinity of a place of worship + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100220 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Church [GENEPIO:0100221]: text: Church [GENEPIO:0100221] + description: A process occuring within or in the vicinity of a church that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100221 is_a: Place of Worship [GENEPIO:0100220] Mosque [GENEPIO:0100222]: text: Mosque [GENEPIO:0100222] + description: A process occuring within or in the vicinity of a mosque that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100222 is_a: Place of Worship [GENEPIO:0100220] Temple [GENEPIO:0100223]: text: Temple [GENEPIO:0100223] + description: A process occuring within or in the vicinity of a temple that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100223 is_a: Place of Worship [GENEPIO:0100220] Restaurant [ECTO:1000040]: text: Restaurant [ECTO:1000040] + description: A exposure event involving the interaction of an exposure receptor + to restaurant. meaning: ECTO:1000040 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Retail Store [ECTO:1000041]: text: Retail Store [ECTO:1000041] + description: A exposure event involving the interaction of an exposure receptor + to shop. meaning: ECTO:1000041 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] School [GENEPIO:0100224]: text: School [GENEPIO:0100224] + description: A process occuring within or in the vicinity of a school that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100224 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Temporary Residence [GENEPIO:0100225]: text: Temporary Residence [GENEPIO:0100225] + description: A process occuring within or in the vicinity of a temporary residence + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100225 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Homeless Shelter [GENEPIO:0100226]: text: Homeless Shelter [GENEPIO:0100226] + description: A process occuring within or in the vicinity of a homeless shelter + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100226 is_a: Temporary Residence [GENEPIO:0100225] Hotel [GENEPIO:0100227]: text: Hotel [GENEPIO:0100227] + description: A process occuring within or in the vicinity of a hotel exposure + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100227 is_a: Temporary Residence [GENEPIO:0100225] Veterinary Care Clinic [GENEPIO:0100228]: text: Veterinary Care Clinic [GENEPIO:0100228] + description: A process occuring within or in the vicinity of a veterinary + facility that exposes the recipient organism to a material entity. meaning: GENEPIO:0100228 is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] Travel Exposure [GENEPIO:0100229]: text: Travel Exposure [GENEPIO:0100229] + description: A process occuring as a result of travel that exposes the recipient + organism to a material entity. meaning: GENEPIO:0100229 Travelled on a Cruise Ship [GENEPIO:0100230]: text: Travelled on a Cruise Ship [GENEPIO:0100230] + description: A process occuring within or in the vicinity of a cruise ship + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100230 is_a: Travel Exposure [GENEPIO:0100229] Travelled on a Plane [GENEPIO:0100231]: text: Travelled on a Plane [GENEPIO:0100231] + description: A process occuring within or in the vicinity of an airplane that + exposes the recipient organism to a material entity. meaning: GENEPIO:0100231 is_a: Travel Exposure [GENEPIO:0100229] Travelled on Ground Transport [GENEPIO:0100232]: text: Travelled on Ground Transport [GENEPIO:0100232] + description: A process occuring within or in the vicinity of ground transport + that exposes the recipient organism to a material entity. meaning: GENEPIO:0100232 is_a: Travel Exposure [GENEPIO:0100229] Other Exposure Setting [GENEPIO:0100235]: text: Other Exposure Setting [GENEPIO:0100235] + description: A process occuring that exposes the recipient organism to a material + entity. meaning: GENEPIO:0100235 - prior Mpox infection menu: - name: prior Mpox infection menu + PriorMpoxInfectionMenu: + name: PriorMpoxInfectionMenu + title: prior Mpox infection menu permissible_values: Prior infection: text: Prior infection + description: Antiviral treatment administered prior to the current regimen + or test. meaning: GENEPIO:0100037 No prior infection: text: No prior infection + description: An absence of antiviral treatment administered prior to the current + regimen or test. meaning: GENEPIO:0100233 - prior Mpox infection international menu: - name: prior Mpox infection international menu + PriorMpoxInfectionInternationalMenu: + name: PriorMpoxInfectionInternationalMenu + title: prior Mpox infection international menu permissible_values: Prior infection [GENEPIO:0100037]: text: Prior infection [GENEPIO:0100037] + description: Antiviral treatment administered prior to the current regimen + or test. meaning: GENEPIO:0100037 No prior infection [GENEPIO:0100233]: text: No prior infection [GENEPIO:0100233] + description: An absence of antiviral treatment administered prior to the current + regimen or test. meaning: GENEPIO:0100233 - prior Mpox antiviral treatment menu: - name: prior Mpox antiviral treatment menu + PriorMpoxAntiviralTreatmentMenu: + name: PriorMpoxAntiviralTreatmentMenu + title: prior Mpox antiviral treatment menu permissible_values: Prior antiviral treatment: text: Prior antiviral treatment + description: Antiviral treatment administered prior to the current regimen + or test. meaning: GENEPIO:0100037 No prior antiviral treatment: text: No prior antiviral treatment + description: An absence of antiviral treatment administered prior to the current + regimen or test. meaning: GENEPIO:0100233 - prior Mpox antiviral treatment international menu: - name: prior Mpox antiviral treatment international menu + PriorMpoxAntiviralTreatmentInternationalMenu: + name: PriorMpoxAntiviralTreatmentInternationalMenu + title: prior Mpox antiviral treatment international menu permissible_values: Prior antiviral treatment [GENEPIO:0100037]: text: Prior antiviral treatment [GENEPIO:0100037] + description: Antiviral treatment administered prior to the current regimen + or test. meaning: GENEPIO:0100037 No prior antiviral treatment [GENEPIO:0100233]: text: No prior antiviral treatment [GENEPIO:0100233] + description: An absence of antiviral treatment administered prior to the current + regimen or test. meaning: GENEPIO:0100233 - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu + title: organism menu permissible_values: Mpox virus: text: Mpox virus + description: A zoonotic virus belonging to the Orthopoxvirus genus and closely + related to the variola, cowpox, and vaccinia viruses. MPV is oval, with + a lipoprotein outer membrane. meaning: NCBITaxon:10244 - organism international menu: - name: organism international menu + OrganismInternationalMenu: + name: OrganismInternationalMenu + title: organism international menu permissible_values: Mpox virus [NCBITaxon:10244]: text: Mpox virus [NCBITaxon:10244] + description: A zoonotic virus belonging to the Orthopoxvirus genus and closely + related to the variola, cowpox, and vaccinia viruses. MPV is oval, with + a lipoprotein outer membrane. meaning: NCBITaxon:10244 - host disease menu: - name: host disease menu + HostDiseaseMenu: + name: HostDiseaseMenu + title: host disease menu permissible_values: Mpox: text: Mpox + description: An infection that is caused by an Orthopoxvirus, which is transmitted + by primates or rodents, and which is characterized by a prodromal syndrome + of fever, chills, headache, myalgia, and lymphedema; initial symptoms are + followed by a generalized papular rash that typically progresses from vesiculation + through crusting over the course of two weeks. meaning: MONDO:0002594 - host disease international menu: - name: host disease international menu + HostDiseaseInternationalMenu: + name: HostDiseaseInternationalMenu + title: host disease international menu permissible_values: Mpox [MONDO:0002594]: text: Mpox [MONDO:0002594] + description: An infection that is caused by an Orthopoxvirus, which is transmitted + by primates or rodents, and which is characterized by a prodromal syndrome + of fever, chills, headache, myalgia, and lymphedema; initial symptoms are + followed by a generalized papular rash that typically progresses from vesiculation + through crusting over the course of two weeks. meaning: MONDO:0002594 - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation: text: Cluster/Outbreak investigation + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. meaning: GENEPIO:0100001 Diagnostic testing: text: Diagnostic testing + description: A sampling strategy in which individuals are sampled in the context + of diagnostic testing. meaning: GENEPIO:0100002 Research: text: Research + description: A sampling strategy in which individuals are sampled in order + to perform research. meaning: GENEPIO:0100003 Surveillance: text: Surveillance + description: A sampling strategy in which individuals are sampled for surveillance + investigations. meaning: GENEPIO:0100004 - purpose of sampling international menu: - name: purpose of sampling international menu + PurposeOfSamplingInternationalMenu: + name: PurposeOfSamplingInternationalMenu + title: purpose of sampling international menu permissible_values: Cluster/Outbreak investigation [GENEPIO:0100001]: text: Cluster/Outbreak investigation [GENEPIO:0100001] + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. meaning: GENEPIO:0100001 Diagnostic testing [GENEPIO:0100002]: text: Diagnostic testing [GENEPIO:0100002] + description: A sampling strategy in which individuals are sampled in the context + of diagnostic testing. meaning: GENEPIO:0100002 Research [GENEPIO:0100003]: text: Research [GENEPIO:0100003] + description: A sampling strategy in which individuals are sampled in order + to perform research. meaning: GENEPIO:0100003 Surveillance [GENEPIO:0100004]: text: Surveillance [GENEPIO:0100004] + description: A sampling strategy in which individuals are sampled for surveillance + investigations. meaning: GENEPIO:0100004 - purpose of sequencing menu: - name: purpose of sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose of sequencing menu permissible_values: Baseline surveillance (random sampling): text: Baseline surveillance (random sampling) + description: A surveillance sampling strategy in which baseline is established + at the beginning of a study or project by the selection of sample units + via random sampling. meaning: GENEPIO:0100005 Targeted surveillance (non-random sampling): text: Targeted surveillance (non-random sampling) + description: A surveillance sampling strategy in which an aspired outcome + is explicity stated. meaning: GENEPIO:0100006 Priority surveillance project: text: Priority surveillance project + description: A targeted surveillance strategy which is considered important + and/or urgent. meaning: GENEPIO:0100007 is_a: Targeted surveillance (non-random sampling) Longitudinal surveillance (repeat sampling of individuals): text: Longitudinal surveillance (repeat sampling of individuals) + description: A priority surveillance strategy in which subsets of a defined + population can be identified who are, have been, or in the future may be + exposed or not exposed - or exposed in different degrees - to a disease + of interest and are selected to under go repeat sampling over a defined + period of time. meaning: GENEPIO:0100009 is_a: Priority surveillance project Re-infection surveillance: text: Re-infection surveillance + description: A priority surveillance strategy in which a population that previously + tested positive for a disease of interest, and since confirmed to have recovered + via a negative test, are monitored for positive test indication of re-infection + with the disease of interest within a defined period of time. meaning: GENEPIO:0100010 is_a: Priority surveillance project Vaccine escape surveillance: text: Vaccine escape surveillance + description: A priority surveillance strategy in which individuals are monitored + for investigation into vaccine escape, i.e., identifying variants that contain + mutations that counteracted the immunity provided by vaccine(s) of interest. meaning: GENEPIO:0100011 is_a: Priority surveillance project Travel-associated surveillance: text: Travel-associated surveillance + description: A priority surveillance strategy in which individuals are selected + if they have a travel history outside of the reporting region within a specified + number of days before onset of symptoms. meaning: GENEPIO:0100012 is_a: Priority surveillance project Domestic travel surveillance: text: Domestic travel surveillance + description: A travel-associated surveillance strategy in which individuals + are selected if they have an intranational travel history within a specified + number of days before onset of symptoms. meaning: GENEPIO:0100013 is_a: Travel-associated surveillance Interstate/ interprovincial travel surveillance: text: Interstate/ interprovincial travel surveillance + description: A domestic travel-associated surveillance strategy in which individuals + are selected if their travel occurred within a state/province within a nation. meaning: GENEPIO:0100275 is_a: Domestic travel surveillance Intra-state/ intra-provincial travel surveillance: text: Intra-state/ intra-provincial travel surveillance + description: A domestic travel-associated surveillance strategy in which individuals + are selected if their travel occurred between states/provinces within a + nation. meaning: GENEPIO:0100276 is_a: Domestic travel surveillance International travel surveillance: text: International travel surveillance + description: A travel-associated surveillance strategy in which individuals + are selected if they have a travel history outside of the reporting country + in a specified number of days before onset of symptoms. meaning: GENEPIO:0100014 is_a: Travel-associated surveillance Cluster/Outbreak investigation: text: Cluster/Outbreak investigation + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. meaning: GENEPIO:0100019 Multi-jurisdictional outbreak investigation: text: Multi-jurisdictional outbreak investigation + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that has connections + to two or more jurisdictions. meaning: GENEPIO:0100020 is_a: Cluster/Outbreak investigation Intra-jurisdictional outbreak investigation: text: Intra-jurisdictional outbreak investigation + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that only has connections + within a single jurisdiction. meaning: GENEPIO:0100021 is_a: Cluster/Outbreak investigation Research: text: Research + description: A sampling strategy in which individuals are sampled in order + to perform research. meaning: GENEPIO:0100022 Viral passage experiment: text: Viral passage experiment + description: A research sampling strategy in which individuals are sampled + in order to perform a viral passage experiment. meaning: GENEPIO:0100023 is_a: Research Protocol testing experiment: text: Protocol testing experiment + description: A research sampling strategy in which individuals are sampled + in order to perform a protocol testing experiment. meaning: GENEPIO:0100024 is_a: Research Retrospective sequencing: text: Retrospective sequencing + description: A sampling strategy in which stored samples from past events + are sequenced. meaning: GENEPIO:0100356 - purpose of sequencing international menu: - name: purpose of sequencing international menu + PurposeOfSequencingInternationalMenu: + name: PurposeOfSequencingInternationalMenu + title: purpose of sequencing international menu permissible_values: Baseline surveillance (random sampling) [GENEPIO:0100005]: text: Baseline surveillance (random sampling) [GENEPIO:0100005] + description: A surveillance sampling strategy in which baseline is established + at the beginning of a study or project by the selection of sample units + via random sampling. meaning: GENEPIO:0100005 Targeted surveillance (non-random sampling) [GENEPIO:0100006]: text: Targeted surveillance (non-random sampling) [GENEPIO:0100006] + description: A surveillance sampling strategy in which an aspired outcome + is explicity stated. meaning: GENEPIO:0100006 Priority surveillance project [GENEPIO:0100007]: text: Priority surveillance project [GENEPIO:0100007] + description: A targeted surveillance strategy which is considered important + and/or urgent. meaning: GENEPIO:0100007 is_a: Targeted surveillance (non-random sampling) [GENEPIO:0100006] Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]: text: Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] + description: A priority surveillance strategy in which subsets of a defined + population can be identified who are, have been, or in the future may be + exposed or not exposed - or exposed in different degrees - to a disease + of interest and are selected to under go repeat sampling over a defined + period of time. meaning: GENEPIO:0100009 is_a: Priority surveillance project [GENEPIO:0100007] Re-infection surveillance [GENEPIO:0100010]: text: Re-infection surveillance [GENEPIO:0100010] + description: A priority surveillance strategy in which a population that previously + tested positive for a disease of interest, and since confirmed to have recovered + via a negative test, are monitored for positive test indication of re-infection + with the disease of interest within a defined period of time. meaning: GENEPIO:0100010 is_a: Priority surveillance project [GENEPIO:0100007] Vaccine escape surveillance [GENEPIO:0100011]: text: Vaccine escape surveillance [GENEPIO:0100011] + description: A priority surveillance strategy in which individuals are monitored + for investigation into vaccine escape, i.e., identifying variants that contain + mutations that counteracted the immunity provided by vaccine(s) of interest. meaning: GENEPIO:0100011 is_a: Priority surveillance project [GENEPIO:0100007] Travel-associated surveillance [GENEPIO:0100012]: text: Travel-associated surveillance [GENEPIO:0100012] + description: A priority surveillance strategy in which individuals are selected + if they have a travel history outside of the reporting region within a specified + number of days before onset of symptoms. meaning: GENEPIO:0100012 is_a: Priority surveillance project [GENEPIO:0100007] Domestic travel surveillance [GENEPIO:0100013]: text: Domestic travel surveillance [GENEPIO:0100013] + description: A travel-associated surveillance strategy in which individuals + are selected if they have an intranational travel history within a specified + number of days before onset of symptoms. meaning: GENEPIO:0100013 is_a: Travel-associated surveillance [GENEPIO:0100012] Interstate/ interprovincial travel surveillance [GENEPIO:0100275]: text: Interstate/ interprovincial travel surveillance [GENEPIO:0100275] + description: A domestic travel-associated surveillance strategy in which individuals + are selected if their travel occurred within a state/province within a nation. meaning: GENEPIO:0100275 is_a: Domestic travel surveillance [GENEPIO:0100013] Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276]: text: Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276] + description: A domestic travel-associated surveillance strategy in which individuals + are selected if their travel occurred between states/provinces within a + nation. meaning: GENEPIO:0100276 is_a: Domestic travel surveillance [GENEPIO:0100013] International travel surveillance [GENEPIO:0100014]: text: International travel surveillance [GENEPIO:0100014] + description: A travel-associated surveillance strategy in which individuals + are selected if they have a travel history outside of the reporting country + in a specified number of days before onset of symptoms. meaning: GENEPIO:0100014 is_a: Travel-associated surveillance [GENEPIO:0100012] Cluster/Outbreak investigation [GENEPIO:0100019]: text: Cluster/Outbreak investigation [GENEPIO:0100019] + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. meaning: GENEPIO:0100019 Multi-jurisdictional outbreak investigation [GENEPIO:0100020]: text: Multi-jurisdictional outbreak investigation [GENEPIO:0100020] + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that has connections + to two or more jurisdictions. meaning: GENEPIO:0100020 is_a: Cluster/Outbreak investigation [GENEPIO:0100019] Intra-jurisdictional outbreak investigation [GENEPIO:0100021]: text: Intra-jurisdictional outbreak investigation [GENEPIO:0100021] + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that only has connections + within a single jurisdiction. meaning: GENEPIO:0100021 is_a: Cluster/Outbreak investigation [GENEPIO:0100019] Research [GENEPIO:0100022]: text: Research [GENEPIO:0100022] + description: A sampling strategy in which individuals are sampled in order + to perform research. meaning: GENEPIO:0100022 Viral passage experiment [GENEPIO:0100023]: text: Viral passage experiment [GENEPIO:0100023] + description: A research sampling strategy in which individuals are sampled + in order to perform a viral passage experiment. meaning: GENEPIO:0100023 is_a: Research [GENEPIO:0100022] Protocol testing experiment [GENEPIO:0100024]: text: Protocol testing experiment [GENEPIO:0100024] + description: A research sampling strategy in which individuals are sampled + in order to perform a protocol testing experiment. meaning: GENEPIO:0100024 is_a: Research [GENEPIO:0100022] Retrospective sequencing [GENEPIO:0100356]: text: Retrospective sequencing [GENEPIO:0100356] + description: A sampling strategy in which stored samples from past events + are sequenced. meaning: GENEPIO:0100356 - sequencing instrument menu: - name: sequencing instrument menu + SequencingAssayTypeMenu: + name: SequencingAssayTypeMenu + title: sequencing assay type menu + permissible_values: + Amplicon sequencing assay: + text: Amplicon sequencing assay + description: A sequencing assay in which a DNA or RNA input molecule is amplified + by PCR and the product sequenced. + meaning: OBI:0002767 + 16S ribosomal gene sequencing assay: + text: 16S ribosomal gene sequencing assay + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. + meaning: OBI:0002763 + is_a: Amplicon sequencing assay + Whole genome sequencing assay: + text: Whole genome sequencing assay + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. + meaning: OBI:0002117 + Whole metagenome sequencing assay: + text: Whole metagenome sequencing assay + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. + meaning: OBI:0002623 + Whole virome sequencing assay: + text: Whole virome sequencing assay + description: A whole metagenome sequencing assay that intends to provide information + on multiple genome sequences from different viruses present in the same + input sample. + meaning: OBI:0002768 + is_a: Whole metagenome sequencing assay + SequencingAssayTypeInternationalMenu: + name: SequencingAssayTypeInternationalMenu + title: sequencing assay type international menu + permissible_values: + Amplicon sequencing assay [OBI:0002767]: + text: Amplicon sequencing assay [OBI:0002767] + description: A sequencing assay in which a DNA or RNA input molecule is amplified + by PCR and the product sequenced. + meaning: OBI:0002767 + 16S ribosomal gene sequencing assay [OBI:0002763]: + text: 16S ribosomal gene sequencing assay [OBI:0002763] + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. + meaning: OBI:0002763 + is_a: Amplicon sequencing assay [OBI:0002767] + Whole genome sequencing assay [OBI:0002117]: + text: Whole genome sequencing assay [OBI:0002117] + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. + meaning: OBI:0002117 + Whole metagenome sequencing assay [OBI:0002623]: + text: Whole metagenome sequencing assay [OBI:0002623] + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. + meaning: OBI:0002623 + Whole virome sequencing assay [OBI:0002768]: + text: Whole virome sequencing assay [OBI:0002768] + description: A whole metagenome sequencing assay that intends to provide information + on multiple genome sequences from different viruses present in the same + input sample. + meaning: OBI:0002768 + is_a: Whole metagenome sequencing assay [OBI:0002623] + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: Illumina: text: Illumina + description: A DNA sequencer manufactured by the Illumina corporation. meaning: GENEPIO:0100105 Illumina Genome Analyzer: text: Illumina Genome Analyzer - meaning: GENEPIO:0100106 + description: A DNA sequencer manufactured by Solexa as one of its first sequencer + lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data + in a single run. + meaning: OBI:0002128 is_a: Illumina Illumina Genome Analyzer II: text: Illumina Genome Analyzer II - meaning: GENEPIO:0100107 + description: A DNA sequencer which is manufactured by Illumina (Solexa) corporation. + it support sequencing of single or paired end clone libraries relying on + sequencing by synthesis technology + meaning: OBI:0000703 is_a: Illumina Genome Analyzer Illumina Genome Analyzer IIx: text: Illumina Genome Analyzer IIx - meaning: GENEPIO:0100108 + description: An Illumina Genome Analyzer II which is manufactured by the Illumina + corporation. It supports sequencing of single, long or short insert paired + end clone libraries relying on sequencing by synthesis technology. The Genome + Analyzer IIx is the most widely adopted next-generation sequencing platform + and proven and published across the broadest range of research applications. + meaning: OBI:0002000 is_a: Illumina Genome Analyzer Illumina HiScanSQ: text: Illumina HiScanSQ + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing + and microarray-based analyses as well as an "SQ Module" to support microfluidics. meaning: GENEPIO:0100109 is_a: Illumina Illumina HiSeq: text: Illumina HiSeq + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, enabling deep sequencing and high yield. meaning: GENEPIO:0100110 is_a: Illumina Illumina HiSeq X: text: Illumina HiSeq X + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that oenabled sufficent depth and coverage + to produce the first 30x human genome for $1000. meaning: GENEPIO:0100111 is_a: Illumina HiSeq Illumina HiSeq X Five: text: Illumina HiSeq X Five + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing + Systems. meaning: GENEPIO:0100112 is_a: Illumina HiSeq X Illumina HiSeq X Ten: text: Illumina HiSeq X Ten - meaning: GENEPIO:0100113 + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. + meaning: OBI:0002129 is_a: Illumina HiSeq X Illumina HiSeq 1000: text: Illumina HiSeq 1000 - meaning: GENEPIO:0100114 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0002022 is_a: Illumina HiSeq Illumina HiSeq 1500: text: Illumina HiSeq 1500 - meaning: GENEPIO:0100115 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell. Built upon sequencing by synthesis technology, + the machine employs dual surface imaging and offers two high-output options + and one rapid-run option. + meaning: OBI:0003386 is_a: Illumina HiSeq Illumina HiSeq 2000: text: Illumina HiSeq 2000 - meaning: GENEPIO:0100116 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. + meaning: OBI:0002001 is_a: Illumina HiSeq Illumina HiSeq 2500: text: Illumina HiSeq 2500 - meaning: GENEPIO:0100117 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. + meaning: OBI:0002002 is_a: Illumina HiSeq Illumina HiSeq 3000: text: Illumina HiSeq 3000 - meaning: GENEPIO:0100118 + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. + meaning: OBI:0002048 is_a: Illumina HiSeq Illumina HiSeq 4000: text: Illumina HiSeq 4000 - meaning: GENEPIO:0100119 + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. + meaning: OBI:0002049 is_a: Illumina HiSeq Illumina iSeq: text: Illumina iSeq + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight. meaning: GENEPIO:0100120 is_a: Illumina Illumina iSeq 100: text: Illumina iSeq 100 + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight and has an output capacity + between 144MB-1.2GB. meaning: GENEPIO:0100121 is_a: Illumina iSeq Illumina NovaSeq: text: Illumina NovaSeq + description: A DNA sequencer manufactured by the Illunina corporation using + sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and + 20 billion reads in dual flow cell mode. meaning: GENEPIO:0100122 is_a: Illumina Illumina NovaSeq 6000: text: Illumina NovaSeq 6000 - meaning: GENEPIO:0100123 + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). + The sequencer utilizes synthesis technology and patterned flow cells to + optimize throughput and even spacing of sequencing clusters. + meaning: OBI:0002630 is_a: Illumina NovaSeq Illumina MiniSeq: text: Illumina MiniSeq - meaning: GENEPIO:0100124 + description: A small benchtop DNA sequencer which is manufactured by the Illumina + corporation with integrated cluster generation, sequencing and data analysis. + The sequencer accommodates various flow cell configurations and can produce + up to 25M single reads or 50M paired-end reads per run. + meaning: OBI:0003114 is_a: Illumina Illumina MiSeq: text: Illumina MiSeq - meaning: GENEPIO:0100125 + description: A DNA sequencer which is manufactured by the Illumina corporation. + Built upon sequencing by synthesis technology, the machine provides an end-to-end + solution (cluster generation, amplification, sequencing, and data analysis) + in a single machine. + meaning: OBI:0002003 is_a: Illumina Illumina NextSeq: text: Illumina NextSeq + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. meaning: GENEPIO:0100126 is_a: Illumina Illumina NextSeq 500: text: Illumina NextSeq 500 - meaning: GENEPIO:0100127 + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. + meaning: OBI:0002021 is_a: Illumina NextSeq Illumina NextSeq 550: text: Illumina NextSeq 550 + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. The 550 is an upgrade on the 500 model. meaning: GENEPIO:0100128 is_a: Illumina NextSeq + Illumina NextSeq 1000: + text: Illumina NextSeq 1000 + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 + and P2 flow cells. + meaning: OBI:0003606 + is_a: Illumina NextSeq Illumina NextSeq 2000: text: Illumina NextSeq 2000 + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 30-360 Gb. meaning: GENEPIO:0100129 is_a: Illumina NextSeq Pacific Biosciences: text: Pacific Biosciences + description: A DNA sequencer manufactured by the Pacific Biosciences corporation. meaning: GENEPIO:0100130 PacBio RS: text: PacBio RS + description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ + \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ + \ The RS was the first model made by the company." meaning: GENEPIO:0100131 is_a: Pacific Biosciences PacBio RS II: text: PacBio RS II - meaning: GENEPIO:0100132 + description: A DNA sequencer which is manufactured by the Pacific Biosciences + corporation. Built upon single molecule real-time sequencing technology, + the machine is optimized for generation with long reads and high consensus + accuracy. + meaning: OBI:0002012 is_a: Pacific Biosciences PacBio Sequel: text: PacBio Sequel - meaning: GENEPIO:0100133 + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation with long reads and high consensus + accuracy, and manufactured by the Pacific Biosciences corporation + meaning: OBI:0002632 is_a: Pacific Biosciences PacBio Sequel II: text: PacBio Sequel II - meaning: GENEPIO:0100134 + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation of highly accurate ("HiFi") long reads, + and which is manufactured by the Pacific Biosciences corporation. + meaning: OBI:0002633 is_a: Pacific Biosciences Ion Torrent: text: Ion Torrent + description: A DNA sequencer manufactured by the Ion Torrent corporation. meaning: GENEPIO:0100135 Ion Torrent PGM: text: Ion Torrent PGM + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of 300 + MB - 1GB. meaning: GENEPIO:0100136 is_a: Ion Torrent Ion Torrent Proton: text: Ion Torrent Proton + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of up to + 15 Gb. meaning: GENEPIO:0100137 is_a: Ion Torrent Ion Torrent S5 XL: text: Ion Torrent S5 XL + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material while producing data faster than the S5 model. meaning: GENEPIO:0100138 is_a: Ion Torrent Ion Torrent S5: text: Ion Torrent S5 + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material. meaning: GENEPIO:0100139 is_a: Ion Torrent Oxford Nanopore: text: Oxford Nanopore + description: A DNA sequencer manufactured by the Oxford Nanopore corporation. meaning: GENEPIO:0100140 + Oxford Nanopore Flongle: + text: Oxford Nanopore Flongle + description: An adapter for MinION or GridION DNA sequencers manufactured + by the Oxford Nanopore corporation that enables sequencing on smaller, single-use + flow cells. + meaning: GENEPIO:0004433 + is_a: Oxford Nanopore Oxford Nanopore GridION: text: Oxford Nanopore GridION + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, that can run and analyze up to five individual flow cells producing + up to 150 Gb of data per run. The sequencer produces real-time results and + utilizes nanopore technology with the option of running the flow cells concurrently + or individual meaning: GENEPIO:0100141 is_a: Oxford Nanopore Oxford Nanopore MinION: text: Oxford Nanopore MinION - meaning: GENEPIO:0100142 + description: A portable DNA sequencer which is manufactured by the Oxford + Nanopore Technologies corporation, that uses consumable flow cells producing + up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time + results and utilizes nanopore technology with up to 512 nanopore channels + in the sensor array. + meaning: OBI:0002750 is_a: Oxford Nanopore Oxford Nanopore PromethION: text: Oxford Nanopore PromethION - meaning: GENEPIO:0100143 + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, capable of running up to 48 flow cells and producing up to + 7.6 Tb of data per run. The sequencer produces real-time results and utilizes + Nanopore technology, with each flow cell allowing up to 3,000 nanopores + to be sequencing simultaneously. + meaning: OBI:0002752 is_a: Oxford Nanopore BGI Genomics: text: BGI Genomics + description: A DNA sequencer manufactured by the BGI Genomics corporation. meaning: GENEPIO:0100144 BGI Genomics BGISEQ-500: text: BGI Genomics BGISEQ-500 + description: A DNA sequencer manufactured by the BGI Genomics corporation + that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". meaning: GENEPIO:0100145 is_a: BGI Genomics MGI: text: MGI + description: A DNA sequencer manufactured by the MGI corporation. meaning: GENEPIO:0100146 MGI DNBSEQ-T7: text: MGI DNBSEQ-T7 + description: A high throughput DNA sequencer manufactured by the MGI corporation + with an output capacity of 1~6TB of data per day. meaning: GENEPIO:0100147 is_a: MGI MGI DNBSEQ-G400: text: MGI DNBSEQ-G400 + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB~1440GB per run. meaning: GENEPIO:0100148 is_a: MGI MGI DNBSEQ-G400 FAST: text: MGI DNBSEQ-G400 FAST + description: A DNA sequencer manufactured by the MGI corporation with an outout + capacity of 55GB~330GB per run, which enables faster sequencing than the + DNBSEQ-G400. meaning: GENEPIO:0100149 is_a: MGI MGI DNBSEQ-G50: text: MGI DNBSEQ-G50 + description: "A DNA sequencer manufactured by the MGI corporation with an\ + \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." meaning: GENEPIO:0100150 is_a: MGI - sequencing instrument international menu: - name: sequencing instrument international menu + SequencingInstrumentInternationalMenu: + name: SequencingInstrumentInternationalMenu + title: sequencing instrument international menu permissible_values: Illumina [GENEPIO:0100105]: text: Illumina [GENEPIO:0100105] + description: A DNA sequencer manufactured by the Illumina corporation. meaning: GENEPIO:0100105 - Illumina Genome Analyzer [GENEPIO:0100106]: - text: Illumina Genome Analyzer [GENEPIO:0100106] - meaning: GENEPIO:0100106 + Illumina Genome Analyzer [OBI:0002128]: + text: Illumina Genome Analyzer [OBI:0002128] + description: A DNA sequencer manufactured by Solexa as one of its first sequencer + lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data + in a single run. + meaning: OBI:0002128 is_a: Illumina [GENEPIO:0100105] - Illumina Genome Analyzer II [GENEPIO:0100107]: - text: Illumina Genome Analyzer II [GENEPIO:0100107] - meaning: GENEPIO:0100107 - is_a: Illumina Genome Analyzer [GENEPIO:0100106] - Illumina Genome Analyzer IIx [GENEPIO:0100108]: - text: Illumina Genome Analyzer IIx [GENEPIO:0100108] - meaning: GENEPIO:0100108 - is_a: Illumina Genome Analyzer [GENEPIO:0100106] + Illumina Genome Analyzer II [OBI:0000703]: + text: Illumina Genome Analyzer II [OBI:0000703] + description: A DNA sequencer which is manufactured by Illumina (Solexa) corporation. + it support sequencing of single or paired end clone libraries relying on + sequencing by synthesis technology + meaning: OBI:0000703 + is_a: Illumina Genome Analyzer [OBI:0002128] + Illumina Genome Analyzer IIx [OBI:0002000]: + text: Illumina Genome Analyzer IIx [OBI:0002000] + description: An Illumina Genome Analyzer II which is manufactured by the Illumina + corporation. It supports sequencing of single, long or short insert paired + end clone libraries relying on sequencing by synthesis technology. The Genome + Analyzer IIx is the most widely adopted next-generation sequencing platform + and proven and published across the broadest range of research applications. + meaning: OBI:0002000 + is_a: Illumina Genome Analyzer [OBI:0002128] Illumina HiScanSQ [GENEPIO:0100109]: text: Illumina HiScanSQ [GENEPIO:0100109] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing + and microarray-based analyses as well as an "SQ Module" to support microfluidics. meaning: GENEPIO:0100109 is_a: Illumina [GENEPIO:0100105] Illumina HiSeq [GENEPIO:0100110]: text: Illumina HiSeq [GENEPIO:0100110] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, enabling deep sequencing and high yield. meaning: GENEPIO:0100110 is_a: Illumina [GENEPIO:0100105] Illumina HiSeq X [GENEPIO:0100111]: text: Illumina HiSeq X [GENEPIO:0100111] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that oenabled sufficent depth and coverage + to produce the first 30x human genome for $1000. meaning: GENEPIO:0100111 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq X Five [GENEPIO:0100112]: text: Illumina HiSeq X Five [GENEPIO:0100112] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing + Systems. meaning: GENEPIO:0100112 is_a: Illumina HiSeq X [GENEPIO:0100111] - Illumina HiSeq X Ten [GENEPIO:0100113]: - text: Illumina HiSeq X Ten [GENEPIO:0100113] - meaning: GENEPIO:0100113 + Illumina HiSeq X Ten [OBI:0002129]: + text: Illumina HiSeq X Ten [OBI:0002129] + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. + meaning: OBI:0002129 is_a: Illumina HiSeq X [GENEPIO:0100111] - Illumina HiSeq 1000 [GENEPIO:0100114]: - text: Illumina HiSeq 1000 [GENEPIO:0100114] - meaning: GENEPIO:0100114 + Illumina HiSeq 1000 [OBI:0002022]: + text: Illumina HiSeq 1000 [OBI:0002022] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0002022 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 1500 [GENEPIO:0100115]: - text: Illumina HiSeq 1500 [GENEPIO:0100115] - meaning: GENEPIO:0100115 + Illumina HiSeq 1500 [OBI:0003386]: + text: Illumina HiSeq 1500 [OBI:0003386] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell. Built upon sequencing by synthesis technology, + the machine employs dual surface imaging and offers two high-output options + and one rapid-run option. + meaning: OBI:0003386 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 2000 [GENEPIO:0100116]: - text: Illumina HiSeq 2000 [GENEPIO:0100116] - meaning: GENEPIO:0100116 + Illumina HiSeq 2000 [OBI:0002001]: + text: Illumina HiSeq 2000 [OBI:0002001] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. + meaning: OBI:0002001 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 2500 [GENEPIO:0100117]: - text: Illumina HiSeq 2500 [GENEPIO:0100117] - meaning: GENEPIO:0100117 + Illumina HiSeq 2500 [OBI:0002002]: + text: Illumina HiSeq 2500 [OBI:0002002] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. + meaning: OBI:0002002 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 3000 [GENEPIO:0100118]: - text: Illumina HiSeq 3000 [GENEPIO:0100118] - meaning: GENEPIO:0100118 + Illumina HiSeq 3000 [OBI:0002048]: + text: Illumina HiSeq 3000 [OBI:0002048] + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. + meaning: OBI:0002048 is_a: Illumina HiSeq [GENEPIO:0100110] - Illumina HiSeq 4000 [GENEPIO:0100119]: - text: Illumina HiSeq 4000 [GENEPIO:0100119] - meaning: GENEPIO:0100119 + Illumina HiSeq 4000 [OBI:0002049]: + text: Illumina HiSeq 4000 [OBI:0002049] + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. + meaning: OBI:0002049 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina iSeq [GENEPIO:0100120]: text: Illumina iSeq [GENEPIO:0100120] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight. meaning: GENEPIO:0100120 is_a: Illumina [GENEPIO:0100105] Illumina iSeq 100 [GENEPIO:0100121]: text: Illumina iSeq 100 [GENEPIO:0100121] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight and has an output capacity + between 144MB-1.2GB. meaning: GENEPIO:0100121 is_a: Illumina iSeq [GENEPIO:0100120] Illumina NovaSeq [GENEPIO:0100122]: text: Illumina NovaSeq [GENEPIO:0100122] + description: A DNA sequencer manufactured by the Illunina corporation using + sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and + 20 billion reads in dual flow cell mode. meaning: GENEPIO:0100122 is_a: Illumina [GENEPIO:0100105] - Illumina NovaSeq 6000 [GENEPIO:0100123]: - text: Illumina NovaSeq 6000 [GENEPIO:0100123] - meaning: GENEPIO:0100123 + Illumina NovaSeq 6000 [OBI:0002630]: + text: Illumina NovaSeq 6000 [OBI:0002630] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). + The sequencer utilizes synthesis technology and patterned flow cells to + optimize throughput and even spacing of sequencing clusters. + meaning: OBI:0002630 is_a: Illumina NovaSeq [GENEPIO:0100122] - Illumina MiniSeq [GENEPIO:0100124]: - text: Illumina MiniSeq [GENEPIO:0100124] - meaning: GENEPIO:0100124 + Illumina MiniSeq [OBI:0003114]: + text: Illumina MiniSeq [OBI:0003114] + description: A small benchtop DNA sequencer which is manufactured by the Illumina + corporation with integrated cluster generation, sequencing and data analysis. + The sequencer accommodates various flow cell configurations and can produce + up to 25M single reads or 50M paired-end reads per run. + meaning: OBI:0003114 is_a: Illumina [GENEPIO:0100105] - Illumina MiSeq [GENEPIO:0100125]: - text: Illumina MiSeq [GENEPIO:0100125] - meaning: GENEPIO:0100125 + Illumina MiSeq [OBI:0002003]: + text: Illumina MiSeq [OBI:0002003] + description: A DNA sequencer which is manufactured by the Illumina corporation. + Built upon sequencing by synthesis technology, the machine provides an end-to-end + solution (cluster generation, amplification, sequencing, and data analysis) + in a single machine. + meaning: OBI:0002003 is_a: Illumina [GENEPIO:0100105] Illumina NextSeq [GENEPIO:0100126]: text: Illumina NextSeq [GENEPIO:0100126] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. meaning: GENEPIO:0100126 is_a: Illumina [GENEPIO:0100105] - Illumina NextSeq 500 [GENEPIO:0100127]: - text: Illumina NextSeq 500 [GENEPIO:0100127] - meaning: GENEPIO:0100127 + Illumina NextSeq 500 [OBI:0002021]: + text: Illumina NextSeq 500 [OBI:0002021] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. + meaning: OBI:0002021 is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 550 [GENEPIO:0100128]: text: Illumina NextSeq 550 [GENEPIO:0100128] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. The 550 is an upgrade on the 500 model. meaning: GENEPIO:0100128 is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 1000 [OBI:0003606]: + text: Illumina NextSeq 1000 [OBI:0003606] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 + and P2 flow cells. + meaning: OBI:0003606 + is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 2000 [GENEPIO:0100129]: text: Illumina NextSeq 2000 [GENEPIO:0100129] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 30-360 Gb. meaning: GENEPIO:0100129 is_a: Illumina NextSeq [GENEPIO:0100126] Pacific Biosciences [GENEPIO:0100130]: text: Pacific Biosciences [GENEPIO:0100130] + description: A DNA sequencer manufactured by the Pacific Biosciences corporation. meaning: GENEPIO:0100130 PacBio RS [GENEPIO:0100131]: text: PacBio RS [GENEPIO:0100131] + description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ + \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ + \ The RS was the first model made by the company." meaning: GENEPIO:0100131 is_a: Pacific Biosciences [GENEPIO:0100130] - PacBio RS II [GENEPIO:0100132]: - text: PacBio RS II [GENEPIO:0100132] - meaning: GENEPIO:0100132 + PacBio RS II [OBI:0002012]: + text: PacBio RS II [OBI:0002012] + description: A DNA sequencer which is manufactured by the Pacific Biosciences + corporation. Built upon single molecule real-time sequencing technology, + the machine is optimized for generation with long reads and high consensus + accuracy. + meaning: OBI:0002012 is_a: Pacific Biosciences [GENEPIO:0100130] - PacBio Sequel [GENEPIO:0100133]: - text: PacBio Sequel [GENEPIO:0100133] - meaning: GENEPIO:0100133 + PacBio Sequel [OBI:0002632]: + text: PacBio Sequel [OBI:0002632] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation with long reads and high consensus + accuracy, and manufactured by the Pacific Biosciences corporation + meaning: OBI:0002632 is_a: Pacific Biosciences [GENEPIO:0100130] - PacBio Sequel II [GENEPIO:0100134]: - text: PacBio Sequel II [GENEPIO:0100134] - meaning: GENEPIO:0100134 + PacBio Sequel II [OBI:0002633]: + text: PacBio Sequel II [OBI:0002633] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation of highly accurate ("HiFi") long reads, + and which is manufactured by the Pacific Biosciences corporation. + meaning: OBI:0002633 is_a: Pacific Biosciences [GENEPIO:0100130] Ion Torrent [GENEPIO:0100135: text: Ion Torrent [GENEPIO:0100135 + description: A DNA sequencer manufactured by the Ion Torrent corporation. meaning: GENEPIO:0100135 - Ion Torrent PGM [GENEPIO:0100136: - text: Ion Torrent PGM [GENEPIO:0100136 + Ion Torrent PGM [GENEPIO:0100136]: + text: Ion Torrent PGM [GENEPIO:0100136] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of 300 + MB - 1GB. meaning: GENEPIO:0100136 is_a: Ion Torrent [GENEPIO:0100135 Ion Torrent Proton [GENEPIO:0100137]: text: Ion Torrent Proton [GENEPIO:0100137] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of up to + 15 Gb. meaning: GENEPIO:0100137 is_a: Ion Torrent [GENEPIO:0100135 Ion Torrent S5 XL [GENEPIO:0100138]: text: Ion Torrent S5 XL [GENEPIO:0100138] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material while producing data faster than the S5 model. meaning: GENEPIO:0100138 is_a: Ion Torrent [GENEPIO:0100135 Ion Torrent S5 [GENEPIO:0100139]: text: Ion Torrent S5 [GENEPIO:0100139] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material. meaning: GENEPIO:0100139 is_a: Ion Torrent [GENEPIO:0100135 Oxford Nanopore [GENEPIO:0100140]: text: Oxford Nanopore [GENEPIO:0100140] + description: A DNA sequencer manufactured by the Oxford Nanopore corporation. meaning: GENEPIO:0100140 - Oxford Nanopore GridION [GENEPIO:0100141: - text: Oxford Nanopore GridION [GENEPIO:0100141 + Oxford Nanopore Flongle [GENEPIO:0004433]: + text: Oxford Nanopore Flongle [GENEPIO:0004433] + description: An adapter for MinION or GridION DNA sequencers manufactured + by the Oxford Nanopore corporation that enables sequencing on smaller, single-use + flow cells. + meaning: GENEPIO:0004433 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore GridION [GENEPIO:0100141]: + text: Oxford Nanopore GridION [GENEPIO:0100141] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, that can run and analyze up to five individual flow cells producing + up to 150 Gb of data per run. The sequencer produces real-time results and + utilizes nanopore technology with the option of running the flow cells concurrently + or individual meaning: GENEPIO:0100141 is_a: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore MinION [GENEPIO:0100142]: - text: Oxford Nanopore MinION [GENEPIO:0100142] - meaning: GENEPIO:0100142 + Oxford Nanopore MinION [OBI:0002750]: + text: Oxford Nanopore MinION [OBI:0002750] + description: A portable DNA sequencer which is manufactured by the Oxford + Nanopore Technologies corporation, that uses consumable flow cells producing + up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time + results and utilizes nanopore technology with up to 512 nanopore channels + in the sensor array. + meaning: OBI:0002750 is_a: Oxford Nanopore [GENEPIO:0100140] - Oxford Nanopore PromethION [GENEPIO:0100143]: - text: Oxford Nanopore PromethION [GENEPIO:0100143] - meaning: GENEPIO:0100143 + Oxford Nanopore PromethION [OBI:0002752]: + text: Oxford Nanopore PromethION [OBI:0002752] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, capable of running up to 48 flow cells and producing up to + 7.6 Tb of data per run. The sequencer produces real-time results and utilizes + Nanopore technology, with each flow cell allowing up to 3,000 nanopores + to be sequencing simultaneously. + meaning: OBI:0002752 is_a: Oxford Nanopore [GENEPIO:0100140] BGI Genomics [GENEPIO:0100144]: text: BGI Genomics [GENEPIO:0100144] + description: A DNA sequencer manufactured by the BGI Genomics corporation. meaning: GENEPIO:0100144 BGI Genomics BGISEQ-500 [GENEPIO:0100145]: text: BGI Genomics BGISEQ-500 [GENEPIO:0100145] + description: A DNA sequencer manufactured by the BGI Genomics corporation + that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". meaning: GENEPIO:0100145 is_a: BGI Genomics [GENEPIO:0100144] MGI [GENEPIO:0100146]: text: MGI [GENEPIO:0100146] + description: A DNA sequencer manufactured by the MGI corporation. meaning: GENEPIO:0100146 MGI DNBSEQ-T7 [GENEPIO:0100147]: text: MGI DNBSEQ-T7 [GENEPIO:0100147] + description: A high throughput DNA sequencer manufactured by the MGI corporation + with an output capacity of 1~6TB of data per day. meaning: GENEPIO:0100147 is_a: MGI [GENEPIO:0100146] MGI DNBSEQ-G400 [GENEPIO:0100148]: text: MGI DNBSEQ-G400 [GENEPIO:0100148] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB~1440GB per run. meaning: GENEPIO:0100148 is_a: MGI [GENEPIO:0100146] MGI DNBSEQ-G400 FAST [GENEPIO:0100149]: text: MGI DNBSEQ-G400 FAST [GENEPIO:0100149] + description: A DNA sequencer manufactured by the MGI corporation with an outout + capacity of 55GB~330GB per run, which enables faster sequencing than the + DNBSEQ-G400. meaning: GENEPIO:0100149 is_a: MGI [GENEPIO:0100146] MGI DNBSEQ-G50 [GENEPIO:0100150]: text: MGI DNBSEQ-G50 [GENEPIO:0100150] + description: "A DNA sequencer manufactured by the MGI corporation with an\ + \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." meaning: GENEPIO:0100150 is_a: MGI [GENEPIO:0100146] - sequence submitted by menu: - name: sequence submitted by menu + GenomicTargetEnrichmentMethodMenu: + name: GenomicTargetEnrichmentMethodMenu + title: genomic target enrichment method menu + permissible_values: + Hybridization capture: + text: Hybridization capture + description: Selection by hybridization in array or solution. + meaning: GENEPIO:0001950 + rRNA depletion method: + text: rRNA depletion method + description: Removal of background RNA for the purposes of enriching the genomic + target. + meaning: GENEPIO:0101020 + GenomicTargetEnrichmentMethodInternationalMenu: + name: GenomicTargetEnrichmentMethodInternationalMenu + title: genomic target enrichment method international menu + permissible_values: + Hybridization capture [GENEPIO:0001950]: + text: Hybridization capture [GENEPIO:0001950] + description: Selection by hybridization in array or solution. + meaning: GENEPIO:0001950 + rRNA depletion method [GENEPIO:0101020]: + text: rRNA depletion method [GENEPIO:0101020] + description: Removal of background RNA for the purposes of enriching the genomic + target. + meaning: GENEPIO:0101020 + QualityControlDeterminationMenu: + name: QualityControlDeterminationMenu + title: quality control determination menu + permissible_values: + No quality control issues identified: + text: No quality control issues identified + description: A data item which is a statement confirming that quality control + processes were carried out and no quality issues were detected. + meaning: GENEPIO:0100562 + Sequence passed quality control: + text: Sequence passed quality control + description: A data item which is a statement confirming that quality control + processes were carried out and that the sequence met the assessment criteria. + meaning: GENEPIO:0100563 + Sequence failed quality control: + text: Sequence failed quality control + description: A data item which is a statement confirming that quality control + processes were carried out and that the sequence did not meet the assessment + criteria. + meaning: GENEPIO:0100564 + Minor quality control issues identified: + text: Minor quality control issues identified + description: A data item which is a statement confirming that quality control + processes were carried out and that the sequence did not meet the assessment + criteria, however the issues detected were minor. + meaning: GENEPIO:0100565 + Sequence flagged for potential quality control issues: + text: Sequence flagged for potential quality control issues + description: A data item which is a statement confirming that quality control + processes were carried out however it is unclear whether the sequence meets + the assessment criteria and the assessment requires review. + meaning: GENEPIO:0100566 + Quality control not performed: + text: Quality control not performed + description: A data item which is a statement confirming that quality control + processes have not been carried out. + meaning: GENEPIO:0100567 + QualityControlDeterminationInternationalMenu: + name: QualityControlDeterminationInternationalMenu + title: quality control determination international menu + permissible_values: + No quality control issues identified [GENEPIO:0100562]: + text: No quality control issues identified [GENEPIO:0100562] + description: A data item which is a statement confirming that quality control + processes were carried out and no quality issues were detected. + meaning: GENEPIO:0100562 + Sequence passed quality control [GENEPIO:0100563]: + text: Sequence passed quality control [GENEPIO:0100563] + description: A data item which is a statement confirming that quality control + processes were carried out and that the sequence met the assessment criteria. + meaning: GENEPIO:0100563 + Sequence failed quality control [GENEPIO:0100564]: + text: Sequence failed quality control [GENEPIO:0100564] + description: A data item which is a statement confirming that quality control + processes were carried out and that the sequence did not meet the assessment + criteria. + meaning: GENEPIO:0100564 + Minor quality control issues identified [GENEPIO:0100565]: + text: Minor quality control issues identified [GENEPIO:0100565] + description: A data item which is a statement confirming that quality control + processes were carried out and that the sequence did not meet the assessment + criteria, however the issues detected were minor. + meaning: GENEPIO:0100565 + Sequence flagged for potential quality control issues [GENEPIO:0100566]: + text: Sequence flagged for potential quality control issues [GENEPIO:0100566] + description: A data item which is a statement confirming that quality control + processes were carried out however it is unclear whether the sequence meets + the assessment criteria and the assessment requires review. + meaning: GENEPIO:0100566 + Quality control not performed [GENEPIO:0100567]: + text: Quality control not performed [GENEPIO:0100567] + description: A data item which is a statement confirming that quality control + processes have not been carried out. + meaning: GENEPIO:0100567 + QualityControlIssuesMenu: + name: QualityControlIssuesMenu + title: quality control issues menu + permissible_values: + Low quality sequence: + text: Low quality sequence + description: A data item that describes sequence data that does not meet quality + control thresholds. + meaning: GENEPIO:0100568 + Sequence contaminated: + text: Sequence contaminated + description: A data item that describes sequence data that contains reads + from unintended targets (e.g. other organisms, other samples) due to contamination + so that it does not faithfully represent the genetic information from the + biological source. + meaning: GENEPIO:0100569 + Low average genome coverage: + text: Low average genome coverage + description: A data item that describes sequence data in which the entire + length of the genome is not sufficiently sequenced (low breadth of coverage), + or particular positions of the genome are not sequenced a prescribed number + of times (low depth of coverage). + meaning: GENEPIO:0100570 + Low percent genome captured: + text: Low percent genome captured + description: A data item that describes sequence data in which the entire + length of the genome is not sufficiently sequenced (low breadth of coverage). + meaning: GENEPIO:0100571 + Read lengths shorter than expected: + text: Read lengths shorter than expected + description: A data item that describes average sequence read lengths that + are below the expected size range given a particular sequencing instrument, + reagents and conditions. + meaning: GENEPIO:0100572 + Sequence amplification artifacts: + text: Sequence amplification artifacts + description: A data item that describes sequence data containing errors generated + during the polymerase chain reaction (PCR) amplification process during + library generation (e.g. mutations, altered read distribution, amplicon + dropouts). + meaning: GENEPIO:0100573 + Low signal to noise ratio: + text: Low signal to noise ratio + description: A data item that describes sequence data containing more errors + or undetermined bases (noise) than sequence representing the biological + source (signal). + meaning: GENEPIO:0100574 + Low coverage of characteristic mutations: + text: Low coverage of characteristic mutations + description: A data item that describes sequence data that contains a lower + than expected number of mutations that are usually observed in the reference + sequence. + meaning: GENEPIO:0100575 + QualityControlIssuesInternationalMenu: + name: QualityControlIssuesInternationalMenu + title: quality control issues international menu + permissible_values: + Low quality sequence [GENEPIO:0100568]: + text: Low quality sequence [GENEPIO:0100568] + description: A data item that describes sequence data that does not meet quality + control thresholds. + meaning: GENEPIO:0100568 + Sequence contaminated [GENEPIO:0100569]: + text: Sequence contaminated [GENEPIO:0100569] + description: A data item that describes sequence data that contains reads + from unintended targets (e.g. other organisms, other samples) due to contamination + so that it does not faithfully represent the genetic information from the + biological source. + meaning: GENEPIO:0100569 + Low average genome coverage [GENEPIO:0100570]: + text: Low average genome coverage [GENEPIO:0100570] + description: A data item that describes sequence data in which the entire + length of the genome is not sufficiently sequenced (low breadth of coverage), + or particular positions of the genome are not sequenced a prescribed number + of times (low depth of coverage). + meaning: GENEPIO:0100570 + Low percent genome captured [GENEPIO:0100571]: + text: Low percent genome captured [GENEPIO:0100571] + description: A data item that describes sequence data in which the entire + length of the genome is not sufficiently sequenced (low breadth of coverage). + meaning: GENEPIO:0100571 + Read lengths shorter than expected [GENEPIO:0100572]: + text: Read lengths shorter than expected [GENEPIO:0100572] + description: A data item that describes average sequence read lengths that + are below the expected size range given a particular sequencing instrument, + reagents and conditions. + meaning: GENEPIO:0100572 + Sequence amplification artifacts [GENEPIO:0100573]: + text: Sequence amplification artifacts [GENEPIO:0100573] + description: A data item that describes sequence data containing errors generated + during the polymerase chain reaction (PCR) amplification process during + library generation (e.g. mutations, altered read distribution, amplicon + dropouts). + meaning: GENEPIO:0100573 + Low signal to noise ratio [GENEPIO:0100574]: + text: Low signal to noise ratio [GENEPIO:0100574] + description: A data item that describes sequence data containing more errors + or undetermined bases (noise) than sequence representing the biological + source (signal). + meaning: GENEPIO:0100574 + Low coverage of characteristic mutations [GENEPIO:0100575]: + text: Low coverage of characteristic mutations [GENEPIO:0100575] + description: A data item that describes sequence data that contains a lower + than expected number of mutations that are usually observed in the reference + sequence. + meaning: GENEPIO:0100575 + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu + title: sequence submitted by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -6349,6 +9682,8 @@ enums: text: Manitoba Cadham Provincial Laboratory McGill University: text: McGill University + description: McGill University is an English-language public research university + located in Montreal, Quebec, Canada. McMaster University: text: McMaster University National Microbiology Laboratory (NML): @@ -6373,8 +9708,9 @@ enums: text: Sunnybrook Health Sciences Centre Thunder Bay Regional Health Sciences Centre: text: Thunder Bay Regional Health Sciences Centre - sequenced by menu: - name: sequenced by menu + SequencedByMenu: + name: SequencedByMenu + title: sequenced by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -6404,6 +9740,8 @@ enums: text: Manitoba Cadham Provincial Laboratory McGill University: text: McGill University + description: McGill University is an English-language public research university + located in Montreal, Quebec, Canada. McMaster University: text: McMaster University National Microbiology Laboratory (NML): @@ -6428,8 +9766,9 @@ enums: text: Sunnybrook Health Sciences Centre Thunder Bay Regional Health Sciences Centre: text: Thunder Bay Regional Health Sciences Centre - sample collected by menu: - name: sample collected by menu + SampleCollectedByMenu: + name: SampleCollectedByMenu + title: sample collected by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -6499,8 +9838,9 @@ enums: text: Unity Health Toronto William Osler Health System: text: William Osler Health System - gene name menu: - name: gene name menu + GeneNameMenu: + name: GeneNameMenu + title: gene name menu permissible_values: MPX (orf B6R): text: MPX (orf B6R) @@ -6519,1637 +9859,5504 @@ enums: RNAse P gene (RNP): text: RNAse P gene (RNP) meaning: GENEPIO:0100508 - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeneSymbolInternationalMenu: + name: GeneSymbolInternationalMenu + title: gene symbol international menu + permissible_values: + opg001 gene (MPOX): + text: opg001 gene (MPOX) + description: A gene that encodes the Chemokine binding protein (MPOX). + meaning: GENEPIO:0101382 + opg002 gene (MPOX): + text: opg002 gene (MPOX) + description: A gene that encodes the Crm-B secreted TNF-alpha-receptor-like + protein (MPOX). + meaning: GENEPIO:0101383 + opg003 gene (MPOX): + text: opg003 gene (MPOX) + description: A gene that encodes the Ankyrin repeat protein (25) (MPOX). + meaning: GENEPIO:0101384 + opg015 gene (MPOX): + text: opg015 gene (MPOX) + description: A gene that encodes the Ankyrin repeat protein (39) (MPOX). + meaning: GENEPIO:0101385 + opg019 gene (MPOX): + text: opg019 gene (MPOX) + description: A gene that encodes the EGF-like domain protein (MPOX). + meaning: GENEPIO:0101386 + opg021 gene (MPOX): + text: opg021 gene (MPOX) + description: A gene that encodes the Zinc finger-like protein (2) (MPOX). + meaning: GENEPIO:0101387 + opg022 gene (MPOX): + text: opg022 gene (MPOX) + description: A gene that encodes the Interleukin-18-binding protein (MPOX). + meaning: GENEPIO:0101388 + opg023 gene (MPOX): + text: opg023 gene (MPOX) + description: A gene that encodes the Ankyrin repeat protein (2) (MPOX). + meaning: GENEPIO:0101389 + opg024 gene (MPOX): + text: opg024 gene (MPOX) + description: A gene that encodes the retroviral pseudoprotease-like protein + (MPOX). + meaning: GENEPIO:0101390 + opg025 gene (MPOX): + text: opg025 gene (MPOX) + description: A gene that encodes the Ankyrin repeat protein (14) (MPOX). + meaning: GENEPIO:0101391 + opg027 gene (MPOX): + text: opg027 gene (MPOX) + description: A gene that encodes the Host range protein (MPOX). + meaning: GENEPIO:0101392 + opg029 gene (MPOX): + text: opg029 gene (MPOX) + description: A gene that encodes the Bcl-2-like protein (MPOX). + meaning: GENEPIO:0101393 + opg030 gene (MPOX): + text: opg030 gene (MPOX) + description: A gene that encodes the Kelch-like protein (1) (MPOX). + meaning: GENEPIO:0101394 + opg031 gene (MPOX): + text: opg031 gene (MPOX) + description: A gene that encodes the C4L/C10L-like family protein (MPOX). + meaning: GENEPIO:0101395 + opg034 gene (MPOX): + text: opg034 gene (MPOX) + description: A gene that encodes the Bcl-2-like protein (MPOX). + meaning: GENEPIO:0101396 + opg035 gene (MPOX): + text: opg035 gene (MPOX) + description: A gene that encodes the Bcl-2-like protein (MPOX). + meaning: GENEPIO:0101397 + opg037 gene (MPOX): + text: opg037 gene (MPOX) + description: A gene that encodes the Ankyrin-like protein (1) (MPOX). + meaning: GENEPIO:0101399 + opg038 gene (MPOX): + text: opg038 gene (MPOX) + description: A gene that encodes the NFkB inhibitor protein (MPOX). + meaning: GENEPIO:0101400 + opg039 gene (MPOX): + text: opg039 gene (MPOX) + description: A gene that encodes the Ankyrin-like protein (3) (MPOX). + meaning: GENEPIO:0101401 + opg040 gene (MPOX): + text: opg040 gene (MPOX) + description: A gene that encodes the Serpin protein (MPOX). + meaning: GENEPIO:0101402 + opg042 gene (MPOX): + text: opg042 gene (MPOX) + description: A gene that encodes the Phospholipase-D-like protein (MPOX). + meaning: GENEPIO:0101403 + opg043 gene (MPOX): + text: opg043 gene (MPOX) + description: A gene that encodes the Putative monoglyceride lipase protein + (MPOX). + meaning: GENEPIO:0101404 + opg045 gene (MPOX): + text: opg045 gene (MPOX) + description: A gene that encodes the Caspase-9 inhibitor protein (MPOX). + meaning: GENEPIO:0101406 + opg046 gene (MPOX): + text: opg046 gene (MPOX) + description: A gene that encodes the dUTPase protein (MPOX). + meaning: GENEPIO:0101407 + opg047 gene (MPOX): + text: opg047 gene (MPOX) + description: A gene that encodes the Kelch-like protein (2) (MPOX). + meaning: GENEPIO:0101408 + opg048 gene (MPOX): + text: opg048 gene (MPOX) + description: A gene that encodes the Ribonucleotide reductase small subunit + protein (MPOX). + meaning: GENEPIO:0101409 + opg049 gene (MPOX): + text: opg049 gene (MPOX) + description: A gene that encodes the Telomere-binding protein I6 (1) (MPOX). + meaning: GENEPIO:0101410 + opg050 gene (MPOX): + text: opg050 gene (MPOX) + description: A gene that encodes the CPXV053 protein (MPOX). + meaning: GENEPIO:0101411 + opg051 gene (MPOX): + text: opg051 gene (MPOX) + description: A gene that encodes the CPXV054 protein (MPOX). + meaning: GENEPIO:0101412 + opg052 gene (MPOX): + text: opg052 gene (MPOX) + description: A gene that encodes the Cytoplasmic protein (MPOX). + meaning: GENEPIO:0101413 + opg053 gene (MPOX): + text: opg053 gene (MPOX) + description: A gene that encodes the IMV membrane protein L1R (MPOX). + meaning: GENEPIO:0101414 + opg054 gene (MPOX): + text: opg054 gene (MPOX) + description: A gene that encodes the Serine/threonine-protein kinase (MPOX). + meaning: GENEPIO:0101415 + opg055 gene (MPOX): + text: opg055 gene (MPOX) + description: A gene that encodes the Protein F11 protein (MPOX). + meaning: GENEPIO:0101416 + opg056 gene (MPOX): + text: opg056 gene (MPOX) + description: A gene that encodes the EEV maturation protein (MPOX). + meaning: GENEPIO:0101417 + opg057 gene (MPOX): + text: opg057 gene (MPOX) + description: A gene that encodes the Palmytilated EEV membrane protein (MPOX). + meaning: GENEPIO:0101418 + opg058 gene (MPOX): + text: opg058 gene (MPOX) + description: A gene that encodes the Protein F14 (1) protein (MPOX). + meaning: GENEPIO:0101419 + opg059 gene (MPOX): + text: opg059 gene (MPOX) + description: A gene that encodes the Cytochrome C oxidase protein (MPOX). + meaning: GENEPIO:0101420 + opg060 gene (MPOX): + text: opg060 gene (MPOX) + description: A gene that encodes the Protein F15 protein (MPOX). + meaning: GENEPIO:0101421 + opg061 gene (MPOX): + text: opg061 gene (MPOX) + description: A gene that encodes the Protein F16 (1) protein (MPOX). + meaning: GENEPIO:0101422 + opg062 gene (MPOX): + text: opg062 gene (MPOX) + description: A gene that encodes the DNA-binding phosphoprotein (1) (MPOX). + meaning: GENEPIO:0101423 + opg063 gene (MPOX): + text: opg063 gene (MPOX) + description: A gene that encodes the Poly(A) polymerase catalytic subunit + (3) protein (MPOX). + meaning: GENEPIO:0101424 + opg064 gene (MPOX): + text: opg064 gene (MPOX) + description: A gene that encodes the Iev morphogenesis protein (MPOX). + meaning: GENEPIO:0101425 + opg065 gene (MPOX): + text: opg065 gene (MPOX) + description: A gene that encodes the Double-stranded RNA binding protein (MPOX). + meaning: GENEPIO:0101426 + opg066 gene (MPOX): + text: opg066 gene (MPOX) + description: A gene that encodes the DNA-directed RNA polymerase 30 kDa polypeptide + protein (MPOX). + meaning: GENEPIO:0101427 + opg068 gene (MPOX): + text: opg068 gene (MPOX) + description: A gene that encodes the IMV membrane protein E6 (MPOX). + meaning: GENEPIO:0101428 + opg069 gene (MPOX): + text: opg069 gene (MPOX) + description: A gene that encodes the Myristoylated protein E7 (MPOX). + meaning: GENEPIO:0101429 + opg070 gene (MPOX): + text: opg070 gene (MPOX) + description: A gene that encodes the Membrane protein E8 (MPOX). + meaning: GENEPIO:0101430 + opg071 gene (MPOX): + text: opg071 gene (MPOX) + description: A gene that encodes the DNA polymerase (2) protein (MPOX). + meaning: GENEPIO:0101431 + opg072 gene (MPOX): + text: opg072 gene (MPOX) + description: A gene that encodes the Sulfhydryl oxidase protein (MPOX). + meaning: GENEPIO:0101432 + opg073 gene (MPOX): + text: opg073 gene (MPOX) + description: A gene that encodes the Virion core protein E11 (MPOX). + meaning: GENEPIO:0101433 + opg074 gene (MPOX): + text: opg074 gene (MPOX) + description: A gene that encodes the Iev morphogenesis protein (MPOX). + meaning: GENEPIO:0101434 + opg075 gene (MPOX): + text: opg075 gene (MPOX) + description: A gene that encodes the Glutaredoxin-1 protein (MPOX). + meaning: GENEPIO:0101435 + opg077 gene (MPOX): + text: opg077 gene (MPOX) + description: A gene that encodes the Telomere-binding protein I1 (MPOX). + meaning: GENEPIO:0101437 + opg078 gene (MPOX): + text: opg078 gene (MPOX) + description: A gene that encodes the IMV membrane protein I2 (MPOX). + meaning: GENEPIO:0101438 + opg079 gene (MPOX): + text: opg079 gene (MPOX) + description: A gene that encodes the DNA-binding phosphoprotein (2) (MPOX). + meaning: GENEPIO:0101439 + opg080 gene (MPOX): + text: opg080 gene (MPOX) + description: A gene that encodes the Ribonucleoside-diphosphate reductase + (2) protein (MPOX). + meaning: GENEPIO:0101440 + opg081 gene (MPOX): + text: opg081 gene (MPOX) + description: A gene that encodes the IMV membrane protein I5 (MPOX). + meaning: GENEPIO:0101441 + opg082 gene (MPOX): + text: opg082 gene (MPOX) + description: A gene that encodes the Telomere-binding protein (MPOX). + meaning: GENEPIO:0101442 + opg083 gene (MPOX): + text: opg083 gene (MPOX) + description: A gene that encodes the Viral core cysteine proteinase (MPOX). + meaning: GENEPIO:0101443 + opg084 gene (MPOX): + text: opg084 gene (MPOX) + description: A gene that encodes the RNA helicase NPH-II (2) protein (MPOX). + meaning: GENEPIO:0101444 + opg085 gene (MPOX): + text: opg085 gene (MPOX) + description: A gene that encodes the Metalloendopeptidase protein (MPOX). + meaning: GENEPIO:0101445 + opg086 gene (MPOX): + text: opg086 gene (MPOX) + description: A gene that encodes the Entry/fusion complex component protein + (MPOX). + meaning: GENEPIO:0101446 + opg087 gene (MPOX): + text: opg087 gene (MPOX) + description: A gene that encodes the Late transcription elongation factor + protein (MPOX). + meaning: GENEPIO:0101447 + opg088 gene (MPOX): + text: opg088 gene (MPOX) + description: A gene that encodes the Glutaredoxin-2 protein (MPOX). + meaning: GENEPIO:0101448 + opg089 gene (MPOX): + text: opg089 gene (MPOX) + description: A gene that encodes the FEN1-like nuclease protein (MPOX). + meaning: GENEPIO:0101449 + opg090 gene (MPOX): + text: opg090 gene (MPOX) + description: A gene that encodes the DNA-directed RNA polymerase 7 kDa subunit + protein (MPOX). + meaning: GENEPIO:0101450 + opg091 gene (MPOX): + text: opg091 gene (MPOX) + description: A gene that encodes the Nlpc/p60 superfamily protein (MPOX). + meaning: GENEPIO:0101451 + opg092 gene (MPOX): + text: opg092 gene (MPOX) + description: A gene that encodes the Assembly protein G7 (MPOX). + meaning: GENEPIO:0101452 + opg093 gene (MPOX): + text: opg093 gene (MPOX) + description: A gene that encodes the Late transcription factor VLTF-1 protein + (MPOX). + meaning: GENEPIO:0101453 + opg094 gene (MPOX): + text: opg094 gene (MPOX) + description: A gene that encodes the Myristylated protein (MPOX). + meaning: GENEPIO:0101454 + opg095 gene (MPOX): + text: opg095 gene (MPOX) + description: A gene that encodes the IMV membrane protein L1R (MPOX). + meaning: GENEPIO:0101455 + opg096 gene (MPOX): + text: opg096 gene (MPOX) + description: A gene that encodes the Crescent membrane and immature virion + formation protein (MPOX). + meaning: GENEPIO:0101456 + opg097 gene (MPOX): + text: opg097 gene (MPOX) + description: A gene that encodes the Internal virion L3/FP4 protein (MPOX). + meaning: GENEPIO:0101457 + opg098 gene (MPOX): + text: opg098 gene (MPOX) + description: A gene that encodes the Nucleic acid binding protein VP8/L4R + (MPOX). + meaning: GENEPIO:0101458 + opg099 gene (MPOX): + text: opg099 gene (MPOX) + description: A gene that encodes the Membrane protein CL5 (MPOX). + meaning: GENEPIO:0101459 + opg100 gene (MPOX): + text: opg100 gene (MPOX) + description: A gene that encodes the IMV membrane protein J1 (MPOX). + meaning: GENEPIO:0101460 + opg101 gene (MPOX): + text: opg101 gene (MPOX) + description: A gene that encodes the Thymidine kinase protein (MPOX). + meaning: GENEPIO:0101461 + opg102 gene (MPOX): + text: opg102 gene (MPOX) + description: A gene that encodes the Cap-specific mRNA protein (MPOX). + meaning: GENEPIO:0101462 + opg103 gene (MPOX): + text: opg103 gene (MPOX) + description: A gene that encodes the DNA-directed RNA polymerase subunit protein + (MPOX). + meaning: GENEPIO:0101463 + opg104 gene (MPOX): + text: opg104 gene (MPOX) + description: A gene that encodes the Myristylated protein (MPOX). + meaning: GENEPIO:0101464 + opg105 gene (MPOX): + text: opg105 gene (MPOX) + description: A gene that encodes the DNA-dependent RNA polymerase subunit + rpo147 protein (MPOX). + meaning: GENEPIO:0101465 + opg106 gene (MPOX): + text: opg106 gene (MPOX) + description: A gene that encodes the Tyr/ser protein phosphatase (MPOX). + meaning: GENEPIO:0101466 + opg107 gene (MPOX): + text: opg107 gene (MPOX) + description: A gene that encodes the Entry-fusion complex essential component + protein (MPOX). + meaning: GENEPIO:0101467 + opg108 gene (MPOX): + text: opg108 gene (MPOX) + description: A gene that encodes the IMV heparin binding surface protein (MPOX). + meaning: GENEPIO:0101468 + opg109 gene (MPOX): + text: opg109 gene (MPOX) + description: A gene that encodes the RNA polymerase-associated transcription-specificity + factor RAP94 protein (MPOX). + meaning: GENEPIO:0101469 + opg110 gene (MPOX): + text: opg110 gene (MPOX) + description: A gene that encodes the Late transcription factor VLTF-4 (1) + protein (MPOX). + meaning: GENEPIO:0101470 + opg111 gene (MPOX): + text: opg111 gene (MPOX) + description: A gene that encodes the DNA topoisomerase type I protein (MPOX). + meaning: GENEPIO:0101471 + opg112 gene (MPOX): + text: opg112 gene (MPOX) + description: A gene that encodes the Late protein H7 (MPOX). + meaning: GENEPIO:0101472 + opg113 gene (MPOX): + text: opg113 gene (MPOX) + description: A gene that encodes the mRNA capping enzyme large subunit protein + (MPOX). + meaning: GENEPIO:0101473 + opg114 gene (MPOX): + text: opg114 gene (MPOX) + description: A gene that encodes the Virion protein D2 (MPOX). + meaning: GENEPIO:0101474 + opg115 gene (MPOX): + text: opg115 gene (MPOX) + description: A gene that encodes the Virion core protein D3 (MPOX). + meaning: GENEPIO:0101475 + opg116 gene (MPOX): + text: opg116 gene (MPOX) + description: A gene that encodes the Uracil DNA glycosylase superfamily protein + (MPOX). + meaning: GENEPIO:0101476 + opg117 gene (MPOX): + text: opg117 gene (MPOX) + description: A gene that encodes the NTPase (1) protein (MPOX). + meaning: GENEPIO:0101477 + opg118 gene (MPOX): + text: opg118 gene (MPOX) + description: A gene that encodes the Early transcription factor 70 kDa subunit + protein (MPOX). + meaning: GENEPIO:0101478 + opg119 gene (MPOX): + text: opg119 gene (MPOX) + description: A gene that encodes the RNA polymerase subunit RPO18 protein + (MPOX). + meaning: GENEPIO:0101479 + opg120 gene (MPOX): + text: opg120 gene (MPOX) + description: A gene that encodes the Carbonic anhydrase protein (MPOX). + meaning: GENEPIO:0101480 + opg121 gene (MPOX): + text: opg121 gene (MPOX) + description: A gene that encodes the NUDIX domain protein (MPOX). + meaning: GENEPIO:0101481 + opg122 gene (MPOX): + text: opg122 gene (MPOX) + description: A gene that encodes the MutT motif protein (MPOX). + meaning: GENEPIO:0101482 + opg123 gene (MPOX): + text: opg123 gene (MPOX) + description: A gene that encodes the Nucleoside triphosphatase I protein (MPOX). + meaning: GENEPIO:0101483 + opg124 gene (MPOX): + text: opg124 gene (MPOX) + description: A gene that encodes the mRNA capping enzyme small subunit protein + (MPOX). + meaning: GENEPIO:0101484 + opg125 gene (MPOX): + text: opg125 gene (MPOX) + description: A gene that encodes the Rifampicin resistance protein (MPOX). + meaning: GENEPIO:0101485 + opg126 gene (MPOX): + text: opg126 gene (MPOX) + description: A gene that encodes the Late transcription factor VLTF-2 (2) + protein (MPOX). + meaning: GENEPIO:0101486 + opg127 gene (MPOX): + text: opg127 gene (MPOX) + description: A gene that encodes the Late transcription factor VLTF-3 (1) + protein (MPOX). + meaning: GENEPIO:0101487 + opg128 gene (MPOX): + text: opg128 gene (MPOX) + description: A gene that encodes the S-S bond formation pathway protein (MPOX). + meaning: GENEPIO:0101488 + opg129 gene (MPOX): + text: opg129 gene (MPOX) + description: A gene that encodes the Virion core protein P4b (MPOX). + meaning: GENEPIO:0101489 + opg130 gene (MPOX): + text: opg130 gene (MPOX) + description: A gene that encodes the A5L protein-like (MPOX). + meaning: GENEPIO:0101490 + opg131 gene (MPOX): + text: opg131 gene (MPOX) + description: A gene that encodes the DNA-directed RNA polymerase 19 kDa subunit + protein (MPOX). + meaning: GENEPIO:0101491 + opg132 gene (MPOX): + text: opg132 gene (MPOX) + description: A gene that encodes the Virion morphogenesis protein (MPOX). + meaning: GENEPIO:0101492 + opg133 gene (MPOX): + text: opg133 gene (MPOX) + description: A gene that encodes the Early transcription factor 82 kDa subunit + protein (MPOX). + meaning: GENEPIO:0101493 + opg134 gene (MPOX): + text: opg134 gene (MPOX) + description: A gene that encodes the Intermediate transcription factor VITF-3 + (1) protein (MPOX). + meaning: GENEPIO:0101494 + opg135 gene (MPOX): + text: opg135 gene (MPOX) + description: A gene that encodes the IMV membrane protein A9 (MPOX). + meaning: GENEPIO:0101495 + opg136 gene (MPOX): + text: opg136 gene (MPOX) + description: A gene that encodes the Virion core protein P4a (MPOX). + meaning: GENEPIO:0101496 + opg137 gene (MPOX): + text: opg137 gene (MPOX) + description: A gene that encodes the Viral membrane formation protein (MPOX). + meaning: GENEPIO:0101497 + opg138 gene (MPOX): + text: opg138 gene (MPOX) + description: A gene that encodes the A12 protein (MPOX). + meaning: GENEPIO:0101498 + opg139 gene (MPOX): + text: opg139 gene (MPOX) + description: A gene that encodes the IMV membrane protein A13L (MPOX). + meaning: GENEPIO:0101499 + opg140 gene (MPOX): + text: opg140 gene (MPOX) + description: A gene that encodes the IMV membrane protein A14 (MPOX). + meaning: GENEPIO:0101500 + opg141 gene (MPOX): + text: opg141 gene (MPOX) + description: A gene that encodes the DUF1029 domain protein (MPOX). + meaning: GENEPIO:0101501 + opg142 gene (MPOX): + text: opg142 gene (MPOX) + description: A gene that encodes the Core protein A15 (MPOX). + meaning: GENEPIO:0101502 + opg143 gene (MPOX): + text: opg143 gene (MPOX) + description: A gene that encodes the Myristylated protein (MPOX). + meaning: GENEPIO:0101503 + opg144 gene (MPOX): + text: opg144 gene (MPOX) + description: A gene that encodes the IMV membrane protein P21 (MPOX). + meaning: GENEPIO:0101504 + opg145 gene (MPOX): + text: opg145 gene (MPOX) + description: A gene that encodes the DNA helicase protein (MPOX). + meaning: GENEPIO:0101505 + opg146 gene (MPOX): + text: opg146 gene (MPOX) + description: A gene that encodes the Zinc finger-like protein (1) (MPOX). + meaning: GENEPIO:0101506 + opg147 gene (MPOX): + text: opg147 gene (MPOX) + description: A gene that encodes the IMV membrane protein A21 (MPOX). + meaning: GENEPIO:0101507 + opg148 gene (MPOX): + text: opg148 gene (MPOX) + description: A gene that encodes the DNA polymerase processivity factor protein + (MPOX). + meaning: GENEPIO:0101508 + opg149 gene (MPOX): + text: opg149 gene (MPOX) + description: A gene that encodes the Holliday junction resolvase protein (MPOX). + meaning: GENEPIO:0101509 + opg150 gene (MPOX): + text: opg150 gene (MPOX) + description: A gene that encodes the Intermediate transcription factor VITF-3 + (2) protein (MPOX). + meaning: GENEPIO:0101510 + opg151 gene (MPOX): + text: opg151 gene (MPOX) + description: A gene that encodes the DNA-dependent RNA polymerase subunit + rpo132 protein (MPOX). + meaning: GENEPIO:0101511 + opg153 gene (MPOX): + text: opg153 gene (MPOX) + description: A gene that encodes the Orthopoxvirus A26L/A30L protein (MPOX). + meaning: GENEPIO:0101512 + opg154 gene (MPOX): + text: opg154 gene (MPOX) + description: A gene that encodes the IMV surface fusion protein (MPOX). + meaning: GENEPIO:0101513 + opg155 gene (MPOX): + text: opg155 gene (MPOX) + description: A gene that encodes the Envelope protein A28 homolog (MPOX). + meaning: GENEPIO:0101514 + opg156 gene (MPOX): + text: opg156 gene (MPOX) + description: A gene that encodes the DNA-directed RNA polymerase 35 kDa subunit + protein (MPOX). + meaning: GENEPIO:0101515 + opg157 gene (MPOX): + text: opg157 gene (MPOX) + description: A gene that encodes the IMV membrane protein A30 (MPOX). + meaning: GENEPIO:0101516 + opg158 gene (MPOX): + text: opg158 gene (MPOX) + description: A gene that encodes the A32.5L protein (MPOX). + meaning: GENEPIO:0101517 + opg159 gene (MPOX): + text: opg159 gene (MPOX) + description: A gene that encodes the CPXV166 protein (MPOX). + meaning: GENEPIO:0101518 + opg160 gene (MPOX): + text: opg160 gene (MPOX) + description: A gene that encodes the ATPase A32 protein (MPOX). + meaning: GENEPIO:0101519 + opg161 gene (MPOX): + text: opg161 gene (MPOX) + description: A gene that encodes the EEV glycoprotein (1) (MPOX). + meaning: GENEPIO:0101520 + opg162 gene (MPOX): + text: opg162 gene (MPOX) + description: A gene that encodes the EEV glycoprotein (2) (MPOX). + meaning: GENEPIO:0101521 + opg163 gene (MPOX): + text: opg163 gene (MPOX) + description: A gene that encodes the MHC class II antigen presentation inhibitor + protein (MPOX). + meaning: GENEPIO:0101522 + opg164 gene (MPOX): + text: opg164 gene (MPOX) + description: A gene that encodes the IEV transmembrane phosphoprotein (MPOX). + meaning: GENEPIO:0101523 + opg165 gene (MPOX): + text: opg165 gene (MPOX) + description: A gene that encodes the CPXV173 protein (MPOX). + meaning: GENEPIO:0101524 + opg166 gene (MPOX): + text: opg166 gene (MPOX) + description: A gene that encodes the hypothetical protein (MPOX). + meaning: GENEPIO:0101525 + opg167 gene (MPOX): + text: opg167 gene (MPOX) + description: A gene that encodes the CD47-like protein (MPOX). + meaning: GENEPIO:0101526 + opg170 gene (MPOX): + text: opg170 gene (MPOX) + description: A gene that encodes the Chemokine binding protein (MPOX). + meaning: GENEPIO:0101527 + opg171 gene (MPOX): + text: opg171 gene (MPOX) + description: A gene that encodes the Profilin domain protein (MPOX). + meaning: GENEPIO:0101528 + opg172 gene (MPOX): + text: opg172 gene (MPOX) + description: A gene that encodes the Type-I membrane glycoprotein (MPOX). + meaning: GENEPIO:0101529 + opg173 gene (MPOX): + text: opg173 gene (MPOX) + description: A gene that encodes the MPXVgp154 protein (MPOX). + meaning: GENEPIO:0101530 + opg174 gene (MPOX): + text: opg174 gene (MPOX) + description: A gene that encodes the Hydroxysteroid dehydrogenase protein + (MPOX). + meaning: GENEPIO:0101531 + opg175 gene (MPOX): + text: opg175 gene (MPOX) + description: A gene that encodes the Copper/zinc superoxide dismutase protein + (MPOX). + meaning: GENEPIO:0101532 + opg176 gene (MPOX): + text: opg176 gene (MPOX) + description: A gene that encodes the Bcl-2-like protein (MPOX). + meaning: GENEPIO:0101533 + opg178 gene (MPOX): + text: opg178 gene (MPOX) + description: A gene that encodes the Thymidylate kinase protein (MPOX). + meaning: GENEPIO:0101534 + opg180 gene (MPOX): + text: opg180 gene (MPOX) + description: A gene that encodes the DNA ligase (2) protein (MPOX). + meaning: GENEPIO:0101535 + opg181 gene (MPOX): + text: opg181 gene (MPOX) + description: A gene that encodes the M137R protein (MPOX). + meaning: GENEPIO:0101536 + opg185 gene (MPOX): + text: opg185 gene (MPOX) + description: A gene that encodes the Hemagglutinin protein (MPOX). + meaning: GENEPIO:0101537 + opg187 gene (MPOX): + text: opg187 gene (MPOX) + description: A gene that encodes the Ser/thr kinase protein (MPOX). + meaning: GENEPIO:0101538 + opg188 gene (MPOX): + text: opg188 gene (MPOX) + description: A gene that encodes the Schlafen (1) protein (MPOX). + meaning: GENEPIO:0101539 + opg189 gene (MPOX): + text: opg189 gene (MPOX) + description: A gene that encodes the Ankyrin repeat protein (25) (MPOX). + meaning: GENEPIO:0101540 + opg190 gene (MPOX): + text: opg190 gene (MPOX) + description: A gene that encodes the EEV type-I membrane glycoprotein (MPOX). + meaning: GENEPIO:0101541 + opg191 gene (MPOX): + text: opg191 gene (MPOX) + description: A gene that encodes the Ankyrin-like protein (46) (MPOX). + meaning: GENEPIO:0101542 + opg192 gene (MPOX): + text: opg192 gene (MPOX) + description: A gene that encodes the Virulence protein (MPOX). + meaning: GENEPIO:0101543 + opg193 gene (MPOX): + text: opg193 gene (MPOX) + description: A gene that encodes the Soluble interferon-gamma receptor-like + protein (MPOX). + meaning: GENEPIO:0101544 + opg195 gene (MPOX): + text: opg195 gene (MPOX) + description: A gene that encodes the Intracellular viral protein (MPOX). + meaning: GENEPIO:0101545 + opg197 gene (MPOX): + text: opg197 gene (MPOX) + description: A gene that encodes the CPXV205 protein (MPOX). + meaning: GENEPIO:0101546 + opg198 gene (MPOX): + text: opg198 gene (MPOX) + description: A gene that encodes the Ser/thr kinase protein (MPOX). + meaning: GENEPIO:0101547 + opg199 gene (MPOX): + text: opg199 gene (MPOX) + description: A gene that encodes the Serpin protein (MPOX). + meaning: GENEPIO:0101548 + opg200 gene (MPOX): + text: opg200 gene (MPOX) + description: A gene that encodes the Bcl-2-like protein (MPOX). + meaning: GENEPIO:0101549 + opg204 gene (MPOX): + text: opg204 gene (MPOX) + description: A gene that encodes the IFN-alpha/beta-receptor-like secreted + glycoprotein (MPOX). + meaning: GENEPIO:0101550 + opg205 gene (MPOX): + text: opg205 gene (MPOX) + description: A gene that encodes the Ankyrin repeat protein (44) (MPOX). + meaning: GENEPIO:0101551 + opg208 gene (MPOX): + text: opg208 gene (MPOX) + description: A gene that encodes the Serpin protein (MPOX). + meaning: GENEPIO:0101552 + opg209 gene (MPOX): + text: opg209 gene (MPOX) + description: A gene that encodes the Virulence protein (MPOX). + meaning: GENEPIO:0101553 + opg210 gene (MPOX): + text: opg210 gene (MPOX) + description: A gene that encodes the B22R family protein (MPOX). + meaning: GENEPIO:0101554 + opg005 gene (MPOX): + text: opg005 gene (MPOX) + description: A gene that encodes the Bcl-2-like protein (MPOX). + meaning: GENEPIO:0101555 + opg016 gene (MPOX): + text: opg016 gene (MPOX) + description: A gene that encodes the Brix domain protein (MPOX). + meaning: GENEPIO:0101556 + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: Afghanistan: text: Afghanistan + description: A landlocked country that is located approximately in the center + of Asia. It is bordered by Pakistan in the south and east Iran in the west, + Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far + northeast. Afghanistan is administratively divided into thirty-four (34) + provinces (welayats). Each province is then divided into many provincial + districts, and each district normally covers a city or several townships. + [ url:http://en.wikipedia.org/wiki/Afghanistan ] meaning: GAZ:00006882 Albania: text: Albania + description: 'A country in South Eastern Europe. Albania is bordered by Greece + to the south-east, Montenegro to the north, Kosovo to the northeast, and + the Republic of Macedonia to the east. It has a coast on the Adriatic Sea + to the west, and on the Ionian Sea to the southwest. From the Strait of + Otranto, Albania is less than 100 km from Italy. Albania is divided into + 12 administrative divisions called (Albanian: official qark/qarku, but often + prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities + (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania + ]' meaning: GAZ:00002953 Algeria: text: Algeria + description: A country in North Africa. It is bordered by Tunisia in the northeast, + Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, + a few km of the Western Sahara in the west, Morocco in the northwest, and + the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), + 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). + [ url:http://en.wikipedia.org/wiki/Algeria ] meaning: GAZ:00000563 American Samoa: text: American Samoa + description: An unincorporated territory of the United States located in the + South Pacific Ocean, southeast of the sovereign State of Samoa. The main + (largest and most populous) island is Tutuila, with the Manu'a Islands, + Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa + ] meaning: GAZ:00003957 Andorra: text: Andorra + description: 'A small landlocked country in western Europe, located in the + eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. + Andorra consists of seven communities known as parishes (Catalan: parroquies, + singular - parroquia). Until relatively recently, it had only six parishes; + the seventh, Escaldes-Engordany, was created in 1978. Some parishes have + a further territorial subdivision. Ordino, La Massana and Sant Julia de + Loria are subdivided into quarts (quarters), while Canillo is subdivided + into veinats (neighborhoods). Those mostly coincide with villages, which + are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]' meaning: GAZ:00002948 Angola: text: Angola + description: A country in south-central Africa bordering Namibia to the south, + Democratic Republic of the Congo to the north, and Zambia to the east, and + with a west coast along the Atlantic Ocean. The exclave province Cabinda + has a border with the Republic of the Congo and the Democratic Republic + of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] meaning: GAZ:00001095 Anguilla: text: Anguilla + description: A British overseas territory in the Caribbean, one of the most + northerly of the Leeward Islands in the Lesser Antilles. It consists of + the main island of Anguilla itself, approximately 26 km long by 5 km wide + at its widest point, together with a number of much smaller islands and + cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila + ] meaning: GAZ:00009159 Antarctica: text: Antarctica + description: The Earth's southernmost continent, overlying the South Pole. + It is situated in the southern hemisphere, almost entirely south of the + Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica + ] meaning: GAZ:00000462 Antigua and Barbuda: text: Antigua and Barbuda + description: An island nation located on the eastern boundary of the Caribbean + Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda + ] meaning: GAZ:00006883 Argentina: text: Argentina + description: 'A South American country, constituted as a federation of twenty-three + provinces and an autonomous city. It is bordered by Paraguay and Bolivia + in the north, Brazil and Uruguay in the northeast, and Chile in the west + and south. The country claims the British controlled territories of the + Falkland Islands and South Georgia and the South Sandwich Islands. Argentina + also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping + other claims made by Chile and the United Kingdom. Argentina is subdivided + into twenty-three provinces (Spanish: provincias, singular provincia) and + one federal district (Capital de la Republica or Capital de la Nacion, informally + the Capital Federal). The federal district and the provinces have their + own constitutions, but exist under a federal system. Provinces are then + divided into departments (Spanish: departamentos, singular departamento), + except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina + ]' meaning: GAZ:00002928 Armenia: text: Armenia + description: A landlocked mountainous country in Eurasia between the Black + Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the + west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan + exclave of Azerbaijan to the south. A transcontinental country at the juncture + of Eastern Europe and Western Asia. A former republic of the Soviet Union. + Armenia is divided into ten marzes (provinces, singular marz), with the + city (kaghak) of Yerevan having special administrative status as the country's + capital. [ url:http://en.wikipedia.org/wiki/Armenia ] meaning: GAZ:00004094 Aruba: text: Aruba + description: An autonomous region within the Kingdom of the Netherlands, Aruba + has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba + ] meaning: GAZ:00004025 Ashmore and Cartier Islands: text: Ashmore and Cartier Islands + description: A Territory of Australia that includes two groups of small low-lying + uninhabited tropical islands in the Indian Ocean situated on the edge of + the continental shelf north-west of Australia and south of the Indonesian + island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands + ] meaning: GAZ:00005901 Australia: text: Australia + description: A country in the southern hemisphere comprising the mainland + of the world's smallest continent, the major island of Tasmania, and a number + of other islands in the Indian and Pacific Oceans. The neighbouring countries + are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon + Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to + the south-east. Australia has six states, two major mainland territories, + and other minor territories. meaning: GAZ:00000463 Austria: text: Austria + description: A landlocked country in Central Europe. It borders both Germany + and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia + and Italy to the south, and Switzerland and Liechtenstein to the west. The + capital is the city of Vienna on the Danube River. Austria is divided into + nine states (Bundeslander). These states are then divided into districts + (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities + (Gemeinden). Cities have the competencies otherwise granted to both districts + and municipalities. meaning: GAZ:00002942 Azerbaijan: text: Azerbaijan + description: A country in the he South Caucasus region of Eurasia, it is bounded + by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, + Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan + is bordered by Armenia to the north and east, Iran to the south and west, + and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts + in Azerbaijan's southwest, have been controlled by Armenia since the end + of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons + 11 city districts (saharlar), and one autonomous republic (muxtar respublika). meaning: GAZ:00004941 Bahamas: text: Bahamas + description: A country consisting of two thousand cays and seven hundred islands + that form an archipelago. It is located in the Atlantic Ocean, southeast + of Florida and the United States, north of Cuba, the island of Hispanola + and the Caribbean, and northwest of the British overseas territory of the + Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, + whose affairs are handled directly by the central government. meaning: GAZ:00002733 Bahrain: text: Bahrain + description: A borderless island country in the Persian Gulf. Saudi Arabia + lies to the west and is connected to Bahrain by the King Fahd Causeway, + and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into + five governorates. meaning: GAZ:00005281 Baker Island: text: Baker Island + description: An uninhabited atoll located just north of the equator in the + central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island + is an unincorporated and unorganized territory of the US. meaning: GAZ:00007117 Bangladesh: text: Bangladesh + description: A country in South Asia. It is bordered by India on all sides + except for a small border with Myanmar to the far southeast and by the Bay + of Bengal to the south. Bangladesh is divided into six administrative divisions. + Divisions are subdivided into districts (zila). There are 64 districts in + Bangladesh, each further subdivided into upazila (subdistricts) or thana + ("police stations"). meaning: GAZ:00003750 Barbados: text: Barbados + description: "An island country in the Lesser Antilles of the West Indies,\ + \ in the Caribbean region of the Americas, and the most easterly of the\ + \ Caribbean Islands. It is 34 kilometres (21 miles) in length and up to\ + \ 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is\ + \ in the western part of the North Atlantic, 100 km (62 mi) east of the\ + \ Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards,\ + \ part of the Lesser Antilles, at roughly 13\xB0N of the equator. It is\ + \ about 168 km (104 mi) east of both the countries of Saint Lucia and Saint\ + \ Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique\ + \ and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside\ + \ the principal Atlantic hurricane belt. Its capital and largest city is\ + \ Bridgetown." meaning: GAZ:00001251 Bassas da India: text: Bassas da India + description: A roughly circular atoll about 10 km in diameter, which corresponds + to a total size (including lagoon) of 80 km2. It is located in the southern + Mozambique Channel, about half-way between Madagascar (which is 385 km to + the east) and Mozambique, and 110 km northwest of Europa Island. It rises + steeply from the seabed 3000 m below. meaning: GAZ:00005810 Belarus: text: Belarus + description: A landlocked country in Eastern Europe, that borders Russia to + the north and east, Ukraine to the south, Poland to the west, and Lithuania + and Latvia to the north. Its capital is Minsk. Belarus is divided into six + voblasts, or provinces. Voblasts are further subdivided into raions (commonly + translated as districts or regions). As of 2002, there are six voblasts, + 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special + status, due to the city serving as the national capital. meaning: GAZ:00006886 Belgium: text: Belgium + description: A country in northwest Europe. Belgium shares borders with France + (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 + km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each + comprise five provinces; the third region, Brussels-Capital Region, is not + a province, nor does it contain any Together, these comprise 589 municipalities, + which in general consist of several sub-municipalities (which were independent + municipalities before the municipal merger operation mainly in 1977). meaning: GAZ:00002938 Belize: text: Belize + description: A country in Central America. It is the only officially English + speaking country in the region. Belize was a British colony for more than + a century and was known as British Honduras until 1973. It became an independent + nation within The Commonwealth in 1981. Belize is divided into 6 districts, + which are further divided into 31 constituencies. meaning: GAZ:00002934 Benin: text: Benin + description: A country in Western Africa. It borders Togo to the west, Nigeria + to the east and Burkina Faso and Niger to the north; its short coastline + to the south leads to the Bight of Benin. Its capital is Porto Novo, but + the seat of government is Cotonou. Benin is divided into 12 departments + and subdivided into 77 communes. meaning: GAZ:00000904 Bermuda: text: Bermuda + description: A British overseas territory in the North Atlantic Ocean. Located + off the east coast of the United States, it is situated around 1770 km NE + of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately + 138 islands. meaning: GAZ:00001264 Bhutan: text: Bhutan + description: A landlocked nation in South Asia. It is located amidst the eastern + end of the Himalaya Mountains and is bordered to the south, east and west + by India and to the north by Tibet. Bhutan is separated from Nepal by the + Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative + zones). Each dzongdey is further divided into dzongkhag (districts). There + are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into + subdistricts known as dungkhag. At the basic level, groups of villages form + a constituency called gewog. meaning: GAZ:00003920 Bolivia: text: Bolivia + description: 'A landlocked country in central South America. It is bordered + by Brazil on the north and east, Paraguay and Argentina on the south, and + Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: + departamentos). Each of the departments is subdivided into provinces (provincias), + which are further subdivided into municipalities (municipios).' meaning: GAZ:00002511 Borneo: text: Borneo + description: 'An island at the grographic centre of Maritime Southeast Adia, + in relation to major Indonesian islands, it is located north of Java, west + of Sulawesi, and east of Sumatra. It is the third-largest island in the + world and the larest in Asia. The island is politically divided among three + countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] + Approximately 73% of the island is Indonesian territory. In the north, the + East Malaysian states of Sabah and Sarawak make up about 26% of the island. + Additionally, the Malaysian federal territory of Labuan is situated on a + small island just off the coast of Borneo. The sovereign state of Brunei, + located on the north coast, comprises about 1% of Borneo''s land area. A + little more than half of the island is in the Northern Hemisphere, including + Brunei and the Malaysian portion, while the Indonesian portion spans the + Northern and Southern hemispheres.' meaning: GAZ:00025355 Bosnia and Herzegovina: text: Bosnia and Herzegovina + description: A country on the Balkan peninsula of Southern Europe. Bordered + by Croatia to the north, west and south, Serbia to the east, and Montenegro + to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 + km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided + into three political regions of which one, the Brcko District is part of + the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. + All three have an equal constitutional status on the whole territory of + Bosnia and Herzegovina. meaning: GAZ:00006887 Botswana: text: Botswana + description: A landlocked nation in Southern Africa. It is bordered by South + Africa to the south and southeast, Namibia to the west, Zambia to the north, + and Zimbabwe to the northeast. Botswana is divided into nine districts, + which are subdivided into a total twenty-eight subdistricts. meaning: GAZ:00001097 Bouvet Island: text: Bouvet Island + description: A sub-antarctic volcanic island in the South Atlantic Ocean, + south-southwest of the Cape of Good Hope (South Africa). It is a dependent + area of Norway and is not subject to the Antarctic Treaty, as it is north + of the latitude south of which claims are suspended. meaning: GAZ:00001453 Brazil: text: Brazil + description: 'A country in South America. Bordered by the Atlantic Ocean and + by Venezuela, Suriname, Guyana and the department of French Guiana to the + north, Colombia to the northwest, Bolivia and Peru to the west, Argentina + and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six + states (estados) and one federal district (Distrito Federal). The states + are subdivided into municipalities. For statistical purposes, the States + are grouped into five main regions: North, Northeast, Central-West, Southeast + and South.' meaning: GAZ:00002828 British Virgin Islands: text: British Virgin Islands + description: A British overseas territory, located in the Caribbean to the + east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, + the remaining islands constituting the US Virgin Islands. The British Virgin + Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and + Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately + fifteen of the islands are inhabited. meaning: GAZ:00003961 Brunei: text: Brunei + description: A country located on the north coast of the island of Borneo, + in Southeast Asia. Apart from its coastline with the South China Sea it + is completely surrounded by the State of Sarawak, Malaysia, and in fact + it is separated into two parts by Limbang, which is part of Sarawak. Brunei + is divided into four districts (daerah), the districts are subdivided into + thirty-eight mukims, which are then divided into kampong (villages). meaning: GAZ:00003901 Bulgaria: text: Bulgaria + description: A country in Southeastern Europe, borders five other countries; + Romania to the north (mostly along the Danube), Serbia and the Republic + of Macedonia to the west, and Greece and Turkey to the south. The Black + Sea defines the extent of the country to the east. Since 1999, it has consisted + of twenty-eight provinces. The provinces subdivide into 264 municipalities. meaning: GAZ:00002950 Burkina Faso: text: Burkina Faso + description: 'A landlocked nation in West Africa. It is surrounded by six + countries: Mali to the north, Niger to the east, Benin to the south east, + Togo and Ghana to the south, and Cote d''Ivoire to the south west. Burkina + Faso is divided into thirteen regions, forty-five provinces, and 301 departments + (communes).' meaning: GAZ:00000905 Burundi: text: Burundi + description: A small country in the Great Lakes region of Africa. It is bordered + by Rwanda on the north, Tanzania on the south and east, and the Democratic + Republic of the Congo on the west. Although the country is landlocked, much + of its western border is adjacent to Lake Tanganyika. Burundi is divided + into 17 provinces, 117 communes, and 2,638 collines. meaning: GAZ:00001090 Cambodia: text: Cambodia + description: A country in Southeast Asia. The country borders Thailand to + its west and northwest, Laos to its northeast, and Vietnam to its east and + southeast. In the south it faces the Gulf of Thailand. meaning: GAZ:00006888 Cameroon: text: Cameroon + description: A country of central and western Africa. It borders Nigeria to + the west; Chad to the northeast; the Central African Republic to the east; + and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. + Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea + and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces + and 58 divisions or departments. The divisions are further sub-divided into + sub-divisions (arrondissements) and districts. meaning: GAZ:00001093 Canada: text: Canada + description: A country occupying most of northern North America, extending + from the Atlantic Ocean in the east to the Pacific Ocean in the west and + northward into the Arctic Ocean. Canada is a federation composed of ten + provinces and three territories; in turn, these may be grouped into regions. + Western Canada consists of British Columbia and the three Prairie provinces + (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec + and Ontario. Atlantic Canada consists of the three Maritime provinces (New + Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland + and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada + together. Three territories (Yukon, Northwest Territories, and Nunavut) + make up Northern Canada. meaning: GAZ:00002560 Cape Verde: text: Cape Verde + description: A republic located on an archipelago in the Macaronesia ecoregion + of the North Atlantic Ocean, off the western coast of Africa. Cape Verde + is divided into 22 municipalities (concelhos), and subdivided into 32 parishes + (freguesias). meaning: GAZ:00001227 Cayman Islands: text: Cayman Islands + description: A British overseas territory located in the western Caribbean + Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. + The Cayman Islands are divided into seven districts. meaning: GAZ:00003986 Central African Republic: text: Central African Republic + description: A landlocked country in Central Africa. It borders Chad in the + north, Sudan in the east, the Republic of the Congo and the Democratic Republic + of the Congo in the south, and Cameroon in the west. The Central African + Republic is divided into 14 administrative prefectures (prefectures), along + with 2 economic prefectures (prefectures economiques) and one autonomous + commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). meaning: GAZ:00001089 Chad: text: Chad + description: A landlocked country in central Africa. It is bordered by Libya + to the north, Sudan to the east, the Central African Republic to the south, + Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided + into 18 regions. The departments are divided into 200 sub-prefectures, which + are in turn composed of 446 cantons. This is due to change. meaning: GAZ:00000586 Chile: text: Chile + description: 'A country in South America occupying a long and narrow coastal + strip wedged between the Andes mountains and the Pacific Ocean. The Pacific + forms the country''s entire western border, with Peru to the north, Bolivia + to the northeast, Argentina to the east, and the Drake Passage at the country''s + southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. + Chile is divided into 15 regions. Every region is further divided into provinces. + Finally each province is divided into communes. Each region is designated + by a name and a Roman numeral, assigned from north to south. The only exception + is the region housing the nation''s capital, which is designated RM, that + stands for Region Metropolitana (Metropolitan Region). Two new regions were + created in 2006: Arica-Parinacota in the north, and Los Rios in the south. + Both became operative in 2007-10.' meaning: GAZ:00002825 China: text: China + description: 'A large country in Northeast Asia. China borders 14 nations + (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, + Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia + and North Korea. Additionally the border between PRC and ROC is located + in territorial waters. The People''s Republic of China has administrative + control over twenty-two provinces and considers Taiwan to be its twenty-third + province. There are also five autonomous regions, each with a designated + minority group; four municipalities; and two Special Administrative Regions + that enjoy considerable autonomy. The People''s Republic of China administers + 33 province-level regions, 333 prefecture-level regions, 2,862 county-level + regions, 41,636 township-level regions, and several village-level regions.' meaning: GAZ:00002845 Christmas Island: text: Christmas Island + description: An island in the Indian Ocean, 500 km south of Indonesia and + about 2600 km northwest of Perth. The island is the flat summit of a submarine + mountain. meaning: GAZ:00005915 Clipperton Island: text: Clipperton Island + description: A nine-square km coral atoll in the North Pacific Ocean, southwest + of Mexico and west of Costa Rica. meaning: GAZ:00005838 Cocos Islands: text: Cocos Islands + description: Islands that located in the Indian Ocean, about halfway between + Australia and Sri Lanka. A territory of Australia. There are two atolls + and twenty-seven coral islands in the group. meaning: GAZ:00009721 Colombia: text: Colombia + description: A country located in the northwestern region of South America. + Colombia is bordered to the east by Venezuela and Brazil; to the south by + Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean + Sea; to the north-west by Panama; and to the west by the Pacific Ocean. + Besides the countries in South America, the Republic of Colombia is recognized + to share maritime borders with the Caribbean countries of Jamaica, Haiti, + the Dominican Republic and the Central American countries of Honduras, Nicaragua, + and Costa Rica. Colombia is divided into 32 departments and one capital + district which is treated as a department. There are in total 10 districts + assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, + Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia + is also subdivided into some municipalities which form departments, each + with a municipal seat capital city assigned. Colombia is also subdivided + into corregimientos which form municipalities. meaning: GAZ:00002929 Comoros: text: Comoros + description: An island nation in the Indian Ocean, located off the eastern + coast of Africa on the northern end of the Mozambique Channel between northern + Madagascar and northeastern Mozambique. meaning: GAZ:00005820 Cook Islands: text: Cook Islands + description: A self-governing parliamentary democracy in free association + with New Zealand. The fifteen small islands in this South Pacific Ocean + country have a total land area of 240 km2, but the Cook Islands Exclusive + Economic Zone (EEZ) covers 1.8 million km2 of ocean. meaning: GAZ:00053798 Coral Sea Islands: text: Coral Sea Islands + description: A Territory of Australia which includes a group of small and + mostly uninhabited tropical islands and reefs in the Coral Sea, northeast + of Queensland, Australia. The only inhabited island is Willis Island. The + territory covers 780,000 km2, extending east and south from the outer edge + of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, + the Willis Group, and fifteen other reef/island groups. meaning: GAZ:00005917 Costa Rica: text: Costa Rica + description: A republic in Central America, bordered by Nicaragua to the north, + Panama to the east-southeast, the Pacific Ocean to the west and south, and + the Caribbean Sea to the east. Costa Rica is composed of seven provinces, + which in turn are divided into 81 cantons. meaning: GAZ:00002901 Cote d'Ivoire: text: Cote d'Ivoire + description: A country in West Africa. It borders Liberia and Guinea to the + west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf + of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). + The regions are further divided into 58 departments. meaning: GAZ:00000906 Croatia: text: Croatia + description: A country at the crossroads of the Mediterranean, Central Europe, + and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and + Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to + the east, Montenegro to the far southeast, and the Adriatic Sea to the south. + Croatia is divided into 21 counties (zupanija) and the capital Zagreb's + city district. meaning: GAZ:00002719 Cuba: text: Cuba + description: A country that consists of the island of Cuba (the largest and + second-most populous island of the Greater Antilles), Isla de la Juventud + and several adjacent small islands. Fourteen provinces and one special municipality + (the Isla de la Juventud) now compose Cuba. meaning: GAZ:00003762 Curacao: text: Curacao + description: One of five island areas of the Netherlands Antilles. meaning: GAZ:00012582 Cyprus: text: Cyprus + description: The third largest island in the Mediterranean Sea (after Sicily + and Sardinia), Cyprus is situated in the eastern Mediterranean, just south + of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, + it is often included in the Middle East (see also Western Asia and Near + East). Turkey is 75 km north; other neighbouring countries include Syria + and Lebanon to the east, Israel to the southeast, Egypt to the south, and + Greece to the west-north-west. meaning: GAZ:00004006 Czech Republic: text: Czech Republic + description: 'A landlocked country in Central Europe. It has borders with + Poland to the north, Germany to the northwest and southwest, Austria to + the south, and Slovakia to the east. The capital and largest city is Prague. + The country is composed of the historic regions of Bohemia and Moravia, + as well as parts of Silesia. Since 2000, the Czech Republic is divided into + thirteen regions (kraje, singular kraj) and the capital city of Prague. + The older seventy-six districts (okresy, singular okres) including three + ''statutory cities'' (without Prague, which had special status) were disbanded + in 1999 in an administrative reform; they remain as territorial division + and seats of various branches of state administration. Since 2003-01-01, + the regions have been divided into around 203 Municipalities with Extended + Competence (unofficially named "Little Districts" (Czech: ''male okresy'') + which took over most of the administration of the former District Authorities. + Some of these are further divided into Municipalities with Commissioned + Local Authority. However, the old districts still exist as territorial units + and remain as seats of some of the offices.' meaning: GAZ:00002954 Democratic Republic of the Congo: text: Democratic Republic of the Congo + description: A country of central Africa. It borders the Central African Republic + and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia + and Angola on the south, the Republic of the Congo on the west, and is separated + from Tanzania by Lake Tanganyika on the east. The country enjoys access + to the ocean through a 40 km stretch of Atlantic coastline at Muanda and + the roughly 9 km wide mouth of the Congo river which opens into the Gulf + of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed + into 25 Provinces from 2.2009. Each Province is divided into Zones. meaning: GAZ:00001086 Denmark: text: Denmark + description: That part of the Kingdom of Denmark located in continental Europe. + The mainland is bordered to the south by Germany; Denmark is located to + the southwest of Sweden and the south of Norway. Denmark borders both the + Baltic and the North Sea. The country consists of a large peninsula, Jutland + (Jylland) and a large number of islands, most notably Zealand (Sjaelland), + Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds + of minor islands often referred to as the Danish Archipelago. meaning: GAZ:00005852 Djibouti: text: Djibouti + description: A country in eastern Africa. Djibouti is bordered by Eritrea + in the north, Ethiopia in the west and south, and Somalia in the southeast. + The remainder of the border is formed by the Red Sea and the Gulf of Aden. + On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the + coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. + Djibouti is divided into 5 regions and one city. It is further subdivided + into 11 districts. meaning: GAZ:00000582 Dominica: text: Dominica + description: An island nation in the Caribbean Sea. Dominica is divided into + ten parishes. meaning: GAZ:00006890 Dominican Republic: text: Dominican Republic + description: A country in the West Indies that occupies the E two-thirds of + the Hispaniola island. The Dominican Republic's shores are washed by the + Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona + Passage, a channel about 130 km wide, separates the country (and the Hispaniola) + from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, + the national capital, Santo Domingo, is contained within its own Distrito + Nacional (National District). The provinces are divided into municipalities + (municipios; singular municipio). meaning: GAZ:00003952 Ecuador: text: Ecuador + description: A country in South America, bordered by Colombia on the north, + by Peru on the east and south, and by the Pacific Ocean to the west. The + country also includes the Galapagos Islands (Archipelago de Colon) in the + Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, + divided into 199 cantons and subdivided into parishes (or parroquias). meaning: GAZ:00002912 Egypt: text: Egypt + description: A country in North Africa that includes the Sinai Peninsula, + a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, + and the Gaza Strip and Israel to the east. The northern coast borders the + Mediterranean Sea and the island of Cyprus; the eastern coast borders the + Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, + singular muhafazah). The governorates are further divided into regions (markazes). meaning: GAZ:00003934 El Salvador: text: El Salvador + description: A country in Central America, bordering the Pacific Ocean between + Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), + which, in turn, are subdivided into 267 municipalities (municipios). meaning: GAZ:00002935 Equatorial Guinea: text: Equatorial Guinea + description: 'A country in Central Africa. It is one of the smallest countries + in continental Africa, and comprises two regions: Rio Muni, continental + region including several offshore islands; and Insular Region containing + Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando + Po) that contains the capital, Malabo. Equatorial Guinea is divided into + seven provinces which are divided into districts.' meaning: GAZ:00001091 Eritrea: text: Eritrea + description: A country situated in northern East Africa. It is bordered by + Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. + The east and northeast of the country have an extensive coastline on the + Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago + and several of the Hanish Islands are part of Eritrea. Eritrea is divided + into six regions (zobas) and subdivided into districts ("sub-zobas"). meaning: GAZ:00000581 Estonia: text: Estonia + description: A country in Northern Europe. Estonia has land borders to the + south with Latvia and to the east with Russia. It is separated from Finland + in the north by the Gulf of Finland and from Sweden in the west by the Baltic + Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). + Estonian counties are divided into rural (vallad, singular vald) and urban + (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) + municipalities. The municipalities comprise populated places (asula or asustusuksus) + - various settlements and territorial units that have no administrative + function. A group of populated places form a rural municipality with local + administration. Most towns constitute separate urban municipalities, while + some have joined with surrounding rural municipalities. meaning: GAZ:00002959 Eswatini: text: Eswatini + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). meaning: GAZ:00001099 Ethiopia: text: Ethiopia + description: 'A country situated in the Horn of Africa that has been landlocked + since the independence of its northern neighbor Eritrea in 1993. Apart from + Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to + the south, Djibouti to the northeast, and Somalia to the east. Since 1996 + Ethiopia has had a tiered government system consisting of a federal government + overseeing ethnically-based regional states, zones, districts (woredas), + and neighborhoods (kebele). It is divided into nine ethnically-based administrative + states (kililoch, singular kilil) and subdivided into sixty-eight zones + and two chartered cities (astedader akababiwoch, singular astedader akababi): + Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and + six special woredas.' meaning: GAZ:00000567 Europa Island: text: Europa Island + description: A 28 km2 low-lying tropical island in the Mozambique Channel, + about a third of the way from southern Madagascar to southern Mozambique. meaning: GAZ:00005811 Falkland Islands (Islas Malvinas): text: Falkland Islands (Islas Malvinas) + description: An archipelago in the South Atlantic Ocean, located 483 km from + the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), + and 940 km north of Antarctica (Elephant Island). They consist of two main + islands, East Falkland and West Falkland, together with 776 smaller islands. meaning: GAZ:00001412 Faroe Islands: text: Faroe Islands + description: An autonomous province of the Kingdom of Denmark since 1948 located + in the Faroes. Administratively, the islands are divided into 34 municipalities + (kommunur) within which 120 or so cities and villages lie. meaning: GAZ:00059206 Fiji: text: Fiji + description: An island nation in the South Pacific Ocean east of Vanuatu, + west of Tonga and south of Tuvalu. The country occupies an archipelago of + about 322 islands, of which 106 are permanently inhabited, and 522 islets. + The two major islands, Viti Levu and Vanua Levu, account for 87% of the + population. meaning: GAZ:00006891 Finland: text: Finland + description: A Nordic country situated in the Fennoscandian region of Northern + Europe. It has borders with Sweden to the west, Russia to the east, and + Norway to the north, while Estonia lies to its south across the Gulf of + Finland. The capital city is Helsinki. Finland is divided into six administrative + provinces (laani, plural laanit). These are divided into 20 regions (maakunt), + 77 subregions (seutukunta) and then into municipalities (kunta). meaning: GAZ:00002937 France: text: France + description: A part of the country of France that extends from the Mediterranean + Sea to the English Channel and the North Sea, and from the Rhine to the + Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, + Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas + departments. meaning: GAZ:00003940 French Guiana: text: French Guiana + description: An overseas department (departement d'outre-mer) of France, located + on the northern coast of South America. It is bordered by Suriname, to the + E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. + French Guiana is divided into 2 departmental arrondissements, 19 cantons + and 22 communes. meaning: GAZ:00002516 French Polynesia: text: French Polynesia + description: 'A French overseas collectivity in the southern Pacific Ocean. + It is made up of several groups of Polynesian islands. French Polynesia + has five administrative subdivisions (French: subdivisions administratives).' meaning: GAZ:00002918 French Southern and Antarctic Lands: text: French Southern and Antarctic Lands + description: The French Southern and Antarctic Lands have formed a territoire + d'outre-mer (an overseas territory) of France since 1955. The territory + is divided into five districts. meaning: GAZ:00003753 Gabon: text: Gabon + description: A country in west central Africa sharing borders with Equatorial + Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital + and largest city is Libreville. Gabon is divided into 9 provinces and further + divided into 37 departments. meaning: GAZ:00001092 Gambia: text: Gambia + description: A country in Western Africa. It is the smallest country on the + African continental mainland and is bordered to the north, east, and south + by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing + through the centre of the country and discharging to the Atlantic Ocean + is the Gambia River. The Gambia is divided into five divisions and one city + (Banjul). The divisions are further subdivided into 37 districts. meaning: GAZ:00000907 Gaza Strip: text: Gaza Strip + description: A Palestinian enclave on the eastern coast of the Mediterranean + Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel + on the east and north along a 51 km (32 mi) border. Gaza and the West Bank + are claimed by the de jure sovereign State of Palestine. meaning: GAZ:00009571 Georgia: text: Georgia + description: 'A Eurasian country in the Caucasus located at the east coast + of the Black Sea. In the north, Georgia has a 723 km common border with + Russia, specifically with the Northern Caucasus federal district. The following + Russian republics/subdivisions: from west to east: border Georgia: Krasnodar + Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, + Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) + to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to + the south-west. It is a transcontinental country, located at the juncture + of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 + autonomous republics (avtonomiuri respublika), and 1 city (k''alak''i). + The regions are further subdivided into 69 districts (raioni).' meaning: GAZ:00004942 Germany: text: Germany + description: A country in Central Europe. It is bordered to the north by the + North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech + Republic; to the south by Austria and Switzerland; and to the west by France, + Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, + Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) + and cities (kreisfreie Stadte). meaning: GAZ:00002646 Ghana: text: Ghana + description: A country in West Africa. It borders Cote d'Ivoire to the west, + Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the + south. Ghana is a divided into 10 regions, subdivided into a total of 138 + districts. meaning: GAZ:00000908 Gibraltar: text: Gibraltar + description: A British overseas territory located near the southernmost tip + of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory + shares a border with Spain to the north. meaning: GAZ:00003987 Glorioso Islands: text: Glorioso Islands + description: A group of islands and rocks totalling 5 km2, in the northern + Mozambique channel, about 160 km northwest of Madagascar. meaning: GAZ:00005808 Greece: text: Greece + description: A country in southeastern Europe, situated on the southern end + of the Balkan Peninsula. It has borders with Albania, the former Yugoslav + Republic of Macedonia and Bulgaria to the north, and Turkey to the east. + The Aegean Sea lies to the east and south of mainland Greece, while the + Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin + feature a vast number of islands. Greece consists of thirteen peripheries + subdivided into a total of fifty-one prefectures (nomoi, singular nomos). + There is also one autonomous area, Mount Athos, which borders the periphery + of Central Macedonia. meaning: GAZ:00002945 Greenland: text: Greenland + description: A self-governing Danish province located between the Arctic and + Atlantic Oceans, east of the Canadian Arctic Archipelago. meaning: GAZ:00001507 Grenada: text: Grenada + description: An island country in the West Indies in the Caribbean Sea at + the southern end of the Grenadines island chain. Grenada consists of the + island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, + and several small islands which lie to the north of the main island and + are a part of the Grenadines. It is located northwest of Trinidad and Tobago, + northeast of Venezuela and southwest of Saint Vincent and the Grenadines. + Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated + population of 112,523 in July 2020. meaning: GAZ:02000573 Guadeloupe: text: Guadeloupe + description: "An archipelago and overseas department and region of France\ + \ in the Caribbean. It consists of six inhabited islands\u2014Basse-Terre,\ + \ Grande-Terre, Marie-Galante, La D\xE9sirade, and the two inhabited \xCE\ + les des Saintes\u2014as well as many uninhabited islands and outcroppings.\ + \ It is south of Antigua and Barbuda and Montserrat, and north of Dominica." meaning: GAZ:00067142 Guam: text: Guam + description: An organized, unincorporated territory of the United States in + the Micronesia subregion of the western Pacific Ocean. It is the westernmost + point and territory of the United States (reckoned from the geographic center + of the U.S.); in Oceania, it is the largest and southernmost of the Mariana + Islands and the largest island in Micronesia. meaning: GAZ:00003706 Guatemala: text: Guatemala + description: A country in Central America bordered by Mexico to the northwest, + the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the + northeast, and Honduras and El Salvador to the southeast. Guatemala is divided + into 22 departments (departamentos) and sub-divided into about 332 municipalities + (municipios). meaning: GAZ:00002936 Guernsey: text: Guernsey + description: A British Crown Dependency in the English Channel off the coast + of Normandy. meaning: GAZ:00001550 Guinea: text: Guinea + description: A nation in West Africa, formerly known as French Guinea. Guinea's + territory has a curved shape, with its base at the Atlantic Ocean, inland + to the east, and turning south. The base borders Guinea-Bissau and Senegal + to the north, and Mali to the north and north-east; the inland part borders + Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone + to the west of the southern tip. meaning: GAZ:00000909 Guinea-Bissau: text: Guinea-Bissau + description: A country in western Africa, and one of the smallest nations + in continental Africa. It is bordered by Senegal to the north, and Guinea + to the south and east, with the Atlantic Ocean to its west. Formerly the + Portuguese colony of Portuguese Guinea, upon independence, the name of its + capital, Bissau, was added to the country's name in order to prevent confusion + between itself and the Republic of Guinea. meaning: GAZ:00000910 Guyana: text: Guyana + description: A country in the N of South America. Guyana lies north of the + equator, in the tropics, and is located on the Atlantic Ocean. Guyana is + bordered to the east by Suriname, to the south and southwest by Brazil and + to the west by Venezuela. Guyana is divided into 10 regions. The regions + of Guyana are divided into 27 neighborhood councils. meaning: GAZ:00002522 Haiti: text: Haiti + description: A country located in the Greater Antilles archipelago on the + Caribbean island of Hispaniola, which it shares with the Dominican Republic. + Haiti is divided into 10 departments. The departments are further divided + into 41 arrondissements, and 133 communes which serve as second and third + level administrative divisions. meaning: GAZ:00003953 Heard Island and McDonald Islands: text: Heard Island and McDonald Islands + description: An Australian external territory comprising a volcanic group + of mostly barren Antarctic islands, about two-thirds of the way from Madagascar + to Antarctica. meaning: GAZ:00009718 Honduras: text: Honduras + description: A republic in Central America. The country is bordered to the + west by Guatemala, to the southwest by El Salvador, to the southeast by + Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and + to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. + Honduras is divided into 18 departments. The capital city is Tegucigalpa + Central District of the department of Francisco Morazan. meaning: GAZ:00002894 Hong Kong: text: Hong Kong + description: A special administrative region of the People's Republic of China + (PRC). The territory lies on the eastern side of the Pearl River Delta, + bordering Guangdong province in the north and facing the South China Sea + in the east, west and south. Hong Kong was a crown colony of the United + Kingdom from 1842 until the transfer of its sovereignty to the People's + Republic of China in 1997. meaning: GAZ:00003203 Howland Island: text: Howland Island + description: An uninhabited coral island located just north of the equator + in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. + The island is almost half way between Hawaii and Australia and is an unincorporated, + unorganized territory of the United States, and is often included as one + of the Phoenix Islands. For statistical purposes, Howland is grouped as + one of the United States Minor Outlying Islands. meaning: GAZ:00007120 Hungary: text: Hungary + description: 'A landlocked country in the Carpathian Basin of Central Europe, + bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. + Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: + megye). In addition, the capital city (fovaros), Budapest, is independent + of any county government. The counties are further subdivided into 173 subregions + (kistersegek), and Budapest is comprised of its own subregion. Since 1996, + the counties and City of Budapest have been grouped into 7 regions for statistical + and development purposes. These seven regions constitute NUTS second-level + units of Hungary.' meaning: GAZ:00002952 Iceland: text: Iceland + description: A country in northern Europe, comprising the island of Iceland + and its outlying islands in the North Atlantic Ocean between the rest of + Europe and Greenland. meaning: GAZ:00000843 India: text: India + description: A country in South Asia. Bounded by the Indian Ocean on the south, + the Arabian Sea on the west, and the Bay of Bengal on the east, India has + a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, + and Bhutan to the north-east; and Bangladesh and Burma to the east. India + is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian + Ocean. India is a federal republic of twenty-eight states and seven Union + Territories. Each state or union territory is divided into basic units of + government and administration called districts. There are nearly 600 districts + in India. The districts in turn are further divided into tehsils and eventually + into villages. meaning: GAZ:00002839 Indonesia: text: Indonesia + description: An archipelagic state in Southeast Asia. The country shares land + borders with Papua New Guinea, East Timor and Malaysia. Other neighboring + countries include Singapore, the Philippines, Australia, and the Indian + territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, + five of which have special status. The provinces are subdivided into regencies + (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), + which are further subdivided into subdistricts (kecamatan), and again into + village groupings (either desa or kelurahan). meaning: GAZ:00003727 Iran: text: Iran + description: A country in Central Eurasia. Iran is bounded by the Gulf of + Oman and the Persian Gulf to the south and the Caspian Sea to its north. + It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and + Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into + 30 provinces (ostan). The provinces are divided into counties (shahrestan), + and subdivided into districts (bakhsh) and sub-districts (dehestan). meaning: GAZ:00004474 Iraq: text: Iraq + description: 'A country in the Middle East spanning most of the northwestern + end of the Zagros mountain range, the eastern part of the Syrian Desert + and the northern part of the Arabian Desert. It shares borders with Kuwait + and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, + Turkey to the north, and Iran to the east. It has a very narrow section + of coastline at Umm Qasr on the Persian Gulf. There are two major flowing + rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates + (or provinces) (muhafazah). The governorates are divided into qadhas (or + districts).' meaning: GAZ:00004483 Ireland: text: Ireland + description: A country in north-western Europe. The modern sovereign state + occupies five-sixths of the island of Ireland, which was partitioned in + 1921. It is bordered by Northern Ireland (part of the United Kingdom) to + the north, by the Atlantic Ocean to the west and by the Irish Sea to the + east. Administration follows the 34 "county-level" counties and cities of + Ireland. Of these twenty-nine are counties, governed by county councils + while the five cities of Dublin, Cork, Limerick, Galway and Waterford have + city councils, (previously known as corporations), and are administered + separately from the counties bearing those names. The City of Kilkenny is + the only city in the republic which does not have a "city council"; it is + still a borough but not a county borough and is administered as part of + County Kilkenny. Ireland is split into eight regions for NUTS statistical + purposes. These are not related to the four traditional provinces but are + based on the administrative counties. meaning: GAZ:00002943 Isle of Man: text: Isle of Man + description: A Crown dependency of the United Kingdom in the centre of the + Irish Sea. It is not part of the United Kingdom, European Union or United + Nations. meaning: GAZ:00052477 Israel: text: Israel + description: 'A country in Western Asia located on the eastern edge of the + Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, + Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, + which are partially administrated by the Palestinian National Authority, + are also adjacent. The State of Israel is divided into six main administrative + districts, known as mehozot (singular mahoz). Districts are further divided + into fifteen sub-districts known as nafot (singular: nafa), which are themselves + partitioned into fifty natural regions.' meaning: GAZ:00002476 Italy: text: Italy + description: A country located on the Italian Peninsula in Southern Europe, + and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. + Italy shares its northern Alpine boundary with France, Switzerland, Austria + and Slovenia. The independent states of San Marino and the Vatican City + are enclaves within the Italian Peninsula, while Campione d'Italia is an + Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, + singular regione). Five of these regions have a special autonomous status + that enables them to enact legislation on some of their local matters. It + is further divided into 109 provinces (province) and 8,101 municipalities + (comuni). meaning: GAZ:00002650 Jamaica: text: Jamaica + description: A nation of the Greater Antilles. Jamaica is divided into 14 + parishes, which are grouped into three historic counties that have no administrative + relevance. meaning: GAZ:00003781 Jan Mayen: text: Jan Mayen + description: 'A volcanic island that is part of the Kingdom of Norway, It + has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus + 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and + 1,000 km west of the Norwegian mainland. The island is mountainous, the + highest summit being the Beerenberg volcano in the north. The isthmus is + the location of the two largest lakes of the island, Sorlaguna (South Lagoon), + and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng + Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.' meaning: GAZ:00005853 Japan: text: Japan + description: An island country in East Asia. Located in the Pacific Ocean, + it lies to the east of China, Korea and Russia, stretching from the Sea + of Okhotsk in the north to the East China Sea in the south. meaning: GAZ:00002747 Jarvis Island: text: Jarvis Island + description: An uninhabited 4.5 km2 coral atoll located in the South Pacific + Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated + territory of the United States administered from Washington, DC by the United + States Fish and Wildlife Service of the United States Department of the + Interior as part of the National Wildlife Refuge system. Jarvis is one of + the southern Line Islands and for statistical purposes is also grouped as + one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. meaning: GAZ:00007118 Jersey: text: Jersey + description: A British Crown Dependency[6] off the coast of Normandy, France. + As well as the island of Jersey itself, the bailiwick includes two groups + of small islands that are no longer permanently inhabited, the Minquiers + and Ecrehous, and the Pierres de Lecq. meaning: GAZ:00001551 Johnston Atoll: text: Johnston Atoll + description: A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 + nm) west of Hawaii. There are four islands located on the coral reef platform, + two natural islands, Johnston Island and Sand Island, which have been expanded + by coral dredging, as well as North Island (Akau) and East Island (Hikina), + artificial islands formed from coral dredging. Johnston is an unincorporated + territory of the United States, administered by the US Fish and Wildlife + Service of the Department of the Interior as part of the United States Pacific + Island Wildlife Refuges. Sits atop Johnston Seamount. meaning: GAZ:00007114 Jordan: text: Jordan + description: A country in Southwest Asia, bordered by Syria to the north, + Iraq to the north-east, Israel and the West Bank to the west, and Saudi + Arabia to the east and south. It shares the coastlines of the Dead Sea, + and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided + into 12 provinces called governorates. The Governorates are subdivided into + approximately fifty-two nahias. meaning: GAZ:00002473 Juan de Nova Island: text: Juan de Nova Island + description: A 4.4 km2 low, flat, tropical island in the narrowest part of + the Mozambique Channel, about one-third of the way between Madagascar and + Mozambique. meaning: GAZ:00005809 Kazakhstan: text: Kazakhstan + description: A country in Central Asia and Europe. It is bordered by Russia, + Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders + on a significant part of the Caspian Sea. Kazakhstan is divided into 14 + provinces and two municipal districts. The provinces of Kazakhstan are divided + into raions. meaning: GAZ:00004999 Kenya: text: Kenya + description: A country in Eastern Africa. It is bordered by Ethiopia to the + north, Somalia to the east, Tanzania to the south, Uganda to the west, and + Sudan to the northwest, with the Indian Ocean running along the southeast + border. Kenya comprises eight provinces each headed by a Provincial Commissioner + (centrally appointed by the president). The provinces (mkoa singular mikoa + plural in Swahili) are subdivided into districts (wilaya). There were 69 + districts as of 1999 census. Districts are then subdivided into 497 divisions + (taarafa). The divisions are then subdivided into 2,427 locations (kata) + and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the + status of a full administrative province. meaning: GAZ:00001101 Kerguelen Archipelago: text: Kerguelen Archipelago + description: A group of islands in the southern Indian Ocean. It is a territory + of France. They are composed primarily of Tertiary flood basalts and a complex + of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano + at the southern end was active during the late Pleistocene. The Rallier + du Baty Peninsula on the SW tip of the island contains two youthful subglacial + eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active + fumarole field is related to a series of Holocene trachytic lava flows and + lahars that extend beyond the icecap. meaning: GAZ:00005682 Kingman Reef: text: Kingman Reef + description: A largely submerged, uninhabited tropical atoll located in the + North Pacific Ocean, roughly half way between Hawaiian Islands and American + Samoa. It is the northernmost of the Northern Line Islands and lies 65 km + NNW of Palmyra Atoll, the next closest island, and has the status of an + unincorporated territory of the United States, administered from Washington, + DC by the US Navy. Sits atop Kingman Reef Seamount. meaning: GAZ:00007116 Kiribati: text: Kiribati + description: 'An island nation located in the central tropical Pacific Ocean. + It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 + km2 straddling the equator and bordering the International Date Line to + the east. It is divided into three island groups which have no administrative + function, including a group which unites the Line Islands and the Phoenix + Islands (ministry at London, Christmas). Each inhabited island has its own + council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two + councils on Tabiteuea).' meaning: GAZ:00006894 Kosovo: text: Kosovo + description: A country on the Balkan Peninsula. Kosovo borders Central Serbia + to the north and east, Montenegro to the northwest, Albania to the west + and the Republic of Macedonia to the south. Kosovo is divided into 7 districts + (Rreth) and 30 municipalities. Serbia does not recognise the unilateral + secession of Kosovo[8] and considers it a United Nations-governed entity + within its sovereign territory, the Autonomous Province of Kosovo and Metohija. meaning: GAZ:00011337 Kuwait: text: Kuwait + description: A sovereign emirate on the coast of the Persian Gulf, enclosed + by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided + into six governorates (muhafazat, singular muhafadhah). meaning: GAZ:00005285 Kyrgyzstan: text: Kyrgyzstan + description: A country in Central Asia. Landlocked and mountainous, it is + bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan + to the southwest and China to the east. Kyrgyzstan is divided into seven + provinces (oblast. The capital, Bishkek, and the second large city Osh are + administratively the independent cities (shaar) with a status equal to a + province. Each province comprises a number of districts (raions). meaning: GAZ:00006893 Laos: text: Laos + description: A landlocked country in southeast Asia, bordered by Burma (Myanmar) + and China to the northwest, Vietnam to the east, Cambodia to the south, + and Thailand to the west. Laos is divided into sixteen provinces (qwang) + and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided + into districts (muang). meaning: GAZ:00006889 Latvia: text: Latvia + description: A country in Northern Europe. Latvia shares land borders with + Estonia to the north and Lithuania to the south, and both Russia and Belarus + to the east. It is separated from Sweden in the west by the Baltic Sea. + The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). + There are also seven cities (lielpilsetas) that have a separate status. + Latvia is also historically, culturally and constitutionally divided in + four or more distinct regions. meaning: GAZ:00002958 Lebanon: text: Lebanon + description: 'A small, mostly mountainous country in Western Asia, on the + eastern shore of the Mediterranean Sea. It is bordered by Syria to the north + and east, and Israel to the south. Lebanon is divided into six governorates + (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, + singular: qadaa).' meaning: GAZ:00002478 Lesotho: text: Lesotho + description: A land-locked country, entirely surrounded by the Republic of + South Africa. Lesotho is divided into ten districts; these are further subdivided + into 80 constituencies, which consists of 129 local community councils. meaning: GAZ:00001098 Liberia: text: Liberia + description: A country on the west coast of Africa, bordered by Sierra Leone, + Guinea, Cote d'Ivoire, and the Atlantic Ocean. meaning: GAZ:00000911 Libya: text: Libya + description: A country in North Africa. Bordering the Mediterranean Sea to + the north, Libya lies between Egypt to the east, Sudan to the southeast, + Chad and Niger to the south, and Algeria and Tunisia to the west. There + are thirty-four municipalities of Libya, known by the Arabic term sha'biyat + (singular sha'biyah). These came recently (in the 1990s to replaced old + Baladiyat systam. The Baladiyat system in turn was introduced to replace + the system of muhafazah (governorates or provinces) that existed from the + 1960s to the 1970s. meaning: GAZ:00000566 Liechtenstein: text: Liechtenstein + description: A tiny, doubly landlocked alpine country in Western Europe, bordered + by Switzerland to its west and by Austria to its east. The principality + of Liechtenstein is divided into 11 municipalities called Gemeinden (singular + Gemeinde). The Gemeinden mostly consist only of a single town. Five of them + fall within the electoral district Unterland (the lower county), and the + remainder within Oberland (the upper county). meaning: GAZ:00003858 Line Islands: text: Line Islands + description: A group of eleven atolls and low coral islands in the central + Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, + while three are United States territories that are grouped with the United + States Minor Outlying Islands. meaning: GAZ:00007144 Lithuania: text: Lithuania + description: 'A country located along the south-eastern shore of the Baltic + Sea, sharing borders with Latvia to the north, Belarus to the southeast, + Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. + Lithuania has a three-tier administrative division: the country is divided + into 10 counties (singular apskritis, plural, apskritys) that are further + subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) + which consist of over 500 elderates (singular seniunija, plural seniunijos).' meaning: GAZ:00002960 Luxembourg: text: Luxembourg + description: A small landlocked country in western Europe, bordered by Belgium, + France, and Germany. Luxembourg is divided into 3 districts, which are further + divided into 12 cantons and then 116 communes. Twelve of the communes have + city status, of which the city of Luxembourg is the largest. meaning: GAZ:00002947 Macau: text: Macau + description: One of the two special administrative regions of the People's + Republic of China, the other being Hong Kong. Macau lies on the western + side of the Pearl River Delta, bordering Guangdong province in the north + and facing the South China Sea in the east and south. Macau is situated + 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the + Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula + is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang + (West River) on the west. It borders the Zhuhai Special Economic Zone in + mainland China. meaning: GAZ:00003202 Madagascar: text: Madagascar + description: An island nation in the Indian Ocean off the southeastern coast + of Africa. The main island, also called Madagascar, is the fourth largest + island in the world, and is home to 5% of the world's plant and animal species, + of which more than 80% are endemic to Madagascar. Most notable are the lemur + infraorder of primates, the carnivorous fossa, three endemic bird families + and six endemic baobab species. Madagascar is divided into six autonomous + provinces (faritany mizakatena), and 22 regions. The regions are further + subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. meaning: GAZ:00001108 Malawi: text: Malawi + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. meaning: GAZ:00001105 Malaysia: text: Malaysia + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. meaning: GAZ:00003902 Maldives: text: Maldives + description: An archipelago which consists of approximately 1,196 coral islands + grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. meaning: GAZ:00006924 Mali: text: Mali + description: A landlocked country in northern Africa. It borders Algeria on + the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the + south, Guinea on the south-west, and Senegal and Mauritania on the west. + Mali is divided into 8 regions (regions) and 1 district, and subdivided + into 49 cercles, totalling 288 arrondissements. meaning: GAZ:00000584 Malta: text: Malta + description: A Southern European country and consists of an archipelago situated + centrally in the Mediterranean. meaning: GAZ:00004017 Marshall Islands: text: Marshall Islands + description: 'An archipelago that consists of twenty-nine atolls and five + isolated islands. The most important atolls and islands form two groups: + the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). + Two-thirds of the nation''s population lives on Majuro (which is also the + capital) and Ebeye. The outer islands are sparsely populated.' meaning: GAZ:00007161 Martinique: text: Martinique + description: An island and an overseas department/region and single territorial + collectivity of France. meaning: GAZ:00067143 Mauritania: text: Mauritania + description: A country in North-West Africa. It is bordered by the Atlantic + Ocean on the west, by Senegal on the southwest, by Mali on the east and + southeast, by Algeria on the northeast, and by Western Sahara on the northwest + (most of which is occupied by Morocco). The capital and largest city is + Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 + regions (regions) and one capital district, which in turn are subdivided + into 44 departments (departements). meaning: GAZ:00000583 Mauritius: text: Mauritius + description: An island nation off the coast of the African continent in the + southwest Indian Ocean, about 900 km east of Madagascar. In addition to + the island of Mauritius, the republic includes the islands of St. Brandon, + Rodrigues and the Agalega Islands. meaning: GAZ:00003745 Mayotte: text: Mayotte + description: An overseas collectivity of France consisting of a main island, + Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and + several islets around these two. meaning: GAZ:00003943 Mexico: text: Mexico + description: A federal constitutional republic in North America. It is bounded + on the north by the United States; on the south and west by the North Pacific + Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and + on the east by the Gulf of Mexico. The United Mexican States comprise a + federation of thirty-one states and a federal district, the capital Mexico + City. meaning: GAZ:00002852 Micronesia: text: Micronesia + description: A subregion of Oceania, comprising hundreds of small islands + in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua + New Guinea and Melanesia to the west and southwest, and Polynesia to the + east. meaning: GAZ:00005862 Midway Islands: text: Midway Islands + description: A 6.2 km2 atoll located in the North Pacific Ocean (near the + northwestern end of the Hawaiian archipelago). It is an unincorporated territory + of the United States, designated an insular area under the authority of + the US Department of the Interior. meaning: GAZ:00007112 Moldova: text: Moldova + description: A landlocked country in Eastern Europe, located between Romania + to the west and Ukraine to the north, east and south. Moldova is divided + into thirty-two districts (raioane, singular raion); three municipalities + (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). + The cities of Comrat and Tiraspol also have municipality status, however + not as first-tier subdivisions of Moldova, but as parts of the regions of + Gagauzia and Transnistria, respectively. The status of Transnistria is however + under dispute. Although it is de jure part of Moldova and is recognized + as such by the international community, Transnistria is not de facto under + the control of the central government of Moldova. It is administered by + an unrecognized breakaway authority under the name Pridnestrovian Moldovan + Republic. meaning: GAZ:00003897 Monaco: text: Monaco + description: A small country that is completely bordered by France to the + north, west, and south; to the east it is bordered by the Mediterranean + Sea. It consists of a single municipality (commune) currently divided into + 4 quartiers and 10 wards. meaning: GAZ:00003857 Mongolia: text: Mongolia + description: A country in East-Central Asia. The landlocked country borders + Russia to the north and China to the south. The capital and largest city + is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are + in turn divided into 315 sums (districts). The capital Ulan Bator is administrated + separately as a khot (municipality) with provincial status. meaning: GAZ:00008744 Montenegro: text: Montenegro + description: A country located in Southeastern Europe. It has a coast on the + Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina + to the northwest, Serbia and its partially recognized breakaway southern + province of Kosovo to the northeast and Albania to the southeast. Its capital + and largest city is Podgorica. Montenegro is divided into twenty-one municipalities + (opstina), and two urban municipalities, subdivisions of Podgorica municipality. meaning: GAZ:00006898 Montserrat: text: Montserrat + description: A British overseas territory located in the Leeward Islands. + Montserrat is divided into three parishes. meaning: GAZ:00003988 Morocco: text: Morocco + description: A country in North Africa. It has a coast on the Atlantic Ocean + that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco + has international borders with Algeria to the east, Spain to the north (a + water border through the Strait and land borders with two small Spanish + autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco + is divided into 16 regions, and subdivided into 62 prefectures and provinces. + Because of the conflict over Western Sahara, the status of both regions + of "Saguia el-Hamra" and "Rio de Oro" is disputed. meaning: GAZ:00000565 Mozambique: text: Mozambique + description: A country in southeastern Africa bordered by the Indian Ocean + to the east, Tanzania to the north, Malawi and Zambia to the northwest, + Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique + is divided into ten provinces (provincias) and one capital city (cidade + capital) with provincial status. The provinces are subdivided into 129 districts + (distritos). Districts are further divided in "Postos Administrativos" (Administrative + Posts) and these in Localidades (Localities) the lowest geographical level + of central state administration. meaning: GAZ:00001100 Myanmar: text: Myanmar + description: A country in SE Asia that is bordered by China on the north, + Laos on the east, Thailand on the southeast, Bangladesh on the west, and + India on the northwest, with the Bay of Bengal to the southwest. Myanmar + is divided into seven states and seven divisions. The administrative divisions + are further subdivided into districts, which are further subdivided into + townships, wards, and villages. meaning: GAZ:00006899 Namibia: text: Namibia + description: A country in southern Africa on the Atlantic coast. It shares + borders with Angola and Zambia to the north, Botswana to the east, and South + Africa to the south. Namibia is divided into 13 regions and subdivided into + 102 constituencies. meaning: GAZ:00001096 Nauru: text: Nauru + description: An island nation in the Micronesian South Pacific. The nearest + neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. + Nauru is divided into fourteen administrative districts which are grouped + into eight electoral constituencies. meaning: GAZ:00006900 Navassa Island: text: Navassa Island + description: A small, uninhabited island in the Caribbean Sea, and is an unorganized + unincorporated territory of the United States, which administers it through + the US Fish and Wildlife Service. The island is also claimed by Haiti. meaning: GAZ:00007119 Nepal: text: Nepal + description: A landlocked nation in South Asia. It is bordered by the Tibet + Autonomous Region of the People's Republic of China to the northeast and + India to the south and west; it is separated from Bhutan by the Indian State + of Sikkim and from Bangladesh by a small strip of the Indian State of West + Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs + across Nepal's north and western parts, and eight of the world's ten highest + mountains, including the highest, Mount Everest are situated within its + territory. Nepal is divided into 14 zones and 75 districts, grouped into + 5 development regions. meaning: GAZ:00004399 Netherlands: text: Netherlands + description: The European part of the Kingdom of the Netherlands. It is bordered + by the North Sea to the north and west, Belgium to the south, and Germany + to the east. The Netherlands is divided into twelve administrative regions, + called provinces. All provinces of the Netherlands are divided into municipalities + (gemeenten), together 443 (2007). meaning: GAZ:00002946 New Caledonia: text: New Caledonia + description: A "sui generis collectivity" (in practice an overseas territory) + of France, made up of a main island (Grande Terre), the Loyalty Islands, + and several smaller islands. It is located in the region of Melanesia in + the southwest Pacific. Administratively, the archipelago is divided into + three provinces, and then into 33 communes. meaning: GAZ:00005206 New Zealand: text: New Zealand + description: A nation in the south-western Pacific Ocean comprising two large + islands (the North Island and the South Island) and numerous smaller islands, + most notably Stewart Island/Rakiura and the Chatham Islands. meaning: GAZ:00000469 Nicaragua: text: Nicaragua + description: A republic in Central America. It is also the least densely populated + with a demographic similar in size to its smaller neighbors. The country + is bordered by Honduras to the north and by Costa Rica to the south. The + Pacific Ocean lies to the west of the country, while the Caribbean Sea lies + to the east. For administrative purposes it is divided into 15 departments + (departamentos) and two self-governing regions (autonomous communities) + based on the Spanish model. The departments are then subdivided into 153 + municipios (municipalities). The two autonomous regions are Region Autonoma + del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred + to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 + they formed the single department of Zelaya. meaning: GAZ:00002978 Niger: text: Niger + description: A landlocked country in Western Africa, named after the Niger + River. It borders Nigeria and Benin to the south, Burkina Faso and Mali + to the west, Algeria and Libya to the north and Chad to the east. The capital + city is Niamey. Niger is divided into 7 departments and one capital district. + The departments are subdivided into 36 arrondissements and further subdivided + into 129 communes. meaning: GAZ:00000585 Nigeria: text: Nigeria + description: A federal constitutional republic comprising thirty-six states + and one Federal Capital Territory. The country is located in West Africa + and shares land borders with the Republic of Benin in the west, Chad and + Cameroon in the east, and Niger in the north. Its coast lies on the Gulf + of Guinea, part of the Atlantic Ocean, in the south. The capital city is + Abuja. Nigeria is divided into thirty-six states and one Federal Capital + Territory, which are further sub-divided into 774 Local Government Areas + (LGAs). meaning: GAZ:00000912 Niue: text: Niue + description: An island nation located in the South Pacific Ocean. Although + self-governing, Niue is in free association with New Zealand, meaning that + the Sovereign in Right of New Zealand is also Niue's head of state. meaning: GAZ:00006902 Norfolk Island: text: Norfolk Island + description: A Territory of Australia that includes Norfolk Island and neighboring + islands. meaning: GAZ:00005908 North Korea: text: North Korea + description: A state in East Asia in the northern half of the Korean Peninsula, + with its capital in the city of Pyongyang. To the south and separated by + the Korean Demilitarized Zone is South Korea, with which it formed one nation + until division following World War II. At its northern Amnok River border + are China and, separated by the Tumen River in the extreme north-east, Russia. meaning: GAZ:00002801 North Macedonia: text: North Macedonia + description: A landlocked country on the Balkan peninsula in southeastern + Europe. It is bordered by Serbia and Kosovo to the north, Albania to the + west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic + of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), + 10 of which comprise Greater Skopje. This is reduced from the previous 123 + municipalities established in 1996-09. Prior to this, local government was + organised into 34 administrative districts. meaning: GAZ:00006895 North Sea: text: North Sea + description: A sea situated between the eastern coasts of the British Isles + and the western coast of Europe. meaning: GAZ:00002284 Northern Mariana Islands: text: Northern Mariana Islands + description: A group of 15 islands about three-quarters of the way from Hawaii + to the Philippines. meaning: GAZ:00003958 Norway: text: Norway + description: A country and constitutional monarchy in Northern Europe that + occupies the western portion of the Scandinavian Peninsula. It is bordered + by Sweden, Finland, and Russia. The Kingdom of Norway also includes the + Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty + over Svalbard is based upon the Svalbard Treaty, but that treaty does not + apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter + I Island and Queen Maud Land in Antarctica are external dependencies, but + those three entities do not form part of the kingdom. meaning: GAZ:00002699 Oman: text: Oman + description: A country in southwest Asia, on the southeast coast of the Arabian + Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia + on the west, and Yemen on the southwest. The coast is formed by the Arabian + Sea on the south and east, and the Gulf of Oman on the northeast. The country + also contains Madha, an exclave enclosed by the United Arab Emirates, and + Musandam, an exclave also separated by Emirati territory. Oman is divided + into four governorates (muhafazah) and five regions (mintaqat). The regions + are subdivided into provinces (wilayat). meaning: GAZ:00005283 Pakistan: text: Pakistan + description: A country in Middle East which lies on the Iranian Plateau and + some parts of South Asia. It is located in the region where South Asia converges + with Central Asia and the Middle East. It has a 1,046 km coastline along + the Arabian Sea in the south, and is bordered by Afghanistan and Iran in + the west, India in the east and China in the far northeast. Pakistan is + subdivided into four provinces and two territories. In addition, the portion + of Kashmir that is administered by the Pakistani government is divided into + two separate administrative units. The provinces are divided into a total + of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly + equivalent to counties). Tehsils may contain villages or municipalities. + There are over five thousand local governments in Pakistan. meaning: GAZ:00005246 Palau: text: Palau + description: A nation that consists of eight principal islands and more than + 250 smaller ones lying roughly 500 miles southeast of the Philippines. meaning: GAZ:00006905 Panama: text: Panama + description: The southernmost country of Central America. Situated on an isthmus, + some categorize it as a transcontinental nation connecting the north and + south part of America. It borders Costa Rica to the north-west, Colombia + to the south-east, the Caribbean Sea to the north and the Pacific Ocean + to the south. Panama's major divisions are nine provinces and five indigenous + territories (comarcas indigenas). The provincial borders have not changed + since they were determined at independence in 1903. The provinces are divided + into districts, which in turn are subdivided into sections called corregimientos. + Configurations of the corregimientos are changed periodically to accommodate + population changes as revealed in the census reports. meaning: GAZ:00002892 Papua New Guinea: text: Papua New Guinea + description: A country in Oceania that comprises the eastern half of the island + of New Guinea and its offshore islands in Melanesia (a region of the southwestern + Pacific Ocean north of Australia). meaning: GAZ:00003922 Paracel Islands: text: Paracel Islands + description: A group of small islands and reefs in the South China Sea, about + one-third of the way from Vietnam to the Philippines. meaning: GAZ:00010832 Paraguay: text: Paraguay + description: A landlocked country in South America. It lies on both banks + of the Paraguay River, bordering Argentina to the south and southwest, Brazil + to the east and northeast, and Bolivia to the northwest, and is located + in the very heart of South America. Paraguay consists of seventeen departments + and one capital district (distrito capital). Each department is divided + into districts. meaning: GAZ:00002933 Peru: text: Peru + description: A country in western South America. It is bordered on the north + by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, + on the south by Chile, and on the west by the Pacific Ocean. Peru is divided + into 25 regions and the province of Lima. These regions are subdivided into + provinces, which are composed of districts (provincias and distritos). There + are 195 provinces and 1833 districts in Peru. The Lima Province, located + in the central coast of the country, is unique in that it doesn't belong + to any of the twenty-five regions. The city of Lima, which is the nation's + capital, is located in this province. Callao is its own region, even though + it only contains one province, the Constitutional Province of Callao. meaning: GAZ:00002932 Philippines: text: Philippines + description: 'An archipelagic nation located in Southeast Asia. The Philippine + archipelago comprises 7,107 islands in the western Pacific Ocean, bordering + countries such as Indonesia, Malaysia, Palau and the Republic of China, + although it is the only Southeast Asian country to share no land borders + with its neighbors. The Philippines is divided into three island groups: + Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, + 136 cities, 1,494 municipalities and 41,995 barangays.' meaning: GAZ:00004525 Pitcairn Islands: text: Pitcairn Islands + description: A group of four islands in the southern Pacific Ocean. The Pitcairn + Islands form the southeasternmost extension of the geological archipelago + of the Tuamotus of French Polynesia. meaning: GAZ:00005867 Poland: text: Poland + description: A country in Central Europe. Poland is bordered by Germany to + the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus + and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a + Russian exclave, to the north. The administrative division of Poland since + 1999 has been based on three levels of subdivision. The territory of Poland + is divided into voivodeships (provinces); these are further divided into + powiats (counties), and these in turn are divided into gminas (communes + or municipalities). Major cities normally have the status of both gmina + and powiat. Poland currently has 16 voivodeships, 379 powiats (including + 65 cities with powiat status), and 2,478 gminas. meaning: GAZ:00002939 Portugal: text: Portugal + description: That part of the Portugese Republic that occupies the W part + of the Iberian Peninsula, and immediately adjacent islands. meaning: GAZ:00004126 Puerto Rico: text: Puerto Rico + description: A semi-autonomous territory composed of an archipelago in the + northeastern Caribbean, east of the Dominican Republic and west of the Virgin + Islands, approximately 2,000 km off the coast of Florida (the nearest of + the mainland United States). meaning: GAZ:00006935 Qatar: text: Qatar + description: 'An Arab emirate in Southwest Asia, occupying the small Qatar + Peninsula on the northeasterly coast of the larger Arabian Peninsula. It + is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds + the state. Qatar is divided into ten municipalities (Arabic: baladiyah), + which are further divided into zones (districts).' meaning: GAZ:00005286 Republic of the Congo: text: Republic of the Congo + description: A country in Central Africa. It is bordered by Gabon, Cameroon, + the Central African Republic, the Democratic Republic of the Congo, the + Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic + of the Congo is divided into 10 regions (regions) and one commune, the capital + Brazzaville. The regions are subdivided into forty-six districts. meaning: GAZ:00001088 Reunion: text: Reunion + description: An island, located in the Indian Ocean east of Madagascar, about + 200 km south west of Mauritius, the nearest island. meaning: GAZ:00003945 Romania: text: Romania + description: A country in Southeastern Europe. It shares a border with Hungary + and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, + and Bulgaria to the south. Romania has a stretch of sea coast along the + Black Sea. It is located roughly in the lower basin of the Danube and almost + all of the Danube Delta is located within its territory. Romania is divided + into forty-one counties (judete), as well as the municipality of Bucharest + (Bucuresti) - which is its own administrative unit. The country is further + subdivided into 319 cities and 2686 communes (rural localities). meaning: GAZ:00002951 Ross Sea: text: Ross Sea + description: A large embayment of the Southern Ocean, extending deeply into + Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck + on the east, at 158degW. meaning: GAZ:00023304 Russia: text: Russia + description: 'A transcontinental country extending over much of northern Eurasia. + Russia shares land borders with the following countries (counter-clockwise + from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania + (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, + Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation + comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais + (territories), 4 autonomous okrugs (autonomous districts), one autonomous + oblast, and two federal cities. The federal subjects are grouped into seven + federal districts. These subjects are divided into districts (raions), cities/towns + and urban-type settlements, and, at level 4, selsovets (rural councils), + towns and urban-type settlements under the jurisdiction of the district + and city districts.' meaning: GAZ:00002721 Rwanda: text: Rwanda + description: A small landlocked country in the Great Lakes region of east-central + Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo + and Tanzania. Rwanda is divided into five provinces (intara) and subdivided + into thirty districts (akarere). The districts are divided into sectors + (imirenge). meaning: GAZ:00001087 Saint Helena: text: Saint Helena + description: An island of volcanic origin and a British overseas territory + in the South Atlantic Ocean. meaning: GAZ:00000849 Saint Kitts and Nevis: text: Saint Kitts and Nevis + description: 'A federal two-island nation in the West Indies. Located in the + Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward + Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, + Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast + are Antigua and Barbuda, and to the southeast is the small uninhabited island + of Redonda, and the island of Montserrat. The federation of Saint Kitts + and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts + and five on Nevis.' meaning: GAZ:00006906 Saint Lucia: text: Saint Lucia + description: An island nation in the eastern Caribbean Sea on the boundary + with the Atlantic Ocean. meaning: GAZ:00006909 Saint Pierre and Miquelon: text: Saint Pierre and Miquelon + description: An Overseas Collectivity of France located in a group of small + islands in the North Atlantic Ocean, the main ones being Saint Pierre and + Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and + Miquelon became an overseas department in 1976, but its status changed to + that of an Overseas collectivity in 1985. meaning: GAZ:00003942 Saint Martin: text: Saint Martin + description: An overseas collectivity of France that came into being on 2007-02-22, + encompassing the northern parts of the island of Saint Martin and neighboring + islets. The southern part of the island, Sint Maarten, is part of the Netherlands + Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. meaning: GAZ:00005841 Saint Vincent and the Grenadines: text: Saint Vincent and the Grenadines + description: An island nation in the Lesser Antilles chain of the Caribbean + Sea. meaning: GAZ:02000565 Samoa: text: Samoa + description: A country governing the western part of the Samoan Islands archipelago + in the South Pacific Ocean. Samoa is made up of eleven itumalo (political + districts). meaning: GAZ:00006910 San Marino: text: San Marino + description: A country in the Apennine Mountains. It is a landlocked enclave, + completely surrounded by Italy. San Marino is an enclave in Italy, on the + border between the regioni of Emilia Romagna and Marche. Its topography + is dominated by the Apennines mountain range. San Marino is divided into + nine municipalities, known locally as Castelli (singular castello). meaning: GAZ:00003102 Sao Tome and Principe: text: Sao Tome and Principe + description: 'An island nation in the Gulf of Guinea, off the western equatorial + coast of Africa. It consists of two islands: Sao Tome and Principe, located + about 140 km apart and about 250 and 225 km respectively, off of the northwestern + coast of Gabon. Both islands are part of an extinct volcanic mountain range. + Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The + provinces are further divided into seven districts, six on Sao Tome and + one on Principe (with Principe having self-government since 1995-04-29).' meaning: GAZ:00006927 Saudi Arabia: text: Saudi Arabia + description: A country on the Arabian Peninsula. It is bordered by Jordan + on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, + and the United Arab Emirates on the east, Oman on the southeast, and Yemen + on the south. The Persian Gulf lies to the northeast and the Red Sea to + its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; + singular mintaqah). Each is then divided into Governorates. meaning: GAZ:00005279 Senegal: text: Senegal + description: A country south of the Senegal River in western Africa. Senegal + is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali + to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies + almost entirely within Senegal, surrounded on the north, east and south; + from its western coast Gambia's territory follows the Gambia River more + than 300 km inland. Dakar is the capital city of Senegal, located on the + Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided + into 11 regions and further subdivided into 34 Departements, 103 Arrondissements + (neither of which have administrative function) and by Collectivites Locales. meaning: GAZ:00000913 Serbia: text: Serbia + description: 'A landlocked country in Central and Southeastern Europe, covering + the southern part of the Pannonian Plain and the central part of the Balkan + Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria + to the east; Republic of Macedonia, Montenegro to the south; Croatia and + Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided + into 29 districts plus the City of Belgrade. The districts and the city + of Belgrade are further divided into municipalities. Serbia has two autonomous + provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), + and Vojvodina in the north (7 districts, 46 municipalities).' meaning: GAZ:00002957 Seychelles: text: Seychelles + description: An archipelagic island country in the Indian Ocean at the eastern + edge of the Somali Sea. It consists of 115 islands. meaning: GAZ:00006922 Sierra Leone: text: Sierra Leone + description: A country in West Africa. It is bordered by Guinea in the north + and east, Liberia in the southeast, and the Atlantic Ocean in the southwest + and west. The Republic of Sierra Leone is composed of 3 provinces and one + area called the Western Area; the provinces are further divided into 12 + districts. The Western Area is also divided into 2 districts. meaning: GAZ:00000914 Singapore: text: Singapore + description: An island nation located at the southern tip of the Malay Peninsula. + It lies 137 km north of the Equator, south of the Malaysian State of Johor + and north of Indonesia's Riau Islands. Singapore consists of 63 islands, + including mainland Singapore. There are two man-made connections to Johor, + Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in + the west. Since 2001-11-24, Singapore has had an administrative subdivision + into 5 districts. It is also divided into five Regions, urban planning subdivisions + with no administrative role. meaning: GAZ:00003923 Sint Maarten: text: Sint Maarten + description: One of five island areas (Eilandgebieden) of the Netherlands + Antilles, encompassing the southern half of the island of Saint Martin/Sint + Maarten. meaning: GAZ:00012579 Slovakia: text: Slovakia + description: A landlocked country in Central Europe. The Slovak Republic borders + the Czech Republic and Austria to the west, Poland to the north, Ukraine + to the east and Hungary to the south. The largest city is its capital, Bratislava. + Slovakia is subdivided into 8 kraje (singular - kraj, usually translated + as regions. The kraje are subdivided into many okresy (singular okres, usually + translated as districts). Slovakia currently has 79 districts. meaning: GAZ:00002956 Slovenia: text: Slovenia + description: A country in southern Central Europe bordering Italy to the west, + the Adriatic Sea to the southwest, Croatia to the south and east, Hungary + to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. + As of 2005-05 Slovenia is divided into 12 statistical regions for legal + and statistical purposes. Slovenia is divided into 210 local municipalities, + eleven of which have urban status. meaning: GAZ:00002955 Solomon Islands: text: Solomon Islands + description: A nation in Melanesia, east of Papua New Guinea, consisting of + nearly one thousand islands. Together they cover a land mass of 28,400 km2. + The capital is Honiara, located on the island of Guadalcanal. meaning: GAZ:00005275 Somalia: text: Somalia + description: A country located in the Horn of Africa. It is bordered by Djibouti + to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on + its north, the Indian Ocean at its east, and Ethiopia to the west. Prior + to the civil war, Somalia was divided into eighteen regions (gobollada, + singular gobol), which were in turn subdivided into districts. On a de facto + basis, northern Somalia is now divided up among the quasi-independent states + of Puntland, Somaliland, Galmudug and Maakhir. meaning: GAZ:00001104 South Africa: text: South Africa + description: 'A country located at the southern tip of Africa. It borders + the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, + Swaziland, and Lesotho, an independent enclave surrounded by South African + territory. It is divided into nine provinces which are further subdivided + into 52 districts: 6 metropolitan and 46 district municipalities. The 46 + district municipalities are further subdivided into 231 local municipalities. + The district municipalities also contain 20 district management areas (mostly + game parks) that are directly governed by the district municipalities. The + six metropolitan municipalities perform the functions of both district and + local municipalities.' meaning: GAZ:00001094 South Georgia and the South Sandwich Islands: text: South Georgia and the South Sandwich Islands + description: A British overseas territory in the southern Atlantic Ocean. + It iconsists of South Georgia and the Sandwich Islands, some 640 km to the + SE. meaning: GAZ:00003990 South Korea: text: South Korea + description: A republic in East Asia, occupying the southern half of the Korean + Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous + province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 + special city (teukbyeolsi). These are further subdivided into a variety + of smaller entities, including cities (si), counties (gun), districts (gu), + towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). meaning: GAZ:00002802 South Sudan: text: South Sudan + description: A state located in Africa with Juba as its capital city. It's + bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic + of the Congo to the south, and the Central African Republic to the west + and Sudan to the North. Southern Sudan includes the vast swamp region of + the Sudd formed by the White Nile, locally called the Bahr el Jebel. meaning: GAZ:00233439 Spain: text: Spain + description: That part of the Kingdom of Spain that occupies the Iberian Peninsula + plus the Balaeric Islands. The Spanish mainland is bordered to the south + and east almost entirely by the Mediterranean Sea (except for a small land + boundary with Gibraltar); to the north by France, Andorra, and the Bay of + Biscay; and to the west by the Atlantic Ocean and Portugal. meaning: GAZ:00000591 Spratly Islands: text: Spratly Islands + description: A group of >100 islands located in the Southeastern Asian group + of reefs and islands in the South China Sea, about two-thirds of the way + from southern Vietnam to the southern Philippines. meaning: GAZ:00010831 Sri Lanka: text: Sri Lanka + description: An island nation in South Asia, located about 31 km off the southern + coast of India. Sri Lanka is divided into 9 provinces and 25 districts. + Districts are divided into Divisional Secretariats. meaning: GAZ:00003924 State of Palestine: text: State of Palestine + description: The territory under the administration of the Palestine National + Authority, as established by the Oslo Accords. The PNA divides the Palestinian + territories into 16 governorates. meaning: GAZ:00002475 Sudan: text: Sudan + description: A country in North Africa. It is bordered by Egypt to the north, + the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and + Uganda to the southeast, Democratic Republic of the Congo and the Central + African Republic to the southwest, Chad to the west and Libya to the northwest. + Sudan is divided into twenty-six states (wilayat, singular wilayah) which + in turn are subdivided into 133 districts. meaning: GAZ:00000560 Suriname: text: Suriname + description: A country in northern South America. It is situated between French + Guiana to the east and Guyana to the west. The southern border is shared + with Brazil and the northern border is the Atlantic coast. The southernmost + border with French Guiana is disputed along the Marowijne river. Suriname + is divided into 10 districts, each of which is divided into Ressorten. meaning: GAZ:00002525 Svalbard: text: Svalbard + description: An archipelago of continental islands lying in the Arctic Ocean + north of mainland Europe, about midway between Norway and the North Pole. meaning: GAZ:00005396 Swaziland: text: Swaziland + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). meaning: GAZ:00001099 Sweden: text: Sweden + description: A Nordic country on the Scandinavian Peninsula in Northern Europe. + It has borders with Norway (west and north) and Finland (northeast). Sweden + is a unitary state, currently divided into twenty-one counties (lan). Each + county further divides into a number of municipalities or kommuner, with + a total of 290 municipalities in 2004. meaning: GAZ:00002729 Switzerland: text: Switzerland + description: 'A federal republic in Europe. Switzerland is bordered by Germany, + France, Italy, Austria and Liechtenstein. The Swiss Confederation consists + of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within + Switzerland there are two enclaves: Busingen belongs to Germany, Campione + d''Italia belongs to Italy.' meaning: GAZ:00002941 Syria: text: Syria + description: 'A country in Southwest Asia, bordering Lebanon, the Mediterranean + Sea and the island of Cyprus to the west, Israel to the southwest, Jordan + to the south, Iraq to the east, and Turkey to the north. Syria has fourteen + governorates, or muhafazat (singular: muhafazah). The governorates are divided + into sixty districts, or manatiq (singular: mintaqah), which are further + divided into sub-districts, or nawahi (singular: nahia).' meaning: GAZ:00002474 Taiwan: text: Taiwan + description: A state in East Asia with de facto rule of the island of Tawain + and adjacent territory. The Republic of China currently administers two + historical provinces of China (one completely and a small part of another + one) and centrally administers two direct-controlled municipalities. meaning: GAZ:00005341 Tajikistan: text: Tajikistan + description: A mountainous landlocked country in Central Asia. Afghanistan + borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and + People's Republic of China to the east. Tajikistan consists of 4 administrative + divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous + province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican + Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly + known as Karotegin Province). Each region is divided into several districts + (nohiya or raion). meaning: GAZ:00006912 Tanzania: text: Tanzania + description: A country in East Africa bordered by Kenya and Uganda on the + north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, + and Zambia, Malawi and Mozambique on the south. To the east it borders the + Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on + the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight + districts (wilaya), each with at least one council, have been created to + further increase local authority; the councils are also known as local government + authorities. Currently there are 114 councils operating in 99 districts; + 22 are urban and 92 are rural. The 22 urban units are further classified + as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, + Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) + or town councils (the remaining eleven communities). meaning: GAZ:00001103 Thailand: text: Thailand + description: 'A country in Southeast Asia. To its east lie Laos and Cambodia; + to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman + Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided + into 75 provinces (changwat), which are gathered into 5 groups of provinces + by location. There are also 2 special governed districts: the capital Bangkok + (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial + level and thus often counted as a 76th province.' meaning: GAZ:00003744 Timor-Leste: text: Timor-Leste + description: A country in Southeast Asia. It comprises the eastern half of + the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, + an exclave on the northwestern side of the island, within Indonesian West + Timor. The small country of 15,410 km2 is located about 640 km northwest + of Darwin, Australia. East Timor is divided into thirteen administrative + districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, + villages and hamlets. meaning: GAZ:00006913 Togo: text: Togo + description: A country in West Africa bordering Ghana in the west, Benin in + the east and Burkina Faso in the north. In the south, it has a short Gulf + of Guinea coast, on which the capital Lome is located. meaning: GAZ:00000915 Tokelau: text: Tokelau + description: 'A dependent territory of New Zealand in the southern Pacific + Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and + Fakaofo. They have a combined land area of 10 km2 (4 sq mi).' meaning: GAZ:00260188 Tonga: text: Tonga + description: A Polynesian country, and also an archipelago comprising 169 + islands, of which 36 are inhabited. The archipelago's total surface area + is about 750 square kilometres (290 sq mi) scattered over 700,000 square + kilometres (270,000 sq mi) of the southern Pacific Ocean. meaning: GAZ:00006916 Trinidad and Tobago: text: Trinidad and Tobago + description: An archipelagic state in the southern Caribbean, lying northeast + of the South American nation of Venezuela and south of Grenada in the Lesser + Antilles. It also shares maritime boundaries with Barbados to the northeast + and Guyana to the southeast. The country covers an area of 5,128 km2and + consists of two main islands, Trinidad and Tobago, and 21 smaller islands. meaning: GAZ:00003767 Tromelin Island: text: Tromelin Island + description: A low, flat 0.8 km2 island in the Indian Ocean, about 350 km + east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 + m long and 700 m wide, surrounded by coral reefs. The island is 7 m high + at its highest point. meaning: GAZ:00005812 Tunisia: text: Tunisia + description: A country situated on the Mediterranean coast of North Africa. + It is bordered by Algeria to the west and Libya to the southeast. Tunisia + is subdivided into 24 governorates, divided into 262 "delegations" or "districts" + (mutamadiyat), and further subdivided into municipalities (shaykhats). meaning: GAZ:00000562 Turkey: text: Turkey + description: 'A Eurasian country that stretches across the Anatolian peninsula + in western Asia and Thrace (Rumelia) in the Balkan region of southeastern + Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece + to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave + of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. + The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago + are to the west; and the Black Sea is to the north. Separating Anatolia + and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus + and the Dardanelles), which are commonly reckoned to delineate the border + between Asia and Europe, thereby making Turkey transcontinental. The territory + of Turkey is subdivided into 81 provinces for administrative purposes. The + provinces are organized into 7 regions for census purposes; however, they + do not represent an administrative structure. Each province is divided into + districts, for a total of 923 districts.' meaning: GAZ:00000558 Turkmenistan: text: Turkmenistan + description: A country in Central Asia. It is bordered by Afghanistan to the + southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan + to the northwest, and the Caspian Sea to the west. It was a constituent + republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan + is divided into five provinces or welayatlar (singular - welayat) and one + independent city. meaning: GAZ:00005018 Turks and Caicos Islands: text: Turks and Caicos Islands + description: A British Overseas Territory consisting of two groups of tropical + islands in the West Indies. The Turks and Caicos Islands are divided into + six administrative districts (two in the Turks Islands and four in the Caicos + Islands. meaning: GAZ:00003955 Tuvalu: text: Tuvalu + description: A Polynesian island nation located in the Pacific Ocean midway + between Hawaii and Australia. meaning: GAZ:00009715 United States of America: text: United States of America + description: A federal constitutional republic comprising fifty states and + a federal district. The country is situated mostly in central North America, + where its forty-eight contiguous states and Washington, DC, the capital + district, lie between the Pacific and Atlantic Oceans, bordered by Canada + to the north and Mexico to the south. The State of Alaska is in the northwest + of the continent, with Canada to its east and Russia to the west across + the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United + States also possesses several territories, or insular areas, that are scattered + around the Caribbean and Pacific. The states are divided into smaller administrative + regions, called counties in most states, exceptions being Alaska (parts + of the state are organized into subdivisions called boroughs; the rest of + the state's territory that is not included in any borough is divided into + "census areas"), and Louisiana (which is divided into county-equivalents + that are called parishes). There are also independent cities which are within + particular states but not part of any particular county or consolidated + city-counties. Another type of organization is where the city and county + are unified and function as an independent city. There are thirty-nine independent + cities in Virginia and other independent cities or city-counties are San + Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, + Colorado and Carson City, Nevada. Counties can include a number of cities, + towns, villages, or hamlets, or sometimes just a part of a city. Counties + have varying degrees of political and legal significance, but they are always + administrative divisions of the state. Counties in many states are further + subdivided into townships, which, by definition, are administrative divisions + of a county. In some states, such as Michigan, a township can file a charter + with the state government, making itself into a "charter township", which + is a type of mixed municipal and township status (giving the township some + of the rights of a city without all of the responsibilities), much in the + way a metropolitan municipality is a mixed municipality and county. meaning: GAZ:00002459 Uganda: text: Uganda + description: 'A landlocked country in East Africa, bordered on the east by + Kenya, the north by Sudan, on the west by the Democratic Republic of the + Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern + part of the country includes a substantial portion of Lake Victoria, within + which it shares borders with Kenya and Tanzania. Uganda is divided into + 80 districts, spread across four administrative regions: Northern, Eastern, + Central and Western. The districts are subdivided into counties.' meaning: GAZ:00001102 Ukraine: text: Ukraine + description: A country in Eastern Europe. It borders Russia to the east, Belarus + to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova + to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine + is subdivided into twenty-four oblasts (provinces) and one autonomous republic + (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, + and Sevastopol, both have a special legal status. The 24 oblasts and Crimea + are subdivided into 490 raions (districts), or second-level administrative + units. meaning: GAZ:00002724 United Arab Emirates: text: United Arab Emirates + description: A Middle Eastern federation of seven states situated in the southeast + of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering + Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, + Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. meaning: GAZ:00005282 United Kingdom: text: United Kingdom + description: A sovereign island country located off the northwestern coast + of mainland Europe comprising of the four constituent countries; England, + Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, + the northeast part of the island of Ireland and many small islands. Apart + from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North + Sea, the English Channel and the Irish Sea. The largest island, Great Britain, + is linked to France by the Channel Tunnel. meaning: GAZ:00002637 Uruguay: text: Uruguay + description: A country located in the southeastern part of South America. + It is bordered by Brazil to the north, by Argentina across the bank of both + the Uruguay River to the west and the estuary of Rio de la Plata to the + southwest, and the South Atlantic Ocean to the southeast. Uraguay consists + of 19 departments (departamentos, singular - departamento). meaning: GAZ:00002930 Uzbekistan: text: Uzbekistan + description: A doubly landlocked country in Central Asia, formerly part of + the Soviet Union. It shares borders with Kazakhstan to the west and to the + north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan + to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one + autonomous republic (respublika and one independent city (shahar). meaning: GAZ:00004979 Vanuatu: text: Vanuatu + description: An island country located in the South Pacific Ocean. The archipelago, + which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern + Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New + Guinea, southeast of the Solomon Islands, and west of Fiji. meaning: GAZ:00006918 Venezuela: text: Venezuela + description: A country on the northern coast of South America. The country + comprises a continental mainland and numerous islands located off the Venezuelan + coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses + borders with Guyana to the east, Brazil to the south, and Colombia to the + west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, + Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just + north, off the Venezuelan coast. Venezuela is divided into twenty-three + states (Estados), a capital district (distrito capital) corresponding to + the city of Caracas, the Federal Dependencies (Dependencias Federales, a + special territory), and Guayana Esequiba (claimed in a border dispute with + Guyana). Venezuela is further subdivided into 335 municipalities (municipios); + these are subdivided into over one thousand parishes (parroquias). meaning: GAZ:00002931 Viet Nam: text: Viet Nam + description: The easternmost country on the Indochina Peninsula in Southeast + Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, + alongside China, Laos, and Cambodia. meaning: GAZ:00003756 Virgin Islands: text: Virgin Islands + description: A group of islands in the Caribbean that are an insular area + of the United States. The islands are geographically part of the Virgin + Islands archipelago and are located in the Leeward Islands of the Lesser + Antilles. The US Virgin Islands are an organized, unincorporated United + States territory. The US Virgin Islands are administratively divided into + two districts and subdivided into 20 sub-districts. meaning: GAZ:00003959 Wake Island: text: Wake Island + description: A coral atoll (despite its name) having a coastline of 19 km + in the North Pacific Ocean, located about two-thirds of the way from Honolulu + (3,700 km west) to Guam (2,430 km east). meaning: GAZ:00007111 Wallis and Futuna: text: Wallis and Futuna + description: A Polynesian French island territory (but not part of, or even + contiguous with, French Polynesia) in the South Pacific between Fiji and + Samoa. It is made up of three main volcanic tropical islands and a number + of tiny islets. meaning: GAZ:00007191 West Bank: text: West Bank + description: A landlocked territory near the Mediterranean coast of Western + Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the + south, west and north.[2] Under Israeli occupation since 1967, the area + is split into 167 Palestinian "islands" under partial Palestinian National + Authority civil rule, and 230 Israeli settlements into which Israeli law + is "pipelined". meaning: GAZ:00009572 Western Sahara: text: Western Sahara + description: A territory of northwestern Africa, bordered by Morocco to the + north, Algeria in the northeast, Mauritania to the east and south, and the + Atlantic Ocean on the west. Western Sahara is administratively divided into + four regions. meaning: GAZ:00000564 Yemen: text: Yemen + description: A country located on the Arabian Peninsula in Southwest Asia. + Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, + the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's + territory includes over 200 islands, the largest of which is Socotra, about + 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen + is divided into twenty governorates (muhafazah) and one municipality. The + population of each governorate is listed in the table below. The governorates + of Yemen are divided into 333 districts (muderiah). The districts are subdivided + into 2,210 sub-districts, and then into 38,284 villages (as of 2001). meaning: GAZ:00005284 Zambia: text: Zambia + description: A landlocked country in Southern Africa. The neighbouring countries + are the Democratic Republic of the Congo to the north, Tanzania to the north-east, + Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, + and Angola to the west. The capital city is Lusaka. Zambia is divided into + nine provinces. Each province is subdivided into several districts with + a total of 73 districts. meaning: GAZ:00001107 Zimbabwe: text: Zimbabwe + description: A landlocked country in the southern part of the continent of + Africa, between the Zambezi and Limpopo rivers. It is bordered by South + Africa to the south, Botswana to the southwest, Zambia to the northwest, + and Mozambique to the east. Zimbabwe is divided into eight provinces and + two cities with provincial status. The provinces are subdivided into 59 + districts and 1,200 municipalities. meaning: GAZ:00001106 - geo_loc_name (country) international menu: - name: geo_loc_name (country) international menu + GeoLocNameCountryInternationalMenu: + name: GeoLocNameCountryInternationalMenu + title: geo_loc_name (country) international menu permissible_values: Afghanistan [GAZ:00006882]: text: Afghanistan [GAZ:00006882] + description: A landlocked country that is located approximately in the center + of Asia. It is bordered by Pakistan in the south and east Iran in the west, + Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far + northeast. Afghanistan is administratively divided into thirty-four (34) + provinces (welayats). Each province is then divided into many provincial + districts, and each district normally covers a city or several townships. + [ url:http://en.wikipedia.org/wiki/Afghanistan ] meaning: GAZ:00006882 Albania [GAZ:00002953]: text: Albania [GAZ:00002953] + description: 'A country in South Eastern Europe. Albania is bordered by Greece + to the south-east, Montenegro to the north, Kosovo to the northeast, and + the Republic of Macedonia to the east. It has a coast on the Adriatic Sea + to the west, and on the Ionian Sea to the southwest. From the Strait of + Otranto, Albania is less than 100 km from Italy. Albania is divided into + 12 administrative divisions called (Albanian: official qark/qarku, but often + prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities + (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania + ]' meaning: GAZ:00002953 Algeria [GAZ:00000563]: text: Algeria [GAZ:00000563] + description: A country in North Africa. It is bordered by Tunisia in the northeast, + Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, + a few km of the Western Sahara in the west, Morocco in the northwest, and + the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), + 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). + [ url:http://en.wikipedia.org/wiki/Algeria ] meaning: GAZ:00000563 American Samoa [GAZ:00003957]: text: American Samoa [GAZ:00003957] + description: An unincorporated territory of the United States located in the + South Pacific Ocean, southeast of the sovereign State of Samoa. The main + (largest and most populous) island is Tutuila, with the Manu'a Islands, + Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa + ] meaning: GAZ:00003957 Andorra [GAZ:00002948]: text: Andorra [GAZ:00002948] + description: 'A small landlocked country in western Europe, located in the + eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. + Andorra consists of seven communities known as parishes (Catalan: parroquies, + singular - parroquia). Until relatively recently, it had only six parishes; + the seventh, Escaldes-Engordany, was created in 1978. Some parishes have + a further territorial subdivision. Ordino, La Massana and Sant Julia de + Loria are subdivided into quarts (quarters), while Canillo is subdivided + into veinats (neighborhoods). Those mostly coincide with villages, which + are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]' meaning: GAZ:00002948 Angola [GAZ:00001095]: text: Angola [GAZ:00001095] + description: A country in south-central Africa bordering Namibia to the south, + Democratic Republic of the Congo to the north, and Zambia to the east, and + with a west coast along the Atlantic Ocean. The exclave province Cabinda + has a border with the Republic of the Congo and the Democratic Republic + of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] meaning: GAZ:00001095 Anguilla [GAZ:00009159]: text: Anguilla [GAZ:00009159] + description: A British overseas territory in the Caribbean, one of the most + northerly of the Leeward Islands in the Lesser Antilles. It consists of + the main island of Anguilla itself, approximately 26 km long by 5 km wide + at its widest point, together with a number of much smaller islands and + cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila + ] meaning: GAZ:00009159 Antarctica [GAZ:00000462]: text: Antarctica [GAZ:00000462] + description: The Earth's southernmost continent, overlying the South Pole. + It is situated in the southern hemisphere, almost entirely south of the + Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica + ] meaning: GAZ:00000462 Antigua and Barbuda [GAZ:00006883]: text: Antigua and Barbuda [GAZ:00006883] + description: An island nation located on the eastern boundary of the Caribbean + Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda + ] meaning: GAZ:00006883 Argentina [GAZ:00002928]: text: Argentina [GAZ:00002928] + description: 'A South American country, constituted as a federation of twenty-three + provinces and an autonomous city. It is bordered by Paraguay and Bolivia + in the north, Brazil and Uruguay in the northeast, and Chile in the west + and south. The country claims the British controlled territories of the + Falkland Islands and South Georgia and the South Sandwich Islands. Argentina + also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping + other claims made by Chile and the United Kingdom. Argentina is subdivided + into twenty-three provinces (Spanish: provincias, singular provincia) and + one federal district (Capital de la Republica or Capital de la Nacion, informally + the Capital Federal). The federal district and the provinces have their + own constitutions, but exist under a federal system. Provinces are then + divided into departments (Spanish: departamentos, singular departamento), + except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina + ]' meaning: GAZ:00002928 Armenia [GAZ:00004094]: text: Armenia [GAZ:00004094] + description: A landlocked mountainous country in Eurasia between the Black + Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the + west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan + exclave of Azerbaijan to the south. A transcontinental country at the juncture + of Eastern Europe and Western Asia. A former republic of the Soviet Union. + Armenia is divided into ten marzes (provinces, singular marz), with the + city (kaghak) of Yerevan having special administrative status as the country's + capital. [ url:http://en.wikipedia.org/wiki/Armenia ] meaning: GAZ:00004094 Aruba [GAZ:00004025]: text: Aruba [GAZ:00004025] + description: An autonomous region within the Kingdom of the Netherlands, Aruba + has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba + ] meaning: GAZ:00004025 Ashmore and Cartier Islands [GAZ:00005901]: text: Ashmore and Cartier Islands [GAZ:00005901] + description: A Territory of Australia that includes two groups of small low-lying + uninhabited tropical islands in the Indian Ocean situated on the edge of + the continental shelf north-west of Australia and south of the Indonesian + island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands + ] meaning: GAZ:00005901 Australia [GAZ:00000463]: text: Australia [GAZ:00000463] + description: A country in the southern hemisphere comprising the mainland + of the world's smallest continent, the major island of Tasmania, and a number + of other islands in the Indian and Pacific Oceans. The neighbouring countries + are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon + Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to + the south-east. Australia has six states, two major mainland territories, + and other minor territories. meaning: GAZ:00000463 Austria [GAZ:00002942]: text: Austria [GAZ:00002942] + description: A landlocked country in Central Europe. It borders both Germany + and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia + and Italy to the south, and Switzerland and Liechtenstein to the west. The + capital is the city of Vienna on the Danube River. Austria is divided into + nine states (Bundeslander). These states are then divided into districts + (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities + (Gemeinden). Cities have the competencies otherwise granted to both districts + and municipalities. meaning: GAZ:00002942 Azerbaijan [GAZ:00004941]: text: Azerbaijan [GAZ:00004941] + description: A country in the he South Caucasus region of Eurasia, it is bounded + by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, + Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan + is bordered by Armenia to the north and east, Iran to the south and west, + and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts + in Azerbaijan's southwest, have been controlled by Armenia since the end + of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons + 11 city districts (saharlar), and one autonomous republic (muxtar respublika). meaning: GAZ:00004941 Bahamas [GAZ:00002733]: text: Bahamas [GAZ:00002733] + description: A country consisting of two thousand cays and seven hundred islands + that form an archipelago. It is located in the Atlantic Ocean, southeast + of Florida and the United States, north of Cuba, the island of Hispanola + and the Caribbean, and northwest of the British overseas territory of the + Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, + whose affairs are handled directly by the central government. meaning: GAZ:00002733 Bahrain [GAZ:00005281]: text: Bahrain [GAZ:00005281] + description: A borderless island country in the Persian Gulf. Saudi Arabia + lies to the west and is connected to Bahrain by the King Fahd Causeway, + and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into + five governorates. meaning: GAZ:00005281 Baker Island [GAZ:00007117]: text: Baker Island [GAZ:00007117] + description: An uninhabited atoll located just north of the equator in the + central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island + is an unincorporated and unorganized territory of the US. meaning: GAZ:00007117 Bangladesh [GAZ:00003750]: text: Bangladesh [GAZ:00003750] + description: A country in South Asia. It is bordered by India on all sides + except for a small border with Myanmar to the far southeast and by the Bay + of Bengal to the south. Bangladesh is divided into six administrative divisions. + Divisions are subdivided into districts (zila). There are 64 districts in + Bangladesh, each further subdivided into upazila (subdistricts) or thana + ("police stations"). meaning: GAZ:00003750 Barbados [GAZ:00001251]: text: Barbados [GAZ:00001251] + description: "An island country in the Lesser Antilles of the West Indies,\ + \ in the Caribbean region of the Americas, and the most easterly of the\ + \ Caribbean Islands. It is 34 kilometres (21 miles) in length and up to\ + \ 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is\ + \ in the western part of the North Atlantic, 100 km (62 mi) east of the\ + \ Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards,\ + \ part of the Lesser Antilles, at roughly 13\xB0N of the equator. It is\ + \ about 168 km (104 mi) east of both the countries of Saint Lucia and Saint\ + \ Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique\ + \ and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside\ + \ the principal Atlantic hurricane belt. Its capital and largest city is\ + \ Bridgetown." meaning: GAZ:00001251 Bassas da India [GAZ:00005810]: text: Bassas da India [GAZ:00005810] + description: A roughly circular atoll about 10 km in diameter, which corresponds + to a total size (including lagoon) of 80 km2. It is located in the southern + Mozambique Channel, about half-way between Madagascar (which is 385 km to + the east) and Mozambique, and 110 km northwest of Europa Island. It rises + steeply from the seabed 3000 m below. meaning: GAZ:00005810 Belarus [GAZ:00006886]: text: Belarus [GAZ:00006886] + description: A landlocked country in Eastern Europe, that borders Russia to + the north and east, Ukraine to the south, Poland to the west, and Lithuania + and Latvia to the north. Its capital is Minsk. Belarus is divided into six + voblasts, or provinces. Voblasts are further subdivided into raions (commonly + translated as districts or regions). As of 2002, there are six voblasts, + 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special + status, due to the city serving as the national capital. meaning: GAZ:00006886 Belgium [GAZ:00002938]: text: Belgium [GAZ:00002938] + description: A country in northwest Europe. Belgium shares borders with France + (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 + km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each + comprise five provinces; the third region, Brussels-Capital Region, is not + a province, nor does it contain any Together, these comprise 589 municipalities, + which in general consist of several sub-municipalities (which were independent + municipalities before the municipal merger operation mainly in 1977). meaning: GAZ:00002938 Belize [GAZ:00002934]: text: Belize [GAZ:00002934] + description: A country in Central America. It is the only officially English + speaking country in the region. Belize was a British colony for more than + a century and was known as British Honduras until 1973. It became an independent + nation within The Commonwealth in 1981. Belize is divided into 6 districts, + which are further divided into 31 constituencies. meaning: GAZ:00002934 Benin [GAZ:00000904]: text: Benin [GAZ:00000904] + description: A country in Western Africa. It borders Togo to the west, Nigeria + to the east and Burkina Faso and Niger to the north; its short coastline + to the south leads to the Bight of Benin. Its capital is Porto Novo, but + the seat of government is Cotonou. Benin is divided into 12 departments + and subdivided into 77 communes. meaning: GAZ:00000904 Bermuda [GAZ:00001264]: text: Bermuda [GAZ:00001264] + description: A British overseas territory in the North Atlantic Ocean. Located + off the east coast of the United States, it is situated around 1770 km NE + of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately + 138 islands. meaning: GAZ:00001264 Bhutan [GAZ:00003920]: text: Bhutan [GAZ:00003920] + description: A landlocked nation in South Asia. It is located amidst the eastern + end of the Himalaya Mountains and is bordered to the south, east and west + by India and to the north by Tibet. Bhutan is separated from Nepal by the + Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative + zones). Each dzongdey is further divided into dzongkhag (districts). There + are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into + subdistricts known as dungkhag. At the basic level, groups of villages form + a constituency called gewog. meaning: GAZ:00003920 Bolivia [GAZ:00002511]: text: Bolivia [GAZ:00002511] + description: 'A landlocked country in central South America. It is bordered + by Brazil on the north and east, Paraguay and Argentina on the south, and + Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: + departamentos). Each of the departments is subdivided into provinces (provincias), + which are further subdivided into municipalities (municipios).' meaning: GAZ:00002511 Borneo [GAZ:00025355]: text: Borneo [GAZ:00025355] + description: 'An island at the grographic centre of Maritime Southeast Adia, + in relation to major Indonesian islands, it is located north of Java, west + of Sulawesi, and east of Sumatra. It is the third-largest island in the + world and the larest in Asia. The island is politically divided among three + countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] + Approximately 73% of the island is Indonesian territory. In the north, the + East Malaysian states of Sabah and Sarawak make up about 26% of the island. + Additionally, the Malaysian federal territory of Labuan is situated on a + small island just off the coast of Borneo. The sovereign state of Brunei, + located on the north coast, comprises about 1% of Borneo''s land area. A + little more than half of the island is in the Northern Hemisphere, including + Brunei and the Malaysian portion, while the Indonesian portion spans the + Northern and Southern hemispheres.' meaning: GAZ:00025355 Bosnia and Herzegovina [GAZ:00006887]: text: Bosnia and Herzegovina [GAZ:00006887] + description: A country on the Balkan peninsula of Southern Europe. Bordered + by Croatia to the north, west and south, Serbia to the east, and Montenegro + to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 + km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided + into three political regions of which one, the Brcko District is part of + the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. + All three have an equal constitutional status on the whole territory of + Bosnia and Herzegovina. meaning: GAZ:00006887 Botswana [GAZ:00001097]: text: Botswana [GAZ:00001097] + description: A landlocked nation in Southern Africa. It is bordered by South + Africa to the south and southeast, Namibia to the west, Zambia to the north, + and Zimbabwe to the northeast. Botswana is divided into nine districts, + which are subdivided into a total twenty-eight subdistricts. meaning: GAZ:00001097 Bouvet Island [GAZ:00001453]: text: Bouvet Island [GAZ:00001453] + description: A sub-antarctic volcanic island in the South Atlantic Ocean, + south-southwest of the Cape of Good Hope (South Africa). It is a dependent + area of Norway and is not subject to the Antarctic Treaty, as it is north + of the latitude south of which claims are suspended. meaning: GAZ:00001453 Brazil [GAZ:00002828]: text: Brazil [GAZ:00002828] + description: 'A country in South America. Bordered by the Atlantic Ocean and + by Venezuela, Suriname, Guyana and the department of French Guiana to the + north, Colombia to the northwest, Bolivia and Peru to the west, Argentina + and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six + states (estados) and one federal district (Distrito Federal). The states + are subdivided into municipalities. For statistical purposes, the States + are grouped into five main regions: North, Northeast, Central-West, Southeast + and South.' meaning: GAZ:00002828 British Virgin Islands [GAZ:00003961]: text: British Virgin Islands [GAZ:00003961] + description: A British overseas territory, located in the Caribbean to the + east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, + the remaining islands constituting the US Virgin Islands. The British Virgin + Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and + Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately + fifteen of the islands are inhabited. meaning: GAZ:00003961 Brunei [GAZ:00003901]: text: Brunei [GAZ:00003901] + description: A country located on the north coast of the island of Borneo, + in Southeast Asia. Apart from its coastline with the South China Sea it + is completely surrounded by the State of Sarawak, Malaysia, and in fact + it is separated into two parts by Limbang, which is part of Sarawak. Brunei + is divided into four districts (daerah), the districts are subdivided into + thirty-eight mukims, which are then divided into kampong (villages). meaning: GAZ:00003901 Bulgaria [GAZ:00002950]: text: Bulgaria [GAZ:00002950] + description: A country in Southeastern Europe, borders five other countries; + Romania to the north (mostly along the Danube), Serbia and the Republic + of Macedonia to the west, and Greece and Turkey to the south. The Black + Sea defines the extent of the country to the east. Since 1999, it has consisted + of twenty-eight provinces. The provinces subdivide into 264 municipalities. meaning: GAZ:00002950 Burkina Faso [GAZ:00000905]: text: Burkina Faso [GAZ:00000905] + description: 'A landlocked nation in West Africa. It is surrounded by six + countries: Mali to the north, Niger to the east, Benin to the south east, + Togo and Ghana to the south, and Cote d''Ivoire to the south west. Burkina + Faso is divided into thirteen regions, forty-five provinces, and 301 departments + (communes).' meaning: GAZ:00000905 Burundi [GAZ:00001090]: text: Burundi [GAZ:00001090] + description: A small country in the Great Lakes region of Africa. It is bordered + by Rwanda on the north, Tanzania on the south and east, and the Democratic + Republic of the Congo on the west. Although the country is landlocked, much + of its western border is adjacent to Lake Tanganyika. Burundi is divided + into 17 provinces, 117 communes, and 2,638 collines. meaning: GAZ:00001090 Cambodia [GAZ:00006888]: text: Cambodia [GAZ:00006888] + description: A country in Southeast Asia. The country borders Thailand to + its west and northwest, Laos to its northeast, and Vietnam to its east and + southeast. In the south it faces the Gulf of Thailand. meaning: GAZ:00006888 Cameroon [GAZ:00001093]: text: Cameroon [GAZ:00001093] + description: A country of central and western Africa. It borders Nigeria to + the west; Chad to the northeast; the Central African Republic to the east; + and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. + Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea + and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces + and 58 divisions or departments. The divisions are further sub-divided into + sub-divisions (arrondissements) and districts. meaning: GAZ:00001093 Canada [GAZ:00002560]: text: Canada [GAZ:00002560] + description: A country occupying most of northern North America, extending + from the Atlantic Ocean in the east to the Pacific Ocean in the west and + northward into the Arctic Ocean. Canada is a federation composed of ten + provinces and three territories; in turn, these may be grouped into regions. + Western Canada consists of British Columbia and the three Prairie provinces + (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec + and Ontario. Atlantic Canada consists of the three Maritime provinces (New + Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland + and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada + together. Three territories (Yukon, Northwest Territories, and Nunavut) + make up Northern Canada. meaning: GAZ:00002560 Cape Verde [GAZ:00001227]: text: Cape Verde [GAZ:00001227] + description: A republic located on an archipelago in the Macaronesia ecoregion + of the North Atlantic Ocean, off the western coast of Africa. Cape Verde + is divided into 22 municipalities (concelhos), and subdivided into 32 parishes + (freguesias). meaning: GAZ:00001227 Cayman Islands [GAZ:00003986]: text: Cayman Islands [GAZ:00003986] + description: A British overseas territory located in the western Caribbean + Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. + The Cayman Islands are divided into seven districts. meaning: GAZ:00003986 Central African Republic [GAZ:00001089]: text: Central African Republic [GAZ:00001089] + description: A landlocked country in Central Africa. It borders Chad in the + north, Sudan in the east, the Republic of the Congo and the Democratic Republic + of the Congo in the south, and Cameroon in the west. The Central African + Republic is divided into 14 administrative prefectures (prefectures), along + with 2 economic prefectures (prefectures economiques) and one autonomous + commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). meaning: GAZ:00001089 Chad [GAZ:00000586]: text: Chad [GAZ:00000586] + description: A landlocked country in central Africa. It is bordered by Libya + to the north, Sudan to the east, the Central African Republic to the south, + Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided + into 18 regions. The departments are divided into 200 sub-prefectures, which + are in turn composed of 446 cantons. This is due to change. meaning: GAZ:00000586 Chile [GAZ:00002825]: text: Chile [GAZ:00002825] + description: 'A country in South America occupying a long and narrow coastal + strip wedged between the Andes mountains and the Pacific Ocean. The Pacific + forms the country''s entire western border, with Peru to the north, Bolivia + to the northeast, Argentina to the east, and the Drake Passage at the country''s + southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. + Chile is divided into 15 regions. Every region is further divided into provinces. + Finally each province is divided into communes. Each region is designated + by a name and a Roman numeral, assigned from north to south. The only exception + is the region housing the nation''s capital, which is designated RM, that + stands for Region Metropolitana (Metropolitan Region). Two new regions were + created in 2006: Arica-Parinacota in the north, and Los Rios in the south. + Both became operative in 2007-10.' meaning: GAZ:00002825 China [GAZ:00002845]: text: China [GAZ:00002845] + description: 'A large country in Northeast Asia. China borders 14 nations + (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, + Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia + and North Korea. Additionally the border between PRC and ROC is located + in territorial waters. The People''s Republic of China has administrative + control over twenty-two provinces and considers Taiwan to be its twenty-third + province. There are also five autonomous regions, each with a designated + minority group; four municipalities; and two Special Administrative Regions + that enjoy considerable autonomy. The People''s Republic of China administers + 33 province-level regions, 333 prefecture-level regions, 2,862 county-level + regions, 41,636 township-level regions, and several village-level regions.' meaning: GAZ:00002845 Christmas Island [GAZ:00005915]: text: Christmas Island [GAZ:00005915] + description: An island in the Indian Ocean, 500 km south of Indonesia and + about 2600 km northwest of Perth. The island is the flat summit of a submarine + mountain. meaning: GAZ:00005915 Clipperton Island [GAZ:00005838]: text: Clipperton Island [GAZ:00005838] + description: A nine-square km coral atoll in the North Pacific Ocean, southwest + of Mexico and west of Costa Rica. meaning: GAZ:00005838 Cocos Islands [GAZ:00009721]: text: Cocos Islands [GAZ:00009721] + description: Islands that located in the Indian Ocean, about halfway between + Australia and Sri Lanka. A territory of Australia. There are two atolls + and twenty-seven coral islands in the group. meaning: GAZ:00009721 Colombia [GAZ:00002929]: text: Colombia [GAZ:00002929] + description: A country located in the northwestern region of South America. + Colombia is bordered to the east by Venezuela and Brazil; to the south by + Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean + Sea; to the north-west by Panama; and to the west by the Pacific Ocean. + Besides the countries in South America, the Republic of Colombia is recognized + to share maritime borders with the Caribbean countries of Jamaica, Haiti, + the Dominican Republic and the Central American countries of Honduras, Nicaragua, + and Costa Rica. Colombia is divided into 32 departments and one capital + district which is treated as a department. There are in total 10 districts + assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, + Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia + is also subdivided into some municipalities which form departments, each + with a municipal seat capital city assigned. Colombia is also subdivided + into corregimientos which form municipalities. meaning: GAZ:00002929 Comoros [GAZ:00005820]: text: Comoros [GAZ:00005820] + description: An island nation in the Indian Ocean, located off the eastern + coast of Africa on the northern end of the Mozambique Channel between northern + Madagascar and northeastern Mozambique. meaning: GAZ:00005820 Cook Islands [GAZ:00053798]: text: Cook Islands [GAZ:00053798] + description: A self-governing parliamentary democracy in free association + with New Zealand. The fifteen small islands in this South Pacific Ocean + country have a total land area of 240 km2, but the Cook Islands Exclusive + Economic Zone (EEZ) covers 1.8 million km2 of ocean. meaning: GAZ:00053798 Coral Sea Islands [GAZ:00005917]: text: Coral Sea Islands [GAZ:00005917] + description: A Territory of Australia which includes a group of small and + mostly uninhabited tropical islands and reefs in the Coral Sea, northeast + of Queensland, Australia. The only inhabited island is Willis Island. The + territory covers 780,000 km2, extending east and south from the outer edge + of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, + the Willis Group, and fifteen other reef/island groups. meaning: GAZ:00005917 Costa Rica [GAZ:00002901]: text: Costa Rica [GAZ:00002901] + description: A republic in Central America, bordered by Nicaragua to the north, + Panama to the east-southeast, the Pacific Ocean to the west and south, and + the Caribbean Sea to the east. Costa Rica is composed of seven provinces, + which in turn are divided into 81 cantons. meaning: GAZ:00002901 Cote d'Ivoire [GAZ:00000906]: text: Cote d'Ivoire [GAZ:00000906] + description: A country in West Africa. It borders Liberia and Guinea to the + west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf + of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). + The regions are further divided into 58 departments. meaning: GAZ:00000906 Croatia [GAZ:00002719]: text: Croatia [GAZ:00002719] + description: A country at the crossroads of the Mediterranean, Central Europe, + and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and + Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to + the east, Montenegro to the far southeast, and the Adriatic Sea to the south. + Croatia is divided into 21 counties (zupanija) and the capital Zagreb's + city district. meaning: GAZ:00002719 Cuba [GAZ:00003762]: text: Cuba [GAZ:00003762] + description: A country that consists of the island of Cuba (the largest and + second-most populous island of the Greater Antilles), Isla de la Juventud + and several adjacent small islands. Fourteen provinces and one special municipality + (the Isla de la Juventud) now compose Cuba. meaning: GAZ:00003762 Curacao [GAZ:00012582]: text: Curacao [GAZ:00012582] + description: One of five island areas of the Netherlands Antilles. meaning: GAZ:00012582 Cyprus [GAZ:00004006]: text: Cyprus [GAZ:00004006] + description: The third largest island in the Mediterranean Sea (after Sicily + and Sardinia), Cyprus is situated in the eastern Mediterranean, just south + of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, + it is often included in the Middle East (see also Western Asia and Near + East). Turkey is 75 km north; other neighbouring countries include Syria + and Lebanon to the east, Israel to the southeast, Egypt to the south, and + Greece to the west-north-west. meaning: GAZ:00004006 Czech Republic [GAZ:00002954]: text: Czech Republic [GAZ:00002954] + description: 'A landlocked country in Central Europe. It has borders with + Poland to the north, Germany to the northwest and southwest, Austria to + the south, and Slovakia to the east. The capital and largest city is Prague. + The country is composed of the historic regions of Bohemia and Moravia, + as well as parts of Silesia. Since 2000, the Czech Republic is divided into + thirteen regions (kraje, singular kraj) and the capital city of Prague. + The older seventy-six districts (okresy, singular okres) including three + ''statutory cities'' (without Prague, which had special status) were disbanded + in 1999 in an administrative reform; they remain as territorial division + and seats of various branches of state administration. Since 2003-01-01, + the regions have been divided into around 203 Municipalities with Extended + Competence (unofficially named "Little Districts" (Czech: ''male okresy'') + which took over most of the administration of the former District Authorities. + Some of these are further divided into Municipalities with Commissioned + Local Authority. However, the old districts still exist as territorial units + and remain as seats of some of the offices.' meaning: GAZ:00002954 Democratic Republic of the Congo [GAZ:00001086]: text: Democratic Republic of the Congo [GAZ:00001086] + description: A country of central Africa. It borders the Central African Republic + and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia + and Angola on the south, the Republic of the Congo on the west, and is separated + from Tanzania by Lake Tanganyika on the east. The country enjoys access + to the ocean through a 40 km stretch of Atlantic coastline at Muanda and + the roughly 9 km wide mouth of the Congo river which opens into the Gulf + of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed + into 25 Provinces from 2.2009. Each Province is divided into Zones. meaning: GAZ:00001086 Denmark [GAZ:00005852]: text: Denmark [GAZ:00005852] + description: That part of the Kingdom of Denmark located in continental Europe. + The mainland is bordered to the south by Germany; Denmark is located to + the southwest of Sweden and the south of Norway. Denmark borders both the + Baltic and the North Sea. The country consists of a large peninsula, Jutland + (Jylland) and a large number of islands, most notably Zealand (Sjaelland), + Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds + of minor islands often referred to as the Danish Archipelago. meaning: GAZ:00005852 Djibouti [GAZ:00000582]: text: Djibouti [GAZ:00000582] + description: A country in eastern Africa. Djibouti is bordered by Eritrea + in the north, Ethiopia in the west and south, and Somalia in the southeast. + The remainder of the border is formed by the Red Sea and the Gulf of Aden. + On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the + coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. + Djibouti is divided into 5 regions and one city. It is further subdivided + into 11 districts. meaning: GAZ:00000582 Dominica [GAZ:00006890]: text: Dominica [GAZ:00006890] + description: An island nation in the Caribbean Sea. Dominica is divided into + ten parishes. meaning: GAZ:00006890 Dominican Republic [GAZ:00003952]: text: Dominican Republic [GAZ:00003952] + description: A country in the West Indies that occupies the E two-thirds of + the Hispaniola island. The Dominican Republic's shores are washed by the + Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona + Passage, a channel about 130 km wide, separates the country (and the Hispaniola) + from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, + the national capital, Santo Domingo, is contained within its own Distrito + Nacional (National District). The provinces are divided into municipalities + (municipios; singular municipio). meaning: GAZ:00003952 Ecuador [GAZ:00002912]: text: Ecuador [GAZ:00002912] + description: A country in South America, bordered by Colombia on the north, + by Peru on the east and south, and by the Pacific Ocean to the west. The + country also includes the Galapagos Islands (Archipelago de Colon) in the + Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, + divided into 199 cantons and subdivided into parishes (or parroquias). meaning: GAZ:00002912 Egypt [GAZ:00003934]: text: Egypt [GAZ:00003934] + description: A country in North Africa that includes the Sinai Peninsula, + a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, + and the Gaza Strip and Israel to the east. The northern coast borders the + Mediterranean Sea and the island of Cyprus; the eastern coast borders the + Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, + singular muhafazah). The governorates are further divided into regions (markazes). meaning: GAZ:00003934 El Salvador [GAZ:00002935]: text: El Salvador [GAZ:00002935] + description: A country in Central America, bordering the Pacific Ocean between + Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), + which, in turn, are subdivided into 267 municipalities (municipios). meaning: GAZ:00002935 Equatorial Guinea [GAZ:00001091]: text: Equatorial Guinea [GAZ:00001091] + description: 'A country in Central Africa. It is one of the smallest countries + in continental Africa, and comprises two regions: Rio Muni, continental + region including several offshore islands; and Insular Region containing + Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando + Po) that contains the capital, Malabo. Equatorial Guinea is divided into + seven provinces which are divided into districts.' meaning: GAZ:00001091 Eritrea [GAZ:00000581]: text: Eritrea [GAZ:00000581] + description: A country situated in northern East Africa. It is bordered by + Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. + The east and northeast of the country have an extensive coastline on the + Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago + and several of the Hanish Islands are part of Eritrea. Eritrea is divided + into six regions (zobas) and subdivided into districts ("sub-zobas"). meaning: GAZ:00000581 Estonia [GAZ:00002959]: text: Estonia [GAZ:00002959] + description: A country in Northern Europe. Estonia has land borders to the + south with Latvia and to the east with Russia. It is separated from Finland + in the north by the Gulf of Finland and from Sweden in the west by the Baltic + Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). + Estonian counties are divided into rural (vallad, singular vald) and urban + (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) + municipalities. The municipalities comprise populated places (asula or asustusuksus) + - various settlements and territorial units that have no administrative + function. A group of populated places form a rural municipality with local + administration. Most towns constitute separate urban municipalities, while + some have joined with surrounding rural municipalities. meaning: GAZ:00002959 Eswatini [GAZ:00001099]: text: Eswatini [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). meaning: GAZ:00001099 Ethiopia [GAZ:00000567]: text: Ethiopia [GAZ:00000567] + description: 'A country situated in the Horn of Africa that has been landlocked + since the independence of its northern neighbor Eritrea in 1993. Apart from + Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to + the south, Djibouti to the northeast, and Somalia to the east. Since 1996 + Ethiopia has had a tiered government system consisting of a federal government + overseeing ethnically-based regional states, zones, districts (woredas), + and neighborhoods (kebele). It is divided into nine ethnically-based administrative + states (kililoch, singular kilil) and subdivided into sixty-eight zones + and two chartered cities (astedader akababiwoch, singular astedader akababi): + Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and + six special woredas.' meaning: GAZ:00000567 Europa Island [GAZ:00005811]: text: Europa Island [GAZ:00005811] + description: A 28 km2 low-lying tropical island in the Mozambique Channel, + about a third of the way from southern Madagascar to southern Mozambique. meaning: GAZ:00005811 Falkland Islands (Islas Malvinas) [GAZ:00001412]: text: Falkland Islands (Islas Malvinas) [GAZ:00001412] + description: An archipelago in the South Atlantic Ocean, located 483 km from + the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), + and 940 km north of Antarctica (Elephant Island). They consist of two main + islands, East Falkland and West Falkland, together with 776 smaller islands. meaning: GAZ:00001412 Faroe Islands [GAZ:00059206]: text: Faroe Islands [GAZ:00059206] + description: An autonomous province of the Kingdom of Denmark since 1948 located + in the Faroes. Administratively, the islands are divided into 34 municipalities + (kommunur) within which 120 or so cities and villages lie. meaning: GAZ:00059206 Fiji [GAZ:00006891]: text: Fiji [GAZ:00006891] + description: An island nation in the South Pacific Ocean east of Vanuatu, + west of Tonga and south of Tuvalu. The country occupies an archipelago of + about 322 islands, of which 106 are permanently inhabited, and 522 islets. + The two major islands, Viti Levu and Vanua Levu, account for 87% of the + population. meaning: GAZ:00006891 Finland [GAZ:00002937]: text: Finland [GAZ:00002937] + description: A Nordic country situated in the Fennoscandian region of Northern + Europe. It has borders with Sweden to the west, Russia to the east, and + Norway to the north, while Estonia lies to its south across the Gulf of + Finland. The capital city is Helsinki. Finland is divided into six administrative + provinces (laani, plural laanit). These are divided into 20 regions (maakunt), + 77 subregions (seutukunta) and then into municipalities (kunta). meaning: GAZ:00002937 France [GAZ:00003940]: text: France [GAZ:00003940] + description: A part of the country of France that extends from the Mediterranean + Sea to the English Channel and the North Sea, and from the Rhine to the + Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, + Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas + departments. meaning: GAZ:00003940 French Guiana [GAZ:00002516]: text: French Guiana [GAZ:00002516] + description: An overseas department (departement d'outre-mer) of France, located + on the northern coast of South America. It is bordered by Suriname, to the + E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. + French Guiana is divided into 2 departmental arrondissements, 19 cantons + and 22 communes. meaning: GAZ:00002516 French Polynesia [GAZ:00002918]: text: French Polynesia [GAZ:00002918] + description: 'A French overseas collectivity in the southern Pacific Ocean. + It is made up of several groups of Polynesian islands. French Polynesia + has five administrative subdivisions (French: subdivisions administratives).' meaning: GAZ:00002918 French Southern and Antarctic Lands [GAZ:00003753]: text: French Southern and Antarctic Lands [GAZ:00003753] + description: The French Southern and Antarctic Lands have formed a territoire + d'outre-mer (an overseas territory) of France since 1955. The territory + is divided into five districts. meaning: GAZ:00003753 Gabon [GAZ:00001092]: text: Gabon [GAZ:00001092] + description: A country in west central Africa sharing borders with Equatorial + Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital + and largest city is Libreville. Gabon is divided into 9 provinces and further + divided into 37 departments. meaning: GAZ:00001092 Gambia [GAZ:00000907]: text: Gambia [GAZ:00000907] + description: A country in Western Africa. It is the smallest country on the + African continental mainland and is bordered to the north, east, and south + by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing + through the centre of the country and discharging to the Atlantic Ocean + is the Gambia River. The Gambia is divided into five divisions and one city + (Banjul). The divisions are further subdivided into 37 districts. meaning: GAZ:00000907 Gaza Strip [GAZ:00009571]: text: Gaza Strip [GAZ:00009571] + description: A Palestinian enclave on the eastern coast of the Mediterranean + Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel + on the east and north along a 51 km (32 mi) border. Gaza and the West Bank + are claimed by the de jure sovereign State of Palestine. meaning: GAZ:00009571 Georgia [GAZ:00004942]: text: Georgia [GAZ:00004942] + description: 'A Eurasian country in the Caucasus located at the east coast + of the Black Sea. In the north, Georgia has a 723 km common border with + Russia, specifically with the Northern Caucasus federal district. The following + Russian republics/subdivisions: from west to east: border Georgia: Krasnodar + Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, + Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) + to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to + the south-west. It is a transcontinental country, located at the juncture + of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 + autonomous republics (avtonomiuri respublika), and 1 city (k''alak''i). + The regions are further subdivided into 69 districts (raioni).' meaning: GAZ:00004942 Germany [GAZ:00002646]: text: Germany [GAZ:00002646] + description: A country in Central Europe. It is bordered to the north by the + North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech + Republic; to the south by Austria and Switzerland; and to the west by France, + Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, + Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) + and cities (kreisfreie Stadte). meaning: GAZ:00002646 Ghana [GAZ:00000908]: text: Ghana [GAZ:00000908] + description: A country in West Africa. It borders Cote d'Ivoire to the west, + Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the + south. Ghana is a divided into 10 regions, subdivided into a total of 138 + districts. meaning: GAZ:00000908 Gibraltar [GAZ:00003987]: text: Gibraltar [GAZ:00003987] + description: A British overseas territory located near the southernmost tip + of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory + shares a border with Spain to the north. meaning: GAZ:00003987 Glorioso Islands [GAZ:00005808]: text: Glorioso Islands [GAZ:00005808] + description: A group of islands and rocks totalling 5 km2, in the northern + Mozambique channel, about 160 km northwest of Madagascar. meaning: GAZ:00005808 Greece [GAZ:00002945]: text: Greece [GAZ:00002945] + description: A country in southeastern Europe, situated on the southern end + of the Balkan Peninsula. It has borders with Albania, the former Yugoslav + Republic of Macedonia and Bulgaria to the north, and Turkey to the east. + The Aegean Sea lies to the east and south of mainland Greece, while the + Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin + feature a vast number of islands. Greece consists of thirteen peripheries + subdivided into a total of fifty-one prefectures (nomoi, singular nomos). + There is also one autonomous area, Mount Athos, which borders the periphery + of Central Macedonia. meaning: GAZ:00002945 Greenland [GAZ:00001507]: text: Greenland [GAZ:00001507] + description: A self-governing Danish province located between the Arctic and + Atlantic Oceans, east of the Canadian Arctic Archipelago. meaning: GAZ:00001507 Grenada [GAZ:02000573]: text: Grenada [GAZ:02000573] + description: An island country in the West Indies in the Caribbean Sea at + the southern end of the Grenadines island chain. Grenada consists of the + island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, + and several small islands which lie to the north of the main island and + are a part of the Grenadines. It is located northwest of Trinidad and Tobago, + northeast of Venezuela and southwest of Saint Vincent and the Grenadines. + Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated + population of 112,523 in July 2020. meaning: GAZ:02000573 Guadeloupe [GAZ:00067142]: text: Guadeloupe [GAZ:00067142] + description: "An archipelago and overseas department and region of France\ + \ in the Caribbean. It consists of six inhabited islands\u2014Basse-Terre,\ + \ Grande-Terre, Marie-Galante, La D\xE9sirade, and the two inhabited \xCE\ + les des Saintes\u2014as well as many uninhabited islands and outcroppings.\ + \ It is south of Antigua and Barbuda and Montserrat, and north of Dominica." meaning: GAZ:00067142 Guam [GAZ:00003706]: text: Guam [GAZ:00003706] + description: An organized, unincorporated territory of the United States in + the Micronesia subregion of the western Pacific Ocean. It is the westernmost + point and territory of the United States (reckoned from the geographic center + of the U.S.); in Oceania, it is the largest and southernmost of the Mariana + Islands and the largest island in Micronesia. meaning: GAZ:00003706 Guatemala [GAZ:00002936]: text: Guatemala [GAZ:00002936] + description: A country in Central America bordered by Mexico to the northwest, + the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the + northeast, and Honduras and El Salvador to the southeast. Guatemala is divided + into 22 departments (departamentos) and sub-divided into about 332 municipalities + (municipios). meaning: GAZ:00002936 Guernsey [GAZ:00001550]: text: Guernsey [GAZ:00001550] + description: A British Crown Dependency in the English Channel off the coast + of Normandy. meaning: GAZ:00001550 Guinea [GAZ:00000909]: text: Guinea [GAZ:00000909] + description: A nation in West Africa, formerly known as French Guinea. Guinea's + territory has a curved shape, with its base at the Atlantic Ocean, inland + to the east, and turning south. The base borders Guinea-Bissau and Senegal + to the north, and Mali to the north and north-east; the inland part borders + Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone + to the west of the southern tip. meaning: GAZ:00000909 Guinea-Bissau [GAZ:00000910]: text: Guinea-Bissau [GAZ:00000910] + description: A country in western Africa, and one of the smallest nations + in continental Africa. It is bordered by Senegal to the north, and Guinea + to the south and east, with the Atlantic Ocean to its west. Formerly the + Portuguese colony of Portuguese Guinea, upon independence, the name of its + capital, Bissau, was added to the country's name in order to prevent confusion + between itself and the Republic of Guinea. meaning: GAZ:00000910 Guyana [GAZ:00002522]: text: Guyana [GAZ:00002522] + description: A country in the N of South America. Guyana lies north of the + equator, in the tropics, and is located on the Atlantic Ocean. Guyana is + bordered to the east by Suriname, to the south and southwest by Brazil and + to the west by Venezuela. Guyana is divided into 10 regions. The regions + of Guyana are divided into 27 neighborhood councils. meaning: GAZ:00002522 Haiti [GAZ:00003953]: text: Haiti [GAZ:00003953] + description: A country located in the Greater Antilles archipelago on the + Caribbean island of Hispaniola, which it shares with the Dominican Republic. + Haiti is divided into 10 departments. The departments are further divided + into 41 arrondissements, and 133 communes which serve as second and third + level administrative divisions. meaning: GAZ:00003953 Heard Island and McDonald Islands [GAZ:00009718]: text: Heard Island and McDonald Islands [GAZ:00009718] + description: An Australian external territory comprising a volcanic group + of mostly barren Antarctic islands, about two-thirds of the way from Madagascar + to Antarctica. meaning: GAZ:00009718 Honduras [GAZ:00002894]: text: Honduras [GAZ:00002894] + description: A republic in Central America. The country is bordered to the + west by Guatemala, to the southwest by El Salvador, to the southeast by + Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and + to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. + Honduras is divided into 18 departments. The capital city is Tegucigalpa + Central District of the department of Francisco Morazan. meaning: GAZ:00002894 Hong Kong [GAZ:00003203]: text: Hong Kong [GAZ:00003203] + description: A special administrative region of the People's Republic of China + (PRC). The territory lies on the eastern side of the Pearl River Delta, + bordering Guangdong province in the north and facing the South China Sea + in the east, west and south. Hong Kong was a crown colony of the United + Kingdom from 1842 until the transfer of its sovereignty to the People's + Republic of China in 1997. meaning: GAZ:00003203 Howland Island [GAZ:00007120]: text: Howland Island [GAZ:00007120] + description: An uninhabited coral island located just north of the equator + in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. + The island is almost half way between Hawaii and Australia and is an unincorporated, + unorganized territory of the United States, and is often included as one + of the Phoenix Islands. For statistical purposes, Howland is grouped as + one of the United States Minor Outlying Islands. meaning: GAZ:00007120 Hungary [GAZ:00002952]: text: Hungary [GAZ:00002952] + description: 'A landlocked country in the Carpathian Basin of Central Europe, + bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. + Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: + megye). In addition, the capital city (fovaros), Budapest, is independent + of any county government. The counties are further subdivided into 173 subregions + (kistersegek), and Budapest is comprised of its own subregion. Since 1996, + the counties and City of Budapest have been grouped into 7 regions for statistical + and development purposes. These seven regions constitute NUTS second-level + units of Hungary.' meaning: GAZ:00002952 Iceland [GAZ:00000843]: text: Iceland [GAZ:00000843] + description: A country in northern Europe, comprising the island of Iceland + and its outlying islands in the North Atlantic Ocean between the rest of + Europe and Greenland. meaning: GAZ:00000843 India [GAZ:00002839]: text: India [GAZ:00002839] + description: A country in South Asia. Bounded by the Indian Ocean on the south, + the Arabian Sea on the west, and the Bay of Bengal on the east, India has + a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, + and Bhutan to the north-east; and Bangladesh and Burma to the east. India + is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian + Ocean. India is a federal republic of twenty-eight states and seven Union + Territories. Each state or union territory is divided into basic units of + government and administration called districts. There are nearly 600 districts + in India. The districts in turn are further divided into tehsils and eventually + into villages. meaning: GAZ:00002839 Indonesia [GAZ:00003727]: text: Indonesia [GAZ:00003727] + description: An archipelagic state in Southeast Asia. The country shares land + borders with Papua New Guinea, East Timor and Malaysia. Other neighboring + countries include Singapore, the Philippines, Australia, and the Indian + territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, + five of which have special status. The provinces are subdivided into regencies + (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), + which are further subdivided into subdistricts (kecamatan), and again into + village groupings (either desa or kelurahan). meaning: GAZ:00003727 Iran [GAZ:00004474]: text: Iran [GAZ:00004474] + description: A country in Central Eurasia. Iran is bounded by the Gulf of + Oman and the Persian Gulf to the south and the Caspian Sea to its north. + It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and + Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into + 30 provinces (ostan). The provinces are divided into counties (shahrestan), + and subdivided into districts (bakhsh) and sub-districts (dehestan). meaning: GAZ:00004474 Iraq [GAZ:00004483]: text: Iraq [GAZ:00004483] + description: 'A country in the Middle East spanning most of the northwestern + end of the Zagros mountain range, the eastern part of the Syrian Desert + and the northern part of the Arabian Desert. It shares borders with Kuwait + and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, + Turkey to the north, and Iran to the east. It has a very narrow section + of coastline at Umm Qasr on the Persian Gulf. There are two major flowing + rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates + (or provinces) (muhafazah). The governorates are divided into qadhas (or + districts).' meaning: GAZ:00004483 Ireland [GAZ:00002943]: text: Ireland [GAZ:00002943] + description: A country in north-western Europe. The modern sovereign state + occupies five-sixths of the island of Ireland, which was partitioned in + 1921. It is bordered by Northern Ireland (part of the United Kingdom) to + the north, by the Atlantic Ocean to the west and by the Irish Sea to the + east. Administration follows the 34 "county-level" counties and cities of + Ireland. Of these twenty-nine are counties, governed by county councils + while the five cities of Dublin, Cork, Limerick, Galway and Waterford have + city councils, (previously known as corporations), and are administered + separately from the counties bearing those names. The City of Kilkenny is + the only city in the republic which does not have a "city council"; it is + still a borough but not a county borough and is administered as part of + County Kilkenny. Ireland is split into eight regions for NUTS statistical + purposes. These are not related to the four traditional provinces but are + based on the administrative counties. meaning: GAZ:00002943 Isle of Man [GAZ:00052477]: text: Isle of Man [GAZ:00052477] + description: A Crown dependency of the United Kingdom in the centre of the + Irish Sea. It is not part of the United Kingdom, European Union or United + Nations. meaning: GAZ:00052477 Israel [GAZ:00002476]: text: Israel [GAZ:00002476] + description: 'A country in Western Asia located on the eastern edge of the + Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, + Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, + which are partially administrated by the Palestinian National Authority, + are also adjacent. The State of Israel is divided into six main administrative + districts, known as mehozot (singular mahoz). Districts are further divided + into fifteen sub-districts known as nafot (singular: nafa), which are themselves + partitioned into fifty natural regions.' meaning: GAZ:00002476 Italy [GAZ:00002650]: text: Italy [GAZ:00002650] + description: A country located on the Italian Peninsula in Southern Europe, + and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. + Italy shares its northern Alpine boundary with France, Switzerland, Austria + and Slovenia. The independent states of San Marino and the Vatican City + are enclaves within the Italian Peninsula, while Campione d'Italia is an + Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, + singular regione). Five of these regions have a special autonomous status + that enables them to enact legislation on some of their local matters. It + is further divided into 109 provinces (province) and 8,101 municipalities + (comuni). meaning: GAZ:00002650 Jamaica [GAZ:00003781]: text: Jamaica [GAZ:00003781] + description: A nation of the Greater Antilles. Jamaica is divided into 14 + parishes, which are grouped into three historic counties that have no administrative + relevance. meaning: GAZ:00003781 Jan Mayen [GAZ:00005853]: text: Jan Mayen [GAZ:00005853] + description: 'A volcanic island that is part of the Kingdom of Norway, It + has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus + 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and + 1,000 km west of the Norwegian mainland. The island is mountainous, the + highest summit being the Beerenberg volcano in the north. The isthmus is + the location of the two largest lakes of the island, Sorlaguna (South Lagoon), + and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng + Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.' meaning: GAZ:00005853 Japan [GAZ:00002747]: text: Japan [GAZ:00002747] + description: An island country in East Asia. Located in the Pacific Ocean, + it lies to the east of China, Korea and Russia, stretching from the Sea + of Okhotsk in the north to the East China Sea in the south. meaning: GAZ:00002747 Jarvis Island [GAZ:00007118]: text: Jarvis Island [GAZ:00007118] + description: An uninhabited 4.5 km2 coral atoll located in the South Pacific + Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated + territory of the United States administered from Washington, DC by the United + States Fish and Wildlife Service of the United States Department of the + Interior as part of the National Wildlife Refuge system. Jarvis is one of + the southern Line Islands and for statistical purposes is also grouped as + one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. meaning: GAZ:00007118 Jersey [GAZ:00001551]: text: Jersey [GAZ:00001551] + description: A British Crown Dependency[6] off the coast of Normandy, France. + As well as the island of Jersey itself, the bailiwick includes two groups + of small islands that are no longer permanently inhabited, the Minquiers + and Ecrehous, and the Pierres de Lecq. meaning: GAZ:00001551 Johnston Atoll [GAZ:00007114]: text: Johnston Atoll [GAZ:00007114] + description: A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 + nm) west of Hawaii. There are four islands located on the coral reef platform, + two natural islands, Johnston Island and Sand Island, which have been expanded + by coral dredging, as well as North Island (Akau) and East Island (Hikina), + artificial islands formed from coral dredging. Johnston is an unincorporated + territory of the United States, administered by the US Fish and Wildlife + Service of the Department of the Interior as part of the United States Pacific + Island Wildlife Refuges. Sits atop Johnston Seamount. meaning: GAZ:00007114 Jordan [GAZ:00002473]: text: Jordan [GAZ:00002473] + description: A country in Southwest Asia, bordered by Syria to the north, + Iraq to the north-east, Israel and the West Bank to the west, and Saudi + Arabia to the east and south. It shares the coastlines of the Dead Sea, + and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided + into 12 provinces called governorates. The Governorates are subdivided into + approximately fifty-two nahias. meaning: GAZ:00002473 Juan de Nova Island [GAZ:00005809]: text: Juan de Nova Island [GAZ:00005809] + description: A 4.4 km2 low, flat, tropical island in the narrowest part of + the Mozambique Channel, about one-third of the way between Madagascar and + Mozambique. meaning: GAZ:00005809 Kazakhstan [GAZ:00004999]: text: Kazakhstan [GAZ:00004999] + description: A country in Central Asia and Europe. It is bordered by Russia, + Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders + on a significant part of the Caspian Sea. Kazakhstan is divided into 14 + provinces and two municipal districts. The provinces of Kazakhstan are divided + into raions. meaning: GAZ:00004999 Kenya [GAZ:00001101]: text: Kenya [GAZ:00001101] + description: A country in Eastern Africa. It is bordered by Ethiopia to the + north, Somalia to the east, Tanzania to the south, Uganda to the west, and + Sudan to the northwest, with the Indian Ocean running along the southeast + border. Kenya comprises eight provinces each headed by a Provincial Commissioner + (centrally appointed by the president). The provinces (mkoa singular mikoa + plural in Swahili) are subdivided into districts (wilaya). There were 69 + districts as of 1999 census. Districts are then subdivided into 497 divisions + (taarafa). The divisions are then subdivided into 2,427 locations (kata) + and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the + status of a full administrative province. meaning: GAZ:00001101 Kerguelen Archipelago [GAZ:00005682]: text: Kerguelen Archipelago [GAZ:00005682] + description: A group of islands in the southern Indian Ocean. It is a territory + of France. They are composed primarily of Tertiary flood basalts and a complex + of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano + at the southern end was active during the late Pleistocene. The Rallier + du Baty Peninsula on the SW tip of the island contains two youthful subglacial + eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active + fumarole field is related to a series of Holocene trachytic lava flows and + lahars that extend beyond the icecap. meaning: GAZ:00005682 Kingman Reef [GAZ:00007116]: text: Kingman Reef [GAZ:00007116] + description: A largely submerged, uninhabited tropical atoll located in the + North Pacific Ocean, roughly half way between Hawaiian Islands and American + Samoa. It is the northernmost of the Northern Line Islands and lies 65 km + NNW of Palmyra Atoll, the next closest island, and has the status of an + unincorporated territory of the United States, administered from Washington, + DC by the US Navy. Sits atop Kingman Reef Seamount. meaning: GAZ:00007116 Kiribati [GAZ:00006894]: text: Kiribati [GAZ:00006894] + description: 'An island nation located in the central tropical Pacific Ocean. + It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 + km2 straddling the equator and bordering the International Date Line to + the east. It is divided into three island groups which have no administrative + function, including a group which unites the Line Islands and the Phoenix + Islands (ministry at London, Christmas). Each inhabited island has its own + council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two + councils on Tabiteuea).' meaning: GAZ:00006894 Kosovo [GAZ:00011337]: text: Kosovo [GAZ:00011337] + description: A country on the Balkan Peninsula. Kosovo borders Central Serbia + to the north and east, Montenegro to the northwest, Albania to the west + and the Republic of Macedonia to the south. Kosovo is divided into 7 districts + (Rreth) and 30 municipalities. Serbia does not recognise the unilateral + secession of Kosovo[8] and considers it a United Nations-governed entity + within its sovereign territory, the Autonomous Province of Kosovo and Metohija. meaning: GAZ:00011337 Kuwait [GAZ:00005285]: text: Kuwait [GAZ:00005285] + description: A sovereign emirate on the coast of the Persian Gulf, enclosed + by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided + into six governorates (muhafazat, singular muhafadhah). meaning: GAZ:00005285 Kyrgyzstan [GAZ:00006893]: text: Kyrgyzstan [GAZ:00006893] + description: A country in Central Asia. Landlocked and mountainous, it is + bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan + to the southwest and China to the east. Kyrgyzstan is divided into seven + provinces (oblast. The capital, Bishkek, and the second large city Osh are + administratively the independent cities (shaar) with a status equal to a + province. Each province comprises a number of districts (raions). meaning: GAZ:00006893 Laos [GAZ:00006889]: text: Laos [GAZ:00006889] + description: A landlocked country in southeast Asia, bordered by Burma (Myanmar) + and China to the northwest, Vietnam to the east, Cambodia to the south, + and Thailand to the west. Laos is divided into sixteen provinces (qwang) + and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided + into districts (muang). meaning: GAZ:00006889 Latvia [GAZ:00002958]: text: Latvia [GAZ:00002958] + description: A country in Northern Europe. Latvia shares land borders with + Estonia to the north and Lithuania to the south, and both Russia and Belarus + to the east. It is separated from Sweden in the west by the Baltic Sea. + The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). + There are also seven cities (lielpilsetas) that have a separate status. + Latvia is also historically, culturally and constitutionally divided in + four or more distinct regions. meaning: GAZ:00002958 Lebanon [GAZ:00002478]: text: Lebanon [GAZ:00002478] + description: 'A small, mostly mountainous country in Western Asia, on the + eastern shore of the Mediterranean Sea. It is bordered by Syria to the north + and east, and Israel to the south. Lebanon is divided into six governorates + (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, + singular: qadaa).' meaning: GAZ:00002478 Lesotho [GAZ:00001098]: text: Lesotho [GAZ:00001098] + description: A land-locked country, entirely surrounded by the Republic of + South Africa. Lesotho is divided into ten districts; these are further subdivided + into 80 constituencies, which consists of 129 local community councils. meaning: GAZ:00001098 Liberia [GAZ:00000911]: text: Liberia [GAZ:00000911] + description: A country on the west coast of Africa, bordered by Sierra Leone, + Guinea, Cote d'Ivoire, and the Atlantic Ocean. meaning: GAZ:00000911 Libya [GAZ:00000566]: text: Libya [GAZ:00000566] + description: A country in North Africa. Bordering the Mediterranean Sea to + the north, Libya lies between Egypt to the east, Sudan to the southeast, + Chad and Niger to the south, and Algeria and Tunisia to the west. There + are thirty-four municipalities of Libya, known by the Arabic term sha'biyat + (singular sha'biyah). These came recently (in the 1990s to replaced old + Baladiyat systam. The Baladiyat system in turn was introduced to replace + the system of muhafazah (governorates or provinces) that existed from the + 1960s to the 1970s. meaning: GAZ:00000566 Liechtenstein [GAZ:00003858]: text: Liechtenstein [GAZ:00003858] + description: A tiny, doubly landlocked alpine country in Western Europe, bordered + by Switzerland to its west and by Austria to its east. The principality + of Liechtenstein is divided into 11 municipalities called Gemeinden (singular + Gemeinde). The Gemeinden mostly consist only of a single town. Five of them + fall within the electoral district Unterland (the lower county), and the + remainder within Oberland (the upper county). meaning: GAZ:00003858 Line Islands [GAZ:00007144]: text: Line Islands [GAZ:00007144] + description: A group of eleven atolls and low coral islands in the central + Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, + while three are United States territories that are grouped with the United + States Minor Outlying Islands. meaning: GAZ:00007144 Lithuania [GAZ:00002960]: text: Lithuania [GAZ:00002960] + description: 'A country located along the south-eastern shore of the Baltic + Sea, sharing borders with Latvia to the north, Belarus to the southeast, + Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. + Lithuania has a three-tier administrative division: the country is divided + into 10 counties (singular apskritis, plural, apskritys) that are further + subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) + which consist of over 500 elderates (singular seniunija, plural seniunijos).' meaning: GAZ:00002960 Luxembourg [GAZ:00002947]: text: Luxembourg [GAZ:00002947] + description: A small landlocked country in western Europe, bordered by Belgium, + France, and Germany. Luxembourg is divided into 3 districts, which are further + divided into 12 cantons and then 116 communes. Twelve of the communes have + city status, of which the city of Luxembourg is the largest. meaning: GAZ:00002947 Macau [GAZ:00003202]: text: Macau [GAZ:00003202] + description: One of the two special administrative regions of the People's + Republic of China, the other being Hong Kong. Macau lies on the western + side of the Pearl River Delta, bordering Guangdong province in the north + and facing the South China Sea in the east and south. Macau is situated + 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the + Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula + is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang + (West River) on the west. It borders the Zhuhai Special Economic Zone in + mainland China. meaning: GAZ:00003202 Madagascar [GAZ:00001108]: text: Madagascar [GAZ:00001108] + description: An island nation in the Indian Ocean off the southeastern coast + of Africa. The main island, also called Madagascar, is the fourth largest + island in the world, and is home to 5% of the world's plant and animal species, + of which more than 80% are endemic to Madagascar. Most notable are the lemur + infraorder of primates, the carnivorous fossa, three endemic bird families + and six endemic baobab species. Madagascar is divided into six autonomous + provinces (faritany mizakatena), and 22 regions. The regions are further + subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. meaning: GAZ:00001108 Malawi [GAZ:00001105]: text: Malawi [GAZ:00001105] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. meaning: GAZ:00001105 Malaysia [GAZ:00003902]: text: Malaysia [GAZ:00003902] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. meaning: GAZ:00003902 Maldives [GAZ:00006924]: text: Maldives [GAZ:00006924] + description: An archipelago which consists of approximately 1,196 coral islands + grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. meaning: GAZ:00006924 Mali [GAZ:00000584]: text: Mali [GAZ:00000584] + description: A landlocked country in northern Africa. It borders Algeria on + the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the + south, Guinea on the south-west, and Senegal and Mauritania on the west. + Mali is divided into 8 regions (regions) and 1 district, and subdivided + into 49 cercles, totalling 288 arrondissements. meaning: GAZ:00000584 Malta [GAZ:00004017]: text: Malta [GAZ:00004017] + description: A Southern European country and consists of an archipelago situated + centrally in the Mediterranean. meaning: GAZ:00004017 Marshall Islands [GAZ:00007161]: text: Marshall Islands [GAZ:00007161] + description: 'An archipelago that consists of twenty-nine atolls and five + isolated islands. The most important atolls and islands form two groups: + the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). + Two-thirds of the nation''s population lives on Majuro (which is also the + capital) and Ebeye. The outer islands are sparsely populated.' meaning: GAZ:00007161 Martinique [GAZ:00067143]: text: Martinique [GAZ:00067143] + description: An island and an overseas department/region and single territorial + collectivity of France. meaning: GAZ:00067143 Mauritania [GAZ:00000583]: text: Mauritania [GAZ:00000583] + description: A country in North-West Africa. It is bordered by the Atlantic + Ocean on the west, by Senegal on the southwest, by Mali on the east and + southeast, by Algeria on the northeast, and by Western Sahara on the northwest + (most of which is occupied by Morocco). The capital and largest city is + Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 + regions (regions) and one capital district, which in turn are subdivided + into 44 departments (departements). meaning: GAZ:00000583 Mauritius [GAZ:00003745]: text: Mauritius [GAZ:00003745] + description: An island nation off the coast of the African continent in the + southwest Indian Ocean, about 900 km east of Madagascar. In addition to + the island of Mauritius, the republic includes the islands of St. Brandon, + Rodrigues and the Agalega Islands. meaning: GAZ:00003745 Mayotte [GAZ:00003943]: text: Mayotte [GAZ:00003943] + description: An overseas collectivity of France consisting of a main island, + Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and + several islets around these two. meaning: GAZ:00003943 Mexico [GAZ:00002852]: text: Mexico [GAZ:00002852] + description: A federal constitutional republic in North America. It is bounded + on the north by the United States; on the south and west by the North Pacific + Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and + on the east by the Gulf of Mexico. The United Mexican States comprise a + federation of thirty-one states and a federal district, the capital Mexico + City. meaning: GAZ:00002852 Micronesia [GAZ:00005862]: text: Micronesia [GAZ:00005862] + description: A subregion of Oceania, comprising hundreds of small islands + in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua + New Guinea and Melanesia to the west and southwest, and Polynesia to the + east. meaning: GAZ:00005862 Midway Islands [GAZ:00007112]: text: Midway Islands [GAZ:00007112] + description: A 6.2 km2 atoll located in the North Pacific Ocean (near the + northwestern end of the Hawaiian archipelago). It is an unincorporated territory + of the United States, designated an insular area under the authority of + the US Department of the Interior. meaning: GAZ:00007112 Moldova [GAZ:00003897]: text: Moldova [GAZ:00003897] + description: A landlocked country in Eastern Europe, located between Romania + to the west and Ukraine to the north, east and south. Moldova is divided + into thirty-two districts (raioane, singular raion); three municipalities + (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). + The cities of Comrat and Tiraspol also have municipality status, however + not as first-tier subdivisions of Moldova, but as parts of the regions of + Gagauzia and Transnistria, respectively. The status of Transnistria is however + under dispute. Although it is de jure part of Moldova and is recognized + as such by the international community, Transnistria is not de facto under + the control of the central government of Moldova. It is administered by + an unrecognized breakaway authority under the name Pridnestrovian Moldovan + Republic. meaning: GAZ:00003897 Monaco [GAZ:00003857]: text: Monaco [GAZ:00003857] + description: A small country that is completely bordered by France to the + north, west, and south; to the east it is bordered by the Mediterranean + Sea. It consists of a single municipality (commune) currently divided into + 4 quartiers and 10 wards. meaning: GAZ:00003857 Mongolia [GAZ:00008744]: text: Mongolia [GAZ:00008744] + description: A country in East-Central Asia. The landlocked country borders + Russia to the north and China to the south. The capital and largest city + is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are + in turn divided into 315 sums (districts). The capital Ulan Bator is administrated + separately as a khot (municipality) with provincial status. meaning: GAZ:00008744 Montenegro [GAZ:00006898]: text: Montenegro [GAZ:00006898] + description: A country located in Southeastern Europe. It has a coast on the + Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina + to the northwest, Serbia and its partially recognized breakaway southern + province of Kosovo to the northeast and Albania to the southeast. Its capital + and largest city is Podgorica. Montenegro is divided into twenty-one municipalities + (opstina), and two urban municipalities, subdivisions of Podgorica municipality. meaning: GAZ:00006898 Montserrat [GAZ:00003988]: text: Montserrat [GAZ:00003988] + description: A British overseas territory located in the Leeward Islands. + Montserrat is divided into three parishes. meaning: GAZ:00003988 Morocco [GAZ:00000565]: text: Morocco [GAZ:00000565] + description: A country in North Africa. It has a coast on the Atlantic Ocean + that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco + has international borders with Algeria to the east, Spain to the north (a + water border through the Strait and land borders with two small Spanish + autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco + is divided into 16 regions, and subdivided into 62 prefectures and provinces. + Because of the conflict over Western Sahara, the status of both regions + of "Saguia el-Hamra" and "Rio de Oro" is disputed. meaning: GAZ:00000565 Mozambique [GAZ:00001100]: text: Mozambique [GAZ:00001100] + description: A country in southeastern Africa bordered by the Indian Ocean + to the east, Tanzania to the north, Malawi and Zambia to the northwest, + Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique + is divided into ten provinces (provincias) and one capital city (cidade + capital) with provincial status. The provinces are subdivided into 129 districts + (distritos). Districts are further divided in "Postos Administrativos" (Administrative + Posts) and these in Localidades (Localities) the lowest geographical level + of central state administration. meaning: GAZ:00001100 Myanmar [GAZ:00006899]: text: Myanmar [GAZ:00006899] + description: A country in SE Asia that is bordered by China on the north, + Laos on the east, Thailand on the southeast, Bangladesh on the west, and + India on the northwest, with the Bay of Bengal to the southwest. Myanmar + is divided into seven states and seven divisions. The administrative divisions + are further subdivided into districts, which are further subdivided into + townships, wards, and villages. meaning: GAZ:00006899 Namibia [GAZ:00001096]: text: Namibia [GAZ:00001096] + description: A country in southern Africa on the Atlantic coast. It shares + borders with Angola and Zambia to the north, Botswana to the east, and South + Africa to the south. Namibia is divided into 13 regions and subdivided into + 102 constituencies. meaning: GAZ:00001096 Nauru [GAZ:00006900]: text: Nauru [GAZ:00006900] + description: An island nation in the Micronesian South Pacific. The nearest + neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. + Nauru is divided into fourteen administrative districts which are grouped + into eight electoral constituencies. meaning: GAZ:00006900 Navassa Island [GAZ:00007119]: text: Navassa Island [GAZ:00007119] + description: A small, uninhabited island in the Caribbean Sea, and is an unorganized + unincorporated territory of the United States, which administers it through + the US Fish and Wildlife Service. The island is also claimed by Haiti. meaning: GAZ:00007119 Nepal [GAZ:00004399]: text: Nepal [GAZ:00004399] + description: A landlocked nation in South Asia. It is bordered by the Tibet + Autonomous Region of the People's Republic of China to the northeast and + India to the south and west; it is separated from Bhutan by the Indian State + of Sikkim and from Bangladesh by a small strip of the Indian State of West + Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs + across Nepal's north and western parts, and eight of the world's ten highest + mountains, including the highest, Mount Everest are situated within its + territory. Nepal is divided into 14 zones and 75 districts, grouped into + 5 development regions. meaning: GAZ:00004399 Netherlands [GAZ:00002946]: text: Netherlands [GAZ:00002946] + description: The European part of the Kingdom of the Netherlands. It is bordered + by the North Sea to the north and west, Belgium to the south, and Germany + to the east. The Netherlands is divided into twelve administrative regions, + called provinces. All provinces of the Netherlands are divided into municipalities + (gemeenten), together 443 (2007). meaning: GAZ:00002946 New Caledonia [GAZ:00005206]: text: New Caledonia [GAZ:00005206] + description: A "sui generis collectivity" (in practice an overseas territory) + of France, made up of a main island (Grande Terre), the Loyalty Islands, + and several smaller islands. It is located in the region of Melanesia in + the southwest Pacific. Administratively, the archipelago is divided into + three provinces, and then into 33 communes. meaning: GAZ:00005206 New Zealand [GAZ:00000469]: text: New Zealand [GAZ:00000469] + description: A nation in the south-western Pacific Ocean comprising two large + islands (the North Island and the South Island) and numerous smaller islands, + most notably Stewart Island/Rakiura and the Chatham Islands. meaning: GAZ:00000469 Nicaragua [GAZ:00002978]: text: Nicaragua [GAZ:00002978] + description: A republic in Central America. It is also the least densely populated + with a demographic similar in size to its smaller neighbors. The country + is bordered by Honduras to the north and by Costa Rica to the south. The + Pacific Ocean lies to the west of the country, while the Caribbean Sea lies + to the east. For administrative purposes it is divided into 15 departments + (departamentos) and two self-governing regions (autonomous communities) + based on the Spanish model. The departments are then subdivided into 153 + municipios (municipalities). The two autonomous regions are Region Autonoma + del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred + to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 + they formed the single department of Zelaya. meaning: GAZ:00002978 Niger [GAZ:00000585]: text: Niger [GAZ:00000585] + description: A landlocked country in Western Africa, named after the Niger + River. It borders Nigeria and Benin to the south, Burkina Faso and Mali + to the west, Algeria and Libya to the north and Chad to the east. The capital + city is Niamey. Niger is divided into 7 departments and one capital district. + The departments are subdivided into 36 arrondissements and further subdivided + into 129 communes. meaning: GAZ:00000585 Nigeria [GAZ:00000912]: text: Nigeria [GAZ:00000912] + description: A federal constitutional republic comprising thirty-six states + and one Federal Capital Territory. The country is located in West Africa + and shares land borders with the Republic of Benin in the west, Chad and + Cameroon in the east, and Niger in the north. Its coast lies on the Gulf + of Guinea, part of the Atlantic Ocean, in the south. The capital city is + Abuja. Nigeria is divided into thirty-six states and one Federal Capital + Territory, which are further sub-divided into 774 Local Government Areas + (LGAs). meaning: GAZ:00000912 Niue [GAZ:00006902]: text: Niue [GAZ:00006902] + description: An island nation located in the South Pacific Ocean. Although + self-governing, Niue is in free association with New Zealand, meaning that + the Sovereign in Right of New Zealand is also Niue's head of state. meaning: GAZ:00006902 Norfolk Island [GAZ:00005908]: text: Norfolk Island [GAZ:00005908] + description: A Territory of Australia that includes Norfolk Island and neighboring + islands. meaning: GAZ:00005908 North Korea [GAZ:00002801]: text: North Korea [GAZ:00002801] + description: A state in East Asia in the northern half of the Korean Peninsula, + with its capital in the city of Pyongyang. To the south and separated by + the Korean Demilitarized Zone is South Korea, with which it formed one nation + until division following World War II. At its northern Amnok River border + are China and, separated by the Tumen River in the extreme north-east, Russia. meaning: GAZ:00002801 North Macedonia [GAZ:00006895]: text: North Macedonia [GAZ:00006895] + description: A landlocked country on the Balkan peninsula in southeastern + Europe. It is bordered by Serbia and Kosovo to the north, Albania to the + west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic + of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), + 10 of which comprise Greater Skopje. This is reduced from the previous 123 + municipalities established in 1996-09. Prior to this, local government was + organised into 34 administrative districts. meaning: GAZ:00006895 North Sea [GAZ:00002284]: text: North Sea [GAZ:00002284] + description: A sea situated between the eastern coasts of the British Isles + and the western coast of Europe. meaning: GAZ:00002284 Northern Mariana Islands [GAZ:00003958]: text: Northern Mariana Islands [GAZ:00003958] + description: A group of 15 islands about three-quarters of the way from Hawaii + to the Philippines. meaning: GAZ:00003958 Norway [GAZ:00002699]: text: Norway [GAZ:00002699] + description: A country and constitutional monarchy in Northern Europe that + occupies the western portion of the Scandinavian Peninsula. It is bordered + by Sweden, Finland, and Russia. The Kingdom of Norway also includes the + Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty + over Svalbard is based upon the Svalbard Treaty, but that treaty does not + apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter + I Island and Queen Maud Land in Antarctica are external dependencies, but + those three entities do not form part of the kingdom. meaning: GAZ:00002699 Oman [GAZ:00005283]: text: Oman [GAZ:00005283] + description: A country in southwest Asia, on the southeast coast of the Arabian + Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia + on the west, and Yemen on the southwest. The coast is formed by the Arabian + Sea on the south and east, and the Gulf of Oman on the northeast. The country + also contains Madha, an exclave enclosed by the United Arab Emirates, and + Musandam, an exclave also separated by Emirati territory. Oman is divided + into four governorates (muhafazah) and five regions (mintaqat). The regions + are subdivided into provinces (wilayat). meaning: GAZ:00005283 Pakistan [GAZ:00005246]: text: Pakistan [GAZ:00005246] + description: A country in Middle East which lies on the Iranian Plateau and + some parts of South Asia. It is located in the region where South Asia converges + with Central Asia and the Middle East. It has a 1,046 km coastline along + the Arabian Sea in the south, and is bordered by Afghanistan and Iran in + the west, India in the east and China in the far northeast. Pakistan is + subdivided into four provinces and two territories. In addition, the portion + of Kashmir that is administered by the Pakistani government is divided into + two separate administrative units. The provinces are divided into a total + of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly + equivalent to counties). Tehsils may contain villages or municipalities. + There are over five thousand local governments in Pakistan. meaning: GAZ:00005246 Palau [GAZ:00006905]: text: Palau [GAZ:00006905] + description: A nation that consists of eight principal islands and more than + 250 smaller ones lying roughly 500 miles southeast of the Philippines. meaning: GAZ:00006905 Panama [GAZ:00002892]: text: Panama [GAZ:00002892] + description: The southernmost country of Central America. Situated on an isthmus, + some categorize it as a transcontinental nation connecting the north and + south part of America. It borders Costa Rica to the north-west, Colombia + to the south-east, the Caribbean Sea to the north and the Pacific Ocean + to the south. Panama's major divisions are nine provinces and five indigenous + territories (comarcas indigenas). The provincial borders have not changed + since they were determined at independence in 1903. The provinces are divided + into districts, which in turn are subdivided into sections called corregimientos. + Configurations of the corregimientos are changed periodically to accommodate + population changes as revealed in the census reports. meaning: GAZ:00002892 Papua New Guinea [GAZ:00003922]: text: Papua New Guinea [GAZ:00003922] + description: A country in Oceania that comprises the eastern half of the island + of New Guinea and its offshore islands in Melanesia (a region of the southwestern + Pacific Ocean north of Australia). meaning: GAZ:00003922 Paracel Islands [GAZ:00010832]: text: Paracel Islands [GAZ:00010832] + description: A group of small islands and reefs in the South China Sea, about + one-third of the way from Vietnam to the Philippines. meaning: GAZ:00010832 Paraguay [GAZ:00002933]: text: Paraguay [GAZ:00002933] + description: A landlocked country in South America. It lies on both banks + of the Paraguay River, bordering Argentina to the south and southwest, Brazil + to the east and northeast, and Bolivia to the northwest, and is located + in the very heart of South America. Paraguay consists of seventeen departments + and one capital district (distrito capital). Each department is divided + into districts. meaning: GAZ:00002933 Peru [GAZ:00002932]: text: Peru [GAZ:00002932] + description: A country in western South America. It is bordered on the north + by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, + on the south by Chile, and on the west by the Pacific Ocean. Peru is divided + into 25 regions and the province of Lima. These regions are subdivided into + provinces, which are composed of districts (provincias and distritos). There + are 195 provinces and 1833 districts in Peru. The Lima Province, located + in the central coast of the country, is unique in that it doesn't belong + to any of the twenty-five regions. The city of Lima, which is the nation's + capital, is located in this province. Callao is its own region, even though + it only contains one province, the Constitutional Province of Callao. meaning: GAZ:00002932 Philippines [GAZ:00004525]: text: Philippines [GAZ:00004525] + description: 'An archipelagic nation located in Southeast Asia. The Philippine + archipelago comprises 7,107 islands in the western Pacific Ocean, bordering + countries such as Indonesia, Malaysia, Palau and the Republic of China, + although it is the only Southeast Asian country to share no land borders + with its neighbors. The Philippines is divided into three island groups: + Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, + 136 cities, 1,494 municipalities and 41,995 barangays.' meaning: GAZ:00004525 Pitcairn Islands [GAZ:00005867]: text: Pitcairn Islands [GAZ:00005867] + description: A group of four islands in the southern Pacific Ocean. The Pitcairn + Islands form the southeasternmost extension of the geological archipelago + of the Tuamotus of French Polynesia. meaning: GAZ:00005867 Poland [GAZ:00002939]: text: Poland [GAZ:00002939] + description: A country in Central Europe. Poland is bordered by Germany to + the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus + and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a + Russian exclave, to the north. The administrative division of Poland since + 1999 has been based on three levels of subdivision. The territory of Poland + is divided into voivodeships (provinces); these are further divided into + powiats (counties), and these in turn are divided into gminas (communes + or municipalities). Major cities normally have the status of both gmina + and powiat. Poland currently has 16 voivodeships, 379 powiats (including + 65 cities with powiat status), and 2,478 gminas. meaning: GAZ:00002939 Portugal [GAZ:00004126]: text: Portugal [GAZ:00004126] + description: That part of the Portugese Republic that occupies the W part + of the Iberian Peninsula, and immediately adjacent islands. meaning: GAZ:00004126 Puerto Rico [GAZ:00006935]: text: Puerto Rico [GAZ:00006935] + description: A semi-autonomous territory composed of an archipelago in the + northeastern Caribbean, east of the Dominican Republic and west of the Virgin + Islands, approximately 2,000 km off the coast of Florida (the nearest of + the mainland United States). meaning: GAZ:00006935 Qatar [GAZ:00005286]: text: Qatar [GAZ:00005286] + description: 'An Arab emirate in Southwest Asia, occupying the small Qatar + Peninsula on the northeasterly coast of the larger Arabian Peninsula. It + is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds + the state. Qatar is divided into ten municipalities (Arabic: baladiyah), + which are further divided into zones (districts).' meaning: GAZ:00005286 Republic of the Congo [GAZ:00001088]: text: Republic of the Congo [GAZ:00001088] + description: A country in Central Africa. It is bordered by Gabon, Cameroon, + the Central African Republic, the Democratic Republic of the Congo, the + Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic + of the Congo is divided into 10 regions (regions) and one commune, the capital + Brazzaville. The regions are subdivided into forty-six districts. meaning: GAZ:00001088 Reunion [GAZ:00003945]: text: Reunion [GAZ:00003945] + description: An island, located in the Indian Ocean east of Madagascar, about + 200 km south west of Mauritius, the nearest island. meaning: GAZ:00003945 Romania [GAZ:00002951]: text: Romania [GAZ:00002951] + description: A country in Southeastern Europe. It shares a border with Hungary + and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, + and Bulgaria to the south. Romania has a stretch of sea coast along the + Black Sea. It is located roughly in the lower basin of the Danube and almost + all of the Danube Delta is located within its territory. Romania is divided + into forty-one counties (judete), as well as the municipality of Bucharest + (Bucuresti) - which is its own administrative unit. The country is further + subdivided into 319 cities and 2686 communes (rural localities). meaning: GAZ:00002951 Ross Sea [GAZ:00023304]: text: Ross Sea [GAZ:00023304] + description: A large embayment of the Southern Ocean, extending deeply into + Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck + on the east, at 158degW. meaning: GAZ:00023304 Russia [GAZ:00002721]: text: Russia [GAZ:00002721] + description: 'A transcontinental country extending over much of northern Eurasia. + Russia shares land borders with the following countries (counter-clockwise + from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania + (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, + Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation + comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais + (territories), 4 autonomous okrugs (autonomous districts), one autonomous + oblast, and two federal cities. The federal subjects are grouped into seven + federal districts. These subjects are divided into districts (raions), cities/towns + and urban-type settlements, and, at level 4, selsovets (rural councils), + towns and urban-type settlements under the jurisdiction of the district + and city districts.' meaning: GAZ:00002721 Rwanda [GAZ:00001087]: text: Rwanda [GAZ:00001087] + description: A small landlocked country in the Great Lakes region of east-central + Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo + and Tanzania. Rwanda is divided into five provinces (intara) and subdivided + into thirty districts (akarere). The districts are divided into sectors + (imirenge). meaning: GAZ:00001087 Saint Helena [GAZ:00000849]: text: Saint Helena [GAZ:00000849] + description: An island of volcanic origin and a British overseas territory + in the South Atlantic Ocean. meaning: GAZ:00000849 Saint Kitts and Nevis [GAZ:00006906]: text: Saint Kitts and Nevis [GAZ:00006906] + description: 'A federal two-island nation in the West Indies. Located in the + Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward + Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, + Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast + are Antigua and Barbuda, and to the southeast is the small uninhabited island + of Redonda, and the island of Montserrat. The federation of Saint Kitts + and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts + and five on Nevis.' meaning: GAZ:00006906 Saint Lucia [GAZ:00006909]: text: Saint Lucia [GAZ:00006909] + description: An island nation in the eastern Caribbean Sea on the boundary + with the Atlantic Ocean. meaning: GAZ:00006909 Saint Pierre and Miquelon [GAZ:00003942]: text: Saint Pierre and Miquelon [GAZ:00003942] + description: An Overseas Collectivity of France located in a group of small + islands in the North Atlantic Ocean, the main ones being Saint Pierre and + Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and + Miquelon became an overseas department in 1976, but its status changed to + that of an Overseas collectivity in 1985. meaning: GAZ:00003942 Saint Martin [GAZ:00005841]: text: Saint Martin [GAZ:00005841] + description: An overseas collectivity of France that came into being on 2007-02-22, + encompassing the northern parts of the island of Saint Martin and neighboring + islets. The southern part of the island, Sint Maarten, is part of the Netherlands + Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. meaning: GAZ:00005841 Saint Vincent and the Grenadines [GAZ:02000565]: text: Saint Vincent and the Grenadines [GAZ:02000565] + description: An island nation in the Lesser Antilles chain of the Caribbean + Sea. meaning: GAZ:02000565 Samoa [GAZ:00006910]: text: Samoa [GAZ:00006910] + description: A country governing the western part of the Samoan Islands archipelago + in the South Pacific Ocean. Samoa is made up of eleven itumalo (political + districts). meaning: GAZ:00006910 San Marino [GAZ:00003102]: text: San Marino [GAZ:00003102] + description: A country in the Apennine Mountains. It is a landlocked enclave, + completely surrounded by Italy. San Marino is an enclave in Italy, on the + border between the regioni of Emilia Romagna and Marche. Its topography + is dominated by the Apennines mountain range. San Marino is divided into + nine municipalities, known locally as Castelli (singular castello). meaning: GAZ:00003102 Sao Tome and Principe [GAZ:00006927]: text: Sao Tome and Principe [GAZ:00006927] + description: 'An island nation in the Gulf of Guinea, off the western equatorial + coast of Africa. It consists of two islands: Sao Tome and Principe, located + about 140 km apart and about 250 and 225 km respectively, off of the northwestern + coast of Gabon. Both islands are part of an extinct volcanic mountain range. + Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The + provinces are further divided into seven districts, six on Sao Tome and + one on Principe (with Principe having self-government since 1995-04-29).' meaning: GAZ:00006927 Saudi Arabia [GAZ:00005279]: text: Saudi Arabia [GAZ:00005279] + description: A country on the Arabian Peninsula. It is bordered by Jordan + on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, + and the United Arab Emirates on the east, Oman on the southeast, and Yemen + on the south. The Persian Gulf lies to the northeast and the Red Sea to + its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; + singular mintaqah). Each is then divided into Governorates. meaning: GAZ:00005279 Senegal [GAZ:00000913]: text: Senegal [GAZ:00000913] + description: A country south of the Senegal River in western Africa. Senegal + is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali + to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies + almost entirely within Senegal, surrounded on the north, east and south; + from its western coast Gambia's territory follows the Gambia River more + than 300 km inland. Dakar is the capital city of Senegal, located on the + Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided + into 11 regions and further subdivided into 34 Departements, 103 Arrondissements + (neither of which have administrative function) and by Collectivites Locales. meaning: GAZ:00000913 Serbia [GAZ:00002957]: text: Serbia [GAZ:00002957] + description: 'A landlocked country in Central and Southeastern Europe, covering + the southern part of the Pannonian Plain and the central part of the Balkan + Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria + to the east; Republic of Macedonia, Montenegro to the south; Croatia and + Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided + into 29 districts plus the City of Belgrade. The districts and the city + of Belgrade are further divided into municipalities. Serbia has two autonomous + provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), + and Vojvodina in the north (7 districts, 46 municipalities).' meaning: GAZ:00002957 Seychelles [GAZ:00006922]: text: Seychelles [GAZ:00006922] + description: An archipelagic island country in the Indian Ocean at the eastern + edge of the Somali Sea. It consists of 115 islands. meaning: GAZ:00006922 Sierra Leone [GAZ:00000914]: text: Sierra Leone [GAZ:00000914] + description: A country in West Africa. It is bordered by Guinea in the north + and east, Liberia in the southeast, and the Atlantic Ocean in the southwest + and west. The Republic of Sierra Leone is composed of 3 provinces and one + area called the Western Area; the provinces are further divided into 12 + districts. The Western Area is also divided into 2 districts. meaning: GAZ:00000914 Singapore [GAZ:00003923]: text: Singapore [GAZ:00003923] + description: An island nation located at the southern tip of the Malay Peninsula. + It lies 137 km north of the Equator, south of the Malaysian State of Johor + and north of Indonesia's Riau Islands. Singapore consists of 63 islands, + including mainland Singapore. There are two man-made connections to Johor, + Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in + the west. Since 2001-11-24, Singapore has had an administrative subdivision + into 5 districts. It is also divided into five Regions, urban planning subdivisions + with no administrative role. meaning: GAZ:00003923 Sint Maarten [GAZ:00012579]: text: Sint Maarten [GAZ:00012579] + description: One of five island areas (Eilandgebieden) of the Netherlands + Antilles, encompassing the southern half of the island of Saint Martin/Sint + Maarten. meaning: GAZ:00012579 Slovakia [GAZ:00002956]: text: Slovakia [GAZ:00002956] + description: A landlocked country in Central Europe. The Slovak Republic borders + the Czech Republic and Austria to the west, Poland to the north, Ukraine + to the east and Hungary to the south. The largest city is its capital, Bratislava. + Slovakia is subdivided into 8 kraje (singular - kraj, usually translated + as regions. The kraje are subdivided into many okresy (singular okres, usually + translated as districts). Slovakia currently has 79 districts. meaning: GAZ:00002956 Slovenia [GAZ:00002955]: text: Slovenia [GAZ:00002955] + description: A country in southern Central Europe bordering Italy to the west, + the Adriatic Sea to the southwest, Croatia to the south and east, Hungary + to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. + As of 2005-05 Slovenia is divided into 12 statistical regions for legal + and statistical purposes. Slovenia is divided into 210 local municipalities, + eleven of which have urban status. meaning: GAZ:00002955 Solomon Islands [GAZ:00005275]: text: Solomon Islands [GAZ:00005275] + description: A nation in Melanesia, east of Papua New Guinea, consisting of + nearly one thousand islands. Together they cover a land mass of 28,400 km2. + The capital is Honiara, located on the island of Guadalcanal. meaning: GAZ:00005275 Somalia [GAZ:00001104]: text: Somalia [GAZ:00001104] + description: A country located in the Horn of Africa. It is bordered by Djibouti + to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on + its north, the Indian Ocean at its east, and Ethiopia to the west. Prior + to the civil war, Somalia was divided into eighteen regions (gobollada, + singular gobol), which were in turn subdivided into districts. On a de facto + basis, northern Somalia is now divided up among the quasi-independent states + of Puntland, Somaliland, Galmudug and Maakhir. meaning: GAZ:00001104 South Africa [GAZ:00001094]: text: South Africa [GAZ:00001094] + description: 'A country located at the southern tip of Africa. It borders + the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, + Swaziland, and Lesotho, an independent enclave surrounded by South African + territory. It is divided into nine provinces which are further subdivided + into 52 districts: 6 metropolitan and 46 district municipalities. The 46 + district municipalities are further subdivided into 231 local municipalities. + The district municipalities also contain 20 district management areas (mostly + game parks) that are directly governed by the district municipalities. The + six metropolitan municipalities perform the functions of both district and + local municipalities.' meaning: GAZ:00001094 South Georgia and the South Sandwich Islands [GAZ:00003990]: text: South Georgia and the South Sandwich Islands [GAZ:00003990] + description: A British overseas territory in the southern Atlantic Ocean. + It iconsists of South Georgia and the Sandwich Islands, some 640 km to the + SE. meaning: GAZ:00003990 South Korea [GAZ:00002802]: text: South Korea [GAZ:00002802] + description: A republic in East Asia, occupying the southern half of the Korean + Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous + province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 + special city (teukbyeolsi). These are further subdivided into a variety + of smaller entities, including cities (si), counties (gun), districts (gu), + towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). meaning: GAZ:00002802 South Sudan [GAZ:00233439]: text: South Sudan [GAZ:00233439] + description: A state located in Africa with Juba as its capital city. It's + bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic + of the Congo to the south, and the Central African Republic to the west + and Sudan to the North. Southern Sudan includes the vast swamp region of + the Sudd formed by the White Nile, locally called the Bahr el Jebel. meaning: GAZ:00233439 Spain [GAZ:00003936]: text: Spain [GAZ:00003936] + description: That part of the Kingdom of Spain that occupies the Iberian Peninsula + plus the Balaeric Islands. The Spanish mainland is bordered to the south + and east almost entirely by the Mediterranean Sea (except for a small land + boundary with Gibraltar); to the north by France, Andorra, and the Bay of + Biscay; and to the west by the Atlantic Ocean and Portugal. meaning: GAZ:00003936 Spratly Islands [GAZ:00010831]: text: Spratly Islands [GAZ:00010831] + description: A group of >100 islands located in the Southeastern Asian group + of reefs and islands in the South China Sea, about two-thirds of the way + from southern Vietnam to the southern Philippines. meaning: GAZ:00010831 Sri Lanka [GAZ:00003924]: text: Sri Lanka [GAZ:00003924] + description: An island nation in South Asia, located about 31 km off the southern + coast of India. Sri Lanka is divided into 9 provinces and 25 districts. + Districts are divided into Divisional Secretariats. meaning: GAZ:00003924 State of Palestine [GAZ:00002475]: text: State of Palestine [GAZ:00002475] + description: The territory under the administration of the Palestine National + Authority, as established by the Oslo Accords. The PNA divides the Palestinian + territories into 16 governorates. meaning: GAZ:00002475 Sudan [GAZ:00000560]: text: Sudan [GAZ:00000560] + description: A country in North Africa. It is bordered by Egypt to the north, + the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and + Uganda to the southeast, Democratic Republic of the Congo and the Central + African Republic to the southwest, Chad to the west and Libya to the northwest. + Sudan is divided into twenty-six states (wilayat, singular wilayah) which + in turn are subdivided into 133 districts. meaning: GAZ:00000560 Suriname [GAZ:00002525]: text: Suriname [GAZ:00002525] + description: A country in northern South America. It is situated between French + Guiana to the east and Guyana to the west. The southern border is shared + with Brazil and the northern border is the Atlantic coast. The southernmost + border with French Guiana is disputed along the Marowijne river. Suriname + is divided into 10 districts, each of which is divided into Ressorten. meaning: GAZ:00002525 Svalbard [GAZ:00005396]: text: Svalbard [GAZ:00005396] + description: An archipelago of continental islands lying in the Arctic Ocean + north of mainland Europe, about midway between Norway and the North Pole. meaning: GAZ:00005396 Swaziland [GAZ:00001099]: text: Swaziland [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). meaning: GAZ:00001099 Sweden [GAZ:00002729]: text: Sweden [GAZ:00002729] + description: A Nordic country on the Scandinavian Peninsula in Northern Europe. + It has borders with Norway (west and north) and Finland (northeast). Sweden + is a unitary state, currently divided into twenty-one counties (lan). Each + county further divides into a number of municipalities or kommuner, with + a total of 290 municipalities in 2004. meaning: GAZ:00002729 Switzerland [GAZ:00002941]: text: Switzerland [GAZ:00002941] + description: 'A federal republic in Europe. Switzerland is bordered by Germany, + France, Italy, Austria and Liechtenstein. The Swiss Confederation consists + of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within + Switzerland there are two enclaves: Busingen belongs to Germany, Campione + d''Italia belongs to Italy.' meaning: GAZ:00002941 Syria [GAZ:00002474]: text: Syria [GAZ:00002474] + description: 'A country in Southwest Asia, bordering Lebanon, the Mediterranean + Sea and the island of Cyprus to the west, Israel to the southwest, Jordan + to the south, Iraq to the east, and Turkey to the north. Syria has fourteen + governorates, or muhafazat (singular: muhafazah). The governorates are divided + into sixty districts, or manatiq (singular: mintaqah), which are further + divided into sub-districts, or nawahi (singular: nahia).' meaning: GAZ:00002474 Taiwan [GAZ:00005341]: text: Taiwan [GAZ:00005341] + description: A state in East Asia with de facto rule of the island of Tawain + and adjacent territory. The Republic of China currently administers two + historical provinces of China (one completely and a small part of another + one) and centrally administers two direct-controlled municipalities. meaning: GAZ:00005341 Tajikistan [GAZ:00006912]: text: Tajikistan [GAZ:00006912] + description: A mountainous landlocked country in Central Asia. Afghanistan + borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and + People's Republic of China to the east. Tajikistan consists of 4 administrative + divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous + province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican + Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly + known as Karotegin Province). Each region is divided into several districts + (nohiya or raion). meaning: GAZ:00006912 Tanzania [GAZ:00001103]: text: Tanzania [GAZ:00001103] + description: A country in East Africa bordered by Kenya and Uganda on the + north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, + and Zambia, Malawi and Mozambique on the south. To the east it borders the + Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on + the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight + districts (wilaya), each with at least one council, have been created to + further increase local authority; the councils are also known as local government + authorities. Currently there are 114 councils operating in 99 districts; + 22 are urban and 92 are rural. The 22 urban units are further classified + as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, + Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) + or town councils (the remaining eleven communities). meaning: GAZ:00001103 Thailand [GAZ:00003744]: text: Thailand [GAZ:00003744] + description: 'A country in Southeast Asia. To its east lie Laos and Cambodia; + to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman + Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided + into 75 provinces (changwat), which are gathered into 5 groups of provinces + by location. There are also 2 special governed districts: the capital Bangkok + (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial + level and thus often counted as a 76th province.' meaning: GAZ:00003744 Timor-Leste [GAZ:00006913]: text: Timor-Leste [GAZ:00006913] + description: A country in Southeast Asia. It comprises the eastern half of + the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, + an exclave on the northwestern side of the island, within Indonesian West + Timor. The small country of 15,410 km2 is located about 640 km northwest + of Darwin, Australia. East Timor is divided into thirteen administrative + districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, + villages and hamlets. meaning: GAZ:00006913 Togo [GAZ:00000915]: text: Togo [GAZ:00000915] + description: A country in West Africa bordering Ghana in the west, Benin in + the east and Burkina Faso in the north. In the south, it has a short Gulf + of Guinea coast, on which the capital Lome is located. meaning: GAZ:00000915 Tokelau [GAZ:00260188]: text: Tokelau [GAZ:00260188] + description: 'A dependent territory of New Zealand in the southern Pacific + Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and + Fakaofo. They have a combined land area of 10 km2 (4 sq mi).' meaning: GAZ:00260188 Tonga [GAZ:00006916]: text: Tonga [GAZ:00006916] + description: A Polynesian country, and also an archipelago comprising 169 + islands, of which 36 are inhabited. The archipelago's total surface area + is about 750 square kilometres (290 sq mi) scattered over 700,000 square + kilometres (270,000 sq mi) of the southern Pacific Ocean. meaning: GAZ:00006916 Trinidad and Tobago [GAZ:00003767]: text: Trinidad and Tobago [GAZ:00003767] + description: An archipelagic state in the southern Caribbean, lying northeast + of the South American nation of Venezuela and south of Grenada in the Lesser + Antilles. It also shares maritime boundaries with Barbados to the northeast + and Guyana to the southeast. The country covers an area of 5,128 km2and + consists of two main islands, Trinidad and Tobago, and 21 smaller islands. meaning: GAZ:00003767 Tromelin Island [GAZ:00005812]: text: Tromelin Island [GAZ:00005812] + description: A low, flat 0.8 km2 island in the Indian Ocean, about 350 km + east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 + m long and 700 m wide, surrounded by coral reefs. The island is 7 m high + at its highest point. meaning: GAZ:00005812 Tunisia [GAZ:00000562]: text: Tunisia [GAZ:00000562] + description: A country situated on the Mediterranean coast of North Africa. + It is bordered by Algeria to the west and Libya to the southeast. Tunisia + is subdivided into 24 governorates, divided into 262 "delegations" or "districts" + (mutamadiyat), and further subdivided into municipalities (shaykhats). meaning: GAZ:00000562 Turkey [GAZ:00000558]: text: Turkey [GAZ:00000558] + description: 'A Eurasian country that stretches across the Anatolian peninsula + in western Asia and Thrace (Rumelia) in the Balkan region of southeastern + Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece + to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave + of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. + The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago + are to the west; and the Black Sea is to the north. Separating Anatolia + and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus + and the Dardanelles), which are commonly reckoned to delineate the border + between Asia and Europe, thereby making Turkey transcontinental. The territory + of Turkey is subdivided into 81 provinces for administrative purposes. The + provinces are organized into 7 regions for census purposes; however, they + do not represent an administrative structure. Each province is divided into + districts, for a total of 923 districts.' meaning: GAZ:00000558 Turkmenistan [GAZ:00005018]: text: Turkmenistan [GAZ:00005018] + description: A country in Central Asia. It is bordered by Afghanistan to the + southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan + to the northwest, and the Caspian Sea to the west. It was a constituent + republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan + is divided into five provinces or welayatlar (singular - welayat) and one + independent city. meaning: GAZ:00005018 Turks and Caicos Islands [GAZ:00003955]: text: Turks and Caicos Islands [GAZ:00003955] + description: A British Overseas Territory consisting of two groups of tropical + islands in the West Indies. The Turks and Caicos Islands are divided into + six administrative districts (two in the Turks Islands and four in the Caicos + Islands. meaning: GAZ:00003955 Tuvalu [GAZ:00009715]: text: Tuvalu [GAZ:00009715] + description: A Polynesian island nation located in the Pacific Ocean midway + between Hawaii and Australia. meaning: GAZ:00009715 United States of America [GAZ:00002459]: text: United States of America [GAZ:00002459] + description: A federal constitutional republic comprising fifty states and + a federal district. The country is situated mostly in central North America, + where its forty-eight contiguous states and Washington, DC, the capital + district, lie between the Pacific and Atlantic Oceans, bordered by Canada + to the north and Mexico to the south. The State of Alaska is in the northwest + of the continent, with Canada to its east and Russia to the west across + the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United + States also possesses several territories, or insular areas, that are scattered + around the Caribbean and Pacific. The states are divided into smaller administrative + regions, called counties in most states, exceptions being Alaska (parts + of the state are organized into subdivisions called boroughs; the rest of + the state's territory that is not included in any borough is divided into + "census areas"), and Louisiana (which is divided into county-equivalents + that are called parishes). There are also independent cities which are within + particular states but not part of any particular county or consolidated + city-counties. Another type of organization is where the city and county + are unified and function as an independent city. There are thirty-nine independent + cities in Virginia and other independent cities or city-counties are San + Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, + Colorado and Carson City, Nevada. Counties can include a number of cities, + towns, villages, or hamlets, or sometimes just a part of a city. Counties + have varying degrees of political and legal significance, but they are always + administrative divisions of the state. Counties in many states are further + subdivided into townships, which, by definition, are administrative divisions + of a county. In some states, such as Michigan, a township can file a charter + with the state government, making itself into a "charter township", which + is a type of mixed municipal and township status (giving the township some + of the rights of a city without all of the responsibilities), much in the + way a metropolitan municipality is a mixed municipality and county. meaning: GAZ:00002459 Uganda [GAZ:00001102]: text: Uganda [GAZ:00001102] + description: 'A landlocked country in East Africa, bordered on the east by + Kenya, the north by Sudan, on the west by the Democratic Republic of the + Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern + part of the country includes a substantial portion of Lake Victoria, within + which it shares borders with Kenya and Tanzania. Uganda is divided into + 80 districts, spread across four administrative regions: Northern, Eastern, + Central and Western. The districts are subdivided into counties.' meaning: GAZ:00001102 Ukraine [GAZ:00002724]: text: Ukraine [GAZ:00002724] + description: A country in Eastern Europe. It borders Russia to the east, Belarus + to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova + to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine + is subdivided into twenty-four oblasts (provinces) and one autonomous republic + (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, + and Sevastopol, both have a special legal status. The 24 oblasts and Crimea + are subdivided into 490 raions (districts), or second-level administrative + units. meaning: GAZ:00002724 United Arab Emirates [GAZ:00005282]: text: United Arab Emirates [GAZ:00005282] + description: A Middle Eastern federation of seven states situated in the southeast + of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering + Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, + Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. meaning: GAZ:00005282 United Kingdom [GAZ:00002637]: text: United Kingdom [GAZ:00002637] + description: A sovereign island country located off the northwestern coast + of mainland Europe comprising of the four constituent countries; England, + Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, + the northeast part of the island of Ireland and many small islands. Apart + from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North + Sea, the English Channel and the Irish Sea. The largest island, Great Britain, + is linked to France by the Channel Tunnel. meaning: GAZ:00002637 Uruguay [GAZ:00002930]: text: Uruguay [GAZ:00002930] + description: A country located in the southeastern part of South America. + It is bordered by Brazil to the north, by Argentina across the bank of both + the Uruguay River to the west and the estuary of Rio de la Plata to the + southwest, and the South Atlantic Ocean to the southeast. Uraguay consists + of 19 departments (departamentos, singular - departamento). meaning: GAZ:00002930 Uzbekistan [GAZ:00004979]: text: Uzbekistan [GAZ:00004979] + description: A doubly landlocked country in Central Asia, formerly part of + the Soviet Union. It shares borders with Kazakhstan to the west and to the + north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan + to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one + autonomous republic (respublika and one independent city (shahar). meaning: GAZ:00004979 Vanuatu [GAZ:00006918]: text: Vanuatu [GAZ:00006918] + description: An island country located in the South Pacific Ocean. The archipelago, + which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern + Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New + Guinea, southeast of the Solomon Islands, and west of Fiji. meaning: GAZ:00006918 Venezuela [GAZ:00002931]: text: Venezuela [GAZ:00002931] + description: A country on the northern coast of South America. The country + comprises a continental mainland and numerous islands located off the Venezuelan + coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses + borders with Guyana to the east, Brazil to the south, and Colombia to the + west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, + Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just + north, off the Venezuelan coast. Venezuela is divided into twenty-three + states (Estados), a capital district (distrito capital) corresponding to + the city of Caracas, the Federal Dependencies (Dependencias Federales, a + special territory), and Guayana Esequiba (claimed in a border dispute with + Guyana). Venezuela is further subdivided into 335 municipalities (municipios); + these are subdivided into over one thousand parishes (parroquias). meaning: GAZ:00002931 Viet Nam [GAZ:00003756]: text: Viet Nam [GAZ:00003756] + description: The easternmost country on the Indochina Peninsula in Southeast + Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, + alongside China, Laos, and Cambodia. meaning: GAZ:00003756 Virgin Islands [GAZ:00003959]: text: Virgin Islands [GAZ:00003959] + description: A group of islands in the Caribbean that are an insular area + of the United States. The islands are geographically part of the Virgin + Islands archipelago and are located in the Leeward Islands of the Lesser + Antilles. The US Virgin Islands are an organized, unincorporated United + States territory. The US Virgin Islands are administratively divided into + two districts and subdivided into 20 sub-districts. meaning: GAZ:00003959 Wake Island [GAZ:00007111]: text: Wake Island [GAZ:00007111] + description: A coral atoll (despite its name) having a coastline of 19 km + in the North Pacific Ocean, located about two-thirds of the way from Honolulu + (3,700 km west) to Guam (2,430 km east). meaning: GAZ:00007111 Wallis and Futuna [GAZ:00007191]: text: Wallis and Futuna [GAZ:00007191] + description: A Polynesian French island territory (but not part of, or even + contiguous with, French Polynesia) in the South Pacific between Fiji and + Samoa. It is made up of three main volcanic tropical islands and a number + of tiny islets. meaning: GAZ:00007191 West Bank [GAZ:00009572]: text: West Bank [GAZ:00009572] + description: A landlocked territory near the Mediterranean coast of Western + Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the + south, west and north.[2] Under Israeli occupation since 1967, the area + is split into 167 Palestinian "islands" under partial Palestinian National + Authority civil rule, and 230 Israeli settlements into which Israeli law + is "pipelined". meaning: GAZ:00009572 Western Sahara [GAZ:00000564]: text: Western Sahara [GAZ:00000564] + description: A territory of northwestern Africa, bordered by Morocco to the + north, Algeria in the northeast, Mauritania to the east and south, and the + Atlantic Ocean on the west. Western Sahara is administratively divided into + four regions. meaning: GAZ:00000564 Yemen [GAZ:00005284]: text: Yemen [GAZ:00005284] + description: A country located on the Arabian Peninsula in Southwest Asia. + Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, + the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's + territory includes over 200 islands, the largest of which is Socotra, about + 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen + is divided into twenty governorates (muhafazah) and one municipality. The + population of each governorate is listed in the table below. The governorates + of Yemen are divided into 333 districts (muderiah). The districts are subdivided + into 2,210 sub-districts, and then into 38,284 villages (as of 2001). meaning: GAZ:00005284 Zambia [GAZ:00001107]: text: Zambia [GAZ:00001107] + description: A landlocked country in Southern Africa. The neighbouring countries + are the Democratic Republic of the Congo to the north, Tanzania to the north-east, + Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, + and Angola to the west. The capital city is Lusaka. Zambia is divided into + nine provinces. Each province is subdivided into several districts with + a total of 73 districts. meaning: GAZ:00001107 Zimbabwe [GAZ:00001106]: text: Zimbabwe [GAZ:00001106] + description: A landlocked country in the southern part of the continent of + Africa, between the Zambezi and Limpopo rivers. It is bordered by South + Africa to the south, Botswana to the southwest, Zambia to the northwest, + and Mozambique to the east. Zimbabwe is divided into eight provinces and + two cities with provincial status. The provinces are subdivided into 59 + districts and 1,200 municipalities. meaning: GAZ:00001106 types: WhitespaceMinimizedString: diff --git a/web/templates/mpox/schema_core.yaml b/web/templates/mpox/schema_core.yaml index d3b0d156..c3bf6ee7 100644 --- a/web/templates/mpox/schema_core.yaml +++ b/web/templates/mpox/schema_core.yaml @@ -1,6 +1,6 @@ id: https://example.com/mpox name: Mpox -version: 5.3.3 +version: 7.5.5 description: "" imports: - 'linkml:types' @@ -18,14 +18,14 @@ classes: is_a: dh_interface see_also: templates/mpox/SOP_Mpox.pdf annotations: - version: 4.3.3 - "Mpox_international": - name: "Mpox_international" + version: 6.5.5 + "MpoxInternational": + name: "MpoxInternational" description: International specification for Mpox clinical virus biosample data gathering is_a: dh_interface see_also: templates/mpox/SOP_Mpox_international.pdf annotations: - version: 5.3.3 + version: 7.5.5 slots: {} enums: {} types: diff --git a/web/templates/mpox/schema_enums.tsv b/web/templates/mpox/schema_enums.tsv index 0dda060b..06cb850b 100644 --- a/web/templates/mpox/schema_enums.tsv +++ b/web/templates/mpox/schema_enums.tsv @@ -1,1574 +1,1821 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal - -null value menu GENEPIO:0001619 Not Applicable - GENEPIO:0001618 Missing - GENEPIO:0001620 Not Collected - GENEPIO:0001668 Not Provided - GENEPIO:0001810 Restricted Access - -geo_loc_name (state/province/territory) menu GAZ:00002566 Alberta - GAZ:00002562 British Columbia - GAZ:00002571 Manitoba - GAZ:00002570 New Brunswick - GAZ:00002567 Newfoundland and Labrador - GAZ:00002575 Northwest Territories - GAZ:00002565 Nova Scotia - GAZ:00002574 Nunavut - GAZ:00002563 Ontario - GAZ:00002572 Prince Edward Island - GAZ:00002569 Quebec - GAZ:00002564 Saskatchewan - GAZ:00002576 Yukon - - -sample collection date precision menu UO:0000036 year - UO:0000035 month - UO:0000033 day - - -NML submitted specimen type menu UBERON:0006314 Bodily fluid - OBI:0001051 DNA - OBI:0001010 Nucleic acid - OBI:0000880 RNA - OBI:0002600 Swab - UBERON:0000479 Tissue - GENEPIO:0001619 Not Applicable - - - -Related specimen relationship type menu HP:0011009 Acute - Convalescent - Familial - EFO:0009642 Follow-up - Reinfection testing - Previously Submitted - Sequencing/bioinformatics methods development/validation - Specimen sampling methods testing - -anatomical material menu UBERON:0000178 Blood - UBERON:0010210 Blood clot - UBERON:0001977 Blood serum - UBERON:0001969 Blood plasma - NCIT:C41067 Whole blood - UBERON:0006314 Fluid - UBERON:0001836 Saliva - UBERON:0001359 Fluid (cerebrospinal (CSF)) - UBERON:0002409 Fluid (pericardial) - UBERON:0001087 Fluid (pleural) - UBERON:0036243 Fluid (vaginal) - UBERON:0000173 Fluid (amniotic) - NCIT:C3824 Lesion - NCIT:C43278 Lesion (Macule) - NCIT:C39690 Lesion (Papule) - NCIT:C78582 Lesion (Pustule) - GENEPIO:0100490 Lesion (Scab) - GENEPIO:0100491 Lesion (Vesicle) - SYMP:0000487 Rash - NCIT:C3426 Ulcer - UBERON:0000479 Tissue - NCIT:C3671 Wound tissue (injury) - -anatomical material international menu UBERON:0000178 Blood [UBERON:0000178] - UBERON:0010210 Blood clot [UBERON:0010210] - UBERON:0001977 Blood serum [UBERON:0001977] - UBERON:0001969 Blood plasma [UBERON:0001969] - NCIT:C41067 Whole blood [NCIT:C41067] - UBERON:0006314 Fluid [UBERON:0006314] - UBERON:0001836 Saliva [UBERON:0001836] - UBERON:0001359 Fluid (cerebrospinal (CSF)) [UBERON:0001359] - UBERON:0002409 Fluid (pericardial) [UBERON:0002409] - UBERON:0001087 Fluid (pleural) [UBERON:0001087] - UBERON:0036243 Fluid (vaginal) [UBERON:0036243] - UBERON:0000173 Fluid (amniotic) [UBERON:0000173] - NCIT:C3824 Lesion [NCIT:C3824] - NCIT:C43278 Lesion (Macule) [NCIT:C43278] - NCIT:C39690 Lesion (Papule) [NCIT:C39690] - NCIT:C78582 Lesion (Pustule) [NCIT:C78582] - GENEPIO:0100490 Lesion (Scab) [GENEPIO:0100490] - GENEPIO:0100491 Lesion (Vesicle) [GENEPIO:0100491] - SYMP:0000487 Rash [SYMP:0000487] - NCIT:C3426 Ulcer [NCIT:C3426] - UBERON:0000479 Tissue [UBERON:0000479] - NCIT:C3671 Wound tissue (injury) [NCIT:C3671] - - -anatomical part menu UBERON:0001245 Anus - UBERON:0012336 Perianal skin - UBERON:0001460 Arm - NCIT:C32628 Arm (forearm) - UBERON:0001461 Elbow - FMA:14181 Back - UBERON:0013691 Buttock - UBERON:0000002 Cervix - UBERON:0001443 Chest - BTO:0000476 Foot - BTO:0003358 Genital area - UBERON:0000989 Penis - UBERON:0035651 Glans (tip of penis) - UBERON:0001332 Prepuce of penis (foreskin) - UBERON:0002356 Perineum - UBERON:0001300 Scrotum - UBERON:0000996 Vagina - UBERON:0002530 Gland - BTO:0004668 Hand - FMA:9666 Finger - FMA:24920 Hand (palm) - UBERON:0000033 Head - UBERON:0006956 Buccal mucosa - UBERON:0001567 Cheek - UBERON:0001690 Ear - NCIT:C103848 Preauricular region - UBERON:0000970 Eye - UBERON:0001456 Face - UBERON:0008200 Forehead - UBERON:0001833 Lip - UBERON:0011595 Jaw - UBERON:0001723 Tongue - UBERON:0013203 Hypogastrium (suprapubic region) - UBERON:0000978 Leg - UBERON:0001512 Ankle - UBERON:0001465 Knee - UBERON:0000376 Thigh - GENEPIO:0100492 Lower body - UBERON:0001707 Nasal Cavity - UBERON:2001427 Anterior Nares - UBERON:0005921 Inferior Nasal Turbinate - UBERON:0005922 Middle Nasal Turbinate - UBERON:0000974 Neck - UBERON:0000341 Pharynx (throat) - UBERON:0001728 Nasopharynx (NP) - UBERON:0001729 Oropharynx (OP) - UBERON:0003126 Trachea - UBERON:0001052 Rectum - UBERON:0001467 Shoulder - UBERON:0001003 Skin - - - - -anatomical part international menu UBERON:0001245 Anus [UBERON:0001245] - UBERON:0012336 Perianal skin [UBERON:0012336] - UBERON:0001460 Arm [UBERON:0001460] - NCIT:C32628 Arm (forearm) [NCIT:C32628] - UBERON:0001461 Elbow [UBERON:0001461] - FMA:14181 Back [FMA:14181] - UBERON:0013691 Buttock [UBERON:0013691] - UBERON:0000002 Cervix [UBERON:0000002] - UBERON:0001443 Chest [UBERON:0001443] - BTO:0000476 Foot [BTO:0000476] - BTO:0003358 Genital area [BTO:0003358] - UBERON:0000989 Penis [UBERON:0000989] - UBERON:0035651 Glans (tip of penis) [UBERON:0035651] - UBERON:0001332 Prepuce of penis (foreskin) - UBERON:0002356 Perineum [UBERON:0002356] - UBERON:0001300 Scrotum [UBERON:0001300] - UBERON:0000996 Vagina [UBERON:0000996] - UBERON:0002530 Gland [UBERON:0002530] - BTO:0004668 Hand [BTO:0004668] - FMA:9666 Finger [FMA:9666] - FMA:24920 Hand (palm) [FMA:24920] - UBERON:0000033 Head [UBERON:0000033] - UBERON:0006956 Buccal mucosa [UBERON:0006956] - UBERON:0001567 Cheek [UBERON:0001567] - UBERON:0001690 Ear [UBERON:0001690] - NCIT:C103848 Preauricular region [NCIT:C103848] - UBERON:0000970 Eye [UBERON:0000970] - UBERON:0001456 Face [UBERON:0001456] - UBERON:0008200 Forehead [UBERON:0008200] - UBERON:0001833 Lip [UBERON:0001833] - UBERON:0011595 Jaw [UBERON:0011595] - UBERON:0001723 Tongue [UBERON:0001723] - UBERON:0013203 Hypogastrium (suprapubic region) [UBERON:0013203] - UBERON:0000978 Leg [UBERON:0000978] - UBERON:0001512 Ankle [UBERON:0001512] - UBERON:0001465 Knee [UBERON:0001465] - UBERON:0000376 Thigh [UBERON:0000376] - GENEPIO:0100492 Lower body [GENEPIO:0100492] - UBERON:0001707 Nasal Cavity [UBERON:0001707] - UBERON:2001427 Anterior Nares [UBERON:2001427] - UBERON:0005921 Inferior Nasal Turbinate [UBERON:0005921] - UBERON:0005922 Middle Nasal Turbinate [UBERON:0005922] - UBERON:0000974 Neck [UBERON:0000974] - UBERON:0000341 Pharynx (throat) [UBERON:0000341] - UBERON:0001728 Nasopharynx (NP) [UBERON:0001728] - UBERON:0001729 Oropharynx (OP) [UBERON:0001729] - UBERON:0003126 Trachea [UBERON:0003126] - UBERON:0001052 Rectum [UBERON:0001052] - UBERON:0001467 Shoulder [UBERON:0001467] - UBERON:0001003 Skin [UBERON:0001003] - - - -body product menu UBERON:0001913 Breast Milk - UBERON:0001988 Feces - SYMP:0000651 Fluid (discharge) - UBERON:0000177 Pus - UBERON:0006530 Fluid (seminal) - UBERON:0000912 Mucus - UBERON:0007311 Sputum - UBERON:0001089 Sweat - UBERON:0001827 Tear - UBERON:0001088 Urine - -body product international menu UBERON:0001913 Breast Milk [UBERON:0001913] - UBERON:0001988 Feces [UBERON:0001988] - SYMP:0000651 Fluid (discharge) [SYMP:0000651] - UBERON:0000177 Pus [UBERON:0000177] - UBERON:0006530 Fluid (seminal) [UBERON:0006530] - UBERON:0000912 Mucus [UBERON:0000912] - UBERON:0007311 Sputum [UBERON:0007311] - UBERON:0001089 Sweat [UBERON:0001089] - UBERON:0001827 Tear [UBERON:0001827] - UBERON:0001088 Urine [UBERON:0001088] - -environmental material international menu Animal carcass - GSSO:005304 Bedding (Bed linen) - GSSO:003405 Clothing - Drinkware - Tableware - Dish - Utensil - - -collection method menu NCIT:C52009 Amniocentesis - NCIT:C15631 Aspiration - GENEPIO:0100028 Suprapubic Aspiration - GENEPIO:0100029 Tracheal aspiration - GENEPIO:0100030 Vacuum Aspiration - OBI:0002650 Biopsy - OBI:0002651 Needle Biopsy - OBI:0302885 Filtration - GENEPIO:0100031 Air filtration - OBI:0600044 Lavage - GENEPIO:0100032 Bronchoalveolar lavage (BAL) - GENEPIO:0100033 Gastric Lavage - NCIT:C15327 Lumbar Puncture - MMO:0000344 Necropsy - NCIT:C28221 Phlebotomy - GENEPIO:0002116 Rinsing - GENEPIO:0100034 Saline gargle (mouth rinse and gargle) - GENEPIO:0100035 Scraping - GENEPIO:0002117 Swabbing - GENEPIO:0100036 Finger Prick - NCIT:C15392 Thoracentesis (chest tap) - -collection method international menu NCIT:C52009 Amniocentesis [NCIT:C52009] - NCIT:C15631 Aspiration [NCIT:C15631] - GENEPIO:0100028 Suprapubic Aspiration [GENEPIO:0100028] - GENEPIO:0100029 Tracheal aspiration [GENEPIO:0100029] - GENEPIO:0100030 Vacuum Aspiration [GENEPIO:0100030] - OBI:0002650 Biopsy [OBI:0002650] - OBI:0002651 Needle Biopsy [OBI:0002651] - OBI:0302885 Filtration [OBI:0302885] - GENEPIO:0100031 Air filtration [GENEPIO:0100031] - OBI:0600044 Lavage [OBI:0600044] - GENEPIO:0100032 Bronchoalveolar lavage (BAL) [GENEPIO:0100032] - GENEPIO:0100033 Gastric Lavage [GENEPIO:0100033] - NCIT:C15327 Lumbar Puncture [NCIT:C15327] - MMO:0000344 Necropsy [MMO:0000344] - NCIT:C28221 Phlebotomy [NCIT:C28221] - GENEPIO:0002116 Rinsing [GENEPIO:0002116] - GENEPIO:0100034 Saline gargle (mouth rinse and gargle) [GENEPIO:0100034] - GENEPIO:0100035 Scraping [GENEPIO:0100035] - GENEPIO:0002117 Swabbing [GENEPIO:0002117] - GENEPIO:0100036 Finger Prick [GENEPIO:0100036] - NCIT:C15392 Thoracentesis (chest tap) [NCIT:C15392] - - -collection device menu OBI:0002859 Blood Collection Tube - OBI:0002826 Bronchoscope - OBI:0002088 Collection Container - GENEPIO:0100026 Collection Cup - GENEPIO:0100103 Filter - OBI:0000436 Needle - OBI:0002860 Serum Collection Tube - OBI:0002861 Sputum Collection Tube - OBI:0002831 Suction Catheter - GENEPIO:0100027 Swab - GENEPIO:0100493 Dry swab - OBI:0002862 Urine Collection Tube - GENEPIO:0100509 Universal Transport Medium (UTM) - OBI:0002866 Virus Transport Medium - - -collection device international menu OBI:0002859 Blood Collection Tube [OBI:0002859] - OBI:0002826 Bronchoscope [OBI:0002826] - OBI:0002088 Collection Container [OBI:0002088] - GENEPIO:0100026 Collection Cup [GENEPIO:0100026] - GENEPIO:0100103 Filter [GENEPIO:0100103] - OBI:0000436 Needle [OBI:0000436] - OBI:0002860 Serum Collection Tube [OBI:0002860] - OBI:0002861 Sputum Collection Tube [OBI:0002861] - OBI:0002831 Suction Catheter [OBI:0002831] - GENEPIO:0100027 Swab [GENEPIO:0100027] - GENEPIO:0100493 Dry swab [GENEPIO:0100493] - OBI:0002862 Urine Collection Tube [OBI:0002862] - GENEPIO:0100509 Universal Transport Medium (UTM) [GENEPIO:0100509] - OBI:0002866 Virus Transport Medium [OBI:0002866] - - -specimen processing menu GENEPIO:0100039 Virus passage - GENEPIO:0100040 RNA re-extraction (post RT-PCR) - OBI:0600016 Specimens pooled - -specimen processing international menu GENEPIO:0100039 Virus passage [GENEPIO:0100039] - GENEPIO:0100040 RNA re-extraction (post RT-PCR) [GENEPIO:0100040] - OBI:0600016 Specimens pooled [OBI:0600016] - - -host (common name) menu NCBITaxon:9606 Human - -host (common name) international menu NCBITaxon:9606 Human [NCBITaxon:9606] - NCBITaxon:9989 Rodent - NCBITaxon:10090 Mouse - Prairie Dog - NCBITaxon:10116 Rat - FOODON:03411389 Squirrel - -host (scientific name) menu NCBITaxon:9606 Homo sapiens - -host (scientific name) international menu NCBITaxon:9606 Homo sapiens [NCBITaxon:9606] - -host health state menu NCIT:C3833 Asymptomatic - NCIT:C28554 Deceased - NCIT:C115935 Healthy - NCIT:C49498 Recovered - NCIT:C25269 Symptomatic - -host health state international menu NCIT:C3833 Asymptomatic [NCIT:C3833] - NCIT:C28554 Deceased [NCIT:C28554] - NCIT:C115935 Healthy [NCIT:C115935] - NCIT:C49498 Recovered [NCIT:C49498] - NCIT:C25269 Symptomatic [NCIT:C25269] - -host health status details menu NCIT:C25179 Hospitalized - GENEPIO:0100045 Hospitalized (Non-ICU) - GENEPIO:0100046 Hospitalized (ICU) - GENEPIO:0100047 Medically Isolated - GENEPIO:0100048 Medically Isolated (Negative Pressure) - NCIT:C173768 Self-quarantining - -host health status details international menu NCIT:C25179 Hospitalized [NCIT:C25179] - GENEPIO:0100045 Hospitalized (Non-ICU) [GENEPIO:0100045] - GENEPIO:0100046 Hospitalized (ICU) [GENEPIO:0100046] - GENEPIO:0100047 Medically Isolated [GENEPIO:0100047] - GENEPIO:0100048 Medically Isolated (Negative Pressure) [GENEPIO:0100048] - NCIT:C173768 Self-quarantining [NCIT:C173768] - -host health outcome menu NCIT:C28554 Deceased - NCIT:C25254 Deteriorating - NCIT:C49498 Recovered - NCIT:C30103 Stable - -host health outcome international menu NCIT:C28554 Deceased [NCIT:C28554] - NCIT:C25254 Deteriorating [NCIT:C25254] - NCIT:C49498 Recovered [NCIT:C49498] - NCIT:C30103 Stable [NCIT:C30103] - - -host age unit menu UO:0000035 month - UO:0000036 year - -host age unit international menu UO:0000035 month [UO:0000035] - UO:0000036 year [UO:0000036] - -host age bin menu GENEPIO:0100049 0 - 9 - GENEPIO:0100050 10 - 19 - GENEPIO:0100051 20 - 29 - GENEPIO:0100052 30 - 39 - GENEPIO:0100053 40 - 49 - GENEPIO:0100054 50 - 59 - GENEPIO:0100055 60 - 69 - GENEPIO:0100056 70 - 79 - GENEPIO:0100057 80 - 89 - GENEPIO:0100058 90 - 99 - GENEPIO:0100059 100+ - -host age bin international menu GENEPIO:0100049 0 - 9 [GENEPIO:0100049] - GENEPIO:0100050 10 - 19 [GENEPIO:0100050] - GENEPIO:0100051 20 - 29 [GENEPIO:0100051] - GENEPIO:0100052 30 - 39 [GENEPIO:0100052] - GENEPIO:0100053 40 - 49 [GENEPIO:0100053] - GENEPIO:0100054 50 - 59 [GENEPIO:0100054] - GENEPIO:0100055 60 - 69 [GENEPIO:0100055] - GENEPIO:0100056 70 - 79 [GENEPIO:0100056] - GENEPIO:0100057 80 - 89 [GENEPIO:0100057] - GENEPIO:0100058 90 - 99 [GENEPIO:0100058] - GENEPIO:0100059 100+ [GENEPIO:0100059] - -host gender menu NCIT:C46110 Female - NCIT:C46109 Male - GSSO:000132 Non-binary gender - GSSO:004004 Transgender (assigned male at birth) - GSSO:004005 Transgender (assigned female at birth) - NCIT:C110959 Undeclared - -host gender international menu NCIT:C46110 Female [NCIT:C46110] - NCIT:C46109 Male [NCIT:C46109] - GSSO:000132 Non-binary gender [GSSO:000132] - GSSO:004004 Transgender (assigned male at birth) [GSSO:004004] - GSSO:004005 Transgender (assigned female at birth) [GSSO:004005] - NCIT:C110959 Undeclared [NCIT:C110959] - - -signs and symptoms menu HP:0025143 Chills (sudden cold sensation) A sudden sensation of feeling cold. - HP:0000509 Conjunctivitis (pink eye) Inflammation of the conjunctiva. - HP:0012735 Cough A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. - HP:0012378 Fatigue (tiredness) A subjective feeling of tiredness characterized by a lack of energy and motivation. - HP:0001945 Fever Body temperature elevated above the normal range. - HP:0002315 Headache Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. - NCIT:C3824 Lesion - NCIT:C43278 Lesion (Macule) - NCIT:C39690 Lesion (Papule) - NCIT:C78582 Lesion (Pustule) - GENEPIO:0100490 Lesion (Scab) - GENEPIO:0100491 Lesion (Vesicle) - HP:0003326 Myalgia (muscle pain) Pain in muscle. - HP:0003418 Back pain - HP:0002018 Nausea A sensation of unease in the stomach together with an urge to vomit. - HP:0000988 Rash A red eruption of the skin. - NCIT:C50747 Sore throat Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. - NCIT:C36172 Sweating - HP:0002716 Swollen Lymph Nodes Enlargment (swelling) of a lymph node. - NCIT:C3426 Ulcer - HP:0002013 Vomiting (throwing up) Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. - - -signs and symptoms international menu HP:0025143 Chills (sudden cold sensation) [HP:0025143] A sudden sensation of feeling cold. - HP:0000509 Conjunctivitis (pink eye) [HP:0000509] Inflammation of the conjunctiva. - HP:0012735 Cough [HP:0012735] A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. - HP:0012378 Fatigue (tiredness) [HP:0012378] A subjective feeling of tiredness characterized by a lack of energy and motivation. - HP:0001945 Fever [HP:0001945] Body temperature elevated above the normal range. - HP:0002315 Headache [HP:0002315] Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. - NCIT:C3824 Lesion [NCIT:C3824] - NCIT:C43278 Lesion (Macule) [NCIT:C43278] - NCIT:C39690 Lesion (Papule) [NCIT:C39690] - NCIT:C78582 Lesion (Pustule) [NCIT:C78582] - GENEPIO:0100490 Lesion (Scab) [GENEPIO:0100490] - GENEPIO:0100491 Lesion (Vesicle) [GENEPIO:0100491] - HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. - HP:0003418 Back pain [HP:0003418] - HP:0002018 Nausea [HP:0002018] A sensation of unease in the stomach together with an urge to vomit. - HP:0000988 Rash [HP:0000988] A red eruption of the skin. - NCIT:C50747 Sore throat [NCIT:C50747] Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. - NCIT:C36172 Sweating [NCIT:C36172] - HP:0002716 Swollen Lymph Nodes [HP:0002716] Enlargment (swelling) of a lymph node. - NCIT:C3426 Ulcer [NCIT:C3426] - HP:0002013 Vomiting (throwing up) [HP:0002013] Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. - - -pre-existing conditions and risk factors menu MONDO:0004992 Cancer - HP:0000819 Diabetes mellitus (diabetes) - HP:0100651 Type I diabetes mellitus (T1D) - HP:0005978 Type II diabetes mellitus (T2D) - NCIT:C14139 Immunocompromised - NCIT:C26726 Infectious disorder - DOID:13778 Chancroid (Haemophilus ducreyi) - DOID:11263 Chlamydia - DOID:7551 Gonorrhea - NCIT:C155871 Herpes Simplex Virus infection (HSV) - MONDO:0005109 Human immunodeficiency virus (HIV) - MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) - MONDO:0005161 Human papilloma virus infection (HPV) - DOID:13819 Lymphogranuloma venereum - NCBITaxon:2097 Mycoplsma genitalium - DOID:4166 Syphilis - DOID:1947 Trichomoniasis - MONDO:0004670 Lupus - NCIT:C25742 Pregnancy - NCIT:C16124 Prior therapy - NCIT:C16212 Cancer treatment - NCIT:C15632 Chemotherapy - NCIT:C16118 HIV and Antiretroviral therapy (ART) - CHEBI:35341 Steroid - NCIT:C159659 Transplant - -pre-existing conditions and risk factors international menu MONDO:0004992 Cancer [MONDO:0004992] - HP:0000819 Diabetes mellitus (diabetes) [HP:0000819] - HP:0100651 Type I diabetes mellitus (T1D) [HP:0100651] - HP:0005978 Type II diabetes mellitus (T2D) [HP:0005978] - NCIT:C14139 Immunocompromised [NCIT:C14139] - NCIT:C26726 Infectious disorder [NCIT:C26726] - DOID:13778 Chancroid (Haemophilus ducreyi) [DOID:13778] - DOID:11263 Chlamydia [DOID:11263] - DOID:7551 Gonorrhea [DOID:7551] - NCIT:C155871 Herpes Simplex Virus infection (HSV) [NCIT:C155871] - MONDO:0005109 Human immunodeficiency virus (HIV) [MONDO:0005109] - MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] - MONDO:0005161 Human papilloma virus infection (HPV) [MONDO:0005161] - DOID:13819 Lymphogranuloma venereum [DOID:13819] - NCBITaxon:2097 Mycoplsma genitalium [NCBITaxon:2097] - DOID:4166 Syphilis [DOID:4166] - DOID:1947 Trichomoniasis [DOID:1947] - MONDO:0004670 Lupus [MONDO:0004670] - NCIT:C25742 Pregnancy [NCIT:C25742] - NCIT:C16124 Prior therapy [NCIT:C16124] - NCIT:C16212 Cancer treatment [NCIT:C16212] - NCIT:C15632 Chemotherapy [NCIT:C15632] - NCIT:C16118 HIV and Antiretroviral therapy (ART) [NCIT:C16118] - CHEBI:35341 Steroid [CHEBI:35341] - NCIT:C159659 Transplant [NCIT:C159659] - -complications menu MONDO:0005682 Bronchopneumonia - MONDO:0023865 Corneal infection - MP:0002908 Delayed wound healing (lesion healing) - DOID:9588 Encephalitis - DOID:820 Myocarditis - IDO:0000567 Secondary infection - HP:0100806 Sepsis - -complications international menu MONDO:0005682 Bronchopneumonia [MONDO:0005682] - MONDO:0023865 Corneal infection [MONDO:0023865] - MP:0002908 Delayed wound healing (lesion healing) [MP:0002908] - DOID:9588 Encephalitis [DOID:9588] - DOID:820 Myocarditis [DOID:820] - IDO:0000567 Secondary infection [IDO:0000567] - HP:0100806 Sepsis [HP:0100806] - -host vaccination status menu GENEPIO:0100100 Fully Vaccinated - GENEPIO:0100102 Not Vaccinated - -host vaccination status international menu GENEPIO:0100100 Fully Vaccinated [GENEPIO:0100100] - GENEPIO:0100102 Not Vaccinated [GENEPIO:0100102] - -exposure event menu GENEPIO:0100237 Mass Gathering - GENEPIO:0100238 Convention (conference) - GENEPIO:0100240 Agricultural Event - PCO:0000033 Social Gathering - PCO:0000034 Community Event - PCO:0000035 Party - Other exposure event - -exposure event international menu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. - GENEPIO:0100238 Convention (conference) [GENEPIO:0100238] A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom. - GENEPIO:0100240 Agricultural Event [GENEPIO:0100240] A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry. - PCO:0000033 Social Gathering [PCO:0000033] A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. - PCO:0000034 Community Event [PCO:0000034] A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. - PCO:0000035 Party [PCO:0000035] A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. - Other exposure event An exposure event not specified in the picklist. - - -exposure contact level menu GENEPIO:0100494 Contact with animal - GENEPIO:0100495 Contact with rodent - GENEPIO:0100496 Contact with fomite - GENEPIO:0100357 Contact with infected individual - TRANS:0000001 Direct (human-to-human contact) - TRANS:0000006 Mother-to-child transmission - NCIT:C19085 Sexual transmission - GENEPIO:0100246 Indirect contact - GENEPIO:0100247 Close contact (face-to-face contact) - GENEPIO:0100248 Casual contact - GENEPIO:0100497 Workplace associated transmission - GENEPIO:0100498 Healthcare associated transmission - GENEPIO:0100499 Laboratory associated transmission - -exposure contact level international menu GENEPIO:0100494 Contact with animal [GENEPIO:0100494] - GENEPIO:0100495 Contact with rodent [GENEPIO:0100495] - GENEPIO:0100496 Contact with fomite [GENEPIO:0100496] - GENEPIO:0100357 Contact with infected individual [GENEPIO:0100357] - TRANS:0000001 Direct (human-to-human contact) [TRANS:0000001] - TRANS:0000006 Mother-to-child transmission [TRANS:0000006] - NCIT:C19085 Sexual transmission [NCIT:C19085] - GENEPIO:0100246 Indirect contact [GENEPIO:0100246] - GENEPIO:0100247 Close contact (face-to-face contact) [GENEPIO:0100247] - GENEPIO:0100248 Casual contact [GENEPIO:0100248] - GENEPIO:0100497 Workplace associated transmission [GENEPIO:0100497] - GENEPIO:0100498 Healthcare associated transmission [GENEPIO:0100498] - GENEPIO:0100499 Laboratory associated transmission [GENEPIO:0100499] - -host role menu GENEPIO:0100249 Attendee - OMRSE:00000058 Student - OMRSE:00000030 Patient - NCIT:C25182 Inpatient - NCIT:C28293 Outpatient - GENEPIO:0100250 Passenger - GENEPIO:0100251 Resident - GENEPIO:0100252 Visitor - GENEPIO:0100253 Volunteer - GENEPIO:0100254 Work - GENEPIO:0100255 Administrator - GENEPIO:0100256 First Responder - GENEPIO:0100260 Housekeeper - GENEPIO:0100261 Kitchen Worker - GENEPIO:0100334 Healthcare Worker - GENEPIO:0100420 Community Healthcare Worker - GENEPIO:0100262 Laboratory Worker - OMRSE:00000014 Nurse - GENEPIO:0100263 Personal Care Aid - GENEPIO:0100264 Pharmacist - OMRSE:00000013 Physician - GENEPIO:0100354 Rotational Worker - GENEPIO:0100355 Seasonal Worker - GSSO:005831 Sex Worker - GENEPIO:0100265 Veterinarian - OMRSE:00000001 Social role - GENEPIO:0100266 Acquaintance of case - GENEPIO:0100267 Relative of case - GENEPIO:0100268 Child of case - GENEPIO:0100269 Parent of case - GENEPIO:0100270 Father of case - GENEPIO:0100271 Mother of case - GENEPIO:0100500 Sexual partner of case - GENEPIO:0100272 Spouse of case - Other Host Role - -host role international menu GENEPIO:0100249 Attendee [GENEPIO:0100249] - OMRSE:00000058 Student [OMRSE:00000058] - OMRSE:00000030 Patient [OMRSE:00000030] - NCIT:C25182 Inpatient [NCIT:C25182] - NCIT:C28293 Outpatient [NCIT:C28293] - GENEPIO:0100250 Passenger [GENEPIO:0100250] - GENEPIO:0100251 Resident [GENEPIO:0100251] - GENEPIO:0100252 Visitor [GENEPIO:0100252] - GENEPIO:0100253 Volunteer [GENEPIO:0100253] - GENEPIO:0100254 Work [GENEPIO:0100254] - GENEPIO:0100255 Administrator [GENEPIO:0100255] - GENEPIO:0100256 First Responder [GENEPIO:0100256] - GENEPIO:0100260 Housekeeper [GENEPIO:0100260] - GENEPIO:0100261 Kitchen Worker [GENEPIO:0100261] - GENEPIO:0100334 Healthcare Worker [GENEPIO:0100334] - GENEPIO:0100420 Community Healthcare Worker [GENEPIO:0100420] - GENEPIO:0100262 Laboratory Worker [GENEPIO:0100262] - OMRSE:00000014 Nurse [OMRSE:00000014] - GENEPIO:0100263 Personal Care Aid [GENEPIO:0100263] - GENEPIO:0100264 Pharmacist [GENEPIO:0100264] - OMRSE:00000013 Physician [OMRSE:00000013] - GENEPIO:0100354 Rotational Worker [GENEPIO:0100354] - GENEPIO:0100355 Seasonal Worker [GENEPIO:0100355] - GSSO:005831 Sex Worker [GSSO:005831] - GENEPIO:0100265 Veterinarian [GENEPIO:0100265] - OMRSE:00000001 Social role [OMRSE:00000001] - GENEPIO:0100266 Acquaintance of case [GENEPIO:0100266] - GENEPIO:0100267 Relative of case [GENEPIO:0100267] - GENEPIO:0100268 Child of case [GENEPIO:0100268] - GENEPIO:0100269 Parent of case [GENEPIO:0100269] - GENEPIO:0100270 Father of case [GENEPIO:0100270] - GENEPIO:0100271 Mother of case [GENEPIO:0100271] - GENEPIO:0100500 Sexual partner of case [GENEPIO:0100500] - GENEPIO:0100272 Spouse of case [GENEPIO:0100272] - Other Host Role - -exposure setting menu ECTO:3000005 Human Exposure - GENEPIO:0100501 Contact with Known Monkeypox Case - GENEPIO:0100185 Contact with Patient - GENEPIO:0100502 Contact with Probable Monkeypox Case - GENEPIO:0100189 Contact with Person who Recently Travelled - GENEPIO:0100190 Occupational, Residency or Patronage Exposure - ECTO:1000033 Abbatoir - GENEPIO:0100191 Animal Rescue - GENEPIO:0100503 Bar (pub) - GENEPIO:0100192 Childcare - GENEPIO:0100193 Daycare - GENEPIO:0100194 Nursery - GENEPIO:0100195 Community Service Centre - GENEPIO:0100196 Correctional Facility - GENEPIO:0100197 Dormitory - ECTO:1000034 Farm - GENEPIO:0100198 First Nations Reserve - GENEPIO:0100199 Funeral Home - GENEPIO:0100200 Group Home - GENEPIO:0100201 Healthcare Setting - GENEPIO:0100202 Ambulance - GENEPIO:0100203 Acute Care Facility - GENEPIO:0100204 Clinic - GENEPIO:0100415 Community Healthcare (At-Home) Setting - GENEPIO:0100205 Community Health Centre - ECTO:1000035 Hospital - GENEPIO:0100206 Emergency Department - GENEPIO:0100207 ICU - GENEPIO:0100208 Ward - ECTO:1000036 Laboratory - GENEPIO:0100209 Long-Term Care Facility - GENEPIO:0100210 Pharmacy - GENEPIO:0100211 Physician's Office - GENEPIO:0100212 Household - GENEPIO:0100213 Insecure Housing (Homeless) - GENEPIO:0100214 Occupational Exposure - GENEPIO:0100215 Worksite - ECTO:1000037 Office - GENEPIO:0100216 Outdoors - ECTO:5000009 Camp/camping - GENEPIO:0100217 Hiking Trail - ECTO:6000030 Hunting Ground - GENEPIO:0100218 Ski Resort - ECTO:5000008 Petting zoo - GENEPIO:0100220 Place of Worship - GENEPIO:0100221 Church - GENEPIO:0100222 Mosque - GENEPIO:0100223 Temple - ECTO:1000040 Restaurant - ECTO:1000041 Retail Store - GENEPIO:0100224 School - GENEPIO:0100225 Temporary Residence - GENEPIO:0100226 Homeless Shelter - GENEPIO:0100227 Hotel - GENEPIO:0100228 Veterinary Care Clinic - GENEPIO:0100229 Travel Exposure - GENEPIO:0100230 Travelled on a Cruise Ship - GENEPIO:0100231 Travelled on a Plane - GENEPIO:0100232 Travelled on Ground Transport - GENEPIO:0100235 Other Exposure Setting - - -exposure setting international menu ECTO:3000005 Human Exposure [ECTO:3000005] - GENEPIO:0100501 Contact with Known Monkeypox Case [GENEPIO:0100501] - GENEPIO:0100185 Contact with Patient [GENEPIO:0100185] - GENEPIO:0100502 Contact with Probable Monkeypox Case [GENEPIO:0100502] - GENEPIO:0100189 Contact with Person who Recently Travelled [GENEPIO:0100189] - GENEPIO:0100190 Occupational, Residency or Patronage Exposure [GENEPIO:0100190] - ECTO:1000033 Abbatoir [ECTO:1000033] - GENEPIO:0100191 Animal Rescue [GENEPIO:0100191] - GENEPIO:0100503 Bar (pub) [GENEPIO:0100503] - GENEPIO:0100192 Childcare [GENEPIO:0100192] - GENEPIO:0100193 Daycare [GENEPIO:0100193] - GENEPIO:0100194 Nursery [GENEPIO:0100194] - GENEPIO:0100195 Community Service Centre [GENEPIO:0100195] - GENEPIO:0100196 Correctional Facility [GENEPIO:0100196] - GENEPIO:0100197 Dormitory [GENEPIO:0100197] - ECTO:1000034 Farm [ECTO:1000034] - GENEPIO:0100198 First Nations Reserve [GENEPIO:0100198] - GENEPIO:0100199 Funeral Home [GENEPIO:0100199] - GENEPIO:0100200 Group Home [GENEPIO:0100200] - GENEPIO:0100201 Healthcare Setting [GENEPIO:0100201] - GENEPIO:0100202 Ambulance [GENEPIO:0100202] - GENEPIO:0100203 Acute Care Facility [GENEPIO:0100203] - GENEPIO:0100204 Clinic [GENEPIO:0100204] - GENEPIO:0100415 Community Healthcare (At-Home) Setting [GENEPIO:0100415] - GENEPIO:0100205 Community Health Centre [GENEPIO:0100205] - ECTO:1000035 Hospital [ECTO:1000035] - GENEPIO:0100206 Emergency Department [GENEPIO:0100206] - GENEPIO:0100207 ICU [GENEPIO:0100207] - GENEPIO:0100208 Ward [GENEPIO:0100208] - ECTO:1000036 Laboratory [ECTO:1000036] - GENEPIO:0100209 Long-Term Care Facility [GENEPIO:0100209] - GENEPIO:0100210 Pharmacy [GENEPIO:0100210] - GENEPIO:0100211 Physician's Office [GENEPIO:0100211] - GENEPIO:0100212 Household [GENEPIO:0100212] - GENEPIO:0100213 Insecure Housing (Homeless) [GENEPIO:0100213] - GENEPIO:0100214 Occupational Exposure [GENEPIO:0100214] - GENEPIO:0100215 Worksite [GENEPIO:0100215] - ECTO:1000037 Office [ECTO:1000037] - GENEPIO:0100216 Outdoors [GENEPIO:0100216] - ECTO:5000009 Camp/camping [ECTO:5000009] - GENEPIO:0100217 Hiking Trail [GENEPIO:0100217] - ECTO:6000030 Hunting Ground [ECTO:6000030] - GENEPIO:0100218 Ski Resort [GENEPIO:0100218] - ECTO:5000008 Petting zoo [ECTO:5000008] - GENEPIO:0100220 Place of Worship [GENEPIO:0100220] - GENEPIO:0100221 Church [GENEPIO:0100221] - GENEPIO:0100222 Mosque [GENEPIO:0100222] - GENEPIO:0100223 Temple [GENEPIO:0100223] - ECTO:1000040 Restaurant [ECTO:1000040] - ECTO:1000041 Retail Store [ECTO:1000041] - GENEPIO:0100224 School [GENEPIO:0100224] - GENEPIO:0100225 Temporary Residence [GENEPIO:0100225] - GENEPIO:0100226 Homeless Shelter [GENEPIO:0100226] - GENEPIO:0100227 Hotel [GENEPIO:0100227] - GENEPIO:0100228 Veterinary Care Clinic [GENEPIO:0100228] - GENEPIO:0100229 Travel Exposure [GENEPIO:0100229] - GENEPIO:0100230 Travelled on a Cruise Ship [GENEPIO:0100230] - GENEPIO:0100231 Travelled on a Plane [GENEPIO:0100231] - GENEPIO:0100232 Travelled on Ground Transport [GENEPIO:0100232] - GENEPIO:0100235 Other Exposure Setting [GENEPIO:0100235] - -prior Mpox infection menu GENEPIO:0100037 Prior infection - GENEPIO:0100233 No prior infection - -prior Mpox infection international menu GENEPIO:0100037 Prior infection [GENEPIO:0100037] - GENEPIO:0100233 No prior infection [GENEPIO:0100233] - -prior Mpox antiviral treatment menu GENEPIO:0100037 Prior antiviral treatment - GENEPIO:0100233 No prior antiviral treatment - -prior Mpox antiviral treatment international menu GENEPIO:0100037 Prior antiviral treatment [GENEPIO:0100037] - GENEPIO:0100233 No prior antiviral treatment [GENEPIO:0100233] - -organism menu NCBITaxon:10244 Mpox virus - -organism international menu NCBITaxon:10244 Mpox virus [NCBITaxon:10244] - -host disease menu MONDO:0002594 Mpox - -host disease international menu MONDO:0002594 Mpox [MONDO:0002594] - - -purpose of sampling menu GENEPIO:0100001 Cluster/Outbreak investigation - GENEPIO:0100002 Diagnostic testing - GENEPIO:0100003 Research - GENEPIO:0100004 Surveillance - -purpose of sampling international menu GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] - GENEPIO:0100002 Diagnostic testing [GENEPIO:0100002] - GENEPIO:0100003 Research [GENEPIO:0100003] - GENEPIO:0100004 Surveillance [GENEPIO:0100004] - -purpose of sequencing menu GENEPIO:0100005 Baseline surveillance (random sampling) - GENEPIO:0100006 Targeted surveillance (non-random sampling) - GENEPIO:0100007 Priority surveillance project - GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) - GENEPIO:0100010 Re-infection surveillance - GENEPIO:0100011 Vaccine escape surveillance - GENEPIO:0100012 Travel-associated surveillance - GENEPIO:0100013 Domestic travel surveillance - GENEPIO:0100275 Interstate/ interprovincial travel surveillance - GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance - GENEPIO:0100014 International travel surveillance - GENEPIO:0100019 Cluster/Outbreak investigation - GENEPIO:0100020 Multi-jurisdictional outbreak investigation - GENEPIO:0100021 Intra-jurisdictional outbreak investigation - GENEPIO:0100022 Research - GENEPIO:0100023 Viral passage experiment - GENEPIO:0100024 Protocol testing experiment - GENEPIO:0100356 Retrospective sequencing - -purpose of sequencing international menu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] - GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] - GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] - GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] - GENEPIO:0100010 Re-infection surveillance [GENEPIO:0100010] - GENEPIO:0100011 Vaccine escape surveillance [GENEPIO:0100011] - GENEPIO:0100012 Travel-associated surveillance [GENEPIO:0100012] - GENEPIO:0100013 Domestic travel surveillance [GENEPIO:0100013] - GENEPIO:0100275 Interstate/ interprovincial travel surveillance [GENEPIO:0100275] - GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276] - GENEPIO:0100014 International travel surveillance [GENEPIO:0100014] - GENEPIO:0100019 Cluster/Outbreak investigation [GENEPIO:0100019] - GENEPIO:0100020 Multi-jurisdictional outbreak investigation [GENEPIO:0100020] - GENEPIO:0100021 Intra-jurisdictional outbreak investigation [GENEPIO:0100021] - GENEPIO:0100022 Research [GENEPIO:0100022] - GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] - GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] - GENEPIO:0100356 Retrospective sequencing [GENEPIO:0100356] - -sequencing instrument menu GENEPIO:0100105 Illumina - GENEPIO:0100106 Illumina Genome Analyzer - GENEPIO:0100107 Illumina Genome Analyzer II - GENEPIO:0100108 Illumina Genome Analyzer IIx - GENEPIO:0100109 Illumina HiScanSQ - GENEPIO:0100110 Illumina HiSeq - GENEPIO:0100111 Illumina HiSeq X - GENEPIO:0100112 Illumina HiSeq X Five - GENEPIO:0100113 Illumina HiSeq X Ten - GENEPIO:0100114 Illumina HiSeq 1000 - GENEPIO:0100115 Illumina HiSeq 1500 - GENEPIO:0100116 Illumina HiSeq 2000 - GENEPIO:0100117 Illumina HiSeq 2500 - GENEPIO:0100118 Illumina HiSeq 3000 - GENEPIO:0100119 Illumina HiSeq 4000 - GENEPIO:0100120 Illumina iSeq - GENEPIO:0100121 Illumina iSeq 100 - GENEPIO:0100122 Illumina NovaSeq - GENEPIO:0100123 Illumina NovaSeq 6000 - GENEPIO:0100124 Illumina MiniSeq - GENEPIO:0100125 Illumina MiSeq - GENEPIO:0100126 Illumina NextSeq - GENEPIO:0100127 Illumina NextSeq 500 - GENEPIO:0100128 Illumina NextSeq 550 - GENEPIO:0100129 Illumina NextSeq 2000 - GENEPIO:0100130 Pacific Biosciences - GENEPIO:0100131 PacBio RS - GENEPIO:0100132 PacBio RS II - GENEPIO:0100133 PacBio Sequel - GENEPIO:0100134 PacBio Sequel II - GENEPIO:0100135 Ion Torrent - GENEPIO:0100136 Ion Torrent PGM - GENEPIO:0100137 Ion Torrent Proton - GENEPIO:0100138 Ion Torrent S5 XL - GENEPIO:0100139 Ion Torrent S5 - GENEPIO:0100140 Oxford Nanopore - GENEPIO:0100141 Oxford Nanopore GridION - GENEPIO:0100142 Oxford Nanopore MinION - GENEPIO:0100143 Oxford Nanopore PromethION - GENEPIO:0100144 BGI Genomics - GENEPIO:0100145 BGI Genomics BGISEQ-500 - GENEPIO:0100146 MGI - GENEPIO:0100147 MGI DNBSEQ-T7 - GENEPIO:0100148 MGI DNBSEQ-G400 - GENEPIO:0100149 MGI DNBSEQ-G400 FAST - GENEPIO:0100150 MGI DNBSEQ-G50 - -sequencing instrument international menu GENEPIO:0100105 Illumina [GENEPIO:0100105] - GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] - GENEPIO:0100107 Illumina Genome Analyzer II [GENEPIO:0100107] - GENEPIO:0100108 Illumina Genome Analyzer IIx [GENEPIO:0100108] - GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] - GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] - GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] - GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] - GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] - GENEPIO:0100114 Illumina HiSeq 1000 [GENEPIO:0100114] - GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] - GENEPIO:0100116 Illumina HiSeq 2000 [GENEPIO:0100116] - GENEPIO:0100117 Illumina HiSeq 2500 [GENEPIO:0100117] - GENEPIO:0100118 Illumina HiSeq 3000 [GENEPIO:0100118] - GENEPIO:0100119 Illumina HiSeq 4000 [GENEPIO:0100119] - GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] - GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] - GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] - GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] - GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] - GENEPIO:0100125 Illumina MiSeq [GENEPIO:0100125] - GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] - GENEPIO:0100127 Illumina NextSeq 500 [GENEPIO:0100127] - GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] - GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] - GENEPIO:0100130 Pacific Biosciences [GENEPIO:0100130] - GENEPIO:0100131 PacBio RS [GENEPIO:0100131] - GENEPIO:0100132 PacBio RS II [GENEPIO:0100132] - GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] - GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] - GENEPIO:0100135 Ion Torrent [GENEPIO:0100135 - GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136 - GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] - GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] - GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] - GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] - GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141 - GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] - GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] - GENEPIO:0100144 BGI Genomics [GENEPIO:0100144] - GENEPIO:0100145 BGI Genomics BGISEQ-500 [GENEPIO:0100145] - GENEPIO:0100146 MGI [GENEPIO:0100146] - GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] - GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] - GENEPIO:0100149 MGI DNBSEQ-G400 FAST [GENEPIO:0100149] - GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] - - -sequence submitted by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Canadore College - The Centre for Applied Genomics (TCAG) - Dynacare - Dynacare (Brampton) - Dynacare (Manitoba) - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Manitoba Cadham Provincial Laboratory - McGill University - McMaster University - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Sunnybrook Health Sciences Centre - Thunder Bay Regional Health Sciences Centre - -sequenced by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Canadore College - The Centre for Applied Genomics (TCAG) - Dynacare - Dynacare (Brampton) - Dynacare (Manitoba) - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Manitoba Cadham Provincial Laboratory - McGill University - McMaster University - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Sunnybrook Health Sciences Centre - Thunder Bay Regional Health Sciences Centre - -sample collected by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Dynacare - Dynacare (Manitoba) - Dynacare (Brampton) - Eastern Ontario Regional Laboratory Association - Hamilton Health Sciences - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Lake of the Woods District Hospital - Ontario - LifeLabs - LifeLabs (Ontario) - Manitoba Cadham Provincial Laboratory - McMaster University - Mount Sinai Hospital - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Nunavut - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Shared Hospital Laboratory - St. John's Rehab at Sunnybrook Hospital - Switch Health - Sunnybrook Health Sciences Centre - Unity Health Toronto - William Osler Health System - -gene name menu GENEPIO:0100505 MPX (orf B6R) - GENEPIO:0100506 OPV (orf 17L) - GENEPIO:0100507 OPHA (orf B2R) - GENEPIO:0100510 G2R_G (TNFR) - G2R_G (WA) - GENEPIO:0100508 RNAse P gene (RNP) - - -geo_loc_name (country) menu GAZ:00006882 Afghanistan - GAZ:00002953 Albania - GAZ:00000563 Algeria - GAZ:00003957 American Samoa - GAZ:00002948 Andorra - GAZ:00001095 Angola - GAZ:00009159 Anguilla - GAZ:00000462 Antarctica - GAZ:00006883 Antigua and Barbuda - GAZ:00002928 Argentina - GAZ:00004094 Armenia - GAZ:00004025 Aruba - GAZ:00005901 Ashmore and Cartier Islands - GAZ:00000463 Australia - GAZ:00002942 Austria - GAZ:00004941 Azerbaijan - GAZ:00002733 Bahamas - GAZ:00005281 Bahrain - GAZ:00007117 Baker Island - GAZ:00003750 Bangladesh - GAZ:00001251 Barbados - GAZ:00005810 Bassas da India - GAZ:00006886 Belarus - GAZ:00002938 Belgium - GAZ:00002934 Belize - GAZ:00000904 Benin - GAZ:00001264 Bermuda - GAZ:00003920 Bhutan - GAZ:00002511 Bolivia - GAZ:00025355 Borneo - GAZ:00006887 Bosnia and Herzegovina - GAZ:00001097 Botswana - GAZ:00001453 Bouvet Island - GAZ:00002828 Brazil - GAZ:00003961 British Virgin Islands - GAZ:00003901 Brunei - GAZ:00002950 Bulgaria - GAZ:00000905 Burkina Faso - GAZ:00001090 Burundi - GAZ:00006888 Cambodia - GAZ:00001093 Cameroon - GAZ:00002560 Canada - GAZ:00001227 Cape Verde - GAZ:00003986 Cayman Islands - GAZ:00001089 Central African Republic - GAZ:00000586 Chad - GAZ:00002825 Chile - GAZ:00002845 China - GAZ:00005915 Christmas Island - GAZ:00005838 Clipperton Island - GAZ:00009721 Cocos Islands - GAZ:00002929 Colombia - GAZ:00005820 Comoros - GAZ:00053798 Cook Islands - GAZ:00005917 Coral Sea Islands - GAZ:00002901 Costa Rica - GAZ:00000906 Cote d'Ivoire - GAZ:00002719 Croatia - GAZ:00003762 Cuba - GAZ:00012582 Curacao - GAZ:00004006 Cyprus - GAZ:00002954 Czech Republic - GAZ:00001086 Democratic Republic of the Congo - GAZ:00005852 Denmark - GAZ:00000582 Djibouti - GAZ:00006890 Dominica - GAZ:00003952 Dominican Republic - GAZ:00002912 Ecuador - GAZ:00003934 Egypt - GAZ:00002935 El Salvador - GAZ:00001091 Equatorial Guinea - GAZ:00000581 Eritrea - GAZ:00002959 Estonia - GAZ:00001099 Eswatini - GAZ:00000567 Ethiopia - GAZ:00005811 Europa Island - GAZ:00001412 Falkland Islands (Islas Malvinas) - GAZ:00059206 Faroe Islands - GAZ:00006891 Fiji - GAZ:00002937 Finland - GAZ:00003940 France - GAZ:00002516 French Guiana - GAZ:00002918 French Polynesia - GAZ:00003753 French Southern and Antarctic Lands - GAZ:00001092 Gabon - GAZ:00000907 Gambia - GAZ:00009571 Gaza Strip - GAZ:00004942 Georgia - GAZ:00002646 Germany - GAZ:00000908 Ghana - GAZ:00003987 Gibraltar - GAZ:00005808 Glorioso Islands - GAZ:00002945 Greece - GAZ:00001507 Greenland - GAZ:02000573 Grenada - GAZ:00067142 Guadeloupe - GAZ:00003706 Guam - GAZ:00002936 Guatemala - GAZ:00001550 Guernsey - GAZ:00000909 Guinea - GAZ:00000910 Guinea-Bissau - GAZ:00002522 Guyana - GAZ:00003953 Haiti - GAZ:00009718 Heard Island and McDonald Islands - GAZ:00002894 Honduras - GAZ:00003203 Hong Kong - GAZ:00007120 Howland Island - GAZ:00002952 Hungary - GAZ:00000843 Iceland - GAZ:00002839 India - GAZ:00003727 Indonesia - GAZ:00004474 Iran - GAZ:00004483 Iraq - GAZ:00002943 Ireland - GAZ:00052477 Isle of Man - GAZ:00002476 Israel - GAZ:00002650 Italy - GAZ:00003781 Jamaica - GAZ:00005853 Jan Mayen - GAZ:00002747 Japan - GAZ:00007118 Jarvis Island - GAZ:00001551 Jersey - GAZ:00007114 Johnston Atoll - GAZ:00002473 Jordan - GAZ:00005809 Juan de Nova Island - GAZ:00004999 Kazakhstan - GAZ:00001101 Kenya - GAZ:00005682 Kerguelen Archipelago - GAZ:00007116 Kingman Reef - GAZ:00006894 Kiribati - GAZ:00011337 Kosovo - GAZ:00005285 Kuwait - GAZ:00006893 Kyrgyzstan - GAZ:00006889 Laos - GAZ:00002958 Latvia - GAZ:00002478 Lebanon - GAZ:00001098 Lesotho - GAZ:00000911 Liberia - GAZ:00000566 Libya - GAZ:00003858 Liechtenstein - GAZ:00007144 Line Islands - GAZ:00002960 Lithuania - GAZ:00002947 Luxembourg - GAZ:00003202 Macau - GAZ:00001108 Madagascar - GAZ:00001105 Malawi - GAZ:00003902 Malaysia - GAZ:00006924 Maldives - GAZ:00000584 Mali - GAZ:00004017 Malta - GAZ:00007161 Marshall Islands - GAZ:00067143 Martinique - GAZ:00000583 Mauritania - GAZ:00003745 Mauritius - GAZ:00003943 Mayotte - GAZ:00002852 Mexico - GAZ:00005862 Micronesia - GAZ:00007112 Midway Islands - GAZ:00003897 Moldova - GAZ:00003857 Monaco - GAZ:00008744 Mongolia - GAZ:00006898 Montenegro - GAZ:00003988 Montserrat - GAZ:00000565 Morocco - GAZ:00001100 Mozambique - GAZ:00006899 Myanmar - GAZ:00001096 Namibia - GAZ:00006900 Nauru - GAZ:00007119 Navassa Island - GAZ:00004399 Nepal - GAZ:00002946 Netherlands - GAZ:00005206 New Caledonia - GAZ:00000469 New Zealand - GAZ:00002978 Nicaragua - GAZ:00000585 Niger - GAZ:00000912 Nigeria - GAZ:00006902 Niue - GAZ:00005908 Norfolk Island - GAZ:00002801 North Korea - GAZ:00006895 North Macedonia - GAZ:00002284 North Sea - GAZ:00003958 Northern Mariana Islands - GAZ:00002699 Norway - GAZ:00005283 Oman - GAZ:00005246 Pakistan - GAZ:00006905 Palau - GAZ:00002892 Panama - GAZ:00003922 Papua New Guinea - GAZ:00010832 Paracel Islands - GAZ:00002933 Paraguay - GAZ:00002932 Peru - GAZ:00004525 Philippines - GAZ:00005867 Pitcairn Islands - GAZ:00002939 Poland - GAZ:00004126 Portugal - GAZ:00006935 Puerto Rico - GAZ:00005286 Qatar - GAZ:00001088 Republic of the Congo - GAZ:00003945 Reunion - GAZ:00002951 Romania - GAZ:00023304 Ross Sea - GAZ:00002721 Russia - GAZ:00001087 Rwanda - GAZ:00000849 Saint Helena - GAZ:00006906 Saint Kitts and Nevis - GAZ:00006909 Saint Lucia - GAZ:00003942 Saint Pierre and Miquelon - GAZ:00005841 Saint Martin - GAZ:02000565 Saint Vincent and the Grenadines - GAZ:00006910 Samoa - GAZ:00003102 San Marino - GAZ:00006927 Sao Tome and Principe - GAZ:00005279 Saudi Arabia - GAZ:00000913 Senegal - GAZ:00002957 Serbia - GAZ:00006922 Seychelles - GAZ:00000914 Sierra Leone - GAZ:00003923 Singapore - GAZ:00012579 Sint Maarten - GAZ:00002956 Slovakia - GAZ:00002955 Slovenia - GAZ:00005275 Solomon Islands - GAZ:00001104 Somalia - GAZ:00001094 South Africa - GAZ:00003990 South Georgia and the South Sandwich Islands - GAZ:00002802 South Korea - GAZ:00233439 South Sudan - GAZ:00000591 Spain - GAZ:00010831 Spratly Islands - GAZ:00003924 Sri Lanka - GAZ:00002475 State of Palestine - GAZ:00000560 Sudan - GAZ:00002525 Suriname - GAZ:00005396 Svalbard - GAZ:00001099 Swaziland - GAZ:00002729 Sweden - GAZ:00002941 Switzerland - GAZ:00002474 Syria - GAZ:00005341 Taiwan - GAZ:00006912 Tajikistan - GAZ:00001103 Tanzania - GAZ:00003744 Thailand - GAZ:00006913 Timor-Leste - GAZ:00000915 Togo - GAZ:00260188 Tokelau - GAZ:00006916 Tonga - GAZ:00003767 Trinidad and Tobago - GAZ:00005812 Tromelin Island - GAZ:00000562 Tunisia - GAZ:00000558 Turkey - GAZ:00005018 Turkmenistan - GAZ:00003955 Turks and Caicos Islands - GAZ:00009715 Tuvalu - GAZ:00002459 United States of America - GAZ:00001102 Uganda - GAZ:00002724 Ukraine - GAZ:00005282 United Arab Emirates - GAZ:00002637 United Kingdom - GAZ:00002930 Uruguay - GAZ:00004979 Uzbekistan - GAZ:00006918 Vanuatu - GAZ:00002931 Venezuela - GAZ:00003756 Viet Nam - GAZ:00003959 Virgin Islands - GAZ:00007111 Wake Island - GAZ:00007191 Wallis and Futuna - GAZ:00009572 West Bank - GAZ:00000564 Western Sahara - GAZ:00005284 Yemen - GAZ:00001107 Zambia - GAZ:00001106 Zimbabwe - -geo_loc_name (country) international menu GAZ:00006882 Afghanistan [GAZ:00006882] - GAZ:00002953 Albania [GAZ:00002953] - GAZ:00000563 Algeria [GAZ:00000563] - GAZ:00003957 American Samoa [GAZ:00003957] - GAZ:00002948 Andorra [GAZ:00002948] - GAZ:00001095 Angola [GAZ:00001095] - GAZ:00009159 Anguilla [GAZ:00009159] - GAZ:00000462 Antarctica [GAZ:00000462] - GAZ:00006883 Antigua and Barbuda [GAZ:00006883] - GAZ:00002928 Argentina [GAZ:00002928] - GAZ:00004094 Armenia [GAZ:00004094] - GAZ:00004025 Aruba [GAZ:00004025] - GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] - GAZ:00000463 Australia [GAZ:00000463] - GAZ:00002942 Austria [GAZ:00002942] - GAZ:00004941 Azerbaijan [GAZ:00004941] - GAZ:00002733 Bahamas [GAZ:00002733] - GAZ:00005281 Bahrain [GAZ:00005281] - GAZ:00007117 Baker Island [GAZ:00007117] - GAZ:00003750 Bangladesh [GAZ:00003750] - GAZ:00001251 Barbados [GAZ:00001251] - GAZ:00005810 Bassas da India [GAZ:00005810] - GAZ:00006886 Belarus [GAZ:00006886] - GAZ:00002938 Belgium [GAZ:00002938] - GAZ:00002934 Belize [GAZ:00002934] - GAZ:00000904 Benin [GAZ:00000904] - GAZ:00001264 Bermuda [GAZ:00001264] - GAZ:00003920 Bhutan [GAZ:00003920] - GAZ:00002511 Bolivia [GAZ:00002511] - GAZ:00025355 Borneo [GAZ:00025355] - GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] - GAZ:00001097 Botswana [GAZ:00001097] - GAZ:00001453 Bouvet Island [GAZ:00001453] - GAZ:00002828 Brazil [GAZ:00002828] - GAZ:00003961 British Virgin Islands [GAZ:00003961] - GAZ:00003901 Brunei [GAZ:00003901] - GAZ:00002950 Bulgaria [GAZ:00002950] - GAZ:00000905 Burkina Faso [GAZ:00000905] - GAZ:00001090 Burundi [GAZ:00001090] - GAZ:00006888 Cambodia [GAZ:00006888] - GAZ:00001093 Cameroon [GAZ:00001093] - GAZ:00002560 Canada [GAZ:00002560] - GAZ:00001227 Cape Verde [GAZ:00001227] - GAZ:00003986 Cayman Islands [GAZ:00003986] - GAZ:00001089 Central African Republic [GAZ:00001089] - GAZ:00000586 Chad [GAZ:00000586] - GAZ:00002825 Chile [GAZ:00002825] - GAZ:00002845 China [GAZ:00002845] - GAZ:00005915 Christmas Island [GAZ:00005915] - GAZ:00005838 Clipperton Island [GAZ:00005838] - GAZ:00009721 Cocos Islands [GAZ:00009721] - GAZ:00002929 Colombia [GAZ:00002929] - GAZ:00005820 Comoros [GAZ:00005820] - GAZ:00053798 Cook Islands [GAZ:00053798] - GAZ:00005917 Coral Sea Islands [GAZ:00005917] - GAZ:00002901 Costa Rica [GAZ:00002901] - GAZ:00000906 Cote d'Ivoire [GAZ:00000906] - GAZ:00002719 Croatia [GAZ:00002719] - GAZ:00003762 Cuba [GAZ:00003762] - GAZ:00012582 Curacao [GAZ:00012582] - GAZ:00004006 Cyprus [GAZ:00004006] - GAZ:00002954 Czech Republic [GAZ:00002954] - GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] - GAZ:00005852 Denmark [GAZ:00005852] - GAZ:00000582 Djibouti [GAZ:00000582] - GAZ:00006890 Dominica [GAZ:00006890] - GAZ:00003952 Dominican Republic [GAZ:00003952] - GAZ:00002912 Ecuador [GAZ:00002912] - GAZ:00003934 Egypt [GAZ:00003934] - GAZ:00002935 El Salvador [GAZ:00002935] - GAZ:00001091 Equatorial Guinea [GAZ:00001091] - GAZ:00000581 Eritrea [GAZ:00000581] - GAZ:00002959 Estonia [GAZ:00002959] - GAZ:00001099 Eswatini [GAZ:00001099] - GAZ:00000567 Ethiopia [GAZ:00000567] - GAZ:00005811 Europa Island [GAZ:00005811] - GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] - GAZ:00059206 Faroe Islands [GAZ:00059206] - GAZ:00006891 Fiji [GAZ:00006891] - GAZ:00002937 Finland [GAZ:00002937] - GAZ:00003940 France [GAZ:00003940] - GAZ:00002516 French Guiana [GAZ:00002516] - GAZ:00002918 French Polynesia [GAZ:00002918] - GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] - GAZ:00001092 Gabon [GAZ:00001092] - GAZ:00000907 Gambia [GAZ:00000907] - GAZ:00009571 Gaza Strip [GAZ:00009571] - GAZ:00004942 Georgia [GAZ:00004942] - GAZ:00002646 Germany [GAZ:00002646] - GAZ:00000908 Ghana [GAZ:00000908] - GAZ:00003987 Gibraltar [GAZ:00003987] - GAZ:00005808 Glorioso Islands [GAZ:00005808] - GAZ:00002945 Greece [GAZ:00002945] - GAZ:00001507 Greenland [GAZ:00001507] - GAZ:02000573 Grenada [GAZ:02000573] - GAZ:00067142 Guadeloupe [GAZ:00067142] - GAZ:00003706 Guam [GAZ:00003706] - GAZ:00002936 Guatemala [GAZ:00002936] - GAZ:00001550 Guernsey [GAZ:00001550] - GAZ:00000909 Guinea [GAZ:00000909] - GAZ:00000910 Guinea-Bissau [GAZ:00000910] - GAZ:00002522 Guyana [GAZ:00002522] - GAZ:00003953 Haiti [GAZ:00003953] - GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] - GAZ:00002894 Honduras [GAZ:00002894] - GAZ:00003203 Hong Kong [GAZ:00003203] - GAZ:00007120 Howland Island [GAZ:00007120] - GAZ:00002952 Hungary [GAZ:00002952] - GAZ:00000843 Iceland [GAZ:00000843] - GAZ:00002839 India [GAZ:00002839] - GAZ:00003727 Indonesia [GAZ:00003727] - GAZ:00004474 Iran [GAZ:00004474] - GAZ:00004483 Iraq [GAZ:00004483] - GAZ:00002943 Ireland [GAZ:00002943] - GAZ:00052477 Isle of Man [GAZ:00052477] - GAZ:00002476 Israel [GAZ:00002476] - GAZ:00002650 Italy [GAZ:00002650] - GAZ:00003781 Jamaica [GAZ:00003781] - GAZ:00005853 Jan Mayen [GAZ:00005853] - GAZ:00002747 Japan [GAZ:00002747] - GAZ:00007118 Jarvis Island [GAZ:00007118] - GAZ:00001551 Jersey [GAZ:00001551] - GAZ:00007114 Johnston Atoll [GAZ:00007114] - GAZ:00002473 Jordan [GAZ:00002473] - GAZ:00005809 Juan de Nova Island [GAZ:00005809] - GAZ:00004999 Kazakhstan [GAZ:00004999] - GAZ:00001101 Kenya [GAZ:00001101] - GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] - GAZ:00007116 Kingman Reef [GAZ:00007116] - GAZ:00006894 Kiribati [GAZ:00006894] - GAZ:00011337 Kosovo [GAZ:00011337] - GAZ:00005285 Kuwait [GAZ:00005285] - GAZ:00006893 Kyrgyzstan [GAZ:00006893] - GAZ:00006889 Laos [GAZ:00006889] - GAZ:00002958 Latvia [GAZ:00002958] - GAZ:00002478 Lebanon [GAZ:00002478] - GAZ:00001098 Lesotho [GAZ:00001098] - GAZ:00000911 Liberia [GAZ:00000911] - GAZ:00000566 Libya [GAZ:00000566] - GAZ:00003858 Liechtenstein [GAZ:00003858] - GAZ:00007144 Line Islands [GAZ:00007144] - GAZ:00002960 Lithuania [GAZ:00002960] - GAZ:00002947 Luxembourg [GAZ:00002947] - GAZ:00003202 Macau [GAZ:00003202] - GAZ:00001108 Madagascar [GAZ:00001108] - GAZ:00001105 Malawi [GAZ:00001105] - GAZ:00003902 Malaysia [GAZ:00003902] - GAZ:00006924 Maldives [GAZ:00006924] - GAZ:00000584 Mali [GAZ:00000584] - GAZ:00004017 Malta [GAZ:00004017] - GAZ:00007161 Marshall Islands [GAZ:00007161] - GAZ:00067143 Martinique [GAZ:00067143] - GAZ:00000583 Mauritania [GAZ:00000583] - GAZ:00003745 Mauritius [GAZ:00003745] - GAZ:00003943 Mayotte [GAZ:00003943] - GAZ:00002852 Mexico [GAZ:00002852] - GAZ:00005862 Micronesia [GAZ:00005862] - GAZ:00007112 Midway Islands [GAZ:00007112] - GAZ:00003897 Moldova [GAZ:00003897] - GAZ:00003857 Monaco [GAZ:00003857] - GAZ:00008744 Mongolia [GAZ:00008744] - GAZ:00006898 Montenegro [GAZ:00006898] - GAZ:00003988 Montserrat [GAZ:00003988] - GAZ:00000565 Morocco [GAZ:00000565] - GAZ:00001100 Mozambique [GAZ:00001100] - GAZ:00006899 Myanmar [GAZ:00006899] - GAZ:00001096 Namibia [GAZ:00001096] - GAZ:00006900 Nauru [GAZ:00006900] - GAZ:00007119 Navassa Island [GAZ:00007119] - GAZ:00004399 Nepal [GAZ:00004399] - GAZ:00002946 Netherlands [GAZ:00002946] - GAZ:00005206 New Caledonia [GAZ:00005206] - GAZ:00000469 New Zealand [GAZ:00000469] - GAZ:00002978 Nicaragua [GAZ:00002978] - GAZ:00000585 Niger [GAZ:00000585] - GAZ:00000912 Nigeria [GAZ:00000912] - GAZ:00006902 Niue [GAZ:00006902] - GAZ:00005908 Norfolk Island [GAZ:00005908] - GAZ:00002801 North Korea [GAZ:00002801] - GAZ:00006895 North Macedonia [GAZ:00006895] - GAZ:00002284 North Sea [GAZ:00002284] - GAZ:00003958 Northern Mariana Islands [GAZ:00003958] - GAZ:00002699 Norway [GAZ:00002699] - GAZ:00005283 Oman [GAZ:00005283] - GAZ:00005246 Pakistan [GAZ:00005246] - GAZ:00006905 Palau [GAZ:00006905] - GAZ:00002892 Panama [GAZ:00002892] - GAZ:00003922 Papua New Guinea [GAZ:00003922] - GAZ:00010832 Paracel Islands [GAZ:00010832] - GAZ:00002933 Paraguay [GAZ:00002933] - GAZ:00002932 Peru [GAZ:00002932] - GAZ:00004525 Philippines [GAZ:00004525] - GAZ:00005867 Pitcairn Islands [GAZ:00005867] - GAZ:00002939 Poland [GAZ:00002939] - GAZ:00004126 Portugal [GAZ:00004126] - GAZ:00006935 Puerto Rico [GAZ:00006935] - GAZ:00005286 Qatar [GAZ:00005286] - GAZ:00001088 Republic of the Congo [GAZ:00001088] - GAZ:00003945 Reunion [GAZ:00003945] - GAZ:00002951 Romania [GAZ:00002951] - GAZ:00023304 Ross Sea [GAZ:00023304] - GAZ:00002721 Russia [GAZ:00002721] - GAZ:00001087 Rwanda [GAZ:00001087] - GAZ:00000849 Saint Helena [GAZ:00000849] - GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] - GAZ:00006909 Saint Lucia [GAZ:00006909] - GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] - GAZ:00005841 Saint Martin [GAZ:00005841] - GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] - GAZ:00006910 Samoa [GAZ:00006910] - GAZ:00003102 San Marino [GAZ:00003102] - GAZ:00006927 Sao Tome and Principe [GAZ:00006927] - GAZ:00005279 Saudi Arabia [GAZ:00005279] - GAZ:00000913 Senegal [GAZ:00000913] - GAZ:00002957 Serbia [GAZ:00002957] - GAZ:00006922 Seychelles [GAZ:00006922] - GAZ:00000914 Sierra Leone [GAZ:00000914] - GAZ:00003923 Singapore [GAZ:00003923] - GAZ:00012579 Sint Maarten [GAZ:00012579] - GAZ:00002956 Slovakia [GAZ:00002956] - GAZ:00002955 Slovenia [GAZ:00002955] - GAZ:00005275 Solomon Islands [GAZ:00005275] - GAZ:00001104 Somalia [GAZ:00001104] - GAZ:00001094 South Africa [GAZ:00001094] - GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] - GAZ:00002802 South Korea [GAZ:00002802] - GAZ:00233439 South Sudan [GAZ:00233439] - GAZ:00003936 Spain [GAZ:00003936] - GAZ:00010831 Spratly Islands [GAZ:00010831] - GAZ:00003924 Sri Lanka [GAZ:00003924] - GAZ:00002475 State of Palestine [GAZ:00002475] - GAZ:00000560 Sudan [GAZ:00000560] - GAZ:00002525 Suriname [GAZ:00002525] - GAZ:00005396 Svalbard [GAZ:00005396] - GAZ:00001099 Swaziland [GAZ:00001099] - GAZ:00002729 Sweden [GAZ:00002729] - GAZ:00002941 Switzerland [GAZ:00002941] - GAZ:00002474 Syria [GAZ:00002474] - GAZ:00005341 Taiwan [GAZ:00005341] - GAZ:00006912 Tajikistan [GAZ:00006912] - GAZ:00001103 Tanzania [GAZ:00001103] - GAZ:00003744 Thailand [GAZ:00003744] - GAZ:00006913 Timor-Leste [GAZ:00006913] - GAZ:00000915 Togo [GAZ:00000915] - GAZ:00260188 Tokelau [GAZ:00260188] - GAZ:00006916 Tonga [GAZ:00006916] - GAZ:00003767 Trinidad and Tobago [GAZ:00003767] - GAZ:00005812 Tromelin Island [GAZ:00005812] - GAZ:00000562 Tunisia [GAZ:00000562] - GAZ:00000558 Turkey [GAZ:00000558] - GAZ:00005018 Turkmenistan [GAZ:00005018] - GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] - GAZ:00009715 Tuvalu [GAZ:00009715] - GAZ:00002459 United States of America [GAZ:00002459] - GAZ:00001102 Uganda [GAZ:00001102] - GAZ:00002724 Ukraine [GAZ:00002724] - GAZ:00005282 United Arab Emirates [GAZ:00005282] - GAZ:00002637 United Kingdom [GAZ:00002637] - GAZ:00002930 Uruguay [GAZ:00002930] - GAZ:00004979 Uzbekistan [GAZ:00004979] - GAZ:00006918 Vanuatu [GAZ:00006918] - GAZ:00002931 Venezuela [GAZ:00002931] - GAZ:00003756 Viet Nam [GAZ:00003756] - GAZ:00003959 Virgin Islands [GAZ:00003959] - GAZ:00007111 Wake Island [GAZ:00007111] - GAZ:00007191 Wallis and Futuna [GAZ:00007191] - GAZ:00009572 West Bank [GAZ:00009572] - GAZ:00000564 Western Sahara [GAZ:00000564] - GAZ:00005284 Yemen [GAZ:00005284] - GAZ:00001107 Zambia [GAZ:00001107] - GAZ:00001106 Zimbabwe [GAZ:00001106] \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal + +null value menu NullValueMenu GENEPIO:0001619 Not Applicable A categorical choice recorded when a datum does not apply to a given context. Mpox;Mpox_international + GENEPIO:0001618 Missing A categorical choice recorded when a datum is not included for an unknown reason. + GENEPIO:0001620 Not Collected A categorical choice recorded when a datum was not measured or collected. + GENEPIO:0001668 Not Provided A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. + GENEPIO:0001810 Restricted Access A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. + +geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu GAZ:00002566 Alberta One of Canada's prairie provinces. It became a province on 1905-09-01. Alberta is located in western Canada, bounded by the provinces of British Columbia to the west and Saskatchewan to the east, Northwest Territories to the north, and by the State of Montana to the south. Statistics Canada divides the province of Alberta into nineteen census divisions, each with one or more municipal governments overseeing county municipalities, improvement districts, special areas, specialized municipalities, municipal districts, regional municipalities, cities, towns, villages, summer villages, Indian settlements, and Indian reserves. Census divisions are not a unit of local government in Alberta. Mpox + GAZ:00002562 British Columbia The westernmost of Canada's provinces. British Columbia is bordered by the Pacific Ocean on the west, by the American State of Alaska on the northwest, and to the north by the Yukon and the Northwest Territories, on the east by the province of Alberta, and on the south by the States of Washington, Idaho, and Montana. The current southern border of British Columbia was established by the 1846 Oregon Treaty, although its history is tied with lands as far south as the California border. British Columbia's rugged coastline stretches for more than 27,000 km, and includes deep, mountainous fjords and about 6,000 islands, most of which are uninhabited. British Columbia is carved into 27 regional districts. These regional districts are federations of member municipalities and electoral areas. The unincorporated area of the regional district is carved into electoral areas. + GAZ:00002571 Manitoba One of Canada's 10 provinces. Manitoba is located at the longitudinal centre of Canada, although it is considered to be part of Western Canada. It borders Saskatchewan to the west, Ontario to the east, Nunavut and Hudson Bay to the north, and the American states of North Dakota and Minnesota to the south. Statistics Canada divides the province of Manitoba into 23 census divisions. Census divisions are not a unit of local government in Manitoba. + GAZ:00002570 New Brunswick One of Canada's three Maritime provinces. New Brunswick is bounded on the north by Quebec's Gaspe Peninsula and by Chaleur Bay. Along the east coast, the Gulf of Saint Lawrence and Northumberland Strait form the boundaries. In the south-east corner of the province, the narrow Isthmus of Chignecto connects New Brunswick to the Nova Scotia peninsula. The south of the province is bounded by the Bay of Fundy, which has the highest tides in the world with a rise of 16 m. To the west, the province borders the American State of Maine. New Brunswick is divided into 15 counties, which no longer have administrative roles except in the court system. The counties are divided into parishes. + GAZ:00002567 Newfoundland and Labrador A province of Canada, the tenth and latest to join the Confederation. Geographically, the province consists of the island of Newfoundland and the mainland Labrador, on Canada's Atlantic coast. + GAZ:00002575 Northwest Territories A territory of Canada. Located in northern Canada, it borders Canada's two other territories, Yukon to the west and Nunavut to the east, and three provinces: British Columbia to the southwest, Alberta to the south, and Saskatchewan to the southeast. The present-day territory was created in 1870-06, when the Hudson's Bay Company transferred Rupert's Land and North-Western Territory to the government of Canada. + GAZ:00002565 Nova Scotia A Canadian province located on Canada's southeastern coast. The province's mainland is the Nova Scotia peninsula surrounded by the Atlantic Ocean, including numerous bays and estuaries. No where in Nova Scotia is more than 67 km from the ocean. Cape Breton Island, a large island to the northeast of the Nova Scotia mainland, is also part of the province, as is Sable Island. + GAZ:00002574 Nunavut The largest and newest territory of Canada; it was separated officially from the Northwest Territories on 1999-04-01. The Territory covers about 1.9 million km2 of land and water in Northern Canada including part of the mainland, most of the Arctic Archipelago, and all of the islands in Hudson Bay, James Bay, and Ungava Bay (including the Belcher Islands) which belonged to the Northwest Territories. Nunavut has land borders with the Northwest Territories on several islands as well as the mainland, a border with Manitoba to the south of the Nunavut mainland, and a tiny land border with Newfoundland and Labrador on Killiniq Island. It also shares aquatic borders with the provinces of Quebec, Ontario and Manitoba and with Greenland. + GAZ:00002563 Ontario A province located in the central part of Canada. Ontario is bordered by the provinces of Manitoba to the west, Quebec to the east, and the States of Michigan, New York, and Minnesota. Most of Ontario's borders with the United States are natural, starting at the Lake of the Woods and continuing through the four Great Lakes: Superior, Huron (which includes Georgian Bay), Erie, and Ontario (for which the province is named), then along the Saint Lawrence River near Cornwall. Ontario is the only Canadian Province that borders the Great Lakes. There are three different types of census divisions: single-tier municipalities, upper-tier municipalities (which can be regional municipalities or counties) and districts. + GAZ:00002572 Prince Edward Island A Canadian province consisting of an island of the same name. It is divided into 3 counties. + GAZ:00002569 Quebec A province in the central part of Canada. Quebec is Canada's largest province by area and its second-largest administrative division; only the territory of Nunavut is larger. It is bordered to the west by the province of Ontario, James Bay and Hudson Bay, to the north by Hudson Strait and Ungava Bay, to the east by the Gulf of Saint Lawrence and the provinces of Newfoundland and Labrador and New Brunswick. It is bordered on the south by the American states of Maine, New Hampshire, Vermont, and New York. It also shares maritime borders with the Territory of Nunavut, the Province of Prince Edward Island and the Province of Nova Scotia. + GAZ:00002564 Saskatchewan A prairie province in Canada. Saskatchewan is bounded on the west by Alberta, on the north by the Northwest Territories, on the east by Manitoba, and on the south by the States of Montana and North Dakota. It is divided into 18 census divisions according to Statistics Canada. + GAZ:00002576 Yukon The westernmost of Canada's three territories. The territory is the approximate shape of a right triangle, bordering the American State of Alaska to the west, the Northwest Territories to the east and British Columbia to the south. Its northern coast is on the Beaufort Sea. Its ragged eastern boundary mostly follows the divide between the Yukon Basin and the Mackenzie River drainage basin to the east in the Mackenzie mountains. Its capital is Whitehorse. + + +sample collection date precision menu SampleCollectionDatePrecisionMenu UO:0000036 year A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days. Mpox + UO:0000035 month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. + UO:0000033 day A time unit which is equal to 24 hours. + + +NML submitted specimen type menu NmlSubmittedSpecimenTypeMenu UBERON:0006314 Bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. Mpox + OBI:0001051 DNA The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. + OBI:0001010 Nucleic acid An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + OBI:0000880 RNA An extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. + OBI:0002600 Swab A device which is a soft, absorbent material mounted on one or both ends of a stick. + UBERON:0000479 Tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + GENEPIO:0001619 Not Applicable A categorical choice recorded when a datum does not apply to a given context. + + + +Related specimen relationship type menu RelatedSpecimenRelationshipTypeMenu HP:0011009 Acute Sudden appearance of disease manifestations over a short period of time. The word acute is applied to different time scales depending on the disease or manifestation and does not have an exact definition in minutes, hours, or days. Mpox + Convalescent A specimen collected from an individual during the recovery phase following the resolution of acute symptoms of a disease, often used to assess immune response or recovery progression. + Familial A specimen obtained from a relative of an individual, often used in studies examining genetic or hereditary factors, or familial transmission of conditions. + EFO:0009642 Follow-up The process by which information about the health status of an individual is obtained after a study has officially closed; an activity that continues something that has already begun or that repeats something that has already been done. + Reinfection testing A specimen collected to determine if an individual has been re-exposed to and reinfected by a pathogen after an initial infection and recovery. + Previously Submitted A specimen that has been previously provided or used in a study or testing but is being considered for re-analysis or additional testing. + Sequencing/bioinformatics methods development/validation A specimen used specifically for the purpose of developing, testing, or validating sequencing or bioinformatics methodologies. + Specimen sampling methods testing A specimen used to test, refine, or validate methods and techniques for collecting and processing samples. + +anatomical material menu AnatomicalMaterialMenu UBERON:0000178 Blood A fluid that is composed of blood plasma and erythrocytes. Mpox + UBERON:0010210 Blood clot Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). + UBERON:0001977 Blood serum The portion of blood plasma that excludes clotting factors. + UBERON:0001969 Blood plasma The liquid component of blood, in which erythrocytes are suspended. + NCIT:C41067 Whole blood Blood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant. + UBERON:0006314 Fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + UBERON:0001836 Saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + UBERON:0001359 Fluid (cerebrospinal (CSF)) A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + UBERON:0002409 Fluid (pericardial) Transudate contained in the pericardial cavity. + UBERON:0001087 Fluid (pleural) Transudate contained in the pleural cavity. + UBERON:0036243 Fluid (vaginal) Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands + UBERON:0000173 Fluid (amniotic) Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. + NCIT:C3824 Lesion A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part. + NCIT:C43278 Lesion (Macule) A flat lesion characterized by change in the skin color. + NCIT:C39690 Lesion (Papule) A small (less than 5-10 mm) elevation of skin that is non-suppurative. + NCIT:C78582 Lesion (Pustule) A circumscribed and elevated skin lesion filled with purulent material. + GENEPIO:0100490 Lesion (Scab) A dry, rough, crust-like lesion that forms over a wound or ulcer as part of the natural healing process. It consists of dried blood, serum, and cellular debris. + GENEPIO:0100491 Lesion (Vesicle) A small, fluid-filled elevation on the skin. Vesicles are often clear or slightly cloudy and can be a sign of various skin conditions or infections. + SYMP:0000487 Rash A skin and integumentary tissue symptom that is characterized by an eruption on the body typically with little or no elevation above the surface. + NCIT:C3426 Ulcer A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. + UBERON:0000479 Tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + NCIT:C3671 Wound tissue (injury) Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. + +anatomical material international menu AnatomicalMaterialInternationalMenu UBERON:0000178 Blood [UBERON:0000178] A fluid that is composed of blood plasma and erythrocytes. Mpox_international + UBERON:0010210 Blood clot [UBERON:0010210] Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). + UBERON:0001977 Blood serum [UBERON:0001977] The portion of blood plasma that excludes clotting factors. + UBERON:0001969 Blood plasma [UBERON:0001969] The liquid component of blood, in which erythrocytes are suspended. + NCIT:C41067 Whole blood [NCIT:C41067] Blood that has not been separated into its various components; blood that has not been modified except for the addition of an anticoagulant. + UBERON:0006314 Fluid [UBERON:0006314] Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + UBERON:0001836 Saliva [UBERON:0001836] A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + UBERON:0001359 Fluid (cerebrospinal (CSF)) [UBERON:0001359] A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + UBERON:0002409 Fluid (pericardial) [UBERON:0002409] Transudate contained in the pericardial cavity. + UBERON:0001087 Fluid (pleural) [UBERON:0001087] Transudate contained in the pleural cavity. + UBERON:0036243 Fluid (vaginal) [UBERON:0036243] Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands + UBERON:0000173 Fluid (amniotic) [UBERON:0000173] Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. + NCIT:C3824 Lesion [NCIT:C3824] A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part. + NCIT:C43278 Lesion (Macule) [NCIT:C43278] A flat lesion characterized by change in the skin color. + NCIT:C39690 Lesion (Papule) [NCIT:C39690] A small (less than 5-10 mm) elevation of skin that is non-suppurative. + NCIT:C78582 Lesion (Pustule) [NCIT:C78582] A circumscribed and elevated skin lesion filled with purulent material. + GENEPIO:0100490 Lesion (Scab) [GENEPIO:0100490] A dry, rough, crust-like lesion that forms over a wound or ulcer as part of the natural healing process. It consists of dried blood, serum, and cellular debris. + GENEPIO:0100491 Lesion (Vesicle) [GENEPIO:0100491] A small, fluid-filled elevation on the skin. Vesicles are often clear or slightly cloudy and can be a sign of various skin conditions or infections. + SYMP:0000487 Rash [SYMP:0000487] A skin and integumentary tissue symptom that is characterized by an eruption on the body typically with little or no elevation above the surface. + NCIT:C3426 Ulcer [NCIT:C3426] A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. + UBERON:0000479 Tissue [UBERON:0000479] Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + NCIT:C3671 Wound tissue (injury) [NCIT:C3671] Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. + + +anatomical part menu AnatomicalPartMenu UBERON:0001245 Anus Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. Mpox + UBERON:0012336 Perianal skin A zone of skin that is part of the area surrounding the anus. + UBERON:0001460 Arm The part of the forelimb extending from the shoulder to the autopod. + NCIT:C32628 Arm (forearm) The structure on the upper limb, between the elbow and the wrist. + UBERON:0001461 Elbow The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. + FMA:14181 Back The rear surface of the human body from the shoulders to the hips. + UBERON:0013691 Buttock A zone of soft tissue located on the posterior of the lateral side of the pelvic region corresponding to the gluteal muscles. + UBERON:0000002 Cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. + UBERON:0001443 Chest Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper + BTO:0000476 Foot The terminal part of the vertebrate leg upon which an individual stands. 2: An invertebrate organ of locomotion or attachment; especially: a ventral muscular surface or process of a mollusk. + BTO:0003358 Genital area The area where the upper thigh meets the trunk. More precisely, the fold or depression marking the juncture of the lower abdomen and the inner part of the thigh. + UBERON:0000989 Penis An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination. + UBERON:0035651 Glans (tip of penis) The bulbous structure at the distal end of the human penis + UBERON:0001332 Prepuce of penis (foreskin) A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. + UBERON:0002356 Perineum The space between the anus and scrotum in the male human, or between the anus and the vulva in the female human. + UBERON:0001300 Scrotum The external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. + UBERON:0000996 Vagina A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles + UBERON:0002530 Gland An organ that functions as a secretory or excretory organ. + BTO:0004668 Hand The terminal part of the vertebrate forelimb when modified, as in humans, as a grasping organ. + FMA:9666 Finger Subdivision of the hand demarcated from the hand proper by the skin crease in line with the distal edge of finger webs. Examples: thumb, right middle finger, left little finger. + FMA:24920 Hand (palm) The inner surface of the hand between the wrist and fingers. + UBERON:0000033 Head The head is the anterior-most division of the body. + UBERON:0006956 Buccal mucosa The inner lining of the cheeks and lips. + UBERON:0001567 Cheek A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. + UBERON:0001690 Ear Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. + NCIT:C103848 Preauricular region Of or pertaining to the area in front of the auricle of the ear. + UBERON:0000970 Eye An organ that detects light. + UBERON:0001456 Face A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). + UBERON:0008200 Forehead The part of the face above the eyes. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond + UBERON:0001833 Lip One of the two fleshy folds which surround the opening of the mouth. + UBERON:0011595 Jaw A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. + UBERON:0001723 Tongue A muscular organ in the floor of the mouth. + UBERON:0013203 Hypogastrium (suprapubic region) The hypogastrium (or hypogastric region, or pubic region) is an area of the human abdomen located below the navel. + UBERON:0000978 Leg The portion of the hindlimb that contains both the stylopod and zeugopod. + UBERON:0001512 Ankle A zone of skin that is part of an ankle + UBERON:0001465 Knee A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. + UBERON:0000376 Thigh The part of the hindlimb between pelvis and the knee, corresponding to the femur. + GENEPIO:0100492 Lower body The part of the body that includes the leg, ankle, and foot. + UBERON:0001707 Nasal Cavity An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. + UBERON:2001427 Anterior Nares The external part of the nose containing the lower nostrils. + UBERON:0005921 Inferior Nasal Turbinate The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. + UBERON:0005922 Middle Nasal Turbinate A turbinal located on the maxilla bone. + UBERON:0000974 Neck An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. + UBERON:0006562 Pharynx (throat) The pharynx is the part of the digestive system immediately posterior to the mouth. + UBERON:0001728 Nasopharynx (NP) The section of the pharynx that lies above the soft palate. + UBERON:0001729 Oropharynx (OP) The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. + UBERON:0003126 Trachea The trachea is the portion of the airway that attaches to the bronchi as it branches. + UBERON:0001052 Rectum The terminal portion of the intestinal tube, terminating with the anus. + UBERON:0001467 Shoulder A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). + UBERON:0001003 Skin The outer epithelial layer of the skin that is superficial to the dermis. + + + + +anatomical part international menu AnatomicalPartInternationalMenu UBERON:0001245 Anus [UBERON:0001245] Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. Mpox_international + UBERON:0012336 Perianal skin [UBERON:0012336] A zone of skin that is part of the area surrounding the anus. + UBERON:0001460 Arm [UBERON:0001460] The part of the forelimb extending from the shoulder to the autopod. + NCIT:C32628 Arm (forearm) [NCIT:C32628] The structure on the upper limb, between the elbow and the wrist. + UBERON:0001461 Elbow [UBERON:0001461] The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. + FMA:14181 Back [FMA:14181] The rear surface of the human body from the shoulders to the hips. + UBERON:0013691 Buttock [UBERON:0013691] A zone of soft tissue located on the posterior of the lateral side of the pelvic region corresponding to the gluteal muscles. + UBERON:0000002 Cervix [UBERON:0000002] Lower, narrow portion of the uterus where it joins with the top end of the vagina. + UBERON:0001443 Chest [UBERON:0001443] Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper + BTO:0000476 Foot [BTO:0000476] The terminal part of the vertebrate leg upon which an individual stands. + BTO:0003358 Genital area [BTO:0003358] The area where the upper thigh meets the trunk. More precisely, the fold or depression marking the juncture of the lower abdomen and the inner part of the thigh. + UBERON:0000989 Penis [UBERON:0000989] An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination. + UBERON:0035651 Glans (tip of penis) [UBERON:0035651] The bulbous structure at the distal end of the human penis + UBERON:0001332 Prepuce of penis (foreskin) A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. + UBERON:0002356 Perineum [UBERON:0002356] The space between the anus and scrotum in the male human, or between the anus and the vulva in the female human. + UBERON:0001300 Scrotum [UBERON:0001300] The external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. + UBERON:0000996 Vagina [UBERON:0000996] A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles + UBERON:0002530 Gland [UBERON:0002530] An organ that functions as a secretory or excretory organ. + BTO:0004668 Hand [BTO:0004668] The terminal part of the vertebrate forelimb when modified, as in humans, as a grasping organ. + FMA:9666 Finger [FMA:9666] Subdivision of the hand demarcated from the hand proper by the skin crease in line with the distal edge of finger webs. Examples: thumb, right middle finger, left little finger. + FMA:24920 Hand (palm) [FMA:24920] The inner surface of the hand between the wrist and fingers. + UBERON:0000033 Head [UBERON:0000033] The head is the anterior-most division of the body. + UBERON:0006956 Buccal mucosa [UBERON:0006956] The inner lining of the cheeks and lips. + UBERON:0001567 Cheek [UBERON:0001567] A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. + UBERON:0001690 Ear [UBERON:0001690] Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. + NCIT:C103848 Preauricular region [NCIT:C103848] Of or pertaining to the area in front of the auricle of the ear. + UBERON:0000970 Eye [UBERON:0000970] An organ that detects light. + UBERON:0001456 Face [UBERON:0001456] A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). + UBERON:0008200 Forehead [UBERON:0008200] The part of the face above the eyes. In human anatomy, the forehead is the fore part of the head. It is, formally, an area of the head bounded by three features, two of the skull and one of the scalp. The top of the forehead is marked by the hairline, the edge of the area where hair on the scalp grows. The bottom of the forehead is marked by the supraorbital ridge, the bone feature of the skull above the eyes. The two sides of the forehead are marked by the temporal ridge, a bone feature that links the supraorbital ridge to the coronal suture line and beyond + UBERON:0001833 Lip [UBERON:0001833] One of the two fleshy folds which surround the opening of the mouth. + UBERON:0011595 Jaw [UBERON:0011595] A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. + UBERON:0001723 Tongue [UBERON:0001723] A muscular organ in the floor of the mouth. + UBERON:0013203 Hypogastrium (suprapubic region) [UBERON:0013203] The hypogastrium (or hypogastric region, or pubic region) is an area of the human abdomen located below the navel. + UBERON:0000978 Leg [UBERON:0000978] The portion of the hindlimb that contains both the stylopod and zeugopod. + UBERON:0001512 Ankle [UBERON:0001512] A zone of skin that is part of an ankle + UBERON:0001465 Knee [UBERON:0001465] A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod. + UBERON:0000376 Thigh [UBERON:0000376] The part of the hindlimb between pelvis and the knee, corresponding to the femur. + GENEPIO:0100492 Lower body [GENEPIO:0100492] The part of the body that includes the leg, ankle, and foot. + UBERON:0001707 Nasal Cavity [UBERON:0001707] An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. + UBERON:2001427 Anterior Nares [UBERON:2001427] The external part of the nose containing the lower nostrils. + UBERON:0005921 Inferior Nasal Turbinate [UBERON:0005921] The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. + UBERON:0005922 Middle Nasal Turbinate [UBERON:0005922] A turbinal located on the maxilla bone. + UBERON:0000974 Neck [UBERON:0000974] An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. + UBERON:0006562 Pharynx (throat) [UBERON:0006562] A zone of skin that is part of an ankle + UBERON:0001728 Nasopharynx (NP) [UBERON:0001728] The section of the pharynx that lies above the soft palate. + UBERON:0001729 Oropharynx (OP) [UBERON:0001729] The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. + UBERON:0003126 Trachea [UBERON:0003126] The trachea is the portion of the airway that attaches to the bronchi as it branches. + UBERON:0001052 Rectum [UBERON:0001052] The terminal portion of the intestinal tube, terminating with the anus. + UBERON:0001467 Shoulder [UBERON:0001467] A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). + UBERON:0001003 Skin [UBERON:0001003] The outer epithelial layer of the skin that is superficial to the dermis. + + + +body product menu BodyProductMenu UBERON:0001913 Breast Milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. Mpox + UBERON:0001988 Feces Portion of semisolid bodily waste discharged through the anus. + SYMP:0000651 Fluid (discharge) A fluid that comes out of the body. + UBERON:0000177 Pus A bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. + UBERON:0006530 Fluid (seminal) A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. + UBERON:0000912 Mucus Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. + UBERON:0007311 Sputum Matter ejected from the lungs, bronchi, and trachea, through the mouth. + UBERON:0001089 Sweat Secretion produced by a sweat gland. + UBERON:0001827 Tear Aqueous substance secreted by the lacrimal gland. + UBERON:0001088 Urine Excretion that is the output of a kidney. + +body product international menu BodyProductInternationalMenu UBERON:0001913 Breast Milk [UBERON:0001913] An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. Mpox_international + UBERON:0001988 Feces [UBERON:0001988] Portion of semisolid bodily waste discharged through the anus. + SYMP:0000651 Fluid (discharge) [SYMP:0000651] A fluid that comes out of the body. + UBERON:0000177 Pus [UBERON:0000177] A bodily fluid consisting of a whitish-yellow or yellow substance produced during inflammatory responses of the body that can be found in regions of pyogenic bacterial infections. + UBERON:0006530 Fluid (seminal) [UBERON:0006530] A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. + UBERON:0000912 Mucus [UBERON:0000912] Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. + UBERON:0007311 Sputum [UBERON:0007311] Matter ejected from the lungs, bronchi, and trachea, through the mouth. + UBERON:0001089 Sweat [UBERON:0001089] Secretion produced by a sweat gland. + UBERON:0001827 Tear [UBERON:0001827] Aqueous substance secreted by the lacrimal gland. + UBERON:0001088 Urine [UBERON:0001088] Excretion that is the output of a kidney. + +environmental material international menu EnvironmentalMaterialInternationalMenu FOODON:02010020 Animal carcass [FOODON:02010020] A carcass of an animal that includes all anatomical parts. This includes a carcass with all organs and skin. Mpox_international + GSSO:005304 Bedding (Bed linen) [GSSO:005304] Bedding is the removable and washable portion of a human sleeping environment. + GSSO:003405 Clothing [GSSO:003405] Fabric or other material used to cover the body. + Drinkware Utensils with an open top that are used to hold liquids for consumption. + ENVO:03501330 Cup [ENVO:03501330] A utensil which is a hand-sized container with an open top. A cup may be used to hold liquids for pouring or drinking, or to store solids for pouring. + Tableware Items used in setting a table and serving food and beverages. This includes various utensils, plates, bowls, cups, glasses, and serving dishes designed for dining and drinking. + Dish A flat, typically round or oval item used for holding or serving food. It can also refer to a specific type of plate, often used to describe the container itself, such as a "plate dish" which is used for placing and serving individual portions of food. + ENVO:03501353 Eating utensil [ENVO:03501353] A utensil used for consuming food. + ENVO:00002001 Wastewater Water that has been adversely affected in quality by anthropogenic influence. + + +collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. Mpox + NCIT:C15631 Aspiration Inspiration of a foreign object into the airway. + GENEPIO:0100028 Suprapubic Aspiration An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample. + GENEPIO:0100029 Tracheal aspiration An aspiration process which collects tracheal secretions. + GENEPIO:0100030 Vacuum Aspiration An aspiration process which uses a vacuum source to remove a sample. + OBI:0002650 Biopsy A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. + OBI:0002651 Needle Biopsy A biopsy that uses a hollow needle to extract cells. + OBI:0302885 Filtration Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device + GENEPIO:0100031 Air filtration A filtration process which removes solid particulates from the air via an air filtration device. + OBI:0600044 Lavage A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid + GENEPIO:0100032 Bronchoalveolar lavage (BAL) The collection of bronchoalveolar lavage fluid (BAL) from the lungs. + GENEPIO:0100033 Gastric Lavage The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. + NCIT:C15327 Lumbar Puncture An invasive procedure in which a hollow needle is introduced through an intervertebral space in the lower back to access the subarachnoid space in order to sample cerebrospinal fluid or to administer medication. + MMO:0000344 Necropsy A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. + NCIT:C28221 Phlebotomy The collection of blood from a vein, most commonly via needle venipuncture. + GENEPIO:0002116 Rinsing The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. + GENEPIO:0100034 Saline gargle (mouth rinse and gargle) A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device. + GENEPIO:0100035 Scraping A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device. + GENEPIO:0002117 Swabbing The process of collecting specimen material using a swab collection device. + GENEPIO:0100036 Finger Prick A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. + NCIT:C15392 Thoracentesis (chest tap) The removal of excess fluid via needle puncture from the thoracic cavity. + +collection method international menu CollectionMethodInternationalMenu NCIT:C52009 Amniocentesis [NCIT:C52009] A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. Mpox_international + NCIT:C15631 Aspiration [NCIT:C15631] Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. + GENEPIO:0100028 Suprapubic Aspiration [GENEPIO:0100028] An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample. + GENEPIO:0100029 Tracheal aspiration [GENEPIO:0100029] An aspiration process which collects tracheal secretions. + GENEPIO:0100030 Vacuum Aspiration [GENEPIO:0100030] An aspiration process which uses a vacuum source to remove a sample. + OBI:0002650 Biopsy [OBI:0002650] A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. + OBI:0002651 Needle Biopsy [OBI:0002651] A biopsy that uses a hollow needle to extract cells. + OBI:0302885 Filtration [OBI:0302885] Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device. + GENEPIO:0100031 Air filtration [GENEPIO:0100031] A filtration process which removes solid particulates from the air via an air filtration device. + OBI:0600044 Lavage [OBI:0600044] A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid. + GENEPIO:0100032 Bronchoalveolar lavage (BAL) [GENEPIO:0100032] The collection of bronchoalveolar lavage fluid (BAL) from the lungs. + GENEPIO:0100033 Gastric Lavage [GENEPIO:0100033] The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. + NCIT:C15327 Lumbar Puncture [NCIT:C15327] An invasive procedure in which a hollow needle is introduced through an intervertebral space in the lower back to access the subarachnoid space in order to sample cerebrospinal fluid or to administer medication. + MMO:0000344 Necropsy [MMO:0000344] A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. + NCIT:C28221 Phlebotomy [NCIT:C28221] The collection of blood from a vein, most commonly via needle venipuncture. + GENEPIO:0002116 Rinsing [GENEPIO:0002116] The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. + GENEPIO:0100034 Saline gargle (mouth rinse and gargle) [GENEPIO:0100034] A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device. + GENEPIO:0100035 Scraping [GENEPIO:0100035] A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device. + GENEPIO:0002117 Swabbing [GENEPIO:0002117] The process of collecting specimen material using a swab collection device. + GENEPIO:0100036 Finger Prick [GENEPIO:0100036] A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. + NCIT:C15392 Thoracentesis (chest tap) [NCIT:C15392] The removal of excess fluid via needle puncture from the thoracic cavity. + + +collection device menu CollectionDeviceMenu OBI:0002859 Blood Collection Tube A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection Mpox + OBI:0002826 Bronchoscope A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung. + OBI:0002088 Collection Container A container with the function of containing a specimen. + GENEPIO:0100026 Collection Cup A device which is used to collect liquid samples. + GENEPIO:0100103 Filter A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass. + OBI:0000436 Needle A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. + OBI:0002860 Serum Collection Tube A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum. + OBI:0002861 Sputum Collection Tube A specimen collection tube which is designed for collecting sputum. + OBI:0002831 Suction Catheter A catheter which is used to remove mucus and other secretions from the body. + GENEPIO:0100027 Swab A device which is a soft, absorbent material mounted on one or both ends of a stick. + GENEPIO:0100493 Dry swab A swab device that consists of soft, absorbent material mounted on one or both ends of a stick, designed to collect samples without the presence of a liquid or preservative medium. + OBI:0002862 Urine Collection Tube A specimen container which is designed for holding urine. + GENEPIO:0100509 Universal Transport Medium (UTM) A sterile, balanced medium designed to preserve and transport clinical specimens, such as viruses, bacteria, and mycoplasma, ensuring the viability of the sample for subsequent analysis or culture. + OBI:0002866 Virus Transport Medium A medium designed to promote longevity of a viral sample. FROM Corona19 + + +collection device international menu CollectionDeviceInternationalMenu OBI:0002859 Blood Collection Tube [OBI:0002859] A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection Mpox_international + OBI:0002826 Bronchoscope [OBI:0002826] A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung. + OBI:0002088 Collection Container [OBI:0002088] A container with the function of containing a specimen. + GENEPIO:0100026 Collection Cup [GENEPIO:0100026] A device which is used to collect liquid samples. + GENEPIO:0100103 Filter [GENEPIO:0100103] A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass. + OBI:0000436 Needle [OBI:0000436] A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. + OBI:0002860 Serum Collection Tube [OBI:0002860] A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum. + OBI:0002861 Sputum Collection Tube [OBI:0002861] A specimen collection tube which is designed for collecting sputum. + OBI:0002831 Suction Catheter [OBI:0002831] A catheter which is used to remove mucus and other secretions from the body. + GENEPIO:0100027 Swab [GENEPIO:0100027] A device which is a soft, absorbent material mounted on one or both ends of a stick. + GENEPIO:0100493 Dry swab [GENEPIO:0100493] A swab device that consists of soft, absorbent material mounted on one or both ends of a stick, designed to collect samples without the presence of a liquid or preservative medium. + OBI:0002862 Urine Collection Tube [OBI:0002862] A specimen container which is designed for holding urine. + GENEPIO:0100509 Universal Transport Medium (UTM) [GENEPIO:0100509] A sterile, balanced medium designed to preserve and transport clinical specimens, such as viruses, bacteria, and mycoplasma, ensuring the viability of the sample for subsequent analysis or culture. + OBI:0002866 Virus Transport Medium [OBI:0002866] A medium designed to promote longevity of a viral sample. FROM Corona19 + + +specimen processing menu SpecimenProcessingMenu GENEPIO:0100039 Virus passage The process of growing a virus in serial iterations. Mpox + OBI:0600016 Specimens pooled Physical combination of several instances of like material. + +specimen processing international menu SpecimenProcessingInternationalMenu GENEPIO:0100039 Virus passage [GENEPIO:0100039] The process of growing a virus in serial iterations. Mpox_international + OBI:0600016 Specimens pooled [OBI:0600016] Physical combination of several instances of like material. + +experimental specimen role type menu ExperimentalSpecimenRoleTypeMenu GENEPIO:0101018 Positive experimental control A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. Mpox + GENEPIO:0101019 Negative experimental control A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment + EFO:0002090 Technical replicate A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. + EFO:0002091 Biological replicate A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. + +experimental specimen role type international menu ExperimentalSpecimenRoleTypeInternationalMenu GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. Mpox_international + GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment + EFO:0002090 Technical replicate [EFO:0002090] A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. + EFO:0002091 Biological replicate [EFO:0002091] A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. + +lineage/clade name international menu LineageCladeNameInternationalMenu GENEPIO:0102029 Mpox virus clade I [GENEPIO:0102029] An Mpox virus clade with at least 99% similarity to the West African/USA-derived Mpox strain. + GENEPIO:0102030 Mpox virus clade Ia [GENEPIO:0102030] An Mpox virus that clusters in phylogenetic trees within the Ia clade. + GENEPIO:0102031 Mpox virus clade Ib [GENEPIO:0102031] An Mpox virus that clusters in phylogenetic trees within the Ib clade. + GENEPIO:0102032 Mpox virus clade II [GENEPIO:0102032] An Mpox virus clade with at least 99% similarity to the Congo Basin-derived Mpox strain. + GENEPIO:0102033 Mpox virus clade IIa [GENEPIO:0102033] An Mpox virus that clusters in phylogenetic trees within the IIa clade. + GENEPIO:0102034 Mpox virus clade IIb [GENEPIO:0102034] An Mpox virus that clusters in phylogenetic trees within the IIb clade. + Mpox virus lineage B.1 + Mpox virus lineage A + +host (common name) menu HostCommonNameMenu NCBITaxon:9606 Human A bipedal primate mammal of the species Homo sapiens. Mpox + +host (common name) international menu HostCommonNameInternationalMenu NCBITaxon:9606 Human [NCBITaxon:9606] A bipedal primate mammal of the species Homo sapiens. Mpox_international + NCBITaxon:9989 Rodent [NCBITaxon:9989] A mammal of the order Rodentia which are characterized by a single pair of continuously growing incisors in each of the upper and lower jaws. + NCBITaxon:10090 Mouse [NCBITaxon:10090] A small rodent that typically has a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. + NCBITaxon:45478 Prairie Dog [NCBITaxon:45478] A herbivorous burrowing ground squirrels native to the grasslands of North America. + NCBITaxon:10116 Rat [NCBITaxon:10116] A medium sized rodent that typically is long tailed. + FOODON:03411389 Squirrel [FOODON:03411389] A small to medium-sized rodent belonging to the family Sciuridae, characterized by a bushy tail, sharp claws, and strong hind legs, commonly found in trees, but some species live on the ground + +host (scientific name) menu HostScientificNameMenu NCBITaxon:9606 Homo sapiens A type of primate characterized by bipedalism and large, complex brain. Mpox + +host (scientific name) international menu HostScientificNameInternationalMenu NCBITaxon:9606 Homo sapiens [NCBITaxon:9606] A bipedal primate mammal of the species Homo sapiens. Mpox_international + +host health state menu HostHealthStateMenu NCIT:C3833 Asymptomatic Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. Mpox + NCIT:C28554 Deceased The cessation of life. + NCIT:C115935 Healthy Having no significant health-related issues. + NCIT:C49498 Recovered One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C25269 Symptomatic Exhibiting the symptoms of a particular disease. + +host health state international menu HostHealthStateInternationalMenu NCIT:C3833 Asymptomatic [NCIT:C3833] Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. Mpox_international + NCIT:C28554 Deceased [NCIT:C28554] The cessation of life. + NCIT:C115935 Healthy [NCIT:C115935] Having no significant health-related issues. + NCIT:C49498 Recovered [NCIT:C49498] One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C25269 Symptomatic [NCIT:C25269] Exhibiting the symptoms of a particular disease. + +host health status details menu HostHealthStatusDetailsMenu NCIT:C25179 Hospitalized The condition of being treated as a patient in a hospital. Mpox + GENEPIO:0100045 Hospitalized (Non-ICU) The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU). + GENEPIO:0100046 Hospitalized (ICU) The condition of being treated as a patient in a hospital intensive care unit (ICU). + GENEPIO:0100047 Medically Isolated Separation of people with a contagious disease from population to reduce the spread of the disease. + GENEPIO:0100048 Medically Isolated (Negative Pressure) Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter. + NCIT:C173768 Self-quarantining A method used by an individual to be kept apart in seclusion from others for a period of time in an attempt to minimize the risk of transmission of an infectious disease. + +host health status details international menu HostHealthStatusDetailsInternationalMenu NCIT:C25179 Hospitalized [NCIT:C25179] The condition of being treated as a patient in a hospital. Mpox_international + GENEPIO:0100045 Hospitalized (Non-ICU) [GENEPIO:0100045] The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU). + GENEPIO:0100046 Hospitalized (ICU) [GENEPIO:0100046] The condition of being treated as a patient in a hospital intensive care unit (ICU). + GENEPIO:0100047 Medically Isolated [GENEPIO:0100047] Separation of people with a contagious disease from population to reduce the spread of the disease. + GENEPIO:0100048 Medically Isolated (Negative Pressure) [GENEPIO:0100048] Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter. + NCIT:C173768 Self-quarantining [NCIT:C173768] A method used by an individual to be kept apart in seclusion from others for a period of time in an attempt to minimize the risk of transmission of an infectious disease. + +host health outcome menu HostHealthOutcomeMenu NCIT:C28554 Deceased The cessation of life. Mpox + NCIT:C25254 Deteriorating Advancing in extent or severity. + NCIT:C49498 Recovered One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C30103 Stable Subject to little fluctuation; showing little if any change. + +host health outcome international menu HostHealthOutcomeInternationalMenu NCIT:C28554 Deceased [NCIT:C28554] The cessation of life. Mpox_international + NCIT:C25254 Deteriorating [NCIT:C25254] Advancing in extent or severity. + NCIT:C49498 Recovered [NCIT:C49498] One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C30103 Stable [NCIT:C30103] Subject to little fluctuation; showing little if any change. + + +host age unit menu HostAgeUnitMenu UO:0000035 month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. Mpox + UO:0000036 year A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days. + +host age unit international menu HostAgeUnitInternationalMenu UO:0000035 month [UO:0000035] A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. Mpox_international + UO:0000036 year [UO:0000036] A time unit which is equal to 12 months which in science is taken to be equal to 365.25 days. + +host age bin menu HostAgeBinMenu GENEPIO:0100049 0 - 9 An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive). Mpox + GENEPIO:0100050 10 - 19 An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive). + GENEPIO:0100051 20 - 29 An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive). + GENEPIO:0100052 30 - 39 An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive). + GENEPIO:0100053 40 - 49 An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive). + GENEPIO:0100054 50 - 59 An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive). + GENEPIO:0100055 60 - 69 An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive). + GENEPIO:0100056 70 - 79 An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive). + GENEPIO:0100057 80 - 89 An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive). + GENEPIO:0100058 90 - 99 An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). + GENEPIO:0100059 100+ An age group that stratifies the age of a case to be greater than or equal to 100 years old. + +host age bin international menu HostAgeBinInternationalMenu GENEPIO:0100049 0 - 9 [GENEPIO:0100049] An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive). Mpox_international + GENEPIO:0100050 10 - 19 [GENEPIO:0100050] An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive). + GENEPIO:0100051 20 - 29 [GENEPIO:0100051] An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive). + GENEPIO:0100052 30 - 39 [GENEPIO:0100052] An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive). + GENEPIO:0100053 40 - 49 [GENEPIO:0100053] An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive). + GENEPIO:0100054 50 - 59 [GENEPIO:0100054] An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive). + GENEPIO:0100055 60 - 69 [GENEPIO:0100055] An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive). + GENEPIO:0100056 70 - 79 [GENEPIO:0100056] An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive). + GENEPIO:0100057 80 - 89 [GENEPIO:0100057] An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive). + GENEPIO:0100058 90 - 99 [GENEPIO:0100058] An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). + GENEPIO:0100059 100+ [GENEPIO:0100059] An age group that stratifies the age of a case to be greater than or equal to 100 years old. + +host gender menu HostGenderMenu NCIT:C46110 Female An individual who reports belonging to the cultural gender role distinction of female. Mpox + NCIT:C46109 Male An individual who reports belonging to the cultural gender role distinction of male. + GSSO:000132 Non-binary gender Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. + GSSO:004004 Transgender (assigned male at birth) Having a feminine gender (identity) which is different from the sex one was assigned at birth. + GSSO:004005 Transgender (assigned female at birth) Having a masculine gender (identity) which is different from the sex one was assigned at birth. + NCIT:C110959 Undeclared A categorical choice recorded when an individual being interviewed is unable or chooses not to provide a datum. + +host gender international menu HostGenderInternationalMenu NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. Mpox_international + NCIT:C46109 Male [NCIT:C46109] An individual who reports belonging to the cultural gender role distinction of male. + GSSO:000132 Non-binary gender [GSSO:000132] Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. + GSSO:004004 Transgender (assigned male at birth) [GSSO:004004] Having a feminine gender (identity) which is different from the sex one was assigned at birth. + GSSO:004005 Transgender (assigned female at birth) [GSSO:004005] Having a masculine gender (identity) which is different from the sex one was assigned at birth. + NCIT:C110959 Undeclared [NCIT:C110959] A categorical choice recorded when an individual being interviewed is unable or chooses not to provide a datum. + + +signs and symptoms menu SignsAndSymptomsMenu HP:0025143 Chills (sudden cold sensation) A sudden sensation of feeling cold. Mpox + HP:0000509 Conjunctivitis (pink eye) Inflammation of the conjunctiva. + HP:0012735 Cough A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. + HP:0012378 Fatigue (tiredness) A subjective feeling of tiredness characterized by a lack of energy and motivation. + HP:0001945 Fever Body temperature elevated above the normal range. + HP:0002315 Headache Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. + NCIT:C3824 Lesion A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part. + NCIT:C43278 Lesion (Macule) A flat lesion characterized by change in the skin color. + NCIT:C39690 Lesion (Papule) A small (less than 5-10 mm) elevation of skin that is non-suppurative. + NCIT:C78582 Lesion (Pustule) A circumscribed and elevated skin lesion filled with purulent material. + GENEPIO:0100490 Lesion (Scab) Dried purulent material on the skin from a skin lesion. + GENEPIO:0100491 Lesion (Vesicle) Small, inflamed, pus-filled, blister-like sores (lesions) on the skin surface. + HP:0003326 Myalgia (muscle pain) Pain in muscle. + HP:0003418 Back pain An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back. + HP:0002018 Nausea A sensation of unease in the stomach together with an urge to vomit. + HP:0000988 Rash A red eruption of the skin. + NCIT:C50747 Sore throat Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. + NCIT:C36172 Sweating A watery secretion by the sweat glands that is primarily composed of salt, urea and minerals. + HP:0002716 Swollen Lymph Nodes Enlargment (swelling) of a lymph node. + NCIT:C3426 Ulcer A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. + HP:0002013 Vomiting (throwing up) Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. + + +signs and symptoms international menu SignsAndSymptomsInternationalMenu HP:0025143 Chills (sudden cold sensation) [HP:0025143] A sudden sensation of feeling cold. Mpox_international + HP:0000509 Conjunctivitis (pink eye) [HP:0000509] Inflammation of the conjunctiva. + HP:0012735 Cough [HP:0012735] A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. + HP:0012378 Fatigue (tiredness) [HP:0012378] A subjective feeling of tiredness characterized by a lack of energy and motivation. + HP:0001945 Fever [HP:0001945] Body temperature elevated above the normal range. + HP:0002315 Headache [HP:0002315] Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. + NCIT:C3824 Lesion [NCIT:C3824] A localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part. + NCIT:C43278 Lesion (Macule) [NCIT:C43278] A flat lesion characterized by change in the skin color. + NCIT:C39690 Lesion (Papule) [NCIT:C39690] A small (less than 5-10 mm) elevation of skin that is non-suppurative. + NCIT:C78582 Lesion (Pustule) [NCIT:C78582] A circumscribed and elevated skin lesion filled with purulent material. + GENEPIO:0100490 Lesion (Scab) [GENEPIO:0100490] Dried purulent material on the skin from a skin lesion. + GENEPIO:0100491 Lesion (Vesicle) [GENEPIO:0100491] Small, inflamed, pus-filled, blister-like sores (lesions) on the skin surface. + HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. + HP:0003418 Back pain [HP:0003418] An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back. + HP:0002018 Nausea [HP:0002018] A sensation of unease in the stomach together with an urge to vomit. + HP:0000988 Rash [HP:0000988] A red eruption of the skin. + NCIT:C50747 Sore throat [NCIT:C50747] Any kind of inflammatory process of the tonsils, pharynx, or/and larynx characterized by pain in swallowing. + NCIT:C36172 Sweating [NCIT:C36172] A watery secretion by the sweat glands that is primarily composed of salt, urea and minerals. + HP:0002716 Swollen Lymph Nodes [HP:0002716] Enlargment (swelling) of a lymph node. + NCIT:C3426 Ulcer [NCIT:C3426] A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. + HP:0002013 Vomiting (throwing up) [HP:0002013] Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. + + +pre-existing conditions and risk factors menu PreExistingConditionsAndRiskFactorsMenu MONDO:0004992 Cancer A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. Mpox + HP:0000819 Diabetes mellitus (diabetes) A group of abnormalities characterized by hyperglycemia and glucose intolerance. + HP:0100651 Type I diabetes mellitus (T1D) A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. + HP:0005978 Type II diabetes mellitus (T2D) A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. + NCIT:C14139 Immunocompromised A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions. + NCIT:C26726 Infectious disorder A disorder resulting from the presence and activity of a microbial, viral, fungal, or parasitic agent. It can be transmitted by direct or indirect contact. + DOID:13778 Chancroid (Haemophilus ducreyi) A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers. + DOID:11263 Chlamydia A commensal bacterial infectious disease that is caused by Chlamydia trachomatis. + DOID:7551 Gonorrhea A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods. + NCIT:C155871 Herpes Simplex Virus infection (HSV) An infection that is caused by herpes simplex virus. + MONDO:0005109 Human immunodeficiency virus (HIV) An infection caused by the human immunodeficiency virus. + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. + MONDO:0005161 Human papilloma virus infection (HPV) An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth. + DOID:13819 Lymphogranuloma venereum A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis. + NCBITaxon:2097 Mycoplsma genitalium A sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans. + DOID:4166 Syphilis A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years. + DOID:1947 Trichomoniasis A parasitic protozoa infectious disease that is caused by singled-celled protozoan parasites Trichomonas vaginalis or Trichomonas tenax, which infect the urogenital tract and mouth respectively. + MONDO:0004670 Lupus An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. + NCIT:C25742 Pregnancy The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. + NCIT:C16124 Prior therapy Prior action or administration of therapeutic agents that produced an effect that is intended to alter or stop a pathologic process. + NCIT:C16212 Cancer treatment Any intervention for management of a malignant neoplasm. + NCIT:C15632 Chemotherapy The use of synthetic or naturally-occurring chemicals for the treatment of diseases. + NCIT:C16118 HIV and Antiretroviral therapy (ART) Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles. + CHEBI:35341 Steroid Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. + NCIT:C159659 Transplant An individual receiving a transplant. + +pre-existing conditions and risk factors international menu PreExistingConditionsAndRiskFactorsInternationalMenu MONDO:0004992 Cancer [MONDO:0004992] A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. Mpox_international + HP:0000819 Diabetes mellitus (diabetes) [HP:0000819] A group of abnormalities characterized by hyperglycemia and glucose intolerance. + HP:0100651 Type I diabetes mellitus (T1D) [HP:0100651] A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. + HP:0005978 Type II diabetes mellitus (T2D) [HP:0005978] A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. + NCIT:C14139 Immunocompromised [NCIT:C14139] A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions. + NCIT:C26726 Infectious disorder [NCIT:C26726] A disorder resulting from the presence and activity of a microbial, viral, fungal, or parasitic agent. It can be transmitted by direct or indirect contact. + DOID:13778 Chancroid (Haemophilus ducreyi) [DOID:13778] A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers. + DOID:11263 Chlamydia [DOID:11263] A commensal bacterial infectious disease that is caused by Chlamydia trachomatis. + DOID:7551 Gonorrhea [DOID:7551] A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods. + NCIT:C155871 Herpes Simplex Virus infection (HSV) [NCIT:C155871] An infection that is caused by herpes simplex virus. + MONDO:0005109 Human immunodeficiency virus (HIV) [MONDO:0005109] An infection caused by the human immunodeficiency virus. + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. + MONDO:0005161 Human papilloma virus infection (HPV) [MONDO:0005161] An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth. + DOID:13819 Lymphogranuloma venereum [DOID:13819] A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis. + NCBITaxon:2097 Mycoplsma genitalium [NCBITaxon:2097] A sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans. + DOID:4166 Syphilis [DOID:4166] A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years. + DOID:1947 Trichomoniasis [DOID:1947] A parasitic protozoa infectious disease that is caused by singled-celled protozoan parasites Trichomonas vaginalis or Trichomonas tenax, which infect the urogenital tract and mouth respectively. + MONDO:0004670 Lupus [MONDO:0004670] An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. + NCIT:C25742 Pregnancy [NCIT:C25742] The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. + NCIT:C16124 Prior therapy [NCIT:C16124] Prior action or administration of therapeutic agents that produced an effect that is intended to alter or stop a pathologic process. + NCIT:C16212 Cancer treatment [NCIT:C16212] Any intervention for management of a malignant neoplasm. + NCIT:C15632 Chemotherapy [NCIT:C15632] The use of synthetic or naturally-occurring chemicals for the treatment of diseases. + NCIT:C16118 HIV and Antiretroviral therapy (ART) [NCIT:C16118] Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles. + CHEBI:35341 Steroid [CHEBI:35341] Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. + NCIT:C159659 Transplant [NCIT:C159659] An individual receiving a transplant. + +complications menu ComplicationsMenu MONDO:0005682 Bronchopneumonia Acute inflammation of the walls of the terminal bronchioles that spreads into the peribronchial alveoli and alveolar ducts. It results in the creation of foci of consolidation, which are surrounded by normal parenchyma. It affects one or more lobes, and is frequently bilateral and basal. It is usually caused by bacteria (e.g., Staphylococcus, Streptococcus, Haemophilus influenzae). Signs and symptoms include fever, cough with production of brown-red sputum, dyspnea, and chest pain. Mpox + MONDO:0023865 Corneal infection A viral or bacterial infectious process affecting the cornea. Symptoms include pain and redness in the eye, photophobia and eye watering. + MP:0002908 Delayed wound healing (lesion healing) Longer time requirement for the ability to self-repair and close wounds than normal + DOID:9588 Encephalitis A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms. + DOID:820 Myocarditis An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle. + IDO:0000567 Secondary infection An infection bearing the secondary infection role. + HP:0100806 Sepsis Systemic inflammatory response to infection. + +complications international menu ComplicationsInternationalMenu MONDO:0005682 Bronchopneumonia [MONDO:0005682] Acute inflammation of the walls of the terminal bronchioles that spreads into the peribronchial alveoli and alveolar ducts. It results in the creation of foci of consolidation, which are surrounded by normal parenchyma. It affects one or more lobes, and is frequently bilateral and basal. It is usually caused by bacteria (e.g., Staphylococcus, Streptococcus, Haemophilus influenzae). Signs and symptoms include fever, cough with production of brown-red sputum, dyspnea, and chest pain. Mpox_international + MONDO:0023865 Corneal infection [MONDO:0023865] A viral or bacterial infectious process affecting the cornea. Symptoms include pain and redness in the eye, photophobia and eye watering. + MP:0002908 Delayed wound healing (lesion healing) [MP:0002908] Longer time requirement for the ability to self-repair and close wounds than normal + DOID:9588 Encephalitis [DOID:9588] A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms. + DOID:820 Myocarditis [DOID:820] An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle. + IDO:0000567 Secondary infection [IDO:0000567] An infection bearing the secondary infection role. + HP:0100806 Sepsis [HP:0100806] Systemic inflammatory response to infection. + +host vaccination status menu HostVaccinationStatusMenu GENEPIO:0100100 Fully Vaccinated Completed a full series of an authorized vaccine according to the regional health institutional guidance. Mpox + GENEPIO:0100102 Not Vaccinated Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance. + +host vaccination status international menu HostVaccinationStatusInternationalMenu GENEPIO:0100100 Fully Vaccinated [GENEPIO:0100100] Completed a full series of an authorized vaccine according to the regional health institutional guidance. Mpox_international + GENEPIO:0100101 Partially Vaccinated [GENEPIO:0100101] Initiated but not yet completed the full series of an authorized vaccine according to the regional health institutional guidance. + GENEPIO:0100102 Not Vaccinated [GENEPIO:0100102] Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance. + +exposure event menu ExposureEventMenu GENEPIO:0100237 Mass Gathering A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. Mpox + GENEPIO:0100238 Convention (conference) A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom. + GENEPIO:0100240 Agricultural Event A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry. + PCO:0000033 Social Gathering A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + PCO:0000034 Community Event A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. + PCO:0000035 Party A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. + Other exposure event An event or situation not classified under other specific exposure types, in which an individual may be exposed to conditions or factors that could impact health or safety. This term encompasses a wide range of gatherings, activities, or circumstances that do not fit into predefined exposure categories. + +exposure event international menu ExposureEventInternationalMenu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. Mpox_international + GENEPIO:0100238 Convention (conference) [GENEPIO:0100238] A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom. + GENEPIO:0100240 Agricultural Event [GENEPIO:0100240] A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry. + PCO:0000033 Social Gathering [PCO:0000033] A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + PCO:0000034 Community Event [PCO:0000034] A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. + PCO:0000035 Party [PCO:0000035] A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. + Other exposure event An exposure event not specified in the picklist. + + +exposure contact level menu ExposureContactLevelMenu GENEPIO:0100494 Contact with animal A type of contact in which an individual comes into contact with an animal, either directly or indirectly, which could include physical interaction or exposure to animal bodily fluids, feces, or other contaminated materials. Mpox + GENEPIO:0100495 Contact with rodent A type of contact in which an individual comes into contact with a rodent, either directly or indirectly, such as through handling, exposure to rodent droppings, urine, or nests, which could potentially lead to the transmission of rodent-borne diseases. + GENEPIO:0100496 Contact with fomite A type of contact in which an individual comes into contact with an inanimate object or surface that has been contaminated with pathogens, such as doorknobs, countertops, or medical equipment, which can transfer infectious agents to the individual. + GENEPIO:0100357 Contact with infected individual A type of contact in which an individual comes in contact with an infected person, either directly or indirectly. + TRANS:0000001 Direct (human-to-human contact) Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. + TRANS:0000006 Mother-to-child transmission A direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth. + NCIT:C19085 Sexual transmission Passage or transfer, as of a disease, from a donor individual to a recipient during or as a result of sexual activity. + GENEPIO:0100246 Indirect contact A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces. + GENEPIO:0100247 Close contact (face-to-face contact) A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time. + GENEPIO:0100248 Casual contact A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission. + GENEPIO:0100497 Workplace associated transmission A type of transmission where an individual acquires an infection or disease as a result of exposure in their workplace environment. This can include direct contact with infected individuals, exposure to contaminated materials or surfaces, or other workplace-specific risk factors. + GENEPIO:0100498 Healthcare associated transmission A type of transmission where an individual acquires an infection or disease as a result of exposure within a healthcare setting. This includes transmission through direct contact with patients, contaminated medical equipment, or surfaces within healthcare facilities, such as hospitals or clinics. + GENEPIO:0100499 Laboratory associated transmission A type of transmission where an individual acquires an infection or disease as a result of exposure within a laboratory setting. This includes contact with infectious agents, contaminated equipment, or laboratory surfaces, as well as potential aerosol exposure or spills of hazardous substances. + +exposure contact level international menu ExposureContactLevelInternationalMenu GENEPIO:0100494 Contact with animal [GENEPIO:0100494] A type of contact in which an individual comes into contact with an animal, either directly or indirectly, which could include physical interaction or exposure to animal bodily fluids, feces, or other contaminated materials. Mpox_international + GENEPIO:0100495 Contact with rodent [GENEPIO:0100495] A type of contact in which an individual comes into contact with a rodent, either directly or indirectly, such as through handling, exposure to rodent droppings, urine, or nests, which could potentially lead to the transmission of rodent-borne diseases. + GENEPIO:0100496 Contact with fomite [GENEPIO:0100496] A type of contact in which an individual comes into contact with an inanimate object or surface that has been contaminated with pathogens, such as doorknobs, countertops, or medical equipment, which can transfer infectious agents to the individual. + GENEPIO:0100357 Contact with infected individual [GENEPIO:0100357] A type of contact in which an individual comes in contact with an infected person, either directly or indirectly. + TRANS:0000001 Direct (human-to-human contact) [TRANS:0000001] Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. + TRANS:0000006 Mother-to-child transmission [TRANS:0000006] A direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth. + NCIT:C19085 Sexual transmission [NCIT:C19085] Passage or transfer, as of a disease, from a donor individual to a recipient during or as a result of sexual activity. + GENEPIO:0100246 Indirect contact [GENEPIO:0100246] A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces. + GENEPIO:0100247 Close contact (face-to-face contact) [GENEPIO:0100247] A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time. + GENEPIO:0100248 Casual contact [GENEPIO:0100248] A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission. + GENEPIO:0100497 Workplace associated transmission [GENEPIO:0100497] A type of transmission where an individual acquires an infection or disease as a result of exposure in their workplace environment. This can include direct contact with infected individuals, exposure to contaminated materials or surfaces, or other workplace-specific risk factors. + GENEPIO:0100498 Healthcare associated transmission [GENEPIO:0100498] A type of transmission where an individual acquires an infection or disease as a result of exposure within a healthcare setting. This includes transmission through direct contact with patients, contaminated medical equipment, or surfaces within healthcare facilities, such as hospitals or clinics. + GENEPIO:0100499 Laboratory associated transmission [GENEPIO:0100499] A type of transmission where an individual acquires an infection or disease as a result of exposure within a laboratory setting. This includes contact with infectious agents, contaminated equipment, or laboratory surfaces, as well as potential aerosol exposure or spills of hazardous substances. + +host role menu HostRoleMenu GENEPIO:0100249 Attendee A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place. Mpox + OMRSE:00000058 Student A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. + OMRSE:00000030 Patient A patient role that inheres in a human being. + NCIT:C25182 Inpatient A patient who is residing in the hospital where he is being treated. + NCIT:C28293 Outpatient A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay. + GENEPIO:0100250 Passenger A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination. + GENEPIO:0100251 Resident A role inhering in a person that is realized when the bearer maintains residency in a given place. + GENEPIO:0100252 Visitor A role inhering in a person that is realized when the bearer pays a visit to a specific place or event. + GENEPIO:0100253 Volunteer A role inhering in a person that is realized when the bearer enters into any service of their own free will. + GENEPIO:0100254 Work A role inhering in a person that is realized when the bearer performs labor for a living. + GENEPIO:0100255 Administrator A role inhering in a person that is realized when the bearer is engaged in administration or administrative work. + GENEPIO:0100256 First Responder A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance. + GENEPIO:0100260 Housekeeper A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff. + GENEPIO:0100261 Kitchen Worker A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen. + GENEPIO:0100334 Healthcare Worker A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting. + GENEPIO:0100420 Community Healthcare Worker A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100262 Laboratory Worker A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory. + OMRSE:00000014 Nurse A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. + GENEPIO:0100263 Personal Care Aid A role inhering in a person that is realized when the bearer works to help another person complete their daily activities. + GENEPIO:0100264 Pharmacist A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility. + OMRSE:00000013 Physician A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. + GENEPIO:0100354 Rotational Worker A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live. + GENEPIO:0100355 Seasonal Worker A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas. + GSSO:005831 Sex Worker A person who supplies sex work (some form of sexual services) in exchange for compensation. This term is promoted along with the idea that what has previously been termed prostitution should be recognized as work on equal terms with that of conventional jobs, with the legal implications this has. It is sometimes regarded as a less offensive alternative to prostitute, although "sex worker" has a much broader meaning. + GENEPIO:0100265 Veterinarian A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine. + OMRSE:00000001 Social role A social role inhering in a human being. + GENEPIO:0100266 Acquaintance of case A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person. + GENEPIO:0100267 Relative of case A role inhering in a person that is realized when the bearer is a relative of the case. + GENEPIO:0100268 Child of case A role inhering in a person that is realized when the bearer is a person younger than the age of majority. + GENEPIO:0100269 Parent of case A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species. + GENEPIO:0100270 Father of case A role inhering in a person that is realized when the bearer is the male parent of a child. + GENEPIO:0100271 Mother of case A role inhering in a person that is realized when the bearer is the female parent of a child. + GENEPIO:0100500 Sexual partner of case A role inhering in a person that is realized when the bearer is a sexual partner of the case. + GENEPIO:0100272 Spouse of case A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage. + Other Host Role A role undertaken by a host that is not categorized under specific predefined host roles. + +host role international menu HostRoleInternationalMenu GENEPIO:0100249 Attendee [GENEPIO:0100249] A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place. Mpox_international + OMRSE:00000058 Student [OMRSE:00000058] A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. + OMRSE:00000030 Patient [OMRSE:00000030] A patient role that inheres in a human being. + NCIT:C25182 Inpatient [NCIT:C25182] A patient who is residing in the hospital where he is being treated. + NCIT:C28293 Outpatient [NCIT:C28293] A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay. + GENEPIO:0100250 Passenger [GENEPIO:0100250] A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination. + GENEPIO:0100251 Resident [GENEPIO:0100251] A role inhering in a person that is realized when the bearer maintains residency in a given place. + GENEPIO:0100252 Visitor [GENEPIO:0100252] A role inhering in a person that is realized when the bearer pays a visit to a specific place or event. + GENEPIO:0100253 Volunteer [GENEPIO:0100253] A role inhering in a person that is realized when the bearer enters into any service of their own free will. + GENEPIO:0100254 Work [GENEPIO:0100254] A role inhering in a person that is realized when the bearer performs labor for a living. + GENEPIO:0100255 Administrator [GENEPIO:0100255] A role inhering in a person that is realized when the bearer is engaged in administration or administrative work. + GENEPIO:0100256 First Responder [GENEPIO:0100256] A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance. + GENEPIO:0100260 Housekeeper [GENEPIO:0100260] A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff. + GENEPIO:0100261 Kitchen Worker [GENEPIO:0100261] A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen. + GENEPIO:0100334 Healthcare Worker [GENEPIO:0100334] A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting. + GENEPIO:0100420 Community Healthcare Worker [GENEPIO:0100420] A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100262 Laboratory Worker [GENEPIO:0100262] A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory. + OMRSE:00000014 Nurse [OMRSE:00000014] A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. + GENEPIO:0100263 Personal Care Aid [GENEPIO:0100263] A role inhering in a person that is realized when the bearer works to help another person complete their daily activities. + GENEPIO:0100264 Pharmacist [GENEPIO:0100264] A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility. + OMRSE:00000013 Physician [OMRSE:00000013] A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. + GENEPIO:0100354 Rotational Worker [GENEPIO:0100354] A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live. + GENEPIO:0100355 Seasonal Worker [GENEPIO:0100355] A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas. + GSSO:005831 Sex Worker [GSSO:005831] A person who supplies sex work (some form of sexual services) in exchange for compensation. This term is promoted along with the idea that what has previously been termed prostitution should be recognized as work on equal terms with that of conventional jobs, with the legal implications this has. It is sometimes regarded as a less offensive alternative to prostitute, although "sex worker" has a much broader meaning. + GENEPIO:0100265 Veterinarian [GENEPIO:0100265] A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine. + OMRSE:00000001 Social role [OMRSE:00000001] A social role inhering in a human being. + GENEPIO:0100266 Acquaintance of case [GENEPIO:0100266] A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person. + GENEPIO:0100267 Relative of case [GENEPIO:0100267] A role inhering in a person that is realized when the bearer is a relative of the case. + GENEPIO:0100268 Child of case [GENEPIO:0100268] A role inhering in a person that is realized when the bearer is a person younger than the age of majority. + GENEPIO:0100269 Parent of case [GENEPIO:0100269] A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species. + GENEPIO:0100270 Father of case [GENEPIO:0100270] A role inhering in a person that is realized when the bearer is the male parent of a child. + GENEPIO:0100271 Mother of case [GENEPIO:0100271] A role inhering in a person that is realized when the bearer is the female parent of a child. + GENEPIO:0100500 Sexual partner of case [GENEPIO:0100500] A role inhering in a person that is realized when the bearer is a sexual partner of the case. + GENEPIO:0100272 Spouse of case [GENEPIO:0100272] A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage. + Other Host Role A role undertaken by a host that is not categorized under specific predefined host roles. + +exposure setting menu ExposureSettingMenu ECTO:3000005 Human Exposure A history of exposure to Homo sapiens. Mpox + GENEPIO:0100501 Contact with Known Monkeypox Case A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox. + GENEPIO:0100185 Contact with Patient A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity. + GENEPIO:0100502 Contact with Probable Monkeypox Case A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox. + GENEPIO:0100189 Contact with Person who Recently Travelled A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity. + GENEPIO:0100190 Occupational, Residency or Patronage Exposure A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity. + ECTO:1000033 Abbatoir A exposure event involving the interaction of an exposure receptor to abattoir. + GENEPIO:0100191 Animal Rescue A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity. + GENEPIO:0100503 Bar (pub) A process occurring within or in the vicinity of a bar or pub environment that exposes the recipient organism to a material entity + GENEPIO:0100192 Childcare A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100193 Daycare A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity. + GENEPIO:0100194 Nursery A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity. + GENEPIO:0100195 Community Service Centre A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity. + GENEPIO:0100196 Correctional Facility A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity. + GENEPIO:0100197 Dormitory A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity. + ECTO:1000034 Farm A exposure event involving the interaction of an exposure receptor to farm + GENEPIO:0100198 First Nations Reserve A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity. + GENEPIO:0100199 Funeral Home A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100200 Group Home A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100201 Healthcare Setting A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100202 Ambulance A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity. + GENEPIO:0100203 Acute Care Facility A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity. + GENEPIO:0100204 Clinic A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity. + GENEPIO:0100415 Community Healthcare (At-Home) Setting A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100205 Community Health Centre A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity. + ECTO:1000035 Hospital A exposure event involving the interaction of an exposure receptor to hospital. + GENEPIO:0100206 Emergency Department A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity. + GENEPIO:0100207 ICU A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity. + GENEPIO:0100208 Ward A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity. + ECTO:1000036 Laboratory A exposure event involving the interaction of an exposure receptor to laboratory facility. + GENEPIO:0100209 Long-Term Care Facility A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity. + GENEPIO:0100210 Pharmacy A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity. + GENEPIO:0100211 Physician's Office A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity. + GENEPIO:0100212 Household A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity. + GENEPIO:0100213 Insecure Housing (Homeless) A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing. + GENEPIO:0100214 Occupational Exposure A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity. + GENEPIO:0100215 Worksite A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity. + ECTO:1000037 Office A exposure event involving the interaction of an exposure receptor to office. + GENEPIO:0100216 Outdoors A process occuring outdoors that exposes the recipient organism to a material entity. + ECTO:5000009 Camp/camping A exposure event involving the interaction of an exposure receptor to campground. + GENEPIO:0100217 Hiking Trail A process that exposes the recipient organism to a material entity as a consequence of hiking. + ECTO:6000030 Hunting Ground An exposure event involving hunting behavior + GENEPIO:0100218 Ski Resort A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity. + ECTO:5000008 Petting zoo A exposure event involving the interaction of an exposure receptor to petting zoo. + GENEPIO:0100220 Place of Worship A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity. + GENEPIO:0100221 Church A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity. + GENEPIO:0100222 Mosque A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity. + GENEPIO:0100223 Temple A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity. + ECTO:1000040 Restaurant A exposure event involving the interaction of an exposure receptor to restaurant. + ECTO:1000041 Retail Store A exposure event involving the interaction of an exposure receptor to shop. + GENEPIO:0100224 School A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity. + GENEPIO:0100225 Temporary Residence A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity. + GENEPIO:0100226 Homeless Shelter A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity. + GENEPIO:0100227 Hotel A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity. + GENEPIO:0100228 Veterinary Care Clinic A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity. + GENEPIO:0100229 Travel Exposure A process occuring as a result of travel that exposes the recipient organism to a material entity. + GENEPIO:0100230 Travelled on a Cruise Ship A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity. + GENEPIO:0100231 Travelled on a Plane A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity. + GENEPIO:0100232 Travelled on Ground Transport A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity. + GENEPIO:0100235 Other Exposure Setting A process occuring that exposes the recipient organism to a material entity. + + +exposure setting international menu ExposureSettingInternationalMenu ECTO:3000005 Human Exposure [ECTO:3000005] A history of exposure to Homo sapiens. Mpox_international + GENEPIO:0100501 Contact with Known Monkeypox Case [GENEPIO:0100501] A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox. + GENEPIO:0100185 Contact with Patient [GENEPIO:0100185] A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity. + GENEPIO:0100502 Contact with Probable Monkeypox Case [GENEPIO:0100502] A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox. + GENEPIO:0100189 Contact with Person who Recently Travelled [GENEPIO:0100189] A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity. + GENEPIO:0100190 Occupational, Residency or Patronage Exposure [GENEPIO:0100190] A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity. + ECTO:1000033 Abbatoir [ECTO:1000033] A exposure event involving the interaction of an exposure receptor to abattoir. + GENEPIO:0100191 Animal Rescue [GENEPIO:0100191] A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity. + GENEPIO:0100503 Bar (pub) [GENEPIO:0100503] A process occurring within or in the vicinity of a bar or pub environment that exposes the recipient organism to a material entity + GENEPIO:0100192 Childcare [GENEPIO:0100192] A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100193 Daycare [GENEPIO:0100193] A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity. + GENEPIO:0100194 Nursery [GENEPIO:0100194] A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity. + GENEPIO:0100195 Community Service Centre [GENEPIO:0100195] A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity. + GENEPIO:0100196 Correctional Facility [GENEPIO:0100196] A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity. + GENEPIO:0100197 Dormitory [GENEPIO:0100197] A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity. + ECTO:1000034 Farm [ECTO:1000034] A exposure event involving the interaction of an exposure receptor to farm + GENEPIO:0100198 First Nations Reserve [GENEPIO:0100198] A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity. + GENEPIO:0100199 Funeral Home [GENEPIO:0100199] A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100200 Group Home [GENEPIO:0100200] A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100201 Healthcare Setting [GENEPIO:0100201] A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100202 Ambulance [GENEPIO:0100202] A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity. + GENEPIO:0100203 Acute Care Facility [GENEPIO:0100203] A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity. + GENEPIO:0100204 Clinic [GENEPIO:0100204] A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity. + GENEPIO:0100415 Community Healthcare (At-Home) Setting [GENEPIO:0100415] A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100205 Community Health Centre [GENEPIO:0100205] A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity. + ECTO:1000035 Hospital [ECTO:1000035] A exposure event involving the interaction of an exposure receptor to hospital. + GENEPIO:0100206 Emergency Department [GENEPIO:0100206] A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity. + GENEPIO:0100207 ICU [GENEPIO:0100207] A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity. + GENEPIO:0100208 Ward [GENEPIO:0100208] A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity. + ECTO:1000036 Laboratory [ECTO:1000036] A exposure event involving the interaction of an exposure receptor to laboratory facility. + GENEPIO:0100209 Long-Term Care Facility [GENEPIO:0100209] A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity. + GENEPIO:0100210 Pharmacy [GENEPIO:0100210] A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity. + GENEPIO:0100211 Physician's Office [GENEPIO:0100211] A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity. + GENEPIO:0100212 Household [GENEPIO:0100212] A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity. + GENEPIO:0100213 Insecure Housing (Homeless) [GENEPIO:0100213] A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing. + GENEPIO:0100214 Occupational Exposure [GENEPIO:0100214] A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity. + GENEPIO:0100215 Worksite [GENEPIO:0100215] A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity. + ECTO:1000037 Office [ECTO:1000037] A exposure event involving the interaction of an exposure receptor to office. + GENEPIO:0100216 Outdoors [GENEPIO:0100216] A process occuring outdoors that exposes the recipient organism to a material entity. + ECTO:5000009 Camp/camping [ECTO:5000009] A exposure event involving the interaction of an exposure receptor to campground. + GENEPIO:0100217 Hiking Trail [GENEPIO:0100217] A process that exposes the recipient organism to a material entity as a consequence of hiking. + ECTO:6000030 Hunting Ground [ECTO:6000030] An exposure event involving hunting behavior + GENEPIO:0100218 Ski Resort [GENEPIO:0100218] A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity. + ECTO:5000008 Petting zoo [ECTO:5000008] A exposure event involving the interaction of an exposure receptor to petting zoo. + GENEPIO:0100220 Place of Worship [GENEPIO:0100220] A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity. + GENEPIO:0100221 Church [GENEPIO:0100221] A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity. + GENEPIO:0100222 Mosque [GENEPIO:0100222] A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity. + GENEPIO:0100223 Temple [GENEPIO:0100223] A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity. + ECTO:1000040 Restaurant [ECTO:1000040] A exposure event involving the interaction of an exposure receptor to restaurant. + ECTO:1000041 Retail Store [ECTO:1000041] A exposure event involving the interaction of an exposure receptor to shop. + GENEPIO:0100224 School [GENEPIO:0100224] A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity. + GENEPIO:0100225 Temporary Residence [GENEPIO:0100225] A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity. + GENEPIO:0100226 Homeless Shelter [GENEPIO:0100226] A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity. + GENEPIO:0100227 Hotel [GENEPIO:0100227] A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity. + GENEPIO:0100228 Veterinary Care Clinic [GENEPIO:0100228] A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity. + GENEPIO:0100229 Travel Exposure [GENEPIO:0100229] A process occuring as a result of travel that exposes the recipient organism to a material entity. + GENEPIO:0100230 Travelled on a Cruise Ship [GENEPIO:0100230] A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity. + GENEPIO:0100231 Travelled on a Plane [GENEPIO:0100231] A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity. + GENEPIO:0100232 Travelled on Ground Transport [GENEPIO:0100232] A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity. + GENEPIO:0100235 Other Exposure Setting [GENEPIO:0100235] A process occuring that exposes the recipient organism to a material entity. + +prior Mpox infection menu PriorMpoxInfectionMenu GENEPIO:0100037 Prior infection Antiviral treatment administered prior to the current regimen or test. MPox + GENEPIO:0100233 No prior infection An absence of antiviral treatment administered prior to the current regimen or test. + +prior Mpox infection international menu PriorMpoxInfectionInternationalMenu GENEPIO:0100037 Prior infection [GENEPIO:0100037] Antiviral treatment administered prior to the current regimen or test. Mpox_international + GENEPIO:0100233 No prior infection [GENEPIO:0100233] An absence of antiviral treatment administered prior to the current regimen or test. + +prior Mpox antiviral treatment menu PriorMpoxAntiviralTreatmentMenu GENEPIO:0100037 Prior antiviral treatment Antiviral treatment administered prior to the current regimen or test. MPox + GENEPIO:0100233 No prior antiviral treatment An absence of antiviral treatment administered prior to the current regimen or test. + +prior Mpox antiviral treatment international menu PriorMpoxAntiviralTreatmentInternationalMenu GENEPIO:0100037 Prior antiviral treatment [GENEPIO:0100037] Antiviral treatment administered prior to the current regimen or test. Mpox_international + GENEPIO:0100233 No prior antiviral treatment [GENEPIO:0100233] An absence of antiviral treatment administered prior to the current regimen or test. + +organism menu OrganismMenu NCBITaxon:10244 Mpox virus A zoonotic virus belonging to the Orthopoxvirus genus and closely related to the variola, cowpox, and vaccinia viruses. MPV is oval, with a lipoprotein outer membrane. Mpox + +organism international menu OrganismInternationalMenu NCBITaxon:10244 Mpox virus [NCBITaxon:10244] A zoonotic virus belonging to the Orthopoxvirus genus and closely related to the variola, cowpox, and vaccinia viruses. MPV is oval, with a lipoprotein outer membrane. Mpox_international + +host disease menu HostDiseaseMenu MONDO:0002594 Mpox An infection that is caused by an Orthopoxvirus, which is transmitted by primates or rodents, and which is characterized by a prodromal syndrome of fever, chills, headache, myalgia, and lymphedema; initial symptoms are followed by a generalized papular rash that typically progresses from vesiculation through crusting over the course of two weeks. Mpox + +host disease international menu HostDiseaseInternationalMenu MONDO:0002594 Mpox [MONDO:0002594] An infection that is caused by an Orthopoxvirus, which is transmitted by primates or rodents, and which is characterized by a prodromal syndrome of fever, chills, headache, myalgia, and lymphedema; initial symptoms are followed by a generalized papular rash that typically progresses from vesiculation through crusting over the course of two weeks. Mpox_international + + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 Cluster/Outbreak investigation A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. Mpox + GENEPIO:0100002 Diagnostic testing A sampling strategy in which individuals are sampled in the context of diagnostic testing. + GENEPIO:0100003 Research A sampling strategy in which individuals are sampled in order to perform research. + GENEPIO:0100004 Surveillance A sampling strategy in which individuals are sampled for surveillance investigations. + +purpose of sampling international menu PurposeOfSamplingInternationalMenu GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. Mpox_international + GENEPIO:0100002 Diagnostic testing [GENEPIO:0100002] A sampling strategy in which individuals are sampled in the context of diagnostic testing. + GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which individuals are sampled in order to perform research. + GENEPIO:0100004 Surveillance [GENEPIO:0100004] A sampling strategy in which individuals are sampled for surveillance investigations. + +purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. Mpox + GENEPIO:0100006 Targeted surveillance (non-random sampling) A surveillance sampling strategy in which an aspired outcome is explicity stated. + GENEPIO:0100007 Priority surveillance project A targeted surveillance strategy which is considered important and/or urgent. + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time. + GENEPIO:0100010 Re-infection surveillance A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time. + GENEPIO:0100011 Vaccine escape surveillance A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest. + GENEPIO:0100012 Travel-associated surveillance A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms. + GENEPIO:0100013 Domestic travel surveillance A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms. + GENEPIO:0100275 Interstate/ interprovincial travel surveillance A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation. + GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation. + GENEPIO:0100014 International travel surveillance A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms. + GENEPIO:0100019 Cluster/Outbreak investigation A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. + GENEPIO:0100020 Multi-jurisdictional outbreak investigation An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions. + GENEPIO:0100021 Intra-jurisdictional outbreak investigation An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction. + GENEPIO:0100022 Research A sampling strategy in which individuals are sampled in order to perform research. + GENEPIO:0100023 Viral passage experiment A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment. + GENEPIO:0100024 Protocol testing experiment A research sampling strategy in which individuals are sampled in order to perform a protocol testing experiment. + GENEPIO:0100356 Retrospective sequencing A sampling strategy in which stored samples from past events are sequenced. + +purpose of sequencing international menu PurposeOfSequencingInternationalMenu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. Mpox_international + GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] A surveillance sampling strategy in which an aspired outcome is explicity stated. + GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] A targeted surveillance strategy which is considered important and/or urgent. + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time. + GENEPIO:0100010 Re-infection surveillance [GENEPIO:0100010] A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time. + GENEPIO:0100011 Vaccine escape surveillance [GENEPIO:0100011] A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest. + GENEPIO:0100012 Travel-associated surveillance [GENEPIO:0100012] A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms. + GENEPIO:0100013 Domestic travel surveillance [GENEPIO:0100013] A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms. + GENEPIO:0100275 Interstate/ interprovincial travel surveillance [GENEPIO:0100275] A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation. + GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276] A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation. + GENEPIO:0100014 International travel surveillance [GENEPIO:0100014] A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms. + GENEPIO:0100019 Cluster/Outbreak investigation [GENEPIO:0100019] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. + GENEPIO:0100020 Multi-jurisdictional outbreak investigation [GENEPIO:0100020] An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions. + GENEPIO:0100021 Intra-jurisdictional outbreak investigation [GENEPIO:0100021] An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction. + GENEPIO:0100022 Research [GENEPIO:0100022] A sampling strategy in which individuals are sampled in order to perform research. + GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment. + GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which individuals are sampled in order to perform a protocol testing experiment. + GENEPIO:0100356 Retrospective sequencing [GENEPIO:0100356] A sampling strategy in which stored samples from past events are sequenced. + +sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. Mpox + OBI:0002763 16S ribosomal gene sequencing assay An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. + OBI:0002117 Whole genome sequencing assay A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002768 Whole virome sequencing assay A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + +sequencing assay type international menu SequencingAssayTypeInternationalMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. Mpox_international + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina A DNA sequencer manufactured by the Illumina corporation. Mpox + OBI:0002128 Illumina Genome Analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + OBI:0000703 Illumina Genome Analyzer II A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + OBI:0002000 Illumina Genome Analyzer IIx An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + GENEPIO:0100109 Illumina HiScanSQ A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + GENEPIO:0100110 Illumina HiSeq A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + GENEPIO:0100111 Illumina HiSeq X A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. + GENEPIO:0100112 Illumina HiSeq X Five A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + OBI:0002129 Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + OBI:0002022 Illumina HiSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + OBI:0003386 Illumina HiSeq 1500 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + OBI:0002001 Illumina HiSeq 2000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + OBI:0002002 Illumina HiSeq 2500 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + OBI:0002048 Illumina HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + OBI:0002049 Illumina HiSeq 4000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + GENEPIO:0100120 Illumina iSeq A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + GENEPIO:0100122 Illumina NovaSeq A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. + OBI:0002630 Illumina NovaSeq 6000 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + OBI:0003114 Illumina MiniSeq A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + OBI:0002003 Illumina MiSeq A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100126 Illumina NextSeq A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002021 Illumina NextSeq 500 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100128 Illumina NextSeq 550 A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + OBI:0003606 Illumina NextSeq 1000 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + GENEPIO:0100129 Illumina NextSeq 2000 A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + GENEPIO:0100130 Pacific Biosciences A DNA sequencer manufactured by the Pacific Biosciences corporation. + GENEPIO:0100131 PacBio RS A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + OBI:0002012 PacBio RS II A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + OBI:0002632 PacBio Sequel A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + OBI:0002633 PacBio Sequel II A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + GENEPIO:0100135 Ion Torrent A DNA sequencer manufactured by the Ion Torrent corporation. + GENEPIO:0100136 Ion Torrent PGM A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + GENEPIO:0100137 Ion Torrent Proton A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + GENEPIO:0100138 Ion Torrent S5 XL A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + GENEPIO:0100139 Ion Torrent S5 A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + GENEPIO:0100140 Oxford Nanopore A DNA sequencer manufactured by the Oxford Nanopore corporation. + GENEPIO:0004433 Oxford Nanopore Flongle An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + GENEPIO:0100141 Oxford Nanopore GridION A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + OBI:0002750 Oxford Nanopore MinION A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + OBI:0002752 Oxford Nanopore PromethION A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + GENEPIO:0100144 BGI Genomics A DNA sequencer manufactured by the BGI Genomics corporation. + GENEPIO:0100145 BGI Genomics BGISEQ-500 A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + GENEPIO:0100146 MGI A DNA sequencer manufactured by the MGI corporation. + GENEPIO:0100147 MGI DNBSEQ-T7 A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. + GENEPIO:0100148 MGI DNBSEQ-G400 A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. + GENEPIO:0100149 MGI DNBSEQ-G400 FAST A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. + GENEPIO:0100150 MGI DNBSEQ-G50 A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + +sequencing instrument international menu SequencingInstrumentInternationalMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. Mpox_international + OBI:0002128 Illumina Genome Analyzer [OBI:0002128] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. + GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + OBI:0002129 Illumina HiSeq X Ten [OBI:0002129] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + OBI:0003386 Illumina HiSeq 1500 [OBI:0003386] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. + OBI:0002630 Illumina NovaSeq 6000 [OBI:0002630] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + OBI:0003114 Illumina MiniSeq [OBI:0003114] A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + OBI:0003606 Illumina NextSeq 1000 [OBI:0003606] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + GENEPIO:0100130 Pacific Biosciences [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + OBI:0002632 PacBio Sequel [OBI:0002632] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + OBI:0002633 PacBio Sequel II [OBI:0002633] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + GENEPIO:0100135 Ion Torrent [GENEPIO:0100135 A DNA sequencer manufactured by the Ion Torrent corporation. + GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + OBI:0002750 Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + OBI:0002752 Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + GENEPIO:0100144 BGI Genomics [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + GENEPIO:0100145 BGI Genomics BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + GENEPIO:0100146 MGI [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. + GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. + GENEPIO:0100149 MGI DNBSEQ-G400 FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. + GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + +genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture Selection by hybridization in array or solution. Mpox + GENEPIO:0101020 rRNA depletion method Removal of background RNA for the purposes of enriching the genomic target. + +genomic target enrichment method international menu GenomicTargetEnrichmentMethodInternationalMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. Mpox_international + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. + +quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected. Mpox + GENEPIO:0100563 Sequence passed quality control A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. + GENEPIO:0100564 Sequence failed quality control A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. + GENEPIO:0100565 Minor quality control issues identified A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. + GENEPIO:0100566 Sequence flagged for potential quality control issues A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. + GENEPIO:0100567 Quality control not performed A data item which is a statement confirming that quality control processes have not been carried out. + +quality control determination international menu QualityControlDeterminationInternationalMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected. Mpox_international + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A data item which is a statement confirming that quality control processes have not been carried out. + +quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence A data item that describes sequence data that does not meet quality control thresholds. Mpox + GENEPIO:0100569 Sequence contaminated A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. + GENEPIO:0100570 Low average genome coverage A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). + GENEPIO:0100571 Low percent genome captured A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). + GENEPIO:0100572 Read lengths shorter than expected A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. + GENEPIO:0100573 Sequence amplification artifacts A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). + GENEPIO:0100574 Low signal to noise ratio A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). + GENEPIO:0100575 Low coverage of characteristic mutations A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. + +quality control issues international menu QualityControlIssuesInternationalMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] A data item that describes sequence data that does not meet quality control thresholds. Mpox_international + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. + + +sequence submitted by menu SequenceSubmittedByMenu Alberta Precision Labs (APL) Mpox + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Canadore College + The Centre for Applied Genomics (TCAG) + Dynacare + Dynacare (Brampton) + Dynacare (Manitoba) + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Manitoba Cadham Provincial Laboratory + McGill University McGill University is an English-language public research university located in Montreal, Quebec, Canada. + McMaster University + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Sunnybrook Health Sciences Centre + Thunder Bay Regional Health Sciences Centre + +sequenced by menu SequencedByMenu Alberta Precision Labs (APL) MPox + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Canadore College + The Centre for Applied Genomics (TCAG) + Dynacare + Dynacare (Brampton) + Dynacare (Manitoba) + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Manitoba Cadham Provincial Laboratory + McGill University McGill University is an English-language public research university located in Montreal, Quebec, Canada. + McMaster University + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Sunnybrook Health Sciences Centre + Thunder Bay Regional Health Sciences Centre + +sample collected by menu SampleCollectedByMenu Alberta Precision Labs (APL) Mpox + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Dynacare + Dynacare (Manitoba) + Dynacare (Brampton) + Eastern Ontario Regional Laboratory Association + Hamilton Health Sciences + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Lake of the Woods District Hospital - Ontario + LifeLabs + LifeLabs (Ontario) + Manitoba Cadham Provincial Laboratory + McMaster University + Mount Sinai Hospital + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Nunavut + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Shared Hospital Laboratory + St. John's Rehab at Sunnybrook Hospital + Switch Health + Sunnybrook Health Sciences Centre + Unity Health Toronto + William Osler Health System + +gene name menu GeneNameMenu GENEPIO:0100505 MPX (orf B6R) Mpox + GENEPIO:0100506 OPV (orf 17L) + GENEPIO:0100507 OPHA (orf B2R) + GENEPIO:0100510 G2R_G (TNFR) + G2R_G (WA) + GENEPIO:0100508 RNAse P gene (RNP) + +gene symbol international menu GeneSymbolInternationalMenu GENEPIO:0101382 opg001 gene (MPOX) A gene that encodes the Chemokine binding protein (MPOX). Mpox_international + GENEPIO:0101383 opg002 gene (MPOX) A gene that encodes the Crm-B secreted TNF-alpha-receptor-like protein (MPOX). + GENEPIO:0101384 opg003 gene (MPOX) A gene that encodes the Ankyrin repeat protein (25) (MPOX). + GENEPIO:0101385 opg015 gene (MPOX) A gene that encodes the Ankyrin repeat protein (39) (MPOX). + GENEPIO:0101386 opg019 gene (MPOX) A gene that encodes the EGF-like domain protein (MPOX). + GENEPIO:0101387 opg021 gene (MPOX) A gene that encodes the Zinc finger-like protein (2) (MPOX). + GENEPIO:0101388 opg022 gene (MPOX) A gene that encodes the Interleukin-18-binding protein (MPOX). + GENEPIO:0101389 opg023 gene (MPOX) A gene that encodes the Ankyrin repeat protein (2) (MPOX). + GENEPIO:0101390 opg024 gene (MPOX) A gene that encodes the retroviral pseudoprotease-like protein (MPOX). + GENEPIO:0101391 opg025 gene (MPOX) A gene that encodes the Ankyrin repeat protein (14) (MPOX). + GENEPIO:0101392 opg027 gene (MPOX) A gene that encodes the Host range protein (MPOX). + GENEPIO:0101393 opg029 gene (MPOX) A gene that encodes the Bcl-2-like protein (MPOX). + GENEPIO:0101394 opg030 gene (MPOX) A gene that encodes the Kelch-like protein (1) (MPOX). + GENEPIO:0101395 opg031 gene (MPOX) A gene that encodes the C4L/C10L-like family protein (MPOX). + GENEPIO:0101396 opg034 gene (MPOX) A gene that encodes the Bcl-2-like protein (MPOX). + GENEPIO:0101397 opg035 gene (MPOX) A gene that encodes the Bcl-2-like protein (MPOX). + GENEPIO:0101399 opg037 gene (MPOX) A gene that encodes the Ankyrin-like protein (1) (MPOX). + GENEPIO:0101400 opg038 gene (MPOX) A gene that encodes the NFkB inhibitor protein (MPOX). + GENEPIO:0101401 opg039 gene (MPOX) A gene that encodes the Ankyrin-like protein (3) (MPOX). + GENEPIO:0101402 opg040 gene (MPOX) A gene that encodes the Serpin protein (MPOX). + GENEPIO:0101403 opg042 gene (MPOX) A gene that encodes the Phospholipase-D-like protein (MPOX). + GENEPIO:0101404 opg043 gene (MPOX) A gene that encodes the Putative monoglyceride lipase protein (MPOX). + GENEPIO:0101406 opg045 gene (MPOX) A gene that encodes the Caspase-9 inhibitor protein (MPOX). + GENEPIO:0101407 opg046 gene (MPOX) A gene that encodes the dUTPase protein (MPOX). + GENEPIO:0101408 opg047 gene (MPOX) A gene that encodes the Kelch-like protein (2) (MPOX). + GENEPIO:0101409 opg048 gene (MPOX) A gene that encodes the Ribonucleotide reductase small subunit protein (MPOX). + GENEPIO:0101410 opg049 gene (MPOX) A gene that encodes the Telomere-binding protein I6 (1) (MPOX). + GENEPIO:0101411 opg050 gene (MPOX) A gene that encodes the CPXV053 protein (MPOX). + GENEPIO:0101412 opg051 gene (MPOX) A gene that encodes the CPXV054 protein (MPOX). + GENEPIO:0101413 opg052 gene (MPOX) A gene that encodes the Cytoplasmic protein (MPOX). + GENEPIO:0101414 opg053 gene (MPOX) A gene that encodes the IMV membrane protein L1R (MPOX). + GENEPIO:0101415 opg054 gene (MPOX) A gene that encodes the Serine/threonine-protein kinase (MPOX). + GENEPIO:0101416 opg055 gene (MPOX) A gene that encodes the Protein F11 protein (MPOX). + GENEPIO:0101417 opg056 gene (MPOX) A gene that encodes the EEV maturation protein (MPOX). + GENEPIO:0101418 opg057 gene (MPOX) A gene that encodes the Palmytilated EEV membrane protein (MPOX). + GENEPIO:0101419 opg058 gene (MPOX) A gene that encodes the Protein F14 (1) protein (MPOX). + GENEPIO:0101420 opg059 gene (MPOX) A gene that encodes the Cytochrome C oxidase protein (MPOX). + GENEPIO:0101421 opg060 gene (MPOX) A gene that encodes the Protein F15 protein (MPOX). + GENEPIO:0101422 opg061 gene (MPOX) A gene that encodes the Protein F16 (1) protein (MPOX). + GENEPIO:0101423 opg062 gene (MPOX) A gene that encodes the DNA-binding phosphoprotein (1) (MPOX). + GENEPIO:0101424 opg063 gene (MPOX) A gene that encodes the Poly(A) polymerase catalytic subunit (3) protein (MPOX). + GENEPIO:0101425 opg064 gene (MPOX) A gene that encodes the Iev morphogenesis protein (MPOX). + GENEPIO:0101426 opg065 gene (MPOX) A gene that encodes the Double-stranded RNA binding protein (MPOX). + GENEPIO:0101427 opg066 gene (MPOX) A gene that encodes the DNA-directed RNA polymerase 30 kDa polypeptide protein (MPOX). + GENEPIO:0101428 opg068 gene (MPOX) A gene that encodes the IMV membrane protein E6 (MPOX). + GENEPIO:0101429 opg069 gene (MPOX) A gene that encodes the Myristoylated protein E7 (MPOX). + GENEPIO:0101430 opg070 gene (MPOX) A gene that encodes the Membrane protein E8 (MPOX). + GENEPIO:0101431 opg071 gene (MPOX) A gene that encodes the DNA polymerase (2) protein (MPOX). + GENEPIO:0101432 opg072 gene (MPOX) A gene that encodes the Sulfhydryl oxidase protein (MPOX). + GENEPIO:0101433 opg073 gene (MPOX) A gene that encodes the Virion core protein E11 (MPOX). + GENEPIO:0101434 opg074 gene (MPOX) A gene that encodes the Iev morphogenesis protein (MPOX). + GENEPIO:0101435 opg075 gene (MPOX) A gene that encodes the Glutaredoxin-1 protein (MPOX). + GENEPIO:0101437 opg077 gene (MPOX) A gene that encodes the Telomere-binding protein I1 (MPOX). + GENEPIO:0101438 opg078 gene (MPOX) A gene that encodes the IMV membrane protein I2 (MPOX). + GENEPIO:0101439 opg079 gene (MPOX) A gene that encodes the DNA-binding phosphoprotein (2) (MPOX). + GENEPIO:0101440 opg080 gene (MPOX) A gene that encodes the Ribonucleoside-diphosphate reductase (2) protein (MPOX). + GENEPIO:0101441 opg081 gene (MPOX) A gene that encodes the IMV membrane protein I5 (MPOX). + GENEPIO:0101442 opg082 gene (MPOX) A gene that encodes the Telomere-binding protein (MPOX). + GENEPIO:0101443 opg083 gene (MPOX) A gene that encodes the Viral core cysteine proteinase (MPOX). + GENEPIO:0101444 opg084 gene (MPOX) A gene that encodes the RNA helicase NPH-II (2) protein (MPOX). + GENEPIO:0101445 opg085 gene (MPOX) A gene that encodes the Metalloendopeptidase protein (MPOX). + GENEPIO:0101446 opg086 gene (MPOX) A gene that encodes the Entry/fusion complex component protein (MPOX). + GENEPIO:0101447 opg087 gene (MPOX) A gene that encodes the Late transcription elongation factor protein (MPOX). + GENEPIO:0101448 opg088 gene (MPOX) A gene that encodes the Glutaredoxin-2 protein (MPOX). + GENEPIO:0101449 opg089 gene (MPOX) A gene that encodes the FEN1-like nuclease protein (MPOX). + GENEPIO:0101450 opg090 gene (MPOX) A gene that encodes the DNA-directed RNA polymerase 7 kDa subunit protein (MPOX). + GENEPIO:0101451 opg091 gene (MPOX) A gene that encodes the Nlpc/p60 superfamily protein (MPOX). + GENEPIO:0101452 opg092 gene (MPOX) A gene that encodes the Assembly protein G7 (MPOX). + GENEPIO:0101453 opg093 gene (MPOX) A gene that encodes the Late transcription factor VLTF-1 protein (MPOX). + GENEPIO:0101454 opg094 gene (MPOX) A gene that encodes the Myristylated protein (MPOX). + GENEPIO:0101455 opg095 gene (MPOX) A gene that encodes the IMV membrane protein L1R (MPOX). + GENEPIO:0101456 opg096 gene (MPOX) A gene that encodes the Crescent membrane and immature virion formation protein (MPOX). + GENEPIO:0101457 opg097 gene (MPOX) A gene that encodes the Internal virion L3/FP4 protein (MPOX). + GENEPIO:0101458 opg098 gene (MPOX) A gene that encodes the Nucleic acid binding protein VP8/L4R (MPOX). + GENEPIO:0101459 opg099 gene (MPOX) A gene that encodes the Membrane protein CL5 (MPOX). + GENEPIO:0101460 opg100 gene (MPOX) A gene that encodes the IMV membrane protein J1 (MPOX). + GENEPIO:0101461 opg101 gene (MPOX) A gene that encodes the Thymidine kinase protein (MPOX). + GENEPIO:0101462 opg102 gene (MPOX) A gene that encodes the Cap-specific mRNA protein (MPOX). + GENEPIO:0101463 opg103 gene (MPOX) A gene that encodes the DNA-directed RNA polymerase subunit protein (MPOX). + GENEPIO:0101464 opg104 gene (MPOX) A gene that encodes the Myristylated protein (MPOX). + GENEPIO:0101465 opg105 gene (MPOX) A gene that encodes the DNA-dependent RNA polymerase subunit rpo147 protein (MPOX). + GENEPIO:0101466 opg106 gene (MPOX) A gene that encodes the Tyr/ser protein phosphatase (MPOX). + GENEPIO:0101467 opg107 gene (MPOX) A gene that encodes the Entry-fusion complex essential component protein (MPOX). + GENEPIO:0101468 opg108 gene (MPOX) A gene that encodes the IMV heparin binding surface protein (MPOX). + GENEPIO:0101469 opg109 gene (MPOX) A gene that encodes the RNA polymerase-associated transcription-specificity factor RAP94 protein (MPOX). + GENEPIO:0101470 opg110 gene (MPOX) A gene that encodes the Late transcription factor VLTF-4 (1) protein (MPOX). + GENEPIO:0101471 opg111 gene (MPOX) A gene that encodes the DNA topoisomerase type I protein (MPOX). + GENEPIO:0101472 opg112 gene (MPOX) A gene that encodes the Late protein H7 (MPOX). + GENEPIO:0101473 opg113 gene (MPOX) A gene that encodes the mRNA capping enzyme large subunit protein (MPOX). + GENEPIO:0101474 opg114 gene (MPOX) A gene that encodes the Virion protein D2 (MPOX). + GENEPIO:0101475 opg115 gene (MPOX) A gene that encodes the Virion core protein D3 (MPOX). + GENEPIO:0101476 opg116 gene (MPOX) A gene that encodes the Uracil DNA glycosylase superfamily protein (MPOX). + GENEPIO:0101477 opg117 gene (MPOX) A gene that encodes the NTPase (1) protein (MPOX). + GENEPIO:0101478 opg118 gene (MPOX) A gene that encodes the Early transcription factor 70 kDa subunit protein (MPOX). + GENEPIO:0101479 opg119 gene (MPOX) A gene that encodes the RNA polymerase subunit RPO18 protein (MPOX). + GENEPIO:0101480 opg120 gene (MPOX) A gene that encodes the Carbonic anhydrase protein (MPOX). + GENEPIO:0101481 opg121 gene (MPOX) A gene that encodes the NUDIX domain protein (MPOX). + GENEPIO:0101482 opg122 gene (MPOX) A gene that encodes the MutT motif protein (MPOX). + GENEPIO:0101483 opg123 gene (MPOX) A gene that encodes the Nucleoside triphosphatase I protein (MPOX). + GENEPIO:0101484 opg124 gene (MPOX) A gene that encodes the mRNA capping enzyme small subunit protein (MPOX). + GENEPIO:0101485 opg125 gene (MPOX) A gene that encodes the Rifampicin resistance protein (MPOX). + GENEPIO:0101486 opg126 gene (MPOX) A gene that encodes the Late transcription factor VLTF-2 (2) protein (MPOX). + GENEPIO:0101487 opg127 gene (MPOX) A gene that encodes the Late transcription factor VLTF-3 (1) protein (MPOX). + GENEPIO:0101488 opg128 gene (MPOX) A gene that encodes the S-S bond formation pathway protein (MPOX). + GENEPIO:0101489 opg129 gene (MPOX) A gene that encodes the Virion core protein P4b (MPOX). + GENEPIO:0101490 opg130 gene (MPOX) A gene that encodes the A5L protein-like (MPOX). + GENEPIO:0101491 opg131 gene (MPOX) A gene that encodes the DNA-directed RNA polymerase 19 kDa subunit protein (MPOX). + GENEPIO:0101492 opg132 gene (MPOX) A gene that encodes the Virion morphogenesis protein (MPOX). + GENEPIO:0101493 opg133 gene (MPOX) A gene that encodes the Early transcription factor 82 kDa subunit protein (MPOX). + GENEPIO:0101494 opg134 gene (MPOX) A gene that encodes the Intermediate transcription factor VITF-3 (1) protein (MPOX). + GENEPIO:0101495 opg135 gene (MPOX) A gene that encodes the IMV membrane protein A9 (MPOX). + GENEPIO:0101496 opg136 gene (MPOX) A gene that encodes the Virion core protein P4a (MPOX). + GENEPIO:0101497 opg137 gene (MPOX) A gene that encodes the Viral membrane formation protein (MPOX). + GENEPIO:0101498 opg138 gene (MPOX) A gene that encodes the A12 protein (MPOX). + GENEPIO:0101499 opg139 gene (MPOX) A gene that encodes the IMV membrane protein A13L (MPOX). + GENEPIO:0101500 opg140 gene (MPOX) A gene that encodes the IMV membrane protein A14 (MPOX). + GENEPIO:0101501 opg141 gene (MPOX) A gene that encodes the DUF1029 domain protein (MPOX). + GENEPIO:0101502 opg142 gene (MPOX) A gene that encodes the Core protein A15 (MPOX). + GENEPIO:0101503 opg143 gene (MPOX) A gene that encodes the Myristylated protein (MPOX). + GENEPIO:0101504 opg144 gene (MPOX) A gene that encodes the IMV membrane protein P21 (MPOX). + GENEPIO:0101505 opg145 gene (MPOX) A gene that encodes the DNA helicase protein (MPOX). + GENEPIO:0101506 opg146 gene (MPOX) A gene that encodes the Zinc finger-like protein (1) (MPOX). + GENEPIO:0101507 opg147 gene (MPOX) A gene that encodes the IMV membrane protein A21 (MPOX). + GENEPIO:0101508 opg148 gene (MPOX) A gene that encodes the DNA polymerase processivity factor protein (MPOX). + GENEPIO:0101509 opg149 gene (MPOX) A gene that encodes the Holliday junction resolvase protein (MPOX). + GENEPIO:0101510 opg150 gene (MPOX) A gene that encodes the Intermediate transcription factor VITF-3 (2) protein (MPOX). + GENEPIO:0101511 opg151 gene (MPOX) A gene that encodes the DNA-dependent RNA polymerase subunit rpo132 protein (MPOX). + GENEPIO:0101512 opg153 gene (MPOX) A gene that encodes the Orthopoxvirus A26L/A30L protein (MPOX). + GENEPIO:0101513 opg154 gene (MPOX) A gene that encodes the IMV surface fusion protein (MPOX). + GENEPIO:0101514 opg155 gene (MPOX) A gene that encodes the Envelope protein A28 homolog (MPOX). + GENEPIO:0101515 opg156 gene (MPOX) A gene that encodes the DNA-directed RNA polymerase 35 kDa subunit protein (MPOX). + GENEPIO:0101516 opg157 gene (MPOX) A gene that encodes the IMV membrane protein A30 (MPOX). + GENEPIO:0101517 opg158 gene (MPOX) A gene that encodes the A32.5L protein (MPOX). + GENEPIO:0101518 opg159 gene (MPOX) A gene that encodes the CPXV166 protein (MPOX). + GENEPIO:0101519 opg160 gene (MPOX) A gene that encodes the ATPase A32 protein (MPOX). + GENEPIO:0101520 opg161 gene (MPOX) A gene that encodes the EEV glycoprotein (1) (MPOX). + GENEPIO:0101521 opg162 gene (MPOX) A gene that encodes the EEV glycoprotein (2) (MPOX). + GENEPIO:0101522 opg163 gene (MPOX) A gene that encodes the MHC class II antigen presentation inhibitor protein (MPOX). + GENEPIO:0101523 opg164 gene (MPOX) A gene that encodes the IEV transmembrane phosphoprotein (MPOX). + GENEPIO:0101524 opg165 gene (MPOX) A gene that encodes the CPXV173 protein (MPOX). + GENEPIO:0101525 opg166 gene (MPOX) A gene that encodes the hypothetical protein (MPOX). + GENEPIO:0101526 opg167 gene (MPOX) A gene that encodes the CD47-like protein (MPOX). + GENEPIO:0101527 opg170 gene (MPOX) A gene that encodes the Chemokine binding protein (MPOX). + GENEPIO:0101528 opg171 gene (MPOX) A gene that encodes the Profilin domain protein (MPOX). + GENEPIO:0101529 opg172 gene (MPOX) A gene that encodes the Type-I membrane glycoprotein (MPOX). + GENEPIO:0101530 opg173 gene (MPOX) A gene that encodes the MPXVgp154 protein (MPOX). + GENEPIO:0101531 opg174 gene (MPOX) A gene that encodes the Hydroxysteroid dehydrogenase protein (MPOX). + GENEPIO:0101532 opg175 gene (MPOX) A gene that encodes the Copper/zinc superoxide dismutase protein (MPOX). + GENEPIO:0101533 opg176 gene (MPOX) A gene that encodes the Bcl-2-like protein (MPOX). + GENEPIO:0101534 opg178 gene (MPOX) A gene that encodes the Thymidylate kinase protein (MPOX). + GENEPIO:0101535 opg180 gene (MPOX) A gene that encodes the DNA ligase (2) protein (MPOX). + GENEPIO:0101536 opg181 gene (MPOX) A gene that encodes the M137R protein (MPOX). + GENEPIO:0101537 opg185 gene (MPOX) A gene that encodes the Hemagglutinin protein (MPOX). + GENEPIO:0101538 opg187 gene (MPOX) A gene that encodes the Ser/thr kinase protein (MPOX). + GENEPIO:0101539 opg188 gene (MPOX) A gene that encodes the Schlafen (1) protein (MPOX). + GENEPIO:0101540 opg189 gene (MPOX) A gene that encodes the Ankyrin repeat protein (25) (MPOX). + GENEPIO:0101541 opg190 gene (MPOX) A gene that encodes the EEV type-I membrane glycoprotein (MPOX). + GENEPIO:0101542 opg191 gene (MPOX) A gene that encodes the Ankyrin-like protein (46) (MPOX). + GENEPIO:0101543 opg192 gene (MPOX) A gene that encodes the Virulence protein (MPOX). + GENEPIO:0101544 opg193 gene (MPOX) A gene that encodes the Soluble interferon-gamma receptor-like protein (MPOX). + GENEPIO:0101545 opg195 gene (MPOX) A gene that encodes the Intracellular viral protein (MPOX). + GENEPIO:0101546 opg197 gene (MPOX) A gene that encodes the CPXV205 protein (MPOX). + GENEPIO:0101547 opg198 gene (MPOX) A gene that encodes the Ser/thr kinase protein (MPOX). + GENEPIO:0101548 opg199 gene (MPOX) A gene that encodes the Serpin protein (MPOX). + GENEPIO:0101549 opg200 gene (MPOX) A gene that encodes the Bcl-2-like protein (MPOX). + GENEPIO:0101550 opg204 gene (MPOX) A gene that encodes the IFN-alpha/beta-receptor-like secreted glycoprotein (MPOX). + GENEPIO:0101551 opg205 gene (MPOX) A gene that encodes the Ankyrin repeat protein (44) (MPOX). + GENEPIO:0101552 opg208 gene (MPOX) A gene that encodes the Serpin protein (MPOX). + GENEPIO:0101553 opg209 gene (MPOX) A gene that encodes the Virulence protein (MPOX). + GENEPIO:0101554 opg210 gene (MPOX) A gene that encodes the B22R family protein (MPOX). + GENEPIO:0101555 opg005 gene (MPOX) A gene that encodes the Bcl-2-like protein (MPOX). + GENEPIO:0101556 opg016 gene (MPOX) A gene that encodes the Brix domain protein (MPOX). + + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] Mpox + GAZ:00002953 Albania A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] + GAZ:00000563 Algeria A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] + GAZ:00003957 American Samoa An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] + GAZ:00002948 Andorra A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] + GAZ:00001095 Angola A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + GAZ:00009159 Anguilla A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] + GAZ:00000462 Antarctica The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] + GAZ:00006883 Antigua and Barbuda An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] + GAZ:00002928 Argentina A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] + GAZ:00004094 Armenia A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + GAZ:00004025 Aruba An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] + GAZ:00005901 Ashmore and Cartier Islands A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] + GAZ:00000463 Australia A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. + GAZ:00002942 Austria A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. + GAZ:00004941 Azerbaijan A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + GAZ:00002733 Bahamas A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. + GAZ:00005281 Bahrain A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. + GAZ:00007117 Baker Island An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. + GAZ:00003750 Bangladesh A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). + GAZ:00001251 Barbados An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. + GAZ:00005810 Bassas da India A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. + GAZ:00006886 Belarus A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. + GAZ:00002938 Belgium A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). + GAZ:00002934 Belize A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. + GAZ:00000904 Benin A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. + GAZ:00001264 Bermuda A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. + GAZ:00003920 Bhutan A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. + GAZ:00002511 Bolivia A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). + GAZ:00025355 Borneo An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. + GAZ:00006887 Bosnia and Herzegovina A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. + GAZ:00001097 Botswana A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. + GAZ:00001453 Bouvet Island A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. + GAZ:00002828 Brazil A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. + GAZ:00003961 British Virgin Islands A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. + GAZ:00003901 Brunei A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). + GAZ:00002950 Bulgaria A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. + GAZ:00000905 Burkina Faso A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). + GAZ:00001090 Burundi A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. + GAZ:00006888 Cambodia A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. + GAZ:00001093 Cameroon A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. + GAZ:00002560 Canada A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. + GAZ:00001227 Cape Verde A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). + GAZ:00003986 Cayman Islands A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. + GAZ:00001089 Central African Republic A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + GAZ:00000586 Chad A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. + GAZ:00002825 Chile A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. + GAZ:00002845 China A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. + GAZ:00005915 Christmas Island An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. + GAZ:00005838 Clipperton Island A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. + GAZ:00009721 Cocos Islands Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. + GAZ:00002929 Colombia A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. + GAZ:00005820 Comoros An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. + GAZ:00053798 Cook Islands A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. + GAZ:00005917 Coral Sea Islands A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. + GAZ:00002901 Costa Rica A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. + GAZ:00000906 Cote d'Ivoire A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. + GAZ:00002719 Croatia A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. + GAZ:00003762 Cuba A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. + GAZ:00012582 Curacao One of five island areas of the Netherlands Antilles. + GAZ:00004006 Cyprus The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. + GAZ:00002954 Czech Republic A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. + GAZ:00001086 Democratic Republic of the Congo A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. + GAZ:00005852 Denmark That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. + GAZ:00000582 Djibouti A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. + GAZ:00006890 Dominica An island nation in the Caribbean Sea. Dominica is divided into ten parishes. + GAZ:00003952 Dominican Republic A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). + GAZ:00002912 Ecuador A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). + GAZ:00003934 Egypt A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). + GAZ:00002935 El Salvador A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). + GAZ:00001091 Equatorial Guinea A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. + GAZ:00000581 Eritrea A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). + GAZ:00002959 Estonia A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. + GAZ:00001099 Eswatini A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00000567 Ethiopia A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. + GAZ:00005811 Europa Island A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. + GAZ:00001412 Falkland Islands (Islas Malvinas) An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. + GAZ:00059206 Faroe Islands An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. + GAZ:00006891 Fiji An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. + GAZ:00002937 Finland A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). + GAZ:00003940 France A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. + GAZ:00002516 French Guiana An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. + GAZ:00002918 French Polynesia A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). + GAZ:00003753 French Southern and Antarctic Lands The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. + GAZ:00001092 Gabon A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. + GAZ:00000907 Gambia A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. + GAZ:00009571 Gaza Strip A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. + GAZ:00004942 Georgia A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). + GAZ:00002646 Germany A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). + GAZ:00000908 Ghana A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. + GAZ:00003987 Gibraltar A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. + GAZ:00005808 Glorioso Islands A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. + GAZ:00002945 Greece A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. + GAZ:00001507 Greenland A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. + GAZ:02000573 Grenada An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. + GAZ:00067142 Guadeloupe An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. + GAZ:00003706 Guam An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. + GAZ:00002936 Guatemala A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). + GAZ:00001550 Guernsey A British Crown Dependency in the English Channel off the coast of Normandy. + GAZ:00000909 Guinea A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. + GAZ:00000910 Guinea-Bissau A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. + GAZ:00002522 Guyana A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. + GAZ:00003953 Haiti A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. + GAZ:00009718 Heard Island and McDonald Islands An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. + GAZ:00002894 Honduras A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. + GAZ:00003203 Hong Kong A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. + GAZ:00007120 Howland Island An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. + GAZ:00002952 Hungary A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. + GAZ:00000843 Iceland A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. + GAZ:00002839 India A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. + GAZ:00003727 Indonesia An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). + GAZ:00004474 Iran A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). + GAZ:00004483 Iraq A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). + GAZ:00002943 Ireland A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. + GAZ:00052477 Isle of Man A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. + GAZ:00002476 Israel A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. + GAZ:00002650 Italy A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). + GAZ:00003781 Jamaica A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. + GAZ:00005853 Jan Mayen A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. + GAZ:00002747 Japan An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. + GAZ:00007118 Jarvis Island An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + GAZ:00001551 Jersey A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. + GAZ:00007114 Johnston Atoll A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. + GAZ:00002473 Jordan A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. + GAZ:00005809 Juan de Nova Island A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. + GAZ:00004999 Kazakhstan A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. + GAZ:00001101 Kenya A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. + GAZ:00005682 Kerguelen Archipelago A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. + GAZ:00007116 Kingman Reef A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. + GAZ:00006894 Kiribati An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). + GAZ:00011337 Kosovo A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + GAZ:00005285 Kuwait A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). + GAZ:00006893 Kyrgyzstan A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). + GAZ:00006889 Laos A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). + GAZ:00002958 Latvia A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. + GAZ:00002478 Lebanon A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). + GAZ:00001098 Lesotho A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. + GAZ:00000911 Liberia A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. + GAZ:00000566 Libya A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. + GAZ:00003858 Liechtenstein A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). + GAZ:00007144 Line Islands A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. + GAZ:00002960 Lithuania A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). + GAZ:00002947 Luxembourg A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. + GAZ:00003202 Macau One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. + GAZ:00001108 Madagascar An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + GAZ:00001105 Malawi A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00003902 Malaysia A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00006924 Maldives An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + GAZ:00000584 Mali A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. + GAZ:00004017 Malta A Southern European country and consists of an archipelago situated centrally in the Mediterranean. + GAZ:00007161 Marshall Islands An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. + GAZ:00067143 Martinique An island and an overseas department/region and single territorial collectivity of France. + GAZ:00000583 Mauritania A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). + GAZ:00003745 Mauritius An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. + GAZ:00003943 Mayotte An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. + GAZ:00002852 Mexico A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. + GAZ:00005862 Micronesia A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. + GAZ:00007112 Midway Islands A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. + GAZ:00003897 Moldova A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. + GAZ:00003857 Monaco A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. + GAZ:00008744 Mongolia A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. + GAZ:00006898 Montenegro A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + GAZ:00003988 Montserrat A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. + GAZ:00000565 Morocco A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. + GAZ:00001100 Mozambique A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. + GAZ:00006899 Myanmar A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. + GAZ:00001096 Namibia A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. + GAZ:00006900 Nauru An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. + GAZ:00007119 Navassa Island A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. + GAZ:00004399 Nepal A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. + GAZ:00002946 Netherlands The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). + GAZ:00005206 New Caledonia A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. + GAZ:00000469 New Zealand A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. + GAZ:00002978 Nicaragua A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. + GAZ:00000585 Niger A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. + GAZ:00000912 Nigeria A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). + GAZ:00006902 Niue An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. + GAZ:00005908 Norfolk Island A Territory of Australia that includes Norfolk Island and neighboring islands. + GAZ:00002801 North Korea A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. + GAZ:00006895 North Macedonia A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. + GAZ:00002284 North Sea A sea situated between the eastern coasts of the British Isles and the western coast of Europe. + GAZ:00003958 Northern Mariana Islands A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. + GAZ:00002699 Norway A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. + GAZ:00005283 Oman A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). + GAZ:00005246 Pakistan A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. + GAZ:00006905 Palau A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. + GAZ:00002892 Panama The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. + GAZ:00003922 Papua New Guinea A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). + GAZ:00010832 Paracel Islands A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. + GAZ:00002933 Paraguay A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. + GAZ:00002932 Peru A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. + GAZ:00004525 Philippines An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. + GAZ:00005867 Pitcairn Islands A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. + GAZ:00002939 Poland A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. + GAZ:00004126 Portugal That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. + GAZ:00006935 Puerto Rico A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). + GAZ:00005286 Qatar An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). + GAZ:00001088 Republic of the Congo A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. + GAZ:00003945 Reunion An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. + GAZ:00002951 Romania A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). + GAZ:00023304 Ross Sea A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. + GAZ:00002721 Russia A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. + GAZ:00001087 Rwanda A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). + GAZ:00000849 Saint Helena An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. + GAZ:00006906 Saint Kitts and Nevis A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. + GAZ:00006909 Saint Lucia An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. + GAZ:00003942 Saint Pierre and Miquelon An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. + GAZ:00005841 Saint Martin An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + GAZ:02000565 Saint Vincent and the Grenadines An island nation in the Lesser Antilles chain of the Caribbean Sea. + GAZ:00006910 Samoa A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). + GAZ:00003102 San Marino A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). + GAZ:00006927 Sao Tome and Principe An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). + GAZ:00005279 Saudi Arabia A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. + GAZ:00000913 Senegal A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. + GAZ:00002957 Serbia A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). + GAZ:00006922 Seychelles An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. + GAZ:00000914 Sierra Leone A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. + GAZ:00003923 Singapore An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. + GAZ:00012579 Sint Maarten One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. + GAZ:00002956 Slovakia A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. + GAZ:00002955 Slovenia A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. + GAZ:00005275 Solomon Islands A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. + GAZ:00001104 Somalia A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. + GAZ:00001094 South Africa A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. + GAZ:00003990 South Georgia and the South Sandwich Islands A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. + GAZ:00002802 South Korea A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + GAZ:00233439 South Sudan A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. + GAZ:00000591 Spain That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. + GAZ:00010831 Spratly Islands A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. + GAZ:00003924 Sri Lanka An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. + GAZ:00002475 State of Palestine The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. + GAZ:00000560 Sudan A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. + GAZ:00002525 Suriname A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. + GAZ:00005396 Svalbard An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. + GAZ:00001099 Swaziland A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00002729 Sweden A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. + GAZ:00002941 Switzerland A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. + GAZ:00002474 Syria A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). + GAZ:00005341 Taiwan A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. + GAZ:00006912 Tajikistan A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). + GAZ:00001103 Tanzania A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). + GAZ:00003744 Thailand A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. + GAZ:00006913 Timor-Leste A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. + GAZ:00000915 Togo A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. + GAZ:00260188 Tokelau A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). + GAZ:00006916 Tonga A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. + GAZ:00003767 Trinidad and Tobago An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + GAZ:00005812 Tromelin Island A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. + GAZ:00000562 Tunisia A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). + GAZ:00000558 Turkey A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. + GAZ:00005018 Turkmenistan A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. + GAZ:00003955 Turks and Caicos Islands A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. + GAZ:00009715 Tuvalu A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. + GAZ:00002459 United States of America A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. + GAZ:00001102 Uganda A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. + GAZ:00002724 Ukraine A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. + GAZ:00005282 United Arab Emirates A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + GAZ:00002637 United Kingdom A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. + GAZ:00002930 Uruguay A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). + GAZ:00004979 Uzbekistan A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). + GAZ:00006918 Vanuatu An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. + GAZ:00002931 Venezuela A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). + GAZ:00003756 Viet Nam The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. + GAZ:00003959 Virgin Islands A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. + GAZ:00007111 Wake Island A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). + GAZ:00007191 Wallis and Futuna A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. + GAZ:00009572 West Bank A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". + GAZ:00000564 Western Sahara A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. + GAZ:00005284 Yemen A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + GAZ:00001107 Zambia A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. + GAZ:00001106 Zimbabwe A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. + +geo_loc_name (country) international menu GeoLocNameCountryInternationalMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] Mpox_international MPox_international + GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] + GAZ:00000563 Algeria [GAZ:00000563] A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] + GAZ:00003957 American Samoa [GAZ:00003957] An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] + GAZ:00002948 Andorra [GAZ:00002948] A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] + GAZ:00001095 Angola [GAZ:00001095] A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + GAZ:00009159 Anguilla [GAZ:00009159] A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] + GAZ:00000462 Antarctica [GAZ:00000462] The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] + GAZ:00006883 Antigua and Barbuda [GAZ:00006883] An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] + GAZ:00002928 Argentina [GAZ:00002928] A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] + GAZ:00004094 Armenia [GAZ:00004094] A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + GAZ:00004025 Aruba [GAZ:00004025] An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] + GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] + GAZ:00000463 Australia [GAZ:00000463] A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. + GAZ:00002942 Austria [GAZ:00002942] A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. + GAZ:00004941 Azerbaijan [GAZ:00004941] A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + GAZ:00002733 Bahamas [GAZ:00002733] A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. + GAZ:00005281 Bahrain [GAZ:00005281] A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. + GAZ:00007117 Baker Island [GAZ:00007117] An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. + GAZ:00003750 Bangladesh [GAZ:00003750] A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). + GAZ:00001251 Barbados [GAZ:00001251] An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. + GAZ:00005810 Bassas da India [GAZ:00005810] A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. + GAZ:00006886 Belarus [GAZ:00006886] A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. + GAZ:00002938 Belgium [GAZ:00002938] A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). + GAZ:00002934 Belize [GAZ:00002934] A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. + GAZ:00000904 Benin [GAZ:00000904] A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. + GAZ:00001264 Bermuda [GAZ:00001264] A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. + GAZ:00003920 Bhutan [GAZ:00003920] A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. + GAZ:00002511 Bolivia [GAZ:00002511] A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). + GAZ:00025355 Borneo [GAZ:00025355] An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. + GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. + GAZ:00001097 Botswana [GAZ:00001097] A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. + GAZ:00001453 Bouvet Island [GAZ:00001453] A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. + GAZ:00002828 Brazil [GAZ:00002828] A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. + GAZ:00003961 British Virgin Islands [GAZ:00003961] A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. + GAZ:00003901 Brunei [GAZ:00003901] A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). + GAZ:00002950 Bulgaria [GAZ:00002950] A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. + GAZ:00000905 Burkina Faso [GAZ:00000905] A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). + GAZ:00001090 Burundi [GAZ:00001090] A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. + GAZ:00006888 Cambodia [GAZ:00006888] A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. + GAZ:00001093 Cameroon [GAZ:00001093] A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. + GAZ:00002560 Canada [GAZ:00002560] A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. + GAZ:00001227 Cape Verde [GAZ:00001227] A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). + GAZ:00003986 Cayman Islands [GAZ:00003986] A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. + GAZ:00001089 Central African Republic [GAZ:00001089] A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + GAZ:00000586 Chad [GAZ:00000586] A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. + GAZ:00002825 Chile [GAZ:00002825] A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. + GAZ:00002845 China [GAZ:00002845] A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. + GAZ:00005915 Christmas Island [GAZ:00005915] An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. + GAZ:00005838 Clipperton Island [GAZ:00005838] A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. + GAZ:00009721 Cocos Islands [GAZ:00009721] Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. + GAZ:00002929 Colombia [GAZ:00002929] A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. + GAZ:00005820 Comoros [GAZ:00005820] An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. + GAZ:00053798 Cook Islands [GAZ:00053798] A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. + GAZ:00005917 Coral Sea Islands [GAZ:00005917] A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. + GAZ:00002901 Costa Rica [GAZ:00002901] A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. + GAZ:00000906 Cote d'Ivoire [GAZ:00000906] A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. + GAZ:00002719 Croatia [GAZ:00002719] A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. + GAZ:00003762 Cuba [GAZ:00003762] A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. + GAZ:00012582 Curacao [GAZ:00012582] One of five island areas of the Netherlands Antilles. + GAZ:00004006 Cyprus [GAZ:00004006] The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. + GAZ:00002954 Czech Republic [GAZ:00002954] A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. + GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. + GAZ:00005852 Denmark [GAZ:00005852] That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. + GAZ:00000582 Djibouti [GAZ:00000582] A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. + GAZ:00006890 Dominica [GAZ:00006890] An island nation in the Caribbean Sea. Dominica is divided into ten parishes. + GAZ:00003952 Dominican Republic [GAZ:00003952] A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). + GAZ:00002912 Ecuador [GAZ:00002912] A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). + GAZ:00003934 Egypt [GAZ:00003934] A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). + GAZ:00002935 El Salvador [GAZ:00002935] A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). + GAZ:00001091 Equatorial Guinea [GAZ:00001091] A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. + GAZ:00000581 Eritrea [GAZ:00000581] A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). + GAZ:00002959 Estonia [GAZ:00002959] A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. + GAZ:00001099 Eswatini [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00000567 Ethiopia [GAZ:00000567] A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. + GAZ:00005811 Europa Island [GAZ:00005811] A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. + GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. + GAZ:00059206 Faroe Islands [GAZ:00059206] An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. + GAZ:00006891 Fiji [GAZ:00006891] An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. + GAZ:00002937 Finland [GAZ:00002937] A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). + GAZ:00003940 France [GAZ:00003940] A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. + GAZ:00002516 French Guiana [GAZ:00002516] An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. + GAZ:00002918 French Polynesia [GAZ:00002918] A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). + GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. + GAZ:00001092 Gabon [GAZ:00001092] A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. + GAZ:00000907 Gambia [GAZ:00000907] A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. + GAZ:00009571 Gaza Strip [GAZ:00009571] A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. + GAZ:00004942 Georgia [GAZ:00004942] A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). + GAZ:00002646 Germany [GAZ:00002646] A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). + GAZ:00000908 Ghana [GAZ:00000908] A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. + GAZ:00003987 Gibraltar [GAZ:00003987] A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. + GAZ:00005808 Glorioso Islands [GAZ:00005808] A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. + GAZ:00002945 Greece [GAZ:00002945] A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. + GAZ:00001507 Greenland [GAZ:00001507] A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. + GAZ:02000573 Grenada [GAZ:02000573] An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. + GAZ:00067142 Guadeloupe [GAZ:00067142] An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. + GAZ:00003706 Guam [GAZ:00003706] An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. + GAZ:00002936 Guatemala [GAZ:00002936] A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). + GAZ:00001550 Guernsey [GAZ:00001550] A British Crown Dependency in the English Channel off the coast of Normandy. + GAZ:00000909 Guinea [GAZ:00000909] A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. + GAZ:00000910 Guinea-Bissau [GAZ:00000910] A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. + GAZ:00002522 Guyana [GAZ:00002522] A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. + GAZ:00003953 Haiti [GAZ:00003953] A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. + GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. + GAZ:00002894 Honduras [GAZ:00002894] A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. + GAZ:00003203 Hong Kong [GAZ:00003203] A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. + GAZ:00007120 Howland Island [GAZ:00007120] An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. + GAZ:00002952 Hungary [GAZ:00002952] A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. + GAZ:00000843 Iceland [GAZ:00000843] A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. + GAZ:00002839 India [GAZ:00002839] A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. + GAZ:00003727 Indonesia [GAZ:00003727] An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). + GAZ:00004474 Iran [GAZ:00004474] A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). + GAZ:00004483 Iraq [GAZ:00004483] A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). + GAZ:00002943 Ireland [GAZ:00002943] A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. + GAZ:00052477 Isle of Man [GAZ:00052477] A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. + GAZ:00002476 Israel [GAZ:00002476] A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. + GAZ:00002650 Italy [GAZ:00002650] A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). + GAZ:00003781 Jamaica [GAZ:00003781] A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. + GAZ:00005853 Jan Mayen [GAZ:00005853] A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. + GAZ:00002747 Japan [GAZ:00002747] An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. + GAZ:00007118 Jarvis Island [GAZ:00007118] An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + GAZ:00001551 Jersey [GAZ:00001551] A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. + GAZ:00007114 Johnston Atoll [GAZ:00007114] A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. + GAZ:00002473 Jordan [GAZ:00002473] A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. + GAZ:00005809 Juan de Nova Island [GAZ:00005809] A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. + GAZ:00004999 Kazakhstan [GAZ:00004999] A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. + GAZ:00001101 Kenya [GAZ:00001101] A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. + GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. + GAZ:00007116 Kingman Reef [GAZ:00007116] A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. + GAZ:00006894 Kiribati [GAZ:00006894] An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). + GAZ:00011337 Kosovo [GAZ:00011337] A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + GAZ:00005285 Kuwait [GAZ:00005285] A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). + GAZ:00006893 Kyrgyzstan [GAZ:00006893] A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). + GAZ:00006889 Laos [GAZ:00006889] A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). + GAZ:00002958 Latvia [GAZ:00002958] A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. + GAZ:00002478 Lebanon [GAZ:00002478] A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). + GAZ:00001098 Lesotho [GAZ:00001098] A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. + GAZ:00000911 Liberia [GAZ:00000911] A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. + GAZ:00000566 Libya [GAZ:00000566] A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. + GAZ:00003858 Liechtenstein [GAZ:00003858] A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). + GAZ:00007144 Line Islands [GAZ:00007144] A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. + GAZ:00002960 Lithuania [GAZ:00002960] A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). + GAZ:00002947 Luxembourg [GAZ:00002947] A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. + GAZ:00003202 Macau [GAZ:00003202] One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. + GAZ:00001108 Madagascar [GAZ:00001108] An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + GAZ:00001105 Malawi [GAZ:00001105] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00003902 Malaysia [GAZ:00003902] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00006924 Maldives [GAZ:00006924] An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + GAZ:00000584 Mali [GAZ:00000584] A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. + GAZ:00004017 Malta [GAZ:00004017] A Southern European country and consists of an archipelago situated centrally in the Mediterranean. + GAZ:00007161 Marshall Islands [GAZ:00007161] An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. + GAZ:00067143 Martinique [GAZ:00067143] An island and an overseas department/region and single territorial collectivity of France. + GAZ:00000583 Mauritania [GAZ:00000583] A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). + GAZ:00003745 Mauritius [GAZ:00003745] An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. + GAZ:00003943 Mayotte [GAZ:00003943] An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. + GAZ:00002852 Mexico [GAZ:00002852] A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. + GAZ:00005862 Micronesia [GAZ:00005862] A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. + GAZ:00007112 Midway Islands [GAZ:00007112] A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. + GAZ:00003897 Moldova [GAZ:00003897] A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. + GAZ:00003857 Monaco [GAZ:00003857] A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. + GAZ:00008744 Mongolia [GAZ:00008744] A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. + GAZ:00006898 Montenegro [GAZ:00006898] A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + GAZ:00003988 Montserrat [GAZ:00003988] A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. + GAZ:00000565 Morocco [GAZ:00000565] A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. + GAZ:00001100 Mozambique [GAZ:00001100] A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. + GAZ:00006899 Myanmar [GAZ:00006899] A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. + GAZ:00001096 Namibia [GAZ:00001096] A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. + GAZ:00006900 Nauru [GAZ:00006900] An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. + GAZ:00007119 Navassa Island [GAZ:00007119] A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. + GAZ:00004399 Nepal [GAZ:00004399] A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. + GAZ:00002946 Netherlands [GAZ:00002946] The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). + GAZ:00005206 New Caledonia [GAZ:00005206] A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. + GAZ:00000469 New Zealand [GAZ:00000469] A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. + GAZ:00002978 Nicaragua [GAZ:00002978] A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. + GAZ:00000585 Niger [GAZ:00000585] A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. + GAZ:00000912 Nigeria [GAZ:00000912] A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). + GAZ:00006902 Niue [GAZ:00006902] An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. + GAZ:00005908 Norfolk Island [GAZ:00005908] A Territory of Australia that includes Norfolk Island and neighboring islands. + GAZ:00002801 North Korea [GAZ:00002801] A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. + GAZ:00006895 North Macedonia [GAZ:00006895] A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. + GAZ:00002284 North Sea [GAZ:00002284] A sea situated between the eastern coasts of the British Isles and the western coast of Europe. + GAZ:00003958 Northern Mariana Islands [GAZ:00003958] A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. + GAZ:00002699 Norway [GAZ:00002699] A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. + GAZ:00005283 Oman [GAZ:00005283] A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). + GAZ:00005246 Pakistan [GAZ:00005246] A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. + GAZ:00006905 Palau [GAZ:00006905] A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. + GAZ:00002892 Panama [GAZ:00002892] The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. + GAZ:00003922 Papua New Guinea [GAZ:00003922] A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). + GAZ:00010832 Paracel Islands [GAZ:00010832] A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. + GAZ:00002933 Paraguay [GAZ:00002933] A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. + GAZ:00002932 Peru [GAZ:00002932] A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. + GAZ:00004525 Philippines [GAZ:00004525] An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. + GAZ:00005867 Pitcairn Islands [GAZ:00005867] A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. + GAZ:00002939 Poland [GAZ:00002939] A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. + GAZ:00004126 Portugal [GAZ:00004126] That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. + GAZ:00006935 Puerto Rico [GAZ:00006935] A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). + GAZ:00005286 Qatar [GAZ:00005286] An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). + GAZ:00001088 Republic of the Congo [GAZ:00001088] A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. + GAZ:00003945 Reunion [GAZ:00003945] An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. + GAZ:00002951 Romania [GAZ:00002951] A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). + GAZ:00023304 Ross Sea [GAZ:00023304] A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. + GAZ:00002721 Russia [GAZ:00002721] A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. + GAZ:00001087 Rwanda [GAZ:00001087] A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). + GAZ:00000849 Saint Helena [GAZ:00000849] An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. + GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. + GAZ:00006909 Saint Lucia [GAZ:00006909] An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. + GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. + GAZ:00005841 Saint Martin [GAZ:00005841] An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] An island nation in the Lesser Antilles chain of the Caribbean Sea. + GAZ:00006910 Samoa [GAZ:00006910] A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). + GAZ:00003102 San Marino [GAZ:00003102] A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). + GAZ:00006927 Sao Tome and Principe [GAZ:00006927] An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). + GAZ:00005279 Saudi Arabia [GAZ:00005279] A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. + GAZ:00000913 Senegal [GAZ:00000913] A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. + GAZ:00002957 Serbia [GAZ:00002957] A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). + GAZ:00006922 Seychelles [GAZ:00006922] An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. + GAZ:00000914 Sierra Leone [GAZ:00000914] A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. + GAZ:00003923 Singapore [GAZ:00003923] An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. + GAZ:00012579 Sint Maarten [GAZ:00012579] One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. + GAZ:00002956 Slovakia [GAZ:00002956] A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. + GAZ:00002955 Slovenia [GAZ:00002955] A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. + GAZ:00005275 Solomon Islands [GAZ:00005275] A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. + GAZ:00001104 Somalia [GAZ:00001104] A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. + GAZ:00001094 South Africa [GAZ:00001094] A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. + GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. + GAZ:00002802 South Korea [GAZ:00002802] A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + GAZ:00233439 South Sudan [GAZ:00233439] A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. + GAZ:00003936 Spain [GAZ:00003936] That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. + GAZ:00010831 Spratly Islands [GAZ:00010831] A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. + GAZ:00003924 Sri Lanka [GAZ:00003924] An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. + GAZ:00002475 State of Palestine [GAZ:00002475] The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. + GAZ:00000560 Sudan [GAZ:00000560] A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. + GAZ:00002525 Suriname [GAZ:00002525] A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. + GAZ:00005396 Svalbard [GAZ:00005396] An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. + GAZ:00001099 Swaziland [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00002729 Sweden [GAZ:00002729] A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. + GAZ:00002941 Switzerland [GAZ:00002941] A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. + GAZ:00002474 Syria [GAZ:00002474] A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). + GAZ:00005341 Taiwan [GAZ:00005341] A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. + GAZ:00006912 Tajikistan [GAZ:00006912] A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). + GAZ:00001103 Tanzania [GAZ:00001103] A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). + GAZ:00003744 Thailand [GAZ:00003744] A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. + GAZ:00006913 Timor-Leste [GAZ:00006913] A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. + GAZ:00000915 Togo [GAZ:00000915] A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. + GAZ:00260188 Tokelau [GAZ:00260188] A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). + GAZ:00006916 Tonga [GAZ:00006916] A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. + GAZ:00003767 Trinidad and Tobago [GAZ:00003767] An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + GAZ:00005812 Tromelin Island [GAZ:00005812] A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. + GAZ:00000562 Tunisia [GAZ:00000562] A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). + GAZ:00000558 Turkey [GAZ:00000558] A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. + GAZ:00005018 Turkmenistan [GAZ:00005018] A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. + GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. + GAZ:00009715 Tuvalu [GAZ:00009715] A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. + GAZ:00002459 United States of America [GAZ:00002459] A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. + GAZ:00001102 Uganda [GAZ:00001102] A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. + GAZ:00002724 Ukraine [GAZ:00002724] A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. + GAZ:00005282 United Arab Emirates [GAZ:00005282] A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + GAZ:00002637 United Kingdom [GAZ:00002637] A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. + GAZ:00002930 Uruguay [GAZ:00002930] A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). + GAZ:00004979 Uzbekistan [GAZ:00004979] A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). + GAZ:00006918 Vanuatu [GAZ:00006918] An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. + GAZ:00002931 Venezuela [GAZ:00002931] A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). + GAZ:00003756 Viet Nam [GAZ:00003756] The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. + GAZ:00003959 Virgin Islands [GAZ:00003959] A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. + GAZ:00007111 Wake Island [GAZ:00007111] A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). + GAZ:00007191 Wallis and Futuna [GAZ:00007191] A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. + GAZ:00009572 West Bank [GAZ:00009572] A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". + GAZ:00000564 Western Sahara [GAZ:00000564] A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. + GAZ:00005284 Yemen [GAZ:00005284] A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + GAZ:00001107 Zambia [GAZ:00001107] A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. + GAZ:00001106 Zimbabwe [GAZ:00001106] A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. \ No newline at end of file diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index a69ca4a2..2cd58db4 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -1,187 +1,235 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -Mpox;Mpox_international GENEPIO:0001122 Database Identifiers -Mpox;Mpox_international Database Identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID -Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID WhitespaceMinimizedString null value menu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID -Mpox;Mpox_international Database Identifiers GENEPIO:0100281 case ID WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID -Mpox;Mpox_international Database Identifiers GENEPIO:0001136 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession -Mpox;Mpox_international Database Identifiers GENEPIO:0001139 biosample accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession -Mpox;Mpox_international Database Identifiers GENEPIO:0001142 SRA accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SUBMISSIONS - SRA Accession -Mpox;Mpox_international Database Identifiers GENEPIO:0001145 GenBank accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 SUBMISSIONS - GenBank Accession -Mpox_international Database Identifiers GENEPIO:0100282 GISAID virus name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name -Mpox;Mpox_international Database Identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession -Mpox;Mpox_international GENEPIO:0001150 Sample collection and processing -Mpox Sample collection and processing GENEPIO:0001153 sample collected by sample collected by menu null value menu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by -Mpox_international Sample collection and processing GENEPIO:0001153 sample collected by WhitespaceMinimizedString null value menu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by -Mpox;Mpox_international Sample collection and processing GENEPIO:0001156 sample collector contact email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email -Mpox;Mpox_international Sample collection and processing GENEPIO:0001158 sample collector contact address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address -Mpox Sample collection and processing GENEPIO:0100416 sequenced by sequence submitted by menu null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by -Mpox_international Sample collection and processing GENEPIO:0100416 sequenced by WhitespaceMinimizedString null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by -Mpox;Mpox_international Sample collection and processing GENEPIO:0100422 sequenced by contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email -Mpox;Mpox_international Sample collection and processing GENEPIO:0100423 sequenced by contact address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequenced by contact address -Mpox Sample collection and processing GENEPIO:0001159 sequence submitted by sequence submitted by menu null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by -Mpox_international Sample collection and processing GENEPIO:0001159 sequence submitted by WhitespaceMinimizedString null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by -Mpox;Mpox_international Sample collection and processing GENEPIO:0001165 sequence submitter contact email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email -Mpox;Mpox_international Sample collection and processing GENEPIO:0001167 sequence submitter contact address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address -Mpox;Mpox_international Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date -Mpox Sample collection and processing GENEPIO:0001177 sample collection date precision sample collection date precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 -Mpox;Mpox_international Sample collection and processing GENEPIO:0001179 sample received date date null value menu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date -Mpox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) -Mpox_international Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) international menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) -Mpox Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name (state/province/territory) menu null value menu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) -Mpox_international Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) WhitespaceMinimizedString null value menu TRUE The state/province/territory where the sample was collected. Provide the state/province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) -Mpox_international Sample collection and processing GENEPIO:0100309 geo_loc latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon -Mpox_international Sample collection and processing GENEPIO:0100310 geo_loc longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon -Mpox Sample collection and processing GENEPIO:0001191 organism organism menu null value menu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus Pathogen HC_CURRENT_ID organism organism -Mpox_international Sample collection and processing GENEPIO:0001191 organism organism international menu null value menu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism -Mpox Sample collection and processing GENEPIO:0001195 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name -Mpox_international Sample collection and processing GENEPIO:0001644 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate -Mpox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling menu null value menu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling -Mpox_international Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling international menu null value menu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling -Mpox;Mpox_international Sample collection and processing GENEPIO:0001200 purpose of sampling details WhitespaceMinimizedString null value menu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Symptomology and history suggested Monkeypox diagnosis. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details -Mpox Sample collection and processing GENEPIO:0001204 NML submitted specimen type NML submitted specimen type menu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Nucleic Acid Specimen Type PH_SPECIMEN_TYPE -Mpox Sample collection and processing GENEPIO:0001209 Related specimen relationship type Related specimen relationship type menu null value menu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Previously Submitted Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE -Mpox Sample collection and processing GENEPIO:0001211 anatomical material anatomical material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material -Mpox_international Sample collection and processing GENEPIO:0001211 anatomical material anatomical material international menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) [NCIT:C78582] Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material -Mpox Sample collection and processing GENEPIO:0001214 anatomical part anatomical part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part -Mpox_international Sample collection and processing GENEPIO:0001214 anatomical part anatomical part international menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part -Mpox Sample collection and processing GENEPIO:0001216 body product body product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product -Mpox_international Sample collection and processing GENEPIO:0001216 body product body product international menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product -Mpox_international Sample collection and processing GENEPIO:0001223 environmental material environmental material international menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material -Mpox Sample collection and processing GENEPIO:0001234 collection device collection device menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device -Mpox_international Sample collection and processing GENEPIO:0001234 collection device collection device international menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device -Mpox Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method -Mpox_international Sample collection and processing GENEPIO:0001241 collection method collection method international menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method -Mpox Sample collection and processing GENEPIO:0001253 specimen processing specimen processing menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing -Mpox_international Sample collection and processing GENEPIO:0001253 specimen processing specimen processing international menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] -Mpox;Mpox_international Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details -Mpox;Mpox_international GENEPIO:0001268 Host Information -Mpox Host Information GENEPIO:0001386 host (common name) host (common name) menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE -Mpox_international Host Information GENEPIO:0001386 host (common name) host (common name) international menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human -Mpox Host Information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) -Mpox_international Host Information GENEPIO:0001387 host (scientific name) host (scientific name) international menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) -Mpox Host Information GENEPIO:0001388 host health state host health state menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state -Mpox_international Host Information GENEPIO:0001388 host health state host health state international menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state -Mpox Host Information GENEPIO:0001389 host health status details host health status details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS -Mpox_international Host Information GENEPIO:0001389 host health status details host health status details international menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] -Mpox Host Information GENEPIO:0001389 host health outcome host health outcome menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome -Mpox_international Host Information GENEPIO:0001389 host health outcome host health outcome international menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome -Mpox Host Information GENEPIO:0001391 host disease host disease menu null value menu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox Host Disease PH_HOST_DISEASE host_disease host disease -Mpox_international Host Information GENEPIO:0001391 host disease host disease international menu null value menu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease -Mpox_international Host Information GENEPIO:0001398 host subject ID WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id -Mpox Host Information GENEPIO:0001392 host age decimal null value menu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age -Mpox_international Host Information GENEPIO:0001392 host age decimal null value menu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age -Mpox Host Information GENEPIO:0001393 host age unit host age unit menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit -Mpox_international Host Information GENEPIO:0001393 host age unit host age unit international menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit -Mpox Host Information GENEPIO:0001394 host age bin host age bin menu null value menu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin -Mpox_international Host Information GENEPIO:0001394 host age bin host age bin international menu null value menu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin -Mpox Host Information GENEPIO:0001395 host gender host gender menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex -Mpox_international Host Information GENEPIO:0001395 host gender host gender international menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex -Mpox Host Information GENEPIO:0001396 host residence geo_loc name (country) geo_loc_name (country) menu null value menu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY -Mpox_international Host Information GENEPIO:0001396 host residence geo_loc name (country) geo_loc_name (country) international menu null value menu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] -Mpox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) geo_loc_name (state/province/territory) menu null value menu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE -Mpox;Mpox_international Host Information GENEPIO:0001399 symptom onset date date null value menu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE -Mpox Host Information GENEPIO:0001400 signs and symptoms signs and symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS -Mpox_international Host Information GENEPIO:0001400 signs and symptoms signs and symptoms international menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] -Mpox Host Information GENEPIO:0001401 pre-existing conditions and risk factors pre-existing conditions and risk factors menu null value menu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors -Mpox_international Host Information GENEPIO:0001401 pre-existing conditions and risk factors pre-existing conditions and risk factors international menu null value menu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors -Mpox Host Information GENEPIO:0001402 complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications -Mpox_international Host Information GENEPIO:0001402 complications complications international menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] -Mpox;Mpox_international Host Information GENEPIO:0100580 antiviral therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy -Mpox;Mpox_international GENEPIO:0001403 Host vaccination information -Mpox Host vaccination information GENEPIO:0001404 host vaccination status host vaccination status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY -Mpox_international Host vaccination information GENEPIO:0001404 host vaccination status host vaccination status international menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY -Mpox;Mpox_international Host vaccination information GENEPIO:0001406 number of vaccine doses received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received -Mpox;Mpox_international Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name WhitespaceMinimizedString null value menu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY -Mpox;Mpox_international Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date date null value menu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY -Mpox;Mpox_international Host vaccination information GENEPIO:0100321 vaccination history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY - -Mpox;Mpox_international GENEPIO:0001409 Host exposure information -Mpox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) geo_loc_name (country) menu null value menu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY -Mpox_international Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) geo_loc_name (country) international menu null value menu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] -Mpox;Mpox_international Host exposure information GENEPIO:0001411 destination of most recent travel (city) WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL -Mpox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) geo_loc_name (state/province/territory) menu null value menu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL -Mpox_international Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California -Mpox Host exposure information GENEPIO:0001413 destination of most recent travel (country) geo_loc_name (country) menu null value menu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL -Mpox_international Host exposure information GENEPIO:0001413 destination of most recent travel (country) geo_loc_name (country) international menu null value menu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] -Mpox;Mpox_international Host exposure information GENEPIO:0001414 most recent travel departure date date null value menu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL -Mpox;Mpox_international Host exposure information GENEPIO:0001415 most recent travel return date date null value menu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL -Mpox;Mpox_international Host exposure information GENEPIO:0001416 travel history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL -Mpox Host exposure information GENEPIO:0001417 exposure event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE -Mpox_international Host exposure information GENEPIO:0001417 exposure event exposure event international menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE -Mpox Host exposure information GENEPIO:0001418 exposure contact level exposure contact level menu null value menu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level -Mpox_international Host exposure information GENEPIO:0001418 exposure contact level exposure contact level international menu null value menu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level -Mpox Host exposure information GENEPIO:0001419 host role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE -Mpox_international Host exposure information GENEPIO:0001419 host role host role international menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE -Mpox Host exposure information GENEPIO:0001428 exposure setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE -Mpox_international Host exposure information GENEPIO:0001428 exposure setting exposure setting international menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE -Mpox;Mpox_international Host exposure information GENEPIO:0001431 exposure details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS - -Mpox;Mpox_international GENEPIO:0001434 Host reinfection information -Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior Monkeypox infection menu null value menu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection -Mpox_international Host reinfection information GENEPIO:0100532 prior Mpox infection prior Monkeypox infection international menu null value menu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] -Mpox;Mpox_international Host reinfection information GENEPIO:0100533 prior Mpox infection date date null value menu The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date -Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior Monkeypox antiviral treatment menu null value menu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment -Mpox_international Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior Monkeypox antiviral treatment international menu null value menu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] -Mpox;Mpox_international Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection - - - - - -Mpox;Mpox_international GENEPIO:0001441 Sequencing -Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing -Mpox_international Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing international menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing -Mpox;Mpox_international Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details -Mpox Sequencing GENEPIO:0001447 sequencing date date null value menu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE -Mpox_international Sequencing GENEPIO:0001447 sequencing date date null value menu {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE -Mpox;Mpox_international Sequencing GENEPIO:0001448 library ID WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID -Mpox;Mpox_international Sequencing GENEPIO:0001449 amplicon size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size -Mpox;Mpox_international Sequencing GENEPIO:0001450 library preparation kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT -Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument -Mpox_international Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument international menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument -Mpox;Mpox_international Sequencing GENEPIO:0001454 sequencing protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol -Mpox;Mpox_international Sequencing GENEPIO:0001455 sequencing kit number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number -Mpox;Mpox_international Sequencing GENEPIO:0001456 amplicon pcr primer scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme -Mpox;Mpox_international GENEPIO:0001457 Bioinformatics and QC metrics -Mpox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method -Mpox_international Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method -Mpox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method -Mpox_international Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001461 consensus sequence filename WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. mpxvassembly.fasta consensus sequence filename -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001462 consensus sequence filepath WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% breadth of coverage value breadth of coverage value -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length -Mpox;Mpox_international Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession -Mpox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol -Mpox_international Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol - -Mpox;Mpox_international GENEPIO:0001506 Pathogen diagnostic testing -Mpox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name -Mpox_international Pathogen diagnostic testing GENEPIO:0001507 gene name 1 WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name -Mpox;Mpox_international Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value -Mpox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 -Mpox_international Pathogen diagnostic testing GENEPIO:0001510 gene name 2 WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 -Mpox;Mpox_international Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 -Mpox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 -Mpox_international Pathogen diagnostic testing GENEPIO:0001513 gene name 3 WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 -Mpox;Mpox_international Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3 -Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4 -Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 -Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 -Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 - - GENEPIO:0001516 Contributor acknowledgement -Mpox;Mpox_international Contributor acknowledgement GENEPIO:0001517 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS -Mpox;Mpox_international Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal For RefGuide Matching +Mpox;MpoxInternational GENEPIO:0001122 Database Identifiers database_identifiers Mpox;MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID Mpox;MpoxInternational +Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID Mpox +Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID Mpox;MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession Mpox;MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession Mpox;MpoxInternational +Mpox;MpoxInternational Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION Mpox;MpoxInternational +Mpox;MpoxInternational Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession Mpox;MpoxInternational +MpoxInternational Database Identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession Mpox;MpoxInternational +Mpox;MpoxInternational GENEPIO:0001150 Sample collection and processing sample_collection_and_processing Mpox;MpoxInternational +Mpox Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by Mpox +MpoxInternational Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by MpoxInternational +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email Mpox;MpoxInternational +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001158 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address Mpox;MpoxInternational +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date Mpox;MpoxInternational +Mpox Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 Mpox +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date Mpox;MpoxInternational +Mpox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) Mpox +MpoxInternational Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) MpoxInternational +Mpox Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) Mpox +MpoxInternational Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the state/province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) MpoxInternational +MpoxInternational Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon MpoxInternational +MpoxInternational Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon MpoxInternational +Mpox Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus Pathogen HC_CURRENT_ID organism organism Mpox +MpoxInternational Sample collection and processing GENEPIO:0001191 organism organism OrganismInternationalMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism MpoxInternational +Mpox Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name Mpox +MpoxInternational Sample collection and processing GENEPIO:0001644 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate MpoxInternational +Mpox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling Mpox +MpoxInternational Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingInternationalMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling MpoxInternational +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Symptomology and history suggested Monkeypox diagnosis. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details Mpox;MpoxInternational +Mpox Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Nucleic Acid Specimen Type PH_SPECIMEN_TYPE Mpox +Mpox Sample collection and processing GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type RelatedSpecimenRelationshipTypeMenu NullValueMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Previously Submitted Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE Mpox +Mpox Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material Mpox +MpoxInternational Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) [NCIT:C78582] Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material MpoxInternational +Mpox Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part Mpox +MpoxInternational Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartInternationalMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part MpoxInternational +Mpox Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product Mpox +MpoxInternational Sample collection and processing GENEPIO:0001216 body product body_product BodyProductInternationalMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product MpoxInternational +MpoxInternational Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material MpoxInternational +Mpox Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device Mpox +MpoxInternational Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceInternationalMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device MpoxInternational +Mpox Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method Mpox +MpoxInternational Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodInternationalMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method MpoxInternational +Mpox Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing Mpox +MpoxInternational Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingInternationalMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] MpoxInternational +Mpox;MpoxInternational Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details Mpox;MpoxInternational +Mpox Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control Mpox +MpoxInternational Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeInternationalMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] MpoxInternational +Mpox;MpoxInternational Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control Mpox;MpoxInternational +Mpox;MpoxInternational GENEPIO:0001498 Lineage and Variant information +MpoxInternational Lineage and Variant information GENEPIO:0001500 lineage/clade name LineageCladeNameINternationalMenu NullValueMenu The name of the lineage or clade. Provide the lineage/clade name. B.1.1.7 PH_LINEAGE_CLADE_NAME +MpoxInternational Lineage and Variant information GENEPIO:0001501 lineage/clade analysis software name WhitespaceMinimizedString NullValueMenu The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin PH_LINEAGE_CLADE_SOFTWARE +MpoxInternational Lineage and Variant information GENEPIO:0001502 lineage/clade analysis software version WhitespaceMinimizedString NullValueMenu The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION +Mpox;MpoxInternational GENEPIO:0001268 Host Information host_information Mpox;MpoxInternational +Mpox Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE Mpox +MpoxInternational Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameInternationalMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human MpoxInternational +Mpox Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) Mpox +MpoxInternational Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameInternationalMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) MpoxInternational +Mpox Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state Mpox +MpoxInternational Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateInternationalMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state MpoxInternational +Mpox Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS Mpox +MpoxInternational Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsInternationalMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] MpoxInternational +Mpox Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome Mpox +MpoxInternational Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeInternationalMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome MpoxInternational +Mpox Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox Host Disease PH_HOST_DISEASE host_disease host disease Mpox +MpoxInternational Host Information GENEPIO:0001391 host disease host_disease HostDiseaseInternationalMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease MpoxInternational +MpoxInternational Host Information GENEPIO:0001398 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id MpoxInternational +Mpox Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age Mpox +MpoxInternational Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age MpoxInternational +Mpox Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit Mpox +MpoxInternational Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitInternationalMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit MpoxInternational +Mpox Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin Mpox +MpoxInternational Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinInternationalMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin MpoxInternational +Mpox Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex Mpox +MpoxInternational Host Information GENEPIO:0001395 host gender host_gender HostGenderInternationalMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex MpoxInternational +Mpox Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY Mpox +MpoxInternational Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] MpoxInternational +Mpox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE Mpox +Mpox;MpoxInternational Host Information GENEPIO:0001399 symptom onset date symptom_onset_date date NullValueMenu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE Mpox;MpoxInternational +Mpox Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS Mpox +MpoxInternational Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsInternationalMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] MpoxInternational +Mpox Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors Mpox +MpoxInternational Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsInternationalMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors MpoxInternational +Mpox Host Information GENEPIO:0001402 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications Mpox +MpoxInternational Host Information GENEPIO:0001402 complications complications ComplicationsInternationalMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] MpoxInternational +Mpox;MpoxInternational Host Information GENEPIO:0100580 antiviral therapy antiviral_therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy Mpox;MpoxInternational +Mpox;MpoxInternational GENEPIO:0001403 Host vaccination information host_vaccination_information Mpox;MpoxInternational +Mpox Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY Mpox +MpoxInternational Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusInternationalMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY MpoxInternational +Mpox;MpoxInternational Host vaccination information GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received Mpox;MpoxInternational +Mpox;MpoxInternational Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name WhitespaceMinimizedString NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY Mpox;MpoxInternational +Mpox;MpoxInternational Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date date NullValueMenu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY Mpox;MpoxInternational +Mpox;MpoxInternational Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY Mpox;MpoxInternational + +Mpox;MpoxInternational GENEPIO:0001409 Host exposure information host_exposure_information Mpox;MpoxInternational +Mpox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY Mpox +MpoxInternational Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] MpoxInternational +Mpox;MpoxInternational Host exposure information GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL Mpox;MpoxInternational +Mpox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL Mpox +MpoxInternational Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California MpoxInternational +Mpox Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL Mpox +MpoxInternational Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryInternationalMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] MpoxInternational +Mpox;MpoxInternational Host exposure information GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL Mpox;MpoxInternational +Mpox;MpoxInternational Host exposure information GENEPIO:0001415 most recent travel return date most_recent_travel_return_date date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL Mpox;MpoxInternational +Mpox;MpoxInternational Host exposure information GENEPIO:0001416 travel history travel_history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL Mpox;MpoxInternational +Mpox Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE Mpox +MpoxInternational Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventInternationalMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE MpoxInternational +Mpox Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level Mpox +MpoxInternational Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelInternationalMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level MpoxInternational +Mpox Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE Mpox +MpoxInternational Host exposure information GENEPIO:0001419 host role host_role HostRoleInternationalMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE MpoxInternational +Mpox Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE Mpox +MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingInternationalMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE MpoxInternational +Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS Mpox;MpoxInternational + +Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information Mpox;MpoxInternational +Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMonkeypoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection Mpox +MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMonkeypoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] MpoxInternational +Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date Mpox;MpoxInternational +Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMonkeypoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment Mpox +MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMonkeypoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] MpoxInternational +Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection Mpox;MpoxInternational + + +Mpox;MpoxInternational GENEPIO:0001441 Sequencing sequencing Mpox;MpoxInternational +Mpox;MpoxInternational Sequence information GENEPIO:0100472 sequencing project name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. MPOX-1356 Mpox;MpoxInternational +Mpox Sequencing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by Mpox +MpoxInternational Sequencing GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Ontario (PHO) sequenced_by MpoxInternational +Mpox Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString NullValueMenu The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab Mpox +MpoxInternational Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequenced by contact address Mpox;MpoxInternational +Mpox Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by Mpox +MpoxInternational Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address Mpox;MpoxInternational +Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Mpox +MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details Mpox;MpoxInternational +Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE Mpox +MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Mpox;MpoxInternational +Mpox Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay Mpox +MpoxInternational Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeInternationalMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] MpoxInternational +Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument Mpox +MpoxInternational Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentInternationalMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument MpoxInternational +Mpox;MpoxInternational Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol__ WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001455 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 Mpox;MpoxInternational +Mpox Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method Mpox +MpoxInternational Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodInternationalMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme Mpox;MpoxInternational + Sequencing GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300bp +Mpox;MpoxInternational GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 Mpox;MpoxInternational +Mpox Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control Mpox +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationInternationalMenu MpoxInternational +Mpox Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage Mpox +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesInternationalMenu MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. Mpox;MpoxInternational +Mpox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method Mpox +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method MpoxInternational +Mpox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method Mpox +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name consensus_sequence_name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta consensus sequence filename Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu TRUE The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu TRUE The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename________ WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath fast5_filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession Mpox;MpoxInternational +Mpox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol Mpox +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol MpoxInternational +MpoxInternational GENEPIO:0101082 Taxonomic identification information +MpoxInternational Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +MpoxInternational Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +MpoxInternational Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +MpoxInternational Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +MpoxInternational Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. MPXV_report123.doc +MpoxInternational Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +MpoxInternational Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +Mpox;MpoxInternational GENEPIO:0001506 Pathogen diagnostic testing pathogen_diagnostic_testing Mpox;MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. MPX (orf B6R) MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0102045 assay target details 1 assay_target_details_1 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name Mpox +MpoxInternational Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg190 gene (MPOX) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. B6R (Li et al., 2006) +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value Mpox;MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OVP (orf 17L) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 Mpox +MpoxInternational Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg002 gene (MPOX) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G). +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 Mpox;MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OPHA (orf B2R) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene_name_3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 Mpox +MpoxInternational Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg188 gene (MPOX) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 MpoxInternational +MpoxInternational Pathogen diagnostic testing GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R_G (Li et al., 2010) assay +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3 Mpox;MpoxInternational +Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4 Mpox +Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 Mpox +Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 Mpox +Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 Mpox + + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement +Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS Mpox;MpoxInternational +Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS Mpox;MpoxInternational \ No newline at end of file From 282b840bfd89c8e5fc61e52ba74f0bea45688099 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 8 Oct 2024 23:42:48 -0700 Subject: [PATCH 49/96] Wastewater update --- web/templates/wastewater/schema.json | 26190 ++++++++++++++------ web/templates/wastewater/schema.yaml | 10319 +++++--- web/templates/wastewater/schema_core.yaml | 8 +- web/templates/wastewater/schema_enums.tsv | 1592 +- web/templates/wastewater/schema_slots.tsv | 484 +- 5 files changed, 26442 insertions(+), 12151 deletions(-) diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index 84c70ad1..e6c15de8 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -2,7 +2,7 @@ "name": "Wastewater", "description": "", "id": "https://example.com/GRDI", - "version": "2.0.0", + "version": "3.1.1", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -296,3370 +296,4178 @@ } }, "enums": { - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "null value menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Not Applicable": { - "text": "Not Applicable", + "Not Applicable [GENEPIO:0001619]": { + "text": "Not Applicable [GENEPIO:0001619]", + "description": "A categorical choice recorded when a datum does not apply to a given context.", "meaning": "GENEPIO:0001619" }, - "Missing": { - "text": "Missing", + "Missing [GENEPIO:0001618]": { + "text": "Missing [GENEPIO:0001618]", + "description": "A categorical choice recorded when a datum is not included for an unknown reason.", "meaning": "GENEPIO:0001618" }, - "Not Collected": { - "text": "Not Collected", + "Not Collected [GENEPIO:0001620]": { + "text": "Not Collected [GENEPIO:0001620]", + "description": "A categorical choice recorded when a datum was not measured or collected.", "meaning": "GENEPIO:0001620" }, - "Not Provided": { - "text": "Not Provided", + "Not Provided [GENEPIO:0001668]": { + "text": "Not Provided [GENEPIO:0001668]", + "description": "A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage.", "meaning": "GENEPIO:0001668" }, - "Restricted Access": { - "text": "Restricted Access", + "Restricted Access [GENEPIO:0001810]": { + "text": "Restricted Access [GENEPIO:0001810]", + "description": "A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns.", "meaning": "GENEPIO:0001810" } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Afghanistan": { - "text": "Afghanistan", + "Afghanistan [GAZ:00006882]": { + "text": "Afghanistan [GAZ:00006882]", + "description": "A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ]", "meaning": "GAZ:00006882" }, - "Albania": { - "text": "Albania", + "Albania [GAZ:00002953]": { + "text": "Albania [GAZ:00002953]", + "description": "A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ]", "meaning": "GAZ:00002953" }, - "Algeria": { - "text": "Algeria", + "Algeria [GAZ:00000563]": { + "text": "Algeria [GAZ:00000563]", + "description": "A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ]", "meaning": "GAZ:00000563" }, - "American Samoa": { - "text": "American Samoa", + "American Samoa [GAZ:00003957]": { + "text": "American Samoa [GAZ:00003957]", + "description": "An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ]", "meaning": "GAZ:00003957" }, - "Andorra": { - "text": "Andorra", + "Andorra [GAZ:00002948]": { + "text": "Andorra [GAZ:00002948]", + "description": "A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]", "meaning": "GAZ:00002948" }, - "Angola": { - "text": "Angola", + "Angola [GAZ:00001095]": { + "text": "Angola [GAZ:00001095]", + "description": "A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ]", "meaning": "GAZ:00001095" }, - "Anguilla": { - "text": "Anguilla", + "Anguilla [GAZ:00009159]": { + "text": "Anguilla [GAZ:00009159]", + "description": "A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ]", "meaning": "GAZ:00009159" }, - "Antarctica": { - "text": "Antarctica", + "Antarctica [GAZ:00000462]": { + "text": "Antarctica [GAZ:00000462]", + "description": "The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ]", "meaning": "GAZ:00000462" }, - "Antigua and Barbuda": { - "text": "Antigua and Barbuda", + "Antigua and Barbuda [GAZ:00006883]": { + "text": "Antigua and Barbuda [GAZ:00006883]", + "description": "An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ]", "meaning": "GAZ:00006883" }, - "Argentina": { - "text": "Argentina", + "Argentina [GAZ:00002928]": { + "text": "Argentina [GAZ:00002928]", + "description": "A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ]", "meaning": "GAZ:00002928" }, - "Armenia": { - "text": "Armenia", + "Armenia [GAZ:00004094]": { + "text": "Armenia [GAZ:00004094]", + "description": "A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ]", "meaning": "GAZ:00004094" }, - "Aruba": { - "text": "Aruba", + "Aruba [GAZ:00004025]": { + "text": "Aruba [GAZ:00004025]", + "description": "An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ]", "meaning": "GAZ:00004025" }, - "Ashmore and Cartier Islands": { - "text": "Ashmore and Cartier Islands", + "Ashmore and Cartier Islands [GAZ:00005901]": { + "text": "Ashmore and Cartier Islands [GAZ:00005901]", + "description": "A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ]", "meaning": "GAZ:00005901" }, - "Australia": { - "text": "Australia", + "Australia [GAZ:00000463]": { + "text": "Australia [GAZ:00000463]", + "description": "A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories.", "meaning": "GAZ:00000463" }, - "Austria": { - "text": "Austria", + "Austria [GAZ:00002942]": { + "text": "Austria [GAZ:00002942]", + "description": "A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities.", "meaning": "GAZ:00002942" }, - "Azerbaijan": { - "text": "Azerbaijan", + "Azerbaijan [GAZ:00004941]": { + "text": "Azerbaijan [GAZ:00004941]", + "description": "A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika).", "meaning": "GAZ:00004941" }, - "Bahamas": { - "text": "Bahamas", + "Bahamas [GAZ:00002733]": { + "text": "Bahamas [GAZ:00002733]", + "description": "A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government.", "meaning": "GAZ:00002733" }, - "Bahrain": { - "text": "Bahrain", + "Bahrain [GAZ:00005281]": { + "text": "Bahrain [GAZ:00005281]", + "description": "A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates.", "meaning": "GAZ:00005281" }, - "Baker Island": { - "text": "Baker Island", + "Baker Island [GAZ:00007117]": { + "text": "Baker Island [GAZ:00007117]", + "description": "An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US.", "meaning": "GAZ:00007117" }, - "Bangladesh": { - "text": "Bangladesh", + "Bangladesh [GAZ:00003750]": { + "text": "Bangladesh [GAZ:00003750]", + "description": "A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana (\"police stations\").", "meaning": "GAZ:00003750" }, - "Barbados": { - "text": "Barbados", + "Barbados [GAZ:00001251]": { + "text": "Barbados [GAZ:00001251]", + "description": "An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown.", "meaning": "GAZ:00001251" }, - "Bassas da India": { - "text": "Bassas da India", + "Bassas da India [GAZ:00005810]": { + "text": "Bassas da India [GAZ:00005810]", + "description": "A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below.", "meaning": "GAZ:00005810" }, - "Belarus": { - "text": "Belarus", + "Belarus [GAZ:00006886]": { + "text": "Belarus [GAZ:00006886]", + "description": "A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital.", "meaning": "GAZ:00006886" }, - "Belgium": { - "text": "Belgium", + "Belgium [GAZ:00002938]": { + "text": "Belgium [GAZ:00002938]", + "description": "A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977).", "meaning": "GAZ:00002938" }, - "Belize": { - "text": "Belize", + "Belize [GAZ:00002934]": { + "text": "Belize [GAZ:00002934]", + "description": "A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies.", "meaning": "GAZ:00002934" }, - "Benin": { - "text": "Benin", + "Benin [GAZ:00000904]": { + "text": "Benin [GAZ:00000904]", + "description": "A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes.", "meaning": "GAZ:00000904" }, - "Bermuda": { - "text": "Bermuda", + "Bermuda [GAZ:00001264]": { + "text": "Bermuda [GAZ:00001264]", + "description": "A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands.", "meaning": "GAZ:00001264" }, - "Bhutan": { - "text": "Bhutan", + "Bhutan [GAZ:00003920]": { + "text": "Bhutan [GAZ:00003920]", + "description": "A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog.", "meaning": "GAZ:00003920" }, - "Bolivia": { - "text": "Bolivia", + "Bolivia [GAZ:00002511]": { + "text": "Bolivia [GAZ:00002511]", + "description": "A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios).", "meaning": "GAZ:00002511" }, - "Borneo": { - "text": "Borneo", + "Borneo [GAZ:00025355]": { + "text": "Borneo [GAZ:00025355]", + "description": "An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres.", "meaning": "GAZ:00025355" }, - "Bosnia and Herzegovina": { - "text": "Bosnia and Herzegovina", + "Bosnia and Herzegovina [GAZ:00006887]": { + "text": "Bosnia and Herzegovina [GAZ:00006887]", + "description": "A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina.", "meaning": "GAZ:00006887" }, - "Botswana": { - "text": "Botswana", + "Botswana [GAZ:00001097]": { + "text": "Botswana [GAZ:00001097]", + "description": "A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts.", "meaning": "GAZ:00001097" }, - "Bouvet Island": { - "text": "Bouvet Island", + "Bouvet Island [GAZ:00001453]": { + "text": "Bouvet Island [GAZ:00001453]", + "description": "A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended.", "meaning": "GAZ:00001453" }, - "Brazil": { - "text": "Brazil", + "Brazil [GAZ:00002828]": { + "text": "Brazil [GAZ:00002828]", + "description": "A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South.", "meaning": "GAZ:00002828" }, - "British Virgin Islands": { - "text": "British Virgin Islands", + "British Virgin Islands [GAZ:00003961]": { + "text": "British Virgin Islands [GAZ:00003961]", + "description": "A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited.", "meaning": "GAZ:00003961" }, - "Brunei": { - "text": "Brunei", + "Brunei [GAZ:00003901]": { + "text": "Brunei [GAZ:00003901]", + "description": "A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages).", "meaning": "GAZ:00003901" }, - "Bulgaria": { - "text": "Bulgaria", + "Bulgaria [GAZ:00002950]": { + "text": "Bulgaria [GAZ:00002950]", + "description": "A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities.", "meaning": "GAZ:00002950" }, - "Burkina Faso": { - "text": "Burkina Faso", + "Burkina Faso [GAZ:00000905]": { + "text": "Burkina Faso [GAZ:00000905]", + "description": "A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes).", "meaning": "GAZ:00000905" }, - "Burundi": { - "text": "Burundi", + "Burundi [GAZ:00001090]": { + "text": "Burundi [GAZ:00001090]", + "description": "A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines.", "meaning": "GAZ:00001090" }, - "Cambodia": { - "text": "Cambodia", + "Cambodia [GAZ:00006888]": { + "text": "Cambodia [GAZ:00006888]", + "description": "A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand.", "meaning": "GAZ:00006888" }, - "Cameroon": { - "text": "Cameroon", + "Cameroon [GAZ:00001093]": { + "text": "Cameroon [GAZ:00001093]", + "description": "A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts.", "meaning": "GAZ:00001093" }, - "Canada": { - "text": "Canada", + "Canada [GAZ:00002560]": { + "text": "Canada [GAZ:00002560]", + "description": "A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada.", "meaning": "GAZ:00002560" }, - "Cape Verde": { - "text": "Cape Verde", + "Cape Verde [GAZ:00001227]": { + "text": "Cape Verde [GAZ:00001227]", + "description": "A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias).", "meaning": "GAZ:00001227" }, - "Cayman Islands": { - "text": "Cayman Islands", + "Cayman Islands [GAZ:00003986]": { + "text": "Cayman Islands [GAZ:00003986]", + "description": "A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts.", "meaning": "GAZ:00003986" }, - "Central African Republic": { - "text": "Central African Republic", + "Central African Republic [GAZ:00001089]": { + "text": "Central African Republic [GAZ:00001089]", + "description": "A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures).", "meaning": "GAZ:00001089" }, - "Chad": { - "text": "Chad", + "Chad [GAZ:00000586]": { + "text": "Chad [GAZ:00000586]", + "description": "A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change.", "meaning": "GAZ:00000586" }, - "Chile": { - "text": "Chile", + "Chile [GAZ:00002825]": { + "text": "Chile [GAZ:00002825]", + "description": "A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10.", "meaning": "GAZ:00002825" }, - "China": { - "text": "China", + "China [GAZ:00002845]": { + "text": "China [GAZ:00002845]", + "description": "A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.", "meaning": "GAZ:00002845" }, - "Christmas Island": { - "text": "Christmas Island", + "Christmas Island [GAZ:00005915]": { + "text": "Christmas Island [GAZ:00005915]", + "description": "An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain.", "meaning": "GAZ:00005915" }, - "Clipperton Island": { - "text": "Clipperton Island", + "Clipperton Island [GAZ:00005838]": { + "text": "Clipperton Island [GAZ:00005838]", + "description": "A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica.", "meaning": "GAZ:00005838" }, - "Cocos Islands": { - "text": "Cocos Islands", + "Cocos Islands [GAZ:00009721]": { + "text": "Cocos Islands [GAZ:00009721]", + "description": "Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group.", "meaning": "GAZ:00009721" }, - "Colombia": { - "text": "Colombia", + "Colombia [GAZ:00002929]": { + "text": "Colombia [GAZ:00002929]", + "description": "A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities.", "meaning": "GAZ:00002929" }, - "Comoros": { - "text": "Comoros", + "Comoros [GAZ:00005820]": { + "text": "Comoros [GAZ:00005820]", + "description": "An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique.", "meaning": "GAZ:00005820" }, - "Cook Islands": { - "text": "Cook Islands", + "Cook Islands [GAZ:00053798]": { + "text": "Cook Islands [GAZ:00053798]", + "description": "A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean.", "meaning": "GAZ:00053798" }, - "Coral Sea Islands": { - "text": "Coral Sea Islands", + "Coral Sea Islands [GAZ:00005917]": { + "text": "Coral Sea Islands [GAZ:00005917]", + "description": "A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups.", "meaning": "GAZ:00005917" }, - "Costa Rica": { - "text": "Costa Rica", + "Costa Rica [GAZ:00002901]": { + "text": "Costa Rica [GAZ:00002901]", + "description": "A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons.", "meaning": "GAZ:00002901" }, - "Cote d'Ivoire": { - "text": "Cote d'Ivoire", + "Cote d'Ivoire [GAZ:00000906]": { + "text": "Cote d'Ivoire [GAZ:00000906]", + "description": "A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments.", "meaning": "GAZ:00000906" }, - "Croatia": { - "text": "Croatia", + "Croatia [GAZ:00002719]": { + "text": "Croatia [GAZ:00002719]", + "description": "A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district.", "meaning": "GAZ:00002719" }, - "Cuba": { - "text": "Cuba", + "Cuba [GAZ:00003762]": { + "text": "Cuba [GAZ:00003762]", + "description": "A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba.", "meaning": "GAZ:00003762" }, - "Curacao": { - "text": "Curacao", + "Curacao [GAZ:00012582]": { + "text": "Curacao [GAZ:00012582]", + "description": "One of five island areas of the Netherlands Antilles.", "meaning": "GAZ:00012582" }, - "Cyprus": { - "text": "Cyprus", + "Cyprus [GAZ:00004006]": { + "text": "Cyprus [GAZ:00004006]", + "description": "The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west.", "meaning": "GAZ:00004006" }, - "Czech Republic": { - "text": "Czech Republic", + "Czech Republic [GAZ:00002954]": { + "text": "Czech Republic [GAZ:00002954]", + "description": "A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named \"Little Districts\" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices.", "meaning": "GAZ:00002954" }, - "Democratic Republic of the Congo": { - "text": "Democratic Republic of the Congo", + "Democratic Republic of the Congo [GAZ:00001086]": { + "text": "Democratic Republic of the Congo [GAZ:00001086]", + "description": "A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones.", "meaning": "GAZ:00001086" }, - "Denmark": { - "text": "Denmark", + "Denmark [GAZ:00005852]": { + "text": "Denmark [GAZ:00005852]", + "description": "That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago.", "meaning": "GAZ:00005852" }, - "Djibouti": { - "text": "Djibouti", + "Djibouti [GAZ:00000582]": { + "text": "Djibouti [GAZ:00000582]", + "description": "A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts.", "meaning": "GAZ:00000582" }, - "Dominica": { - "text": "Dominica", + "Dominica [GAZ:00006890]": { + "text": "Dominica [GAZ:00006890]", + "description": "An island nation in the Caribbean Sea. Dominica is divided into ten parishes.", "meaning": "GAZ:00006890" }, - "Dominican Republic": { - "text": "Dominican Republic", + "Dominican Republic [GAZ:00003952]": { + "text": "Dominican Republic [GAZ:00003952]", + "description": "A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio).", "meaning": "GAZ:00003952" }, - "Ecuador": { - "text": "Ecuador", + "Ecuador [GAZ:00002912]": { + "text": "Ecuador [GAZ:00002912]", + "description": "A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias).", "meaning": "GAZ:00002912" }, - "Egypt": { - "text": "Egypt", + "Egypt [GAZ:00003934]": { + "text": "Egypt [GAZ:00003934]", + "description": "A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes).", "meaning": "GAZ:00003934" }, - "El Salvador": { - "text": "El Salvador", + "El Salvador [GAZ:00002935]": { + "text": "El Salvador [GAZ:00002935]", + "description": "A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios).", "meaning": "GAZ:00002935" }, - "Equatorial Guinea": { - "text": "Equatorial Guinea", + "Equatorial Guinea [GAZ:00001091]": { + "text": "Equatorial Guinea [GAZ:00001091]", + "description": "A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts.", "meaning": "GAZ:00001091" }, - "Eritrea": { - "text": "Eritrea", + "Eritrea [GAZ:00000581]": { + "text": "Eritrea [GAZ:00000581]", + "description": "A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts (\"sub-zobas\").", "meaning": "GAZ:00000581" }, - "Estonia": { - "text": "Estonia", + "Estonia [GAZ:00002959]": { + "text": "Estonia [GAZ:00002959]", + "description": "A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities.", "meaning": "GAZ:00002959" }, - "Eswatini": { - "text": "Eswatini", + "Eswatini [GAZ:00001099]": { + "text": "Eswatini [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", "meaning": "GAZ:00001099" }, - "Ethiopia": { - "text": "Ethiopia", + "Ethiopia [GAZ:00000567]": { + "text": "Ethiopia [GAZ:00000567]", + "description": "A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas.", "meaning": "GAZ:00000567" }, - "Europa Island": { - "text": "Europa Island", + "Europa Island [GAZ:00005811]": { + "text": "Europa Island [GAZ:00005811]", + "description": "A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique.", "meaning": "GAZ:00005811" }, - "Falkland Islands (Islas Malvinas)": { - "text": "Falkland Islands (Islas Malvinas)", + "Falkland Islands (Islas Malvinas) [GAZ:00001412]": { + "text": "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "description": "An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands.", "meaning": "GAZ:00001412" }, - "Faroe Islands": { - "text": "Faroe Islands", + "Faroe Islands [GAZ:00059206]": { + "text": "Faroe Islands [GAZ:00059206]", + "description": "An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie.", "meaning": "GAZ:00059206" }, - "Fiji": { - "text": "Fiji", + "Fiji [GAZ:00006891]": { + "text": "Fiji [GAZ:00006891]", + "description": "An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population.", "meaning": "GAZ:00006891" }, - "Finland": { - "text": "Finland", + "Finland [GAZ:00002937]": { + "text": "Finland [GAZ:00002937]", + "description": "A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta).", "meaning": "GAZ:00002937" }, - "France": { - "text": "France", + "France [GAZ:00003940]": { + "text": "France [GAZ:00003940]", + "description": "A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments.", "meaning": "GAZ:00003940" }, - "French Guiana": { - "text": "French Guiana", + "French Guiana [GAZ:00002516]": { + "text": "French Guiana [GAZ:00002516]", + "description": "An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes.", "meaning": "GAZ:00002516" }, - "French Polynesia": { - "text": "French Polynesia", + "French Polynesia [GAZ:00002918]": { + "text": "French Polynesia [GAZ:00002918]", + "description": "A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives).", "meaning": "GAZ:00002918" }, - "French Southern and Antarctic Lands": { - "text": "French Southern and Antarctic Lands", + "French Southern and Antarctic Lands [GAZ:00003753]": { + "text": "French Southern and Antarctic Lands [GAZ:00003753]", + "description": "The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts.", "meaning": "GAZ:00003753" }, - "Gabon": { - "text": "Gabon", + "Gabon [GAZ:00001092]": { + "text": "Gabon [GAZ:00001092]", + "description": "A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments.", "meaning": "GAZ:00001092" }, - "Gambia": { - "text": "Gambia", + "Gambia [GAZ:00000907]": { + "text": "Gambia [GAZ:00000907]", + "description": "A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts.", "meaning": "GAZ:00000907" }, - "Gaza Strip": { - "text": "Gaza Strip", + "Gaza Strip [GAZ:00009571]": { + "text": "Gaza Strip [GAZ:00009571]", + "description": "A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine.", "meaning": "GAZ:00009571" }, - "Georgia": { - "text": "Georgia", + "Georgia [GAZ:00004942]": { + "text": "Georgia [GAZ:00004942]", + "description": "A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni).", "meaning": "GAZ:00004942" }, - "Germany": { - "text": "Germany", + "Germany [GAZ:00002646]": { + "text": "Germany [GAZ:00002646]", + "description": "A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte).", "meaning": "GAZ:00002646" }, - "Ghana": { - "text": "Ghana", + "Ghana [GAZ:00000908]": { + "text": "Ghana [GAZ:00000908]", + "description": "A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts.", "meaning": "GAZ:00000908" }, - "Gibraltar": { - "text": "Gibraltar", + "Gibraltar [GAZ:00003987]": { + "text": "Gibraltar [GAZ:00003987]", + "description": "A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north.", "meaning": "GAZ:00003987" }, - "Glorioso Islands": { - "text": "Glorioso Islands", + "Glorioso Islands [GAZ:00005808]": { + "text": "Glorioso Islands [GAZ:00005808]", + "description": "A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar.", "meaning": "GAZ:00005808" }, - "Greece": { - "text": "Greece", + "Greece [GAZ:00002945]": { + "text": "Greece [GAZ:00002945]", + "description": "A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia.", "meaning": "GAZ:00002945" }, - "Greenland": { - "text": "Greenland", + "Greenland [GAZ:00001507]": { + "text": "Greenland [GAZ:00001507]", + "description": "A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago.", "meaning": "GAZ:00001507" }, - "Grenada": { - "text": "Grenada", + "Grenada [GAZ:02000573]": { + "text": "Grenada [GAZ:02000573]", + "description": "An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020.", "meaning": "GAZ:02000573" }, - "Guadeloupe": { - "text": "Guadeloupe", + "Guadeloupe [GAZ:00067142]": { + "text": "Guadeloupe [GAZ:00067142]", + "description": "An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica.", "meaning": "GAZ:00067142" }, - "Guam": { - "text": "Guam", + "Guam [GAZ:00003706]": { + "text": "Guam [GAZ:00003706]", + "description": "An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia.", "meaning": "GAZ:00003706" }, - "Guatemala": { - "text": "Guatemala", + "Guatemala [GAZ:00002936]": { + "text": "Guatemala [GAZ:00002936]", + "description": "A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios).", "meaning": "GAZ:00002936" }, - "Guernsey": { - "text": "Guernsey", + "Guernsey [GAZ:00001550]": { + "text": "Guernsey [GAZ:00001550]", + "description": "A British Crown Dependency in the English Channel off the coast of Normandy.", "meaning": "GAZ:00001550" }, - "Guinea": { - "text": "Guinea", + "Guinea [GAZ:00000909]": { + "text": "Guinea [GAZ:00000909]", + "description": "A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip.", "meaning": "GAZ:00000909" }, - "Guinea-Bissau": { - "text": "Guinea-Bissau", + "Guinea-Bissau [GAZ:00000910]": { + "text": "Guinea-Bissau [GAZ:00000910]", + "description": "A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea.", "meaning": "GAZ:00000910" }, - "Guyana": { - "text": "Guyana", + "Guyana [GAZ:00002522]": { + "text": "Guyana [GAZ:00002522]", + "description": "A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils.", "meaning": "GAZ:00002522" }, - "Haiti": { - "text": "Haiti", + "Haiti [GAZ:00003953]": { + "text": "Haiti [GAZ:00003953]", + "description": "A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions.", "meaning": "GAZ:00003953" }, - "Heard Island and McDonald Islands": { - "text": "Heard Island and McDonald Islands", + "Heard Island and McDonald Islands [GAZ:00009718]": { + "text": "Heard Island and McDonald Islands [GAZ:00009718]", + "description": "An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica.", "meaning": "GAZ:00009718" }, - "Honduras": { - "text": "Honduras", + "Honduras [GAZ:00002894]": { + "text": "Honduras [GAZ:00002894]", + "description": "A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan.", "meaning": "GAZ:00002894" }, - "Hong Kong": { - "text": "Hong Kong", + "Hong Kong [GAZ:00003203]": { + "text": "Hong Kong [GAZ:00003203]", + "description": "A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997.", "meaning": "GAZ:00003203" }, - "Howland Island": { - "text": "Howland Island", + "Howland Island [GAZ:00007120]": { + "text": "Howland Island [GAZ:00007120]", + "description": "An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands.", "meaning": "GAZ:00007120" }, - "Hungary": { - "text": "Hungary", + "Hungary [GAZ:00002952]": { + "text": "Hungary [GAZ:00002952]", + "description": "A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary.", "meaning": "GAZ:00002952" }, - "Iceland": { - "text": "Iceland", + "Iceland [GAZ:00000843]": { + "text": "Iceland [GAZ:00000843]", + "description": "A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland.", "meaning": "GAZ:00000843" }, - "India": { - "text": "India", + "India [GAZ:00002839]": { + "text": "India [GAZ:00002839]", + "description": "A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages.", "meaning": "GAZ:00002839" }, - "Indonesia": { - "text": "Indonesia", + "Indonesia [GAZ:00003727]": { + "text": "Indonesia [GAZ:00003727]", + "description": "An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan).", "meaning": "GAZ:00003727" }, - "Iran": { - "text": "Iran", + "Iran [GAZ:00004474]": { + "text": "Iran [GAZ:00004474]", + "description": "A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan).", "meaning": "GAZ:00004474" }, - "Iraq": { - "text": "Iraq", + "Iraq [GAZ:00004483]": { + "text": "Iraq [GAZ:00004483]", + "description": "A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts).", "meaning": "GAZ:00004483" }, - "Ireland": { - "text": "Ireland", + "Ireland [GAZ:00002943]": { + "text": "Ireland [GAZ:00002943]", + "description": "A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 \"county-level\" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a \"city council\"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties.", "meaning": "GAZ:00002943" }, - "Isle of Man": { - "text": "Isle of Man", + "Isle of Man [GAZ:00052477]": { + "text": "Isle of Man [GAZ:00052477]", + "description": "A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations.", "meaning": "GAZ:00052477" }, - "Israel": { - "text": "Israel", + "Israel [GAZ:00002476]": { + "text": "Israel [GAZ:00002476]", + "description": "A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions.", "meaning": "GAZ:00002476" }, - "Italy": { - "text": "Italy", + "Italy [GAZ:00002650]": { + "text": "Italy [GAZ:00002650]", + "description": "A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni).", "meaning": "GAZ:00002650" }, - "Jamaica": { - "text": "Jamaica", + "Jamaica [GAZ:00003781]": { + "text": "Jamaica [GAZ:00003781]", + "description": "A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance.", "meaning": "GAZ:00003781" }, - "Jan Mayen": { - "text": "Jan Mayen", + "Jan Mayen [GAZ:00005853]": { + "text": "Jan Mayen [GAZ:00005853]", + "description": "A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.", "meaning": "GAZ:00005853" }, - "Japan": { - "text": "Japan", + "Japan [GAZ:00002747]": { + "text": "Japan [GAZ:00002747]", + "description": "An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.", "meaning": "GAZ:00002747" }, - "Jarvis Island": { - "text": "Jarvis Island", + "Jarvis Island [GAZ:00007118]": { + "text": "Jarvis Island [GAZ:00007118]", + "description": "An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount.", "meaning": "GAZ:00007118" }, - "Jersey": { - "text": "Jersey", + "Jersey [GAZ:00001551]": { + "text": "Jersey [GAZ:00001551]", + "description": "A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq.", "meaning": "GAZ:00001551" }, - "Johnston Atoll": { - "text": "Johnston Atoll", + "Johnston Atoll [GAZ:00007114]": { + "text": "Johnston Atoll [GAZ:00007114]", + "description": "A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount.", "meaning": "GAZ:00007114" }, - "Jordan": { - "text": "Jordan", + "Jordan [GAZ:00002473]": { + "text": "Jordan [GAZ:00002473]", + "description": "A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias.", "meaning": "GAZ:00002473" }, - "Juan de Nova Island": { - "text": "Juan de Nova Island", + "Juan de Nova Island [GAZ:00005809]": { + "text": "Juan de Nova Island [GAZ:00005809]", + "description": "A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique.", "meaning": "GAZ:00005809" }, - "Kazakhstan": { - "text": "Kazakhstan", + "Kazakhstan [GAZ:00004999]": { + "text": "Kazakhstan [GAZ:00004999]", + "description": "A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions.", "meaning": "GAZ:00004999" }, - "Kenya": { - "text": "Kenya", + "Kenya [GAZ:00001101]": { + "text": "Kenya [GAZ:00001101]", + "description": "A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province.", "meaning": "GAZ:00001101" }, - "Kerguelen Archipelago": { - "text": "Kerguelen Archipelago", + "Kerguelen Archipelago [GAZ:00005682]": { + "text": "Kerguelen Archipelago [GAZ:00005682]", + "description": "A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap.", "meaning": "GAZ:00005682" }, - "Kingman Reef": { - "text": "Kingman Reef", + "Kingman Reef [GAZ:00007116]": { + "text": "Kingman Reef [GAZ:00007116]", + "description": "A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount.", "meaning": "GAZ:00007116" }, - "Kiribati": { - "text": "Kiribati", + "Kiribati [GAZ:00006894]": { + "text": "Kiribati [GAZ:00006894]", + "description": "An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea).", "meaning": "GAZ:00006894" }, - "Kosovo": { - "text": "Kosovo", + "Kosovo [GAZ:00011337]": { + "text": "Kosovo [GAZ:00011337]", + "description": "A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija.", "meaning": "GAZ:00011337" }, - "Kuwait": { - "text": "Kuwait", + "Kuwait [GAZ:00005285]": { + "text": "Kuwait [GAZ:00005285]", + "description": "A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah).", "meaning": "GAZ:00005285" }, - "Kyrgyzstan": { - "text": "Kyrgyzstan", + "Kyrgyzstan [GAZ:00006893]": { + "text": "Kyrgyzstan [GAZ:00006893]", + "description": "A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions).", "meaning": "GAZ:00006893" }, - "Laos": { - "text": "Laos", + "Laos [GAZ:00006889]": { + "text": "Laos [GAZ:00006889]", + "description": "A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang).", "meaning": "GAZ:00006889" }, - "Latvia": { - "text": "Latvia", + "Latvia [GAZ:00002958]": { + "text": "Latvia [GAZ:00002958]", + "description": "A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions.", "meaning": "GAZ:00002958" }, - "Lebanon": { - "text": "Lebanon", + "Lebanon [GAZ:00002478]": { + "text": "Lebanon [GAZ:00002478]", + "description": "A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa).", "meaning": "GAZ:00002478" }, - "Lesotho": { - "text": "Lesotho", + "Lesotho [GAZ:00001098]": { + "text": "Lesotho [GAZ:00001098]", + "description": "A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils.", "meaning": "GAZ:00001098" }, - "Liberia": { - "text": "Liberia", + "Liberia [GAZ:00000911]": { + "text": "Liberia [GAZ:00000911]", + "description": "A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean.", "meaning": "GAZ:00000911" }, - "Libya": { - "text": "Libya", + "Libya [GAZ:00000566]": { + "text": "Libya [GAZ:00000566]", + "description": "A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s.", "meaning": "GAZ:00000566" }, - "Liechtenstein": { - "text": "Liechtenstein", + "Liechtenstein [GAZ:00003858]": { + "text": "Liechtenstein [GAZ:00003858]", + "description": "A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county).", "meaning": "GAZ:00003858" }, - "Line Islands": { - "text": "Line Islands", + "Line Islands [GAZ:00007144]": { + "text": "Line Islands [GAZ:00007144]", + "description": "A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands.", "meaning": "GAZ:00007144" }, - "Lithuania": { - "text": "Lithuania", + "Lithuania [GAZ:00002960]": { + "text": "Lithuania [GAZ:00002960]", + "description": "A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos).", "meaning": "GAZ:00002960" }, - "Luxembourg": { - "text": "Luxembourg", + "Luxembourg [GAZ:00002947]": { + "text": "Luxembourg [GAZ:00002947]", + "description": "A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest.", "meaning": "GAZ:00002947" }, - "Macau": { - "text": "Macau", + "Macau [GAZ:00003202]": { + "text": "Macau [GAZ:00003202]", + "description": "One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China.", "meaning": "GAZ:00003202" }, - "Madagascar": { - "text": "Madagascar", + "Madagascar [GAZ:00001108]": { + "text": "Madagascar [GAZ:00001108]", + "description": "An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany.", "meaning": "GAZ:00001108" }, - "Malawi": { - "text": "Malawi", + "Malawi [GAZ:00001105]": { + "text": "Malawi [GAZ:00001105]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", "meaning": "GAZ:00001105" }, - "Malaysia": { - "text": "Malaysia", + "Malaysia [GAZ:00003902]": { + "text": "Malaysia [GAZ:00003902]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", "meaning": "GAZ:00003902" }, - "Maldives": { - "text": "Maldives", + "Maldives [GAZ:00006924]": { + "text": "Maldives [GAZ:00006924]", + "description": "An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2.", "meaning": "GAZ:00006924" }, - "Mali": { - "text": "Mali", + "Mali [GAZ:00000584]": { + "text": "Mali [GAZ:00000584]", + "description": "A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements.", "meaning": "GAZ:00000584" }, - "Malta": { - "text": "Malta", + "Malta [GAZ:00004017]": { + "text": "Malta [GAZ:00004017]", + "description": "A Southern European country and consists of an archipelago situated centrally in the Mediterranean.", "meaning": "GAZ:00004017" }, - "Marshall Islands": { - "text": "Marshall Islands", + "Marshall Islands [GAZ:00007161]": { + "text": "Marshall Islands [GAZ:00007161]", + "description": "An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning \"sunrise\" and \"sunset\" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated.", "meaning": "GAZ:00007161" }, - "Martinique": { - "text": "Martinique", + "Martinique [GAZ:00067143]": { + "text": "Martinique [GAZ:00067143]", + "description": "An island and an overseas department/region and single territorial collectivity of France.", "meaning": "GAZ:00067143" }, - "Mauritania": { - "text": "Mauritania", + "Mauritania [GAZ:00000583]": { + "text": "Mauritania [GAZ:00000583]", + "description": "A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements).", "meaning": "GAZ:00000583" }, - "Mauritius": { - "text": "Mauritius", + "Mauritius [GAZ:00003745]": { + "text": "Mauritius [GAZ:00003745]", + "description": "An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands.", "meaning": "GAZ:00003745" }, - "Mayotte": { - "text": "Mayotte", + "Mayotte [GAZ:00003943]": { + "text": "Mayotte [GAZ:00003943]", + "description": "An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two.", "meaning": "GAZ:00003943" }, - "Mexico": { - "text": "Mexico", + "Mexico [GAZ:00002852]": { + "text": "Mexico [GAZ:00002852]", + "description": "A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City.", "meaning": "GAZ:00002852" }, - "Micronesia": { - "text": "Micronesia", + "Micronesia [GAZ:00005862]": { + "text": "Micronesia [GAZ:00005862]", + "description": "A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east.", "meaning": "GAZ:00005862" }, - "Midway Islands": { - "text": "Midway Islands", + "Midway Islands [GAZ:00007112]": { + "text": "Midway Islands [GAZ:00007112]", + "description": "A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior.", "meaning": "GAZ:00007112" }, - "Moldova": { - "text": "Moldova", + "Moldova [GAZ:00003897]": { + "text": "Moldova [GAZ:00003897]", + "description": "A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic.", "meaning": "GAZ:00003897" }, - "Monaco": { - "text": "Monaco", + "Monaco [GAZ:00003857]": { + "text": "Monaco [GAZ:00003857]", + "description": "A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards.", "meaning": "GAZ:00003857" }, - "Mongolia": { - "text": "Mongolia", + "Mongolia [GAZ:00008744]": { + "text": "Mongolia [GAZ:00008744]", + "description": "A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status.", "meaning": "GAZ:00008744" }, - "Montenegro": { - "text": "Montenegro", + "Montenegro [GAZ:00006898]": { + "text": "Montenegro [GAZ:00006898]", + "description": "A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality.", "meaning": "GAZ:00006898" }, - "Montserrat": { - "text": "Montserrat", + "Montserrat [GAZ:00003988]": { + "text": "Montserrat [GAZ:00003988]", + "description": "A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes.", "meaning": "GAZ:00003988" }, - "Morocco": { - "text": "Morocco", + "Morocco [GAZ:00000565]": { + "text": "Morocco [GAZ:00000565]", + "description": "A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of \"Saguia el-Hamra\" and \"Rio de Oro\" is disputed.", "meaning": "GAZ:00000565" }, - "Mozambique": { - "text": "Mozambique", + "Mozambique [GAZ:00001100]": { + "text": "Mozambique [GAZ:00001100]", + "description": "A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in \"Postos Administrativos\" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration.", "meaning": "GAZ:00001100" }, - "Myanmar": { - "text": "Myanmar", + "Myanmar [GAZ:00006899]": { + "text": "Myanmar [GAZ:00006899]", + "description": "A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages.", "meaning": "GAZ:00006899" }, - "Namibia": { - "text": "Namibia", + "Namibia [GAZ:00001096]": { + "text": "Namibia [GAZ:00001096]", + "description": "A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies.", "meaning": "GAZ:00001096" }, - "Nauru": { - "text": "Nauru", + "Nauru [GAZ:00006900]": { + "text": "Nauru [GAZ:00006900]", + "description": "An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies.", "meaning": "GAZ:00006900" }, - "Navassa Island": { - "text": "Navassa Island", + "Navassa Island [GAZ:00007119]": { + "text": "Navassa Island [GAZ:00007119]", + "description": "A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti.", "meaning": "GAZ:00007119" }, - "Nepal": { - "text": "Nepal", + "Nepal [GAZ:00004399]": { + "text": "Nepal [GAZ:00004399]", + "description": "A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the \"Chicken's Neck\". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions.", "meaning": "GAZ:00004399" }, - "Netherlands": { - "text": "Netherlands", + "Netherlands [GAZ:00002946]": { + "text": "Netherlands [GAZ:00002946]", + "description": "The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007).", "meaning": "GAZ:00002946" }, - "New Caledonia": { - "text": "New Caledonia", + "New Caledonia [GAZ:00005206]": { + "text": "New Caledonia [GAZ:00005206]", + "description": "A \"sui generis collectivity\" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes.", "meaning": "GAZ:00005206" }, - "New Zealand": { - "text": "New Zealand", + "New Zealand [GAZ:00000469]": { + "text": "New Zealand [GAZ:00000469]", + "description": "A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands.", "meaning": "GAZ:00000469" }, - "Nicaragua": { - "text": "Nicaragua", + "Nicaragua [GAZ:00002978]": { + "text": "Nicaragua [GAZ:00002978]", + "description": "A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya.", "meaning": "GAZ:00002978" }, - "Niger": { - "text": "Niger", + "Niger [GAZ:00000585]": { + "text": "Niger [GAZ:00000585]", + "description": "A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes.", "meaning": "GAZ:00000585" }, - "Nigeria": { - "text": "Nigeria", + "Nigeria [GAZ:00000912]": { + "text": "Nigeria [GAZ:00000912]", + "description": "A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs).", "meaning": "GAZ:00000912" }, - "Niue": { - "text": "Niue", + "Niue [GAZ:00006902]": { + "text": "Niue [GAZ:00006902]", + "description": "An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state.", "meaning": "GAZ:00006902" }, - "Norfolk Island": { - "text": "Norfolk Island", + "Norfolk Island [GAZ:00005908]": { + "text": "Norfolk Island [GAZ:00005908]", + "description": "A Territory of Australia that includes Norfolk Island and neighboring islands.", "meaning": "GAZ:00005908" }, - "North Korea": { - "text": "North Korea", + "North Korea [GAZ:00002801]": { + "text": "North Korea [GAZ:00002801]", + "description": "A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia.", "meaning": "GAZ:00002801" }, - "North Macedonia": { - "text": "North Macedonia", + "North Macedonia [GAZ:00006895]": { + "text": "North Macedonia [GAZ:00006895]", + "description": "A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts.", "meaning": "GAZ:00006895" }, - "North Sea": { - "text": "North Sea", + "North Sea [GAZ:00002284]": { + "text": "North Sea [GAZ:00002284]", + "description": "A sea situated between the eastern coasts of the British Isles and the western coast of Europe.", "meaning": "GAZ:00002284" }, - "Northern Mariana Islands": { - "text": "Northern Mariana Islands", + "Northern Mariana Islands [GAZ:00003958]": { + "text": "Northern Mariana Islands [GAZ:00003958]", + "description": "A group of 15 islands about three-quarters of the way from Hawaii to the Philippines.", "meaning": "GAZ:00003958" }, - "Norway": { - "text": "Norway", + "Norway [GAZ:00002699]": { + "text": "Norway [GAZ:00002699]", + "description": "A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom.", "meaning": "GAZ:00002699" }, - "Oman": { - "text": "Oman", + "Oman [GAZ:00005283]": { + "text": "Oman [GAZ:00005283]", + "description": "A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat).", "meaning": "GAZ:00005283" }, - "Pakistan": { - "text": "Pakistan", + "Pakistan [GAZ:00005246]": { + "text": "Pakistan [GAZ:00005246]", + "description": "A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan.", "meaning": "GAZ:00005246" }, - "Palau": { - "text": "Palau", + "Palau [GAZ:00006905]": { + "text": "Palau [GAZ:00006905]", + "description": "A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines.", "meaning": "GAZ:00006905" }, - "Panama": { - "text": "Panama", + "Panama [GAZ:00002892]": { + "text": "Panama [GAZ:00002892]", + "description": "The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports.", "meaning": "GAZ:00002892" }, - "Papua New Guinea": { - "text": "Papua New Guinea", + "Papua New Guinea [GAZ:00003922]": { + "text": "Papua New Guinea [GAZ:00003922]", + "description": "A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia).", "meaning": "GAZ:00003922" }, - "Paracel Islands": { - "text": "Paracel Islands", + "Paracel Islands [GAZ:00010832]": { + "text": "Paracel Islands [GAZ:00010832]", + "description": "A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines.", "meaning": "GAZ:00010832" }, - "Paraguay": { - "text": "Paraguay", + "Paraguay [GAZ:00002933]": { + "text": "Paraguay [GAZ:00002933]", + "description": "A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts.", "meaning": "GAZ:00002933" }, - "Peru": { - "text": "Peru", + "Peru [GAZ:00002932]": { + "text": "Peru [GAZ:00002932]", + "description": "A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao.", "meaning": "GAZ:00002932" }, - "Philippines": { - "text": "Philippines", + "Philippines [GAZ:00004525]": { + "text": "Philippines [GAZ:00004525]", + "description": "An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays.", "meaning": "GAZ:00004525" }, - "Pitcairn Islands": { - "text": "Pitcairn Islands", + "Pitcairn Islands [GAZ:00005867]": { + "text": "Pitcairn Islands [GAZ:00005867]", + "description": "A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia.", "meaning": "GAZ:00005867" }, - "Poland": { - "text": "Poland", + "Poland [GAZ:00002939]": { + "text": "Poland [GAZ:00002939]", + "description": "A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas.", "meaning": "GAZ:00002939" }, - "Portugal": { - "text": "Portugal", + "Portugal [GAZ:00004126]": { + "text": "Portugal [GAZ:00004126]", + "description": "That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands.", "meaning": "GAZ:00004126" }, - "Puerto Rico": { - "text": "Puerto Rico", + "Puerto Rico [GAZ:00006935]": { + "text": "Puerto Rico [GAZ:00006935]", + "description": "A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States).", "meaning": "GAZ:00006935" }, - "Qatar": { - "text": "Qatar", + "Qatar [GAZ:00005286]": { + "text": "Qatar [GAZ:00005286]", + "description": "An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts).", "meaning": "GAZ:00005286" }, - "Republic of the Congo": { - "text": "Republic of the Congo", + "Republic of the Congo [GAZ:00001088]": { + "text": "Republic of the Congo [GAZ:00001088]", + "description": "A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts.", "meaning": "GAZ:00001088" }, - "Reunion": { - "text": "Reunion", + "Reunion [GAZ:00003945]": { + "text": "Reunion [GAZ:00003945]", + "description": "An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island.", "meaning": "GAZ:00003945" }, - "Romania": { - "text": "Romania", + "Romania [GAZ:00002951]": { + "text": "Romania [GAZ:00002951]", + "description": "A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities).", "meaning": "GAZ:00002951" }, - "Ross Sea": { - "text": "Ross Sea", + "Ross Sea [GAZ:00023304]": { + "text": "Ross Sea [GAZ:00023304]", + "description": "A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW.", "meaning": "GAZ:00023304" }, - "Russia": { - "text": "Russia", + "Russia [GAZ:00002721]": { + "text": "Russia [GAZ:00002721]", + "description": "A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts.", "meaning": "GAZ:00002721" }, - "Rwanda": { - "text": "Rwanda", + "Rwanda [GAZ:00001087]": { + "text": "Rwanda [GAZ:00001087]", + "description": "A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge).", "meaning": "GAZ:00001087" }, - "Saint Helena": { - "text": "Saint Helena", + "Saint Helena [GAZ:00000849]": { + "text": "Saint Helena [GAZ:00000849]", + "description": "An island of volcanic origin and a British overseas territory in the South Atlantic Ocean.", "meaning": "GAZ:00000849" }, - "Saint Kitts and Nevis": { - "text": "Saint Kitts and Nevis", + "Saint Kitts and Nevis [GAZ:00006906]": { + "text": "Saint Kitts and Nevis [GAZ:00006906]", + "description": "A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis.", "meaning": "GAZ:00006906" }, - "Saint Lucia": { - "text": "Saint Lucia", + "Saint Lucia [GAZ:00006909]": { + "text": "Saint Lucia [GAZ:00006909]", + "description": "An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean.", "meaning": "GAZ:00006909" }, - "Saint Pierre and Miquelon": { - "text": "Saint Pierre and Miquelon", + "Saint Pierre and Miquelon [GAZ:00003942]": { + "text": "Saint Pierre and Miquelon [GAZ:00003942]", + "description": "An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985.", "meaning": "GAZ:00003942" }, - "Saint Martin": { - "text": "Saint Martin", + "Saint Martin [GAZ:00005841]": { + "text": "Saint Martin [GAZ:00005841]", + "description": "An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe.", "meaning": "GAZ:00005841" }, - "Saint Vincent and the Grenadines": { - "text": "Saint Vincent and the Grenadines", + "Saint Vincent and the Grenadines [GAZ:02000565]": { + "text": "Saint Vincent and the Grenadines [GAZ:02000565]", + "description": "An island nation in the Lesser Antilles chain of the Caribbean Sea.", "meaning": "GAZ:02000565" }, - "Samoa": { - "text": "Samoa", + "Samoa [GAZ:00006910]": { + "text": "Samoa [GAZ:00006910]", + "description": "A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts).", "meaning": "GAZ:00006910" }, - "San Marino": { - "text": "San Marino", + "San Marino [GAZ:00003102]": { + "text": "San Marino [GAZ:00003102]", + "description": "A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello).", "meaning": "GAZ:00003102" }, - "Sao Tome and Principe": { - "text": "Sao Tome and Principe", + "Sao Tome and Principe [GAZ:00006927]": { + "text": "Sao Tome and Principe [GAZ:00006927]", + "description": "An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29).", "meaning": "GAZ:00006927" }, - "Saudi Arabia": { - "text": "Saudi Arabia", + "Saudi Arabia [GAZ:00005279]": { + "text": "Saudi Arabia [GAZ:00005279]", + "description": "A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates.", "meaning": "GAZ:00005279" }, - "Senegal": { - "text": "Senegal", + "Senegal [GAZ:00000913]": { + "text": "Senegal [GAZ:00000913]", + "description": "A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales.", "meaning": "GAZ:00000913" }, - "Serbia": { - "text": "Serbia", + "Serbia [GAZ:00002957]": { + "text": "Serbia [GAZ:00002957]", + "description": "A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities).", "meaning": "GAZ:00002957" }, - "Seychelles": { - "text": "Seychelles", + "Seychelles [GAZ:00006922]": { + "text": "Seychelles [GAZ:00006922]", + "description": "An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands.", "meaning": "GAZ:00006922" }, - "Sierra Leone": { - "text": "Sierra Leone", + "Sierra Leone [GAZ:00000914]": { + "text": "Sierra Leone [GAZ:00000914]", + "description": "A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts.", "meaning": "GAZ:00000914" }, - "Singapore": { - "text": "Singapore", + "Singapore [GAZ:00003923]": { + "text": "Singapore [GAZ:00003923]", + "description": "An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role.", "meaning": "GAZ:00003923" }, - "Sint Maarten": { - "text": "Sint Maarten", + "Sint Maarten [GAZ:00012579]": { + "text": "Sint Maarten [GAZ:00012579]", + "description": "One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten.", "meaning": "GAZ:00012579" }, - "Slovakia": { - "text": "Slovakia", + "Slovakia [GAZ:00002956]": { + "text": "Slovakia [GAZ:00002956]", + "description": "A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts.", "meaning": "GAZ:00002956" }, - "Slovenia": { - "text": "Slovenia", + "Slovenia [GAZ:00002955]": { + "text": "Slovenia [GAZ:00002955]", + "description": "A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status.", "meaning": "GAZ:00002955" }, - "Solomon Islands": { - "text": "Solomon Islands", + "Solomon Islands [GAZ:00005275]": { + "text": "Solomon Islands [GAZ:00005275]", + "description": "A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal.", "meaning": "GAZ:00005275" }, - "Somalia": { - "text": "Somalia", + "Somalia [GAZ:00001104]": { + "text": "Somalia [GAZ:00001104]", + "description": "A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir.", "meaning": "GAZ:00001104" }, - "South Africa": { - "text": "South Africa", + "South Africa [GAZ:00001094]": { + "text": "South Africa [GAZ:00001094]", + "description": "A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities.", "meaning": "GAZ:00001094" }, - "South Georgia and the South Sandwich Islands": { - "text": "South Georgia and the South Sandwich Islands", + "South Georgia and the South Sandwich Islands [GAZ:00003990]": { + "text": "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "description": "A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE.", "meaning": "GAZ:00003990" }, - "South Korea": { - "text": "South Korea", + "South Korea [GAZ:00002802]": { + "text": "South Korea [GAZ:00002802]", + "description": "A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri).", "meaning": "GAZ:00002802" }, - "South Sudan": { - "text": "South Sudan", + "South Sudan [GAZ:00233439]": { + "text": "South Sudan [GAZ:00233439]", + "description": "A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel.", "meaning": "GAZ:00233439" }, - "Spain": { - "text": "Spain", + "Spain [GAZ:00000591]": { + "text": "Spain [GAZ:00000591]", + "description": "That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal.", "meaning": "GAZ:00000591" }, - "Spratly Islands": { - "text": "Spratly Islands", + "Spratly Islands [GAZ:00010831]": { + "text": "Spratly Islands [GAZ:00010831]", + "description": "A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines.", "meaning": "GAZ:00010831" }, - "Sri Lanka": { - "text": "Sri Lanka", + "Sri Lanka [GAZ:00003924]": { + "text": "Sri Lanka [GAZ:00003924]", + "description": "An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats.", "meaning": "GAZ:00003924" }, - "State of Palestine": { - "text": "State of Palestine", + "State of Palestine [GAZ:00002475]": { + "text": "State of Palestine [GAZ:00002475]", + "description": "The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates.", "meaning": "GAZ:00002475" }, - "Sudan": { - "text": "Sudan", + "Sudan [GAZ:00000560]": { + "text": "Sudan [GAZ:00000560]", + "description": "A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts.", "meaning": "GAZ:00000560" }, - "Suriname": { - "text": "Suriname", + "Suriname [GAZ:00002525]": { + "text": "Suriname [GAZ:00002525]", + "description": "A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten.", "meaning": "GAZ:00002525" }, - "Svalbard": { - "text": "Svalbard", + "Svalbard [GAZ:00005396]": { + "text": "Svalbard [GAZ:00005396]", + "description": "An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole.", "meaning": "GAZ:00005396" }, - "Swaziland": { - "text": "Swaziland", - "meaning": "GAZ:00001099" - }, - "Sweden": { - "text": "Sweden", + "Sweden [GAZ:00002729]": { + "text": "Sweden [GAZ:00002729]", + "description": "A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004.", "meaning": "GAZ:00002729" }, - "Switzerland": { - "text": "Switzerland", + "Switzerland [GAZ:00002941]": { + "text": "Switzerland [GAZ:00002941]", + "description": "A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy.", "meaning": "GAZ:00002941" }, - "Syria": { - "text": "Syria", + "Syria [GAZ:00002474]": { + "text": "Syria [GAZ:00002474]", + "description": "A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia).", "meaning": "GAZ:00002474" }, - "Taiwan": { - "text": "Taiwan", + "Taiwan [GAZ:00005341]": { + "text": "Taiwan [GAZ:00005341]", + "description": "A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities.", "meaning": "GAZ:00005341" }, - "Tajikistan": { - "text": "Tajikistan", + "Tajikistan [GAZ:00006912]": { + "text": "Tajikistan [GAZ:00006912]", + "description": "A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion).", "meaning": "GAZ:00006912" }, - "Tanzania": { - "text": "Tanzania", + "Tanzania [GAZ:00001103]": { + "text": "Tanzania [GAZ:00001103]", + "description": "A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities).", "meaning": "GAZ:00001103" }, - "Thailand": { - "text": "Thailand", + "Thailand [GAZ:00003744]": { + "text": "Thailand [GAZ:00003744]", + "description": "A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province.", "meaning": "GAZ:00003744" }, - "Timor-Leste": { - "text": "Timor-Leste", + "Timor-Leste [GAZ:00006913]": { + "text": "Timor-Leste [GAZ:00006913]", + "description": "A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets.", "meaning": "GAZ:00006913" }, - "Togo": { - "text": "Togo", + "Togo [GAZ:00000915]": { + "text": "Togo [GAZ:00000915]", + "description": "A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located.", "meaning": "GAZ:00000915" }, - "Tokelau": { - "text": "Tokelau", + "Tokelau [GAZ:00260188]": { + "text": "Tokelau [GAZ:00260188]", + "description": "A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi).", "meaning": "GAZ:00260188" }, - "Tonga": { - "text": "Tonga", + "Tonga [GAZ:00006916]": { + "text": "Tonga [GAZ:00006916]", + "description": "A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean.", "meaning": "GAZ:00006916" }, - "Trinidad and Tobago": { - "text": "Trinidad and Tobago", + "Trinidad and Tobago [GAZ:00003767]": { + "text": "Trinidad and Tobago [GAZ:00003767]", + "description": "An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands.", "meaning": "GAZ:00003767" }, - "Tromelin Island": { - "text": "Tromelin Island", + "Tromelin Island [GAZ:00005812]": { + "text": "Tromelin Island [GAZ:00005812]", + "description": "A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point.", "meaning": "GAZ:00005812" }, - "Tunisia": { - "text": "Tunisia", + "Tunisia [GAZ:00000562]": { + "text": "Tunisia [GAZ:00000562]", + "description": "A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 \"delegations\" or \"districts\" (mutamadiyat), and further subdivided into municipalities (shaykhats).", "meaning": "GAZ:00000562" }, - "Turkey": { - "text": "Turkey", + "Turkey [GAZ:00000558]": { + "text": "Turkey [GAZ:00000558]", + "description": "A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts.", "meaning": "GAZ:00000558" }, - "Turkmenistan": { - "text": "Turkmenistan", + "Turkmenistan [GAZ:00005018]": { + "text": "Turkmenistan [GAZ:00005018]", + "description": "A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city.", "meaning": "GAZ:00005018" }, - "Turks and Caicos Islands": { - "text": "Turks and Caicos Islands", + "Turks and Caicos Islands [GAZ:00003955]": { + "text": "Turks and Caicos Islands [GAZ:00003955]", + "description": "A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands.", "meaning": "GAZ:00003955" }, - "Tuvalu": { - "text": "Tuvalu", + "Tuvalu [GAZ:00009715]": { + "text": "Tuvalu [GAZ:00009715]", + "description": "A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia.", "meaning": "GAZ:00009715" }, - "United States of America": { - "text": "United States of America", + "United States of America [GAZ:00002459]": { + "text": "United States of America [GAZ:00002459]", + "description": "A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into \"census areas\"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a \"charter township\", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.", "meaning": "GAZ:00002459" }, - "Uganda": { - "text": "Uganda", + "Uganda [GAZ:00001102]": { + "text": "Uganda [GAZ:00001102]", + "description": "A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.", "meaning": "GAZ:00001102" }, - "Ukraine": { - "text": "Ukraine", + "Ukraine [GAZ:00002724]": { + "text": "Ukraine [GAZ:00002724]", + "description": "A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units.", "meaning": "GAZ:00002724" }, - "United Arab Emirates": { - "text": "United Arab Emirates", + "United Arab Emirates [GAZ:00005282]": { + "text": "United Arab Emirates [GAZ:00005282]", + "description": "A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain.", "meaning": "GAZ:00005282" }, - "United Kingdom": { - "text": "United Kingdom", + "United Kingdom [GAZ:00002637]": { + "text": "United Kingdom [GAZ:00002637]", + "description": "A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.", "meaning": "GAZ:00002637" }, - "Uruguay": { - "text": "Uruguay", + "Uruguay [GAZ:00002930]": { + "text": "Uruguay [GAZ:00002930]", + "description": "A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento).", "meaning": "GAZ:00002930" }, - "Uzbekistan": { - "text": "Uzbekistan", + "Uzbekistan [GAZ:00004979]": { + "text": "Uzbekistan [GAZ:00004979]", + "description": "A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar).", "meaning": "GAZ:00004979" }, - "Vanuatu": { - "text": "Vanuatu", + "Vanuatu [GAZ:00006918]": { + "text": "Vanuatu [GAZ:00006918]", + "description": "An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji.", "meaning": "GAZ:00006918" }, - "Venezuela": { - "text": "Venezuela", + "Venezuela [GAZ:00002931]": { + "text": "Venezuela [GAZ:00002931]", + "description": "A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias).", "meaning": "GAZ:00002931" }, - "Viet Nam": { - "text": "Viet Nam", + "Viet Nam [GAZ:00003756]": { + "text": "Viet Nam [GAZ:00003756]", + "description": "The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia.", "meaning": "GAZ:00003756" }, - "Virgin Islands": { - "text": "Virgin Islands", + "Virgin Islands [GAZ:00003959]": { + "text": "Virgin Islands [GAZ:00003959]", + "description": "A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts.", "meaning": "GAZ:00003959" }, - "Wake Island": { - "text": "Wake Island", + "Wake Island [GAZ:00007111]": { + "text": "Wake Island [GAZ:00007111]", + "description": "A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east).", "meaning": "GAZ:00007111" }, - "Wallis and Futuna": { - "text": "Wallis and Futuna", + "Wallis and Futuna [GAZ:00007191]": { + "text": "Wallis and Futuna [GAZ:00007191]", + "description": "A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets.", "meaning": "GAZ:00007191" }, - "West Bank": { - "text": "West Bank", + "West Bank [GAZ:00009572]": { + "text": "West Bank [GAZ:00009572]", + "description": "A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian \"islands\" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is \"pipelined\".", "meaning": "GAZ:00009572" }, - "Western Sahara": { - "text": "Western Sahara", + "Western Sahara [GAZ:00000564]": { + "text": "Western Sahara [GAZ:00000564]", + "description": "A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions.", "meaning": "GAZ:00000564" }, - "Yemen": { - "text": "Yemen", + "Yemen [GAZ:00005284]": { + "text": "Yemen [GAZ:00005284]", + "description": "A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001).", "meaning": "GAZ:00005284" }, - "Zambia": { - "text": "Zambia", + "Zambia [GAZ:00001107]": { + "text": "Zambia [GAZ:00001107]", + "description": "A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts.", "meaning": "GAZ:00001107" }, - "Zimbabwe": { - "text": "Zimbabwe", + "Zimbabwe [GAZ:00001106]": { + "text": "Zimbabwe [GAZ:00001106]", + "description": "A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities.", "meaning": "GAZ:00001106" } } }, - "geo_loc_name (state/province/territory) menu": { - "name": "geo_loc_name (state/province/territory) menu", - "from_schema": "https://example.com/GRDI", - "permissible_values": { - "Alberta": { - "text": "Alberta", - "meaning": "GAZ:00002566" - }, - "British Columbia": { - "text": "British Columbia", - "meaning": "GAZ:00002562" - }, - "Manitoba": { - "text": "Manitoba", - "meaning": "GAZ:00002571" - }, - "New Brunswick": { - "text": "New Brunswick", - "meaning": "GAZ:00002570" - }, - "Newfoundland and Labrador": { - "text": "Newfoundland and Labrador", - "meaning": "GAZ:00002567" - }, - "Northwest Territories": { - "text": "Northwest Territories", - "meaning": "GAZ:00002575" - }, - "Nova Scotia": { - "text": "Nova Scotia", - "meaning": "GAZ:00002565" - }, - "Nunavut": { - "text": "Nunavut", - "meaning": "GAZ:00002574" - }, - "Ontario": { - "text": "Ontario", - "meaning": "GAZ:00002563" - }, - "Prince Edward Island": { - "text": "Prince Edward Island", - "meaning": "GAZ:00002572" - }, - "Quebec": { - "text": "Quebec", - "meaning": "GAZ:00002569" - }, - "Saskatchewan": { - "text": "Saskatchewan", - "meaning": "GAZ:00002564" - }, - "Yukon": { - "text": "Yukon", - "meaning": "GAZ:00002576" - } - } - }, - "watershed shapefile availability menu": { - "name": "watershed shapefile availability menu", + "WatershedShapefileAvailabilityMenu": { + "name": "WatershedShapefileAvailabilityMenu", + "title": "watershed shapefile availability menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Available": { - "text": "Available", + "Available [GENEPIO:0100993]": { + "text": "Available [GENEPIO:0100993]", + "description": "A datum status in which the required datum is able to be used, obtained or selected.", "meaning": "GENEPIO:0100993" }, - "Unknown": { - "text": "Unknown", + "Unknown [GENEPIO:0100995]": { + "text": "Unknown [GENEPIO:0100995]", + "description": "A datum status in which the availabilty or presence of the required datum is not known.", "meaning": "GENEPIO:0100995" } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Severe acute respiratory syndrome coronavirus 2": { - "text": "Severe acute respiratory syndrome coronavirus 2", + "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]": { + "text": "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]", + "description": "A strain of the species Betacoronavirus pandemicum, a coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic.", "meaning": "NCBITaxon:2697049" } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Wastewater treatment efficiency assessment": { - "text": "Wastewater treatment efficiency assessment", + "Wastewater treatment efficiency assessment [GENEPIO:0100869]": { + "text": "Wastewater treatment efficiency assessment [GENEPIO:0100869]", + "description": "An environmental sampling strategy in which wastewater effluent is collected to assess the efficiency of wastewater treatment.", "meaning": "GENEPIO:0100869" }, - "Wastewater chemical surveillance": { - "text": "Wastewater chemical surveillance", + "Wastewater chemical surveillance [GENEPIO:0100870]": { + "text": "Wastewater chemical surveillance [GENEPIO:0100870]", + "description": "An environmental sampling strategy in which wastewater samples are collected to monitor for chemical contamination.", "meaning": "GENEPIO:0100870" }, - "Wastewater drug surveillance": { - "text": "Wastewater drug surveillance", + "Wastewater drug surveillance [GENEPIO:0100871]": { + "text": "Wastewater drug surveillance [GENEPIO:0100871]", + "description": "An environmental sampling strategy in which wastewater samples are collected to monitor for community drug use.", "meaning": "GENEPIO:0100871" }, - "Wastewater pathogen surveillance": { - "text": "Wastewater pathogen surveillance", + "Wastewater pathogen surveillance [GENEPIO:0100872]": { + "text": "Wastewater pathogen surveillance [GENEPIO:0100872]", + "description": "An environmental sampling strategy in which samples are collected to identify and/or monitor the presence of pathogens.", "meaning": "GENEPIO:0100872" }, - "Research": { - "text": "Research", + "Research [GENEPIO:0100003]": { + "text": "Research [GENEPIO:0100003]", + "description": "A sampling strategy in which samples are collected in order to perform research.", "meaning": "GENEPIO:0100003" }, - "Environmental survey (profiling)": { - "text": "Environmental survey (profiling)", + "Environmental survey (profiling) [GENEPIO:0100873]": { + "text": "Environmental survey (profiling) [GENEPIO:0100873]", + "description": "A research sampling strategy in which samples are collected in order to survey/profile entities in, or characteristics of, an environment.", "meaning": "GENEPIO:0100873", - "is_a": "Research" + "is_a": "Research [GENEPIO:0100003]" }, - "Protocol testing": { - "text": "Protocol testing", + "Protocol testing [GENEPIO:0100024]": { + "text": "Protocol testing [GENEPIO:0100024]", + "description": "A research sampling strategy in which samples are collected in order to test a method or protocol.", "meaning": "GENEPIO:0100024", - "is_a": "Research" + "is_a": "Research [GENEPIO:0100003]" } } }, - "scale of sampling menu": { - "name": "scale of sampling menu", + "ScaleOfSamplingMenu": { + "name": "ScaleOfSamplingMenu", + "title": "scale of sampling menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Community-level surveillance": { - "text": "Community-level surveillance", + "Community-level surveillance [GENEPIO:0100874]": { + "text": "Community-level surveillance [GENEPIO:0100874]", + "description": "A surveillance strategy in which sites are sampled at the community level.", "meaning": "GENEPIO:0100874" }, - "Institution-level surveillance": { - "text": "Institution-level surveillance", + "Institution-level surveillance [GENEPIO:0100875]": { + "text": "Institution-level surveillance [GENEPIO:0100875]", + "description": "A surveillance strategy in which sites are sampled at the institution level.", "meaning": "GENEPIO:0100875" }, - "Building-level surveillance": { - "text": "Building-level surveillance", + "Building-level surveillance [GENEPIO:0100876]": { + "text": "Building-level surveillance [GENEPIO:0100876]", + "description": "A surveillance strategy in which sites are sampled at the building level.", "meaning": "GENEPIO:0100876" } } }, - "sample collection time of day menu": { - "name": "sample collection time of day menu", + "SampleCollectionTimeOfDayMenu": { + "name": "SampleCollectionTimeOfDayMenu", + "title": "sample collection time of day menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Morning": { - "text": "Morning", + "Morning [NCIT:C64934]": { + "text": "Morning [NCIT:C64934]", + "description": "The time period between dawn and noon.", "meaning": "NCIT:C64934" }, - "Afternoon": { - "text": "Afternoon", + "Afternoon [NCIT:C64935]": { + "text": "Afternoon [NCIT:C64935]", + "description": "The time period between noon and sunset.", "meaning": "NCIT:C64935" }, - "Evening": { - "text": "Evening", + "Evening [NCIT:C64936]": { + "text": "Evening [NCIT:C64936]", + "description": "The time period between late afternoon and bedtime.", "meaning": "NCIT:C64936" }, - "Night": { - "text": "Night", + "Night [NCIT:C65001]": { + "text": "Night [NCIT:C65001]", + "description": "The time in every 24 hour period when it is dark.", "meaning": "NCIT:C65001" } } }, - "sample collection duration unit menu": { - "name": "sample collection duration unit menu", + "SampleCollectionDurationUnitMenu": { + "name": "SampleCollectionDurationUnitMenu", + "title": "sample collection duration unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Second": { - "text": "Second", + "Second [UO:0000010]": { + "text": "Second [UO:0000010]", + "description": "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.", "meaning": "UO:0000010" }, - "Minute": { - "text": "Minute", + "Minute [UO:0000031]": { + "text": "Minute [UO:0000031]", + "description": "A time unit which is equal to 60 seconds.", "meaning": "UO:0000031" }, - "Hour": { - "text": "Hour", + "Hour [UO:0000032]": { + "text": "Hour [UO:0000032]", + "description": "A time unit which is equal to 60 minutes.", "meaning": "UO:0000032" }, - "Day": { - "text": "Day", + "Day [UO:0000033]": { + "text": "Day [UO:0000033]", + "description": "A time unit which is equal to 24 hours.", "meaning": "UO:0000033" }, - "Week": { - "text": "Week", + "Week [UO:0000034]": { + "text": "Week [UO:0000034]", + "description": "A time unit which is equal to 7 days.", "meaning": "UO:0000034" }, - "Month": { - "text": "Month", + "Month [UO:0000035]": { + "text": "Month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", "meaning": "UO:0000035" }, - "Year": { - "text": "Year", + "Year [UO:0000036]": { + "text": "Year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", "meaning": "UO:0000036" } } }, - "presampling activity menu": { - "name": "presampling activity menu", + "PresamplingActivityMenu": { + "name": "PresamplingActivityMenu", + "title": "presampling activity menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Agricultural activity": { - "text": "Agricultural activity", + "Agricultural activity [ENVO:01001442]": { + "text": "Agricultural activity [ENVO:01001442]", + "description": "A land use process during which terrestrial environments are modified such that they can grow crop plants or allow the rearing of animals to provide food, fiber, medicines, or other products used by humans.", "meaning": "ENVO:01001442" }, - "Animal husbandry": { - "text": "Animal husbandry", + "Animal husbandry [ENVO:01001248]": { + "text": "Animal husbandry [ENVO:01001248]", + "description": "An agricultural process during which humans rear animals on land for harvest and consumption.", "meaning": "ENVO:01001248" }, - "Industrial activity": { - "text": "Industrial activity", + "Industrial activity [ENVO:01001450]": { + "text": "Industrial activity [ENVO:01001450]", + "description": "A process that leads to the production of goods.", "meaning": "ENVO:01001450" }, - "Healthcare activity": { - "text": "Healthcare activity", + "Healthcare activity [NCIT:C16205]": { + "text": "Healthcare activity [NCIT:C16205]", + "description": "A process that includes the prevention, treatment, and management of physical and mental illness.", "meaning": "NCIT:C16205" }, - "Wastewater treatment": { - "text": "Wastewater treatment", + "Wastewater treatment [ENVO:06105300]": { + "text": "Wastewater treatment [ENVO:06105300]", + "description": "A recycling process during which wastewater is treated.", "meaning": "ENVO:06105300" }, - "Wastewater filtration": { - "text": "Wastewater filtration", - "meaning": "GENEPIO:0100881", - "is_a": "Wastewater treatment" - }, - "Wastewater grit removal": { - "text": "Wastewater grit removal", - "meaning": "GENEPIO:0100882", - "is_a": "Wastewater treatment" - }, - "Wastewater microbial pre-treatment": { - "text": "Wastewater microbial pre-treatment", - "meaning": "GENEPIO:0100883", - "is_a": "Wastewater treatment" - }, - "Wastewater primary sedimentation": { - "text": "Wastewater primary sedimentation", - "meaning": "GENEPIO:0100884", - "is_a": "Wastewater treatment" - }, - "Wastewater secondary sedimentation": { - "text": "Wastewater secondary sedimentation", - "meaning": "GENEPIO:0100885", - "is_a": "Wastewater treatment" + "Wastewater screening process [GENEPIO:0101198]": { + "text": "Wastewater screening process [GENEPIO:0101198]", + "description": "A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances.", + "meaning": "GENEPIO:0101198", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "wastewater comminution process [GENEPIO:0101719]": { + "text": "wastewater comminution process [GENEPIO:0101719]", + "description": "A wastewater treatment process which involves the mechanical reduction of solid materials in wastewater into smaller, more manageable particles through devices like comminutors or grinders to shred debris.", + "meaning": "GENEPIO:0101719", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater filtration [ENVO:03501445]": { + "text": "Wastewater filtration [ENVO:03501445]", + "description": "A wastewater treatment process which removes solid particles from wastewater by means of filtration.", + "meaning": "ENVO:03501445", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater grit removal [ENVO:03501446]": { + "text": "Wastewater grit removal [ENVO:03501446]", + "description": "A wastewater treatment process which removes sand, silt, and grit from wastewater.", + "meaning": "ENVO:03501446", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater primary sedimentation [ENVO:03501448]": { + "text": "Wastewater primary sedimentation [ENVO:03501448]", + "description": "A wastewater treatment process which removes solids and large particles from influent through gravitational force.", + "meaning": "ENVO:03501448", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater microbial treatment [ENVO:03501447]": { + "text": "Wastewater microbial treatment [ENVO:03501447]", + "description": "A wastewater treatment process in which microbes are used to degrade the biological material in wastewater.", + "meaning": "ENVO:03501447", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater aerobic digestion [GENEPIO:0101199]": { + "text": "Wastewater aerobic digestion [GENEPIO:0101199]", + "description": "A wastewater microbial treatment process in which organic material is broken down in the presence of oxygen.", + "meaning": "GENEPIO:0101199", + "is_a": "Wastewater microbial treatment [ENVO:03501447]" + }, + "Wastewater anaerobic digestion [GENEPIO:0101200]": { + "text": "Wastewater anaerobic digestion [GENEPIO:0101200]", + "description": "A wastewater microbial treatment process in which organic material is broken down in the absence of oxygen by anaerobic bacteria.", + "meaning": "GENEPIO:0101200", + "is_a": "Wastewater microbial treatment [ENVO:03501447]" + }, + "Wastewater secondary sedimentation [ENVO:03501449]": { + "text": "Wastewater secondary sedimentation [ENVO:03501449]", + "description": "A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force.", + "meaning": "ENVO:03501449", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater sludge removal [GENEPIO:0101201]": { + "text": "Wastewater sludge removal [GENEPIO:0101201]", + "description": "A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances.", + "meaning": "GENEPIO:0101201", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater sludge dewatering [GENEPIO:0101202]": { + "text": "Wastewater sludge dewatering [GENEPIO:0101202]", + "description": "A wastewater treatment process which mechanically reduces the water content of wastewater sludge using equipment like centrifuges or belt presses, resulting in a semi-solid material that is easier to handle and transport", + "meaning": "GENEPIO:0101202", + "is_a": "Wastewater treatment [ENVO:06105300]" + }, + "Wastewater sludge drying [GENEPIO:0101718]": { + "text": "Wastewater sludge drying [GENEPIO:0101718]", + "description": "A wastewater treatment process which further reduces the moisture content of dewatered sludge, typically through thermal or air drying methods, producing a dry, stable material for easier disposal or use.", + "meaning": "GENEPIO:0101718", + "is_a": "Wastewater treatment [ENVO:06105300]" } } }, - "sample volume measurement unit menu": { - "name": "sample volume measurement unit menu", + "SampleVolumeMeasurementUnitMenu": { + "name": "SampleVolumeMeasurementUnitMenu", + "title": "sample volume measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "microliter (uL)": { - "text": "microliter (uL)", + "microliter (uL) [UO:0000101]": { + "text": "microliter (uL) [UO:0000101]", + "description": "A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter.", "meaning": "UO:0000101" }, - "milliliter (mL)": { - "text": "milliliter (mL)", + "milliliter (mL) [UO:0000098]": { + "text": "milliliter (mL) [UO:0000098]", + "description": "A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter.", "meaning": "UO:0000098" }, - "liter (L)": { - "text": "liter (L)", + "liter (L) [UO:0000099]": { + "text": "liter (L) [UO:0000099]", + "description": "A metric unit of volume equivalent to 1000 cubic centimeters", "meaning": "UO:0000099" } } }, - "sample storage duration unit menu": { - "name": "sample storage duration unit menu", + "SampleStorageDurationUnitMenu": { + "name": "SampleStorageDurationUnitMenu", + "title": "sample storage duration unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Second": { - "text": "Second", + "Second [UO:0000010]": { + "text": "Second [UO:0000010]", + "description": "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.", "meaning": "UO:0000010" }, - "Minute": { - "text": "Minute", + "Minute [UO:0000031]": { + "text": "Minute [UO:0000031]", + "description": "A time unit which is equal to 60 seconds.", "meaning": "UO:0000031" }, - "Hour": { - "text": "Hour", + "Hour [UO:0000032]": { + "text": "Hour [UO:0000032]", + "description": "A time unit which is equal to 60 minutes.", "meaning": "UO:0000032" }, - "Day": { - "text": "Day", + "Day [UO:0000033]": { + "text": "Day [UO:0000033]", + "description": "A time unit which is equal to 24 hours.", "meaning": "UO:0000033" }, - "Week": { - "text": "Week", + "Week [UO:0000034]": { + "text": "Week [UO:0000034]", + "description": "A time unit which is equal to 7 days.", "meaning": "UO:0000034" }, - "Month": { - "text": "Month", + "Month [UO:0000035]": { + "text": "Month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", "meaning": "UO:0000035" }, - "Year": { - "text": "Year", + "Year [UO:0000036]": { + "text": "Year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", "meaning": "UO:0000036" } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Concentration": { - "text": "Concentration", + "Concentration [OBI:0600041]": { + "text": "Concentration [OBI:0600041]", + "description": "A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest.", "meaning": "OBI:0600041" }, - "Centrifugation": { - "text": "Centrifugation", + "Centrifugation [OBI:0302886]": { + "text": "Centrifugation [OBI:0302886]", + "description": "A process separating molecules by size or density using centrifugal forces generated by a spinning rotor.", "meaning": "OBI:0302886" }, - "Filtration": { - "text": "Filtration", + "Filtration [OBI:0302885]": { + "text": "Filtration [OBI:0302885]", + "description": "A process which separates components suspended in a fluid based on granularity properties relying on a filter device.", "meaning": "OBI:0302885" }, - "Flocculation": { - "text": "Flocculation", + "Flocculation [NCIT:C154798]": { + "text": "Flocculation [NCIT:C154798]", + "description": "A process in which microscopic particles in suspension aggregate to form loosely clumped masses that are often macroscopically observable.", "meaning": "NCIT:C154798" }, - "Magnetic nanobead binding": { - "text": "Magnetic nanobead binding", + "Magnetic nanobead binding [GENEPIO:0100886]": { + "text": "Magnetic nanobead binding [GENEPIO:0100886]", + "description": "A process that uses nanobeads to bind to particles or microbes of interest.", "meaning": "GENEPIO:0100886" }, - "Precipitation": { - "text": "Precipitation", + "Precipitation [OBI:0600034]": { + "text": "Precipitation [OBI:0600034]", + "description": "A protocol application to cause a material to precipitate (becoming a solid) out of solution.", "meaning": "OBI:0600034" }, - "Gravity separation": { - "text": "Gravity separation", + "Gravity separation [GENEPIO:0101011]": { + "text": "Gravity separation [GENEPIO:0101011]", + "description": "A process through which solids are separated from a liquid by allowing the solids to settle by gravity.", "meaning": "GENEPIO:0101011" }, - "Pasteurization": { - "text": "Pasteurization", + "Pasteurization [IDO:0100170]": { + "text": "Pasteurization [IDO:0100170]", + "description": "A planned process of heating a liquid entity, to a specific temperature of a defined length of time span, and then cooling it immediately. It has an objective of prevent the microbial's growth in the liquid entity, which is a specific input of this planned process.", "meaning": "IDO:0100170" }, - "Growth in enrichment broth": { - "text": "Growth in enrichment broth", + "Growth in enrichment broth [GENEPIO:0101012]": { + "text": "Growth in enrichment broth [GENEPIO:0101012]", + "description": "A process in which microorganisms, present in a collected sample, undergo cultivation within a nutrient-rich liquid medium, that facilitates growth.", "meaning": "GENEPIO:0101012" }, - "Pooling specimens": { - "text": "Pooling specimens", + "Pooling specimens [OBI:0600016]": { + "text": "Pooling specimens [OBI:0600016]", + "description": "Physical combination of several instances of like material.", "meaning": "OBI:0600016" }, - "Technical replicate process": { - "text": "Technical replicate process", + "Technical replicate process [GENEPIO:0101021]": { + "text": "Technical replicate process [GENEPIO:0101021]", + "description": "A specimen collection process in which a replicate(s) is collected to assess technical variation within an experiment. For technical replicates the same BioSample is used e.g. the same pool of RNA is used to assess technical (as opposed to biological) variation.", "meaning": "GENEPIO:0101021" }, - "Biological replicate process": { - "text": "Biological replicate process", + "Biological replicate process [GENEPIO:0101022]": { + "text": "Biological replicate process [GENEPIO:0101022]", + "description": "A specimen collection process in which a replicate(s) is collected in parallel to assess for biological variation within an experiment. Biological replicates would have distinct BioSamples records.", "meaning": "GENEPIO:0101022" } } }, - "environmental site menu": { - "name": "environmental site menu", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental site menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Correctional facility": { - "text": "Correctional facility", + "Correctional facility [ENVO:01001481]": { + "text": "Correctional facility [ENVO:01001481]", + "description": "A prison facility which is owned and operated by a state.", "meaning": "ENVO:01001481" }, - "Healthcare facility": { - "text": "Healthcare facility", + "Healthcare facility [ENVO:03501134]": { + "text": "Healthcare facility [ENVO:03501134]", + "description": "A human construction in which healthcare is provided.", "meaning": "ENVO:03501134" }, - "Hospital": { - "text": "Hospital", + "Hospital [ENVO:00002173]": { + "text": "Hospital [ENVO:00002173]", + "description": "A building in which health care services are provided by specialized staff and equipment.", "meaning": "ENVO:00002173", - "is_a": "Healthcare facility" + "is_a": "Healthcare facility [ENVO:03501134]" }, - "Clinic": { - "text": "Clinic", + "Clinic [ENVO:03501182]": { + "text": "Clinic [ENVO:03501182]", + "description": "A facility which is used to provide treatment, remedial work, and/or instruction.", "meaning": "ENVO:03501182", - "is_a": "Healthcare facility" + "is_a": "Healthcare facility [ENVO:03501134]" }, - "Educational facility": { - "text": "Educational facility", + "Educational facility [ENVO:03501129]": { + "text": "Educational facility [ENVO:03501129]", + "description": "A human construction in which people are educated.", "meaning": "ENVO:03501129" }, - "Daycare facility": { - "text": "Daycare facility", + "Daycare facility [ENVO:03501335]": { + "text": "Daycare facility [ENVO:03501335]", + "description": "A child care facility in which day care services are provided, by specialized staff and equipment, to a human child during the working day.", "meaning": "ENVO:03501335", - "is_a": "Educational facility" + "is_a": "Educational facility [ENVO:03501129]" }, - "School": { - "text": "School", + "School [ENVO:03501130]": { + "text": "School [ENVO:03501130]", + "description": "An institutional building in which students are educated.", "meaning": "ENVO:03501130", - "is_a": "Educational facility" + "is_a": "Educational facility [ENVO:03501129]" }, - "College or university": { - "text": "College or university", + "College or university [ENVO:03501131]": { + "text": "College or university [ENVO:03501131]", + "description": "An institutional building in which university services are performed.", "meaning": "ENVO:03501131", - "is_a": "Educational facility" - }, - "Residential building": { - "text": "Residential building", + "is_a": "Educational facility [ENVO:03501129]" + }, + "Commercial building [ENVO:01001222]": { + "text": "Commercial building [ENVO:01001222]", + "description": "A building which is primarily used to facilitate the buying or selling of goods or services. \"Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally.\"", + "meaning": "ENVO:01001222" + }, + "Office [ENVO:01001221]": { + "text": "Office [ENVO:01001221]", + "description": "A commercial building which contains parts used as workplaces primarily for administrative and managerial workers. \"An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets.\"", + "meaning": "ENVO:01001221", + "is_a": "Commercial building [ENVO:01001222]" + }, + "Restaurant [ENVO:01000934]": { + "text": "Restaurant [ENVO:01000934]", + "description": "A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services.", + "meaning": "ENVO:01000934", + "is_a": "Commercial building [ENVO:01001222]" + }, + "Shopping mall [ENVO:03501207]": { + "text": "Shopping mall [ENVO:03501207]", + "description": "A shopping center in which a large indoor pedestrian promenade provides access to stores and other facilities.", + "meaning": "ENVO:03501207", + "is_a": "Commercial building [ENVO:01001222]" + }, + "Residential building [ENVO:01000933]": { + "text": "Residential building [ENVO:01000933]", + "description": "A human house which serves as a long-term shelter for its inhabitants and within which they store personal property.", "meaning": "ENVO:01000933" }, - "Homeless shelter": { - "text": "Homeless shelter", + "Homeless shelter [ENVO:03501133]": { + "text": "Homeless shelter [ENVO:03501133]", + "description": "An institutional building which temporarily houses homeless people.", "meaning": "ENVO:03501133", - "is_a": "Residential building" + "is_a": "Residential building [ENVO:01000933]" }, - "Long-term care facility": { - "text": "Long-term care facility", + "Long-term care facility [ENVO:01000932]": { + "text": "Long-term care facility [ENVO:01000932]", + "description": "A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living.", "meaning": "ENVO:01000932", - "is_a": "Residential building" + "is_a": "Residential building [ENVO:01000933]" }, - "Transport hub": { - "text": "Transport hub", + "Transport hub [ENVO:03501117]": { + "text": "Transport hub [ENVO:03501117]", + "description": "A place where passengers and cargo are exchanged between vehicles or/and between transport modes.", "meaning": "ENVO:03501117" }, - "Airport": { - "text": "Airport", + "Airport [ENVO:03501122]": { + "text": "Airport [ENVO:03501122]", + "description": "A human construction with extended facilities from which aircraft flight operations take place.", "meaning": "ENVO:03501122", - "is_a": "Transport hub" + "is_a": "Transport hub [ENVO:03501117]" }, - "Farm": { - "text": "Farm", + "Farm [ENVO:00000078]": { + "text": "Farm [ENVO:00000078]", + "description": "An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.", "meaning": "ENVO:00000078" }, - "Refugee camp": { - "text": "Refugee camp", + "Refugee camp [NCIT:C85867]": { + "text": "Refugee camp [NCIT:C85867]", + "description": "A temporary, often makeshift shelter for persons displaced by war, political oppression, or for religious beliefs.", "meaning": "NCIT:C85867" }, - "Road": { - "text": "Road", + "Road [ENVO:00000064]": { + "text": "Road [ENVO:00000064]", + "description": "An open way for the passage of vehicles, persons, or animals on land.", "meaning": "ENVO:00000064" }, - "Roadside": { - "text": "Roadside", + "Roadside [ENVO:01000447]": { + "text": "Roadside [ENVO:01000447]", + "description": "An environmental zone of varying area which is adjacent to a road.", "meaning": "ENVO:01000447" }, - "Industrial plant": { - "text": "Industrial plant", + "Industrial plant [ENVO:00003861]": { + "text": "Industrial plant [ENVO:00003861]", + "description": "A building within which goods are produced and, optionally, stored or within which services are rendered.", "meaning": "ENVO:00003861" }, - "Meat processing plant": { - "text": "Meat processing plant", + "Meat processing plant [ENVO:03501297]": { + "text": "Meat processing plant [ENVO:03501297]", + "description": "A processing plant for slaughtering, processing, packaging, labelling, handling, and storing of food animal carcasses, parts of carcasses, and meat products.", "meaning": "ENVO:03501297", - "is_a": "Industrial plant" + "is_a": "Industrial plant [ENVO:00003861]" }, - "Pharmaceutical manufacturing plant": { - "text": "Pharmaceutical manufacturing plant", - "meaning": "GENEPIO:0100887", - "is_a": "Industrial plant" + "Pharmaceutical manufacturing plant [ENVO:03501450]": { + "text": "Pharmaceutical manufacturing plant [ENVO:03501450]", + "description": "An industrial building in which pharamceutical drugs are synthesised and processed on an industrial scale.", + "meaning": "ENVO:03501450", + "is_a": "Industrial plant [ENVO:00003861]" }, - "Body of water": { - "text": "Body of water", + "Body of water [ENVO:00000063]": { + "text": "Body of water [ENVO:00000063]", + "description": "An accumulation of water of varying size.", "meaning": "ENVO:00000063" }, - "Surface water": { - "text": "Surface water", + "Surface water [ENVO:00002042]": { + "text": "Surface water [ENVO:00002042]", + "description": "Water that is found on the surface of an astronomical object.", "meaning": "ENVO:00002042", - "is_a": "Body of water" + "is_a": "Body of water [ENVO:00000063]" }, - "Lake": { - "text": "Lake", + "Lake [ENVO:00000020]": { + "text": "Lake [ENVO:00000020]", + "description": "A body of water or other liquid of considerable size contained in a depression on a landmass.", "meaning": "ENVO:00000020", - "is_a": "Surface water" + "is_a": "Surface water [ENVO:00002042]" }, - "Stream": { - "text": "Stream", + "Stream [ENVO:00000023]": { + "text": "Stream [ENVO:00000023]", + "description": "A watercourse which is linear and flows across the solid portion of a planetary surface.", "meaning": "ENVO:00000023", - "is_a": "Surface water" + "is_a": "Surface water [ENVO:00002042]" }, - "River": { - "text": "River", + "River [ENVO:00000022]": { + "text": "River [ENVO:00000022]", + "description": "A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.", "meaning": "ENVO:00000022", - "is_a": "Stream" + "is_a": "Stream [ENVO:00000023]" }, - "Ocean": { - "text": "Ocean", + "Ocean [ENVO:00000015]": { + "text": "Ocean [ENVO:00000015]", + "description": "A marine water body which is constitutes the majority of an astronomical body's hydrosphere.", "meaning": "ENVO:00000015", - "is_a": "Surface water" + "is_a": "Surface water [ENVO:00002042]" }, - "Sea": { - "text": "Sea", + "Sea [ENVO:00000016]": { + "text": "Sea [ENVO:00000016]", + "description": "A large expanse of saline water usually connected with an ocean.", "meaning": "ENVO:00000016", - "is_a": "Surface water" + "is_a": "Surface water [ENVO:00002042]" }, - "Canal": { - "text": "Canal", + "Canal [ENVO:00000014]": { + "text": "Canal [ENVO:00000014]", + "description": "Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation.", "meaning": "ENVO:00000014", - "is_a": "Surface water" + "is_a": "Surface water [ENVO:00002042]" }, - "Reservoir": { - "text": "Reservoir", + "Reservoir [ENVO:00000025]": { + "text": "Reservoir [ENVO:00000025]", + "description": "An artificial body of water, often contained by a dam, constructed for the purpose of water storage.", "meaning": "ENVO:00000025", - "is_a": "Surface water" + "is_a": "Surface water [ENVO:00002042]" }, - "Ground water": { - "text": "Ground water", + "Ground water [ENVO:01001004]": { + "text": "Ground water [ENVO:01001004]", + "description": "Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.", "meaning": "ENVO:01001004", - "is_a": "Body of water" + "is_a": "Body of water [ENVO:00000063]" }, - "Well": { - "text": "Well", + "Well [ENVO:00000026]": { + "text": "Well [ENVO:00000026]", + "description": "A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface.", "meaning": "ENVO:00000026", - "is_a": "Ground water" + "is_a": "Ground water [ENVO:01001004]" }, - "Spring": { - "text": "Spring", + "Spring [ENVO:00000027]": { + "text": "Spring [ENVO:00000027]", + "description": "A surface landform which provides an egress for groundwater or steam to flow out of the ground.", "meaning": "ENVO:00000027", - "is_a": "Ground water" + "is_a": "Ground water [ENVO:01001004]" }, - "Wastewater treatment plant": { - "text": "Wastewater treatment plant", + "Wastewater treatment plant [ENVO:00002272]": { + "text": "Wastewater treatment plant [ENVO:00002272]", + "description": "A plant in which wastewater is treated.", "meaning": "ENVO:00002272" }, - "Waste stabilization pond (lagoon)": { - "text": "Waste stabilization pond (lagoon)", + "Influent pump station [ENVO:03501465]": { + "text": "Influent pump station [ENVO:03501465]", + "description": "A facility within a wastewater treatment plant designed to receive and lift incoming wastewater (influent) to a higher elevation for subsequent treatment processes. The influent pump station typically houses pumps, controls, and associated equipment necessary to move wastewater through the treatment process.", + "meaning": "ENVO:03501465", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Grit chamber [ENVO:03501467]": { + "text": "Grit chamber [ENVO:03501467]", + "description": "A physical structure or equipment within a wastewater treatment plant where grit and other heavy inorganic particles are removed from the influent through sedimentation. The grit chamber helps protect downstream equipment from abrasion and reduces the accumulation of grit in subsequent treatment processes.", + "meaning": "ENVO:03501467", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Communitor [ENVO:03501472]": { + "text": "Communitor [ENVO:03501472]", + "description": "A mechanical device designed to reduce the size of solid materials in wastewater. It uses rotating drums or cutting blades to shred large debris into smaller pieces, protecting downstream equipment and enhancing the efficiency of subsequent treatment processes.", + "meaning": "ENVO:03501472", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Primary clarifer [ENVO:03501468]": { + "text": "Primary clarifer [ENVO:03501468]", + "description": "A large, sedimentation tank in a wastewater treatment plant where the primary stage of solids separation occurs. In the primary clarifier, suspended solids settle to the bottom as sludge, while lighter materials, such as oils and greases, rise to the surface for removal.", + "meaning": "ENVO:03501468", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Aeration tank [ENVO:03501469]": { + "text": "Aeration tank [ENVO:03501469]", + "description": "A tank or basin in a wastewater treatment plant where oxygen is introduced into the wastewater to promote the growth of aerobic microorganisms. These microorganisms break down organic pollutants in the water, facilitating the biological treatment process. The aeration tank is essential for reducing the organic load before the water moves to subsequent treatment stages.", + "meaning": "ENVO:03501469", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Secondary clarifer [ENVO:03501471]": { + "text": "Secondary clarifer [ENVO:03501471]", + "description": "A sedimentation tank in a wastewater treatment plant used in the secondary treatment process. The secondary clarifier allows for the settling and removal of biological floc or sludge produced in the aeration tank, further clarifying the treated wastewater before discharge or further treatment.", + "meaning": "ENVO:03501471", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Sludge dryer [ENVO:03501473]": { + "text": "Sludge dryer [ENVO:03501473]", + "description": "A device designed to remove moisture from sludge through thermal drying methods, resulting in a dry, granular material that is easier to handle, store, or utilize in other applications.", + "meaning": "ENVO:03501473", + "is_a": "Wastewater treatment plant [ENVO:00002272]" + }, + "Waste stabilization pond (lagoon) [ENVO:03600076]": { + "text": "Waste stabilization pond (lagoon) [ENVO:03600076]", + "description": "A human construction which confines wastewater in a depression enclosed by earthen structures.", "meaning": "ENVO:03600076" }, - "Sewer": { - "text": "Sewer", + "Sewer [ENVO:01000924]": { + "text": "Sewer [ENVO:01000924]", + "description": "An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed.", "meaning": "ENVO:01000924" }, - "Transportation vehicle": { - "text": "Transportation vehicle", + "Transportation vehicle [ENVO:01000604]": { + "text": "Transportation vehicle [ENVO:01000604]", + "description": "A vehicle is a mobile machine which transports people or cargo.", "meaning": "ENVO:01000604" }, - "Boat": { - "text": "Boat", + "Boat [ENVO:01000608]": { + "text": "Boat [ENVO:01000608]", + "description": "A boat is a watercraft of any size which is able to float or plane on water.", "meaning": "ENVO:01000608", - "is_a": "Transportation vehicle" + "is_a": "Transportation vehicle [ENVO:01000604]" }, - "Airplane": { - "text": "Airplane", + "Airplane [ENVO:03501349]": { + "text": "Airplane [ENVO:03501349]", + "description": "An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine.", "meaning": "ENVO:03501349", - "is_a": "Transportation vehicle" + "is_a": "Transportation vehicle [ENVO:01000604]" } } }, "environmental material menu": { "name": "environmental material menu", + "title": "environmental material menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Surface water": { - "text": "Surface water", + "Bar screen [ENVO:03501474]": { + "text": "Bar screen [ENVO:03501474]", + "description": "A mechanical filter used to remove large objects, such as rags and plastics, from wastewater", + "meaning": "ENVO:03501474" + }, + "Surface water [ENVO:00002042]": { + "text": "Surface water [ENVO:00002042]", + "description": "Water that is found on the surface of an astronomical object.", "meaning": "ENVO:00002042" }, - "Wastewater": { - "text": "Wastewater", + "Wastewater [ENVO:00002001]": { + "text": "Wastewater [ENVO:00002001]", + "description": "Water that has been adversely affected in quality by anthropogenic influence", "meaning": "ENVO:00002001" }, - "Wastewater sediment": { - "text": "Wastewater sediment", - "meaning": "GENEPIO:0100890" + "Wastewater sediment [ENVO:03501456]": { + "text": "Wastewater sediment [ENVO:03501456]", + "description": "A sediment which is removed from waste water during a waste water treatment process.", + "meaning": "ENVO:03501456" }, - "Sludge": { - "text": "Sludge", + "Sludge [ENVO:00002044]": { + "text": "Sludge [ENVO:00002044]", + "description": "The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.", "meaning": "ENVO:00002044" }, - "Primary sludge": { - "text": "Primary sludge", + "Primary sludge [ENVO:00002057]": { + "text": "Primary sludge [ENVO:00002057]", + "description": "Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment.", "meaning": "ENVO:00002057", - "is_a": "Sludge" + "is_a": "Sludge [ENVO:00002044]" }, - "Secondary sludge": { - "text": "Secondary sludge", + "Secondary sludge [ENVO:00002058]": { + "text": "Secondary sludge [ENVO:00002058]", + "description": "Activated waste biomass generated during wastewater treatment.", "meaning": "ENVO:00002058", - "is_a": "Sludge" + "is_a": "Sludge [ENVO:00002044]" }, - "Wastewater effluent": { - "text": "Wastewater effluent", - "meaning": "GENEPIO:0100891" + "Wastewater effluent [ENVO:03501457]": { + "text": "Wastewater effluent [ENVO:03501457]", + "description": "A wastewater which has been discharged from any item of equipment at a stage of a wastewater treatment process.", + "meaning": "ENVO:03501457" }, - "Primary wastewater effluent": { - "text": "Primary wastewater effluent", + "Primary wastewater effluent [GENEPIO:0100892]": { + "text": "Primary wastewater effluent [GENEPIO:0100892]", + "description": "A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation.", "meaning": "GENEPIO:0100892", - "is_a": "Wastewater effluent" + "is_a": "Wastewater effluent [ENVO:03501457]" }, - "Secondary wastewater effluent": { - "text": "Secondary wastewater effluent", + "Secondary wastewater effluent [GENEPIO:0100893]": { + "text": "Secondary wastewater effluent [GENEPIO:0100893]", + "description": "A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation.", "meaning": "GENEPIO:0100893", - "is_a": "Wastewater effluent" + "is_a": "Wastewater effluent [ENVO:03501457]" } } }, - "environmental material properties menu": { - "name": "environmental material properties menu", + "EnvironmentalMaterialPropertiesMenu": { + "name": "EnvironmentalMaterialPropertiesMenu", + "title": "environmental material properties menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Fluid (stagnant)": { - "text": "Fluid (stagnant)", + "Fluid (stagnant) [GENEPIO:0101004]": { + "text": "Fluid (stagnant) [GENEPIO:0101004]", + "description": "A quality of a body of water wherein it has no current or flow.", "meaning": "GENEPIO:0101004" }, - "Fluid (slow)": { - "text": "Fluid (slow)", + "Fluid (slow) [GENEPIO:0101005]": { + "text": "Fluid (slow) [GENEPIO:0101005]", + "description": "A quality of a body of water wherein there is a slow flow.", "meaning": "GENEPIO:0101005" }, - "Fluid (fast)": { - "text": "Fluid (fast)", + "Fluid (fast) [GENEPIO:0101006]": { + "text": "Fluid (fast) [GENEPIO:0101006]", + "description": "A quality of a body of water wherein there is a fast flow.", "meaning": "GENEPIO:0101006" }, - "Contamination": { - "text": "Contamination", + "Contamination [PATO:0015031]": { + "text": "Contamination [PATO:0015031]", + "description": "The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity.", "meaning": "PATO:0015031" }, - "Fecal-contaminated": { - "text": "Fecal-contaminated", + "Fecal-contaminated [GENEPIO:0101010]": { + "text": "Fecal-contaminated [GENEPIO:0101010]", + "description": "A contamination quality in which fecal matter is a key component of the contamination.", "meaning": "GENEPIO:0101010", - "is_a": "Contamination" + "is_a": "Contamination [PATO:0015031]" }, - "Liquid": { - "text": "Liquid", + "Liquid [PATO:0001735]": { + "text": "Liquid [PATO:0001735]", + "description": "A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids.", "meaning": "PATO:0001735" }, - "Slurry-like": { - "text": "Slurry-like", + "Slurry-like [GENEPIO:0101007]": { + "text": "Slurry-like [GENEPIO:0101007]", + "description": "An quality in which the fluid like material is more viscous due to the suspension of insoluble solid particles.", "meaning": "GENEPIO:0101007" }, - "Semi-solid": { - "text": "Semi-solid", + "Semi-solid [NCIT:C149895]": { + "text": "Semi-solid [NCIT:C149895]", + "description": "A state of matter consisting of molecules in a non-rigid structure that can retain its shape and volume but that is not resistant to such change.", "meaning": "NCIT:C149895" }, - "Solid": { - "text": "Solid", + "Solid [PATO:0001736]": { + "text": "Solid [PATO:0001736]", + "description": "A quality in which an object or material exhibits characteristics of solids, lacking movement or flow.", "meaning": "PATO:0001736" }, - "Treated": { - "text": "Treated", + "Treated [GENEPIO:0101008]": { + "text": "Treated [GENEPIO:0101008]", + "description": "A quality which denotes an altered state of an item resulting from purposeful interventions or processes.", "meaning": "GENEPIO:0101008" }, - "Untreated": { - "text": "Untreated", + "Untreated [GENEPIO:0101009]": { + "text": "Untreated [GENEPIO:0101009]", + "description": "A quality which denotes an absence of purposeful intervention or processes on an item.", "meaning": "GENEPIO:0101009" } } }, - "wastewater system type menu": { - "name": "wastewater system type menu", + "WastewaterSystemTypeMenu": { + "name": "WastewaterSystemTypeMenu", + "title": "wastewater system type menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Combined sewer system": { - "text": "Combined sewer system" - }, - "Sanitary sewer system": { - "text": "Sanitary sewer system" - }, - "Waste stabilization pond": { - "text": "Waste stabilization pond", + "Combined sewer system [ENVO:03501453]": { + "text": "Combined sewer system [ENVO:03501453]", + "description": "A sewered sanitation system that collects rainwater runoff, domestic sewage, and industrial wastewater.", + "meaning": "ENVO:03501453" + }, + "Sanitary sewer system [ENVO:03501454]": { + "text": "Sanitary sewer system [ENVO:03501454]", + "description": "A sewered sanitation system that collects only domestic sewage.", + "meaning": "ENVO:03501454" + }, + "Waste stabilization pond [ENVO:03600076]": { + "text": "Waste stabilization pond [ENVO:03600076]", + "description": "A human construction which confines wastewater in a depression enclosed by earthen structures.", "meaning": "ENVO:03600076" }, - "Latrine": { - "text": "Latrine", + "Latrine [ENVO:01000519]": { + "text": "Latrine [ENVO:01000519]", + "description": "A latrine is a toilet which is of simple construction (relative to a flush or chemical toilet) and typically intended for communal use.", "meaning": "ENVO:01000519" }, - "Septic tank": { - "text": "Septic tank" + "Septic tank [ENVO:03501451]": { + "text": "Septic tank [ENVO:03501451]", + "description": "An underground holding and treatment site for domestic wastewater.", + "meaning": "ENVO:03501451" }, - "Cesspit": { - "text": "Cesspit" + "Cesspit [ENVO:03501452]": { + "text": "Cesspit [ENVO:03501452]", + "description": "A pit for the disposal and storage of sewage.", + "meaning": "ENVO:03501452" }, - "Composting toilet": { - "text": "Composting toilet", + "Composting toilet [ENVO:01000550]": { + "text": "Composting toilet [ENVO:01000550]", + "description": "A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils.", "meaning": "ENVO:01000550" }, - "Plumbing drain": { - "text": "Plumbing drain", + "Sewer drain [ENVO:01000924]": { + "text": "Sewer drain [ENVO:01000924]", + "description": "An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed.", "meaning": "ENVO:01000924" } } }, - "experimental specimen role type menu": { - "name": "experimental specimen role type menu", + "ExperimentalSpecimenRoleTypeMenu": { + "name": "ExperimentalSpecimenRoleTypeMenu", + "title": "experimental specimen role type menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Positive experimental control": { - "text": "Positive experimental control", + "Positive experimental control [GENEPIO:0101018]": { + "text": "Positive experimental control [GENEPIO:0101018]", + "description": "A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment.", "meaning": "GENEPIO:0101018" }, - "Negative experimental control": { - "text": "Negative experimental control", + "Negative experimental control [GENEPIO:0101019]": { + "text": "Negative experimental control [GENEPIO:0101019]", + "description": "A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment", "meaning": "GENEPIO:0101019" }, - "Technical replicate": { - "text": "Technical replicate", + "Technical replicate [EFO:0002090]": { + "text": "Technical replicate [EFO:0002090]", + "description": "A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.", "meaning": "EFO:0002090" }, - "Biological replicate": { - "text": "Biological replicate", + "Biological replicate [EFO:0002091]": { + "text": "Biological replicate [EFO:0002091]", + "description": "A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples.", "meaning": "EFO:0002091" } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Grab sampler": { - "text": "Grab sampler", + "Grab sampler [GENEPIO:0100941]": { + "text": "Grab sampler [GENEPIO:0100941]", + "description": "A specimen collection device which is used to collect discrete, instantaneous samples of water, soil, or other substances from a specific point in a body of water or at a specific location.", "meaning": "GENEPIO:0100941" }, - "Core sampling device": { - "text": "Core sampling device", + "Bag filtration device [GENEPIO:0102027]": { + "text": "Bag filtration device [GENEPIO:0102027]", + "meaning": "GENEPIO:0102027", + "is_a": "Grab sampler [GENEPIO:0100941]" + }, + "Core sampling device [GENEPIO:0100943]": { + "text": "Core sampling device [GENEPIO:0100943]", + "description": "A grab sampler that captures a vertical section of the substrate matrix of fecal sludge.", "meaning": "GENEPIO:0100943", - "is_a": "Grab sampler" + "is_a": "Grab sampler [GENEPIO:0100941]" }, - "Vacuum sludge sampling device": { - "text": "Vacuum sludge sampling device", + "Vacuum sludge sampling device [GENEPIO:0100944]": { + "text": "Vacuum sludge sampling device [GENEPIO:0100944]", + "description": "A grab sampler that takes a sample at a designated depth with minimal disturbance to surrounding layers.", "meaning": "GENEPIO:0100944", - "is_a": "Grab sampler" + "is_a": "Grab sampler [GENEPIO:0100941]" }, - "Cone-shaped sampling device": { - "text": "Cone-shaped sampling device", + "Cone-shaped sampling device [GENEPIO:0100945]": { + "text": "Cone-shaped sampling device [GENEPIO:0100945]", + "description": "A grab sample that has a controlled valve that opens to take a sample from a specific depth, then closes to bring the sample out.", "meaning": "GENEPIO:0100945", - "is_a": "Grab sampler" + "is_a": "Grab sampler [GENEPIO:0100941]" }, - "Horizontal grab sampling device": { - "text": "Horizontal grab sampling device", + "Horizontal grab sampling device [GENEPIO:0100946]": { + "text": "Horizontal grab sampling device [GENEPIO:0100946]", + "description": "A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting discharge from a pipe or truck.", "meaning": "GENEPIO:0100946", - "is_a": "Grab sampler" + "is_a": "Grab sampler [GENEPIO:0100941]" }, - "Vertical grab sampling device": { - "text": "Vertical grab sampling device", + "Vertical grab sampling device [GENEPIO:0100947]": { + "text": "Vertical grab sampling device [GENEPIO:0100947]", + "description": "A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting waste from a tank.", "meaning": "GENEPIO:0100947", - "is_a": "Grab sampler" + "is_a": "Grab sampler [GENEPIO:0100941]" }, - "Composite sampler": { - "text": "Composite sampler", + "Composite sampler [GENEPIO:0100942]": { + "text": "Composite sampler [GENEPIO:0100942]", + "description": "A specimen collection device that collects material over different times or locations.", "meaning": "GENEPIO:0100942" }, - "Passive (trap) sampler": { - "text": "Passive (trap) sampler", + "Passive (trap) sampler [GENEPIO:0100948]": { + "text": "Passive (trap) sampler [GENEPIO:0100948]", + "description": "A composite sampler that passively collects a sample without use of electricity or a battery.", "meaning": "GENEPIO:0100948", - "is_a": "Composite sampler" + "is_a": "Composite sampler [GENEPIO:0100942]" }, - "Moore swab": { - "text": "Moore swab", + "Moore swab [GENEPIO:0100949]": { + "text": "Moore swab [GENEPIO:0100949]", + "description": "A composite sampler which consists of gauze pad tied with string, suspended in flowing water or wastewater, in order to collect a wastewater sample.", "meaning": "GENEPIO:0100949", - "is_a": "Passive (trap) sampler" + "is_a": "Passive (trap) sampler [GENEPIO:0100948]" }, - "Automatic composite sampler": { - "text": "Automatic composite sampler", + "Automatic composite sampler [GENEPIO:0100950]": { + "text": "Automatic composite sampler [GENEPIO:0100950]", + "description": "A composite sampler which is automated to collect and store multiple wastewater samples across multiple time points.", "meaning": "GENEPIO:0100950", - "is_a": "Composite sampler" + "is_a": "Composite sampler [GENEPIO:0100942]" }, - "Automatic flow-proportional sampler": { - "text": "Automatic flow-proportional sampler", + "Automatic flow-proportional sampler [GENEPIO:0100951]": { + "text": "Automatic flow-proportional sampler [GENEPIO:0100951]", + "description": "A composite sampler which is automated to collect and store multiple wastewater samples in a manner proportional to flow.", "meaning": "GENEPIO:0100951", - "is_a": "Automatic composite sampler" + "is_a": "Automatic composite sampler [GENEPIO:0100950]" }, - "Automatic sequential (time-proportional) sampler": { - "text": "Automatic sequential (time-proportional) sampler", + "Automatic sequential (time-proportional) sampler [GENEPIO:0100952]": { + "text": "Automatic sequential (time-proportional) sampler [GENEPIO:0100952]", + "description": "A composite sampler which is automated to collect and combine multiple samples of equal volume taken at a set time interval.", "meaning": "GENEPIO:0100952", - "is_a": "Automatic composite sampler" + "is_a": "Automatic composite sampler [GENEPIO:0100950]" } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Grab sampling": { - "text": "Grab sampling", + "Grab sampling [GENEPIO:0100953]": { + "text": "Grab sampling [GENEPIO:0100953]", + "description": "An environmental material collection process in which a water or soil sample is taken at a single point of time using a container type known as a grab sampler.", "meaning": "GENEPIO:0100953" }, - "Composite sampling": { - "text": "Composite sampling", + "Bag Mediated Filtration [GENEPIO:0102028]": { + "text": "Bag Mediated Filtration [GENEPIO:0102028]", + "meaning": "GENEPIO:0102028" + }, + "Composite sampling [GENEPIO:0100954]": { + "text": "Composite sampling [GENEPIO:0100954]", + "description": "An environmental material collection process in which mutliple water or soil samples are taken at different time points and combined to produce a composite. Samples can be collected continuously or at discrete time points.", "meaning": "GENEPIO:0100954" }, - "Passive composite sampling": { - "text": "Passive composite sampling", + "Passive composite sampling [GENEPIO:0100955]": { + "text": "Passive composite sampling [GENEPIO:0100955]", + "description": "A method of composite sampling in which a continuous sample is collected passively without electrical input minimizing cost.", "meaning": "GENEPIO:0100955", - "is_a": "Composite sampling" + "is_a": "Composite sampling [GENEPIO:0100954]" }, - "Automatic composite sampling": { - "text": "Automatic composite sampling", + "Automatic composite sampling [GENEPIO:0100956]": { + "text": "Automatic composite sampling [GENEPIO:0100956]", + "description": "A method of composite sampling which utilizes an automated system to collect multiple samples, continuously or at discrete timepoints.", "meaning": "GENEPIO:0100956", - "is_a": "Composite sampling" + "is_a": "Composite sampling [GENEPIO:0100954]" }, - "Manual composite sampling": { - "text": "Manual composite sampling", + "Manual composite sampling [GENEPIO:0100957]": { + "text": "Manual composite sampling [GENEPIO:0100957]", + "description": "A method of composite sampling in which multiple grab samples from discrete time points are taken and then combined to produce a single composite sample.", "meaning": "GENEPIO:0100957", - "is_a": "Composite sampling" + "is_a": "Composite sampling [GENEPIO:0100954]" } } }, - "water catchment area human population range menu": { - "name": "water catchment area human population range menu", + "WaterCatchmentAreaHumanPopulationRangeMenu": { + "name": "WaterCatchmentAreaHumanPopulationRangeMenu", + "title": "water catchment area human population range menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "<10 people": { - "text": "<10 people" + "text": "<10 people", + "description": "An estimation of population size for a group smaller than 10 people." }, "10 - 100 people": { - "text": "10 - 100 people" + "text": "10 - 100 people", + "description": "An estimation of population size for a group smaller than 100 people and larger than 10 people." }, "100 - 1,000 people": { - "text": "100 - 1,000 people" + "text": "100 - 1,000 people", + "description": "An estimation of population size for a group smaller than 1,000 people and larger than 100 people." }, "1,000 - 10,000 people": { - "text": "1,000 - 10,000 people" + "text": "1,000 - 10,000 people", + "description": "An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people." }, "10,000 - 100,000 people": { - "text": "10,000 - 100,000 people" + "text": "10,000 - 100,000 people", + "description": "An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people." }, "100,000 - 1,000,000 people": { - "text": "100,000 - 1,000,000 people" + "text": "100,000 - 1,000,000 people", + "description": "An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people." }, "1,000,000+ people": { - "text": "1,000,000+ people" + "text": "1,000,000+ people", + "description": "An estimation of population size for a group larger than 1,000,000 people." } } }, - "water catchment area human population density unit menu": { - "name": "water catchment area human population density unit menu", + "WaterCatchmentAreaHumanPopulationDensityUnitMenu": { + "name": "WaterCatchmentAreaHumanPopulationDensityUnitMenu", + "title": "water catchment area human population density unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "persons per square mile": { - "text": "persons per square mile", + "persons per square mile [GENEPIO:0100989]": { + "text": "persons per square mile [GENEPIO:0100989]", + "description": "A unit of population density that describes the average number of people in a square mile of a given area.", "meaning": "GENEPIO:0100989" }, - "persons per square kilometer": { - "text": "persons per square kilometer", + "persons per square kilometer [GENEPIO:0100990]": { + "text": "persons per square kilometer [GENEPIO:0100990]", + "description": "A unit of population density that describes the average number of people in a square kilometer of a given area.", "meaning": "GENEPIO:0100990" }, - "residents per square mile": { - "text": "residents per square mile", + "residents per square mile [GENEPIO:0100991]": { + "text": "residents per square mile [GENEPIO:0100991]", + "description": "A unit of population density that describes the average number of registered residents in a square mile of a given area.", "meaning": "GENEPIO:0100991" }, - "residents per square kilometer": { - "text": "residents per square kilometer", + "residents per square kilometer [GENEPIO:0100992]": { + "text": "residents per square kilometer [GENEPIO:0100992]", + "description": "A unit of population density that describes the average number of registered residents in a square kilometer of a given area.", "meaning": "GENEPIO:0100992" } } }, - "populated area type menu": { - "name": "populated area type menu", + "PopulatedAreaTypeMenu": { + "name": "PopulatedAreaTypeMenu", + "title": "populated area type menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Suburban": { - "text": "Suburban", + "Suburban [GSSO:011077]": { + "text": "Suburban [GSSO:011077]", + "description": "A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities.", "meaning": "GSSO:011077" }, - "Rural": { - "text": "Rural", + "Rural [GSSO:011078]": { + "text": "Rural [GSSO:011078]", + "description": "A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements.", "meaning": "GSSO:011078" }, - "Urban": { - "text": "Urban", + "Urban [GSSO:011080]": { + "text": "Urban [GSSO:011080]", + "description": "A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment.", "meaning": "GSSO:011080" } } }, - "sampling weather conditions menu": { - "name": "sampling weather conditions menu", + "SamplingWeatherConditionsMenu": { + "name": "SamplingWeatherConditionsMenu", + "title": "sampling weather conditions menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Cloudy/Overcast": { - "text": "Cloudy/Overcast", + "Cloudy/Overcast [ENVO:03501418]": { + "text": "Cloudy/Overcast [ENVO:03501418]", + "description": "Atmospheric weather in which the sky is mostly or completely obscured by clouds.", "meaning": "ENVO:03501418" }, - "Partially cloudy": { - "text": "Partially cloudy", + "Partially cloudy [ENVO:03501419]": { + "text": "Partially cloudy [ENVO:03501419]", + "description": "Atmospheric weather in which the sky is partially obscured by clouds.", "meaning": "ENVO:03501419", - "is_a": "Cloudy/Overcast" + "is_a": "Cloudy/Overcast [ENVO:03501418]" }, - "Drizzle": { - "text": "Drizzle", + "Drizzle [ENVO:03501420]": { + "text": "Drizzle [ENVO:03501420]", + "description": "An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process.", "meaning": "ENVO:03501420" }, - "Fog": { - "text": "Fog", + "Fog [ENVO:01000844]": { + "text": "Fog [ENVO:01000844]", + "description": "A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.", "meaning": "ENVO:01000844" }, - "Rain": { - "text": "Rain", + "Rain [ENVO:01001564]": { + "text": "Rain [ENVO:01001564]", + "description": "An aggregate of raindrops falling to a planetary surface during a precipitation process.", "meaning": "ENVO:01001564" }, - "Snow": { - "text": "Snow", + "Snow [ENVO:01000406]": { + "text": "Snow [ENVO:01000406]", + "description": "Snow is an environmental material which is primarily composed of flakes of crystalline water ice.", "meaning": "ENVO:01000406" }, - "Storm": { - "text": "Storm", + "Storm [ENVO:01000876]": { + "text": "Storm [ENVO:01000876]", + "description": "A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.", "meaning": "ENVO:01000876" }, - "Sunny/Clear": { - "text": "Sunny/Clear", + "Sunny/Clear [ENVO:03501421]": { + "text": "Sunny/Clear [ENVO:03501421]", + "description": "Atmospheric weather in which the sun can be seen to shine brightly.", "meaning": "ENVO:03501421" } } }, - "presampling weather conditions menu": { - "name": "presampling weather conditions menu", + "PresamplingWeatherConditionsMenu": { + "name": "PresamplingWeatherConditionsMenu", + "title": "presampling weather conditions menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Cloudy/Overcast": { - "text": "Cloudy/Overcast", + "Cloudy/Overcast [ENVO:03501418]": { + "text": "Cloudy/Overcast [ENVO:03501418]", + "description": "Atmospheric weather in which the sky is mostly or completely obscured by clouds.", "meaning": "ENVO:03501418" }, - "Partially cloudy": { - "text": "Partially cloudy", + "Partially cloudy [ENVO:03501419]": { + "text": "Partially cloudy [ENVO:03501419]", + "description": "Atmospheric weather in which the sky is partially obscured by clouds.", "meaning": "ENVO:03501419", - "is_a": "Cloudy/Overcast" + "is_a": "Cloudy/Overcast [ENVO:03501418]" }, - "Drizzle": { - "text": "Drizzle", + "Drizzle [ENVO:03501420]": { + "text": "Drizzle [ENVO:03501420]", + "description": "An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process.", "meaning": "ENVO:03501420" }, - "Fog": { - "text": "Fog", + "Fog [ENVO:01000844]": { + "text": "Fog [ENVO:01000844]", + "description": "A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.", "meaning": "ENVO:01000844" }, - "Rain": { - "text": "Rain", + "Rain [ENVO:01001564]": { + "text": "Rain [ENVO:01001564]", + "description": "An aggregate of raindrops falling to a planetary surface during a precipitation process.", "meaning": "ENVO:01001564" }, - "Snow": { - "text": "Snow", + "Snow [ENVO:01000406]": { + "text": "Snow [ENVO:01000406]", + "description": "Snow is an environmental material which is primarily composed of flakes of crystalline water ice.", "meaning": "ENVO:01000406" }, - "Storm": { - "text": "Storm", + "Storm [ENVO:01000876]": { + "text": "Storm [ENVO:01000876]", + "description": "A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.", "meaning": "ENVO:01000876" }, - "Sunny/Clear": { - "text": "Sunny/Clear", + "Sunny/Clear [ENVO:03501421]": { + "text": "Sunny/Clear [ENVO:03501421]", + "description": "Atmospheric weather in which the sun can be seen to shine brightly.", "meaning": "ENVO:03501421" } } }, - "precipitation measurement unit menu": { - "name": "precipitation measurement unit menu", + "PrecipitationMeasurementUnitMenu": { + "name": "PrecipitationMeasurementUnitMenu", + "title": "precipitation measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "millimeter (mm)": { - "text": "millimeter (mm)", + "millimeter (mm) [UO:0000016]": { + "text": "millimeter (mm) [UO:0000016]", + "description": "A length unit which is defined as one thousandth of a meter.", "meaning": "UO:0000016" }, - "centimeter (cm)": { - "text": "centimeter (cm)", + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", "meaning": "UO:0000015" }, - "meter (m)": { - "text": "meter (m)", + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", "meaning": "UO:0000008" }, - "inch (in)": { - "text": "inch (in)", + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", "meaning": "UO:0010011" }, - "foot (ft)": { - "text": "foot (ft)", + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", "meaning": "UO:0010013" } } }, - "air pressure measurement unit menu": { - "name": "air pressure measurement unit menu", + "AirPressureMeasurementUnitMenu": { + "name": "AirPressureMeasurementUnitMenu", + "title": "air pressure measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "atmosphere (atm)": { - "text": "atmosphere (atm)", + "atmosphere (atm) [EFO:0005212]": { + "text": "atmosphere (atm) [EFO:0005212]", + "description": "A non-SI unit of pressure defined as 101,325 pascals (Pa).", "meaning": "EFO:0005212" }, "bar": { "text": "bar" }, - "pascal": { - "text": "pascal", + "pascal [UO:0000110]": { + "text": "pascal [UO:0000110]", + "description": "An SI unit of pressure defined as one newton per square meter (N/m^2).", "meaning": "UO:0000110" } } }, - "ambient temperature measurement unit menu": { - "name": "ambient temperature measurement unit menu", + "AmbientTemperatureMeasurementUnitMenu": { + "name": "AmbientTemperatureMeasurementUnitMenu", + "title": "ambient temperature measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "degree Fahrenheit (F)": { - "text": "degree Fahrenheit (F)", + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", "meaning": "UO:0000195" }, - "degree Celsius (C)": { - "text": "degree Celsius (C)", + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", "meaning": "UO:0000027" } } }, - "total daily flow rate measurement unit menu": { - "name": "total daily flow rate measurement unit menu", + "TotalDailyFlowRateMeasurementUnitMenu": { + "name": "TotalDailyFlowRateMeasurementUnitMenu", + "title": "total daily flow rate measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "cubic meter per second (m^3/s)": { - "text": "cubic meter per second (m^3/s)" + "text": "cubic meter per second (m^3/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second." }, "cubic meter per minute (m^3/min)": { - "text": "cubic meter per minute (m^3/min)" + "text": "cubic meter per minute (m^3/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute." }, "cubic meter per hour (m^3/h)": { - "text": "cubic meter per hour (m^3/h)" + "text": "cubic meter per hour (m^3/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour." }, "liter per second (L/s)": { - "text": "liter per second (L/s)" + "text": "liter per second (L/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second." }, "liter per minute (L/min)": { - "text": "liter per minute (L/min)" + "text": "liter per minute (L/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute." }, "liter per hour (L/h)": { - "text": "liter per hour (L/h)" + "text": "liter per hour (L/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour." }, "liter per day (L/day)": { - "text": "liter per day (L/day)" + "text": "liter per day (L/day)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day." }, "million gallons per day (MGD)": { - "text": "million gallons per day (MGD)" + "text": "million gallons per day (MGD)", + "description": "A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day." } } }, - "instantaneous flow rate measurement unit menu": { - "name": "instantaneous flow rate measurement unit menu", + "InstantaneousFlowRateMeasurementUnitMenu": { + "name": "InstantaneousFlowRateMeasurementUnitMenu", + "title": "instantaneous flow rate measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "cubic meter per second (m^3/s)": { - "text": "cubic meter per second (m^3/s)" + "text": "cubic meter per second (m^3/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second." }, "cubic meter per minute (m^3/min)": { - "text": "cubic meter per minute (m^3/min)" + "text": "cubic meter per minute (m^3/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute." }, "cubic meter per hour (m^3/h)": { - "text": "cubic meter per hour (m^3/h)" + "text": "cubic meter per hour (m^3/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour." }, "liter per second (L/s)": { - "text": "liter per second (L/s)" + "text": "liter per second (L/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second." }, "liter per minute (L/min)": { - "text": "liter per minute (L/min)" + "text": "liter per minute (L/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute." }, "liter per hour (L/h)": { - "text": "liter per hour (L/h)" + "text": "liter per hour (L/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour." }, "liter per day (L/day)": { - "text": "liter per day (L/day)" + "text": "liter per day (L/day)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day." }, "million gallons per day (MGD)": { - "text": "million gallons per day (MGD)" + "text": "million gallons per day (MGD)", + "description": "A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day." } } }, - "turbidity measurement unit menu": { - "name": "turbidity measurement unit menu", + "TurbidityMeasurementUnitMenu": { + "name": "TurbidityMeasurementUnitMenu", + "title": "turbidity measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "nephelometric turbidity unit (NTU)": { - "text": "nephelometric turbidity unit (NTU)" + "text": "nephelometric turbidity unit (NTU)", + "description": "A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample." }, - "formazin nephelometric unit (FNU)": { - "text": "formazin nephelometric unit (FNU)", + "formazin nephelometric unit (FNU) [UO:0000318]": { + "text": "formazin nephelometric unit (FNU) [UO:0000318]", + "description": "A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin.", "meaning": "UO:0000318" } } }, - "dissolved oxygen measurement unit menu": { - "name": "dissolved oxygen measurement unit menu", + "DissolvedOxygenMeasurementUnitMenu": { + "name": "DissolvedOxygenMeasurementUnitMenu", + "title": "dissolved oxygen measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "milligram per liter (mg/L)": { - "text": "milligram per liter (mg/L)", + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", "meaning": "UO:0000273" }, - "kilogram per cubic meter (kg/m^3)": { - "text": "kilogram per cubic meter (kg/m^3)", + "kilogram per cubic meter (kg/m^3) [UO:0000083]": { + "text": "kilogram per cubic meter (kg/m^3) [UO:0000083]", + "description": "An SI unit of density that is one thousandth of the density of water.", "meaning": "UO:0000083" }, - "part per million (ppm)": { - "text": "part per million (ppm)", + "part per million (ppm) [UO:0000169]": { + "text": "part per million (ppm) [UO:0000169]", + "description": "A unitless measure of density that represents one item out of a million.", "meaning": "UO:0000169" } } }, - "oxygen reduction potential (ORP) measurement unit menu": { - "name": "oxygen reduction potential (ORP) measurement unit menu", + "OxygenReductionPotentialOrpMeasurementUnitMenu": { + "name": "OxygenReductionPotentialOrpMeasurementUnitMenu", + "title": "oxygen reduction potential (ORP) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "milliVolt (mV)": { - "text": "milliVolt (mV)", + "milliVolt (mV) [UO:0000247]": { + "text": "milliVolt (mV) [UO:0000247]", + "description": "A non-SI unit of electromotive force that is one thousandth of a volt.", "meaning": "UO:0000247" } } }, - "chemical oxygen demand (COD) measurement unit menu": { - "name": "chemical oxygen demand (COD) measurement unit menu", + "ChemicalOxygenDemandCodMeasurementUnitMenu": { + "name": "ChemicalOxygenDemandCodMeasurementUnitMenu", + "title": "chemical oxygen demand (COD) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "milligram per liter (mg/L)": { - "text": "milligram per liter (mg/L)", + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", "meaning": "UO:0000273" } } }, - "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu", + "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu": { + "name": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu", + "title": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "milligram per liter (mg/L)": { - "text": "milligram per liter (mg/L)", + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", "meaning": "UO:0000273" } } }, - "total suspended solids (TSS) measurement unit menu": { - "name": "total suspended solids (TSS) measurement unit menu", + "TotalSuspendedSolidsTssMeasurementUnitMenu": { + "name": "TotalSuspendedSolidsTssMeasurementUnitMenu", + "title": "total suspended solids (TSS) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "percent (%)": { - "text": "percent (%)", + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", "meaning": "UO:0000187" }, - "gram per liter (g/L)": { - "text": "gram per liter (g/L)", + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", "meaning": "UO:0000175" } } }, - "total dissolved solids (TDS) measurement unit menu": { - "name": "total dissolved solids (TDS) measurement unit menu", + "TotalDissolvedSolidsTdsMeasurementUnitMenu": { + "name": "TotalDissolvedSolidsTdsMeasurementUnitMenu", + "title": "total dissolved solids (TDS) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "percent (%)": { - "text": "percent (%)", + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", "meaning": "UO:0000187" }, - "gram per liter (g/L)": { - "text": "gram per liter (g/L)", + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", "meaning": "UO:0000175" } } }, - "total solids (TS) measurement unit menu": { - "name": "total solids (TS) measurement unit menu", + "TotalSolidsTsMeasurementUnitMenu": { + "name": "TotalSolidsTsMeasurementUnitMenu", + "title": "total solids (TS) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "percent (%)": { - "text": "percent (%)", + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", "meaning": "UO:0000187" }, - "gram per liter (g/L)": { - "text": "gram per liter (g/L)", + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", "meaning": "UO:0000175" } } }, - "alkalinity measurement unit menu": { - "name": "alkalinity measurement unit menu", + "AlkalinityMeasurementUnitMenu": { + "name": "AlkalinityMeasurementUnitMenu", + "title": "alkalinity measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "milliequivalent per liter (meq/L)": { - "text": "milliequivalent per liter (meq/L)" + "text": "milliequivalent per liter (meq/L)", + "description": "A unit of ion concentration that represents chemical activity per volume." }, - "milligram per liter (mg/L)": { - "text": "milligram per liter (mg/L)", + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", "meaning": "UO:0000273" }, - "parts per million": { - "text": "parts per million", + "parts per million [UO:0000169]": { + "text": "parts per million [UO:0000169]", + "description": "A unitless measure of density that represents one item out of a million.", "meaning": "UO:0000169" } } }, - "conductivity measurement unit menu": { - "name": "conductivity measurement unit menu", + "ConductivityMeasurementUnitMenu": { + "name": "ConductivityMeasurementUnitMenu", + "title": "conductivity measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "milliSiemen per centimeter (mS/cm)": { - "text": "milliSiemen per centimeter (mS/cm)" + "text": "milliSiemen per centimeter (mS/cm)", + "description": "A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m)." }, "microSiemen per centimeter (μS/cm)": { - "text": "microSiemen per centimeter (μS/cm)" + "text": "microSiemen per centimeter (μS/cm)", + "description": "A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m)." }, "Siemen per meter (S/m)": { - "text": "Siemen per meter (S/m)" + "text": "Siemen per meter (S/m)", + "description": "An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m)." } } }, - "salinity measurement unit menu": { - "name": "salinity measurement unit menu", + "SalinityMeasurementUnitMenu": { + "name": "SalinityMeasurementUnitMenu", + "title": "salinity measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "practical salinity unit (PSU)": { - "text": "practical salinity unit (PSU)" + "text": "practical salinity unit (PSU)", + "description": "A unitless measure of salinity that is equivalent to per thousand." }, "weight for weight (% w/w)": { - "text": "weight for weight (% w/w)" + "text": "weight for weight (% w/w)", + "description": "A unitless comparison based on weight rather than volume, which is equivalent to per hundred." }, - "parts per thousand": { - "text": "parts per thousand", + "parts per thousand [UO:0000168]": { + "text": "parts per thousand [UO:0000168]", + "description": "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same.", "meaning": "UO:0000168" }, - "gram per liter (g/L)": { - "text": "gram per liter (g/L)", + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", "meaning": "UO:0000175" } } }, - "total nitrogen (TN) measurement unit menu": { - "name": "total nitrogen (TN) measurement unit menu", + "TotalNitrogenTnMeasurementUnitMenu": { + "name": "TotalNitrogenTnMeasurementUnitMenu", + "title": "total nitrogen (TN) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "milligram per liter (mg/L)": { - "text": "milligram per liter (mg/L)", + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", "meaning": "UO:0000273" }, - "gram per liter (g/L)": { - "text": "gram per liter (g/L)", + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", "meaning": "UO:0000175" - }, + } + } + }, + "total nitrogen (TN) measurement unit menu": { + "name": "total nitrogen (TN) measurement unit menu", + "title": "total nitrogen (TN) measurement unit menu", + "from_schema": "https://example.com/GRDI", + "permissible_values": { "gram per total solids (g/gTS)": { - "text": "gram per total solids (g/gTS)" + "text": "gram per total solids (g/gTS)", + "description": "A unitless comparison of the weight of a substance as a proportion to the weight of total solids." } } }, - "total phosphorpus (TP) measurement unit menu": { - "name": "total phosphorpus (TP) measurement unit menu", + "TotalPhosphorpusTpMeasurementUnitMenu": { + "name": "TotalPhosphorpusTpMeasurementUnitMenu", + "title": "total phosphorpus (TP) measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "gram per total solids (g/gTS)": { - "text": "gram per total solids (g/gTS)" + "text": "gram per total solids (g/gTS)", + "description": "A unitless comparison of the weight of a substance as a proportion to the weight of total solids." }, - "orthophosphate as phosphorus per total solids (gPO4-P/gTS)": { - "text": "orthophosphate as phosphorus per total solids (gPO4-P/gTS)", + "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]": { + "text": "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]", + "description": "A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids.", "meaning": "GENEPIO:0100998" }, - "milligrams per liter (mg/L)": { - "text": "milligrams per liter (mg/L)", + "milligrams per liter (mg/L) [UO:0000273]": { + "text": "milligrams per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", "meaning": "UO:0000273" }, - "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)": { - "text": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)", + "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]": { + "text": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]", + "description": "A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume.", "meaning": "GENEPIO:0100999" } } }, - "fecal contamination indicator menu": { - "name": "fecal contamination indicator menu", + "FecalContaminationIndicatorMenu": { + "name": "FecalContaminationIndicatorMenu", + "title": "fecal contamination indicator menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "crAssphage": { - "text": "crAssphage", + "crAssphage [NCBITaxon:1211417]": { + "text": "crAssphage [NCBITaxon:1211417]", + "description": "CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome.", "meaning": "NCBITaxon:1211417" }, - "PMMoV / pepper mild mottle virus": { - "text": "PMMoV / pepper mild mottle virus", + "PMMoV / pepper mild mottle virus [NCBITaxon:12239]": { + "text": "PMMoV / pepper mild mottle virus [NCBITaxon:12239]", + "description": "A plant RNA virus that is abundant in human feces.", "meaning": "NCBITaxon:12239" }, - "Bacteroides HF183": { - "text": "Bacteroides HF183", + "Bacteroides HF183 [GENEPIO:0101000]": { + "text": "Bacteroides HF183 [GENEPIO:0101000]", + "description": "A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus.", "meaning": "GENEPIO:0101000" }, - "Lachnospiraceae Lachno3": { - "text": "Lachnospiraceae Lachno3", + "Lachnospiraceae Lachno3 [GENEPIO:0101001]": { + "text": "Lachnospiraceae Lachno3 [GENEPIO:0101001]", + "description": "A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria.", "meaning": "GENEPIO:0101001" }, - "F+ (male specific) coliphages": { - "text": "F+ (male specific) coliphages", + "F+ (male specific) coliphages [GENEPIO:0101002]": { + "text": "F+ (male specific) coliphages [GENEPIO:0101002]", + "description": "A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment.", "meaning": "GENEPIO:0101002" }, - "Stercobilin": { - "text": "Stercobilin", + "Stercobilin [CHEBI:26756]": { + "text": "Stercobilin [CHEBI:26756]", + "description": "Bile pigment found in fecal material.", "meaning": "CHEBI:26756" } } }, - "fecal contamination unit menu": { - "name": "fecal contamination unit menu", + "FecalContaminationUnitMenu": { + "name": "FecalContaminationUnitMenu", + "title": "fecal contamination unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "log10 gene copies per 100 milliliter (log10 GC/100 mL)": { - "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)" + "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)", + "description": "A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material." }, "gene copies per liter (GC/L)": { - "text": "gene copies per liter (GC/L)" + "text": "gene copies per liter (GC/L)", + "description": "A unit that measures the number of copies of a given gene within a liter of a biological material." }, - "PCR quantification cycle": { - "text": "PCR quantification cycle", + "PCR quantification cycle [UO:0010077]": { + "text": "PCR quantification cycle [UO:0010077]", + "description": "A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line.", "meaning": "UO:0010077" }, "log10 gene copies per nanogram total DNA": { - "text": "log10 gene copies per nanogram total DNA" + "text": "log10 gene copies per nanogram total DNA", + "description": "A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material." } } }, - "urinary contamination indicator menu": { - "name": "urinary contamination indicator menu", + "UrinaryContaminationIndicatorMenu": { + "name": "UrinaryContaminationIndicatorMenu", + "title": "urinary contamination indicator menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Urobilin": { - "text": "Urobilin", + "Urobilin [CHEBI:36378]": { + "text": "Urobilin [CHEBI:36378]", + "description": "A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome.", "meaning": "CHEBI:36378" } } }, - "urinary contamination unit menu": { - "name": "urinary contamination unit menu", + "UrinaryContaminationUnitMenu": { + "name": "UrinaryContaminationUnitMenu", + "title": "urinary contamination unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "nanograms per liter (ng/L)": { - "text": "nanograms per liter (ng/L)", + "nanograms per liter (ng/L) [EFO:0004382]": { + "text": "nanograms per liter (ng/L) [EFO:0004382]", + "description": "A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters.", "meaning": "EFO:0004382" } } }, - "fecal coliform count unit menu": { - "name": "fecal coliform count unit menu", + "FecalColiformCountUnitMenu": { + "name": "FecalColiformCountUnitMenu", + "title": "fecal coliform count unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "colony forming units per milliliter (CFU/mL)": { - "text": "colony forming units per milliliter (CFU/mL)", + "colony forming units per milliliter (CFU/mL) [UO:0000213]": { + "text": "colony forming units per milliliter (CFU/mL) [UO:0000213]", + "description": "A unit of microbial density that describes the number of colony forming units within a milliliter of material.", "meaning": "UO:0000213" }, "colony forming units per 100 milliliter (CFU/100 mL)": { - "text": "colony forming units per 100 milliliter (CFU/100 mL)" + "text": "colony forming units per 100 milliliter (CFU/100 mL)", + "description": "A unit of microbial density that describes the number of colony forming units within 100 milliliters of material." }, "colony forming units per grams total solids (CFU/gTS)": { - "text": "colony forming units per grams total solids (CFU/gTS)" + "text": "colony forming units per grams total solids (CFU/gTS)", + "description": "A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material." }, "most probable number per milliliter (MPN/mL)": { - "text": "most probable number per milliliter (MPN/mL)" + "text": "most probable number per milliliter (MPN/mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within one milliliter of material." }, "most probable number per 100 milliliter (MPN/100 mL)": { - "text": "most probable number per 100 milliliter (MPN/100 mL)" + "text": "most probable number per 100 milliliter (MPN/100 mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material." } } }, - "sample temperature unit (at collection) menu": { - "name": "sample temperature unit (at collection) menu", + "SampleTemperatureUnitAtCollectionMenu": { + "name": "SampleTemperatureUnitAtCollectionMenu", + "title": "sample temperature unit (at collection) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "degree Fahrenheit (F)": { - "text": "degree Fahrenheit (F)", + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", "meaning": "UO:0000195" }, - "degree Celsius (C)": { - "text": "degree Celsius (C)", + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", "meaning": "UO:0000027" } } }, - "sample temperature unit (when received) menu": { - "name": "sample temperature unit (when received) menu", + "SampleTemperatureUnitWhenReceivedMenu": { + "name": "SampleTemperatureUnitWhenReceivedMenu", + "title": "sample temperature unit (when received) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "degree Fahrenheit (F)": { - "text": "degree Fahrenheit (F)", + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", "meaning": "UO:0000195" }, - "degree Celsius (C)": { - "text": "degree Celsius (C)", + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", "meaning": "UO:0000027" } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose of sequencing menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Baseline surveillance (random sampling)": { - "text": "Baseline surveillance (random sampling)", + "Baseline surveillance (random sampling) [GENEPIO:0100005]": { + "text": "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "description": "A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.", "meaning": "GENEPIO:0100005" }, - "Targeted surveillance (non-random sampling)": { - "text": "Targeted surveillance (non-random sampling)", + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]": { + "text": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "description": "A surveillance sampling strategy in which an aspired outcome is explicitly stated.", "meaning": "GENEPIO:0100006" }, - "Priority surveillance project": { - "text": "Priority surveillance project", + "Priority surveillance project [GENEPIO:0100007]": { + "text": "Priority surveillance project [GENEPIO:0100007]", + "description": "A targeted surveillance strategy which is considered important and/or urgent.", "meaning": "GENEPIO:0100007" }, - "Longitudinal surveillance (repeat sampling)": { - "text": "Longitudinal surveillance (repeat sampling)", + "Longitudinal surveillance (repeat sampling) [GENEPIO:0100009]": { + "text": "Longitudinal surveillance (repeat sampling) [GENEPIO:0100009]", + "description": "A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time.", "meaning": "GENEPIO:0100009" }, - "Travel-associated surveillance": { - "text": "Travel-associated surveillance", + "Travel-associated surveillance [GENEPIO:0100012]": { + "text": "Travel-associated surveillance [GENEPIO:0100012]", + "description": "A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored.", "meaning": "GENEPIO:0100012" }, - "Domestic travel surveillance": { - "text": "Domestic travel surveillance", + "Domestic travel surveillance [GENEPIO:0100013]": { + "text": "Domestic travel surveillance [GENEPIO:0100013]", + "description": "A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to domestic travel.", "meaning": "GENEPIO:0100013", - "is_a": "Travel-associated surveillance" + "is_a": "Travel-associated surveillance [GENEPIO:0100012]" }, - "International travel surveillance": { - "text": "International travel surveillance", + "International travel surveillance [GENEPIO:0100014]": { + "text": "International travel surveillance [GENEPIO:0100014]", + "description": "A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to international travel.", "meaning": "GENEPIO:0100014", - "is_a": "Travel-associated surveillance" + "is_a": "Travel-associated surveillance [GENEPIO:0100012]" }, - "Research": { - "text": "Research", + "Research [GENEPIO:0100022]": { + "text": "Research [GENEPIO:0100022]", + "description": "A sampling strategy in which sites are sampled in order to perform research.", "meaning": "GENEPIO:0100022" }, - "Viral passage experiment": { - "text": "Viral passage experiment", + "Viral passage experiment [GENEPIO:0100023]": { + "text": "Viral passage experiment [GENEPIO:0100023]", + "description": "A research sampling strategy in which samples are selected in order to perform a viral passage experiment.", "meaning": "GENEPIO:0100023", - "is_a": "Research" + "is_a": "Research [GENEPIO:0100022]" }, - "Protocol testing experiment": { - "text": "Protocol testing experiment", + "Protocol testing experiment [GENEPIO:0100024]": { + "text": "Protocol testing experiment [GENEPIO:0100024]", + "description": "A research sampling strategy in which samples are collected in order to test a method or protocol.", "meaning": "GENEPIO:0100024", - "is_a": "Research" + "is_a": "Research [GENEPIO:0100022]" } } }, - "sequencing platform menu": { - "name": "sequencing platform menu", + "SequencingPlatformMenu": { + "name": "SequencingPlatformMenu", + "title": "sequencing platform menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Illumina": { - "text": "Illumina", + "Illumina [GENEPIO:0001923]": { + "text": "Illumina [GENEPIO:0001923]", + "description": "A sequencing platform provided by the Illumina company.", "meaning": "GENEPIO:0001923" }, - "Pacific Biosciences": { - "text": "Pacific Biosciences", + "Pacific Biosciences [GENEPIO:0001927]": { + "text": "Pacific Biosciences [GENEPIO:0001927]", + "description": "A sequencing platform provided by the Pacific Biosciences company.", "meaning": "GENEPIO:0001927" }, - "Ion Torrent": { - "text": "Ion Torrent", + "Ion Torrent [GENEPIO:0002683]": { + "text": "Ion Torrent [GENEPIO:0002683]", + "description": "A sequencing platform provided by the Ion Torrent company.", "meaning": "GENEPIO:0002683" }, - "Oxford Nanopore Technologies": { - "text": "Oxford Nanopore Technologies", + "Oxford Nanopore Technologies [GENEPIO:0100986]": { + "text": "Oxford Nanopore Technologies [GENEPIO:0100986]", + "description": "An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK.", "meaning": "GENEPIO:0100986" }, - "BGI Genomics": { - "text": "BGI Genomics", + "BGI Genomics [GENEPIO:0004324]": { + "text": "BGI Genomics [GENEPIO:0004324]", + "description": "A sequencing platform provided by the BGI Genomics company.", "meaning": "GENEPIO:0004324" }, - "MGI": { - "text": "MGI", + "MGI [GENEPIO:0004325]": { + "text": "MGI [GENEPIO:0004325]", + "description": "A sequencing platform provided by the MGI company.", "meaning": "GENEPIO:0004325" }, - "Roche LS454": { - "text": "Roche LS454", + "Roche LS454 [GENEPIO:0001926]": { + "text": "Roche LS454 [GENEPIO:0001926]", + "description": "A sequencing platform provided by the 454 Life Sciences company.", "meaning": "GENEPIO:0001926" }, - "SOLiD sequencing": { - "text": "SOLiD sequencing", + "SOLiD sequencing [GENEPIO:0002684]": { + "text": "SOLiD sequencing [GENEPIO:0002684]", + "description": "A sequencing platform provided by Life Technologies Corporation.", "meaning": "GENEPIO:0002684" }, - "Complete Genomics": { - "text": "Complete Genomics", + "Complete Genomics [GENEPIO:0001924]": { + "text": "Complete Genomics [GENEPIO:0001924]", + "description": "An in-house sequencing platform provided by Complete Genomics.", "meaning": "GENEPIO:0001924" }, - "Helicos": { - "text": "Helicos", + "Helicos [GENEPIO:0002682]": { + "text": "Helicos [GENEPIO:0002682]", + "description": "A sequencing platform brand provided by Helicos corporation (now defunct).", "meaning": "GENEPIO:0002682" }, - "Applied Biosystems": { - "text": "Applied Biosystems", + "Applied Biosystems [GENEPIO:0100985]": { + "text": "Applied Biosystems [GENEPIO:0100985]", + "description": "A sequencing platform provided by ThermoFisher.", "meaning": "GENEPIO:0100985" } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Illumina": { - "text": "Illumina", + "Illumina [GENEPIO:0100105]": { + "text": "Illumina [GENEPIO:0100105]", + "description": "A DNA sequencer manufactured by the Illumina corporation.", "meaning": "GENEPIO:0100105" }, - "Illumina Genome Analyzer": { - "text": "Illumina Genome Analyzer", + "Illumina Genome Analyzer [GENEPIO:0100106]": { + "text": "Illumina Genome Analyzer [GENEPIO:0100106]", + "description": "A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.", "meaning": "GENEPIO:0100106", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina Genome Analyzer II": { - "text": "Illumina Genome Analyzer II", + "Illumina Genome Analyzer II [OBI:0000703]": { + "text": "Illumina Genome Analyzer II [OBI:0000703]", + "description": "A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology.", "meaning": "OBI:0000703", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina Genome Analyzer IIx": { - "text": "Illumina Genome Analyzer IIx", + "Illumina Genome Analyzer IIx [OBI:0002000]": { + "text": "Illumina Genome Analyzer IIx [OBI:0002000]", + "description": "An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", "meaning": "OBI:0002000", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina HiScanSQ": { - "text": "Illumina HiScanSQ", + "Illumina HiScanSQ [GENEPIO:0100109]": { + "text": "Illumina HiScanSQ [GENEPIO:0100109]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an \"SQ Module\" to support microfluidics.", "meaning": "GENEPIO:0100109", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina HiSeq": { - "text": "Illumina HiSeq", + "Illumina HiSeq [GENEPIO:0100110]": { + "text": "Illumina HiSeq [GENEPIO:0100110]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.", "meaning": "GENEPIO:0100110", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina HiSeq X": { - "text": "Illumina HiSeq X", + "Illumina HiSeq X [GENEPIO:0100111]": { + "text": "Illumina HiSeq X [GENEPIO:0100111]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000.", "meaning": "GENEPIO:0100111", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq X Five": { - "text": "Illumina HiSeq X Five", + "Illumina HiSeq X Five [GENEPIO:0100112]": { + "text": "Illumina HiSeq X Five [GENEPIO:0100112]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", "meaning": "GENEPIO:0100112", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq X Ten": { - "text": "Illumina HiSeq X Ten", + "Illumina HiSeq X Ten [GENEPIO:0100113]": { + "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", + "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", "meaning": "GENEPIO:0100113", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 1000": { - "text": "Illumina HiSeq 1000", + "Illumina HiSeq 1000 [OBI:0002022]": { + "text": "Illumina HiSeq 1000 [OBI:0002022]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", "meaning": "OBI:0002022", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 1500": { - "text": "Illumina HiSeq 1500", + "Illumina HiSeq 1500 [GENEPIO:0100115]": { + "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day.", "meaning": "GENEPIO:0100115", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 2000": { - "text": "Illumina HiSeq 2000", + "Illumina HiSeq 2000 [OBI:0002001]": { + "text": "Illumina HiSeq 2000 [OBI:0002001]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", "meaning": "OBI:0002001", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 2500": { - "text": "Illumina HiSeq 2500", + "Illumina HiSeq 2500 [OBI:0002002]": { + "text": "Illumina HiSeq 2500 [OBI:0002002]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", "meaning": "OBI:0002002", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 3000": { - "text": "Illumina HiSeq 3000", + "Illumina HiSeq 3000 [OBI:0002048]": { + "text": "Illumina HiSeq 3000 [OBI:0002048]", + "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", "meaning": "OBI:0002048", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina HiSeq 4000": { - "text": "Illumina HiSeq 4000", + "Illumina HiSeq 4000 [OBI:0002049]": { + "text": "Illumina HiSeq 4000 [OBI:0002049]", + "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", "meaning": "OBI:0002049", - "is_a": "Illumina HiSeq" + "is_a": "Illumina HiSeq [GENEPIO:0100110]" }, - "Illumina iSeq": { - "text": "Illumina iSeq", + "Illumina iSeq [GENEPIO:0100120]": { + "text": "Illumina iSeq [GENEPIO:0100120]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", "meaning": "GENEPIO:0100120", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina iSeq 100": { - "text": "Illumina iSeq 100", + "Illumina iSeq 100 [GENEPIO:0100121]": { + "text": "Illumina iSeq 100 [GENEPIO:0100121]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", "meaning": "GENEPIO:0100121", - "is_a": "Illumina iSeq" + "is_a": "Illumina iSeq [GENEPIO:0100120]" }, - "Illumina NovaSeq": { - "text": "Illumina NovaSeq", + "Illumina NovaSeq [GENEPIO:0100122]": { + "text": "Illumina NovaSeq [GENEPIO:0100122]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode.", "meaning": "GENEPIO:0100122", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina NovaSeq 6000": { - "text": "Illumina NovaSeq 6000", + "Illumina NovaSeq 6000 [GENEPIO:0100123]": { + "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", "meaning": "GENEPIO:0100123", - "is_a": "Illumina NovaSeq" + "is_a": "Illumina NovaSeq [GENEPIO:0100122]" }, - "Illumina MiniSeq": { - "text": "Illumina MiniSeq", + "Illumina MiniSeq [GENEPIO:0100124]": { + "text": "Illumina MiniSeq [GENEPIO:0100124]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", "meaning": "GENEPIO:0100124", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina MiSeq": { - "text": "Illumina MiSeq", + "Illumina MiSeq [OBI:0002003]": { + "text": "Illumina MiSeq [OBI:0002003]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", "meaning": "OBI:0002003", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina NextSeq": { - "text": "Illumina NextSeq", + "Illumina NextSeq [GENEPIO:0100126]": { + "text": "Illumina NextSeq [GENEPIO:0100126]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", "meaning": "GENEPIO:0100126", - "is_a": "Illumina" + "is_a": "Illumina [GENEPIO:0100105]" }, - "Illumina NextSeq 500": { - "text": "Illumina NextSeq 500", + "Illumina NextSeq 500 [OBI:0002021]": { + "text": "Illumina NextSeq 500 [OBI:0002021]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", "meaning": "OBI:0002021", - "is_a": "Illumina NextSeq" + "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, - "Illumina NextSeq 550": { - "text": "Illumina NextSeq 550", + "Illumina NextSeq 550 [GENEPIO:0100128]": { + "text": "Illumina NextSeq 550 [GENEPIO:0100128]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", "meaning": "GENEPIO:0100128", - "is_a": "Illumina NextSeq" + "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, - "Illumina NextSeq 1000": { - "text": "Illumina NextSeq 1000", + "Illumina NextSeq 1000 [GENEPIO:0004432]": { + "text": "Illumina NextSeq 1000 [GENEPIO:0004432]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", "meaning": "GENEPIO:0004432", - "is_a": "Illumina NextSeq" + "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, - "Illumina NextSeq 2000": { - "text": "Illumina NextSeq 2000", + "Illumina NextSeq 2000 [GENEPIO:0100129]": { + "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", "meaning": "GENEPIO:0100129", - "is_a": "Illumina NextSeq" + "is_a": "Illumina NextSeq [GENEPIO:0100126]" }, - "PacBio": { - "text": "PacBio", + "PacBio [GENEPIO:0100130]": { + "text": "PacBio [GENEPIO:0100130]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation.", "meaning": "GENEPIO:0100130" }, - "PacBio RS": { - "text": "PacBio RS", + "PacBio RS [GENEPIO:0100131]": { + "text": "PacBio RS [GENEPIO:0100131]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", "meaning": "GENEPIO:0100131", - "is_a": "PacBio" + "is_a": "PacBio [GENEPIO:0100130]" }, - "PacBio RS II": { - "text": "PacBio RS II", + "PacBio RS II [OBI:0002012]": { + "text": "PacBio RS II [OBI:0002012]", + "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", "meaning": "OBI:0002012", - "is_a": "PacBio" + "is_a": "PacBio [GENEPIO:0100130]" }, - "PacBio Sequel": { - "text": "PacBio Sequel", + "PacBio Sequel [GENEPIO:0100133]": { + "text": "PacBio Sequel [GENEPIO:0100133]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", "meaning": "GENEPIO:0100133", - "is_a": "PacBio" + "is_a": "PacBio [GENEPIO:0100130]" }, - "PacBio Sequel II": { - "text": "PacBio Sequel II", + "PacBio Sequel II [GENEPIO:0100134]": { + "text": "PacBio Sequel II [GENEPIO:0100134]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", "meaning": "GENEPIO:0100134", - "is_a": "PacBio" + "is_a": "PacBio [GENEPIO:0100130]" }, - "Ion Torrent": { - "text": "Ion Torrent", + "Ion Torrent [GENEPIO:0100135]": { + "text": "Ion Torrent [GENEPIO:0100135]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation.", "meaning": "GENEPIO:0100135" }, - "Ion Torrent PGM": { - "text": "Ion Torrent PGM", + "Ion Torrent PGM [GENEPIO:0100136]": { + "text": "Ion Torrent PGM [GENEPIO:0100136]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", "meaning": "GENEPIO:0100136", - "is_a": "Ion Torrent" + "is_a": "Ion Torrent [GENEPIO:0100135]" }, - "Ion Torrent Proton": { - "text": "Ion Torrent Proton", + "Ion Torrent Proton [GENEPIO:0100137]": { + "text": "Ion Torrent Proton [GENEPIO:0100137]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", "meaning": "GENEPIO:0100137", - "is_a": "Ion Torrent" + "is_a": "Ion Torrent [GENEPIO:0100135]" }, - "Ion Torrent S5 XL": { - "text": "Ion Torrent S5 XL", + "Ion Torrent S5 XL [GENEPIO:0100138]": { + "text": "Ion Torrent S5 XL [GENEPIO:0100138]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", "meaning": "GENEPIO:0100138", - "is_a": "Ion Torrent" + "is_a": "Ion Torrent [GENEPIO:0100135]" }, - "Ion Torrent S5": { - "text": "Ion Torrent S5", + "Ion Torrent S5 [GENEPIO:0100139]": { + "text": "Ion Torrent S5 [GENEPIO:0100139]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", "meaning": "GENEPIO:0100139", - "is_a": "Ion Torrent" + "is_a": "Ion Torrent [GENEPIO:0100135]" }, - "Oxford Nanopore": { - "text": "Oxford Nanopore", + "Oxford Nanopore [GENEPIO:0100140]": { + "text": "Oxford Nanopore [GENEPIO:0100140]", + "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation.", "meaning": "GENEPIO:0100140" }, - "Oxford Nanopore Flongle": { - "text": "Oxford Nanopore Flongle", + "Oxford Nanopore Flongle [GENEPIO:0004433]": { + "text": "Oxford Nanopore Flongle [GENEPIO:0004433]", + "description": "An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.", "meaning": "GENEPIO:0004433", - "is_a": "Oxford Nanopore" + "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore GridION": { - "text": "Oxford Nanopore GridION", + "Oxford Nanopore GridION [GENEPIO:0100141]": { + "text": "Oxford Nanopore GridION [GENEPIO:0100141]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", "meaning": "GENEPIO:0100141", - "is_a": "Oxford Nanopore" + "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore MinION": { - "text": "Oxford Nanopore MinION", + "Oxford Nanopore MinION [GENEPIO:0100142]": { + "text": "Oxford Nanopore MinION [GENEPIO:0100142]", + "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", "meaning": "GENEPIO:0100142", - "is_a": "Oxford Nanopore" + "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "Oxford Nanopore PromethION": { - "text": "Oxford Nanopore PromethION", + "Oxford Nanopore PromethION [GENEPIO:0100143]": { + "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", "meaning": "GENEPIO:0100143", - "is_a": "Oxford Nanopore" + "is_a": "Oxford Nanopore [GENEPIO:0100140]" }, - "BGI Genomics sequencing instrument": { - "text": "BGI Genomics sequencing instrument", + "BGI Genomics sequencing instrument [GENEPIO:0100144]": { + "text": "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation.", "meaning": "GENEPIO:0100144" }, - "BGISEQ-500": { - "text": "BGISEQ-500", + "BGISEQ-500 [GENEPIO:0100145]": { + "text": "BGISEQ-500 [GENEPIO:0100145]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", "meaning": "GENEPIO:0100145", - "is_a": "BGI Genomics sequencing instrument" + "is_a": "BGI Genomics sequencing instrument [GENEPIO:0100144]" }, - "MGI sequencing instrument": { - "text": "MGI sequencing instrument", + "MGI sequencing instrument [GENEPIO:0100146]": { + "text": "MGI sequencing instrument [GENEPIO:0100146]", + "description": "A DNA sequencer manufactured by the MGI corporation.", "meaning": "GENEPIO:0100146" }, - "MGISEQ-2000RS": { - "text": "MGISEQ-2000RS", + "MGISEQ-2000RS [GENEPIO:0100971]": { + "text": "MGISEQ-2000RS [GENEPIO:0100971]", + "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing.", "meaning": "GENEPIO:0100971", - "is_a": "MGI sequencing instrument" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" }, - "MGI DNBSEQ-G99": { - "text": "MGI DNBSEQ-G99", + "MGI DNBSEQ-G99 [GENEPIO:0100972]": { + "text": "MGI DNBSEQ-G99 [GENEPIO:0100972]", + "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds.", "meaning": "GENEPIO:0100972", - "is_a": "MGI sequencing instrument" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" }, - "MGI DNBSEQ-G400": { - "text": "MGI DNBSEQ-G400", + "MGI DNBSEQ-G400 [GENEPIO:0100148]": { + "text": "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run.", "meaning": "GENEPIO:0100148", - "is_a": "MGI sequencing instrument" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" }, - "MGI DNBSEQ-G400RS FAST": { - "text": "MGI DNBSEQ-G400RS FAST", + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]": { + "text": "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400.", "meaning": "GENEPIO:0100149", - "is_a": "MGI DNBSEQ-G400" + "is_a": "MGI DNBSEQ-G400 [GENEPIO:0100148]" }, - "MGI DNBSEQ-T7": { - "text": "MGI DNBSEQ-T7", + "MGI DNBSEQ-T7 [GENEPIO:0100147]": { + "text": "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day.", "meaning": "GENEPIO:0100147", - "is_a": "MGI sequencing instrument" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" }, - "MGI DNBSEQ-E25": { - "text": "MGI DNBSEQ-E25", + "MGI DNBSEQ-E25 [GENEPIO:0100973]": { + "text": "MGI DNBSEQ-E25 [GENEPIO:0100973]", + "description": "An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab.", "meaning": "GENEPIO:0100973", - "is_a": "MGI sequencing instrument" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" }, - "MGI DNBSEQ-G50": { - "text": "MGI DNBSEQ-G50", + "MGI DNBSEQ-G50 [GENEPIO:0100150]": { + "text": "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", "meaning": "GENEPIO:0100150", - "is_a": "MGI sequencing instrument" + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" }, - "454 Genome Sequencer": { - "text": "454 Genome Sequencer", + "454 Genome Sequencer [GENEPIO:0001937]": { + "text": "454 Genome Sequencer [GENEPIO:0001937]", + "description": "A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing.", "meaning": "GENEPIO:0001937" }, - "454 Genome Sequencer 20": { - "text": "454 Genome Sequencer 20", + "454 Genome Sequencer 20 [OBI:0000689]": { + "text": "454 Genome Sequencer 20 [OBI:0000689]", + "description": "A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem.", "meaning": "OBI:0000689", - "is_a": "454 Genome Sequencer" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" }, - "454 Genome Sequencer FLX": { - "text": "454 Genome Sequencer FLX", + "454 Genome Sequencer FLX [OBI:0000702]": { + "text": "454 Genome Sequencer FLX [OBI:0000702]", + "description": "A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.", "meaning": "OBI:0000702", - "is_a": "454 Genome Sequencer" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" }, - "454 Genome Sequencer FLX+": { - "text": "454 Genome Sequencer FLX+", + "454 Genome Sequencer FLX+ [GENEPIO:0100982]": { + "text": "454 Genome Sequencer FLX+ [GENEPIO:0100982]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+.", "meaning": "GENEPIO:0100982", - "is_a": "454 Genome Sequencer" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" }, - "454 Genome Sequencer FLX Titanium": { - "text": "454 Genome Sequencer FLX Titanium", + "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]": { + "text": "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads.", "meaning": "GENEPIO:0001936", - "is_a": "454 Genome Sequencer" + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" }, - "454 Genome Sequencer Junior": { - "text": "454 Genome Sequencer Junior", - "meaning": "GENEPIO:0100983", - "is_a": "454 Genome Sequencer" + "454 Genome Sequencer Junior [GENEPIO:0001938]": { + "text": "454 Genome Sequencer Junior [GENEPIO:0001938]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and is more compact.", + "meaning": "GENEPIO:0001938", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" }, - "SOLiD System": { - "text": "SOLiD System", + "SOLiD System [OBI:0000696]": { + "text": "SOLiD System [OBI:0000696]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation.", "meaning": "OBI:0000696" }, - "SOLiD 5500": { - "text": "SOLiD 5500", + "SOLiD 5500 [GENEPIO:0001929]": { + "text": "SOLiD 5500 [GENEPIO:0001929]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series.", "meaning": "GENEPIO:0001929", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD 5500xl Genetic Analyzer": { - "text": "SOLiD 5500xl Genetic Analyzer", + "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]": { + "text": "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model.", "meaning": "GENEPIO:0001930", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD 5500x-Wl Genetic Analyzer": { - "text": "SOLiD 5500x-Wl Genetic Analyzer", + "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]": { + "text": "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer.", "meaning": "GENEPIO:0100984", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD 3 Plus System": { - "text": "SOLiD 3 Plus System", + "SOLiD 3 Plus System [OBI:0002007]": { + "text": "SOLiD 3 Plus System [OBI:0002007]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.", "meaning": "OBI:0002007", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD 4 System": { - "text": "SOLiD 4 System", + "SOLiD 4 System [OBI:0002024]": { + "text": "SOLiD 4 System [OBI:0002024]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput.", "meaning": "OBI:0002024", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD 4hq System": { - "text": "SOLiD 4hq System", + "SOLiD 4hq System [GENEPIO:0001928]": { + "text": "SOLiD 4hq System [GENEPIO:0001928]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput.", "meaning": "GENEPIO:0001928", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD PI System": { - "text": "SOLiD PI System", + "SOLiD PI System [GENEPIO:0001931]": { + "text": "SOLiD PI System [GENEPIO:0001931]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput.", "meaning": "GENEPIO:0001931", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD System 2.0": { - "text": "SOLiD System 2.0", + "SOLiD System 2.0 [GENEPIO:0001932]": { + "text": "SOLiD System 2.0 [GENEPIO:0001932]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", "meaning": "GENEPIO:0001932", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "SOLiD System 3.0": { - "text": "SOLiD System 3.0", + "SOLiD System 3.0 [GENEPIO:0001933]": { + "text": "SOLiD System 3.0 [GENEPIO:0001933]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", "meaning": "GENEPIO:0001933", - "is_a": "SOLiD System" + "is_a": "SOLiD System [OBI:0000696]" }, - "HeliScope Single Molecule Sequencer": { - "text": "HeliScope Single Molecule Sequencer", + "HeliScope Single Molecule Sequencer [OBI:0000717]": { + "text": "HeliScope Single Molecule Sequencer [OBI:0000717]", + "description": "A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry.", "meaning": "OBI:0000717" }, - "Applied Biosystems sequencing instrument model": { - "text": "Applied Biosystems sequencing instrument model", + "Applied Biosystems sequencing instrument model [GENEPIO:0100974]": { + "text": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "description": "A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis.", "meaning": "GENEPIO:0100974" }, - "AB 310 Genetic Analyzer": { - "text": "AB 310 Genetic Analyzer", + "AB 310 Genetic Analyzer [GENEPIO:0100975]": { + "text": "AB 310 Genetic Analyzer [GENEPIO:0100975]", + "description": "An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated.", "meaning": "GENEPIO:0100975", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" }, - "AB 3130 Genetic Analyzer": { - "text": "AB 3130 Genetic Analyzer", + "AB 3130 Genetic Analyzer [GENEPIO:0100976]": { + "text": "AB 3130 Genetic Analyzer [GENEPIO:0100976]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries.", "meaning": "GENEPIO:0100976", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" }, - "AB 3130xL Genetic Analyzer": { - "text": "AB 3130xL Genetic Analyzer", + "AB 3130xL Genetic Analyzer [GENEPIO:0100977]": { + "text": "AB 3130xL Genetic Analyzer [GENEPIO:0100977]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries.", "meaning": "GENEPIO:0100977", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" }, - "AB 3500 Genetic Analyzer": { - "text": "AB 3500 Genetic Analyzer", + "AB 3500 Genetic Analyzer [GENEPIO:0100978]": { + "text": "AB 3500 Genetic Analyzer [GENEPIO:0100978]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates.", "meaning": "GENEPIO:0100978", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" }, - "AB 3500xL Genetic Analyzer": { - "text": "AB 3500xL Genetic Analyzer", + "AB 3500xL Genetic Analyzer [GENEPIO:0100979]": { + "text": "AB 3500xL Genetic Analyzer [GENEPIO:0100979]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates.", "meaning": "GENEPIO:0100979", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" }, - "AB 3730 Genetic Analyzer": { - "text": "AB 3730 Genetic Analyzer", + "AB 3730 Genetic Analyzer [GENEPIO:0100980]": { + "text": "AB 3730 Genetic Analyzer [GENEPIO:0100980]", + "description": "An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing.", "meaning": "GENEPIO:0100980", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" }, - "AB 3730xL Genetic Analyzer": { - "text": "AB 3730xL Genetic Analyzer", + "AB 3730xL Genetic Analyzer [GENEPIO:0100981]": { + "text": "AB 3730xL Genetic Analyzer [GENEPIO:0100981]", + "description": "An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing.", "meaning": "GENEPIO:0100981", - "is_a": "Applied Biosystems sequencing instrument model" + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" } } }, - "sequencing assay type menu": { - "name": "sequencing assay type menu", + "SequencingAssayTypeMenu": { + "name": "SequencingAssayTypeMenu", + "title": "sequencing assay type menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Amplicon sequencing assay": { - "text": "Amplicon sequencing assay", + "Amplicon sequencing assay [OBI:0002767]": { + "text": "Amplicon sequencing assay [OBI:0002767]", + "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", "meaning": "OBI:0002767" }, - "16S ribosomal gene sequencing assay": { - "text": "16S ribosomal gene sequencing assay", + "16S ribosomal gene sequencing assay [OBI:0002763]": { + "text": "16S ribosomal gene sequencing assay [OBI:0002763]", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", "meaning": "OBI:0002763", - "is_a": "Amplicon sequencing assay" + "is_a": "Amplicon sequencing assay [OBI:0002767]" }, - "Whole genome sequencing assay": { - "text": "Whole genome sequencing assay", + "Whole genome sequencing assay [OBI:0002117]": { + "text": "Whole genome sequencing assay [OBI:0002117]", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", "meaning": "OBI:0002117" }, - "Whole metagenome sequencing assay": { - "text": "Whole metagenome sequencing assay", + "Whole metagenome sequencing assay [OBI:0002623]": { + "text": "Whole metagenome sequencing assay [OBI:0002623]", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", "meaning": "OBI:0002623" }, - "Whole virome sequencing assay": { - "text": "Whole virome sequencing assay", + "Whole virome sequencing assay [OBI:0002768]": { + "text": "Whole virome sequencing assay [OBI:0002768]", + "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", "meaning": "OBI:0002768", - "is_a": "Whole metagenome sequencing assay" + "is_a": "Whole metagenome sequencing assay [OBI:0002623]" } } }, - "amplicon pcr primer scheme menu": { - "name": "amplicon pcr primer scheme menu", + "AmpliconPcrPrimerSchemeMenu": { + "name": "AmpliconPcrPrimerSchemeMenu", + "title": "amplicon pcr primer scheme menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "artic-v1": { - "text": "artic-v1", + "artic-v1 [GENEPIO:0100847]": { + "text": "artic-v1 [GENEPIO:0100847]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0.", "meaning": "GENEPIO:0100847" }, - "artic-v2": { - "text": "artic-v2", + "artic-v2 [GENEPIO:0100848]": { + "text": "artic-v2 [GENEPIO:0100848]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0.", "meaning": "GENEPIO:0100848" }, - "artic-v3": { - "text": "artic-v3", + "artic-v3 [GENEPIO:0100849]": { + "text": "artic-v3 [GENEPIO:0100849]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0.", "meaning": "GENEPIO:0100849" }, - "artic-v4": { - "text": "artic-v4", + "artic-v4 [GENEPIO:0100850]": { + "text": "artic-v4 [GENEPIO:0100850]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0.", "meaning": "GENEPIO:0100850" }, - "artic-v4.1": { - "text": "artic-v4.1", + "artic-v4.1 [GENEPIO:0100851]": { + "text": "artic-v4.1 [GENEPIO:0100851]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0.", "meaning": "GENEPIO:0100851" }, - "artic-v5.0.0_400": { - "text": "artic-v5.0.0_400", + "artic-v5.0.0_400 [GENEPIO:0100852]": { + "text": "artic-v5.0.0_400 [GENEPIO:0100852]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length.", "meaning": "GENEPIO:0100852" }, - "artic-v5.1.0_400": { - "text": "artic-v5.1.0_400", + "artic-v5.1.0_400 [GENEPIO:0100853]": { + "text": "artic-v5.1.0_400 [GENEPIO:0100853]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length.", "meaning": "GENEPIO:0100853" }, - "artic-v5.2.0_1200": { - "text": "artic-v5.2.0_1200", + "artic-v5.2.0_1200 [GENEPIO:0100854]": { + "text": "artic-v5.2.0_1200 [GENEPIO:0100854]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100854" }, - "artic-v5.2.0_400": { - "text": "artic-v5.2.0_400", + "artic-v5.2.0_400 [GENEPIO:0100855]": { + "text": "artic-v5.2.0_400 [GENEPIO:0100855]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length.", "meaning": "GENEPIO:0100855" }, - "artic-v5.3.2_400": { - "text": "artic-v5.3.2_400", + "artic-v5.3.2_400 [GENEPIO:0100856]": { + "text": "artic-v5.3.2_400 [GENEPIO:0100856]", + "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length.", "meaning": "GENEPIO:0100856" }, - "eden-v1": { - "text": "eden-v1", + "eden-v1 [GENEPIO:0100857]": { + "text": "eden-v1 [GENEPIO:0100857]", + "description": "An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length.", "meaning": "GENEPIO:0100857" }, - "midnight-bccdc-v1": { - "text": "midnight-bccdc-v1", + "midnight-bccdc-v1 [GENEPIO:0100858]": { + "text": "midnight-bccdc-v1 [GENEPIO:0100858]", + "description": "An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100858" }, - "midnight-bccdc-v2": { - "text": "midnight-bccdc-v2", + "midnight-bccdc-v2 [GENEPIO:0100859]": { + "text": "midnight-bccdc-v2 [GENEPIO:0100859]", + "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100859" }, - "midnight-bccdc-v3": { - "text": "midnight-bccdc-v3", + "midnight-bccdc-v3 [GENEPIO:0100860]": { + "text": "midnight-bccdc-v3 [GENEPIO:0100860]", + "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100860" }, - "midnight-bccdc-v4": { - "text": "midnight-bccdc-v4", + "midnight-bccdc-v4 [GENEPIO:0100861]": { + "text": "midnight-bccdc-v4 [GENEPIO:0100861]", + "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100861" }, - "midnight-ont-v3": { - "text": "midnight-ont-v3", + "midnight-ont-v3 [GENEPIO:0100862]": { + "text": "midnight-ont-v3 [GENEPIO:0100862]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100862" }, - "midnight-v1": { - "text": "midnight-v1", + "midnight-v1 [GENEPIO:0100863]": { + "text": "midnight-v1 [GENEPIO:0100863]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100863" }, - "midnight-v2": { - "text": "midnight-v2", + "midnight-v2 [GENEPIO:0100864]": { + "text": "midnight-v2 [GENEPIO:0100864]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", "meaning": "GENEPIO:0100864" }, - "varskip-vsl1a": { - "text": "varskip-vsl1a", + "varskip-vsl1a [GENEPIO:0100865]": { + "text": "varskip-vsl1a [GENEPIO:0100865]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long.", "meaning": "GENEPIO:0100865" }, - "varskip-vss1a": { - "text": "varskip-vss1a", + "varskip-vss1a [GENEPIO:0100866]": { + "text": "varskip-vss1a [GENEPIO:0100866]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short.", "meaning": "GENEPIO:0100866" }, - "varskip-vss2a": { - "text": "varskip-vss2a", + "varskip-vss2a [GENEPIO:0100867]": { + "text": "varskip-vss2a [GENEPIO:0100867]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a.", "meaning": "GENEPIO:0100867" }, - "varskip-vss2b": { - "text": "varskip-vss2b", + "varskip-vss2b [GENEPIO:0100868]": { + "text": "varskip-vss2b [GENEPIO:0100868]", + "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b.", "meaning": "GENEPIO:0100868" } } }, - "genomic target enrichment method menu": { - "name": "genomic target enrichment method menu", + "GenomicTargetEnrichmentMethodMenu": { + "name": "GenomicTargetEnrichmentMethodMenu", + "title": "genomic target enrichment method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Hybrid selection method": { - "text": "Hybrid selection method", + "Hybridization capture [GENEPIO:0001950]": { + "text": "Hybridization capture [GENEPIO:0001950]", + "description": "Selection by hybridization in array or solution.", "meaning": "GENEPIO:0001950" }, - "rRNA depletion method": { - "text": "rRNA depletion method", + "rRNA depletion method [GENEPIO:0101020]": { + "text": "rRNA depletion method [GENEPIO:0101020]", + "description": "Removal of background RNA for the purposes of enriching the genomic target.", "meaning": "GENEPIO:0101020" } } }, - "quality control determination menu": { - "name": "quality control determination menu", + "QualityControlDeterminationMenu": { + "name": "QualityControlDeterminationMenu", + "title": "quality control determination menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "No quality control issues identified": { - "text": "No quality control issues identified", + "No quality control issues identified [GENEPIO:0100562]": { + "text": "No quality control issues identified [GENEPIO:0100562]", + "description": "A statement confirming that quality control processes were carried out and no quality issues were detected.", "meaning": "GENEPIO:0100562" }, - "Sequence passed quality control": { - "text": "Sequence passed quality control", + "Sequence passed quality control [GENEPIO:0100563]": { + "text": "Sequence passed quality control [GENEPIO:0100563]", + "description": "A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", "meaning": "GENEPIO:0100563" }, - "Sequence failed quality control": { - "text": "Sequence failed quality control", + "Sequence failed quality control [GENEPIO:0100564]": { + "text": "Sequence failed quality control [GENEPIO:0100564]", + "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", "meaning": "GENEPIO:0100564" }, - "Minor quality control issues identified": { - "text": "Minor quality control issues identified", + "Minor quality control issues identified [GENEPIO:0100565]": { + "text": "Minor quality control issues identified [GENEPIO:0100565]", + "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", "meaning": "GENEPIO:0100565" }, - "Sequence flagged for potential quality control issues": { - "text": "Sequence flagged for potential quality control issues", + "Sequence flagged for potential quality control issues [GENEPIO:0100566]": { + "text": "Sequence flagged for potential quality control issues [GENEPIO:0100566]", + "description": "A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", "meaning": "GENEPIO:0100566" }, - "Quality control not performed": { - "text": "Quality control not performed", + "Quality control not performed [GENEPIO:0100567]": { + "text": "Quality control not performed [GENEPIO:0100567]", + "description": "A statement confirming that quality control processes have not been carried out.", "meaning": "GENEPIO:0100567" } } }, - "quality control issues menu": { - "name": "quality control issues menu", + "QualityControlIssuesMenu": { + "name": "QualityControlIssuesMenu", + "title": "quality control issues menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Low quality sequence": { - "text": "Low quality sequence", + "Low quality sequence [GENEPIO:0100568]": { + "text": "Low quality sequence [GENEPIO:0100568]", + "description": "Sequence data that does not meet quality control thresholds.", "meaning": "GENEPIO:0100568" }, - "Sequence contaminated": { - "text": "Sequence contaminated", + "Sequence contaminated [GENEPIO:0100569]": { + "text": "Sequence contaminated [GENEPIO:0100569]", + "description": "Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", "meaning": "GENEPIO:0100569" }, - "Low average genome coverage": { - "text": "Low average genome coverage", + "Low average genome coverage [GENEPIO:0100570]": { + "text": "Low average genome coverage [GENEPIO:0100570]", + "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", "meaning": "GENEPIO:0100570" }, - "Low percent genome captured": { - "text": "Low percent genome captured", + "Low percent genome captured [GENEPIO:0100571]": { + "text": "Low percent genome captured [GENEPIO:0100571]", + "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", "meaning": "GENEPIO:0100571" }, - "Read lengths shorter than expected": { - "text": "Read lengths shorter than expected", + "Read lengths shorter than expected [GENEPIO:0100572]": { + "text": "Read lengths shorter than expected [GENEPIO:0100572]", + "description": "Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", "meaning": "GENEPIO:0100572" }, - "Sequence amplification artifacts": { - "text": "Sequence amplification artifacts", + "Sequence amplification artifacts [GENEPIO:0100573]": { + "text": "Sequence amplification artifacts [GENEPIO:0100573]", + "description": "Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", "meaning": "GENEPIO:0100573" }, - "Low signal to noise ratio": { - "text": "Low signal to noise ratio", + "Low signal to noise ratio [GENEPIO:0100574]": { + "text": "Low signal to noise ratio [GENEPIO:0100574]", + "description": "Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", "meaning": "GENEPIO:0100574" }, - "Low coverage of characteristic mutations": { - "text": "Low coverage of characteristic mutations", + "Low coverage of characteristic mutations [GENEPIO:0100575]": { + "text": "Low coverage of characteristic mutations [GENEPIO:0100575]", + "description": "Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", "meaning": "GENEPIO:0100575" } } }, - "gene name menu": { - "name": "gene name menu", + "GeneSymbolMenu": { + "name": "GeneSymbolMenu", + "title": "gene symbol menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "E gene (orf4)": { - "text": "E gene (orf4)", + "E gene (orf4) [GENEPIO:0100151]": { + "text": "E gene (orf4) [GENEPIO:0100151]", "meaning": "GENEPIO:0100151" }, - "M gene (orf5)": { - "text": "M gene (orf5)", + "M gene (orf5) [GENEPIO:0100152]": { + "text": "M gene (orf5) [GENEPIO:0100152]", "meaning": "GENEPIO:0100152" }, - "N gene (orf9)": { - "text": "N gene (orf9)", + "N gene (orf9) [GENEPIO:0100153]": { + "text": "N gene (orf9) [GENEPIO:0100153]", "meaning": "GENEPIO:0100153" }, - "Spike gene (orf2)": { - "text": "Spike gene (orf2)", + "Spike gene (orf2) [GENEPIO:0100154]": { + "text": "Spike gene (orf2) [GENEPIO:0100154]", "meaning": "GENEPIO:0100154" }, - "orf1ab (rep)": { - "text": "orf1ab (rep)", + "orf1ab (rep) [GENEPIO:0100155]": { + "text": "orf1ab (rep) [GENEPIO:0100155]", "meaning": "GENEPIO:0100155" }, - "orf1a (pp1a)": { - "text": "orf1a (pp1a)", + "orf1a (pp1a) [GENEPIO:0100156]": { + "text": "orf1a (pp1a) [GENEPIO:0100156]", "meaning": "GENEPIO:0100156", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp11": { - "text": "nsp11", + "nsp11 [GENEPIO:0100157]": { + "text": "nsp11 [GENEPIO:0100157]", "meaning": "GENEPIO:0100157", - "is_a": "orf1a (pp1a)" + "is_a": "orf1a (pp1a) [GENEPIO:0100156]" }, - "nsp1": { - "text": "nsp1", + "nsp1 [GENEPIO:0100158]": { + "text": "nsp1 [GENEPIO:0100158]", "meaning": "GENEPIO:0100158", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp2": { - "text": "nsp2", + "nsp2 [GENEPIO:0100159]": { + "text": "nsp2 [GENEPIO:0100159]", "meaning": "GENEPIO:0100159", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp3": { - "text": "nsp3", + "nsp3 [GENEPIO:0100160]": { + "text": "nsp3 [GENEPIO:0100160]", "meaning": "GENEPIO:0100160", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp4": { - "text": "nsp4", + "nsp4 [GENEPIO:0100161]": { + "text": "nsp4 [GENEPIO:0100161]", "meaning": "GENEPIO:0100161", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp5": { - "text": "nsp5", + "nsp5 [GENEPIO:0100162]": { + "text": "nsp5 [GENEPIO:0100162]", "meaning": "GENEPIO:0100162", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp6": { - "text": "nsp6", + "nsp6 [GENEPIO:0100163]": { + "text": "nsp6 [GENEPIO:0100163]", "meaning": "GENEPIO:0100163", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp7": { - "text": "nsp7", + "nsp7 [GENEPIO:0100164]": { + "text": "nsp7 [GENEPIO:0100164]", "meaning": "GENEPIO:0100164", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp8": { - "text": "nsp8", + "nsp8 [GENEPIO:0100165]": { + "text": "nsp8 [GENEPIO:0100165]", "meaning": "GENEPIO:0100165", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp9": { - "text": "nsp9", + "nsp9 [GENEPIO:0100166]": { + "text": "nsp9 [GENEPIO:0100166]", "meaning": "GENEPIO:0100166", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp10": { - "text": "nsp10", + "nsp10 [GENEPIO:0100167]": { + "text": "nsp10 [GENEPIO:0100167]", "meaning": "GENEPIO:0100167", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "RdRp gene (nsp12)": { - "text": "RdRp gene (nsp12)", + "RdRp gene (nsp12) [GENEPIO:0100168]": { + "text": "RdRp gene (nsp12) [GENEPIO:0100168]", "meaning": "GENEPIO:0100168", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "hel gene (nsp13)": { - "text": "hel gene (nsp13)", + "hel gene (nsp13) [GENEPIO:0100169]": { + "text": "hel gene (nsp13) [GENEPIO:0100169]", "meaning": "GENEPIO:0100169", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "exoN gene (nsp14)": { - "text": "exoN gene (nsp14)", + "exoN gene (nsp14) [GENEPIO:0100170]": { + "text": "exoN gene (nsp14) [GENEPIO:0100170]", "meaning": "GENEPIO:0100170", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp15": { - "text": "nsp15", + "nsp15 [GENEPIO:0100171]": { + "text": "nsp15 [GENEPIO:0100171]", "meaning": "GENEPIO:0100171", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "nsp16": { - "text": "nsp16", + "nsp16 [GENEPIO:0100172]": { + "text": "nsp16 [GENEPIO:0100172]", "meaning": "GENEPIO:0100172", - "is_a": "orf1ab (rep)" + "is_a": "orf1ab (rep) [GENEPIO:0100155]" }, - "orf3a": { - "text": "orf3a", + "orf3a [GENEPIO:0100173]": { + "text": "orf3a [GENEPIO:0100173]", "meaning": "GENEPIO:0100173" }, - "orf3b": { - "text": "orf3b", + "orf3b [GENEPIO:0100174]": { + "text": "orf3b [GENEPIO:0100174]", "meaning": "GENEPIO:0100174" }, - "orf6 (ns6)": { - "text": "orf6 (ns6)", + "orf6 (ns6) [GENEPIO:0100175]": { + "text": "orf6 (ns6) [GENEPIO:0100175]", "meaning": "GENEPIO:0100175" }, - "orf7a": { - "text": "orf7a", + "orf7a [GENEPIO:0100176]": { + "text": "orf7a [GENEPIO:0100176]", "meaning": "GENEPIO:0100176" }, - "orf7b (ns7b)": { - "text": "orf7b (ns7b)", + "orf7b (ns7b) [GENEPIO:0100177]": { + "text": "orf7b (ns7b) [GENEPIO:0100177]", "meaning": "GENEPIO:0100177" }, - "orf8 (ns8)": { - "text": "orf8 (ns8)", + "orf8 (ns8) [GENEPIO:0100178]": { + "text": "orf8 (ns8) [GENEPIO:0100178]", "meaning": "GENEPIO:0100178" }, - "orf9b": { - "text": "orf9b", + "orf9b [GENEPIO:0100179]": { + "text": "orf9b [GENEPIO:0100179]", "meaning": "GENEPIO:0100179" }, - "orf9c": { - "text": "orf9c", + "orf9c [GENEPIO:0100180]": { + "text": "orf9c [GENEPIO:0100180]", "meaning": "GENEPIO:0100180" }, - "orf10": { - "text": "orf10", + "orf10 [GENEPIO:0100181]": { + "text": "orf10 [GENEPIO:0100181]", "meaning": "GENEPIO:0100181" }, - "orf14": { - "text": "orf14", + "orf14 [GENEPIO:0100182]": { + "text": "orf14 [GENEPIO:0100182]", "meaning": "GENEPIO:0100182" }, - "SARS-COV-2 5' UTR": { - "text": "SARS-COV-2 5' UTR", + "SARS-COV-2 5' UTR [GENEPIO:0100183]": { + "text": "SARS-COV-2 5' UTR [GENEPIO:0100183]", "meaning": "GENEPIO:0100183" } } }, - "diagnostic target presence menu": { - "name": "diagnostic target presence menu", + "DiagnosticTargetPresenceMenu": { + "name": "DiagnosticTargetPresenceMenu", + "title": "diagnostic target presence menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "diagnostic target present": { - "text": "diagnostic target present", + "diagnostic target present [GENEPIO:0100987]": { + "text": "diagnostic target present [GENEPIO:0100987]", + "description": "A quality inhering in a bearer by virtue of the bearer's existence.", "meaning": "GENEPIO:0100987" }, - "diagnostic target absent": { - "text": "diagnostic target absent", + "diagnostic target absent [GENEPIO:0100988]": { + "text": "diagnostic target absent [GENEPIO:0100988]", + "description": "Aquality denoting the lack of an entity.", "meaning": "GENEPIO:0100988" } } }, - "diagnostic measurement unit menu": { - "name": "diagnostic measurement unit menu", + "DiagnosticMeasurementUnitMenu": { + "name": "DiagnosticMeasurementUnitMenu", + "title": "diagnostic measurement unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { "gene copies per liter (GC/L)": { - "text": "gene copies per liter (GC/L)" + "text": "gene copies per liter (GC/L)", + "description": "A unit that measures the number of copies of a given gene within a liter of a biological material." }, - "cycle threshold (Ct)": { - "text": "cycle threshold (Ct)", + "cycle threshold (Ct) [GENEPIO:0100657]": { + "text": "cycle threshold (Ct) [GENEPIO:0100657]", + "description": "A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test.", "meaning": "GENEPIO:0100657" }, - "colony forming units per milliliter (CFU/mL)": { - "text": "colony forming units per milliliter (CFU/mL)", + "colony forming units per milliliter (CFU/mL) [UO:0000213]": { + "text": "colony forming units per milliliter (CFU/mL) [UO:0000213]", + "description": "A unit of microbial density that describes the number of colony forming units within a milliliter of material.", "meaning": "UO:0000213" }, "colony forming units per 100 milliliter (CFU/100 mL)": { - "text": "colony forming units per 100 milliliter (CFU/100 mL)" + "text": "colony forming units per 100 milliliter (CFU/100 mL)", + "description": "A unit of microbial density that describes the number of colony forming units within 100 milliliters of material." }, "colony forming units per grams total solids (CFU/gTS)": { - "text": "colony forming units per grams total solids (CFU/gTS)" + "text": "colony forming units per grams total solids (CFU/gTS)", + "description": "A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material." }, "most probable number per milliliter (MPN/mL)": { - "text": "most probable number per milliliter (MPN/mL)" + "text": "most probable number per milliliter (MPN/mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within one milliliter of material." }, "most probable number per 100 milliliter (MPN/100 mL)": { - "text": "most probable number per 100 milliliter (MPN/100 mL)" + "text": "most probable number per 100 milliliter (MPN/100 mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material." } } }, - "diagnostic measurement method menu": { - "name": "diagnostic measurement method menu", + "DiagnosticMeasurementMethodMenu": { + "name": "DiagnosticMeasurementMethodMenu", + "title": "diagnostic measurement method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { - "Quantitative real time polymerase chain reaction (qPCR)": { - "text": "Quantitative real time polymerase chain reaction (qPCR)", + "Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]": { + "text": "Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]", + "description": "An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.", "meaning": "OBI:0000893" }, "Digital real time polymerase chain reaction (dPCR)": { - "text": "Digital real time polymerase chain reaction (dPCR)" + "text": "Digital real time polymerase chain reaction (dPCR)", + "description": "A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction" }, "Bacteria culture test": { - "text": "Bacteria culture test" + "text": "Bacteria culture test", + "description": "An assay to identify the presence of bacteria" } } } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -3671,13 +4479,22 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sample_name", + "NCBI_SRA:sample_name" + ], "slot_uri": "GENEPIO:0001123", "identifier": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "required": true }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", "description": "The user-defined identifier assigned to a portion of the original sample.", "title": "specimen collector subsample ID", "comments": [ @@ -3689,11 +4506,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_id" + ], "slot_uri": "GENEPIO:0100752", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "pooled sample ID": { - "name": "pooled sample ID", + "pooled_sample_id": { + "name": "pooled_sample_id", "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", "title": "pooled sample ID", "comments": [ @@ -3706,10 +4531,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100996", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "metagenome-assembled genome (MAG) ID": { - "name": "metagenome-assembled genome (MAG) ID", + "metagenomeassembled_genome_mag_id": { + "name": "metagenomeassembled_genome_mag_id", "description": "The user-defined identifier assigned to a genome reconstructed from metagenomic data.", "title": "metagenome-assembled genome (MAG) ID", "comments": [ @@ -3722,21 +4552,33 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100753", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "specimen collector project ID": { - "name": "specimen collector project ID", + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", "description": "The user-defined project name assigned to a sequencing project.", "title": "specimen collector project ID", "comments": [ "If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here." ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:project_name" + ], "slot_uri": "GENEPIO:0100918", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "BioProject accession": { - "name": "BioProject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", "title": "BioProject accession", "comments": [ @@ -3748,7 +4590,15 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:bioproject_accession" + ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -3757,8 +4607,8 @@ "partial_match": false } }, - "BioSample accession": { - "name": "BioSample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", "title": "BioSample accession", "comments": [ @@ -3766,11 +4616,16 @@ ], "examples": [ { - "value": "SAMN14180202, SAMD00000001" + "value": "SAMN14180202, SAMEA00000002, SAMD00000001" } ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true, "pattern": "{UPPER_CASE}", @@ -3780,42 +4635,25 @@ "partial_match": false } }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", - "description": "The versioned identifier assigned to an assembly or consensus sequence in GenBank archives.", - "title": "GenBank accession (versioned)", + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", "comments": [ - "Store the versioned GenBank accession assigned to the submitted sequence." + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." ], "examples": [ { - "value": "LZ986655.1" + "value": "ERR123456, DRR123456, CRR123456" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100754", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", - "comments": [ - "Store the accession assigned to the submitted sequence. NCBI-SRA accessions start with SRR." - ], - "examples": [ - { - "value": "SRR11177792" - } + "slot_uri": "GENEPIO:0101203", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001142", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -3824,42 +4662,25 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", - "title": "GISAID accession", + "enterobase_accession": { + "name": "enterobase_accession", + "description": "The identifier assigned to a sequence in Enterobase archives.", + "title": "Enterobase accession", "comments": [ - "Store the accession assigned to the submitted sequence. GISAID accessions start with EPI." + "Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism." ], "examples": [ { - "value": "EPI_ISL_402131" + "value": "SAL_AA0019AA_ST" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001147", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "GISAID virus name": { - "name": "GISAID virus name", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "title": "GISAID virus name", - "comments": [ - "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\"." - ], - "examples": [ - { - "value": "hCoV-19/Canada/prov_rona_99/2020" - } + "slot_uri": "GENEPIO:0100759", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100282", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -3868,42 +4689,25 @@ "partial_match": false } }, - "ENA accession": { - "name": "ENA accession", - "description": "The identifier assigned to a sequence in the European Nucleotide Archive (ENA).", - "title": "ENA accession", + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", "comments": [ - "Store the accession assigned to the submitted sequence. ENA sequence accessions start with ERR." + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." ], "examples": [ { - "value": "ERR123456" + "value": "LZ986655.1" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100755", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "DRA accession": { - "name": "DRA accession", - "description": "The identifier assigned to a sequence in DNA Data Bank of Japan (DDBJ) sequence read archives.", - "title": "DRA accession", - "comments": [ - "Store the accession assigned to the submitted sequence. DRA accessions start with DRR." - ], - "examples": [ - { - "value": "DRR123456" - } + "slot_uri": "GENEPIO:0101204", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" ], - "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100757", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -3912,20 +4716,25 @@ "partial_match": false } }, - "GSA accession": { - "name": "GSA accession", - "description": "The identifier assigned to a BioSample in GSA (Genome Sequence Archive) archives.", - "title": "GSA accession", + "gisaid_accession": { + "name": "gisaid_accession", + "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", + "title": "GISAID accession", "comments": [ - "Store the accession assigned to the submitted sequence. GSA accessions start with CRR." + "Store the accession assigned to the submitted sequence. GISAID accessions start with EPI." ], "examples": [ { - "value": "CRR123456" + "value": "EPI_ISL_402131" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100758", + "slot_uri": "GENEPIO:0001147", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -3934,20 +4743,25 @@ "partial_match": false } }, - "Enterobase accession": { - "name": "Enterobase accession", - "description": "The identifier assigned to a sequence in Enterobase archives.", - "title": "Enterobase accession", + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "title": "GISAID virus name", "comments": [ - "Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism." + "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\"." ], "examples": [ { - "value": "SAL_AA0019AA_ST" + "value": "hCoV-19/Canada/prov_rona_99/2020" } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100759", + "slot_uri": "GENEPIO:0100282", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -3956,8 +4770,8 @@ "partial_match": false } }, - "sampling site ID": { - "name": "sampling site ID", + "sampling_site_id": { + "name": "sampling_site_id", "description": "The user-defined identifier assigned to a specific location from which samples are taken.", "title": "sampling site ID", "comments": [ @@ -3969,12 +4783,20 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_site_id" + ], "slot_uri": "GENEPIO:0100760", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sampling event ID": { - "name": "sampling event ID", + "sampling_event_id": { + "name": "sampling_event_id", "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", "title": "sampling event ID", "comments": [ @@ -3987,11 +4809,16 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100761", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sample collection data steward name": { - "name": "sample collection data steward name", + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", "title": "sample collection data steward name", "comments": [ @@ -4004,10 +4831,36 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100762", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "description": "The specific laboratory affiliation of the sample collector.", + "title": "sample collected by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100428", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the organization with which the sample collector is affiliated.", "title": "sample collected by", "comments": [ @@ -4019,19 +4872,48 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collected_by" + ], "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "description": "The name or job title of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100432", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "comments": [ @@ -4044,11 +4926,16 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "geo loc name (country)": { - "name": "geo loc name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo loc name (country)", "comments": [ @@ -4061,18 +4948,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The state/province/territory of origin of the sample.", "title": "geo loc name (state/province/territory)", "comments": [ @@ -4085,18 +4977,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "description": "The county/region of origin of the sample.", "title": "geo loc name (county/region)", "comments": [ @@ -4109,10 +5006,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100280", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "geo loc name (city)": { - "name": "geo loc name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city of origin of the sample.", "title": "geo loc name (city)", "comments": [ @@ -4125,10 +5027,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001189", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "geo loc name (site)": { - "name": "geo loc name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo loc name (site)", "comments": [ @@ -4141,10 +5048,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100436", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "geo loc latitude": { - "name": "geo loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo loc latitude", "comments": [ @@ -4157,10 +5069,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100309", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "geo loc longitude": { - "name": "geo loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo loc longitude", "comments": [ @@ -4173,10 +5090,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100310", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", "description": "The availability status of a shapefile descriping the catchment contributing to a watershed.", "title": "watershed shapefile availability", "comments": [ @@ -4189,17 +5111,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100919", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "watershed shapefile availability menu" + "range": "WatershedShapefileAvailabilityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", "description": "The name of the watershed shapefile.", "title": "watershed shapefile filename", "comments": [ @@ -4212,6 +5139,11 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100920", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, "organism": { @@ -4219,10 +5151,19 @@ "description": "Taxonomic name of the organism.", "title": "organism", "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0001191" + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1" + ], + "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "multivalued": true }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", "comments": [ @@ -4234,20 +5175,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], "slot_uri": "GENEPIO:0001198", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "scale of sampling": { - "name": "scale of sampling", + "scale_of_sampling": { + "name": "scale_of_sampling", "description": "The range of locations or entities sampled expressed in general terms.", "title": "scale of sampling", "comments": [ @@ -4259,19 +5208,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], "slot_uri": "GENEPIO:0100877", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "scale of sampling menu" + "range": "ScaleOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", "comments": [ @@ -4284,19 +5241,24 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_start_date": { + "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", - "title": "sample collection date", + "title": "sample collection start date", "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -4307,18 +5269,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection end date": { - "name": "sample collection end date", + "sample_collection_end_date": { + "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", "comments": [ @@ -4331,18 +5298,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101071", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample processing date": { - "name": "sample processing date", + "sample_processing_date": { + "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", "comments": [ @@ -4355,17 +5327,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100763", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection start time": { - "name": "sample collection start time", + "sample_collection_start_time": { + "name": "sample_collection_start_time", "description": "The time at which sample collection began.", "title": "sample collection start time", "comments": [ @@ -4378,18 +5355,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101072", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection end time": { - "name": "sample collection end time", + "sample_collection_end_time": { + "name": "sample_collection_end_time", "description": "The time at which sample collection ended.", "title": "sample collection end time", "comments": [ @@ -4402,18 +5384,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101073", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection time of day": { - "name": "sample collection time of day", + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", "description": "The descriptive time of day during which the sample was collected.", "title": "sample collection time of day", "comments": [ @@ -4426,17 +5413,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100765", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "sample collection time of day menu" + "range": "SampleCollectionTimeOfDayMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection time duration value": { - "name": "sample collection time duration value", + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", "description": "The amount of time over which the sample was collected.", "title": "sample collection time duration value", "comments": [ @@ -4448,19 +5440,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], "slot_uri": "GENEPIO:0100766", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", "description": "The units of the time duration measurement of sample collection.", "title": "sample collection time duration unit", "comments": [ @@ -4472,19 +5472,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], "slot_uri": "GENEPIO:0100767", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "sample collection duration unit menu" + "range": "SampleCollectionDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "presampling activity": { - "name": "presampling activity", + "presampling_activity": { + "name": "presampling_activity", "description": "The activities or variables upstream of sample collection that may affect the sample.", "title": "presampling activity", "comments": [ @@ -4497,18 +5505,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100433", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "presampling activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "presampling activity details": { - "name": "presampling activity details", + "presampling_activity_details": { + "name": "presampling_activity_details", "description": "The details of the activities or variables that affected the sample collected.", "title": "presampling activity details", "comments": [ @@ -4521,17 +5534,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100434", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample volume measurement value": { - "name": "sample volume measurement value", + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", "description": "The numerical value of the volume measurement of the sample collected.", "title": "sample volume measurement value", "comments": [ @@ -4543,11 +5561,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], "slot_uri": "GENEPIO:0100768", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample volume measurement unit": { - "name": "sample volume measurement unit", + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", "description": "The units of the volume measurement of the sample collected.", "title": "sample volume measurement unit", "comments": [ @@ -4559,18 +5585,26 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], "slot_uri": "GENEPIO:0100769", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "sample volume measurement unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample storage method": { - "name": "sample storage method", + "sample_storage_method": { + "name": "sample_storage_method", "description": "The process used to store the sample.", "title": "sample storage method", "comments": [ @@ -4583,10 +5617,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100448", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample storage medium": { - "name": "sample storage medium", + "sample_storage_medium": { + "name": "sample_storage_medium", "description": "The medium in which a sample is stored.", "title": "sample storage medium", "comments": [ @@ -4599,10 +5638,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100449", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample storage duration value": { - "name": "sample storage duration value", + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", "description": "The numerical value of the time measurement during which a sample is in storage.", "title": "sample storage duration value", "comments": [ @@ -4615,10 +5659,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101014", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample storage duration unit": { - "name": "sample storage duration unit", + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", "description": "The units of a measured sample storage duration.", "title": "sample storage duration unit", "comments": [ @@ -4631,17 +5680,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101015", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "sample storage duration unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -4653,19 +5707,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing" + ], "slot_uri": "GENEPIO:0001253", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "specimen processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "The details of the processing applied to the sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -4677,11 +5739,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_details" + ], "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "experimental protocol field": { - "name": "experimental protocol field", + "experimental_protocol_field": { + "name": "experimental_protocol_field", "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", "title": "experimental protocol field", "comments": [ @@ -4689,10 +5759,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101029", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", "comments": [ @@ -4704,20 +5779,50 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_site" + ], "slot_uri": "GENEPIO:0001232", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "environmental site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", + "proximal_environmental_site": { + "name": "proximal_environmental_site", + "description": "An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample.", + "title": "proximal environmental site", + "comments": [ + "Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Farm" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101205", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "EnvironmentalSiteMenu", + "multivalued": true + }, + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", "comments": [ @@ -4729,20 +5834,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_matrix" + ], "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "environmental material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material properties": { - "name": "environmental material properties", + "environmental_material_properties": { + "name": "environmental_material_properties", "description": "The properties, characteristics and qualities of a substance obtained from the natural or man-made environment.", "title": "environmental material properties", "comments": [ @@ -4755,19 +5868,24 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100770", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "environmental material properties menu" + "range": "EnvironmentalMaterialPropertiesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "wastewater system type": { - "name": "wastewater system type", + "wastewater_system_type": { + "name": "wastewater_system_type", "description": "The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine", "title": "wastewater system type", "comments": [ @@ -4780,18 +5898,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100771", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "wastewater system type menu" + "range": "WastewaterSystemTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "experimental specimen role type": { - "name": "experimental specimen role type", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", "description": "The type of role that the sample represents in the experiment.", "title": "experimental specimen role type", "comments": [ @@ -4804,18 +5927,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100921", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "experimental specimen role type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "experimental control details": { - "name": "experimental control details", + "experimental_control_details": { + "name": "experimental_control_details", "description": "The details regarding the experimental control contained in the sample.", "title": "experimental control details", "comments": [ @@ -4828,10 +5956,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100922", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. grab sampler.", "title": "collection device", "comments": [ @@ -4844,18 +5977,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001234", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample.", "title": "collection method", "comments": [ @@ -4867,20 +6005,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_type" + ], "slot_uri": "GENEPIO:0001241", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "collection method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", "title": "nucleic acid extraction method", "comments": [ @@ -4892,11 +6038,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:extraction_method" + ], "slot_uri": "GENEPIO:0100939", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "description": "The kit used to extract genomic material from a sample", "title": "nucleic acid extraction kit", "comments": [ @@ -4909,22 +6063,35 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100772", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "endogenous control details": { - "name": "endogenous control details", + "endogenous_control_details": { + "name": "endogenous_control_details", "description": "The description of the endogenous controls included when extracting a sample.", "title": "endogenous control details", "comments": [ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_endog_control_1" + ], "slot_uri": "GENEPIO:0100923", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "extraction recovery efficiency measurement value": { - "name": "extraction recovery efficiency measurement value", + "extraction_recovery_efficiency_measurement_value": { + "name": "extraction_recovery_efficiency_measurement_value", "description": "The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected.", "title": "extraction recovery efficiency measurement value", "comments": [ @@ -4932,10 +6099,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100924", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "extraction recovery efficiency measurement method": { - "name": "extraction recovery efficiency measurement method", + "extraction_recovery_efficiency_measurement_method": { + "name": "extraction_recovery_efficiency_measurement_method", "description": "The method by which recovery efficiency of an extraction was calculated.", "title": "extraction recovery efficiency measurement method", "comments": [ @@ -4943,10 +6115,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100925", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "microbiological method": { - "name": "microbiological method", + "microbiological_method": { + "name": "microbiological_method", "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", "title": "microbiological method", "comments": [ @@ -4959,6 +6136,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100454", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -4976,10 +6156,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100455", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "isolate ID": { - "name": "isolate ID", + "isolate_id": { + "name": "isolate_id", "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", "title": "isolate ID", "comments": [ @@ -4992,18 +6175,21 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100456", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "alternative isolate ID": { - "name": "alternative isolate ID", + "alternative_isolate_id": { + "name": "alternative_isolate_id", "description": "An alternative isolate_ID assigned to the isolate by another organization.", "title": "alternative isolate ID", "comments": [ @@ -5019,12 +6205,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100457", - "multivalued": true, + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", - "recommended": true + "recommended": true, + "multivalued": true }, - "progeny isolate ID": { - "name": "progeny isolate ID", + "progeny_isolate_id": { + "name": "progeny_isolate_id", "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", "title": "progeny isolate ID", "comments": [ @@ -5037,10 +6226,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100458", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "isolated by": { - "name": "isolated by", + "isolated_by": { + "name": "isolated_by", "description": "The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.", "title": "isolated by", "comments": [ @@ -5053,10 +6245,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100461", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "isolated by laboratory name": { - "name": "isolated by laboratory name", + "isolated_by_laboratory_name": { + "name": "isolated_by_laboratory_name", "description": "The specific laboratory affiliation of the individual who performed the isolation procedure.", "title": "isolated by laboratory name", "comments": [ @@ -5069,10 +6264,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100462", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "isolated by contact name": { - "name": "isolated by contact name", + "isolated_by_contact_name": { + "name": "isolated_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the isolate.", "title": "isolated by contact name", "comments": [ @@ -5085,10 +6283,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100463", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "isolated by contact email": { - "name": "isolated by contact email", + "isolated_by_contact_email": { + "name": "isolated_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the isolate.", "title": "isolated by contact email", "comments": [ @@ -5101,10 +6302,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100464", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "isolation date": { - "name": "isolation date", + "isolation_date": { + "name": "isolation_date", "description": "The date on which the isolate was isolated from a sample.", "title": "isolation date", "comments": [ @@ -5117,10 +6321,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100465", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "date" }, - "isolate received date": { - "name": "isolate received date", + "isolate_received_date": { + "name": "isolate_received_date", "description": "The date on which the isolate was received by the laboratory.", "title": "isolate received date", "comments": [ @@ -5133,6 +6340,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100466", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, "serovar": { @@ -5149,11 +6359,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100467", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "serotyping method": { - "name": "serotyping method", + "serotyping_method": { + "name": "serotyping_method", "description": "The method used to determine the serovar.", "title": "serotyping method", "comments": [ @@ -5166,6 +6379,9 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100468", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, @@ -5183,10 +6399,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100469", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "water catchment area human population measurement value": { - "name": "water catchment area human population measurement value", + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", "title": "water catchment area human population measurement value", "comments": [ @@ -5198,19 +6417,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population" + ], "slot_uri": "GENEPIO:0100773", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "integer" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "water catchment area human population range": { - "name": "water catchment area human population range", + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", "title": "water catchment area human population range", "comments": [ @@ -5223,17 +6450,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100774", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "water catchment area human population range menu" + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "water catchment area human population measurement method": { - "name": "water catchment area human population measurement method", + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", "description": "The method by which a water catchment 's human population size was measured or estimated", "title": "water catchment area human population measurement method", "comments": [ @@ -5245,11 +6477,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population_source" + ], "slot_uri": "GENEPIO:0100775", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "water catchment area human population density value": { - "name": "water catchment area human population density value", + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", "description": "The numerical value describing the number of humans per geographical area in a water catchment.", "title": "water catchment area human population density value", "comments": [ @@ -5262,10 +6502,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100776", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "water catchment area human population density unit": { - "name": "water catchment area human population density unit", + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", "description": "The unit describing the number of humans per geographical area in a water catchment.", "title": "water catchment area human population density unit", "comments": [ @@ -5278,17 +6523,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100777", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "water catchment area human population density unit menu" + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "populated area type": { - "name": "populated area type", + "populated_area_type": { + "name": "populated_area_type", "description": "A type of area that is populated by humans to different degrees.", "title": "populated area type", "comments": [ @@ -5301,17 +6551,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100778", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sampling weather conditions": { - "name": "sampling weather conditions", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", "title": "sampling weather conditions", "comments": [ @@ -5324,18 +6579,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100779", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "sampling weather conditions menu" + "range": "SamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "presampling weather conditions": { - "name": "presampling weather conditions", + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", "description": "Weather conditions prior to collection that may affect the sample.", "title": "presampling weather conditions", "comments": [ @@ -5348,18 +6608,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100780", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "presampling weather conditions menu" + "range": "PresamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "precipitation measurement value": { - "name": "precipitation measurement value", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", "description": "The amount of water which has fallen during a precipitation process.", "title": "precipitation measurement value", "comments": [ @@ -5372,18 +6637,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100911", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "precipitation measurement unit": { - "name": "precipitation measurement unit", + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", "title": "precipitation measurement unit", "comments": [ @@ -5396,18 +6666,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100912", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "precipitation measurement unit menu" + "range": "PrecipitationMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "precipitation measurement method": { - "name": "precipitation measurement method", + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", "description": "The process used to measure the amount of water which has fallen during a precipitation process.", "title": "precipitation measurement method", "comments": [ @@ -5420,10 +6695,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100913", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "ambient temperature measurement value": { - "name": "ambient temperature measurement value", + "ambient_temperature_measurement_value": { + "name": "ambient_temperature_measurement_value", "description": "The numerical value of a measurement of the ambient temperature.", "title": "ambient temperature measurement value", "comments": [ @@ -5436,10 +6716,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100935", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "ambient temperature measurement unit": { - "name": "ambient temperature measurement unit", + "ambient_temperature_measurement_unit": { + "name": "ambient_temperature_measurement_unit", "description": "The units of a measurement of the ambient temperature.", "title": "ambient temperature measurement unit", "comments": [ @@ -5452,17 +6737,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100936", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "ambient temperature measurement unit menu" + "range": "AmbientTemperatureMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "pH measurement value": { - "name": "pH measurement value", + "ph_measurement_value": { + "name": "ph_measurement_value", "description": "The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution.", "title": "pH measurement value", "comments": [ @@ -5474,11 +6764,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_ph" + ], "slot_uri": "GENEPIO:0001736", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "pH measurement method": { - "name": "pH measurement method", + "ph_measurement_method": { + "name": "ph_measurement_method", "description": "The process used to measure pH value.", "title": "pH measurement method", "comments": [ @@ -5491,10 +6789,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100781", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement value": { - "name": "total daily flow rate measurement value", + "total_daily_flow_rate_measurement_value": { + "name": "total_daily_flow_rate_measurement_value", "description": "The numerical value of a measured fluid flow rate over the course of a day.", "title": "total daily flow rate measurement value", "comments": [ @@ -5506,11 +6809,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], "slot_uri": "GENEPIO:0100905", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement unit": { - "name": "total daily flow rate measurement unit", + "total_daily_flow_rate_measurement_unit": { + "name": "total_daily_flow_rate_measurement_unit", "description": "The units of a measured fluid flow rate over the course of a day.", "title": "total daily flow rate measurement unit", "comments": [ @@ -5522,18 +6833,26 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], "slot_uri": "GENEPIO:0100906", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "total daily flow rate measurement unit menu" + "range": "TotalDailyFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "total daily flow rate measurement method": { - "name": "total daily flow rate measurement method", + "total_daily_flow_rate_measurement_method": { + "name": "total_daily_flow_rate_measurement_method", "description": "The process used to measure total daily fluid flow rate.", "title": "total daily flow rate measurement method", "comments": [ @@ -5546,10 +6865,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100907", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement value": { - "name": "instantaneous flow rate measurement value", + "instantaneous_flow_rate_measurement_value": { + "name": "instantaneous_flow_rate_measurement_value", "description": "The numerical value of a measured instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement value", "comments": [ @@ -5562,10 +6886,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100908", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement unit": { - "name": "instantaneous flow rate measurement unit", + "instantaneous_flow_rate_measurement_unit": { + "name": "instantaneous_flow_rate_measurement_unit", "description": "The units of a measured instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement unit", "comments": [ @@ -5578,17 +6907,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100909", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "instantaneous flow rate measurement unit menu" + "range": "InstantaneousFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "instantaneous flow rate measurement method": { - "name": "instantaneous flow rate measurement method", + "instantaneous_flow_rate_measurement_method": { + "name": "instantaneous_flow_rate_measurement_method", "description": "The process used to measure instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement method", "comments": [ @@ -5601,10 +6935,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100910", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "turbidity measurement value": { - "name": "turbidity measurement value", + "turbidity_measurement_value": { + "name": "turbidity_measurement_value", "description": "The numerical value of a measurement of turbidity.", "title": "turbidity measurement value", "comments": [ @@ -5617,11 +6956,16 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100783", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "turbidity measurement unit": { - "name": "turbidity measurement unit", + "turbidity_measurement_unit": { + "name": "turbidity_measurement_unit", "description": "The units of a measurement of turbidity.", "title": "turbidity measurement unit", "comments": [ @@ -5634,18 +6978,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100914", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "turbidity measurement unit menu" + "range": "TurbidityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "turbidity measurement method": { - "name": "turbidity measurement method", + "turbidity_measurement_method": { + "name": "turbidity_measurement_method", "description": "The process used to measure turbidity.", "title": "turbidity measurement method", "comments": [ @@ -5658,10 +7007,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101013", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement value": { - "name": "dissolved oxygen measurement value", + "dissolved_oxygen_measurement_value": { + "name": "dissolved_oxygen_measurement_value", "description": "The numerical value of a measurement of dissolved oxygen.", "title": "dissolved oxygen measurement value", "comments": [ @@ -5673,11 +7027,16 @@ } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100915", + "slot_uri": "GENEPIO:0000035", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement unit": { - "name": "dissolved oxygen measurement unit", + "dissolved_oxygen_measurement_unit": { + "name": "dissolved_oxygen_measurement_unit", "description": "The units of a measurement of dissolved oxygen.", "title": "dissolved oxygen measurement unit", "comments": [ @@ -5690,17 +7049,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100784", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "dissolved oxygen measurement unit menu" + "range": "DissolvedOxygenMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "dissolved oxygen measurement method": { - "name": "dissolved oxygen measurement method", + "dissolved_oxygen_measurement_method": { + "name": "dissolved_oxygen_measurement_method", "description": "The method used to measure dissolved oxygen.", "title": "dissolved oxygen measurement method", "comments": [ @@ -5713,10 +7077,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100785", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement value": { - "name": "oxygen reduction potential (ORP) measurement value", + "oxygen_reduction_potential_orp_measurement_value": { + "name": "oxygen_reduction_potential_orp_measurement_value", "description": "The numerical value of a measurement of oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement value", "comments": [ @@ -5728,11 +7097,16 @@ } ], "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100917", + "slot_uri": "FIX:0000278", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement unit": { - "name": "oxygen reduction potential (ORP) measurement unit", + "oxygen_reduction_potential_orp_measurement_unit": { + "name": "oxygen_reduction_potential_orp_measurement_unit", "description": "The units of a measurement of oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement unit", "comments": [ @@ -5745,17 +7119,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100786", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "oxygen reduction potential (ORP) measurement unit menu" + "range": "OxygenReductionPotentialOrpMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "oxygen reduction potential (ORP) measurement method": { - "name": "oxygen reduction potential (ORP) measurement method", + "oxygen_reduction_potential_orp_measurement_method": { + "name": "oxygen_reduction_potential_orp_measurement_method", "description": "The method used to measure oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement method", "comments": [ @@ -5768,10 +7147,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100787", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement value": { - "name": "chemical oxygen demand (COD) measurement value", + "chemical_oxygen_demand_cod_measurement_value": { + "name": "chemical_oxygen_demand_cod_measurement_value", "description": "The measured value from a chemical oxygen demand (COD) test.", "title": "chemical oxygen demand (COD) measurement value", "comments": [ @@ -5784,10 +7168,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100788", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement unit": { - "name": "chemical oxygen demand (COD) measurement unit", + "chemical_oxygen_demand_cod_measurement_unit": { + "name": "chemical_oxygen_demand_cod_measurement_unit", "description": "The units associated with a value from a chemical oxygen demand (COD) test.", "title": "chemical oxygen demand (COD) measurement unit", "comments": [ @@ -5800,17 +7189,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100789", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "chemical oxygen demand (COD) measurement unit menu" + "range": "ChemicalOxygenDemandCodMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "chemical oxygen demand (COD) measurement method": { - "name": "chemical oxygen demand (COD) measurement method", + "chemical_oxygen_demand_cod_measurement_method": { + "name": "chemical_oxygen_demand_cod_measurement_method", "description": "The method used to measure chemical oxygen demand (COD).", "title": "chemical oxygen demand (COD) measurement method", "comments": [ @@ -5823,10 +7217,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100790", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - 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"range": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu" + "range": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "carbonaceous biochemical oxygen demand (CBOD) measurement method": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "description": "The method used to measure carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement method", "comments": [ @@ -5878,10 +7287,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100793", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement value": { - "name": "total suspended solids (TSS) measurement value", + "total_suspended_solids_tss_measurement_value": { + "name": "total_suspended_solids_tss_measurement_value", "description": "The numerical value from a total suspended solids (TSS) test.", "title": "total suspended solids (TSS) measurement value", "comments": [ @@ -5893,11 +7307,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], "slot_uri": "GENEPIO:0100794", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement unit": { - "name": "total suspended solids (TSS) measurement unit", + "total_suspended_solids_tss_measurement_unit": { + "name": "total_suspended_solids_tss_measurement_unit", "description": "The units associated with a value from a total suspended solids (TSS) test.", "title": "total suspended solids (TSS) measurement unit", "comments": [ @@ -5909,18 +7331,26 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], "slot_uri": "GENEPIO:0100795", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "total suspended solids (TSS) measurement unit menu" + "range": "TotalSuspendedSolidsTssMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "total suspended solids (TSS) measurement method": { - "name": "total suspended solids (TSS) measurement method", + "total_suspended_solids_tss_measurement_method": { + "name": "total_suspended_solids_tss_measurement_method", "description": "The method used to measure total suspended solids (TSS).", "title": "total suspended solids (TSS) measurement method", "comments": [ @@ -5933,10 +7363,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100796", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement value": { - "name": "total dissolved solids (TDS) measurement value", + "total_dissolved_solids_tds_measurement_value": { + "name": "total_dissolved_solids_tds_measurement_value", "description": "The numerical value from a total dissolved solids (TDS) test.", "title": "total dissolved solids (TDS) measurement value", "comments": [ @@ -5949,10 +7384,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100797", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement unit": { - "name": "total dissolved solids (TDS) measurement unit", + "total_dissolved_solids_tds_measurement_unit": { + "name": "total_dissolved_solids_tds_measurement_unit", "description": "The units associated with a value from a total dissolved solids (TDS) test.", "title": "total dissolved solids (TDS) measurement unit", "comments": [ @@ -5965,17 +7405,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100798", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "total dissolved solids (TDS) measurement unit menu" + "range": "TotalDissolvedSolidsTdsMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "total dissolved solids (TDS) measurement method": { - "name": "total dissolved solids (TDS) measurement method", + "total_dissolved_solids_tds_measurement_method": { + "name": "total_dissolved_solids_tds_measurement_method", "description": "The method used to measure total dissolved solids (TDS).", "title": "total dissolved solids (TDS) measurement method", "comments": [ @@ -5988,10 +7433,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100799", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total solids (TS) measurement value": { - "name": "total solids (TS) measurement value", + "total_solids_ts_measurement_value": { + "name": "total_solids_ts_measurement_value", "description": "The numerical value from a total solids (TS) test.", "title": "total solids (TS) measurement value", "comments": [ @@ -6004,10 +7454,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100800", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total solids (TS) measurement unit": { - "name": "total solids (TS) measurement unit", + "total_solids_ts_measurement_unit": { + "name": "total_solids_ts_measurement_unit", "description": "The units associated with a value from a total solids (TS) test.", "title": "total solids (TS) measurement unit", "comments": [ @@ -6020,17 +7475,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100801", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "total solids (TS) measurement unit menu" + "range": "TotalSolidsTsMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "total solids (TS) measurement method": { - "name": "total solids (TS) measurement method", + "total_solids_ts_measurement_method": { + "name": "total_solids_ts_measurement_method", "description": "The method used to measure total solids (TS).", "title": "total solids (TS) measurement method", "comments": [ @@ -6043,10 +7503,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100802", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "alkalinity measurement value": { - "name": "alkalinity measurement value", + "alkalinity_measurement_value": { + "name": "alkalinity_measurement_value", "description": "The numerical value of a measurement of alkalinity.", "title": "alkalinity measurement value", "comments": [ @@ -6059,10 +7524,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100878", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "alkalinity measurement unit": { - "name": "alkalinity measurement unit", + "alkalinity_measurement_unit": { + "name": "alkalinity_measurement_unit", "description": "The units of a measurement of alkalinity.", "title": "alkalinity measurement unit", "comments": [ @@ -6075,17 +7545,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100879", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "alkalinity measurement unit menu" + "range": "AlkalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "alkalinity measurement method": { - "name": "alkalinity measurement method", + "alkalinity_measurement_method": { + "name": "alkalinity_measurement_method", "description": "The process used to measure alkalinity.", "title": "alkalinity measurement method", "comments": [ @@ -6098,10 +7573,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100880", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "conductivity measurement value": { - "name": "conductivity measurement value", + "conductivity_measurement_value": { + "name": "conductivity_measurement_value", "description": "The numerical value of a measurement of conductivity.", "title": "conductivity measurement value", "comments": [ @@ -6114,10 +7594,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100916", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "conductivity measurement unit": { - "name": "conductivity measurement unit", + "conductivity_measurement_unit": { + "name": "conductivity_measurement_unit", "description": "The units of a measurement of conductivity.", "title": "conductivity measurement unit", "comments": [ @@ -6130,17 +7615,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100803", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "conductivity measurement unit menu" + "range": "ConductivityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "conductivity measurement method": { - "name": "conductivity measurement method", + "conductivity_measurement_method": { + "name": "conductivity_measurement_method", "description": "The method used to measure conductivity.", "title": "conductivity measurement method", "comments": [ @@ -6153,10 +7643,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100804", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "salinity measurement value": { - "name": "salinity measurement value", + "salinity_measurement_value": { + "name": "salinity_measurement_value", "description": "The numerical value of a measurement of salinity.", "title": "salinity measurement value", "comments": [ @@ -6168,11 +7663,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], "slot_uri": "GENEPIO:0100805", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "salinity measurement unit": { - "name": "salinity measurement unit", + "salinity_measurement_unit": { + "name": "salinity_measurement_unit", "description": "The units of a measurement of salinity.", "title": "salinity measurement unit", "comments": [ @@ -6184,18 +7687,26 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], "slot_uri": "GENEPIO:0100806", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "salinity measurement unit menu" + "range": "SalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "salinity measurement method": { - "name": "salinity measurement method", + "salinity_measurement_method": { + "name": "salinity_measurement_method", "description": "The method used to measure salinity.", "title": "salinity measurement method", "comments": [ @@ -6208,10 +7719,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100807", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement value": { - "name": "total nitrogen (TN) measurement value", + "total_nitrogen_tn_measurement_value": { + "name": "total_nitrogen_tn_measurement_value", "description": "The numerical value of a measurement of total nitrogen (TN).", "title": "total nitrogen (TN) measurement value", "comments": [ @@ -6224,10 +7740,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100808", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement unit": { - "name": "total nitrogen (TN) measurement unit", + "total_nitrogen_tn_measurement_unit": { + "name": "total_nitrogen_tn_measurement_unit", "description": "The units of a measurement of total nitrogen (TN).", "title": "total nitrogen (TN) measurement unit", "comments": [ @@ -6240,17 +7761,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100809", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "total nitrogen (TN) measurement unit menu" + "range": "TotalNitrogenTnMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "total nitrogen (TN) measurement method": { - "name": "total nitrogen (TN) measurement method", + "total_nitrogen_tn_measurement_method": { + "name": "total_nitrogen_tn_measurement_method", "description": "The method used to measure total nitrogen (TN).", "title": "total nitrogen (TN) measurement method", "comments": [ @@ -6263,10 +7789,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100810", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement value": { - "name": "total phosphorus (TP) measurement value", + "total_phosphorus_tp_measurement_value": { + "name": "total_phosphorus_tp_measurement_value", "description": "The numerical value of a measurement of total phosphorus (TP).", "title": "total phosphorus (TP) measurement value", "comments": [ @@ -6279,10 +7810,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100811", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement unit": { - "name": "total phosphorus (TP) measurement unit", + "total_phosphorus_tp_measurement_unit": { + "name": "total_phosphorus_tp_measurement_unit", "description": "The units of a measurement of total phosphorus (TP).", "title": "total phosphorus (TP) measurement unit", "comments": [ @@ -6295,17 +7831,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100812", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "total phosphorus (TP) measurement unit menu" + "range": "TotalPhosphorusTpMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "total phosphorus (TP) measurement method": { - "name": "total phosphorus (TP) measurement method", + "total_phosphorus_tp_measurement_method": { + "name": "total_phosphorus_tp_measurement_method", "description": "The method used to measure total phosphorus (TP).", "title": "total phosphorus (TP) measurement method", "comments": [ @@ -6318,10 +7859,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100813", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "fecal contamination indicator": { - "name": "fecal contamination indicator", + "fecal_contamination_indicator": { + "name": "fecal_contamination_indicator", "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", "title": "fecal contamination indicator", "comments": [ @@ -6334,18 +7880,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100814", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "fecal contamination indicator menu" + "range": "FecalContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "fecal contamination value": { - "name": "fecal contamination value", + "fecal_contamination_value": { + "name": "fecal_contamination_value", "description": "The numerical value of a measurement of fecal contamination.", "title": "fecal contamination value", "comments": [ @@ -6358,11 +7909,16 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100815", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "fecal contamination unit": { - "name": "fecal contamination unit", + "fecal_contamination_unit": { + "name": "fecal_contamination_unit", "description": "The units of a measurement of fecal contamination.", "title": "fecal contamination unit", "comments": [ @@ -6375,18 +7931,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100816", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "fecal contamination unit menu" + "range": "FecalContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "fecal contamination method": { - "name": "fecal contamination method", + "fecal_contamination_method": { + "name": "fecal_contamination_method", "description": "The method used to measure fecal contamination.", "title": "fecal contamination method", "comments": [ @@ -6399,10 +7960,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100817", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "fecal coliform count value": { - "name": "fecal coliform count value", + "fecal_coliform_count_value": { + "name": "fecal_coliform_count_value", "description": "The numerical value of a measurement of fecal coliforms within a sample.", "title": "fecal coliform count value", "comments": [ @@ -6415,10 +7981,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100818", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "fecal coliform count unit": { - "name": "fecal coliform count unit", + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", "description": "The units of a measurement of fecal coliforms.", "title": "fecal coliform count unit", "comments": [ @@ -6431,17 +8002,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100819", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "fecal coliform count unit menu" + "range": "FecalColiformCountUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "fecal coliform count method": { - "name": "fecal coliform count method", + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", "description": "The method used to measure fecal coliforms.", "title": "fecal coliform count method", "comments": [ @@ -6454,10 +8030,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100820", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "urinary contamination indicator": { - "name": "urinary contamination indicator", + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", "title": "urinary contamination indicator", "comments": [ @@ -6470,17 +8051,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100837", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "urinary contamination indicator menu" + "range": "UrinaryContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "urinary contamination value": { - "name": "urinary contamination value", + "urinary_contamination_value": { + "name": "urinary_contamination_value", "description": "The numerical value of a measurement of urinary contamination.", "title": "urinary contamination value", "comments": [ @@ -6493,10 +8079,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100838", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "urinary contamination unit": { - "name": "urinary contamination unit", + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", "description": "The units of a measurement of urinary contamination.", "title": "urinary contamination unit", "comments": [ @@ -6509,17 +8100,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100839", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "urinary contamination unit menu" + "range": "UrinaryContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "urinary contamination method": { - "name": "urinary contamination method", + "urinary_contamination_method": { + "name": "urinary_contamination_method", "description": "The method used to measure urinary contamination.", "title": "urinary contamination method", "comments": [ @@ -6532,10 +8128,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100840", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample temperature value (at collection)": { - "name": "sample temperature value (at collection)", + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", "description": "The numerical value of a measurement of temperature of a sample at collection.", "title": "sample temperature value (at collection)", "comments": [ @@ -6547,11 +8148,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], "slot_uri": "GENEPIO:0100821", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample temperature unit (at collection)": { - "name": "sample temperature unit (at collection)", + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", "description": "The units of a measurement of temperature of a sample at the time of collection.", "title": "sample temperature unit (at collection)", "comments": [ @@ -6563,18 +8172,26 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], "slot_uri": "GENEPIO:0100822", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "sample temperature unit (at collection) menu" + "range": "SampleTemperatureUnitAtCollectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample temperature value (when received)": { - "name": "sample temperature value (when received)", + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", "description": "The numerical value of a measurement of temperature of a sample upon receipt.", "title": "sample temperature value (when received)", "comments": [ @@ -6587,10 +8204,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100823", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sample temperature unit (when received)": { - "name": "sample temperature unit (when received)", + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", "description": "The units of a measurement of temperature of a sample at the time upon receipt.", "title": "sample temperature unit (when received)", "comments": [ @@ -6603,17 +8225,22 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100824", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "sample temperature unit (when received) menu" + "range": "SampleTemperatureUnitWhenReceivedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", "comments": [ @@ -6625,20 +8252,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sequencing" + ], "slot_uri": "GENEPIO:0001445", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "purpose of sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "comments": [ @@ -6651,10 +8286,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", "title": "sequenced by", "comments": [ @@ -6670,18 +8310,44 @@ "GISAID:sequenced_by" ], "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0100470", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact name", "comments": [ @@ -6689,23 +8355,28 @@ ], "examples": [ { - "value": "Enterics Lab Manager" + "value": "Joe Bloggs, Enterics Lab Manager" } ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", "comments": [ @@ -6718,18 +8389,23 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that submitted the sequence to a database.", "title": "sequence submitted by", "comments": [ @@ -6741,19 +8417,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sequenced_by" + ], "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", "comments": [ @@ -6765,7 +8449,15 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:sequence_submitter_contact_email" + ], "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "pattern": "^\\S+@\\S+\\.\\S+$", "any_of": [ @@ -6773,12 +8465,12 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ @@ -6794,10 +8486,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "date" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", "comments": [ @@ -6809,11 +8506,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:library_ID" + ], "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sequencing platform": { - "name": "sequencing platform", + "sequencing_platform": { + "name": "sequencing_platform", "description": "The platform technology used to perform the sequencing.", "title": "sequencing platform", "comments": [ @@ -6825,19 +8530,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:platform" + ], "slot_uri": "GENEPIO:0100473", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "sequencing platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", "comments": [ @@ -6849,20 +8562,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:instrument_model" + ], "slot_uri": "GENEPIO:0001452", - "multivalued": true, + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "sequencing instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing assay type": { - "name": "sequencing assay type", + "sequencing_assay_type": { + "name": "sequencing_assay_type", "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", "title": "sequencing assay type", "comments": [ @@ -6874,19 +8595,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:library_strategy" + ], "slot_uri": "GENEPIO:0100997", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "sequencing assay type menu" + "range": "SequencingAssayTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", "comments": [ @@ -6898,11 +8627,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:library_preparation_kit" + ], "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol or method used for sequencing.", "title": "sequencing protocol", "comments": [ @@ -6915,11 +8652,16 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DNA fragment length": { - "name": "DNA fragment length", + "dna_fragment_length": { + "name": "dna_fragment_length", "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", "title": "DNA fragment length", "comments": [ @@ -6932,10 +8674,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100843", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method", "comments": [ @@ -6947,20 +8693,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:library_selection" + ], "slot_uri": "GENEPIO:0100966", - "multivalued": true, + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "genomic target enrichment method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method details", "comments": [ @@ -6973,10 +8726,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100967", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", "comments": [ @@ -6988,19 +8745,26 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:amplicon_PCR_primer_scheme" + ], "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "amplicon pcr primer scheme menu" + "range": "AmpliconPcrPrimerSchemeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", "comments": [ @@ -7012,11 +8776,18 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:amplicon_size" + ], "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "quality control method name": { - "name": "quality control method name", + "quality_control_method_name": { + "name": "quality_control_method_name", "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method name", "comments": [ @@ -7028,11 +8799,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:quality_control_method" + ], "slot_uri": "GENEPIO:0100557", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_version": { + "name": "quality_control_method_version", "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method version", "comments": [ @@ -7044,11 +8823,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:quality_control_method_version" + ], "slot_uri": "GENEPIO:0100558", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_determination": { + "name": "quality_control_determination", "description": "The determination of a quality control assessment.", "title": "quality control determination", "comments": [ @@ -7060,19 +8847,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:quality_control_determination" + ], "slot_uri": "GENEPIO:0100559", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "quality control determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "quality control issues": { - "name": "quality control issues", + "quality_control_issues": { + "name": "quality_control_issues", "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", "title": "quality control issues", "comments": [ @@ -7084,19 +8879,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:quality_control_issues" + ], "slot_uri": "GENEPIO:0100560", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "multivalued": true, "any_of": [ { - "range": "quality control issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "quality control details": { - "name": "quality control details", + "quality_control_details": { + "name": "quality_control_details", "description": "The details surrounding a low quality determination in a quality control assessment.", "title": "quality control details", "comments": [ @@ -7108,11 +8911,19 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:quality_control_details" + ], "slot_uri": "GENEPIO:0100561", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "comments": [ @@ -7124,19 +8935,27 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:raw_sequence_data_processing_method" + ], "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "comments": [ @@ -7148,19 +8967,83 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:dehosting_method" + ], "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" + } + ] + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101715", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", + "comments": [ + "Provide the filepath of the genome sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101716", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" } ] }, - "sequence assembly software name": { - "name": "sequence assembly software name", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", "description": "The name of the software used to assemble a sequence.", "title": "sequence assembly software name", "comments": [ @@ -7173,17 +9056,21 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100825", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence assembly software version": { - "name": "sequence assembly software version", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", "description": "The version of the software used to assemble a sequence.", "title": "sequence assembly software version", "comments": [ @@ -7196,17 +9083,21 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100826", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of the software used to generate the consensus sequence.", "title": "consensus sequence software name", "comments": [ @@ -7219,17 +9110,20 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "comments": [ @@ -7242,17 +9136,20 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", "comments": [ @@ -7265,10 +9162,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", "comments": [ @@ -7281,10 +9183,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", "comments": [ @@ -7297,10 +9204,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "genome completeness": { - "name": "genome completeness", + "genome_completeness": { + "name": "genome_completeness", "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", "title": "genome completeness", "comments": [ @@ -7313,10 +9225,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100844", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", "comments": [ @@ -7329,10 +9245,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "number of total reads": { - "name": "number of total reads", + "number_of_total_reads": { + "name": "number_of_total_reads", "description": "The total number of non-unique reads generated by the sequencing process.", "title": "number of total reads", "comments": [ @@ -7345,10 +9266,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100827", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "number of unique reads": { - "name": "number of unique reads", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "description": "The number of unique reads generated by the sequencing process.", "title": "number of unique reads", "comments": [ @@ -7361,10 +9287,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100828", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", "title": "minimum post-trimming read length", "comments": [ @@ -7377,10 +9308,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100829", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "number of contigs": { - "name": "number of contigs", + "number_of_contigs": { + "name": "number_of_contigs", "description": "The number of contigs (contiguous sequences) in a sequence assembly.", "title": "number of contigs", "comments": [ @@ -7393,10 +9329,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100937", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", "title": "percent Ns across total genome length", "comments": [ @@ -7409,10 +9349,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100830", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", "title": "Ns per 100 kbp", "comments": [ @@ -7425,10 +9369,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "range": "integer" }, - "N50": { - "name": "N50", + "n50": { + "name": "n50", "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", "title": "N50", "comments": [ @@ -7441,10 +9388,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100938", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "percent read contamination": { - "name": "percent read contamination", + "percent_read_contamination": { + "name": "percent_read_contamination", "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", "title": "percent read contamination", "comments": [ @@ -7457,10 +9408,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100845", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "sequence assembly length": { - "name": "sequence assembly length", + "sequence_assembly_length": { + "name": "sequence_assembly_length", "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", "title": "sequence assembly length", "comments": [ @@ -7473,10 +9428,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100846", + "domain_of": [ + "WastewaterPathogenAgnostic" + ], "range": "integer" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "The length of the genome defined by the most common nucleotides at each position.", "title": "consensus genome length", "comments": [ @@ -7489,10 +9447,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "range": "integer" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", "comments": [ @@ -7504,11 +9465,18 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_SRA:assembly" + ], "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "deduplication method": { - "name": "deduplication method", + "deduplication_method": { + "name": "deduplication_method", "description": "The method used to remove duplicated reads in a sequence read dataset.", "title": "deduplication method", "comments": [ @@ -7521,10 +9489,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100831", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "comments": [ @@ -7537,10 +9509,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "read mapping software name": { - "name": "read mapping software name", + "read_mapping_software_name": { + "name": "read_mapping_software_name", "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software name", "comments": [ @@ -7553,10 +9530,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100832", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "read mapping software version": { - "name": "read mapping software version", + "read_mapping_software_version": { + "name": "read_mapping_software_version", "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software version", "comments": [ @@ -7569,10 +9550,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100833", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", "description": "The name of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database name", "comments": [ @@ -7585,11 +9570,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100834", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", "description": "The version of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database version", "comments": [ @@ -7602,11 +9591,15 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100835", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", "description": "The filename of the report containing the results of a taxonomic analysis.", "title": "taxonomic analysis report filename", "comments": [ @@ -7619,10 +9612,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101074", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", "comments": [ @@ -7635,10 +9632,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101075", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "date" }, - "read mapping criteria": { - "name": "read mapping criteria", + "read_mapping_criteria": { + "name": "read_mapping_criteria", "description": "A description of the criteria used to map reads to a reference sequence.", "title": "read mapping criteria", "comments": [ @@ -7651,10 +9652,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100836", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "AMR analysis software name": { - "name": "AMR analysis software name", + "amr_analysis_software_name": { + "name": "amr_analysis_software_name", "description": "The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis.", "title": "AMR analysis software name", "comments": [ @@ -7667,11 +9672,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101076", + "domain_of": [ + "WastewaterAMR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR analysis software version": { - "name": "AMR analysis software version", + "amr_analysis_software_version": { + "name": "amr_analysis_software_version", "description": "The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis.", "title": "AMR analysis software version", "comments": [ @@ -7684,11 +9692,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101077", + "domain_of": [ + "WastewaterAMR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR reference database name": { - "name": "AMR reference database name", + "amr_reference_database_name": { + "name": "amr_reference_database_name", "description": "Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis.", "title": "AMR reference database name", "comments": [ @@ -7701,11 +9712,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101078", + "domain_of": [ + "WastewaterAMR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR reference database version": { - "name": "AMR reference database version", + "amr_reference_database_version": { + "name": "amr_reference_database_version", "description": "The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis.", "title": "AMR reference database version", "comments": [ @@ -7718,11 +9732,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101079", + "domain_of": [ + "WastewaterAMR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR analysis report filename": { - "name": "AMR analysis report filename", + "amr_analysis_report_filename": { + "name": "amr_analysis_report_filename", "description": "The filename of the report containing the results of an in silico antimicrobial resistance analysis.", "title": "AMR analysis report filename", "comments": [ @@ -7735,11 +9752,14 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101080", + "domain_of": [ + "WastewaterAMR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "description": "The name of the lineage or clade.", "title": "lineage/clade name", "comments": [ @@ -7752,10 +9772,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001500", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "description": "The name of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software name", "comments": [ @@ -7768,10 +9791,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001501", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "description": "The version of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software version", "comments": [ @@ -7784,10 +9810,13 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0001502", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis report filename": { - "name": "lineage/clade analysis report filename", + "lineage_clade_analysis_report_filename": { + "name": "lineage_clade_analysis_report_filename", "description": "The filename of the report containing the results of a lineage/clade analysis.", "title": "lineage/clade analysis report filename", "comments": [ @@ -7800,19 +9829,66 @@ ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0101081", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], + "range": "WhitespaceMinimizedString" + }, + "assay_target_name_1": { + "name": "assay_target_name_1", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 1", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0101206", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_details": { + "name": "assay_target_details", + "description": "Describe any details of the assay target.", + "title": "assay target details", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/GRDI", + "slot_uri": "GENEPIO:0102040", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "gene name": { - "name": "gene name", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name", + "gene_symbol_1": { + "name": "gene_symbol_1", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 1", "from_schema": "https://example.com/GRDI", - "slot_uri": "GENEPIO:0100655" + "slot_uri": "GENEPIO:0102041", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", "description": "The binary value of the result from a diagnostic test.", - "title": "diagnostic target presence", + "title": "diagnostic target presence 1", "comments": [ "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." ], @@ -7822,20 +9898,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_known_present" + ], "slot_uri": "GENEPIO:0100962", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", "description": "The value of the result from a diagnostic test.", - "title": "diagnostic measurement value", + "title": "diagnostic measurement value 1", "comments": [ "Provide the numerical result of a diagnostic test (no need to include units)." ], @@ -7845,13 +9929,21 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc" + ], "slot_uri": "GENEPIO:0100963", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", "description": "The unit of the result from a diagnostic test.", - "title": "diagnostic measurement unit", + "title": "diagnostic measurement unit 1", "comments": [ "Select a value from the pick list provided, to describe the units of the given diagnostic test." ], @@ -7861,20 +9953,28 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc_unit" + ], "slot_uri": "GENEPIO:0100964", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", "description": "The method by which a diagnostic result was determined.", - "title": "diagnostic measurement method", + "title": "diagnostic measurement method 1", "comments": [ "Select a value from the pick list provided to describe the method used for a given diagnostic test." ], @@ -7884,64 +9984,319 @@ } ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_protocol" + ], "slot_uri": "GENEPIO:0100965", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", + "assay_target_name_2": { + "name": "assay_target_name_2", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 2", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "assay_target_details_2": { + "name": "assay_target_details_2", + "description": "Describe any details of the assay target.", + "title": "assay target details 2", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "gene_symbol_2": { + "name": "gene_symbol_2", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 2", + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_gene" + ], + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ] + }, + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 2", "comments": [ - "Include the first and last names of all individuals that should be attributed, separated by a semicolon." + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." ], "examples": [ { - "value": "Tejinder Singh" - }, + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_known_present" + ], + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ { - "value": "Fei Hu" + "range": "DiagnosticTargetPresenceMenu" }, { - "value": "Joe Blogs" + "range": "NullValueMenu" + } + ] + }, + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 2", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "GISAID:Authors", - "CNPHI:Authors", - "NML_LIMS:PH_CANCOGEN_AUTHORS" + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc" ], - "slot_uri": "GENEPIO:0001517", - "range": "WhitespaceMinimizedString", - "recommended": true + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 2", "comments": [ - "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + "Select a value from the pick list provided, to describe the units of the given diagnostic test." ], "examples": [ { - "value": "DataHarmonizer v3.3.3, Influenza v1.0.0" + "value": "cycle threshold (Ct)" } ], "from_schema": "https://example.com/GRDI", "exact_mappings": [ - "GISAID:DataHarmonizer%20provenance", - "CNPHI:Additional%20Comments", - "NML_LIMS:HC_COMMENTS" + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc_unit" + ], + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 2", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "assay_target_name_3": { + "name": "assay_target_name_3", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 3", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "assay_target_details_3": { + "name": "assay_target_details_3", + "description": "Describe any details of the assay target.", + "title": "assay target details 3", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "gene_symbol_3": { + "name": "gene_symbol_3", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 3", + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ] + }, + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 3", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 3", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 3", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 3", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } ], - "slot_uri": "GENEPIO:0001518", - "range": "Provenance" + "from_schema": "https://example.com/GRDI", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] } }, "classes": { @@ -7952,150 +10307,151 @@ }, "WastewaterSARS-CoV-2": { "name": "WastewaterSARS-CoV-2", + "annotations": { + "version": { + "tag": "version", + "value": "3.1.1" + } + }, "description": "Specification for Wastewater SARS-CoV-2 virus biosample data gathering", "from_schema": "https://example.com/GRDI", "is_a": "dh_interface", "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 1, "slot_group": "Database identifiers" }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", "rank": 2, "slot_group": "Database identifiers" }, - "pooled sample ID": { - "name": "pooled sample ID", + "pooled_sample_id": { + "name": "pooled_sample_id", "rank": 3, "slot_group": "Database identifiers" }, - "specimen collector project ID": { - "name": "specimen collector project ID", + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", "rank": 4, "slot_group": "Database identifiers" }, - "BioProject accession": { - "name": "BioProject accession", + "bioproject_accession": { + "name": "bioproject_accession", "rank": 5, "slot_group": "Database identifiers" }, - "BioSample accession": { - "name": "BioSample accession", + "biosample_accession": { + "name": "biosample_accession", "rank": 6, "slot_group": "Database identifiers" }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", "rank": 7, "slot_group": "Database identifiers" }, - "SRA accession": { - "name": "SRA accession", + "enterobase_accession": { + "name": "enterobase_accession", "rank": 8, "slot_group": "Database identifiers" }, - "GISAID accession": { - "name": "GISAID accession", + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", "rank": 9, "slot_group": "Database identifiers" }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_accession": { + "name": "gisaid_accession", "rank": 10, "slot_group": "Database identifiers" }, - "ENA accession": { - "name": "ENA accession", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "rank": 11, "slot_group": "Database identifiers" }, - "DRA accession": { - "name": "DRA accession", + "sampling_site_id": { + "name": "sampling_site_id", "rank": 12, "slot_group": "Database identifiers" }, - "GSA accession": { - "name": "GSA accession", + "sampling_event_id": { + "name": "sampling_event_id", "rank": 13, "slot_group": "Database identifiers" }, - "Enterobase accession": { - "name": "Enterobase accession", + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", "rank": 14, - "slot_group": "Database identifiers" + "slot_group": "Sample collection and processing" }, - "sampling site ID": { - "name": "sampling site ID", + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", "rank": 15, - "slot_group": "Database identifiers" + "slot_group": "Sample collection and processing" }, - "sampling event ID": { - "name": "sampling event ID", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 16, - "slot_group": "Database identifiers" + "slot_group": "Sample collection and processing" }, - "sample collection data steward name": { - "name": "sample collection data steward name", + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", "rank": 17, "slot_group": "Sample collection and processing" }, - "sample collected by": { - "name": "sample collected by", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "rank": 18, "slot_group": "Sample collection and processing" }, - "sample collector contact email": { - "name": "sample collector contact email", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 19, "slot_group": "Sample collection and processing" }, - "geo loc name (country)": { - "name": "geo loc name (country)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 20, "slot_group": "Sample collection and processing" }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "rank": 21, "slot_group": "Sample collection and processing" }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "rank": 22, "slot_group": "Sample collection and processing" }, - "geo loc name (city)": { - "name": "geo loc name (city)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 23, "slot_group": "Sample collection and processing" }, - "geo loc name (site)": { - "name": "geo loc name (site)", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "rank": 24, "slot_group": "Sample collection and processing" }, - "geo loc latitude": { - "name": "geo loc latitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "rank": 25, "slot_group": "Sample collection and processing" }, - "geo loc longitude": { - "name": "geo loc longitude", + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", "rank": 26, "slot_group": "Sample collection and processing" }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", "rank": 27, "slot_group": "Sample collection and processing" }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", - "rank": 28, - "slot_group": "Sample collection and processing" - }, "organism": { "name": "organism", "comments": [ @@ -8106,801 +10462,830 @@ "value": "Severe acute respiratory syndrome coronavirus 2" } ], - "rank": 29, - "multivalued": true, + "rank": 28, "slot_group": "Sample collection and processing", "required": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "rank": 29, + "slot_group": "Sample collection and processing" + }, + "scale_of_sampling": { + "name": "scale_of_sampling", "rank": 30, "slot_group": "Sample collection and processing" }, - "scale of sampling": { - "name": "scale of sampling", + "sample_received_date": { + "name": "sample_received_date", "rank": 31, "slot_group": "Sample collection and processing" }, - "sample received date": { - "name": "sample received date", + "sample_collection_start_date": { + "name": "sample_collection_start_date", "rank": 32, "slot_group": "Sample collection and processing" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_end_date": { + "name": "sample_collection_end_date", "rank": 33, "slot_group": "Sample collection and processing" }, - "sample collection end date": { - "name": "sample collection end date", + "sample_processing_date": { + "name": "sample_processing_date", "rank": 34, "slot_group": "Sample collection and processing" }, - "sample processing date": { - "name": "sample processing date", + "sample_collection_start_time": { + "name": "sample_collection_start_time", "rank": 35, "slot_group": "Sample collection and processing" }, - "sample collection start time": { - "name": "sample collection start time", + "sample_collection_end_time": { + "name": "sample_collection_end_time", "rank": 36, "slot_group": "Sample collection and processing" }, - "sample collection end time": { - "name": "sample collection end time", + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", "rank": 37, "slot_group": "Sample collection and processing" }, - "sample collection time of day": { - "name": "sample collection time of day", + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", "rank": 38, "slot_group": "Sample collection and processing" }, - "sample collection time duration value": { - "name": "sample collection time duration value", + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", "rank": 39, "slot_group": "Sample collection and processing" }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", + "presampling_activity": { + "name": "presampling_activity", "rank": 40, "slot_group": "Sample collection and processing" }, - "presampling activity": { - "name": "presampling activity", + "presampling_activity_details": { + "name": "presampling_activity_details", "rank": 41, "slot_group": "Sample collection and processing" }, - "presampling activity details": { - "name": "presampling activity details", + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", "rank": 42, "slot_group": "Sample collection and processing" }, - "sample volume measurement value": { - "name": "sample volume measurement value", + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", "rank": 43, "slot_group": "Sample collection and processing" }, - 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"sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "rank": 144, "slot_group": "Sequence information" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "rank": 145, "slot_group": "Sequence information" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 146, "slot_group": "Sequence information" }, - "sequencing date": { - "name": "sequencing date", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "rank": 147, "slot_group": "Sequence information" }, - "library ID": { - "name": "library ID", + "sequencing_date": { + "name": "sequencing_date", "rank": 148, "slot_group": "Sequence information" }, - "sequencing platform": { - "name": "sequencing platform", + "library_id": { + "name": "library_id", "rank": 149, "slot_group": "Sequence information" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_platform": { + "name": "sequencing_platform", "rank": 150, "slot_group": "Sequence information" }, - "sequencing assay type": { - "name": "sequencing assay type", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 151, "slot_group": "Sequence information" }, - "library preparation kit": { - "name": "library preparation kit", + "sequencing_assay_type": { + "name": "sequencing_assay_type", "rank": 152, "slot_group": "Sequence information" }, - "sequencing protocol": { - "name": "sequencing protocol", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 153, "slot_group": "Sequence information" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 154, "slot_group": "Sequence information" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 155, "slot_group": "Sequence information" }, - "quality control method name": { - "name": "quality control method name", + "amplicon_size": { + "name": "amplicon_size", "rank": 156, - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Sequence information" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_name": { + "name": "quality_control_method_name", "rank": 157, "slot_group": "Bioinformatics and QC metrics" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_method_version": { + "name": "quality_control_method_version", "rank": 158, "slot_group": "Bioinformatics and QC metrics" }, - "quality control issues": { - "name": "quality control issues", + "quality_control_determination": { + "name": "quality_control_determination", "rank": 159, "slot_group": "Bioinformatics and QC metrics" }, - "quality control details": { - "name": "quality control details", + "quality_control_issues": { + "name": "quality_control_issues", "rank": 160, "slot_group": "Bioinformatics and QC metrics" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "quality_control_details": { + "name": "quality_control_details", "rank": 161, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 162, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "dehosting_method": { + "name": "dehosting_method", "rank": 163, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", "rank": 164, "slot_group": "Bioinformatics and QC metrics" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", "rank": 165, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage value": { - "name": "depth of coverage value", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 166, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 167, "slot_group": "Bioinformatics and QC metrics" }, - "genome completeness": { - "name": "genome completeness", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 168, "slot_group": "Bioinformatics and QC metrics" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 169, "slot_group": "Bioinformatics and QC metrics" }, - "number of total reads": { - "name": "number of total reads", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 170, "slot_group": "Bioinformatics and QC metrics" }, - "number of unique reads": { - "name": "number of unique reads", + "genome_completeness": { + "name": "genome_completeness", "rank": 171, "slot_group": "Bioinformatics and QC metrics" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 172, "slot_group": "Bioinformatics and QC metrics" }, - "number of contigs": { - "name": "number of contigs", + "number_of_total_reads": { + "name": "number_of_total_reads", "rank": 173, "slot_group": "Bioinformatics and QC metrics" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "rank": 174, "slot_group": "Bioinformatics and QC metrics" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "rank": 175, "slot_group": "Bioinformatics and QC metrics" }, - "N50": { - "name": "N50", + "number_of_contigs": { + "name": "number_of_contigs", "rank": 176, "slot_group": "Bioinformatics and QC metrics" }, - "percent read contamination": { - "name": "percent read contamination", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "rank": 177, "slot_group": "Bioinformatics and QC metrics" }, - "consensus genome length": { - "name": "consensus genome length", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "rank": 178, "slot_group": "Bioinformatics and QC metrics" }, - "reference genome accession": { - "name": "reference genome accession", + "n50": { + "name": "n50", "rank": 179, "slot_group": "Bioinformatics and QC metrics" }, - "deduplication method": { - "name": "deduplication method", + "percent_read_contamination": { + "name": "percent_read_contamination", "rank": 180, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "consensus_genome_length": { + "name": "consensus_genome_length", "rank": 181, "slot_group": "Bioinformatics and QC metrics" }, - "lineage/clade name": { - "name": "lineage/clade name", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 182, - "slot_group": "Lineage/clade information" + "slot_group": "Bioinformatics and QC metrics" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "deduplication_method": { + "name": "deduplication_method", "rank": 183, - "slot_group": "Lineage/clade information" + "slot_group": "Bioinformatics and QC metrics" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 184, - "slot_group": "Lineage/clade information" + "slot_group": "Bioinformatics and QC metrics" }, - "lineage/clade analysis report filename": { - "name": "lineage/clade analysis report filename", + "lineage_clade_name": { + "name": "lineage_clade_name", "rank": 185, "slot_group": "Lineage/clade information" }, - "gene name": { - "name": "gene name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", + "rank": 186, + "slot_group": "Lineage/clade information" + }, + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", + "rank": 187, + "slot_group": "Lineage/clade information" + }, + "lineage_clade_analysis_report_filename": { + "name": "lineage_clade_analysis_report_filename", + "rank": 188, + "slot_group": "Lineage/clade information" + }, + "assay_target_name_1": { + "name": "assay_target_name_1", + "rank": 189, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details": { + "name": "assay_target_details", + "rank": 190, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_1": { + "name": "gene_symbol_1", "comments": [ "Select a gene name value from the pick list provided." ], @@ -8909,76 +11294,191 @@ "value": "E gene (orf4)" } ], - "rank": 186, + "rank": 191, "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name menu" + "range": "GeneSymbolMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", - "rank": 187, + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", + "rank": 192, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", - "rank": 188, + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", + "rank": 193, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", - "rank": 189, + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", + "rank": 194, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", - "rank": 190, + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", + "rank": 195, "slot_group": "Pathogen diagnostic testing" }, - "authors": { - "name": "authors", - "rank": 191, - "slot_group": "Contributor acknowledgement" + "assay_target_name_2": { + "name": "assay_target_name_2", + "rank": 196, + "slot_group": "Pathogen diagnostic testing" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 192, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "The user-defined name for the sample.", - "title": "specimen collector sample ID", - "from_schema": "https://example.com/GRDI", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "specimen_collector_sample_ID", - "owner": "WastewaterSARS-CoV-2", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "assay_target_details_2": { + "name": "assay_target_details_2", + "rank": 197, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_2": { + "name": "gene_symbol_2", + "comments": [ + "Select a gene name value from the pick list provided." + ], + "examples": [ + { + "value": "E gene (orf4)" + } + ], + "rank": 198, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "rank": 199, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "rank": 200, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "rank": 201, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "rank": 202, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_name_3": { + "name": "assay_target_name_3", + "rank": 203, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details_3": { + "name": "assay_target_details_3", + "rank": 204, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_3": { + "name": "gene_symbol_3", + "comments": [ + "Select a gene name value from the pick list provided." + ], + "examples": [ + { + "value": "E gene (orf4)" + } + ], + "rank": 205, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", + "rank": 206, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", + "rank": 207, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", + "rank": 208, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sample_name", + "NCBI_SRA:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" ], "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", "description": "The user-defined identifier assigned to a portion of the original sample.", "title": "specimen collector subsample ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_id" + ], "rank": 2, "slot_uri": "GENEPIO:0100752", - "alias": "specimen_collector_subsample_ID", + "alias": "specimen_collector_subsample_id", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -8988,14 +11488,22 @@ "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString" }, - "pooled sample ID": { - "name": "pooled sample ID", + "pooled_sample_id": { + "name": "pooled_sample_id", "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", "title": "pooled sample ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], "from_schema": "https://example.com/GRDI", "rank": 3, "slot_uri": "GENEPIO:0100996", - "alias": "pooled_sample_ID", + "alias": "pooled_sample_id", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9005,14 +11513,20 @@ "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString" }, - "specimen collector project ID": { - "name": "specimen collector project ID", + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", "description": "The user-defined project name assigned to a sequencing project.", "title": "specimen collector project ID", + "comments": [ + "If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here." + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:project_name" + ], "rank": 4, "slot_uri": "GENEPIO:0100918", - "alias": "specimen_collector_project_ID", + "alias": "specimen_collector_project_id", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9022,14 +11536,25 @@ "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString" }, - "BioProject accession": { - "name": "BioProject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", "title": "BioProject accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:bioproject_accession" + ], "rank": 5, "slot_uri": "GENEPIO:0001136", - "alias": "BioProject_accession", + "alias": "bioproject_accession", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9045,14 +11570,22 @@ "partial_match": false } }, - "BioSample accession": { - "name": "BioSample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", "title": "BioSample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMEA00000002, SAMD00000001" + } + ], "from_schema": "https://example.com/GRDI", "rank": 6, "slot_uri": "GENEPIO:0001139", - "alias": "BioSample_accession", + "alias": "biosample_accession", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9069,14 +11602,22 @@ "partial_match": false } }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", - "description": "The versioned identifier assigned to an assembly or consensus sequence in GenBank archives.", - "title": "GenBank accession (versioned)", + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], "from_schema": "https://example.com/GRDI", "rank": 7, - "slot_uri": "GENEPIO:0100754", - "alias": "GenBank_accession_(versioned)", + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9092,14 +11633,22 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", + "enterobase_accession": { + "name": "enterobase_accession", + "description": "The identifier assigned to a sequence in Enterobase archives.", + "title": "Enterobase accession", + "comments": [ + "Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism." + ], + "examples": [ + { + "value": "SAL_AA0019AA_ST" + } + ], "from_schema": "https://example.com/GRDI", "rank": 8, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "slot_uri": "GENEPIO:0100759", + "alias": "enterobase_accession", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9115,14 +11664,22 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", - "title": "GISAID accession", + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], "from_schema": "https://example.com/GRDI", "rank": 9, - "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9138,60 +11695,22 @@ "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "title": "GISAID virus name", - "from_schema": "https://example.com/GRDI", - "rank": 10, - "slot_uri": "GENEPIO:0100282", - "alias": "GISAID_virus_name", - "owner": "WastewaterSARS-CoV-2", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "gisaid_accession": { + "name": "gisaid_accession", + "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", + "title": "GISAID accession", + "comments": [ + "Store the accession assigned to the submitted sequence. GISAID accessions start with EPI." ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "ENA accession": { - "name": "ENA accession", - "description": "The identifier assigned to a sequence in the European Nucleotide Archive (ENA).", - "title": "ENA accession", - "from_schema": "https://example.com/GRDI", - "rank": 11, - "slot_uri": "GENEPIO:0100755", - "alias": "ENA_accession", - "owner": "WastewaterSARS-CoV-2", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "examples": [ + { + "value": "EPI_ISL_402131" + } ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "DRA accession": { - "name": "DRA accession", - "description": "The identifier assigned to a sequence in DNA Data Bank of Japan (DDBJ) sequence read archives.", - "title": "DRA accession", "from_schema": "https://example.com/GRDI", - "rank": 12, - "slot_uri": "GENEPIO:0100757", - "alias": "DRA_accession", + "rank": 10, + "slot_uri": "GENEPIO:0001147", + "alias": "gisaid_accession", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9207,37 +11726,22 @@ "partial_match": false } }, - "GSA accession": { - "name": "GSA accession", - "description": "The identifier assigned to a BioSample in GSA (Genome Sequence Archive) archives.", - "title": "GSA accession", - "from_schema": "https://example.com/GRDI", - "rank": 13, - "slot_uri": "GENEPIO:0100758", - "alias": "GSA_accession", - "owner": "WastewaterSARS-CoV-2", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "title": "GISAID virus name", + "comments": [ + "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\"." + ], + "examples": [ + { + "value": "hCoV-19/Canada/prov_rona_99/2020" + } ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } - }, - "Enterobase accession": { - "name": "Enterobase accession", - "description": "The identifier assigned to a sequence in Enterobase archives.", - "title": "Enterobase accession", "from_schema": "https://example.com/GRDI", - "rank": 14, - "slot_uri": "GENEPIO:0100759", - "alias": "Enterobase_accession", + "rank": 11, + "slot_uri": "GENEPIO:0100282", + "alias": "gisaid_virus_name", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9253,14 +11757,25 @@ "partial_match": false } }, - "sampling site ID": { - "name": "sampling site ID", + "sampling_site_id": { + "name": "sampling_site_id", "description": "The user-defined identifier assigned to a specific location from which samples are taken.", "title": "sampling site ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 15, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_site_id" + ], + "rank": 12, "slot_uri": "GENEPIO:0100760", - "alias": "sampling_site_ID", + "alias": "sampling_site_id", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9271,14 +11786,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "sampling event ID": { - "name": "sampling event ID", + "sampling_event_id": { + "name": "sampling_event_id", "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", "title": "sampling event ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 16, + "rank": 13, "slot_uri": "GENEPIO:0100761", - "alias": "sampling_event_ID", + "alias": "sampling_event_id", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9289,12 +11812,20 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "sample collection data steward name": { - "name": "sample collection data steward name", + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", "title": "sample collection data steward name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 17, + "rank": 14, "slot_uri": "GENEPIO:0100762", "alias": "sample_collection_data_steward_name", "owner": "WastewaterSARS-CoV-2", @@ -9306,14 +11837,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collected by": { - "name": "sample collected by", - "description": "The name of the organization with which the sample collector is affiliated.", - "title": "sample collected by", + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "description": "The specific laboratory affiliation of the sample collector.", + "title": "sample collected by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 18, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", + "rank": 15, + "slot_uri": "GENEPIO:0100428", + "alias": "sample_collected_by_laboratory_name", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9321,14 +11860,83 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "range": "WhitespaceMinimizedString" }, - "sample collector contact email": { - "name": "sample collector contact email", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "title": "sample collector contact email", - "from_schema": "https://example.com/GRDI", - "rank": 19, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample collected by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collected_by" + ], + "rank": 16, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "description": "The name or job title of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 17, + "slot_uri": "GENEPIO:0100432", + "alias": "sample_collector_contact_name", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 18, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "WastewaterSARS-CoV-2", @@ -9341,14 +11949,22 @@ "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "geo loc name (country)": { - "name": "geo loc name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo loc name (country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 20, + "rank": 19, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "alias": "geo_loc_name_country", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9356,16 +11972,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The state/province/territory of origin of the sample.", "title": "geo loc name (state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 21, + "rank": 20, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "alias": "geo_loc_name_state_province_territory", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9373,16 +12005,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "description": "The county/region of origin of the sample.", "title": "geo loc name (county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 22, + "rank": 21, "slot_uri": "GENEPIO:0100280", - "alias": "geo_loc_name_(county/region)", + "alias": "geo_loc_name_county_region", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9392,14 +12040,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc name (city)": { - "name": "geo loc name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city of origin of the sample.", "title": "geo loc name (city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 23, + "rank": 22, "slot_uri": "GENEPIO:0001189", - "alias": "geo_loc_name_(city)", + "alias": "geo_loc_name_city", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9409,14 +12065,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc name (site)": { - "name": "geo loc name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo loc name (site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 24, + "rank": 23, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_(site)", + "alias": "geo_loc_name_site", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9426,12 +12090,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc latitude": { - "name": "geo loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo loc latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 25, + "rank": 24, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", "owner": "WastewaterSARS-CoV-2", @@ -9443,12 +12115,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc longitude": { - "name": "geo loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo loc longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 26, + "rank": 25, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", "owner": "WastewaterSARS-CoV-2", @@ -9460,12 +12140,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", "description": "The availability status of a shapefile descriping the catchment contributing to a watershed.", "title": "watershed shapefile availability", + "comments": [ + "Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request." + ], + "examples": [ + { + "value": "watershed shapefile available" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 27, + "rank": 26, "slot_uri": "GENEPIO:0100919", "alias": "watershed_shapefile_availability", "owner": "WastewaterSARS-CoV-2", @@ -9474,14 +12162,30 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WatershedShapefileAvailabilityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", "description": "The name of the watershed shapefile.", "title": "watershed shapefile filename", + "comments": [ + "Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas." + ], + "examples": [ + { + "value": "siteAD17.shp, siteAD17.kml" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 28, + "rank": 27, "slot_uri": "GENEPIO:0100920", "alias": "watershed_shapefile_filename", "owner": "WastewaterSARS-CoV-2", @@ -9506,9 +12210,11 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 29, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1" + ], + "rank": 28, "slot_uri": "GENEPIO:0001191", - "multivalued": true, "alias": "organism", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9518,23 +12224,34 @@ ], "slot_group": "Sample collection and processing", "required": true, + "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 30, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], + "rank": 29, "slot_uri": "GENEPIO:0001198", - "multivalued": true, "alias": "purpose_of_sampling", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9543,14 +12260,34 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "scale of sampling": { - "name": "scale of sampling", + "scale_of_sampling": { + "name": "scale_of_sampling", "description": "The range of locations or entities sampled expressed in general terms.", "title": "scale of sampling", + "comments": [ + "Provide the scale of wastewater sampling by selecting a value from the picklist." + ], + "examples": [ + { + "value": "Community-level surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 31, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], + "rank": 30, "slot_uri": "GENEPIO:0100877", "alias": "scale_of_sampling", "owner": "WastewaterSARS-CoV-2", @@ -9560,14 +12297,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "ScaleOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 32, + "rank": 31, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "WastewaterSARS-CoV-2", @@ -9576,16 +12329,32 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_start_date": { + "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", - "title": "sample collection date", + "title": "sample collection start date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 33, + "rank": 32, "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", + "alias": "sample_collection_start_date", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -9593,14 +12362,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end date": { - "name": "sample collection end date", + "sample_collection_end_date": { + "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 34, + "rank": 33, "slot_uri": "GENEPIO:0101071", "alias": "sample_collection_end_date", "owner": "WastewaterSARS-CoV-2", @@ -9610,14 +12395,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample processing date": { - "name": "sample processing date", + "sample_processing_date": { + "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 35, + "rank": 34, "slot_uri": "GENEPIO:0100763", "alias": "sample_processing_date", "owner": "WastewaterSARS-CoV-2", @@ -9626,14 +12427,30 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" - }, - "sample collection start time": { - "name": "sample collection start time", - "description": "The time at which sample collection began.", - "title": "sample collection start time", - "from_schema": "https://example.com/GRDI", - "rank": 36, + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample collection start time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 35, "slot_uri": "GENEPIO:0101072", "alias": "sample_collection_start_time", "owner": "WastewaterSARS-CoV-2", @@ -9643,14 +12460,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end time": { - "name": "sample collection end time", + "sample_collection_end_time": { + "name": "sample_collection_end_time", "description": "The time at which sample collection ended.", "title": "sample collection end time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 37, + "rank": 36, "slot_uri": "GENEPIO:0101073", "alias": "sample_collection_end_time", "owner": "WastewaterSARS-CoV-2", @@ -9660,14 +12493,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time of day": { - "name": "sample collection time of day", + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", "description": "The descriptive time of day during which the sample was collected.", "title": "sample collection time of day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 38, + "rank": 37, "slot_uri": "GENEPIO:0100765", "alias": "sample_collection_time_of_day", "owner": "WastewaterSARS-CoV-2", @@ -9676,14 +12525,33 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleCollectionTimeOfDayMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time duration value": { - "name": "sample collection time duration value", + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", "description": "The amount of time over which the sample was collected.", "title": "sample collection time duration value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 39, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], + "rank": 38, "slot_uri": "GENEPIO:0100766", "alias": "sample_collection_time_duration_value", "owner": "WastewaterSARS-CoV-2", @@ -9693,14 +12561,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", "description": "The units of the time duration measurement of sample collection.", "title": "sample collection time duration unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 40, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], + "rank": 39, "slot_uri": "GENEPIO:0100767", "alias": "sample_collection_time_duration_unit", "owner": "WastewaterSARS-CoV-2", @@ -9710,16 +12597,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "SampleCollectionDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling activity": { - "name": "presampling activity", + "presampling_activity": { + "name": "presampling_activity", "description": "The activities or variables upstream of sample collection that may affect the sample.", "title": "presampling activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 41, + "rank": 40, "slot_uri": "GENEPIO:0100433", - "multivalued": true, "alias": "presampling_activity", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9727,14 +12629,31 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "PresamplingActivityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling activity details": { - "name": "presampling activity details", + "presampling_activity_details": { + "name": "presampling_activity_details", "description": "The details of the activities or variables that affected the sample collected.", "title": "presampling activity details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 42, + "rank": 41, "slot_uri": "GENEPIO:0100434", "alias": "presampling_activity_details", "owner": "WastewaterSARS-CoV-2", @@ -9743,14 +12662,33 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample volume measurement value": { - "name": "sample volume measurement value", + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", "description": "The numerical value of the volume measurement of the sample collected.", "title": "sample volume measurement value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 43, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], + "rank": 42, "slot_uri": "GENEPIO:0100768", "alias": "sample_volume_measurement_value", "owner": "WastewaterSARS-CoV-2", @@ -9762,12 +12700,23 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample volume measurement unit": { - "name": "sample volume measurement unit", + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", "description": "The units of the volume measurement of the sample collected.", "title": "sample volume measurement unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "mL" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 44, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], + "rank": 43, "slot_uri": "GENEPIO:0100769", "alias": "sample_volume_measurement_unit", "owner": "WastewaterSARS-CoV-2", @@ -9776,14 +12725,30 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleVolumeMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample storage method": { - "name": "sample storage method", + "sample_storage_method": { + "name": "sample_storage_method", "description": "The process used to store the sample.", "title": "sample storage method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 45, + "rank": 44, "slot_uri": "GENEPIO:0100448", "alias": "sample_storage_method", "owner": "WastewaterSARS-CoV-2", @@ -9795,12 +12760,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample storage medium": { - "name": "sample storage medium", + "sample_storage_medium": { + "name": "sample_storage_medium", "description": "The medium in which a sample is stored.", "title": "sample storage medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 46, + "rank": 45, "slot_uri": "GENEPIO:0100449", "alias": "sample_storage_medium", "owner": "WastewaterSARS-CoV-2", @@ -9812,12 +12785,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample storage duration value": { - "name": "sample storage duration value", + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", "description": "The numerical value of the time measurement during which a sample is in storage.", "title": "sample storage duration value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 47, + "rank": 46, "slot_uri": "GENEPIO:0101014", "alias": "sample_storage_duration_value", "owner": "WastewaterSARS-CoV-2", @@ -9829,12 +12810,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample storage duration unit": { - "name": "sample storage duration unit", + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", "description": "The units of a measured sample storage duration.", "title": "sample storage duration unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 48, + "rank": 47, "slot_uri": "GENEPIO:0101015", "alias": "sample_storage_duration_unit", "owner": "WastewaterSARS-CoV-2", @@ -9843,16 +12832,34 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleStorageDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 49, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing" + ], + "rank": 48, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9860,14 +12867,34 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "The details of the processing applied to the sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 50, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_details" + ], + "rank": 49, "slot_uri": "GENEPIO:0100311", "alias": "specimen_processing_details", "owner": "WastewaterSARS-CoV-2", @@ -9879,12 +12906,15 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "experimental protocol field": { - "name": "experimental protocol field", + "experimental_protocol_field": { + "name": "experimental_protocol_field", "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", "title": "experimental protocol field", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], "from_schema": "https://example.com/GRDI", - "rank": 51, + "rank": 50, "slot_uri": "GENEPIO:0101029", "alias": "experimental_protocol_field", "owner": "WastewaterSARS-CoV-2", @@ -9896,14 +12926,24 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", + "comments": [ + "Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Meat processing plant" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 52, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_site" + ], + "rank": 51, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9912,16 +12952,61 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material": { - "name": "environmental material", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", - "title": "environmental material", + "proximal_environmental_site": { + "name": "proximal_environmental_site", + "description": "An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample.", + "title": "proximal environmental site", + "comments": [ + "Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Farm" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 53, - "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "rank": 52, + "slot_uri": "GENEPIO:0101205", + "alias": "proximal_environmental_site", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "EnvironmentalSiteMenu", + "multivalued": true + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", + "title": "environmental material", + "comments": [ + "Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Raw wastewater" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_matrix" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001223", "alias": "environmental_material", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9930,16 +13015,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material properties": { - "name": "environmental material properties", + "environmental_material_properties": { + "name": "environmental_material_properties", "description": "The properties, characteristics and qualities of a substance obtained from the natural or man-made environment.", "title": "environmental material properties", + "comments": [ + "Provide the environmental material properties by selecting descriptors from the pick list." + ], + "examples": [ + { + "value": "Stagnant" + } + ], "from_schema": "https://example.com/GRDI", "rank": 54, "slot_uri": "GENEPIO:0100770", - "multivalued": true, "alias": "environmental_material_properties", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9948,12 +13049,29 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialPropertiesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "wastewater system type": { - "name": "wastewater system type", + "wastewater_system_type": { + "name": "wastewater_system_type", "description": "The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine", "title": "wastewater system type", + "comments": [ + "Provide the classification of the wastewater system by selecting from the provided pick list." + ], + "examples": [ + { + "value": "Sanitary sewer" + } + ], "from_schema": "https://example.com/GRDI", "rank": 55, "slot_uri": "GENEPIO:0100771", @@ -9965,16 +13083,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WastewaterSystemTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "experimental specimen role type": { - "name": "experimental specimen role type", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", "description": "The type of role that the sample represents in the experiment.", "title": "experimental specimen role type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], "from_schema": "https://example.com/GRDI", "rank": 56, "slot_uri": "GENEPIO:0100921", - "multivalued": true, "alias": "experimental_specimen_role_type", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -9982,12 +13115,29 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "ExperimentalSpecimenRoleTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "experimental control details": { - "name": "experimental control details", + "experimental_control_details": { + "name": "experimental_control_details", "description": "The details regarding the experimental control contained in the sample.", "title": "experimental control details", + "comments": [ + "Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor." + ], + "examples": [ + { + "value": "Human coronavirus 229E (HCoV-229E) spiked in sample as process control" + } + ], "from_schema": "https://example.com/GRDI", "rank": 57, "slot_uri": "GENEPIO:0100922", @@ -10001,14 +13151,21 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. grab sampler.", "title": "collection device", + "comments": [ + "Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Automatic flow-proportional sampler" + } + ], "from_schema": "https://example.com/GRDI", "rank": 58, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -10016,16 +13173,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample.", "title": "collection method", + "comments": [ + "Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Automatic composite sampling" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_type" + ], "rank": 59, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -10034,13 +13210,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", "title": "nucleic acid extraction method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:extraction_method" + ], "rank": 60, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", @@ -10053,10 +13249,18 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "description": "The kit used to extract genomic material from a sample", "title": "nucleic acid extraction kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 61, "slot_uri": "GENEPIO:0100772", @@ -10070,11 +13274,17 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "endogenous control details": { - "name": "endogenous control details", + "endogenous_control_details": { + "name": "endogenous_control_details", "description": "The description of the endogenous controls included when extracting a sample.", "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_endog_control_1" + ], "rank": 62, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", @@ -10088,10 +13298,13 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "extraction recovery efficiency measurement value": { - "name": "extraction recovery efficiency measurement value", + "extraction_recovery_efficiency_measurement_value": { + "name": "extraction_recovery_efficiency_measurement_value", "description": "The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected.", "title": "extraction recovery efficiency measurement value", + "comments": [ + "Provide value as a percent." + ], "from_schema": "https://example.com/GRDI", "rank": 63, "slot_uri": "GENEPIO:0100924", @@ -10105,10 +13318,13 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "extraction recovery efficiency measurement method": { - "name": "extraction recovery efficiency measurement method", + "extraction_recovery_efficiency_measurement_method": { + "name": "extraction_recovery_efficiency_measurement_method", "description": "The method by which recovery efficiency of an extraction was calculated.", "title": "extraction recovery efficiency measurement method", + "comments": [ + "Provide a brief description of how extraction recovery efficiency was measured or estimated." + ], "from_schema": "https://example.com/GRDI", "rank": 64, "slot_uri": "GENEPIO:0100925", @@ -10122,11 +13338,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "water catchment area human population measurement value": { - "name": "water catchment area human population measurement value", + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", "title": "water catchment area human population measurement value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population" + ], "rank": 65, "slot_uri": "GENEPIO:0100773", "alias": "water_catchment_area_human_population_measurement_value", @@ -10137,12 +13364,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "NullValueMenu" + } + ] }, - "water catchment area human population range": { - "name": "water catchment area human population range", + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", "title": "water catchment area human population range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], "from_schema": "https://example.com/GRDI", "rank": 66, "slot_uri": "GENEPIO:0100774", @@ -10153,13 +13396,32 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "water catchment area human population measurement method": { - "name": "water catchment area human population measurement method", + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", "description": "The method by which a water catchment 's human population size was measured or estimated", "title": "water catchment area human population measurement method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population_source" + ], "rank": 67, "slot_uri": "GENEPIO:0100775", "alias": "water_catchment_area_human_population_measurement_method", @@ -10172,10 +13434,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population density value": { - "name": "water catchment area human population density value", + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", "description": "The numerical value describing the number of humans per geographical area in a water catchment.", "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", "rank": 68, "slot_uri": "GENEPIO:0100776", @@ -10189,10 +13459,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population density unit": { - "name": "water catchment area human population density unit", + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", "description": "The unit describing the number of humans per geographical area in a water catchment.", "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 69, "slot_uri": "GENEPIO:0100777", @@ -10203,12 +13481,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "populated area type": { - "name": "populated area type", + "populated_area_type": { + "name": "populated_area_type", "description": "A type of area that is populated by humans to different degrees.", "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], "from_schema": "https://example.com/GRDI", "rank": 70, "slot_uri": "GENEPIO:0100778", @@ -10219,16 +13513,31 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "PopulatedAreaTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sampling weather conditions": { - "name": "sampling weather conditions", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], "from_schema": "https://example.com/GRDI", "rank": 71, "slot_uri": "GENEPIO:0100779", - "multivalued": true, "alias": "sampling_weather_conditions", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -10236,16 +13545,32 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "SamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling weather conditions": { - "name": "presampling weather conditions", + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", "description": "Weather conditions prior to collection that may affect the sample.", "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], "from_schema": "https://example.com/GRDI", "rank": 72, "slot_uri": "GENEPIO:0100780", - "multivalued": true, "alias": "presampling_weather_conditions", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -10253,12 +13578,29 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "PresamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement value": { - "name": "precipitation measurement value", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", "description": "The amount of water which has fallen during a precipitation process.", "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], "from_schema": "https://example.com/GRDI", "rank": 73, "slot_uri": "GENEPIO:0100911", @@ -10270,16 +13612,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement unit": { - "name": "precipitation measurement unit", + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", "title": "precipitation measurement unit", - "from_schema": "https://example.com/GRDI", - "rank": 74, - "slot_uri": "GENEPIO:0100912", - "alias": "precipitation_measurement_unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 74, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10287,12 +13645,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "PrecipitationMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement method": { - "name": "precipitation measurement method", + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", "description": "The process used to measure the amount of water which has fallen during a precipitation process.", "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample collection" + } + ], "from_schema": "https://example.com/GRDI", "rank": 75, "slot_uri": "GENEPIO:0100913", @@ -10306,10 +13680,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "ambient temperature measurement value": { - "name": "ambient temperature measurement value", + "ambient_temperature_measurement_value": { + "name": "ambient_temperature_measurement_value", "description": "The numerical value of a measurement of the ambient temperature.", "title": "ambient temperature measurement value", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "70" + } + ], "from_schema": "https://example.com/GRDI", "rank": 76, "slot_uri": "GENEPIO:0100935", @@ -10323,10 +13705,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "ambient temperature measurement unit": { - "name": "ambient temperature measurement unit", + "ambient_temperature_measurement_unit": { + "name": "ambient_temperature_measurement_unit", "description": "The units of a measurement of the ambient temperature.", "title": "ambient temperature measurement unit", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 77, "slot_uri": "GENEPIO:0100936", @@ -10337,16 +13727,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "AmbientTemperatureMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "pH measurement value": { - "name": "pH measurement value", + "ph_measurement_value": { + "name": "ph_measurement_value", "description": "The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution.", "title": "pH measurement value", + "comments": [ + "Provide the numerical value of the measured pH." + ], + "examples": [ + { + "value": "7.4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_ph" + ], "rank": 78, "slot_uri": "GENEPIO:0001736", - "alias": "pH_measurement_value", + "alias": "ph_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10356,14 +13765,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "pH measurement method": { - "name": "pH measurement method", + "ph_measurement_method": { + "name": "ph_measurement_method", "description": "The process used to measure pH value.", "title": "pH measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure pH." + ], + "examples": [ + { + "value": "pH test strip (litmus test)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 79, "slot_uri": "GENEPIO:0100781", - "alias": "pH_measurement_method", + "alias": "ph_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10373,11 +13790,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement value": { - "name": "total daily flow rate measurement value", + "total_daily_flow_rate_measurement_value": { + "name": "total_daily_flow_rate_measurement_value", "description": "The numerical value of a measured fluid flow rate over the course of a day.", "title": "total daily flow rate measurement value", + "comments": [ + "Provide the numerical value of the measured flow rate." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], "rank": 80, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", @@ -10390,11 +13818,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement unit": { - "name": "total daily flow rate measurement unit", + "total_daily_flow_rate_measurement_unit": { + "name": "total_daily_flow_rate_measurement_unit", "description": "The units of a measured fluid flow rate over the course of a day.", "title": "total daily flow rate measurement unit", + "comments": [ + "Provide the units of the measured flow rate by selecting a value from the pick list." + ], + "examples": [ + { + "value": "million gallons per day (MGD)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], "rank": 81, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", @@ -10404,12 +13843,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalDailyFlowRateMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total daily flow rate measurement method": { - "name": "total daily flow rate measurement method", + "total_daily_flow_rate_measurement_method": { + "name": "total_daily_flow_rate_measurement_method", "description": "The process used to measure total daily fluid flow rate.", "title": "total daily flow rate measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure flow rate." + ], + "examples": [ + { + "value": "Flow meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 82, "slot_uri": "GENEPIO:0100907", @@ -10423,10 +13878,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement value": { - "name": "instantaneous flow rate measurement value", + "instantaneous_flow_rate_measurement_value": { + "name": "instantaneous_flow_rate_measurement_value", "description": "The numerical value of a measured instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement value", + "comments": [ + "Provide the numerical value of the measured flow rate." + ], + "examples": [ + { + "value": "25" + } + ], "from_schema": "https://example.com/GRDI", "rank": 83, "slot_uri": "GENEPIO:0100908", @@ -10440,10 +13903,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement unit": { - "name": "instantaneous flow rate measurement unit", + "instantaneous_flow_rate_measurement_unit": { + "name": "instantaneous_flow_rate_measurement_unit", "description": "The units of a measured instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement unit", + "comments": [ + "Provide the units of the measured flow rate by selecting a value from the pick list." + ], + "examples": [ + { + "value": "cubic meter per hour (m^3/h)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 84, "slot_uri": "GENEPIO:0100909", @@ -10454,12 +13925,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "InstantaneousFlowRateMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "instantaneous flow rate measurement method": { - "name": "instantaneous flow rate measurement method", + "instantaneous_flow_rate_measurement_method": { + "name": "instantaneous_flow_rate_measurement_method", "description": "The process used to measure instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure flow rate." + ], + "examples": [ + { + "value": "Flow meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 85, "slot_uri": "GENEPIO:0100910", @@ -10473,10 +13960,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "turbidity measurement value": { - "name": "turbidity measurement value", + "turbidity_measurement_value": { + "name": "turbidity_measurement_value", "description": "The numerical value of a measurement of turbidity.", "title": "turbidity measurement value", + "comments": [ + "Provide the numerical value of the measured turbidity." + ], + "examples": [ + { + "value": "0.02" + } + ], "from_schema": "https://example.com/GRDI", "rank": 86, "slot_uri": "GENEPIO:0100783", @@ -10491,10 +13986,18 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "turbidity measurement unit": { - "name": "turbidity measurement unit", + "turbidity_measurement_unit": { + "name": "turbidity_measurement_unit", "description": "The units of a measurement of turbidity.", "title": "turbidity measurement unit", + "comments": [ + "Provide the units of the measured turbidity by selecting a value from the pick list." + ], + "examples": [ + { + "value": "nephelometric turbidity unit (NTU)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 87, "slot_uri": "GENEPIO:0100914", @@ -10506,12 +14009,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "TurbidityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "turbidity measurement method": { - "name": "turbidity measurement method", + "turbidity_measurement_method": { + "name": "turbidity_measurement_method", "description": "The process used to measure turbidity.", "title": "turbidity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure turbidity." + ], + "examples": [ + { + "value": "Nephelometric method" + } + ], "from_schema": "https://example.com/GRDI", "rank": 88, "slot_uri": "GENEPIO:0101013", @@ -10525,13 +14044,21 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement value": { - "name": "dissolved oxygen measurement value", + "dissolved_oxygen_measurement_value": { + "name": "dissolved_oxygen_measurement_value", "description": "The numerical value of a measurement of dissolved oxygen.", "title": "dissolved oxygen measurement value", + "comments": [ + "Provide the numerical value of the measured dissolved oxygen." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 89, - "slot_uri": "GENEPIO:0100915", + "slot_uri": "GENEPIO:0000035", "alias": "dissolved_oxygen_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -10542,10 +14069,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement unit": { - "name": "dissolved oxygen measurement unit", + "dissolved_oxygen_measurement_unit": { + "name": "dissolved_oxygen_measurement_unit", "description": "The units of a measurement of dissolved oxygen.", "title": "dissolved oxygen measurement unit", + "comments": [ + "Provide the units of the measured dissolved oxygen by selecting a value from the pick list." + ], + "examples": [ + { + "value": "part per million (ppm)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 90, "slot_uri": "GENEPIO:0100784", @@ -10556,12 +14091,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "DissolvedOxygenMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "dissolved oxygen measurement method": { - "name": "dissolved oxygen measurement method", + "dissolved_oxygen_measurement_method": { + "name": "dissolved_oxygen_measurement_method", "description": "The method used to measure dissolved oxygen.", "title": "dissolved oxygen measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure dissolved oxygen." + ], + "examples": [ + { + "value": "Dissolved oxygen meter in vertical direction" + } + ], "from_schema": "https://example.com/GRDI", "rank": 91, "slot_uri": "GENEPIO:0100785", @@ -10575,14 +14126,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement value": { - "name": "oxygen reduction potential (ORP) measurement value", + "oxygen_reduction_potential_orp_measurement_value": { + "name": "oxygen_reduction_potential_orp_measurement_value", "description": "The numerical value of a measurement of oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement value", + "comments": [ + "Provide the numerical value of the measured oxygen reduction potential." + ], + "examples": [ + { + "value": "-50" + } + ], "from_schema": "https://example.com/GRDI", "rank": 92, - "slot_uri": "GENEPIO:0100917", - "alias": "oxygen_reduction_potential_(ORP)_measurement_value", + "slot_uri": "FIX:0000278", + "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10592,30 +14151,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement unit": { - "name": "oxygen reduction potential (ORP) measurement unit", + "oxygen_reduction_potential_orp_measurement_unit": { + "name": "oxygen_reduction_potential_orp_measurement_unit", "description": "The units of a measurement of oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement unit", + "comments": [ + "Provide the units of the measured oxygen reduction potential by selecting a value from the pick list." + ], + "examples": [ + { + "value": "milliVolt (mV)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 93, "slot_uri": "GENEPIO:0100786", - "alias": "oxygen_reduction_potential_(ORP)_measurement_unit", + "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "OxygenReductionPotentialOrpMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "oxygen reduction potential (ORP) measurement method": { - "name": "oxygen reduction potential (ORP) measurement method", + "oxygen_reduction_potential_orp_measurement_method": { + "name": "oxygen_reduction_potential_orp_measurement_method", "description": "The method used to measure oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure oxygen reduction potential." + ], + "examples": [ + { + "value": "ORP sensor" + } + ], "from_schema": "https://example.com/GRDI", "rank": 94, "slot_uri": "GENEPIO:0100787", - "alias": "oxygen_reduction_potential_(ORP)_measurement_method", + "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10625,14 +14208,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement value": { - "name": "chemical oxygen demand (COD) measurement value", + "chemical_oxygen_demand_cod_measurement_value": { + "name": "chemical_oxygen_demand_cod_measurement_value", "description": "The measured value from a chemical oxygen demand (COD) test.", "title": "chemical oxygen demand (COD) measurement value", + "comments": [ + "Provide the numerical value of the COD test result." + ], + "examples": [ + { + "value": "26" + } + ], "from_schema": "https://example.com/GRDI", "rank": 95, "slot_uri": "GENEPIO:0100788", - "alias": "chemical_oxygen_demand_(COD)_measurement_value", + "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10642,30 +14233,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement unit": { - "name": "chemical oxygen demand (COD) measurement unit", + "chemical_oxygen_demand_cod_measurement_unit": { + "name": "chemical_oxygen_demand_cod_measurement_unit", "description": "The units associated with a value from a chemical oxygen demand (COD) test.", "title": "chemical oxygen demand (COD) measurement unit", + "comments": [ + "Provide the units of the COD test result." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 96, "slot_uri": "GENEPIO:0100789", - "alias": "chemical_oxygen_demand_(COD)_measurement_unit", + "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "ChemicalOxygenDemandCodMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "chemical oxygen demand (COD) measurement method": { - "name": "chemical oxygen demand (COD) measurement method", + "chemical_oxygen_demand_cod_measurement_method": { + "name": "chemical_oxygen_demand_cod_measurement_method", "description": "The method used to measure chemical oxygen demand (COD).", "title": "chemical oxygen demand (COD) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure COD." + ], + "examples": [ + { + "value": "Hach LCK test kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 97, "slot_uri": "GENEPIO:0100790", - "alias": "chemical_oxygen_demand_(COD)_measurement_method", + "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10675,14 +14290,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement value": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement value", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "description": "The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement value", + "comments": [ + "Provide the numerical value of the measured CBOD." + ], + "examples": [ + { + "value": "20" + } + ], "from_schema": "https://example.com/GRDI", "rank": 98, "slot_uri": "GENEPIO:0100791", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_value", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10692,30 +14315,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement unit": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement unit", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "description": "The units of a measurement of carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement unit", + "comments": [ + "Provide the units of the measured CBOD by selecting a value from the pick list." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 99, "slot_uri": "GENEPIO:0100792", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "carbonaceous biochemical oxygen demand (CBOD) measurement method": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "description": "The method used to measure carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure CBOD." + ], + "examples": [ + { + "value": "CBOD measurement by optical probe" + } + ], "from_schema": "https://example.com/GRDI", "rank": 100, "slot_uri": "GENEPIO:0100793", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_method", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10725,14 +14372,25 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement value": { - "name": "total suspended solids (TSS) measurement value", + "total_suspended_solids_tss_measurement_value": { + "name": "total_suspended_solids_tss_measurement_value", "description": "The numerical value from a total suspended solids (TSS) test.", "title": "total suspended solids (TSS) measurement value", + "comments": [ + "Provide the numerical value of the measured TSS." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], "rank": 101, "slot_uri": "GENEPIO:0100794", - "alias": "total_suspended_solids_(TSS)_measurement_value", + "alias": "total_suspended_solids_tss_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10742,30 +14400,57 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement unit": { - "name": "total suspended solids (TSS) measurement unit", + "total_suspended_solids_tss_measurement_unit": { + "name": "total_suspended_solids_tss_measurement_unit", "description": "The units associated with a value from a total suspended solids (TSS) test.", "title": "total suspended solids (TSS) measurement unit", + "comments": [ + "Provide the units of the measured TSS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], "rank": 102, "slot_uri": "GENEPIO:0100795", - "alias": "total_suspended_solids_(TSS)_measurement_unit", + "alias": "total_suspended_solids_tss_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalSuspendedSolidsTssMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total suspended solids (TSS) measurement method": { - "name": "total suspended solids (TSS) measurement method", + "total_suspended_solids_tss_measurement_method": { + "name": "total_suspended_solids_tss_measurement_method", "description": "The method used to measure total suspended solids (TSS).", "title": "total suspended solids (TSS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TSS." + ], + "examples": [ + { + "value": "Vacuum filter through a 2-micron filter, then oven-dried and weighed sample" + } + ], "from_schema": "https://example.com/GRDI", "rank": 103, "slot_uri": "GENEPIO:0100796", - "alias": "total_suspended_solids_(TSS)_measurement_method", + "alias": "total_suspended_solids_tss_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10775,14 +14460,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement value": { - "name": "total dissolved solids (TDS) measurement value", + "total_dissolved_solids_tds_measurement_value": { + "name": "total_dissolved_solids_tds_measurement_value", "description": "The numerical value from a total dissolved solids (TDS) test.", "title": "total dissolved solids (TDS) measurement value", + "comments": [ + "Provide the numerical value of the measured TDS." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 104, "slot_uri": "GENEPIO:0100797", - "alias": "total_dissolved_solids_(TDS)_measurement_value", + "alias": "total_dissolved_solids_tds_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10792,30 +14485,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement unit": { - "name": "total dissolved solids (TDS) measurement unit", + "total_dissolved_solids_tds_measurement_unit": { + "name": "total_dissolved_solids_tds_measurement_unit", "description": "The units associated with a value from a total dissolved solids (TDS) test.", "title": "total dissolved solids (TDS) measurement unit", + "comments": [ + "Provide the units of the measured TDS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 105, "slot_uri": "GENEPIO:0100798", - "alias": "total_dissolved_solids_(TDS)_measurement_unit", + "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalDissolvedSolidsTdsMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total dissolved solids (TDS) measurement method": { - "name": "total dissolved solids (TDS) measurement method", + "total_dissolved_solids_tds_measurement_method": { + "name": "total_dissolved_solids_tds_measurement_method", "description": "The method used to measure total dissolved solids (TDS).", "title": "total dissolved solids (TDS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TDS." + ], + "examples": [ + { + "value": "Subtract calculated TSS from calculated TS" + } + ], "from_schema": "https://example.com/GRDI", "rank": 106, "slot_uri": "GENEPIO:0100799", - "alias": "total_dissolved_solids_(TDS)_measurement_method", + "alias": "total_dissolved_solids_tds_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10825,14 +14542,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total solids (TS) measurement value": { - "name": "total solids (TS) measurement value", + "total_solids_ts_measurement_value": { + "name": "total_solids_ts_measurement_value", "description": "The numerical value from a total solids (TS) test.", "title": "total solids (TS) measurement value", + "comments": [ + "Provide the numerical value of the measured TS." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", "rank": 107, "slot_uri": "GENEPIO:0100800", - "alias": "total_solids_(TS)_measurement_value", + "alias": "total_solids_ts_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10842,30 +14567,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total solids (TS) measurement unit": { - "name": "total solids (TS) measurement unit", + "total_solids_ts_measurement_unit": { + "name": "total_solids_ts_measurement_unit", "description": "The units associated with a value from a total solids (TS) test.", "title": "total solids (TS) measurement unit", + "comments": [ + "Provide the units of the measured TS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 108, "slot_uri": "GENEPIO:0100801", - "alias": "total_solids_(TS)_measurement_unit", + "alias": "total_solids_ts_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalSolidsTsMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total solids (TS) measurement method": { - "name": "total solids (TS) measurement method", + "total_solids_ts_measurement_method": { + "name": "total_solids_ts_measurement_method", "description": "The method used to measure total solids (TS).", "title": "total solids (TS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TS." + ], + "examples": [ + { + "value": "Gravimetric method by oven drying, then weighing" + } + ], "from_schema": "https://example.com/GRDI", "rank": 109, "slot_uri": "GENEPIO:0100802", - "alias": "total_solids_(TS)_measurement_method", + "alias": "total_solids_ts_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -10875,10 +14624,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "alkalinity measurement value": { - "name": "alkalinity measurement value", + "alkalinity_measurement_value": { + "name": "alkalinity_measurement_value", "description": "The numerical value of a measurement of alkalinity.", "title": "alkalinity measurement value", + "comments": [ + "Provide the numerical value of the measured alkalinity." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 110, "slot_uri": "GENEPIO:0100878", @@ -10892,10 +14649,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "alkalinity measurement unit": { - "name": "alkalinity measurement unit", + "alkalinity_measurement_unit": { + "name": "alkalinity_measurement_unit", "description": "The units of a measurement of alkalinity.", "title": "alkalinity measurement unit", + "comments": [ + "Provide the units of the measured alkalinity." + ], + "examples": [ + { + "value": "milligram per liter of calcium carbonate (mg/L CaCO3)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 111, "slot_uri": "GENEPIO:0100879", @@ -10906,12 +14671,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "AlkalinityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "alkalinity measurement method": { - "name": "alkalinity measurement method", + "alkalinity_measurement_method": { + "name": "alkalinity_measurement_method", "description": "The process used to measure alkalinity.", "title": "alkalinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure alkalinity." + ], + "examples": [ + { + "value": "Titration method" + } + ], "from_schema": "https://example.com/GRDI", "rank": 112, "slot_uri": "GENEPIO:0100880", @@ -10925,10 +14706,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "conductivity measurement value": { - "name": "conductivity measurement value", + "conductivity_measurement_value": { + "name": "conductivity_measurement_value", "description": "The numerical value of a measurement of conductivity.", "title": "conductivity measurement value", + "comments": [ + "Provide the numerical value of the measured conductivity." + ], + "examples": [ + { + "value": "1412" + } + ], "from_schema": "https://example.com/GRDI", "rank": 113, "slot_uri": "GENEPIO:0100916", @@ -10942,10 +14731,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "conductivity measurement unit": { - "name": "conductivity measurement unit", + "conductivity_measurement_unit": { + "name": "conductivity_measurement_unit", "description": "The units of a measurement of conductivity.", "title": "conductivity measurement unit", + "comments": [ + "Provide the units of the measured conductivity." + ], + "examples": [ + { + "value": "microSiemen per centimeter (μS/cm)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 114, "slot_uri": "GENEPIO:0100803", @@ -10956,12 +14753,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "ConductivityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "conductivity measurement method": { - "name": "conductivity measurement method", + "conductivity_measurement_method": { + "name": "conductivity_measurement_method", "description": "The method used to measure conductivity.", "title": "conductivity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure conductivity." + ], + "examples": [ + { + "value": "Conductivity electrode and meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 115, "slot_uri": "GENEPIO:0100804", @@ -10975,11 +14788,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "salinity measurement value": { - "name": "salinity measurement value", + "salinity_measurement_value": { + "name": "salinity_measurement_value", "description": "The numerical value of a measurement of salinity.", "title": "salinity measurement value", + "comments": [ + "Provide the numerical value of the measured salinity." + ], + "examples": [ + { + "value": "35" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], "rank": 116, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", @@ -10992,11 +14816,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "salinity measurement unit": { - "name": "salinity measurement unit", + "salinity_measurement_unit": { + "name": "salinity_measurement_unit", "description": "The units of a measurement of salinity.", "title": "salinity measurement unit", + "comments": [ + "Provide the units of the measured salinity." + ], + "examples": [ + { + "value": "practical salinity unit (PSU)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], "rank": 117, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", @@ -11006,12 +14841,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SalinityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "salinity measurement method": { - "name": "salinity measurement method", + "salinity_measurement_method": { + "name": "salinity_measurement_method", "description": "The method used to measure salinity.", "title": "salinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure salinity." + ], + "examples": [ + { + "value": "conductivity meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 118, "slot_uri": "GENEPIO:0100807", @@ -11025,14 +14876,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement value": { - "name": "total nitrogen (TN) measurement value", + "total_nitrogen_tn_measurement_value": { + "name": "total_nitrogen_tn_measurement_value", "description": "The numerical value of a measurement of total nitrogen (TN).", "title": "total nitrogen (TN) measurement value", + "comments": [ + "Provide the numerical value of the measured TN." + ], + "examples": [ + { + "value": "120" + } + ], "from_schema": "https://example.com/GRDI", "rank": 119, "slot_uri": "GENEPIO:0100808", - "alias": "total_nitrogen_(TN)_measurement_value", + "alias": "total_nitrogen_tn_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11042,30 +14901,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement unit": { - "name": "total nitrogen (TN) measurement unit", + "total_nitrogen_tn_measurement_unit": { + "name": "total_nitrogen_tn_measurement_unit", "description": "The units of a measurement of total nitrogen (TN).", "title": "total nitrogen (TN) measurement unit", + "comments": [ + "Provide the units of the measured TN." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 120, "slot_uri": "GENEPIO:0100809", - "alias": "total_nitrogen_(TN)_measurement_unit", + "alias": "total_nitrogen_tn_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalNitrogenTnMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total nitrogen (TN) measurement method": { - "name": "total nitrogen (TN) measurement method", + "total_nitrogen_tn_measurement_method": { + "name": "total_nitrogen_tn_measurement_method", "description": "The method used to measure total nitrogen (TN).", "title": "total nitrogen (TN) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TN." + ], + "examples": [ + { + "value": "Hach total nitrogen spectrophotometric test" + } + ], "from_schema": "https://example.com/GRDI", "rank": 121, "slot_uri": "GENEPIO:0100810", - "alias": "total_nitrogen_(TN)_measurement_method", + "alias": "total_nitrogen_tn_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11075,14 +14958,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement value": { - "name": "total phosphorus (TP) measurement value", + "total_phosphorus_tp_measurement_value": { + "name": "total_phosphorus_tp_measurement_value", "description": "The numerical value of a measurement of total phosphorus (TP).", "title": "total phosphorus (TP) measurement value", + "comments": [ + "Provide the numerical value of the measured TP." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 122, "slot_uri": "GENEPIO:0100811", - "alias": "total_phosphorus_(TP)_measurement_value", + "alias": "total_phosphorus_tp_measurement_value", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11092,30 +14983,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement unit": { - "name": "total phosphorus (TP) measurement unit", + "total_phosphorus_tp_measurement_unit": { + "name": "total_phosphorus_tp_measurement_unit", "description": "The units of a measurement of total phosphorus (TP).", "title": "total phosphorus (TP) measurement unit", + "comments": [ + "Provide the units of the measured TP." + ], + "examples": [ + { + "value": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 123, "slot_uri": "GENEPIO:0100812", - "alias": "total_phosphorus_(TP)_measurement_unit", + "alias": "total_phosphorus_tp_measurement_unit", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalPhosphorusTpMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total phosphorus (TP) measurement method": { - "name": "total phosphorus (TP) measurement method", + "total_phosphorus_tp_measurement_method": { + "name": "total_phosphorus_tp_measurement_method", "description": "The method used to measure total phosphorus (TP).", "title": "total phosphorus (TP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TP." + ], + "examples": [ + { + "value": "Merck phosphate spectrophotometric test kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 124, "slot_uri": "GENEPIO:0100813", - "alias": "total_phosphorus_(TP)_measurement_method", + "alias": "total_phosphorus_tp_measurement_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11125,10 +15040,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "fecal contamination indicator": { - "name": "fecal contamination indicator", + "fecal_contamination_indicator": { + "name": "fecal_contamination_indicator", "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", "title": "fecal contamination indicator", + "comments": [ + "If a fecal contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "crAssphage" + } + ], "from_schema": "https://example.com/GRDI", "rank": 125, "slot_uri": "GENEPIO:0100814", @@ -11140,12 +15063,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "FecalContaminationIndicatorMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination value": { - "name": "fecal contamination value", + "fecal_contamination_value": { + "name": "fecal_contamination_value", "description": "The numerical value of a measurement of fecal contamination.", "title": "fecal contamination value", + "comments": [ + "Provide the numerical value of the measured fecal contamination." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", "rank": 126, "slot_uri": "GENEPIO:0100815", @@ -11160,10 +15099,18 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "fecal contamination unit": { - "name": "fecal contamination unit", + "fecal_contamination_unit": { + "name": "fecal_contamination_unit", "description": "The units of a measurement of fecal contamination.", "title": "fecal contamination unit", + "comments": [ + "Provide the units of the measured fecal contamination." + ], + "examples": [ + { + "value": "cycle threshold (Ct) / quantification cycle (Cq)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 127, "slot_uri": "GENEPIO:0100816", @@ -11175,12 +15122,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "FecalContaminationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination method": { - "name": "fecal contamination method", + "fecal_contamination_method": { + "name": "fecal_contamination_method", "description": "The method used to measure fecal contamination.", "title": "fecal contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal contamination." + ], + "examples": [ + { + "value": "quantitative PCR assay" + } + ], "from_schema": "https://example.com/GRDI", "rank": 128, "slot_uri": "GENEPIO:0100817", @@ -11194,10 +15157,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "fecal coliform count value": { - "name": "fecal coliform count value", + "fecal_coliform_count_value": { + "name": "fecal_coliform_count_value", "description": "The numerical value of a measurement of fecal coliforms within a sample.", "title": "fecal coliform count value", + "comments": [ + "Provide the numerical value of the measured fecal coliforms." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 129, "slot_uri": "GENEPIO:0100818", @@ -11211,10 +15182,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "fecal coliform count unit": { - "name": "fecal coliform count unit", + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", "description": "The units of a measurement of fecal coliforms.", "title": "fecal coliform count unit", + "comments": [ + "Provide the units of the measured fecal coliforms." + ], + "examples": [ + { + "value": "most probable number per milliliter (MPN/mL)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 130, "slot_uri": "GENEPIO:0100819", @@ -11225,15 +15204,31 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" - }, - "fecal coliform count method": { - "name": "fecal coliform count method", - "description": "The method used to measure fecal coliforms.", - "title": "fecal coliform count method", - "from_schema": "https://example.com/GRDI", - "rank": 131, - "slot_uri": "GENEPIO:0100820", + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "FecalColiformCountUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", + "description": "The method used to measure fecal coliforms.", + "title": "fecal coliform count method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal coliforms." + ], + "examples": [ + { + "value": "MPN method via serial dilutions until lack of growth" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 131, + "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -11244,10 +15239,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "urinary contamination indicator": { - "name": "urinary contamination indicator", + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", "title": "urinary contamination indicator", + "comments": [ + "If a urinary contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "urobilin" + } + ], "from_schema": "https://example.com/GRDI", "rank": 132, "slot_uri": "GENEPIO:0100837", @@ -11258,12 +15261,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "UrinaryContaminationIndicatorMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination value": { - "name": "urinary contamination value", + "urinary_contamination_value": { + "name": "urinary_contamination_value", "description": "The numerical value of a measurement of urinary contamination.", "title": "urinary contamination value", + "comments": [ + "Provide the numerical value of the measured urinary contamination." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 133, "slot_uri": "GENEPIO:0100838", @@ -11277,10 +15296,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "urinary contamination unit": { - "name": "urinary contamination unit", + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", "description": "The units of a measurement of urinary contamination.", "title": "urinary contamination unit", + "comments": [ + "Provide the units of the measured urinary contamination." + ], + "examples": [ + { + "value": "nanograms per liter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 134, "slot_uri": "GENEPIO:0100839", @@ -11291,12 +15318,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "UrinaryContaminationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination method": { - "name": "urinary contamination method", + "urinary_contamination_method": { + "name": "urinary_contamination_method", "description": "The method used to measure urinary contamination.", "title": "urinary contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure urinary contamination." + ], + "examples": [ + { + "value": "Urobilin Concentration Test" + } + ], "from_schema": "https://example.com/GRDI", "rank": 135, "slot_uri": "GENEPIO:0100840", @@ -11310,14 +15353,25 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "sample temperature value (at collection)": { - "name": "sample temperature value (at collection)", + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", "description": "The numerical value of a measurement of temperature of a sample at collection.", "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], "rank": 136, "slot_uri": "GENEPIO:0100821", - "alias": "sample_temperature_value_(at_collection)", + "alias": "sample_temperature_value_at_collection", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11327,30 +15381,57 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "sample temperature unit (at collection)": { - "name": "sample temperature unit (at collection)", + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", "description": "The units of a measurement of temperature of a sample at the time of collection.", "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], "rank": 137, "slot_uri": "GENEPIO:0100822", - "alias": "sample_temperature_unit_(at_collection)", + "alias": "sample_temperature_unit_at_collection", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SampleTemperatureUnitAtCollectionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample temperature value (when received)": { - "name": "sample temperature value (when received)", + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", "description": "The numerical value of a measurement of temperature of a sample upon receipt.", "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], "from_schema": "https://example.com/GRDI", "rank": 138, "slot_uri": "GENEPIO:0100823", - "alias": "sample_temperature_value_(when_received)", + "alias": "sample_temperature_value_when_received", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11360,30 +15441,56 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "sample temperature unit (when received)": { - "name": "sample temperature unit (when received)", + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", "description": "The units of a measurement of temperature of a sample at the time upon receipt.", "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 139, "slot_uri": "GENEPIO:0100824", - "alias": "sample_temperature_unit_(when_received)", + "alias": "sample_temperature_unit_when_received", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SampleTemperatureUnitWhenReceivedMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sequencing" + ], "rank": 140, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -11392,12 +15499,29 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], "from_schema": "https://example.com/GRDI", "rank": 141, "slot_uri": "GENEPIO:0001446", @@ -11411,11 +15535,22 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", "title": "sequenced by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "GISAID:sequenced_by" + ], "rank": 142, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", @@ -11426,14 +15561,55 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 143, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 143, + "rank": 144, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "WastewaterSARS-CoV-2", @@ -11443,14 +15619,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 144, + "rank": 145, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_email", "owner": "WastewaterSARS-CoV-2", @@ -11460,14 +15652,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that submitted the sequence to a database.", "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 145, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sequenced_by" + ], + "rank": 146, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "WastewaterSARS-CoV-2", @@ -11477,14 +15688,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 146, + "exact_mappings": [ + "NCBI_SRA:sequence_submitter_contact_email" + ], + "rank": 147, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "WastewaterSARS-CoV-2", @@ -11495,14 +15725,33 @@ ], "slot_group": "Sequence information", "recommended": true, - "pattern": "^\\S+@\\S+\\.\\S+$" + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 147, + "rank": 148, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "WastewaterSARS-CoV-2", @@ -11514,14 +15763,25 @@ "slot_group": "Sequence information", "range": "date" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 148, + "exact_mappings": [ + "NCBI_SRA:library_ID" + ], + "rank": 149, "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", + "alias": "library_id", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11531,14 +15791,24 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequencing platform": { - "name": "sequencing platform", + "sequencing_platform": { + "name": "sequencing_platform", "description": "The platform technology used to perform the sequencing.", "title": "sequencing platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 149, + "exact_mappings": [ + "NCBI_SRA:platform" + ], + "rank": 150, "slot_uri": "GENEPIO:0100473", - "multivalued": true, "alias": "sequencing_platform", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -11546,16 +15816,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information" - }, - "sequencing instrument": { - "name": "sequencing instrument", + "slot_group": "Sequence information", + "multivalued": true, + "any_of": [ + { + "range": "SequencingPlatformMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 150, + "exact_mappings": [ + "NCBI_SRA:instrument_model" + ], + "rank": 151, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -11564,14 +15853,34 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing assay type": { - "name": "sequencing assay type", + "sequencing_assay_type": { + "name": "sequencing_assay_type", "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", "title": "sequencing assay type", + "comments": [ + "Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 151, + "exact_mappings": [ + "NCBI_SRA:library_strategy" + ], + "rank": 152, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "WastewaterSARS-CoV-2", @@ -11581,14 +15890,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "SequencingAssayTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 152, + "exact_mappings": [ + "NCBI_SRA:library_preparation_kit" + ], + "rank": 153, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "WastewaterSARS-CoV-2", @@ -11600,12 +15928,20 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol or method used for sequencing.", "title": "sequencing protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 153, + "rank": 154, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "WastewaterSARS-CoV-2", @@ -11618,12 +15954,23 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 154, + "exact_mappings": [ + "NCBI_SRA:amplicon_PCR_primer_scheme" + ], + "rank": 155, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "WastewaterSARS-CoV-2", @@ -11632,14 +15979,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "AmpliconPcrPrimerSchemeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 155, + "exact_mappings": [ + "NCBI_SRA:amplicon_size" + ], + "rank": 156, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "WastewaterSARS-CoV-2", @@ -11650,12 +16016,23 @@ "slot_group": "Sequence information", "range": "integer" }, - "quality control method name": { - "name": "quality control method name", + "quality_control_method_name": { + "name": "quality_control_method_name", "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 156, + "exact_mappings": [ + "NCBI_SRA:quality_control_method" + ], + "rank": 157, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "WastewaterSARS-CoV-2", @@ -11667,12 +16044,23 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_version": { + "name": "quality_control_method_version", "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 157, + "exact_mappings": [ + "NCBI_SRA:quality_control_method_version" + ], + "rank": 158, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "WastewaterSARS-CoV-2", @@ -11684,14 +16072,24 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_determination": { + "name": "quality_control_determination", "description": "The determination of a quality control assessment.", "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 158, + "exact_mappings": [ + "NCBI_SRA:quality_control_determination" + ], + "rank": 159, "slot_uri": "GENEPIO:0100559", - "multivalued": true, "alias": "quality_control_determination", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -11699,16 +16097,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlDeterminationMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "quality control issues": { - "name": "quality control issues", + "quality_control_issues": { + "name": "quality_control_issues", "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 159, + "exact_mappings": [ + "NCBI_SRA:quality_control_issues" + ], + "rank": 160, "slot_uri": "GENEPIO:0100560", - "multivalued": true, "alias": "quality_control_issues", "owner": "WastewaterSARS-CoV-2", "domain_of": [ @@ -11716,14 +16133,34 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlIssuesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "quality control details": { - "name": "quality control details", + "quality_control_details": { + "name": "quality_control_details", "description": "The details surrounding a low quality determination in a quality control assessment.", "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 160, + "exact_mappings": [ + "NCBI_SRA:quality_control_details" + ], + "rank": 161, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "WastewaterSARS-CoV-2", @@ -11735,12 +16172,23 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 161, + "exact_mappings": [ + "NCBI_SRA:raw_sequence_data_processing_method" + ], + "rank": 162, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "WastewaterSARS-CoV-2", @@ -11750,14 +16198,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 162, + "exact_mappings": [ + "NCBI_SRA:dehosting_method" + ], + "rank": 163, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "WastewaterSARS-CoV-2", @@ -11767,44 +16234,64 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "The name of the software used to generate the consensus sequence.", - "title": "consensus sequence software name", - "from_schema": "https://example.com/GRDI", - "rank": 163, - "slot_uri": "GENEPIO:0001463", - "alias": "consensus_sequence_software_name", - "owner": "WastewaterSARS-CoV-2", - "domain_of": [ - "WastewaterSARS-CoV-2" + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } ], - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "The version of the software used to generate the consensus sequence.", - "title": "consensus sequence software version", "from_schema": "https://example.com/GRDI", "rank": 164, - "slot_uri": "GENEPIO:0001469", - "alias": "consensus_sequence_software_version", + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", "owner": "WastewaterSARS-CoV-2", "domain_of": [ - "WastewaterSARS-CoV-2" + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth of coverage value", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", + "comments": [ + "Provide the filepath of the genome sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" + } + ], "from_schema": "https://example.com/GRDI", "rank": 165, - "slot_uri": "GENEPIO:0001472", - "alias": "breadth_of_coverage_value", + "slot_uri": "GENEPIO:0101716", + "alias": "genome_sequence_file_path", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11812,31 +16299,139 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], "from_schema": "https://example.com/GRDI", "rank": 166, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", "owner": "WastewaterSARS-CoV-2", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", + "WastewaterSARS-CoV-2" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 167, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 168, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 169, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 167, + "rank": 170, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "WastewaterSARS-CoV-2", @@ -11848,12 +16443,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "genome completeness": { - "name": "genome completeness", + "genome_completeness": { + "name": "genome_completeness", "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 168, + "rank": 171, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "WastewaterSARS-CoV-2", @@ -11864,12 +16467,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 169, + "rank": 172, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "WastewaterSARS-CoV-2", @@ -11881,12 +16492,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of total reads": { - "name": "number of total reads", + "number_of_total_reads": { + "name": "number_of_total_reads", "description": "The total number of non-unique reads generated by the sequencing process.", "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 170, + "rank": 173, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "WastewaterSARS-CoV-2", @@ -11898,12 +16517,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of unique reads": { - "name": "number of unique reads", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "description": "The number of unique reads generated by the sequencing process.", "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 171, + "rank": 174, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "WastewaterSARS-CoV-2", @@ -11915,14 +16542,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 172, + "rank": 175, "slot_uri": "GENEPIO:0100829", - "alias": "minimum_post_trimming_read_length", + "alias": "minimum_posttrimming_read_length", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11932,12 +16567,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of contigs": { - "name": "number of contigs", + "number_of_contigs": { + "name": "number_of_contigs", "description": "The number of contigs (contiguous sequences) in a sequence assembly.", "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 173, + "rank": 176, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "WastewaterSARS-CoV-2", @@ -11948,14 +16591,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 174, + "rank": 177, "slot_uri": "GENEPIO:0100830", - "alias": "percent_Ns_across_total_genome_length", + "alias": "percent_ns_across_total_genome_length", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11964,14 +16615,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 175, + "rank": 178, "slot_uri": "GENEPIO:0001484", - "alias": "Ns_per_100_kbp", + "alias": "ns_per_100_kbp", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2" @@ -11979,14 +16638,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "N50": { - "name": "N50", + "n50": { + "name": "n50", "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 176, + "rank": 179, "slot_uri": "GENEPIO:0100938", - "alias": "N50", + "alias": "n50", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -11995,12 +16662,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "percent read contamination": { - "name": "percent read contamination", + "percent_read_contamination": { + "name": "percent_read_contamination", "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 177, + "rank": 180, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination", "owner": "WastewaterSARS-CoV-2", @@ -12011,12 +16686,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "The length of the genome defined by the most common nucleotides at each position.", "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 178, + "rank": 181, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "WastewaterSARS-CoV-2", @@ -12026,12 +16709,23 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 179, + "exact_mappings": [ + "NCBI_SRA:assembly" + ], + "rank": 182, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "WastewaterSARS-CoV-2", @@ -12042,12 +16736,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "deduplication method": { - "name": "deduplication method", + "deduplication_method": { + "name": "deduplication_method", "description": "The method used to remove duplicated reads in a sequence read dataset.", "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 180, + "rank": 183, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "WastewaterSARS-CoV-2", @@ -12058,12 +16760,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 181, + "rank": 184, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "WastewaterSARS-CoV-2", @@ -12075,14 +16785,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "description": "The name of the lineage or clade.", "title": "lineage/clade name", + "comments": [ + "Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon." + ], + "examples": [ + { + "value": "B.1.1.7" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 182, + "rank": 185, "slot_uri": "GENEPIO:0001500", - "alias": "lineage/clade_name", + "alias": "lineage_clade_name", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2" @@ -12090,14 +16808,22 @@ "slot_group": "Lineage/clade information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "description": "The name of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software name", + "comments": [ + "Provide the name of the software used to determine the lineage/clade." + ], + "examples": [ + { + "value": "Freyja" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 183, + "rank": 186, "slot_uri": "GENEPIO:0001501", - "alias": "lineage/clade_analysis_software_name", + "alias": "lineage_clade_analysis_software_name", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2" @@ -12105,14 +16831,22 @@ "slot_group": "Lineage/clade information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "description": "The version of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software version", + "comments": [ + "Provide the version of the software used ot determine the lineage/clade." + ], + "examples": [ + { + "value": "1.5.0" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 184, + "rank": 187, "slot_uri": "GENEPIO:0001502", - "alias": "lineage/clade_analysis_software_version", + "alias": "lineage_clade_analysis_software_version", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2" @@ -12120,14 +16854,22 @@ "slot_group": "Lineage/clade information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis report filename": { - "name": "lineage/clade analysis report filename", + "lineage_clade_analysis_report_filename": { + "name": "lineage_clade_analysis_report_filename", "description": "The filename of the report containing the results of a lineage/clade analysis.", "title": "lineage/clade analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the lineage/clade analysis." + ], + "examples": [ + { + "value": "aggregated-WWSC2-ABC-b_1234.tsv" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 185, + "rank": 188, "slot_uri": "GENEPIO:0101081", - "alias": "lineage/clade_analysis_report_filename", + "alias": "lineage_clade_analysis_report_filename", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2" @@ -12135,22 +16877,17 @@ "slot_group": "Lineage/clade information", "range": "WhitespaceMinimizedString" }, - "gene name": { - "name": "gene name", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name", + "assay_target_name_1": { + "name": "assay_target_name_1", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 1", "comments": [ - "Select a gene name value from the pick list provided." - ], - "examples": [ - { - "value": "E gene (orf4)" - } + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." ], "from_schema": "https://example.com/GRDI", - "rank": 186, - "slot_uri": "GENEPIO:0100655", - "alias": "gene_name", + "rank": 189, + "slot_uri": "GENEPIO:0101206", + "alias": "assay_target_name_1", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -12160,37 +16897,119 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "gene name menu" + "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", - "description": "The binary value of the result from a diagnostic test.", - "title": "diagnostic target presence", + "assay_target_details": { + "name": "assay_target_details", + "description": "Describe any details of the assay target.", + "title": "assay target details", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/GRDI", - "rank": 187, - "slot_uri": "GENEPIO:0100962", - "alias": "diagnostic_target_presence", + "rank": 190, + "slot_uri": "GENEPIO:0102040", + "alias": "assay_target_details", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", - "description": "The value of the result from a diagnostic test.", - "title": "diagnostic measurement value", + "gene_symbol_1": { + "name": "gene_symbol_1", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 1", + "comments": [ + "Select a gene name value from the pick list provided." + ], + "examples": [ + { + "value": "E gene (orf4)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 188, - "slot_uri": "GENEPIO:0100963", - "alias": "diagnostic_measurement_value", + "rank": 191, + "slot_uri": "GENEPIO:0102041", + "alias": "gene_symbol_1", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneSymbolMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 1", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_known_present" + ], + "rank": 192, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence_1", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 1", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc" + ], + "rank": 193, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value_1", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", @@ -12200,1032 +17019,1450 @@ "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", "description": "The unit of the result from a diagnostic test.", - "title": "diagnostic measurement unit", + "title": "diagnostic measurement unit 1", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 189, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc_unit" + ], + "rank": 194, "slot_uri": "GENEPIO:0100964", - "alias": "diagnostic_measurement_unit", + "alias": "diagnostic_measurement_unit_1", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", "description": "The method by which a diagnostic result was determined.", - "title": "diagnostic measurement method", + "title": "diagnostic measurement method 1", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 190, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_protocol" + ], + "rank": 195, "slot_uri": "GENEPIO:0100965", - "alias": "diagnostic_measurement_method", + "alias": "diagnostic_measurement_method_1", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", + "assay_target_name_2": { + "name": "assay_target_name_2", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 2", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], "from_schema": "https://example.com/GRDI", - "rank": 191, - "slot_uri": "GENEPIO:0001517", - "alias": "authors", + "rank": 196, + "alias": "assay_target_name_2", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Contributor acknowledgement", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", + "assay_target_details_2": { + "name": "assay_target_details_2", + "description": "Describe any details of the assay target.", + "title": "assay target details 2", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/GRDI", - "rank": 192, - "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "rank": 197, + "alias": "assay_target_details_2", "owner": "WastewaterSARS-CoV-2", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Contributor acknowledgement", - "range": "Provenance" - } - } - }, - "WastewaterAMR": { - "name": "WastewaterAMR", - "description": "Specification for Wastewater AMR biosample data gathering", - "from_schema": "https://example.com/GRDI", - "is_a": "dh_interface", - "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "rank": 1, - "slot_group": "Database identifiers" - }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", - "rank": 2, - "slot_group": "Database identifiers" - }, - "pooled sample ID": { - "name": "pooled sample ID", - "rank": 3, - "slot_group": "Database identifiers" - }, - "metagenome-assembled genome (MAG) ID": { - "name": "metagenome-assembled genome (MAG) ID", - "rank": 4, - "slot_group": "Database identifiers" - }, - "specimen collector project ID": { - "name": "specimen collector project ID", - "rank": 5, - "slot_group": "Database identifiers" - }, - "BioProject accession": { - "name": "BioProject accession", - "rank": 6, - "slot_group": "Database identifiers" - }, - "BioSample accession": { - "name": "BioSample accession", - "rank": 7, - "slot_group": "Database identifiers" - }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", - "rank": 8, - "slot_group": "Database identifiers" - }, - "SRA accession": { - "name": "SRA accession", - "rank": 9, - "slot_group": "Database identifiers" - }, - "GISAID accession": { - "name": "GISAID accession", - "rank": 10, - "slot_group": "Database identifiers" - }, - "GISAID virus name": { - "name": "GISAID virus name", - "rank": 11, - "slot_group": "Database identifiers" - }, - "ENA accession": { - "name": "ENA accession", - "rank": 12, - "slot_group": "Database identifiers" - }, - "DRA accession": { - "name": "DRA accession", - "rank": 13, - "slot_group": "Database identifiers" - }, - "GSA accession": { - "name": "GSA accession", - "rank": 14, - "slot_group": "Database identifiers" - }, - "Enterobase accession": { - "name": "Enterobase accession", - "rank": 15, - "slot_group": "Database identifiers" - }, - "sampling site ID": { - "name": "sampling site ID", - "rank": 16, - "slot_group": "Database identifiers" - }, - "sampling event ID": { - "name": "sampling event ID", - "rank": 17, - "slot_group": "Database identifiers" - }, - "sample collection data steward name": { - "name": "sample collection data steward name", - "rank": 18, - "slot_group": "Sample collection and processing" - }, - "sample collected by": { - "name": "sample collected by", - "rank": 19, - "slot_group": "Sample collection and processing" - }, - "sample collector contact email": { - "name": "sample collector contact email", - "rank": 20, - "slot_group": "Sample collection and processing" - }, - "geo loc name (country)": { - "name": "geo loc name (country)", - "rank": 21, - "slot_group": "Sample collection and processing" - }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", - "rank": 22, - "slot_group": "Sample collection and processing" - }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", - "rank": 23, - "slot_group": "Sample collection and processing" - }, - "geo loc name (city)": { - "name": "geo loc name (city)", - "rank": 24, - "slot_group": "Sample collection and processing" - }, - "geo loc name (site)": { - "name": "geo loc name (site)", - "rank": 25, - "slot_group": "Sample collection and processing" - }, - "geo loc latitude": { - "name": "geo loc latitude", - "rank": 26, - "slot_group": "Sample collection and processing" - }, - "geo loc longitude": { - "name": "geo loc longitude", - "rank": 27, - "slot_group": "Sample collection and processing" - }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", - "rank": 28, - "slot_group": "Sample collection and processing" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", - "rank": 29, - "slot_group": "Sample collection and processing" + "gene_symbol_2": { + "name": "gene_symbol_2", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 2", + "comments": [ + "Select a gene name value from the pick list provided." + ], + "examples": [ + { + "value": "E gene (orf4)" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_gene" + ], + "rank": 198, + "alias": "gene_symbol_2", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "organism": { - "name": "organism", + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 2", "comments": [ - "Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." ], "examples": [ { - "value": "Vibrio cholerae" + "value": "diagnostic target present" } ], - "rank": 30, - "slot_group": "Sample collection and processing", - "recommended": true, + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_known_present" + ], + "rank": 199, + "alias": "diagnostic_target_presence_2", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", - "rank": 31, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 2", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc" + ], + "rank": 200, + "alias": "diagnostic_measurement_value_2", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "scale of sampling": { - "name": "scale of sampling", - "rank": 32, - "slot_group": "Sample collection and processing" - }, - "sample received date": { - "name": "sample received date", - "rank": 33, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 2", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc_unit" + ], + "rank": 201, + "alias": "diagnostic_measurement_unit_2", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", - "rank": 34, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 2", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 202, + "alias": "diagnostic_measurement_method_2", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end date": { - "name": "sample collection end date", - "rank": 35, - "slot_group": "Sample collection and processing" + "assay_target_name_3": { + "name": "assay_target_name_3", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 3", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "from_schema": "https://example.com/GRDI", + "rank": 203, + "alias": "assay_target_name_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample processing date": { - "name": "sample processing date", - "rank": 36, - "slot_group": "Sample collection and processing" + "assay_target_details_3": { + "name": "assay_target_details_3", + "description": "Describe any details of the assay target.", + "title": "assay target details 3", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/GRDI", + "rank": 204, + "alias": "assay_target_details_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample collection start time": { - "name": "sample collection start time", - "rank": 37, - "slot_group": "Sample collection and processing" + "gene_symbol_3": { + "name": "gene_symbol_3", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 3", + "comments": [ + "Select a gene name value from the pick list provided." + ], + "examples": [ + { + "value": "E gene (orf4)" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 205, + "alias": "gene_symbol_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end time": { - "name": "sample collection end time", - "rank": 38, - "slot_group": "Sample collection and processing" + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 3", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 206, + "alias": "diagnostic_target_presence_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time of day": { - "name": "sample collection time of day", - "rank": 39, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 3", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 207, + "alias": "diagnostic_measurement_value_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample collection time duration value": { - "name": "sample collection time duration value", - "rank": 40, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 3", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 208, + "alias": "diagnostic_measurement_unit_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", - "rank": 41, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 3", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 209, + "alias": "diagnostic_measurement_method_3", + "owner": "WastewaterSARS-CoV-2", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + } + } + }, + "WastewaterAMR": { + "name": "WastewaterAMR", + "annotations": { + "version": { + "tag": "version", + "value": "3.1.1" + } + }, + "description": "Specification for Wastewater AMR biosample data gathering", + "from_schema": "https://example.com/GRDI", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" }, - "presampling activity": { - "name": "presampling activity", - "rank": 42, - "slot_group": "Sample collection and processing" + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" }, - "presampling activity details": { - "name": "presampling activity details", - "rank": 43, - "slot_group": "Sample collection and processing" + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" }, - "sample volume measurement value": { - "name": "sample volume measurement value", - "rank": 44, - "slot_group": "Sample collection and processing" + "metagenomeassembled_genome_mag_id": { + "name": "metagenomeassembled_genome_mag_id", + "rank": 4, + "slot_group": "Database identifiers" }, - "sample volume measurement unit": { - "name": "sample volume measurement unit", - "rank": 45, - "slot_group": "Sample collection and processing" + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", + "rank": 5, + "slot_group": "Database identifiers" }, - "sample storage method": { - "name": "sample storage method", - "rank": 46, - "slot_group": "Sample collection and processing" + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" }, - "sample storage medium": { - "name": "sample storage medium", - "rank": 47, - "slot_group": "Sample collection and processing" + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" }, - "sample storage duration value": { - "name": "sample storage duration value", - "rank": 48, - "slot_group": "Sample collection and processing" + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" }, - "sample storage duration unit": { - "name": "sample storage duration unit", - "rank": 49, - "slot_group": "Sample collection and processing" + "enterobase_accession": { + "name": "enterobase_accession", + "rank": 9, + "slot_group": "Database identifiers" }, - "specimen processing": { - "name": "specimen processing", - "rank": 50, - "slot_group": "Sample collection and processing" + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 10, + "slot_group": "Database identifiers" }, - "specimen processing details": { - "name": "specimen processing details", - "rank": 51, - "slot_group": "Sample collection and processing" + "gisaid_accession": { + "name": "gisaid_accession", + "rank": 11, + "slot_group": "Database identifiers" }, - "experimental protocol field": { - "name": "experimental protocol field", - "rank": 52, - "slot_group": "Sample collection and processing" + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "rank": 12, + "slot_group": "Database identifiers" }, - "environmental site": { - "name": "environmental site", - "rank": 53, - "slot_group": "Sample collection and processing" + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 13, + "slot_group": "Database identifiers" }, - "environmental material": { - "name": "environmental material", + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 14, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 17, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "rank": 18, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 19, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 20, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 21, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 22, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 23, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_site": { + "name": "geo_loc_name_site", + "rank": 24, + "slot_group": "Sample collection and processing" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "rank": 25, + "slot_group": "Sample collection and processing" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "rank": 26, + "slot_group": "Sample collection and processing" + }, + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", + "rank": 27, + "slot_group": "Sample collection and processing" + }, + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", + "rank": 28, + "slot_group": "Sample collection and processing" + }, + "organism": { + "name": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "rank": 29, + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "rank": 30, + "slot_group": "Sample collection and processing" + }, + "scale_of_sampling": { + "name": "scale_of_sampling", + "rank": 31, + "slot_group": "Sample collection and processing" + }, + "sample_received_date": { + "name": "sample_received_date", + "rank": 32, + "slot_group": "Sample collection and processing" + }, + "sample_collection_start_date": { + "name": "sample_collection_start_date", + "rank": 33, + "slot_group": "Sample collection and processing" + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "rank": 34, + "slot_group": "Sample collection and processing" + }, + "sample_processing_date": { + "name": "sample_processing_date", + "rank": 35, + "slot_group": "Sample collection and processing" + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "rank": 36, + "slot_group": "Sample collection and processing" + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "rank": 37, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "rank": 38, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "rank": 39, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "rank": 40, + "slot_group": "Sample collection and processing" + }, + "presampling_activity": { + "name": "presampling_activity", + "rank": 41, + "slot_group": "Sample collection and processing" + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "rank": 42, + "slot_group": "Sample collection and processing" + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "rank": 43, + "slot_group": "Sample collection and processing" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "rank": 44, + "slot_group": "Sample collection and processing" + }, + "sample_storage_method": { + "name": "sample_storage_method", + "rank": 45, + "slot_group": "Sample collection and processing" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "rank": 46, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "rank": 47, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "rank": 48, + "slot_group": "Sample collection and processing" + }, + "specimen_processing": { + "name": "specimen_processing", + "rank": 49, + "slot_group": "Sample collection and processing" + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 50, + "slot_group": "Sample collection and processing" + }, + "experimental_protocol_field": { + "name": "experimental_protocol_field", + "rank": 51, + "slot_group": "Sample collection and processing" + }, + "environmental_site": { + "name": "environmental_site", + "rank": 52, + "slot_group": "Sample collection and processing" + }, + "proximal_environmental_site": { + "name": "proximal_environmental_site", + "rank": 53, + "slot_group": "Sample collection and processing" + }, + "environmental_material": { + "name": "environmental_material", "rank": 54, "slot_group": "Sample collection and processing" }, - "environmental material properties": { - "name": "environmental material properties", + "environmental_material_properties": { + "name": "environmental_material_properties", "rank": 55, "slot_group": "Sample collection and processing" }, - "wastewater system type": { - "name": "wastewater system type", + "wastewater_system_type": { + "name": "wastewater_system_type", "rank": 56, "slot_group": "Sample collection and processing" }, - "experimental specimen role type": { - "name": "experimental specimen role type", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", "rank": 57, "slot_group": "Sample collection and processing" }, - "experimental control details": { - "name": "experimental control details", + "experimental_control_details": { + "name": "experimental_control_details", "rank": 58, "slot_group": "Sample collection and processing" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 59, "slot_group": "Sample collection and processing" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 60, "slot_group": "Sample collection and processing" }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "rank": 61, "slot_group": "Sample collection and processing" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "rank": 62, "slot_group": "Sample collection and processing" }, - "endogenous control details": { - "name": "endogenous control details", + "endogenous_control_details": { + "name": "endogenous_control_details", "rank": 63, "slot_group": "Sample collection and processing" }, - "extraction recovery efficiency measurement value": { - "name": "extraction recovery efficiency measurement value", + "extraction_recovery_efficiency_measurement_value": { + "name": "extraction_recovery_efficiency_measurement_value", "rank": 64, "slot_group": "Sample collection and processing" }, - "extraction recovery efficiency measurement method": { - "name": "extraction recovery efficiency measurement method", + "extraction_recovery_efficiency_measurement_method": { + "name": "extraction_recovery_efficiency_measurement_method", "rank": 65, "slot_group": "Sample collection and processing" }, - "water catchment area human population measurement value": { - "name": "water catchment area human population measurement value", + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", "rank": 66, "slot_group": "Environmental conditions and measurements" }, - "water catchment area human population range": { - "name": "water catchment area human population range", + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", "rank": 67, "slot_group": "Environmental conditions and measurements" }, - "water catchment area human population measurement method": { - "name": "water catchment area human population measurement method", + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", "rank": 68, "slot_group": "Environmental conditions and measurements" }, - "water catchment area human population density value": { - "name": "water catchment area human population density value", + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", "rank": 69, "slot_group": "Environmental conditions and measurements" }, - "water catchment area human population density unit": { - "name": "water catchment area human population density unit", + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", "rank": 70, "slot_group": "Environmental conditions and measurements" }, - "populated area type": { - "name": "populated area type", + "populated_area_type": { + "name": "populated_area_type", "rank": 71, "slot_group": "Environmental conditions and measurements" }, - "sampling weather conditions": { - "name": "sampling weather conditions", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", "rank": 72, "slot_group": "Environmental conditions and measurements" }, - "presampling weather conditions": { - "name": "presampling weather conditions", + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", "rank": 73, "slot_group": "Environmental conditions and measurements" }, - "precipitation measurement value": { - "name": "precipitation measurement value", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", "rank": 74, "slot_group": "Environmental conditions and measurements" }, - "precipitation measurement unit": { - "name": "precipitation measurement unit", + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", "rank": 75, "slot_group": "Environmental conditions and measurements" }, - "precipitation measurement method": { - "name": "precipitation measurement method", + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", "rank": 76, "slot_group": "Environmental conditions and measurements" }, - "ambient temperature measurement value": { - "name": "ambient temperature measurement value", + "ambient_temperature_measurement_value": { + "name": "ambient_temperature_measurement_value", "rank": 77, "slot_group": "Environmental conditions and measurements" }, - "ambient temperature measurement unit": { - "name": "ambient temperature measurement unit", + "ambient_temperature_measurement_unit": { + "name": "ambient_temperature_measurement_unit", "rank": 78, "slot_group": "Environmental conditions and measurements" }, - "pH measurement value": { - "name": "pH measurement value", + "ph_measurement_value": { + "name": "ph_measurement_value", "rank": 79, "slot_group": "Environmental conditions and measurements" }, - "pH measurement method": { - "name": "pH measurement method", + "ph_measurement_method": { + "name": "ph_measurement_method", "rank": 80, "slot_group": "Environmental conditions and measurements" }, - "total daily flow rate measurement value": { - "name": "total daily flow rate measurement value", + "total_daily_flow_rate_measurement_value": { + "name": "total_daily_flow_rate_measurement_value", "rank": 81, "slot_group": "Environmental conditions and measurements" }, - "total daily flow rate measurement unit": { - "name": "total daily flow rate measurement unit", + "total_daily_flow_rate_measurement_unit": { + "name": "total_daily_flow_rate_measurement_unit", "rank": 82, "slot_group": "Environmental conditions and measurements" }, - "total daily flow rate measurement method": { - "name": "total daily flow rate measurement method", + "total_daily_flow_rate_measurement_method": { + "name": "total_daily_flow_rate_measurement_method", "rank": 83, "slot_group": "Environmental conditions and measurements" }, - "instantaneous flow rate measurement value": { - "name": "instantaneous flow rate measurement value", + "instantaneous_flow_rate_measurement_value": { + "name": "instantaneous_flow_rate_measurement_value", "rank": 84, "slot_group": "Environmental conditions and measurements" }, - "instantaneous flow rate measurement unit": { - "name": "instantaneous flow rate measurement unit", + "instantaneous_flow_rate_measurement_unit": { + "name": "instantaneous_flow_rate_measurement_unit", "rank": 85, "slot_group": "Environmental conditions and measurements" }, - "instantaneous flow rate measurement method": { - "name": "instantaneous flow rate measurement method", + "instantaneous_flow_rate_measurement_method": { + "name": "instantaneous_flow_rate_measurement_method", "rank": 86, "slot_group": "Environmental conditions and measurements" }, - "turbidity measurement value": { - "name": "turbidity measurement value", + "turbidity_measurement_value": { + "name": "turbidity_measurement_value", "rank": 87, "slot_group": "Environmental conditions and measurements" }, - "turbidity measurement unit": { - "name": "turbidity measurement unit", + "turbidity_measurement_unit": { + "name": "turbidity_measurement_unit", "rank": 88, "slot_group": "Environmental conditions and measurements" }, - "turbidity measurement method": { - "name": "turbidity measurement method", + "turbidity_measurement_method": { + "name": "turbidity_measurement_method", "rank": 89, "slot_group": "Environmental conditions and measurements" }, - "dissolved oxygen measurement value": { - "name": "dissolved oxygen measurement value", + "dissolved_oxygen_measurement_value": { + "name": "dissolved_oxygen_measurement_value", "rank": 90, "slot_group": "Environmental conditions and measurements" }, - "dissolved oxygen measurement unit": { - "name": "dissolved oxygen measurement unit", + "dissolved_oxygen_measurement_unit": { + "name": "dissolved_oxygen_measurement_unit", "rank": 91, "slot_group": "Environmental conditions and measurements" }, - "dissolved oxygen measurement method": { - "name": "dissolved oxygen measurement method", + "dissolved_oxygen_measurement_method": { + "name": "dissolved_oxygen_measurement_method", "rank": 92, "slot_group": "Environmental conditions and measurements" }, - "oxygen reduction potential (ORP) measurement value": { - "name": "oxygen reduction potential (ORP) measurement value", + "oxygen_reduction_potential_orp_measurement_value": { + "name": "oxygen_reduction_potential_orp_measurement_value", "rank": 93, "slot_group": "Environmental conditions and measurements" }, - "oxygen reduction potential (ORP) measurement unit": { - "name": "oxygen reduction potential (ORP) measurement unit", + "oxygen_reduction_potential_orp_measurement_unit": { + "name": "oxygen_reduction_potential_orp_measurement_unit", "rank": 94, "slot_group": "Environmental conditions and measurements" }, - "oxygen reduction potential (ORP) measurement method": { - "name": "oxygen reduction potential (ORP) measurement method", + "oxygen_reduction_potential_orp_measurement_method": { + "name": "oxygen_reduction_potential_orp_measurement_method", "rank": 95, "slot_group": "Environmental conditions and measurements" }, - "chemical oxygen demand (COD) measurement value": { - "name": "chemical oxygen demand (COD) measurement value", + "chemical_oxygen_demand_cod_measurement_value": { + "name": "chemical_oxygen_demand_cod_measurement_value", "rank": 96, "slot_group": "Environmental conditions and measurements" }, - "chemical oxygen demand (COD) measurement unit": { - "name": "chemical oxygen demand (COD) measurement unit", + "chemical_oxygen_demand_cod_measurement_unit": { + "name": "chemical_oxygen_demand_cod_measurement_unit", "rank": 97, "slot_group": "Environmental conditions and measurements" }, - "chemical oxygen demand (COD) measurement method": { - "name": "chemical oxygen demand (COD) measurement method", + "chemical_oxygen_demand_cod_measurement_method": { + "name": "chemical_oxygen_demand_cod_measurement_method", "rank": 98, "slot_group": "Environmental conditions and measurements" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement value": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement value", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "rank": 99, "slot_group": "Environmental conditions and measurements" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement unit": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement unit", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "rank": 100, "slot_group": "Environmental conditions and measurements" }, - 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"fecal coliform count unit": { - "name": "fecal coliform count unit", + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", "rank": 131, "slot_group": "Environmental conditions and measurements" }, - "fecal coliform count method": { - "name": "fecal coliform count method", + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", "rank": 132, "slot_group": "Environmental conditions and measurements" }, - "urinary contamination indicator": { - "name": "urinary contamination indicator", + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", "rank": 133, "slot_group": "Environmental conditions and measurements" }, - "urinary contamination value": { - "name": "urinary contamination value", + "urinary_contamination_value": { + "name": "urinary_contamination_value", "rank": 134, "slot_group": "Environmental conditions and measurements" }, - "urinary contamination unit": { - "name": "urinary contamination unit", + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", "rank": 135, "slot_group": "Environmental conditions and measurements" }, - "urinary contamination method": { - "name": "urinary contamination method", + "urinary_contamination_method": { + "name": "urinary_contamination_method", "rank": 136, "slot_group": "Environmental conditions and measurements" }, - "sample temperature value (at collection)": { - "name": "sample temperature value (at collection)", + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", "rank": 137, "slot_group": "Environmental conditions and measurements" }, - "sample temperature unit (at collection)": { - "name": "sample temperature unit (at collection)", + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", "rank": 138, "slot_group": "Environmental conditions and measurements" }, - "sample temperature value (when received)": { - "name": "sample temperature value (when received)", + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", "rank": 139, "slot_group": "Environmental conditions and measurements" }, - 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"name": "AMR reference database name", + "read_mapping_criteria": { + "name": "read_mapping_criteria", "rank": 184, - "slot_group": "AMR detection information" + "slot_group": "Taxonomic identification information" }, - "AMR reference database version": { - "name": "AMR reference database version", + "amr_analysis_software_name": { + "name": "amr_analysis_software_name", "rank": 185, "slot_group": "AMR detection information" }, - "AMR analysis report filename": { - "name": "AMR analysis report filename", + "amr_analysis_software_version": { + "name": "amr_analysis_software_version", "rank": 186, "slot_group": "AMR detection information" }, - "gene name": { - "name": "gene name", + "amr_reference_database_name": { + "name": "amr_reference_database_name", + "rank": 187, + "slot_group": "AMR detection information" + }, + "amr_reference_database_version": { + "name": "amr_reference_database_version", + "rank": 188, + "slot_group": "AMR detection information" + }, + "amr_analysis_report_filename": { + "name": "amr_analysis_report_filename", + "rank": 189, + "slot_group": "AMR detection information" + }, + "assay_target_name_1": { + "name": "assay_target_name_1", + "rank": 190, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details": { + "name": "assay_target_details", + "rank": 191, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_1": { + "name": "gene_symbol_1", "comments": [ "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" ], @@ -13234,126 +18471,191 @@ "value": "gyrase A" } ], - "rank": 187, + "rank": 192, "slot_group": "Pathogen diagnostic testing", "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", - "rank": 188, + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", + "rank": 193, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", - "rank": 189, + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", + "rank": 194, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", - "rank": 190, + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", + "rank": 195, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", - "rank": 191, + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", + "rank": 196, "slot_group": "Pathogen diagnostic testing" }, - "authors": { - "name": "authors", - "rank": 192, - "slot_group": "Contributor acknowledgement" + "assay_target_name_2": { + "name": "assay_target_name_2", + "rank": 197, + "slot_group": "Pathogen diagnostic testing" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 193, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "The user-defined name for the sample.", - "title": "specimen collector sample ID", - "from_schema": "https://example.com/GRDI", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "specimen_collector_sample_ID", - "owner": "WastewaterAMR", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" - ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "required": true + "assay_target_details_2": { + "name": "assay_target_details_2", + "rank": 198, + "slot_group": "Pathogen diagnostic testing" }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", - "description": "The user-defined identifier assigned to a portion of the original sample.", - "title": "specimen collector subsample ID", - "from_schema": "https://example.com/GRDI", - "rank": 2, - "slot_uri": "GENEPIO:0100752", - "alias": "specimen_collector_subsample_ID", - "owner": "WastewaterAMR", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "gene_symbol_2": { + "name": "gene_symbol_2", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString" - }, - "pooled sample ID": { - "name": "pooled sample ID", - "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", - "title": "pooled sample ID", - "from_schema": "https://example.com/GRDI", - "rank": 3, - "slot_uri": "GENEPIO:0100996", - "alias": "pooled_sample_ID", - "owner": "WastewaterAMR", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "examples": [ + { + "value": "gyrase A" + } ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString" + "rank": 199, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "metagenome-assembled genome (MAG) ID": { - "name": "metagenome-assembled genome (MAG) ID", - "description": "The user-defined identifier assigned to a genome reconstructed from metagenomic data.", - "title": "metagenome-assembled genome (MAG) ID", - "from_schema": "https://example.com/GRDI", - "rank": 4, - "slot_uri": "GENEPIO:0100753", - "alias": "metagenome_assembled_genome_(MAG)_ID", - "owner": "WastewaterAMR", - "domain_of": [ + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "rank": 200, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "rank": 201, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "rank": 202, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "rank": 203, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_name_3": { + "name": "assay_target_name_3", + "rank": 204, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details_3": { + "name": "assay_target_details_3", + "rank": 205, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_3": { + "name": "gene_symbol_3", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "rank": 206, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", + "rank": 207, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", + "rank": 208, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", + "rank": 210, + "slot_group": "Pathogen diagnostic testing" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sample_name", + "NCBI_SRA:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString" + "range": "WhitespaceMinimizedString", + "required": true }, - "specimen collector project ID": { - "name": "specimen collector project ID", - "description": "The user-defined project name assigned to a sequencing project.", - "title": "specimen collector project ID", + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen collector subsample ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 5, - "slot_uri": "GENEPIO:0100918", - "alias": "specimen_collector_project_ID", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_id" + ], + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13363,14 +18665,22 @@ "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString" }, - "BioProject accession": { - "name": "BioProject accession", - "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", - "title": "BioProject accession", + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled sample ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 6, - "slot_uri": "GENEPIO:0001136", - "alias": "BioProject_accession", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13378,46 +18688,46 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "range": "WhitespaceMinimizedString" }, - "BioSample accession": { - "name": "BioSample accession", - "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", - "title": "BioSample accession", + "metagenomeassembled_genome_mag_id": { + "name": "metagenomeassembled_genome_mag_id", + "description": "The user-defined identifier assigned to a genome reconstructed from metagenomic data.", + "title": "metagenome-assembled genome (MAG) ID", + "comments": [ + "Store the MAG ID." + ], + "examples": [ + { + "value": "XYZ1234.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 7, - "slot_uri": "GENEPIO:0001139", - "alias": "BioSample_accession", + "rank": 4, + "slot_uri": "GENEPIO:0100753", + "alias": "metagenomeassembled_genome_mag_id", "owner": "WastewaterAMR", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "recommended": true, - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "range": "WhitespaceMinimizedString" }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", - "description": "The versioned identifier assigned to an assembly or consensus sequence in GenBank archives.", - "title": "GenBank accession (versioned)", + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", + "description": "The user-defined project name assigned to a sequencing project.", + "title": "specimen collector project ID", + "comments": [ + "If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here." + ], "from_schema": "https://example.com/GRDI", - "rank": 8, - "slot_uri": "GENEPIO:0100754", - "alias": "GenBank_accession_(versioned)", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:project_name" + ], + "rank": 5, + "slot_uri": "GENEPIO:0100918", + "alias": "specimen_collector_project_id", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13425,22 +18735,27 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "range": "WhitespaceMinimizedString" }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 9, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13456,14 +18771,22 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", - "title": "GISAID accession", + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMEA00000002, SAMD00000001" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 10, - "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13472,6 +18795,7 @@ ], "slot_group": "Database identifiers", "range": "WhitespaceMinimizedString", + "recommended": true, "pattern": "{UPPER_CASE}", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -13479,14 +18803,22 @@ "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "title": "GISAID virus name", + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 11, - "slot_uri": "GENEPIO:0100282", - "alias": "GISAID_virus_name", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13502,14 +18834,22 @@ "partial_match": false } }, - "ENA accession": { - "name": "ENA accession", - "description": "The identifier assigned to a sequence in the European Nucleotide Archive (ENA).", - "title": "ENA accession", + "enterobase_accession": { + "name": "enterobase_accession", + "description": "The identifier assigned to a sequence in Enterobase archives.", + "title": "Enterobase accession", + "comments": [ + "Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism." + ], + "examples": [ + { + "value": "SAL_AA0019AA_ST" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 12, - "slot_uri": "GENEPIO:0100755", - "alias": "ENA_accession", + "rank": 9, + "slot_uri": "GENEPIO:0100759", + "alias": "enterobase_accession", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13525,14 +18865,22 @@ "partial_match": false } }, - "DRA accession": { - "name": "DRA accession", - "description": "The identifier assigned to a sequence in DNA Data Bank of Japan (DDBJ) sequence read archives.", - "title": "DRA accession", + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 13, - "slot_uri": "GENEPIO:0100757", - "alias": "DRA_accession", + "rank": 10, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13548,14 +18896,22 @@ "partial_match": false } }, - "GSA accession": { - "name": "GSA accession", - "description": "The identifier assigned to a BioSample in GSA (Genome Sequence Archive) archives.", - "title": "GSA accession", + "gisaid_accession": { + "name": "gisaid_accession", + "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", + "title": "GISAID accession", + "comments": [ + "Store the accession assigned to the submitted sequence. GISAID accessions start with EPI." + ], + "examples": [ + { + "value": "EPI_ISL_402131" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 14, - "slot_uri": "GENEPIO:0100758", - "alias": "GSA_accession", + "rank": 11, + "slot_uri": "GENEPIO:0001147", + "alias": "gisaid_accession", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13571,14 +18927,22 @@ "partial_match": false } }, - "Enterobase accession": { - "name": "Enterobase accession", - "description": "The identifier assigned to a sequence in Enterobase archives.", - "title": "Enterobase accession", + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "title": "GISAID virus name", + "comments": [ + "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\"." + ], + "examples": [ + { + "value": "hCoV-19/Canada/prov_rona_99/2020" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 15, - "slot_uri": "GENEPIO:0100759", - "alias": "Enterobase_accession", + "rank": 12, + "slot_uri": "GENEPIO:0100282", + "alias": "gisaid_virus_name", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13594,14 +18958,25 @@ "partial_match": false } }, - "sampling site ID": { - "name": "sampling site ID", + "sampling_site_id": { + "name": "sampling_site_id", "description": "The user-defined identifier assigned to a specific location from which samples are taken.", "title": "sampling site ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 16, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_site_id" + ], + "rank": 13, "slot_uri": "GENEPIO:0100760", - "alias": "sampling_site_ID", + "alias": "sampling_site_id", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13612,14 +18987,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "sampling event ID": { - "name": "sampling event ID", + "sampling_event_id": { + "name": "sampling_event_id", "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", "title": "sampling event ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 17, + "rank": 14, "slot_uri": "GENEPIO:0100761", - "alias": "sampling_event_ID", + "alias": "sampling_event_id", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13630,12 +19013,20 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "sample collection data steward name": { - "name": "sample collection data steward name", + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", "title": "sample collection data steward name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 18, + "rank": 15, "slot_uri": "GENEPIO:0100762", "alias": "sample_collection_data_steward_name", "owner": "WastewaterAMR", @@ -13647,12 +19038,48 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collected by": { - "name": "sample collected by", - "description": "The name of the organization with which the sample collector is affiliated.", - "title": "sample collected by", - "from_schema": "https://example.com/GRDI", - "rank": 19, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "description": "The specific laboratory affiliation of the sample collector.", + "title": "sample collected by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 16, + "slot_uri": "GENEPIO:0100428", + "alias": "sample_collected_by_laboratory_name", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample collected by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collected_by" + ], + "rank": 17, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", "owner": "WastewaterAMR", @@ -13662,14 +19089,55 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "description": "The name or job title of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 18, + "slot_uri": "GENEPIO:0100432", + "alias": "sample_collector_contact_name", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 20, + "rank": 19, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "WastewaterAMR", @@ -13682,14 +19150,22 @@ "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "geo loc name (country)": { - "name": "geo loc name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo loc name (country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 21, + "rank": 20, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "alias": "geo_loc_name_country", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13697,16 +19173,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The state/province/territory of origin of the sample.", "title": "geo loc name (state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 22, + "rank": 21, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "alias": "geo_loc_name_state_province_territory", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13714,16 +19206,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "description": "The county/region of origin of the sample.", "title": "geo loc name (county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 23, + "rank": 22, "slot_uri": "GENEPIO:0100280", - "alias": "geo_loc_name_(county/region)", + "alias": "geo_loc_name_county_region", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13733,14 +19241,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc name (city)": { - "name": "geo loc name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city of origin of the sample.", "title": "geo loc name (city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 24, + "rank": 23, "slot_uri": "GENEPIO:0001189", - "alias": "geo_loc_name_(city)", + "alias": "geo_loc_name_city", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13750,14 +19266,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc name (site)": { - "name": "geo loc name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo loc name (site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 25, + "rank": 24, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_(site)", + "alias": "geo_loc_name_site", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13767,12 +19291,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc latitude": { - "name": "geo loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo loc latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 26, + "rank": 25, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", "owner": "WastewaterAMR", @@ -13784,12 +19316,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc longitude": { - "name": "geo loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo loc longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 27, + "rank": 26, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", "owner": "WastewaterAMR", @@ -13801,12 +19341,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", "description": "The availability status of a shapefile descriping the catchment contributing to a watershed.", "title": "watershed shapefile availability", + "comments": [ + "Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request." + ], + "examples": [ + { + "value": "watershed shapefile available" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 28, + "rank": 27, "slot_uri": "GENEPIO:0100919", "alias": "watershed_shapefile_availability", "owner": "WastewaterAMR", @@ -13815,14 +19363,30 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WatershedShapefileAvailabilityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", "description": "The name of the watershed shapefile.", "title": "watershed shapefile filename", + "comments": [ + "Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas." + ], + "examples": [ + { + "value": "siteAD17.shp, siteAD17.kml" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 29, + "rank": 28, "slot_uri": "GENEPIO:0100920", "alias": "watershed_shapefile_filename", "owner": "WastewaterAMR", @@ -13847,7 +19411,10 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 30, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1" + ], + "rank": 29, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "WastewaterAMR", @@ -13858,23 +19425,34 @@ ], "slot_group": "Sample collection and processing", "recommended": true, + "multivalued": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 31, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], + "rank": 30, "slot_uri": "GENEPIO:0001198", - "multivalued": true, "alias": "purpose_of_sampling", "owner": "WastewaterAMR", "domain_of": [ @@ -13883,14 +19461,34 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "scale of sampling": { - "name": "scale of sampling", + "scale_of_sampling": { + "name": "scale_of_sampling", "description": "The range of locations or entities sampled expressed in general terms.", "title": "scale of sampling", + "comments": [ + "Provide the scale of wastewater sampling by selecting a value from the picklist." + ], + "examples": [ + { + "value": "Community-level surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 32, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], + "rank": 31, "slot_uri": "GENEPIO:0100877", "alias": "scale_of_sampling", "owner": "WastewaterAMR", @@ -13900,14 +19498,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "ScaleOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 33, + "rank": 32, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "WastewaterAMR", @@ -13916,16 +19530,32 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_start_date": { + "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", - "title": "sample collection date", + "title": "sample collection start date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 34, + "rank": 33, "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", + "alias": "sample_collection_start_date", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -13933,14 +19563,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end date": { - "name": "sample collection end date", + "sample_collection_end_date": { + "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 35, + "rank": 34, "slot_uri": "GENEPIO:0101071", "alias": "sample_collection_end_date", "owner": "WastewaterAMR", @@ -13950,14 +19596,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample processing date": { - "name": "sample processing date", + "sample_processing_date": { + "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 36, + "rank": 35, "slot_uri": "GENEPIO:0100763", "alias": "sample_processing_date", "owner": "WastewaterAMR", @@ -13966,14 +19628,30 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection start time": { - "name": "sample collection start time", + "sample_collection_start_time": { + "name": "sample_collection_start_time", "description": "The time at which sample collection began.", "title": "sample collection start time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 37, + "rank": 36, "slot_uri": "GENEPIO:0101072", "alias": "sample_collection_start_time", "owner": "WastewaterAMR", @@ -13983,14 +19661,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end time": { - "name": "sample collection end time", + "sample_collection_end_time": { + "name": "sample_collection_end_time", "description": "The time at which sample collection ended.", "title": "sample collection end time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 38, + "rank": 37, "slot_uri": "GENEPIO:0101073", "alias": "sample_collection_end_time", "owner": "WastewaterAMR", @@ -14000,14 +19694,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time of day": { - "name": "sample collection time of day", + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", "description": "The descriptive time of day during which the sample was collected.", "title": "sample collection time of day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 39, + "rank": 38, "slot_uri": "GENEPIO:0100765", "alias": "sample_collection_time_of_day", "owner": "WastewaterAMR", @@ -14016,14 +19726,33 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleCollectionTimeOfDayMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time duration value": { - "name": "sample collection time duration value", + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", "description": "The amount of time over which the sample was collected.", "title": "sample collection time duration value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 40, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], + "rank": 39, "slot_uri": "GENEPIO:0100766", "alias": "sample_collection_time_duration_value", "owner": "WastewaterAMR", @@ -14033,14 +19762,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", "description": "The units of the time duration measurement of sample collection.", "title": "sample collection time duration unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 41, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], + "rank": 40, "slot_uri": "GENEPIO:0100767", "alias": "sample_collection_time_duration_unit", "owner": "WastewaterAMR", @@ -14050,16 +19798,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "SampleCollectionDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling activity": { - "name": "presampling activity", + "presampling_activity": { + "name": "presampling_activity", "description": "The activities or variables upstream of sample collection that may affect the sample.", "title": "presampling activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 42, + "rank": 41, "slot_uri": "GENEPIO:0100433", - "multivalued": true, "alias": "presampling_activity", "owner": "WastewaterAMR", "domain_of": [ @@ -14067,14 +19830,31 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "PresamplingActivityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling activity details": { - "name": "presampling activity details", + "presampling_activity_details": { + "name": "presampling_activity_details", "description": "The details of the activities or variables that affected the sample collected.", "title": "presampling activity details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 43, + "rank": 42, "slot_uri": "GENEPIO:0100434", "alias": "presampling_activity_details", "owner": "WastewaterAMR", @@ -14083,14 +19863,33 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample volume measurement value": { - "name": "sample volume measurement value", + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", "description": "The numerical value of the volume measurement of the sample collected.", "title": "sample volume measurement value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 44, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], + "rank": 43, "slot_uri": "GENEPIO:0100768", "alias": "sample_volume_measurement_value", "owner": "WastewaterAMR", @@ -14102,12 +19901,23 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample volume measurement unit": { - "name": "sample volume measurement unit", + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", "description": "The units of the volume measurement of the sample collected.", "title": "sample volume measurement unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "mL" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 45, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], + "rank": 44, "slot_uri": "GENEPIO:0100769", "alias": "sample_volume_measurement_unit", "owner": "WastewaterAMR", @@ -14116,14 +19926,30 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleVolumeMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample storage method": { - "name": "sample storage method", + "sample_storage_method": { + "name": "sample_storage_method", "description": "The process used to store the sample.", "title": "sample storage method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 46, + "rank": 45, "slot_uri": "GENEPIO:0100448", "alias": "sample_storage_method", "owner": "WastewaterAMR", @@ -14135,12 +19961,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample storage medium": { - "name": "sample storage medium", + "sample_storage_medium": { + "name": "sample_storage_medium", "description": "The medium in which a sample is stored.", "title": "sample storage medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 47, + "rank": 46, "slot_uri": "GENEPIO:0100449", "alias": "sample_storage_medium", "owner": "WastewaterAMR", @@ -14152,12 +19986,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample storage duration value": { - "name": "sample storage duration value", + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", "description": "The numerical value of the time measurement during which a sample is in storage.", "title": "sample storage duration value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 48, + "rank": 47, "slot_uri": "GENEPIO:0101014", "alias": "sample_storage_duration_value", "owner": "WastewaterAMR", @@ -14169,12 +20011,20 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample storage duration unit": { - "name": "sample storage duration unit", + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", "description": "The units of a measured sample storage duration.", "title": "sample storage duration unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 49, + "rank": 48, "slot_uri": "GENEPIO:0101015", "alias": "sample_storage_duration_unit", "owner": "WastewaterAMR", @@ -14183,16 +20033,34 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleStorageDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 50, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing" + ], + "rank": 49, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", "owner": "WastewaterAMR", "domain_of": [ @@ -14200,14 +20068,34 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "The details of the processing applied to the sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 51, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_details" + ], + "rank": 50, "slot_uri": "GENEPIO:0100311", "alias": "specimen_processing_details", "owner": "WastewaterAMR", @@ -14219,12 +20107,15 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "experimental protocol field": { - "name": "experimental protocol field", + "experimental_protocol_field": { + "name": "experimental_protocol_field", "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", "title": "experimental protocol field", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], "from_schema": "https://example.com/GRDI", - "rank": 52, + "rank": 51, "slot_uri": "GENEPIO:0101029", "alias": "experimental_protocol_field", "owner": "WastewaterAMR", @@ -14236,14 +20127,24 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", + "comments": [ + "Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Meat processing plant" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 53, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_site" + ], + "rank": 52, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", "owner": "WastewaterAMR", "domain_of": [ @@ -14252,17 +20153,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material": { - "name": "environmental material", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", - "title": "environmental material", + "proximal_environmental_site": { + "name": "proximal_environmental_site", + "description": "An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample.", + "title": "proximal environmental site", + "comments": [ + "Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Farm" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 54, - "slot_uri": "GENEPIO:0001223", - "multivalued": true, - "alias": "environmental_material", + "rank": 53, + "slot_uri": "GENEPIO:0101205", + "alias": "proximal_environmental_site", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14270,16 +20187,61 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "range": "EnvironmentalSiteMenu", + "multivalued": true + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", + "title": "environmental material", + "comments": [ + "Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Raw wastewater" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_matrix" + ], + "rank": 54, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material properties": { - "name": "environmental material properties", + "environmental_material_properties": { + "name": "environmental_material_properties", "description": "The properties, characteristics and qualities of a substance obtained from the natural or man-made environment.", "title": "environmental material properties", + "comments": [ + "Provide the environmental material properties by selecting descriptors from the pick list." + ], + "examples": [ + { + "value": "Stagnant" + } + ], "from_schema": "https://example.com/GRDI", "rank": 55, "slot_uri": "GENEPIO:0100770", - "multivalued": true, "alias": "environmental_material_properties", "owner": "WastewaterAMR", "domain_of": [ @@ -14288,12 +20250,29 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialPropertiesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "wastewater system type": { - "name": "wastewater system type", + "wastewater_system_type": { + "name": "wastewater_system_type", "description": "The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine", "title": "wastewater system type", + "comments": [ + "Provide the classification of the wastewater system by selecting from the provided pick list." + ], + "examples": [ + { + "value": "Sanitary sewer" + } + ], "from_schema": "https://example.com/GRDI", "rank": 56, "slot_uri": "GENEPIO:0100771", @@ -14305,16 +20284,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WastewaterSystemTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "experimental specimen role type": { - "name": "experimental specimen role type", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", "description": "The type of role that the sample represents in the experiment.", "title": "experimental specimen role type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], "from_schema": "https://example.com/GRDI", "rank": 57, "slot_uri": "GENEPIO:0100921", - "multivalued": true, "alias": "experimental_specimen_role_type", "owner": "WastewaterAMR", "domain_of": [ @@ -14322,12 +20316,29 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "ExperimentalSpecimenRoleTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "experimental control details": { - "name": "experimental control details", + "experimental_control_details": { + "name": "experimental_control_details", "description": "The details regarding the experimental control contained in the sample.", "title": "experimental control details", + "comments": [ + "Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor." + ], + "examples": [ + { + "value": "Human coronavirus 229E (HCoV-229E) spiked in sample as process control" + } + ], "from_schema": "https://example.com/GRDI", "rank": 58, "slot_uri": "GENEPIO:0100922", @@ -14341,14 +20352,21 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. grab sampler.", "title": "collection device", + "comments": [ + "Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Automatic flow-proportional sampler" + } + ], "from_schema": "https://example.com/GRDI", "rank": 59, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", "owner": "WastewaterAMR", "domain_of": [ @@ -14356,16 +20374,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample.", "title": "collection method", + "comments": [ + "Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Automatic composite sampling" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_type" + ], "rank": 60, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", "owner": "WastewaterAMR", "domain_of": [ @@ -14374,13 +20411,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", "description": "The process used to extract genomic material from a sample.", "title": "nucleic acid extraction method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:extraction_method" + ], "rank": 61, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", @@ -14393,10 +20450,18 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", "description": "The kit used to extract genomic material from a sample", "title": "nucleic acid extraction kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 62, "slot_uri": "GENEPIO:0100772", @@ -14410,11 +20475,17 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "endogenous control details": { - "name": "endogenous control details", + "endogenous_control_details": { + "name": "endogenous_control_details", "description": "The description of the endogenous controls included when extracting a sample.", "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_endog_control_1" + ], "rank": 63, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", @@ -14428,10 +20499,13 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "extraction recovery efficiency measurement value": { - "name": "extraction recovery efficiency measurement value", + "extraction_recovery_efficiency_measurement_value": { + "name": "extraction_recovery_efficiency_measurement_value", "description": "The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected.", "title": "extraction recovery efficiency measurement value", + "comments": [ + "Provide value as a percent." + ], "from_schema": "https://example.com/GRDI", "rank": 64, "slot_uri": "GENEPIO:0100924", @@ -14445,10 +20519,13 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "extraction recovery efficiency measurement method": { - "name": "extraction recovery efficiency measurement method", + "extraction_recovery_efficiency_measurement_method": { + "name": "extraction_recovery_efficiency_measurement_method", "description": "The method by which recovery efficiency of an extraction was calculated.", "title": "extraction recovery efficiency measurement method", + "comments": [ + "Provide a brief description of how extraction recovery efficiency was measured or estimated." + ], "from_schema": "https://example.com/GRDI", "rank": 65, "slot_uri": "GENEPIO:0100925", @@ -14462,11 +20539,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "water catchment area human population measurement value": { - "name": "water catchment area human population measurement value", + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", "title": "water catchment area human population measurement value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population" + ], "rank": 66, "slot_uri": "GENEPIO:0100773", "alias": "water_catchment_area_human_population_measurement_value", @@ -14477,12 +20565,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "NullValueMenu" + } + ] }, - "water catchment area human population range": { - "name": "water catchment area human population range", + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", "title": "water catchment area human population range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], "from_schema": "https://example.com/GRDI", "rank": 67, "slot_uri": "GENEPIO:0100774", @@ -14493,13 +20597,32 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "water catchment area human population measurement method": { - "name": "water catchment area human population measurement method", + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", "description": "The method by which a water catchment 's human population size was measured or estimated", "title": "water catchment area human population measurement method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population_source" + ], "rank": 68, "slot_uri": "GENEPIO:0100775", "alias": "water_catchment_area_human_population_measurement_method", @@ -14512,10 +20635,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population density value": { - "name": "water catchment area human population density value", + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", "description": "The numerical value describing the number of humans per geographical area in a water catchment.", "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", "rank": 69, "slot_uri": "GENEPIO:0100776", @@ -14529,10 +20660,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population density unit": { - "name": "water catchment area human population density unit", + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", "description": "The unit describing the number of humans per geographical area in a water catchment.", "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 70, "slot_uri": "GENEPIO:0100777", @@ -14543,12 +20682,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "populated area type": { - "name": "populated area type", + "populated_area_type": { + "name": "populated_area_type", "description": "A type of area that is populated by humans to different degrees.", "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], "from_schema": "https://example.com/GRDI", "rank": 71, "slot_uri": "GENEPIO:0100778", @@ -14559,16 +20714,31 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "PopulatedAreaTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sampling weather conditions": { - "name": "sampling weather conditions", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], "from_schema": "https://example.com/GRDI", "rank": 72, "slot_uri": "GENEPIO:0100779", - "multivalued": true, "alias": "sampling_weather_conditions", "owner": "WastewaterAMR", "domain_of": [ @@ -14576,16 +20746,32 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "SamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling weather conditions": { - "name": "presampling weather conditions", + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", "description": "Weather conditions prior to collection that may affect the sample.", "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], "from_schema": "https://example.com/GRDI", "rank": 73, "slot_uri": "GENEPIO:0100780", - "multivalued": true, "alias": "presampling_weather_conditions", "owner": "WastewaterAMR", "domain_of": [ @@ -14593,12 +20779,29 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "PresamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement value": { - "name": "precipitation measurement value", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", "description": "The amount of water which has fallen during a precipitation process.", "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], "from_schema": "https://example.com/GRDI", "rank": 74, "slot_uri": "GENEPIO:0100911", @@ -14610,16 +20813,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement unit": { - "name": "precipitation measurement unit", + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", "title": "precipitation measurement unit", - "from_schema": "https://example.com/GRDI", - "rank": 75, - "slot_uri": "GENEPIO:0100912", - "alias": "precipitation_measurement_unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 75, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14627,12 +20846,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "PrecipitationMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement method": { - "name": "precipitation measurement method", + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", "description": "The process used to measure the amount of water which has fallen during a precipitation process.", "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample collection" + } + ], "from_schema": "https://example.com/GRDI", "rank": 76, "slot_uri": "GENEPIO:0100913", @@ -14646,10 +20881,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "ambient temperature measurement value": { - "name": "ambient temperature measurement value", + "ambient_temperature_measurement_value": { + "name": "ambient_temperature_measurement_value", "description": "The numerical value of a measurement of the ambient temperature.", "title": "ambient temperature measurement value", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "70" + } + ], "from_schema": "https://example.com/GRDI", "rank": 77, "slot_uri": "GENEPIO:0100935", @@ -14663,10 +20906,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "ambient temperature measurement unit": { - "name": "ambient temperature measurement unit", + "ambient_temperature_measurement_unit": { + "name": "ambient_temperature_measurement_unit", "description": "The units of a measurement of the ambient temperature.", "title": "ambient temperature measurement unit", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 78, "slot_uri": "GENEPIO:0100936", @@ -14677,16 +20928,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "AmbientTemperatureMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "pH measurement value": { - "name": "pH measurement value", + "ph_measurement_value": { + "name": "ph_measurement_value", "description": "The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution.", "title": "pH measurement value", + "comments": [ + "Provide the numerical value of the measured pH." + ], + "examples": [ + { + "value": "7.4" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_ph" + ], "rank": 79, "slot_uri": "GENEPIO:0001736", - "alias": "pH_measurement_value", + "alias": "ph_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14696,14 +20966,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "pH measurement method": { - "name": "pH measurement method", + "ph_measurement_method": { + "name": "ph_measurement_method", "description": "The process used to measure pH value.", "title": "pH measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure pH." + ], + "examples": [ + { + "value": "pH test strip (litmus test)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 80, "slot_uri": "GENEPIO:0100781", - "alias": "pH_measurement_method", + "alias": "ph_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14713,11 +20991,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement value": { - "name": "total daily flow rate measurement value", + "total_daily_flow_rate_measurement_value": { + "name": "total_daily_flow_rate_measurement_value", "description": "The numerical value of a measured fluid flow rate over the course of a day.", "title": "total daily flow rate measurement value", + "comments": [ + "Provide the numerical value of the measured flow rate." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], "rank": 81, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", @@ -14730,11 +21019,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement unit": { - "name": "total daily flow rate measurement unit", + "total_daily_flow_rate_measurement_unit": { + "name": "total_daily_flow_rate_measurement_unit", "description": "The units of a measured fluid flow rate over the course of a day.", "title": "total daily flow rate measurement unit", + "comments": [ + "Provide the units of the measured flow rate by selecting a value from the pick list." + ], + "examples": [ + { + "value": "million gallons per day (MGD)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], "rank": 82, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", @@ -14744,12 +21044,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalDailyFlowRateMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total daily flow rate measurement method": { - "name": "total daily flow rate measurement method", + "total_daily_flow_rate_measurement_method": { + "name": "total_daily_flow_rate_measurement_method", "description": "The process used to measure total daily fluid flow rate.", "title": "total daily flow rate measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure flow rate." + ], + "examples": [ + { + "value": "Flow meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 83, "slot_uri": "GENEPIO:0100907", @@ -14763,10 +21079,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement value": { - "name": "instantaneous flow rate measurement value", + "instantaneous_flow_rate_measurement_value": { + "name": "instantaneous_flow_rate_measurement_value", "description": "The numerical value of a measured instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement value", + "comments": [ + "Provide the numerical value of the measured flow rate." + ], + "examples": [ + { + "value": "25" + } + ], "from_schema": "https://example.com/GRDI", "rank": 84, "slot_uri": "GENEPIO:0100908", @@ -14780,10 +21104,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement unit": { - "name": "instantaneous flow rate measurement unit", + "instantaneous_flow_rate_measurement_unit": { + "name": "instantaneous_flow_rate_measurement_unit", "description": "The units of a measured instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement unit", + "comments": [ + "Provide the units of the measured flow rate by selecting a value from the pick list." + ], + "examples": [ + { + "value": "cubic meter per hour (m^3/h)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 85, "slot_uri": "GENEPIO:0100909", @@ -14794,12 +21126,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "InstantaneousFlowRateMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "instantaneous flow rate measurement method": { - "name": "instantaneous flow rate measurement method", + "instantaneous_flow_rate_measurement_method": { + "name": "instantaneous_flow_rate_measurement_method", "description": "The process used to measure instantaneous fluid flow rate.", "title": "instantaneous flow rate measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure flow rate." + ], + "examples": [ + { + "value": "Flow meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 86, "slot_uri": "GENEPIO:0100910", @@ -14813,10 +21161,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "turbidity measurement value": { - "name": "turbidity measurement value", + "turbidity_measurement_value": { + "name": "turbidity_measurement_value", "description": "The numerical value of a measurement of turbidity.", "title": "turbidity measurement value", + "comments": [ + "Provide the numerical value of the measured turbidity." + ], + "examples": [ + { + "value": "0.02" + } + ], "from_schema": "https://example.com/GRDI", "rank": 87, "slot_uri": "GENEPIO:0100783", @@ -14831,10 +21187,18 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "turbidity measurement unit": { - "name": "turbidity measurement unit", + "turbidity_measurement_unit": { + "name": "turbidity_measurement_unit", "description": "The units of a measurement of turbidity.", "title": "turbidity measurement unit", + "comments": [ + "Provide the units of the measured turbidity by selecting a value from the pick list." + ], + "examples": [ + { + "value": "nephelometric turbidity unit (NTU)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 88, "slot_uri": "GENEPIO:0100914", @@ -14846,12 +21210,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "TurbidityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "turbidity measurement method": { - "name": "turbidity measurement method", + "turbidity_measurement_method": { + "name": "turbidity_measurement_method", "description": "The process used to measure turbidity.", "title": "turbidity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure turbidity." + ], + "examples": [ + { + "value": "Nephelometric method" + } + ], "from_schema": "https://example.com/GRDI", "rank": 89, "slot_uri": "GENEPIO:0101013", @@ -14865,13 +21245,21 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement value": { - "name": "dissolved oxygen measurement value", + "dissolved_oxygen_measurement_value": { + "name": "dissolved_oxygen_measurement_value", "description": "The numerical value of a measurement of dissolved oxygen.", "title": "dissolved oxygen measurement value", + "comments": [ + "Provide the numerical value of the measured dissolved oxygen." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 90, - "slot_uri": "GENEPIO:0100915", + "slot_uri": "GENEPIO:0000035", "alias": "dissolved_oxygen_measurement_value", "owner": "WastewaterAMR", "domain_of": [ @@ -14882,10 +21270,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement unit": { - "name": "dissolved oxygen measurement unit", + "dissolved_oxygen_measurement_unit": { + "name": "dissolved_oxygen_measurement_unit", "description": "The units of a measurement of dissolved oxygen.", "title": "dissolved oxygen measurement unit", + "comments": [ + "Provide the units of the measured dissolved oxygen by selecting a value from the pick list." + ], + "examples": [ + { + "value": "part per million (ppm)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 91, "slot_uri": "GENEPIO:0100784", @@ -14896,12 +21292,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "DissolvedOxygenMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "dissolved oxygen measurement method": { - "name": "dissolved oxygen measurement method", + "dissolved_oxygen_measurement_method": { + "name": "dissolved_oxygen_measurement_method", "description": "The method used to measure dissolved oxygen.", "title": "dissolved oxygen measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure dissolved oxygen." + ], + "examples": [ + { + "value": "Dissolved oxygen meter in vertical direction" + } + ], "from_schema": "https://example.com/GRDI", "rank": 92, "slot_uri": "GENEPIO:0100785", @@ -14915,14 +21327,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement value": { - "name": "oxygen reduction potential (ORP) measurement value", + "oxygen_reduction_potential_orp_measurement_value": { + "name": "oxygen_reduction_potential_orp_measurement_value", "description": "The numerical value of a measurement of oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement value", + "comments": [ + "Provide the numerical value of the measured oxygen reduction potential." + ], + "examples": [ + { + "value": "-50" + } + ], "from_schema": "https://example.com/GRDI", "rank": 93, - "slot_uri": "GENEPIO:0100917", - "alias": "oxygen_reduction_potential_(ORP)_measurement_value", + "slot_uri": "FIX:0000278", + "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14932,30 +21352,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement unit": { - "name": "oxygen reduction potential (ORP) measurement unit", + "oxygen_reduction_potential_orp_measurement_unit": { + "name": "oxygen_reduction_potential_orp_measurement_unit", "description": "The units of a measurement of oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement unit", + "comments": [ + "Provide the units of the measured oxygen reduction potential by selecting a value from the pick list." + ], + "examples": [ + { + "value": "milliVolt (mV)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 94, "slot_uri": "GENEPIO:0100786", - "alias": "oxygen_reduction_potential_(ORP)_measurement_unit", + "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "OxygenReductionPotentialOrpMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "oxygen reduction potential (ORP) measurement method": { - "name": "oxygen reduction potential (ORP) measurement method", + "oxygen_reduction_potential_orp_measurement_method": { + "name": "oxygen_reduction_potential_orp_measurement_method", "description": "The method used to measure oxygen reduction potential (ORP).", "title": "oxygen reduction potential (ORP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure oxygen reduction potential." + ], + "examples": [ + { + "value": "ORP sensor" + } + ], "from_schema": "https://example.com/GRDI", "rank": 95, "slot_uri": "GENEPIO:0100787", - "alias": "oxygen_reduction_potential_(ORP)_measurement_method", + "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14965,14 +21409,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement value": { - "name": "chemical oxygen demand (COD) measurement value", + "chemical_oxygen_demand_cod_measurement_value": { + "name": "chemical_oxygen_demand_cod_measurement_value", "description": "The measured value from a chemical oxygen demand (COD) test.", "title": "chemical oxygen demand (COD) measurement value", + "comments": [ + "Provide the numerical value of the COD test result." + ], + "examples": [ + { + "value": "26" + } + ], "from_schema": "https://example.com/GRDI", "rank": 96, "slot_uri": "GENEPIO:0100788", - "alias": "chemical_oxygen_demand_(COD)_measurement_value", + "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -14982,30 +21434,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement unit": { - "name": "chemical oxygen demand (COD) measurement unit", + "chemical_oxygen_demand_cod_measurement_unit": { + "name": "chemical_oxygen_demand_cod_measurement_unit", "description": "The units associated with a value from a chemical oxygen demand (COD) test.", "title": "chemical oxygen demand (COD) measurement unit", + "comments": [ + "Provide the units of the COD test result." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 97, "slot_uri": "GENEPIO:0100789", - "alias": "chemical_oxygen_demand_(COD)_measurement_unit", + "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "ChemicalOxygenDemandCodMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "chemical oxygen demand (COD) measurement method": { - "name": "chemical oxygen demand (COD) measurement method", + "chemical_oxygen_demand_cod_measurement_method": { + "name": "chemical_oxygen_demand_cod_measurement_method", "description": "The method used to measure chemical oxygen demand (COD).", "title": "chemical oxygen demand (COD) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure COD." + ], + "examples": [ + { + "value": "Hach LCK test kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 98, "slot_uri": "GENEPIO:0100790", - "alias": "chemical_oxygen_demand_(COD)_measurement_method", + "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15015,14 +21491,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement value": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement value", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "description": "The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement value", + "comments": [ + "Provide the numerical value of the measured CBOD." + ], + "examples": [ + { + "value": "20" + } + ], "from_schema": "https://example.com/GRDI", "rank": 99, "slot_uri": "GENEPIO:0100791", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_value", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15032,30 +21516,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement unit": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement unit", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "description": "The units of a measurement of carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement unit", + "comments": [ + "Provide the units of the measured CBOD by selecting a value from the pick list." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 100, "slot_uri": "GENEPIO:0100792", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "carbonaceous biochemical oxygen demand (CBOD) measurement method": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "description": "The method used to measure carbonaceous biochemical oxygen demand (CBOD).", "title": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure CBOD." + ], + "examples": [ + { + "value": "CBOD measurement by optical probe" + } + ], "from_schema": "https://example.com/GRDI", "rank": 101, "slot_uri": "GENEPIO:0100793", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_method", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15065,14 +21573,25 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement value": { - "name": "total suspended solids (TSS) measurement value", + "total_suspended_solids_tss_measurement_value": { + "name": "total_suspended_solids_tss_measurement_value", "description": "The numerical value from a total suspended solids (TSS) test.", "title": "total suspended solids (TSS) measurement value", + "comments": [ + "Provide the numerical value of the measured TSS." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], "rank": 102, "slot_uri": "GENEPIO:0100794", - "alias": "total_suspended_solids_(TSS)_measurement_value", + "alias": "total_suspended_solids_tss_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15082,30 +21601,57 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement unit": { - "name": "total suspended solids (TSS) measurement unit", + "total_suspended_solids_tss_measurement_unit": { + "name": "total_suspended_solids_tss_measurement_unit", "description": "The units associated with a value from a total suspended solids (TSS) test.", "title": "total suspended solids (TSS) measurement unit", + "comments": [ + "Provide the units of the measured TSS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], "rank": 103, "slot_uri": "GENEPIO:0100795", - "alias": "total_suspended_solids_(TSS)_measurement_unit", + "alias": "total_suspended_solids_tss_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalSuspendedSolidsTssMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total suspended solids (TSS) measurement method": { - "name": "total suspended solids (TSS) measurement method", + "total_suspended_solids_tss_measurement_method": { + "name": "total_suspended_solids_tss_measurement_method", "description": "The method used to measure total suspended solids (TSS).", "title": "total suspended solids (TSS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TSS." + ], + "examples": [ + { + "value": "Vacuum filter through a 2-micron filter, then oven-dried and weighed sample" + } + ], "from_schema": "https://example.com/GRDI", "rank": 104, "slot_uri": "GENEPIO:0100796", - "alias": "total_suspended_solids_(TSS)_measurement_method", + "alias": "total_suspended_solids_tss_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15115,14 +21661,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement value": { - "name": "total dissolved solids (TDS) measurement value", + "total_dissolved_solids_tds_measurement_value": { + "name": "total_dissolved_solids_tds_measurement_value", "description": "The numerical value from a total dissolved solids (TDS) test.", "title": "total dissolved solids (TDS) measurement value", + "comments": [ + "Provide the numerical value of the measured TDS." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 105, "slot_uri": "GENEPIO:0100797", - "alias": "total_dissolved_solids_(TDS)_measurement_value", + "alias": "total_dissolved_solids_tds_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15132,30 +21686,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement unit": { - "name": "total dissolved solids (TDS) measurement unit", + "total_dissolved_solids_tds_measurement_unit": { + "name": "total_dissolved_solids_tds_measurement_unit", "description": "The units associated with a value from a total dissolved solids (TDS) test.", "title": "total dissolved solids (TDS) measurement unit", + "comments": [ + "Provide the units of the measured TDS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 106, "slot_uri": "GENEPIO:0100798", - "alias": "total_dissolved_solids_(TDS)_measurement_unit", + "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalDissolvedSolidsTdsMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total dissolved solids (TDS) measurement method": { - "name": "total dissolved solids (TDS) measurement method", + "total_dissolved_solids_tds_measurement_method": { + "name": "total_dissolved_solids_tds_measurement_method", "description": "The method used to measure total dissolved solids (TDS).", "title": "total dissolved solids (TDS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TDS." + ], + "examples": [ + { + "value": "Subtract calculated TSS from calculated TS" + } + ], "from_schema": "https://example.com/GRDI", "rank": 107, "slot_uri": "GENEPIO:0100799", - "alias": "total_dissolved_solids_(TDS)_measurement_method", + "alias": "total_dissolved_solids_tds_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15165,14 +21743,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total solids (TS) measurement value": { - "name": "total solids (TS) measurement value", + "total_solids_ts_measurement_value": { + "name": "total_solids_ts_measurement_value", "description": "The numerical value from a total solids (TS) test.", "title": "total solids (TS) measurement value", + "comments": [ + "Provide the numerical value of the measured TS." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", "rank": 108, "slot_uri": "GENEPIO:0100800", - "alias": "total_solids_(TS)_measurement_value", + "alias": "total_solids_ts_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15182,30 +21768,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total solids (TS) measurement unit": { - "name": "total solids (TS) measurement unit", + "total_solids_ts_measurement_unit": { + "name": "total_solids_ts_measurement_unit", "description": "The units associated with a value from a total solids (TS) test.", "title": "total solids (TS) measurement unit", + "comments": [ + "Provide the units of the measured TS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 109, "slot_uri": "GENEPIO:0100801", - "alias": "total_solids_(TS)_measurement_unit", + "alias": "total_solids_ts_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalSolidsTsMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total solids (TS) measurement method": { - "name": "total solids (TS) measurement method", + "total_solids_ts_measurement_method": { + "name": "total_solids_ts_measurement_method", "description": "The method used to measure total solids (TS).", "title": "total solids (TS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TS." + ], + "examples": [ + { + "value": "Gravimetric method by oven drying, then weighing" + } + ], "from_schema": "https://example.com/GRDI", "rank": 110, "slot_uri": "GENEPIO:0100802", - "alias": "total_solids_(TS)_measurement_method", + "alias": "total_solids_ts_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15215,10 +21825,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "alkalinity measurement value": { - "name": "alkalinity measurement value", + "alkalinity_measurement_value": { + "name": "alkalinity_measurement_value", "description": "The numerical value of a measurement of alkalinity.", "title": "alkalinity measurement value", + "comments": [ + "Provide the numerical value of the measured alkalinity." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 111, "slot_uri": "GENEPIO:0100878", @@ -15232,10 +21850,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "alkalinity measurement unit": { - "name": "alkalinity measurement unit", + "alkalinity_measurement_unit": { + "name": "alkalinity_measurement_unit", "description": "The units of a measurement of alkalinity.", "title": "alkalinity measurement unit", + "comments": [ + "Provide the units of the measured alkalinity." + ], + "examples": [ + { + "value": "milligram per liter of calcium carbonate (mg/L CaCO3)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 112, "slot_uri": "GENEPIO:0100879", @@ -15246,12 +21872,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "AlkalinityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "alkalinity measurement method": { - "name": "alkalinity measurement method", + "alkalinity_measurement_method": { + "name": "alkalinity_measurement_method", "description": "The process used to measure alkalinity.", "title": "alkalinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure alkalinity." + ], + "examples": [ + { + "value": "Titration method" + } + ], "from_schema": "https://example.com/GRDI", "rank": 113, "slot_uri": "GENEPIO:0100880", @@ -15265,10 +21907,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "conductivity measurement value": { - "name": "conductivity measurement value", + "conductivity_measurement_value": { + "name": "conductivity_measurement_value", "description": "The numerical value of a measurement of conductivity.", "title": "conductivity measurement value", + "comments": [ + "Provide the numerical value of the measured conductivity." + ], + "examples": [ + { + "value": "1412" + } + ], "from_schema": "https://example.com/GRDI", "rank": 114, "slot_uri": "GENEPIO:0100916", @@ -15282,10 +21932,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "conductivity measurement unit": { - "name": "conductivity measurement unit", + "conductivity_measurement_unit": { + "name": "conductivity_measurement_unit", "description": "The units of a measurement of conductivity.", "title": "conductivity measurement unit", + "comments": [ + "Provide the units of the measured conductivity." + ], + "examples": [ + { + "value": "microSiemen per centimeter (μS/cm)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 115, "slot_uri": "GENEPIO:0100803", @@ -15296,12 +21954,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "ConductivityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "conductivity measurement method": { - "name": "conductivity measurement method", + "conductivity_measurement_method": { + "name": "conductivity_measurement_method", "description": "The method used to measure conductivity.", "title": "conductivity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure conductivity." + ], + "examples": [ + { + "value": "Conductivity electrode and meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 116, "slot_uri": "GENEPIO:0100804", @@ -15315,11 +21989,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "salinity measurement value": { - "name": "salinity measurement value", + "salinity_measurement_value": { + "name": "salinity_measurement_value", "description": "The numerical value of a measurement of salinity.", "title": "salinity measurement value", + "comments": [ + "Provide the numerical value of the measured salinity." + ], + "examples": [ + { + "value": "35" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], "rank": 117, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", @@ -15332,11 +22017,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "salinity measurement unit": { - "name": "salinity measurement unit", + "salinity_measurement_unit": { + "name": "salinity_measurement_unit", "description": "The units of a measurement of salinity.", "title": "salinity measurement unit", + "comments": [ + "Provide the units of the measured salinity." + ], + "examples": [ + { + "value": "practical salinity unit (PSU)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], "rank": 118, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", @@ -15346,12 +22042,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SalinityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "salinity measurement method": { - "name": "salinity measurement method", + "salinity_measurement_method": { + "name": "salinity_measurement_method", "description": "The method used to measure salinity.", "title": "salinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure salinity." + ], + "examples": [ + { + "value": "conductivity meter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 119, "slot_uri": "GENEPIO:0100807", @@ -15365,14 +22077,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement value": { - "name": "total nitrogen (TN) measurement value", + "total_nitrogen_tn_measurement_value": { + "name": "total_nitrogen_tn_measurement_value", "description": "The numerical value of a measurement of total nitrogen (TN).", "title": "total nitrogen (TN) measurement value", + "comments": [ + "Provide the numerical value of the measured TN." + ], + "examples": [ + { + "value": "120" + } + ], "from_schema": "https://example.com/GRDI", "rank": 120, "slot_uri": "GENEPIO:0100808", - "alias": "total_nitrogen_(TN)_measurement_value", + "alias": "total_nitrogen_tn_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15382,30 +22102,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement unit": { - "name": "total nitrogen (TN) measurement unit", + "total_nitrogen_tn_measurement_unit": { + "name": "total_nitrogen_tn_measurement_unit", "description": "The units of a measurement of total nitrogen (TN).", "title": "total nitrogen (TN) measurement unit", + "comments": [ + "Provide the units of the measured TN." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 121, "slot_uri": "GENEPIO:0100809", - "alias": "total_nitrogen_(TN)_measurement_unit", + "alias": "total_nitrogen_tn_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalNitrogenTnMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total nitrogen (TN) measurement method": { - "name": "total nitrogen (TN) measurement method", + "total_nitrogen_tn_measurement_method": { + "name": "total_nitrogen_tn_measurement_method", "description": "The method used to measure total nitrogen (TN).", "title": "total nitrogen (TN) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TN." + ], + "examples": [ + { + "value": "Hach total nitrogen spectrophotometric test" + } + ], "from_schema": "https://example.com/GRDI", "rank": 122, "slot_uri": "GENEPIO:0100810", - "alias": "total_nitrogen_(TN)_measurement_method", + "alias": "total_nitrogen_tn_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15415,14 +22159,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement value": { - "name": "total phosphorus (TP) measurement value", + "total_phosphorus_tp_measurement_value": { + "name": "total_phosphorus_tp_measurement_value", "description": "The numerical value of a measurement of total phosphorus (TP).", "title": "total phosphorus (TP) measurement value", + "comments": [ + "Provide the numerical value of the measured TP." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", "rank": 123, "slot_uri": "GENEPIO:0100811", - "alias": "total_phosphorus_(TP)_measurement_value", + "alias": "total_phosphorus_tp_measurement_value", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15432,30 +22184,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement unit": { - "name": "total phosphorus (TP) measurement unit", + "total_phosphorus_tp_measurement_unit": { + "name": "total_phosphorus_tp_measurement_unit", "description": "The units of a measurement of total phosphorus (TP).", "title": "total phosphorus (TP) measurement unit", + "comments": [ + "Provide the units of the measured TP." + ], + "examples": [ + { + "value": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 124, "slot_uri": "GENEPIO:0100812", - "alias": "total_phosphorus_(TP)_measurement_unit", + "alias": "total_phosphorus_tp_measurement_unit", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalPhosphorusTpMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total phosphorus (TP) measurement method": { - "name": "total phosphorus (TP) measurement method", + "total_phosphorus_tp_measurement_method": { + "name": "total_phosphorus_tp_measurement_method", "description": "The method used to measure total phosphorus (TP).", "title": "total phosphorus (TP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TP." + ], + "examples": [ + { + "value": "Merck phosphate spectrophotometric test kit" + } + ], "from_schema": "https://example.com/GRDI", "rank": 125, "slot_uri": "GENEPIO:0100813", - "alias": "total_phosphorus_(TP)_measurement_method", + "alias": "total_phosphorus_tp_measurement_method", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15465,10 +22241,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "fecal contamination indicator": { - "name": "fecal contamination indicator", + "fecal_contamination_indicator": { + "name": "fecal_contamination_indicator", "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", "title": "fecal contamination indicator", + "comments": [ + "If a fecal contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "crAssphage" + } + ], "from_schema": "https://example.com/GRDI", "rank": 126, "slot_uri": "GENEPIO:0100814", @@ -15480,12 +22264,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "FecalContaminationIndicatorMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination value": { - "name": "fecal contamination value", + "fecal_contamination_value": { + "name": "fecal_contamination_value", "description": "The numerical value of a measurement of fecal contamination.", "title": "fecal contamination value", + "comments": [ + "Provide the numerical value of the measured fecal contamination." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", "rank": 127, "slot_uri": "GENEPIO:0100815", @@ -15500,10 +22300,18 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "fecal contamination unit": { - "name": "fecal contamination unit", + "fecal_contamination_unit": { + "name": "fecal_contamination_unit", "description": "The units of a measurement of fecal contamination.", "title": "fecal contamination unit", + "comments": [ + "Provide the units of the measured fecal contamination." + ], + "examples": [ + { + "value": "cycle threshold (Ct) / quantification cycle (Cq)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 128, "slot_uri": "GENEPIO:0100816", @@ -15515,12 +22323,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "FecalContaminationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination method": { - "name": "fecal contamination method", + "fecal_contamination_method": { + "name": "fecal_contamination_method", "description": "The method used to measure fecal contamination.", "title": "fecal contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal contamination." + ], + "examples": [ + { + "value": "quantitative PCR assay" + } + ], "from_schema": "https://example.com/GRDI", "rank": 129, "slot_uri": "GENEPIO:0100817", @@ -15534,10 +22358,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "fecal coliform count value": { - "name": "fecal coliform count value", + "fecal_coliform_count_value": { + "name": "fecal_coliform_count_value", "description": "The numerical value of a measurement of fecal coliforms within a sample.", "title": "fecal coliform count value", + "comments": [ + "Provide the numerical value of the measured fecal coliforms." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 130, "slot_uri": "GENEPIO:0100818", @@ -15551,10 +22383,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "fecal coliform count unit": { - "name": "fecal coliform count unit", + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", "description": "The units of a measurement of fecal coliforms.", "title": "fecal coliform count unit", + "comments": [ + "Provide the units of the measured fecal coliforms." + ], + "examples": [ + { + "value": "most probable number per milliliter (MPN/mL)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 131, "slot_uri": "GENEPIO:0100819", @@ -15565,15 +22405,31 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" - }, - "fecal coliform count method": { - "name": "fecal coliform count method", - "description": "The method used to measure fecal coliforms.", - "title": "fecal coliform count method", - "from_schema": "https://example.com/GRDI", - "rank": 132, - "slot_uri": "GENEPIO:0100820", + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "FecalColiformCountUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", + "description": "The method used to measure fecal coliforms.", + "title": "fecal coliform count method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal coliforms." + ], + "examples": [ + { + "value": "MPN method via serial dilutions until lack of growth" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 132, + "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "WastewaterAMR", "domain_of": [ @@ -15584,10 +22440,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "urinary contamination indicator": { - "name": "urinary contamination indicator", + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", "title": "urinary contamination indicator", + "comments": [ + "If a urinary contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "urobilin" + } + ], "from_schema": "https://example.com/GRDI", "rank": 133, "slot_uri": "GENEPIO:0100837", @@ -15598,12 +22462,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "UrinaryContaminationIndicatorMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination value": { - "name": "urinary contamination value", + "urinary_contamination_value": { + "name": "urinary_contamination_value", "description": "The numerical value of a measurement of urinary contamination.", "title": "urinary contamination value", + "comments": [ + "Provide the numerical value of the measured urinary contamination." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", "rank": 134, "slot_uri": "GENEPIO:0100838", @@ -15617,10 +22497,18 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "urinary contamination unit": { - "name": "urinary contamination unit", + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", "description": "The units of a measurement of urinary contamination.", "title": "urinary contamination unit", + "comments": [ + "Provide the units of the measured urinary contamination." + ], + "examples": [ + { + "value": "nanograms per liter" + } + ], "from_schema": "https://example.com/GRDI", "rank": 135, "slot_uri": "GENEPIO:0100839", @@ -15631,12 +22519,28 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "UrinaryContaminationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination method": { - "name": "urinary contamination method", + "urinary_contamination_method": { + "name": "urinary_contamination_method", "description": "The method used to measure urinary contamination.", "title": "urinary contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure urinary contamination." + ], + "examples": [ + { + "value": "Urobilin Concentration Test" + } + ], "from_schema": "https://example.com/GRDI", "rank": 136, "slot_uri": "GENEPIO:0100840", @@ -15650,14 +22554,25 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "sample temperature value (at collection)": { - "name": "sample temperature value (at collection)", + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", "description": "The numerical value of a measurement of temperature of a sample at collection.", "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], "rank": 137, "slot_uri": "GENEPIO:0100821", - "alias": "sample_temperature_value_(at_collection)", + "alias": "sample_temperature_value_at_collection", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15667,30 +22582,57 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "sample temperature unit (at collection)": { - "name": "sample temperature unit (at collection)", + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", "description": "The units of a measurement of temperature of a sample at the time of collection.", "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], "rank": 138, "slot_uri": "GENEPIO:0100822", - "alias": "sample_temperature_unit_(at_collection)", + "alias": "sample_temperature_unit_at_collection", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SampleTemperatureUnitAtCollectionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample temperature value (when received)": { - "name": "sample temperature value (when received)", + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", "description": "The numerical value of a measurement of temperature of a sample upon receipt.", "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], "from_schema": "https://example.com/GRDI", "rank": 139, "slot_uri": "GENEPIO:0100823", - "alias": "sample_temperature_value_(when_received)", + "alias": "sample_temperature_value_when_received", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15700,30 +22642,56 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "sample temperature unit (when received)": { - "name": "sample temperature unit (when received)", + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", "description": "The units of a measurement of temperature of a sample at the time upon receipt.", "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", "rank": 140, "slot_uri": "GENEPIO:0100824", - "alias": "sample_temperature_unit_(when_received)", + "alias": "sample_temperature_unit_when_received", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SampleTemperatureUnitWhenReceivedMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sequencing" + ], "rank": 141, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", "owner": "WastewaterAMR", "domain_of": [ @@ -15732,12 +22700,29 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], "from_schema": "https://example.com/GRDI", "rank": 142, "slot_uri": "GENEPIO:0001446", @@ -15751,11 +22736,22 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", "title": "sequenced by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "GISAID:sequenced_by" + ], "rank": 143, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", @@ -15766,14 +22762,55 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 144, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 144, + "rank": 145, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "WastewaterAMR", @@ -15783,14 +22820,30 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 145, + "rank": 146, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_email", "owner": "WastewaterAMR", @@ -15800,14 +22853,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that submitted the sequence to a database.", "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 146, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sequenced_by" + ], + "rank": 147, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "WastewaterAMR", @@ -15817,14 +22889,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 147, + "exact_mappings": [ + "NCBI_SRA:sequence_submitter_contact_email" + ], + "rank": 148, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "WastewaterAMR", @@ -15835,14 +22926,33 @@ ], "slot_group": "Sequence information", "recommended": true, - "pattern": "^\\S+@\\S+\\.\\S+$" + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 148, + "rank": 149, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "WastewaterAMR", @@ -15854,14 +22964,25 @@ "slot_group": "Sequence information", "range": "date" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 149, + "exact_mappings": [ + "NCBI_SRA:library_ID" + ], + "rank": 150, "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", + "alias": "library_id", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -15871,14 +22992,24 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequencing platform": { - "name": "sequencing platform", + "sequencing_platform": { + "name": "sequencing_platform", "description": "The platform technology used to perform the sequencing.", "title": "sequencing platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 150, + "exact_mappings": [ + "NCBI_SRA:platform" + ], + "rank": 151, "slot_uri": "GENEPIO:0100473", - "multivalued": true, "alias": "sequencing_platform", "owner": "WastewaterAMR", "domain_of": [ @@ -15886,16 +23017,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information" - }, - "sequencing instrument": { - "name": "sequencing instrument", + "slot_group": "Sequence information", + "multivalued": true, + "any_of": [ + { + "range": "SequencingPlatformMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 151, + "exact_mappings": [ + "NCBI_SRA:instrument_model" + ], + "rank": 152, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", "owner": "WastewaterAMR", "domain_of": [ @@ -15904,14 +23054,34 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing assay type": { - "name": "sequencing assay type", + "sequencing_assay_type": { + "name": "sequencing_assay_type", "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", "title": "sequencing assay type", + "comments": [ + "Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 152, + "exact_mappings": [ + "NCBI_SRA:library_strategy" + ], + "rank": 153, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "WastewaterAMR", @@ -15921,14 +23091,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "SequencingAssayTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 153, + "exact_mappings": [ + "NCBI_SRA:library_preparation_kit" + ], + "rank": 154, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "WastewaterAMR", @@ -15940,12 +23129,20 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol or method used for sequencing.", "title": "sequencing protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 154, + "rank": 155, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "WastewaterAMR", @@ -15958,14 +23155,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "DNA fragment length": { - "name": "DNA fragment length", + "dna_fragment_length": { + "name": "dna_fragment_length", "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", "title": "DNA fragment length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 155, + "rank": 156, "slot_uri": "GENEPIO:0100843", - "alias": "DNA_fragment_length", + "alias": "dna_fragment_length", "owner": "WastewaterAMR", "domain_of": [ "WastewaterAMR", @@ -15974,14 +23179,24 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "hybrid selection method" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 156, + "exact_mappings": [ + "NCBI_SRA:library_selection" + ], + "rank": 157, "slot_uri": "GENEPIO:0100966", - "multivalued": true, "alias": "genomic_target_enrichment_method", "owner": "WastewaterAMR", "domain_of": [ @@ -15989,14 +23204,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "GenomicTargetEnrichmentMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", "title": "genomic target enrichment method details", + "comments": [ + "Provide details that are applicable to the method you used." + ], + "examples": [ + { + "value": "enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 157, + "rank": 158, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "WastewaterAMR", @@ -16007,12 +23239,23 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "quality control method name": { - "name": "quality control method name", + "quality_control_method_name": { + "name": "quality_control_method_name", "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 158, + "exact_mappings": [ + "NCBI_SRA:quality_control_method" + ], + "rank": 159, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "WastewaterAMR", @@ -16024,12 +23267,23 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_version": { + "name": "quality_control_method_version", "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 159, + "exact_mappings": [ + "NCBI_SRA:quality_control_method_version" + ], + "rank": 160, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "WastewaterAMR", @@ -16041,14 +23295,24 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_determination": { + "name": "quality_control_determination", "description": "The determination of a quality control assessment.", "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 160, + "exact_mappings": [ + "NCBI_SRA:quality_control_determination" + ], + "rank": 161, "slot_uri": "GENEPIO:0100559", - "multivalued": true, "alias": "quality_control_determination", "owner": "WastewaterAMR", "domain_of": [ @@ -16056,16 +23320,35 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlDeterminationMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "quality control issues": { - "name": "quality control issues", + "quality_control_issues": { + "name": "quality_control_issues", "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 161, + "exact_mappings": [ + "NCBI_SRA:quality_control_issues" + ], + "rank": 162, "slot_uri": "GENEPIO:0100560", - "multivalued": true, "alias": "quality_control_issues", "owner": "WastewaterAMR", "domain_of": [ @@ -16073,14 +23356,34 @@ "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlIssuesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "quality control details": { - "name": "quality control details", + "quality_control_details": { + "name": "quality_control_details", "description": "The details surrounding a low quality determination in a quality control assessment.", "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 162, + "exact_mappings": [ + "NCBI_SRA:quality_control_details" + ], + "rank": 163, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "WastewaterAMR", @@ -16092,12 +23395,23 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 163, + "exact_mappings": [ + "NCBI_SRA:raw_sequence_data_processing_method" + ], + "rank": 164, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "WastewaterAMR", @@ -16107,14 +23421,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 164, + "exact_mappings": [ + "NCBI_SRA:dehosting_method" + ], + "rank": 165, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "WastewaterAMR", @@ -16124,46 +23457,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence assembly software name": { - "name": "sequence assembly software name", - "description": "The name of the software used to assemble a sequence.", - "title": "sequence assembly software name", - "from_schema": "https://example.com/GRDI", - "rank": 165, - "slot_uri": "GENEPIO:0100825", - "alias": "sequence_assembly_software_name", - "owner": "WastewaterAMR", - "domain_of": [ - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." ], - "slot_group": "Bioinformatics and QC metrics" - }, - "sequence assembly software version": { - "name": "sequence assembly software version", - "description": "The version of the software used to assemble a sequence.", - "title": "sequence assembly software version", - "from_schema": "https://example.com/GRDI", - "rank": 166, - "slot_uri": "GENEPIO:0100826", - "alias": "sequence_assembly_software_version", - "owner": "WastewaterAMR", - "domain_of": [ - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "examples": [ + { + "value": "mpxvassembly.fasta" + } ], - "slot_group": "Bioinformatics and QC metrics" - }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth of coverage value", "from_schema": "https://example.com/GRDI", - "rank": 167, - "slot_uri": "GENEPIO:0001472", - "alias": "breadth_of_coverage_value", + "rank": 166, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -16171,16 +23490,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", + "comments": [ + "Provide the filepath of the genome sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 168, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", + "rank": 167, + "slot_uri": "GENEPIO:0101716", + "alias": "genome_sequence_file_path", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -16188,14 +23522,141 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth of coverage threshold", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 168, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], "from_schema": "https://example.com/GRDI", "rank": 169, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 170, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 171, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 172, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "WastewaterAMR", @@ -16207,12 +23668,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 170, + "rank": 173, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "WastewaterAMR", @@ -16224,12 +23693,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of total reads": { - "name": "number of total reads", + "number_of_total_reads": { + "name": "number_of_total_reads", "description": "The total number of non-unique reads generated by the sequencing process.", "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 171, + "rank": 174, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "WastewaterAMR", @@ -16241,12 +23718,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "number of unique reads": { - "name": "number of unique reads", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "description": "The number of unique reads generated by the sequencing process.", "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 172, + "rank": 175, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "WastewaterAMR", @@ -16258,14 +23743,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 173, + "rank": 176, "slot_uri": "GENEPIO:0100829", - "alias": "minimum_post_trimming_read_length", + "alias": "minimum_posttrimming_read_length", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -16275,12 +23768,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 174, + "rank": 177, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "WastewaterAMR", @@ -16292,12 +23793,20 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "read mapping software name": { - "name": "read mapping software name", + "read_mapping_software_name": { + "name": "read_mapping_software_name", "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 175, + "rank": 178, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "WastewaterAMR", @@ -16309,12 +23818,20 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "read mapping software version": { - "name": "read mapping software version", + "read_mapping_software_version": { + "name": "read_mapping_software_version", "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 176, + "rank": 179, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "WastewaterAMR", @@ -16326,12 +23843,20 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", "description": "The name of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 177, + "rank": 180, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "WastewaterAMR", @@ -16343,12 +23868,20 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", "description": "The version of the taxonomic reference database used to identify the organism.", "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 178, + "rank": 181, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "WastewaterAMR", @@ -16360,12 +23893,20 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", "description": "The filename of the report containing the results of a taxonomic analysis.", "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 179, + "rank": 182, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "WastewaterAMR", @@ -16376,12 +23917,20 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 180, + "rank": 183, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "WastewaterAMR", @@ -16392,12 +23941,20 @@ "slot_group": "Taxonomic identification information", "range": "date" }, - "read mapping criteria": { - "name": "read mapping criteria", + "read_mapping_criteria": { + "name": "read_mapping_criteria", "description": "A description of the criteria used to map reads to a reference sequence.", "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 181, + "rank": 184, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "WastewaterAMR", @@ -16408,14 +23965,22 @@ "slot_group": "Taxonomic identification information", "range": "WhitespaceMinimizedString" }, - "AMR analysis software name": { - "name": "AMR analysis software name", + "amr_analysis_software_name": { + "name": "amr_analysis_software_name", "description": "The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis.", "title": "AMR analysis software name", + "comments": [ + "Provide the name of the software used for AMR analysis." + ], + "examples": [ + { + "value": "Resistance Gene Identifier" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 182, + "rank": 185, "slot_uri": "GENEPIO:0101076", - "alias": "AMR_analysis_software_name", + "alias": "amr_analysis_software_name", "owner": "WastewaterAMR", "domain_of": [ "WastewaterAMR" @@ -16424,14 +23989,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR analysis software version": { - "name": "AMR analysis software version", + "amr_analysis_software_version": { + "name": "amr_analysis_software_version", "description": "The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis.", "title": "AMR analysis software version", + "comments": [ + "Provide the version number of the software used for AMR analysis." + ], + "examples": [ + { + "value": "6.0.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 183, + "rank": 186, "slot_uri": "GENEPIO:0101077", - "alias": "AMR_analysis_software_version", + "alias": "amr_analysis_software_version", "owner": "WastewaterAMR", "domain_of": [ "WastewaterAMR" @@ -16440,14 +24013,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR reference database name": { - "name": "AMR reference database name", + "amr_reference_database_name": { + "name": "amr_reference_database_name", "description": "Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis.", "title": "AMR reference database name", + "comments": [ + "Provide the name of the reference database used for AMR analysis." + ], + "examples": [ + { + "value": "Comprehensive Antibiotic Resistance Database (CARD)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 184, + "rank": 187, "slot_uri": "GENEPIO:0101078", - "alias": "AMR_reference_database_name", + "alias": "amr_reference_database_name", "owner": "WastewaterAMR", "domain_of": [ "WastewaterAMR" @@ -16456,14 +24037,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR reference database version": { - "name": "AMR reference database version", + "amr_reference_database_version": { + "name": "amr_reference_database_version", "description": "The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis.", "title": "AMR reference database version", + "comments": [ + "Provide the version number of the reference database used for AMR analysis." + ], + "examples": [ + { + "value": "3.2.9" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 185, + "rank": 188, "slot_uri": "GENEPIO:0101079", - "alias": "AMR_reference_database_version", + "alias": "amr_reference_database_version", "owner": "WastewaterAMR", "domain_of": [ "WastewaterAMR" @@ -16472,14 +24061,22 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "AMR analysis report filename": { - "name": "AMR analysis report filename", + "amr_analysis_report_filename": { + "name": "amr_analysis_report_filename", "description": "The filename of the report containing the results of an in silico antimicrobial resistance analysis.", "title": "AMR analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the AMR analysis." + ], + "examples": [ + { + "value": "WWAMR_report_Feb1_2024.doc" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 186, + "rank": 189, "slot_uri": "GENEPIO:0101080", - "alias": "AMR_analysis_report_filename", + "alias": "amr_analysis_report_filename", "owner": "WastewaterAMR", "domain_of": [ "WastewaterAMR" @@ -16488,22 +24085,17 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "gene name": { - "name": "gene name", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name", + "assay_target_name_1": { + "name": "assay_target_name_1", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 1", "comments": [ - "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" - ], - "examples": [ - { - "value": "gyrase A" - } + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." ], "from_schema": "https://example.com/GRDI", - "rank": 187, - "slot_uri": "GENEPIO:0100655", - "alias": "gene_name", + "rank": 190, + "slot_uri": "GENEPIO:0101206", + "alias": "assay_target_name_1", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -16516,34 +24108,116 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", - "description": "The binary value of the result from a diagnostic test.", - "title": "diagnostic target presence", - "from_schema": "https://example.com/GRDI", - "rank": 188, + "assay_target_details": { + "name": "assay_target_details", + "description": "Describe any details of the assay target.", + "title": "assay target details", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/GRDI", + "rank": 191, + "slot_uri": "GENEPIO:0102040", + "alias": "assay_target_details", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "gene_symbol_1": { + "name": "gene_symbol_1", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 1", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 192, + "slot_uri": "GENEPIO:0102041", + "alias": "gene_symbol_1", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 1", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_known_present" + ], + "rank": 193, "slot_uri": "GENEPIO:0100962", - "alias": "diagnostic_target_presence", + "alias": "diagnostic_target_presence_1", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", "description": "The value of the result from a diagnostic test.", - "title": "diagnostic measurement value", + "title": "diagnostic measurement value 1", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 189, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc" + ], + "rank": 194, "slot_uri": "GENEPIO:0100963", - "alias": "diagnostic_measurement_value", + "alias": "diagnostic_measurement_value_1", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", @@ -16553,425 +24227,818 @@ "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", "description": "The unit of the result from a diagnostic test.", - "title": "diagnostic measurement unit", + "title": "diagnostic measurement unit 1", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 190, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc_unit" + ], + "rank": 195, "slot_uri": "GENEPIO:0100964", - "alias": "diagnostic_measurement_unit", + "alias": "diagnostic_measurement_unit_1", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", "description": "The method by which a diagnostic result was determined.", - "title": "diagnostic measurement method", + "title": "diagnostic measurement method 1", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 191, + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_protocol" + ], + "rank": 196, "slot_uri": "GENEPIO:0100965", - "alias": "diagnostic_measurement_method", + "alias": "diagnostic_measurement_method_1", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", + "assay_target_name_2": { + "name": "assay_target_name_2", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 2", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], "from_schema": "https://example.com/GRDI", - "rank": 192, - "slot_uri": "GENEPIO:0001517", - "alias": "authors", + "rank": 197, + "alias": "assay_target_name_2", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Contributor acknowledgement", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", + "assay_target_details_2": { + "name": "assay_target_details_2", + "description": "Describe any details of the assay target.", + "title": "assay target details 2", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/GRDI", - "rank": 193, - "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "rank": 198, + "alias": "assay_target_details_2", "owner": "WastewaterAMR", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Contributor acknowledgement", - "range": "Provenance" - } - } - }, - "WastewaterPathogenAgnostic": { - "name": "WastewaterPathogenAgnostic", - "description": "Specification for Wastewater Pathogen Agnostic biosample data gathering", - "from_schema": "https://example.com/GRDI", - "is_a": "dh_interface", - "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "rank": 1, - "slot_group": "Database identifiers" - }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", - "rank": 2, - "slot_group": "Database identifiers" - }, - "pooled sample ID": { - "name": "pooled sample ID", - "rank": 3, - "slot_group": "Database identifiers" - }, - "metagenome-assembled genome (MAG) ID": { - "name": "metagenome-assembled genome (MAG) ID", - "rank": 4, - "slot_group": "Database identifiers" - }, - "specimen collector project ID": { - "name": "specimen collector project ID", - "rank": 5, - "slot_group": "Database identifiers" - }, - "BioProject accession": { - "name": "BioProject accession", - "rank": 6, - "slot_group": "Database identifiers" - }, - "BioSample accession": { - "name": "BioSample accession", - "rank": 7, - "slot_group": "Database identifiers" - }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", - "rank": 8, - "slot_group": "Database identifiers" - }, - "SRA accession": { - "name": "SRA accession", - "rank": 9, - "slot_group": "Database identifiers" - }, - "GISAID accession": { - "name": "GISAID accession", - "rank": 10, - "slot_group": "Database identifiers" - }, - "GISAID virus name": { - "name": "GISAID virus name", - "rank": 11, - "slot_group": "Database identifiers" - }, - "ENA accession": { - "name": "ENA accession", - "rank": 12, - "slot_group": "Database identifiers" - }, - "DRA accession": { - "name": "DRA accession", - "rank": 13, - "slot_group": "Database identifiers" - }, - "GSA accession": { - "name": "GSA accession", - "rank": 14, - "slot_group": "Database identifiers" - }, - "Enterobase accession": { - "name": "Enterobase accession", - "rank": 15, - "slot_group": "Database identifiers" - }, - "sampling site ID": { - "name": "sampling site ID", - "rank": 16, - "slot_group": "Database identifiers" - }, - "sampling event ID": { - "name": "sampling event ID", - "rank": 17, - "slot_group": "Database identifiers" - }, - "sample collection data steward name": { - "name": "sample collection data steward name", - "rank": 18, - "slot_group": "Sample collection and processing" - }, - "sample collected by": { - "name": "sample collected by", - "rank": 19, - "slot_group": "Sample collection and processing" - }, - "sample collector contact email": { - "name": "sample collector contact email", - "rank": 20, - "slot_group": "Sample collection and processing" - }, - "geo loc name (country)": { - "name": "geo loc name (country)", - "rank": 21, - "slot_group": "Sample collection and processing" - }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", - "rank": 22, - "slot_group": "Sample collection and processing" - }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", - "rank": 23, - "slot_group": "Sample collection and processing" - }, - "geo loc name (city)": { - "name": "geo loc name (city)", - "rank": 24, - "slot_group": "Sample collection and processing" - }, - "geo loc name (site)": { - "name": "geo loc name (site)", - "rank": 25, - "slot_group": "Sample collection and processing" - }, - "geo loc latitude": { - "name": "geo loc latitude", - "rank": 26, - "slot_group": "Sample collection and processing" - }, - "geo loc longitude": { - "name": "geo loc longitude", - "rank": 27, - "slot_group": "Sample collection and processing" - }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", - "rank": 28, - "slot_group": "Sample collection and processing" - }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", - "rank": 29, - "slot_group": "Sample collection and processing" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "organism": { - "name": "organism", + "gene_symbol_2": { + "name": "gene_symbol_2", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 2", "comments": [ - "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" ], "examples": [ { - "value": "Vibrio cholerae" + "value": "gyrase A" } ], - "rank": 30, - "slot_group": "Sample collection and processing", - "required": true, + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_gene" + ], + "rank": 199, + "alias": "gene_symbol_2", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", - "rank": 31, - "slot_group": "Sample collection and processing" - }, - "scale of sampling": { - "name": "scale of sampling", - "rank": 32, - "slot_group": "Sample collection and processing" + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 2", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_known_present" + ], + "rank": 200, + "alias": "diagnostic_target_presence_2", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", - "rank": 33, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 2", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc" + ], + "rank": 201, + "alias": "diagnostic_measurement_value_2", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", - "rank": 34, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 2", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc_unit" + ], + "rank": 202, + "alias": "diagnostic_measurement_unit_2", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection end date": { - "name": "sample collection end date", - "rank": 35, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 2", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 203, + "alias": "diagnostic_measurement_method_2", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample processing date": { - "name": "sample processing date", - "rank": 36, - "slot_group": "Sample collection and processing" + "assay_target_name_3": { + "name": "assay_target_name_3", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 3", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], + "from_schema": "https://example.com/GRDI", + "rank": 204, + "alias": "assay_target_name_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample collection start time": { - "name": "sample collection start time", - "rank": 37, - "slot_group": "Sample collection and processing" + "assay_target_details_3": { + "name": "assay_target_details_3", + "description": "Describe any details of the assay target.", + "title": "assay target details 3", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], + "from_schema": "https://example.com/GRDI", + "rank": 205, + "alias": "assay_target_details_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample collection end time": { - "name": "sample collection end time", - "rank": 38, - "slot_group": "Sample collection and processing" + "gene_symbol_3": { + "name": "gene_symbol_3", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 3", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 206, + "alias": "gene_symbol_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time of day": { - "name": "sample collection time of day", - "rank": 39, - "slot_group": "Sample collection and processing" + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 3", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 207, + "alias": "diagnostic_target_presence_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection time duration value": { - "name": "sample collection time duration value", - "rank": 40, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 3", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 208, + "alias": "diagnostic_measurement_value_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", - "rank": 41, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 3", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 209, + "alias": "diagnostic_measurement_unit_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling activity": { - "name": "presampling activity", - "rank": 42, - "slot_group": "Sample collection and processing" + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 3", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 210, + "alias": "diagnostic_measurement_method_3", + "owner": "WastewaterAMR", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + } + } + }, + "WastewaterPathogenAgnostic": { + "name": "WastewaterPathogenAgnostic", + "annotations": { + "version": { + "tag": "version", + "value": "3.1.1" + } + }, + "description": "Specification for Wastewater Pathogen Agnostic biosample data gathering", + "from_schema": "https://example.com/GRDI", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" }, - "presampling activity details": { - "name": "presampling activity details", - "rank": 43, - "slot_group": "Sample collection and processing" + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" }, - "sample volume measurement value": { - "name": "sample volume measurement value", - "rank": 44, - "slot_group": "Sample collection and processing" + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" }, - "sample volume measurement unit": { - "name": "sample volume measurement unit", - "rank": 45, - "slot_group": "Sample collection and processing" + "metagenomeassembled_genome_mag_id": { + "name": "metagenomeassembled_genome_mag_id", + "rank": 4, + "slot_group": "Database identifiers" }, - "sample storage method": { - "name": "sample storage method", - "rank": 46, - "slot_group": "Sample collection and processing" + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", + "rank": 5, + "slot_group": "Database identifiers" }, - "sample storage medium": { - "name": "sample storage medium", - "rank": 47, - "slot_group": "Sample collection and processing" + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" }, - "sample storage duration value": { - "name": "sample storage duration value", - "rank": 48, - "slot_group": "Sample collection and processing" + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" }, - "sample storage duration unit": { - "name": "sample storage duration unit", - "rank": 49, - "slot_group": "Sample collection and processing" + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" }, - "specimen processing": { - "name": "specimen processing", - "rank": 50, + "enterobase_accession": { + "name": "enterobase_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 10, + "slot_group": "Database identifiers" + }, + "gisaid_accession": { + "name": "gisaid_accession", + "rank": 11, + "slot_group": "Database identifiers" + }, + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "rank": 12, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 13, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 14, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 17, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "rank": 18, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 19, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 20, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 21, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 22, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 23, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_site": { + "name": "geo_loc_name_site", + "rank": 24, + "slot_group": "Sample collection and processing" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "rank": 25, + "slot_group": "Sample collection and processing" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "rank": 26, + "slot_group": "Sample collection and processing" + }, + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", + "rank": 27, + "slot_group": "Sample collection and processing" + }, + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", + "rank": 28, + "slot_group": "Sample collection and processing" + }, + "organism": { + "name": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "rank": 29, + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "rank": 30, + "slot_group": "Sample collection and processing" + }, + "scale_of_sampling": { + "name": "scale_of_sampling", + "rank": 31, + "slot_group": "Sample collection and processing" + }, + "sample_received_date": { + "name": "sample_received_date", + "rank": 32, + "slot_group": "Sample collection and processing" + }, + "sample_collection_start_date": { + "name": "sample_collection_start_date", + "rank": 33, + "slot_group": "Sample collection and processing" + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "rank": 34, + "slot_group": "Sample collection and processing" + }, + "sample_processing_date": { + "name": "sample_processing_date", + "rank": 35, + "slot_group": "Sample collection and processing" + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "rank": 36, + "slot_group": "Sample collection and processing" + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "rank": 37, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "rank": 38, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "rank": 39, + "slot_group": "Sample collection and processing" + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "rank": 40, + "slot_group": "Sample collection and processing" + }, + "presampling_activity": { + "name": "presampling_activity", + "rank": 41, + "slot_group": "Sample collection and processing" + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "rank": 42, + "slot_group": "Sample collection and processing" + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "rank": 43, + "slot_group": "Sample collection and processing" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "rank": 44, + "slot_group": "Sample collection and processing" + }, + "sample_storage_method": { + "name": "sample_storage_method", + "rank": 45, + "slot_group": "Sample collection and processing" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "rank": 46, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "rank": 47, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "rank": 48, "slot_group": "Sample collection and processing" }, - 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"urinary contamination method": { - "name": "urinary contamination method", + "urinary_contamination_method": { + "name": "urinary_contamination_method", "rank": 150, "slot_group": "Environmental conditions and measurements" }, - "sample temperature value (at collection)": { - "name": "sample temperature value (at collection)", + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", "rank": 151, "slot_group": "Environmental conditions and measurements" }, - "sample temperature unit (at collection)": { - "name": "sample temperature unit (at collection)", + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", "rank": 152, "slot_group": "Environmental conditions and measurements" }, - "sample temperature value (when received)": { - "name": "sample temperature value (when received)", + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", "rank": 153, "slot_group": "Environmental conditions and measurements" }, - "sample temperature unit (when received)": { - "name": "sample temperature unit (when received)", + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", "rank": 154, "slot_group": "Environmental conditions and measurements" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 155, "slot_group": "Sequence information" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 156, "slot_group": "Sequence information" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "rank": 157, "slot_group": "Sequence information" }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", "rank": 158, "slot_group": "Sequence information" }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "rank": 159, "slot_group": "Sequence information" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "rank": 160, "slot_group": "Sequence information" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 161, "slot_group": "Sequence information" }, - "sequencing date": { - "name": "sequencing date", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "rank": 162, "slot_group": "Sequence information" }, - "library ID": { - "name": "library ID", + "sequencing_date": { + "name": "sequencing_date", "rank": 163, "slot_group": "Sequence information" }, - "sequencing platform": { - "name": "sequencing platform", + "library_id": { + "name": "library_id", "rank": 164, "slot_group": "Sequence information" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_platform": { + "name": "sequencing_platform", "rank": 165, "slot_group": "Sequence information" }, - "sequencing assay type": { - "name": "sequencing assay type", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 166, "slot_group": "Sequence information" }, - "library preparation kit": { - "name": "library preparation kit", + "sequencing_assay_type": { + "name": "sequencing_assay_type", "rank": 167, "slot_group": "Sequence information" }, - "sequencing protocol": { - "name": "sequencing protocol", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 168, "slot_group": "Sequence information" }, - "DNA fragment length": { - "name": "DNA fragment length", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 169, "slot_group": "Sequence information" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", + "dna_fragment_length": { + "name": "dna_fragment_length", "rank": 170, "slot_group": "Sequence information" }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", "rank": 171, "slot_group": "Sequence information" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", "rank": 172, "slot_group": "Sequence information" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 173, "slot_group": "Sequence information" }, - "quality control method name": { - "name": "quality control method name", + "amplicon_size": { + "name": "amplicon_size", "rank": 174, - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Sequence information" }, - "quality control method version": { - "name": "quality control method version", + "quality_control_method_name": { + "name": "quality_control_method_name", "rank": 175, "slot_group": "Bioinformatics and QC metrics" }, - "quality control determination": { - "name": "quality control determination", + "quality_control_method_version": { + "name": "quality_control_method_version", "rank": 176, "slot_group": "Bioinformatics and QC metrics" }, - "quality control issues": { - "name": "quality control issues", + "quality_control_determination": { + "name": "quality_control_determination", "rank": 177, "slot_group": "Bioinformatics and QC metrics" }, - "quality control details": { - "name": "quality control details", + "quality_control_issues": { + "name": "quality_control_issues", "rank": 178, "slot_group": "Bioinformatics and QC metrics" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "quality_control_details": { + "name": "quality_control_details", "rank": 179, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 180, "slot_group": "Bioinformatics and QC metrics" }, - "sequence assembly software name": { - "name": "sequence assembly software name", + "dehosting_method": { + "name": "dehosting_method", "rank": 181, "slot_group": "Bioinformatics and QC metrics" }, - "sequence assembly software version": { - "name": "sequence assembly software version", + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", "rank": 182, "slot_group": "Bioinformatics and QC metrics" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", "rank": 183, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage value": { - "name": "depth of coverage value", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", "rank": 184, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", "rank": 185, "slot_group": "Bioinformatics and QC metrics" }, - "genome completeness": { - "name": "genome completeness", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 186, "slot_group": "Bioinformatics and QC metrics" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 187, "slot_group": "Bioinformatics and QC metrics" }, - "number of total reads": { - "name": "number of total reads", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 188, "slot_group": "Bioinformatics and QC metrics" }, - "number of unique reads": { - "name": "number of unique reads", + "genome_completeness": { + "name": "genome_completeness", "rank": 189, "slot_group": "Bioinformatics and QC metrics" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 190, "slot_group": "Bioinformatics and QC metrics" }, - "number of contigs": { - "name": "number of contigs", + "number_of_total_reads": { + "name": "number_of_total_reads", "rank": 191, "slot_group": "Bioinformatics and QC metrics" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", + "number_of_unique_reads": { + "name": "number_of_unique_reads", "rank": 192, "slot_group": "Bioinformatics and QC metrics" }, - "N50": { - "name": "N50", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", "rank": 193, "slot_group": "Bioinformatics and QC metrics" }, - "percent read contamination": { - "name": "percent read contamination", + "number_of_contigs": { + "name": "number_of_contigs", "rank": 194, "slot_group": "Bioinformatics and QC metrics" }, - "sequence assembly length": { - "name": "sequence assembly length", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", "rank": 195, "slot_group": "Bioinformatics and QC metrics" }, - "reference genome accession": { - "name": "reference genome accession", + "n50": { + "name": "n50", "rank": 196, "slot_group": "Bioinformatics and QC metrics" }, - "deduplication method": { - "name": "deduplication method", + "percent_read_contamination": { + "name": "percent_read_contamination", "rank": 197, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "sequence_assembly_length": { + "name": "sequence_assembly_length", "rank": 198, "slot_group": "Bioinformatics and QC metrics" }, - "read mapping software name": { - "name": "read mapping software name", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 199, + "slot_group": "Bioinformatics and QC metrics" + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 200, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 201, + "slot_group": "Bioinformatics and QC metrics" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "rank": 202, "slot_group": "Taxonomic identification information", "required": true }, - "read mapping software version": { - "name": "read mapping software version", - "rank": 200, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "rank": 203, "slot_group": "Taxonomic identification information", "required": true }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", - "rank": 201, - "slot_group": "Taxonomic identification information" + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "rank": 204, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "rank": 205, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "rank": 206, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "rank": 207, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "rank": 208, + "slot_group": "Taxonomic identification information" + }, + "assay_target_name_1": { + "name": "assay_target_name_1", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details": { + "name": "assay_target_details", + "rank": 210, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_1": { + "name": "gene_symbol_1", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "rank": 211, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", + "rank": 212, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", + "rank": 213, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", + "rank": 214, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", + "rank": 215, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_name_2": { + "name": "assay_target_name_2", + "rank": 216, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details_2": { + "name": "assay_target_details_2", + "rank": 217, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_2": { + "name": "gene_symbol_2", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "rank": 218, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "rank": 219, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "rank": 220, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "rank": 221, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "rank": 222, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_name_3": { + "name": "assay_target_name_3", + "rank": 223, + "slot_group": "Pathogen diagnostic testing" + }, + "assay_target_details_3": { + "name": "assay_target_details_3", + "rank": 224, + "slot_group": "Pathogen diagnostic testing" + }, + "gene_symbol_3": { + "name": "gene_symbol_3", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "rank": 225, + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", + "rank": 226, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", + "rank": 227, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", + "rank": 228, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", + "rank": 229, + "slot_group": "Pathogen diagnostic testing" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sample_name", + "NCBI_SRA:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen collector subsample ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_id" + ], + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled sample ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "metagenomeassembled_genome_mag_id": { + "name": "metagenomeassembled_genome_mag_id", + "description": "The user-defined identifier assigned to a genome reconstructed from metagenomic data.", + "title": "metagenome-assembled genome (MAG) ID", + "comments": [ + "Store the MAG ID." + ], + "examples": [ + { + "value": "XYZ1234.1" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 4, + "slot_uri": "GENEPIO:0100753", + "alias": "metagenomeassembled_genome_mag_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "specimen_collector_project_id": { + "name": "specimen_collector_project_id", + "description": "The user-defined project name assigned to a sequencing project.", + "title": "specimen collector project ID", + "comments": [ + "If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here." + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:project_name" + ], + "rank": 5, + "slot_uri": "GENEPIO:0100918", + "alias": "specimen_collector_project_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMEA00000002, SAMD00000001" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "enterobase_accession": { + "name": "enterobase_accession", + "description": "The identifier assigned to a sequence in Enterobase archives.", + "title": "Enterobase accession", + "comments": [ + "Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism." + ], + "examples": [ + { + "value": "SAL_AA0019AA_ST" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 9, + "slot_uri": "GENEPIO:0100759", + "alias": "enterobase_accession", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 10, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "gisaid_accession": { + "name": "gisaid_accession", + "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", + "title": "GISAID accession", + "comments": [ + "Store the accession assigned to the submitted sequence. GISAID accessions start with EPI." + ], + "examples": [ + { + "value": "EPI_ISL_402131" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 11, + "slot_uri": "GENEPIO:0001147", + "alias": "gisaid_accession", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "gisaid_virus_name": { + "name": "gisaid_virus_name", + "description": "The user-defined GISAID virus name assigned to the sequence.", + "title": "GISAID virus name", + "comments": [ + "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\"." + ], + "examples": [ + { + "value": "hCoV-19/Canada/prov_rona_99/2020" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 12, + "slot_uri": "GENEPIO:0100282", + "alias": "gisaid_virus_name", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling site ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_site_id" + ], + "rank": 13, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling event ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 14, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample collection data steward name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 15, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by_laboratory_name": { + "name": "sample_collected_by_laboratory_name", + "description": "The specific laboratory affiliation of the sample collector.", + "title": "sample collected by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 16, + "slot_uri": "GENEPIO:0100428", + "alias": "sample_collected_by_laboratory_name", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", - "rank": 202, - "slot_group": "Taxonomic identification information" + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample collected by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/GRDI", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collected_by" + ], + "rank": 17, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", - "rank": 203, - "slot_group": "Taxonomic identification information" + "sample_collector_contact_name": { + "name": "sample_collector_contact_name", + "description": "The name or job title of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 18, + "slot_uri": "GENEPIO:0100432", + "alias": "sample_collector_contact_name", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", - "rank": 204, - "slot_group": "Taxonomic identification information" + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 19, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" }, - "read mapping criteria": { - "name": "read mapping criteria", - "rank": 205, - "slot_group": "Taxonomic identification information" + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo loc name (country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 20, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "gene name": { - "name": "gene name", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo loc name (state/province/territory)", "comments": [ - "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" ], "examples": [ { - "value": "gyrase A" + "value": "Western Cape" } ], - "rank": 206, - "slot_group": "Pathogen diagnostic testing", + "from_schema": "https://example.com/GRDI", + "rank": 21, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", - "rank": 207, - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", - "rank": 208, - "slot_group": "Pathogen diagnostic testing" - }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", - "rank": 209, - "slot_group": "Pathogen diagnostic testing" + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo loc name (county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 22, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", - "rank": 210, - "slot_group": "Pathogen diagnostic testing" + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo loc name (city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 23, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "authors": { - "name": "authors", - "rank": 211, - "slot_group": "Contributor acknowledgement" + "geo_loc_name_site": { + "name": "geo_loc_name_site", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo loc name (site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/GRDI", + "rank": 24, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site", + "owner": "WastewaterPathogenAgnostic", + "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", + "WastewaterPathogenAgnostic" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "rank": 212, - "slot_group": "Contributor acknowledgement" - } - }, - "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "The user-defined name for the sample.", - "title": "specimen collector sample ID", + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo loc latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 1, - "slot_uri": "GENEPIO:0001123", - "identifier": true, - "alias": "specimen_collector_sample_ID", + "rank": 25, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "required": true + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" }, - "specimen collector subsample ID": { - "name": "specimen collector subsample ID", - "description": "The user-defined identifier assigned to a portion of the original sample.", - "title": "specimen collector subsample ID", + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo loc longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 2, - "slot_uri": "GENEPIO:0100752", - "alias": "specimen_collector_subsample_ID", + "rank": 26, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", + "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "pooled sample ID": { - "name": "pooled sample ID", - "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", - "title": "pooled sample ID", + "watershed_shapefile_availability": { + "name": "watershed_shapefile_availability", + "description": "The availability status of a shapefile descriping the catchment contributing to a watershed.", + "title": "watershed shapefile availability", + "comments": [ + "Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request." + ], + "examples": [ + { + "value": "watershed shapefile available" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 3, - "slot_uri": "GENEPIO:0100996", - "alias": "pooled_sample_ID", + "rank": 27, + "slot_uri": "GENEPIO:0100919", + "alias": "watershed_shapefile_availability", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WatershedShapefileAvailabilityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "metagenome-assembled genome (MAG) ID": { - "name": "metagenome-assembled genome (MAG) ID", - "description": "The user-defined identifier assigned to a genome reconstructed from metagenomic data.", - "title": "metagenome-assembled genome (MAG) ID", + "watershed_shapefile_filename": { + "name": "watershed_shapefile_filename", + "description": "The name of the watershed shapefile.", + "title": "watershed shapefile filename", + "comments": [ + "Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas." + ], + "examples": [ + { + "value": "siteAD17.shp, siteAD17.kml" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 4, - "slot_uri": "GENEPIO:0100753", - "alias": "metagenome_assembled_genome_(MAG)_ID", + "rank": 28, + "slot_uri": "GENEPIO:0100920", + "alias": "watershed_shapefile_filename", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", + "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "specimen collector project ID": { - "name": "specimen collector project ID", - "description": "The user-defined project name assigned to a sequencing project.", - "title": "specimen collector project ID", + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 5, - "slot_uri": "GENEPIO:0100918", - "alias": "specimen_collector_project_ID", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1" + ], + "rank": 29, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString" + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "BioProject accession": { - "name": "BioProject accession", - "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", - "title": "BioProject accession", + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 6, - "slot_uri": "GENEPIO:0001136", - "alias": "BioProject_accession", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], + "rank": 30, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "BioSample accession": { - "name": "BioSample accession", - "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", - "title": "BioSample accession", + "scale_of_sampling": { + "name": "scale_of_sampling", + "description": "The range of locations or entities sampled expressed in general terms.", + "title": "scale of sampling", + "comments": [ + "Provide the scale of wastewater sampling by selecting a value from the picklist." + ], + "examples": [ + { + "value": "Community-level surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 7, - "slot_uri": "GENEPIO:0001139", - "alias": "BioSample_accession", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling" + ], + "rank": 31, + "slot_uri": "GENEPIO:0100877", + "alias": "scale_of_sampling", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", + "slot_group": "Sample collection and processing", "recommended": true, - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "any_of": [ + { + "range": "ScaleOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "GenBank accession (versioned)": { - "name": "GenBank accession (versioned)", - "description": "The versioned identifier assigned to an assembly or consensus sequence in GenBank archives.", - "title": "GenBank accession (versioned)", + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 8, - "slot_uri": "GENEPIO:0100754", - "alias": "GenBank_accession_(versioned)", + "rank": 32, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "SRA accession": { - "name": "SRA accession", - "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", - "title": "SRA accession", + "sample_collection_start_date": { + "name": "sample_collection_start_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample collection start date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 9, - "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "rank": 33, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_start_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "GISAID accession": { - "name": "GISAID accession", - "description": "The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives.", - "title": "GISAID accession", + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample collection end date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 10, - "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "rank": 34, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "GISAID virus name": { - "name": "GISAID virus name", - "description": "The user-defined GISAID virus name assigned to the sequence.", - "title": "GISAID virus name", + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 11, - "slot_uri": "GENEPIO:0100282", - "alias": "GISAID_virus_name", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "ENA accession": { - "name": "ENA accession", - "description": "The identifier assigned to a sequence in the European Nucleotide Archive (ENA).", - "title": "ENA accession", + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample collection start time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 12, - "slot_uri": "GENEPIO:0100755", - "alias": "ENA_accession", + "rank": 36, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "DRA accession": { - "name": "DRA accession", - "description": "The identifier assigned to a sequence in DNA Data Bank of Japan (DDBJ) sequence read archives.", - "title": "DRA accession", + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample collection end time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 13, - "slot_uri": "GENEPIO:0100757", - "alias": "DRA_accession", + "rank": 37, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "NullValueMenu" + } + ] }, - "GSA accession": { - "name": "GSA accession", - "description": "The identifier assigned to a BioSample in GSA (Genome Sequence Archive) archives.", - "title": "GSA accession", + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample collection time of day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 14, - "slot_uri": "GENEPIO:0100758", - "alias": "GSA_accession", + "rank": 38, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleCollectionTimeOfDayMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "Enterobase accession": { - "name": "Enterobase accession", - "description": "The identifier assigned to a sequence in Enterobase archives.", - "title": "Enterobase accession", + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample collection time duration value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 15, - "slot_uri": "GENEPIO:0100759", - "alias": "Enterobase_accession", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], + "rank": 39, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "pattern": "{UPPER_CASE}", - "structured_pattern": { - "syntax": "{UPPER_CASE}", - "interpolated": true, - "partial_match": false - } + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sampling site ID": { - "name": "sampling site ID", - "description": "The user-defined identifier assigned to a specific location from which samples are taken.", - "title": "sampling site ID", + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample collection time duration unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 16, - "slot_uri": "GENEPIO:0100760", - "alias": "sampling_site_ID", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration" + ], + "rank": 40, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "SampleCollectionDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sampling event ID": { - "name": "sampling event ID", - "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", - "title": "sampling event ID", + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 17, - "slot_uri": "GENEPIO:0100761", - "alias": "sampling_event_ID", + "rank": 41, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Database identifiers", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "PresamplingActivityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection data steward name": { - "name": "sample collection data steward name", - "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", - "title": "sample collection data steward name", + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling activity details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 18, - "slot_uri": "GENEPIO:0100762", - "alias": "sample_collection_data_steward_name", + "rank": 42, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18093,16 +27167,34 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collected by": { - "name": "sample collected by", - "description": "The name of the organization with which the sample collector is affiliated.", - "title": "sample collected by", + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample volume measurement value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 19, - "slot_uri": "GENEPIO:0001153", - "alias": "sample_collected_by", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], + "rank": 43, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18110,16 +27202,27 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "range": "WhitespaceMinimizedString" }, - "sample collector contact email": { - "name": "sample collector contact email", - "description": "The email address of the contact responsible for follow-up regarding the sample.", - "title": "sample collector contact email", + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample volume measurement unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "mL" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 20, - "slot_uri": "GENEPIO:0001156", - "alias": "sample_collector_contact_email", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume" + ], + "rank": 44, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18127,17 +27230,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "pattern": "^\\S+@\\S+\\.\\S+$" + "any_of": [ + { + "range": "SampleVolumeMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc name (country)": { - "name": "geo loc name (country)", - "description": "The country of origin of the sample.", - "title": "geo loc name (country)", + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample storage method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 21, - "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "rank": 45, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18145,16 +27262,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "range": "WhitespaceMinimizedString" }, - "geo loc name (state/province/territory)": { - "name": "geo loc name (state/province/territory)", - "description": "The state/province/territory of origin of the sample.", - "title": "geo loc name (state/province/territory)", + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample storage medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 22, - "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "rank": 46, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18162,16 +27287,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "range": "WhitespaceMinimizedString" }, - "geo loc name (county/region)": { - "name": "geo loc name (county/region)", - "description": "The county/region of origin of the sample.", - "title": "geo loc name (county/region)", + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample storage duration value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 23, - "slot_uri": "GENEPIO:0100280", - "alias": "geo_loc_name_(county/region)", + "rank": 47, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18181,14 +27314,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc name (city)": { - "name": "geo loc name (city)", - "description": "The city of origin of the sample.", - "title": "geo loc name (city)", + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample storage duration unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 24, - "slot_uri": "GENEPIO:0001189", - "alias": "geo_loc_name_(city)", + "rank": 48, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18196,16 +27337,34 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "SampleStorageDurationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc name (site)": { - "name": "geo loc name (site)", - "description": "The name of a specific geographical location e.g. Credit River (rather than river).", - "title": "geo loc name (site)", + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 25, - "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_(site)", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing" + ], + "rank": 49, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18213,16 +27372,35 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo loc latitude": { - "name": "geo loc latitude", - "description": "The latitude coordinates of the geographical location of sample collection.", - "title": "geo loc latitude", + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen processing details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 26, - "slot_uri": "GENEPIO:0100309", - "alias": "geo_loc_latitude", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_details" + ], + "rank": 50, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18232,14 +27410,17 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo loc longitude": { - "name": "geo loc longitude", - "description": "The longitude coordinates of the geographical location of sample collection.", - "title": "geo loc longitude", + "experimental_protocol_field": { + "name": "experimental_protocol_field", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental protocol field", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], "from_schema": "https://example.com/GRDI", - "rank": 27, - "slot_uri": "GENEPIO:0100310", - "alias": "geo_loc_longitude", + "rank": 51, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol_field", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18249,30 +27430,59 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "watershed shapefile availability": { - "name": "watershed shapefile availability", - "description": "The availability status of a shapefile descriping the catchment contributing to a watershed.", - "title": "watershed shapefile availability", + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", + "title": "environmental site", + "comments": [ + "Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Meat processing plant" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 28, - "slot_uri": "GENEPIO:0100919", - "alias": "watershed_shapefile_availability", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_site" + ], + "rank": 52, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "watershed shapefile filename": { - "name": "watershed shapefile filename", - "description": "The name of the watershed shapefile.", - "title": "watershed shapefile filename", + "proximal_environmental_site": { + "name": "proximal_environmental_site", + "description": "An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample.", + "title": "proximal environmental site", + "comments": [ + "Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Farm" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 29, - "slot_uri": "GENEPIO:0100920", - "alias": "watershed_shapefile_filename", + "rank": 53, + "slot_uri": "GENEPIO:0101205", + "alias": "proximal_environmental_site", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18280,24 +27490,28 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "range": "EnvironmentalSiteMenu", + "multivalued": true }, - "organism": { - "name": "organism", - "description": "Taxonomic name of the organism.", - "title": "organism", + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", + "title": "environmental material", "comments": [ - "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + "Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value." ], "examples": [ { - "value": "Vibrio cholerae" + "value": "Raw wastewater" } ], "from_schema": "https://example.com/GRDI", - "rank": 30, - "slot_uri": "GENEPIO:0001191", - "alias": "organism", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_matrix" + ], + "rank": 54, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18305,25 +27519,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true, + "recommended": true, + "multivalued": true, "any_of": [ { - "range": "WhitespaceMinimizedString" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", - "description": "The reason that the sample was collected.", - "title": "purpose of sampling", + "environmental_material_properties": { + "name": "environmental_material_properties", + "description": "The properties, characteristics and qualities of a substance obtained from the natural or man-made environment.", + "title": "environmental material properties", + "comments": [ + "Provide the environmental material properties by selecting descriptors from the pick list." + ], + "examples": [ + { + "value": "Stagnant" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 31, - "slot_uri": "GENEPIO:0001198", - "multivalued": true, - "alias": "purpose_of_sampling", + "rank": 55, + "slot_uri": "GENEPIO:0100770", + "alias": "environmental_material_properties", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18331,16 +27553,33 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialPropertiesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "scale of sampling": { - "name": "scale of sampling", - "description": "The range of locations or entities sampled expressed in general terms.", - "title": "scale of sampling", + "wastewater_system_type": { + "name": "wastewater_system_type", + "description": "The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine", + "title": "wastewater system type", + "comments": [ + "Provide the classification of the wastewater system by selecting from the provided pick list." + ], + "examples": [ + { + "value": "Sanitary sewer" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 32, - "slot_uri": "GENEPIO:0100877", - "alias": "scale_of_sampling", + "rank": 56, + "slot_uri": "GENEPIO:0100771", + "alias": "wastewater_system_type", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18348,32 +27587,65 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WastewaterSystemTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", - "description": "The date on which the sample was received.", - "title": "sample received date", + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental specimen role type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 33, - "slot_uri": "GENEPIO:0001179", - "alias": "sample_received_date", + "rank": 57, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "ExperimentalSpecimenRoleTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", - "description": "The date on which the sample was collected, or sampling began for a continuous sample.", - "title": "sample collection date", + "experimental_control_details": { + "name": "experimental_control_details", + "description": "The details regarding the experimental control contained in the sample.", + "title": "experimental control details", + "comments": [ + "Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor." + ], + "examples": [ + { + "value": "Human coronavirus 229E (HCoV-229E) spiked in sample as process control" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 34, - "slot_uri": "GENEPIO:0001174", - "alias": "sample_collection_date", + "rank": 58, + "slot_uri": "GENEPIO:0100922", + "alias": "experimental_control_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18381,16 +27653,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "range": "WhitespaceMinimizedString" }, - "sample collection end date": { - "name": "sample collection end date", - "description": "The date on which sample collection ended for a continuous sample.", - "title": "sample collection end date", + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. grab sampler.", + "title": "collection device", + "comments": [ + "Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Automatic flow-proportional sampler" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 35, - "slot_uri": "GENEPIO:0101071", - "alias": "sample_collection_end_date", + "rank": 59, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18398,32 +27678,72 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample processing date": { - "name": "sample processing date", - "description": "The date on which the sample was processed.", - "title": "sample processing date", + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample.", + "title": "collection method", + "comments": [ + "Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value." + ], + "examples": [ + { + "value": "Automatic composite sampling" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 36, - "slot_uri": "GENEPIO:0100763", - "alias": "sample_processing_date", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_type" + ], + "rank": 60, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection start time": { - "name": "sample collection start time", - "description": "The time at which sample collection began.", - "title": "sample collection start time", + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic acid extraction method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 37, - "slot_uri": "GENEPIO:0101072", - "alias": "sample_collection_start_time", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:extraction_method" + ], + "rank": 61, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18431,16 +27751,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "sample collection end time": { - "name": "sample collection end time", - "description": "The time at which sample collection ended.", - "title": "sample collection end time", + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic acid extraction kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 38, - "slot_uri": "GENEPIO:0101073", - "alias": "sample_collection_end_time", + "rank": 62, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18448,32 +27776,43 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "sample collection time of day": { - "name": "sample collection time of day", - "description": "The descriptive time of day during which the sample was collected.", - "title": "sample collection time of day", + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], "from_schema": "https://example.com/GRDI", - "rank": 39, - "slot_uri": "GENEPIO:0100765", - "alias": "sample_collection_time_of_day", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_endog_control_1" + ], + "rank": 63, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "sample collection time duration value": { - "name": "sample collection time duration value", - "description": "The amount of time over which the sample was collected.", - "title": "sample collection time duration value", + "extraction_recovery_efficiency_measurement_value": { + "name": "extraction_recovery_efficiency_measurement_value", + "description": "The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected.", + "title": "extraction recovery efficiency measurement value", + "comments": [ + "Provide value as a percent." + ], "from_schema": "https://example.com/GRDI", - "rank": 40, - "slot_uri": "GENEPIO:0100766", - "alias": "sample_collection_time_duration_value", + "rank": 64, + "slot_uri": "GENEPIO:0100924", + "alias": "extraction_recovery_efficiency_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18481,16 +27820,19 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "sample collection time duration unit": { - "name": "sample collection time duration unit", - "description": "The units of the time duration measurement of sample collection.", - "title": "sample collection time duration unit", + "extraction_recovery_efficiency_measurement_method": { + "name": "extraction_recovery_efficiency_measurement_method", + "description": "The method by which recovery efficiency of an extraction was calculated.", + "title": "extraction recovery efficiency measurement method", + "comments": [ + "Provide a brief description of how extraction recovery efficiency was measured or estimated." + ], "from_schema": "https://example.com/GRDI", - "rank": 41, - "slot_uri": "GENEPIO:0100767", - "alias": "sample_collection_time_duration_unit", + "rank": 65, + "slot_uri": "GENEPIO:0100925", + "alias": "extraction_recovery_efficiency_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -18498,641 +27840,984 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "presampling activity": { - "name": "presampling activity", - "description": "The activities or variables upstream of sample collection that may affect the sample.", - "title": "presampling activity", + "microbiological_method": { + "name": "microbiological_method", + "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", + "title": "microbiological method", + "comments": [ + "Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure." + ], + "examples": [ + { + "value": "MFHPB-30" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 42, - "slot_uri": "GENEPIO:0100433", - "multivalued": true, - "alias": "presampling_activity", + "rank": 66, + "slot_uri": "GENEPIO:0100454", + "alias": "microbiological_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "presampling activity details": { - "name": "presampling activity details", - "description": "The details of the activities or variables that affected the sample collected.", - "title": "presampling activity details", + "strain": { + "name": "strain", + "description": "The strain identifier.", + "title": "strain", + "comments": [ + "If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier." + ], + "examples": [ + { + "value": "K12" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 43, - "slot_uri": "GENEPIO:0100434", - "alias": "presampling_activity_details", + "rank": 67, + "slot_uri": "GENEPIO:0100455", + "alias": "strain", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "sample volume measurement value": { - "name": "sample volume measurement value", - "description": "The numerical value of the volume measurement of the sample collected.", - "title": "sample volume measurement value", + "isolate_id": { + "name": "isolate_id", + "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", + "title": "isolate ID", + "comments": [ + "Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field." + ], + "examples": [ + { + "value": "SA20131043" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 44, - "slot_uri": "GENEPIO:0100768", - "alias": "sample_volume_measurement_value", + "rank": 68, + "slot_uri": "GENEPIO:0100456", + "alias": "isolate_id", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Strain and isolation information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample volume measurement unit": { - "name": "sample volume measurement unit", - "description": "The units of the volume measurement of the sample collected.", - "title": "sample volume measurement unit", + "alternative_isolate_id": { + "name": "alternative_isolate_id", + "description": "An alternative isolate_ID assigned to the isolate by another organization.", + "title": "alternative isolate ID", + "comments": [ + "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons." + ], + "examples": [ + { + "value": "GHIF3456[PHAC]" + }, + { + "value": "QWICK222[CFIA]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 45, - "slot_uri": "GENEPIO:0100769", - "alias": "sample_volume_measurement_unit", + "rank": 69, + "slot_uri": "GENEPIO:0100457", + "alias": "alternative_isolate_id", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", + "recommended": true, + "multivalued": true }, - "sample storage method": { - "name": "sample storage method", - "description": "The process used to store the sample.", - "title": "sample storage method", + "progeny_isolate_id": { + "name": "progeny_isolate_id", + "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", + "title": "progeny isolate ID", + "comments": [ + "If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID." + ], + "examples": [ + { + "value": "SUB_ON_1526" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 46, - "slot_uri": "GENEPIO:0100448", - "alias": "sample_storage_method", + "rank": 70, + "slot_uri": "GENEPIO:0100458", + "alias": "progeny_isolate_id", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" - }, - "sample storage medium": { - "name": "sample storage medium", - "description": "The medium in which a sample is stored.", - "title": "sample storage medium", + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" + }, + "isolated_by": { + "name": "isolated_by", + "description": "The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.", + "title": "isolated by", + "comments": [ + "Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 47, - "slot_uri": "GENEPIO:0100449", - "alias": "sample_storage_medium", + "rank": 71, + "slot_uri": "GENEPIO:0100461", + "alias": "isolated_by", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "sample storage duration value": { - "name": "sample storage duration value", - "description": "The numerical value of the time measurement during which a sample is in storage.", - "title": "sample storage duration value", + "isolated_by_laboratory_name": { + "name": "isolated_by_laboratory_name", + "description": "The specific laboratory affiliation of the individual who performed the isolation procedure.", + "title": "isolated by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 48, - "slot_uri": "GENEPIO:0101014", - "alias": "sample_storage_duration_value", + "rank": 72, + "slot_uri": "GENEPIO:0100462", + "alias": "isolated_by_laboratory_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "sample storage duration unit": { - "name": "sample storage duration unit", - "description": "The units of a measured sample storage duration.", - "title": "sample storage duration unit", + "isolated_by_contact_name": { + "name": "isolated_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the isolate.", + "title": "isolated by contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 49, - "slot_uri": "GENEPIO:0101015", - "alias": "sample_storage_duration_unit", + "rank": 73, + "slot_uri": "GENEPIO:0100463", + "alias": "isolated_by_contact_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", - "description": "Any processing applied to the sample during or after receiving the sample.", - "title": "specimen processing", + "isolated_by_contact_email": { + "name": "isolated_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the isolate.", + "title": "isolated by contact email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 50, - "slot_uri": "GENEPIO:0001253", - "multivalued": true, - "alias": "specimen_processing", + "rank": 74, + "slot_uri": "GENEPIO:0100464", + "alias": "isolated_by_contact_email", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "specimen processing details": { - "name": "specimen processing details", - "description": "The details of the processing applied to the sample during or after receiving the sample.", - "title": "specimen processing details", + "isolation_date": { + "name": "isolation_date", + "description": "The date on which the isolate was isolated from a sample.", + "title": "isolation date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2020-10-30" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 51, - "slot_uri": "GENEPIO:0100311", - "alias": "specimen_processing_details", + "rank": 75, + "slot_uri": "GENEPIO:0100465", + "alias": "isolation_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Strain and isolation information", + "range": "date" }, - "experimental protocol field": { - "name": "experimental protocol field", - "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", - "title": "experimental protocol field", + "isolate_received_date": { + "name": "isolate_received_date", + "description": "The date on which the isolate was received by the laboratory.", + "title": "isolate received date", + "comments": [ + "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." + ], + "examples": [ + { + "value": "2020-11-15" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 52, - "slot_uri": "GENEPIO:0101029", - "alias": "experimental_protocol_field", + "rank": 76, + "slot_uri": "GENEPIO:0100466", + "alias": "isolate_received_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", + "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString" }, - "environmental site": { - "name": "environmental site", - "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", - "title": "environmental site", + "serovar": { + "name": "serovar", + "description": "The serovar of the organism.", + "title": "serovar", + "comments": [ + "Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR." + ], + "examples": [ + { + "value": "Heidelberg" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 53, - "slot_uri": "GENEPIO:0001232", - "multivalued": true, - "alias": "environmental_site", + "rank": 77, + "slot_uri": "GENEPIO:0100467", + "alias": "serovar", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", "recommended": true }, - "environmental material": { - "name": "environmental material", - "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", - "title": "environmental material", + "serotyping_method": { + "name": "serotyping_method", + "description": "The method used to determine the serovar.", + "title": "serotyping method", + "comments": [ + "If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software." + ], + "examples": [ + { + "value": "SISTR 1.0.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 54, - "slot_uri": "GENEPIO:0001223", - "multivalued": true, - "alias": "environmental_material", + "rank": 78, + "slot_uri": "GENEPIO:0100468", + "alias": "serotyping_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString", "recommended": true }, - "environmental material properties": { - "name": "environmental material properties", - "description": "The properties, characteristics and qualities of a substance obtained from the natural or man-made environment.", - "title": "environmental material properties", + "phagetype": { + "name": "phagetype", + "description": "The phagetype of the organism.", + "title": "phagetype", + "comments": [ + "Provide if known. If unknown, put “missing”." + ], + "examples": [ + { + "value": "47" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 55, - "slot_uri": "GENEPIO:0100770", - "multivalued": true, - "alias": "environmental_material_properties", + "rank": 79, + "slot_uri": "GENEPIO:0100469", + "alias": "phagetype", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "recommended": true + "slot_group": "Strain and isolation information", + "range": "WhitespaceMinimizedString" }, - "wastewater system type": { - "name": "wastewater system type", - "description": "The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine", - "title": "wastewater system type", + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water catchment area human population measurement value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 56, - "slot_uri": "GENEPIO:0100771", - "alias": "wastewater_system_type", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population" + ], + "rank": 80, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "recommended": true + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "NullValueMenu" + } + ] }, - "experimental specimen role type": { - "name": "experimental specimen role type", - "description": "The type of role that the sample represents in the experiment.", - "title": "experimental specimen role type", + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water catchment area human population range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 57, - "slot_uri": "GENEPIO:0100921", - "multivalued": true, - "alias": "experimental_specimen_role_type", + "rank": 81, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "experimental control details": { - "name": "experimental control details", - "description": "The details regarding the experimental control contained in the sample.", - "title": "experimental control details", + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water catchment area human population measurement method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 58, - "slot_uri": "GENEPIO:0100922", - "alias": "experimental_control_details", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population_source" + ], + "rank": 82, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "collection device": { - "name": "collection device", - "description": "The instrument or container used to collect the sample e.g. grab sampler.", - "title": "collection device", + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 59, - "slot_uri": "GENEPIO:0001234", - "multivalued": true, - "alias": "collection_device", + "rank": 83, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "collection method": { - "name": "collection method", - "description": "The process used to collect the sample.", - "title": "collection method", + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 60, - "slot_uri": "GENEPIO:0001241", - "multivalued": true, - "alias": "collection_method", + "rank": 84, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "recommended": true + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic acid extraction method": { - "name": "nucleic acid extraction method", - "description": "The process used to extract genomic material from a sample.", - "title": "nucleic acid extraction method", + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 61, - "slot_uri": "GENEPIO:0100939", - "alias": "nucleic_acid_extraction_method", + "rank": 85, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "PopulatedAreaTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "nucleic acid extraction kit": { - "name": "nucleic acid extraction kit", - "description": "The kit used to extract genomic material from a sample", - "title": "nucleic acid extraction kit", + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 62, - "slot_uri": "GENEPIO:0100772", - "alias": "nucleic_acid_extraction_kit", + "rank": 86, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "SamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "endogenous control details": { - "name": "endogenous control details", - "description": "The description of the endogenous controls included when extracting a sample.", - "title": "endogenous control details", + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 63, - "slot_uri": "GENEPIO:0100923", - "alias": "endogenous_control_details", + "rank": 87, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "PresamplingWeatherConditionsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "extraction recovery efficiency measurement value": { - "name": "extraction recovery efficiency measurement value", - "description": "The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected.", - "title": "extraction recovery efficiency measurement value", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 64, - "slot_uri": "GENEPIO:0100924", - "alias": "extraction_recovery_efficiency_measurement_value", + "rank": 88, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "extraction recovery efficiency measurement method": { - "name": "extraction recovery efficiency measurement method", - "description": "The method by which recovery efficiency of an extraction was calculated.", - "title": "extraction recovery efficiency measurement method", + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 65, - "slot_uri": "GENEPIO:0100925", - "alias": "extraction_recovery_efficiency_measurement_method", + "rank": 89, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sample collection and processing", - "range": "WhitespaceMinimizedString" + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "PrecipitationMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "microbiological method": { - "name": "microbiological method", - "description": "The laboratory method used to grow, prepare, and/or isolate the microbial isolate.", - "title": "microbiological method", - "from_schema": "https://example.com/GRDI", - "rank": 66, - "slot_uri": "GENEPIO:0100454", - "alias": "microbiological_method", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterPathogenAgnostic" + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample collection" + } ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "strain": { - "name": "strain", - "description": "The strain identifier.", - "title": "strain", "from_schema": "https://example.com/GRDI", - "rank": 67, - "slot_uri": "GENEPIO:0100455", - "alias": "strain", + "rank": 90, + "slot_uri": "GENEPIO:0100913", + "alias": "precipitation_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "isolate ID": { - "name": "isolate ID", - "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", - "title": "isolate ID", - "from_schema": "https://example.com/GRDI", - "rank": 68, - "slot_uri": "GENEPIO:0100456", - "alias": "isolate_ID", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterPathogenAgnostic" + "ambient_temperature_measurement_value": { + "name": "ambient_temperature_measurement_value", + "description": "The numerical value of a measurement of the ambient temperature.", + "title": "ambient temperature measurement value", + "comments": [ + "Provide the numerical value of the measured temperature." ], - "slot_group": "Strain and isolation information", - "required": true - }, - "alternative isolate ID": { - "name": "alternative isolate ID", - "description": "An alternative isolate_ID assigned to the isolate by another organization.", - "title": "alternative isolate ID", - "from_schema": "https://example.com/GRDI", - "rank": 69, - "slot_uri": "GENEPIO:0100457", - "multivalued": true, - "alias": "alternative_isolate_ID", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterPathogenAgnostic" + "examples": [ + { + "value": "70" + } ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "progeny isolate ID": { - "name": "progeny isolate ID", - "description": "The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample.", - "title": "progeny isolate ID", "from_schema": "https://example.com/GRDI", - "rank": 70, - "slot_uri": "GENEPIO:0100458", - "alias": "progeny_isolate_ID", + "rank": 91, + "slot_uri": "GENEPIO:0100935", + "alias": "ambient_temperature_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "isolated by": { - "name": "isolated by", - "description": "The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated.", - "title": "isolated by", + "ambient_temperature_measurement_unit": { + "name": "ambient_temperature_measurement_unit", + "description": "The units of a measurement of the ambient temperature.", + "title": "ambient temperature measurement unit", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 71, - "slot_uri": "GENEPIO:0100461", - "alias": "isolated_by", + "rank": 92, + "slot_uri": "GENEPIO:0100936", + "alias": "ambient_temperature_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "AmbientTemperatureMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "isolated by laboratory name": { - "name": "isolated by laboratory name", - "description": "The specific laboratory affiliation of the individual who performed the isolation procedure.", - "title": "isolated by laboratory name", + "ph_measurement_value": { + "name": "ph_measurement_value", + "description": "The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution.", + "title": "pH measurement value", + "comments": [ + "Provide the numerical value of the measured pH." + ], + "examples": [ + { + "value": "7.4" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 72, - "slot_uri": "GENEPIO:0100462", - "alias": "isolated_by_laboratory_name", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_ph" + ], + "rank": 93, + "slot_uri": "GENEPIO:0001736", + "alias": "ph_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "isolated by contact name": { - "name": "isolated by contact name", - "description": "The name or title of the contact responsible for follow-up regarding the isolate.", - "title": "isolated by contact name", + "ph_measurement_method": { + "name": "ph_measurement_method", + "description": "The process used to measure pH value.", + "title": "pH measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure pH." + ], + "examples": [ + { + "value": "pH test strip (litmus test)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 73, - "slot_uri": "GENEPIO:0100463", - "alias": "isolated_by_contact_name", + "rank": 94, + "slot_uri": "GENEPIO:0100781", + "alias": "ph_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "isolated by contact email": { - "name": "isolated by contact email", - "description": "The email address of the contact responsible for follow-up regarding the isolate.", - "title": "isolated by contact email", + "total_daily_flow_rate_measurement_value": { + "name": "total_daily_flow_rate_measurement_value", + "description": "The numerical value of a measured fluid flow rate over the course of a day.", + "title": "total daily flow rate measurement value", + "comments": [ + "Provide the numerical value of the measured flow rate." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 74, - "slot_uri": "GENEPIO:0100464", - "alias": "isolated_by_contact_email", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], + "rank": 95, + "slot_uri": "GENEPIO:0100905", + "alias": "total_daily_flow_rate_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "isolation date": { - "name": "isolation date", - "description": "The date on which the isolate was isolated from a sample.", - "title": "isolation date", + "total_daily_flow_rate_measurement_unit": { + "name": "total_daily_flow_rate_measurement_unit", + "description": "The units of a measured fluid flow rate over the course of a day.", + "title": "total daily flow rate measurement unit", + "comments": [ + "Provide the units of the measured flow rate by selecting a value from the pick list." + ], + "examples": [ + { + "value": "million gallons per day (MGD)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 75, - "slot_uri": "GENEPIO:0100465", - "alias": "isolation_date", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow" + ], + "rank": 96, + "slot_uri": "GENEPIO:0100906", + "alias": "total_daily_flow_rate_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", - "range": "date" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalDailyFlowRateMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "isolate received date": { - "name": "isolate received date", - "description": "The date on which the isolate was received by the laboratory.", - "title": "isolate received date", + "total_daily_flow_rate_measurement_method": { + "name": "total_daily_flow_rate_measurement_method", + "description": "The process used to measure total daily fluid flow rate.", + "title": "total daily flow rate measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure flow rate." + ], + "examples": [ + { + "value": "Flow meter" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 76, - "slot_uri": "GENEPIO:0100466", - "alias": "isolate_received_date", + "rank": 97, + "slot_uri": "GENEPIO:0100907", + "alias": "total_daily_flow_rate_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "serovar": { - "name": "serovar", - "description": "The serovar of the organism.", - "title": "serovar", + "instantaneous_flow_rate_measurement_value": { + "name": "instantaneous_flow_rate_measurement_value", + "description": "The numerical value of a measured instantaneous fluid flow rate.", + "title": "instantaneous flow rate measurement value", + "comments": [ + "Provide the numerical value of the measured flow rate." + ], + "examples": [ + { + "value": "25" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 77, - "slot_uri": "GENEPIO:0100467", - "alias": "serovar", + "rank": 98, + "slot_uri": "GENEPIO:0100908", + "alias": "instantaneous_flow_rate_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "serotyping method": { - "name": "serotyping method", - "description": "The method used to determine the serovar.", - "title": "serotyping method", + "instantaneous_flow_rate_measurement_unit": { + "name": "instantaneous_flow_rate_measurement_unit", + "description": "The units of a measured instantaneous fluid flow rate.", + "title": "instantaneous flow rate measurement unit", + "comments": [ + "Provide the units of the measured flow rate by selecting a value from the pick list." + ], + "examples": [ + { + "value": "cubic meter per hour (m^3/h)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 78, - "slot_uri": "GENEPIO:0100468", - "alias": "serotyping_method", + "rank": 99, + "slot_uri": "GENEPIO:0100909", + "alias": "instantaneous_flow_rate_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "InstantaneousFlowRateMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "phagetype": { - "name": "phagetype", - "description": "The phagetype of the organism.", - "title": "phagetype", + "instantaneous_flow_rate_measurement_method": { + "name": "instantaneous_flow_rate_measurement_method", + "description": "The process used to measure instantaneous fluid flow rate.", + "title": "instantaneous flow rate measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure flow rate." + ], + "examples": [ + { + "value": "Flow meter" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 79, - "slot_uri": "GENEPIO:0100469", - "alias": "phagetype", + "rank": 100, + "slot_uri": "GENEPIO:0100910", + "alias": "instantaneous_flow_rate_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Strain and isolation information", + "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population measurement value": { - "name": "water catchment area human population measurement value", - "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", - "title": "water catchment area human population measurement value", + "turbidity_measurement_value": { + "name": "turbidity_measurement_value", + "description": "The numerical value of a measurement of turbidity.", + "title": "turbidity measurement value", + "comments": [ + "Provide the numerical value of the measured turbidity." + ], + "examples": [ + { + "value": "0.02" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 80, - "slot_uri": "GENEPIO:0100773", - "alias": "water_catchment_area_human_population_measurement_value", + "rank": 101, + "slot_uri": "GENEPIO:0100783", + "alias": "turbidity_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19140,32 +28825,58 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString", "recommended": true }, - "water catchment area human population range": { - "name": "water catchment area human population range", - "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", - "title": "water catchment area human population range", + "turbidity_measurement_unit": { + "name": "turbidity_measurement_unit", + "description": "The units of a measurement of turbidity.", + "title": "turbidity measurement unit", + "comments": [ + "Provide the units of the measured turbidity by selecting a value from the pick list." + ], + "examples": [ + { + "value": "nephelometric turbidity unit (NTU)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 81, - "slot_uri": "GENEPIO:0100774", - "alias": "water_catchment_area_human_population_range", + "rank": 102, + "slot_uri": "GENEPIO:0100914", + "alias": "turbidity_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "TurbidityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "water catchment area human population measurement method": { - "name": "water catchment area human population measurement method", - "description": "The method by which a water catchment 's human population size was measured or estimated", - "title": "water catchment area human population measurement method", + "turbidity_measurement_method": { + "name": "turbidity_measurement_method", + "description": "The process used to measure turbidity.", + "title": "turbidity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure turbidity." + ], + "examples": [ + { + "value": "Nephelometric method" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 82, - "slot_uri": "GENEPIO:0100775", - "alias": "water_catchment_area_human_population_measurement_method", + "rank": 103, + "slot_uri": "GENEPIO:0101013", + "alias": "turbidity_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19175,14 +28886,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population density value": { - "name": "water catchment area human population density value", - "description": "The numerical value describing the number of humans per geographical area in a water catchment.", - "title": "water catchment area human population density value", + "dissolved_oxygen_measurement_value": { + "name": "dissolved_oxygen_measurement_value", + "description": "The numerical value of a measurement of dissolved oxygen.", + "title": "dissolved oxygen measurement value", + "comments": [ + "Provide the numerical value of the measured dissolved oxygen." + ], + "examples": [ + { + "value": "5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 83, - "slot_uri": "GENEPIO:0100776", - "alias": "water_catchment_area_human_population_density_value", + "rank": 104, + "slot_uri": "GENEPIO:0000035", + "alias": "dissolved_oxygen_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19192,80 +28911,136 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "water catchment area human population density unit": { - "name": "water catchment area human population density unit", - "description": "The unit describing the number of humans per geographical area in a water catchment.", - "title": "water catchment area human population density unit", + "dissolved_oxygen_measurement_unit": { + "name": "dissolved_oxygen_measurement_unit", + "description": "The units of a measurement of dissolved oxygen.", + "title": "dissolved oxygen measurement unit", + "comments": [ + "Provide the units of the measured dissolved oxygen by selecting a value from the pick list." + ], + "examples": [ + { + "value": "part per million (ppm)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 84, - "slot_uri": "GENEPIO:0100777", - "alias": "water_catchment_area_human_population_density_unit", + "rank": 105, + "slot_uri": "GENEPIO:0100784", + "alias": "dissolved_oxygen_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "DissolvedOxygenMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "populated area type": { - "name": "populated area type", - "description": "A type of area that is populated by humans to different degrees.", - "title": "populated area type", + "dissolved_oxygen_measurement_method": { + "name": "dissolved_oxygen_measurement_method", + "description": "The method used to measure dissolved oxygen.", + "title": "dissolved oxygen measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure dissolved oxygen." + ], + "examples": [ + { + "value": "Dissolved oxygen meter in vertical direction" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 85, - "slot_uri": "GENEPIO:0100778", - "alias": "populated_area_type", + "rank": 106, + "slot_uri": "GENEPIO:0100785", + "alias": "dissolved_oxygen_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "sampling weather conditions": { - "name": "sampling weather conditions", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "sampling weather conditions", + "oxygen_reduction_potential_orp_measurement_value": { + "name": "oxygen_reduction_potential_orp_measurement_value", + "description": "The numerical value of a measurement of oxygen reduction potential (ORP).", + "title": "oxygen reduction potential (ORP) measurement value", + "comments": [ + "Provide the numerical value of the measured oxygen reduction potential." + ], + "examples": [ + { + "value": "-50" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 86, - "slot_uri": "GENEPIO:0100779", - "multivalued": true, - "alias": "sampling_weather_conditions", + "rank": 107, + "slot_uri": "FIX:0000278", + "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "presampling weather conditions": { - "name": "presampling weather conditions", - "description": "Weather conditions prior to collection that may affect the sample.", - "title": "presampling weather conditions", + "oxygen_reduction_potential_orp_measurement_unit": { + "name": "oxygen_reduction_potential_orp_measurement_unit", + "description": "The units of a measurement of oxygen reduction potential (ORP).", + "title": "oxygen reduction potential (ORP) measurement unit", + "comments": [ + "Provide the units of the measured oxygen reduction potential by selecting a value from the pick list." + ], + "examples": [ + { + "value": "milliVolt (mV)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 87, - "slot_uri": "GENEPIO:0100780", - "multivalued": true, - "alias": "presampling_weather_conditions", + "rank": 108, + "slot_uri": "GENEPIO:0100786", + "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "OxygenReductionPotentialOrpMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "precipitation measurement value": { - "name": "precipitation measurement value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", + "oxygen_reduction_potential_orp_measurement_method": { + "name": "oxygen_reduction_potential_orp_measurement_method", + "description": "The method used to measure oxygen reduction potential (ORP).", + "title": "oxygen reduction potential (ORP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure oxygen reduction potential." + ], + "examples": [ + { + "value": "ORP sensor" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 88, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", + "rank": 109, + "slot_uri": "GENEPIO:0100787", + "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19273,16 +29048,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "precipitation measurement unit": { - "name": "precipitation measurement unit", - "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement unit", + "chemical_oxygen_demand_cod_measurement_value": { + "name": "chemical_oxygen_demand_cod_measurement_value", + "description": "The measured value from a chemical oxygen demand (COD) test.", + "title": "chemical oxygen demand (COD) measurement value", + "comments": [ + "Provide the numerical value of the COD test result." + ], + "examples": [ + { + "value": "26" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 89, - "slot_uri": "GENEPIO:0100912", - "alias": "precipitation_measurement_unit", + "rank": 110, + "slot_uri": "GENEPIO:0100788", + "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19290,16 +29073,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "precipitation measurement method": { - "name": "precipitation measurement method", - "description": "The process used to measure the amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement method", + "chemical_oxygen_demand_cod_measurement_unit": { + "name": "chemical_oxygen_demand_cod_measurement_unit", + "description": "The units associated with a value from a chemical oxygen demand (COD) test.", + "title": "chemical oxygen demand (COD) measurement unit", + "comments": [ + "Provide the units of the COD test result." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 90, - "slot_uri": "GENEPIO:0100913", - "alias": "precipitation_measurement_method", + "rank": 111, + "slot_uri": "GENEPIO:0100789", + "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19307,16 +29098,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "ChemicalOxygenDemandCodMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "ambient temperature measurement value": { - "name": "ambient temperature measurement value", - "description": "The numerical value of a measurement of the ambient temperature.", - "title": "ambient temperature measurement value", + "chemical_oxygen_demand_cod_measurement_method": { + "name": "chemical_oxygen_demand_cod_measurement_method", + "description": "The method used to measure chemical oxygen demand (COD).", + "title": "chemical oxygen demand (COD) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure COD." + ], + "examples": [ + { + "value": "Hach LCK test kit" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 91, - "slot_uri": "GENEPIO:0100935", - "alias": "ambient_temperature_measurement_value", + "rank": 112, + "slot_uri": "GENEPIO:0100790", + "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19326,30 +29132,47 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - 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"slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "pH measurement value": { - "name": "pH measurement value", - "description": "The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution.", - "title": "pH measurement value", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", + "description": "The units of a measurement of carbonaceous biochemical oxygen demand (CBOD).", + "title": "carbonaceous biochemical oxygen demand (CBOD) measurement unit", + "comments": [ + "Provide the units of the measured CBOD by selecting a value from the pick list." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 93, - "slot_uri": "GENEPIO:0001736", - "alias": "pH_measurement_value", + "rank": 114, + "slot_uri": "GENEPIO:0100792", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19357,16 +29180,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "pH measurement method": { - "name": "pH measurement method", - "description": "The process used to measure pH value.", - "title": "pH measurement method", + "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { + "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", + "description": "The method used to measure carbonaceous biochemical oxygen demand (CBOD).", + "title": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure CBOD." + ], + "examples": [ + { + "value": "CBOD measurement by optical probe" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 94, - "slot_uri": "GENEPIO:0100781", - "alias": "pH_measurement_method", + "rank": 115, + "slot_uri": "GENEPIO:0100793", + "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19376,14 +29214,25 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement value": { - "name": "total daily flow rate measurement value", - "description": "The numerical value of a measured fluid flow rate over the course of a day.", - "title": "total daily flow rate measurement value", + "total_suspended_solids_tss_measurement_value": { + "name": "total_suspended_solids_tss_measurement_value", + "description": "The numerical value from a total suspended solids (TSS) test.", + "title": "total suspended solids (TSS) measurement value", + "comments": [ + "Provide the numerical value of the measured TSS." + ], + "examples": [ + { + "value": "8" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 95, - "slot_uri": "GENEPIO:0100905", - "alias": "total_daily_flow_rate_measurement_value", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], + "rank": 116, + "slot_uri": "GENEPIO:0100794", + "alias": "total_suspended_solids_tss_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19393,30 +29242,57 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total daily flow rate measurement unit": { - "name": "total daily flow rate measurement unit", - "description": "The units of a measured fluid flow rate over the course of a day.", - "title": "total daily flow rate measurement unit", + "total_suspended_solids_tss_measurement_unit": { + "name": "total_suspended_solids_tss_measurement_unit", + "description": "The units associated with a value from a total suspended solids (TSS) test.", + "title": "total suspended solids (TSS) measurement unit", + "comments": [ + "Provide the units of the measured TSS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 96, - "slot_uri": "GENEPIO:0100906", - "alias": "total_daily_flow_rate_measurement_unit", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids" + ], + "rank": 117, + "slot_uri": "GENEPIO:0100795", + "alias": "total_suspended_solids_tss_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalSuspendedSolidsTssMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total daily flow rate measurement method": { - "name": "total daily flow rate measurement method", - "description": "The process used to measure total daily fluid flow rate.", - "title": "total daily flow rate measurement method", + "total_suspended_solids_tss_measurement_method": { + "name": "total_suspended_solids_tss_measurement_method", + "description": "The method used to measure total suspended solids (TSS).", + "title": "total suspended solids (TSS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TSS." + ], + "examples": [ + { + "value": "Vacuum filter through a 2-micron filter, then oven-dried and weighed sample" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 97, - "slot_uri": "GENEPIO:0100907", - "alias": "total_daily_flow_rate_measurement_method", + "rank": 118, + "slot_uri": "GENEPIO:0100796", + "alias": "total_suspended_solids_tss_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19426,14 +29302,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement value": { - "name": "instantaneous flow rate measurement value", - "description": "The numerical value of a measured instantaneous fluid flow rate.", - "title": "instantaneous flow rate measurement value", + "total_dissolved_solids_tds_measurement_value": { + "name": "total_dissolved_solids_tds_measurement_value", + "description": "The numerical value from a total dissolved solids (TDS) test.", + "title": "total dissolved solids (TDS) measurement value", + "comments": [ + "Provide the numerical value of the measured TDS." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 98, - "slot_uri": "GENEPIO:0100908", - "alias": "instantaneous_flow_rate_measurement_value", + "rank": 119, + "slot_uri": "GENEPIO:0100797", + "alias": "total_dissolved_solids_tds_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19443,30 +29327,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "instantaneous flow rate measurement unit": { - "name": "instantaneous flow rate measurement unit", - "description": "The units of a measured instantaneous fluid flow rate.", - "title": "instantaneous flow rate measurement unit", + "total_dissolved_solids_tds_measurement_unit": { + "name": "total_dissolved_solids_tds_measurement_unit", + "description": "The units associated with a value from a total dissolved solids (TDS) test.", + "title": "total dissolved solids (TDS) measurement unit", + "comments": [ + "Provide the units of the measured TDS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 99, - "slot_uri": "GENEPIO:0100909", - "alias": "instantaneous_flow_rate_measurement_unit", + "rank": 120, + "slot_uri": "GENEPIO:0100798", + "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalDissolvedSolidsTdsMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "instantaneous flow rate measurement method": { - "name": "instantaneous flow rate measurement method", - "description": "The process used to measure instantaneous fluid flow rate.", - "title": "instantaneous flow rate measurement method", + "total_dissolved_solids_tds_measurement_method": { + "name": "total_dissolved_solids_tds_measurement_method", + "description": "The method used to measure total dissolved solids (TDS).", + "title": "total dissolved solids (TDS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TDS." + ], + "examples": [ + { + "value": "Subtract calculated TSS from calculated TS" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 100, - "slot_uri": "GENEPIO:0100910", - "alias": "instantaneous_flow_rate_measurement_method", + "rank": 121, + "slot_uri": "GENEPIO:0100799", + "alias": "total_dissolved_solids_tds_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19476,14 +29384,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "turbidity measurement value": { - "name": "turbidity measurement value", - "description": "The numerical value of a measurement of turbidity.", - "title": "turbidity measurement value", + "total_solids_ts_measurement_value": { + "name": "total_solids_ts_measurement_value", + "description": "The numerical value from a total solids (TS) test.", + "title": "total solids (TS) measurement value", + "comments": [ + "Provide the numerical value of the measured TS." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 101, - "slot_uri": "GENEPIO:0100783", - "alias": "turbidity_measurement_value", + "rank": 122, + "slot_uri": "GENEPIO:0100800", + "alias": "total_solids_ts_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19491,17 +29407,24 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "turbidity measurement unit": { - "name": "turbidity measurement unit", - "description": "The units of a measurement of turbidity.", - "title": "turbidity measurement unit", + "total_solids_ts_measurement_unit": { + "name": "total_solids_ts_measurement_unit", + "description": "The units associated with a value from a total solids (TS) test.", + "title": "total solids (TS) measurement unit", + "comments": [ + "Provide the units of the measured TS." + ], + "examples": [ + { + "value": "percent (%)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 102, - "slot_uri": "GENEPIO:0100914", - "alias": "turbidity_measurement_unit", + "rank": 123, + "slot_uri": "GENEPIO:0100801", + "alias": "total_solids_ts_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19509,16 +29432,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "recommended": true + "any_of": [ + { + "range": "TotalSolidsTsMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "turbidity measurement method": { - "name": "turbidity measurement method", - "description": "The process used to measure turbidity.", - "title": "turbidity measurement method", + "total_solids_ts_measurement_method": { + "name": "total_solids_ts_measurement_method", + "description": "The method used to measure total solids (TS).", + "title": "total solids (TS) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TS." + ], + "examples": [ + { + "value": "Gravimetric method by oven drying, then weighing" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 103, - "slot_uri": "GENEPIO:0101013", - "alias": "turbidity_measurement_method", + "rank": 124, + "slot_uri": "GENEPIO:0100802", + "alias": "total_solids_ts_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19528,14 +29466,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement value": { - "name": "dissolved oxygen measurement value", - "description": "The numerical value of a measurement of dissolved oxygen.", - "title": "dissolved oxygen measurement value", + "alkalinity_measurement_value": { + "name": "alkalinity_measurement_value", + "description": "The numerical value of a measurement of alkalinity.", + "title": "alkalinity measurement value", + "comments": [ + "Provide the numerical value of the measured alkalinity." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 104, - "slot_uri": "GENEPIO:0100915", - "alias": "dissolved_oxygen_measurement_value", + "rank": 125, + "slot_uri": "GENEPIO:0100878", + "alias": "alkalinity_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19545,30 +29491,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "dissolved oxygen measurement unit": { - "name": "dissolved oxygen measurement unit", - "description": "The units of a measurement of dissolved oxygen.", - "title": "dissolved oxygen measurement unit", + "alkalinity_measurement_unit": { + "name": "alkalinity_measurement_unit", + "description": "The units of a measurement of alkalinity.", + "title": "alkalinity measurement unit", + "comments": [ + "Provide the units of the measured alkalinity." + ], + "examples": [ + { + "value": "milligram per liter of calcium carbonate (mg/L CaCO3)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 105, - "slot_uri": "GENEPIO:0100784", - "alias": "dissolved_oxygen_measurement_unit", + "rank": 126, + "slot_uri": "GENEPIO:0100879", + "alias": "alkalinity_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "AlkalinityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "dissolved oxygen measurement method": { - "name": "dissolved oxygen measurement method", - "description": "The method used to measure dissolved oxygen.", - "title": "dissolved oxygen measurement method", + "alkalinity_measurement_method": { + "name": "alkalinity_measurement_method", + "description": "The process used to measure alkalinity.", + "title": "alkalinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure alkalinity." + ], + "examples": [ + { + "value": "Titration method" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 106, - "slot_uri": "GENEPIO:0100785", - "alias": "dissolved_oxygen_measurement_method", + "rank": 127, + "slot_uri": "GENEPIO:0100880", + "alias": "alkalinity_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19578,14 +29548,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement value": { - "name": "oxygen reduction potential (ORP) measurement value", - "description": "The numerical value of a measurement of oxygen reduction potential (ORP).", - "title": "oxygen reduction potential (ORP) measurement value", + "conductivity_measurement_value": { + "name": "conductivity_measurement_value", + "description": "The numerical value of a measurement of conductivity.", + "title": "conductivity measurement value", + "comments": [ + "Provide the numerical value of the measured conductivity." + ], + "examples": [ + { + "value": "1412" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 107, - "slot_uri": "GENEPIO:0100917", - "alias": "oxygen_reduction_potential_(ORP)_measurement_value", + "rank": 128, + "slot_uri": "GENEPIO:0100916", + "alias": "conductivity_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19595,30 +29573,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "oxygen reduction potential (ORP) measurement unit": { - "name": "oxygen reduction potential (ORP) measurement unit", - "description": "The units of a measurement of oxygen reduction potential (ORP).", - "title": "oxygen reduction potential (ORP) measurement unit", + "conductivity_measurement_unit": { + "name": "conductivity_measurement_unit", + "description": "The units of a measurement of conductivity.", + "title": "conductivity measurement unit", + "comments": [ + "Provide the units of the measured conductivity." + ], + "examples": [ + { + "value": "microSiemen per centimeter (μS/cm)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 108, - "slot_uri": "GENEPIO:0100786", - "alias": "oxygen_reduction_potential_(ORP)_measurement_unit", + "rank": 129, + "slot_uri": "GENEPIO:0100803", + "alias": "conductivity_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "ConductivityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "oxygen reduction potential (ORP) measurement method": { - "name": "oxygen reduction potential (ORP) measurement method", - "description": "The method used to measure oxygen reduction potential (ORP).", - "title": "oxygen reduction potential (ORP) measurement method", + "conductivity_measurement_method": { + "name": "conductivity_measurement_method", + "description": "The method used to measure conductivity.", + "title": "conductivity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure conductivity." + ], + "examples": [ + { + "value": "Conductivity electrode and meter" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 109, - "slot_uri": "GENEPIO:0100787", - "alias": "oxygen_reduction_potential_(ORP)_measurement_method", + "rank": 130, + "slot_uri": "GENEPIO:0100804", + "alias": "conductivity_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19628,14 +29630,25 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "chemical oxygen demand (COD) measurement value": { - "name": "chemical oxygen demand (COD) measurement value", - "description": "The measured value from a chemical oxygen demand (COD) test.", - "title": "chemical oxygen demand (COD) measurement value", + "salinity_measurement_value": { + "name": "salinity_measurement_value", + "description": "The numerical value of a measurement of salinity.", + "title": "salinity measurement value", + "comments": [ + "Provide the numerical value of the measured salinity." + ], + "examples": [ + { + "value": "35" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 110, - "slot_uri": "GENEPIO:0100788", - "alias": "chemical_oxygen_demand_(COD)_measurement_value", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity" + ], + "rank": 131, + "slot_uri": "GENEPIO:0100805", + "alias": "salinity_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19645,30 +29658,57 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - 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"slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SalinityMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "chemical oxygen demand (COD) measurement method": { - "name": "chemical oxygen demand (COD) measurement method", - "description": "The method used to measure chemical oxygen demand (COD).", - "title": "chemical oxygen demand (COD) measurement method", + "salinity_measurement_method": { + "name": "salinity_measurement_method", + "description": "The method used to measure salinity.", + "title": "salinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure salinity." + ], + "examples": [ + { + "value": "conductivity meter" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 112, - "slot_uri": "GENEPIO:0100790", - "alias": "chemical_oxygen_demand_(COD)_measurement_method", + "rank": 133, + "slot_uri": "GENEPIO:0100807", + "alias": "salinity_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19678,14 +29718,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "carbonaceous biochemical oxygen demand (CBOD) measurement value": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement value", - "description": "The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD).", - "title": "carbonaceous biochemical oxygen demand (CBOD) measurement value", + "total_nitrogen_tn_measurement_value": { + "name": "total_nitrogen_tn_measurement_value", + "description": "The numerical value of a measurement of total nitrogen (TN).", + "title": "total nitrogen (TN) measurement value", + "comments": [ + "Provide the numerical value of the measured TN." + ], + "examples": [ + { + "value": "120" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 113, - "slot_uri": "GENEPIO:0100791", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_value", + "rank": 134, + "slot_uri": "GENEPIO:0100808", + "alias": "total_nitrogen_tn_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19695,30 +29743,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - 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"slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "TotalNitrogenTnMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "carbonaceous biochemical oxygen demand (CBOD) measurement method": { - "name": "carbonaceous biochemical oxygen demand (CBOD) measurement method", - "description": "The method used to measure carbonaceous biochemical oxygen demand (CBOD).", - "title": "carbonaceous biochemical oxygen demand (CBOD) measurement method", + "total_nitrogen_tn_measurement_method": { + "name": "total_nitrogen_tn_measurement_method", + "description": "The method used to measure total nitrogen (TN).", + "title": "total nitrogen (TN) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TN." + ], + "examples": [ + { + "value": "Hach total nitrogen spectrophotometric test" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 115, - "slot_uri": "GENEPIO:0100793", - "alias": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_method", + "rank": 136, + "slot_uri": "GENEPIO:0100810", + "alias": "total_nitrogen_tn_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19728,14 +29800,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement value": { - "name": "total suspended solids (TSS) measurement value", - "description": "The numerical value from a total suspended solids (TSS) test.", - "title": "total suspended solids (TSS) measurement value", + "total_phosphorus_tp_measurement_value": { + "name": "total_phosphorus_tp_measurement_value", + "description": "The numerical value of a measurement of total phosphorus (TP).", + "title": "total phosphorus (TP) measurement value", + "comments": [ + "Provide the numerical value of the measured TP." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 116, - "slot_uri": "GENEPIO:0100794", - "alias": "total_suspended_solids_(TSS)_measurement_value", + "rank": 137, + "slot_uri": "GENEPIO:0100811", + "alias": "total_phosphorus_tp_measurement_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19745,30 +29825,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total suspended solids (TSS) measurement unit": { - "name": "total suspended solids (TSS) measurement unit", - "description": "The units associated with a value from a total suspended solids (TSS) test.", - "title": "total suspended solids (TSS) measurement unit", - "from_schema": "https://example.com/GRDI", - "rank": 117, - "slot_uri": "GENEPIO:0100795", - "alias": "total_suspended_solids_(TSS)_measurement_unit", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "total_phosphorus_tp_measurement_unit": { + "name": "total_phosphorus_tp_measurement_unit", + "description": "The units of a measurement of total phosphorus (TP).", + "title": "total phosphorus (TP) measurement unit", + "comments": [ + "Provide the units of the measured TP." + ], + "examples": [ + { + "value": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)" + } ], - "slot_group": "Environmental conditions and measurements" - }, - "total suspended solids (TSS) measurement method": { - "name": "total suspended solids (TSS) measurement method", - "description": "The method used to measure total suspended solids (TSS).", - "title": "total suspended solids (TSS) measurement method", "from_schema": "https://example.com/GRDI", - "rank": 118, - "slot_uri": "GENEPIO:0100796", - "alias": "total_suspended_solids_(TSS)_measurement_method", + "rank": 138, + "slot_uri": "GENEPIO:0100812", + "alias": "total_phosphorus_tp_measurement_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19776,16 +29848,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "TotalPhosphorusTpMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total dissolved solids (TDS) measurement value": { - "name": "total dissolved solids (TDS) measurement value", - "description": "The numerical value from a total dissolved solids (TDS) test.", - "title": "total dissolved solids (TDS) measurement value", + "total_phosphorus_tp_measurement_method": { + "name": "total_phosphorus_tp_measurement_method", + "description": "The method used to measure total phosphorus (TP).", + "title": "total phosphorus (TP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TP." + ], + "examples": [ + { + "value": "Merck phosphate spectrophotometric test kit" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 119, - "slot_uri": "GENEPIO:0100797", - "alias": "total_dissolved_solids_(TDS)_measurement_value", + "rank": 139, + "slot_uri": "GENEPIO:0100813", + "alias": "total_phosphorus_tp_measurement_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19795,30 +29882,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total dissolved solids (TDS) measurement unit": { - "name": "total dissolved solids (TDS) measurement unit", - "description": "The units associated with a value from a total dissolved solids (TDS) test.", - "title": "total dissolved solids (TDS) measurement unit", - "from_schema": "https://example.com/GRDI", - "rank": 120, - "slot_uri": "GENEPIO:0100798", - "alias": "total_dissolved_solids_(TDS)_measurement_unit", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "fecal_contamination_indicator": { + "name": "fecal_contamination_indicator", + "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", + "title": "fecal contamination indicator", + "comments": [ + "If a fecal contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "crAssphage" + } ], - "slot_group": "Environmental conditions and measurements" - }, - "total dissolved solids (TDS) measurement method": { - "name": "total dissolved solids (TDS) measurement method", - "description": "The method used to measure total dissolved solids (TDS).", - "title": "total dissolved solids (TDS) measurement method", "from_schema": "https://example.com/GRDI", - "rank": 121, - "slot_uri": "GENEPIO:0100799", - "alias": "total_dissolved_solids_(TDS)_measurement_method", + "rank": 140, + "slot_uri": "GENEPIO:0100814", + "alias": "fecal_contamination_indicator", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19826,16 +29905,32 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "recommended": true, + "any_of": [ + { + "range": "FecalContaminationIndicatorMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total solids (TS) measurement value": { - "name": "total solids (TS) measurement value", - "description": "The numerical value from a total solids (TS) test.", - "title": "total solids (TS) measurement value", + "fecal_contamination_value": { + "name": "fecal_contamination_value", + "description": "The numerical value of a measurement of fecal contamination.", + "title": "fecal contamination value", + "comments": [ + "Provide the numerical value of the measured fecal contamination." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 122, - "slot_uri": "GENEPIO:0100800", - "alias": "total_solids_(TS)_measurement_value", + "rank": 141, + "slot_uri": "GENEPIO:0100815", + "alias": "fecal_contamination_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19843,32 +29938,58 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "range": "WhitespaceMinimizedString", + "recommended": true }, - "total solids (TS) measurement unit": { - "name": "total solids (TS) measurement unit", - "description": "The units associated with a value from a total solids (TS) test.", - "title": "total solids (TS) measurement unit", + "fecal_contamination_unit": { + "name": "fecal_contamination_unit", + "description": "The units of a measurement of fecal contamination.", + "title": "fecal contamination unit", + "comments": [ + "Provide the units of the measured fecal contamination." + ], + "examples": [ + { + "value": "cycle threshold (Ct) / quantification cycle (Cq)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 123, - "slot_uri": "GENEPIO:0100801", - "alias": "total_solids_(TS)_measurement_unit", + "rank": 142, + "slot_uri": "GENEPIO:0100816", + "alias": "fecal_contamination_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "FecalContaminationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total solids (TS) measurement method": { - "name": "total solids (TS) measurement method", - "description": "The method used to measure total solids (TS).", - "title": "total solids (TS) measurement method", + "fecal_contamination_method": { + "name": "fecal_contamination_method", + "description": "The method used to measure fecal contamination.", + "title": "fecal contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal contamination." + ], + "examples": [ + { + "value": "quantitative PCR assay" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 124, - "slot_uri": "GENEPIO:0100802", - "alias": "total_solids_(TS)_measurement_method", + "rank": 143, + "slot_uri": "GENEPIO:0100817", + "alias": "fecal_contamination_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19878,14 +29999,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "alkalinity measurement value": { - "name": "alkalinity measurement value", - "description": "The numerical value of a measurement of alkalinity.", - "title": "alkalinity measurement value", + "fecal_coliform_count_value": { + "name": "fecal_coliform_count_value", + "description": "The numerical value of a measurement of fecal coliforms within a sample.", + "title": "fecal coliform count value", + "comments": [ + "Provide the numerical value of the measured fecal coliforms." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 125, - "slot_uri": "GENEPIO:0100878", - "alias": "alkalinity_measurement_value", + "rank": 144, + "slot_uri": "GENEPIO:0100818", + "alias": "fecal_coliform_count_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19895,30 +30024,54 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "alkalinity measurement unit": { - "name": "alkalinity measurement unit", - "description": "The units of a measurement of alkalinity.", - "title": "alkalinity measurement unit", + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", + "description": "The units of a measurement of fecal coliforms.", + "title": "fecal coliform count unit", + "comments": [ + "Provide the units of the measured fecal coliforms." + ], + "examples": [ + { + "value": "most probable number per milliliter (MPN/mL)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 126, - "slot_uri": "GENEPIO:0100879", - "alias": "alkalinity_measurement_unit", + "rank": 145, + "slot_uri": "GENEPIO:0100819", + "alias": "fecal_coliform_count_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "FecalColiformCountUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "alkalinity measurement method": { - "name": "alkalinity measurement method", - "description": "The process used to measure alkalinity.", - "title": "alkalinity measurement method", + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", + "description": "The method used to measure fecal coliforms.", + "title": "fecal coliform count method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal coliforms." + ], + "examples": [ + { + "value": "MPN method via serial dilutions until lack of growth" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 127, - "slot_uri": "GENEPIO:0100880", - "alias": "alkalinity_measurement_method", + "rank": 146, + "slot_uri": "GENEPIO:0100820", + "alias": "fecal_coliform_count_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19928,14 +30081,22 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "conductivity measurement value": { - "name": "conductivity measurement value", - "description": "The numerical value of a measurement of conductivity.", - "title": "conductivity measurement value", + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", + "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", + "title": "urinary contamination indicator", + "comments": [ + "If a urinary contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "urobilin" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 128, - "slot_uri": "GENEPIO:0100916", - "alias": "conductivity_measurement_value", + "rank": 147, + "slot_uri": "GENEPIO:0100837", + "alias": "urinary_contamination_indicator", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19943,32 +30104,56 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "UrinaryContaminationIndicatorMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "conductivity measurement unit": { - "name": "conductivity measurement unit", - "description": "The units of a measurement of conductivity.", - "title": "conductivity measurement unit", + "urinary_contamination_value": { + "name": "urinary_contamination_value", + "description": "The numerical value of a measurement of urinary contamination.", + "title": "urinary contamination value", + "comments": [ + "Provide the numerical value of the measured urinary contamination." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 129, - "slot_uri": "GENEPIO:0100803", - "alias": "conductivity_measurement_unit", + "rank": 148, + "slot_uri": "GENEPIO:0100838", + "alias": "urinary_contamination_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "conductivity measurement method": { - "name": "conductivity measurement method", - "description": "The method used to measure conductivity.", - "title": "conductivity measurement method", + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", + "description": "The units of a measurement of urinary contamination.", + "title": "urinary contamination unit", + "comments": [ + "Provide the units of the measured urinary contamination." + ], + "examples": [ + { + "value": "nanograms per liter" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 130, - "slot_uri": "GENEPIO:0100804", - "alias": "conductivity_measurement_method", + "rank": 149, + "slot_uri": "GENEPIO:0100839", + "alias": "urinary_contamination_unit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19976,16 +30161,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "UrinaryContaminationUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "salinity measurement value": { - "name": "salinity measurement value", - "description": "The numerical value of a measurement of salinity.", - "title": "salinity measurement value", + "urinary_contamination_method": { + "name": "urinary_contamination_method", + "description": "The method used to measure urinary contamination.", + "title": "urinary contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure urinary contamination." + ], + "examples": [ + { + "value": "Urobilin Concentration Test" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 131, - "slot_uri": "GENEPIO:0100805", - "alias": "salinity_measurement_value", + "rank": 150, + "slot_uri": "GENEPIO:0100840", + "alias": "urinary_contamination_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -19995,30 +30195,53 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "salinity measurement unit": { - "name": "salinity measurement unit", - "description": "The units of a measurement of salinity.", - "title": "salinity measurement unit", + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", + "description": "The numerical value of a measurement of temperature of a sample at collection.", + "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 132, - "slot_uri": "GENEPIO:0100806", - "alias": "salinity_measurement_unit", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], + "rank": 151, + "slot_uri": "GENEPIO:0100821", + "alias": "sample_temperature_value_at_collection", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" }, - "salinity measurement method": { - "name": "salinity measurement method", - "description": "The method used to measure salinity.", - "title": "salinity measurement method", + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", + "description": "The units of a measurement of temperature of a sample at the time of collection.", + "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 133, - "slot_uri": "GENEPIO:0100807", - "alias": "salinity_measurement_method", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature" + ], + "rank": 152, + "slot_uri": "GENEPIO:0100822", + "alias": "sample_temperature_unit_at_collection", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -20026,16 +30249,31 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "any_of": [ + { + "range": "SampleTemperatureUnitAtCollectionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total nitrogen (TN) measurement value": { - "name": "total nitrogen (TN) measurement value", - "description": "The numerical value of a measurement of total nitrogen (TN).", - "title": "total nitrogen (TN) measurement value", + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 134, - "slot_uri": "GENEPIO:0100808", - "alias": "total_nitrogen_(TN)_measurement_value", + "rank": 153, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -20045,671 +30283,1209 @@ "slot_group": "Environmental conditions and measurements", "range": "WhitespaceMinimizedString" }, - "total nitrogen (TN) measurement unit": { - "name": "total nitrogen (TN) measurement unit", - "description": "The units of a measurement of total nitrogen (TN).", - "title": "total nitrogen (TN) measurement unit", + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 135, - "slot_uri": "GENEPIO:0100809", - "alias": "total_nitrogen_(TN)_measurement_unit", + "rank": 154, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "SampleTemperatureUnitWhenReceivedMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total nitrogen (TN) measurement method": { - "name": "total nitrogen (TN) measurement method", - "description": "The method used to measure total nitrogen (TN).", - "title": "total nitrogen (TN) measurement method", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "The reason that the sample was sequenced.", + "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 136, - "slot_uri": "GENEPIO:0100810", - "alias": "total_nitrogen_(TN)_measurement_method", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sequencing" + ], + "rank": 155, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "total phosphorus (TP) measurement value": { - "name": "total phosphorus (TP) measurement value", - "description": "The numerical value of a measurement of total phosphorus (TP).", - "title": "total phosphorus (TP) measurement value", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 137, - "slot_uri": "GENEPIO:0100811", - "alias": "total_phosphorus_(TP)_measurement_value", + "rank": 156, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "total phosphorus (TP) measurement unit": { - "name": "total phosphorus (TP) measurement unit", - "description": "The units of a measurement of total phosphorus (TP).", - "title": "total phosphorus (TP) measurement unit", + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 138, - "slot_uri": "GENEPIO:0100812", - "alias": "total_phosphorus_(TP)_measurement_unit", + "exact_mappings": [ + "GISAID:sequenced_by" + ], + "rank": 157, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "total phosphorus (TP) measurement method": { - "name": "total phosphorus (TP) measurement method", - "description": "The method used to measure total phosphorus (TP).", - "title": "total phosphorus (TP) measurement method", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 139, - "slot_uri": "GENEPIO:0100813", - "alias": "total_phosphorus_(TP)_measurement_method", + "rank": 158, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "fecal contamination indicator": { - "name": "fecal contamination indicator", - "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", - "title": "fecal contamination indicator", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Bloggs, Enterics Lab Manager" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 140, - "slot_uri": "GENEPIO:0100814", - "alias": "fecal_contamination_indicator", + "rank": 159, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "recommended": true + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination value": { - "name": "fecal contamination value", - "description": "The numerical value of a measurement of fecal contamination.", - "title": "fecal contamination value", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced by contact email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 141, - "slot_uri": "GENEPIO:0100815", - "alias": "fecal_contamination_value", + "rank": 160, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_email", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination unit": { - "name": "fecal contamination unit", - "description": "The units of a measurement of fecal contamination.", - "title": "fecal contamination unit", + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 142, - "slot_uri": "GENEPIO:0100816", - "alias": "fecal_contamination_unit", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:sequenced_by" + ], + "rank": 161, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "recommended": true + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal contamination method": { - "name": "fecal contamination method", - "description": "The method used to measure fecal contamination.", - "title": "fecal contamination method", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 143, - "slot_uri": "GENEPIO:0100817", - "alias": "fecal_contamination_method", + "exact_mappings": [ + "NCBI_SRA:sequence_submitter_contact_email" + ], + "rank": 162, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "fecal coliform count value": { - "name": "fecal coliform count value", - "description": "The numerical value of a measurement of fecal coliforms within a sample.", - "title": "fecal coliform count value", + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 144, - "slot_uri": "GENEPIO:0100818", - "alias": "fecal_coliform_count_value", + "rank": 163, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "range": "date" }, - "fecal coliform count unit": { - "name": "fecal coliform count unit", - "description": "The units of a measurement of fecal coliforms.", - "title": "fecal coliform count unit", + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 145, - "slot_uri": "GENEPIO:0100819", - "alias": "fecal_coliform_count_unit", + "exact_mappings": [ + "NCBI_SRA:library_ID" + ], + "rank": 164, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "fecal coliform count method": { - "name": "fecal coliform count method", - "description": "The method used to measure fecal coliforms.", - "title": "fecal coliform count method", + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 146, - "slot_uri": "GENEPIO:0100820", - "alias": "fecal_coliform_count_method", + "exact_mappings": [ + "NCBI_SRA:platform" + ], + "rank": 165, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "multivalued": true, + "any_of": [ + { + "range": "SequencingPlatformMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination indicator": { - "name": "urinary contamination indicator", - "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", - "title": "urinary contamination indicator", + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 147, - "slot_uri": "GENEPIO:0100837", - "alias": "urinary_contamination_indicator", + "exact_mappings": [ + "NCBI_SRA:instrument_model" + ], + "rank": 166, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination value": { - "name": "urinary contamination value", - "description": "The numerical value of a measurement of urinary contamination.", - "title": "urinary contamination value", + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing assay type", + "comments": [ + "Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 148, - "slot_uri": "GENEPIO:0100838", - "alias": "urinary_contamination_value", + "exact_mappings": [ + "NCBI_SRA:library_strategy" + ], + "rank": 167, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "SequencingAssayTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "urinary contamination unit": { - "name": "urinary contamination unit", - "description": "The units of a measurement of urinary contamination.", - "title": "urinary contamination unit", + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 149, - "slot_uri": "GENEPIO:0100839", - "alias": "urinary_contamination_unit", + "exact_mappings": [ + "NCBI_SRA:library_preparation_kit" + ], + "rank": 168, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" }, - "urinary contamination method": { - "name": "urinary contamination method", - "description": "The method used to measure urinary contamination.", - "title": "urinary contamination method", + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 150, - "slot_uri": "GENEPIO:0100840", - "alias": "urinary_contamination_method", + "rank": 169, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", - "range": "WhitespaceMinimizedString" + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "sample temperature value (at collection)": { - "name": "sample temperature value (at collection)", - "description": "The numerical value of a measurement of temperature of a sample at collection.", - "title": "sample temperature value (at collection)", + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA fragment length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 151, - "slot_uri": "GENEPIO:0100821", - "alias": "sample_temperature_value_(at_collection)", + "rank": 170, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sample temperature unit (at collection)": { - "name": "sample temperature unit (at collection)", - "description": "The units of a measurement of temperature of a sample at the time of collection.", - "title": "sample temperature unit (at collection)", + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "hybrid selection method" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 152, - "slot_uri": "GENEPIO:0100822", - "alias": "sample_temperature_unit_(at_collection)", + "exact_mappings": [ + "NCBI_SRA:library_selection" + ], + "rank": 171, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Sequence information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "GenomicTargetEnrichmentMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample temperature value (when received)": { - "name": "sample temperature value (when received)", - "description": "The numerical value of a measurement of temperature of a sample upon receipt.", - "title": "sample temperature value (when received)", + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic target enrichment method details", + "comments": [ + "Provide details that are applicable to the method you used." + ], + "examples": [ + { + "value": "enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 153, - "slot_uri": "GENEPIO:0100823", - "alias": "sample_temperature_value_(when_received)", + "rank": 172, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sample temperature unit (when received)": { - "name": "sample temperature unit (when received)", - "description": "The units of a measurement of temperature of a sample at the time upon receipt.", - "title": "sample temperature unit (when received)", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 154, - "slot_uri": "GENEPIO:0100824", - "alias": "sample_temperature_unit_(when_received)", + "exact_mappings": [ + "NCBI_SRA:amplicon_PCR_primer_scheme" + ], + "rank": 173, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Environmental conditions and measurements" + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "AmpliconPcrPrimerSchemeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing": { - "name": "purpose of sequencing", - "description": "The reason that the sample was sequenced.", - "title": "purpose of sequencing", + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 155, - "slot_uri": "GENEPIO:0001445", - "multivalued": true, - "alias": "purpose_of_sequencing", + "exact_mappings": [ + "NCBI_SRA:amplicon_size" + ], + "rank": 174, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Sequence information", - "required": true + "range": "integer" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "description": "The description of why the sample was sequenced providing specific details.", - "title": "purpose of sequencing details", + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 156, - "slot_uri": "GENEPIO:0001446", - "alias": "purpose_of_sequencing_details", + "exact_mappings": [ + "NCBI_SRA:quality_control_method" + ], + "rank": 175, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "sequenced by": { - "name": "sequenced by", - "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", - "title": "sequenced by", + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 157, - "slot_uri": "GENEPIO:0100416", - "alias": "sequenced_by", + "exact_mappings": [ + "NCBI_SRA:quality_control_method_version" + ], + "rank": 176, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "required": true + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "sequenced by contact name": { - "name": "sequenced by contact name", - "description": "The name or title of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced by contact name", + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 158, - "slot_uri": "GENEPIO:0100471", - "alias": "sequenced_by_contact_name", + "exact_mappings": [ + "NCBI_SRA:quality_control_determination" + ], + "rank": 177, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "required": true + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlDeterminationMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequenced by contact email": { - "name": "sequenced by contact email", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "title": "sequenced by contact email", + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 159, - "slot_uri": "GENEPIO:0100471", - "alias": "sequenced_by_contact_email", + "exact_mappings": [ + "NCBI_SRA:quality_control_issues" + ], + "rank": 178, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "required": true + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "QualityControlIssuesMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "The name of the agency that submitted the sequence to a database.", - "title": "sequence submitted by", + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], "from_schema": "https://example.com/GRDI", - "rank": 160, - "slot_uri": "GENEPIO:0001159", - "alias": "sequence_submitted_by", + "exact_mappings": [ + "NCBI_SRA:quality_control_details" + ], + "rank": 179, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "description": "The email address of the contact responsible for follow-up regarding the sequence.", - "title": "sequence submitter contact email", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 161, - "slot_uri": "GENEPIO:0001165", - "alias": "sequence_submitter_contact_email", + "exact_mappings": [ + "NCBI_SRA:raw_sequence_data_processing_method" + ], + "rank": 180, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "recommended": true, - "pattern": "^\\S+@\\S+\\.\\S+$" + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", - "description": "The date the sample was sequenced.", - "title": "sequencing date", + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 162, - "slot_uri": "GENEPIO:0001447", - "alias": "sequencing_date", + "exact_mappings": [ + "NCBI_SRA:dehosting_method" + ], + "rank": 181, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "range": "date" + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "library ID": { - "name": "library ID", - "description": "The user-specified identifier for the library prepared for sequencing.", - "title": "library ID", + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the consensus sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 163, - "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", + "rank": 182, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing platform": { - "name": "sequencing platform", - "description": "The platform technology used to perform the sequencing.", - "title": "sequencing platform", + "genome_sequence_file_path": { + "name": "genome_sequence_file_path", + "description": "The filepath of the consensus sequence file.", + "title": "genome sequence file path", + "comments": [ + "Provide the filepath of the genome sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 164, - "slot_uri": "GENEPIO:0100473", - "multivalued": true, - "alias": "sequencing_platform", + "rank": 183, + "slot_uri": "GENEPIO:0101716", + "alias": "genome_sequence_file_path", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information" + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing instrument": { - "name": "sequencing instrument", - "description": "The model of the sequencing instrument used.", - "title": "sequencing instrument", + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 165, - "slot_uri": "GENEPIO:0001452", - "multivalued": true, - "alias": "sequencing_instrument", + "rank": 184, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "required": true + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing assay type": { - "name": "sequencing assay type", - "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", - "title": "sequencing assay type", + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 166, - "slot_uri": "GENEPIO:0100997", - "alias": "sequencing_assay_type", + "rank": 185, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "library preparation kit": { - "name": "library preparation kit", - "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", - "title": "library preparation kit", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 167, - "slot_uri": "GENEPIO:0001450", - "alias": "library_preparation_kit", + "rank": 186, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "sequencing protocol": { - "name": "sequencing protocol", - "description": "The protocol or method used for sequencing.", - "title": "sequencing protocol", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 168, - "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol", + "rank": 187, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "DNA fragment length": { - "name": "DNA fragment length", - "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", - "title": "DNA fragment length", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 169, - "slot_uri": "GENEPIO:0100843", - "alias": "DNA_fragment_length", + "rank": 188, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "genomic target enrichment method": { - "name": "genomic target enrichment method", - "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", - "title": "genomic target enrichment method", + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 170, - "slot_uri": "GENEPIO:0100966", - "multivalued": true, - "alias": "genomic_target_enrichment_method", + "rank": 189, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterAMR", + "WastewaterSARS-CoV-2", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "genomic target enrichment method details": { - "name": "genomic target enrichment method details", - "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", - "title": "genomic target enrichment method details", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 171, - "slot_uri": "GENEPIO:0100967", - "alias": "genomic_target_enrichment_method_details", + "rank": 190, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "title": "amplicon pcr primer scheme", + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 172, - "slot_uri": "GENEPIO:0001456", - "alias": "amplicon_pcr_primer_scheme", + "rank": 191, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", - "recommended": true + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "amplicon size": { - "name": "amplicon size", - "description": "The length of the amplicon generated by PCR amplification.", - "title": "amplicon size", + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 173, - "slot_uri": "GENEPIO:0001449", - "alias": "amplicon_size", + "rank": 192, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Sequence information", + "slot_group": "Bioinformatics and QC metrics", "range": "integer" }, - "quality control method name": { - "name": "quality control method name", - "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", - "title": "quality control method name", + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 174, - "slot_uri": "GENEPIO:0100557", - "alias": "quality_control_method_name", + "rank": 193, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -20717,523 +31493,827 @@ "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "integer" }, - "quality control method version": { - "name": "quality control method version", - "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", - "title": "quality control method version", + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 175, - "slot_uri": "GENEPIO:0100558", - "alias": "quality_control_method_version", + "rank": 194, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "integer" }, - "quality control determination": { - "name": "quality control determination", - "description": "The determination of a quality control assessment.", - "title": "quality control determination", + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 176, - "slot_uri": "GENEPIO:0100559", - "multivalued": true, - "alias": "quality_control_determination", + "rank": 195, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "quality control issues": { - "name": "quality control issues", - "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", - "title": "quality control issues", + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 177, - "slot_uri": "GENEPIO:0100560", - "multivalued": true, - "alias": "quality_control_issues", + "rank": 196, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" }, - "quality control details": { - "name": "quality control details", - "description": "The details surrounding a low quality determination in a quality control assessment.", - "title": "quality control details", + "percent_read_contamination": { + "name": "percent_read_contamination", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 178, - "slot_uri": "GENEPIO:0100561", - "alias": "quality_control_details", + "rank": 197, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "integer" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", - "title": "raw sequence data processing method", + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 179, - "slot_uri": "GENEPIO:0001458", - "alias": "raw_sequence_data_processing_method", + "rank": 198, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true + "range": "integer" }, - "dehosting method": { - "name": "dehosting method", - "description": "The method used to remove host reads from the pathogen sequence.", - "title": "dehosting method", + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 180, - "slot_uri": "GENEPIO:0001459", - "alias": "dehosting_method", + "exact_mappings": [ + "NCBI_SRA:assembly" + ], + "rank": 199, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", - "WastewaterAMR", "WastewaterPathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", - "recommended": true + "range": "WhitespaceMinimizedString" }, - "sequence assembly software name": { - "name": "sequence assembly software name", - "description": "The name of the software used to assemble a sequence.", - "title": "sequence assembly software name", + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 181, - "slot_uri": "GENEPIO:0100825", - "alias": "sequence_assembly_software_name", + "rank": 200, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterAMR", + "WastewaterSARS-CoV-2", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "sequence assembly software version": { - "name": "sequence assembly software version", - "description": "The version of the software used to assemble a sequence.", - "title": "sequence assembly software version", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 182, - "slot_uri": "GENEPIO:0100826", - "alias": "sequence_assembly_software_version", + "rank": 201, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics" + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", - "title": "breadth of coverage value", + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 183, - "slot_uri": "GENEPIO:0001472", - "alias": "breadth_of_coverage_value", + "rank": 202, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString", + "required": true }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 184, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", + "rank": 203, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString", + "required": true }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth of coverage threshold", + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 185, - "slot_uri": "GENEPIO:0001475", - "alias": "depth_of_coverage_threshold", + "rank": 204, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "genome completeness": { - "name": "genome completeness", - "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", - "title": "genome completeness", + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 186, - "slot_uri": "GENEPIO:0100844", - "alias": "genome_completeness", + "rank": 205, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString", + "recommended": true }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "The number of total base pairs generated by the sequencing process.", - "title": "number of base pairs sequenced", + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 187, - "slot_uri": "GENEPIO:0001482", - "alias": "number_of_base_pairs_sequenced", + "rank": 206, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "number of total reads": { - "name": "number of total reads", - "description": "The total number of non-unique reads generated by the sequencing process.", - "title": "number of total reads", + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 188, - "slot_uri": "GENEPIO:0100827", - "alias": "number_of_total_reads", + "rank": 207, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Taxonomic identification information", + "range": "date" }, - "number of unique reads": { - "name": "number of unique reads", - "description": "The number of unique reads generated by the sequencing process.", - "title": "number of unique reads", + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 189, - "slot_uri": "GENEPIO:0100828", - "alias": "number_of_unique_reads", + "rank": 208, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", "owner": "WastewaterPathogenAgnostic", "domain_of": [ - "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" }, - "minimum post-trimming read length": { - "name": "minimum post-trimming read length", - "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", - "title": "minimum post-trimming read length", + "assay_target_name_1": { + "name": "assay_target_name_1", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 1", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], "from_schema": "https://example.com/GRDI", - "rank": 190, - "slot_uri": "GENEPIO:0100829", - "alias": "minimum_post_trimming_read_length", + "rank": 209, + "slot_uri": "GENEPIO:0101206", + "alias": "assay_target_name_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "number of contigs": { - "name": "number of contigs", - "description": "The number of contigs (contiguous sequences) in a sequence assembly.", - "title": "number of contigs", + "assay_target_details": { + "name": "assay_target_details", + "description": "Describe any details of the assay target.", + "title": "assay target details", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/GRDI", - "rank": 191, - "slot_uri": "GENEPIO:0100937", - "alias": "number_of_contigs", + "rank": 210, + "slot_uri": "GENEPIO:0102040", + "alias": "assay_target_details", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "percent Ns across total genome length": { - "name": "percent Ns across total genome length", - "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", - "title": "percent Ns across total genome length", + "gene_symbol_1": { + "name": "gene_symbol_1", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 1", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 192, - "slot_uri": "GENEPIO:0100830", - "alias": "percent_Ns_across_total_genome_length", + "rank": 211, + "slot_uri": "GENEPIO:0102041", + "alias": "gene_symbol_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "N50": { - "name": "N50", - "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", - "title": "N50", + "diagnostic_target_presence_1": { + "name": "diagnostic_target_presence_1", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 1", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 193, - "slot_uri": "GENEPIO:0100938", - "alias": "N50", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_known_present" + ], + "rank": 212, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "percent read contamination": { - "name": "percent read contamination", - "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", - "title": "percent read contamination", + "diagnostic_measurement_value_1": { + "name": "diagnostic_measurement_value_1", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 1", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 194, - "slot_uri": "GENEPIO:0100845", - "alias": "percent_read_contamination", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc" + ], + "rank": 213, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "sequence assembly length": { - "name": "sequence assembly length", - "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", - "title": "sequence assembly length", + "diagnostic_measurement_unit_1": { + "name": "diagnostic_measurement_unit_1", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 1", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 195, - "slot_uri": "GENEPIO:0100846", - "alias": "sequence_assembly_length", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc_unit" + ], + "rank": 214, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "integer" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "reference genome accession": { - "name": "reference genome accession", - "description": "A persistent, unique identifier of a genome database entry.", - "title": "reference genome accession", + "diagnostic_measurement_method_1": { + "name": "diagnostic_measurement_method_1", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 1", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 196, - "slot_uri": "GENEPIO:0001485", - "alias": "reference_genome_accession", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_protocol" + ], + "rank": 215, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method_1", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "deduplication method": { - "name": "deduplication method", - "description": "The method used to remove duplicated reads in a sequence read dataset.", - "title": "deduplication method", + "assay_target_name_2": { + "name": "assay_target_name_2", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 2", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], "from_schema": "https://example.com/GRDI", - "rank": 197, - "slot_uri": "GENEPIO:0100831", - "alias": "deduplication_method", + "rank": 216, + "alias": "assay_target_name_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", + "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "A description of the overall bioinformatics strategy used.", - "title": "bioinformatics protocol", + "assay_target_details_2": { + "name": "assay_target_details_2", + "description": "Describe any details of the assay target.", + "title": "assay target details 2", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/GRDI", - "rank": 198, - "slot_uri": "GENEPIO:0001489", - "alias": "bioinformatics_protocol", + "rank": 217, + "alias": "assay_target_details_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Bioinformatics and QC metrics", + "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "read mapping software name": { - "name": "read mapping software name", - "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", - "title": "read mapping software name", + "gene_symbol_2": { + "name": "gene_symbol_2", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 2", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 199, - "slot_uri": "GENEPIO:0100832", - "alias": "read_mapping_software_name", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_gene" + ], + "rank": 218, + "alias": "gene_symbol_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString", - "required": true + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "read mapping software version": { - "name": "read mapping software version", - "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", - "title": "read mapping software version", + "diagnostic_target_presence_2": { + "name": "diagnostic_target_presence_2", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence 2", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 200, - "slot_uri": "GENEPIO:0100833", - "alias": "read_mapping_software_version", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_known_present" + ], + "rank": 219, + "alias": "diagnostic_target_presence_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString", - "required": true + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic reference database name": { - "name": "taxonomic reference database name", - "description": "The name of the taxonomic reference database used to identify the organism.", - "title": "taxonomic reference database name", + "diagnostic_measurement_value_2": { + "name": "diagnostic_measurement_value_2", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value 2", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 201, - "slot_uri": "GENEPIO:0100834", - "alias": "taxonomic_reference_database_name", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc" + ], + "rank": 220, + "alias": "diagnostic_measurement_value_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "taxonomic reference database version": { - "name": "taxonomic reference database version", - "description": "The version of the taxonomic reference database used to identify the organism.", - "title": "taxonomic reference database version", + "diagnostic_measurement_unit_2": { + "name": "diagnostic_measurement_unit_2", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit 2", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 202, - "slot_uri": "GENEPIO:0100835", - "alias": "taxonomic_reference_database_version", + "exact_mappings": [ + "NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc_unit" + ], + "rank": 221, + "alias": "diagnostic_measurement_unit_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString", - "recommended": true + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic analysis report filename": { - "name": "taxonomic analysis report filename", - "description": "The filename of the report containing the results of a taxonomic analysis.", - "title": "taxonomic analysis report filename", + "diagnostic_measurement_method_2": { + "name": "diagnostic_measurement_method_2", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method 2", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 203, - "slot_uri": "GENEPIO:0101074", - "alias": "taxonomic_analysis_report_filename", + "rank": 222, + "alias": "diagnostic_measurement_method_2", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", - "range": "WhitespaceMinimizedString" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "taxonomic analysis date": { - "name": "taxonomic analysis date", - "description": "The date a taxonomic analysis was performed.", - "title": "taxonomic analysis date", + "assay_target_name_3": { + "name": "assay_target_name_3", + "description": "The name of the assay target used in the diagnostic RT-PCR test.", + "title": "assay target name 3", + "comments": [ + "The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities." + ], "from_schema": "https://example.com/GRDI", - "rank": 204, - "slot_uri": "GENEPIO:0101075", - "alias": "taxonomic_analysis_date", + "rank": 223, + "alias": "assay_target_name_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", - "range": "date" + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" }, - "read mapping criteria": { - "name": "read mapping criteria", - "description": "A description of the criteria used to map reads to a reference sequence.", - "title": "read mapping criteria", + "assay_target_details_3": { + "name": "assay_target_details_3", + "description": "Describe any details of the assay target.", + "title": "assay target details 3", + "comments": [ + "Provide details that are applicable to the assay used for the diagnostic test." + ], "from_schema": "https://example.com/GRDI", - "rank": 205, - "slot_uri": "GENEPIO:0100836", - "alias": "read_mapping_criteria", + "rank": 224, + "alias": "assay_target_details_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ + "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Taxonomic identification information", + "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "gene name": { - "name": "gene name", - "description": "The name of the gene used in the diagnostic RT-PCR test.", - "title": "gene name", + "gene_symbol_3": { + "name": "gene_symbol_3", + "description": "The symbol of the gene used in the diagnostic RT-PCR test.", + "title": "gene symbol 3", "comments": [ "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" ], @@ -21243,9 +32323,8 @@ } ], "from_schema": "https://example.com/GRDI", - "rank": 206, - "slot_uri": "GENEPIO:0100655", - "alias": "gene_name", + "rank": 225, + "alias": "gene_symbol_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -21258,34 +32337,56 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic target presence": { - "name": "diagnostic target presence", + "diagnostic_target_presence_3": { + "name": "diagnostic_target_presence_3", "description": "The binary value of the result from a diagnostic test.", - "title": "diagnostic target presence", + "title": "diagnostic target presence 3", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 207, - "slot_uri": "GENEPIO:0100962", - "alias": "diagnostic_target_presence", + "rank": 226, + "alias": "diagnostic_target_presence_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticTargetPresenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic measurement value": { - "name": "diagnostic measurement value", + "diagnostic_measurement_value_3": { + "name": "diagnostic_measurement_value_3", "description": "The value of the result from a diagnostic test.", - "title": "diagnostic measurement value", + "title": "diagnostic measurement value 3", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 208, - "slot_uri": "GENEPIO:0100963", - "alias": "diagnostic_measurement_value", + "rank": 227, + "alias": "diagnostic_measurement_value_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", @@ -21295,72 +32396,67 @@ "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic measurement unit": { - "name": "diagnostic measurement unit", + "diagnostic_measurement_unit_3": { + "name": "diagnostic_measurement_unit_3", "description": "The unit of the result from a diagnostic test.", - "title": "diagnostic measurement unit", + "title": "diagnostic measurement unit 3", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], "from_schema": "https://example.com/GRDI", - "rank": 209, - "slot_uri": "GENEPIO:0100964", - "alias": "diagnostic_measurement_unit", + "rank": 228, + "alias": "diagnostic_measurement_unit_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic measurement method": { - "name": "diagnostic measurement method", + "diagnostic_measurement_method_3": { + "name": "diagnostic_measurement_method_3", "description": "The method by which a diagnostic result was determined.", - "title": "diagnostic measurement method", - "from_schema": "https://example.com/GRDI", - "rank": 210, - "slot_uri": "GENEPIO:0100965", - "alias": "diagnostic_measurement_method", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "title": "diagnostic measurement method 3", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." ], - "slot_group": "Pathogen diagnostic testing" - }, - "authors": { - "name": "authors", - "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", - "title": "authors", - "from_schema": "https://example.com/GRDI", - "rank": 211, - "slot_uri": "GENEPIO:0001517", - "alias": "authors", - "owner": "WastewaterPathogenAgnostic", - "domain_of": [ - "WastewaterSARS-CoV-2", - "WastewaterAMR", - "WastewaterPathogenAgnostic" + "examples": [ + { + "value": "qPCR" + } ], - "slot_group": "Contributor acknowledgement", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software and template version provenance.", - "title": "DataHarmonizer provenance", "from_schema": "https://example.com/GRDI", - "rank": 212, - "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "rank": 229, + "alias": "diagnostic_measurement_method_3", "owner": "WastewaterPathogenAgnostic", "domain_of": [ "WastewaterSARS-CoV-2", "WastewaterAMR", "WastewaterPathogenAgnostic" ], - "slot_group": "Contributor acknowledgement", - "range": "Provenance" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "DiagnosticMeasurementMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] } } } diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index cbac32b8..277473ad 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/GRDI name: Wastewater description: '' -version: 2.0.0 +version: 3.1.1 imports: - linkml:types prefixes: @@ -16,1080 +16,1177 @@ classes: name: WastewaterSARS-CoV-2 description: Specification for Wastewater SARS-CoV-2 virus biosample data gathering is_a: dh_interface + annotations: + version: 3.1.1 slots: - - specimen collector sample ID - - specimen collector subsample ID - - pooled sample ID - - specimen collector project ID - - BioProject accession - - BioSample accession - - GenBank accession (versioned) - - SRA accession - - GISAID accession - - GISAID virus name - - ENA accession - - DRA accession - - GSA accession - - Enterobase accession - - sampling site ID - - sampling event ID - - sample collection data steward name - - sample collected by - - sample collector contact email - - geo loc name (country) - - geo loc name (state/province/territory) - - geo loc name (county/region) - - geo loc name (city) - - geo loc name (site) - - geo loc latitude - - geo loc longitude - - watershed shapefile availability - - watershed shapefile filename + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - specimen_collector_project_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - enterobase_accession + - insdc_assembly_accession + - gisaid_accession + - gisaid_virus_name + - sampling_site_id + - sampling_event_id + - sample_collection_data_steward_name + - sample_collected_by_laboratory_name + - sample_collected_by + - sample_collector_contact_name + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site + - geo_loc_latitude + - geo_loc_longitude + - watershed_shapefile_availability + - watershed_shapefile_filename - organism - - purpose of sampling - - scale of sampling - - sample received date - - sample collection date - - sample collection end date - - sample processing date - - sample collection start time - - sample collection end time - - sample collection time of day - - sample collection time duration value - - sample collection time duration unit - - presampling activity - - presampling activity details - - sample volume measurement value - - sample volume measurement unit - - sample storage method - - sample storage medium - - sample storage duration value - - sample storage duration unit - - specimen processing - - specimen processing details - - experimental protocol field - - environmental site - - environmental material - - environmental material properties - - wastewater system type - - experimental specimen role type - - experimental control details - - collection device - - collection method - - nucleic acid extraction method - - nucleic acid extraction kit - - endogenous control details - - extraction recovery efficiency measurement value - - extraction recovery efficiency measurement method - - water catchment area human population measurement value - - water catchment area human population range - - water catchment area human population measurement method - - water catchment area human population density value - - water catchment area human population density unit - - populated area type - - sampling weather conditions - - presampling weather conditions - - precipitation measurement value - - precipitation measurement unit - - precipitation measurement method - - ambient temperature measurement value - - ambient temperature measurement unit - - pH measurement value - - pH measurement method - - total daily flow rate measurement value - - total daily flow rate measurement unit - - total daily flow rate measurement method - - instantaneous flow rate measurement value - - instantaneous flow rate measurement unit - - instantaneous flow rate measurement method - - turbidity measurement value - - turbidity measurement unit - - turbidity measurement method - - dissolved oxygen measurement value - - dissolved oxygen measurement unit - - dissolved oxygen measurement method - - oxygen reduction potential (ORP) measurement value - - oxygen reduction potential (ORP) measurement unit - - oxygen reduction potential (ORP) measurement method - - chemical oxygen demand (COD) measurement value - - chemical oxygen demand (COD) measurement unit - - chemical oxygen demand (COD) measurement method - - carbonaceous biochemical oxygen demand (CBOD) measurement value - - carbonaceous biochemical oxygen demand (CBOD) measurement unit - - carbonaceous biochemical oxygen demand (CBOD) measurement method - - total suspended solids (TSS) measurement value - - total suspended solids (TSS) measurement unit - - total suspended solids (TSS) measurement method - - total dissolved solids (TDS) measurement value - - total dissolved solids (TDS) measurement unit - - total dissolved solids (TDS) measurement method - - total solids (TS) measurement value - - total solids (TS) measurement unit - - total solids (TS) measurement method - - alkalinity measurement value - - alkalinity measurement unit - - alkalinity measurement method - - conductivity measurement value - - conductivity measurement unit - - conductivity measurement method - - salinity measurement value - - salinity measurement unit - - salinity measurement method - - total nitrogen (TN) measurement value - - total nitrogen (TN) measurement unit - - total nitrogen (TN) measurement method - - total phosphorus (TP) measurement value - - total phosphorus (TP) measurement unit - - total phosphorus (TP) measurement method - - fecal contamination indicator - - fecal contamination value - - fecal contamination unit - - fecal contamination method - - fecal coliform count value - - fecal coliform count unit - - fecal coliform count method - - urinary contamination indicator - - urinary contamination value - - urinary contamination unit - - urinary contamination method - - sample temperature value (at collection) - - sample temperature unit (at collection) - - sample temperature value (when received) - - sample temperature unit (when received) - - purpose of sequencing - - purpose of sequencing details - - sequenced by - - sequenced by contact name - - sequenced by contact email - - sequence submitted by - - sequence submitter contact email - - sequencing date - - library ID - - sequencing platform - - sequencing instrument - - sequencing assay type - - library preparation kit - - sequencing protocol - - amplicon pcr primer scheme - - amplicon size - - quality control method name - - quality control method version - - quality control determination - - quality control issues - - quality control details - - raw sequence data processing method - - dehosting method - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - genome completeness - - number of base pairs sequenced - - number of total reads - - number of unique reads - - minimum post-trimming read length - - number of contigs - - percent Ns across total genome length - - Ns per 100 kbp - - N50 - - percent read contamination - - consensus genome length - - reference genome accession - - deduplication method - - bioinformatics protocol - - lineage/clade name - - lineage/clade analysis software name - - lineage/clade analysis software version - - lineage/clade analysis report filename - - gene name - - diagnostic target presence - - diagnostic measurement value - - diagnostic measurement unit - - diagnostic measurement method - - authors - - DataHarmonizer provenance + - purpose_of_sampling + - scale_of_sampling + - sample_received_date + - sample_collection_start_date + - sample_collection_end_date + - sample_processing_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - presampling_activity + - presampling_activity_details + - sample_volume_measurement_value + - sample_volume_measurement_unit + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol_field + - environmental_site + - proximal_environmental_site + - environmental_material + - environmental_material_properties + - wastewater_system_type + - experimental_specimen_role_type + - experimental_control_details + - collection_device + - collection_method + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - extraction_recovery_efficiency_measurement_value + - extraction_recovery_efficiency_measurement_method + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - sequencing_date + - library_id + - sequencing_platform + - sequencing_instrument + - sequencing_assay_type + - library_preparation_kit + - sequencing_protocol + - amplicon_pcr_primer_scheme + - amplicon_size + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - genome_sequence_file_name + - genome_sequence_file_path + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - lineage_clade_name + - lineage_clade_analysis_software_name + - lineage_clade_analysis_software_version + - lineage_clade_analysis_report_filename + - assay_target_name_1 + - assay_target_details + - gene_symbol_1 + - diagnostic_target_presence_1 + - diagnostic_measurement_value_1 + - diagnostic_measurement_unit_1 + - diagnostic_measurement_method_1 + - assay_target_name_2 + - assay_target_details_2 + - gene_symbol_2 + - diagnostic_target_presence_2 + - diagnostic_measurement_value_2 + - diagnostic_measurement_unit_2 + - diagnostic_measurement_method_2 + - assay_target_name_3 + - assay_target_details_3 + - gene_symbol_3 + - diagnostic_target_presence_3 + - diagnostic_measurement_value_3 + - diagnostic_measurement_unit_3 + - diagnostic_measurement_method_3 slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database identifiers - specimen collector subsample ID: + specimen_collector_subsample_id: rank: 2 slot_group: Database identifiers - pooled sample ID: + pooled_sample_id: rank: 3 slot_group: Database identifiers - specimen collector project ID: + specimen_collector_project_id: rank: 4 slot_group: Database identifiers - BioProject accession: + bioproject_accession: rank: 5 slot_group: Database identifiers - BioSample accession: + biosample_accession: rank: 6 slot_group: Database identifiers - GenBank accession (versioned): + insdc_sequence_read_accession: rank: 7 slot_group: Database identifiers - SRA accession: + enterobase_accession: rank: 8 slot_group: Database identifiers - GISAID accession: + insdc_assembly_accession: rank: 9 slot_group: Database identifiers - GISAID virus name: + gisaid_accession: rank: 10 slot_group: Database identifiers - ENA accession: + gisaid_virus_name: rank: 11 slot_group: Database identifiers - DRA accession: + sampling_site_id: rank: 12 slot_group: Database identifiers - GSA accession: + sampling_event_id: rank: 13 slot_group: Database identifiers - Enterobase accession: + sample_collection_data_steward_name: rank: 14 - slot_group: Database identifiers - sampling site ID: + slot_group: Sample collection and processing + sample_collected_by_laboratory_name: rank: 15 - slot_group: Database identifiers - sampling event ID: + slot_group: Sample collection and processing + sample_collected_by: rank: 16 - slot_group: Database identifiers - sample collection data steward name: + slot_group: Sample collection and processing + sample_collector_contact_name: rank: 17 slot_group: Sample collection and processing - sample collected by: + sample_collector_contact_email: rank: 18 slot_group: Sample collection and processing - sample collector contact email: + geo_loc_name_country: rank: 19 slot_group: Sample collection and processing - geo loc name (country): + geo_loc_name_state_province_territory: rank: 20 slot_group: Sample collection and processing - geo loc name (state/province/territory): + geo_loc_name_county_region: rank: 21 slot_group: Sample collection and processing - geo loc name (county/region): + geo_loc_name_city: rank: 22 slot_group: Sample collection and processing - geo loc name (city): + geo_loc_name_site: rank: 23 slot_group: Sample collection and processing - geo loc name (site): + geo_loc_latitude: rank: 24 slot_group: Sample collection and processing - geo loc latitude: + geo_loc_longitude: rank: 25 slot_group: Sample collection and processing - geo loc longitude: + watershed_shapefile_availability: rank: 26 slot_group: Sample collection and processing - watershed shapefile availability: + watershed_shapefile_filename: rank: 27 slot_group: Sample collection and processing - watershed shapefile filename: - rank: 28 - slot_group: Sample collection and processing organism: - rank: 29 + rank: 28 slot_group: Sample collection and processing - multivalued: true comments: Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. examples: - value: Severe acute respiratory syndrome coronavirus 2 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu required: true - purpose of sampling: + purpose_of_sampling: + rank: 29 + slot_group: Sample collection and processing + scale_of_sampling: rank: 30 slot_group: Sample collection and processing - scale of sampling: + sample_received_date: rank: 31 slot_group: Sample collection and processing - sample received date: + sample_collection_start_date: rank: 32 slot_group: Sample collection and processing - sample collection date: + sample_collection_end_date: rank: 33 slot_group: Sample collection and processing - sample collection end date: + sample_processing_date: rank: 34 slot_group: Sample collection and processing - sample processing date: + sample_collection_start_time: rank: 35 slot_group: Sample collection and processing - sample collection start time: + sample_collection_end_time: rank: 36 slot_group: Sample collection and processing - sample collection end time: + sample_collection_time_of_day: rank: 37 slot_group: Sample collection and processing - sample collection time of day: + sample_collection_time_duration_value: rank: 38 slot_group: Sample collection and processing - sample collection time duration value: + sample_collection_time_duration_unit: rank: 39 slot_group: Sample collection and processing - sample collection time duration unit: + presampling_activity: rank: 40 slot_group: Sample collection and processing - presampling activity: + presampling_activity_details: rank: 41 slot_group: Sample collection and processing - presampling activity details: + sample_volume_measurement_value: rank: 42 slot_group: Sample collection and processing - sample volume measurement value: + sample_volume_measurement_unit: rank: 43 slot_group: Sample collection and processing - sample volume measurement unit: + sample_storage_method: rank: 44 slot_group: Sample collection and processing - sample storage method: + sample_storage_medium: rank: 45 slot_group: Sample collection and processing - sample storage medium: + sample_storage_duration_value: rank: 46 slot_group: Sample collection and processing - sample storage duration value: + sample_storage_duration_unit: rank: 47 slot_group: Sample collection and processing - sample storage duration unit: + specimen_processing: rank: 48 slot_group: Sample collection and processing - specimen processing: + specimen_processing_details: rank: 49 slot_group: Sample collection and processing - specimen processing details: + experimental_protocol_field: rank: 50 slot_group: Sample collection and processing - experimental protocol field: + environmental_site: rank: 51 slot_group: Sample collection and processing - environmental site: + proximal_environmental_site: rank: 52 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 53 slot_group: Sample collection and processing - environmental material properties: + environmental_material_properties: rank: 54 slot_group: Sample collection and processing - wastewater system type: + wastewater_system_type: rank: 55 slot_group: Sample collection and processing - experimental specimen role type: + experimental_specimen_role_type: rank: 56 slot_group: Sample collection and processing - experimental control details: + experimental_control_details: rank: 57 slot_group: Sample collection and processing - collection device: + collection_device: rank: 58 slot_group: Sample collection and processing - collection method: + collection_method: rank: 59 slot_group: Sample collection and processing - nucleic acid extraction method: + nucleic_acid_extraction_method: rank: 60 slot_group: Sample collection and processing - nucleic acid extraction kit: + nucleic_acid_extraction_kit: rank: 61 slot_group: Sample collection and processing - endogenous control details: + endogenous_control_details: rank: 62 slot_group: Sample collection and processing - extraction recovery efficiency measurement value: + extraction_recovery_efficiency_measurement_value: rank: 63 slot_group: Sample collection and processing - extraction recovery efficiency measurement method: + extraction_recovery_efficiency_measurement_method: rank: 64 slot_group: Sample collection and processing - water catchment area human population measurement value: + water_catchment_area_human_population_measurement_value: rank: 65 slot_group: Environmental conditions and measurements - water catchment area human population range: + water_catchment_area_human_population_range: rank: 66 slot_group: Environmental conditions and measurements - water catchment area human population measurement method: + water_catchment_area_human_population_measurement_method: rank: 67 slot_group: Environmental conditions and measurements - water catchment area human population density value: + water_catchment_area_human_population_density_value: rank: 68 slot_group: Environmental conditions and measurements - water catchment area human population density unit: + water_catchment_area_human_population_density_unit: rank: 69 slot_group: Environmental conditions and measurements - populated area type: + populated_area_type: rank: 70 slot_group: Environmental conditions and measurements - sampling weather conditions: + sampling_weather_conditions: rank: 71 slot_group: Environmental conditions and measurements - presampling weather conditions: + presampling_weather_conditions: rank: 72 slot_group: Environmental conditions and measurements - precipitation measurement value: + precipitation_measurement_value: rank: 73 slot_group: Environmental conditions and measurements - precipitation measurement unit: + precipitation_measurement_unit: rank: 74 slot_group: Environmental conditions and measurements - precipitation measurement method: + precipitation_measurement_method: rank: 75 slot_group: Environmental conditions and measurements - ambient temperature measurement value: + ambient_temperature_measurement_value: rank: 76 slot_group: Environmental conditions and measurements - ambient temperature measurement unit: + ambient_temperature_measurement_unit: rank: 77 slot_group: Environmental conditions and measurements - pH measurement value: + ph_measurement_value: rank: 78 slot_group: Environmental conditions and measurements - pH measurement method: + ph_measurement_method: rank: 79 slot_group: Environmental conditions and measurements - total daily flow rate measurement value: + total_daily_flow_rate_measurement_value: rank: 80 slot_group: Environmental conditions and measurements - total daily flow rate measurement unit: + total_daily_flow_rate_measurement_unit: rank: 81 slot_group: Environmental conditions and measurements - total daily flow rate measurement method: + total_daily_flow_rate_measurement_method: rank: 82 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement value: + instantaneous_flow_rate_measurement_value: rank: 83 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement unit: + instantaneous_flow_rate_measurement_unit: rank: 84 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement method: + instantaneous_flow_rate_measurement_method: rank: 85 slot_group: Environmental conditions and measurements - turbidity measurement value: + turbidity_measurement_value: rank: 86 slot_group: Environmental conditions and measurements - turbidity measurement unit: + turbidity_measurement_unit: rank: 87 slot_group: Environmental conditions and measurements - turbidity measurement method: + turbidity_measurement_method: rank: 88 slot_group: Environmental conditions and measurements - dissolved oxygen measurement value: + dissolved_oxygen_measurement_value: rank: 89 slot_group: Environmental conditions and measurements - dissolved oxygen measurement unit: + dissolved_oxygen_measurement_unit: rank: 90 slot_group: Environmental conditions and measurements - dissolved oxygen measurement method: + dissolved_oxygen_measurement_method: rank: 91 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement value: + oxygen_reduction_potential_orp_measurement_value: rank: 92 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement unit: + oxygen_reduction_potential_orp_measurement_unit: rank: 93 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement method: + oxygen_reduction_potential_orp_measurement_method: rank: 94 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement value: + chemical_oxygen_demand_cod_measurement_value: rank: 95 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement unit: + chemical_oxygen_demand_cod_measurement_unit: rank: 96 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement method: + chemical_oxygen_demand_cod_measurement_method: rank: 97 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement value: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: rank: 98 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement unit: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: rank: 99 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement method: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: rank: 100 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement value: + total_suspended_solids_tss_measurement_value: rank: 101 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement unit: + total_suspended_solids_tss_measurement_unit: rank: 102 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement method: + total_suspended_solids_tss_measurement_method: rank: 103 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement value: + total_dissolved_solids_tds_measurement_value: rank: 104 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement unit: + total_dissolved_solids_tds_measurement_unit: rank: 105 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement method: + total_dissolved_solids_tds_measurement_method: rank: 106 slot_group: Environmental conditions and measurements - total solids (TS) measurement value: + total_solids_ts_measurement_value: rank: 107 slot_group: Environmental conditions and measurements - total solids (TS) measurement unit: + total_solids_ts_measurement_unit: rank: 108 slot_group: Environmental conditions and measurements - total solids (TS) measurement method: + total_solids_ts_measurement_method: rank: 109 slot_group: Environmental conditions and measurements - alkalinity measurement value: + alkalinity_measurement_value: rank: 110 slot_group: Environmental conditions and measurements - alkalinity measurement unit: + alkalinity_measurement_unit: rank: 111 slot_group: Environmental conditions and measurements - alkalinity measurement method: + alkalinity_measurement_method: rank: 112 slot_group: Environmental conditions and measurements - conductivity measurement value: + conductivity_measurement_value: rank: 113 slot_group: Environmental conditions and measurements - conductivity measurement unit: + conductivity_measurement_unit: rank: 114 slot_group: Environmental conditions and measurements - conductivity measurement method: + conductivity_measurement_method: rank: 115 slot_group: Environmental conditions and measurements - salinity measurement value: + salinity_measurement_value: rank: 116 slot_group: Environmental conditions and measurements - salinity measurement unit: + salinity_measurement_unit: rank: 117 slot_group: Environmental conditions and measurements - salinity measurement method: + salinity_measurement_method: rank: 118 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement value: + total_nitrogen_tn_measurement_value: rank: 119 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement unit: + total_nitrogen_tn_measurement_unit: rank: 120 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement method: + total_nitrogen_tn_measurement_method: rank: 121 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement value: + total_phosphorus_tp_measurement_value: rank: 122 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement unit: + total_phosphorus_tp_measurement_unit: rank: 123 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement method: + total_phosphorus_tp_measurement_method: rank: 124 slot_group: Environmental conditions and measurements - fecal contamination indicator: + fecal_contamination_indicator: rank: 125 slot_group: Environmental conditions and measurements - fecal contamination value: + fecal_contamination_value: rank: 126 slot_group: Environmental conditions and measurements - fecal contamination unit: + fecal_contamination_unit: rank: 127 slot_group: Environmental conditions and measurements - fecal contamination method: + fecal_contamination_method: rank: 128 slot_group: Environmental conditions and measurements - fecal coliform count value: + fecal_coliform_count_value: rank: 129 slot_group: Environmental conditions and measurements - fecal coliform count unit: + fecal_coliform_count_unit: rank: 130 slot_group: Environmental conditions and measurements - fecal coliform count method: + fecal_coliform_count_method: rank: 131 slot_group: Environmental conditions and measurements - urinary contamination indicator: + urinary_contamination_indicator: rank: 132 slot_group: Environmental conditions and measurements - urinary contamination value: + urinary_contamination_value: rank: 133 slot_group: Environmental conditions and measurements - urinary contamination unit: + urinary_contamination_unit: rank: 134 slot_group: Environmental conditions and measurements - urinary contamination method: + urinary_contamination_method: rank: 135 slot_group: Environmental conditions and measurements - sample temperature value (at collection): + sample_temperature_value_at_collection: rank: 136 slot_group: Environmental conditions and measurements - sample temperature unit (at collection): + sample_temperature_unit_at_collection: rank: 137 slot_group: Environmental conditions and measurements - sample temperature value (when received): + sample_temperature_value_when_received: rank: 138 slot_group: Environmental conditions and measurements - sample temperature unit (when received): + sample_temperature_unit_when_received: rank: 139 slot_group: Environmental conditions and measurements - purpose of sequencing: + purpose_of_sequencing: rank: 140 slot_group: Sequence information - purpose of sequencing details: + purpose_of_sequencing_details: rank: 141 slot_group: Sequence information - sequenced by: + sequenced_by: rank: 142 slot_group: Sequence information - sequenced by contact name: + sequenced_by_laboratory_name: rank: 143 slot_group: Sequence information - sequenced by contact email: + sequenced_by_contact_name: rank: 144 slot_group: Sequence information - sequence submitted by: + sequenced_by_contact_email: rank: 145 slot_group: Sequence information - sequence submitter contact email: + sequence_submitted_by: rank: 146 slot_group: Sequence information - sequencing date: + sequence_submitter_contact_email: rank: 147 slot_group: Sequence information - library ID: + sequencing_date: rank: 148 slot_group: Sequence information - sequencing platform: + library_id: rank: 149 slot_group: Sequence information - sequencing instrument: + sequencing_platform: rank: 150 slot_group: Sequence information - sequencing assay type: + sequencing_instrument: rank: 151 slot_group: Sequence information - library preparation kit: + sequencing_assay_type: rank: 152 slot_group: Sequence information - sequencing protocol: + library_preparation_kit: rank: 153 slot_group: Sequence information - amplicon pcr primer scheme: + sequencing_protocol: rank: 154 slot_group: Sequence information - amplicon size: + amplicon_pcr_primer_scheme: rank: 155 slot_group: Sequence information - quality control method name: + amplicon_size: rank: 156 - slot_group: Bioinformatics and QC metrics - quality control method version: + slot_group: Sequence information + quality_control_method_name: rank: 157 slot_group: Bioinformatics and QC metrics - quality control determination: + quality_control_method_version: rank: 158 slot_group: Bioinformatics and QC metrics - quality control issues: + quality_control_determination: rank: 159 slot_group: Bioinformatics and QC metrics - quality control details: + quality_control_issues: rank: 160 slot_group: Bioinformatics and QC metrics - raw sequence data processing method: + quality_control_details: rank: 161 slot_group: Bioinformatics and QC metrics - dehosting method: + raw_sequence_data_processing_method: rank: 162 slot_group: Bioinformatics and QC metrics - consensus sequence software name: + dehosting_method: rank: 163 slot_group: Bioinformatics and QC metrics - consensus sequence software version: + genome_sequence_file_name: rank: 164 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + genome_sequence_file_path: rank: 165 slot_group: Bioinformatics and QC metrics - depth of coverage value: + consensus_sequence_software_name: rank: 166 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + consensus_sequence_software_version: rank: 167 slot_group: Bioinformatics and QC metrics - genome completeness: + breadth_of_coverage_value: rank: 168 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + depth_of_coverage_value: rank: 169 slot_group: Bioinformatics and QC metrics - number of total reads: + depth_of_coverage_threshold: rank: 170 slot_group: Bioinformatics and QC metrics - number of unique reads: + genome_completeness: rank: 171 slot_group: Bioinformatics and QC metrics - minimum post-trimming read length: + number_of_base_pairs_sequenced: rank: 172 slot_group: Bioinformatics and QC metrics - number of contigs: + number_of_total_reads: rank: 173 slot_group: Bioinformatics and QC metrics - percent Ns across total genome length: + number_of_unique_reads: rank: 174 slot_group: Bioinformatics and QC metrics - Ns per 100 kbp: + minimum_posttrimming_read_length: rank: 175 slot_group: Bioinformatics and QC metrics - N50: + number_of_contigs: rank: 176 slot_group: Bioinformatics and QC metrics - percent read contamination: + percent_ns_across_total_genome_length: rank: 177 slot_group: Bioinformatics and QC metrics - consensus genome length: + ns_per_100_kbp: rank: 178 slot_group: Bioinformatics and QC metrics - reference genome accession: + n50: rank: 179 slot_group: Bioinformatics and QC metrics - deduplication method: + percent_read_contamination: rank: 180 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + consensus_genome_length: rank: 181 slot_group: Bioinformatics and QC metrics - lineage/clade name: + reference_genome_accession: rank: 182 - slot_group: Lineage/clade information - lineage/clade analysis software name: + slot_group: Bioinformatics and QC metrics + deduplication_method: rank: 183 - slot_group: Lineage/clade information - lineage/clade analysis software version: + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: rank: 184 - slot_group: Lineage/clade information - lineage/clade analysis report filename: + slot_group: Bioinformatics and QC metrics + lineage_clade_name: rank: 185 slot_group: Lineage/clade information - gene name: + lineage_clade_analysis_software_name: rank: 186 + slot_group: Lineage/clade information + lineage_clade_analysis_software_version: + rank: 187 + slot_group: Lineage/clade information + lineage_clade_analysis_report_filename: + rank: 188 + slot_group: Lineage/clade information + assay_target_name_1: + rank: 189 + slot_group: Pathogen diagnostic testing + assay_target_details: + rank: 190 + slot_group: Pathogen diagnostic testing + gene_symbol_1: + rank: 191 slot_group: Pathogen diagnostic testing comments: Select a gene name value from the pick list provided. examples: - value: E gene (orf4) any_of: - - range: gene name menu - - range: null value menu - diagnostic target presence: - rank: 187 + - range: GeneSymbolMenu + - range: NullValueMenu + diagnostic_target_presence_1: + rank: 192 slot_group: Pathogen diagnostic testing - diagnostic measurement value: - rank: 188 + diagnostic_measurement_value_1: + rank: 193 slot_group: Pathogen diagnostic testing - diagnostic measurement unit: - rank: 189 + diagnostic_measurement_unit_1: + rank: 194 slot_group: Pathogen diagnostic testing - diagnostic measurement method: - rank: 190 + diagnostic_measurement_method_1: + rank: 195 + slot_group: Pathogen diagnostic testing + assay_target_name_2: + rank: 196 + slot_group: Pathogen diagnostic testing + assay_target_details_2: + rank: 197 + slot_group: Pathogen diagnostic testing + gene_symbol_2: + rank: 198 + slot_group: Pathogen diagnostic testing + comments: Select a gene name value from the pick list provided. + examples: + - value: E gene (orf4) + any_of: + - range: GeneNameMenu + - range: NullValueMenu + diagnostic_target_presence_2: + rank: 199 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value_2: + rank: 200 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit_2: + rank: 201 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method_2: + rank: 202 + slot_group: Pathogen diagnostic testing + assay_target_name_3: + rank: 203 + slot_group: Pathogen diagnostic testing + assay_target_details_3: + rank: 204 + slot_group: Pathogen diagnostic testing + gene_symbol_3: + rank: 205 + slot_group: Pathogen diagnostic testing + comments: Select a gene name value from the pick list provided. + examples: + - value: E gene (orf4) + any_of: + - range: GeneNameMenu + - range: NullValueMenu + diagnostic_target_presence_3: + rank: 206 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value_3: + rank: 207 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit_3: + rank: 208 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method_3: + rank: 209 slot_group: Pathogen diagnostic testing - authors: - rank: 191 - slot_group: Contributor acknowledgement - DataHarmonizer provenance: - rank: 192 - slot_group: Contributor acknowledgement WastewaterAMR: name: WastewaterAMR description: Specification for Wastewater AMR biosample data gathering is_a: dh_interface + annotations: + version: 3.1.1 slots: - - specimen collector sample ID - - specimen collector subsample ID - - pooled sample ID - - metagenome-assembled genome (MAG) ID - - specimen collector project ID - - BioProject accession - - BioSample accession - - GenBank accession (versioned) - - SRA accession - - GISAID accession - - GISAID virus name - - ENA accession - - DRA accession - - GSA accession - - Enterobase accession - - sampling site ID - - sampling event ID - - sample collection data steward name - - sample collected by - - sample collector contact email - - geo loc name (country) - - geo loc name (state/province/territory) - - geo loc name (county/region) - - geo loc name (city) - - geo loc name (site) - - geo loc latitude - - geo loc longitude - - watershed shapefile availability - - watershed shapefile filename + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - metagenomeassembled_genome_mag_id + - specimen_collector_project_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - enterobase_accession + - insdc_assembly_accession + - gisaid_accession + - gisaid_virus_name + - sampling_site_id + - sampling_event_id + - sample_collection_data_steward_name + - sample_collected_by_laboratory_name + - sample_collected_by + - sample_collector_contact_name + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site + - geo_loc_latitude + - geo_loc_longitude + - watershed_shapefile_availability + - watershed_shapefile_filename - organism - - purpose of sampling - - scale of sampling - - sample received date - - sample collection date - - sample collection end date - - sample processing date - - sample collection start time - - sample collection end time - - sample collection time of day - - sample collection time duration value - - sample collection time duration unit - - presampling activity - - presampling activity details - - sample volume measurement value - - sample volume measurement unit - - sample storage method - - sample storage medium - - sample storage duration value - - sample storage duration unit - - specimen processing - - specimen processing details - - experimental protocol field - - environmental site - - environmental material - - environmental material properties - - wastewater system type - - experimental specimen role type - - experimental control details - - collection device - - collection method - - nucleic acid extraction method - - nucleic acid extraction kit - - endogenous control details - - extraction recovery efficiency measurement value - - extraction recovery efficiency measurement method - - water catchment area human population measurement value - - water catchment area human population range - - water catchment area human population measurement method - - water catchment area human population density value - - water catchment area human population density unit - - populated area type - - sampling weather conditions - - presampling weather conditions - - precipitation measurement value - - precipitation measurement unit - - precipitation measurement method - - ambient temperature measurement value - - ambient temperature measurement unit - - pH measurement value - - pH measurement method - - total daily flow rate measurement value - - total daily flow rate measurement unit - - total daily flow rate measurement method - - instantaneous flow rate measurement value - - instantaneous flow rate measurement unit - - instantaneous flow rate measurement method - - turbidity measurement value - - turbidity measurement unit - - turbidity measurement method - - dissolved oxygen measurement value - - dissolved oxygen measurement unit - - dissolved oxygen measurement method - - oxygen reduction potential (ORP) measurement value - - oxygen reduction potential (ORP) measurement unit - - oxygen reduction potential (ORP) measurement method - - chemical oxygen demand (COD) measurement value - - chemical oxygen demand (COD) measurement unit - - chemical oxygen demand (COD) measurement method - - carbonaceous biochemical oxygen demand (CBOD) measurement value - - carbonaceous biochemical oxygen demand (CBOD) measurement unit - - carbonaceous biochemical oxygen demand (CBOD) measurement method - - total suspended solids (TSS) measurement value - - total suspended solids (TSS) measurement unit - - total suspended solids (TSS) measurement method - - total dissolved solids (TDS) measurement value - - total dissolved solids (TDS) measurement unit - - total dissolved solids (TDS) measurement method - - total solids (TS) measurement value - - total solids (TS) measurement unit - - total solids (TS) measurement method - - alkalinity measurement value - - alkalinity measurement unit - - alkalinity measurement method - - conductivity measurement value - - conductivity measurement unit - - conductivity measurement method - - salinity measurement value - - salinity measurement unit - - salinity measurement method - - total nitrogen (TN) measurement value - - total nitrogen (TN) measurement unit - - total nitrogen (TN) measurement method - - total phosphorus (TP) measurement value - - total phosphorus (TP) measurement unit - - total phosphorus (TP) measurement method - - fecal contamination indicator - - fecal contamination value - - fecal contamination unit - - fecal contamination method - - fecal coliform count value - - fecal coliform count unit - - fecal coliform count method - - urinary contamination indicator - - urinary contamination value - - urinary contamination unit - - urinary contamination method - - sample temperature value (at collection) - - sample temperature unit (at collection) - - sample temperature value (when received) - - sample temperature unit (when received) - - purpose of sequencing - - purpose of sequencing details - - sequenced by - - sequenced by contact name - - sequenced by contact email - - sequence submitted by - - sequence submitter contact email - - sequencing date - - library ID - - sequencing platform - - sequencing instrument - - sequencing assay type - - library preparation kit - - sequencing protocol - - DNA fragment length - - genomic target enrichment method - - genomic target enrichment method details - - quality control method name - - quality control method version - - quality control determination - - quality control issues - - quality control details - - raw sequence data processing method - - dehosting method - - sequence assembly software name - - sequence assembly software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - number of base pairs sequenced - - number of total reads - - number of unique reads - - minimum post-trimming read length - - bioinformatics protocol - - read mapping software name - - read mapping software version - - taxonomic reference database name - - taxonomic reference database version - - taxonomic analysis report filename - - taxonomic analysis date - - read mapping criteria - - AMR analysis software name - - AMR analysis software version - - AMR reference database name - - AMR reference database version - - AMR analysis report filename - - gene name - - diagnostic target presence - - diagnostic measurement value - - diagnostic measurement unit - - diagnostic measurement method - - authors - - DataHarmonizer provenance + - purpose_of_sampling + - scale_of_sampling + - sample_received_date + - sample_collection_start_date + - sample_collection_end_date + - sample_processing_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - presampling_activity + - presampling_activity_details + - sample_volume_measurement_value + - sample_volume_measurement_unit + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol_field + - environmental_site + - proximal_environmental_site + - environmental_material + - environmental_material_properties + - wastewater_system_type + - experimental_specimen_role_type + - experimental_control_details + - collection_device + - collection_method + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - extraction_recovery_efficiency_measurement_value + - extraction_recovery_efficiency_measurement_method + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - sequencing_date + - library_id + - sequencing_platform + - sequencing_instrument + - sequencing_assay_type + - library_preparation_kit + - sequencing_protocol + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - genome_sequence_file_name + - genome_sequence_file_path + - sequence_assembly_software_name + - sequence_assembly_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - amr_analysis_software_name + - amr_analysis_software_version + - amr_reference_database_name + - amr_reference_database_version + - amr_analysis_report_filename + - assay_target_name_1 + - assay_target_details + - gene_symbol_1 + - diagnostic_target_presence_1 + - diagnostic_measurement_value_1 + - diagnostic_measurement_unit_1 + - diagnostic_measurement_method_1 + - assay_target_name_2 + - assay_target_details_2 + - gene_symbol_2 + - diagnostic_target_presence_2 + - diagnostic_measurement_value_2 + - diagnostic_measurement_unit_2 + - diagnostic_measurement_method_2 + - assay_target_name_3 + - assay_target_details_3 + - gene_symbol_3 + - diagnostic_target_presence_3 + - diagnostic_measurement_value_3 + - diagnostic_measurement_unit_3 + - diagnostic_measurement_method_3 slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database identifiers - specimen collector subsample ID: + specimen_collector_subsample_id: rank: 2 slot_group: Database identifiers - pooled sample ID: + pooled_sample_id: rank: 3 slot_group: Database identifiers - metagenome-assembled genome (MAG) ID: + metagenomeassembled_genome_mag_id: rank: 4 slot_group: Database identifiers - specimen collector project ID: + specimen_collector_project_id: rank: 5 slot_group: Database identifiers - BioProject accession: + bioproject_accession: rank: 6 slot_group: Database identifiers - BioSample accession: + biosample_accession: rank: 7 slot_group: Database identifiers - GenBank accession (versioned): + insdc_sequence_read_accession: rank: 8 slot_group: Database identifiers - SRA accession: + enterobase_accession: rank: 9 slot_group: Database identifiers - GISAID accession: + insdc_assembly_accession: rank: 10 slot_group: Database identifiers - GISAID virus name: + gisaid_accession: rank: 11 slot_group: Database identifiers - ENA accession: + gisaid_virus_name: rank: 12 slot_group: Database identifiers - DRA accession: + sampling_site_id: rank: 13 slot_group: Database identifiers - GSA accession: + sampling_event_id: rank: 14 slot_group: Database identifiers - Enterobase accession: + sample_collection_data_steward_name: rank: 15 - slot_group: Database identifiers - sampling site ID: + slot_group: Sample collection and processing + sample_collected_by_laboratory_name: rank: 16 - slot_group: Database identifiers - sampling event ID: + slot_group: Sample collection and processing + sample_collected_by: rank: 17 - slot_group: Database identifiers - sample collection data steward name: + slot_group: Sample collection and processing + sample_collector_contact_name: rank: 18 slot_group: Sample collection and processing - sample collected by: + sample_collector_contact_email: rank: 19 slot_group: Sample collection and processing - sample collector contact email: + geo_loc_name_country: rank: 20 slot_group: Sample collection and processing - geo loc name (country): + geo_loc_name_state_province_territory: rank: 21 slot_group: Sample collection and processing - geo loc name (state/province/territory): + geo_loc_name_county_region: rank: 22 slot_group: Sample collection and processing - geo loc name (county/region): + geo_loc_name_city: rank: 23 slot_group: Sample collection and processing - geo loc name (city): + geo_loc_name_site: rank: 24 slot_group: Sample collection and processing - geo loc name (site): + geo_loc_latitude: rank: 25 slot_group: Sample collection and processing - geo loc latitude: + geo_loc_longitude: rank: 26 slot_group: Sample collection and processing - geo loc longitude: + watershed_shapefile_availability: rank: 27 slot_group: Sample collection and processing - watershed shapefile availability: + watershed_shapefile_filename: rank: 28 slot_group: Sample collection and processing - watershed shapefile filename: - rank: 29 - slot_group: Sample collection and processing organism: - rank: 30 + rank: 29 slot_group: Sample collection and processing recommended: true comments: 'Provide the official nomenclature for the organism(s) present in @@ -1100,479 +1197,497 @@ classes: - value: Vibrio cholerae any_of: - range: WhitespaceMinimizedString - - range: null value menu - purpose of sampling: + - range: NullValueMenu + purpose_of_sampling: + rank: 30 + slot_group: Sample collection and processing + scale_of_sampling: rank: 31 slot_group: Sample collection and processing - scale of sampling: + sample_received_date: rank: 32 slot_group: Sample collection and processing - sample received date: + sample_collection_start_date: rank: 33 slot_group: Sample collection and processing - sample collection date: + sample_collection_end_date: rank: 34 slot_group: Sample collection and processing - sample collection end date: + sample_processing_date: rank: 35 slot_group: Sample collection and processing - sample processing date: + sample_collection_start_time: rank: 36 slot_group: Sample collection and processing - sample collection start time: + sample_collection_end_time: rank: 37 slot_group: Sample collection and processing - sample collection end time: + sample_collection_time_of_day: rank: 38 slot_group: Sample collection and processing - sample collection time of day: + sample_collection_time_duration_value: rank: 39 slot_group: Sample collection and processing - sample collection time duration value: + sample_collection_time_duration_unit: rank: 40 slot_group: Sample collection and processing - sample collection time duration unit: + presampling_activity: rank: 41 slot_group: Sample collection and processing - presampling activity: + presampling_activity_details: rank: 42 slot_group: Sample collection and processing - presampling activity details: + sample_volume_measurement_value: rank: 43 slot_group: Sample collection and processing - sample volume measurement value: + sample_volume_measurement_unit: rank: 44 slot_group: Sample collection and processing - sample volume measurement unit: + sample_storage_method: rank: 45 slot_group: Sample collection and processing - sample storage method: + sample_storage_medium: rank: 46 slot_group: Sample collection and processing - sample storage medium: + sample_storage_duration_value: rank: 47 slot_group: Sample collection and processing - sample storage duration value: + sample_storage_duration_unit: rank: 48 slot_group: Sample collection and processing - sample storage duration unit: + specimen_processing: rank: 49 slot_group: Sample collection and processing - specimen processing: + specimen_processing_details: rank: 50 slot_group: Sample collection and processing - specimen processing details: + experimental_protocol_field: rank: 51 slot_group: Sample collection and processing - experimental protocol field: + environmental_site: rank: 52 slot_group: Sample collection and processing - environmental site: + proximal_environmental_site: rank: 53 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 54 slot_group: Sample collection and processing - environmental material properties: + environmental_material_properties: rank: 55 slot_group: Sample collection and processing - wastewater system type: + wastewater_system_type: rank: 56 slot_group: Sample collection and processing - experimental specimen role type: + experimental_specimen_role_type: rank: 57 slot_group: Sample collection and processing - experimental control details: + experimental_control_details: rank: 58 slot_group: Sample collection and processing - collection device: + collection_device: rank: 59 slot_group: Sample collection and processing - collection method: + collection_method: rank: 60 slot_group: Sample collection and processing - nucleic acid extraction method: + nucleic_acid_extraction_method: rank: 61 slot_group: Sample collection and processing - nucleic acid extraction kit: + nucleic_acid_extraction_kit: rank: 62 slot_group: Sample collection and processing - endogenous control details: + endogenous_control_details: rank: 63 slot_group: Sample collection and processing - extraction recovery efficiency measurement value: + extraction_recovery_efficiency_measurement_value: rank: 64 slot_group: Sample collection and processing - extraction recovery efficiency measurement method: + extraction_recovery_efficiency_measurement_method: rank: 65 slot_group: Sample collection and processing - water catchment area human population measurement value: + water_catchment_area_human_population_measurement_value: rank: 66 slot_group: Environmental conditions and measurements - water catchment area human population range: + water_catchment_area_human_population_range: rank: 67 slot_group: Environmental conditions and measurements - water catchment area human population measurement method: + water_catchment_area_human_population_measurement_method: rank: 68 slot_group: Environmental conditions and measurements - water catchment area human population density value: + water_catchment_area_human_population_density_value: rank: 69 slot_group: Environmental conditions and measurements - water catchment area human population density unit: + water_catchment_area_human_population_density_unit: rank: 70 slot_group: Environmental conditions and measurements - populated area type: + populated_area_type: rank: 71 slot_group: Environmental conditions and measurements - sampling weather conditions: + sampling_weather_conditions: rank: 72 slot_group: Environmental conditions and measurements - presampling weather conditions: + presampling_weather_conditions: rank: 73 slot_group: Environmental conditions and measurements - precipitation measurement value: + precipitation_measurement_value: rank: 74 slot_group: Environmental conditions and measurements - precipitation measurement unit: + precipitation_measurement_unit: rank: 75 slot_group: Environmental conditions and measurements - precipitation measurement method: + precipitation_measurement_method: rank: 76 slot_group: Environmental conditions and measurements - ambient temperature measurement value: + ambient_temperature_measurement_value: rank: 77 slot_group: Environmental conditions and measurements - ambient temperature measurement unit: + ambient_temperature_measurement_unit: rank: 78 slot_group: Environmental conditions and measurements - pH measurement value: + ph_measurement_value: rank: 79 slot_group: Environmental conditions and measurements - pH measurement method: + ph_measurement_method: rank: 80 slot_group: Environmental conditions and measurements - total daily flow rate measurement value: + total_daily_flow_rate_measurement_value: rank: 81 slot_group: Environmental conditions and measurements - total daily flow rate measurement unit: + total_daily_flow_rate_measurement_unit: rank: 82 slot_group: Environmental conditions and measurements - total daily flow rate measurement method: + total_daily_flow_rate_measurement_method: rank: 83 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement value: + instantaneous_flow_rate_measurement_value: rank: 84 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement unit: + instantaneous_flow_rate_measurement_unit: rank: 85 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement method: + instantaneous_flow_rate_measurement_method: rank: 86 slot_group: Environmental conditions and measurements - turbidity measurement value: + turbidity_measurement_value: rank: 87 slot_group: Environmental conditions and measurements - turbidity measurement unit: + turbidity_measurement_unit: rank: 88 slot_group: Environmental conditions and measurements - turbidity measurement method: + turbidity_measurement_method: rank: 89 slot_group: Environmental conditions and measurements - dissolved oxygen measurement value: + dissolved_oxygen_measurement_value: rank: 90 slot_group: Environmental conditions and measurements - dissolved oxygen measurement unit: + dissolved_oxygen_measurement_unit: rank: 91 slot_group: Environmental conditions and measurements - dissolved oxygen measurement method: + dissolved_oxygen_measurement_method: rank: 92 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement value: + oxygen_reduction_potential_orp_measurement_value: rank: 93 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement unit: + oxygen_reduction_potential_orp_measurement_unit: rank: 94 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement method: + oxygen_reduction_potential_orp_measurement_method: rank: 95 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement value: + chemical_oxygen_demand_cod_measurement_value: rank: 96 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement unit: + chemical_oxygen_demand_cod_measurement_unit: rank: 97 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement method: + chemical_oxygen_demand_cod_measurement_method: rank: 98 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement value: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: rank: 99 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement unit: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: rank: 100 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement method: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: rank: 101 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement value: + total_suspended_solids_tss_measurement_value: rank: 102 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement unit: + total_suspended_solids_tss_measurement_unit: rank: 103 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement method: + total_suspended_solids_tss_measurement_method: rank: 104 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement value: + total_dissolved_solids_tds_measurement_value: rank: 105 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement unit: + total_dissolved_solids_tds_measurement_unit: rank: 106 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement method: + total_dissolved_solids_tds_measurement_method: rank: 107 slot_group: Environmental conditions and measurements - total solids (TS) measurement value: + total_solids_ts_measurement_value: rank: 108 slot_group: Environmental conditions and measurements - total solids (TS) measurement unit: + total_solids_ts_measurement_unit: rank: 109 slot_group: Environmental conditions and measurements - total solids (TS) measurement method: + total_solids_ts_measurement_method: rank: 110 slot_group: Environmental conditions and measurements - alkalinity measurement value: + alkalinity_measurement_value: rank: 111 slot_group: Environmental conditions and measurements - alkalinity measurement unit: + alkalinity_measurement_unit: rank: 112 slot_group: Environmental conditions and measurements - alkalinity measurement method: + alkalinity_measurement_method: rank: 113 slot_group: Environmental conditions and measurements - conductivity measurement value: + conductivity_measurement_value: rank: 114 slot_group: Environmental conditions and measurements - conductivity measurement unit: + conductivity_measurement_unit: rank: 115 slot_group: Environmental conditions and measurements - conductivity measurement method: + conductivity_measurement_method: rank: 116 slot_group: Environmental conditions and measurements - salinity measurement value: + salinity_measurement_value: rank: 117 slot_group: Environmental conditions and measurements - salinity measurement unit: + salinity_measurement_unit: rank: 118 slot_group: Environmental conditions and measurements - salinity measurement method: + salinity_measurement_method: rank: 119 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement value: + total_nitrogen_tn_measurement_value: rank: 120 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement unit: + total_nitrogen_tn_measurement_unit: rank: 121 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement method: + total_nitrogen_tn_measurement_method: rank: 122 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement value: + total_phosphorus_tp_measurement_value: rank: 123 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement unit: + total_phosphorus_tp_measurement_unit: rank: 124 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement method: + total_phosphorus_tp_measurement_method: rank: 125 slot_group: Environmental conditions and measurements - fecal contamination indicator: + fecal_contamination_indicator: rank: 126 slot_group: Environmental conditions and measurements - fecal contamination value: + fecal_contamination_value: rank: 127 slot_group: Environmental conditions and measurements - fecal contamination unit: + fecal_contamination_unit: rank: 128 slot_group: Environmental conditions and measurements - fecal contamination method: + fecal_contamination_method: rank: 129 slot_group: Environmental conditions and measurements - fecal coliform count value: + fecal_coliform_count_value: rank: 130 slot_group: Environmental conditions and measurements - fecal coliform count unit: + fecal_coliform_count_unit: rank: 131 slot_group: Environmental conditions and measurements - fecal coliform count method: + fecal_coliform_count_method: rank: 132 slot_group: Environmental conditions and measurements - urinary contamination indicator: + urinary_contamination_indicator: rank: 133 slot_group: Environmental conditions and measurements - urinary contamination value: + urinary_contamination_value: rank: 134 slot_group: Environmental conditions and measurements - urinary contamination unit: + urinary_contamination_unit: rank: 135 slot_group: Environmental conditions and measurements - urinary contamination method: + urinary_contamination_method: rank: 136 slot_group: Environmental conditions and measurements - sample temperature value (at collection): + sample_temperature_value_at_collection: rank: 137 slot_group: Environmental conditions and measurements - sample temperature unit (at collection): + sample_temperature_unit_at_collection: rank: 138 slot_group: Environmental conditions and measurements - sample temperature value (when received): + sample_temperature_value_when_received: rank: 139 slot_group: Environmental conditions and measurements - sample temperature unit (when received): + sample_temperature_unit_when_received: rank: 140 slot_group: Environmental conditions and measurements - purpose of sequencing: + purpose_of_sequencing: rank: 141 slot_group: Sequence information - purpose of sequencing details: + purpose_of_sequencing_details: rank: 142 slot_group: Sequence information - sequenced by: + sequenced_by: rank: 143 slot_group: Sequence information - sequenced by contact name: + sequenced_by_laboratory_name: rank: 144 slot_group: Sequence information - sequenced by contact email: + sequenced_by_contact_name: rank: 145 slot_group: Sequence information - sequence submitted by: + sequenced_by_contact_email: rank: 146 slot_group: Sequence information - sequence submitter contact email: + sequence_submitted_by: rank: 147 slot_group: Sequence information - sequencing date: + sequence_submitter_contact_email: rank: 148 slot_group: Sequence information - library ID: + sequencing_date: rank: 149 slot_group: Sequence information - sequencing platform: + library_id: rank: 150 slot_group: Sequence information - sequencing instrument: + sequencing_platform: rank: 151 slot_group: Sequence information - sequencing assay type: + sequencing_instrument: rank: 152 slot_group: Sequence information - library preparation kit: + sequencing_assay_type: rank: 153 slot_group: Sequence information - sequencing protocol: + library_preparation_kit: rank: 154 slot_group: Sequence information - DNA fragment length: + sequencing_protocol: rank: 155 slot_group: Sequence information - genomic target enrichment method: + dna_fragment_length: rank: 156 slot_group: Sequence information - genomic target enrichment method details: + genomic_target_enrichment_method: rank: 157 slot_group: Sequence information - quality control method name: + genomic_target_enrichment_method_details: rank: 158 - slot_group: Bioinformatics and QC metrics - quality control method version: + slot_group: Sequence information + quality_control_method_name: rank: 159 slot_group: Bioinformatics and QC metrics - quality control determination: + quality_control_method_version: rank: 160 slot_group: Bioinformatics and QC metrics - quality control issues: + quality_control_determination: rank: 161 slot_group: Bioinformatics and QC metrics - quality control details: + quality_control_issues: rank: 162 slot_group: Bioinformatics and QC metrics - raw sequence data processing method: + quality_control_details: rank: 163 slot_group: Bioinformatics and QC metrics - dehosting method: + raw_sequence_data_processing_method: rank: 164 slot_group: Bioinformatics and QC metrics - sequence assembly software name: + dehosting_method: rank: 165 slot_group: Bioinformatics and QC metrics - sequence assembly software version: + genome_sequence_file_name: rank: 166 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + genome_sequence_file_path: rank: 167 slot_group: Bioinformatics and QC metrics - depth of coverage value: + sequence_assembly_software_name: rank: 168 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + sequence_assembly_software_version: rank: 169 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + breadth_of_coverage_value: rank: 170 slot_group: Bioinformatics and QC metrics - number of total reads: + depth_of_coverage_value: rank: 171 slot_group: Bioinformatics and QC metrics - number of unique reads: + depth_of_coverage_threshold: rank: 172 slot_group: Bioinformatics and QC metrics - minimum post-trimming read length: + number_of_base_pairs_sequenced: rank: 173 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + number_of_total_reads: rank: 174 slot_group: Bioinformatics and QC metrics - read mapping software name: + number_of_unique_reads: rank: 175 - slot_group: Taxonomic identification information - recommended: true - read mapping software version: + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: rank: 176 - slot_group: Taxonomic identification information - recommended: true - taxonomic reference database name: + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: rank: 177 - slot_group: Taxonomic identification information - taxonomic reference database version: + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: rank: 178 slot_group: Taxonomic identification information - taxonomic analysis report filename: + recommended: true + read_mapping_software_version: rank: 179 slot_group: Taxonomic identification information - taxonomic analysis date: + recommended: true + taxonomic_reference_database_name: rank: 180 slot_group: Taxonomic identification information - read mapping criteria: + taxonomic_reference_database_version: rank: 181 slot_group: Taxonomic identification information - AMR analysis software name: + taxonomic_analysis_report_filename: rank: 182 - slot_group: AMR detection information - AMR analysis software version: + slot_group: Taxonomic identification information + taxonomic_analysis_date: rank: 183 - slot_group: AMR detection information - AMR reference database name: + slot_group: Taxonomic identification information + read_mapping_criteria: rank: 184 - slot_group: AMR detection information - AMR reference database version: + slot_group: Taxonomic identification information + amr_analysis_software_name: rank: 185 slot_group: AMR detection information - AMR analysis report filename: + amr_analysis_software_version: rank: 186 slot_group: AMR detection information - gene name: + amr_reference_database_name: rank: 187 + slot_group: AMR detection information + amr_reference_database_version: + rank: 188 + slot_group: AMR detection information + amr_analysis_report_filename: + rank: 189 + slot_group: AMR detection information + assay_target_name_1: + rank: 190 + slot_group: Pathogen diagnostic testing + assay_target_details: + rank: 191 + slot_group: Pathogen diagnostic testing + gene_symbol_1: + rank: 192 slot_group: Pathogen diagnostic testing comments: 'Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: @@ -1581,332 +1696,400 @@ classes: - value: gyrase A any_of: - range: WhitespaceMinimizedString - - range: null value menu - diagnostic target presence: - rank: 188 + - range: NullValueMenu + diagnostic_target_presence_1: + rank: 193 slot_group: Pathogen diagnostic testing - diagnostic measurement value: - rank: 189 + diagnostic_measurement_value_1: + rank: 194 slot_group: Pathogen diagnostic testing - diagnostic measurement unit: - rank: 190 + diagnostic_measurement_unit_1: + rank: 195 slot_group: Pathogen diagnostic testing - diagnostic measurement method: - rank: 191 + diagnostic_measurement_method_1: + rank: 196 + slot_group: Pathogen diagnostic testing + assay_target_name_2: + rank: 197 + slot_group: Pathogen diagnostic testing + assay_target_details_2: + rank: 198 + slot_group: Pathogen diagnostic testing + gene_symbol_2: + rank: 199 + slot_group: Pathogen diagnostic testing + comments: 'Provide the full name of the gene used in the test. Standardized + gene names can be found in the Gene Ontology using this look-up service: + https://bit.ly/2Sq1LbI' + examples: + - value: gyrase A + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + diagnostic_target_presence_2: + rank: 200 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value_2: + rank: 201 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit_2: + rank: 202 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method_2: + rank: 203 + slot_group: Pathogen diagnostic testing + assay_target_name_3: + rank: 204 + slot_group: Pathogen diagnostic testing + assay_target_details_3: + rank: 205 + slot_group: Pathogen diagnostic testing + gene_symbol_3: + rank: 206 + slot_group: Pathogen diagnostic testing + comments: 'Provide the full name of the gene used in the test. Standardized + gene names can be found in the Gene Ontology using this look-up service: + https://bit.ly/2Sq1LbI' + examples: + - value: gyrase A + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + diagnostic_target_presence_3: + rank: 207 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value_3: + rank: 208 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit_3: + rank: 209 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method_3: + rank: 210 slot_group: Pathogen diagnostic testing - authors: - rank: 192 - slot_group: Contributor acknowledgement - DataHarmonizer provenance: - rank: 193 - slot_group: Contributor acknowledgement WastewaterPathogenAgnostic: name: WastewaterPathogenAgnostic description: Specification for Wastewater Pathogen Agnostic biosample data gathering is_a: dh_interface + annotations: + version: 3.1.1 slots: - - specimen collector sample ID - - specimen collector subsample ID - - pooled sample ID - - metagenome-assembled genome (MAG) ID - - specimen collector project ID - - BioProject accession - - BioSample accession - - GenBank accession (versioned) - - SRA accession - - GISAID accession - - GISAID virus name - - ENA accession - - DRA accession - - GSA accession - - Enterobase accession - - sampling site ID - - sampling event ID - - sample collection data steward name - - sample collected by - - sample collector contact email - - geo loc name (country) - - geo loc name (state/province/territory) - - geo loc name (county/region) - - geo loc name (city) - - geo loc name (site) - - geo loc latitude - - geo loc longitude - - watershed shapefile availability - - watershed shapefile filename + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - metagenomeassembled_genome_mag_id + - specimen_collector_project_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - enterobase_accession + - insdc_assembly_accession + - gisaid_accession + - gisaid_virus_name + - sampling_site_id + - sampling_event_id + - sample_collection_data_steward_name + - sample_collected_by_laboratory_name + - sample_collected_by + - sample_collector_contact_name + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site + - geo_loc_latitude + - geo_loc_longitude + - watershed_shapefile_availability + - watershed_shapefile_filename - organism - - purpose of sampling - - scale of sampling - - sample received date - - sample collection date - - sample collection end date - - sample processing date - - sample collection start time - - sample collection end time - - sample collection time of day - - sample collection time duration value - - sample collection time duration unit - - presampling activity - - presampling activity details - - sample volume measurement value - - sample volume measurement unit - - sample storage method - - sample storage medium - - sample storage duration value - - sample storage duration unit - - specimen processing - - specimen processing details - - experimental protocol field - - environmental site - - environmental material - - environmental material properties - - wastewater system type - - experimental specimen role type - - experimental control details - - collection device - - collection method - - nucleic acid extraction method - - nucleic acid extraction kit - - endogenous control details - - extraction recovery efficiency measurement value - - extraction recovery efficiency measurement method - - microbiological method + - purpose_of_sampling + - scale_of_sampling + - sample_received_date + - sample_collection_start_date + - sample_collection_end_date + - sample_processing_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - presampling_activity + - presampling_activity_details + - sample_volume_measurement_value + - sample_volume_measurement_unit + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol_field + - environmental_site + - proximal_environmental_site + - environmental_material + - environmental_material_properties + - wastewater_system_type + - experimental_specimen_role_type + - experimental_control_details + - collection_device + - collection_method + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - extraction_recovery_efficiency_measurement_value + - extraction_recovery_efficiency_measurement_method + - microbiological_method - strain - - isolate ID - - alternative isolate ID - - progeny isolate ID - - isolated by - - isolated by laboratory name - - isolated by contact name - - isolated by contact email - - isolation date - - isolate received date + - isolate_id + - alternative_isolate_id + - progeny_isolate_id + - isolated_by + - isolated_by_laboratory_name + - isolated_by_contact_name + - isolated_by_contact_email + - isolation_date + - isolate_received_date - serovar - - serotyping method + - serotyping_method - phagetype - - water catchment area human population measurement value - - water catchment area human population range - - water catchment area human population measurement method - - water catchment area human population density value - - water catchment area human population density unit - - populated area type - - sampling weather conditions - - presampling weather conditions - - precipitation measurement value - - precipitation measurement unit - - precipitation measurement method - - ambient temperature measurement value - - ambient temperature measurement unit - - pH measurement value - - pH measurement method - - total daily flow rate measurement value - - total daily flow rate measurement unit - - total daily flow rate measurement method - - instantaneous flow rate measurement value - - instantaneous flow rate measurement unit - - instantaneous flow rate measurement method - - turbidity measurement value - - turbidity measurement unit - - turbidity measurement method - - dissolved oxygen measurement value - - dissolved oxygen measurement unit - - dissolved oxygen measurement method - - oxygen reduction potential (ORP) measurement value - - oxygen reduction potential (ORP) measurement unit - - oxygen reduction potential (ORP) measurement method - - chemical oxygen demand (COD) measurement value - - chemical oxygen demand (COD) measurement unit - - chemical oxygen demand (COD) measurement method - - carbonaceous biochemical oxygen demand (CBOD) measurement value - - carbonaceous biochemical oxygen demand (CBOD) measurement unit - - carbonaceous biochemical oxygen demand (CBOD) measurement method - - total suspended solids (TSS) measurement value - - total suspended solids (TSS) measurement unit - - total suspended solids (TSS) measurement method - - total dissolved solids (TDS) measurement value - - total dissolved solids (TDS) measurement unit - - total dissolved solids (TDS) measurement method - - total solids (TS) measurement value - - total solids (TS) measurement unit - - total solids (TS) measurement method - - alkalinity measurement value - - alkalinity measurement unit - - alkalinity measurement method - - conductivity measurement value - - conductivity measurement unit - - conductivity measurement method - - salinity measurement value - - salinity measurement unit - - salinity measurement method - - total nitrogen (TN) measurement value - - total nitrogen (TN) measurement unit - - total nitrogen (TN) measurement method - - total phosphorus (TP) measurement value - - total phosphorus (TP) measurement unit - - total phosphorus (TP) measurement method - - fecal contamination indicator - - fecal contamination value - - fecal contamination unit - - fecal contamination method - - fecal coliform count value - - fecal coliform count unit - - fecal coliform count method - - urinary contamination indicator - - urinary contamination value - - urinary contamination unit - - urinary contamination method - - sample temperature value (at collection) - - sample temperature unit (at collection) - - sample temperature value (when received) - - sample temperature unit (when received) - - purpose of sequencing - - purpose of sequencing details - - sequenced by - - sequenced by contact name - - sequenced by contact email - - sequence submitted by - - sequence submitter contact email - - sequencing date - - library ID - - sequencing platform - - sequencing instrument - - sequencing assay type - - library preparation kit - - sequencing protocol - - DNA fragment length - - genomic target enrichment method - - genomic target enrichment method details - - amplicon pcr primer scheme - - amplicon size - - quality control method name - - quality control method version - - quality control determination - - quality control issues - - quality control details - - raw sequence data processing method - - dehosting method - - sequence assembly software name - - sequence assembly software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - genome completeness - - number of base pairs sequenced - - number of total reads - - number of unique reads - - minimum post-trimming read length - - number of contigs - - percent Ns across total genome length - - N50 - - percent read contamination - - sequence assembly length - - reference genome accession - - deduplication method - - bioinformatics protocol - - read mapping software name - - read mapping software version - - taxonomic reference database name - - taxonomic reference database version - - taxonomic analysis report filename - - taxonomic analysis date - - read mapping criteria - - gene name - - diagnostic target presence - - diagnostic measurement value - - diagnostic measurement unit - - diagnostic measurement method - - authors - - DataHarmonizer provenance + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - sequencing_date + - library_id + - sequencing_platform + - sequencing_instrument + - sequencing_assay_type + - library_preparation_kit + - sequencing_protocol + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - genome_sequence_file_name + - genome_sequence_file_path + - sequence_assembly_software_name + - sequence_assembly_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - n50 + - percent_read_contamination + - sequence_assembly_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - assay_target_name_1 + - assay_target_details + - gene_symbol_1 + - diagnostic_target_presence_1 + - diagnostic_measurement_value_1 + - diagnostic_measurement_unit_1 + - diagnostic_measurement_method_1 + - assay_target_name_2 + - assay_target_details_2 + - gene_symbol_2 + - diagnostic_target_presence_2 + - diagnostic_measurement_value_2 + - diagnostic_measurement_unit_2 + - diagnostic_measurement_method_2 + - assay_target_name_3 + - assay_target_details_3 + - gene_symbol_3 + - diagnostic_target_presence_3 + - diagnostic_measurement_value_3 + - diagnostic_measurement_unit_3 + - diagnostic_measurement_method_3 slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database identifiers - specimen collector subsample ID: + specimen_collector_subsample_id: rank: 2 slot_group: Database identifiers - pooled sample ID: + pooled_sample_id: rank: 3 slot_group: Database identifiers - metagenome-assembled genome (MAG) ID: + metagenomeassembled_genome_mag_id: rank: 4 slot_group: Database identifiers - specimen collector project ID: + specimen_collector_project_id: rank: 5 slot_group: Database identifiers - BioProject accession: + bioproject_accession: rank: 6 slot_group: Database identifiers - BioSample accession: + biosample_accession: rank: 7 slot_group: Database identifiers - GenBank accession (versioned): + insdc_sequence_read_accession: rank: 8 slot_group: Database identifiers - SRA accession: + enterobase_accession: rank: 9 slot_group: Database identifiers - GISAID accession: + insdc_assembly_accession: rank: 10 slot_group: Database identifiers - GISAID virus name: + gisaid_accession: rank: 11 slot_group: Database identifiers - ENA accession: + gisaid_virus_name: rank: 12 slot_group: Database identifiers - DRA accession: + sampling_site_id: rank: 13 slot_group: Database identifiers - GSA accession: + sampling_event_id: rank: 14 slot_group: Database identifiers - Enterobase accession: + sample_collection_data_steward_name: rank: 15 - slot_group: Database identifiers - sampling site ID: + slot_group: Sample collection and processing + sample_collected_by_laboratory_name: rank: 16 - slot_group: Database identifiers - sampling event ID: + slot_group: Sample collection and processing + sample_collected_by: rank: 17 - slot_group: Database identifiers - sample collection data steward name: + slot_group: Sample collection and processing + sample_collector_contact_name: rank: 18 slot_group: Sample collection and processing - sample collected by: + sample_collector_contact_email: rank: 19 slot_group: Sample collection and processing - sample collector contact email: + geo_loc_name_country: rank: 20 slot_group: Sample collection and processing - geo loc name (country): + geo_loc_name_state_province_territory: rank: 21 slot_group: Sample collection and processing - geo loc name (state/province/territory): + geo_loc_name_county_region: rank: 22 slot_group: Sample collection and processing - geo loc name (county/region): + geo_loc_name_city: rank: 23 slot_group: Sample collection and processing - geo loc name (city): + geo_loc_name_site: rank: 24 slot_group: Sample collection and processing - geo loc name (site): + geo_loc_latitude: rank: 25 slot_group: Sample collection and processing - geo loc latitude: + geo_loc_longitude: rank: 26 slot_group: Sample collection and processing - geo loc longitude: + watershed_shapefile_availability: rank: 27 slot_group: Sample collection and processing - watershed shapefile availability: + watershed_shapefile_filename: rank: 28 slot_group: Sample collection and processing - watershed shapefile filename: - rank: 29 - slot_group: Sample collection and processing organism: - rank: 30 + rank: 29 slot_group: Sample collection and processing comments: 'Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. @@ -1915,537 +2098,555 @@ classes: - value: Vibrio cholerae any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - purpose of sampling: + purpose_of_sampling: + rank: 30 + slot_group: Sample collection and processing + scale_of_sampling: rank: 31 slot_group: Sample collection and processing - scale of sampling: + sample_received_date: rank: 32 slot_group: Sample collection and processing - sample received date: + sample_collection_start_date: rank: 33 slot_group: Sample collection and processing - sample collection date: + sample_collection_end_date: rank: 34 slot_group: Sample collection and processing - sample collection end date: + sample_processing_date: rank: 35 slot_group: Sample collection and processing - sample processing date: + sample_collection_start_time: rank: 36 slot_group: Sample collection and processing - sample collection start time: + sample_collection_end_time: rank: 37 slot_group: Sample collection and processing - sample collection end time: + sample_collection_time_of_day: rank: 38 slot_group: Sample collection and processing - sample collection time of day: + sample_collection_time_duration_value: rank: 39 slot_group: Sample collection and processing - sample collection time duration value: + sample_collection_time_duration_unit: rank: 40 slot_group: Sample collection and processing - sample collection time duration unit: + presampling_activity: rank: 41 slot_group: Sample collection and processing - presampling activity: + presampling_activity_details: rank: 42 slot_group: Sample collection and processing - presampling activity details: + sample_volume_measurement_value: rank: 43 slot_group: Sample collection and processing - sample volume measurement value: + sample_volume_measurement_unit: rank: 44 slot_group: Sample collection and processing - sample volume measurement unit: + sample_storage_method: rank: 45 slot_group: Sample collection and processing - sample storage method: + sample_storage_medium: rank: 46 slot_group: Sample collection and processing - sample storage medium: + sample_storage_duration_value: rank: 47 slot_group: Sample collection and processing - sample storage duration value: + sample_storage_duration_unit: rank: 48 slot_group: Sample collection and processing - sample storage duration unit: + specimen_processing: rank: 49 slot_group: Sample collection and processing - specimen processing: + specimen_processing_details: rank: 50 slot_group: Sample collection and processing - specimen processing details: + experimental_protocol_field: rank: 51 slot_group: Sample collection and processing - experimental protocol field: + environmental_site: rank: 52 slot_group: Sample collection and processing - environmental site: + proximal_environmental_site: rank: 53 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 54 slot_group: Sample collection and processing - environmental material properties: + environmental_material_properties: rank: 55 slot_group: Sample collection and processing - wastewater system type: + wastewater_system_type: rank: 56 slot_group: Sample collection and processing - experimental specimen role type: + experimental_specimen_role_type: rank: 57 slot_group: Sample collection and processing - experimental control details: + experimental_control_details: rank: 58 slot_group: Sample collection and processing - collection device: + collection_device: rank: 59 slot_group: Sample collection and processing - collection method: + collection_method: rank: 60 slot_group: Sample collection and processing - nucleic acid extraction method: + nucleic_acid_extraction_method: rank: 61 slot_group: Sample collection and processing - nucleic acid extraction kit: + nucleic_acid_extraction_kit: rank: 62 slot_group: Sample collection and processing - endogenous control details: + endogenous_control_details: rank: 63 slot_group: Sample collection and processing - extraction recovery efficiency measurement value: + extraction_recovery_efficiency_measurement_value: rank: 64 slot_group: Sample collection and processing - extraction recovery efficiency measurement method: + extraction_recovery_efficiency_measurement_method: rank: 65 slot_group: Sample collection and processing - microbiological method: + microbiological_method: rank: 66 slot_group: Strain and isolation information strain: rank: 67 slot_group: Strain and isolation information - isolate ID: + isolate_id: rank: 68 slot_group: Strain and isolation information - alternative isolate ID: + alternative_isolate_id: rank: 69 slot_group: Strain and isolation information - progeny isolate ID: + progeny_isolate_id: rank: 70 slot_group: Strain and isolation information - isolated by: + isolated_by: rank: 71 slot_group: Strain and isolation information - isolated by laboratory name: + isolated_by_laboratory_name: rank: 72 slot_group: Strain and isolation information - isolated by contact name: + isolated_by_contact_name: rank: 73 slot_group: Strain and isolation information - isolated by contact email: + isolated_by_contact_email: rank: 74 slot_group: Strain and isolation information - isolation date: + isolation_date: rank: 75 slot_group: Strain and isolation information - isolate received date: + isolate_received_date: rank: 76 slot_group: Strain and isolation information serovar: rank: 77 slot_group: Strain and isolation information - serotyping method: + serotyping_method: rank: 78 slot_group: Strain and isolation information phagetype: rank: 79 slot_group: Strain and isolation information - water catchment area human population measurement value: + water_catchment_area_human_population_measurement_value: rank: 80 slot_group: Environmental conditions and measurements - water catchment area human population range: + water_catchment_area_human_population_range: rank: 81 slot_group: Environmental conditions and measurements - water catchment area human population measurement method: + water_catchment_area_human_population_measurement_method: rank: 82 slot_group: Environmental conditions and measurements - water catchment area human population density value: + water_catchment_area_human_population_density_value: rank: 83 slot_group: Environmental conditions and measurements - water catchment area human population density unit: + water_catchment_area_human_population_density_unit: rank: 84 slot_group: Environmental conditions and measurements - populated area type: + populated_area_type: rank: 85 slot_group: Environmental conditions and measurements - sampling weather conditions: + sampling_weather_conditions: rank: 86 slot_group: Environmental conditions and measurements - presampling weather conditions: + presampling_weather_conditions: rank: 87 slot_group: Environmental conditions and measurements - precipitation measurement value: + precipitation_measurement_value: rank: 88 slot_group: Environmental conditions and measurements - precipitation measurement unit: + precipitation_measurement_unit: rank: 89 slot_group: Environmental conditions and measurements - precipitation measurement method: + precipitation_measurement_method: rank: 90 slot_group: Environmental conditions and measurements - ambient temperature measurement value: + ambient_temperature_measurement_value: rank: 91 slot_group: Environmental conditions and measurements - ambient temperature measurement unit: + ambient_temperature_measurement_unit: rank: 92 slot_group: Environmental conditions and measurements - pH measurement value: + ph_measurement_value: rank: 93 slot_group: Environmental conditions and measurements - pH measurement method: + ph_measurement_method: rank: 94 slot_group: Environmental conditions and measurements - total daily flow rate measurement value: + total_daily_flow_rate_measurement_value: rank: 95 slot_group: Environmental conditions and measurements - total daily flow rate measurement unit: + total_daily_flow_rate_measurement_unit: rank: 96 slot_group: Environmental conditions and measurements - total daily flow rate measurement method: + total_daily_flow_rate_measurement_method: rank: 97 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement value: + instantaneous_flow_rate_measurement_value: rank: 98 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement unit: + instantaneous_flow_rate_measurement_unit: rank: 99 slot_group: Environmental conditions and measurements - instantaneous flow rate measurement method: + instantaneous_flow_rate_measurement_method: rank: 100 slot_group: Environmental conditions and measurements - turbidity measurement value: + turbidity_measurement_value: rank: 101 slot_group: Environmental conditions and measurements - turbidity measurement unit: + turbidity_measurement_unit: rank: 102 slot_group: Environmental conditions and measurements - turbidity measurement method: + turbidity_measurement_method: rank: 103 slot_group: Environmental conditions and measurements - dissolved oxygen measurement value: + dissolved_oxygen_measurement_value: rank: 104 slot_group: Environmental conditions and measurements - dissolved oxygen measurement unit: + dissolved_oxygen_measurement_unit: rank: 105 slot_group: Environmental conditions and measurements - dissolved oxygen measurement method: + dissolved_oxygen_measurement_method: rank: 106 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement value: + oxygen_reduction_potential_orp_measurement_value: rank: 107 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement unit: + oxygen_reduction_potential_orp_measurement_unit: rank: 108 slot_group: Environmental conditions and measurements - oxygen reduction potential (ORP) measurement method: + oxygen_reduction_potential_orp_measurement_method: rank: 109 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement value: + chemical_oxygen_demand_cod_measurement_value: rank: 110 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement unit: + chemical_oxygen_demand_cod_measurement_unit: rank: 111 slot_group: Environmental conditions and measurements - chemical oxygen demand (COD) measurement method: + chemical_oxygen_demand_cod_measurement_method: rank: 112 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement value: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: rank: 113 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement unit: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: rank: 114 slot_group: Environmental conditions and measurements - carbonaceous biochemical oxygen demand (CBOD) measurement method: + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: rank: 115 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement value: + total_suspended_solids_tss_measurement_value: rank: 116 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement unit: + total_suspended_solids_tss_measurement_unit: rank: 117 slot_group: Environmental conditions and measurements - total suspended solids (TSS) measurement method: + total_suspended_solids_tss_measurement_method: rank: 118 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement value: + total_dissolved_solids_tds_measurement_value: rank: 119 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement unit: + total_dissolved_solids_tds_measurement_unit: rank: 120 slot_group: Environmental conditions and measurements - total dissolved solids (TDS) measurement method: + total_dissolved_solids_tds_measurement_method: rank: 121 slot_group: Environmental conditions and measurements - total solids (TS) measurement value: + total_solids_ts_measurement_value: rank: 122 slot_group: Environmental conditions and measurements - total solids (TS) measurement unit: + total_solids_ts_measurement_unit: rank: 123 slot_group: Environmental conditions and measurements - total solids (TS) measurement method: + total_solids_ts_measurement_method: rank: 124 slot_group: Environmental conditions and measurements - alkalinity measurement value: + alkalinity_measurement_value: rank: 125 slot_group: Environmental conditions and measurements - alkalinity measurement unit: + alkalinity_measurement_unit: rank: 126 slot_group: Environmental conditions and measurements - alkalinity measurement method: + alkalinity_measurement_method: rank: 127 slot_group: Environmental conditions and measurements - conductivity measurement value: + conductivity_measurement_value: rank: 128 slot_group: Environmental conditions and measurements - conductivity measurement unit: + conductivity_measurement_unit: rank: 129 slot_group: Environmental conditions and measurements - conductivity measurement method: + conductivity_measurement_method: rank: 130 slot_group: Environmental conditions and measurements - salinity measurement value: + salinity_measurement_value: rank: 131 slot_group: Environmental conditions and measurements - salinity measurement unit: + salinity_measurement_unit: rank: 132 slot_group: Environmental conditions and measurements - salinity measurement method: + salinity_measurement_method: rank: 133 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement value: + total_nitrogen_tn_measurement_value: rank: 134 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement unit: + total_nitrogen_tn_measurement_unit: rank: 135 slot_group: Environmental conditions and measurements - total nitrogen (TN) measurement method: + total_nitrogen_tn_measurement_method: rank: 136 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement value: + total_phosphorus_tp_measurement_value: rank: 137 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement unit: + total_phosphorus_tp_measurement_unit: rank: 138 slot_group: Environmental conditions and measurements - total phosphorus (TP) measurement method: + total_phosphorus_tp_measurement_method: rank: 139 slot_group: Environmental conditions and measurements - fecal contamination indicator: + fecal_contamination_indicator: rank: 140 slot_group: Environmental conditions and measurements - fecal contamination value: + fecal_contamination_value: rank: 141 slot_group: Environmental conditions and measurements - fecal contamination unit: + fecal_contamination_unit: rank: 142 slot_group: Environmental conditions and measurements - fecal contamination method: + fecal_contamination_method: rank: 143 slot_group: Environmental conditions and measurements - fecal coliform count value: + fecal_coliform_count_value: rank: 144 slot_group: Environmental conditions and measurements - fecal coliform count unit: + fecal_coliform_count_unit: rank: 145 slot_group: Environmental conditions and measurements - fecal coliform count method: + fecal_coliform_count_method: rank: 146 slot_group: Environmental conditions and measurements - urinary contamination indicator: + urinary_contamination_indicator: rank: 147 slot_group: Environmental conditions and measurements - urinary contamination value: + urinary_contamination_value: rank: 148 slot_group: Environmental conditions and measurements - urinary contamination unit: + urinary_contamination_unit: rank: 149 slot_group: Environmental conditions and measurements - urinary contamination method: + urinary_contamination_method: rank: 150 slot_group: Environmental conditions and measurements - sample temperature value (at collection): + sample_temperature_value_at_collection: rank: 151 slot_group: Environmental conditions and measurements - sample temperature unit (at collection): + sample_temperature_unit_at_collection: rank: 152 slot_group: Environmental conditions and measurements - sample temperature value (when received): + sample_temperature_value_when_received: rank: 153 slot_group: Environmental conditions and measurements - sample temperature unit (when received): + sample_temperature_unit_when_received: rank: 154 slot_group: Environmental conditions and measurements - purpose of sequencing: + purpose_of_sequencing: rank: 155 slot_group: Sequence information - purpose of sequencing details: + purpose_of_sequencing_details: rank: 156 slot_group: Sequence information - sequenced by: + sequenced_by: rank: 157 slot_group: Sequence information - sequenced by contact name: + sequenced_by_laboratory_name: rank: 158 slot_group: Sequence information - sequenced by contact email: + sequenced_by_contact_name: rank: 159 slot_group: Sequence information - sequence submitted by: + sequenced_by_contact_email: rank: 160 slot_group: Sequence information - sequence submitter contact email: + sequence_submitted_by: rank: 161 slot_group: Sequence information - sequencing date: + sequence_submitter_contact_email: rank: 162 slot_group: Sequence information - library ID: + sequencing_date: rank: 163 slot_group: Sequence information - sequencing platform: + library_id: rank: 164 slot_group: Sequence information - sequencing instrument: + sequencing_platform: rank: 165 slot_group: Sequence information - sequencing assay type: + sequencing_instrument: rank: 166 slot_group: Sequence information - library preparation kit: + sequencing_assay_type: rank: 167 slot_group: Sequence information - sequencing protocol: + library_preparation_kit: rank: 168 slot_group: Sequence information - DNA fragment length: + sequencing_protocol: rank: 169 slot_group: Sequence information - genomic target enrichment method: + dna_fragment_length: rank: 170 slot_group: Sequence information - genomic target enrichment method details: + genomic_target_enrichment_method: rank: 171 slot_group: Sequence information - amplicon pcr primer scheme: + genomic_target_enrichment_method_details: rank: 172 slot_group: Sequence information - amplicon size: + amplicon_pcr_primer_scheme: rank: 173 slot_group: Sequence information - quality control method name: + amplicon_size: rank: 174 - slot_group: Bioinformatics and QC metrics - quality control method version: + slot_group: Sequence information + quality_control_method_name: rank: 175 slot_group: Bioinformatics and QC metrics - quality control determination: + quality_control_method_version: rank: 176 slot_group: Bioinformatics and QC metrics - quality control issues: + quality_control_determination: rank: 177 slot_group: Bioinformatics and QC metrics - quality control details: + quality_control_issues: rank: 178 slot_group: Bioinformatics and QC metrics - raw sequence data processing method: + quality_control_details: rank: 179 slot_group: Bioinformatics and QC metrics - dehosting method: + raw_sequence_data_processing_method: rank: 180 slot_group: Bioinformatics and QC metrics - sequence assembly software name: + dehosting_method: rank: 181 slot_group: Bioinformatics and QC metrics - sequence assembly software version: + genome_sequence_file_name: rank: 182 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + genome_sequence_file_path: rank: 183 slot_group: Bioinformatics and QC metrics - depth of coverage value: + sequence_assembly_software_name: rank: 184 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + sequence_assembly_software_version: rank: 185 slot_group: Bioinformatics and QC metrics - genome completeness: + breadth_of_coverage_value: rank: 186 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + depth_of_coverage_value: rank: 187 slot_group: Bioinformatics and QC metrics - number of total reads: + depth_of_coverage_threshold: rank: 188 slot_group: Bioinformatics and QC metrics - number of unique reads: + genome_completeness: rank: 189 slot_group: Bioinformatics and QC metrics - minimum post-trimming read length: + number_of_base_pairs_sequenced: rank: 190 slot_group: Bioinformatics and QC metrics - number of contigs: + number_of_total_reads: rank: 191 slot_group: Bioinformatics and QC metrics - percent Ns across total genome length: + number_of_unique_reads: rank: 192 slot_group: Bioinformatics and QC metrics - N50: + minimum_posttrimming_read_length: rank: 193 slot_group: Bioinformatics and QC metrics - percent read contamination: + number_of_contigs: rank: 194 slot_group: Bioinformatics and QC metrics - sequence assembly length: + percent_ns_across_total_genome_length: rank: 195 slot_group: Bioinformatics and QC metrics - reference genome accession: + n50: rank: 196 slot_group: Bioinformatics and QC metrics - deduplication method: + percent_read_contamination: rank: 197 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + sequence_assembly_length: rank: 198 slot_group: Bioinformatics and QC metrics - read mapping software name: + reference_genome_accession: rank: 199 - slot_group: Taxonomic identification information - required: true - read mapping software version: + slot_group: Bioinformatics and QC metrics + deduplication_method: rank: 200 - slot_group: Taxonomic identification information - required: true - taxonomic reference database name: + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: rank: 201 - slot_group: Taxonomic identification information - taxonomic reference database version: + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: rank: 202 slot_group: Taxonomic identification information - taxonomic analysis report filename: + required: true + read_mapping_software_version: rank: 203 slot_group: Taxonomic identification information - taxonomic analysis date: + required: true + taxonomic_reference_database_name: rank: 204 slot_group: Taxonomic identification information - read mapping criteria: + taxonomic_reference_database_version: rank: 205 slot_group: Taxonomic identification information - gene name: + taxonomic_analysis_report_filename: rank: 206 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 207 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 208 + slot_group: Taxonomic identification information + assay_target_name_1: + rank: 209 + slot_group: Pathogen diagnostic testing + assay_target_details: + rank: 210 + slot_group: Pathogen diagnostic testing + gene_symbol_1: + rank: 211 slot_group: Pathogen diagnostic testing comments: 'Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: @@ -2454,28 +2655,80 @@ classes: - value: gyrase A any_of: - range: WhitespaceMinimizedString - - range: null value menu - diagnostic target presence: - rank: 207 + - range: NullValueMenu + diagnostic_target_presence_1: + rank: 212 slot_group: Pathogen diagnostic testing - diagnostic measurement value: - rank: 208 + diagnostic_measurement_value_1: + rank: 213 slot_group: Pathogen diagnostic testing - diagnostic measurement unit: - rank: 209 + diagnostic_measurement_unit_1: + rank: 214 slot_group: Pathogen diagnostic testing - diagnostic measurement method: - rank: 210 + diagnostic_measurement_method_1: + rank: 215 + slot_group: Pathogen diagnostic testing + assay_target_name_2: + rank: 216 + slot_group: Pathogen diagnostic testing + assay_target_details_2: + rank: 217 + slot_group: Pathogen diagnostic testing + gene_symbol_2: + rank: 218 + slot_group: Pathogen diagnostic testing + comments: 'Provide the full name of the gene used in the test. Standardized + gene names can be found in the Gene Ontology using this look-up service: + https://bit.ly/2Sq1LbI' + examples: + - value: gyrase A + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + diagnostic_target_presence_2: + rank: 219 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value_2: + rank: 220 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit_2: + rank: 221 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method_2: + rank: 222 + slot_group: Pathogen diagnostic testing + assay_target_name_3: + rank: 223 + slot_group: Pathogen diagnostic testing + assay_target_details_3: + rank: 224 + slot_group: Pathogen diagnostic testing + gene_symbol_3: + rank: 225 + slot_group: Pathogen diagnostic testing + comments: 'Provide the full name of the gene used in the test. Standardized + gene names can be found in the Gene Ontology using this look-up service: + https://bit.ly/2Sq1LbI' + examples: + - value: gyrase A + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + diagnostic_target_presence_3: + rank: 226 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value_3: + rank: 227 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit_3: + rank: 228 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method_3: + rank: 229 slot_group: Pathogen diagnostic testing - authors: - rank: 211 - slot_group: Contributor acknowledgement - DataHarmonizer provenance: - rank: 212 - slot_group: Contributor acknowledgement slots: - specimen collector sample ID: - name: specimen collector sample ID + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. comments: Store the collector sample ID. If this number is considered identifiable @@ -2490,8 +2743,11 @@ slots: required: true examples: - value: ASDFG123 - specimen collector subsample ID: - name: specimen collector subsample ID + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:sample_name + - NCBI_SRA:sample_name + specimen_collector_subsample_id: + name: specimen_collector_subsample_id title: specimen collector subsample ID description: The user-defined identifier assigned to a portion of the original sample. @@ -2500,8 +2756,10 @@ slots: range: WhitespaceMinimizedString examples: - value: ASDFG123_12 - pooled sample ID: - name: pooled sample ID + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_id + pooled_sample_id: + name: pooled_sample_id title: pooled sample ID description: The user-defined identifier assigned to a combined (pooled) set of samples. @@ -2511,8 +2769,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 12345AYZ - metagenome-assembled genome (MAG) ID: - name: metagenome-assembled genome (MAG) ID + metagenomeassembled_genome_mag_id: + name: metagenomeassembled_genome_mag_id title: metagenome-assembled genome (MAG) ID description: The user-defined identifier assigned to a genome reconstructed from metagenomic data. @@ -2521,16 +2779,18 @@ slots: range: WhitespaceMinimizedString examples: - value: XYZ1234.1 - specimen collector project ID: - name: specimen collector project ID + specimen_collector_project_id: + name: specimen_collector_project_id title: specimen collector project ID description: The user-defined project name assigned to a sequencing project. comments: If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. slot_uri: GENEPIO:0100918 range: WhitespaceMinimizedString - BioProject accession: - name: BioProject accession + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:project_name + bioproject_accession: + name: bioproject_accession title: BioProject accession description: The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. @@ -2549,8 +2809,10 @@ slots: interpolated: true examples: - value: PRJNA608651 - BioSample accession: - name: BioSample accession + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:bioproject_accession + biosample_accession: + name: biosample_accession title: BioSample accession description: The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. @@ -2565,14 +2827,17 @@ slots: partial_match: false interpolated: true examples: - - value: SAMN14180202, SAMD00000001 - GenBank accession (versioned): - name: GenBank accession (versioned) - title: GenBank accession (versioned) - description: The versioned identifier assigned to an assembly or consensus sequence - in GenBank archives. - comments: Store the versioned GenBank accession assigned to the submitted sequence. - slot_uri: GENEPIO:0100754 + - value: SAMN14180202, SAMEA00000002, SAMD00000001 + insdc_sequence_read_accession: + name: insdc_sequence_read_accession + title: INSDC sequence read accession + description: The identifier assigned to a sequence in one of the International + Nucleotide Sequence Database Collaboration (INSDC) repositories. + comments: Store the accession assigned to the submitted sequence. European Nucleotide + Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start + with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome + Sequence Archive (GSA) accessions start with CRR. + slot_uri: GENEPIO:0101203 range: WhitespaceMinimizedString pattern: '{UPPER_CASE}' structured_pattern: @@ -2580,15 +2845,14 @@ slots: partial_match: false interpolated: true examples: - - value: LZ986655.1 - SRA accession: - name: SRA accession - title: SRA accession - description: The Sequence Read Archive (SRA) identifier linking raw read data, - methodological metadata and quality control metrics submitted to the INSDC. - comments: Store the accession assigned to the submitted sequence. NCBI-SRA accessions - start with SRR. - slot_uri: GENEPIO:0001142 + - value: ERR123456, DRR123456, CRR123456 + enterobase_accession: + name: enterobase_accession + title: Enterobase accession + description: The identifier assigned to a sequence in Enterobase archives. + comments: Store the barcode assigned to the submitted sequence. Enterobase barcodes + start with different 3 letter codes depending on the organism. + slot_uri: GENEPIO:0100759 range: WhitespaceMinimizedString pattern: '{UPPER_CASE}' structured_pattern: @@ -2596,9 +2860,26 @@ slots: partial_match: false interpolated: true examples: - - value: SRR11177792 - GISAID accession: - name: GISAID accession + - value: SAL_AA0019AA_ST + insdc_assembly_accession: + name: insdc_assembly_accession + title: INSDC assembly accession + description: The versioned identifier assigned to an assembly or consensus sequence + in one of the International Nucleotide Sequence Database Collaboration (INSDC) + repositories. + comments: Store the versioned accession assigned to the submitted sequence e.g. + the GenBank accession version. + slot_uri: GENEPIO:0101204 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: LZ986655.1 + gisaid_accession: + name: gisaid_accession title: GISAID accession description: The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. @@ -2613,8 +2894,8 @@ slots: interpolated: true examples: - value: EPI_ISL_402131 - GISAID virus name: - name: GISAID virus name + gisaid_virus_name: + name: gisaid_virus_name title: GISAID virus name description: The user-defined GISAID virus name assigned to the sequence. comments: GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". @@ -2627,71 +2908,8 @@ slots: interpolated: true examples: - value: hCoV-19/Canada/prov_rona_99/2020 - ENA accession: - name: ENA accession - title: ENA accession - description: The identifier assigned to a sequence in the European Nucleotide - Archive (ENA). - comments: Store the accession assigned to the submitted sequence. ENA sequence - accessions start with ERR. - slot_uri: GENEPIO:0100755 - range: WhitespaceMinimizedString - pattern: '{UPPER_CASE}' - structured_pattern: - syntax: '{UPPER_CASE}' - partial_match: false - interpolated: true - examples: - - value: ERR123456 - DRA accession: - name: DRA accession - title: DRA accession - description: The identifier assigned to a sequence in DNA Data Bank of Japan (DDBJ) - sequence read archives. - comments: Store the accession assigned to the submitted sequence. DRA accessions - start with DRR. - slot_uri: GENEPIO:0100757 - range: WhitespaceMinimizedString - pattern: '{UPPER_CASE}' - structured_pattern: - syntax: '{UPPER_CASE}' - partial_match: false - interpolated: true - examples: - - value: DRR123456 - GSA accession: - name: GSA accession - title: GSA accession - description: The identifier assigned to a BioSample in GSA (Genome Sequence Archive) - archives. - comments: Store the accession assigned to the submitted sequence. GSA accessions - start with CRR. - slot_uri: GENEPIO:0100758 - range: WhitespaceMinimizedString - pattern: '{UPPER_CASE}' - structured_pattern: - syntax: '{UPPER_CASE}' - partial_match: false - interpolated: true - examples: - - value: CRR123456 - Enterobase accession: - name: Enterobase accession - title: Enterobase accession - description: The identifier assigned to a sequence in Enterobase archives. - comments: Store the barcode assigned to the submitted sequence. Enterobase barcodes - start with different 3 letter codes depending on the organism. - slot_uri: GENEPIO:0100759 - range: WhitespaceMinimizedString - pattern: '{UPPER_CASE}' - structured_pattern: - syntax: '{UPPER_CASE}' - partial_match: false - interpolated: true - examples: - - value: SAL_AA0019AA_ST - sampling site ID: - name: sampling site ID + sampling_site_id: + name: sampling_site_id title: sampling site ID description: The user-defined identifier assigned to a specific location from which samples are taken. @@ -2705,8 +2923,10 @@ slots: recommended: true examples: - value: Site 12A - sampling event ID: - name: sampling event ID + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_site_id + sampling_event_id: + name: sampling_event_id title: sampling event ID description: The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. @@ -2718,8 +2938,8 @@ slots: recommended: true examples: - value: Event 120522.1 - sample collection data steward name: - name: sample collection data steward name + sample_collection_data_steward_name: + name: sample_collection_data_steward_name title: sample collection data steward name description: The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. @@ -2728,8 +2948,19 @@ slots: range: WhitespaceMinimizedString examples: - value: Joe Bloggs - sample collected by: - name: sample collected by + sample_collected_by_laboratory_name: + name: sample_collected_by_laboratory_name + title: sample collected by laboratory name + description: The specific laboratory affiliation of the sample collector. + comments: Provide the name of the specific laboratory that collected the sample + (avoid abbreviations). If the information is unknown or cannot be provided, + leave blank or provide a null value. + slot_uri: GENEPIO:0100428 + range: WhitespaceMinimizedString + examples: + - value: Topp Lab + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the organization with which the sample collector is affiliated. comments: The name of the agency should be written out in full, (with minor exceptions) @@ -2737,12 +2968,28 @@ slots: slot_uri: GENEPIO:0001153 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Public Health Agency of Canada - sample collector contact email: - name: sample collector contact email + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:collected_by + sample_collector_contact_name: + name: sample_collector_contact_name + title: sample collector contact name + description: The name or job title of the contact responsible for follow-up regarding + the sample. + comments: Provide the name of an individual or their job title. As personnel turnover + may render the contact's name obsolete, it is more preferable to provide a job + title for ensuring accuracy of information and institutional memory. If the + information is unknown or cannot be provided, leave blank or provide a null + value. + slot_uri: GENEPIO:0100432 + range: WhitespaceMinimizedString + examples: + - value: Joe Bloggs, Enterics Lab Manager + sample_collector_contact_email: + name: sample_collector_contact_email title: sample collector contact email description: The email address of the contact responsible for follow-up regarding the sample. @@ -2753,20 +3000,20 @@ slots: pattern: ^\S+@\S+\.\S+$ examples: - value: WaterTester@facility.ca - geo loc name (country): - name: geo loc name (country) + geo_loc_name_country: + name: geo_loc_name_country title: geo loc name (country) description: The country of origin of the sample. comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true examples: - value: Canada - geo loc name (state/province/territory): - name: geo loc name (state/province/territory) + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo loc name (state/province/territory) description: The state/province/territory of origin of the sample. comments: 'Provide the state/province/territory name from the GAZ geography ontology. @@ -2774,12 +3021,12 @@ slots: slot_uri: GENEPIO:0001185 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Western Cape - geo loc name (county/region): - name: geo loc name (county/region) + geo_loc_name_county_region: + name: geo_loc_name_county_region title: geo loc name (county/region) description: The county/region of origin of the sample. comments: 'Provide the county/region name from the GAZ geography ontology. Search @@ -2788,8 +3035,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Derbyshire - geo loc name (city): - name: geo loc name (city) + geo_loc_name_city: + name: geo_loc_name_city title: geo loc name (city) description: The city of origin of the sample. comments: 'Provide the city name from the GAZ geography ontology. Search for geography @@ -2798,8 +3045,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Vancouver - geo loc name (site): - name: geo loc name (site) + geo_loc_name_site: + name: geo_loc_name_site title: geo loc name (site) description: The name of a specific geographical location e.g. Credit River (rather than river). @@ -2809,8 +3056,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Credit River - geo loc latitude: - name: geo loc latitude + geo_loc_latitude: + name: geo_loc_latitude title: geo loc latitude description: The latitude coordinates of the geographical location of sample collection. comments: Provide latitude coordinates if available. Do not use the centre of @@ -2821,8 +3068,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 38.98 N - geo loc longitude: - name: geo loc longitude + geo_loc_longitude: + name: geo_loc_longitude title: geo loc longitude description: The longitude coordinates of the geographical location of sample collection. @@ -2834,8 +3081,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 77.11 W - watershed shapefile availability: - name: watershed shapefile availability + watershed_shapefile_availability: + name: watershed_shapefile_availability title: watershed shapefile availability description: The availability status of a shapefile descriping the catchment contributing to a watershed. @@ -2843,12 +3090,12 @@ slots: shapefile would be available upon request. slot_uri: GENEPIO:0100919 any_of: - - range: watershed shapefile availability menu - - range: null value menu + - range: WatershedShapefileAvailabilityMenu + - range: NullValueMenu examples: - value: watershed shapefile available - watershed shapefile filename: - name: watershed shapefile filename + watershed_shapefile_filename: + name: watershed_shapefile_filename title: watershed shapefile filename description: The name of the watershed shapefile. comments: Provide the shapefile filename corresponding to the watershed from which @@ -2863,8 +3110,11 @@ slots: title: organism description: Taxonomic name of the organism. slot_uri: GENEPIO:0001191 - purpose of sampling: - name: purpose of sampling + multivalued: true + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1 + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: The reason a sample was collected may provide information about potential @@ -2875,39 +3125,43 @@ slots: of sequencing" field. slot_uri: GENEPIO:0001198 any_of: - - range: purpose of sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu multivalued: true required: true examples: - value: Public health surveillance - scale of sampling: - name: scale of sampling + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling + scale_of_sampling: + name: scale_of_sampling title: scale of sampling description: The range of locations or entities sampled expressed in general terms. comments: Provide the scale of wastewater sampling by selecting a value from the picklist. slot_uri: GENEPIO:0100877 any_of: - - range: scale of sampling menu - - range: null value menu + - range: ScaleOfSamplingMenu + - range: NullValueMenu recommended: true examples: - value: Community-level surveillance - sample received date: - name: sample received date + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sampling + sample_received_date: + name: sample_received_date title: sample received date description: The date on which the sample was received. comments: Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". slot_uri: GENEPIO:0001179 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-28' - sample collection date: - name: sample collection date - title: sample collection date + sample_collection_start_date: + name: sample_collection_start_date + title: sample collection start date description: The date on which the sample was collected, or sampling began for a continuous sample. comments: If your sample is a continuous sample please use this field to capture @@ -2917,12 +3171,12 @@ slots: slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu + - range: NullValueMenu required: true examples: - value: '2020-03-16' - sample collection end date: - name: sample collection end date + sample_collection_end_date: + name: sample_collection_end_date title: sample collection end date description: The date on which sample collection ended for a continuous sample. comments: Provide the date that sample collection ended in ISO 8601 format i.e. @@ -2930,12 +3184,12 @@ slots: slot_uri: GENEPIO:0101071 any_of: - range: date - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: '2020-03-18' - sample processing date: - name: sample processing date + sample_processing_date: + name: sample_processing_date title: sample processing date description: The date on which the sample was processed. comments: Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". @@ -2944,35 +3198,35 @@ slots: slot_uri: GENEPIO:0100763 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-16' - sample collection start time: - name: sample collection start time + sample_collection_start_time: + name: sample_collection_start_time title: sample collection start time description: The time at which sample collection began. comments: Provide this time in ISO 8601 24hr format, in your local time. slot_uri: GENEPIO:0101072 any_of: - range: time - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 17:15 PST - sample collection end time: - name: sample collection end time + sample_collection_end_time: + name: sample_collection_end_time title: sample collection end time description: The time at which sample collection ended. comments: Provide this time in ISO 8601 24hr format, in your local time. slot_uri: GENEPIO:0101073 any_of: - range: time - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 19:15 PST - sample collection time of day: - name: sample collection time of day + sample_collection_time_of_day: + name: sample_collection_time_of_day title: sample collection time of day description: The descriptive time of day during which the sample was collected. comments: If known, select a value from the pick list. The time of sample processing @@ -2980,36 +3234,40 @@ slots: over the course of the day. slot_uri: GENEPIO:0100765 any_of: - - range: sample collection time of day menu - - range: null value menu + - range: SampleCollectionTimeOfDayMenu + - range: NullValueMenu examples: - value: Morning - sample collection time duration value: - name: sample collection time duration value + sample_collection_time_duration_value: + name: sample_collection_time_duration_value title: sample collection time duration value description: The amount of time over which the sample was collected. comments: Provide the numerical value of time. slot_uri: GENEPIO:0100766 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: '4' - sample collection time duration unit: - name: sample collection time duration unit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration + sample_collection_time_duration_unit: + name: sample_collection_time_duration_unit title: sample collection time duration unit description: The units of the time duration measurement of sample collection. comments: Provide the units from the pick list. slot_uri: GENEPIO:0100767 any_of: - - range: sample collection duration unit menu - - range: null value menu + - range: SampleCollectionDurationUnitMenu + - range: NullValueMenu recommended: true examples: - value: Hour - presampling activity: - name: presampling activity + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_duration + presampling_activity: + name: presampling_activity title: presampling activity description: The activities or variables upstream of sample collection that may affect the sample. @@ -3019,13 +3277,13 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100433 any_of: - - range: presampling activity menu - - range: null value menu + - range: PresamplingActivityMenu + - range: NullValueMenu multivalued: true examples: - value: Agricultural activity - presampling activity details: - name: presampling activity details + presampling_activity_details: + name: presampling_activity_details title: presampling activity details description: The details of the activities or variables that affected the sample collected. @@ -3033,11 +3291,11 @@ slots: slot_uri: GENEPIO:0100434 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: Agricultural waste from large farm contributes waste to the site sampled. - sample volume measurement value: - name: sample volume measurement value + sample_volume_measurement_value: + name: sample_volume_measurement_value title: sample volume measurement value description: The numerical value of the volume measurement of the sample collected. comments: Provide the numerical value of volume. @@ -3045,19 +3303,23 @@ slots: range: WhitespaceMinimizedString examples: - value: '5' - sample volume measurement unit: - name: sample volume measurement unit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume + sample_volume_measurement_unit: + name: sample_volume_measurement_unit title: sample volume measurement unit description: The units of the volume measurement of the sample collected. comments: Provide the units from the pick list. slot_uri: GENEPIO:0100769 any_of: - - range: sample volume measurement unit menu - - range: null value menu + - range: SampleVolumeMeasurementUnitMenu + - range: NullValueMenu examples: - value: mL - sample storage method: - name: sample storage method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:collection_volume + sample_storage_method: + name: sample_storage_method title: sample storage method description: The process used to store the sample. comments: Provide details of how the sample was stored from time of collection @@ -3070,8 +3332,8 @@ slots: (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. - sample storage medium: - name: sample storage medium + sample_storage_medium: + name: sample_storage_medium title: sample storage medium description: The medium in which a sample is stored. comments: Provide the name of the transport medium or storage medium used for @@ -3080,8 +3342,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Cary-Blair transport medium - sample storage duration value: - name: sample storage duration value + sample_storage_duration_value: + name: sample_storage_duration_value title: sample storage duration value description: The numerical value of the time measurement during which a sample is in storage. @@ -3090,32 +3352,34 @@ slots: range: WhitespaceMinimizedString examples: - value: '5' - sample storage duration unit: - name: sample storage duration unit + sample_storage_duration_unit: + name: sample_storage_duration_unit title: sample storage duration unit description: The units of a measured sample storage duration. comments: Provide the units from the pick list. slot_uri: GENEPIO:0101015 any_of: - - range: sample storage duration unit menu - - range: null value menu + - range: SampleStorageDurationUnitMenu + - range: NullValueMenu examples: - value: Day - specimen processing: - name: specimen processing + specimen_processing: + name: specimen_processing title: specimen processing description: Any processing applied to the sample during or after receiving the sample. comments: Select processes from the picklist that were applied to this sample. slot_uri: GENEPIO:0001253 any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true examples: - value: Centrifugation - specimen processing details: - name: specimen processing details + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing + specimen_processing_details: + name: specimen_processing_details title: specimen processing details description: The details of the processing applied to the sample during or after receiving the sample. @@ -3125,8 +3389,10 @@ slots: examples: - value: 25 samples were pooled and further prepared as a single sample during library prep. - experimental protocol field: - name: experimental protocol field + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:specimen_processing_details + experimental_protocol_field: + name: experimental_protocol_field title: experimental protocol field description: The name of the overarching experimental methodology that was used to process the biomaterial. @@ -3134,8 +3400,8 @@ slots: provide a link to the protocol. slot_uri: GENEPIO:0101029 range: WhitespaceMinimizedString - environmental site: - name: environmental site + environmental_site: + name: environmental_site title: environmental site description: An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. @@ -3143,14 +3409,29 @@ slots: provided in the template. If not applicable, choose a null value. slot_uri: GENEPIO:0001232 any_of: - - range: environmental site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true recommended: true examples: - value: Meat processing plant - environmental material: - name: environmental material + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_site + proximal_environmental_site: + name: proximal_environmental_site + title: proximal environmental site + description: An environmental location in the natural or built environment, that + is proximal to a sampling location and which can impact a sample. + comments: Provide a descriptor of the environmental site close to the sampling + site. Use the picklist provided in the template. If not applicable, choose a + null value. + slot_uri: GENEPIO:0101205 + range: EnvironmentalSiteMenu + multivalued: true + examples: + - value: Farm + environmental_material: + name: environmental_material title: environmental material description: A substance obtained from the natural or man-made environment e.g. soil, water, sewage. @@ -3158,14 +3439,16 @@ slots: picklist provided in the template. If not applicable, choose a null value. slot_uri: GENEPIO:0001223 any_of: - - range: environmental material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true examples: - value: Raw wastewater - environmental material properties: - name: environmental material properties + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_matrix + environmental_material_properties: + name: environmental_material_properties title: environmental material properties description: The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. @@ -3173,14 +3456,14 @@ slots: from the pick list. slot_uri: GENEPIO:0100770 any_of: - - range: environmental material properties menu - - range: null value menu + - range: EnvironmentalMaterialPropertiesMenu + - range: NullValueMenu multivalued: true recommended: true examples: - value: Stagnant - wastewater system type: - name: wastewater system type + wastewater_system_type: + name: wastewater_system_type title: wastewater system type description: The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine @@ -3188,13 +3471,13 @@ slots: the provided pick list. slot_uri: GENEPIO:0100771 any_of: - - range: wastewater system type menu - - range: null value menu + - range: WastewaterSystemTypeMenu + - range: NullValueMenu recommended: true examples: - value: Sanitary sewer - experimental specimen role type: - name: experimental specimen role type + experimental_specimen_role_type: + name: experimental_specimen_role_type title: experimental specimen role type description: The type of role that the sample represents in the experiment. comments: Samples can play different types of roles in experiments. A sample under @@ -3205,13 +3488,13 @@ slots: a control, leave blank or select "Not Applicable". slot_uri: GENEPIO:0100921 any_of: - - range: experimental specimen role type menu - - range: null value menu + - range: ExperimentalSpecimenRoleTypeMenu + - range: NullValueMenu multivalued: true examples: - value: Positive experimental control - experimental control details: - name: experimental control details + experimental_control_details: + name: experimental_control_details title: experimental control details description: The details regarding the experimental control contained in the sample. comments: Provide details regarding the nature of the reference strain used as @@ -3220,8 +3503,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Human coronavirus 229E (HCoV-229E) spiked in sample as process control - collection device: - name: collection device + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. grab sampler. @@ -3229,27 +3512,29 @@ slots: provided in the template. If not applicable, choose a null value. slot_uri: GENEPIO:0001234 any_of: - - range: collection device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu multivalued: true examples: - value: Automatic flow-proportional sampler - collection method: - name: collection method + collection_method: + name: collection_method title: collection method description: The process used to collect the sample. comments: Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. slot_uri: GENEPIO:0001241 any_of: - - range: collection method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu multivalued: true recommended: true examples: - value: Automatic composite sampling - nucleic acid extraction method: - name: nucleic acid extraction method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_type + nucleic_acid_extraction_method: + name: nucleic_acid_extraction_method title: nucleic acid extraction method description: The process used to extract genomic material from a sample. comments: Briefly describe the extraction method used. @@ -3258,8 +3543,10 @@ slots: examples: - value: Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 - nucleic acid extraction kit: - name: nucleic acid extraction kit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:extraction_method + nucleic_acid_extraction_kit: + name: nucleic_acid_extraction_kit title: nucleic acid extraction kit description: The kit used to extract genomic material from a sample comments: Provide the name of the genomic extraction kit used. @@ -3267,8 +3554,8 @@ slots: range: WhitespaceMinimizedString examples: - value: QIAamp PowerFecal Pro DNA Kit - endogenous control details: - name: endogenous control details + endogenous_control_details: + name: endogenous_control_details title: endogenous control details description: The description of the endogenous controls included when extracting a sample. @@ -3278,8 +3565,10 @@ slots: slot_uri: GENEPIO:0100923 range: WhitespaceMinimizedString recommended: true - extraction recovery efficiency measurement value: - name: extraction recovery efficiency measurement value + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_endog_control_1 + extraction_recovery_efficiency_measurement_value: + name: extraction_recovery_efficiency_measurement_value title: extraction recovery efficiency measurement value description: The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the @@ -3287,16 +3576,16 @@ slots: comments: Provide value as a percent. slot_uri: GENEPIO:0100924 range: WhitespaceMinimizedString - extraction recovery efficiency measurement method: - name: extraction recovery efficiency measurement method + extraction_recovery_efficiency_measurement_method: + name: extraction_recovery_efficiency_measurement_method title: extraction recovery efficiency measurement method description: The method by which recovery efficiency of an extraction was calculated. comments: Provide a brief description of how extraction recovery efficiency was measured or estimated. slot_uri: GENEPIO:0100925 range: WhitespaceMinimizedString - microbiological method: - name: microbiological method + microbiological_method: + name: microbiological_method title: microbiological method description: The laboratory method used to grow, prepare, and/or isolate the microbial isolate. @@ -3318,8 +3607,8 @@ slots: range: WhitespaceMinimizedString examples: - value: K12 - isolate ID: - name: isolate ID + isolate_id: + name: isolate_id title: isolate ID description: The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. @@ -3331,12 +3620,12 @@ slots: slot_uri: GENEPIO:0100456 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: SA20131043 - alternative isolate ID: - name: alternative isolate ID + alternative_isolate_id: + name: alternative_isolate_id title: alternative isolate ID description: An alternative isolate_ID assigned to the isolate by another organization. comments: "Alternative isolate IDs should be provided in the in a prescribed format\ @@ -3352,8 +3641,8 @@ slots: examples: - value: GHIF3456[PHAC] - value: QWICK222[CFIA] - progeny isolate ID: - name: progeny isolate ID + progeny_isolate_id: + name: progeny_isolate_id title: progeny isolate ID description: The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. @@ -3363,8 +3652,8 @@ slots: range: WhitespaceMinimizedString examples: - value: SUB_ON_1526 - isolated by: - name: isolated by + isolated_by: + name: isolated_by title: isolated by description: The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. @@ -3375,8 +3664,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - isolated by laboratory name: - name: isolated by laboratory name + isolated_by_laboratory_name: + name: isolated_by_laboratory_name title: isolated by laboratory name description: The specific laboratory affiliation of the individual who performed the isolation procedure. @@ -3387,8 +3676,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Topp Lab - isolated by contact name: - name: isolated by contact name + isolated_by_contact_name: + name: isolated_by_contact_name title: isolated by contact name description: The name or title of the contact responsible for follow-up regarding the isolate. @@ -3400,8 +3689,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Enterics Lab Manager - isolated by contact email: - name: isolated by contact email + isolated_by_contact_email: + name: isolated_by_contact_email title: isolated by contact email description: The email address of the contact responsible for follow-up regarding the isolate. @@ -3414,8 +3703,8 @@ slots: range: WhitespaceMinimizedString examples: - value: enterics@lab.ca - isolation date: - name: isolation date + isolation_date: + name: isolation_date title: isolation date description: The date on which the isolate was isolated from a sample. comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" @@ -3424,8 +3713,8 @@ slots: range: date examples: - value: '2020-10-30' - isolate received date: - name: isolate received date + isolate_received_date: + name: isolate_received_date title: isolate received date description: The date on which the isolate was received by the laboratory. comments: Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" @@ -3445,8 +3734,8 @@ slots: recommended: true examples: - value: Heidelberg - serotyping method: - name: serotyping method + serotyping_method: + name: serotyping_method title: serotyping method description: The method used to determine the serovar. comments: "If the serovar was determined via traditional serotyping methods, put\ @@ -3466,8 +3755,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '47' - water catchment area human population measurement value: - name: water catchment area human population measurement value + water_catchment_area_human_population_measurement_value: + name: water_catchment_area_human_population_measurement_value title: water catchment area human population measurement value description: The numerical value of the human population measurement that contributes to the composition of water in a catchment area. @@ -3476,12 +3765,14 @@ slots: slot_uri: GENEPIO:0100773 any_of: - range: integer - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 10,500 - water catchment area human population range: - name: water catchment area human population range + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population + water_catchment_area_human_population_range: + name: water_catchment_area_human_population_range title: water catchment area human population range description: The human population range of the water catchment that contributes effluent to a wastewater site. @@ -3489,12 +3780,12 @@ slots: of population size by selecting a value from the picklist. slot_uri: GENEPIO:0100774 any_of: - - range: water catchment area human population range menu - - range: null value menu + - range: WaterCatchmentAreaHumanPopulationRangeMenu + - range: NullValueMenu examples: - value: 1,000 - 10,000 people - water catchment area human population measurement method: - name: water catchment area human population measurement method + water_catchment_area_human_population_measurement_method: + name: water_catchment_area_human_population_measurement_method title: water catchment area human population measurement method description: The method by which a water catchment 's human population size was measured or estimated @@ -3504,8 +3795,10 @@ slots: range: WhitespaceMinimizedString examples: - value: population of jurisdiction encompassing the wastewater service area - water catchment area human population density value: - name: water catchment area human population density value + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_population_source + water_catchment_area_human_population_density_value: + name: water_catchment_area_human_population_density_value title: water catchment area human population density value description: The numerical value describing the number of humans per geographical area in a water catchment. @@ -3515,56 +3808,56 @@ slots: range: WhitespaceMinimizedString examples: - value: '4' - water catchment area human population density unit: - name: water catchment area human population density unit + water_catchment_area_human_population_density_unit: + name: water_catchment_area_human_population_density_unit title: water catchment area human population density unit description: The unit describing the number of humans per geographical area in a water catchment. comments: Provide the unit of the population density in the catchement area. slot_uri: GENEPIO:0100777 any_of: - - range: water catchment area human population density unit menu - - range: null value menu + - range: WaterCatchmentAreaHumanPopulationDensityUnitMenu + - range: NullValueMenu examples: - value: persons per Km^2 - populated area type: - name: populated area type + populated_area_type: + name: populated_area_type title: populated area type description: A type of area that is populated by humans to different degrees. comments: Provide the populated area type from the pick list. slot_uri: GENEPIO:0100778 any_of: - - range: populated area type menu - - range: null value menu + - range: PopulatedAreaTypeMenu + - range: NullValueMenu examples: - value: Urban area - sampling weather conditions: - name: sampling weather conditions + sampling_weather_conditions: + name: sampling_weather_conditions title: sampling weather conditions description: The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. comments: Provide the weather conditions at the time of sample collection. slot_uri: GENEPIO:0100779 any_of: - - range: sampling weather conditions menu - - range: null value menu + - range: SamplingWeatherConditionsMenu + - range: NullValueMenu multivalued: true examples: - value: Rain - presampling weather conditions: - name: presampling weather conditions + presampling_weather_conditions: + name: presampling_weather_conditions title: presampling weather conditions description: Weather conditions prior to collection that may affect the sample. comments: Provide the weather conditions prior to sample collection. slot_uri: GENEPIO:0100780 any_of: - - range: presampling weather conditions menu - - range: null value menu + - range: PresamplingWeatherConditionsMenu + - range: NullValueMenu multivalued: true examples: - value: Drizzle - precipitation measurement value: - name: precipitation measurement value + precipitation_measurement_value: + name: precipitation_measurement_value title: precipitation measurement value description: The amount of water which has fallen during a precipitation process. comments: Provide the quantity of precipitation in the area leading up to the @@ -3572,12 +3865,12 @@ slots: slot_uri: GENEPIO:0100911 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: '12' - precipitation measurement unit: - name: precipitation measurement unit + precipitation_measurement_unit: + name: precipitation_measurement_unit title: precipitation measurement unit description: The units of measurement for the amount of water which has fallen during a precipitation process. @@ -3585,13 +3878,13 @@ slots: list. slot_uri: GENEPIO:0100912 any_of: - - range: precipitation measurement unit menu - - range: null value menu + - range: PrecipitationMeasurementUnitMenu + - range: NullValueMenu recommended: true examples: - value: inch - precipitation measurement method: - name: precipitation measurement method + precipitation_measurement_method: + name: precipitation_measurement_method title: precipitation measurement method description: The process used to measure the amount of water which has fallen during a precipitation process. @@ -3600,8 +3893,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Rain gauge over a 12 hour period prior to sample collection - ambient temperature measurement value: - name: ambient temperature measurement value + ambient_temperature_measurement_value: + name: ambient_temperature_measurement_value title: ambient temperature measurement value description: The numerical value of a measurement of the ambient temperature. comments: Provide the numerical value of the measured temperature. @@ -3609,19 +3902,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '70' - ambient temperature measurement unit: - name: ambient temperature measurement unit + ambient_temperature_measurement_unit: + name: ambient_temperature_measurement_unit title: ambient temperature measurement unit description: The units of a measurement of the ambient temperature. comments: Provide the units of the measured temperature. slot_uri: GENEPIO:0100936 any_of: - - range: ambient temperature measurement unit menu - - range: null value menu + - range: AmbientTemperatureMeasurementUnitMenu + - range: NullValueMenu examples: - value: degree Celsius (C) - pH measurement value: - name: pH measurement value + ph_measurement_value: + name: ph_measurement_value title: pH measurement value description: The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. @@ -3630,8 +3923,10 @@ slots: range: WhitespaceMinimizedString examples: - value: '7.4' - pH measurement method: - name: pH measurement method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_ph + ph_measurement_method: + name: ph_measurement_method title: pH measurement method description: The process used to measure pH value. comments: Provide the name of the procedure or technology used to measure pH. @@ -3639,8 +3934,8 @@ slots: range: WhitespaceMinimizedString examples: - value: pH test strip (litmus test) - total daily flow rate measurement value: - name: total daily flow rate measurement value + total_daily_flow_rate_measurement_value: + name: total_daily_flow_rate_measurement_value title: total daily flow rate measurement value description: The numerical value of a measured fluid flow rate over the course of a day. @@ -3649,20 +3944,24 @@ slots: range: WhitespaceMinimizedString examples: - value: '10' - total daily flow rate measurement unit: - name: total daily flow rate measurement unit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow + total_daily_flow_rate_measurement_unit: + name: total_daily_flow_rate_measurement_unit title: total daily flow rate measurement unit description: The units of a measured fluid flow rate over the course of a day. comments: Provide the units of the measured flow rate by selecting a value from the pick list. slot_uri: GENEPIO:0100906 any_of: - - range: total daily flow rate measurement unit menu - - range: null value menu + - range: TotalDailyFlowRateMeasurementUnitMenu + - range: NullValueMenu examples: - value: million gallons per day (MGD) - total daily flow rate measurement method: - name: total daily flow rate measurement method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_flow + total_daily_flow_rate_measurement_method: + name: total_daily_flow_rate_measurement_method title: total daily flow rate measurement method description: The process used to measure total daily fluid flow rate. comments: Provide the name of the procedure or technology used to measure flow @@ -3671,8 +3970,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Flow meter - instantaneous flow rate measurement value: - name: instantaneous flow rate measurement value + instantaneous_flow_rate_measurement_value: + name: instantaneous_flow_rate_measurement_value title: instantaneous flow rate measurement value description: The numerical value of a measured instantaneous fluid flow rate. comments: Provide the numerical value of the measured flow rate. @@ -3680,20 +3979,20 @@ slots: range: WhitespaceMinimizedString examples: - value: '25' - instantaneous flow rate measurement unit: - name: instantaneous flow rate measurement unit + instantaneous_flow_rate_measurement_unit: + name: instantaneous_flow_rate_measurement_unit title: instantaneous flow rate measurement unit description: The units of a measured instantaneous fluid flow rate. comments: Provide the units of the measured flow rate by selecting a value from the pick list. slot_uri: GENEPIO:0100909 any_of: - - range: instantaneous flow rate measurement unit menu - - range: null value menu + - range: InstantaneousFlowRateMeasurementUnitMenu + - range: NullValueMenu examples: - value: cubic meter per hour (m^3/h) - instantaneous flow rate measurement method: - name: instantaneous flow rate measurement method + instantaneous_flow_rate_measurement_method: + name: instantaneous_flow_rate_measurement_method title: instantaneous flow rate measurement method description: The process used to measure instantaneous fluid flow rate. comments: Provide the name of the procedure or technology used to measure flow @@ -3702,8 +4001,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Flow meter - turbidity measurement value: - name: turbidity measurement value + turbidity_measurement_value: + name: turbidity_measurement_value title: turbidity measurement value description: The numerical value of a measurement of turbidity. comments: Provide the numerical value of the measured turbidity. @@ -3712,21 +4011,21 @@ slots: recommended: true examples: - value: '0.02' - turbidity measurement unit: - name: turbidity measurement unit + turbidity_measurement_unit: + name: turbidity_measurement_unit title: turbidity measurement unit description: The units of a measurement of turbidity. comments: Provide the units of the measured turbidity by selecting a value from the pick list. slot_uri: GENEPIO:0100914 any_of: - - range: turbidity measurement unit menu - - range: null value menu + - range: TurbidityMeasurementUnitMenu + - range: NullValueMenu recommended: true examples: - value: nephelometric turbidity unit (NTU) - turbidity measurement method: - name: turbidity measurement method + turbidity_measurement_method: + name: turbidity_measurement_method title: turbidity measurement method description: The process used to measure turbidity. comments: Provide the name of the procedure or technology used to measure turbidity. @@ -3734,29 +4033,29 @@ slots: range: WhitespaceMinimizedString examples: - value: Nephelometric method - dissolved oxygen measurement value: - name: dissolved oxygen measurement value + dissolved_oxygen_measurement_value: + name: dissolved_oxygen_measurement_value title: dissolved oxygen measurement value description: The numerical value of a measurement of dissolved oxygen. comments: Provide the numerical value of the measured dissolved oxygen. - slot_uri: GENEPIO:0100915 + slot_uri: GENEPIO:0000035 range: WhitespaceMinimizedString examples: - value: '5' - dissolved oxygen measurement unit: - name: dissolved oxygen measurement unit + dissolved_oxygen_measurement_unit: + name: dissolved_oxygen_measurement_unit title: dissolved oxygen measurement unit description: The units of a measurement of dissolved oxygen. comments: Provide the units of the measured dissolved oxygen by selecting a value from the pick list. slot_uri: GENEPIO:0100784 any_of: - - range: dissolved oxygen measurement unit menu - - range: null value menu + - range: DissolvedOxygenMeasurementUnitMenu + - range: NullValueMenu examples: - value: part per million (ppm) - dissolved oxygen measurement method: - name: dissolved oxygen measurement method + dissolved_oxygen_measurement_method: + name: dissolved_oxygen_measurement_method title: dissolved oxygen measurement method description: The method used to measure dissolved oxygen. comments: Provide the name of the procedure or technology used to measure dissolved @@ -3765,30 +4064,30 @@ slots: range: WhitespaceMinimizedString examples: - value: Dissolved oxygen meter in vertical direction - oxygen reduction potential (ORP) measurement value: - name: oxygen reduction potential (ORP) measurement value + oxygen_reduction_potential_orp_measurement_value: + name: oxygen_reduction_potential_orp_measurement_value title: oxygen reduction potential (ORP) measurement value description: The numerical value of a measurement of oxygen reduction potential (ORP). comments: Provide the numerical value of the measured oxygen reduction potential. - slot_uri: GENEPIO:0100917 + slot_uri: FIX:0000278 range: WhitespaceMinimizedString examples: - value: '-50' - oxygen reduction potential (ORP) measurement unit: - name: oxygen reduction potential (ORP) measurement unit + oxygen_reduction_potential_orp_measurement_unit: + name: oxygen_reduction_potential_orp_measurement_unit title: oxygen reduction potential (ORP) measurement unit description: The units of a measurement of oxygen reduction potential (ORP). comments: Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. slot_uri: GENEPIO:0100786 any_of: - - range: oxygen reduction potential (ORP) measurement unit menu - - range: null value menu + - range: OxygenReductionPotentialOrpMeasurementUnitMenu + - range: NullValueMenu examples: - value: milliVolt (mV) - oxygen reduction potential (ORP) measurement method: - name: oxygen reduction potential (ORP) measurement method + oxygen_reduction_potential_orp_measurement_method: + name: oxygen_reduction_potential_orp_measurement_method title: oxygen reduction potential (ORP) measurement method description: The method used to measure oxygen reduction potential (ORP). comments: Provide the name of the procedure or technology used to measure oxygen @@ -3797,8 +4096,8 @@ slots: range: WhitespaceMinimizedString examples: - value: ORP sensor - chemical oxygen demand (COD) measurement value: - name: chemical oxygen demand (COD) measurement value + chemical_oxygen_demand_cod_measurement_value: + name: chemical_oxygen_demand_cod_measurement_value title: chemical oxygen demand (COD) measurement value description: The measured value from a chemical oxygen demand (COD) test. comments: Provide the numerical value of the COD test result. @@ -3806,20 +4105,20 @@ slots: range: WhitespaceMinimizedString examples: - value: '26' - chemical oxygen demand (COD) measurement unit: - name: chemical oxygen demand (COD) measurement unit + chemical_oxygen_demand_cod_measurement_unit: + name: chemical_oxygen_demand_cod_measurement_unit title: chemical oxygen demand (COD) measurement unit description: The units associated with a value from a chemical oxygen demand (COD) test. comments: Provide the units of the COD test result. slot_uri: GENEPIO:0100789 any_of: - - range: chemical oxygen demand (COD) measurement unit menu - - range: null value menu + - range: ChemicalOxygenDemandCodMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter (mg/L) - chemical oxygen demand (COD) measurement method: - name: chemical oxygen demand (COD) measurement method + chemical_oxygen_demand_cod_measurement_method: + name: chemical_oxygen_demand_cod_measurement_method title: chemical oxygen demand (COD) measurement method description: The method used to measure chemical oxygen demand (COD). comments: Provide the name of the procedure or technology used to measure COD. @@ -3827,8 +4126,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Hach LCK test kit - carbonaceous biochemical oxygen demand (CBOD) measurement value: - name: carbonaceous biochemical oxygen demand (CBOD) measurement value + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_value title: carbonaceous biochemical oxygen demand (CBOD) measurement value description: The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). @@ -3837,8 +4136,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '20' - carbonaceous biochemical oxygen demand (CBOD) measurement unit: - name: carbonaceous biochemical oxygen demand (CBOD) measurement unit + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit title: carbonaceous biochemical oxygen demand (CBOD) measurement unit description: The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). @@ -3846,12 +4145,12 @@ slots: pick list. slot_uri: GENEPIO:0100792 any_of: - - range: carbonaceous biochemical oxygen demand (CBOD) measurement unit menu - - range: null value menu + - range: CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter (mg/L) - carbonaceous biochemical oxygen demand (CBOD) measurement method: - name: carbonaceous biochemical oxygen demand (CBOD) measurement method + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_method title: carbonaceous biochemical oxygen demand (CBOD) measurement method description: The method used to measure carbonaceous biochemical oxygen demand (CBOD). @@ -3860,8 +4159,8 @@ slots: range: WhitespaceMinimizedString examples: - value: CBOD measurement by optical probe - total suspended solids (TSS) measurement value: - name: total suspended solids (TSS) measurement value + total_suspended_solids_tss_measurement_value: + name: total_suspended_solids_tss_measurement_value title: total suspended solids (TSS) measurement value description: The numerical value from a total suspended solids (TSS) test. comments: Provide the numerical value of the measured TSS. @@ -3869,20 +4168,24 @@ slots: range: WhitespaceMinimizedString examples: - value: '8' - total suspended solids (TSS) measurement unit: - name: total suspended solids (TSS) measurement unit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids + total_suspended_solids_tss_measurement_unit: + name: total_suspended_solids_tss_measurement_unit title: total suspended solids (TSS) measurement unit description: The units associated with a value from a total suspended solids (TSS) test. comments: Provide the units of the measured TSS. slot_uri: GENEPIO:0100795 any_of: - - range: total suspended solids (TSS) measurement unit menu - - range: null value menu + - range: TotalSuspendedSolidsTssMeasurementUnitMenu + - range: NullValueMenu examples: - value: percent (%) - total suspended solids (TSS) measurement method: - name: total suspended solids (TSS) measurement method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_total_suspended_solids + total_suspended_solids_tss_measurement_method: + name: total_suspended_solids_tss_measurement_method title: total suspended solids (TSS) measurement method description: The method used to measure total suspended solids (TSS). comments: Provide the name of the procedure or technology used to measure TSS. @@ -3891,8 +4194,8 @@ slots: examples: - value: Vacuum filter through a 2-micron filter, then oven-dried and weighed sample - total dissolved solids (TDS) measurement value: - name: total dissolved solids (TDS) measurement value + total_dissolved_solids_tds_measurement_value: + name: total_dissolved_solids_tds_measurement_value title: total dissolved solids (TDS) measurement value description: The numerical value from a total dissolved solids (TDS) test. comments: Provide the numerical value of the measured TDS. @@ -3900,20 +4203,20 @@ slots: range: WhitespaceMinimizedString examples: - value: '2' - total dissolved solids (TDS) measurement unit: - name: total dissolved solids (TDS) measurement unit + total_dissolved_solids_tds_measurement_unit: + name: total_dissolved_solids_tds_measurement_unit title: total dissolved solids (TDS) measurement unit description: The units associated with a value from a total dissolved solids (TDS) test. comments: Provide the units of the measured TDS. slot_uri: GENEPIO:0100798 any_of: - - range: total dissolved solids (TDS) measurement unit menu - - range: null value menu + - range: TotalDissolvedSolidsTdsMeasurementUnitMenu + - range: NullValueMenu examples: - value: percent (%) - total dissolved solids (TDS) measurement method: - name: total dissolved solids (TDS) measurement method + total_dissolved_solids_tds_measurement_method: + name: total_dissolved_solids_tds_measurement_method title: total dissolved solids (TDS) measurement method description: The method used to measure total dissolved solids (TDS). comments: Provide the name of the procedure or technology used to measure TDS. @@ -3921,8 +4224,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Subtract calculated TSS from calculated TS - total solids (TS) measurement value: - name: total solids (TS) measurement value + total_solids_ts_measurement_value: + name: total_solids_ts_measurement_value title: total solids (TS) measurement value description: The numerical value from a total solids (TS) test. comments: Provide the numerical value of the measured TS. @@ -3930,19 +4233,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '10' - total solids (TS) measurement unit: - name: total solids (TS) measurement unit + total_solids_ts_measurement_unit: + name: total_solids_ts_measurement_unit title: total solids (TS) measurement unit description: The units associated with a value from a total solids (TS) test. comments: Provide the units of the measured TS. slot_uri: GENEPIO:0100801 any_of: - - range: total solids (TS) measurement unit menu - - range: null value menu + - range: TotalSolidsTsMeasurementUnitMenu + - range: NullValueMenu examples: - value: percent (%) - total solids (TS) measurement method: - name: total solids (TS) measurement method + total_solids_ts_measurement_method: + name: total_solids_ts_measurement_method title: total solids (TS) measurement method description: The method used to measure total solids (TS). comments: Provide the name of the procedure or technology used to measure TS. @@ -3950,8 +4253,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Gravimetric method by oven drying, then weighing - alkalinity measurement value: - name: alkalinity measurement value + alkalinity_measurement_value: + name: alkalinity_measurement_value title: alkalinity measurement value description: The numerical value of a measurement of alkalinity. comments: Provide the numerical value of the measured alkalinity. @@ -3959,19 +4262,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '3' - alkalinity measurement unit: - name: alkalinity measurement unit + alkalinity_measurement_unit: + name: alkalinity_measurement_unit title: alkalinity measurement unit description: The units of a measurement of alkalinity. comments: Provide the units of the measured alkalinity. slot_uri: GENEPIO:0100879 any_of: - - range: alkalinity measurement unit menu - - range: null value menu + - range: AlkalinityMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter of calcium carbonate (mg/L CaCO3) - alkalinity measurement method: - name: alkalinity measurement method + alkalinity_measurement_method: + name: alkalinity_measurement_method title: alkalinity measurement method description: The process used to measure alkalinity. comments: Provide the name of the procedure or technology used to measure alkalinity. @@ -3979,8 +4282,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Titration method - conductivity measurement value: - name: conductivity measurement value + conductivity_measurement_value: + name: conductivity_measurement_value title: conductivity measurement value description: The numerical value of a measurement of conductivity. comments: Provide the numerical value of the measured conductivity. @@ -3988,19 +4291,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '1412' - conductivity measurement unit: - name: conductivity measurement unit + conductivity_measurement_unit: + name: conductivity_measurement_unit title: conductivity measurement unit description: The units of a measurement of conductivity. comments: Provide the units of the measured conductivity. slot_uri: GENEPIO:0100803 any_of: - - range: conductivity measurement unit menu - - range: null value menu + - range: ConductivityMeasurementUnitMenu + - range: NullValueMenu examples: - value: "microSiemen per centimeter (\u03BCS/cm)" - conductivity measurement method: - name: conductivity measurement method + conductivity_measurement_method: + name: conductivity_measurement_method title: conductivity measurement method description: The method used to measure conductivity. comments: Provide the name of the procedure or technology used to measure conductivity. @@ -4008,8 +4311,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Conductivity electrode and meter - salinity measurement value: - name: salinity measurement value + salinity_measurement_value: + name: salinity_measurement_value title: salinity measurement value description: The numerical value of a measurement of salinity. comments: Provide the numerical value of the measured salinity. @@ -4017,19 +4320,23 @@ slots: range: WhitespaceMinimizedString examples: - value: '35' - salinity measurement unit: - name: salinity measurement unit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity + salinity_measurement_unit: + name: salinity_measurement_unit title: salinity measurement unit description: The units of a measurement of salinity. comments: Provide the units of the measured salinity. slot_uri: GENEPIO:0100806 any_of: - - range: salinity measurement unit menu - - range: null value menu + - range: SalinityMeasurementUnitMenu + - range: NullValueMenu examples: - value: practical salinity unit (PSU) - salinity measurement method: - name: salinity measurement method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_sample_salinity + salinity_measurement_method: + name: salinity_measurement_method title: salinity measurement method description: The method used to measure salinity. comments: Provide the name of the procedure or technology used to measure salinity. @@ -4037,8 +4344,8 @@ slots: range: WhitespaceMinimizedString examples: - value: conductivity meter - total nitrogen (TN) measurement value: - name: total nitrogen (TN) measurement value + total_nitrogen_tn_measurement_value: + name: total_nitrogen_tn_measurement_value title: total nitrogen (TN) measurement value description: The numerical value of a measurement of total nitrogen (TN). comments: Provide the numerical value of the measured TN. @@ -4046,19 +4353,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '120' - total nitrogen (TN) measurement unit: - name: total nitrogen (TN) measurement unit + total_nitrogen_tn_measurement_unit: + name: total_nitrogen_tn_measurement_unit title: total nitrogen (TN) measurement unit description: The units of a measurement of total nitrogen (TN). comments: Provide the units of the measured TN. slot_uri: GENEPIO:0100809 any_of: - - range: total nitrogen (TN) measurement unit menu - - range: null value menu + - range: TotalNitrogenTnMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter (mg/L) - total nitrogen (TN) measurement method: - name: total nitrogen (TN) measurement method + total_nitrogen_tn_measurement_method: + name: total_nitrogen_tn_measurement_method title: total nitrogen (TN) measurement method description: The method used to measure total nitrogen (TN). comments: Provide the name of the procedure or technology used to measure TN. @@ -4066,8 +4373,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Hach total nitrogen spectrophotometric test - total phosphorus (TP) measurement value: - name: total phosphorus (TP) measurement value + total_phosphorus_tp_measurement_value: + name: total_phosphorus_tp_measurement_value title: total phosphorus (TP) measurement value description: The numerical value of a measurement of total phosphorus (TP). comments: Provide the numerical value of the measured TP. @@ -4075,19 +4382,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '2' - total phosphorus (TP) measurement unit: - name: total phosphorus (TP) measurement unit + total_phosphorus_tp_measurement_unit: + name: total_phosphorus_tp_measurement_unit title: total phosphorus (TP) measurement unit description: The units of a measurement of total phosphorus (TP). comments: Provide the units of the measured TP. slot_uri: GENEPIO:0100812 any_of: - - range: total phosphorus (TP) measurement unit menu - - range: null value menu + - range: TotalPhosphorusTpMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) - total phosphorus (TP) measurement method: - name: total phosphorus (TP) measurement method + total_phosphorus_tp_measurement_method: + name: total_phosphorus_tp_measurement_method title: total phosphorus (TP) measurement method description: The method used to measure total phosphorus (TP). comments: Provide the name of the procedure or technology used to measure TP. @@ -4095,8 +4402,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Merck phosphate spectrophotometric test kit - fecal contamination indicator: - name: fecal contamination indicator + fecal_contamination_indicator: + name: fecal_contamination_indicator title: fecal contamination indicator description: A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. @@ -4104,13 +4411,13 @@ slots: picklist. slot_uri: GENEPIO:0100814 any_of: - - range: fecal contamination indicator menu - - range: null value menu + - range: FecalContaminationIndicatorMenu + - range: NullValueMenu recommended: true examples: - value: crAssphage - fecal contamination value: - name: fecal contamination value + fecal_contamination_value: + name: fecal_contamination_value title: fecal contamination value description: The numerical value of a measurement of fecal contamination. comments: Provide the numerical value of the measured fecal contamination. @@ -4119,20 +4426,20 @@ slots: recommended: true examples: - value: '10' - fecal contamination unit: - name: fecal contamination unit + fecal_contamination_unit: + name: fecal_contamination_unit title: fecal contamination unit description: The units of a measurement of fecal contamination. comments: Provide the units of the measured fecal contamination. slot_uri: GENEPIO:0100816 any_of: - - range: fecal contamination unit menu - - range: null value menu + - range: FecalContaminationUnitMenu + - range: NullValueMenu recommended: true examples: - value: cycle threshold (Ct) / quantification cycle (Cq) - fecal contamination method: - name: fecal contamination method + fecal_contamination_method: + name: fecal_contamination_method title: fecal contamination method description: The method used to measure fecal contamination. comments: Provide the name of the procedure or technology used to measure fecal @@ -4141,8 +4448,8 @@ slots: range: WhitespaceMinimizedString examples: - value: quantitative PCR assay - fecal coliform count value: - name: fecal coliform count value + fecal_coliform_count_value: + name: fecal_coliform_count_value title: fecal coliform count value description: The numerical value of a measurement of fecal coliforms within a sample. @@ -4151,19 +4458,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '3' - fecal coliform count unit: - name: fecal coliform count unit + fecal_coliform_count_unit: + name: fecal_coliform_count_unit title: fecal coliform count unit description: The units of a measurement of fecal coliforms. comments: Provide the units of the measured fecal coliforms. slot_uri: GENEPIO:0100819 any_of: - - range: fecal coliform count unit menu - - range: null value menu + - range: FecalColiformCountUnitMenu + - range: NullValueMenu examples: - value: most probable number per milliliter (MPN/mL) - fecal coliform count method: - name: fecal coliform count method + fecal_coliform_count_method: + name: fecal_coliform_count_method title: fecal coliform count method description: The method used to measure fecal coliforms. comments: Provide the name of the procedure or technology used to measure fecal @@ -4172,8 +4479,8 @@ slots: range: WhitespaceMinimizedString examples: - value: MPN method via serial dilutions until lack of growth - urinary contamination indicator: - name: urinary contamination indicator + urinary_contamination_indicator: + name: urinary_contamination_indicator title: urinary contamination indicator description: A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. @@ -4181,12 +4488,12 @@ slots: picklist. slot_uri: GENEPIO:0100837 any_of: - - range: urinary contamination indicator menu - - range: null value menu + - range: UrinaryContaminationIndicatorMenu + - range: NullValueMenu examples: - value: urobilin - urinary contamination value: - name: urinary contamination value + urinary_contamination_value: + name: urinary_contamination_value title: urinary contamination value description: The numerical value of a measurement of urinary contamination. comments: Provide the numerical value of the measured urinary contamination. @@ -4194,19 +4501,19 @@ slots: range: WhitespaceMinimizedString examples: - value: '3' - urinary contamination unit: - name: urinary contamination unit + urinary_contamination_unit: + name: urinary_contamination_unit title: urinary contamination unit description: The units of a measurement of urinary contamination. comments: Provide the units of the measured urinary contamination. slot_uri: GENEPIO:0100839 any_of: - - range: urinary contamination unit menu - - range: null value menu + - range: UrinaryContaminationUnitMenu + - range: NullValueMenu examples: - value: nanograms per liter - urinary contamination method: - name: urinary contamination method + urinary_contamination_method: + name: urinary_contamination_method title: urinary contamination method description: The method used to measure urinary contamination. comments: Provide the name of the procedure or technology used to measure urinary @@ -4215,8 +4522,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Urobilin Concentration Test - sample temperature value (at collection): - name: sample temperature value (at collection) + sample_temperature_value_at_collection: + name: sample_temperature_value_at_collection title: sample temperature value (at collection) description: The numerical value of a measurement of temperature of a sample at collection. @@ -4225,20 +4532,24 @@ slots: range: WhitespaceMinimizedString examples: - value: '20' - sample temperature unit (at collection): - name: sample temperature unit (at collection) + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature + sample_temperature_unit_at_collection: + name: sample_temperature_unit_at_collection title: sample temperature unit (at collection) description: The units of a measurement of temperature of a sample at the time of collection. comments: Provide the units of the measured temperature. slot_uri: GENEPIO:0100822 any_of: - - range: sample temperature unit (at collection) menu - - range: null value menu + - range: SampleTemperatureUnitAtCollectionMenu + - range: NullValueMenu examples: - value: degree Celsius (C) - sample temperature value (when received): - name: sample temperature value (when received) + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_temperature + sample_temperature_value_when_received: + name: sample_temperature_value_when_received title: sample temperature value (when received) description: The numerical value of a measurement of temperature of a sample upon receipt. @@ -4247,20 +4558,20 @@ slots: range: WhitespaceMinimizedString examples: - value: '22' - sample temperature unit (when received): - name: sample temperature unit (when received) + sample_temperature_unit_when_received: + name: sample_temperature_unit_when_received title: sample temperature unit (when received) description: The units of a measurement of temperature of a sample at the time upon receipt. comments: Provide the units of the measured temperature. slot_uri: GENEPIO:0100824 any_of: - - range: sample temperature unit (when received) menu - - range: null value menu + - range: SampleTemperatureUnitWhenReceivedMenu + - range: NullValueMenu examples: - value: degree Celsius (C) - purpose of sequencing: - name: purpose of sequencing + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the @@ -4270,14 +4581,16 @@ slots: sample collection should be indicated in the "purpose of sampling" field. slot_uri: GENEPIO:0001445 any_of: - - range: purpose of sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true examples: - value: Travel-associated surveillance - purpose of sequencing details: - name: purpose of sequencing details + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:purpose_of_ww_sequencing + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details description: The description of why the sample was sequenced providing specific details. @@ -4292,8 +4605,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Investigating schools/universities - sequenced by: - name: sequenced by + sequenced_by: + name: sequenced_by title: sequenced by description: The name of the agency, organization or institution responsible for sequencing the isolate's genome. @@ -4303,14 +4616,26 @@ slots: slot_uri: GENEPIO:0100416 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] exact_mappings: - GISAID:sequenced_by - sequenced by contact name: - name: sequenced by contact name + sequenced_by_laboratory_name: + name: sequenced_by_laboratory_name + title: sequenced by laboratory name + description: The specific laboratory affiliation of the responsible for sequencing + the isolate's genome. + comments: Provide the name of the specific laboratory that that performed the + sequencing in full (avoid abbreviations). If the information is unknown or cannot + be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100470 + range: WhitespaceMinimizedString + examples: + - value: Topp Lab + sequenced_by_contact_name: + name: sequenced_by_contact_name title: sequenced by contact name description: The name or title of the contact responsible for follow-up regarding the sequence. @@ -4322,12 +4647,12 @@ slots: slot_uri: GENEPIO:0100471 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - - value: Enterics Lab Manager - sequenced by contact email: - name: sequenced by contact email + - value: Joe Bloggs, Enterics Lab Manager + sequenced_by_contact_email: + name: sequenced_by_contact_email title: sequenced by contact email description: The email address of the contact responsible for follow-up regarding the sequence. @@ -4339,12 +4664,12 @@ slots: slot_uri: GENEPIO:0100471 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: enterics@lab.ca - sequence submitted by: - name: sequence submitted by + sequence_submitted_by: + name: sequence_submitted_by title: sequence submitted by description: The name of the agency that submitted the sequence to a database. comments: The name of the agency should be written out in full, (with minor exceptions) @@ -4354,12 +4679,14 @@ slots: slot_uri: GENEPIO:0001159 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Public Health Ontario (PHO) - sequence submitter contact email: - name: sequence submitter contact email + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:sequenced_by + sequence_submitter_contact_email: + name: sequence_submitter_contact_email title: sequence submitter contact email description: The email address of the contact responsible for follow-up regarding the sequence. @@ -4367,13 +4694,15 @@ slots: slot_uri: GENEPIO:0001165 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true pattern: ^\S+@\S+\.\S+$ examples: - value: RespLab@lab.ca - sequencing date: - name: sequencing date + exact_mappings: + - NCBI_SRA:sequence_submitter_contact_email + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: ISO 8601 standard "YYYY-MM-DD". @@ -4383,8 +4712,8 @@ slots: - '>={sample collection date}' examples: - value: '2020-06-22' - library ID: - name: library ID + library_id: + name: library_id title: library ID description: The user-specified identifier for the library prepared for sequencing. comments: The library name should be unique, and can be an autogenerated ID from @@ -4393,8 +4722,10 @@ slots: range: WhitespaceMinimizedString examples: - value: XYZ_123345 - sequencing platform: - name: sequencing platform + exact_mappings: + - NCBI_SRA:library_ID + sequencing_platform: + name: sequencing_platform title: sequencing platform description: The platform technology used to perform the sequencing. comments: Provide the name of the company that created the sequencing instrument @@ -4402,13 +4733,15 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100473 any_of: - - range: sequencing platform menu - - range: null value menu + - range: SequencingPlatformMenu + - range: NullValueMenu multivalued: true examples: - value: Illumina [GENEPIO:0001923] - sequencing instrument: - name: sequencing instrument + exact_mappings: + - NCBI_SRA:platform + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Provide the model sequencing instrument by selecting a value from the @@ -4416,14 +4749,16 @@ slots: blank or provide a null value. slot_uri: GENEPIO:0001452 any_of: - - range: sequencing instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu multivalued: true required: true examples: - value: Illumina HiSeq 2500 [GENEPIO:0100117] - sequencing assay type: - name: sequencing assay type + exact_mappings: + - NCBI_SRA:instrument_model + sequencing_assay_type: + name: sequencing_assay_type title: sequencing assay type description: The overarching sequencing methodology that was used to determine the sequence of a biomaterial. @@ -4431,13 +4766,15 @@ slots: study. If unsure refer to the protocol documentation, or provide a null value. slot_uri: GENEPIO:0100997 any_of: - - range: sequencing assay type menu - - range: null value menu + - range: SequencingAssayTypeMenu + - range: NullValueMenu recommended: true examples: - value: whole genome sequencing assay - library preparation kit: - name: library preparation kit + exact_mappings: + - NCBI_SRA:library_strategy + library_preparation_kit: + name: library_preparation_kit title: library preparation kit description: The name of the DNA library preparation kit used to generate the library being sequenced. @@ -4446,8 +4783,10 @@ slots: range: WhitespaceMinimizedString examples: - value: Nextera XT - sequencing protocol: - name: sequencing protocol + exact_mappings: + - NCBI_SRA:library_preparation_kit + sequencing_protocol: + name: sequencing_protocol title: sequencing protocol description: The protocol or method used for sequencing. comments: Provide the name and version of the procedure or protocol used for sequencing. @@ -4457,8 +4796,8 @@ slots: recommended: true examples: - value: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no - DNA fragment length: - name: DNA fragment length + dna_fragment_length: + name: dna_fragment_length title: DNA fragment length description: The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. @@ -4467,22 +4806,24 @@ slots: range: WhitespaceMinimizedString examples: - value: '400' - genomic target enrichment method: - name: genomic target enrichment method + genomic_target_enrichment_method: + name: genomic_target_enrichment_method title: genomic target enrichment method description: The molecular technique used to selectively capture and amplify specific regions of interest from a genome. comments: Provide the name of the enrichment method slot_uri: GENEPIO:0100966 any_of: - - range: genomic target enrichment method menu - - range: null value menu + - range: GenomicTargetEnrichmentMethodMenu + - range: NullValueMenu multivalued: true recommended: true examples: - value: hybrid selection method - genomic target enrichment method details: - name: genomic target enrichment method details + exact_mappings: + - NCBI_SRA:library_selection + genomic_target_enrichment_method_details: + name: genomic_target_enrichment_method_details title: genomic target enrichment method details description: Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a @@ -4493,8 +4834,8 @@ slots: examples: - value: enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. - amplicon pcr primer scheme: - name: amplicon pcr primer scheme + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme title: amplicon pcr primer scheme description: The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. @@ -4502,13 +4843,15 @@ slots: amplicons for sequencing. slot_uri: GENEPIO:0001456 any_of: - - range: amplicon pcr primer scheme menu - - range: null value menu + - range: AmpliconPcrPrimerSchemeMenu + - range: NullValueMenu recommended: true examples: - value: artic v3 - amplicon size: - name: amplicon size + exact_mappings: + - NCBI_SRA:amplicon_PCR_primer_scheme + amplicon_size: + name: amplicon_size title: amplicon size description: The length of the amplicon generated by PCR amplification. comments: Provide the amplicon size expressed in base pairs. @@ -4516,8 +4859,10 @@ slots: range: integer examples: - value: '300' - quality control method name: - name: quality control method name + exact_mappings: + - NCBI_SRA:amplicon_size + quality_control_method_name: + name: quality_control_method_name title: quality control method name description: The name of the method used to assess whether a sequence passed a predetermined quality control threshold. @@ -4530,8 +4875,10 @@ slots: range: WhitespaceMinimizedString examples: - value: ncov-tools - quality control method version: - name: quality control method version + exact_mappings: + - NCBI_SRA:quality_control_method + quality_control_method_version: + name: quality_control_method_version title: quality control method version description: The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. @@ -4544,8 +4891,10 @@ slots: range: WhitespaceMinimizedString examples: - value: 1.2.3 - quality control determination: - name: quality control determination + exact_mappings: + - NCBI_SRA:quality_control_method_version + quality_control_determination: + name: quality_control_determination title: quality control determination description: The determination of a quality control assessment. comments: Select a value from the pick list provided. If a desired value is missing, @@ -4553,13 +4902,15 @@ slots: New Term Request form. slot_uri: GENEPIO:0100559 any_of: - - range: quality control determination menu - - range: null value menu + - range: QualityControlDeterminationMenu + - range: NullValueMenu multivalued: true examples: - value: sequence failed quality control - quality control issues: - name: quality control issues + exact_mappings: + - NCBI_SRA:quality_control_determination + quality_control_issues: + name: quality_control_issues title: quality control issues description: The reason contributing to, or causing, a low quality determination in a quality control assessment. @@ -4568,13 +4919,15 @@ slots: New Term Request form. slot_uri: GENEPIO:0100560 any_of: - - range: quality control issues menu - - range: null value menu + - range: QualityControlIssuesMenu + - range: NullValueMenu multivalued: true examples: - value: low average genome coverage - quality control details: - name: quality control details + exact_mappings: + - NCBI_SRA:quality_control_issues + quality_control_details: + name: quality_control_details title: quality control details description: The details surrounding a low quality determination in a quality control assessment. @@ -4583,8 +4936,10 @@ slots: range: WhitespaceMinimizedString examples: - value: CT value of 39. Low viral load. Low DNA concentration after amplification. - raw sequence data processing method: - name: raw sequence data processing method + exact_mappings: + - NCBI_SRA:quality_control_details + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method description: The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. @@ -4593,12 +4948,14 @@ slots: slot_uri: GENEPIO:0001458 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Porechop 0.2.3 - dehosting method: - name: dehosting method + exact_mappings: + - NCBI_SRA:raw_sequence_data_processing_method + dehosting_method: + name: dehosting_method title: dehosting method description: The method used to remove host reads from the pathogen sequence. comments: Provide the name and version number of the software used to remove host @@ -4606,56 +4963,82 @@ slots: slot_uri: GENEPIO:0001459 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Nanostripper - sequence assembly software name: - name: sequence assembly software name + exact_mappings: + - NCBI_SRA:dehosting_method + genome_sequence_file_name: + name: genome_sequence_file_name + title: genome sequence file name + description: The name of the consensus sequence file. + comments: Provide the name and version number, with the file extension, of the + processed genome sequence file e.g. a consensus sequence FASTA file or a genome + assembly file. + slot_uri: GENEPIO:0101715 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: mpxvassembly.fasta + genome_sequence_file_path: + name: genome_sequence_file_path + title: genome sequence file path + description: The filepath of the consensus sequence file. + comments: Provide the filepath of the genome sequence FASTA file. + slot_uri: GENEPIO:0101716 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: /User/Documents/ViralLab/Data/mpxvassembly.fasta + sequence_assembly_software_name: + name: sequence_assembly_software_name title: sequence assembly software name description: The name of the software used to assemble a sequence. comments: Provide the name of the software used to assemble the sequence. slot_uri: GENEPIO:0100825 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet - sequence assembly software version: - name: sequence assembly software version + sequence_assembly_software_version: + name: sequence_assembly_software_version title: sequence assembly software version description: The version of the software used to assemble a sequence. comments: Provide the version of the software used to assemble the sequence. slot_uri: GENEPIO:0100826 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: 3.15.5 - consensus sequence software name: - name: consensus sequence software name + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name description: The name of the software used to generate the consensus sequence. comments: Provide the name of the software used to generate the consensus sequence. slot_uri: GENEPIO:0001463 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: iVar - consensus sequence software version: - name: consensus sequence software version + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version description: The version of the software used to generate the consensus sequence. comments: Provide the version of the software used to generate the consensus sequence. slot_uri: GENEPIO:0001469 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: '1.3' - breadth of coverage value: - name: breadth of coverage value + breadth_of_coverage_value: + name: breadth_of_coverage_value title: breadth of coverage value description: The percentage of the reference genome covered by the sequenced data, to a prescribed depth. @@ -4664,8 +5047,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '95' - depth of coverage value: - name: depth of coverage value + depth_of_coverage_value: + name: depth_of_coverage_value title: depth of coverage value description: The average number of reads representing a given nucleotide in the reconstructed sequence. @@ -4674,8 +5057,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '400' - depth of coverage threshold: - name: depth of coverage threshold + depth_of_coverage_threshold: + name: depth_of_coverage_threshold title: depth of coverage threshold description: The threshold used as a cut-off for the depth of coverage. comments: Provide the threshold fold coverage. @@ -4683,8 +5066,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '100' - genome completeness: - name: genome completeness + genome_completeness: + name: genome_completeness title: genome completeness description: The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. @@ -4693,8 +5076,8 @@ slots: range: WhitespaceMinimizedString examples: - value: '85' - number of base pairs sequenced: - name: number of base pairs sequenced + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced title: number of base pairs sequenced description: The number of total base pairs generated by the sequencing process. comments: Provide a numerical value (no need to include units). @@ -4702,8 +5085,8 @@ slots: range: integer examples: - value: '387566' - number of total reads: - name: number of total reads + number_of_total_reads: + name: number_of_total_reads title: number of total reads description: The total number of non-unique reads generated by the sequencing process. @@ -4712,8 +5095,8 @@ slots: range: integer examples: - value: '423867' - number of unique reads: - name: number of unique reads + number_of_unique_reads: + name: number_of_unique_reads title: number of unique reads description: The number of unique reads generated by the sequencing process. comments: Provide a numerical value (no need to include units). @@ -4721,8 +5104,8 @@ slots: range: integer examples: - value: '248236' - minimum post-trimming read length: - name: minimum post-trimming read length + minimum_posttrimming_read_length: + name: minimum_posttrimming_read_length title: minimum post-trimming read length description: The threshold used as a cut-off for the minimum length of a read after trimming. @@ -4731,8 +5114,8 @@ slots: range: integer examples: - value: '150' - number of contigs: - name: number of contigs + number_of_contigs: + name: number_of_contigs title: number of contigs description: The number of contigs (contiguous sequences) in a sequence assembly. comments: Provide a numerical value. @@ -4740,8 +5123,8 @@ slots: range: integer examples: - value: '10' - percent Ns across total genome length: - name: percent Ns across total genome length + percent_ns_across_total_genome_length: + name: percent_ns_across_total_genome_length title: percent Ns across total genome length description: The percentage of the assembly that consists of ambiguous bases (Ns). comments: Provide a numerical value (no need to include units). @@ -4749,8 +5132,8 @@ slots: range: integer examples: - value: '2' - Ns per 100 kbp: - name: Ns per 100 kbp + ns_per_100_kbp: + name: ns_per_100_kbp title: Ns per 100 kbp description: The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). @@ -4759,8 +5142,8 @@ slots: range: integer examples: - value: '342' - N50: - name: N50 + n50: + name: n50 title: N50 description: The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. @@ -4769,8 +5152,8 @@ slots: range: integer examples: - value: '150' - percent read contamination: - name: percent read contamination + percent_read_contamination: + name: percent_read_contamination title: percent read contamination description: The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. @@ -4779,8 +5162,8 @@ slots: range: integer examples: - value: '2' - sequence assembly length: - name: sequence assembly length + sequence_assembly_length: + name: sequence_assembly_length title: sequence assembly length description: The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. @@ -4789,8 +5172,8 @@ slots: range: integer examples: - value: '34272' - consensus genome length: - name: consensus genome length + consensus_genome_length: + name: consensus_genome_length title: consensus genome length description: The length of the genome defined by the most common nucleotides at each position. @@ -4799,8 +5182,8 @@ slots: range: integer examples: - value: '38677' - reference genome accession: - name: reference genome accession + reference_genome_accession: + name: reference_genome_accession title: reference genome accession description: A persistent, unique identifier of a genome database entry. comments: Provide the accession number of the reference genome. @@ -4808,8 +5191,10 @@ slots: range: WhitespaceMinimizedString examples: - value: NC_045512.2 - deduplication method: - name: deduplication method + exact_mappings: + - NCBI_SRA:assembly + deduplication_method: + name: deduplication_method title: deduplication method description: The method used to remove duplicated reads in a sequence read dataset. comments: Provide the deduplication software name followed by the version, or @@ -4818,8 +5203,8 @@ slots: range: WhitespaceMinimizedString examples: - value: DeDup 0.12.8 - bioinformatics protocol: - name: bioinformatics protocol + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Further details regarding the methods used to process raw data, and/or @@ -4830,8 +5215,8 @@ slots: range: WhitespaceMinimizedString examples: - value: https://github.com/phac-nml/ncov2019-artic-nf - read mapping software name: - name: read mapping software name + read_mapping_software_name: + name: read_mapping_software_name title: read mapping software name description: The name of the software used to map sequence reads to a reference genome or set of reference genes. @@ -4840,8 +5225,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Bowtie2, BWA-MEM, TopHat - read mapping software version: - name: read mapping software version + read_mapping_software_version: + name: read_mapping_software_version title: read mapping software version description: The version of the software used to map sequence reads to a reference genome or set of reference genes. @@ -4850,8 +5235,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 2.5.1 - taxonomic reference database name: - name: taxonomic reference database name + taxonomic_reference_database_name: + name: taxonomic_reference_database_name title: taxonomic reference database name description: The name of the taxonomic reference database used to identify the organism. @@ -4861,8 +5246,8 @@ slots: recommended: true examples: - value: NCBITaxon - taxonomic reference database version: - name: taxonomic reference database version + taxonomic_reference_database_version: + name: taxonomic_reference_database_version title: taxonomic reference database version description: The version of the taxonomic reference database used to identify the organism. @@ -4872,8 +5257,8 @@ slots: recommended: true examples: - value: '1.3' - taxonomic analysis report filename: - name: taxonomic analysis report filename + taxonomic_analysis_report_filename: + name: taxonomic_analysis_report_filename title: taxonomic analysis report filename description: The filename of the report containing the results of a taxonomic analysis. @@ -4883,8 +5268,8 @@ slots: range: WhitespaceMinimizedString examples: - value: WWtax_report_Feb1_2024.doc - taxonomic analysis date: - name: taxonomic analysis date + taxonomic_analysis_date: + name: taxonomic_analysis_date title: taxonomic analysis date description: The date a taxonomic analysis was performed. comments: Providing the date that an analyis was performed can help provide context @@ -4894,8 +5279,8 @@ slots: range: date examples: - value: '2024-02-01' - read mapping criteria: - name: read mapping criteria + read_mapping_criteria: + name: read_mapping_criteria title: read mapping criteria description: A description of the criteria used to map reads to a reference sequence. comments: Provide a description of the read mapping criteria. @@ -4903,8 +5288,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Phred score >20 - AMR analysis software name: - name: AMR analysis software name + amr_analysis_software_name: + name: amr_analysis_software_name title: AMR analysis software name description: The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. @@ -4914,8 +5299,8 @@ slots: recommended: true examples: - value: Resistance Gene Identifier - AMR analysis software version: - name: AMR analysis software version + amr_analysis_software_version: + name: amr_analysis_software_version title: AMR analysis software version description: The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. @@ -4925,8 +5310,8 @@ slots: recommended: true examples: - value: 6.0.3 - AMR reference database name: - name: AMR reference database name + amr_reference_database_name: + name: amr_reference_database_name title: AMR reference database name description: Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. @@ -4936,8 +5321,8 @@ slots: recommended: true examples: - value: Comprehensive Antibiotic Resistance Database (CARD) - AMR reference database version: - name: AMR reference database version + amr_reference_database_version: + name: amr_reference_database_version title: AMR reference database version description: The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. @@ -4947,8 +5332,8 @@ slots: recommended: true examples: - value: 3.2.9 - AMR analysis report filename: - name: AMR analysis report filename + amr_analysis_report_filename: + name: amr_analysis_report_filename title: AMR analysis report filename description: The filename of the report containing the results of an in silico antimicrobial resistance analysis. @@ -4959,8 +5344,8 @@ slots: recommended: true examples: - value: WWAMR_report_Feb1_2024.doc - lineage/clade name: - name: lineage/clade name + lineage_clade_name: + name: lineage_clade_name title: lineage/clade name description: The name of the lineage or clade. comments: Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades @@ -4969,8 +5354,8 @@ slots: range: WhitespaceMinimizedString examples: - value: B.1.1.7 - lineage/clade analysis software name: - name: lineage/clade analysis software name + lineage_clade_analysis_software_name: + name: lineage_clade_analysis_software_name title: lineage/clade analysis software name description: The name of the software used to determine the lineage/clade. comments: Provide the name of the software used to determine the lineage/clade. @@ -4978,8 +5363,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Freyja - lineage/clade analysis software version: - name: lineage/clade analysis software version + lineage_clade_analysis_software_version: + name: lineage_clade_analysis_software_version title: lineage/clade analysis software version description: The version of the software used to determine the lineage/clade. comments: Provide the version of the software used ot determine the lineage/clade. @@ -4987,8 +5372,8 @@ slots: range: WhitespaceMinimizedString examples: - value: 1.5.0 - lineage/clade analysis report filename: - name: lineage/clade analysis report filename + lineage_clade_analysis_report_filename: + name: lineage_clade_analysis_report_filename title: lineage/clade analysis report filename description: The filename of the report containing the results of a lineage/clade analysis. @@ -4998,26 +5383,48 @@ slots: range: WhitespaceMinimizedString examples: - value: aggregated-WWSC2-ABC-b_1234.tsv - gene name: - name: gene name - title: gene name - description: The name of the gene used in the diagnostic RT-PCR test. - slot_uri: GENEPIO:0100655 - diagnostic target presence: - name: diagnostic target presence - title: diagnostic target presence + assay_target_name_1: + name: assay_target_name_1 + title: assay target name 1 + description: The name of the assay target used in the diagnostic RT-PCR test. + comments: The specific genomic region, sequence, or variant targeted by the assay + in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, + or other genetic elements that serve as a marker for detecting the presence + of a pathogen or other relevant entities. + slot_uri: GENEPIO:0101206 + any_of: + - range: WhitespaceMinimizedString + - range: NullValueMenu + assay_target_details: + name: assay_target_details + title: assay target details + description: Describe any details of the assay target. + comments: Provide details that are applicable to the assay used for the diagnostic + test. + slot_uri: GENEPIO:0102040 + range: WhitespaceMinimizedString + gene_symbol_1: + name: gene_symbol_1 + title: gene symbol 1 + description: The symbol of the gene used in the diagnostic RT-PCR test. + slot_uri: GENEPIO:0102041 + diagnostic_target_presence_1: + name: diagnostic_target_presence_1 + title: diagnostic target presence 1 description: The binary value of the result from a diagnostic test. comments: Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. slot_uri: GENEPIO:0100962 any_of: - - range: diagnostic target presence menu - - range: null value menu + - range: DiagnosticTargetPresenceMenu + - range: NullValueMenu examples: - value: diagnostic target present - diagnostic measurement value: - name: diagnostic measurement value - title: diagnostic measurement value + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_known_present + diagnostic_measurement_value_1: + name: diagnostic_measurement_value_1 + title: diagnostic measurement value 1 description: The value of the result from a diagnostic test. comments: Provide the numerical result of a diagnostic test (no need to include units). @@ -5025,2513 +5432,5267 @@ slots: range: WhitespaceMinimizedString examples: - value: '1000' - diagnostic measurement unit: - name: diagnostic measurement unit - title: diagnostic measurement unit + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc + diagnostic_measurement_unit_1: + name: diagnostic_measurement_unit_1 + title: diagnostic measurement unit 1 description: The unit of the result from a diagnostic test. comments: Select a value from the pick list provided, to describe the units of the given diagnostic test. slot_uri: GENEPIO:0100964 any_of: - - range: diagnostic measurement unit menu - - range: null value menu + - range: DiagnosticMeasurementUnitMenu + - range: NullValueMenu examples: - value: cycle threshold (Ct) - diagnostic measurement method: - name: diagnostic measurement method - title: diagnostic measurement method + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_conc_unit + diagnostic_measurement_method_1: + name: diagnostic_measurement_method_1 + title: diagnostic measurement method 1 description: The method by which a diagnostic result was determined. comments: Select a value from the pick list provided to describe the method used for a given diagnostic test. slot_uri: GENEPIO:0100965 any_of: - - range: diagnostic measurement method menu - - range: null value menu + - range: DiagnosticMeasurementMethodMenu + - range: NullValueMenu examples: - value: qPCR - authors: - name: authors - title: authors - description: Names of individuals contributing to the processes of sample collection, - sequence generation, analysis, and data submission. - comments: Include the first and last names of all individuals that should be attributed, - separated by a semicolon. - slot_uri: GENEPIO:0001517 + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_1_protocol + assay_target_name_2: + name: assay_target_name_2 + title: assay target name 2 + description: The name of the assay target used in the diagnostic RT-PCR test. + comments: The specific genomic region, sequence, or variant targeted by the assay + in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, + or other genetic elements that serve as a marker for detecting the presence + of a pathogen or other relevant entities. range: WhitespaceMinimizedString - recommended: true + assay_target_details_2: + name: assay_target_details_2 + title: assay target details 2 + description: Describe any details of the assay target. + comments: Provide details that are applicable to the assay used for the diagnostic + test. + range: WhitespaceMinimizedString + gene_symbol_2: + name: gene_symbol_2 + title: gene symbol 2 + description: The symbol of the gene used in the diagnostic RT-PCR test. + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_gene + diagnostic_target_presence_2: + name: diagnostic_target_presence_2 + title: diagnostic target presence 2 + description: The binary value of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe whether a target + was determined to be present or absent within a sample. + any_of: + - range: DiagnosticTargetPresenceMenu + - range: NullValueMenu examples: - - value: Tejinder Singh - - value: Fei Hu - - value: Joe Blogs + - value: diagnostic target present exact_mappings: - - GISAID:Authors - - CNPHI:Authors - - NML_LIMS:PH_CANCOGEN_AUTHORS - DataHarmonizer provenance: - name: DataHarmonizer provenance - title: DataHarmonizer provenance - description: The DataHarmonizer software and template version provenance. - comments: The current software and template version information will be automatically - generated in this field after the user utilizes the "validate" function. This - information will be generated regardless as to whether the row is valid of not. - slot_uri: GENEPIO:0001518 - range: Provenance - examples: - - value: DataHarmonizer v3.3.3, Influenza v1.0.0 + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_known_present + diagnostic_measurement_value_2: + name: diagnostic_measurement_value_2 + title: diagnostic measurement value 2 + description: The value of the result from a diagnostic test. + comments: Provide the numerical result of a diagnostic test (no need to include + units). + range: WhitespaceMinimizedString + examples: + - value: '1000' + exact_mappings: + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc + diagnostic_measurement_unit_2: + name: diagnostic_measurement_unit_2 + title: diagnostic measurement unit 2 + description: The unit of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe the units of + the given diagnostic test. + any_of: + - range: DiagnosticMeasurementUnitMenu + - range: NullValueMenu + examples: + - value: cycle threshold (Ct) exact_mappings: - - GISAID:DataHarmonizer%20provenance - - CNPHI:Additional%20Comments - - NML_LIMS:HC_COMMENTS + - NCBI_BIOSAMPLE_SARS-COV-2_WWS:ww_surv_target_2_conc_unit + diagnostic_measurement_method_2: + name: diagnostic_measurement_method_2 + title: diagnostic measurement method 2 + description: The method by which a diagnostic result was determined. + comments: Select a value from the pick list provided to describe the method used + for a given diagnostic test. + any_of: + - range: DiagnosticMeasurementMethodMenu + - range: NullValueMenu + examples: + - value: qPCR + assay_target_name_3: + name: assay_target_name_3 + title: assay target name 3 + description: The name of the assay target used in the diagnostic RT-PCR test. + comments: The specific genomic region, sequence, or variant targeted by the assay + in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, + or other genetic elements that serve as a marker for detecting the presence + of a pathogen or other relevant entities. + range: WhitespaceMinimizedString + assay_target_details_3: + name: assay_target_details_3 + title: assay target details 3 + description: Describe any details of the assay target. + comments: Provide details that are applicable to the assay used for the diagnostic + test. + range: WhitespaceMinimizedString + gene_symbol_3: + name: gene_symbol_3 + title: gene symbol 3 + description: The symbol of the gene used in the diagnostic RT-PCR test. + diagnostic_target_presence_3: + name: diagnostic_target_presence_3 + title: diagnostic target presence 3 + description: The binary value of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe whether a target + was determined to be present or absent within a sample. + any_of: + - range: DiagnosticTargetPresenceMenu + - range: NullValueMenu + examples: + - value: diagnostic target present + diagnostic_measurement_value_3: + name: diagnostic_measurement_value_3 + title: diagnostic measurement value 3 + description: The value of the result from a diagnostic test. + comments: Provide the numerical result of a diagnostic test (no need to include + units). + range: WhitespaceMinimizedString + examples: + - value: '1000' + diagnostic_measurement_unit_3: + name: diagnostic_measurement_unit_3 + title: diagnostic measurement unit 3 + description: The unit of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe the units of + the given diagnostic test. + any_of: + - range: DiagnosticMeasurementUnitMenu + - range: NullValueMenu + examples: + - value: cycle threshold (Ct) + diagnostic_measurement_method_3: + name: diagnostic_measurement_method_3 + title: diagnostic measurement method 3 + description: The method by which a diagnostic result was determined. + comments: Select a value from the pick list provided to describe the method used + for a given diagnostic test. + any_of: + - range: DiagnosticMeasurementMethodMenu + - range: NullValueMenu + examples: + - value: qPCR enums: - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu + title: null value menu permissible_values: - Not Applicable: - text: Not Applicable + Not Applicable [GENEPIO:0001619]: + text: Not Applicable [GENEPIO:0001619] + description: A categorical choice recorded when a datum does not apply to + a given context. meaning: GENEPIO:0001619 - Missing: - text: Missing + Missing [GENEPIO:0001618]: + text: Missing [GENEPIO:0001618] + description: A categorical choice recorded when a datum is not included for + an unknown reason. meaning: GENEPIO:0001618 - Not Collected: - text: Not Collected + Not Collected [GENEPIO:0001620]: + text: Not Collected [GENEPIO:0001620] + description: A categorical choice recorded when a datum was not measured or + collected. meaning: GENEPIO:0001620 - Not Provided: - text: Not Provided + Not Provided [GENEPIO:0001668]: + text: Not Provided [GENEPIO:0001668] + description: A categorical choice recorded when a datum was collected but + is not currently provided in the information being shared. This value indicates + the information may be shared at the later stage. meaning: GENEPIO:0001668 - Restricted Access: - text: Restricted Access + Restricted Access [GENEPIO:0001810]: + text: Restricted Access [GENEPIO:0001810] + description: A categorical choice recorded when a given datum is available + but not shared publicly because of information privacy concerns. meaning: GENEPIO:0001810 - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: - Afghanistan: - text: Afghanistan + Afghanistan [GAZ:00006882]: + text: Afghanistan [GAZ:00006882] + description: A landlocked country that is located approximately in the center + of Asia. It is bordered by Pakistan in the south and east Iran in the west, + Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far + northeast. Afghanistan is administratively divided into thirty-four (34) + provinces (welayats). Each province is then divided into many provincial + districts, and each district normally covers a city or several townships. + [ url:http://en.wikipedia.org/wiki/Afghanistan ] meaning: GAZ:00006882 - Albania: - text: Albania + Albania [GAZ:00002953]: + text: Albania [GAZ:00002953] + description: 'A country in South Eastern Europe. Albania is bordered by Greece + to the south-east, Montenegro to the north, Kosovo to the northeast, and + the Republic of Macedonia to the east. It has a coast on the Adriatic Sea + to the west, and on the Ionian Sea to the southwest. From the Strait of + Otranto, Albania is less than 100 km from Italy. Albania is divided into + 12 administrative divisions called (Albanian: official qark/qarku, but often + prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities + (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania + ]' meaning: GAZ:00002953 - Algeria: - text: Algeria + Algeria [GAZ:00000563]: + text: Algeria [GAZ:00000563] + description: A country in North Africa. It is bordered by Tunisia in the northeast, + Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, + a few km of the Western Sahara in the west, Morocco in the northwest, and + the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), + 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). + [ url:http://en.wikipedia.org/wiki/Algeria ] meaning: GAZ:00000563 - American Samoa: - text: American Samoa + American Samoa [GAZ:00003957]: + text: American Samoa [GAZ:00003957] + description: An unincorporated territory of the United States located in the + South Pacific Ocean, southeast of the sovereign State of Samoa. The main + (largest and most populous) island is Tutuila, with the Manu'a Islands, + Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa + ] meaning: GAZ:00003957 - Andorra: - text: Andorra + Andorra [GAZ:00002948]: + text: Andorra [GAZ:00002948] + description: 'A small landlocked country in western Europe, located in the + eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. + Andorra consists of seven communities known as parishes (Catalan: parroquies, + singular - parroquia). Until relatively recently, it had only six parishes; + the seventh, Escaldes-Engordany, was created in 1978. Some parishes have + a further territorial subdivision. Ordino, La Massana and Sant Julia de + Loria are subdivided into quarts (quarters), while Canillo is subdivided + into veinats (neighborhoods). Those mostly coincide with villages, which + are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]' meaning: GAZ:00002948 - Angola: - text: Angola + Angola [GAZ:00001095]: + text: Angola [GAZ:00001095] + description: A country in south-central Africa bordering Namibia to the south, + Democratic Republic of the Congo to the north, and Zambia to the east, and + with a west coast along the Atlantic Ocean. The exclave province Cabinda + has a border with the Republic of the Congo and the Democratic Republic + of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] meaning: GAZ:00001095 - Anguilla: - text: Anguilla + Anguilla [GAZ:00009159]: + text: Anguilla [GAZ:00009159] + description: A British overseas territory in the Caribbean, one of the most + northerly of the Leeward Islands in the Lesser Antilles. It consists of + the main island of Anguilla itself, approximately 26 km long by 5 km wide + at its widest point, together with a number of much smaller islands and + cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila + ] meaning: GAZ:00009159 - Antarctica: - text: Antarctica + Antarctica [GAZ:00000462]: + text: Antarctica [GAZ:00000462] + description: The Earth's southernmost continent, overlying the South Pole. + It is situated in the southern hemisphere, almost entirely south of the + Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica + ] meaning: GAZ:00000462 - Antigua and Barbuda: - text: Antigua and Barbuda + Antigua and Barbuda [GAZ:00006883]: + text: Antigua and Barbuda [GAZ:00006883] + description: An island nation located on the eastern boundary of the Caribbean + Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda + ] meaning: GAZ:00006883 - Argentina: - text: Argentina + Argentina [GAZ:00002928]: + text: Argentina [GAZ:00002928] + description: 'A South American country, constituted as a federation of twenty-three + provinces and an autonomous city. It is bordered by Paraguay and Bolivia + in the north, Brazil and Uruguay in the northeast, and Chile in the west + and south. The country claims the British controlled territories of the + Falkland Islands and South Georgia and the South Sandwich Islands. Argentina + also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping + other claims made by Chile and the United Kingdom. Argentina is subdivided + into twenty-three provinces (Spanish: provincias, singular provincia) and + one federal district (Capital de la Republica or Capital de la Nacion, informally + the Capital Federal). The federal district and the provinces have their + own constitutions, but exist under a federal system. Provinces are then + divided into departments (Spanish: departamentos, singular departamento), + except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina + ]' meaning: GAZ:00002928 - Armenia: - text: Armenia + Armenia [GAZ:00004094]: + text: Armenia [GAZ:00004094] + description: A landlocked mountainous country in Eurasia between the Black + Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the + west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan + exclave of Azerbaijan to the south. A transcontinental country at the juncture + of Eastern Europe and Western Asia. A former republic of the Soviet Union. + Armenia is divided into ten marzes (provinces, singular marz), with the + city (kaghak) of Yerevan having special administrative status as the country's + capital. [ url:http://en.wikipedia.org/wiki/Armenia ] meaning: GAZ:00004094 - Aruba: - text: Aruba + Aruba [GAZ:00004025]: + text: Aruba [GAZ:00004025] + description: An autonomous region within the Kingdom of the Netherlands, Aruba + has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba + ] meaning: GAZ:00004025 - Ashmore and Cartier Islands: - text: Ashmore and Cartier Islands + Ashmore and Cartier Islands [GAZ:00005901]: + text: Ashmore and Cartier Islands [GAZ:00005901] + description: A Territory of Australia that includes two groups of small low-lying + uninhabited tropical islands in the Indian Ocean situated on the edge of + the continental shelf north-west of Australia and south of the Indonesian + island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands + ] meaning: GAZ:00005901 - Australia: - text: Australia + Australia [GAZ:00000463]: + text: Australia [GAZ:00000463] + description: A country in the southern hemisphere comprising the mainland + of the world's smallest continent, the major island of Tasmania, and a number + of other islands in the Indian and Pacific Oceans. The neighbouring countries + are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon + Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to + the south-east. Australia has six states, two major mainland territories, + and other minor territories. meaning: GAZ:00000463 - Austria: - text: Austria + Austria [GAZ:00002942]: + text: Austria [GAZ:00002942] + description: A landlocked country in Central Europe. It borders both Germany + and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia + and Italy to the south, and Switzerland and Liechtenstein to the west. The + capital is the city of Vienna on the Danube River. Austria is divided into + nine states (Bundeslander). These states are then divided into districts + (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities + (Gemeinden). Cities have the competencies otherwise granted to both districts + and municipalities. meaning: GAZ:00002942 - Azerbaijan: - text: Azerbaijan + Azerbaijan [GAZ:00004941]: + text: Azerbaijan [GAZ:00004941] + description: A country in the he South Caucasus region of Eurasia, it is bounded + by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, + Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan + is bordered by Armenia to the north and east, Iran to the south and west, + and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts + in Azerbaijan's southwest, have been controlled by Armenia since the end + of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons + 11 city districts (saharlar), and one autonomous republic (muxtar respublika). meaning: GAZ:00004941 - Bahamas: - text: Bahamas + Bahamas [GAZ:00002733]: + text: Bahamas [GAZ:00002733] + description: A country consisting of two thousand cays and seven hundred islands + that form an archipelago. It is located in the Atlantic Ocean, southeast + of Florida and the United States, north of Cuba, the island of Hispanola + and the Caribbean, and northwest of the British overseas territory of the + Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, + whose affairs are handled directly by the central government. meaning: GAZ:00002733 - Bahrain: - text: Bahrain + Bahrain [GAZ:00005281]: + text: Bahrain [GAZ:00005281] + description: A borderless island country in the Persian Gulf. Saudi Arabia + lies to the west and is connected to Bahrain by the King Fahd Causeway, + and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into + five governorates. meaning: GAZ:00005281 - Baker Island: - text: Baker Island + Baker Island [GAZ:00007117]: + text: Baker Island [GAZ:00007117] + description: An uninhabited atoll located just north of the equator in the + central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island + is an unincorporated and unorganized territory of the US. meaning: GAZ:00007117 - Bangladesh: - text: Bangladesh + Bangladesh [GAZ:00003750]: + text: Bangladesh [GAZ:00003750] + description: A country in South Asia. It is bordered by India on all sides + except for a small border with Myanmar to the far southeast and by the Bay + of Bengal to the south. Bangladesh is divided into six administrative divisions. + Divisions are subdivided into districts (zila). There are 64 districts in + Bangladesh, each further subdivided into upazila (subdistricts) or thana + ("police stations"). meaning: GAZ:00003750 - Barbados: - text: Barbados + Barbados [GAZ:00001251]: + text: Barbados [GAZ:00001251] + description: "An island country in the Lesser Antilles of the West Indies,\ + \ in the Caribbean region of the Americas, and the most easterly of the\ + \ Caribbean Islands. It is 34 kilometres (21 miles) in length and up to\ + \ 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is\ + \ in the western part of the North Atlantic, 100 km (62 mi) east of the\ + \ Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards,\ + \ part of the Lesser Antilles, at roughly 13\xB0N of the equator. It is\ + \ about 168 km (104 mi) east of both the countries of Saint Lucia and Saint\ + \ Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique\ + \ and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside\ + \ the principal Atlantic hurricane belt. Its capital and largest city is\ + \ Bridgetown." meaning: GAZ:00001251 - Bassas da India: - text: Bassas da India + Bassas da India [GAZ:00005810]: + text: Bassas da India [GAZ:00005810] + description: A roughly circular atoll about 10 km in diameter, which corresponds + to a total size (including lagoon) of 80 km2. It is located in the southern + Mozambique Channel, about half-way between Madagascar (which is 385 km to + the east) and Mozambique, and 110 km northwest of Europa Island. It rises + steeply from the seabed 3000 m below. meaning: GAZ:00005810 - Belarus: - text: Belarus + Belarus [GAZ:00006886]: + text: Belarus [GAZ:00006886] + description: A landlocked country in Eastern Europe, that borders Russia to + the north and east, Ukraine to the south, Poland to the west, and Lithuania + and Latvia to the north. Its capital is Minsk. Belarus is divided into six + voblasts, or provinces. Voblasts are further subdivided into raions (commonly + translated as districts or regions). As of 2002, there are six voblasts, + 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special + status, due to the city serving as the national capital. meaning: GAZ:00006886 - Belgium: - text: Belgium + Belgium [GAZ:00002938]: + text: Belgium [GAZ:00002938] + description: A country in northwest Europe. Belgium shares borders with France + (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 + km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each + comprise five provinces; the third region, Brussels-Capital Region, is not + a province, nor does it contain any Together, these comprise 589 municipalities, + which in general consist of several sub-municipalities (which were independent + municipalities before the municipal merger operation mainly in 1977). meaning: GAZ:00002938 - Belize: - text: Belize + Belize [GAZ:00002934]: + text: Belize [GAZ:00002934] + description: A country in Central America. It is the only officially English + speaking country in the region. Belize was a British colony for more than + a century and was known as British Honduras until 1973. It became an independent + nation within The Commonwealth in 1981. Belize is divided into 6 districts, + which are further divided into 31 constituencies. meaning: GAZ:00002934 - Benin: - text: Benin + Benin [GAZ:00000904]: + text: Benin [GAZ:00000904] + description: A country in Western Africa. It borders Togo to the west, Nigeria + to the east and Burkina Faso and Niger to the north; its short coastline + to the south leads to the Bight of Benin. Its capital is Porto Novo, but + the seat of government is Cotonou. Benin is divided into 12 departments + and subdivided into 77 communes. meaning: GAZ:00000904 - Bermuda: - text: Bermuda + Bermuda [GAZ:00001264]: + text: Bermuda [GAZ:00001264] + description: A British overseas territory in the North Atlantic Ocean. Located + off the east coast of the United States, it is situated around 1770 km NE + of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately + 138 islands. meaning: GAZ:00001264 - Bhutan: - text: Bhutan + Bhutan [GAZ:00003920]: + text: Bhutan [GAZ:00003920] + description: A landlocked nation in South Asia. It is located amidst the eastern + end of the Himalaya Mountains and is bordered to the south, east and west + by India and to the north by Tibet. Bhutan is separated from Nepal by the + Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative + zones). Each dzongdey is further divided into dzongkhag (districts). There + are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into + subdistricts known as dungkhag. At the basic level, groups of villages form + a constituency called gewog. meaning: GAZ:00003920 - Bolivia: - text: Bolivia + Bolivia [GAZ:00002511]: + text: Bolivia [GAZ:00002511] + description: 'A landlocked country in central South America. It is bordered + by Brazil on the north and east, Paraguay and Argentina on the south, and + Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: + departamentos). Each of the departments is subdivided into provinces (provincias), + which are further subdivided into municipalities (municipios).' meaning: GAZ:00002511 - Borneo: - text: Borneo + Borneo [GAZ:00025355]: + text: Borneo [GAZ:00025355] + description: 'An island at the grographic centre of Maritime Southeast Adia, + in relation to major Indonesian islands, it is located north of Java, west + of Sulawesi, and east of Sumatra. It is the third-largest island in the + world and the larest in Asia. The island is politically divided among three + countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] + Approximately 73% of the island is Indonesian territory. In the north, the + East Malaysian states of Sabah and Sarawak make up about 26% of the island. + Additionally, the Malaysian federal territory of Labuan is situated on a + small island just off the coast of Borneo. The sovereign state of Brunei, + located on the north coast, comprises about 1% of Borneo''s land area. A + little more than half of the island is in the Northern Hemisphere, including + Brunei and the Malaysian portion, while the Indonesian portion spans the + Northern and Southern hemispheres.' meaning: GAZ:00025355 - Bosnia and Herzegovina: - text: Bosnia and Herzegovina + Bosnia and Herzegovina [GAZ:00006887]: + text: Bosnia and Herzegovina [GAZ:00006887] + description: A country on the Balkan peninsula of Southern Europe. Bordered + by Croatia to the north, west and south, Serbia to the east, and Montenegro + to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 + km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided + into three political regions of which one, the Brcko District is part of + the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. + All three have an equal constitutional status on the whole territory of + Bosnia and Herzegovina. meaning: GAZ:00006887 - Botswana: - text: Botswana + Botswana [GAZ:00001097]: + text: Botswana [GAZ:00001097] + description: A landlocked nation in Southern Africa. It is bordered by South + Africa to the south and southeast, Namibia to the west, Zambia to the north, + and Zimbabwe to the northeast. Botswana is divided into nine districts, + which are subdivided into a total twenty-eight subdistricts. meaning: GAZ:00001097 - Bouvet Island: - text: Bouvet Island + Bouvet Island [GAZ:00001453]: + text: Bouvet Island [GAZ:00001453] + description: A sub-antarctic volcanic island in the South Atlantic Ocean, + south-southwest of the Cape of Good Hope (South Africa). It is a dependent + area of Norway and is not subject to the Antarctic Treaty, as it is north + of the latitude south of which claims are suspended. meaning: GAZ:00001453 - Brazil: - text: Brazil + Brazil [GAZ:00002828]: + text: Brazil [GAZ:00002828] + description: 'A country in South America. Bordered by the Atlantic Ocean and + by Venezuela, Suriname, Guyana and the department of French Guiana to the + north, Colombia to the northwest, Bolivia and Peru to the west, Argentina + and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six + states (estados) and one federal district (Distrito Federal). The states + are subdivided into municipalities. For statistical purposes, the States + are grouped into five main regions: North, Northeast, Central-West, Southeast + and South.' meaning: GAZ:00002828 - British Virgin Islands: - text: British Virgin Islands + British Virgin Islands [GAZ:00003961]: + text: British Virgin Islands [GAZ:00003961] + description: A British overseas territory, located in the Caribbean to the + east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, + the remaining islands constituting the US Virgin Islands. The British Virgin + Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and + Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately + fifteen of the islands are inhabited. meaning: GAZ:00003961 - Brunei: - text: Brunei + Brunei [GAZ:00003901]: + text: Brunei [GAZ:00003901] + description: A country located on the north coast of the island of Borneo, + in Southeast Asia. Apart from its coastline with the South China Sea it + is completely surrounded by the State of Sarawak, Malaysia, and in fact + it is separated into two parts by Limbang, which is part of Sarawak. Brunei + is divided into four districts (daerah), the districts are subdivided into + thirty-eight mukims, which are then divided into kampong (villages). meaning: GAZ:00003901 - Bulgaria: - text: Bulgaria + Bulgaria [GAZ:00002950]: + text: Bulgaria [GAZ:00002950] + description: A country in Southeastern Europe, borders five other countries; + Romania to the north (mostly along the Danube), Serbia and the Republic + of Macedonia to the west, and Greece and Turkey to the south. The Black + Sea defines the extent of the country to the east. Since 1999, it has consisted + of twenty-eight provinces. The provinces subdivide into 264 municipalities. meaning: GAZ:00002950 - Burkina Faso: - text: Burkina Faso + Burkina Faso [GAZ:00000905]: + text: Burkina Faso [GAZ:00000905] + description: 'A landlocked nation in West Africa. It is surrounded by six + countries: Mali to the north, Niger to the east, Benin to the south east, + Togo and Ghana to the south, and Cote d''Ivoire to the south west. Burkina + Faso is divided into thirteen regions, forty-five provinces, and 301 departments + (communes).' meaning: GAZ:00000905 - Burundi: - text: Burundi + Burundi [GAZ:00001090]: + text: Burundi [GAZ:00001090] + description: A small country in the Great Lakes region of Africa. It is bordered + by Rwanda on the north, Tanzania on the south and east, and the Democratic + Republic of the Congo on the west. Although the country is landlocked, much + of its western border is adjacent to Lake Tanganyika. Burundi is divided + into 17 provinces, 117 communes, and 2,638 collines. meaning: GAZ:00001090 - Cambodia: - text: Cambodia + Cambodia [GAZ:00006888]: + text: Cambodia [GAZ:00006888] + description: A country in Southeast Asia. The country borders Thailand to + its west and northwest, Laos to its northeast, and Vietnam to its east and + southeast. In the south it faces the Gulf of Thailand. meaning: GAZ:00006888 - Cameroon: - text: Cameroon + Cameroon [GAZ:00001093]: + text: Cameroon [GAZ:00001093] + description: A country of central and western Africa. It borders Nigeria to + the west; Chad to the northeast; the Central African Republic to the east; + and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. + Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea + and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces + and 58 divisions or departments. The divisions are further sub-divided into + sub-divisions (arrondissements) and districts. meaning: GAZ:00001093 - Canada: - text: Canada + Canada [GAZ:00002560]: + text: Canada [GAZ:00002560] + description: A country occupying most of northern North America, extending + from the Atlantic Ocean in the east to the Pacific Ocean in the west and + northward into the Arctic Ocean. Canada is a federation composed of ten + provinces and three territories; in turn, these may be grouped into regions. + Western Canada consists of British Columbia and the three Prairie provinces + (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec + and Ontario. Atlantic Canada consists of the three Maritime provinces (New + Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland + and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada + together. Three territories (Yukon, Northwest Territories, and Nunavut) + make up Northern Canada. meaning: GAZ:00002560 - Cape Verde: - text: Cape Verde + Cape Verde [GAZ:00001227]: + text: Cape Verde [GAZ:00001227] + description: A republic located on an archipelago in the Macaronesia ecoregion + of the North Atlantic Ocean, off the western coast of Africa. Cape Verde + is divided into 22 municipalities (concelhos), and subdivided into 32 parishes + (freguesias). meaning: GAZ:00001227 - Cayman Islands: - text: Cayman Islands + Cayman Islands [GAZ:00003986]: + text: Cayman Islands [GAZ:00003986] + description: A British overseas territory located in the western Caribbean + Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. + The Cayman Islands are divided into seven districts. meaning: GAZ:00003986 - Central African Republic: - text: Central African Republic + Central African Republic [GAZ:00001089]: + text: Central African Republic [GAZ:00001089] + description: A landlocked country in Central Africa. It borders Chad in the + north, Sudan in the east, the Republic of the Congo and the Democratic Republic + of the Congo in the south, and Cameroon in the west. The Central African + Republic is divided into 14 administrative prefectures (prefectures), along + with 2 economic prefectures (prefectures economiques) and one autonomous + commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). meaning: GAZ:00001089 - Chad: - text: Chad + Chad [GAZ:00000586]: + text: Chad [GAZ:00000586] + description: A landlocked country in central Africa. It is bordered by Libya + to the north, Sudan to the east, the Central African Republic to the south, + Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided + into 18 regions. The departments are divided into 200 sub-prefectures, which + are in turn composed of 446 cantons. This is due to change. meaning: GAZ:00000586 - Chile: - text: Chile + Chile [GAZ:00002825]: + text: Chile [GAZ:00002825] + description: 'A country in South America occupying a long and narrow coastal + strip wedged between the Andes mountains and the Pacific Ocean. The Pacific + forms the country''s entire western border, with Peru to the north, Bolivia + to the northeast, Argentina to the east, and the Drake Passage at the country''s + southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. + Chile is divided into 15 regions. Every region is further divided into provinces. + Finally each province is divided into communes. Each region is designated + by a name and a Roman numeral, assigned from north to south. The only exception + is the region housing the nation''s capital, which is designated RM, that + stands for Region Metropolitana (Metropolitan Region). Two new regions were + created in 2006: Arica-Parinacota in the north, and Los Rios in the south. + Both became operative in 2007-10.' meaning: GAZ:00002825 - China: - text: China + China [GAZ:00002845]: + text: China [GAZ:00002845] + description: 'A large country in Northeast Asia. China borders 14 nations + (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, + Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia + and North Korea. Additionally the border between PRC and ROC is located + in territorial waters. The People''s Republic of China has administrative + control over twenty-two provinces and considers Taiwan to be its twenty-third + province. There are also five autonomous regions, each with a designated + minority group; four municipalities; and two Special Administrative Regions + that enjoy considerable autonomy. The People''s Republic of China administers + 33 province-level regions, 333 prefecture-level regions, 2,862 county-level + regions, 41,636 township-level regions, and several village-level regions.' meaning: GAZ:00002845 - Christmas Island: - text: Christmas Island + Christmas Island [GAZ:00005915]: + text: Christmas Island [GAZ:00005915] + description: An island in the Indian Ocean, 500 km south of Indonesia and + about 2600 km northwest of Perth. The island is the flat summit of a submarine + mountain. meaning: GAZ:00005915 - Clipperton Island: - text: Clipperton Island + Clipperton Island [GAZ:00005838]: + text: Clipperton Island [GAZ:00005838] + description: A nine-square km coral atoll in the North Pacific Ocean, southwest + of Mexico and west of Costa Rica. meaning: GAZ:00005838 - Cocos Islands: - text: Cocos Islands + Cocos Islands [GAZ:00009721]: + text: Cocos Islands [GAZ:00009721] + description: Islands that located in the Indian Ocean, about halfway between + Australia and Sri Lanka. A territory of Australia. There are two atolls + and twenty-seven coral islands in the group. meaning: GAZ:00009721 - Colombia: - text: Colombia + Colombia [GAZ:00002929]: + text: Colombia [GAZ:00002929] + description: A country located in the northwestern region of South America. + Colombia is bordered to the east by Venezuela and Brazil; to the south by + Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean + Sea; to the north-west by Panama; and to the west by the Pacific Ocean. + Besides the countries in South America, the Republic of Colombia is recognized + to share maritime borders with the Caribbean countries of Jamaica, Haiti, + the Dominican Republic and the Central American countries of Honduras, Nicaragua, + and Costa Rica. Colombia is divided into 32 departments and one capital + district which is treated as a department. There are in total 10 districts + assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, + Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia + is also subdivided into some municipalities which form departments, each + with a municipal seat capital city assigned. Colombia is also subdivided + into corregimientos which form municipalities. meaning: GAZ:00002929 - Comoros: - text: Comoros + Comoros [GAZ:00005820]: + text: Comoros [GAZ:00005820] + description: An island nation in the Indian Ocean, located off the eastern + coast of Africa on the northern end of the Mozambique Channel between northern + Madagascar and northeastern Mozambique. meaning: GAZ:00005820 - Cook Islands: - text: Cook Islands + Cook Islands [GAZ:00053798]: + text: Cook Islands [GAZ:00053798] + description: A self-governing parliamentary democracy in free association + with New Zealand. The fifteen small islands in this South Pacific Ocean + country have a total land area of 240 km2, but the Cook Islands Exclusive + Economic Zone (EEZ) covers 1.8 million km2 of ocean. meaning: GAZ:00053798 - Coral Sea Islands: - text: Coral Sea Islands + Coral Sea Islands [GAZ:00005917]: + text: Coral Sea Islands [GAZ:00005917] + description: A Territory of Australia which includes a group of small and + mostly uninhabited tropical islands and reefs in the Coral Sea, northeast + of Queensland, Australia. The only inhabited island is Willis Island. The + territory covers 780,000 km2, extending east and south from the outer edge + of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, + the Willis Group, and fifteen other reef/island groups. meaning: GAZ:00005917 - Costa Rica: - text: Costa Rica + Costa Rica [GAZ:00002901]: + text: Costa Rica [GAZ:00002901] + description: A republic in Central America, bordered by Nicaragua to the north, + Panama to the east-southeast, the Pacific Ocean to the west and south, and + the Caribbean Sea to the east. Costa Rica is composed of seven provinces, + which in turn are divided into 81 cantons. meaning: GAZ:00002901 - Cote d'Ivoire: - text: Cote d'Ivoire + Cote d'Ivoire [GAZ:00000906]: + text: Cote d'Ivoire [GAZ:00000906] + description: A country in West Africa. It borders Liberia and Guinea to the + west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf + of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). + The regions are further divided into 58 departments. meaning: GAZ:00000906 - Croatia: - text: Croatia + Croatia [GAZ:00002719]: + text: Croatia [GAZ:00002719] + description: A country at the crossroads of the Mediterranean, Central Europe, + and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and + Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to + the east, Montenegro to the far southeast, and the Adriatic Sea to the south. + Croatia is divided into 21 counties (zupanija) and the capital Zagreb's + city district. meaning: GAZ:00002719 - Cuba: - text: Cuba + Cuba [GAZ:00003762]: + text: Cuba [GAZ:00003762] + description: A country that consists of the island of Cuba (the largest and + second-most populous island of the Greater Antilles), Isla de la Juventud + and several adjacent small islands. Fourteen provinces and one special municipality + (the Isla de la Juventud) now compose Cuba. meaning: GAZ:00003762 - Curacao: - text: Curacao + Curacao [GAZ:00012582]: + text: Curacao [GAZ:00012582] + description: One of five island areas of the Netherlands Antilles. meaning: GAZ:00012582 - Cyprus: - text: Cyprus + Cyprus [GAZ:00004006]: + text: Cyprus [GAZ:00004006] + description: The third largest island in the Mediterranean Sea (after Sicily + and Sardinia), Cyprus is situated in the eastern Mediterranean, just south + of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, + it is often included in the Middle East (see also Western Asia and Near + East). Turkey is 75 km north; other neighbouring countries include Syria + and Lebanon to the east, Israel to the southeast, Egypt to the south, and + Greece to the west-north-west. meaning: GAZ:00004006 - Czech Republic: - text: Czech Republic + Czech Republic [GAZ:00002954]: + text: Czech Republic [GAZ:00002954] + description: 'A landlocked country in Central Europe. It has borders with + Poland to the north, Germany to the northwest and southwest, Austria to + the south, and Slovakia to the east. The capital and largest city is Prague. + The country is composed of the historic regions of Bohemia and Moravia, + as well as parts of Silesia. Since 2000, the Czech Republic is divided into + thirteen regions (kraje, singular kraj) and the capital city of Prague. + The older seventy-six districts (okresy, singular okres) including three + ''statutory cities'' (without Prague, which had special status) were disbanded + in 1999 in an administrative reform; they remain as territorial division + and seats of various branches of state administration. Since 2003-01-01, + the regions have been divided into around 203 Municipalities with Extended + Competence (unofficially named "Little Districts" (Czech: ''male okresy'') + which took over most of the administration of the former District Authorities. + Some of these are further divided into Municipalities with Commissioned + Local Authority. However, the old districts still exist as territorial units + and remain as seats of some of the offices.' meaning: GAZ:00002954 - Democratic Republic of the Congo: - text: Democratic Republic of the Congo + Democratic Republic of the Congo [GAZ:00001086]: + text: Democratic Republic of the Congo [GAZ:00001086] + description: A country of central Africa. It borders the Central African Republic + and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia + and Angola on the south, the Republic of the Congo on the west, and is separated + from Tanzania by Lake Tanganyika on the east. The country enjoys access + to the ocean through a 40 km stretch of Atlantic coastline at Muanda and + the roughly 9 km wide mouth of the Congo river which opens into the Gulf + of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed + into 25 Provinces from 2.2009. Each Province is divided into Zones. meaning: GAZ:00001086 - Denmark: - text: Denmark + Denmark [GAZ:00005852]: + text: Denmark [GAZ:00005852] + description: That part of the Kingdom of Denmark located in continental Europe. + The mainland is bordered to the south by Germany; Denmark is located to + the southwest of Sweden and the south of Norway. Denmark borders both the + Baltic and the North Sea. The country consists of a large peninsula, Jutland + (Jylland) and a large number of islands, most notably Zealand (Sjaelland), + Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds + of minor islands often referred to as the Danish Archipelago. meaning: GAZ:00005852 - Djibouti: - text: Djibouti + Djibouti [GAZ:00000582]: + text: Djibouti [GAZ:00000582] + description: A country in eastern Africa. Djibouti is bordered by Eritrea + in the north, Ethiopia in the west and south, and Somalia in the southeast. + The remainder of the border is formed by the Red Sea and the Gulf of Aden. + On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the + coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. + Djibouti is divided into 5 regions and one city. It is further subdivided + into 11 districts. meaning: GAZ:00000582 - Dominica: - text: Dominica + Dominica [GAZ:00006890]: + text: Dominica [GAZ:00006890] + description: An island nation in the Caribbean Sea. Dominica is divided into + ten parishes. meaning: GAZ:00006890 - Dominican Republic: - text: Dominican Republic + Dominican Republic [GAZ:00003952]: + text: Dominican Republic [GAZ:00003952] + description: A country in the West Indies that occupies the E two-thirds of + the Hispaniola island. The Dominican Republic's shores are washed by the + Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona + Passage, a channel about 130 km wide, separates the country (and the Hispaniola) + from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, + the national capital, Santo Domingo, is contained within its own Distrito + Nacional (National District). The provinces are divided into municipalities + (municipios; singular municipio). meaning: GAZ:00003952 - Ecuador: - text: Ecuador + Ecuador [GAZ:00002912]: + text: Ecuador [GAZ:00002912] + description: A country in South America, bordered by Colombia on the north, + by Peru on the east and south, and by the Pacific Ocean to the west. The + country also includes the Galapagos Islands (Archipelago de Colon) in the + Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, + divided into 199 cantons and subdivided into parishes (or parroquias). meaning: GAZ:00002912 - Egypt: - text: Egypt + Egypt [GAZ:00003934]: + text: Egypt [GAZ:00003934] + description: A country in North Africa that includes the Sinai Peninsula, + a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, + and the Gaza Strip and Israel to the east. The northern coast borders the + Mediterranean Sea and the island of Cyprus; the eastern coast borders the + Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, + singular muhafazah). The governorates are further divided into regions (markazes). meaning: GAZ:00003934 - El Salvador: - text: El Salvador + El Salvador [GAZ:00002935]: + text: El Salvador [GAZ:00002935] + description: A country in Central America, bordering the Pacific Ocean between + Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), + which, in turn, are subdivided into 267 municipalities (municipios). meaning: GAZ:00002935 - Equatorial Guinea: - text: Equatorial Guinea + Equatorial Guinea [GAZ:00001091]: + text: Equatorial Guinea [GAZ:00001091] + description: 'A country in Central Africa. It is one of the smallest countries + in continental Africa, and comprises two regions: Rio Muni, continental + region including several offshore islands; and Insular Region containing + Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando + Po) that contains the capital, Malabo. Equatorial Guinea is divided into + seven provinces which are divided into districts.' meaning: GAZ:00001091 - Eritrea: - text: Eritrea + Eritrea [GAZ:00000581]: + text: Eritrea [GAZ:00000581] + description: A country situated in northern East Africa. It is bordered by + Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. + The east and northeast of the country have an extensive coastline on the + Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago + and several of the Hanish Islands are part of Eritrea. Eritrea is divided + into six regions (zobas) and subdivided into districts ("sub-zobas"). meaning: GAZ:00000581 - Estonia: - text: Estonia + Estonia [GAZ:00002959]: + text: Estonia [GAZ:00002959] + description: A country in Northern Europe. Estonia has land borders to the + south with Latvia and to the east with Russia. It is separated from Finland + in the north by the Gulf of Finland and from Sweden in the west by the Baltic + Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). + Estonian counties are divided into rural (vallad, singular vald) and urban + (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) + municipalities. The municipalities comprise populated places (asula or asustusuksus) + - various settlements and territorial units that have no administrative + function. A group of populated places form a rural municipality with local + administration. Most towns constitute separate urban municipalities, while + some have joined with surrounding rural municipalities. meaning: GAZ:00002959 - Eswatini: - text: Eswatini + Eswatini [GAZ:00001099]: + text: Eswatini [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). meaning: GAZ:00001099 - Ethiopia: - text: Ethiopia + Ethiopia [GAZ:00000567]: + text: Ethiopia [GAZ:00000567] + description: 'A country situated in the Horn of Africa that has been landlocked + since the independence of its northern neighbor Eritrea in 1993. Apart from + Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to + the south, Djibouti to the northeast, and Somalia to the east. Since 1996 + Ethiopia has had a tiered government system consisting of a federal government + overseeing ethnically-based regional states, zones, districts (woredas), + and neighborhoods (kebele). It is divided into nine ethnically-based administrative + states (kililoch, singular kilil) and subdivided into sixty-eight zones + and two chartered cities (astedader akababiwoch, singular astedader akababi): + Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and + six special woredas.' meaning: GAZ:00000567 - Europa Island: - text: Europa Island + Europa Island [GAZ:00005811]: + text: Europa Island [GAZ:00005811] + description: A 28 km2 low-lying tropical island in the Mozambique Channel, + about a third of the way from southern Madagascar to southern Mozambique. meaning: GAZ:00005811 - Falkland Islands (Islas Malvinas): - text: Falkland Islands (Islas Malvinas) + Falkland Islands (Islas Malvinas) [GAZ:00001412]: + text: Falkland Islands (Islas Malvinas) [GAZ:00001412] + description: An archipelago in the South Atlantic Ocean, located 483 km from + the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), + and 940 km north of Antarctica (Elephant Island). They consist of two main + islands, East Falkland and West Falkland, together with 776 smaller islands. meaning: GAZ:00001412 - Faroe Islands: - text: Faroe Islands + Faroe Islands [GAZ:00059206]: + text: Faroe Islands [GAZ:00059206] + description: An autonomous province of the Kingdom of Denmark since 1948 located + in the Faroes. Administratively, the islands are divided into 34 municipalities + (kommunur) within which 120 or so cities and villages lie. meaning: GAZ:00059206 - Fiji: - text: Fiji + Fiji [GAZ:00006891]: + text: Fiji [GAZ:00006891] + description: An island nation in the South Pacific Ocean east of Vanuatu, + west of Tonga and south of Tuvalu. The country occupies an archipelago of + about 322 islands, of which 106 are permanently inhabited, and 522 islets. + The two major islands, Viti Levu and Vanua Levu, account for 87% of the + population. meaning: GAZ:00006891 - Finland: - text: Finland + Finland [GAZ:00002937]: + text: Finland [GAZ:00002937] + description: A Nordic country situated in the Fennoscandian region of Northern + Europe. It has borders with Sweden to the west, Russia to the east, and + Norway to the north, while Estonia lies to its south across the Gulf of + Finland. The capital city is Helsinki. Finland is divided into six administrative + provinces (laani, plural laanit). These are divided into 20 regions (maakunt), + 77 subregions (seutukunta) and then into municipalities (kunta). meaning: GAZ:00002937 - France: - text: France + France [GAZ:00003940]: + text: France [GAZ:00003940] + description: A part of the country of France that extends from the Mediterranean + Sea to the English Channel and the North Sea, and from the Rhine to the + Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, + Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas + departments. meaning: GAZ:00003940 - French Guiana: - text: French Guiana + French Guiana [GAZ:00002516]: + text: French Guiana [GAZ:00002516] + description: An overseas department (departement d'outre-mer) of France, located + on the northern coast of South America. It is bordered by Suriname, to the + E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. + French Guiana is divided into 2 departmental arrondissements, 19 cantons + and 22 communes. meaning: GAZ:00002516 - French Polynesia: - text: French Polynesia + French Polynesia [GAZ:00002918]: + text: French Polynesia [GAZ:00002918] + description: 'A French overseas collectivity in the southern Pacific Ocean. + It is made up of several groups of Polynesian islands. French Polynesia + has five administrative subdivisions (French: subdivisions administratives).' meaning: GAZ:00002918 - French Southern and Antarctic Lands: - text: French Southern and Antarctic Lands + French Southern and Antarctic Lands [GAZ:00003753]: + text: French Southern and Antarctic Lands [GAZ:00003753] + description: The French Southern and Antarctic Lands have formed a territoire + d'outre-mer (an overseas territory) of France since 1955. The territory + is divided into five districts. meaning: GAZ:00003753 - Gabon: - text: Gabon + Gabon [GAZ:00001092]: + text: Gabon [GAZ:00001092] + description: A country in west central Africa sharing borders with Equatorial + Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital + and largest city is Libreville. Gabon is divided into 9 provinces and further + divided into 37 departments. meaning: GAZ:00001092 - Gambia: - text: Gambia + Gambia [GAZ:00000907]: + text: Gambia [GAZ:00000907] + description: A country in Western Africa. It is the smallest country on the + African continental mainland and is bordered to the north, east, and south + by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing + through the centre of the country and discharging to the Atlantic Ocean + is the Gambia River. The Gambia is divided into five divisions and one city + (Banjul). The divisions are further subdivided into 37 districts. meaning: GAZ:00000907 - Gaza Strip: - text: Gaza Strip + Gaza Strip [GAZ:00009571]: + text: Gaza Strip [GAZ:00009571] + description: A Palestinian enclave on the eastern coast of the Mediterranean + Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel + on the east and north along a 51 km (32 mi) border. Gaza and the West Bank + are claimed by the de jure sovereign State of Palestine. meaning: GAZ:00009571 - Georgia: - text: Georgia + Georgia [GAZ:00004942]: + text: Georgia [GAZ:00004942] + description: 'A Eurasian country in the Caucasus located at the east coast + of the Black Sea. In the north, Georgia has a 723 km common border with + Russia, specifically with the Northern Caucasus federal district. The following + Russian republics/subdivisions: from west to east: border Georgia: Krasnodar + Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, + Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) + to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to + the south-west. It is a transcontinental country, located at the juncture + of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 + autonomous republics (avtonomiuri respublika), and 1 city (k''alak''i). + The regions are further subdivided into 69 districts (raioni).' meaning: GAZ:00004942 - Germany: - text: Germany + Germany [GAZ:00002646]: + text: Germany [GAZ:00002646] + description: A country in Central Europe. It is bordered to the north by the + North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech + Republic; to the south by Austria and Switzerland; and to the west by France, + Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, + Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) + and cities (kreisfreie Stadte). meaning: GAZ:00002646 - Ghana: - text: Ghana + Ghana [GAZ:00000908]: + text: Ghana [GAZ:00000908] + description: A country in West Africa. It borders Cote d'Ivoire to the west, + Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the + south. Ghana is a divided into 10 regions, subdivided into a total of 138 + districts. meaning: GAZ:00000908 - Gibraltar: - text: Gibraltar + Gibraltar [GAZ:00003987]: + text: Gibraltar [GAZ:00003987] + description: A British overseas territory located near the southernmost tip + of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory + shares a border with Spain to the north. meaning: GAZ:00003987 - Glorioso Islands: - text: Glorioso Islands + Glorioso Islands [GAZ:00005808]: + text: Glorioso Islands [GAZ:00005808] + description: A group of islands and rocks totalling 5 km2, in the northern + Mozambique channel, about 160 km northwest of Madagascar. meaning: GAZ:00005808 - Greece: - text: Greece + Greece [GAZ:00002945]: + text: Greece [GAZ:00002945] + description: A country in southeastern Europe, situated on the southern end + of the Balkan Peninsula. It has borders with Albania, the former Yugoslav + Republic of Macedonia and Bulgaria to the north, and Turkey to the east. + The Aegean Sea lies to the east and south of mainland Greece, while the + Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin + feature a vast number of islands. Greece consists of thirteen peripheries + subdivided into a total of fifty-one prefectures (nomoi, singular nomos). + There is also one autonomous area, Mount Athos, which borders the periphery + of Central Macedonia. meaning: GAZ:00002945 - Greenland: - text: Greenland + Greenland [GAZ:00001507]: + text: Greenland [GAZ:00001507] + description: A self-governing Danish province located between the Arctic and + Atlantic Oceans, east of the Canadian Arctic Archipelago. meaning: GAZ:00001507 - Grenada: - text: Grenada + Grenada [GAZ:02000573]: + text: Grenada [GAZ:02000573] + description: An island country in the West Indies in the Caribbean Sea at + the southern end of the Grenadines island chain. Grenada consists of the + island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, + and several small islands which lie to the north of the main island and + are a part of the Grenadines. It is located northwest of Trinidad and Tobago, + northeast of Venezuela and southwest of Saint Vincent and the Grenadines. + Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated + population of 112,523 in July 2020. meaning: GAZ:02000573 - Guadeloupe: - text: Guadeloupe + Guadeloupe [GAZ:00067142]: + text: Guadeloupe [GAZ:00067142] + description: "An archipelago and overseas department and region of France\ + \ in the Caribbean. It consists of six inhabited islands\u2014Basse-Terre,\ + \ Grande-Terre, Marie-Galante, La D\xE9sirade, and the two inhabited \xCE\ + les des Saintes\u2014as well as many uninhabited islands and outcroppings.\ + \ It is south of Antigua and Barbuda and Montserrat, and north of Dominica." meaning: GAZ:00067142 - Guam: - text: Guam + Guam [GAZ:00003706]: + text: Guam [GAZ:00003706] + description: An organized, unincorporated territory of the United States in + the Micronesia subregion of the western Pacific Ocean. It is the westernmost + point and territory of the United States (reckoned from the geographic center + of the U.S.); in Oceania, it is the largest and southernmost of the Mariana + Islands and the largest island in Micronesia. meaning: GAZ:00003706 - Guatemala: - text: Guatemala + Guatemala [GAZ:00002936]: + text: Guatemala [GAZ:00002936] + description: A country in Central America bordered by Mexico to the northwest, + the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the + northeast, and Honduras and El Salvador to the southeast. Guatemala is divided + into 22 departments (departamentos) and sub-divided into about 332 municipalities + (municipios). meaning: GAZ:00002936 - Guernsey: - text: Guernsey + Guernsey [GAZ:00001550]: + text: Guernsey [GAZ:00001550] + description: A British Crown Dependency in the English Channel off the coast + of Normandy. meaning: GAZ:00001550 - Guinea: - text: Guinea + Guinea [GAZ:00000909]: + text: Guinea [GAZ:00000909] + description: A nation in West Africa, formerly known as French Guinea. Guinea's + territory has a curved shape, with its base at the Atlantic Ocean, inland + to the east, and turning south. The base borders Guinea-Bissau and Senegal + to the north, and Mali to the north and north-east; the inland part borders + Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone + to the west of the southern tip. meaning: GAZ:00000909 - Guinea-Bissau: - text: Guinea-Bissau + Guinea-Bissau [GAZ:00000910]: + text: Guinea-Bissau [GAZ:00000910] + description: A country in western Africa, and one of the smallest nations + in continental Africa. It is bordered by Senegal to the north, and Guinea + to the south and east, with the Atlantic Ocean to its west. Formerly the + Portuguese colony of Portuguese Guinea, upon independence, the name of its + capital, Bissau, was added to the country's name in order to prevent confusion + between itself and the Republic of Guinea. meaning: GAZ:00000910 - Guyana: - text: Guyana + Guyana [GAZ:00002522]: + text: Guyana [GAZ:00002522] + description: A country in the N of South America. Guyana lies north of the + equator, in the tropics, and is located on the Atlantic Ocean. Guyana is + bordered to the east by Suriname, to the south and southwest by Brazil and + to the west by Venezuela. Guyana is divided into 10 regions. The regions + of Guyana are divided into 27 neighborhood councils. meaning: GAZ:00002522 - Haiti: - text: Haiti + Haiti [GAZ:00003953]: + text: Haiti [GAZ:00003953] + description: A country located in the Greater Antilles archipelago on the + Caribbean island of Hispaniola, which it shares with the Dominican Republic. + Haiti is divided into 10 departments. The departments are further divided + into 41 arrondissements, and 133 communes which serve as second and third + level administrative divisions. meaning: GAZ:00003953 - Heard Island and McDonald Islands: - text: Heard Island and McDonald Islands + Heard Island and McDonald Islands [GAZ:00009718]: + text: Heard Island and McDonald Islands [GAZ:00009718] + description: An Australian external territory comprising a volcanic group + of mostly barren Antarctic islands, about two-thirds of the way from Madagascar + to Antarctica. meaning: GAZ:00009718 - Honduras: - text: Honduras + Honduras [GAZ:00002894]: + text: Honduras [GAZ:00002894] + description: A republic in Central America. The country is bordered to the + west by Guatemala, to the southwest by El Salvador, to the southeast by + Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and + to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. + Honduras is divided into 18 departments. The capital city is Tegucigalpa + Central District of the department of Francisco Morazan. meaning: GAZ:00002894 - Hong Kong: - text: Hong Kong + Hong Kong [GAZ:00003203]: + text: Hong Kong [GAZ:00003203] + description: A special administrative region of the People's Republic of China + (PRC). The territory lies on the eastern side of the Pearl River Delta, + bordering Guangdong province in the north and facing the South China Sea + in the east, west and south. Hong Kong was a crown colony of the United + Kingdom from 1842 until the transfer of its sovereignty to the People's + Republic of China in 1997. meaning: GAZ:00003203 - Howland Island: - text: Howland Island + Howland Island [GAZ:00007120]: + text: Howland Island [GAZ:00007120] + description: An uninhabited coral island located just north of the equator + in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. + The island is almost half way between Hawaii and Australia and is an unincorporated, + unorganized territory of the United States, and is often included as one + of the Phoenix Islands. For statistical purposes, Howland is grouped as + one of the United States Minor Outlying Islands. meaning: GAZ:00007120 - Hungary: - text: Hungary + Hungary [GAZ:00002952]: + text: Hungary [GAZ:00002952] + description: 'A landlocked country in the Carpathian Basin of Central Europe, + bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. + Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: + megye). In addition, the capital city (fovaros), Budapest, is independent + of any county government. The counties are further subdivided into 173 subregions + (kistersegek), and Budapest is comprised of its own subregion. Since 1996, + the counties and City of Budapest have been grouped into 7 regions for statistical + and development purposes. These seven regions constitute NUTS second-level + units of Hungary.' meaning: GAZ:00002952 - Iceland: - text: Iceland + Iceland [GAZ:00000843]: + text: Iceland [GAZ:00000843] + description: A country in northern Europe, comprising the island of Iceland + and its outlying islands in the North Atlantic Ocean between the rest of + Europe and Greenland. meaning: GAZ:00000843 - India: - text: India + India [GAZ:00002839]: + text: India [GAZ:00002839] + description: A country in South Asia. Bounded by the Indian Ocean on the south, + the Arabian Sea on the west, and the Bay of Bengal on the east, India has + a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, + and Bhutan to the north-east; and Bangladesh and Burma to the east. India + is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian + Ocean. India is a federal republic of twenty-eight states and seven Union + Territories. Each state or union territory is divided into basic units of + government and administration called districts. There are nearly 600 districts + in India. The districts in turn are further divided into tehsils and eventually + into villages. meaning: GAZ:00002839 - Indonesia: - text: Indonesia + Indonesia [GAZ:00003727]: + text: Indonesia [GAZ:00003727] + description: An archipelagic state in Southeast Asia. The country shares land + borders with Papua New Guinea, East Timor and Malaysia. Other neighboring + countries include Singapore, the Philippines, Australia, and the Indian + territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, + five of which have special status. The provinces are subdivided into regencies + (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), + which are further subdivided into subdistricts (kecamatan), and again into + village groupings (either desa or kelurahan). meaning: GAZ:00003727 - Iran: - text: Iran + Iran [GAZ:00004474]: + text: Iran [GAZ:00004474] + description: A country in Central Eurasia. Iran is bounded by the Gulf of + Oman and the Persian Gulf to the south and the Caspian Sea to its north. + It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and + Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into + 30 provinces (ostan). The provinces are divided into counties (shahrestan), + and subdivided into districts (bakhsh) and sub-districts (dehestan). meaning: GAZ:00004474 - Iraq: - text: Iraq + Iraq [GAZ:00004483]: + text: Iraq [GAZ:00004483] + description: 'A country in the Middle East spanning most of the northwestern + end of the Zagros mountain range, the eastern part of the Syrian Desert + and the northern part of the Arabian Desert. It shares borders with Kuwait + and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, + Turkey to the north, and Iran to the east. It has a very narrow section + of coastline at Umm Qasr on the Persian Gulf. There are two major flowing + rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates + (or provinces) (muhafazah). The governorates are divided into qadhas (or + districts).' meaning: GAZ:00004483 - Ireland: - text: Ireland + Ireland [GAZ:00002943]: + text: Ireland [GAZ:00002943] + description: A country in north-western Europe. The modern sovereign state + occupies five-sixths of the island of Ireland, which was partitioned in + 1921. It is bordered by Northern Ireland (part of the United Kingdom) to + the north, by the Atlantic Ocean to the west and by the Irish Sea to the + east. Administration follows the 34 "county-level" counties and cities of + Ireland. Of these twenty-nine are counties, governed by county councils + while the five cities of Dublin, Cork, Limerick, Galway and Waterford have + city councils, (previously known as corporations), and are administered + separately from the counties bearing those names. The City of Kilkenny is + the only city in the republic which does not have a "city council"; it is + still a borough but not a county borough and is administered as part of + County Kilkenny. Ireland is split into eight regions for NUTS statistical + purposes. These are not related to the four traditional provinces but are + based on the administrative counties. meaning: GAZ:00002943 - Isle of Man: - text: Isle of Man + Isle of Man [GAZ:00052477]: + text: Isle of Man [GAZ:00052477] + description: A Crown dependency of the United Kingdom in the centre of the + Irish Sea. It is not part of the United Kingdom, European Union or United + Nations. meaning: GAZ:00052477 - Israel: - text: Israel + Israel [GAZ:00002476]: + text: Israel [GAZ:00002476] + description: 'A country in Western Asia located on the eastern edge of the + Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, + Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, + which are partially administrated by the Palestinian National Authority, + are also adjacent. The State of Israel is divided into six main administrative + districts, known as mehozot (singular mahoz). Districts are further divided + into fifteen sub-districts known as nafot (singular: nafa), which are themselves + partitioned into fifty natural regions.' meaning: GAZ:00002476 - Italy: - text: Italy + Italy [GAZ:00002650]: + text: Italy [GAZ:00002650] + description: A country located on the Italian Peninsula in Southern Europe, + and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. + Italy shares its northern Alpine boundary with France, Switzerland, Austria + and Slovenia. The independent states of San Marino and the Vatican City + are enclaves within the Italian Peninsula, while Campione d'Italia is an + Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, + singular regione). Five of these regions have a special autonomous status + that enables them to enact legislation on some of their local matters. It + is further divided into 109 provinces (province) and 8,101 municipalities + (comuni). meaning: GAZ:00002650 - Jamaica: - text: Jamaica + Jamaica [GAZ:00003781]: + text: Jamaica [GAZ:00003781] + description: A nation of the Greater Antilles. Jamaica is divided into 14 + parishes, which are grouped into three historic counties that have no administrative + relevance. meaning: GAZ:00003781 - Jan Mayen: - text: Jan Mayen + Jan Mayen [GAZ:00005853]: + text: Jan Mayen [GAZ:00005853] + description: 'A volcanic island that is part of the Kingdom of Norway, It + has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus + 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and + 1,000 km west of the Norwegian mainland. The island is mountainous, the + highest summit being the Beerenberg volcano in the north. The isthmus is + the location of the two largest lakes of the island, Sorlaguna (South Lagoon), + and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng + Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.' meaning: GAZ:00005853 - Japan: - text: Japan + Japan [GAZ:00002747]: + text: Japan [GAZ:00002747] + description: An island country in East Asia. Located in the Pacific Ocean, + it lies to the east of China, Korea and Russia, stretching from the Sea + of Okhotsk in the north to the East China Sea in the south. meaning: GAZ:00002747 - Jarvis Island: - text: Jarvis Island + Jarvis Island [GAZ:00007118]: + text: Jarvis Island [GAZ:00007118] + description: An uninhabited 4.5 km2 coral atoll located in the South Pacific + Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated + territory of the United States administered from Washington, DC by the United + States Fish and Wildlife Service of the United States Department of the + Interior as part of the National Wildlife Refuge system. Jarvis is one of + the southern Line Islands and for statistical purposes is also grouped as + one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. meaning: GAZ:00007118 - Jersey: - text: Jersey + Jersey [GAZ:00001551]: + text: Jersey [GAZ:00001551] + description: A British Crown Dependency[6] off the coast of Normandy, France. + As well as the island of Jersey itself, the bailiwick includes two groups + of small islands that are no longer permanently inhabited, the Minquiers + and Ecrehous, and the Pierres de Lecq. meaning: GAZ:00001551 - Johnston Atoll: - text: Johnston Atoll + Johnston Atoll [GAZ:00007114]: + text: Johnston Atoll [GAZ:00007114] + description: A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 + nm) west of Hawaii. There are four islands located on the coral reef platform, + two natural islands, Johnston Island and Sand Island, which have been expanded + by coral dredging, as well as North Island (Akau) and East Island (Hikina), + artificial islands formed from coral dredging. Johnston is an unincorporated + territory of the United States, administered by the US Fish and Wildlife + Service of the Department of the Interior as part of the United States Pacific + Island Wildlife Refuges. Sits atop Johnston Seamount. meaning: GAZ:00007114 - Jordan: - text: Jordan + Jordan [GAZ:00002473]: + text: Jordan [GAZ:00002473] + description: A country in Southwest Asia, bordered by Syria to the north, + Iraq to the north-east, Israel and the West Bank to the west, and Saudi + Arabia to the east and south. It shares the coastlines of the Dead Sea, + and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided + into 12 provinces called governorates. The Governorates are subdivided into + approximately fifty-two nahias. meaning: GAZ:00002473 - Juan de Nova Island: - text: Juan de Nova Island + Juan de Nova Island [GAZ:00005809]: + text: Juan de Nova Island [GAZ:00005809] + description: A 4.4 km2 low, flat, tropical island in the narrowest part of + the Mozambique Channel, about one-third of the way between Madagascar and + Mozambique. meaning: GAZ:00005809 - Kazakhstan: - text: Kazakhstan + Kazakhstan [GAZ:00004999]: + text: Kazakhstan [GAZ:00004999] + description: A country in Central Asia and Europe. It is bordered by Russia, + Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders + on a significant part of the Caspian Sea. Kazakhstan is divided into 14 + provinces and two municipal districts. The provinces of Kazakhstan are divided + into raions. meaning: GAZ:00004999 - Kenya: - text: Kenya + Kenya [GAZ:00001101]: + text: Kenya [GAZ:00001101] + description: A country in Eastern Africa. It is bordered by Ethiopia to the + north, Somalia to the east, Tanzania to the south, Uganda to the west, and + Sudan to the northwest, with the Indian Ocean running along the southeast + border. Kenya comprises eight provinces each headed by a Provincial Commissioner + (centrally appointed by the president). The provinces (mkoa singular mikoa + plural in Swahili) are subdivided into districts (wilaya). There were 69 + districts as of 1999 census. Districts are then subdivided into 497 divisions + (taarafa). The divisions are then subdivided into 2,427 locations (kata) + and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the + status of a full administrative province. meaning: GAZ:00001101 - Kerguelen Archipelago: - text: Kerguelen Archipelago + Kerguelen Archipelago [GAZ:00005682]: + text: Kerguelen Archipelago [GAZ:00005682] + description: A group of islands in the southern Indian Ocean. It is a territory + of France. They are composed primarily of Tertiary flood basalts and a complex + of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano + at the southern end was active during the late Pleistocene. The Rallier + du Baty Peninsula on the SW tip of the island contains two youthful subglacial + eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active + fumarole field is related to a series of Holocene trachytic lava flows and + lahars that extend beyond the icecap. meaning: GAZ:00005682 - Kingman Reef: - text: Kingman Reef + Kingman Reef [GAZ:00007116]: + text: Kingman Reef [GAZ:00007116] + description: A largely submerged, uninhabited tropical atoll located in the + North Pacific Ocean, roughly half way between Hawaiian Islands and American + Samoa. It is the northernmost of the Northern Line Islands and lies 65 km + NNW of Palmyra Atoll, the next closest island, and has the status of an + unincorporated territory of the United States, administered from Washington, + DC by the US Navy. Sits atop Kingman Reef Seamount. meaning: GAZ:00007116 - Kiribati: - text: Kiribati + Kiribati [GAZ:00006894]: + text: Kiribati [GAZ:00006894] + description: 'An island nation located in the central tropical Pacific Ocean. + It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 + km2 straddling the equator and bordering the International Date Line to + the east. It is divided into three island groups which have no administrative + function, including a group which unites the Line Islands and the Phoenix + Islands (ministry at London, Christmas). Each inhabited island has its own + council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two + councils on Tabiteuea).' meaning: GAZ:00006894 - Kosovo: - text: Kosovo + Kosovo [GAZ:00011337]: + text: Kosovo [GAZ:00011337] + description: A country on the Balkan Peninsula. Kosovo borders Central Serbia + to the north and east, Montenegro to the northwest, Albania to the west + and the Republic of Macedonia to the south. Kosovo is divided into 7 districts + (Rreth) and 30 municipalities. Serbia does not recognise the unilateral + secession of Kosovo[8] and considers it a United Nations-governed entity + within its sovereign territory, the Autonomous Province of Kosovo and Metohija. meaning: GAZ:00011337 - Kuwait: - text: Kuwait + Kuwait [GAZ:00005285]: + text: Kuwait [GAZ:00005285] + description: A sovereign emirate on the coast of the Persian Gulf, enclosed + by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided + into six governorates (muhafazat, singular muhafadhah). meaning: GAZ:00005285 - Kyrgyzstan: - text: Kyrgyzstan + Kyrgyzstan [GAZ:00006893]: + text: Kyrgyzstan [GAZ:00006893] + description: A country in Central Asia. Landlocked and mountainous, it is + bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan + to the southwest and China to the east. Kyrgyzstan is divided into seven + provinces (oblast. The capital, Bishkek, and the second large city Osh are + administratively the independent cities (shaar) with a status equal to a + province. Each province comprises a number of districts (raions). meaning: GAZ:00006893 - Laos: - text: Laos + Laos [GAZ:00006889]: + text: Laos [GAZ:00006889] + description: A landlocked country in southeast Asia, bordered by Burma (Myanmar) + and China to the northwest, Vietnam to the east, Cambodia to the south, + and Thailand to the west. Laos is divided into sixteen provinces (qwang) + and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided + into districts (muang). meaning: GAZ:00006889 - Latvia: - text: Latvia + Latvia [GAZ:00002958]: + text: Latvia [GAZ:00002958] + description: A country in Northern Europe. Latvia shares land borders with + Estonia to the north and Lithuania to the south, and both Russia and Belarus + to the east. It is separated from Sweden in the west by the Baltic Sea. + The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). + There are also seven cities (lielpilsetas) that have a separate status. + Latvia is also historically, culturally and constitutionally divided in + four or more distinct regions. meaning: GAZ:00002958 - Lebanon: - text: Lebanon + Lebanon [GAZ:00002478]: + text: Lebanon [GAZ:00002478] + description: 'A small, mostly mountainous country in Western Asia, on the + eastern shore of the Mediterranean Sea. It is bordered by Syria to the north + and east, and Israel to the south. Lebanon is divided into six governorates + (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, + singular: qadaa).' meaning: GAZ:00002478 - Lesotho: - text: Lesotho + Lesotho [GAZ:00001098]: + text: Lesotho [GAZ:00001098] + description: A land-locked country, entirely surrounded by the Republic of + South Africa. Lesotho is divided into ten districts; these are further subdivided + into 80 constituencies, which consists of 129 local community councils. meaning: GAZ:00001098 - Liberia: - text: Liberia + Liberia [GAZ:00000911]: + text: Liberia [GAZ:00000911] + description: A country on the west coast of Africa, bordered by Sierra Leone, + Guinea, Cote d'Ivoire, and the Atlantic Ocean. meaning: GAZ:00000911 - Libya: - text: Libya + Libya [GAZ:00000566]: + text: Libya [GAZ:00000566] + description: A country in North Africa. Bordering the Mediterranean Sea to + the north, Libya lies between Egypt to the east, Sudan to the southeast, + Chad and Niger to the south, and Algeria and Tunisia to the west. There + are thirty-four municipalities of Libya, known by the Arabic term sha'biyat + (singular sha'biyah). These came recently (in the 1990s to replaced old + Baladiyat systam. The Baladiyat system in turn was introduced to replace + the system of muhafazah (governorates or provinces) that existed from the + 1960s to the 1970s. meaning: GAZ:00000566 - Liechtenstein: - text: Liechtenstein + Liechtenstein [GAZ:00003858]: + text: Liechtenstein [GAZ:00003858] + description: A tiny, doubly landlocked alpine country in Western Europe, bordered + by Switzerland to its west and by Austria to its east. The principality + of Liechtenstein is divided into 11 municipalities called Gemeinden (singular + Gemeinde). The Gemeinden mostly consist only of a single town. Five of them + fall within the electoral district Unterland (the lower county), and the + remainder within Oberland (the upper county). meaning: GAZ:00003858 - Line Islands: - text: Line Islands + Line Islands [GAZ:00007144]: + text: Line Islands [GAZ:00007144] + description: A group of eleven atolls and low coral islands in the central + Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, + while three are United States territories that are grouped with the United + States Minor Outlying Islands. meaning: GAZ:00007144 - Lithuania: - text: Lithuania + Lithuania [GAZ:00002960]: + text: Lithuania [GAZ:00002960] + description: 'A country located along the south-eastern shore of the Baltic + Sea, sharing borders with Latvia to the north, Belarus to the southeast, + Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. + Lithuania has a three-tier administrative division: the country is divided + into 10 counties (singular apskritis, plural, apskritys) that are further + subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) + which consist of over 500 elderates (singular seniunija, plural seniunijos).' meaning: GAZ:00002960 - Luxembourg: - text: Luxembourg + Luxembourg [GAZ:00002947]: + text: Luxembourg [GAZ:00002947] + description: A small landlocked country in western Europe, bordered by Belgium, + France, and Germany. Luxembourg is divided into 3 districts, which are further + divided into 12 cantons and then 116 communes. Twelve of the communes have + city status, of which the city of Luxembourg is the largest. meaning: GAZ:00002947 - Macau: - text: Macau + Macau [GAZ:00003202]: + text: Macau [GAZ:00003202] + description: One of the two special administrative regions of the People's + Republic of China, the other being Hong Kong. Macau lies on the western + side of the Pearl River Delta, bordering Guangdong province in the north + and facing the South China Sea in the east and south. Macau is situated + 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the + Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula + is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang + (West River) on the west. It borders the Zhuhai Special Economic Zone in + mainland China. meaning: GAZ:00003202 - Madagascar: - text: Madagascar + Madagascar [GAZ:00001108]: + text: Madagascar [GAZ:00001108] + description: An island nation in the Indian Ocean off the southeastern coast + of Africa. The main island, also called Madagascar, is the fourth largest + island in the world, and is home to 5% of the world's plant and animal species, + of which more than 80% are endemic to Madagascar. Most notable are the lemur + infraorder of primates, the carnivorous fossa, three endemic bird families + and six endemic baobab species. Madagascar is divided into six autonomous + provinces (faritany mizakatena), and 22 regions. The regions are further + subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. meaning: GAZ:00001108 - Malawi: - text: Malawi + Malawi [GAZ:00001105]: + text: Malawi [GAZ:00001105] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. meaning: GAZ:00001105 - Malaysia: - text: Malaysia + Malaysia [GAZ:00003902]: + text: Malaysia [GAZ:00003902] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. meaning: GAZ:00003902 - Maldives: - text: Maldives + Maldives [GAZ:00006924]: + text: Maldives [GAZ:00006924] + description: An archipelago which consists of approximately 1,196 coral islands + grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. meaning: GAZ:00006924 - Mali: - text: Mali + Mali [GAZ:00000584]: + text: Mali [GAZ:00000584] + description: A landlocked country in northern Africa. It borders Algeria on + the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the + south, Guinea on the south-west, and Senegal and Mauritania on the west. + Mali is divided into 8 regions (regions) and 1 district, and subdivided + into 49 cercles, totalling 288 arrondissements. meaning: GAZ:00000584 - Malta: - text: Malta + Malta [GAZ:00004017]: + text: Malta [GAZ:00004017] + description: A Southern European country and consists of an archipelago situated + centrally in the Mediterranean. meaning: GAZ:00004017 - Marshall Islands: - text: Marshall Islands + Marshall Islands [GAZ:00007161]: + text: Marshall Islands [GAZ:00007161] + description: 'An archipelago that consists of twenty-nine atolls and five + isolated islands. The most important atolls and islands form two groups: + the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). + Two-thirds of the nation''s population lives on Majuro (which is also the + capital) and Ebeye. The outer islands are sparsely populated.' meaning: GAZ:00007161 - Martinique: - text: Martinique + Martinique [GAZ:00067143]: + text: Martinique [GAZ:00067143] + description: An island and an overseas department/region and single territorial + collectivity of France. meaning: GAZ:00067143 - Mauritania: - text: Mauritania + Mauritania [GAZ:00000583]: + text: Mauritania [GAZ:00000583] + description: A country in North-West Africa. It is bordered by the Atlantic + Ocean on the west, by Senegal on the southwest, by Mali on the east and + southeast, by Algeria on the northeast, and by Western Sahara on the northwest + (most of which is occupied by Morocco). The capital and largest city is + Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 + regions (regions) and one capital district, which in turn are subdivided + into 44 departments (departements). meaning: GAZ:00000583 - Mauritius: - text: Mauritius + Mauritius [GAZ:00003745]: + text: Mauritius [GAZ:00003745] + description: An island nation off the coast of the African continent in the + southwest Indian Ocean, about 900 km east of Madagascar. In addition to + the island of Mauritius, the republic includes the islands of St. Brandon, + Rodrigues and the Agalega Islands. meaning: GAZ:00003745 - Mayotte: - text: Mayotte + Mayotte [GAZ:00003943]: + text: Mayotte [GAZ:00003943] + description: An overseas collectivity of France consisting of a main island, + Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and + several islets around these two. meaning: GAZ:00003943 - Mexico: - text: Mexico + Mexico [GAZ:00002852]: + text: Mexico [GAZ:00002852] + description: A federal constitutional republic in North America. It is bounded + on the north by the United States; on the south and west by the North Pacific + Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and + on the east by the Gulf of Mexico. The United Mexican States comprise a + federation of thirty-one states and a federal district, the capital Mexico + City. meaning: GAZ:00002852 - Micronesia: - text: Micronesia + Micronesia [GAZ:00005862]: + text: Micronesia [GAZ:00005862] + description: A subregion of Oceania, comprising hundreds of small islands + in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua + New Guinea and Melanesia to the west and southwest, and Polynesia to the + east. meaning: GAZ:00005862 - Midway Islands: - text: Midway Islands + Midway Islands [GAZ:00007112]: + text: Midway Islands [GAZ:00007112] + description: A 6.2 km2 atoll located in the North Pacific Ocean (near the + northwestern end of the Hawaiian archipelago). It is an unincorporated territory + of the United States, designated an insular area under the authority of + the US Department of the Interior. meaning: GAZ:00007112 - Moldova: - text: Moldova + Moldova [GAZ:00003897]: + text: Moldova [GAZ:00003897] + description: A landlocked country in Eastern Europe, located between Romania + to the west and Ukraine to the north, east and south. Moldova is divided + into thirty-two districts (raioane, singular raion); three municipalities + (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). + The cities of Comrat and Tiraspol also have municipality status, however + not as first-tier subdivisions of Moldova, but as parts of the regions of + Gagauzia and Transnistria, respectively. The status of Transnistria is however + under dispute. Although it is de jure part of Moldova and is recognized + as such by the international community, Transnistria is not de facto under + the control of the central government of Moldova. It is administered by + an unrecognized breakaway authority under the name Pridnestrovian Moldovan + Republic. meaning: GAZ:00003897 - Monaco: - text: Monaco + Monaco [GAZ:00003857]: + text: Monaco [GAZ:00003857] + description: A small country that is completely bordered by France to the + north, west, and south; to the east it is bordered by the Mediterranean + Sea. It consists of a single municipality (commune) currently divided into + 4 quartiers and 10 wards. meaning: GAZ:00003857 - Mongolia: - text: Mongolia + Mongolia [GAZ:00008744]: + text: Mongolia [GAZ:00008744] + description: A country in East-Central Asia. The landlocked country borders + Russia to the north and China to the south. The capital and largest city + is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are + in turn divided into 315 sums (districts). The capital Ulan Bator is administrated + separately as a khot (municipality) with provincial status. meaning: GAZ:00008744 - Montenegro: - text: Montenegro + Montenegro [GAZ:00006898]: + text: Montenegro [GAZ:00006898] + description: A country located in Southeastern Europe. It has a coast on the + Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina + to the northwest, Serbia and its partially recognized breakaway southern + province of Kosovo to the northeast and Albania to the southeast. Its capital + and largest city is Podgorica. Montenegro is divided into twenty-one municipalities + (opstina), and two urban municipalities, subdivisions of Podgorica municipality. meaning: GAZ:00006898 - Montserrat: - text: Montserrat + Montserrat [GAZ:00003988]: + text: Montserrat [GAZ:00003988] + description: A British overseas territory located in the Leeward Islands. + Montserrat is divided into three parishes. meaning: GAZ:00003988 - Morocco: - text: Morocco + Morocco [GAZ:00000565]: + text: Morocco [GAZ:00000565] + description: A country in North Africa. It has a coast on the Atlantic Ocean + that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco + has international borders with Algeria to the east, Spain to the north (a + water border through the Strait and land borders with two small Spanish + autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco + is divided into 16 regions, and subdivided into 62 prefectures and provinces. + Because of the conflict over Western Sahara, the status of both regions + of "Saguia el-Hamra" and "Rio de Oro" is disputed. meaning: GAZ:00000565 - Mozambique: - text: Mozambique + Mozambique [GAZ:00001100]: + text: Mozambique [GAZ:00001100] + description: A country in southeastern Africa bordered by the Indian Ocean + to the east, Tanzania to the north, Malawi and Zambia to the northwest, + Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique + is divided into ten provinces (provincias) and one capital city (cidade + capital) with provincial status. The provinces are subdivided into 129 districts + (distritos). Districts are further divided in "Postos Administrativos" (Administrative + Posts) and these in Localidades (Localities) the lowest geographical level + of central state administration. meaning: GAZ:00001100 - Myanmar: - text: Myanmar + Myanmar [GAZ:00006899]: + text: Myanmar [GAZ:00006899] + description: A country in SE Asia that is bordered by China on the north, + Laos on the east, Thailand on the southeast, Bangladesh on the west, and + India on the northwest, with the Bay of Bengal to the southwest. Myanmar + is divided into seven states and seven divisions. The administrative divisions + are further subdivided into districts, which are further subdivided into + townships, wards, and villages. meaning: GAZ:00006899 - Namibia: - text: Namibia + Namibia [GAZ:00001096]: + text: Namibia [GAZ:00001096] + description: A country in southern Africa on the Atlantic coast. It shares + borders with Angola and Zambia to the north, Botswana to the east, and South + Africa to the south. Namibia is divided into 13 regions and subdivided into + 102 constituencies. meaning: GAZ:00001096 - Nauru: - text: Nauru + Nauru [GAZ:00006900]: + text: Nauru [GAZ:00006900] + description: An island nation in the Micronesian South Pacific. The nearest + neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. + Nauru is divided into fourteen administrative districts which are grouped + into eight electoral constituencies. meaning: GAZ:00006900 - Navassa Island: - text: Navassa Island + Navassa Island [GAZ:00007119]: + text: Navassa Island [GAZ:00007119] + description: A small, uninhabited island in the Caribbean Sea, and is an unorganized + unincorporated territory of the United States, which administers it through + the US Fish and Wildlife Service. The island is also claimed by Haiti. meaning: GAZ:00007119 - Nepal: - text: Nepal + Nepal [GAZ:00004399]: + text: Nepal [GAZ:00004399] + description: A landlocked nation in South Asia. It is bordered by the Tibet + Autonomous Region of the People's Republic of China to the northeast and + India to the south and west; it is separated from Bhutan by the Indian State + of Sikkim and from Bangladesh by a small strip of the Indian State of West + Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs + across Nepal's north and western parts, and eight of the world's ten highest + mountains, including the highest, Mount Everest are situated within its + territory. Nepal is divided into 14 zones and 75 districts, grouped into + 5 development regions. meaning: GAZ:00004399 - Netherlands: - text: Netherlands + Netherlands [GAZ:00002946]: + text: Netherlands [GAZ:00002946] + description: The European part of the Kingdom of the Netherlands. It is bordered + by the North Sea to the north and west, Belgium to the south, and Germany + to the east. The Netherlands is divided into twelve administrative regions, + called provinces. All provinces of the Netherlands are divided into municipalities + (gemeenten), together 443 (2007). meaning: GAZ:00002946 - New Caledonia: - text: New Caledonia + New Caledonia [GAZ:00005206]: + text: New Caledonia [GAZ:00005206] + description: A "sui generis collectivity" (in practice an overseas territory) + of France, made up of a main island (Grande Terre), the Loyalty Islands, + and several smaller islands. It is located in the region of Melanesia in + the southwest Pacific. Administratively, the archipelago is divided into + three provinces, and then into 33 communes. meaning: GAZ:00005206 - New Zealand: - text: New Zealand + New Zealand [GAZ:00000469]: + text: New Zealand [GAZ:00000469] + description: A nation in the south-western Pacific Ocean comprising two large + islands (the North Island and the South Island) and numerous smaller islands, + most notably Stewart Island/Rakiura and the Chatham Islands. meaning: GAZ:00000469 - Nicaragua: - text: Nicaragua + Nicaragua [GAZ:00002978]: + text: Nicaragua [GAZ:00002978] + description: A republic in Central America. It is also the least densely populated + with a demographic similar in size to its smaller neighbors. The country + is bordered by Honduras to the north and by Costa Rica to the south. The + Pacific Ocean lies to the west of the country, while the Caribbean Sea lies + to the east. For administrative purposes it is divided into 15 departments + (departamentos) and two self-governing regions (autonomous communities) + based on the Spanish model. The departments are then subdivided into 153 + municipios (municipalities). The two autonomous regions are Region Autonoma + del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred + to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 + they formed the single department of Zelaya. meaning: GAZ:00002978 - Niger: - text: Niger + Niger [GAZ:00000585]: + text: Niger [GAZ:00000585] + description: A landlocked country in Western Africa, named after the Niger + River. It borders Nigeria and Benin to the south, Burkina Faso and Mali + to the west, Algeria and Libya to the north and Chad to the east. The capital + city is Niamey. Niger is divided into 7 departments and one capital district. + The departments are subdivided into 36 arrondissements and further subdivided + into 129 communes. meaning: GAZ:00000585 - Nigeria: - text: Nigeria + Nigeria [GAZ:00000912]: + text: Nigeria [GAZ:00000912] + description: A federal constitutional republic comprising thirty-six states + and one Federal Capital Territory. The country is located in West Africa + and shares land borders with the Republic of Benin in the west, Chad and + Cameroon in the east, and Niger in the north. Its coast lies on the Gulf + of Guinea, part of the Atlantic Ocean, in the south. The capital city is + Abuja. Nigeria is divided into thirty-six states and one Federal Capital + Territory, which are further sub-divided into 774 Local Government Areas + (LGAs). meaning: GAZ:00000912 - Niue: - text: Niue + Niue [GAZ:00006902]: + text: Niue [GAZ:00006902] + description: An island nation located in the South Pacific Ocean. Although + self-governing, Niue is in free association with New Zealand, meaning that + the Sovereign in Right of New Zealand is also Niue's head of state. meaning: GAZ:00006902 - Norfolk Island: - text: Norfolk Island + Norfolk Island [GAZ:00005908]: + text: Norfolk Island [GAZ:00005908] + description: A Territory of Australia that includes Norfolk Island and neighboring + islands. meaning: GAZ:00005908 - North Korea: - text: North Korea + North Korea [GAZ:00002801]: + text: North Korea [GAZ:00002801] + description: A state in East Asia in the northern half of the Korean Peninsula, + with its capital in the city of Pyongyang. To the south and separated by + the Korean Demilitarized Zone is South Korea, with which it formed one nation + until division following World War II. At its northern Amnok River border + are China and, separated by the Tumen River in the extreme north-east, Russia. meaning: GAZ:00002801 - North Macedonia: - text: North Macedonia + North Macedonia [GAZ:00006895]: + text: North Macedonia [GAZ:00006895] + description: A landlocked country on the Balkan peninsula in southeastern + Europe. It is bordered by Serbia and Kosovo to the north, Albania to the + west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic + of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), + 10 of which comprise Greater Skopje. This is reduced from the previous 123 + municipalities established in 1996-09. Prior to this, local government was + organised into 34 administrative districts. meaning: GAZ:00006895 - North Sea: - text: North Sea + North Sea [GAZ:00002284]: + text: North Sea [GAZ:00002284] + description: A sea situated between the eastern coasts of the British Isles + and the western coast of Europe. meaning: GAZ:00002284 - Northern Mariana Islands: - text: Northern Mariana Islands + Northern Mariana Islands [GAZ:00003958]: + text: Northern Mariana Islands [GAZ:00003958] + description: A group of 15 islands about three-quarters of the way from Hawaii + to the Philippines. meaning: GAZ:00003958 - Norway: - text: Norway + Norway [GAZ:00002699]: + text: Norway [GAZ:00002699] + description: A country and constitutional monarchy in Northern Europe that + occupies the western portion of the Scandinavian Peninsula. It is bordered + by Sweden, Finland, and Russia. The Kingdom of Norway also includes the + Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty + over Svalbard is based upon the Svalbard Treaty, but that treaty does not + apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter + I Island and Queen Maud Land in Antarctica are external dependencies, but + those three entities do not form part of the kingdom. meaning: GAZ:00002699 - Oman: - text: Oman + Oman [GAZ:00005283]: + text: Oman [GAZ:00005283] + description: A country in southwest Asia, on the southeast coast of the Arabian + Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia + on the west, and Yemen on the southwest. The coast is formed by the Arabian + Sea on the south and east, and the Gulf of Oman on the northeast. The country + also contains Madha, an exclave enclosed by the United Arab Emirates, and + Musandam, an exclave also separated by Emirati territory. Oman is divided + into four governorates (muhafazah) and five regions (mintaqat). The regions + are subdivided into provinces (wilayat). meaning: GAZ:00005283 - Pakistan: - text: Pakistan + Pakistan [GAZ:00005246]: + text: Pakistan [GAZ:00005246] + description: A country in Middle East which lies on the Iranian Plateau and + some parts of South Asia. It is located in the region where South Asia converges + with Central Asia and the Middle East. It has a 1,046 km coastline along + the Arabian Sea in the south, and is bordered by Afghanistan and Iran in + the west, India in the east and China in the far northeast. Pakistan is + subdivided into four provinces and two territories. In addition, the portion + of Kashmir that is administered by the Pakistani government is divided into + two separate administrative units. The provinces are divided into a total + of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly + equivalent to counties). Tehsils may contain villages or municipalities. + There are over five thousand local governments in Pakistan. meaning: GAZ:00005246 - Palau: - text: Palau + Palau [GAZ:00006905]: + text: Palau [GAZ:00006905] + description: A nation that consists of eight principal islands and more than + 250 smaller ones lying roughly 500 miles southeast of the Philippines. meaning: GAZ:00006905 - Panama: - text: Panama + Panama [GAZ:00002892]: + text: Panama [GAZ:00002892] + description: The southernmost country of Central America. Situated on an isthmus, + some categorize it as a transcontinental nation connecting the north and + south part of America. It borders Costa Rica to the north-west, Colombia + to the south-east, the Caribbean Sea to the north and the Pacific Ocean + to the south. Panama's major divisions are nine provinces and five indigenous + territories (comarcas indigenas). The provincial borders have not changed + since they were determined at independence in 1903. The provinces are divided + into districts, which in turn are subdivided into sections called corregimientos. + Configurations of the corregimientos are changed periodically to accommodate + population changes as revealed in the census reports. meaning: GAZ:00002892 - Papua New Guinea: - text: Papua New Guinea + Papua New Guinea [GAZ:00003922]: + text: Papua New Guinea [GAZ:00003922] + description: A country in Oceania that comprises the eastern half of the island + of New Guinea and its offshore islands in Melanesia (a region of the southwestern + Pacific Ocean north of Australia). meaning: GAZ:00003922 - Paracel Islands: - text: Paracel Islands + Paracel Islands [GAZ:00010832]: + text: Paracel Islands [GAZ:00010832] + description: A group of small islands and reefs in the South China Sea, about + one-third of the way from Vietnam to the Philippines. meaning: GAZ:00010832 - Paraguay: - text: Paraguay + Paraguay [GAZ:00002933]: + text: Paraguay [GAZ:00002933] + description: A landlocked country in South America. It lies on both banks + of the Paraguay River, bordering Argentina to the south and southwest, Brazil + to the east and northeast, and Bolivia to the northwest, and is located + in the very heart of South America. Paraguay consists of seventeen departments + and one capital district (distrito capital). Each department is divided + into districts. meaning: GAZ:00002933 - Peru: - text: Peru + Peru [GAZ:00002932]: + text: Peru [GAZ:00002932] + description: A country in western South America. It is bordered on the north + by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, + on the south by Chile, and on the west by the Pacific Ocean. Peru is divided + into 25 regions and the province of Lima. These regions are subdivided into + provinces, which are composed of districts (provincias and distritos). There + are 195 provinces and 1833 districts in Peru. The Lima Province, located + in the central coast of the country, is unique in that it doesn't belong + to any of the twenty-five regions. The city of Lima, which is the nation's + capital, is located in this province. Callao is its own region, even though + it only contains one province, the Constitutional Province of Callao. meaning: GAZ:00002932 - Philippines: - text: Philippines + Philippines [GAZ:00004525]: + text: Philippines [GAZ:00004525] + description: 'An archipelagic nation located in Southeast Asia. The Philippine + archipelago comprises 7,107 islands in the western Pacific Ocean, bordering + countries such as Indonesia, Malaysia, Palau and the Republic of China, + although it is the only Southeast Asian country to share no land borders + with its neighbors. The Philippines is divided into three island groups: + Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, + 136 cities, 1,494 municipalities and 41,995 barangays.' meaning: GAZ:00004525 - Pitcairn Islands: - text: Pitcairn Islands + Pitcairn Islands [GAZ:00005867]: + text: Pitcairn Islands [GAZ:00005867] + description: A group of four islands in the southern Pacific Ocean. The Pitcairn + Islands form the southeasternmost extension of the geological archipelago + of the Tuamotus of French Polynesia. meaning: GAZ:00005867 - Poland: - text: Poland + Poland [GAZ:00002939]: + text: Poland [GAZ:00002939] + description: A country in Central Europe. Poland is bordered by Germany to + the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus + and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a + Russian exclave, to the north. The administrative division of Poland since + 1999 has been based on three levels of subdivision. The territory of Poland + is divided into voivodeships (provinces); these are further divided into + powiats (counties), and these in turn are divided into gminas (communes + or municipalities). Major cities normally have the status of both gmina + and powiat. Poland currently has 16 voivodeships, 379 powiats (including + 65 cities with powiat status), and 2,478 gminas. meaning: GAZ:00002939 - Portugal: - text: Portugal + Portugal [GAZ:00004126]: + text: Portugal [GAZ:00004126] + description: That part of the Portugese Republic that occupies the W part + of the Iberian Peninsula, and immediately adjacent islands. meaning: GAZ:00004126 - Puerto Rico: - text: Puerto Rico + Puerto Rico [GAZ:00006935]: + text: Puerto Rico [GAZ:00006935] + description: A semi-autonomous territory composed of an archipelago in the + northeastern Caribbean, east of the Dominican Republic and west of the Virgin + Islands, approximately 2,000 km off the coast of Florida (the nearest of + the mainland United States). meaning: GAZ:00006935 - Qatar: - text: Qatar + Qatar [GAZ:00005286]: + text: Qatar [GAZ:00005286] + description: 'An Arab emirate in Southwest Asia, occupying the small Qatar + Peninsula on the northeasterly coast of the larger Arabian Peninsula. It + is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds + the state. Qatar is divided into ten municipalities (Arabic: baladiyah), + which are further divided into zones (districts).' meaning: GAZ:00005286 - Republic of the Congo: - text: Republic of the Congo + Republic of the Congo [GAZ:00001088]: + text: Republic of the Congo [GAZ:00001088] + description: A country in Central Africa. It is bordered by Gabon, Cameroon, + the Central African Republic, the Democratic Republic of the Congo, the + Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic + of the Congo is divided into 10 regions (regions) and one commune, the capital + Brazzaville. The regions are subdivided into forty-six districts. meaning: GAZ:00001088 - Reunion: - text: Reunion + Reunion [GAZ:00003945]: + text: Reunion [GAZ:00003945] + description: An island, located in the Indian Ocean east of Madagascar, about + 200 km south west of Mauritius, the nearest island. meaning: GAZ:00003945 - Romania: - text: Romania + Romania [GAZ:00002951]: + text: Romania [GAZ:00002951] + description: A country in Southeastern Europe. It shares a border with Hungary + and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, + and Bulgaria to the south. Romania has a stretch of sea coast along the + Black Sea. It is located roughly in the lower basin of the Danube and almost + all of the Danube Delta is located within its territory. Romania is divided + into forty-one counties (judete), as well as the municipality of Bucharest + (Bucuresti) - which is its own administrative unit. The country is further + subdivided into 319 cities and 2686 communes (rural localities). meaning: GAZ:00002951 - Ross Sea: - text: Ross Sea + Ross Sea [GAZ:00023304]: + text: Ross Sea [GAZ:00023304] + description: A large embayment of the Southern Ocean, extending deeply into + Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck + on the east, at 158degW. meaning: GAZ:00023304 - Russia: - text: Russia + Russia [GAZ:00002721]: + text: Russia [GAZ:00002721] + description: 'A transcontinental country extending over much of northern Eurasia. + Russia shares land borders with the following countries (counter-clockwise + from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania + (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, + Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation + comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais + (territories), 4 autonomous okrugs (autonomous districts), one autonomous + oblast, and two federal cities. The federal subjects are grouped into seven + federal districts. These subjects are divided into districts (raions), cities/towns + and urban-type settlements, and, at level 4, selsovets (rural councils), + towns and urban-type settlements under the jurisdiction of the district + and city districts.' meaning: GAZ:00002721 - Rwanda: - text: Rwanda + Rwanda [GAZ:00001087]: + text: Rwanda [GAZ:00001087] + description: A small landlocked country in the Great Lakes region of east-central + Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo + and Tanzania. Rwanda is divided into five provinces (intara) and subdivided + into thirty districts (akarere). The districts are divided into sectors + (imirenge). meaning: GAZ:00001087 - Saint Helena: - text: Saint Helena + Saint Helena [GAZ:00000849]: + text: Saint Helena [GAZ:00000849] + description: An island of volcanic origin and a British overseas territory + in the South Atlantic Ocean. meaning: GAZ:00000849 - Saint Kitts and Nevis: - text: Saint Kitts and Nevis + Saint Kitts and Nevis [GAZ:00006906]: + text: Saint Kitts and Nevis [GAZ:00006906] + description: 'A federal two-island nation in the West Indies. Located in the + Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward + Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, + Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast + are Antigua and Barbuda, and to the southeast is the small uninhabited island + of Redonda, and the island of Montserrat. The federation of Saint Kitts + and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts + and five on Nevis.' meaning: GAZ:00006906 - Saint Lucia: - text: Saint Lucia + Saint Lucia [GAZ:00006909]: + text: Saint Lucia [GAZ:00006909] + description: An island nation in the eastern Caribbean Sea on the boundary + with the Atlantic Ocean. meaning: GAZ:00006909 - Saint Pierre and Miquelon: - text: Saint Pierre and Miquelon + Saint Pierre and Miquelon [GAZ:00003942]: + text: Saint Pierre and Miquelon [GAZ:00003942] + description: An Overseas Collectivity of France located in a group of small + islands in the North Atlantic Ocean, the main ones being Saint Pierre and + Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and + Miquelon became an overseas department in 1976, but its status changed to + that of an Overseas collectivity in 1985. meaning: GAZ:00003942 - Saint Martin: - text: Saint Martin + Saint Martin [GAZ:00005841]: + text: Saint Martin [GAZ:00005841] + description: An overseas collectivity of France that came into being on 2007-02-22, + encompassing the northern parts of the island of Saint Martin and neighboring + islets. The southern part of the island, Sint Maarten, is part of the Netherlands + Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. meaning: GAZ:00005841 - Saint Vincent and the Grenadines: - text: Saint Vincent and the Grenadines + Saint Vincent and the Grenadines [GAZ:02000565]: + text: Saint Vincent and the Grenadines [GAZ:02000565] + description: An island nation in the Lesser Antilles chain of the Caribbean + Sea. meaning: GAZ:02000565 - Samoa: - text: Samoa + Samoa [GAZ:00006910]: + text: Samoa [GAZ:00006910] + description: A country governing the western part of the Samoan Islands archipelago + in the South Pacific Ocean. Samoa is made up of eleven itumalo (political + districts). meaning: GAZ:00006910 - San Marino: - text: San Marino + San Marino [GAZ:00003102]: + text: San Marino [GAZ:00003102] + description: A country in the Apennine Mountains. It is a landlocked enclave, + completely surrounded by Italy. San Marino is an enclave in Italy, on the + border between the regioni of Emilia Romagna and Marche. Its topography + is dominated by the Apennines mountain range. San Marino is divided into + nine municipalities, known locally as Castelli (singular castello). meaning: GAZ:00003102 - Sao Tome and Principe: - text: Sao Tome and Principe + Sao Tome and Principe [GAZ:00006927]: + text: Sao Tome and Principe [GAZ:00006927] + description: 'An island nation in the Gulf of Guinea, off the western equatorial + coast of Africa. It consists of two islands: Sao Tome and Principe, located + about 140 km apart and about 250 and 225 km respectively, off of the northwestern + coast of Gabon. Both islands are part of an extinct volcanic mountain range. + Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The + provinces are further divided into seven districts, six on Sao Tome and + one on Principe (with Principe having self-government since 1995-04-29).' meaning: GAZ:00006927 - Saudi Arabia: - text: Saudi Arabia + Saudi Arabia [GAZ:00005279]: + text: Saudi Arabia [GAZ:00005279] + description: A country on the Arabian Peninsula. It is bordered by Jordan + on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, + and the United Arab Emirates on the east, Oman on the southeast, and Yemen + on the south. The Persian Gulf lies to the northeast and the Red Sea to + its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; + singular mintaqah). Each is then divided into Governorates. meaning: GAZ:00005279 - Senegal: - text: Senegal + Senegal [GAZ:00000913]: + text: Senegal [GAZ:00000913] + description: A country south of the Senegal River in western Africa. Senegal + is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali + to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies + almost entirely within Senegal, surrounded on the north, east and south; + from its western coast Gambia's territory follows the Gambia River more + than 300 km inland. Dakar is the capital city of Senegal, located on the + Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided + into 11 regions and further subdivided into 34 Departements, 103 Arrondissements + (neither of which have administrative function) and by Collectivites Locales. meaning: GAZ:00000913 - Serbia: - text: Serbia + Serbia [GAZ:00002957]: + text: Serbia [GAZ:00002957] + description: 'A landlocked country in Central and Southeastern Europe, covering + the southern part of the Pannonian Plain and the central part of the Balkan + Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria + to the east; Republic of Macedonia, Montenegro to the south; Croatia and + Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided + into 29 districts plus the City of Belgrade. The districts and the city + of Belgrade are further divided into municipalities. Serbia has two autonomous + provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), + and Vojvodina in the north (7 districts, 46 municipalities).' meaning: GAZ:00002957 - Seychelles: - text: Seychelles + Seychelles [GAZ:00006922]: + text: Seychelles [GAZ:00006922] + description: An archipelagic island country in the Indian Ocean at the eastern + edge of the Somali Sea. It consists of 115 islands. meaning: GAZ:00006922 - Sierra Leone: - text: Sierra Leone + Sierra Leone [GAZ:00000914]: + text: Sierra Leone [GAZ:00000914] + description: A country in West Africa. It is bordered by Guinea in the north + and east, Liberia in the southeast, and the Atlantic Ocean in the southwest + and west. The Republic of Sierra Leone is composed of 3 provinces and one + area called the Western Area; the provinces are further divided into 12 + districts. The Western Area is also divided into 2 districts. meaning: GAZ:00000914 - Singapore: - text: Singapore + Singapore [GAZ:00003923]: + text: Singapore [GAZ:00003923] + description: An island nation located at the southern tip of the Malay Peninsula. + It lies 137 km north of the Equator, south of the Malaysian State of Johor + and north of Indonesia's Riau Islands. Singapore consists of 63 islands, + including mainland Singapore. There are two man-made connections to Johor, + Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in + the west. Since 2001-11-24, Singapore has had an administrative subdivision + into 5 districts. It is also divided into five Regions, urban planning subdivisions + with no administrative role. meaning: GAZ:00003923 - Sint Maarten: - text: Sint Maarten + Sint Maarten [GAZ:00012579]: + text: Sint Maarten [GAZ:00012579] + description: One of five island areas (Eilandgebieden) of the Netherlands + Antilles, encompassing the southern half of the island of Saint Martin/Sint + Maarten. meaning: GAZ:00012579 - Slovakia: - text: Slovakia + Slovakia [GAZ:00002956]: + text: Slovakia [GAZ:00002956] + description: A landlocked country in Central Europe. The Slovak Republic borders + the Czech Republic and Austria to the west, Poland to the north, Ukraine + to the east and Hungary to the south. The largest city is its capital, Bratislava. + Slovakia is subdivided into 8 kraje (singular - kraj, usually translated + as regions. The kraje are subdivided into many okresy (singular okres, usually + translated as districts). Slovakia currently has 79 districts. meaning: GAZ:00002956 - Slovenia: - text: Slovenia + Slovenia [GAZ:00002955]: + text: Slovenia [GAZ:00002955] + description: A country in southern Central Europe bordering Italy to the west, + the Adriatic Sea to the southwest, Croatia to the south and east, Hungary + to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. + As of 2005-05 Slovenia is divided into 12 statistical regions for legal + and statistical purposes. Slovenia is divided into 210 local municipalities, + eleven of which have urban status. meaning: GAZ:00002955 - Solomon Islands: - text: Solomon Islands + Solomon Islands [GAZ:00005275]: + text: Solomon Islands [GAZ:00005275] + description: A nation in Melanesia, east of Papua New Guinea, consisting of + nearly one thousand islands. Together they cover a land mass of 28,400 km2. + The capital is Honiara, located on the island of Guadalcanal. meaning: GAZ:00005275 - Somalia: - text: Somalia + Somalia [GAZ:00001104]: + text: Somalia [GAZ:00001104] + description: A country located in the Horn of Africa. It is bordered by Djibouti + to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on + its north, the Indian Ocean at its east, and Ethiopia to the west. Prior + to the civil war, Somalia was divided into eighteen regions (gobollada, + singular gobol), which were in turn subdivided into districts. On a de facto + basis, northern Somalia is now divided up among the quasi-independent states + of Puntland, Somaliland, Galmudug and Maakhir. meaning: GAZ:00001104 - South Africa: - text: South Africa + South Africa [GAZ:00001094]: + text: South Africa [GAZ:00001094] + description: 'A country located at the southern tip of Africa. It borders + the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, + Swaziland, and Lesotho, an independent enclave surrounded by South African + territory. It is divided into nine provinces which are further subdivided + into 52 districts: 6 metropolitan and 46 district municipalities. The 46 + district municipalities are further subdivided into 231 local municipalities. + The district municipalities also contain 20 district management areas (mostly + game parks) that are directly governed by the district municipalities. The + six metropolitan municipalities perform the functions of both district and + local municipalities.' meaning: GAZ:00001094 - South Georgia and the South Sandwich Islands: - text: South Georgia and the South Sandwich Islands + South Georgia and the South Sandwich Islands [GAZ:00003990]: + text: South Georgia and the South Sandwich Islands [GAZ:00003990] + description: A British overseas territory in the southern Atlantic Ocean. + It iconsists of South Georgia and the Sandwich Islands, some 640 km to the + SE. meaning: GAZ:00003990 - South Korea: - text: South Korea + South Korea [GAZ:00002802]: + text: South Korea [GAZ:00002802] + description: A republic in East Asia, occupying the southern half of the Korean + Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous + province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 + special city (teukbyeolsi). These are further subdivided into a variety + of smaller entities, including cities (si), counties (gun), districts (gu), + towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). meaning: GAZ:00002802 - South Sudan: - text: South Sudan + South Sudan [GAZ:00233439]: + text: South Sudan [GAZ:00233439] + description: A state located in Africa with Juba as its capital city. It's + bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic + of the Congo to the south, and the Central African Republic to the west + and Sudan to the North. Southern Sudan includes the vast swamp region of + the Sudd formed by the White Nile, locally called the Bahr el Jebel. meaning: GAZ:00233439 - Spain: - text: Spain + Spain [GAZ:00000591]: + text: Spain [GAZ:00000591] + description: That part of the Kingdom of Spain that occupies the Iberian Peninsula + plus the Balaeric Islands. The Spanish mainland is bordered to the south + and east almost entirely by the Mediterranean Sea (except for a small land + boundary with Gibraltar); to the north by France, Andorra, and the Bay of + Biscay; and to the west by the Atlantic Ocean and Portugal. meaning: GAZ:00000591 - Spratly Islands: - text: Spratly Islands + Spratly Islands [GAZ:00010831]: + text: Spratly Islands [GAZ:00010831] + description: A group of >100 islands located in the Southeastern Asian group + of reefs and islands in the South China Sea, about two-thirds of the way + from southern Vietnam to the southern Philippines. meaning: GAZ:00010831 - Sri Lanka: - text: Sri Lanka + Sri Lanka [GAZ:00003924]: + text: Sri Lanka [GAZ:00003924] + description: An island nation in South Asia, located about 31 km off the southern + coast of India. Sri Lanka is divided into 9 provinces and 25 districts. + Districts are divided into Divisional Secretariats. meaning: GAZ:00003924 - State of Palestine: - text: State of Palestine + State of Palestine [GAZ:00002475]: + text: State of Palestine [GAZ:00002475] + description: The territory under the administration of the Palestine National + Authority, as established by the Oslo Accords. The PNA divides the Palestinian + territories into 16 governorates. meaning: GAZ:00002475 - Sudan: - text: Sudan + Sudan [GAZ:00000560]: + text: Sudan [GAZ:00000560] + description: A country in North Africa. It is bordered by Egypt to the north, + the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and + Uganda to the southeast, Democratic Republic of the Congo and the Central + African Republic to the southwest, Chad to the west and Libya to the northwest. + Sudan is divided into twenty-six states (wilayat, singular wilayah) which + in turn are subdivided into 133 districts. meaning: GAZ:00000560 - Suriname: - text: Suriname + Suriname [GAZ:00002525]: + text: Suriname [GAZ:00002525] + description: A country in northern South America. It is situated between French + Guiana to the east and Guyana to the west. The southern border is shared + with Brazil and the northern border is the Atlantic coast. The southernmost + border with French Guiana is disputed along the Marowijne river. Suriname + is divided into 10 districts, each of which is divided into Ressorten. meaning: GAZ:00002525 - Svalbard: - text: Svalbard + Svalbard [GAZ:00005396]: + text: Svalbard [GAZ:00005396] + description: An archipelago of continental islands lying in the Arctic Ocean + north of mainland Europe, about midway between Norway and the North Pole. meaning: GAZ:00005396 - Swaziland: - text: Swaziland - meaning: GAZ:00001099 - Sweden: - text: Sweden + Sweden [GAZ:00002729]: + text: Sweden [GAZ:00002729] + description: A Nordic country on the Scandinavian Peninsula in Northern Europe. + It has borders with Norway (west and north) and Finland (northeast). Sweden + is a unitary state, currently divided into twenty-one counties (lan). Each + county further divides into a number of municipalities or kommuner, with + a total of 290 municipalities in 2004. meaning: GAZ:00002729 - Switzerland: - text: Switzerland + Switzerland [GAZ:00002941]: + text: Switzerland [GAZ:00002941] + description: 'A federal republic in Europe. Switzerland is bordered by Germany, + France, Italy, Austria and Liechtenstein. The Swiss Confederation consists + of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within + Switzerland there are two enclaves: Busingen belongs to Germany, Campione + d''Italia belongs to Italy.' meaning: GAZ:00002941 - Syria: - text: Syria + Syria [GAZ:00002474]: + text: Syria [GAZ:00002474] + description: 'A country in Southwest Asia, bordering Lebanon, the Mediterranean + Sea and the island of Cyprus to the west, Israel to the southwest, Jordan + to the south, Iraq to the east, and Turkey to the north. Syria has fourteen + governorates, or muhafazat (singular: muhafazah). The governorates are divided + into sixty districts, or manatiq (singular: mintaqah), which are further + divided into sub-districts, or nawahi (singular: nahia).' meaning: GAZ:00002474 - Taiwan: - text: Taiwan + Taiwan [GAZ:00005341]: + text: Taiwan [GAZ:00005341] + description: A state in East Asia with de facto rule of the island of Tawain + and adjacent territory. The Republic of China currently administers two + historical provinces of China (one completely and a small part of another + one) and centrally administers two direct-controlled municipalities. meaning: GAZ:00005341 - Tajikistan: - text: Tajikistan + Tajikistan [GAZ:00006912]: + text: Tajikistan [GAZ:00006912] + description: A mountainous landlocked country in Central Asia. Afghanistan + borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and + People's Republic of China to the east. Tajikistan consists of 4 administrative + divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous + province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican + Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly + known as Karotegin Province). Each region is divided into several districts + (nohiya or raion). meaning: GAZ:00006912 - Tanzania: - text: Tanzania + Tanzania [GAZ:00001103]: + text: Tanzania [GAZ:00001103] + description: A country in East Africa bordered by Kenya and Uganda on the + north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, + and Zambia, Malawi and Mozambique on the south. To the east it borders the + Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on + the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight + districts (wilaya), each with at least one council, have been created to + further increase local authority; the councils are also known as local government + authorities. Currently there are 114 councils operating in 99 districts; + 22 are urban and 92 are rural. The 22 urban units are further classified + as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, + Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) + or town councils (the remaining eleven communities). meaning: GAZ:00001103 - Thailand: - text: Thailand + Thailand [GAZ:00003744]: + text: Thailand [GAZ:00003744] + description: 'A country in Southeast Asia. To its east lie Laos and Cambodia; + to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman + Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided + into 75 provinces (changwat), which are gathered into 5 groups of provinces + by location. There are also 2 special governed districts: the capital Bangkok + (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial + level and thus often counted as a 76th province.' meaning: GAZ:00003744 - Timor-Leste: - text: Timor-Leste + Timor-Leste [GAZ:00006913]: + text: Timor-Leste [GAZ:00006913] + description: A country in Southeast Asia. It comprises the eastern half of + the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, + an exclave on the northwestern side of the island, within Indonesian West + Timor. The small country of 15,410 km2 is located about 640 km northwest + of Darwin, Australia. East Timor is divided into thirteen administrative + districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, + villages and hamlets. meaning: GAZ:00006913 - Togo: - text: Togo + Togo [GAZ:00000915]: + text: Togo [GAZ:00000915] + description: A country in West Africa bordering Ghana in the west, Benin in + the east and Burkina Faso in the north. In the south, it has a short Gulf + of Guinea coast, on which the capital Lome is located. meaning: GAZ:00000915 - Tokelau: - text: Tokelau + Tokelau [GAZ:00260188]: + text: Tokelau [GAZ:00260188] + description: 'A dependent territory of New Zealand in the southern Pacific + Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and + Fakaofo. They have a combined land area of 10 km2 (4 sq mi).' meaning: GAZ:00260188 - Tonga: - text: Tonga + Tonga [GAZ:00006916]: + text: Tonga [GAZ:00006916] + description: A Polynesian country, and also an archipelago comprising 169 + islands, of which 36 are inhabited. The archipelago's total surface area + is about 750 square kilometres (290 sq mi) scattered over 700,000 square + kilometres (270,000 sq mi) of the southern Pacific Ocean. meaning: GAZ:00006916 - Trinidad and Tobago: - text: Trinidad and Tobago + Trinidad and Tobago [GAZ:00003767]: + text: Trinidad and Tobago [GAZ:00003767] + description: An archipelagic state in the southern Caribbean, lying northeast + of the South American nation of Venezuela and south of Grenada in the Lesser + Antilles. It also shares maritime boundaries with Barbados to the northeast + and Guyana to the southeast. The country covers an area of 5,128 km2and + consists of two main islands, Trinidad and Tobago, and 21 smaller islands. meaning: GAZ:00003767 - Tromelin Island: - text: Tromelin Island + Tromelin Island [GAZ:00005812]: + text: Tromelin Island [GAZ:00005812] + description: A low, flat 0.8 km2 island in the Indian Ocean, about 350 km + east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 + m long and 700 m wide, surrounded by coral reefs. The island is 7 m high + at its highest point. meaning: GAZ:00005812 - Tunisia: - text: Tunisia + Tunisia [GAZ:00000562]: + text: Tunisia [GAZ:00000562] + description: A country situated on the Mediterranean coast of North Africa. + It is bordered by Algeria to the west and Libya to the southeast. Tunisia + is subdivided into 24 governorates, divided into 262 "delegations" or "districts" + (mutamadiyat), and further subdivided into municipalities (shaykhats). meaning: GAZ:00000562 - Turkey: - text: Turkey + Turkey [GAZ:00000558]: + text: Turkey [GAZ:00000558] + description: 'A Eurasian country that stretches across the Anatolian peninsula + in western Asia and Thrace (Rumelia) in the Balkan region of southeastern + Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece + to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave + of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. + The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago + are to the west; and the Black Sea is to the north. Separating Anatolia + and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus + and the Dardanelles), which are commonly reckoned to delineate the border + between Asia and Europe, thereby making Turkey transcontinental. The territory + of Turkey is subdivided into 81 provinces for administrative purposes. The + provinces are organized into 7 regions for census purposes; however, they + do not represent an administrative structure. Each province is divided into + districts, for a total of 923 districts.' meaning: GAZ:00000558 - Turkmenistan: - text: Turkmenistan + Turkmenistan [GAZ:00005018]: + text: Turkmenistan [GAZ:00005018] + description: A country in Central Asia. It is bordered by Afghanistan to the + southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan + to the northwest, and the Caspian Sea to the west. It was a constituent + republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan + is divided into five provinces or welayatlar (singular - welayat) and one + independent city. meaning: GAZ:00005018 - Turks and Caicos Islands: - text: Turks and Caicos Islands + Turks and Caicos Islands [GAZ:00003955]: + text: Turks and Caicos Islands [GAZ:00003955] + description: A British Overseas Territory consisting of two groups of tropical + islands in the West Indies. The Turks and Caicos Islands are divided into + six administrative districts (two in the Turks Islands and four in the Caicos + Islands. meaning: GAZ:00003955 - Tuvalu: - text: Tuvalu + Tuvalu [GAZ:00009715]: + text: Tuvalu [GAZ:00009715] + description: A Polynesian island nation located in the Pacific Ocean midway + between Hawaii and Australia. meaning: GAZ:00009715 - United States of America: - text: United States of America + United States of America [GAZ:00002459]: + text: United States of America [GAZ:00002459] + description: A federal constitutional republic comprising fifty states and + a federal district. The country is situated mostly in central North America, + where its forty-eight contiguous states and Washington, DC, the capital + district, lie between the Pacific and Atlantic Oceans, bordered by Canada + to the north and Mexico to the south. The State of Alaska is in the northwest + of the continent, with Canada to its east and Russia to the west across + the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United + States also possesses several territories, or insular areas, that are scattered + around the Caribbean and Pacific. The states are divided into smaller administrative + regions, called counties in most states, exceptions being Alaska (parts + of the state are organized into subdivisions called boroughs; the rest of + the state's territory that is not included in any borough is divided into + "census areas"), and Louisiana (which is divided into county-equivalents + that are called parishes). There are also independent cities which are within + particular states but not part of any particular county or consolidated + city-counties. Another type of organization is where the city and county + are unified and function as an independent city. There are thirty-nine independent + cities in Virginia and other independent cities or city-counties are San + Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, + Colorado and Carson City, Nevada. Counties can include a number of cities, + towns, villages, or hamlets, or sometimes just a part of a city. Counties + have varying degrees of political and legal significance, but they are always + administrative divisions of the state. Counties in many states are further + subdivided into townships, which, by definition, are administrative divisions + of a county. In some states, such as Michigan, a township can file a charter + with the state government, making itself into a "charter township", which + is a type of mixed municipal and township status (giving the township some + of the rights of a city without all of the responsibilities), much in the + way a metropolitan municipality is a mixed municipality and county. meaning: GAZ:00002459 - Uganda: - text: Uganda + Uganda [GAZ:00001102]: + text: Uganda [GAZ:00001102] + description: 'A landlocked country in East Africa, bordered on the east by + Kenya, the north by Sudan, on the west by the Democratic Republic of the + Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern + part of the country includes a substantial portion of Lake Victoria, within + which it shares borders with Kenya and Tanzania. Uganda is divided into + 80 districts, spread across four administrative regions: Northern, Eastern, + Central and Western. The districts are subdivided into counties.' meaning: GAZ:00001102 - Ukraine: - text: Ukraine + Ukraine [GAZ:00002724]: + text: Ukraine [GAZ:00002724] + description: A country in Eastern Europe. It borders Russia to the east, Belarus + to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova + to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine + is subdivided into twenty-four oblasts (provinces) and one autonomous republic + (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, + and Sevastopol, both have a special legal status. The 24 oblasts and Crimea + are subdivided into 490 raions (districts), or second-level administrative + units. meaning: GAZ:00002724 - United Arab Emirates: - text: United Arab Emirates + United Arab Emirates [GAZ:00005282]: + text: United Arab Emirates [GAZ:00005282] + description: A Middle Eastern federation of seven states situated in the southeast + of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering + Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, + Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. meaning: GAZ:00005282 - United Kingdom: - text: United Kingdom + United Kingdom [GAZ:00002637]: + text: United Kingdom [GAZ:00002637] + description: A sovereign island country located off the northwestern coast + of mainland Europe comprising of the four constituent countries; England, + Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, + the northeast part of the island of Ireland and many small islands. Apart + from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North + Sea, the English Channel and the Irish Sea. The largest island, Great Britain, + is linked to France by the Channel Tunnel. meaning: GAZ:00002637 - Uruguay: - text: Uruguay + Uruguay [GAZ:00002930]: + text: Uruguay [GAZ:00002930] + description: A country located in the southeastern part of South America. + It is bordered by Brazil to the north, by Argentina across the bank of both + the Uruguay River to the west and the estuary of Rio de la Plata to the + southwest, and the South Atlantic Ocean to the southeast. Uraguay consists + of 19 departments (departamentos, singular - departamento). meaning: GAZ:00002930 - Uzbekistan: - text: Uzbekistan + Uzbekistan [GAZ:00004979]: + text: Uzbekistan [GAZ:00004979] + description: A doubly landlocked country in Central Asia, formerly part of + the Soviet Union. It shares borders with Kazakhstan to the west and to the + north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan + to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one + autonomous republic (respublika and one independent city (shahar). meaning: GAZ:00004979 - Vanuatu: - text: Vanuatu + Vanuatu [GAZ:00006918]: + text: Vanuatu [GAZ:00006918] + description: An island country located in the South Pacific Ocean. The archipelago, + which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern + Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New + Guinea, southeast of the Solomon Islands, and west of Fiji. meaning: GAZ:00006918 - Venezuela: - text: Venezuela + Venezuela [GAZ:00002931]: + text: Venezuela [GAZ:00002931] + description: A country on the northern coast of South America. The country + comprises a continental mainland and numerous islands located off the Venezuelan + coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses + borders with Guyana to the east, Brazil to the south, and Colombia to the + west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, + Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just + north, off the Venezuelan coast. Venezuela is divided into twenty-three + states (Estados), a capital district (distrito capital) corresponding to + the city of Caracas, the Federal Dependencies (Dependencias Federales, a + special territory), and Guayana Esequiba (claimed in a border dispute with + Guyana). Venezuela is further subdivided into 335 municipalities (municipios); + these are subdivided into over one thousand parishes (parroquias). meaning: GAZ:00002931 - Viet Nam: - text: Viet Nam + Viet Nam [GAZ:00003756]: + text: Viet Nam [GAZ:00003756] + description: The easternmost country on the Indochina Peninsula in Southeast + Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, + alongside China, Laos, and Cambodia. meaning: GAZ:00003756 - Virgin Islands: - text: Virgin Islands + Virgin Islands [GAZ:00003959]: + text: Virgin Islands [GAZ:00003959] + description: A group of islands in the Caribbean that are an insular area + of the United States. The islands are geographically part of the Virgin + Islands archipelago and are located in the Leeward Islands of the Lesser + Antilles. The US Virgin Islands are an organized, unincorporated United + States territory. The US Virgin Islands are administratively divided into + two districts and subdivided into 20 sub-districts. meaning: GAZ:00003959 - Wake Island: - text: Wake Island + Wake Island [GAZ:00007111]: + text: Wake Island [GAZ:00007111] + description: A coral atoll (despite its name) having a coastline of 19 km + in the North Pacific Ocean, located about two-thirds of the way from Honolulu + (3,700 km west) to Guam (2,430 km east). meaning: GAZ:00007111 - Wallis and Futuna: - text: Wallis and Futuna + Wallis and Futuna [GAZ:00007191]: + text: Wallis and Futuna [GAZ:00007191] + description: A Polynesian French island territory (but not part of, or even + contiguous with, French Polynesia) in the South Pacific between Fiji and + Samoa. It is made up of three main volcanic tropical islands and a number + of tiny islets. meaning: GAZ:00007191 - West Bank: - text: West Bank + West Bank [GAZ:00009572]: + text: West Bank [GAZ:00009572] + description: A landlocked territory near the Mediterranean coast of Western + Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the + south, west and north.[2] Under Israeli occupation since 1967, the area + is split into 167 Palestinian "islands" under partial Palestinian National + Authority civil rule, and 230 Israeli settlements into which Israeli law + is "pipelined". meaning: GAZ:00009572 - Western Sahara: - text: Western Sahara + Western Sahara [GAZ:00000564]: + text: Western Sahara [GAZ:00000564] + description: A territory of northwestern Africa, bordered by Morocco to the + north, Algeria in the northeast, Mauritania to the east and south, and the + Atlantic Ocean on the west. Western Sahara is administratively divided into + four regions. meaning: GAZ:00000564 - Yemen: - text: Yemen + Yemen [GAZ:00005284]: + text: Yemen [GAZ:00005284] + description: A country located on the Arabian Peninsula in Southwest Asia. + Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, + the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's + territory includes over 200 islands, the largest of which is Socotra, about + 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen + is divided into twenty governorates (muhafazah) and one municipality. The + population of each governorate is listed in the table below. The governorates + of Yemen are divided into 333 districts (muderiah). The districts are subdivided + into 2,210 sub-districts, and then into 38,284 villages (as of 2001). meaning: GAZ:00005284 - Zambia: - text: Zambia + Zambia [GAZ:00001107]: + text: Zambia [GAZ:00001107] + description: A landlocked country in Southern Africa. The neighbouring countries + are the Democratic Republic of the Congo to the north, Tanzania to the north-east, + Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, + and Angola to the west. The capital city is Lusaka. Zambia is divided into + nine provinces. Each province is subdivided into several districts with + a total of 73 districts. meaning: GAZ:00001107 - Zimbabwe: - text: Zimbabwe + Zimbabwe [GAZ:00001106]: + text: Zimbabwe [GAZ:00001106] + description: A landlocked country in the southern part of the continent of + Africa, between the Zambezi and Limpopo rivers. It is bordered by South + Africa to the south, Botswana to the southwest, Zambia to the northwest, + and Mozambique to the east. Zimbabwe is divided into eight provinces and + two cities with provincial status. The provinces are subdivided into 59 + districts and 1,200 municipalities. meaning: GAZ:00001106 - geo_loc_name (state/province/territory) menu: - name: geo_loc_name (state/province/territory) menu + WatershedShapefileAvailabilityMenu: + name: WatershedShapefileAvailabilityMenu + title: watershed shapefile availability menu permissible_values: - Alberta: - text: Alberta - meaning: GAZ:00002566 - British Columbia: - text: British Columbia - meaning: GAZ:00002562 - Manitoba: - text: Manitoba - meaning: GAZ:00002571 - New Brunswick: - text: New Brunswick - meaning: GAZ:00002570 - Newfoundland and Labrador: - text: Newfoundland and Labrador - meaning: GAZ:00002567 - Northwest Territories: - text: Northwest Territories - meaning: GAZ:00002575 - Nova Scotia: - text: Nova Scotia - meaning: GAZ:00002565 - Nunavut: - text: Nunavut - meaning: GAZ:00002574 - Ontario: - text: Ontario - meaning: GAZ:00002563 - Prince Edward Island: - text: Prince Edward Island - meaning: GAZ:00002572 - Quebec: - text: Quebec - meaning: GAZ:00002569 - Saskatchewan: - text: Saskatchewan - meaning: GAZ:00002564 - Yukon: - text: Yukon - meaning: GAZ:00002576 - watershed shapefile availability menu: - name: watershed shapefile availability menu - permissible_values: - Available: - text: Available + Available [GENEPIO:0100993]: + text: Available [GENEPIO:0100993] + description: A datum status in which the required datum is able to be used, + obtained or selected. meaning: GENEPIO:0100993 - Unknown: - text: Unknown + Unknown [GENEPIO:0100995]: + text: Unknown [GENEPIO:0100995] + description: A datum status in which the availabilty or presence of the required + datum is not known. meaning: GENEPIO:0100995 - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu + title: organism menu permissible_values: - Severe acute respiratory syndrome coronavirus 2: - text: Severe acute respiratory syndrome coronavirus 2 + Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]: + text: Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] + description: A strain of the species Betacoronavirus pandemicum, a coronavirus + that causes COVID-19, the respiratory illness responsible for the COVID-19 + pandemic. meaning: NCBITaxon:2697049 - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: - Wastewater treatment efficiency assessment: - text: Wastewater treatment efficiency assessment + Wastewater treatment efficiency assessment [GENEPIO:0100869]: + text: Wastewater treatment efficiency assessment [GENEPIO:0100869] + description: An environmental sampling strategy in which wastewater effluent + is collected to assess the efficiency of wastewater treatment. meaning: GENEPIO:0100869 - Wastewater chemical surveillance: - text: Wastewater chemical surveillance + Wastewater chemical surveillance [GENEPIO:0100870]: + text: Wastewater chemical surveillance [GENEPIO:0100870] + description: An environmental sampling strategy in which wastewater samples + are collected to monitor for chemical contamination. meaning: GENEPIO:0100870 - Wastewater drug surveillance: - text: Wastewater drug surveillance + Wastewater drug surveillance [GENEPIO:0100871]: + text: Wastewater drug surveillance [GENEPIO:0100871] + description: An environmental sampling strategy in which wastewater samples + are collected to monitor for community drug use. meaning: GENEPIO:0100871 - Wastewater pathogen surveillance: - text: Wastewater pathogen surveillance + Wastewater pathogen surveillance [GENEPIO:0100872]: + text: Wastewater pathogen surveillance [GENEPIO:0100872] + description: An environmental sampling strategy in which samples are collected + to identify and/or monitor the presence of pathogens. meaning: GENEPIO:0100872 - Research: - text: Research + Research [GENEPIO:0100003]: + text: Research [GENEPIO:0100003] + description: A sampling strategy in which samples are collected in order to + perform research. meaning: GENEPIO:0100003 - Environmental survey (profiling): - text: Environmental survey (profiling) + Environmental survey (profiling) [GENEPIO:0100873]: + text: Environmental survey (profiling) [GENEPIO:0100873] + description: A research sampling strategy in which samples are collected in + order to survey/profile entities in, or characteristics of, an environment. meaning: GENEPIO:0100873 - is_a: Research - Protocol testing: - text: Protocol testing + is_a: Research [GENEPIO:0100003] + Protocol testing [GENEPIO:0100024]: + text: Protocol testing [GENEPIO:0100024] + description: A research sampling strategy in which samples are collected in + order to test a method or protocol. meaning: GENEPIO:0100024 - is_a: Research - scale of sampling menu: - name: scale of sampling menu + is_a: Research [GENEPIO:0100003] + ScaleOfSamplingMenu: + name: ScaleOfSamplingMenu + title: scale of sampling menu permissible_values: - Community-level surveillance: - text: Community-level surveillance + Community-level surveillance [GENEPIO:0100874]: + text: Community-level surveillance [GENEPIO:0100874] + description: A surveillance strategy in which sites are sampled at the community + level. meaning: GENEPIO:0100874 - Institution-level surveillance: - text: Institution-level surveillance + Institution-level surveillance [GENEPIO:0100875]: + text: Institution-level surveillance [GENEPIO:0100875] + description: A surveillance strategy in which sites are sampled at the institution + level. meaning: GENEPIO:0100875 - Building-level surveillance: - text: Building-level surveillance + Building-level surveillance [GENEPIO:0100876]: + text: Building-level surveillance [GENEPIO:0100876] + description: A surveillance strategy in which sites are sampled at the building + level. meaning: GENEPIO:0100876 - sample collection time of day menu: - name: sample collection time of day menu + SampleCollectionTimeOfDayMenu: + name: SampleCollectionTimeOfDayMenu + title: sample collection time of day menu permissible_values: - Morning: - text: Morning + Morning [NCIT:C64934]: + text: Morning [NCIT:C64934] + description: The time period between dawn and noon. meaning: NCIT:C64934 - Afternoon: - text: Afternoon + Afternoon [NCIT:C64935]: + text: Afternoon [NCIT:C64935] + description: The time period between noon and sunset. meaning: NCIT:C64935 - Evening: - text: Evening + Evening [NCIT:C64936]: + text: Evening [NCIT:C64936] + description: The time period between late afternoon and bedtime. meaning: NCIT:C64936 - Night: - text: Night + Night [NCIT:C65001]: + text: Night [NCIT:C65001] + description: The time in every 24 hour period when it is dark. meaning: NCIT:C65001 - sample collection duration unit menu: - name: sample collection duration unit menu + SampleCollectionDurationUnitMenu: + name: SampleCollectionDurationUnitMenu + title: sample collection duration unit menu permissible_values: - Second: - text: Second + Second [UO:0000010]: + text: Second [UO:0000010] + description: A time unit which is equal to the duration of 9 192 631 770 periods + of the radiation corresponding to the transition between the two hyperfine + levels of the ground state of the caesium 133 atom. meaning: UO:0000010 - Minute: - text: Minute + Minute [UO:0000031]: + text: Minute [UO:0000031] + description: A time unit which is equal to 60 seconds. meaning: UO:0000031 - Hour: - text: Hour + Hour [UO:0000032]: + text: Hour [UO:0000032] + description: A time unit which is equal to 60 minutes. meaning: UO:0000032 - Day: - text: Day + Day [UO:0000033]: + text: Day [UO:0000033] + description: A time unit which is equal to 24 hours. meaning: UO:0000033 - Week: - text: Week + Week [UO:0000034]: + text: Week [UO:0000034] + description: A time unit which is equal to 7 days. meaning: UO:0000034 - Month: - text: Month + Month [UO:0000035]: + text: Month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. meaning: UO:0000035 - Year: - text: Year + Year [UO:0000036]: + text: Year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. meaning: UO:0000036 - presampling activity menu: - name: presampling activity menu + PresamplingActivityMenu: + name: PresamplingActivityMenu + title: presampling activity menu permissible_values: - Agricultural activity: - text: Agricultural activity + Agricultural activity [ENVO:01001442]: + text: Agricultural activity [ENVO:01001442] + description: A land use process during which terrestrial environments are + modified such that they can grow crop plants or allow the rearing of animals + to provide food, fiber, medicines, or other products used by humans. meaning: ENVO:01001442 - Animal husbandry: - text: Animal husbandry + Animal husbandry [ENVO:01001248]: + text: Animal husbandry [ENVO:01001248] + description: An agricultural process during which humans rear animals on land + for harvest and consumption. meaning: ENVO:01001248 - Industrial activity: - text: Industrial activity + Industrial activity [ENVO:01001450]: + text: Industrial activity [ENVO:01001450] + description: A process that leads to the production of goods. meaning: ENVO:01001450 - Healthcare activity: - text: Healthcare activity + Healthcare activity [NCIT:C16205]: + text: Healthcare activity [NCIT:C16205] + description: A process that includes the prevention, treatment, and management + of physical and mental illness. meaning: NCIT:C16205 - Wastewater treatment: - text: Wastewater treatment + Wastewater treatment [ENVO:06105300]: + text: Wastewater treatment [ENVO:06105300] + description: A recycling process during which wastewater is treated. meaning: ENVO:06105300 - Wastewater filtration: - text: Wastewater filtration - meaning: GENEPIO:0100881 - is_a: Wastewater treatment - Wastewater grit removal: - text: Wastewater grit removal - meaning: GENEPIO:0100882 - is_a: Wastewater treatment - Wastewater microbial pre-treatment: - text: Wastewater microbial pre-treatment - meaning: GENEPIO:0100883 - is_a: Wastewater treatment - Wastewater primary sedimentation: - text: Wastewater primary sedimentation - meaning: GENEPIO:0100884 - is_a: Wastewater treatment - Wastewater secondary sedimentation: - text: Wastewater secondary sedimentation - meaning: GENEPIO:0100885 - is_a: Wastewater treatment - sample volume measurement unit menu: - name: sample volume measurement unit menu + Wastewater screening process [GENEPIO:0101198]: + text: Wastewater screening process [GENEPIO:0101198] + description: A wastewater treatment process which removes large objects such + as rags, paper, plastics, and metals to prevent damage and clogging of downstream + equipment, piping, and appurtenances. + meaning: GENEPIO:0101198 + is_a: Wastewater treatment [ENVO:06105300] + wastewater comminution process [GENEPIO:0101719]: + text: wastewater comminution process [GENEPIO:0101719] + description: A wastewater treatment process which involves the mechanical + reduction of solid materials in wastewater into smaller, more manageable + particles through devices like comminutors or grinders to shred debris. + meaning: GENEPIO:0101719 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater filtration [ENVO:03501445]: + text: Wastewater filtration [ENVO:03501445] + description: A wastewater treatment process which removes solid particles + from wastewater by means of filtration. + meaning: ENVO:03501445 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater grit removal [ENVO:03501446]: + text: Wastewater grit removal [ENVO:03501446] + description: A wastewater treatment process which removes sand, silt, and + grit from wastewater. + meaning: ENVO:03501446 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater primary sedimentation [ENVO:03501448]: + text: Wastewater primary sedimentation [ENVO:03501448] + description: A wastewater treatment process which removes solids and large + particles from influent through gravitational force. + meaning: ENVO:03501448 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater microbial treatment [ENVO:03501447]: + text: Wastewater microbial treatment [ENVO:03501447] + description: A wastewater treatment process in which microbes are used to + degrade the biological material in wastewater. + meaning: ENVO:03501447 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater aerobic digestion [GENEPIO:0101199]: + text: Wastewater aerobic digestion [GENEPIO:0101199] + description: A wastewater microbial treatment process in which organic material + is broken down in the presence of oxygen. + meaning: GENEPIO:0101199 + is_a: Wastewater microbial treatment [ENVO:03501447] + Wastewater anaerobic digestion [GENEPIO:0101200]: + text: Wastewater anaerobic digestion [GENEPIO:0101200] + description: A wastewater microbial treatment process in which organic material + is broken down in the absence of oxygen by anaerobic bacteria. + meaning: GENEPIO:0101200 + is_a: Wastewater microbial treatment [ENVO:03501447] + Wastewater secondary sedimentation [ENVO:03501449]: + text: Wastewater secondary sedimentation [ENVO:03501449] + description: A wastewater treatment process which removes biomass produced + in aeration from influent through gravitational force. + meaning: ENVO:03501449 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater sludge removal [GENEPIO:0101201]: + text: Wastewater sludge removal [GENEPIO:0101201] + description: A wastewater treatment process which removes large objects such + as rags, paper, plastics, and metals to prevent damage and clogging of downstream + equipment, piping, and appurtenances. + meaning: GENEPIO:0101201 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater sludge dewatering [GENEPIO:0101202]: + text: Wastewater sludge dewatering [GENEPIO:0101202] + description: A wastewater treatment process which mechanically reduces the + water content of wastewater sludge using equipment like centrifuges or belt + presses, resulting in a semi-solid material that is easier to handle and + transport + meaning: GENEPIO:0101202 + is_a: Wastewater treatment [ENVO:06105300] + Wastewater sludge drying [GENEPIO:0101718]: + text: Wastewater sludge drying [GENEPIO:0101718] + description: A wastewater treatment process which further reduces the moisture + content of dewatered sludge, typically through thermal or air drying methods, + producing a dry, stable material for easier disposal or use. + meaning: GENEPIO:0101718 + is_a: Wastewater treatment [ENVO:06105300] + SampleVolumeMeasurementUnitMenu: + name: SampleVolumeMeasurementUnitMenu + title: sample volume measurement unit menu permissible_values: - microliter (uL): - text: microliter (uL) + microliter (uL) [UO:0000101]: + text: microliter (uL) [UO:0000101] + description: A metric unit of volume equivalent to one thousandth of a cubic + centimeter or one millionth of a liter. meaning: UO:0000101 - milliliter (mL): - text: milliliter (mL) + milliliter (mL) [UO:0000098]: + text: milliliter (mL) [UO:0000098] + description: A metric unit of volume equivalent to one cubic centimeter or + one thousandth of a liter. meaning: UO:0000098 - liter (L): - text: liter (L) + liter (L) [UO:0000099]: + text: liter (L) [UO:0000099] + description: A metric unit of volume equivalent to 1000 cubic centimeters meaning: UO:0000099 - sample storage duration unit menu: - name: sample storage duration unit menu + SampleStorageDurationUnitMenu: + name: SampleStorageDurationUnitMenu + title: sample storage duration unit menu permissible_values: - Second: - text: Second + Second [UO:0000010]: + text: Second [UO:0000010] + description: A time unit which is equal to the duration of 9 192 631 770 periods + of the radiation corresponding to the transition between the two hyperfine + levels of the ground state of the caesium 133 atom. meaning: UO:0000010 - Minute: - text: Minute + Minute [UO:0000031]: + text: Minute [UO:0000031] + description: A time unit which is equal to 60 seconds. meaning: UO:0000031 - Hour: - text: Hour + Hour [UO:0000032]: + text: Hour [UO:0000032] + description: A time unit which is equal to 60 minutes. meaning: UO:0000032 - Day: - text: Day + Day [UO:0000033]: + text: Day [UO:0000033] + description: A time unit which is equal to 24 hours. meaning: UO:0000033 - Week: - text: Week + Week [UO:0000034]: + text: Week [UO:0000034] + description: A time unit which is equal to 7 days. meaning: UO:0000034 - Month: - text: Month + Month [UO:0000035]: + text: Month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. meaning: UO:0000035 - Year: - text: Year + Year [UO:0000036]: + text: Year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. meaning: UO:0000036 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: - Concentration: - text: Concentration + Concentration [OBI:0600041]: + text: Concentration [OBI:0600041] + description: A process used to increase the density of a material of interest + by removing other materials in the entity containing the material of interest. meaning: OBI:0600041 - Centrifugation: - text: Centrifugation + Centrifugation [OBI:0302886]: + text: Centrifugation [OBI:0302886] + description: A process separating molecules by size or density using centrifugal + forces generated by a spinning rotor. meaning: OBI:0302886 - Filtration: - text: Filtration + Filtration [OBI:0302885]: + text: Filtration [OBI:0302885] + description: A process which separates components suspended in a fluid based + on granularity properties relying on a filter device. meaning: OBI:0302885 - Flocculation: - text: Flocculation + Flocculation [NCIT:C154798]: + text: Flocculation [NCIT:C154798] + description: A process in which microscopic particles in suspension aggregate + to form loosely clumped masses that are often macroscopically observable. meaning: NCIT:C154798 - Magnetic nanobead binding: - text: Magnetic nanobead binding + Magnetic nanobead binding [GENEPIO:0100886]: + text: Magnetic nanobead binding [GENEPIO:0100886] + description: A process that uses nanobeads to bind to particles or microbes + of interest. meaning: GENEPIO:0100886 - Precipitation: - text: Precipitation + Precipitation [OBI:0600034]: + text: Precipitation [OBI:0600034] + description: A protocol application to cause a material to precipitate (becoming + a solid) out of solution. meaning: OBI:0600034 - Gravity separation: - text: Gravity separation + Gravity separation [GENEPIO:0101011]: + text: Gravity separation [GENEPIO:0101011] + description: A process through which solids are separated from a liquid by + allowing the solids to settle by gravity. meaning: GENEPIO:0101011 - Pasteurization: - text: Pasteurization + Pasteurization [IDO:0100170]: + text: Pasteurization [IDO:0100170] + description: A planned process of heating a liquid entity, to a specific temperature + of a defined length of time span, and then cooling it immediately. It has + an objective of prevent the microbial's growth in the liquid entity, which + is a specific input of this planned process. meaning: IDO:0100170 - Growth in enrichment broth: - text: Growth in enrichment broth + Growth in enrichment broth [GENEPIO:0101012]: + text: Growth in enrichment broth [GENEPIO:0101012] + description: A process in which microorganisms, present in a collected sample, + undergo cultivation within a nutrient-rich liquid medium, that facilitates + growth. meaning: GENEPIO:0101012 - Pooling specimens: - text: Pooling specimens + Pooling specimens [OBI:0600016]: + text: Pooling specimens [OBI:0600016] + description: Physical combination of several instances of like material. meaning: OBI:0600016 - Technical replicate process: - text: Technical replicate process + Technical replicate process [GENEPIO:0101021]: + text: Technical replicate process [GENEPIO:0101021] + description: A specimen collection process in which a replicate(s) is collected + to assess technical variation within an experiment. For technical replicates + the same BioSample is used e.g. the same pool of RNA is used to assess technical + (as opposed to biological) variation. meaning: GENEPIO:0101021 - Biological replicate process: - text: Biological replicate process + Biological replicate process [GENEPIO:0101022]: + text: Biological replicate process [GENEPIO:0101022] + description: A specimen collection process in which a replicate(s) is collected + in parallel to assess for biological variation within an experiment. Biological + replicates would have distinct BioSamples records. meaning: GENEPIO:0101022 - environmental site menu: - name: environmental site menu + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental site menu permissible_values: - Correctional facility: - text: Correctional facility + Correctional facility [ENVO:01001481]: + text: Correctional facility [ENVO:01001481] + description: A prison facility which is owned and operated by a state. meaning: ENVO:01001481 - Healthcare facility: - text: Healthcare facility + Healthcare facility [ENVO:03501134]: + text: Healthcare facility [ENVO:03501134] + description: A human construction in which healthcare is provided. meaning: ENVO:03501134 - Hospital: - text: Hospital + Hospital [ENVO:00002173]: + text: Hospital [ENVO:00002173] + description: A building in which health care services are provided by specialized + staff and equipment. meaning: ENVO:00002173 - is_a: Healthcare facility - Clinic: - text: Clinic + is_a: Healthcare facility [ENVO:03501134] + Clinic [ENVO:03501182]: + text: Clinic [ENVO:03501182] + description: A facility which is used to provide treatment, remedial work, + and/or instruction. meaning: ENVO:03501182 - is_a: Healthcare facility - Educational facility: - text: Educational facility + is_a: Healthcare facility [ENVO:03501134] + Educational facility [ENVO:03501129]: + text: Educational facility [ENVO:03501129] + description: A human construction in which people are educated. meaning: ENVO:03501129 - Daycare facility: - text: Daycare facility + Daycare facility [ENVO:03501335]: + text: Daycare facility [ENVO:03501335] + description: A child care facility in which day care services are provided, + by specialized staff and equipment, to a human child during the working + day. meaning: ENVO:03501335 - is_a: Educational facility - School: - text: School + is_a: Educational facility [ENVO:03501129] + School [ENVO:03501130]: + text: School [ENVO:03501130] + description: An institutional building in which students are educated. meaning: ENVO:03501130 - is_a: Educational facility - College or university: - text: College or university + is_a: Educational facility [ENVO:03501129] + College or university [ENVO:03501131]: + text: College or university [ENVO:03501131] + description: An institutional building in which university services are performed. meaning: ENVO:03501131 - is_a: Educational facility - Residential building: - text: Residential building + is_a: Educational facility [ENVO:03501129] + Commercial building [ENVO:01001222]: + text: Commercial building [ENVO:01001222] + description: A building which is primarily used to facilitate the buying or + selling of goods or services. "Commerce includes legal, economic, political, + social, cultural and technological systems that are in operation in any + country or internationally." + meaning: ENVO:01001222 + Office [ENVO:01001221]: + text: Office [ENVO:01001221] + description: A commercial building which contains parts used as workplaces + primarily for administrative and managerial workers. "An office building + will be divided into sections for different companies or may be dedicated + to one company. In either case, each company will typically have a reception + area, one or several meeting rooms, singular or open-plan offices, as well + as toilets." + meaning: ENVO:01001221 + is_a: Commercial building [ENVO:01001222] + Restaurant [ENVO:01000934]: + text: Restaurant [ENVO:01000934] + description: A building within which food and drink are prepared and served + to customers in exchange for money or other goods and/or services. + meaning: ENVO:01000934 + is_a: Commercial building [ENVO:01001222] + Shopping mall [ENVO:03501207]: + text: Shopping mall [ENVO:03501207] + description: A shopping center in which a large indoor pedestrian promenade + provides access to stores and other facilities. + meaning: ENVO:03501207 + is_a: Commercial building [ENVO:01001222] + Residential building [ENVO:01000933]: + text: Residential building [ENVO:01000933] + description: A human house which serves as a long-term shelter for its inhabitants + and within which they store personal property. meaning: ENVO:01000933 - Homeless shelter: - text: Homeless shelter + Homeless shelter [ENVO:03501133]: + text: Homeless shelter [ENVO:03501133] + description: An institutional building which temporarily houses homeless people. meaning: ENVO:03501133 - is_a: Residential building - Long-term care facility: - text: Long-term care facility + is_a: Residential building [ENVO:01000933] + Long-term care facility [ENVO:01000932]: + text: Long-term care facility [ENVO:01000932] + description: A building in which nursing aides and skilled nurses provide + care and treatment to residents who have significant difficulty coping with + the required activities of daily living. meaning: ENVO:01000932 - is_a: Residential building - Transport hub: - text: Transport hub + is_a: Residential building [ENVO:01000933] + Transport hub [ENVO:03501117]: + text: Transport hub [ENVO:03501117] + description: A place where passengers and cargo are exchanged between vehicles + or/and between transport modes. meaning: ENVO:03501117 - Airport: - text: Airport + Airport [ENVO:03501122]: + text: Airport [ENVO:03501122] + description: A human construction with extended facilities from which aircraft + flight operations take place. meaning: ENVO:03501122 - is_a: Transport hub - Farm: - text: Farm + is_a: Transport hub [ENVO:03501117] + Farm [ENVO:00000078]: + text: Farm [ENVO:00000078] + description: An area of land which is used for the cultivation of crops or + grazing of livestock, including any agricultural constructions therein. meaning: ENVO:00000078 - Refugee camp: - text: Refugee camp + Refugee camp [NCIT:C85867]: + text: Refugee camp [NCIT:C85867] + description: A temporary, often makeshift shelter for persons displaced by + war, political oppression, or for religious beliefs. meaning: NCIT:C85867 - Road: - text: Road + Road [ENVO:00000064]: + text: Road [ENVO:00000064] + description: An open way for the passage of vehicles, persons, or animals + on land. meaning: ENVO:00000064 - Roadside: - text: Roadside + Roadside [ENVO:01000447]: + text: Roadside [ENVO:01000447] + description: An environmental zone of varying area which is adjacent to a + road. meaning: ENVO:01000447 - Industrial plant: - text: Industrial plant + Industrial plant [ENVO:00003861]: + text: Industrial plant [ENVO:00003861] + description: A building within which goods are produced and, optionally, stored + or within which services are rendered. meaning: ENVO:00003861 - Meat processing plant: - text: Meat processing plant + Meat processing plant [ENVO:03501297]: + text: Meat processing plant [ENVO:03501297] + description: A processing plant for slaughtering, processing, packaging, labelling, + handling, and storing of food animal carcasses, parts of carcasses, and + meat products. meaning: ENVO:03501297 - is_a: Industrial plant - Pharmaceutical manufacturing plant: - text: Pharmaceutical manufacturing plant - meaning: GENEPIO:0100887 - is_a: Industrial plant - Body of water: - text: Body of water + is_a: Industrial plant [ENVO:00003861] + Pharmaceutical manufacturing plant [ENVO:03501450]: + text: Pharmaceutical manufacturing plant [ENVO:03501450] + description: An industrial building in which pharamceutical drugs are synthesised + and processed on an industrial scale. + meaning: ENVO:03501450 + is_a: Industrial plant [ENVO:00003861] + Body of water [ENVO:00000063]: + text: Body of water [ENVO:00000063] + description: An accumulation of water of varying size. meaning: ENVO:00000063 - Surface water: - text: Surface water + Surface water [ENVO:00002042]: + text: Surface water [ENVO:00002042] + description: Water that is found on the surface of an astronomical object. meaning: ENVO:00002042 - is_a: Body of water - Lake: - text: Lake + is_a: Body of water [ENVO:00000063] + Lake [ENVO:00000020]: + text: Lake [ENVO:00000020] + description: A body of water or other liquid of considerable size contained + in a depression on a landmass. meaning: ENVO:00000020 - is_a: Surface water - Stream: - text: Stream + is_a: Surface water [ENVO:00002042] + Stream [ENVO:00000023]: + text: Stream [ENVO:00000023] + description: A watercourse which is linear and flows across the solid portion + of a planetary surface. meaning: ENVO:00000023 - is_a: Surface water - River: - text: River + is_a: Surface water [ENVO:00002042] + River [ENVO:00000022]: + text: River [ENVO:00000022] + description: A stream which, through permanent or seasonal flow processes, + moves from elevated land towards lower elevations through a definite channel + and empties either into a sea, lake, or another river or ends on land as + bed seepage and evapotranspiration exceed water supply. meaning: ENVO:00000022 - is_a: Stream - Ocean: - text: Ocean + is_a: Stream [ENVO:00000023] + Ocean [ENVO:00000015]: + text: Ocean [ENVO:00000015] + description: A marine water body which is constitutes the majority of an astronomical + body's hydrosphere. meaning: ENVO:00000015 - is_a: Surface water - Sea: - text: Sea + is_a: Surface water [ENVO:00002042] + Sea [ENVO:00000016]: + text: Sea [ENVO:00000016] + description: A large expanse of saline water usually connected with an ocean. meaning: ENVO:00000016 - is_a: Surface water - Canal: - text: Canal + is_a: Surface water [ENVO:00002042] + Canal [ENVO:00000014]: + text: Canal [ENVO:00000014] + description: Artificial watercourse with no flow or a controlled flow used + for navigation, drainage or irrigation. meaning: ENVO:00000014 - is_a: Surface water - Reservoir: - text: Reservoir + is_a: Surface water [ENVO:00002042] + Reservoir [ENVO:00000025]: + text: Reservoir [ENVO:00000025] + description: An artificial body of water, often contained by a dam, constructed + for the purpose of water storage. meaning: ENVO:00000025 - is_a: Surface water - Ground water: - text: Ground water + is_a: Surface water [ENVO:00002042] + Ground water [ENVO:01001004]: + text: Ground water [ENVO:01001004] + description: Underground water which is located in pore spaces found in rock + or unconsolidated deposits such as soil, clay, or gravel. meaning: ENVO:01001004 - is_a: Body of water - Well: - text: Well + is_a: Body of water [ENVO:00000063] + Well [ENVO:00000026]: + text: Well [ENVO:00000026] + description: A cylindrical hole, pit, or tunnel drilled or dug down to a depth + from which water, oil, or gas can be pumped or brought to the surface. meaning: ENVO:00000026 - is_a: Ground water - Spring: - text: Spring + is_a: Ground water [ENVO:01001004] + Spring [ENVO:00000027]: + text: Spring [ENVO:00000027] + description: A surface landform which provides an egress for groundwater or + steam to flow out of the ground. meaning: ENVO:00000027 - is_a: Ground water - Wastewater treatment plant: - text: Wastewater treatment plant + is_a: Ground water [ENVO:01001004] + Wastewater treatment plant [ENVO:00002272]: + text: Wastewater treatment plant [ENVO:00002272] + description: A plant in which wastewater is treated. meaning: ENVO:00002272 - Waste stabilization pond (lagoon): - text: Waste stabilization pond (lagoon) + Influent pump station [ENVO:03501465]: + text: Influent pump station [ENVO:03501465] + description: A facility within a wastewater treatment plant designed to receive + and lift incoming wastewater (influent) to a higher elevation for subsequent + treatment processes. The influent pump station typically houses pumps, controls, + and associated equipment necessary to move wastewater through the treatment + process. + meaning: ENVO:03501465 + is_a: Wastewater treatment plant [ENVO:00002272] + Grit chamber [ENVO:03501467]: + text: Grit chamber [ENVO:03501467] + description: A physical structure or equipment within a wastewater treatment + plant where grit and other heavy inorganic particles are removed from the + influent through sedimentation. The grit chamber helps protect downstream + equipment from abrasion and reduces the accumulation of grit in subsequent + treatment processes. + meaning: ENVO:03501467 + is_a: Wastewater treatment plant [ENVO:00002272] + Communitor [ENVO:03501472]: + text: Communitor [ENVO:03501472] + description: A mechanical device designed to reduce the size of solid materials + in wastewater. It uses rotating drums or cutting blades to shred large debris + into smaller pieces, protecting downstream equipment and enhancing the efficiency + of subsequent treatment processes. + meaning: ENVO:03501472 + is_a: Wastewater treatment plant [ENVO:00002272] + Primary clarifer [ENVO:03501468]: + text: Primary clarifer [ENVO:03501468] + description: A large, sedimentation tank in a wastewater treatment plant where + the primary stage of solids separation occurs. In the primary clarifier, + suspended solids settle to the bottom as sludge, while lighter materials, + such as oils and greases, rise to the surface for removal. + meaning: ENVO:03501468 + is_a: Wastewater treatment plant [ENVO:00002272] + Aeration tank [ENVO:03501469]: + text: Aeration tank [ENVO:03501469] + description: A tank or basin in a wastewater treatment plant where oxygen + is introduced into the wastewater to promote the growth of aerobic microorganisms. + These microorganisms break down organic pollutants in the water, facilitating + the biological treatment process. The aeration tank is essential for reducing + the organic load before the water moves to subsequent treatment stages. + meaning: ENVO:03501469 + is_a: Wastewater treatment plant [ENVO:00002272] + Secondary clarifer [ENVO:03501471]: + text: Secondary clarifer [ENVO:03501471] + description: A sedimentation tank in a wastewater treatment plant used in + the secondary treatment process. The secondary clarifier allows for the + settling and removal of biological floc or sludge produced in the aeration + tank, further clarifying the treated wastewater before discharge or further + treatment. + meaning: ENVO:03501471 + is_a: Wastewater treatment plant [ENVO:00002272] + Sludge dryer [ENVO:03501473]: + text: Sludge dryer [ENVO:03501473] + description: A device designed to remove moisture from sludge through thermal + drying methods, resulting in a dry, granular material that is easier to + handle, store, or utilize in other applications. + meaning: ENVO:03501473 + is_a: Wastewater treatment plant [ENVO:00002272] + Waste stabilization pond (lagoon) [ENVO:03600076]: + text: Waste stabilization pond (lagoon) [ENVO:03600076] + description: A human construction which confines wastewater in a depression + enclosed by earthen structures. meaning: ENVO:03600076 - Sewer: - text: Sewer + Sewer [ENVO:01000924]: + text: Sewer [ENVO:01000924] + description: An artificial channel which transports unwanted water or waste + liquids away from their source, either to a more useful area, a receptacle, + or into sewers or stormwater mains as waste discharge to be released or + processed. meaning: ENVO:01000924 - Transportation vehicle: - text: Transportation vehicle + Transportation vehicle [ENVO:01000604]: + text: Transportation vehicle [ENVO:01000604] + description: A vehicle is a mobile machine which transports people or cargo. meaning: ENVO:01000604 - Boat: - text: Boat + Boat [ENVO:01000608]: + text: Boat [ENVO:01000608] + description: A boat is a watercraft of any size which is able to float or + plane on water. meaning: ENVO:01000608 - is_a: Transportation vehicle - Airplane: - text: Airplane + is_a: Transportation vehicle [ENVO:01000604] + Airplane [ENVO:03501349]: + text: Airplane [ENVO:03501349] + description: An aircraft which 1) has fixed wings and 2) is propelled by a + thrust from a jet engine, propeller, or rocket engine. meaning: ENVO:03501349 - is_a: Transportation vehicle + is_a: Transportation vehicle [ENVO:01000604] environmental material menu: name: environmental material menu + title: environmental material menu permissible_values: - Surface water: - text: Surface water + Bar screen [ENVO:03501474]: + text: Bar screen [ENVO:03501474] + description: A mechanical filter used to remove large objects, such as rags + and plastics, from wastewater + meaning: ENVO:03501474 + Surface water [ENVO:00002042]: + text: Surface water [ENVO:00002042] + description: Water that is found on the surface of an astronomical object. meaning: ENVO:00002042 - Wastewater: - text: Wastewater + Wastewater [ENVO:00002001]: + text: Wastewater [ENVO:00002001] + description: Water that has been adversely affected in quality by anthropogenic + influence meaning: ENVO:00002001 - Wastewater sediment: - text: Wastewater sediment - meaning: GENEPIO:0100890 - Sludge: - text: Sludge + Wastewater sediment [ENVO:03501456]: + text: Wastewater sediment [ENVO:03501456] + description: A sediment which is removed from waste water during a waste water + treatment process. + meaning: ENVO:03501456 + Sludge [ENVO:00002044]: + text: Sludge [ENVO:00002044] + description: The residual semi-solid material left from domestic or industrial + processes, or wastewater treatment processes. meaning: ENVO:00002044 - Primary sludge: - text: Primary sludge + Primary sludge [ENVO:00002057]: + text: Primary sludge [ENVO:00002057] + description: Sludge generated from the initial processes (i.e., precipitation, + sedimentation) of wastewater treatment. meaning: ENVO:00002057 - is_a: Sludge - Secondary sludge: - text: Secondary sludge + is_a: Sludge [ENVO:00002044] + Secondary sludge [ENVO:00002058]: + text: Secondary sludge [ENVO:00002058] + description: Activated waste biomass generated during wastewater treatment. meaning: ENVO:00002058 - is_a: Sludge - Wastewater effluent: - text: Wastewater effluent - meaning: GENEPIO:0100891 - Primary wastewater effluent: - text: Primary wastewater effluent + is_a: Sludge [ENVO:00002044] + Wastewater effluent [ENVO:03501457]: + text: Wastewater effluent [ENVO:03501457] + description: A wastewater which has been discharged from any item of equipment + at a stage of a wastewater treatment process. + meaning: ENVO:03501457 + Primary wastewater effluent [GENEPIO:0100892]: + text: Primary wastewater effluent [GENEPIO:0100892] + description: A wastewater effluent which has been discharged from a primary + clarifier after the first stage of sedimentation. meaning: GENEPIO:0100892 - is_a: Wastewater effluent - Secondary wastewater effluent: - text: Secondary wastewater effluent + is_a: Wastewater effluent [ENVO:03501457] + Secondary wastewater effluent [GENEPIO:0100893]: + text: Secondary wastewater effluent [GENEPIO:0100893] + description: A wastewater effluent which has been discharged from a secondary + clarifier after the second stage of sedimentation. meaning: GENEPIO:0100893 - is_a: Wastewater effluent - environmental material properties menu: - name: environmental material properties menu + is_a: Wastewater effluent [ENVO:03501457] + EnvironmentalMaterialPropertiesMenu: + name: EnvironmentalMaterialPropertiesMenu + title: environmental material properties menu permissible_values: - Fluid (stagnant): - text: Fluid (stagnant) + Fluid (stagnant) [GENEPIO:0101004]: + text: Fluid (stagnant) [GENEPIO:0101004] + description: A quality of a body of water wherein it has no current or flow. meaning: GENEPIO:0101004 - Fluid (slow): - text: Fluid (slow) + Fluid (slow) [GENEPIO:0101005]: + text: Fluid (slow) [GENEPIO:0101005] + description: A quality of a body of water wherein there is a slow flow. meaning: GENEPIO:0101005 - Fluid (fast): - text: Fluid (fast) + Fluid (fast) [GENEPIO:0101006]: + text: Fluid (fast) [GENEPIO:0101006] + description: A quality of a body of water wherein there is a fast flow. meaning: GENEPIO:0101006 - Contamination: - text: Contamination + Contamination [PATO:0015031]: + text: Contamination [PATO:0015031] + description: The presence of a constituent, impurity, or some other undesirable + element that spoils, corrupts, infects, makes unfit, or makes inferior a + material, physical body, natural environment, place of human occupancy, + or other material entity. meaning: PATO:0015031 - Fecal-contaminated: - text: Fecal-contaminated + Fecal-contaminated [GENEPIO:0101010]: + text: Fecal-contaminated [GENEPIO:0101010] + description: A contamination quality in which fecal matter is a key component + of the contamination. meaning: GENEPIO:0101010 - is_a: Contamination - Liquid: - text: Liquid + is_a: Contamination [PATO:0015031] + Liquid [PATO:0001735]: + text: Liquid [PATO:0001735] + description: A physical quality inhering in a bearer by virtue of the bearer's + parts having the arrangement which exhibits characteristics of liquids. meaning: PATO:0001735 - Slurry-like: - text: Slurry-like + Slurry-like [GENEPIO:0101007]: + text: Slurry-like [GENEPIO:0101007] + description: An quality in which the fluid like material is more viscous due + to the suspension of insoluble solid particles. meaning: GENEPIO:0101007 - Semi-solid: - text: Semi-solid + Semi-solid [NCIT:C149895]: + text: Semi-solid [NCIT:C149895] + description: A state of matter consisting of molecules in a non-rigid structure + that can retain its shape and volume but that is not resistant to such change. meaning: NCIT:C149895 - Solid: - text: Solid + Solid [PATO:0001736]: + text: Solid [PATO:0001736] + description: A quality in which an object or material exhibits characteristics + of solids, lacking movement or flow. meaning: PATO:0001736 - Treated: - text: Treated + Treated [GENEPIO:0101008]: + text: Treated [GENEPIO:0101008] + description: A quality which denotes an altered state of an item resulting + from purposeful interventions or processes. meaning: GENEPIO:0101008 - Untreated: - text: Untreated + Untreated [GENEPIO:0101009]: + text: Untreated [GENEPIO:0101009] + description: A quality which denotes an absence of purposeful intervention + or processes on an item. meaning: GENEPIO:0101009 - wastewater system type menu: - name: wastewater system type menu + WastewaterSystemTypeMenu: + name: WastewaterSystemTypeMenu + title: wastewater system type menu permissible_values: - Combined sewer system: - text: Combined sewer system - Sanitary sewer system: - text: Sanitary sewer system - Waste stabilization pond: - text: Waste stabilization pond + Combined sewer system [ENVO:03501453]: + text: Combined sewer system [ENVO:03501453] + description: A sewered sanitation system that collects rainwater runoff, domestic + sewage, and industrial wastewater. + meaning: ENVO:03501453 + Sanitary sewer system [ENVO:03501454]: + text: Sanitary sewer system [ENVO:03501454] + description: A sewered sanitation system that collects only domestic sewage. + meaning: ENVO:03501454 + Waste stabilization pond [ENVO:03600076]: + text: Waste stabilization pond [ENVO:03600076] + description: A human construction which confines wastewater in a depression + enclosed by earthen structures. meaning: ENVO:03600076 - Latrine: - text: Latrine + Latrine [ENVO:01000519]: + text: Latrine [ENVO:01000519] + description: A latrine is a toilet which is of simple construction (relative + to a flush or chemical toilet) and typically intended for communal use. meaning: ENVO:01000519 - Septic tank: - text: Septic tank - Cesspit: - text: Cesspit - Composting toilet: - text: Composting toilet + Septic tank [ENVO:03501451]: + text: Septic tank [ENVO:03501451] + description: An underground holding and treatment site for domestic wastewater. + meaning: ENVO:03501451 + Cesspit [ENVO:03501452]: + text: Cesspit [ENVO:03501452] + description: A pit for the disposal and storage of sewage. + meaning: ENVO:03501452 + Composting toilet [ENVO:01000550]: + text: Composting toilet [ENVO:01000550] + description: A composting toilet fixture is a dry toilet fixture in which + managed, aerobic decomposition converts human excreta into organic matter + suitable for the fertilisation or amendment of soils. meaning: ENVO:01000550 - Plumbing drain: - text: Plumbing drain + Sewer drain [ENVO:01000924]: + text: Sewer drain [ENVO:01000924] + description: An artificial channel which transports unwanted water or waste + liquids away from their source, either to a more useful area, a receptacle, + or into sewers or stormwater mains as waste discharge to be released or + processed. meaning: ENVO:01000924 - experimental specimen role type menu: - name: experimental specimen role type menu + ExperimentalSpecimenRoleTypeMenu: + name: ExperimentalSpecimenRoleTypeMenu + title: experimental specimen role type menu permissible_values: - Positive experimental control: - text: Positive experimental control + Positive experimental control [GENEPIO:0101018]: + text: Positive experimental control [GENEPIO:0101018] + description: A control specimen that is expected to yield a positive result, + to establish a reference baseline for an experiment. meaning: GENEPIO:0101018 - Negative experimental control: - text: Negative experimental control + Negative experimental control [GENEPIO:0101019]: + text: Negative experimental control [GENEPIO:0101019] + description: A control specimen that is expected to yield a negative result, + to establish a reference baseline for an experiment meaning: GENEPIO:0101019 - Technical replicate: - text: Technical replicate + Technical replicate [EFO:0002090]: + text: Technical replicate [EFO:0002090] + description: A technical replicate is a replicate role where the same BioSample + is use e.g. the same pool of RNA used to assess technical (as opposed to + biological) variation within an experiment. meaning: EFO:0002090 - Biological replicate: - text: Biological replicate + Biological replicate [EFO:0002091]: + text: Biological replicate [EFO:0002091] + description: A biological replicate is a replicate role that consists of independent + biological replicates made from different individual biosamples. meaning: EFO:0002091 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: - Grab sampler: - text: Grab sampler + Grab sampler [GENEPIO:0100941]: + text: Grab sampler [GENEPIO:0100941] + description: A specimen collection device which is used to collect discrete, + instantaneous samples of water, soil, or other substances from a specific + point in a body of water or at a specific location. meaning: GENEPIO:0100941 - Core sampling device: - text: Core sampling device + Bag filtration device [GENEPIO:0102027]: + text: Bag filtration device [GENEPIO:0102027] + meaning: GENEPIO:0102027 + is_a: Grab sampler [GENEPIO:0100941] + Core sampling device [GENEPIO:0100943]: + text: Core sampling device [GENEPIO:0100943] + description: A grab sampler that captures a vertical section of the substrate + matrix of fecal sludge. meaning: GENEPIO:0100943 - is_a: Grab sampler - Vacuum sludge sampling device: - text: Vacuum sludge sampling device + is_a: Grab sampler [GENEPIO:0100941] + Vacuum sludge sampling device [GENEPIO:0100944]: + text: Vacuum sludge sampling device [GENEPIO:0100944] + description: A grab sampler that takes a sample at a designated depth with + minimal disturbance to surrounding layers. meaning: GENEPIO:0100944 - is_a: Grab sampler - Cone-shaped sampling device: - text: Cone-shaped sampling device + is_a: Grab sampler [GENEPIO:0100941] + Cone-shaped sampling device [GENEPIO:0100945]: + text: Cone-shaped sampling device [GENEPIO:0100945] + description: A grab sample that has a controlled valve that opens to take + a sample from a specific depth, then closes to bring the sample out. meaning: GENEPIO:0100945 - is_a: Grab sampler - Horizontal grab sampling device: - text: Horizontal grab sampling device + is_a: Grab sampler [GENEPIO:0100941] + Horizontal grab sampling device [GENEPIO:0100946]: + text: Horizontal grab sampling device [GENEPIO:0100946] + description: A grab sampler in which the container for the sample is mounted + on the end of a rod, which is suitable for collecting discharge from a pipe + or truck. meaning: GENEPIO:0100946 - is_a: Grab sampler - Vertical grab sampling device: - text: Vertical grab sampling device + is_a: Grab sampler [GENEPIO:0100941] + Vertical grab sampling device [GENEPIO:0100947]: + text: Vertical grab sampling device [GENEPIO:0100947] + description: A grab sampler in which the container for the sample is mounted + on the end of a rod, which is suitable for collecting waste from a tank. meaning: GENEPIO:0100947 - is_a: Grab sampler - Composite sampler: - text: Composite sampler + is_a: Grab sampler [GENEPIO:0100941] + Composite sampler [GENEPIO:0100942]: + text: Composite sampler [GENEPIO:0100942] + description: A specimen collection device that collects material over different + times or locations. meaning: GENEPIO:0100942 - Passive (trap) sampler: - text: Passive (trap) sampler + Passive (trap) sampler [GENEPIO:0100948]: + text: Passive (trap) sampler [GENEPIO:0100948] + description: A composite sampler that passively collects a sample without + use of electricity or a battery. meaning: GENEPIO:0100948 - is_a: Composite sampler - Moore swab: - text: Moore swab + is_a: Composite sampler [GENEPIO:0100942] + Moore swab [GENEPIO:0100949]: + text: Moore swab [GENEPIO:0100949] + description: A composite sampler which consists of gauze pad tied with string, + suspended in flowing water or wastewater, in order to collect a wastewater + sample. meaning: GENEPIO:0100949 - is_a: Passive (trap) sampler - Automatic composite sampler: - text: Automatic composite sampler + is_a: Passive (trap) sampler [GENEPIO:0100948] + Automatic composite sampler [GENEPIO:0100950]: + text: Automatic composite sampler [GENEPIO:0100950] + description: A composite sampler which is automated to collect and store multiple + wastewater samples across multiple time points. meaning: GENEPIO:0100950 - is_a: Composite sampler - Automatic flow-proportional sampler: - text: Automatic flow-proportional sampler + is_a: Composite sampler [GENEPIO:0100942] + Automatic flow-proportional sampler [GENEPIO:0100951]: + text: Automatic flow-proportional sampler [GENEPIO:0100951] + description: A composite sampler which is automated to collect and store multiple + wastewater samples in a manner proportional to flow. meaning: GENEPIO:0100951 - is_a: Automatic composite sampler - Automatic sequential (time-proportional) sampler: - text: Automatic sequential (time-proportional) sampler + is_a: Automatic composite sampler [GENEPIO:0100950] + Automatic sequential (time-proportional) sampler [GENEPIO:0100952]: + text: Automatic sequential (time-proportional) sampler [GENEPIO:0100952] + description: A composite sampler which is automated to collect and combine + multiple samples of equal volume taken at a set time interval. meaning: GENEPIO:0100952 - is_a: Automatic composite sampler - collection method menu: - name: collection method menu + is_a: Automatic composite sampler [GENEPIO:0100950] + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: - Grab sampling: - text: Grab sampling + Grab sampling [GENEPIO:0100953]: + text: Grab sampling [GENEPIO:0100953] + description: An environmental material collection process in which a water + or soil sample is taken at a single point of time using a container type + known as a grab sampler. meaning: GENEPIO:0100953 - Composite sampling: - text: Composite sampling + Bag Mediated Filtration [GENEPIO:0102028]: + text: Bag Mediated Filtration [GENEPIO:0102028] + meaning: GENEPIO:0102028 + Composite sampling [GENEPIO:0100954]: + text: Composite sampling [GENEPIO:0100954] + description: An environmental material collection process in which mutliple + water or soil samples are taken at different time points and combined to + produce a composite. Samples can be collected continuously or at discrete + time points. meaning: GENEPIO:0100954 - Passive composite sampling: - text: Passive composite sampling + Passive composite sampling [GENEPIO:0100955]: + text: Passive composite sampling [GENEPIO:0100955] + description: A method of composite sampling in which a continuous sample is + collected passively without electrical input minimizing cost. meaning: GENEPIO:0100955 - is_a: Composite sampling - Automatic composite sampling: - text: Automatic composite sampling + is_a: Composite sampling [GENEPIO:0100954] + Automatic composite sampling [GENEPIO:0100956]: + text: Automatic composite sampling [GENEPIO:0100956] + description: A method of composite sampling which utilizes an automated system + to collect multiple samples, continuously or at discrete timepoints. meaning: GENEPIO:0100956 - is_a: Composite sampling - Manual composite sampling: - text: Manual composite sampling + is_a: Composite sampling [GENEPIO:0100954] + Manual composite sampling [GENEPIO:0100957]: + text: Manual composite sampling [GENEPIO:0100957] + description: A method of composite sampling in which multiple grab samples + from discrete time points are taken and then combined to produce a single + composite sample. meaning: GENEPIO:0100957 - is_a: Composite sampling - water catchment area human population range menu: - name: water catchment area human population range menu + is_a: Composite sampling [GENEPIO:0100954] + WaterCatchmentAreaHumanPopulationRangeMenu: + name: WaterCatchmentAreaHumanPopulationRangeMenu + title: water catchment area human population range menu permissible_values: <10 people: text: <10 people + description: An estimation of population size for a group smaller than 10 + people. 10 - 100 people: text: 10 - 100 people + description: An estimation of population size for a group smaller than 100 + people and larger than 10 people. 100 - 1,000 people: text: 100 - 1,000 people + description: An estimation of population size for a group smaller than 1,000 + people and larger than 100 people. 1,000 - 10,000 people: text: 1,000 - 10,000 people + description: An estimation of population size for a group smaller than 10,000 + people and larger than 1,000 people. 10,000 - 100,000 people: text: 10,000 - 100,000 people + description: An estimation of population size for a group smaller than 100,000 + people and larger than 10,000 people. 100,000 - 1,000,000 people: text: 100,000 - 1,000,000 people + description: An estimation of population size for a group smaller than 1,000,000 + people and larger than 100,000 people. 1,000,000+ people: text: 1,000,000+ people - water catchment area human population density unit menu: - name: water catchment area human population density unit menu + description: An estimation of population size for a group larger than 1,000,000 + people. + WaterCatchmentAreaHumanPopulationDensityUnitMenu: + name: WaterCatchmentAreaHumanPopulationDensityUnitMenu + title: water catchment area human population density unit menu permissible_values: - persons per square mile: - text: persons per square mile + persons per square mile [GENEPIO:0100989]: + text: persons per square mile [GENEPIO:0100989] + description: A unit of population density that describes the average number + of people in a square mile of a given area. meaning: GENEPIO:0100989 - persons per square kilometer: - text: persons per square kilometer + persons per square kilometer [GENEPIO:0100990]: + text: persons per square kilometer [GENEPIO:0100990] + description: A unit of population density that describes the average number + of people in a square kilometer of a given area. meaning: GENEPIO:0100990 - residents per square mile: - text: residents per square mile + residents per square mile [GENEPIO:0100991]: + text: residents per square mile [GENEPIO:0100991] + description: A unit of population density that describes the average number + of registered residents in a square mile of a given area. meaning: GENEPIO:0100991 - residents per square kilometer: - text: residents per square kilometer + residents per square kilometer [GENEPIO:0100992]: + text: residents per square kilometer [GENEPIO:0100992] + description: A unit of population density that describes the average number + of registered residents in a square kilometer of a given area. meaning: GENEPIO:0100992 - populated area type menu: - name: populated area type menu + PopulatedAreaTypeMenu: + name: PopulatedAreaTypeMenu + title: populated area type menu permissible_values: - Suburban: - text: Suburban + Suburban [GSSO:011077]: + text: Suburban [GSSO:011077] + description: A mixed-use or residential area, existing either as part of a + city/urban area, or as a separate residential community within commuting + distance of one. Suburbs might have their own political or legal jurisdiction, + especially in the United States, but this is not always the case, especially + in the United Kingdom where most suburbs are located within the administrative + boundaries of cities. meaning: GSSO:011077 - Rural: - text: Rural + Rural [GSSO:011078]: + text: Rural [GSSO:011078] + description: A geographic area that is located outside towns and cities. Rural + areas are primarily used for agriculture or pastoralism and may contain + rural settlements. meaning: GSSO:011078 - Urban: - text: Urban + Urban [GSSO:011080]: + text: Urban [GSSO:011080] + description: A human settlement with a high population density and infrastructure + of built environment. Urban areas are created through urbanization and are + categorized by urban morphology as cities, towns, conurbations or suburbs. + In urbanism, the term contrasts to rural areas such as villages and hamlets; + in urban sociology or urban anthropology it contrasts with natural environment. meaning: GSSO:011080 - sampling weather conditions menu: - name: sampling weather conditions menu + SamplingWeatherConditionsMenu: + name: SamplingWeatherConditionsMenu + title: sampling weather conditions menu permissible_values: - Cloudy/Overcast: - text: Cloudy/Overcast + Cloudy/Overcast [ENVO:03501418]: + text: Cloudy/Overcast [ENVO:03501418] + description: Atmospheric weather in which the sky is mostly or completely + obscured by clouds. meaning: ENVO:03501418 - Partially cloudy: - text: Partially cloudy + Partially cloudy [ENVO:03501419]: + text: Partially cloudy [ENVO:03501419] + description: Atmospheric weather in which the sky is partially obscured by + clouds. meaning: ENVO:03501419 - is_a: Cloudy/Overcast - Drizzle: - text: Drizzle + is_a: Cloudy/Overcast [ENVO:03501418] + Drizzle [ENVO:03501420]: + text: Drizzle [ENVO:03501420] + description: An aggregate of water drops smaller than those of rain which + falls on a planetary surface during a precipitation process. meaning: ENVO:03501420 - Fog: - text: Fog + Fog [ENVO:01000844]: + text: Fog [ENVO:01000844] + description: A visible mass of cloud water droplets or ice crystals suspended + in the air at or near the surface of an astronomical body. meaning: ENVO:01000844 - Rain: - text: Rain + Rain [ENVO:01001564]: + text: Rain [ENVO:01001564] + description: An aggregate of raindrops falling to a planetary surface during + a precipitation process. meaning: ENVO:01001564 - Snow: - text: Snow + Snow [ENVO:01000406]: + text: Snow [ENVO:01000406] + description: Snow is an environmental material which is primarily composed + of flakes of crystalline water ice. meaning: ENVO:01000406 - Storm: - text: Storm + Storm [ENVO:01000876]: + text: Storm [ENVO:01000876] + description: A storm is an environmental process in which an environmental + system and the processes it participates in are strongly perturbed by external + forcings. These forcings typically increase the rates of processes unfolding + in the system, relative to their normal rates. meaning: ENVO:01000876 - Sunny/Clear: - text: Sunny/Clear + Sunny/Clear [ENVO:03501421]: + text: Sunny/Clear [ENVO:03501421] + description: Atmospheric weather in which the sun can be seen to shine brightly. meaning: ENVO:03501421 - presampling weather conditions menu: - name: presampling weather conditions menu + PresamplingWeatherConditionsMenu: + name: PresamplingWeatherConditionsMenu + title: presampling weather conditions menu permissible_values: - Cloudy/Overcast: - text: Cloudy/Overcast + Cloudy/Overcast [ENVO:03501418]: + text: Cloudy/Overcast [ENVO:03501418] + description: Atmospheric weather in which the sky is mostly or completely + obscured by clouds. meaning: ENVO:03501418 - Partially cloudy: - text: Partially cloudy + Partially cloudy [ENVO:03501419]: + text: Partially cloudy [ENVO:03501419] + description: Atmospheric weather in which the sky is partially obscured by + clouds. meaning: ENVO:03501419 - is_a: Cloudy/Overcast - Drizzle: - text: Drizzle + is_a: Cloudy/Overcast [ENVO:03501418] + Drizzle [ENVO:03501420]: + text: Drizzle [ENVO:03501420] + description: An aggregate of water drops smaller than those of rain which + falls on a planetary surface during a precipitation process. meaning: ENVO:03501420 - Fog: - text: Fog + Fog [ENVO:01000844]: + text: Fog [ENVO:01000844] + description: A visible mass of cloud water droplets or ice crystals suspended + in the air at or near the surface of an astronomical body. meaning: ENVO:01000844 - Rain: - text: Rain + Rain [ENVO:01001564]: + text: Rain [ENVO:01001564] + description: An aggregate of raindrops falling to a planetary surface during + a precipitation process. meaning: ENVO:01001564 - Snow: - text: Snow + Snow [ENVO:01000406]: + text: Snow [ENVO:01000406] + description: Snow is an environmental material which is primarily composed + of flakes of crystalline water ice. meaning: ENVO:01000406 - Storm: - text: Storm + Storm [ENVO:01000876]: + text: Storm [ENVO:01000876] + description: A storm is an environmental process in which an environmental + system and the processes it participates in are strongly perturbed by external + forcings. These forcings typically increase the rates of processes unfolding + in the system, relative to their normal rates. meaning: ENVO:01000876 - Sunny/Clear: - text: Sunny/Clear + Sunny/Clear [ENVO:03501421]: + text: Sunny/Clear [ENVO:03501421] + description: Atmospheric weather in which the sun can be seen to shine brightly. meaning: ENVO:03501421 - precipitation measurement unit menu: - name: precipitation measurement unit menu + PrecipitationMeasurementUnitMenu: + name: PrecipitationMeasurementUnitMenu + title: precipitation measurement unit menu permissible_values: - millimeter (mm): - text: millimeter (mm) + millimeter (mm) [UO:0000016]: + text: millimeter (mm) [UO:0000016] + description: A length unit which is defined as one thousandth of a meter. meaning: UO:0000016 - centimeter (cm): - text: centimeter (cm) + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m meaning: UO:0000015 - meter (m): - text: meter (m) + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. meaning: UO:0000008 - inch (in): - text: inch (in) + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. meaning: UO:0010011 - foot (ft): - text: foot (ft) + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. meaning: UO:0010013 - air pressure measurement unit menu: - name: air pressure measurement unit menu + AirPressureMeasurementUnitMenu: + name: AirPressureMeasurementUnitMenu + title: air pressure measurement unit menu permissible_values: - atmosphere (atm): - text: atmosphere (atm) + atmosphere (atm) [EFO:0005212]: + text: atmosphere (atm) [EFO:0005212] + description: A non-SI unit of pressure defined as 101,325 pascals (Pa). meaning: EFO:0005212 bar: text: bar - pascal: - text: pascal + pascal [UO:0000110]: + text: pascal [UO:0000110] + description: An SI unit of pressure defined as one newton per square meter + (N/m^2). meaning: UO:0000110 - ambient temperature measurement unit menu: - name: ambient temperature measurement unit menu + AmbientTemperatureMeasurementUnitMenu: + name: AmbientTemperatureMeasurementUnitMenu + title: ambient temperature measurement unit menu permissible_values: - degree Fahrenheit (F): - text: degree Fahrenheit (F) + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. meaning: UO:0000195 - degree Celsius (C): - text: degree Celsius (C) + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. meaning: UO:0000027 - total daily flow rate measurement unit menu: - name: total daily flow rate measurement unit menu + TotalDailyFlowRateMeasurementUnitMenu: + name: TotalDailyFlowRateMeasurementUnitMenu + title: total daily flow rate measurement unit menu permissible_values: cubic meter per second (m^3/s): text: cubic meter per second (m^3/s) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one second. cubic meter per minute (m^3/min): text: cubic meter per minute (m^3/min) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one minute. cubic meter per hour (m^3/h): text: cubic meter per hour (m^3/h) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one hour. liter per second (L/s): text: liter per second (L/s) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one second. liter per minute (L/min): text: liter per minute (L/min) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one minute. liter per hour (L/h): text: liter per hour (L/h) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one hour. liter per day (L/day): text: liter per day (L/day) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one day. million gallons per day (MGD): text: million gallons per day (MGD) - instantaneous flow rate measurement unit menu: - name: instantaneous flow rate measurement unit menu + description: A volumetric flow rate unit which is the measure of the volume + of one million gallons of matter crosses a given surface during the period + of time equal to one day. + InstantaneousFlowRateMeasurementUnitMenu: + name: InstantaneousFlowRateMeasurementUnitMenu + title: instantaneous flow rate measurement unit menu permissible_values: cubic meter per second (m^3/s): text: cubic meter per second (m^3/s) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one second. cubic meter per minute (m^3/min): text: cubic meter per minute (m^3/min) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one minute. cubic meter per hour (m^3/h): text: cubic meter per hour (m^3/h) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one hour. liter per second (L/s): text: liter per second (L/s) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one second. liter per minute (L/min): text: liter per minute (L/min) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one minute. liter per hour (L/h): text: liter per hour (L/h) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one hour. liter per day (L/day): text: liter per day (L/day) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one day. million gallons per day (MGD): text: million gallons per day (MGD) - turbidity measurement unit menu: - name: turbidity measurement unit menu + description: A volumetric flow rate unit which is the measure of the volume + of one million gallons of matter crosses a given surface during the period + of time equal to one day. + TurbidityMeasurementUnitMenu: + name: TurbidityMeasurementUnitMenu + title: turbidity measurement unit menu permissible_values: nephelometric turbidity unit (NTU): text: nephelometric turbidity unit (NTU) - formazin nephelometric unit (FNU): - text: formazin nephelometric unit (FNU) + description: A measure of turbidity calculated by using a nephelometer to + compare how white light is scattered in a water sample. + formazin nephelometric unit (FNU) [UO:0000318]: + text: formazin nephelometric unit (FNU) [UO:0000318] + description: A measure of turbidity calculated by comparing how infrared light + is scattered in a water sample against the amount of infrared light scattered + in a reference solution containing formazin. meaning: UO:0000318 - dissolved oxygen measurement unit menu: - name: dissolved oxygen measurement unit menu + DissolvedOxygenMeasurementUnitMenu: + name: DissolvedOxygenMeasurementUnitMenu + title: dissolved oxygen measurement unit menu permissible_values: - milligram per liter (mg/L): - text: milligram per liter (mg/L) + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. meaning: UO:0000273 - kilogram per cubic meter (kg/m^3): - text: kilogram per cubic meter (kg/m^3) + kilogram per cubic meter (kg/m^3) [UO:0000083]: + text: kilogram per cubic meter (kg/m^3) [UO:0000083] + description: An SI unit of density that is one thousandth of the density of + water. meaning: UO:0000083 - part per million (ppm): - text: part per million (ppm) + part per million (ppm) [UO:0000169]: + text: part per million (ppm) [UO:0000169] + description: A unitless measure of density that represents one item out of + a million. meaning: UO:0000169 - oxygen reduction potential (ORP) measurement unit menu: - name: oxygen reduction potential (ORP) measurement unit menu + OxygenReductionPotentialOrpMeasurementUnitMenu: + name: OxygenReductionPotentialOrpMeasurementUnitMenu + title: oxygen reduction potential (ORP) measurement unit menu permissible_values: - milliVolt (mV): - text: milliVolt (mV) + milliVolt (mV) [UO:0000247]: + text: milliVolt (mV) [UO:0000247] + description: A non-SI unit of electromotive force that is one thousandth of + a volt. meaning: UO:0000247 - chemical oxygen demand (COD) measurement unit menu: - name: chemical oxygen demand (COD) measurement unit menu + ChemicalOxygenDemandCodMeasurementUnitMenu: + name: ChemicalOxygenDemandCodMeasurementUnitMenu + title: chemical oxygen demand (COD) measurement unit menu permissible_values: - milligram per liter (mg/L): - text: milligram per liter (mg/L) + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. meaning: UO:0000273 - carbonaceous biochemical oxygen demand (CBOD) measurement unit menu: - name: carbonaceous biochemical oxygen demand (CBOD) measurement unit menu + CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu: + name: CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu + title: carbonaceous biochemical oxygen demand (CBOD) measurement unit menu permissible_values: - milligram per liter (mg/L): - text: milligram per liter (mg/L) + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. meaning: UO:0000273 - total suspended solids (TSS) measurement unit menu: - name: total suspended solids (TSS) measurement unit menu + TotalSuspendedSolidsTssMeasurementUnitMenu: + name: TotalSuspendedSolidsTssMeasurementUnitMenu + title: total suspended solids (TSS) measurement unit menu permissible_values: - percent (%): - text: percent (%) + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. meaning: UO:0000187 - gram per liter (g/L): - text: gram per liter (g/L) + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. meaning: UO:0000175 - total dissolved solids (TDS) measurement unit menu: - name: total dissolved solids (TDS) measurement unit menu + TotalDissolvedSolidsTdsMeasurementUnitMenu: + name: TotalDissolvedSolidsTdsMeasurementUnitMenu + title: total dissolved solids (TDS) measurement unit menu permissible_values: - percent (%): - text: percent (%) + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. meaning: UO:0000187 - gram per liter (g/L): - text: gram per liter (g/L) + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. meaning: UO:0000175 - total solids (TS) measurement unit menu: - name: total solids (TS) measurement unit menu + TotalSolidsTsMeasurementUnitMenu: + name: TotalSolidsTsMeasurementUnitMenu + title: total solids (TS) measurement unit menu permissible_values: - percent (%): - text: percent (%) + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. meaning: UO:0000187 - gram per liter (g/L): - text: gram per liter (g/L) + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. meaning: UO:0000175 - alkalinity measurement unit menu: - name: alkalinity measurement unit menu + AlkalinityMeasurementUnitMenu: + name: AlkalinityMeasurementUnitMenu + title: alkalinity measurement unit menu permissible_values: milliequivalent per liter (meq/L): text: milliequivalent per liter (meq/L) - milligram per liter (mg/L): - text: milligram per liter (mg/L) + description: A unit of ion concentration that represents chemical activity + per volume. + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. meaning: UO:0000273 - parts per million: - text: parts per million + parts per million [UO:0000169]: + text: parts per million [UO:0000169] + description: A unitless measure of density that represents one item out of + a million. meaning: UO:0000169 - conductivity measurement unit menu: - name: conductivity measurement unit menu + ConductivityMeasurementUnitMenu: + name: ConductivityMeasurementUnitMenu + title: conductivity measurement unit menu permissible_values: milliSiemen per centimeter (mS/cm): text: milliSiemen per centimeter (mS/cm) + description: A non-SI unit of electrical conductivity that is equivalent to + one tenth of a Siemen per meter (S/m). "microSiemen per centimeter (\u03BCS/cm)": text: "microSiemen per centimeter (\u03BCS/cm)" + description: A non-SI unit of electrical conductivity that is equivalent to + one ten thousandth of a Siemen per meter (S/m). Siemen per meter (S/m): text: Siemen per meter (S/m) - salinity measurement unit menu: - name: salinity measurement unit menu + description: An SI unit of electrical conductivity that is equivalent to an + ampere per volt per meter (A/v/m). + SalinityMeasurementUnitMenu: + name: SalinityMeasurementUnitMenu + title: salinity measurement unit menu permissible_values: practical salinity unit (PSU): text: practical salinity unit (PSU) + description: A unitless measure of salinity that is equivalent to per thousand. weight for weight (% w/w): text: weight for weight (% w/w) - parts per thousand: - text: parts per thousand + description: A unitless comparison based on weight rather than volume, which + is equivalent to per hundred. + parts per thousand [UO:0000168]: + text: parts per thousand [UO:0000168] + description: A dimensionless concentration notation which denotes the amount + of a given substance in a total amount of 1000 regardless of the units of + measure as long as they are the same. meaning: UO:0000168 - gram per liter (g/L): - text: gram per liter (g/L) + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. meaning: UO:0000175 - total nitrogen (TN) measurement unit menu: - name: total nitrogen (TN) measurement unit menu + TotalNitrogenTnMeasurementUnitMenu: + name: TotalNitrogenTnMeasurementUnitMenu + title: total nitrogen (TN) measurement unit menu permissible_values: - milligram per liter (mg/L): - text: milligram per liter (mg/L) + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. meaning: UO:0000273 - gram per liter (g/L): - text: gram per liter (g/L) + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. meaning: UO:0000175 + total nitrogen (TN) measurement unit menu: + name: total nitrogen (TN) measurement unit menu + title: total nitrogen (TN) measurement unit menu + permissible_values: gram per total solids (g/gTS): text: gram per total solids (g/gTS) - total phosphorpus (TP) measurement unit menu: - name: total phosphorpus (TP) measurement unit menu + description: A unitless comparison of the weight of a substance as a proportion + to the weight of total solids. + TotalPhosphorpusTpMeasurementUnitMenu: + name: TotalPhosphorpusTpMeasurementUnitMenu + title: total phosphorpus (TP) measurement unit menu permissible_values: gram per total solids (g/gTS): text: gram per total solids (g/gTS) - orthophosphate as phosphorus per total solids (gPO4-P/gTS): - text: orthophosphate as phosphorus per total solids (gPO4-P/gTS) + description: A unitless comparison of the weight of a substance as a proportion + to the weight of total solids. + orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]: + text: orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] + description: A substance unit which describes the weight of orthophosphate + as phosphorus (gPO4-P) within a sample to the weight of total solids. meaning: GENEPIO:0100998 - milligrams per liter (mg/L): - text: milligrams per liter (mg/L) + milligrams per liter (mg/L) [UO:0000273]: + text: milligrams per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. meaning: UO:0000273 - milligrams orthophosphate as phosphorus per liter (mg PO4-P/L): - text: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) + milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]: + text: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] + description: A density unit comparing the weight of orthophosphate as phosphorus + (PO4-P) in milligrams within a standard liter volume. meaning: GENEPIO:0100999 - fecal contamination indicator menu: - name: fecal contamination indicator menu + FecalContaminationIndicatorMenu: + name: FecalContaminationIndicatorMenu + title: fecal contamination indicator menu permissible_values: - crAssphage: - text: crAssphage + crAssphage [NCBITaxon:1211417]: + text: crAssphage [NCBITaxon:1211417] + description: CrAss-like phage, a bacteriophage discovered in 2014 in the human + fecal metagenome. meaning: NCBITaxon:1211417 - PMMoV / pepper mild mottle virus: - text: PMMoV / pepper mild mottle virus + PMMoV / pepper mild mottle virus [NCBITaxon:12239]: + text: PMMoV / pepper mild mottle virus [NCBITaxon:12239] + description: A plant RNA virus that is abundant in human feces. meaning: NCBITaxon:12239 - Bacteroides HF183: - text: Bacteroides HF183 + Bacteroides HF183 [GENEPIO:0101000]: + text: Bacteroides HF183 [GENEPIO:0101000] + description: A fecal indicator which is the most commonly used sewage-associated + marker gene, belonging to the Bacteroides genus. meaning: GENEPIO:0101000 - Lachnospiraceae Lachno3: - text: Lachnospiraceae Lachno3 + Lachnospiraceae Lachno3 [GENEPIO:0101001]: + text: Lachnospiraceae Lachno3 [GENEPIO:0101001] + description: A fecal indicator which is a human-associated genetic marker + in the Lachnospiraceae family of bacteria. meaning: GENEPIO:0101001 - F+ (male specific) coliphages: - text: F+ (male specific) coliphages + F+ (male specific) coliphages [GENEPIO:0101002]: + text: F+ (male specific) coliphages [GENEPIO:0101002] + description: A fecal indicator which is a bacteriophage that infects coliform + bacteria and is used in water assessment. meaning: GENEPIO:0101002 - Stercobilin: - text: Stercobilin + Stercobilin [CHEBI:26756]: + text: Stercobilin [CHEBI:26756] + description: Bile pigment found in fecal material. meaning: CHEBI:26756 - fecal contamination unit menu: - name: fecal contamination unit menu + FecalContaminationUnitMenu: + name: FecalContaminationUnitMenu + title: fecal contamination unit menu permissible_values: log10 gene copies per 100 milliliter (log10 GC/100 mL): text: log10 gene copies per 100 milliliter (log10 GC/100 mL) + description: A unit that expresses on a logarithmic scale the number of copies + of a given gene within one hundred milliliters of a biological material. gene copies per liter (GC/L): text: gene copies per liter (GC/L) - PCR quantification cycle: - text: PCR quantification cycle + description: A unit that measures the number of copies of a given gene within + a liter of a biological material. + PCR quantification cycle [UO:0010077]: + text: PCR quantification cycle [UO:0010077] + description: A count unit of how many Polymerase Chain Reaction (PCR) cycles + it took to detect a real signal from a sample. Equivalent to the PCR cycle + number at which a sample's reaction curve intersects the threshold line. meaning: UO:0010077 log10 gene copies per nanogram total DNA: text: log10 gene copies per nanogram total DNA - urinary contamination indicator menu: - name: urinary contamination indicator menu + description: A unit that expresses on a logarithmic scale the number of copies + within a nanogram of deoxyribonucleic acid genetic material. + UrinaryContaminationIndicatorMenu: + name: UrinaryContaminationIndicatorMenu + title: urinary contamination indicator menu permissible_values: - Urobilin: - text: Urobilin + Urobilin [CHEBI:36378]: + text: Urobilin [CHEBI:36378] + description: A tetrapyrroledicarboxylic acid that causes the yellow color + in urine. Also known as urochrome. meaning: CHEBI:36378 - urinary contamination unit menu: - name: urinary contamination unit menu + UrinaryContaminationUnitMenu: + name: UrinaryContaminationUnitMenu + title: urinary contamination unit menu permissible_values: - nanograms per liter (ng/L): - text: nanograms per liter (ng/L) + nanograms per liter (ng/L) [EFO:0004382]: + text: nanograms per liter (ng/L) [EFO:0004382] + description: A mass unit density which is equal to mass of an object in nanograms + divided by the volume in liters. meaning: EFO:0004382 - fecal coliform count unit menu: - name: fecal coliform count unit menu + FecalColiformCountUnitMenu: + name: FecalColiformCountUnitMenu + title: fecal coliform count unit menu permissible_values: - colony forming units per milliliter (CFU/mL): - text: colony forming units per milliliter (CFU/mL) + colony forming units per milliliter (CFU/mL) [UO:0000213]: + text: colony forming units per milliliter (CFU/mL) [UO:0000213] + description: A unit of microbial density that describes the number of colony + forming units within a milliliter of material. meaning: UO:0000213 colony forming units per 100 milliliter (CFU/100 mL): text: colony forming units per 100 milliliter (CFU/100 mL) + description: A unit of microbial density that describes the number of colony + forming units within 100 milliliters of material. colony forming units per grams total solids (CFU/gTS): text: colony forming units per grams total solids (CFU/gTS) + description: A unit of microbial density that describes the number of colony + forming units within a gram of total solids in waste material. most probable number per milliliter (MPN/mL): text: most probable number per milliliter (MPN/mL) + description: A unit of microbial density that describes the most probable + number of microbes within one milliliter of material. most probable number per 100 milliliter (MPN/100 mL): text: most probable number per 100 milliliter (MPN/100 mL) - sample temperature unit (at collection) menu: - name: sample temperature unit (at collection) menu + description: A unit of microbial density that describes the most probable + number of microbes within 100 milliliters of material. + SampleTemperatureUnitAtCollectionMenu: + name: SampleTemperatureUnitAtCollectionMenu + title: sample temperature unit (at collection) menu permissible_values: - degree Fahrenheit (F): - text: degree Fahrenheit (F) + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. meaning: UO:0000195 - degree Celsius (C): - text: degree Celsius (C) + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. meaning: UO:0000027 - sample temperature unit (when received) menu: - name: sample temperature unit (when received) menu + SampleTemperatureUnitWhenReceivedMenu: + name: SampleTemperatureUnitWhenReceivedMenu + title: sample temperature unit (when received) menu permissible_values: - degree Fahrenheit (F): - text: degree Fahrenheit (F) + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. meaning: UO:0000195 - degree Celsius (C): - text: degree Celsius (C) + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. meaning: UO:0000027 - purpose of sequencing menu: - name: purpose of sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose of sequencing menu permissible_values: - Baseline surveillance (random sampling): - text: Baseline surveillance (random sampling) + Baseline surveillance (random sampling) [GENEPIO:0100005]: + text: Baseline surveillance (random sampling) [GENEPIO:0100005] + description: A surveillance sampling strategy in which baseline is established + at the beginning of a study or project by the selection of sample units + via random sampling. meaning: GENEPIO:0100005 - Targeted surveillance (non-random sampling): - text: Targeted surveillance (non-random sampling) + Targeted surveillance (non-random sampling) [GENEPIO:0100006]: + text: Targeted surveillance (non-random sampling) [GENEPIO:0100006] + description: A surveillance sampling strategy in which an aspired outcome + is explicitly stated. meaning: GENEPIO:0100006 - Priority surveillance project: - text: Priority surveillance project + Priority surveillance project [GENEPIO:0100007]: + text: Priority surveillance project [GENEPIO:0100007] + description: A targeted surveillance strategy which is considered important + and/or urgent. meaning: GENEPIO:0100007 - Longitudinal surveillance (repeat sampling): - text: Longitudinal surveillance (repeat sampling) + Longitudinal surveillance (repeat sampling) [GENEPIO:0100009]: + text: Longitudinal surveillance (repeat sampling) [GENEPIO:0100009] + description: A surveillance strategy in which an individual or site is selected + to undergo repeat sampling over a defined period of time. meaning: GENEPIO:0100009 - Travel-associated surveillance: - text: Travel-associated surveillance + Travel-associated surveillance [GENEPIO:0100012]: + text: Travel-associated surveillance [GENEPIO:0100012] + description: A surveillance strategy in which wastewater produced within travel + hubs or travel vehicles are monitored. meaning: GENEPIO:0100012 - Domestic travel surveillance: - text: Domestic travel surveillance + Domestic travel surveillance [GENEPIO:0100013]: + text: Domestic travel surveillance [GENEPIO:0100013] + description: A surveillance strategy in which wastewater produced within travel + hubs or travel vehicles are monitored, related to domestic travel. meaning: GENEPIO:0100013 - is_a: Travel-associated surveillance - International travel surveillance: - text: International travel surveillance + is_a: Travel-associated surveillance [GENEPIO:0100012] + International travel surveillance [GENEPIO:0100014]: + text: International travel surveillance [GENEPIO:0100014] + description: A surveillance strategy in which wastewater produced within travel + hubs or travel vehicles are monitored, related to international travel. meaning: GENEPIO:0100014 - is_a: Travel-associated surveillance - Research: - text: Research + is_a: Travel-associated surveillance [GENEPIO:0100012] + Research [GENEPIO:0100022]: + text: Research [GENEPIO:0100022] + description: A sampling strategy in which sites are sampled in order to perform + research. meaning: GENEPIO:0100022 - Viral passage experiment: - text: Viral passage experiment + Viral passage experiment [GENEPIO:0100023]: + text: Viral passage experiment [GENEPIO:0100023] + description: A research sampling strategy in which samples are selected in + order to perform a viral passage experiment. meaning: GENEPIO:0100023 - is_a: Research - Protocol testing experiment: - text: Protocol testing experiment + is_a: Research [GENEPIO:0100022] + Protocol testing experiment [GENEPIO:0100024]: + text: Protocol testing experiment [GENEPIO:0100024] + description: A research sampling strategy in which samples are collected in + order to test a method or protocol. meaning: GENEPIO:0100024 - is_a: Research - sequencing platform menu: - name: sequencing platform menu + is_a: Research [GENEPIO:0100022] + SequencingPlatformMenu: + name: SequencingPlatformMenu + title: sequencing platform menu permissible_values: - Illumina: - text: Illumina + Illumina [GENEPIO:0001923]: + text: Illumina [GENEPIO:0001923] + description: A sequencing platform provided by the Illumina company. meaning: GENEPIO:0001923 - Pacific Biosciences: - text: Pacific Biosciences + Pacific Biosciences [GENEPIO:0001927]: + text: Pacific Biosciences [GENEPIO:0001927] + description: A sequencing platform provided by the Pacific Biosciences company. meaning: GENEPIO:0001927 - Ion Torrent: - text: Ion Torrent + Ion Torrent [GENEPIO:0002683]: + text: Ion Torrent [GENEPIO:0002683] + description: A sequencing platform provided by the Ion Torrent company. meaning: GENEPIO:0002683 - Oxford Nanopore Technologies: - text: Oxford Nanopore Technologies + Oxford Nanopore Technologies [GENEPIO:0100986]: + text: Oxford Nanopore Technologies [GENEPIO:0100986] + description: An sequencing platform that is developing and selling nanopore + sequencing products and is based in the UK. meaning: GENEPIO:0100986 - BGI Genomics: - text: BGI Genomics + BGI Genomics [GENEPIO:0004324]: + text: BGI Genomics [GENEPIO:0004324] + description: A sequencing platform provided by the BGI Genomics company. meaning: GENEPIO:0004324 - MGI: - text: MGI + MGI [GENEPIO:0004325]: + text: MGI [GENEPIO:0004325] + description: A sequencing platform provided by the MGI company. meaning: GENEPIO:0004325 - Roche LS454: - text: Roche LS454 + Roche LS454 [GENEPIO:0001926]: + text: Roche LS454 [GENEPIO:0001926] + description: A sequencing platform provided by the 454 Life Sciences company. meaning: GENEPIO:0001926 - SOLiD sequencing: - text: SOLiD sequencing + SOLiD sequencing [GENEPIO:0002684]: + text: SOLiD sequencing [GENEPIO:0002684] + description: A sequencing platform provided by Life Technologies Corporation. meaning: GENEPIO:0002684 - Complete Genomics: - text: Complete Genomics + Complete Genomics [GENEPIO:0001924]: + text: Complete Genomics [GENEPIO:0001924] + description: An in-house sequencing platform provided by Complete Genomics. meaning: GENEPIO:0001924 - Helicos: - text: Helicos + Helicos [GENEPIO:0002682]: + text: Helicos [GENEPIO:0002682] + description: A sequencing platform brand provided by Helicos corporation (now + defunct). meaning: GENEPIO:0002682 - Applied Biosystems: - text: Applied Biosystems + Applied Biosystems [GENEPIO:0100985]: + text: Applied Biosystems [GENEPIO:0100985] + description: A sequencing platform provided by ThermoFisher. meaning: GENEPIO:0100985 - sequencing instrument menu: - name: sequencing instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: - Illumina: - text: Illumina + Illumina [GENEPIO:0100105]: + text: Illumina [GENEPIO:0100105] + description: A DNA sequencer manufactured by the Illumina corporation. meaning: GENEPIO:0100105 - Illumina Genome Analyzer: - text: Illumina Genome Analyzer + Illumina Genome Analyzer [GENEPIO:0100106]: + text: Illumina Genome Analyzer [GENEPIO:0100106] + description: A DNA sequencer manufactured by Solexa as one of its first sequencer + lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data + in a single run. meaning: GENEPIO:0100106 - is_a: Illumina - Illumina Genome Analyzer II: - text: Illumina Genome Analyzer II + is_a: Illumina [GENEPIO:0100105] + Illumina Genome Analyzer II [OBI:0000703]: + text: Illumina Genome Analyzer II [OBI:0000703] + description: A DNA sequencer manufactured by the Illumina (Solexa) corporation, + which supports sequencing of single or paired end clone libraries relying + on sequencing by synthesis technology. meaning: OBI:0000703 - is_a: Illumina - Illumina Genome Analyzer IIx: - text: Illumina Genome Analyzer IIx + is_a: Illumina [GENEPIO:0100105] + Illumina Genome Analyzer IIx [OBI:0002000]: + text: Illumina Genome Analyzer IIx [OBI:0002000] + description: An Illumina Genome Analyzer II which is manufactured by the Illumina + corporation. It supports sequencing of single, long or short insert paired + end clone libraries relying on sequencing by synthesis technology. The Genome + Analyzer IIx is the most widely adopted next-generation sequencing platform + and proven and published across the broadest range of research applications. meaning: OBI:0002000 - is_a: Illumina - Illumina HiScanSQ: - text: Illumina HiScanSQ + is_a: Illumina [GENEPIO:0100105] + Illumina HiScanSQ [GENEPIO:0100109]: + text: Illumina HiScanSQ [GENEPIO:0100109] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing + and microarray-based analyses as well as an "SQ Module" to support microfluidics. meaning: GENEPIO:0100109 - is_a: Illumina - Illumina HiSeq: - text: Illumina HiSeq + is_a: Illumina [GENEPIO:0100105] + Illumina HiSeq [GENEPIO:0100110]: + text: Illumina HiSeq [GENEPIO:0100110] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, enabling deep sequencing and high yield. meaning: GENEPIO:0100110 - is_a: Illumina - Illumina HiSeq X: - text: Illumina HiSeq X + is_a: Illumina [GENEPIO:0100105] + Illumina HiSeq X [GENEPIO:0100111]: + text: Illumina HiSeq X [GENEPIO:0100111] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that enables sufficient depth and coverage + to produce the first 30x human genome for $1000. meaning: GENEPIO:0100111 - is_a: Illumina HiSeq - Illumina HiSeq X Five: - text: Illumina HiSeq X Five + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X Five [GENEPIO:0100112]: + text: Illumina HiSeq X Five [GENEPIO:0100112] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing + Systems. meaning: GENEPIO:0100112 - is_a: Illumina HiSeq - Illumina HiSeq X Ten: - text: Illumina HiSeq X Ten + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X Ten [GENEPIO:0100113]: + text: Illumina HiSeq X Ten [GENEPIO:0100113] + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. meaning: GENEPIO:0100113 - is_a: Illumina HiSeq - Illumina HiSeq 1000: - text: Illumina HiSeq 1000 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 1000 [OBI:0002022]: + text: Illumina HiSeq 1000 [OBI:0002022] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. meaning: OBI:0002022 - is_a: Illumina HiSeq - Illumina HiSeq 1500: - text: Illumina HiSeq 1500 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 1500 [GENEPIO:0100115]: + text: Illumina HiSeq 1500 [GENEPIO:0100115] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35-50 Gb per day. meaning: GENEPIO:0100115 - is_a: Illumina HiSeq - Illumina HiSeq 2000: - text: Illumina HiSeq 2000 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 2000 [OBI:0002001]: + text: Illumina HiSeq 2000 [OBI:0002001] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. meaning: OBI:0002001 - is_a: Illumina HiSeq - Illumina HiSeq 2500: - text: Illumina HiSeq 2500 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 2500 [OBI:0002002]: + text: Illumina HiSeq 2500 [OBI:0002002] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. meaning: OBI:0002002 - is_a: Illumina HiSeq - Illumina HiSeq 3000: - text: Illumina HiSeq 3000 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 3000 [OBI:0002048]: + text: Illumina HiSeq 3000 [OBI:0002048] + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. meaning: OBI:0002048 - is_a: Illumina HiSeq - Illumina HiSeq 4000: - text: Illumina HiSeq 4000 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 4000 [OBI:0002049]: + text: Illumina HiSeq 4000 [OBI:0002049] + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. meaning: OBI:0002049 - is_a: Illumina HiSeq - Illumina iSeq: - text: Illumina iSeq + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina iSeq [GENEPIO:0100120]: + text: Illumina iSeq [GENEPIO:0100120] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight. meaning: GENEPIO:0100120 - is_a: Illumina - Illumina iSeq 100: - text: Illumina iSeq 100 + is_a: Illumina [GENEPIO:0100105] + Illumina iSeq 100 [GENEPIO:0100121]: + text: Illumina iSeq 100 [GENEPIO:0100121] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight and has an output capacity + between 144MB-1.2GB. meaning: GENEPIO:0100121 - is_a: Illumina iSeq - Illumina NovaSeq: - text: Illumina NovaSeq + is_a: Illumina iSeq [GENEPIO:0100120] + Illumina NovaSeq [GENEPIO:0100122]: + text: Illumina NovaSeq [GENEPIO:0100122] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that has an output capacity of 6 Tb and + 20 billion reads in dual flow cell mode. meaning: GENEPIO:0100122 - is_a: Illumina - Illumina NovaSeq 6000: - text: Illumina NovaSeq 6000 + is_a: Illumina [GENEPIO:0100105] + Illumina NovaSeq 6000 [GENEPIO:0100123]: + text: Illumina NovaSeq 6000 [GENEPIO:0100123] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). + The sequencer utilizes synthesis technology and patterned flow cells to + optimize throughput and even spacing of sequencing clusters. meaning: GENEPIO:0100123 - is_a: Illumina NovaSeq - Illumina MiniSeq: - text: Illumina MiniSeq + is_a: Illumina NovaSeq [GENEPIO:0100122] + Illumina MiniSeq [GENEPIO:0100124]: + text: Illumina MiniSeq [GENEPIO:0100124] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. meaning: GENEPIO:0100124 - is_a: Illumina - Illumina MiSeq: - text: Illumina MiSeq + is_a: Illumina [GENEPIO:0100105] + Illumina MiSeq [OBI:0002003]: + text: Illumina MiSeq [OBI:0002003] + description: A DNA sequencer which is manufactured by the Illumina corporation. + Built upon sequencing by synthesis technology, the machine provides an end-to-end + solution (cluster generation, amplification, sequencing, and data analysis) + in a single machine. meaning: OBI:0002003 - is_a: Illumina - Illumina NextSeq: - text: Illumina NextSeq + is_a: Illumina [GENEPIO:0100105] + Illumina NextSeq [GENEPIO:0100126]: + text: Illumina NextSeq [GENEPIO:0100126] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. meaning: GENEPIO:0100126 - is_a: Illumina - Illumina NextSeq 500: - text: Illumina NextSeq 500 + is_a: Illumina [GENEPIO:0100105] + Illumina NextSeq 500 [OBI:0002021]: + text: Illumina NextSeq 500 [OBI:0002021] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. meaning: OBI:0002021 - is_a: Illumina NextSeq - Illumina NextSeq 550: - text: Illumina NextSeq 550 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 550 [GENEPIO:0100128]: + text: Illumina NextSeq 550 [GENEPIO:0100128] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. The 550 is an upgrade on the 500 model. meaning: GENEPIO:0100128 - is_a: Illumina NextSeq - Illumina NextSeq 1000: - text: Illumina NextSeq 1000 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 1000 [GENEPIO:0004432]: + text: Illumina NextSeq 1000 [GENEPIO:0004432] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 + and P2 flow cells. meaning: GENEPIO:0004432 - is_a: Illumina NextSeq - Illumina NextSeq 2000: - text: Illumina NextSeq 2000 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 2000 [GENEPIO:0100129]: + text: Illumina NextSeq 2000 [GENEPIO:0100129] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 30-360 Gb. meaning: GENEPIO:0100129 - is_a: Illumina NextSeq - PacBio: - text: PacBio + is_a: Illumina NextSeq [GENEPIO:0100126] + PacBio [GENEPIO:0100130]: + text: PacBio [GENEPIO:0100130] + description: A DNA sequencer manufactured by the Pacific Biosciences corporation. meaning: GENEPIO:0100130 - PacBio RS: - text: PacBio RS + PacBio RS [GENEPIO:0100131]: + text: PacBio RS [GENEPIO:0100131] + description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ + \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ + \ The RS was the first model made by the company." meaning: GENEPIO:0100131 - is_a: PacBio - PacBio RS II: - text: PacBio RS II + is_a: PacBio [GENEPIO:0100130] + PacBio RS II [OBI:0002012]: + text: PacBio RS II [OBI:0002012] + description: A DNA sequencer which is manufactured by the Pacific Biosciences + corporation. Built upon single molecule real-time sequencing technology, + the machine is optimized for generation with long reads and high consensus + accuracy. meaning: OBI:0002012 - is_a: PacBio - PacBio Sequel: - text: PacBio Sequel + is_a: PacBio [GENEPIO:0100130] + PacBio Sequel [GENEPIO:0100133]: + text: PacBio Sequel [GENEPIO:0100133] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation with long reads and high consensus + accuracy, and manufactured by the Pacific Biosciences corporation meaning: GENEPIO:0100133 - is_a: PacBio - PacBio Sequel II: - text: PacBio Sequel II + is_a: PacBio [GENEPIO:0100130] + PacBio Sequel II [GENEPIO:0100134]: + text: PacBio Sequel II [GENEPIO:0100134] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation of highly accurate ("HiFi") long reads, + and which is manufactured by the Pacific Biosciences corporation. meaning: GENEPIO:0100134 - is_a: PacBio - Ion Torrent: - text: Ion Torrent + is_a: PacBio [GENEPIO:0100130] + Ion Torrent [GENEPIO:0100135]: + text: Ion Torrent [GENEPIO:0100135] + description: A DNA sequencer manufactured by the Ion Torrent corporation. meaning: GENEPIO:0100135 - Ion Torrent PGM: - text: Ion Torrent PGM + Ion Torrent PGM [GENEPIO:0100136]: + text: Ion Torrent PGM [GENEPIO:0100136] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of 300 + MB - 1GB. meaning: GENEPIO:0100136 - is_a: Ion Torrent - Ion Torrent Proton: - text: Ion Torrent Proton + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent Proton [GENEPIO:0100137]: + text: Ion Torrent Proton [GENEPIO:0100137] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of up to + 15 Gb. meaning: GENEPIO:0100137 - is_a: Ion Torrent - Ion Torrent S5 XL: - text: Ion Torrent S5 XL + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent S5 XL [GENEPIO:0100138]: + text: Ion Torrent S5 XL [GENEPIO:0100138] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material while producing data faster than the S5 model. meaning: GENEPIO:0100138 - is_a: Ion Torrent - Ion Torrent S5: - text: Ion Torrent S5 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent S5 [GENEPIO:0100139]: + text: Ion Torrent S5 [GENEPIO:0100139] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material. meaning: GENEPIO:0100139 - is_a: Ion Torrent - Oxford Nanopore: - text: Oxford Nanopore + is_a: Ion Torrent [GENEPIO:0100135] + Oxford Nanopore [GENEPIO:0100140]: + text: Oxford Nanopore [GENEPIO:0100140] + description: A DNA sequencer manufactured by the Oxford Nanopore corporation. meaning: GENEPIO:0100140 - Oxford Nanopore Flongle: - text: Oxford Nanopore Flongle + Oxford Nanopore Flongle [GENEPIO:0004433]: + text: Oxford Nanopore Flongle [GENEPIO:0004433] + description: An adapter for MinION or GridION DNA sequencers manufactured + by the Oxford Nanopore corporation that enables sequencing on smaller, single-use + flow cells. meaning: GENEPIO:0004433 - is_a: Oxford Nanopore - Oxford Nanopore GridION: - text: Oxford Nanopore GridION + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore GridION [GENEPIO:0100141]: + text: Oxford Nanopore GridION [GENEPIO:0100141] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, that can run and analyze up to five individual flow cells producing + up to 150 Gb of data per run. The sequencer produces real-time results and + utilizes nanopore technology with the option of running the flow cells concurrently + or individual meaning: GENEPIO:0100141 - is_a: Oxford Nanopore - Oxford Nanopore MinION: - text: Oxford Nanopore MinION + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore MinION [GENEPIO:0100142]: + text: Oxford Nanopore MinION [GENEPIO:0100142] + description: A portable DNA sequencer which is manufactured by the Oxford + Nanopore Technologies corporation, that uses consumable flow cells producing + up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time + results and utilizes nanopore technology with up to 512 nanopore channels + in the sensor array. meaning: GENEPIO:0100142 - is_a: Oxford Nanopore - Oxford Nanopore PromethION: - text: Oxford Nanopore PromethION + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore PromethION [GENEPIO:0100143]: + text: Oxford Nanopore PromethION [GENEPIO:0100143] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, capable of running up to 48 flow cells and producing up to + 7.6 Tb of data per run. The sequencer produces real-time results and utilizes + Nanopore technology, with each flow cell allowing up to 3,000 nanopores + to be sequencing simultaneously. meaning: GENEPIO:0100143 - is_a: Oxford Nanopore - BGI Genomics sequencing instrument: - text: BGI Genomics sequencing instrument + is_a: Oxford Nanopore [GENEPIO:0100140] + BGI Genomics sequencing instrument [GENEPIO:0100144]: + text: BGI Genomics sequencing instrument [GENEPIO:0100144] + description: A DNA sequencer manufactured by the BGI Genomics corporation. meaning: GENEPIO:0100144 - BGISEQ-500: - text: BGISEQ-500 + BGISEQ-500 [GENEPIO:0100145]: + text: BGISEQ-500 [GENEPIO:0100145] + description: A DNA sequencer manufactured by the BGI Genomics corporation + that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". meaning: GENEPIO:0100145 - is_a: BGI Genomics sequencing instrument - MGI sequencing instrument: - text: MGI sequencing instrument + is_a: BGI Genomics sequencing instrument [GENEPIO:0100144] + MGI sequencing instrument [GENEPIO:0100146]: + text: MGI sequencing instrument [GENEPIO:0100146] + description: A DNA sequencer manufactured by the MGI corporation. meaning: GENEPIO:0100146 - MGISEQ-2000RS: - text: MGISEQ-2000RS + MGISEQ-2000RS [GENEPIO:0100971]: + text: MGISEQ-2000RS [GENEPIO:0100971] + description: An MGI sequencing instrument model that utilises DNA nanoball + and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing + ad which is capable of medium to high throughput sequencing. meaning: GENEPIO:0100971 - is_a: MGI sequencing instrument - MGI DNBSEQ-G99: - text: MGI DNBSEQ-G99 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G99 [GENEPIO:0100972]: + text: MGI DNBSEQ-G99 [GENEPIO:0100972] + description: An MGI sequencing instrument model that utilises DNA nanoball + and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing + and which adopts triangular matrix signal spots on sequencing flow cell, + for low throughput at highspeeds. meaning: GENEPIO:0100972 - is_a: MGI sequencing instrument - MGI DNBSEQ-G400: - text: MGI DNBSEQ-G400 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G400 [GENEPIO:0100148]: + text: MGI DNBSEQ-G400 [GENEPIO:0100148] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB; 1440GB per run. meaning: GENEPIO:0100148 - is_a: MGI sequencing instrument - MGI DNBSEQ-G400RS FAST: - text: MGI DNBSEQ-G400RS FAST + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]: + text: MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB; 330GB per run, which enables faster sequencing than the + DNBSEQ-G400. meaning: GENEPIO:0100149 - is_a: MGI DNBSEQ-G400 - MGI DNBSEQ-T7: - text: MGI DNBSEQ-T7 + is_a: MGI DNBSEQ-G400 [GENEPIO:0100148] + MGI DNBSEQ-T7 [GENEPIO:0100147]: + text: MGI DNBSEQ-T7 [GENEPIO:0100147] + description: A high throughput DNA sequencer manufactured by the MGI corporation + with an output capacity of 1; 6TB of data per day. meaning: GENEPIO:0100147 - is_a: MGI sequencing instrument - MGI DNBSEQ-E25: - text: MGI DNBSEQ-E25 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-E25 [GENEPIO:0100973]: + text: MGI DNBSEQ-E25 [GENEPIO:0100973] + description: An MGI sequencing instrument model that is a compact and lightweight + standalone system which can bu used inside or outside the lab. meaning: GENEPIO:0100973 - is_a: MGI sequencing instrument - MGI DNBSEQ-G50: - text: MGI DNBSEQ-G50 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G50 [GENEPIO:0100150]: + text: MGI DNBSEQ-G50 [GENEPIO:0100150] + description: "A DNA sequencer manufactured by the MGI corporation with an\ + \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." meaning: GENEPIO:0100150 - is_a: MGI sequencing instrument - 454 Genome Sequencer: - text: 454 Genome Sequencer + is_a: MGI sequencing instrument [GENEPIO:0100146] + 454 Genome Sequencer [GENEPIO:0001937]: + text: 454 Genome Sequencer [GENEPIO:0001937] + description: A DNA sequencer first manufactured by 454 Life Science Corporation + that conducts pyrosequencing. meaning: GENEPIO:0001937 - 454 Genome Sequencer 20: - text: 454 Genome Sequencer 20 + 454 Genome Sequencer 20 [OBI:0000689]: + text: 454 Genome Sequencer 20 [OBI:0000689] + description: A DNA sequencer first manufactured by 454 Life Science Corporation + in 2005, and enables pyrosequencing to be performed. It comprises both optics + and fluidics subsystems, which are controlled by a computer subsystem. meaning: OBI:0000689 - is_a: 454 Genome Sequencer - 454 Genome Sequencer FLX: - text: 454 Genome Sequencer FLX + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX [OBI:0000702]: + text: 454 Genome Sequencer FLX [OBI:0000702] + description: A DNA sequencer which was first manufactured by 454 Life Science + Corporation in 2008 and enables pyrosequencing to be performed. It comprises + both optics and fluidics subsystems, which are controlled by a computer + subsystem. It has the ability to sequence 400-600 million base pairs per + run with 400-500 base pair read lengths. meaning: OBI:0000702 - is_a: 454 Genome Sequencer - 454 Genome Sequencer FLX+: - text: 454 Genome Sequencer FLX+ + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX+ [GENEPIO:0100982]: + text: 454 Genome Sequencer FLX+ [GENEPIO:0100982] + description: A 454 Genome Sequencer that performs pyrosequencing and comprises + both optics and fluidics subsystems and can be used for longer reads when + used with the long-read Sequencing Kit XL+. meaning: GENEPIO:0100982 - is_a: 454 Genome Sequencer - 454 Genome Sequencer FLX Titanium: - text: 454 Genome Sequencer FLX Titanium + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX Titanium [GENEPIO:0001936]: + text: 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] + description: A 454 Genome Sequencer that performs pyrosequencing and has enhanced + capacity and generates longer reads. meaning: GENEPIO:0001936 - is_a: 454 Genome Sequencer - 454 Genome Sequencer Junior: - text: 454 Genome Sequencer Junior - meaning: GENEPIO:0100983 - is_a: 454 Genome Sequencer - SOLiD System: - text: SOLiD System + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer Junior [GENEPIO:0001938]: + text: 454 Genome Sequencer Junior [GENEPIO:0001938] + description: A 454 Genome Sequencer that performs pyrosequencing and is more + compact. + meaning: GENEPIO:0001938 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + SOLiD System [OBI:0000696]: + text: SOLiD System [OBI:0000696] + description: A DNA sequencer which is manufactured by Applied Biosystems and + which enable DNA sequencing by ligation. meaning: OBI:0000696 - SOLiD 5500: - text: SOLiD 5500 + SOLiD 5500 [GENEPIO:0001929]: + text: SOLiD 5500 [GENEPIO:0001929] + description: A DNA sequencer which is manufactured by Applied Biosystems and + utillizes sequencing by ligation technology and faster run times than the + SOLiD 4 series. meaning: GENEPIO:0001929 - is_a: SOLiD System - SOLiD 5500xl Genetic Analyzer: - text: SOLiD 5500xl Genetic Analyzer + is_a: SOLiD System [OBI:0000696] + SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]: + text: SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] + description: A DNA sequencer which is manufactured by Applied Biosystems and + has two FlowChips for across 12 lanes and with a higher throughput than + the 5500 model. meaning: GENEPIO:0001930 - is_a: SOLiD System - SOLiD 5500x-Wl Genetic Analyzer: - text: SOLiD 5500x-Wl Genetic Analyzer + is_a: SOLiD System [OBI:0000696] + SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]: + text: SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology and with a higher throughput + than SOLiD 5500xl Genetic Analyzer. meaning: GENEPIO:0100984 - is_a: SOLiD System - SOLiD 3 Plus System: - text: SOLiD 3 Plus System + is_a: SOLiD System [OBI:0000696] + SOLiD 3 Plus System [OBI:0002007]: + text: SOLiD 3 Plus System [OBI:0002007] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology, the machine generates + greater than 1 billion mappable reads per run. meaning: OBI:0002007 - is_a: SOLiD System - SOLiD 4 System: - text: SOLiD 4 System + is_a: SOLiD System [OBI:0000696] + SOLiD 4 System [OBI:0002024]: + text: SOLiD 4 System [OBI:0002024] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology with 100 Gb mappable + throughput. meaning: OBI:0002024 - is_a: SOLiD System - SOLiD 4hq System: - text: SOLiD 4hq System + is_a: SOLiD System [OBI:0000696] + SOLiD 4hq System [GENEPIO:0001928]: + text: SOLiD 4hq System [GENEPIO:0001928] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology with 300 Gb mappable + throughput. meaning: GENEPIO:0001928 - is_a: SOLiD System - SOLiD PI System: - text: SOLiD PI System + is_a: SOLiD System [OBI:0000696] + SOLiD PI System [GENEPIO:0001931]: + text: SOLiD PI System [GENEPIO:0001931] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology, the machine offers + 50Gb mappable throughput. meaning: GENEPIO:0001931 - is_a: SOLiD System - SOLiD System 2.0: - text: SOLiD System 2.0 + is_a: SOLiD System [OBI:0000696] + SOLiD System 2.0 [GENEPIO:0001932]: + text: SOLiD System 2.0 [GENEPIO:0001932] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. meaning: GENEPIO:0001932 - is_a: SOLiD System - SOLiD System 3.0: - text: SOLiD System 3.0 + is_a: SOLiD System [OBI:0000696] + SOLiD System 3.0 [GENEPIO:0001933]: + text: SOLiD System 3.0 [GENEPIO:0001933] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. meaning: GENEPIO:0001933 - is_a: SOLiD System - HeliScope Single Molecule Sequencer: - text: HeliScope Single Molecule Sequencer + is_a: SOLiD System [OBI:0000696] + HeliScope Single Molecule Sequencer [OBI:0000717]: + text: HeliScope Single Molecule Sequencer [OBI:0000717] + description: A DNA sequencer manufacturer by Helicos Corporation to carry + out Single Molecule sequencing using reversible termination chemistry. meaning: OBI:0000717 - Applied Biosystems sequencing instrument model: - text: Applied Biosystems sequencing instrument model + Applied Biosystems sequencing instrument model [GENEPIO:0100974]: + text: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + description: A sequencing instrument model that is manufactured by Applied + Biosystems and which performs Sanger sequencing and fragment analysis by + capillary electrophoresis. meaning: GENEPIO:0100974 - AB 310 Genetic Analyzer: - text: AB 310 Genetic Analyzer + AB 310 Genetic Analyzer [GENEPIO:0100975]: + text: AB 310 Genetic Analyzer [GENEPIO:0100975] + description: An Applied Biosystems sequencing instrument model which utilises + a single capillary electrophoresis system to perform Sanger sequencing and + fragment analysis that is automated. meaning: GENEPIO:0100975 - is_a: Applied Biosystems sequencing instrument model - AB 3130 Genetic Analyzer: - text: AB 3130 Genetic Analyzer + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3130 Genetic Analyzer [GENEPIO:0100976]: + text: AB 3130 Genetic Analyzer [GENEPIO:0100976] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 4 capillaries. meaning: GENEPIO:0100976 - is_a: Applied Biosystems sequencing instrument model - AB 3130xL Genetic Analyzer: - text: AB 3130xL Genetic Analyzer + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3130xL Genetic Analyzer [GENEPIO:0100977]: + text: AB 3130xL Genetic Analyzer [GENEPIO:0100977] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 16 capillaries. meaning: GENEPIO:0100977 - is_a: Applied Biosystems sequencing instrument model - AB 3500 Genetic Analyzer: - text: AB 3500 Genetic Analyzer + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3500 Genetic Analyzer [GENEPIO:0100978]: + text: AB 3500 Genetic Analyzer [GENEPIO:0100978] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 8 capillaries, which can + run 96 well plates. meaning: GENEPIO:0100978 - is_a: Applied Biosystems sequencing instrument model - AB 3500xL Genetic Analyzer: - text: AB 3500xL Genetic Analyzer + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3500xL Genetic Analyzer [GENEPIO:0100979]: + text: AB 3500xL Genetic Analyzer [GENEPIO:0100979] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 24 capillaries, which + can run 384 well plates. meaning: GENEPIO:0100979 - is_a: Applied Biosystems sequencing instrument model - AB 3730 Genetic Analyzer: - text: AB 3730 Genetic Analyzer + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3730 Genetic Analyzer [GENEPIO:0100980]: + text: AB 3730 Genetic Analyzer [GENEPIO:0100980] + description: An Applied Biosystems sequencing instrument model which utilises + an 48 capillary array electrophoresis system for sequencing. meaning: GENEPIO:0100980 - is_a: Applied Biosystems sequencing instrument model - AB 3730xL Genetic Analyzer: - text: AB 3730xL Genetic Analyzer + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3730xL Genetic Analyzer [GENEPIO:0100981]: + text: AB 3730xL Genetic Analyzer [GENEPIO:0100981] + description: An Applied Biosystems sequencing instrument model which utilises + an 96 capillary array electrophoresis system for sequencing. meaning: GENEPIO:0100981 - is_a: Applied Biosystems sequencing instrument model - sequencing assay type menu: - name: sequencing assay type menu + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + SequencingAssayTypeMenu: + name: SequencingAssayTypeMenu + title: sequencing assay type menu permissible_values: - Amplicon sequencing assay: - text: Amplicon sequencing assay + Amplicon sequencing assay [OBI:0002767]: + text: Amplicon sequencing assay [OBI:0002767] + description: A sequencing assay in which a DNA or RNA input molecule is amplified + by PCR and the product sequenced. meaning: OBI:0002767 - 16S ribosomal gene sequencing assay: - text: 16S ribosomal gene sequencing assay + 16S ribosomal gene sequencing assay [OBI:0002763]: + text: 16S ribosomal gene sequencing assay [OBI:0002763] + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting + sequences are compared to reference 16S sequence databases to identify or + classify bacteria present within a given sample. meaning: OBI:0002763 - is_a: Amplicon sequencing assay - Whole genome sequencing assay: - text: Whole genome sequencing assay + is_a: Amplicon sequencing assay [OBI:0002767] + Whole genome sequencing assay [OBI:0002117]: + text: Whole genome sequencing assay [OBI:0002117] + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. meaning: OBI:0002117 - Whole metagenome sequencing assay: - text: Whole metagenome sequencing assay + Whole metagenome sequencing assay [OBI:0002623]: + text: Whole metagenome sequencing assay [OBI:0002623] + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. meaning: OBI:0002623 - Whole virome sequencing assay: - text: Whole virome sequencing assay + Whole virome sequencing assay [OBI:0002768]: + text: Whole virome sequencing assay [OBI:0002768] + description: A whole metagenome sequencing assay that intends to provide information + on multiple genome sequences from different viruses present in the same + input sample. meaning: OBI:0002768 - is_a: Whole metagenome sequencing assay - amplicon pcr primer scheme menu: - name: amplicon pcr primer scheme menu + is_a: Whole metagenome sequencing assay [OBI:0002623] + AmpliconPcrPrimerSchemeMenu: + name: AmpliconPcrPrimerSchemeMenu + title: amplicon pcr primer scheme menu permissible_values: - artic-v1: - text: artic-v1 + artic-v1 [GENEPIO:0100847]: + text: artic-v1 [GENEPIO:0100847] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 1.0.0. meaning: GENEPIO:0100847 - artic-v2: - text: artic-v2 + artic-v2 [GENEPIO:0100848]: + text: artic-v2 [GENEPIO:0100848] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 2.0.0. meaning: GENEPIO:0100848 - artic-v3: - text: artic-v3 + artic-v3 [GENEPIO:0100849]: + text: artic-v3 [GENEPIO:0100849] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 3.0.0. meaning: GENEPIO:0100849 - artic-v4: - text: artic-v4 + artic-v4 [GENEPIO:0100850]: + text: artic-v4 [GENEPIO:0100850] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 4.0.0. meaning: GENEPIO:0100850 - artic-v4.1: - text: artic-v4.1 + artic-v4.1 [GENEPIO:0100851]: + text: artic-v4.1 [GENEPIO:0100851] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 4.1.0. meaning: GENEPIO:0100851 - artic-v5.0.0_400: - text: artic-v5.0.0_400 + artic-v5.0.0_400 [GENEPIO:0100852]: + text: artic-v5.0.0_400 [GENEPIO:0100852] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons + approximately 400bp in length. meaning: GENEPIO:0100852 - artic-v5.1.0_400: - text: artic-v5.1.0_400 + artic-v5.1.0_400 [GENEPIO:0100853]: + text: artic-v5.1.0_400 [GENEPIO:0100853] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons + approximately 400bp in length. meaning: GENEPIO:0100853 - artic-v5.2.0_1200: - text: artic-v5.2.0_1200 + artic-v5.2.0_1200 [GENEPIO:0100854]: + text: artic-v5.2.0_1200 [GENEPIO:0100854] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons + approximately 1200bp in length. meaning: GENEPIO:0100854 - artic-v5.2.0_400: - text: artic-v5.2.0_400 + artic-v5.2.0_400 [GENEPIO:0100855]: + text: artic-v5.2.0_400 [GENEPIO:0100855] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons + approximately 400bp in length. meaning: GENEPIO:0100855 - artic-v5.3.2_400: - text: artic-v5.3.2_400 + artic-v5.3.2_400 [GENEPIO:0100856]: + text: artic-v5.3.2_400 [GENEPIO:0100856] + description: An amplicon strategy which was developed by the ARTIC consortium + for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons + approximately 400bp in length. meaning: GENEPIO:0100856 - eden-v1: - text: eden-v1 + eden-v1 [GENEPIO:0100857]: + text: eden-v1 [GENEPIO:0100857] + description: An amplicon strategy which was developed by John-Sebastian Eden + with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces + amplicons approximately 2500bp in length. meaning: GENEPIO:0100857 - midnight-bccdc-v1: - text: midnight-bccdc-v1 + midnight-bccdc-v1 [GENEPIO:0100858]: + text: midnight-bccdc-v1 [GENEPIO:0100858] + description: An amplicon strategy which is for SARS-CoV-2 and based on the + original Midnight scheme developed by Oxford Nanopore Technologies, and + adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 + which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100858 - midnight-bccdc-v2: - text: midnight-bccdc-v2 + midnight-bccdc-v2 [GENEPIO:0100859]: + text: midnight-bccdc-v2 [GENEPIO:0100859] + description: An amplicon strategy which targets SARS-CoV-2 and is based on + the original Midnight scheme developed by Oxford Nanopore Technologies, + and adapted by the BCCDC Public Health Lab with the attributes of version + 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100859 - midnight-bccdc-v3: - text: midnight-bccdc-v3 + midnight-bccdc-v3 [GENEPIO:0100860]: + text: midnight-bccdc-v3 [GENEPIO:0100860] + description: An amplicon strategy which targets SARS-CoV-2 and is based on + the original Midnight scheme developed by Oxford Nanopore Technologies, + and adapted by the BCCDC Public Health Lab with the attributes of version + 3.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100860 - midnight-bccdc-v4: - text: midnight-bccdc-v4 + midnight-bccdc-v4 [GENEPIO:0100861]: + text: midnight-bccdc-v4 [GENEPIO:0100861] + description: An amplicon strategy which targets SARS-CoV-2 and is based on + the original Midnight scheme developed by Oxford Nanopore Technologies, + and adapted by the BCCDC Public Health Lab with the attributes of version + 4.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100861 - midnight-ont-v3: - text: midnight-ont-v3 + midnight-ont-v3 [GENEPIO:0100862]: + text: midnight-ont-v3 [GENEPIO:0100862] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by Oxford Nanopore Technologies with the attributes of version 2.0.0 which + produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100862 - midnight-v1: - text: midnight-v1 + midnight-v1 [GENEPIO:0100863]: + text: midnight-v1 [GENEPIO:0100863] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by Oxford Nanopore Technologies with the attributes of version 1.0.0 which + produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100863 - midnight-v2: - text: midnight-v2 + midnight-v2 [GENEPIO:0100864]: + text: midnight-v2 [GENEPIO:0100864] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by Oxford Nanopore Technologies with the attributes of version 2.0.0 which + produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100864 - varskip-vsl1a: - text: varskip-vsl1a + varskip-vsl1a [GENEPIO:0100865]: + text: varskip-vsl1a [GENEPIO:0100865] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by New England BioLabs using PrimalSeq to reduce effects of variants with + the attributes of version 1a long. meaning: GENEPIO:0100865 - varskip-vss1a: - text: varskip-vss1a + varskip-vss1a [GENEPIO:0100866]: + text: varskip-vss1a [GENEPIO:0100866] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by New England BioLabs using PrimalSeq to reduce effects of variants with + the attributes of version 1a short. meaning: GENEPIO:0100866 - varskip-vss2a: - text: varskip-vss2a + varskip-vss2a [GENEPIO:0100867]: + text: varskip-vss2a [GENEPIO:0100867] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by New England BioLabs using PrimalSeq to reduce effects of variants with + the attributes of version 2a. meaning: GENEPIO:0100867 - varskip-vss2b: - text: varskip-vss2b + varskip-vss2b [GENEPIO:0100868]: + text: varskip-vss2b [GENEPIO:0100868] + description: An amplicon strategy which targets SARS-CoV-2 and was developed + by New England BioLabs using PrimalSeq to reduce effects of variants with + the attributes of version 2b. meaning: GENEPIO:0100868 - genomic target enrichment method menu: - name: genomic target enrichment method menu + GenomicTargetEnrichmentMethodMenu: + name: GenomicTargetEnrichmentMethodMenu + title: genomic target enrichment method menu permissible_values: - Hybrid selection method: - text: Hybrid selection method + Hybridization capture [GENEPIO:0001950]: + text: Hybridization capture [GENEPIO:0001950] + description: Selection by hybridization in array or solution. meaning: GENEPIO:0001950 - rRNA depletion method: - text: rRNA depletion method + rRNA depletion method [GENEPIO:0101020]: + text: rRNA depletion method [GENEPIO:0101020] + description: Removal of background RNA for the purposes of enriching the genomic + target. meaning: GENEPIO:0101020 - quality control determination menu: - name: quality control determination menu + QualityControlDeterminationMenu: + name: QualityControlDeterminationMenu + title: quality control determination menu permissible_values: - No quality control issues identified: - text: No quality control issues identified + No quality control issues identified [GENEPIO:0100562]: + text: No quality control issues identified [GENEPIO:0100562] + description: A statement confirming that quality control processes were carried + out and no quality issues were detected. meaning: GENEPIO:0100562 - Sequence passed quality control: - text: Sequence passed quality control + Sequence passed quality control [GENEPIO:0100563]: + text: Sequence passed quality control [GENEPIO:0100563] + description: A statement confirming that quality control processes were carried + out and that the sequence met the assessment criteria. meaning: GENEPIO:0100563 - Sequence failed quality control: - text: Sequence failed quality control + Sequence failed quality control [GENEPIO:0100564]: + text: Sequence failed quality control [GENEPIO:0100564] + description: A statement confirming that quality control processes were carried + out and that the sequence did not meet the assessment criteria. meaning: GENEPIO:0100564 - Minor quality control issues identified: - text: Minor quality control issues identified + Minor quality control issues identified [GENEPIO:0100565]: + text: Minor quality control issues identified [GENEPIO:0100565] + description: A statement confirming that quality control processes were carried + out and that the sequence did not meet the assessment criteria, however + the issues detected were minor. meaning: GENEPIO:0100565 - Sequence flagged for potential quality control issues: - text: Sequence flagged for potential quality control issues + Sequence flagged for potential quality control issues [GENEPIO:0100566]: + text: Sequence flagged for potential quality control issues [GENEPIO:0100566] + description: A statement confirming that quality control processes were carried + out however it is unclear whether the sequence meets the assessment criteria + and the assessment requires review. meaning: GENEPIO:0100566 - Quality control not performed: - text: Quality control not performed + Quality control not performed [GENEPIO:0100567]: + text: Quality control not performed [GENEPIO:0100567] + description: A statement confirming that quality control processes have not + been carried out. meaning: GENEPIO:0100567 - quality control issues menu: - name: quality control issues menu + QualityControlIssuesMenu: + name: QualityControlIssuesMenu + title: quality control issues menu permissible_values: - Low quality sequence: - text: Low quality sequence + Low quality sequence [GENEPIO:0100568]: + text: Low quality sequence [GENEPIO:0100568] + description: Sequence data that does not meet quality control thresholds. meaning: GENEPIO:0100568 - Sequence contaminated: - text: Sequence contaminated + Sequence contaminated [GENEPIO:0100569]: + text: Sequence contaminated [GENEPIO:0100569] + description: Sequence data that contains reads from unintended targets (e.g. + other organisms, other samples) due to contamination so that it does not + faithfully represent the genetic information from the biological source. meaning: GENEPIO:0100569 - Low average genome coverage: - text: Low average genome coverage + Low average genome coverage [GENEPIO:0100570]: + text: Low average genome coverage [GENEPIO:0100570] + description: Sequence data in which the entire length of the genome is not + sufficiently sequenced (low breadth of coverage), or particular positions + of the genome are not sequenced a prescribed number of times (low depth + of coverage). meaning: GENEPIO:0100570 - Low percent genome captured: - text: Low percent genome captured + Low percent genome captured [GENEPIO:0100571]: + text: Low percent genome captured [GENEPIO:0100571] + description: Sequence data in which the entire length of the genome is not + sufficiently sequenced (low breadth of coverage). meaning: GENEPIO:0100571 - Read lengths shorter than expected: - text: Read lengths shorter than expected + Read lengths shorter than expected [GENEPIO:0100572]: + text: Read lengths shorter than expected [GENEPIO:0100572] + description: Average sequence read lengths that are below the expected size + range given a particular sequencing instrument, reagents and conditions. meaning: GENEPIO:0100572 - Sequence amplification artifacts: - text: Sequence amplification artifacts + Sequence amplification artifacts [GENEPIO:0100573]: + text: Sequence amplification artifacts [GENEPIO:0100573] + description: Sequence data containing errors generated during the PCR amplification + process during library generation (e.g. mutations, altered read distribution, + amplicon dropouts). meaning: GENEPIO:0100573 - Low signal to noise ratio: - text: Low signal to noise ratio + Low signal to noise ratio [GENEPIO:0100574]: + text: Low signal to noise ratio [GENEPIO:0100574] + description: Sequence data containing more errors or undetermined bases (noise) + than sequence representing the biological source (signal). meaning: GENEPIO:0100574 - Low coverage of characteristic mutations: - text: Low coverage of characteristic mutations + Low coverage of characteristic mutations [GENEPIO:0100575]: + text: Low coverage of characteristic mutations [GENEPIO:0100575] + description: Sequence data that contains a lower than expected number of mutations + that are usually observed in the reference sequence. meaning: GENEPIO:0100575 - gene name menu: - name: gene name menu + GeneSymbolMenu: + name: GeneSymbolMenu + title: gene symbol menu permissible_values: - E gene (orf4): - text: E gene (orf4) + E gene (orf4) [GENEPIO:0100151]: + text: E gene (orf4) [GENEPIO:0100151] meaning: GENEPIO:0100151 - M gene (orf5): - text: M gene (orf5) + M gene (orf5) [GENEPIO:0100152]: + text: M gene (orf5) [GENEPIO:0100152] meaning: GENEPIO:0100152 - N gene (orf9): - text: N gene (orf9) + N gene (orf9) [GENEPIO:0100153]: + text: N gene (orf9) [GENEPIO:0100153] meaning: GENEPIO:0100153 - Spike gene (orf2): - text: Spike gene (orf2) + Spike gene (orf2) [GENEPIO:0100154]: + text: Spike gene (orf2) [GENEPIO:0100154] meaning: GENEPIO:0100154 - orf1ab (rep): - text: orf1ab (rep) + orf1ab (rep) [GENEPIO:0100155]: + text: orf1ab (rep) [GENEPIO:0100155] meaning: GENEPIO:0100155 - orf1a (pp1a): - text: orf1a (pp1a) + orf1a (pp1a) [GENEPIO:0100156]: + text: orf1a (pp1a) [GENEPIO:0100156] meaning: GENEPIO:0100156 - is_a: orf1ab (rep) - nsp11: - text: nsp11 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp11 [GENEPIO:0100157]: + text: nsp11 [GENEPIO:0100157] meaning: GENEPIO:0100157 - is_a: orf1a (pp1a) - nsp1: - text: nsp1 + is_a: orf1a (pp1a) [GENEPIO:0100156] + nsp1 [GENEPIO:0100158]: + text: nsp1 [GENEPIO:0100158] meaning: GENEPIO:0100158 - is_a: orf1ab (rep) - nsp2: - text: nsp2 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp2 [GENEPIO:0100159]: + text: nsp2 [GENEPIO:0100159] meaning: GENEPIO:0100159 - is_a: orf1ab (rep) - nsp3: - text: nsp3 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp3 [GENEPIO:0100160]: + text: nsp3 [GENEPIO:0100160] meaning: GENEPIO:0100160 - is_a: orf1ab (rep) - nsp4: - text: nsp4 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp4 [GENEPIO:0100161]: + text: nsp4 [GENEPIO:0100161] meaning: GENEPIO:0100161 - is_a: orf1ab (rep) - nsp5: - text: nsp5 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp5 [GENEPIO:0100162]: + text: nsp5 [GENEPIO:0100162] meaning: GENEPIO:0100162 - is_a: orf1ab (rep) - nsp6: - text: nsp6 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp6 [GENEPIO:0100163]: + text: nsp6 [GENEPIO:0100163] meaning: GENEPIO:0100163 - is_a: orf1ab (rep) - nsp7: - text: nsp7 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp7 [GENEPIO:0100164]: + text: nsp7 [GENEPIO:0100164] meaning: GENEPIO:0100164 - is_a: orf1ab (rep) - nsp8: - text: nsp8 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp8 [GENEPIO:0100165]: + text: nsp8 [GENEPIO:0100165] meaning: GENEPIO:0100165 - is_a: orf1ab (rep) - nsp9: - text: nsp9 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp9 [GENEPIO:0100166]: + text: nsp9 [GENEPIO:0100166] meaning: GENEPIO:0100166 - is_a: orf1ab (rep) - nsp10: - text: nsp10 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp10 [GENEPIO:0100167]: + text: nsp10 [GENEPIO:0100167] meaning: GENEPIO:0100167 - is_a: orf1ab (rep) - RdRp gene (nsp12): - text: RdRp gene (nsp12) + is_a: orf1ab (rep) [GENEPIO:0100155] + RdRp gene (nsp12) [GENEPIO:0100168]: + text: RdRp gene (nsp12) [GENEPIO:0100168] meaning: GENEPIO:0100168 - is_a: orf1ab (rep) - hel gene (nsp13): - text: hel gene (nsp13) + is_a: orf1ab (rep) [GENEPIO:0100155] + hel gene (nsp13) [GENEPIO:0100169]: + text: hel gene (nsp13) [GENEPIO:0100169] meaning: GENEPIO:0100169 - is_a: orf1ab (rep) - exoN gene (nsp14): - text: exoN gene (nsp14) + is_a: orf1ab (rep) [GENEPIO:0100155] + exoN gene (nsp14) [GENEPIO:0100170]: + text: exoN gene (nsp14) [GENEPIO:0100170] meaning: GENEPIO:0100170 - is_a: orf1ab (rep) - nsp15: - text: nsp15 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp15 [GENEPIO:0100171]: + text: nsp15 [GENEPIO:0100171] meaning: GENEPIO:0100171 - is_a: orf1ab (rep) - nsp16: - text: nsp16 + is_a: orf1ab (rep) [GENEPIO:0100155] + nsp16 [GENEPIO:0100172]: + text: nsp16 [GENEPIO:0100172] meaning: GENEPIO:0100172 - is_a: orf1ab (rep) - orf3a: - text: orf3a + is_a: orf1ab (rep) [GENEPIO:0100155] + orf3a [GENEPIO:0100173]: + text: orf3a [GENEPIO:0100173] meaning: GENEPIO:0100173 - orf3b: - text: orf3b + orf3b [GENEPIO:0100174]: + text: orf3b [GENEPIO:0100174] meaning: GENEPIO:0100174 - orf6 (ns6): - text: orf6 (ns6) + orf6 (ns6) [GENEPIO:0100175]: + text: orf6 (ns6) [GENEPIO:0100175] meaning: GENEPIO:0100175 - orf7a: - text: orf7a + orf7a [GENEPIO:0100176]: + text: orf7a [GENEPIO:0100176] meaning: GENEPIO:0100176 - orf7b (ns7b): - text: orf7b (ns7b) + orf7b (ns7b) [GENEPIO:0100177]: + text: orf7b (ns7b) [GENEPIO:0100177] meaning: GENEPIO:0100177 - orf8 (ns8): - text: orf8 (ns8) + orf8 (ns8) [GENEPIO:0100178]: + text: orf8 (ns8) [GENEPIO:0100178] meaning: GENEPIO:0100178 - orf9b: - text: orf9b + orf9b [GENEPIO:0100179]: + text: orf9b [GENEPIO:0100179] meaning: GENEPIO:0100179 - orf9c: - text: orf9c + orf9c [GENEPIO:0100180]: + text: orf9c [GENEPIO:0100180] meaning: GENEPIO:0100180 - orf10: - text: orf10 + orf10 [GENEPIO:0100181]: + text: orf10 [GENEPIO:0100181] meaning: GENEPIO:0100181 - orf14: - text: orf14 + orf14 [GENEPIO:0100182]: + text: orf14 [GENEPIO:0100182] meaning: GENEPIO:0100182 - SARS-COV-2 5' UTR: - text: SARS-COV-2 5' UTR + SARS-COV-2 5' UTR [GENEPIO:0100183]: + text: SARS-COV-2 5' UTR [GENEPIO:0100183] meaning: GENEPIO:0100183 - diagnostic target presence menu: - name: diagnostic target presence menu + DiagnosticTargetPresenceMenu: + name: DiagnosticTargetPresenceMenu + title: diagnostic target presence menu permissible_values: - diagnostic target present: - text: diagnostic target present + diagnostic target present [GENEPIO:0100987]: + text: diagnostic target present [GENEPIO:0100987] + description: A quality inhering in a bearer by virtue of the bearer's existence. meaning: GENEPIO:0100987 - diagnostic target absent: - text: diagnostic target absent + diagnostic target absent [GENEPIO:0100988]: + text: diagnostic target absent [GENEPIO:0100988] + description: Aquality denoting the lack of an entity. meaning: GENEPIO:0100988 - diagnostic measurement unit menu: - name: diagnostic measurement unit menu + DiagnosticMeasurementUnitMenu: + name: DiagnosticMeasurementUnitMenu + title: diagnostic measurement unit menu permissible_values: gene copies per liter (GC/L): text: gene copies per liter (GC/L) - cycle threshold (Ct): - text: cycle threshold (Ct) + description: A unit that measures the number of copies of a given gene within + a liter of a biological material. + cycle threshold (Ct) [GENEPIO:0100657]: + text: cycle threshold (Ct) [GENEPIO:0100657] + description: A data field which describes the cycle threshold (Ct) value result + from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) + test. meaning: GENEPIO:0100657 - colony forming units per milliliter (CFU/mL): - text: colony forming units per milliliter (CFU/mL) + colony forming units per milliliter (CFU/mL) [UO:0000213]: + text: colony forming units per milliliter (CFU/mL) [UO:0000213] + description: A unit of microbial density that describes the number of colony + forming units within a milliliter of material. meaning: UO:0000213 colony forming units per 100 milliliter (CFU/100 mL): text: colony forming units per 100 milliliter (CFU/100 mL) + description: A unit of microbial density that describes the number of colony + forming units within 100 milliliters of material. colony forming units per grams total solids (CFU/gTS): text: colony forming units per grams total solids (CFU/gTS) + description: A unit of microbial density that describes the number of colony + forming units within a gram of total solids in waste material. most probable number per milliliter (MPN/mL): text: most probable number per milliliter (MPN/mL) + description: A unit of microbial density that describes the most probable + number of microbes within one milliliter of material. most probable number per 100 milliliter (MPN/100 mL): text: most probable number per 100 milliliter (MPN/100 mL) - diagnostic measurement method menu: - name: diagnostic measurement method menu + description: A unit of microbial density that describes the most probable + number of microbes within 100 milliliters of material. + DiagnosticMeasurementMethodMenu: + name: DiagnosticMeasurementMethodMenu + title: diagnostic measurement method menu permissible_values: - Quantitative real time polymerase chain reaction (qPCR): - text: Quantitative real time polymerase chain reaction (qPCR) + Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]: + text: Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] + description: An assay, based on the PCR, that amplifies and simultaneously + quantifies a specific DNA molecule based on the use of complementary probes/primers. + It enables both detection and quantification (as absolute number of copies + or relative amount when normalized to DNA input or additional normalizing + genes) of one or more specific sequences in a DNA sample. meaning: OBI:0000893 Digital real time polymerase chain reaction (dPCR): text: Digital real time polymerase chain reaction (dPCR) + description: A type of polymerase chain reaction technique in which the sample + is fractionated, within which individual PCR reactions occur in each fraction Bacteria culture test: text: Bacteria culture test + description: An assay to identify the presence of bacteria types: WhitespaceMinimizedString: name: WhitespaceMinimizedString diff --git a/web/templates/wastewater/schema_core.yaml b/web/templates/wastewater/schema_core.yaml index c7f4a98d..42dc7744 100644 --- a/web/templates/wastewater/schema_core.yaml +++ b/web/templates/wastewater/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/GRDI name: "Wastewater" description: "" -version: 2.0.0 +version: 3.1.1 imports: - 'linkml:types' prefixes: @@ -16,14 +16,20 @@ classes: name: 'WastewaterSARS-CoV-2' description: Specification for Wastewater SARS-CoV-2 virus biosample data gathering is_a: dh_interface + annotations: + version: 3.1.1 'WastewaterAMR': name: 'WastewaterAMR' description: Specification for Wastewater AMR biosample data gathering is_a: dh_interface + annotations: + version: 3.1.1 'WastewaterPathogenAgnostic': name: 'WastewaterPathogenAgnostic' description: Specification for Wastewater Pathogen Agnostic biosample data gathering is_a: dh_interface + annotations: + version: 3.1.1 slots: {} enums: {} types: diff --git a/web/templates/wastewater/schema_enums.tsv b/web/templates/wastewater/schema_enums.tsv index ff7fd162..222799e6 100644 --- a/web/templates/wastewater/schema_enums.tsv +++ b/web/templates/wastewater/schema_enums.tsv @@ -1,792 +1,800 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal - -null value menu GENEPIO:0001619 Not Applicable - GENEPIO:0001618 Missing - GENEPIO:0001620 Not Collected - GENEPIO:0001668 Not Provided - GENEPIO:0001810 Restricted Access - -geo_loc_name (country) menu GAZ:00006882 Afghanistan - GAZ:00002953 Albania - GAZ:00000563 Algeria - GAZ:00003957 American Samoa - GAZ:00002948 Andorra - GAZ:00001095 Angola - GAZ:00009159 Anguilla - GAZ:00000462 Antarctica - GAZ:00006883 Antigua and Barbuda - GAZ:00002928 Argentina - GAZ:00004094 Armenia - GAZ:00004025 Aruba - GAZ:00005901 Ashmore and Cartier Islands - GAZ:00000463 Australia - GAZ:00002942 Austria - GAZ:00004941 Azerbaijan - GAZ:00002733 Bahamas - GAZ:00005281 Bahrain - GAZ:00007117 Baker Island - GAZ:00003750 Bangladesh - GAZ:00001251 Barbados - GAZ:00005810 Bassas da India - GAZ:00006886 Belarus - GAZ:00002938 Belgium - GAZ:00002934 Belize - GAZ:00000904 Benin - GAZ:00001264 Bermuda - GAZ:00003920 Bhutan - GAZ:00002511 Bolivia - GAZ:00025355 Borneo - GAZ:00006887 Bosnia and Herzegovina - GAZ:00001097 Botswana - GAZ:00001453 Bouvet Island - GAZ:00002828 Brazil - GAZ:00003961 British Virgin Islands - GAZ:00003901 Brunei - GAZ:00002950 Bulgaria - GAZ:00000905 Burkina Faso - GAZ:00001090 Burundi - GAZ:00006888 Cambodia - GAZ:00001093 Cameroon - GAZ:00002560 Canada - GAZ:00001227 Cape Verde - GAZ:00003986 Cayman Islands - GAZ:00001089 Central African Republic - GAZ:00000586 Chad - GAZ:00002825 Chile - GAZ:00002845 China - GAZ:00005915 Christmas Island - GAZ:00005838 Clipperton Island - GAZ:00009721 Cocos Islands - GAZ:00002929 Colombia - GAZ:00005820 Comoros - GAZ:00053798 Cook Islands - GAZ:00005917 Coral Sea Islands - GAZ:00002901 Costa Rica - GAZ:00000906 Cote d'Ivoire - GAZ:00002719 Croatia - GAZ:00003762 Cuba - GAZ:00012582 Curacao - GAZ:00004006 Cyprus - GAZ:00002954 Czech Republic - GAZ:00001086 Democratic Republic of the Congo - GAZ:00005852 Denmark - GAZ:00000582 Djibouti - GAZ:00006890 Dominica - GAZ:00003952 Dominican Republic - GAZ:00002912 Ecuador - GAZ:00003934 Egypt - GAZ:00002935 El Salvador - GAZ:00001091 Equatorial Guinea - GAZ:00000581 Eritrea - GAZ:00002959 Estonia - GAZ:00001099 Eswatini - GAZ:00000567 Ethiopia - GAZ:00005811 Europa Island - GAZ:00001412 Falkland Islands (Islas Malvinas) - GAZ:00059206 Faroe Islands - GAZ:00006891 Fiji - GAZ:00002937 Finland - GAZ:00003940 France - GAZ:00002516 French Guiana - GAZ:00002918 French Polynesia - GAZ:00003753 French Southern and Antarctic Lands - GAZ:00001092 Gabon - GAZ:00000907 Gambia - GAZ:00009571 Gaza Strip - GAZ:00004942 Georgia - GAZ:00002646 Germany - GAZ:00000908 Ghana - GAZ:00003987 Gibraltar - GAZ:00005808 Glorioso Islands - GAZ:00002945 Greece - GAZ:00001507 Greenland - GAZ:02000573 Grenada - GAZ:00067142 Guadeloupe - GAZ:00003706 Guam - GAZ:00002936 Guatemala - GAZ:00001550 Guernsey - GAZ:00000909 Guinea - GAZ:00000910 Guinea-Bissau - GAZ:00002522 Guyana - GAZ:00003953 Haiti - GAZ:00009718 Heard Island and McDonald Islands - GAZ:00002894 Honduras - GAZ:00003203 Hong Kong - GAZ:00007120 Howland Island - GAZ:00002952 Hungary - GAZ:00000843 Iceland - GAZ:00002839 India - GAZ:00003727 Indonesia - GAZ:00004474 Iran - GAZ:00004483 Iraq - GAZ:00002943 Ireland - GAZ:00052477 Isle of Man - GAZ:00002476 Israel - GAZ:00002650 Italy - GAZ:00003781 Jamaica - GAZ:00005853 Jan Mayen - GAZ:00002747 Japan - GAZ:00007118 Jarvis Island - GAZ:00001551 Jersey - GAZ:00007114 Johnston Atoll - GAZ:00002473 Jordan - GAZ:00005809 Juan de Nova Island - GAZ:00004999 Kazakhstan - GAZ:00001101 Kenya - GAZ:00005682 Kerguelen Archipelago - GAZ:00007116 Kingman Reef - GAZ:00006894 Kiribati - GAZ:00011337 Kosovo - GAZ:00005285 Kuwait - GAZ:00006893 Kyrgyzstan - GAZ:00006889 Laos - GAZ:00002958 Latvia - GAZ:00002478 Lebanon - GAZ:00001098 Lesotho - GAZ:00000911 Liberia - GAZ:00000566 Libya - GAZ:00003858 Liechtenstein - GAZ:00007144 Line Islands - GAZ:00002960 Lithuania - GAZ:00002947 Luxembourg - GAZ:00003202 Macau - GAZ:00001108 Madagascar - GAZ:00001105 Malawi - GAZ:00003902 Malaysia - GAZ:00006924 Maldives - GAZ:00000584 Mali - GAZ:00004017 Malta - GAZ:00007161 Marshall Islands - GAZ:00067143 Martinique - GAZ:00000583 Mauritania - GAZ:00003745 Mauritius - GAZ:00003943 Mayotte - GAZ:00002852 Mexico - GAZ:00005862 Micronesia - GAZ:00007112 Midway Islands - GAZ:00003897 Moldova - GAZ:00003857 Monaco - GAZ:00008744 Mongolia - GAZ:00006898 Montenegro - GAZ:00003988 Montserrat - GAZ:00000565 Morocco - GAZ:00001100 Mozambique - GAZ:00006899 Myanmar - GAZ:00001096 Namibia - GAZ:00006900 Nauru - GAZ:00007119 Navassa Island - GAZ:00004399 Nepal - GAZ:00002946 Netherlands - GAZ:00005206 New Caledonia - GAZ:00000469 New Zealand - GAZ:00002978 Nicaragua - GAZ:00000585 Niger - GAZ:00000912 Nigeria - GAZ:00006902 Niue - GAZ:00005908 Norfolk Island - GAZ:00002801 North Korea - GAZ:00006895 North Macedonia - GAZ:00002284 North Sea - GAZ:00003958 Northern Mariana Islands - GAZ:00002699 Norway - GAZ:00005283 Oman - GAZ:00005246 Pakistan - GAZ:00006905 Palau - GAZ:00002892 Panama - GAZ:00003922 Papua New Guinea - GAZ:00010832 Paracel Islands - GAZ:00002933 Paraguay - GAZ:00002932 Peru - GAZ:00004525 Philippines - GAZ:00005867 Pitcairn Islands - GAZ:00002939 Poland - GAZ:00004126 Portugal - GAZ:00006935 Puerto Rico - GAZ:00005286 Qatar - GAZ:00001088 Republic of the Congo - GAZ:00003945 Reunion - GAZ:00002951 Romania - GAZ:00023304 Ross Sea - GAZ:00002721 Russia - GAZ:00001087 Rwanda - GAZ:00000849 Saint Helena - GAZ:00006906 Saint Kitts and Nevis - GAZ:00006909 Saint Lucia - GAZ:00003942 Saint Pierre and Miquelon - GAZ:00005841 Saint Martin - GAZ:02000565 Saint Vincent and the Grenadines - GAZ:00006910 Samoa - GAZ:00003102 San Marino - GAZ:00006927 Sao Tome and Principe - GAZ:00005279 Saudi Arabia - GAZ:00000913 Senegal - GAZ:00002957 Serbia - GAZ:00006922 Seychelles - GAZ:00000914 Sierra Leone - GAZ:00003923 Singapore - GAZ:00012579 Sint Maarten - GAZ:00002956 Slovakia - GAZ:00002955 Slovenia - GAZ:00005275 Solomon Islands - GAZ:00001104 Somalia - GAZ:00001094 South Africa - GAZ:00003990 South Georgia and the South Sandwich Islands - GAZ:00002802 South Korea - GAZ:00233439 South Sudan - GAZ:00000591 Spain - GAZ:00010831 Spratly Islands - GAZ:00003924 Sri Lanka - GAZ:00002475 State of Palestine - GAZ:00000560 Sudan - GAZ:00002525 Suriname - GAZ:00005396 Svalbard - GAZ:00001099 Swaziland - GAZ:00002729 Sweden - GAZ:00002941 Switzerland - GAZ:00002474 Syria - GAZ:00005341 Taiwan - GAZ:00006912 Tajikistan - GAZ:00001103 Tanzania - GAZ:00003744 Thailand - GAZ:00006913 Timor-Leste - GAZ:00000915 Togo - GAZ:00260188 Tokelau - GAZ:00006916 Tonga - GAZ:00003767 Trinidad and Tobago - GAZ:00005812 Tromelin Island - GAZ:00000562 Tunisia - GAZ:00000558 Turkey - GAZ:00005018 Turkmenistan - GAZ:00003955 Turks and Caicos Islands - GAZ:00009715 Tuvalu - GAZ:00002459 United States of America - GAZ:00001102 Uganda - GAZ:00002724 Ukraine - GAZ:00005282 United Arab Emirates - GAZ:00002637 United Kingdom - GAZ:00002930 Uruguay - GAZ:00004979 Uzbekistan - GAZ:00006918 Vanuatu - GAZ:00002931 Venezuela - GAZ:00003756 Viet Nam - GAZ:00003959 Virgin Islands - GAZ:00007111 Wake Island - GAZ:00007191 Wallis and Futuna - GAZ:00009572 West Bank - GAZ:00000564 Western Sahara - GAZ:00005284 Yemen - GAZ:00001107 Zambia - GAZ:00001106 Zimbabwe - -geo_loc_name (state/province/territory) menu GAZ:00002566 Alberta - GAZ:00002562 British Columbia - GAZ:00002571 Manitoba - GAZ:00002570 New Brunswick - GAZ:00002567 Newfoundland and Labrador - GAZ:00002575 Northwest Territories - GAZ:00002565 Nova Scotia - GAZ:00002574 Nunavut - GAZ:00002563 Ontario - GAZ:00002572 Prince Edward Island - GAZ:00002569 Quebec - GAZ:00002564 Saskatchewan - GAZ:00002576 Yukon - - -watershed shapefile availability menu GENEPIO:0100993 Available - GENEPIO:0100995 Unknown - -organism menu NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 - -purpose of sampling menu GENEPIO:0100869 Wastewater treatment efficiency assessment - GENEPIO:0100870 Wastewater chemical surveillance - GENEPIO:0100871 Wastewater drug surveillance - GENEPIO:0100872 Wastewater pathogen surveillance - GENEPIO:0100003 Research - GENEPIO:0100873 Environmental survey (profiling) - GENEPIO:0100024 Protocol testing - -scale of sampling menu GENEPIO:0100874 Community-level surveillance - GENEPIO:0100875 Institution-level surveillance - GENEPIO:0100876 Building-level surveillance - -sample collection time of day menu NCIT:C64934 Morning - NCIT:C64935 Afternoon - NCIT:C64936 Evening - NCIT:C65001 Night - -sample collection duration unit menu UO:0000010 Second - UO:0000031 Minute - UO:0000032 Hour - UO:0000033 Day - UO:0000034 Week - UO:0000035 Month - UO:0000036 Year - -presampling activity menu ENVO:01001442 Agricultural activity - ENVO:01001248 Animal husbandry - ENVO:01001450 Industrial activity - NCIT:C16205 Healthcare activity - ENVO:06105300 Wastewater treatment - GENEPIO:0100881 Wastewater filtration - GENEPIO:0100882 Wastewater grit removal - GENEPIO:0100883 Wastewater microbial pre-treatment - GENEPIO:0100884 Wastewater primary sedimentation - GENEPIO:0100885 Wastewater secondary sedimentation - -sample volume measurement unit menu UO:0000101 microliter (uL) - UO:0000098 milliliter (mL) - UO:0000099 liter (L) - -sample storage duration unit menu UO:0000010 Second - UO:0000031 Minute - UO:0000032 Hour - UO:0000033 Day - UO:0000034 Week - UO:0000035 Month - UO:0000036 Year - -specimen processing menu OBI:0600041 Concentration - OBI:0302886 Centrifugation - OBI:0302885 Filtration - NCIT:C154798 Flocculation - GENEPIO:0100886 Magnetic nanobead binding - OBI:0600034 Precipitation - GENEPIO:0101011 Gravity separation - IDO:0100170 Pasteurization - GENEPIO:0101012 Growth in enrichment broth - OBI:0600016 Pooling specimens - GENEPIO:0101021 Technical replicate process - GENEPIO:0101022 Biological replicate process - -environmental site menu ENVO:01001481 Correctional facility - ENVO:03501134 Healthcare facility - ENVO:00002173 Hospital - ENVO:03501182 Clinic - ENVO:03501129 Educational facility - ENVO:03501335 Daycare facility - ENVO:03501130 School - ENVO:03501131 College or university - ENVO:01000933 Residential building - ENVO:03501133 Homeless shelter - ENVO:01000932 Long-term care facility - ENVO:03501117 Transport hub - ENVO:03501122 Airport - ENVO:00000078 Farm - NCIT:C85867 Refugee camp - ENVO:00000064 Road - ENVO:01000447 Roadside - ENVO:00003861 Industrial plant - ENVO:03501297 Meat processing plant - GENEPIO:0100887 Pharmaceutical manufacturing plant - ENVO:00000063 Body of water - ENVO:00002042 Surface water - ENVO:00000020 Lake - ENVO:00000023 Stream - ENVO:00000022 River - ENVO:00000015 Ocean - ENVO:00000016 Sea - ENVO:00000014 Canal - ENVO:00000025 Reservoir - ENVO:01001004 Ground water - ENVO:00000026 Well - ENVO:00000027 Spring - ENVO:00002272 Wastewater treatment plant - ENVO:03600076 Waste stabilization pond (lagoon) - ENVO:01000924 Sewer - ENVO:01000604 Transportation vehicle - ENVO:01000608 Boat - ENVO:03501349 Airplane - -environmental material menu ENVO:00002042 Surface water - ENVO:00002001 Wastewater - GENEPIO:0100890 Wastewater sediment - ENVO:00002044 Sludge - ENVO:00002057 Primary sludge - ENVO:00002058 Secondary sludge - GENEPIO:0100891 Wastewater effluent - GENEPIO:0100892 Primary wastewater effluent - GENEPIO:0100893 Secondary wastewater effluent - -environmental material properties menu GENEPIO:0101004 Fluid (stagnant) - GENEPIO:0101005 Fluid (slow) - GENEPIO:0101006 Fluid (fast) - PATO:0015031 Contamination - GENEPIO:0101010 Fecal-contaminated - PATO:0001735 Liquid - GENEPIO:0101007 Slurry-like - NCIT:C149895 Semi-solid - PATO:0001736 Solid - GENEPIO:0101008 Treated - GENEPIO:0101009 Untreated - -wastewater system type menu Combined sewer system - Sanitary sewer system - ENVO:03600076 Waste stabilization pond - ENVO:01000519 Latrine - Septic tank - Cesspit - ENVO:01000550 Composting toilet - ENVO:01000924 Plumbing drain - - - -experimental specimen role type menu GENEPIO:0101018 Positive experimental control - GENEPIO:0101019 Negative experimental control - EFO:0002090 Technical replicate - EFO:0002091 Biological replicate - -collection device menu GENEPIO:0100941 Grab sampler - GENEPIO:0100943 Core sampling device - GENEPIO:0100944 Vacuum sludge sampling device - GENEPIO:0100945 Cone-shaped sampling device - GENEPIO:0100946 Horizontal grab sampling device - GENEPIO:0100947 Vertical grab sampling device - GENEPIO:0100942 Composite sampler - GENEPIO:0100948 Passive (trap) sampler - GENEPIO:0100949 Moore swab - GENEPIO:0100950 Automatic composite sampler - GENEPIO:0100951 Automatic flow-proportional sampler - GENEPIO:0100952 Automatic sequential (time-proportional) sampler - -collection method menu GENEPIO:0100953 Grab sampling - GENEPIO:0100954 Composite sampling - GENEPIO:0100955 Passive composite sampling - GENEPIO:0100956 Automatic composite sampling - GENEPIO:0100957 Manual composite sampling - -water catchment area human population range menu <10 people - 10 - 100 people - 100 - 1,000 people - 1,000 - 10,000 people - 10,000 - 100,000 people - 100,000 - 1,000,000 people - 1,000,000+ people - -water catchment area human population density unit menu GENEPIO:0100989 persons per square mile - GENEPIO:0100990 persons per square kilometer - GENEPIO:0100991 residents per square mile - GENEPIO:0100992 residents per square kilometer - -populated area type menu GSSO:011077 Suburban - GSSO:011078 Rural - GSSO:011080 Urban - -sampling weather conditions menu ENVO:03501418 Cloudy/Overcast - ENVO:03501419 Partially cloudy - ENVO:03501420 Drizzle - ENVO:01000844 Fog - ENVO:01001564 Rain - ENVO:01000406 Snow - ENVO:01000876 Storm - ENVO:03501421 Sunny/Clear - -presampling weather conditions menu ENVO:03501418 Cloudy/Overcast - ENVO:03501419 Partially cloudy - ENVO:03501420 Drizzle - ENVO:01000844 Fog - ENVO:01001564 Rain - ENVO:01000406 Snow - ENVO:01000876 Storm - ENVO:03501421 Sunny/Clear - -precipitation measurement unit menu UO:0000016 millimeter (mm) - UO:0000015 centimeter (cm) - UO:0000008 meter (m) - UO:0010011 inch (in) - UO:0010013 foot (ft) - -air pressure measurement unit menu EFO:0005212 atmosphere (atm) - bar - UO:0000110 pascal - -ambient temperature measurement unit menu UO:0000195 degree Fahrenheit (F) - UO:0000027 degree Celsius (C) - -total daily flow rate measurement unit menu cubic meter per second (m^3/s) - cubic meter per minute (m^3/min) - cubic meter per hour (m^3/h) - liter per second (L/s) - liter per minute (L/min) - liter per hour (L/h) - liter per day (L/day) - million gallons per day (MGD) - -instantaneous flow rate measurement unit menu cubic meter per second (m^3/s) - cubic meter per minute (m^3/min) - cubic meter per hour (m^3/h) - liter per second (L/s) - liter per minute (L/min) - liter per hour (L/h) - liter per day (L/day) - million gallons per day (MGD) - -turbidity measurement unit menu nephelometric turbidity unit (NTU) - UO:0000318 formazin nephelometric unit (FNU) - -dissolved oxygen measurement unit menu UO:0000273 milligram per liter (mg/L) - UO:0000083 kilogram per cubic meter (kg/m^3) - UO:0000169 part per million (ppm) - -oxygen reduction potential (ORP) measurement unit menu UO:0000247 milliVolt (mV) - -chemical oxygen demand (COD) measurement unit menu UO:0000273 milligram per liter (mg/L) - -carbonaceous biochemical oxygen demand (CBOD) measurement unit menu UO:0000273 milligram per liter (mg/L) - -total suspended solids (TSS) measurement unit menu UO:0000187 percent (%) - UO:0000175 gram per liter (g/L) - -total dissolved solids (TDS) measurement unit menu UO:0000187 percent (%) - UO:0000175 gram per liter (g/L) - -total solids (TS) measurement unit menu UO:0000187 percent (%) - UO:0000175 gram per liter (g/L) - -alkalinity measurement unit menu milliequivalent per liter (meq/L) - UO:0000273 milligram per liter (mg/L) - UO:0000169 parts per million - -conductivity measurement unit menu milliSiemen per centimeter (mS/cm) - microSiemen per centimeter (μS/cm) - Siemen per meter (S/m) - -salinity measurement unit menu practical salinity unit (PSU) - weight for weight (% w/w) - UO:0000168 parts per thousand - UO:0000175 gram per liter (g/L) - -total nitrogen (TN) measurement unit menu UO:0000273 milligram per liter (mg/L) - UO:0000175 gram per liter (g/L) - gram per total solids (g/gTS) - -total phosphorpus (TP) measurement unit menu gram per total solids (g/gTS) - GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) - UO:0000273 milligrams per liter (mg/L) - GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) - -fecal contamination indicator menu NCBITaxon:1211417 crAssphage - NCBITaxon:12239 PMMoV / pepper mild mottle virus - GENEPIO:0101000 Bacteroides HF183 - GENEPIO:0101001 Lachnospiraceae Lachno3 - GENEPIO:0101002 F+ (male specific) coliphages - CHEBI:26756 Stercobilin - -fecal contamination unit menu log10 gene copies per 100 milliliter (log10 GC/100 mL) - gene copies per liter (GC/L) - UO:0010077 PCR quantification cycle - log10 gene copies per nanogram total DNA - -urinary contamination indicator menu CHEBI:36378 Urobilin - -urinary contamination unit menu EFO:0004382 nanograms per liter (ng/L) - -fecal coliform count unit menu UO:0000213 colony forming units per milliliter (CFU/mL) - colony forming units per 100 milliliter (CFU/100 mL) - colony forming units per grams total solids (CFU/gTS) - most probable number per milliliter (MPN/mL) - most probable number per 100 milliliter (MPN/100 mL) - -sample temperature unit (at collection) menu UO:0000195 degree Fahrenheit (F) - UO:0000027 degree Celsius (C) - -sample temperature unit (when received) menu UO:0000195 degree Fahrenheit (F) - UO:0000027 degree Celsius (C) - -purpose of sequencing menu GENEPIO:0100005 Baseline surveillance (random sampling) - GENEPIO:0100006 Targeted surveillance (non-random sampling) - GENEPIO:0100007 Priority surveillance project - GENEPIO:0100009 Longitudinal surveillance (repeat sampling) - GENEPIO:0100012 Travel-associated surveillance - GENEPIO:0100013 Domestic travel surveillance - GENEPIO:0100014 International travel surveillance - GENEPIO:0100022 Research - GENEPIO:0100023 Viral passage experiment - GENEPIO:0100024 Protocol testing experiment - -sequencing platform menu GENEPIO:0001923 Illumina - GENEPIO:0001927 Pacific Biosciences - GENEPIO:0002683 Ion Torrent - GENEPIO:0100986 Oxford Nanopore Technologies - GENEPIO:0004324 BGI Genomics - GENEPIO:0004325 MGI - GENEPIO:0001926 Roche LS454 - GENEPIO:0002684 SOLiD sequencing - GENEPIO:0001924 Complete Genomics - GENEPIO:0002682 Helicos - GENEPIO:0100985 Applied Biosystems - -sequencing instrument menu GENEPIO:0100105 Illumina - GENEPIO:0100106 Illumina Genome Analyzer - OBI:0000703 Illumina Genome Analyzer II - OBI:0002000 Illumina Genome Analyzer IIx - GENEPIO:0100109 Illumina HiScanSQ - GENEPIO:0100110 Illumina HiSeq - GENEPIO:0100111 Illumina HiSeq X - GENEPIO:0100112 Illumina HiSeq X Five - GENEPIO:0100113 Illumina HiSeq X Ten - OBI:0002022 Illumina HiSeq 1000 - GENEPIO:0100115 Illumina HiSeq 1500 - OBI:0002001 Illumina HiSeq 2000 - OBI:0002002 Illumina HiSeq 2500 - OBI:0002048 Illumina HiSeq 3000 - OBI:0002049 Illumina HiSeq 4000 - GENEPIO:0100120 Illumina iSeq - GENEPIO:0100121 Illumina iSeq 100 - GENEPIO:0100122 Illumina NovaSeq - GENEPIO:0100123 Illumina NovaSeq 6000 - GENEPIO:0100124 Illumina MiniSeq - OBI:0002003 Illumina MiSeq - GENEPIO:0100126 Illumina NextSeq - OBI:0002021 Illumina NextSeq 500 - GENEPIO:0100128 Illumina NextSeq 550 - GENEPIO:0004432 Illumina NextSeq 1000 - GENEPIO:0100129 Illumina NextSeq 2000 - GENEPIO:0100130 PacBio - GENEPIO:0100131 PacBio RS - OBI:0002012 PacBio RS II - GENEPIO:0100133 PacBio Sequel - GENEPIO:0100134 PacBio Sequel II - GENEPIO:0100135 Ion Torrent - GENEPIO:0100136 Ion Torrent PGM - GENEPIO:0100137 Ion Torrent Proton - GENEPIO:0100138 Ion Torrent S5 XL - GENEPIO:0100139 Ion Torrent S5 - GENEPIO:0100140 Oxford Nanopore - GENEPIO:0004433 Oxford Nanopore Flongle - GENEPIO:0100141 Oxford Nanopore GridION - GENEPIO:0100142 Oxford Nanopore MinION - GENEPIO:0100143 Oxford Nanopore PromethION - GENEPIO:0100144 BGI Genomics sequencing instrument - GENEPIO:0100145 BGISEQ-500 - GENEPIO:0100146 MGI sequencing instrument - GENEPIO:0100971 MGISEQ-2000RS - GENEPIO:0100972 MGI DNBSEQ-G99 - GENEPIO:0100148 MGI DNBSEQ-G400 - GENEPIO:0100149 MGI DNBSEQ-G400RS FAST - GENEPIO:0100147 MGI DNBSEQ-T7 - GENEPIO:0100973 MGI DNBSEQ-E25 - GENEPIO:0100150 MGI DNBSEQ-G50 - GENEPIO:0001937 454 Genome Sequencer - OBI:0000689 454 Genome Sequencer 20 - OBI:0000702 454 Genome Sequencer FLX - GENEPIO:0100982 454 Genome Sequencer FLX+ - GENEPIO:0001936 454 Genome Sequencer FLX Titanium - GENEPIO:0100983 454 Genome Sequencer Junior - OBI:0000696 SOLiD System - GENEPIO:0001929 SOLiD 5500 - GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer - GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer - OBI:0002007 SOLiD 3 Plus System - OBI:0002024 SOLiD 4 System - GENEPIO:0001928 SOLiD 4hq System - GENEPIO:0001931 SOLiD PI System - GENEPIO:0001932 SOLiD System 2.0 - GENEPIO:0001933 SOLiD System 3.0 - OBI:0000717 HeliScope Single Molecule Sequencer - GENEPIO:0100974 Applied Biosystems sequencing instrument model - GENEPIO:0100975 AB 310 Genetic Analyzer - GENEPIO:0100976 AB 3130 Genetic Analyzer - GENEPIO:0100977 AB 3130xL Genetic Analyzer - GENEPIO:0100978 AB 3500 Genetic Analyzer - GENEPIO:0100979 AB 3500xL Genetic Analyzer - GENEPIO:0100980 AB 3730 Genetic Analyzer - GENEPIO:0100981 AB 3730xL Genetic Analyzer - -sequencing assay type menu OBI:0002767 Amplicon sequencing assay - OBI:0002763 16S ribosomal gene sequencing assay - OBI:0002117 Whole genome sequencing assay - OBI:0002623 Whole metagenome sequencing assay - OBI:0002768 Whole virome sequencing assay - -amplicon pcr primer scheme menu GENEPIO:0100847 artic-v1 - GENEPIO:0100848 artic-v2 - GENEPIO:0100849 artic-v3 - GENEPIO:0100850 artic-v4 - GENEPIO:0100851 artic-v4.1 - GENEPIO:0100852 artic-v5.0.0_400 - GENEPIO:0100853 artic-v5.1.0_400 - GENEPIO:0100854 artic-v5.2.0_1200 - GENEPIO:0100855 artic-v5.2.0_400 - GENEPIO:0100856 artic-v5.3.2_400 - GENEPIO:0100857 eden-v1 - GENEPIO:0100858 midnight-bccdc-v1 - GENEPIO:0100859 midnight-bccdc-v2 - GENEPIO:0100860 midnight-bccdc-v3 - GENEPIO:0100861 midnight-bccdc-v4 - GENEPIO:0100862 midnight-ont-v3 - GENEPIO:0100863 midnight-v1 - GENEPIO:0100864 midnight-v2 - GENEPIO:0100865 varskip-vsl1a - GENEPIO:0100866 varskip-vss1a - GENEPIO:0100867 varskip-vss2a - GENEPIO:0100868 varskip-vss2b - -genomic target enrichment method menu GENEPIO:0001950 Hybrid selection method - GENEPIO:0101020 rRNA depletion method - -quality control determination menu GENEPIO:0100562 No quality control issues identified - GENEPIO:0100563 Sequence passed quality control - GENEPIO:0100564 Sequence failed quality control - GENEPIO:0100565 Minor quality control issues identified - GENEPIO:0100566 Sequence flagged for potential quality control issues - GENEPIO:0100567 Quality control not performed - -quality control issues menu GENEPIO:0100568 Low quality sequence - GENEPIO:0100569 Sequence contaminated - GENEPIO:0100570 Low average genome coverage - GENEPIO:0100571 Low percent genome captured - GENEPIO:0100572 Read lengths shorter than expected - GENEPIO:0100573 Sequence amplification artifacts - GENEPIO:0100574 Low signal to noise ratio - GENEPIO:0100575 Low coverage of characteristic mutations - -gene name menu GENEPIO:0100151 E gene (orf4) - GENEPIO:0100152 M gene (orf5) - GENEPIO:0100153 N gene (orf9) - GENEPIO:0100154 Spike gene (orf2) - GENEPIO:0100155 orf1ab (rep) - GENEPIO:0100156 orf1a (pp1a) - GENEPIO:0100157 nsp11 - GENEPIO:0100158 nsp1 - GENEPIO:0100159 nsp2 - GENEPIO:0100160 nsp3 - GENEPIO:0100161 nsp4 - GENEPIO:0100162 nsp5 - GENEPIO:0100163 nsp6 - GENEPIO:0100164 nsp7 - GENEPIO:0100165 nsp8 - GENEPIO:0100166 nsp9 - GENEPIO:0100167 nsp10 - GENEPIO:0100168 RdRp gene (nsp12) - GENEPIO:0100169 hel gene (nsp13) - GENEPIO:0100170 exoN gene (nsp14) - GENEPIO:0100171 nsp15 - GENEPIO:0100172 nsp16 - GENEPIO:0100173 orf3a - GENEPIO:0100174 orf3b - GENEPIO:0100175 orf6 (ns6) - GENEPIO:0100176 orf7a - GENEPIO:0100177 orf7b (ns7b) - GENEPIO:0100178 orf8 (ns8) - GENEPIO:0100179 orf9b - GENEPIO:0100180 orf9c - GENEPIO:0100181 orf10 - GENEPIO:0100182 orf14 - GENEPIO:0100183 SARS-COV-2 5' UTR - -diagnostic target presence menu GENEPIO:0100987 diagnostic target present - GENEPIO:0100988 diagnostic target absent - -diagnostic measurement unit menu gene copies per liter (GC/L) - GENEPIO:0100657 cycle threshold (Ct) - UO:0000213 colony forming units per milliliter (CFU/mL) - colony forming units per 100 milliliter (CFU/100 mL) - colony forming units per grams total solids (CFU/gTS) - most probable number per milliliter (MPN/mL) - most probable number per 100 milliliter (MPN/100 mL) - -diagnostic measurement method menu OBI:0000893 Quantitative real time polymerase chain reaction (qPCR) - Digital real time polymerase chain reaction (dPCR) - Bacteria culture test - \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal + +null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. + GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. + GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. + GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. + GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] + GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] + GAZ:00000563 Algeria [GAZ:00000563] A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] + GAZ:00003957 American Samoa [GAZ:00003957] An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] + GAZ:00002948 Andorra [GAZ:00002948] A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] + GAZ:00001095 Angola [GAZ:00001095] A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + GAZ:00009159 Anguilla [GAZ:00009159] A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] + GAZ:00000462 Antarctica [GAZ:00000462] The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] + GAZ:00006883 Antigua and Barbuda [GAZ:00006883] An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] + GAZ:00002928 Argentina [GAZ:00002928] A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] + GAZ:00004094 Armenia [GAZ:00004094] A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + GAZ:00004025 Aruba [GAZ:00004025] An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] + GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] + GAZ:00000463 Australia [GAZ:00000463] A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. + GAZ:00002942 Austria [GAZ:00002942] A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. + GAZ:00004941 Azerbaijan [GAZ:00004941] A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + GAZ:00002733 Bahamas [GAZ:00002733] A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. + GAZ:00005281 Bahrain [GAZ:00005281] A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. + GAZ:00007117 Baker Island [GAZ:00007117] An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. + GAZ:00003750 Bangladesh [GAZ:00003750] A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). + GAZ:00001251 Barbados [GAZ:00001251] An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. + GAZ:00005810 Bassas da India [GAZ:00005810] A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. + GAZ:00006886 Belarus [GAZ:00006886] A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. + GAZ:00002938 Belgium [GAZ:00002938] A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). + GAZ:00002934 Belize [GAZ:00002934] A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. + GAZ:00000904 Benin [GAZ:00000904] A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. + GAZ:00001264 Bermuda [GAZ:00001264] A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. + GAZ:00003920 Bhutan [GAZ:00003920] A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. + GAZ:00002511 Bolivia [GAZ:00002511] A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). + GAZ:00025355 Borneo [GAZ:00025355] An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. + GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. + GAZ:00001097 Botswana [GAZ:00001097] A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. + GAZ:00001453 Bouvet Island [GAZ:00001453] A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. + GAZ:00002828 Brazil [GAZ:00002828] A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. + GAZ:00003961 British Virgin Islands [GAZ:00003961] A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. + GAZ:00003901 Brunei [GAZ:00003901] A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). + GAZ:00002950 Bulgaria [GAZ:00002950] A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. + GAZ:00000905 Burkina Faso [GAZ:00000905] A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). + GAZ:00001090 Burundi [GAZ:00001090] A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. + GAZ:00006888 Cambodia [GAZ:00006888] A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. + GAZ:00001093 Cameroon [GAZ:00001093] A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. + GAZ:00002560 Canada [GAZ:00002560] A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. + GAZ:00001227 Cape Verde [GAZ:00001227] A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). + GAZ:00003986 Cayman Islands [GAZ:00003986] A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. + GAZ:00001089 Central African Republic [GAZ:00001089] A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + GAZ:00000586 Chad [GAZ:00000586] A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. + GAZ:00002825 Chile [GAZ:00002825] A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. + GAZ:00002845 China [GAZ:00002845] A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. + GAZ:00005915 Christmas Island [GAZ:00005915] An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. + GAZ:00005838 Clipperton Island [GAZ:00005838] A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. + GAZ:00009721 Cocos Islands [GAZ:00009721] Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. + GAZ:00002929 Colombia [GAZ:00002929] A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. + GAZ:00005820 Comoros [GAZ:00005820] An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. + GAZ:00053798 Cook Islands [GAZ:00053798] A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. + GAZ:00005917 Coral Sea Islands [GAZ:00005917] A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. + GAZ:00002901 Costa Rica [GAZ:00002901] A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. + GAZ:00000906 Cote d'Ivoire [GAZ:00000906] A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. + GAZ:00002719 Croatia [GAZ:00002719] A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. + GAZ:00003762 Cuba [GAZ:00003762] A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. + GAZ:00012582 Curacao [GAZ:00012582] One of five island areas of the Netherlands Antilles. + GAZ:00004006 Cyprus [GAZ:00004006] The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. + GAZ:00002954 Czech Republic [GAZ:00002954] A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. + GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. + GAZ:00005852 Denmark [GAZ:00005852] That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. + GAZ:00000582 Djibouti [GAZ:00000582] A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. + GAZ:00006890 Dominica [GAZ:00006890] An island nation in the Caribbean Sea. Dominica is divided into ten parishes. + GAZ:00003952 Dominican Republic [GAZ:00003952] A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). + GAZ:00002912 Ecuador [GAZ:00002912] A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). + GAZ:00003934 Egypt [GAZ:00003934] A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). + GAZ:00002935 El Salvador [GAZ:00002935] A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). + GAZ:00001091 Equatorial Guinea [GAZ:00001091] A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. + GAZ:00000581 Eritrea [GAZ:00000581] A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). + GAZ:00002959 Estonia [GAZ:00002959] A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. + GAZ:00001099 Eswatini [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00000567 Ethiopia [GAZ:00000567] A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. + GAZ:00005811 Europa Island [GAZ:00005811] A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. + GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. + GAZ:00059206 Faroe Islands [GAZ:00059206] An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. + GAZ:00006891 Fiji [GAZ:00006891] An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. + GAZ:00002937 Finland [GAZ:00002937] A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). + GAZ:00003940 France [GAZ:00003940] A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. + GAZ:00002516 French Guiana [GAZ:00002516] An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. + GAZ:00002918 French Polynesia [GAZ:00002918] A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). + GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. + GAZ:00001092 Gabon [GAZ:00001092] A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. + GAZ:00000907 Gambia [GAZ:00000907] A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. + GAZ:00009571 Gaza Strip [GAZ:00009571] A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. + GAZ:00004942 Georgia [GAZ:00004942] A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). + GAZ:00002646 Germany [GAZ:00002646] A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). + GAZ:00000908 Ghana [GAZ:00000908] A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. + GAZ:00003987 Gibraltar [GAZ:00003987] A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. + GAZ:00005808 Glorioso Islands [GAZ:00005808] A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. + GAZ:00002945 Greece [GAZ:00002945] A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. + GAZ:00001507 Greenland [GAZ:00001507] A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. + GAZ:02000573 Grenada [GAZ:02000573] An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. + GAZ:00067142 Guadeloupe [GAZ:00067142] An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. + GAZ:00003706 Guam [GAZ:00003706] An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. + GAZ:00002936 Guatemala [GAZ:00002936] A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). + GAZ:00001550 Guernsey [GAZ:00001550] A British Crown Dependency in the English Channel off the coast of Normandy. + GAZ:00000909 Guinea [GAZ:00000909] A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. + GAZ:00000910 Guinea-Bissau [GAZ:00000910] A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. + GAZ:00002522 Guyana [GAZ:00002522] A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. + GAZ:00003953 Haiti [GAZ:00003953] A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. + GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. + GAZ:00002894 Honduras [GAZ:00002894] A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. + GAZ:00003203 Hong Kong [GAZ:00003203] A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. + GAZ:00007120 Howland Island [GAZ:00007120] An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. + GAZ:00002952 Hungary [GAZ:00002952] A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. + GAZ:00000843 Iceland [GAZ:00000843] A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. + GAZ:00002839 India [GAZ:00002839] A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. + GAZ:00003727 Indonesia [GAZ:00003727] An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). + GAZ:00004474 Iran [GAZ:00004474] A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). + GAZ:00004483 Iraq [GAZ:00004483] A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). + GAZ:00002943 Ireland [GAZ:00002943] A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. + GAZ:00052477 Isle of Man [GAZ:00052477] A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. + GAZ:00002476 Israel [GAZ:00002476] A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. + GAZ:00002650 Italy [GAZ:00002650] A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). + GAZ:00003781 Jamaica [GAZ:00003781] A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. + GAZ:00005853 Jan Mayen [GAZ:00005853] A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. + GAZ:00002747 Japan [GAZ:00002747] An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. + GAZ:00007118 Jarvis Island [GAZ:00007118] An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + GAZ:00001551 Jersey [GAZ:00001551] A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. + GAZ:00007114 Johnston Atoll [GAZ:00007114] A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. + GAZ:00002473 Jordan [GAZ:00002473] A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. + GAZ:00005809 Juan de Nova Island [GAZ:00005809] A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. + GAZ:00004999 Kazakhstan [GAZ:00004999] A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. + GAZ:00001101 Kenya [GAZ:00001101] A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. + GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. + GAZ:00007116 Kingman Reef [GAZ:00007116] A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. + GAZ:00006894 Kiribati [GAZ:00006894] An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). + GAZ:00011337 Kosovo [GAZ:00011337] A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + GAZ:00005285 Kuwait [GAZ:00005285] A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). + GAZ:00006893 Kyrgyzstan [GAZ:00006893] A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). + GAZ:00006889 Laos [GAZ:00006889] A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). + GAZ:00002958 Latvia [GAZ:00002958] A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. + GAZ:00002478 Lebanon [GAZ:00002478] A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). + GAZ:00001098 Lesotho [GAZ:00001098] A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. + GAZ:00000911 Liberia [GAZ:00000911] A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. + GAZ:00000566 Libya [GAZ:00000566] A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. + GAZ:00003858 Liechtenstein [GAZ:00003858] A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). + GAZ:00007144 Line Islands [GAZ:00007144] A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. + GAZ:00002960 Lithuania [GAZ:00002960] A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). + GAZ:00002947 Luxembourg [GAZ:00002947] A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. + GAZ:00003202 Macau [GAZ:00003202] One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. + GAZ:00001108 Madagascar [GAZ:00001108] An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + GAZ:00001105 Malawi [GAZ:00001105] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00003902 Malaysia [GAZ:00003902] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00006924 Maldives [GAZ:00006924] An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + GAZ:00000584 Mali [GAZ:00000584] A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. + GAZ:00004017 Malta [GAZ:00004017] A Southern European country and consists of an archipelago situated centrally in the Mediterranean. + GAZ:00007161 Marshall Islands [GAZ:00007161] An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. + GAZ:00067143 Martinique [GAZ:00067143] An island and an overseas department/region and single territorial collectivity of France. + GAZ:00000583 Mauritania [GAZ:00000583] A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). + GAZ:00003745 Mauritius [GAZ:00003745] An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. + GAZ:00003943 Mayotte [GAZ:00003943] An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. + GAZ:00002852 Mexico [GAZ:00002852] A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. + GAZ:00005862 Micronesia [GAZ:00005862] A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. + GAZ:00007112 Midway Islands [GAZ:00007112] A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. + GAZ:00003897 Moldova [GAZ:00003897] A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. + GAZ:00003857 Monaco [GAZ:00003857] A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. + GAZ:00008744 Mongolia [GAZ:00008744] A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. + GAZ:00006898 Montenegro [GAZ:00006898] A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + GAZ:00003988 Montserrat [GAZ:00003988] A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. + GAZ:00000565 Morocco [GAZ:00000565] A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. + GAZ:00001100 Mozambique [GAZ:00001100] A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. + GAZ:00006899 Myanmar [GAZ:00006899] A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. + GAZ:00001096 Namibia [GAZ:00001096] A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. + GAZ:00006900 Nauru [GAZ:00006900] An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. + GAZ:00007119 Navassa Island [GAZ:00007119] A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. + GAZ:00004399 Nepal [GAZ:00004399] A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. + GAZ:00002946 Netherlands [GAZ:00002946] The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). + GAZ:00005206 New Caledonia [GAZ:00005206] A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. + GAZ:00000469 New Zealand [GAZ:00000469] A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. + GAZ:00002978 Nicaragua [GAZ:00002978] A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. + GAZ:00000585 Niger [GAZ:00000585] A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. + GAZ:00000912 Nigeria [GAZ:00000912] A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). + GAZ:00006902 Niue [GAZ:00006902] An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. + GAZ:00005908 Norfolk Island [GAZ:00005908] A Territory of Australia that includes Norfolk Island and neighboring islands. + GAZ:00002801 North Korea [GAZ:00002801] A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. + GAZ:00006895 North Macedonia [GAZ:00006895] A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. + GAZ:00002284 North Sea [GAZ:00002284] A sea situated between the eastern coasts of the British Isles and the western coast of Europe. + GAZ:00003958 Northern Mariana Islands [GAZ:00003958] A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. + GAZ:00002699 Norway [GAZ:00002699] A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. + GAZ:00005283 Oman [GAZ:00005283] A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). + GAZ:00005246 Pakistan [GAZ:00005246] A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. + GAZ:00006905 Palau [GAZ:00006905] A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. + GAZ:00002892 Panama [GAZ:00002892] The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. + GAZ:00003922 Papua New Guinea [GAZ:00003922] A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). + GAZ:00010832 Paracel Islands [GAZ:00010832] A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. + GAZ:00002933 Paraguay [GAZ:00002933] A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. + GAZ:00002932 Peru [GAZ:00002932] A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. + GAZ:00004525 Philippines [GAZ:00004525] An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. + GAZ:00005867 Pitcairn Islands [GAZ:00005867] A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. + GAZ:00002939 Poland [GAZ:00002939] A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. + GAZ:00004126 Portugal [GAZ:00004126] That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. + GAZ:00006935 Puerto Rico [GAZ:00006935] A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). + GAZ:00005286 Qatar [GAZ:00005286] An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). + GAZ:00001088 Republic of the Congo [GAZ:00001088] A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. + GAZ:00003945 Reunion [GAZ:00003945] An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. + GAZ:00002951 Romania [GAZ:00002951] A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). + GAZ:00023304 Ross Sea [GAZ:00023304] A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. + GAZ:00002721 Russia [GAZ:00002721] A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. + GAZ:00001087 Rwanda [GAZ:00001087] A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). + GAZ:00000849 Saint Helena [GAZ:00000849] An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. + GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. + GAZ:00006909 Saint Lucia [GAZ:00006909] An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. + GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. + GAZ:00005841 Saint Martin [GAZ:00005841] An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] An island nation in the Lesser Antilles chain of the Caribbean Sea. + GAZ:00006910 Samoa [GAZ:00006910] A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). + GAZ:00003102 San Marino [GAZ:00003102] A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). + GAZ:00006927 Sao Tome and Principe [GAZ:00006927] An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). + GAZ:00005279 Saudi Arabia [GAZ:00005279] A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. + GAZ:00000913 Senegal [GAZ:00000913] A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. + GAZ:00002957 Serbia [GAZ:00002957] A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). + GAZ:00006922 Seychelles [GAZ:00006922] An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. + GAZ:00000914 Sierra Leone [GAZ:00000914] A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. + GAZ:00003923 Singapore [GAZ:00003923] An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. + GAZ:00012579 Sint Maarten [GAZ:00012579] One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. + GAZ:00002956 Slovakia [GAZ:00002956] A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. + GAZ:00002955 Slovenia [GAZ:00002955] A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. + GAZ:00005275 Solomon Islands [GAZ:00005275] A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. + GAZ:00001104 Somalia [GAZ:00001104] A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. + GAZ:00001094 South Africa [GAZ:00001094] A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. + GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. + GAZ:00002802 South Korea [GAZ:00002802] A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + GAZ:00233439 South Sudan [GAZ:00233439] A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. + GAZ:00000591 Spain [GAZ:00000591] That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. + GAZ:00010831 Spratly Islands [GAZ:00010831] A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. + GAZ:00003924 Sri Lanka [GAZ:00003924] An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. + GAZ:00002475 State of Palestine [GAZ:00002475] The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. + GAZ:00000560 Sudan [GAZ:00000560] A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. + GAZ:00002525 Suriname [GAZ:00002525] A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. + GAZ:00005396 Svalbard [GAZ:00005396] An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. + GAZ:00002729 Sweden [GAZ:00002729] A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. + GAZ:00002941 Switzerland [GAZ:00002941] A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. + GAZ:00002474 Syria [GAZ:00002474] A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). + GAZ:00005341 Taiwan [GAZ:00005341] A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. + GAZ:00006912 Tajikistan [GAZ:00006912] A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). + GAZ:00001103 Tanzania [GAZ:00001103] A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). + GAZ:00003744 Thailand [GAZ:00003744] A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. + GAZ:00006913 Timor-Leste [GAZ:00006913] A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. + GAZ:00000915 Togo [GAZ:00000915] A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. + GAZ:00260188 Tokelau [GAZ:00260188] A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). + GAZ:00006916 Tonga [GAZ:00006916] A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. + GAZ:00003767 Trinidad and Tobago [GAZ:00003767] An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + GAZ:00005812 Tromelin Island [GAZ:00005812] A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. + GAZ:00000562 Tunisia [GAZ:00000562] A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). + GAZ:00000558 Turkey [GAZ:00000558] A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. + GAZ:00005018 Turkmenistan [GAZ:00005018] A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. + GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. + GAZ:00009715 Tuvalu [GAZ:00009715] A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. + GAZ:00002459 United States of America [GAZ:00002459] A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. + GAZ:00001102 Uganda [GAZ:00001102] A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. + GAZ:00002724 Ukraine [GAZ:00002724] A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. + GAZ:00005282 United Arab Emirates [GAZ:00005282] A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + GAZ:00002637 United Kingdom [GAZ:00002637] A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. + GAZ:00002930 Uruguay [GAZ:00002930] A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). + GAZ:00004979 Uzbekistan [GAZ:00004979] A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). + GAZ:00006918 Vanuatu [GAZ:00006918] An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. + GAZ:00002931 Venezuela [GAZ:00002931] A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). + GAZ:00003756 Viet Nam [GAZ:00003756] The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. + GAZ:00003959 Virgin Islands [GAZ:00003959] A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. + GAZ:00007111 Wake Island [GAZ:00007111] A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). + GAZ:00007191 Wallis and Futuna [GAZ:00007191] A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. + GAZ:00009572 West Bank [GAZ:00009572] A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". + GAZ:00000564 Western Sahara [GAZ:00000564] A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. + GAZ:00005284 Yemen [GAZ:00005284] A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + GAZ:00001107 Zambia [GAZ:00001107] A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. + GAZ:00001106 Zimbabwe [GAZ:00001106] A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. + + + +watershed shapefile availability menu WatershedShapefileAvailabilityMenu GENEPIO:0100993 Available [GENEPIO:0100993] A datum status in which the required datum is able to be used, obtained or selected. + GENEPIO:0100995 Unknown [GENEPIO:0100995] A datum status in which the availabilty or presence of the required datum is not known. + +organism menu OrganismMenu NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] A strain of the species Betacoronavirus pandemicum, a coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic. + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100869 Wastewater treatment efficiency assessment [GENEPIO:0100869] An environmental sampling strategy in which wastewater effluent is collected to assess the efficiency of wastewater treatment. + GENEPIO:0100870 Wastewater chemical surveillance [GENEPIO:0100870] An environmental sampling strategy in which wastewater samples are collected to monitor for chemical contamination. + GENEPIO:0100871 Wastewater drug surveillance [GENEPIO:0100871] An environmental sampling strategy in which wastewater samples are collected to monitor for community drug use. + GENEPIO:0100872 Wastewater pathogen surveillance [GENEPIO:0100872] An environmental sampling strategy in which samples are collected to identify and/or monitor the presence of pathogens. + GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. + GENEPIO:0100873 Environmental survey (profiling) [GENEPIO:0100873] A research sampling strategy in which samples are collected in order to survey/profile entities in, or characteristics of, an environment. + GENEPIO:0100024 Protocol testing [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. + +scale of sampling menu ScaleOfSamplingMenu GENEPIO:0100874 Community-level surveillance [GENEPIO:0100874] A surveillance strategy in which sites are sampled at the community level. + GENEPIO:0100875 Institution-level surveillance [GENEPIO:0100875] A surveillance strategy in which sites are sampled at the institution level. + GENEPIO:0100876 Building-level surveillance [GENEPIO:0100876] A surveillance strategy in which sites are sampled at the building level. + +sample collection time of day menu SampleCollectionTimeOfDayMenu NCIT:C64934 Morning [NCIT:C64934] The time period between dawn and noon. + NCIT:C64935 Afternoon [NCIT:C64935] The time period between noon and sunset. + NCIT:C64936 Evening [NCIT:C64936] The time period between late afternoon and bedtime. + NCIT:C65001 Night [NCIT:C65001] The time in every 24 hour period when it is dark. + +sample collection duration unit menu SampleCollectionDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + +presampling activity menu PresamplingActivityMenu ENVO:01001442 Agricultural activity [ENVO:01001442] A land use process during which terrestrial environments are modified such that they can grow crop plants or allow the rearing of animals to provide food, fiber, medicines, or other products used by humans. + ENVO:01001248 Animal husbandry [ENVO:01001248] An agricultural process during which humans rear animals on land for harvest and consumption. + ENVO:01001450 Industrial activity [ENVO:01001450] A process that leads to the production of goods. + NCIT:C16205 Healthcare activity [NCIT:C16205] A process that includes the prevention, treatment, and management of physical and mental illness. + ENVO:06105300 Wastewater treatment [ENVO:06105300] A recycling process during which wastewater is treated. + GENEPIO:0101198 Wastewater screening process [GENEPIO:0101198] A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances. + GENEPIO:0101719 wastewater comminution process [GENEPIO:0101719] A wastewater treatment process which involves the mechanical reduction of solid materials in wastewater into smaller, more manageable particles through devices like comminutors or grinders to shred debris. + ENVO:03501445 Wastewater filtration [ENVO:03501445] A wastewater treatment process which removes solid particles from wastewater by means of filtration. + ENVO:03501446 Wastewater grit removal [ENVO:03501446] A wastewater treatment process which removes sand, silt, and grit from wastewater. + ENVO:03501448 Wastewater primary sedimentation [ENVO:03501448] A wastewater treatment process which removes solids and large particles from influent through gravitational force. + ENVO:03501447 Wastewater microbial treatment [ENVO:03501447] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. + GENEPIO:0101199 Wastewater aerobic digestion [GENEPIO:0101199] A wastewater microbial treatment process in which organic material is broken down in the presence of oxygen. + GENEPIO:0101200 Wastewater anaerobic digestion [GENEPIO:0101200] A wastewater microbial treatment process in which organic material is broken down in the absence of oxygen by anaerobic bacteria. + ENVO:03501449 Wastewater secondary sedimentation [ENVO:03501449] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. + GENEPIO:0101201 Wastewater sludge removal [GENEPIO:0101201] A wastewater treatment process which removes large objects such as rags, paper, plastics, and metals to prevent damage and clogging of downstream equipment, piping, and appurtenances. + GENEPIO:0101202 Wastewater sludge dewatering [GENEPIO:0101202] A wastewater treatment process which mechanically reduces the water content of wastewater sludge using equipment like centrifuges or belt presses, resulting in a semi-solid material that is easier to handle and transport + GENEPIO:0101718 Wastewater sludge drying [GENEPIO:0101718] A wastewater treatment process which further reduces the moisture content of dewatered sludge, typically through thermal or air drying methods, producing a dry, stable material for easier disposal or use. + + +sample volume measurement unit menu SampleVolumeMeasurementUnitMenu UO:0000101 microliter (uL) [UO:0000101] A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter. + UO:0000098 milliliter (mL) [UO:0000098] A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter. + UO:0000099 liter (L) [UO:0000099] A metric unit of volume equivalent to 1000 cubic centimeters + +sample storage duration unit menu SampleStorageDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + +specimen processing menu SpecimenProcessingMenu OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. + OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. + OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. + NCIT:C154798 Flocculation [NCIT:C154798] A process in which microscopic particles in suspension aggregate to form loosely clumped masses that are often macroscopically observable. + GENEPIO:0100886 Magnetic nanobead binding [GENEPIO:0100886] A process that uses nanobeads to bind to particles or microbes of interest. + OBI:0600034 Precipitation [OBI:0600034] A protocol application to cause a material to precipitate (becoming a solid) out of solution. + GENEPIO:0101011 Gravity separation [GENEPIO:0101011] A process through which solids are separated from a liquid by allowing the solids to settle by gravity. + IDO:0100170 Pasteurization [IDO:0100170] A planned process of heating a liquid entity, to a specific temperature of a defined length of time span, and then cooling it immediately. It has an objective of prevent the microbial's growth in the liquid entity, which is a specific input of this planned process. + GENEPIO:0101012 Growth in enrichment broth [GENEPIO:0101012] A process in which microorganisms, present in a collected sample, undergo cultivation within a nutrient-rich liquid medium, that facilitates growth. + OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. + GENEPIO:0101021 Technical replicate process [GENEPIO:0101021] A specimen collection process in which a replicate(s) is collected to assess technical variation within an experiment. For technical replicates the same BioSample is used e.g. the same pool of RNA is used to assess technical (as opposed to biological) variation. + GENEPIO:0101022 Biological replicate process [GENEPIO:0101022] A specimen collection process in which a replicate(s) is collected in parallel to assess for biological variation within an experiment. Biological replicates would have distinct BioSamples records. + +environmental site menu EnvironmentalSiteMenu ENVO:01001481 Correctional facility [ENVO:01001481] A prison facility which is owned and operated by a state. + ENVO:03501134 Healthcare facility [ENVO:03501134] A human construction in which healthcare is provided. + ENVO:00002173 Hospital [ENVO:00002173] A building in which health care services are provided by specialized staff and equipment. + ENVO:03501182 Clinic [ENVO:03501182] A facility which is used to provide treatment, remedial work, and/or instruction. + ENVO:03501129 Educational facility [ENVO:03501129] A human construction in which people are educated. + ENVO:03501335 Daycare facility [ENVO:03501335] A child care facility in which day care services are provided, by specialized staff and equipment, to a human child during the working day. + ENVO:03501130 School [ENVO:03501130] An institutional building in which students are educated. + ENVO:03501131 College or university [ENVO:03501131] An institutional building in which university services are performed. + ENVO:01001222 Commercial building [ENVO:01001222] A building which is primarily used to facilitate the buying or selling of goods or services. "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." + ENVO:01001221 Office [ENVO:01001221] A commercial building which contains parts used as workplaces primarily for administrative and managerial workers. "An office building will be divided into sections for different companies or may be dedicated to one company. In either case, each company will typically have a reception area, one or several meeting rooms, singular or open-plan offices, as well as toilets." + ENVO:01000934 Restaurant [ENVO:01000934] A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services. + ENVO:03501207 Shopping mall [ENVO:03501207] A shopping center in which a large indoor pedestrian promenade provides access to stores and other facilities. + ENVO:01000933 Residential building [ENVO:01000933] A human house which serves as a long-term shelter for its inhabitants and within which they store personal property. + ENVO:03501133 Homeless shelter [ENVO:03501133] An institutional building which temporarily houses homeless people. + ENVO:01000932 Long-term care facility [ENVO:01000932] A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living. + ENVO:03501117 Transport hub [ENVO:03501117] A place where passengers and cargo are exchanged between vehicles or/and between transport modes. + ENVO:03501122 Airport [ENVO:03501122] A human construction with extended facilities from which aircraft flight operations take place. + ENVO:00000078 Farm [ENVO:00000078] An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. + NCIT:C85867 Refugee camp [NCIT:C85867] A temporary, often makeshift shelter for persons displaced by war, political oppression, or for religious beliefs. + ENVO:00000064 Road [ENVO:00000064] An open way for the passage of vehicles, persons, or animals on land. + ENVO:01000447 Roadside [ENVO:01000447] An environmental zone of varying area which is adjacent to a road. + ENVO:00003861 Industrial plant [ENVO:00003861] A building within which goods are produced and, optionally, stored or within which services are rendered. + ENVO:03501297 Meat processing plant [ENVO:03501297] A processing plant for slaughtering, processing, packaging, labelling, handling, and storing of food animal carcasses, parts of carcasses, and meat products. + ENVO:03501450 Pharmaceutical manufacturing plant [ENVO:03501450] An industrial building in which pharamceutical drugs are synthesised and processed on an industrial scale. + ENVO:00000063 Body of water [ENVO:00000063] An accumulation of water of varying size. + ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. + ENVO:00000020 Lake [ENVO:00000020] A body of water or other liquid of considerable size contained in a depression on a landmass. + ENVO:00000023 Stream [ENVO:00000023] A watercourse which is linear and flows across the solid portion of a planetary surface. + ENVO:00000022 River [ENVO:00000022] A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. + ENVO:00000015 Ocean [ENVO:00000015] A marine water body which is constitutes the majority of an astronomical body's hydrosphere. + ENVO:00000016 Sea [ENVO:00000016] A large expanse of saline water usually connected with an ocean. + ENVO:00000014 Canal [ENVO:00000014] Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation. + ENVO:00000025 Reservoir [ENVO:00000025] An artificial body of water, often contained by a dam, constructed for the purpose of water storage. + ENVO:01001004 Ground water [ENVO:01001004] Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel. + ENVO:00000026 Well [ENVO:00000026] A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface. + ENVO:00000027 Spring [ENVO:00000027] A surface landform which provides an egress for groundwater or steam to flow out of the ground. + ENVO:00002272 Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. + ENVO:03501465 Influent pump station [ENVO:03501465] A facility within a wastewater treatment plant designed to receive and lift incoming wastewater (influent) to a higher elevation for subsequent treatment processes. The influent pump station typically houses pumps, controls, and associated equipment necessary to move wastewater through the treatment process. + ENVO:03501467 Grit chamber [ENVO:03501467] A physical structure or equipment within a wastewater treatment plant where grit and other heavy inorganic particles are removed from the influent through sedimentation. The grit chamber helps protect downstream equipment from abrasion and reduces the accumulation of grit in subsequent treatment processes. + ENVO:03501472 Communitor [ENVO:03501472] A mechanical device designed to reduce the size of solid materials in wastewater. It uses rotating drums or cutting blades to shred large debris into smaller pieces, protecting downstream equipment and enhancing the efficiency of subsequent treatment processes. + ENVO:03501468 Primary clarifer [ENVO:03501468] A large, sedimentation tank in a wastewater treatment plant where the primary stage of solids separation occurs. In the primary clarifier, suspended solids settle to the bottom as sludge, while lighter materials, such as oils and greases, rise to the surface for removal. + ENVO:03501469 Aeration tank [ENVO:03501469] A tank or basin in a wastewater treatment plant where oxygen is introduced into the wastewater to promote the growth of aerobic microorganisms. These microorganisms break down organic pollutants in the water, facilitating the biological treatment process. The aeration tank is essential for reducing the organic load before the water moves to subsequent treatment stages. + ENVO:03501471 Secondary clarifer [ENVO:03501471] A sedimentation tank in a wastewater treatment plant used in the secondary treatment process. The secondary clarifier allows for the settling and removal of biological floc or sludge produced in the aeration tank, further clarifying the treated wastewater before discharge or further treatment. + ENVO:03501473 Sludge dryer [ENVO:03501473] A device designed to remove moisture from sludge through thermal drying methods, resulting in a dry, granular material that is easier to handle, store, or utilize in other applications. + ENVO:03600076 Waste stabilization pond (lagoon) [ENVO:03600076] A human construction which confines wastewater in a depression enclosed by earthen structures. + ENVO:01000924 Sewer [ENVO:01000924] An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. + ENVO:01000604 Transportation vehicle [ENVO:01000604] A vehicle is a mobile machine which transports people or cargo. + ENVO:01000608 Boat [ENVO:01000608] A boat is a watercraft of any size which is able to float or plane on water. + ENVO:03501349 Airplane [ENVO:03501349] An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine. + +environmental material menu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater + ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. + ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence + ENVO:03501456 Wastewater sediment [ENVO:03501456] A sediment which is removed from waste water during a waste water treatment process. + ENVO:00002044 Sludge [ENVO:00002044] The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. + ENVO:00002057 Primary sludge [ENVO:00002057] Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment. + ENVO:00002058 Secondary sludge [ENVO:00002058] Activated waste biomass generated during wastewater treatment. + ENVO:03501457 Wastewater effluent [ENVO:03501457] A wastewater which has been discharged from any item of equipment at a stage of a wastewater treatment process. + GENEPIO:0100892 Primary wastewater effluent [GENEPIO:0100892] A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation. + GENEPIO:0100893 Secondary wastewater effluent [GENEPIO:0100893] A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation. + +environmental material properties menu EnvironmentalMaterialPropertiesMenu GENEPIO:0101004 Fluid (stagnant) [GENEPIO:0101004] A quality of a body of water wherein it has no current or flow. + GENEPIO:0101005 Fluid (slow) [GENEPIO:0101005] A quality of a body of water wherein there is a slow flow. + GENEPIO:0101006 Fluid (fast) [GENEPIO:0101006] A quality of a body of water wherein there is a fast flow. + PATO:0015031 Contamination [PATO:0015031] The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. + GENEPIO:0101010 Fecal-contaminated [GENEPIO:0101010] A contamination quality in which fecal matter is a key component of the contamination. + PATO:0001735 Liquid [PATO:0001735] A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. + GENEPIO:0101007 Slurry-like [GENEPIO:0101007] An quality in which the fluid like material is more viscous due to the suspension of insoluble solid particles. + NCIT:C149895 Semi-solid [NCIT:C149895] A state of matter consisting of molecules in a non-rigid structure that can retain its shape and volume but that is not resistant to such change. + PATO:0001736 Solid [PATO:0001736] A quality in which an object or material exhibits characteristics of solids, lacking movement or flow. + GENEPIO:0101008 Treated [GENEPIO:0101008] A quality which denotes an altered state of an item resulting from purposeful interventions or processes. + GENEPIO:0101009 Untreated [GENEPIO:0101009] A quality which denotes an absence of purposeful intervention or processes on an item. + +wastewater system type menu WastewaterSystemTypeMenu ENVO:03501453 Combined sewer system [ENVO:03501453] A sewered sanitation system that collects rainwater runoff, domestic sewage, and industrial wastewater. + ENVO:03501454 Sanitary sewer system [ENVO:03501454] A sewered sanitation system that collects only domestic sewage. + ENVO:03600076 Waste stabilization pond [ENVO:03600076] A human construction which confines wastewater in a depression enclosed by earthen structures. + ENVO:01000519 Latrine [ENVO:01000519] A latrine is a toilet which is of simple construction (relative to a flush or chemical toilet) and typically intended for communal use. + ENVO:03501451 Septic tank [ENVO:03501451] An underground holding and treatment site for domestic wastewater. + ENVO:03501452 Cesspit [ENVO:03501452] A pit for the disposal and storage of sewage. + ENVO:01000550 Composting toilet [ENVO:01000550] A composting toilet fixture is a dry toilet fixture in which managed, aerobic decomposition converts human excreta into organic matter suitable for the fertilisation or amendment of soils. + ENVO:01000924 Sewer drain [ENVO:01000924] An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. + + + +experimental specimen role type menu ExperimentalSpecimenRoleTypeMenu GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. + GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment + EFO:0002090 Technical replicate [EFO:0002090] A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. + EFO:0002091 Biological replicate [EFO:0002091] A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. + +collection device menu CollectionDeviceMenu GENEPIO:0100941 Grab sampler [GENEPIO:0100941] A specimen collection device which is used to collect discrete, instantaneous samples of water, soil, or other substances from a specific point in a body of water or at a specific location. + GENEPIO:0102027 Bag filtration device [GENEPIO:0102027] + GENEPIO:0100943 Core sampling device [GENEPIO:0100943] A grab sampler that captures a vertical section of the substrate matrix of fecal sludge. + GENEPIO:0100944 Vacuum sludge sampling device [GENEPIO:0100944] A grab sampler that takes a sample at a designated depth with minimal disturbance to surrounding layers. + GENEPIO:0100945 Cone-shaped sampling device [GENEPIO:0100945] A grab sample that has a controlled valve that opens to take a sample from a specific depth, then closes to bring the sample out. + GENEPIO:0100946 Horizontal grab sampling device [GENEPIO:0100946] A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting discharge from a pipe or truck. + GENEPIO:0100947 Vertical grab sampling device [GENEPIO:0100947] A grab sampler in which the container for the sample is mounted on the end of a rod, which is suitable for collecting waste from a tank. + GENEPIO:0100942 Composite sampler [GENEPIO:0100942] A specimen collection device that collects material over different times or locations. + GENEPIO:0100948 Passive (trap) sampler [GENEPIO:0100948] A composite sampler that passively collects a sample without use of electricity or a battery. + GENEPIO:0100949 Moore swab [GENEPIO:0100949] A composite sampler which consists of gauze pad tied with string, suspended in flowing water or wastewater, in order to collect a wastewater sample. + GENEPIO:0100950 Automatic composite sampler [GENEPIO:0100950] A composite sampler which is automated to collect and store multiple wastewater samples across multiple time points. + GENEPIO:0100951 Automatic flow-proportional sampler [GENEPIO:0100951] A composite sampler which is automated to collect and store multiple wastewater samples in a manner proportional to flow. + GENEPIO:0100952 Automatic sequential (time-proportional) sampler [GENEPIO:0100952] A composite sampler which is automated to collect and combine multiple samples of equal volume taken at a set time interval. + +collection method menu CollectionMethodMenu GENEPIO:0100953 Grab sampling [GENEPIO:0100953] An environmental material collection process in which a water or soil sample is taken at a single point of time using a container type known as a grab sampler. + GENEPIO:0102028 Bag Mediated Filtration [GENEPIO:0102028] + GENEPIO:0100954 Composite sampling [GENEPIO:0100954] An environmental material collection process in which mutliple water or soil samples are taken at different time points and combined to produce a composite. Samples can be collected continuously or at discrete time points. + GENEPIO:0100955 Passive composite sampling [GENEPIO:0100955] A method of composite sampling in which a continuous sample is collected passively without electrical input minimizing cost. + GENEPIO:0100956 Automatic composite sampling [GENEPIO:0100956] A method of composite sampling which utilizes an automated system to collect multiple samples, continuously or at discrete timepoints. + GENEPIO:0100957 Manual composite sampling [GENEPIO:0100957] A method of composite sampling in which multiple grab samples from discrete time points are taken and then combined to produce a single composite sample. + +water catchment area human population range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people An estimation of population size for a group smaller than 10 people. + 10 - 100 people An estimation of population size for a group smaller than 100 people and larger than 10 people. + 100 - 1,000 people An estimation of population size for a group smaller than 1,000 people and larger than 100 people. + 1,000 - 10,000 people An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people. + 10,000 - 100,000 people An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people. + 100,000 - 1,000,000 people An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people. + 1,000,000+ people An estimation of population size for a group larger than 1,000,000 people. + +water catchment area human population density unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. + GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. + GENEPIO:0100991 residents per square mile [GENEPIO:0100991] A unit of population density that describes the average number of registered residents in a square mile of a given area. + GENEPIO:0100992 residents per square kilometer [GENEPIO:0100992] A unit of population density that describes the average number of registered residents in a square kilometer of a given area. + +populated area type menu PopulatedAreaTypeMenu GSSO:011077 Suburban [GSSO:011077] A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities. + GSSO:011078 Rural [GSSO:011078] A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements. + GSSO:011080 Urban [GSSO:011080] A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment. + +sampling weather conditions menu SamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +presampling weather conditions menu PresamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +precipitation measurement unit menu PrecipitationMeasurementUnitMenu UO:0000016 millimeter (mm) [UO:0000016] A length unit which is defined as one thousandth of a meter. + UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +air pressure measurement unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). + bar + UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). + +ambient temperature measurement unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +total daily flow rate measurement unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +instantaneous flow rate measurement unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +turbidity measurement unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample. + UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. + +dissolved oxygen measurement unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000083 kilogram per cubic meter (kg/m^3) [UO:0000083] An SI unit of density that is one thousandth of the density of water. + UO:0000169 part per million (ppm) [UO:0000169] A unitless measure of density that represents one item out of a million. + +oxygen reduction potential (ORP) measurement unit menu OxygenReductionPotentialOrpMeasurementUnitMenu UO:0000247 milliVolt (mV) [UO:0000247] A non-SI unit of electromotive force that is one thousandth of a volt. + +chemical oxygen demand (COD) measurement unit menu ChemicalOxygenDemandCodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +carbonaceous biochemical oxygen demand (CBOD) measurement unit menu CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +total suspended solids (TSS) measurement unit menu TotalSuspendedSolidsTssMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total dissolved solids (TDS) measurement unit menu TotalDissolvedSolidsTdsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total solids (TS) measurement unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +alkalinity measurement unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) A unit of ion concentration that represents chemical activity per volume. + UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. + +conductivity measurement unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m). + microSiemen per centimeter (μS/cm) A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m). + Siemen per meter (S/m) An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m). + +salinity measurement unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) A unitless measure of salinity that is equivalent to per thousand. + weight for weight (% w/w) A unitless comparison based on weight rather than volume, which is equivalent to per hundred. + UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total nitrogen (TN) measurement unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. +total nitrogen (TN) measurement unit menu gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. + +total phosphorpus (TP) measurement unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. + GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. + UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. + +fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:1211417 crAssphage [NCBITaxon:1211417] CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome. + NCBITaxon:12239 PMMoV / pepper mild mottle virus [NCBITaxon:12239] A plant RNA virus that is abundant in human feces. + GENEPIO:0101000 Bacteroides HF183 [GENEPIO:0101000] A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus. + GENEPIO:0101001 Lachnospiraceae Lachno3 [GENEPIO:0101001] A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria. + GENEPIO:0101002 F+ (male specific) coliphages [GENEPIO:0101002] A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. + CHEBI:26756 Stercobilin [CHEBI:26756] Bile pigment found in fecal material. + +fecal contamination unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material. + gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. + UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. + log10 gene copies per nanogram total DNA A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material. + +urinary contamination indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. + +urinary contamination unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. + +fecal coliform count unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. + +sample temperature unit (at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sample temperature unit (when received) menu SampleTemperatureUnitWhenReceivedMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. + GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] A surveillance sampling strategy in which an aspired outcome is explicitly stated. + GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] A targeted surveillance strategy which is considered important and/or urgent. + GENEPIO:0100009 Longitudinal surveillance (repeat sampling) [GENEPIO:0100009] A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time. + GENEPIO:0100012 Travel-associated surveillance [GENEPIO:0100012] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored. + GENEPIO:0100013 Domestic travel surveillance [GENEPIO:0100013] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to domestic travel. + GENEPIO:0100014 International travel surveillance [GENEPIO:0100014] A surveillance strategy in which wastewater produced within travel hubs or travel vehicles are monitored, related to international travel. + GENEPIO:0100022 Research [GENEPIO:0100022] A sampling strategy in which sites are sampled in order to perform research. + GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. + GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. + +sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. + GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. + GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. + GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. + GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. + GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. + GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. + GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. + GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. + GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). + GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. + GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. + OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. + GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. + OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. + GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. + GENEPIO:0100972 MGI DNBSEQ-G99 [GENEPIO:0100972] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds. + GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. + GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. + GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. + GENEPIO:0100973 MGI DNBSEQ-E25 [GENEPIO:0100973] An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab. + GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. + OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. + OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. + GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. + GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. + OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. + GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. + GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. + GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. + OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. + GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. + GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. + GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. + GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. + GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. + GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. + GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. + GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. + GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. + GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. + GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. + +sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + +amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. + GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. + GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. + GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. + GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. + GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. + GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. + GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. + GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. + GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. + GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. + GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. + GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. + GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. + GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. + +genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. + +quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. + +quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. + +gene symbol menu GeneSymbolMenu GENEPIO:0100151 E gene (orf4) [GENEPIO:0100151] + GENEPIO:0100152 M gene (orf5) [GENEPIO:0100152] + GENEPIO:0100153 N gene (orf9) [GENEPIO:0100153] + GENEPIO:0100154 Spike gene (orf2) [GENEPIO:0100154] + GENEPIO:0100155 orf1ab (rep) [GENEPIO:0100155] + GENEPIO:0100156 orf1a (pp1a) [GENEPIO:0100156] + GENEPIO:0100157 nsp11 [GENEPIO:0100157] + GENEPIO:0100158 nsp1 [GENEPIO:0100158] + GENEPIO:0100159 nsp2 [GENEPIO:0100159] + GENEPIO:0100160 nsp3 [GENEPIO:0100160] + GENEPIO:0100161 nsp4 [GENEPIO:0100161] + GENEPIO:0100162 nsp5 [GENEPIO:0100162] + GENEPIO:0100163 nsp6 [GENEPIO:0100163] + GENEPIO:0100164 nsp7 [GENEPIO:0100164] + GENEPIO:0100165 nsp8 [GENEPIO:0100165] + GENEPIO:0100166 nsp9 [GENEPIO:0100166] + GENEPIO:0100167 nsp10 [GENEPIO:0100167] + GENEPIO:0100168 RdRp gene (nsp12) [GENEPIO:0100168] + GENEPIO:0100169 hel gene (nsp13) [GENEPIO:0100169] + GENEPIO:0100170 exoN gene (nsp14) [GENEPIO:0100170] + GENEPIO:0100171 nsp15 [GENEPIO:0100171] + GENEPIO:0100172 nsp16 [GENEPIO:0100172] + GENEPIO:0100173 orf3a [GENEPIO:0100173] + GENEPIO:0100174 orf3b [GENEPIO:0100174] + GENEPIO:0100175 orf6 (ns6) [GENEPIO:0100175] + GENEPIO:0100176 orf7a [GENEPIO:0100176] + GENEPIO:0100177 orf7b (ns7b) [GENEPIO:0100177] + GENEPIO:0100178 orf8 (ns8) [GENEPIO:0100178] + GENEPIO:0100179 orf9b [GENEPIO:0100179] + GENEPIO:0100180 orf9c [GENEPIO:0100180] + GENEPIO:0100181 orf10 [GENEPIO:0100181] + GENEPIO:0100182 orf14 [GENEPIO:0100182] + GENEPIO:0100183 SARS-COV-2 5' UTR [GENEPIO:0100183] + +diagnostic target presence menu DiagnosticTargetPresenceMenu GENEPIO:0100987 diagnostic target present [GENEPIO:0100987] A quality inhering in a bearer by virtue of the bearer's existence. + GENEPIO:0100988 diagnostic target absent [GENEPIO:0100988] Aquality denoting the lack of an entity. + +diagnostic measurement unit menu DiagnosticMeasurementUnitMenu gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. + GENEPIO:0100657 cycle threshold (Ct) [GENEPIO:0100657] A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. + UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. + +diagnostic measurement method menu DiagnosticMeasurementMethodMenu OBI:0000893 Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + Digital real time polymerase chain reaction (dPCR) A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction + Bacteria culture test An assay to identify the presence of bacteria + \ No newline at end of file diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index a14caa58..bddf02b9 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -1,243 +1,263 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ -WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMD00000001 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100754 GenBank accession (versioned) WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in GenBank archives. Store the versioned GenBank accession assigned to the submitted sequence. LZ986655.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001142 SRA accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted sequence. NCBI-SRA accessions start with SRR. SRR11177792 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100755 ENA accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in the European Nucleotide Archive (ENA). Store the accession assigned to the submitted sequence. ENA sequence accessions start with ERR. ERR123456 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100757 DRA accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in DNA Data Bank of Japan (DDBJ) sequence read archives. Store the accession assigned to the submitted sequence. DRA accessions start with DRR. DRR123456 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100758 GSA accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in GSA (Genome Sequence Archive) archives. Store the accession assigned to the submitted sequence. GSA accessions start with CRR. CRR123456 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ +WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by WhitespaceMinimizedString null value menu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name (country) menu null value menu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) WhitespaceMinimizedString null value menu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed shapefile availability menu null value menu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml -WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 -WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism WhitespaceMinimizedString null value menu TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae -WastewaterAMR Sample collection and processing GENEPIO:0001191 organism WhitespaceMinimizedString null value menu TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling menu null value menu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale of sampling menu null value menu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date date null value menu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date date null value menu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date date null value menu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time time null value menu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time time null value menu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample collection time of day menu null value menu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value WhitespaceMinimizedString null value menu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample collection duration unit menu null value menu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling activity menu null value menu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details WhitespaceMinimizedString null value menu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample volume measurement unit menu null value menu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample storage duration unit menu null value menu The units of a measured sample storage duration. Provide the units from the pick list. Day -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen processing menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental material properties menu null value menu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater system type menu null value menu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental specimen role type menu null value menu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection device menu null value menu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml +WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 +WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID WhitespaceMinimizedString null value menu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value integer null value menu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water catchment area human population range menu null value menu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water catchment area human population density unit menu null value menu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated area type menu null value menu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling weather conditions menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling weather conditions menu null value menu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value WhitespaceMinimizedString null value menu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation measurement unit menu null value menu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient temperature measurement unit menu null value menu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total daily flow rate measurement unit menu null value menu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous flow rate measurement unit menu null value menu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity measurement unit menu null value menu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100915 dissolved oxygen measurement value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved oxygen measurement unit menu null value menu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100917 oxygen reduction potential (ORP) measurement value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen reduction potential (ORP) measurement unit menu null value menu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical oxygen demand (COD) measurement unit menu null value menu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous biochemical oxygen demand (CBOD) measurement unit menu null value menu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total suspended solids (TSS) measurement unit menu null value menu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total dissolved solids (TDS) measurement unit menu null value menu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total solids (TS) measurement unit menu null value menu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity measurement unit menu null value menu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity measurement unit menu null value menu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity measurement unit menu null value menu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total nitrogen (TN) measurement unit menu null value menu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total phosphorus (TP) measurement unit menu null value menu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal contamination indicator menu null value menu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal contamination unit menu null value menu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal coliform count unit menu null value menu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary contamination indicator menu null value menu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary contamination unit menu null value menu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample temperature unit (at collection) menu null value menu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample temperature unit (when received) menu null value menu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by WhitespaceMinimizedString null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by WhitespaceMinimizedString null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email WhitespaceMinimizedString null value menu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing platform menu null value menu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing assay type menu null value menu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic target enrichment method menu null value menu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon pcr primer scheme menu null value menu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality control determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality control issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 -WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 +WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information -WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 WastewaterAMR GENEPIO:0100479 AMR detection information -WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier -WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 -WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) -WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 -WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc +WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier +WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 +WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) +WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 +WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing - -WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0100655 gene name gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100655 gene name WhitespaceMinimizedString null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence diagnostic target presence menu null value menu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit diagnostic measurement unit menu null value menu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method diagnostic measurement method menu null value menu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 2 gene_symbol_2 GeneNameMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 3 gene_symbol_3 GeneNameMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS \ No newline at end of file +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors Authors +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance Additional Comments \ No newline at end of file From 7b486f27a6134593b5f036d6f962a845d35ba1cd Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 9 Oct 2024 00:06:44 -0700 Subject: [PATCH 50/96] New HPAI schema --- web/templates/hpai/export.js | 2 + web/templates/hpai/schema.json | 49098 ++++++++++++++++++++++++++ web/templates/hpai/schema.yaml | 15257 ++++++++ web/templates/hpai/schema_core.yaml | 73 + web/templates/hpai/schema_enums.tsv | 1429 + web/templates/hpai/schema_slots.tsv | 283 + web/templates/menu.json | 27 + 7 files changed, 66169 insertions(+) create mode 100644 web/templates/hpai/export.js create mode 100644 web/templates/hpai/schema.json create mode 100644 web/templates/hpai/schema.yaml create mode 100644 web/templates/hpai/schema_core.yaml create mode 100644 web/templates/hpai/schema_enums.tsv create mode 100644 web/templates/hpai/schema_slots.tsv diff --git a/web/templates/hpai/export.js b/web/templates/hpai/export.js new file mode 100644 index 00000000..592ad2d1 --- /dev/null +++ b/web/templates/hpai/export.js @@ -0,0 +1,2 @@ +// A dictionary of possible export formats +export default {}; diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json new file mode 100644 index 00000000..ca465096 --- /dev/null +++ b/web/templates/hpai/schema.json @@ -0,0 +1,49098 @@ +{ + "name": "Mpox", + "description": "The HPAI specification was developed by the Public Health Alliance for Genomic Epidemiology (PHA4GE) to better enable harmonization of highly pathogenic avian influenza genomic surveillance contextual data. The specification is intended to support H5N1 monitoring, and provides standardized, ontology-based fields and terms for samples, sequences, and bioinformatics analysis.", + "id": "https://example.com/hpai", + "version": "4.3.3", + "prefixes": { + "linkml": { + "prefix_prefix": "linkml", + "prefix_reference": "https://w3id.org/linkml/" + }, + "GENEPIO": { + "prefix_prefix": "GENEPIO", + "prefix_reference": "http://purl.obolibrary.org/obo/GENEPIO_" + }, + "xsd": { + "prefix_prefix": "xsd", + "prefix_reference": "http://www.w3.org/2001/XMLSchema#" + }, + "shex": { + "prefix_prefix": "shex", + "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" + } + }, + "default_prefix": "https://example.com/hpai/", + "types": { + "WhitespaceMinimizedString": { + "name": "WhitespaceMinimizedString", + "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/hpai", + "typeof": "string", + "base": "str", + "uri": "xsd:token" + }, + "Provenance": { + "name": "Provenance", + "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/hpai", + "typeof": "string", + "base": "str", + "uri": "xsd:token" + }, + "string": { + "name": "string", + "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Text" + ], + "base": "str", + "uri": "xsd:string" + }, + "integer": { + "name": "integer", + "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Integer" + ], + "base": "int", + "uri": "xsd:integer" + }, + "boolean": { + "name": "boolean", + "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Boolean" + ], + "base": "Bool", + "uri": "xsd:boolean", + "repr": "bool" + }, + "float": { + "name": "float", + "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:float" + }, + "double": { + "name": "double", + "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/hpai", + "close_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:double" + }, + "decimal": { + "name": "decimal", + "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/hpai", + "broad_mappings": [ + "schema:Number" + ], + "base": "Decimal", + "uri": "xsd:decimal" + }, + "time": { + "name": "time", + "description": "A time object represents a (local) time of day, independent of any particular day", + "notes": [ + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Time" + ], + "base": "XSDTime", + "uri": "xsd:time", + "repr": "str" + }, + "date": { + "name": "date", + "description": "a date (year, month and day) in an idealized calendar", + "notes": [ + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:Date" + ], + "base": "XSDDate", + "uri": "xsd:date", + "repr": "str" + }, + "datetime": { + "name": "datetime", + "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "schema:DateTime" + ], + "base": "XSDDateTime", + "uri": "xsd:dateTime", + "repr": "str" + }, + "date_or_datetime": { + "name": "date_or_datetime", + "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "linkml:DateOrDatetime", + "repr": "str" + }, + "uriorcurie": { + "name": "uriorcurie", + "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/hpai", + "base": "URIorCURIE", + "uri": "xsd:anyURI", + "repr": "str" + }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/hpai", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, + "uri": { + "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", + "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/hpai", + "close_mappings": [ + "schema:URL" + ], + "base": "URI", + "uri": "xsd:anyURI", + "repr": "str" + }, + "ncname": { + "name": "ncname", + "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/hpai", + "base": "NCName", + "uri": "xsd:string", + "repr": "str" + }, + "objectidentifier": { + "name": "objectidentifier", + "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/hpai", + "base": "ElementIdentifier", + "uri": "shex:iri", + "repr": "str" + }, + "nodeidentifier": { + "name": "nodeidentifier", + "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/hpai", + "base": "NodeIdentifier", + "uri": "shex:nonLiteral", + "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/hpai", + "base": "str", + "uri": "xsd:string", + "repr": "str" + } + }, + "enums": { + "NullValue": { + "name": "NullValue", + "title": "null value", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Not Applicable [GENEPIO:0001619]": { + "text": "Not Applicable [GENEPIO:0001619]", + "description": "A categorical choice recorded when a datum does not apply to a given context.", + "meaning": "GENEPIO:0001619" + }, + "Missing [GENEPIO:0001618]": { + "text": "Missing [GENEPIO:0001618]", + "description": "A categorical choice recorded when a datum is not included for an unknown reason.", + "meaning": "GENEPIO:0001618" + }, + "Not Collected [GENEPIO:0001620]": { + "text": "Not Collected [GENEPIO:0001620]", + "description": "A categorical choice recorded when a datum was not measured or collected.", + "meaning": "GENEPIO:0001620" + }, + "Not Provided [GENEPIO:0001668]": { + "text": "Not Provided [GENEPIO:0001668]", + "description": "A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage.", + "meaning": "GENEPIO:0001668" + }, + "Restricted Access [GENEPIO:0001810]": { + "text": "Restricted Access [GENEPIO:0001810]", + "description": "A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns.", + "meaning": "GENEPIO:0001810" + } + } + }, + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Influenza A virus [NCBITaxon:11320]": { + "text": "Influenza A virus [NCBITaxon:11320]", + "meaning": "NCBITaxon:11320" + } + } + }, + "InfluenzaSubtypeMenu": { + "name": "InfluenzaSubtypeMenu", + "title": "influenza_subtype menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "H5N1 subtype (Influenza A virus) [NCBITaxon:102793]": { + "text": "H5N1 subtype (Influenza A virus) [NCBITaxon:102793]", + "meaning": "NCBITaxon:102793" + } + } + }, + "InfluenzaSubtypingSchemeNameMenu": { + "name": "InfluenzaSubtypingSchemeNameMenu", + "title": "influenza_subtyping_scheme_name menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Tripartite Influenza A scheme [GENEPIO:0101121]": { + "text": "Tripartite Influenza A scheme [GENEPIO:0101121]", + "meaning": "GENEPIO:0101121" + }, + "USDA GenoFLU scheme [GENEPIO:0101122]": { + "text": "USDA GenoFLU scheme [GENEPIO:0101122]", + "meaning": "GENEPIO:0101122" + } + } + }, + "TaxonomicIdentificationProcessMenu": { + "name": "TaxonomicIdentificationProcessMenu", + "title": "taxonomic_identification_process menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Whole genome sequencing assay [OBI:0002117]": { + "text": "Whole genome sequencing assay [OBI:0002117]", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", + "meaning": "OBI:0002117" + }, + "Whole metagenome sequencing assay [OBI:0002623]": { + "text": "Whole metagenome sequencing assay [OBI:0002623]", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", + "meaning": "OBI:0002623" + }, + "16S ribosomal gene sequencing assay [OBI:0002763]": { + "text": "16S ribosomal gene sequencing assay [OBI:0002763]", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", + "meaning": "OBI:0002763" + }, + "PCR assay [OBI:0002740]": { + "text": "PCR assay [OBI:0002740]", + "description": "An organism identification assay that is based on PCR.", + "meaning": "OBI:0002740" + }, + "Comparative phenotypic assessment [OBI:0001546]": { + "text": "Comparative phenotypic assessment [OBI:0001546]", + "description": "Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference", + "meaning": "OBI:0001546" + } + } + }, + "SampleCollectionTimeOfDayMenu": { + "name": "SampleCollectionTimeOfDayMenu", + "title": "sample_collection_time_of_day menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Morning [NCIT:C64934]": { + "text": "Morning [NCIT:C64934]", + "description": "The time period between dawn and noon.", + "meaning": "NCIT:C64934" + }, + "Afternoon [NCIT:C64935]": { + "text": "Afternoon [NCIT:C64935]", + "description": "The time period between noon and sunset.", + "meaning": "NCIT:C64935" + }, + "Evening [NCIT:C64936]": { + "text": "Evening [NCIT:C64936]", + "description": "The time period between late afternoon and bedtime.", + "meaning": "NCIT:C64936" + }, + "Night [NCIT:C65001]": { + "text": "Night [NCIT:C65001]", + "description": "The time in every 24 hour period when it is dark.", + "meaning": "NCIT:C65001" + } + } + }, + "SampleCollectionDurationUnitMenu": { + "name": "SampleCollectionDurationUnitMenu", + "title": "sample_collection_duration_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Second [UO:0000010]": { + "text": "Second [UO:0000010]", + "description": "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.", + "meaning": "UO:0000010" + }, + "Minute [UO:0000031]": { + "text": "Minute [UO:0000031]", + "description": "A time unit which is equal to 60 seconds.", + "meaning": "UO:0000031" + }, + "Hour [UO:0000032]": { + "text": "Hour [UO:0000032]", + "description": "A time unit which is equal to 60 minutes.", + "meaning": "UO:0000032" + }, + "Day [UO:0000033]": { + "text": "Day [UO:0000033]", + "description": "A time unit which is equal to 24 hours.", + "meaning": "UO:0000033" + }, + "Week [UO:0000034]": { + "text": "Week [UO:0000034]", + "description": "A time unit which is equal to 7 days.", + "meaning": "UO:0000034" + }, + "Month [UO:0000035]": { + "text": "Month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", + "meaning": "UO:0000035" + }, + "Year [UO:0000036]": { + "text": "Year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", + "meaning": "UO:0000036" + } + } + }, + "FoodProductMenu": { + "name": "FoodProductMenu", + "title": "food_product menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Animal feed [ENVO:02000047]": { + "text": "Animal feed [ENVO:02000047]", + "description": "Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs.", + "meaning": "ENVO:02000047" + }, + "Blood meal [FOODON:00001564]": { + "text": "Blood meal [FOODON:00001564]", + "description": "Blood meal is a dry, inert powder made from blood used as a high-nitrogen organic fertilizer and a high protein animal feed.", + "meaning": "FOODON:00001564", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Bone meal [ENVO:02000054]": { + "text": "Bone meal [ENVO:02000054]", + "description": "A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed.", + "meaning": "ENVO:02000054", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Brassica carinata meal [FOODON:00004310]": { + "text": "Brassica carinata meal [FOODON:00004310]", + "description": "A meal that is a co-product produced after the extraction of oil from the seed of the Ethiopian mustard plant (Brassica carinata).", + "meaning": "FOODON:00004310", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Canola meal [FOODON:00002694]": { + "text": "Canola meal [FOODON:00002694]", + "description": "Canola meal is an oilseed meal made from canola grain. Canola meal is a by-product of the oil crushing process.", + "meaning": "FOODON:00002694", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Compound feed premix [FOODON:00004323]": { + "text": "Compound feed premix [FOODON:00004323]", + "description": "A formula mixture of micronutrients that is used as a component in compound feed.", + "meaning": "FOODON:00004323", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Compound feed premix (medicated) [FOODON:00004324]": { + "text": "Compound feed premix (medicated) [FOODON:00004324]", + "description": "A compound feed premix in which medicinal substance has been added.", + "meaning": "FOODON:00004324", + "is_a": "Compound feed premix [FOODON:00004323]" + }, + "Feather meal [FOODON:00003927]": { + "text": "Feather meal [FOODON:00003927]", + "description": "A by product of processing poultry which is made from poultry feathers by partially grinding them under elevated heat and pressure, and then grinding and drying.", + "meaning": "FOODON:00003927", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Fish meal [FOODON:03301620]": { + "text": "Fish meal [FOODON:03301620]", + "description": "Fish meal is primarily used as a protein supplement in compound feed. As of 2010, about 56% of fish meal was used to feed farmed fish, about 20% was used in pig feed, about 12% in poultry feed, and about 12% in other uses, which included fertilizer.", + "meaning": "FOODON:03301620", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Lay ration [FOODON:00004286]": { + "text": "Lay ration [FOODON:00004286]", + "description": "Food formulated for the laying hens to increase egg production and egg shell quality.", + "meaning": "FOODON:00004286", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Meat and bone meal [FOODON:00002738]": { + "text": "Meat and bone meal [FOODON:00002738]", + "description": "Meat and bone meal (MBM) is a product of the rendering industry. It is typically about 48–52% protein, 33–35% ash, 8–12% fat, and 4–7% water. It is primarily used in the formulation of animal feed to improve the amino acid profile of the feed.", + "meaning": "FOODON:00002738", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Meat meal [FOODON:00004282]": { + "text": "Meat meal [FOODON:00004282]", + "description": "A meal that is obtained by cooking, defatting, sterilizing, grinding, and sifting by-products of an animal.", + "meaning": "FOODON:00004282", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Pet food [FOODON:00002682]": { + "text": "Pet food [FOODON:00002682]", + "description": "Pet food is plant or animal material intended for consumption by pets.", + "meaning": "FOODON:00002682", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Soybean meal [FOODON:03302757]": { + "text": "Soybean meal [FOODON:03302757]", + "description": "A type of ground protein-rich residue from the production of soybean oil used chiefly in animal feeds, in adhesives and plastics, in making synthetic protein fibers, and in fermentation media (as for the production of antibiotics).", + "meaning": "FOODON:03302757", + "is_a": "Animal feed [ENVO:02000047]" + }, + "Animal feed ingredient [FOODON:00004322]": { + "text": "Animal feed ingredient [FOODON:00004322]", + "description": "An ingredient that is used in the preparation of animal feed.", + "meaning": "FOODON:00004322" + }, + "Dairy food product [FOODON:00001256]": { + "text": "Dairy food product [FOODON:00001256]", + "description": "A dairy food product has mammilian milk or a milk component as an ingredient.", + "meaning": "FOODON:00001256" + }, + "Cheese block (whole or parts) [FOODON:03000287]": { + "text": "Cheese block (whole or parts) [FOODON:03000287]", + "description": "A whole cheese block or some substance made from a block of processed cheese.", + "meaning": "FOODON:03000287", + "is_a": "Dairy food product [FOODON:00001256]" + }, + "Cow skim milk (powdered) [FOODON:03310016]": { + "text": "Cow skim milk (powdered) [FOODON:03310016]", + "description": "Milk powder that is obtained by removing all of the water from pasteurized skim milk.", + "meaning": "FOODON:03310016", + "is_a": "Dairy food product [FOODON:00001256]" + }, + "Milk [UBERON:0001913]": { + "text": "Milk [UBERON:0001913]", + "description": "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.", + "meaning": "UBERON:0001913", + "is_a": "Dairy food product [FOODON:00001256]" + }, + "Meat, poultry and fish (organizational term)": { + "text": "Meat, poultry and fish (organizational term)" + }, + "Beef (ground or minced) [FOODON:00001282]": { + "text": "Beef (ground or minced) [FOODON:00001282]", + "description": "A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese.", + "meaning": "FOODON:00001282", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef (ground or minced, boneless) [FOODON:03000412]": { + "text": "Beef (ground or minced, boneless) [FOODON:03000412]", + "meaning": "FOODON:03000412", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, extra lean) [FOODON:03000398]": { + "text": "Beef (ground or minced, extra lean) [FOODON:03000398]", + "meaning": "FOODON:03000398", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, lean) [FOODON:03000394]": { + "text": "Beef (ground or minced, lean) [FOODON:03000394]", + "meaning": "FOODON:03000394", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, medium) [FOODON:03000402]": { + "text": "Beef (ground or minced, medium) [FOODON:03000402]", + "meaning": "FOODON:03000402", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, regular) [FOODON:03000406]": { + "text": "Beef (ground or minced, regular) [FOODON:03000406]", + "meaning": "FOODON:03000406", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef (ground or minced, sirloin) [FOODON:03000408]": { + "text": "Beef (ground or minced, sirloin) [FOODON:03000408]", + "meaning": "FOODON:03000408", + "is_a": "Beef (ground or minced) [FOODON:00001282]" + }, + "Beef hamburger (dish) [FOODON:00002737]": { + "text": "Beef hamburger (dish) [FOODON:00002737]", + "description": "A hamburger (short: burger) is a sandwich consisting of one or more cooked patties of ground meat, usually beef, placed inside a sliced bread roll or bun. The patty may be pan fried, grilled, or flame broiled.", + "meaning": "FOODON:00002737", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef shoulder [FOODON:03000377]": { + "text": "Beef shoulder [FOODON:03000377]", + "meaning": "FOODON:03000377", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef shoulder chop [FOODON:03000387]": { + "text": "Beef shoulder chop [FOODON:03000387]", + "description": "Meat chop from the shoulder region of beef.", + "meaning": "FOODON:03000387", + "is_a": "Beef shoulder [FOODON:03000377]" + }, + "Beef sirloin chop [FOODON:03000389]": { + "text": "Beef sirloin chop [FOODON:03000389]", + "description": "Meat chop from the sirloin region of beef", + "meaning": "FOODON:03000389", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef stew chunk [FOODON:00004288]": { + "text": "Beef stew chunk [FOODON:00004288]", + "description": "A chunk of beef used as an ingredient in making stew.", + "meaning": "FOODON:00004288", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef tenderloin [FOODON:00003302]": { + "text": "Beef tenderloin [FOODON:00003302]", + "description": "A cut of beef corresponding to the psoas major muscle, which is very tender.", + "meaning": "FOODON:00003302", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Beef (whole cut or parts) [FOODON:03000333]": { + "text": "Beef (whole cut or parts) [FOODON:03000333]", + "meaning": "FOODON:03000333", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Brisket [FOODON:03530020]": { + "text": "Brisket [FOODON:03530020]", + "description": "A cut of meat from the breast or lower chest of beef or veal.", + "meaning": "FOODON:03530020", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken breast [FOODON:00002703]": { + "text": "Chicken breast [FOODON:00002703]", + "description": "Chicken breast consists mainly of the breast meat portion of a chicken, and may or may not include connected bone (boneless versus \"with bone\") and skin.", + "meaning": "FOODON:00002703", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken breast (back off) [FOODON:03000385]": { + "text": "Chicken breast (back off) [FOODON:03000385]", + "description": "A chicken breast with its backbone removed.", + "meaning": "FOODON:03000385", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast (skinless) [FOODON:00003332]": { + "text": "Chicken breast (skinless) [FOODON:00003332]", + "meaning": "FOODON:00003332", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast (with skin) [FOODON:03000374]": { + "text": "Chicken breast (with skin) [FOODON:03000374]", + "meaning": "FOODON:03000374", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast (skinless, boneless) [FOODON:00003364]": { + "text": "Chicken breast (skinless, boneless) [FOODON:00003364]", + "meaning": "FOODON:00003364", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken breast cutlet [FOODON:00004308]": { + "text": "Chicken breast cutlet [FOODON:00004308]", + "description": "A cutlet made from chicken breast.", + "meaning": "FOODON:00004308", + "is_a": "Chicken breast [FOODON:00002703]" + }, + "Chicken drumstick [FOODON:00002716]": { + "text": "Chicken drumstick [FOODON:00002716]", + "description": "The segment of a chicken's leg between the thigh and tarsus (ankle).", + "meaning": "FOODON:00002716", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken drumstick (skinless) [FOODON:03000366]": { + "text": "Chicken drumstick (skinless) [FOODON:03000366]", + "meaning": "FOODON:03000366", + "is_a": "Chicken drumstick [FOODON:00002716]" + }, + "Chicken drumstick (with skin) [FOODON:03000368]": { + "text": "Chicken drumstick (with skin) [FOODON:03000368]", + "meaning": "FOODON:03000368", + "is_a": "Chicken drumstick [FOODON:00002716]" + }, + "Chicken meat [FOODON:00001040]": { + "text": "Chicken meat [FOODON:00001040]", + "meaning": "FOODON:00001040", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken meat (ground or minced) [FOODON:03311826]": { + "text": "Chicken meat (ground or minced) [FOODON:03311826]", + "description": "A food product made of ground or minced chicken meat.", + "meaning": "FOODON:03311826", + "is_a": "Chicken meat [FOODON:00001040]" + }, + "Chicken meat (ground or minced, lean) [FOODON:03000392]": { + "text": "Chicken meat (ground or minced, lean) [FOODON:03000392]", + "description": "A food product made of lean, ground or minced chicken meat.", + "meaning": "FOODON:03000392", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, extra lean) [FOODON:03000396]": { + "text": "Chicken meat (ground or minced, extra lean) [FOODON:03000396]", + "description": "A food product made of extra lean, ground or minced chicken meat.", + "meaning": "FOODON:03000396", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, medium) [FOODON:03000400]": { + "text": "Chicken meat (ground or minced, medium) [FOODON:03000400]", + "description": "A food product made of medium, ground or minced chicken meat.", + "meaning": "FOODON:03000400", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, regular) [FOODON:03000404]": { + "text": "Chicken meat (ground or minced, regular) [FOODON:03000404]", + "description": "A food product made of regular, ground or minced chicken meat.", + "meaning": "FOODON:03000404", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken meat (ground or minced, boneless) [FOODON:03000410]": { + "text": "Chicken meat (ground or minced, boneless) [FOODON:03000410]", + "meaning": "FOODON:03000410", + "is_a": "Chicken meat (ground or minced) [FOODON:03311826]" + }, + "Chicken nugget [FOODON:00002672]": { + "text": "Chicken nugget [FOODON:00002672]", + "description": "A chicken nugget is a chicken product made from chicken meat that is breaded or battered, then deep-fried or baked.", + "meaning": "FOODON:00002672", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken thigh [FOODON:02020219]": { + "text": "Chicken thigh [FOODON:02020219]", + "description": "A whole thigh that derives from a chicken.", + "meaning": "FOODON:02020219", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Chicken thigh (skinless) [FOODON:00003331]": { + "text": "Chicken thigh (skinless) [FOODON:00003331]", + "description": "A chicken thigh after the skin has been removed.", + "meaning": "FOODON:00003331", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken thigh (skinless, with bone) [FOODON:02020227]": { + "text": "Chicken thigh (skinless, with bone) [FOODON:02020227]", + "description": "A chicken thigh that is skinless and contains bone element.", + "meaning": "FOODON:02020227", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken thigh (skinless, boneless) [FOODON:03000417]": { + "text": "Chicken thigh (skinless, boneless) [FOODON:03000417]", + "meaning": "FOODON:03000417", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken upper thigh [FOODON:03000381]": { + "text": "Chicken upper thigh [FOODON:03000381]", + "description": "Meat from the upper thigh of a chicken.", + "meaning": "FOODON:03000381", + "is_a": "Chicken thigh (skinless, boneless) [FOODON:03000417]" + }, + "Chicken thigh (with skin) [FOODON:00003330]": { + "text": "Chicken thigh (with skin) [FOODON:00003330]", + "meaning": "FOODON:00003330", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken thigh (with skin, with bone) [FOODON_00003363]": { + "text": "Chicken thigh (with skin, with bone) [FOODON_00003363]", + "description": "A chicken thigh that contains skin and bone material.", + "meaning": "FOODON:00003363", + "is_a": "Chicken thigh [FOODON:02020219]" + }, + "Chicken wing [FOODON:00002674]": { + "text": "Chicken wing [FOODON:00002674]", + "description": "A whole wing that derives from a chicken.", + "meaning": "FOODON:00002674", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Fish food product [FOODON:00001248]": { + "text": "Fish food product [FOODON:00001248]", + "description": "A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins).", + "meaning": "FOODON:00001248", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Fish steak [FOODON:00002986]": { + "text": "Fish steak [FOODON:00002986]", + "description": "A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless.", + "meaning": "FOODON:00002986", + "is_a": "Fish food product [FOODON:00001248]" + }, + "Ham food product [FOODON:00002502]": { + "text": "Ham food product [FOODON:00002502]", + "description": "Ham is pork from a leg cut that has been preserved by wet or dry curing, with or without smoking. As a processed meat, the term \"ham\" includes both whole cuts of meat and ones that have been mechanically formed.", + "meaning": "FOODON:00002502", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Head cheese [FOODON:03315658]": { + "text": "Head cheese [FOODON:03315658]", + "description": "Head cheese is a cold cut that originated in Europe. Head cheese is not a dairy cheese, but a terrine or meat jelly made with flesh from the head of a calf or pig, or less commonly a sheep or cow, and often set in aspic. A version pickled with vinegar is known as souse.", + "meaning": "FOODON:03315658", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Lamb [FOODON:03411669]": { + "text": "Lamb [FOODON:03411669]", + "description": "A whole lamb or some material processed from a lamb.", + "meaning": "FOODON:03411669", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Meat strip [FOODON:00004285]": { + "text": "Meat strip [FOODON:00004285]", + "description": "A cut of meat which is long, narrow and boneless.", + "meaning": "FOODON:00004285", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Mutton [FOODON:00002912]": { + "text": "Mutton [FOODON:00002912]", + "description": "The meat of an adult sheep is mutton, a term only used for the meat, not the living animals.", + "meaning": "FOODON:00002912", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork chop [FOODON:00001049]": { + "text": "Pork chop [FOODON:00001049]", + "description": "A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion.", + "meaning": "FOODON:00001049", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork meat (ground or minced) [FOODON:03309969]": { + "text": "Pork meat (ground or minced) [FOODON:03309969]", + "description": "Meat from a pig that has been ground or minced.", + "meaning": "FOODON:03309969", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork meat (ground or minced, boneless) [FOODON:03000413]": { + "text": "Pork meat (ground or minced, boneless) [FOODON:03000413]", + "meaning": "FOODON:03000413", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, extra lean) [FOODON:03000399]": { + "text": "Pork meat (ground or minced, extra lean) [FOODON:03000399]", + "description": "A food product made of extra-lean, ground or minced pork meat.", + "meaning": "FOODON:03000399", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, lean) [FOODON:03000395]": { + "text": "Pork meat (ground or minced, lean) [FOODON:03000395]", + "description": "A food product made of lean, ground or minced pork meat.", + "meaning": "FOODON:03000395", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, medium) [FOODON:03000403]": { + "text": "Pork meat (ground or minced, medium) [FOODON:03000403]", + "description": "A food product made of medium, ground or minced pork meat.", + "meaning": "FOODON:03000403", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, regular) [FOODON:03000407]": { + "text": "Pork meat (ground or minced, regular) [FOODON:03000407]", + "description": "A food product made of regular, ground or minced pork meat.", + "meaning": "FOODON:03000407", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork meat (ground or minced, Sirloin) [FOODON:03000409]": { + "text": "Pork meat (ground or minced, Sirloin) [FOODON:03000409]", + "description": "Ground or minced pork meat that comes from the sirloin region.", + "meaning": "FOODON:03000409", + "is_a": "Pork meat (ground or minced) [FOODON:03309969]" + }, + "Pork shoulder [FOODON:03000376]": { + "text": "Pork shoulder [FOODON:03000376]", + "meaning": "FOODON:03000376", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork shoulder chop [FOODON:03000388]": { + "text": "Pork shoulder chop [FOODON:03000388]", + "description": "Meat chop from the blade roast of pork.", + "meaning": "FOODON:03000388", + "is_a": "Pork shoulder [FOODON:03000376]" + }, + "Pork sirloin chop [FOODON:03000390]": { + "text": "Pork sirloin chop [FOODON:03000390]", + "meaning": "FOODON:03000390", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork steak [FOODON:00003148]": { + "text": "Pork steak [FOODON:00003148]", + "meaning": "FOODON:00003148", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pork tenderloin [FOODON:03000416]": { + "text": "Pork tenderloin [FOODON:03000416]", + "meaning": "FOODON:03000416", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Poultry meat [FOODON:03315883]": { + "text": "Poultry meat [FOODON:03315883]", + "description": "Any meat from one or more poultry birds.", + "meaning": "FOODON:03315883", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Leg (poultry meat cut) [FOODON:03530159]": { + "text": "Leg (poultry meat cut) [FOODON:03530159]", + "description": "The leg cut of a poultry bird.", + "meaning": "FOODON:03530159", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Poultry drumstick [FOODON:00003469]": { + "text": "Poultry drumstick [FOODON:00003469]", + "description": "The calf part of a poultry hindleg (hindlimb zeugopod)", + "meaning": "FOODON:00003469", + "is_a": "Leg (poultry meat cut) [FOODON:03530159]" + }, + "Neck (poultry meat cut) [FOODON:03530294]": { + "text": "Neck (poultry meat cut) [FOODON:03530294]", + "description": "The neck cut of a poultry bird.", + "meaning": "FOODON:03530294", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Thigh (poultry meat cut) [FOODON:03530160]": { + "text": "Thigh (poultry meat cut) [FOODON:03530160]", + "description": "The thigh cut of a poultry bird.", + "meaning": "FOODON:03530160", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Wing (poultry meat cut) [FOODON:03530157]": { + "text": "Wing (poultry meat cut) [FOODON:03530157]", + "description": "The wing cut of a poultry bird.", + "meaning": "FOODON:03530157", + "is_a": "Poultry meat [FOODON:03315883]" + }, + "Sausage (whole) [FOODON:03315904]": { + "text": "Sausage (whole) [FOODON:03315904]", + "description": "A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder.", + "meaning": "FOODON:03315904", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Pepperoni [FOODON:03311003]": { + "text": "Pepperoni [FOODON:03311003]", + "description": "A highly seasoned and spicy beef or pork sausage.", + "meaning": "FOODON:03311003", + "is_a": "Sausage (whole) [FOODON:03315904]" + }, + "Salami [FOODON:03312067]": { + "text": "Salami [FOODON:03312067]", + "description": "A cured sausage which consists of fermented and air-dried meat, typically pork.", + "meaning": "FOODON:03312067", + "is_a": "Sausage (whole) [FOODON:03315904]" + }, + "Shellfish [FOODON:03411433]": { + "text": "Shellfish [FOODON:03411433]", + "description": "The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates.", + "meaning": "FOODON:03411433", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Shrimp [FOODON:03301673]": { + "text": "Shrimp [FOODON:03301673]", + "description": "A whole shrimp or some material processed from a shrimp.", + "meaning": "FOODON:03301673", + "is_a": "Shellfish [FOODON:03411433]" + }, + "Scallop [FOODON:03411489]": { + "text": "Scallop [FOODON:03411489]", + "meaning": "FOODON:03411489", + "is_a": "Shellfish [FOODON:03411433]" + }, + "Turkey breast [FOODON:00002690]": { + "text": "Turkey breast [FOODON:00002690]", + "description": "Turkey breast consists mainly of the breast meat portion of a turkey, and may or may not include connected bone (\"deboned or boneless versus bone-in\") and skin.", + "meaning": "FOODON:00002690", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey breast (back off) [FOODON:03000386]": { + "text": "Turkey breast (back off) [FOODON:03000386]", + "description": "A turkey breast with its backbone removed.", + "meaning": "FOODON:03000386", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey breast (skinless) [FOODON:03000372]": { + "text": "Turkey breast (skinless) [FOODON:03000372]", + "meaning": "FOODON:03000372", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey breast (skinless, boneless) [FOODON:03000373]": { + "text": "Turkey breast (skinless, boneless) [FOODON:03000373]", + "meaning": "FOODON:03000373", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey breast (with skin) [FOODON:03000375]": { + "text": "Turkey breast (with skin) [FOODON:03000375]", + "meaning": "FOODON:03000375", + "is_a": "Turkey breast [FOODON:00002690]" + }, + "Turkey drumstick [FOODON:03000365]": { + "text": "Turkey drumstick [FOODON:03000365]", + "meaning": "FOODON:03000365", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey drumstick (skinless) [FOODON:03000367]": { + "text": "Turkey drumstick (skinless) [FOODON:03000367]", + "meaning": "FOODON:03000367", + "is_a": "Turkey drumstick [FOODON:03000365]" + }, + "Turkey drumstick (with skin) [FOODON:03000369]": { + "text": "Turkey drumstick (with skin) [FOODON:03000369]", + "meaning": "FOODON:03000369", + "is_a": "Turkey drumstick [FOODON:03000365]" + }, + "Turkey meat [FOODON:00001286]": { + "text": "Turkey meat [FOODON:00001286]", + "description": "A turkey meat food product is any food product made predominantly of turkey parts.", + "meaning": "FOODON:00001286", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey meat (ground or minced) [FOODON:00002714]": { + "text": "Turkey meat (ground or minced) [FOODON:00002714]", + "description": "A food product made of ground or minced turkey meat.", + "meaning": "FOODON:00002714", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, lean) [FOODON:03000393]": { + "text": "Turkey meat (ground or minced, lean) [FOODON:03000393]", + "description": "A food product made of lean, ground or minced turkey meat.", + "meaning": "FOODON:03000393", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, extra lean) [FOODON:03000397]": { + "text": "Turkey meat (ground or minced, extra lean) [FOODON:03000397]", + "description": "A food product made of extra-lean, ground or minced turkey meat.", + "meaning": "FOODON:03000397", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, medium) [FOODON:03000401]": { + "text": "Turkey meat (ground or minced, medium) [FOODON:03000401]", + "description": "A food product made of medium, ground or minced turkey meat.", + "meaning": "FOODON:03000401", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, regular) [FOODON:03000405]": { + "text": "Turkey meat (ground or minced, regular) [FOODON:03000405]", + "description": "A food product made of regular, ground or minced turkey meat.", + "meaning": "FOODON:03000405", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey meat (ground or minced, boneless) [FOODON:03000411]": { + "text": "Turkey meat (ground or minced, boneless) [FOODON:03000411]", + "meaning": "FOODON:03000411", + "is_a": "Turkey meat [FOODON:00001286]" + }, + "Turkey thigh [FOODON:00003325]": { + "text": "Turkey thigh [FOODON:00003325]", + "description": "A thigh poultry cut of turkey.", + "meaning": "FOODON:00003325", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Turkey thigh (skinless) [FOODON:00003329]": { + "text": "Turkey thigh (skinless) [FOODON:00003329]", + "description": "A turkey thigh after the skin has been removed.", + "meaning": "FOODON:00003329", + "is_a": "Turkey thigh [FOODON:00003325]" + }, + "Turkey thigh (skinless, boneless) [FOODON:03000370]": { + "text": "Turkey thigh (skinless, boneless) [FOODON:03000370]", + "meaning": "FOODON:03000370", + "is_a": "Turkey thigh [FOODON:00003325]" + }, + "Turkey thigh (with skin) [FOODON:00003328]": { + "text": "Turkey thigh (with skin) [FOODON:00003328]", + "description": "A turkey thigh that still contains the skin.", + "meaning": "FOODON:00003328", + "is_a": "Turkey thigh [FOODON:00003325]" + }, + "Turkey upper thigh [FOODON:03000382]": { + "text": "Turkey upper thigh [FOODON:03000382]", + "description": "Meat from the upper thigh of a turkey.", + "meaning": "FOODON:03000382", + "is_a": "Turkey thigh (with skin) [FOODON:00003328]" + }, + "Turkey upper thigh (with skin) [FOODON:03000384]": { + "text": "Turkey upper thigh (with skin) [FOODON:03000384]", + "description": "Turkey's upper thigh that contains the skin.", + "meaning": "FOODON:03000384", + "is_a": "Turkey thigh (with skin) [FOODON:00003328]" + }, + "Turkey wing [FOODON:03000371]": { + "text": "Turkey wing [FOODON:03000371]", + "meaning": "FOODON:03000371", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Veal [FOODON:00003083]": { + "text": "Veal [FOODON:00003083]", + "description": "Veal is the meat of calves, in contrast to the beef from older cattle. Veal can be produced from a calf of either sex and any breed; however, most veal comes from young males of dairy breeds which are not used for breeding.", + "meaning": "FOODON:00003083", + "is_a": "Meat, poultry and fish (organizational term)" + }, + "Formula fed veal [FOODON:000039111]": { + "text": "Formula fed veal [FOODON:000039111]", + "meaning": "OODON:000039111", + "is_a": "Veal [FOODON:00003083]" + }, + "Grain-fed veal [FOODON:00004280]": { + "text": "Grain-fed veal [FOODON:00004280]", + "description": "Meat from a calf that is raised on grain, hay, or other solid food, in addition to milk", + "meaning": "FOODON:00004280", + "is_a": "Veal [FOODON:00003083]" + } + } + }, + "FoodProductPropertiesMenu": { + "name": "FoodProductPropertiesMenu", + "title": "food_product_properties menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Organic food claim or use [FOODON:03510128]": { + "text": "Organic food claim or use [FOODON:03510128]", + "description": "USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF]", + "meaning": "FOODON:03510128" + }, + "Food (raw) [FOODON:03311126]": { + "text": "Food (raw) [FOODON:03311126]", + "description": "A food material that has not been cooked.", + "meaning": "FOODON:03311126" + }, + "Food (heat treated) [FOODON:03316043]": { + "text": "Food (heat treated) [FOODON:03316043]", + "meaning": "FOODON:03316043" + }, + "Food (pasteurized) [FOODON:00002654]": { + "text": "Food (pasteurized) [FOODON:00002654]", + "meaning": "FOODON:00002654" + }, + "Dairy product (no fat removed, whole)": { + "text": "Dairy product (no fat removed, whole)" + }, + "Dairy product (skimmed, non-fat)": { + "text": "Dairy product (skimmed, non-fat)" + }, + "Dairy product (semi-skimmed, reduced fat, 1%)": { + "text": "Dairy product (semi-skimmed, reduced fat, 1%)" + }, + "Dairy product (semi-skimmed, reduced fat, 2%)": { + "text": "Dairy product (semi-skimmed, reduced fat, 2%)" + } + } + }, + "FoodPackagingMenu": { + "name": "FoodPackagingMenu", + "title": "food_packaging menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Bottle [FOODON:03490214": { + "text": "Bottle [FOODON:03490214", + "description": "A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle.", + "meaning": "FOODON:03490214" + }, + "Bag [FOODON:03490197]": { + "text": "Bag [FOODON:03490197]", + "description": "According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack", + "meaning": "FOODON:03490197" + }, + "Carton [FOODON:03490213]": { + "text": "Carton [FOODON:03490213]", + "meaning": "FOODON:03490213" + } + } + }, + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental_site menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Abattoir [ENVO:01000925]": { + "text": "Abattoir [ENVO:01000925]", + "description": "A facility in which non-human animals are slaughtered and processed for human consumption.", + "meaning": "ENVO:01000925" + }, + "Agricultural Field [ENVO:00000114]": { + "text": "Agricultural Field [ENVO:00000114]", + "description": "A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops.", + "meaning": "ENVO:00000114" + }, + "Animal cage [ENVO:01000922]": { + "text": "Animal cage [ENVO:01000922]", + "description": "A manufactured cage which may be used to confine, contain, or protect an animal.", + "meaning": "ENVO:01000922" + }, + "Artificial wetland [ENVO:03501406]": { + "text": "Artificial wetland [ENVO:03501406]", + "description": "A wetland ecosystem which is constructed to treat municipal or industrial wastewater, greywater or stormwater runoff.", + "meaning": "ENVO:03501406" + }, + "Breeding ground [ENVO:03501441]": { + "text": "Breeding ground [ENVO:03501441]", + "description": "A place where animals breed.", + "meaning": "ENVO:03501441" + }, + "Building [ENVO:00000073]": { + "text": "Building [ENVO:00000073]", + "description": "A permanent walled and roofed construction.", + "meaning": "ENVO:00000073" + }, + "Barn [ENVO:03501257]": { + "text": "Barn [ENVO:03501257]", + "description": "A farm building used for housing livestock, storing machinery or crops etc", + "meaning": "ENVO:03501257" + }, + "Breeder barn [ENVO:03501383]": { + "text": "Breeder barn [ENVO:03501383]", + "description": "A barn where animals are kept for breeding purposes.", + "meaning": "ENVO:03501383", + "is_a": "Barn [ENVO:03501257]" + }, + "Broiler barn [ENVO:03501386]": { + "text": "Broiler barn [ENVO:03501386]", + "description": "A barn where broiler chickens are reared.", + "meaning": "ENVO:03501386", + "is_a": "Barn [ENVO:03501257]" + }, + "Sheep barn [ENVO:03501385]": { + "text": "Sheep barn [ENVO:03501385]", + "description": "A barn where sheep are kept.", + "meaning": "ENVO:03501385", + "is_a": "Barn [ENVO:03501257]" + }, + "Dairy [ENVO:00003862]": { + "text": "Dairy [ENVO:00003862]", + "description": "A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption.", + "meaning": "ENVO:00003862" + }, + "Farm [ENVO:00000078]": { + "text": "Farm [ENVO:00000078]", + "description": "An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein.", + "meaning": "ENVO:00000078" + }, + "Beef farm [ENVO:03501443]": { + "text": "Beef farm [ENVO:03501443]", + "description": "A farm where cows are kept for the purpose of meat production.", + "meaning": "ENVO:03501443", + "is_a": "Farm [ENVO:00000078]" + }, + "Breeder farm [ENVO:03501384]": { + "text": "Breeder farm [ENVO:03501384]", + "description": "A farm where animals are kept for breeding purposes.", + "meaning": "ENVO:03501384", + "is_a": "Farm [ENVO:00000078]" + }, + "Dairy farm [ENVO:03501416]": { + "text": "Dairy farm [ENVO:03501416]", + "description": "A farm where cows are kept for the purpose of producing milk and other dairy products.", + "meaning": "ENVO:03501416", + "is_a": "Farm [ENVO:00000078]" + }, + "Feedlot [ENVO:01000627]": { + "text": "Feedlot [ENVO:01000627]", + "description": "A feedlot is a plot of land on which livestock are fattened for market [URL:http://www.merriam-webster.com/dictionary/feedlot ].", + "meaning": "ENVO:01000627", + "is_a": "Farm [ENVO:00000078]" + }, + "Beef cattle feedlot [ENVO:03501444]": { + "text": "Beef cattle feedlot [ENVO:03501444]", + "description": "A feedlot where beef cattle are kept with a focus on efficient growth and weight gain of the animals.", + "meaning": "ENVO:03501444", + "is_a": "Feedlot [ENVO:01000627]" + }, + "Fish farm [ENVO:00000294]": { + "text": "Fish farm [ENVO:00000294]", + "description": "A facility in which fish are raised commercially in tanks or enclosures, usually for food.", + "meaning": "ENVO:00000294", + "is_a": "Farm [ENVO:00000078]" + }, + "Research farm [ENVO:03501417]": { + "text": "Research farm [ENVO:03501417]", + "description": "A farm which is used for conducting agricultural research.", + "meaning": "ENVO:03501417", + "is_a": "Farm [ENVO:00000078]" + }, + "Central Experimental Farm [GAZ:00004603]": { + "text": "Central Experimental Farm [GAZ:00004603]", + "description": "An agricultural facility, working farm, and research centre of the Research Branch of Agriculture and Agri-Food Canada. This farm is centrally located in and completely surrounded by the City of Ottawa, Ontario, Canada. The CEF is bordered by the Rideau Canal (a National Historic Site as well) to the east, by Baseline Road to the south, by Merivale and Fisher Roads to the west, and Carling Avenue to the north.", + "meaning": "GAZ:00004603", + "is_a": "Farm [ENVO:00000078]" + }, + "Freshwater environment [ENVO:01000306]": { + "text": "Freshwater environment [ENVO:01000306]", + "description": "An aquatic environment which is determined by freshwater.", + "meaning": "ENVO:01000306" + }, + "Hatchery [ENVO:01001873]": { + "text": "Hatchery [ENVO:01001873]", + "description": "A construction in which eggs are hatched under artificial conditions.", + "meaning": "ENVO:01001873" + }, + "Poultry hatchery [ENVO:01001874]": { + "text": "Poultry hatchery [ENVO:01001874]", + "description": "A hatchery in which the eggs of poultry are hatched under artificial conditions", + "meaning": "ENVO:01001874", + "is_a": "Hatchery [ENVO:01001873]" + }, + "Hospital [ENVO:00002173]": { + "text": "Hospital [ENVO:00002173]", + "description": "A building in which health care services are provided by specialized staff and equipment.", + "meaning": "ENVO:00002173" + }, + "Lake [ENVO:00000020]": { + "text": "Lake [ENVO:00000020]", + "description": "A body of water or other liquid of considerable size contained in a depression on a landmass.", + "meaning": "ENVO:00000020" + }, + "Pond [ENVO:00000033]": { + "text": "Pond [ENVO:00000033]", + "description": "A body of water, usually of smaller size than a lake.", + "meaning": "ENVO:00000033" + }, + "Reservoir [ENVO:00000025]": { + "text": "Reservoir [ENVO:00000025]", + "description": "An artificial body of water, often contained by a dam, constructed for the purpose of water storage.", + "meaning": "ENVO:00000025" + }, + "Irrigation reservoir [ENVO:00000450]": { + "text": "Irrigation reservoir [ENVO:00000450]", + "description": "A reservoir constructed for the purpose of providing water for irrigation.", + "meaning": "ENVO:00000450", + "is_a": "Reservoir [ENVO:00000025]" + }, + "Retail environment [ENVO:01001448]": { + "text": "Retail environment [ENVO:01001448]", + "description": "A planned environmental usage process during which an environment supports the sale of goods to ultimate consumers, usually in small quantities.", + "meaning": "ENVO:01001448" + }, + "Shop [ENVO:00002221]": { + "text": "Shop [ENVO:00002221]", + "description": "A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods.", + "meaning": "ENVO:00002221", + "is_a": "Retail environment [ENVO:01001448]" + }, + "Supermarket [ENVO:01000984]": { + "text": "Supermarket [ENVO:01000984]", + "description": "A food shop in which food products are the primary offer for sale or trade.", + "meaning": "ENVO:01000984", + "is_a": "Shop [ENVO:00002221]" + }, + "River [ENVO:00000022]": { + "text": "River [ENVO:00000022]", + "description": "A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply.", + "meaning": "ENVO:00000022" + }, + "Roost (bird) [ENVO:03501439]": { + "text": "Roost (bird) [ENVO:03501439]", + "description": "A perch on which birds rest.", + "meaning": "ENVO:03501439" + }, + "Wastewater treatment plant [ENVO:00002272]": { + "text": "Wastewater treatment plant [ENVO:00002272]", + "description": "A plant in which wastewater is treated.", + "meaning": "ENVO:00002272" + }, + "Wetland [ENVO:00000043]": { + "text": "Wetland [ENVO:00000043]", + "description": "An area that is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions.", + "meaning": "ENVO:00000043" + } + } + }, + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "environmental_material menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Air [ENVO:00002005]": { + "text": "Air [ENVO:00002005]", + "description": "The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.", + "meaning": "ENVO:00002005" + }, + "Animal manure [AGRO:00000079]": { + "text": "Animal manure [AGRO:00000079]", + "description": "Organic matter mostly derived from animal feces which can be used as organic fertilizer in agriculture.", + "meaning": "AGRO:00000079" + }, + "Animal feeding equipment [AGRO:00000675]": { + "text": "Animal feeding equipment [AGRO:00000675]", + "description": "An equipment used to feed and water livestock animals.", + "meaning": "AGRO:00000675" + }, + "Animal feeder [AGRO:00000679]": { + "text": "Animal feeder [AGRO:00000679]", + "description": "An animal feeding equipment that has a food storage unit and which enables livestock to obtain their own food.", + "meaning": "AGRO:00000679", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Animal drinker [AGRO:00000680]": { + "text": "Animal drinker [AGRO:00000680]", + "description": "An animal feeding equipment that has a water storage unit which enables livestock to obtain their own water.", + "meaning": "AGRO:00000680", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Feed pan [AGRO:00000676]": { + "text": "Feed pan [AGRO:00000676]", + "description": "A bowl or pan which is used to feed livestock.", + "meaning": "AGRO:00000676", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Watering bowl [AGRO:00000677]": { + "text": "Watering bowl [AGRO:00000677]", + "description": "A bowl from which animals can drink.", + "meaning": "AGRO:00000677", + "is_a": "Animal feeding equipment [AGRO:00000675]" + }, + "Animal transportation equipment [AGRO:00000671]": { + "text": "Animal transportation equipment [AGRO:00000671]", + "description": "An equipment used in the transportation of an animal", + "meaning": "AGRO:00000671" + }, + "Dead haul trailer [GENEPIO:0100896]": { + "text": "Dead haul trailer [GENEPIO:0100896]", + "description": "A trailer used by a dead haul truck to transport dead animal from an abattoir.", + "meaning": "GENEPIO:0100896", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Dead haul truck [AGRO:00000673]": { + "text": "Dead haul truck [AGRO:00000673]", + "description": "A truck used to haul dead animals from an abattoir.", + "meaning": "AGRO:00000673", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Live haul trailer [GENEPIO:0100897]": { + "text": "Live haul trailer [GENEPIO:0100897]", + "description": "A trailer used by a live haul truck to transport live animals.", + "meaning": "GENEPIO:0100897", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Live haul truck [AGRO:00000674]": { + "text": "Live haul truck [AGRO:00000674]", + "description": "A truck used to haul live animals.", + "meaning": "AGRO:00000674", + "is_a": "Animal transportation equipment [AGRO:00000671]" + }, + "Belt [NCIT:C49844]": { + "text": "Belt [NCIT:C49844]", + "description": "A device consisting of a narrow loop of material moving over shafts or pulleys.", + "meaning": "NCIT:C49844" + }, + "Egg belt [AGRO:00000670]": { + "text": "Egg belt [AGRO:00000670]", + "description": "A conveyor belt used to collect eggs in an industrial egg production environment.", + "meaning": "AGRO:00000670", + "is_a": "Belt [NCIT:C49844]" + }, + "Plucking belt [AGRO:00000669]": { + "text": "Plucking belt [AGRO:00000669]", + "description": "A part of the plucking machine that moves the birds through the stages of plucking within the plucking apparatus.", + "meaning": "AGRO:00000669", + "is_a": "Belt [NCIT:C49844]" + }, + "Biosolids [ENVO:00002059]": { + "text": "Biosolids [ENVO:00002059]", + "description": "A treated form of sludge, sometimes used as a fertilizer in agriculture.", + "meaning": "ENVO:00002059" + }, + "Boot [GSSO:012935]": { + "text": "Boot [GSSO:012935]", + "description": "A footwear which covers the foot, the ankle, and sometimes the leg below the knee.", + "meaning": "GSSO:012935" + }, + "Boot cover [OBI:0002806]": { + "text": "Boot cover [OBI:0002806]", + "description": "A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants.", + "meaning": "OBI:0002806", + "is_a": "Boot [GSSO:012935]" + }, + "Broom [ENVO:03501431]": { + "text": "Broom [ENVO:03501431]", + "description": "A cleaning equipment piece which is a bundle of fibres attached to a long handle, and is used for sweeping.", + "meaning": "ENVO:03501431" + }, + "Bulk tank [ENVO:03501379]": { + "text": "Bulk tank [ENVO:03501379]", + "description": "A manufactured product which used to safely store and/or transport solids, liquids, gases and a variety of compounds and mixtures.", + "meaning": "ENVO:03501379" + }, + "Chick box [AGRO:00000678]": { + "text": "Chick box [AGRO:00000678]", + "description": "The box which is used to transport chick (juvenile chicken).", + "meaning": "AGRO:00000678" + }, + "Chick pad [AGRO:00000672]": { + "text": "Chick pad [AGRO:00000672]", + "description": "The lining of a box or crate used to transport chicks (juvenile chickens).", + "meaning": "AGRO:00000672" + }, + "Cleaning equipment [ENVO:03501430]": { + "text": "Cleaning equipment [ENVO:03501430]", + "description": "An equipment piece used for cleaning a built environment or a manufactured product.", + "meaning": "ENVO:03501430" + }, + "Compost [ENVO:00002170]": { + "text": "Compost [ENVO:00002170]", + "description": "The aerobically decomposed remnants of organic materials.", + "meaning": "ENVO:00002170" + }, + "Crate [ENVO:03501372]": { + "text": "Crate [ENVO:03501372]", + "description": "A manufactured product which is a container, traditionally made of wooden slates, designed to protect transported goods from damage.", + "meaning": "ENVO:03501372" + }, + "Dumpster [ENVO:03501400]": { + "text": "Dumpster [ENVO:03501400]", + "description": "A manufactured product which is a reusable container that accumulates waste until it is periodically emptied or replaced.", + "meaning": "ENVO:03501400" + }, + "Dust [ENVO:00002008]": { + "text": "Dust [ENVO:00002008]", + "description": "Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere.", + "meaning": "ENVO:00002008" + }, + "Fan [NCIT:C49947]": { + "text": "Fan [NCIT:C49947]", + "description": "A device designed to create an air current through the rotation of a planar surface.", + "meaning": "NCIT:C49947" + }, + "Freezer [ENVO:03501415]": { + "text": "Freezer [ENVO:03501415]", + "description": "A manufactured product which is a device used to keep things frozen by maintaining a temperature below the freezing point of water.", + "meaning": "ENVO:03501415" + }, + "Freezer handle [ENVO:03501414]": { + "text": "Freezer handle [ENVO:03501414]", + "description": "A manufactured product which is the handle of a freezer door.", + "meaning": "ENVO:03501414", + "is_a": "Freezer [ENVO:03501415]" + }, + "Manure digester equipment [ENVO:03501424]": { + "text": "Manure digester equipment [ENVO:03501424]", + "description": "An equipment piece which is used in the aerobic or anaerobic microbial digestion of manure.", + "meaning": "ENVO:03501424" + }, + "Nest [ENVO:03501432]": { + "text": "Nest [ENVO:03501432]", + "description": "A structure that is built for certain animals to hold eggs or young.", + "meaning": "ENVO:03501432" + }, + "Bird's nest [ENVO:00005805]": { + "text": "Bird's nest [ENVO:00005805]", + "description": "A bird nest is the spot in which a bird lays and incubates its eggs and raises its young. [ https://en.wikipedia.org/wiki/Bird_nest ]", + "meaning": "ENVO:00005805", + "is_a": "Nest [ENVO:03501432]" + }, + "Permafrost [ENVO:00000134]": { + "text": "Permafrost [ENVO:00000134]", + "description": "Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years.", + "meaning": "ENVO:00000134" + }, + "Poultry fluff [UBERON:0008291]": { + "text": "Poultry fluff [UBERON:0008291]", + "description": "A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus.", + "meaning": "UBERON:0008291" + }, + "Poultry litter [AGRO:00000080]": { + "text": "Poultry litter [AGRO:00000080]", + "description": "Manure which is primarily composed of pig feces.", + "meaning": "AGRO:00000080" + }, + "Sediment [ENVO:00002007]": { + "text": "Sediment [ENVO:00002007]", + "description": "Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.", + "meaning": "ENVO:00002007" + }, + "Soil [ENVO:00001998]": { + "text": "Soil [ENVO:00001998]", + "description": "Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.", + "meaning": "ENVO:00001998" + }, + "Agricultural soil [ENVO:00002259]": { + "text": "Agricultural soil [ENVO:00002259]", + "description": "A type of soil used for agriculture that supports the physical, chemical, and biological needs of the desired crop during production.", + "meaning": "ENVO:00002259", + "is_a": "Soil [ENVO:00001998]" + }, + "Forest soil [ENVO:00002261]": { + "text": "Forest soil [ENVO:00002261]", + "description": "A portion of soil which is found in a forested area.", + "meaning": "ENVO:00002261", + "is_a": "Soil [ENVO:00001998]" + }, + "Straw [ENVO:00003869]": { + "text": "Straw [ENVO:00003869]", + "description": "An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed.", + "meaning": "ENVO:00003869" + }, + "Water [CHEBI:15377]": { + "text": "Water [CHEBI:15377]", + "description": "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.", + "meaning": "CHEBI:15377" + }, + "Drinking water [ENVO:00003064]": { + "text": "Drinking water [ENVO:00003064]", + "description": "Water which is suitable for consumption by humans", + "meaning": "ENVO:00003064", + "is_a": "Water [CHEBI:15377]" + }, + "Fecal slurry [ENVO:03501436]": { + "text": "Fecal slurry [ENVO:03501436]", + "description": "A mixture of fecal material mixed, buffer, and other materials, that is homogenized and strained and used in fecal microbiota translpantation.", + "meaning": "ENVO:03501436", + "is_a": "Water [CHEBI:15377]" + }, + "Fluid from meat rinse [GENEPIO:0004323]": { + "text": "Fluid from meat rinse [GENEPIO:0004323]", + "meaning": "GENEPIO:0004323", + "is_a": "Water [CHEBI:15377]" + }, + "Groundwater [ENVO:01001004]": { + "text": "Groundwater [ENVO:01001004]", + "description": "Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel.", + "meaning": "ENVO:01001004", + "is_a": "Water [CHEBI:15377]" + }, + "Poultry plucking water [AGRO_00000693]": { + "text": "Poultry plucking water [AGRO_00000693]", + "description": "A type of water obtained from rinsing poultry carcasses during the feather plucking process.", + "meaning": "AGRO:00000693", + "is_a": "Water [CHEBI:15377]" + }, + "Surface runoff [ENVO:03501408]": { + "text": "Surface runoff [ENVO:03501408]", + "description": "Surface water which is 1) from some rainwater, stormwater, meltwater, or other local source and 2) which can no longer sufficiently rapidly infiltrate into soil, and instead flows along a drainage slope.", + "meaning": "ENVO:03501408", + "is_a": "Water [CHEBI:15377]" + }, + "Surface water [ENVO:00002042]": { + "text": "Surface water [ENVO:00002042]", + "description": "Water that is found on the surface of an astronomical object.", + "meaning": "ENVO:00002042", + "is_a": "Water [CHEBI:15377]" + }, + "Wastewater [ENVO:00002001]": { + "text": "Wastewater [ENVO:00002001]", + "description": "Water that has been adversely affected in quality by anthropogenic influence", + "meaning": "ENVO:00002001", + "is_a": "Water [CHEBI:15377]" + }, + "Sludge [ENVO:00002044]": { + "text": "Sludge [ENVO:00002044]", + "description": "The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes.", + "meaning": "ENVO:00002044", + "is_a": "Wastewater [ENVO:00002001]" + }, + "Primary sludge [ENVO:00002057]": { + "text": "Primary sludge [ENVO:00002057]", + "description": "Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment.", + "meaning": "ENVO:00002057", + "is_a": "Sludge [ENVO:00002044]" + }, + "Secondary sludge [ENVO:00002058]": { + "text": "Secondary sludge [ENVO:00002058]", + "description": "Activated waste biomass generated during wastewater treatment.", + "meaning": "ENVO:00002058", + "is_a": "Sludge [ENVO:00002044]" + }, + "Wastewater effluent [GENEPIO:0100891]": { + "text": "Wastewater effluent [GENEPIO:0100891]", + "meaning": "GENEPIO:0100891", + "is_a": "Wastewater [ENVO:00002001]" + }, + "Primary wastewater effluent [GENEPIO:0100892]": { + "text": "Primary wastewater effluent [GENEPIO:0100892]", + "description": "A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation.", + "meaning": "GENEPIO:0100892", + "is_a": "Wastewater effluent [GENEPIO:0100891]" + }, + "Secondary wastewater effluent [GENEPIO:0100893]": { + "text": "Secondary wastewater effluent [GENEPIO:0100893]", + "description": "A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation.", + "meaning": "GENEPIO:0100893", + "is_a": "Wastewater effluent [GENEPIO:0100891]" + }, + "Wastewater sediment [GENEPIO:0100890]": { + "text": "Wastewater sediment [GENEPIO:0100890]", + "meaning": "GENEPIO:0100890", + "is_a": "Wastewater [ENVO:00002001]" + }, + "Weep fluid [AGRO:00000692]": { + "text": "Weep fluid [AGRO:00000692]", + "description": "A fluid that leaks from a bag containing an animal carcass, and can include water, chemicals and anatomical fluids.", + "meaning": "AGRO:00000692", + "is_a": "Water [CHEBI:15377]" + } + } + }, + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical_material menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Blood [UBERON:0000178]": { + "text": "Blood [UBERON:0000178]", + "description": "A fluid that is composed of blood plasma and erythrocytes.", + "meaning": "UBERON:0000178" + }, + "Fluid [UBERON:0006314]": { + "text": "Fluid [UBERON:0006314]", + "description": "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", + "meaning": "UBERON:0006314" + }, + "Fluid (cerebrospinal (CSF)) [UBERON:0001359]": { + "text": "Fluid (cerebrospinal (CSF)) [UBERON:0001359]", + "description": "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.", + "meaning": "UBERON:0001359", + "is_a": "Fluid [UBERON:0006314]" + }, + "Fluid (amniotic) [UBERON:0000173]": { + "text": "Fluid (amniotic) [UBERON:0000173]", + "description": "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion.", + "meaning": "UBERON:0000173", + "is_a": "Fluid [UBERON:0006314]" + }, + "Saliva [UBERON:0001836]": { + "text": "Saliva [UBERON:0001836]", + "description": "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.", + "meaning": "UBERON:0001836", + "is_a": "Fluid [UBERON:0006314]" + }, + "Tissue [UBERON:0000479]": { + "text": "Tissue [UBERON:0000479]", + "description": "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", + "meaning": "UBERON:0000479" + } + } + }, + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body_product menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Digestive tract substance [GENEPIO:0100898]": { + "text": "Digestive tract substance [GENEPIO:0100898]", + "description": "Undigested food material, microbiota, and other materials found in the digestive tract.", + "meaning": "GENEPIO:0100898" + }, + "Caecal content [GENEPIO:0100899]": { + "text": "Caecal content [GENEPIO:0100899]", + "description": "Undigested food material, microbiota, and other materials found in the cecum", + "meaning": "GENEPIO:0100899", + "is_a": "Digestive tract substance [GENEPIO:0100898]" + }, + "Intestinal content [GENEPIO:0100900]": { + "text": "Intestinal content [GENEPIO:0100900]", + "description": "Undigested food material, microbiota, and other materials found in the intestine", + "meaning": "GENEPIO:0100900", + "is_a": "Digestive tract substance [GENEPIO:0100898]" + }, + "Stomach content [GENEPIO:0100901]": { + "text": "Stomach content [GENEPIO:0100901]", + "description": "Undigested food material, microbiota, and other materials found in the stomach", + "meaning": "GENEPIO:0100901", + "is_a": "Digestive tract substance [GENEPIO:0100898]" + }, + "Feces [UBERON:0001988]": { + "text": "Feces [UBERON:0001988]", + "description": "Portion of semisolid bodily waste discharged through the anus.", + "meaning": "UBERON:0001988" + }, + "Fecal composite [GENEPIO:0004512]": { + "text": "Fecal composite [GENEPIO:0004512]", + "description": "A mixture of feces obtained from multiple individuals.", + "meaning": "GENEPIO:0004512", + "is_a": "Feces [UBERON:0001988]" + }, + "Feces (fresh) [GENEPIO:0004513]": { + "text": "Feces (fresh) [GENEPIO:0004513]", + "description": "Feces that was recently excreted.", + "meaning": "GENEPIO:0004513", + "is_a": "Feces [UBERON:0001988]" + }, + "Feces (environmental) [GENEPIO:0004514]": { + "text": "Feces (environmental) [GENEPIO:0004514]", + "description": "Feces which is deposited in the environment.", + "meaning": "GENEPIO:0004514", + "is_a": "Feces [UBERON:0001988]" + }, + "Meconium [UBERON:0007109]": { + "text": "Meconium [UBERON:0007109]", + "description": "A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth.", + "meaning": "UBERON:0007109", + "is_a": "Feces [UBERON:0001988]" + }, + "Milk [UBERON:0001913]": { + "text": "Milk [UBERON:0001913]", + "description": "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation.", + "meaning": "UBERON:0001913" + }, + "Colostrum [UBERON:0001914]": { + "text": "Colostrum [UBERON:0001914]", + "description": "The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates. [ MESH : A12.200.194 http://en.wikipedia.org/wiki/Colostrum ]", + "meaning": "UBERON:0001914", + "is_a": "Milk [UBERON:0001913]" + }, + "Mucus [UBERON:0000912]": { + "text": "Mucus [UBERON:0000912]", + "description": "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.", + "meaning": "UBERON:0000912" + }, + "Urine [UBERON:0001088]": { + "text": "Urine [UBERON:0001088]", + "description": "Excretion that is the output of a kidney.", + "meaning": "UBERON:0001088" + } + } + }, + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical_part menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Carcass [UBERON:0008979]": { + "text": "Carcass [UBERON:0008979]", + "description": "A body of a multi-cellular organism that is no longer living.", + "meaning": "UBERON:0008979" + }, + "Digestive system [UBERON:0001007]": { + "text": "Digestive system [UBERON:0001007]", + "description": "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.", + "meaning": "UBERON:0001007" + }, + "Caecum [UBERON:0001153]": { + "text": "Caecum [UBERON:0001153]", + "description": "pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.", + "meaning": "UBERON:0001153", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Colon [UBERON:0001155]": { + "text": "Colon [UBERON:0001155]", + "description": "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal.", + "meaning": "UBERON:0001155", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Digestive gland [UBERON:0006925]": { + "text": "Digestive gland [UBERON:0006925]", + "description": "Any gland that is part of the digestive system.", + "meaning": "UBERON:0006925", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Foregut [UBERON:0001041]": { + "text": "Foregut [UBERON:0001041]", + "description": "Anterior subdivision of a digestive tract.", + "meaning": "UBERON:0001041", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Gall bladder [UBERON:0002110]": { + "text": "Gall bladder [UBERON:0002110]", + "description": "An organ that aids digestion and stores bile produced by the liver.", + "meaning": "UBERON:0002110", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Gastrointestinal system mucosa [UBERON:0004786]": { + "text": "Gastrointestinal system mucosa [UBERON:0004786]", + "description": "A mucosa that is part of a gastrointestinal system.", + "meaning": "UBERON:0004786", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Gizzard [UBERON:0005052]": { + "text": "Gizzard [UBERON:0005052]", + "description": "The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus.", + "meaning": "UBERON:0005052", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Hindgut [UBERON:0001046]": { + "text": "Hindgut [UBERON:0001046]", + "description": "The caudalmost subdivision of a digestive tract.", + "meaning": "UBERON:0001046", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Intestine [UBERON:0000160]": { + "text": "Intestine [UBERON:0000160]", + "description": "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.", + "meaning": "UBERON:0000160", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Small intestine [UBERON:0002108]": { + "text": "Small intestine [UBERON:0002108]", + "description": "Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum.", + "meaning": "UBERON:0002108", + "is_a": "Intestine [UBERON:0000160]" + }, + "Duodenum [UBERON:0002114]": { + "text": "Duodenum [UBERON:0002114]", + "description": "The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).", + "meaning": "UBERON:0002114", + "is_a": "Small intestine [UBERON:0002108]" + }, + "Ileum [UBERON:0002116]": { + "text": "Ileum [UBERON:0002116]", + "description": "The portion of the small intestine that extends from the jejunum to the colon.", + "meaning": "UBERON:0002116", + "is_a": "Small intestine [UBERON:0002108]" + }, + "Jejunum [UBERON:0002115]": { + "text": "Jejunum [UBERON:0002115]", + "description": "The portion of the small intestine that extends from the duodenum to the ileum.", + "meaning": "UBERON:0002115", + "is_a": "Small intestine [UBERON:0002108]" + }, + "Stomach [UBERON:0000945]": { + "text": "Stomach [UBERON:0000945]", + "description": "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.", + "meaning": "UBERON:0000945", + "is_a": "Digestive system [UBERON:0001007]" + }, + "Abomasum [UBERON:0007358]": { + "text": "Abomasum [UBERON:0007358]", + "description": "The fourth stomach of ruminating animals, which is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine.", + "meaning": "UBERON:0007358", + "is_a": "Stomach [UBERON:0000945]" + }, + "Rumen [UBERON:0007365]": { + "text": "Rumen [UBERON:0007365]", + "description": "The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity.", + "meaning": "UBERON:0007365", + "is_a": "Stomach [UBERON:0000945]" + }, + "Excretory system (organizational term)": { + "text": "Excretory system (organizational term)" + }, + "Anus [UBERON:0001245]": { + "text": "Anus [UBERON:0001245]", + "description": "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.", + "meaning": "UBERON:0001245", + "is_a": "Excretory system (organizational term)" + }, + "Anal gland [UBERON:0011253]": { + "text": "Anal gland [UBERON:0011253]", + "description": "A type of gland occurring as solitary or in pairs or groups, near the anus and sometimes opening into the rectum.", + "meaning": "UBERON:0011253", + "is_a": "Excretory system (organizational term)" + }, + "Cloaca [UBERON:0000162]": { + "text": "Cloaca [UBERON:0000162]", + "description": "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.", + "meaning": "UBERON:0000162", + "is_a": "Excretory system (organizational term)" + }, + "Liver [UBERON:0002107]": { + "text": "Liver [UBERON:0002107]", + "description": "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes", + "meaning": "UBERON:0002107", + "is_a": "Excretory system (organizational term)" + }, + "Kidney [UBERON:0002113]": { + "text": "Kidney [UBERON:0002113]", + "description": "A paired organ of the urinary tract which has the production of urine as its primary function.", + "meaning": "UBERON:0002113", + "is_a": "Excretory system (organizational term)" + }, + "Rectum [UBERON:0001052]": { + "text": "Rectum [UBERON:0001052]", + "description": "The terminal portion of the intestinal tube, terminating with the anus.", + "meaning": "UBERON:0001052", + "is_a": "Excretory system (organizational term)" + }, + "Spleen [UBERON:0002106]": { + "text": "Spleen [UBERON:0002106]", + "description": "The organ that functions to filter blood and to store red corpuscles and platelets.", + "meaning": "UBERON:0002106", + "is_a": "Excretory system (organizational term)" + }, + "Urinary bladder [UBERON:0001255]": { + "text": "Urinary bladder [UBERON:0001255]", + "description": "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion.", + "meaning": "UBERON:0001255", + "is_a": "Excretory system (organizational term)" + }, + "Foot [UBERON:0002387]": { + "text": "Foot [UBERON:0002387]", + "description": "The terminal part of the vertebrate leg upon which an individual stands. 2: An invertebrate organ of locomotion or attachment; especially: a ventral muscular surface or process of a mollusk.", + "meaning": "UBERON:0002387" + }, + "Head [UBERON:0000033]": { + "text": "Head [UBERON:0000033]", + "description": "The head is the anterior-most division of the body.", + "meaning": "UBERON:0000033", + "is_a": "Foot [UBERON:0002387]" + }, + "Brain [UBERON:0000955]": { + "text": "Brain [UBERON:0000955]", + "description": "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell.", + "meaning": "UBERON:0000955", + "is_a": "Foot [UBERON:0002387]" + }, + "Ear [UBERON:0001690]": { + "text": "Ear [UBERON:0001690]", + "description": "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.", + "meaning": "UBERON:0001690", + "is_a": "Foot [UBERON:0002387]" + }, + "Eye [UBERON:0000970]": { + "text": "Eye [UBERON:0000970]", + "description": "An organ that detects light.", + "meaning": "UBERON:0000970", + "is_a": "Foot [UBERON:0002387]" + }, + "Mouth [UBERON:0000165]": { + "text": "Mouth [UBERON:0000165]", + "description": "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "meaning": "UBERON:0000165", + "is_a": "Foot [UBERON:0002387]" + }, + "Nose [UBERON:0000004]": { + "text": "Nose [UBERON:0000004]", + "description": "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.", + "meaning": "UBERON:0000004", + "is_a": "Foot [UBERON:0002387]" + }, + "Nasal turbinal [UBERON:0035612]": { + "text": "Nasal turbinal [UBERON:0035612]", + "description": "A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning.", + "meaning": "UBERON:0035612", + "is_a": "Nose [UBERON:0000004]" + }, + "Nasopharynx (NP) [UBERON:0001728]": { + "text": "Nasopharynx (NP) [UBERON:0001728]", + "description": "The section of the pharynx that lies above the soft palate.", + "meaning": "UBERON:0001728", + "is_a": "Nose [UBERON:0000004]" + }, + "Pair of nares [UBERON:0002109]": { + "text": "Pair of nares [UBERON:0002109]", + "description": "Pair of nostrils.", + "meaning": "UBERON:0002109", + "is_a": "Nose [UBERON:0000004]" + }, + "Paranasal sinus [UBERON:0001825]": { + "text": "Paranasal sinus [UBERON:0001825]", + "description": "The paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity.", + "meaning": "UBERON:0001825", + "is_a": "Nose [UBERON:0000004]" + }, + "Snout [UBERON:0006333]": { + "text": "Snout [UBERON:0006333]", + "description": "The projecting nose and mouth of an animal, especially a mammal.", + "meaning": "UBERON:0006333", + "is_a": "Nose [UBERON:0000004]" + }, + "Lymphatic system [UBERON:0006558]": { + "text": "Lymphatic system [UBERON:0006558]", + "description": "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system.", + "meaning": "UBERON:0006558" + }, + "Lymph node [UBERON:0000029]": { + "text": "Lymph node [UBERON:0000029]", + "description": "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph.", + "meaning": "UBERON:0000029", + "is_a": "Lymphatic system [UBERON:0006558]" + }, + "Mesenteric lymph node [UBERON:0002509]": { + "text": "Mesenteric lymph node [UBERON:0002509]", + "description": "The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.", + "meaning": "UBERON:0002509", + "is_a": "Lymph node [UBERON:0000029]" + }, + "Mantle (bird) [GENEPIO:0100927]": { + "text": "Mantle (bird) [GENEPIO:0100927]", + "description": "The forward area of a bird's upper side that is sandwiched between the nape and the start of the back.", + "meaning": "GENEPIO:0100927" + }, + "Neck [UBERON:0000974]": { + "text": "Neck [UBERON:0000974]", + "description": "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.", + "meaning": "UBERON:0000974" + }, + "Esophagus [UBERON:0001043]": { + "text": "Esophagus [UBERON:0001043]", + "description": "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation.", + "meaning": "UBERON:0001043", + "is_a": "Neck [UBERON:0000974]" + }, + "Trachea [UBERON:0003126]": { + "text": "Trachea [UBERON:0003126]", + "description": "The trachea is the portion of the airway that attaches to the bronchi as it branches.", + "meaning": "UBERON:0003126", + "is_a": "Neck [UBERON:0000974]" + }, + "Nerve [UBERON:0001021]": { + "text": "Nerve [UBERON:0001021]", + "description": "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.", + "meaning": "UBERON:0001021" + }, + "Spinal cord [UBERON:0002240]": { + "text": "Spinal cord [UBERON:0002240]", + "description": "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal.", + "meaning": "UBERON:0002240", + "is_a": "Nerve [UBERON:0001021]" + }, + "Organs or organ parts [GENEPIO:0001117]": { + "text": "Organs or organ parts [GENEPIO:0001117]", + "description": "An object aggregate which has as members whole organs or parts of organs, possibly from different organisms.", + "meaning": "GENEPIO:0001117" + }, + "Organ [UBERON:0000062]": { + "text": "Organ [UBERON:0000062]", + "description": "Anatomical structure that performs a specific function or group of functions", + "meaning": "UBERON:0000062", + "is_a": "Organs or organ parts [GENEPIO:0001117]" + }, + "Muscle organ [UBERON:0001630]": { + "text": "Muscle organ [UBERON:0001630]", + "description": "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.", + "meaning": "UBERON:0001630", + "is_a": "Organ [UBERON:0000062]" + }, + "Skin of body [UBERON:0002097]": { + "text": "Skin of body [UBERON:0002097]", + "description": "The organ covering the body that consists of the dermis and epidermis.", + "meaning": "UBERON:0002097", + "is_a": "Organ [UBERON:0000062]" + }, + "Reproductive system [UBERON:0000990]": { + "text": "Reproductive system [UBERON:0000990]", + "description": "Anatomical system that has as its parts the organs concerned with reproduction.", + "meaning": "UBERON:0000990" + }, + "Embryo [UBERON:0000922]": { + "text": "Embryo [UBERON:0000922]", + "description": "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", + "meaning": "UBERON:0000922", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Fetus [UBERON:0000323]": { + "text": "Fetus [UBERON:0000323]", + "description": "An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching", + "meaning": "UBERON:0000323", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Ovary [UBERON:0000992]": { + "text": "Ovary [UBERON:0000992]", + "description": "The gonad of a female organism which contains germ cells.", + "meaning": "UBERON:0000992", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Oviduct [UBERON:0000993]": { + "text": "Oviduct [UBERON:0000993]", + "description": "A tube or collection of tubes in an animal from the ovaries to the outside of the body.", + "meaning": "UBERON:0000993", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Placenta [UBERON:0001987]": { + "text": "Placenta [UBERON:0001987]", + "description": "Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.", + "meaning": "UBERON:0001987", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Testis [UBERON:0000473]": { + "text": "Testis [UBERON:0000473]", + "description": "A gonad of a male animal. A gonad produces and releases sperm.", + "meaning": "UBERON:0000473", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Udder [UBERON:0013216]": { + "text": "Udder [UBERON:0013216]", + "description": "A large pendulous organ consisting of two or more mammary glands enclosed in a common envelope and each provided with a single nipple.", + "meaning": "UBERON:0013216", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Uterus [UBERON:0000995]": { + "text": "Uterus [UBERON:0000995]", + "description": "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.", + "meaning": "UBERON:0000995", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Vagina [UBERON:0000996]": { + "text": "Vagina [UBERON:0000996]", + "description": "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles", + "meaning": "UBERON:0000996", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Yolk sac [UBERON:0001040]": { + "text": "Yolk sac [UBERON:0001040]", + "description": "A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes.", + "meaning": "UBERON:0001040", + "is_a": "Reproductive system [UBERON:0000990]" + }, + "Respiratory system [UBERON:0001004]": { + "text": "Respiratory system [UBERON:0001004]", + "description": "Functional system which consists of structures involved in respiration.", + "meaning": "UBERON:0001004" + }, + "Air sac [UBERON:0009060]": { + "text": "Air sac [UBERON:0009060]", + "description": "Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs.", + "meaning": "UBERON:0009060", + "is_a": "Respiratory system [UBERON:0001004]" + }, + "Lung [UBERON:0002048]": { + "text": "Lung [UBERON:0002048]", + "description": "Respiration organ that develops as an outpocketing of the esophagus", + "meaning": "UBERON:0002048", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Pleura [UBERON:0000977]": { + "text": "Pleura [UBERON:0000977]", + "description": "The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).", + "meaning": "UBERON:0000977", + "is_a": "Respiratory system [UBERON:0001004]" + }, + "Respiratory system mucosa [UBERON:0004785]": { + "text": "Respiratory system mucosa [UBERON:0004785]", + "description": "The mucous membrane lining the respiratory tract.", + "meaning": "UBERON:0004785", + "is_a": "Respiratory system [UBERON:0001004]" + }, + "Skeletal system [UBERON:0001434]": { + "text": "Skeletal system [UBERON:0001434]", + "description": "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.", + "meaning": "UBERON:0001434" + }, + "Skeletal joint [UBERON:0000982]": { + "text": "Skeletal joint [UBERON:0000982]", + "description": "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue.", + "meaning": "UBERON:0000982", + "is_a": "Skeletal system [UBERON:0001434]" + }, + "Bone element [UBERON:0001474]": { + "text": "Bone element [UBERON:0001474]", + "description": "Skeletal element that is composed of bone tissue.", + "meaning": "UBERON:0001474", + "is_a": "Skeletal system [UBERON:0001434]" + }, + "Thoracic segment of trunk [UBERON:0000915]": { + "text": "Thoracic segment of trunk [UBERON:0000915]", + "description": "Subdivision of trunk that lies between the head and the abdomen.", + "meaning": "UBERON:0000915" + }, + "Abdomen [UBERON:0000916]": { + "text": "Abdomen [UBERON:0000916]", + "description": "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.", + "meaning": "UBERON:0000916", + "is_a": "Thoracic segment of trunk [UBERON:0000915]" + }, + "Muscle of abdomen [UBERON:0002378]": { + "text": "Muscle of abdomen [UBERON:0002378]", + "description": "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.", + "meaning": "UBERON:0002378", + "is_a": "Abdomen [UBERON:0000916]" + }, + "Peritoneum [UBERON:0002358]": { + "text": "Peritoneum [UBERON:0002358]", + "description": "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.", + "meaning": "UBERON:0002358", + "is_a": "Abdomen [UBERON:0000916]" + }, + "Vascular system [UBERON:0007798]": { + "text": "Vascular system [UBERON:0007798]", + "description": "Anatomical system that consists of all blood and lymph vessels.", + "meaning": "UBERON:0007798" + }, + "Blood vessel [UBERON:0001981]": { + "text": "Blood vessel [UBERON:0001981]", + "description": "A vessel through which blood circulates in the body.", + "meaning": "UBERON:0001981", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Bursa of Fabricius [UBERON:0003903]": { + "text": "Bursa of Fabricius [UBERON:0003903]", + "description": "An epithelial and lymphoid organ that develops as a dorsal diverticulum of the proctodeal region of the cloaca in birds. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells. The bursa is an organ found in birds involved in B cell differentiation.", + "meaning": "UBERON:0003903", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Gill [UBERON:0002535]": { + "text": "Gill [UBERON:0002535]", + "description": "Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians. [ http://en.wikipedia.org/wiki/Gill ]", + "meaning": "UBERON:0002535", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Heart [UBERON:0000948]": { + "text": "Heart [UBERON:0000948]", + "description": "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.", + "meaning": "UBERON:0000948", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Pericardium [UBERON:0002407]": { + "text": "Pericardium [UBERON:0002407]", + "description": "The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.", + "meaning": "UBERON:0002407", + "is_a": "Vascular system [UBERON:0007798]" + }, + "Vent (anatomical) [UBERON:2000298]": { + "text": "Vent (anatomical) [UBERON:2000298]", + "description": "The external opening of the rectum or cloaca.", + "meaning": "UBERON:2000298" + }, + "Bird vent [UBERON:0012464]": { + "text": "Bird vent [UBERON:0012464]", + "description": "The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. [ http://orcid.org/0000-0002-6601-2165 ]", + "meaning": "UBERON:0012464", + "is_a": "Vent (anatomical) [UBERON:2000298]" + }, + "Fish vent [GENEPIO:0100902]": { + "text": "Fish vent [GENEPIO:0100902]", + "description": "The external opening which opens to the reproductive and digestive tracts of the fish. During spawning, the vent serves as an outlet for eggs and sperm. In most fishes, the vent is in front of the anal fin.", + "meaning": "GENEPIO:0100902", + "is_a": "Vent (anatomical) [UBERON:2000298]" + } + } + }, + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection_device menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Air filter [ENVO:00003968]": { + "text": "Air filter [ENVO:00003968]", + "meaning": "ENVO:00003968" + }, + "Auger (earth auger) [AGRO:00000405]": { + "text": "Auger (earth auger) [AGRO:00000405]", + "description": "Manually operated hand tool that consists of cutter head having semicircular blades connected to pipe with the help of clamp and flange. The connecting pipe is further connected to a handle.", + "meaning": "AGRO:00000405" + }, + "Bag [GSSO:008558]": { + "text": "Bag [GSSO:008558]", + "description": "A sac or pouch.", + "meaning": "GSSO:008558" + }, + "Whirlpak sampling bag [GENEPIO:0002122]": { + "text": "Whirlpak sampling bag [GENEPIO:0002122]", + "description": "A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures.", + "meaning": "GENEPIO:0002122", + "is_a": "Bag [GSSO:008558]" + }, + "Bottle [FOODON:03490214]": { + "text": "Bottle [FOODON:03490214]", + "description": "A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle.", + "meaning": "FOODON:03490214" + }, + "Box corer [GENEPIO:0100928]": { + "text": "Box corer [GENEPIO:0100928]", + "description": "A specimen collection device that is used to collect soft sediments in lakes or oceans.", + "meaning": "GENEPIO:0100928" + }, + "Bronchoscope [OBI:0002826]": { + "text": "Bronchoscope [OBI:0002826]", + "description": "A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung.", + "meaning": "OBI:0002826" + }, + "Collection Container [OBI:0002088]": { + "text": "Collection Container [OBI:0002088]", + "description": "A container with the function of containing a specimen.", + "meaning": "OBI:0002088" + }, + "Collection Cup [GENEPIO:0100026]": { + "text": "Collection Cup [GENEPIO:0100026]", + "description": "A device which is used to collect liquid samples.", + "meaning": "GENEPIO:0100026" + }, + "Culture plate [GENEPIO:0004318]": { + "text": "Culture plate [GENEPIO:0004318]", + "description": "A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium.", + "meaning": "GENEPIO:0004318" + }, + "Petri dish [NCIT:C96141]": { + "text": "Petri dish [NCIT:C96141]", + "description": "A shallow dish with a lid used to culture cells.", + "meaning": "NCIT:C96141", + "is_a": "Culture plate [GENEPIO:0004318]" + }, + "Fibrobronchoscope Brush [OBI:0002825]": { + "text": "Fibrobronchoscope Brush [OBI:0002825]", + "meaning": "OBI:0002825" + }, + "Filter [GENEPIO:0100103]": { + "text": "Filter [GENEPIO:0100103]", + "description": "A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass.", + "meaning": "GENEPIO:0100103" + }, + "Fine Needle [OBI:0002827]": { + "text": "Fine Needle [OBI:0002827]", + "meaning": "OBI:0002827" + }, + "Micropipette [OBI:0001128]": { + "text": "Micropipette [OBI:0001128]", + "meaning": "OBI:0001128" + }, + "Needle [OBI:0000436]": { + "text": "Needle [OBI:0000436]", + "description": "A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.", + "meaning": "OBI:0000436" + }, + "PONAR grab sampler [GENEPIO:0100929]": { + "text": "PONAR grab sampler [GENEPIO:0100929]", + "description": "A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay.\"", + "meaning": "GENEPIO:0100929" + }, + "Scoop [GENEPIO:0002125]": { + "text": "Scoop [GENEPIO:0002125]", + "description": "A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion.", + "meaning": "GENEPIO:0002125" + }, + "Soil sample probe [GENEPIO:0100930]": { + "text": "Soil sample probe [GENEPIO:0100930]", + "description": "A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores.", + "meaning": "GENEPIO:0100930" + }, + "Spatula [NCIT:C149941]": { + "text": "Spatula [NCIT:C149941]", + "meaning": "CIT:C149941" + }, + "Sponge [OBI:0002819]": { + "text": "Sponge [OBI:0002819]", + "description": "A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter.", + "meaning": "OBI:0002819" + }, + "Suction Catheter [OBI:0002831]": { + "text": "Suction Catheter [OBI:0002831]", + "description": "A catheter which is used to remove mucus and other secretions from the body.", + "meaning": "OBI:0002831" + }, + "Swab [GENEPIO:0100027]": { + "text": "Swab [GENEPIO:0100027]", + "description": "A device which is a soft, absorbent material mounted on one or both ends of a stick.", + "meaning": "GENEPIO:0100027" + }, + "Drag swab [OBI:0002822]": { + "text": "Drag swab [OBI:0002822]", + "description": "A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string", + "meaning": "OBI:0002822", + "is_a": "Swab [GENEPIO:0100027]" + }, + "Surface wipe [OBI:0002824]": { + "text": "Surface wipe [OBI:0002824]", + "description": "A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces.", + "meaning": "OBI:0002824", + "is_a": "Swab [GENEPIO:0100027]" + }, + "Tube [GENEPIO:0101196]": { + "text": "Tube [GENEPIO:0101196]", + "description": "A sample collection device which is cylindrical shape that is open at one end, used to collect material.", + "meaning": "GENEPIO:0101196" + }, + "Blood Collection Tube [OBI:0002859]": { + "text": "Blood Collection Tube [OBI:0002859]", + "description": "A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection", + "meaning": "OBI:0002859", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Microcapillary tube [OBI:0002858]": { + "text": "Microcapillary tube [OBI:0002858]", + "meaning": "OBI:0002858", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Serum Collection Tube [OBI:0002860]": { + "text": "Serum Collection Tube [OBI:0002860]", + "description": "A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum.", + "meaning": "OBI:0002860", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Sputum Collection Tube [OBI:0002861]": { + "text": "Sputum Collection Tube [OBI:0002861]", + "description": "A specimen collection tube which is designed for collecting sputum.", + "meaning": "OBI:0002861", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Urine Collection Tube [OBI:0002862]": { + "text": "Urine Collection Tube [OBI:0002862]", + "description": "A specimen container which is designed for holding urine.", + "meaning": "OBI:0002862", + "is_a": "Tube [GENEPIO:0101196]" + }, + "Vacuum device [GENEPIO:0002127]": { + "text": "Vacuum device [GENEPIO:0002127]", + "description": "A device which generates a vacuum to provide suction of material.", + "meaning": "GENEPIO:0002127" + }, + "Vacutainer [OBIB:0000032]": { + "text": "Vacutainer [OBIB:0000032]", + "description": "A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing.", + "meaning": "OBIB:0000032", + "is_a": "Vacuum device [GENEPIO:0002127]" + } + } + }, + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection_method menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Aspiration [HP:0002835]": { + "text": "Aspiration [HP:0002835]", + "description": "Inspiration of a foreign object into the airway.", + "meaning": "HP:0002835" + }, + "Biopsy [OBI:0002650]": { + "text": "Biopsy [OBI:0002650]", + "description": "A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.", + "meaning": "OBI:0002650" + }, + "Fecal grab [GENEPIO:0004326]": { + "text": "Fecal grab [GENEPIO:0004326]", + "description": "A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted.", + "meaning": "GENEPIO:0004326" + }, + "Filtration [OBI:0302885]": { + "text": "Filtration [OBI:0302885]", + "description": "A process which separates components suspended in a fluid based on granularity properties relying on a filter device.", + "meaning": "OBI:0302885" + }, + "Air filtration [GENEPIO:0100031]": { + "text": "Air filtration [GENEPIO:0100031]", + "description": "A filtration process which removes solid particulates from the air via an air filtration device.", + "meaning": "GENEPIO:0100031", + "is_a": "Filtration [OBI:0302885]" + }, + "Water filtration [GENEPIO:0100931]": { + "text": "Water filtration [GENEPIO:0100931]", + "description": "A filtration process which removes or reduces the concentration of particulate matter, including suspended particles, parasites, bacteria, algae, viruses, and fungi, as well as other undesirable chemical and biological contaminants from contaminated water using water filters to produce safe and clean water.", + "meaning": "GENEPIO:0100931", + "is_a": "Filtration [OBI:0302885]" + }, + "Lavage [OBI:0600044]": { + "text": "Lavage [OBI:0600044]", + "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid", + "meaning": "OBI:0600044" + }, + "Bronchoalveolar lavage [GENEPIO:0100032]": { + "text": "Bronchoalveolar lavage [GENEPIO:0100032]", + "description": "The collection of bronchoalveolar lavage fluid (BAL) from the lungs.", + "meaning": "GENEPIO:0100032", + "is_a": "Lavage [OBI:0600044]" + }, + "Gastric lavage [GENEPIO:0100033]": { + "text": "Gastric lavage [GENEPIO:0100033]", + "description": "The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach.", + "meaning": "GENEPIO:0100033", + "is_a": "Lavage [OBI:0600044]" + }, + "Necropsy [MMO:0000344]": { + "text": "Necropsy [MMO:0000344]", + "description": "A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease.", + "meaning": "MMO:0000344" + }, + "Phlebotomy [NCIT:C28221]": { + "text": "Phlebotomy [NCIT:C28221]", + "description": "The collection of blood from a vein, most commonly via needle venipuncture.", + "meaning": "NCIT:C28221" + }, + "Rinsing for specimen collection [GENEPIO_0002116]": { + "text": "Rinsing for specimen collection [GENEPIO_0002116]", + "description": "The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids.", + "meaning": "GENEPIO:0002116" + }, + "Scooping [GENEPIO:0100932]": { + "text": "Scooping [GENEPIO:0100932]", + "description": "A specimen collection process that is used to dig out an amount of sample using a scoop.", + "meaning": "GENEPIO:0100932" + }, + "Sediment collection [GENEPIO:0100933]": { + "text": "Sediment collection [GENEPIO:0100933]", + "description": "A specimen collection process that is used to collect a sediment sample.", + "meaning": "GENEPIO:0100933" + }, + "Soil coring [GENEPIO:0100934]": { + "text": "Soil coring [GENEPIO:0100934]", + "description": "A specimen collection process that is used to collect soil sample cores.", + "meaning": "GENEPIO:0100934" + }, + "Weep fluid collection (pouring) [GENEPIO:0101003]": { + "text": "Weep fluid collection (pouring) [GENEPIO:0101003]", + "description": "A specimen collection process that is used to collect weep fluid via pouring from the source container into the sample collection device. (e.g. bag or tube)", + "meaning": "GENEPIO:0101003" + } + } + }, + "SampleVolumeMeasurementUnitMenu": { + "name": "SampleVolumeMeasurementUnitMenu", + "title": "sample_volume_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "microliter (uL) [UO:0000101]": { + "text": "microliter (uL) [UO:0000101]", + "description": "A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter.", + "meaning": "UO:0000101" + }, + "milliliter (mL) [UO:0000098]": { + "text": "milliliter (mL) [UO:0000098]", + "description": "A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter.", + "meaning": "UO:0000098" + }, + "liter (L) [UO:0000099]": { + "text": "liter (L) [UO:0000099]", + "description": "A metric unit of volume equivalent to 1000 cubic centimeters", + "meaning": "UO:0000099" + } + } + }, + "ResidualSampleStatusMenu": { + "name": "ResidualSampleStatusMenu", + "title": "residual_sample_status menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Residual sample remaining (some sample left) [GENEPIO:0101087]": { + "text": "Residual sample remaining (some sample left) [GENEPIO:0101087]", + "meaning": "GENEPIO:0101087" + }, + "No residual sample (sample all used) [GENEPIO:0101088]": { + "text": "No residual sample (sample all used) [GENEPIO:0101088]", + "meaning": "GENEPIO:0101088" + }, + "Residual sample status unkown [GENEPIO:0101089]": { + "text": "Residual sample status unkown [GENEPIO:0101089]", + "meaning": "GENEPIO:0101089" + } + } + }, + "PurposeOfSampling": { + "name": "PurposeOfSampling", + "title": "purpose of sampling", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cluster/Outbreak investigation [GENEPIO:0100001]": { + "text": "Cluster/Outbreak investigation [GENEPIO:0100001]", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", + "meaning": "GENEPIO:0100001" + }, + "Diagnostic testing [GENEPIO:0100002]": { + "text": "Diagnostic testing [GENEPIO:0100002]", + "description": "A sampling strategy in which individuals are sampled in the context of diagnostic testing.", + "meaning": "GENEPIO:0100002" + }, + "Environmental testing [GENEPIO:0100548]": { + "text": "Environmental testing [GENEPIO:0100548]", + "description": "A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena.", + "meaning": "GENEPIO:0100548" + }, + "Research [GENEPIO:0100003]": { + "text": "Research [GENEPIO:0100003]", + "description": "A sampling strategy in which samples are collected in order to perform research.", + "meaning": "GENEPIO:0100003" + }, + "Clinical trial [GENEPIO:0100549]": { + "text": "Clinical trial [GENEPIO:0100549]", + "description": "A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research.", + "meaning": "GENEPIO:0100549", + "is_a": "Research [GENEPIO:0100003]" + }, + "Field experiment [GENEPIO:0100550]": { + "text": "Field experiment [GENEPIO:0100550]", + "description": "A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work.", + "meaning": "GENEPIO:0100550", + "is_a": "Research [GENEPIO:0100003]" + }, + "Survey study [GENEPIO:0100582]": { + "text": "Survey study [GENEPIO:0100582]", + "description": "A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes.", + "meaning": "GENEPIO:0100582", + "is_a": "Research [GENEPIO:0100003]" + }, + "Surveillance [GENEPIO:0100004]": { + "text": "Surveillance [GENEPIO:0100004]", + "description": "A sampling strategy in which individuals are sampled for surveillance investigations.", + "meaning": "GENEPIO:0100004" + } + } + }, + "PresamplingActivity": { + "name": "PresamplingActivity", + "title": "presampling activity", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Addition of substances to food/water [GENEPIO:0100536]": { + "text": "Addition of substances to food/water [GENEPIO:0100536]", + "description": "The addition of substances to food or water administered to an individual or group of individuals.", + "meaning": "GENEPIO:0100536" + }, + "Antimicrobial pre-treatment [GENEPIO:0100537]": { + "text": "Antimicrobial pre-treatment [GENEPIO:0100537]", + "description": "The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity.", + "meaning": "GENEPIO:0100537" + }, + "Certified animal husbandry practices [GENEPIO:0100538]": { + "text": "Certified animal husbandry practices [GENEPIO:0100538]", + "description": "The implementation of animal husbandy practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100538" + }, + "Certified humane animal husbandry practices [GENEPIO:0100894]": { + "text": "Certified humane animal husbandry practices [GENEPIO:0100894]", + "description": "A certification organization in Washington DC that is dedicated to improving the lives of farm animals in food production from birth through slaughter.", + "meaning": "GENEPIO:0100894", + "is_a": "Certified animal husbandry practices [GENEPIO:0100538]" + }, + "Certified organic farming practices [GENEPIO:0100539]": { + "text": "Certified organic farming practices [GENEPIO:0100539]", + "description": "The implementation of organic farming practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100539" + }, + "Conventional farming practices [GENEPIO:0100895]": { + "text": "Conventional farming practices [GENEPIO:0100895]", + "description": "The implementation of farming practices that include man-made inputs such as chemical fertilizers and genetically-modified seeds.", + "meaning": "GENEPIO:0100895" + }, + "Change in storage conditions [GENEPIO:0100540]": { + "text": "Change in storage conditions [GENEPIO:0100540]", + "description": "A change in the storage conditions of a material or a substance.", + "meaning": "GENEPIO:0100540" + }, + "Cleaning/disinfection [GENEPIO:0100541]": { + "text": "Cleaning/disinfection [GENEPIO:0100541]", + "description": "A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment.", + "meaning": "GENEPIO:0100541" + }, + "Extended downtime between activities [GENEPIO:0100542]": { + "text": "Extended downtime between activities [GENEPIO:0100542]", + "description": "A prolonged period of inactivity between processes or events.", + "meaning": "GENEPIO:0100542" + }, + "Microbial pre-treatment [GENEPIO:0100546]": { + "text": "Microbial pre-treatment [GENEPIO:0100546]", + "description": "The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity.", + "meaning": "GENEPIO:0100546" + }, + "Probiotic pre-treatment [GENEPIO:0100547]": { + "text": "Probiotic pre-treatment [GENEPIO:0100547]", + "description": "The addition of a probiotic substance to an individual or material prior to some other event or activity.", + "meaning": "GENEPIO:0100547" + }, + "Vaccination [NCIT:C15346]": { + "text": "Vaccination [NCIT:C15346]", + "description": "Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment.", + "meaning": "NCIT:C15346" + } + } + }, + "SampleStorageDurationUnit": { + "name": "SampleStorageDurationUnit", + "title": "sample storage duration unit", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Second [UO:0000010]": { + "text": "Second [UO:0000010]", + "description": "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.", + "meaning": "UO:0000010" + }, + "Minute [UO:0000031]": { + "text": "Minute [UO:0000031]", + "description": "A time unit which is equal to 60 seconds.", + "meaning": "UO:0000031" + }, + "Hour [UO:0000032]": { + "text": "Hour [UO:0000032]", + "description": "A time unit which is equal to 60 minutes.", + "meaning": "UO:0000032" + }, + "Day [UO:0000033]": { + "text": "Day [UO:0000033]", + "description": "A time unit which is equal to 24 hours.", + "meaning": "UO:0000033" + }, + "Week [UO:0000034]": { + "text": "Week [UO:0000034]", + "description": "A time unit which is equal to 7 days.", + "meaning": "UO:0000034" + }, + "Month [UO:0000035]": { + "text": "Month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", + "meaning": "UO:0000035" + }, + "Year [UO:0000036]": { + "text": "Year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", + "meaning": "UO:0000036" + } + } + }, + "SpecimenProcessing": { + "name": "SpecimenProcessing", + "title": "specimen processing", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Concentration [OBI:0600041]": { + "text": "Concentration [OBI:0600041]", + "description": "A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest.", + "meaning": "OBI:0600041" + }, + "Centrifugation [OBI:0302886]": { + "text": "Centrifugation [OBI:0302886]", + "description": "A process separating molecules by size or density using centrifugal forces generated by a spinning rotor.", + "meaning": "OBI:0302886" + }, + "Filtration [OBI:0302885]": { + "text": "Filtration [OBI:0302885]", + "description": "A process which separates components suspended in a fluid based on granularity properties relying on a filter device.", + "meaning": "OBI:0302885" + }, + "Pooling specimens [OBI:0600016]": { + "text": "Pooling specimens [OBI:0600016]", + "description": "Physical combination of several instances of like material.", + "meaning": "OBI:0600016" + } + } + }, + "ExperimentalSpecimenRoleType": { + "name": "ExperimentalSpecimenRoleType", + "title": "experimental specimen role type", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Positive experimental control [GENEPIO:0101018]": { + "text": "Positive experimental control [GENEPIO:0101018]", + "description": "A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment.", + "meaning": "GENEPIO:0101018" + }, + "Validation strain [GENEPIO:0101123]": { + "text": "Validation strain [GENEPIO:0101123]", + "meaning": "GENEPIO:0101123", + "is_a": "Positive experimental control [GENEPIO:0101018]" + }, + "Proficiency test isolate [GENEPIO:0101124]": { + "text": "Proficiency test isolate [GENEPIO:0101124]", + "meaning": "GENEPIO:0101124", + "is_a": "Positive experimental control [GENEPIO:0101018]" + }, + "Negative experimental control [GENEPIO:0101019]": { + "text": "Negative experimental control [GENEPIO:0101019]", + "description": "A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment", + "meaning": "GENEPIO:0101019" + }, + "Technical replicate [EFO:0002090]": { + "text": "Technical replicate [EFO:0002090]", + "description": "A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.", + "meaning": "EFO:0002090" + }, + "Biological replicate [EFO:0002091]": { + "text": "Biological replicate [EFO:0002091]", + "description": "A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples.", + "meaning": "EFO:0002091" + }, + "Synthetic lab construct [GENEPIO:0101039]": { + "text": "Synthetic lab construct [GENEPIO:0101039]", + "meaning": "GENEPIO:0101039" + }, + "Negative sample [GENEPIO:0101120]": { + "text": "Negative sample [GENEPIO:0101120]", + "meaning": "GENEPIO:0101120" + } + } + }, + "AvailableDataTypesMenu": { + "name": "AvailableDataTypesMenu", + "title": "available_data_types menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Documentation [GENEPIO:0100702]": { + "text": "Documentation [GENEPIO:0100702]", + "description": "A dataset attribute bundle which indicates the presence of documentation data.", + "meaning": "GENEPIO:0100702" + }, + "Experimental parameters documentation [GENEPIO:0100703]": { + "text": "Experimental parameters documentation [GENEPIO:0100703]", + "description": "A documentation data tag which indicates the presence of data that describes experimental parameters.", + "meaning": "GENEPIO:0100703", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Feed history [GENEPIO:0100704]": { + "text": "Feed history [GENEPIO:0100704]", + "description": "A documentation data tag which indicates the presence of data that describes feed history.", + "meaning": "GENEPIO:0100704", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Land use information [GENEPIO:0100705]": { + "text": "Land use information [GENEPIO:0100705]", + "description": "A documentation data tag which indicates the presence of data that describes land use information.", + "meaning": "GENEPIO:0100705", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Therapeutic administration history [GENEPIO:0100706]": { + "text": "Therapeutic administration history [GENEPIO:0100706]", + "description": "A documentation data tag which indicates the presence of data that describes a history of therapeutic administration.", + "meaning": "GENEPIO:0100706", + "is_a": "Documentation [GENEPIO:0100702]" + }, + "Chemical characterization [GENEPIO:0100707]": { + "text": "Chemical characterization [GENEPIO:0100707]", + "description": "A dataset attribute bundle which indicates the presence of chemical characterization data.", + "meaning": "GENEPIO:0100707" + }, + "Microbiological characterization [GENEPIO:0100714]": { + "text": "Microbiological characterization [GENEPIO:0100714]", + "description": "A dataset attribute bundle which indicates the presence of microbiological characterization data.", + "meaning": "GENEPIO:0100714" + }, + "Microbiological identification [GENEPIO:0100715]": { + "text": "Microbiological identification [GENEPIO:0100715]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data.", + "meaning": "GENEPIO:0100715", + "is_a": "Microbiological characterization [GENEPIO:0100714]" + }, + "Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]": { + "text": "Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Beckson Dickson BBL Crystal identification system.", + "meaning": "GENEPIO:0100716", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (bioMérieux API) [GENEPIO:0100717]": { + "text": "Microbiological identification (bioMérieux API) [GENEPIO:0100717]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data dervied using the bioMérieux API identification system.", + "meaning": "GENEPIO:0100717", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (Biolog) [GENEPIO:0100718]": { + "text": "Microbiological identification (Biolog) [GENEPIO:0100718]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Biolog identification system.", + "meaning": "GENEPIO:0100718", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (FAME) [GENEPIO:0100719]": { + "text": "Microbiological identification (FAME) [GENEPIO:0100719]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Fatty acid methyl esters (FAME) identification system.", + "meaning": "GENEPIO:0100719", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (Sensititre) [GENEPIO:0100720]": { + "text": "Microbiological identification (Sensititre) [GENEPIO:0100720]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Sensititre identification system.", + "meaning": "GENEPIO:0100720", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Microbiological identification (ViTek) [GENEPIO:0100721]": { + "text": "Microbiological identification (ViTek) [GENEPIO:0100721]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the ViTek identification system.", + "meaning": "GENEPIO:0100721", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Phage type [GENEPIO:0100722]": { + "text": "Phage type [GENEPIO:0100722]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using phage type identification.", + "meaning": "GENEPIO:0100722", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Serotype [GENEPIO:0100723]": { + "text": "Serotype [GENEPIO:0100723]", + "description": "A microbiological characterization data tag which indicates the presence of microbiological identification data derived using serotype identification.", + "meaning": "GENEPIO:0100723", + "is_a": "Microbiological identification [GENEPIO:0100715]" + }, + "Phenotypic microbiological characterization [GENEPIO:0100724]": { + "text": "Phenotypic microbiological characterization [GENEPIO:0100724]", + "description": "A microbiological characterization data tag which indicates the presence of phenotypic microbiological characterization data.", + "meaning": "GENEPIO:0100724", + "is_a": "Microbiological characterization [GENEPIO:0100714]" + }, + "AMR phenotypic testing [GENEPIO:0100725]": { + "text": "AMR phenotypic testing [GENEPIO:0100725]", + "description": "A phenotypic microbiological characterization data tag which indicates the presence of antimicrobial resistance (AMR) phenotypic testing characterization data.", + "meaning": "GENEPIO:0100725", + "is_a": "Phenotypic microbiological characterization [GENEPIO:0100724]" + }, + "Biolog phenotype microarray [GENEPIO:0100726]": { + "text": "Biolog phenotype microarray [GENEPIO:0100726]", + "description": "A phenotypic microbiological characterization data tag which indicates the presence of biolog phenotype microarray characterization data.", + "meaning": "GENEPIO:0100726", + "is_a": "Phenotypic microbiological characterization [GENEPIO:0100724]" + }, + "Microbiological quantification [GENEPIO:0100727]": { + "text": "Microbiological quantification [GENEPIO:0100727]", + "description": "A dataset attribute bundle which indicates the presence of microbiological quantification data.", + "meaning": "GENEPIO:0100727" + }, + "Colony count [GENEPIO:0100728]": { + "text": "Colony count [GENEPIO:0100728]", + "description": "A microbiological quantification data tag which indicates the presence of colony count data.", + "meaning": "GENEPIO:0100728", + "is_a": "Microbiological quantification [GENEPIO:0100727]" + }, + "Total coliform count [GENEPIO:0100729]": { + "text": "Total coliform count [GENEPIO:0100729]", + "description": "A colony count microbiological quantification data tag which indicates the presence of data that describes total colony count of coliforms.", + "meaning": "GENEPIO:0100729", + "is_a": "Colony count [GENEPIO:0100728]" + }, + "Total fecal coliform count [GENEPIO:0100730]": { + "text": "Total fecal coliform count [GENEPIO:0100730]", + "description": "A colony count microbiological quantification data tag that indicates the presence of data which describes total colony count of fecal coliforms.", + "meaning": "GENEPIO:0100730", + "is_a": "Colony count [GENEPIO:0100728]" + }, + "Infectivity assay [GENEPIO:0100731]": { + "text": "Infectivity assay [GENEPIO:0100731]", + "description": "A microbiological quantification data tag which indicates the presence of infectivity assay data.", + "meaning": "GENEPIO:0100731", + "is_a": "Microbiological quantification [GENEPIO:0100727]" + }, + "ELISA toxin binding [GENEPIO:0100732]": { + "text": "ELISA toxin binding [GENEPIO:0100732]", + "description": "A microbiological quantification data tag which indicates the presence of data which describes enzyme-linked immunosorbent assay (ELISA) toxin binding.", + "meaning": "GENEPIO:0100732", + "is_a": "Microbiological quantification [GENEPIO:0100727]" + }, + "Molecular characterization [GENEPIO:0100733]": { + "text": "Molecular characterization [GENEPIO:0100733]", + "description": "A dataset attribute bundle which indicates the presence of molecular characterization data.", + "meaning": "GENEPIO:0100733" + }, + "16S rRNA Sanger sequencing [GENEPIO:0100734]": { + "text": "16S rRNA Sanger sequencing [GENEPIO:0100734]", + "description": "A molecular characterization data tag which indicates the presence of 16S rRNA Sanger sequencing characterization data.", + "meaning": "GENEPIO:0100734", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "Metagenomic sequencing [GENEPIO:0101024]": { + "text": "Metagenomic sequencing [GENEPIO:0101024]", + "description": "A molecular characterization data tag which indicates the presence of metagenomic sequencing characterization data.", + "meaning": "GENEPIO:0101024", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "PCR marker detection [GENEPIO:0100735]": { + "text": "PCR marker detection [GENEPIO:0100735]", + "description": "A molecular characterization data tag which indicates the presence of polymerase chain reaction (PCR) marker detection characterization data.", + "meaning": "GENEPIO:0100735", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "BOX PCR fingerprint [GENEPIO:0100736]": { + "text": "BOX PCR fingerprint [GENEPIO:0100736]", + "description": "A PCR marker detection characterization data tag which indicates the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data.", + "meaning": "GENEPIO:0100736", + "is_a": "PCR marker detection [GENEPIO:0100735]" + }, + "ERIC PCR fingerprint [GENEPIO:0100737]": { + "text": "ERIC PCR fingerprint [GENEPIO:0100737]", + "description": "A PCR marker detection characterization data tag which indicates the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint data.", + "meaning": "GENEPIO:0100737", + "is_a": "PCR marker detection [GENEPIO:0100735]" + }, + "Plasmid type [GENEPIO:0100738]": { + "text": "Plasmid type [GENEPIO:0100738]", + "description": "A molecular characterization data tag which indicates the presence of plasmid type characterization data.", + "meaning": "GENEPIO:0100738", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "Ribotype [GENEPIO:0100739]": { + "text": "Ribotype [GENEPIO:0100739]", + "description": "A molecular characterization data tag which indicates the presence of ribotype characterization data.", + "meaning": "GENEPIO:0100739", + "is_a": "Molecular characterization [GENEPIO:0100733]" + }, + "Molecular quantification [GENEPIO:0100740]": { + "text": "Molecular quantification [GENEPIO:0100740]", + "description": "A dataset attribute bundle which indicates the presence of molecular quantification data.", + "meaning": "GENEPIO:0100740" + }, + "qPCR marker organism quantification [GENEPIO:0100741]": { + "text": "qPCR marker organism quantification [GENEPIO:0100741]", + "description": "A molecular quantification data tag which indicates the presence of quantitative polymerase chain reaction (qPCR) marker organism quantification data.", + "meaning": "GENEPIO:0100741", + "is_a": "Molecular quantification [GENEPIO:0100740]" + }, + "Physical characterization [GENEPIO:0100742]": { + "text": "Physical characterization [GENEPIO:0100742]", + "description": "A dataset attribute bundle which indicates the presence of physical characterization data.", + "meaning": "GENEPIO:0100742" + }, + "Conductivity measurement [GENEPIO:0100743]": { + "text": "Conductivity measurement [GENEPIO:0100743]", + "description": "A physical characterization data tag which indicates the presence of data that describes conductivity measurement characterization.", + "meaning": "GENEPIO:0100743", + "is_a": "Physical characterization [GENEPIO:0100742]" + }, + "Mollusc shell measurement [GENEPIO:0100744]": { + "text": "Mollusc shell measurement [GENEPIO:0100744]", + "description": "A physical characterization data tag which indicates the presence of data that describes a measurement of a mollusc shell.", + "meaning": "GENEPIO:0100744", + "is_a": "Physical characterization [GENEPIO:0100742]" + }, + "Matter compostion [GENEPIO:0100746]": { + "text": "Matter compostion [GENEPIO:0100746]", + "description": "A physical characterization data tag which indicates the presence of matter compostion characterization data.", + "meaning": "GENEPIO:0100746", + "is_a": "Physical characterization [GENEPIO:0100742]" + }, + "Dry matter composition [GENEPIO:0100747]": { + "text": "Dry matter composition [GENEPIO:0100747]", + "description": "A matter composition characterization data tag which indicates the presence of data that describes dry matter composition.", + "meaning": "GENEPIO:0100747", + "is_a": "Matter compostion [GENEPIO:0100746]" + }, + "Organic matter composition [GENEPIO:0100748]": { + "text": "Organic matter composition [GENEPIO:0100748]", + "description": "A matter composition characterization data tag which indicates the presence of data that describes organic matter composition.", + "meaning": "GENEPIO:0100748", + "is_a": "Matter compostion [GENEPIO:0100746]" + } + } + }, + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Bird [NCBITaxon:8782]": { + "text": "Bird [NCBITaxon:8782]", + "description": "A group of warm-blooded vertebrates in class Aves, that are characterized by feathers, wings, toothless beaked jaws and the laying of hard-shelled eggs and are usually able to fly.", + "meaning": "NCBITaxon:8782" + }, + "Chicken [NCBITaxon:9031]": { + "text": "Chicken [NCBITaxon:9031]", + "description": "A domesticated junglefowl of the species Gallus gallus.", + "meaning": "NCBITaxon:9031", + "is_a": "Bird [NCBITaxon:8782]" + }, + "Seabird [FOODON:00004504]": { + "text": "Seabird [FOODON:00004504]", + "description": "A bird that is adapted to live within the marine environment.", + "meaning": "FOODON:00004504", + "is_a": "Bird [NCBITaxon:8782]" + }, + "Cormorant [NCBITaxon:9206]": { + "text": "Cormorant [NCBITaxon:9206]", + "description": "A family of aquatic birds (Phalacrocoracidae).", + "meaning": "NCBITaxon:9206", + "is_a": "Seabird [FOODON:00004504]" + }, + "Double Crested Cormorant [NCBITaxon:56069]": { + "text": "Double Crested Cormorant [NCBITaxon:56069]", + "description": "A species of the cormorant family of water birds (Phalacrocorax auritus).", + "meaning": "NCBITaxon:56069", + "is_a": "Cormorant [NCBITaxon:9206]" + }, + "Crane [NCBITaxon:9109]": { + "text": "Crane [NCBITaxon:9109]", + "description": "A family of large, long-legged, and long-necked birds (Gruidae).", + "meaning": "NCBITaxon:9109", + "is_a": "Seabird [FOODON:00004504]" + }, + "Whooping Crane [NCBITaxon:9117]": { + "text": "Whooping Crane [NCBITaxon:9117]", + "description": "An endangered crane species that is native to North America and is named for its whooping sound.", + "meaning": "NCBITaxon:9117", + "is_a": "Crane [NCBITaxon:9109]" + }, + "Gull (Seagull) [NCBITaxon:8911]": { + "text": "Gull (Seagull) [NCBITaxon:8911]", + "description": "A large genus of gulls within the family Laridae.", + "meaning": "NCBITaxon:8911", + "is_a": "Seabird [FOODON:00004504]" + }, + "Glaucous-winged Gull [NCBITaxon:119606]": { + "text": "Glaucous-winged Gull [NCBITaxon:119606]", + "description": "A species of large, white-headed gull (Larus glaucescens).", + "meaning": "NCBITaxon:119606", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Great Black-backed Gull [NCBITaxon:8912]": { + "text": "Great Black-backed Gull [NCBITaxon:8912]", + "description": "A species of white gull that has a black back and wings (Larus marinus).", + "meaning": "NCBITaxon:8912", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Herring Gull [NCBITaxon:35669]": { + "text": "Herring Gull [NCBITaxon:35669]", + "description": "A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus).", + "meaning": "NCBITaxon:35669", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Ring-billed Gull [NCBITaxon:126683]": { + "text": "Ring-billed Gull [NCBITaxon:126683]", + "description": "A species of ring-billed gull that has a black ring around its bill (Larus delawarensis).", + "meaning": "NCBITaxon:126683", + "is_a": "Gull (Seagull) [NCBITaxon:8911]" + }, + "Eider [NCBITaxon:50366]": { + "text": "Eider [NCBITaxon:50366]", + "description": "A genus of large seaducks (Somateria).", + "meaning": "NCBITaxon:50366", + "is_a": "Seabird [FOODON:00004504]" + }, + "Common Eider [NCBITaxon:76058]": { + "text": "Common Eider [NCBITaxon:76058]", + "description": "A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima).", + "meaning": "NCBITaxon:76058", + "is_a": "Eider [NCBITaxon:50366]" + }, + "Turkey [NCBITaxon:9103]": { + "text": "Turkey [NCBITaxon:9103]", + "description": "A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo.", + "meaning": "NCBITaxon:9103", + "is_a": "Bird [NCBITaxon:8782]" + }, + "Fish [FOODON:03411222]": { + "text": "Fish [FOODON:03411222]", + "description": "Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic (\"cold-blooded\"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature.", + "meaning": "FOODON:03411222" + }, + "Mammal [FOODON:03411134]": { + "text": "Mammal [FOODON:03411134]", + "description": "Mammals (from Latin mamma \"breast\") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones.", + "meaning": "FOODON:03411134" + }, + "Companion animal [FOODON:03000300]": { + "text": "Companion animal [FOODON:03000300]", + "description": "An animal that is kept as a companion.", + "meaning": "FOODON:03000300", + "is_a": "Mammal [FOODON:03411134]" + }, + "Cow [NCBITaxon:9913]": { + "text": "Cow [NCBITaxon:9913]", + "description": "A group of large, domesticated, cloven-hooved herbivores.", + "meaning": "NCBITaxon:9913", + "is_a": "Mammal [FOODON:03411134]" + }, + "Deer [NCBITaxon:9850]": { + "text": "Deer [NCBITaxon:9850]", + "meaning": "NCBITaxon:9850", + "is_a": "Mammal [FOODON:03411134]" + }, + "Human [NCBITaxon:9606]": { + "text": "Human [NCBITaxon:9606]", + "description": "A bipedal primate mammal of the species Homo sapiens.", + "meaning": "NCBITaxon:9606", + "is_a": "Mammal [FOODON:03411134]" + }, + "Pig [NCBITaxon:9823]": { + "text": "Pig [NCBITaxon:9823]", + "description": "A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles.", + "meaning": "NCBITaxon:9823", + "is_a": "Mammal [FOODON:03411134]" + }, + "Sheep [NCBITaxon:9940]": { + "text": "Sheep [NCBITaxon:9940]", + "description": "A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries.", + "meaning": "NCBITaxon:9940", + "is_a": "Mammal [FOODON:03411134]" + }, + "Shellfish [FOODON:03411433]": { + "text": "Shellfish [FOODON:03411433]", + "description": "The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates.", + "meaning": "FOODON:03411433" + } + } + }, + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Anoplopoma fimbria [NCBITaxon:229290]": { + "text": "Anoplopoma fimbria [NCBITaxon:229290]", + "description": "One of two members of the fish family Anoplopomatidae and the only species in the genus Anoplopoma.", + "meaning": "NCBITaxon:229290" + }, + "Bos taurus [NCBITaxon:9913]": { + "text": "Bos taurus [NCBITaxon:9913]", + "description": "A group of large, domesticated, cloven-hooved herbivores.", + "meaning": "NCBITaxon:9913" + }, + "Crassostrea virginica [NCBITaxon:6565]": { + "text": "Crassostrea virginica [NCBITaxon:6565]", + "description": "A species of true oyster (Crassostrea virginica).", + "meaning": "NCBITaxon:6565" + }, + "Gallus gallus [NCBITaxon:9031]": { + "text": "Gallus gallus [NCBITaxon:9031]", + "description": "A domesticated junglefowl of the species Gallus gallus.", + "meaning": "NCBITaxon:9031" + }, + "Grus americana [NCBITaxon:9117]": { + "text": "Grus americana [NCBITaxon:9117]", + "description": "An endangered crane species that is native to North America and is named for its whooping sound.", + "meaning": "NCBITaxon:9117" + }, + "Homarus americanus [NCBITaxon:6706]": { + "text": "Homarus americanus [NCBITaxon:6706]", + "description": "A species of lobster that is found on the Atlantic coast of North America (Homarus americanus).", + "meaning": "NCBITaxon:6706" + }, + "Homo sapiens [NCBITaxon:9606]": { + "text": "Homo sapiens [NCBITaxon:9606]", + "description": "A bipedal primate mammal of the species Homo sapiens.", + "meaning": "NCBITaxon:9606" + }, + "Larus argentatus [NCBITaxon:35669]": { + "text": "Larus argentatus [NCBITaxon:35669]", + "description": "A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus).", + "meaning": "NCBITaxon:35669" + }, + "Larus delawarensis [NCBITaxon:126683]": { + "text": "Larus delawarensis [NCBITaxon:126683]", + "description": "A species of ring-billed gull that has a black ring around its bill (Larus delawarensis).", + "meaning": "NCBITaxon:126683" + }, + "Larus glaucescens [NCBITaxon:119606]": { + "text": "Larus glaucescens [NCBITaxon:119606]", + "description": "A species of large, white-headed gull (Larus glaucescens).", + "meaning": "NCBITaxon:119606" + }, + "Larus marinus [NCBITaxon:8912]": { + "text": "Larus marinus [NCBITaxon:8912]", + "description": "A species of white gull that has a black back and wings (Larus marinus).", + "meaning": "NCBITaxon:8912" + }, + "Meleagris gallopavo [NCBITaxon:9103]": { + "text": "Meleagris gallopavo [NCBITaxon:9103]", + "description": "A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo.", + "meaning": "NCBITaxon:9103" + }, + "Mytilus edulis [NCBITaxon:6550]": { + "text": "Mytilus edulis [NCBITaxon:6550]", + "description": "A medium-sized edible marine bivalve mollusc in the family Mytilidae, the mussels.", + "meaning": "NCBITaxon:6550" + }, + "Oncorhynchus kisutch [NCBITaxon:8019]": { + "text": "Oncorhynchus kisutch [NCBITaxon:8019]", + "description": "A species of pacific salmon in North America, that is commonly called as coho salmon.", + "meaning": "NCBITaxon:8019" + }, + "Oncorhynchus mykiss [NCBITaxon:8022]": { + "text": "Oncorhynchus mykiss [NCBITaxon:8022]", + "description": "A species of trout native to cold-water tributaries of the Pacific Ocean in Asia and North America (Oncorhynchus mykiss).", + "meaning": "NCBITaxon:8022" + }, + "Oncorhynchus tshawytscha [NCBITaxon:74940]": { + "text": "Oncorhynchus tshawytscha [NCBITaxon:74940]", + "description": "The largest species of pacific salmon in North America (Oncorhynchus tshawytscha).", + "meaning": "NCBITaxon:74940" + }, + "Ovis aries [NCBITaxon:9940]": { + "text": "Ovis aries [NCBITaxon:9940]", + "description": "A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries.", + "meaning": "NCBITaxon:9940" + }, + "Phalacrocorax auritus [NCBITaxon:56069]": { + "text": "Phalacrocorax auritus [NCBITaxon:56069]", + "description": "A species of the cormorant family of water birds (Phalacrocorax auritus).", + "meaning": "NCBITaxon:56069" + }, + "Salmo salar [NCBITaxon:8030]": { + "text": "Salmo salar [NCBITaxon:8030]", + "description": "A species of ray-finned fish in the family Salmonidae (Salmo salar).", + "meaning": "NCBITaxon:8030" + }, + "Somateria mollissima [NCBITaxon:76058]": { + "text": "Somateria mollissima [NCBITaxon:76058]", + "description": "A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima).", + "meaning": "NCBITaxon:76058" + }, + "Sus scrofa domesticus [NCBITaxon:9825]": { + "text": "Sus scrofa domesticus [NCBITaxon:9825]", + "description": "A stout-bodied, hooved and short-legged, omnivorous mammal, with thick skin usually sparsely coated with short bristles raised for its meat.", + "meaning": "NCBITaxon:9825" + } + } + }, + "HostFoodProductionNameMenu": { + "name": "HostFoodProductionNameMenu", + "title": "host (food production name) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cow (by age/production stage) (organizational term)": { + "text": "Cow (by age/production stage) (organizational term)" + }, + "Calf [FOODON:03411349]": { + "text": "Calf [FOODON:03411349]", + "description": "Calves are the young of domestic cattle. Calves are reared to become adult cattle, or are slaughtered for their meat, called veal.", + "meaning": "FOODON:03411349", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Dry cow [FOODON:00004411]": { + "text": "Dry cow [FOODON:00004411]", + "description": "A cow that is in a stage of its lactation cycle where milk production ceases prior to calving.", + "meaning": "FOODON:00004411", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Feeder cow [FOODON:00004292]": { + "text": "Feeder cow [FOODON:00004292]", + "description": "A young cow mature enough either to undergo backgrounding or to be fattened in preparation for slaughter.", + "meaning": "FOODON:00004292", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Finisher cow [FOODON:00004293]": { + "text": "Finisher cow [FOODON:00004293]", + "meaning": "FOODON:00004293", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Milker cow [FOODON:03411201]": { + "text": "Milker cow [FOODON:03411201]", + "description": "A cow that is bred specifically for milk production.", + "meaning": "FOODON:03411201", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Stocker cow [FOODON:00004294]": { + "text": "Stocker cow [FOODON:00004294]", + "description": "A type of cow that has been weaned and is being fed in a way to add physical bulk to its body.", + "meaning": "FOODON:00004294", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Weanling cow [FOODON:00004295]": { + "text": "Weanling cow [FOODON:00004295]", + "description": "A type of young cow that has been weaned and consumes solid food.", + "meaning": "FOODON:00004295", + "is_a": "Cow (by age/production stage) (organizational term)" + }, + "Cow (by sex/reproductive stage) (organizational term)": { + "text": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Bull [FOODON:00000015]": { + "text": "Bull [FOODON:00000015]", + "description": "A cattle bull is an adult \"intact\" (i.e. not castrated) male of a cattle species.", + "meaning": "FOODON:00000015", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Cow [NCBITaxon:9913]": { + "text": "Cow [NCBITaxon:9913]", + "description": "A group of large, domesticated, cloven-hooved herbivores.", + "meaning": "NCBITaxon:9913", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Freemartin [FOODON:00004296]": { + "text": "Freemartin [FOODON:00004296]", + "description": "A cow that is genetically female, but has many characteristics of a male and is usually infertile.", + "meaning": "FOODON:00004296", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Heifer [FOODON:00002518]": { + "text": "Heifer [FOODON:00002518]", + "description": "A heifer is a young female, under three years of age, of a cattle species before she has had a calf of her own.", + "meaning": "FOODON:00002518", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Steer [FOODON:00002531]": { + "text": "Steer [FOODON:00002531]", + "description": "A cattle steer is an adult castrated male of a cattle species.", + "meaning": "FOODON:00002531", + "is_a": "Cow (by sex/reproductive stage) (organizational term)" + }, + "Pig (by age/production stage) (organizational term)": { + "text": "Pig (by age/production stage) (organizational term)" + }, + "Finisher pig [FOODON:00003371]": { + "text": "Finisher pig [FOODON:00003371]", + "description": "A grower pig over 70 kg (150 lb) liveweight.", + "meaning": "FOODON:00003371", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Grower pig [FOODON:00003370]": { + "text": "Grower pig [FOODON:00003370]", + "description": "A pig between weaning and sale or transfer to the breeding herd, sold for slaughter or killed for rations.", + "meaning": "FOODON:00003370", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Nursing pig [FOODON:00004297 ]": { + "text": "Nursing pig [FOODON:00004297 ]", + "meaning": "OODON:00004297", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Pig [NCBITaxon:9823]": { + "text": "Pig [NCBITaxon:9823]", + "description": "A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles.", + "meaning": "NCBITaxon:9823", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Piglet [FOODON:00003952]": { + "text": "Piglet [FOODON:00003952]", + "description": "An unweaned or immature pig.", + "meaning": "FOODON:00003952", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Weanling (weaner) pig [FOODON:00003373]": { + "text": "Weanling (weaner) pig [FOODON:00003373]", + "description": "A young pig recently separated from the sow", + "meaning": "FOODON:00003373", + "is_a": "Pig (by age/production stage) (organizational term)" + }, + "Pig (by sex/reproductive stage) (organizational term)": { + "text": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Barrow [FOODON:03411280]": { + "text": "Barrow [FOODON:03411280]", + "description": "A male swine castrated before sexual maturity.", + "meaning": "FOODON:03411280", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Boar [FOODON:03412248]": { + "text": "Boar [FOODON:03412248]", + "description": "An adult male swine.", + "meaning": "FOODON:03412248", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Gilt [FOODON:00003369]": { + "text": "Gilt [FOODON:00003369]", + "description": "A female pig under the age of 1 year. The term is also often used to refer to a pig who has not farrowed, or given birth to a litter.", + "meaning": "FOODON:00003369", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Sow [FOODON:00003333]": { + "text": "Sow [FOODON:00003333]", + "description": "An adult female swine.", + "meaning": "FOODON:00003333", + "is_a": "Pig (by sex/reproductive stage) (organizational term)" + }, + "Poultry or game bird [FOODON:03411563]": { + "text": "Poultry or game bird [FOODON:03411563]", + "description": "Domesticated birds kept by humans for their eggs, their meat or their feathers.", + "meaning": "FOODON:03411563" + }, + "Broiler or fryer chicken [FOODON:03411198]": { + "text": "Broiler or fryer chicken [FOODON:03411198]", + "description": "A chicken younger than 10 weeks old (previously younger than 13 weeks), of either sex, that is tender-meated with soft, pliable, smooth-textured skin and flexible breastbone cartilage.", + "meaning": "FOODON:03411198", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Capon [FOODON:03411711]": { + "text": "Capon [FOODON:03411711]", + "description": "A surgically neutered male chicken younger than four months old (previously younger than eight months) that is tender-meated with soft, pliable, smooth-textured skin.", + "meaning": "FOODON:03411711", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Chick [FOODON:00004299]": { + "text": "Chick [FOODON:00004299]", + "description": "A young offspring of any bird.", + "meaning": "FOODON:00004299", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Chicken [NCBITaxon:9031]": { + "text": "Chicken [NCBITaxon:9031]", + "description": "A domesticated junglefowl of the species Gallus gallus.", + "meaning": "NCBITaxon:9031", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Egg [UBERON:0007379]": { + "text": "Egg [UBERON:0007379]", + "description": "The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food.", + "meaning": "UBERON:0007379", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Hatchling [FOODON:00004300]": { + "text": "Hatchling [FOODON:00004300]", + "description": "A young animal that has recently emerged from its egg.", + "meaning": "FOODON:00004300", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Hen [FOODON:00003282]": { + "text": "Hen [FOODON:00003282]", + "description": "An adult female chicken.", + "meaning": "FOODON:00003282", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Layer chicken [FOODON:00004301]": { + "text": "Layer chicken [FOODON:00004301]", + "description": "A type of chicken kept for laying eggs.", + "meaning": "FOODON:00004301", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Layer turkey [FOODON:00004302]": { + "text": "Layer turkey [FOODON:00004302]", + "description": "A type of turkey kept for laying eggs.", + "meaning": "FOODON:00004302", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Poult [FOODON:00002962]": { + "text": "Poult [FOODON:00002962]", + "description": "A poult is a young domestic chicken, turkey, pheasant, or other fowl being raised for food.", + "meaning": "FOODON:00002962", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Pullet [FOODON:00004303]": { + "text": "Pullet [FOODON:00004303]", + "description": "A young hen, especially one less than one year old.", + "meaning": "FOODON:00004303", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Rooster [FOODON:03411714]": { + "text": "Rooster [FOODON:03411714]", + "description": "A mature male chicken with coarse skin, toughened and darkened meat, and hardened breastbone tip.", + "meaning": "FOODON:03411714", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Tom (Gobbler) [FOODON:00004304 ]": { + "text": "Tom (Gobbler) [FOODON:00004304 ]", + "meaning": "OODON:00004304", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Turkey [NCBITaxon:9103]": { + "text": "Turkey [NCBITaxon:9103]", + "description": "A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo.", + "meaning": "NCBITaxon:9103", + "is_a": "Poultry or game bird [FOODON:03411563]" + }, + "Sheep [NCBITaxon:9940]": { + "text": "Sheep [NCBITaxon:9940]", + "description": "A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries.", + "meaning": "NCBITaxon:9940" + }, + "Ram [FOODON:00004305]": { + "text": "Ram [FOODON:00004305]", + "description": "An adult male sheep kept for breeding and for wool production.", + "meaning": "FOODON:00004305", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Wether sheep [FOODON:00004306]": { + "text": "Wether sheep [FOODON:00004306]", + "description": "A castrated male sheep.", + "meaning": "FOODON:00004306", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Ewe [FOODON:03412610]": { + "text": "Ewe [FOODON:03412610]", + "description": "A ewe is a female sheep.", + "meaning": "FOODON:03412610", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Lamb [FOODON:03411669]": { + "text": "Lamb [FOODON:03411669]", + "description": "A whole lamb or some material processed from a lamb.", + "meaning": "FOODON:03411669", + "is_a": "Sheep [NCBITaxon:9940]" + }, + "Fish [FOODON:03411222]": { + "text": "Fish [FOODON:03411222]", + "description": "Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic (\"cold-blooded\"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature.", + "meaning": "FOODON:03411222" + }, + "Fish egg [FOODON_00004319]": { + "text": "Fish egg [FOODON_00004319]", + "description": "An egg or spawn of a fish that is contained within or separated from the ovary.", + "meaning": "FOODON:00004319", + "is_a": "Fish [FOODON:03411222]" + }, + "Fry (fish) [FOODON_00004318]": { + "text": "Fry (fish) [FOODON_00004318]", + "description": "A fish that is recently hatched and has reached the stage where its yolk-sac has almost disappeared and its swim bladder is operational to the point where the fish can actively feed for itself.", + "meaning": "FOODON:00004318", + "is_a": "Fish [FOODON:03411222]" + }, + "Juvenile fish [FOODON_00004317]": { + "text": "Juvenile fish [FOODON_00004317]", + "description": "A fish that has not reached to sexual maturity.", + "meaning": "FOODON:00004317", + "is_a": "Fish [FOODON:03411222]" + } + } + }, + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host_age_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "month [UO:0000035]": { + "text": "month [UO:0000035]", + "description": "A time unit which is equal to approximately 4-4.5 weeks or 28-31 days.", + "meaning": "UO:0000035" + }, + "year [UO:0000036]": { + "text": "year [UO:0000036]", + "description": "A time unit which is equal to 365 days, or 366 days during a leap year.", + "meaning": "UO:0000036" + } + } + }, + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host_age_bin menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "First winter [GENEPIO:0100684]": { + "text": "First winter [GENEPIO:0100684]", + "description": "An age group used to classify birds identified by their first winter nonbreeding plumage, generally indicating a juvenile bird.", + "meaning": "GENEPIO:0100684" + }, + "First summer [GENEPIO:0100685]": { + "text": "First summer [GENEPIO:0100685]", + "description": "An age group used to classify birds identified by their first summer nonbreeding plumage, generally indicating a juvenile bird.", + "meaning": "GENEPIO:0100685" + }, + "Second winter [GENEPIO:0100686]": { + "text": "Second winter [GENEPIO:0100686]", + "description": "An age group used to classify birds identified by their second winter plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100686" + }, + "Second summer [GENEPIO:0100687]": { + "text": "Second summer [GENEPIO:0100687]", + "description": "An age group used to classify birds identified by their second summer plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100687" + }, + "Third winter [GENEPIO:0100688]": { + "text": "Third winter [GENEPIO:0100688]", + "description": "An age group used to classify birds identified by their third winter plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100688" + }, + "Third summer [GENEPIO:0100689]": { + "text": "Third summer [GENEPIO:0100689]", + "description": "An age group used to classify birds identified by their third summer plumage (many types of birds molt several times during the same season).", + "meaning": "GENEPIO:0100689" + }, + "0 - 9 [GENEPIO:0100049]]": { + "text": "0 - 9 [GENEPIO:0100049]]", + "meaning": "ENEPIO:0100049" + }, + "10 - 19 [GENEPIO:0100050]": { + "text": "10 - 19 [GENEPIO:0100050]", + "description": "An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive).", + "meaning": "GENEPIO:0100050" + }, + "20 - 29 [GENEPIO:0100051]": { + "text": "20 - 29 [GENEPIO:0100051]", + "description": "An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive).", + "meaning": "GENEPIO:0100051" + }, + "30 - 39 [GENEPIO:0100052]": { + "text": "30 - 39 [GENEPIO:0100052]", + "description": "An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive).", + "meaning": "GENEPIO:0100052" + }, + "40 - 49 [GENEPIO:0100053]": { + "text": "40 - 49 [GENEPIO:0100053]", + "description": "An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive).", + "meaning": "GENEPIO:0100053" + }, + "50 - 59 [GENEPIO:0100054]": { + "text": "50 - 59 [GENEPIO:0100054]", + "description": "An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive).", + "meaning": "GENEPIO:0100054" + }, + "60 - 69 [GENEPIO:0100055]": { + "text": "60 - 69 [GENEPIO:0100055]", + "description": "An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive).", + "meaning": "GENEPIO:0100055" + }, + "70 - 79 [GENEPIO:0100056]": { + "text": "70 - 79 [GENEPIO:0100056]", + "description": "An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive).", + "meaning": "GENEPIO:0100056" + }, + "80 - 89 [GENEPIO:0100057]": { + "text": "80 - 89 [GENEPIO:0100057]", + "description": "An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive).", + "meaning": "GENEPIO:0100057" + }, + "90 - 99 [GENEPIO:0100058]": { + "text": "90 - 99 [GENEPIO:0100058]", + "description": "An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive).", + "meaning": "GENEPIO:0100058" + }, + "100+ [GENEPIO:0100059]": { + "text": "100+ [GENEPIO:0100059]", + "description": "An age group that stratifies the age of a case to be greater than or equal to 100 years old.", + "meaning": "GENEPIO:0100059" + } + } + }, + "HostGender": { + "name": "HostGender", + "title": "host_gender", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Female [NCIT:C46110]": { + "text": "Female [NCIT:C46110]", + "description": "An individual who reports belonging to the cultural gender role distinction of female.", + "meaning": "NCIT:C46110" + }, + "Male [NCIT:C46109]": { + "text": "Male [NCIT:C46109]", + "description": "An individual who reports belonging to the cultural gender role distinction of male.", + "meaning": "NCIT:C46109" + }, + "Non-binary gender [GSSO:000132]": { + "text": "Non-binary gender [GSSO:000132]", + "description": "Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female.", + "meaning": "GSSO:000132" + }, + "Transgender (assigned male at birth) [GSSO:004004]": { + "text": "Transgender (assigned male at birth) [GSSO:004004]", + "description": "Having a feminine gender (identity) which is different from the sex one was assigned at birth.", + "meaning": "GSSO:004004" + }, + "Transgender (assigned female at birth) [GSSO:004005]": { + "text": "Transgender (assigned female at birth) [GSSO:004005]", + "description": "Having a masculine gender (identity) which is different from the sex one was assigned at birth.", + "meaning": "GSSO:004005" + }, + "Undeclared [NCIT:C110959]": { + "text": "Undeclared [NCIT:C110959]", + "meaning": "CIT:C110959" + } + } + }, + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host_disease menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Highly pathogenic avian influenza A (HPAI)": { + "text": "Highly pathogenic avian influenza A (HPAI)" + } + } + }, + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "host_health_state menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Asymptomatic [NCIT:C3833]": { + "text": "Asymptomatic [NCIT:C3833]", + "description": "Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction.", + "meaning": "NCIT:C3833" + }, + "Deceased [NCIT:C28554]": { + "text": "Deceased [NCIT:C28554]", + "description": "The cessation of life.", + "meaning": "NCIT:C28554" + }, + "Healthy [NCIT:C115935]": { + "text": "Healthy [NCIT:C115935]", + "meaning": "CIT:C115935" + }, + "Recovered [NCIT:C49498]": { + "text": "Recovered [NCIT:C49498]", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", + "meaning": "NCIT:C49498" + }, + "Symptomatic [NCIT:C25269]": { + "text": "Symptomatic [NCIT:C25269]", + "description": "Exhibiting the symptoms of a particular disease.", + "meaning": "NCIT:C25269" + } + } + }, + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "host_health_status_details menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Hospitalized [NCIT:C25179]": { + "text": "Hospitalized [NCIT:C25179]", + "description": "The condition of being treated as a patient in a hospital.", + "meaning": "NCIT:C25179" + }, + "Hospitalized (Non-ICU) [GENEPIO:0100045]": { + "text": "Hospitalized (Non-ICU) [GENEPIO:0100045]", + "description": "The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU).", + "meaning": "GENEPIO:0100045", + "is_a": "Hospitalized [NCIT:C25179]" + }, + "Hospitalized (ICU) [GENEPIO:0100046]": { + "text": "Hospitalized (ICU) [GENEPIO:0100046]", + "description": "The condition of being treated as a patient in a hospital intensive care unit (ICU).", + "meaning": "GENEPIO:0100046", + "is_a": "Hospitalized [NCIT:C25179]" + }, + "Mechanical Ventilation [NCIT:C70909]": { + "text": "Mechanical Ventilation [NCIT:C70909]", + "meaning": "NCIT:C70909" + }, + "Medically Isolated [GENEPIO:0100047]": { + "text": "Medically Isolated [GENEPIO:0100047]", + "description": "Separation of people with a contagious disease from population to reduce the spread of the disease.", + "meaning": "GENEPIO:0100047" + }, + "Medically Isolated (Negative Pressure) [GENEPIO:0100048]": { + "text": "Medically Isolated (Negative Pressure) [GENEPIO:0100048]", + "description": "Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter.", + "meaning": "GENEPIO:0100048", + "is_a": "Medically Isolated [GENEPIO:0100047]" + }, + "Self-quarantining [NCIT:C173768]": { + "text": "Self-quarantining [NCIT:C173768]", + "meaning": "CIT:C173768" + } + } + }, + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "host_health_outcome menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Deceased [NCIT:C28554]": { + "text": "Deceased [NCIT:C28554]", + "description": "The cessation of life.", + "meaning": "NCIT:C28554" + }, + "Deteriorating [NCIT:C25254]": { + "text": "Deteriorating [NCIT:C25254]", + "description": "Advancing in extent or severity.", + "meaning": "NCIT:C25254" + }, + "Recovered [NCIT:C49498]": { + "text": "Recovered [NCIT:C49498]", + "description": "One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated.", + "meaning": "NCIT:C49498" + }, + "Stable [NCIT:C30103]": { + "text": "Stable [NCIT:C30103]", + "description": "Subject to little fluctuation; showing little if any change.", + "meaning": "NCIT:C30103" + } + } + }, + "SignsAndSymptomsMenu": { + "name": "SignsAndSymptomsMenu", + "title": "signs_and_symptoms menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Abnormal lung auscultation [HP:0030829]": { + "text": "Abnormal lung auscultation [HP:0030829]", + "meaning": "HP:0030829" + }, + "Acute Respiratory Distress Syndrome [HP:0033677]": { + "text": "Acute Respiratory Distress Syndrome [HP:0033677]", + "meaning": "HP:0033677" + }, + "Altered mental status [HP:0011446]": { + "text": "Altered mental status [HP:0011446]", + "meaning": "HP:0011446" + }, + "Cognitive impairment [HP:0100543]": { + "text": "Cognitive impairment [HP:0100543]", + "meaning": "HP:0100543", + "is_a": "Altered mental status [HP:0011446]" + }, + "Coma [HP:0001259]": { + "text": "Coma [HP:0001259]", + "meaning": "HP:0001259", + "is_a": "Altered mental status [HP:0011446]" + }, + "Confusion [HP:0001289]": { + "text": "Confusion [HP:0001289]", + "meaning": "HP:0001289", + "is_a": "Altered mental status [HP:0011446]" + }, + "Delirium (sudden severe confusion) [HP:0031258]": { + "text": "Delirium (sudden severe confusion) [HP:0031258]", + "meaning": "HP:0031258", + "is_a": "Confusion [HP:0001289]" + }, + "Arrhythmia [HP:0011675]": { + "text": "Arrhythmia [HP:0011675]", + "meaning": "HP:0011675" + }, + "Asthenia (generalized weakness) [HP:0025406]": { + "text": "Asthenia (generalized weakness) [HP:0025406]", + "meaning": "HP:0025406" + }, + "Bleeding gums [GENEPIO:0101182]": { + "text": "Bleeding gums [GENEPIO:0101182]", + "meaning": "GENEPIO:0101182" + }, + "Chest tightness or pressure [HP:0031352]": { + "text": "Chest tightness or pressure [HP:0031352]", + "meaning": "HP:0031352" + }, + "Rigors (fever shakes) [HP:0025145]": { + "text": "Rigors (fever shakes) [HP:0025145]", + "meaning": "HP:0025145", + "is_a": "Chest tightness or pressure [HP:0031352]" + }, + "Chills (sudden cold sensation) [HP:0025143]": { + "text": "Chills (sudden cold sensation) [HP:0025143]", + "description": "A sudden sensation of feeling cold.", + "meaning": "HP:0025143" + }, + "Conjunctivitis (pink eye) [HP:0000509]": { + "text": "Conjunctivitis (pink eye) [HP:0000509]", + "description": "Inflammation of the conjunctiva.", + "meaning": "HP:0000509" + }, + "Coryza (rhinitis) [MP:0001867]": { + "text": "Coryza (rhinitis) [MP:0001867]", + "meaning": "MP:0001867" + }, + "Cough [HP:0012735]": { + "text": "Cough [HP:0012735]", + "description": "A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation.", + "meaning": "HP:0012735" + }, + "Nonproductive cough (dry cough) [HP:0031246]": { + "text": "Nonproductive cough (dry cough) [HP:0031246]", + "meaning": "HP:0031246", + "is_a": "Cough [HP:0012735]" + }, + "Productive cough (wet cough) [HP:0031245]": { + "text": "Productive cough (wet cough) [HP:0031245]", + "meaning": "HP:0031245", + "is_a": "Cough [HP:0012735]" + }, + "Diarrhea [DOID:13250]": { + "text": "Diarrhea [DOID:13250]", + "meaning": "DOID:13250" + }, + "Dyspnea (breathing difficulty) [HP:0002094]": { + "text": "Dyspnea (breathing difficulty) [HP:0002094]", + "meaning": "HP:0002094" + }, + "Fatigue (tiredness) [HP:0012378]": { + "text": "Fatigue (tiredness) [HP:0012378]", + "description": "A subjective feeling of tiredness characterized by a lack of energy and motivation.", + "meaning": "HP:0012378" + }, + "Fever [HP:0001945]": { + "text": "Fever [HP:0001945]", + "description": "Body temperature elevated above the normal range.", + "meaning": "HP:0001945" + }, + "Fever (>=38°C) [GENEPIO:0100066]": { + "text": "Fever (>=38°C) [GENEPIO:0100066]", + "meaning": "GENEPIO:0100066", + "is_a": "Fever [HP:0001945]" + }, + "Headache [HP:0002315]": { + "text": "Headache [HP:0002315]", + "description": "Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve.", + "meaning": "HP:0002315" + }, + "Hypoxemia (low blood oxygen) [HP:0012418]": { + "text": "Hypoxemia (low blood oxygen) [HP:0012418]", + "meaning": "HP:0012418" + }, + "Silent hypoxemia [GENEPIO:0100068]": { + "text": "Silent hypoxemia [GENEPIO:0100068]", + "meaning": "GENEPIO:0100068", + "is_a": "Hypoxemia (low blood oxygen) [HP:0012418]" + }, + "Malaise (general discomfort/unease) [HP:0033834]": { + "text": "Malaise (general discomfort/unease) [HP:0033834]", + "meaning": "HP:0033834" + }, + "Muscle weakness [HP:0001324]": { + "text": "Muscle weakness [HP:0001324]", + "meaning": "HP:0001324" + }, + "Nasal obstruction (stuffy nose) [HP:0001742]": { + "text": "Nasal obstruction (stuffy nose) [HP:0001742]", + "meaning": "HP:0001742" + }, + "Nausea [HP:0002018]": { + "text": "Nausea [HP:0002018]", + "description": "A sensation of unease in the stomach together with an urge to vomit.", + "meaning": "HP:0002018" + }, + "Pain [HP:0012531]": { + "text": "Pain [HP:0012531]", + "meaning": "HP:0012531" + }, + "Arthralgia (painful joints) [HP:0002829]": { + "text": "Arthralgia (painful joints) [HP:0002829]", + "meaning": "HP:0002829", + "is_a": "Pain [HP:0012531]" + }, + "Myalgia (muscle pain) [HP:0003326]": { + "text": "Myalgia (muscle pain) [HP:0003326]", + "description": "Pain in muscle.", + "meaning": "HP:0003326", + "is_a": "Pain [HP:0012531]" + }, + "Pharyngitis (sore throat) [HP:0025439]": { + "text": "Pharyngitis (sore throat) [HP:0025439]", + "meaning": "HP:0025439" + }, + "Rhinorrhea (runny nose) [HP:0031417]": { + "text": "Rhinorrhea (runny nose) [HP:0031417]", + "meaning": "HP:0031417" + }, + "Shivering (involuntary muscle twitching) [HP:0025144]": { + "text": "Shivering (involuntary muscle twitching) [HP:0025144]", + "meaning": "HP:0025144" + }, + "Sneezing [HP:0025095]": { + "text": "Sneezing [HP:0025095]", + "meaning": "HP:0025095" + }, + "Sputum Production [HP:0033709]": { + "text": "Sputum Production [HP:0033709]", + "meaning": "HP:0033709" + }, + "Swollen Lymph Nodes [HP:0002716]": { + "text": "Swollen Lymph Nodes [HP:0002716]", + "description": "Enlargment (swelling) of a lymph node.", + "meaning": "HP:0002716" + }, + "Tachypnea (accelerated respiratory rate) [HP:0002789]": { + "text": "Tachypnea (accelerated respiratory rate) [HP:0002789]", + "meaning": "HP:0002789" + }, + "Vomiting (throwing up) [HP:0002013]": { + "text": "Vomiting (throwing up) [HP:0002013]", + "description": "Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions.", + "meaning": "HP:0002013" + } + } + }, + "PreExistingConditionsAndRiskFactorsMenu": { + "name": "PreExistingConditionsAndRiskFactorsMenu", + "title": "pre-existing_conditions_and_risk_factors menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Age 60+ [VO:0004925]": { + "text": "Age 60+ [VO:0004925]", + "meaning": "VO:0004925" + }, + "Anemia [DOID:2355]": { + "text": "Anemia [DOID:2355]", + "meaning": "DOID:2355" + }, + "Hemoglobinopathy [DOID:2860]": { + "text": "Hemoglobinopathy [DOID:2860]", + "meaning": "DOID:2860", + "is_a": "Anemia [DOID:2355]" + }, + "Anorexia [HP:0002039]": { + "text": "Anorexia [HP:0002039]", + "meaning": "HP:0002039" + }, + "Birthing labor [NCIT:C92743]": { + "text": "Birthing labor [NCIT:C92743]", + "meaning": "NCIT:C92743" + }, + "Bone marrow failure [NCIT:C80693]": { + "text": "Bone marrow failure [NCIT:C80693]", + "meaning": "NCIT:C80693" + }, + "Cancer [MONDO:0004992]": { + "text": "Cancer [MONDO:0004992]", + "description": "A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.", + "meaning": "MONDO:0004992" + }, + "Breast cancer [MONDO:0007254]": { + "text": "Breast cancer [MONDO:0007254]", + "meaning": "MONDO:0007254", + "is_a": "Cancer [MONDO:0004992]" + }, + "Colorectal cancer [MONDO:0005575]": { + "text": "Colorectal cancer [MONDO:0005575]", + "meaning": "MONDO:0005575", + "is_a": "Cancer [MONDO:0004992]" + }, + "Hematologic malignancy (cancer of the blood) [DOID:2531]": { + "text": "Hematologic malignancy (cancer of the blood) [DOID:2531]", + "meaning": "DOID:2531", + "is_a": "Cancer [MONDO:0004992]" + }, + "Lung cancer [MONDO:0008903]": { + "text": "Lung cancer [MONDO:0008903]", + "meaning": "MONDO:0008903", + "is_a": "Cancer [MONDO:0004992]" + }, + "Metastatic disease [MONDO:0024880]": { + "text": "Metastatic disease [MONDO:0024880]", + "meaning": "MONDO:0024880", + "is_a": "Cancer [MONDO:0004992]" + }, + "Cancer treatment [NCIT:C16212]": { + "text": "Cancer treatment [NCIT:C16212]", + "description": "Any intervention for management of a malignant neoplasm.", + "meaning": "NCIT:C16212" + }, + "Cancer surgery [NCIT:C157740]": { + "text": "Cancer surgery [NCIT:C157740]", + "meaning": "NCIT:C157740", + "is_a": "Cancer treatment [NCIT:C16212]" + }, + "Chemotherapy [NCIT:C15632]": { + "text": "Chemotherapy [NCIT:C15632]", + "description": "The use of synthetic or naturally-occurring chemicals for the treatment of diseases.", + "meaning": "NCIT:C15632", + "is_a": "Cancer treatment [NCIT:C16212]" + }, + "Adjuvant chemotherapy [NCIT:C15360]": { + "text": "Adjuvant chemotherapy [NCIT:C15360]", + "meaning": "NCIT:C15360", + "is_a": "Chemotherapy [NCIT:C15632]" + }, + "Cardiac disorder [NCIT:C3079]": { + "text": "Cardiac disorder [NCIT:C3079]", + "meaning": "NCIT:C3079" + }, + "Arrhythmia [HP:0011675]": { + "text": "Arrhythmia [HP:0011675]", + "meaning": "HP:0011675", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cardiac disease [MONDO:0005267]": { + "text": "Cardiac disease [MONDO:0005267]", + "meaning": "MONDO:0005267", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cardiomyopathy [HP:0001638]": { + "text": "Cardiomyopathy [HP:0001638]", + "meaning": "HP:0001638", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cardiac injury [GENEPIO:0100074]": { + "text": "Cardiac injury [GENEPIO:0100074]", + "meaning": "GENEPIO:0100074", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Hypertension (high blood pressure) [HP:0000822]": { + "text": "Hypertension (high blood pressure) [HP:0000822]", + "meaning": "HP:0000822", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Hypotension (low blood pressure) [HP:0002615]": { + "text": "Hypotension (low blood pressure) [HP:0002615]", + "meaning": "HP:0002615", + "is_a": "Cardiac disorder [NCIT:C3079]" + }, + "Cesarean section [HP:0011410]": { + "text": "Cesarean section [HP:0011410]", + "meaning": "HP:0011410" + }, + "Chronic cough [GENEPIO:0100075]": { + "text": "Chronic cough [GENEPIO:0100075]", + "meaning": "GENEPIO:0100075" + }, + "Chronic gastrointestinal disease [GENEPIO:0100076]": { + "text": "Chronic gastrointestinal disease [GENEPIO:0100076]", + "meaning": "GENEPIO:0100076" + }, + "Corticosteroids [NCIT:C211]": { + "text": "Corticosteroids [NCIT:C211]", + "meaning": "NCIT:C211" + }, + "Diabetes mellitus (diabetes) [HP:0000819]": { + "text": "Diabetes mellitus (diabetes) [HP:0000819]", + "description": "A group of abnormalities characterized by hyperglycemia and glucose intolerance.", + "meaning": "HP:0000819" + }, + "Type I diabetes mellitus (T1D) [HP:0100651]": { + "text": "Type I diabetes mellitus (T1D) [HP:0100651]", + "description": "A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin.", + "meaning": "HP:0100651", + "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" + }, + "Type II diabetes mellitus (T2D) [HP:0005978]": { + "text": "Type II diabetes mellitus (T2D) [HP:0005978]", + "description": "A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia.", + "meaning": "HP:0005978", + "is_a": "Diabetes mellitus (diabetes) [HP:0000819]" + }, + "Eczema [HP:0000964]": { + "text": "Eczema [HP:0000964]", + "meaning": "HP:0000964" + }, + "Electrolyte disturbance [HP:0003111]": { + "text": "Electrolyte disturbance [HP:0003111]", + "meaning": "HP:0003111" + }, + "Hypocalcemia [HP:0002901]": { + "text": "Hypocalcemia [HP:0002901]", + "meaning": "HP:0002901", + "is_a": "Electrolyte disturbance [HP:0003111]" + }, + "Hypokalemia [HP:0002900]": { + "text": "Hypokalemia [HP:0002900]", + "meaning": "HP:0002900", + "is_a": "Electrolyte disturbance [HP:0003111]" + }, + "Hypomagnesemia [HP:0002917]": { + "text": "Hypomagnesemia [HP:0002917]", + "meaning": "HP:0002917", + "is_a": "Electrolyte disturbance [HP:0003111]" + }, + "Encephalitis (brain inflammation) [HP:0002383]": { + "text": "Encephalitis (brain inflammation) [HP:0002383]", + "meaning": "HP:0002383" + }, + "Epilepsy [MONDO:0005027]": { + "text": "Epilepsy [MONDO:0005027]", + "meaning": "MONDO:0005027" + }, + "Hemodialysis [NCIT:C15248]": { + "text": "Hemodialysis [NCIT:C15248]", + "meaning": "NCIT:C15248" + }, + "Hemoglobinopathy [MONDO:0044348]": { + "text": "Hemoglobinopathy [MONDO:0044348]", + "meaning": "MONDO:0044348" + }, + "Human immunodeficiency virus (HIV) [MONDO:0005109]": { + "text": "Human immunodeficiency virus (HIV) [MONDO:0005109]", + "description": "An infection caused by the human immunodeficiency virus.", + "meaning": "MONDO:0005109" + }, + "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]": { + "text": "Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]", + "description": "A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes.", + "meaning": "MONDO:0012268", + "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" + }, + "HIV and antiretroviral therapy (ART) [NCIT:C16118]": { + "text": "HIV and antiretroviral therapy (ART) [NCIT:C16118]", + "description": "Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles.", + "meaning": "NCIT:C16118", + "is_a": "Human immunodeficiency virus (HIV) [MONDO:0005109]" + }, + "Immunocompromised [NCIT:C14139]": { + "text": "Immunocompromised [NCIT:C14139]", + "description": "A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions.", + "meaning": "NCIT:C14139" + }, + "Lupus [MONDO:0004670]": { + "text": "Lupus [MONDO:0004670]", + "description": "An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus.", + "meaning": "MONDO:0004670", + "is_a": "Immunocompromised [NCIT:C14139]" + }, + "Inflammatory bowel disease (IBD) [MONDO:0005265]": { + "text": "Inflammatory bowel disease (IBD) [MONDO:0005265]", + "meaning": "MONDO:0005265" + }, + "Colitis [HP:0002583]": { + "text": "Colitis [HP:0002583]", + "meaning": "HP:0002583", + "is_a": "Inflammatory bowel disease (IBD) [MONDO:0005265]" + }, + "Ulcerative colitis [HP:0100279]": { + "text": "Ulcerative colitis [HP:0100279]", + "meaning": "HP:0100279", + "is_a": "Colitis [HP:0002583]" + }, + "Crohn's disease [HP:0100280]": { + "text": "Crohn's disease [HP:0100280]", + "meaning": "HP:0100280", + "is_a": "Inflammatory bowel disease (IBD) [MONDO:0005265]" + }, + "Renal disorder [NCIT:C3149]": { + "text": "Renal disorder [NCIT:C3149]", + "meaning": "NCIT:C3149" + }, + "Renal disease [MONDO:0005240]": { + "text": "Renal disease [MONDO:0005240]", + "meaning": "MONDO:0005240", + "is_a": "Renal disorder [NCIT:C3149]" + }, + "Chronic renal disease [HP:0012622]": { + "text": "Chronic renal disease [HP:0012622]", + "meaning": "HP:0012622", + "is_a": "Renal disease [MONDO:0005240]" + }, + "Renal failure [HP:0000083]": { + "text": "Renal failure [HP:0000083]", + "meaning": "HP:0000083", + "is_a": "Renal disorder [NCIT:C3149]" + }, + "Liver disease [MONDO:0005154]": { + "text": "Liver disease [MONDO:0005154]", + "meaning": "MONDO:0005154" + }, + "Chronic liver disease [NCIT:C113609]": { + "text": "Chronic liver disease [NCIT:C113609]", + "meaning": "NCIT:C113609", + "is_a": "Liver disease [MONDO:0005154]" + }, + "Fatty liver disease (FLD) [HP:0001397]": { + "text": "Fatty liver disease (FLD) [HP:0001397]", + "meaning": "HP:0001397", + "is_a": "Chronic liver disease [NCIT:C113609]" + }, + "Myalgia (muscle pain) [HP:0003326]": { + "text": "Myalgia (muscle pain) [HP:0003326]", + "description": "Pain in muscle.", + "meaning": "HP:0003326" + }, + "Myalgic encephalomyelitis (ME) [MONDO:0005404]": { + "text": "Myalgic encephalomyelitis (ME) [MONDO:0005404]", + "meaning": "MONDO:0005404" + }, + "Neurological disorder [MONDO:0005071]": { + "text": "Neurological disorder [MONDO:0005071]", + "meaning": "MONDO:0005071" + }, + "Neuromuscular disorder [MONDO:0019056]": { + "text": "Neuromuscular disorder [MONDO:0019056]", + "meaning": "MONDO:0019056", + "is_a": "Neurological disorder [MONDO:0005071]" + }, + "Obesity [HP:0001513]": { + "text": "Obesity [HP:0001513]", + "meaning": "HP:0001513" + }, + "Severe obesity [MONDO:0005139]": { + "text": "Severe obesity [MONDO:0005139]", + "meaning": "MONDO:0005139", + "is_a": "Obesity [HP:0001513]" + }, + "Respiratory disorder [MONDO:0005087]": { + "text": "Respiratory disorder [MONDO:0005087]", + "meaning": "MONDO:0005087" + }, + "Asthma [HP:0002099]": { + "text": "Asthma [HP:0002099]", + "meaning": "HP:0002099", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Chronic bronchitis [HP:0004469]": { + "text": "Chronic bronchitis [HP:0004469]", + "meaning": "HP:0004469", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Chronic obstructive pulmonary disease [HP:0006510]": { + "text": "Chronic obstructive pulmonary disease [HP:0006510]", + "meaning": "HP:0006510", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Emphysema [HP:0002097]": { + "text": "Emphysema [HP:0002097]", + "meaning": "HP:0002097", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Lung disease [MONDO:0005275]": { + "text": "Lung disease [MONDO:0005275]", + "meaning": "MONDO:0005275", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Chronic lung disease [HP:0006528]": { + "text": "Chronic lung disease [HP:0006528]", + "meaning": "HP:0006528", + "is_a": "Lung disease [MONDO:0005275]" + }, + "Pulmonary fibrosis [HP:0002206]": { + "text": "Pulmonary fibrosis [HP:0002206]", + "meaning": "HP:0002206", + "is_a": "Lung disease [MONDO:0005275]" + }, + "Pneumonia [HP:0002090]": { + "text": "Pneumonia [HP:0002090]", + "meaning": "HP:0002090", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Respiratory failure [HP:0002878]": { + "text": "Respiratory failure [HP:0002878]", + "meaning": "HP:0002878", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Adult respiratory distress syndrome [HP:0033677]": { + "text": "Adult respiratory distress syndrome [HP:0033677]", + "meaning": "HP:0033677", + "is_a": "Respiratory failure [HP:0002878]" + }, + "Newborn respiratory distress syndrome [MONDO:0009971]": { + "text": "Newborn respiratory distress syndrome [MONDO:0009971]", + "meaning": "MONDO:0009971", + "is_a": "Respiratory failure [HP:0002878]" + }, + "Tuberculosis [MONDO:0018076]": { + "text": "Tuberculosis [MONDO:0018076]", + "meaning": "MONDO:0018076", + "is_a": "Respiratory disorder [MONDO:0005087]" + }, + "Postpartum (≤6 weeks) [GENEPIO:0100077]": { + "text": "Postpartum (≤6 weeks) [GENEPIO:0100077]", + "meaning": "GENEPIO:0100077" + }, + "Pregnancy [NCIT:C25742]": { + "text": "Pregnancy [NCIT:C25742]", + "description": "The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.", + "meaning": "NCIT:C25742" + }, + "Reye syndrome [DOID:14525]": { + "text": "Reye syndrome [DOID:14525]", + "meaning": "DOID:14525" + }, + "Rheumatic disease [MONDO:0005554]": { + "text": "Rheumatic disease [MONDO:0005554]", + "meaning": "MONDO:0005554" + }, + "Sickle cell disease [MONDO:0011382]": { + "text": "Sickle cell disease [MONDO:0011382]", + "meaning": "MONDO:0011382" + }, + "Substance use [NBO:0001845]": { + "text": "Substance use [NBO:0001845]", + "meaning": "NBO:0001845" + }, + "Alcohol abuse [MONDO:0002046]": { + "text": "Alcohol abuse [MONDO:0002046]", + "meaning": "MONDO:0002046", + "is_a": "Substance use [NBO:0001845]" + }, + "Drug abuse [GENEPIO:0100078]": { + "text": "Drug abuse [GENEPIO:0100078]", + "meaning": "GENEPIO:0100078", + "is_a": "Substance use [NBO:0001845]" + }, + "Injection drug abuse [GENEPIO:0100079]": { + "text": "Injection drug abuse [GENEPIO:0100079]", + "meaning": "GENEPIO:0100079", + "is_a": "Drug abuse [GENEPIO:0100078]" + }, + "Smoking [NBO:0015005]": { + "text": "Smoking [NBO:0015005]", + "meaning": "NBO:0015005", + "is_a": "Substance use [NBO:0001845]" + }, + "Vaping [NCIT:C173621]": { + "text": "Vaping [NCIT:C173621]", + "meaning": "NCIT:C173621", + "is_a": "Substance use [NBO:0001845]" + }, + "Tachypnea (accelerated respiratory rate) [HP:0002789]": { + "text": "Tachypnea (accelerated respiratory rate) [HP:0002789]", + "meaning": "HP:0002789" + }, + "Transplant [NCIT:C159659]": { + "text": "Transplant [NCIT:C159659]", + "meaning": "CIT:C159659" + }, + "Cardiac transplant [NCIT:C131759]": { + "text": "Cardiac transplant [NCIT:C131759]", + "meaning": "NCIT:C131759", + "is_a": "Transplant [NCIT:C159659]" + }, + "Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080]": { + "text": "Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080]", + "meaning": "GENEPIO:0100080", + "is_a": "Transplant [NCIT:C159659]" + }, + "Kidney transplant [NCIT:C157332]": { + "text": "Kidney transplant [NCIT:C157332]", + "meaning": "NCIT:C157332", + "is_a": "Transplant [NCIT:C159659]" + }, + "Liver transplant [GENEPIO:0100081]": { + "text": "Liver transplant [GENEPIO:0100081]", + "meaning": "GENEPIO:0100081", + "is_a": "Transplant [NCIT:C159659]" + } + } + }, + "ComplicationsMenu": { + "name": "ComplicationsMenu", + "title": "complications menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Abnormal blood oxygen level [HP:0500165]": { + "text": "Abnormal blood oxygen level [HP:0500165]", + "meaning": "HP:0500165" + }, + "Acute lung injury [MONDO:0015796]": { + "text": "Acute lung injury [MONDO:0015796]", + "meaning": "MONDO:0015796" + }, + "Ventilation induced lung injury (VILI) [GENEPIO:0100092]": { + "text": "Ventilation induced lung injury (VILI) [GENEPIO:0100092]", + "meaning": "GENEPIO:0100092", + "is_a": "Acute lung injury [MONDO:0015796]" + }, + "Acute respiratory failure [MONDO:0001208]": { + "text": "Acute respiratory failure [MONDO:0001208]", + "meaning": "MONDO:0001208" + }, + "Arrhythmia (complication) [HP:0011675]": { + "text": "Arrhythmia (complication) [HP:0011675]", + "meaning": "HP:0011675" + }, + "Tachycardia [HP:0001649]": { + "text": "Tachycardia [HP:0001649]", + "meaning": "HP:0001649", + "is_a": "Arrhythmia (complication) [HP:0011675]" + }, + "Cardiac injury [GENEPIO:0100074]": { + "text": "Cardiac injury [GENEPIO:0100074]", + "meaning": "GENEPIO:0100074" + }, + "Cardiac arrest [HP:0001695]": { + "text": "Cardiac arrest [HP:0001695]", + "meaning": "HP:0001695" + }, + "Blood clot [HP:0001977]": { + "text": "Blood clot [HP:0001977]", + "meaning": "HP:0001977" + }, + "Arterial clot [HP:0004420]": { + "text": "Arterial clot [HP:0004420]", + "meaning": "HP:0004420", + "is_a": "Blood clot [HP:0001977]" + }, + "Deep vein thrombosis (DVT) [HP:0002625]": { + "text": "Deep vein thrombosis (DVT) [HP:0002625]", + "meaning": "HP:0002625", + "is_a": "Blood clot [HP:0001977]" + }, + "Pulmonary embolism (PE) [HP:0002204]": { + "text": "Pulmonary embolism (PE) [HP:0002204]", + "meaning": "HP:0002204", + "is_a": "Blood clot [HP:0001977]" + }, + "Cardiomyopathy [HP:0001638]": { + "text": "Cardiomyopathy [HP:0001638]", + "meaning": "HP:0001638" + }, + "Central nervous system invasion [MONDO:0024619]": { + "text": "Central nervous system invasion [MONDO:0024619]", + "meaning": "MONDO:0024619" + }, + "Stroke (complication) [HP:0001297]": { + "text": "Stroke (complication) [HP:0001297]", + "meaning": "HP:0001297" + }, + "Central Nervous System Vasculitis [MONDO:0003346]": { + "text": "Central Nervous System Vasculitis [MONDO:0003346]", + "meaning": "MONDO:0003346", + "is_a": "Stroke (complication) [HP:0001297]" + }, + "Acute ischemic stroke [HP:0002140]": { + "text": "Acute ischemic stroke [HP:0002140]", + "meaning": "HP:0002140", + "is_a": "Stroke (complication) [HP:0001297]" + }, + "Coma [HP:0001259]": { + "text": "Coma [HP:0001259]", + "meaning": "HP:0001259" + }, + "Convulsions [HP:0011097]": { + "text": "Convulsions [HP:0011097]", + "meaning": "HP:0011097" + }, + "Cystic fibrosis [MONDO:0009061]": { + "text": "Cystic fibrosis [MONDO:0009061]", + "meaning": "MONDO:0009061" + }, + "Cytokine release syndrome [MONDO:0600008]": { + "text": "Cytokine release syndrome [MONDO:0600008]", + "meaning": "MONDO:0600008" + }, + "Disseminated intravascular coagulation (DIC) [MPATH:108]": { + "text": "Disseminated intravascular coagulation (DIC) [MPATH:108]", + "meaning": "MPATH:108" + }, + "Encephalopathy [HP:0001298]": { + "text": "Encephalopathy [HP:0001298]", + "meaning": "HP:0001298" + }, + "Fulminant myocarditis [GENEPIO:0100088]": { + "text": "Fulminant myocarditis [GENEPIO:0100088]", + "meaning": "GENEPIO:0100088" + }, + "Guillain-Barré syndrome [MONDO:0016218]": { + "text": "Guillain-Barré syndrome [MONDO:0016218]", + "meaning": "MONDO:0016218" + }, + "Internal hemorrhage (complication; internal bleeding) [HP:0011029]": { + "text": "Internal hemorrhage (complication; internal bleeding) [HP:0011029]", + "meaning": "HP:0011029" + }, + "Intracerebral haemorrhage [MONDO:0013792]": { + "text": "Intracerebral haemorrhage [MONDO:0013792]", + "meaning": "MONDO:0013792", + "is_a": "Internal hemorrhage (complication; internal bleeding) [HP:0011029]" + }, + "Kawasaki disease [MONDO:0012727]": { + "text": "Kawasaki disease [MONDO:0012727]", + "meaning": "MONDO:0012727" + }, + "Complete Kawasaki disease [GENEPIO:0100089]": { + "text": "Complete Kawasaki disease [GENEPIO:0100089]", + "meaning": "GENEPIO:0100089", + "is_a": "Kawasaki disease [MONDO:0012727]" + }, + "Incomplete Kawasaki disease [GENEPIO:0100090]": { + "text": "Incomplete Kawasaki disease [GENEPIO:0100090]", + "meaning": "GENEPIO:0100090", + "is_a": "Kawasaki disease [MONDO:0012727]" + }, + "Liver dysfunction [HP:0001410]": { + "text": "Liver dysfunction [HP:0001410]", + "meaning": "HP:0001410" + }, + "Acute liver injury [GENEPIO:0100091]": { + "text": "Acute liver injury [GENEPIO:0100091]", + "meaning": "GENEPIO:0100091", + "is_a": "Liver dysfunction [HP:0001410]" + }, + "Long COVID-19 [MONDO:0100233]": { + "text": "Long COVID-19 [MONDO:0100233]", + "meaning": "MONDO:0100233" + }, + "Meningitis [HP:0001287]": { + "text": "Meningitis [HP:0001287]", + "meaning": "HP:0001287" + }, + "Migraine [HP:0002076]": { + "text": "Migraine [HP:0002076]", + "meaning": "HP:0002076" + }, + "Miscarriage [HP:0005268]": { + "text": "Miscarriage [HP:0005268]", + "meaning": "HP:0005268" + }, + "Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]": { + "text": "Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]", + "meaning": "MONDO:0100163" + }, + "Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319]": { + "text": "Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319]", + "meaning": "MONDO:0100319" + }, + "Muscle injury [GENEPIO:0100093]": { + "text": "Muscle injury [GENEPIO:0100093]", + "meaning": "GENEPIO:0100093" + }, + "Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]": { + "text": "Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]", + "meaning": "MONDO:0005404" + }, + "Myocardial infarction (heart attack) [MONDO:0005068]": { + "text": "Myocardial infarction (heart attack) [MONDO:0005068]", + "meaning": "MONDO:0005068" + }, + "Myocardial injury [HP:0001700]": { + "text": "Myocardial injury [HP:0001700]", + "meaning": "HP:0001700" + }, + "Neonatal complications [NCIT:C168498]": { + "text": "Neonatal complications [NCIT:C168498]", + "meaning": "CIT:C168498" + }, + "Noncardiogenic pulmonary edema [GENEPIO:0100085]": { + "text": "Noncardiogenic pulmonary edema [GENEPIO:0100085]", + "meaning": "GENEPIO:0100085" + }, + "Acute respiratory distress syndrome (ARDS) [HP:0033677]": { + "text": "Acute respiratory distress syndrome (ARDS) [HP:0033677]", + "meaning": "HP:0033677", + "is_a": "Noncardiogenic pulmonary edema [GENEPIO:0100085]" + }, + "Organ failure [GENEPIO:0100094]": { + "text": "Organ failure [GENEPIO:0100094]", + "meaning": "GENEPIO:0100094" + }, + "Paralysis [HP:0003470]": { + "text": "Paralysis [HP:0003470]", + "meaning": "HP:0003470" + }, + "Pneumothorax (collapsed lung) [HP:0002107]": { + "text": "Pneumothorax (collapsed lung) [HP:0002107]", + "meaning": "HP:0002107" + }, + "Pneumonia (complication) [HP:0002090]": { + "text": "Pneumonia (complication) [HP:0002090]", + "meaning": "HP:0002090" + }, + "Pregancy complications [HP:0001197]": { + "text": "Pregancy complications [HP:0001197]", + "meaning": "HP:0001197" + }, + "Rhabdomyolysis [HP:0003201]": { + "text": "Rhabdomyolysis [HP:0003201]", + "meaning": "HP:0003201" + }, + "Secondary infection [IDO:0000567]": { + "text": "Secondary infection [IDO:0000567]", + "description": "An infection bearing the secondary infection role.", + "meaning": "IDO:0000567" + }, + "Seizure (complication) [HP:0001250]": { + "text": "Seizure (complication) [HP:0001250]", + "meaning": "HP:0001250" + }, + "Sepsis/Septicemia [HP:0100806]": { + "text": "Sepsis/Septicemia [HP:0100806]", + "description": "Systemic inflammatory response to infection.", + "meaning": "HP:0100806" + }, + "Sepsis (systemic inflammatory response to infection) [IDO:0000636]": { + "text": "Sepsis (systemic inflammatory response to infection) [IDO:0000636]", + "meaning": "IDO:0000636", + "is_a": "Sepsis/Septicemia [HP:0100806]" + }, + "Septicemia (bloodstream infection) [NCIT:C3364]": { + "text": "Septicemia (bloodstream infection) [NCIT:C3364]", + "meaning": "NCIT:C3364", + "is_a": "Sepsis/Septicemia [HP:0100806]" + }, + "Shock [HP:0031273]": { + "text": "Shock [HP:0031273]", + "meaning": "HP:0031273" + }, + "Hyperinflammatory shock [GENEPIO:0100097]": { + "text": "Hyperinflammatory shock [GENEPIO:0100097]", + "meaning": "GENEPIO:0100097", + "is_a": "Shock [HP:0031273]" + }, + "Septic shock [NCIT:C35018]": { + "text": "Septic shock [NCIT:C35018]", + "meaning": "NCIT:C35018", + "is_a": "Shock [HP:0031273]" + }, + "Vasculitis [HP:0002633]": { + "text": "Vasculitis [HP:0002633]", + "meaning": "HP:0002633" + } + } + }, + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "exposure_event menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Mass Gathering [GENEPIO:0100237]": { + "text": "Mass Gathering [GENEPIO:0100237]", + "description": "A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held.", + "meaning": "GENEPIO:0100237" + }, + "Convention [GENEPIO:0100238]": { + "text": "Convention [GENEPIO:0100238]", + "description": "A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom.", + "meaning": "GENEPIO:0100238", + "is_a": "Mass Gathering [GENEPIO:0100237]" + }, + "Convocation [GENEPIO:0100239]": { + "text": "Convocation [GENEPIO:0100239]", + "meaning": "GENEPIO:0100239", + "is_a": "Mass Gathering [GENEPIO:0100237]" + }, + "Agricultural Event [GENEPIO:0100240]": { + "text": "Agricultural Event [GENEPIO:0100240]", + "description": "A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry.", + "meaning": "GENEPIO:0100240", + "is_a": "Mass Gathering [GENEPIO:0100237]" + }, + "Religious Gathering [GENEPIO:0100241]": { + "text": "Religious Gathering [GENEPIO:0100241]", + "meaning": "GENEPIO:0100241" + }, + "Mass [GENEPIO:0100242]": { + "text": "Mass [GENEPIO:0100242]", + "meaning": "GENEPIO:0100242", + "is_a": "Religious Gathering [GENEPIO:0100241]" + }, + "Social Gathering [PCO:0000033]": { + "text": "Social Gathering [PCO:0000033]", + "description": "A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially.", + "meaning": "PCO:0000033" + }, + "Baby Shower [PCO:0000039]": { + "text": "Baby Shower [PCO:0000039]", + "meaning": "PCO:0000039", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Community Event [PCO:0000034]": { + "text": "Community Event [PCO:0000034]", + "meaning": "PCO:0000034", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Family Gathering [GENEPIO:0100243]": { + "text": "Family Gathering [GENEPIO:0100243]", + "meaning": "GENEPIO:0100243", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Family Reunion [GENEPIO:0100244]": { + "text": "Family Reunion [GENEPIO:0100244]", + "meaning": "GENEPIO:0100244", + "is_a": "Family Gathering [GENEPIO:0100243]" + }, + "Funeral [GENEPIO:0100245]": { + "text": "Funeral [GENEPIO:0100245]", + "meaning": "GENEPIO:0100245", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Party [PCO:0000035]": { + "text": "Party [PCO:0000035]", + "meaning": "PCO:0000035", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Potluck [PCO:0000037]": { + "text": "Potluck [PCO:0000037]", + "meaning": "PCO:0000037", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Wedding [PCO:0000038]": { + "text": "Wedding [PCO:0000038]", + "meaning": "PCO:0000038", + "is_a": "Social Gathering [PCO:0000033]" + }, + "Animal contact event [GENEPIO:0101183]": { + "text": "Animal contact event [GENEPIO:0101183]", + "meaning": "GENEPIO:0101183" + }, + "Trip to a live animal market [GENEPIO:0101185]": { + "text": "Trip to a live animal market [GENEPIO:0101185]", + "meaning": "GENEPIO:0101185", + "is_a": "Animal contact event [GENEPIO:0101183]" + }, + "Trip to a farm [GENEPIO:0101186]": { + "text": "Trip to a farm [GENEPIO:0101186]", + "meaning": "GENEPIO:0101186", + "is_a": "Animal contact event [GENEPIO:0101183]" + }, + "Wildlife encounter [GENEPIO:0101188]": { + "text": "Wildlife encounter [GENEPIO:0101188]", + "meaning": "GENEPIO:0101188", + "is_a": "Animal contact event [GENEPIO:0101183]" + }, + "Hunting trip [GENEPIO:0101184]": { + "text": "Hunting trip [GENEPIO:0101184]", + "meaning": "GENEPIO:0101184", + "is_a": "Wildlife encounter [GENEPIO:0101188]" + }, + "Animal transportation event [GENEPIO:0101187]": { + "text": "Animal transportation event [GENEPIO:0101187]", + "meaning": "GENEPIO:0101187" + }, + "Other exposure event": { + "text": "Other exposure event" + } + } + }, + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "exposure_contact_level menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Contact with infected animal [GENEPIO:0101189]": { + "text": "Contact with infected animal [GENEPIO:0101189]", + "meaning": "GENEPIO:0101189" + }, + "Direct (host-to-animal contact) [GENEPIO:0101190]": { + "text": "Direct (host-to-animal contact) [GENEPIO:0101190]", + "meaning": "GENEPIO:0101190", + "is_a": "Contact with infected animal [GENEPIO:0101189]" + }, + "Indirect contact (host-to-animal) [GENEPIO:0101191]": { + "text": "Indirect contact (host-to-animal) [GENEPIO:0101191]", + "meaning": "GENEPIO:0101191", + "is_a": "Contact with infected animal [GENEPIO:0101189]" + }, + "Close animal contact (face-to-face contact) [GENEPIO:0101192]": { + "text": "Close animal contact (face-to-face contact) [GENEPIO:0101192]", + "meaning": "GENEPIO:0101192", + "is_a": "Indirect contact (host-to-animal) [GENEPIO:0101191]" + }, + "Casual animal contact [GENEPIO:0101193]": { + "text": "Casual animal contact [GENEPIO:0101193]", + "meaning": "GENEPIO:0101193", + "is_a": "Indirect contact (host-to-animal) [GENEPIO:0101191]" + }, + "Contact with infected individual": { + "text": "Contact with infected individual" + }, + "Direct (human-to-human contact) [TRANS:0000001]": { + "text": "Direct (human-to-human contact) [TRANS:0000001]", + "description": "Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission.", + "meaning": "TRANS:0000001", + "is_a": "Contact with infected individual" + }, + "Indirect contact [GENEPIO:0100246]": { + "text": "Indirect contact [GENEPIO:0100246]", + "description": "A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces.", + "meaning": "GENEPIO:0100246", + "is_a": "Contact with infected individual" + }, + "Close contact (face-to-face contact) [GENEPIO:0100247]": { + "text": "Close contact (face-to-face contact) [GENEPIO:0100247]", + "description": "A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time.", + "meaning": "GENEPIO:0100247", + "is_a": "Indirect contact [GENEPIO:0100246]" + }, + "Casual contact [GENEPIO:0100248]": { + "text": "Casual contact [GENEPIO:0100248]", + "description": "A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission.", + "meaning": "GENEPIO:0100248", + "is_a": "Indirect contact [GENEPIO:0100246]" + } + } + }, + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "host_role menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Attendee [GENEPIO:0100249]": { + "text": "Attendee [GENEPIO:0100249]", + "description": "A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place.", + "meaning": "GENEPIO:0100249" + }, + "Student [OMRSE:00000058]": { + "text": "Student [OMRSE:00000058]", + "description": "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes.", + "meaning": "OMRSE:00000058", + "is_a": "Attendee [GENEPIO:0100249]" + }, + "Patient [OMRSE:00000030]": { + "text": "Patient [OMRSE:00000030]", + "description": "A patient role that inheres in a human being.", + "meaning": "OMRSE:00000030" + }, + "Inpatient [NCIT:C25182]": { + "text": "Inpatient [NCIT:C25182]", + "description": "A patient who is residing in the hospital where he is being treated.", + "meaning": "NCIT:C25182", + "is_a": "Patient [OMRSE:00000030]" + }, + "Outpatient [NCIT:C28293]": { + "text": "Outpatient [NCIT:C28293]", + "description": "A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay.", + "meaning": "NCIT:C28293", + "is_a": "Patient [OMRSE:00000030]" + }, + "Passenger [GENEPIO:0100250]": { + "text": "Passenger [GENEPIO:0100250]", + "description": "A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination.", + "meaning": "GENEPIO:0100250" + }, + "Resident [GENEPIO:0100251]": { + "text": "Resident [GENEPIO:0100251]", + "description": "A role inhering in a person that is realized when the bearer maintains residency in a given place.", + "meaning": "GENEPIO:0100251" + }, + "Visitor [GENEPIO:0100252]": { + "text": "Visitor [GENEPIO:0100252]", + "description": "A role inhering in a person that is realized when the bearer pays a visit to a specific place or event.", + "meaning": "GENEPIO:0100252" + }, + "Volunteer [GENEPIO:0100253]": { + "text": "Volunteer [GENEPIO:0100253]", + "description": "A role inhering in a person that is realized when the bearer enters into any service of their own free will.", + "meaning": "GENEPIO:0100253" + }, + "Work [GENEPIO:0100254]": { + "text": "Work [GENEPIO:0100254]", + "description": "A role inhering in a person that is realized when the bearer performs labor for a living.", + "meaning": "GENEPIO:0100254" + }, + "Administrator [GENEPIO:0100255]": { + "text": "Administrator [GENEPIO:0100255]", + "description": "A role inhering in a person that is realized when the bearer is engaged in administration or administrative work.", + "meaning": "GENEPIO:0100255", + "is_a": "Work [GENEPIO:0100254]" + }, + "First Responder [GENEPIO:0100256]": { + "text": "First Responder [GENEPIO:0100256]", + "description": "A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance.", + "meaning": "GENEPIO:0100256", + "is_a": "Work [GENEPIO:0100254]" + }, + "Firefighter [GENEPIO:0100257]": { + "text": "Firefighter [GENEPIO:0100257]", + "meaning": "GENEPIO:0100257", + "is_a": "First Responder [GENEPIO:0100256]" + }, + "Paramedic [GENEPIO:0100258]": { + "text": "Paramedic [GENEPIO:0100258]", + "meaning": "GENEPIO:0100258", + "is_a": "First Responder [GENEPIO:0100256]" + }, + "Police Officer [GENEPIO:0100259]": { + "text": "Police Officer [GENEPIO:0100259]", + "meaning": "GENEPIO:0100259", + "is_a": "First Responder [GENEPIO:0100256]" + }, + "Housekeeper [GENEPIO:0100260]": { + "text": "Housekeeper [GENEPIO:0100260]", + "description": "A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff.", + "meaning": "GENEPIO:0100260", + "is_a": "Work [GENEPIO:0100254]" + }, + "Kitchen Worker [GENEPIO:0100261]": { + "text": "Kitchen Worker [GENEPIO:0100261]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen.", + "meaning": "GENEPIO:0100261", + "is_a": "Work [GENEPIO:0100254]" + }, + "Healthcare Worker [GENEPIO:0100334]": { + "text": "Healthcare Worker [GENEPIO:0100334]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting.", + "meaning": "GENEPIO:0100334", + "is_a": "Work [GENEPIO:0100254]" + }, + "Community Healthcare Worker [GENEPIO:0100420]": { + "text": "Community Healthcare Worker [GENEPIO:0100420]", + "description": "A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home.", + "meaning": "GENEPIO:0100420", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Laboratory Worker [GENEPIO:0100262]": { + "text": "Laboratory Worker [GENEPIO:0100262]", + "description": "A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory.", + "meaning": "GENEPIO:0100262", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Nurse [OMRSE:00000014]": { + "text": "Nurse [OMRSE:00000014]", + "description": "A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life.", + "meaning": "OMRSE:00000014", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Personal Care Aid [GENEPIO:0100263]": { + "text": "Personal Care Aid [GENEPIO:0100263]", + "description": "A role inhering in a person that is realized when the bearer works to help another person complete their daily activities.", + "meaning": "GENEPIO:0100263", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Pharmacist [GENEPIO:0100264]": { + "text": "Pharmacist [GENEPIO:0100264]", + "description": "A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility.", + "meaning": "GENEPIO:0100264", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Physician [OMRSE:00000013]": { + "text": "Physician [OMRSE:00000013]", + "description": "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments.", + "meaning": "OMRSE:00000013", + "is_a": "Healthcare Worker [GENEPIO:0100334]" + }, + "Rotational Worker [GENEPIO:0100354]": { + "text": "Rotational Worker [GENEPIO:0100354]", + "description": "A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live.", + "meaning": "GENEPIO:0100354", + "is_a": "Work [GENEPIO:0100254]" + }, + "Seasonal Worker [GENEPIO:0100355]": { + "text": "Seasonal Worker [GENEPIO:0100355]", + "description": "A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas.", + "meaning": "GENEPIO:0100355", + "is_a": "Work [GENEPIO:0100254]" + }, + "Veterinarian [GENEPIO:0100265]": { + "text": "Veterinarian [GENEPIO:0100265]", + "description": "A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine.", + "meaning": "GENEPIO:0100265", + "is_a": "Work [GENEPIO:0100254]" + }, + "Social role [OMRSE:00000001]": { + "text": "Social role [OMRSE:00000001]", + "description": "A social role inhering in a human being.", + "meaning": "OMRSE:00000001" + }, + "Acquaintance of case [GENEPIO:0100266]": { + "text": "Acquaintance of case [GENEPIO:0100266]", + "description": "A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person.", + "meaning": "GENEPIO:0100266", + "is_a": "Social role [OMRSE:00000001]" + }, + "Relative of case [GENEPIO:0100267]": { + "text": "Relative of case [GENEPIO:0100267]", + "description": "A role inhering in a person that is realized when the bearer is a relative of the case.", + "meaning": "GENEPIO:0100267", + "is_a": "Social role [OMRSE:00000001]" + }, + "Child of case [GENEPIO:0100268]": { + "text": "Child of case [GENEPIO:0100268]", + "description": "A role inhering in a person that is realized when the bearer is a person younger than the age of majority.", + "meaning": "GENEPIO:0100268", + "is_a": "Relative of case [GENEPIO:0100267]" + }, + "Parent of case [GENEPIO:0100269]": { + "text": "Parent of case [GENEPIO:0100269]", + "description": "A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species.", + "meaning": "GENEPIO:0100269", + "is_a": "Relative of case [GENEPIO:0100267]" + }, + "Father of case [GENEPIO:0100270]": { + "text": "Father of case [GENEPIO:0100270]", + "description": "A role inhering in a person that is realized when the bearer is the male parent of a child.", + "meaning": "GENEPIO:0100270", + "is_a": "Parent of case [GENEPIO:0100269]" + }, + "Mother of case [GENEPIO:0100271]": { + "text": "Mother of case [GENEPIO:0100271]", + "description": "A role inhering in a person that is realized when the bearer is the female parent of a child.", + "meaning": "GENEPIO:0100271", + "is_a": "Parent of case [GENEPIO:0100269]" + }, + "Spouse of case [GENEPIO:0100272]": { + "text": "Spouse of case [GENEPIO:0100272]", + "description": "A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage.", + "meaning": "GENEPIO:0100272", + "is_a": "Social role [OMRSE:00000001]" + }, + "Other Host Role": { + "text": "Other Host Role" + } + } + }, + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "exposure_setting menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Human Exposure [ECTO:3000005]": { + "text": "Human Exposure [ECTO:3000005]", + "description": "A history of exposure to Homo sapiens.", + "meaning": "ECTO:3000005" + }, + "Contact with Patient [GENEPIO:0100185]": { + "text": "Contact with Patient [GENEPIO:0100185]", + "description": "A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100185", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]": { + "text": "Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]", + "meaning": "GENEPIO:0100187", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Contact with Person with Fever and/or Cough [GENEPIO:0100188]": { + "text": "Contact with Person with Fever and/or Cough [GENEPIO:0100188]", + "meaning": "GENEPIO:0100188", + "is_a": "Human Exposure [ECTO:3000005]" + }, + "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]": { + "text": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]", + "description": "A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100190" + }, + "Abbatoir [ECTO:1000033]": { + "text": "Abbatoir [ECTO:1000033]", + "description": "A exposure event involving the interaction of an exposure receptor to abattoir.", + "meaning": "ECTO:1000033", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Animal Rescue [GENEPIO:0100191]": { + "text": "Animal Rescue [GENEPIO:0100191]", + "description": "A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100191", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Childcare [GENEPIO:0100192]": { + "text": "Childcare [GENEPIO:0100192]", + "description": "A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100192", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Daycare [GENEPIO:0100193]": { + "text": "Daycare [GENEPIO:0100193]", + "description": "A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100193", + "is_a": "Childcare [GENEPIO:0100192]" + }, + "Nursery [GENEPIO:0100194]": { + "text": "Nursery [GENEPIO:0100194]", + "description": "A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100194", + "is_a": "Childcare [GENEPIO:0100192]" + }, + "Community Service Centre [GENEPIO:0100195]": { + "text": "Community Service Centre [GENEPIO:0100195]", + "description": "A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100195", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Correctional Facility [GENEPIO:0100196]": { + "text": "Correctional Facility [GENEPIO:0100196]", + "description": "A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100196", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Dormitory [GENEPIO:0100197]": { + "text": "Dormitory [GENEPIO:0100197]", + "description": "A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100197", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Farm [ECTO:1000034]": { + "text": "Farm [ECTO:1000034]", + "description": "A exposure event involving the interaction of an exposure receptor to farm", + "meaning": "ECTO:1000034", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "First Nations Reserve [GENEPIO:0100198]": { + "text": "First Nations Reserve [GENEPIO:0100198]", + "description": "A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100198", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Funeral Home [GENEPIO:0100199]": { + "text": "Funeral Home [GENEPIO:0100199]", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100199", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Group Home [GENEPIO:0100200]": { + "text": "Group Home [GENEPIO:0100200]", + "description": "A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100200", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Healthcare Setting [GENEPIO:0100201]": { + "text": "Healthcare Setting [GENEPIO:0100201]", + "description": "A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100201", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Ambulance [GENEPIO:0100202]": { + "text": "Ambulance [GENEPIO:0100202]", + "description": "A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100202", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Acute Care Facility [GENEPIO:0100203]": { + "text": "Acute Care Facility [GENEPIO:0100203]", + "description": "A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100203", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Clinic [GENEPIO:0100204]": { + "text": "Clinic [GENEPIO:0100204]", + "description": "A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100204", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Community Healthcare (At-Home) Setting [GENEPIO:0100415]": { + "text": "Community Healthcare (At-Home) Setting [GENEPIO:0100415]", + "description": "A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home.", + "meaning": "GENEPIO:0100415", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Community Health Centre [GENEPIO:0100205]": { + "text": "Community Health Centre [GENEPIO:0100205]", + "description": "A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100205", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Hospital [ECTO:1000035]": { + "text": "Hospital [ECTO:1000035]", + "description": "A exposure event involving the interaction of an exposure receptor to hospital.", + "meaning": "ECTO:1000035", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Emergency Department [GENEPIO:0100206]": { + "text": "Emergency Department [GENEPIO:0100206]", + "description": "A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100206", + "is_a": "Hospital [ECTO:1000035]" + }, + "ICU [GENEPIO:0100207]": { + "text": "ICU [GENEPIO:0100207]", + "description": "A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100207", + "is_a": "Hospital [ECTO:1000035]" + }, + "Ward [GENEPIO:0100208]": { + "text": "Ward [GENEPIO:0100208]", + "description": "A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100208", + "is_a": "Hospital [ECTO:1000035]" + }, + "Laboratory [ECTO:1000036]": { + "text": "Laboratory [ECTO:1000036]", + "description": "A exposure event involving the interaction of an exposure receptor to laboratory facility.", + "meaning": "ECTO:1000036", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Long-Term Care Facility [GENEPIO:0100209]": { + "text": "Long-Term Care Facility [GENEPIO:0100209]", + "description": "A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100209", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Pharmacy [GENEPIO:0100210]": { + "text": "Pharmacy [GENEPIO:0100210]", + "description": "A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100210", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Physician's Office [GENEPIO:0100211]": { + "text": "Physician's Office [GENEPIO:0100211]", + "description": "A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100211", + "is_a": "Healthcare Setting [GENEPIO:0100201]" + }, + "Household [GENEPIO:0100212]": { + "text": "Household [GENEPIO:0100212]", + "description": "A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100212", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Insecure Housing (Homeless) [GENEPIO:0100213]": { + "text": "Insecure Housing (Homeless) [GENEPIO:0100213]", + "description": "A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing.", + "meaning": "GENEPIO:0100213", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Occupational Exposure [GENEPIO:0100214]": { + "text": "Occupational Exposure [GENEPIO:0100214]", + "description": "A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100214", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Worksite [GENEPIO:0100215]": { + "text": "Worksite [GENEPIO:0100215]", + "description": "A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100215", + "is_a": "Occupational Exposure [GENEPIO:0100214]" + }, + "Office [ECTO:1000037]": { + "text": "Office [ECTO:1000037]", + "description": "A exposure event involving the interaction of an exposure receptor to office.", + "meaning": "ECTO:1000037", + "is_a": "Worksite [GENEPIO:0100215]" + }, + "Outdoors [GENEPIO:0100216]": { + "text": "Outdoors [GENEPIO:0100216]", + "description": "A process occuring outdoors that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100216", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Camp/camping [ECTO:5000009]": { + "text": "Camp/camping [ECTO:5000009]", + "description": "A exposure event involving the interaction of an exposure receptor to campground.", + "meaning": "ECTO:5000009", + "is_a": "Outdoors [GENEPIO:0100216]" + }, + "Hiking Trail [GENEPIO:0100217]": { + "text": "Hiking Trail [GENEPIO:0100217]", + "description": "A process that exposes the recipient organism to a material entity as a consequence of hiking.", + "meaning": "GENEPIO:0100217", + "is_a": "Outdoors [GENEPIO:0100216]" + }, + "Hunting Ground [ECTO:6000030]": { + "text": "Hunting Ground [ECTO:6000030]", + "description": "An exposure event involving hunting behavior", + "meaning": "ECTO:6000030", + "is_a": "Outdoors [GENEPIO:0100216]" + }, + "Petting zoo [ECTO:5000008]": { + "text": "Petting zoo [ECTO:5000008]", + "description": "A exposure event involving the interaction of an exposure receptor to petting zoo.", + "meaning": "ECTO:5000008", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Place of Worship [GENEPIO:0100220]": { + "text": "Place of Worship [GENEPIO:0100220]", + "description": "A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100220", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Church [GENEPIO:0100221]": { + "text": "Church [GENEPIO:0100221]", + "description": "A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100221", + "is_a": "Place of Worship [GENEPIO:0100220]" + }, + "Mosque [GENEPIO:0100222]": { + "text": "Mosque [GENEPIO:0100222]", + "description": "A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100222", + "is_a": "Place of Worship [GENEPIO:0100220]" + }, + "Temple [GENEPIO:0100223]": { + "text": "Temple [GENEPIO:0100223]", + "description": "A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100223", + "is_a": "Place of Worship [GENEPIO:0100220]" + }, + "Restaurant [ECTO:1000040]": { + "text": "Restaurant [ECTO:1000040]", + "description": "A exposure event involving the interaction of an exposure receptor to restaurant.", + "meaning": "ECTO:1000040", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Retail Store [ECTO:1000041]": { + "text": "Retail Store [ECTO:1000041]", + "description": "A exposure event involving the interaction of an exposure receptor to shop.", + "meaning": "ECTO:1000041", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "School [GENEPIO:0100224]": { + "text": "School [GENEPIO:0100224]", + "description": "A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100224", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Temporary Residence [GENEPIO:0100225]": { + "text": "Temporary Residence [GENEPIO:0100225]", + "description": "A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100225", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Homeless Shelter [GENEPIO:0100226]": { + "text": "Homeless Shelter [GENEPIO:0100226]", + "description": "A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100226", + "is_a": "Temporary Residence [GENEPIO:0100225]" + }, + "Hotel [GENEPIO:0100227]": { + "text": "Hotel [GENEPIO:0100227]", + "description": "A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100227", + "is_a": "Temporary Residence [GENEPIO:0100225]" + }, + "Veterinary Care Clinic [GENEPIO:0100228]": { + "text": "Veterinary Care Clinic [GENEPIO:0100228]", + "description": "A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100228", + "is_a": "Occupational, Residency or Patronage Exposure [GENEPIO:0100190]" + }, + "Travel Exposure [GENEPIO:0100229]": { + "text": "Travel Exposure [GENEPIO:0100229]", + "description": "A process occuring as a result of travel that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100229" + }, + "Travelled on a Cruise Ship [GENEPIO:0100230]": { + "text": "Travelled on a Cruise Ship [GENEPIO:0100230]", + "description": "A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100230", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled on a Plane [GENEPIO:0100231]": { + "text": "Travelled on a Plane [GENEPIO:0100231]", + "description": "A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100231", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled on Ground Transport [GENEPIO:0100232]": { + "text": "Travelled on Ground Transport [GENEPIO:0100232]", + "description": "A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100232", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled outside Province/Territory [GENEPIO:0001118]": { + "text": "Travelled outside Province/Territory [GENEPIO:0001118]", + "meaning": "GENEPIO:0001118", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Travelled outside Canada [GENEPIO:0001119]": { + "text": "Travelled outside Canada [GENEPIO:0001119]", + "meaning": "GENEPIO:0001119", + "is_a": "Travel Exposure [GENEPIO:0100229]" + }, + "Other Exposure Setting [GENEPIO:0100235]": { + "text": "Other Exposure Setting [GENEPIO:0100235]", + "description": "A process occuring that exposes the recipient organism to a material entity.", + "meaning": "GENEPIO:0100235" + } + } + }, + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "host_vaccination_status menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Fully Vaccinated [GENEPIO:0100100]": { + "text": "Fully Vaccinated [GENEPIO:0100100]", + "description": "Completed a full series of an authorized vaccine according to the regional health institutional guidance.", + "meaning": "GENEPIO:0100100" + }, + "Not Vaccinated [GENEPIO:0100102]": { + "text": "Not Vaccinated [GENEPIO:0100102]", + "description": "Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance.", + "meaning": "GENEPIO:0100102" + } + } + }, + "InfluenzaAntiviralTreatmentAdministrationMenu": { + "name": "InfluenzaAntiviralTreatmentAdministrationMenu", + "title": "influenza_antiviral_treatment_administration menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Influenza antiviral treatment administered [GENEPIO:0101194]": { + "text": "Influenza antiviral treatment administered [GENEPIO:0101194]", + "meaning": "GENEPIO:0101194" + }, + "No influenza antiviral treatment administered [GENEPIO:0101195]": { + "text": "No influenza antiviral treatment administered [GENEPIO:0101195]", + "meaning": "GENEPIO:0101195" + } + } + }, + "WaterCatchmentAreaHumanPopulationRangeMenu": { + "name": "WaterCatchmentAreaHumanPopulationRangeMenu", + "title": "water_catchment_area_human_population_range menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "<10 people": { + "text": "<10 people" + }, + "10 - 100 people": { + "text": "10 - 100 people" + }, + "100 - 1,000 people": { + "text": "100 - 1,000 people" + }, + "1,000 - 10,000 people": { + "text": "1,000 - 10,000 people" + }, + "10,000 - 100,000 people": { + "text": "10,000 - 100,000 people" + }, + "100,000 - 1,000,000 people": { + "text": "100,000 - 1,000,000 people" + }, + "1,000,000+ people": { + "text": "1,000,000+ people" + } + } + }, + "WaterCatchmentAreaHumanPopulationDensityUnitMenu": { + "name": "WaterCatchmentAreaHumanPopulationDensityUnitMenu", + "title": "water_catchment_area_human_population_density_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "persons per square mile [GENEPIO:0100989]": { + "text": "persons per square mile [GENEPIO:0100989]", + "description": "A unit of population density that describes the average number of people in a square mile of a given area.", + "meaning": "GENEPIO:0100989" + }, + "persons per square kilometer [GENEPIO:0100990]": { + "text": "persons per square kilometer [GENEPIO:0100990]", + "description": "A unit of population density that describes the average number of people in a square kilometer of a given area.", + "meaning": "GENEPIO:0100990" + }, + "residents per square mile [GENEPIO:0100991]": { + "text": "residents per square mile [GENEPIO:0100991]", + "description": "A unit of population density that describes the average number of registered residents in a square mile of a given area.", + "meaning": "GENEPIO:0100991" + }, + "residents per square kilometer [GENEPIO:0100992]": { + "text": "residents per square kilometer [GENEPIO:0100992]", + "description": "A unit of population density that describes the average number of registered residents in a square kilometer of a given area.", + "meaning": "GENEPIO:0100992" + } + } + }, + "PopulatedAreaTypeMenu": { + "name": "PopulatedAreaTypeMenu", + "title": "populated_area_type menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Suburban [GSSO:011077]": { + "text": "Suburban [GSSO:011077]", + "description": "A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities.", + "meaning": "GSSO:011077" + }, + "Rural [GSSO:011078]": { + "text": "Rural [GSSO:011078]", + "description": "A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements.", + "meaning": "GSSO:011078" + }, + "Urban [GSSO:011080]": { + "text": "Urban [GSSO:011080]", + "description": "A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment.", + "meaning": "GSSO:011080" + } + } + }, + "SamplingWeatherConditionsMenu": { + "name": "SamplingWeatherConditionsMenu", + "title": "sampling_weather_conditions menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cloudy/Overcast [ENVO:03501418]": { + "text": "Cloudy/Overcast [ENVO:03501418]", + "description": "Atmospheric weather in which the sky is mostly or completely obscured by clouds.", + "meaning": "ENVO:03501418" + }, + "Partially cloudy [ENVO:03501419]": { + "text": "Partially cloudy [ENVO:03501419]", + "description": "Atmospheric weather in which the sky is partially obscured by clouds.", + "meaning": "ENVO:03501419", + "is_a": "Cloudy/Overcast [ENVO:03501418]" + }, + "Drizzle [ENVO:03501420]": { + "text": "Drizzle [ENVO:03501420]", + "description": "An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process.", + "meaning": "ENVO:03501420" + }, + "Fog [ENVO:01000844]": { + "text": "Fog [ENVO:01000844]", + "description": "A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.", + "meaning": "ENVO:01000844" + }, + "Rain [ENVO:01001564]": { + "text": "Rain [ENVO:01001564]", + "description": "An aggregate of raindrops falling to a planetary surface during a precipitation process.", + "meaning": "ENVO:01001564" + }, + "Snow [ENVO:01000406]": { + "text": "Snow [ENVO:01000406]", + "description": "Snow is an environmental material which is primarily composed of flakes of crystalline water ice.", + "meaning": "ENVO:01000406" + }, + "Storm [ENVO:01000876]": { + "text": "Storm [ENVO:01000876]", + "description": "A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.", + "meaning": "ENVO:01000876" + }, + "Sunny/Clear [ENVO:03501421]": { + "text": "Sunny/Clear [ENVO:03501421]", + "description": "Atmospheric weather in which the sun can be seen to shine brightly.", + "meaning": "ENVO:03501421" + } + } + }, + "PresamplingWeatherConditionsMenu": { + "name": "PresamplingWeatherConditionsMenu", + "title": "presampling_weather_conditions menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Cloudy/Overcast [ENVO:03501418]": { + "text": "Cloudy/Overcast [ENVO:03501418]", + "description": "Atmospheric weather in which the sky is mostly or completely obscured by clouds.", + "meaning": "ENVO:03501418" + }, + "Partially cloudy [ENVO:03501419]": { + "text": "Partially cloudy [ENVO:03501419]", + "description": "Atmospheric weather in which the sky is partially obscured by clouds.", + "meaning": "ENVO:03501419", + "is_a": "Cloudy/Overcast [ENVO:03501418]" + }, + "Drizzle [ENVO:03501420]": { + "text": "Drizzle [ENVO:03501420]", + "description": "An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process.", + "meaning": "ENVO:03501420" + }, + "Fog [ENVO:01000844]": { + "text": "Fog [ENVO:01000844]", + "description": "A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body.", + "meaning": "ENVO:01000844" + }, + "Rain [ENVO:01001564]": { + "text": "Rain [ENVO:01001564]", + "description": "An aggregate of raindrops falling to a planetary surface during a precipitation process.", + "meaning": "ENVO:01001564" + }, + "Snow [ENVO:01000406]": { + "text": "Snow [ENVO:01000406]", + "description": "Snow is an environmental material which is primarily composed of flakes of crystalline water ice.", + "meaning": "ENVO:01000406" + }, + "Storm [ENVO:01000876]": { + "text": "Storm [ENVO:01000876]", + "description": "A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates.", + "meaning": "ENVO:01000876" + }, + "Sunny/Clear [ENVO:03501421]": { + "text": "Sunny/Clear [ENVO:03501421]", + "description": "Atmospheric weather in which the sun can be seen to shine brightly.", + "meaning": "ENVO:03501421" + } + } + }, + "PrecipitationMeasurementUnitMenu": { + "name": "PrecipitationMeasurementUnitMenu", + "title": "precipitation_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "millimeter (mm) [UO:0000016]": { + "text": "millimeter (mm) [UO:0000016]", + "description": "A length unit which is defined as one thousandth of a meter.", + "meaning": "UO:0000016" + }, + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", + "meaning": "UO:0000015" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", + "meaning": "UO:0000008" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", + "meaning": "UO:0010011" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", + "meaning": "UO:0010013" + } + } + }, + "AirPressureMeasurementUnitMenu": { + "name": "AirPressureMeasurementUnitMenu", + "title": "air_pressure_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "atmosphere (atm) [EFO:0005212]": { + "text": "atmosphere (atm) [EFO:0005212]", + "description": "A non-SI unit of pressure defined as 101,325 pascals (Pa).", + "meaning": "EFO:0005212" + }, + "bar": { + "text": "bar" + }, + "pascal [UO:0000110]": { + "text": "pascal [UO:0000110]", + "description": "An SI unit of pressure defined as one newton per square meter (N/m^2).", + "meaning": "UO:0000110" + } + } + }, + "AmbientTemperatureMeasurementUnitMenu": { + "name": "AmbientTemperatureMeasurementUnitMenu", + "title": "ambient_temperature_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "TotalDailyFlowRateMeasurementUnitMenu": { + "name": "TotalDailyFlowRateMeasurementUnitMenu", + "title": "total_daily_flow_rate_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "cubic meter per second (m^3/s)": { + "text": "cubic meter per second (m^3/s)" + }, + "cubic meter per minute (m^3/min)": { + "text": "cubic meter per minute (m^3/min)" + }, + "cubic meter per hour (m^3/h)": { + "text": "cubic meter per hour (m^3/h)" + }, + "liter per second (L/s)": { + "text": "liter per second (L/s)" + }, + "liter per minute (L/min)": { + "text": "liter per minute (L/min)" + }, + "liter per hour (L/h)": { + "text": "liter per hour (L/h)" + }, + "liter per day (L/day)": { + "text": "liter per day (L/day)" + }, + "million gallons per day (MGD)": { + "text": "million gallons per day (MGD)" + } + } + }, + "InstantaneousFlowRateMeasurementUnitMenu": { + "name": "InstantaneousFlowRateMeasurementUnitMenu", + "title": "instantaneous_flow_rate_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "cubic meter per second (m^3/s)": { + "text": "cubic meter per second (m^3/s)" + }, + "cubic meter per minute (m^3/min)": { + "text": "cubic meter per minute (m^3/min)" + }, + "cubic meter per hour (m^3/h)": { + "text": "cubic meter per hour (m^3/h)" + }, + "liter per second (L/s)": { + "text": "liter per second (L/s)" + }, + "liter per minute (L/min)": { + "text": "liter per minute (L/min)" + }, + "liter per hour (L/h)": { + "text": "liter per hour (L/h)" + }, + "liter per day (L/day)": { + "text": "liter per day (L/day)" + }, + "million gallons per day (MGD)": { + "text": "million gallons per day (MGD)" + } + } + }, + "TurbidityMeasurementUnitMenu": { + "name": "TurbidityMeasurementUnitMenu", + "title": "turbidity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "nephelometric turbidity unit (NTU)": { + "text": "nephelometric turbidity unit (NTU)" + }, + "formazin nephelometric unit (FNU) [UO:0000318]": { + "text": "formazin nephelometric unit (FNU) [UO:0000318]", + "description": "A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin.", + "meaning": "UO:0000318" + } + } + }, + "DissolvedOxygenMeasurementUnitMenu": { + "name": "DissolvedOxygenMeasurementUnitMenu", + "title": "dissolved_oxygen_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "kilogram per cubic meter (kg/m^3) [UO:0000083]": { + "text": "kilogram per cubic meter (kg/m^3) [UO:0000083]", + "description": "An SI unit of density that is one thousandth of the density of water.", + "meaning": "UO:0000083" + }, + "part per million (ppm) [UO:0000169]": { + "text": "part per million (ppm) [UO:0000169]", + "description": "A unitless measure of density that represents one item out of a million.", + "meaning": "UO:0000169" + } + } + }, + "OxygenReductionPotentialOrpMeasurementUnitMenu": { + "name": "OxygenReductionPotentialOrpMeasurementUnitMenu", + "title": "oxygen_reduction_potential_(ORP)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milliVolt (mV) [UO:0000247]": { + "text": "milliVolt (mV) [UO:0000247]", + "description": "A non-SI unit of electromotive force that is one thousandth of a volt.", + "meaning": "UO:0000247" + } + } + }, + "ChemicalOxygenDemandCodMeasurementUnitMenu": { + "name": "ChemicalOxygenDemandCodMeasurementUnitMenu", + "title": "chemical_oxygen_demand_(COD)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + } + } + }, + "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu": { + "name": "CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu", + "title": "carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + } + } + }, + "TotalSuspendedSolidsTssMeasurementUnitMenu": { + "name": "TotalSuspendedSolidsTssMeasurementUnitMenu", + "title": "total_suspended_solids_(TSS)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", + "meaning": "UO:0000187" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "TotalDissolvedSolidsTdsMeasurementUnitMenu": { + "name": "TotalDissolvedSolidsTdsMeasurementUnitMenu", + "title": "total_dissolved_solids_(TDS)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", + "meaning": "UO:0000187" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "TotalSolidsTsMeasurementUnitMenu": { + "name": "TotalSolidsTsMeasurementUnitMenu", + "title": "total_solids_(TS)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "percent (%) [UO:0000187]": { + "text": "percent (%) [UO:0000187]", + "description": "A unitless measure that represents one in a hundred.", + "meaning": "UO:0000187" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "AlkalinityMeasurementUnitMenu": { + "name": "AlkalinityMeasurementUnitMenu", + "title": "alkalinity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milliequivalent per liter (meq/L)": { + "text": "milliequivalent per liter (meq/L)" + }, + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "parts per million [UO:0000169]": { + "text": "parts per million [UO:0000169]", + "description": "A unitless measure of density that represents one item out of a million.", + "meaning": "UO:0000169" + } + } + }, + "ConductivityMeasurementUnitMenu": { + "name": "ConductivityMeasurementUnitMenu", + "title": "conductivity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milliSiemen per centimeter (mS/cm)": { + "text": "milliSiemen per centimeter (mS/cm)" + }, + "microSiemen per centimeter (μS/cm)": { + "text": "microSiemen per centimeter (μS/cm)" + }, + "Siemen per meter (S/m)": { + "text": "Siemen per meter (S/m)" + } + } + }, + "SalinityMeasurementUnitMenu": { + "name": "SalinityMeasurementUnitMenu", + "title": "salinity_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "practical salinity unit (PSU)": { + "text": "practical salinity unit (PSU)" + }, + "weight for weight (% w/w)": { + "text": "weight for weight (% w/w)" + }, + "parts per thousand [UO:0000168]": { + "text": "parts per thousand [UO:0000168]", + "description": "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same.", + "meaning": "UO:0000168" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + } + } + }, + "TotalNitrogenTnMeasurementUnitMenu": { + "name": "TotalNitrogenTnMeasurementUnitMenu", + "title": "total_nitrogen_(TN)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "milligram per liter (mg/L) [UO:0000273]": { + "text": "milligram per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "gram per liter (g/L) [UO:0000175]": { + "text": "gram per liter (g/L) [UO:0000175]", + "description": "A non-SI unit of density that is a thousand kilograms per cubic meter.", + "meaning": "UO:0000175" + }, + "gram per total solids (g/gTS)": { + "text": "gram per total solids (g/gTS)" + } + } + }, + "TotalPhosphorpusTpMeasurementUnitMenu": { + "name": "TotalPhosphorpusTpMeasurementUnitMenu", + "title": "total_phosphorpus_(TP)_measurement_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "gram per total solids (g/gTS)": { + "text": "gram per total solids (g/gTS)" + }, + "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]": { + "text": "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]", + "description": "A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids.", + "meaning": "GENEPIO:0100998" + }, + "milligrams per liter (mg/L) [UO:0000273]": { + "text": "milligrams per liter (mg/L) [UO:0000273]", + "description": "A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter.", + "meaning": "UO:0000273" + }, + "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]": { + "text": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]", + "description": "A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume.", + "meaning": "GENEPIO:0100999" + } + } + }, + "FecalContaminationIndicatorMenu": { + "name": "FecalContaminationIndicatorMenu", + "title": "fecal contamination indicator menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "crAssphage [NCBITaxon:1211417]": { + "text": "crAssphage [NCBITaxon:1211417]", + "description": "CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome.", + "meaning": "NCBITaxon:1211417" + }, + "PMMoV / pepper mild mottle virus [NCBITaxon:12239]": { + "text": "PMMoV / pepper mild mottle virus [NCBITaxon:12239]", + "description": "A plant RNA virus that is abundant in human feces.", + "meaning": "NCBITaxon:12239" + }, + "Bacteroides HF183": { + "text": "Bacteroides HF183", + "description": "A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus.", + "meaning": "GENEPIO:0101000" + }, + "Lachnospiraceae Lachno3": { + "text": "Lachnospiraceae Lachno3", + "description": "A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria.", + "meaning": "GENEPIO:0101001" + }, + "F+ (male specific) coliphages": { + "text": "F+ (male specific) coliphages", + "description": "A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment.", + "meaning": "GENEPIO:0101002" + }, + "Stercobilin": { + "text": "Stercobilin", + "description": "Bile pigment found in fecal material.", + "meaning": "CHEBI:26756" + } + } + }, + "FecalContaminationUnitMenu": { + "name": "FecalContaminationUnitMenu", + "title": "fecal_contamination_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "log10 gene copies per 100 milliliter (log10 GC/100 mL)": { + "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)" + }, + "gene copies per liter (GC/L)": { + "text": "gene copies per liter (GC/L)" + }, + "PCR quantification cycle [UO:0010077]": { + "text": "PCR quantification cycle [UO:0010077]", + "description": "A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line.", + "meaning": "UO:0010077" + }, + "log10 gene copies per nanogram total DNA": { + "text": "log10 gene copies per nanogram total DNA" + } + } + }, + "UrinaryContaminationIndicatorMenu": { + "name": "UrinaryContaminationIndicatorMenu", + "title": "urinary_contamination_indicator menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Urobilin [CHEBI:36378]": { + "text": "Urobilin [CHEBI:36378]", + "description": "A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome.", + "meaning": "CHEBI:36378" + } + } + }, + "UrinaryContaminationUnitMenu": { + "name": "UrinaryContaminationUnitMenu", + "title": "urinary_contamination_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "nanograms per liter (ng/L) [EFO:0004382]": { + "text": "nanograms per liter (ng/L) [EFO:0004382]", + "description": "A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters.", + "meaning": "EFO:0004382" + } + } + }, + "FecalColiformCountUnitMenu": { + "name": "FecalColiformCountUnitMenu", + "title": "fecal_coliform_count_unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "colony forming units per milliliter (CFU/mL) [UO:0000213]": { + "text": "colony forming units per milliliter (CFU/mL) [UO:0000213]", + "description": "A unit of microbial density that describes the number of colony forming units within a milliliter of material.", + "meaning": "UO:0000213" + }, + "colony forming units per 100 milliliter (CFU/100 mL)": { + "text": "colony forming units per 100 milliliter (CFU/100 mL)" + }, + "colony forming units per grams total solids (CFU/gTS)": { + "text": "colony forming units per grams total solids (CFU/gTS)" + }, + "most probable number per milliliter (MPN/mL)": { + "text": "most probable number per milliliter (MPN/mL)" + }, + "most probable number per 100 milliliter (MPN/100 mL)": { + "text": "most probable number per 100 milliliter (MPN/100 mL)" + } + } + }, + "SampleTemperatureUnitAtCollectionMenu": { + "name": "SampleTemperatureUnitAtCollectionMenu", + "title": "sample_temperature_unit_(at collection) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "SampleTemperatureUnitWhenReceivedMenu": { + "name": "SampleTemperatureUnitWhenReceivedMenu", + "title": "sample_temperature_unit_(when received) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "SequencingAssayTypeMenu": { + "name": "SequencingAssayTypeMenu", + "title": "sequencing_assay_type menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Amplicon sequencing assay [OBI:0002767]": { + "text": "Amplicon sequencing assay [OBI:0002767]", + "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", + "meaning": "OBI:0002767" + }, + "16S ribosomal gene sequencing assay [OBI:0002763]": { + "text": "16S ribosomal gene sequencing assay [OBI:0002763]", + "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", + "meaning": "OBI:0002763", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "CRISPR amplicon sequencing assay [GENEPIO:0101128]": { + "text": "CRISPR amplicon sequencing assay [GENEPIO:0101128]", + "meaning": "GENEPIO:0101128", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "Primal tiling amplicon sequencing assay [GENEPIO:0101129]": { + "text": "Primal tiling amplicon sequencing assay [GENEPIO:0101129]", + "meaning": "GENEPIO:0101129", + "is_a": "Amplicon sequencing assay [OBI:0002767]" + }, + "Whole genome sequencing assay [OBI:0002117]": { + "text": "Whole genome sequencing assay [OBI:0002117]", + "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", + "meaning": "OBI:0002117" + }, + "Whole metagenome sequencing assay [OBI:0002623]": { + "text": "Whole metagenome sequencing assay [OBI:0002623]", + "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", + "meaning": "OBI:0002623" + }, + "Whole virome sequencing assay [OBI:0002768]": { + "text": "Whole virome sequencing assay [OBI:0002768]", + "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", + "meaning": "OBI:0002768", + "is_a": "Whole metagenome sequencing assay [OBI:0002623]" + } + } + }, + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose_of_sequencing menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Baseline surveillance (random sampling) [GENEPIO:0100005]": { + "text": "Baseline surveillance (random sampling) [GENEPIO:0100005]", + "description": "A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling.", + "meaning": "GENEPIO:0100005" + }, + "Targeted surveillance (non-random sampling) [GENEPIO:0100006]": { + "text": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]", + "description": "A surveillance sampling strategy in which an aspired outcome is explicitly stated.", + "meaning": "GENEPIO:0100006" + }, + "Priority surveillance project [GENEPIO:0100007]": { + "text": "Priority surveillance project [GENEPIO:0100007]", + "description": "A targeted surveillance strategy which is considered important and/or urgent.", + "meaning": "GENEPIO:0100007", + "is_a": "Targeted surveillance (non-random sampling) [GENEPIO:0100006]" + }, + "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]": { + "text": "Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]", + "description": "A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time.", + "meaning": "GENEPIO:0100009", + "is_a": "Priority surveillance project [GENEPIO:0100007]" + }, + "Cluster/Outbreak investigation [GENEPIO:0100019]": { + "text": "Cluster/Outbreak investigation [GENEPIO:0100019]", + "description": "A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak.", + "meaning": "GENEPIO:0100019" + }, + "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]": { + "text": "Multi-jurisdictional outbreak investigation [GENEPIO:0100020]", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions.", + "meaning": "GENEPIO:0100020", + "is_a": "Cluster/Outbreak investigation [GENEPIO:0100019]" + }, + "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]": { + "text": "Intra-jurisdictional outbreak investigation [GENEPIO:0100021]", + "description": "An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction.", + "meaning": "GENEPIO:0100021", + "is_a": "Cluster/Outbreak investigation [GENEPIO:0100019]" + }, + "Research [GENEPIO:0100022]": { + "text": "Research [GENEPIO:0100022]", + "description": "A sampling strategy in which sites are sampled in order to perform research.", + "meaning": "GENEPIO:0100022" + }, + "Viral passage experiment [GENEPIO:0100023]": { + "text": "Viral passage experiment [GENEPIO:0100023]", + "description": "A research sampling strategy in which samples are selected in order to perform a viral passage experiment.", + "meaning": "GENEPIO:0100023", + "is_a": "Research [GENEPIO:0100022]" + }, + "Protocol testing experiment [GENEPIO:0100024]": { + "text": "Protocol testing experiment [GENEPIO:0100024]", + "description": "A research sampling strategy in which samples are collected in order to test a method or protocol.", + "meaning": "GENEPIO:0100024", + "is_a": "Research [GENEPIO:0100022]" + }, + "Retrospective sequencing [GENEPIO:0100356]": { + "text": "Retrospective sequencing [GENEPIO:0100356]", + "description": "A sampling strategy in which stored samples from past events are sequenced.", + "meaning": "GENEPIO:0100356" + } + } + }, + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name_(country) menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Afghanistan [GAZ:00006882]": { + "text": "Afghanistan [GAZ:00006882]", + "description": "A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ]", + "meaning": "GAZ:00006882" + }, + "Albania [GAZ:00002953]": { + "text": "Albania [GAZ:00002953]", + "description": "A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ]", + "meaning": "GAZ:00002953" + }, + "Algeria [GAZ:00000563]": { + "text": "Algeria [GAZ:00000563]", + "description": "A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ]", + "meaning": "GAZ:00000563" + }, + "American Samoa [GAZ:00003957]": { + "text": "American Samoa [GAZ:00003957]", + "description": "An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ]", + "meaning": "GAZ:00003957" + }, + "Andorra [GAZ:00002948]": { + "text": "Andorra [GAZ:00002948]", + "description": "A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]", + "meaning": "GAZ:00002948" + }, + "Angola [GAZ:00001095]": { + "text": "Angola [GAZ:00001095]", + "description": "A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ]", + "meaning": "GAZ:00001095" + }, + "Anguilla [GAZ:00009159]": { + "text": "Anguilla [GAZ:00009159]", + "description": "A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ]", + "meaning": "GAZ:00009159" + }, + "Antarctica [GAZ:00000462]": { + "text": "Antarctica [GAZ:00000462]", + "description": "The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ]", + "meaning": "GAZ:00000462" + }, + "Antigua and Barbuda [GAZ:00006883]": { + "text": "Antigua and Barbuda [GAZ:00006883]", + "description": "An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ]", + "meaning": "GAZ:00006883" + }, + "Argentina [GAZ:00002928]": { + "text": "Argentina [GAZ:00002928]", + "description": "A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ]", + "meaning": "GAZ:00002928" + }, + "Armenia [GAZ:00004094]": { + "text": "Armenia [GAZ:00004094]", + "description": "A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ]", + "meaning": "GAZ:00004094" + }, + "Aruba [GAZ:00004025]": { + "text": "Aruba [GAZ:00004025]", + "description": "An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ]", + "meaning": "GAZ:00004025" + }, + "Ashmore and Cartier Islands [GAZ:00005901]": { + "text": "Ashmore and Cartier Islands [GAZ:00005901]", + "description": "A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ]", + "meaning": "GAZ:00005901" + }, + "Australia [GAZ:00000463]": { + "text": "Australia [GAZ:00000463]", + "description": "A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories.", + "meaning": "GAZ:00000463" + }, + "Austria [GAZ:00002942]": { + "text": "Austria [GAZ:00002942]", + "description": "A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities.", + "meaning": "GAZ:00002942" + }, + "Azerbaijan [GAZ:00004941]": { + "text": "Azerbaijan [GAZ:00004941]", + "description": "A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika).", + "meaning": "GAZ:00004941" + }, + "Bahamas [GAZ:00002733]": { + "text": "Bahamas [GAZ:00002733]", + "description": "A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government.", + "meaning": "GAZ:00002733" + }, + "Bahrain [GAZ:00005281]": { + "text": "Bahrain [GAZ:00005281]", + "description": "A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates.", + "meaning": "GAZ:00005281" + }, + "Baker Island [GAZ:00007117]": { + "text": "Baker Island [GAZ:00007117]", + "description": "An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US.", + "meaning": "GAZ:00007117" + }, + "Bangladesh [GAZ:00003750]": { + "text": "Bangladesh [GAZ:00003750]", + "description": "A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana (\"police stations\").", + "meaning": "GAZ:00003750" + }, + "Barbados [GAZ:00001251]": { + "text": "Barbados [GAZ:00001251]", + "description": "An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown.", + "meaning": "GAZ:00001251" + }, + "Bassas da India [GAZ:00005810]": { + "text": "Bassas da India [GAZ:00005810]", + "description": "A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below.", + "meaning": "GAZ:00005810" + }, + "Belarus [GAZ:00006886]": { + "text": "Belarus [GAZ:00006886]", + "description": "A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital.", + "meaning": "GAZ:00006886" + }, + "Belgium [GAZ:00002938]": { + "text": "Belgium [GAZ:00002938]", + "description": "A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977).", + "meaning": "GAZ:00002938" + }, + "Belize [GAZ:00002934]": { + "text": "Belize [GAZ:00002934]", + "description": "A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies.", + "meaning": "GAZ:00002934" + }, + "Benin [GAZ:00000904]": { + "text": "Benin [GAZ:00000904]", + "description": "A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes.", + "meaning": "GAZ:00000904" + }, + "Bermuda [GAZ:00001264]": { + "text": "Bermuda [GAZ:00001264]", + "description": "A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands.", + "meaning": "GAZ:00001264" + }, + "Bhutan [GAZ:00003920]": { + "text": "Bhutan [GAZ:00003920]", + "description": "A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog.", + "meaning": "GAZ:00003920" + }, + "Bolivia [GAZ:00002511]": { + "text": "Bolivia [GAZ:00002511]", + "description": "A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios).", + "meaning": "GAZ:00002511" + }, + "Borneo [GAZ:00025355]": { + "text": "Borneo [GAZ:00025355]", + "description": "An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres.", + "meaning": "GAZ:00025355" + }, + "Bosnia and Herzegovina [GAZ:00006887]": { + "text": "Bosnia and Herzegovina [GAZ:00006887]", + "description": "A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina.", + "meaning": "GAZ:00006887" + }, + "Botswana [GAZ:00001097]": { + "text": "Botswana [GAZ:00001097]", + "description": "A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts.", + "meaning": "GAZ:00001097" + }, + "Bouvet Island [GAZ:00001453]": { + "text": "Bouvet Island [GAZ:00001453]", + "description": "A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended.", + "meaning": "GAZ:00001453" + }, + "Brazil [GAZ:00002828]": { + "text": "Brazil [GAZ:00002828]", + "description": "A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South.", + "meaning": "GAZ:00002828" + }, + "British Virgin Islands [GAZ:00003961]": { + "text": "British Virgin Islands [GAZ:00003961]", + "description": "A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited.", + "meaning": "GAZ:00003961" + }, + "Brunei [GAZ:00003901]": { + "text": "Brunei [GAZ:00003901]", + "description": "A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages).", + "meaning": "GAZ:00003901" + }, + "Bulgaria [GAZ:00002950]": { + "text": "Bulgaria [GAZ:00002950]", + "description": "A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities.", + "meaning": "GAZ:00002950" + }, + "Burkina Faso [GAZ:00000905]": { + "text": "Burkina Faso [GAZ:00000905]", + "description": "A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes).", + "meaning": "GAZ:00000905" + }, + "Burundi [GAZ:00001090]": { + "text": "Burundi [GAZ:00001090]", + "description": "A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines.", + "meaning": "GAZ:00001090" + }, + "Cambodia [GAZ:00006888]": { + "text": "Cambodia [GAZ:00006888]", + "description": "A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand.", + "meaning": "GAZ:00006888" + }, + "Cameroon [GAZ:00001093]": { + "text": "Cameroon [GAZ:00001093]", + "description": "A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts.", + "meaning": "GAZ:00001093" + }, + "Canada [GAZ:00002560]": { + "text": "Canada [GAZ:00002560]", + "description": "A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada.", + "meaning": "GAZ:00002560" + }, + "Cape Verde [GAZ:00001227]": { + "text": "Cape Verde [GAZ:00001227]", + "description": "A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias).", + "meaning": "GAZ:00001227" + }, + "Cayman Islands [GAZ:00003986]": { + "text": "Cayman Islands [GAZ:00003986]", + "description": "A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts.", + "meaning": "GAZ:00003986" + }, + "Central African Republic [GAZ:00001089]": { + "text": "Central African Republic [GAZ:00001089]", + "description": "A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures).", + "meaning": "GAZ:00001089" + }, + "Chad [GAZ:00000586]": { + "text": "Chad [GAZ:00000586]", + "description": "A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change.", + "meaning": "GAZ:00000586" + }, + "Chile [GAZ:00002825]": { + "text": "Chile [GAZ:00002825]", + "description": "A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10.", + "meaning": "GAZ:00002825" + }, + "China [GAZ:00002845]": { + "text": "China [GAZ:00002845]", + "description": "A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions.", + "meaning": "GAZ:00002845" + }, + "Christmas Island [GAZ:00005915]": { + "text": "Christmas Island [GAZ:00005915]", + "description": "An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain.", + "meaning": "GAZ:00005915" + }, + "Clipperton Island [GAZ:00005838]": { + "text": "Clipperton Island [GAZ:00005838]", + "description": "A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica.", + "meaning": "GAZ:00005838" + }, + "Cocos Islands [GAZ:00009721]": { + "text": "Cocos Islands [GAZ:00009721]", + "description": "Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group.", + "meaning": "GAZ:00009721" + }, + "Colombia [GAZ:00002929]": { + "text": "Colombia [GAZ:00002929]", + "description": "A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities.", + "meaning": "GAZ:00002929" + }, + "Comoros [GAZ:00005820]": { + "text": "Comoros [GAZ:00005820]", + "description": "An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique.", + "meaning": "GAZ:00005820" + }, + "Cook Islands [GAZ:00053798]": { + "text": "Cook Islands [GAZ:00053798]", + "description": "A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean.", + "meaning": "GAZ:00053798" + }, + "Coral Sea Islands [GAZ:00005917]": { + "text": "Coral Sea Islands [GAZ:00005917]", + "description": "A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups.", + "meaning": "GAZ:00005917" + }, + "Costa Rica [GAZ:00002901]": { + "text": "Costa Rica [GAZ:00002901]", + "description": "A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons.", + "meaning": "GAZ:00002901" + }, + "Cote d'Ivoire [GAZ:00000906]": { + "text": "Cote d'Ivoire [GAZ:00000906]", + "description": "A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments.", + "meaning": "GAZ:00000906" + }, + "Croatia [GAZ:00002719]": { + "text": "Croatia [GAZ:00002719]", + "description": "A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district.", + "meaning": "GAZ:00002719" + }, + "Cuba [GAZ:00003762]": { + "text": "Cuba [GAZ:00003762]", + "description": "A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba.", + "meaning": "GAZ:00003762" + }, + "Curacao [GAZ:00012582]": { + "text": "Curacao [GAZ:00012582]", + "description": "One of five island areas of the Netherlands Antilles.", + "meaning": "GAZ:00012582" + }, + "Cyprus [GAZ:00004006]": { + "text": "Cyprus [GAZ:00004006]", + "description": "The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west.", + "meaning": "GAZ:00004006" + }, + "Czech Republic [GAZ:00002954]": { + "text": "Czech Republic [GAZ:00002954]", + "description": "A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named \"Little Districts\" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices.", + "meaning": "GAZ:00002954" + }, + "Democratic Republic of the Congo [GAZ:00001086]": { + "text": "Democratic Republic of the Congo [GAZ:00001086]", + "description": "A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones.", + "meaning": "GAZ:00001086" + }, + "Denmark [GAZ:00005852]": { + "text": "Denmark [GAZ:00005852]", + "description": "That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago.", + "meaning": "GAZ:00005852" + }, + "Djibouti [GAZ:00000582]": { + "text": "Djibouti [GAZ:00000582]", + "description": "A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts.", + "meaning": "GAZ:00000582" + }, + "Dominica [GAZ:00006890]": { + "text": "Dominica [GAZ:00006890]", + "description": "An island nation in the Caribbean Sea. Dominica is divided into ten parishes.", + "meaning": "GAZ:00006890" + }, + "Dominican Republic [GAZ:00003952]": { + "text": "Dominican Republic [GAZ:00003952]", + "description": "A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio).", + "meaning": "GAZ:00003952" + }, + "Ecuador [GAZ:00002912]": { + "text": "Ecuador [GAZ:00002912]", + "description": "A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias).", + "meaning": "GAZ:00002912" + }, + "Egypt [GAZ:00003934]": { + "text": "Egypt [GAZ:00003934]", + "description": "A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes).", + "meaning": "GAZ:00003934" + }, + "El Salvador [GAZ:00002935]": { + "text": "El Salvador [GAZ:00002935]", + "description": "A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios).", + "meaning": "GAZ:00002935" + }, + "Equatorial Guinea [GAZ:00001091]": { + "text": "Equatorial Guinea [GAZ:00001091]", + "description": "A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts.", + "meaning": "GAZ:00001091" + }, + "Eritrea [GAZ:00000581]": { + "text": "Eritrea [GAZ:00000581]", + "description": "A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts (\"sub-zobas\").", + "meaning": "GAZ:00000581" + }, + "Estonia [GAZ:00002959]": { + "text": "Estonia [GAZ:00002959]", + "description": "A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities.", + "meaning": "GAZ:00002959" + }, + "Eswatini [GAZ:00001099]": { + "text": "Eswatini [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", + "meaning": "GAZ:00001099" + }, + "Ethiopia [GAZ:00000567]": { + "text": "Ethiopia [GAZ:00000567]", + "description": "A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas.", + "meaning": "GAZ:00000567" + }, + "Europa Island [GAZ:00005811]": { + "text": "Europa Island [GAZ:00005811]", + "description": "A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique.", + "meaning": "GAZ:00005811" + }, + "Falkland Islands (Islas Malvinas) [GAZ:00001412]": { + "text": "Falkland Islands (Islas Malvinas) [GAZ:00001412]", + "description": "An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands.", + "meaning": "GAZ:00001412" + }, + "Faroe Islands [GAZ:00059206]": { + "text": "Faroe Islands [GAZ:00059206]", + "description": "An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie.", + "meaning": "GAZ:00059206" + }, + "Fiji [GAZ:00006891]": { + "text": "Fiji [GAZ:00006891]", + "description": "An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population.", + "meaning": "GAZ:00006891" + }, + "Finland [GAZ:00002937]": { + "text": "Finland [GAZ:00002937]", + "description": "A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta).", + "meaning": "GAZ:00002937" + }, + "France [GAZ:00003940]": { + "text": "France [GAZ:00003940]", + "description": "A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments.", + "meaning": "GAZ:00003940" + }, + "French Guiana [GAZ:00002516]": { + "text": "French Guiana [GAZ:00002516]", + "description": "An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes.", + "meaning": "GAZ:00002516" + }, + "French Polynesia [GAZ:00002918]": { + "text": "French Polynesia [GAZ:00002918]", + "description": "A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives).", + "meaning": "GAZ:00002918" + }, + "French Southern and Antarctic Lands [GAZ:00003753]": { + "text": "French Southern and Antarctic Lands [GAZ:00003753]", + "description": "The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts.", + "meaning": "GAZ:00003753" + }, + "Gabon [GAZ:00001092]": { + "text": "Gabon [GAZ:00001092]", + "description": "A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments.", + "meaning": "GAZ:00001092" + }, + "Gambia [GAZ:00000907]": { + "text": "Gambia [GAZ:00000907]", + "description": "A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts.", + "meaning": "GAZ:00000907" + }, + "Gaza Strip [GAZ:00009571]": { + "text": "Gaza Strip [GAZ:00009571]", + "description": "A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine.", + "meaning": "GAZ:00009571" + }, + "Georgia [GAZ:00004942]": { + "text": "Georgia [GAZ:00004942]", + "description": "A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni).", + "meaning": "GAZ:00004942" + }, + "Germany [GAZ:00002646]": { + "text": "Germany [GAZ:00002646]", + "description": "A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte).", + "meaning": "GAZ:00002646" + }, + "Ghana [GAZ:00000908]": { + "text": "Ghana [GAZ:00000908]", + "description": "A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts.", + "meaning": "GAZ:00000908" + }, + "Gibraltar [GAZ:00003987]": { + "text": "Gibraltar [GAZ:00003987]", + "description": "A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north.", + "meaning": "GAZ:00003987" + }, + "Glorioso Islands [GAZ:00005808]": { + "text": "Glorioso Islands [GAZ:00005808]", + "description": "A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar.", + "meaning": "GAZ:00005808" + }, + "Greece [GAZ:00002945]": { + "text": "Greece [GAZ:00002945]", + "description": "A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia.", + "meaning": "GAZ:00002945" + }, + "Greenland [GAZ:00001507]": { + "text": "Greenland [GAZ:00001507]", + "description": "A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago.", + "meaning": "GAZ:00001507" + }, + "Grenada [GAZ:02000573]": { + "text": "Grenada [GAZ:02000573]", + "description": "An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020.", + "meaning": "GAZ:02000573" + }, + "Guadeloupe [GAZ:00067142]": { + "text": "Guadeloupe [GAZ:00067142]", + "description": "An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica.", + "meaning": "GAZ:00067142" + }, + "Guam [GAZ:00003706]": { + "text": "Guam [GAZ:00003706]", + "description": "An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia.", + "meaning": "GAZ:00003706" + }, + "Guatemala [GAZ:00002936]": { + "text": "Guatemala [GAZ:00002936]", + "description": "A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios).", + "meaning": "GAZ:00002936" + }, + "Guernsey [GAZ:00001550]": { + "text": "Guernsey [GAZ:00001550]", + "description": "A British Crown Dependency in the English Channel off the coast of Normandy.", + "meaning": "GAZ:00001550" + }, + "Guinea [GAZ:00000909]": { + "text": "Guinea [GAZ:00000909]", + "description": "A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip.", + "meaning": "GAZ:00000909" + }, + "Guinea-Bissau [GAZ:00000910]": { + "text": "Guinea-Bissau [GAZ:00000910]", + "description": "A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea.", + "meaning": "GAZ:00000910" + }, + "Guyana [GAZ:00002522]": { + "text": "Guyana [GAZ:00002522]", + "description": "A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils.", + "meaning": "GAZ:00002522" + }, + "Haiti [GAZ:00003953]": { + "text": "Haiti [GAZ:00003953]", + "description": "A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions.", + "meaning": "GAZ:00003953" + }, + "Heard Island and McDonald Islands [GAZ:00009718]": { + "text": "Heard Island and McDonald Islands [GAZ:00009718]", + "description": "An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica.", + "meaning": "GAZ:00009718" + }, + "Honduras [GAZ:00002894]": { + "text": "Honduras [GAZ:00002894]", + "description": "A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan.", + "meaning": "GAZ:00002894" + }, + "Hong Kong [GAZ:00003203]": { + "text": "Hong Kong [GAZ:00003203]", + "description": "A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997.", + "meaning": "GAZ:00003203" + }, + "Howland Island [GAZ:00007120]": { + "text": "Howland Island [GAZ:00007120]", + "description": "An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands.", + "meaning": "GAZ:00007120" + }, + "Hungary [GAZ:00002952]": { + "text": "Hungary [GAZ:00002952]", + "description": "A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary.", + "meaning": "GAZ:00002952" + }, + "Iceland [GAZ:00000843]": { + "text": "Iceland [GAZ:00000843]", + "description": "A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland.", + "meaning": "GAZ:00000843" + }, + "India [GAZ:00002839]": { + "text": "India [GAZ:00002839]", + "description": "A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages.", + "meaning": "GAZ:00002839" + }, + "Indonesia [GAZ:00003727]": { + "text": "Indonesia [GAZ:00003727]", + "description": "An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan).", + "meaning": "GAZ:00003727" + }, + "Iran [GAZ:00004474]": { + "text": "Iran [GAZ:00004474]", + "description": "A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan).", + "meaning": "GAZ:00004474" + }, + "Iraq [GAZ:00004483]": { + "text": "Iraq [GAZ:00004483]", + "description": "A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts).", + "meaning": "GAZ:00004483" + }, + "Ireland [GAZ:00002943]": { + "text": "Ireland [GAZ:00002943]", + "description": "A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 \"county-level\" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a \"city council\"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties.", + "meaning": "GAZ:00002943" + }, + "Isle of Man [GAZ:00052477]": { + "text": "Isle of Man [GAZ:00052477]", + "description": "A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations.", + "meaning": "GAZ:00052477" + }, + "Israel [GAZ:00002476]": { + "text": "Israel [GAZ:00002476]", + "description": "A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions.", + "meaning": "GAZ:00002476" + }, + "Italy [GAZ:00002650]": { + "text": "Italy [GAZ:00002650]", + "description": "A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni).", + "meaning": "GAZ:00002650" + }, + "Jamaica [GAZ:00003781]": { + "text": "Jamaica [GAZ:00003781]", + "description": "A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance.", + "meaning": "GAZ:00003781" + }, + "Jan Mayen [GAZ:00005853]": { + "text": "Jan Mayen [GAZ:00005853]", + "description": "A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.", + "meaning": "GAZ:00005853" + }, + "Japan [GAZ:00002747]": { + "text": "Japan [GAZ:00002747]", + "description": "An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south.", + "meaning": "GAZ:00002747" + }, + "Jarvis Island [GAZ:00007118]": { + "text": "Jarvis Island [GAZ:00007118]", + "description": "An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount.", + "meaning": "GAZ:00007118" + }, + "Jersey [GAZ:00001551]": { + "text": "Jersey [GAZ:00001551]", + "description": "A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq.", + "meaning": "GAZ:00001551" + }, + "Johnston Atoll [GAZ:00007114]": { + "text": "Johnston Atoll [GAZ:00007114]", + "description": "A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount.", + "meaning": "GAZ:00007114" + }, + "Jordan [GAZ:00002473]": { + "text": "Jordan [GAZ:00002473]", + "description": "A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias.", + "meaning": "GAZ:00002473" + }, + "Juan de Nova Island [GAZ:00005809]": { + "text": "Juan de Nova Island [GAZ:00005809]", + "description": "A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique.", + "meaning": "GAZ:00005809" + }, + "Kazakhstan [GAZ:00004999]": { + "text": "Kazakhstan [GAZ:00004999]", + "description": "A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions.", + "meaning": "GAZ:00004999" + }, + "Kenya [GAZ:00001101]": { + "text": "Kenya [GAZ:00001101]", + "description": "A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province.", + "meaning": "GAZ:00001101" + }, + "Kerguelen Archipelago [GAZ:00005682]": { + "text": "Kerguelen Archipelago [GAZ:00005682]", + "description": "A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap.", + "meaning": "GAZ:00005682" + }, + "Kingman Reef [GAZ:00007116]": { + "text": "Kingman Reef [GAZ:00007116]", + "description": "A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount.", + "meaning": "GAZ:00007116" + }, + "Kiribati [GAZ:00006894]": { + "text": "Kiribati [GAZ:00006894]", + "description": "An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea).", + "meaning": "GAZ:00006894" + }, + "Kosovo [GAZ:00011337]": { + "text": "Kosovo [GAZ:00011337]", + "description": "A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija.", + "meaning": "GAZ:00011337" + }, + "Kuwait [GAZ:00005285]": { + "text": "Kuwait [GAZ:00005285]", + "description": "A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah).", + "meaning": "GAZ:00005285" + }, + "Kyrgyzstan [GAZ:00006893]": { + "text": "Kyrgyzstan [GAZ:00006893]", + "description": "A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions).", + "meaning": "GAZ:00006893" + }, + "Laos [GAZ:00006889]": { + "text": "Laos [GAZ:00006889]", + "description": "A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang).", + "meaning": "GAZ:00006889" + }, + "Latvia [GAZ:00002958]": { + "text": "Latvia [GAZ:00002958]", + "description": "A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions.", + "meaning": "GAZ:00002958" + }, + "Lebanon [GAZ:00002478]": { + "text": "Lebanon [GAZ:00002478]", + "description": "A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa).", + "meaning": "GAZ:00002478" + }, + "Lesotho [GAZ:00001098]": { + "text": "Lesotho [GAZ:00001098]", + "description": "A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils.", + "meaning": "GAZ:00001098" + }, + "Liberia [GAZ:00000911]": { + "text": "Liberia [GAZ:00000911]", + "description": "A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean.", + "meaning": "GAZ:00000911" + }, + "Libya [GAZ:00000566]": { + "text": "Libya [GAZ:00000566]", + "description": "A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s.", + "meaning": "GAZ:00000566" + }, + "Liechtenstein [GAZ:00003858]": { + "text": "Liechtenstein [GAZ:00003858]", + "description": "A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county).", + "meaning": "GAZ:00003858" + }, + "Line Islands [GAZ:00007144]": { + "text": "Line Islands [GAZ:00007144]", + "description": "A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands.", + "meaning": "GAZ:00007144" + }, + "Lithuania [GAZ:00002960]": { + "text": "Lithuania [GAZ:00002960]", + "description": "A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos).", + "meaning": "GAZ:00002960" + }, + "Luxembourg [GAZ:00002947]": { + "text": "Luxembourg [GAZ:00002947]", + "description": "A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest.", + "meaning": "GAZ:00002947" + }, + "Macau [GAZ:00003202]": { + "text": "Macau [GAZ:00003202]", + "description": "One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China.", + "meaning": "GAZ:00003202" + }, + "Madagascar [GAZ:00001108]": { + "text": "Madagascar [GAZ:00001108]", + "description": "An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany.", + "meaning": "GAZ:00001108" + }, + "Malawi [GAZ:00001105]": { + "text": "Malawi [GAZ:00001105]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", + "meaning": "GAZ:00001105" + }, + "Malaysia [GAZ:00003902]": { + "text": "Malaysia [GAZ:00003902]", + "description": "A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms.", + "meaning": "GAZ:00003902" + }, + "Maldives [GAZ:00006924]": { + "text": "Maldives [GAZ:00006924]", + "description": "An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2.", + "meaning": "GAZ:00006924" + }, + "Mali [GAZ:00000584]": { + "text": "Mali [GAZ:00000584]", + "description": "A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements.", + "meaning": "GAZ:00000584" + }, + "Malta [GAZ:00004017]": { + "text": "Malta [GAZ:00004017]", + "description": "A Southern European country and consists of an archipelago situated centrally in the Mediterranean.", + "meaning": "GAZ:00004017" + }, + "Marshall Islands [GAZ:00007161]": { + "text": "Marshall Islands [GAZ:00007161]", + "description": "An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning \"sunrise\" and \"sunset\" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated.", + "meaning": "GAZ:00007161" + }, + "Martinique [GAZ:00067143]": { + "text": "Martinique [GAZ:00067143]", + "description": "An island and an overseas department/region and single territorial collectivity of France.", + "meaning": "GAZ:00067143" + }, + "Mauritania [GAZ:00000583]": { + "text": "Mauritania [GAZ:00000583]", + "description": "A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements).", + "meaning": "GAZ:00000583" + }, + "Mauritius [GAZ:00003745]": { + "text": "Mauritius [GAZ:00003745]", + "description": "An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands.", + "meaning": "GAZ:00003745" + }, + "Mayotte [GAZ:00003943]": { + "text": "Mayotte [GAZ:00003943]", + "description": "An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two.", + "meaning": "GAZ:00003943" + }, + "Mexico [GAZ:00002852]": { + "text": "Mexico [GAZ:00002852]", + "description": "A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City.", + "meaning": "GAZ:00002852" + }, + "Micronesia [GAZ:00005862]": { + "text": "Micronesia [GAZ:00005862]", + "description": "A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east.", + "meaning": "GAZ:00005862" + }, + "Midway Islands [GAZ:00007112]": { + "text": "Midway Islands [GAZ:00007112]", + "description": "A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior.", + "meaning": "GAZ:00007112" + }, + "Moldova [GAZ:00003897]": { + "text": "Moldova [GAZ:00003897]", + "description": "A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic.", + "meaning": "GAZ:00003897" + }, + "Monaco [GAZ:00003857]": { + "text": "Monaco [GAZ:00003857]", + "description": "A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards.", + "meaning": "GAZ:00003857" + }, + "Mongolia [GAZ:00008744]": { + "text": "Mongolia [GAZ:00008744]", + "description": "A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status.", + "meaning": "GAZ:00008744" + }, + "Montenegro [GAZ:00006898]": { + "text": "Montenegro [GAZ:00006898]", + "description": "A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality.", + "meaning": "GAZ:00006898" + }, + "Montserrat [GAZ:00003988]": { + "text": "Montserrat [GAZ:00003988]", + "description": "A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes.", + "meaning": "GAZ:00003988" + }, + "Morocco [GAZ:00000565]": { + "text": "Morocco [GAZ:00000565]", + "description": "A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of \"Saguia el-Hamra\" and \"Rio de Oro\" is disputed.", + "meaning": "GAZ:00000565" + }, + "Mozambique [GAZ:00001100]": { + "text": "Mozambique [GAZ:00001100]", + "description": "A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in \"Postos Administrativos\" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration.", + "meaning": "GAZ:00001100" + }, + "Myanmar [GAZ:00006899]": { + "text": "Myanmar [GAZ:00006899]", + "description": "A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages.", + "meaning": "GAZ:00006899" + }, + "Namibia [GAZ:00001096]": { + "text": "Namibia [GAZ:00001096]", + "description": "A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies.", + "meaning": "GAZ:00001096" + }, + "Nauru [GAZ:00006900]": { + "text": "Nauru [GAZ:00006900]", + "description": "An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies.", + "meaning": "GAZ:00006900" + }, + "Navassa Island [GAZ:00007119]": { + "text": "Navassa Island [GAZ:00007119]", + "description": "A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti.", + "meaning": "GAZ:00007119" + }, + "Nepal [GAZ:00004399]": { + "text": "Nepal [GAZ:00004399]", + "description": "A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the \"Chicken's Neck\". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions.", + "meaning": "GAZ:00004399" + }, + "Netherlands [GAZ:00002946]": { + "text": "Netherlands [GAZ:00002946]", + "description": "The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007).", + "meaning": "GAZ:00002946" + }, + "New Caledonia [GAZ:00005206]": { + "text": "New Caledonia [GAZ:00005206]", + "description": "A \"sui generis collectivity\" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes.", + "meaning": "GAZ:00005206" + }, + "New Zealand [GAZ:00000469]": { + "text": "New Zealand [GAZ:00000469]", + "description": "A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands.", + "meaning": "GAZ:00000469" + }, + "Nicaragua [GAZ:00002978]": { + "text": "Nicaragua [GAZ:00002978]", + "description": "A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya.", + "meaning": "GAZ:00002978" + }, + "Niger [GAZ:00000585]": { + "text": "Niger [GAZ:00000585]", + "description": "A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes.", + "meaning": "GAZ:00000585" + }, + "Nigeria [GAZ:00000912]": { + "text": "Nigeria [GAZ:00000912]", + "description": "A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs).", + "meaning": "GAZ:00000912" + }, + "Niue [GAZ:00006902]": { + "text": "Niue [GAZ:00006902]", + "description": "An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state.", + "meaning": "GAZ:00006902" + }, + "Norfolk Island [GAZ:00005908]": { + "text": "Norfolk Island [GAZ:00005908]", + "description": "A Territory of Australia that includes Norfolk Island and neighboring islands.", + "meaning": "GAZ:00005908" + }, + "North Korea [GAZ:00002801]": { + "text": "North Korea [GAZ:00002801]", + "description": "A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia.", + "meaning": "GAZ:00002801" + }, + "North Macedonia [GAZ:00006895]": { + "text": "North Macedonia [GAZ:00006895]", + "description": "A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts.", + "meaning": "GAZ:00006895" + }, + "North Sea [GAZ:00002284]": { + "text": "North Sea [GAZ:00002284]", + "description": "A sea situated between the eastern coasts of the British Isles and the western coast of Europe.", + "meaning": "GAZ:00002284" + }, + "Northern Mariana Islands [GAZ:00003958]": { + "text": "Northern Mariana Islands [GAZ:00003958]", + "description": "A group of 15 islands about three-quarters of the way from Hawaii to the Philippines.", + "meaning": "GAZ:00003958" + }, + "Norway [GAZ:00002699]": { + "text": "Norway [GAZ:00002699]", + "description": "A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom.", + "meaning": "GAZ:00002699" + }, + "Oman [GAZ:00005283]": { + "text": "Oman [GAZ:00005283]", + "description": "A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat).", + "meaning": "GAZ:00005283" + }, + "Pakistan [GAZ:00005246]": { + "text": "Pakistan [GAZ:00005246]", + "description": "A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan.", + "meaning": "GAZ:00005246" + }, + "Palau [GAZ:00006905]": { + "text": "Palau [GAZ:00006905]", + "description": "A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines.", + "meaning": "GAZ:00006905" + }, + "Panama [GAZ:00002892]": { + "text": "Panama [GAZ:00002892]", + "description": "The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports.", + "meaning": "GAZ:00002892" + }, + "Papua New Guinea [GAZ:00003922]": { + "text": "Papua New Guinea [GAZ:00003922]", + "description": "A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia).", + "meaning": "GAZ:00003922" + }, + "Paracel Islands [GAZ:00010832]": { + "text": "Paracel Islands [GAZ:00010832]", + "description": "A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines.", + "meaning": "GAZ:00010832" + }, + "Paraguay [GAZ:00002933]": { + "text": "Paraguay [GAZ:00002933]", + "description": "A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts.", + "meaning": "GAZ:00002933" + }, + "Peru [GAZ:00002932]": { + "text": "Peru [GAZ:00002932]", + "description": "A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao.", + "meaning": "GAZ:00002932" + }, + "Philippines [GAZ:00004525]": { + "text": "Philippines [GAZ:00004525]", + "description": "An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays.", + "meaning": "GAZ:00004525" + }, + "Pitcairn Islands [GAZ:00005867]": { + "text": "Pitcairn Islands [GAZ:00005867]", + "description": "A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia.", + "meaning": "GAZ:00005867" + }, + "Poland [GAZ:00002939]": { + "text": "Poland [GAZ:00002939]", + "description": "A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas.", + "meaning": "GAZ:00002939" + }, + "Portugal [GAZ:00004126]": { + "text": "Portugal [GAZ:00004126]", + "description": "That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands.", + "meaning": "GAZ:00004126" + }, + "Puerto Rico [GAZ:00006935]": { + "text": "Puerto Rico [GAZ:00006935]", + "description": "A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States).", + "meaning": "GAZ:00006935" + }, + "Qatar [GAZ:00005286]": { + "text": "Qatar [GAZ:00005286]", + "description": "An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts).", + "meaning": "GAZ:00005286" + }, + "Republic of the Congo [GAZ:00001088]": { + "text": "Republic of the Congo [GAZ:00001088]", + "description": "A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts.", + "meaning": "GAZ:00001088" + }, + "Reunion [GAZ:00003945]": { + "text": "Reunion [GAZ:00003945]", + "description": "An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island.", + "meaning": "GAZ:00003945" + }, + "Romania [GAZ:00002951]": { + "text": "Romania [GAZ:00002951]", + "description": "A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities).", + "meaning": "GAZ:00002951" + }, + "Ross Sea [GAZ:00023304]": { + "text": "Ross Sea [GAZ:00023304]", + "description": "A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW.", + "meaning": "GAZ:00023304" + }, + "Russia [GAZ:00002721]": { + "text": "Russia [GAZ:00002721]", + "description": "A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts.", + "meaning": "GAZ:00002721" + }, + "Rwanda [GAZ:00001087]": { + "text": "Rwanda [GAZ:00001087]", + "description": "A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge).", + "meaning": "GAZ:00001087" + }, + "Saint Helena [GAZ:00000849]": { + "text": "Saint Helena [GAZ:00000849]", + "description": "An island of volcanic origin and a British overseas territory in the South Atlantic Ocean.", + "meaning": "GAZ:00000849" + }, + "Saint Kitts and Nevis [GAZ:00006906]": { + "text": "Saint Kitts and Nevis [GAZ:00006906]", + "description": "A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis.", + "meaning": "GAZ:00006906" + }, + "Saint Lucia [GAZ:00006909]": { + "text": "Saint Lucia [GAZ:00006909]", + "description": "An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean.", + "meaning": "GAZ:00006909" + }, + "Saint Pierre and Miquelon [GAZ:00003942]": { + "text": "Saint Pierre and Miquelon [GAZ:00003942]", + "description": "An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985.", + "meaning": "GAZ:00003942" + }, + "Saint Martin [GAZ:00005841]": { + "text": "Saint Martin [GAZ:00005841]", + "description": "An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe.", + "meaning": "GAZ:00005841" + }, + "Saint Vincent and the Grenadines [GAZ:02000565]": { + "text": "Saint Vincent and the Grenadines [GAZ:02000565]", + "description": "An island nation in the Lesser Antilles chain of the Caribbean Sea.", + "meaning": "GAZ:02000565" + }, + "Samoa [GAZ:00006910]": { + "text": "Samoa [GAZ:00006910]", + "description": "A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts).", + "meaning": "GAZ:00006910" + }, + "San Marino [GAZ:00003102]": { + "text": "San Marino [GAZ:00003102]", + "description": "A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello).", + "meaning": "GAZ:00003102" + }, + "Sao Tome and Principe [GAZ:00006927]": { + "text": "Sao Tome and Principe [GAZ:00006927]", + "description": "An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29).", + "meaning": "GAZ:00006927" + }, + "Saudi Arabia [GAZ:00005279]": { + "text": "Saudi Arabia [GAZ:00005279]", + "description": "A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates.", + "meaning": "GAZ:00005279" + }, + "Senegal [GAZ:00000913]": { + "text": "Senegal [GAZ:00000913]", + "description": "A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales.", + "meaning": "GAZ:00000913" + }, + "Serbia [GAZ:00002957]": { + "text": "Serbia [GAZ:00002957]", + "description": "A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities).", + "meaning": "GAZ:00002957" + }, + "Seychelles [GAZ:00006922]": { + "text": "Seychelles [GAZ:00006922]", + "description": "An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands.", + "meaning": "GAZ:00006922" + }, + "Sierra Leone [GAZ:00000914]": { + "text": "Sierra Leone [GAZ:00000914]", + "description": "A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts.", + "meaning": "GAZ:00000914" + }, + "Singapore [GAZ:00003923]": { + "text": "Singapore [GAZ:00003923]", + "description": "An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role.", + "meaning": "GAZ:00003923" + }, + "Sint Maarten [GAZ:00012579]": { + "text": "Sint Maarten [GAZ:00012579]", + "description": "One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten.", + "meaning": "GAZ:00012579" + }, + "Slovakia [GAZ:00002956]": { + "text": "Slovakia [GAZ:00002956]", + "description": "A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts.", + "meaning": "GAZ:00002956" + }, + "Slovenia [GAZ:00002955]": { + "text": "Slovenia [GAZ:00002955]", + "description": "A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status.", + "meaning": "GAZ:00002955" + }, + "Solomon Islands [GAZ:00005275]": { + "text": "Solomon Islands [GAZ:00005275]", + "description": "A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal.", + "meaning": "GAZ:00005275" + }, + "Somalia [GAZ:00001104]": { + "text": "Somalia [GAZ:00001104]", + "description": "A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir.", + "meaning": "GAZ:00001104" + }, + "South Africa [GAZ:00001094]": { + "text": "South Africa [GAZ:00001094]", + "description": "A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities.", + "meaning": "GAZ:00001094" + }, + "South Georgia and the South Sandwich Islands [GAZ:00003990]": { + "text": "South Georgia and the South Sandwich Islands [GAZ:00003990]", + "description": "A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE.", + "meaning": "GAZ:00003990" + }, + "South Korea [GAZ:00002802]": { + "text": "South Korea [GAZ:00002802]", + "description": "A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri).", + "meaning": "GAZ:00002802" + }, + "South Sudan [GAZ:00233439]": { + "text": "South Sudan [GAZ:00233439]", + "description": "A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel.", + "meaning": "GAZ:00233439" + }, + "Spain [GAZ:00003936]": { + "text": "Spain [GAZ:00003936]", + "description": "That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal.", + "meaning": "GAZ:00003936" + }, + "Spratly Islands [GAZ:00010831]": { + "text": "Spratly Islands [GAZ:00010831]", + "description": "A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines.", + "meaning": "GAZ:00010831" + }, + "Sri Lanka [GAZ:00003924]": { + "text": "Sri Lanka [GAZ:00003924]", + "description": "An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats.", + "meaning": "GAZ:00003924" + }, + "State of Palestine [GAZ:00002475]": { + "text": "State of Palestine [GAZ:00002475]", + "description": "The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates.", + "meaning": "GAZ:00002475" + }, + "Sudan [GAZ:00000560]": { + "text": "Sudan [GAZ:00000560]", + "description": "A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts.", + "meaning": "GAZ:00000560" + }, + "Suriname [GAZ:00002525]": { + "text": "Suriname [GAZ:00002525]", + "description": "A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten.", + "meaning": "GAZ:00002525" + }, + "Svalbard [GAZ:00005396]": { + "text": "Svalbard [GAZ:00005396]", + "description": "An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole.", + "meaning": "GAZ:00005396" + }, + "Swaziland [GAZ:00001099]": { + "text": "Swaziland [GAZ:00001099]", + "description": "A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla).", + "meaning": "GAZ:00001099" + }, + "Sweden [GAZ:00002729]": { + "text": "Sweden [GAZ:00002729]", + "description": "A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004.", + "meaning": "GAZ:00002729" + }, + "Switzerland [GAZ:00002941]": { + "text": "Switzerland [GAZ:00002941]", + "description": "A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy.", + "meaning": "GAZ:00002941" + }, + "Syria [GAZ:00002474]": { + "text": "Syria [GAZ:00002474]", + "description": "A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia).", + "meaning": "GAZ:00002474" + }, + "Taiwan [GAZ:00005341]": { + "text": "Taiwan [GAZ:00005341]", + "description": "A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities.", + "meaning": "GAZ:00005341" + }, + "Tajikistan [GAZ:00006912]": { + "text": "Tajikistan [GAZ:00006912]", + "description": "A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion).", + "meaning": "GAZ:00006912" + }, + "Tanzania [GAZ:00001103]": { + "text": "Tanzania [GAZ:00001103]", + "description": "A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities).", + "meaning": "GAZ:00001103" + }, + "Thailand [GAZ:00003744]": { + "text": "Thailand [GAZ:00003744]", + "description": "A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province.", + "meaning": "GAZ:00003744" + }, + "Timor-Leste [GAZ:00006913]": { + "text": "Timor-Leste [GAZ:00006913]", + "description": "A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets.", + "meaning": "GAZ:00006913" + }, + "Togo [GAZ:00000915]": { + "text": "Togo [GAZ:00000915]", + "description": "A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located.", + "meaning": "GAZ:00000915" + }, + "Tokelau [GAZ:00260188]": { + "text": "Tokelau [GAZ:00260188]", + "description": "A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi).", + "meaning": "GAZ:00260188" + }, + "Tonga [GAZ:00006916]": { + "text": "Tonga [GAZ:00006916]", + "description": "A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean.", + "meaning": "GAZ:00006916" + }, + "Trinidad and Tobago [GAZ:00003767]": { + "text": "Trinidad and Tobago [GAZ:00003767]", + "description": "An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands.", + "meaning": "GAZ:00003767" + }, + "Tromelin Island [GAZ:00005812]": { + "text": "Tromelin Island [GAZ:00005812]", + "description": "A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point.", + "meaning": "GAZ:00005812" + }, + "Tunisia [GAZ:00000562]": { + "text": "Tunisia [GAZ:00000562]", + "description": "A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 \"delegations\" or \"districts\" (mutamadiyat), and further subdivided into municipalities (shaykhats).", + "meaning": "GAZ:00000562" + }, + "Turkey [GAZ:00000558]": { + "text": "Turkey [GAZ:00000558]", + "description": "A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts.", + "meaning": "GAZ:00000558" + }, + "Turkmenistan [GAZ:00005018]": { + "text": "Turkmenistan [GAZ:00005018]", + "description": "A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city.", + "meaning": "GAZ:00005018" + }, + "Turks and Caicos Islands [GAZ:00003955]": { + "text": "Turks and Caicos Islands [GAZ:00003955]", + "description": "A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands.", + "meaning": "GAZ:00003955" + }, + "Tuvalu [GAZ:00009715]": { + "text": "Tuvalu [GAZ:00009715]", + "description": "A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia.", + "meaning": "GAZ:00009715" + }, + "United States of America [GAZ:00002459]": { + "text": "United States of America [GAZ:00002459]", + "description": "A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into \"census areas\"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a \"charter township\", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county.", + "meaning": "GAZ:00002459" + }, + "Uganda [GAZ:00001102]": { + "text": "Uganda [GAZ:00001102]", + "description": "A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties.", + "meaning": "GAZ:00001102" + }, + "Ukraine [GAZ:00002724]": { + "text": "Ukraine [GAZ:00002724]", + "description": "A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units.", + "meaning": "GAZ:00002724" + }, + "United Arab Emirates [GAZ:00005282]": { + "text": "United Arab Emirates [GAZ:00005282]", + "description": "A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain.", + "meaning": "GAZ:00005282" + }, + "United Kingdom [GAZ:00002637]": { + "text": "United Kingdom [GAZ:00002637]", + "description": "A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel.", + "meaning": "GAZ:00002637" + }, + "Uruguay [GAZ:00002930]": { + "text": "Uruguay [GAZ:00002930]", + "description": "A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento).", + "meaning": "GAZ:00002930" + }, + "Uzbekistan [GAZ:00004979]": { + "text": "Uzbekistan [GAZ:00004979]", + "description": "A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar).", + "meaning": "GAZ:00004979" + }, + "Vanuatu [GAZ:00006918]": { + "text": "Vanuatu [GAZ:00006918]", + "description": "An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji.", + "meaning": "GAZ:00006918" + }, + "Venezuela [GAZ:00002931]": { + "text": "Venezuela [GAZ:00002931]", + "description": "A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias).", + "meaning": "GAZ:00002931" + }, + "Viet Nam [GAZ:00003756]": { + "text": "Viet Nam [GAZ:00003756]", + "description": "The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia.", + "meaning": "GAZ:00003756" + }, + "Virgin Islands [GAZ:00003959]": { + "text": "Virgin Islands [GAZ:00003959]", + "description": "A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts.", + "meaning": "GAZ:00003959" + }, + "Wake Island [GAZ:00007111]": { + "text": "Wake Island [GAZ:00007111]", + "description": "A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east).", + "meaning": "GAZ:00007111" + }, + "Wallis and Futuna [GAZ:00007191]": { + "text": "Wallis and Futuna [GAZ:00007191]", + "description": "A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets.", + "meaning": "GAZ:00007191" + }, + "West Bank [GAZ:00009572]": { + "text": "West Bank [GAZ:00009572]", + "description": "A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian \"islands\" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is \"pipelined\".", + "meaning": "GAZ:00009572" + }, + "Western Sahara [GAZ:00000564]": { + "text": "Western Sahara [GAZ:00000564]", + "description": "A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions.", + "meaning": "GAZ:00000564" + }, + "Yemen [GAZ:00005284]": { + "text": "Yemen [GAZ:00005284]", + "description": "A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001).", + "meaning": "GAZ:00005284" + }, + "Zambia [GAZ:00001107]": { + "text": "Zambia [GAZ:00001107]", + "description": "A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts.", + "meaning": "GAZ:00001107" + }, + "Zimbabwe [GAZ:00001106]": { + "text": "Zimbabwe [GAZ:00001106]", + "description": "A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities.", + "meaning": "GAZ:00001106" + } + } + } + }, + "slots": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100752", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100996", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100760", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100761", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101203", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101204", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100762", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101107", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100280", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001189", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100436", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "slot_uri": "GENEPIO:0100309", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "slot_uri": "GENEPIO:0100310", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101108", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101109", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100583", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101110", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101111", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101071", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101072", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101073", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100765", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100766", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100767", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100763", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100438", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_origin" + ], + "slot_uri": "GENEPIO:0100437", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:food_product_type" + ], + "slot_uri": "GENEPIO:0100444", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", + "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product_properties", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0100445", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_packaging", + "BIOSAMPLE_Enterics:food_contain_wrap" + ], + "slot_uri": "GENEPIO:0100447", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_quality_date" + ], + "slot_uri": "GENEPIO:0100615", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "range": "date" + }, + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100616", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "range": "date" + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "slot_uri": "GENEPIO:0001232", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001223", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_material", + "BIOSAMPLE_Enterics:host_tissue_sampled", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001211", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:body_product", + "BIOSAMPLE_Enterics:host_body_product", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001216", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_part", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001214", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001234", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "slot_uri": "GENEPIO:0001241", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100768", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100769", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101090", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100433", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100434", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100448", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100449", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101014", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101015", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001253", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101029", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100921", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101112", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100690", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101023", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host_(common_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host_(scientific_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:host" + ], + "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host_(ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_variety" + ], + "slot_uri": "GENEPIO:0100450", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host_(breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host_disease", + "BIOSAMPLE_Enterics:host_animal_breed" + ], + "slot_uri": "GENEPIO:0100451", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host_(food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "slot_uri": "GENEPIO:0100452", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host_age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:host_age" + ], + "slot_uri": "GENEPIO:0001392", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "required": true, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host_age_unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "host_age_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_age" + ], + "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_disease" + ], + "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_disease menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host_health_state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:host_health_state" + ], + "slot_uri": "GENEPIO:0001388", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_health_state menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host_health_status_details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_health_status_details menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host_health_outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_disease_outcome" + ], + "slot_uri": "GENEPIO:0001390", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_health_outcome menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "title": "host_subject_ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_subject_id" + ], + "slot_uri": "GENEPIO:0001398", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case_ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom_onset_date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001399", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs_and_symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001400", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "signs_and_symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing_conditions_and_risk_factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001401", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "pre-existing_conditions_and_risk_factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001402", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "slot_uri": "GENEPIO:0001417", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "slot_uri": "GENEPIO:0001418", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "slot_uri": "GENEPIO:0001419", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "host role menu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "slot_uri": "GENEPIO:0001428", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "exposure setting menu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "slot_uri": "GENEPIO:0001431", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host_vaccination_status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:prior_sars_cov_2_vaccination" + ], + "slot_uri": "GENEPIO:0001404", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "host_vaccination_status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number_of_vaccine_doses_received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001406", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "integer", + "minimum_value": 0 + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination_dose_1_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100313", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination_dose_1_vaccination_date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100314", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "date" + }, + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", + "title": "vaccination_dose_2_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100315", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "The date the second dose of a vaccine was administered.", + "title": "vaccination_dose_2_vaccination_date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100316", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "date" + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], + "slot_uri": "GENEPIO:0100321", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_administration": { + "name": "influenza_antiviral_treatment_administration", + "description": "An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen.", + "title": "influenza_antiviral_treatment_administration", + "examples": [ + { + "value": "Influenza antiviral treatment administered [GENEPIO:0101194]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101113", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "any_of": [ + { + "range": "influenza_antiviral_treatment_administration menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_antiviral_agent__": { + "name": "influenza_antiviral_agent__", + "description": "A substance that destroys or inhibits replication of viruses.", + "title": "influenza_antiviral_agent", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101114", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_date": { + "name": "influenza_antiviral_treatment_date", + "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", + "title": "influenza_antiviral_treatment_date", + "comments": [ + "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101115", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "range": "date" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100773", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100774", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100775", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100776", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100777", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100778", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100779", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100780", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100911", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100440", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101025", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100697", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101026", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100441", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101027", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100698", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101028", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "weather_type": { + "name": "weather_type", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "weather_type", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100442", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "multivalued": true, + "any_of": [ + { + "range": "weather_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100912", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "precipitation measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample collection" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100913", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "ambient_temperature_measurement_value": { + "name": "ambient_temperature_measurement_value", + "description": "The numerical value of a measurement of the ambient temperature.", + "title": "ambient temperature measurement value", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "70" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100935", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "ambient_temperature_measurement_unit": { + "name": 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"alkalinity_measurement_method": { + "name": "alkalinity_measurement_method", + "description": "The process used to measure alkalinity.", + "title": "alkalinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure alkalinity." + ], + "examples": [ + { + "value": "Titration method" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100880", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "conductivity_measurement_value": { + "name": "conductivity_measurement_value", + "description": "The numerical value of a measurement of conductivity.", + "title": "conductivity measurement value", + "comments": [ + "Provide the numerical value of the measured conductivity." + ], + "examples": [ + { + "value": "1412" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100916", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "conductivity_measurement_unit": { + "name": "conductivity_measurement_unit", + "description": "The units of a measurement of conductivity.", + "title": "conductivity measurement unit", + "comments": [ + "Provide the units of the measured conductivity." + ], + "examples": [ + { + "value": "microSiemen per centimeter (μS/cm)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100803", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "conductivity measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "conductivity_measurement_method": { + "name": "conductivity_measurement_method", + "description": "The method used to measure conductivity.", + "title": "conductivity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure conductivity." + ], + "examples": [ + { + "value": "Conductivity electrode and meter" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100804", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "salinity_measurement_value": { + "name": "salinity_measurement_value", + "description": "The numerical value of a measurement of salinity.", + "title": "salinity measurement value", + "comments": [ + "Provide the numerical value of the measured salinity." + ], + "examples": [ + { + "value": "35" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100805", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "salinity_measurement_unit": { + "name": "salinity_measurement_unit", + "description": "The units of a measurement of salinity.", + "title": "salinity measurement unit", + "comments": [ + "Provide the units of the measured salinity." + ], + "examples": [ + { + "value": "practical salinity unit (PSU)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100806", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "salinity measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "salinity_measurement_method": { + "name": "salinity_measurement_method", + "description": "The method used to measure salinity.", + "title": "salinity measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure salinity." + ], + "examples": [ + { + "value": "conductivity meter" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100807", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_nitrogen_tn_measurement_value": { + "name": "total_nitrogen_tn_measurement_value", + "description": "The numerical value of a measurement of total nitrogen (TN).", + "title": "total nitrogen (TN) measurement value", + "comments": [ + "Provide the numerical value of the measured TN." + ], + "examples": [ + { + "value": "120" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100808", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_nitrogen_tn_measurement_unit": { + "name": "total_nitrogen_tn_measurement_unit", + "description": "The units of a measurement of total nitrogen (TN).", + "title": "total nitrogen (TN) measurement unit", + "comments": [ + "Provide the units of the measured TN." + ], + "examples": [ + { + "value": "milligram per liter (mg/L)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100809", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "total nitrogen (TN) measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "total_nitrogen_tn_measurement_method": { + "name": "total_nitrogen_tn_measurement_method", + "description": "The method used to measure total nitrogen (TN).", + "title": "total nitrogen (TN) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TN." + ], + "examples": [ + { + "value": "Hach total nitrogen spectrophotometric test" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100810", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_phosphorus_tp_measurement_value": { + "name": "total_phosphorus_tp_measurement_value", + "description": "The numerical value of a measurement of total phosphorus (TP).", + "title": "total phosphorus (TP) measurement value", + "comments": [ + "Provide the numerical value of the measured TP." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100811", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "total_phosphorus_tp_measurement_unit": { + "name": "total_phosphorus_tp_measurement_unit", + "description": "The units of a measurement of total phosphorus (TP).", + "title": "total phosphorus (TP) measurement unit", + "comments": [ + "Provide the units of the measured TP." + ], + "examples": [ + { + "value": "milligrams orthophosphate as phosphorus per liter (mg PO4-P/L)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100812", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "total phosphorus (TP) measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "total_phosphorus_tp_measurement_method": { + "name": "total_phosphorus_tp_measurement_method", + "description": "The method used to measure total phosphorus (TP).", + "title": "total phosphorus (TP) measurement method", + "comments": [ + "Provide the name of the procedure or technology used to measure TP." + ], + "examples": [ + { + "value": "Merck phosphate spectrophotometric test kit" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100813", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "fecal_contamination_indicator_": { + "name": "fecal_contamination_indicator_", + "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination.", + "title": "fecal contamination indicator", + "comments": [ + "If a fecal contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "crAssphage" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100814", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "fecal contamination indicator menu" + }, + { + "range": "null value menu" + } + ] + }, + "fecal_contamination_value": { + "name": "fecal_contamination_value", + "description": "The numerical value of a measurement of fecal contamination.", + "title": "fecal contamination value", + "comments": [ + "Provide the numerical value of the measured fecal contamination." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100815", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "fecal_contamination_unit": { + "name": "fecal_contamination_unit", + "description": "The units of a measurement of fecal contamination.", + "title": "fecal contamination unit", + "comments": [ + "Provide the units of the measured fecal contamination." + ], + "examples": [ + { + "value": "cycle threshold (Ct) / quantification cycle (Cq)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100816", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "recommended": true, + "any_of": [ + { + "range": "fecal contamination unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "fecal_contamination_method": { + "name": "fecal_contamination_method", + "description": "The method used to measure fecal contamination.", + "title": "fecal contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal contamination." + ], + "examples": [ + { + "value": "quantitative PCR assay" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100817", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "fecal_coliform_count_value": { + "name": "fecal_coliform_count_value", + "description": "The numerical value of a measurement of fecal coliforms within a sample.", + "title": "fecal coliform count value", + "comments": [ + "Provide the numerical value of the measured fecal coliforms." + ], + "examples": [ + { + "value": "3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100818", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "fecal_coliform_count_unit": { + "name": "fecal_coliform_count_unit", + "description": "The units of a measurement of fecal coliforms.", + "title": "fecal coliform count unit", + "comments": [ + "Provide the units of the measured fecal coliforms." + ], + "examples": [ + { + "value": "most probable number per milliliter (MPN/mL)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100819", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "fecal coliform count unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "fecal_coliform_count_method": { + "name": "fecal_coliform_count_method", + "description": "The method used to measure fecal coliforms.", + "title": "fecal coliform count method", + "comments": [ + "Provide the name of the procedure or technology used to measure fecal coliforms." + ], + "examples": [ + { + "value": "MPN method via serial dilutions until lack of growth" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100820", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "urinary_contamination_indicator": { + "name": "urinary_contamination_indicator", + "description": "A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination.", + "title": "urinary contamination indicator", + "comments": [ + "If a urinary contamination indicator was measured, select it from the picklist." + ], + "examples": [ + { + "value": "urobilin" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100837", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "urinary contamination indicator menu" + }, + { + "range": "null value menu" + } + ] + }, + "urinary_contamination_value": { + "name": "urinary_contamination_value", + "description": "The numerical value of a measurement of urinary contamination.", + "title": "urinary contamination value", + "comments": [ + "Provide the numerical value of the measured urinary contamination." + ], + "examples": [ + { + "value": "3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100838", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "urinary_contamination_unit": { + "name": "urinary_contamination_unit", + "description": "The units of a measurement of urinary contamination.", + "title": "urinary contamination unit", + "comments": [ + "Provide the units of the measured urinary contamination." + ], + "examples": [ + { + "value": "nanograms per liter" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100839", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "urinary contamination unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "urinary_contamination_method": { + "name": "urinary_contamination_method", + "description": "The method used to measure urinary contamination.", + "title": "urinary contamination method", + "comments": [ + "Provide the name of the procedure or technology used to measure urinary contamination." + ], + "examples": [ + { + "value": "Urobilin Concentration Test" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100840", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_value_at_collection": { + "name": "sample_temperature_value_at_collection", + "description": "The numerical value of a measurement of temperature of a sample at collection.", + "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100821", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", + "description": "The units of a measurement of temperature of a sample at the time of collection.", + "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100822", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sample temperature unit (at collection) menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100823", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100824", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100997", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001445", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100470", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100422", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100939", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100772", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100923", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100472", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100473", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001452", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100843", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100966", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100967", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101102", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001476", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001477", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001480", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101715", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001461", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100557", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100558", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100559", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100560", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100561", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100825", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100826", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100844", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100827", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100828", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100829", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100937", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100830", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100938", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100845", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100846", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100831", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100832", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100833", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100834", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100835", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101074", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101075", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100836", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101116", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101117", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101118", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100962", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100963", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100964", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100965", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101104", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101105", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101106", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100480", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100481", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100482", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100483", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100484", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "range": "WhitespaceMinimizedString", + "recommended": true + } + }, + "classes": { + "dh_interface": { + "name": "dh_interface", + "description": "A DataHarmonizer interface", + "from_schema": "https://example.com/hpai" + }, + "HPAI": { + "name": "HPAI", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + 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If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 31, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 32, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 33, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 34, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 36, + "slot_uri": "GENEPIO:0100438", + "alias": "host_origin_geo_loc_name_country", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_origin" + ], + "rank": 37, + "slot_uri": "GENEPIO:0100437", + "alias": "food_product_origin_geo_loc_name_country", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:food_product_type" + ], + "rank": 38, + "slot_uri": "GENEPIO:0100444", + "alias": "food_product", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", + "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product_properties", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0100445", + "alias": "food_product_properties", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_packaging", + "BIOSAMPLE_Enterics:food_contain_wrap" + ], + "rank": 40, + "slot_uri": "GENEPIO:0100447", + "alias": "food_packaging", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_quality_date" + ], + "rank": 41, + "slot_uri": "GENEPIO:0100615", + "alias": "food_quality_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0100616", + "alias": "food_packaging_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 44, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_material", + "BIOSAMPLE_Enterics:host_tissue_sampled", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 45, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:body_product", + "BIOSAMPLE_Enterics:host_body_product", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 46, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_part", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 47, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 48, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 49, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 62, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host_(common_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 67, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host_(scientific_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:host" + ], + "rank": 68, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host_(ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_variety" + ], + "rank": 69, + "slot_uri": "GENEPIO:0100450", + "alias": "host_ecotype", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host_(breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host_disease", + "BIOSAMPLE_Enterics:host_animal_breed" + ], + "rank": 70, + "slot_uri": "GENEPIO:0100451", + "alias": "host_breed", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host_(food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 71, + "slot_uri": "GENEPIO:0100452", + "alias": "host_food_production_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host_age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:host_age" + ], + "rank": 72, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host_age_unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "host_age_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_age" + ], + "rank": 74, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_disease" + ], + "rank": 75, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_disease menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host_health_state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:host_health_state" + ], + "rank": 76, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_state menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host_health_status_details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 77, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_status_details menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host_health_outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_disease_outcome" + ], + "rank": 78, + "slot_uri": "GENEPIO:0001390", + "alias": "host_health_outcome", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_outcome menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "title": "host_subject_ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_subject_id" + ], + "rank": 79, + "slot_uri": "GENEPIO:0001398", + "alias": "host_subject_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case_ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 80, + "slot_uri": "GENEPIO:0100281", + "alias": "case_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom_onset_date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 81, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs_and_symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 82, + "slot_uri": "GENEPIO:0001400", + "alias": "signs_and_symptoms", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "signs_and_symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing_conditions_and_risk_factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 83, + "slot_uri": "GENEPIO:0001401", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "pre-existing_conditions_and_risk_factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 84, + "slot_uri": "GENEPIO:0001402", + "alias": "complications", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 85, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "rank": 86, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "rank": 87, + "slot_uri": "GENEPIO:0001419", + "alias": "host_role", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "host role menu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 88, + "slot_uri": "GENEPIO:0001428", + "alias": "exposure_setting", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "exposure setting menu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "rank": 89, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host_vaccination_status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:prior_sars_cov_2_vaccination" + ], + "rank": 90, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host_vaccination_status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number_of_vaccine_doses_received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 91, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "integer", + "minimum_value": 0 + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination_dose_1_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 92, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination_dose_1_vaccination_date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 93, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", + "title": "vaccination_dose_2_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 94, + "slot_uri": "GENEPIO:0100315", + "alias": "vaccination_dose_2_vaccine_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "The date the second dose of a vaccine was administered.", + "title": "vaccination_dose_2_vaccination_date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 95, + "slot_uri": "GENEPIO:0100316", + "alias": "vaccination_dose_2_vaccination_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], + "rank": 96, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_administration": { + "name": "influenza_antiviral_treatment_administration", + "description": "An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen.", + "title": "influenza_antiviral_treatment_administration", + "examples": [ + { + "value": "Influenza antiviral treatment administered [GENEPIO:0101194]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 97, + "slot_uri": "GENEPIO:0101113", + "alias": "influenza_antiviral_treatment_administration", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "any_of": [ + { + "range": "influenza_antiviral_treatment_administration menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_antiviral_agent__": { + "name": "influenza_antiviral_agent__", + "description": "A substance that destroys or inhibits replication of viruses.", + "title": "influenza_antiviral_agent", + "from_schema": "https://example.com/hpai", + "rank": 98, + "slot_uri": "GENEPIO:0101114", + "alias": "influenza_antiviral_agent__", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_date": { + "name": "influenza_antiviral_treatment_date", + "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", + "title": "influenza_antiviral_treatment_date", + "comments": [ + "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." + ], + "from_schema": "https://example.com/hpai", + "rank": 99, + "slot_uri": "GENEPIO:0101115", + "alias": "influenza_antiviral_treatment_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "date" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 100, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 101, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 102, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 103, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 104, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 105, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 106, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 107, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 108, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 109, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 110, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 111, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 112, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 113, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 114, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 115, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 116, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "weather_type": { + "name": "weather_type", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "weather_type", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 117, + "slot_uri": "GENEPIO:0100442", + "alias": "weather_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "weather_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_unit": { + "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 118, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "precipitation measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period 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"sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 182, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 183, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 184, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 185, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 186, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 187, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 188, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 189, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 190, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 191, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 192, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 193, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 194, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 195, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 196, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 197, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 198, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 199, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 200, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 201, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 202, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 203, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 204, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 205, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 206, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 207, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 208, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 209, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 210, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 211, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 212, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 213, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 214, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 215, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 216, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 217, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 218, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 219, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 220, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 221, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 222, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 223, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 224, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 225, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 226, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 227, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 228, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 229, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 230, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 231, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 232, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 233, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 234, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 235, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 236, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 237, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 238, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 239, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 240, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 241, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 242, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 243, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 244, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 245, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 246, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 247, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 248, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 249, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 250, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 251, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 252, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 253, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 254, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 255, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 256, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 257, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 258, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 259, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 260, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 261, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 262, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 263, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 264, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAI", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIFood": { + "name": "HPAIFood", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Food", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 4, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 5, + "slot_group": "Database identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 17, + "slot_group": "Sample 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If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_origin_geo_loc_name_country": { + "name": "food_product_origin_geo_loc_name_country", + "description": "The country of origin of a food product.", + "title": "food_product_origin_geo_loc_name (country)", + "comments": [ + "If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "United States of America [GAZ:00002459]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_origin" + ], + "rank": 30, + "slot_uri": "GENEPIO:0100437", + "alias": "food_product_origin_geo_loc_name_country", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product": { + "name": "food_product", + "description": "A material consumed and digested for nutritional value or enjoyment.", + "title": "food_product", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feather meal [FOODON:00003927]" + }, + { + "value": "Bone meal [ENVO:02000054]" + }, + { + "value": "Chicken breast [FOODON:00002703]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:food_product_type" + ], + "rank": 31, + "slot_uri": "GENEPIO:0100444", + "alias": "food_product", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_product_properties": { + "name": "food_product_properties", + "description": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.", + "title": "food_product_properties", + "comments": [ + "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free)." + ], + "examples": [ + { + "value": "Food (chopped) [FOODON:00002777]" + }, + { + "value": "Ready-to-eat (RTE) [FOODON:03316636]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_product_properties", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 32, + "slot_uri": "GENEPIO:0100445", + "alias": "food_product_properties", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_product_properties menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_packaging": { + "name": "food_packaging", + "description": "The type of packaging used to contain a food product.", + "title": "food_packaging", + "comments": [ + "If known, provide information regarding how the food product was packaged." + ], + "examples": [ + { + "value": "Plastic tray or pan [FOODON:03490126]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:food_packaging", + "BIOSAMPLE_Enterics:food_contain_wrap" + ], + "rank": 33, + "slot_uri": "GENEPIO:0100447", + "alias": "food_packaging", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "food_packaging menu" + }, + { + "range": "null value menu" + } + ] + }, + "food_quality_date": { + "name": "food_quality_date", + "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", + "title": "food_quality_date", + "comments": [ + "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:food_quality_date" + ], + "rank": 34, + "slot_uri": "GENEPIO:0100615", + "alias": "food_quality_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "food_packaging_date": { + "name": "food_packaging_date", + "description": "A food product's packaging date as marked by a food manufacturer or retailer.", + "title": "food_packaging_date", + "comments": [ + "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." + ], + "examples": [ + { + "value": "2020-05-25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100616", + "alias": "food_packaging_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood" + ], + "slot_group": "Sample collection and processing", + "range": "date" + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 53, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 62, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 71, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 72, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 74, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 75, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 76, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 77, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 78, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 79, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 80, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 81, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 82, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 83, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 84, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 85, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 86, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 87, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 88, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 89, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 90, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 91, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 92, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 93, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 94, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 95, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 96, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 97, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 98, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 99, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 100, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 101, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 102, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 103, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 104, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 105, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 106, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 107, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 108, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 109, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 110, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 111, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 112, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 113, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 114, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 115, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 116, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 117, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 118, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 119, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 120, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 121, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 122, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 123, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 124, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 125, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 126, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 127, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 128, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 129, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 130, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 131, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 132, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 133, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 134, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 135, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 136, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 137, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIFood", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIWW": { + "name": "HPAIWW", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Wastewater", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 4, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 5, + "slot_group": "Database identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 17, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "rank": 18, + "slot_group": "Sample collection and processing" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "rank": 19, + "slot_group": "Sample collection and processing" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "rank": 20, + "slot_group": "Sample collection and processing" + }, + "organism": { + "name": "organism", + "rank": 21, + "slot_group": "Sample collection and processing" + }, + "influenza_subtype": { + "name": "influenza_subtype", + "rank": 22, + "slot_group": "Sample collection and processing" + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "rank": 23, + "slot_group": "Sample collection and processing" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "rank": 24, + "slot_group": "Sample collection and processing" + }, + "virus_identifier": { + "name": 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"percent_read_contamination_", + "rank": 194, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "rank": 195, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "rank": 196, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "rank": 197, + "slot_group": "Bioinformatics and QC metrics" + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 198, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 199, + "slot_group": "Bioinformatics and QC metrics" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "rank": 200, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "rank": 201, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "rank": 202, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "rank": 203, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "rank": 204, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "rank": 205, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "rank": 206, + "slot_group": "Taxonomic identification information" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "rank": 207, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region": { + "name": "genetic_target_region", + "rank": 208, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "rank": 210, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "rank": 211, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "rank": 212, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "rank": 213, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "rank": 214, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "rank": 215, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "rank": 216, + "slot_group": "Pathogen diagnostic testing" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "rank": 217, + "slot_group": "Risk assessment information" + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "rank": 218, + "slot_group": "Risk assessment information" + }, + "stage_of_production": { + "name": "stage_of_production", + "rank": 219, + "slot_group": "Risk assessment information" + }, + "experimental_intervention": { + "name": "experimental_intervention", + "rank": 220, + "slot_group": "Risk assessment information" + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "rank": 221, + "slot_group": "Risk assessment information" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 31, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 32, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 33, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 34, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 53, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 62, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 71, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 72, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + }, + { + "range": "null value 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"comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 75, + "slot_uri": "GENEPIO:0100912", + "alias": "precipitation_measurement_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "precipitation measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_method": { + "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample 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value menu" + } + ] + }, + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 139, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 140, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 141, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 142, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 143, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 144, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 145, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 146, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 147, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 148, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 149, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 150, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 151, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 152, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 153, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 154, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 155, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 156, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 157, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 158, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 159, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 160, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 161, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 162, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 163, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 164, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 165, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 166, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 167, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 168, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 169, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 170, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 171, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 172, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 173, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 174, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 175, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 176, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 177, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 178, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 179, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 180, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 181, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 182, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 183, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 184, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 185, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 186, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 187, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 188, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 189, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 190, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 191, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 192, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 193, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 194, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 195, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 196, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 197, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 198, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 199, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 200, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 201, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 202, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 203, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 204, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 205, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 206, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 207, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 208, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 209, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 210, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 211, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 212, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 213, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 214, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 215, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 216, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 217, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 218, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 219, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 220, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 221, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIWW", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIEnviro": { + "name": "HPAIEnviro", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Environmental", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + 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"name": "quality_control_determination", + "rank": 173, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_issues": { + "name": "quality_control_issues", + "rank": 174, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_details": { + "name": "quality_control_details", + "rank": 175, + "slot_group": "Bioinformatics and QC metrics" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "rank": 176, + "slot_group": "Bioinformatics and QC metrics" + }, + "dehosting_method": { + "name": "dehosting_method", + "rank": 177, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "rank": 178, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "rank": 179, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "rank": 180, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "rank": 181, + "slot_group": "Bioinformatics and QC metrics" + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "rank": 182, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "rank": 183, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "rank": 184, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_completeness": { + "name": "genome_completeness", + "rank": 185, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "rank": 186, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "rank": 187, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "rank": 188, + "slot_group": "Bioinformatics and QC metrics" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "rank": 189, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "rank": 190, + "slot_group": "Bioinformatics and QC metrics" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "rank": 191, + "slot_group": "Bioinformatics and QC metrics" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "rank": 192, + "slot_group": "Bioinformatics and QC metrics" + }, + "n50": { + "name": "n50", + "rank": 193, + "slot_group": "Bioinformatics and QC metrics" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "rank": 194, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "rank": 195, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "rank": 196, + "slot_group": "Bioinformatics and QC metrics" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "rank": 197, + "slot_group": "Bioinformatics and QC metrics" + }, + "deduplication_method": { + "name": "deduplication_method", + "rank": 198, + "slot_group": "Bioinformatics and QC metrics" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "rank": 199, + "slot_group": "Bioinformatics and QC metrics" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "rank": 200, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "rank": 201, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "rank": 202, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "rank": 203, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "rank": 204, + "slot_group": "Taxonomic identification information" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "rank": 205, + "slot_group": "Taxonomic identification information" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "rank": 206, + "slot_group": "Taxonomic identification information" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "rank": 207, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region": { + "name": "genetic_target_region", + "rank": 208, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "rank": 209, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "rank": 210, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "rank": 211, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "rank": 212, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "rank": 213, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "rank": 214, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "rank": 215, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "rank": 216, + "slot_group": "Pathogen diagnostic testing" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "rank": 217, + "slot_group": "Risk assessment information" + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "rank": 218, + "slot_group": "Risk assessment information" + }, + "stage_of_production": { + "name": "stage_of_production", + "rank": 219, + "slot_group": "Risk assessment information" + }, + "experimental_intervention": { + "name": "experimental_intervention", + "rank": 220, + "slot_group": "Risk assessment information" + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "rank": 221, + "slot_group": "Risk assessment information" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_date": { + "name": "sample_collection_end_date", + "description": "The date on which sample collection ended for a continuous sample.", + "title": "sample_collection_end_date", + "comments": [ + "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" + ], + "examples": [ + { + "value": "2020-03-18" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0101071", + "alias": "sample_collection_end_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_start_time": { + "name": "sample_collection_start_time", + "description": "The time at which sample collection began.", + "title": "sample_collection_start_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "17:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0101072", + "alias": "sample_collection_start_time", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_end_time": { + "name": "sample_collection_end_time", + "description": "The time at which sample collection ended.", + "title": "sample_collection_end_time", + "comments": [ + "Provide this time in ISO 8601 24hr format, in your local time." + ], + "examples": [ + { + "value": "19:15 PST" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0101073", + "alias": "sample_collection_end_time", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "time" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_of_day": { + "name": "sample_collection_time_of_day", + "description": "The descriptive time of day during which the sample was collected.", + "title": "sample_collection_time_of_day", + "comments": [ + "If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day." + ], + "examples": [ + { + "value": "Morning" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 31, + "slot_uri": "GENEPIO:0100765", + "alias": "sample_collection_time_of_day", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_collection_time_of_day menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_value": { + "name": "sample_collection_time_duration_value", + "description": "The amount of time over which the sample was collected.", + "title": "sample_collection_time_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 32, + "slot_uri": "GENEPIO:0100766", + "alias": "sample_collection_time_duration_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collection_time_duration_unit": { + "name": "sample_collection_time_duration_unit", + "description": "The units of the time duration measurement of sample collection.", + "title": "sample_collection_time_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Hour" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 33, + "slot_uri": "GENEPIO:0100767", + "alias": "sample_collection_time_duration_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "sample_collection_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 34, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 35, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_site": { + "name": "environmental_site", + "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", + "title": "environmental_site", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Poultry hatchery [ENVO:01001874]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_site", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:animal_env" + ], + "rank": 36, + "slot_uri": "GENEPIO:0001232", + "alias": "environmental_site", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_site menu" + }, + { + "range": "null value menu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", + "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", + "title": "environmental_material", + "comments": [ + "If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Soil [ENVO:00001998]" + }, + { + "value": "Water [CHEBI:15377]" + }, + { + "value": "Wastewater [ENVO:00002001]" + }, + { + "value": "Broom [ENVO:03501377]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:environmental_material", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 37, + "slot_uri": "GENEPIO:0001223", + "alias": "environmental_material", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "environmental_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 38, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 43, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 53, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 54, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 55, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 56, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_measurement_value": { + "name": "water_catchment_area_human_population_measurement_value", + "description": "The numerical value of the human population measurement that contributes to the composition of water in a catchment area.", + "title": "water_catchment_area_human_population_measurement_value", + "comments": [ + "Where known, provide the numerical value of population size, i.e. the number of people." + ], + "examples": [ + { + "value": "10,500" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 57, + "slot_uri": "GENEPIO:0100773", + "alias": "water_catchment_area_human_population_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "integer" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_range": { + "name": "water_catchment_area_human_population_range", + "description": "The human population range of the water catchment that contributes effluent to a wastewater site.", + "title": "water_catchment_area_human_population_range", + "comments": [ + "Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist." + ], + "examples": [ + { + "value": "1,000 - 10,000 people" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 58, + "slot_uri": "GENEPIO:0100774", + "alias": "water_catchment_area_human_population_range", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population range menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_catchment_area_human_population_measurement_method": { + "name": "water_catchment_area_human_population_measurement_method", + "description": "The method by which a water catchment 's human population size was measured or estimated", + "title": "water_catchment_area_human_population_measurement_method", + "comments": [ + "Provide a brief description of how catchment population size was measured or estimated." + ], + "examples": [ + { + "value": "population of jurisdiction encompassing the wastewater service area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0100775", + "alias": "water_catchment_area_human_population_measurement_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_value": { + "name": "water_catchment_area_human_population_density_value", + "description": "The numerical value describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density value", + "comments": [ + "Provide the numerical value of the population density in the catchement area." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 60, + "slot_uri": "GENEPIO:0100776", + "alias": "water_catchment_area_human_population_density_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_catchment_area_human_population_density_unit": { + "name": "water_catchment_area_human_population_density_unit", + "description": "The unit describing the number of humans per geographical area in a water catchment.", + "title": "water catchment area human population density unit", + "comments": [ + "Provide the unit of the population density in the catchement area." + ], + "examples": [ + { + "value": "persons per Km^2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 61, + "slot_uri": "GENEPIO:0100777", + "alias": "water_catchment_area_human_population_density_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water catchment area human population density unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "populated_area_type": { + "name": "populated_area_type", + "description": "A type of area that is populated by humans to different degrees.", + "title": "populated area type", + "comments": [ + "Provide the populated area type from the pick list." + ], + "examples": [ + { + "value": "Urban area" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 62, + "slot_uri": "GENEPIO:0100778", + "alias": "populated_area_type", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "populated area type menu" + }, + { + "range": "null value menu" + } + ] + }, + "sampling_weather_conditions": { + "name": "sampling_weather_conditions", + "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", + "title": "sampling weather conditions", + "comments": [ + "Provide the weather conditions at the time of sample collection." + ], + "examples": [ + { + "value": "Rain" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0100779", + "alias": "sampling_weather_conditions", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "sampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_weather_conditions": { + "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", + "title": "presampling weather conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Drizzle" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 64, + "slot_uri": "GENEPIO:0100780", + "alias": "presampling_weather_conditions", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "multivalued": true, + "any_of": [ + { + "range": "presampling weather conditions menu" + }, + { + "range": "null value menu" + } + ] + }, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 65, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0100440", + "alias": "water_depth", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0101025", + "alias": "water_depth_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0100697", + "alias": "sediment_depth", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0101026", + "alias": "sediment_depth_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sediment_depth_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0100441", + "alias": "air_temperature", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 71, + "slot_uri": "GENEPIO:0101027", + "alias": "air_temperature_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "air_temperature_units menu" + }, + { + "range": "null value menu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 72, + "slot_uri": "GENEPIO:0100698", + "alias": "water_temperature", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 73, + "slot_uri": "GENEPIO:0101028", + "alias": "water_temperature_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "water_temperature_units menu" + 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collection.", + "title": "sample temperature value (at collection)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 137, + "slot_uri": "GENEPIO:0100821", + "alias": "sample_temperature_value_at_collection", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_at_collection": { + "name": "sample_temperature_unit_at_collection", + "description": "The units of a measurement of temperature of a sample at the time of collection.", + "title": "sample temperature unit (at collection)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 138, + "slot_uri": "GENEPIO:0100822", + "alias": "sample_temperature_unit_at_collection", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (at collection) menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_temperature_value_when_received": { + "name": "sample_temperature_value_when_received", + "description": "The numerical value of a measurement of temperature of a sample upon receipt.", + "title": "sample temperature value (when received)", + "comments": [ + "Provide the numerical value of the measured temperature." + ], + "examples": [ + { + "value": "22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 139, + "slot_uri": "GENEPIO:0100823", + "alias": "sample_temperature_value_when_received", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "range": "WhitespaceMinimizedString" + }, + "sample_temperature_unit_when_received": { + "name": "sample_temperature_unit_when_received", + "description": "The units of a measurement of temperature of a sample at the time upon receipt.", + "title": "sample temperature unit (when received)", + "comments": [ + "Provide the units of the measured temperature." + ], + "examples": [ + { + "value": "degree Celsius (C)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 140, + "slot_uri": "GENEPIO:0100824", + "alias": "sample_temperature_unit_when_received", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "slot_group": "Environmental conditions and measurements", + "any_of": [ + { + "range": "sample temperature unit (when received) menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 141, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 142, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 143, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 144, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 145, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 146, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 147, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 148, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 149, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 150, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 151, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 152, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 153, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 154, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 155, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 156, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 157, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 158, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 159, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 160, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 161, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 162, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 163, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 164, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 165, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 166, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 167, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 168, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 169, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 170, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 171, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 172, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 173, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 174, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 175, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 176, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 177, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 178, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 179, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 180, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 181, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 182, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 183, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 184, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 185, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 186, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 187, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 188, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 189, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 190, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 191, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 192, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 193, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 194, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 195, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 196, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 197, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 198, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 199, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 200, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 201, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 202, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 203, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 204, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 205, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 206, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 207, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 208, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 209, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 210, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 211, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 212, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 213, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 214, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 215, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 216, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 217, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 218, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 219, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 220, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 221, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIEnviro", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + }, + "HPAIHost": { + "name": "HPAIHost", + "annotations": { + "version": { + "tag": "version", + "value": "1.0.0" + } + }, + "title": "HPAI Host", + "from_schema": "https://example.com/hpai", + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database identifiers" + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "rank": 2, + "slot_group": "Database identifiers" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "rank": 3, + "slot_group": "Database identifiers" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "rank": 4, + "slot_group": "Database identifiers" + }, + "sampling_event_id": { + "name": "sampling_event_id", + "rank": 5, + "slot_group": "Database identifiers" + }, + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 6, + "slot_group": "Database identifiers" + }, + "biosample_accession": { + "name": "biosample_accession", + "rank": 7, + "slot_group": "Database identifiers" + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "rank": 8, + "slot_group": "Database identifiers" + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "rank": 9, + "slot_group": "Database identifiers" + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "rank": 10, + "slot_group": "Sample collection and processing" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "rank": 11, + "slot_group": "Sample collection and processing" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "rank": 12, + "slot_group": "Sample collection and processing" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "rank": 13, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "rank": 14, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "rank": 15, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "rank": 16, + "slot_group": "Sample collection and processing" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "rank": 17, + "slot_group": "Sample 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"presampling_activity": { + "name": "presampling_activity", + "rank": 40, + "slot_group": "Sample collection and processing" + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "rank": 41, + "slot_group": "Sample collection and processing" + }, + "sample_storage_method": { + "name": "sample_storage_method", + "rank": 42, + "slot_group": "Sample collection and processing" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "rank": 43, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "rank": 44, + "slot_group": "Sample collection and processing" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "rank": 45, + "slot_group": "Sample collection and processing" + }, + "specimen_processing": { + "name": "specimen_processing", + "rank": 46, + "slot_group": "Sample collection and processing" + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "rank": 47, + "slot_group": "Sample collection and processing" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "rank": 48, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "rank": 49, + "slot_group": "Sample collection and processing" + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "rank": 50, + "slot_group": "Sample collection and processing" + }, + "available_data_types": { + "name": "available_data_types", + "rank": 51, + "slot_group": "Sample collection and processing" + }, + "available_data_type_details": { + "name": "available_data_type_details", + "rank": 52, + "slot_group": "Sample collection and processing" + }, + "host_common_name": { + "name": "host_common_name", + "rank": 53, + "slot_group": "Host information" + }, + "host_scientific_name": { + "name": "host_scientific_name", + "rank": 54, + "slot_group": "Host information" + }, + "host_ecotype": { + "name": "host_ecotype", + "rank": 55, + "slot_group": "Host information" + }, + "host_breed": { + "name": "host_breed", + "rank": 56, + "slot_group": "Host information" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "rank": 57, + "slot_group": "Host information" + }, + "host_age": { + "name": "host_age", + "rank": 58, + "slot_group": "Host Information" + }, + "host_age_unit": { + "name": "host_age_unit", + "rank": 59, + "slot_group": "Host Information" + }, + "host_age_bin": { + "name": "host_age_bin", + "rank": 60, + "slot_group": "Host information" + }, + "host_disease": { + "name": "host_disease", + "rank": 61, + "slot_group": "Host information" + }, + "host_health_state": { + "name": "host_health_state", + "rank": 62, + "slot_group": "Host Information" + }, + "host_health_status_details": { + "name": "host_health_status_details", + "rank": 63, + "slot_group": "Host Information" + }, + "host_health_outcome": { + "name": "host_health_outcome", + "rank": 64, + "slot_group": "Host Information" + }, + "host_subject_id": { + "name": "host_subject_id", + "rank": 65, + "slot_group": "Host Information" + }, + "case_id": { + "name": "case_id", + "rank": 66, + "slot_group": "Host Information" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "rank": 67, + "slot_group": "Host Information" + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "rank": 68, + "slot_group": "Host Information" + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "rank": 69, + "slot_group": "Host Information" + }, + "complications": { + "name": "complications", + "rank": 70, + "slot_group": "Host Information" + }, + "exposure_event": { + "name": "exposure_event", + "rank": 71, + "slot_group": "Host exposure information" + }, + "exposure_contact_level": { + "name": 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"slot_group": "Sequence information" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "rank": 87, + "slot_group": "Sequence information" + }, + "sequencing_date": { + "name": "sequencing_date", + "rank": 88, + "slot_group": "Sequence information" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "rank": 89, + "slot_group": "Sequence information" + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "rank": 90, + "slot_group": "Sequence information" + }, + "sequenced_by": { + "name": "sequenced_by", + "rank": 91, + "slot_group": "Sequence information" + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "rank": 92, + "slot_group": "Sequence information" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "rank": 93, + "slot_group": "Sequence information" + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "rank": 94, + "slot_group": "Sequence information" + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "rank": 95, + "slot_group": "Sequence information" + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "rank": 96, + "slot_group": "Sequence information" + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "rank": 97, + "slot_group": "Sample collection and processing" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "rank": 98, + "slot_group": "Sample collection and processing" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "rank": 99, + "slot_group": "Sample collection and processing" + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "rank": 100, + "slot_group": "Sequence information" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "rank": 101, + "slot_group": "Sequence information" + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "rank": 102, + "slot_group": "Sequence information" + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "rank": 103, + "slot_group": "Sequence information" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "rank": 104, + "slot_group": "Sequence information" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "rank": 105, + "slot_group": "Sequence information" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "rank": 106, + "slot_group": "Sequence information" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "rank": 107, + "slot_group": "Sequence information" + }, + "amplicon_size": { + "name": "amplicon_size", + "rank": 108, + "slot_group": "Sequence information" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "rank": 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"slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "rank": 118, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_issues": { + "name": "quality_control_issues", + "rank": 119, + "slot_group": "Bioinformatics and QC metrics" + }, + "quality_control_details": { + "name": "quality_control_details", + "rank": 120, + "slot_group": "Bioinformatics and QC metrics" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "rank": 121, + "slot_group": "Bioinformatics and QC metrics" + }, + "dehosting_method": { + "name": "dehosting_method", + "rank": 122, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "rank": 123, + "slot_group": "Bioinformatics and QC metrics" + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "rank": 124, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "rank": 125, + "slot_group": "Bioinformatics and QC metrics" + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "rank": 126, + "slot_group": "Bioinformatics and QC metrics" + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "rank": 127, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "rank": 128, + "slot_group": "Bioinformatics and QC metrics" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "rank": 129, + "slot_group": "Bioinformatics and QC metrics" + }, + "genome_completeness": { + "name": "genome_completeness", + "rank": 130, + "slot_group": "Bioinformatics and QC metrics" + }, + "number_of_base_pairs_sequenced": { + "name": 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"genetic_target_name", + "rank": 152, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region": { + "name": "genetic_target_region", + "rank": 153, + "slot_group": "Pathogen diagnostic testing" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "rank": 154, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "rank": 155, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "rank": 156, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "rank": 157, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "rank": 158, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "rank": 159, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "rank": 160, + "slot_group": "Pathogen diagnostic testing" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "rank": 161, + "slot_group": "Pathogen diagnostic testing" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "rank": 162, + "slot_group": "Risk assessment information" + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "rank": 163, + "slot_group": "Risk assessment information" + }, + "stage_of_production": { + "name": "stage_of_production", + "rank": 164, + "slot_group": "Risk assessment information" + }, + "experimental_intervention": { + "name": "experimental_intervention", + "rank": 165, + "slot_group": "Risk assessment information" + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "rank": 166, + "slot_group": "Risk assessment information" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen_collector_sample_ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "ASDFG123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:sample_name" + ], + "rank": 1, + "slot_uri": "GENEPIO:0001123", + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "specimen_collector_subsample_id": { + "name": "specimen_collector_subsample_id", + "description": "The user-defined identifier assigned to a portion of the original sample.", + "title": "specimen_collector_subsample_ID", + "comments": [ + "Store the ID for the subsample/aliquot." + ], + "examples": [ + { + "value": "ASDFG123_12" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 2, + "slot_uri": "GENEPIO:0100752", + "alias": "specimen_collector_subsample_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "pooled_sample_id": { + "name": "pooled_sample_id", + "description": "The user-defined identifier assigned to a combined (pooled) set of samples.", + "title": "pooled_sample_ID", + "comments": [ + "If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID." + ], + "examples": [ + { + "value": "12345AYZ" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 3, + "slot_uri": "GENEPIO:0100996", + "alias": "pooled_sample_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString" + }, + "sampling_site_id": { + "name": "sampling_site_id", + "description": "The user-defined identifier assigned to a specific location from which samples are taken.", + "title": "sampling_site_ID", + "comments": [ + "Store the ID for the site from which a sample was taken. The \"site\" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID." + ], + "examples": [ + { + "value": "Site 12A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 4, + "slot_uri": "GENEPIO:0100760", + "alias": "sampling_site_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sampling_event_id": { + "name": "sampling_event_id", + "description": "The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites.", + "title": "sampling_event_ID", + "comments": [ + "Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site." + ], + "examples": [ + { + "value": "Event 120522.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 5, + "slot_uri": "GENEPIO:0100761", + "alias": "sampling_event_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "bioproject_accession": { + "name": "bioproject_accession", + "description": "The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs.", + "title": "BioProject_accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:bioproject_accession" + ], + "rank": 6, + "slot_uri": "GENEPIO:0001136", + "alias": "bioproject_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "biosample_accession": { + "name": "biosample_accession", + "description": "The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives.", + "title": "BioSample_accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD" + ], + "examples": [ + { + "value": "SAMN14180202, SAMD00000001" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 7, + "slot_uri": "GENEPIO:0001139", + "alias": "biosample_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "recommended": true, + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_sequence_read_accession": { + "name": "insdc_sequence_read_accession", + "description": "The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC sequence read accession", + "comments": [ + "Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR." + ], + "examples": [ + { + "value": "ERR123456, DRR123456, CRR123456" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 8, + "slot_uri": "GENEPIO:0101203", + "alias": "insdc_sequence_read_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "insdc_assembly_accession": { + "name": "insdc_assembly_accession", + "description": "The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories.", + "title": "INSDC assembly accession", + "comments": [ + "Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version." + ], + "examples": [ + { + "value": "LZ986655.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 9, + "slot_uri": "GENEPIO:0101204", + "alias": "insdc_assembly_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Database identifiers", + "range": "WhitespaceMinimizedString", + "pattern": "{UPPER_CASE}", + "structured_pattern": { + "syntax": "{UPPER_CASE}", + "interpolated": true, + "partial_match": false + } + }, + "sample_collection_data_steward_name": { + "name": "sample_collection_data_steward_name", + "description": "The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_name", + "comments": [ + "Provide the name of the sample collection data steward." + ], + "examples": [ + { + "value": "Joe Bloggs" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 10, + "slot_uri": "GENEPIO:0100762", + "alias": "sample_collection_data_steward_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_data_steward_contact_email": { + "name": "sample_collection_data_steward_contact_email", + "description": "The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample.", + "title": "sample_collection_data_steward_contact_email", + "comments": [ + "Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the \"sample collector contact email\"." + ], + "examples": [ + { + "value": "bloggsj@aglab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 11, + "slot_uri": "GENEPIO:0101107", + "alias": "sample_collection_data_steward_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collected_by": { + "name": "sample_collected_by", + "description": "The name of the organization with which the sample collector is affiliated.", + "title": "sample_collected_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collected_by" + ], + "rank": 12, + "slot_uri": "GENEPIO:0001153", + "alias": "sample_collected_by", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sample.", + "title": "sample_collector_contact_email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "WaterTester@facility.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 13, + "slot_uri": "GENEPIO:0001156", + "alias": "sample_collector_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "The country of origin of the sample.", + "title": "geo_loc_name_(country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 14, + "slot_uri": "GENEPIO:0001181", + "alias": "geo_loc_name_country", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "geo_loc_name_(country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "The state/province/territory of origin of the sample.", + "title": "geo_loc_name_(state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga" + ], + "examples": [ + { + "value": "Western Cape" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:geo_loc_name" + ], + "rank": 15, + "slot_uri": "GENEPIO:0001185", + "alias": "geo_loc_name_state_province_territory", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", + "description": "The county/region of origin of the sample.", + "title": "geo_loc_name_(county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 16, + "slot_uri": "GENEPIO:0100280", + "alias": "geo_loc_name_county_region", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "The city of origin of the sample.", + "title": "geo_loc_name_(city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 17, + "slot_uri": "GENEPIO:0001189", + "alias": "geo_loc_name_city", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_name_site__": { + "name": "geo_loc_name_site__", + "description": "The name of a specific geographical location e.g. Credit River (rather than river).", + "title": "geo_loc_name_(site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Credit River" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 18, + "slot_uri": "GENEPIO:0100436", + "alias": "geo_loc_name_site__", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_latitude": { + "name": "geo_loc_latitude", + "description": "The latitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 19, + "slot_uri": "GENEPIO:0100309", + "alias": "geo_loc_latitude", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "geo_loc_longitude": { + "name": "geo_loc_longitude", + "description": "The longitude coordinates of the geographical location of sample collection.", + "title": "geo_loc_longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:lat_lon" + ], + "rank": 20, + "slot_uri": "GENEPIO:0100310", + "alias": "geo_loc_longitude", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "organism": { + "name": "organism", + "description": "Taxonomic name of the organism.", + "title": "organism", + "comments": [ + "Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy." + ], + "examples": [ + { + "value": "Vibrio cholerae" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:organism" + ], + "rank": 21, + "slot_uri": "GENEPIO:0001191", + "alias": "organism", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "organism menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_subtype": { + "name": "influenza_subtype", + "title": "influenza_subtype", + "from_schema": "https://example.com/hpai", + "rank": 22, + "slot_uri": "GENEPIO:0101108", + "alias": "influenza_subtype", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subsubtype menu", + "required": true, + "multivalued": true + }, + "influenza_subtyping_scheme_name": { + "name": "influenza_subtyping_scheme_name", + "title": "influenza_subtyping_scheme_name", + "from_schema": "https://example.com/hpai", + "rank": 23, + "slot_uri": "GENEPIO:0101109", + "alias": "influenza_subtyping_scheme_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "influenza_subtyping_scheme_name menu" + }, + "taxonomic_identification_process": { + "name": "taxonomic_identification_process", + "title": "taxonomic_identification_process", + "from_schema": "https://example.com/hpai", + "rank": 24, + "slot_uri": "GENEPIO:0100583", + "alias": "taxonomic_identification_process", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "taxonomic_identification_process menu" + }, + "virus_identifier": { + "name": "virus_identifier", + "title": "virus_identifier", + "from_schema": "https://example.com/hpai", + "rank": 25, + "slot_uri": "GENEPIO:0101110", + "alias": "virus_identifier", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "who_oie_fao_h5_clade": { + "name": "who_oie_fao_h5_clade", + "title": "WHO/OIE/FAO_H5_clade", + "from_schema": "https://example.com/hpai", + "rank": 26, + "slot_uri": "GENEPIO:0101111", + "alias": "who_oie_fao_h5_clade", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "The date on which the sample was collected, or sampling began for a continuous sample.", + "title": "sample_collection_date", + "comments": [ + "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:collection_date" + ], + "rank": 27, + "slot_uri": "GENEPIO:0001174", + "alias": "sample_collection_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "The date on which the sample was received.", + "title": "sample received date", + "comments": [ + "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-28" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 28, + "slot_uri": "GENEPIO:0001179", + "alias": "sample_received_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "sample_processing_date": { + "name": "sample_processing_date", + "description": "The date on which the sample was processed.", + "title": "sample processing date", + "comments": [ + "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 29, + "slot_uri": "GENEPIO:0100763", + "alias": "sample_processing_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "host_origin_geo_loc_name_country": { + "name": "host_origin_geo_loc_name_country", + "description": "The country of origin of the host.", + "title": "host_origin_geo_loc_name (country)", + "comments": [ + "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 30, + "slot_uri": "GENEPIO:0100438", + "alias": "host_origin_geo_loc_name_country", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "geo_loc_name (country) menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_material": { + "name": "anatomical_material", + "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", + "title": "anatomical_material", + "comments": [ + "An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Tissue [UBERON:0000479]" + }, + { + "value": "Blood [UBERON:0000178]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_material", + "BIOSAMPLE_Enterics:host_tissue_sampled", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 31, + "slot_uri": "GENEPIO:0001211", + "alias": "anatomical_material", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_material menu" + }, + { + "range": "null value menu" + } + ] + }, + "body_product": { + "name": "body_product", + "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", + "title": "body_product", + "comments": [ + "A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + }, + { + "value": "Urine [UBERON:0001088]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:body_product", + "BIOSAMPLE_Enterics:host_body_product", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 32, + "slot_uri": "GENEPIO:0001216", + "alias": "body_product", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "body_product menu" + }, + { + "range": "null value menu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", + "description": "An anatomical part of an organism e.g. oropharynx.", + "title": "anatomical_part", + "comments": [ + "An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Snout [UBERON:0006333]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:anatomical_part", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 33, + "slot_uri": "GENEPIO:0001214", + "alias": "anatomical_part", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "anatomical_part menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_device": { + "name": "collection_device", + "description": "The instrument or container used to collect the sample e.g. swab.", + "title": "collection_device", + "comments": [ + "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Drag swab [OBI:0002822]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_device", + "BIOSAMPLE_Enterics:samp_collect_device", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 34, + "slot_uri": "GENEPIO:0001234", + "alias": "collection_device", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_device menu" + }, + { + "range": "null value menu" + } + ] + }, + "collection_method": { + "name": "collection_method", + "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", + "title": "collection_method", + "comments": [ + "If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon." + ], + "examples": [ + { + "value": "Rinsing for specimen collection [GENEPIO_0002116]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:isolation_source", + "GISAID:collection_method", + "BIOSAMPLE_Enterics:isolation_source" + ], + "rank": 35, + "slot_uri": "GENEPIO:0001241", + "alias": "collection_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "recommended": true, + "any_of": [ + { + "range": "collection_method menu" + }, + { + "range": "null value menu" + } + ] + }, + "sample_volume_measurement_value": { + "name": "sample_volume_measurement_value", + "description": "The numerical value of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_value", + "comments": [ + "Provide the numerical value of volume." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 36, + "slot_uri": "GENEPIO:0100768", + "alias": "sample_volume_measurement_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_volume_measurement_unit": { + "name": "sample_volume_measurement_unit", + "description": "The units of the volume measurement of the sample collected.", + "title": "sample_volume_measurement_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "milliliter (mL) [UO:0000098]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 37, + "slot_uri": "GENEPIO:0100769", + "alias": "sample_volume_measurement_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "sample_volume_measurement_unit menu" + }, + "residual_sample_status": { + "name": "residual_sample_status", + "description": "The status of the residual sample (whether any sample remains after its original use).", + "title": "residual_sample_status", + "comments": [ + "Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select \"Residual sample remaining (some sample left)\"." + ], + "examples": [ + { + "value": "No residual sample (sample all used) [GENEPIO:0101088]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 38, + "slot_uri": "GENEPIO:0101090", + "alias": "residual_sample_status", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "residual_sample_status menu" + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "The reason that the sample was collected.", + "title": "purpose_of_sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Public health surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:purpose_of_sampling" + ], + "rank": 39, + "slot_uri": "GENEPIO:0001198", + "alias": "purpose_of_sampling", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sampling menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity": { + "name": "presampling_activity", + "description": "The activities or variables upstream of sample collection that may affect the sample.", + "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Agricultural activity" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 40, + "slot_uri": "GENEPIO:0100433", + "alias": "presampling_activity", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "presampling_activity menu" + }, + { + "range": "null value menu" + } + ] + }, + "presampling_activity_details": { + "name": "presampling_activity_details", + "description": "The details of the activities or variables that affected the sample collected.", + "title": "presampling_activity_details", + "comments": [ + "Briefly describe the presampling activities using free text." + ], + "examples": [ + { + "value": "Agricultural waste from large farm contributes waste to the site sampled." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 41, + "slot_uri": "GENEPIO:0100434", + "alias": "presampling_activity_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sample_storage_method": { + "name": "sample_storage_method", + "description": "The process used to store the sample.", + "title": "sample_storage_method", + "comments": [ + "Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here." + ], + "examples": [ + { + "value": "The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 42, + "slot_uri": "GENEPIO:0100448", + "alias": "sample_storage_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_medium": { + "name": "sample_storage_medium", + "description": "The medium in which a sample is stored.", + "title": "sample_storage_medium", + "comments": [ + "Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write \"None\"." + ], + "examples": [ + { + "value": "Cary-Blair transport medium" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 43, + "slot_uri": "GENEPIO:0100449", + "alias": "sample_storage_medium", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_value": { + "name": "sample_storage_duration_value", + "description": "The numerical value of the time measurement during which a sample is in storage.", + "title": "sample_storage_duration_value", + "comments": [ + "Provide the numerical value of time." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 44, + "slot_uri": "GENEPIO:0101014", + "alias": "sample_storage_duration_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "sample_storage_duration_unit": { + "name": "sample_storage_duration_unit", + "description": "The units of a measured sample storage duration.", + "title": "sample_storage_duration_unit", + "comments": [ + "Provide the units from the pick list." + ], + "examples": [ + { + "value": "Day" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 45, + "slot_uri": "GENEPIO:0101015", + "alias": "sample_storage_duration_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "sample_storage_duration_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing": { + "name": "specimen_processing", + "description": "Any processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing", + "comments": [ + "Select processes from the picklist that were applied to this sample." + ], + "examples": [ + { + "value": "Centrifugation" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 46, + "slot_uri": "GENEPIO:0001253", + "alias": "specimen_processing", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "specimen_processing menu" + }, + { + "range": "null value menu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "The details of the processing applied to the sample during or after receiving the sample.", + "title": "specimen_processing_details", + "comments": [ + "Briefly describe the processes applied to the sample." + ], + "examples": [ + { + "value": "25 samples were pooled and further prepared as a single sample during library prep." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 47, + "slot_uri": "GENEPIO:0100311", + "alias": "specimen_processing_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_protocol": { + "name": "experimental_protocol", + "description": "The name of the overarching experimental methodology that was used to process the biomaterial.", + "title": "experimental_protocol", + "comments": [ + "Provide the name of the methodology used in your study. If available, provide a link to the protocol." + ], + "from_schema": "https://example.com/hpai", + "rank": 48, + "slot_uri": "GENEPIO:0101029", + "alias": "experimental_protocol", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "experimental_specimen_role_type": { + "name": "experimental_specimen_role_type", + "description": "The type of role that the sample represents in the experiment.", + "title": "experimental_specimen_role_type", + "comments": [ + "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\"." + ], + "examples": [ + { + "value": "Positive experimental control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 49, + "slot_uri": "GENEPIO:0100921", + "alias": "experimental_specimen_role_type", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "experimental_specimen_role_type menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_specimen_details": { + "name": "experimental_specimen_details", + "title": "experimental_specimen_details", + "from_schema": "https://example.com/hpai", + "rank": 50, + "slot_uri": "GENEPIO:0101112", + "alias": "experimental_specimen_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "available_data_types": { + "name": "available_data_types", + "description": "The type of data that is available, that may or may not require permission to access.", + "title": "available_data_types", + "comments": [ + "This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information." + ], + "examples": [ + { + "value": "Total coliform count [GENEPIO:0100729]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 51, + "slot_uri": "GENEPIO:0100690", + "alias": "available_data_types", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "available_data_types menu" + }, + { + "range": "null value menu" + } + ] + }, + "available_data_type_details": { + "name": "available_data_type_details", + "description": "Detailed information regarding other available data types.", + "title": "available_data_type_details", + "comments": [ + "Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data." + ], + "examples": [ + { + "value": "Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 52, + "slot_uri": "GENEPIO:0101023", + "alias": "available_data_type_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "host_common_name": { + "name": "host_common_name", + "description": "The commonly used name of the host.", + "title": "host_(common_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name." + ], + "examples": [ + { + "value": "Cow [NCBITaxon:9913]" + }, + { + "value": "Chicken [NCBITaxon:9913], Human [NCBITaxon:9606]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 53, + "slot_uri": "GENEPIO:0001386", + "alias": "host_common_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (common name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", + "description": "The taxonomic, or scientific name of the host.", + "title": "host_(scientific_name)", + "comments": [ + "If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided." + ], + "examples": [ + { + "value": "Bos taurus [NCBITaxon:9913]" + }, + { + "value": "Homo sapiens [NCBITaxon:9103]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host", + "BIOSAMPLE_Enterics:isolation_source", + "BIOSAMPLE_Enterics:host" + ], + "rank": 54, + "slot_uri": "GENEPIO:0001387", + "alias": "host_scientific_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "recommended": true, + "any_of": [ + { + "range": "host (scientific name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_ecotype": { + "name": "host_ecotype", + "description": "The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler.", + "title": "host_(ecotype)", + "comments": [ + "Provide the name of the ecotype of the host organism." + ], + "examples": [ + { + "value": "Sea ecotype" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_variety" + ], + "rank": 55, + "slot_uri": "GENEPIO:0100450", + "alias": "host_ecotype", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_breed": { + "name": "host_breed", + "description": "A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding.", + "title": "host_(breed)", + "comments": [ + "Provide the name of the breed of the host organism." + ], + "examples": [ + { + "value": "Holstein" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:host_disease", + "BIOSAMPLE_Enterics:host_animal_breed" + ], + "rank": 56, + "slot_uri": "GENEPIO:0100451", + "alias": "host_breed", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "range": "WhitespaceMinimizedString" + }, + "host_food_production_name": { + "name": "host_food_production_name", + "description": "The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity.", + "title": "host_(food production name)", + "comments": [ + "Select the host's food production name from the pick list." + ], + "examples": [ + { + "value": "Calf [FOODON:03411349]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host" + ], + "rank": 57, + "slot_uri": "GENEPIO:0100452", + "alias": "host_food_production_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host (food production name) menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age": { + "name": "host_age", + "description": "Age of host at the time of sampling.", + "title": "host_age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:host_age" + ], + "rank": 58, + "slot_uri": "GENEPIO:0001392", + "alias": "host_age", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_unit": { + "name": "host_age_unit", + "description": "The units used to measure the host's age.", + "title": "host_age_unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 59, + "slot_uri": "GENEPIO:0001393", + "alias": "host_age_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "required": true, + "any_of": [ + { + "range": "host_age_unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_age_bin": { + "name": "host_age_bin", + "description": "Age of host at the time of sampling, expressed as an age group.", + "title": "host_age_bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank." + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_age" + ], + "rank": 60, + "slot_uri": "GENEPIO:0001394", + "alias": "host_age_bin", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_age_bin menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_disease": { + "name": "host_disease", + "description": "The name of the disease experienced by the host.", + "title": "host_disease", + "comments": [ + "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”." + ], + "examples": [ + { + "value": "mastitis, gastroenteritis" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "BIOSAMPLE_Enterics:host_disease" + ], + "rank": 61, + "slot_uri": "GENEPIO:0001391", + "alias": "host_disease", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host information", + "any_of": [ + { + "range": "host_disease menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_state": { + "name": "host_health_state", + "description": "Health status of the host at the time of sample collection.", + "title": "host_health_state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:host_health_state" + ], + "rank": 62, + "slot_uri": "GENEPIO:0001388", + "alias": "host_health_state", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_state menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Further details pertaining to the health or disease status of the host at time of collection.", + "title": "host_health_status_details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 63, + "slot_uri": "GENEPIO:0001389", + "alias": "host_health_status_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_status_details menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Disease outcome in the host.", + "title": "host_health_outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_disease_outcome" + ], + "rank": 64, + "slot_uri": "GENEPIO:0001390", + "alias": "host_health_outcome", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "host_health_outcome menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_subject_id": { + "name": "host_subject_id", + "description": "A unique identifier by which each host can be referred to e.g. #131", + "title": "host_subject_ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:host_subject_id" + ], + "rank": 65, + "slot_uri": "GENEPIO:0001398", + "alias": "host_subject_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "case_id": { + "name": "case_id", + "description": "The identifier used to specify an epidemiologically detected case of disease.", + "title": "case_ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 66, + "slot_uri": "GENEPIO:0100281", + "alias": "case_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "range": "WhitespaceMinimizedString" + }, + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "The date on which the symptoms began or were first noted.", + "title": "symptom_onset_date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 67, + "slot_uri": "GENEPIO:0001399", + "alias": "symptom_onset_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "null value menu" + } + ] + }, + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", + "title": "signs_and_symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 68, + "slot_uri": "GENEPIO:0001400", + "alias": "signs_and_symptoms", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "signs_and_symptoms menu" + }, + { + "range": "null value menu" + } + ] + }, + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", + "title": "pre-existing_conditions_and_risk_factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 69, + "slot_uri": "GENEPIO:0001401", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "pre-existing_conditions_and_risk_factors menu" + }, + { + "range": "null value menu" + } + ] + }, + "complications": { + "name": "complications", + "description": "Patient medical complications that are believed to have occurred as a result of host disease.", + "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 70, + "slot_uri": "GENEPIO:0001402", + "alias": "complications", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host Information", + "recommended": true, + "any_of": [ + { + "range": "complications menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_event": { + "name": "exposure_event", + "description": "Event leading to exposure.", + "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 71, + "slot_uri": "GENEPIO:0001417", + "alias": "exposure_event", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure event menu" + }, + { + "range": "null value menu" + } + ] + }, + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "The exposure transmission contact type.", + "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], + "rank": 72, + "slot_uri": "GENEPIO:0001418", + "alias": "exposure_contact_level", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "exposure contact level menu" + }, + { + "range": "null value menu" + } + ] + }, + "host_role": { + "name": "host_role", + "description": "The role of the host in relation to the exposure setting.", + "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], + "rank": 73, + "slot_uri": "GENEPIO:0001419", + "alias": "host_role", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "host role menu", + "multivalued": true + }, + "exposure_setting": { + "name": "exposure_setting", + "description": "The setting leading to exposure.", + "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], + "rank": 74, + "slot_uri": "GENEPIO:0001428", + "alias": "exposure_setting", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "exposure setting menu", + "multivalued": true + }, + "exposure_details": { + "name": "exposure_details", + "description": "Additional host exposure information.", + "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], + "rank": 75, + "slot_uri": "GENEPIO:0001431", + "alias": "exposure_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host exposure information", + "range": "WhitespaceMinimizedString" + }, + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", + "title": "host_vaccination_status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "CNPHI:prior_sars_cov_2_vaccination" + ], + "rank": 76, + "slot_uri": "GENEPIO:0001404", + "alias": "host_vaccination_status", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host_vaccination_status menu" + }, + { + "range": "null value menu" + } + ] + }, + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "The number of doses of the vaccine recived by the host.", + "title": "number_of_vaccine_doses_received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 77, + "slot_uri": "GENEPIO:0001406", + "alias": "number_of_vaccine_doses_received", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "integer", + "minimum_value": 0 + }, + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", + "title": "vaccination_dose_1_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 78, + "slot_uri": "GENEPIO:0100313", + "alias": "vaccination_dose_1_vaccine_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "The date the first dose of a vaccine was administered.", + "title": "vaccination_dose_1_vaccination_date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 79, + "slot_uri": "GENEPIO:0100314", + "alias": "vaccination_dose_1_vaccination_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", + "title": "vaccination_dose_2_vaccine_name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 80, + "slot_uri": "GENEPIO:0100315", + "alias": "vaccination_dose_2_vaccine_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "The date the second dose of a vaccine was administered.", + "title": "vaccination_dose_2_vaccination_date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 81, + "slot_uri": "GENEPIO:0100316", + "alias": "vaccination_dose_2_vaccination_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "date" + }, + "vaccination_history": { + "name": "vaccination_history", + "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", + "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], + "rank": 82, + "slot_uri": "GENEPIO:0100321", + "alias": "vaccination_history", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host vaccination information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_administration": { + "name": "influenza_antiviral_treatment_administration", + "description": "An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen.", + "title": "influenza_antiviral_treatment_administration", + "examples": [ + { + "value": "Influenza antiviral treatment administered [GENEPIO:0101194]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 83, + "slot_uri": "GENEPIO:0101113", + "alias": "influenza_antiviral_treatment_administration", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "any_of": [ + { + "range": "influenza_antiviral_treatment_administration menu" + }, + { + "range": "null value menu" + } + ] + }, + "influenza_antiviral_agent__": { + "name": "influenza_antiviral_agent__", + "description": "A substance that destroys or inhibits replication of viruses.", + "title": "influenza_antiviral_agent", + "from_schema": "https://example.com/hpai", + "rank": 84, + "slot_uri": "GENEPIO:0101114", + "alias": "influenza_antiviral_agent__", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "WhitespaceMinimizedString" + }, + "influenza_antiviral_treatment_date": { + "name": "influenza_antiviral_treatment_date", + "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", + "title": "influenza_antiviral_treatment_date", + "comments": [ + "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." + ], + "from_schema": "https://example.com/hpai", + "rank": 85, + "slot_uri": "GENEPIO:0101115", + "alias": "influenza_antiviral_treatment_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIHost" + ], + "slot_group": "Host treatment information", + "range": "date" + }, + "library_id": { + "name": "library_id", + "description": "The user-specified identifier for the library prepared for sequencing.", + "title": "library_ID", + "comments": [ + "Every \"library ID\" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "LS_2010_NP_123446" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 86, + "slot_uri": "GENEPIO:0001448", + "alias": "library_id", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_assay_type": { + "name": "sequencing_assay_type", + "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", + "title": "sequencing_assay_type", + "comments": [ + "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." + ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 87, + "slot_uri": "GENEPIO:0100997", + "alias": "sequencing_assay_type", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "sequencing_assay_type menu" + }, + "sequencing_date": { + "name": "sequencing_date", + "description": "The date the sample was sequenced.", + "title": "sequencing_date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 88, + "slot_uri": "GENEPIO:0001447", + "alias": "sequencing_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "date" + }, + "purpose_of_sequencing__": { + "name": "purpose_of_sequencing__", + "description": "The reason that the sample was sequenced.", + "title": "purpose_of_sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Travel-associated surveillance" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 89, + "slot_uri": "GENEPIO:0001445", + "alias": "purpose_of_sequencing__", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "purpose_of_sequencing menu" + }, + { + "range": "null value menu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "The description of why the sample was sequenced providing specific details.", + "title": "purpose_of_sequencing_details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities." + ], + "examples": [ + { + "value": "Investigating schools/universities" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 90, + "slot_uri": "GENEPIO:0001446", + "alias": "purpose_of_sequencing_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", + "title": "sequenced_by", + "comments": [ + "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]" + } + ], + "from_schema": "https://example.com/hpai", + "exact_mappings": [ + "GISAID:sequenced_by", + "BIOSAMPLE_Enterics:sequenced_by" + ], + "rank": 91, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced_by_laboratory_name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 92, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", + "description": "The name or title of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Enterics Lab Manager" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 93, + "slot_uri": "GENEPIO:0100471", + "alias": "sequenced_by_contact_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequenced_by_contact_email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "enterics@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 94, + "slot_uri": "GENEPIO:0100422", + "alias": "sequenced_by_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "The name of the agency that submitted the sequence to a database.", + "title": "sequence_submitted_by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 95, + "slot_uri": "GENEPIO:0001159", + "alias": "sequence_submitted_by", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "The email address of the contact responsible for follow-up regarding the sequence.", + "title": "sequence_submitter_contact_email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 96, + "slot_uri": "GENEPIO:0001165", + "alias": "sequence_submitter_contact_email", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "recommended": true, + "pattern": "^\\S+@\\S+\\.\\S+$", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "nucleic_acid_extraction_method": { + "name": "nucleic_acid_extraction_method", + "description": "The process used to extract genomic material from a sample.", + "title": "nucleic_acid_extraction_method", + "comments": [ + "Briefly describe the extraction method used." + ], + "examples": [ + { + "value": "Direct wastewater RNA capture and purification via the \"Sewage, Salt, Silica and SARS-CoV-2 (4S)\" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 97, + "slot_uri": "GENEPIO:0100939", + "alias": "nucleic_acid_extraction_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "nucleic_acid_extraction_kit": { + "name": "nucleic_acid_extraction_kit", + "description": "The kit used to extract genomic material from a sample", + "title": "nucleic_acid_extraction_kit", + "comments": [ + "Provide the name of the genomic extraction kit used." + ], + "examples": [ + { + "value": "QIAamp PowerFecal Pro DNA Kit" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 98, + "slot_uri": "GENEPIO:0100772", + "alias": "nucleic_acid_extraction_kit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString" + }, + "endogenous_control_details": { + "name": "endogenous_control_details", + "description": "The description of the endogenous controls included when extracting a sample.", + "title": "endogenous control details", + "comments": [ + "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." + ], + "from_schema": "https://example.com/hpai", + "rank": 99, + "slot_uri": "GENEPIO:0100923", + "alias": "endogenous_control_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sample collection and processing", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "sequencing_project_name": { + "name": "sequencing_project_name", + "description": "The name of the project/initiative/program for which sequencing was performed.", + "title": "sequencing_project_name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "AMR-GRDI (PA-1356)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 100, + "slot_uri": "GENEPIO:0100472", + "alias": "sequencing_project_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_platform": { + "name": "sequencing_platform", + "description": "The platform technology used to perform the sequencing.", + "title": "sequencing_platform", + "comments": [ + "Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina [GENEPIO:0001923]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 101, + "slot_uri": "GENEPIO:0100473", + "alias": "sequencing_platform", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_platform menu" + }, + { + "range": "null value menu" + } + ] + }, + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "The model of the sequencing instrument used.", + "title": "sequencing_instrument", + "comments": [ + "Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Illumina HiSeq 2500 [GENEPIO:0100117]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 102, + "slot_uri": "GENEPIO:0001452", + "alias": "sequencing_instrument", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "any_of": [ + { + "range": "sequencing_instrument menu" + }, + { + "range": "null value menu" + } + ] + }, + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", + "title": "library_preparation_kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 103, + "slot_uri": "GENEPIO:0001450", + "alias": "library_preparation_kit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "dna_fragment_length": { + "name": "dna_fragment_length", + "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", + "title": "DNA_fragment_length", + "comments": [ + "Provide the fragment length in base pairs (do not include the units)." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 104, + "slot_uri": "GENEPIO:0100843", + "alias": "dna_fragment_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "genomic_target_enrichment_method": { + "name": "genomic_target_enrichment_method", + "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method", + "comments": [ + "Provide the name of the enrichment method" + ], + "examples": [ + { + "value": "Hybrid selection method (bait-capture) [GENEPIO:0001950]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 105, + "slot_uri": "GENEPIO:0100966", + "alias": "genomic_target_enrichment_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "genomic_target_enrichment_method menu" + }, + "genomic_target_enrichment_method_details": { + "name": "genomic_target_enrichment_method_details", + "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", + "title": "genomic_target_enrichment_method_details", + "comments": [ + "Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information)." + ], + "examples": [ + { + "value": "enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 106, + "slot_uri": "GENEPIO:0100967", + "alias": "genomic_target_enrichment_method_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon_pcr_primer_scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "artic v3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 107, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon_size", + "comments": [ + "Provide the amplicon size expressed in base pairs." + ], + "examples": [ + { + "value": "300" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 108, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "Integer" + }, + "sequencing_flow_cell_version": { + "name": "sequencing_flow_cell_version", + "description": "The version number of the flow cell used for generating sequence data.", + "title": "sequencing_flow_cell_version", + "comments": [ + "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." + ], + "examples": [ + { + "value": "R.9.4.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 109, + "slot_uri": "GENEPIO:0101102", + "alias": "sequencing_flow_cell_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "The protocol or method used for sequencing.", + "title": "sequencing_protocol", + "comments": [ + "Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 110, + "slot_uri": "GENEPIO:0001454", + "alias": "sequencing_protocol", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1_fastq_filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 111, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2_fastq_filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 112, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5_filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "batch1a_sequences.fast5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 113, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "genome_sequence_file_name": { + "name": "genome_sequence_file_name", + "description": "The name of the sequence file.", + "title": "genome sequence file name", + "comments": [ + "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + ], + "examples": [ + { + "value": "mpxvassembly.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 114, + "slot_uri": "GENEPIO:0101715", + "alias": "genome_sequence_file_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "assembly_filename": { + "name": "assembly_filename", + "description": "The user-defined filename of the FASTA file.", + "title": "assembly_filename", + "comments": [ + "Provide the FASTA filename." + ], + "examples": [ + { + "value": "pathogenassembly123.fasta" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 115, + "slot_uri": "GENEPIO:0001461", + "alias": "assembly_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Sequence information", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_name": { + "name": "quality_control_method_name", + "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method name", + "comments": [ + "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." + ], + "examples": [ + { + "value": "ncov-tools" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 116, + "slot_uri": "GENEPIO:0100557", + "alias": "quality_control_method_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_method_version": { + "name": "quality_control_method_version", + "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", + "title": "quality control method version", + "comments": [ + "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." + ], + "examples": [ + { + "value": "1.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 117, + "slot_uri": "GENEPIO:0100558", + "alias": "quality_control_method_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "quality_control_determination": { + "name": "quality_control_determination", + "description": "The determination of a quality control assessment.", + "title": "quality control determination", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "sequence failed quality control" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 118, + "slot_uri": "GENEPIO:0100559", + "alias": "quality_control_determination", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_determination menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_issues": { + "name": "quality_control_issues", + "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", + "title": "quality control issues", + "comments": [ + "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." + ], + "examples": [ + { + "value": "low average genome coverage" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 119, + "slot_uri": "GENEPIO:0100560", + "alias": "quality_control_issues", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "multivalued": true, + "any_of": [ + { + "range": "quality_control_issues menu" + }, + { + "range": "null value menu" + } + ] + }, + "quality_control_details": { + "name": "quality_control_details", + "description": "The details surrounding a low quality determination in a quality control assessment.", + "title": "quality control details", + "comments": [ + "Provide notes or details regarding QC results using free text." + ], + "examples": [ + { + "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 120, + "slot_uri": "GENEPIO:0100561", + "alias": "quality_control_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "title": "raw sequence data processing method", + "comments": [ + "Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 121, + "slot_uri": "GENEPIO:0001458", + "alias": "raw_sequence_data_processing_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "dehosting_method": { + "name": "dehosting_method", + "description": "The method used to remove host reads from the pathogen sequence.", + "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 122, + "slot_uri": "GENEPIO:0001459", + "alias": "dehosting_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_name": { + "name": "sequence_assembly_software_name", + "description": "The name of the software used to assemble a sequence.", + "title": "sequence assembly software name", + "comments": [ + "Provide the name of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 123, + "slot_uri": "GENEPIO:0100825", + "alias": "sequence_assembly_software_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "sequence_assembly_software_version": { + "name": "sequence_assembly_software_version", + "description": "The version of the software used to assemble a sequence.", + "title": "sequence assembly software version", + "comments": [ + "Provide the version of the software used to assemble the sequence." + ], + "examples": [ + { + "value": "3.15.5" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 124, + "slot_uri": "GENEPIO:0100826", + "alias": "sequence_assembly_software_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of the software used to generate the consensus sequence.", + "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 125, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 126, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 127, + "slot_uri": "GENEPIO:0001472", + "alias": "breadth_of_coverage_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 128, + "slot_uri": "GENEPIO:0001474", + "alias": "depth_of_coverage_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "The threshold used as a cut-off for the depth of coverage.", + "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 129, + "slot_uri": "GENEPIO:0001475", + "alias": "depth_of_coverage_threshold", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "genome_completeness": { + "name": "genome_completeness", + "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", + "title": "genome completeness", + "comments": [ + "Provide the genome completeness as a percent (no need to include units)." + ], + "examples": [ + { + "value": "85" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 130, + "slot_uri": "GENEPIO:0100844", + "alias": "genome_completeness", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 131, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_total_reads": { + "name": "number_of_total_reads", + "description": "The total number of non-unique reads generated by the sequencing process.", + "title": "number of total reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "423867" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 132, + "slot_uri": "GENEPIO:0100827", + "alias": "number_of_total_reads", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_unique_reads": { + "name": "number_of_unique_reads", + "description": "The number of unique reads generated by the sequencing process.", + "title": "number of unique reads", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "248236" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 133, + "slot_uri": "GENEPIO:0100828", + "alias": "number_of_unique_reads", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "minimum_posttrimming_read_length": { + "name": "minimum_posttrimming_read_length", + "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", + "title": "minimum post-trimming read length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 134, + "slot_uri": "GENEPIO:0100829", + "alias": "minimum_posttrimming_read_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "number_of_contigs": { + "name": "number_of_contigs", + "description": "The number of contigs (contiguous sequences) in a sequence assembly.", + "title": "number of contigs", + "comments": [ + "Provide a numerical value." + ], + "examples": [ + { + "value": "10" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 135, + "slot_uri": "GENEPIO:0100937", + "alias": "number_of_contigs", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_ns_across_total_genome_length": { + "name": "percent_ns_across_total_genome_length", + "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", + "title": "percent Ns across total genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 136, + "slot_uri": "GENEPIO:0100830", + "alias": "percent_ns_across_total_genome_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", + "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "342" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 137, + "slot_uri": "GENEPIO:0001484", + "alias": "ns_per_100_kbp", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "n50": { + "name": "n50", + "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", + "title": "N50", + "comments": [ + "Provide the N50 value in Mb." + ], + "examples": [ + { + "value": "150" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 138, + "slot_uri": "GENEPIO:0100938", + "alias": "n50", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "percent_read_contamination_": { + "name": "percent_read_contamination_", + "description": "The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset.", + "title": "percent read contamination", + "comments": [ + "Provide the percent contamination value (no need to include units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 139, + "slot_uri": "GENEPIO:0100845", + "alias": "percent_read_contamination_", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "sequence_assembly_length": { + "name": "sequence_assembly_length", + "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", + "title": "sequence assembly length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "34272" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 140, + "slot_uri": "GENEPIO:0100846", + "alias": "sequence_assembly_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "The length of the genome defined by the most common nucleotides at each position.", + "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 141, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "integer" + }, + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "A persistent, unique identifier of a genome database entry.", + "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 142, + "slot_uri": "GENEPIO:0001485", + "alias": "reference_genome_accession", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "deduplication_method": { + "name": "deduplication_method", + "description": "The method used to remove duplicated reads in a sequence read dataset.", + "title": "deduplication method", + "comments": [ + "Provide the deduplication software name followed by the version, or a link to a tool or method." + ], + "examples": [ + { + "value": "DeDup 0.12.8" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 143, + "slot_uri": "GENEPIO:0100831", + "alias": "deduplication_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "A description of the overall bioinformatics strategy used.", + "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 144, + "slot_uri": "GENEPIO:0001489", + "alias": "bioinformatics_protocol", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Bioinformatics and QC metrics", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_name": { + "name": "read_mapping_software_name", + "description": "The name of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software name", + "comments": [ + "Provide the name of the read mapping software." + ], + "examples": [ + { + "value": "Bowtie2, BWA-MEM, TopHat" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 145, + "slot_uri": "GENEPIO:0100832", + "alias": "read_mapping_software_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "read_mapping_software_version": { + "name": "read_mapping_software_version", + "description": "The version of the software used to map sequence reads to a reference genome or set of reference genes.", + "title": "read mapping software version", + "comments": [ + "Provide the version number of the read mapping software." + ], + "examples": [ + { + "value": "2.5.1" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 146, + "slot_uri": "GENEPIO:0100833", + "alias": "read_mapping_software_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_name": { + "name": "taxonomic_reference_database_name", + "description": "The name of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database name", + "comments": [ + "Provide the name of the taxonomic reference database." + ], + "examples": [ + { + "value": "NCBITaxon" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 147, + "slot_uri": "GENEPIO:0100834", + "alias": "taxonomic_reference_database_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_reference_database_version": { + "name": "taxonomic_reference_database_version", + "description": "The version of the taxonomic reference database used to identify the organism.", + "title": "taxonomic reference database version", + "comments": [ + "Provide the version number of the taxonomic reference database." + ], + "examples": [ + { + "value": "1.3" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 148, + "slot_uri": "GENEPIO:0100835", + "alias": "taxonomic_reference_database_version", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_report_filename": { + "name": "taxonomic_analysis_report_filename", + "description": "The filename of the report containing the results of a taxonomic analysis.", + "title": "taxonomic analysis report filename", + "comments": [ + "Provide the filename of the report containing the results of the taxonomic analysis." + ], + "examples": [ + { + "value": "WWtax_report_Feb1_2024.doc" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 149, + "slot_uri": "GENEPIO:0101074", + "alias": "taxonomic_analysis_report_filename", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "taxonomic_analysis_date": { + "name": "taxonomic_analysis_date", + "description": "The date a taxonomic analysis was performed.", + "title": "taxonomic analysis date", + "comments": [ + "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2024-02-01" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 150, + "slot_uri": "GENEPIO:0101075", + "alias": "taxonomic_analysis_date", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "date" + }, + "read_mapping_criteria": { + "name": "read_mapping_criteria", + "description": "A description of the criteria used to map reads to a reference sequence.", + "title": "read mapping criteria", + "comments": [ + "Provide a description of the read mapping criteria." + ], + "examples": [ + { + "value": "Phred score >20" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 151, + "slot_uri": "GENEPIO:0100836", + "alias": "read_mapping_criteria", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Taxonomic identification information", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_name": { + "name": "genetic_target_name", + "description": "The name of the genetic marker used for testing.", + "title": "genetic target name", + "comments": [ + "Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "gyrase A" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 152, + "slot_uri": "GENEPIO:0101116", + "alias": "genetic_target_name", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "null value menu" + } + ] + }, + "genetic_target_region": { + "name": "genetic_target_region", + "description": "The specific region or segment of a genetic sequence used for testing or analysis.", + "title": "genetic target region", + "from_schema": "https://example.com/hpai", + "rank": 153, + "slot_uri": "GENEPIO:0101117", + "alias": "genetic_target_region", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "genetic_target_region_reference_genome": { + "name": "genetic_target_region_reference_genome", + "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", + "title": "genetic target region reference genome", + "from_schema": "https://example.com/hpai", + "rank": 154, + "slot_uri": "GENEPIO:0101118", + "alias": "genetic_target_region_reference_genome", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_target_presence": { + "name": "diagnostic_target_presence", + "description": "The binary value of the result from a diagnostic test.", + "title": "diagnostic target presence", + "comments": [ + "Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample." + ], + "examples": [ + { + "value": "diagnostic target present" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 155, + "slot_uri": "GENEPIO:0100962", + "alias": "diagnostic_target_presence", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic target presence menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_value": { + "name": "diagnostic_measurement_value", + "description": "The value of the result from a diagnostic test.", + "title": "diagnostic measurement value", + "comments": [ + "Provide the numerical result of a diagnostic test (no need to include units)." + ], + "examples": [ + { + "value": "1000" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 156, + "slot_uri": "GENEPIO:0100963", + "alias": "diagnostic_measurement_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_measurement_unit": { + "name": "diagnostic_measurement_unit", + "description": "The unit of the result from a diagnostic test.", + "title": "diagnostic measurement unit", + "comments": [ + "Select a value from the pick list provided, to describe the units of the given diagnostic test." + ], + "examples": [ + { + "value": "cycle threshold (Ct)" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 157, + "slot_uri": "GENEPIO:0100964", + "alias": "diagnostic_measurement_unit", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement unit menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_measurement_method": { + "name": "diagnostic_measurement_method", + "description": "The method by which a diagnostic result was determined.", + "title": "diagnostic measurement method", + "comments": [ + "Select a value from the pick list provided to describe the method used for a given diagnostic test." + ], + "examples": [ + { + "value": "qPCR" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 158, + "slot_uri": "GENEPIO:0100965", + "alias": "diagnostic_measurement_method", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "diagnostic measurement method menu" + }, + { + "range": "null value menu" + } + ] + }, + "diagnostic_testing_threshold_value": { + "name": "diagnostic_testing_threshold_value", + "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold value", + "from_schema": "https://example.com/hpai", + "rank": 159, + "slot_uri": "GENEPIO:0101104", + "alias": "diagnostic_testing_threshold_value", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "integer" + }, + "diagnostic_testing_threshold_units": { + "name": "diagnostic_testing_threshold_units", + "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", + "title": "diagnostic testing threshold units", + "from_schema": "https://example.com/hpai", + "rank": 160, + "slot_uri": "GENEPIO:0101105", + "alias": "diagnostic_testing_threshold_units", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "diagnostic_testing_details": { + "name": "diagnostic_testing_details", + "description": "Describe any details of the diagnsotic testing.", + "title": "diagnostic testing details", + "from_schema": "https://example.com/hpai", + "rank": 161, + "slot_uri": "GENEPIO:0101106", + "alias": "diagnostic_testing_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Pathogen diagnostic testing", + "range": "WhitespaceMinimizedString" + }, + "prevalence_metrics": { + "name": "prevalence_metrics", + "description": "Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project.", + "title": "prevalence_metrics", + "comments": [ + "Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are \" Number of total samples collected\", \"Number of positive samples\", \"Average count of hazard organism\", \"Average count of indicator organism\". You do not need to provide the actual values, just indicate that the information is available." + ], + "examples": [ + { + "value": "Number of total samples collected, Number of positive samples" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 162, + "slot_uri": "GENEPIO:0100480", + "alias": "prevalence_metrics", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "prevalence_metrics_details": { + "name": "prevalence_metrics_details", + "description": "The details pertaining to the prevalence metrics from a surveillance project.", + "title": "prevalence_metrics_details", + "comments": [ + "If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text." + ], + "examples": [ + { + "value": "Hazard organism counts (i.e. Salmonella) do not distinguish between serovars." + } + ], + "from_schema": "https://example.com/hpai", + "rank": 163, + "slot_uri": "GENEPIO:0100481", + "alias": "prevalence_metrics_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + }, + "stage_of_production": { + "name": "stage_of_production", + "description": "The stage of food production.", + "title": "stage_of_production", + "comments": [ + "Provide the stage of food production as free text." + ], + "examples": [ + { + "value": "Abattoir [ENVO:01000925]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 164, + "slot_uri": "GENEPIO:0100482", + "alias": "stage_of_production", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "any_of": [ + { + "range": "stage_of_production menu" + }, + { + "range": "null value menu" + } + ] + }, + "experimental_intervention": { + "name": "experimental_intervention", + "description": "The category of the experimental intervention applied in the food production system.", + "title": "experimental_intervention", + "comments": [ + "In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided." + ], + "examples": [ + { + "value": "Vaccination [NCIT:C15346]" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 165, + "slot_uri": "GENEPIO:0100483", + "alias": "experimental_intervention", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "experimental_intervention menu" + }, + { + "range": "null value menu" + } + ] + }, + "experiment_intervention_details": { + "name": "experiment_intervention_details", + "description": "The details of the experimental intervention applied in the food production system.", + "title": "experiment_intervention_details", + "comments": [ + "If an experimental intervention was applied in the survey, provide details in this field as free text." + ], + "examples": [ + { + "value": "2% cranberry solution mixed in feed" + } + ], + "from_schema": "https://example.com/hpai", + "rank": 166, + "slot_uri": "GENEPIO:0100484", + "alias": "experiment_intervention_details", + "owner": "HPAIHost", + "domain_of": [ + "HPAI", + "HPAIFood", + "HPAIWW", + "HPAIEnviro", + "HPAIHost" + ], + "slot_group": "Risk assessment information", + "range": "WhitespaceMinimizedString", + "recommended": true + } + } + } + }, + "settings": { + "Title_Case": { + "setting_key": "Title_Case", + "setting_value": "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" + }, + "UPPER_CASE": { + "setting_key": "UPPER_CASE", + "setting_value": "[A-Z\\W\\d_]*" + }, + "lower_case": { + "setting_key": "lower_case", + "setting_value": "[a-z\\W\\d_]*" + } + }, + "@type": "SchemaDefinition" +} \ No newline at end of file diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml new file mode 100644 index 00000000..83dafead --- /dev/null +++ b/web/templates/hpai/schema.yaml @@ -0,0 +1,15257 @@ +id: https://example.com/hpai +name: Mpox +version: 4.3.3 +description: The HPAI specification was developed by the Public Health Alliance for + Genomic Epidemiology (PHA4GE) to better enable harmonization of highly pathogenic + avian influenza genomic surveillance contextual data. The specification is intended + to support H5N1 monitoring, and provides standardized, ontology-based fields and + terms for samples, sequences, and bioinformatics analysis. +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ +classes: + dh_interface: + name: dh_interface + description: A DataHarmonizer interface + from_schema: https://example.com/hpai + HPAI: + name: HPAI + title: HPAI + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_collection_end_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - sample_received_date + - sample_processing_date + - host_origin_geo_loc_name_country + - food_product_origin_geo_loc_name_country + - food_product + - food_product_properties + - food_packaging + - food_quality_date + - food_packaging_date + - environmental_site + - environmental_material + - anatomical_material + - body_product + - anatomical_part + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - host_common_name + - host_scientific_name + - host_ecotype + - host_breed + - host_food_production_name + - host_age + - host_age_unit + - host_age_bin + - host_disease + - host_health_state + - host_health_status_details + - host_health_outcome + - host_subject_id + - case_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors + - complications + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_history + - influenza_antiviral_treatment_administration + - influenza_antiviral_agent__ + - influenza_antiviral_treatment_date + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - water_depth + - water_depth_units + - sediment_depth + - sediment_depth_units + - air_temperature + - air_temperature_units + - water_temperature + - water_temperature_units + - weather_type + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator_ + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_collection_end_date: + rank: 28 + slot_group: Sample collection and processing + sample_collection_start_time: + rank: 29 + slot_group: Sample collection and processing + sample_collection_end_time: + rank: 30 + slot_group: Sample collection and processing + sample_collection_time_of_day: + rank: 31 + slot_group: Sample collection and processing + sample_collection_time_duration_value: + rank: 32 + slot_group: Sample collection and processing + sample_collection_time_duration_unit: + rank: 33 + slot_group: Sample collection and processing + sample_received_date: + rank: 34 + slot_group: Sample collection and processing + sample_processing_date: + rank: 35 + slot_group: Sample collection and processing + host_origin_geo_loc_name_country: + rank: 36 + slot_group: Sample collection and processing + food_product_origin_geo_loc_name_country: + rank: 37 + slot_group: Sample collection and processing + food_product: + rank: 38 + slot_group: Sample collection and processing + food_product_properties: + rank: 39 + slot_group: Sample collection and processing + food_packaging: + rank: 40 + slot_group: Sample collection and processing + food_quality_date: + rank: 41 + slot_group: Sample collection and processing + food_packaging_date: + rank: 42 + slot_group: Sample collection and processing + environmental_site: + rank: 43 + slot_group: Sample collection and processing + environmental_material: + rank: 44 + slot_group: Sample collection and processing + anatomical_material: + rank: 45 + slot_group: Sample collection and processing + body_product: + rank: 46 + slot_group: Sample collection and processing + anatomical_part: + rank: 47 + slot_group: Sample collection and processing + collection_device: + rank: 48 + slot_group: Sample collection and processing + collection_method: + rank: 49 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 50 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 51 + slot_group: Sample collection and processing + residual_sample_status: + rank: 52 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 53 + slot_group: Sample collection and processing + presampling_activity: + rank: 54 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 55 + slot_group: Sample collection and processing + sample_storage_method: + rank: 56 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 57 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 58 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 59 + slot_group: Sample collection and processing + specimen_processing: + rank: 60 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 61 + slot_group: Sample collection and processing + experimental_protocol: + rank: 62 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 63 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 64 + slot_group: Sample collection and processing + available_data_types: + rank: 65 + slot_group: Sample collection and processing + available_data_type_details: + rank: 66 + slot_group: Sample collection and processing + host_common_name: + rank: 67 + slot_group: Host information + host_scientific_name: + rank: 68 + slot_group: Host information + host_ecotype: + rank: 69 + slot_group: Host information + host_breed: + rank: 70 + slot_group: Host information + host_food_production_name: + rank: 71 + slot_group: Host information + host_age: + rank: 72 + slot_group: Host Information + host_age_unit: + rank: 73 + slot_group: Host Information + host_age_bin: + rank: 74 + slot_group: Host information + host_disease: + rank: 75 + slot_group: Host information + host_health_state: + rank: 76 + slot_group: Host Information + host_health_status_details: + rank: 77 + slot_group: Host Information + host_health_outcome: + rank: 78 + slot_group: Host Information + host_subject_id: + rank: 79 + slot_group: Host Information + case_id: + rank: 80 + slot_group: Host Information + symptom_onset_date: + rank: 81 + slot_group: Host Information + signs_and_symptoms: + rank: 82 + slot_group: Host Information + preexisting_conditions_and_risk_factors: + rank: 83 + slot_group: Host Information + complications: + rank: 84 + slot_group: Host Information + exposure_event: + rank: 85 + slot_group: Host exposure information + exposure_contact_level: + rank: 86 + slot_group: Host exposure information + host_role: + rank: 87 + slot_group: Host exposure information + exposure_setting: + rank: 88 + slot_group: Host exposure information + exposure_details: + rank: 89 + slot_group: Host exposure information + host_vaccination_status: + rank: 90 + slot_group: Host vaccination information + number_of_vaccine_doses_received: + rank: 91 + slot_group: Host vaccination information + vaccination_dose_1_vaccine_name: + rank: 92 + slot_group: Host vaccination information + vaccination_dose_1_vaccination_date: + rank: 93 + slot_group: Host vaccination information + vaccination_dose_2_vaccine_name: + rank: 94 + slot_group: Host vaccination information + vaccination_dose_2_vaccination_date: + rank: 95 + slot_group: Host vaccination information + vaccination_history: + rank: 96 + slot_group: Host vaccination information + influenza_antiviral_treatment_administration: + rank: 97 + slot_group: Host treatment information + influenza_antiviral_agent__: + rank: 98 + slot_group: Host treatment information + influenza_antiviral_treatment_date: + rank: 99 + slot_group: Host treatment information + water_catchment_area_human_population_measurement_value: + rank: 100 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_range: + rank: 101 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_measurement_method: + rank: 102 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_value: + rank: 103 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_unit: + rank: 104 + slot_group: Environmental conditions and measurements + populated_area_type: + rank: 105 + slot_group: Environmental conditions and measurements + sampling_weather_conditions: + rank: 106 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 107 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 108 + slot_group: Environmental conditions and measurements + water_depth: + rank: 109 + slot_group: Environmental conditions and measurements + water_depth_units: + rank: 110 + slot_group: Environmental conditions and measurements + sediment_depth: + rank: 111 + slot_group: Environmental conditions and measurements + sediment_depth_units: + rank: 112 + slot_group: Environmental conditions and measurements + air_temperature: + rank: 113 + slot_group: Environmental conditions and measurements + air_temperature_units: + rank: 114 + slot_group: Environmental conditions and measurements + water_temperature: + rank: 115 + slot_group: Environmental conditions and measurements + water_temperature_units: + rank: 116 + slot_group: Environmental conditions and measurements + weather_type: + rank: 117 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 118 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 119 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_value: + rank: 120 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_unit: + rank: 121 + slot_group: Environmental conditions and measurements + ph_measurement_value: + rank: 122 + slot_group: Environmental conditions and measurements + ph_measurement_method: + rank: 123 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_value: + rank: 124 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_unit: + rank: 125 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_method: + rank: 126 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_value: + rank: 127 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_unit: + rank: 128 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_method: + rank: 129 + slot_group: Environmental conditions and measurements + turbidity_measurement_value: + rank: 130 + slot_group: Environmental conditions and measurements + turbidity_measurement_unit: + rank: 131 + slot_group: Environmental conditions and measurements + turbidity_measurement_method: + rank: 132 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_value: + rank: 133 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_unit: + rank: 134 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_method: + rank: 135 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_value: + rank: 136 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_unit: + rank: 137 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_method: + rank: 138 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_value: + rank: 139 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_unit: + rank: 140 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_method: + rank: 141 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + rank: 142 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + rank: 143 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + rank: 144 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_value: + rank: 145 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_unit: + rank: 146 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_method: + rank: 147 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_value: + rank: 148 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_unit: + rank: 149 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_method: + rank: 150 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_value: + rank: 151 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_unit: + rank: 152 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_method: + rank: 153 + slot_group: Environmental conditions and measurements + alkalinity_measurement_value: + rank: 154 + slot_group: Environmental conditions and measurements + alkalinity_measurement_unit: + rank: 155 + slot_group: Environmental conditions and measurements + alkalinity_measurement_method: + rank: 156 + slot_group: Environmental conditions and measurements + conductivity_measurement_value: + rank: 157 + slot_group: Environmental conditions and measurements + conductivity_measurement_unit: + rank: 158 + slot_group: Environmental conditions and measurements + conductivity_measurement_method: + rank: 159 + slot_group: Environmental conditions and measurements + salinity_measurement_value: + rank: 160 + slot_group: Environmental conditions and measurements + salinity_measurement_unit: + rank: 161 + slot_group: Environmental conditions and measurements + salinity_measurement_method: + rank: 162 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_value: + rank: 163 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_unit: + rank: 164 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_method: + rank: 165 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_value: + rank: 166 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_unit: + rank: 167 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_method: + rank: 168 + slot_group: Environmental conditions and measurements + fecal_contamination_indicator_: + rank: 169 + slot_group: Environmental conditions and measurements + fecal_contamination_value: + rank: 170 + slot_group: Environmental conditions and measurements + fecal_contamination_unit: + rank: 171 + slot_group: Environmental conditions and measurements + fecal_contamination_method: + rank: 172 + slot_group: Environmental conditions and measurements + fecal_coliform_count_value: + rank: 173 + slot_group: Environmental conditions and measurements + fecal_coliform_count_unit: + rank: 174 + slot_group: Environmental conditions and measurements + fecal_coliform_count_method: + rank: 175 + slot_group: Environmental conditions and measurements + urinary_contamination_indicator: + rank: 176 + slot_group: Environmental conditions and measurements + urinary_contamination_value: + rank: 177 + slot_group: Environmental conditions and measurements + urinary_contamination_unit: + rank: 178 + slot_group: Environmental conditions and measurements + urinary_contamination_method: + rank: 179 + slot_group: Environmental conditions and measurements + sample_temperature_value_at_collection: + rank: 180 + slot_group: Environmental conditions and measurements + sample_temperature_unit_at_collection: + rank: 181 + slot_group: Environmental conditions and measurements + sample_temperature_value_when_received: + rank: 182 + slot_group: Environmental conditions and measurements + sample_temperature_unit_when_received: + rank: 183 + slot_group: Environmental conditions and measurements + library_id: + rank: 184 + slot_group: Sequence information + sequencing_assay_type: + rank: 185 + slot_group: Sequence information + sequencing_date: + rank: 186 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 187 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 188 + slot_group: Sequence information + sequenced_by: + rank: 189 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 190 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 191 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 192 + slot_group: Sequence information + sequence_submitted_by: + rank: 193 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 194 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 195 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 196 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 197 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 198 + slot_group: Sequence information + sequencing_platform: + rank: 199 + slot_group: Sequence information + sequencing_instrument: + rank: 200 + slot_group: Sequence information + library_preparation_kit: + rank: 201 + slot_group: Sequence information + dna_fragment_length: + rank: 202 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 203 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 204 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 205 + slot_group: Sequence information + amplicon_size: + rank: 206 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 207 + slot_group: Sequence information + sequencing_protocol: + rank: 208 + slot_group: Sequence information + r1_fastq_filename: + rank: 209 + slot_group: Sequence information + r2_fastq_filename: + rank: 210 + slot_group: Sequence information + fast5_filename: + rank: 211 + slot_group: Sequence information + genome_sequence_file_name: + rank: 212 + slot_group: Sequence information + assembly_filename: + rank: 213 + slot_group: Sequence information + quality_control_method_name: + rank: 214 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 215 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 216 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 217 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 218 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 219 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 220 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 221 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 222 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 223 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 224 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 225 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 226 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 227 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 228 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 229 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 230 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 231 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 232 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 233 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 234 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 235 + slot_group: Bioinformatics and QC metrics + n50: + rank: 236 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 237 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 238 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 239 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 240 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 241 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 242 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 243 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 244 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 245 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 246 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 247 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 248 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 249 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 250 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 251 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 252 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 253 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 254 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 255 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 256 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 257 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 258 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 259 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 260 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 261 + slot_group: Risk assessment information + stage_of_production: + rank: 262 + slot_group: Risk assessment information + experimental_intervention: + rank: 263 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 264 + slot_group: Risk assessment information + HPAIFood: + name: HPAIFood + title: HPAI Food + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_received_date + - sample_processing_date + - food_product_origin_geo_loc_name_country + - food_product + - food_product_properties + - food_packaging + - food_quality_date + - food_packaging_date + - environmental_site + - environmental_material + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_received_date: + rank: 28 + slot_group: Sample collection and processing + sample_processing_date: + rank: 29 + slot_group: Sample collection and processing + food_product_origin_geo_loc_name_country: + rank: 30 + slot_group: Sample collection and processing + food_product: + rank: 31 + slot_group: Sample collection and processing + food_product_properties: + rank: 32 + slot_group: Sample collection and processing + food_packaging: + rank: 33 + slot_group: Sample collection and processing + food_quality_date: + rank: 34 + slot_group: Sample collection and processing + food_packaging_date: + rank: 35 + slot_group: Sample collection and processing + environmental_site: + rank: 36 + slot_group: Sample collection and processing + environmental_material: + rank: 37 + slot_group: Sample collection and processing + collection_device: + rank: 38 + slot_group: Sample collection and processing + collection_method: + rank: 39 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 40 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 41 + slot_group: Sample collection and processing + residual_sample_status: + rank: 42 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 43 + slot_group: Sample collection and processing + presampling_activity: + rank: 44 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 45 + slot_group: Sample collection and processing + sample_storage_method: + rank: 46 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 47 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 48 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 49 + slot_group: Sample collection and processing + specimen_processing: + rank: 50 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 51 + slot_group: Sample collection and processing + experimental_protocol: + rank: 52 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 53 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 54 + slot_group: Sample collection and processing + available_data_types: + rank: 55 + slot_group: Sample collection and processing + available_data_type_details: + rank: 56 + slot_group: Sample collection and processing + library_id: + rank: 57 + slot_group: Sequence information + sequencing_assay_type: + rank: 58 + slot_group: Sequence information + sequencing_date: + rank: 59 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 60 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 61 + slot_group: Sequence information + sequenced_by: + rank: 62 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 63 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 64 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 65 + slot_group: Sequence information + sequence_submitted_by: + rank: 66 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 67 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 68 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 69 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 70 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 71 + slot_group: Sequence information + sequencing_platform: + rank: 72 + slot_group: Sequence information + sequencing_instrument: + rank: 73 + slot_group: Sequence information + library_preparation_kit: + rank: 74 + slot_group: Sequence information + dna_fragment_length: + rank: 75 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 76 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 77 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 78 + slot_group: Sequence information + amplicon_size: + rank: 79 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 80 + slot_group: Sequence information + sequencing_protocol: + rank: 81 + slot_group: Sequence information + r1_fastq_filename: + rank: 82 + slot_group: Sequence information + r2_fastq_filename: + rank: 83 + slot_group: Sequence information + fast5_filename: + rank: 84 + slot_group: Sequence information + genome_sequence_file_name: + rank: 85 + slot_group: Sequence information + assembly_filename: + rank: 86 + slot_group: Sequence information + quality_control_method_name: + rank: 87 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 88 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 89 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 90 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 91 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 92 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 93 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 94 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 95 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 96 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 97 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 98 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 99 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 100 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 101 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 102 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 103 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 104 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 105 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 106 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 107 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 108 + slot_group: Bioinformatics and QC metrics + n50: + rank: 109 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 110 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 111 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 112 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 113 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 114 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 115 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 116 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 117 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 118 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 119 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 120 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 121 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 122 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 123 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 124 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 125 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 126 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 127 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 128 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 129 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 130 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 131 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 132 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 133 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 134 + slot_group: Risk assessment information + stage_of_production: + rank: 135 + slot_group: Risk assessment information + experimental_intervention: + rank: 136 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 137 + slot_group: Risk assessment information + HPAIWW: + name: HPAIWW + title: HPAI Wastewater + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_collection_end_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - sample_received_date + - sample_processing_date + - environmental_site + - environmental_material + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - water_depth + - water_depth_units + - sediment_depth + - sediment_depth_units + - air_temperature + - air_temperature_units + - water_temperature + - water_temperature_units + - weather_type + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator_ + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_collection_end_date: + rank: 28 + slot_group: Sample collection and processing + sample_collection_start_time: + rank: 29 + slot_group: Sample collection and processing + sample_collection_end_time: + rank: 30 + slot_group: Sample collection and processing + sample_collection_time_of_day: + rank: 31 + slot_group: Sample collection and processing + sample_collection_time_duration_value: + rank: 32 + slot_group: Sample collection and processing + sample_collection_time_duration_unit: + rank: 33 + slot_group: Sample collection and processing + sample_received_date: + rank: 34 + slot_group: Sample collection and processing + sample_processing_date: + rank: 35 + slot_group: Sample collection and processing + environmental_site: + rank: 36 + slot_group: Sample collection and processing + environmental_material: + rank: 37 + slot_group: Sample collection and processing + collection_device: + rank: 38 + slot_group: Sample collection and processing + collection_method: + rank: 39 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 40 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 41 + slot_group: Sample collection and processing + residual_sample_status: + rank: 42 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 43 + slot_group: Sample collection and processing + presampling_activity: + rank: 44 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 45 + slot_group: Sample collection and processing + sample_storage_method: + rank: 46 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 47 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 48 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 49 + slot_group: Sample collection and processing + specimen_processing: + rank: 50 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 51 + slot_group: Sample collection and processing + experimental_protocol: + rank: 52 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 53 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 54 + slot_group: Sample collection and processing + available_data_types: + rank: 55 + slot_group: Sample collection and processing + available_data_type_details: + rank: 56 + slot_group: Sample collection and processing + water_catchment_area_human_population_measurement_value: + rank: 57 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_range: + rank: 58 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_measurement_method: + rank: 59 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_value: + rank: 60 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_unit: + rank: 61 + slot_group: Environmental conditions and measurements + populated_area_type: + rank: 62 + slot_group: Environmental conditions and measurements + sampling_weather_conditions: + rank: 63 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 64 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 65 + slot_group: Environmental conditions and measurements + water_depth: + rank: 66 + slot_group: Environmental conditions and measurements + water_depth_units: + rank: 67 + slot_group: Environmental conditions and measurements + sediment_depth: + rank: 68 + slot_group: Environmental conditions and measurements + sediment_depth_units: + rank: 69 + slot_group: Environmental conditions and measurements + air_temperature: + rank: 70 + slot_group: Environmental conditions and measurements + air_temperature_units: + rank: 71 + slot_group: Environmental conditions and measurements + water_temperature: + rank: 72 + slot_group: Environmental conditions and measurements + water_temperature_units: + rank: 73 + slot_group: Environmental conditions and measurements + weather_type: + rank: 74 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 75 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 76 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_value: + rank: 77 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_unit: + rank: 78 + slot_group: Environmental conditions and measurements + ph_measurement_value: + rank: 79 + slot_group: Environmental conditions and measurements + ph_measurement_method: + rank: 80 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_value: + rank: 81 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_unit: + rank: 82 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_method: + rank: 83 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_value: + rank: 84 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_unit: + rank: 85 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_method: + rank: 86 + slot_group: Environmental conditions and measurements + turbidity_measurement_value: + rank: 87 + slot_group: Environmental conditions and measurements + turbidity_measurement_unit: + rank: 88 + slot_group: Environmental conditions and measurements + turbidity_measurement_method: + rank: 89 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_value: + rank: 90 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_unit: + rank: 91 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_method: + rank: 92 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_value: + rank: 93 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_unit: + rank: 94 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_method: + rank: 95 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_value: + rank: 96 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_unit: + rank: 97 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_method: + rank: 98 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + rank: 99 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + rank: 100 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + rank: 101 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_value: + rank: 102 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_unit: + rank: 103 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_method: + rank: 104 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_value: + rank: 105 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_unit: + rank: 106 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_method: + rank: 107 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_value: + rank: 108 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_unit: + rank: 109 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_method: + rank: 110 + slot_group: Environmental conditions and measurements + alkalinity_measurement_value: + rank: 111 + slot_group: Environmental conditions and measurements + alkalinity_measurement_unit: + rank: 112 + slot_group: Environmental conditions and measurements + alkalinity_measurement_method: + rank: 113 + slot_group: Environmental conditions and measurements + conductivity_measurement_value: + rank: 114 + slot_group: Environmental conditions and measurements + conductivity_measurement_unit: + rank: 115 + slot_group: Environmental conditions and measurements + conductivity_measurement_method: + rank: 116 + slot_group: Environmental conditions and measurements + salinity_measurement_value: + rank: 117 + slot_group: Environmental conditions and measurements + salinity_measurement_unit: + rank: 118 + slot_group: Environmental conditions and measurements + salinity_measurement_method: + rank: 119 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_value: + rank: 120 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_unit: + rank: 121 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_method: + rank: 122 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_value: + rank: 123 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_unit: + rank: 124 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_method: + rank: 125 + slot_group: Environmental conditions and measurements + fecal_contamination_indicator_: + rank: 126 + slot_group: Environmental conditions and measurements + fecal_contamination_value: + rank: 127 + slot_group: Environmental conditions and measurements + fecal_contamination_unit: + rank: 128 + slot_group: Environmental conditions and measurements + fecal_contamination_method: + rank: 129 + slot_group: Environmental conditions and measurements + fecal_coliform_count_value: + rank: 130 + slot_group: Environmental conditions and measurements + fecal_coliform_count_unit: + rank: 131 + slot_group: Environmental conditions and measurements + fecal_coliform_count_method: + rank: 132 + slot_group: Environmental conditions and measurements + urinary_contamination_indicator: + rank: 133 + slot_group: Environmental conditions and measurements + urinary_contamination_value: + rank: 134 + slot_group: Environmental conditions and measurements + urinary_contamination_unit: + rank: 135 + slot_group: Environmental conditions and measurements + urinary_contamination_method: + rank: 136 + slot_group: Environmental conditions and measurements + sample_temperature_value_at_collection: + rank: 137 + slot_group: Environmental conditions and measurements + sample_temperature_unit_at_collection: + rank: 138 + slot_group: Environmental conditions and measurements + sample_temperature_value_when_received: + rank: 139 + slot_group: Environmental conditions and measurements + sample_temperature_unit_when_received: + rank: 140 + slot_group: Environmental conditions and measurements + library_id: + rank: 141 + slot_group: Sequence information + sequencing_assay_type: + rank: 142 + slot_group: Sequence information + sequencing_date: + rank: 143 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 144 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 145 + slot_group: Sequence information + sequenced_by: + rank: 146 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 147 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 148 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 149 + slot_group: Sequence information + sequence_submitted_by: + rank: 150 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 151 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 152 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 153 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 154 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 155 + slot_group: Sequence information + sequencing_platform: + rank: 156 + slot_group: Sequence information + sequencing_instrument: + rank: 157 + slot_group: Sequence information + library_preparation_kit: + rank: 158 + slot_group: Sequence information + dna_fragment_length: + rank: 159 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 160 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 161 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 162 + slot_group: Sequence information + amplicon_size: + rank: 163 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 164 + slot_group: Sequence information + sequencing_protocol: + rank: 165 + slot_group: Sequence information + r1_fastq_filename: + rank: 166 + slot_group: Sequence information + r2_fastq_filename: + rank: 167 + slot_group: Sequence information + fast5_filename: + rank: 168 + slot_group: Sequence information + genome_sequence_file_name: + rank: 169 + slot_group: Sequence information + assembly_filename: + rank: 170 + slot_group: Sequence information + quality_control_method_name: + rank: 171 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 172 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 173 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 174 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 175 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 176 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 177 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 178 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 179 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 180 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 181 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 182 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 183 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 184 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 185 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 186 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 187 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 188 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 189 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 190 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 191 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 192 + slot_group: Bioinformatics and QC metrics + n50: + rank: 193 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 194 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 195 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 196 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 197 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 198 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 199 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 200 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 201 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 202 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 203 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 204 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 205 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 206 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 207 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 208 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 209 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 210 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 211 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 212 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 213 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 214 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 215 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 216 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 217 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 218 + slot_group: Risk assessment information + stage_of_production: + rank: 219 + slot_group: Risk assessment information + experimental_intervention: + rank: 220 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 221 + slot_group: Risk assessment information + HPAIEnviro: + name: HPAIEnviro + title: HPAI Environmental + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_collection_end_date + - sample_collection_start_time + - sample_collection_end_time + - sample_collection_time_of_day + - sample_collection_time_duration_value + - sample_collection_time_duration_unit + - sample_received_date + - sample_processing_date + - environmental_site + - environmental_material + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - water_catchment_area_human_population_measurement_value + - water_catchment_area_human_population_range + - water_catchment_area_human_population_measurement_method + - water_catchment_area_human_population_density_value + - water_catchment_area_human_population_density_unit + - populated_area_type + - sampling_weather_conditions + - presampling_weather_conditions + - precipitation_measurement_value + - water_depth + - water_depth_units + - sediment_depth + - sediment_depth_units + - air_temperature + - air_temperature_units + - water_temperature + - water_temperature_units + - weather_type + - precipitation_measurement_unit + - precipitation_measurement_method + - ambient_temperature_measurement_value + - ambient_temperature_measurement_unit + - ph_measurement_value + - ph_measurement_method + - total_daily_flow_rate_measurement_value + - total_daily_flow_rate_measurement_unit + - total_daily_flow_rate_measurement_method + - instantaneous_flow_rate_measurement_value + - instantaneous_flow_rate_measurement_unit + - instantaneous_flow_rate_measurement_method + - turbidity_measurement_value + - turbidity_measurement_unit + - turbidity_measurement_method + - dissolved_oxygen_measurement_value + - dissolved_oxygen_measurement_unit + - dissolved_oxygen_measurement_method + - oxygen_reduction_potential_orp_measurement_value + - oxygen_reduction_potential_orp_measurement_unit + - oxygen_reduction_potential_orp_measurement_method + - chemical_oxygen_demand_cod_measurement_value + - chemical_oxygen_demand_cod_measurement_unit + - chemical_oxygen_demand_cod_measurement_method + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + - carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + - total_suspended_solids_tss_measurement_value + - total_suspended_solids_tss_measurement_unit + - total_suspended_solids_tss_measurement_method + - total_dissolved_solids_tds_measurement_value + - total_dissolved_solids_tds_measurement_unit + - total_dissolved_solids_tds_measurement_method + - total_solids_ts_measurement_value + - total_solids_ts_measurement_unit + - total_solids_ts_measurement_method + - alkalinity_measurement_value + - alkalinity_measurement_unit + - alkalinity_measurement_method + - conductivity_measurement_value + - conductivity_measurement_unit + - conductivity_measurement_method + - salinity_measurement_value + - salinity_measurement_unit + - salinity_measurement_method + - total_nitrogen_tn_measurement_value + - total_nitrogen_tn_measurement_unit + - total_nitrogen_tn_measurement_method + - total_phosphorus_tp_measurement_value + - total_phosphorus_tp_measurement_unit + - total_phosphorus_tp_measurement_method + - fecal_contamination_indicator_ + - fecal_contamination_value + - fecal_contamination_unit + - fecal_contamination_method + - fecal_coliform_count_value + - fecal_coliform_count_unit + - fecal_coliform_count_method + - urinary_contamination_indicator + - urinary_contamination_value + - urinary_contamination_unit + - urinary_contamination_method + - sample_temperature_value_at_collection + - sample_temperature_unit_at_collection + - sample_temperature_value_when_received + - sample_temperature_unit_when_received + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_collection_end_date: + rank: 28 + slot_group: Sample collection and processing + sample_collection_start_time: + rank: 29 + slot_group: Sample collection and processing + sample_collection_end_time: + rank: 30 + slot_group: Sample collection and processing + sample_collection_time_of_day: + rank: 31 + slot_group: Sample collection and processing + sample_collection_time_duration_value: + rank: 32 + slot_group: Sample collection and processing + sample_collection_time_duration_unit: + rank: 33 + slot_group: Sample collection and processing + sample_received_date: + rank: 34 + slot_group: Sample collection and processing + sample_processing_date: + rank: 35 + slot_group: Sample collection and processing + environmental_site: + rank: 36 + slot_group: Sample collection and processing + environmental_material: + rank: 37 + slot_group: Sample collection and processing + collection_device: + rank: 38 + slot_group: Sample collection and processing + collection_method: + rank: 39 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 40 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 41 + slot_group: Sample collection and processing + residual_sample_status: + rank: 42 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 43 + slot_group: Sample collection and processing + presampling_activity: + rank: 44 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 45 + slot_group: Sample collection and processing + sample_storage_method: + rank: 46 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 47 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 48 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 49 + slot_group: Sample collection and processing + specimen_processing: + rank: 50 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 51 + slot_group: Sample collection and processing + experimental_protocol: + rank: 52 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 53 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 54 + slot_group: Sample collection and processing + available_data_types: + rank: 55 + slot_group: Sample collection and processing + available_data_type_details: + rank: 56 + slot_group: Sample collection and processing + water_catchment_area_human_population_measurement_value: + rank: 57 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_range: + rank: 58 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_measurement_method: + rank: 59 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_value: + rank: 60 + slot_group: Environmental conditions and measurements + water_catchment_area_human_population_density_unit: + rank: 61 + slot_group: Environmental conditions and measurements + populated_area_type: + rank: 62 + slot_group: Environmental conditions and measurements + sampling_weather_conditions: + rank: 63 + slot_group: Environmental conditions and measurements + presampling_weather_conditions: + rank: 64 + slot_group: Environmental conditions and measurements + precipitation_measurement_value: + rank: 65 + slot_group: Environmental conditions and measurements + water_depth: + rank: 66 + slot_group: Environmental conditions and measurements + water_depth_units: + rank: 67 + slot_group: Environmental conditions and measurements + sediment_depth: + rank: 68 + slot_group: Environmental conditions and measurements + sediment_depth_units: + rank: 69 + slot_group: Environmental conditions and measurements + air_temperature: + rank: 70 + slot_group: Environmental conditions and measurements + air_temperature_units: + rank: 71 + slot_group: Environmental conditions and measurements + water_temperature: + rank: 72 + slot_group: Environmental conditions and measurements + water_temperature_units: + rank: 73 + slot_group: Environmental conditions and measurements + weather_type: + rank: 74 + slot_group: Environmental conditions and measurements + precipitation_measurement_unit: + rank: 75 + slot_group: Environmental conditions and measurements + precipitation_measurement_method: + rank: 76 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_value: + rank: 77 + slot_group: Environmental conditions and measurements + ambient_temperature_measurement_unit: + rank: 78 + slot_group: Environmental conditions and measurements + ph_measurement_value: + rank: 79 + slot_group: Environmental conditions and measurements + ph_measurement_method: + rank: 80 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_value: + rank: 81 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_unit: + rank: 82 + slot_group: Environmental conditions and measurements + total_daily_flow_rate_measurement_method: + rank: 83 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_value: + rank: 84 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_unit: + rank: 85 + slot_group: Environmental conditions and measurements + instantaneous_flow_rate_measurement_method: + rank: 86 + slot_group: Environmental conditions and measurements + turbidity_measurement_value: + rank: 87 + slot_group: Environmental conditions and measurements + turbidity_measurement_unit: + rank: 88 + slot_group: Environmental conditions and measurements + turbidity_measurement_method: + rank: 89 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_value: + rank: 90 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_unit: + rank: 91 + slot_group: Environmental conditions and measurements + dissolved_oxygen_measurement_method: + rank: 92 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_value: + rank: 93 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_unit: + rank: 94 + slot_group: Environmental conditions and measurements + oxygen_reduction_potential_orp_measurement_method: + rank: 95 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_value: + rank: 96 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_unit: + rank: 97 + slot_group: Environmental conditions and measurements + chemical_oxygen_demand_cod_measurement_method: + rank: 98 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + rank: 99 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + rank: 100 + slot_group: Environmental conditions and measurements + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + rank: 101 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_value: + rank: 102 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_unit: + rank: 103 + slot_group: Environmental conditions and measurements + total_suspended_solids_tss_measurement_method: + rank: 104 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_value: + rank: 105 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_unit: + rank: 106 + slot_group: Environmental conditions and measurements + total_dissolved_solids_tds_measurement_method: + rank: 107 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_value: + rank: 108 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_unit: + rank: 109 + slot_group: Environmental conditions and measurements + total_solids_ts_measurement_method: + rank: 110 + slot_group: Environmental conditions and measurements + alkalinity_measurement_value: + rank: 111 + slot_group: Environmental conditions and measurements + alkalinity_measurement_unit: + rank: 112 + slot_group: Environmental conditions and measurements + alkalinity_measurement_method: + rank: 113 + slot_group: Environmental conditions and measurements + conductivity_measurement_value: + rank: 114 + slot_group: Environmental conditions and measurements + conductivity_measurement_unit: + rank: 115 + slot_group: Environmental conditions and measurements + conductivity_measurement_method: + rank: 116 + slot_group: Environmental conditions and measurements + salinity_measurement_value: + rank: 117 + slot_group: Environmental conditions and measurements + salinity_measurement_unit: + rank: 118 + slot_group: Environmental conditions and measurements + salinity_measurement_method: + rank: 119 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_value: + rank: 120 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_unit: + rank: 121 + slot_group: Environmental conditions and measurements + total_nitrogen_tn_measurement_method: + rank: 122 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_value: + rank: 123 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_unit: + rank: 124 + slot_group: Environmental conditions and measurements + total_phosphorus_tp_measurement_method: + rank: 125 + slot_group: Environmental conditions and measurements + fecal_contamination_indicator_: + rank: 126 + slot_group: Environmental conditions and measurements + fecal_contamination_value: + rank: 127 + slot_group: Environmental conditions and measurements + fecal_contamination_unit: + rank: 128 + slot_group: Environmental conditions and measurements + fecal_contamination_method: + rank: 129 + slot_group: Environmental conditions and measurements + fecal_coliform_count_value: + rank: 130 + slot_group: Environmental conditions and measurements + fecal_coliform_count_unit: + rank: 131 + slot_group: Environmental conditions and measurements + fecal_coliform_count_method: + rank: 132 + slot_group: Environmental conditions and measurements + urinary_contamination_indicator: + rank: 133 + slot_group: Environmental conditions and measurements + urinary_contamination_value: + rank: 134 + slot_group: Environmental conditions and measurements + urinary_contamination_unit: + rank: 135 + slot_group: Environmental conditions and measurements + urinary_contamination_method: + rank: 136 + slot_group: Environmental conditions and measurements + sample_temperature_value_at_collection: + rank: 137 + slot_group: Environmental conditions and measurements + sample_temperature_unit_at_collection: + rank: 138 + slot_group: Environmental conditions and measurements + sample_temperature_value_when_received: + rank: 139 + slot_group: Environmental conditions and measurements + sample_temperature_unit_when_received: + rank: 140 + slot_group: Environmental conditions and measurements + library_id: + rank: 141 + slot_group: Sequence information + sequencing_assay_type: + rank: 142 + slot_group: Sequence information + sequencing_date: + rank: 143 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 144 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 145 + slot_group: Sequence information + sequenced_by: + rank: 146 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 147 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 148 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 149 + slot_group: Sequence information + sequence_submitted_by: + rank: 150 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 151 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 152 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 153 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 154 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 155 + slot_group: Sequence information + sequencing_platform: + rank: 156 + slot_group: Sequence information + sequencing_instrument: + rank: 157 + slot_group: Sequence information + library_preparation_kit: + rank: 158 + slot_group: Sequence information + dna_fragment_length: + rank: 159 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 160 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 161 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 162 + slot_group: Sequence information + amplicon_size: + rank: 163 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 164 + slot_group: Sequence information + sequencing_protocol: + rank: 165 + slot_group: Sequence information + r1_fastq_filename: + rank: 166 + slot_group: Sequence information + r2_fastq_filename: + rank: 167 + slot_group: Sequence information + fast5_filename: + rank: 168 + slot_group: Sequence information + genome_sequence_file_name: + rank: 169 + slot_group: Sequence information + assembly_filename: + rank: 170 + slot_group: Sequence information + quality_control_method_name: + rank: 171 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 172 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 173 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 174 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 175 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 176 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 177 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 178 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 179 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 180 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 181 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 182 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 183 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 184 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 185 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 186 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 187 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 188 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 189 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 190 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 191 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 192 + slot_group: Bioinformatics and QC metrics + n50: + rank: 193 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 194 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 195 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 196 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 197 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 198 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 199 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 200 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 201 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 202 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 203 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 204 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 205 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 206 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 207 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 208 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 209 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 210 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 211 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 212 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 213 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 214 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 215 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 216 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 217 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 218 + slot_group: Risk assessment information + stage_of_production: + rank: 219 + slot_group: Risk assessment information + experimental_intervention: + rank: 220 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 221 + slot_group: Risk assessment information + HPAIHost: + name: HPAIHost + title: HPAI Host + description: null + is_a: dh_interface + see_also: null + annotations: + version: 1.0.0 + slots: + - specimen_collector_sample_id + - specimen_collector_subsample_id + - pooled_sample_id + - sampling_site_id + - sampling_event_id + - bioproject_accession + - biosample_accession + - insdc_sequence_read_accession + - insdc_assembly_accession + - sample_collection_data_steward_name + - sample_collection_data_steward_contact_email + - sample_collected_by + - sample_collector_contact_email + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_name_site__ + - geo_loc_latitude + - geo_loc_longitude + - organism + - influenza_subtype + - influenza_subtyping_scheme_name + - taxonomic_identification_process + - virus_identifier + - who_oie_fao_h5_clade + - sample_collection_date + - sample_received_date + - sample_processing_date + - host_origin_geo_loc_name_country + - anatomical_material + - body_product + - anatomical_part + - collection_device + - collection_method + - sample_volume_measurement_value + - sample_volume_measurement_unit + - residual_sample_status + - purpose_of_sampling + - presampling_activity + - presampling_activity_details + - sample_storage_method + - sample_storage_medium + - sample_storage_duration_value + - sample_storage_duration_unit + - specimen_processing + - specimen_processing_details + - experimental_protocol + - experimental_specimen_role_type + - experimental_specimen_details + - available_data_types + - available_data_type_details + - host_common_name + - host_scientific_name + - host_ecotype + - host_breed + - host_food_production_name + - host_age + - host_age_unit + - host_age_bin + - host_disease + - host_health_state + - host_health_status_details + - host_health_outcome + - host_subject_id + - case_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors + - complications + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_history + - influenza_antiviral_treatment_administration + - influenza_antiviral_agent__ + - influenza_antiviral_treatment_date + - library_id + - sequencing_assay_type + - sequencing_date + - purpose_of_sequencing__ + - purpose_of_sequencing_details + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - sequence_submitted_by + - sequence_submitter_contact_email + - nucleic_acid_extraction_method + - nucleic_acid_extraction_kit + - endogenous_control_details + - sequencing_project_name + - sequencing_platform + - sequencing_instrument + - library_preparation_kit + - dna_fragment_length + - genomic_target_enrichment_method + - genomic_target_enrichment_method_details + - amplicon_pcr_primer_scheme + - amplicon_size + - sequencing_flow_cell_version + - sequencing_protocol + - r1_fastq_filename + - r2_fastq_filename + - fast5_filename + - genome_sequence_file_name + - assembly_filename + - quality_control_method_name + - quality_control_method_version + - quality_control_determination + - quality_control_issues + - quality_control_details + - raw_sequence_data_processing_method + - dehosting_method + - sequence_assembly_software_name + - sequence_assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - genome_completeness + - number_of_base_pairs_sequenced + - number_of_total_reads + - number_of_unique_reads + - minimum_posttrimming_read_length + - number_of_contigs + - percent_ns_across_total_genome_length + - ns_per_100_kbp + - n50 + - percent_read_contamination_ + - sequence_assembly_length + - consensus_genome_length + - reference_genome_accession + - deduplication_method + - bioinformatics_protocol + - read_mapping_software_name + - read_mapping_software_version + - taxonomic_reference_database_name + - taxonomic_reference_database_version + - taxonomic_analysis_report_filename + - taxonomic_analysis_date + - read_mapping_criteria + - genetic_target_name + - genetic_target_region + - genetic_target_region_reference_genome + - diagnostic_target_presence + - diagnostic_measurement_value + - diagnostic_measurement_unit + - diagnostic_measurement_method + - diagnostic_testing_threshold_value + - diagnostic_testing_threshold_units + - diagnostic_testing_details + - prevalence_metrics + - prevalence_metrics_details + - stage_of_production + - experimental_intervention + - experiment_intervention_details + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database identifiers + specimen_collector_subsample_id: + rank: 2 + slot_group: Database identifiers + pooled_sample_id: + rank: 3 + slot_group: Database identifiers + sampling_site_id: + rank: 4 + slot_group: Database identifiers + sampling_event_id: + rank: 5 + slot_group: Database identifiers + bioproject_accession: + rank: 6 + slot_group: Database identifiers + biosample_accession: + rank: 7 + slot_group: Database identifiers + insdc_sequence_read_accession: + rank: 8 + slot_group: Database identifiers + insdc_assembly_accession: + rank: 9 + slot_group: Database identifiers + sample_collection_data_steward_name: + rank: 10 + slot_group: Sample collection and processing + sample_collection_data_steward_contact_email: + rank: 11 + slot_group: Sample collection and processing + sample_collected_by: + rank: 12 + slot_group: Sample collection and processing + sample_collector_contact_email: + rank: 13 + slot_group: Sample collection and processing + geo_loc_name_country: + rank: 14 + slot_group: Sample collection and processing + geo_loc_name_state_province_territory: + rank: 15 + slot_group: Sample collection and processing + geo_loc_name_county_region: + rank: 16 + slot_group: Sample collection and processing + geo_loc_name_city: + rank: 17 + slot_group: Sample collection and processing + geo_loc_name_site__: + rank: 18 + slot_group: Sample collection and processing + geo_loc_latitude: + rank: 19 + slot_group: Sample collection and processing + geo_loc_longitude: + rank: 20 + slot_group: Sample collection and processing + organism: + rank: 21 + slot_group: Sample collection and processing + influenza_subtype: + rank: 22 + slot_group: Sample collection and processing + influenza_subtyping_scheme_name: + rank: 23 + slot_group: Sample collection and processing + taxonomic_identification_process: + rank: 24 + slot_group: Sample collection and processing + virus_identifier: + rank: 25 + slot_group: Sample collection and processing + who_oie_fao_h5_clade: + rank: 26 + slot_group: Sample collection and processing + sample_collection_date: + rank: 27 + slot_group: Sample collection and processing + sample_received_date: + rank: 28 + slot_group: Sample collection and processing + sample_processing_date: + rank: 29 + slot_group: Sample collection and processing + host_origin_geo_loc_name_country: + rank: 30 + slot_group: Sample collection and processing + anatomical_material: + rank: 31 + slot_group: Sample collection and processing + body_product: + rank: 32 + slot_group: Sample collection and processing + anatomical_part: + rank: 33 + slot_group: Sample collection and processing + collection_device: + rank: 34 + slot_group: Sample collection and processing + collection_method: + rank: 35 + slot_group: Sample collection and processing + sample_volume_measurement_value: + rank: 36 + slot_group: Sample collection and processing + sample_volume_measurement_unit: + rank: 37 + slot_group: Sample collection and processing + residual_sample_status: + rank: 38 + slot_group: Sample collection and processing + purpose_of_sampling: + rank: 39 + slot_group: Sample collection and processing + presampling_activity: + rank: 40 + slot_group: Sample collection and processing + presampling_activity_details: + rank: 41 + slot_group: Sample collection and processing + sample_storage_method: + rank: 42 + slot_group: Sample collection and processing + sample_storage_medium: + rank: 43 + slot_group: Sample collection and processing + sample_storage_duration_value: + rank: 44 + slot_group: Sample collection and processing + sample_storage_duration_unit: + rank: 45 + slot_group: Sample collection and processing + specimen_processing: + rank: 46 + slot_group: Sample collection and processing + specimen_processing_details: + rank: 47 + slot_group: Sample collection and processing + experimental_protocol: + rank: 48 + slot_group: Sample collection and processing + experimental_specimen_role_type: + rank: 49 + slot_group: Sample collection and processing + experimental_specimen_details: + rank: 50 + slot_group: Sample collection and processing + available_data_types: + rank: 51 + slot_group: Sample collection and processing + available_data_type_details: + rank: 52 + slot_group: Sample collection and processing + host_common_name: + rank: 53 + slot_group: Host information + host_scientific_name: + rank: 54 + slot_group: Host information + host_ecotype: + rank: 55 + slot_group: Host information + host_breed: + rank: 56 + slot_group: Host information + host_food_production_name: + rank: 57 + slot_group: Host information + host_age: + rank: 58 + slot_group: Host Information + host_age_unit: + rank: 59 + slot_group: Host Information + host_age_bin: + rank: 60 + slot_group: Host information + host_disease: + rank: 61 + slot_group: Host information + host_health_state: + rank: 62 + slot_group: Host Information + host_health_status_details: + rank: 63 + slot_group: Host Information + host_health_outcome: + rank: 64 + slot_group: Host Information + host_subject_id: + rank: 65 + slot_group: Host Information + case_id: + rank: 66 + slot_group: Host Information + symptom_onset_date: + rank: 67 + slot_group: Host Information + signs_and_symptoms: + rank: 68 + slot_group: Host Information + preexisting_conditions_and_risk_factors: + rank: 69 + slot_group: Host Information + complications: + rank: 70 + slot_group: Host Information + exposure_event: + rank: 71 + slot_group: Host exposure information + exposure_contact_level: + rank: 72 + slot_group: Host exposure information + host_role: + rank: 73 + slot_group: Host exposure information + exposure_setting: + rank: 74 + slot_group: Host exposure information + exposure_details: + rank: 75 + slot_group: Host exposure information + host_vaccination_status: + rank: 76 + slot_group: Host vaccination information + number_of_vaccine_doses_received: + rank: 77 + slot_group: Host vaccination information + vaccination_dose_1_vaccine_name: + rank: 78 + slot_group: Host vaccination information + vaccination_dose_1_vaccination_date: + rank: 79 + slot_group: Host vaccination information + vaccination_dose_2_vaccine_name: + rank: 80 + slot_group: Host vaccination information + vaccination_dose_2_vaccination_date: + rank: 81 + slot_group: Host vaccination information + vaccination_history: + rank: 82 + slot_group: Host vaccination information + influenza_antiviral_treatment_administration: + rank: 83 + slot_group: Host treatment information + influenza_antiviral_agent__: + rank: 84 + slot_group: Host treatment information + influenza_antiviral_treatment_date: + rank: 85 + slot_group: Host treatment information + library_id: + rank: 86 + slot_group: Sequence information + sequencing_assay_type: + rank: 87 + slot_group: Sequence information + sequencing_date: + rank: 88 + slot_group: Sequence information + purpose_of_sequencing__: + rank: 89 + slot_group: Sequence information + purpose_of_sequencing_details: + rank: 90 + slot_group: Sequence information + sequenced_by: + rank: 91 + slot_group: Sequence information + sequenced_by_laboratory_name: + rank: 92 + slot_group: Sequence information + sequenced_by_contact_name: + rank: 93 + slot_group: Sequence information + sequenced_by_contact_email: + rank: 94 + slot_group: Sequence information + sequence_submitted_by: + rank: 95 + slot_group: Sequence information + sequence_submitter_contact_email: + rank: 96 + slot_group: Sequence information + nucleic_acid_extraction_method: + rank: 97 + slot_group: Sample collection and processing + nucleic_acid_extraction_kit: + rank: 98 + slot_group: Sample collection and processing + endogenous_control_details: + rank: 99 + slot_group: Sample collection and processing + sequencing_project_name: + rank: 100 + slot_group: Sequence information + sequencing_platform: + rank: 101 + slot_group: Sequence information + sequencing_instrument: + rank: 102 + slot_group: Sequence information + library_preparation_kit: + rank: 103 + slot_group: Sequence information + dna_fragment_length: + rank: 104 + slot_group: Sequence information + genomic_target_enrichment_method: + rank: 105 + slot_group: Sequence information + genomic_target_enrichment_method_details: + rank: 106 + slot_group: Sequence information + amplicon_pcr_primer_scheme: + rank: 107 + slot_group: Sequence information + amplicon_size: + rank: 108 + slot_group: Sequence information + sequencing_flow_cell_version: + rank: 109 + slot_group: Sequence information + sequencing_protocol: + rank: 110 + slot_group: Sequence information + r1_fastq_filename: + rank: 111 + slot_group: Sequence information + r2_fastq_filename: + rank: 112 + slot_group: Sequence information + fast5_filename: + rank: 113 + slot_group: Sequence information + genome_sequence_file_name: + rank: 114 + slot_group: Sequence information + assembly_filename: + rank: 115 + slot_group: Sequence information + quality_control_method_name: + rank: 116 + slot_group: Bioinformatics and QC metrics + quality_control_method_version: + rank: 117 + slot_group: Bioinformatics and QC metrics + quality_control_determination: + rank: 118 + slot_group: Bioinformatics and QC metrics + quality_control_issues: + rank: 119 + slot_group: Bioinformatics and QC metrics + quality_control_details: + rank: 120 + slot_group: Bioinformatics and QC metrics + raw_sequence_data_processing_method: + rank: 121 + slot_group: Bioinformatics and QC metrics + dehosting_method: + rank: 122 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_name: + rank: 123 + slot_group: Bioinformatics and QC metrics + sequence_assembly_software_version: + rank: 124 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_name: + rank: 125 + slot_group: Bioinformatics and QC metrics + consensus_sequence_software_version: + rank: 126 + slot_group: Bioinformatics and QC metrics + breadth_of_coverage_value: + rank: 127 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_value: + rank: 128 + slot_group: Bioinformatics and QC metrics + depth_of_coverage_threshold: + rank: 129 + slot_group: Bioinformatics and QC metrics + genome_completeness: + rank: 130 + slot_group: Bioinformatics and QC metrics + number_of_base_pairs_sequenced: + rank: 131 + slot_group: Bioinformatics and QC metrics + number_of_total_reads: + rank: 132 + slot_group: Bioinformatics and QC metrics + number_of_unique_reads: + rank: 133 + slot_group: Bioinformatics and QC metrics + minimum_posttrimming_read_length: + rank: 134 + slot_group: Bioinformatics and QC metrics + number_of_contigs: + rank: 135 + slot_group: Bioinformatics and QC metrics + percent_ns_across_total_genome_length: + rank: 136 + slot_group: Bioinformatics and QC metrics + ns_per_100_kbp: + rank: 137 + slot_group: Bioinformatics and QC metrics + n50: + rank: 138 + slot_group: Bioinformatics and QC metrics + percent_read_contamination_: + rank: 139 + slot_group: Bioinformatics and QC metrics + sequence_assembly_length: + rank: 140 + slot_group: Bioinformatics and QC metrics + consensus_genome_length: + rank: 141 + slot_group: Bioinformatics and QC metrics + reference_genome_accession: + rank: 142 + slot_group: Bioinformatics and QC metrics + deduplication_method: + rank: 143 + slot_group: Bioinformatics and QC metrics + bioinformatics_protocol: + rank: 144 + slot_group: Bioinformatics and QC metrics + read_mapping_software_name: + rank: 145 + slot_group: Taxonomic identification information + read_mapping_software_version: + rank: 146 + slot_group: Taxonomic identification information + taxonomic_reference_database_name: + rank: 147 + slot_group: Taxonomic identification information + taxonomic_reference_database_version: + rank: 148 + slot_group: Taxonomic identification information + taxonomic_analysis_report_filename: + rank: 149 + slot_group: Taxonomic identification information + taxonomic_analysis_date: + rank: 150 + slot_group: Taxonomic identification information + read_mapping_criteria: + rank: 151 + slot_group: Taxonomic identification information + genetic_target_name: + rank: 152 + slot_group: Pathogen diagnostic testing + genetic_target_region: + rank: 153 + slot_group: Pathogen diagnostic testing + genetic_target_region_reference_genome: + rank: 154 + slot_group: Pathogen diagnostic testing + diagnostic_target_presence: + rank: 155 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_value: + rank: 156 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_unit: + rank: 157 + slot_group: Pathogen diagnostic testing + diagnostic_measurement_method: + rank: 158 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_value: + rank: 159 + slot_group: Pathogen diagnostic testing + diagnostic_testing_threshold_units: + rank: 160 + slot_group: Pathogen diagnostic testing + diagnostic_testing_details: + rank: 161 + slot_group: Pathogen diagnostic testing + prevalence_metrics: + rank: 162 + slot_group: Risk assessment information + prevalence_metrics_details: + rank: 163 + slot_group: Risk assessment information + stage_of_production: + rank: 164 + slot_group: Risk assessment information + experimental_intervention: + rank: 165 + slot_group: Risk assessment information + experiment_intervention_details: + rank: 166 + slot_group: Risk assessment information +slots: + specimen_collector_sample_id: + name: specimen_collector_sample_id + title: specimen_collector_sample_ID + description: The user-defined name for the sample. + comments: Store the collector sample ID. If this number is considered identifiable + information, provide an alternative ID. Be sure to store the key that maps between + the original and alternative IDs for traceability and follow up if necessary. + Every collector sample ID from a single submitter must be unique. It can have + any format, but we suggest that you make it concise, unique and consistent within + your lab. + slot_uri: GENEPIO:0001123 + identifier: true + range: WhitespaceMinimizedString + required: true + examples: + - value: ASDFG123 + exact_mappings: + - BIOSAMPLE_Enterics:sample_name + specimen_collector_subsample_id: + name: specimen_collector_subsample_id + title: specimen_collector_subsample_ID + description: The user-defined identifier assigned to a portion of the original + sample. + comments: Store the ID for the subsample/aliquot. + slot_uri: GENEPIO:0100752 + range: WhitespaceMinimizedString + examples: + - value: ASDFG123_12 + pooled_sample_id: + name: pooled_sample_id + title: pooled_sample_ID + description: The user-defined identifier assigned to a combined (pooled) set of + samples. + comments: If the sample being analyzed is the result of pooling individual samples, + rename the pooled sample with a new identifier. Store the pooled sample ID. + slot_uri: GENEPIO:0100996 + range: WhitespaceMinimizedString + examples: + - value: 12345AYZ + sampling_site_id: + name: sampling_site_id + title: sampling_site_ID + description: The user-defined identifier assigned to a specific location from + which samples are taken. + comments: Store the ID for the site from which a sample was taken. The "site" + is user defined (e.g. it may be a building and its environs, a specific entity + within an environment). Please use the same site ID for all samples from a given + site, regardless of when these samples were taken. Any important changes in + site location, should be represented with a new site ID. + slot_uri: GENEPIO:0100760 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Site 12A + sampling_event_id: + name: sampling_event_id + title: sampling_event_ID + description: The user-defined identifier assigned to a specific event during which + one or more samples are taken, from one or more sites. + comments: Store the ID for the event during which a sample or samples were taken. + For example, an event could be one person taking samples from multiple sites, + or multiple people taking samples from one site. + slot_uri: GENEPIO:0100761 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Event 120522.1 + bioproject_accession: + name: bioproject_accession + title: BioProject_accession + description: The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) + to which the BioSample belongs. + comments: Store the BioProject accession number. BioProjects are an organizing + tool that links together raw sequence data, assemblies, and their associated + metadata. Each province will be assigned a different bioproject accession number + by the National Microbiology Lab. A valid NCBI BioProject accession has prefix + PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing + project. + slot_uri: GENEPIO:0001136 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: PRJNA608651 + exact_mappings: + - BIOSAMPLE_Enterics:bioproject_accession + biosample_accession: + name: biosample_accession + title: BioSample_accession + description: The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, + or DDBJ) archives. + comments: Store the accession returned from the BioSample submission. NCBI BioSamples + will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD + slot_uri: GENEPIO:0001139 + range: WhitespaceMinimizedString + recommended: true + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: SAMN14180202, SAMD00000001 + insdc_sequence_read_accession: + name: insdc_sequence_read_accession + title: INSDC sequence read accession + description: The identifier assigned to a sequence in one of the International + Nucleotide Sequence Database Collaboration (INSDC) repositories. + comments: Store the accession assigned to the submitted sequence. European Nucleotide + Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start + with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome + Sequence Archive (GSA) accessions start with CRR. + slot_uri: GENEPIO:0101203 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: ERR123456, DRR123456, CRR123456 + insdc_assembly_accession: + name: insdc_assembly_accession + title: INSDC assembly accession + description: The versioned identifier assigned to an assembly or consensus sequence + in one of the International Nucleotide Sequence Database Collaboration (INSDC) + repositories. + comments: Store the versioned accession assigned to the submitted sequence e.g. + the GenBank accession version. + slot_uri: GENEPIO:0101204 + range: WhitespaceMinimizedString + pattern: '{UPPER_CASE}' + structured_pattern: + syntax: '{UPPER_CASE}' + partial_match: false + interpolated: true + examples: + - value: LZ986655.1 + sample_collection_data_steward_name: + name: sample_collection_data_steward_name + title: sample_collection_data_steward_name + description: The name of the individual responsible for the data governance, (meta)data + usage and distribution of the sample. + comments: Provide the name of the sample collection data steward. + slot_uri: GENEPIO:0100762 + range: WhitespaceMinimizedString + examples: + - value: Joe Bloggs + sample_collection_data_steward_contact_email: + name: sample_collection_data_steward_contact_email + title: sample_collection_data_steward_contact_email + description: The email address of the individual responsible for the data governance, + (meta)data usage and distribution of the sample. + comments: Provide the email address of the sample collection data steward. This + may or may not be the same individual/organization that collected the sample. + If the contact is the same, provide the same address as the "sample collector + contact email". + slot_uri: GENEPIO:0101107 + range: WhitespaceMinimizedString + examples: + - value: bloggsj@aglab.ca + sample_collected_by: + name: sample_collected_by + title: sample_collected_by + description: The name of the organization with which the sample collector is affiliated. + comments: The name of the agency should be written out in full, (with minor exceptions) + and be consistent across multiple submissions. + slot_uri: GENEPIO:0001153 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Public Health Agency of Canada + exact_mappings: + - BIOSAMPLE_Enterics:collected_by + sample_collector_contact_email: + name: sample_collector_contact_email + title: sample_collector_contact_email + description: The email address of the contact responsible for follow-up regarding + the sample. + comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, + or RespLab@lab.ca + slot_uri: GENEPIO:0001156 + range: WhitespaceMinimizedString + pattern: ^\S+@\S+\.\S+$ + examples: + - value: WaterTester@facility.ca + geo_loc_name_country: + name: geo_loc_name_country + title: geo_loc_name_(country) + description: The country of origin of the sample. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001181 + any_of: + - range: geo_loc_name_(country) menu + - range: null value menu + required: true + examples: + - value: Canada + exact_mappings: + - BIOSAMPLE_Enterics:geo_loc_name + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory + title: geo_loc_name_(state/province/territory) + description: The state/province/territory of origin of the sample. + comments: 'Provide the state/province/territory name from the GAZ geography ontology. + Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga' + slot_uri: GENEPIO:0001185 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Western Cape + exact_mappings: + - BIOSAMPLE_Enterics:geo_loc_name + geo_loc_name_county_region: + name: geo_loc_name_county_region + title: geo_loc_name_(county/region) + description: The county/region of origin of the sample. + comments: 'Provide the county/region name from the GAZ geography ontology. Search + for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' + slot_uri: GENEPIO:0100280 + range: WhitespaceMinimizedString + examples: + - value: Derbyshire + geo_loc_name_city: + name: geo_loc_name_city + title: geo_loc_name_(city) + description: The city of origin of the sample. + comments: 'Provide the city name from the GAZ geography ontology. Search for geography + terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' + slot_uri: GENEPIO:0001189 + range: WhitespaceMinimizedString + examples: + - value: Vancouver + geo_loc_name_site__: + name: geo_loc_name_site__ + title: geo_loc_name_(site) + description: The name of a specific geographical location e.g. Credit River (rather + than river). + comments: Provide the name of the specific geographical site using a specific + noun (a word that names a certain place, thing). + slot_uri: GENEPIO:0100436 + range: WhitespaceMinimizedString + examples: + - value: Credit River + geo_loc_latitude: + name: geo_loc_latitude + title: geo_loc_latitude + description: The latitude coordinates of the geographical location of sample collection. + comments: Provide latitude coordinates if available. Do not use the centre of + the city/region/province/state/country or the location of your agency as a proxy, + as this implicates a real location and is misleading. Specify as degrees latitude + in format "d[d.dddd] N|S". + slot_uri: GENEPIO:0100309 + range: WhitespaceMinimizedString + examples: + - value: 38.98 N + exact_mappings: + - BIOSAMPLE_Enterics:lat_lon + geo_loc_longitude: + name: geo_loc_longitude + title: geo_loc_longitude + description: The longitude coordinates of the geographical location of sample + collection. + comments: Provide longitude coordinates if available. Do not use the centre of + the city/region/province/state/country or the location of your agency as a proxy, + as this implicates a real location and is misleading. Specify as degrees longitude + in format "d[dd.dddd] W|E". + slot_uri: GENEPIO:0100310 + range: WhitespaceMinimizedString + examples: + - value: 77.11 W + exact_mappings: + - BIOSAMPLE_Enterics:lat_lon + organism: + name: organism + title: organism + description: Taxonomic name of the organism. + comments: 'Provide the official nomenclature for the organism(s) present in the + sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. + Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy.' + slot_uri: GENEPIO:0001191 + any_of: + - range: organism menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Vibrio cholerae + exact_mappings: + - BIOSAMPLE_Enterics:organism + influenza_subtype: + name: influenza_subtype + title: influenza_subtype + slot_uri: GENEPIO:0101108 + range: influenza_subsubtype menu + multivalued: true + required: true + influenza_subtyping_scheme_name: + name: influenza_subtyping_scheme_name + title: influenza_subtyping_scheme_name + slot_uri: GENEPIO:0101109 + range: influenza_subtyping_scheme_name menu + taxonomic_identification_process: + name: taxonomic_identification_process + title: taxonomic_identification_process + slot_uri: GENEPIO:0100583 + range: taxonomic_identification_process menu + virus_identifier: + name: virus_identifier + title: virus_identifier + slot_uri: GENEPIO:0101110 + range: WhitespaceMinimizedString + who_oie_fao_h5_clade: + name: who_oie_fao_h5_clade + title: WHO/OIE/FAO_H5_clade + slot_uri: GENEPIO:0101111 + range: WhitespaceMinimizedString + sample_collection_date: + name: sample_collection_date + title: sample_collection_date + description: The date on which the sample was collected, or sampling began for + a continuous sample. + comments: If your sample is a continuous sample please use this field to capture + your start date. Sample collection date is critical for surveillance and many + types of analyses. Required granularity includes year, month and day. The date + should be provided in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0001174 + any_of: + - range: date + - range: null value menu + required: true + examples: + - value: '2020-03-16' + exact_mappings: + - BIOSAMPLE_Enterics:collection_date + sample_collection_end_date: + name: sample_collection_end_date + title: sample_collection_end_date + description: The date on which sample collection ended for a continuous sample. + comments: Provide the date that sample collection ended in ISO 8601 format i.e. + YYYY-MM-DD + slot_uri: GENEPIO:0101071 + any_of: + - range: date + - range: null value menu + recommended: true + examples: + - value: '2020-03-18' + sample_collection_start_time: + name: sample_collection_start_time + title: sample_collection_start_time + description: The time at which sample collection began. + comments: Provide this time in ISO 8601 24hr format, in your local time. + slot_uri: GENEPIO:0101072 + any_of: + - range: time + - range: null value menu + recommended: true + examples: + - value: 17:15 PST + sample_collection_end_time: + name: sample_collection_end_time + title: sample_collection_end_time + description: The time at which sample collection ended. + comments: Provide this time in ISO 8601 24hr format, in your local time. + slot_uri: GENEPIO:0101073 + any_of: + - range: time + - range: null value menu + recommended: true + examples: + - value: 19:15 PST + sample_collection_time_of_day: + name: sample_collection_time_of_day + title: sample_collection_time_of_day + description: The descriptive time of day during which the sample was collected. + comments: If known, select a value from the pick list. The time of sample processing + matters especially for grab samples, as fecal concentration in wastewater fluctuates + over the course of the day. + slot_uri: GENEPIO:0100765 + any_of: + - range: sample_collection_time_of_day menu + - range: null value menu + examples: + - value: Morning + sample_collection_time_duration_value: + name: sample_collection_time_duration_value + title: sample_collection_time_duration_value + description: The amount of time over which the sample was collected. + comments: Provide the numerical value of time. + slot_uri: GENEPIO:0100766 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: '4' + sample_collection_time_duration_unit: + name: sample_collection_time_duration_unit + title: sample_collection_time_duration_unit + description: The units of the time duration measurement of sample collection. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0100767 + any_of: + - range: sample_collection_duration_unit menu + - range: null value menu + recommended: true + examples: + - value: Hour + sample_received_date: + name: sample_received_date + title: sample received date + description: The date on which the sample was received. + comments: Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". + slot_uri: GENEPIO:0001179 + any_of: + - range: date + - range: null value menu + examples: + - value: '2020-03-28' + sample_processing_date: + name: sample_processing_date + title: sample processing date + description: The date on which the sample was processed. + comments: Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". + The sample may be collected and processed (e.g. filtered, extraction) on the + same day, or on different dates. + slot_uri: GENEPIO:0100763 + any_of: + - range: date + - range: null value menu + examples: + - value: '2020-03-16' + host_origin_geo_loc_name_country: + name: host_origin_geo_loc_name_country + title: host_origin_geo_loc_name (country) + description: The country of origin of the host. + comments: If a sample is from a human or animal host that originated from outside + of Canada, provide the the name of the country where the host originated by + selecting a value from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100438 + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + examples: + - value: South Africa [GAZ:00001094] + food_product_origin_geo_loc_name_country: + name: food_product_origin_geo_loc_name_country + title: food_product_origin_geo_loc_name (country) + description: The country of origin of a food product. + comments: If a food product was sampled and the food product was manufactured + outside of Canada, provide the name of the country where the food product originated + by selecting a value from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100437 + any_of: + - range: geo_loc_name (country) menu + - range: null value menu + examples: + - value: United States of America [GAZ:00002459] + exact_mappings: + - BIOSAMPLE_Enterics:food_origin + food_product: + name: food_product + title: food_product + description: A material consumed and digested for nutritional value or enjoyment. + comments: This field includes animal feed. If applicable, select the standardized + term and ontology ID for the anatomical material from the picklist provided. + Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0100444 + any_of: + - range: food_product menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Feather meal [FOODON:00003927] + - value: Bone meal [ENVO:02000054] + - value: Chicken breast [FOODON:00002703] + exact_mappings: + - GISAID:isolation_source + - GISAID:food_product + - BIOSAMPLE_Enterics:isolation_source + - BIOSAMPLE_Enterics:food_product_type + food_product_properties: + name: food_product_properties + title: food_product_properties + description: Any characteristic of the food product pertaining to its state, processing, + a label claim, or implications for consumers. + comments: Provide any characteristics of the food product including whether it + has been cooked, processed, preserved, any known information about its state + (e.g. raw, ready-to-eat), any known information about its containment (e.g. + canned), and any information about a label claim (e.g. organic, fat-free). + slot_uri: GENEPIO:0100445 + any_of: + - range: food_product_properties menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Food (chopped) [FOODON:00002777] + - value: Ready-to-eat (RTE) [FOODON:03316636] + exact_mappings: + - GISAID:isolation_source + - GISAID:food_product_properties + - BIOSAMPLE_Enterics:isolation_source + food_packaging: + name: food_packaging + title: food_packaging + description: The type of packaging used to contain a food product. + comments: If known, provide information regarding how the food product was packaged. + slot_uri: GENEPIO:0100447 + any_of: + - range: food_packaging menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Plastic tray or pan [FOODON:03490126] + exact_mappings: + - GISAID:isolation_source + - GISAID:food_packaging + - BIOSAMPLE_Enterics:food_contain_wrap + food_quality_date: + name: food_quality_date + title: food_quality_date + description: A date recommended for the use of a product while at peak quality, + this date is not a reflection of safety unless used on infant formula. + comments: This date is typically labeled on a food product as "best if used by", + best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave + blank or provide a null value. + slot_uri: GENEPIO:0100615 + range: date + examples: + - value: '2020-05-25' + exact_mappings: + - BIOSAMPLE_Enterics:food_quality_date + food_packaging_date: + name: food_packaging_date + title: food_packaging_date + description: A food product's packaging date as marked by a food manufacturer + or retailer. + comments: The packaging date should not be confused with, nor replaced by a Best + Before date or other food quality date. If the date is known, leave blank or + provide a null value. + slot_uri: GENEPIO:0100616 + range: date + examples: + - value: '2020-05-25' + environmental_site: + name: environmental_site + title: environmental_site + description: An environmental location may describe a site in the natural or built + environment e.g. hospital, wet market, bat cave. + comments: If applicable, select the standardized term and ontology ID for the + environmental site from the picklist provided. Multiple values can be provided, + separated by a semi-colon. + slot_uri: GENEPIO:0001232 + any_of: + - range: environmental_site menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Poultry hatchery [ENVO:01001874] + exact_mappings: + - GISAID:isolation_source + - GISAID:environmental_site + - BIOSAMPLE_Enterics:isolation_source + - BIOSAMPLE_Enterics:animal_env + environmental_material: + name: environmental_material + title: environmental_material + description: A substance obtained from the natural or man-made environment e.g. + soil, water, sewage, door handle, bed handrail, face mask. + comments: If applicable, select the standardized term and ontology ID for the + environmental material from the picklist provided. Multiple values can be provided, + separated by a semi-colon. + slot_uri: GENEPIO:0001223 + any_of: + - range: environmental_material menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Soil [ENVO:00001998] + - value: Water [CHEBI:15377] + - value: Wastewater [ENVO:00002001] + - value: Broom [ENVO:03501377] + exact_mappings: + - GISAID:isolation_source + - GISAID:environmental_material + - BIOSAMPLE_Enterics:isolation_source + anatomical_material: + name: anatomical_material + title: anatomical_material + description: A substance obtained from an anatomical part of an organism e.g. + tissue, blood. + comments: An anatomical material is a substance taken from the body. If applicable, + select the standardized term and ontology ID for the anatomical material from + the picklist provided. Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001211 + any_of: + - range: anatomical_material menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Tissue [UBERON:0000479] + - value: Blood [UBERON:0000178] + exact_mappings: + - GISAID:isolation_source + - GISAID:anatomical_material + - BIOSAMPLE_Enterics:host_tissue_sampled + - BIOSAMPLE_Enterics:isolation_source + body_product: + name: body_product + title: body_product + description: A substance excreted/secreted from an organism e.g. feces, urine, + sweat. + comments: A body product is a substance produced by the body but meant to be excreted/secreted + (i.e. not part of the body). If applicable, select the standardized term and + ontology ID for the body product from the picklist provided. Multiple values + can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001216 + any_of: + - range: body_product menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Feces [UBERON:0001988] + - value: Urine [UBERON:0001088] + exact_mappings: + - GISAID:isolation_source + - GISAID:body_product + - BIOSAMPLE_Enterics:host_body_product + - BIOSAMPLE_Enterics:isolation_source + anatomical_part: + name: anatomical_part + title: anatomical_part + description: An anatomical part of an organism e.g. oropharynx. + comments: An anatomical part is a structure or location in the body. If applicable, + select the standardized term and ontology ID for the anatomical material from + the picklist provided. Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001214 + any_of: + - range: anatomical_part menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Snout [UBERON:0006333] + exact_mappings: + - GISAID:isolation_source + - GISAID:anatomical_part + - BIOSAMPLE_Enterics:isolation_source + collection_device: + name: collection_device + title: collection_device + description: The instrument or container used to collect the sample e.g. swab. + comments: This field includes animal feed. If applicable, select the standardized + term and ontology ID for the anatomical material from the picklist provided. + Multiple values can be provided, separated by a semi-colon. + slot_uri: GENEPIO:0001234 + any_of: + - range: collection_device menu + - range: null value menu + recommended: true + examples: + - value: Drag swab [OBI:0002822] + exact_mappings: + - GISAID:isolation_source + - GISAID:collection_device + - BIOSAMPLE_Enterics:samp_collect_device + - BIOSAMPLE_Enterics:isolation_source + collection_method: + name: collection_method + title: collection_method + description: The process used to collect the sample e.g. phlebotomy, necropsy. + comments: If applicable, provide the standardized term and ontology ID for the + anatomical material from the picklist provided. Multiple values can be provided, + separated by a semi-colon. + slot_uri: GENEPIO:0001241 + any_of: + - range: collection_method menu + - range: null value menu + recommended: true + examples: + - value: Rinsing for specimen collection [GENEPIO_0002116] + exact_mappings: + - GISAID:isolation_source + - GISAID:collection_method + - BIOSAMPLE_Enterics:isolation_source + sample_volume_measurement_value: + name: sample_volume_measurement_value + title: sample_volume_measurement_value + description: The numerical value of the volume measurement of the sample collected. + comments: Provide the numerical value of volume. + slot_uri: GENEPIO:0100768 + range: WhitespaceMinimizedString + examples: + - value: '5' + sample_volume_measurement_unit: + name: sample_volume_measurement_unit + title: sample_volume_measurement_unit + description: The units of the volume measurement of the sample collected. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0100769 + range: sample_volume_measurement_unit menu + examples: + - value: milliliter (mL) [UO:0000098] + residual_sample_status: + name: residual_sample_status + title: residual_sample_status + description: The status of the residual sample (whether any sample remains after + its original use). + comments: Residual samples are samples that remain after the sample material was + used for its original purpose. Select a residual sample status from the picklist. + If sample still exists, select "Residual sample remaining (some sample left)". + slot_uri: GENEPIO:0101090 + range: residual_sample_status menu + examples: + - value: No residual sample (sample all used) [GENEPIO:0101088] + purpose_of_sampling: + name: purpose_of_sampling + title: purpose_of_sampling + description: The reason that the sample was collected. + comments: The reason a sample was collected may provide information about potential + biases in sampling strategy. Provide the purpose of sampling from the picklist + in the template. Most likely, the sample was collected for Public health surveillance. + The reason why a sample was originally collected may differ from the reason + why it was selected for sequencing, which should be indicated in the "purpose + of sequencing" field. + slot_uri: GENEPIO:0001198 + any_of: + - range: purpose_of_sampling menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Public health surveillance + exact_mappings: + - BIOSAMPLE_Enterics:purpose_of_sampling + presampling_activity: + name: presampling_activity + title: presampling_activity + description: The activities or variables upstream of sample collection that may + affect the sample. + comments: If there was an activity that would affect the sample prior to collection + (this is different than sample processing), provide the activities by selecting + one or more values from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100433 + any_of: + - range: presampling_activity menu + - range: null value menu + multivalued: true + examples: + - value: Agricultural activity + presampling_activity_details: + name: presampling_activity_details + title: presampling_activity_details + description: The details of the activities or variables that affected the sample + collected. + comments: Briefly describe the presampling activities using free text. + slot_uri: GENEPIO:0100434 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: Agricultural waste from large farm contributes waste to the site sampled. + sample_storage_method: + name: sample_storage_method + title: sample_storage_method + description: The process used to store the sample. + comments: Provide details of how the sample was stored from time of collection + until time of processing. If there were issues with the cold chain storage, + note those here. + slot_uri: GENEPIO:0100448 + range: WhitespaceMinimizedString + examples: + - value: The sample was placed in a tube in a cooler bag during transportation + (~3 hours) to the lab site. At this point the sample was placed in storage + medium and put in a -10C freezer until it was processed and extracted 5 days + later. + sample_storage_medium: + name: sample_storage_medium + title: sample_storage_medium + description: The medium in which a sample is stored. + comments: Provide the name of the transport medium or storage medium used for + this sample. If none was used, leave blank or write "None". + slot_uri: GENEPIO:0100449 + range: WhitespaceMinimizedString + examples: + - value: Cary-Blair transport medium + sample_storage_duration_value: + name: sample_storage_duration_value + title: sample_storage_duration_value + description: The numerical value of the time measurement during which a sample + is in storage. + comments: Provide the numerical value of time. + slot_uri: GENEPIO:0101014 + range: WhitespaceMinimizedString + examples: + - value: '5' + sample_storage_duration_unit: + name: sample_storage_duration_unit + title: sample_storage_duration_unit + description: The units of a measured sample storage duration. + comments: Provide the units from the pick list. + slot_uri: GENEPIO:0101015 + any_of: + - range: sample_storage_duration_unit menu + - range: null value menu + examples: + - value: Day + specimen_processing: + name: specimen_processing + title: specimen_processing + description: Any processing applied to the sample during or after receiving the + sample. + comments: Select processes from the picklist that were applied to this sample. + slot_uri: GENEPIO:0001253 + any_of: + - range: specimen_processing menu + - range: null value menu + multivalued: true + examples: + - value: Centrifugation + specimen_processing_details: + name: specimen_processing_details + title: specimen_processing_details + description: The details of the processing applied to the sample during or after + receiving the sample. + comments: Briefly describe the processes applied to the sample. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString + examples: + - value: 25 samples were pooled and further prepared as a single sample during + library prep. + experimental_protocol: + name: experimental_protocol + title: experimental_protocol + description: The name of the overarching experimental methodology that was used + to process the biomaterial. + comments: Provide the name of the methodology used in your study. If available, + provide a link to the protocol. + slot_uri: GENEPIO:0101029 + range: WhitespaceMinimizedString + experimental_specimen_role_type: + name: experimental_specimen_role_type + title: experimental_specimen_role_type + description: The type of role that the sample represents in the experiment. + comments: Samples can play different types of roles in experiments. A sample under + study in one experiment may act as a control or be a replicate of another sample + in another experiment. This field is used to distinguish samples under study + from controls, replicates, etc. If the sample acted as an experimental control + or a replicate, select a role type from the picklist. If the sample was not + a control, leave blank or select "Not Applicable". + slot_uri: GENEPIO:0100921 + any_of: + - range: experimental_specimen_role_type menu + - range: null value menu + multivalued: true + examples: + - value: Positive experimental control + experimental_specimen_details: + name: experimental_specimen_details + title: experimental_specimen_details + slot_uri: GENEPIO:0101112 + range: WhitespaceMinimizedString + available_data_types: + name: available_data_types + title: available_data_types + description: The type of data that is available, that may or may not require permission + to access. + comments: This field provides information about additional data types that are + available that may provide context for interpretation of the sequence data. + Provide a term from the picklist for additional data types that are available. + Additional data types may require special permission to access. Contact the + data provider for more information. + slot_uri: GENEPIO:0100690 + any_of: + - range: available_data_types menu + - range: null value menu + multivalued: true + examples: + - value: Total coliform count [GENEPIO:0100729] + available_data_type_details: + name: available_data_type_details + title: available_data_type_details + description: Detailed information regarding other available data types. + comments: Use this field to provide free text details describing other available + data types that may provide context for interpreting genomic sequence data. + slot_uri: GENEPIO:0101023 + range: WhitespaceMinimizedString + examples: + - value: Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) + bacteria + host_common_name: + name: host_common_name + title: host_(common_name) + description: The commonly used name of the host. + comments: If the sample is directly from a host, either a common or scientific + name must be provided (although both can be included, if known). If known, + provide the common name. + slot_uri: GENEPIO:0001386 + any_of: + - range: host (common name) menu + - range: null value menu + recommended: true + examples: + - value: Cow [NCBITaxon:9913] + - value: Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] + exact_mappings: + - BIOSAMPLE_Enterics:host + host_scientific_name: + name: host_scientific_name + title: host_(scientific_name) + description: The taxonomic, or scientific name of the host. + comments: If the sample is directly from a host, either a common or scientific + name must be provided (although both can be included, if known). If known, + select the scientific name from the picklist provided. + slot_uri: GENEPIO:0001387 + any_of: + - range: host (scientific name) menu + - range: null value menu + recommended: true + examples: + - value: Bos taurus [NCBITaxon:9913] + - value: Homo sapiens [NCBITaxon:9103] + exact_mappings: + - GISAID:host + - BIOSAMPLE_Enterics:isolation_source + - BIOSAMPLE_Enterics:host + host_ecotype: + name: host_ecotype + title: host_(ecotype) + description: The biotype resulting from selection in a particular habitat, e.g. + the A. thaliana Ecotype Ler. + comments: Provide the name of the ecotype of the host organism. + slot_uri: GENEPIO:0100450 + range: WhitespaceMinimizedString + examples: + - value: Sea ecotype + exact_mappings: + - BIOSAMPLE_Enterics:host_variety + host_breed: + name: host_breed + title: host_(breed) + description: A breed is a specific group of domestic animals or plants having + homogeneous appearance, homogeneous behavior, and other characteristics that + distinguish it from other animals or plants of the same species and that were + arrived at through selective breeding. + comments: Provide the name of the breed of the host organism. + slot_uri: GENEPIO:0100451 + range: WhitespaceMinimizedString + examples: + - value: Holstein + exact_mappings: + - GISAID:host_disease + - BIOSAMPLE_Enterics:host_animal_breed + host_food_production_name: + name: host_food_production_name + title: host_(food production name) + description: The name of the host at a certain stage of food production, which + may depend on its age or stage of sexual maturity. + comments: Select the host's food production name from the pick list. + slot_uri: GENEPIO:0100452 + any_of: + - range: host (food production name) menu + - range: null value menu + examples: + - value: Calf [FOODON:03411349] + exact_mappings: + - BIOSAMPLE_Enterics:host + host_age: + name: host_age + title: host_age + description: Age of host at the time of sampling. + comments: If known, provide age. Age-binning is also acceptable. + slot_uri: GENEPIO:0001392 + any_of: + - range: decimal + - range: null value menu + maximum_value: 130 + required: true + examples: + - value: '79' + exact_mappings: + - GISAID:Patient%20age + - CNPHI:host_age + host_age_unit: + name: host_age_unit + title: host_age_unit + description: The units used to measure the host's age. + comments: If known, provide the age units used to measure the host's age from + the pick list. + slot_uri: GENEPIO:0001393 + any_of: + - range: host_age_unit menu + - range: null value menu + required: true + examples: + - value: year [UO:0000036] + host_age_bin: + name: host_age_bin + title: host_age_bin + description: Age of host at the time of sampling, expressed as an age group. + comments: Select the corresponding host age bin from the pick list provided in + the template. If not available, provide a null value or leave blank. + slot_uri: GENEPIO:0001394 + any_of: + - range: host_age_bin menu + - range: null value menu + exact_mappings: + - BIOSAMPLE_Enterics:host_age + host_disease: + name: host_disease + title: host_disease + description: The name of the disease experienced by the host. + comments: "This field is only required if the Pathogen.cl package was selected.\ + \ If the host was sick, provide the name of the disease.The standardized term\ + \ can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid\ + \ If the disease is not known, put \u201Cmissing\u201D." + slot_uri: GENEPIO:0001391 + any_of: + - range: host_disease menu + - range: null value menu + examples: + - value: mastitis, gastroenteritis + exact_mappings: + - BIOSAMPLE_Enterics:host_disease + host_health_state: + name: host_health_state + title: host_health_state + description: Health status of the host at the time of sample collection. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001388 + any_of: + - range: host_health_state menu + - range: null value menu + examples: + - value: Asymptomatic [NCIT:C3833] + exact_mappings: + - GISAID:Patient%20status + - CNPHI:host_health_state + host_health_status_details: + name: host_health_status_details + title: host_health_status_details + description: Further details pertaining to the health or disease status of the + host at time of collection. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001389 + any_of: + - range: host_health_status_details menu + - range: null value menu + examples: + - value: Hospitalized (ICU) [GENEPIO:0100046] + host_health_outcome: + name: host_health_outcome + title: host_health_outcome + description: Disease outcome in the host. + comments: If known, select a value from the pick list. + slot_uri: GENEPIO:0001390 + any_of: + - range: host_health_outcome menu + - range: null value menu + examples: + - value: Recovered [NCIT:C49498] + exact_mappings: + - CNPHI:host_disease_outcome + host_subject_id: + name: host_subject_id + title: host_subject_ID + description: 'A unique identifier by which each host can be referred to e.g. #131' + comments: Should be a unique, user-defined identifier. This ID can help link laboratory + data with epidemiological data, however, is likely sensitive information. Consult + the data steward. + slot_uri: GENEPIO:0001398 + range: WhitespaceMinimizedString + examples: + - value: BCxy123 + exact_mappings: + - CNPHI:host_subject_id + case_id: + name: case_id + title: case_ID + description: The identifier used to specify an epidemiologically detected case + of disease. + comments: Provide the case identifer. The case ID greatly facilitates linkage + between laboratory and epidemiological data. The case ID may be considered identifiable + information. Consult the data steward before sharing. + slot_uri: GENEPIO:0100281 + range: WhitespaceMinimizedString + examples: + - value: ABCD1234 + symptom_onset_date: + name: symptom_onset_date + title: symptom_onset_date + description: The date on which the symptoms began or were first noted. + comments: If known, provide the symptom onset date in ISO 8601 standard format + "YYYY-MM-DD". + slot_uri: GENEPIO:0001399 + any_of: + - range: date + - range: null value menu + examples: + - value: '2020-03-16' + signs_and_symptoms: + name: signs_and_symptoms + title: signs_and_symptoms + description: A perceived change in function or sensation, (loss, disturbance or + appearance) indicative of a disease, reported by a patient. + comments: Select all of the symptoms experienced by the host from the pick list. + slot_uri: GENEPIO:0001400 + any_of: + - range: signs_and_symptoms menu + - range: null value menu + recommended: true + examples: + - value: Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] + preexisting_conditions_and_risk_factors: + name: preexisting_conditions_and_risk_factors + title: pre-existing_conditions_and_risk_factors + description: 'Patient pre-existing conditions and risk factors. + + Pre-existing condition: A medical condition that existed prior to the current + infection. + + Risk Factor: A variable associated with an increased risk of disease or infection.' + comments: Select all of the pre-existing conditions and risk factors experienced + by the host from the pick list. If the desired term is missing, contact the + curation team. + slot_uri: GENEPIO:0001401 + any_of: + - range: pre-existing_conditions_and_risk_factors menu + - range: null value menu + recommended: true + examples: + - value: Asthma [HP:0002099] + complications: + name: complications + title: complications + description: Patient medical complications that are believed to have occurred + as a result of host disease. + comments: Select all of the complications experienced by the host from the pick + list. + slot_uri: GENEPIO:0001402 + any_of: + - range: complications menu + - range: null value menu + recommended: true + examples: + - value: Acute respiratory failure [MONDO:0001208] + exposure_event: + name: exposure_event + title: exposure event + description: Event leading to exposure. + comments: Select an exposure event from the pick list provided in the template. + If the desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001417 + any_of: + - range: exposure event menu + - range: null value menu + examples: + - value: Social Gathering + exact_mappings: + - GISAID:Additional%20location%20information + - CNPHI:Exposure%20Event + - NML_LIMS:PH_EXPOSURE + exposure_contact_level: + name: exposure_contact_level + title: exposure contact level + description: The exposure transmission contact type. + comments: Select direct or indirect exposure from the pick-list. + slot_uri: GENEPIO:0001418 + any_of: + - range: exposure contact level menu + - range: null value menu + examples: + - value: Direct + exact_mappings: + - NML_LIMS:exposure%20contact%20level + host_role: + name: host_role + title: host role + description: The role of the host in relation to the exposure setting. + comments: Select the host's personal role(s) from the pick list provided in the + template. If the desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001419 + range: host role menu + multivalued: true + examples: + - value: Inpatient + exact_mappings: + - NML_LIMS:PH_HOST_ROLE + exposure_setting: + name: exposure_setting + title: exposure setting + description: The setting leading to exposure. + comments: Select the host exposure setting(s) from the pick list provided in the + template. If a desired term is missing, contact the curation team. + slot_uri: GENEPIO:0001428 + range: exposure setting menu + multivalued: true + examples: + - value: Healthcare Setting + exact_mappings: + - NML_LIMS:PH_EXPOSURE + exposure_details: + name: exposure_details + title: exposure details + description: Additional host exposure information. + comments: Free text description of the exposure. + slot_uri: GENEPIO:0001431 + range: WhitespaceMinimizedString + examples: + - value: Case infected family at home + exact_mappings: + - NML_LIMS:PH_EXPOSURE_DETAILS + host_vaccination_status: + name: host_vaccination_status + title: host_vaccination_status + description: The vaccination status of the host (fully vaccinated, partially vaccinated, + or not vaccinated). + comments: Select the vaccination status of the host from the pick list. + slot_uri: GENEPIO:0001404 + any_of: + - range: host_vaccination_status menu + - range: null value menu + examples: + - value: Fully Vaccinated [GENEPIO:0100100] + exact_mappings: + - CNPHI:prior_sars_cov_2_vaccination + number_of_vaccine_doses_received: + name: number_of_vaccine_doses_received + title: number_of_vaccine_doses_received + description: The number of doses of the vaccine recived by the host. + comments: Record how many doses of the vaccine the host has received. + slot_uri: GENEPIO:0001406 + range: integer + minimum_value: 0 + examples: + - value: '2' + vaccination_dose_1_vaccine_name: + name: vaccination_dose_1_vaccine_name + title: vaccination_dose_1_vaccine_name + description: The name of the vaccine administered as the first dose of a vaccine + regimen. + comments: Provide the name and the corresponding manufacturer of the COVID-19 + vaccine administered as the first dose by selecting a value from the pick list + slot_uri: GENEPIO:0100313 + range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_1_vaccination_date: + name: vaccination_dose_1_vaccination_date + title: vaccination_dose_1_vaccination_date + description: The date the first dose of a vaccine was administered. + comments: Provide the date the first dose of COVID-19 vaccine was administered. + The date should be provided in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0100314 + range: date + examples: + - value: '2021-03-01' + vaccination_dose_2_vaccine_name: + name: vaccination_dose_2_vaccine_name + title: vaccination_dose_2_vaccine_name + description: The name of the vaccine administered as the second dose of a vaccine + regimen. + comments: Provide the name and the corresponding manufacturer of the COVID-19 + vaccine administered as the second dose by selecting a value from the pick list + slot_uri: GENEPIO:0100315 + range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_2_vaccination_date: + name: vaccination_dose_2_vaccination_date + title: vaccination_dose_2_vaccination_date + description: The date the second dose of a vaccine was administered. + comments: Provide the date the second dose of COVID-19 vaccine was administered. + The date should be provided in ISO 8601 standard format "YYYY-MM-DD". + slot_uri: GENEPIO:0100316 + range: date + examples: + - value: '2021-09-01' + vaccination_history: + name: vaccination_history + title: vaccination history + description: A description of the vaccines received and the administration dates + of a series of vaccinations against a specific disease or a set of diseases. + comments: Free text description of the dates and vaccines administered against + a particular disease/set of diseases. It is also acceptable to concatenate the + individual dose information (vaccine name, vaccination date) separated by semicolons. + slot_uri: GENEPIO:0100321 + range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + - value: '2021-03-01' + - value: Pfizer-BioNTech (Comirnaty) + - value: '2022-01-15' + exact_mappings: + - GISAID:Last%20vaccinated + influenza_antiviral_treatment_administration: + name: influenza_antiviral_treatment_administration + title: influenza_antiviral_treatment_administration + description: An action of giving or applying an influenza antiviral agent to a + patient as part of a treatment regimen. + slot_uri: GENEPIO:0101113 + any_of: + - range: influenza_antiviral_treatment_administration menu + - range: null value menu + examples: + - value: Influenza antiviral treatment administered [GENEPIO:0101194] + influenza_antiviral_agent__: + name: influenza_antiviral_agent__ + title: influenza_antiviral_agent + description: A substance that destroys or inhibits replication of viruses. + slot_uri: GENEPIO:0101114 + range: WhitespaceMinimizedString + influenza_antiviral_treatment_date: + name: influenza_antiviral_treatment_date + title: influenza_antiviral_treatment_date + description: The date on which the influenza antiviral agent was administered + to a patient as part of treatment + comments: This field records the exact date when the antiviral treatment was administered. + The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect + the first administration date if multiple doses were given. + slot_uri: GENEPIO:0101115 + range: date + water_catchment_area_human_population_measurement_value: + name: water_catchment_area_human_population_measurement_value + title: water_catchment_area_human_population_measurement_value + description: The numerical value of the human population measurement that contributes + to the composition of water in a catchment area. + comments: Where known, provide the numerical value of population size, i.e. the + number of people. + slot_uri: GENEPIO:0100773 + any_of: + - range: integer + - range: null value menu + recommended: true + examples: + - value: 10,500 + water_catchment_area_human_population_range: + name: water_catchment_area_human_population_range + title: water_catchment_area_human_population_range + description: The human population range of the water catchment that contributes + effluent to a wastewater site. + comments: Where catchment population is not well known, provide an estimation + of population size by selecting a value from the picklist. + slot_uri: GENEPIO:0100774 + any_of: + - range: water catchment area human population range menu + - range: null value menu + examples: + - value: 1,000 - 10,000 people + water_catchment_area_human_population_measurement_method: + name: water_catchment_area_human_population_measurement_method + title: water_catchment_area_human_population_measurement_method + description: The method by which a water catchment 's human population size was + measured or estimated + comments: Provide a brief description of how catchment population size was measured + or estimated. + slot_uri: GENEPIO:0100775 + range: WhitespaceMinimizedString + examples: + - value: population of jurisdiction encompassing the wastewater service area + water_catchment_area_human_population_density_value: + name: water_catchment_area_human_population_density_value + title: water catchment area human population density value + description: The numerical value describing the number of humans per geographical + area in a water catchment. + comments: Provide the numerical value of the population density in the catchement + area. + slot_uri: GENEPIO:0100776 + range: WhitespaceMinimizedString + examples: + - value: '4' + water_catchment_area_human_population_density_unit: + name: water_catchment_area_human_population_density_unit + title: water catchment area human population density unit + description: The unit describing the number of humans per geographical area in + a water catchment. + comments: Provide the unit of the population density in the catchement area. + slot_uri: GENEPIO:0100777 + any_of: + - range: water catchment area human population density unit menu + - range: null value menu + examples: + - value: persons per Km^2 + populated_area_type: + name: populated_area_type + title: populated area type + description: A type of area that is populated by humans to different degrees. + comments: Provide the populated area type from the pick list. + slot_uri: GENEPIO:0100778 + any_of: + - range: populated area type menu + - range: null value menu + examples: + - value: Urban area + sampling_weather_conditions: + name: sampling_weather_conditions + title: sampling weather conditions + description: The state of the atmosphere at a place and time as regards heat, + dryness, sunshine, wind, rain, etc. + comments: Provide the weather conditions at the time of sample collection. + slot_uri: GENEPIO:0100779 + any_of: + - range: sampling weather conditions menu + - range: null value menu + multivalued: true + examples: + - value: Rain + presampling_weather_conditions: + name: presampling_weather_conditions + title: presampling weather conditions + description: Weather conditions prior to collection that may affect the sample. + comments: Provide the weather conditions prior to sample collection. + slot_uri: GENEPIO:0100780 + any_of: + - range: presampling weather conditions menu + - range: null value menu + multivalued: true + examples: + - value: Drizzle + precipitation_measurement_value: + name: precipitation_measurement_value + title: precipitation measurement value + description: The amount of water which has fallen during a precipitation process. + comments: Provide the quantity of precipitation in the area leading up to the + time of sample collection. + slot_uri: GENEPIO:0100911 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: '12' + water_depth: + name: water_depth + title: water_depth + description: The depth of some water. + comments: Provide the numerical depth only of water only (without units). + slot_uri: GENEPIO:0100440 + range: WhitespaceMinimizedString + examples: + - value: '5' + water_depth_units: + name: water_depth_units + title: water_depth_units + description: The units of measurement for water depth. + comments: Provide the units of measurement for which the depth was recorded. + slot_uri: GENEPIO:0101025 + any_of: + - range: water_depth_units menu + - range: null value menu + examples: + - value: meter (m) [UO:0000008] + sediment_depth: + name: sediment_depth + title: sediment_depth + description: The depth of some sediment. + comments: Provide the numerical depth only of the sediment (without units). + slot_uri: GENEPIO:0100697 + range: WhitespaceMinimizedString + examples: + - value: '2' + sediment_depth_units: + name: sediment_depth_units + title: sediment_depth_units + description: The units of measurement for sediment depth. + comments: Provide the units of measurement for which the depth was recorded. + slot_uri: GENEPIO:0101026 + any_of: + - range: sediment_depth_units menu + - range: null value menu + examples: + - value: meter (m) [UO:0000008] + air_temperature: + name: air_temperature + title: air_temperature + description: The temperature of some air. + comments: Provide the numerical value for the temperature of the air (without + units). + slot_uri: GENEPIO:0100441 + range: WhitespaceMinimizedString + examples: + - value: '25' + air_temperature_units: + name: air_temperature_units + title: air_temperature_units + description: The units of measurement for air temperature. + comments: Provide the units of measurement for which the temperature was recorded. + slot_uri: GENEPIO:0101027 + any_of: + - range: air_temperature_units menu + - range: null value menu + examples: + - value: degree Celsius (C) [UO:0000027] + water_temperature: + name: water_temperature + title: water_temperature + description: The temperature of some water. + comments: Provide the numerical value for the temperature of the water (without + units). + slot_uri: GENEPIO:0100698 + range: WhitespaceMinimizedString + examples: + - value: '4' + water_temperature_units: + name: water_temperature_units + title: water_temperature_units + description: The units of measurement for water temperature. + comments: Provide the units of measurement for which the temperature was recorded. + slot_uri: GENEPIO:0101028 + any_of: + - range: water_temperature_units menu + - range: null value menu + examples: + - value: degree Celsius (C) [UO:0000027] + weather_type: + name: weather_type + title: weather_type + description: The state of the atmosphere at a place and time as regards heat, + dryness, sunshine, wind, rain, etc. + comments: Provide the weather conditions at the time of sample collection. + slot_uri: GENEPIO:0100442 + any_of: + - range: weather_type menu + - range: null value menu + multivalued: true + examples: + - value: Rain [ENVO:01001564] + precipitation_measurement_unit: + name: precipitation_measurement_unit + title: precipitation measurement unit + description: The units of measurement for the amount of water which has fallen + during a precipitation process. + comments: Provide the units of precipitation by selecting a value from the pick + list. + slot_uri: GENEPIO:0100912 + any_of: + - range: precipitation measurement unit menu + - range: null value menu + recommended: true + examples: + - value: inch + precipitation_measurement_method: + name: precipitation_measurement_method + title: precipitation measurement method + description: The process used to measure the amount of water which has fallen + during a precipitation process. + comments: Provide the name of the procedure or method used to measure precipitation. + slot_uri: GENEPIO:0100913 + range: WhitespaceMinimizedString + examples: + - value: Rain gauge over a 12 hour period prior to sample collection + ambient_temperature_measurement_value: + name: ambient_temperature_measurement_value + title: ambient temperature measurement value + description: The numerical value of a measurement of the ambient temperature. + comments: Provide the numerical value of the measured temperature. + slot_uri: GENEPIO:0100935 + range: WhitespaceMinimizedString + examples: + - value: '70' + ambient_temperature_measurement_unit: + name: ambient_temperature_measurement_unit + title: ambient temperature measurement unit + description: The units of a measurement of the ambient temperature. + comments: Provide the units of the measured temperature. + slot_uri: GENEPIO:0100936 + any_of: + - range: ambient temperature measurement unit menu + - range: null value menu + examples: + - value: degree Celsius (C) + ph_measurement_value: + name: ph_measurement_value + title: pH measurement value + description: The measured pH value indicating the acidity or basicity(alkalinity) + of an aqueous solution. + comments: Provide the numerical value of the measured pH. + slot_uri: GENEPIO:0001736 + range: WhitespaceMinimizedString + examples: + - value: '7.4' + ph_measurement_method: + name: ph_measurement_method + title: pH measurement method + description: The process used to measure pH value. + comments: Provide the name of the procedure or technology used to measure pH. + slot_uri: GENEPIO:0100781 + range: WhitespaceMinimizedString + examples: + - value: pH test strip (litmus test) + total_daily_flow_rate_measurement_value: + name: total_daily_flow_rate_measurement_value + title: total daily flow rate measurement value + description: The numerical value of a measured fluid flow rate over the course + of a day. + comments: Provide the numerical value of the measured flow rate. + slot_uri: GENEPIO:0100905 + range: WhitespaceMinimizedString + examples: + - value: '10' + total_daily_flow_rate_measurement_unit: + name: total_daily_flow_rate_measurement_unit + title: total daily flow rate measurement unit + description: The units of a measured fluid flow rate over the course of a day. + comments: Provide the units of the measured flow rate by selecting a value from + the pick list. + slot_uri: GENEPIO:0100906 + any_of: + - range: total daily flow rate measurement unit menu + - range: null value menu + examples: + - value: million gallons per day (MGD) + total_daily_flow_rate_measurement_method: + name: total_daily_flow_rate_measurement_method + title: total daily flow rate measurement method + description: The process used to measure total daily fluid flow rate. + comments: Provide the name of the procedure or technology used to measure flow + rate. + slot_uri: GENEPIO:0100907 + range: WhitespaceMinimizedString + examples: + - value: Flow meter + instantaneous_flow_rate_measurement_value: + name: instantaneous_flow_rate_measurement_value + title: instantaneous flow rate measurement value + description: The numerical value of a measured instantaneous fluid flow rate. + comments: Provide the numerical value of the measured flow rate. + slot_uri: GENEPIO:0100908 + range: WhitespaceMinimizedString + examples: + - value: '25' + instantaneous_flow_rate_measurement_unit: + name: instantaneous_flow_rate_measurement_unit + title: instantaneous flow rate measurement unit + description: The units of a measured instantaneous fluid flow rate. + comments: Provide the units of the measured flow rate by selecting a value from + the pick list. + slot_uri: GENEPIO:0100909 + any_of: + - range: instantaneous flow rate measurement unit menu + - range: null value menu + examples: + - value: cubic meter per hour (m^3/h) + instantaneous_flow_rate_measurement_method: + name: instantaneous_flow_rate_measurement_method + title: instantaneous flow rate measurement method + description: The process used to measure instantaneous fluid flow rate. + comments: Provide the name of the procedure or technology used to measure flow + rate. + slot_uri: GENEPIO:0100910 + range: WhitespaceMinimizedString + examples: + - value: Flow meter + turbidity_measurement_value: + name: turbidity_measurement_value + title: turbidity measurement value + description: The numerical value of a measurement of turbidity. + comments: Provide the numerical value of the measured turbidity. + slot_uri: GENEPIO:0100783 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: '0.02' + turbidity_measurement_unit: + name: turbidity_measurement_unit + title: turbidity measurement unit + description: The units of a measurement of turbidity. + comments: Provide the units of the measured turbidity by selecting a value from + the pick list. + slot_uri: GENEPIO:0100914 + any_of: + - range: turbidity measurement unit menu + - range: null value menu + recommended: true + examples: + - value: nephelometric turbidity unit (NTU) + turbidity_measurement_method: + name: turbidity_measurement_method + title: turbidity measurement method + description: The process used to measure turbidity. + comments: Provide the name of the procedure or technology used to measure turbidity. + slot_uri: GENEPIO:0101013 + range: WhitespaceMinimizedString + examples: + - value: Nephelometric method + dissolved_oxygen_measurement_value: + name: dissolved_oxygen_measurement_value + title: dissolved oxygen measurement value + description: The numerical value of a measurement of dissolved oxygen. + comments: Provide the numerical value of the measured dissolved oxygen. + slot_uri: GENEPIO:0100915 + range: WhitespaceMinimizedString + examples: + - value: '5' + dissolved_oxygen_measurement_unit: + name: dissolved_oxygen_measurement_unit + title: dissolved oxygen measurement unit + description: The units of a measurement of dissolved oxygen. + comments: Provide the units of the measured dissolved oxygen by selecting a value + from the pick list. + slot_uri: GENEPIO:0100784 + any_of: + - range: dissolved oxygen measurement unit menu + - range: null value menu + examples: + - value: part per million (ppm) + dissolved_oxygen_measurement_method: + name: dissolved_oxygen_measurement_method + title: dissolved oxygen measurement method + description: The method used to measure dissolved oxygen. + comments: Provide the name of the procedure or technology used to measure dissolved + oxygen. + slot_uri: GENEPIO:0100785 + range: WhitespaceMinimizedString + examples: + - value: Dissolved oxygen meter in vertical direction + oxygen_reduction_potential_orp_measurement_value: + name: oxygen_reduction_potential_orp_measurement_value + title: oxygen reduction potential (ORP) measurement value + description: The numerical value of a measurement of oxygen reduction potential + (ORP). + comments: Provide the numerical value of the measured oxygen reduction potential. + slot_uri: GENEPIO:0100917 + range: WhitespaceMinimizedString + examples: + - value: '-50' + oxygen_reduction_potential_orp_measurement_unit: + name: oxygen_reduction_potential_orp_measurement_unit + title: oxygen reduction potential (ORP) measurement unit + description: The units of a measurement of oxygen reduction potential (ORP). + comments: Provide the units of the measured oxygen reduction potential by selecting + a value from the pick list. + slot_uri: GENEPIO:0100786 + any_of: + - range: oxygen reduction potential (ORP) measurement unit menu + - range: null value menu + examples: + - value: milliVolt (mV) + oxygen_reduction_potential_orp_measurement_method: + name: oxygen_reduction_potential_orp_measurement_method + title: oxygen reduction potential (ORP) measurement method + description: The method used to measure oxygen reduction potential (ORP). + comments: Provide the name of the procedure or technology used to measure oxygen + reduction potential. + slot_uri: GENEPIO:0100787 + range: WhitespaceMinimizedString + examples: + - value: ORP sensor + chemical_oxygen_demand_cod_measurement_value: + name: chemical_oxygen_demand_cod_measurement_value + title: chemical oxygen demand (COD) measurement value + description: The measured value from a chemical oxygen demand (COD) test. + comments: Provide the numerical value of the COD test result. + slot_uri: GENEPIO:0100788 + range: WhitespaceMinimizedString + examples: + - value: '26' + chemical_oxygen_demand_cod_measurement_unit: + name: chemical_oxygen_demand_cod_measurement_unit + title: chemical oxygen demand (COD) measurement unit + description: The units associated with a value from a chemical oxygen demand (COD) + test. + comments: Provide the units of the COD test result. + slot_uri: GENEPIO:0100789 + any_of: + - range: chemical oxygen demand (COD) measurement unit menu + - range: null value menu + examples: + - value: milligram per liter (mg/L) + chemical_oxygen_demand_cod_measurement_method: + name: chemical_oxygen_demand_cod_measurement_method + title: chemical oxygen demand (COD) measurement method + description: The method used to measure chemical oxygen demand (COD). + comments: Provide the name of the procedure or technology used to measure COD. + slot_uri: GENEPIO:0100790 + range: WhitespaceMinimizedString + examples: + - value: Hach LCK test kit + carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_value + title: carbonaceous biochemical oxygen demand (CBOD) measurement value + description: The numerical value of a measurement of carbonaceous biochemical + oxygen demand (CBOD). + comments: Provide the numerical value of the measured CBOD. + slot_uri: GENEPIO:0100791 + range: WhitespaceMinimizedString + examples: + - value: '20' + carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit + title: carbonaceous biochemical oxygen demand (CBOD) measurement unit + description: The units of a measurement of carbonaceous biochemical oxygen demand + (CBOD). + comments: Provide the units of the measured CBOD by selecting a value from the + pick list. + slot_uri: GENEPIO:0100792 + any_of: + - range: carbonaceous biochemical oxygen demand (CBOD) measurement unit menu + - range: null value menu + examples: + - value: milligram per liter (mg/L) + carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: + name: carbonaceous_biochemical_oxygen_demand_cbod_measurement_method + title: carbonaceous biochemical oxygen demand (CBOD) measurement method + description: The method used to measure carbonaceous biochemical oxygen demand + (CBOD). + comments: Provide the name of the procedure or technology used to measure CBOD. + slot_uri: GENEPIO:0100793 + range: WhitespaceMinimizedString + examples: + - value: CBOD measurement by optical probe + total_suspended_solids_tss_measurement_value: + name: total_suspended_solids_tss_measurement_value + title: total suspended solids (TSS) measurement value + description: The numerical value from a total suspended solids (TSS) test. + comments: Provide the numerical value of the measured TSS. + slot_uri: GENEPIO:0100794 + range: WhitespaceMinimizedString + examples: + - value: '8' + total_suspended_solids_tss_measurement_unit: + name: total_suspended_solids_tss_measurement_unit + title: total suspended solids (TSS) measurement unit + description: The units associated with a value from a total suspended solids (TSS) + test. + comments: Provide the units of the measured TSS. + slot_uri: GENEPIO:0100795 + any_of: + - range: total suspended solids (TSS) measurement unit menu + - range: null value menu + examples: + - value: percent (%) + total_suspended_solids_tss_measurement_method: + name: total_suspended_solids_tss_measurement_method + title: total suspended solids (TSS) measurement method + description: The method used to measure total suspended solids (TSS). + comments: Provide the name of the procedure or technology used to measure TSS. + slot_uri: GENEPIO:0100796 + range: WhitespaceMinimizedString + examples: + - value: Vacuum filter through a 2-micron filter, then oven-dried and weighed + sample + total_dissolved_solids_tds_measurement_value: + name: total_dissolved_solids_tds_measurement_value + title: total dissolved solids (TDS) measurement value + description: The numerical value from a total dissolved solids (TDS) test. + comments: Provide the numerical value of the measured TDS. + slot_uri: GENEPIO:0100797 + range: WhitespaceMinimizedString + examples: + - value: '2' + total_dissolved_solids_tds_measurement_unit: + name: total_dissolved_solids_tds_measurement_unit + title: total dissolved solids (TDS) measurement unit + description: The units associated with a value from a total dissolved solids (TDS) + test. + comments: Provide the units of the measured TDS. + slot_uri: GENEPIO:0100798 + any_of: + - range: total dissolved solids (TDS) measurement unit menu + - range: null value menu + examples: + - value: percent (%) + total_dissolved_solids_tds_measurement_method: + name: total_dissolved_solids_tds_measurement_method + title: total dissolved solids (TDS) measurement method + description: The method used to measure total dissolved solids (TDS). + comments: Provide the name of the procedure or technology used to measure TDS. + slot_uri: GENEPIO:0100799 + range: WhitespaceMinimizedString + examples: + - value: Subtract calculated TSS from calculated TS + total_solids_ts_measurement_value: + name: total_solids_ts_measurement_value + title: total solids (TS) measurement value + description: The numerical value from a total solids (TS) test. + comments: Provide the numerical value of the measured TS. + slot_uri: GENEPIO:0100800 + range: WhitespaceMinimizedString + examples: + - value: '10' + total_solids_ts_measurement_unit: + name: total_solids_ts_measurement_unit + title: total solids (TS) measurement unit + description: The units associated with a value from a total solids (TS) test. + comments: Provide the units of the measured TS. + slot_uri: GENEPIO:0100801 + any_of: + - range: total solids (TS) measurement unit menu + - range: null value menu + examples: + - value: percent (%) + total_solids_ts_measurement_method: + name: total_solids_ts_measurement_method + title: total solids (TS) measurement method + description: The method used to measure total solids (TS). + comments: Provide the name of the procedure or technology used to measure TS. + slot_uri: GENEPIO:0100802 + range: WhitespaceMinimizedString + examples: + - value: Gravimetric method by oven drying, then weighing + alkalinity_measurement_value: + name: alkalinity_measurement_value + title: alkalinity measurement value + description: The numerical value of a measurement of alkalinity. + comments: Provide the numerical value of the measured alkalinity. + slot_uri: GENEPIO:0100878 + range: WhitespaceMinimizedString + examples: + - value: '3' + alkalinity_measurement_unit: + name: alkalinity_measurement_unit + title: alkalinity measurement unit + description: The units of a measurement of alkalinity. + comments: Provide the units of the measured alkalinity. + slot_uri: GENEPIO:0100879 + any_of: + - range: alkalinity measurement unit menu + - range: null value menu + examples: + - value: milligram per liter of calcium carbonate (mg/L CaCO3) + alkalinity_measurement_method: + name: alkalinity_measurement_method + title: alkalinity measurement method + description: The process used to measure alkalinity. + comments: Provide the name of the procedure or technology used to measure alkalinity. + slot_uri: GENEPIO:0100880 + range: WhitespaceMinimizedString + examples: + - value: Titration method + conductivity_measurement_value: + name: conductivity_measurement_value + title: conductivity measurement value + description: The numerical value of a measurement of conductivity. + comments: Provide the numerical value of the measured conductivity. + slot_uri: GENEPIO:0100916 + range: WhitespaceMinimizedString + examples: + - value: '1412' + conductivity_measurement_unit: + name: conductivity_measurement_unit + title: conductivity measurement unit + description: The units of a measurement of conductivity. + comments: Provide the units of the measured conductivity. + slot_uri: GENEPIO:0100803 + any_of: + - range: conductivity measurement unit menu + - range: null value menu + examples: + - value: "microSiemen per centimeter (\u03BCS/cm)" + conductivity_measurement_method: + name: conductivity_measurement_method + title: conductivity measurement method + description: The method used to measure conductivity. + comments: Provide the name of the procedure or technology used to measure conductivity. + slot_uri: GENEPIO:0100804 + range: WhitespaceMinimizedString + examples: + - value: Conductivity electrode and meter + salinity_measurement_value: + name: salinity_measurement_value + title: salinity measurement value + description: The numerical value of a measurement of salinity. + comments: Provide the numerical value of the measured salinity. + slot_uri: GENEPIO:0100805 + range: WhitespaceMinimizedString + examples: + - value: '35' + salinity_measurement_unit: + name: salinity_measurement_unit + title: salinity measurement unit + description: The units of a measurement of salinity. + comments: Provide the units of the measured salinity. + slot_uri: GENEPIO:0100806 + any_of: + - range: salinity measurement unit menu + - range: null value menu + examples: + - value: practical salinity unit (PSU) + salinity_measurement_method: + name: salinity_measurement_method + title: salinity measurement method + description: The method used to measure salinity. + comments: Provide the name of the procedure or technology used to measure salinity. + slot_uri: GENEPIO:0100807 + range: WhitespaceMinimizedString + examples: + - value: conductivity meter + total_nitrogen_tn_measurement_value: + name: total_nitrogen_tn_measurement_value + title: total nitrogen (TN) measurement value + description: The numerical value of a measurement of total nitrogen (TN). + comments: Provide the numerical value of the measured TN. + slot_uri: GENEPIO:0100808 + range: WhitespaceMinimizedString + examples: + - value: '120' + total_nitrogen_tn_measurement_unit: + name: total_nitrogen_tn_measurement_unit + title: total nitrogen (TN) measurement unit + description: The units of a measurement of total nitrogen (TN). + comments: Provide the units of the measured TN. + slot_uri: GENEPIO:0100809 + any_of: + - range: total nitrogen (TN) measurement unit menu + - range: null value menu + examples: + - value: milligram per liter (mg/L) + total_nitrogen_tn_measurement_method: + name: total_nitrogen_tn_measurement_method + title: total nitrogen (TN) measurement method + description: The method used to measure total nitrogen (TN). + comments: Provide the name of the procedure or technology used to measure TN. + slot_uri: GENEPIO:0100810 + range: WhitespaceMinimizedString + examples: + - value: Hach total nitrogen spectrophotometric test + total_phosphorus_tp_measurement_value: + name: total_phosphorus_tp_measurement_value + title: total phosphorus (TP) measurement value + description: The numerical value of a measurement of total phosphorus (TP). + comments: Provide the numerical value of the measured TP. + slot_uri: GENEPIO:0100811 + range: WhitespaceMinimizedString + examples: + - value: '2' + total_phosphorus_tp_measurement_unit: + name: total_phosphorus_tp_measurement_unit + title: total phosphorus (TP) measurement unit + description: The units of a measurement of total phosphorus (TP). + comments: Provide the units of the measured TP. + slot_uri: GENEPIO:0100812 + any_of: + - range: total phosphorus (TP) measurement unit menu + - range: null value menu + examples: + - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) + total_phosphorus_tp_measurement_method: + name: total_phosphorus_tp_measurement_method + title: total phosphorus (TP) measurement method + description: The method used to measure total phosphorus (TP). + comments: Provide the name of the procedure or technology used to measure TP. + slot_uri: GENEPIO:0100813 + range: WhitespaceMinimizedString + examples: + - value: Merck phosphate spectrophotometric test kit + fecal_contamination_indicator_: + name: fecal_contamination_indicator_ + title: fecal contamination indicator + description: A gene, virus, bacteria, or substance used to measure the sanitary + quality of water in regards to fecal contamination. + comments: If a fecal contamination indicator was measured, select it from the + picklist. + slot_uri: GENEPIO:0100814 + any_of: + - range: fecal contamination indicator menu + - range: null value menu + recommended: true + examples: + - value: crAssphage + fecal_contamination_value: + name: fecal_contamination_value + title: fecal contamination value + description: The numerical value of a measurement of fecal contamination. + comments: Provide the numerical value of the measured fecal contamination. + slot_uri: GENEPIO:0100815 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: '10' + fecal_contamination_unit: + name: fecal_contamination_unit + title: fecal contamination unit + description: The units of a measurement of fecal contamination. + comments: Provide the units of the measured fecal contamination. + slot_uri: GENEPIO:0100816 + any_of: + - range: fecal contamination unit menu + - range: null value menu + recommended: true + examples: + - value: cycle threshold (Ct) / quantification cycle (Cq) + fecal_contamination_method: + name: fecal_contamination_method + title: fecal contamination method + description: The method used to measure fecal contamination. + comments: Provide the name of the procedure or technology used to measure fecal + contamination. + slot_uri: GENEPIO:0100817 + range: WhitespaceMinimizedString + examples: + - value: quantitative PCR assay + fecal_coliform_count_value: + name: fecal_coliform_count_value + title: fecal coliform count value + description: The numerical value of a measurement of fecal coliforms within a + sample. + comments: Provide the numerical value of the measured fecal coliforms. + slot_uri: GENEPIO:0100818 + range: WhitespaceMinimizedString + examples: + - value: '3' + fecal_coliform_count_unit: + name: fecal_coliform_count_unit + title: fecal coliform count unit + description: The units of a measurement of fecal coliforms. + comments: Provide the units of the measured fecal coliforms. + slot_uri: GENEPIO:0100819 + any_of: + - range: fecal coliform count unit menu + - range: null value menu + examples: + - value: most probable number per milliliter (MPN/mL) + fecal_coliform_count_method: + name: fecal_coliform_count_method + title: fecal coliform count method + description: The method used to measure fecal coliforms. + comments: Provide the name of the procedure or technology used to measure fecal + coliforms. + slot_uri: GENEPIO:0100820 + range: WhitespaceMinimizedString + examples: + - value: MPN method via serial dilutions until lack of growth + urinary_contamination_indicator: + name: urinary_contamination_indicator + title: urinary contamination indicator + description: A gene, virus, bacteria, or substance used to measure the sanitary + quality of water in regards to urinary contamination. + comments: If a urinary contamination indicator was measured, select it from the + picklist. + slot_uri: GENEPIO:0100837 + any_of: + - range: urinary contamination indicator menu + - range: null value menu + examples: + - value: urobilin + urinary_contamination_value: + name: urinary_contamination_value + title: urinary contamination value + description: The numerical value of a measurement of urinary contamination. + comments: Provide the numerical value of the measured urinary contamination. + slot_uri: GENEPIO:0100838 + range: WhitespaceMinimizedString + examples: + - value: '3' + urinary_contamination_unit: + name: urinary_contamination_unit + title: urinary contamination unit + description: The units of a measurement of urinary contamination. + comments: Provide the units of the measured urinary contamination. + slot_uri: GENEPIO:0100839 + any_of: + - range: urinary contamination unit menu + - range: null value menu + examples: + - value: nanograms per liter + urinary_contamination_method: + name: urinary_contamination_method + title: urinary contamination method + description: The method used to measure urinary contamination. + comments: Provide the name of the procedure or technology used to measure urinary + contamination. + slot_uri: GENEPIO:0100840 + range: WhitespaceMinimizedString + examples: + - value: Urobilin Concentration Test + sample_temperature_value_at_collection: + name: sample_temperature_value_at_collection + title: sample temperature value (at collection) + description: The numerical value of a measurement of temperature of a sample at + collection. + comments: Provide the numerical value of the measured temperature. + slot_uri: GENEPIO:0100821 + range: WhitespaceMinimizedString + examples: + - value: '20' + sample_temperature_unit_at_collection: + name: sample_temperature_unit_at_collection + title: sample temperature unit (at collection) + description: The units of a measurement of temperature of a sample at the time + of collection. + comments: Provide the units of the measured temperature. + slot_uri: GENEPIO:0100822 + any_of: + - range: sample temperature unit (at collection) menu + - range: null value menu + examples: + - value: degree Celsius (C) + sample_temperature_value_when_received: + name: sample_temperature_value_when_received + title: sample temperature value (when received) + description: The numerical value of a measurement of temperature of a sample upon + receipt. + comments: Provide the numerical value of the measured temperature. + slot_uri: GENEPIO:0100823 + range: WhitespaceMinimizedString + examples: + - value: '22' + sample_temperature_unit_when_received: + name: sample_temperature_unit_when_received + title: sample temperature unit (when received) + description: The units of a measurement of temperature of a sample at the time + upon receipt. + comments: Provide the units of the measured temperature. + slot_uri: GENEPIO:0100824 + any_of: + - range: sample temperature unit (when received) menu + - range: null value menu + examples: + - value: degree Celsius (C) + library_id: + name: library_id + title: library_ID + description: The user-specified identifier for the library prepared for sequencing. + comments: Every "library ID" from a single submitter must be unique. It can have + any format, but we suggest that you make it concise, unique and consistent within + your lab, and as informative as possible. + slot_uri: GENEPIO:0001448 + range: WhitespaceMinimizedString + examples: + - value: LS_2010_NP_123446 + sequencing_assay_type: + name: sequencing_assay_type + title: sequencing_assay_type + description: The overarching sequencing methodology that was used to determine + the sequence of a biomaterial. + comments: 'Example Guidance: Provide the name of the DNA or RNA sequencing technology + used in your study. If unsure refer to the protocol documentation, or provide + a null value.' + slot_uri: GENEPIO:0100997 + range: sequencing_assay_type menu + examples: + - value: whole genome sequencing assay [OBI:0002117] + sequencing_date: + name: sequencing_date + title: sequencing_date + description: The date the sample was sequenced. + comments: ISO 8601 standard "YYYY-MM-DD". + slot_uri: GENEPIO:0001447 + range: date + todos: + - '>={sample collection date}' + examples: + - value: '2020-06-22' + purpose_of_sequencing__: + name: purpose_of_sequencing__ + title: purpose_of_sequencing + description: The reason that the sample was sequenced. + comments: The reason why a sample was originally collected may differ from the + reason why it was selected for sequencing. The reason a sample was sequenced + may provide information about potential biases in sequencing strategy. Provide + the purpose of sequencing from the picklist in the template. The reason for + sample collection should be indicated in the "purpose of sampling" field. + slot_uri: GENEPIO:0001445 + any_of: + - range: purpose_of_sequencing menu + - range: null value menu + multivalued: true + required: true + examples: + - value: Travel-associated surveillance + purpose_of_sequencing_details: + name: purpose_of_sequencing_details + title: purpose_of_sequencing_details + description: The description of why the sample was sequenced providing specific + details. + comments: 'Provide an expanded description of why the sample was sequenced using + free text. The description may include the importance of the sequences for a + particular public health investigation/surveillance activity/research question. + Suggested standardized descriptions include: Assessing public health control + measures, Determining early introductions and spread, Investigating airline-related + exposures, Investigating remote regions, Investigating health care workers, + Investigating schools/universities.' + slot_uri: GENEPIO:0001446 + range: WhitespaceMinimizedString + examples: + - value: Investigating schools/universities + sequenced_by: + name: sequenced_by + title: sequenced_by + description: The name of the agency, organization or institution responsible for + sequencing the isolate's genome. + comments: Provide the name of the agency, organization or institution that performed + the sequencing in full (avoid abbreviations). If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100416 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + exact_mappings: + - GISAID:sequenced_by + - BIOSAMPLE_Enterics:sequenced_by + sequenced_by_laboratory_name: + name: sequenced_by_laboratory_name + title: sequenced_by_laboratory_name + description: The specific laboratory affiliation of the responsible for sequencing + the isolate's genome. + comments: Provide the name of the specific laboratory that that performed the + sequencing in full (avoid abbreviations). If the information is unknown or cannot + be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100470 + range: WhitespaceMinimizedString + examples: + - value: Topp Lab + sequenced_by_contact_name: + name: sequenced_by_contact_name + title: sequenced_by_contact_name + description: The name or title of the contact responsible for follow-up regarding + the sequence. + comments: Provide the name of an individual or their job title. As personnel turnover + may render the contact's name obsolete, it is more prefereable to provide a + job title for ensuring accuracy of information and institutional memory. If + the information is unknown or cannot be provided, leave blank or provide a null + value. + slot_uri: GENEPIO:0100471 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: Enterics Lab Manager + sequenced_by_contact_email: + name: sequenced_by_contact_email + title: sequenced_by_contact_email + description: The email address of the contact responsible for follow-up regarding + the sequence. + comments: Provide the email associated with the listed contact. As personnel turnover + may render an individual's email obsolete, it is more prefereable to provide + an address for a position or lab, to ensure accuracy of information and institutional + memory. If the information is unknown or cannot be provided, leave blank or + provide a null value. + slot_uri: GENEPIO:0100422 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + required: true + examples: + - value: enterics@lab.ca + sequence_submitted_by: + name: sequence_submitted_by + title: sequence_submitted_by + description: The name of the agency that submitted the sequence to a database. + comments: The name of the agency should be written out in full, (with minor exceptions) + and be consistent across multiple submissions. For Canadian institutions submitting + specimens rather than sequencing data, please put the "National Microbiology + Laboratory (NML)". + slot_uri: GENEPIO:0001159 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: Public Health Ontario (PHO) + sequence_submitter_contact_email: + name: sequence_submitter_contact_email + title: sequence_submitter_contact_email + description: The email address of the contact responsible for follow-up regarding + the sequence. + comments: The email address can represent a specific individual or laboratory. + slot_uri: GENEPIO:0001165 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + pattern: ^\S+@\S+\.\S+$ + examples: + - value: RespLab@lab.ca + nucleic_acid_extraction_method: + name: nucleic_acid_extraction_method + title: nucleic_acid_extraction_method + description: The process used to extract genomic material from a sample. + comments: Briefly describe the extraction method used. + slot_uri: GENEPIO:0100939 + range: WhitespaceMinimizedString + examples: + - value: Direct wastewater RNA capture and purification via the "Sewage, Salt, + Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 + nucleic_acid_extraction_kit: + name: nucleic_acid_extraction_kit + title: nucleic_acid_extraction_kit + description: The kit used to extract genomic material from a sample + comments: Provide the name of the genomic extraction kit used. + slot_uri: GENEPIO:0100772 + range: WhitespaceMinimizedString + examples: + - value: QIAamp PowerFecal Pro DNA Kit + endogenous_control_details: + name: endogenous_control_details + title: endogenous control details + description: The description of the endogenous controls included when extracting + a sample. + comments: Provide the names of endogenous controls that were used as a reference + during extraction. If relevant, include titers of these controls, as well as + whether any controls were expected but not identified in the sample. + slot_uri: GENEPIO:0100923 + range: WhitespaceMinimizedString + recommended: true + sequencing_project_name: + name: sequencing_project_name + title: sequencing_project_name + description: The name of the project/initiative/program for which sequencing was + performed. + comments: Provide the name of the project and/or the project ID here. If the information + is unknown or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100472 + range: WhitespaceMinimizedString + examples: + - value: AMR-GRDI (PA-1356) + sequencing_platform: + name: sequencing_platform + title: sequencing_platform + description: The platform technology used to perform the sequencing. + comments: Provide the name of the company that created the sequencing instrument + by selecting a value from the template pick list. If the information is unknown + or cannot be provided, leave blank or provide a null value. + slot_uri: GENEPIO:0100473 + any_of: + - range: sequencing_platform menu + - range: null value menu + examples: + - value: Illumina [GENEPIO:0001923] + sequencing_instrument: + name: sequencing_instrument + title: sequencing_instrument + description: The model of the sequencing instrument used. + comments: Provide the model sequencing instrument by selecting a value from the + template pick list. If the information is unknown or cannot be provided, leave + blank or provide a null value. + slot_uri: GENEPIO:0001452 + any_of: + - range: sequencing_instrument menu + - range: null value menu + examples: + - value: Illumina HiSeq 2500 [GENEPIO:0100117] + library_preparation_kit: + name: library_preparation_kit + title: library_preparation_kit + description: The name of the DNA library preparation kit used to generate the + library being sequenced. + comments: Provide the name of the library preparation kit used. + slot_uri: GENEPIO:0001450 + range: WhitespaceMinimizedString + examples: + - value: Nextera XT + dna_fragment_length: + name: dna_fragment_length + title: DNA_fragment_length + description: The length of the DNA fragment generated by mechanical shearing or + enzymatic digestion for the purposes of library preparation. + comments: Provide the fragment length in base pairs (do not include the units). + slot_uri: GENEPIO:0100843 + range: Integer + examples: + - value: '400' + genomic_target_enrichment_method: + name: genomic_target_enrichment_method + title: genomic_target_enrichment_method + description: The molecular technique used to selectively capture and amplify specific + regions of interest from a genome. + comments: Provide the name of the enrichment method + slot_uri: GENEPIO:0100966 + range: genomic_target_enrichment_method menu + examples: + - value: Hybrid selection method (bait-capture) [GENEPIO:0001950] + genomic_target_enrichment_method_details: + name: genomic_target_enrichment_method_details + title: genomic_target_enrichment_method_details + description: Details that provide additional context to the molecular technique + used to selectively capture and amplify specific regions of interest from a + genome. + comments: 'Provide details that are applicable to the method you used. Note: If + bait-capture methods were used for enrichment, provide the panel name and version + number (or a URL providing that information).' + slot_uri: GENEPIO:0100967 + range: WhitespaceMinimizedString + examples: + - value: 'enrichment was done using Twist''s respiratory virus research panel: + https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel' + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme + title: amplicon_pcr_primer_scheme + description: The specifications of the primers (primer sequences, binding positions, + fragment size generated etc) used to generate the amplicons to be sequenced. + comments: Provide the name and version of the primer scheme used to generate the + amplicons for sequencing. + slot_uri: GENEPIO:0001456 + range: WhitespaceMinimizedString + examples: + - value: artic v3 + amplicon_size: + name: amplicon_size + title: amplicon_size + description: The length of the amplicon generated by PCR amplification. + comments: Provide the amplicon size expressed in base pairs. + slot_uri: GENEPIO:0001449 + range: Integer + examples: + - value: '300' + sequencing_flow_cell_version: + name: sequencing_flow_cell_version + title: sequencing_flow_cell_version + description: The version number of the flow cell used for generating sequence + data. + comments: Flow cells can vary in terms of design, chemistry, capacity, etc. The + version of the flow cell used to generate sequence data can affect sequence + quantity and quality. Record the version of the flow cell used to generate sequence + data. Do not include "version" or "v" in the version number. + slot_uri: GENEPIO:0101102 + range: WhitespaceMinimizedString + examples: + - value: R.9.4.1 + sequencing_protocol: + name: sequencing_protocol + title: sequencing_protocol + description: The protocol or method used for sequencing. + comments: Provide the name and version of the procedure or protocol used for sequencing. + You can also provide a link to a protocol online. + slot_uri: GENEPIO:0001454 + range: WhitespaceMinimizedString + examples: + - value: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no + r1_fastq_filename: + name: r1_fastq_filename + title: r1_fastq_filename + description: The user-specified filename of the r1 FASTQ file. + comments: Provide the r1 FASTQ filename. + slot_uri: GENEPIO:0001476 + range: WhitespaceMinimizedString + examples: + - value: ABC123_S1_L001_R1_001.fastq.gz + r2_fastq_filename: + name: r2_fastq_filename + title: r2_fastq_filename + description: The user-specified filename of the r2 FASTQ file. + comments: Provide the r2 FASTQ filename. + slot_uri: GENEPIO:0001477 + range: WhitespaceMinimizedString + examples: + - value: ABC123_S1_L001_R2_001.fastq.gz + fast5_filename: + name: fast5_filename + title: fast5_filename + description: The user-specified filename of the FAST5 file. + comments: Provide the FAST5 filename. + slot_uri: GENEPIO:0001480 + range: WhitespaceMinimizedString + examples: + - value: batch1a_sequences.fast5 + genome_sequence_file_name: + name: genome_sequence_file_name + title: genome sequence file name + description: The name of the sequence file. + comments: Provide the name and version number, with the file extension, of the + processed genome sequence file e.g. a consensus sequence FASTA file or a genome + assembly file. + slot_uri: GENEPIO:0101715 + range: WhitespaceMinimizedString + examples: + - value: mpxvassembly.fasta + assembly_filename: + name: assembly_filename + title: assembly_filename + description: The user-defined filename of the FASTA file. + comments: Provide the FASTA filename. + slot_uri: GENEPIO:0001461 + range: WhitespaceMinimizedString + examples: + - value: pathogenassembly123.fasta + quality_control_method_name: + name: quality_control_method_name + title: quality control method name + description: The name of the method used to assess whether a sequence passed a + predetermined quality control threshold. + comments: Providing the name of the method used for quality control is very important + for interpreting the rest of the QC information. Method names can be provided + as the name of a pipeline or a link to a GitHub repository. Multiple methods + should be listed and separated by a semi-colon. Do not include QC tags in other + fields if no method name is provided. + slot_uri: GENEPIO:0100557 + range: WhitespaceMinimizedString + examples: + - value: ncov-tools + quality_control_method_version: + name: quality_control_method_version + title: quality control method version + description: The version number of the method used to assess whether a sequence + passed a predetermined quality control threshold. + comments: Methods updates can make big differences to their outputs. Provide the + version of the method used for quality control. The version can be expressed + using whatever convention the developer implements (e.g. date, semantic versioning). + If multiple methods were used, record the version numbers in the same order + as the method names. Separate the version numbers using a semi-colon. + slot_uri: GENEPIO:0100558 + range: WhitespaceMinimizedString + examples: + - value: 1.2.3 + quality_control_determination: + name: quality_control_determination + title: quality control determination + description: The determination of a quality control assessment. + comments: Select a value from the pick list provided. If a desired value is missing, + submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the + New Term Request form. + slot_uri: GENEPIO:0100559 + any_of: + - range: quality_control_determination menu + - range: null value menu + multivalued: true + examples: + - value: sequence failed quality control + quality_control_issues: + name: quality_control_issues + title: quality control issues + description: The reason contributing to, or causing, a low quality determination + in a quality control assessment. + comments: Select a value from the pick list provided. If a desired value is missing, + submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the + New Term Request form. + slot_uri: GENEPIO:0100560 + any_of: + - range: quality_control_issues menu + - range: null value menu + multivalued: true + examples: + - value: low average genome coverage + quality_control_details: + name: quality_control_details + title: quality control details + description: The details surrounding a low quality determination in a quality + control assessment. + comments: Provide notes or details regarding QC results using free text. + slot_uri: GENEPIO:0100561 + range: WhitespaceMinimizedString + examples: + - value: CT value of 39. Low viral load. Low DNA concentration after amplification. + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method + title: raw sequence data processing method + description: The method used for raw data processing such as removing barcodes, + adapter trimming, filtering etc. + comments: Raw data processing can have a significant impact on data quality and + how it can be used. Provide the names and version numbers of software used for + trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop + v. 0.2.3), or a link to a GitHub protocol. + slot_uri: GENEPIO:0001458 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: Porechop 0.2.3 + dehosting_method: + name: dehosting_method + title: dehosting method + description: The method used to remove host reads from the pathogen sequence. + comments: Provide the name and version number of the software used to remove host + reads. + slot_uri: GENEPIO:0001459 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + recommended: true + examples: + - value: Nanostripper + sequence_assembly_software_name: + name: sequence_assembly_software_name + title: sequence assembly software name + description: The name of the software used to assemble a sequence. + comments: Provide the name of the software used to assemble the sequence. + slot_uri: GENEPIO:0100825 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet + sequence_assembly_software_version: + name: sequence_assembly_software_version + title: sequence assembly software version + description: The version of the software used to assemble a sequence. + comments: Provide the version of the software used to assemble the sequence. + slot_uri: GENEPIO:0100826 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: 3.15.5 + consensus_sequence_software_name: + name: consensus_sequence_software_name + title: consensus sequence software name + description: The name of the software used to generate the consensus sequence. + comments: Provide the name of the software used to generate the consensus sequence. + slot_uri: GENEPIO:0001463 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: iVar + consensus_sequence_software_version: + name: consensus_sequence_software_version + title: consensus sequence software version + description: The version of the software used to generate the consensus sequence. + comments: Provide the version of the software used to generate the consensus sequence. + slot_uri: GENEPIO:0001469 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: '1.3' + breadth_of_coverage_value: + name: breadth_of_coverage_value + title: breadth of coverage value + description: The percentage of the reference genome covered by the sequenced data, + to a prescribed depth. + comments: Provide value as a percent. + slot_uri: GENEPIO:0001472 + range: WhitespaceMinimizedString + examples: + - value: '95' + depth_of_coverage_value: + name: depth_of_coverage_value + title: depth of coverage value + description: The average number of reads representing a given nucleotide in the + reconstructed sequence. + comments: Provide value as a fold of coverage. + slot_uri: GENEPIO:0001474 + range: WhitespaceMinimizedString + examples: + - value: '400' + depth_of_coverage_threshold: + name: depth_of_coverage_threshold + title: depth of coverage threshold + description: The threshold used as a cut-off for the depth of coverage. + comments: Provide the threshold fold coverage. + slot_uri: GENEPIO:0001475 + range: WhitespaceMinimizedString + examples: + - value: '100' + genome_completeness: + name: genome_completeness + title: genome completeness + description: The percentage of expected genes identified in the genome being sequenced. + Missing genes indicate missing genomic regions (incompleteness) in the data. + comments: Provide the genome completeness as a percent (no need to include units). + slot_uri: GENEPIO:0100844 + range: WhitespaceMinimizedString + examples: + - value: '85' + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced + title: number of base pairs sequenced + description: The number of total base pairs generated by the sequencing process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001482 + range: integer + examples: + - value: '387566' + number_of_total_reads: + name: number_of_total_reads + title: number of total reads + description: The total number of non-unique reads generated by the sequencing + process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100827 + range: integer + examples: + - value: '423867' + number_of_unique_reads: + name: number_of_unique_reads + title: number of unique reads + description: The number of unique reads generated by the sequencing process. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100828 + range: integer + examples: + - value: '248236' + minimum_posttrimming_read_length: + name: minimum_posttrimming_read_length + title: minimum post-trimming read length + description: The threshold used as a cut-off for the minimum length of a read + after trimming. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100829 + range: integer + examples: + - value: '150' + number_of_contigs: + name: number_of_contigs + title: number of contigs + description: The number of contigs (contiguous sequences) in a sequence assembly. + comments: Provide a numerical value. + slot_uri: GENEPIO:0100937 + range: integer + examples: + - value: '10' + percent_ns_across_total_genome_length: + name: percent_ns_across_total_genome_length + title: percent Ns across total genome length + description: The percentage of the assembly that consists of ambiguous bases (Ns). + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100830 + range: integer + examples: + - value: '2' + ns_per_100_kbp: + name: ns_per_100_kbp + title: Ns per 100 kbp + description: The number of ambiguous bases (Ns) normalized per 100 kilobasepairs + (kbp). + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001484 + range: integer + examples: + - value: '342' + n50: + name: n50 + title: N50 + description: The length of the shortest read that, together with other reads, + represents at least 50% of the nucleotides in a set of sequences. + comments: Provide the N50 value in Mb. + slot_uri: GENEPIO:0100938 + range: integer + examples: + - value: '150' + percent_read_contamination_: + name: percent_read_contamination_ + title: percent read contamination + description: The percent of the total number of reads identified as contamination + (not belonging to the target organism) in a sequence dataset. + comments: Provide the percent contamination value (no need to include units). + slot_uri: GENEPIO:0100845 + range: integer + examples: + - value: '2' + sequence_assembly_length: + name: sequence_assembly_length + title: sequence assembly length + description: The length of the genome generated by assembling reads using a scaffold + or by reference-based mapping. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0100846 + range: integer + examples: + - value: '34272' + consensus_genome_length: + name: consensus_genome_length + title: consensus genome length + description: The length of the genome defined by the most common nucleotides at + each position. + comments: Provide a numerical value (no need to include units). + slot_uri: GENEPIO:0001483 + range: integer + examples: + - value: '38677' + reference_genome_accession: + name: reference_genome_accession + title: reference genome accession + description: A persistent, unique identifier of a genome database entry. + comments: Provide the accession number of the reference genome. + slot_uri: GENEPIO:0001485 + range: WhitespaceMinimizedString + examples: + - value: NC_045512.2 + deduplication_method: + name: deduplication_method + title: deduplication method + description: The method used to remove duplicated reads in a sequence read dataset. + comments: Provide the deduplication software name followed by the version, or + a link to a tool or method. + slot_uri: GENEPIO:0100831 + range: WhitespaceMinimizedString + examples: + - value: DeDup 0.12.8 + bioinformatics_protocol: + name: bioinformatics_protocol + title: bioinformatics protocol + description: A description of the overall bioinformatics strategy used. + comments: Further details regarding the methods used to process raw data, and/or + generate assemblies, and/or generate consensus sequences can. This information + can be provided in an SOP or protocol or pipeline/workflow. Provide the name + and version number of the protocol, or a GitHub link to a pipeline or workflow. + slot_uri: GENEPIO:0001489 + range: WhitespaceMinimizedString + examples: + - value: https://github.com/phac-nml/ncov2019-artic-nf + read_mapping_software_name: + name: read_mapping_software_name + title: read mapping software name + description: The name of the software used to map sequence reads to a reference + genome or set of reference genes. + comments: Provide the name of the read mapping software. + slot_uri: GENEPIO:0100832 + range: WhitespaceMinimizedString + examples: + - value: Bowtie2, BWA-MEM, TopHat + read_mapping_software_version: + name: read_mapping_software_version + title: read mapping software version + description: The version of the software used to map sequence reads to a reference + genome or set of reference genes. + comments: Provide the version number of the read mapping software. + slot_uri: GENEPIO:0100833 + range: WhitespaceMinimizedString + examples: + - value: 2.5.1 + taxonomic_reference_database_name: + name: taxonomic_reference_database_name + title: taxonomic reference database name + description: The name of the taxonomic reference database used to identify the + organism. + comments: Provide the name of the taxonomic reference database. + slot_uri: GENEPIO:0100834 + range: WhitespaceMinimizedString + examples: + - value: NCBITaxon + taxonomic_reference_database_version: + name: taxonomic_reference_database_version + title: taxonomic reference database version + description: The version of the taxonomic reference database used to identify + the organism. + comments: Provide the version number of the taxonomic reference database. + slot_uri: GENEPIO:0100835 + range: WhitespaceMinimizedString + examples: + - value: '1.3' + taxonomic_analysis_report_filename: + name: taxonomic_analysis_report_filename + title: taxonomic analysis report filename + description: The filename of the report containing the results of a taxonomic + analysis. + comments: Provide the filename of the report containing the results of the taxonomic + analysis. + slot_uri: GENEPIO:0101074 + range: WhitespaceMinimizedString + examples: + - value: WWtax_report_Feb1_2024.doc + taxonomic_analysis_date: + name: taxonomic_analysis_date + title: taxonomic analysis date + description: The date a taxonomic analysis was performed. + comments: Providing the date that an analyis was performed can help provide context + for tool and reference database versions. Provide the date that the taxonomic + analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". + slot_uri: GENEPIO:0101075 + range: date + examples: + - value: '2024-02-01' + read_mapping_criteria: + name: read_mapping_criteria + title: read mapping criteria + description: A description of the criteria used to map reads to a reference sequence. + comments: Provide a description of the read mapping criteria. + slot_uri: GENEPIO:0100836 + range: WhitespaceMinimizedString + examples: + - value: Phred score >20 + genetic_target_name: + name: genetic_target_name + title: genetic target name + description: The name of the genetic marker used for testing. + comments: 'Provide the full name of the gene used in the test. Standardized gene + names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' + slot_uri: GENEPIO:0101116 + any_of: + - range: WhitespaceMinimizedString + - range: null value menu + examples: + - value: gyrase A + genetic_target_region: + name: genetic_target_region + title: genetic target region + description: The specific region or segment of a genetic sequence used for testing + or analysis. + slot_uri: GENEPIO:0101117 + range: WhitespaceMinimizedString + genetic_target_region_reference_genome: + name: genetic_target_region_reference_genome + title: genetic target region reference genome + description: The reference genome version used to determine the coordinates or + identity of the genetic target region in testing or analysis. + slot_uri: GENEPIO:0101118 + range: WhitespaceMinimizedString + diagnostic_target_presence: + name: diagnostic_target_presence + title: diagnostic target presence + description: The binary value of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe whether a target + was determined to be present or absent within a sample. + slot_uri: GENEPIO:0100962 + any_of: + - range: diagnostic target presence menu + - range: null value menu + examples: + - value: diagnostic target present + diagnostic_measurement_value: + name: diagnostic_measurement_value + title: diagnostic measurement value + description: The value of the result from a diagnostic test. + comments: Provide the numerical result of a diagnostic test (no need to include + units). + slot_uri: GENEPIO:0100963 + range: WhitespaceMinimizedString + examples: + - value: '1000' + diagnostic_measurement_unit: + name: diagnostic_measurement_unit + title: diagnostic measurement unit + description: The unit of the result from a diagnostic test. + comments: Select a value from the pick list provided, to describe the units of + the given diagnostic test. + slot_uri: GENEPIO:0100964 + any_of: + - range: diagnostic measurement unit menu + - range: null value menu + examples: + - value: cycle threshold (Ct) + diagnostic_measurement_method: + name: diagnostic_measurement_method + title: diagnostic measurement method + description: The method by which a diagnostic result was determined. + comments: Select a value from the pick list provided to describe the method used + for a given diagnostic test. + slot_uri: GENEPIO:0100965 + any_of: + - range: diagnostic measurement method menu + - range: null value menu + examples: + - value: qPCR + diagnostic_testing_threshold_value: + name: diagnostic_testing_threshold_value + title: diagnostic testing threshold value + description: The numerical value which represents the threshold above/below which + interpretation can be drawn on the diagnostic test + slot_uri: GENEPIO:0101104 + range: integer + diagnostic_testing_threshold_units: + name: diagnostic_testing_threshold_units + title: diagnostic testing threshold units + description: The unit which are attributed to the threshold above/below which + interpretation can be drawn on the diagnostic test + slot_uri: GENEPIO:0101105 + range: WhitespaceMinimizedString + diagnostic_testing_details: + name: diagnostic_testing_details + title: diagnostic testing details + description: Describe any details of the diagnsotic testing. + slot_uri: GENEPIO:0101106 + range: WhitespaceMinimizedString + prevalence_metrics: + name: prevalence_metrics + title: prevalence_metrics + description: Metrics regarding the prevalence of the pathogen of interest obtained + from a surveillance project. + comments: Risk assessment requires detailed information regarding the quantities + of a pathogen in a specified location, commodity, or environment. As such, it + is useful for risk assessors to know what types of information are available + through documented methods and results. Provide the metric types that are available + in the surveillance project sample plan by selecting them from the pick list. + The metrics of interest are " Number of total samples collected", "Number of + positive samples", "Average count of hazard organism", "Average count of indicator + organism". You do not need to provide the actual values, just indicate that + the information is available. + slot_uri: GENEPIO:0100480 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Number of total samples collected, Number of positive samples + prevalence_metrics_details: + name: prevalence_metrics_details + title: prevalence_metrics_details + description: The details pertaining to the prevalence metrics from a surveillance + project. + comments: If there are details pertaining to samples or organism counts in the + sample plan that might be informative, provide details using free text. + slot_uri: GENEPIO:0100481 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. + stage_of_production: + name: stage_of_production + title: stage_of_production + description: The stage of food production. + comments: Provide the stage of food production as free text. + slot_uri: GENEPIO:0100482 + any_of: + - range: stage_of_production menu + - range: null value menu + recommended: true + examples: + - value: Abattoir [ENVO:01000925] + experimental_intervention: + name: experimental_intervention + title: experimental_intervention + description: The category of the experimental intervention applied in the food + production system. + comments: In some surveys, a particular intervention in the food supply chain + in studied. If there was an intervention specified in the sample plan, select + the intervention category from the pick list provided. + slot_uri: GENEPIO:0100483 + any_of: + - range: experimental_intervention menu + - range: null value menu + multivalued: true + recommended: true + examples: + - value: Vaccination [NCIT:C15346] + experiment_intervention_details: + name: experiment_intervention_details + title: experiment_intervention_details + description: The details of the experimental intervention applied in the food + production system. + comments: If an experimental intervention was applied in the survey, provide details + in this field as free text. + slot_uri: GENEPIO:0100484 + range: WhitespaceMinimizedString + recommended: true + examples: + - value: 2% cranberry solution mixed in feed +enums: + NullValue: + name: NullValue + title: null value + permissible_values: + Not Applicable [GENEPIO:0001619]: + text: Not Applicable [GENEPIO:0001619] + description: A categorical choice recorded when a datum does not apply to + a given context. + meaning: GENEPIO:0001619 + Missing [GENEPIO:0001618]: + text: Missing [GENEPIO:0001618] + description: A categorical choice recorded when a datum is not included for + an unknown reason. + meaning: GENEPIO:0001618 + Not Collected [GENEPIO:0001620]: + text: Not Collected [GENEPIO:0001620] + description: A categorical choice recorded when a datum was not measured or + collected. + meaning: GENEPIO:0001620 + Not Provided [GENEPIO:0001668]: + text: Not Provided [GENEPIO:0001668] + description: A categorical choice recorded when a datum was collected but + is not currently provided in the information being shared. This value indicates + the information may be shared at the later stage. + meaning: GENEPIO:0001668 + Restricted Access [GENEPIO:0001810]: + text: Restricted Access [GENEPIO:0001810] + description: A categorical choice recorded when a given datum is available + but not shared publicly because of information privacy concerns. + meaning: GENEPIO:0001810 + OrganismMenu: + name: OrganismMenu + title: organism menu + permissible_values: + Influenza A virus [NCBITaxon:11320]: + text: Influenza A virus [NCBITaxon:11320] + meaning: NCBITaxon:11320 + InfluenzaSubtypeMenu: + name: InfluenzaSubtypeMenu + title: influenza_subtype menu + permissible_values: + H5N1 subtype (Influenza A virus) [NCBITaxon:102793]: + text: H5N1 subtype (Influenza A virus) [NCBITaxon:102793] + meaning: NCBITaxon:102793 + InfluenzaSubtypingSchemeNameMenu: + name: InfluenzaSubtypingSchemeNameMenu + title: influenza_subtyping_scheme_name menu + permissible_values: + Tripartite Influenza A scheme [GENEPIO:0101121]: + text: Tripartite Influenza A scheme [GENEPIO:0101121] + meaning: GENEPIO:0101121 + USDA GenoFLU scheme [GENEPIO:0101122]: + text: USDA GenoFLU scheme [GENEPIO:0101122] + meaning: GENEPIO:0101122 + TaxonomicIdentificationProcessMenu: + name: TaxonomicIdentificationProcessMenu + title: taxonomic_identification_process menu + permissible_values: + Whole genome sequencing assay [OBI:0002117]: + text: Whole genome sequencing assay [OBI:0002117] + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. + meaning: OBI:0002117 + Whole metagenome sequencing assay [OBI:0002623]: + text: Whole metagenome sequencing assay [OBI:0002623] + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. + meaning: OBI:0002623 + 16S ribosomal gene sequencing assay [OBI:0002763]: + text: 16S ribosomal gene sequencing assay [OBI:0002763] + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting + sequences are compared to reference 16S sequence databases to identify or + classify bacteria present within a given sample. + meaning: OBI:0002763 + PCR assay [OBI:0002740]: + text: PCR assay [OBI:0002740] + description: An organism identification assay that is based on PCR. + meaning: OBI:0002740 + Comparative phenotypic assessment [OBI:0001546]: + text: Comparative phenotypic assessment [OBI:0001546] + description: Interpreting data from assays that evaluate the qualities or + dispositions inhering in an organism or organism part and comparing it to + data from other organisms to make a conclusion about a phenotypic difference + meaning: OBI:0001546 + SampleCollectionTimeOfDayMenu: + name: SampleCollectionTimeOfDayMenu + title: sample_collection_time_of_day menu + permissible_values: + Morning [NCIT:C64934]: + text: Morning [NCIT:C64934] + description: The time period between dawn and noon. + meaning: NCIT:C64934 + Afternoon [NCIT:C64935]: + text: Afternoon [NCIT:C64935] + description: The time period between noon and sunset. + meaning: NCIT:C64935 + Evening [NCIT:C64936]: + text: Evening [NCIT:C64936] + description: The time period between late afternoon and bedtime. + meaning: NCIT:C64936 + Night [NCIT:C65001]: + text: Night [NCIT:C65001] + description: The time in every 24 hour period when it is dark. + meaning: NCIT:C65001 + SampleCollectionDurationUnitMenu: + name: SampleCollectionDurationUnitMenu + title: sample_collection_duration_unit menu + permissible_values: + Second [UO:0000010]: + text: Second [UO:0000010] + description: A time unit which is equal to the duration of 9 192 631 770 periods + of the radiation corresponding to the transition between the two hyperfine + levels of the ground state of the caesium 133 atom. + meaning: UO:0000010 + Minute [UO:0000031]: + text: Minute [UO:0000031] + description: A time unit which is equal to 60 seconds. + meaning: UO:0000031 + Hour [UO:0000032]: + text: Hour [UO:0000032] + description: A time unit which is equal to 60 minutes. + meaning: UO:0000032 + Day [UO:0000033]: + text: Day [UO:0000033] + description: A time unit which is equal to 24 hours. + meaning: UO:0000033 + Week [UO:0000034]: + text: Week [UO:0000034] + description: A time unit which is equal to 7 days. + meaning: UO:0000034 + Month [UO:0000035]: + text: Month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. + meaning: UO:0000035 + Year [UO:0000036]: + text: Year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. + meaning: UO:0000036 + FoodProductMenu: + name: FoodProductMenu + title: food_product menu + permissible_values: + Animal feed [ENVO:02000047]: + text: Animal feed [ENVO:02000047] + description: Food material which can be used to meet nutritional requirements + of animals, particularly livestock such as cattle, goats, sheep, horses, + chickens and pigs. + meaning: ENVO:02000047 + Blood meal [FOODON:00001564]: + text: Blood meal [FOODON:00001564] + description: Blood meal is a dry, inert powder made from blood used as a high-nitrogen + organic fertilizer and a high protein animal feed. + meaning: FOODON:00001564 + is_a: Animal feed [ENVO:02000047] + Bone meal [ENVO:02000054]: + text: Bone meal [ENVO:02000054] + description: A mixture of crushed and coarsely ground bones that is used as + an organic fertilizer for plants and formerly in animal feed. + meaning: ENVO:02000054 + is_a: Animal feed [ENVO:02000047] + Brassica carinata meal [FOODON:00004310]: + text: Brassica carinata meal [FOODON:00004310] + description: A meal that is a co-product produced after the extraction of + oil from the seed of the Ethiopian mustard plant (Brassica carinata). + meaning: FOODON:00004310 + is_a: Animal feed [ENVO:02000047] + Canola meal [FOODON:00002694]: + text: Canola meal [FOODON:00002694] + description: Canola meal is an oilseed meal made from canola grain. Canola + meal is a by-product of the oil crushing process. + meaning: FOODON:00002694 + is_a: Animal feed [ENVO:02000047] + Compound feed premix [FOODON:00004323]: + text: Compound feed premix [FOODON:00004323] + description: A formula mixture of micronutrients that is used as a component + in compound feed. + meaning: FOODON:00004323 + is_a: Animal feed [ENVO:02000047] + Compound feed premix (medicated) [FOODON:00004324]: + text: Compound feed premix (medicated) [FOODON:00004324] + description: A compound feed premix in which medicinal substance has been + added. + meaning: FOODON:00004324 + is_a: Compound feed premix [FOODON:00004323] + Feather meal [FOODON:00003927]: + text: Feather meal [FOODON:00003927] + description: A by product of processing poultry which is made from poultry + feathers by partially grinding them under elevated heat and pressure, and + then grinding and drying. + meaning: FOODON:00003927 + is_a: Animal feed [ENVO:02000047] + Fish meal [FOODON:03301620]: + text: Fish meal [FOODON:03301620] + description: Fish meal is primarily used as a protein supplement in compound + feed. As of 2010, about 56% of fish meal was used to feed farmed fish, about + 20% was used in pig feed, about 12% in poultry feed, and about 12% in other + uses, which included fertilizer. + meaning: FOODON:03301620 + is_a: Animal feed [ENVO:02000047] + Lay ration [FOODON:00004286]: + text: Lay ration [FOODON:00004286] + description: Food formulated for the laying hens to increase egg production + and egg shell quality. + meaning: FOODON:00004286 + is_a: Animal feed [ENVO:02000047] + Meat and bone meal [FOODON:00002738]: + text: Meat and bone meal [FOODON:00002738] + description: "Meat and bone meal (MBM) is a product of the rendering industry.\ + \ It is typically about 48\u201352% protein, 33\u201335% ash, 8\u201312%\ + \ fat, and 4\u20137% water. It is primarily used in the formulation of animal\ + \ feed to improve the amino acid profile of the feed." + meaning: FOODON:00002738 + is_a: Animal feed [ENVO:02000047] + Meat meal [FOODON:00004282]: + text: Meat meal [FOODON:00004282] + description: A meal that is obtained by cooking, defatting, sterilizing, grinding, + and sifting by-products of an animal. + meaning: FOODON:00004282 + is_a: Animal feed [ENVO:02000047] + Pet food [FOODON:00002682]: + text: Pet food [FOODON:00002682] + description: Pet food is plant or animal material intended for consumption + by pets. + meaning: FOODON:00002682 + is_a: Animal feed [ENVO:02000047] + Soybean meal [FOODON:03302757]: + text: Soybean meal [FOODON:03302757] + description: A type of ground protein-rich residue from the production of + soybean oil used chiefly in animal feeds, in adhesives and plastics, in + making synthetic protein fibers, and in fermentation media (as for the production + of antibiotics). + meaning: FOODON:03302757 + is_a: Animal feed [ENVO:02000047] + Animal feed ingredient [FOODON:00004322]: + text: Animal feed ingredient [FOODON:00004322] + description: An ingredient that is used in the preparation of animal feed. + meaning: FOODON:00004322 + Dairy food product [FOODON:00001256]: + text: Dairy food product [FOODON:00001256] + description: A dairy food product has mammilian milk or a milk component as + an ingredient. + meaning: FOODON:00001256 + Cheese block (whole or parts) [FOODON:03000287]: + text: Cheese block (whole or parts) [FOODON:03000287] + description: A whole cheese block or some substance made from a block of processed + cheese. + meaning: FOODON:03000287 + is_a: Dairy food product [FOODON:00001256] + Cow skim milk (powdered) [FOODON:03310016]: + text: Cow skim milk (powdered) [FOODON:03310016] + description: Milk powder that is obtained by removing all of the water from + pasteurized skim milk. + meaning: FOODON:03310016 + is_a: Dairy food product [FOODON:00001256] + Milk [UBERON:0001913]: + text: Milk [UBERON:0001913] + description: An emulsion of fat globules within a fluid that is secreted by + the mammary gland during lactation. + meaning: UBERON:0001913 + is_a: Dairy food product [FOODON:00001256] + Meat, poultry and fish (organizational term): + text: Meat, poultry and fish (organizational term) + Beef (ground or minced) [FOODON:00001282]: + text: Beef (ground or minced) [FOODON:00001282] + description: A ground beef product is made of beef that has been finely chopped + with a knife or a meat grinder (American English) or mincing machine (British + English). Ground beef is used in many recipes including hamburgers and spaghetti + Bolognese. + meaning: FOODON:00001282 + is_a: Meat, poultry and fish (organizational term) + Beef (ground or minced, boneless) [FOODON:03000412]: + text: Beef (ground or minced, boneless) [FOODON:03000412] + meaning: FOODON:03000412 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, extra lean) [FOODON:03000398]: + text: Beef (ground or minced, extra lean) [FOODON:03000398] + meaning: FOODON:03000398 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, lean) [FOODON:03000394]: + text: Beef (ground or minced, lean) [FOODON:03000394] + meaning: FOODON:03000394 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, medium) [FOODON:03000402]: + text: Beef (ground or minced, medium) [FOODON:03000402] + meaning: FOODON:03000402 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, regular) [FOODON:03000406]: + text: Beef (ground or minced, regular) [FOODON:03000406] + meaning: FOODON:03000406 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, sirloin) [FOODON:03000408]: + text: Beef (ground or minced, sirloin) [FOODON:03000408] + meaning: FOODON:03000408 + is_a: Beef (ground or minced) [FOODON:00001282] + Beef hamburger (dish) [FOODON:00002737]: + text: Beef hamburger (dish) [FOODON:00002737] + description: 'A hamburger (short: burger) is a sandwich consisting of one + or more cooked patties of ground meat, usually beef, placed inside a sliced + bread roll or bun. The patty may be pan fried, grilled, or flame broiled.' + meaning: FOODON:00002737 + is_a: Meat, poultry and fish (organizational term) + Beef shoulder [FOODON:03000377]: + text: Beef shoulder [FOODON:03000377] + meaning: FOODON:03000377 + is_a: Meat, poultry and fish (organizational term) + Beef shoulder chop [FOODON:03000387]: + text: Beef shoulder chop [FOODON:03000387] + description: Meat chop from the shoulder region of beef. + meaning: FOODON:03000387 + is_a: Beef shoulder [FOODON:03000377] + Beef sirloin chop [FOODON:03000389]: + text: Beef sirloin chop [FOODON:03000389] + description: Meat chop from the sirloin region of beef + meaning: FOODON:03000389 + is_a: Meat, poultry and fish (organizational term) + Beef stew chunk [FOODON:00004288]: + text: Beef stew chunk [FOODON:00004288] + description: A chunk of beef used as an ingredient in making stew. + meaning: FOODON:00004288 + is_a: Meat, poultry and fish (organizational term) + Beef tenderloin [FOODON:00003302]: + text: Beef tenderloin [FOODON:00003302] + description: A cut of beef corresponding to the psoas major muscle, which + is very tender. + meaning: FOODON:00003302 + is_a: Meat, poultry and fish (organizational term) + Beef (whole cut or parts) [FOODON:03000333]: + text: Beef (whole cut or parts) [FOODON:03000333] + meaning: FOODON:03000333 + is_a: Meat, poultry and fish (organizational term) + Brisket [FOODON:03530020]: + text: Brisket [FOODON:03530020] + description: A cut of meat from the breast or lower chest of beef or veal. + meaning: FOODON:03530020 + is_a: Meat, poultry and fish (organizational term) + Chicken breast [FOODON:00002703]: + text: Chicken breast [FOODON:00002703] + description: Chicken breast consists mainly of the breast meat portion of + a chicken, and may or may not include connected bone (boneless versus "with + bone") and skin. + meaning: FOODON:00002703 + is_a: Meat, poultry and fish (organizational term) + Chicken breast (back off) [FOODON:03000385]: + text: Chicken breast (back off) [FOODON:03000385] + description: A chicken breast with its backbone removed. + meaning: FOODON:03000385 + is_a: Chicken breast [FOODON:00002703] + Chicken breast (skinless) [FOODON:00003332]: + text: Chicken breast (skinless) [FOODON:00003332] + meaning: FOODON:00003332 + is_a: Chicken breast [FOODON:00002703] + Chicken breast (with skin) [FOODON:03000374]: + text: Chicken breast (with skin) [FOODON:03000374] + meaning: FOODON:03000374 + is_a: Chicken breast [FOODON:00002703] + Chicken breast (skinless, boneless) [FOODON:00003364]: + text: Chicken breast (skinless, boneless) [FOODON:00003364] + meaning: FOODON:00003364 + is_a: Chicken breast [FOODON:00002703] + Chicken breast cutlet [FOODON:00004308]: + text: Chicken breast cutlet [FOODON:00004308] + description: A cutlet made from chicken breast. + meaning: FOODON:00004308 + is_a: Chicken breast [FOODON:00002703] + Chicken drumstick [FOODON:00002716]: + text: Chicken drumstick [FOODON:00002716] + description: The segment of a chicken's leg between the thigh and tarsus (ankle). + meaning: FOODON:00002716 + is_a: Meat, poultry and fish (organizational term) + Chicken drumstick (skinless) [FOODON:03000366]: + text: Chicken drumstick (skinless) [FOODON:03000366] + meaning: FOODON:03000366 + is_a: Chicken drumstick [FOODON:00002716] + Chicken drumstick (with skin) [FOODON:03000368]: + text: Chicken drumstick (with skin) [FOODON:03000368] + meaning: FOODON:03000368 + is_a: Chicken drumstick [FOODON:00002716] + Chicken meat [FOODON:00001040]: + text: Chicken meat [FOODON:00001040] + meaning: FOODON:00001040 + is_a: Meat, poultry and fish (organizational term) + Chicken meat (ground or minced) [FOODON:03311826]: + text: Chicken meat (ground or minced) [FOODON:03311826] + description: A food product made of ground or minced chicken meat. + meaning: FOODON:03311826 + is_a: Chicken meat [FOODON:00001040] + Chicken meat (ground or minced, lean) [FOODON:03000392]: + text: Chicken meat (ground or minced, lean) [FOODON:03000392] + description: A food product made of lean, ground or minced chicken meat. + meaning: FOODON:03000392 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, extra lean) [FOODON:03000396]: + text: Chicken meat (ground or minced, extra lean) [FOODON:03000396] + description: A food product made of extra lean, ground or minced chicken meat. + meaning: FOODON:03000396 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, medium) [FOODON:03000400]: + text: Chicken meat (ground or minced, medium) [FOODON:03000400] + description: A food product made of medium, ground or minced chicken meat. + meaning: FOODON:03000400 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, regular) [FOODON:03000404]: + text: Chicken meat (ground or minced, regular) [FOODON:03000404] + description: A food product made of regular, ground or minced chicken meat. + meaning: FOODON:03000404 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken meat (ground or minced, boneless) [FOODON:03000410]: + text: Chicken meat (ground or minced, boneless) [FOODON:03000410] + meaning: FOODON:03000410 + is_a: Chicken meat (ground or minced) [FOODON:03311826] + Chicken nugget [FOODON:00002672]: + text: Chicken nugget [FOODON:00002672] + description: A chicken nugget is a chicken product made from chicken meat + that is breaded or battered, then deep-fried or baked. + meaning: FOODON:00002672 + is_a: Meat, poultry and fish (organizational term) + Chicken thigh [FOODON:02020219]: + text: Chicken thigh [FOODON:02020219] + description: A whole thigh that derives from a chicken. + meaning: FOODON:02020219 + is_a: Meat, poultry and fish (organizational term) + Chicken thigh (skinless) [FOODON:00003331]: + text: Chicken thigh (skinless) [FOODON:00003331] + description: A chicken thigh after the skin has been removed. + meaning: FOODON:00003331 + is_a: Chicken thigh [FOODON:02020219] + Chicken thigh (skinless, with bone) [FOODON:02020227]: + text: Chicken thigh (skinless, with bone) [FOODON:02020227] + description: A chicken thigh that is skinless and contains bone element. + meaning: FOODON:02020227 + is_a: Chicken thigh [FOODON:02020219] + Chicken thigh (skinless, boneless) [FOODON:03000417]: + text: Chicken thigh (skinless, boneless) [FOODON:03000417] + meaning: FOODON:03000417 + is_a: Chicken thigh [FOODON:02020219] + Chicken upper thigh [FOODON:03000381]: + text: Chicken upper thigh [FOODON:03000381] + description: Meat from the upper thigh of a chicken. + meaning: FOODON:03000381 + is_a: Chicken thigh (skinless, boneless) [FOODON:03000417] + Chicken thigh (with skin) [FOODON:00003330]: + text: Chicken thigh (with skin) [FOODON:00003330] + meaning: FOODON:00003330 + is_a: Chicken thigh [FOODON:02020219] + Chicken thigh (with skin, with bone) [FOODON_00003363]: + text: Chicken thigh (with skin, with bone) [FOODON_00003363] + description: A chicken thigh that contains skin and bone material. + meaning: FOODON:00003363 + is_a: Chicken thigh [FOODON:02020219] + Chicken wing [FOODON:00002674]: + text: Chicken wing [FOODON:00002674] + description: A whole wing that derives from a chicken. + meaning: FOODON:00002674 + is_a: Meat, poultry and fish (organizational term) + Fish food product [FOODON:00001248]: + text: Fish food product [FOODON:00001248] + description: A fish food product includes products made from any fish species + (aquatic vertebrate with gills and fins). + meaning: FOODON:00001248 + is_a: Meat, poultry and fish (organizational term) + Fish steak [FOODON:00002986]: + text: Fish steak [FOODON:00002986] + description: A fish steak, alternatively known as a fish cutlet, is a cut + of fish which is cut perpendicular to the spine and can either include the + bones or be boneless. + meaning: FOODON:00002986 + is_a: Fish food product [FOODON:00001248] + Ham food product [FOODON:00002502]: + text: Ham food product [FOODON:00002502] + description: Ham is pork from a leg cut that has been preserved by wet or + dry curing, with or without smoking. As a processed meat, the term "ham" + includes both whole cuts of meat and ones that have been mechanically formed. + meaning: FOODON:00002502 + is_a: Meat, poultry and fish (organizational term) + Head cheese [FOODON:03315658]: + text: Head cheese [FOODON:03315658] + description: Head cheese is a cold cut that originated in Europe. Head cheese + is not a dairy cheese, but a terrine or meat jelly made with flesh from + the head of a calf or pig, or less commonly a sheep or cow, and often set + in aspic. A version pickled with vinegar is known as souse. + meaning: FOODON:03315658 + is_a: Meat, poultry and fish (organizational term) + Lamb [FOODON:03411669]: + text: Lamb [FOODON:03411669] + description: A whole lamb or some material processed from a lamb. + meaning: FOODON:03411669 + is_a: Meat, poultry and fish (organizational term) + Meat strip [FOODON:00004285]: + text: Meat strip [FOODON:00004285] + description: A cut of meat which is long, narrow and boneless. + meaning: FOODON:00004285 + is_a: Meat, poultry and fish (organizational term) + Mutton [FOODON:00002912]: + text: Mutton [FOODON:00002912] + description: The meat of an adult sheep is mutton, a term only used for the + meat, not the living animals. + meaning: FOODON:00002912 + is_a: Meat, poultry and fish (organizational term) + Pork chop [FOODON:00001049]: + text: Pork chop [FOODON:00001049] + description: A cut of meat (a meat chop) cut perpendicularly to the spine + of the pig and usually containing a rib or part of a vertebra, served as + an individual portion. + meaning: FOODON:00001049 + is_a: Meat, poultry and fish (organizational term) + Pork meat (ground or minced) [FOODON:03309969]: + text: Pork meat (ground or minced) [FOODON:03309969] + description: Meat from a pig that has been ground or minced. + meaning: FOODON:03309969 + is_a: Meat, poultry and fish (organizational term) + Pork meat (ground or minced, boneless) [FOODON:03000413]: + text: Pork meat (ground or minced, boneless) [FOODON:03000413] + meaning: FOODON:03000413 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, extra lean) [FOODON:03000399]: + text: Pork meat (ground or minced, extra lean) [FOODON:03000399] + description: A food product made of extra-lean, ground or minced pork meat. + meaning: FOODON:03000399 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, lean) [FOODON:03000395]: + text: Pork meat (ground or minced, lean) [FOODON:03000395] + description: A food product made of lean, ground or minced pork meat. + meaning: FOODON:03000395 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, medium) [FOODON:03000403]: + text: Pork meat (ground or minced, medium) [FOODON:03000403] + description: A food product made of medium, ground or minced pork meat. + meaning: FOODON:03000403 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, regular) [FOODON:03000407]: + text: Pork meat (ground or minced, regular) [FOODON:03000407] + description: A food product made of regular, ground or minced pork meat. + meaning: FOODON:03000407 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork meat (ground or minced, Sirloin) [FOODON:03000409]: + text: Pork meat (ground or minced, Sirloin) [FOODON:03000409] + description: Ground or minced pork meat that comes from the sirloin region. + meaning: FOODON:03000409 + is_a: Pork meat (ground or minced) [FOODON:03309969] + Pork shoulder [FOODON:03000376]: + text: Pork shoulder [FOODON:03000376] + meaning: FOODON:03000376 + is_a: Meat, poultry and fish (organizational term) + Pork shoulder chop [FOODON:03000388]: + text: Pork shoulder chop [FOODON:03000388] + description: Meat chop from the blade roast of pork. + meaning: FOODON:03000388 + is_a: Pork shoulder [FOODON:03000376] + Pork sirloin chop [FOODON:03000390]: + text: Pork sirloin chop [FOODON:03000390] + meaning: FOODON:03000390 + is_a: Meat, poultry and fish (organizational term) + Pork steak [FOODON:00003148]: + text: Pork steak [FOODON:00003148] + meaning: FOODON:00003148 + is_a: Meat, poultry and fish (organizational term) + Pork tenderloin [FOODON:03000416]: + text: Pork tenderloin [FOODON:03000416] + meaning: FOODON:03000416 + is_a: Meat, poultry and fish (organizational term) + Poultry meat [FOODON:03315883]: + text: Poultry meat [FOODON:03315883] + description: Any meat from one or more poultry birds. + meaning: FOODON:03315883 + is_a: Meat, poultry and fish (organizational term) + Leg (poultry meat cut) [FOODON:03530159]: + text: Leg (poultry meat cut) [FOODON:03530159] + description: The leg cut of a poultry bird. + meaning: FOODON:03530159 + is_a: Poultry meat [FOODON:03315883] + Poultry drumstick [FOODON:00003469]: + text: Poultry drumstick [FOODON:00003469] + description: The calf part of a poultry hindleg (hindlimb zeugopod) + meaning: FOODON:00003469 + is_a: Leg (poultry meat cut) [FOODON:03530159] + Neck (poultry meat cut) [FOODON:03530294]: + text: Neck (poultry meat cut) [FOODON:03530294] + description: The neck cut of a poultry bird. + meaning: FOODON:03530294 + is_a: Poultry meat [FOODON:03315883] + Thigh (poultry meat cut) [FOODON:03530160]: + text: Thigh (poultry meat cut) [FOODON:03530160] + description: The thigh cut of a poultry bird. + meaning: FOODON:03530160 + is_a: Poultry meat [FOODON:03315883] + Wing (poultry meat cut) [FOODON:03530157]: + text: Wing (poultry meat cut) [FOODON:03530157] + description: The wing cut of a poultry bird. + meaning: FOODON:03530157 + is_a: Poultry meat [FOODON:03315883] + Sausage (whole) [FOODON:03315904]: + text: Sausage (whole) [FOODON:03315904] + description: A food product that is highly seasoned minced meat and is encased + in a skin in the shape of a cylinder. + meaning: FOODON:03315904 + is_a: Meat, poultry and fish (organizational term) + Pepperoni [FOODON:03311003]: + text: Pepperoni [FOODON:03311003] + description: A highly seasoned and spicy beef or pork sausage. + meaning: FOODON:03311003 + is_a: Sausage (whole) [FOODON:03315904] + Salami [FOODON:03312067]: + text: Salami [FOODON:03312067] + description: A cured sausage which consists of fermented and air-dried meat, + typically pork. + meaning: FOODON:03312067 + is_a: Sausage (whole) [FOODON:03315904] + Shellfish [FOODON:03411433]: + text: Shellfish [FOODON:03411433] + description: The term shellfish is used both broadly and specifically. For + regulatory purposes it is often narrowly defined as filter-feeding molluscs + such as clams, mussels, and oyster to the exclusion of crustaceans and all + else. Although their shells may differ, all shellfish are invertebrates. + meaning: FOODON:03411433 + is_a: Meat, poultry and fish (organizational term) + Shrimp [FOODON:03301673]: + text: Shrimp [FOODON:03301673] + description: A whole shrimp or some material processed from a shrimp. + meaning: FOODON:03301673 + is_a: Shellfish [FOODON:03411433] + Scallop [FOODON:03411489]: + text: Scallop [FOODON:03411489] + meaning: FOODON:03411489 + is_a: Shellfish [FOODON:03411433] + Turkey breast [FOODON:00002690]: + text: Turkey breast [FOODON:00002690] + description: Turkey breast consists mainly of the breast meat portion of a + turkey, and may or may not include connected bone ("deboned or boneless + versus bone-in") and skin. + meaning: FOODON:00002690 + is_a: Meat, poultry and fish (organizational term) + Turkey breast (back off) [FOODON:03000386]: + text: Turkey breast (back off) [FOODON:03000386] + description: A turkey breast with its backbone removed. + meaning: FOODON:03000386 + is_a: Turkey breast [FOODON:00002690] + Turkey breast (skinless) [FOODON:03000372]: + text: Turkey breast (skinless) [FOODON:03000372] + meaning: FOODON:03000372 + is_a: Turkey breast [FOODON:00002690] + Turkey breast (skinless, boneless) [FOODON:03000373]: + text: Turkey breast (skinless, boneless) [FOODON:03000373] + meaning: FOODON:03000373 + is_a: Turkey breast [FOODON:00002690] + Turkey breast (with skin) [FOODON:03000375]: + text: Turkey breast (with skin) [FOODON:03000375] + meaning: FOODON:03000375 + is_a: Turkey breast [FOODON:00002690] + Turkey drumstick [FOODON:03000365]: + text: Turkey drumstick [FOODON:03000365] + meaning: FOODON:03000365 + is_a: Meat, poultry and fish (organizational term) + Turkey drumstick (skinless) [FOODON:03000367]: + text: Turkey drumstick (skinless) [FOODON:03000367] + meaning: FOODON:03000367 + is_a: Turkey drumstick [FOODON:03000365] + Turkey drumstick (with skin) [FOODON:03000369]: + text: Turkey drumstick (with skin) [FOODON:03000369] + meaning: FOODON:03000369 + is_a: Turkey drumstick [FOODON:03000365] + Turkey meat [FOODON:00001286]: + text: Turkey meat [FOODON:00001286] + description: A turkey meat food product is any food product made predominantly + of turkey parts. + meaning: FOODON:00001286 + is_a: Meat, poultry and fish (organizational term) + Turkey meat (ground or minced) [FOODON:00002714]: + text: Turkey meat (ground or minced) [FOODON:00002714] + description: A food product made of ground or minced turkey meat. + meaning: FOODON:00002714 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, lean) [FOODON:03000393]: + text: Turkey meat (ground or minced, lean) [FOODON:03000393] + description: A food product made of lean, ground or minced turkey meat. + meaning: FOODON:03000393 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, extra lean) [FOODON:03000397]: + text: Turkey meat (ground or minced, extra lean) [FOODON:03000397] + description: A food product made of extra-lean, ground or minced turkey meat. + meaning: FOODON:03000397 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, medium) [FOODON:03000401]: + text: Turkey meat (ground or minced, medium) [FOODON:03000401] + description: A food product made of medium, ground or minced turkey meat. + meaning: FOODON:03000401 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, regular) [FOODON:03000405]: + text: Turkey meat (ground or minced, regular) [FOODON:03000405] + description: A food product made of regular, ground or minced turkey meat. + meaning: FOODON:03000405 + is_a: Turkey meat [FOODON:00001286] + Turkey meat (ground or minced, boneless) [FOODON:03000411]: + text: Turkey meat (ground or minced, boneless) [FOODON:03000411] + meaning: FOODON:03000411 + is_a: Turkey meat [FOODON:00001286] + Turkey thigh [FOODON:00003325]: + text: Turkey thigh [FOODON:00003325] + description: A thigh poultry cut of turkey. + meaning: FOODON:00003325 + is_a: Meat, poultry and fish (organizational term) + Turkey thigh (skinless) [FOODON:00003329]: + text: Turkey thigh (skinless) [FOODON:00003329] + description: A turkey thigh after the skin has been removed. + meaning: FOODON:00003329 + is_a: Turkey thigh [FOODON:00003325] + Turkey thigh (skinless, boneless) [FOODON:03000370]: + text: Turkey thigh (skinless, boneless) [FOODON:03000370] + meaning: FOODON:03000370 + is_a: Turkey thigh [FOODON:00003325] + Turkey thigh (with skin) [FOODON:00003328]: + text: Turkey thigh (with skin) [FOODON:00003328] + description: A turkey thigh that still contains the skin. + meaning: FOODON:00003328 + is_a: Turkey thigh [FOODON:00003325] + Turkey upper thigh [FOODON:03000382]: + text: Turkey upper thigh [FOODON:03000382] + description: Meat from the upper thigh of a turkey. + meaning: FOODON:03000382 + is_a: Turkey thigh (with skin) [FOODON:00003328] + Turkey upper thigh (with skin) [FOODON:03000384]: + text: Turkey upper thigh (with skin) [FOODON:03000384] + description: Turkey's upper thigh that contains the skin. + meaning: FOODON:03000384 + is_a: Turkey thigh (with skin) [FOODON:00003328] + Turkey wing [FOODON:03000371]: + text: Turkey wing [FOODON:03000371] + meaning: FOODON:03000371 + is_a: Meat, poultry and fish (organizational term) + Veal [FOODON:00003083]: + text: Veal [FOODON:00003083] + description: Veal is the meat of calves, in contrast to the beef from older + cattle. Veal can be produced from a calf of either sex and any breed; however, + most veal comes from young males of dairy breeds which are not used for + breeding. + meaning: FOODON:00003083 + is_a: Meat, poultry and fish (organizational term) + Formula fed veal [FOODON:000039111]: + text: Formula fed veal [FOODON:000039111] + meaning: OODON:000039111 + is_a: Veal [FOODON:00003083] + Grain-fed veal [FOODON:00004280]: + text: Grain-fed veal [FOODON:00004280] + description: Meat from a calf that is raised on grain, hay, or other solid + food, in addition to milk + meaning: FOODON:00004280 + is_a: Veal [FOODON:00003083] + FoodProductPropertiesMenu: + name: FoodProductPropertiesMenu + title: food_product_properties menu + permissible_values: + Organic food claim or use [FOODON:03510128]: + text: Organic food claim or use [FOODON:03510128] + description: 'USA: The 1990 Farm Act specifies that a food labeled ''organic'' + must meet four requirements: 1) the food must be raised by specified methods + to replenish and maintain the fertility of the soil; 2) the food must be + certified as having been produced with a nationally approved list of materials + and practices; 3) to be eligible for certification at least three years + must have elapsed between the first organic harvest and first use of nationally + approved materials on land and crops;and 4) organic foods must meet all + local, state and federal regulations governing the quality and safety of + the food supply. Europe: Foods produced in accordance with Council Regulation + (EC) No 834/2007 of 28 June 2007 on organic production and labelling of + organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF]' + meaning: FOODON:03510128 + Food (raw) [FOODON:03311126]: + text: Food (raw) [FOODON:03311126] + description: A food material that has not been cooked. + meaning: FOODON:03311126 + Food (heat treated) [FOODON:03316043]: + text: Food (heat treated) [FOODON:03316043] + meaning: FOODON:03316043 + Food (pasteurized) [FOODON:00002654]: + text: Food (pasteurized) [FOODON:00002654] + meaning: FOODON:00002654 + Dairy product (no fat removed, whole): + text: Dairy product (no fat removed, whole) + Dairy product (skimmed, non-fat): + text: Dairy product (skimmed, non-fat) + Dairy product (semi-skimmed, reduced fat, 1%): + text: Dairy product (semi-skimmed, reduced fat, 1%) + Dairy product (semi-skimmed, reduced fat, 2%): + text: Dairy product (semi-skimmed, reduced fat, 2%) + FoodPackagingMenu: + name: FoodPackagingMenu + title: food_packaging menu + permissible_values: + Bottle [FOODON:03490214: + text: Bottle [FOODON:03490214 + description: A rigid or semirigid container typically of glass or plastic + having a comparatively narrow neck or mouth and usually no handle. + meaning: FOODON:03490214 + Bag [FOODON:03490197]: + text: Bag [FOODON:03490197] + description: According to FSTA Thesaurus Packaging 3.1 package types, includes + boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, + valve bag, and valve sack + meaning: FOODON:03490197 + Carton [FOODON:03490213]: + text: Carton [FOODON:03490213] + meaning: FOODON:03490213 + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental_site menu + permissible_values: + Abattoir [ENVO:01000925]: + text: Abattoir [ENVO:01000925] + description: A facility in which non-human animals are slaughtered and processed + for human consumption. + meaning: ENVO:01000925 + Agricultural Field [ENVO:00000114]: + text: Agricultural Field [ENVO:00000114] + description: A field which is located on land and used for agricultural purposes, + such as the grazing of livestock or the cultivation of crops. + meaning: ENVO:00000114 + Animal cage [ENVO:01000922]: + text: Animal cage [ENVO:01000922] + description: A manufactured cage which may be used to confine, contain, or + protect an animal. + meaning: ENVO:01000922 + Artificial wetland [ENVO:03501406]: + text: Artificial wetland [ENVO:03501406] + description: A wetland ecosystem which is constructed to treat municipal or + industrial wastewater, greywater or stormwater runoff. + meaning: ENVO:03501406 + Breeding ground [ENVO:03501441]: + text: Breeding ground [ENVO:03501441] + description: A place where animals breed. + meaning: ENVO:03501441 + Building [ENVO:00000073]: + text: Building [ENVO:00000073] + description: A permanent walled and roofed construction. + meaning: ENVO:00000073 + Barn [ENVO:03501257]: + text: Barn [ENVO:03501257] + description: A farm building used for housing livestock, storing machinery + or crops etc + meaning: ENVO:03501257 + Breeder barn [ENVO:03501383]: + text: Breeder barn [ENVO:03501383] + description: A barn where animals are kept for breeding purposes. + meaning: ENVO:03501383 + is_a: Barn [ENVO:03501257] + Broiler barn [ENVO:03501386]: + text: Broiler barn [ENVO:03501386] + description: A barn where broiler chickens are reared. + meaning: ENVO:03501386 + is_a: Barn [ENVO:03501257] + Sheep barn [ENVO:03501385]: + text: Sheep barn [ENVO:03501385] + description: A barn where sheep are kept. + meaning: ENVO:03501385 + is_a: Barn [ENVO:03501257] + Dairy [ENVO:00003862]: + text: Dairy [ENVO:00003862] + description: A dairy is a building in which animal milk is harvested and, + optionally, processed for human consumption. + meaning: ENVO:00003862 + Farm [ENVO:00000078]: + text: Farm [ENVO:00000078] + description: An area of land which is used for the cultivation of crops or + grazing of livestock, including any agricultural constructions therein. + meaning: ENVO:00000078 + Beef farm [ENVO:03501443]: + text: Beef farm [ENVO:03501443] + description: A farm where cows are kept for the purpose of meat production. + meaning: ENVO:03501443 + is_a: Farm [ENVO:00000078] + Breeder farm [ENVO:03501384]: + text: Breeder farm [ENVO:03501384] + description: A farm where animals are kept for breeding purposes. + meaning: ENVO:03501384 + is_a: Farm [ENVO:00000078] + Dairy farm [ENVO:03501416]: + text: Dairy farm [ENVO:03501416] + description: A farm where cows are kept for the purpose of producing milk + and other dairy products. + meaning: ENVO:03501416 + is_a: Farm [ENVO:00000078] + Feedlot [ENVO:01000627]: + text: Feedlot [ENVO:01000627] + description: A feedlot is a plot of land on which livestock are fattened for + market [URL:http://www.merriam-webster.com/dictionary/feedlot ]. + meaning: ENVO:01000627 + is_a: Farm [ENVO:00000078] + Beef cattle feedlot [ENVO:03501444]: + text: Beef cattle feedlot [ENVO:03501444] + description: A feedlot where beef cattle are kept with a focus on efficient + growth and weight gain of the animals. + meaning: ENVO:03501444 + is_a: Feedlot [ENVO:01000627] + Fish farm [ENVO:00000294]: + text: Fish farm [ENVO:00000294] + description: A facility in which fish are raised commercially in tanks or + enclosures, usually for food. + meaning: ENVO:00000294 + is_a: Farm [ENVO:00000078] + Research farm [ENVO:03501417]: + text: Research farm [ENVO:03501417] + description: A farm which is used for conducting agricultural research. + meaning: ENVO:03501417 + is_a: Farm [ENVO:00000078] + Central Experimental Farm [GAZ:00004603]: + text: Central Experimental Farm [GAZ:00004603] + description: An agricultural facility, working farm, and research centre of + the Research Branch of Agriculture and Agri-Food Canada. This farm is centrally + located in and completely surrounded by the City of Ottawa, Ontario, Canada. + The CEF is bordered by the Rideau Canal (a National Historic Site as well) + to the east, by Baseline Road to the south, by Merivale and Fisher Roads + to the west, and Carling Avenue to the north. + meaning: GAZ:00004603 + is_a: Farm [ENVO:00000078] + Freshwater environment [ENVO:01000306]: + text: Freshwater environment [ENVO:01000306] + description: An aquatic environment which is determined by freshwater. + meaning: ENVO:01000306 + Hatchery [ENVO:01001873]: + text: Hatchery [ENVO:01001873] + description: A construction in which eggs are hatched under artificial conditions. + meaning: ENVO:01001873 + Poultry hatchery [ENVO:01001874]: + text: Poultry hatchery [ENVO:01001874] + description: A hatchery in which the eggs of poultry are hatched under artificial + conditions + meaning: ENVO:01001874 + is_a: Hatchery [ENVO:01001873] + Hospital [ENVO:00002173]: + text: Hospital [ENVO:00002173] + description: A building in which health care services are provided by specialized + staff and equipment. + meaning: ENVO:00002173 + Lake [ENVO:00000020]: + text: Lake [ENVO:00000020] + description: A body of water or other liquid of considerable size contained + in a depression on a landmass. + meaning: ENVO:00000020 + Pond [ENVO:00000033]: + text: Pond [ENVO:00000033] + description: A body of water, usually of smaller size than a lake. + meaning: ENVO:00000033 + Reservoir [ENVO:00000025]: + text: Reservoir [ENVO:00000025] + description: An artificial body of water, often contained by a dam, constructed + for the purpose of water storage. + meaning: ENVO:00000025 + Irrigation reservoir [ENVO:00000450]: + text: Irrigation reservoir [ENVO:00000450] + description: A reservoir constructed for the purpose of providing water for + irrigation. + meaning: ENVO:00000450 + is_a: Reservoir [ENVO:00000025] + Retail environment [ENVO:01001448]: + text: Retail environment [ENVO:01001448] + description: A planned environmental usage process during which an environment + supports the sale of goods to ultimate consumers, usually in small quantities. + meaning: ENVO:01001448 + Shop [ENVO:00002221]: + text: Shop [ENVO:00002221] + description: A building in which a business presents a selection of goods + and offers to trade or sell them to customers for money or other goods. + meaning: ENVO:00002221 + is_a: Retail environment [ENVO:01001448] + Supermarket [ENVO:01000984]: + text: Supermarket [ENVO:01000984] + description: A food shop in which food products are the primary offer for + sale or trade. + meaning: ENVO:01000984 + is_a: Shop [ENVO:00002221] + River [ENVO:00000022]: + text: River [ENVO:00000022] + description: A stream which, through permanent or seasonal flow processes, + moves from elevated land towards lower elevations through a definite channel + and empties either into a sea, lake, or another river or ends on land as + bed seepage and evapotranspiration exceed water supply. + meaning: ENVO:00000022 + Roost (bird) [ENVO:03501439]: + text: Roost (bird) [ENVO:03501439] + description: A perch on which birds rest. + meaning: ENVO:03501439 + Wastewater treatment plant [ENVO:00002272]: + text: Wastewater treatment plant [ENVO:00002272] + description: A plant in which wastewater is treated. + meaning: ENVO:00002272 + Wetland [ENVO:00000043]: + text: Wetland [ENVO:00000043] + description: An area that is inundated or saturated by surface or ground water + at a frequency and duration sufficient to support, and that under normal + circumstances do support, a prevalence of vegetation typically adapted for + life in saturated soil conditions. + meaning: ENVO:00000043 + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu + title: environmental_material menu + permissible_values: + Air [ENVO:00002005]: + text: Air [ENVO:00002005] + description: 'The mixture of gases (roughly (by molar content/volume: 78% + nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts + of other gases, and a variable amount (average around 1%) of water vapor) + that surrounds the planet Earth.' + meaning: ENVO:00002005 + Animal manure [AGRO:00000079]: + text: Animal manure [AGRO:00000079] + description: Organic matter mostly derived from animal feces which can be + used as organic fertilizer in agriculture. + meaning: AGRO:00000079 + Animal feeding equipment [AGRO:00000675]: + text: Animal feeding equipment [AGRO:00000675] + description: An equipment used to feed and water livestock animals. + meaning: AGRO:00000675 + Animal feeder [AGRO:00000679]: + text: Animal feeder [AGRO:00000679] + description: An animal feeding equipment that has a food storage unit and + which enables livestock to obtain their own food. + meaning: AGRO:00000679 + is_a: Animal feeding equipment [AGRO:00000675] + Animal drinker [AGRO:00000680]: + text: Animal drinker [AGRO:00000680] + description: An animal feeding equipment that has a water storage unit which + enables livestock to obtain their own water. + meaning: AGRO:00000680 + is_a: Animal feeding equipment [AGRO:00000675] + Feed pan [AGRO:00000676]: + text: Feed pan [AGRO:00000676] + description: A bowl or pan which is used to feed livestock. + meaning: AGRO:00000676 + is_a: Animal feeding equipment [AGRO:00000675] + Watering bowl [AGRO:00000677]: + text: Watering bowl [AGRO:00000677] + description: A bowl from which animals can drink. + meaning: AGRO:00000677 + is_a: Animal feeding equipment [AGRO:00000675] + Animal transportation equipment [AGRO:00000671]: + text: Animal transportation equipment [AGRO:00000671] + description: An equipment used in the transportation of an animal + meaning: AGRO:00000671 + Dead haul trailer [GENEPIO:0100896]: + text: Dead haul trailer [GENEPIO:0100896] + description: A trailer used by a dead haul truck to transport dead animal + from an abattoir. + meaning: GENEPIO:0100896 + is_a: Animal transportation equipment [AGRO:00000671] + Dead haul truck [AGRO:00000673]: + text: Dead haul truck [AGRO:00000673] + description: A truck used to haul dead animals from an abattoir. + meaning: AGRO:00000673 + is_a: Animal transportation equipment [AGRO:00000671] + Live haul trailer [GENEPIO:0100897]: + text: Live haul trailer [GENEPIO:0100897] + description: A trailer used by a live haul truck to transport live animals. + meaning: GENEPIO:0100897 + is_a: Animal transportation equipment [AGRO:00000671] + Live haul truck [AGRO:00000674]: + text: Live haul truck [AGRO:00000674] + description: A truck used to haul live animals. + meaning: AGRO:00000674 + is_a: Animal transportation equipment [AGRO:00000671] + Belt [NCIT:C49844]: + text: Belt [NCIT:C49844] + description: A device consisting of a narrow loop of material moving over + shafts or pulleys. + meaning: NCIT:C49844 + Egg belt [AGRO:00000670]: + text: Egg belt [AGRO:00000670] + description: A conveyor belt used to collect eggs in an industrial egg production + environment. + meaning: AGRO:00000670 + is_a: Belt [NCIT:C49844] + Plucking belt [AGRO:00000669]: + text: Plucking belt [AGRO:00000669] + description: A part of the plucking machine that moves the birds through the + stages of plucking within the plucking apparatus. + meaning: AGRO:00000669 + is_a: Belt [NCIT:C49844] + Biosolids [ENVO:00002059]: + text: Biosolids [ENVO:00002059] + description: A treated form of sludge, sometimes used as a fertilizer in agriculture. + meaning: ENVO:00002059 + Boot [GSSO:012935]: + text: Boot [GSSO:012935] + description: A footwear which covers the foot, the ankle, and sometimes the + leg below the knee. + meaning: GSSO:012935 + Boot cover [OBI:0002806]: + text: Boot cover [OBI:0002806] + description: A personal protective device which is an impermiable material + which covers a shoe or boot in order to prevent spread of specific environmental + contaminants. + meaning: OBI:0002806 + is_a: Boot [GSSO:012935] + Broom [ENVO:03501431]: + text: Broom [ENVO:03501431] + description: A cleaning equipment piece which is a bundle of fibres attached + to a long handle, and is used for sweeping. + meaning: ENVO:03501431 + Bulk tank [ENVO:03501379]: + text: Bulk tank [ENVO:03501379] + description: A manufactured product which used to safely store and/or transport + solids, liquids, gases and a variety of compounds and mixtures. + meaning: ENVO:03501379 + Chick box [AGRO:00000678]: + text: Chick box [AGRO:00000678] + description: The box which is used to transport chick (juvenile chicken). + meaning: AGRO:00000678 + Chick pad [AGRO:00000672]: + text: Chick pad [AGRO:00000672] + description: The lining of a box or crate used to transport chicks (juvenile + chickens). + meaning: AGRO:00000672 + Cleaning equipment [ENVO:03501430]: + text: Cleaning equipment [ENVO:03501430] + description: An equipment piece used for cleaning a built environment or a + manufactured product. + meaning: ENVO:03501430 + Compost [ENVO:00002170]: + text: Compost [ENVO:00002170] + description: The aerobically decomposed remnants of organic materials. + meaning: ENVO:00002170 + Crate [ENVO:03501372]: + text: Crate [ENVO:03501372] + description: A manufactured product which is a container, traditionally made + of wooden slates, designed to protect transported goods from damage. + meaning: ENVO:03501372 + Dumpster [ENVO:03501400]: + text: Dumpster [ENVO:03501400] + description: A manufactured product which is a reusable container that accumulates + waste until it is periodically emptied or replaced. + meaning: ENVO:03501400 + Dust [ENVO:00002008]: + text: Dust [ENVO:00002008] + description: Minute solid particles with diameters less than 500 micrometers. + Occurs in and may be deposited from, the atmosphere. + meaning: ENVO:00002008 + Fan [NCIT:C49947]: + text: Fan [NCIT:C49947] + description: A device designed to create an air current through the rotation + of a planar surface. + meaning: NCIT:C49947 + Freezer [ENVO:03501415]: + text: Freezer [ENVO:03501415] + description: A manufactured product which is a device used to keep things + frozen by maintaining a temperature below the freezing point of water. + meaning: ENVO:03501415 + Freezer handle [ENVO:03501414]: + text: Freezer handle [ENVO:03501414] + description: A manufactured product which is the handle of a freezer door. + meaning: ENVO:03501414 + is_a: Freezer [ENVO:03501415] + Manure digester equipment [ENVO:03501424]: + text: Manure digester equipment [ENVO:03501424] + description: An equipment piece which is used in the aerobic or anaerobic + microbial digestion of manure. + meaning: ENVO:03501424 + Nest [ENVO:03501432]: + text: Nest [ENVO:03501432] + description: A structure that is built for certain animals to hold eggs or + young. + meaning: ENVO:03501432 + Bird's nest [ENVO:00005805]: + text: Bird's nest [ENVO:00005805] + description: A bird nest is the spot in which a bird lays and incubates its + eggs and raises its young. [ https://en.wikipedia.org/wiki/Bird_nest ] + meaning: ENVO:00005805 + is_a: Nest [ENVO:03501432] + Permafrost [ENVO:00000134]: + text: Permafrost [ENVO:00000134] + description: Soil or rock and included ice or organic material at or below + the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) + for two or more years. + meaning: ENVO:00000134 + Poultry fluff [UBERON:0008291]: + text: Poultry fluff [UBERON:0008291] + description: A feather lacking a vane and having a rudimentary rachis and + a tuft of non-interlocked barbs with elongated barbules extending from the + calamus. + meaning: UBERON:0008291 + Poultry litter [AGRO:00000080]: + text: Poultry litter [AGRO:00000080] + description: Manure which is primarily composed of pig feces. + meaning: AGRO:00000080 + Sediment [ENVO:00002007]: + text: Sediment [ENVO:00002007] + description: Sediment is an environmental substance comprised of any particulate + matter that can be transported by fluid flow and which eventually is deposited + as a layer of solid particles on the bedor bottom of a body of water or + other liquid. + meaning: ENVO:00002007 + Soil [ENVO:00001998]: + text: Soil [ENVO:00001998] + description: Soil is an environmental material which is primarily composed + of minerals, varying proportions of sand, silt, and clay, organic material + such as humus, gases, liquids, and a broad range of resident micro- and + macroorganisms. + meaning: ENVO:00001998 + Agricultural soil [ENVO:00002259]: + text: Agricultural soil [ENVO:00002259] + description: A type of soil used for agriculture that supports the physical, + chemical, and biological needs of the desired crop during production. + meaning: ENVO:00002259 + is_a: Soil [ENVO:00001998] + Forest soil [ENVO:00002261]: + text: Forest soil [ENVO:00002261] + description: A portion of soil which is found in a forested area. + meaning: ENVO:00002261 + is_a: Soil [ENVO:00001998] + Straw [ENVO:00003869]: + text: Straw [ENVO:00003869] + description: An agricultural byproduct, the dry stalk of a cereal plant, after + the nutrient grain or seed has been removed. + meaning: ENVO:00003869 + Water [CHEBI:15377]: + text: Water [CHEBI:15377] + description: An oxygen hydride consisting of an oxygen atom that is covalently + bonded to two hydrogen atoms. + meaning: CHEBI:15377 + Drinking water [ENVO:00003064]: + text: Drinking water [ENVO:00003064] + description: Water which is suitable for consumption by humans + meaning: ENVO:00003064 + is_a: Water [CHEBI:15377] + Fecal slurry [ENVO:03501436]: + text: Fecal slurry [ENVO:03501436] + description: A mixture of fecal material mixed, buffer, and other materials, + that is homogenized and strained and used in fecal microbiota translpantation. + meaning: ENVO:03501436 + is_a: Water [CHEBI:15377] + Fluid from meat rinse [GENEPIO:0004323]: + text: Fluid from meat rinse [GENEPIO:0004323] + meaning: GENEPIO:0004323 + is_a: Water [CHEBI:15377] + Groundwater [ENVO:01001004]: + text: Groundwater [ENVO:01001004] + description: Underground water which is located in pore spaces found in rock + or unconsolidated deposits such as soil, clay, or gravel. + meaning: ENVO:01001004 + is_a: Water [CHEBI:15377] + Poultry plucking water [AGRO_00000693]: + text: Poultry plucking water [AGRO_00000693] + description: A type of water obtained from rinsing poultry carcasses during + the feather plucking process. + meaning: AGRO:00000693 + is_a: Water [CHEBI:15377] + Surface runoff [ENVO:03501408]: + text: Surface runoff [ENVO:03501408] + description: Surface water which is 1) from some rainwater, stormwater, meltwater, + or other local source and 2) which can no longer sufficiently rapidly infiltrate + into soil, and instead flows along a drainage slope. + meaning: ENVO:03501408 + is_a: Water [CHEBI:15377] + Surface water [ENVO:00002042]: + text: Surface water [ENVO:00002042] + description: Water that is found on the surface of an astronomical object. + meaning: ENVO:00002042 + is_a: Water [CHEBI:15377] + Wastewater [ENVO:00002001]: + text: Wastewater [ENVO:00002001] + description: Water that has been adversely affected in quality by anthropogenic + influence + meaning: ENVO:00002001 + is_a: Water [CHEBI:15377] + Sludge [ENVO:00002044]: + text: Sludge [ENVO:00002044] + description: The residual semi-solid material left from domestic or industrial + processes, or wastewater treatment processes. + meaning: ENVO:00002044 + is_a: Wastewater [ENVO:00002001] + Primary sludge [ENVO:00002057]: + text: Primary sludge [ENVO:00002057] + description: Sludge generated from the initial processes (i.e., precipitation, + sedimentation) of wastewater treatment. + meaning: ENVO:00002057 + is_a: Sludge [ENVO:00002044] + Secondary sludge [ENVO:00002058]: + text: Secondary sludge [ENVO:00002058] + description: Activated waste biomass generated during wastewater treatment. + meaning: ENVO:00002058 + is_a: Sludge [ENVO:00002044] + Wastewater effluent [GENEPIO:0100891]: + text: Wastewater effluent [GENEPIO:0100891] + meaning: GENEPIO:0100891 + is_a: Wastewater [ENVO:00002001] + Primary wastewater effluent [GENEPIO:0100892]: + text: Primary wastewater effluent [GENEPIO:0100892] + description: A wastewater effluent which has been discharged from a primary + clarifier after the first stage of sedimentation. + meaning: GENEPIO:0100892 + is_a: Wastewater effluent [GENEPIO:0100891] + Secondary wastewater effluent [GENEPIO:0100893]: + text: Secondary wastewater effluent [GENEPIO:0100893] + description: A wastewater effluent which has been discharged from a secondary + clarifier after the second stage of sedimentation. + meaning: GENEPIO:0100893 + is_a: Wastewater effluent [GENEPIO:0100891] + Wastewater sediment [GENEPIO:0100890]: + text: Wastewater sediment [GENEPIO:0100890] + meaning: GENEPIO:0100890 + is_a: Wastewater [ENVO:00002001] + Weep fluid [AGRO:00000692]: + text: Weep fluid [AGRO:00000692] + description: A fluid that leaks from a bag containing an animal carcass, and + can include water, chemicals and anatomical fluids. + meaning: AGRO:00000692 + is_a: Water [CHEBI:15377] + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical_material menu + permissible_values: + Blood [UBERON:0000178]: + text: Blood [UBERON:0000178] + description: A fluid that is composed of blood plasma and erythrocytes. + meaning: UBERON:0000178 + Fluid [UBERON:0006314]: + text: Fluid [UBERON:0006314] + description: Liquid components of living organisms. includes fluids that are + excreted or secreted from the body as well as body water that normally is + not. + meaning: UBERON:0006314 + Fluid (cerebrospinal (CSF)) [UBERON:0001359]: + text: Fluid (cerebrospinal (CSF)) [UBERON:0001359] + description: A clear, colorless, bodily fluid, that occupies the subarachnoid + space and the ventricular system around and inside the brain and spinal + cord. + meaning: UBERON:0001359 + is_a: Fluid [UBERON:0006314] + Fluid (amniotic) [UBERON:0000173]: + text: Fluid (amniotic) [UBERON:0000173] + description: Amniotic fluid is a bodily fluid consisting of watery liquid + surrounding and cushioning a growing fetus within the amnion. + meaning: UBERON:0000173 + is_a: Fluid [UBERON:0006314] + Saliva [UBERON:0001836]: + text: Saliva [UBERON:0001836] + description: A fluid produced in the oral cavity by salivary glands, typically + used in predigestion, but also in other functions. + meaning: UBERON:0001836 + is_a: Fluid [UBERON:0006314] + Tissue [UBERON:0000479]: + text: Tissue [UBERON:0000479] + description: Multicellular anatomical structure that consists of many cells + of one or a few types, arranged in an extracellular matrix such that their + long-range organisation is at least partly a repetition of their short-range + organisation. + meaning: UBERON:0000479 + BodyProductMenu: + name: BodyProductMenu + title: body_product menu + permissible_values: + Digestive tract substance [GENEPIO:0100898]: + text: Digestive tract substance [GENEPIO:0100898] + description: Undigested food material, microbiota, and other materials found + in the digestive tract. + meaning: GENEPIO:0100898 + Caecal content [GENEPIO:0100899]: + text: Caecal content [GENEPIO:0100899] + description: Undigested food material, microbiota, and other materials found + in the cecum + meaning: GENEPIO:0100899 + is_a: Digestive tract substance [GENEPIO:0100898] + Intestinal content [GENEPIO:0100900]: + text: Intestinal content [GENEPIO:0100900] + description: Undigested food material, microbiota, and other materials found + in the intestine + meaning: GENEPIO:0100900 + is_a: Digestive tract substance [GENEPIO:0100898] + Stomach content [GENEPIO:0100901]: + text: Stomach content [GENEPIO:0100901] + description: Undigested food material, microbiota, and other materials found + in the stomach + meaning: GENEPIO:0100901 + is_a: Digestive tract substance [GENEPIO:0100898] + Feces [UBERON:0001988]: + text: Feces [UBERON:0001988] + description: Portion of semisolid bodily waste discharged through the anus. + meaning: UBERON:0001988 + Fecal composite [GENEPIO:0004512]: + text: Fecal composite [GENEPIO:0004512] + description: A mixture of feces obtained from multiple individuals. + meaning: GENEPIO:0004512 + is_a: Feces [UBERON:0001988] + Feces (fresh) [GENEPIO:0004513]: + text: Feces (fresh) [GENEPIO:0004513] + description: Feces that was recently excreted. + meaning: GENEPIO:0004513 + is_a: Feces [UBERON:0001988] + Feces (environmental) [GENEPIO:0004514]: + text: Feces (environmental) [GENEPIO:0004514] + description: Feces which is deposited in the environment. + meaning: GENEPIO:0004514 + is_a: Feces [UBERON:0001988] + Meconium [UBERON:0007109]: + text: Meconium [UBERON:0007109] + description: A dark greenish mass that accumulates in the bowel during fetal + life and is discharged shortly after birth. + meaning: UBERON:0007109 + is_a: Feces [UBERON:0001988] + Milk [UBERON:0001913]: + text: Milk [UBERON:0001913] + description: An emulsion of fat globules within a fluid that is secreted by + the mammary gland during lactation. + meaning: UBERON:0001913 + Colostrum [UBERON:0001914]: + text: Colostrum [UBERON:0001914] + description: 'The thin, yellow, serous fluid secreted by the mammary glands + during pregnancy and immediately postpartum before lactation begins. It + consists of immunologically active substances, white blood cells, water, + protein, fat, and carbohydrates. [ MESH : A12.200.194 http://en.wikipedia.org/wiki/Colostrum + ]' + meaning: UBERON:0001914 + is_a: Milk [UBERON:0001913] + Mucus [UBERON:0000912]: + text: Mucus [UBERON:0000912] + description: Mucus is a bodily fluid consisting of a slippery secretion of + the lining of the mucous membranes in the body. It is a viscous colloid + containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus + is produced by goblet cells in the mucous membranes that cover the surfaces + of the membranes. It is made up of mucins and inorganic salts suspended + in water. + meaning: UBERON:0000912 + Urine [UBERON:0001088]: + text: Urine [UBERON:0001088] + description: Excretion that is the output of a kidney. + meaning: UBERON:0001088 + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical_part menu + permissible_values: + Carcass [UBERON:0008979]: + text: Carcass [UBERON:0008979] + description: A body of a multi-cellular organism that is no longer living. + meaning: UBERON:0008979 + Digestive system [UBERON:0001007]: + text: Digestive system [UBERON:0001007] + description: Anatomical system that has as its parts the organs devoted to + the ingestion, digestion, and assimilation of food and the discharge of + residual wastes. + meaning: UBERON:0001007 + Caecum [UBERON:0001153]: + text: Caecum [UBERON:0001153] + description: pouch in the digestive tract that connects the ileum with the + ascending colon of the large intestine. It is separated from the ileum by + the ileocecal valve, and is the beginning of the large intestine. It is + also separated from the colon by the cecocolic junction. + meaning: UBERON:0001153 + is_a: Digestive system [UBERON:0001007] + Colon [UBERON:0001155]: + text: Colon [UBERON:0001155] + description: A portion of the large intestine before it becomes the rectum. + In mammals, the colon is the most part of the large intestine, excluding + the vermiform appendix, the rectum and the anal canal. + meaning: UBERON:0001155 + is_a: Digestive system [UBERON:0001007] + Digestive gland [UBERON:0006925]: + text: Digestive gland [UBERON:0006925] + description: Any gland that is part of the digestive system. + meaning: UBERON:0006925 + is_a: Digestive system [UBERON:0001007] + Foregut [UBERON:0001041]: + text: Foregut [UBERON:0001041] + description: Anterior subdivision of a digestive tract. + meaning: UBERON:0001041 + is_a: Digestive system [UBERON:0001007] + Gall bladder [UBERON:0002110]: + text: Gall bladder [UBERON:0002110] + description: An organ that aids digestion and stores bile produced by the + liver. + meaning: UBERON:0002110 + is_a: Digestive system [UBERON:0001007] + Gastrointestinal system mucosa [UBERON:0004786]: + text: Gastrointestinal system mucosa [UBERON:0004786] + description: A mucosa that is part of a gastrointestinal system. + meaning: UBERON:0004786 + is_a: Digestive system [UBERON:0001007] + Gizzard [UBERON:0005052]: + text: Gizzard [UBERON:0005052] + description: The muscular enlargement of the alimentary canal that has usually + thick muscular walls and a tough horny lining for grinding the food and + when the crop is present follows it and the proventriculus. + meaning: UBERON:0005052 + is_a: Digestive system [UBERON:0001007] + Hindgut [UBERON:0001046]: + text: Hindgut [UBERON:0001046] + description: The caudalmost subdivision of a digestive tract. + meaning: UBERON:0001046 + is_a: Digestive system [UBERON:0001007] + Intestine [UBERON:0000160]: + text: Intestine [UBERON:0000160] + description: Segment of the alimentary canal extending from the stomach to + the anus and, in humans and other mammals, consists of two segments, the + small intestine and the large intestine. + meaning: UBERON:0000160 + is_a: Digestive system [UBERON:0001007] + Small intestine [UBERON:0002108]: + text: Small intestine [UBERON:0002108] + description: 'Subdivision of digestive tract that connects the stomach to + the large intestine and is where much of the digestion and absorption of + food takes place (with the exception of ruminants). The mammalian small + intestine is long and coiled and can be differentiated histologically into: + duodenum, jejunem, ileum.' + meaning: UBERON:0002108 + is_a: Intestine [UBERON:0000160] + Duodenum [UBERON:0002114]: + text: Duodenum [UBERON:0002114] + description: The first part of the small intestine. At the junction of the + stomach and the duodenum the alimentary canal is inflected. The duodenum + first goes anteriorly for a short distance, turns dorsally, and eventually + caudally, thus it is a U-shaped structure with two horizontal sections (a + ventral and a dorsal one). + meaning: UBERON:0002114 + is_a: Small intestine [UBERON:0002108] + Ileum [UBERON:0002116]: + text: Ileum [UBERON:0002116] + description: The portion of the small intestine that extends from the jejunum + to the colon. + meaning: UBERON:0002116 + is_a: Small intestine [UBERON:0002108] + Jejunum [UBERON:0002115]: + text: Jejunum [UBERON:0002115] + description: The portion of the small intestine that extends from the duodenum + to the ileum. + meaning: UBERON:0002115 + is_a: Small intestine [UBERON:0002108] + Stomach [UBERON:0000945]: + text: Stomach [UBERON:0000945] + description: An expanded region of the vertebrate alimentary tract that serves + as a food storage compartment and digestive organ. A stomach is lined, in + whole or in part by a glandular epithelium. + meaning: UBERON:0000945 + is_a: Digestive system [UBERON:0001007] + Abomasum [UBERON:0007358]: + text: Abomasum [UBERON:0007358] + description: The fourth stomach of ruminating animals, which is an elongated + pear-shaped sac lying on the floor of the abdomen, on the right-hand side, + and roughly between the seventh and twelfth ribs. It leads to the beginning + of the small intestine. + meaning: UBERON:0007358 + is_a: Stomach [UBERON:0000945] + Rumen [UBERON:0007365]: + text: Rumen [UBERON:0007365] + description: The first compartment of the ruminant stomach. It lies on the + left side of the body, occupying the whole of the left side of the abdomen + and even stretching across the median plane of the body to the right side. + It is capacious, divided into an upper and a lower sac, each of which has + a blind sac at its posterior extremity. + meaning: UBERON:0007365 + is_a: Stomach [UBERON:0000945] + Excretory system (organizational term): + text: Excretory system (organizational term) + Anus [UBERON:0001245]: + text: Anus [UBERON:0001245] + description: 'Orifice at the opposite end of an animal''s digestive tract + from the mouth. Its function is to expel feces, unwanted semi-solid matter + produced during digestion, which, depending on the type of animal, may be + one or more of: matter which the animal cannot digest, such as bones; food + material after all the nutrients have been extracted, for example cellulose + or lignin; ingested matter which would be toxic if it remained in the digestive + tract; and dead or excess gut bacteria and other endosymbionts.' + meaning: UBERON:0001245 + is_a: Excretory system (organizational term) + Anal gland [UBERON:0011253]: + text: Anal gland [UBERON:0011253] + description: A type of gland occurring as solitary or in pairs or groups, + near the anus and sometimes opening into the rectum. + meaning: UBERON:0011253 + is_a: Excretory system (organizational term) + Cloaca [UBERON:0000162]: + text: Cloaca [UBERON:0000162] + description: Common chamber into which the intestines and excretory system + opens. Arises during development in all vertebrates, but in many it becomes + subdivided, lost or incorporated into other structures. + meaning: UBERON:0000162 + is_a: Excretory system (organizational term) + Liver [UBERON:0002107]: + text: Liver [UBERON:0002107] + description: An exocrine gland which secretes bile and functions in metabolism + of protein and carbohydrate and fat, synthesizes substances involved in + the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, + stores glycogen, and breaks down worn-out erythrocytes + meaning: UBERON:0002107 + is_a: Excretory system (organizational term) + Kidney [UBERON:0002113]: + text: Kidney [UBERON:0002113] + description: A paired organ of the urinary tract which has the production + of urine as its primary function. + meaning: UBERON:0002113 + is_a: Excretory system (organizational term) + Rectum [UBERON:0001052]: + text: Rectum [UBERON:0001052] + description: The terminal portion of the intestinal tube, terminating with + the anus. + meaning: UBERON:0001052 + is_a: Excretory system (organizational term) + Spleen [UBERON:0002106]: + text: Spleen [UBERON:0002106] + description: The organ that functions to filter blood and to store red corpuscles + and platelets. + meaning: UBERON:0002106 + is_a: Excretory system (organizational term) + Urinary bladder [UBERON:0001255]: + text: Urinary bladder [UBERON:0001255] + description: Distensible musculomembranous organ situated in the anterior + part of the pelvic cavity in which urine collects before excretion. + meaning: UBERON:0001255 + is_a: Excretory system (organizational term) + Foot [UBERON:0002387]: + text: Foot [UBERON:0002387] + description: 'The terminal part of the vertebrate leg upon which an individual + stands. 2: An invertebrate organ of locomotion or attachment; especially: + a ventral muscular surface or process of a mollusk.' + meaning: UBERON:0002387 + Head [UBERON:0000033]: + text: Head [UBERON:0000033] + description: The head is the anterior-most division of the body. + meaning: UBERON:0000033 + is_a: Foot [UBERON:0002387] + Brain [UBERON:0000955]: + text: Brain [UBERON:0000955] + description: The brain is the center of the nervous system in all vertebrate, + and most invertebrate, animals. Some primitive animals such as jellyfish + and starfish have a decentralized nervous system without a brain, while + sponges lack any nervous system at all. In vertebrates, the brain is located + in the head, protected by the skull and close to the primary sensory apparatus + of vision, hearing, balance, taste, and smell. + meaning: UBERON:0000955 + is_a: Foot [UBERON:0002387] + Ear [UBERON:0001690]: + text: Ear [UBERON:0001690] + description: Sense organ in vertebrates that is specialized for the detection + of sound, and the maintenance of balance. Includes the outer ear and middle + ear, which collect and transmit sound waves; and the inner ear, which contains + the organs of balance and (except in fish) hearing. Also includes the pinna, + the visible part of the outer ear, present in some mammals. + meaning: UBERON:0001690 + is_a: Foot [UBERON:0002387] + Eye [UBERON:0000970]: + text: Eye [UBERON:0000970] + description: An organ that detects light. + meaning: UBERON:0000970 + is_a: Foot [UBERON:0002387] + Mouth [UBERON:0000165]: + text: Mouth [UBERON:0000165] + description: The proximal portion of the digestive tract, containing the oral + cavity and bounded by the oral opening. In vertebrates, this extends to + the pharynx and includes gums, lips, tongue and parts of the palate. Typically + also includes the teeth, except where these occur elsewhere (e.g. pharyngeal + jaws) or protrude from the mouth (tusks). + meaning: UBERON:0000165 + is_a: Foot [UBERON:0002387] + Nose [UBERON:0000004]: + text: Nose [UBERON:0000004] + description: The olfactory organ of vertebrates, consisting of nares, olfactory + epithelia and the structures and skeletal framework of the nasal cavity. + meaning: UBERON:0000004 + is_a: Foot [UBERON:0002387] + Nasal turbinal [UBERON:0035612]: + text: Nasal turbinal [UBERON:0035612] + description: A skeletal element of the ethmoid region with complex morphology + that are lined with mucuous membranes involved in either olfaction or air + conditioning. + meaning: UBERON:0035612 + is_a: Nose [UBERON:0000004] + Nasopharynx (NP) [UBERON:0001728]: + text: Nasopharynx (NP) [UBERON:0001728] + description: The section of the pharynx that lies above the soft palate. + meaning: UBERON:0001728 + is_a: Nose [UBERON:0000004] + Pair of nares [UBERON:0002109]: + text: Pair of nares [UBERON:0002109] + description: Pair of nostrils. + meaning: UBERON:0002109 + is_a: Nose [UBERON:0000004] + Paranasal sinus [UBERON:0001825]: + text: Paranasal sinus [UBERON:0001825] + description: The paired air-filled cavities surrounded by the bones of the + face that are lined by mucous membranes and are continuous with the nasal + cavity. + meaning: UBERON:0001825 + is_a: Nose [UBERON:0000004] + Snout [UBERON:0006333]: + text: Snout [UBERON:0006333] + description: The projecting nose and mouth of an animal, especially a mammal. + meaning: UBERON:0006333 + is_a: Nose [UBERON:0000004] + Lymphatic system [UBERON:0006558]: + text: Lymphatic system [UBERON:0006558] + description: An organ system subdivision that is a network of vessels capable + of removing accumulating protein and fluid from the interstitial space and + returning it to the vascular space. In some species, this network is connected + to the immune system via lymph nodes and lymphocyte-producing organs, with + the whole being the lymphoid system. + meaning: UBERON:0006558 + Lymph node [UBERON:0000029]: + text: Lymph node [UBERON:0000029] + description: Any of the rounded masses of lymphoid tissue that are surrounded + by a capsule of connective tissue, are distributed along the lymphatic vessels, + and contain numerous lymphocytes which filter the flow of lymph. + meaning: UBERON:0000029 + is_a: Lymphatic system [UBERON:0006558] + Mesenteric lymph node [UBERON:0002509]: + text: Mesenteric lymph node [UBERON:0002509] + description: 'The lymph nodes located in the mesentery, of which there are + 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group.' + meaning: UBERON:0002509 + is_a: Lymph node [UBERON:0000029] + Mantle (bird) [GENEPIO:0100927]: + text: Mantle (bird) [GENEPIO:0100927] + description: The forward area of a bird's upper side that is sandwiched between + the nape and the start of the back. + meaning: GENEPIO:0100927 + Neck [UBERON:0000974]: + text: Neck [UBERON:0000974] + description: An organism subdivision that extends from the head to the pectoral + girdle, encompassing the cervical vertebral column. + meaning: UBERON:0000974 + Esophagus [UBERON:0001043]: + text: Esophagus [UBERON:0001043] + description: Tube that connects the pharynx to the stomach. In mammals, the + oesophagus connects the buccal cavity with the stomach. The stratified squamous + non-keratinised epithelium lining the buccal cavity is continued through + the pharynx down into the oesophagus. The lowest part of the oesophagus + (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main + body of the oesophagus is lined with small, simple mucous glands. Each gland + opens into the lumen by a long duct which pierces the muscularis mucosae + (Wilson and Washington, 1989). A sphincter is situated at the point where + the oesophagus enters the stomach to prevent gastro-oesophageal reflux, + i.e. to prevent acidic gastric contents from reaching stratified epithelia + of the oesophagus, where they can cause inflammation and irritation. + meaning: UBERON:0001043 + is_a: Neck [UBERON:0000974] + Trachea [UBERON:0003126]: + text: Trachea [UBERON:0003126] + description: The trachea is the portion of the airway that attaches to the + bronchi as it branches. + meaning: UBERON:0003126 + is_a: Neck [UBERON:0000974] + Nerve [UBERON:0001021]: + text: Nerve [UBERON:0001021] + description: An enclosed, cable-like bundle of axons in the peripheral nervous + system originating in a nerve root in the central nervous system (or a condensed + nervous structure) connecting with peripheral structures. + meaning: UBERON:0001021 + Spinal cord [UBERON:0002240]: + text: Spinal cord [UBERON:0002240] + description: Part of the central nervous system located in the vertebral canal + continuous with and caudal to the brain; demarcated from brain by plane + of foramen magnum. It is composed of an inner core of gray matter in which + nerve cells predominate, and an outer layer of white matter in which myelinated + nerve fibers predominate, and surrounds the central canal. + meaning: UBERON:0002240 + is_a: Nerve [UBERON:0001021] + Organs or organ parts [GENEPIO:0001117]: + text: Organs or organ parts [GENEPIO:0001117] + description: An object aggregate which has as members whole organs or parts + of organs, possibly from different organisms. + meaning: GENEPIO:0001117 + Organ [UBERON:0000062]: + text: Organ [UBERON:0000062] + description: Anatomical structure that performs a specific function or group + of functions + meaning: UBERON:0000062 + is_a: Organs or organ parts [GENEPIO:0001117] + Muscle organ [UBERON:0001630]: + text: Muscle organ [UBERON:0001630] + description: Organ consisting of a tissue made up of various elongated cells + that are specialized to contract and thus to produce movement and mechanical + work. + meaning: UBERON:0001630 + is_a: Organ [UBERON:0000062] + Skin of body [UBERON:0002097]: + text: Skin of body [UBERON:0002097] + description: The organ covering the body that consists of the dermis and epidermis. + meaning: UBERON:0002097 + is_a: Organ [UBERON:0000062] + Reproductive system [UBERON:0000990]: + text: Reproductive system [UBERON:0000990] + description: Anatomical system that has as its parts the organs concerned + with reproduction. + meaning: UBERON:0000990 + Embryo [UBERON:0000922]: + text: Embryo [UBERON:0000922] + description: Anatomical entity that comprises the organism in the early stages + of growth and differentiation that are characterized by cleavage, the laying + down of fundamental tissues, and the formation of primitive organs and organ + systems. For example, for mammals, the process would begin with zygote formation + and end with birth. For insects, the process would begin at zygote formation + and end with larval hatching. For plant zygotic embryos, this would be from + zygote formation to the end of seed dormancy. For plant vegetative embryos, + this would be from the initial determination of the cell or group of cells + to form an embryo until the point when the embryo becomes independent of + the parent plant. + meaning: UBERON:0000922 + is_a: Reproductive system [UBERON:0000990] + Fetus [UBERON:0000323]: + text: Fetus [UBERON:0000323] + description: An embryo that is at the late embryonic stage; this stage covers + late steps of the embryogenesis with a fully formed embryo still developing + before birth or egg hatching + meaning: UBERON:0000323 + is_a: Reproductive system [UBERON:0000990] + Ovary [UBERON:0000992]: + text: Ovary [UBERON:0000992] + description: The gonad of a female organism which contains germ cells. + meaning: UBERON:0000992 + is_a: Reproductive system [UBERON:0000990] + Oviduct [UBERON:0000993]: + text: Oviduct [UBERON:0000993] + description: A tube or collection of tubes in an animal from the ovaries to + the outside of the body. + meaning: UBERON:0000993 + is_a: Reproductive system [UBERON:0000990] + Placenta [UBERON:0001987]: + text: Placenta [UBERON:0001987] + description: Organ of metabolic interchange between fetus and mother, partly + of embryonic origin and partly of maternal origin[GO]. The fetal portion + of the placenta is known as the villous chorion. The maternal portion is + known as the decidua basalis. The two portions are held together by anchoring + villi that are anchored to the decidua basalis by the cytotrophoblastic + shell. + meaning: UBERON:0001987 + is_a: Reproductive system [UBERON:0000990] + Testis [UBERON:0000473]: + text: Testis [UBERON:0000473] + description: A gonad of a male animal. A gonad produces and releases sperm. + meaning: UBERON:0000473 + is_a: Reproductive system [UBERON:0000990] + Udder [UBERON:0013216]: + text: Udder [UBERON:0013216] + description: A large pendulous organ consisting of two or more mammary glands + enclosed in a common envelope and each provided with a single nipple. + meaning: UBERON:0013216 + is_a: Reproductive system [UBERON:0000990] + Uterus [UBERON:0000995]: + text: Uterus [UBERON:0000995] + description: The female muscular organ of gestation in which the developing + embryo or fetus is nourished until birth. + meaning: UBERON:0000995 + is_a: Reproductive system [UBERON:0000990] + Vagina [UBERON:0000996]: + text: Vagina [UBERON:0000996] + description: A fibromuscular tubular tract leading from the uterus to the + exterior of the body in female placental mammals and marsupials, or to the + cloaca in female birds, monotremes, and some reptiles + meaning: UBERON:0000996 + is_a: Reproductive system [UBERON:0000990] + Yolk sac [UBERON:0001040]: + text: Yolk sac [UBERON:0001040] + description: A sac-like expansion of the ventral wall of the intestine, narrowed + into a yolk stalk near the body[Hyman's]. Membranous sac attached to an + embryo, providing early nourishment in the form of yolk in bony fishes, + sharks, reptiles, birds, and primitive mammals. It functions as the developmental + circulatory system of the human embryo, before internal circulation begins. + In the mouse, the yolk sac is the first site of blood formation, generating + primitive macrophages and erythrocytes. + meaning: UBERON:0001040 + is_a: Reproductive system [UBERON:0000990] + Respiratory system [UBERON:0001004]: + text: Respiratory system [UBERON:0001004] + description: Functional system which consists of structures involved in respiration. + meaning: UBERON:0001004 + Air sac [UBERON:0009060]: + text: Air sac [UBERON:0009060] + description: Any of the membranous air-filled extensions of the lungs of birds, + which increase the efficiency of gaseous exchange in the lungs. + meaning: UBERON:0009060 + is_a: Respiratory system [UBERON:0001004] + Lung [UBERON:0002048]: + text: Lung [UBERON:0002048] + description: Respiration organ that develops as an outpocketing of the esophagus + meaning: UBERON:0002048 + is_a: Vascular system [UBERON:0007798] + Pleura [UBERON:0000977]: + text: Pleura [UBERON:0000977] + description: The invaginated serous membrane that surrounds the lungs (the + visceral portion) and lines the walls of the pleural cavity (parietal portion). + meaning: UBERON:0000977 + is_a: Respiratory system [UBERON:0001004] + Respiratory system mucosa [UBERON:0004785]: + text: Respiratory system mucosa [UBERON:0004785] + description: The mucous membrane lining the respiratory tract. + meaning: UBERON:0004785 + is_a: Respiratory system [UBERON:0001004] + Skeletal system [UBERON:0001434]: + text: Skeletal system [UBERON:0001434] + description: Anatomical system that is a multi-element, multi-tissue anatomical + cluster that consists of the skeleton and the articular system. + meaning: UBERON:0001434 + Skeletal joint [UBERON:0000982]: + text: Skeletal joint [UBERON:0000982] + description: Anatomical cluster that consists of two or more adjacent skeletal + structures, which may be interconnected by various types of tissue. + meaning: UBERON:0000982 + is_a: Skeletal system [UBERON:0001434] + Bone element [UBERON:0001474]: + text: Bone element [UBERON:0001474] + description: Skeletal element that is composed of bone tissue. + meaning: UBERON:0001474 + is_a: Skeletal system [UBERON:0001434] + Thoracic segment of trunk [UBERON:0000915]: + text: Thoracic segment of trunk [UBERON:0000915] + description: Subdivision of trunk that lies between the head and the abdomen. + meaning: UBERON:0000915 + Abdomen [UBERON:0000916]: + text: Abdomen [UBERON:0000916] + description: The subdivision of the vertebrate body between the thorax and + pelvis. The ventral part of the abdomen contains the abdominal cavity and + visceral organs. The dorsal part includes the abdominal section of the vertebral + column. + meaning: UBERON:0000916 + is_a: Thoracic segment of trunk [UBERON:0000915] + Muscle of abdomen [UBERON:0002378]: + text: Muscle of abdomen [UBERON:0002378] + description: 'Muscle (organ) which is a part of the abdomen. Examples: external + oblique, rectus abdominis.' + meaning: UBERON:0002378 + is_a: Abdomen [UBERON:0000916] + Peritoneum [UBERON:0002358]: + text: Peritoneum [UBERON:0002358] + description: 'Muscle (organ) which is a part of the abdomen. Examples: external + oblique, rectus abdominis.' + meaning: UBERON:0002358 + is_a: Abdomen [UBERON:0000916] + Vascular system [UBERON:0007798]: + text: Vascular system [UBERON:0007798] + description: Anatomical system that consists of all blood and lymph vessels. + meaning: UBERON:0007798 + Blood vessel [UBERON:0001981]: + text: Blood vessel [UBERON:0001981] + description: A vessel through which blood circulates in the body. + meaning: UBERON:0001981 + is_a: Vascular system [UBERON:0007798] + Bursa of Fabricius [UBERON:0003903]: + text: Bursa of Fabricius [UBERON:0003903] + description: An epithelial and lymphoid organ that develops as a dorsal diverticulum + of the proctodeal region of the cloaca in birds. The luminal (interior) + surface of the bursa is plicated with as many as 15 primary and 7 secondary + plicae or folds. These plicae have hundreds of bursal follicles containing + follicle-associated epithelial cells, lymphocytes, macrophages, and plasma + cells. Lymphoid stem cells migrate from the fetal liver to the bursa during + ontogeny. In the bursa, these stem cells acquire the characteristics of + mature, immunocompetent B cells. The bursa is an organ found in birds involved + in B cell differentiation. + meaning: UBERON:0003903 + is_a: Vascular system [UBERON:0007798] + Gill [UBERON:0002535]: + text: Gill [UBERON:0002535] + description: Anatomical surface structure found in many aquatic organisms. + It is a respiration organ whose function is the extraction of oxygen from + water and the excretion of carbon dioxide. The microscopic structure of + a gill is such that it presents a very large surface area to the external + environment. Gills usually consist of thin filaments of tissue, branches, + or slender tufted processes which have a highly folded surface to increase + surface area. A high surface area is crucial to the gas exchange of aquatic + organisms as water contains only 1/20 parts dissolved Oxygen compared to + air. With the exception of some aquatic insects, the filaments and lamellae + (folds) contain blood or coelomic fluid, from which gases are exchanged + through the thin walls. Oxygen is carried by the blood to other parts of + the body. Carbon dioxide passes from the blood through the thin gill tissue + into the water. Gills or gill-like organs, located in different parts of + the body, are found in various groups of aquatic animals, including mollusks, + crustaceans, insects, fish, and amphibians. [ http://en.wikipedia.org/wiki/Gill + ] + meaning: UBERON:0002535 + is_a: Vascular system [UBERON:0007798] + Heart [UBERON:0000948]: + text: Heart [UBERON:0000948] + description: A myogenic muscular circulatory organ found in the vertebrate + cardiovascular system composed of chambers of cardiac muscle. It is the + primary circulatory organ. + meaning: UBERON:0000948 + is_a: Vascular system [UBERON:0007798] + Pericardium [UBERON:0002407]: + text: Pericardium [UBERON:0002407] + description: The combination of pericardial sac (a double-walled sac containing + the heart and the roots of the great vessels) plus fibrous pericardium. + meaning: UBERON:0002407 + is_a: Vascular system [UBERON:0007798] + Vent (anatomical) [UBERON:2000298]: + text: Vent (anatomical) [UBERON:2000298] + description: The external opening of the rectum or cloaca. + meaning: UBERON:2000298 + Bird vent [UBERON:0012464]: + text: Bird vent [UBERON:0012464] + description: The opening of the cloacal chamber to the outside of the organism. + Birds maintain a single cloacal opening throughout their lives. [ http://orcid.org/0000-0002-6601-2165 + ] + meaning: UBERON:0012464 + is_a: Vent (anatomical) [UBERON:2000298] + Fish vent [GENEPIO:0100902]: + text: Fish vent [GENEPIO:0100902] + description: The external opening which opens to the reproductive and digestive + tracts of the fish. During spawning, the vent serves as an outlet for eggs + and sperm. In most fishes, the vent is in front of the anal fin. + meaning: GENEPIO:0100902 + is_a: Vent (anatomical) [UBERON:2000298] + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection_device menu + permissible_values: + Air filter [ENVO:00003968]: + text: Air filter [ENVO:00003968] + meaning: ENVO:00003968 + Auger (earth auger) [AGRO:00000405]: + text: Auger (earth auger) [AGRO:00000405] + description: Manually operated hand tool that consists of cutter head having + semicircular blades connected to pipe with the help of clamp and flange. + The connecting pipe is further connected to a handle. + meaning: AGRO:00000405 + Bag [GSSO:008558]: + text: Bag [GSSO:008558] + description: A sac or pouch. + meaning: GSSO:008558 + Whirlpak sampling bag [GENEPIO:0002122]: + text: Whirlpak sampling bag [GENEPIO:0002122] + description: A sterilized sampling bag that is puncture proof tabs for protection + from damage due to wire-end protrusion and leak-proof closures. + meaning: GENEPIO:0002122 + is_a: Bag [GSSO:008558] + Bottle [FOODON:03490214]: + text: Bottle [FOODON:03490214] + description: A rigid or semirigid container typically of glass or plastic + having a comparatively narrow neck or mouth and usually no handle. + meaning: FOODON:03490214 + Box corer [GENEPIO:0100928]: + text: Box corer [GENEPIO:0100928] + description: A specimen collection device that is used to collect soft sediments + in lakes or oceans. + meaning: GENEPIO:0100928 + Bronchoscope [OBI:0002826]: + text: Bronchoscope [OBI:0002826] + description: A device which is a thin, tube-like instrument which includes + a light and a lens used to examine a lung. + meaning: OBI:0002826 + Collection Container [OBI:0002088]: + text: Collection Container [OBI:0002088] + description: A container with the function of containing a specimen. + meaning: OBI:0002088 + Collection Cup [GENEPIO:0100026]: + text: Collection Cup [GENEPIO:0100026] + description: A device which is used to collect liquid samples. + meaning: GENEPIO:0100026 + Culture plate [GENEPIO:0004318]: + text: Culture plate [GENEPIO:0004318] + description: A low flat-bottomed laboratory container for growing a layer + of organisms such as bacteria, molds, and cells on a thin layer of nutrient + medium. + meaning: GENEPIO:0004318 + Petri dish [NCIT:C96141]: + text: Petri dish [NCIT:C96141] + description: A shallow dish with a lid used to culture cells. + meaning: NCIT:C96141 + is_a: Culture plate [GENEPIO:0004318] + Fibrobronchoscope Brush [OBI:0002825]: + text: Fibrobronchoscope Brush [OBI:0002825] + meaning: OBI:0002825 + Filter [GENEPIO:0100103]: + text: Filter [GENEPIO:0100103] + description: A manufactured product which separates solids from fluids by + adding a medium through which only a fluid can pass. + meaning: GENEPIO:0100103 + Fine Needle [OBI:0002827]: + text: Fine Needle [OBI:0002827] + meaning: OBI:0002827 + Micropipette [OBI:0001128]: + text: Micropipette [OBI:0001128] + meaning: OBI:0001128 + Needle [OBI:0000436]: + text: Needle [OBI:0000436] + description: A needle is a sharp, hollow device used to penetrate tissue or + soft material. When attached to a syringe. it allows delivery of a specific + volume of liquid or gaseous mixture. + meaning: OBI:0000436 + PONAR grab sampler [GENEPIO:0100929]: + text: PONAR grab sampler [GENEPIO:0100929] + description: A specimen collection device that is designed to collect sediment + samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated + marl or clay." + meaning: GENEPIO:0100929 + Scoop [GENEPIO:0002125]: + text: Scoop [GENEPIO:0002125] + description: A shovel-like utensil that has a deep curved dish and a short + handle and is used for digging into a soft substance for lifting out a portion. + meaning: GENEPIO:0002125 + Soil sample probe [GENEPIO:0100930]: + text: Soil sample probe [GENEPIO:0100930] + description: A specimen collection device designed to penetrate soil with + a hollow tube to collect soil sample cores. + meaning: GENEPIO:0100930 + Spatula [NCIT:C149941]: + text: Spatula [NCIT:C149941] + meaning: CIT:C149941 + Sponge [OBI:0002819]: + text: Sponge [OBI:0002819] + description: A sample collection device consisting of a soft flexible, absorbent + pad usually made from natural material such as gauze or cotton, used to + absorb specimen fluid or particulate matter. + meaning: OBI:0002819 + Suction Catheter [OBI:0002831]: + text: Suction Catheter [OBI:0002831] + description: A catheter which is used to remove mucus and other secretions + from the body. + meaning: OBI:0002831 + Swab [GENEPIO:0100027]: + text: Swab [GENEPIO:0100027] + description: A device which is a soft, absorbent material mounted on one or + both ends of a stick. + meaning: GENEPIO:0100027 + Drag swab [OBI:0002822]: + text: Drag swab [OBI:0002822] + description: A specimen collection device consisting of a specimen pad made + of sterile gauze which is aseptically attached to a pole by clips or to + a string + meaning: OBI:0002822 + is_a: Swab [GENEPIO:0100027] + Surface wipe [OBI:0002824]: + text: Surface wipe [OBI:0002824] + description: A sample collection device consisting of a thin, less absorbent + sheet, used to collect material from surfaces. + meaning: OBI:0002824 + is_a: Swab [GENEPIO:0100027] + Tube [GENEPIO:0101196]: + text: Tube [GENEPIO:0101196] + description: A sample collection device which is cylindrical shape that is + open at one end, used to collect material. + meaning: GENEPIO:0101196 + Blood Collection Tube [OBI:0002859]: + text: Blood Collection Tube [OBI:0002859] + description: 'A specimen collection tube which is designed for the collection + of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection' + meaning: OBI:0002859 + is_a: Tube [GENEPIO:0101196] + Microcapillary tube [OBI:0002858]: + text: Microcapillary tube [OBI:0002858] + meaning: OBI:0002858 + is_a: Tube [GENEPIO:0101196] + Serum Collection Tube [OBI:0002860]: + text: Serum Collection Tube [OBI:0002860] + description: A specimen collection tube which is designed for collecting whole + blood and enabling the separation of serum. + meaning: OBI:0002860 + is_a: Tube [GENEPIO:0101196] + Sputum Collection Tube [OBI:0002861]: + text: Sputum Collection Tube [OBI:0002861] + description: A specimen collection tube which is designed for collecting sputum. + meaning: OBI:0002861 + is_a: Tube [GENEPIO:0101196] + Urine Collection Tube [OBI:0002862]: + text: Urine Collection Tube [OBI:0002862] + description: A specimen container which is designed for holding urine. + meaning: OBI:0002862 + is_a: Tube [GENEPIO:0101196] + Vacuum device [GENEPIO:0002127]: + text: Vacuum device [GENEPIO:0002127] + description: A device which generates a vacuum to provide suction of material. + meaning: GENEPIO:0002127 + Vacutainer [OBIB:0000032]: + text: Vacutainer [OBIB:0000032] + description: A test tube which is either a sterile glass or plastic tube with + a closure that is evacuated to create a vacuum inside the tube facilitating + the draw of a predetermined volume of liquid. Most commonly used to draw + a blood sample directly from the vein, these also are used to collect urine + samples. Vacutainer tube may contain additives designed to stabilize and + preserve the specimen prior to analytical testing. + meaning: OBIB:0000032 + is_a: Vacuum device [GENEPIO:0002127] + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection_method menu + permissible_values: + Aspiration [HP:0002835]: + text: Aspiration [HP:0002835] + description: Inspiration of a foreign object into the airway. + meaning: HP:0002835 + Biopsy [OBI:0002650]: + text: Biopsy [OBI:0002650] + description: A specimen collection that obtains a sample of tissue or cell + from a living multicellular organism body for diagnostic purposes by means + intended to be minimally invasive. + meaning: OBI:0002650 + Fecal grab [GENEPIO:0004326]: + text: Fecal grab [GENEPIO:0004326] + description: A fecal specimen collection method in which feces is obtained + by inserting the collection device into the anus of the host, or the feces + is captured as it is excreted. + meaning: GENEPIO:0004326 + Filtration [OBI:0302885]: + text: Filtration [OBI:0302885] + description: A process which separates components suspended in a fluid based + on granularity properties relying on a filter device. + meaning: OBI:0302885 + Air filtration [GENEPIO:0100031]: + text: Air filtration [GENEPIO:0100031] + description: A filtration process which removes solid particulates from the + air via an air filtration device. + meaning: GENEPIO:0100031 + is_a: Filtration [OBI:0302885] + Water filtration [GENEPIO:0100931]: + text: Water filtration [GENEPIO:0100931] + description: A filtration process which removes or reduces the concentration + of particulate matter, including suspended particles, parasites, bacteria, + algae, viruses, and fungi, as well as other undesirable chemical and biological + contaminants from contaminated water using water filters to produce safe + and clean water. + meaning: GENEPIO:0100931 + is_a: Filtration [OBI:0302885] + Lavage [OBI:0600044]: + text: Lavage [OBI:0600044] + description: A protocol application to separate cells and/or cellular secretions + from an anatomical space by the introduction and removal of fluid + meaning: OBI:0600044 + Bronchoalveolar lavage [GENEPIO:0100032]: + text: Bronchoalveolar lavage [GENEPIO:0100032] + description: The collection of bronchoalveolar lavage fluid (BAL) from the + lungs. + meaning: GENEPIO:0100032 + is_a: Lavage [OBI:0600044] + Gastric lavage [GENEPIO:0100033]: + text: Gastric lavage [GENEPIO:0100033] + description: The administration and evacuation of small volumes of liquid + through an orogastric tube to remove toxic substances within the stomach. + meaning: GENEPIO:0100033 + is_a: Lavage [OBI:0600044] + Necropsy [MMO:0000344]: + text: Necropsy [MMO:0000344] + description: A postmortem examination of the body of an animal to determine + the cause of death or the character and extent of changes produced by disease. + meaning: MMO:0000344 + Phlebotomy [NCIT:C28221]: + text: Phlebotomy [NCIT:C28221] + description: The collection of blood from a vein, most commonly via needle + venipuncture. + meaning: NCIT:C28221 + Rinsing for specimen collection [GENEPIO_0002116]: + text: Rinsing for specimen collection [GENEPIO_0002116] + description: The process of removal and collection of specimen material from + the surface of an entity by washing, or a similar application of fluids. + meaning: GENEPIO:0002116 + Scooping [GENEPIO:0100932]: + text: Scooping [GENEPIO:0100932] + description: A specimen collection process that is used to dig out an amount + of sample using a scoop. + meaning: GENEPIO:0100932 + Sediment collection [GENEPIO:0100933]: + text: Sediment collection [GENEPIO:0100933] + description: A specimen collection process that is used to collect a sediment + sample. + meaning: GENEPIO:0100933 + Soil coring [GENEPIO:0100934]: + text: Soil coring [GENEPIO:0100934] + description: A specimen collection process that is used to collect soil sample + cores. + meaning: GENEPIO:0100934 + Weep fluid collection (pouring) [GENEPIO:0101003]: + text: Weep fluid collection (pouring) [GENEPIO:0101003] + description: A specimen collection process that is used to collect weep fluid + via pouring from the source container into the sample collection device. + (e.g. bag or tube) + meaning: GENEPIO:0101003 + SampleVolumeMeasurementUnitMenu: + name: SampleVolumeMeasurementUnitMenu + title: sample_volume_measurement_unit menu + permissible_values: + microliter (uL) [UO:0000101]: + text: microliter (uL) [UO:0000101] + description: A metric unit of volume equivalent to one thousandth of a cubic + centimeter or one millionth of a liter. + meaning: UO:0000101 + milliliter (mL) [UO:0000098]: + text: milliliter (mL) [UO:0000098] + description: A metric unit of volume equivalent to one cubic centimeter or + one thousandth of a liter. + meaning: UO:0000098 + liter (L) [UO:0000099]: + text: liter (L) [UO:0000099] + description: A metric unit of volume equivalent to 1000 cubic centimeters + meaning: UO:0000099 + ResidualSampleStatusMenu: + name: ResidualSampleStatusMenu + title: residual_sample_status menu + permissible_values: + Residual sample remaining (some sample left) [GENEPIO:0101087]: + text: Residual sample remaining (some sample left) [GENEPIO:0101087] + meaning: GENEPIO:0101087 + No residual sample (sample all used) [GENEPIO:0101088]: + text: No residual sample (sample all used) [GENEPIO:0101088] + meaning: GENEPIO:0101088 + Residual sample status unkown [GENEPIO:0101089]: + text: Residual sample status unkown [GENEPIO:0101089] + meaning: GENEPIO:0101089 + PurposeOfSampling: + name: PurposeOfSampling + title: purpose of sampling + permissible_values: + Cluster/Outbreak investigation [GENEPIO:0100001]: + text: Cluster/Outbreak investigation [GENEPIO:0100001] + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. + meaning: GENEPIO:0100001 + Diagnostic testing [GENEPIO:0100002]: + text: Diagnostic testing [GENEPIO:0100002] + description: A sampling strategy in which individuals are sampled in the context + of diagnostic testing. + meaning: GENEPIO:0100002 + Environmental testing [GENEPIO:0100548]: + text: Environmental testing [GENEPIO:0100548] + description: A sampling strategy in which environments are sampled in the + context of testing for the presence of, or change in the levels of, chemicals, + pathogens or other phenomena. + meaning: GENEPIO:0100548 + Research [GENEPIO:0100003]: + text: Research [GENEPIO:0100003] + description: A sampling strategy in which samples are collected in order to + perform research. + meaning: GENEPIO:0100003 + Clinical trial [GENEPIO:0100549]: + text: Clinical trial [GENEPIO:0100549] + description: A sampling strategy in which individuals are sampled in the context + of experiments or observations performed as part of clinical research. + meaning: GENEPIO:0100549 + is_a: Research [GENEPIO:0100003] + Field experiment [GENEPIO:0100550]: + text: Field experiment [GENEPIO:0100550] + description: A sampling strategy in which samples are taken during real-life + experiments which test directly whether proposed interventions actually + work. + meaning: GENEPIO:0100550 + is_a: Research [GENEPIO:0100003] + Survey study [GENEPIO:0100582]: + text: Survey study [GENEPIO:0100582] + description: A sampling strategy in which individuals and/or materials are + sampled for surveillance performed for research purposes. + meaning: GENEPIO:0100582 + is_a: Research [GENEPIO:0100003] + Surveillance [GENEPIO:0100004]: + text: Surveillance [GENEPIO:0100004] + description: A sampling strategy in which individuals are sampled for surveillance + investigations. + meaning: GENEPIO:0100004 + PresamplingActivity: + name: PresamplingActivity + title: presampling activity + permissible_values: + Addition of substances to food/water [GENEPIO:0100536]: + text: Addition of substances to food/water [GENEPIO:0100536] + description: The addition of substances to food or water administered to an + individual or group of individuals. + meaning: GENEPIO:0100536 + Antimicrobial pre-treatment [GENEPIO:0100537]: + text: Antimicrobial pre-treatment [GENEPIO:0100537] + description: The administration of an antimicrobial agent to an individual + or its addition to a substance prior to some other event or activity. + meaning: GENEPIO:0100537 + Certified animal husbandry practices [GENEPIO:0100538]: + text: Certified animal husbandry practices [GENEPIO:0100538] + description: The implementation of animal husbandy practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100538 + Certified humane animal husbandry practices [GENEPIO:0100894]: + text: Certified humane animal husbandry practices [GENEPIO:0100894] + description: A certification organization in Washington DC that is dedicated + to improving the lives of farm animals in food production from birth through + slaughter. + meaning: GENEPIO:0100894 + is_a: Certified animal husbandry practices [GENEPIO:0100538] + Certified organic farming practices [GENEPIO:0100539]: + text: Certified organic farming practices [GENEPIO:0100539] + description: The implementation of organic farming practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100539 + Conventional farming practices [GENEPIO:0100895]: + text: Conventional farming practices [GENEPIO:0100895] + description: The implementation of farming practices that include man-made + inputs such as chemical fertilizers and genetically-modified seeds. + meaning: GENEPIO:0100895 + Change in storage conditions [GENEPIO:0100540]: + text: Change in storage conditions [GENEPIO:0100540] + description: A change in the storage conditions of a material or a substance. + meaning: GENEPIO:0100540 + Cleaning/disinfection [GENEPIO:0100541]: + text: Cleaning/disinfection [GENEPIO:0100541] + description: A process of removing unwanted substances, such as dirt, infectious + agents, and other impurities, from an object or environment. + meaning: GENEPIO:0100541 + Extended downtime between activities [GENEPIO:0100542]: + text: Extended downtime between activities [GENEPIO:0100542] + description: A prolonged period of inactivity between processes or events. + meaning: GENEPIO:0100542 + Microbial pre-treatment [GENEPIO:0100546]: + text: Microbial pre-treatment [GENEPIO:0100546] + description: The deliberate addition of microbes or a mixture of microbes + to an individual or substance prior to some other event or activity. + meaning: GENEPIO:0100546 + Probiotic pre-treatment [GENEPIO:0100547]: + text: Probiotic pre-treatment [GENEPIO:0100547] + description: The addition of a probiotic substance to an individual or material + prior to some other event or activity. + meaning: GENEPIO:0100547 + Vaccination [NCIT:C15346]: + text: Vaccination [NCIT:C15346] + description: Administration of vaccines to stimulate the host's immune response. + This includes any preparation intended for active immunological prophylaxis + or treatment. + meaning: NCIT:C15346 + SampleStorageDurationUnit: + name: SampleStorageDurationUnit + title: sample storage duration unit + permissible_values: + Second [UO:0000010]: + text: Second [UO:0000010] + description: A time unit which is equal to the duration of 9 192 631 770 periods + of the radiation corresponding to the transition between the two hyperfine + levels of the ground state of the caesium 133 atom. + meaning: UO:0000010 + Minute [UO:0000031]: + text: Minute [UO:0000031] + description: A time unit which is equal to 60 seconds. + meaning: UO:0000031 + Hour [UO:0000032]: + text: Hour [UO:0000032] + description: A time unit which is equal to 60 minutes. + meaning: UO:0000032 + Day [UO:0000033]: + text: Day [UO:0000033] + description: A time unit which is equal to 24 hours. + meaning: UO:0000033 + Week [UO:0000034]: + text: Week [UO:0000034] + description: A time unit which is equal to 7 days. + meaning: UO:0000034 + Month [UO:0000035]: + text: Month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. + meaning: UO:0000035 + Year [UO:0000036]: + text: Year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. + meaning: UO:0000036 + SpecimenProcessing: + name: SpecimenProcessing + title: specimen processing + permissible_values: + Concentration [OBI:0600041]: + text: Concentration [OBI:0600041] + description: A process used to increase the density of a material of interest + by removing other materials in the entity containing the material of interest. + meaning: OBI:0600041 + Centrifugation [OBI:0302886]: + text: Centrifugation [OBI:0302886] + description: A process separating molecules by size or density using centrifugal + forces generated by a spinning rotor. + meaning: OBI:0302886 + Filtration [OBI:0302885]: + text: Filtration [OBI:0302885] + description: A process which separates components suspended in a fluid based + on granularity properties relying on a filter device. + meaning: OBI:0302885 + Pooling specimens [OBI:0600016]: + text: Pooling specimens [OBI:0600016] + description: Physical combination of several instances of like material. + meaning: OBI:0600016 + ExperimentalSpecimenRoleType: + name: ExperimentalSpecimenRoleType + title: experimental specimen role type + permissible_values: + Positive experimental control [GENEPIO:0101018]: + text: Positive experimental control [GENEPIO:0101018] + description: A control specimen that is expected to yield a positive result, + to establish a reference baseline for an experiment. + meaning: GENEPIO:0101018 + Validation strain [GENEPIO:0101123]: + text: Validation strain [GENEPIO:0101123] + meaning: GENEPIO:0101123 + is_a: Positive experimental control [GENEPIO:0101018] + Proficiency test isolate [GENEPIO:0101124]: + text: Proficiency test isolate [GENEPIO:0101124] + meaning: GENEPIO:0101124 + is_a: Positive experimental control [GENEPIO:0101018] + Negative experimental control [GENEPIO:0101019]: + text: Negative experimental control [GENEPIO:0101019] + description: A control specimen that is expected to yield a negative result, + to establish a reference baseline for an experiment + meaning: GENEPIO:0101019 + Technical replicate [EFO:0002090]: + text: Technical replicate [EFO:0002090] + description: A technical replicate is a replicate role where the same BioSample + is use e.g. the same pool of RNA used to assess technical (as opposed to + biological) variation within an experiment. + meaning: EFO:0002090 + Biological replicate [EFO:0002091]: + text: Biological replicate [EFO:0002091] + description: A biological replicate is a replicate role that consists of independent + biological replicates made from different individual biosamples. + meaning: EFO:0002091 + Synthetic lab construct [GENEPIO:0101039]: + text: Synthetic lab construct [GENEPIO:0101039] + meaning: GENEPIO:0101039 + Negative sample [GENEPIO:0101120]: + text: Negative sample [GENEPIO:0101120] + meaning: GENEPIO:0101120 + AvailableDataTypesMenu: + name: AvailableDataTypesMenu + title: available_data_types menu + permissible_values: + Documentation [GENEPIO:0100702]: + text: Documentation [GENEPIO:0100702] + description: A dataset attribute bundle which indicates the presence of documentation + data. + meaning: GENEPIO:0100702 + Experimental parameters documentation [GENEPIO:0100703]: + text: Experimental parameters documentation [GENEPIO:0100703] + description: A documentation data tag which indicates the presence of data + that describes experimental parameters. + meaning: GENEPIO:0100703 + is_a: Documentation [GENEPIO:0100702] + Feed history [GENEPIO:0100704]: + text: Feed history [GENEPIO:0100704] + description: A documentation data tag which indicates the presence of data + that describes feed history. + meaning: GENEPIO:0100704 + is_a: Documentation [GENEPIO:0100702] + Land use information [GENEPIO:0100705]: + text: Land use information [GENEPIO:0100705] + description: A documentation data tag which indicates the presence of data + that describes land use information. + meaning: GENEPIO:0100705 + is_a: Documentation [GENEPIO:0100702] + Therapeutic administration history [GENEPIO:0100706]: + text: Therapeutic administration history [GENEPIO:0100706] + description: A documentation data tag which indicates the presence of data + that describes a history of therapeutic administration. + meaning: GENEPIO:0100706 + is_a: Documentation [GENEPIO:0100702] + Chemical characterization [GENEPIO:0100707]: + text: Chemical characterization [GENEPIO:0100707] + description: A dataset attribute bundle which indicates the presence of chemical + characterization data. + meaning: GENEPIO:0100707 + Microbiological characterization [GENEPIO:0100714]: + text: Microbiological characterization [GENEPIO:0100714] + description: A dataset attribute bundle which indicates the presence of microbiological + characterization data. + meaning: GENEPIO:0100714 + Microbiological identification [GENEPIO:0100715]: + text: Microbiological identification [GENEPIO:0100715] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data. + meaning: GENEPIO:0100715 + is_a: Microbiological characterization [GENEPIO:0100714] + Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716]: + text: Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Beckson + Dickson BBL Crystal identification system. + meaning: GENEPIO:0100716 + is_a: Microbiological identification [GENEPIO:0100715] + "Microbiological identification (bioM\xE9rieux API) [GENEPIO:0100717]": + text: "Microbiological identification (bioM\xE9rieux API) [GENEPIO:0100717]" + description: "A microbiological characterization data tag which indicates\ + \ the presence of microbiological identification data dervied using the\ + \ bioM\xE9rieux API identification system." + meaning: GENEPIO:0100717 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (Biolog) [GENEPIO:0100718]: + text: Microbiological identification (Biolog) [GENEPIO:0100718] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Biolog + identification system. + meaning: GENEPIO:0100718 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (FAME) [GENEPIO:0100719]: + text: Microbiological identification (FAME) [GENEPIO:0100719] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Fatty + acid methyl esters (FAME) identification system. + meaning: GENEPIO:0100719 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (Sensititre) [GENEPIO:0100720]: + text: Microbiological identification (Sensititre) [GENEPIO:0100720] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the Sensititre + identification system. + meaning: GENEPIO:0100720 + is_a: Microbiological identification [GENEPIO:0100715] + Microbiological identification (ViTek) [GENEPIO:0100721]: + text: Microbiological identification (ViTek) [GENEPIO:0100721] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using the ViTek + identification system. + meaning: GENEPIO:0100721 + is_a: Microbiological identification [GENEPIO:0100715] + Phage type [GENEPIO:0100722]: + text: Phage type [GENEPIO:0100722] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using phage type + identification. + meaning: GENEPIO:0100722 + is_a: Microbiological identification [GENEPIO:0100715] + Serotype [GENEPIO:0100723]: + text: Serotype [GENEPIO:0100723] + description: A microbiological characterization data tag which indicates the + presence of microbiological identification data derived using serotype identification. + meaning: GENEPIO:0100723 + is_a: Microbiological identification [GENEPIO:0100715] + Phenotypic microbiological characterization [GENEPIO:0100724]: + text: Phenotypic microbiological characterization [GENEPIO:0100724] + description: A microbiological characterization data tag which indicates the + presence of phenotypic microbiological characterization data. + meaning: GENEPIO:0100724 + is_a: Microbiological characterization [GENEPIO:0100714] + AMR phenotypic testing [GENEPIO:0100725]: + text: AMR phenotypic testing [GENEPIO:0100725] + description: A phenotypic microbiological characterization data tag which + indicates the presence of antimicrobial resistance (AMR) phenotypic testing + characterization data. + meaning: GENEPIO:0100725 + is_a: Phenotypic microbiological characterization [GENEPIO:0100724] + Biolog phenotype microarray [GENEPIO:0100726]: + text: Biolog phenotype microarray [GENEPIO:0100726] + description: A phenotypic microbiological characterization data tag which + indicates the presence of biolog phenotype microarray characterization data. + meaning: GENEPIO:0100726 + is_a: Phenotypic microbiological characterization [GENEPIO:0100724] + Microbiological quantification [GENEPIO:0100727]: + text: Microbiological quantification [GENEPIO:0100727] + description: A dataset attribute bundle which indicates the presence of microbiological + quantification data. + meaning: GENEPIO:0100727 + Colony count [GENEPIO:0100728]: + text: Colony count [GENEPIO:0100728] + description: A microbiological quantification data tag which indicates the + presence of colony count data. + meaning: GENEPIO:0100728 + is_a: Microbiological quantification [GENEPIO:0100727] + Total coliform count [GENEPIO:0100729]: + text: Total coliform count [GENEPIO:0100729] + description: A colony count microbiological quantification data tag which + indicates the presence of data that describes total colony count of coliforms. + meaning: GENEPIO:0100729 + is_a: Colony count [GENEPIO:0100728] + Total fecal coliform count [GENEPIO:0100730]: + text: Total fecal coliform count [GENEPIO:0100730] + description: A colony count microbiological quantification data tag that indicates + the presence of data which describes total colony count of fecal coliforms. + meaning: GENEPIO:0100730 + is_a: Colony count [GENEPIO:0100728] + Infectivity assay [GENEPIO:0100731]: + text: Infectivity assay [GENEPIO:0100731] + description: A microbiological quantification data tag which indicates the + presence of infectivity assay data. + meaning: GENEPIO:0100731 + is_a: Microbiological quantification [GENEPIO:0100727] + ELISA toxin binding [GENEPIO:0100732]: + text: ELISA toxin binding [GENEPIO:0100732] + description: A microbiological quantification data tag which indicates the + presence of data which describes enzyme-linked immunosorbent assay (ELISA) + toxin binding. + meaning: GENEPIO:0100732 + is_a: Microbiological quantification [GENEPIO:0100727] + Molecular characterization [GENEPIO:0100733]: + text: Molecular characterization [GENEPIO:0100733] + description: A dataset attribute bundle which indicates the presence of molecular + characterization data. + meaning: GENEPIO:0100733 + 16S rRNA Sanger sequencing [GENEPIO:0100734]: + text: 16S rRNA Sanger sequencing [GENEPIO:0100734] + description: A molecular characterization data tag which indicates the presence + of 16S rRNA Sanger sequencing characterization data. + meaning: GENEPIO:0100734 + is_a: Molecular characterization [GENEPIO:0100733] + Metagenomic sequencing [GENEPIO:0101024]: + text: Metagenomic sequencing [GENEPIO:0101024] + description: A molecular characterization data tag which indicates the presence + of metagenomic sequencing characterization data. + meaning: GENEPIO:0101024 + is_a: Molecular characterization [GENEPIO:0100733] + PCR marker detection [GENEPIO:0100735]: + text: PCR marker detection [GENEPIO:0100735] + description: A molecular characterization data tag which indicates the presence + of polymerase chain reaction (PCR) marker detection characterization data. + meaning: GENEPIO:0100735 + is_a: Molecular characterization [GENEPIO:0100733] + BOX PCR fingerprint [GENEPIO:0100736]: + text: BOX PCR fingerprint [GENEPIO:0100736] + description: A PCR marker detection characterization data tag which indicates + the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR + fingerprint data. + meaning: GENEPIO:0100736 + is_a: PCR marker detection [GENEPIO:0100735] + ERIC PCR fingerprint [GENEPIO:0100737]: + text: ERIC PCR fingerprint [GENEPIO:0100737] + description: A PCR marker detection characterization data tag which indicates + the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR + fingerprint data. + meaning: GENEPIO:0100737 + is_a: PCR marker detection [GENEPIO:0100735] + Plasmid type [GENEPIO:0100738]: + text: Plasmid type [GENEPIO:0100738] + description: A molecular characterization data tag which indicates the presence + of plasmid type characterization data. + meaning: GENEPIO:0100738 + is_a: Molecular characterization [GENEPIO:0100733] + Ribotype [GENEPIO:0100739]: + text: Ribotype [GENEPIO:0100739] + description: A molecular characterization data tag which indicates the presence + of ribotype characterization data. + meaning: GENEPIO:0100739 + is_a: Molecular characterization [GENEPIO:0100733] + Molecular quantification [GENEPIO:0100740]: + text: Molecular quantification [GENEPIO:0100740] + description: A dataset attribute bundle which indicates the presence of molecular + quantification data. + meaning: GENEPIO:0100740 + qPCR marker organism quantification [GENEPIO:0100741]: + text: qPCR marker organism quantification [GENEPIO:0100741] + description: A molecular quantification data tag which indicates the presence + of quantitative polymerase chain reaction (qPCR) marker organism quantification + data. + meaning: GENEPIO:0100741 + is_a: Molecular quantification [GENEPIO:0100740] + Physical characterization [GENEPIO:0100742]: + text: Physical characterization [GENEPIO:0100742] + description: A dataset attribute bundle which indicates the presence of physical + characterization data. + meaning: GENEPIO:0100742 + Conductivity measurement [GENEPIO:0100743]: + text: Conductivity measurement [GENEPIO:0100743] + description: A physical characterization data tag which indicates the presence + of data that describes conductivity measurement characterization. + meaning: GENEPIO:0100743 + is_a: Physical characterization [GENEPIO:0100742] + Mollusc shell measurement [GENEPIO:0100744]: + text: Mollusc shell measurement [GENEPIO:0100744] + description: A physical characterization data tag which indicates the presence + of data that describes a measurement of a mollusc shell. + meaning: GENEPIO:0100744 + is_a: Physical characterization [GENEPIO:0100742] + Matter compostion [GENEPIO:0100746]: + text: Matter compostion [GENEPIO:0100746] + description: A physical characterization data tag which indicates the presence + of matter compostion characterization data. + meaning: GENEPIO:0100746 + is_a: Physical characterization [GENEPIO:0100742] + Dry matter composition [GENEPIO:0100747]: + text: Dry matter composition [GENEPIO:0100747] + description: A matter composition characterization data tag which indicates + the presence of data that describes dry matter composition. + meaning: GENEPIO:0100747 + is_a: Matter compostion [GENEPIO:0100746] + Organic matter composition [GENEPIO:0100748]: + text: Organic matter composition [GENEPIO:0100748] + description: A matter composition characterization data tag which indicates + the presence of data that describes organic matter composition. + meaning: GENEPIO:0100748 + is_a: Matter compostion [GENEPIO:0100746] + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu + permissible_values: + Bird [NCBITaxon:8782]: + text: Bird [NCBITaxon:8782] + description: A group of warm-blooded vertebrates in class Aves, that are characterized + by feathers, wings, toothless beaked jaws and the laying of hard-shelled + eggs and are usually able to fly. + meaning: NCBITaxon:8782 + Chicken [NCBITaxon:9031]: + text: Chicken [NCBITaxon:9031] + description: A domesticated junglefowl of the species Gallus gallus. + meaning: NCBITaxon:9031 + is_a: Bird [NCBITaxon:8782] + Seabird [FOODON:00004504]: + text: Seabird [FOODON:00004504] + description: A bird that is adapted to live within the marine environment. + meaning: FOODON:00004504 + is_a: Bird [NCBITaxon:8782] + Cormorant [NCBITaxon:9206]: + text: Cormorant [NCBITaxon:9206] + description: A family of aquatic birds (Phalacrocoracidae). + meaning: NCBITaxon:9206 + is_a: Seabird [FOODON:00004504] + Double Crested Cormorant [NCBITaxon:56069]: + text: Double Crested Cormorant [NCBITaxon:56069] + description: A species of the cormorant family of water birds (Phalacrocorax + auritus). + meaning: NCBITaxon:56069 + is_a: Cormorant [NCBITaxon:9206] + Crane [NCBITaxon:9109]: + text: Crane [NCBITaxon:9109] + description: A family of large, long-legged, and long-necked birds (Gruidae). + meaning: NCBITaxon:9109 + is_a: Seabird [FOODON:00004504] + Whooping Crane [NCBITaxon:9117]: + text: Whooping Crane [NCBITaxon:9117] + description: An endangered crane species that is native to North America and + is named for its whooping sound. + meaning: NCBITaxon:9117 + is_a: Crane [NCBITaxon:9109] + Gull (Seagull) [NCBITaxon:8911]: + text: Gull (Seagull) [NCBITaxon:8911] + description: A large genus of gulls within the family Laridae. + meaning: NCBITaxon:8911 + is_a: Seabird [FOODON:00004504] + Glaucous-winged Gull [NCBITaxon:119606]: + text: Glaucous-winged Gull [NCBITaxon:119606] + description: A species of large, white-headed gull (Larus glaucescens). + meaning: NCBITaxon:119606 + is_a: Gull (Seagull) [NCBITaxon:8911] + Great Black-backed Gull [NCBITaxon:8912]: + text: Great Black-backed Gull [NCBITaxon:8912] + description: A species of white gull that has a black back and wings (Larus + marinus). + meaning: NCBITaxon:8912 + is_a: Gull (Seagull) [NCBITaxon:8911] + Herring Gull [NCBITaxon:35669]: + text: Herring Gull [NCBITaxon:35669] + description: A species of large gull, that is up to 66 cm (26 in) long (Larus + argentatus). + meaning: NCBITaxon:35669 + is_a: Gull (Seagull) [NCBITaxon:8911] + Ring-billed Gull [NCBITaxon:126683]: + text: Ring-billed Gull [NCBITaxon:126683] + description: A species of ring-billed gull that has a black ring around its + bill (Larus delawarensis). + meaning: NCBITaxon:126683 + is_a: Gull (Seagull) [NCBITaxon:8911] + Eider [NCBITaxon:50366]: + text: Eider [NCBITaxon:50366] + description: A genus of large seaducks (Somateria). + meaning: NCBITaxon:50366 + is_a: Seabird [FOODON:00004504] + Common Eider [NCBITaxon:76058]: + text: Common Eider [NCBITaxon:76058] + description: A species of a large sea-duck that is distributed over the northern + coasts of Europe, North America and eastern Siberia (Somateria mollissima). + meaning: NCBITaxon:76058 + is_a: Eider [NCBITaxon:50366] + Turkey [NCBITaxon:9103]: + text: Turkey [NCBITaxon:9103] + description: A large, mainly domesticated game bird characterized by a bald + head and wattles (in the male) of the species Meleagris gallopavo. + meaning: NCBITaxon:9103 + is_a: Bird [NCBITaxon:8782] + Fish [FOODON:03411222]: + text: Fish [FOODON:03411222] + description: Fish are the gill-bearing aquatic craniate animals that lack + limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing + their body temperatures to vary as ambient temperatures change, though some + of the large active swimmers like white shark and tuna can hold a higher + core temperature. + meaning: FOODON:03411222 + Mammal [FOODON:03411134]: + text: Mammal [FOODON:03411134] + description: Mammals (from Latin mamma "breast") are vertebrate animals constituting + the class Mammalia, and characterized by the presence of mammary glands + which in females produce milk for feeding (nursing) their young, a neocortex + (a region of the brain), fur or hair, and three middle ear bones. + meaning: FOODON:03411134 + Companion animal [FOODON:03000300]: + text: Companion animal [FOODON:03000300] + description: An animal that is kept as a companion. + meaning: FOODON:03000300 + is_a: Mammal [FOODON:03411134] + Cow [NCBITaxon:9913]: + text: Cow [NCBITaxon:9913] + description: A group of large, domesticated, cloven-hooved herbivores. + meaning: NCBITaxon:9913 + is_a: Mammal [FOODON:03411134] + Deer [NCBITaxon:9850]: + text: Deer [NCBITaxon:9850] + meaning: NCBITaxon:9850 + is_a: Mammal [FOODON:03411134] + Human [NCBITaxon:9606]: + text: Human [NCBITaxon:9606] + description: A bipedal primate mammal of the species Homo sapiens. + meaning: NCBITaxon:9606 + is_a: Mammal [FOODON:03411134] + Pig [NCBITaxon:9823]: + text: Pig [NCBITaxon:9823] + description: A stout-bodied, hooved and short-legged, omnivorous mammal from + the species Sus scofus, with thick skin usually sparsely coated with short + bristles. + meaning: NCBITaxon:9823 + is_a: Mammal [FOODON:03411134] + Sheep [NCBITaxon:9940]: + text: Sheep [NCBITaxon:9940] + description: A domesticated, even-toed, ungluate, ruminant mammal typically + kept as livestock for its wool and meat, usually of the species Ovis aries. + meaning: NCBITaxon:9940 + is_a: Mammal [FOODON:03411134] + Shellfish [FOODON:03411433]: + text: Shellfish [FOODON:03411433] + description: The term shellfish is used both broadly and specifically. For + regulatory purposes it is often narrowly defined as filter-feeding molluscs + such as clams, mussels, and oyster to the exclusion of crustaceans and all + else. Although their shells may differ, all shellfish are invertebrates. + meaning: FOODON:03411433 + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu + permissible_values: + Anoplopoma fimbria [NCBITaxon:229290]: + text: Anoplopoma fimbria [NCBITaxon:229290] + description: One of two members of the fish family Anoplopomatidae and the + only species in the genus Anoplopoma. + meaning: NCBITaxon:229290 + Bos taurus [NCBITaxon:9913]: + text: Bos taurus [NCBITaxon:9913] + description: A group of large, domesticated, cloven-hooved herbivores. + meaning: NCBITaxon:9913 + Crassostrea virginica [NCBITaxon:6565]: + text: Crassostrea virginica [NCBITaxon:6565] + description: A species of true oyster (Crassostrea virginica). + meaning: NCBITaxon:6565 + Gallus gallus [NCBITaxon:9031]: + text: Gallus gallus [NCBITaxon:9031] + description: A domesticated junglefowl of the species Gallus gallus. + meaning: NCBITaxon:9031 + Grus americana [NCBITaxon:9117]: + text: Grus americana [NCBITaxon:9117] + description: An endangered crane species that is native to North America and + is named for its whooping sound. + meaning: NCBITaxon:9117 + Homarus americanus [NCBITaxon:6706]: + text: Homarus americanus [NCBITaxon:6706] + description: A species of lobster that is found on the Atlantic coast of North + America (Homarus americanus). + meaning: NCBITaxon:6706 + Homo sapiens [NCBITaxon:9606]: + text: Homo sapiens [NCBITaxon:9606] + description: A bipedal primate mammal of the species Homo sapiens. + meaning: NCBITaxon:9606 + Larus argentatus [NCBITaxon:35669]: + text: Larus argentatus [NCBITaxon:35669] + description: A species of large gull, that is up to 66 cm (26 in) long (Larus + argentatus). + meaning: NCBITaxon:35669 + Larus delawarensis [NCBITaxon:126683]: + text: Larus delawarensis [NCBITaxon:126683] + description: A species of ring-billed gull that has a black ring around its + bill (Larus delawarensis). + meaning: NCBITaxon:126683 + Larus glaucescens [NCBITaxon:119606]: + text: Larus glaucescens [NCBITaxon:119606] + description: A species of large, white-headed gull (Larus glaucescens). + meaning: NCBITaxon:119606 + Larus marinus [NCBITaxon:8912]: + text: Larus marinus [NCBITaxon:8912] + description: A species of white gull that has a black back and wings (Larus + marinus). + meaning: NCBITaxon:8912 + Meleagris gallopavo [NCBITaxon:9103]: + text: Meleagris gallopavo [NCBITaxon:9103] + description: A large, mainly domesticated game bird characterized by a bald + head and wattles (in the male) of the species Meleagris gallopavo. + meaning: NCBITaxon:9103 + Mytilus edulis [NCBITaxon:6550]: + text: Mytilus edulis [NCBITaxon:6550] + description: A medium-sized edible marine bivalve mollusc in the family Mytilidae, + the mussels. + meaning: NCBITaxon:6550 + Oncorhynchus kisutch [NCBITaxon:8019]: + text: Oncorhynchus kisutch [NCBITaxon:8019] + description: A species of pacific salmon in North America, that is commonly + called as coho salmon. + meaning: NCBITaxon:8019 + Oncorhynchus mykiss [NCBITaxon:8022]: + text: Oncorhynchus mykiss [NCBITaxon:8022] + description: A species of trout native to cold-water tributaries of the Pacific + Ocean in Asia and North America (Oncorhynchus mykiss). + meaning: NCBITaxon:8022 + Oncorhynchus tshawytscha [NCBITaxon:74940]: + text: Oncorhynchus tshawytscha [NCBITaxon:74940] + description: The largest species of pacific salmon in North America (Oncorhynchus + tshawytscha). + meaning: NCBITaxon:74940 + Ovis aries [NCBITaxon:9940]: + text: Ovis aries [NCBITaxon:9940] + description: A domesticated, even-toed, ungluate, ruminant mammal typically + kept as livestock for its wool and meat, usually of the species Ovis aries. + meaning: NCBITaxon:9940 + Phalacrocorax auritus [NCBITaxon:56069]: + text: Phalacrocorax auritus [NCBITaxon:56069] + description: A species of the cormorant family of water birds (Phalacrocorax + auritus). + meaning: NCBITaxon:56069 + Salmo salar [NCBITaxon:8030]: + text: Salmo salar [NCBITaxon:8030] + description: A species of ray-finned fish in the family Salmonidae (Salmo + salar). + meaning: NCBITaxon:8030 + Somateria mollissima [NCBITaxon:76058]: + text: Somateria mollissima [NCBITaxon:76058] + description: A species of a large sea-duck that is distributed over the northern + coasts of Europe, North America and eastern Siberia (Somateria mollissima). + meaning: NCBITaxon:76058 + Sus scrofa domesticus [NCBITaxon:9825]: + text: Sus scrofa domesticus [NCBITaxon:9825] + description: A stout-bodied, hooved and short-legged, omnivorous mammal, with + thick skin usually sparsely coated with short bristles raised for its meat. + meaning: NCBITaxon:9825 + HostFoodProductionNameMenu: + name: HostFoodProductionNameMenu + title: host (food production name) menu + permissible_values: + Cow (by age/production stage) (organizational term): + text: Cow (by age/production stage) (organizational term) + Calf [FOODON:03411349]: + text: Calf [FOODON:03411349] + description: Calves are the young of domestic cattle. Calves are reared to + become adult cattle, or are slaughtered for their meat, called veal. + meaning: FOODON:03411349 + is_a: Cow (by age/production stage) (organizational term) + Dry cow [FOODON:00004411]: + text: Dry cow [FOODON:00004411] + description: A cow that is in a stage of its lactation cycle where milk production + ceases prior to calving. + meaning: FOODON:00004411 + is_a: Cow (by age/production stage) (organizational term) + Feeder cow [FOODON:00004292]: + text: Feeder cow [FOODON:00004292] + description: A young cow mature enough either to undergo backgrounding or + to be fattened in preparation for slaughter. + meaning: FOODON:00004292 + is_a: Cow (by age/production stage) (organizational term) + Finisher cow [FOODON:00004293]: + text: Finisher cow [FOODON:00004293] + meaning: FOODON:00004293 + is_a: Cow (by age/production stage) (organizational term) + Milker cow [FOODON:03411201]: + text: Milker cow [FOODON:03411201] + description: A cow that is bred specifically for milk production. + meaning: FOODON:03411201 + is_a: Cow (by age/production stage) (organizational term) + Stocker cow [FOODON:00004294]: + text: Stocker cow [FOODON:00004294] + description: A type of cow that has been weaned and is being fed in a way + to add physical bulk to its body. + meaning: FOODON:00004294 + is_a: Cow (by age/production stage) (organizational term) + Weanling cow [FOODON:00004295]: + text: Weanling cow [FOODON:00004295] + description: A type of young cow that has been weaned and consumes solid food. + meaning: FOODON:00004295 + is_a: Cow (by age/production stage) (organizational term) + Cow (by sex/reproductive stage) (organizational term): + text: Cow (by sex/reproductive stage) (organizational term) + Bull [FOODON:00000015]: + text: Bull [FOODON:00000015] + description: A cattle bull is an adult "intact" (i.e. not castrated) male + of a cattle species. + meaning: FOODON:00000015 + is_a: Cow (by sex/reproductive stage) (organizational term) + Cow [NCBITaxon:9913]: + text: Cow [NCBITaxon:9913] + description: A group of large, domesticated, cloven-hooved herbivores. + meaning: NCBITaxon:9913 + is_a: Cow (by sex/reproductive stage) (organizational term) + Freemartin [FOODON:00004296]: + text: Freemartin [FOODON:00004296] + description: A cow that is genetically female, but has many characteristics + of a male and is usually infertile. + meaning: FOODON:00004296 + is_a: Cow (by sex/reproductive stage) (organizational term) + Heifer [FOODON:00002518]: + text: Heifer [FOODON:00002518] + description: A heifer is a young female, under three years of age, of a cattle + species before she has had a calf of her own. + meaning: FOODON:00002518 + is_a: Cow (by sex/reproductive stage) (organizational term) + Steer [FOODON:00002531]: + text: Steer [FOODON:00002531] + description: A cattle steer is an adult castrated male of a cattle species. + meaning: FOODON:00002531 + is_a: Cow (by sex/reproductive stage) (organizational term) + Pig (by age/production stage) (organizational term): + text: Pig (by age/production stage) (organizational term) + Finisher pig [FOODON:00003371]: + text: Finisher pig [FOODON:00003371] + description: A grower pig over 70 kg (150 lb) liveweight. + meaning: FOODON:00003371 + is_a: Pig (by age/production stage) (organizational term) + Grower pig [FOODON:00003370]: + text: Grower pig [FOODON:00003370] + description: A pig between weaning and sale or transfer to the breeding herd, + sold for slaughter or killed for rations. + meaning: FOODON:00003370 + is_a: Pig (by age/production stage) (organizational term) + Nursing pig [FOODON:00004297 ]: + text: Nursing pig [FOODON:00004297 ] + meaning: OODON:00004297 + is_a: Pig (by age/production stage) (organizational term) + Pig [NCBITaxon:9823]: + text: Pig [NCBITaxon:9823] + description: A stout-bodied, hooved and short-legged, omnivorous mammal from + the species Sus scofus, with thick skin usually sparsely coated with short + bristles. + meaning: NCBITaxon:9823 + is_a: Pig (by age/production stage) (organizational term) + Piglet [FOODON:00003952]: + text: Piglet [FOODON:00003952] + description: An unweaned or immature pig. + meaning: FOODON:00003952 + is_a: Pig (by age/production stage) (organizational term) + Weanling (weaner) pig [FOODON:00003373]: + text: Weanling (weaner) pig [FOODON:00003373] + description: A young pig recently separated from the sow + meaning: FOODON:00003373 + is_a: Pig (by age/production stage) (organizational term) + Pig (by sex/reproductive stage) (organizational term): + text: Pig (by sex/reproductive stage) (organizational term) + Barrow [FOODON:03411280]: + text: Barrow [FOODON:03411280] + description: A male swine castrated before sexual maturity. + meaning: FOODON:03411280 + is_a: Pig (by sex/reproductive stage) (organizational term) + Boar [FOODON:03412248]: + text: Boar [FOODON:03412248] + description: An adult male swine. + meaning: FOODON:03412248 + is_a: Pig (by sex/reproductive stage) (organizational term) + Gilt [FOODON:00003369]: + text: Gilt [FOODON:00003369] + description: A female pig under the age of 1 year. The term is also often + used to refer to a pig who has not farrowed, or given birth to a litter. + meaning: FOODON:00003369 + is_a: Pig (by sex/reproductive stage) (organizational term) + Sow [FOODON:00003333]: + text: Sow [FOODON:00003333] + description: An adult female swine. + meaning: FOODON:00003333 + is_a: Pig (by sex/reproductive stage) (organizational term) + Poultry or game bird [FOODON:03411563]: + text: Poultry or game bird [FOODON:03411563] + description: Domesticated birds kept by humans for their eggs, their meat + or their feathers. + meaning: FOODON:03411563 + Broiler or fryer chicken [FOODON:03411198]: + text: Broiler or fryer chicken [FOODON:03411198] + description: A chicken younger than 10 weeks old (previously younger than + 13 weeks), of either sex, that is tender-meated with soft, pliable, smooth-textured + skin and flexible breastbone cartilage. + meaning: FOODON:03411198 + is_a: Poultry or game bird [FOODON:03411563] + Capon [FOODON:03411711]: + text: Capon [FOODON:03411711] + description: A surgically neutered male chicken younger than four months old + (previously younger than eight months) that is tender-meated with soft, + pliable, smooth-textured skin. + meaning: FOODON:03411711 + is_a: Poultry or game bird [FOODON:03411563] + Chick [FOODON:00004299]: + text: Chick [FOODON:00004299] + description: A young offspring of any bird. + meaning: FOODON:00004299 + is_a: Poultry or game bird [FOODON:03411563] + Chicken [NCBITaxon:9031]: + text: Chicken [NCBITaxon:9031] + description: A domesticated junglefowl of the species Gallus gallus. + meaning: NCBITaxon:9031 + is_a: Poultry or game bird [FOODON:03411563] + Egg [UBERON:0007379]: + text: Egg [UBERON:0007379] + description: 'The hard-shelled reproductive body produced by a bird (especially + by the common domestic chicken) or a reptile; also: its contents used as + food.' + meaning: UBERON:0007379 + is_a: Poultry or game bird [FOODON:03411563] + Hatchling [FOODON:00004300]: + text: Hatchling [FOODON:00004300] + description: A young animal that has recently emerged from its egg. + meaning: FOODON:00004300 + is_a: Poultry or game bird [FOODON:03411563] + Hen [FOODON:00003282]: + text: Hen [FOODON:00003282] + description: An adult female chicken. + meaning: FOODON:00003282 + is_a: Poultry or game bird [FOODON:03411563] + Layer chicken [FOODON:00004301]: + text: Layer chicken [FOODON:00004301] + description: A type of chicken kept for laying eggs. + meaning: FOODON:00004301 + is_a: Poultry or game bird [FOODON:03411563] + Layer turkey [FOODON:00004302]: + text: Layer turkey [FOODON:00004302] + description: A type of turkey kept for laying eggs. + meaning: FOODON:00004302 + is_a: Poultry or game bird [FOODON:03411563] + Poult [FOODON:00002962]: + text: Poult [FOODON:00002962] + description: A poult is a young domestic chicken, turkey, pheasant, or other + fowl being raised for food. + meaning: FOODON:00002962 + is_a: Poultry or game bird [FOODON:03411563] + Pullet [FOODON:00004303]: + text: Pullet [FOODON:00004303] + description: A young hen, especially one less than one year old. + meaning: FOODON:00004303 + is_a: Poultry or game bird [FOODON:03411563] + Rooster [FOODON:03411714]: + text: Rooster [FOODON:03411714] + description: A mature male chicken with coarse skin, toughened and darkened + meat, and hardened breastbone tip. + meaning: FOODON:03411714 + is_a: Poultry or game bird [FOODON:03411563] + Tom (Gobbler) [FOODON:00004304 ]: + text: Tom (Gobbler) [FOODON:00004304 ] + meaning: OODON:00004304 + is_a: Poultry or game bird [FOODON:03411563] + Turkey [NCBITaxon:9103]: + text: Turkey [NCBITaxon:9103] + description: A large, mainly domesticated game bird characterized by a bald + head and wattles (in the male) of the species Meleagris gallopavo. + meaning: NCBITaxon:9103 + is_a: Poultry or game bird [FOODON:03411563] + Sheep [NCBITaxon:9940]: + text: Sheep [NCBITaxon:9940] + description: A domesticated, even-toed, ungluate, ruminant mammal typically + kept as livestock for its wool and meat, usually of the species Ovis aries. + meaning: NCBITaxon:9940 + Ram [FOODON:00004305]: + text: Ram [FOODON:00004305] + description: An adult male sheep kept for breeding and for wool production. + meaning: FOODON:00004305 + is_a: Sheep [NCBITaxon:9940] + Wether sheep [FOODON:00004306]: + text: Wether sheep [FOODON:00004306] + description: A castrated male sheep. + meaning: FOODON:00004306 + is_a: Sheep [NCBITaxon:9940] + Ewe [FOODON:03412610]: + text: Ewe [FOODON:03412610] + description: A ewe is a female sheep. + meaning: FOODON:03412610 + is_a: Sheep [NCBITaxon:9940] + Lamb [FOODON:03411669]: + text: Lamb [FOODON:03411669] + description: A whole lamb or some material processed from a lamb. + meaning: FOODON:03411669 + is_a: Sheep [NCBITaxon:9940] + Fish [FOODON:03411222]: + text: Fish [FOODON:03411222] + description: Fish are the gill-bearing aquatic craniate animals that lack + limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing + their body temperatures to vary as ambient temperatures change, though some + of the large active swimmers like white shark and tuna can hold a higher + core temperature. + meaning: FOODON:03411222 + Fish egg [FOODON_00004319]: + text: Fish egg [FOODON_00004319] + description: An egg or spawn of a fish that is contained within or separated + from the ovary. + meaning: FOODON:00004319 + is_a: Fish [FOODON:03411222] + Fry (fish) [FOODON_00004318]: + text: Fry (fish) [FOODON_00004318] + description: A fish that is recently hatched and has reached the stage where + its yolk-sac has almost disappeared and its swim bladder is operational + to the point where the fish can actively feed for itself. + meaning: FOODON:00004318 + is_a: Fish [FOODON:03411222] + Juvenile fish [FOODON_00004317]: + text: Juvenile fish [FOODON_00004317] + description: A fish that has not reached to sexual maturity. + meaning: FOODON:00004317 + is_a: Fish [FOODON:03411222] + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host_age_unit menu + permissible_values: + month [UO:0000035]: + text: month [UO:0000035] + description: A time unit which is equal to approximately 4-4.5 weeks or 28-31 + days. + meaning: UO:0000035 + year [UO:0000036]: + text: year [UO:0000036] + description: A time unit which is equal to 365 days, or 366 days during a + leap year. + meaning: UO:0000036 + HostAgeBinMenu: + name: HostAgeBinMenu + title: host_age_bin menu + permissible_values: + First winter [GENEPIO:0100684]: + text: First winter [GENEPIO:0100684] + description: An age group used to classify birds identified by their first + winter nonbreeding plumage, generally indicating a juvenile bird. + meaning: GENEPIO:0100684 + First summer [GENEPIO:0100685]: + text: First summer [GENEPIO:0100685] + description: An age group used to classify birds identified by their first + summer nonbreeding plumage, generally indicating a juvenile bird. + meaning: GENEPIO:0100685 + Second winter [GENEPIO:0100686]: + text: Second winter [GENEPIO:0100686] + description: An age group used to classify birds identified by their second + winter plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100686 + Second summer [GENEPIO:0100687]: + text: Second summer [GENEPIO:0100687] + description: An age group used to classify birds identified by their second + summer plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100687 + Third winter [GENEPIO:0100688]: + text: Third winter [GENEPIO:0100688] + description: An age group used to classify birds identified by their third + winter plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100688 + Third summer [GENEPIO:0100689]: + text: Third summer [GENEPIO:0100689] + description: An age group used to classify birds identified by their third + summer plumage (many types of birds molt several times during the same season). + meaning: GENEPIO:0100689 + 0 - 9 [GENEPIO:0100049]]: + text: 0 - 9 [GENEPIO:0100049]] + meaning: ENEPIO:0100049 + 10 - 19 [GENEPIO:0100050]: + text: 10 - 19 [GENEPIO:0100050] + description: An age group that stratifies the age of a case to be between + 10 to 19 years old (inclusive). + meaning: GENEPIO:0100050 + 20 - 29 [GENEPIO:0100051]: + text: 20 - 29 [GENEPIO:0100051] + description: An age group that stratifies the age of a case to be between + 20 to 29 years old (inclusive). + meaning: GENEPIO:0100051 + 30 - 39 [GENEPIO:0100052]: + text: 30 - 39 [GENEPIO:0100052] + description: An age group that stratifies the age of a case to be between + 30 to 39 years old (inclusive). + meaning: GENEPIO:0100052 + 40 - 49 [GENEPIO:0100053]: + text: 40 - 49 [GENEPIO:0100053] + description: An age group that stratifies the age of a case to be between + 40 to 49 years old (inclusive). + meaning: GENEPIO:0100053 + 50 - 59 [GENEPIO:0100054]: + text: 50 - 59 [GENEPIO:0100054] + description: An age group that stratifies the age of a case to be between + 50 to 59 years old (inclusive). + meaning: GENEPIO:0100054 + 60 - 69 [GENEPIO:0100055]: + text: 60 - 69 [GENEPIO:0100055] + description: An age group that stratifies the age of a case to be between + 60 to 69 years old (inclusive). + meaning: GENEPIO:0100055 + 70 - 79 [GENEPIO:0100056]: + text: 70 - 79 [GENEPIO:0100056] + description: An age group that stratifies the age of a case to be between + 70 to 79 years old (inclusive). + meaning: GENEPIO:0100056 + 80 - 89 [GENEPIO:0100057]: + text: 80 - 89 [GENEPIO:0100057] + description: An age group that stratifies the age of a case to be between + 80 to 89 years old (inclusive). + meaning: GENEPIO:0100057 + 90 - 99 [GENEPIO:0100058]: + text: 90 - 99 [GENEPIO:0100058] + description: An age group that stratifies the age of a case to be between + 90 to 99 years old (inclusive). + meaning: GENEPIO:0100058 + 100+ [GENEPIO:0100059]: + text: 100+ [GENEPIO:0100059] + description: An age group that stratifies the age of a case to be greater + than or equal to 100 years old. + meaning: GENEPIO:0100059 + HostGender: + name: HostGender + title: host_gender + permissible_values: + Female [NCIT:C46110]: + text: Female [NCIT:C46110] + description: An individual who reports belonging to the cultural gender role + distinction of female. + meaning: NCIT:C46110 + Male [NCIT:C46109]: + text: Male [NCIT:C46109] + description: An individual who reports belonging to the cultural gender role + distinction of male. + meaning: NCIT:C46109 + Non-binary gender [GSSO:000132]: + text: Non-binary gender [GSSO:000132] + description: Either, a specific gender identity which is not male or female; + or, more broadly, an umbrella term for gender identities not considered + male or female. + meaning: GSSO:000132 + Transgender (assigned male at birth) [GSSO:004004]: + text: Transgender (assigned male at birth) [GSSO:004004] + description: Having a feminine gender (identity) which is different from the + sex one was assigned at birth. + meaning: GSSO:004004 + Transgender (assigned female at birth) [GSSO:004005]: + text: Transgender (assigned female at birth) [GSSO:004005] + description: Having a masculine gender (identity) which is different from + the sex one was assigned at birth. + meaning: GSSO:004005 + Undeclared [NCIT:C110959]: + text: Undeclared [NCIT:C110959] + meaning: CIT:C110959 + HostDiseaseMenu: + name: HostDiseaseMenu + title: host_disease menu + permissible_values: + Highly pathogenic avian influenza A (HPAI): + text: Highly pathogenic avian influenza A (HPAI) + HostHealthStateMenu: + name: HostHealthStateMenu + title: host_health_state menu + permissible_values: + Asymptomatic [NCIT:C3833]: + text: Asymptomatic [NCIT:C3833] + description: Without clinical signs or indications that raise the possibility + of a particular disorder or dysfunction. + meaning: NCIT:C3833 + Deceased [NCIT:C28554]: + text: Deceased [NCIT:C28554] + description: The cessation of life. + meaning: NCIT:C28554 + Healthy [NCIT:C115935]: + text: Healthy [NCIT:C115935] + meaning: CIT:C115935 + Recovered [NCIT:C49498]: + text: Recovered [NCIT:C49498] + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. + meaning: NCIT:C49498 + Symptomatic [NCIT:C25269]: + text: Symptomatic [NCIT:C25269] + description: Exhibiting the symptoms of a particular disease. + meaning: NCIT:C25269 + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu + title: host_health_status_details menu + permissible_values: + Hospitalized [NCIT:C25179]: + text: Hospitalized [NCIT:C25179] + description: The condition of being treated as a patient in a hospital. + meaning: NCIT:C25179 + Hospitalized (Non-ICU) [GENEPIO:0100045]: + text: Hospitalized (Non-ICU) [GENEPIO:0100045] + description: The condition of being treated as a patient in a hospital without + admission to an intensive care unit (ICU). + meaning: GENEPIO:0100045 + is_a: Hospitalized [NCIT:C25179] + Hospitalized (ICU) [GENEPIO:0100046]: + text: Hospitalized (ICU) [GENEPIO:0100046] + description: The condition of being treated as a patient in a hospital intensive + care unit (ICU). + meaning: GENEPIO:0100046 + is_a: Hospitalized [NCIT:C25179] + Mechanical Ventilation [NCIT:C70909]: + text: Mechanical Ventilation [NCIT:C70909] + meaning: NCIT:C70909 + Medically Isolated [GENEPIO:0100047]: + text: Medically Isolated [GENEPIO:0100047] + description: Separation of people with a contagious disease from population + to reduce the spread of the disease. + meaning: GENEPIO:0100047 + Medically Isolated (Negative Pressure) [GENEPIO:0100048]: + text: Medically Isolated (Negative Pressure) [GENEPIO:0100048] + description: 'Medical isolation in a negative pressure environment: 6 to 12 + air exchanges per hour, and direct exhaust to the outside or through a high + efficiency particulate air filter.' + meaning: GENEPIO:0100048 + is_a: Medically Isolated [GENEPIO:0100047] + Self-quarantining [NCIT:C173768]: + text: Self-quarantining [NCIT:C173768] + meaning: CIT:C173768 + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu + title: host_health_outcome menu + permissible_values: + Deceased [NCIT:C28554]: + text: Deceased [NCIT:C28554] + description: The cessation of life. + meaning: NCIT:C28554 + Deteriorating [NCIT:C25254]: + text: Deteriorating [NCIT:C25254] + description: Advancing in extent or severity. + meaning: NCIT:C25254 + Recovered [NCIT:C49498]: + text: Recovered [NCIT:C49498] + description: One of the possible results of an adverse event outcome that + indicates that the event has improved or recuperated. + meaning: NCIT:C49498 + Stable [NCIT:C30103]: + text: Stable [NCIT:C30103] + description: Subject to little fluctuation; showing little if any change. + meaning: NCIT:C30103 + SignsAndSymptomsMenu: + name: SignsAndSymptomsMenu + title: signs_and_symptoms menu + permissible_values: + Abnormal lung auscultation [HP:0030829]: + text: Abnormal lung auscultation [HP:0030829] + meaning: HP:0030829 + Acute Respiratory Distress Syndrome [HP:0033677]: + text: Acute Respiratory Distress Syndrome [HP:0033677] + meaning: HP:0033677 + Altered mental status [HP:0011446]: + text: Altered mental status [HP:0011446] + meaning: HP:0011446 + Cognitive impairment [HP:0100543]: + text: Cognitive impairment [HP:0100543] + meaning: HP:0100543 + is_a: Altered mental status [HP:0011446] + Coma [HP:0001259]: + text: Coma [HP:0001259] + meaning: HP:0001259 + is_a: Altered mental status [HP:0011446] + Confusion [HP:0001289]: + text: Confusion [HP:0001289] + meaning: HP:0001289 + is_a: Altered mental status [HP:0011446] + Delirium (sudden severe confusion) [HP:0031258]: + text: Delirium (sudden severe confusion) [HP:0031258] + meaning: HP:0031258 + is_a: Confusion [HP:0001289] + Arrhythmia [HP:0011675]: + text: Arrhythmia [HP:0011675] + meaning: HP:0011675 + Asthenia (generalized weakness) [HP:0025406]: + text: Asthenia (generalized weakness) [HP:0025406] + meaning: HP:0025406 + Bleeding gums [GENEPIO:0101182]: + text: Bleeding gums [GENEPIO:0101182] + meaning: GENEPIO:0101182 + Chest tightness or pressure [HP:0031352]: + text: Chest tightness or pressure [HP:0031352] + meaning: HP:0031352 + Rigors (fever shakes) [HP:0025145]: + text: Rigors (fever shakes) [HP:0025145] + meaning: HP:0025145 + is_a: Chest tightness or pressure [HP:0031352] + Chills (sudden cold sensation) [HP:0025143]: + text: Chills (sudden cold sensation) [HP:0025143] + description: A sudden sensation of feeling cold. + meaning: HP:0025143 + Conjunctivitis (pink eye) [HP:0000509]: + text: Conjunctivitis (pink eye) [HP:0000509] + description: Inflammation of the conjunctiva. + meaning: HP:0000509 + Coryza (rhinitis) [MP:0001867]: + text: Coryza (rhinitis) [MP:0001867] + meaning: MP:0001867 + Cough [HP:0012735]: + text: Cough [HP:0012735] + description: A sudden, audible expulsion of air from the lungs through a partially + closed glottis, preceded by inhalation. + meaning: HP:0012735 + Nonproductive cough (dry cough) [HP:0031246]: + text: Nonproductive cough (dry cough) [HP:0031246] + meaning: HP:0031246 + is_a: Cough [HP:0012735] + Productive cough (wet cough) [HP:0031245]: + text: Productive cough (wet cough) [HP:0031245] + meaning: HP:0031245 + is_a: Cough [HP:0012735] + Diarrhea [DOID:13250]: + text: Diarrhea [DOID:13250] + meaning: DOID:13250 + Dyspnea (breathing difficulty) [HP:0002094]: + text: Dyspnea (breathing difficulty) [HP:0002094] + meaning: HP:0002094 + Fatigue (tiredness) [HP:0012378]: + text: Fatigue (tiredness) [HP:0012378] + description: A subjective feeling of tiredness characterized by a lack of + energy and motivation. + meaning: HP:0012378 + Fever [HP:0001945]: + text: Fever [HP:0001945] + description: Body temperature elevated above the normal range. + meaning: HP:0001945 + "Fever (>=38\xB0C) [GENEPIO:0100066]": + text: "Fever (>=38\xB0C) [GENEPIO:0100066]" + meaning: GENEPIO:0100066 + is_a: Fever [HP:0001945] + Headache [HP:0002315]: + text: Headache [HP:0002315] + description: Cephalgia, or pain sensed in various parts of the head, not confined + to the area of distribution of any nerve. + meaning: HP:0002315 + Hypoxemia (low blood oxygen) [HP:0012418]: + text: Hypoxemia (low blood oxygen) [HP:0012418] + meaning: HP:0012418 + Silent hypoxemia [GENEPIO:0100068]: + text: Silent hypoxemia [GENEPIO:0100068] + meaning: GENEPIO:0100068 + is_a: Hypoxemia (low blood oxygen) [HP:0012418] + Malaise (general discomfort/unease) [HP:0033834]: + text: Malaise (general discomfort/unease) [HP:0033834] + meaning: HP:0033834 + Muscle weakness [HP:0001324]: + text: Muscle weakness [HP:0001324] + meaning: HP:0001324 + Nasal obstruction (stuffy nose) [HP:0001742]: + text: Nasal obstruction (stuffy nose) [HP:0001742] + meaning: HP:0001742 + Nausea [HP:0002018]: + text: Nausea [HP:0002018] + description: A sensation of unease in the stomach together with an urge to + vomit. + meaning: HP:0002018 + Pain [HP:0012531]: + text: Pain [HP:0012531] + meaning: HP:0012531 + Arthralgia (painful joints) [HP:0002829]: + text: Arthralgia (painful joints) [HP:0002829] + meaning: HP:0002829 + is_a: Pain [HP:0012531] + Myalgia (muscle pain) [HP:0003326]: + text: Myalgia (muscle pain) [HP:0003326] + description: Pain in muscle. + meaning: HP:0003326 + is_a: Pain [HP:0012531] + Pharyngitis (sore throat) [HP:0025439]: + text: Pharyngitis (sore throat) [HP:0025439] + meaning: HP:0025439 + Rhinorrhea (runny nose) [HP:0031417]: + text: Rhinorrhea (runny nose) [HP:0031417] + meaning: HP:0031417 + Shivering (involuntary muscle twitching) [HP:0025144]: + text: Shivering (involuntary muscle twitching) [HP:0025144] + meaning: HP:0025144 + Sneezing [HP:0025095]: + text: Sneezing [HP:0025095] + meaning: HP:0025095 + Sputum Production [HP:0033709]: + text: Sputum Production [HP:0033709] + meaning: HP:0033709 + Swollen Lymph Nodes [HP:0002716]: + text: Swollen Lymph Nodes [HP:0002716] + description: Enlargment (swelling) of a lymph node. + meaning: HP:0002716 + Tachypnea (accelerated respiratory rate) [HP:0002789]: + text: Tachypnea (accelerated respiratory rate) [HP:0002789] + meaning: HP:0002789 + Vomiting (throwing up) [HP:0002013]: + text: Vomiting (throwing up) [HP:0002013] + description: Forceful ejection of the contents of the stomach through the + mouth by means of a series of involuntary spasmic contractions. + meaning: HP:0002013 + PreExistingConditionsAndRiskFactorsMenu: + name: PreExistingConditionsAndRiskFactorsMenu + title: pre-existing_conditions_and_risk_factors menu + permissible_values: + Age 60+ [VO:0004925]: + text: Age 60+ [VO:0004925] + meaning: VO:0004925 + Anemia [DOID:2355]: + text: Anemia [DOID:2355] + meaning: DOID:2355 + Hemoglobinopathy [DOID:2860]: + text: Hemoglobinopathy [DOID:2860] + meaning: DOID:2860 + is_a: Anemia [DOID:2355] + Anorexia [HP:0002039]: + text: Anorexia [HP:0002039] + meaning: HP:0002039 + Birthing labor [NCIT:C92743]: + text: Birthing labor [NCIT:C92743] + meaning: NCIT:C92743 + Bone marrow failure [NCIT:C80693]: + text: Bone marrow failure [NCIT:C80693] + meaning: NCIT:C80693 + Cancer [MONDO:0004992]: + text: Cancer [MONDO:0004992] + description: A tumor composed of atypical neoplastic, often pleomorphic cells + that invade other tissues. Malignant neoplasms often metastasize to distant + anatomic sites and may recur after excision. The most common malignant neoplasms + are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and + non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. + meaning: MONDO:0004992 + Breast cancer [MONDO:0007254]: + text: Breast cancer [MONDO:0007254] + meaning: MONDO:0007254 + is_a: Cancer [MONDO:0004992] + Colorectal cancer [MONDO:0005575]: + text: Colorectal cancer [MONDO:0005575] + meaning: MONDO:0005575 + is_a: Cancer [MONDO:0004992] + Hematologic malignancy (cancer of the blood) [DOID:2531]: + text: Hematologic malignancy (cancer of the blood) [DOID:2531] + meaning: DOID:2531 + is_a: Cancer [MONDO:0004992] + Lung cancer [MONDO:0008903]: + text: Lung cancer [MONDO:0008903] + meaning: MONDO:0008903 + is_a: Cancer [MONDO:0004992] + Metastatic disease [MONDO:0024880]: + text: Metastatic disease [MONDO:0024880] + meaning: MONDO:0024880 + is_a: Cancer [MONDO:0004992] + Cancer treatment [NCIT:C16212]: + text: Cancer treatment [NCIT:C16212] + description: Any intervention for management of a malignant neoplasm. + meaning: NCIT:C16212 + Cancer surgery [NCIT:C157740]: + text: Cancer surgery [NCIT:C157740] + meaning: NCIT:C157740 + is_a: Cancer treatment [NCIT:C16212] + Chemotherapy [NCIT:C15632]: + text: Chemotherapy [NCIT:C15632] + description: The use of synthetic or naturally-occurring chemicals for the + treatment of diseases. + meaning: NCIT:C15632 + is_a: Cancer treatment [NCIT:C16212] + Adjuvant chemotherapy [NCIT:C15360]: + text: Adjuvant chemotherapy [NCIT:C15360] + meaning: NCIT:C15360 + is_a: Chemotherapy [NCIT:C15632] + Cardiac disorder [NCIT:C3079]: + text: Cardiac disorder [NCIT:C3079] + meaning: NCIT:C3079 + Arrhythmia [HP:0011675]: + text: Arrhythmia [HP:0011675] + meaning: HP:0011675 + is_a: Cardiac disorder [NCIT:C3079] + Cardiac disease [MONDO:0005267]: + text: Cardiac disease [MONDO:0005267] + meaning: MONDO:0005267 + is_a: Cardiac disorder [NCIT:C3079] + Cardiomyopathy [HP:0001638]: + text: Cardiomyopathy [HP:0001638] + meaning: HP:0001638 + is_a: Cardiac disorder [NCIT:C3079] + Cardiac injury [GENEPIO:0100074]: + text: Cardiac injury [GENEPIO:0100074] + meaning: GENEPIO:0100074 + is_a: Cardiac disorder [NCIT:C3079] + Hypertension (high blood pressure) [HP:0000822]: + text: Hypertension (high blood pressure) [HP:0000822] + meaning: HP:0000822 + is_a: Cardiac disorder [NCIT:C3079] + Hypotension (low blood pressure) [HP:0002615]: + text: Hypotension (low blood pressure) [HP:0002615] + meaning: HP:0002615 + is_a: Cardiac disorder [NCIT:C3079] + Cesarean section [HP:0011410]: + text: Cesarean section [HP:0011410] + meaning: HP:0011410 + Chronic cough [GENEPIO:0100075]: + text: Chronic cough [GENEPIO:0100075] + meaning: GENEPIO:0100075 + Chronic gastrointestinal disease [GENEPIO:0100076]: + text: Chronic gastrointestinal disease [GENEPIO:0100076] + meaning: GENEPIO:0100076 + Corticosteroids [NCIT:C211]: + text: Corticosteroids [NCIT:C211] + meaning: NCIT:C211 + Diabetes mellitus (diabetes) [HP:0000819]: + text: Diabetes mellitus (diabetes) [HP:0000819] + description: A group of abnormalities characterized by hyperglycemia and glucose + intolerance. + meaning: HP:0000819 + Type I diabetes mellitus (T1D) [HP:0100651]: + text: Type I diabetes mellitus (T1D) [HP:0100651] + description: A chronic condition in which the pancreas produces little or + no insulin. Type I diabetes mellitus is manifested by the sudden onset of + severe hyperglycemia with rapid progression to diabetic ketoacidosis unless + treated with insulin. + meaning: HP:0100651 + is_a: Diabetes mellitus (diabetes) [HP:0000819] + Type II diabetes mellitus (T2D) [HP:0005978]: + text: Type II diabetes mellitus (T2D) [HP:0005978] + description: A type of diabetes mellitus initially characterized by insulin + resistance and hyperinsulinemia and subsequently by glucose interolerance + and hyperglycemia. + meaning: HP:0005978 + is_a: Diabetes mellitus (diabetes) [HP:0000819] + Eczema [HP:0000964]: + text: Eczema [HP:0000964] + meaning: HP:0000964 + Electrolyte disturbance [HP:0003111]: + text: Electrolyte disturbance [HP:0003111] + meaning: HP:0003111 + Hypocalcemia [HP:0002901]: + text: Hypocalcemia [HP:0002901] + meaning: HP:0002901 + is_a: Electrolyte disturbance [HP:0003111] + Hypokalemia [HP:0002900]: + text: Hypokalemia [HP:0002900] + meaning: HP:0002900 + is_a: Electrolyte disturbance [HP:0003111] + Hypomagnesemia [HP:0002917]: + text: Hypomagnesemia [HP:0002917] + meaning: HP:0002917 + is_a: Electrolyte disturbance [HP:0003111] + Encephalitis (brain inflammation) [HP:0002383]: + text: Encephalitis (brain inflammation) [HP:0002383] + meaning: HP:0002383 + Epilepsy [MONDO:0005027]: + text: Epilepsy [MONDO:0005027] + meaning: MONDO:0005027 + Hemodialysis [NCIT:C15248]: + text: Hemodialysis [NCIT:C15248] + meaning: NCIT:C15248 + Hemoglobinopathy [MONDO:0044348]: + text: Hemoglobinopathy [MONDO:0044348] + meaning: MONDO:0044348 + Human immunodeficiency virus (HIV) [MONDO:0005109]: + text: Human immunodeficiency virus (HIV) [MONDO:0005109] + description: An infection caused by the human immunodeficiency virus. + meaning: MONDO:0005109 + Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268]: + text: Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] + description: A syndrome resulting from the acquired deficiency of cellular + immunity caused by the human immunodeficiency virus (HIV). It is characterized + by the reduction of the Helper T-lymphocytes in the peripheral blood and + the lymph nodes. + meaning: MONDO:0012268 + is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] + HIV and antiretroviral therapy (ART) [NCIT:C16118]: + text: HIV and antiretroviral therapy (ART) [NCIT:C16118] + description: Treatment of human immunodeficiency virus (HIV) infections with + medications that target the virus directly, limiting the ability of infected + cells to produce new HIV particles. + meaning: NCIT:C16118 + is_a: Human immunodeficiency virus (HIV) [MONDO:0005109] + Immunocompromised [NCIT:C14139]: + text: Immunocompromised [NCIT:C14139] + description: A loss of any arm of immune functions, resulting in potential + or actual increase in infections. This state may be reached secondary to + specific genetic lesions, syndromes with unidentified or polygenic causes, + acquired deficits from other disease states, or as result of therapy for + other diseases or conditions. + meaning: NCIT:C14139 + Lupus [MONDO:0004670]: + text: Lupus [MONDO:0004670] + description: An autoimmune, connective tissue chronic inflammatory disorder + affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood + cells. It is more commonly seen in women than men. Variants include discoid + and systemic lupus erythematosus. + meaning: MONDO:0004670 + is_a: Immunocompromised [NCIT:C14139] + Inflammatory bowel disease (IBD) [MONDO:0005265]: + text: Inflammatory bowel disease (IBD) [MONDO:0005265] + meaning: MONDO:0005265 + Colitis [HP:0002583]: + text: Colitis [HP:0002583] + meaning: HP:0002583 + is_a: Inflammatory bowel disease (IBD) [MONDO:0005265] + Ulcerative colitis [HP:0100279]: + text: Ulcerative colitis [HP:0100279] + meaning: HP:0100279 + is_a: Colitis [HP:0002583] + Crohn's disease [HP:0100280]: + text: Crohn's disease [HP:0100280] + meaning: HP:0100280 + is_a: Inflammatory bowel disease (IBD) [MONDO:0005265] + Renal disorder [NCIT:C3149]: + text: Renal disorder [NCIT:C3149] + meaning: NCIT:C3149 + Renal disease [MONDO:0005240]: + text: Renal disease [MONDO:0005240] + meaning: MONDO:0005240 + is_a: Renal disorder [NCIT:C3149] + Chronic renal disease [HP:0012622]: + text: Chronic renal disease [HP:0012622] + meaning: HP:0012622 + is_a: Renal disease [MONDO:0005240] + Renal failure [HP:0000083]: + text: Renal failure [HP:0000083] + meaning: HP:0000083 + is_a: Renal disorder [NCIT:C3149] + Liver disease [MONDO:0005154]: + text: Liver disease [MONDO:0005154] + meaning: MONDO:0005154 + Chronic liver disease [NCIT:C113609]: + text: Chronic liver disease [NCIT:C113609] + meaning: NCIT:C113609 + is_a: Liver disease [MONDO:0005154] + Fatty liver disease (FLD) [HP:0001397]: + text: Fatty liver disease (FLD) [HP:0001397] + meaning: HP:0001397 + is_a: Chronic liver disease [NCIT:C113609] + Myalgia (muscle pain) [HP:0003326]: + text: Myalgia (muscle pain) [HP:0003326] + description: Pain in muscle. + meaning: HP:0003326 + Myalgic encephalomyelitis (ME) [MONDO:0005404]: + text: Myalgic encephalomyelitis (ME) [MONDO:0005404] + meaning: MONDO:0005404 + Neurological disorder [MONDO:0005071]: + text: Neurological disorder [MONDO:0005071] + meaning: MONDO:0005071 + Neuromuscular disorder [MONDO:0019056]: + text: Neuromuscular disorder [MONDO:0019056] + meaning: MONDO:0019056 + is_a: Neurological disorder [MONDO:0005071] + Obesity [HP:0001513]: + text: Obesity [HP:0001513] + meaning: HP:0001513 + Severe obesity [MONDO:0005139]: + text: Severe obesity [MONDO:0005139] + meaning: MONDO:0005139 + is_a: Obesity [HP:0001513] + Respiratory disorder [MONDO:0005087]: + text: Respiratory disorder [MONDO:0005087] + meaning: MONDO:0005087 + Asthma [HP:0002099]: + text: Asthma [HP:0002099] + meaning: HP:0002099 + is_a: Respiratory disorder [MONDO:0005087] + Chronic bronchitis [HP:0004469]: + text: Chronic bronchitis [HP:0004469] + meaning: HP:0004469 + is_a: Respiratory disorder [MONDO:0005087] + Chronic obstructive pulmonary disease [HP:0006510]: + text: Chronic obstructive pulmonary disease [HP:0006510] + meaning: HP:0006510 + is_a: Respiratory disorder [MONDO:0005087] + Emphysema [HP:0002097]: + text: Emphysema [HP:0002097] + meaning: HP:0002097 + is_a: Respiratory disorder [MONDO:0005087] + Lung disease [MONDO:0005275]: + text: Lung disease [MONDO:0005275] + meaning: MONDO:0005275 + is_a: Respiratory disorder [MONDO:0005087] + Chronic lung disease [HP:0006528]: + text: Chronic lung disease [HP:0006528] + meaning: HP:0006528 + is_a: Lung disease [MONDO:0005275] + Pulmonary fibrosis [HP:0002206]: + text: Pulmonary fibrosis [HP:0002206] + meaning: HP:0002206 + is_a: Lung disease [MONDO:0005275] + Pneumonia [HP:0002090]: + text: Pneumonia [HP:0002090] + meaning: HP:0002090 + is_a: Respiratory disorder [MONDO:0005087] + Respiratory failure [HP:0002878]: + text: Respiratory failure [HP:0002878] + meaning: HP:0002878 + is_a: Respiratory disorder [MONDO:0005087] + Adult respiratory distress syndrome [HP:0033677]: + text: Adult respiratory distress syndrome [HP:0033677] + meaning: HP:0033677 + is_a: Respiratory failure [HP:0002878] + Newborn respiratory distress syndrome [MONDO:0009971]: + text: Newborn respiratory distress syndrome [MONDO:0009971] + meaning: MONDO:0009971 + is_a: Respiratory failure [HP:0002878] + Tuberculosis [MONDO:0018076]: + text: Tuberculosis [MONDO:0018076] + meaning: MONDO:0018076 + is_a: Respiratory disorder [MONDO:0005087] + "Postpartum (\u22646 weeks) [GENEPIO:0100077]": + text: "Postpartum (\u22646 weeks) [GENEPIO:0100077]" + meaning: GENEPIO:0100077 + Pregnancy [NCIT:C25742]: + text: Pregnancy [NCIT:C25742] + description: The state or condition of having a developing embryo or fetus + in the body (uterus), after union of an ovum and spermatozoon, during the + period from conception to birth. + meaning: NCIT:C25742 + Reye syndrome [DOID:14525]: + text: Reye syndrome [DOID:14525] + meaning: DOID:14525 + Rheumatic disease [MONDO:0005554]: + text: Rheumatic disease [MONDO:0005554] + meaning: MONDO:0005554 + Sickle cell disease [MONDO:0011382]: + text: Sickle cell disease [MONDO:0011382] + meaning: MONDO:0011382 + Substance use [NBO:0001845]: + text: Substance use [NBO:0001845] + meaning: NBO:0001845 + Alcohol abuse [MONDO:0002046]: + text: Alcohol abuse [MONDO:0002046] + meaning: MONDO:0002046 + is_a: Substance use [NBO:0001845] + Drug abuse [GENEPIO:0100078]: + text: Drug abuse [GENEPIO:0100078] + meaning: GENEPIO:0100078 + is_a: Substance use [NBO:0001845] + Injection drug abuse [GENEPIO:0100079]: + text: Injection drug abuse [GENEPIO:0100079] + meaning: GENEPIO:0100079 + is_a: Drug abuse [GENEPIO:0100078] + Smoking [NBO:0015005]: + text: Smoking [NBO:0015005] + meaning: NBO:0015005 + is_a: Substance use [NBO:0001845] + Vaping [NCIT:C173621]: + text: Vaping [NCIT:C173621] + meaning: NCIT:C173621 + is_a: Substance use [NBO:0001845] + Tachypnea (accelerated respiratory rate) [HP:0002789]: + text: Tachypnea (accelerated respiratory rate) [HP:0002789] + meaning: HP:0002789 + Transplant [NCIT:C159659]: + text: Transplant [NCIT:C159659] + meaning: CIT:C159659 + Cardiac transplant [NCIT:C131759]: + text: Cardiac transplant [NCIT:C131759] + meaning: NCIT:C131759 + is_a: Transplant [NCIT:C159659] + Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080]: + text: Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080] + meaning: GENEPIO:0100080 + is_a: Transplant [NCIT:C159659] + Kidney transplant [NCIT:C157332]: + text: Kidney transplant [NCIT:C157332] + meaning: NCIT:C157332 + is_a: Transplant [NCIT:C159659] + Liver transplant [GENEPIO:0100081]: + text: Liver transplant [GENEPIO:0100081] + meaning: GENEPIO:0100081 + is_a: Transplant [NCIT:C159659] + ComplicationsMenu: + name: ComplicationsMenu + title: complications menu + permissible_values: + Abnormal blood oxygen level [HP:0500165]: + text: Abnormal blood oxygen level [HP:0500165] + meaning: HP:0500165 + Acute lung injury [MONDO:0015796]: + text: Acute lung injury [MONDO:0015796] + meaning: MONDO:0015796 + Ventilation induced lung injury (VILI) [GENEPIO:0100092]: + text: Ventilation induced lung injury (VILI) [GENEPIO:0100092] + meaning: GENEPIO:0100092 + is_a: Acute lung injury [MONDO:0015796] + Acute respiratory failure [MONDO:0001208]: + text: Acute respiratory failure [MONDO:0001208] + meaning: MONDO:0001208 + Arrhythmia (complication) [HP:0011675]: + text: Arrhythmia (complication) [HP:0011675] + meaning: HP:0011675 + Tachycardia [HP:0001649]: + text: Tachycardia [HP:0001649] + meaning: HP:0001649 + is_a: Arrhythmia (complication) [HP:0011675] + Cardiac injury [GENEPIO:0100074]: + text: Cardiac injury [GENEPIO:0100074] + meaning: GENEPIO:0100074 + Cardiac arrest [HP:0001695]: + text: Cardiac arrest [HP:0001695] + meaning: HP:0001695 + Blood clot [HP:0001977]: + text: Blood clot [HP:0001977] + meaning: HP:0001977 + Arterial clot [HP:0004420]: + text: Arterial clot [HP:0004420] + meaning: HP:0004420 + is_a: Blood clot [HP:0001977] + Deep vein thrombosis (DVT) [HP:0002625]: + text: Deep vein thrombosis (DVT) [HP:0002625] + meaning: HP:0002625 + is_a: Blood clot [HP:0001977] + Pulmonary embolism (PE) [HP:0002204]: + text: Pulmonary embolism (PE) [HP:0002204] + meaning: HP:0002204 + is_a: Blood clot [HP:0001977] + Cardiomyopathy [HP:0001638]: + text: Cardiomyopathy [HP:0001638] + meaning: HP:0001638 + Central nervous system invasion [MONDO:0024619]: + text: Central nervous system invasion [MONDO:0024619] + meaning: MONDO:0024619 + Stroke (complication) [HP:0001297]: + text: Stroke (complication) [HP:0001297] + meaning: HP:0001297 + Central Nervous System Vasculitis [MONDO:0003346]: + text: Central Nervous System Vasculitis [MONDO:0003346] + meaning: MONDO:0003346 + is_a: Stroke (complication) [HP:0001297] + Acute ischemic stroke [HP:0002140]: + text: Acute ischemic stroke [HP:0002140] + meaning: HP:0002140 + is_a: Stroke (complication) [HP:0001297] + Coma [HP:0001259]: + text: Coma [HP:0001259] + meaning: HP:0001259 + Convulsions [HP:0011097]: + text: Convulsions [HP:0011097] + meaning: HP:0011097 + Cystic fibrosis [MONDO:0009061]: + text: Cystic fibrosis [MONDO:0009061] + meaning: MONDO:0009061 + Cytokine release syndrome [MONDO:0600008]: + text: Cytokine release syndrome [MONDO:0600008] + meaning: MONDO:0600008 + Disseminated intravascular coagulation (DIC) [MPATH:108]: + text: Disseminated intravascular coagulation (DIC) [MPATH:108] + meaning: MPATH:108 + Encephalopathy [HP:0001298]: + text: Encephalopathy [HP:0001298] + meaning: HP:0001298 + Fulminant myocarditis [GENEPIO:0100088]: + text: Fulminant myocarditis [GENEPIO:0100088] + meaning: GENEPIO:0100088 + "Guillain-Barr\xE9 syndrome [MONDO:0016218]": + text: "Guillain-Barr\xE9 syndrome [MONDO:0016218]" + meaning: MONDO:0016218 + Internal hemorrhage (complication; internal bleeding) [HP:0011029]: + text: Internal hemorrhage (complication; internal bleeding) [HP:0011029] + meaning: HP:0011029 + Intracerebral haemorrhage [MONDO:0013792]: + text: Intracerebral haemorrhage [MONDO:0013792] + meaning: MONDO:0013792 + is_a: Internal hemorrhage (complication; internal bleeding) [HP:0011029] + Kawasaki disease [MONDO:0012727]: + text: Kawasaki disease [MONDO:0012727] + meaning: MONDO:0012727 + Complete Kawasaki disease [GENEPIO:0100089]: + text: Complete Kawasaki disease [GENEPIO:0100089] + meaning: GENEPIO:0100089 + is_a: Kawasaki disease [MONDO:0012727] + Incomplete Kawasaki disease [GENEPIO:0100090]: + text: Incomplete Kawasaki disease [GENEPIO:0100090] + meaning: GENEPIO:0100090 + is_a: Kawasaki disease [MONDO:0012727] + Liver dysfunction [HP:0001410]: + text: Liver dysfunction [HP:0001410] + meaning: HP:0001410 + Acute liver injury [GENEPIO:0100091]: + text: Acute liver injury [GENEPIO:0100091] + meaning: GENEPIO:0100091 + is_a: Liver dysfunction [HP:0001410] + Long COVID-19 [MONDO:0100233]: + text: Long COVID-19 [MONDO:0100233] + meaning: MONDO:0100233 + Meningitis [HP:0001287]: + text: Meningitis [HP:0001287] + meaning: HP:0001287 + Migraine [HP:0002076]: + text: Migraine [HP:0002076] + meaning: HP:0002076 + Miscarriage [HP:0005268]: + text: Miscarriage [HP:0005268] + meaning: HP:0005268 + Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163]: + text: Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163] + meaning: MONDO:0100163 + Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319]: + text: Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319] + meaning: MONDO:0100319 + Muscle injury [GENEPIO:0100093]: + text: Muscle injury [GENEPIO:0100093] + meaning: GENEPIO:0100093 + Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404]: + text: Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404] + meaning: MONDO:0005404 + Myocardial infarction (heart attack) [MONDO:0005068]: + text: Myocardial infarction (heart attack) [MONDO:0005068] + meaning: MONDO:0005068 + Myocardial injury [HP:0001700]: + text: Myocardial injury [HP:0001700] + meaning: HP:0001700 + Neonatal complications [NCIT:C168498]: + text: Neonatal complications [NCIT:C168498] + meaning: CIT:C168498 + Noncardiogenic pulmonary edema [GENEPIO:0100085]: + text: Noncardiogenic pulmonary edema [GENEPIO:0100085] + meaning: GENEPIO:0100085 + Acute respiratory distress syndrome (ARDS) [HP:0033677]: + text: Acute respiratory distress syndrome (ARDS) [HP:0033677] + meaning: HP:0033677 + is_a: Noncardiogenic pulmonary edema [GENEPIO:0100085] + Organ failure [GENEPIO:0100094]: + text: Organ failure [GENEPIO:0100094] + meaning: GENEPIO:0100094 + Paralysis [HP:0003470]: + text: Paralysis [HP:0003470] + meaning: HP:0003470 + Pneumothorax (collapsed lung) [HP:0002107]: + text: Pneumothorax (collapsed lung) [HP:0002107] + meaning: HP:0002107 + Pneumonia (complication) [HP:0002090]: + text: Pneumonia (complication) [HP:0002090] + meaning: HP:0002090 + Pregancy complications [HP:0001197]: + text: Pregancy complications [HP:0001197] + meaning: HP:0001197 + Rhabdomyolysis [HP:0003201]: + text: Rhabdomyolysis [HP:0003201] + meaning: HP:0003201 + Secondary infection [IDO:0000567]: + text: Secondary infection [IDO:0000567] + description: An infection bearing the secondary infection role. + meaning: IDO:0000567 + Seizure (complication) [HP:0001250]: + text: Seizure (complication) [HP:0001250] + meaning: HP:0001250 + Sepsis/Septicemia [HP:0100806]: + text: Sepsis/Septicemia [HP:0100806] + description: Systemic inflammatory response to infection. + meaning: HP:0100806 + Sepsis (systemic inflammatory response to infection) [IDO:0000636]: + text: Sepsis (systemic inflammatory response to infection) [IDO:0000636] + meaning: IDO:0000636 + is_a: Sepsis/Septicemia [HP:0100806] + Septicemia (bloodstream infection) [NCIT:C3364]: + text: Septicemia (bloodstream infection) [NCIT:C3364] + meaning: NCIT:C3364 + is_a: Sepsis/Septicemia [HP:0100806] + Shock [HP:0031273]: + text: Shock [HP:0031273] + meaning: HP:0031273 + Hyperinflammatory shock [GENEPIO:0100097]: + text: Hyperinflammatory shock [GENEPIO:0100097] + meaning: GENEPIO:0100097 + is_a: Shock [HP:0031273] + Septic shock [NCIT:C35018]: + text: Septic shock [NCIT:C35018] + meaning: NCIT:C35018 + is_a: Shock [HP:0031273] + Vasculitis [HP:0002633]: + text: Vasculitis [HP:0002633] + meaning: HP:0002633 + ExposureEventMenu: + name: ExposureEventMenu + title: exposure_event menu + permissible_values: + Mass Gathering [GENEPIO:0100237]: + text: Mass Gathering [GENEPIO:0100237] + description: A gathering or event attended by a sufficient number of people + to strain the planning and response resources of the host community, state/province, + nation, or region where it is being held. + meaning: GENEPIO:0100237 + Convention [GENEPIO:0100238]: + text: Convention [GENEPIO:0100238] + description: A gathering of individuals who meet at an arranged place and + time in order to discuss or engage in some common interest. The most common + conventions are based upon industry, profession, and fandom. + meaning: GENEPIO:0100238 + is_a: Mass Gathering [GENEPIO:0100237] + Convocation [GENEPIO:0100239]: + text: Convocation [GENEPIO:0100239] + meaning: GENEPIO:0100239 + is_a: Mass Gathering [GENEPIO:0100237] + Agricultural Event [GENEPIO:0100240]: + text: Agricultural Event [GENEPIO:0100240] + description: A gathering exhibiting the equipment, animals, sports and recreation + associated with agriculture and animal husbandry. + meaning: GENEPIO:0100240 + is_a: Mass Gathering [GENEPIO:0100237] + Religious Gathering [GENEPIO:0100241]: + text: Religious Gathering [GENEPIO:0100241] + meaning: GENEPIO:0100241 + Mass [GENEPIO:0100242]: + text: Mass [GENEPIO:0100242] + meaning: GENEPIO:0100242 + is_a: Religious Gathering [GENEPIO:0100241] + Social Gathering [PCO:0000033]: + text: Social Gathering [PCO:0000033] + description: A type of social behavior in which a collection of humans intentionally + gathers together on a temporary basis to engage socially. + meaning: PCO:0000033 + Baby Shower [PCO:0000039]: + text: Baby Shower [PCO:0000039] + meaning: PCO:0000039 + is_a: Social Gathering [PCO:0000033] + Community Event [PCO:0000034]: + text: Community Event [PCO:0000034] + meaning: PCO:0000034 + is_a: Social Gathering [PCO:0000033] + Family Gathering [GENEPIO:0100243]: + text: Family Gathering [GENEPIO:0100243] + meaning: GENEPIO:0100243 + is_a: Social Gathering [PCO:0000033] + Family Reunion [GENEPIO:0100244]: + text: Family Reunion [GENEPIO:0100244] + meaning: GENEPIO:0100244 + is_a: Family Gathering [GENEPIO:0100243] + Funeral [GENEPIO:0100245]: + text: Funeral [GENEPIO:0100245] + meaning: GENEPIO:0100245 + is_a: Social Gathering [PCO:0000033] + Party [PCO:0000035]: + text: Party [PCO:0000035] + meaning: PCO:0000035 + is_a: Social Gathering [PCO:0000033] + Potluck [PCO:0000037]: + text: Potluck [PCO:0000037] + meaning: PCO:0000037 + is_a: Social Gathering [PCO:0000033] + Wedding [PCO:0000038]: + text: Wedding [PCO:0000038] + meaning: PCO:0000038 + is_a: Social Gathering [PCO:0000033] + Animal contact event [GENEPIO:0101183]: + text: Animal contact event [GENEPIO:0101183] + meaning: GENEPIO:0101183 + Trip to a live animal market [GENEPIO:0101185]: + text: Trip to a live animal market [GENEPIO:0101185] + meaning: GENEPIO:0101185 + is_a: Animal contact event [GENEPIO:0101183] + Trip to a farm [GENEPIO:0101186]: + text: Trip to a farm [GENEPIO:0101186] + meaning: GENEPIO:0101186 + is_a: Animal contact event [GENEPIO:0101183] + Wildlife encounter [GENEPIO:0101188]: + text: Wildlife encounter [GENEPIO:0101188] + meaning: GENEPIO:0101188 + is_a: Animal contact event [GENEPIO:0101183] + Hunting trip [GENEPIO:0101184]: + text: Hunting trip [GENEPIO:0101184] + meaning: GENEPIO:0101184 + is_a: Wildlife encounter [GENEPIO:0101188] + Animal transportation event [GENEPIO:0101187]: + text: Animal transportation event [GENEPIO:0101187] + meaning: GENEPIO:0101187 + Other exposure event: + text: Other exposure event + ExposureContactLevelMenu: + name: ExposureContactLevelMenu + title: exposure_contact_level menu + permissible_values: + Contact with infected animal [GENEPIO:0101189]: + text: Contact with infected animal [GENEPIO:0101189] + meaning: GENEPIO:0101189 + Direct (host-to-animal contact) [GENEPIO:0101190]: + text: Direct (host-to-animal contact) [GENEPIO:0101190] + meaning: GENEPIO:0101190 + is_a: Contact with infected animal [GENEPIO:0101189] + Indirect contact (host-to-animal) [GENEPIO:0101191]: + text: Indirect contact (host-to-animal) [GENEPIO:0101191] + meaning: GENEPIO:0101191 + is_a: Contact with infected animal [GENEPIO:0101189] + Close animal contact (face-to-face contact) [GENEPIO:0101192]: + text: Close animal contact (face-to-face contact) [GENEPIO:0101192] + meaning: GENEPIO:0101192 + is_a: Indirect contact (host-to-animal) [GENEPIO:0101191] + Casual animal contact [GENEPIO:0101193]: + text: Casual animal contact [GENEPIO:0101193] + meaning: GENEPIO:0101193 + is_a: Indirect contact (host-to-animal) [GENEPIO:0101191] + Contact with infected individual: + text: Contact with infected individual + Direct (human-to-human contact) [TRANS:0000001]: + text: Direct (human-to-human contact) [TRANS:0000001] + description: Direct and essentially immediate transfer of infectious agents + to a receptive portal of entry through which human or animal infection may + take place. This may be by direct contact such as touching, kissing, biting, + or sexual intercourse or by the direct projection (droplet spread) of droplet + spray onto the conjunctiva or the mucous membranes of the eyes, nose, or + mouth. It may also be by direct exposure of susceptible tissue to an agent + in soil, compost, or decaying vegetable matter or by the bite of a rabid + animal. Transplacental transmission is another form of direct transmission. + meaning: TRANS:0000001 + is_a: Contact with infected individual + Indirect contact [GENEPIO:0100246]: + text: Indirect contact [GENEPIO:0100246] + description: A type of contact in which an individual does not come in direct + contact with a source of infection e.g. through airborne transmission, contact + with contaminated surfaces. + meaning: GENEPIO:0100246 + is_a: Contact with infected individual + Close contact (face-to-face contact) [GENEPIO:0100247]: + text: Close contact (face-to-face contact) [GENEPIO:0100247] + description: A type of indirect contact where an individual sustains unprotected + exposure by being within 6 feet of an infected individual over a sustained + period of time. + meaning: GENEPIO:0100247 + is_a: Indirect contact [GENEPIO:0100246] + Casual contact [GENEPIO:0100248]: + text: Casual contact [GENEPIO:0100248] + description: A type of indirect contact where an individual may at the same + location at the same time as a positive case; however, they may have been + there only briefly, or it may have been a location that carries a lower + risk of transmission. + meaning: GENEPIO:0100248 + is_a: Indirect contact [GENEPIO:0100246] + HostRoleMenu: + name: HostRoleMenu + title: host_role menu + permissible_values: + Attendee [GENEPIO:0100249]: + text: Attendee [GENEPIO:0100249] + description: A role inhering in a person that is realized when the bearer + is present on a given occasion or at a given place. + meaning: GENEPIO:0100249 + Student [OMRSE:00000058]: + text: Student [OMRSE:00000058] + description: A human social role that, if realized, is realized by the process + of formal education that the bearer undergoes. + meaning: OMRSE:00000058 + is_a: Attendee [GENEPIO:0100249] + Patient [OMRSE:00000030]: + text: Patient [OMRSE:00000030] + description: A patient role that inheres in a human being. + meaning: OMRSE:00000030 + Inpatient [NCIT:C25182]: + text: Inpatient [NCIT:C25182] + description: A patient who is residing in the hospital where he is being treated. + meaning: NCIT:C25182 + is_a: Patient [OMRSE:00000030] + Outpatient [NCIT:C28293]: + text: Outpatient [NCIT:C28293] + description: A patient who comes to a healthcare facility for diagnosis or + treatment but is not admitted for an overnight stay. + meaning: NCIT:C28293 + is_a: Patient [OMRSE:00000030] + Passenger [GENEPIO:0100250]: + text: Passenger [GENEPIO:0100250] + description: A role inhering in a person that is realized when the bearer + travels in a vehicle but bears little to no responsibility for vehicle operation + nor arrival at its destination. + meaning: GENEPIO:0100250 + Resident [GENEPIO:0100251]: + text: Resident [GENEPIO:0100251] + description: A role inhering in a person that is realized when the bearer + maintains residency in a given place. + meaning: GENEPIO:0100251 + Visitor [GENEPIO:0100252]: + text: Visitor [GENEPIO:0100252] + description: A role inhering in a person that is realized when the bearer + pays a visit to a specific place or event. + meaning: GENEPIO:0100252 + Volunteer [GENEPIO:0100253]: + text: Volunteer [GENEPIO:0100253] + description: A role inhering in a person that is realized when the bearer + enters into any service of their own free will. + meaning: GENEPIO:0100253 + Work [GENEPIO:0100254]: + text: Work [GENEPIO:0100254] + description: A role inhering in a person that is realized when the bearer + performs labor for a living. + meaning: GENEPIO:0100254 + Administrator [GENEPIO:0100255]: + text: Administrator [GENEPIO:0100255] + description: A role inhering in a person that is realized when the bearer + is engaged in administration or administrative work. + meaning: GENEPIO:0100255 + is_a: Work [GENEPIO:0100254] + First Responder [GENEPIO:0100256]: + text: First Responder [GENEPIO:0100256] + description: A role inhering in a person that is realized when the bearer + is among the first to arrive at the scene of an emergency and has specialized + training to provide assistance. + meaning: GENEPIO:0100256 + is_a: Work [GENEPIO:0100254] + Firefighter [GENEPIO:0100257]: + text: Firefighter [GENEPIO:0100257] + meaning: GENEPIO:0100257 + is_a: First Responder [GENEPIO:0100256] + Paramedic [GENEPIO:0100258]: + text: Paramedic [GENEPIO:0100258] + meaning: GENEPIO:0100258 + is_a: First Responder [GENEPIO:0100256] + Police Officer [GENEPIO:0100259]: + text: Police Officer [GENEPIO:0100259] + meaning: GENEPIO:0100259 + is_a: First Responder [GENEPIO:0100256] + Housekeeper [GENEPIO:0100260]: + text: Housekeeper [GENEPIO:0100260] + description: A role inhering in a person that is realized when the bearer + is an individual who performs cleaning duties and/or is responsible for + the supervision of cleaning staff. + meaning: GENEPIO:0100260 + is_a: Work [GENEPIO:0100254] + Kitchen Worker [GENEPIO:0100261]: + text: Kitchen Worker [GENEPIO:0100261] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a kitchen. + meaning: GENEPIO:0100261 + is_a: Work [GENEPIO:0100254] + Healthcare Worker [GENEPIO:0100334]: + text: Healthcare Worker [GENEPIO:0100334] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a healthcare setting. + meaning: GENEPIO:0100334 + is_a: Work [GENEPIO:0100254] + Community Healthcare Worker [GENEPIO:0100420]: + text: Community Healthcare Worker [GENEPIO:0100420] + description: A role inhering in a person that is realized when the bearer + a professional caregiver that provides health care or supportive care in + the individual home where the patient or client is living, as opposed to + care provided in group accommodations like clinics or nursing home. + meaning: GENEPIO:0100420 + is_a: Healthcare Worker [GENEPIO:0100334] + Laboratory Worker [GENEPIO:0100262]: + text: Laboratory Worker [GENEPIO:0100262] + description: A role inhering in a person that is realized when the bearer + is an employee that performs labor in a laboratory. + meaning: GENEPIO:0100262 + is_a: Healthcare Worker [GENEPIO:0100334] + Nurse [OMRSE:00000014]: + text: Nurse [OMRSE:00000014] + description: A health care role borne by a human being and realized by the + care of individuals, families, and communities so they may attain, maintain, + or recover optimal health and quality of life. + meaning: OMRSE:00000014 + is_a: Healthcare Worker [GENEPIO:0100334] + Personal Care Aid [GENEPIO:0100263]: + text: Personal Care Aid [GENEPIO:0100263] + description: A role inhering in a person that is realized when the bearer + works to help another person complete their daily activities. + meaning: GENEPIO:0100263 + is_a: Healthcare Worker [GENEPIO:0100334] + Pharmacist [GENEPIO:0100264]: + text: Pharmacist [GENEPIO:0100264] + description: A role inhering in a person that is realized when the bearer + is a health professional who specializes in dispensing prescription drugs + at a healthcare facility. + meaning: GENEPIO:0100264 + is_a: Healthcare Worker [GENEPIO:0100334] + Physician [OMRSE:00000013]: + text: Physician [OMRSE:00000013] + description: A health care role borne by a human being and realized by promoting, + maintaining or restoring human health through the study, diagnosis, and + treatment of disease, injury and other physical and mental impairments. + meaning: OMRSE:00000013 + is_a: Healthcare Worker [GENEPIO:0100334] + Rotational Worker [GENEPIO:0100354]: + text: Rotational Worker [GENEPIO:0100354] + description: A role inhering in a person that is realized when the bearer + performs labor on a regular schedule, often requiring travel to geographic + locations other than where they live. + meaning: GENEPIO:0100354 + is_a: Work [GENEPIO:0100254] + Seasonal Worker [GENEPIO:0100355]: + text: Seasonal Worker [GENEPIO:0100355] + description: A role inhering in a person that is realized when the bearer + performs labor for a particular period of the year, such as harvest, or + Christmas. + meaning: GENEPIO:0100355 + is_a: Work [GENEPIO:0100254] + Veterinarian [GENEPIO:0100265]: + text: Veterinarian [GENEPIO:0100265] + description: A role inhering in a person that is realized when the bearer + is a professional who practices veterinary medicine. + meaning: GENEPIO:0100265 + is_a: Work [GENEPIO:0100254] + Social role [OMRSE:00000001]: + text: Social role [OMRSE:00000001] + description: A social role inhering in a human being. + meaning: OMRSE:00000001 + Acquaintance of case [GENEPIO:0100266]: + text: Acquaintance of case [GENEPIO:0100266] + description: A role inhering in a person that is realized when the bearer + is in a state of being acquainted with a person. + meaning: GENEPIO:0100266 + is_a: Social role [OMRSE:00000001] + Relative of case [GENEPIO:0100267]: + text: Relative of case [GENEPIO:0100267] + description: A role inhering in a person that is realized when the bearer + is a relative of the case. + meaning: GENEPIO:0100267 + is_a: Social role [OMRSE:00000001] + Child of case [GENEPIO:0100268]: + text: Child of case [GENEPIO:0100268] + description: A role inhering in a person that is realized when the bearer + is a person younger than the age of majority. + meaning: GENEPIO:0100268 + is_a: Relative of case [GENEPIO:0100267] + Parent of case [GENEPIO:0100269]: + text: Parent of case [GENEPIO:0100269] + description: A role inhering in a person that is realized when the bearer + is a caregiver of the offspring of their own species. + meaning: GENEPIO:0100269 + is_a: Relative of case [GENEPIO:0100267] + Father of case [GENEPIO:0100270]: + text: Father of case [GENEPIO:0100270] + description: A role inhering in a person that is realized when the bearer + is the male parent of a child. + meaning: GENEPIO:0100270 + is_a: Parent of case [GENEPIO:0100269] + Mother of case [GENEPIO:0100271]: + text: Mother of case [GENEPIO:0100271] + description: A role inhering in a person that is realized when the bearer + is the female parent of a child. + meaning: GENEPIO:0100271 + is_a: Parent of case [GENEPIO:0100269] + Spouse of case [GENEPIO:0100272]: + text: Spouse of case [GENEPIO:0100272] + description: A role inhering in a person that is realized when the bearer + is a significant other in a marriage, civil union, or common-law marriage. + meaning: GENEPIO:0100272 + is_a: Social role [OMRSE:00000001] + Other Host Role: + text: Other Host Role + ExposureSettingMenu: + name: ExposureSettingMenu + title: exposure_setting menu + permissible_values: + Human Exposure [ECTO:3000005]: + text: Human Exposure [ECTO:3000005] + description: A history of exposure to Homo sapiens. + meaning: ECTO:3000005 + Contact with Patient [GENEPIO:0100185]: + text: Contact with Patient [GENEPIO:0100185] + description: A process occuring within or in the vicinity of a human patient + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100185 + is_a: Human Exposure [ECTO:3000005] + Contact with Person with Acute Respiratory Illness [GENEPIO:0100187]: + text: Contact with Person with Acute Respiratory Illness [GENEPIO:0100187] + meaning: GENEPIO:0100187 + is_a: Human Exposure [ECTO:3000005] + Contact with Person with Fever and/or Cough [GENEPIO:0100188]: + text: Contact with Person with Fever and/or Cough [GENEPIO:0100188] + meaning: GENEPIO:0100188 + is_a: Human Exposure [ECTO:3000005] + Occupational, Residency or Patronage Exposure [GENEPIO:0100190]: + text: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + description: A process occuring within or in the vicinity of a human residential + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100190 + Abbatoir [ECTO:1000033]: + text: Abbatoir [ECTO:1000033] + description: A exposure event involving the interaction of an exposure receptor + to abattoir. + meaning: ECTO:1000033 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Animal Rescue [GENEPIO:0100191]: + text: Animal Rescue [GENEPIO:0100191] + description: A process occuring within or in the vicinity of an animal rescue + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100191 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Childcare [GENEPIO:0100192]: + text: Childcare [GENEPIO:0100192] + description: A process occuring within or in the vicinity of a human childcare + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100192 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Daycare [GENEPIO:0100193]: + text: Daycare [GENEPIO:0100193] + description: A process occuring within or in the vicinity of a human daycare + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100193 + is_a: Childcare [GENEPIO:0100192] + Nursery [GENEPIO:0100194]: + text: Nursery [GENEPIO:0100194] + description: A process occuring within or in the vicinity of a human nursery + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100194 + is_a: Childcare [GENEPIO:0100192] + Community Service Centre [GENEPIO:0100195]: + text: Community Service Centre [GENEPIO:0100195] + description: A process occuring within or in the vicinity of a community service + centre that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100195 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Correctional Facility [GENEPIO:0100196]: + text: Correctional Facility [GENEPIO:0100196] + description: A process occuring within or in the vicinity of a correctional + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100196 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Dormitory [GENEPIO:0100197]: + text: Dormitory [GENEPIO:0100197] + description: A process occuring within or in the vicinity of a dormitory that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100197 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Farm [ECTO:1000034]: + text: Farm [ECTO:1000034] + description: A exposure event involving the interaction of an exposure receptor + to farm + meaning: ECTO:1000034 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + First Nations Reserve [GENEPIO:0100198]: + text: First Nations Reserve [GENEPIO:0100198] + description: A process occuring within or in the vicinity of a first nations + reserve that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100198 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Funeral Home [GENEPIO:0100199]: + text: Funeral Home [GENEPIO:0100199] + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100199 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Group Home [GENEPIO:0100200]: + text: Group Home [GENEPIO:0100200] + description: A process occuring within or in the vicinity of a group home + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100200 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Healthcare Setting [GENEPIO:0100201]: + text: Healthcare Setting [GENEPIO:0100201] + description: A process occuring within or in the vicinity of a healthcare + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100201 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Ambulance [GENEPIO:0100202]: + text: Ambulance [GENEPIO:0100202] + description: A process occuring within or in the vicinity of an ambulance + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100202 + is_a: Healthcare Setting [GENEPIO:0100201] + Acute Care Facility [GENEPIO:0100203]: + text: Acute Care Facility [GENEPIO:0100203] + description: A process occuring within or in the vicinity of an acute care + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100203 + is_a: Healthcare Setting [GENEPIO:0100201] + Clinic [GENEPIO:0100204]: + text: Clinic [GENEPIO:0100204] + description: A process occuring within or in the vicinity of a medical clinic + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100204 + is_a: Healthcare Setting [GENEPIO:0100201] + Community Healthcare (At-Home) Setting [GENEPIO:0100415]: + text: Community Healthcare (At-Home) Setting [GENEPIO:0100415] + description: A process occuring within or in the vicinty of a the individual + home where the patient or client is living and health care or supportive + care is being being delivered, as opposed to care provided in group accommodations + like clinics or nursing home. + meaning: GENEPIO:0100415 + is_a: Healthcare Setting [GENEPIO:0100201] + Community Health Centre [GENEPIO:0100205]: + text: Community Health Centre [GENEPIO:0100205] + description: A process occuring within or in the vicinity of a community health + centre that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100205 + is_a: Healthcare Setting [GENEPIO:0100201] + Hospital [ECTO:1000035]: + text: Hospital [ECTO:1000035] + description: A exposure event involving the interaction of an exposure receptor + to hospital. + meaning: ECTO:1000035 + is_a: Healthcare Setting [GENEPIO:0100201] + Emergency Department [GENEPIO:0100206]: + text: Emergency Department [GENEPIO:0100206] + description: A process occuring within or in the vicinity of an emergency + department that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100206 + is_a: Hospital [ECTO:1000035] + ICU [GENEPIO:0100207]: + text: ICU [GENEPIO:0100207] + description: A process occuring within or in the vicinity of an ICU that exposes + the recipient organism to a material entity. + meaning: GENEPIO:0100207 + is_a: Hospital [ECTO:1000035] + Ward [GENEPIO:0100208]: + text: Ward [GENEPIO:0100208] + description: A process occuring within or in the vicinity of a hospital ward + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100208 + is_a: Hospital [ECTO:1000035] + Laboratory [ECTO:1000036]: + text: Laboratory [ECTO:1000036] + description: A exposure event involving the interaction of an exposure receptor + to laboratory facility. + meaning: ECTO:1000036 + is_a: Healthcare Setting [GENEPIO:0100201] + Long-Term Care Facility [GENEPIO:0100209]: + text: Long-Term Care Facility [GENEPIO:0100209] + description: A process occuring within or in the vicinity of a long-term care + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100209 + is_a: Healthcare Setting [GENEPIO:0100201] + Pharmacy [GENEPIO:0100210]: + text: Pharmacy [GENEPIO:0100210] + description: A process occuring within or in the vicinity of a pharmacy that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100210 + is_a: Healthcare Setting [GENEPIO:0100201] + Physician's Office [GENEPIO:0100211]: + text: Physician's Office [GENEPIO:0100211] + description: A process occuring within or in the vicinity of a physician's + office that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100211 + is_a: Healthcare Setting [GENEPIO:0100201] + Household [GENEPIO:0100212]: + text: Household [GENEPIO:0100212] + description: A process occuring within or in the vicinity of a household that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100212 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Insecure Housing (Homeless) [GENEPIO:0100213]: + text: Insecure Housing (Homeless) [GENEPIO:0100213] + description: A process occuring that exposes the recipient organism to a material + entity as a consequence of said organism having insecure housing. + meaning: GENEPIO:0100213 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Occupational Exposure [GENEPIO:0100214]: + text: Occupational Exposure [GENEPIO:0100214] + description: A process occuring within or in the vicinity of a human occupational + environment that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100214 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Worksite [GENEPIO:0100215]: + text: Worksite [GENEPIO:0100215] + description: A process occuring within or in the vicinity of an office that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100215 + is_a: Occupational Exposure [GENEPIO:0100214] + Office [ECTO:1000037]: + text: Office [ECTO:1000037] + description: A exposure event involving the interaction of an exposure receptor + to office. + meaning: ECTO:1000037 + is_a: Worksite [GENEPIO:0100215] + Outdoors [GENEPIO:0100216]: + text: Outdoors [GENEPIO:0100216] + description: A process occuring outdoors that exposes the recipient organism + to a material entity. + meaning: GENEPIO:0100216 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Camp/camping [ECTO:5000009]: + text: Camp/camping [ECTO:5000009] + description: A exposure event involving the interaction of an exposure receptor + to campground. + meaning: ECTO:5000009 + is_a: Outdoors [GENEPIO:0100216] + Hiking Trail [GENEPIO:0100217]: + text: Hiking Trail [GENEPIO:0100217] + description: A process that exposes the recipient organism to a material entity + as a consequence of hiking. + meaning: GENEPIO:0100217 + is_a: Outdoors [GENEPIO:0100216] + Hunting Ground [ECTO:6000030]: + text: Hunting Ground [ECTO:6000030] + description: An exposure event involving hunting behavior + meaning: ECTO:6000030 + is_a: Outdoors [GENEPIO:0100216] + Petting zoo [ECTO:5000008]: + text: Petting zoo [ECTO:5000008] + description: A exposure event involving the interaction of an exposure receptor + to petting zoo. + meaning: ECTO:5000008 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Place of Worship [GENEPIO:0100220]: + text: Place of Worship [GENEPIO:0100220] + description: A process occuring within or in the vicinity of a place of worship + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100220 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Church [GENEPIO:0100221]: + text: Church [GENEPIO:0100221] + description: A process occuring within or in the vicinity of a church that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100221 + is_a: Place of Worship [GENEPIO:0100220] + Mosque [GENEPIO:0100222]: + text: Mosque [GENEPIO:0100222] + description: A process occuring within or in the vicinity of a mosque that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100222 + is_a: Place of Worship [GENEPIO:0100220] + Temple [GENEPIO:0100223]: + text: Temple [GENEPIO:0100223] + description: A process occuring within or in the vicinity of a temple that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100223 + is_a: Place of Worship [GENEPIO:0100220] + Restaurant [ECTO:1000040]: + text: Restaurant [ECTO:1000040] + description: A exposure event involving the interaction of an exposure receptor + to restaurant. + meaning: ECTO:1000040 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Retail Store [ECTO:1000041]: + text: Retail Store [ECTO:1000041] + description: A exposure event involving the interaction of an exposure receptor + to shop. + meaning: ECTO:1000041 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + School [GENEPIO:0100224]: + text: School [GENEPIO:0100224] + description: A process occuring within or in the vicinity of a school that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100224 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Temporary Residence [GENEPIO:0100225]: + text: Temporary Residence [GENEPIO:0100225] + description: A process occuring within or in the vicinity of a temporary residence + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100225 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Homeless Shelter [GENEPIO:0100226]: + text: Homeless Shelter [GENEPIO:0100226] + description: A process occuring within or in the vicinity of a homeless shelter + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100226 + is_a: Temporary Residence [GENEPIO:0100225] + Hotel [GENEPIO:0100227]: + text: Hotel [GENEPIO:0100227] + description: A process occuring within or in the vicinity of a hotel exposure + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100227 + is_a: Temporary Residence [GENEPIO:0100225] + Veterinary Care Clinic [GENEPIO:0100228]: + text: Veterinary Care Clinic [GENEPIO:0100228] + description: A process occuring within or in the vicinity of a veterinary + facility that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100228 + is_a: Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + Travel Exposure [GENEPIO:0100229]: + text: Travel Exposure [GENEPIO:0100229] + description: A process occuring as a result of travel that exposes the recipient + organism to a material entity. + meaning: GENEPIO:0100229 + Travelled on a Cruise Ship [GENEPIO:0100230]: + text: Travelled on a Cruise Ship [GENEPIO:0100230] + description: A process occuring within or in the vicinity of a cruise ship + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100230 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled on a Plane [GENEPIO:0100231]: + text: Travelled on a Plane [GENEPIO:0100231] + description: A process occuring within or in the vicinity of an airplane that + exposes the recipient organism to a material entity. + meaning: GENEPIO:0100231 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled on Ground Transport [GENEPIO:0100232]: + text: Travelled on Ground Transport [GENEPIO:0100232] + description: A process occuring within or in the vicinity of ground transport + that exposes the recipient organism to a material entity. + meaning: GENEPIO:0100232 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled outside Province/Territory [GENEPIO:0001118]: + text: Travelled outside Province/Territory [GENEPIO:0001118] + meaning: GENEPIO:0001118 + is_a: Travel Exposure [GENEPIO:0100229] + Travelled outside Canada [GENEPIO:0001119]: + text: Travelled outside Canada [GENEPIO:0001119] + meaning: GENEPIO:0001119 + is_a: Travel Exposure [GENEPIO:0100229] + Other Exposure Setting [GENEPIO:0100235]: + text: Other Exposure Setting [GENEPIO:0100235] + description: A process occuring that exposes the recipient organism to a material + entity. + meaning: GENEPIO:0100235 + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu + title: host_vaccination_status menu + permissible_values: + Fully Vaccinated [GENEPIO:0100100]: + text: Fully Vaccinated [GENEPIO:0100100] + description: Completed a full series of an authorized vaccine according to + the regional health institutional guidance. + meaning: GENEPIO:0100100 + Not Vaccinated [GENEPIO:0100102]: + text: Not Vaccinated [GENEPIO:0100102] + description: Have not completed or initiated a vaccine series authorized and + administered according to the regional health institutional guidance. + meaning: GENEPIO:0100102 + InfluenzaAntiviralTreatmentAdministrationMenu: + name: InfluenzaAntiviralTreatmentAdministrationMenu + title: influenza_antiviral_treatment_administration menu + permissible_values: + Influenza antiviral treatment administered [GENEPIO:0101194]: + text: Influenza antiviral treatment administered [GENEPIO:0101194] + meaning: GENEPIO:0101194 + No influenza antiviral treatment administered [GENEPIO:0101195]: + text: No influenza antiviral treatment administered [GENEPIO:0101195] + meaning: GENEPIO:0101195 + WaterCatchmentAreaHumanPopulationRangeMenu: + name: WaterCatchmentAreaHumanPopulationRangeMenu + title: water_catchment_area_human_population_range menu + permissible_values: + <10 people: + text: <10 people + 10 - 100 people: + text: 10 - 100 people + 100 - 1,000 people: + text: 100 - 1,000 people + 1,000 - 10,000 people: + text: 1,000 - 10,000 people + 10,000 - 100,000 people: + text: 10,000 - 100,000 people + 100,000 - 1,000,000 people: + text: 100,000 - 1,000,000 people + 1,000,000+ people: + text: 1,000,000+ people + WaterCatchmentAreaHumanPopulationDensityUnitMenu: + name: WaterCatchmentAreaHumanPopulationDensityUnitMenu + title: water_catchment_area_human_population_density_unit menu + permissible_values: + persons per square mile [GENEPIO:0100989]: + text: persons per square mile [GENEPIO:0100989] + description: A unit of population density that describes the average number + of people in a square mile of a given area. + meaning: GENEPIO:0100989 + persons per square kilometer [GENEPIO:0100990]: + text: persons per square kilometer [GENEPIO:0100990] + description: A unit of population density that describes the average number + of people in a square kilometer of a given area. + meaning: GENEPIO:0100990 + residents per square mile [GENEPIO:0100991]: + text: residents per square mile [GENEPIO:0100991] + description: A unit of population density that describes the average number + of registered residents in a square mile of a given area. + meaning: GENEPIO:0100991 + residents per square kilometer [GENEPIO:0100992]: + text: residents per square kilometer [GENEPIO:0100992] + description: A unit of population density that describes the average number + of registered residents in a square kilometer of a given area. + meaning: GENEPIO:0100992 + PopulatedAreaTypeMenu: + name: PopulatedAreaTypeMenu + title: populated_area_type menu + permissible_values: + Suburban [GSSO:011077]: + text: Suburban [GSSO:011077] + description: A mixed-use or residential area, existing either as part of a + city/urban area, or as a separate residential community within commuting + distance of one. Suburbs might have their own political or legal jurisdiction, + especially in the United States, but this is not always the case, especially + in the United Kingdom where most suburbs are located within the administrative + boundaries of cities. + meaning: GSSO:011077 + Rural [GSSO:011078]: + text: Rural [GSSO:011078] + description: A geographic area that is located outside towns and cities. Rural + areas are primarily used for agriculture or pastoralism and may contain + rural settlements. + meaning: GSSO:011078 + Urban [GSSO:011080]: + text: Urban [GSSO:011080] + description: A human settlement with a high population density and infrastructure + of built environment. Urban areas are created through urbanization and are + categorized by urban morphology as cities, towns, conurbations or suburbs. + In urbanism, the term contrasts to rural areas such as villages and hamlets; + in urban sociology or urban anthropology it contrasts with natural environment. + meaning: GSSO:011080 + SamplingWeatherConditionsMenu: + name: SamplingWeatherConditionsMenu + title: sampling_weather_conditions menu + permissible_values: + Cloudy/Overcast [ENVO:03501418]: + text: Cloudy/Overcast [ENVO:03501418] + description: Atmospheric weather in which the sky is mostly or completely + obscured by clouds. + meaning: ENVO:03501418 + Partially cloudy [ENVO:03501419]: + text: Partially cloudy [ENVO:03501419] + description: Atmospheric weather in which the sky is partially obscured by + clouds. + meaning: ENVO:03501419 + is_a: Cloudy/Overcast [ENVO:03501418] + Drizzle [ENVO:03501420]: + text: Drizzle [ENVO:03501420] + description: An aggregate of water drops smaller than those of rain which + falls on a planetary surface during a precipitation process. + meaning: ENVO:03501420 + Fog [ENVO:01000844]: + text: Fog [ENVO:01000844] + description: A visible mass of cloud water droplets or ice crystals suspended + in the air at or near the surface of an astronomical body. + meaning: ENVO:01000844 + Rain [ENVO:01001564]: + text: Rain [ENVO:01001564] + description: An aggregate of raindrops falling to a planetary surface during + a precipitation process. + meaning: ENVO:01001564 + Snow [ENVO:01000406]: + text: Snow [ENVO:01000406] + description: Snow is an environmental material which is primarily composed + of flakes of crystalline water ice. + meaning: ENVO:01000406 + Storm [ENVO:01000876]: + text: Storm [ENVO:01000876] + description: A storm is an environmental process in which an environmental + system and the processes it participates in are strongly perturbed by external + forcings. These forcings typically increase the rates of processes unfolding + in the system, relative to their normal rates. + meaning: ENVO:01000876 + Sunny/Clear [ENVO:03501421]: + text: Sunny/Clear [ENVO:03501421] + description: Atmospheric weather in which the sun can be seen to shine brightly. + meaning: ENVO:03501421 + PresamplingWeatherConditionsMenu: + name: PresamplingWeatherConditionsMenu + title: presampling_weather_conditions menu + permissible_values: + Cloudy/Overcast [ENVO:03501418]: + text: Cloudy/Overcast [ENVO:03501418] + description: Atmospheric weather in which the sky is mostly or completely + obscured by clouds. + meaning: ENVO:03501418 + Partially cloudy [ENVO:03501419]: + text: Partially cloudy [ENVO:03501419] + description: Atmospheric weather in which the sky is partially obscured by + clouds. + meaning: ENVO:03501419 + is_a: Cloudy/Overcast [ENVO:03501418] + Drizzle [ENVO:03501420]: + text: Drizzle [ENVO:03501420] + description: An aggregate of water drops smaller than those of rain which + falls on a planetary surface during a precipitation process. + meaning: ENVO:03501420 + Fog [ENVO:01000844]: + text: Fog [ENVO:01000844] + description: A visible mass of cloud water droplets or ice crystals suspended + in the air at or near the surface of an astronomical body. + meaning: ENVO:01000844 + Rain [ENVO:01001564]: + text: Rain [ENVO:01001564] + description: An aggregate of raindrops falling to a planetary surface during + a precipitation process. + meaning: ENVO:01001564 + Snow [ENVO:01000406]: + text: Snow [ENVO:01000406] + description: Snow is an environmental material which is primarily composed + of flakes of crystalline water ice. + meaning: ENVO:01000406 + Storm [ENVO:01000876]: + text: Storm [ENVO:01000876] + description: A storm is an environmental process in which an environmental + system and the processes it participates in are strongly perturbed by external + forcings. These forcings typically increase the rates of processes unfolding + in the system, relative to their normal rates. + meaning: ENVO:01000876 + Sunny/Clear [ENVO:03501421]: + text: Sunny/Clear [ENVO:03501421] + description: Atmospheric weather in which the sun can be seen to shine brightly. + meaning: ENVO:03501421 + PrecipitationMeasurementUnitMenu: + name: PrecipitationMeasurementUnitMenu + title: precipitation_measurement_unit menu + permissible_values: + millimeter (mm) [UO:0000016]: + text: millimeter (mm) [UO:0000016] + description: A length unit which is defined as one thousandth of a meter. + meaning: UO:0000016 + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m + meaning: UO:0000015 + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. + meaning: UO:0000008 + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. + meaning: UO:0010011 + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. + meaning: UO:0010013 + AirPressureMeasurementUnitMenu: + name: AirPressureMeasurementUnitMenu + title: air_pressure_measurement_unit menu + permissible_values: + atmosphere (atm) [EFO:0005212]: + text: atmosphere (atm) [EFO:0005212] + description: A non-SI unit of pressure defined as 101,325 pascals (Pa). + meaning: EFO:0005212 + bar: + text: bar + pascal [UO:0000110]: + text: pascal [UO:0000110] + description: An SI unit of pressure defined as one newton per square meter + (N/m^2). + meaning: UO:0000110 + AmbientTemperatureMeasurementUnitMenu: + name: AmbientTemperatureMeasurementUnitMenu + title: ambient_temperature_measurement_unit menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + TotalDailyFlowRateMeasurementUnitMenu: + name: TotalDailyFlowRateMeasurementUnitMenu + title: total_daily_flow_rate_measurement_unit menu + permissible_values: + cubic meter per second (m^3/s): + text: cubic meter per second (m^3/s) + cubic meter per minute (m^3/min): + text: cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h): + text: cubic meter per hour (m^3/h) + liter per second (L/s): + text: liter per second (L/s) + liter per minute (L/min): + text: liter per minute (L/min) + liter per hour (L/h): + text: liter per hour (L/h) + liter per day (L/day): + text: liter per day (L/day) + million gallons per day (MGD): + text: million gallons per day (MGD) + InstantaneousFlowRateMeasurementUnitMenu: + name: InstantaneousFlowRateMeasurementUnitMenu + title: instantaneous_flow_rate_measurement_unit menu + permissible_values: + cubic meter per second (m^3/s): + text: cubic meter per second (m^3/s) + cubic meter per minute (m^3/min): + text: cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h): + text: cubic meter per hour (m^3/h) + liter per second (L/s): + text: liter per second (L/s) + liter per minute (L/min): + text: liter per minute (L/min) + liter per hour (L/h): + text: liter per hour (L/h) + liter per day (L/day): + text: liter per day (L/day) + million gallons per day (MGD): + text: million gallons per day (MGD) + TurbidityMeasurementUnitMenu: + name: TurbidityMeasurementUnitMenu + title: turbidity_measurement_unit menu + permissible_values: + nephelometric turbidity unit (NTU): + text: nephelometric turbidity unit (NTU) + formazin nephelometric unit (FNU) [UO:0000318]: + text: formazin nephelometric unit (FNU) [UO:0000318] + description: A measure of turbidity calculated by comparing how infrared light + is scattered in a water sample against the amount of infrared light scattered + in a reference solution containing formazin. + meaning: UO:0000318 + DissolvedOxygenMeasurementUnitMenu: + name: DissolvedOxygenMeasurementUnitMenu + title: dissolved_oxygen_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + kilogram per cubic meter (kg/m^3) [UO:0000083]: + text: kilogram per cubic meter (kg/m^3) [UO:0000083] + description: An SI unit of density that is one thousandth of the density of + water. + meaning: UO:0000083 + part per million (ppm) [UO:0000169]: + text: part per million (ppm) [UO:0000169] + description: A unitless measure of density that represents one item out of + a million. + meaning: UO:0000169 + OxygenReductionPotentialOrpMeasurementUnitMenu: + name: OxygenReductionPotentialOrpMeasurementUnitMenu + title: oxygen_reduction_potential_(ORP)_measurement_unit menu + permissible_values: + milliVolt (mV) [UO:0000247]: + text: milliVolt (mV) [UO:0000247] + description: A non-SI unit of electromotive force that is one thousandth of + a volt. + meaning: UO:0000247 + ChemicalOxygenDemandCodMeasurementUnitMenu: + name: ChemicalOxygenDemandCodMeasurementUnitMenu + title: chemical_oxygen_demand_(COD)_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu: + name: CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu + title: carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + TotalSuspendedSolidsTssMeasurementUnitMenu: + name: TotalSuspendedSolidsTssMeasurementUnitMenu + title: total_suspended_solids_(TSS)_measurement_unit menu + permissible_values: + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. + meaning: UO:0000187 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + TotalDissolvedSolidsTdsMeasurementUnitMenu: + name: TotalDissolvedSolidsTdsMeasurementUnitMenu + title: total_dissolved_solids_(TDS)_measurement_unit menu + permissible_values: + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. + meaning: UO:0000187 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + TotalSolidsTsMeasurementUnitMenu: + name: TotalSolidsTsMeasurementUnitMenu + title: total_solids_(TS)_measurement_unit menu + permissible_values: + percent (%) [UO:0000187]: + text: percent (%) [UO:0000187] + description: A unitless measure that represents one in a hundred. + meaning: UO:0000187 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + AlkalinityMeasurementUnitMenu: + name: AlkalinityMeasurementUnitMenu + title: alkalinity_measurement_unit menu + permissible_values: + milliequivalent per liter (meq/L): + text: milliequivalent per liter (meq/L) + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + parts per million [UO:0000169]: + text: parts per million [UO:0000169] + description: A unitless measure of density that represents one item out of + a million. + meaning: UO:0000169 + ConductivityMeasurementUnitMenu: + name: ConductivityMeasurementUnitMenu + title: conductivity_measurement_unit menu + permissible_values: + milliSiemen per centimeter (mS/cm): + text: milliSiemen per centimeter (mS/cm) + "microSiemen per centimeter (\u03BCS/cm)": + text: "microSiemen per centimeter (\u03BCS/cm)" + Siemen per meter (S/m): + text: Siemen per meter (S/m) + SalinityMeasurementUnitMenu: + name: SalinityMeasurementUnitMenu + title: salinity_measurement_unit menu + permissible_values: + practical salinity unit (PSU): + text: practical salinity unit (PSU) + weight for weight (% w/w): + text: weight for weight (% w/w) + parts per thousand [UO:0000168]: + text: parts per thousand [UO:0000168] + description: A dimensionless concentration notation which denotes the amount + of a given substance in a total amount of 1000 regardless of the units of + measure as long as they are the same. + meaning: UO:0000168 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + TotalNitrogenTnMeasurementUnitMenu: + name: TotalNitrogenTnMeasurementUnitMenu + title: total_nitrogen_(TN)_measurement_unit menu + permissible_values: + milligram per liter (mg/L) [UO:0000273]: + text: milligram per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + gram per liter (g/L) [UO:0000175]: + text: gram per liter (g/L) [UO:0000175] + description: A non-SI unit of density that is a thousand kilograms per cubic + meter. + meaning: UO:0000175 + gram per total solids (g/gTS): + text: gram per total solids (g/gTS) + TotalPhosphorpusTpMeasurementUnitMenu: + name: TotalPhosphorpusTpMeasurementUnitMenu + title: total_phosphorpus_(TP)_measurement_unit menu + permissible_values: + gram per total solids (g/gTS): + text: gram per total solids (g/gTS) + orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]: + text: orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] + description: A substance unit which describes the weight of orthophosphate + as phosphorus (gPO4-P) within a sample to the weight of total solids. + meaning: GENEPIO:0100998 + milligrams per liter (mg/L) [UO:0000273]: + text: milligrams per liter (mg/L) [UO:0000273] + description: A non-SI unit of density that is equivalent to the SI metric + kilogram per cubic meter. + meaning: UO:0000273 + milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999]: + text: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] + description: A density unit comparing the weight of orthophosphate as phosphorus + (PO4-P) in milligrams within a standard liter volume. + meaning: GENEPIO:0100999 + FecalContaminationIndicatorMenu: + name: FecalContaminationIndicatorMenu + title: fecal contamination indicator menu + permissible_values: + crAssphage [NCBITaxon:1211417]: + text: crAssphage [NCBITaxon:1211417] + description: CrAss-like phage, a bacteriophage discovered in 2014 in the human + fecal metagenome. + meaning: NCBITaxon:1211417 + PMMoV / pepper mild mottle virus [NCBITaxon:12239]: + text: PMMoV / pepper mild mottle virus [NCBITaxon:12239] + description: A plant RNA virus that is abundant in human feces. + meaning: NCBITaxon:12239 + Bacteroides HF183: + text: Bacteroides HF183 + description: A fecal indicator which is the most commonly used sewage-associated + marker gene, belonging to the Bacteroides genus. + meaning: GENEPIO:0101000 + Lachnospiraceae Lachno3: + text: Lachnospiraceae Lachno3 + description: A fecal indicator which is a human-associated genetic marker + in the Lachnospiraceae family of bacteria. + meaning: GENEPIO:0101001 + F+ (male specific) coliphages: + text: F+ (male specific) coliphages + description: A fecal indicator which is a bacteriophage that infects coliform + bacteria and is used in water assessment. + meaning: GENEPIO:0101002 + Stercobilin: + text: Stercobilin + description: Bile pigment found in fecal material. + meaning: CHEBI:26756 + FecalContaminationUnitMenu: + name: FecalContaminationUnitMenu + title: fecal_contamination_unit menu + permissible_values: + log10 gene copies per 100 milliliter (log10 GC/100 mL): + text: log10 gene copies per 100 milliliter (log10 GC/100 mL) + gene copies per liter (GC/L): + text: gene copies per liter (GC/L) + PCR quantification cycle [UO:0010077]: + text: PCR quantification cycle [UO:0010077] + description: A count unit of how many Polymerase Chain Reaction (PCR) cycles + it took to detect a real signal from a sample. Equivalent to the PCR cycle + number at which a sample's reaction curve intersects the threshold line. + meaning: UO:0010077 + log10 gene copies per nanogram total DNA: + text: log10 gene copies per nanogram total DNA + UrinaryContaminationIndicatorMenu: + name: UrinaryContaminationIndicatorMenu + title: urinary_contamination_indicator menu + permissible_values: + Urobilin [CHEBI:36378]: + text: Urobilin [CHEBI:36378] + description: A tetrapyrroledicarboxylic acid that causes the yellow color + in urine. Also known as urochrome. + meaning: CHEBI:36378 + UrinaryContaminationUnitMenu: + name: UrinaryContaminationUnitMenu + title: urinary_contamination_unit menu + permissible_values: + nanograms per liter (ng/L) [EFO:0004382]: + text: nanograms per liter (ng/L) [EFO:0004382] + description: A mass unit density which is equal to mass of an object in nanograms + divided by the volume in liters. + meaning: EFO:0004382 + FecalColiformCountUnitMenu: + name: FecalColiformCountUnitMenu + title: fecal_coliform_count_unit menu + permissible_values: + colony forming units per milliliter (CFU/mL) [UO:0000213]: + text: colony forming units per milliliter (CFU/mL) [UO:0000213] + description: A unit of microbial density that describes the number of colony + forming units within a milliliter of material. + meaning: UO:0000213 + colony forming units per 100 milliliter (CFU/100 mL): + text: colony forming units per 100 milliliter (CFU/100 mL) + colony forming units per grams total solids (CFU/gTS): + text: colony forming units per grams total solids (CFU/gTS) + most probable number per milliliter (MPN/mL): + text: most probable number per milliliter (MPN/mL) + most probable number per 100 milliliter (MPN/100 mL): + text: most probable number per 100 milliliter (MPN/100 mL) + SampleTemperatureUnitAtCollectionMenu: + name: SampleTemperatureUnitAtCollectionMenu + title: sample_temperature_unit_(at collection) menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + SampleTemperatureUnitWhenReceivedMenu: + name: SampleTemperatureUnitWhenReceivedMenu + title: sample_temperature_unit_(when received) menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + SequencingAssayTypeMenu: + name: SequencingAssayTypeMenu + title: sequencing_assay_type menu + permissible_values: + Amplicon sequencing assay [OBI:0002767]: + text: Amplicon sequencing assay [OBI:0002767] + description: A sequencing assay in which a DNA or RNA input molecule is amplified + by PCR and the product sequenced. + meaning: OBI:0002767 + 16S ribosomal gene sequencing assay [OBI:0002763]: + text: 16S ribosomal gene sequencing assay [OBI:0002763] + description: An amplicon sequencing assay in which the amplicon is derived + from universal primers used to amplify the 16S ribosomal RNA gene from isolate + bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting + sequences are compared to reference 16S sequence databases to identify or + classify bacteria present within a given sample. + meaning: OBI:0002763 + is_a: Amplicon sequencing assay [OBI:0002767] + CRISPR amplicon sequencing assay [GENEPIO:0101128]: + text: CRISPR amplicon sequencing assay [GENEPIO:0101128] + meaning: GENEPIO:0101128 + is_a: Amplicon sequencing assay [OBI:0002767] + Primal tiling amplicon sequencing assay [GENEPIO:0101129]: + text: Primal tiling amplicon sequencing assay [GENEPIO:0101129] + meaning: GENEPIO:0101129 + is_a: Amplicon sequencing assay [OBI:0002767] + Whole genome sequencing assay [OBI:0002117]: + text: Whole genome sequencing assay [OBI:0002117] + description: A DNA sequencing assay that intends to provide information about + the sequence of an entire genome of an organism. + meaning: OBI:0002117 + Whole metagenome sequencing assay [OBI:0002623]: + text: Whole metagenome sequencing assay [OBI:0002623] + description: A DNA sequencing assay that intends to provide information on + the DNA sequences of multiple genomes (a metagenome) from different organisms + present in the same input sample. + meaning: OBI:0002623 + Whole virome sequencing assay [OBI:0002768]: + text: Whole virome sequencing assay [OBI:0002768] + description: A whole metagenome sequencing assay that intends to provide information + on multiple genome sequences from different viruses present in the same + input sample. + meaning: OBI:0002768 + is_a: Whole metagenome sequencing assay [OBI:0002623] + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose_of_sequencing menu + permissible_values: + Baseline surveillance (random sampling) [GENEPIO:0100005]: + text: Baseline surveillance (random sampling) [GENEPIO:0100005] + description: A surveillance sampling strategy in which baseline is established + at the beginning of a study or project by the selection of sample units + via random sampling. + meaning: GENEPIO:0100005 + Targeted surveillance (non-random sampling) [GENEPIO:0100006]: + text: Targeted surveillance (non-random sampling) [GENEPIO:0100006] + description: A surveillance sampling strategy in which an aspired outcome + is explicitly stated. + meaning: GENEPIO:0100006 + Priority surveillance project [GENEPIO:0100007]: + text: Priority surveillance project [GENEPIO:0100007] + description: A targeted surveillance strategy which is considered important + and/or urgent. + meaning: GENEPIO:0100007 + is_a: Targeted surveillance (non-random sampling) [GENEPIO:0100006] + Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009]: + text: Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] + description: A surveillance strategy in which an individual or site is selected + to undergo repeat sampling over a defined period of time. + meaning: GENEPIO:0100009 + is_a: Priority surveillance project [GENEPIO:0100007] + Cluster/Outbreak investigation [GENEPIO:0100019]: + text: Cluster/Outbreak investigation [GENEPIO:0100019] + description: A sampling strategy in which individuals are chosen for investigation + into a disease cluster or outbreak. + meaning: GENEPIO:0100019 + Multi-jurisdictional outbreak investigation [GENEPIO:0100020]: + text: Multi-jurisdictional outbreak investigation [GENEPIO:0100020] + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that has connections + to two or more jurisdictions. + meaning: GENEPIO:0100020 + is_a: Cluster/Outbreak investigation [GENEPIO:0100019] + Intra-jurisdictional outbreak investigation [GENEPIO:0100021]: + text: Intra-jurisdictional outbreak investigation [GENEPIO:0100021] + description: An outbreak investigation sampling strategy in which individuals + are chosen for investigation into a disease outbreak that only has connections + within a single jurisdiction. + meaning: GENEPIO:0100021 + is_a: Cluster/Outbreak investigation [GENEPIO:0100019] + Research [GENEPIO:0100022]: + text: Research [GENEPIO:0100022] + description: A sampling strategy in which sites are sampled in order to perform + research. + meaning: GENEPIO:0100022 + Viral passage experiment [GENEPIO:0100023]: + text: Viral passage experiment [GENEPIO:0100023] + description: A research sampling strategy in which samples are selected in + order to perform a viral passage experiment. + meaning: GENEPIO:0100023 + is_a: Research [GENEPIO:0100022] + Protocol testing experiment [GENEPIO:0100024]: + text: Protocol testing experiment [GENEPIO:0100024] + description: A research sampling strategy in which samples are collected in + order to test a method or protocol. + meaning: GENEPIO:0100024 + is_a: Research [GENEPIO:0100022] + Retrospective sequencing [GENEPIO:0100356]: + text: Retrospective sequencing [GENEPIO:0100356] + description: A sampling strategy in which stored samples from past events + are sequenced. + meaning: GENEPIO:0100356 + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name_(country) menu + permissible_values: + Afghanistan [GAZ:00006882]: + text: Afghanistan [GAZ:00006882] + description: A landlocked country that is located approximately in the center + of Asia. It is bordered by Pakistan in the south and east Iran in the west, + Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far + northeast. Afghanistan is administratively divided into thirty-four (34) + provinces (welayats). Each province is then divided into many provincial + districts, and each district normally covers a city or several townships. + [ url:http://en.wikipedia.org/wiki/Afghanistan ] + meaning: GAZ:00006882 + Albania [GAZ:00002953]: + text: Albania [GAZ:00002953] + description: 'A country in South Eastern Europe. Albania is bordered by Greece + to the south-east, Montenegro to the north, Kosovo to the northeast, and + the Republic of Macedonia to the east. It has a coast on the Adriatic Sea + to the west, and on the Ionian Sea to the southwest. From the Strait of + Otranto, Albania is less than 100 km from Italy. Albania is divided into + 12 administrative divisions called (Albanian: official qark/qarku, but often + prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities + (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania + ]' + meaning: GAZ:00002953 + Algeria [GAZ:00000563]: + text: Algeria [GAZ:00000563] + description: A country in North Africa. It is bordered by Tunisia in the northeast, + Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, + a few km of the Western Sahara in the west, Morocco in the northwest, and + the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), + 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). + [ url:http://en.wikipedia.org/wiki/Algeria ] + meaning: GAZ:00000563 + American Samoa [GAZ:00003957]: + text: American Samoa [GAZ:00003957] + description: An unincorporated territory of the United States located in the + South Pacific Ocean, southeast of the sovereign State of Samoa. The main + (largest and most populous) island is Tutuila, with the Manu'a Islands, + Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa + ] + meaning: GAZ:00003957 + Andorra [GAZ:00002948]: + text: Andorra [GAZ:00002948] + description: 'A small landlocked country in western Europe, located in the + eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. + Andorra consists of seven communities known as parishes (Catalan: parroquies, + singular - parroquia). Until relatively recently, it had only six parishes; + the seventh, Escaldes-Engordany, was created in 1978. Some parishes have + a further territorial subdivision. Ordino, La Massana and Sant Julia de + Loria are subdivided into quarts (quarters), while Canillo is subdivided + into veinats (neighborhoods). Those mostly coincide with villages, which + are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ]' + meaning: GAZ:00002948 + Angola [GAZ:00001095]: + text: Angola [GAZ:00001095] + description: A country in south-central Africa bordering Namibia to the south, + Democratic Republic of the Congo to the north, and Zambia to the east, and + with a west coast along the Atlantic Ocean. The exclave province Cabinda + has a border with the Republic of the Congo and the Democratic Republic + of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + meaning: GAZ:00001095 + Anguilla [GAZ:00009159]: + text: Anguilla [GAZ:00009159] + description: A British overseas territory in the Caribbean, one of the most + northerly of the Leeward Islands in the Lesser Antilles. It consists of + the main island of Anguilla itself, approximately 26 km long by 5 km wide + at its widest point, together with a number of much smaller islands and + cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila + ] + meaning: GAZ:00009159 + Antarctica [GAZ:00000462]: + text: Antarctica [GAZ:00000462] + description: The Earth's southernmost continent, overlying the South Pole. + It is situated in the southern hemisphere, almost entirely south of the + Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica + ] + meaning: GAZ:00000462 + Antigua and Barbuda [GAZ:00006883]: + text: Antigua and Barbuda [GAZ:00006883] + description: An island nation located on the eastern boundary of the Caribbean + Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda + ] + meaning: GAZ:00006883 + Argentina [GAZ:00002928]: + text: Argentina [GAZ:00002928] + description: 'A South American country, constituted as a federation of twenty-three + provinces and an autonomous city. It is bordered by Paraguay and Bolivia + in the north, Brazil and Uruguay in the northeast, and Chile in the west + and south. The country claims the British controlled territories of the + Falkland Islands and South Georgia and the South Sandwich Islands. Argentina + also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping + other claims made by Chile and the United Kingdom. Argentina is subdivided + into twenty-three provinces (Spanish: provincias, singular provincia) and + one federal district (Capital de la Republica or Capital de la Nacion, informally + the Capital Federal). The federal district and the provinces have their + own constitutions, but exist under a federal system. Provinces are then + divided into departments (Spanish: departamentos, singular departamento), + except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina + ]' + meaning: GAZ:00002928 + Armenia [GAZ:00004094]: + text: Armenia [GAZ:00004094] + description: A landlocked mountainous country in Eurasia between the Black + Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the + west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan + exclave of Azerbaijan to the south. A transcontinental country at the juncture + of Eastern Europe and Western Asia. A former republic of the Soviet Union. + Armenia is divided into ten marzes (provinces, singular marz), with the + city (kaghak) of Yerevan having special administrative status as the country's + capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + meaning: GAZ:00004094 + Aruba [GAZ:00004025]: + text: Aruba [GAZ:00004025] + description: An autonomous region within the Kingdom of the Netherlands, Aruba + has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba + ] + meaning: GAZ:00004025 + Ashmore and Cartier Islands [GAZ:00005901]: + text: Ashmore and Cartier Islands [GAZ:00005901] + description: A Territory of Australia that includes two groups of small low-lying + uninhabited tropical islands in the Indian Ocean situated on the edge of + the continental shelf north-west of Australia and south of the Indonesian + island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands + ] + meaning: GAZ:00005901 + Australia [GAZ:00000463]: + text: Australia [GAZ:00000463] + description: A country in the southern hemisphere comprising the mainland + of the world's smallest continent, the major island of Tasmania, and a number + of other islands in the Indian and Pacific Oceans. The neighbouring countries + are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon + Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to + the south-east. Australia has six states, two major mainland territories, + and other minor territories. + meaning: GAZ:00000463 + Austria [GAZ:00002942]: + text: Austria [GAZ:00002942] + description: A landlocked country in Central Europe. It borders both Germany + and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia + and Italy to the south, and Switzerland and Liechtenstein to the west. The + capital is the city of Vienna on the Danube River. Austria is divided into + nine states (Bundeslander). These states are then divided into districts + (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities + (Gemeinden). Cities have the competencies otherwise granted to both districts + and municipalities. + meaning: GAZ:00002942 + Azerbaijan [GAZ:00004941]: + text: Azerbaijan [GAZ:00004941] + description: A country in the he South Caucasus region of Eurasia, it is bounded + by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, + Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan + is bordered by Armenia to the north and east, Iran to the south and west, + and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts + in Azerbaijan's southwest, have been controlled by Armenia since the end + of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons + 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + meaning: GAZ:00004941 + Bahamas [GAZ:00002733]: + text: Bahamas [GAZ:00002733] + description: A country consisting of two thousand cays and seven hundred islands + that form an archipelago. It is located in the Atlantic Ocean, southeast + of Florida and the United States, north of Cuba, the island of Hispanola + and the Caribbean, and northwest of the British overseas territory of the + Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, + whose affairs are handled directly by the central government. + meaning: GAZ:00002733 + Bahrain [GAZ:00005281]: + text: Bahrain [GAZ:00005281] + description: A borderless island country in the Persian Gulf. Saudi Arabia + lies to the west and is connected to Bahrain by the King Fahd Causeway, + and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into + five governorates. + meaning: GAZ:00005281 + Baker Island [GAZ:00007117]: + text: Baker Island [GAZ:00007117] + description: An uninhabited atoll located just north of the equator in the + central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island + is an unincorporated and unorganized territory of the US. + meaning: GAZ:00007117 + Bangladesh [GAZ:00003750]: + text: Bangladesh [GAZ:00003750] + description: A country in South Asia. It is bordered by India on all sides + except for a small border with Myanmar to the far southeast and by the Bay + of Bengal to the south. Bangladesh is divided into six administrative divisions. + Divisions are subdivided into districts (zila). There are 64 districts in + Bangladesh, each further subdivided into upazila (subdistricts) or thana + ("police stations"). + meaning: GAZ:00003750 + Barbados [GAZ:00001251]: + text: Barbados [GAZ:00001251] + description: "An island country in the Lesser Antilles of the West Indies,\ + \ in the Caribbean region of the Americas, and the most easterly of the\ + \ Caribbean Islands. It is 34 kilometres (21 miles) in length and up to\ + \ 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is\ + \ in the western part of the North Atlantic, 100 km (62 mi) east of the\ + \ Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards,\ + \ part of the Lesser Antilles, at roughly 13\xB0N of the equator. It is\ + \ about 168 km (104 mi) east of both the countries of Saint Lucia and Saint\ + \ Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique\ + \ and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside\ + \ the principal Atlantic hurricane belt. Its capital and largest city is\ + \ Bridgetown." + meaning: GAZ:00001251 + Bassas da India [GAZ:00005810]: + text: Bassas da India [GAZ:00005810] + description: A roughly circular atoll about 10 km in diameter, which corresponds + to a total size (including lagoon) of 80 km2. It is located in the southern + Mozambique Channel, about half-way between Madagascar (which is 385 km to + the east) and Mozambique, and 110 km northwest of Europa Island. It rises + steeply from the seabed 3000 m below. + meaning: GAZ:00005810 + Belarus [GAZ:00006886]: + text: Belarus [GAZ:00006886] + description: A landlocked country in Eastern Europe, that borders Russia to + the north and east, Ukraine to the south, Poland to the west, and Lithuania + and Latvia to the north. Its capital is Minsk. Belarus is divided into six + voblasts, or provinces. Voblasts are further subdivided into raions (commonly + translated as districts or regions). As of 2002, there are six voblasts, + 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special + status, due to the city serving as the national capital. + meaning: GAZ:00006886 + Belgium [GAZ:00002938]: + text: Belgium [GAZ:00002938] + description: A country in northwest Europe. Belgium shares borders with France + (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 + km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each + comprise five provinces; the third region, Brussels-Capital Region, is not + a province, nor does it contain any Together, these comprise 589 municipalities, + which in general consist of several sub-municipalities (which were independent + municipalities before the municipal merger operation mainly in 1977). + meaning: GAZ:00002938 + Belize [GAZ:00002934]: + text: Belize [GAZ:00002934] + description: A country in Central America. It is the only officially English + speaking country in the region. Belize was a British colony for more than + a century and was known as British Honduras until 1973. It became an independent + nation within The Commonwealth in 1981. Belize is divided into 6 districts, + which are further divided into 31 constituencies. + meaning: GAZ:00002934 + Benin [GAZ:00000904]: + text: Benin [GAZ:00000904] + description: A country in Western Africa. It borders Togo to the west, Nigeria + to the east and Burkina Faso and Niger to the north; its short coastline + to the south leads to the Bight of Benin. Its capital is Porto Novo, but + the seat of government is Cotonou. Benin is divided into 12 departments + and subdivided into 77 communes. + meaning: GAZ:00000904 + Bermuda [GAZ:00001264]: + text: Bermuda [GAZ:00001264] + description: A British overseas territory in the North Atlantic Ocean. Located + off the east coast of the United States, it is situated around 1770 km NE + of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately + 138 islands. + meaning: GAZ:00001264 + Bhutan [GAZ:00003920]: + text: Bhutan [GAZ:00003920] + description: A landlocked nation in South Asia. It is located amidst the eastern + end of the Himalaya Mountains and is bordered to the south, east and west + by India and to the north by Tibet. Bhutan is separated from Nepal by the + Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative + zones). Each dzongdey is further divided into dzongkhag (districts). There + are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into + subdistricts known as dungkhag. At the basic level, groups of villages form + a constituency called gewog. + meaning: GAZ:00003920 + Bolivia [GAZ:00002511]: + text: Bolivia [GAZ:00002511] + description: 'A landlocked country in central South America. It is bordered + by Brazil on the north and east, Paraguay and Argentina on the south, and + Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: + departamentos). Each of the departments is subdivided into provinces (provincias), + which are further subdivided into municipalities (municipios).' + meaning: GAZ:00002511 + Borneo [GAZ:00025355]: + text: Borneo [GAZ:00025355] + description: 'An island at the grographic centre of Maritime Southeast Adia, + in relation to major Indonesian islands, it is located north of Java, west + of Sulawesi, and east of Sumatra. It is the third-largest island in the + world and the larest in Asia. The island is politically divided among three + countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] + Approximately 73% of the island is Indonesian territory. In the north, the + East Malaysian states of Sabah and Sarawak make up about 26% of the island. + Additionally, the Malaysian federal territory of Labuan is situated on a + small island just off the coast of Borneo. The sovereign state of Brunei, + located on the north coast, comprises about 1% of Borneo''s land area. A + little more than half of the island is in the Northern Hemisphere, including + Brunei and the Malaysian portion, while the Indonesian portion spans the + Northern and Southern hemispheres.' + meaning: GAZ:00025355 + Bosnia and Herzegovina [GAZ:00006887]: + text: Bosnia and Herzegovina [GAZ:00006887] + description: A country on the Balkan peninsula of Southern Europe. Bordered + by Croatia to the north, west and south, Serbia to the east, and Montenegro + to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 + km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided + into three political regions of which one, the Brcko District is part of + the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. + All three have an equal constitutional status on the whole territory of + Bosnia and Herzegovina. + meaning: GAZ:00006887 + Botswana [GAZ:00001097]: + text: Botswana [GAZ:00001097] + description: A landlocked nation in Southern Africa. It is bordered by South + Africa to the south and southeast, Namibia to the west, Zambia to the north, + and Zimbabwe to the northeast. Botswana is divided into nine districts, + which are subdivided into a total twenty-eight subdistricts. + meaning: GAZ:00001097 + Bouvet Island [GAZ:00001453]: + text: Bouvet Island [GAZ:00001453] + description: A sub-antarctic volcanic island in the South Atlantic Ocean, + south-southwest of the Cape of Good Hope (South Africa). It is a dependent + area of Norway and is not subject to the Antarctic Treaty, as it is north + of the latitude south of which claims are suspended. + meaning: GAZ:00001453 + Brazil [GAZ:00002828]: + text: Brazil [GAZ:00002828] + description: 'A country in South America. Bordered by the Atlantic Ocean and + by Venezuela, Suriname, Guyana and the department of French Guiana to the + north, Colombia to the northwest, Bolivia and Peru to the west, Argentina + and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six + states (estados) and one federal district (Distrito Federal). The states + are subdivided into municipalities. For statistical purposes, the States + are grouped into five main regions: North, Northeast, Central-West, Southeast + and South.' + meaning: GAZ:00002828 + British Virgin Islands [GAZ:00003961]: + text: British Virgin Islands [GAZ:00003961] + description: A British overseas territory, located in the Caribbean to the + east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, + the remaining islands constituting the US Virgin Islands. The British Virgin + Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and + Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately + fifteen of the islands are inhabited. + meaning: GAZ:00003961 + Brunei [GAZ:00003901]: + text: Brunei [GAZ:00003901] + description: A country located on the north coast of the island of Borneo, + in Southeast Asia. Apart from its coastline with the South China Sea it + is completely surrounded by the State of Sarawak, Malaysia, and in fact + it is separated into two parts by Limbang, which is part of Sarawak. Brunei + is divided into four districts (daerah), the districts are subdivided into + thirty-eight mukims, which are then divided into kampong (villages). + meaning: GAZ:00003901 + Bulgaria [GAZ:00002950]: + text: Bulgaria [GAZ:00002950] + description: A country in Southeastern Europe, borders five other countries; + Romania to the north (mostly along the Danube), Serbia and the Republic + of Macedonia to the west, and Greece and Turkey to the south. The Black + Sea defines the extent of the country to the east. Since 1999, it has consisted + of twenty-eight provinces. The provinces subdivide into 264 municipalities. + meaning: GAZ:00002950 + Burkina Faso [GAZ:00000905]: + text: Burkina Faso [GAZ:00000905] + description: 'A landlocked nation in West Africa. It is surrounded by six + countries: Mali to the north, Niger to the east, Benin to the south east, + Togo and Ghana to the south, and Cote d''Ivoire to the south west. Burkina + Faso is divided into thirteen regions, forty-five provinces, and 301 departments + (communes).' + meaning: GAZ:00000905 + Burundi [GAZ:00001090]: + text: Burundi [GAZ:00001090] + description: A small country in the Great Lakes region of Africa. It is bordered + by Rwanda on the north, Tanzania on the south and east, and the Democratic + Republic of the Congo on the west. Although the country is landlocked, much + of its western border is adjacent to Lake Tanganyika. Burundi is divided + into 17 provinces, 117 communes, and 2,638 collines. + meaning: GAZ:00001090 + Cambodia [GAZ:00006888]: + text: Cambodia [GAZ:00006888] + description: A country in Southeast Asia. The country borders Thailand to + its west and northwest, Laos to its northeast, and Vietnam to its east and + southeast. In the south it faces the Gulf of Thailand. + meaning: GAZ:00006888 + Cameroon [GAZ:00001093]: + text: Cameroon [GAZ:00001093] + description: A country of central and western Africa. It borders Nigeria to + the west; Chad to the northeast; the Central African Republic to the east; + and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. + Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea + and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces + and 58 divisions or departments. The divisions are further sub-divided into + sub-divisions (arrondissements) and districts. + meaning: GAZ:00001093 + Canada [GAZ:00002560]: + text: Canada [GAZ:00002560] + description: A country occupying most of northern North America, extending + from the Atlantic Ocean in the east to the Pacific Ocean in the west and + northward into the Arctic Ocean. Canada is a federation composed of ten + provinces and three territories; in turn, these may be grouped into regions. + Western Canada consists of British Columbia and the three Prairie provinces + (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec + and Ontario. Atlantic Canada consists of the three Maritime provinces (New + Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland + and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada + together. Three territories (Yukon, Northwest Territories, and Nunavut) + make up Northern Canada. + meaning: GAZ:00002560 + Cape Verde [GAZ:00001227]: + text: Cape Verde [GAZ:00001227] + description: A republic located on an archipelago in the Macaronesia ecoregion + of the North Atlantic Ocean, off the western coast of Africa. Cape Verde + is divided into 22 municipalities (concelhos), and subdivided into 32 parishes + (freguesias). + meaning: GAZ:00001227 + Cayman Islands [GAZ:00003986]: + text: Cayman Islands [GAZ:00003986] + description: A British overseas territory located in the western Caribbean + Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. + The Cayman Islands are divided into seven districts. + meaning: GAZ:00003986 + Central African Republic [GAZ:00001089]: + text: Central African Republic [GAZ:00001089] + description: A landlocked country in Central Africa. It borders Chad in the + north, Sudan in the east, the Republic of the Congo and the Democratic Republic + of the Congo in the south, and Cameroon in the west. The Central African + Republic is divided into 14 administrative prefectures (prefectures), along + with 2 economic prefectures (prefectures economiques) and one autonomous + commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + meaning: GAZ:00001089 + Chad [GAZ:00000586]: + text: Chad [GAZ:00000586] + description: A landlocked country in central Africa. It is bordered by Libya + to the north, Sudan to the east, the Central African Republic to the south, + Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided + into 18 regions. The departments are divided into 200 sub-prefectures, which + are in turn composed of 446 cantons. This is due to change. + meaning: GAZ:00000586 + Chile [GAZ:00002825]: + text: Chile [GAZ:00002825] + description: 'A country in South America occupying a long and narrow coastal + strip wedged between the Andes mountains and the Pacific Ocean. The Pacific + forms the country''s entire western border, with Peru to the north, Bolivia + to the northeast, Argentina to the east, and the Drake Passage at the country''s + southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. + Chile is divided into 15 regions. Every region is further divided into provinces. + Finally each province is divided into communes. Each region is designated + by a name and a Roman numeral, assigned from north to south. The only exception + is the region housing the nation''s capital, which is designated RM, that + stands for Region Metropolitana (Metropolitan Region). Two new regions were + created in 2006: Arica-Parinacota in the north, and Los Rios in the south. + Both became operative in 2007-10.' + meaning: GAZ:00002825 + China [GAZ:00002845]: + text: China [GAZ:00002845] + description: 'A large country in Northeast Asia. China borders 14 nations + (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, + Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia + and North Korea. Additionally the border between PRC and ROC is located + in territorial waters. The People''s Republic of China has administrative + control over twenty-two provinces and considers Taiwan to be its twenty-third + province. There are also five autonomous regions, each with a designated + minority group; four municipalities; and two Special Administrative Regions + that enjoy considerable autonomy. The People''s Republic of China administers + 33 province-level regions, 333 prefecture-level regions, 2,862 county-level + regions, 41,636 township-level regions, and several village-level regions.' + meaning: GAZ:00002845 + Christmas Island [GAZ:00005915]: + text: Christmas Island [GAZ:00005915] + description: An island in the Indian Ocean, 500 km south of Indonesia and + about 2600 km northwest of Perth. The island is the flat summit of a submarine + mountain. + meaning: GAZ:00005915 + Clipperton Island [GAZ:00005838]: + text: Clipperton Island [GAZ:00005838] + description: A nine-square km coral atoll in the North Pacific Ocean, southwest + of Mexico and west of Costa Rica. + meaning: GAZ:00005838 + Cocos Islands [GAZ:00009721]: + text: Cocos Islands [GAZ:00009721] + description: Islands that located in the Indian Ocean, about halfway between + Australia and Sri Lanka. A territory of Australia. There are two atolls + and twenty-seven coral islands in the group. + meaning: GAZ:00009721 + Colombia [GAZ:00002929]: + text: Colombia [GAZ:00002929] + description: A country located in the northwestern region of South America. + Colombia is bordered to the east by Venezuela and Brazil; to the south by + Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean + Sea; to the north-west by Panama; and to the west by the Pacific Ocean. + Besides the countries in South America, the Republic of Colombia is recognized + to share maritime borders with the Caribbean countries of Jamaica, Haiti, + the Dominican Republic and the Central American countries of Honduras, Nicaragua, + and Costa Rica. Colombia is divided into 32 departments and one capital + district which is treated as a department. There are in total 10 districts + assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, + Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia + is also subdivided into some municipalities which form departments, each + with a municipal seat capital city assigned. Colombia is also subdivided + into corregimientos which form municipalities. + meaning: GAZ:00002929 + Comoros [GAZ:00005820]: + text: Comoros [GAZ:00005820] + description: An island nation in the Indian Ocean, located off the eastern + coast of Africa on the northern end of the Mozambique Channel between northern + Madagascar and northeastern Mozambique. + meaning: GAZ:00005820 + Cook Islands [GAZ:00053798]: + text: Cook Islands [GAZ:00053798] + description: A self-governing parliamentary democracy in free association + with New Zealand. The fifteen small islands in this South Pacific Ocean + country have a total land area of 240 km2, but the Cook Islands Exclusive + Economic Zone (EEZ) covers 1.8 million km2 of ocean. + meaning: GAZ:00053798 + Coral Sea Islands [GAZ:00005917]: + text: Coral Sea Islands [GAZ:00005917] + description: A Territory of Australia which includes a group of small and + mostly uninhabited tropical islands and reefs in the Coral Sea, northeast + of Queensland, Australia. The only inhabited island is Willis Island. The + territory covers 780,000 km2, extending east and south from the outer edge + of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, + the Willis Group, and fifteen other reef/island groups. + meaning: GAZ:00005917 + Costa Rica [GAZ:00002901]: + text: Costa Rica [GAZ:00002901] + description: A republic in Central America, bordered by Nicaragua to the north, + Panama to the east-southeast, the Pacific Ocean to the west and south, and + the Caribbean Sea to the east. Costa Rica is composed of seven provinces, + which in turn are divided into 81 cantons. + meaning: GAZ:00002901 + Cote d'Ivoire [GAZ:00000906]: + text: Cote d'Ivoire [GAZ:00000906] + description: A country in West Africa. It borders Liberia and Guinea to the + west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf + of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). + The regions are further divided into 58 departments. + meaning: GAZ:00000906 + Croatia [GAZ:00002719]: + text: Croatia [GAZ:00002719] + description: A country at the crossroads of the Mediterranean, Central Europe, + and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and + Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to + the east, Montenegro to the far southeast, and the Adriatic Sea to the south. + Croatia is divided into 21 counties (zupanija) and the capital Zagreb's + city district. + meaning: GAZ:00002719 + Cuba [GAZ:00003762]: + text: Cuba [GAZ:00003762] + description: A country that consists of the island of Cuba (the largest and + second-most populous island of the Greater Antilles), Isla de la Juventud + and several adjacent small islands. Fourteen provinces and one special municipality + (the Isla de la Juventud) now compose Cuba. + meaning: GAZ:00003762 + Curacao [GAZ:00012582]: + text: Curacao [GAZ:00012582] + description: One of five island areas of the Netherlands Antilles. + meaning: GAZ:00012582 + Cyprus [GAZ:00004006]: + text: Cyprus [GAZ:00004006] + description: The third largest island in the Mediterranean Sea (after Sicily + and Sardinia), Cyprus is situated in the eastern Mediterranean, just south + of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, + it is often included in the Middle East (see also Western Asia and Near + East). Turkey is 75 km north; other neighbouring countries include Syria + and Lebanon to the east, Israel to the southeast, Egypt to the south, and + Greece to the west-north-west. + meaning: GAZ:00004006 + Czech Republic [GAZ:00002954]: + text: Czech Republic [GAZ:00002954] + description: 'A landlocked country in Central Europe. It has borders with + Poland to the north, Germany to the northwest and southwest, Austria to + the south, and Slovakia to the east. The capital and largest city is Prague. + The country is composed of the historic regions of Bohemia and Moravia, + as well as parts of Silesia. Since 2000, the Czech Republic is divided into + thirteen regions (kraje, singular kraj) and the capital city of Prague. + The older seventy-six districts (okresy, singular okres) including three + ''statutory cities'' (without Prague, which had special status) were disbanded + in 1999 in an administrative reform; they remain as territorial division + and seats of various branches of state administration. Since 2003-01-01, + the regions have been divided into around 203 Municipalities with Extended + Competence (unofficially named "Little Districts" (Czech: ''male okresy'') + which took over most of the administration of the former District Authorities. + Some of these are further divided into Municipalities with Commissioned + Local Authority. However, the old districts still exist as territorial units + and remain as seats of some of the offices.' + meaning: GAZ:00002954 + Democratic Republic of the Congo [GAZ:00001086]: + text: Democratic Republic of the Congo [GAZ:00001086] + description: A country of central Africa. It borders the Central African Republic + and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia + and Angola on the south, the Republic of the Congo on the west, and is separated + from Tanzania by Lake Tanganyika on the east. The country enjoys access + to the ocean through a 40 km stretch of Atlantic coastline at Muanda and + the roughly 9 km wide mouth of the Congo river which opens into the Gulf + of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed + into 25 Provinces from 2.2009. Each Province is divided into Zones. + meaning: GAZ:00001086 + Denmark [GAZ:00005852]: + text: Denmark [GAZ:00005852] + description: That part of the Kingdom of Denmark located in continental Europe. + The mainland is bordered to the south by Germany; Denmark is located to + the southwest of Sweden and the south of Norway. Denmark borders both the + Baltic and the North Sea. The country consists of a large peninsula, Jutland + (Jylland) and a large number of islands, most notably Zealand (Sjaelland), + Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds + of minor islands often referred to as the Danish Archipelago. + meaning: GAZ:00005852 + Djibouti [GAZ:00000582]: + text: Djibouti [GAZ:00000582] + description: A country in eastern Africa. Djibouti is bordered by Eritrea + in the north, Ethiopia in the west and south, and Somalia in the southeast. + The remainder of the border is formed by the Red Sea and the Gulf of Aden. + On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the + coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. + Djibouti is divided into 5 regions and one city. It is further subdivided + into 11 districts. + meaning: GAZ:00000582 + Dominica [GAZ:00006890]: + text: Dominica [GAZ:00006890] + description: An island nation in the Caribbean Sea. Dominica is divided into + ten parishes. + meaning: GAZ:00006890 + Dominican Republic [GAZ:00003952]: + text: Dominican Republic [GAZ:00003952] + description: A country in the West Indies that occupies the E two-thirds of + the Hispaniola island. The Dominican Republic's shores are washed by the + Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona + Passage, a channel about 130 km wide, separates the country (and the Hispaniola) + from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, + the national capital, Santo Domingo, is contained within its own Distrito + Nacional (National District). The provinces are divided into municipalities + (municipios; singular municipio). + meaning: GAZ:00003952 + Ecuador [GAZ:00002912]: + text: Ecuador [GAZ:00002912] + description: A country in South America, bordered by Colombia on the north, + by Peru on the east and south, and by the Pacific Ocean to the west. The + country also includes the Galapagos Islands (Archipelago de Colon) in the + Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, + divided into 199 cantons and subdivided into parishes (or parroquias). + meaning: GAZ:00002912 + Egypt [GAZ:00003934]: + text: Egypt [GAZ:00003934] + description: A country in North Africa that includes the Sinai Peninsula, + a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, + and the Gaza Strip and Israel to the east. The northern coast borders the + Mediterranean Sea and the island of Cyprus; the eastern coast borders the + Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, + singular muhafazah). The governorates are further divided into regions (markazes). + meaning: GAZ:00003934 + El Salvador [GAZ:00002935]: + text: El Salvador [GAZ:00002935] + description: A country in Central America, bordering the Pacific Ocean between + Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), + which, in turn, are subdivided into 267 municipalities (municipios). + meaning: GAZ:00002935 + Equatorial Guinea [GAZ:00001091]: + text: Equatorial Guinea [GAZ:00001091] + description: 'A country in Central Africa. It is one of the smallest countries + in continental Africa, and comprises two regions: Rio Muni, continental + region including several offshore islands; and Insular Region containing + Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando + Po) that contains the capital, Malabo. Equatorial Guinea is divided into + seven provinces which are divided into districts.' + meaning: GAZ:00001091 + Eritrea [GAZ:00000581]: + text: Eritrea [GAZ:00000581] + description: A country situated in northern East Africa. It is bordered by + Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. + The east and northeast of the country have an extensive coastline on the + Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago + and several of the Hanish Islands are part of Eritrea. Eritrea is divided + into six regions (zobas) and subdivided into districts ("sub-zobas"). + meaning: GAZ:00000581 + Estonia [GAZ:00002959]: + text: Estonia [GAZ:00002959] + description: A country in Northern Europe. Estonia has land borders to the + south with Latvia and to the east with Russia. It is separated from Finland + in the north by the Gulf of Finland and from Sweden in the west by the Baltic + Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). + Estonian counties are divided into rural (vallad, singular vald) and urban + (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) + municipalities. The municipalities comprise populated places (asula or asustusuksus) + - various settlements and territorial units that have no administrative + function. A group of populated places form a rural municipality with local + administration. Most towns constitute separate urban municipalities, while + some have joined with surrounding rural municipalities. + meaning: GAZ:00002959 + Eswatini [GAZ:00001099]: + text: Eswatini [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). + meaning: GAZ:00001099 + Ethiopia [GAZ:00000567]: + text: Ethiopia [GAZ:00000567] + description: 'A country situated in the Horn of Africa that has been landlocked + since the independence of its northern neighbor Eritrea in 1993. Apart from + Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to + the south, Djibouti to the northeast, and Somalia to the east. Since 1996 + Ethiopia has had a tiered government system consisting of a federal government + overseeing ethnically-based regional states, zones, districts (woredas), + and neighborhoods (kebele). It is divided into nine ethnically-based administrative + states (kililoch, singular kilil) and subdivided into sixty-eight zones + and two chartered cities (astedader akababiwoch, singular astedader akababi): + Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and + six special woredas.' + meaning: GAZ:00000567 + Europa Island [GAZ:00005811]: + text: Europa Island [GAZ:00005811] + description: A 28 km2 low-lying tropical island in the Mozambique Channel, + about a third of the way from southern Madagascar to southern Mozambique. + meaning: GAZ:00005811 + Falkland Islands (Islas Malvinas) [GAZ:00001412]: + text: Falkland Islands (Islas Malvinas) [GAZ:00001412] + description: An archipelago in the South Atlantic Ocean, located 483 km from + the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), + and 940 km north of Antarctica (Elephant Island). They consist of two main + islands, East Falkland and West Falkland, together with 776 smaller islands. + meaning: GAZ:00001412 + Faroe Islands [GAZ:00059206]: + text: Faroe Islands [GAZ:00059206] + description: An autonomous province of the Kingdom of Denmark since 1948 located + in the Faroes. Administratively, the islands are divided into 34 municipalities + (kommunur) within which 120 or so cities and villages lie. + meaning: GAZ:00059206 + Fiji [GAZ:00006891]: + text: Fiji [GAZ:00006891] + description: An island nation in the South Pacific Ocean east of Vanuatu, + west of Tonga and south of Tuvalu. The country occupies an archipelago of + about 322 islands, of which 106 are permanently inhabited, and 522 islets. + The two major islands, Viti Levu and Vanua Levu, account for 87% of the + population. + meaning: GAZ:00006891 + Finland [GAZ:00002937]: + text: Finland [GAZ:00002937] + description: A Nordic country situated in the Fennoscandian region of Northern + Europe. It has borders with Sweden to the west, Russia to the east, and + Norway to the north, while Estonia lies to its south across the Gulf of + Finland. The capital city is Helsinki. Finland is divided into six administrative + provinces (laani, plural laanit). These are divided into 20 regions (maakunt), + 77 subregions (seutukunta) and then into municipalities (kunta). + meaning: GAZ:00002937 + France [GAZ:00003940]: + text: France [GAZ:00003940] + description: A part of the country of France that extends from the Mediterranean + Sea to the English Channel and the North Sea, and from the Rhine to the + Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, + Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas + departments. + meaning: GAZ:00003940 + French Guiana [GAZ:00002516]: + text: French Guiana [GAZ:00002516] + description: An overseas department (departement d'outre-mer) of France, located + on the northern coast of South America. It is bordered by Suriname, to the + E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. + French Guiana is divided into 2 departmental arrondissements, 19 cantons + and 22 communes. + meaning: GAZ:00002516 + French Polynesia [GAZ:00002918]: + text: French Polynesia [GAZ:00002918] + description: 'A French overseas collectivity in the southern Pacific Ocean. + It is made up of several groups of Polynesian islands. French Polynesia + has five administrative subdivisions (French: subdivisions administratives).' + meaning: GAZ:00002918 + French Southern and Antarctic Lands [GAZ:00003753]: + text: French Southern and Antarctic Lands [GAZ:00003753] + description: The French Southern and Antarctic Lands have formed a territoire + d'outre-mer (an overseas territory) of France since 1955. The territory + is divided into five districts. + meaning: GAZ:00003753 + Gabon [GAZ:00001092]: + text: Gabon [GAZ:00001092] + description: A country in west central Africa sharing borders with Equatorial + Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital + and largest city is Libreville. Gabon is divided into 9 provinces and further + divided into 37 departments. + meaning: GAZ:00001092 + Gambia [GAZ:00000907]: + text: Gambia [GAZ:00000907] + description: A country in Western Africa. It is the smallest country on the + African continental mainland and is bordered to the north, east, and south + by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing + through the centre of the country and discharging to the Atlantic Ocean + is the Gambia River. The Gambia is divided into five divisions and one city + (Banjul). The divisions are further subdivided into 37 districts. + meaning: GAZ:00000907 + Gaza Strip [GAZ:00009571]: + text: Gaza Strip [GAZ:00009571] + description: A Palestinian enclave on the eastern coast of the Mediterranean + Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel + on the east and north along a 51 km (32 mi) border. Gaza and the West Bank + are claimed by the de jure sovereign State of Palestine. + meaning: GAZ:00009571 + Georgia [GAZ:00004942]: + text: Georgia [GAZ:00004942] + description: 'A Eurasian country in the Caucasus located at the east coast + of the Black Sea. In the north, Georgia has a 723 km common border with + Russia, specifically with the Northern Caucasus federal district. The following + Russian republics/subdivisions: from west to east: border Georgia: Krasnodar + Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, + Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) + to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to + the south-west. It is a transcontinental country, located at the juncture + of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 + autonomous republics (avtonomiuri respublika), and 1 city (k''alak''i). + The regions are further subdivided into 69 districts (raioni).' + meaning: GAZ:00004942 + Germany [GAZ:00002646]: + text: Germany [GAZ:00002646] + description: A country in Central Europe. It is bordered to the north by the + North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech + Republic; to the south by Austria and Switzerland; and to the west by France, + Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, + Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) + and cities (kreisfreie Stadte). + meaning: GAZ:00002646 + Ghana [GAZ:00000908]: + text: Ghana [GAZ:00000908] + description: A country in West Africa. It borders Cote d'Ivoire to the west, + Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the + south. Ghana is a divided into 10 regions, subdivided into a total of 138 + districts. + meaning: GAZ:00000908 + Gibraltar [GAZ:00003987]: + text: Gibraltar [GAZ:00003987] + description: A British overseas territory located near the southernmost tip + of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory + shares a border with Spain to the north. + meaning: GAZ:00003987 + Glorioso Islands [GAZ:00005808]: + text: Glorioso Islands [GAZ:00005808] + description: A group of islands and rocks totalling 5 km2, in the northern + Mozambique channel, about 160 km northwest of Madagascar. + meaning: GAZ:00005808 + Greece [GAZ:00002945]: + text: Greece [GAZ:00002945] + description: A country in southeastern Europe, situated on the southern end + of the Balkan Peninsula. It has borders with Albania, the former Yugoslav + Republic of Macedonia and Bulgaria to the north, and Turkey to the east. + The Aegean Sea lies to the east and south of mainland Greece, while the + Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin + feature a vast number of islands. Greece consists of thirteen peripheries + subdivided into a total of fifty-one prefectures (nomoi, singular nomos). + There is also one autonomous area, Mount Athos, which borders the periphery + of Central Macedonia. + meaning: GAZ:00002945 + Greenland [GAZ:00001507]: + text: Greenland [GAZ:00001507] + description: A self-governing Danish province located between the Arctic and + Atlantic Oceans, east of the Canadian Arctic Archipelago. + meaning: GAZ:00001507 + Grenada [GAZ:02000573]: + text: Grenada [GAZ:02000573] + description: An island country in the West Indies in the Caribbean Sea at + the southern end of the Grenadines island chain. Grenada consists of the + island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, + and several small islands which lie to the north of the main island and + are a part of the Grenadines. It is located northwest of Trinidad and Tobago, + northeast of Venezuela and southwest of Saint Vincent and the Grenadines. + Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated + population of 112,523 in July 2020. + meaning: GAZ:02000573 + Guadeloupe [GAZ:00067142]: + text: Guadeloupe [GAZ:00067142] + description: "An archipelago and overseas department and region of France\ + \ in the Caribbean. It consists of six inhabited islands\u2014Basse-Terre,\ + \ Grande-Terre, Marie-Galante, La D\xE9sirade, and the two inhabited \xCE\ + les des Saintes\u2014as well as many uninhabited islands and outcroppings.\ + \ It is south of Antigua and Barbuda and Montserrat, and north of Dominica." + meaning: GAZ:00067142 + Guam [GAZ:00003706]: + text: Guam [GAZ:00003706] + description: An organized, unincorporated territory of the United States in + the Micronesia subregion of the western Pacific Ocean. It is the westernmost + point and territory of the United States (reckoned from the geographic center + of the U.S.); in Oceania, it is the largest and southernmost of the Mariana + Islands and the largest island in Micronesia. + meaning: GAZ:00003706 + Guatemala [GAZ:00002936]: + text: Guatemala [GAZ:00002936] + description: A country in Central America bordered by Mexico to the northwest, + the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the + northeast, and Honduras and El Salvador to the southeast. Guatemala is divided + into 22 departments (departamentos) and sub-divided into about 332 municipalities + (municipios). + meaning: GAZ:00002936 + Guernsey [GAZ:00001550]: + text: Guernsey [GAZ:00001550] + description: A British Crown Dependency in the English Channel off the coast + of Normandy. + meaning: GAZ:00001550 + Guinea [GAZ:00000909]: + text: Guinea [GAZ:00000909] + description: A nation in West Africa, formerly known as French Guinea. Guinea's + territory has a curved shape, with its base at the Atlantic Ocean, inland + to the east, and turning south. The base borders Guinea-Bissau and Senegal + to the north, and Mali to the north and north-east; the inland part borders + Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone + to the west of the southern tip. + meaning: GAZ:00000909 + Guinea-Bissau [GAZ:00000910]: + text: Guinea-Bissau [GAZ:00000910] + description: A country in western Africa, and one of the smallest nations + in continental Africa. It is bordered by Senegal to the north, and Guinea + to the south and east, with the Atlantic Ocean to its west. Formerly the + Portuguese colony of Portuguese Guinea, upon independence, the name of its + capital, Bissau, was added to the country's name in order to prevent confusion + between itself and the Republic of Guinea. + meaning: GAZ:00000910 + Guyana [GAZ:00002522]: + text: Guyana [GAZ:00002522] + description: A country in the N of South America. Guyana lies north of the + equator, in the tropics, and is located on the Atlantic Ocean. Guyana is + bordered to the east by Suriname, to the south and southwest by Brazil and + to the west by Venezuela. Guyana is divided into 10 regions. The regions + of Guyana are divided into 27 neighborhood councils. + meaning: GAZ:00002522 + Haiti [GAZ:00003953]: + text: Haiti [GAZ:00003953] + description: A country located in the Greater Antilles archipelago on the + Caribbean island of Hispaniola, which it shares with the Dominican Republic. + Haiti is divided into 10 departments. The departments are further divided + into 41 arrondissements, and 133 communes which serve as second and third + level administrative divisions. + meaning: GAZ:00003953 + Heard Island and McDonald Islands [GAZ:00009718]: + text: Heard Island and McDonald Islands [GAZ:00009718] + description: An Australian external territory comprising a volcanic group + of mostly barren Antarctic islands, about two-thirds of the way from Madagascar + to Antarctica. + meaning: GAZ:00009718 + Honduras [GAZ:00002894]: + text: Honduras [GAZ:00002894] + description: A republic in Central America. The country is bordered to the + west by Guatemala, to the southwest by El Salvador, to the southeast by + Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and + to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. + Honduras is divided into 18 departments. The capital city is Tegucigalpa + Central District of the department of Francisco Morazan. + meaning: GAZ:00002894 + Hong Kong [GAZ:00003203]: + text: Hong Kong [GAZ:00003203] + description: A special administrative region of the People's Republic of China + (PRC). The territory lies on the eastern side of the Pearl River Delta, + bordering Guangdong province in the north and facing the South China Sea + in the east, west and south. Hong Kong was a crown colony of the United + Kingdom from 1842 until the transfer of its sovereignty to the People's + Republic of China in 1997. + meaning: GAZ:00003203 + Howland Island [GAZ:00007120]: + text: Howland Island [GAZ:00007120] + description: An uninhabited coral island located just north of the equator + in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. + The island is almost half way between Hawaii and Australia and is an unincorporated, + unorganized territory of the United States, and is often included as one + of the Phoenix Islands. For statistical purposes, Howland is grouped as + one of the United States Minor Outlying Islands. + meaning: GAZ:00007120 + Hungary [GAZ:00002952]: + text: Hungary [GAZ:00002952] + description: 'A landlocked country in the Carpathian Basin of Central Europe, + bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. + Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: + megye). In addition, the capital city (fovaros), Budapest, is independent + of any county government. The counties are further subdivided into 173 subregions + (kistersegek), and Budapest is comprised of its own subregion. Since 1996, + the counties and City of Budapest have been grouped into 7 regions for statistical + and development purposes. These seven regions constitute NUTS second-level + units of Hungary.' + meaning: GAZ:00002952 + Iceland [GAZ:00000843]: + text: Iceland [GAZ:00000843] + description: A country in northern Europe, comprising the island of Iceland + and its outlying islands in the North Atlantic Ocean between the rest of + Europe and Greenland. + meaning: GAZ:00000843 + India [GAZ:00002839]: + text: India [GAZ:00002839] + description: A country in South Asia. Bounded by the Indian Ocean on the south, + the Arabian Sea on the west, and the Bay of Bengal on the east, India has + a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, + and Bhutan to the north-east; and Bangladesh and Burma to the east. India + is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian + Ocean. India is a federal republic of twenty-eight states and seven Union + Territories. Each state or union territory is divided into basic units of + government and administration called districts. There are nearly 600 districts + in India. The districts in turn are further divided into tehsils and eventually + into villages. + meaning: GAZ:00002839 + Indonesia [GAZ:00003727]: + text: Indonesia [GAZ:00003727] + description: An archipelagic state in Southeast Asia. The country shares land + borders with Papua New Guinea, East Timor and Malaysia. Other neighboring + countries include Singapore, the Philippines, Australia, and the Indian + territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, + five of which have special status. The provinces are subdivided into regencies + (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), + which are further subdivided into subdistricts (kecamatan), and again into + village groupings (either desa or kelurahan). + meaning: GAZ:00003727 + Iran [GAZ:00004474]: + text: Iran [GAZ:00004474] + description: A country in Central Eurasia. Iran is bounded by the Gulf of + Oman and the Persian Gulf to the south and the Caspian Sea to its north. + It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and + Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into + 30 provinces (ostan). The provinces are divided into counties (shahrestan), + and subdivided into districts (bakhsh) and sub-districts (dehestan). + meaning: GAZ:00004474 + Iraq [GAZ:00004483]: + text: Iraq [GAZ:00004483] + description: 'A country in the Middle East spanning most of the northwestern + end of the Zagros mountain range, the eastern part of the Syrian Desert + and the northern part of the Arabian Desert. It shares borders with Kuwait + and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, + Turkey to the north, and Iran to the east. It has a very narrow section + of coastline at Umm Qasr on the Persian Gulf. There are two major flowing + rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates + (or provinces) (muhafazah). The governorates are divided into qadhas (or + districts).' + meaning: GAZ:00004483 + Ireland [GAZ:00002943]: + text: Ireland [GAZ:00002943] + description: A country in north-western Europe. The modern sovereign state + occupies five-sixths of the island of Ireland, which was partitioned in + 1921. It is bordered by Northern Ireland (part of the United Kingdom) to + the north, by the Atlantic Ocean to the west and by the Irish Sea to the + east. Administration follows the 34 "county-level" counties and cities of + Ireland. Of these twenty-nine are counties, governed by county councils + while the five cities of Dublin, Cork, Limerick, Galway and Waterford have + city councils, (previously known as corporations), and are administered + separately from the counties bearing those names. The City of Kilkenny is + the only city in the republic which does not have a "city council"; it is + still a borough but not a county borough and is administered as part of + County Kilkenny. Ireland is split into eight regions for NUTS statistical + purposes. These are not related to the four traditional provinces but are + based on the administrative counties. + meaning: GAZ:00002943 + Isle of Man [GAZ:00052477]: + text: Isle of Man [GAZ:00052477] + description: A Crown dependency of the United Kingdom in the centre of the + Irish Sea. It is not part of the United Kingdom, European Union or United + Nations. + meaning: GAZ:00052477 + Israel [GAZ:00002476]: + text: Israel [GAZ:00002476] + description: 'A country in Western Asia located on the eastern edge of the + Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, + Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, + which are partially administrated by the Palestinian National Authority, + are also adjacent. The State of Israel is divided into six main administrative + districts, known as mehozot (singular mahoz). Districts are further divided + into fifteen sub-districts known as nafot (singular: nafa), which are themselves + partitioned into fifty natural regions.' + meaning: GAZ:00002476 + Italy [GAZ:00002650]: + text: Italy [GAZ:00002650] + description: A country located on the Italian Peninsula in Southern Europe, + and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. + Italy shares its northern Alpine boundary with France, Switzerland, Austria + and Slovenia. The independent states of San Marino and the Vatican City + are enclaves within the Italian Peninsula, while Campione d'Italia is an + Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, + singular regione). Five of these regions have a special autonomous status + that enables them to enact legislation on some of their local matters. It + is further divided into 109 provinces (province) and 8,101 municipalities + (comuni). + meaning: GAZ:00002650 + Jamaica [GAZ:00003781]: + text: Jamaica [GAZ:00003781] + description: A nation of the Greater Antilles. Jamaica is divided into 14 + parishes, which are grouped into three historic counties that have no administrative + relevance. + meaning: GAZ:00003781 + Jan Mayen [GAZ:00005853]: + text: Jan Mayen [GAZ:00005853] + description: 'A volcanic island that is part of the Kingdom of Norway, It + has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus + 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and + 1,000 km west of the Norwegian mainland. The island is mountainous, the + highest summit being the Beerenberg volcano in the north. The isthmus is + the location of the two largest lakes of the island, Sorlaguna (South Lagoon), + and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng + Lagoon). Jan Mayen was formed by the Jan Mayen hotspot.' + meaning: GAZ:00005853 + Japan [GAZ:00002747]: + text: Japan [GAZ:00002747] + description: An island country in East Asia. Located in the Pacific Ocean, + it lies to the east of China, Korea and Russia, stretching from the Sea + of Okhotsk in the north to the East China Sea in the south. + meaning: GAZ:00002747 + Jarvis Island [GAZ:00007118]: + text: Jarvis Island [GAZ:00007118] + description: An uninhabited 4.5 km2 coral atoll located in the South Pacific + Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated + territory of the United States administered from Washington, DC by the United + States Fish and Wildlife Service of the United States Department of the + Interior as part of the National Wildlife Refuge system. Jarvis is one of + the southern Line Islands and for statistical purposes is also grouped as + one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + meaning: GAZ:00007118 + Jersey [GAZ:00001551]: + text: Jersey [GAZ:00001551] + description: A British Crown Dependency[6] off the coast of Normandy, France. + As well as the island of Jersey itself, the bailiwick includes two groups + of small islands that are no longer permanently inhabited, the Minquiers + and Ecrehous, and the Pierres de Lecq. + meaning: GAZ:00001551 + Johnston Atoll [GAZ:00007114]: + text: Johnston Atoll [GAZ:00007114] + description: A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 + nm) west of Hawaii. There are four islands located on the coral reef platform, + two natural islands, Johnston Island and Sand Island, which have been expanded + by coral dredging, as well as North Island (Akau) and East Island (Hikina), + artificial islands formed from coral dredging. Johnston is an unincorporated + territory of the United States, administered by the US Fish and Wildlife + Service of the Department of the Interior as part of the United States Pacific + Island Wildlife Refuges. Sits atop Johnston Seamount. + meaning: GAZ:00007114 + Jordan [GAZ:00002473]: + text: Jordan [GAZ:00002473] + description: A country in Southwest Asia, bordered by Syria to the north, + Iraq to the north-east, Israel and the West Bank to the west, and Saudi + Arabia to the east and south. It shares the coastlines of the Dead Sea, + and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided + into 12 provinces called governorates. The Governorates are subdivided into + approximately fifty-two nahias. + meaning: GAZ:00002473 + Juan de Nova Island [GAZ:00005809]: + text: Juan de Nova Island [GAZ:00005809] + description: A 4.4 km2 low, flat, tropical island in the narrowest part of + the Mozambique Channel, about one-third of the way between Madagascar and + Mozambique. + meaning: GAZ:00005809 + Kazakhstan [GAZ:00004999]: + text: Kazakhstan [GAZ:00004999] + description: A country in Central Asia and Europe. It is bordered by Russia, + Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders + on a significant part of the Caspian Sea. Kazakhstan is divided into 14 + provinces and two municipal districts. The provinces of Kazakhstan are divided + into raions. + meaning: GAZ:00004999 + Kenya [GAZ:00001101]: + text: Kenya [GAZ:00001101] + description: A country in Eastern Africa. It is bordered by Ethiopia to the + north, Somalia to the east, Tanzania to the south, Uganda to the west, and + Sudan to the northwest, with the Indian Ocean running along the southeast + border. Kenya comprises eight provinces each headed by a Provincial Commissioner + (centrally appointed by the president). The provinces (mkoa singular mikoa + plural in Swahili) are subdivided into districts (wilaya). There were 69 + districts as of 1999 census. Districts are then subdivided into 497 divisions + (taarafa). The divisions are then subdivided into 2,427 locations (kata) + and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the + status of a full administrative province. + meaning: GAZ:00001101 + Kerguelen Archipelago [GAZ:00005682]: + text: Kerguelen Archipelago [GAZ:00005682] + description: A group of islands in the southern Indian Ocean. It is a territory + of France. They are composed primarily of Tertiary flood basalts and a complex + of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano + at the southern end was active during the late Pleistocene. The Rallier + du Baty Peninsula on the SW tip of the island contains two youthful subglacial + eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active + fumarole field is related to a series of Holocene trachytic lava flows and + lahars that extend beyond the icecap. + meaning: GAZ:00005682 + Kingman Reef [GAZ:00007116]: + text: Kingman Reef [GAZ:00007116] + description: A largely submerged, uninhabited tropical atoll located in the + North Pacific Ocean, roughly half way between Hawaiian Islands and American + Samoa. It is the northernmost of the Northern Line Islands and lies 65 km + NNW of Palmyra Atoll, the next closest island, and has the status of an + unincorporated territory of the United States, administered from Washington, + DC by the US Navy. Sits atop Kingman Reef Seamount. + meaning: GAZ:00007116 + Kiribati [GAZ:00006894]: + text: Kiribati [GAZ:00006894] + description: 'An island nation located in the central tropical Pacific Ocean. + It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 + km2 straddling the equator and bordering the International Date Line to + the east. It is divided into three island groups which have no administrative + function, including a group which unites the Line Islands and the Phoenix + Islands (ministry at London, Christmas). Each inhabited island has its own + council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two + councils on Tabiteuea).' + meaning: GAZ:00006894 + Kosovo [GAZ:00011337]: + text: Kosovo [GAZ:00011337] + description: A country on the Balkan Peninsula. Kosovo borders Central Serbia + to the north and east, Montenegro to the northwest, Albania to the west + and the Republic of Macedonia to the south. Kosovo is divided into 7 districts + (Rreth) and 30 municipalities. Serbia does not recognise the unilateral + secession of Kosovo[8] and considers it a United Nations-governed entity + within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + meaning: GAZ:00011337 + Kuwait [GAZ:00005285]: + text: Kuwait [GAZ:00005285] + description: A sovereign emirate on the coast of the Persian Gulf, enclosed + by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided + into six governorates (muhafazat, singular muhafadhah). + meaning: GAZ:00005285 + Kyrgyzstan [GAZ:00006893]: + text: Kyrgyzstan [GAZ:00006893] + description: A country in Central Asia. Landlocked and mountainous, it is + bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan + to the southwest and China to the east. Kyrgyzstan is divided into seven + provinces (oblast. The capital, Bishkek, and the second large city Osh are + administratively the independent cities (shaar) with a status equal to a + province. Each province comprises a number of districts (raions). + meaning: GAZ:00006893 + Laos [GAZ:00006889]: + text: Laos [GAZ:00006889] + description: A landlocked country in southeast Asia, bordered by Burma (Myanmar) + and China to the northwest, Vietnam to the east, Cambodia to the south, + and Thailand to the west. Laos is divided into sixteen provinces (qwang) + and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided + into districts (muang). + meaning: GAZ:00006889 + Latvia [GAZ:00002958]: + text: Latvia [GAZ:00002958] + description: A country in Northern Europe. Latvia shares land borders with + Estonia to the north and Lithuania to the south, and both Russia and Belarus + to the east. It is separated from Sweden in the west by the Baltic Sea. + The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). + There are also seven cities (lielpilsetas) that have a separate status. + Latvia is also historically, culturally and constitutionally divided in + four or more distinct regions. + meaning: GAZ:00002958 + Lebanon [GAZ:00002478]: + text: Lebanon [GAZ:00002478] + description: 'A small, mostly mountainous country in Western Asia, on the + eastern shore of the Mediterranean Sea. It is bordered by Syria to the north + and east, and Israel to the south. Lebanon is divided into six governorates + (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, + singular: qadaa).' + meaning: GAZ:00002478 + Lesotho [GAZ:00001098]: + text: Lesotho [GAZ:00001098] + description: A land-locked country, entirely surrounded by the Republic of + South Africa. Lesotho is divided into ten districts; these are further subdivided + into 80 constituencies, which consists of 129 local community councils. + meaning: GAZ:00001098 + Liberia [GAZ:00000911]: + text: Liberia [GAZ:00000911] + description: A country on the west coast of Africa, bordered by Sierra Leone, + Guinea, Cote d'Ivoire, and the Atlantic Ocean. + meaning: GAZ:00000911 + Libya [GAZ:00000566]: + text: Libya [GAZ:00000566] + description: A country in North Africa. Bordering the Mediterranean Sea to + the north, Libya lies between Egypt to the east, Sudan to the southeast, + Chad and Niger to the south, and Algeria and Tunisia to the west. There + are thirty-four municipalities of Libya, known by the Arabic term sha'biyat + (singular sha'biyah). These came recently (in the 1990s to replaced old + Baladiyat systam. The Baladiyat system in turn was introduced to replace + the system of muhafazah (governorates or provinces) that existed from the + 1960s to the 1970s. + meaning: GAZ:00000566 + Liechtenstein [GAZ:00003858]: + text: Liechtenstein [GAZ:00003858] + description: A tiny, doubly landlocked alpine country in Western Europe, bordered + by Switzerland to its west and by Austria to its east. The principality + of Liechtenstein is divided into 11 municipalities called Gemeinden (singular + Gemeinde). The Gemeinden mostly consist only of a single town. Five of them + fall within the electoral district Unterland (the lower county), and the + remainder within Oberland (the upper county). + meaning: GAZ:00003858 + Line Islands [GAZ:00007144]: + text: Line Islands [GAZ:00007144] + description: A group of eleven atolls and low coral islands in the central + Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, + while three are United States territories that are grouped with the United + States Minor Outlying Islands. + meaning: GAZ:00007144 + Lithuania [GAZ:00002960]: + text: Lithuania [GAZ:00002960] + description: 'A country located along the south-eastern shore of the Baltic + Sea, sharing borders with Latvia to the north, Belarus to the southeast, + Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. + Lithuania has a three-tier administrative division: the country is divided + into 10 counties (singular apskritis, plural, apskritys) that are further + subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) + which consist of over 500 elderates (singular seniunija, plural seniunijos).' + meaning: GAZ:00002960 + Luxembourg [GAZ:00002947]: + text: Luxembourg [GAZ:00002947] + description: A small landlocked country in western Europe, bordered by Belgium, + France, and Germany. Luxembourg is divided into 3 districts, which are further + divided into 12 cantons and then 116 communes. Twelve of the communes have + city status, of which the city of Luxembourg is the largest. + meaning: GAZ:00002947 + Macau [GAZ:00003202]: + text: Macau [GAZ:00003202] + description: One of the two special administrative regions of the People's + Republic of China, the other being Hong Kong. Macau lies on the western + side of the Pearl River Delta, bordering Guangdong province in the north + and facing the South China Sea in the east and south. Macau is situated + 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the + Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula + is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang + (West River) on the west. It borders the Zhuhai Special Economic Zone in + mainland China. + meaning: GAZ:00003202 + Madagascar [GAZ:00001108]: + text: Madagascar [GAZ:00001108] + description: An island nation in the Indian Ocean off the southeastern coast + of Africa. The main island, also called Madagascar, is the fourth largest + island in the world, and is home to 5% of the world's plant and animal species, + of which more than 80% are endemic to Madagascar. Most notable are the lemur + infraorder of primates, the carnivorous fossa, three endemic bird families + and six endemic baobab species. Madagascar is divided into six autonomous + provinces (faritany mizakatena), and 22 regions. The regions are further + subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + meaning: GAZ:00001108 + Malawi [GAZ:00001105]: + text: Malawi [GAZ:00001105] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. + meaning: GAZ:00001105 + Malaysia [GAZ:00003902]: + text: Malaysia [GAZ:00003902] + description: A country in southeastern Africa. It is bordered by Zambia to + the north-west, Tanzania to the north and Mozambique, which surrounds it + on the east, south and west. Malawi is divided into three regions (the Northern, + Central and Southern regions), which are further divided into twenty-seven + districts, which in turn are further divided into 137 traditional authorities + and 68 sub-chiefdoms. + meaning: GAZ:00003902 + Maldives [GAZ:00006924]: + text: Maldives [GAZ:00006924] + description: An archipelago which consists of approximately 1,196 coral islands + grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + meaning: GAZ:00006924 + Mali [GAZ:00000584]: + text: Mali [GAZ:00000584] + description: A landlocked country in northern Africa. It borders Algeria on + the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the + south, Guinea on the south-west, and Senegal and Mauritania on the west. + Mali is divided into 8 regions (regions) and 1 district, and subdivided + into 49 cercles, totalling 288 arrondissements. + meaning: GAZ:00000584 + Malta [GAZ:00004017]: + text: Malta [GAZ:00004017] + description: A Southern European country and consists of an archipelago situated + centrally in the Mediterranean. + meaning: GAZ:00004017 + Marshall Islands [GAZ:00007161]: + text: Marshall Islands [GAZ:00007161] + description: 'An archipelago that consists of twenty-nine atolls and five + isolated islands. The most important atolls and islands form two groups: + the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). + Two-thirds of the nation''s population lives on Majuro (which is also the + capital) and Ebeye. The outer islands are sparsely populated.' + meaning: GAZ:00007161 + Martinique [GAZ:00067143]: + text: Martinique [GAZ:00067143] + description: An island and an overseas department/region and single territorial + collectivity of France. + meaning: GAZ:00067143 + Mauritania [GAZ:00000583]: + text: Mauritania [GAZ:00000583] + description: A country in North-West Africa. It is bordered by the Atlantic + Ocean on the west, by Senegal on the southwest, by Mali on the east and + southeast, by Algeria on the northeast, and by Western Sahara on the northwest + (most of which is occupied by Morocco). The capital and largest city is + Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 + regions (regions) and one capital district, which in turn are subdivided + into 44 departments (departements). + meaning: GAZ:00000583 + Mauritius [GAZ:00003745]: + text: Mauritius [GAZ:00003745] + description: An island nation off the coast of the African continent in the + southwest Indian Ocean, about 900 km east of Madagascar. In addition to + the island of Mauritius, the republic includes the islands of St. Brandon, + Rodrigues and the Agalega Islands. + meaning: GAZ:00003745 + Mayotte [GAZ:00003943]: + text: Mayotte [GAZ:00003943] + description: An overseas collectivity of France consisting of a main island, + Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and + several islets around these two. + meaning: GAZ:00003943 + Mexico [GAZ:00002852]: + text: Mexico [GAZ:00002852] + description: A federal constitutional republic in North America. It is bounded + on the north by the United States; on the south and west by the North Pacific + Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and + on the east by the Gulf of Mexico. The United Mexican States comprise a + federation of thirty-one states and a federal district, the capital Mexico + City. + meaning: GAZ:00002852 + Micronesia [GAZ:00005862]: + text: Micronesia [GAZ:00005862] + description: A subregion of Oceania, comprising hundreds of small islands + in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua + New Guinea and Melanesia to the west and southwest, and Polynesia to the + east. + meaning: GAZ:00005862 + Midway Islands [GAZ:00007112]: + text: Midway Islands [GAZ:00007112] + description: A 6.2 km2 atoll located in the North Pacific Ocean (near the + northwestern end of the Hawaiian archipelago). It is an unincorporated territory + of the United States, designated an insular area under the authority of + the US Department of the Interior. + meaning: GAZ:00007112 + Moldova [GAZ:00003897]: + text: Moldova [GAZ:00003897] + description: A landlocked country in Eastern Europe, located between Romania + to the west and Ukraine to the north, east and south. Moldova is divided + into thirty-two districts (raioane, singular raion); three municipalities + (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). + The cities of Comrat and Tiraspol also have municipality status, however + not as first-tier subdivisions of Moldova, but as parts of the regions of + Gagauzia and Transnistria, respectively. The status of Transnistria is however + under dispute. Although it is de jure part of Moldova and is recognized + as such by the international community, Transnistria is not de facto under + the control of the central government of Moldova. It is administered by + an unrecognized breakaway authority under the name Pridnestrovian Moldovan + Republic. + meaning: GAZ:00003897 + Monaco [GAZ:00003857]: + text: Monaco [GAZ:00003857] + description: A small country that is completely bordered by France to the + north, west, and south; to the east it is bordered by the Mediterranean + Sea. It consists of a single municipality (commune) currently divided into + 4 quartiers and 10 wards. + meaning: GAZ:00003857 + Mongolia [GAZ:00008744]: + text: Mongolia [GAZ:00008744] + description: A country in East-Central Asia. The landlocked country borders + Russia to the north and China to the south. The capital and largest city + is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are + in turn divided into 315 sums (districts). The capital Ulan Bator is administrated + separately as a khot (municipality) with provincial status. + meaning: GAZ:00008744 + Montenegro [GAZ:00006898]: + text: Montenegro [GAZ:00006898] + description: A country located in Southeastern Europe. It has a coast on the + Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina + to the northwest, Serbia and its partially recognized breakaway southern + province of Kosovo to the northeast and Albania to the southeast. Its capital + and largest city is Podgorica. Montenegro is divided into twenty-one municipalities + (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + meaning: GAZ:00006898 + Montserrat [GAZ:00003988]: + text: Montserrat [GAZ:00003988] + description: A British overseas territory located in the Leeward Islands. + Montserrat is divided into three parishes. + meaning: GAZ:00003988 + Morocco [GAZ:00000565]: + text: Morocco [GAZ:00000565] + description: A country in North Africa. It has a coast on the Atlantic Ocean + that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco + has international borders with Algeria to the east, Spain to the north (a + water border through the Strait and land borders with two small Spanish + autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco + is divided into 16 regions, and subdivided into 62 prefectures and provinces. + Because of the conflict over Western Sahara, the status of both regions + of "Saguia el-Hamra" and "Rio de Oro" is disputed. + meaning: GAZ:00000565 + Mozambique [GAZ:00001100]: + text: Mozambique [GAZ:00001100] + description: A country in southeastern Africa bordered by the Indian Ocean + to the east, Tanzania to the north, Malawi and Zambia to the northwest, + Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique + is divided into ten provinces (provincias) and one capital city (cidade + capital) with provincial status. The provinces are subdivided into 129 districts + (distritos). Districts are further divided in "Postos Administrativos" (Administrative + Posts) and these in Localidades (Localities) the lowest geographical level + of central state administration. + meaning: GAZ:00001100 + Myanmar [GAZ:00006899]: + text: Myanmar [GAZ:00006899] + description: A country in SE Asia that is bordered by China on the north, + Laos on the east, Thailand on the southeast, Bangladesh on the west, and + India on the northwest, with the Bay of Bengal to the southwest. Myanmar + is divided into seven states and seven divisions. The administrative divisions + are further subdivided into districts, which are further subdivided into + townships, wards, and villages. + meaning: GAZ:00006899 + Namibia [GAZ:00001096]: + text: Namibia [GAZ:00001096] + description: A country in southern Africa on the Atlantic coast. It shares + borders with Angola and Zambia to the north, Botswana to the east, and South + Africa to the south. Namibia is divided into 13 regions and subdivided into + 102 constituencies. + meaning: GAZ:00001096 + Nauru [GAZ:00006900]: + text: Nauru [GAZ:00006900] + description: An island nation in the Micronesian South Pacific. The nearest + neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. + Nauru is divided into fourteen administrative districts which are grouped + into eight electoral constituencies. + meaning: GAZ:00006900 + Navassa Island [GAZ:00007119]: + text: Navassa Island [GAZ:00007119] + description: A small, uninhabited island in the Caribbean Sea, and is an unorganized + unincorporated territory of the United States, which administers it through + the US Fish and Wildlife Service. The island is also claimed by Haiti. + meaning: GAZ:00007119 + Nepal [GAZ:00004399]: + text: Nepal [GAZ:00004399] + description: A landlocked nation in South Asia. It is bordered by the Tibet + Autonomous Region of the People's Republic of China to the northeast and + India to the south and west; it is separated from Bhutan by the Indian State + of Sikkim and from Bangladesh by a small strip of the Indian State of West + Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs + across Nepal's north and western parts, and eight of the world's ten highest + mountains, including the highest, Mount Everest are situated within its + territory. Nepal is divided into 14 zones and 75 districts, grouped into + 5 development regions. + meaning: GAZ:00004399 + Netherlands [GAZ:00002946]: + text: Netherlands [GAZ:00002946] + description: The European part of the Kingdom of the Netherlands. It is bordered + by the North Sea to the north and west, Belgium to the south, and Germany + to the east. The Netherlands is divided into twelve administrative regions, + called provinces. All provinces of the Netherlands are divided into municipalities + (gemeenten), together 443 (2007). + meaning: GAZ:00002946 + New Caledonia [GAZ:00005206]: + text: New Caledonia [GAZ:00005206] + description: A "sui generis collectivity" (in practice an overseas territory) + of France, made up of a main island (Grande Terre), the Loyalty Islands, + and several smaller islands. It is located in the region of Melanesia in + the southwest Pacific. Administratively, the archipelago is divided into + three provinces, and then into 33 communes. + meaning: GAZ:00005206 + New Zealand [GAZ:00000469]: + text: New Zealand [GAZ:00000469] + description: A nation in the south-western Pacific Ocean comprising two large + islands (the North Island and the South Island) and numerous smaller islands, + most notably Stewart Island/Rakiura and the Chatham Islands. + meaning: GAZ:00000469 + Nicaragua [GAZ:00002978]: + text: Nicaragua [GAZ:00002978] + description: A republic in Central America. It is also the least densely populated + with a demographic similar in size to its smaller neighbors. The country + is bordered by Honduras to the north and by Costa Rica to the south. The + Pacific Ocean lies to the west of the country, while the Caribbean Sea lies + to the east. For administrative purposes it is divided into 15 departments + (departamentos) and two self-governing regions (autonomous communities) + based on the Spanish model. The departments are then subdivided into 153 + municipios (municipalities). The two autonomous regions are Region Autonoma + del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred + to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 + they formed the single department of Zelaya. + meaning: GAZ:00002978 + Niger [GAZ:00000585]: + text: Niger [GAZ:00000585] + description: A landlocked country in Western Africa, named after the Niger + River. It borders Nigeria and Benin to the south, Burkina Faso and Mali + to the west, Algeria and Libya to the north and Chad to the east. The capital + city is Niamey. Niger is divided into 7 departments and one capital district. + The departments are subdivided into 36 arrondissements and further subdivided + into 129 communes. + meaning: GAZ:00000585 + Nigeria [GAZ:00000912]: + text: Nigeria [GAZ:00000912] + description: A federal constitutional republic comprising thirty-six states + and one Federal Capital Territory. The country is located in West Africa + and shares land borders with the Republic of Benin in the west, Chad and + Cameroon in the east, and Niger in the north. Its coast lies on the Gulf + of Guinea, part of the Atlantic Ocean, in the south. The capital city is + Abuja. Nigeria is divided into thirty-six states and one Federal Capital + Territory, which are further sub-divided into 774 Local Government Areas + (LGAs). + meaning: GAZ:00000912 + Niue [GAZ:00006902]: + text: Niue [GAZ:00006902] + description: An island nation located in the South Pacific Ocean. Although + self-governing, Niue is in free association with New Zealand, meaning that + the Sovereign in Right of New Zealand is also Niue's head of state. + meaning: GAZ:00006902 + Norfolk Island [GAZ:00005908]: + text: Norfolk Island [GAZ:00005908] + description: A Territory of Australia that includes Norfolk Island and neighboring + islands. + meaning: GAZ:00005908 + North Korea [GAZ:00002801]: + text: North Korea [GAZ:00002801] + description: A state in East Asia in the northern half of the Korean Peninsula, + with its capital in the city of Pyongyang. To the south and separated by + the Korean Demilitarized Zone is South Korea, with which it formed one nation + until division following World War II. At its northern Amnok River border + are China and, separated by the Tumen River in the extreme north-east, Russia. + meaning: GAZ:00002801 + North Macedonia [GAZ:00006895]: + text: North Macedonia [GAZ:00006895] + description: A landlocked country on the Balkan peninsula in southeastern + Europe. It is bordered by Serbia and Kosovo to the north, Albania to the + west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic + of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), + 10 of which comprise Greater Skopje. This is reduced from the previous 123 + municipalities established in 1996-09. Prior to this, local government was + organised into 34 administrative districts. + meaning: GAZ:00006895 + North Sea [GAZ:00002284]: + text: North Sea [GAZ:00002284] + description: A sea situated between the eastern coasts of the British Isles + and the western coast of Europe. + meaning: GAZ:00002284 + Northern Mariana Islands [GAZ:00003958]: + text: Northern Mariana Islands [GAZ:00003958] + description: A group of 15 islands about three-quarters of the way from Hawaii + to the Philippines. + meaning: GAZ:00003958 + Norway [GAZ:00002699]: + text: Norway [GAZ:00002699] + description: A country and constitutional monarchy in Northern Europe that + occupies the western portion of the Scandinavian Peninsula. It is bordered + by Sweden, Finland, and Russia. The Kingdom of Norway also includes the + Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty + over Svalbard is based upon the Svalbard Treaty, but that treaty does not + apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter + I Island and Queen Maud Land in Antarctica are external dependencies, but + those three entities do not form part of the kingdom. + meaning: GAZ:00002699 + Oman [GAZ:00005283]: + text: Oman [GAZ:00005283] + description: A country in southwest Asia, on the southeast coast of the Arabian + Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia + on the west, and Yemen on the southwest. The coast is formed by the Arabian + Sea on the south and east, and the Gulf of Oman on the northeast. The country + also contains Madha, an exclave enclosed by the United Arab Emirates, and + Musandam, an exclave also separated by Emirati territory. Oman is divided + into four governorates (muhafazah) and five regions (mintaqat). The regions + are subdivided into provinces (wilayat). + meaning: GAZ:00005283 + Pakistan [GAZ:00005246]: + text: Pakistan [GAZ:00005246] + description: A country in Middle East which lies on the Iranian Plateau and + some parts of South Asia. It is located in the region where South Asia converges + with Central Asia and the Middle East. It has a 1,046 km coastline along + the Arabian Sea in the south, and is bordered by Afghanistan and Iran in + the west, India in the east and China in the far northeast. Pakistan is + subdivided into four provinces and two territories. In addition, the portion + of Kashmir that is administered by the Pakistani government is divided into + two separate administrative units. The provinces are divided into a total + of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly + equivalent to counties). Tehsils may contain villages or municipalities. + There are over five thousand local governments in Pakistan. + meaning: GAZ:00005246 + Palau [GAZ:00006905]: + text: Palau [GAZ:00006905] + description: A nation that consists of eight principal islands and more than + 250 smaller ones lying roughly 500 miles southeast of the Philippines. + meaning: GAZ:00006905 + Panama [GAZ:00002892]: + text: Panama [GAZ:00002892] + description: The southernmost country of Central America. Situated on an isthmus, + some categorize it as a transcontinental nation connecting the north and + south part of America. It borders Costa Rica to the north-west, Colombia + to the south-east, the Caribbean Sea to the north and the Pacific Ocean + to the south. Panama's major divisions are nine provinces and five indigenous + territories (comarcas indigenas). The provincial borders have not changed + since they were determined at independence in 1903. The provinces are divided + into districts, which in turn are subdivided into sections called corregimientos. + Configurations of the corregimientos are changed periodically to accommodate + population changes as revealed in the census reports. + meaning: GAZ:00002892 + Papua New Guinea [GAZ:00003922]: + text: Papua New Guinea [GAZ:00003922] + description: A country in Oceania that comprises the eastern half of the island + of New Guinea and its offshore islands in Melanesia (a region of the southwestern + Pacific Ocean north of Australia). + meaning: GAZ:00003922 + Paracel Islands [GAZ:00010832]: + text: Paracel Islands [GAZ:00010832] + description: A group of small islands and reefs in the South China Sea, about + one-third of the way from Vietnam to the Philippines. + meaning: GAZ:00010832 + Paraguay [GAZ:00002933]: + text: Paraguay [GAZ:00002933] + description: A landlocked country in South America. It lies on both banks + of the Paraguay River, bordering Argentina to the south and southwest, Brazil + to the east and northeast, and Bolivia to the northwest, and is located + in the very heart of South America. Paraguay consists of seventeen departments + and one capital district (distrito capital). Each department is divided + into districts. + meaning: GAZ:00002933 + Peru [GAZ:00002932]: + text: Peru [GAZ:00002932] + description: A country in western South America. It is bordered on the north + by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, + on the south by Chile, and on the west by the Pacific Ocean. Peru is divided + into 25 regions and the province of Lima. These regions are subdivided into + provinces, which are composed of districts (provincias and distritos). There + are 195 provinces and 1833 districts in Peru. The Lima Province, located + in the central coast of the country, is unique in that it doesn't belong + to any of the twenty-five regions. The city of Lima, which is the nation's + capital, is located in this province. Callao is its own region, even though + it only contains one province, the Constitutional Province of Callao. + meaning: GAZ:00002932 + Philippines [GAZ:00004525]: + text: Philippines [GAZ:00004525] + description: 'An archipelagic nation located in Southeast Asia. The Philippine + archipelago comprises 7,107 islands in the western Pacific Ocean, bordering + countries such as Indonesia, Malaysia, Palau and the Republic of China, + although it is the only Southeast Asian country to share no land borders + with its neighbors. The Philippines is divided into three island groups: + Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, + 136 cities, 1,494 municipalities and 41,995 barangays.' + meaning: GAZ:00004525 + Pitcairn Islands [GAZ:00005867]: + text: Pitcairn Islands [GAZ:00005867] + description: A group of four islands in the southern Pacific Ocean. The Pitcairn + Islands form the southeasternmost extension of the geological archipelago + of the Tuamotus of French Polynesia. + meaning: GAZ:00005867 + Poland [GAZ:00002939]: + text: Poland [GAZ:00002939] + description: A country in Central Europe. Poland is bordered by Germany to + the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus + and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a + Russian exclave, to the north. The administrative division of Poland since + 1999 has been based on three levels of subdivision. The territory of Poland + is divided into voivodeships (provinces); these are further divided into + powiats (counties), and these in turn are divided into gminas (communes + or municipalities). Major cities normally have the status of both gmina + and powiat. Poland currently has 16 voivodeships, 379 powiats (including + 65 cities with powiat status), and 2,478 gminas. + meaning: GAZ:00002939 + Portugal [GAZ:00004126]: + text: Portugal [GAZ:00004126] + description: That part of the Portugese Republic that occupies the W part + of the Iberian Peninsula, and immediately adjacent islands. + meaning: GAZ:00004126 + Puerto Rico [GAZ:00006935]: + text: Puerto Rico [GAZ:00006935] + description: A semi-autonomous territory composed of an archipelago in the + northeastern Caribbean, east of the Dominican Republic and west of the Virgin + Islands, approximately 2,000 km off the coast of Florida (the nearest of + the mainland United States). + meaning: GAZ:00006935 + Qatar [GAZ:00005286]: + text: Qatar [GAZ:00005286] + description: 'An Arab emirate in Southwest Asia, occupying the small Qatar + Peninsula on the northeasterly coast of the larger Arabian Peninsula. It + is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds + the state. Qatar is divided into ten municipalities (Arabic: baladiyah), + which are further divided into zones (districts).' + meaning: GAZ:00005286 + Republic of the Congo [GAZ:00001088]: + text: Republic of the Congo [GAZ:00001088] + description: A country in Central Africa. It is bordered by Gabon, Cameroon, + the Central African Republic, the Democratic Republic of the Congo, the + Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic + of the Congo is divided into 10 regions (regions) and one commune, the capital + Brazzaville. The regions are subdivided into forty-six districts. + meaning: GAZ:00001088 + Reunion [GAZ:00003945]: + text: Reunion [GAZ:00003945] + description: An island, located in the Indian Ocean east of Madagascar, about + 200 km south west of Mauritius, the nearest island. + meaning: GAZ:00003945 + Romania [GAZ:00002951]: + text: Romania [GAZ:00002951] + description: A country in Southeastern Europe. It shares a border with Hungary + and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, + and Bulgaria to the south. Romania has a stretch of sea coast along the + Black Sea. It is located roughly in the lower basin of the Danube and almost + all of the Danube Delta is located within its territory. Romania is divided + into forty-one counties (judete), as well as the municipality of Bucharest + (Bucuresti) - which is its own administrative unit. The country is further + subdivided into 319 cities and 2686 communes (rural localities). + meaning: GAZ:00002951 + Ross Sea [GAZ:00023304]: + text: Ross Sea [GAZ:00023304] + description: A large embayment of the Southern Ocean, extending deeply into + Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck + on the east, at 158degW. + meaning: GAZ:00023304 + Russia [GAZ:00002721]: + text: Russia [GAZ:00002721] + description: 'A transcontinental country extending over much of northern Eurasia. + Russia shares land borders with the following countries (counter-clockwise + from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania + (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, + Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation + comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais + (territories), 4 autonomous okrugs (autonomous districts), one autonomous + oblast, and two federal cities. The federal subjects are grouped into seven + federal districts. These subjects are divided into districts (raions), cities/towns + and urban-type settlements, and, at level 4, selsovets (rural councils), + towns and urban-type settlements under the jurisdiction of the district + and city districts.' + meaning: GAZ:00002721 + Rwanda [GAZ:00001087]: + text: Rwanda [GAZ:00001087] + description: A small landlocked country in the Great Lakes region of east-central + Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo + and Tanzania. Rwanda is divided into five provinces (intara) and subdivided + into thirty districts (akarere). The districts are divided into sectors + (imirenge). + meaning: GAZ:00001087 + Saint Helena [GAZ:00000849]: + text: Saint Helena [GAZ:00000849] + description: An island of volcanic origin and a British overseas territory + in the South Atlantic Ocean. + meaning: GAZ:00000849 + Saint Kitts and Nevis [GAZ:00006906]: + text: Saint Kitts and Nevis [GAZ:00006906] + description: 'A federal two-island nation in the West Indies. Located in the + Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward + Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, + Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast + are Antigua and Barbuda, and to the southeast is the small uninhabited island + of Redonda, and the island of Montserrat. The federation of Saint Kitts + and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts + and five on Nevis.' + meaning: GAZ:00006906 + Saint Lucia [GAZ:00006909]: + text: Saint Lucia [GAZ:00006909] + description: An island nation in the eastern Caribbean Sea on the boundary + with the Atlantic Ocean. + meaning: GAZ:00006909 + Saint Pierre and Miquelon [GAZ:00003942]: + text: Saint Pierre and Miquelon [GAZ:00003942] + description: An Overseas Collectivity of France located in a group of small + islands in the North Atlantic Ocean, the main ones being Saint Pierre and + Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and + Miquelon became an overseas department in 1976, but its status changed to + that of an Overseas collectivity in 1985. + meaning: GAZ:00003942 + Saint Martin [GAZ:00005841]: + text: Saint Martin [GAZ:00005841] + description: An overseas collectivity of France that came into being on 2007-02-22, + encompassing the northern parts of the island of Saint Martin and neighboring + islets. The southern part of the island, Sint Maarten, is part of the Netherlands + Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + meaning: GAZ:00005841 + Saint Vincent and the Grenadines [GAZ:02000565]: + text: Saint Vincent and the Grenadines [GAZ:02000565] + description: An island nation in the Lesser Antilles chain of the Caribbean + Sea. + meaning: GAZ:02000565 + Samoa [GAZ:00006910]: + text: Samoa [GAZ:00006910] + description: A country governing the western part of the Samoan Islands archipelago + in the South Pacific Ocean. Samoa is made up of eleven itumalo (political + districts). + meaning: GAZ:00006910 + San Marino [GAZ:00003102]: + text: San Marino [GAZ:00003102] + description: A country in the Apennine Mountains. It is a landlocked enclave, + completely surrounded by Italy. San Marino is an enclave in Italy, on the + border between the regioni of Emilia Romagna and Marche. Its topography + is dominated by the Apennines mountain range. San Marino is divided into + nine municipalities, known locally as Castelli (singular castello). + meaning: GAZ:00003102 + Sao Tome and Principe [GAZ:00006927]: + text: Sao Tome and Principe [GAZ:00006927] + description: 'An island nation in the Gulf of Guinea, off the western equatorial + coast of Africa. It consists of two islands: Sao Tome and Principe, located + about 140 km apart and about 250 and 225 km respectively, off of the northwestern + coast of Gabon. Both islands are part of an extinct volcanic mountain range. + Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The + provinces are further divided into seven districts, six on Sao Tome and + one on Principe (with Principe having self-government since 1995-04-29).' + meaning: GAZ:00006927 + Saudi Arabia [GAZ:00005279]: + text: Saudi Arabia [GAZ:00005279] + description: A country on the Arabian Peninsula. It is bordered by Jordan + on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, + and the United Arab Emirates on the east, Oman on the southeast, and Yemen + on the south. The Persian Gulf lies to the northeast and the Red Sea to + its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; + singular mintaqah). Each is then divided into Governorates. + meaning: GAZ:00005279 + Senegal [GAZ:00000913]: + text: Senegal [GAZ:00000913] + description: A country south of the Senegal River in western Africa. Senegal + is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali + to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies + almost entirely within Senegal, surrounded on the north, east and south; + from its western coast Gambia's territory follows the Gambia River more + than 300 km inland. Dakar is the capital city of Senegal, located on the + Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided + into 11 regions and further subdivided into 34 Departements, 103 Arrondissements + (neither of which have administrative function) and by Collectivites Locales. + meaning: GAZ:00000913 + Serbia [GAZ:00002957]: + text: Serbia [GAZ:00002957] + description: 'A landlocked country in Central and Southeastern Europe, covering + the southern part of the Pannonian Plain and the central part of the Balkan + Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria + to the east; Republic of Macedonia, Montenegro to the south; Croatia and + Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided + into 29 districts plus the City of Belgrade. The districts and the city + of Belgrade are further divided into municipalities. Serbia has two autonomous + provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), + and Vojvodina in the north (7 districts, 46 municipalities).' + meaning: GAZ:00002957 + Seychelles [GAZ:00006922]: + text: Seychelles [GAZ:00006922] + description: An archipelagic island country in the Indian Ocean at the eastern + edge of the Somali Sea. It consists of 115 islands. + meaning: GAZ:00006922 + Sierra Leone [GAZ:00000914]: + text: Sierra Leone [GAZ:00000914] + description: A country in West Africa. It is bordered by Guinea in the north + and east, Liberia in the southeast, and the Atlantic Ocean in the southwest + and west. The Republic of Sierra Leone is composed of 3 provinces and one + area called the Western Area; the provinces are further divided into 12 + districts. The Western Area is also divided into 2 districts. + meaning: GAZ:00000914 + Singapore [GAZ:00003923]: + text: Singapore [GAZ:00003923] + description: An island nation located at the southern tip of the Malay Peninsula. + It lies 137 km north of the Equator, south of the Malaysian State of Johor + and north of Indonesia's Riau Islands. Singapore consists of 63 islands, + including mainland Singapore. There are two man-made connections to Johor, + Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in + the west. Since 2001-11-24, Singapore has had an administrative subdivision + into 5 districts. It is also divided into five Regions, urban planning subdivisions + with no administrative role. + meaning: GAZ:00003923 + Sint Maarten [GAZ:00012579]: + text: Sint Maarten [GAZ:00012579] + description: One of five island areas (Eilandgebieden) of the Netherlands + Antilles, encompassing the southern half of the island of Saint Martin/Sint + Maarten. + meaning: GAZ:00012579 + Slovakia [GAZ:00002956]: + text: Slovakia [GAZ:00002956] + description: A landlocked country in Central Europe. The Slovak Republic borders + the Czech Republic and Austria to the west, Poland to the north, Ukraine + to the east and Hungary to the south. The largest city is its capital, Bratislava. + Slovakia is subdivided into 8 kraje (singular - kraj, usually translated + as regions. The kraje are subdivided into many okresy (singular okres, usually + translated as districts). Slovakia currently has 79 districts. + meaning: GAZ:00002956 + Slovenia [GAZ:00002955]: + text: Slovenia [GAZ:00002955] + description: A country in southern Central Europe bordering Italy to the west, + the Adriatic Sea to the southwest, Croatia to the south and east, Hungary + to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. + As of 2005-05 Slovenia is divided into 12 statistical regions for legal + and statistical purposes. Slovenia is divided into 210 local municipalities, + eleven of which have urban status. + meaning: GAZ:00002955 + Solomon Islands [GAZ:00005275]: + text: Solomon Islands [GAZ:00005275] + description: A nation in Melanesia, east of Papua New Guinea, consisting of + nearly one thousand islands. Together they cover a land mass of 28,400 km2. + The capital is Honiara, located on the island of Guadalcanal. + meaning: GAZ:00005275 + Somalia [GAZ:00001104]: + text: Somalia [GAZ:00001104] + description: A country located in the Horn of Africa. It is bordered by Djibouti + to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on + its north, the Indian Ocean at its east, and Ethiopia to the west. Prior + to the civil war, Somalia was divided into eighteen regions (gobollada, + singular gobol), which were in turn subdivided into districts. On a de facto + basis, northern Somalia is now divided up among the quasi-independent states + of Puntland, Somaliland, Galmudug and Maakhir. + meaning: GAZ:00001104 + South Africa [GAZ:00001094]: + text: South Africa [GAZ:00001094] + description: 'A country located at the southern tip of Africa. It borders + the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, + Swaziland, and Lesotho, an independent enclave surrounded by South African + territory. It is divided into nine provinces which are further subdivided + into 52 districts: 6 metropolitan and 46 district municipalities. The 46 + district municipalities are further subdivided into 231 local municipalities. + The district municipalities also contain 20 district management areas (mostly + game parks) that are directly governed by the district municipalities. The + six metropolitan municipalities perform the functions of both district and + local municipalities.' + meaning: GAZ:00001094 + South Georgia and the South Sandwich Islands [GAZ:00003990]: + text: South Georgia and the South Sandwich Islands [GAZ:00003990] + description: A British overseas territory in the southern Atlantic Ocean. + It iconsists of South Georgia and the Sandwich Islands, some 640 km to the + SE. + meaning: GAZ:00003990 + South Korea [GAZ:00002802]: + text: South Korea [GAZ:00002802] + description: A republic in East Asia, occupying the southern half of the Korean + Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous + province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 + special city (teukbyeolsi). These are further subdivided into a variety + of smaller entities, including cities (si), counties (gun), districts (gu), + towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + meaning: GAZ:00002802 + South Sudan [GAZ:00233439]: + text: South Sudan [GAZ:00233439] + description: A state located in Africa with Juba as its capital city. It's + bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic + of the Congo to the south, and the Central African Republic to the west + and Sudan to the North. Southern Sudan includes the vast swamp region of + the Sudd formed by the White Nile, locally called the Bahr el Jebel. + meaning: GAZ:00233439 + Spain [GAZ:00003936]: + text: Spain [GAZ:00003936] + description: That part of the Kingdom of Spain that occupies the Iberian Peninsula + plus the Balaeric Islands. The Spanish mainland is bordered to the south + and east almost entirely by the Mediterranean Sea (except for a small land + boundary with Gibraltar); to the north by France, Andorra, and the Bay of + Biscay; and to the west by the Atlantic Ocean and Portugal. + meaning: GAZ:00003936 + Spratly Islands [GAZ:00010831]: + text: Spratly Islands [GAZ:00010831] + description: A group of >100 islands located in the Southeastern Asian group + of reefs and islands in the South China Sea, about two-thirds of the way + from southern Vietnam to the southern Philippines. + meaning: GAZ:00010831 + Sri Lanka [GAZ:00003924]: + text: Sri Lanka [GAZ:00003924] + description: An island nation in South Asia, located about 31 km off the southern + coast of India. Sri Lanka is divided into 9 provinces and 25 districts. + Districts are divided into Divisional Secretariats. + meaning: GAZ:00003924 + State of Palestine [GAZ:00002475]: + text: State of Palestine [GAZ:00002475] + description: The territory under the administration of the Palestine National + Authority, as established by the Oslo Accords. The PNA divides the Palestinian + territories into 16 governorates. + meaning: GAZ:00002475 + Sudan [GAZ:00000560]: + text: Sudan [GAZ:00000560] + description: A country in North Africa. It is bordered by Egypt to the north, + the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and + Uganda to the southeast, Democratic Republic of the Congo and the Central + African Republic to the southwest, Chad to the west and Libya to the northwest. + Sudan is divided into twenty-six states (wilayat, singular wilayah) which + in turn are subdivided into 133 districts. + meaning: GAZ:00000560 + Suriname [GAZ:00002525]: + text: Suriname [GAZ:00002525] + description: A country in northern South America. It is situated between French + Guiana to the east and Guyana to the west. The southern border is shared + with Brazil and the northern border is the Atlantic coast. The southernmost + border with French Guiana is disputed along the Marowijne river. Suriname + is divided into 10 districts, each of which is divided into Ressorten. + meaning: GAZ:00002525 + Svalbard [GAZ:00005396]: + text: Svalbard [GAZ:00005396] + description: An archipelago of continental islands lying in the Arctic Ocean + north of mainland Europe, about midway between Norway and the North Pole. + meaning: GAZ:00005396 + Swaziland [GAZ:00001099]: + text: Swaziland [GAZ:00001099] + description: A small, landlocked country in Africa embedded between South + Africa in the west, north and south and Mozambique in the east. Swaziland + is divided into four districts, each of which is divided into Tinkhundla + (singular, Inkhundla). + meaning: GAZ:00001099 + Sweden [GAZ:00002729]: + text: Sweden [GAZ:00002729] + description: A Nordic country on the Scandinavian Peninsula in Northern Europe. + It has borders with Norway (west and north) and Finland (northeast). Sweden + is a unitary state, currently divided into twenty-one counties (lan). Each + county further divides into a number of municipalities or kommuner, with + a total of 290 municipalities in 2004. + meaning: GAZ:00002729 + Switzerland [GAZ:00002941]: + text: Switzerland [GAZ:00002941] + description: 'A federal republic in Europe. Switzerland is bordered by Germany, + France, Italy, Austria and Liechtenstein. The Swiss Confederation consists + of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within + Switzerland there are two enclaves: Busingen belongs to Germany, Campione + d''Italia belongs to Italy.' + meaning: GAZ:00002941 + Syria [GAZ:00002474]: + text: Syria [GAZ:00002474] + description: 'A country in Southwest Asia, bordering Lebanon, the Mediterranean + Sea and the island of Cyprus to the west, Israel to the southwest, Jordan + to the south, Iraq to the east, and Turkey to the north. Syria has fourteen + governorates, or muhafazat (singular: muhafazah). The governorates are divided + into sixty districts, or manatiq (singular: mintaqah), which are further + divided into sub-districts, or nawahi (singular: nahia).' + meaning: GAZ:00002474 + Taiwan [GAZ:00005341]: + text: Taiwan [GAZ:00005341] + description: A state in East Asia with de facto rule of the island of Tawain + and adjacent territory. The Republic of China currently administers two + historical provinces of China (one completely and a small part of another + one) and centrally administers two direct-controlled municipalities. + meaning: GAZ:00005341 + Tajikistan [GAZ:00006912]: + text: Tajikistan [GAZ:00006912] + description: A mountainous landlocked country in Central Asia. Afghanistan + borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and + People's Republic of China to the east. Tajikistan consists of 4 administrative + divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous + province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican + Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly + known as Karotegin Province). Each region is divided into several districts + (nohiya or raion). + meaning: GAZ:00006912 + Tanzania [GAZ:00001103]: + text: Tanzania [GAZ:00001103] + description: A country in East Africa bordered by Kenya and Uganda on the + north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, + and Zambia, Malawi and Mozambique on the south. To the east it borders the + Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on + the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight + districts (wilaya), each with at least one council, have been created to + further increase local authority; the councils are also known as local government + authorities. Currently there are 114 councils operating in 99 districts; + 22 are urban and 92 are rural. The 22 urban units are further classified + as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, + Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) + or town councils (the remaining eleven communities). + meaning: GAZ:00001103 + Thailand [GAZ:00003744]: + text: Thailand [GAZ:00003744] + description: 'A country in Southeast Asia. To its east lie Laos and Cambodia; + to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman + Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided + into 75 provinces (changwat), which are gathered into 5 groups of provinces + by location. There are also 2 special governed districts: the capital Bangkok + (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial + level and thus often counted as a 76th province.' + meaning: GAZ:00003744 + Timor-Leste [GAZ:00006913]: + text: Timor-Leste [GAZ:00006913] + description: A country in Southeast Asia. It comprises the eastern half of + the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, + an exclave on the northwestern side of the island, within Indonesian West + Timor. The small country of 15,410 km2 is located about 640 km northwest + of Darwin, Australia. East Timor is divided into thirteen administrative + districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, + villages and hamlets. + meaning: GAZ:00006913 + Togo [GAZ:00000915]: + text: Togo [GAZ:00000915] + description: A country in West Africa bordering Ghana in the west, Benin in + the east and Burkina Faso in the north. In the south, it has a short Gulf + of Guinea coast, on which the capital Lome is located. + meaning: GAZ:00000915 + Tokelau [GAZ:00260188]: + text: Tokelau [GAZ:00260188] + description: 'A dependent territory of New Zealand in the southern Pacific + Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and + Fakaofo. They have a combined land area of 10 km2 (4 sq mi).' + meaning: GAZ:00260188 + Tonga [GAZ:00006916]: + text: Tonga [GAZ:00006916] + description: A Polynesian country, and also an archipelago comprising 169 + islands, of which 36 are inhabited. The archipelago's total surface area + is about 750 square kilometres (290 sq mi) scattered over 700,000 square + kilometres (270,000 sq mi) of the southern Pacific Ocean. + meaning: GAZ:00006916 + Trinidad and Tobago [GAZ:00003767]: + text: Trinidad and Tobago [GAZ:00003767] + description: An archipelagic state in the southern Caribbean, lying northeast + of the South American nation of Venezuela and south of Grenada in the Lesser + Antilles. It also shares maritime boundaries with Barbados to the northeast + and Guyana to the southeast. The country covers an area of 5,128 km2and + consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + meaning: GAZ:00003767 + Tromelin Island [GAZ:00005812]: + text: Tromelin Island [GAZ:00005812] + description: A low, flat 0.8 km2 island in the Indian Ocean, about 350 km + east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 + m long and 700 m wide, surrounded by coral reefs. The island is 7 m high + at its highest point. + meaning: GAZ:00005812 + Tunisia [GAZ:00000562]: + text: Tunisia [GAZ:00000562] + description: A country situated on the Mediterranean coast of North Africa. + It is bordered by Algeria to the west and Libya to the southeast. Tunisia + is subdivided into 24 governorates, divided into 262 "delegations" or "districts" + (mutamadiyat), and further subdivided into municipalities (shaykhats). + meaning: GAZ:00000562 + Turkey [GAZ:00000558]: + text: Turkey [GAZ:00000558] + description: 'A Eurasian country that stretches across the Anatolian peninsula + in western Asia and Thrace (Rumelia) in the Balkan region of southeastern + Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece + to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave + of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. + The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago + are to the west; and the Black Sea is to the north. Separating Anatolia + and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus + and the Dardanelles), which are commonly reckoned to delineate the border + between Asia and Europe, thereby making Turkey transcontinental. The territory + of Turkey is subdivided into 81 provinces for administrative purposes. The + provinces are organized into 7 regions for census purposes; however, they + do not represent an administrative structure. Each province is divided into + districts, for a total of 923 districts.' + meaning: GAZ:00000558 + Turkmenistan [GAZ:00005018]: + text: Turkmenistan [GAZ:00005018] + description: A country in Central Asia. It is bordered by Afghanistan to the + southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan + to the northwest, and the Caspian Sea to the west. It was a constituent + republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan + is divided into five provinces or welayatlar (singular - welayat) and one + independent city. + meaning: GAZ:00005018 + Turks and Caicos Islands [GAZ:00003955]: + text: Turks and Caicos Islands [GAZ:00003955] + description: A British Overseas Territory consisting of two groups of tropical + islands in the West Indies. The Turks and Caicos Islands are divided into + six administrative districts (two in the Turks Islands and four in the Caicos + Islands. + meaning: GAZ:00003955 + Tuvalu [GAZ:00009715]: + text: Tuvalu [GAZ:00009715] + description: A Polynesian island nation located in the Pacific Ocean midway + between Hawaii and Australia. + meaning: GAZ:00009715 + United States of America [GAZ:00002459]: + text: United States of America [GAZ:00002459] + description: A federal constitutional republic comprising fifty states and + a federal district. The country is situated mostly in central North America, + where its forty-eight contiguous states and Washington, DC, the capital + district, lie between the Pacific and Atlantic Oceans, bordered by Canada + to the north and Mexico to the south. The State of Alaska is in the northwest + of the continent, with Canada to its east and Russia to the west across + the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United + States also possesses several territories, or insular areas, that are scattered + around the Caribbean and Pacific. The states are divided into smaller administrative + regions, called counties in most states, exceptions being Alaska (parts + of the state are organized into subdivisions called boroughs; the rest of + the state's territory that is not included in any borough is divided into + "census areas"), and Louisiana (which is divided into county-equivalents + that are called parishes). There are also independent cities which are within + particular states but not part of any particular county or consolidated + city-counties. Another type of organization is where the city and county + are unified and function as an independent city. There are thirty-nine independent + cities in Virginia and other independent cities or city-counties are San + Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, + Colorado and Carson City, Nevada. Counties can include a number of cities, + towns, villages, or hamlets, or sometimes just a part of a city. Counties + have varying degrees of political and legal significance, but they are always + administrative divisions of the state. Counties in many states are further + subdivided into townships, which, by definition, are administrative divisions + of a county. In some states, such as Michigan, a township can file a charter + with the state government, making itself into a "charter township", which + is a type of mixed municipal and township status (giving the township some + of the rights of a city without all of the responsibilities), much in the + way a metropolitan municipality is a mixed municipality and county. + meaning: GAZ:00002459 + Uganda [GAZ:00001102]: + text: Uganda [GAZ:00001102] + description: 'A landlocked country in East Africa, bordered on the east by + Kenya, the north by Sudan, on the west by the Democratic Republic of the + Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern + part of the country includes a substantial portion of Lake Victoria, within + which it shares borders with Kenya and Tanzania. Uganda is divided into + 80 districts, spread across four administrative regions: Northern, Eastern, + Central and Western. The districts are subdivided into counties.' + meaning: GAZ:00001102 + Ukraine [GAZ:00002724]: + text: Ukraine [GAZ:00002724] + description: A country in Eastern Europe. It borders Russia to the east, Belarus + to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova + to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine + is subdivided into twenty-four oblasts (provinces) and one autonomous republic + (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, + and Sevastopol, both have a special legal status. The 24 oblasts and Crimea + are subdivided into 490 raions (districts), or second-level administrative + units. + meaning: GAZ:00002724 + United Arab Emirates [GAZ:00005282]: + text: United Arab Emirates [GAZ:00005282] + description: A Middle Eastern federation of seven states situated in the southeast + of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering + Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, + Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + meaning: GAZ:00005282 + United Kingdom [GAZ:00002637]: + text: United Kingdom [GAZ:00002637] + description: A sovereign island country located off the northwestern coast + of mainland Europe comprising of the four constituent countries; England, + Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, + the northeast part of the island of Ireland and many small islands. Apart + from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North + Sea, the English Channel and the Irish Sea. The largest island, Great Britain, + is linked to France by the Channel Tunnel. + meaning: GAZ:00002637 + Uruguay [GAZ:00002930]: + text: Uruguay [GAZ:00002930] + description: A country located in the southeastern part of South America. + It is bordered by Brazil to the north, by Argentina across the bank of both + the Uruguay River to the west and the estuary of Rio de la Plata to the + southwest, and the South Atlantic Ocean to the southeast. Uraguay consists + of 19 departments (departamentos, singular - departamento). + meaning: GAZ:00002930 + Uzbekistan [GAZ:00004979]: + text: Uzbekistan [GAZ:00004979] + description: A doubly landlocked country in Central Asia, formerly part of + the Soviet Union. It shares borders with Kazakhstan to the west and to the + north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan + to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one + autonomous republic (respublika and one independent city (shahar). + meaning: GAZ:00004979 + Vanuatu [GAZ:00006918]: + text: Vanuatu [GAZ:00006918] + description: An island country located in the South Pacific Ocean. The archipelago, + which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern + Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New + Guinea, southeast of the Solomon Islands, and west of Fiji. + meaning: GAZ:00006918 + Venezuela [GAZ:00002931]: + text: Venezuela [GAZ:00002931] + description: A country on the northern coast of South America. The country + comprises a continental mainland and numerous islands located off the Venezuelan + coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses + borders with Guyana to the east, Brazil to the south, and Colombia to the + west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, + Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just + north, off the Venezuelan coast. Venezuela is divided into twenty-three + states (Estados), a capital district (distrito capital) corresponding to + the city of Caracas, the Federal Dependencies (Dependencias Federales, a + special territory), and Guayana Esequiba (claimed in a border dispute with + Guyana). Venezuela is further subdivided into 335 municipalities (municipios); + these are subdivided into over one thousand parishes (parroquias). + meaning: GAZ:00002931 + Viet Nam [GAZ:00003756]: + text: Viet Nam [GAZ:00003756] + description: The easternmost country on the Indochina Peninsula in Southeast + Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, + alongside China, Laos, and Cambodia. + meaning: GAZ:00003756 + Virgin Islands [GAZ:00003959]: + text: Virgin Islands [GAZ:00003959] + description: A group of islands in the Caribbean that are an insular area + of the United States. The islands are geographically part of the Virgin + Islands archipelago and are located in the Leeward Islands of the Lesser + Antilles. The US Virgin Islands are an organized, unincorporated United + States territory. The US Virgin Islands are administratively divided into + two districts and subdivided into 20 sub-districts. + meaning: GAZ:00003959 + Wake Island [GAZ:00007111]: + text: Wake Island [GAZ:00007111] + description: A coral atoll (despite its name) having a coastline of 19 km + in the North Pacific Ocean, located about two-thirds of the way from Honolulu + (3,700 km west) to Guam (2,430 km east). + meaning: GAZ:00007111 + Wallis and Futuna [GAZ:00007191]: + text: Wallis and Futuna [GAZ:00007191] + description: A Polynesian French island territory (but not part of, or even + contiguous with, French Polynesia) in the South Pacific between Fiji and + Samoa. It is made up of three main volcanic tropical islands and a number + of tiny islets. + meaning: GAZ:00007191 + West Bank [GAZ:00009572]: + text: West Bank [GAZ:00009572] + description: A landlocked territory near the Mediterranean coast of Western + Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the + south, west and north.[2] Under Israeli occupation since 1967, the area + is split into 167 Palestinian "islands" under partial Palestinian National + Authority civil rule, and 230 Israeli settlements into which Israeli law + is "pipelined". + meaning: GAZ:00009572 + Western Sahara [GAZ:00000564]: + text: Western Sahara [GAZ:00000564] + description: A territory of northwestern Africa, bordered by Morocco to the + north, Algeria in the northeast, Mauritania to the east and south, and the + Atlantic Ocean on the west. Western Sahara is administratively divided into + four regions. + meaning: GAZ:00000564 + Yemen [GAZ:00005284]: + text: Yemen [GAZ:00005284] + description: A country located on the Arabian Peninsula in Southwest Asia. + Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, + the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's + territory includes over 200 islands, the largest of which is Socotra, about + 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen + is divided into twenty governorates (muhafazah) and one municipality. The + population of each governorate is listed in the table below. The governorates + of Yemen are divided into 333 districts (muderiah). The districts are subdivided + into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + meaning: GAZ:00005284 + Zambia [GAZ:00001107]: + text: Zambia [GAZ:00001107] + description: A landlocked country in Southern Africa. The neighbouring countries + are the Democratic Republic of the Congo to the north, Tanzania to the north-east, + Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, + and Angola to the west. The capital city is Lusaka. Zambia is divided into + nine provinces. Each province is subdivided into several districts with + a total of 73 districts. + meaning: GAZ:00001107 + Zimbabwe [GAZ:00001106]: + text: Zimbabwe [GAZ:00001106] + description: A landlocked country in the southern part of the continent of + Africa, between the Zambezi and Limpopo rivers. It is bordered by South + Africa to the south, Botswana to the southwest, Zambia to the northwest, + and Mozambique to the east. Zimbabwe is divided into eight provinces and + two cities with provincial status. The provinces are subdivided into 59 + districts and 1,200 municipalities. + meaning: GAZ:00001106 +types: + WhitespaceMinimizedString: + name: WhitespaceMinimizedString + typeof: string + description: 'A string that has all whitespace trimmed off of beginning and end, + and all internal whitespace segments reduced to single spaces. Whitespace includes + #x9 (tab), #xA (linefeed), and #xD (carriage return).' + base: str + uri: xsd:token + Provenance: + name: Provenance + typeof: string + description: A field containing a DataHarmonizer versioning marker. It is issued + by DataHarmonizer when validation is applied to a given row of data. + base: str + uri: xsd:token +settings: + Title_Case: (((?<=\b)[^a-z\W]\w*?|[\W])+) + UPPER_CASE: '[A-Z\W\d_]*' + lower_case: '[a-z\W\d_]*' diff --git a/web/templates/hpai/schema_core.yaml b/web/templates/hpai/schema_core.yaml new file mode 100644 index 00000000..d960a6e8 --- /dev/null +++ b/web/templates/hpai/schema_core.yaml @@ -0,0 +1,73 @@ +id: https://example.com/hpai +name: Mpox +version: 4.3.3 +description: "The HPAI specification was developed by the Public Health Alliance for Genomic Epidemiology (PHA4GE) to better enable harmonization of highly pathogenic avian influenza genomic surveillance contextual data. The specification is intended to support H5N1 monitoring, and provides standardized, ontology-based fields and terms for samples, sequences, and bioinformatics analysis." +imports: + - 'linkml:types' +prefixes: + linkml: 'https://w3id.org/linkml/' + GENEPIO: 'http://purl.obolibrary.org/obo/GENEPIO_' +classes: + dh_interface: + name: dh_interface + description: 'A DataHarmonizer interface' + from_schema: https://example.com/hpai + 'HPAI': + name: 'HPAI' + title: 'HPAI' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIFood': + name: 'HPAIFood' + title: 'HPAI Food' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIWW': + name: 'HPAIWW' + title: 'HPAI Wastewater' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIEnviro': + name: 'HPAIEnviro' + title: 'HPAI Environmental' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 + 'HPAIHost': + name: 'HPAIHost' + title: 'HPAI Host' + description: + is_a: dh_interface + see_also: + annotations: + version: 1.0.0 +slots: {} +enums: {} +types: + WhitespaceMinimizedString: + name: 'WhitespaceMinimizedString' + typeof: string + description: 'A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).' + base: str + uri: xsd:token + Provenance: + name: 'Provenance' + typeof: string + description: 'A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.' + base: str + uri: xsd:token +settings: + Title_Case: "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" + UPPER_CASE: "[A-Z\\W\\d_]*" + lower_case: "[a-z\\W\\d_]*" diff --git a/web/templates/hpai/schema_enums.tsv b/web/templates/hpai/schema_enums.tsv new file mode 100644 index 00000000..913d4fde --- /dev/null +++ b/web/templates/hpai/schema_enums.tsv @@ -0,0 +1,1429 @@ +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description + +null value NullValue GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. + GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. + GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. + GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. + GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. + +organism menu OrganismMenu NCBITaxon:11320 Influenza A virus [NCBITaxon:11320] + +influenza_subtype menu InfluenzaSubtypeMenu NCBITaxon:102793 H5N1 subtype (Influenza A virus) [NCBITaxon:102793] + +influenza_subtyping_scheme_name menu InfluenzaSubtypingSchemeNameMenu GENEPIO:0101121 Tripartite Influenza A scheme [GENEPIO:0101121] Tripartite Influenza A scheme (A/goose/Guangdong/1/96-like viruses) [GENEPIO:0101121] + GENEPIO:0101122 USDA GenoFLU scheme [GENEPIO:0101122] USDA GenoFLU scheme (8 segment eurasian/american genotypes) [GENEPIO:0101122] + +taxonomic_identification_process menu TaxonomicIdentificationProcessMenu OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + OBI:0002740 PCR assay [OBI:0002740] An organism identification assay that is based on PCR. + OBI:0001546 Comparative phenotypic assessment [OBI:0001546] Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference + +sample_collection_time_of_day menu SampleCollectionTimeOfDayMenu NCIT:C64934 Morning [NCIT:C64934] The time period between dawn and noon. + NCIT:C64935 Afternoon [NCIT:C64935] The time period between noon and sunset. + NCIT:C64936 Evening [NCIT:C64936] The time period between late afternoon and bedtime. + NCIT:C65001 Night [NCIT:C65001] The time in every 24 hour period when it is dark. + +sample_collection_duration_unit menu SampleCollectionDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + + +food_product menu FoodProductMenu ENVO:02000047 Animal feed [ENVO:02000047] Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. + FOODON:00001564 Blood meal [FOODON:00001564] Blood meal is a dry, inert powder made from blood used as a high-nitrogen organic fertilizer and a high protein animal feed. + ENVO:02000054 Bone meal [ENVO:02000054] A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed. + FOODON:00004310 Brassica carinata meal [FOODON:00004310] A meal that is a co-product produced after the extraction of oil from the seed of the Ethiopian mustard plant (Brassica carinata). + FOODON:00002694 Canola meal [FOODON:00002694] Canola meal is an oilseed meal made from canola grain. Canola meal is a by-product of the oil crushing process. + FOODON:00004323 Compound feed premix [FOODON:00004323] A formula mixture of micronutrients that is used as a component in compound feed. + FOODON:00004324 Compound feed premix (medicated) [FOODON:00004324] A compound feed premix in which medicinal substance has been added. + FOODON:00003927 Feather meal [FOODON:00003927] A by product of processing poultry which is made from poultry feathers by partially grinding them under elevated heat and pressure, and then grinding and drying. + FOODON:03301620 Fish meal [FOODON:03301620] Fish meal is primarily used as a protein supplement in compound feed. As of 2010, about 56% of fish meal was used to feed farmed fish, about 20% was used in pig feed, about 12% in poultry feed, and about 12% in other uses, which included fertilizer. + FOODON:00004286 Lay ration [FOODON:00004286] Food formulated for the laying hens to increase egg production and egg shell quality. + FOODON:00002738 Meat and bone meal [FOODON:00002738] Meat and bone meal (MBM) is a product of the rendering industry. It is typically about 48–52% protein, 33–35% ash, 8–12% fat, and 4–7% water. It is primarily used in the formulation of animal feed to improve the amino acid profile of the feed. + FOODON:00004282 Meat meal [FOODON:00004282] A meal that is obtained by cooking, defatting, sterilizing, grinding, and sifting by-products of an animal. + FOODON:00002682 Pet food [FOODON:00002682] Pet food is plant or animal material intended for consumption by pets. + FOODON:03302757 Soybean meal [FOODON:03302757] A type of ground protein-rich residue from the production of soybean oil used chiefly in animal feeds, in adhesives and plastics, in making synthetic protein fibers, and in fermentation media (as for the production of antibiotics). + FOODON:00004322 Animal feed ingredient [FOODON:00004322] An ingredient that is used in the preparation of animal feed. + FOODON:00001256 Dairy food product [FOODON:00001256] A dairy food product has mammilian milk or a milk component as an ingredient. + FOODON:03000287 Cheese block (whole or parts) [FOODON:03000287] A whole cheese block or some substance made from a block of processed cheese. + FOODON:03310016 Cow skim milk (powdered) [FOODON:03310016] Milk powder that is obtained by removing all of the water from pasteurized skim milk. + UBERON:0001913 Milk [UBERON:0001913] An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + Meat, poultry and fish (organizational term) + FOODON:00001282 Beef (ground or minced) [FOODON:00001282] A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. + FOODON:03000412 Beef (ground or minced, boneless) [FOODON:03000412] + FOODON:03000398 Beef (ground or minced, extra lean) [FOODON:03000398] + FOODON:03000394 Beef (ground or minced, lean) [FOODON:03000394] + FOODON:03000402 Beef (ground or minced, medium) [FOODON:03000402] + FOODON:03000406 Beef (ground or minced, regular) [FOODON:03000406] + FOODON:03000408 Beef (ground or minced, sirloin) [FOODON:03000408] + FOODON:00002737 Beef hamburger (dish) [FOODON:00002737] A hamburger (short: burger) is a sandwich consisting of one or more cooked patties of ground meat, usually beef, placed inside a sliced bread roll or bun. The patty may be pan fried, grilled, or flame broiled. + FOODON:03000377 Beef shoulder [FOODON:03000377] + FOODON:03000387 Beef shoulder chop [FOODON:03000387] Meat chop from the shoulder region of beef. + FOODON:03000389 Beef sirloin chop [FOODON:03000389] Meat chop from the sirloin region of beef + FOODON:00004288 Beef stew chunk [FOODON:00004288] A chunk of beef used as an ingredient in making stew. + FOODON:00003302 Beef tenderloin [FOODON:00003302] A cut of beef corresponding to the psoas major muscle, which is very tender. + FOODON:03000333 Beef (whole cut or parts) [FOODON:03000333] + FOODON:03530020 Brisket [FOODON:03530020] A cut of meat from the breast or lower chest of beef or veal. + FOODON:00002703 Chicken breast [FOODON:00002703] Chicken breast consists mainly of the breast meat portion of a chicken, and may or may not include connected bone (boneless versus "with bone") and skin. + FOODON:03000385 Chicken breast (back off) [FOODON:03000385] A chicken breast with its backbone removed. + FOODON:00003332 Chicken breast (skinless) [FOODON:00003332] + FOODON:03000374 Chicken breast (with skin) [FOODON:03000374] + FOODON:00003364 Chicken breast (skinless, boneless) [FOODON:00003364] + FOODON:00004308 Chicken breast cutlet [FOODON:00004308] A cutlet made from chicken breast. + FOODON:00002716 Chicken drumstick [FOODON:00002716] The segment of a chicken's leg between the thigh and tarsus (ankle). + FOODON:03000366 Chicken drumstick (skinless) [FOODON:03000366] + FOODON:03000368 Chicken drumstick (with skin) [FOODON:03000368] + FOODON:00001040 Chicken meat [FOODON:00001040] + FOODON:03311826 Chicken meat (ground or minced) [FOODON:03311826] A food product made of ground or minced chicken meat. + FOODON:03000392 Chicken meat (ground or minced, lean) [FOODON:03000392] A food product made of lean, ground or minced chicken meat. + FOODON:03000396 Chicken meat (ground or minced, extra lean) [FOODON:03000396] A food product made of extra lean, ground or minced chicken meat. + FOODON:03000400 Chicken meat (ground or minced, medium) [FOODON:03000400] A food product made of medium, ground or minced chicken meat. + FOODON:03000404 Chicken meat (ground or minced, regular) [FOODON:03000404] A food product made of regular, ground or minced chicken meat. + FOODON:03000410 Chicken meat (ground or minced, boneless) [FOODON:03000410] + FOODON:00002672 Chicken nugget [FOODON:00002672] A chicken nugget is a chicken product made from chicken meat that is breaded or battered, then deep-fried or baked. + FOODON:02020219 Chicken thigh [FOODON:02020219] A whole thigh that derives from a chicken. + FOODON:00003331 Chicken thigh (skinless) [FOODON:00003331] A chicken thigh after the skin has been removed. + FOODON:02020227 Chicken thigh (skinless, with bone) [FOODON:02020227] A chicken thigh that is skinless and contains bone element. + FOODON:03000417 Chicken thigh (skinless, boneless) [FOODON:03000417] + FOODON:03000381 Chicken upper thigh [FOODON:03000381] Meat from the upper thigh of a chicken. + FOODON:00003330 Chicken thigh (with skin) [FOODON:00003330] + FOODON:00003363 Chicken thigh (with skin, with bone) [FOODON_00003363] A chicken thigh that contains skin and bone material. + FOODON:00002674 Chicken wing [FOODON:00002674] A whole wing that derives from a chicken. + FOODON:00001248 Fish food product [FOODON:00001248] A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). + FOODON:00002986 Fish steak [FOODON:00002986] A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless. + FOODON:00002502 Ham food product [FOODON:00002502] Ham is pork from a leg cut that has been preserved by wet or dry curing, with or without smoking. As a processed meat, the term "ham" includes both whole cuts of meat and ones that have been mechanically formed. + FOODON:03315658 Head cheese [FOODON:03315658] Head cheese is a cold cut that originated in Europe. Head cheese is not a dairy cheese, but a terrine or meat jelly made with flesh from the head of a calf or pig, or less commonly a sheep or cow, and often set in aspic. A version pickled with vinegar is known as souse. + FOODON:03411669 Lamb [FOODON:03411669] A whole lamb or some material processed from a lamb. + FOODON:00004285 Meat strip [FOODON:00004285] A cut of meat which is long, narrow and boneless. + FOODON:00002912 Mutton [FOODON:00002912] The meat of an adult sheep is mutton, a term only used for the meat, not the living animals. + FOODON:00001049 Pork chop [FOODON:00001049] A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion. + FOODON:03309969 Pork meat (ground or minced) [FOODON:03309969] Meat from a pig that has been ground or minced. + FOODON:03000413 Pork meat (ground or minced, boneless) [FOODON:03000413] + FOODON:03000399 Pork meat (ground or minced, extra lean) [FOODON:03000399] A food product made of extra-lean, ground or minced pork meat. + FOODON:03000395 Pork meat (ground or minced, lean) [FOODON:03000395] A food product made of lean, ground or minced pork meat. + FOODON:03000403 Pork meat (ground or minced, medium) [FOODON:03000403] A food product made of medium, ground or minced pork meat. + FOODON:03000407 Pork meat (ground or minced, regular) [FOODON:03000407] A food product made of regular, ground or minced pork meat. + FOODON:03000409 Pork meat (ground or minced, Sirloin) [FOODON:03000409] Ground or minced pork meat that comes from the sirloin region. + FOODON:03000376 Pork shoulder [FOODON:03000376] + FOODON:03000388 Pork shoulder chop [FOODON:03000388] Meat chop from the blade roast of pork. + FOODON:03000390 Pork sirloin chop [FOODON:03000390] + FOODON:00003148 Pork steak [FOODON:00003148] + FOODON:03000416 Pork tenderloin [FOODON:03000416] + FOODON:03315883 Poultry meat [FOODON:03315883] Any meat from one or more poultry birds. + FOODON:03530159 Leg (poultry meat cut) [FOODON:03530159] The leg cut of a poultry bird. + FOODON:00003469 Poultry drumstick [FOODON:00003469] The calf part of a poultry hindleg (hindlimb zeugopod) + FOODON:03530294 Neck (poultry meat cut) [FOODON:03530294] The neck cut of a poultry bird. + FOODON:03530160 Thigh (poultry meat cut) [FOODON:03530160] The thigh cut of a poultry bird. + FOODON:03530157 Wing (poultry meat cut) [FOODON:03530157] The wing cut of a poultry bird. + FOODON:03315904 Sausage (whole) [FOODON:03315904] A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder. + FOODON:03311003 Pepperoni [FOODON:03311003] A highly seasoned and spicy beef or pork sausage. + FOODON:03312067 Salami [FOODON:03312067] A cured sausage which consists of fermented and air-dried meat, typically pork. + FOODON:03411433 Shellfish [FOODON:03411433] The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. + FOODON:03301673 Shrimp [FOODON:03301673] A whole shrimp or some material processed from a shrimp. + FOODON:03411489 Scallop [FOODON:03411489] + FOODON:00002690 Turkey breast [FOODON:00002690] Turkey breast consists mainly of the breast meat portion of a turkey, and may or may not include connected bone ("deboned or boneless versus bone-in") and skin. + FOODON:03000386 Turkey breast (back off) [FOODON:03000386] A turkey breast with its backbone removed. + FOODON:03000372 Turkey breast (skinless) [FOODON:03000372] + FOODON:03000373 Turkey breast (skinless, boneless) [FOODON:03000373] + FOODON:03000375 Turkey breast (with skin) [FOODON:03000375] + FOODON:03000365 Turkey drumstick [FOODON:03000365] + FOODON:03000367 Turkey drumstick (skinless) [FOODON:03000367] + FOODON:03000369 Turkey drumstick (with skin) [FOODON:03000369] + FOODON:00001286 Turkey meat [FOODON:00001286] A turkey meat food product is any food product made predominantly of turkey parts. + FOODON:00002714 Turkey meat (ground or minced) [FOODON:00002714] A food product made of ground or minced turkey meat. + FOODON:03000393 Turkey meat (ground or minced, lean) [FOODON:03000393] A food product made of lean, ground or minced turkey meat. + FOODON:03000397 Turkey meat (ground or minced, extra lean) [FOODON:03000397] A food product made of extra-lean, ground or minced turkey meat. + FOODON:03000401 Turkey meat (ground or minced, medium) [FOODON:03000401] A food product made of medium, ground or minced turkey meat. + FOODON:03000405 Turkey meat (ground or minced, regular) [FOODON:03000405] A food product made of regular, ground or minced turkey meat. + FOODON:03000411 Turkey meat (ground or minced, boneless) [FOODON:03000411] + FOODON:00003325 Turkey thigh [FOODON:00003325] A thigh poultry cut of turkey. + FOODON:00003329 Turkey thigh (skinless) [FOODON:00003329] A turkey thigh after the skin has been removed. + FOODON:03000370 Turkey thigh (skinless, boneless) [FOODON:03000370] + FOODON:00003328 Turkey thigh (with skin) [FOODON:00003328] A turkey thigh that still contains the skin. + FOODON:03000382 Turkey upper thigh [FOODON:03000382] Meat from the upper thigh of a turkey. + FOODON:03000384 Turkey upper thigh (with skin) [FOODON:03000384] Turkey's upper thigh that contains the skin. + FOODON:03000371 Turkey wing [FOODON:03000371] + FOODON:00003083 Veal [FOODON:00003083] Veal is the meat of calves, in contrast to the beef from older cattle. Veal can be produced from a calf of either sex and any breed; however, most veal comes from young males of dairy breeds which are not used for breeding. + OODON:000039111 Formula fed veal [FOODON:000039111] + FOODON:00004280 Grain-fed veal [FOODON:00004280] Meat from a calf that is raised on grain, hay, or other solid food, in addition to milk + + +food_product_properties menu FoodProductPropertiesMenu FOODON:03510128 Organic food claim or use [FOODON:03510128] USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] + FOODON:03311126 Food (raw) [FOODON:03311126] A food material that has not been cooked. + FOODON:03316043 Food (heat treated) [FOODON:03316043] + FOODON:00002654 Food (pasteurized) [FOODON:00002654] + Dairy product (no fat removed, whole) + Dairy product (skimmed, non-fat) + Dairy product (semi-skimmed, reduced fat, 1%) + Dairy product (semi-skimmed, reduced fat, 2%) + +food_packaging menu FoodPackagingMenu FOODON:03490214 Bottle [FOODON:03490214 A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle. + FOODON:03490197 Bag [FOODON:03490197] According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack + FOODON:03490213 Carton [FOODON:03490213] + +environmental_site menu EnvironmentalSiteMenu ENVO:01000925 Abattoir [ENVO:01000925] A facility in which non-human animals are slaughtered and processed for human consumption. + ENVO:00000114 Agricultural Field [ENVO:00000114] A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops. + ENVO:01000922 Animal cage [ENVO:01000922] A manufactured cage which may be used to confine, contain, or protect an animal. + ENVO:03501406 Artificial wetland [ENVO:03501406] A wetland ecosystem which is constructed to treat municipal or industrial wastewater, greywater or stormwater runoff. + ENVO:03501441 Breeding ground [ENVO:03501441] A place where animals breed. + ENVO:00000073 Building [ENVO:00000073] A permanent walled and roofed construction. + ENVO:03501257 Barn [ENVO:03501257] A farm building used for housing livestock, storing machinery or crops etc + ENVO:03501383 Breeder barn [ENVO:03501383] A barn where animals are kept for breeding purposes. + ENVO:03501386 Broiler barn [ENVO:03501386] A barn where broiler chickens are reared. + ENVO:03501385 Sheep barn [ENVO:03501385] A barn where sheep are kept. + ENVO:00003862 Dairy [ENVO:00003862] A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption. + ENVO:00000078 Farm [ENVO:00000078] An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. + ENVO:03501443 Beef farm [ENVO:03501443] A farm where cows are kept for the purpose of meat production. + ENVO:03501384 Breeder farm [ENVO:03501384] A farm where animals are kept for breeding purposes. + ENVO:03501416 Dairy farm [ENVO:03501416] A farm where cows are kept for the purpose of producing milk and other dairy products. + ENVO:01000627 Feedlot [ENVO:01000627] A feedlot is a plot of land on which livestock are fattened for market [URL:http://www.merriam-webster.com/dictionary/feedlot ]. + ENVO:03501444 Beef cattle feedlot [ENVO:03501444] A feedlot where beef cattle are kept with a focus on efficient growth and weight gain of the animals. + ENVO:00000294 Fish farm [ENVO:00000294] A facility in which fish are raised commercially in tanks or enclosures, usually for food. + ENVO:03501417 Research farm [ENVO:03501417] A farm which is used for conducting agricultural research. + GAZ:00004603 Central Experimental Farm [GAZ:00004603] An agricultural facility, working farm, and research centre of the Research Branch of Agriculture and Agri-Food Canada. This farm is centrally located in and completely surrounded by the City of Ottawa, Ontario, Canada. The CEF is bordered by the Rideau Canal (a National Historic Site as well) to the east, by Baseline Road to the south, by Merivale and Fisher Roads to the west, and Carling Avenue to the north. + ENVO:01000306 Freshwater environment [ENVO:01000306] An aquatic environment which is determined by freshwater. + ENVO:01001873 Hatchery [ENVO:01001873] A construction in which eggs are hatched under artificial conditions. + ENVO:01001874 Poultry hatchery [ENVO:01001874] A hatchery in which the eggs of poultry are hatched under artificial conditions + ENVO:00002173 Hospital [ENVO:00002173] A building in which health care services are provided by specialized staff and equipment. + ENVO:00000020 Lake [ENVO:00000020] A body of water or other liquid of considerable size contained in a depression on a landmass. + ENVO:00000033 Pond [ENVO:00000033] A body of water, usually of smaller size than a lake. + ENVO:00000025 Reservoir [ENVO:00000025] An artificial body of water, often contained by a dam, constructed for the purpose of water storage. + ENVO:00000450 Irrigation reservoir [ENVO:00000450] A reservoir constructed for the purpose of providing water for irrigation. + ENVO:01001448 Retail environment [ENVO:01001448] A planned environmental usage process during which an environment supports the sale of goods to ultimate consumers, usually in small quantities. + ENVO:00002221 Shop [ENVO:00002221] A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods. + ENVO:01000984 Supermarket [ENVO:01000984] A food shop in which food products are the primary offer for sale or trade. + ENVO:00000022 River [ENVO:00000022] A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. + ENVO:03501439 Roost (bird) [ENVO:03501439] A perch on which birds rest. + ENVO:00002272 Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. + ENVO:00000043 Wetland [ENVO:00000043] An area that is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances do support, a prevalence of vegetation typically adapted for life in saturated soil conditions. + +environmental_material menu EnvironmentalMaterialMenu ENVO:00002005 Air [ENVO:00002005] The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. + AGRO:00000079 Animal manure [AGRO:00000079] Organic matter mostly derived from animal feces which can be used as organic fertilizer in agriculture. + AGRO:00000675 Animal feeding equipment [AGRO:00000675] An equipment used to feed and water livestock animals. + AGRO:00000679 Animal feeder [AGRO:00000679] An animal feeding equipment that has a food storage unit and which enables livestock to obtain their own food. + AGRO:00000680 Animal drinker [AGRO:00000680] An animal feeding equipment that has a water storage unit which enables livestock to obtain their own water. + AGRO:00000676 Feed pan [AGRO:00000676] A bowl or pan which is used to feed livestock. + AGRO:00000677 Watering bowl [AGRO:00000677] A bowl from which animals can drink. + AGRO:00000671 Animal transportation equipment [AGRO:00000671] An equipment used in the transportation of an animal + GENEPIO:0100896 Dead haul trailer [GENEPIO:0100896] A trailer used by a dead haul truck to transport dead animal from an abattoir. + AGRO:00000673 Dead haul truck [AGRO:00000673] A truck used to haul dead animals from an abattoir. + GENEPIO:0100897 Live haul trailer [GENEPIO:0100897] A trailer used by a live haul truck to transport live animals. + AGRO:00000674 Live haul truck [AGRO:00000674] A truck used to haul live animals. + NCIT:C49844 Belt [NCIT:C49844] A device consisting of a narrow loop of material moving over shafts or pulleys. + AGRO:00000670 Egg belt [AGRO:00000670] A conveyor belt used to collect eggs in an industrial egg production environment. + AGRO:00000669 Plucking belt [AGRO:00000669] A part of the plucking machine that moves the birds through the stages of plucking within the plucking apparatus. + ENVO:00002059 Biosolids [ENVO:00002059] A treated form of sludge, sometimes used as a fertilizer in agriculture. + GSSO:012935 Boot [GSSO:012935] A footwear which covers the foot, the ankle, and sometimes the leg below the knee. + OBI:0002806 Boot cover [OBI:0002806] A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. + ENVO:03501431 Broom [ENVO:03501431] A cleaning equipment piece which is a bundle of fibres attached to a long handle, and is used for sweeping. + ENVO:03501379 Bulk tank [ENVO:03501379] A manufactured product which used to safely store and/or transport solids, liquids, gases and a variety of compounds and mixtures. + AGRO:00000678 Chick box [AGRO:00000678] The box which is used to transport chick (juvenile chicken). + AGRO:00000672 Chick pad [AGRO:00000672] The lining of a box or crate used to transport chicks (juvenile chickens). + ENVO:03501430 Cleaning equipment [ENVO:03501430] An equipment piece used for cleaning a built environment or a manufactured product. + ENVO:00002170 Compost [ENVO:00002170] The aerobically decomposed remnants of organic materials. + ENVO:03501372 Crate [ENVO:03501372] A manufactured product which is a container, traditionally made of wooden slates, designed to protect transported goods from damage. + ENVO:03501400 Dumpster [ENVO:03501400] A manufactured product which is a reusable container that accumulates waste until it is periodically emptied or replaced. + ENVO:00002008 Dust [ENVO:00002008] Minute solid particles with diameters less than 500 micrometers. Occurs in and may be deposited from, the atmosphere. + NCIT:C49947 Fan [NCIT:C49947] A device designed to create an air current through the rotation of a planar surface. + ENVO:03501415 Freezer [ENVO:03501415] A manufactured product which is a device used to keep things frozen by maintaining a temperature below the freezing point of water. + ENVO:03501414 Freezer handle [ENVO:03501414] A manufactured product which is the handle of a freezer door. + ENVO:03501424 Manure digester equipment [ENVO:03501424] An equipment piece which is used in the aerobic or anaerobic microbial digestion of manure. + ENVO:03501432 Nest [ENVO:03501432] A structure that is built for certain animals to hold eggs or young. + ENVO:00005805 Bird's nest [ENVO:00005805] A bird nest is the spot in which a bird lays and incubates its eggs and raises its young. [ https://en.wikipedia.org/wiki/Bird_nest ] + ENVO:00000134 Permafrost [ENVO:00000134] Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years. + UBERON:0008291 Poultry fluff [UBERON:0008291] A feather lacking a vane and having a rudimentary rachis and a tuft of non-interlocked barbs with elongated barbules extending from the calamus. + AGRO:00000080 Poultry litter [AGRO:00000080] Manure which is primarily composed of pig feces. + ENVO:00002007 Sediment [ENVO:00002007] Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid. + ENVO:00001998 Soil [ENVO:00001998] Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. + ENVO:00002259 Agricultural soil [ENVO:00002259] A type of soil used for agriculture that supports the physical, chemical, and biological needs of the desired crop during production. + ENVO:00002261 Forest soil [ENVO:00002261] A portion of soil which is found in a forested area. + ENVO:00003869 Straw [ENVO:00003869] An agricultural byproduct, the dry stalk of a cereal plant, after the nutrient grain or seed has been removed. + CHEBI:15377 Water [CHEBI:15377] An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + ENVO:00003064 Drinking water [ENVO:00003064] Water which is suitable for consumption by humans + ENVO:03501436 Fecal slurry [ENVO:03501436] A mixture of fecal material mixed, buffer, and other materials, that is homogenized and strained and used in fecal microbiota translpantation. + GENEPIO:0004323 Fluid from meat rinse [GENEPIO:0004323] + ENVO:01001004 Groundwater [ENVO:01001004] Underground water which is located in pore spaces found in rock or unconsolidated deposits such as soil, clay, or gravel. + AGRO:00000693 Poultry plucking water [AGRO_00000693] A type of water obtained from rinsing poultry carcasses during the feather plucking process. + ENVO:03501408 Surface runoff [ENVO:03501408] Surface water which is 1) from some rainwater, stormwater, meltwater, or other local source and 2) which can no longer sufficiently rapidly infiltrate into soil, and instead flows along a drainage slope. + ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. + ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence + ENVO:00002044 Sludge [ENVO:00002044] The residual semi-solid material left from domestic or industrial processes, or wastewater treatment processes. + ENVO:00002057 Primary sludge [ENVO:00002057] Sludge generated from the initial processes (i.e., precipitation, sedimentation) of wastewater treatment. + ENVO:00002058 Secondary sludge [ENVO:00002058] Activated waste biomass generated during wastewater treatment. + GENEPIO:0100891 Wastewater effluent [GENEPIO:0100891] + GENEPIO:0100892 Primary wastewater effluent [GENEPIO:0100892] A wastewater effluent which has been discharged from a primary clarifier after the first stage of sedimentation. + GENEPIO:0100893 Secondary wastewater effluent [GENEPIO:0100893] A wastewater effluent which has been discharged from a secondary clarifier after the second stage of sedimentation. + GENEPIO:0100890 Wastewater sediment [GENEPIO:0100890] + AGRO:00000692 Weep fluid [AGRO:00000692] A fluid that leaks from a bag containing an animal carcass, and can include water, chemicals and anatomical fluids. + +anatomical_material menu AnatomicalMaterialMenu UBERON:0000178 Blood [UBERON:0000178] A fluid that is composed of blood plasma and erythrocytes. + UBERON:0006314 Fluid [UBERON:0006314] Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + UBERON:0001359 Fluid (cerebrospinal (CSF)) [UBERON:0001359] A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + UBERON:0000173 Fluid (amniotic) [UBERON:0000173] Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. + UBERON:0001836 Saliva [UBERON:0001836] A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + UBERON:0000479 Tissue [UBERON:0000479] Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + +body_product menu BodyProductMenu GENEPIO:0100898 Digestive tract substance [GENEPIO:0100898] Undigested food material, microbiota, and other materials found in the digestive tract. + GENEPIO:0100899 Caecal content [GENEPIO:0100899] Undigested food material, microbiota, and other materials found in the cecum + GENEPIO:0100900 Intestinal content [GENEPIO:0100900] Undigested food material, microbiota, and other materials found in the intestine + GENEPIO:0100901 Stomach content [GENEPIO:0100901] Undigested food material, microbiota, and other materials found in the stomach + UBERON:0001988 Feces [UBERON:0001988] Portion of semisolid bodily waste discharged through the anus. + GENEPIO:0004512 Fecal composite [GENEPIO:0004512] A mixture of feces obtained from multiple individuals. + GENEPIO:0004513 Feces (fresh) [GENEPIO:0004513] Feces that was recently excreted. + GENEPIO:0004514 Feces (environmental) [GENEPIO:0004514] Feces which is deposited in the environment. + UBERON:0007109 Meconium [UBERON:0007109] A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. + UBERON:0001913 Milk [UBERON:0001913] An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + UBERON:0001914 Colostrum [UBERON:0001914] The thin, yellow, serous fluid secreted by the mammary glands during pregnancy and immediately postpartum before lactation begins. It consists of immunologically active substances, white blood cells, water, protein, fat, and carbohydrates. [ MESH : A12.200.194 http://en.wikipedia.org/wiki/Colostrum ] + UBERON:0000912 Mucus [UBERON:0000912] Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. + UBERON:0001088 Urine [UBERON:0001088] Excretion that is the output of a kidney. + +anatomical_part menu AnatomicalPartMenu UBERON:0008979 Carcass [UBERON:0008979] A body of a multi-cellular organism that is no longer living. + UBERON:0001007 Digestive system [UBERON:0001007] Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. + UBERON:0001153 Caecum [UBERON:0001153] pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. + UBERON:0001155 Colon [UBERON:0001155] A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. + UBERON:0006925 Digestive gland [UBERON:0006925] Any gland that is part of the digestive system. + UBERON:0001041 Foregut [UBERON:0001041] Anterior subdivision of a digestive tract. + UBERON:0002110 Gall bladder [UBERON:0002110] An organ that aids digestion and stores bile produced by the liver. + UBERON:0004786 Gastrointestinal system mucosa [UBERON:0004786] A mucosa that is part of a gastrointestinal system. + UBERON:0005052 Gizzard [UBERON:0005052] The muscular enlargement of the alimentary canal that has usually thick muscular walls and a tough horny lining for grinding the food and when the crop is present follows it and the proventriculus. + UBERON:0001046 Hindgut [UBERON:0001046] The caudalmost subdivision of a digestive tract. + UBERON:0000160 Intestine [UBERON:0000160] Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. + UBERON:0002108 Small intestine [UBERON:0002108] Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum. + UBERON:0002114 Duodenum [UBERON:0002114] The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). + UBERON:0002116 Ileum [UBERON:0002116] The portion of the small intestine that extends from the jejunum to the colon. + UBERON:0002115 Jejunum [UBERON:0002115] The portion of the small intestine that extends from the duodenum to the ileum. + UBERON:0000945 Stomach [UBERON:0000945] An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. + UBERON:0007358 Abomasum [UBERON:0007358] The fourth stomach of ruminating animals, which is an elongated pear-shaped sac lying on the floor of the abdomen, on the right-hand side, and roughly between the seventh and twelfth ribs. It leads to the beginning of the small intestine. + UBERON:0007365 Rumen [UBERON:0007365] The first compartment of the ruminant stomach. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. + Excretory system (organizational term) + UBERON:0001245 Anus [UBERON:0001245] Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. + UBERON:0011253 Anal gland [UBERON:0011253] A type of gland occurring as solitary or in pairs or groups, near the anus and sometimes opening into the rectum. + UBERON:0000162 Cloaca [UBERON:0000162] Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. + UBERON:0002107 Liver [UBERON:0002107] An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes + UBERON:0002113 Kidney [UBERON:0002113] A paired organ of the urinary tract which has the production of urine as its primary function. + UBERON:0001052 Rectum [UBERON:0001052] The terminal portion of the intestinal tube, terminating with the anus. + UBERON:0002106 Spleen [UBERON:0002106] The organ that functions to filter blood and to store red corpuscles and platelets. + UBERON:0001255 Urinary bladder [UBERON:0001255] Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion. + UBERON:0002387 Foot [UBERON:0002387] The terminal part of the vertebrate leg upon which an individual stands. 2: An invertebrate organ of locomotion or attachment; especially: a ventral muscular surface or process of a mollusk. + UBERON:0000033 Head [UBERON:0000033] The head is the anterior-most division of the body. + UBERON:0000955 Brain [UBERON:0000955] The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell. + UBERON:0001690 Ear [UBERON:0001690] Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. + UBERON:0000970 Eye [UBERON:0000970] An organ that detects light. + UBERON:0000165 Mouth [UBERON:0000165] The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + UBERON:0000004 Nose [UBERON:0000004] The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. + UBERON:0035612 Nasal turbinal [UBERON:0035612] A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. + UBERON:0001728 Nasopharynx (NP) [UBERON:0001728] The section of the pharynx that lies above the soft palate. + UBERON:0002109 Pair of nares [UBERON:0002109] Pair of nostrils. + UBERON:0001825 Paranasal sinus [UBERON:0001825] The paired air-filled cavities surrounded by the bones of the face that are lined by mucous membranes and are continuous with the nasal cavity. + UBERON:0006333 Snout [UBERON:0006333] The projecting nose and mouth of an animal, especially a mammal. + UBERON:0006558 Lymphatic system [UBERON:0006558] An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. + UBERON:0000029 Lymph node [UBERON:0000029] Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. + UBERON:0002509 Mesenteric lymph node [UBERON:0002509] The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. + GENEPIO:0100927 Mantle (bird) [GENEPIO:0100927] The forward area of a bird's upper side that is sandwiched between the nape and the start of the back. + UBERON:0000974 Neck [UBERON:0000974] An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. + UBERON:0001043 Esophagus [UBERON:0001043] Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation. + UBERON:0003126 Trachea [UBERON:0003126] The trachea is the portion of the airway that attaches to the bronchi as it branches. + UBERON:0001021 Nerve [UBERON:0001021] An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. + UBERON:0002240 Spinal cord [UBERON:0002240] Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. + GENEPIO:0001117 Organs or organ parts [GENEPIO:0001117] An object aggregate which has as members whole organs or parts of organs, possibly from different organisms. + UBERON:0000062 Organ [UBERON:0000062] Anatomical structure that performs a specific function or group of functions + UBERON:0001630 Muscle organ [UBERON:0001630] Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work. + UBERON:0002097 Skin of body [UBERON:0002097] The organ covering the body that consists of the dermis and epidermis. + UBERON:0000990 Reproductive system [UBERON:0000990] Anatomical system that has as its parts the organs concerned with reproduction. + UBERON:0000922 Embryo [UBERON:0000922] Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + UBERON:0000323 Fetus [UBERON:0000323] An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching + UBERON:0000992 Ovary [UBERON:0000992] The gonad of a female organism which contains germ cells. + UBERON:0000993 Oviduct [UBERON:0000993] A tube or collection of tubes in an animal from the ovaries to the outside of the body. + UBERON:0001987 Placenta [UBERON:0001987] Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. + UBERON:0000473 Testis [UBERON:0000473] A gonad of a male animal. A gonad produces and releases sperm. + UBERON:0013216 Udder [UBERON:0013216] A large pendulous organ consisting of two or more mammary glands enclosed in a common envelope and each provided with a single nipple. + UBERON:0000995 Uterus [UBERON:0000995] The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. + UBERON:0000996 Vagina [UBERON:0000996] A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles + UBERON:0001040 Yolk sac [UBERON:0001040] A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes. + UBERON:0001004 Respiratory system [UBERON:0001004] Functional system which consists of structures involved in respiration. + UBERON:0009060 Air sac [UBERON:0009060] Any of the membranous air-filled extensions of the lungs of birds, which increase the efficiency of gaseous exchange in the lungs. + UBERON:0002048 Lung [UBERON:0002048] Respiration organ that develops as an outpocketing of the esophagus + UBERON:0000977 Pleura [UBERON:0000977] The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). + UBERON:0004785 Respiratory system mucosa [UBERON:0004785] The mucous membrane lining the respiratory tract. + UBERON:0001434 Skeletal system [UBERON:0001434] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + UBERON:0000982 Skeletal joint [UBERON:0000982] Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue. + UBERON:0001474 Bone element [UBERON:0001474] Skeletal element that is composed of bone tissue. + UBERON:0000915 Thoracic segment of trunk [UBERON:0000915] Subdivision of trunk that lies between the head and the abdomen. + UBERON:0000916 Abdomen [UBERON:0000916] The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + UBERON:0002378 Muscle of abdomen [UBERON:0002378] Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. + UBERON:0002358 Peritoneum [UBERON:0002358] Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. + UBERON:0007798 Vascular system [UBERON:0007798] Anatomical system that consists of all blood and lymph vessels. + UBERON:0001981 Blood vessel [UBERON:0001981] A vessel through which blood circulates in the body. + UBERON:0003903 Bursa of Fabricius [UBERON:0003903] An epithelial and lymphoid organ that develops as a dorsal diverticulum of the proctodeal region of the cloaca in birds. The luminal (interior) surface of the bursa is plicated with as many as 15 primary and 7 secondary plicae or folds. These plicae have hundreds of bursal follicles containing follicle-associated epithelial cells, lymphocytes, macrophages, and plasma cells. Lymphoid stem cells migrate from the fetal liver to the bursa during ontogeny. In the bursa, these stem cells acquire the characteristics of mature, immunocompetent B cells. The bursa is an organ found in birds involved in B cell differentiation. + UBERON:0002535 Gill [UBERON:0002535] Anatomical surface structure found in many aquatic organisms. It is a respiration organ whose function is the extraction of oxygen from water and the excretion of carbon dioxide. The microscopic structure of a gill is such that it presents a very large surface area to the external environment. Gills usually consist of thin filaments of tissue, branches, or slender tufted processes which have a highly folded surface to increase surface area. A high surface area is crucial to the gas exchange of aquatic organisms as water contains only 1/20 parts dissolved Oxygen compared to air. With the exception of some aquatic insects, the filaments and lamellae (folds) contain blood or coelomic fluid, from which gases are exchanged through the thin walls. Oxygen is carried by the blood to other parts of the body. Carbon dioxide passes from the blood through the thin gill tissue into the water. Gills or gill-like organs, located in different parts of the body, are found in various groups of aquatic animals, including mollusks, crustaceans, insects, fish, and amphibians. [ http://en.wikipedia.org/wiki/Gill ] + UBERON:0000948 Heart [UBERON:0000948] A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. + UBERON:0002048 Lung [UBERON:0002048] Respiration organ that develops as an outpocketing of the esophagus + UBERON:0002407 Pericardium [UBERON:0002407] The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. + UBERON:2000298 Vent (anatomical) [UBERON:2000298] The external opening of the rectum or cloaca. + UBERON:0012464 Bird vent [UBERON:0012464] The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. [ http://orcid.org/0000-0002-6601-2165 ] + GENEPIO:0100902 Fish vent [GENEPIO:0100902] The external opening which opens to the reproductive and digestive tracts of the fish. During spawning, the vent serves as an outlet for eggs and sperm. In most fishes, the vent is in front of the anal fin. + +collection_device menu CollectionDeviceMenu ENVO:00003968 Air filter [ENVO:00003968] + AGRO:00000405 Auger (earth auger) [AGRO:00000405] Manually operated hand tool that consists of cutter head having semicircular blades connected to pipe with the help of clamp and flange. The connecting pipe is further connected to a handle. + GSSO:008558 Bag [GSSO:008558] A sac or pouch. + GENEPIO:0002122 Whirlpak sampling bag [GENEPIO:0002122] A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures. + FOODON:03490214 Bottle [FOODON:03490214] A rigid or semirigid container typically of glass or plastic having a comparatively narrow neck or mouth and usually no handle. + GENEPIO:0100928 Box corer [GENEPIO:0100928] A specimen collection device that is used to collect soft sediments in lakes or oceans. + OBI:0002826 Bronchoscope [OBI:0002826] A device which is a thin, tube-like instrument which includes a light and a lens used to examine a lung. + OBI:0002088 Collection Container [OBI:0002088] A container with the function of containing a specimen. + GENEPIO:0100026 Collection Cup [GENEPIO:0100026] A device which is used to collect liquid samples. + GENEPIO:0004318 Culture plate [GENEPIO:0004318] A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium. + NCIT:C96141 Petri dish [NCIT:C96141] A shallow dish with a lid used to culture cells. + OBI:0002825 Fibrobronchoscope Brush [OBI:0002825] + GENEPIO:0100103 Filter [GENEPIO:0100103] A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass. + OBI:0002827 Fine Needle [OBI:0002827] + OBI:0001128 Micropipette [OBI:0001128] + OBI:0000436 Needle [OBI:0000436] A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. + GENEPIO:0100929 PONAR grab sampler [GENEPIO:0100929] A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay." + GENEPIO:0002125 Scoop [GENEPIO:0002125] A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion. + GENEPIO:0100930 Soil sample probe [GENEPIO:0100930] A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores. + CIT:C149941 Spatula [NCIT:C149941] + OBI:0002819 Sponge [OBI:0002819] A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. + OBI:0002831 Suction Catheter [OBI:0002831] A catheter which is used to remove mucus and other secretions from the body. + GENEPIO:0100027 Swab [GENEPIO:0100027] A device which is a soft, absorbent material mounted on one or both ends of a stick. + OBI:0002822 Drag swab [OBI:0002822] A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string + OBI:0002824 Surface wipe [OBI:0002824] A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. + GENEPIO:0101196 Tube [GENEPIO:0101196] A sample collection device which is cylindrical shape that is open at one end, used to collect material. + OBI:0002859 Blood Collection Tube [OBI:0002859] A specimen collection tube which is designed for the collection of whole blood. See also: https://en.wikipedia.org/wiki/Blood_culture#Collection + OBI:0002858 Microcapillary tube [OBI:0002858] + OBI:0002860 Serum Collection Tube [OBI:0002860] A specimen collection tube which is designed for collecting whole blood and enabling the separation of serum. + OBI:0002861 Sputum Collection Tube [OBI:0002861] A specimen collection tube which is designed for collecting sputum. + OBI:0002862 Urine Collection Tube [OBI:0002862] A specimen container which is designed for holding urine. + GENEPIO:0002127 Vacuum device [GENEPIO:0002127] A device which generates a vacuum to provide suction of material. + OBIB:0000032 Vacutainer [OBIB:0000032] A test tube which is either a sterile glass or plastic tube with a closure that is evacuated to create a vacuum inside the tube facilitating the draw of a predetermined volume of liquid. Most commonly used to draw a blood sample directly from the vein, these also are used to collect urine samples. Vacutainer tube may contain additives designed to stabilize and preserve the specimen prior to analytical testing. + +collection_method menu CollectionMethodMenu HP:0002835 Aspiration [HP:0002835] Inspiration of a foreign object into the airway. + OBI:0002650 Biopsy [OBI:0002650] A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. + GENEPIO:0004326 Fecal grab [GENEPIO:0004326] A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted. + OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. + GENEPIO:0100031 Air filtration [GENEPIO:0100031] A filtration process which removes solid particulates from the air via an air filtration device. + GENEPIO:0100931 Water filtration [GENEPIO:0100931] A filtration process which removes or reduces the concentration of particulate matter, including suspended particles, parasites, bacteria, algae, viruses, and fungi, as well as other undesirable chemical and biological contaminants from contaminated water using water filters to produce safe and clean water. + OBI:0600044 Lavage [OBI:0600044] A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid + GENEPIO:0100032 Bronchoalveolar lavage [GENEPIO:0100032] The collection of bronchoalveolar lavage fluid (BAL) from the lungs. + GENEPIO:0100033 Gastric lavage [GENEPIO:0100033] The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. + MMO:0000344 Necropsy [MMO:0000344] A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. + NCIT:C28221 Phlebotomy [NCIT:C28221] The collection of blood from a vein, most commonly via needle venipuncture. + GENEPIO:0002116 Rinsing for specimen collection [GENEPIO_0002116] The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. + GENEPIO:0100932 Scooping [GENEPIO:0100932] A specimen collection process that is used to dig out an amount of sample using a scoop. + GENEPIO:0100933 Sediment collection [GENEPIO:0100933] A specimen collection process that is used to collect a sediment sample. + GENEPIO:0100934 Soil coring [GENEPIO:0100934] A specimen collection process that is used to collect soil sample cores. + GENEPIO:0101003 Weep fluid collection (pouring) [GENEPIO:0101003] A specimen collection process that is used to collect weep fluid via pouring from the source container into the sample collection device. (e.g. bag or tube) + +sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu UO:0000101 microliter (uL) [UO:0000101] A metric unit of volume equivalent to one thousandth of a cubic centimeter or one millionth of a liter. + UO:0000098 milliliter (mL) [UO:0000098] A metric unit of volume equivalent to one cubic centimeter or one thousandth of a liter. + UO:0000099 liter (L) [UO:0000099] A metric unit of volume equivalent to 1000 cubic centimeters + +residual_sample_status menu ResidualSampleStatusMenu GENEPIO:0101087 Residual sample remaining (some sample left) [GENEPIO:0101087] + GENEPIO:0101088 No residual sample (sample all used) [GENEPIO:0101088] + GENEPIO:0101089 Residual sample status unkown [GENEPIO:0101089] + + +purpose of sampling PurposeOfSampling GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. + GENEPIO:0100002 Diagnostic testing [GENEPIO:0100002] A sampling strategy in which individuals are sampled in the context of diagnostic testing. + GENEPIO:0100548 Environmental testing [GENEPIO:0100548] A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena. + GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. + GENEPIO:0100549 Clinical trial [GENEPIO:0100549] A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research. + GENEPIO:0100550 Field experiment [GENEPIO:0100550] A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work. + GENEPIO:0100582 Survey study [GENEPIO:0100582] A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes. + GENEPIO:0100004 Surveillance [GENEPIO:0100004] A sampling strategy in which individuals are sampled for surveillance investigations. + +presampling activity PresamplingActivity GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. + GENEPIO:0100537 Antimicrobial pre-treatment [GENEPIO:0100537] The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity. + GENEPIO:0100538 Certified animal husbandry practices [GENEPIO:0100538] The implementation of animal husbandy practices that have been certified by an authorized organization. + GENEPIO:0100894 Certified humane animal husbandry practices [GENEPIO:0100894] A certification organization in Washington DC that is dedicated to improving the lives of farm animals in food production from birth through slaughter. + GENEPIO:0100539 Certified organic farming practices [GENEPIO:0100539] The implementation of organic farming practices that have been certified by an authorized organization. + GENEPIO:0100895 Conventional farming practices [GENEPIO:0100895] The implementation of farming practices that include man-made inputs such as chemical fertilizers and genetically-modified seeds. + GENEPIO:0100540 Change in storage conditions [GENEPIO:0100540] A change in the storage conditions of a material or a substance. + GENEPIO:0100541 Cleaning/disinfection [GENEPIO:0100541] A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment. + GENEPIO:0100542 Extended downtime between activities [GENEPIO:0100542] A prolonged period of inactivity between processes or events. + GENEPIO:0100546 Microbial pre-treatment [GENEPIO:0100546] The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity. + GENEPIO:0100547 Probiotic pre-treatment [GENEPIO:0100547] The addition of a probiotic substance to an individual or material prior to some other event or activity. + NCIT:C15346 Vaccination [NCIT:C15346] Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. + +sample storage duration unit SampleStorageDurationUnit UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. + UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. + UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. + UO:0000034 Week [UO:0000034] A time unit which is equal to 7 days. + UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + +specimen processing SpecimenProcessing OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. + OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. + OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. + OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. + +experimental specimen role type ExperimentalSpecimenRoleType GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. + GENEPIO:0101123 Validation strain [GENEPIO:0101123] + GENEPIO:0101124 Proficiency test isolate [GENEPIO:0101124] + GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment + EFO:0002090 Technical replicate [EFO:0002090] A technical replicate is a replicate role where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment. + EFO:0002091 Biological replicate [EFO:0002091] A biological replicate is a replicate role that consists of independent biological replicates made from different individual biosamples. + GENEPIO:0101039 Synthetic lab construct [GENEPIO:0101039] + GENEPIO:0101120 Negative sample [GENEPIO:0101120] + +available_data_types menu AvailableDataTypesMenu GENEPIO:0100702 Documentation [GENEPIO:0100702] A dataset attribute bundle which indicates the presence of documentation data. + GENEPIO:0100703 Experimental parameters documentation [GENEPIO:0100703] A documentation data tag which indicates the presence of data that describes experimental parameters. + GENEPIO:0100704 Feed history [GENEPIO:0100704] A documentation data tag which indicates the presence of data that describes feed history. + GENEPIO:0100705 Land use information [GENEPIO:0100705] A documentation data tag which indicates the presence of data that describes land use information. + GENEPIO:0100706 Therapeutic administration history [GENEPIO:0100706] A documentation data tag which indicates the presence of data that describes a history of therapeutic administration. + GENEPIO:0100707 Chemical characterization [GENEPIO:0100707] A dataset attribute bundle which indicates the presence of chemical characterization data. + GENEPIO:0100714 Microbiological characterization [GENEPIO:0100714] A dataset attribute bundle which indicates the presence of microbiological characterization data. + GENEPIO:0100715 Microbiological identification [GENEPIO:0100715] A microbiological characterization data tag which indicates the presence of microbiological identification data. + GENEPIO:0100716 Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Beckson Dickson BBL Crystal identification system. + GENEPIO:0100717 Microbiological identification (bioMérieux API) [GENEPIO:0100717] A microbiological characterization data tag which indicates the presence of microbiological identification data dervied using the bioMérieux API identification system. + GENEPIO:0100718 Microbiological identification (Biolog) [GENEPIO:0100718] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Biolog identification system. + GENEPIO:0100719 Microbiological identification (FAME) [GENEPIO:0100719] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Fatty acid methyl esters (FAME) identification system. + GENEPIO:0100720 Microbiological identification (Sensititre) [GENEPIO:0100720] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Sensititre identification system. + GENEPIO:0100721 Microbiological identification (ViTek) [GENEPIO:0100721] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the ViTek identification system. + GENEPIO:0100722 Phage type [GENEPIO:0100722] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using phage type identification. + GENEPIO:0100723 Serotype [GENEPIO:0100723] A microbiological characterization data tag which indicates the presence of microbiological identification data derived using serotype identification. + GENEPIO:0100724 Phenotypic microbiological characterization [GENEPIO:0100724] A microbiological characterization data tag which indicates the presence of phenotypic microbiological characterization data. + GENEPIO:0100725 AMR phenotypic testing [GENEPIO:0100725] A phenotypic microbiological characterization data tag which indicates the presence of antimicrobial resistance (AMR) phenotypic testing characterization data. + GENEPIO:0100726 Biolog phenotype microarray [GENEPIO:0100726] A phenotypic microbiological characterization data tag which indicates the presence of biolog phenotype microarray characterization data. + GENEPIO:0100727 Microbiological quantification [GENEPIO:0100727] A dataset attribute bundle which indicates the presence of microbiological quantification data. + GENEPIO:0100728 Colony count [GENEPIO:0100728] A microbiological quantification data tag which indicates the presence of colony count data. + GENEPIO:0100729 Total coliform count [GENEPIO:0100729] A colony count microbiological quantification data tag which indicates the presence of data that describes total colony count of coliforms. + GENEPIO:0100730 Total fecal coliform count [GENEPIO:0100730] A colony count microbiological quantification data tag that indicates the presence of data which describes total colony count of fecal coliforms. + GENEPIO:0100731 Infectivity assay [GENEPIO:0100731] A microbiological quantification data tag which indicates the presence of infectivity assay data. + GENEPIO:0100732 ELISA toxin binding [GENEPIO:0100732] A microbiological quantification data tag which indicates the presence of data which describes enzyme-linked immunosorbent assay (ELISA) toxin binding. + GENEPIO:0100733 Molecular characterization [GENEPIO:0100733] A dataset attribute bundle which indicates the presence of molecular characterization data. + GENEPIO:0100734 16S rRNA Sanger sequencing [GENEPIO:0100734] A molecular characterization data tag which indicates the presence of 16S rRNA Sanger sequencing characterization data. + GENEPIO:0101024 Metagenomic sequencing [GENEPIO:0101024] A molecular characterization data tag which indicates the presence of metagenomic sequencing characterization data. + GENEPIO:0100735 PCR marker detection [GENEPIO:0100735] A molecular characterization data tag which indicates the presence of polymerase chain reaction (PCR) marker detection characterization data. + GENEPIO:0100736 BOX PCR fingerprint [GENEPIO:0100736] A PCR marker detection characterization data tag which indicates the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data. + GENEPIO:0100737 ERIC PCR fingerprint [GENEPIO:0100737] A PCR marker detection characterization data tag which indicates the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint data. + GENEPIO:0100738 Plasmid type [GENEPIO:0100738] A molecular characterization data tag which indicates the presence of plasmid type characterization data. + GENEPIO:0100739 Ribotype [GENEPIO:0100739] A molecular characterization data tag which indicates the presence of ribotype characterization data. + GENEPIO:0100740 Molecular quantification [GENEPIO:0100740] A dataset attribute bundle which indicates the presence of molecular quantification data. + GENEPIO:0100741 qPCR marker organism quantification [GENEPIO:0100741] A molecular quantification data tag which indicates the presence of quantitative polymerase chain reaction (qPCR) marker organism quantification data. + GENEPIO:0100742 Physical characterization [GENEPIO:0100742] A dataset attribute bundle which indicates the presence of physical characterization data. + GENEPIO:0100743 Conductivity measurement [GENEPIO:0100743] A physical characterization data tag which indicates the presence of data that describes conductivity measurement characterization. + GENEPIO:0100744 Mollusc shell measurement [GENEPIO:0100744] A physical characterization data tag which indicates the presence of data that describes a measurement of a mollusc shell. + GENEPIO:0100746 Matter compostion [GENEPIO:0100746] A physical characterization data tag which indicates the presence of matter compostion characterization data. + GENEPIO:0100747 Dry matter composition [GENEPIO:0100747] A matter composition characterization data tag which indicates the presence of data that describes dry matter composition. + GENEPIO:0100748 Organic matter composition [GENEPIO:0100748] A matter composition characterization data tag which indicates the presence of data that describes organic matter composition. + +host (common name) menu HostCommonNameMenu NCBITaxon:8782 Bird [NCBITaxon:8782] A group of warm-blooded vertebrates in class Aves, that are characterized by feathers, wings, toothless beaked jaws and the laying of hard-shelled eggs and are usually able to fly. + NCBITaxon:9031 Chicken [NCBITaxon:9031] "A domesticated junglefowl of the species Gallus gallus. " + FOODON:00004504 Seabird [FOODON:00004504] A bird that is adapted to live within the marine environment. + NCBITaxon:9206 Cormorant [NCBITaxon:9206] A family of aquatic birds (Phalacrocoracidae). + NCBITaxon:56069 Double Crested Cormorant [NCBITaxon:56069] A species of the cormorant family of water birds (Phalacrocorax auritus). + NCBITaxon:9109 Crane [NCBITaxon:9109] A family of large, long-legged, and long-necked birds (Gruidae). + NCBITaxon:9117 Whooping Crane [NCBITaxon:9117] An endangered crane species that is native to North America and is named for its whooping sound. + NCBITaxon:8911 Gull (Seagull) [NCBITaxon:8911] A large genus of gulls within the family Laridae. + NCBITaxon:119606 Glaucous-winged Gull [NCBITaxon:119606] A species of large, white-headed gull (Larus glaucescens). + NCBITaxon:8912 Great Black-backed Gull [NCBITaxon:8912] A species of white gull that has a black back and wings (Larus marinus). + NCBITaxon:35669 Herring Gull [NCBITaxon:35669] A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus). + NCBITaxon:126683 Ring-billed Gull [NCBITaxon:126683] A species of ring-billed gull that has a black ring around its bill (Larus delawarensis). + NCBITaxon:50366 Eider [NCBITaxon:50366] A genus of large seaducks (Somateria). + NCBITaxon:76058 Common Eider [NCBITaxon:76058] A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima). + NCBITaxon:9103 Turkey [NCBITaxon:9103] A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo. + FOODON:03411222 Fish [FOODON:03411222] Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. + FOODON:03411134 Mammal [FOODON:03411134] Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. + FOODON:03000300 Companion animal [FOODON:03000300] An animal that is kept as a companion. + NCBITaxon:9913 Cow [NCBITaxon:9913] A group of large, domesticated, cloven-hooved herbivores. + NCBITaxon:9850 Deer [NCBITaxon:9850] + NCBITaxon:9606 Human [NCBITaxon:9606] A bipedal primate mammal of the species Homo sapiens. + NCBITaxon:9823 Pig [NCBITaxon:9823] A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles. + NCBITaxon:9940 Sheep [NCBITaxon:9940] A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries. + FOODON:03411433 Shellfish [FOODON:03411433] The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. + + +host (scientific name) menu HostScientificNameMenu NCBITaxon:229290 Anoplopoma fimbria [NCBITaxon:229290] One of two members of the fish family Anoplopomatidae and the only species in the genus Anoplopoma. + NCBITaxon:9913 Bos taurus [NCBITaxon:9913] A group of large, domesticated, cloven-hooved herbivores. + NCBITaxon:6565 Crassostrea virginica [NCBITaxon:6565] A species of true oyster (Crassostrea virginica). + NCBITaxon:9031 Gallus gallus [NCBITaxon:9031] "A domesticated junglefowl of the species Gallus gallus. " + NCBITaxon:9117 Grus americana [NCBITaxon:9117] An endangered crane species that is native to North America and is named for its whooping sound. + NCBITaxon:6706 Homarus americanus [NCBITaxon:6706] A species of lobster that is found on the Atlantic coast of North America (Homarus americanus). + NCBITaxon:9606 Homo sapiens [NCBITaxon:9606] A bipedal primate mammal of the species Homo sapiens. + NCBITaxon:35669 Larus argentatus [NCBITaxon:35669] A species of large gull, that is up to 66 cm (26 in) long (Larus argentatus). + NCBITaxon:126683 Larus delawarensis [NCBITaxon:126683] A species of ring-billed gull that has a black ring around its bill (Larus delawarensis). + NCBITaxon:119606 Larus glaucescens [NCBITaxon:119606] A species of large, white-headed gull (Larus glaucescens). + NCBITaxon:8912 Larus marinus [NCBITaxon:8912] A species of white gull that has a black back and wings (Larus marinus). + NCBITaxon:9103 Meleagris gallopavo [NCBITaxon:9103] A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo. + NCBITaxon:6550 Mytilus edulis [NCBITaxon:6550] A medium-sized edible marine bivalve mollusc in the family Mytilidae, the mussels. + NCBITaxon:8019 Oncorhynchus kisutch [NCBITaxon:8019] A species of pacific salmon in North America, that is commonly called as coho salmon. + NCBITaxon:8022 Oncorhynchus mykiss [NCBITaxon:8022] A species of trout native to cold-water tributaries of the Pacific Ocean in Asia and North America (Oncorhynchus mykiss). + NCBITaxon:74940 Oncorhynchus tshawytscha [NCBITaxon:74940] The largest species of pacific salmon in North America (Oncorhynchus tshawytscha). + NCBITaxon:9940 Ovis aries [NCBITaxon:9940] A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries. + NCBITaxon:56069 Phalacrocorax auritus [NCBITaxon:56069] A species of the cormorant family of water birds (Phalacrocorax auritus). + NCBITaxon:8030 Salmo salar [NCBITaxon:8030] A species of ray-finned fish in the family Salmonidae (Salmo salar). + NCBITaxon:76058 Somateria mollissima [NCBITaxon:76058] A species of a large sea-duck that is distributed over the northern coasts of Europe, North America and eastern Siberia (Somateria mollissima). + NCBITaxon:9825 Sus scrofa domesticus [NCBITaxon:9825] A stout-bodied, hooved and short-legged, omnivorous mammal, with thick skin usually sparsely coated with short bristles raised for its meat. + + +host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) + FOODON:03411349 Calf [FOODON:03411349] Calves are the young of domestic cattle. Calves are reared to become adult cattle, or are slaughtered for their meat, called veal. + FOODON:00004411 Dry cow [FOODON:00004411] A cow that is in a stage of its lactation cycle where milk production ceases prior to calving. + FOODON:00004292 Feeder cow [FOODON:00004292] A young cow mature enough either to undergo backgrounding or to be fattened in preparation for slaughter. + FOODON:00004293 Finisher cow [FOODON:00004293] + FOODON:03411201 Milker cow [FOODON:03411201] A cow that is bred specifically for milk production. + FOODON:00004294 Stocker cow [FOODON:00004294] A type of cow that has been weaned and is being fed in a way to add physical bulk to its body. + FOODON:00004295 Weanling cow [FOODON:00004295] A type of young cow that has been weaned and consumes solid food. + Cow (by sex/reproductive stage) (organizational term) + FOODON:00000015 Bull [FOODON:00000015] A cattle bull is an adult "intact" (i.e. not castrated) male of a cattle species. + NCBITaxon:9913 Cow [NCBITaxon:9913] A group of large, domesticated, cloven-hooved herbivores. + FOODON:00004296 Freemartin [FOODON:00004296] A cow that is genetically female, but has many characteristics of a male and is usually infertile. + FOODON:00002518 Heifer [FOODON:00002518] A heifer is a young female, under three years of age, of a cattle species before she has had a calf of her own. + FOODON:00002531 Steer [FOODON:00002531] A cattle steer is an adult castrated male of a cattle species. + Pig (by age/production stage) (organizational term) + FOODON:00003371 Finisher pig [FOODON:00003371] A grower pig over 70 kg (150 lb) liveweight. + FOODON:00003370 Grower pig [FOODON:00003370] A pig between weaning and sale or transfer to the breeding herd, sold for slaughter or killed for rations. + OODON:00004297 Nursing pig [FOODON:00004297 ] + NCBITaxon:9823 Pig [NCBITaxon:9823] A stout-bodied, hooved and short-legged, omnivorous mammal from the species Sus scofus, with thick skin usually sparsely coated with short bristles. + FOODON:00003952 Piglet [FOODON:00003952] An unweaned or immature pig. + FOODON:00003373 Weanling (weaner) pig [FOODON:00003373] A young pig recently separated from the sow + Pig (by sex/reproductive stage) (organizational term) + FOODON:03411280 Barrow [FOODON:03411280] A male swine castrated before sexual maturity. + FOODON:03412248 Boar [FOODON:03412248] An adult male swine. + FOODON:00003369 Gilt [FOODON:00003369] A female pig under the age of 1 year. The term is also often used to refer to a pig who has not farrowed, or given birth to a litter. + FOODON:00003333 Sow [FOODON:00003333] An adult female swine. + FOODON:03411563 Poultry or game bird [FOODON:03411563] Domesticated birds kept by humans for their eggs, their meat or their feathers. + FOODON:03411198 Broiler or fryer chicken [FOODON:03411198] A chicken younger than 10 weeks old (previously younger than 13 weeks), of either sex, that is tender-meated with soft, pliable, smooth-textured skin and flexible breastbone cartilage. + FOODON:03411711 Capon [FOODON:03411711] A surgically neutered male chicken younger than four months old (previously younger than eight months) that is tender-meated with soft, pliable, smooth-textured skin. + FOODON:00004299 Chick [FOODON:00004299] A young offspring of any bird. + NCBITaxon:9031 Chicken [NCBITaxon:9031] "A domesticated junglefowl of the species Gallus gallus. " + UBERON:0007379 Egg [UBERON:0007379] The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. + FOODON:00004300 Hatchling [FOODON:00004300] A young animal that has recently emerged from its egg. + FOODON:00003282 Hen [FOODON:00003282] An adult female chicken. + FOODON:00004301 Layer chicken [FOODON:00004301] A type of chicken kept for laying eggs. + FOODON:00004302 Layer turkey [FOODON:00004302] A type of turkey kept for laying eggs. + FOODON:00002962 Poult [FOODON:00002962] A poult is a young domestic chicken, turkey, pheasant, or other fowl being raised for food. + FOODON:00004303 Pullet [FOODON:00004303] A young hen, especially one less than one year old. + FOODON:03411714 Rooster [FOODON:03411714] A mature male chicken with coarse skin, toughened and darkened meat, and hardened breastbone tip. + OODON:00004304 Tom (Gobbler) [FOODON:00004304 ] + NCBITaxon:9103 Turkey [NCBITaxon:9103] A large, mainly domesticated game bird characterized by a bald head and wattles (in the male) of the species Meleagris gallopavo. + NCBITaxon:9940 Sheep [NCBITaxon:9940] A domesticated, even-toed, ungluate, ruminant mammal typically kept as livestock for its wool and meat, usually of the species Ovis aries. + FOODON:00004305 Ram [FOODON:00004305] An adult male sheep kept for breeding and for wool production. + FOODON:00004306 Wether sheep [FOODON:00004306] A castrated male sheep. + FOODON:03412610 Ewe [FOODON:03412610] A ewe is a female sheep. + FOODON:03411669 Lamb [FOODON:03411669] A whole lamb or some material processed from a lamb. + FOODON:03411222 Fish [FOODON:03411222] Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. + FOODON:00004319 Fish egg [FOODON_00004319] An egg or spawn of a fish that is contained within or separated from the ovary. + FOODON:00004318 Fry (fish) [FOODON_00004318] A fish that is recently hatched and has reached the stage where its yolk-sac has almost disappeared and its swim bladder is operational to the point where the fish can actively feed for itself. + FOODON:00004317 Juvenile fish [FOODON_00004317] A fish that has not reached to sexual maturity. + +host_age_unit menu HostAgeUnitMenu UO:0000035 month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. + UO:0000036 year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. + + +host_age_bin menu HostAgeBinMenu GENEPIO:0100684 First winter [GENEPIO:0100684] An age group used to classify birds identified by their first winter nonbreeding plumage, generally indicating a juvenile bird. + GENEPIO:0100685 First summer [GENEPIO:0100685] An age group used to classify birds identified by their first summer nonbreeding plumage, generally indicating a juvenile bird. + GENEPIO:0100686 Second winter [GENEPIO:0100686] An age group used to classify birds identified by their second winter plumage (many types of birds molt several times during the same season). + GENEPIO:0100687 Second summer [GENEPIO:0100687] An age group used to classify birds identified by their second summer plumage (many types of birds molt several times during the same season). + GENEPIO:0100688 Third winter [GENEPIO:0100688] An age group used to classify birds identified by their third winter plumage (many types of birds molt several times during the same season). + GENEPIO:0100689 Third summer [GENEPIO:0100689] An age group used to classify birds identified by their third summer plumage (many types of birds molt several times during the same season). + ENEPIO:0100049 0 - 9 [GENEPIO:0100049]] + GENEPIO:0100050 10 - 19 [GENEPIO:0100050] An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive). + GENEPIO:0100051 20 - 29 [GENEPIO:0100051] An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive). + GENEPIO:0100052 30 - 39 [GENEPIO:0100052] An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive). + GENEPIO:0100053 40 - 49 [GENEPIO:0100053] An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive). + GENEPIO:0100054 50 - 59 [GENEPIO:0100054] An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive). + GENEPIO:0100055 60 - 69 [GENEPIO:0100055] An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive). + GENEPIO:0100056 70 - 79 [GENEPIO:0100056] An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive). + GENEPIO:0100057 80 - 89 [GENEPIO:0100057] An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive). + GENEPIO:0100058 90 - 99 [GENEPIO:0100058] An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). + GENEPIO:0100059 100+ [GENEPIO:0100059] An age group that stratifies the age of a case to be greater than or equal to 100 years old. + +host_gender HostGender NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. + NCIT:C46109 Male [NCIT:C46109] An individual who reports belonging to the cultural gender role distinction of male. + GSSO:000132 Non-binary gender [GSSO:000132] Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. + GSSO:004004 Transgender (assigned male at birth) [GSSO:004004] Having a feminine gender (identity) which is different from the sex one was assigned at birth. + GSSO:004005 Transgender (assigned female at birth) [GSSO:004005] Having a masculine gender (identity) which is different from the sex one was assigned at birth. + CIT:C110959 Undeclared [NCIT:C110959] + + + +host_disease menu HostDiseaseMenu Highly pathogenic avian influenza A (HPAI) + +host_health_state menu HostHealthStateMenu NCIT:C3833 Asymptomatic [NCIT:C3833] Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. + NCIT:C28554 Deceased [NCIT:C28554] The cessation of life. + CIT:C115935 Healthy [NCIT:C115935] + NCIT:C49498 Recovered [NCIT:C49498] One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C25269 Symptomatic [NCIT:C25269] Exhibiting the symptoms of a particular disease. + +host_health_status_details menu HostHealthStatusDetailsMenu NCIT:C25179 Hospitalized [NCIT:C25179] The condition of being treated as a patient in a hospital. + GENEPIO:0100045 Hospitalized (Non-ICU) [GENEPIO:0100045] The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU). + GENEPIO:0100046 Hospitalized (ICU) [GENEPIO:0100046] The condition of being treated as a patient in a hospital intensive care unit (ICU). + NCIT:C70909 Mechanical Ventilation [NCIT:C70909] + GENEPIO:0100047 Medically Isolated [GENEPIO:0100047] Separation of people with a contagious disease from population to reduce the spread of the disease. + GENEPIO:0100048 Medically Isolated (Negative Pressure) [GENEPIO:0100048] Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter. + CIT:C173768 Self-quarantining [NCIT:C173768] + +host_health_outcome menu HostHealthOutcomeMenu NCIT:C28554 Deceased [NCIT:C28554] The cessation of life. + NCIT:C25254 Deteriorating [NCIT:C25254] Advancing in extent or severity. + NCIT:C49498 Recovered [NCIT:C49498] One of the possible results of an adverse event outcome that indicates that the event has improved or recuperated. + NCIT:C30103 Stable [NCIT:C30103] Subject to little fluctuation; showing little if any change. + +signs_and_symptoms menu SignsAndSymptomsMenu HP:0030829 Abnormal lung auscultation [HP:0030829] + HP:0033677 Acute Respiratory Distress Syndrome [HP:0033677] + HP:0011446 Altered mental status [HP:0011446] + HP:0100543 Cognitive impairment [HP:0100543] + HP:0001259 Coma [HP:0001259] + HP:0001289 Confusion [HP:0001289] + HP:0031258 Delirium (sudden severe confusion) [HP:0031258] + HP:0011675 Arrhythmia [HP:0011675] + HP:0025406 Asthenia (generalized weakness) [HP:0025406] + GENEPIO:0101182 Bleeding gums [GENEPIO:0101182] + HP:0031352 Chest tightness or pressure [HP:0031352] + HP:0025145 Rigors (fever shakes) [HP:0025145] + HP:0025143 Chills (sudden cold sensation) [HP:0025143] A sudden sensation of feeling cold. + HP:0000509 Conjunctivitis (pink eye) [HP:0000509] Inflammation of the conjunctiva. + MP:0001867 Coryza (rhinitis) [MP:0001867] + HP:0012735 Cough [HP:0012735] A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. + HP:0031246 Nonproductive cough (dry cough) [HP:0031246] + HP:0031245 Productive cough (wet cough) [HP:0031245] + DOID:13250 Diarrhea [DOID:13250] + HP:0002094 Dyspnea (breathing difficulty) [HP:0002094] + HP:0012378 Fatigue (tiredness) [HP:0012378] A subjective feeling of tiredness characterized by a lack of energy and motivation. + HP:0001945 Fever [HP:0001945] Body temperature elevated above the normal range. + GENEPIO:0100066 Fever (>=38°C) [GENEPIO:0100066] + HP:0002315 Headache [HP:0002315] Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. + HP:0012418 Hypoxemia (low blood oxygen) [HP:0012418] + GENEPIO:0100068 Silent hypoxemia [GENEPIO:0100068] + HP:0033834 Malaise (general discomfort/unease) [HP:0033834] + HP:0001324 Muscle weakness [HP:0001324] + HP:0001742 Nasal obstruction (stuffy nose) [HP:0001742] + HP:0002018 Nausea [HP:0002018] A sensation of unease in the stomach together with an urge to vomit. + HP:0012531 Pain [HP:0012531] + HP:0002829 Arthralgia (painful joints) [HP:0002829] + HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. + HP:0025439 Pharyngitis (sore throat) [HP:0025439] + HP:0031417 Rhinorrhea (runny nose) [HP:0031417] + HP:0025144 Shivering (involuntary muscle twitching) [HP:0025144] + HP:0025095 Sneezing [HP:0025095] + HP:0033709 Sputum Production [HP:0033709] + HP:0002716 Swollen Lymph Nodes [HP:0002716] Enlargment (swelling) of a lymph node. + HP:0002789 Tachypnea (accelerated respiratory rate) [HP:0002789] + HP:0002013 Vomiting (throwing up) [HP:0002013] Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. + +pre-existing_conditions_and_risk_factors menu PreExistingConditionsAndRiskFactorsMenu VO:0004925 Age 60+ [VO:0004925] + DOID:2355 Anemia [DOID:2355] + DOID:2860 Hemoglobinopathy [DOID:2860] + HP:0002039 Anorexia [HP:0002039] + NCIT:C92743 Birthing labor [NCIT:C92743] + NCIT:C80693 Bone marrow failure [NCIT:C80693] + MONDO:0004992 Cancer [MONDO:0004992] A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. + MONDO:0007254 Breast cancer [MONDO:0007254] + MONDO:0005575 Colorectal cancer [MONDO:0005575] + DOID:2531 Hematologic malignancy (cancer of the blood) [DOID:2531] + MONDO:0008903 Lung cancer [MONDO:0008903] + MONDO:0024880 Metastatic disease [MONDO:0024880] + NCIT:C16212 Cancer treatment [NCIT:C16212] Any intervention for management of a malignant neoplasm. + NCIT:C157740 Cancer surgery [NCIT:C157740] + NCIT:C15632 Chemotherapy [NCIT:C15632] The use of synthetic or naturally-occurring chemicals for the treatment of diseases. + NCIT:C15360 Adjuvant chemotherapy [NCIT:C15360] + NCIT:C3079 Cardiac disorder [NCIT:C3079] + HP:0011675 Arrhythmia [HP:0011675] + MONDO:0005267 Cardiac disease [MONDO:0005267] + HP:0001638 Cardiomyopathy [HP:0001638] + GENEPIO:0100074 Cardiac injury [GENEPIO:0100074] + HP:0000822 Hypertension (high blood pressure) [HP:0000822] + HP:0002615 Hypotension (low blood pressure) [HP:0002615] + HP:0011410 Cesarean section [HP:0011410] + GENEPIO:0100075 Chronic cough [GENEPIO:0100075] + GENEPIO:0100076 Chronic gastrointestinal disease [GENEPIO:0100076] + NCIT:C211 Corticosteroids [NCIT:C211] + HP:0000819 Diabetes mellitus (diabetes) [HP:0000819] A group of abnormalities characterized by hyperglycemia and glucose intolerance. + HP:0100651 Type I diabetes mellitus (T1D) [HP:0100651] A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. + HP:0005978 Type II diabetes mellitus (T2D) [HP:0005978] A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. + HP:0000964 Eczema [HP:0000964] + HP:0003111 Electrolyte disturbance [HP:0003111] + HP:0002901 Hypocalcemia [HP:0002901] + HP:0002900 Hypokalemia [HP:0002900] + HP:0002917 Hypomagnesemia [HP:0002917] + HP:0002383 Encephalitis (brain inflammation) [HP:0002383] + MONDO:0005027 Epilepsy [MONDO:0005027] + NCIT:C15248 Hemodialysis [NCIT:C15248] + MONDO:0044348 Hemoglobinopathy [MONDO:0044348] + MONDO:0005109 Human immunodeficiency virus (HIV) [MONDO:0005109] An infection caused by the human immunodeficiency virus. + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. + NCIT:C16118 HIV and antiretroviral therapy (ART) [NCIT:C16118] Treatment of human immunodeficiency virus (HIV) infections with medications that target the virus directly, limiting the ability of infected cells to produce new HIV particles. + NCIT:C14139 Immunocompromised [NCIT:C14139] A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions. + MONDO:0004670 Lupus [MONDO:0004670] An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. + MONDO:0005265 Inflammatory bowel disease (IBD) [MONDO:0005265] + HP:0002583 Colitis [HP:0002583] + HP:0100279 Ulcerative colitis [HP:0100279] + HP:0100280 Crohn's disease [HP:0100280] + NCIT:C3149 Renal disorder [NCIT:C3149] + MONDO:0005240 Renal disease [MONDO:0005240] + HP:0012622 Chronic renal disease [HP:0012622] + HP:0000083 Renal failure [HP:0000083] + MONDO:0005154 Liver disease [MONDO:0005154] + NCIT:C113609 Chronic liver disease [NCIT:C113609] + HP:0001397 Fatty liver disease (FLD) [HP:0001397] + HP:0003326 Myalgia (muscle pain) [HP:0003326] Pain in muscle. + MONDO:0005404 Myalgic encephalomyelitis (ME) [MONDO:0005404] + MONDO:0005071 Neurological disorder [MONDO:0005071] + MONDO:0019056 Neuromuscular disorder [MONDO:0019056] + HP:0001513 Obesity [HP:0001513] + MONDO:0005139 Severe obesity [MONDO:0005139] + MONDO:0005087 Respiratory disorder [MONDO:0005087] + HP:0002099 Asthma [HP:0002099] + HP:0004469 Chronic bronchitis [HP:0004469] + HP:0006510 Chronic obstructive pulmonary disease [HP:0006510] + HP:0002097 Emphysema [HP:0002097] + MONDO:0005275 Lung disease [MONDO:0005275] + HP:0006528 Chronic lung disease [HP:0006528] + HP:0002206 Pulmonary fibrosis [HP:0002206] + HP:0002090 Pneumonia [HP:0002090] + HP:0002878 Respiratory failure [HP:0002878] + HP:0033677 Adult respiratory distress syndrome [HP:0033677] + MONDO:0009971 Newborn respiratory distress syndrome [MONDO:0009971] + MONDO:0018076 Tuberculosis [MONDO:0018076] + GENEPIO:0100077 Postpartum (≤6 weeks) [GENEPIO:0100077] + NCIT:C25742 Pregnancy [NCIT:C25742] The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. + DOID:14525 Reye syndrome [DOID:14525] + MONDO:0005554 Rheumatic disease [MONDO:0005554] + MONDO:0011382 Sickle cell disease [MONDO:0011382] + NBO:0001845 Substance use [NBO:0001845] + MONDO:0002046 Alcohol abuse [MONDO:0002046] + GENEPIO:0100078 Drug abuse [GENEPIO:0100078] + GENEPIO:0100079 Injection drug abuse [GENEPIO:0100079] + NBO:0015005 Smoking [NBO:0015005] + NCIT:C173621 Vaping [NCIT:C173621] + HP:0002789 Tachypnea (accelerated respiratory rate) [HP:0002789] + CIT:C159659 Transplant [NCIT:C159659] + NCIT:C131759 Cardiac transplant [NCIT:C131759] + GENEPIO:0100080 Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080] + NCIT:C157332 Kidney transplant [NCIT:C157332] + GENEPIO:0100081 Liver transplant [GENEPIO:0100081] + +complications menu ComplicationsMenu HP:0500165 Abnormal blood oxygen level [HP:0500165] + MONDO:0015796 Acute lung injury [MONDO:0015796] + GENEPIO:0100092 Ventilation induced lung injury (VILI) [GENEPIO:0100092] + MONDO:0001208 Acute respiratory failure [MONDO:0001208] + HP:0011675 Arrhythmia (complication) [HP:0011675] + HP:0001649 Tachycardia [HP:0001649] + GENEPIO:0100074 Cardiac injury [GENEPIO:0100074] + HP:0001695 Cardiac arrest [HP:0001695] + HP:0001977 Blood clot [HP:0001977] + HP:0004420 Arterial clot [HP:0004420] + HP:0002625 Deep vein thrombosis (DVT) [HP:0002625] + HP:0002204 Pulmonary embolism (PE) [HP:0002204] + HP:0001638 Cardiomyopathy [HP:0001638] + MONDO:0024619 Central nervous system invasion [MONDO:0024619] + HP:0001297 Stroke (complication) [HP:0001297] + MONDO:0003346 Central Nervous System Vasculitis [MONDO:0003346] + HP:0002140 Acute ischemic stroke [HP:0002140] + HP:0001259 Coma [HP:0001259] + HP:0011097 Convulsions [HP:0011097] + MONDO:0009061 Cystic fibrosis [MONDO:0009061] + MONDO:0600008 Cytokine release syndrome [MONDO:0600008] + MPATH:108 Disseminated intravascular coagulation (DIC) [MPATH:108] + HP:0001298 Encephalopathy [HP:0001298] + GENEPIO:0100088 Fulminant myocarditis [GENEPIO:0100088] + MONDO:0016218 Guillain-Barré syndrome [MONDO:0016218] + HP:0011029 Internal hemorrhage (complication; internal bleeding) [HP:0011029] + MONDO:0013792 Intracerebral haemorrhage [MONDO:0013792] + MONDO:0012727 Kawasaki disease [MONDO:0012727] + GENEPIO:0100089 Complete Kawasaki disease [GENEPIO:0100089] + GENEPIO:0100090 Incomplete Kawasaki disease [GENEPIO:0100090] + HP:0001410 Liver dysfunction [HP:0001410] + GENEPIO:0100091 Acute liver injury [GENEPIO:0100091] + MONDO:0100233 Long COVID-19 [MONDO:0100233] + HP:0001287 Meningitis [HP:0001287] + HP:0002076 Migraine [HP:0002076] + HP:0005268 Miscarriage [HP:0005268] + MONDO:0100163 Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163] + MONDO:0100319 Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319] + GENEPIO:0100093 Muscle injury [GENEPIO:0100093] + MONDO:0005404 Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404] + MONDO:0005068 Myocardial infarction (heart attack) [MONDO:0005068] + HP:0001700 Myocardial injury [HP:0001700] + CIT:C168498 Neonatal complications [NCIT:C168498] + GENEPIO:0100085 Noncardiogenic pulmonary edema [GENEPIO:0100085] + HP:0033677 Acute respiratory distress syndrome (ARDS) [HP:0033677] + GENEPIO:0100094 Organ failure [GENEPIO:0100094] + HP:0003470 Paralysis [HP:0003470] + HP:0002107 Pneumothorax (collapsed lung) [HP:0002107] + HP:0002090 Pneumonia (complication) [HP:0002090] + HP:0001197 Pregancy complications [HP:0001197] + HP:0003201 Rhabdomyolysis [HP:0003201] + IDO:0000567 Secondary infection [IDO:0000567] An infection bearing the secondary infection role. + HP:0001250 Seizure (complication) [HP:0001250] + HP:0100806 Sepsis/Septicemia [HP:0100806] Systemic inflammatory response to infection. + IDO:0000636 Sepsis (systemic inflammatory response to infection) [IDO:0000636] + NCIT:C3364 Septicemia (bloodstream infection) [NCIT:C3364] + HP:0031273 Shock [HP:0031273] + GENEPIO:0100097 Hyperinflammatory shock [GENEPIO:0100097] + NCIT:C35018 Septic shock [NCIT:C35018] + HP:0002633 Vasculitis [HP:0002633] + +exposure_event menu ExposureEventMenu GENEPIO:0100237 Mass Gathering [GENEPIO:0100237] A gathering or event attended by a sufficient number of people to strain the planning and response resources of the host community, state/province, nation, or region where it is being held. + GENEPIO:0100238 Convention [GENEPIO:0100238] A gathering of individuals who meet at an arranged place and time in order to discuss or engage in some common interest. The most common conventions are based upon industry, profession, and fandom. + GENEPIO:0100239 Convocation [GENEPIO:0100239] + GENEPIO:0100240 Agricultural Event [GENEPIO:0100240] A gathering exhibiting the equipment, animals, sports and recreation associated with agriculture and animal husbandry. + GENEPIO:0100241 Religious Gathering [GENEPIO:0100241] + GENEPIO:0100242 Mass [GENEPIO:0100242] + PCO:0000033 Social Gathering [PCO:0000033] A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. + PCO:0000039 Baby Shower [PCO:0000039] + PCO:0000034 Community Event [PCO:0000034] + GENEPIO:0100243 Family Gathering [GENEPIO:0100243] + GENEPIO:0100244 Family Reunion [GENEPIO:0100244] + GENEPIO:0100245 Funeral [GENEPIO:0100245] + PCO:0000035 Party [PCO:0000035] + PCO:0000037 Potluck [PCO:0000037] + PCO:0000038 Wedding [PCO:0000038] + GENEPIO:0101183 Animal contact event [GENEPIO:0101183] + GENEPIO:0101185 Trip to a live animal market [GENEPIO:0101185] + GENEPIO:0101186 Trip to a farm [GENEPIO:0101186] + GENEPIO:0101188 Wildlife encounter [GENEPIO:0101188] + GENEPIO:0101184 Hunting trip [GENEPIO:0101184] + GENEPIO:0101187 Animal transportation event [GENEPIO:0101187] + Other exposure event + +exposure_contact_level menu ExposureContactLevelMenu GENEPIO:0101189 Contact with infected animal [GENEPIO:0101189] + GENEPIO:0101190 Direct (host-to-animal contact) [GENEPIO:0101190] + GENEPIO:0101191 Indirect contact (host-to-animal) [GENEPIO:0101191] + GENEPIO:0101192 Close animal contact (face-to-face contact) [GENEPIO:0101192] + GENEPIO:0101193 Casual animal contact [GENEPIO:0101193] + Contact with infected individual + TRANS:0000001 Direct (human-to-human contact) [TRANS:0000001] Direct and essentially immediate transfer of infectious agents to a receptive portal of entry through which human or animal infection may take place. This may be by direct contact such as touching, kissing, biting, or sexual intercourse or by the direct projection (droplet spread) of droplet spray onto the conjunctiva or the mucous membranes of the eyes, nose, or mouth. It may also be by direct exposure of susceptible tissue to an agent in soil, compost, or decaying vegetable matter or by the bite of a rabid animal. Transplacental transmission is another form of direct transmission. + GENEPIO:0100246 Indirect contact [GENEPIO:0100246] A type of contact in which an individual does not come in direct contact with a source of infection e.g. through airborne transmission, contact with contaminated surfaces. + GENEPIO:0100247 Close contact (face-to-face contact) [GENEPIO:0100247] A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time. + GENEPIO:0100248 Casual contact [GENEPIO:0100248] A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission. + +host_role menu HostRoleMenu GENEPIO:0100249 Attendee [GENEPIO:0100249] A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place. + OMRSE:00000058 Student [OMRSE:00000058] A human social role that, if realized, is realized by the process of formal education that the bearer undergoes. + OMRSE:00000030 Patient [OMRSE:00000030] A patient role that inheres in a human being. + NCIT:C25182 Inpatient [NCIT:C25182] A patient who is residing in the hospital where he is being treated. + NCIT:C28293 Outpatient [NCIT:C28293] A patient who comes to a healthcare facility for diagnosis or treatment but is not admitted for an overnight stay. + GENEPIO:0100250 Passenger [GENEPIO:0100250] A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination. + GENEPIO:0100251 Resident [GENEPIO:0100251] A role inhering in a person that is realized when the bearer maintains residency in a given place. + GENEPIO:0100252 Visitor [GENEPIO:0100252] A role inhering in a person that is realized when the bearer pays a visit to a specific place or event. + GENEPIO:0100253 Volunteer [GENEPIO:0100253] A role inhering in a person that is realized when the bearer enters into any service of their own free will. + GENEPIO:0100254 Work [GENEPIO:0100254] A role inhering in a person that is realized when the bearer performs labor for a living. + GENEPIO:0100255 Administrator [GENEPIO:0100255] A role inhering in a person that is realized when the bearer is engaged in administration or administrative work. + GENEPIO:0100256 First Responder [GENEPIO:0100256] A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance. + GENEPIO:0100257 Firefighter [GENEPIO:0100257] + GENEPIO:0100258 Paramedic [GENEPIO:0100258] + GENEPIO:0100259 Police Officer [GENEPIO:0100259] + GENEPIO:0100260 Housekeeper [GENEPIO:0100260] A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff. + GENEPIO:0100261 Kitchen Worker [GENEPIO:0100261] A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen. + GENEPIO:0100334 Healthcare Worker [GENEPIO:0100334] A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting. + GENEPIO:0100420 Community Healthcare Worker [GENEPIO:0100420] A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100262 Laboratory Worker [GENEPIO:0100262] A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory. + OMRSE:00000014 Nurse [OMRSE:00000014] A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. + GENEPIO:0100263 Personal Care Aid [GENEPIO:0100263] A role inhering in a person that is realized when the bearer works to help another person complete their daily activities. + GENEPIO:0100264 Pharmacist [GENEPIO:0100264] A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility. + OMRSE:00000013 Physician [OMRSE:00000013] A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. + GENEPIO:0100354 Rotational Worker [GENEPIO:0100354] A role inhering in a person that is realized when the bearer performs labor on a regular schedule, often requiring travel to geographic locations other than where they live. + GENEPIO:0100355 Seasonal Worker [GENEPIO:0100355] A role inhering in a person that is realized when the bearer performs labor for a particular period of the year, such as harvest, or Christmas. + GENEPIO:0100265 Veterinarian [GENEPIO:0100265] A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine. + OMRSE:00000001 Social role [OMRSE:00000001] A social role inhering in a human being. + GENEPIO:0100266 Acquaintance of case [GENEPIO:0100266] A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person. + GENEPIO:0100267 Relative of case [GENEPIO:0100267] A role inhering in a person that is realized when the bearer is a relative of the case. + GENEPIO:0100268 Child of case [GENEPIO:0100268] A role inhering in a person that is realized when the bearer is a person younger than the age of majority. + GENEPIO:0100269 Parent of case [GENEPIO:0100269] A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species. + GENEPIO:0100270 Father of case [GENEPIO:0100270] A role inhering in a person that is realized when the bearer is the male parent of a child. + GENEPIO:0100271 Mother of case [GENEPIO:0100271] A role inhering in a person that is realized when the bearer is the female parent of a child. + GENEPIO:0100272 Spouse of case [GENEPIO:0100272] A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage. + Other Host Role + +exposure_setting menu ExposureSettingMenu ECTO:3000005 Human Exposure [ECTO:3000005] A history of exposure to Homo sapiens. + GENEPIO:0100185 Contact with Patient [GENEPIO:0100185] A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity. + GENEPIO:0100187 Contact with Person with Acute Respiratory Illness [GENEPIO:0100187] + GENEPIO:0100188 Contact with Person with Fever and/or Cough [GENEPIO:0100188] + GENEPIO:0100190 Occupational, Residency or Patronage Exposure [GENEPIO:0100190] A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity. + ECTO:1000033 Abbatoir [ECTO:1000033] A exposure event involving the interaction of an exposure receptor to abattoir. + GENEPIO:0100191 Animal Rescue [GENEPIO:0100191] A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity. + GENEPIO:0100192 Childcare [GENEPIO:0100192] A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100193 Daycare [GENEPIO:0100193] A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity. + GENEPIO:0100194 Nursery [GENEPIO:0100194] A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity. + GENEPIO:0100195 Community Service Centre [GENEPIO:0100195] A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity. + GENEPIO:0100196 Correctional Facility [GENEPIO:0100196] A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity. + GENEPIO:0100197 Dormitory [GENEPIO:0100197] A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity. + ECTO:1000034 Farm [ECTO:1000034] A exposure event involving the interaction of an exposure receptor to farm + GENEPIO:0100198 First Nations Reserve [GENEPIO:0100198] A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity. + GENEPIO:0100199 Funeral Home [GENEPIO:0100199] A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100200 Group Home [GENEPIO:0100200] A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. + GENEPIO:0100201 Healthcare Setting [GENEPIO:0100201] A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity. + GENEPIO:0100202 Ambulance [GENEPIO:0100202] A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity. + GENEPIO:0100203 Acute Care Facility [GENEPIO:0100203] A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity. + GENEPIO:0100204 Clinic [GENEPIO:0100204] A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity. + GENEPIO:0100415 Community Healthcare (At-Home) Setting [GENEPIO:0100415] A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home. + GENEPIO:0100205 Community Health Centre [GENEPIO:0100205] A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity. + ECTO:1000035 Hospital [ECTO:1000035] A exposure event involving the interaction of an exposure receptor to hospital. + GENEPIO:0100206 Emergency Department [GENEPIO:0100206] A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity. + GENEPIO:0100207 ICU [GENEPIO:0100207] A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity. + GENEPIO:0100208 Ward [GENEPIO:0100208] A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity. + ECTO:1000036 Laboratory [ECTO:1000036] A exposure event involving the interaction of an exposure receptor to laboratory facility. + GENEPIO:0100209 Long-Term Care Facility [GENEPIO:0100209] A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity. + GENEPIO:0100210 Pharmacy [GENEPIO:0100210] A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity. + GENEPIO:0100211 Physician's Office [GENEPIO:0100211] A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity. + GENEPIO:0100212 Household [GENEPIO:0100212] A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity. + GENEPIO:0100213 Insecure Housing (Homeless) [GENEPIO:0100213] A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing. + GENEPIO:0100214 Occupational Exposure [GENEPIO:0100214] A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity. + GENEPIO:0100215 Worksite [GENEPIO:0100215] A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity. + ECTO:1000037 Office [ECTO:1000037] A exposure event involving the interaction of an exposure receptor to office. + GENEPIO:0100216 Outdoors [GENEPIO:0100216] A process occuring outdoors that exposes the recipient organism to a material entity. + ECTO:5000009 Camp/camping [ECTO:5000009] A exposure event involving the interaction of an exposure receptor to campground. + GENEPIO:0100217 Hiking Trail [GENEPIO:0100217] A process that exposes the recipient organism to a material entity as a consequence of hiking. + ECTO:6000030 Hunting Ground [ECTO:6000030] An exposure event involving hunting behavior + ECTO:5000008 Petting zoo [ECTO:5000008] A exposure event involving the interaction of an exposure receptor to petting zoo. + GENEPIO:0100220 Place of Worship [GENEPIO:0100220] A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity. + GENEPIO:0100221 Church [GENEPIO:0100221] A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity. + GENEPIO:0100222 Mosque [GENEPIO:0100222] A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity. + GENEPIO:0100223 Temple [GENEPIO:0100223] A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity. + ECTO:1000040 Restaurant [ECTO:1000040] A exposure event involving the interaction of an exposure receptor to restaurant. + ECTO:1000041 Retail Store [ECTO:1000041] A exposure event involving the interaction of an exposure receptor to shop. + GENEPIO:0100224 School [GENEPIO:0100224] A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity. + GENEPIO:0100225 Temporary Residence [GENEPIO:0100225] A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity. + GENEPIO:0100226 Homeless Shelter [GENEPIO:0100226] A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity. + GENEPIO:0100227 Hotel [GENEPIO:0100227] A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity. + GENEPIO:0100228 Veterinary Care Clinic [GENEPIO:0100228] A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity. + GENEPIO:0100229 Travel Exposure [GENEPIO:0100229] A process occuring as a result of travel that exposes the recipient organism to a material entity. + GENEPIO:0100230 Travelled on a Cruise Ship [GENEPIO:0100230] A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity. + GENEPIO:0100231 Travelled on a Plane [GENEPIO:0100231] A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity. + GENEPIO:0100232 Travelled on Ground Transport [GENEPIO:0100232] A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity. + GENEPIO:0001118 Travelled outside Province/Territory [GENEPIO:0001118] + GENEPIO:0001119 Travelled outside Canada [GENEPIO:0001119] + GENEPIO:0100235 Other Exposure Setting [GENEPIO:0100235] A process occuring that exposes the recipient organism to a material entity. + +host_vaccination_status menu HostVaccinationStatusMenu GENEPIO:0100100 Fully Vaccinated [GENEPIO:0100100] Completed a full series of an authorized vaccine according to the regional health institutional guidance. + GENEPIO:0100102 Not Vaccinated [GENEPIO:0100102] Have not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance. + +influenza_antiviral_treatment_administration menu InfluenzaAntiviralTreatmentAdministrationMenu GENEPIO:0101194 Influenza antiviral treatment administered [GENEPIO:0101194] + GENEPIO:0101195 No influenza antiviral treatment administered [GENEPIO:0101195] + +water_catchment_area_human_population_range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people + 10 - 100 people + 100 - 1,000 people + 1,000 - 10,000 people + 10,000 - 100,000 people + 100,000 - 1,000,000 people + 1,000,000+ people + +water_catchment_area_human_population_density_unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. + GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. + GENEPIO:0100991 residents per square mile [GENEPIO:0100991] A unit of population density that describes the average number of registered residents in a square mile of a given area. + GENEPIO:0100992 residents per square kilometer [GENEPIO:0100992] A unit of population density that describes the average number of registered residents in a square kilometer of a given area. + +populated_area_type menu PopulatedAreaTypeMenu GSSO:011077 Suburban [GSSO:011077] A mixed-use or residential area, existing either as part of a city/urban area, or as a separate residential community within commuting distance of one. Suburbs might have their own political or legal jurisdiction, especially in the United States, but this is not always the case, especially in the United Kingdom where most suburbs are located within the administrative boundaries of cities. + GSSO:011078 Rural [GSSO:011078] A geographic area that is located outside towns and cities. Rural areas are primarily used for agriculture or pastoralism and may contain rural settlements. + GSSO:011080 Urban [GSSO:011080] A human settlement with a high population density and infrastructure of built environment. Urban areas are created through urbanization and are categorized by urban morphology as cities, towns, conurbations or suburbs. In urbanism, the term contrasts to rural areas such as villages and hamlets; in urban sociology or urban anthropology it contrasts with natural environment. + +sampling_weather_conditions menu SamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +presampling_weather_conditions menu PresamplingWeatherConditionsMenu ENVO:03501418 Cloudy/Overcast [ENVO:03501418] Atmospheric weather in which the sky is mostly or completely obscured by clouds. + ENVO:03501419 Partially cloudy [ENVO:03501419] Atmospheric weather in which the sky is partially obscured by clouds. + ENVO:03501420 Drizzle [ENVO:03501420] An aggregate of water drops smaller than those of rain which falls on a planetary surface during a precipitation process. + ENVO:01000844 Fog [ENVO:01000844] A visible mass of cloud water droplets or ice crystals suspended in the air at or near the surface of an astronomical body. + ENVO:01001564 Rain [ENVO:01001564] An aggregate of raindrops falling to a planetary surface during a precipitation process. + ENVO:01000406 Snow [ENVO:01000406] Snow is an environmental material which is primarily composed of flakes of crystalline water ice. + ENVO:01000876 Storm [ENVO:01000876] A storm is an environmental process in which an environmental system and the processes it participates in are strongly perturbed by external forcings. These forcings typically increase the rates of processes unfolding in the system, relative to their normal rates. + ENVO:03501421 Sunny/Clear [ENVO:03501421] Atmospheric weather in which the sun can be seen to shine brightly. + +precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu UO:0000016 millimeter (mm) [UO:0000016] A length unit which is defined as one thousandth of a meter. + UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +air_pressure_measurement_unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). + bar + UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). + +ambient_temperature_measurement_unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +total_daily_flow_rate_measurement_unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) + cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h) + liter per second (L/s) + liter per minute (L/min) + liter per hour (L/h) + liter per day (L/day) + million gallons per day (MGD) + +instantaneous_flow_rate_measurement_unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) + cubic meter per minute (m^3/min) + cubic meter per hour (m^3/h) + liter per second (L/s) + liter per minute (L/min) + liter per hour (L/h) + liter per day (L/day) + million gallons per day (MGD) + +turbidity_measurement_unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) + UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. + +dissolved_oxygen_measurement_unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000083 kilogram per cubic meter (kg/m^3) [UO:0000083] An SI unit of density that is one thousandth of the density of water. + UO:0000169 part per million (ppm) [UO:0000169] A unitless measure of density that represents one item out of a million. + +oxygen_reduction_potential_(ORP)_measurement_unit menu OxygenReductionPotentialOrpMeasurementUnitMenu UO:0000247 milliVolt (mV) [UO:0000247] A non-SI unit of electromotive force that is one thousandth of a volt. + +chemical_oxygen_demand_(COD)_measurement_unit menu ChemicalOxygenDemandCodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +carbonaceous_biochemical_oxygen_demand_(CBOD)_measurement_unit menu CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + +total_suspended_solids_(TSS)_measurement_unit menu TotalSuspendedSolidsTssMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total_dissolved_solids_(TDS)_measurement_unit menu TotalDissolvedSolidsTdsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total_solids_(TS)_measurement_unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +alkalinity_measurement_unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) + UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. + +conductivity_measurement_unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) + microSiemen per centimeter (μS/cm) + Siemen per meter (S/m) + +salinity_measurement_unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) + weight for weight (% w/w) + UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + +total_nitrogen_(TN)_measurement_unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. + gram per total solids (g/gTS) + +total_phosphorpus_(TP)_measurement_unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) + GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. + UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. + GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. + +fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:1211417 crAssphage [NCBITaxon:1211417] CrAss-like phage, a bacteriophage discovered in 2014 in the human fecal metagenome. + NCBITaxon:12239 PMMoV / pepper mild mottle virus [NCBITaxon:12239] A plant RNA virus that is abundant in human feces. + GENEPIO:0101000 Bacteroides HF183 A fecal indicator which is the most commonly used sewage-associated marker gene, belonging to the Bacteroides genus. + GENEPIO:0101001 Lachnospiraceae Lachno3 A fecal indicator which is a human-associated genetic marker in the Lachnospiraceae family of bacteria. + GENEPIO:0101002 F+ (male specific) coliphages A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. + CHEBI:26756 Stercobilin Bile pigment found in fecal material. + +fecal_contamination_unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) + gene copies per liter (GC/L) + UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. + log10 gene copies per nanogram total DNA + +urinary_contamination_indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. + +urinary_contamination_unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. + +fecal_coliform_count_unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) + colony forming units per grams total solids (CFU/gTS) + most probable number per milliliter (MPN/mL) + most probable number per 100 milliliter (MPN/100 mL) + +sample_temperature_unit_(at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sample_temperature_unit_(when received) menu SampleTemperatureUnitWhenReceivedMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sequencing_assay_type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + GENEPIO:0101128 CRISPR amplicon sequencing assay [GENEPIO:0101128] + GENEPIO:0101129 Primal tiling amplicon sequencing assay [GENEPIO:0101129] + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + +purpose_of_sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) [GENEPIO:0100005] A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. + GENEPIO:0100006 Targeted surveillance (non-random sampling) [GENEPIO:0100006] A surveillance sampling strategy in which an aspired outcome is explicitly stated. + GENEPIO:0100007 Priority surveillance project [GENEPIO:0100007] A targeted surveillance strategy which is considered important and/or urgent. + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] A surveillance strategy in which an individual or site is selected to undergo repeat sampling over a defined period of time. + GENEPIO:0100019 Cluster/Outbreak investigation [GENEPIO:0100019] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. + GENEPIO:0100020 Multi-jurisdictional outbreak investigation [GENEPIO:0100020] An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions. + GENEPIO:0100021 Intra-jurisdictional outbreak investigation [GENEPIO:0100021] An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction. + GENEPIO:0100022 Research [GENEPIO:0100022] A sampling strategy in which sites are sampled in order to perform research. + GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. + GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. + GENEPIO:0100356 Retrospective sequencing [GENEPIO:0100356] A sampling strategy in which stored samples from past events are sequenced. + +geo_loc_name_(country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] + GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] + GAZ:00000563 Algeria [GAZ:00000563] A country in North Africa. It is bordered by Tunisia in the northeast, Libya in the east, Niger in the southeast, Mali and Mauritania in the southwest, a few km of the Western Sahara in the west, Morocco in the northwest, and the Mediterranean Sea in the north. It divided into 48 provinces (wilayas), 553 districts (dairas) and 1,541 municipalities (communes, baladiyahs). [ url:http://en.wikipedia.org/wiki/Algeria ] + GAZ:00003957 American Samoa [GAZ:00003957] An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. [ url:http://en.wikipedia.org/wiki/American_Samoa ] + GAZ:00002948 Andorra [GAZ:00002948] A small landlocked country in western Europe, located in the eastern Pyrenees mountains and bordered by Spain (Catalonia) and France. Andorra consists of seven communities known as parishes (Catalan: parroquies, singular - parroquia). Until relatively recently, it had only six parishes; the seventh, Escaldes-Engordany, was created in 1978. Some parishes have a further territorial subdivision. Ordino, La Massana and Sant Julia de Loria are subdivided into quarts (quarters), while Canillo is subdivided into veinats (neighborhoods). Those mostly coincide with villages, which are found in all parishes. [ url:http://en.wikipedia.org/wiki/Andorra ] + GAZ:00001095 Angola [GAZ:00001095] A country in south-central Africa bordering Namibia to the south, Democratic Republic of the Congo to the north, and Zambia to the east, and with a west coast along the Atlantic Ocean. The exclave province Cabinda has a border with the Republic of the Congo and the Democratic Republic of the Congo. [ url:http://en.wikipedia.org/wiki/Angola ] + GAZ:00009159 Anguilla [GAZ:00009159] A British overseas territory in the Caribbean, one of the most northerly of the Leeward Islands in the Lesser Antilles. It consists of the main island of Anguilla itself, approximately 26 km long by 5 km wide at its widest point, together with a number of much smaller islands and cays with no permanent population. [ url:http://en.wikipedia.org/wiki/Anguila ] + GAZ:00000462 Antarctica [GAZ:00000462] The Earth's southernmost continent, overlying the South Pole. It is situated in the southern hemisphere, almost entirely south of the Antarctic Circle, and is surrounded by the Southern Ocean. [ url:http://en.wikipedia.org/wiki/Antarctica ] + GAZ:00006883 Antigua and Barbuda [GAZ:00006883] An island nation located on the eastern boundary of the Caribbean Sea with the Atlantic Ocean. [ url:http://en.wikipedia.org/wiki/Antigua_and_Barbuda ] + GAZ:00002928 Argentina [GAZ:00002928] A South American country, constituted as a federation of twenty-three provinces and an autonomous city. It is bordered by Paraguay and Bolivia in the north, Brazil and Uruguay in the northeast, and Chile in the west and south. The country claims the British controlled territories of the Falkland Islands and South Georgia and the South Sandwich Islands. Argentina also claims 969,464 km2 of Antarctica, known as Argentine Antarctica, overlapping other claims made by Chile and the United Kingdom. Argentina is subdivided into twenty-three provinces (Spanish: provincias, singular provincia) and one federal district (Capital de la Republica or Capital de la Nacion, informally the Capital Federal). The federal district and the provinces have their own constitutions, but exist under a federal system. Provinces are then divided into departments (Spanish: departamentos, singular departamento), except for Buenos Aires Province, which is divided into partidos. [ url:http://en.wikipedia.org/wiki/Argentina ] + GAZ:00004094 Armenia [GAZ:00004094] A landlocked mountainous country in Eurasia between the Black Sea and the Caspian Sea in the Southern Caucasus. It borders Turkey to the west, Georgia to the north, Azerbaijan to the east, and Iran and the Nakhchivan exclave of Azerbaijan to the south. A transcontinental country at the juncture of Eastern Europe and Western Asia. A former republic of the Soviet Union. Armenia is divided into ten marzes (provinces, singular marz), with the city (kaghak) of Yerevan having special administrative status as the country's capital. [ url:http://en.wikipedia.org/wiki/Armenia ] + GAZ:00004025 Aruba [GAZ:00004025] An autonomous region within the Kingdom of the Netherlands, Aruba has no administrative subdivisions. [ url:http://en.wikipedia.org/wiki/Aruba ] + GAZ:00005901 Ashmore and Cartier Islands [GAZ:00005901] A Territory of Australia that includes two groups of small low-lying uninhabited tropical islands in the Indian Ocean situated on the edge of the continental shelf north-west of Australia and south of the Indonesian island of Roti. [ url:http://en.wikipedia.org/wiki/Ashmore_and_Cartier_Islands ] + GAZ:00000463 Australia [GAZ:00000463] A country in the southern hemisphere comprising the mainland of the world's smallest continent, the major island of Tasmania, and a number of other islands in the Indian and Pacific Oceans. The neighbouring countries are Indonesia, East Timor, and Papua New Guinea to the north, the Solomon Islands, Vanuatu, and New Caledonia to the north-east, and New Zealand to the south-east. Australia has six states, two major mainland territories, and other minor territories. + GAZ:00002942 Austria [GAZ:00002942] A landlocked country in Central Europe. It borders both Germany and the Czech Republic to the north, Slovakia and Hungary to the east, Slovenia and Italy to the south, and Switzerland and Liechtenstein to the west. The capital is the city of Vienna on the Danube River. Austria is divided into nine states (Bundeslander). These states are then divided into districts (Bezirke) and cities (Statutarstadte). Districts are subdivided into municipalities (Gemeinden). Cities have the competencies otherwise granted to both districts and municipalities. + GAZ:00004941 Azerbaijan [GAZ:00004941] A country in the he South Caucasus region of Eurasia, it is bounded by the Caspian Sea to the east, Russia to the north, Georgia to the northwest, Armenia to the west, and Iran to the south. The Azerbaijani exclave of Nakhchivan is bordered by Armenia to the north and east, Iran to the south and west, and Turkey to the northwest. Nagorno-Karabakh, along with 7 other districts in Azerbaijan's southwest, have been controlled by Armenia since the end of the Nagorno-Karabakh War in 1994. Azerbaijan is divided into 59 rayons 11 city districts (saharlar), and one autonomous republic (muxtar respublika). + GAZ:00002733 Bahamas [GAZ:00002733] A country consisting of two thousand cays and seven hundred islands that form an archipelago. It is located in the Atlantic Ocean, southeast of Florida and the United States, north of Cuba, the island of Hispanola and the Caribbean, and northwest of the British overseas territory of the Turks and Caicos Islands. It is divided into 32 districts, plus New Providence, whose affairs are handled directly by the central government. + GAZ:00005281 Bahrain [GAZ:00005281] A borderless island country in the Persian Gulf. Saudi Arabia lies to the west and is connected to Bahrain by the King Fahd Causeway, and Qatar is to the south across the Gulf of Bahrain. Bahrain is split into five governorates. + GAZ:00007117 Baker Island [GAZ:00007117] An uninhabited atoll located just north of the equator in the central Pacific Ocean about 3,100 km southwest of Honolulu. Baker Island is an unincorporated and unorganized territory of the US. + GAZ:00003750 Bangladesh [GAZ:00003750] A country in South Asia. It is bordered by India on all sides except for a small border with Myanmar to the far southeast and by the Bay of Bengal to the south. Bangladesh is divided into six administrative divisions. Divisions are subdivided into districts (zila). There are 64 districts in Bangladesh, each further subdivided into upazila (subdistricts) or thana ("police stations"). + GAZ:00001251 Barbados [GAZ:00001251] An island country in the Lesser Antilles of the West Indies, in the Caribbean region of the Americas, and the most easterly of the Caribbean Islands. It is 34 kilometres (21 miles) in length and up to 23 km (14 mi) in width, covering an area of 432 km2 (167 sq mi). It is in the western part of the North Atlantic, 100 km (62 mi) east of the Windward Islands and the Caribbean Sea.[7] Barbados is east of the Windwards, part of the Lesser Antilles, at roughly 13°N of the equator. It is about 168 km (104 mi) east of both the countries of Saint Lucia and Saint Vincent and the Grenadines and 180 km (110 mi) south-east of Martinique and 400 km (250 mi) north-east of Trinidad and Tobago. Barbados is outside the principal Atlantic hurricane belt. Its capital and largest city is Bridgetown. + GAZ:00005810 Bassas da India [GAZ:00005810] A roughly circular atoll about 10 km in diameter, which corresponds to a total size (including lagoon) of 80 km2. It is located in the southern Mozambique Channel, about half-way between Madagascar (which is 385 km to the east) and Mozambique, and 110 km northwest of Europa Island. It rises steeply from the seabed 3000 m below. + GAZ:00006886 Belarus [GAZ:00006886] A landlocked country in Eastern Europe, that borders Russia to the north and east, Ukraine to the south, Poland to the west, and Lithuania and Latvia to the north. Its capital is Minsk. Belarus is divided into six voblasts, or provinces. Voblasts are further subdivided into raions (commonly translated as districts or regions). As of 2002, there are six voblasts, 118 raions, 102 towns and 108 urbanized settlements. Minsk is given a special status, due to the city serving as the national capital. + GAZ:00002938 Belgium [GAZ:00002938] A country in northwest Europe. Belgium shares borders with France (620 km), Germany (167 km), Luxembourg (148 km) and the Netherlands (450 km). The Flemish Region (Flanders) and the Walloon Region (Wallonia) each comprise five provinces; the third region, Brussels-Capital Region, is not a province, nor does it contain any Together, these comprise 589 municipalities, which in general consist of several sub-municipalities (which were independent municipalities before the municipal merger operation mainly in 1977). + GAZ:00002934 Belize [GAZ:00002934] A country in Central America. It is the only officially English speaking country in the region. Belize was a British colony for more than a century and was known as British Honduras until 1973. It became an independent nation within The Commonwealth in 1981. Belize is divided into 6 districts, which are further divided into 31 constituencies. + GAZ:00000904 Benin [GAZ:00000904] A country in Western Africa. It borders Togo to the west, Nigeria to the east and Burkina Faso and Niger to the north; its short coastline to the south leads to the Bight of Benin. Its capital is Porto Novo, but the seat of government is Cotonou. Benin is divided into 12 departments and subdivided into 77 communes. + GAZ:00001264 Bermuda [GAZ:00001264] A British overseas territory in the North Atlantic Ocean. Located off the east coast of the United States, it is situated around 1770 km NE of Miami, Florida and 1350 km S of Halifax, Nova Scotia. Comprised of approximately 138 islands. + GAZ:00003920 Bhutan [GAZ:00003920] A landlocked nation in South Asia. It is located amidst the eastern end of the Himalaya Mountains and is bordered to the south, east and west by India and to the north by Tibet. Bhutan is separated from Nepal by the Indian State of Sikkim. Bhutan is divided into four dzongdey (administrative zones). Each dzongdey is further divided into dzongkhag (districts). There are twenty dzongkhag in Bhutan. Large dzongkhags are further divided into subdistricts known as dungkhag. At the basic level, groups of villages form a constituency called gewog. + GAZ:00002511 Bolivia [GAZ:00002511] A landlocked country in central South America. It is bordered by Brazil on the north and east, Paraguay and Argentina on the south, and Chile and Peru on the west. Bolivia is divided into 9 departments (Spanish: departamentos). Each of the departments is subdivided into provinces (provincias), which are further subdivided into municipalities (municipios). + GAZ:00025355 Borneo [GAZ:00025355] An island at the grographic centre of Maritime Southeast Adia, in relation to major Indonesian islands, it is located north of Java, west of Sulawesi, and east of Sumatra. It is the third-largest island in the world and the larest in Asia. The island is politically divided among three countries: Malaysia and Brunei in the north, and Indonesia to the south.[1] Approximately 73% of the island is Indonesian territory. In the north, the East Malaysian states of Sabah and Sarawak make up about 26% of the island. Additionally, the Malaysian federal territory of Labuan is situated on a small island just off the coast of Borneo. The sovereign state of Brunei, located on the north coast, comprises about 1% of Borneo's land area. A little more than half of the island is in the Northern Hemisphere, including Brunei and the Malaysian portion, while the Indonesian portion spans the Northern and Southern hemispheres. + GAZ:00006887 Bosnia and Herzegovina [GAZ:00006887] A country on the Balkan peninsula of Southern Europe. Bordered by Croatia to the north, west and south, Serbia to the east, and Montenegro to the south, Bosnia and Herzegovina is mostly landlocked, except for 26 km of the Adriatic Sea coastline. Bosnia and Herzegovina is now divided into three political regions of which one, the Brcko District is part of the other two, the Federacija Bosne i Hercegovine and the Republika Srpska. All three have an equal constitutional status on the whole territory of Bosnia and Herzegovina. + GAZ:00001097 Botswana [GAZ:00001097] A landlocked nation in Southern Africa. It is bordered by South Africa to the south and southeast, Namibia to the west, Zambia to the north, and Zimbabwe to the northeast. Botswana is divided into nine districts, which are subdivided into a total twenty-eight subdistricts. + GAZ:00001453 Bouvet Island [GAZ:00001453] A sub-antarctic volcanic island in the South Atlantic Ocean, south-southwest of the Cape of Good Hope (South Africa). It is a dependent area of Norway and is not subject to the Antarctic Treaty, as it is north of the latitude south of which claims are suspended. + GAZ:00002828 Brazil [GAZ:00002828] A country in South America. Bordered by the Atlantic Ocean and by Venezuela, Suriname, Guyana and the department of French Guiana to the north, Colombia to the northwest, Bolivia and Peru to the west, Argentina and Paraguay to the southwest, and Uruguay to the south. Federation of twenty-six states (estados) and one federal district (Distrito Federal). The states are subdivided into municipalities. For statistical purposes, the States are grouped into five main regions: North, Northeast, Central-West, Southeast and South. + GAZ:00003961 British Virgin Islands [GAZ:00003961] A British overseas territory, located in the Caribbean to the east of Puerto Rico. The islands make up part of the Virgin Islands archipelago, the remaining islands constituting the US Virgin Islands. The British Virgin Islands consist of the main islands of Tortola, Virgin Gorda, Anegada and Jost Van Dyke, along with over fifty other smaller islands and cays. Approximately fifteen of the islands are inhabited. + GAZ:00003901 Brunei [GAZ:00003901] A country located on the north coast of the island of Borneo, in Southeast Asia. Apart from its coastline with the South China Sea it is completely surrounded by the State of Sarawak, Malaysia, and in fact it is separated into two parts by Limbang, which is part of Sarawak. Brunei is divided into four districts (daerah), the districts are subdivided into thirty-eight mukims, which are then divided into kampong (villages). + GAZ:00002950 Bulgaria [GAZ:00002950] A country in Southeastern Europe, borders five other countries; Romania to the north (mostly along the Danube), Serbia and the Republic of Macedonia to the west, and Greece and Turkey to the south. The Black Sea defines the extent of the country to the east. Since 1999, it has consisted of twenty-eight provinces. The provinces subdivide into 264 municipalities. + GAZ:00000905 Burkina Faso [GAZ:00000905] A landlocked nation in West Africa. It is surrounded by six countries: Mali to the north, Niger to the east, Benin to the south east, Togo and Ghana to the south, and Cote d'Ivoire to the south west. Burkina Faso is divided into thirteen regions, forty-five provinces, and 301 departments (communes). + GAZ:00001090 Burundi [GAZ:00001090] A small country in the Great Lakes region of Africa. It is bordered by Rwanda on the north, Tanzania on the south and east, and the Democratic Republic of the Congo on the west. Although the country is landlocked, much of its western border is adjacent to Lake Tanganyika. Burundi is divided into 17 provinces, 117 communes, and 2,638 collines. + GAZ:00006888 Cambodia [GAZ:00006888] A country in Southeast Asia. The country borders Thailand to its west and northwest, Laos to its northeast, and Vietnam to its east and southeast. In the south it faces the Gulf of Thailand. + GAZ:00001093 Cameroon [GAZ:00001093] A country of central and western Africa. It borders Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the Bight of Bonny, part of the Gulf of Guinea and the Atlantic Ocean. The Republic of Cameroon is divided into ten provinces and 58 divisions or departments. The divisions are further sub-divided into sub-divisions (arrondissements) and districts. + GAZ:00002560 Canada [GAZ:00002560] A country occupying most of northern North America, extending from the Atlantic Ocean in the east to the Pacific Ocean in the west and northward into the Arctic Ocean. Canada is a federation composed of ten provinces and three territories; in turn, these may be grouped into regions. Western Canada consists of British Columbia and the three Prairie provinces (Alberta, Saskatchewan, and Manitoba). Central Canada consists of Quebec and Ontario. Atlantic Canada consists of the three Maritime provinces (New Brunswick, Prince Edward Island, and Nova Scotia), along with Newfoundland and Labrador. Eastern Canada refers to Central Canada and Atlantic Canada together. Three territories (Yukon, Northwest Territories, and Nunavut) make up Northern Canada. + GAZ:00001227 Cape Verde [GAZ:00001227] A republic located on an archipelago in the Macaronesia ecoregion of the North Atlantic Ocean, off the western coast of Africa. Cape Verde is divided into 22 municipalities (concelhos), and subdivided into 32 parishes (freguesias). + GAZ:00003986 Cayman Islands [GAZ:00003986] A British overseas territory located in the western Caribbean Sea, comprising the islands of Grand Cayman, Cayman Brac, and Little Cayman. The Cayman Islands are divided into seven districts. + GAZ:00001089 Central African Republic [GAZ:00001089] A landlocked country in Central Africa. It borders Chad in the north, Sudan in the east, the Republic of the Congo and the Democratic Republic of the Congo in the south, and Cameroon in the west. The Central African Republic is divided into 14 administrative prefectures (prefectures), along with 2 economic prefectures (prefectures economiques) and one autonomous commune. The prefectures are further divided into 71 sub-prefectures (sous-prefectures). + GAZ:00000586 Chad [GAZ:00000586] A landlocked country in central Africa. It is bordered by Libya to the north, Sudan to the east, the Central African Republic to the south, Cameroon and Nigeria to the southwest, and Niger to the west. Chad is divided into 18 regions. The departments are divided into 200 sub-prefectures, which are in turn composed of 446 cantons. This is due to change. + GAZ:00002825 Chile [GAZ:00002825] A country in South America occupying a long and narrow coastal strip wedged between the Andes mountains and the Pacific Ocean. The Pacific forms the country's entire western border, with Peru to the north, Bolivia to the northeast, Argentina to the east, and the Drake Passage at the country's southernmost tip. Chile claims 1,250,000 km2 of territory in Antarctica. Chile is divided into 15 regions. Every region is further divided into provinces. Finally each province is divided into communes. Each region is designated by a name and a Roman numeral, assigned from north to south. The only exception is the region housing the nation's capital, which is designated RM, that stands for Region Metropolitana (Metropolitan Region). Two new regions were created in 2006: Arica-Parinacota in the north, and Los Rios in the south. Both became operative in 2007-10. + GAZ:00002845 China [GAZ:00002845] A large country in Northeast Asia. China borders 14 nations (counted clockwise from south): Vietnam, Laos, Burma, India, Bhutan, Nepal, Pakistan, Afghanistan, Tajikistan, Kyrgyzstan, Kazakhstan, Russia, Mongolia and North Korea. Additionally the border between PRC and ROC is located in territorial waters. The People's Republic of China has administrative control over twenty-two provinces and considers Taiwan to be its twenty-third province. There are also five autonomous regions, each with a designated minority group; four municipalities; and two Special Administrative Regions that enjoy considerable autonomy. The People's Republic of China administers 33 province-level regions, 333 prefecture-level regions, 2,862 county-level regions, 41,636 township-level regions, and several village-level regions. + GAZ:00005915 Christmas Island [GAZ:00005915] An island in the Indian Ocean, 500 km south of Indonesia and about 2600 km northwest of Perth. The island is the flat summit of a submarine mountain. + GAZ:00005838 Clipperton Island [GAZ:00005838] A nine-square km coral atoll in the North Pacific Ocean, southwest of Mexico and west of Costa Rica. + GAZ:00009721 Cocos Islands [GAZ:00009721] Islands that located in the Indian Ocean, about halfway between Australia and Sri Lanka. A territory of Australia. There are two atolls and twenty-seven coral islands in the group. + GAZ:00002929 Colombia [GAZ:00002929] A country located in the northwestern region of South America. Colombia is bordered to the east by Venezuela and Brazil; to the south by Ecuador and Peru; to the North by the Atlantic Ocean, through the Caribbean Sea; to the north-west by Panama; and to the west by the Pacific Ocean. Besides the countries in South America, the Republic of Colombia is recognized to share maritime borders with the Caribbean countries of Jamaica, Haiti, the Dominican Republic and the Central American countries of Honduras, Nicaragua, and Costa Rica. Colombia is divided into 32 departments and one capital district which is treated as a department. There are in total 10 districts assigned to cities in Colombia including Bogota, Barranquilla, Cartagena, Santa Marta, Tunja, Cucuta, Popayan, Buenaventura, Tumaco and Turbo. Colombia is also subdivided into some municipalities which form departments, each with a municipal seat capital city assigned. Colombia is also subdivided into corregimientos which form municipalities. + GAZ:00005820 Comoros [GAZ:00005820] An island nation in the Indian Ocean, located off the eastern coast of Africa on the northern end of the Mozambique Channel between northern Madagascar and northeastern Mozambique. + GAZ:00053798 Cook Islands [GAZ:00053798] A self-governing parliamentary democracy in free association with New Zealand. The fifteen small islands in this South Pacific Ocean country have a total land area of 240 km2, but the Cook Islands Exclusive Economic Zone (EEZ) covers 1.8 million km2 of ocean. + GAZ:00005917 Coral Sea Islands [GAZ:00005917] A Territory of Australia which includes a group of small and mostly uninhabited tropical islands and reefs in the Coral Sea, northeast of Queensland, Australia. The only inhabited island is Willis Island. The territory covers 780,000 km2, extending east and south from the outer edge of the Great Barrier Reef, and including Heralds Beacon Island, Osprey Reef, the Willis Group, and fifteen other reef/island groups. + GAZ:00002901 Costa Rica [GAZ:00002901] A republic in Central America, bordered by Nicaragua to the north, Panama to the east-southeast, the Pacific Ocean to the west and south, and the Caribbean Sea to the east. Costa Rica is composed of seven provinces, which in turn are divided into 81 cantons. + GAZ:00000906 Cote d'Ivoire [GAZ:00000906] A country in West Africa. It borders Liberia and Guinea to the west, Mali and Burkina Faso to the north, Ghana to the east, and the Gulf of Guinea to the south. Cote d'Ivoire is divided into nineteen regions (regions). The regions are further divided into 58 departments. + GAZ:00002719 Croatia [GAZ:00002719] A country at the crossroads of the Mediterranean, Central Europe, and the Balkans. Its capital is Zagreb. Croatia borders with Slovenia and Hungary to the north, Serbia to the northeast, Bosnia and Herzegovina to the east, Montenegro to the far southeast, and the Adriatic Sea to the south. Croatia is divided into 21 counties (zupanija) and the capital Zagreb's city district. + GAZ:00003762 Cuba [GAZ:00003762] A country that consists of the island of Cuba (the largest and second-most populous island of the Greater Antilles), Isla de la Juventud and several adjacent small islands. Fourteen provinces and one special municipality (the Isla de la Juventud) now compose Cuba. + GAZ:00012582 Curacao [GAZ:00012582] One of five island areas of the Netherlands Antilles. + GAZ:00004006 Cyprus [GAZ:00004006] The third largest island in the Mediterranean Sea (after Sicily and Sardinia), Cyprus is situated in the eastern Mediterranean, just south of the Anatolian peninsula (or Asia Minor) of the Asian mainland; thus, it is often included in the Middle East (see also Western Asia and Near East). Turkey is 75 km north; other neighbouring countries include Syria and Lebanon to the east, Israel to the southeast, Egypt to the south, and Greece to the west-north-west. + GAZ:00002954 Czech Republic [GAZ:00002954] A landlocked country in Central Europe. It has borders with Poland to the north, Germany to the northwest and southwest, Austria to the south, and Slovakia to the east. The capital and largest city is Prague. The country is composed of the historic regions of Bohemia and Moravia, as well as parts of Silesia. Since 2000, the Czech Republic is divided into thirteen regions (kraje, singular kraj) and the capital city of Prague. The older seventy-six districts (okresy, singular okres) including three 'statutory cities' (without Prague, which had special status) were disbanded in 1999 in an administrative reform; they remain as territorial division and seats of various branches of state administration. Since 2003-01-01, the regions have been divided into around 203 Municipalities with Extended Competence (unofficially named "Little Districts" (Czech: 'male okresy') which took over most of the administration of the former District Authorities. Some of these are further divided into Municipalities with Commissioned Local Authority. However, the old districts still exist as territorial units and remain as seats of some of the offices. + GAZ:00001086 Democratic Republic of the Congo [GAZ:00001086] A country of central Africa. It borders the Central African Republic and Sudan on the north, Uganda, Rwanda, and Burundi on the east, Zambia and Angola on the south, the Republic of the Congo on the west, and is separated from Tanzania by Lake Tanganyika on the east. The country enjoys access to the ocean through a 40 km stretch of Atlantic coastline at Muanda and the roughly 9 km wide mouth of the Congo river which opens into the Gulf of Guinea. Congo Kinshasa is now divided into 11 Provinces, to be redistributed into 25 Provinces from 2.2009. Each Province is divided into Zones. + GAZ:00005852 Denmark [GAZ:00005852] That part of the Kingdom of Denmark located in continental Europe. The mainland is bordered to the south by Germany; Denmark is located to the southwest of Sweden and the south of Norway. Denmark borders both the Baltic and the North Sea. The country consists of a large peninsula, Jutland (Jylland) and a large number of islands, most notably Zealand (Sjaelland), Funen (Fyn), Vendsyssel-Thy, Lolland, Falster and Bornholm as well as hundreds of minor islands often referred to as the Danish Archipelago. + GAZ:00000582 Djibouti [GAZ:00000582] A country in eastern Africa. Djibouti is bordered by Eritrea in the north, Ethiopia in the west and south, and Somalia in the southeast. The remainder of the border is formed by the Red Sea and the Gulf of Aden. On the other side of the Red Sea, on the Arabian Peninsula, 20 km from the coast of Djibouti, is Yemen. The capital of Djibouti is the city of Djibouti. Djibouti is divided into 5 regions and one city. It is further subdivided into 11 districts. + GAZ:00006890 Dominica [GAZ:00006890] An island nation in the Caribbean Sea. Dominica is divided into ten parishes. + GAZ:00003952 Dominican Republic [GAZ:00003952] A country in the West Indies that occupies the E two-thirds of the Hispaniola island. The Dominican Republic's shores are washed by the Atlantic Ocean to the north and the Caribbean Sea to the south. The Mona Passage, a channel about 130 km wide, separates the country (and the Hispaniola) from Puerto Rico. The Dominican Republic is divided into 31 provinces. Additionally, the national capital, Santo Domingo, is contained within its own Distrito Nacional (National District). The provinces are divided into municipalities (municipios; singular municipio). + GAZ:00002912 Ecuador [GAZ:00002912] A country in South America, bordered by Colombia on the north, by Peru on the east and south, and by the Pacific Ocean to the west. The country also includes the Galapagos Islands (Archipelago de Colon) in the Pacific, about 965 km west of the mainland. Ecuador is divided into 24 provinces, divided into 199 cantons and subdivided into parishes (or parroquias). + GAZ:00003934 Egypt [GAZ:00003934] A country in North Africa that includes the Sinai Peninsula, a land bridge to Asia. Egypt borders Libya to the west, Sudan to the south, and the Gaza Strip and Israel to the east. The northern coast borders the Mediterranean Sea and the island of Cyprus; the eastern coast borders the Red Sea. Egypt is divided into 26 governorates (in Arabic, called muhafazat, singular muhafazah). The governorates are further divided into regions (markazes). + GAZ:00002935 El Salvador [GAZ:00002935] A country in Central America, bordering the Pacific Ocean between Guatemala and Honduras. El Salvador is divided into 14 departments (departamentos), which, in turn, are subdivided into 267 municipalities (municipios). + GAZ:00001091 Equatorial Guinea [GAZ:00001091] A country in Central Africa. It is one of the smallest countries in continental Africa, and comprises two regions: Rio Muni, continental region including several offshore islands; and Insular Region containing Annobon island in the South Atlantic Ocean, and Bioko island (formerly Fernando Po) that contains the capital, Malabo. Equatorial Guinea is divided into seven provinces which are divided into districts. + GAZ:00000581 Eritrea [GAZ:00000581] A country situated in northern East Africa. It is bordered by Sudan in the west, Ethiopia in the south, and Djibouti in the southeast. The east and northeast of the country have an extensive coastline on the Red Sea, directly across from Saudi Arabia and Yemen. The Dahlak Archipelago and several of the Hanish Islands are part of Eritrea. Eritrea is divided into six regions (zobas) and subdivided into districts ("sub-zobas"). + GAZ:00002959 Estonia [GAZ:00002959] A country in Northern Europe. Estonia has land borders to the south with Latvia and to the east with Russia. It is separated from Finland in the north by the Gulf of Finland and from Sweden in the west by the Baltic Sea. Estonia is divided into 15 counties. (maakonnad; sing. - maakond). Estonian counties are divided into rural (vallad, singular vald) and urban (linnad, singular linn; alevid, singular alev; alevikud, singular alevik) municipalities. The municipalities comprise populated places (asula or asustusuksus) - various settlements and territorial units that have no administrative function. A group of populated places form a rural municipality with local administration. Most towns constitute separate urban municipalities, while some have joined with surrounding rural municipalities. + GAZ:00001099 Eswatini [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00000567 Ethiopia [GAZ:00000567] A country situated in the Horn of Africa that has been landlocked since the independence of its northern neighbor Eritrea in 1993. Apart from Eritrea to the north, Ethiopia is bordered by Sudan to the west, Kenya to the south, Djibouti to the northeast, and Somalia to the east. Since 1996 Ethiopia has had a tiered government system consisting of a federal government overseeing ethnically-based regional states, zones, districts (woredas), and neighborhoods (kebele). It is divided into nine ethnically-based administrative states (kililoch, singular kilil) and subdivided into sixty-eight zones and two chartered cities (astedader akababiwoch, singular astedader akababi): Addis Ababa and Dire Dawa. It is further subdivided into 550 woredas and six special woredas. + GAZ:00005811 Europa Island [GAZ:00005811] A 28 km2 low-lying tropical island in the Mozambique Channel, about a third of the way from southern Madagascar to southern Mozambique. + GAZ:00001412 Falkland Islands (Islas Malvinas) [GAZ:00001412] An archipelago in the South Atlantic Ocean, located 483 km from the coast of Argentina, 1,080 km west of the Shag Rocks (South Georgia), and 940 km north of Antarctica (Elephant Island). They consist of two main islands, East Falkland and West Falkland, together with 776 smaller islands. + GAZ:00059206 Faroe Islands [GAZ:00059206] An autonomous province of the Kingdom of Denmark since 1948 located in the Faroes. Administratively, the islands are divided into 34 municipalities (kommunur) within which 120 or so cities and villages lie. + GAZ:00006891 Fiji [GAZ:00006891] An island nation in the South Pacific Ocean east of Vanuatu, west of Tonga and south of Tuvalu. The country occupies an archipelago of about 322 islands, of which 106 are permanently inhabited, and 522 islets. The two major islands, Viti Levu and Vanua Levu, account for 87% of the population. + GAZ:00002937 Finland [GAZ:00002937] A Nordic country situated in the Fennoscandian region of Northern Europe. It has borders with Sweden to the west, Russia to the east, and Norway to the north, while Estonia lies to its south across the Gulf of Finland. The capital city is Helsinki. Finland is divided into six administrative provinces (laani, plural laanit). These are divided into 20 regions (maakunt), 77 subregions (seutukunta) and then into municipalities (kunta). + GAZ:00003940 France [GAZ:00003940] A part of the country of France that extends from the Mediterranean Sea to the English Channel and the North Sea, and from the Rhine to the Atlantic Ocean. Metropolitan France is bordered by Belgium, Luxembourg, Germany, Switzerland, Italy, Monaco, Andorra, and Spain. Due to its overseas departments. + GAZ:00002516 French Guiana [GAZ:00002516] An overseas department (departement d'outre-mer) of France, located on the northern coast of South America. It is bordered by Suriname, to the E, and Brazil, to the S and W, and by the North Atlantic Ocean, to the N. French Guiana is divided into 2 departmental arrondissements, 19 cantons and 22 communes. + GAZ:00002918 French Polynesia [GAZ:00002918] A French overseas collectivity in the southern Pacific Ocean. It is made up of several groups of Polynesian islands. French Polynesia has five administrative subdivisions (French: subdivisions administratives). + GAZ:00003753 French Southern and Antarctic Lands [GAZ:00003753] The French Southern and Antarctic Lands have formed a territoire d'outre-mer (an overseas territory) of France since 1955. The territory is divided into five districts. + GAZ:00001092 Gabon [GAZ:00001092] A country in west central Africa sharing borders with Equatorial Guinea, Cameroon, Republic of the Congo and the Gulf of Guinea. The capital and largest city is Libreville. Gabon is divided into 9 provinces and further divided into 37 departments. + GAZ:00000907 Gambia [GAZ:00000907] A country in Western Africa. It is the smallest country on the African continental mainland and is bordered to the north, east, and south by Senegal, and has a small coast on the Atlantic Ocean in the west. Flowing through the centre of the country and discharging to the Atlantic Ocean is the Gambia River. The Gambia is divided into five divisions and one city (Banjul). The divisions are further subdivided into 37 districts. + GAZ:00009571 Gaza Strip [GAZ:00009571] A Palestinian enclave on the eastern coast of the Mediterranean Sea. It borders Egypt on the southwest for 11 kilometers (6.8 mi) and Israel on the east and north along a 51 km (32 mi) border. Gaza and the West Bank are claimed by the de jure sovereign State of Palestine. + GAZ:00004942 Georgia [GAZ:00004942] A Eurasian country in the Caucasus located at the east coast of the Black Sea. In the north, Georgia has a 723 km common border with Russia, specifically with the Northern Caucasus federal district. The following Russian republics/subdivisions: from west to east: border Georgia: Krasnodar Krai, Karachay-Cherkessia, Kabardino-Balkaria, North Ossetia-Alania, Ingushetia, Chechnya, Dagestan. Georgia also shares borders with Azerbaijan (322 km) to the south-east, Armenia (164 km) to the south, and Turkey (252 km) to the south-west. It is a transcontinental country, located at the juncture of Eastern Europe and Western Asia. Georgia is divided into 9 regions, 2 autonomous republics (avtonomiuri respublika), and 1 city (k'alak'i). The regions are further subdivided into 69 districts (raioni). + GAZ:00002646 Germany [GAZ:00002646] A country in Central Europe. It is bordered to the north by the North Sea, Denmark, and the Baltic Sea; to the east by Poland and the Czech Republic; to the south by Austria and Switzerland; and to the west by France, Luxembourg, Belgium, and the Netherlands. Germany comprises 16 states (Lander, Bundeslander), which are further subdivided into 439 districts (Kreise/Landkreise) and cities (kreisfreie Stadte). + GAZ:00000908 Ghana [GAZ:00000908] A country in West Africa. It borders Cote d'Ivoire to the west, Burkina Faso to the north, Togo to the east, and the Gulf of Guinea to the south. Ghana is a divided into 10 regions, subdivided into a total of 138 districts. + GAZ:00003987 Gibraltar [GAZ:00003987] A British overseas territory located near the southernmost tip of the Iberian Peninsula overlooking the Strait of Gibraltar. The territory shares a border with Spain to the north. + GAZ:00005808 Glorioso Islands [GAZ:00005808] A group of islands and rocks totalling 5 km2, in the northern Mozambique channel, about 160 km northwest of Madagascar. + GAZ:00002945 Greece [GAZ:00002945] A country in southeastern Europe, situated on the southern end of the Balkan Peninsula. It has borders with Albania, the former Yugoslav Republic of Macedonia and Bulgaria to the north, and Turkey to the east. The Aegean Sea lies to the east and south of mainland Greece, while the Ionian Sea lies to the west. Both parts of the Eastern Mediterranean basin feature a vast number of islands. Greece consists of thirteen peripheries subdivided into a total of fifty-one prefectures (nomoi, singular nomos). There is also one autonomous area, Mount Athos, which borders the periphery of Central Macedonia. + GAZ:00001507 Greenland [GAZ:00001507] A self-governing Danish province located between the Arctic and Atlantic Oceans, east of the Canadian Arctic Archipelago. + GAZ:02000573 Grenada [GAZ:02000573] An island country in the West Indies in the Caribbean Sea at the southern end of the Grenadines island chain. Grenada consists of the island of Grenada itself, two smaller islands, Carriacou and Petite Martinique, and several small islands which lie to the north of the main island and are a part of the Grenadines. It is located northwest of Trinidad and Tobago, northeast of Venezuela and southwest of Saint Vincent and the Grenadines. Its size is 348.5 square kilometres (134.6 sq mi), and it had an estimated population of 112,523 in July 2020. + GAZ:00067142 Guadeloupe [GAZ:00067142] An archipelago and overseas department and region of France in the Caribbean. It consists of six inhabited islands—Basse-Terre, Grande-Terre, Marie-Galante, La Désirade, and the two inhabited Îles des Saintes—as well as many uninhabited islands and outcroppings. It is south of Antigua and Barbuda and Montserrat, and north of Dominica. + GAZ:00003706 Guam [GAZ:00003706] An organized, unincorporated territory of the United States in the Micronesia subregion of the western Pacific Ocean. It is the westernmost point and territory of the United States (reckoned from the geographic center of the U.S.); in Oceania, it is the largest and southernmost of the Mariana Islands and the largest island in Micronesia. + GAZ:00002936 Guatemala [GAZ:00002936] A country in Central America bordered by Mexico to the northwest, the Pacific Ocean to the southwest, Belize and the Caribbean Sea to the northeast, and Honduras and El Salvador to the southeast. Guatemala is divided into 22 departments (departamentos) and sub-divided into about 332 municipalities (municipios). + GAZ:00001550 Guernsey [GAZ:00001550] A British Crown Dependency in the English Channel off the coast of Normandy. + GAZ:00000909 Guinea [GAZ:00000909] A nation in West Africa, formerly known as French Guinea. Guinea's territory has a curved shape, with its base at the Atlantic Ocean, inland to the east, and turning south. The base borders Guinea-Bissau and Senegal to the north, and Mali to the north and north-east; the inland part borders Cote d'Ivoire to the south-east, Liberia to the south, and Sierra Leone to the west of the southern tip. + GAZ:00000910 Guinea-Bissau [GAZ:00000910] A country in western Africa, and one of the smallest nations in continental Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west. Formerly the Portuguese colony of Portuguese Guinea, upon independence, the name of its capital, Bissau, was added to the country's name in order to prevent confusion between itself and the Republic of Guinea. + GAZ:00002522 Guyana [GAZ:00002522] A country in the N of South America. Guyana lies north of the equator, in the tropics, and is located on the Atlantic Ocean. Guyana is bordered to the east by Suriname, to the south and southwest by Brazil and to the west by Venezuela. Guyana is divided into 10 regions. The regions of Guyana are divided into 27 neighborhood councils. + GAZ:00003953 Haiti [GAZ:00003953] A country located in the Greater Antilles archipelago on the Caribbean island of Hispaniola, which it shares with the Dominican Republic. Haiti is divided into 10 departments. The departments are further divided into 41 arrondissements, and 133 communes which serve as second and third level administrative divisions. + GAZ:00009718 Heard Island and McDonald Islands [GAZ:00009718] An Australian external territory comprising a volcanic group of mostly barren Antarctic islands, about two-thirds of the way from Madagascar to Antarctica. + GAZ:00002894 Honduras [GAZ:00002894] A republic in Central America. The country is bordered to the west by Guatemala, to the southwest by El Salvador, to the southeast by Nicaragua, to the south by the Pacific Ocean at the Gulf of Fonseca, and to the north by the Gulf of Honduras, a large inlet of the Caribbean Sea. Honduras is divided into 18 departments. The capital city is Tegucigalpa Central District of the department of Francisco Morazan. + GAZ:00003203 Hong Kong [GAZ:00003203] A special administrative region of the People's Republic of China (PRC). The territory lies on the eastern side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east, west and south. Hong Kong was a crown colony of the United Kingdom from 1842 until the transfer of its sovereignty to the People's Republic of China in 1997. + GAZ:00007120 Howland Island [GAZ:00007120] An uninhabited coral island located just north of the equator in the central Pacific Ocean, about 3,100 km (1,670 nm) southwest of Honolulu. The island is almost half way between Hawaii and Australia and is an unincorporated, unorganized territory of the United States, and is often included as one of the Phoenix Islands. For statistical purposes, Howland is grouped as one of the United States Minor Outlying Islands. + GAZ:00002952 Hungary [GAZ:00002952] A landlocked country in the Carpathian Basin of Central Europe, bordered by Austria, Slovakia, Ukraine, Romania, Serbia, Croatia, and Slovenia. Its capital is Budapest. Hungary is divided into 19 counties (megyek, singular: megye). In addition, the capital city (fovaros), Budapest, is independent of any county government. The counties are further subdivided into 173 subregions (kistersegek), and Budapest is comprised of its own subregion. Since 1996, the counties and City of Budapest have been grouped into 7 regions for statistical and development purposes. These seven regions constitute NUTS second-level units of Hungary. + GAZ:00000843 Iceland [GAZ:00000843] A country in northern Europe, comprising the island of Iceland and its outlying islands in the North Atlantic Ocean between the rest of Europe and Greenland. + GAZ:00002839 India [GAZ:00002839] A country in South Asia. Bounded by the Indian Ocean on the south, the Arabian Sea on the west, and the Bay of Bengal on the east, India has a coastline of 7,517 km. It borders Pakistan to the west; China, Nepal, and Bhutan to the north-east; and Bangladesh and Burma to the east. India is in the vicinity of Sri Lanka, the Maldives, and Indonesia in the Indian Ocean. India is a federal republic of twenty-eight states and seven Union Territories. Each state or union territory is divided into basic units of government and administration called districts. There are nearly 600 districts in India. The districts in turn are further divided into tehsils and eventually into villages. + GAZ:00003727 Indonesia [GAZ:00003727] An archipelagic state in Southeast Asia. The country shares land borders with Papua New Guinea, East Timor and Malaysia. Other neighboring countries include Singapore, the Philippines, Australia, and the Indian territory of the Andaman and Nicobar Islands. Indonesia consists of 33 provinces, five of which have special status. The provinces are subdivided into regencies (kabupaten, distrik in Papua and West Papua Provinces) and cities (kota), which are further subdivided into subdistricts (kecamatan), and again into village groupings (either desa or kelurahan). + GAZ:00004474 Iran [GAZ:00004474] A country in Central Eurasia. Iran is bounded by the Gulf of Oman and the Persian Gulf to the south and the Caspian Sea to its north. It borders Armenia, Azerbaijan, Turkmenistan to the north, Afghanistan and Pakistan to the east, and Turkey and Iraq to the west. Iran is divided into 30 provinces (ostan). The provinces are divided into counties (shahrestan), and subdivided into districts (bakhsh) and sub-districts (dehestan). + GAZ:00004483 Iraq [GAZ:00004483] A country in the Middle East spanning most of the northwestern end of the Zagros mountain range, the eastern part of the Syrian Desert and the northern part of the Arabian Desert. It shares borders with Kuwait and Saudi Arabia to the south, Jordan to the west, Syria to the northwest, Turkey to the north, and Iran to the east. It has a very narrow section of coastline at Umm Qasr on the Persian Gulf. There are two major flowing rivers: the Tigris and the Euphrates. Iraq is divided into 18 governorates (or provinces) (muhafazah). The governorates are divided into qadhas (or districts). + GAZ:00002943 Ireland [GAZ:00002943] A country in north-western Europe. The modern sovereign state occupies five-sixths of the island of Ireland, which was partitioned in 1921. It is bordered by Northern Ireland (part of the United Kingdom) to the north, by the Atlantic Ocean to the west and by the Irish Sea to the east. Administration follows the 34 "county-level" counties and cities of Ireland. Of these twenty-nine are counties, governed by county councils while the five cities of Dublin, Cork, Limerick, Galway and Waterford have city councils, (previously known as corporations), and are administered separately from the counties bearing those names. The City of Kilkenny is the only city in the republic which does not have a "city council"; it is still a borough but not a county borough and is administered as part of County Kilkenny. Ireland is split into eight regions for NUTS statistical purposes. These are not related to the four traditional provinces but are based on the administrative counties. + GAZ:00052477 Isle of Man [GAZ:00052477] A Crown dependency of the United Kingdom in the centre of the Irish Sea. It is not part of the United Kingdom, European Union or United Nations. + GAZ:00002476 Israel [GAZ:00002476] A country in Western Asia located on the eastern edge of the Mediterranean Sea. It borders Lebanon in the north, Syria in the northeast, Jordan in the east, and Egypt on the southwest. The West Bank and Gaza Strip, which are partially administrated by the Palestinian National Authority, are also adjacent. The State of Israel is divided into six main administrative districts, known as mehozot (singular mahoz). Districts are further divided into fifteen sub-districts known as nafot (singular: nafa), which are themselves partitioned into fifty natural regions. + GAZ:00002650 Italy [GAZ:00002650] A country located on the Italian Peninsula in Southern Europe, and on the two largest islands in the Mediterranean Sea, Sicily and Sardinia. Italy shares its northern Alpine boundary with France, Switzerland, Austria and Slovenia. The independent states of San Marino and the Vatican City are enclaves within the Italian Peninsula, while Campione d'Italia is an Italian exclave in Switzerland. Italy is subdivided into 20 regions (regioni, singular regione). Five of these regions have a special autonomous status that enables them to enact legislation on some of their local matters. It is further divided into 109 provinces (province) and 8,101 municipalities (comuni). + GAZ:00003781 Jamaica [GAZ:00003781] A nation of the Greater Antilles. Jamaica is divided into 14 parishes, which are grouped into three historic counties that have no administrative relevance. + GAZ:00005853 Jan Mayen [GAZ:00005853] A volcanic island that is part of the Kingdom of Norway, It has two parts: larger Nord-Jan and smaller Sor-Jan, linked by an isthmus 2.5 km wide. It lies 600 km north of Iceland, 500 km east of Greenland and 1,000 km west of the Norwegian mainland. The island is mountainous, the highest summit being the Beerenberg volcano in the north. The isthmus is the location of the two largest lakes of the island, Sorlaguna (South Lagoon), and Nordlaguna (North Lagoon). A third lake is called Ullerenglaguna (Ullereng Lagoon). Jan Mayen was formed by the Jan Mayen hotspot. + GAZ:00002747 Japan [GAZ:00002747] An island country in East Asia. Located in the Pacific Ocean, it lies to the east of China, Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea in the south. + GAZ:00007118 Jarvis Island [GAZ:00007118] An uninhabited 4.5 km2 coral atoll located in the South Pacific Ocean about halfway between Hawaii and the Cook Islands. It is an unincorporated territory of the United States administered from Washington, DC by the United States Fish and Wildlife Service of the United States Department of the Interior as part of the National Wildlife Refuge system. Jarvis is one of the southern Line Islands and for statistical purposes is also grouped as one of the United States Minor Outlying Islands. Sits atop the Jarvis Seamount. + GAZ:00001551 Jersey [GAZ:00001551] A British Crown Dependency[6] off the coast of Normandy, France. As well as the island of Jersey itself, the bailiwick includes two groups of small islands that are no longer permanently inhabited, the Minquiers and Ecrehous, and the Pierres de Lecq. + GAZ:00007114 Johnston Atoll [GAZ:00007114] A 130 km2 atoll in the North Pacific Ocean about 1400 km (750 nm) west of Hawaii. There are four islands located on the coral reef platform, two natural islands, Johnston Island and Sand Island, which have been expanded by coral dredging, as well as North Island (Akau) and East Island (Hikina), artificial islands formed from coral dredging. Johnston is an unincorporated territory of the United States, administered by the US Fish and Wildlife Service of the Department of the Interior as part of the United States Pacific Island Wildlife Refuges. Sits atop Johnston Seamount. + GAZ:00002473 Jordan [GAZ:00002473] A country in Southwest Asia, bordered by Syria to the north, Iraq to the north-east, Israel and the West Bank to the west, and Saudi Arabia to the east and south. It shares the coastlines of the Dead Sea, and the Gulf of Aqaba with Israel, Saudi Arabia, and Egypt. Jordan is divided into 12 provinces called governorates. The Governorates are subdivided into approximately fifty-two nahias. + GAZ:00005809 Juan de Nova Island [GAZ:00005809] A 4.4 km2 low, flat, tropical island in the narrowest part of the Mozambique Channel, about one-third of the way between Madagascar and Mozambique. + GAZ:00004999 Kazakhstan [GAZ:00004999] A country in Central Asia and Europe. It is bordered by Russia, Kyrgyzstan, Turkmenistan, Uzbekistan and China. The country also borders on a significant part of the Caspian Sea. Kazakhstan is divided into 14 provinces and two municipal districts. The provinces of Kazakhstan are divided into raions. + GAZ:00001101 Kenya [GAZ:00001101] A country in Eastern Africa. It is bordered by Ethiopia to the north, Somalia to the east, Tanzania to the south, Uganda to the west, and Sudan to the northwest, with the Indian Ocean running along the southeast border. Kenya comprises eight provinces each headed by a Provincial Commissioner (centrally appointed by the president). The provinces (mkoa singular mikoa plural in Swahili) are subdivided into districts (wilaya). There were 69 districts as of 1999 census. Districts are then subdivided into 497 divisions (taarafa). The divisions are then subdivided into 2,427 locations (kata) and then 6,612 sublocations (kata ndogo). The City of Nairobi enjoys the status of a full administrative province. + GAZ:00005682 Kerguelen Archipelago [GAZ:00005682] A group of islands in the southern Indian Ocean. It is a territory of France. They are composed primarily of Tertiary flood basalts and a complex of plutonic rocks. The trachybasaltic-to-trachytic Mount Ross stratovolcano at the southern end was active during the late Pleistocene. The Rallier du Baty Peninsula on the SW tip of the island contains two youthful subglacial eruptive centers, Mont St. Allouarn and Mont Henri Rallier du Baty. An active fumarole field is related to a series of Holocene trachytic lava flows and lahars that extend beyond the icecap. + GAZ:00007116 Kingman Reef [GAZ:00007116] A largely submerged, uninhabited tropical atoll located in the North Pacific Ocean, roughly half way between Hawaiian Islands and American Samoa. It is the northernmost of the Northern Line Islands and lies 65 km NNW of Palmyra Atoll, the next closest island, and has the status of an unincorporated territory of the United States, administered from Washington, DC by the US Navy. Sits atop Kingman Reef Seamount. + GAZ:00006894 Kiribati [GAZ:00006894] An island nation located in the central tropical Pacific Ocean. It is composed of 32 atolls and one raised coral island dispersed over 3,500,000 km2 straddling the equator and bordering the International Date Line to the east. It is divided into three island groups which have no administrative function, including a group which unites the Line Islands and the Phoenix Islands (ministry at London, Christmas). Each inhabited island has its own council (three councils on Tarawa: Betio, South-Tarawa, North-Tarawa; two councils on Tabiteuea). + GAZ:00011337 Kosovo [GAZ:00011337] A country on the Balkan Peninsula. Kosovo borders Central Serbia to the north and east, Montenegro to the northwest, Albania to the west and the Republic of Macedonia to the south. Kosovo is divided into 7 districts (Rreth) and 30 municipalities. Serbia does not recognise the unilateral secession of Kosovo[8] and considers it a United Nations-governed entity within its sovereign territory, the Autonomous Province of Kosovo and Metohija. + GAZ:00005285 Kuwait [GAZ:00005285] A sovereign emirate on the coast of the Persian Gulf, enclosed by Saudi Arabia to the south and Iraq to the north and west. Kuwait is divided into six governorates (muhafazat, singular muhafadhah). + GAZ:00006893 Kyrgyzstan [GAZ:00006893] A country in Central Asia. Landlocked and mountainous, it is bordered by Kazakhstan to the north, Uzbekistan to the west, Tajikistan to the southwest and China to the east. Kyrgyzstan is divided into seven provinces (oblast. The capital, Bishkek, and the second large city Osh are administratively the independent cities (shaar) with a status equal to a province. Each province comprises a number of districts (raions). + GAZ:00006889 Laos [GAZ:00006889] A landlocked country in southeast Asia, bordered by Burma (Myanmar) and China to the northwest, Vietnam to the east, Cambodia to the south, and Thailand to the west. Laos is divided into sixteen provinces (qwang) and Vientiane Capital (Na Kone Luang Vientiane). The provinces further divided into districts (muang). + GAZ:00002958 Latvia [GAZ:00002958] A country in Northern Europe. Latvia shares land borders with Estonia to the north and Lithuania to the south, and both Russia and Belarus to the east. It is separated from Sweden in the west by the Baltic Sea. The capital of Latvia is Riga. Latvia is divided into 26 districts (raioni). There are also seven cities (lielpilsetas) that have a separate status. Latvia is also historically, culturally and constitutionally divided in four or more distinct regions. + GAZ:00002478 Lebanon [GAZ:00002478] A small, mostly mountainous country in Western Asia, on the eastern shore of the Mediterranean Sea. It is bordered by Syria to the north and east, and Israel to the south. Lebanon is divided into six governorates (mohaafazaat, which are further subdivided into twenty-five districts (aqdya, singular: qadaa). + GAZ:00001098 Lesotho [GAZ:00001098] A land-locked country, entirely surrounded by the Republic of South Africa. Lesotho is divided into ten districts; these are further subdivided into 80 constituencies, which consists of 129 local community councils. + GAZ:00000911 Liberia [GAZ:00000911] A country on the west coast of Africa, bordered by Sierra Leone, Guinea, Cote d'Ivoire, and the Atlantic Ocean. + GAZ:00000566 Libya [GAZ:00000566] A country in North Africa. Bordering the Mediterranean Sea to the north, Libya lies between Egypt to the east, Sudan to the southeast, Chad and Niger to the south, and Algeria and Tunisia to the west. There are thirty-four municipalities of Libya, known by the Arabic term sha'biyat (singular sha'biyah). These came recently (in the 1990s to replaced old Baladiyat systam. The Baladiyat system in turn was introduced to replace the system of muhafazah (governorates or provinces) that existed from the 1960s to the 1970s. + GAZ:00003858 Liechtenstein [GAZ:00003858] A tiny, doubly landlocked alpine country in Western Europe, bordered by Switzerland to its west and by Austria to its east. The principality of Liechtenstein is divided into 11 municipalities called Gemeinden (singular Gemeinde). The Gemeinden mostly consist only of a single town. Five of them fall within the electoral district Unterland (the lower county), and the remainder within Oberland (the upper county). + GAZ:00007144 Line Islands [GAZ:00007144] A group of eleven atolls and low coral islands in the central Pacific Ocean south of the Hawaiian Islands, eight of which belong to Kiribati, while three are United States territories that are grouped with the United States Minor Outlying Islands. + GAZ:00002960 Lithuania [GAZ:00002960] A country located along the south-eastern shore of the Baltic Sea, sharing borders with Latvia to the north, Belarus to the southeast, Poland, and the Russian exclave of the Kaliningrad Oblast to the southwest. Lithuania has a three-tier administrative division: the country is divided into 10 counties (singular apskritis, plural, apskritys) that are further subdivided into 60 municipalities (singular savivaldybe, plural savivaldybes) which consist of over 500 elderates (singular seniunija, plural seniunijos). + GAZ:00002947 Luxembourg [GAZ:00002947] A small landlocked country in western Europe, bordered by Belgium, France, and Germany. Luxembourg is divided into 3 districts, which are further divided into 12 cantons and then 116 communes. Twelve of the communes have city status, of which the city of Luxembourg is the largest. + GAZ:00003202 Macau [GAZ:00003202] One of the two special administrative regions of the People's Republic of China, the other being Hong Kong. Macau lies on the western side of the Pearl River Delta, bordering Guangdong province in the north and facing the South China Sea in the east and south. Macau is situated 60 kmsouthwest of Hong Kong and 145 km from Guangzhou. It consists of the Macau Peninsula itself and the islands of Taipa and Coloane. The peninsula is formed by the Zhujiang (Pearl River) estuary on the east and the Xijiang (West River) on the west. It borders the Zhuhai Special Economic Zone in mainland China. + GAZ:00001108 Madagascar [GAZ:00001108] An island nation in the Indian Ocean off the southeastern coast of Africa. The main island, also called Madagascar, is the fourth largest island in the world, and is home to 5% of the world's plant and animal species, of which more than 80% are endemic to Madagascar. Most notable are the lemur infraorder of primates, the carnivorous fossa, three endemic bird families and six endemic baobab species. Madagascar is divided into six autonomous provinces (faritany mizakatena), and 22 regions. The regions are further subdivided into 116 districts, 1,548 communes, and 16,969 fokontany. + GAZ:00001105 Malawi [GAZ:00001105] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00003902 Malaysia [GAZ:00003902] A country in southeastern Africa. It is bordered by Zambia to the north-west, Tanzania to the north and Mozambique, which surrounds it on the east, south and west. Malawi is divided into three regions (the Northern, Central and Southern regions), which are further divided into twenty-seven districts, which in turn are further divided into 137 traditional authorities and 68 sub-chiefdoms. + GAZ:00006924 Maldives [GAZ:00006924] An archipelago which consists of approximately 1,196 coral islands grouped in a double chain of 27 atolls, spread over roughly 90,000 km2. + GAZ:00000584 Mali [GAZ:00000584] A landlocked country in northern Africa. It borders Algeria on the north, Niger on the east, Burkina Faso and the Cote d'Ivoire on the south, Guinea on the south-west, and Senegal and Mauritania on the west. Mali is divided into 8 regions (regions) and 1 district, and subdivided into 49 cercles, totalling 288 arrondissements. + GAZ:00004017 Malta [GAZ:00004017] A Southern European country and consists of an archipelago situated centrally in the Mediterranean. + GAZ:00007161 Marshall Islands [GAZ:00007161] An archipelago that consists of twenty-nine atolls and five isolated islands. The most important atolls and islands form two groups: the Ratak Chain and the Ralik Chain (meaning "sunrise" and "sunset" chains). Two-thirds of the nation's population lives on Majuro (which is also the capital) and Ebeye. The outer islands are sparsely populated. + GAZ:00067143 Martinique [GAZ:00067143] An island and an overseas department/region and single territorial collectivity of France. + GAZ:00000583 Mauritania [GAZ:00000583] A country in North-West Africa. It is bordered by the Atlantic Ocean on the west, by Senegal on the southwest, by Mali on the east and southeast, by Algeria on the northeast, and by Western Sahara on the northwest (most of which is occupied by Morocco). The capital and largest city is Nouakchott, located on the Atlantic coast. Mauritania is divided into 12 regions (regions) and one capital district, which in turn are subdivided into 44 departments (departements). + GAZ:00003745 Mauritius [GAZ:00003745] An island nation off the coast of the African continent in the southwest Indian Ocean, about 900 km east of Madagascar. In addition to the island of Mauritius, the republic includes the islands of St. Brandon, Rodrigues and the Agalega Islands. + GAZ:00003943 Mayotte [GAZ:00003943] An overseas collectivity of France consisting of a main island, Grande-Terre (or Mahore), a smaller island, Petite-Terre (or Pamanzi), and several islets around these two. + GAZ:00002852 Mexico [GAZ:00002852] A federal constitutional republic in North America. It is bounded on the north by the United States; on the south and west by the North Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of Mexico. The United Mexican States comprise a federation of thirty-one states and a federal district, the capital Mexico City. + GAZ:00005862 Micronesia [GAZ:00005862] A subregion of Oceania, comprising hundreds of small islands in the Pacific Ocean. The Philippines lie to the northwest, Indonesia, Papua New Guinea and Melanesia to the west and southwest, and Polynesia to the east. + GAZ:00007112 Midway Islands [GAZ:00007112] A 6.2 km2 atoll located in the North Pacific Ocean (near the northwestern end of the Hawaiian archipelago). It is an unincorporated territory of the United States, designated an insular area under the authority of the US Department of the Interior. + GAZ:00003897 Moldova [GAZ:00003897] A landlocked country in Eastern Europe, located between Romania to the west and Ukraine to the north, east and south. Moldova is divided into thirty-two districts (raioane, singular raion); three municipalities (Balti, Chisinau, Tighina); and two autonomous regions (Gagauzia and Transnistria). The cities of Comrat and Tiraspol also have municipality status, however not as first-tier subdivisions of Moldova, but as parts of the regions of Gagauzia and Transnistria, respectively. The status of Transnistria is however under dispute. Although it is de jure part of Moldova and is recognized as such by the international community, Transnistria is not de facto under the control of the central government of Moldova. It is administered by an unrecognized breakaway authority under the name Pridnestrovian Moldovan Republic. + GAZ:00003857 Monaco [GAZ:00003857] A small country that is completely bordered by France to the north, west, and south; to the east it is bordered by the Mediterranean Sea. It consists of a single municipality (commune) currently divided into 4 quartiers and 10 wards. + GAZ:00008744 Mongolia [GAZ:00008744] A country in East-Central Asia. The landlocked country borders Russia to the north and China to the south. The capital and largest city is Ulan Bator. Mongolia is divided into 21 aimags (provinces), which are in turn divided into 315 sums (districts). The capital Ulan Bator is administrated separately as a khot (municipality) with provincial status. + GAZ:00006898 Montenegro [GAZ:00006898] A country located in Southeastern Europe. It has a coast on the Adriatic Sea to the south and borders Croatia to the west, Bosnia and Herzegovina to the northwest, Serbia and its partially recognized breakaway southern province of Kosovo to the northeast and Albania to the southeast. Its capital and largest city is Podgorica. Montenegro is divided into twenty-one municipalities (opstina), and two urban municipalities, subdivisions of Podgorica municipality. + GAZ:00003988 Montserrat [GAZ:00003988] A British overseas territory located in the Leeward Islands. Montserrat is divided into three parishes. + GAZ:00000565 Morocco [GAZ:00000565] A country in North Africa. It has a coast on the Atlantic Ocean that reaches past the Strait of Gibraltar into the Mediterranean Sea. Morocco has international borders with Algeria to the east, Spain to the north (a water border through the Strait and land borders with two small Spanish autonomous cities, Ceuta and Melilla), and Mauritania to the south. Morocco is divided into 16 regions, and subdivided into 62 prefectures and provinces. Because of the conflict over Western Sahara, the status of both regions of "Saguia el-Hamra" and "Rio de Oro" is disputed. + GAZ:00001100 Mozambique [GAZ:00001100] A country in southeastern Africa bordered by the Indian Ocean to the east, Tanzania to the north, Malawi and Zambia to the northwest, Zimbabwe to the west and Swaziland and South Africa to the southwest. Mozambique is divided into ten provinces (provincias) and one capital city (cidade capital) with provincial status. The provinces are subdivided into 129 districts (distritos). Districts are further divided in "Postos Administrativos" (Administrative Posts) and these in Localidades (Localities) the lowest geographical level of central state administration. + GAZ:00006899 Myanmar [GAZ:00006899] A country in SE Asia that is bordered by China on the north, Laos on the east, Thailand on the southeast, Bangladesh on the west, and India on the northwest, with the Bay of Bengal to the southwest. Myanmar is divided into seven states and seven divisions. The administrative divisions are further subdivided into districts, which are further subdivided into townships, wards, and villages. + GAZ:00001096 Namibia [GAZ:00001096] A country in southern Africa on the Atlantic coast. It shares borders with Angola and Zambia to the north, Botswana to the east, and South Africa to the south. Namibia is divided into 13 regions and subdivided into 102 constituencies. + GAZ:00006900 Nauru [GAZ:00006900] An island nation in the Micronesian South Pacific. The nearest neighbour is Banaba Island in the Republic of Kiribati, 300 km due east. Nauru is divided into fourteen administrative districts which are grouped into eight electoral constituencies. + GAZ:00007119 Navassa Island [GAZ:00007119] A small, uninhabited island in the Caribbean Sea, and is an unorganized unincorporated territory of the United States, which administers it through the US Fish and Wildlife Service. The island is also claimed by Haiti. + GAZ:00004399 Nepal [GAZ:00004399] A landlocked nation in South Asia. It is bordered by the Tibet Autonomous Region of the People's Republic of China to the northeast and India to the south and west; it is separated from Bhutan by the Indian State of Sikkim and from Bangladesh by a small strip of the Indian State of West Bengal, known as the "Chicken's Neck". The Himalaya mountain range runs across Nepal's north and western parts, and eight of the world's ten highest mountains, including the highest, Mount Everest are situated within its territory. Nepal is divided into 14 zones and 75 districts, grouped into 5 development regions. + GAZ:00002946 Netherlands [GAZ:00002946] The European part of the Kingdom of the Netherlands. It is bordered by the North Sea to the north and west, Belgium to the south, and Germany to the east. The Netherlands is divided into twelve administrative regions, called provinces. All provinces of the Netherlands are divided into municipalities (gemeenten), together 443 (2007). + GAZ:00005206 New Caledonia [GAZ:00005206] A "sui generis collectivity" (in practice an overseas territory) of France, made up of a main island (Grande Terre), the Loyalty Islands, and several smaller islands. It is located in the region of Melanesia in the southwest Pacific. Administratively, the archipelago is divided into three provinces, and then into 33 communes. + GAZ:00000469 New Zealand [GAZ:00000469] A nation in the south-western Pacific Ocean comprising two large islands (the North Island and the South Island) and numerous smaller islands, most notably Stewart Island/Rakiura and the Chatham Islands. + GAZ:00002978 Nicaragua [GAZ:00002978] A republic in Central America. It is also the least densely populated with a demographic similar in size to its smaller neighbors. The country is bordered by Honduras to the north and by Costa Rica to the south. The Pacific Ocean lies to the west of the country, while the Caribbean Sea lies to the east. For administrative purposes it is divided into 15 departments (departamentos) and two self-governing regions (autonomous communities) based on the Spanish model. The departments are then subdivided into 153 municipios (municipalities). The two autonomous regions are Region Autonoma del Atlantico Norte and Region Autonoma del Atlantico Sur, often referred to as RAAN and RAAS, respectively. Until they were granted autonomy in 1985 they formed the single department of Zelaya. + GAZ:00000585 Niger [GAZ:00000585] A landlocked country in Western Africa, named after the Niger River. It borders Nigeria and Benin to the south, Burkina Faso and Mali to the west, Algeria and Libya to the north and Chad to the east. The capital city is Niamey. Niger is divided into 7 departments and one capital district. The departments are subdivided into 36 arrondissements and further subdivided into 129 communes. + GAZ:00000912 Nigeria [GAZ:00000912] A federal constitutional republic comprising thirty-six states and one Federal Capital Territory. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in the north. Its coast lies on the Gulf of Guinea, part of the Atlantic Ocean, in the south. The capital city is Abuja. Nigeria is divided into thirty-six states and one Federal Capital Territory, which are further sub-divided into 774 Local Government Areas (LGAs). + GAZ:00006902 Niue [GAZ:00006902] An island nation located in the South Pacific Ocean. Although self-governing, Niue is in free association with New Zealand, meaning that the Sovereign in Right of New Zealand is also Niue's head of state. + GAZ:00005908 Norfolk Island [GAZ:00005908] A Territory of Australia that includes Norfolk Island and neighboring islands. + GAZ:00002801 North Korea [GAZ:00002801] A state in East Asia in the northern half of the Korean Peninsula, with its capital in the city of Pyongyang. To the south and separated by the Korean Demilitarized Zone is South Korea, with which it formed one nation until division following World War II. At its northern Amnok River border are China and, separated by the Tumen River in the extreme north-east, Russia. + GAZ:00006895 North Macedonia [GAZ:00006895] A landlocked country on the Balkan peninsula in southeastern Europe. It is bordered by Serbia and Kosovo to the north, Albania to the west, Greece to the south, and Bulgaria to the east. In 2004-08, the Republic of Macedonia was reorganised into 85 municipalities (opstini; singular opstina), 10 of which comprise Greater Skopje. This is reduced from the previous 123 municipalities established in 1996-09. Prior to this, local government was organised into 34 administrative districts. + GAZ:00002284 North Sea [GAZ:00002284] A sea situated between the eastern coasts of the British Isles and the western coast of Europe. + GAZ:00003958 Northern Mariana Islands [GAZ:00003958] A group of 15 islands about three-quarters of the way from Hawaii to the Philippines. + GAZ:00002699 Norway [GAZ:00002699] A country and constitutional monarchy in Northern Europe that occupies the western portion of the Scandinavian Peninsula. It is bordered by Sweden, Finland, and Russia. The Kingdom of Norway also includes the Arctic island territories of Svalbard and Jan Mayen. Norwegian sovereignty over Svalbard is based upon the Svalbard Treaty, but that treaty does not apply to Jan Mayen. Bouvet Island in the South Atlantic Ocean and Peter I Island and Queen Maud Land in Antarctica are external dependencies, but those three entities do not form part of the kingdom. + GAZ:00005283 Oman [GAZ:00005283] A country in southwest Asia, on the southeast coast of the Arabian Peninsula. It borders the United Arab Emirates on the northwest, Saudi Arabia on the west, and Yemen on the southwest. The coast is formed by the Arabian Sea on the south and east, and the Gulf of Oman on the northeast. The country also contains Madha, an exclave enclosed by the United Arab Emirates, and Musandam, an exclave also separated by Emirati territory. Oman is divided into four governorates (muhafazah) and five regions (mintaqat). The regions are subdivided into provinces (wilayat). + GAZ:00005246 Pakistan [GAZ:00005246] A country in Middle East which lies on the Iranian Plateau and some parts of South Asia. It is located in the region where South Asia converges with Central Asia and the Middle East. It has a 1,046 km coastline along the Arabian Sea in the south, and is bordered by Afghanistan and Iran in the west, India in the east and China in the far northeast. Pakistan is subdivided into four provinces and two territories. In addition, the portion of Kashmir that is administered by the Pakistani government is divided into two separate administrative units. The provinces are divided into a total of 105 zillas (districts). A zilla is further subdivided into tehsils (roughly equivalent to counties). Tehsils may contain villages or municipalities. There are over five thousand local governments in Pakistan. + GAZ:00006905 Palau [GAZ:00006905] A nation that consists of eight principal islands and more than 250 smaller ones lying roughly 500 miles southeast of the Philippines. + GAZ:00002892 Panama [GAZ:00002892] The southernmost country of Central America. Situated on an isthmus, some categorize it as a transcontinental nation connecting the north and south part of America. It borders Costa Rica to the north-west, Colombia to the south-east, the Caribbean Sea to the north and the Pacific Ocean to the south. Panama's major divisions are nine provinces and five indigenous territories (comarcas indigenas). The provincial borders have not changed since they were determined at independence in 1903. The provinces are divided into districts, which in turn are subdivided into sections called corregimientos. Configurations of the corregimientos are changed periodically to accommodate population changes as revealed in the census reports. + GAZ:00003922 Papua New Guinea [GAZ:00003922] A country in Oceania that comprises the eastern half of the island of New Guinea and its offshore islands in Melanesia (a region of the southwestern Pacific Ocean north of Australia). + GAZ:00010832 Paracel Islands [GAZ:00010832] A group of small islands and reefs in the South China Sea, about one-third of the way from Vietnam to the Philippines. + GAZ:00002933 Paraguay [GAZ:00002933] A landlocked country in South America. It lies on both banks of the Paraguay River, bordering Argentina to the south and southwest, Brazil to the east and northeast, and Bolivia to the northwest, and is located in the very heart of South America. Paraguay consists of seventeen departments and one capital district (distrito capital). Each department is divided into districts. + GAZ:00002932 Peru [GAZ:00002932] A country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean. Peru is divided into 25 regions and the province of Lima. These regions are subdivided into provinces, which are composed of districts (provincias and distritos). There are 195 provinces and 1833 districts in Peru. The Lima Province, located in the central coast of the country, is unique in that it doesn't belong to any of the twenty-five regions. The city of Lima, which is the nation's capital, is located in this province. Callao is its own region, even though it only contains one province, the Constitutional Province of Callao. + GAZ:00004525 Philippines [GAZ:00004525] An archipelagic nation located in Southeast Asia. The Philippine archipelago comprises 7,107 islands in the western Pacific Ocean, bordering countries such as Indonesia, Malaysia, Palau and the Republic of China, although it is the only Southeast Asian country to share no land borders with its neighbors. The Philippines is divided into three island groups: Luzon, Visayas, and Mindanao. These are divided into 17 regions, 81 provinces, 136 cities, 1,494 municipalities and 41,995 barangays. + GAZ:00005867 Pitcairn Islands [GAZ:00005867] A group of four islands in the southern Pacific Ocean. The Pitcairn Islands form the southeasternmost extension of the geological archipelago of the Tuamotus of French Polynesia. + GAZ:00002939 Poland [GAZ:00002939] A country in Central Europe. Poland is bordered by Germany to the west; the Czech Republic and Slovakia to the south; Ukraine, Belarus and Lithuania to the east; and the Baltic Sea and Kaliningrad Oblast, a Russian exclave, to the north. The administrative division of Poland since 1999 has been based on three levels of subdivision. The territory of Poland is divided into voivodeships (provinces); these are further divided into powiats (counties), and these in turn are divided into gminas (communes or municipalities). Major cities normally have the status of both gmina and powiat. Poland currently has 16 voivodeships, 379 powiats (including 65 cities with powiat status), and 2,478 gminas. + GAZ:00004126 Portugal [GAZ:00004126] That part of the Portugese Republic that occupies the W part of the Iberian Peninsula, and immediately adjacent islands. + GAZ:00006935 Puerto Rico [GAZ:00006935] A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). + GAZ:00005286 Qatar [GAZ:00005286] An Arab emirate in Southwest Asia, occupying the small Qatar Peninsula on the northeasterly coast of the larger Arabian Peninsula. It is bordered by Saudi Arabia to the south; otherwise the Persian Gulf surrounds the state. Qatar is divided into ten municipalities (Arabic: baladiyah), which are further divided into zones (districts). + GAZ:00001088 Republic of the Congo [GAZ:00001088] A country in Central Africa. It is bordered by Gabon, Cameroon, the Central African Republic, the Democratic Republic of the Congo, the Angolan exclave province of Cabinda, and the Gulf of Guinea. The Republic of the Congo is divided into 10 regions (regions) and one commune, the capital Brazzaville. The regions are subdivided into forty-six districts. + GAZ:00003945 Reunion [GAZ:00003945] An island, located in the Indian Ocean east of Madagascar, about 200 km south west of Mauritius, the nearest island. + GAZ:00002951 Romania [GAZ:00002951] A country in Southeastern Europe. It shares a border with Hungary and Serbia to the west, Ukraine and the Republic of Moldova to the northeast, and Bulgaria to the south. Romania has a stretch of sea coast along the Black Sea. It is located roughly in the lower basin of the Danube and almost all of the Danube Delta is located within its territory. Romania is divided into forty-one counties (judete), as well as the municipality of Bucharest (Bucuresti) - which is its own administrative unit. The country is further subdivided into 319 cities and 2686 communes (rural localities). + GAZ:00023304 Ross Sea [GAZ:00023304] A large embayment of the Southern Ocean, extending deeply into Antarctica between Cape Adare, at 170degE, on the west and Cape Colbeck on the east, at 158degW. + GAZ:00002721 Russia [GAZ:00002721] A transcontinental country extending over much of northern Eurasia. Russia shares land borders with the following countries (counter-clockwise from northwest to southeast): Norway, Finland, Estonia, Latvia, Lithuania (Kaliningrad Oblast), Poland (Kaliningrad Oblast), Belarus, Ukraine, Georgia, Azerbaijan, Kazakhstan, China, Mongolia and North Korea. The Russian Federation comprises 83 federal subjectsm 46 oblasts(provinces), 21 republics, 9 krais (territories), 4 autonomous okrugs (autonomous districts), one autonomous oblast, and two federal cities. The federal subjects are grouped into seven federal districts. These subjects are divided into districts (raions), cities/towns and urban-type settlements, and, at level 4, selsovets (rural councils), towns and urban-type settlements under the jurisdiction of the district and city districts. + GAZ:00001087 Rwanda [GAZ:00001087] A small landlocked country in the Great Lakes region of east-central Africa, bordered by Uganda, Burundi, the Democratic Republic of the Congo and Tanzania. Rwanda is divided into five provinces (intara) and subdivided into thirty districts (akarere). The districts are divided into sectors (imirenge). + GAZ:00000849 Saint Helena [GAZ:00000849] An island of volcanic origin and a British overseas territory in the South Atlantic Ocean. + GAZ:00006906 Saint Kitts and Nevis [GAZ:00006906] A federal two-island nation in the West Indies. Located in the Leeward Islands. Saint Kitts and Nevis are geographically part of the Leeward Islands. To the north-northwest lie the islands of Saint Eustatius, Saba, Saint Barthelemy, and Saint-Martin/Sint Maarten. To the east and northeast are Antigua and Barbuda, and to the southeast is the small uninhabited island of Redonda, and the island of Montserrat. The federation of Saint Kitts and Nevis is divided into fourteen parishes: nine divisions on Saint Kitts and five on Nevis. + GAZ:00006909 Saint Lucia [GAZ:00006909] An island nation in the eastern Caribbean Sea on the boundary with the Atlantic Ocean. + GAZ:00003942 Saint Pierre and Miquelon [GAZ:00003942] An Overseas Collectivity of France located in a group of small islands in the North Atlantic Ocean, the main ones being Saint Pierre and Miquelon, 25 km off the coast of Newfoundland, Canada. Saint Pierre and Miquelon became an overseas department in 1976, but its status changed to that of an Overseas collectivity in 1985. + GAZ:00005841 Saint Martin [GAZ:00005841] An overseas collectivity of France that came into being on 2007-02-22, encompassing the northern parts of the island of Saint Martin and neighboring islets. The southern part of the island, Sint Maarten, is part of the Netherlands Antilles. Formerly, with Saint-Barthelemy, an arrondissement of Guadeloupe. + GAZ:02000565 Saint Vincent and the Grenadines [GAZ:02000565] An island nation in the Lesser Antilles chain of the Caribbean Sea. + GAZ:00006910 Samoa [GAZ:00006910] A country governing the western part of the Samoan Islands archipelago in the South Pacific Ocean. Samoa is made up of eleven itumalo (political districts). + GAZ:00003102 San Marino [GAZ:00003102] A country in the Apennine Mountains. It is a landlocked enclave, completely surrounded by Italy. San Marino is an enclave in Italy, on the border between the regioni of Emilia Romagna and Marche. Its topography is dominated by the Apennines mountain range. San Marino is divided into nine municipalities, known locally as Castelli (singular castello). + GAZ:00006927 Sao Tome and Principe [GAZ:00006927] An island nation in the Gulf of Guinea, off the western equatorial coast of Africa. It consists of two islands: Sao Tome and Principe, located about 140 km apart and about 250 and 225 km respectively, off of the northwestern coast of Gabon. Both islands are part of an extinct volcanic mountain range. Sao Tome and Principe is divided into 2 provinces: Principe, Sao Tome. The provinces are further divided into seven districts, six on Sao Tome and one on Principe (with Principe having self-government since 1995-04-29). + GAZ:00005279 Saudi Arabia [GAZ:00005279] A country on the Arabian Peninsula. It is bordered by Jordan on the northwest, Iraq on the north and northeast, Kuwait, Qatar, Bahrain, and the United Arab Emirates on the east, Oman on the southeast, and Yemen on the south. The Persian Gulf lies to the northeast and the Red Sea to its west. Saudi Arabia is divided into 13 provinces or regions (manatiq; singular mintaqah). Each is then divided into Governorates. + GAZ:00000913 Senegal [GAZ:00000913] A country south of the Senegal River in western Africa. Senegal is bounded by the Atlantic Ocean to the west, Mauritania to the north, Mali to the east, and Guinea and Guinea-Bissau to the south. The Gambia lies almost entirely within Senegal, surrounded on the north, east and south; from its western coast Gambia's territory follows the Gambia River more than 300 km inland. Dakar is the capital city of Senegal, located on the Cape Verde Peninsula on the country's Atlantic coast. Senegal is subdivided into 11 regions and further subdivided into 34 Departements, 103 Arrondissements (neither of which have administrative function) and by Collectivites Locales. + GAZ:00002957 Serbia [GAZ:00002957] A landlocked country in Central and Southeastern Europe, covering the southern part of the Pannonian Plain and the central part of the Balkan Peninsula. It is bordered by Hungary to the north; Romania and Bulgaria to the east; Republic of Macedonia, Montenegro to the south; Croatia and Bosnia and Herzegovina to the west. The capital is Belgrade. Serbia is divided into 29 districts plus the City of Belgrade. The districts and the city of Belgrade are further divided into municipalities. Serbia has two autonomous provinces: Kosovo and Metohija in the south (5 districts, 30 municipalities), and Vojvodina in the north (7 districts, 46 municipalities). + GAZ:00006922 Seychelles [GAZ:00006922] An archipelagic island country in the Indian Ocean at the eastern edge of the Somali Sea. It consists of 115 islands. + GAZ:00000914 Sierra Leone [GAZ:00000914] A country in West Africa. It is bordered by Guinea in the north and east, Liberia in the southeast, and the Atlantic Ocean in the southwest and west. The Republic of Sierra Leone is composed of 3 provinces and one area called the Western Area; the provinces are further divided into 12 districts. The Western Area is also divided into 2 districts. + GAZ:00003923 Singapore [GAZ:00003923] An island nation located at the southern tip of the Malay Peninsula. It lies 137 km north of the Equator, south of the Malaysian State of Johor and north of Indonesia's Riau Islands. Singapore consists of 63 islands, including mainland Singapore. There are two man-made connections to Johor, Malaysia, Johor-Singapore Causeway in the north, and Tuas Second Link in the west. Since 2001-11-24, Singapore has had an administrative subdivision into 5 districts. It is also divided into five Regions, urban planning subdivisions with no administrative role. + GAZ:00012579 Sint Maarten [GAZ:00012579] One of five island areas (Eilandgebieden) of the Netherlands Antilles, encompassing the southern half of the island of Saint Martin/Sint Maarten. + GAZ:00002956 Slovakia [GAZ:00002956] A landlocked country in Central Europe. The Slovak Republic borders the Czech Republic and Austria to the west, Poland to the north, Ukraine to the east and Hungary to the south. The largest city is its capital, Bratislava. Slovakia is subdivided into 8 kraje (singular - kraj, usually translated as regions. The kraje are subdivided into many okresy (singular okres, usually translated as districts). Slovakia currently has 79 districts. + GAZ:00002955 Slovenia [GAZ:00002955] A country in southern Central Europe bordering Italy to the west, the Adriatic Sea to the southwest, Croatia to the south and east, Hungary to the northeast, and Austria to the north. The capital of Slovenia is Ljubljana. As of 2005-05 Slovenia is divided into 12 statistical regions for legal and statistical purposes. Slovenia is divided into 210 local municipalities, eleven of which have urban status. + GAZ:00005275 Solomon Islands [GAZ:00005275] A nation in Melanesia, east of Papua New Guinea, consisting of nearly one thousand islands. Together they cover a land mass of 28,400 km2. The capital is Honiara, located on the island of Guadalcanal. + GAZ:00001104 Somalia [GAZ:00001104] A country located in the Horn of Africa. It is bordered by Djibouti to the northwest, Kenya on its southwest, the Gulf of Aden with Yemen on its north, the Indian Ocean at its east, and Ethiopia to the west. Prior to the civil war, Somalia was divided into eighteen regions (gobollada, singular gobol), which were in turn subdivided into districts. On a de facto basis, northern Somalia is now divided up among the quasi-independent states of Puntland, Somaliland, Galmudug and Maakhir. + GAZ:00001094 South Africa [GAZ:00001094] A country located at the southern tip of Africa. It borders the Atlantic and Indian oceans and Namibia, Botswana, Zimbabwe, Mozambique, Swaziland, and Lesotho, an independent enclave surrounded by South African territory. It is divided into nine provinces which are further subdivided into 52 districts: 6 metropolitan and 46 district municipalities. The 46 district municipalities are further subdivided into 231 local municipalities. The district municipalities also contain 20 district management areas (mostly game parks) that are directly governed by the district municipalities. The six metropolitan municipalities perform the functions of both district and local municipalities. + GAZ:00003990 South Georgia and the South Sandwich Islands [GAZ:00003990] A British overseas territory in the southern Atlantic Ocean. It iconsists of South Georgia and the Sandwich Islands, some 640 km to the SE. + GAZ:00002802 South Korea [GAZ:00002802] A republic in East Asia, occupying the southern half of the Korean Peninsula. South Korea is divided into 8 provinces (do), 1 special autonomous province (teukbyeol jachido), 6 metropolitan cities (gwangyeoksi), and 1 special city (teukbyeolsi). These are further subdivided into a variety of smaller entities, including cities (si), counties (gun), districts (gu), towns (eup), townships (myeon), neighborhoods (dong) and villages (ri). + GAZ:00233439 South Sudan [GAZ:00233439] A state located in Africa with Juba as its capital city. It's bordered by Ethiopia to the east, Kenya, Uganda, and the Democratic Republic of the Congo to the south, and the Central African Republic to the west and Sudan to the North. Southern Sudan includes the vast swamp region of the Sudd formed by the White Nile, locally called the Bahr el Jebel. + GAZ:00003936 Spain [GAZ:00003936] That part of the Kingdom of Spain that occupies the Iberian Peninsula plus the Balaeric Islands. The Spanish mainland is bordered to the south and east almost entirely by the Mediterranean Sea (except for a small land boundary with Gibraltar); to the north by France, Andorra, and the Bay of Biscay; and to the west by the Atlantic Ocean and Portugal. + GAZ:00010831 Spratly Islands [GAZ:00010831] A group of >100 islands located in the Southeastern Asian group of reefs and islands in the South China Sea, about two-thirds of the way from southern Vietnam to the southern Philippines. + GAZ:00003924 Sri Lanka [GAZ:00003924] An island nation in South Asia, located about 31 km off the southern coast of India. Sri Lanka is divided into 9 provinces and 25 districts. Districts are divided into Divisional Secretariats. + GAZ:00002475 State of Palestine [GAZ:00002475] The territory under the administration of the Palestine National Authority, as established by the Oslo Accords. The PNA divides the Palestinian territories into 16 governorates. + GAZ:00000560 Sudan [GAZ:00000560] A country in North Africa. It is bordered by Egypt to the north, the Red Sea to the northeast, Eritrea and Ethiopia to the east, Kenya and Uganda to the southeast, Democratic Republic of the Congo and the Central African Republic to the southwest, Chad to the west and Libya to the northwest. Sudan is divided into twenty-six states (wilayat, singular wilayah) which in turn are subdivided into 133 districts. + GAZ:00002525 Suriname [GAZ:00002525] A country in northern South America. It is situated between French Guiana to the east and Guyana to the west. The southern border is shared with Brazil and the northern border is the Atlantic coast. The southernmost border with French Guiana is disputed along the Marowijne river. Suriname is divided into 10 districts, each of which is divided into Ressorten. + GAZ:00005396 Svalbard [GAZ:00005396] An archipelago of continental islands lying in the Arctic Ocean north of mainland Europe, about midway between Norway and the North Pole. + GAZ:00001099 Swaziland [GAZ:00001099] A small, landlocked country in Africa embedded between South Africa in the west, north and south and Mozambique in the east. Swaziland is divided into four districts, each of which is divided into Tinkhundla (singular, Inkhundla). + GAZ:00002729 Sweden [GAZ:00002729] A Nordic country on the Scandinavian Peninsula in Northern Europe. It has borders with Norway (west and north) and Finland (northeast). Sweden is a unitary state, currently divided into twenty-one counties (lan). Each county further divides into a number of municipalities or kommuner, with a total of 290 municipalities in 2004. + GAZ:00002941 Switzerland [GAZ:00002941] A federal republic in Europe. Switzerland is bordered by Germany, France, Italy, Austria and Liechtenstein. The Swiss Confederation consists of 26 cantons. The Cantons comprise a total of 2,889 municipalities. Within Switzerland there are two enclaves: Busingen belongs to Germany, Campione d'Italia belongs to Italy. + GAZ:00002474 Syria [GAZ:00002474] A country in Southwest Asia, bordering Lebanon, the Mediterranean Sea and the island of Cyprus to the west, Israel to the southwest, Jordan to the south, Iraq to the east, and Turkey to the north. Syria has fourteen governorates, or muhafazat (singular: muhafazah). The governorates are divided into sixty districts, or manatiq (singular: mintaqah), which are further divided into sub-districts, or nawahi (singular: nahia). + GAZ:00005341 Taiwan [GAZ:00005341] A state in East Asia with de facto rule of the island of Tawain and adjacent territory. The Republic of China currently administers two historical provinces of China (one completely and a small part of another one) and centrally administers two direct-controlled municipalities. + GAZ:00006912 Tajikistan [GAZ:00006912] A mountainous landlocked country in Central Asia. Afghanistan borders to the south, Uzbekistan to the west, Kyrgyzstan to the north, and People's Republic of China to the east. Tajikistan consists of 4 administrative divisions. These are the provinces (viloyat) of Sughd and Khatlon, the autonomous province of Gorno-Badakhshan (abbreviated as GBAO), and the Region of Republican Subordination (RRP, Raiony Respublikanskogo Podchineniya in Russian; formerly known as Karotegin Province). Each region is divided into several districts (nohiya or raion). + GAZ:00001103 Tanzania [GAZ:00001103] A country in East Africa bordered by Kenya and Uganda on the north, Rwanda, Burundi and the Democratic Republic of the Congo on the west, and Zambia, Malawi and Mozambique on the south. To the east it borders the Indian Ocean. Tanzania is divided into 26 regions (mkoa), twenty-one on the mainland and five on Zanzibar (three on Unguja, two on Pemba). Ninety-eight districts (wilaya), each with at least one council, have been created to further increase local authority; the councils are also known as local government authorities. Currently there are 114 councils operating in 99 districts; 22 are urban and 92 are rural. The 22 urban units are further classified as city councils (Dar es Salaam and Mwanza), municipal councils (Arusha, Dodoma, Iringa, Kilimanjaro, Mbeya, Morogoro, Shinyanga, Tabora, and Tanga) or town councils (the remaining eleven communities). + GAZ:00003744 Thailand [GAZ:00003744] A country in Southeast Asia. To its east lie Laos and Cambodia; to its south, the Gulf of Thailand and Malaysia; and to its west, the Andaman Sea and Burma. Its capital and largest city is Bangkok. Thailand is divided into 75 provinces (changwat), which are gathered into 5 groups of provinces by location. There are also 2 special governed districts: the capital Bangkok (Krung Thep Maha Nakhon) and Pattaya, of which Bangkok is at provincial level and thus often counted as a 76th province. + GAZ:00006913 Timor-Leste [GAZ:00006913] A country in Southeast Asia. It comprises the eastern half of the island of Timor, the nearby islands of Atauro and Jaco, and Oecussi-Ambeno, an exclave on the northwestern side of the island, within Indonesian West Timor. The small country of 15,410 km2 is located about 640 km northwest of Darwin, Australia. East Timor is divided into thirteen administrative districts, are subdivided into 65 subdistricts, 443 sucos and 2,336 towns, villages and hamlets. + GAZ:00000915 Togo [GAZ:00000915] A country in West Africa bordering Ghana in the west, Benin in the east and Burkina Faso in the north. In the south, it has a short Gulf of Guinea coast, on which the capital Lome is located. + GAZ:00260188 Tokelau [GAZ:00260188] A dependent territory of New Zealand in the southern Pacific Ocean. It consists of three tropical coral atolls: Atafu, Nukunonu, and Fakaofo. They have a combined land area of 10 km2 (4 sq mi). + GAZ:00006916 Tonga [GAZ:00006916] A Polynesian country, and also an archipelago comprising 169 islands, of which 36 are inhabited. The archipelago's total surface area is about 750 square kilometres (290 sq mi) scattered over 700,000 square kilometres (270,000 sq mi) of the southern Pacific Ocean. + GAZ:00003767 Trinidad and Tobago [GAZ:00003767] An archipelagic state in the southern Caribbean, lying northeast of the South American nation of Venezuela and south of Grenada in the Lesser Antilles. It also shares maritime boundaries with Barbados to the northeast and Guyana to the southeast. The country covers an area of 5,128 km2and consists of two main islands, Trinidad and Tobago, and 21 smaller islands. + GAZ:00005812 Tromelin Island [GAZ:00005812] A low, flat 0.8 km2 island in the Indian Ocean, about 350 km east of Madagascar. Tromelin is a low, scrub-covered sandbank about 1,700 m long and 700 m wide, surrounded by coral reefs. The island is 7 m high at its highest point. + GAZ:00000562 Tunisia [GAZ:00000562] A country situated on the Mediterranean coast of North Africa. It is bordered by Algeria to the west and Libya to the southeast. Tunisia is subdivided into 24 governorates, divided into 262 "delegations" or "districts" (mutamadiyat), and further subdivided into municipalities (shaykhats). + GAZ:00000558 Turkey [GAZ:00000558] A Eurasian country that stretches across the Anatolian peninsula in western Asia and Thrace (Rumelia) in the Balkan region of southeastern Europe. Turkey borders eight countries: Bulgaria to the northwest; Greece to the west, Georgia to the northeast; Armenia, Azerbaijan (the exclave of Nakhichevan), and Iran to the east; and Iraq and Syria to the southeast. The Mediterranean Sea and Cyprus are to the south; the Aegean Sea and Archipelago are to the west; and the Black Sea is to the north. Separating Anatolia and Thrace are the Sea of Marmara and the Turkish Straits (the Bosporus and the Dardanelles), which are commonly reckoned to delineate the border between Asia and Europe, thereby making Turkey transcontinental. The territory of Turkey is subdivided into 81 provinces for administrative purposes. The provinces are organized into 7 regions for census purposes; however, they do not represent an administrative structure. Each province is divided into districts, for a total of 923 districts. + GAZ:00005018 Turkmenistan [GAZ:00005018] A country in Central Asia. It is bordered by Afghanistan to the southeast, Iran to the southwest, Uzbekistan to the northeast, Kazakhstan to the northwest, and the Caspian Sea to the west. It was a constituent republic of the Soviet Union, the Turkmen Soviet Socialist Republic. Turkmenistan is divided into five provinces or welayatlar (singular - welayat) and one independent city. + GAZ:00003955 Turks and Caicos Islands [GAZ:00003955] A British Overseas Territory consisting of two groups of tropical islands in the West Indies. The Turks and Caicos Islands are divided into six administrative districts (two in the Turks Islands and four in the Caicos Islands. + GAZ:00009715 Tuvalu [GAZ:00009715] A Polynesian island nation located in the Pacific Ocean midway between Hawaii and Australia. + GAZ:00002459 United States of America [GAZ:00002459] A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. + GAZ:00001102 Uganda [GAZ:00001102] A landlocked country in East Africa, bordered on the east by Kenya, the north by Sudan, on the west by the Democratic Republic of the Congo, on the southwest by Rwanda, and on the south by Tanzania. The southern part of the country includes a substantial portion of Lake Victoria, within which it shares borders with Kenya and Tanzania. Uganda is divided into 80 districts, spread across four administrative regions: Northern, Eastern, Central and Western. The districts are subdivided into counties. + GAZ:00002724 Ukraine [GAZ:00002724] A country in Eastern Europe. It borders Russia to the east, Belarus to the north, Poland, Slovakia and Hungary to the west, Romania and Moldova to the southwest, and the Black Sea and Sea of Azov to the south. Ukraine is subdivided into twenty-four oblasts (provinces) and one autonomous republic (avtonomna respublika), Crimea. Additionally, the cities of Kiev, the capital, and Sevastopol, both have a special legal status. The 24 oblasts and Crimea are subdivided into 490 raions (districts), or second-level administrative units. + GAZ:00005282 United Arab Emirates [GAZ:00005282] A Middle Eastern federation of seven states situated in the southeast of the Arabian Peninsula in Southwest Asia on the Persian Gulf, bordering Oman and Saudi Arabia. The seven states, termed emirates, are Abu Dhabi, Ajman, Dubai, Fujairah, Ras al-Khaimah, Sharjah, and Umm al-Quwain. + GAZ:00002637 United Kingdom [GAZ:00002637] A sovereign island country located off the northwestern coast of mainland Europe comprising of the four constituent countries; England, Scotland, Wales and Northern Ireland. It comprises the island of Great Britain, the northeast part of the island of Ireland and many small islands. Apart from Northern Ireland the UK is surrounded by the Atlantic Ocean, the North Sea, the English Channel and the Irish Sea. The largest island, Great Britain, is linked to France by the Channel Tunnel. + GAZ:00002930 Uruguay [GAZ:00002930] A country located in the southeastern part of South America. It is bordered by Brazil to the north, by Argentina across the bank of both the Uruguay River to the west and the estuary of Rio de la Plata to the southwest, and the South Atlantic Ocean to the southeast. Uraguay consists of 19 departments (departamentos, singular - departamento). + GAZ:00004979 Uzbekistan [GAZ:00004979] A doubly landlocked country in Central Asia, formerly part of the Soviet Union. It shares borders with Kazakhstan to the west and to the north, Kyrgyzstan and Tajikistan to the east, and Afghanistan and Turkmenistan to the south. Uzbekistan is divided into twelve provinces (viloyatlar) one autonomous republic (respublika and one independent city (shahar). + GAZ:00006918 Vanuatu [GAZ:00006918] An island country located in the South Pacific Ocean. The archipelago, which is of volcanic origin, is 1,750 kilometres (1,090 mi) east of northern Australia, 540 kilometres (340 mi) northeast of New Caledonia, east of New Guinea, southeast of the Solomon Islands, and west of Fiji. + GAZ:00002931 Venezuela [GAZ:00002931] A country on the northern coast of South America. The country comprises a continental mainland and numerous islands located off the Venezuelan coastline in the Caribbean Sea. The Bolivarian Republic of Venezuela possesses borders with Guyana to the east, Brazil to the south, and Colombia to the west. Trinidad and Tobago, Grenada, St. Lucia, Barbados, Curacao, Bonaire, Aruba, Saint Vincent and the Grenadines and the Leeward Antilles lie just north, off the Venezuelan coast. Venezuela is divided into twenty-three states (Estados), a capital district (distrito capital) corresponding to the city of Caracas, the Federal Dependencies (Dependencias Federales, a special territory), and Guayana Esequiba (claimed in a border dispute with Guyana). Venezuela is further subdivided into 335 municipalities (municipios); these are subdivided into over one thousand parishes (parroquias). + GAZ:00003756 Viet Nam [GAZ:00003756] The easternmost country on the Indochina Peninsula in Southeast Asia. It borders the Gulf of Thailand, Gulf of Tonkin, and South China Sea, alongside China, Laos, and Cambodia. + GAZ:00003959 Virgin Islands [GAZ:00003959] A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. + GAZ:00007111 Wake Island [GAZ:00007111] A coral atoll (despite its name) having a coastline of 19 km in the North Pacific Ocean, located about two-thirds of the way from Honolulu (3,700 km west) to Guam (2,430 km east). + GAZ:00007191 Wallis and Futuna [GAZ:00007191] A Polynesian French island territory (but not part of, or even contiguous with, French Polynesia) in the South Pacific between Fiji and Samoa. It is made up of three main volcanic tropical islands and a number of tiny islets. + GAZ:00009572 West Bank [GAZ:00009572] A landlocked territory near the Mediterranean coast of Western Asia, bordered by Jordan and the Dead Sea to the east and by Israel to the south, west and north.[2] Under Israeli occupation since 1967, the area is split into 167 Palestinian "islands" under partial Palestinian National Authority civil rule, and 230 Israeli settlements into which Israeli law is "pipelined". + GAZ:00000564 Western Sahara [GAZ:00000564] A territory of northwestern Africa, bordered by Morocco to the north, Algeria in the northeast, Mauritania to the east and south, and the Atlantic Ocean on the west. Western Sahara is administratively divided into four regions. + GAZ:00005284 Yemen [GAZ:00005284] A country located on the Arabian Peninsula in Southwest Asia. Yemen is bordered by Saudi Arabia to the North, the Red Sea to the West, the Arabian Sea and Gulf of Aden to the South, and Oman to the east. Yemen's territory includes over 200 islands, the largest of which is Socotra, about 415 km to the south of Yemen, off the coast of Somalia. As of 2004-02, Yemen is divided into twenty governorates (muhafazah) and one municipality. The population of each governorate is listed in the table below. The governorates of Yemen are divided into 333 districts (muderiah). The districts are subdivided into 2,210 sub-districts, and then into 38,284 villages (as of 2001). + GAZ:00001107 Zambia [GAZ:00001107] A landlocked country in Southern Africa. The neighbouring countries are the Democratic Republic of the Congo to the north, Tanzania to the north-east, Malawi to the east, Mozambique, Zimbabwe, Botswana, and Namibia to the south, and Angola to the west. The capital city is Lusaka. Zambia is divided into nine provinces. Each province is subdivided into several districts with a total of 73 districts. + GAZ:00001106 Zimbabwe [GAZ:00001106] A landlocked country in the southern part of the continent of Africa, between the Zambezi and Limpopo rivers. It is bordered by South Africa to the south, Botswana to the southwest, Zambia to the northwest, and Mozambique to the east. Zimbabwe is divided into eight provinces and two cities with provincial status. The provinces are subdivided into 59 districts and 1,200 municipalities. + \ No newline at end of file diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv new file mode 100644 index 00000000..d0a14efd --- /dev/null +++ b/web/templates/hpai/schema_slots.tsv @@ -0,0 +1,283 @@ +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_BIOSAMPLE_Enterics EXPORT_VirusSeq_Portal +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001122 Database Identifiers +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0001123 specimen_collector_sample_ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100752 specimen_collector_subsample_ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100996 pooled_sample_ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100760 sampling_site_ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0100761 sampling_event_ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0001136 BioProject_accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0001139 BioSample_accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMD00000001 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001150 Sample collection and processing +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100762 sample_collection_data_steward_name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101107 sample_collection_data_steward_contact_email sample_collection_data_steward_contact_email WhitespaceMinimizedString The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the "sample collector contact email". bloggsj@aglab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by WhitespaceMinimizedString null value menu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001181 geo_loc_name_(country) geo_loc_name_country geo_loc_name_(country) menu null value menu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada geo_loc_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001185 geo_loc_name_(state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString null value menu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape geo_loc_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100280 geo_loc_name_(county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001189 geo_loc_name_(city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100436 geo_loc_name_(site) geo_loc_name_site__ WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100309 geo_loc_latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100310 geo_loc_longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype influenza_subsubtype menu TRUE TRUE +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101109 influenza_subtyping_scheme_name influenza_subtyping_scheme_name influenza_subtyping_scheme_name menu +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process taxonomic_identification_process menu +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101110 virus_identifier virus_identifier WhitespaceMinimizedString +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101111 WHO/OIE/FAO_H5_clade who_oie_fao_h5_clade WhitespaceMinimizedString +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date null value menu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 collection_date +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date null value menu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time null value menu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time null value menu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day sample_collection_time_of_day menu null value menu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString null value menu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit sample_collection_duration_unit menu null value menu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date null value menu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date null value menu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +HPAI;HPAIHost Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] +HPAI;HPAIFood Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin +HPAI;HPAIFood Sample collection and processing GENEPIO:0100444 food_product food_product food_product menu null value menu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type +HPAI;HPAIFood Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties food_product_properties menu null value menu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source +HPAI;HPAIFood Sample collection and processing GENEPIO:0100447 food_packaging food_packaging food_packaging menu null value menu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap +HPAI;HPAIFood Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date +HPAI;HPAIFood Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 +HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001232 environmental_site environmental_site environmental_site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env +HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001223 environmental_material environmental_material environmental_material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material anatomical_material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001216 body_product body_product body_product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part anatomical_part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001234 collection_device collection_device collection_device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001241 collection_method collection_method collection_method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit sample_volume_measurement_unit menu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status residual_sample_status menu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling purpose_of_sampling menu null value menu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_sampling +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity presampling_activity menu null value menu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString null value menu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit sample_storage_duration_unit menu null value menu The units of a measured sample storage duration. Provide the units from the pick list. Day +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001253 specimen_processing specimen_processing specimen_processing menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101029 experimental_protocol experimental_protocol WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type experimental_specimen_role_type menu null value menu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101112 experimental_specimen_details experimental_specimen_details WhitespaceMinimizedString +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100690 available_data_types available_data_types available_data_types menu null value menu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria +HPAI;HPAIHost GENEPIO:0001268 Host information +HPAI;HPAIHost Host information GENEPIO:0001386 host_(common_name) host_common_name host (common name) menu null value menu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host +HPAI;HPAIHost Host information GENEPIO:0001387 host_(scientific_name) host_scientific_name host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host +HPAI;HPAIHost Host information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety +HPAI;HPAIHost Host information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed +HPAI;HPAIHost Host information GENEPIO:0100452 host_(food production name) host_food_production_name host (food production name) menu null value menu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host +HPAI;HPAIHost Host Information GENEPIO:0001392 host_age host_age decimal null value menu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +HPAI;HPAIHost Host Information GENEPIO:0001393 host_age_unit host_age_unit host_age_unit menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] +HPAI;HPAIHost Host information GENEPIO:0001394 host_age_bin host_age_bin host_age_bin menu null value menu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + host_gender host_gender +HPAI;HPAIHost Host information GENEPIO:0001391 host_disease host_disease host_disease menu null value menu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease +HPAI;HPAIHost Host Information GENEPIO:0001388 host_health_state host_health_state host_health_state menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state +HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_health_status_details host_health_status_details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] +HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome host_health_outcome menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome +HPAI;HPAIHost Host Information GENEPIO:0001398 host_subject_ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. BCxy123 host_subject_id +HPAI;HPAIHost Host Information GENEPIO:0100281 case_ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 +HPAI;HPAIHost Host Information GENEPIO:0001399 symptom_onset_date symptom_onset_date date null value menu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +HPAI;HPAIHost Host Information GENEPIO:0001400 signs_and_symptoms signs_and_symptoms signs_and_symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] +HPAI;HPAIHost Host Information GENEPIO:0001401 pre-existing_conditions_and_risk_factors preexisting_conditions_and_risk_factors pre-existing_conditions_and_risk_factors menu null value menu TRUE "Patient pre-existing conditions and risk factors. +Pre-existing condition: A medical condition that existed prior to the current infection. +Risk Factor: A variable associated with an increased risk of disease or infection." Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma [HP:0002099] +HPAI;HPAIHost Host Information GENEPIO:0001402 complications complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. Acute respiratory failure [MONDO:0001208] +HPAI;HPAIHost GENEPIO:0001409 Host exposure information +HPAI;HPAIHost Host exposure information GENEPIO:0001417 exposure event exposure_event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Social Gathering Additional location information Exposure Event PH_EXPOSURE +HPAI;HPAIHost Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level exposure contact level menu null value menu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct exposure contact level +HPAI;HPAIHost Host exposure information GENEPIO:0001419 host role host_role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Inpatient PH_HOST_ROLE +HPAI;HPAIHost Host exposure information GENEPIO:0001428 exposure setting exposure_setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting PH_EXPOSURE +HPAI;HPAIHost Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Case infected family at home PH_EXPOSURE_DETAILS +HPAI;HPAIHost GENEPIO:0001403 Host vaccination information +HPAI;HPAIHost Host vaccination information GENEPIO:0001404 host_vaccination_status host_vaccination_status host_vaccination_status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination +HPAI;HPAIHost Host vaccination information GENEPIO:0001406 number_of_vaccine_doses_received number_of_vaccine_doses_received integer 0 The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 +HPAI;HPAIHost Host vaccination information GENEPIO:0100313 vaccination_dose_1_vaccine_name vaccination_dose_1_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) +HPAI;HPAIHost Host vaccination information GENEPIO:0100314 vaccination_dose_1_vaccination_date vaccination_dose_1_vaccination_date date The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 +HPAI;HPAIHost Host vaccination information GENEPIO:0100315 vaccination_dose_2_vaccine_name vaccination_dose_2_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the second dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) +HPAI;HPAIHost Host vaccination information GENEPIO:0100316 vaccination_dose_2_vaccination_date vaccination_dose_2_vaccination_date date The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 +HPAI;HPAIHost Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated +HPAI;HPAIHost Host treatment information +HPAI;HPAIHost Host treatment information GENEPIO:0101113 influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration menu null value menu An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen. Influenza antiviral treatment administered [GENEPIO:0101194] +HPAI;HPAIHost Host treatment information GENEPIO:0101114 influenza_antiviral_agent influenza_antiviral_agent__ WhitespaceMinimizedString A substance that destroys or inhibits replication of viruses. +HPAI;HPAIHost Host treatment information GENEPIO:0101115 influenza_antiviral_treatment_date influenza_antiviral_treatment_date date The date on which the influenza antiviral agent was administered to a patient as part of treatment "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given. + +" +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100773 water_catchment_area_human_population_measurement_value water_catchment_area_human_population_measurement_value integer null value menu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100774 water_catchment_area_human_population_range water_catchment_area_human_population_range water catchment area human population range menu null value menu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100775 water_catchment_area_human_population_measurement_method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit water catchment area human population density unit menu null value menu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type populated area type menu null value menu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions sampling weather conditions menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions presampling weather conditions menu null value menu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString null value menu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units water_depth_units menu null value menu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units sediment_depth_units menu null value menu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units air_temperature_units menu null value menu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units water_temperature_units menu null value menu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type weather_type menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit precipitation measurement unit menu null value menu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit ambient temperature measurement unit menu null value menu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit total daily flow rate measurement unit menu null value menu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit instantaneous flow rate measurement unit menu null value menu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit turbidity measurement unit menu null value menu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100915 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit dissolved oxygen measurement unit menu null value menu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100917 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit oxygen reduction potential (ORP) measurement unit menu null value menu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit chemical oxygen demand (COD) measurement unit menu null value menu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit carbonaceous biochemical oxygen demand (CBOD) measurement unit menu null value menu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit total suspended solids (TSS) measurement unit menu null value menu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit total dissolved solids (TDS) measurement unit menu null value menu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit total solids (TS) measurement unit menu null value menu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit alkalinity measurement unit menu null value menu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit conductivity measurement unit menu null value menu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit salinity measurement unit menu null value menu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit total nitrogen (TN) measurement unit menu null value menu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit total phosphorus (TP) measurement unit menu null value menu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator_ fecal contamination indicator menu null value menu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit fecal contamination unit menu null value menu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit fecal coliform count unit menu null value menu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator urinary contamination indicator menu null value menu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit urinary contamination unit menu null value menu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection sample temperature unit (at collection) menu null value menu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received sample temperature unit (when received) menu null value menu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001441 Sequence information +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing__ purpose_of_sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001446 purpose_of_sequencing_details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by WhitespaceMinimizedString null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001165 sequence_submitter_contact_email sequence_submitter_contact_email WhitespaceMinimizedString null value menu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100843 DNA_fragment_length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100966 genomic_target_enrichment_method genomic_target_enrichment_method genomic_target_enrichment_method menu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100967 genomic_target_enrichment_method_details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001456 amplicon_pcr_primer_scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001449 amplicon_size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0101102 sequencing_flow_cell_version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001461 assembly_filename assembly_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001457 Bioinformatics and QC metrics +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination quality_control_determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues quality_control_issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0101082 Taxonomic identification information +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001506 Pathogen diagnostic testing +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101116 genetic target name genetic_target_name WhitespaceMinimizedString null value menu The name of the genetic marker used for testing. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101117 genetic target region genetic_target_region WhitespaceMinimizedString The specific region or segment of a genetic sequence used for testing or analysis. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101118 genetic target region reference genome genetic_target_region_reference_genome WhitespaceMinimizedString The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence diagnostic_target_presence diagnostic target presence menu null value menu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value diagnostic_measurement_value WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit diagnostic_measurement_unit diagnostic measurement unit menu null value menu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method diagnostic_measurement_method diagnostic measurement method menu null value menu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101104 diagnostic testing threshold value diagnostic_testing_threshold_value integer The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101105 diagnostic testing threshold units diagnostic_testing_threshold_units WhitespaceMinimizedString The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101106 diagnostic testing details diagnostic_testing_details WhitespaceMinimizedString Describe any details of the diagnsotic testing. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0100478 Risk assessment information +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production stage_of_production menu null value menu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention experimental_intervention menu null value menu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed + \ No newline at end of file diff --git a/web/templates/menu.json b/web/templates/menu.json index 5117e66f..735a7e07 100644 --- a/web/templates/menu.json +++ b/web/templates/menu.json @@ -83,5 +83,32 @@ "status": "published", "display": true } + }, + "hpai": { + "HPAI": { + "name": "HPAI", + "status": "published", + "display": true + }, + "HPAIFood": { + "name": "HPAIFood", + "status": "published", + "display": true + }, + "HPAIWW": { + "name": "HPAIWW", + "status": "published", + "display": true + }, + "HPAIEnviro": { + "name": "HPAIEnviro", + "status": "published", + "display": true + }, + "HPAIHost": { + "name": "HPAIHost", + "status": "published", + "display": true + } } } \ No newline at end of file From 66c504f1107f5422ff31cab091a750f2b50428fc Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 9 Oct 2024 01:19:27 -0700 Subject: [PATCH 51/96] New HPAI schema --- web/templates/hpai/schema.json | 1752 +++++++++++++-------------- web/templates/hpai/schema.yaml | 400 +++--- web/templates/hpai/schema_enums.tsv | 2 +- web/templates/hpai/schema_slots.tsv | 234 ++-- web/templates/menu.json | 8 +- 5 files changed, 1198 insertions(+), 1198 deletions(-) diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index ca465096..08b813be 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -296,8 +296,8 @@ } }, "enums": { - "NullValue": { - "name": "NullValue", + "NullValueMenu": { + "name": "NullValueMenu", "title": "null value", "from_schema": "https://example.com/hpai", "permissible_values": { @@ -8045,7 +8045,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8100,10 +8100,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name_(country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8137,7 +8137,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8290,10 +8290,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8309,7 +8309,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "influenza_subsubtype menu", + "range": "InfluenzaSubsubtypeMenu", "required": true, "multivalued": true }, @@ -8325,7 +8325,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "influenza_subtyping_scheme_name menu" + "range": "InfluenzaSubtypingSchemeNameMenu" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", @@ -8339,7 +8339,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, "virus_identifier": { "name": "virus_identifier", @@ -8399,7 +8399,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8428,7 +8428,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8457,7 +8457,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8486,7 +8486,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8511,10 +8511,10 @@ ], "any_of": [ { - "range": "sample_collection_time_of_day menu" + "range": "SampleCollectionTimeOfDayMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8543,7 +8543,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8569,10 +8569,10 @@ "recommended": true, "any_of": [ { - "range": "sample_collection_duration_unit menu" + "range": "SampleCollectionDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8602,7 +8602,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8632,7 +8632,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8656,10 +8656,10 @@ ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8686,10 +8686,10 @@ ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8727,10 +8727,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product menu" + "range": "FoodProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8764,10 +8764,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product_properties menu" + "range": "FoodProductPropertiesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8798,10 +8798,10 @@ "multivalued": true, "any_of": [ { - "range": "food_packaging menu" + "range": "FoodPackagingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8878,10 +8878,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8923,10 +8923,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8961,10 +8961,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8999,10 +8999,10 @@ "multivalued": true, "any_of": [ { - "range": "body_product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9033,10 +9033,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9070,10 +9070,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9106,10 +9106,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9157,7 +9157,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -9180,7 +9180,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "purpose_of_sampling": { "name": "purpose_of_sampling", @@ -9210,10 +9210,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9241,10 +9241,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9274,7 +9274,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9370,10 +9370,10 @@ ], "any_of": [ { - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9401,10 +9401,10 @@ "multivalued": true, "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9473,10 +9473,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9518,10 +9518,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9575,10 +9575,10 @@ "recommended": true, "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9611,10 +9611,10 @@ "recommended": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9688,10 +9688,10 @@ ], "any_of": [ { - "range": "host (food production name) menu" + "range": "HostFoodProductionNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9724,7 +9724,7 @@ "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9749,10 +9749,10 @@ "required": true, "any_of": [ { - "range": "host_age_unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9774,10 +9774,10 @@ ], "any_of": [ { - "range": "host_age_bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9804,10 +9804,10 @@ ], "any_of": [ { - "range": "host_disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9835,10 +9835,10 @@ ], "any_of": [ { - "range": "host_health_state menu" + "range": "HostHealthStateMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9862,10 +9862,10 @@ ], "any_of": [ { - "range": "host_health_status_details menu" + "range": "HostHealthStatusDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9892,10 +9892,10 @@ ], "any_of": [ { - "range": "host_health_outcome menu" + "range": "HostHealthOutcomeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9965,7 +9965,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -9990,10 +9990,10 @@ "recommended": true, "any_of": [ { - "range": "signs_and_symptoms menu" + "range": "SignsAndSymptomsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10018,10 +10018,10 @@ "recommended": true, "any_of": [ { - "range": "pre-existing_conditions_and_risk_factors menu" + "range": "PreexistingConditionsAndRiskFactorsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10046,10 +10046,10 @@ "recommended": true, "any_of": [ { - "range": "complications menu" + "range": "ComplicationsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10078,10 +10078,10 @@ ], "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10108,10 +10108,10 @@ ], "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10136,7 +10136,7 @@ "HPAI", "HPAIHost" ], - "range": "host role menu", + "range": "HostRoleMenu", "multivalued": true }, "exposure_setting": { @@ -10160,7 +10160,7 @@ "HPAI", "HPAIHost" ], - "range": "exposure setting menu", + "range": "ExposureSettingMenu", "multivalued": true }, "exposure_details": { @@ -10209,10 +10209,10 @@ ], "any_of": [ { - "range": "host_vaccination_status menu" + "range": "HostVaccinationStatusMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10366,10 +10366,10 @@ ], "any_of": [ { - "range": "influenza_antiviral_treatment_administration menu" + "range": "InfluenzaAntiviralTreatmentAdministrationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10425,7 +10425,7 @@ "range": "integer" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10450,10 +10450,10 @@ ], "any_of": [ { - "range": "water catchment area human population range menu" + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10520,10 +10520,10 @@ ], "any_of": [ { - "range": "water catchment area human population density unit menu" + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10551,7 +10551,7 @@ "range": "populated area type menu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10577,10 +10577,10 @@ "multivalued": true, "any_of": [ { - "range": "sampling weather conditions menu" + "range": "SamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10606,10 +10606,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling weather conditions menu" + "range": "PresamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10638,7 +10638,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10684,10 +10684,10 @@ ], "any_of": [ { - "range": "water_depth_units menu" + "range": "WaterDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10733,10 +10733,10 @@ ], "any_of": [ { - "range": "sediment_depth_units menu" + "range": "SedimentDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10782,10 +10782,10 @@ ], "any_of": [ { - "range": "air_temperature_units menu" + "range": "AirTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10831,10 +10831,10 @@ ], "any_of": [ { - "range": "water_temperature_units menu" + "range": "WaterTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10860,10 +10860,10 @@ "multivalued": true, "any_of": [ { - "range": "weather_type menu" + "range": "WeatherTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10889,10 +10889,10 @@ "recommended": true, "any_of": [ { - "range": "precipitation measurement unit menu" + "range": "PrecipitationMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -10959,10 +10959,10 @@ ], "any_of": [ { - "range": "ambient temperature measurement unit menu" + "range": "AmbientTemperatureMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11050,10 +11050,10 @@ ], "any_of": [ { - "range": "total daily flow rate measurement unit menu" + "range": "TotalDailyFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11120,10 +11120,10 @@ ], "any_of": [ { - "range": "instantaneous flow rate measurement unit menu" + "range": "InstantaneousFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11192,10 +11192,10 @@ "recommended": true, "any_of": [ { - "range": "turbidity measurement unit menu" + "range": "TurbidityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11262,10 +11262,10 @@ ], "any_of": [ { - "range": "dissolved oxygen measurement unit menu" + "range": "DissolvedOxygenMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11332,10 +11332,10 @@ ], "any_of": [ { - "range": "oxygen reduction potential (ORP) measurement unit menu" + "range": "OxygenReductionPotentialORPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11402,10 +11402,10 @@ ], "any_of": [ { - "range": "chemical oxygen demand (COD) measurement unit menu" + "range": "ChemicalOxygenDemandCODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11472,10 +11472,10 @@ ], "any_of": [ { - "range": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu" + "range": "CarbonaceousBiochemicalOxygenDemandCBODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11542,10 +11542,10 @@ ], "any_of": [ { - "range": "total suspended solids (TSS) measurement unit menu" + "range": "TotalSuspendedSolidsTSSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11612,10 +11612,10 @@ ], "any_of": [ { - "range": "total dissolved solids (TDS) measurement unit menu" + "range": "TotalDissolvedSolidsTDSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11682,10 +11682,10 @@ ], "any_of": [ { - "range": "total solids (TS) measurement unit menu" + "range": "TotalSolidsTSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11752,10 +11752,10 @@ ], "any_of": [ { - "range": "alkalinity measurement unit menu" + "range": "AlkalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11822,10 +11822,10 @@ ], "any_of": [ { - "range": "conductivity measurement unit menu" + "range": "ConductivityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11892,10 +11892,10 @@ ], "any_of": [ { - "range": "salinity measurement unit menu" + "range": "SalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -11962,10 +11962,10 @@ ], "any_of": [ { - "range": "total nitrogen (TN) measurement unit menu" + "range": "TotalNitrogenTNMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12032,10 +12032,10 @@ ], "any_of": [ { - "range": "total phosphorus (TP) measurement unit menu" + "range": "TotalPhosphorusTPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12082,10 +12082,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination indicator menu" + "range": "FecalContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12133,10 +12133,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination unit menu" + "range": "FecalContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12203,10 +12203,10 @@ ], "any_of": [ { - "range": "fecal coliform count unit menu" + "range": "FecalColiformCountUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12252,10 +12252,10 @@ ], "any_of": [ { - "range": "urinary contamination indicator menu" + "range": "UrinaryContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12301,10 +12301,10 @@ ], "any_of": [ { - "range": "urinary contamination unit menu" + "range": "UrinaryContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12371,10 +12371,10 @@ ], "any_of": [ { - "range": "sample temperature unit (at collection) menu" + "range": "SampleTemperatureUnitAtCollectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12420,10 +12420,10 @@ ], "any_of": [ { - "range": "sample temperature unit (when received) menu" + "range": "SampleTemperatureUnitWhenReceivedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12471,7 +12471,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "sequencing_date": { "name": "sequencing_date", @@ -12524,10 +12524,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12585,7 +12585,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12639,7 +12639,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12670,7 +12670,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12701,7 +12701,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12733,7 +12733,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12848,10 +12848,10 @@ ], "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12878,10 +12878,10 @@ ], "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -12952,7 +12952,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -13254,10 +13254,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13285,10 +13285,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13342,7 +13342,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13373,7 +13373,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13403,7 +13403,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13433,7 +13433,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13463,7 +13463,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -13493,7 +13493,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14098,7 +14098,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14155,10 +14155,10 @@ ], "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14208,10 +14208,10 @@ ], "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14238,10 +14238,10 @@ ], "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14362,10 +14362,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -14394,10 +14394,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16132,7 +16132,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16195,10 +16195,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name_(country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16236,7 +16236,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16413,10 +16413,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16436,7 +16436,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subsubtype menu", + "range": "InfluenzaSubsubtypeMenu", "required": true, "multivalued": true }, @@ -16456,7 +16456,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subtyping_scheme_name menu" + "range": "InfluenzaSubtypingSchemeNameMenu" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", @@ -16474,7 +16474,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, "virus_identifier": { "name": "virus_identifier", @@ -16546,7 +16546,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16579,7 +16579,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16612,7 +16612,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16645,7 +16645,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16674,10 +16674,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_collection_time_of_day menu" + "range": "SampleCollectionTimeOfDayMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16710,7 +16710,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16740,10 +16740,10 @@ "recommended": true, "any_of": [ { - "range": "sample_collection_duration_unit menu" + "range": "SampleCollectionDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16777,7 +16777,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16811,7 +16811,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16839,10 +16839,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16873,10 +16873,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16918,10 +16918,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product menu" + "range": "FoodProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16959,10 +16959,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product_properties menu" + "range": "FoodProductPropertiesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -16997,10 +16997,10 @@ "multivalued": true, "any_of": [ { - "range": "food_packaging menu" + "range": "FoodPackagingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17089,10 +17089,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17138,10 +17138,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17180,10 +17180,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17222,10 +17222,10 @@ "multivalued": true, "any_of": [ { - "range": "body_product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17260,10 +17260,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17301,10 +17301,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17341,10 +17341,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17400,7 +17400,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -17427,7 +17427,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "purpose_of_sampling": { "name": "purpose_of_sampling", @@ -17461,10 +17461,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17496,10 +17496,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17533,7 +17533,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17645,10 +17645,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17680,10 +17680,10 @@ "multivalued": true, "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17764,10 +17764,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17817,10 +17817,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17882,10 +17882,10 @@ "recommended": true, "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -17922,10 +17922,10 @@ "recommended": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18011,10 +18011,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host (food production name) menu" + "range": "HostFoodProductionNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18051,7 +18051,7 @@ "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18080,10 +18080,10 @@ "required": true, "any_of": [ { - "range": "host_age_unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18109,10 +18109,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host_age_bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18143,10 +18143,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host_disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18178,10 +18178,10 @@ "slot_group": "Host Information", "any_of": [ { - "range": "host_health_state menu" + "range": "HostHealthStateMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18209,10 +18209,10 @@ "slot_group": "Host Information", "any_of": [ { - "range": "host_health_status_details menu" + "range": "HostHealthStatusDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18243,10 +18243,10 @@ "slot_group": "Host Information", "any_of": [ { - "range": "host_health_outcome menu" + "range": "HostHealthOutcomeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18328,7 +18328,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18357,10 +18357,10 @@ "recommended": true, "any_of": [ { - "range": "signs_and_symptoms menu" + "range": "SignsAndSymptomsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18389,10 +18389,10 @@ "recommended": true, "any_of": [ { - "range": "pre-existing_conditions_and_risk_factors menu" + "range": "PreexistingConditionsAndRiskFactorsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18421,10 +18421,10 @@ "recommended": true, "any_of": [ { - "range": "complications menu" + "range": "ComplicationsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18457,10 +18457,10 @@ "slot_group": "Host exposure information", "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18491,10 +18491,10 @@ "slot_group": "Host exposure information", "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18523,7 +18523,7 @@ "HPAIHost" ], "slot_group": "Host exposure information", - "range": "host role menu", + "range": "HostRoleMenu", "multivalued": true }, "exposure_setting": { @@ -18551,7 +18551,7 @@ "HPAIHost" ], "slot_group": "Host exposure information", - "range": "exposure setting menu", + "range": "ExposureSettingMenu", "multivalued": true }, "exposure_details": { @@ -18608,10 +18608,10 @@ "slot_group": "Host vaccination information", "any_of": [ { - "range": "host_vaccination_status menu" + "range": "HostVaccinationStatusMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18793,10 +18793,10 @@ "slot_group": "Host treatment information", "any_of": [ { - "range": "influenza_antiviral_treatment_administration menu" + "range": "InfluenzaAntiviralTreatmentAdministrationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18864,7 +18864,7 @@ "range": "integer" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18893,10 +18893,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water catchment area human population range menu" + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -18975,10 +18975,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water catchment area human population density unit menu" + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19010,7 +19010,7 @@ "range": "populated area type menu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19040,10 +19040,10 @@ "multivalued": true, "any_of": [ { - "range": "sampling weather conditions menu" + "range": "SamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19073,10 +19073,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling weather conditions menu" + "range": "PresamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19109,7 +19109,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19163,10 +19163,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_depth_units menu" + "range": "WaterDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19220,10 +19220,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sediment_depth_units menu" + "range": "SedimentDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19277,10 +19277,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "air_temperature_units menu" + "range": "AirTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19334,10 +19334,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_temperature_units menu" + "range": "WaterTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19367,10 +19367,10 @@ "multivalued": true, "any_of": [ { - "range": "weather_type menu" + "range": "WeatherTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19400,10 +19400,10 @@ "recommended": true, "any_of": [ { - "range": "precipitation measurement unit menu" + "range": "PrecipitationMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19482,10 +19482,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "ambient temperature measurement unit menu" + "range": "AmbientTemperatureMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19589,10 +19589,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total daily flow rate measurement unit menu" + "range": "TotalDailyFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19671,10 +19671,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "instantaneous flow rate measurement unit menu" + "range": "InstantaneousFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19755,10 +19755,10 @@ "recommended": true, "any_of": [ { - "range": "turbidity measurement unit menu" + "range": "TurbidityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19837,10 +19837,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "dissolved oxygen measurement unit menu" + "range": "DissolvedOxygenMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -19919,10 +19919,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "oxygen reduction potential (ORP) measurement unit menu" + "range": "OxygenReductionPotentialORPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20001,10 +20001,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "chemical oxygen demand (COD) measurement unit menu" + "range": "ChemicalOxygenDemandCODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20083,10 +20083,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu" + "range": "CarbonaceousBiochemicalOxygenDemandCBODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20165,10 +20165,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total suspended solids (TSS) measurement unit menu" + "range": "TotalSuspendedSolidsTSSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20247,10 +20247,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total dissolved solids (TDS) measurement unit menu" + "range": "TotalDissolvedSolidsTDSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20329,10 +20329,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total solids (TS) measurement unit menu" + "range": "TotalSolidsTSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20411,10 +20411,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "alkalinity measurement unit menu" + "range": "AlkalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20493,10 +20493,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "conductivity measurement unit menu" + "range": "ConductivityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20575,10 +20575,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "salinity measurement unit menu" + "range": "SalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20657,10 +20657,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total nitrogen (TN) measurement unit menu" + "range": "TotalNitrogenTNMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20739,10 +20739,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total phosphorus (TP) measurement unit menu" + "range": "TotalPhosphorusTPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20797,10 +20797,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination indicator menu" + "range": "FecalContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20856,10 +20856,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination unit menu" + "range": "FecalContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20938,10 +20938,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "fecal coliform count unit menu" + "range": "FecalColiformCountUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -20995,10 +20995,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "urinary contamination indicator menu" + "range": "UrinaryContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21052,10 +21052,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "urinary contamination unit menu" + "range": "UrinaryContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21134,10 +21134,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sample temperature unit (at collection) menu" + "range": "SampleTemperatureUnitAtCollectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21191,10 +21191,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sample temperature unit (when received) menu" + "range": "SampleTemperatureUnitWhenReceivedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21250,7 +21250,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "sequencing_date": { "name": "sequencing_date", @@ -21311,10 +21311,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21380,7 +21380,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21442,7 +21442,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21477,7 +21477,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21512,7 +21512,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21548,7 +21548,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21683,10 +21683,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21717,10 +21717,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -21803,7 +21803,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -22157,10 +22157,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22192,10 +22192,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22257,7 +22257,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22292,7 +22292,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22326,7 +22326,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22360,7 +22360,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22394,7 +22394,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -22428,7 +22428,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23137,7 +23137,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23206,10 +23206,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23267,10 +23267,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23301,10 +23301,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23449,10 +23449,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -23485,10 +23485,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24587,7 +24587,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24650,10 +24650,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name_(country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24691,7 +24691,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24868,10 +24868,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -24891,7 +24891,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subsubtype menu", + "range": "InfluenzaSubsubtypeMenu", "required": true, "multivalued": true }, @@ -24911,7 +24911,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subtyping_scheme_name menu" + "range": "InfluenzaSubtypingSchemeNameMenu" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", @@ -24929,7 +24929,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, "virus_identifier": { "name": "virus_identifier", @@ -25001,7 +25001,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25035,7 +25035,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25069,7 +25069,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25100,10 +25100,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25145,10 +25145,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product menu" + "range": "FoodProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25186,10 +25186,10 @@ "multivalued": true, "any_of": [ { - "range": "food_product_properties menu" + "range": "FoodProductPropertiesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25224,10 +25224,10 @@ "multivalued": true, "any_of": [ { - "range": "food_packaging menu" + "range": "FoodPackagingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25316,10 +25316,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25365,10 +25365,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25406,10 +25406,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25446,10 +25446,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25505,7 +25505,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -25532,7 +25532,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "purpose_of_sampling": { "name": "purpose_of_sampling", @@ -25566,10 +25566,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25601,10 +25601,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25638,7 +25638,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25750,10 +25750,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25785,10 +25785,10 @@ "multivalued": true, "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25869,10 +25869,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -25922,10 +25922,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26008,7 +26008,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "sequencing_date": { "name": "sequencing_date", @@ -26069,10 +26069,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26138,7 +26138,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26200,7 +26200,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26235,7 +26235,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26270,7 +26270,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26306,7 +26306,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26441,10 +26441,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26475,10 +26475,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26561,7 +26561,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -26915,10 +26915,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -26950,10 +26950,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27015,7 +27015,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27050,7 +27050,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27084,7 +27084,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27118,7 +27118,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27152,7 +27152,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27186,7 +27186,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27895,7 +27895,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -27964,10 +27964,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28025,10 +28025,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28059,10 +28059,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28207,10 +28207,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -28243,10 +28243,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29765,7 +29765,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29828,10 +29828,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name_(country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -29869,7 +29869,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30046,10 +30046,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30069,7 +30069,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subsubtype menu", + "range": "InfluenzaSubsubtypeMenu", "required": true, "multivalued": true }, @@ -30089,7 +30089,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subtyping_scheme_name menu" + "range": "InfluenzaSubtypingSchemeNameMenu" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", @@ -30107,7 +30107,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, "virus_identifier": { "name": "virus_identifier", @@ -30179,7 +30179,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30212,7 +30212,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30245,7 +30245,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30278,7 +30278,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30307,10 +30307,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_collection_time_of_day menu" + "range": "SampleCollectionTimeOfDayMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30343,7 +30343,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30373,10 +30373,10 @@ "recommended": true, "any_of": [ { - "range": "sample_collection_duration_unit menu" + "range": "SampleCollectionDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30410,7 +30410,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30444,7 +30444,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30482,10 +30482,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30531,10 +30531,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30572,10 +30572,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30612,10 +30612,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30671,7 +30671,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -30698,7 +30698,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "purpose_of_sampling": { "name": "purpose_of_sampling", @@ -30732,10 +30732,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30767,10 +30767,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30804,7 +30804,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30916,10 +30916,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -30951,10 +30951,10 @@ "multivalued": true, "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31035,10 +31035,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31088,10 +31088,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31151,7 +31151,7 @@ "range": "integer" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31180,10 +31180,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water catchment area human population range menu" + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31262,10 +31262,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water catchment area human population density unit menu" + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31297,7 +31297,7 @@ "range": "populated area type menu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31327,10 +31327,10 @@ "multivalued": true, "any_of": [ { - "range": "sampling weather conditions menu" + "range": "SamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31360,10 +31360,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling weather conditions menu" + "range": "PresamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31396,7 +31396,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31450,10 +31450,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_depth_units menu" + "range": "WaterDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31507,10 +31507,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sediment_depth_units menu" + "range": "SedimentDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31564,10 +31564,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "air_temperature_units menu" + "range": "AirTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31621,10 +31621,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_temperature_units menu" + "range": "WaterTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31654,10 +31654,10 @@ "multivalued": true, "any_of": [ { - "range": "weather_type menu" + "range": "WeatherTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31687,10 +31687,10 @@ "recommended": true, "any_of": [ { - "range": "precipitation measurement unit menu" + "range": "PrecipitationMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31769,10 +31769,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "ambient temperature measurement unit menu" + "range": "AmbientTemperatureMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31876,10 +31876,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total daily flow rate measurement unit menu" + "range": "TotalDailyFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -31958,10 +31958,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "instantaneous flow rate measurement unit menu" + "range": "InstantaneousFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32042,10 +32042,10 @@ "recommended": true, "any_of": [ { - "range": "turbidity measurement unit menu" + "range": "TurbidityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32124,10 +32124,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "dissolved oxygen measurement unit menu" + "range": "DissolvedOxygenMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32206,10 +32206,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "oxygen reduction potential (ORP) measurement unit menu" + "range": "OxygenReductionPotentialORPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32288,10 +32288,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "chemical oxygen demand (COD) measurement unit menu" + "range": "ChemicalOxygenDemandCODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32370,10 +32370,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu" + "range": "CarbonaceousBiochemicalOxygenDemandCBODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32452,10 +32452,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total suspended solids (TSS) measurement unit menu" + "range": "TotalSuspendedSolidsTSSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32534,10 +32534,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total dissolved solids (TDS) measurement unit menu" + "range": "TotalDissolvedSolidsTDSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32616,10 +32616,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total solids (TS) measurement unit menu" + "range": "TotalSolidsTSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32698,10 +32698,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "alkalinity measurement unit menu" + "range": "AlkalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32780,10 +32780,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "conductivity measurement unit menu" + "range": "ConductivityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32862,10 +32862,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "salinity measurement unit menu" + "range": "SalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -32944,10 +32944,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total nitrogen (TN) measurement unit menu" + "range": "TotalNitrogenTNMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33026,10 +33026,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total phosphorus (TP) measurement unit menu" + "range": "TotalPhosphorusTPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33084,10 +33084,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination indicator menu" + "range": "FecalContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33143,10 +33143,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination unit menu" + "range": "FecalContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33225,10 +33225,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "fecal coliform count unit menu" + "range": "FecalColiformCountUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33282,10 +33282,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "urinary contamination indicator menu" + "range": "UrinaryContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33339,10 +33339,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "urinary contamination unit menu" + "range": "UrinaryContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33421,10 +33421,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sample temperature unit (at collection) menu" + "range": "SampleTemperatureUnitAtCollectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33478,10 +33478,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sample temperature unit (when received) menu" + "range": "SampleTemperatureUnitWhenReceivedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33537,7 +33537,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "sequencing_date": { "name": "sequencing_date", @@ -33598,10 +33598,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33667,7 +33667,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33729,7 +33729,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33764,7 +33764,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33799,7 +33799,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33835,7 +33835,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -33970,10 +33970,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34004,10 +34004,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34090,7 +34090,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -34444,10 +34444,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34479,10 +34479,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34544,7 +34544,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34579,7 +34579,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34613,7 +34613,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34647,7 +34647,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34681,7 +34681,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -34715,7 +34715,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35424,7 +35424,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35493,10 +35493,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35554,10 +35554,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35588,10 +35588,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35736,10 +35736,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -35772,10 +35772,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37294,7 +37294,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37357,10 +37357,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name_(country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37398,7 +37398,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37575,10 +37575,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37598,7 +37598,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subsubtype menu", + "range": "InfluenzaSubsubtypeMenu", "required": true, "multivalued": true }, @@ -37618,7 +37618,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subtyping_scheme_name menu" + "range": "InfluenzaSubtypingSchemeNameMenu" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", @@ -37636,7 +37636,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, "virus_identifier": { "name": "virus_identifier", @@ -37708,7 +37708,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37741,7 +37741,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37774,7 +37774,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37807,7 +37807,7 @@ "range": "time" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37836,10 +37836,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_collection_time_of_day menu" + "range": "SampleCollectionTimeOfDayMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37872,7 +37872,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37902,10 +37902,10 @@ "recommended": true, "any_of": [ { - "range": "sample_collection_duration_unit menu" + "range": "SampleCollectionDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37939,7 +37939,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -37973,7 +37973,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38011,10 +38011,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38060,10 +38060,10 @@ "multivalued": true, "any_of": [ { - "range": "environmental_material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38101,10 +38101,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38141,10 +38141,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38200,7 +38200,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -38227,7 +38227,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "purpose_of_sampling": { "name": "purpose_of_sampling", @@ -38261,10 +38261,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38296,10 +38296,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38333,7 +38333,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38445,10 +38445,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38480,10 +38480,10 @@ "multivalued": true, "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38564,10 +38564,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38617,10 +38617,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38680,7 +38680,7 @@ "range": "integer" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38709,10 +38709,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water catchment area human population range menu" + "range": "WaterCatchmentAreaHumanPopulationRangeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38791,10 +38791,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water catchment area human population density unit menu" + "range": "WaterCatchmentAreaHumanPopulationDensityUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38826,7 +38826,7 @@ "range": "populated area type menu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38856,10 +38856,10 @@ "multivalued": true, "any_of": [ { - "range": "sampling weather conditions menu" + "range": "SamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38889,10 +38889,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling weather conditions menu" + "range": "PresamplingWeatherConditionsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38925,7 +38925,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -38979,10 +38979,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_depth_units menu" + "range": "WaterDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39036,10 +39036,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sediment_depth_units menu" + "range": "SedimentDepthUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39093,10 +39093,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "air_temperature_units menu" + "range": "AirTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39150,10 +39150,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "water_temperature_units menu" + "range": "WaterTemperatureUnitsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39183,10 +39183,10 @@ "multivalued": true, "any_of": [ { - "range": "weather_type menu" + "range": "WeatherTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39216,10 +39216,10 @@ "recommended": true, "any_of": [ { - "range": "precipitation measurement unit menu" + "range": "PrecipitationMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39298,10 +39298,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "ambient temperature measurement unit menu" + "range": "AmbientTemperatureMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39405,10 +39405,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total daily flow rate measurement unit menu" + "range": "TotalDailyFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39487,10 +39487,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "instantaneous flow rate measurement unit menu" + "range": "InstantaneousFlowRateMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39571,10 +39571,10 @@ "recommended": true, "any_of": [ { - "range": "turbidity measurement unit menu" + "range": "TurbidityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39653,10 +39653,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "dissolved oxygen measurement unit menu" + "range": "DissolvedOxygenMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39735,10 +39735,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "oxygen reduction potential (ORP) measurement unit menu" + "range": "OxygenReductionPotentialORPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39817,10 +39817,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "chemical oxygen demand (COD) measurement unit menu" + "range": "ChemicalOxygenDemandCODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39899,10 +39899,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "carbonaceous biochemical oxygen demand (CBOD) measurement unit menu" + "range": "CarbonaceousBiochemicalOxygenDemandCBODMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -39981,10 +39981,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total suspended solids (TSS) measurement unit menu" + "range": "TotalSuspendedSolidsTSSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40063,10 +40063,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total dissolved solids (TDS) measurement unit menu" + "range": "TotalDissolvedSolidsTDSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40145,10 +40145,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total solids (TS) measurement unit menu" + "range": "TotalSolidsTSMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40227,10 +40227,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "alkalinity measurement unit menu" + "range": "AlkalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40309,10 +40309,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "conductivity measurement unit menu" + "range": "ConductivityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40391,10 +40391,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "salinity measurement unit menu" + "range": "SalinityMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40473,10 +40473,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total nitrogen (TN) measurement unit menu" + "range": "TotalNitrogenTNMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40555,10 +40555,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "total phosphorus (TP) measurement unit menu" + "range": "TotalPhosphorusTPMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40613,10 +40613,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination indicator menu" + "range": "FecalContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40672,10 +40672,10 @@ "recommended": true, "any_of": [ { - "range": "fecal contamination unit menu" + "range": "FecalContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40754,10 +40754,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "fecal coliform count unit menu" + "range": "FecalColiformCountUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40811,10 +40811,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "urinary contamination indicator menu" + "range": "UrinaryContaminationIndicatorMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40868,10 +40868,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "urinary contamination unit menu" + "range": "UrinaryContaminationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -40950,10 +40950,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sample temperature unit (at collection) menu" + "range": "SampleTemperatureUnitAtCollectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41007,10 +41007,10 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "sample temperature unit (when received) menu" + "range": "SampleTemperatureUnitWhenReceivedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41066,7 +41066,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "sequencing_date": { "name": "sequencing_date", @@ -41127,10 +41127,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41196,7 +41196,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41258,7 +41258,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41293,7 +41293,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41328,7 +41328,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41364,7 +41364,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41499,10 +41499,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41533,10 +41533,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -41619,7 +41619,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -41973,10 +41973,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42008,10 +42008,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42073,7 +42073,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42108,7 +42108,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42142,7 +42142,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42176,7 +42176,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42210,7 +42210,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42244,7 +42244,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -42953,7 +42953,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43022,10 +43022,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43083,10 +43083,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43117,10 +43117,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43265,10 +43265,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -43301,10 +43301,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44548,7 +44548,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44611,10 +44611,10 @@ "required": true, "any_of": [ { - "range": "geo_loc_name_(country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44652,7 +44652,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44829,10 +44829,10 @@ "multivalued": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44852,7 +44852,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subsubtype menu", + "range": "InfluenzaSubsubtypeMenu", "required": true, "multivalued": true }, @@ -44872,7 +44872,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "influenza_subtyping_scheme_name menu" + "range": "InfluenzaSubtypingSchemeNameMenu" }, "taxonomic_identification_process": { "name": "taxonomic_identification_process", @@ -44890,7 +44890,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "taxonomic_identification_process menu" + "range": "TaxonomicIdentificationProcessMenu" }, "virus_identifier": { "name": "virus_identifier", @@ -44962,7 +44962,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -44996,7 +44996,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45030,7 +45030,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45058,10 +45058,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45100,10 +45100,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45142,10 +45142,10 @@ "multivalued": true, "any_of": [ { - "range": "body_product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45180,10 +45180,10 @@ "multivalued": true, "any_of": [ { - "range": "anatomical_part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45221,10 +45221,10 @@ "recommended": true, "any_of": [ { - "range": "collection_device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45261,10 +45261,10 @@ "recommended": true, "any_of": [ { - "range": "collection_method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45320,7 +45320,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "sample_volume_measurement_unit menu" + "range": "SampleVolumeMeasurementUnitMenu" }, "residual_sample_status": { "name": "residual_sample_status", @@ -45347,7 +45347,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "residual_sample_status menu" + "range": "ResidualSampleStatusMenu" }, "purpose_of_sampling": { "name": "purpose_of_sampling", @@ -45381,10 +45381,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45416,10 +45416,10 @@ "multivalued": true, "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45453,7 +45453,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45565,10 +45565,10 @@ "slot_group": "Sample collection and processing", "any_of": [ { - "range": "sample_storage_duration_unit menu" + "range": "SampleStorageDurationUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45600,10 +45600,10 @@ "multivalued": true, "any_of": [ { - "range": "specimen_processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45684,10 +45684,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_specimen_role_type menu" + "range": "ExperimentalSpecimenRoleTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45737,10 +45737,10 @@ "multivalued": true, "any_of": [ { - "range": "available_data_types menu" + "range": "AvailableDataTypesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45802,10 +45802,10 @@ "recommended": true, "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45842,10 +45842,10 @@ "recommended": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45931,10 +45931,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host (food production name) menu" + "range": "HostFoodProductionNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -45971,7 +45971,7 @@ "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46000,10 +46000,10 @@ "required": true, "any_of": [ { - "range": "host_age_unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46029,10 +46029,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host_age_bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46063,10 +46063,10 @@ "slot_group": "Host information", "any_of": [ { - "range": "host_disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46098,10 +46098,10 @@ "slot_group": "Host Information", "any_of": [ { - "range": "host_health_state menu" + "range": "HostHealthStateMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46129,10 +46129,10 @@ "slot_group": "Host Information", "any_of": [ { - "range": "host_health_status_details menu" + "range": "HostHealthStatusDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46163,10 +46163,10 @@ "slot_group": "Host Information", "any_of": [ { - "range": "host_health_outcome menu" + "range": "HostHealthOutcomeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46248,7 +46248,7 @@ "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46277,10 +46277,10 @@ "recommended": true, "any_of": [ { - "range": "signs_and_symptoms menu" + "range": "SignsAndSymptomsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46309,10 +46309,10 @@ "recommended": true, "any_of": [ { - "range": "pre-existing_conditions_and_risk_factors menu" + "range": "PreexistingConditionsAndRiskFactorsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46341,10 +46341,10 @@ "recommended": true, "any_of": [ { - "range": "complications menu" + "range": "ComplicationsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46377,10 +46377,10 @@ "slot_group": "Host exposure information", "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46411,10 +46411,10 @@ "slot_group": "Host exposure information", "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46443,7 +46443,7 @@ "HPAIHost" ], "slot_group": "Host exposure information", - "range": "host role menu", + "range": "HostRoleMenu", "multivalued": true }, "exposure_setting": { @@ -46471,7 +46471,7 @@ "HPAIHost" ], "slot_group": "Host exposure information", - "range": "exposure setting menu", + "range": "ExposureSettingMenu", "multivalued": true }, "exposure_details": { @@ -46528,10 +46528,10 @@ "slot_group": "Host vaccination information", "any_of": [ { - "range": "host_vaccination_status menu" + "range": "HostVaccinationStatusMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46713,10 +46713,10 @@ "slot_group": "Host treatment information", "any_of": [ { - "range": "influenza_antiviral_treatment_administration menu" + "range": "InfluenzaAntiviralTreatmentAdministrationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46807,7 +46807,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "sequencing_assay_type menu" + "range": "SequencingAssayTypeMenu" }, "sequencing_date": { "name": "sequencing_date", @@ -46868,10 +46868,10 @@ "multivalued": true, "any_of": [ { - "range": "purpose_of_sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46937,7 +46937,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -46999,7 +46999,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47034,7 +47034,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47069,7 +47069,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47105,7 +47105,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47240,10 +47240,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_platform menu" + "range": "SequencingPlatformMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47274,10 +47274,10 @@ "slot_group": "Sequence information", "any_of": [ { - "range": "sequencing_instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47360,7 +47360,7 @@ "HPAIHost" ], "slot_group": "Sequence information", - "range": "genomic_target_enrichment_method menu" + "range": "GenomicTargetEnrichmentMethodMenu" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -47714,10 +47714,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_determination menu" + "range": "QualityControlDeterminationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47749,10 +47749,10 @@ "multivalued": true, "any_of": [ { - "range": "quality_control_issues menu" + "range": "QualityControlIssuesMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47814,7 +47814,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47849,7 +47849,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47883,7 +47883,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47917,7 +47917,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47951,7 +47951,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -47985,7 +47985,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48694,7 +48694,7 @@ "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48763,10 +48763,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic target presence menu" + "range": "DiagnosticTargetPresenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48824,10 +48824,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement unit menu" + "range": "DiagnosticMeasurementUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -48858,10 +48858,10 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "diagnostic measurement method menu" + "range": "DiagnosticMeasurementMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49006,10 +49006,10 @@ "recommended": true, "any_of": [ { - "range": "stage_of_production menu" + "range": "StageOfProductionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -49042,10 +49042,10 @@ "multivalued": true, "any_of": [ { - "range": "experimental_intervention menu" + "range": "ExperimentalInterventionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index 83dafead..3bfe72a4 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -4276,7 +4276,7 @@ slots: slot_uri: GENEPIO:0001153 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Public Health Agency of Canada @@ -4301,8 +4301,8 @@ slots: comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name_(country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true examples: - value: Canada @@ -4317,7 +4317,7 @@ slots: slot_uri: GENEPIO:0001185 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Western Cape @@ -4392,8 +4392,8 @@ slots: Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy.' slot_uri: GENEPIO:0001191 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -4404,19 +4404,19 @@ slots: name: influenza_subtype title: influenza_subtype slot_uri: GENEPIO:0101108 - range: influenza_subsubtype menu + range: InfluenzaSubsubtypeMenu multivalued: true required: true influenza_subtyping_scheme_name: name: influenza_subtyping_scheme_name title: influenza_subtyping_scheme_name slot_uri: GENEPIO:0101109 - range: influenza_subtyping_scheme_name menu + range: InfluenzaSubtypingSchemeNameMenu taxonomic_identification_process: name: taxonomic_identification_process title: taxonomic_identification_process slot_uri: GENEPIO:0100583 - range: taxonomic_identification_process menu + range: TaxonomicIdentificationProcessMenu virus_identifier: name: virus_identifier title: virus_identifier @@ -4439,7 +4439,7 @@ slots: slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu + - range: NullValueMenu required: true examples: - value: '2020-03-16' @@ -4454,7 +4454,7 @@ slots: slot_uri: GENEPIO:0101071 any_of: - range: date - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: '2020-03-18' @@ -4466,7 +4466,7 @@ slots: slot_uri: GENEPIO:0101072 any_of: - range: time - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 17:15 PST @@ -4478,7 +4478,7 @@ slots: slot_uri: GENEPIO:0101073 any_of: - range: time - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 19:15 PST @@ -4491,8 +4491,8 @@ slots: over the course of the day. slot_uri: GENEPIO:0100765 any_of: - - range: sample_collection_time_of_day menu - - range: null value menu + - range: SampleCollectionTimeOfDayMenu + - range: NullValueMenu examples: - value: Morning sample_collection_time_duration_value: @@ -4503,7 +4503,7 @@ slots: slot_uri: GENEPIO:0100766 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: '4' @@ -4514,8 +4514,8 @@ slots: comments: Provide the units from the pick list. slot_uri: GENEPIO:0100767 any_of: - - range: sample_collection_duration_unit menu - - range: null value menu + - range: SampleCollectionDurationUnitMenu + - range: NullValueMenu recommended: true examples: - value: Hour @@ -4527,7 +4527,7 @@ slots: slot_uri: GENEPIO:0001179 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-28' sample_processing_date: @@ -4540,7 +4540,7 @@ slots: slot_uri: GENEPIO:0100763 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-16' host_origin_geo_loc_name_country: @@ -4553,8 +4553,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100438 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: South Africa [GAZ:00001094] food_product_origin_geo_loc_name_country: @@ -4567,8 +4567,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100437 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: United States of America [GAZ:00002459] exact_mappings: @@ -4582,8 +4582,8 @@ slots: Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0100444 any_of: - - range: food_product menu - - range: null value menu + - range: FoodProductMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -4606,8 +4606,8 @@ slots: canned), and any information about a label claim (e.g. organic, fat-free). slot_uri: GENEPIO:0100445 any_of: - - range: food_product_properties menu - - range: null value menu + - range: FoodProductPropertiesMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4624,8 +4624,8 @@ slots: comments: If known, provide information regarding how the food product was packaged. slot_uri: GENEPIO:0100447 any_of: - - range: food_packaging menu - - range: null value menu + - range: FoodPackagingMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4670,8 +4670,8 @@ slots: separated by a semi-colon. slot_uri: GENEPIO:0001232 any_of: - - range: environmental_site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4691,8 +4691,8 @@ slots: separated by a semi-colon. slot_uri: GENEPIO:0001223 any_of: - - range: environmental_material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4714,8 +4714,8 @@ slots: the picklist provided. Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001211 any_of: - - range: anatomical_material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4737,8 +4737,8 @@ slots: can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001216 any_of: - - range: body_product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4758,8 +4758,8 @@ slots: the picklist provided. Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001214 any_of: - - range: anatomical_part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -4777,8 +4777,8 @@ slots: Multiple values can be provided, separated by a semi-colon. slot_uri: GENEPIO:0001234 any_of: - - range: collection_device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu recommended: true examples: - value: Drag swab [OBI:0002822] @@ -4796,8 +4796,8 @@ slots: separated by a semi-colon. slot_uri: GENEPIO:0001241 any_of: - - range: collection_method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu recommended: true examples: - value: Rinsing for specimen collection [GENEPIO_0002116] @@ -4820,7 +4820,7 @@ slots: description: The units of the volume measurement of the sample collected. comments: Provide the units from the pick list. slot_uri: GENEPIO:0100769 - range: sample_volume_measurement_unit menu + range: SampleVolumeMeasurementUnitMenu examples: - value: milliliter (mL) [UO:0000098] residual_sample_status: @@ -4832,7 +4832,7 @@ slots: used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". slot_uri: GENEPIO:0101090 - range: residual_sample_status menu + range: ResidualSampleStatusMenu examples: - value: No residual sample (sample all used) [GENEPIO:0101088] purpose_of_sampling: @@ -4847,8 +4847,8 @@ slots: of sequencing" field. slot_uri: GENEPIO:0001198 any_of: - - range: purpose_of_sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -4866,8 +4866,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100433 any_of: - - range: presampling_activity menu - - range: null value menu + - range: PresamplingActivityMenu + - range: NullValueMenu multivalued: true examples: - value: Agricultural activity @@ -4880,7 +4880,7 @@ slots: slot_uri: GENEPIO:0100434 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: Agricultural waste from large farm contributes waste to the site sampled. sample_storage_method: @@ -4924,8 +4924,8 @@ slots: comments: Provide the units from the pick list. slot_uri: GENEPIO:0101015 any_of: - - range: sample_storage_duration_unit menu - - range: null value menu + - range: SampleStorageDurationUnitMenu + - range: NullValueMenu examples: - value: Day specimen_processing: @@ -4936,8 +4936,8 @@ slots: comments: Select processes from the picklist that were applied to this sample. slot_uri: GENEPIO:0001253 any_of: - - range: specimen_processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true examples: - value: Centrifugation @@ -4973,8 +4973,8 @@ slots: a control, leave blank or select "Not Applicable". slot_uri: GENEPIO:0100921 any_of: - - range: experimental_specimen_role_type menu - - range: null value menu + - range: ExperimentalSpecimenRoleTypeMenu + - range: NullValueMenu multivalued: true examples: - value: Positive experimental control @@ -4995,8 +4995,8 @@ slots: data provider for more information. slot_uri: GENEPIO:0100690 any_of: - - range: available_data_types menu - - range: null value menu + - range: AvailableDataTypesMenu + - range: NullValueMenu multivalued: true examples: - value: Total coliform count [GENEPIO:0100729] @@ -5020,8 +5020,8 @@ slots: provide the common name. slot_uri: GENEPIO:0001386 any_of: - - range: host (common name) menu - - range: null value menu + - range: HostCommonNameMenu + - range: NullValueMenu recommended: true examples: - value: Cow [NCBITaxon:9913] @@ -5037,8 +5037,8 @@ slots: select the scientific name from the picklist provided. slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu + - range: HostScientificNameMenu + - range: NullValueMenu recommended: true examples: - value: Bos taurus [NCBITaxon:9913] @@ -5082,8 +5082,8 @@ slots: comments: Select the host's food production name from the pick list. slot_uri: GENEPIO:0100452 any_of: - - range: host (food production name) menu - - range: null value menu + - range: HostFoodProductionNameMenu + - range: NullValueMenu examples: - value: Calf [FOODON:03411349] exact_mappings: @@ -5096,7 +5096,7 @@ slots: slot_uri: GENEPIO:0001392 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu maximum_value: 130 required: true examples: @@ -5112,8 +5112,8 @@ slots: the pick list. slot_uri: GENEPIO:0001393 any_of: - - range: host_age_unit menu - - range: null value menu + - range: HostAgeUnitMenu + - range: NullValueMenu required: true examples: - value: year [UO:0000036] @@ -5125,8 +5125,8 @@ slots: the template. If not available, provide a null value or leave blank. slot_uri: GENEPIO:0001394 any_of: - - range: host_age_bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu exact_mappings: - BIOSAMPLE_Enterics:host_age host_disease: @@ -5139,8 +5139,8 @@ slots: \ If the disease is not known, put \u201Cmissing\u201D." slot_uri: GENEPIO:0001391 any_of: - - range: host_disease menu - - range: null value menu + - range: HostDiseaseMenu + - range: NullValueMenu examples: - value: mastitis, gastroenteritis exact_mappings: @@ -5152,8 +5152,8 @@ slots: comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001388 any_of: - - range: host_health_state menu - - range: null value menu + - range: HostHealthStateMenu + - range: NullValueMenu examples: - value: Asymptomatic [NCIT:C3833] exact_mappings: @@ -5167,8 +5167,8 @@ slots: comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001389 any_of: - - range: host_health_status_details menu - - range: null value menu + - range: HostHealthStatusDetailsMenu + - range: NullValueMenu examples: - value: Hospitalized (ICU) [GENEPIO:0100046] host_health_outcome: @@ -5178,8 +5178,8 @@ slots: comments: If known, select a value from the pick list. slot_uri: GENEPIO:0001390 any_of: - - range: host_health_outcome menu - - range: null value menu + - range: HostHealthOutcomeMenu + - range: NullValueMenu examples: - value: Recovered [NCIT:C49498] exact_mappings: @@ -5218,7 +5218,7 @@ slots: slot_uri: GENEPIO:0001399 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-16' signs_and_symptoms: @@ -5229,8 +5229,8 @@ slots: comments: Select all of the symptoms experienced by the host from the pick list. slot_uri: GENEPIO:0001400 any_of: - - range: signs_and_symptoms menu - - range: null value menu + - range: SignsAndSymptomsMenu + - range: NullValueMenu recommended: true examples: - value: Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] @@ -5248,8 +5248,8 @@ slots: curation team. slot_uri: GENEPIO:0001401 any_of: - - range: pre-existing_conditions_and_risk_factors menu - - range: null value menu + - range: PreexistingConditionsAndRiskFactorsMenu + - range: NullValueMenu recommended: true examples: - value: Asthma [HP:0002099] @@ -5262,8 +5262,8 @@ slots: list. slot_uri: GENEPIO:0001402 any_of: - - range: complications menu - - range: null value menu + - range: ComplicationsMenu + - range: NullValueMenu recommended: true examples: - value: Acute respiratory failure [MONDO:0001208] @@ -5275,8 +5275,8 @@ slots: If the desired term is missing, contact the curation team. slot_uri: GENEPIO:0001417 any_of: - - range: exposure event menu - - range: null value menu + - range: ExposureEventMenu + - range: NullValueMenu examples: - value: Social Gathering exact_mappings: @@ -5290,8 +5290,8 @@ slots: comments: Select direct or indirect exposure from the pick-list. slot_uri: GENEPIO:0001418 any_of: - - range: exposure contact level menu - - range: null value menu + - range: ExposureContactLevelMenu + - range: NullValueMenu examples: - value: Direct exact_mappings: @@ -5303,7 +5303,7 @@ slots: comments: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. slot_uri: GENEPIO:0001419 - range: host role menu + range: HostRoleMenu multivalued: true examples: - value: Inpatient @@ -5316,7 +5316,7 @@ slots: comments: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. slot_uri: GENEPIO:0001428 - range: exposure setting menu + range: ExposureSettingMenu multivalued: true examples: - value: Healthcare Setting @@ -5341,8 +5341,8 @@ slots: comments: Select the vaccination status of the host from the pick list. slot_uri: GENEPIO:0001404 any_of: - - range: host_vaccination_status menu - - range: null value menu + - range: HostVaccinationStatusMenu + - range: NullValueMenu examples: - value: Fully Vaccinated [GENEPIO:0100100] exact_mappings: @@ -5423,8 +5423,8 @@ slots: patient as part of a treatment regimen. slot_uri: GENEPIO:0101113 any_of: - - range: influenza_antiviral_treatment_administration menu - - range: null value menu + - range: InfluenzaAntiviralTreatmentAdministrationMenu + - range: NullValueMenu examples: - value: Influenza antiviral treatment administered [GENEPIO:0101194] influenza_antiviral_agent__: @@ -5453,7 +5453,7 @@ slots: slot_uri: GENEPIO:0100773 any_of: - range: integer - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 10,500 @@ -5466,8 +5466,8 @@ slots: of population size by selecting a value from the picklist. slot_uri: GENEPIO:0100774 any_of: - - range: water catchment area human population range menu - - range: null value menu + - range: WaterCatchmentAreaHumanPopulationRangeMenu + - range: NullValueMenu examples: - value: 1,000 - 10,000 people water_catchment_area_human_population_measurement_method: @@ -5500,8 +5500,8 @@ slots: comments: Provide the unit of the population density in the catchement area. slot_uri: GENEPIO:0100777 any_of: - - range: water catchment area human population density unit menu - - range: null value menu + - range: WaterCatchmentAreaHumanPopulationDensityUnitMenu + - range: NullValueMenu examples: - value: persons per Km^2 populated_area_type: @@ -5512,7 +5512,7 @@ slots: slot_uri: GENEPIO:0100778 any_of: - range: populated area type menu - - range: null value menu + - range: NullValueMenu examples: - value: Urban area sampling_weather_conditions: @@ -5523,8 +5523,8 @@ slots: comments: Provide the weather conditions at the time of sample collection. slot_uri: GENEPIO:0100779 any_of: - - range: sampling weather conditions menu - - range: null value menu + - range: SamplingWeatherConditionsMenu + - range: NullValueMenu multivalued: true examples: - value: Rain @@ -5535,8 +5535,8 @@ slots: comments: Provide the weather conditions prior to sample collection. slot_uri: GENEPIO:0100780 any_of: - - range: presampling weather conditions menu - - range: null value menu + - range: PresamplingWeatherConditionsMenu + - range: NullValueMenu multivalued: true examples: - value: Drizzle @@ -5549,7 +5549,7 @@ slots: slot_uri: GENEPIO:0100911 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: '12' @@ -5569,8 +5569,8 @@ slots: comments: Provide the units of measurement for which the depth was recorded. slot_uri: GENEPIO:0101025 any_of: - - range: water_depth_units menu - - range: null value menu + - range: WaterDepthUnitsMenu + - range: NullValueMenu examples: - value: meter (m) [UO:0000008] sediment_depth: @@ -5589,8 +5589,8 @@ slots: comments: Provide the units of measurement for which the depth was recorded. slot_uri: GENEPIO:0101026 any_of: - - range: sediment_depth_units menu - - range: null value menu + - range: SedimentDepthUnitsMenu + - range: NullValueMenu examples: - value: meter (m) [UO:0000008] air_temperature: @@ -5610,8 +5610,8 @@ slots: comments: Provide the units of measurement for which the temperature was recorded. slot_uri: GENEPIO:0101027 any_of: - - range: air_temperature_units menu - - range: null value menu + - range: AirTemperatureUnitsMenu + - range: NullValueMenu examples: - value: degree Celsius (C) [UO:0000027] water_temperature: @@ -5631,8 +5631,8 @@ slots: comments: Provide the units of measurement for which the temperature was recorded. slot_uri: GENEPIO:0101028 any_of: - - range: water_temperature_units menu - - range: null value menu + - range: WaterTemperatureUnitsMenu + - range: NullValueMenu examples: - value: degree Celsius (C) [UO:0000027] weather_type: @@ -5643,8 +5643,8 @@ slots: comments: Provide the weather conditions at the time of sample collection. slot_uri: GENEPIO:0100442 any_of: - - range: weather_type menu - - range: null value menu + - range: WeatherTypeMenu + - range: NullValueMenu multivalued: true examples: - value: Rain [ENVO:01001564] @@ -5657,8 +5657,8 @@ slots: list. slot_uri: GENEPIO:0100912 any_of: - - range: precipitation measurement unit menu - - range: null value menu + - range: PrecipitationMeasurementUnitMenu + - range: NullValueMenu recommended: true examples: - value: inch @@ -5688,8 +5688,8 @@ slots: comments: Provide the units of the measured temperature. slot_uri: GENEPIO:0100936 any_of: - - range: ambient temperature measurement unit menu - - range: null value menu + - range: AmbientTemperatureMeasurementUnitMenu + - range: NullValueMenu examples: - value: degree Celsius (C) ph_measurement_value: @@ -5729,8 +5729,8 @@ slots: the pick list. slot_uri: GENEPIO:0100906 any_of: - - range: total daily flow rate measurement unit menu - - range: null value menu + - range: TotalDailyFlowRateMeasurementUnitMenu + - range: NullValueMenu examples: - value: million gallons per day (MGD) total_daily_flow_rate_measurement_method: @@ -5760,8 +5760,8 @@ slots: the pick list. slot_uri: GENEPIO:0100909 any_of: - - range: instantaneous flow rate measurement unit menu - - range: null value menu + - range: InstantaneousFlowRateMeasurementUnitMenu + - range: NullValueMenu examples: - value: cubic meter per hour (m^3/h) instantaneous_flow_rate_measurement_method: @@ -5792,8 +5792,8 @@ slots: the pick list. slot_uri: GENEPIO:0100914 any_of: - - range: turbidity measurement unit menu - - range: null value menu + - range: TurbidityMeasurementUnitMenu + - range: NullValueMenu recommended: true examples: - value: nephelometric turbidity unit (NTU) @@ -5823,8 +5823,8 @@ slots: from the pick list. slot_uri: GENEPIO:0100784 any_of: - - range: dissolved oxygen measurement unit menu - - range: null value menu + - range: DissolvedOxygenMeasurementUnitMenu + - range: NullValueMenu examples: - value: part per million (ppm) dissolved_oxygen_measurement_method: @@ -5855,8 +5855,8 @@ slots: a value from the pick list. slot_uri: GENEPIO:0100786 any_of: - - range: oxygen reduction potential (ORP) measurement unit menu - - range: null value menu + - range: OxygenReductionPotentialORPMeasurementUnitMenu + - range: NullValueMenu examples: - value: milliVolt (mV) oxygen_reduction_potential_orp_measurement_method: @@ -5886,8 +5886,8 @@ slots: comments: Provide the units of the COD test result. slot_uri: GENEPIO:0100789 any_of: - - range: chemical oxygen demand (COD) measurement unit menu - - range: null value menu + - range: ChemicalOxygenDemandCODMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter (mg/L) chemical_oxygen_demand_cod_measurement_method: @@ -5918,8 +5918,8 @@ slots: pick list. slot_uri: GENEPIO:0100792 any_of: - - range: carbonaceous biochemical oxygen demand (CBOD) measurement unit menu - - range: null value menu + - range: CarbonaceousBiochemicalOxygenDemandCBODMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter (mg/L) carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: @@ -5949,8 +5949,8 @@ slots: comments: Provide the units of the measured TSS. slot_uri: GENEPIO:0100795 any_of: - - range: total suspended solids (TSS) measurement unit menu - - range: null value menu + - range: TotalSuspendedSolidsTSSMeasurementUnitMenu + - range: NullValueMenu examples: - value: percent (%) total_suspended_solids_tss_measurement_method: @@ -5980,8 +5980,8 @@ slots: comments: Provide the units of the measured TDS. slot_uri: GENEPIO:0100798 any_of: - - range: total dissolved solids (TDS) measurement unit menu - - range: null value menu + - range: TotalDissolvedSolidsTDSMeasurementUnitMenu + - range: NullValueMenu examples: - value: percent (%) total_dissolved_solids_tds_measurement_method: @@ -6009,8 +6009,8 @@ slots: comments: Provide the units of the measured TS. slot_uri: GENEPIO:0100801 any_of: - - range: total solids (TS) measurement unit menu - - range: null value menu + - range: TotalSolidsTSMeasurementUnitMenu + - range: NullValueMenu examples: - value: percent (%) total_solids_ts_measurement_method: @@ -6038,8 +6038,8 @@ slots: comments: Provide the units of the measured alkalinity. slot_uri: GENEPIO:0100879 any_of: - - range: alkalinity measurement unit menu - - range: null value menu + - range: AlkalinityMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter of calcium carbonate (mg/L CaCO3) alkalinity_measurement_method: @@ -6067,8 +6067,8 @@ slots: comments: Provide the units of the measured conductivity. slot_uri: GENEPIO:0100803 any_of: - - range: conductivity measurement unit menu - - range: null value menu + - range: ConductivityMeasurementUnitMenu + - range: NullValueMenu examples: - value: "microSiemen per centimeter (\u03BCS/cm)" conductivity_measurement_method: @@ -6096,8 +6096,8 @@ slots: comments: Provide the units of the measured salinity. slot_uri: GENEPIO:0100806 any_of: - - range: salinity measurement unit menu - - range: null value menu + - range: SalinityMeasurementUnitMenu + - range: NullValueMenu examples: - value: practical salinity unit (PSU) salinity_measurement_method: @@ -6125,8 +6125,8 @@ slots: comments: Provide the units of the measured TN. slot_uri: GENEPIO:0100809 any_of: - - range: total nitrogen (TN) measurement unit menu - - range: null value menu + - range: TotalNitrogenTNMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligram per liter (mg/L) total_nitrogen_tn_measurement_method: @@ -6154,8 +6154,8 @@ slots: comments: Provide the units of the measured TP. slot_uri: GENEPIO:0100812 any_of: - - range: total phosphorus (TP) measurement unit menu - - range: null value menu + - range: TotalPhosphorusTPMeasurementUnitMenu + - range: NullValueMenu examples: - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) total_phosphorus_tp_measurement_method: @@ -6176,8 +6176,8 @@ slots: picklist. slot_uri: GENEPIO:0100814 any_of: - - range: fecal contamination indicator menu - - range: null value menu + - range: FecalContaminationIndicatorMenu + - range: NullValueMenu recommended: true examples: - value: crAssphage @@ -6198,8 +6198,8 @@ slots: comments: Provide the units of the measured fecal contamination. slot_uri: GENEPIO:0100816 any_of: - - range: fecal contamination unit menu - - range: null value menu + - range: FecalContaminationUnitMenu + - range: NullValueMenu recommended: true examples: - value: cycle threshold (Ct) / quantification cycle (Cq) @@ -6230,8 +6230,8 @@ slots: comments: Provide the units of the measured fecal coliforms. slot_uri: GENEPIO:0100819 any_of: - - range: fecal coliform count unit menu - - range: null value menu + - range: FecalColiformCountUnitMenu + - range: NullValueMenu examples: - value: most probable number per milliliter (MPN/mL) fecal_coliform_count_method: @@ -6253,8 +6253,8 @@ slots: picklist. slot_uri: GENEPIO:0100837 any_of: - - range: urinary contamination indicator menu - - range: null value menu + - range: UrinaryContaminationIndicatorMenu + - range: NullValueMenu examples: - value: urobilin urinary_contamination_value: @@ -6273,8 +6273,8 @@ slots: comments: Provide the units of the measured urinary contamination. slot_uri: GENEPIO:0100839 any_of: - - range: urinary contamination unit menu - - range: null value menu + - range: UrinaryContaminationUnitMenu + - range: NullValueMenu examples: - value: nanograms per liter urinary_contamination_method: @@ -6305,8 +6305,8 @@ slots: comments: Provide the units of the measured temperature. slot_uri: GENEPIO:0100822 any_of: - - range: sample temperature unit (at collection) menu - - range: null value menu + - range: SampleTemperatureUnitAtCollectionMenu + - range: NullValueMenu examples: - value: degree Celsius (C) sample_temperature_value_when_received: @@ -6327,8 +6327,8 @@ slots: comments: Provide the units of the measured temperature. slot_uri: GENEPIO:0100824 any_of: - - range: sample temperature unit (when received) menu - - range: null value menu + - range: SampleTemperatureUnitWhenReceivedMenu + - range: NullValueMenu examples: - value: degree Celsius (C) library_id: @@ -6351,7 +6351,7 @@ slots: used in your study. If unsure refer to the protocol documentation, or provide a null value.' slot_uri: GENEPIO:0100997 - range: sequencing_assay_type menu + range: SequencingAssayTypeMenu examples: - value: whole genome sequencing assay [OBI:0002117] sequencing_date: @@ -6376,8 +6376,8 @@ slots: sample collection should be indicated in the "purpose of sampling" field. slot_uri: GENEPIO:0001445 any_of: - - range: purpose_of_sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -6409,7 +6409,7 @@ slots: slot_uri: GENEPIO:0100416 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -6441,7 +6441,7 @@ slots: slot_uri: GENEPIO:0100471 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Enterics Lab Manager @@ -6458,7 +6458,7 @@ slots: slot_uri: GENEPIO:0100422 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: enterics@lab.ca @@ -6473,7 +6473,7 @@ slots: slot_uri: GENEPIO:0001159 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Public Health Ontario (PHO) @@ -6486,7 +6486,7 @@ slots: slot_uri: GENEPIO:0001165 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true pattern: ^\S+@\S+\.\S+$ examples: @@ -6541,8 +6541,8 @@ slots: or cannot be provided, leave blank or provide a null value. slot_uri: GENEPIO:0100473 any_of: - - range: sequencing_platform menu - - range: null value menu + - range: SequencingPlatformMenu + - range: NullValueMenu examples: - value: Illumina [GENEPIO:0001923] sequencing_instrument: @@ -6554,8 +6554,8 @@ slots: blank or provide a null value. slot_uri: GENEPIO:0001452 any_of: - - range: sequencing_instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu examples: - value: Illumina HiSeq 2500 [GENEPIO:0100117] library_preparation_kit: @@ -6585,7 +6585,7 @@ slots: regions of interest from a genome. comments: Provide the name of the enrichment method slot_uri: GENEPIO:0100966 - range: genomic_target_enrichment_method menu + range: GenomicTargetEnrichmentMethodMenu examples: - value: Hybrid selection method (bait-capture) [GENEPIO:0001950] genomic_target_enrichment_method_details: @@ -6729,8 +6729,8 @@ slots: New Term Request form. slot_uri: GENEPIO:0100559 any_of: - - range: quality_control_determination menu - - range: null value menu + - range: QualityControlDeterminationMenu + - range: NullValueMenu multivalued: true examples: - value: sequence failed quality control @@ -6744,8 +6744,8 @@ slots: New Term Request form. slot_uri: GENEPIO:0100560 any_of: - - range: quality_control_issues menu - - range: null value menu + - range: QualityControlIssuesMenu + - range: NullValueMenu multivalued: true examples: - value: low average genome coverage @@ -6771,7 +6771,7 @@ slots: slot_uri: GENEPIO:0001458 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Porechop 0.2.3 @@ -6784,7 +6784,7 @@ slots: slot_uri: GENEPIO:0001459 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: Nanostripper @@ -6796,7 +6796,7 @@ slots: slot_uri: GENEPIO:0100825 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: SPAdes Genome Assembler, Canu, wtdbg2, velvet sequence_assembly_software_version: @@ -6807,7 +6807,7 @@ slots: slot_uri: GENEPIO:0100826 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: 3.15.5 consensus_sequence_software_name: @@ -6818,7 +6818,7 @@ slots: slot_uri: GENEPIO:0001463 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: iVar consensus_sequence_software_version: @@ -6829,7 +6829,7 @@ slots: slot_uri: GENEPIO:0001469 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: '1.3' breadth_of_coverage_value: @@ -7088,7 +7088,7 @@ slots: slot_uri: GENEPIO:0101116 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: gyrase A genetic_target_region: @@ -7113,8 +7113,8 @@ slots: was determined to be present or absent within a sample. slot_uri: GENEPIO:0100962 any_of: - - range: diagnostic target presence menu - - range: null value menu + - range: DiagnosticTargetPresenceMenu + - range: NullValueMenu examples: - value: diagnostic target present diagnostic_measurement_value: @@ -7135,8 +7135,8 @@ slots: the given diagnostic test. slot_uri: GENEPIO:0100964 any_of: - - range: diagnostic measurement unit menu - - range: null value menu + - range: DiagnosticMeasurementUnitMenu + - range: NullValueMenu examples: - value: cycle threshold (Ct) diagnostic_measurement_method: @@ -7147,8 +7147,8 @@ slots: for a given diagnostic test. slot_uri: GENEPIO:0100965 any_of: - - range: diagnostic measurement method menu - - range: null value menu + - range: DiagnosticMeasurementMethodMenu + - range: NullValueMenu examples: - value: qPCR diagnostic_testing_threshold_value: @@ -7209,8 +7209,8 @@ slots: comments: Provide the stage of food production as free text. slot_uri: GENEPIO:0100482 any_of: - - range: stage_of_production menu - - range: null value menu + - range: StageOfProductionMenu + - range: NullValueMenu recommended: true examples: - value: Abattoir [ENVO:01000925] @@ -7224,8 +7224,8 @@ slots: the intervention category from the pick list provided. slot_uri: GENEPIO:0100483 any_of: - - range: experimental_intervention menu - - range: null value menu + - range: ExperimentalInterventionMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -7243,8 +7243,8 @@ slots: examples: - value: 2% cranberry solution mixed in feed enums: - NullValue: - name: NullValue + NullValueMenu: + name: NullValueMenu title: null value permissible_values: Not Applicable [GENEPIO:0001619]: diff --git a/web/templates/hpai/schema_enums.tsv b/web/templates/hpai/schema_enums.tsv index 913d4fde..f742904b 100644 --- a/web/templates/hpai/schema_enums.tsv +++ b/web/templates/hpai/schema_enums.tsv @@ -1,6 +1,6 @@ title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description -null value NullValue GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. +null value NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv index d0a14efd..334908f3 100644 --- a/web/templates/hpai/schema_slots.tsv +++ b/web/templates/hpai/schema_slots.tsv @@ -12,91 +12,91 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Database identifiers GENEPIO:0101204 IN HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001150 Sample collection and processing HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100762 sample_collection_data_steward_name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101107 sample_collection_data_steward_contact_email sample_collection_data_steward_contact_email WhitespaceMinimizedString The email address of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the email address of the sample collection data steward. This may or may not be the same individual/organization that collected the sample. If the contact is the same, provide the same address as the "sample collector contact email". bloggsj@aglab.ca -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by WhitespaceMinimizedString null value menu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001181 geo_loc_name_(country) geo_loc_name_country geo_loc_name_(country) menu null value menu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada geo_loc_name -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001185 geo_loc_name_(state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString null value menu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape geo_loc_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001181 geo_loc_name_(country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada geo_loc_name +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001185 geo_loc_name_(state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape geo_loc_name HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100280 geo_loc_name_(county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001189 geo_loc_name_(city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100436 geo_loc_name_(site) geo_loc_name_site__ WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100309 geo_loc_latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100310 geo_loc_longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism organism menu null value menu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype influenza_subsubtype menu TRUE TRUE -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101109 influenza_subtyping_scheme_name influenza_subtyping_scheme_name influenza_subtyping_scheme_name menu -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process taxonomic_identification_process menu +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype InfluenzaSubsubtypeMenu TRUE TRUE +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101109 influenza_subtyping_scheme_name influenza_subtyping_scheme_name InfluenzaSubtypingSchemeNameMenu +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101110 virus_identifier virus_identifier WhitespaceMinimizedString HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101111 WHO/OIE/FAO_H5_clade who_oie_fao_h5_clade WhitespaceMinimizedString -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date null value menu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 collection_date -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date null value menu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time null value menu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time null value menu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day sample_collection_time_of_day menu null value menu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString null value menu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit sample_collection_duration_unit menu null value menu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date null value menu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date null value menu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 -HPAI;HPAIHost Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] -HPAI;HPAIFood Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country geo_loc_name (country) menu null value menu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin -HPAI;HPAIFood Sample collection and processing GENEPIO:0100444 food_product food_product food_product menu null value menu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type -HPAI;HPAIFood Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties food_product_properties menu null value menu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source -HPAI;HPAIFood Sample collection and processing GENEPIO:0100447 food_packaging food_packaging food_packaging menu null value menu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 collection_date +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +HPAI;HPAIHost Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] +HPAI;HPAIFood Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin +HPAI;HPAIFood Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type +HPAI;HPAIFood Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source +HPAI;HPAIFood Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap HPAI;HPAIFood Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date HPAI;HPAIFood Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 -HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001232 environmental_site environmental_site environmental_site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env -HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001223 environmental_material environmental_material environmental_material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source -HPAI;HPAIHost Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material anatomical_material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source -HPAI;HPAIHost Sample collection and processing GENEPIO:0001216 body_product body_product body_product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source -HPAI;HPAIHost Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part anatomical_part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001234 collection_device collection_device collection_device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001241 collection_method collection_method collection_method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source +HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env +HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source +HPAI;HPAIHost Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit sample_volume_measurement_unit menu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status residual_sample_status menu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling purpose_of_sampling menu null value menu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_sampling -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity presampling_activity menu null value menu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString null value menu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_sampling +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit sample_storage_duration_unit menu null value menu The units of a measured sample storage duration. Provide the units from the pick list. Day -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001253 specimen_processing specimen_processing specimen_processing menu null value menu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001253 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101029 experimental_protocol experimental_protocol WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type experimental_specimen_role_type menu null value menu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101112 experimental_specimen_details experimental_specimen_details WhitespaceMinimizedString -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100690 available_data_types available_data_types available_data_types menu null value menu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria HPAI;HPAIHost GENEPIO:0001268 Host information -HPAI;HPAIHost Host information GENEPIO:0001386 host_(common_name) host_common_name host (common name) menu null value menu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host -HPAI;HPAIHost Host information GENEPIO:0001387 host_(scientific_name) host_scientific_name host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host +HPAI;HPAIHost Host information GENEPIO:0001386 host_(common_name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host +HPAI;HPAIHost Host information GENEPIO:0001387 host_(scientific_name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host HPAI;HPAIHost Host information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety HPAI;HPAIHost Host information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed -HPAI;HPAIHost Host information GENEPIO:0100452 host_(food production name) host_food_production_name host (food production name) menu null value menu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host -HPAI;HPAIHost Host Information GENEPIO:0001392 host_age host_age decimal null value menu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age -HPAI;HPAIHost Host Information GENEPIO:0001393 host_age_unit host_age_unit host_age_unit menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] -HPAI;HPAIHost Host information GENEPIO:0001394 host_age_bin host_age_bin host_age_bin menu null value menu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age +HPAI;HPAIHost Host information GENEPIO:0100452 host_(food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host +HPAI;HPAIHost Host Information GENEPIO:0001392 host_age host_age decimal NullValueMenu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +HPAI;HPAIHost Host Information GENEPIO:0001393 host_age_unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] +HPAI;HPAIHost Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age host_gender host_gender -HPAI;HPAIHost Host information GENEPIO:0001391 host_disease host_disease host_disease menu null value menu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease -HPAI;HPAIHost Host Information GENEPIO:0001388 host_health_state host_health_state host_health_state menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state -HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_health_status_details host_health_status_details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] -HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome host_health_outcome menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome +HPAI;HPAIHost Host information GENEPIO:0001391 host_disease host_disease HostDiseaseMenu NullValueMenu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease +HPAI;HPAIHost Host Information GENEPIO:0001388 host_health_state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state +HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] +HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome HPAI;HPAIHost Host Information GENEPIO:0001398 host_subject_ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. BCxy123 host_subject_id HPAI;HPAIHost Host Information GENEPIO:0100281 case_ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 -HPAI;HPAIHost Host Information GENEPIO:0001399 symptom_onset_date symptom_onset_date date null value menu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 -HPAI;HPAIHost Host Information GENEPIO:0001400 signs_and_symptoms signs_and_symptoms signs_and_symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] -HPAI;HPAIHost Host Information GENEPIO:0001401 pre-existing_conditions_and_risk_factors preexisting_conditions_and_risk_factors pre-existing_conditions_and_risk_factors menu null value menu TRUE "Patient pre-existing conditions and risk factors. +HPAI;HPAIHost Host Information GENEPIO:0001399 symptom_onset_date symptom_onset_date date NullValueMenu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +HPAI;HPAIHost Host Information GENEPIO:0001400 signs_and_symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] +HPAI;HPAIHost Host Information GENEPIO:0001401 pre-existing_conditions_and_risk_factors preexisting_conditions_and_risk_factors PreexistingConditionsAndRiskFactorsMenu NullValueMenu TRUE "Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection." Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma [HP:0002099] -HPAI;HPAIHost Host Information GENEPIO:0001402 complications complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. Acute respiratory failure [MONDO:0001208] +HPAI;HPAIHost Host Information GENEPIO:0001402 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. Acute respiratory failure [MONDO:0001208] HPAI;HPAIHost GENEPIO:0001409 Host exposure information -HPAI;HPAIHost Host exposure information GENEPIO:0001417 exposure event exposure_event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Social Gathering Additional location information Exposure Event PH_EXPOSURE -HPAI;HPAIHost Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level exposure contact level menu null value menu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct exposure contact level -HPAI;HPAIHost Host exposure information GENEPIO:0001419 host role host_role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Inpatient PH_HOST_ROLE -HPAI;HPAIHost Host exposure information GENEPIO:0001428 exposure setting exposure_setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting PH_EXPOSURE +HPAI;HPAIHost Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Social Gathering Additional location information Exposure Event PH_EXPOSURE +HPAI;HPAIHost Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct exposure contact level +HPAI;HPAIHost Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Inpatient PH_HOST_ROLE +HPAI;HPAIHost Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting PH_EXPOSURE HPAI;HPAIHost Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Case infected family at home PH_EXPOSURE_DETAILS HPAI;HPAIHost GENEPIO:0001403 Host vaccination information -HPAI;HPAIHost Host vaccination information GENEPIO:0001404 host_vaccination_status host_vaccination_status host_vaccination_status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination +HPAI;HPAIHost Host vaccination information GENEPIO:0001404 host_vaccination_status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination HPAI;HPAIHost Host vaccination information GENEPIO:0001406 number_of_vaccine_doses_received number_of_vaccine_doses_received integer 0 The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 HPAI;HPAIHost Host vaccination information GENEPIO:0100313 vaccination_dose_1_vaccine_name vaccination_dose_1_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) HPAI;HPAIHost Host vaccination information GENEPIO:0100314 vaccination_dose_1_vaccination_date vaccination_dose_1_vaccination_date date The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 @@ -104,117 +104,117 @@ HPAI;HPAIHost Host vaccination information GENEPIO:0100315 vaccination_dose_2_va HPAI;HPAIHost Host vaccination information GENEPIO:0100316 vaccination_dose_2_vaccination_date vaccination_dose_2_vaccination_date date The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 HPAI;HPAIHost Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated HPAI;HPAIHost Host treatment information -HPAI;HPAIHost Host treatment information GENEPIO:0101113 influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration menu null value menu An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen. Influenza antiviral treatment administered [GENEPIO:0101194] +HPAI;HPAIHost Host treatment information GENEPIO:0101113 influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration InfluenzaAntiviralTreatmentAdministrationMenu NullValueMenu An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen. Influenza antiviral treatment administered [GENEPIO:0101194] HPAI;HPAIHost Host treatment information GENEPIO:0101114 influenza_antiviral_agent influenza_antiviral_agent__ WhitespaceMinimizedString A substance that destroys or inhibits replication of viruses. HPAI;HPAIHost Host treatment information GENEPIO:0101115 influenza_antiviral_treatment_date influenza_antiviral_treatment_date date The date on which the influenza antiviral agent was administered to a patient as part of treatment "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given. " HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100773 water_catchment_area_human_population_measurement_value water_catchment_area_human_population_measurement_value integer null value menu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100774 water_catchment_area_human_population_range water_catchment_area_human_population_range water catchment area human population range menu null value menu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100773 water_catchment_area_human_population_measurement_value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100774 water_catchment_area_human_population_range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100775 water_catchment_area_human_population_measurement_method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit water catchment area human population density unit menu null value menu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type populated area type menu null value menu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions sampling weather conditions menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions presampling weather conditions menu null value menu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString null value menu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type populated area type menu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units water_depth_units menu null value menu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units sediment_depth_units menu null value menu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units air_temperature_units menu null value menu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units water_temperature_units menu null value menu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type weather_type menu null value menu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit precipitation measurement unit menu null value menu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type WeatherTypeMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit ambient temperature measurement unit menu null value menu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit total daily flow rate measurement unit menu null value menu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit instantaneous flow rate measurement unit menu null value menu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit turbidity measurement unit menu null value menu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100915 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit dissolved oxygen measurement unit menu null value menu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100917 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit oxygen reduction potential (ORP) measurement unit menu null value menu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialORPMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit chemical oxygen demand (COD) measurement unit menu null value menu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCODMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit carbonaceous biochemical oxygen demand (CBOD) measurement unit menu null value menu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCBODMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit total suspended solids (TSS) measurement unit menu null value menu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTSSMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit total dissolved solids (TDS) measurement unit menu null value menu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTDSMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit total solids (TS) measurement unit menu null value menu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTSMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit alkalinity measurement unit menu null value menu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit conductivity measurement unit menu null value menu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit salinity measurement unit menu null value menu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit total nitrogen (TN) measurement unit menu null value menu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTNMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit total phosphorus (TP) measurement unit menu null value menu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorusTPMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator_ fecal contamination indicator menu null value menu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator_ FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit fecal contamination unit menu null value menu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit fecal coliform count unit menu null value menu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator urinary contamination indicator menu null value menu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit urinary contamination unit menu null value menu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection sample temperature unit (at collection) menu null value menu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received sample temperature unit (when received) menu null value menu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001441 Sequence information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type sequencing_assay_type menu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing__ purpose_of_sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing__ PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001446 purpose_of_sequencing_details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString null value menu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString null value menu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString null value menu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by WhitespaceMinimizedString null value menu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001165 sequence_submitter_contact_email sequence_submitter_contact_email WhitespaceMinimizedString null value menu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001165 sequence_submitter_contact_email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform sequencing_platform menu null value menu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument sequencing_instrument menu null value menu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100843 DNA_fragment_length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100966 genomic_target_enrichment_method genomic_target_enrichment_method genomic_target_enrichment_method menu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100966 genomic_target_enrichment_method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100967 genomic_target_enrichment_method_details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001456 amplicon_pcr_primer_scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001449 amplicon_size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 @@ -228,15 +228,15 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001461 as HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001457 Bioinformatics and QC metrics HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination quality_control_determination menu null value menu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues quality_control_issues menu null value menu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString null value menu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString null value menu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString null value menu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString null value menu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString null value menu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString null value menu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 @@ -264,20 +264,20 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GE HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001506 Pathogen diagnostic testing -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101116 genetic target name genetic_target_name WhitespaceMinimizedString null value menu The name of the genetic marker used for testing. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101116 genetic target name genetic_target_name WhitespaceMinimizedString NullValueMenu The name of the genetic marker used for testing. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101117 genetic target region genetic_target_region WhitespaceMinimizedString The specific region or segment of a genetic sequence used for testing or analysis. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101118 genetic target region reference genome genetic_target_region_reference_genome WhitespaceMinimizedString The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis. -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence diagnostic_target_presence diagnostic target presence menu null value menu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence diagnostic_target_presence DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value diagnostic_measurement_value WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit diagnostic_measurement_unit diagnostic measurement unit menu null value menu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method diagnostic_measurement_method diagnostic measurement method menu null value menu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit diagnostic_measurement_unit DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method diagnostic_measurement_method DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101104 diagnostic testing threshold value diagnostic_testing_threshold_value integer The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101105 diagnostic testing threshold units diagnostic_testing_threshold_units WhitespaceMinimizedString The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101106 diagnostic testing details diagnostic_testing_details WhitespaceMinimizedString Describe any details of the diagnsotic testing. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0100478 Risk assessment information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production stage_of_production menu null value menu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention experimental_intervention menu null value menu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed \ No newline at end of file diff --git a/web/templates/menu.json b/web/templates/menu.json index 735a7e07..ac7bc408 100644 --- a/web/templates/menu.json +++ b/web/templates/menu.json @@ -28,8 +28,8 @@ } }, "phac_dexa": { - "PHAC Dexa": { - "name": "PHAC Dexa", + "PHACDexa": { + "name": "PHACDexa", "status": "published", "display": true } @@ -61,8 +61,8 @@ "status": "published", "display": true }, - "Mpox_international": { - "name": "Mpox_international", + "MpoxInternational": { + "name": "MpoxInternational", "status": "published", "display": true } From 3b4996b2a5eaa2e051d32af483ce96b7081b5ab7 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 9 Oct 2024 01:19:40 -0700 Subject: [PATCH 52/96] GRDI version bump --- web/templates/grdi/schema_core.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/templates/grdi/schema_core.yaml b/web/templates/grdi/schema_core.yaml index ed9f2964..af2ce543 100644 --- a/web/templates/grdi/schema_core.yaml +++ b/web/templates/grdi/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/GRDI name: "GRDI" description: "" -version: 12.2.2 +version: 13.3.3 imports: - 'linkml:types' prefixes: From 371c4acec60d096153d359029e940b29566b39a7 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 9 Oct 2024 01:20:00 -0700 Subject: [PATCH 53/96] PHAC DEXA update --- web/templates/phac_dexa/schema.json | 5795 +++++++++++++++------- web/templates/phac_dexa/schema.yaml | 2369 ++++----- web/templates/phac_dexa/schema_core.yaml | 5 +- web/templates/phac_dexa/schema_enums.tsv | 1490 +++--- web/templates/phac_dexa/schema_slots.tsv | 308 +- 5 files changed, 6085 insertions(+), 3882 deletions(-) diff --git a/web/templates/phac_dexa/schema.json b/web/templates/phac_dexa/schema.json index 6552bdef..7d087bd3 100644 --- a/web/templates/phac_dexa/schema.json +++ b/web/templates/phac_dexa/schema.json @@ -19,6 +19,10 @@ "shex": { "prefix_prefix": "shex", "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" } }, "default_prefix": "https://example.com/PHAC_Dexa/", @@ -26,6 +30,7 @@ "WhitespaceMinimizedString": { "name": "WhitespaceMinimizedString", "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/PHAC_Dexa", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -33,6 +38,7 @@ "Provenance": { "name": "Provenance", "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/PHAC_Dexa", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -40,18 +46,39 @@ "string": { "name": "string", "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "xsd:string" }, "integer": { "name": "integer", "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "xsd:integer" }, "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "xsd:boolean", "repr": "bool" @@ -59,18 +86,39 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:float" }, "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:double" }, "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "xsd:decimal" }, @@ -78,17 +126,27 @@ "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:Time" ], "base": "XSDTime", - "uri": "xsd:dateTime", + "uri": "xsd:time", "repr": "str" }, "date": { "name": "date", "description": "a date (year, month and day) in an idealized calendar", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:Date" ], "base": "XSDDate", "uri": "xsd:date", @@ -97,6 +155,13 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "xsd:dateTime", "repr": "str" @@ -104,6 +169,10 @@ "date_or_datetime": { "name": "date_or_datetime", "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", "base": "str", "uri": "linkml:DateOrDatetime", "repr": "str" @@ -111,13 +180,44 @@ "uriorcurie": { "name": "uriorcurie", "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", "base": "URIorCURIE", "uri": "xsd:anyURI", "repr": "str" }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/PHAC_Dexa", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, "uri": { "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/PHAC_Dexa", + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "xsd:anyURI", "repr": "str" @@ -125,6 +225,10 @@ "ncname": { "name": "ncname", "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", "base": "NCName", "uri": "xsd:string", "repr": "str" @@ -132,7 +236,13 @@ "objectidentifier": { "name": "objectidentifier", "description": "A URI or CURIE that represents an object in the model.", - "comments": ["Used for inheritence and type checking"], + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/PHAC_Dexa", "base": "ElementIdentifier", "uri": "shex:iri", "repr": "str" @@ -140,118 +250,203 @@ "nodeidentifier": { "name": "nodeidentifier", "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", "base": "NodeIdentifier", "uri": "shex:nonLiteral", "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/PHAC_Dexa", + "base": "str", + "uri": "xsd:string", + "repr": "str" } }, "enums": { - "SUBJECT_DESCRIPTIONS menu": { - "name": "SUBJECT_DESCRIPTIONS menu", + "SubjectDescriptionsMenu": { + "name": "SubjectDescriptionsMenu", + "title": "SUBJECT_DESCRIPTIONS menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "1/2 breast": { "text": "1/2 breast", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Avian Ingredients": { "text": "Avian Ingredients", "meaning": "FOODON:00002616", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Back": { "text": "Back", "meaning": "PATO:0001901", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Balut": { "text": "Balut", "meaning": "FOODON:03302184", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Black Pepper": { "text": "Black Pepper", "meaning": "FOODON:03411191", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Blade Steak": { "text": "Blade Steak", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Blood Meal": { "text": "Blood Meal", "meaning": "FOODON:00001564", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Bone Meal": { "text": "Bone Meal", "meaning": "ENVO:02000054", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Bovine Ingredients": { "text": "Bovine Ingredients", "meaning": "FOODON:03414374", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast": { "text": "Breast", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast back off": { "text": "Breast back off", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast cutlets": { "text": "Breast cutlets", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast Skinless": { "text": "Breast Skinless", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast Skinless Boneless": { "text": "Breast Skinless Boneless", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast with Skin": { "text": "Breast with Skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Brisket": { "text": "Brisket", "meaning": "FOODON:03530020", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Burger": { "text": "Burger", "meaning": "FOODON:00002737", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Calf": { "text": "Calf", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Canola Meal": { "text": "Canola Meal", "meaning": "FOODON:00002694", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Carinata Meal": { "text": "Carinata Meal", "meaning": "FOODON:03316468", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chop": { "text": "Chop", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chops": { "text": "Chops", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "coli": { "text": "coli" @@ -259,505 +454,716 @@ "Complete Feed": { "text": "Complete Feed", "meaning": "FOODON:03309997", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Corn": { "text": "Corn", "meaning": "FOODON:00001765", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Cow": { "text": "Cow", "meaning": "FOODON:03411161", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Cubes": { "text": "Cubes", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Cutlet": { "text": "Cutlet", "meaning": "FOODON:00003001", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Drumstick": { "text": "Drumstick", "meaning": "CURATION:0001378", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Drumstick Skinless": { "text": "Drumstick Skinless", "meaning": "CURATION:0001378", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Drumstick with Skin": { "text": "Drumstick with Skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Drumsticks": { "text": "Drumsticks", "meaning": "CURATION:0001378", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Egg Flour": { "text": "Egg Flour", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Feather Meal": { "text": "Feather Meal", "meaning": "CURATION:0001357", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Feed": { "text": "Feed", "meaning": "FOODON:03309997", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Filet": { "text": "Filet", "meaning": "FOODON:03530144", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Fish Ingredients": { "text": "Fish Ingredients", "meaning": "FOODON:03411222", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Fish Meal": { "text": "Fish Meal", "meaning": "FOODON:03301620", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Grain": { "text": "Grain", "meaning": "FOODON:03311095", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground": { "text": "Ground", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground ( lean)": { "text": "Ground ( lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Angus)": { "text": "Ground (Angus)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Extra Lean)": { "text": "Ground (Extra Lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (extra-lan)": { "text": "Ground (extra-lan)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Extra-Lean)": { "text": "Ground (Extra-Lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Lean)": { "text": "Ground (Lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Medium)": { "text": "Ground (Medium)", "meaning": "FOODON:03430117", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Regular)": { "text": "Ground (Regular)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (Sirloin)": { "text": "Ground (Sirloin)", "meaning": "CURATION:0001614", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground Boneless": { "text": "Ground Boneless", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground extra lean": { "text": "Ground extra lean", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground regular": { "text": "Ground regular", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "ground( extra lean)": { "text": "ground( extra lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "ground( medium)": { "text": "ground( medium)", "meaning": "FOODON:03430117", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground(Extra lean)": { "text": "Ground(Extra lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground(Lean)": { "text": "Ground(Lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground(medium)": { "text": "Ground(medium)", "meaning": "FOODON:03430117", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "ground(regular)": { "text": "ground(regular)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Groundextra lean)": { "text": "Groundextra lean)", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground-Lean": { "text": "Ground-Lean", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground-Regular": { "text": "Ground-Regular", "meaning": "FOODON:03430136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Heifer": { "text": "Heifer", "meaning": "FOODON:00002518", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Hummus": { "text": "Hummus", "meaning": "FOODON:00003049", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "In-Shell": { "text": "In-Shell", "meaning": "UBERON:0006612", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Lay Ration": { "text": "Lay Ration", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Leg": { "text": "Leg", "meaning": "UBERON:0000978", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Leg with Skin-Drumstick and Thigh": { "text": "Leg with Skin-Drumstick and Thigh", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Liver": { "text": "Liver", "meaning": "UBERON:0002107", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Loin Center Chop": { "text": "Loin Center Chop", "meaning": "FOODON:03530031", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Meat and Bone Meal": { "text": "Meat and Bone Meal", "meaning": "FOODON:00002738", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Meat Flour/Meal": { "text": "Meat Flour/Meal", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Meat Meal": { "text": "Meat Meal", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mild italian style burger": { "text": "Mild italian style burger", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Necks": { "text": "Necks", "meaning": "UBERON:0000974", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Nuggets": { "text": "Nuggets", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other": { "text": "Other", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Other cut": { "text": "Other cut", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other Cut (Not Ground)": { "text": "Other Cut (Not Ground)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other Cut Boneless": { "text": "Other Cut Boneless", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other Cut Boneless (Not Ground)": { "text": "Other Cut Boneless (Not Ground)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ovine Ingredients": { "text": "Ovine Ingredients", "meaning": "FOODON:03411183", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pet Food": { "text": "Pet Food", "meaning": "FOODON:00002682", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Porcine Ingredients": { "text": "Porcine Ingredients", "meaning": "FOODON:03411136", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pork Chop (Cut Unknown)": { "text": "Pork Chop (Cut Unknown)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Premix": { "text": "Premix", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Premix (Medicated)": { "text": "Premix (Medicated)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Processed (Other)": { "text": "Processed (Other)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Raw": { "text": "Raw", "meaning": "FOODON:03311126", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Rib Chop": { "text": "Rib Chop", "meaning": "UBERON:0002228", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ribs": { "text": "Ribs", "meaning": "UBERON:0002228", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Roast": { "text": "Roast", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Salami": { "text": "Salami", "meaning": "FOODON:03312067", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sausage": { "text": "Sausage", "meaning": "FOODON:03315904", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sausage (Pepper)": { "text": "Sausage (Pepper)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Scallopini": { "text": "Scallopini", "meaning": "FOODON:00003017", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shell on": { "text": "Shell on", "meaning": "UBERON:0006612", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shelled": { "text": "Shelled", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shoulder": { "text": "Shoulder", "meaning": "UBERON:0001467", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shoulder Chop": { "text": "Shoulder Chop", "meaning": "UBERON:0001467", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sirloin Chop": { "text": "Sirloin Chop", "meaning": "FOODON:03530027", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Skim milk powder": { "text": "Skim milk powder", "meaning": "FOODON:03301484", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Soft": { "text": "Soft", "meaning": "PATO:0000387", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Soyabean Meal": { "text": "Soyabean Meal", "meaning": "FOODON:03316468", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Starter Ration": { "text": "Starter Ration", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Steak": { "text": "Steak", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Stew Chunks": { "text": "Stew Chunks", "meaning": "FOODON:00003140", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Supplements": { "text": "Supplements", "meaning": "FOODON:00001874", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "T. high": { "text": "T. high", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Tahini": { "text": "Tahini", "meaning": "FOODON:03304154", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Tender loin": { "text": "Tender loin", "meaning": "FOODON:03530217", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Tenderloin": { "text": "Tenderloin", "meaning": "FOODON:03530217", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Thigh": { "text": "Thigh", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Thigh Skinless": { "text": "Thigh Skinless", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Thigh Skinless Boneless": { "text": "Thigh Skinless Boneless", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Thigh with Skin": { "text": "Thigh with Skin", "meaning": "UBERON:0000014", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Trim": { "text": "Trim", "meaning": "FOODON:00001568", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Unknown Meal": { "text": "Unknown Meal", "meaning": "FOODON:03316468", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Unspecified Feed/Ingredient": { "text": "Unspecified Feed/Ingredient", "meaning": "FOODON:03309997", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Upper Thigh": { "text": "Upper Thigh", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Upper Thigh with Skin": { "text": "Upper Thigh with Skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "upper thight": { "text": "upper thight", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Upperthigh": { "text": "Upperthigh", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "White Pepper": { "text": "White Pepper", "meaning": "FOODON:03304045", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Whole": { "text": "Whole", "meaning": "FOODON:03430131", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Whole Carcass": { "text": "Whole Carcass", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Whole with Skin": { "text": "Whole with Skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Wing": { "text": "Wing", "meaning": "UBERON:0000023", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Wings": { "text": "Wings", "meaning": "UBERON:0000023", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] } } }, - "SPECIES menu": { - "name": "SPECIES menu", + "SpeciesMenu": { + "name": "SpeciesMenu", + "title": "SPECIES menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "2": { @@ -1393,8 +1799,9 @@ } } }, - "STTYPE menu": { - "name": "STTYPE menu", + "STTypeMenu": { + "name": "STTypeMenu", + "title": "STTYPE menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "0": { @@ -1406,25 +1813,31 @@ "ANIMAL": { "text": "ANIMAL", "meaning": "FOODON:00003004", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "ENVIRONMENT": { "text": "ENVIRONMENT", "meaning": "ENVO:01000254", "exact_mappings": [ - "GRDI:environmental_material:", - "GRDI:environmental_site:" + "GRDI:environmental_material%3A", + "GRDI:environmental_site%3A" ] }, "FOOD": { "text": "FOOD", "meaning": "CHEBI:33290", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "HUMAN": { "text": "HUMAN", "meaning": "NCBITAXON:9606", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "PRODUCT": { "text": "PRODUCT" @@ -1434,7 +1847,9 @@ }, "UNKNOWN": { "text": "UNKNOWN", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "2": { "text": "2" @@ -1448,123 +1863,173 @@ "Amphibian": { "text": "Amphibian", "meaning": "FOODON:03411624", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Aquatic Mammal": { "text": "Aquatic Mammal", "meaning": "FOODON:03411134", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Armadillo": { "text": "Armadillo", "meaning": "FOODON:03411626", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Avian": { "text": "Avian", "meaning": "FOODON:00002616", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Bat": { "text": "Bat", "meaning": "CURATION:0001601", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Biosolids": { "text": "Biosolids", "meaning": "ENVO:00002059", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Bovine": { "text": "Bovine", "meaning": "FOODON:03414374", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Building": { "text": "Building", "meaning": "ENVO:00000073", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Camelid": { "text": "Camelid", "meaning": "FOODON:03412103", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Canine": { "text": "Canine", "meaning": "FOODON:03414847", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Caprine": { "text": "Caprine", "meaning": "FOODON:03411328", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Caprine and Ovine": { "text": "Caprine and Ovine", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Cereal": { "text": "Cereal", "meaning": "FOODON:00001709", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Cereal/Bread/Snack": { "text": "Cereal/Bread/Snack", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Cervid": { "text": "Cervid", "meaning": "FOODON:03411500", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Compost": { "text": "Compost", "meaning": "CURATION:0001527", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Confections/Nuts/Condiments": { "text": "Confections/Nuts/Condiments", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Crocuta": { "text": "Crocuta", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Crustacean": { "text": "Crustacean", "meaning": "FOODON:03411374", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Dairy": { "text": "Dairy", "meaning": "ENVO:00003862", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Dust": { "text": "Dust", "meaning": "ENVO:00002008", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Egg": { "text": "Egg", "meaning": "FOODON:00001274", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Elephant": { "text": "Elephant", "meaning": "FOODON:03412129", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Equine": { "text": "Equine", "meaning": "CURATION:0001431", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Equipment": { "text": "Equipment", "meaning": "CURATION:0000348", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "ERROR": { "text": "ERROR" @@ -1572,183 +2037,259 @@ "Feed and Ingredients": { "text": "Feed and Ingredients", "meaning": "FOODON:03309997", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Feline": { "text": "Feline", "meaning": "NCIT:C14191", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Ferret": { "text": "Ferret", "meaning": "CURATION:0001411", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Fertilizer": { "text": "Fertilizer", "meaning": "CHEBI:33287", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Fish": { "text": "Fish", "meaning": "FOODON:03411222", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Food": { "text": "Food", "meaning": "CHEBI:33290", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Fruit": { "text": "Fruit", "meaning": "PO:0009001", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Fruits and Vegetables": { "text": "Fruits and Vegetables", "meaning": "FOODON:00002141", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Health (medicine)": { "text": "Health (medicine)" }, "Herbs and Spices": { "text": "Herbs and Spices", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Herpestidae": { "text": "Herpestidae", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Hippopotamidae": { "text": "Hippopotamidae", "meaning": "NCBITAXON:9831", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Lapine": { "text": "Lapine", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Litter/Manure": { "text": "Litter/Manure", "meaning": "CURATION:0001446", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Manure": { "text": "Manure", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Marsupial": { "text": "Marsupial", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Meat": { "text": "Meat", "meaning": "FOODON:00001006", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mephitida": { "text": "Mephitida", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Mink": { "text": "Mink", "meaning": "FOODON:00002723", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Mixed food": { "text": "Mixed food", "meaning": "CHEBI:33290", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mixed Food/Meat": { "text": "Mixed Food/Meat", "meaning": "FOODON:03315600", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mollusk": { "text": "Mollusk", "meaning": "FOODON:03412112", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Mustelid": { "text": "Mustelid", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "n/a": { "text": "n/a", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Other": { "text": "Other", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Ovine": { "text": "Ovine", "meaning": "FOODON:03411183", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Personnel Clothing": { "text": "Personnel Clothing", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Porcine": { "text": "Porcine", "meaning": "FOODON:03411136", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Primate": { "text": "Primate", "meaning": "NCBITAXON:9443", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Raccoon": { "text": "Raccoon", "meaning": "FOODON:03411461", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Reptile": { "text": "Reptile", "meaning": "FOODON:03411625", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Rodent": { "text": "Rodent", "meaning": "NCBITAXON:9989", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Sewage": { "text": "Sewage", "meaning": "ENVO:00002018", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Soil": { "text": "Soil", "meaning": "ENVO:00001998", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Transportation Supplies": { "text": "Transportation Supplies", "meaning": "ENVO:02000125", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Transportation Vehicles": { "text": "Transportation Vehicles", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Turkey": { "text": "Turkey", "meaning": "FOODON:03414166", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Unknown": { "text": "Unknown", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Unknown Food": { "text": "Unknown Food", "meaning": "CHEBI:33290", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Unspecified": { "text": "Unspecified" @@ -1756,16 +2297,22 @@ "Unspecified Animal": { "text": "Unspecified Animal", "meaning": "FOODON:00003004", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Unspecified Environmental": { "text": "Unspecified Environmental", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Unspecified Food": { "text": "Unspecified Food", "meaning": "CURATION:0001610", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Unspecified Product": { "text": "Unspecified Product", @@ -1773,21 +2320,28 @@ }, "Ursine": { "text": "Ursine", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Vegetable/Spice": { "text": "Vegetable/Spice", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Water": { "text": "Water", "meaning": "CHEBI:15377", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] } } }, - "COMMODITY menu": { - "name": "COMMODITY menu", + "CommodityMenu": { + "name": "CommodityMenu", + "title": "COMMODITY menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "<=16": { @@ -1796,17 +2350,23 @@ "Beef": { "text": "Beef", "meaning": "FOODON:00001041", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Broiler": { "text": "Broiler", "meaning": "FOODON:03411198", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Dairy": { "text": "Dairy", "meaning": "ENVO:00003862", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Domestic/Farmed": { "text": "Domestic/Farmed" @@ -1814,50 +2374,70 @@ "Egg": { "text": "Egg", "meaning": "FOODON:00001274", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Laboratory": { "text": "Laboratory", "meaning": "NCIT:C37984", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Meat": { "text": "Meat", "meaning": "FOODON:00001006", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mutton": { "text": "Mutton", "meaning": "FOODON:00002912", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pet": { "text": "Pet", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Pet/Zoo": { "text": "Pet/Zoo", "meaning": "ENVO:00010625", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Red Veal": { "text": "Red Veal", "meaning": "FOODON:00003083", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Unknown": { "text": "Unknown", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Veal": { "text": "Veal", "meaning": "FOODON:00003083", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "White Veal": { "text": "White Veal", "meaning": "FOODON:00003083", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Wild": { "text": "Wild", @@ -1865,8 +2445,9 @@ } } }, - "SPECIMENSOURCE_1 menu": { - "name": "SPECIMENSOURCE_1 menu", + "SpecimenSource1Menu": { + "name": "SpecimenSource1Menu", + "title": "SPECIMENSOURCE_1 menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "2": { @@ -1882,21 +2463,29 @@ "Blood": { "text": "Blood", "meaning": "UBERON:0000178", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Blood Meal": { "text": "Blood Meal", "meaning": "FOODON:00001564", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Body Fluid/Excretion": { "text": "Body Fluid/Excretion", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Carcass": { "text": "Carcass", "meaning": "UBERON:0008979", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Check Sample": { "text": "Check Sample", @@ -1904,7 +2493,9 @@ }, "Contact plate": { "text": "Contact plate", - "exact_mappings": ["GRDI:collection_device:"] + "exact_mappings": [ + "GRDI:collection_device%3A" + ] }, "Culture": { "text": "Culture", @@ -1913,12 +2504,16 @@ "Dust": { "text": "Dust", "meaning": "ENVO:00002008", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Egg": { "text": "Egg", "meaning": "FOODON:00001274", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Environment (Animal)": { "text": "Environment (Animal)" @@ -1927,27 +2522,35 @@ "text": "Environmental", "meaning": "CURATION:0001610", "exact_mappings": [ - "GRDI:environmental_material:", - "GRDI:environmental_site:" + "GRDI:environmental_material%3A", + "GRDI:environmental_site%3A" ] }, "Feces": { "text": "Feces", "meaning": "UBERON:0001988", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Fetus/Embryo": { "text": "Fetus/Embryo", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Organ": { "text": "Organ", "meaning": "UBERON:0000062", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Organ/Tissue": { "text": "Organ/Tissue", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Proficiency Isolate": { "text": "Proficiency Isolate", @@ -1960,31 +2563,43 @@ "Rinse": { "text": "Rinse", "meaning": "CURATION:0001629", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Septage": { "text": "Septage", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Soya Meal": { "text": "Soya Meal", "meaning": "FOODON:03316468", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Stool": { "text": "Stool", "meaning": "UBERON:0001988", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Swab": { "text": "Swab", "meaning": "NCIT:C17627", - "exact_mappings": ["GRDI:collection_device:"] + "exact_mappings": [ + "GRDI:collection_device%3A" + ] }, "Tissue": { "text": "Tissue", "meaning": "UBERON:0000479", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Unit (Pre-Packaged)": { "text": "Unit (Pre-Packaged)", @@ -1992,7 +2607,9 @@ }, "Unknown": { "text": "Unknown", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Unspecified": { "text": "Unspecified" @@ -2000,12 +2617,15 @@ "Urine": { "text": "Urine", "meaning": "UBERON:0001088", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] } } }, - "SPECIMENSUBSOURCE_1 menu": { - "name": "SPECIMENSUBSOURCE_1 menu", + "SpecimenSubsource1Menu": { + "name": "SpecimenSubsource1Menu", + "title": "SPECIMENSUBSOURCE_1 menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "0.25": { @@ -2023,300 +2643,422 @@ "Abdomen": { "text": "Abdomen", "meaning": "UBERON:0000916", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Abdominal Muscle": { "text": "Abdominal Muscle", "meaning": "UBERON:0002378", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Abomasum": { "text": "Abomasum", "meaning": "UBERON:0007358", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Abscess": { "text": "Abscess", "meaning": "HP:0025615", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Air Intake": { "text": "Air Intake", "meaning": "ENVO:00002005", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Air Sac": { "text": "Air Sac", "meaning": "UBERON:0009060", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Anal Gland": { "text": "Anal Gland", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Animal Pen": { "text": "Animal Pen", "meaning": "FOODON:00003004", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Balut": { "text": "Balut", "meaning": "FOODON:03302184", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Belt": { "text": "Belt", "meaning": "CURATION:0000406", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Bladder": { "text": "Bladder", "meaning": "CURATION:0000504", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Blood": { "text": "Blood", "meaning": "UBERON:0000178", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Blood vessel": { "text": "Blood vessel", "meaning": "UBERON:0001981", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Bone": { "text": "Bone", "meaning": "UBERON:0001474", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Bone Marrow": { "text": "Bone Marrow", "meaning": "UBERON:0002371", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Bootie": { "text": "Bootie", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Boots": { "text": "Boots", "meaning": "CURATION:0000401", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Brain": { "text": "Brain", "meaning": "UBERON:0000955", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Bursa of Fabricus": { "text": "Bursa of Fabricus", "meaning": "CURATION:0000502", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Cages": { "text": "Cages", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Cavity Fluid (Unspecified)": { "text": "Cavity Fluid (Unspecified)", "meaning": "CURATION:0000480", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Cavity fluid unspecified": { "text": "Cavity fluid unspecified", "meaning": "CURATION:0000480", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Cecal Content": { "text": "Cecal Content", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Cecum": { "text": "Cecum", "meaning": "CURATION:0000495", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Chick Boxes": { "text": "Chick Boxes", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Chick Pads": { "text": "Chick Pads", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Cloacae": { "text": "Cloacae", "meaning": "CURATION:0000491", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Cloacal swab": { "text": "Cloacal swab", "meaning": "NCIT:C17627", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Colon": { "text": "Colon", "meaning": "UBERON:0001155", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Confirmation": { "text": "Confirmation", - "exact_mappings": ["GRDI:?"] + "exact_mappings": [ + "GRDI:%3F" + ] }, "Crates": { "text": "Crates", "meaning": "FOODON:03490213", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Crop": { "text": "Crop", "meaning": "UBERON:0007356", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Culture Plate": { "text": "Culture Plate", - "exact_mappings": ["GRDI:collection_device:"] + "exact_mappings": [ + "GRDI:collection_device%3A" + ] }, "Digestive System (Unspecified)": { "text": "Digestive System (Unspecified)", "meaning": "UBERON:0001007", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Duodenum": { "text": "Duodenum", "meaning": "UBERON:0002114", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Dust": { "text": "Dust", "meaning": "ENVO:00002008", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Ear": { "text": "Ear", "meaning": "UBERON:0001690", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Egg Belt": { "text": "Egg Belt", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Environment Swab": { "text": "Environment Swab", - "exact_mappings": ["GRDI:collection_device:"] + "exact_mappings": [ + "GRDI:collection_device%3A" + ] }, "Environment Swab (Hatchery)": { "text": "Environment Swab (Hatchery)", "exact_mappings": [ - "GRDI:environmental_site:hatchery", - "GRDI:collection_device:swab" + "GRDI:environmental_site%3Ahatchery", + "GRDI:collection_device%3Aswab" ] }, "Esophagus": { "text": "Esophagus", "meaning": "UBERON:0001043", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "External Quality Assurance": { "text": "External Quality Assurance", "meaning": "BFO:0000019", - "exact_mappings": ["GRDI:?"] + "exact_mappings": [ + "GRDI:%3F" + ] }, "Eye": { "text": "Eye", "meaning": "UBERON:0000970", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Fan": { "text": "Fan", "meaning": "ENVO:00000104", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Fecal Slurry": { "text": "Fecal Slurry", "meaning": "UBERON:0001988", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Feces": { "text": "Feces", "meaning": "UBERON:0001988", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Feed": { "text": "Feed", "meaning": "FOODON:03309997", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Feeders and Drinkers": { "text": "Feeders and Drinkers", "meaning": "CURATION:0000419", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Fetal Tissue": { "text": "Fetal Tissue", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Final Wash": { "text": "Final Wash", "meaning": "CURATION:0001488", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Floor": { "text": "Floor", "meaning": "CURATION:0000335", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Fluff": { "text": "Fluff", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Fluff (Hatchery)": { "text": "Fluff (Hatchery)", "meaning": "ENVO:01001873", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Foot": { "text": "Foot", "meaning": "UO:0010013", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Gall Bladder": { "text": "Gall Bladder", "meaning": "UBERON:0002110", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Gallbladder": { "text": "Gallbladder", "meaning": "UBERON:0002110", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Ganglion": { "text": "Ganglion", "meaning": "UBERON:0000045", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Gizzard": { "text": "Gizzard", "meaning": "UBERON:0005052", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Growth / lesion (unspecified tissue)": { "text": "Growth / lesion (unspecified tissue)", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Growth/Lesion (Unspecified Tissue)": { "text": "Growth/Lesion (Unspecified Tissue)", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Heart": { "text": "Heart", "meaning": "UBERON:0000948", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Ileum": { "text": "Ileum", "meaning": "UBERON:0002116", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "In-House": { "text": "In-House", @@ -2328,211 +3070,297 @@ }, "Intestinal Contents": { "text": "Intestinal Contents", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Intestine": { "text": "Intestine", "meaning": "UBERON:0000160", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Jejunum": { "text": "Jejunum", "meaning": "UBERON:0002115", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Joint": { "text": "Joint", "meaning": "UBERON:0004905", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Joint Fluid": { "text": "Joint Fluid", "meaning": "UBERON:0001090", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Kidney": { "text": "Kidney", "meaning": "UBERON:0002113", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Levage/peritoneal": { "text": "Levage/peritoneal", "meaning": "CURATION:0000463", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Levage/Tracheal": { "text": "Levage/Tracheal", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Litter": { "text": "Litter", "meaning": "CURATION:0001446", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Litter/Manure": { "text": "Litter/Manure", "meaning": "CURATION:0001446", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Live Haul Truck": { "text": "Live Haul Truck", "meaning": "ENVO:01000602", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Live Haul Truck/Trailer": { "text": "Live Haul Truck/Trailer", "meaning": "ENVO:01000602", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Liver": { "text": "Liver", "meaning": "UBERON:0002107", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Lung": { "text": "Lung", "meaning": "UBERON:0002048", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Lymph Node": { "text": "Lymph Node", "meaning": "UBERON:0000029", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Manure Pit": { "text": "Manure Pit", "meaning": "ENVO:01001872", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Meconium": { "text": "Meconium", "meaning": "UBERON:0007109", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Mesenteric Lymph Node": { "text": "Mesenteric Lymph Node", "meaning": "UBERON:0002509", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Milk/Colostrum": { "text": "Milk/Colostrum", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Mixed": { "text": "Mixed", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Mixed Organs": { "text": "Mixed Organs", "meaning": "UBERON:0000062", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Mixed Tissues": { "text": "Mixed Tissues", "meaning": "UBERON:0000479", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Mouth": { "text": "Mouth", "meaning": "UBERON:0000165", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Mucous membrane (gut)": { "text": "Mucous membrane (gut)", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Mucous membrane (resp)": { "text": "Mucous membrane (resp)", "meaning": "UBERON:0000344", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Mucus": { "text": "Mucus", "meaning": "UBERON:0000912", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Muscle": { "text": "Muscle", "meaning": "CURATION:0001428", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Muscle/Meat": { "text": "Muscle/Meat", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Nasal Turbinate": { "text": "Nasal Turbinate", "meaning": "UBERON:0035612", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Nasal/Naries": { "text": "Nasal/Naries", "meaning": "CURATION:0000466", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Organ Unspecified": { "text": "Organ Unspecified", "meaning": "UBERON:0000062", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Ovary": { "text": "Ovary", "meaning": "UBERON:0000992", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Oviduct": { "text": "Oviduct", "meaning": "UBERON:0000993", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Pericardium": { "text": "Pericardium", "meaning": "UBERON:0002407", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Peritoneal Fluid": { "text": "Peritoneal Fluid", "meaning": "UBERON:0001268", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Peritoneum": { "text": "Peritoneum", "meaning": "UBERON:0002358", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Placenta": { "text": "Placenta", "meaning": "UBERON:0001987", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Pleura": { "text": "Pleura", "meaning": "UBERON:0000977", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Plucking Belt": { "text": "Plucking Belt", "meaning": "CURATION:0000406", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Plucking Water": { "text": "Plucking Water", "meaning": "CHEBI:15377", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Pooled Feces": { "text": "Pooled Feces", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Rectal Swab": { "text": "Rectal Swab", "meaning": "CURATION:0000457", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Rectum": { "text": "Rectum", "meaning": "UBERON:0001052", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Research": { "text": "Research", @@ -2541,162 +3369,227 @@ "Rinse": { "text": "Rinse", "meaning": "CURATION:0001629", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Rumen": { "text": "Rumen", "meaning": "UBERON:0007365", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Shell": { "text": "Shell", "meaning": "UBERON:0006612", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Shell egg": { "text": "Shell egg", "meaning": "UBERON:0005079", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sinus": { "text": "Sinus", "meaning": "CURATION:0000455", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Skin": { "text": "Skin", "meaning": "UBERON:0000014", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Small Intestine": { "text": "Small Intestine", "meaning": "UBERON:0002108", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Soil": { "text": "Soil", "meaning": "ENVO:00001998", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Spinal Cord": { "text": "Spinal Cord", "meaning": "UBERON:0002240", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Spleen": { "text": "Spleen", "meaning": "UBERON:0002106", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Stall": { "text": "Stall", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Stomach": { "text": "Stomach", "meaning": "UBERON:0000945", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Stomach Contents": { "text": "Stomach Contents", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Swab": { "text": "Swab", "meaning": "NCIT:C17627", - "exact_mappings": ["GRDI:collection_device:"] + "exact_mappings": [ + "GRDI:collection_device%3A" + ] }, "Swab (Nasal)": { "text": "Swab (Nasal)", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Swab (Rectal)": { "text": "Swab (Rectal)", "meaning": "CURATION:0000457", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Swab (Tissue Fluid-Unspecified)": { "text": "Swab (Tissue Fluid-Unspecified)", - "exact_mappings": ["GRDI:anatomical_material:"] + "exact_mappings": [ + "GRDI:anatomical_material%3A" + ] }, "Testicle": { "text": "Testicle", "meaning": "UBERON:0000473", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Thorax": { "text": "Thorax", "meaning": "UBERON:0000915", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Trachea": { "text": "Trachea", "meaning": "UBERON:0003126", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Unknown organ": { "text": "Unknown organ", "meaning": "UBERON:0000062", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Unspecified Organ/Tissue": { "text": "Unspecified Organ/Tissue", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Urine": { "text": "Urine", "meaning": "UBERON:0001088", - "exact_mappings": ["GRDI:body_product:"] + "exact_mappings": [ + "GRDI:body_product%3A" + ] }, "Uterus": { "text": "Uterus", "meaning": "UBERON:0000995", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Vagina": { "text": "Vagina", "meaning": "UBERON:0000996", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Walls": { "text": "Walls", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Water": { "text": "Water", "meaning": "CHEBI:15377", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Watering Bowl/Equipment": { "text": "Watering Bowl/Equipment", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Weekly": { "text": "Weekly" }, "Weep": { "text": "Weep", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Whole": { "text": "Whole", "meaning": "FOODON:03430131", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Yolk": { "text": "Yolk", "meaning": "UBERON:2000084", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Yolk Sac": { "text": "Yolk Sac", "meaning": "UBERON:0001040", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] } } }, - "SUBJECT_SUBTYPE menu": { - "name": "SUBJECT_SUBTYPE menu", + "SubjectSubtypeMenu": { + "name": "SubjectSubtypeMenu", + "title": "SUBJECT_SUBTYPE menu", "from_schema": "https://example.com/PHAC_Dexa", "permissible_values": { "<=32": { @@ -2711,313 +3604,445 @@ "Alfalfa Sprouts": { "text": "Alfalfa Sprouts", "meaning": "FOODON:00002670", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Almond": { "text": "Almond", "meaning": "FOODON:03301355", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Animal pen": { "text": "Animal pen", "meaning": "FOODON:00003004", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Artificial wetland": { "text": "Artificial wetland", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Arugula": { "text": "Arugula", "meaning": "FOODON:00002426", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Basil": { "text": "Basil", "meaning": "FOODON:00003044", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Bean Sprouts": { "text": "Bean Sprouts", "meaning": "FOODON:00002576", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Biosolid": { "text": "Biosolid", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Biosolid/Sludge": { "text": "Biosolid/Sludge", "meaning": "ENVO:00002044", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Bootie": { "text": "Bootie", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Boots": { "text": "Boots", "meaning": "CURATION:0000401", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Breast": { "text": "Breast", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast skinless": { "text": "Breast skinless", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast skinless boneless": { "text": "Breast skinless boneless", "meaning": "UBERON:0000310", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Breast with skin": { "text": "Breast with skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Broom": { "text": "Broom", "meaning": "CURATION:0000397", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Bulk Tank": { "text": "Bulk Tank", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Cantaloupe": { "text": "Cantaloupe", "meaning": "CURATION:0001383", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Carcass (whole)": { "text": "Carcass (whole)", - "exact_mappings": ["GRDI:anatomical_part:"] + "exact_mappings": [ + "GRDI:anatomical_part%3A" + ] }, "Cheese": { "text": "Cheese", "meaning": "FOODON:00001013", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chia Powder": { "text": "Chia Powder", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chia Seeds": { "text": "Chia Seeds", "meaning": "CURATION:0001385", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chia Sprouts": { "text": "Chia Sprouts", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chick Boxes": { "text": "Chick Boxes", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Chick Pads": { "text": "Chick Pads", "meaning": "UBERON:2001977", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Chickpea": { "text": "Chickpea", "meaning": "FOODON:03306811", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chili": { "text": "Chili", "meaning": "FOODON:03301511", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chilli Pepper": { "text": "Chilli Pepper", "meaning": "FOODON:03315873", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chives": { "text": "Chives", "meaning": "FOODON:03311167", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Chops": { "text": "Chops", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Coconut": { "text": "Coconut", "meaning": "FOODON:03303085", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Compost": { "text": "Compost", "meaning": "CURATION:0001527", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Cooler Line": { "text": "Cooler Line", "meaning": "SIO:000511", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Coriander Seeds": { "text": "Coriander Seeds", "meaning": "PO:0009010", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Coriander-Cumin Powder": { "text": "Coriander-Cumin Powder", "meaning": "FOODON:00002976", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Cottage": { "text": "Cottage", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Cucumber": { "text": "Cucumber", "meaning": "FOODON:03301545", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Curry Leaves": { "text": "Curry Leaves", "meaning": "FOODON:03306648", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Curry powder": { "text": "Curry powder", "meaning": "FOODON:03301842", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Cut": { "text": "Cut", "meaning": "ENVO:00000474", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Dead Haul Truck / Trailer": { "text": "Dead Haul Truck / Trailer", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Dill": { "text": "Dill", "meaning": "FOODON:00001811", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Drumstick": { "text": "Drumstick", "meaning": "CURATION:0001378", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Dumpster": { "text": "Dumpster", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Effluent": { "text": "Effluent", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Egg": { "text": "Egg", "meaning": "FOODON:00001274", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Egg Belt": { "text": "Egg Belt", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Fan": { "text": "Fan", "meaning": "ENVO:00000104", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Feed Pans": { "text": "Feed Pans", "meaning": "FOODON:03309997", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Fennel": { "text": "Fennel", "meaning": "FOODON:03309953", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Filet": { "text": "Filet", "meaning": "FOODON:03530144", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Flax and Chia Powder": { "text": "Flax and Chia Powder", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Flax Powder": { "text": "Flax Powder", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Floor": { "text": "Floor", "meaning": "CURATION:0000335", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "For Avian": { "text": "For Avian", "meaning": "FOODON:00002616", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Beef Cattle": { "text": "For Beef Cattle", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Cats": { "text": "For Cats", "meaning": "CURATION:0001354", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Cattle (Beef)": { "text": "For Cattle (Beef)", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Cattle (Dairy)": { "text": "For Cattle (Dairy)", "meaning": "FOODON:00002505", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Chicken": { "text": "For Chicken", "meaning": "FOODON:03411457", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Dairy Cows": { "text": "For Dairy Cows", "meaning": "FOODON:03411201", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Dogs": { "text": "For Dogs", "meaning": "CURATION:0001351", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Fish": { "text": "For Fish", "meaning": "FOODON:03411222", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Goats": { "text": "For Goats", "meaning": "FOODON:03411328", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Horse": { "text": "For Horse", "meaning": "FOODON:03411229", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Mink": { "text": "For Mink", "meaning": "FOODON:00002723", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Others": { "text": "For Others" @@ -3025,237 +4050,339 @@ "For Poultry": { "text": "For Poultry", "meaning": "FOODON:00001131", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Swine": { "text": "For Swine", "meaning": "FOODON:03411136", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Turkeys": { "text": "For Turkeys", "meaning": "FOODON:03414166", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "For Unknown": { "text": "For Unknown" }, "For Unspecified": { "text": "For Unspecified", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Garlic Powder": { "text": "Garlic Powder", "meaning": "FOODON:03301844", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ginger": { "text": "Ginger", "meaning": "FOODON:00002718", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Green Onion": { "text": "Green Onion", "meaning": "FOODON:03411478", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground": { "text": "Ground", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (extra lean)": { "text": "Ground (extra lean)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (lean)": { "text": "Ground (lean)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (medium)": { "text": "Ground (medium)", "meaning": "FOODON:03430117", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground (regular)": { "text": "Ground (regular)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Ground Water": { "text": "Ground Water", "meaning": "ENVO:00002041", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Ham": { "text": "Ham", "meaning": "FOODON:00002502", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Hazelnut / Filbert": { "text": "Hazelnut / Filbert", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Headcheese": { "text": "Headcheese", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Herb/Spice (Unspecified)": { "text": "Herb/Spice (Unspecified)", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Irrigation": { "text": "Irrigation", "meaning": "CURATION:0000309", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Kale": { "text": "Kale", "meaning": "FOODON:03304859", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Kalonji Whole Seed": { "text": "Kalonji Whole Seed", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Lab Surface": { "text": "Lab Surface", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Lake": { "text": "Lake", "meaning": "ENVO:00000020", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Leg": { "text": "Leg", "meaning": "UBERON:0000978", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Lettuce": { "text": "Lettuce", "meaning": "FOODON:00001998", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Liquid whole": { "text": "Liquid whole", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Liver": { "text": "Liver", "meaning": "UBERON:0002107", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Loin center chop non-seasoned": { "text": "Loin center chop non-seasoned", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mango": { "text": "Mango", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Meat": { "text": "Meat", "meaning": "FOODON:00001006", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Milk": { "text": "Milk", "meaning": "UBERON:0001913", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mint": { "text": "Mint", "meaning": "FOODON:00002432", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mixed": { "text": "Mixed", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Mixed Salad/Mixed Greens": { "text": "Mixed Salad/Mixed Greens", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mixed Sprouts": { "text": "Mixed Sprouts", "meaning": "FOODON:03420183", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Mung Bean Sprouts": { "text": "Mung Bean Sprouts", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Oregano": { "text": "Oregano", "meaning": "FOODON:03301482", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other": { "text": "Other", - "exact_mappings": ["GRDI:host (common name):"] + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ] }, "Other chicken": { "text": "Other chicken", "meaning": "FOODON:03411457", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other cut (not ground)": { "text": "Other cut (not ground)", "meaning": "ENVO:00000474", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Other variety meats": { "text": "Other variety meats", "meaning": "FOODON:03420218", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Papaya": { "text": "Papaya", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Paprika": { "text": "Paprika", "meaning": "FOODON:03301105", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Parsley": { "text": "Parsley", "meaning": "FOODON:00002942", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pea Sprouts": { "text": "Pea Sprouts", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pepper": { "text": "Pepper", "meaning": "FOODON:00001649", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pepper Powder": { "text": "Pepper Powder", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Pepperoni": { "text": "Pepperoni", "meaning": "FOODON:03311003", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Rasam Powder Spice": { "text": "Rasam Powder Spice", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "River": { "text": "River", "meaning": "ENVO:00000022", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "River Surface": { "text": "River Surface", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Roast": { "text": "Roast", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Rolled": { "text": "Rolled" @@ -3263,139 +4390,197 @@ "Run Off": { "text": "Run Off", "meaning": "ENVO:00000029", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Sausage": { "text": "Sausage", "meaning": "FOODON:03315904", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Scallopini": { "text": "Scallopini", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sediment": { "text": "Sediment", "meaning": "ENVO:00002007", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Sesame Seed": { "text": "Sesame Seed", "meaning": "FOODON:03310306", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shelf / Sill": { "text": "Shelf / Sill", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Shellfish": { "text": "Shellfish", "meaning": "FOODON:03411433", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shoulder": { "text": "Shoulder", "meaning": "UBERON:0001467", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shoulder Chop": { "text": "Shoulder Chop", "meaning": "UBERON:0001467", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Shoulder chop non-seasoned": { "text": "Shoulder chop non-seasoned", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Soft": { "text": "Soft", "meaning": "PATO:0000387", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Soybean": { "text": "Soybean", "meaning": "FOODON:03301415", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Spinach": { "text": "Spinach", "meaning": "FOODON:03301716", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sprouted Seeds": { "text": "Sprouted Seeds", "meaning": "FOODON:03420102", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Sprouts": { "text": "Sprouts", "meaning": "FOODON:03420183", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Stall": { "text": "Stall", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Steak": { "text": "Steak", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Stew Chunks": { "text": "Stew Chunks", "meaning": "FOODON:00003140", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Surface - Other": { "text": "Surface - Other", "meaning": "CURATION:0000247", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Surface - River": { "text": "Surface - River", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Surface unspecified": { "text": "Surface unspecified", "meaning": "CURATION:0000247", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Surface Water": { "text": "Surface Water", "meaning": "ENVO:00002042", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Tenderloin": { "text": "Tenderloin", "meaning": "FOODON:03530217", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Thigh": { "text": "Thigh", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Thigh with skin": { "text": "Thigh with skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Transformer": { "text": "Transformer", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Truck / Trailer": { "text": "Truck / Trailer", "meaning": "ENVO:01000602", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Truck/Trailer": { "text": "Truck/Trailer", "meaning": "ENVO:01000602", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Turmeric": { "text": "Turmeric", "meaning": "FOODON:03310841", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Unknown": { "text": "Unknown" @@ -3403,7 +4588,9 @@ "Unknown Surface": { "text": "Unknown Surface", "meaning": "CURATION:0000247", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Unspecified": { "text": "Unspecified" @@ -3411,986 +4598,1493 @@ "Upper Thigh": { "text": "Upper Thigh", "meaning": "UBERON:0000376", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Upper Thigh with Skin": { "text": "Upper Thigh with Skin", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Wall": { "text": "Wall", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Walnut": { "text": "Walnut", "meaning": "FOODON:03315233", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Waste Water": { "text": "Waste Water", "meaning": "ENVO:00002001", - "exact_mappings": ["GRDI:environmental_material:"] + "exact_mappings": [ + "GRDI:environmental_material%3A" + ] }, "Watering bowl/equipment": { "text": "Watering bowl/equipment", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Whole": { "text": "Whole", "meaning": "FOODON:03430131", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Wings": { "text": "Wings", "meaning": "UBERON:0000023", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] }, "Working Surface": { "text": "Working Surface", "meaning": "CURATION:0000247", - "exact_mappings": ["GRDI:environmental_site:"] + "exact_mappings": [ + "GRDI:environmental_site%3A" + ] }, "Yeast": { "text": "Yeast", "meaning": "FOODON:03411345", - "exact_mappings": ["GRDI:food_product:"] + "exact_mappings": [ + "GRDI:food_product%3A" + ] } } } }, "slots": { - "SPECIMEN_ID": { - "name": "SPECIMEN_ID", + "specimen_id": { + "name": "specimen_id", "title": "SPECIMEN_ID", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:alternative_sample_ID"], + "exact_mappings": [ + "GRDI:alternative_sample_ID" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "ISOLATE_ID": { - "name": "ISOLATE_ID", + "isolate_id": { + "name": "isolate_id", "title": "ISOLATE_ID", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:isolate_ID"], + "exact_mappings": [ + "GRDI:isolate_ID" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString", "required": true }, - "SAMPLE_ID": { - "name": "SAMPLE_ID", + "sample_id": { + "name": "sample_id", "title": "SAMPLE_ID", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:sample_collector_sample_ID"], + "exact_mappings": [ + "GRDI:sample_collector_sample_ID" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString", "required": true }, - "SENTINEL_SITE": { - "name": "SENTINEL_SITE", + "sentinel_site": { + "name": "sentinel_site", "title": "SENTINEL_SITE", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "LFZ_ADDITIONAL_SAMPLE_ID": { - "name": "LFZ_ADDITIONAL_SAMPLE_ID", + "lfz_additional_sample_id": { + "name": "lfz_additional_sample_id", "title": "LFZ_ADDITIONAL_SAMPLE_ID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "LFZ_ORIGIN_COUNTRY": { - "name": "LFZ_ORIGIN_COUNTRY", + "lfz_origin_country": { + "name": "lfz_origin_country", "title": "LFZ_ORIGIN_COUNTRY", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SUBJECT_CODE": { - "name": "SUBJECT_CODE", + "subject_code": { + "name": "subject_code", "title": "SUBJECT_CODE", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SUBJECT_DESCRIPTIONS": { - "name": "SUBJECT_DESCRIPTIONS", + "subject_descriptions": { + "name": "subject_descriptions", "title": "SUBJECT_DESCRIPTIONS", "from_schema": "https://example.com/PHAC_Dexa", - "range": "SUBJECT_DESCRIPTIONS menu" + "domain_of": [ + "PHACDexa" + ], + "range": "SubjectDescriptionsMenu" }, - "SUBMITTINGORG_1": { - "name": "SUBMITTINGORG_1", + "submittingorg_1": { + "name": "submittingorg_1", "title": "SUBMITTINGORG_1", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:collected_by"], + "exact_mappings": [ + "GRDI:collected_by" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SUBMITTINGLAB_1": { - "name": "SUBMITTINGLAB_1", + "submittinglab_1": { + "name": "submittinglab_1", "title": "SUBMITTINGLAB_1", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:laboratory_name"], + "exact_mappings": [ + "GRDI:laboratory_name" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "PROJECT_1": { - "name": "PROJECT_1", + "project_1": { + "name": "project_1", "title": "PROJECT_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "COUNTRY_1": { - "name": "COUNTRY_1", + "country_1": { + "name": "country_1", "title": "COUNTRY_1", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:geo_loc_name (country)"], + "exact_mappings": [ + "GRDI:geo_loc_name%20%28country%29" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "PROVINCE_1": { - "name": "PROVINCE_1", + "province_1": { + "name": "province_1", "title": "PROVINCE_1", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:geo_loc_name (state/province/region)"], + "exact_mappings": [ + "GRDI:geo_loc_name%20%28state/province/region%29" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CENSUSDIVISION_1": { - "name": "CENSUSDIVISION_1", + "censusdivision_1": { + "name": "censusdivision_1", "title": "CENSUSDIVISION_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "REGION": { - "name": "REGION", + "region": { + "name": "region", "title": "REGION", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "YEAR": { - "name": "YEAR", + "year": { + "name": "year", "title": "YEAR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MONTH": { - "name": "MONTH", + "month": { + "name": "month", "title": "MONTH", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "QTR": { - "name": "QTR", + "qtr": { + "name": "qtr", "title": "QTR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "DATECOLLECTED_1": { - "name": "DATECOLLECTED_1", + "datecollected_1": { + "name": "datecollected_1", "title": "DATECOLLECTED_1", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:sample_collection_date"], + "exact_mappings": [ + "GRDI:sample_collection_date" + ], + "domain_of": [ + "PHACDexa" + ], "range": "date" }, - "DATERECEIVED_1": { - "name": "DATERECEIVED_1", + "datereceived_1": { + "name": "datereceived_1", "title": "DATERECEIVED_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "DATESHIPPED_1": { - "name": "DATESHIPPED_1", + "dateshipped_1": { + "name": "dateshipped_1", "title": "DATESHIPPED_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "ESTABLISHMENT_1": { - "name": "ESTABLISHMENT_1", + "establishment_1": { + "name": "establishment_1", "title": "ESTABLISHMENT_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SPECIES": { - "name": "SPECIES", + "species": { + "name": "species", "title": "SPECIES", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:host (common name):"], - "range": "SPECIES menu" + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ], + "domain_of": [ + "PHACDexa" + ], + "range": "SpeciesMenu" }, - "STTYPE": { - "name": "STTYPE", + "sttype": { + "name": "sttype", "title": "STTYPE", "from_schema": "https://example.com/PHAC_Dexa", - "range": "STTYPE menu" + "domain_of": [ + "PHACDexa" + ], + "range": "STTypeMenu" }, - "STYPE": { - "name": "STYPE", + "stype": { + "name": "stype", "title": "STYPE", "from_schema": "https://example.com/PHAC_Dexa", - "range": "STYPE menu" + "domain_of": [ + "PHACDexa" + ], + "range": "STypeMenu" }, - "COMMODITY": { - "name": "COMMODITY", + "commodity": { + "name": "commodity", "title": "COMMODITY", "from_schema": "https://example.com/PHAC_Dexa", - "range": "COMMODITY menu" + "domain_of": [ + "PHACDexa" + ], + "range": "CommodityMenu" }, - "SPECIMENSOURCE_1": { - "name": "SPECIMENSOURCE_1", + "specimensource_1": { + "name": "specimensource_1", "title": "SPECIMENSOURCE_1", "from_schema": "https://example.com/PHAC_Dexa", - "range": "SPECIMENSOURCE_1 menu" + "domain_of": [ + "PHACDexa" + ], + "range": "SpecimenSource1Menu" }, - "SPECIMENSUBSOURCE_1": { - "name": "SPECIMENSUBSOURCE_1", + "specimensubsource_1": { + "name": "specimensubsource_1", "title": "SPECIMENSUBSOURCE_1", "from_schema": "https://example.com/PHAC_Dexa", - "range": "SPECIMENSUBSOURCE_1 menu" + "domain_of": [ + "PHACDexa" + ], + "range": "SpecimenSubsource1Menu" }, - "SUBJECT_SUBTYPE": { - "name": "SUBJECT_SUBTYPE", + "subject_subtype": { + "name": "subject_subtype", "title": "SUBJECT_SUBTYPE", "from_schema": "https://example.com/PHAC_Dexa", - "range": "SUBJECT_SUBTYPE menu" + "domain_of": [ + "PHACDexa" + ], + "range": "SubjectSubtypeMenu" }, - "FIELDSTAFF_1": { - "name": "FIELDSTAFF_1", + "fieldstaff_1": { + "name": "fieldstaff_1", "title": "FIELDSTAFF_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "IN_STORE_PROCESSING": { - "name": "IN_STORE_PROCESSING", + "in_store_processing": { + "name": "in_store_processing", "title": "IN_STORE_PROCESSING", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MAYCONTAINFROZENMEAT_1": { - "name": "MAYCONTAINFROZENMEAT_1", + "maycontainfrozenmeat_1": { + "name": "maycontainfrozenmeat_1", "title": "MAYCONTAINFROZENMEAT_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "NOOFCASHREGISTERS_1": { - "name": "NOOFCASHREGISTERS_1", + "noofcashregisters_1": { + "name": "noofcashregisters_1", "title": "NOOFCASHREGISTERS_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "PRICEPERKG_1": { - "name": "PRICEPERKG_1", + "priceperkg_1": { + "name": "priceperkg_1", "title": "PRICEPERKG_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "STORETYPE_SAMPLINGSITE_1": { - "name": "STORETYPE_SAMPLINGSITE_1", + "storetype_samplingsite_1": { + "name": "storetype_samplingsite_1", "title": "STORETYPE_SAMPLINGSITE_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "TEMPERATUREMAX_1": { - "name": "TEMPERATUREMAX_1", + "temperaturemax_1": { + "name": "temperaturemax_1", "title": "TEMPERATUREMAX_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "TEMPERATUREMIN_1": { - "name": "TEMPERATUREMIN_1", + "temperaturemin_1": { + "name": "temperaturemin_1", "title": "TEMPERATUREMIN_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "TEMPERATUREARRIVAL_1": { - "name": "TEMPERATUREARRIVAL_1", + "temperaturearrival_1": { + "name": "temperaturearrival_1", "title": "TEMPERATUREARRIVAL_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "VETID": { - "name": "VETID", + "vetid": { + "name": "vetid", "title": "VETID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "ROOMID": { - "name": "ROOMID", + "roomid": { + "name": "roomid", "title": "ROOMID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "PENID": { - "name": "PENID", + "penid": { + "name": "penid", "title": "PENID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SAMPLING_TYPE": { - "name": "SAMPLING_TYPE", + "sampling_type": { + "name": "sampling_type", "title": "SAMPLING_TYPE", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "BARN_ID": { - "name": "BARN_ID", + "barn_id": { + "name": "barn_id", "title": "BARN_ID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "DATE_PACKED": { - "name": "DATE_PACKED", + "date_packed": { + "name": "date_packed", "title": "DATE_PACKED", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FINAL_ID_GENUS": { - "name": "FINAL_ID_GENUS", + "final_id_genus": { + "name": "final_id_genus", "title": "FINAL_ID_GENUS", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:organism"], + "exact_mappings": [ + "GRDI:organism" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FINAL_ID_SPECIES": { - "name": "FINAL_ID_SPECIES", + "final_id_species": { + "name": "final_id_species", "title": "FINAL_ID_SPECIES", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:organism"], + "exact_mappings": [ + "GRDI:organism" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FINAL_ID_SUBSPECIES": { - "name": "FINAL_ID_SUBSPECIES", + "final_id_subspecies": { + "name": "final_id_subspecies", "title": "FINAL_ID_SUBSPECIES", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FINAL_ID_SEROTYPE": { - "name": "FINAL_ID_SEROTYPE", + "final_id_serotype": { + "name": "final_id_serotype", "title": "FINAL_ID_SEROTYPE", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:serovar"], + "exact_mappings": [ + "GRDI:serovar" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FINAL_ID_ANTIGEN": { - "name": "FINAL_ID_ANTIGEN", + "final_id_antigen": { + "name": "final_id_antigen", "title": "FINAL_ID_ANTIGEN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FINAL_ID_PHAGETYPE": { - "name": "FINAL_ID_PHAGETYPE", + "final_id_phagetype": { + "name": "final_id_phagetype", "title": "FINAL_ID_PHAGETYPE", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:phagetype"], + "exact_mappings": [ + "GRDI:phagetype" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SA_Serotype_Method": { - "name": "SA_Serotype_Method", + "sa_serotype_method": { + "name": "sa_serotype_method", "title": "SA_Serotype_Method", "from_schema": "https://example.com/PHAC_Dexa", - "exact_mappings": ["GRDI:serotyping_method"], + "exact_mappings": [ + "GRDI:serotyping_method" + ], + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SEROTYPE_GR": { - "name": "SEROTYPE_GR", + "serotype_gr": { + "name": "serotype_gr", "title": "SEROTYPE_GR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_AMC": { - "name": "MIC_AMC", + "mic_amc": { + "name": "mic_amc", "title": "MIC_AMC", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_AMK": { - "name": "MIC_AMK", + "mic_amk": { + "name": "mic_amk", "title": "MIC_AMK", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_AMP": { - "name": "MIC_AMP", + "mic_amp": { + "name": "mic_amp", "title": "MIC_AMP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_AZM": { - "name": "MIC_AZM", + "mic_azm": { + "name": "mic_azm", "title": "MIC_AZM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_CEP": { - "name": "MIC_CEP", + "mic_cep": { + "name": "mic_cep", "title": "MIC_CEP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_CHL": { - "name": "MIC_CHL", + "mic_chl": { + "name": "mic_chl", "title": "MIC_CHL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_CIP": { - "name": "MIC_CIP", + "mic_cip": { + "name": "mic_cip", "title": "MIC_CIP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_CRO": { - "name": "MIC_CRO", + "mic_cro": { + "name": "mic_cro", "title": "MIC_CRO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_FOX": { - "name": "MIC_FOX", + "mic_fox": { + "name": "mic_fox", "title": "MIC_FOX", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_GEN": { - "name": "MIC_GEN", + "mic_gen": { + "name": "mic_gen", "title": "MIC_GEN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_KAN": { - "name": "MIC_KAN", + "mic_kan": { + "name": "mic_kan", "title": "MIC_KAN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_MEM": { - "name": "MIC_MEM", + "mic_mem": { + "name": "mic_mem", "title": "MIC_MEM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_NAL": { - "name": "MIC_NAL", + "mic_nal": { + "name": "mic_nal", "title": "MIC_NAL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_SSS": { - "name": "MIC_SSS", + "mic_sss": { + "name": "mic_sss", "title": "MIC_SSS", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_STR": { - "name": "MIC_STR", + "mic_str": { + "name": "mic_str", "title": "MIC_STR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_SXT": { - "name": "MIC_SXT", + "mic_sxt": { + "name": "mic_sxt", "title": "MIC_SXT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_TET": { - "name": "MIC_TET", + "mic_tet": { + "name": "mic_tet", "title": "MIC_TET", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MIC_TIO": { - "name": "MIC_TIO", + "mic_tio": { + "name": "mic_tio", "title": "MIC_TIO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "N_OF_RESISTANCE": { - "name": "N_OF_RESISTANCE", + "n_of_resistance": { + "name": "n_of_resistance", "title": "N_OF_RESISTANCE", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "NBTESTED": { - "name": "NBTESTED", + "nbtested": { + "name": "nbtested", "title": "NBTESTED", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "R_PATTERN": { - "name": "R_PATTERN", + "r_pattern": { + "name": "r_pattern", "title": "R_PATTERN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "AMR_PA2C": { - "name": "AMR_PA2C", + "amr_pa2c": { + "name": "amr_pa2c", "title": "AMR_PA2C", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RLEAST1": { - "name": "RLEAST1", + "rleast1": { + "name": "rleast1", "title": "RLEAST1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RLEAST2": { - "name": "RLEAST2", + "rleast2": { + "name": "rleast2", "title": "RLEAST2", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RLEAST3": { - "name": "RLEAST3", + "rleast3": { + "name": "rleast3", "title": "RLEAST3", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RLEAST4": { - "name": "RLEAST4", + "rleast4": { + "name": "rleast4", "title": "RLEAST4", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RLEAST5": { - "name": "RLEAST5", + "rleast5": { + "name": "rleast5", "title": "RLEAST5", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_AMC": { - "name": "SIR_AMC", + "sir_amc": { + "name": "sir_amc", "title": "SIR_AMC", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_AMK": { - "name": "SIR_AMK", + "sir_amk": { + "name": "sir_amk", "title": "SIR_AMK", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_AMP": { - "name": "SIR_AMP", + "sir_amp": { + "name": "sir_amp", "title": "SIR_AMP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_AZM": { - "name": "SIR_AZM", + "sir_azm": { + "name": "sir_azm", "title": "SIR_AZM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_CEP": { - "name": "SIR_CEP", + "sir_cep": { + "name": "sir_cep", "title": "SIR_CEP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_CHL": { - "name": "SIR_CHL", + "sir_chl": { + "name": "sir_chl", "title": "SIR_CHL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_CIP": { - "name": "SIR_CIP", + "sir_cip": { + "name": "sir_cip", "title": "SIR_CIP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_CRO": { - "name": "SIR_CRO", + "sir_cro": { + "name": "sir_cro", "title": "SIR_CRO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_FOX": { - "name": "SIR_FOX", + "sir_fox": { + "name": "sir_fox", "title": "SIR_FOX", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_GEN": { - "name": "SIR_GEN", + "sir_gen": { + "name": "sir_gen", "title": "SIR_GEN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_KAN": { - "name": "SIR_KAN", + "sir_kan": { + "name": "sir_kan", "title": "SIR_KAN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_MEM": { - "name": "SIR_MEM", + "sir_mem": { + "name": "sir_mem", "title": "SIR_MEM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_NAL": { - "name": "SIR_NAL", + "sir_nal": { + "name": "sir_nal", "title": "SIR_NAL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_SSS": { - "name": "SIR_SSS", + "sir_sss": { + "name": "sir_sss", "title": "SIR_SSS", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_STR": { - "name": "SIR_STR", + "sir_str": { + "name": "sir_str", "title": "SIR_STR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_SXT": { - "name": "SIR_SXT", + "sir_sxt": { + "name": "sir_sxt", "title": "SIR_SXT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_TET": { - "name": "SIR_TET", + "sir_tet": { + "name": "sir_tet", "title": "SIR_TET", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "SIR_TIO": { - "name": "SIR_TIO", + "sir_tio": { + "name": "sir_tio", "title": "SIR_TIO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RAMC": { - "name": "RAMC", + "ramc": { + "name": "ramc", "title": "RAMC", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RAMK": { - "name": "RAMK", + "ramk": { + "name": "ramk", "title": "RAMK", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RAMP": { - "name": "RAMP", + "ramp": { + "name": "ramp", "title": "RAMP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RAZM": { - "name": "RAZM", + "razm": { + "name": "razm", "title": "RAZM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RCEP": { - "name": "RCEP", + "rcep": { + "name": "rcep", "title": "RCEP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RCHL": { - "name": "RCHL", + "rchl": { + "name": "rchl", "title": "RCHL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RCIP": { - "name": "RCIP", + "rcip": { + "name": "rcip", "title": "RCIP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RCRO": { - "name": "RCRO", + "rcro": { + "name": "rcro", "title": "RCRO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RFOX": { - "name": "RFOX", + "rfox": { + "name": "rfox", "title": "RFOX", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RGEN": { - "name": "RGEN", + "rgen": { + "name": "rgen", "title": "RGEN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RKAN": { - "name": "RKAN", + "rkan": { + "name": "rkan", "title": "RKAN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RMEM": { - "name": "RMEM", + "rmem": { + "name": "rmem", "title": "RMEM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RNAL": { - "name": "RNAL", + "rnal": { + "name": "rnal", "title": "RNAL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RSSS": { - "name": "RSSS", + "rsss": { + "name": "rsss", "title": "RSSS", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RSTR": { - "name": "RSTR", + "rstr": { + "name": "rstr", "title": "RSTR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RSXT": { - "name": "RSXT", + "rsxt": { + "name": "rsxt", "title": "RSXT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RTET": { - "name": "RTET", + "rtet": { + "name": "rtet", "title": "RTET", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RTIO": { - "name": "RTIO", + "rtio": { + "name": "rtio", "title": "RTIO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "A2C": { - "name": "A2C", + "a2c": { + "name": "a2c", "title": "A2C", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CAMC": { - "name": "CAMC", + "camc": { + "name": "camc", "title": "CAMC", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CAMK": { - "name": "CAMK", + "camk": { + "name": "camk", "title": "CAMK", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CAMP": { - "name": "CAMP", + "camp": { + "name": "camp", "title": "CAMP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CAZM": { - "name": "CAZM", + "cazm": { + "name": "cazm", "title": "CAZM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CCEP": { - "name": "CCEP", + "ccep": { + "name": "ccep", "title": "CCEP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CCHL": { - "name": "CCHL", + "cchl": { + "name": "cchl", "title": "CCHL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CCIP": { - "name": "CCIP", + "ccip": { + "name": "ccip", "title": "CCIP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CCRO": { - "name": "CCRO", + "ccro": { + "name": "ccro", "title": "CCRO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CFOX": { - "name": "CFOX", + "cfox": { + "name": "cfox", "title": "CFOX", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CGEN": { - "name": "CGEN", + "cgen": { + "name": "cgen", "title": "CGEN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CKAN": { - "name": "CKAN", + "ckan": { + "name": "ckan", "title": "CKAN", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CMEM": { - "name": "CMEM", + "cmem": { + "name": "cmem", "title": "CMEM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CNAL": { - "name": "CNAL", + "cnal": { + "name": "cnal", "title": "CNAL", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CSSS": { - "name": "CSSS", + "csss": { + "name": "csss", "title": "CSSS", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CSTR": { - "name": "CSTR", + "cstr": { + "name": "cstr", "title": "CSTR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CSXT": { - "name": "CSXT", + "csxt": { + "name": "csxt", "title": "CSXT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CTET": { - "name": "CTET", + "ctet": { + "name": "ctet", "title": "CTET", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "CTIO": { - "name": "CTIO", + "ctio": { + "name": "ctio", "title": "CTIO", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "STHY_TESTSRC_ID": { - "name": "STHY_TESTSRC_ID", + "sthy_testsrc_id": { + "name": "sthy_testsrc_id", "title": "STHY_TESTSRC_ID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "WINN_TESTSRC_ID": { - "name": "WINN_TESTSRC_ID", + "winn_testsrc_id": { + "name": "winn_testsrc_id", "title": "WINN_TESTSRC_ID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "GUEL_TESTSRC_ID": { - "name": "GUEL_TESTSRC_ID", + "guel_testsrc_id": { + "name": "guel_testsrc_id", "title": "GUEL_TESTSRC_ID", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RCIP_DANMAP": { - "name": "RCIP_DANMAP", + "rcip_danmap": { + "name": "rcip_danmap", "title": "RCIP_DANMAP", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "EPIDATESTAMP_1": { - "name": "EPIDATESTAMP_1", + "epidatestamp_1": { + "name": "epidatestamp_1", "title": "EPIDATESTAMP_1", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "ACSSUT": { - "name": "ACSSUT", + "acssut": { + "name": "acssut", "title": "ACSSUT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "AKSSUT": { - "name": "AKSSUT", + "akssut": { + "name": "akssut", "title": "AKSSUT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "ACKSSUT": { - "name": "ACKSSUT", + "ackssut": { + "name": "ackssut", "title": "ACKSSUT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MDR_A_SSUT": { - "name": "MDR_A_SSUT", + "mdr_a_ssut": { + "name": "mdr_a_ssut", "title": "MDR_A_SSUT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "EXCLUSION": { - "name": "EXCLUSION", + "exclusion": { + "name": "exclusion", "title": "EXCLUSION", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RAMINOGLY": { - "name": "RAMINOGLY", + "raminogly": { + "name": "raminogly", "title": "RAMINOGLY", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RBETALACTAM": { - "name": "RBETALACTAM", + "rbetalactam": { + "name": "rbetalactam", "title": "RBETALACTAM", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RQUINOLONES": { - "name": "RQUINOLONES", + "rquinolones": { + "name": "rquinolones", "title": "RQUINOLONES", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "RFOLINHIBITOR": { - "name": "RFOLINHIBITOR", + "rfolinhibitor": { + "name": "rfolinhibitor", "title": "RFOLINHIBITOR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "MDR": { - "name": "MDR", + "mdr": { + "name": "mdr", "title": "MDR", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, "specimen_number": { "name": "specimen_number", "title": "specimen_number", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "EXTERNAL_AGENT": { - "name": "EXTERNAL_AGENT", + "external_agent": { + "name": "external_agent", "title": "EXTERNAL_AGENT", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "FARM_FLAG": { - "name": "FARM_FLAG", + "farm_flag": { + "name": "farm_flag", "title": "FARM_FLAG", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" }, - "AMIKACINGELET": { - "name": "AMIKACINGELET", + "amikacingelet": { + "name": "amikacingelet", "title": "AMIKACINGELET", "from_schema": "https://example.com/PHAC_Dexa", + "domain_of": [ + "PHACDexa" + ], "range": "WhitespaceMinimizedString" } }, @@ -4400,754 +6094,755 @@ "description": "A DataHarmonizer interface", "from_schema": "https://example.com/PHAC_Dexa" }, - "PHAC Dexa": { - "name": "PHAC Dexa", + "PHACDexa": { + "name": "PHACDexa", "description": "Specification for PHAC Dexa clinical virus biosample data gathering", + "title": "PHAC Dexa", "from_schema": "https://example.com/PHAC_Dexa", "is_a": "dh_interface", "slot_usage": { - "SPECIMEN_ID": { - "name": "SPECIMEN_ID", + "specimen_id": { + "name": "specimen_id", "rank": 1, "slot_group": "Database Identifiers" }, - "ISOLATE_ID": { - "name": "ISOLATE_ID", + "isolate_id": { + "name": "isolate_id", "rank": 2, "slot_group": "Database Identifiers" }, - "SAMPLE_ID": { - "name": "SAMPLE_ID", + "sample_id": { + "name": "sample_id", "rank": 3, "slot_group": "Database Identifiers" }, - "SENTINEL_SITE": { - "name": "SENTINEL_SITE", + "sentinel_site": { + "name": "sentinel_site", "rank": 4, "slot_group": "Fields to put in sections" }, - "LFZ_ADDITIONAL_SAMPLE_ID": { - "name": "LFZ_ADDITIONAL_SAMPLE_ID", + "lfz_additional_sample_id": { + "name": "lfz_additional_sample_id", "rank": 5, "slot_group": "Fields to put in sections" }, - "LFZ_ORIGIN_COUNTRY": { - "name": "LFZ_ORIGIN_COUNTRY", + "lfz_origin_country": { + "name": "lfz_origin_country", "rank": 6, "slot_group": "Fields to put in sections" }, - "SUBJECT_CODE": { - "name": "SUBJECT_CODE", + "subject_code": { + "name": "subject_code", "rank": 7, "slot_group": "Fields to put in sections" }, - "SUBJECT_DESCRIPTIONS": { - "name": "SUBJECT_DESCRIPTIONS", + "subject_descriptions": { + "name": "subject_descriptions", "rank": 8, "slot_group": "Fields to put in sections" }, - "SUBMITTINGORG_1": { - "name": "SUBMITTINGORG_1", + "submittingorg_1": { + "name": "submittingorg_1", "rank": 9, "slot_group": "Fields to put in sections" }, - "SUBMITTINGLAB_1": { - "name": "SUBMITTINGLAB_1", + "submittinglab_1": { + "name": "submittinglab_1", "rank": 10, "slot_group": "Fields to put in sections" }, - "PROJECT_1": { - "name": "PROJECT_1", + "project_1": { + "name": "project_1", "rank": 11, "slot_group": "Fields to put in sections" }, - "COUNTRY_1": { - "name": "COUNTRY_1", + "country_1": { + "name": "country_1", "rank": 12, "slot_group": "Fields to put in sections" }, - "PROVINCE_1": { - "name": "PROVINCE_1", + "province_1": { + "name": "province_1", "rank": 13, "slot_group": "Fields to put in sections" }, - "CENSUSDIVISION_1": { - "name": "CENSUSDIVISION_1", + "censusdivision_1": { + "name": "censusdivision_1", "rank": 14, "slot_group": "Fields to put in sections" }, - "REGION": { - "name": "REGION", + "region": { + "name": "region", "rank": 15, "slot_group": "Fields to put in sections" }, - "YEAR": { - "name": "YEAR", + "year": { + "name": "year", "rank": 16, "slot_group": "Fields to put in sections" }, - "MONTH": { - "name": "MONTH", + "month": { + "name": "month", "rank": 17, "slot_group": "Fields to put in sections" }, - "QTR": { - "name": "QTR", + "qtr": { + "name": "qtr", "rank": 18, "slot_group": "Fields to put in sections" }, - "DATECOLLECTED_1": { - "name": "DATECOLLECTED_1", + "datecollected_1": { + "name": "datecollected_1", "rank": 19, "slot_group": "Fields to put in sections" }, - "DATERECEIVED_1": { - "name": "DATERECEIVED_1", + "datereceived_1": { + "name": "datereceived_1", "rank": 20, "slot_group": "Fields to put in sections" }, - "DATESHIPPED_1": { - "name": "DATESHIPPED_1", + "dateshipped_1": { + "name": "dateshipped_1", "rank": 21, "slot_group": "Fields to put in sections" }, - "ESTABLISHMENT_1": { - "name": "ESTABLISHMENT_1", + "establishment_1": { + "name": "establishment_1", "rank": 22, "slot_group": "Fields to put in sections" }, - "SPECIES": { - "name": "SPECIES", + "species": { + "name": "species", "rank": 23, "slot_group": "Fields to put in sections" }, - "STTYPE": { - "name": "STTYPE", + "sttype": { + "name": "sttype", "rank": 24, "slot_group": "Fields to put in sections" }, - "STYPE": { - "name": "STYPE", + "stype": { + "name": "stype", "rank": 25, "slot_group": "Fields to put in sections" }, - "COMMODITY": { - "name": "COMMODITY", + "commodity": { + "name": "commodity", "rank": 26, "slot_group": "Fields to put in sections" }, - "SPECIMENSOURCE_1": { - "name": "SPECIMENSOURCE_1", + "specimensource_1": { + "name": "specimensource_1", "rank": 27, "slot_group": "Fields to put in sections" }, - "SPECIMENSUBSOURCE_1": { - "name": "SPECIMENSUBSOURCE_1", + "specimensubsource_1": { + "name": "specimensubsource_1", "rank": 28, "slot_group": "Fields to put in sections" }, - "SUBJECT_SUBTYPE": { - "name": "SUBJECT_SUBTYPE", + "subject_subtype": { + "name": "subject_subtype", "rank": 29, "slot_group": "Fields to put in sections" }, - "FIELDSTAFF_1": { - "name": "FIELDSTAFF_1", + "fieldstaff_1": { + "name": "fieldstaff_1", "rank": 30, "slot_group": "Fields to put in sections" }, - "IN_STORE_PROCESSING": { - "name": "IN_STORE_PROCESSING", + "in_store_processing": { + "name": "in_store_processing", "rank": 31, "slot_group": "Fields to put in sections" }, - "MAYCONTAINFROZENMEAT_1": { - "name": "MAYCONTAINFROZENMEAT_1", + "maycontainfrozenmeat_1": { + "name": "maycontainfrozenmeat_1", "rank": 32, "slot_group": "Fields to put in sections" }, - "NOOFCASHREGISTERS_1": { - "name": "NOOFCASHREGISTERS_1", + "noofcashregisters_1": { + "name": "noofcashregisters_1", "rank": 33, "slot_group": "Fields to put in sections" }, - "PRICEPERKG_1": { - "name": "PRICEPERKG_1", + "priceperkg_1": { + "name": "priceperkg_1", "rank": 34, "slot_group": "Fields to put in sections" }, - "STORETYPE_SAMPLINGSITE_1": { - "name": "STORETYPE_SAMPLINGSITE_1", + "storetype_samplingsite_1": { + "name": "storetype_samplingsite_1", "rank": 35, "slot_group": "Fields to put in sections" }, - "TEMPERATUREMAX_1": { - "name": "TEMPERATUREMAX_1", + "temperaturemax_1": { + "name": "temperaturemax_1", "rank": 36, "slot_group": "Fields to put in sections" }, - "TEMPERATUREMIN_1": { - "name": "TEMPERATUREMIN_1", + "temperaturemin_1": { + "name": "temperaturemin_1", "rank": 37, "slot_group": "Fields to put in sections" }, - "TEMPERATUREARRIVAL_1": { - "name": "TEMPERATUREARRIVAL_1", + "temperaturearrival_1": { + "name": "temperaturearrival_1", "rank": 38, "slot_group": "Fields to put in sections" }, - "VETID": { - "name": "VETID", + "vetid": { + "name": "vetid", "rank": 39, "slot_group": "Fields to put in sections" }, - "ROOMID": { - "name": "ROOMID", + "roomid": { + "name": "roomid", "rank": 40, "slot_group": "Fields to put in sections" }, - "PENID": { - "name": "PENID", + "penid": { + "name": "penid", "rank": 41, "slot_group": "Fields to put in sections" }, - "SAMPLING_TYPE": { - "name": "SAMPLING_TYPE", + "sampling_type": { + "name": "sampling_type", "rank": 42, "slot_group": "Fields to put in sections" }, - "BARN_ID": { - "name": "BARN_ID", + "barn_id": { + "name": "barn_id", "rank": 43, "slot_group": "Fields to put in sections" }, - "DATE_PACKED": { - "name": "DATE_PACKED", + "date_packed": { + "name": "date_packed", "rank": 44, "slot_group": "Fields to put in sections" }, - "FINAL_ID_GENUS": { - "name": "FINAL_ID_GENUS", + "final_id_genus": { + "name": "final_id_genus", "rank": 45, "slot_group": "Fields to put in sections" }, - "FINAL_ID_SPECIES": { - "name": "FINAL_ID_SPECIES", + "final_id_species": { + "name": "final_id_species", "rank": 46, "slot_group": "Fields to put in sections" }, - "FINAL_ID_SUBSPECIES": { - "name": "FINAL_ID_SUBSPECIES", + "final_id_subspecies": { + "name": "final_id_subspecies", "rank": 47, "slot_group": "Fields to put in sections" }, - "FINAL_ID_SEROTYPE": { - "name": "FINAL_ID_SEROTYPE", + "final_id_serotype": { + "name": "final_id_serotype", "rank": 48, "slot_group": "Fields to put in sections" }, - "FINAL_ID_ANTIGEN": { - "name": "FINAL_ID_ANTIGEN", + "final_id_antigen": { + "name": "final_id_antigen", "rank": 49, "slot_group": "Fields to put in sections" }, - "FINAL_ID_PHAGETYPE": { - "name": "FINAL_ID_PHAGETYPE", + "final_id_phagetype": { + "name": "final_id_phagetype", "rank": 50, "slot_group": "Fields to put in sections" }, - "SA_Serotype_Method": { - "name": "SA_Serotype_Method", + "sa_serotype_method": { + "name": "sa_serotype_method", "rank": 51, "slot_group": "Fields to put in sections" }, - "SEROTYPE_GR": { - "name": "SEROTYPE_GR", + "serotype_gr": { + "name": "serotype_gr", "rank": 52, "slot_group": "Fields to put in sections" }, - "MIC_AMC": { - "name": "MIC_AMC", + "mic_amc": { + "name": "mic_amc", "rank": 53, "slot_group": "Fields to put in sections" }, - "MIC_AMK": { - "name": "MIC_AMK", + "mic_amk": { + "name": "mic_amk", "rank": 54, "slot_group": "Fields to put in sections" }, - "MIC_AMP": { - "name": "MIC_AMP", + "mic_amp": { + "name": "mic_amp", "rank": 55, "slot_group": "Fields to put in sections" }, - "MIC_AZM": { - "name": "MIC_AZM", + "mic_azm": { + "name": "mic_azm", "rank": 56, "slot_group": "Fields to put in sections" }, - "MIC_CEP": { - "name": "MIC_CEP", + "mic_cep": { + "name": "mic_cep", "rank": 57, "slot_group": "Fields to put in sections" }, - "MIC_CHL": { - "name": "MIC_CHL", + "mic_chl": { + "name": "mic_chl", "rank": 58, "slot_group": "Fields to put in sections" }, - "MIC_CIP": { - "name": "MIC_CIP", + "mic_cip": { + "name": "mic_cip", "rank": 59, "slot_group": "Fields to put in sections" }, - "MIC_CRO": { - "name": "MIC_CRO", + "mic_cro": { + "name": "mic_cro", "rank": 60, "slot_group": "Fields to put in sections" }, - "MIC_FOX": { - "name": "MIC_FOX", + "mic_fox": { + "name": "mic_fox", "rank": 61, "slot_group": "Fields to put in sections" }, - "MIC_GEN": { - "name": "MIC_GEN", + "mic_gen": { + "name": "mic_gen", "rank": 62, "slot_group": "Fields to put in sections" }, - "MIC_KAN": { - "name": "MIC_KAN", + "mic_kan": { + "name": "mic_kan", "rank": 63, "slot_group": "Fields to put in sections" }, - "MIC_MEM": { - "name": "MIC_MEM", + "mic_mem": { + "name": "mic_mem", "rank": 64, "slot_group": "Fields to put in sections" }, - "MIC_NAL": { - "name": "MIC_NAL", + "mic_nal": { + "name": "mic_nal", "rank": 65, "slot_group": "Fields to put in sections" }, - "MIC_SSS": { - "name": "MIC_SSS", + "mic_sss": { + "name": "mic_sss", "rank": 66, "slot_group": "Fields to put in sections" }, - "MIC_STR": { - "name": "MIC_STR", + "mic_str": { + "name": "mic_str", "rank": 67, "slot_group": "Fields to put in sections" }, - "MIC_SXT": { - "name": "MIC_SXT", + "mic_sxt": { + "name": "mic_sxt", "rank": 68, "slot_group": "Fields to put in sections" }, - "MIC_TET": { - "name": "MIC_TET", + "mic_tet": { + "name": "mic_tet", "rank": 69, "slot_group": "Fields to put in sections" }, - "MIC_TIO": { - "name": "MIC_TIO", + "mic_tio": { + "name": "mic_tio", "rank": 70, "slot_group": "Fields to put in sections" }, - "N_OF_RESISTANCE": { - "name": "N_OF_RESISTANCE", + "n_of_resistance": { + "name": "n_of_resistance", "rank": 71, "slot_group": "Fields to put in sections" }, - "NBTESTED": { - "name": "NBTESTED", + "nbtested": { + "name": "nbtested", "rank": 72, "slot_group": "Fields to put in sections" }, - "R_PATTERN": { - "name": "R_PATTERN", + "r_pattern": { + "name": "r_pattern", "rank": 73, "slot_group": "Fields to put in sections" }, - "AMR_PA2C": { - "name": "AMR_PA2C", + "amr_pa2c": { + "name": "amr_pa2c", "rank": 74, "slot_group": "Fields to put in sections" }, - "RLEAST1": { - "name": "RLEAST1", + "rleast1": { + "name": "rleast1", "rank": 75, "slot_group": "Fields to put in sections" }, - "RLEAST2": { - "name": "RLEAST2", + "rleast2": { + "name": "rleast2", "rank": 76, "slot_group": "Fields to put in sections" }, - "RLEAST3": { - "name": "RLEAST3", + "rleast3": { + "name": "rleast3", "rank": 77, "slot_group": "Fields to put in sections" }, - "RLEAST4": { - "name": "RLEAST4", + "rleast4": { + "name": "rleast4", "rank": 78, "slot_group": "Fields to put in sections" }, - "RLEAST5": { - "name": "RLEAST5", + "rleast5": { + "name": "rleast5", "rank": 79, "slot_group": "Fields to put in sections" }, - "SIR_AMC": { - "name": "SIR_AMC", + "sir_amc": { + "name": "sir_amc", "rank": 80, "slot_group": "Fields to put in sections" }, - "SIR_AMK": { - "name": "SIR_AMK", + "sir_amk": { + "name": "sir_amk", "rank": 81, "slot_group": "Fields to put in sections" }, - "SIR_AMP": { - "name": "SIR_AMP", + "sir_amp": { + "name": "sir_amp", "rank": 82, "slot_group": "Fields to put in sections" }, - "SIR_AZM": { - "name": "SIR_AZM", + "sir_azm": { + "name": "sir_azm", "rank": 83, "slot_group": "Fields to put in sections" }, - "SIR_CEP": { - "name": "SIR_CEP", + "sir_cep": { + "name": "sir_cep", "rank": 84, "slot_group": "Fields to put in sections" }, - "SIR_CHL": { - "name": "SIR_CHL", + "sir_chl": { + "name": "sir_chl", "rank": 85, "slot_group": "Fields to put in sections" }, - "SIR_CIP": { - "name": "SIR_CIP", + "sir_cip": { + "name": "sir_cip", "rank": 86, "slot_group": "Fields to put in sections" }, - "SIR_CRO": { - "name": "SIR_CRO", + "sir_cro": { + "name": "sir_cro", "rank": 87, "slot_group": "Fields to put in sections" }, - "SIR_FOX": { - "name": "SIR_FOX", + "sir_fox": { + "name": "sir_fox", "rank": 88, "slot_group": "Fields to put in sections" }, - "SIR_GEN": { - "name": "SIR_GEN", + "sir_gen": { + "name": "sir_gen", "rank": 89, "slot_group": "Fields to put in sections" }, - "SIR_KAN": { - "name": "SIR_KAN", + "sir_kan": { + "name": "sir_kan", "rank": 90, "slot_group": "Fields to put in sections" }, - "SIR_MEM": { - "name": "SIR_MEM", + "sir_mem": { + "name": "sir_mem", "rank": 91, "slot_group": "Fields to put in sections" }, - "SIR_NAL": { - "name": "SIR_NAL", + "sir_nal": { + "name": "sir_nal", "rank": 92, "slot_group": "Fields to put in sections" }, - "SIR_SSS": { - "name": "SIR_SSS", + "sir_sss": { + "name": "sir_sss", "rank": 93, "slot_group": "Fields to put in sections" }, - "SIR_STR": { - "name": "SIR_STR", + "sir_str": { + "name": "sir_str", "rank": 94, "slot_group": "Fields to put in sections" }, - "SIR_SXT": { - "name": "SIR_SXT", + "sir_sxt": { + "name": "sir_sxt", "rank": 95, "slot_group": "Fields to put in sections" }, - "SIR_TET": { - "name": "SIR_TET", + "sir_tet": { + "name": "sir_tet", "rank": 96, "slot_group": "Fields to put in sections" }, - "SIR_TIO": { - "name": "SIR_TIO", + "sir_tio": { + "name": "sir_tio", "rank": 97, "slot_group": "Fields to put in sections" }, - "RAMC": { - "name": "RAMC", + "ramc": { + "name": "ramc", "rank": 98, "slot_group": "Fields to put in sections" }, - "RAMK": { - "name": "RAMK", + "ramk": { + "name": "ramk", "rank": 99, "slot_group": "Fields to put in sections" }, - "RAMP": { - "name": "RAMP", + "ramp": { + "name": "ramp", "rank": 100, "slot_group": "Fields to put in sections" }, - "RAZM": { - "name": "RAZM", + "razm": { + "name": "razm", "rank": 101, "slot_group": "Fields to put in sections" }, - "RCEP": { - "name": "RCEP", + "rcep": { + "name": "rcep", "rank": 102, "slot_group": "Fields to put in sections" }, - "RCHL": { - "name": "RCHL", + "rchl": { + "name": "rchl", "rank": 103, "slot_group": "Fields to put in sections" }, - "RCIP": { - "name": "RCIP", + "rcip": { + "name": "rcip", "rank": 104, "slot_group": "Fields to put in sections" }, - "RCRO": { - "name": "RCRO", + "rcro": { + "name": "rcro", "rank": 105, "slot_group": "Fields to put in sections" }, - "RFOX": { - "name": "RFOX", + "rfox": { + "name": "rfox", "rank": 106, "slot_group": "Fields to put in sections" }, - "RGEN": { - "name": "RGEN", + "rgen": { + "name": "rgen", "rank": 107, "slot_group": "Fields to put in sections" }, - "RKAN": { - "name": "RKAN", + "rkan": { + "name": "rkan", "rank": 108, "slot_group": "Fields to put in sections" }, - "RMEM": { - "name": "RMEM", + "rmem": { + "name": "rmem", "rank": 109, "slot_group": "Fields to put in sections" }, - "RNAL": { - "name": "RNAL", + "rnal": { + "name": "rnal", "rank": 110, "slot_group": "Fields to put in sections" }, - "RSSS": { - "name": "RSSS", + "rsss": { + "name": "rsss", "rank": 111, "slot_group": "Fields to put in sections" }, - "RSTR": { - "name": "RSTR", + "rstr": { + "name": "rstr", "rank": 112, "slot_group": "Fields to put in sections" }, - "RSXT": { - "name": "RSXT", + "rsxt": { + "name": "rsxt", "rank": 113, "slot_group": "Fields to put in sections" }, - "RTET": { - "name": "RTET", + "rtet": { + "name": "rtet", "rank": 114, "slot_group": "Fields to put in sections" }, - "RTIO": { - "name": "RTIO", + "rtio": { + "name": "rtio", "rank": 115, "slot_group": "Fields to put in sections" }, - "A2C": { - "name": "A2C", + "a2c": { + "name": "a2c", "rank": 116, "slot_group": "Fields to put in sections" }, - "CAMC": { - "name": "CAMC", + "camc": { + "name": "camc", "rank": 117, "slot_group": "Fields to put in sections" }, - "CAMK": { - "name": "CAMK", + "camk": { + "name": "camk", "rank": 118, "slot_group": "Fields to put in sections" }, - "CAMP": { - "name": "CAMP", + "camp": { + "name": "camp", "rank": 119, "slot_group": "Fields to put in sections" }, - "CAZM": { - "name": "CAZM", + "cazm": { + "name": "cazm", "rank": 120, "slot_group": "Fields to put in sections" }, - "CCEP": { - "name": "CCEP", + "ccep": { + "name": "ccep", "rank": 121, "slot_group": "Fields to put in sections" }, - "CCHL": { - "name": "CCHL", + "cchl": { + "name": "cchl", "rank": 122, "slot_group": "Fields to put in sections" }, - "CCIP": { - "name": "CCIP", + "ccip": { + "name": "ccip", "rank": 123, "slot_group": "Fields to put in sections" }, - "CCRO": { - "name": "CCRO", + "ccro": { + "name": "ccro", "rank": 124, "slot_group": "Fields to put in sections" }, - "CFOX": { - "name": "CFOX", + "cfox": { + "name": "cfox", "rank": 125, "slot_group": "Fields to put in sections" }, - "CGEN": { - "name": "CGEN", + "cgen": { + "name": "cgen", "rank": 126, "slot_group": "Fields to put in sections" }, - "CKAN": { - "name": "CKAN", + "ckan": { + "name": "ckan", "rank": 127, "slot_group": "Fields to put in sections" }, - "CMEM": { - "name": "CMEM", + "cmem": { + "name": "cmem", "rank": 128, "slot_group": "Fields to put in sections" }, - "CNAL": { - "name": "CNAL", + "cnal": { + "name": "cnal", "rank": 129, "slot_group": "Fields to put in sections" }, - "CSSS": { - "name": "CSSS", + "csss": { + "name": "csss", "rank": 130, "slot_group": "Fields to put in sections" }, - "CSTR": { - "name": "CSTR", + "cstr": { + "name": "cstr", "rank": 131, "slot_group": "Fields to put in sections" }, - "CSXT": { - "name": "CSXT", + "csxt": { + "name": "csxt", "rank": 132, "slot_group": "Fields to put in sections" }, - "CTET": { - "name": "CTET", + "ctet": { + "name": "ctet", "rank": 133, "slot_group": "Fields to put in sections" }, - "CTIO": { - "name": "CTIO", + "ctio": { + "name": "ctio", "rank": 134, "slot_group": "Fields to put in sections" }, - "STHY_TESTSRC_ID": { - "name": "STHY_TESTSRC_ID", + "sthy_testsrc_id": { + "name": "sthy_testsrc_id", "rank": 135, "slot_group": "Fields to put in sections" }, - "WINN_TESTSRC_ID": { - "name": "WINN_TESTSRC_ID", + "winn_testsrc_id": { + "name": "winn_testsrc_id", "rank": 136, "slot_group": "Fields to put in sections" }, - "GUEL_TESTSRC_ID": { - "name": "GUEL_TESTSRC_ID", + "guel_testsrc_id": { + "name": "guel_testsrc_id", "rank": 137, "slot_group": "Fields to put in sections" }, - "RCIP_DANMAP": { - "name": "RCIP_DANMAP", + "rcip_danmap": { + "name": "rcip_danmap", "rank": 138, "slot_group": "Fields to put in sections" }, - "EPIDATESTAMP_1": { - "name": "EPIDATESTAMP_1", + "epidatestamp_1": { + "name": "epidatestamp_1", "rank": 139, "slot_group": "Fields to put in sections" }, - "ACSSUT": { - "name": "ACSSUT", + "acssut": { + "name": "acssut", "rank": 140, "slot_group": "Fields to put in sections" }, - "AKSSUT": { - "name": "AKSSUT", + "akssut": { + "name": "akssut", "rank": 141, "slot_group": "Fields to put in sections" }, - "ACKSSUT": { - "name": "ACKSSUT", + "ackssut": { + "name": "ackssut", "rank": 142, "slot_group": "Fields to put in sections" }, - "MDR_A_SSUT": { - "name": "MDR_A_SSUT", + "mdr_a_ssut": { + "name": "mdr_a_ssut", "rank": 143, "slot_group": "Fields to put in sections" }, - "EXCLUSION": { - "name": "EXCLUSION", + "exclusion": { + "name": "exclusion", "rank": 144, "slot_group": "Fields to put in sections" }, - "RAMINOGLY": { - "name": "RAMINOGLY", + "raminogly": { + "name": "raminogly", "rank": 145, "slot_group": "Fields to put in sections" }, - "RBETALACTAM": { - "name": "RBETALACTAM", + "rbetalactam": { + "name": "rbetalactam", "rank": 146, "slot_group": "Fields to put in sections" }, - "RQUINOLONES": { - "name": "RQUINOLONES", + "rquinolones": { + "name": "rquinolones", "rank": 147, "slot_group": "Fields to put in sections" }, - "RFOLINHIBITOR": { - "name": "RFOLINHIBITOR", + "rfolinhibitor": { + "name": "rfolinhibitor", "rank": 148, "slot_group": "Fields to put in sections" }, - "MDR": { - "name": "MDR", + "mdr": { + "name": "mdr", "rank": 149, "slot_group": "Fields to put in sections" }, @@ -5156,1512 +6851,2001 @@ "rank": 150, "slot_group": "Fields to put in sections" }, - "EXTERNAL_AGENT": { - "name": "EXTERNAL_AGENT", + "external_agent": { + "name": "external_agent", "rank": 151, "slot_group": "Fields to put in sections" }, - "FARM_FLAG": { - "name": "FARM_FLAG", + "farm_flag": { + "name": "farm_flag", "rank": 152, "slot_group": "Fields to put in sections" }, - "AMIKACINGELET": { - "name": "AMIKACINGELET", + "amikacingelet": { + "name": "amikacingelet", "rank": 153, "slot_group": "Fields to put in sections" } }, "attributes": { - "SPECIMEN_ID": { - "name": "SPECIMEN_ID", + "specimen_id": { + "name": "specimen_id", "title": "SPECIMEN_ID", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:alternative_sample_ID" + ], "rank": 1, - "alias": "SPECIMEN_ID", - "owner": "PHAC Dexa", + "alias": "specimen_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "ISOLATE_ID": { - "name": "ISOLATE_ID", + "isolate_id": { + "name": "isolate_id", "title": "ISOLATE_ID", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:isolate_ID" + ], "rank": 2, - "alias": "ISOLATE_ID", - "owner": "PHAC Dexa", + "alias": "isolate_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "SAMPLE_ID": { - "name": "SAMPLE_ID", + "sample_id": { + "name": "sample_id", "title": "SAMPLE_ID", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:sample_collector_sample_ID" + ], "rank": 3, - "alias": "SAMPLE_ID", - "owner": "PHAC Dexa", + "alias": "sample_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "SENTINEL_SITE": { - "name": "SENTINEL_SITE", + "sentinel_site": { + "name": "sentinel_site", "title": "SENTINEL_SITE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 4, - "alias": "SENTINEL_SITE", - "owner": "PHAC Dexa", + "alias": "sentinel_site", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "LFZ_ADDITIONAL_SAMPLE_ID": { - "name": "LFZ_ADDITIONAL_SAMPLE_ID", + "lfz_additional_sample_id": { + "name": "lfz_additional_sample_id", "title": "LFZ_ADDITIONAL_SAMPLE_ID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 5, - "alias": "LFZ_ADDITIONAL_SAMPLE_ID", - "owner": "PHAC Dexa", + "alias": "lfz_additional_sample_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "LFZ_ORIGIN_COUNTRY": { - "name": "LFZ_ORIGIN_COUNTRY", + "lfz_origin_country": { + "name": "lfz_origin_country", "title": "LFZ_ORIGIN_COUNTRY", "from_schema": "https://example.com/PHAC_Dexa", "rank": 6, - "alias": "LFZ_ORIGIN_COUNTRY", - "owner": "PHAC Dexa", + "alias": "lfz_origin_country", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SUBJECT_CODE": { - "name": "SUBJECT_CODE", + "subject_code": { + "name": "subject_code", "title": "SUBJECT_CODE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 7, - "alias": "SUBJECT_CODE", - "owner": "PHAC Dexa", + "alias": "subject_code", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SUBJECT_DESCRIPTIONS": { - "name": "SUBJECT_DESCRIPTIONS", + "subject_descriptions": { + "name": "subject_descriptions", "title": "SUBJECT_DESCRIPTIONS", "from_schema": "https://example.com/PHAC_Dexa", "rank": 8, - "alias": "SUBJECT_DESCRIPTIONS", - "owner": "PHAC Dexa", + "alias": "subject_descriptions", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "SUBJECT_DESCRIPTIONS menu" + "range": "SubjectDescriptionsMenu" }, - "SUBMITTINGORG_1": { - "name": "SUBMITTINGORG_1", + "submittingorg_1": { + "name": "submittingorg_1", "title": "SUBMITTINGORG_1", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:collected_by" + ], "rank": 9, - "alias": "SUBMITTINGORG_1", - "owner": "PHAC Dexa", + "alias": "submittingorg_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SUBMITTINGLAB_1": { - "name": "SUBMITTINGLAB_1", + "submittinglab_1": { + "name": "submittinglab_1", "title": "SUBMITTINGLAB_1", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:laboratory_name" + ], "rank": 10, - "alias": "SUBMITTINGLAB_1", - "owner": "PHAC Dexa", + "alias": "submittinglab_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "PROJECT_1": { - "name": "PROJECT_1", + "project_1": { + "name": "project_1", "title": "PROJECT_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 11, - "alias": "PROJECT_1", - "owner": "PHAC Dexa", + "alias": "project_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "COUNTRY_1": { - "name": "COUNTRY_1", + "country_1": { + "name": "country_1", "title": "COUNTRY_1", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:geo_loc_name%20%28country%29" + ], "rank": 12, - "alias": "COUNTRY_1", - "owner": "PHAC Dexa", + "alias": "country_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "PROVINCE_1": { - "name": "PROVINCE_1", + "province_1": { + "name": "province_1", "title": "PROVINCE_1", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:geo_loc_name%20%28state/province/region%29" + ], "rank": 13, - "alias": "PROVINCE_1", - "owner": "PHAC Dexa", + "alias": "province_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CENSUSDIVISION_1": { - "name": "CENSUSDIVISION_1", + "censusdivision_1": { + "name": "censusdivision_1", "title": "CENSUSDIVISION_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 14, - "alias": "CENSUSDIVISION_1", - "owner": "PHAC Dexa", + "alias": "censusdivision_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "REGION": { - "name": "REGION", + "region": { + "name": "region", "title": "REGION", "from_schema": "https://example.com/PHAC_Dexa", "rank": 15, - "alias": "REGION", - "owner": "PHAC Dexa", + "alias": "region", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "YEAR": { - "name": "YEAR", + "year": { + "name": "year", "title": "YEAR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 16, - "alias": "YEAR", - "owner": "PHAC Dexa", + "alias": "year", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MONTH": { - "name": "MONTH", + "month": { + "name": "month", "title": "MONTH", "from_schema": "https://example.com/PHAC_Dexa", "rank": 17, - "alias": "MONTH", - "owner": "PHAC Dexa", + "alias": "month", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "QTR": { - "name": "QTR", + "qtr": { + "name": "qtr", "title": "QTR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 18, - "alias": "QTR", - "owner": "PHAC Dexa", + "alias": "qtr", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "DATECOLLECTED_1": { - "name": "DATECOLLECTED_1", + "datecollected_1": { + "name": "datecollected_1", "title": "DATECOLLECTED_1", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:sample_collection_date" + ], "rank": 19, - "alias": "DATECOLLECTED_1", - "owner": "PHAC Dexa", + "alias": "datecollected_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "date" }, - "DATERECEIVED_1": { - "name": "DATERECEIVED_1", + "datereceived_1": { + "name": "datereceived_1", "title": "DATERECEIVED_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 20, - "alias": "DATERECEIVED_1", - "owner": "PHAC Dexa", + "alias": "datereceived_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "DATESHIPPED_1": { - "name": "DATESHIPPED_1", + "dateshipped_1": { + "name": "dateshipped_1", "title": "DATESHIPPED_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 21, - "alias": "DATESHIPPED_1", - "owner": "PHAC Dexa", + "alias": "dateshipped_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "ESTABLISHMENT_1": { - "name": "ESTABLISHMENT_1", + "establishment_1": { + "name": "establishment_1", "title": "ESTABLISHMENT_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 22, - "alias": "ESTABLISHMENT_1", - "owner": "PHAC Dexa", + "alias": "establishment_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SPECIES": { - "name": "SPECIES", + "species": { + "name": "species", "title": "SPECIES", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:host%20%28common%20name%29%3A" + ], "rank": 23, - "alias": "SPECIES", - "owner": "PHAC Dexa", + "alias": "species", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "SPECIES menu" + "range": "SpeciesMenu" }, - "STTYPE": { - "name": "STTYPE", + "sttype": { + "name": "sttype", "title": "STTYPE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 24, - "alias": "STTYPE", - "owner": "PHAC Dexa", + "alias": "sttype", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "STTYPE menu" + "range": "STTypeMenu" }, - "STYPE": { - "name": "STYPE", + "stype": { + "name": "stype", "title": "STYPE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 25, - "alias": "STYPE", - "owner": "PHAC Dexa", + "alias": "stype", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "STYPE menu" + "range": "STypeMenu" }, - "COMMODITY": { - "name": "COMMODITY", + "commodity": { + "name": "commodity", "title": "COMMODITY", "from_schema": "https://example.com/PHAC_Dexa", "rank": 26, - "alias": "COMMODITY", - "owner": "PHAC Dexa", + "alias": "commodity", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "COMMODITY menu" + "range": "CommodityMenu" }, - "SPECIMENSOURCE_1": { - "name": "SPECIMENSOURCE_1", + "specimensource_1": { + "name": "specimensource_1", "title": "SPECIMENSOURCE_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 27, - "alias": "SPECIMENSOURCE_1", - "owner": "PHAC Dexa", + "alias": "specimensource_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "SPECIMENSOURCE_1 menu" + "range": "SpecimenSource1Menu" }, - "SPECIMENSUBSOURCE_1": { - "name": "SPECIMENSUBSOURCE_1", + "specimensubsource_1": { + "name": "specimensubsource_1", "title": "SPECIMENSUBSOURCE_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 28, - "alias": "SPECIMENSUBSOURCE_1", - "owner": "PHAC Dexa", + "alias": "specimensubsource_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "SPECIMENSUBSOURCE_1 menu" + "range": "SpecimenSubsource1Menu" }, - "SUBJECT_SUBTYPE": { - "name": "SUBJECT_SUBTYPE", + "subject_subtype": { + "name": "subject_subtype", "title": "SUBJECT_SUBTYPE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 29, - "alias": "SUBJECT_SUBTYPE", - "owner": "PHAC Dexa", + "alias": "subject_subtype", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", - "range": "SUBJECT_SUBTYPE menu" + "range": "SubjectSubtypeMenu" }, - "FIELDSTAFF_1": { - "name": "FIELDSTAFF_1", + "fieldstaff_1": { + "name": "fieldstaff_1", "title": "FIELDSTAFF_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 30, - "alias": "FIELDSTAFF_1", - "owner": "PHAC Dexa", + "alias": "fieldstaff_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "IN_STORE_PROCESSING": { - "name": "IN_STORE_PROCESSING", + "in_store_processing": { + "name": "in_store_processing", "title": "IN_STORE_PROCESSING", "from_schema": "https://example.com/PHAC_Dexa", "rank": 31, - "alias": "IN_STORE_PROCESSING", - "owner": "PHAC Dexa", + "alias": "in_store_processing", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MAYCONTAINFROZENMEAT_1": { - "name": "MAYCONTAINFROZENMEAT_1", + "maycontainfrozenmeat_1": { + "name": "maycontainfrozenmeat_1", "title": "MAYCONTAINFROZENMEAT_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 32, - "alias": "MAYCONTAINFROZENMEAT_1", - "owner": "PHAC Dexa", + "alias": "maycontainfrozenmeat_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "NOOFCASHREGISTERS_1": { - "name": "NOOFCASHREGISTERS_1", + "noofcashregisters_1": { + "name": "noofcashregisters_1", "title": "NOOFCASHREGISTERS_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 33, - "alias": "NOOFCASHREGISTERS_1", - "owner": "PHAC Dexa", + "alias": "noofcashregisters_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "PRICEPERKG_1": { - "name": "PRICEPERKG_1", + "priceperkg_1": { + "name": "priceperkg_1", "title": "PRICEPERKG_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 34, - "alias": "PRICEPERKG_1", - "owner": "PHAC Dexa", + "alias": "priceperkg_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "STORETYPE_SAMPLINGSITE_1": { - "name": "STORETYPE_SAMPLINGSITE_1", + "storetype_samplingsite_1": { + "name": "storetype_samplingsite_1", "title": "STORETYPE_SAMPLINGSITE_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 35, - "alias": "STORETYPE_SAMPLINGSITE_1", - "owner": "PHAC Dexa", + "alias": "storetype_samplingsite_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "TEMPERATUREMAX_1": { - "name": "TEMPERATUREMAX_1", + "temperaturemax_1": { + "name": "temperaturemax_1", "title": "TEMPERATUREMAX_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 36, - "alias": "TEMPERATUREMAX_1", - "owner": "PHAC Dexa", + "alias": "temperaturemax_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "TEMPERATUREMIN_1": { - "name": "TEMPERATUREMIN_1", + "temperaturemin_1": { + "name": "temperaturemin_1", "title": "TEMPERATUREMIN_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 37, - "alias": "TEMPERATUREMIN_1", - "owner": "PHAC Dexa", + "alias": "temperaturemin_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "TEMPERATUREARRIVAL_1": { - "name": "TEMPERATUREARRIVAL_1", + "temperaturearrival_1": { + "name": "temperaturearrival_1", "title": "TEMPERATUREARRIVAL_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 38, - "alias": "TEMPERATUREARRIVAL_1", - "owner": "PHAC Dexa", + "alias": "temperaturearrival_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "VETID": { - "name": "VETID", + "vetid": { + "name": "vetid", "title": "VETID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 39, - "alias": "VETID", - "owner": "PHAC Dexa", + "alias": "vetid", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "ROOMID": { - "name": "ROOMID", + "roomid": { + "name": "roomid", "title": "ROOMID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 40, - "alias": "ROOMID", - "owner": "PHAC Dexa", + "alias": "roomid", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "PENID": { - "name": "PENID", + "penid": { + "name": "penid", "title": "PENID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 41, - "alias": "PENID", - "owner": "PHAC Dexa", + "alias": "penid", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SAMPLING_TYPE": { - "name": "SAMPLING_TYPE", + "sampling_type": { + "name": "sampling_type", "title": "SAMPLING_TYPE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 42, - "alias": "SAMPLING_TYPE", - "owner": "PHAC Dexa", + "alias": "sampling_type", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "BARN_ID": { - "name": "BARN_ID", + "barn_id": { + "name": "barn_id", "title": "BARN_ID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 43, - "alias": "BARN_ID", - "owner": "PHAC Dexa", + "alias": "barn_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "DATE_PACKED": { - "name": "DATE_PACKED", + "date_packed": { + "name": "date_packed", "title": "DATE_PACKED", "from_schema": "https://example.com/PHAC_Dexa", "rank": 44, - "alias": "DATE_PACKED", - "owner": "PHAC Dexa", + "alias": "date_packed", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FINAL_ID_GENUS": { - "name": "FINAL_ID_GENUS", + "final_id_genus": { + "name": "final_id_genus", "title": "FINAL_ID_GENUS", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:organism" + ], "rank": 45, - "alias": "FINAL_ID_GENUS", - "owner": "PHAC Dexa", + "alias": "final_id_genus", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FINAL_ID_SPECIES": { - "name": "FINAL_ID_SPECIES", + "final_id_species": { + "name": "final_id_species", "title": "FINAL_ID_SPECIES", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:organism" + ], "rank": 46, - "alias": "FINAL_ID_SPECIES", - "owner": "PHAC Dexa", + "alias": "final_id_species", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FINAL_ID_SUBSPECIES": { - "name": "FINAL_ID_SUBSPECIES", + "final_id_subspecies": { + "name": "final_id_subspecies", "title": "FINAL_ID_SUBSPECIES", "from_schema": "https://example.com/PHAC_Dexa", "rank": 47, - "alias": "FINAL_ID_SUBSPECIES", - "owner": "PHAC Dexa", + "alias": "final_id_subspecies", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FINAL_ID_SEROTYPE": { - "name": "FINAL_ID_SEROTYPE", + "final_id_serotype": { + "name": "final_id_serotype", "title": "FINAL_ID_SEROTYPE", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:serovar" + ], "rank": 48, - "alias": "FINAL_ID_SEROTYPE", - "owner": "PHAC Dexa", + "alias": "final_id_serotype", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FINAL_ID_ANTIGEN": { - "name": "FINAL_ID_ANTIGEN", + "final_id_antigen": { + "name": "final_id_antigen", "title": "FINAL_ID_ANTIGEN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 49, - "alias": "FINAL_ID_ANTIGEN", - "owner": "PHAC Dexa", + "alias": "final_id_antigen", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FINAL_ID_PHAGETYPE": { - "name": "FINAL_ID_PHAGETYPE", + "final_id_phagetype": { + "name": "final_id_phagetype", "title": "FINAL_ID_PHAGETYPE", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:phagetype" + ], "rank": 50, - "alias": "FINAL_ID_PHAGETYPE", - "owner": "PHAC Dexa", + "alias": "final_id_phagetype", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SA_Serotype_Method": { - "name": "SA_Serotype_Method", + "sa_serotype_method": { + "name": "sa_serotype_method", "title": "SA_Serotype_Method", "from_schema": "https://example.com/PHAC_Dexa", + "exact_mappings": [ + "GRDI:serotyping_method" + ], "rank": 51, - "alias": "SA_Serotype_Method", - "owner": "PHAC Dexa", + "alias": "sa_serotype_method", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SEROTYPE_GR": { - "name": "SEROTYPE_GR", + "serotype_gr": { + "name": "serotype_gr", "title": "SEROTYPE_GR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 52, - "alias": "SEROTYPE_GR", - "owner": "PHAC Dexa", + "alias": "serotype_gr", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_AMC": { - "name": "MIC_AMC", + "mic_amc": { + "name": "mic_amc", "title": "MIC_AMC", "from_schema": "https://example.com/PHAC_Dexa", "rank": 53, - "alias": "MIC_AMC", - "owner": "PHAC Dexa", + "alias": "mic_amc", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_AMK": { - "name": "MIC_AMK", + "mic_amk": { + "name": "mic_amk", "title": "MIC_AMK", "from_schema": "https://example.com/PHAC_Dexa", "rank": 54, - "alias": "MIC_AMK", - "owner": "PHAC Dexa", + "alias": "mic_amk", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_AMP": { - "name": "MIC_AMP", + "mic_amp": { + "name": "mic_amp", "title": "MIC_AMP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 55, - "alias": "MIC_AMP", - "owner": "PHAC Dexa", + "alias": "mic_amp", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_AZM": { - "name": "MIC_AZM", + "mic_azm": { + "name": "mic_azm", "title": "MIC_AZM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 56, - "alias": "MIC_AZM", - "owner": "PHAC Dexa", + "alias": "mic_azm", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_CEP": { - "name": "MIC_CEP", + "mic_cep": { + "name": "mic_cep", "title": "MIC_CEP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 57, - "alias": "MIC_CEP", - "owner": "PHAC Dexa", + "alias": "mic_cep", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_CHL": { - "name": "MIC_CHL", + "mic_chl": { + "name": "mic_chl", "title": "MIC_CHL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 58, - "alias": "MIC_CHL", - "owner": "PHAC Dexa", + "alias": "mic_chl", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_CIP": { - "name": "MIC_CIP", + "mic_cip": { + "name": "mic_cip", "title": "MIC_CIP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 59, - "alias": "MIC_CIP", - "owner": "PHAC Dexa", + "alias": "mic_cip", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_CRO": { - "name": "MIC_CRO", + "mic_cro": { + "name": "mic_cro", "title": "MIC_CRO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 60, - "alias": "MIC_CRO", - "owner": "PHAC Dexa", + "alias": "mic_cro", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_FOX": { - "name": "MIC_FOX", + "mic_fox": { + "name": "mic_fox", "title": "MIC_FOX", "from_schema": "https://example.com/PHAC_Dexa", "rank": 61, - "alias": "MIC_FOX", - "owner": "PHAC Dexa", + "alias": "mic_fox", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_GEN": { - "name": "MIC_GEN", + "mic_gen": { + "name": "mic_gen", "title": "MIC_GEN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 62, - "alias": "MIC_GEN", - "owner": "PHAC Dexa", + "alias": "mic_gen", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_KAN": { - "name": "MIC_KAN", + "mic_kan": { + "name": "mic_kan", "title": "MIC_KAN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 63, - "alias": "MIC_KAN", - "owner": "PHAC Dexa", + "alias": "mic_kan", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_MEM": { - "name": "MIC_MEM", + "mic_mem": { + "name": "mic_mem", "title": "MIC_MEM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 64, - "alias": "MIC_MEM", - "owner": "PHAC Dexa", + "alias": "mic_mem", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_NAL": { - "name": "MIC_NAL", + "mic_nal": { + "name": "mic_nal", "title": "MIC_NAL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 65, - "alias": "MIC_NAL", - "owner": "PHAC Dexa", + "alias": "mic_nal", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_SSS": { - "name": "MIC_SSS", + "mic_sss": { + "name": "mic_sss", "title": "MIC_SSS", "from_schema": "https://example.com/PHAC_Dexa", "rank": 66, - "alias": "MIC_SSS", - "owner": "PHAC Dexa", + "alias": "mic_sss", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_STR": { - "name": "MIC_STR", + "mic_str": { + "name": "mic_str", "title": "MIC_STR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 67, - "alias": "MIC_STR", - "owner": "PHAC Dexa", + "alias": "mic_str", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_SXT": { - "name": "MIC_SXT", + "mic_sxt": { + "name": "mic_sxt", "title": "MIC_SXT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 68, - "alias": "MIC_SXT", - "owner": "PHAC Dexa", + "alias": "mic_sxt", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_TET": { - "name": "MIC_TET", + "mic_tet": { + "name": "mic_tet", "title": "MIC_TET", "from_schema": "https://example.com/PHAC_Dexa", "rank": 69, - "alias": "MIC_TET", - "owner": "PHAC Dexa", + "alias": "mic_tet", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MIC_TIO": { - "name": "MIC_TIO", + "mic_tio": { + "name": "mic_tio", "title": "MIC_TIO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 70, - "alias": "MIC_TIO", - "owner": "PHAC Dexa", + "alias": "mic_tio", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "N_OF_RESISTANCE": { - "name": "N_OF_RESISTANCE", + "n_of_resistance": { + "name": "n_of_resistance", "title": "N_OF_RESISTANCE", "from_schema": "https://example.com/PHAC_Dexa", "rank": 71, - "alias": "N_OF_RESISTANCE", - "owner": "PHAC Dexa", + "alias": "n_of_resistance", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "NBTESTED": { - "name": "NBTESTED", + "nbtested": { + "name": "nbtested", "title": "NBTESTED", "from_schema": "https://example.com/PHAC_Dexa", "rank": 72, - "alias": "NBTESTED", - "owner": "PHAC Dexa", + "alias": "nbtested", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "R_PATTERN": { - "name": "R_PATTERN", + "r_pattern": { + "name": "r_pattern", "title": "R_PATTERN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 73, - "alias": "R_PATTERN", - "owner": "PHAC Dexa", + "alias": "r_pattern", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "AMR_PA2C": { - "name": "AMR_PA2C", + "amr_pa2c": { + "name": "amr_pa2c", "title": "AMR_PA2C", "from_schema": "https://example.com/PHAC_Dexa", "rank": 74, - "alias": "AMR_PA2C", - "owner": "PHAC Dexa", + "alias": "amr_pa2c", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RLEAST1": { - "name": "RLEAST1", + "rleast1": { + "name": "rleast1", "title": "RLEAST1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 75, - "alias": "RLEAST1", - "owner": "PHAC Dexa", + "alias": "rleast1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RLEAST2": { - "name": "RLEAST2", + "rleast2": { + "name": "rleast2", "title": "RLEAST2", "from_schema": "https://example.com/PHAC_Dexa", "rank": 76, - "alias": "RLEAST2", - "owner": "PHAC Dexa", + "alias": "rleast2", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RLEAST3": { - "name": "RLEAST3", + "rleast3": { + "name": "rleast3", "title": "RLEAST3", "from_schema": "https://example.com/PHAC_Dexa", "rank": 77, - "alias": "RLEAST3", - "owner": "PHAC Dexa", + "alias": "rleast3", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RLEAST4": { - "name": "RLEAST4", + "rleast4": { + "name": "rleast4", "title": "RLEAST4", "from_schema": "https://example.com/PHAC_Dexa", "rank": 78, - "alias": "RLEAST4", - "owner": "PHAC Dexa", + "alias": "rleast4", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RLEAST5": { - "name": "RLEAST5", + "rleast5": { + "name": "rleast5", "title": "RLEAST5", "from_schema": "https://example.com/PHAC_Dexa", "rank": 79, - "alias": "RLEAST5", - "owner": "PHAC Dexa", + "alias": "rleast5", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_AMC": { - "name": "SIR_AMC", + "sir_amc": { + "name": "sir_amc", "title": "SIR_AMC", "from_schema": "https://example.com/PHAC_Dexa", "rank": 80, - "alias": "SIR_AMC", - "owner": "PHAC Dexa", + "alias": "sir_amc", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_AMK": { - "name": "SIR_AMK", + "sir_amk": { + "name": "sir_amk", "title": "SIR_AMK", "from_schema": "https://example.com/PHAC_Dexa", "rank": 81, - "alias": "SIR_AMK", - "owner": "PHAC Dexa", + "alias": "sir_amk", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_AMP": { - "name": "SIR_AMP", + "sir_amp": { + "name": "sir_amp", "title": "SIR_AMP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 82, - "alias": "SIR_AMP", - "owner": "PHAC Dexa", + "alias": "sir_amp", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_AZM": { - "name": "SIR_AZM", + "sir_azm": { + "name": "sir_azm", "title": "SIR_AZM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 83, - "alias": "SIR_AZM", - "owner": "PHAC Dexa", + "alias": "sir_azm", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_CEP": { - "name": "SIR_CEP", + "sir_cep": { + "name": "sir_cep", "title": "SIR_CEP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 84, - "alias": "SIR_CEP", - "owner": "PHAC Dexa", + "alias": "sir_cep", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_CHL": { - "name": "SIR_CHL", + "sir_chl": { + "name": "sir_chl", "title": "SIR_CHL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 85, - "alias": "SIR_CHL", - "owner": "PHAC Dexa", + "alias": "sir_chl", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_CIP": { - "name": "SIR_CIP", + "sir_cip": { + "name": "sir_cip", "title": "SIR_CIP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 86, - "alias": "SIR_CIP", - "owner": "PHAC Dexa", + "alias": "sir_cip", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_CRO": { - "name": "SIR_CRO", + "sir_cro": { + "name": "sir_cro", "title": "SIR_CRO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 87, - "alias": "SIR_CRO", - "owner": "PHAC Dexa", + "alias": "sir_cro", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_FOX": { - "name": "SIR_FOX", + "sir_fox": { + "name": "sir_fox", "title": "SIR_FOX", "from_schema": "https://example.com/PHAC_Dexa", "rank": 88, - "alias": "SIR_FOX", - "owner": "PHAC Dexa", + "alias": "sir_fox", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_GEN": { - "name": "SIR_GEN", + "sir_gen": { + "name": "sir_gen", "title": "SIR_GEN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 89, - "alias": "SIR_GEN", - "owner": "PHAC Dexa", + "alias": "sir_gen", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_KAN": { - "name": "SIR_KAN", + "sir_kan": { + "name": "sir_kan", "title": "SIR_KAN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 90, - "alias": "SIR_KAN", - "owner": "PHAC Dexa", + "alias": "sir_kan", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_MEM": { - "name": "SIR_MEM", + "sir_mem": { + "name": "sir_mem", "title": "SIR_MEM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 91, - "alias": "SIR_MEM", - "owner": "PHAC Dexa", + "alias": "sir_mem", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_NAL": { - "name": "SIR_NAL", + "sir_nal": { + "name": "sir_nal", "title": "SIR_NAL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 92, - "alias": "SIR_NAL", - "owner": "PHAC Dexa", + "alias": "sir_nal", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_SSS": { - "name": "SIR_SSS", + "sir_sss": { + "name": "sir_sss", "title": "SIR_SSS", "from_schema": "https://example.com/PHAC_Dexa", "rank": 93, - "alias": "SIR_SSS", - "owner": "PHAC Dexa", + "alias": "sir_sss", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_STR": { - "name": "SIR_STR", + "sir_str": { + "name": "sir_str", "title": "SIR_STR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 94, - "alias": "SIR_STR", - "owner": "PHAC Dexa", + "alias": "sir_str", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_SXT": { - "name": "SIR_SXT", + "sir_sxt": { + "name": "sir_sxt", "title": "SIR_SXT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 95, - "alias": "SIR_SXT", - "owner": "PHAC Dexa", + "alias": "sir_sxt", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_TET": { - "name": "SIR_TET", + "sir_tet": { + "name": "sir_tet", "title": "SIR_TET", "from_schema": "https://example.com/PHAC_Dexa", "rank": 96, - "alias": "SIR_TET", - "owner": "PHAC Dexa", + "alias": "sir_tet", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "SIR_TIO": { - "name": "SIR_TIO", + "sir_tio": { + "name": "sir_tio", "title": "SIR_TIO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 97, - "alias": "SIR_TIO", - "owner": "PHAC Dexa", + "alias": "sir_tio", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RAMC": { - "name": "RAMC", + "ramc": { + "name": "ramc", "title": "RAMC", "from_schema": "https://example.com/PHAC_Dexa", "rank": 98, - "alias": "RAMC", - "owner": "PHAC Dexa", + "alias": "ramc", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RAMK": { - "name": "RAMK", + "ramk": { + "name": "ramk", "title": "RAMK", "from_schema": "https://example.com/PHAC_Dexa", "rank": 99, - "alias": "RAMK", - "owner": "PHAC Dexa", + "alias": "ramk", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RAMP": { - "name": "RAMP", + "ramp": { + "name": "ramp", "title": "RAMP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 100, - "alias": "RAMP", - "owner": "PHAC Dexa", + "alias": "ramp", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RAZM": { - "name": "RAZM", + "razm": { + "name": "razm", "title": "RAZM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 101, - "alias": "RAZM", - "owner": "PHAC Dexa", + "alias": "razm", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RCEP": { - "name": "RCEP", + "rcep": { + "name": "rcep", "title": "RCEP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 102, - "alias": "RCEP", - "owner": "PHAC Dexa", + "alias": "rcep", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RCHL": { - "name": "RCHL", + "rchl": { + "name": "rchl", "title": "RCHL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 103, - "alias": "RCHL", - "owner": "PHAC Dexa", + "alias": "rchl", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RCIP": { - "name": "RCIP", + "rcip": { + "name": "rcip", "title": "RCIP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 104, - "alias": "RCIP", - "owner": "PHAC Dexa", + "alias": "rcip", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RCRO": { - "name": "RCRO", + "rcro": { + "name": "rcro", "title": "RCRO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 105, - "alias": "RCRO", - "owner": "PHAC Dexa", + "alias": "rcro", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RFOX": { - "name": "RFOX", + "rfox": { + "name": "rfox", "title": "RFOX", "from_schema": "https://example.com/PHAC_Dexa", "rank": 106, - "alias": "RFOX", - "owner": "PHAC Dexa", + "alias": "rfox", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RGEN": { - "name": "RGEN", + "rgen": { + "name": "rgen", "title": "RGEN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 107, - "alias": "RGEN", - "owner": "PHAC Dexa", + "alias": "rgen", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RKAN": { - "name": "RKAN", + "rkan": { + "name": "rkan", "title": "RKAN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 108, - "alias": "RKAN", - "owner": "PHAC Dexa", + "alias": "rkan", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RMEM": { - "name": "RMEM", + "rmem": { + "name": "rmem", "title": "RMEM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 109, - "alias": "RMEM", - "owner": "PHAC Dexa", + "alias": "rmem", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RNAL": { - "name": "RNAL", + "rnal": { + "name": "rnal", "title": "RNAL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 110, - "alias": "RNAL", - "owner": "PHAC Dexa", + "alias": "rnal", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RSSS": { - "name": "RSSS", + "rsss": { + "name": "rsss", "title": "RSSS", "from_schema": "https://example.com/PHAC_Dexa", "rank": 111, - "alias": "RSSS", - "owner": "PHAC Dexa", + "alias": "rsss", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RSTR": { - "name": "RSTR", + "rstr": { + "name": "rstr", "title": "RSTR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 112, - "alias": "RSTR", - "owner": "PHAC Dexa", + "alias": "rstr", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RSXT": { - "name": "RSXT", + "rsxt": { + "name": "rsxt", "title": "RSXT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 113, - "alias": "RSXT", - "owner": "PHAC Dexa", + "alias": "rsxt", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RTET": { - "name": "RTET", + "rtet": { + "name": "rtet", "title": "RTET", "from_schema": "https://example.com/PHAC_Dexa", "rank": 114, - "alias": "RTET", - "owner": "PHAC Dexa", + "alias": "rtet", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RTIO": { - "name": "RTIO", + "rtio": { + "name": "rtio", "title": "RTIO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 115, - "alias": "RTIO", - "owner": "PHAC Dexa", + "alias": "rtio", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "A2C": { - "name": "A2C", + "a2c": { + "name": "a2c", "title": "A2C", "from_schema": "https://example.com/PHAC_Dexa", "rank": 116, - "alias": "A2C", - "owner": "PHAC Dexa", + "alias": "a2c", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CAMC": { - "name": "CAMC", + "camc": { + "name": "camc", "title": "CAMC", "from_schema": "https://example.com/PHAC_Dexa", "rank": 117, - "alias": "CAMC", - "owner": "PHAC Dexa", + "alias": "camc", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CAMK": { - "name": "CAMK", + "camk": { + "name": "camk", "title": "CAMK", "from_schema": "https://example.com/PHAC_Dexa", "rank": 118, - "alias": "CAMK", - "owner": "PHAC Dexa", + "alias": "camk", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CAMP": { - "name": "CAMP", + "camp": { + "name": "camp", "title": "CAMP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 119, - "alias": "CAMP", - "owner": "PHAC Dexa", + "alias": "camp", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CAZM": { - "name": "CAZM", + "cazm": { + "name": "cazm", "title": "CAZM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 120, - "alias": "CAZM", - "owner": "PHAC Dexa", + "alias": "cazm", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CCEP": { - "name": "CCEP", + "ccep": { + "name": "ccep", "title": "CCEP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 121, - "alias": "CCEP", - "owner": "PHAC Dexa", + "alias": "ccep", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CCHL": { - "name": "CCHL", + "cchl": { + "name": "cchl", "title": "CCHL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 122, - "alias": "CCHL", - "owner": "PHAC Dexa", + "alias": "cchl", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CCIP": { - "name": "CCIP", + "ccip": { + "name": "ccip", "title": "CCIP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 123, - "alias": "CCIP", - "owner": "PHAC Dexa", + "alias": "ccip", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CCRO": { - "name": "CCRO", + "ccro": { + "name": "ccro", "title": "CCRO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 124, - "alias": "CCRO", - "owner": "PHAC Dexa", + "alias": "ccro", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CFOX": { - "name": "CFOX", + "cfox": { + "name": "cfox", "title": "CFOX", "from_schema": "https://example.com/PHAC_Dexa", "rank": 125, - "alias": "CFOX", - "owner": "PHAC Dexa", + "alias": "cfox", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CGEN": { - "name": "CGEN", + "cgen": { + "name": "cgen", "title": "CGEN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 126, - "alias": "CGEN", - "owner": "PHAC Dexa", + "alias": "cgen", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CKAN": { - "name": "CKAN", + "ckan": { + "name": "ckan", "title": "CKAN", "from_schema": "https://example.com/PHAC_Dexa", "rank": 127, - "alias": "CKAN", - "owner": "PHAC Dexa", + "alias": "ckan", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CMEM": { - "name": "CMEM", + "cmem": { + "name": "cmem", "title": "CMEM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 128, - "alias": "CMEM", - "owner": "PHAC Dexa", + "alias": "cmem", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CNAL": { - "name": "CNAL", + "cnal": { + "name": "cnal", "title": "CNAL", "from_schema": "https://example.com/PHAC_Dexa", "rank": 129, - "alias": "CNAL", - "owner": "PHAC Dexa", + "alias": "cnal", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CSSS": { - "name": "CSSS", + "csss": { + "name": "csss", "title": "CSSS", "from_schema": "https://example.com/PHAC_Dexa", "rank": 130, - "alias": "CSSS", - "owner": "PHAC Dexa", + "alias": "csss", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CSTR": { - "name": "CSTR", + "cstr": { + "name": "cstr", "title": "CSTR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 131, - "alias": "CSTR", - "owner": "PHAC Dexa", + "alias": "cstr", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CSXT": { - "name": "CSXT", + "csxt": { + "name": "csxt", "title": "CSXT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 132, - "alias": "CSXT", - "owner": "PHAC Dexa", + "alias": "csxt", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CTET": { - "name": "CTET", + "ctet": { + "name": "ctet", "title": "CTET", "from_schema": "https://example.com/PHAC_Dexa", "rank": 133, - "alias": "CTET", - "owner": "PHAC Dexa", + "alias": "ctet", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "CTIO": { - "name": "CTIO", + "ctio": { + "name": "ctio", "title": "CTIO", "from_schema": "https://example.com/PHAC_Dexa", "rank": 134, - "alias": "CTIO", - "owner": "PHAC Dexa", + "alias": "ctio", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "STHY_TESTSRC_ID": { - "name": "STHY_TESTSRC_ID", + "sthy_testsrc_id": { + "name": "sthy_testsrc_id", "title": "STHY_TESTSRC_ID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 135, - "alias": "STHY_TESTSRC_ID", - "owner": "PHAC Dexa", + "alias": "sthy_testsrc_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "WINN_TESTSRC_ID": { - "name": "WINN_TESTSRC_ID", + "winn_testsrc_id": { + "name": "winn_testsrc_id", "title": "WINN_TESTSRC_ID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 136, - "alias": "WINN_TESTSRC_ID", - "owner": "PHAC Dexa", + "alias": "winn_testsrc_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "GUEL_TESTSRC_ID": { - "name": "GUEL_TESTSRC_ID", + "guel_testsrc_id": { + "name": "guel_testsrc_id", "title": "GUEL_TESTSRC_ID", "from_schema": "https://example.com/PHAC_Dexa", "rank": 137, - "alias": "GUEL_TESTSRC_ID", - "owner": "PHAC Dexa", + "alias": "guel_testsrc_id", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RCIP_DANMAP": { - "name": "RCIP_DANMAP", + "rcip_danmap": { + "name": "rcip_danmap", "title": "RCIP_DANMAP", "from_schema": "https://example.com/PHAC_Dexa", "rank": 138, - "alias": "RCIP_DANMAP", - "owner": "PHAC Dexa", + "alias": "rcip_danmap", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "EPIDATESTAMP_1": { - "name": "EPIDATESTAMP_1", + "epidatestamp_1": { + "name": "epidatestamp_1", "title": "EPIDATESTAMP_1", "from_schema": "https://example.com/PHAC_Dexa", "rank": 139, - "alias": "EPIDATESTAMP_1", - "owner": "PHAC Dexa", + "alias": "epidatestamp_1", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "ACSSUT": { - "name": "ACSSUT", + "acssut": { + "name": "acssut", "title": "ACSSUT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 140, - "alias": "ACSSUT", - "owner": "PHAC Dexa", + "alias": "acssut", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "AKSSUT": { - "name": "AKSSUT", + "akssut": { + "name": "akssut", "title": "AKSSUT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 141, - "alias": "AKSSUT", - "owner": "PHAC Dexa", + "alias": "akssut", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "ACKSSUT": { - "name": "ACKSSUT", + "ackssut": { + "name": "ackssut", "title": "ACKSSUT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 142, - "alias": "ACKSSUT", - "owner": "PHAC Dexa", + "alias": "ackssut", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MDR_A_SSUT": { - "name": "MDR_A_SSUT", + "mdr_a_ssut": { + "name": "mdr_a_ssut", "title": "MDR_A_SSUT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 143, - "alias": "MDR_A_SSUT", - "owner": "PHAC Dexa", + "alias": "mdr_a_ssut", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "EXCLUSION": { - "name": "EXCLUSION", + "exclusion": { + "name": "exclusion", "title": "EXCLUSION", "from_schema": "https://example.com/PHAC_Dexa", "rank": 144, - "alias": "EXCLUSION", - "owner": "PHAC Dexa", + "alias": "exclusion", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RAMINOGLY": { - "name": "RAMINOGLY", + "raminogly": { + "name": "raminogly", "title": "RAMINOGLY", "from_schema": "https://example.com/PHAC_Dexa", "rank": 145, - "alias": "RAMINOGLY", - "owner": "PHAC Dexa", + "alias": "raminogly", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RBETALACTAM": { - "name": "RBETALACTAM", + "rbetalactam": { + "name": "rbetalactam", "title": "RBETALACTAM", "from_schema": "https://example.com/PHAC_Dexa", "rank": 146, - "alias": "RBETALACTAM", - "owner": "PHAC Dexa", + "alias": "rbetalactam", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RQUINOLONES": { - "name": "RQUINOLONES", + "rquinolones": { + "name": "rquinolones", "title": "RQUINOLONES", "from_schema": "https://example.com/PHAC_Dexa", "rank": 147, - "alias": "RQUINOLONES", - "owner": "PHAC Dexa", + "alias": "rquinolones", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "RFOLINHIBITOR": { - "name": "RFOLINHIBITOR", + "rfolinhibitor": { + "name": "rfolinhibitor", "title": "RFOLINHIBITOR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 148, - "alias": "RFOLINHIBITOR", - "owner": "PHAC Dexa", + "alias": "rfolinhibitor", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "MDR": { - "name": "MDR", + "mdr": { + "name": "mdr", "title": "MDR", "from_schema": "https://example.com/PHAC_Dexa", "rank": 149, - "alias": "MDR", - "owner": "PHAC Dexa", + "alias": "mdr", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, @@ -6671,44 +8855,55 @@ "from_schema": "https://example.com/PHAC_Dexa", "rank": 150, "alias": "specimen_number", - "owner": "PHAC Dexa", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "EXTERNAL_AGENT": { - "name": "EXTERNAL_AGENT", + "external_agent": { + "name": "external_agent", "title": "EXTERNAL_AGENT", "from_schema": "https://example.com/PHAC_Dexa", "rank": 151, - "alias": "EXTERNAL_AGENT", - "owner": "PHAC Dexa", + "alias": "external_agent", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "FARM_FLAG": { - "name": "FARM_FLAG", + "farm_flag": { + "name": "farm_flag", "title": "FARM_FLAG", "from_schema": "https://example.com/PHAC_Dexa", "rank": 152, - "alias": "FARM_FLAG", - "owner": "PHAC Dexa", + "alias": "farm_flag", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" }, - "AMIKACINGELET": { - "name": "AMIKACINGELET", + "amikacingelet": { + "name": "amikacingelet", "title": "AMIKACINGELET", "from_schema": "https://example.com/PHAC_Dexa", "rank": 153, - "alias": "AMIKACINGELET", - "owner": "PHAC Dexa", + "alias": "amikacingelet", + "owner": "PHACDexa", + "domain_of": [ + "PHACDexa" + ], "slot_group": "Fields to put in sections", "range": "WhitespaceMinimizedString" } } } }, - "source_file": "schema.yaml", "settings": { "Title_Case": { "setting_key": "Title_Case", @@ -6724,4 +8919,4 @@ } }, "@type": "SchemaDefinition" -} +} \ No newline at end of file diff --git a/web/templates/phac_dexa/schema.yaml b/web/templates/phac_dexa/schema.yaml index 9a00d690..cad62978 100644 --- a/web/templates/phac_dexa/schema.yaml +++ b/web/templates/phac_dexa/schema.yaml @@ -3,7 +3,7 @@ name: PHAC_Dexa description: '' version: 1.0.0 imports: - - linkml:types +- linkml:types prefixes: linkml: https://w3id.org/linkml/ GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ @@ -12,1876 +12,1879 @@ classes: name: dh_interface description: A DataHarmonizer interface from_schema: https://example.com/PHAC_Dexa - PHAC Dexa: - name: PHAC Dexa + PHACDexa: + name: PHACDexa + title: PHAC Dexa description: Specification for PHAC Dexa clinical virus biosample data gathering is_a: dh_interface slots: - - SPECIMEN_ID - - ISOLATE_ID - - SAMPLE_ID - - SENTINEL_SITE - - LFZ_ADDITIONAL_SAMPLE_ID - - LFZ_ORIGIN_COUNTRY - - SUBJECT_CODE - - SUBJECT_DESCRIPTIONS - - SUBMITTINGORG_1 - - SUBMITTINGLAB_1 - - PROJECT_1 - - COUNTRY_1 - - PROVINCE_1 - - CENSUSDIVISION_1 - - REGION - - YEAR - - MONTH - - QTR - - DATECOLLECTED_1 - - DATERECEIVED_1 - - DATESHIPPED_1 - - ESTABLISHMENT_1 - - SPECIES - - STTYPE - - STYPE - - COMMODITY - - SPECIMENSOURCE_1 - - SPECIMENSUBSOURCE_1 - - SUBJECT_SUBTYPE - - FIELDSTAFF_1 - - IN_STORE_PROCESSING - - MAYCONTAINFROZENMEAT_1 - - NOOFCASHREGISTERS_1 - - PRICEPERKG_1 - - STORETYPE_SAMPLINGSITE_1 - - TEMPERATUREMAX_1 - - TEMPERATUREMIN_1 - - TEMPERATUREARRIVAL_1 - - VETID - - ROOMID - - PENID - - SAMPLING_TYPE - - BARN_ID - - DATE_PACKED - - FINAL_ID_GENUS - - FINAL_ID_SPECIES - - FINAL_ID_SUBSPECIES - - FINAL_ID_SEROTYPE - - FINAL_ID_ANTIGEN - - FINAL_ID_PHAGETYPE - - SA_Serotype_Method - - SEROTYPE_GR - - MIC_AMC - - MIC_AMK - - MIC_AMP - - MIC_AZM - - MIC_CEP - - MIC_CHL - - MIC_CIP - - MIC_CRO - - MIC_FOX - - MIC_GEN - - MIC_KAN - - MIC_MEM - - MIC_NAL - - MIC_SSS - - MIC_STR - - MIC_SXT - - MIC_TET - - MIC_TIO - - N_OF_RESISTANCE - - NBTESTED - - R_PATTERN - - AMR_PA2C - - RLEAST1 - - RLEAST2 - - RLEAST3 - - RLEAST4 - - RLEAST5 - - SIR_AMC - - SIR_AMK - - SIR_AMP - - SIR_AZM - - SIR_CEP - - SIR_CHL - - SIR_CIP - - SIR_CRO - - SIR_FOX - - SIR_GEN - - SIR_KAN - - SIR_MEM - - SIR_NAL - - SIR_SSS - - SIR_STR - - SIR_SXT - - SIR_TET - - SIR_TIO - - RAMC - - RAMK - - RAMP - - RAZM - - RCEP - - RCHL - - RCIP - - RCRO - - RFOX - - RGEN - - RKAN - - RMEM - - RNAL - - RSSS - - RSTR - - RSXT - - RTET - - RTIO - - A2C - - CAMC - - CAMK - - CAMP - - CAZM - - CCEP - - CCHL - - CCIP - - CCRO - - CFOX - - CGEN - - CKAN - - CMEM - - CNAL - - CSSS - - CSTR - - CSXT - - CTET - - CTIO - - STHY_TESTSRC_ID - - WINN_TESTSRC_ID - - GUEL_TESTSRC_ID - - RCIP_DANMAP - - EPIDATESTAMP_1 - - ACSSUT - - AKSSUT - - ACKSSUT - - MDR_A_SSUT - - EXCLUSION - - RAMINOGLY - - RBETALACTAM - - RQUINOLONES - - RFOLINHIBITOR - - MDR - - specimen_number - - EXTERNAL_AGENT - - FARM_FLAG - - AMIKACINGELET + - specimen_id + - isolate_id + - sample_id + - sentinel_site + - lfz_additional_sample_id + - lfz_origin_country + - subject_code + - subject_descriptions + - submittingorg_1 + - submittinglab_1 + - project_1 + - country_1 + - province_1 + - censusdivision_1 + - region + - year + - month + - qtr + - datecollected_1 + - datereceived_1 + - dateshipped_1 + - establishment_1 + - species + - sttype + - stype + - commodity + - specimensource_1 + - specimensubsource_1 + - subject_subtype + - fieldstaff_1 + - in_store_processing + - maycontainfrozenmeat_1 + - noofcashregisters_1 + - priceperkg_1 + - storetype_samplingsite_1 + - temperaturemax_1 + - temperaturemin_1 + - temperaturearrival_1 + - vetid + - roomid + - penid + - sampling_type + - barn_id + - date_packed + - final_id_genus + - final_id_species + - final_id_subspecies + - final_id_serotype + - final_id_antigen + - final_id_phagetype + - sa_serotype_method + - serotype_gr + - mic_amc + - mic_amk + - mic_amp + - mic_azm + - mic_cep + - mic_chl + - mic_cip + - mic_cro + - mic_fox + - mic_gen + - mic_kan + - mic_mem + - mic_nal + - mic_sss + - mic_str + - mic_sxt + - mic_tet + - mic_tio + - n_of_resistance + - nbtested + - r_pattern + - amr_pa2c + - rleast1 + - rleast2 + - rleast3 + - rleast4 + - rleast5 + - sir_amc + - sir_amk + - sir_amp + - sir_azm + - sir_cep + - sir_chl + - sir_cip + - sir_cro + - sir_fox + - sir_gen + - sir_kan + - sir_mem + - sir_nal + - sir_sss + - sir_str + - sir_sxt + - sir_tet + - sir_tio + - ramc + - ramk + - ramp + - razm + - rcep + - rchl + - rcip + - rcro + - rfox + - rgen + - rkan + - rmem + - rnal + - rsss + - rstr + - rsxt + - rtet + - rtio + - a2c + - camc + - camk + - camp + - cazm + - ccep + - cchl + - ccip + - ccro + - cfox + - cgen + - ckan + - cmem + - cnal + - csss + - cstr + - csxt + - ctet + - ctio + - sthy_testsrc_id + - winn_testsrc_id + - guel_testsrc_id + - rcip_danmap + - epidatestamp_1 + - acssut + - akssut + - ackssut + - mdr_a_ssut + - exclusion + - raminogly + - rbetalactam + - rquinolones + - rfolinhibitor + - mdr + - specimen_number + - external_agent + - farm_flag + - amikacingelet slot_usage: - SPECIMEN_ID: + specimen_id: rank: 1 slot_group: Database Identifiers - ISOLATE_ID: + isolate_id: rank: 2 slot_group: Database Identifiers - SAMPLE_ID: + sample_id: rank: 3 slot_group: Database Identifiers - SENTINEL_SITE: + sentinel_site: rank: 4 slot_group: Fields to put in sections - LFZ_ADDITIONAL_SAMPLE_ID: + lfz_additional_sample_id: rank: 5 slot_group: Fields to put in sections - LFZ_ORIGIN_COUNTRY: + lfz_origin_country: rank: 6 slot_group: Fields to put in sections - SUBJECT_CODE: + subject_code: rank: 7 slot_group: Fields to put in sections - SUBJECT_DESCRIPTIONS: + subject_descriptions: rank: 8 slot_group: Fields to put in sections - SUBMITTINGORG_1: + submittingorg_1: rank: 9 slot_group: Fields to put in sections - SUBMITTINGLAB_1: + submittinglab_1: rank: 10 slot_group: Fields to put in sections - PROJECT_1: + project_1: rank: 11 slot_group: Fields to put in sections - COUNTRY_1: + country_1: rank: 12 slot_group: Fields to put in sections - PROVINCE_1: + province_1: rank: 13 slot_group: Fields to put in sections - CENSUSDIVISION_1: + censusdivision_1: rank: 14 slot_group: Fields to put in sections - REGION: + region: rank: 15 slot_group: Fields to put in sections - YEAR: + year: rank: 16 slot_group: Fields to put in sections - MONTH: + month: rank: 17 slot_group: Fields to put in sections - QTR: + qtr: rank: 18 slot_group: Fields to put in sections - DATECOLLECTED_1: + datecollected_1: rank: 19 slot_group: Fields to put in sections - DATERECEIVED_1: + datereceived_1: rank: 20 slot_group: Fields to put in sections - DATESHIPPED_1: + dateshipped_1: rank: 21 slot_group: Fields to put in sections - ESTABLISHMENT_1: + establishment_1: rank: 22 slot_group: Fields to put in sections - SPECIES: + species: rank: 23 slot_group: Fields to put in sections - STTYPE: + sttype: rank: 24 slot_group: Fields to put in sections - STYPE: + stype: rank: 25 slot_group: Fields to put in sections - COMMODITY: + commodity: rank: 26 slot_group: Fields to put in sections - SPECIMENSOURCE_1: + specimensource_1: rank: 27 slot_group: Fields to put in sections - SPECIMENSUBSOURCE_1: + specimensubsource_1: rank: 28 slot_group: Fields to put in sections - SUBJECT_SUBTYPE: + subject_subtype: rank: 29 slot_group: Fields to put in sections - FIELDSTAFF_1: + fieldstaff_1: rank: 30 slot_group: Fields to put in sections - IN_STORE_PROCESSING: + in_store_processing: rank: 31 slot_group: Fields to put in sections - MAYCONTAINFROZENMEAT_1: + maycontainfrozenmeat_1: rank: 32 slot_group: Fields to put in sections - NOOFCASHREGISTERS_1: + noofcashregisters_1: rank: 33 slot_group: Fields to put in sections - PRICEPERKG_1: + priceperkg_1: rank: 34 slot_group: Fields to put in sections - STORETYPE_SAMPLINGSITE_1: + storetype_samplingsite_1: rank: 35 slot_group: Fields to put in sections - TEMPERATUREMAX_1: + temperaturemax_1: rank: 36 slot_group: Fields to put in sections - TEMPERATUREMIN_1: + temperaturemin_1: rank: 37 slot_group: Fields to put in sections - TEMPERATUREARRIVAL_1: + temperaturearrival_1: rank: 38 slot_group: Fields to put in sections - VETID: + vetid: rank: 39 slot_group: Fields to put in sections - ROOMID: + roomid: rank: 40 slot_group: Fields to put in sections - PENID: + penid: rank: 41 slot_group: Fields to put in sections - SAMPLING_TYPE: + sampling_type: rank: 42 slot_group: Fields to put in sections - BARN_ID: + barn_id: rank: 43 slot_group: Fields to put in sections - DATE_PACKED: + date_packed: rank: 44 slot_group: Fields to put in sections - FINAL_ID_GENUS: + final_id_genus: rank: 45 slot_group: Fields to put in sections - FINAL_ID_SPECIES: + final_id_species: rank: 46 slot_group: Fields to put in sections - FINAL_ID_SUBSPECIES: + final_id_subspecies: rank: 47 slot_group: Fields to put in sections - FINAL_ID_SEROTYPE: + final_id_serotype: rank: 48 slot_group: Fields to put in sections - FINAL_ID_ANTIGEN: + final_id_antigen: rank: 49 slot_group: Fields to put in sections - FINAL_ID_PHAGETYPE: + final_id_phagetype: rank: 50 slot_group: Fields to put in sections - SA_Serotype_Method: + sa_serotype_method: rank: 51 slot_group: Fields to put in sections - SEROTYPE_GR: + serotype_gr: rank: 52 slot_group: Fields to put in sections - MIC_AMC: + mic_amc: rank: 53 slot_group: Fields to put in sections - MIC_AMK: + mic_amk: rank: 54 slot_group: Fields to put in sections - MIC_AMP: + mic_amp: rank: 55 slot_group: Fields to put in sections - MIC_AZM: + mic_azm: rank: 56 slot_group: Fields to put in sections - MIC_CEP: + mic_cep: rank: 57 slot_group: Fields to put in sections - MIC_CHL: + mic_chl: rank: 58 slot_group: Fields to put in sections - MIC_CIP: + mic_cip: rank: 59 slot_group: Fields to put in sections - MIC_CRO: + mic_cro: rank: 60 slot_group: Fields to put in sections - MIC_FOX: + mic_fox: rank: 61 slot_group: Fields to put in sections - MIC_GEN: + mic_gen: rank: 62 slot_group: Fields to put in sections - MIC_KAN: + mic_kan: rank: 63 slot_group: Fields to put in sections - MIC_MEM: + mic_mem: rank: 64 slot_group: Fields to put in sections - MIC_NAL: + mic_nal: rank: 65 slot_group: Fields to put in sections - MIC_SSS: + mic_sss: rank: 66 slot_group: Fields to put in sections - MIC_STR: + mic_str: rank: 67 slot_group: Fields to put in sections - MIC_SXT: + mic_sxt: rank: 68 slot_group: Fields to put in sections - MIC_TET: + mic_tet: rank: 69 slot_group: Fields to put in sections - MIC_TIO: + mic_tio: rank: 70 slot_group: Fields to put in sections - N_OF_RESISTANCE: + n_of_resistance: rank: 71 slot_group: Fields to put in sections - NBTESTED: + nbtested: rank: 72 slot_group: Fields to put in sections - R_PATTERN: + r_pattern: rank: 73 slot_group: Fields to put in sections - AMR_PA2C: + amr_pa2c: rank: 74 slot_group: Fields to put in sections - RLEAST1: + rleast1: rank: 75 slot_group: Fields to put in sections - RLEAST2: + rleast2: rank: 76 slot_group: Fields to put in sections - RLEAST3: + rleast3: rank: 77 slot_group: Fields to put in sections - RLEAST4: + rleast4: rank: 78 slot_group: Fields to put in sections - RLEAST5: + rleast5: rank: 79 slot_group: Fields to put in sections - SIR_AMC: + sir_amc: rank: 80 slot_group: Fields to put in sections - SIR_AMK: + sir_amk: rank: 81 slot_group: Fields to put in sections - SIR_AMP: + sir_amp: rank: 82 slot_group: Fields to put in sections - SIR_AZM: + sir_azm: rank: 83 slot_group: Fields to put in sections - SIR_CEP: + sir_cep: rank: 84 slot_group: Fields to put in sections - SIR_CHL: + sir_chl: rank: 85 slot_group: Fields to put in sections - SIR_CIP: + sir_cip: rank: 86 slot_group: Fields to put in sections - SIR_CRO: + sir_cro: rank: 87 slot_group: Fields to put in sections - SIR_FOX: + sir_fox: rank: 88 slot_group: Fields to put in sections - SIR_GEN: + sir_gen: rank: 89 slot_group: Fields to put in sections - SIR_KAN: + sir_kan: rank: 90 slot_group: Fields to put in sections - SIR_MEM: + sir_mem: rank: 91 slot_group: Fields to put in sections - SIR_NAL: + sir_nal: rank: 92 slot_group: Fields to put in sections - SIR_SSS: + sir_sss: rank: 93 slot_group: Fields to put in sections - SIR_STR: + sir_str: rank: 94 slot_group: Fields to put in sections - SIR_SXT: + sir_sxt: rank: 95 slot_group: Fields to put in sections - SIR_TET: + sir_tet: rank: 96 slot_group: Fields to put in sections - SIR_TIO: + sir_tio: rank: 97 slot_group: Fields to put in sections - RAMC: + ramc: rank: 98 slot_group: Fields to put in sections - RAMK: + ramk: rank: 99 slot_group: Fields to put in sections - RAMP: + ramp: rank: 100 slot_group: Fields to put in sections - RAZM: + razm: rank: 101 slot_group: Fields to put in sections - RCEP: + rcep: rank: 102 slot_group: Fields to put in sections - RCHL: + rchl: rank: 103 slot_group: Fields to put in sections - RCIP: + rcip: rank: 104 slot_group: Fields to put in sections - RCRO: + rcro: rank: 105 slot_group: Fields to put in sections - RFOX: + rfox: rank: 106 slot_group: Fields to put in sections - RGEN: + rgen: rank: 107 slot_group: Fields to put in sections - RKAN: + rkan: rank: 108 slot_group: Fields to put in sections - RMEM: + rmem: rank: 109 slot_group: Fields to put in sections - RNAL: + rnal: rank: 110 slot_group: Fields to put in sections - RSSS: + rsss: rank: 111 slot_group: Fields to put in sections - RSTR: + rstr: rank: 112 slot_group: Fields to put in sections - RSXT: + rsxt: rank: 113 slot_group: Fields to put in sections - RTET: + rtet: rank: 114 slot_group: Fields to put in sections - RTIO: + rtio: rank: 115 slot_group: Fields to put in sections - A2C: + a2c: rank: 116 slot_group: Fields to put in sections - CAMC: + camc: rank: 117 slot_group: Fields to put in sections - CAMK: + camk: rank: 118 slot_group: Fields to put in sections - CAMP: + camp: rank: 119 slot_group: Fields to put in sections - CAZM: + cazm: rank: 120 slot_group: Fields to put in sections - CCEP: + ccep: rank: 121 slot_group: Fields to put in sections - CCHL: + cchl: rank: 122 slot_group: Fields to put in sections - CCIP: + ccip: rank: 123 slot_group: Fields to put in sections - CCRO: + ccro: rank: 124 slot_group: Fields to put in sections - CFOX: + cfox: rank: 125 slot_group: Fields to put in sections - CGEN: + cgen: rank: 126 slot_group: Fields to put in sections - CKAN: + ckan: rank: 127 slot_group: Fields to put in sections - CMEM: + cmem: rank: 128 slot_group: Fields to put in sections - CNAL: + cnal: rank: 129 slot_group: Fields to put in sections - CSSS: + csss: rank: 130 slot_group: Fields to put in sections - CSTR: + cstr: rank: 131 slot_group: Fields to put in sections - CSXT: + csxt: rank: 132 slot_group: Fields to put in sections - CTET: + ctet: rank: 133 slot_group: Fields to put in sections - CTIO: + ctio: rank: 134 slot_group: Fields to put in sections - STHY_TESTSRC_ID: + sthy_testsrc_id: rank: 135 slot_group: Fields to put in sections - WINN_TESTSRC_ID: + winn_testsrc_id: rank: 136 slot_group: Fields to put in sections - GUEL_TESTSRC_ID: + guel_testsrc_id: rank: 137 slot_group: Fields to put in sections - RCIP_DANMAP: + rcip_danmap: rank: 138 slot_group: Fields to put in sections - EPIDATESTAMP_1: + epidatestamp_1: rank: 139 slot_group: Fields to put in sections - ACSSUT: + acssut: rank: 140 slot_group: Fields to put in sections - AKSSUT: + akssut: rank: 141 slot_group: Fields to put in sections - ACKSSUT: + ackssut: rank: 142 slot_group: Fields to put in sections - MDR_A_SSUT: + mdr_a_ssut: rank: 143 slot_group: Fields to put in sections - EXCLUSION: + exclusion: rank: 144 slot_group: Fields to put in sections - RAMINOGLY: + raminogly: rank: 145 slot_group: Fields to put in sections - RBETALACTAM: + rbetalactam: rank: 146 slot_group: Fields to put in sections - RQUINOLONES: + rquinolones: rank: 147 slot_group: Fields to put in sections - RFOLINHIBITOR: + rfolinhibitor: rank: 148 slot_group: Fields to put in sections - MDR: + mdr: rank: 149 slot_group: Fields to put in sections specimen_number: rank: 150 slot_group: Fields to put in sections - EXTERNAL_AGENT: + external_agent: rank: 151 slot_group: Fields to put in sections - FARM_FLAG: + farm_flag: rank: 152 slot_group: Fields to put in sections - AMIKACINGELET: + amikacingelet: rank: 153 slot_group: Fields to put in sections slots: - SPECIMEN_ID: - name: SPECIMEN_ID + specimen_id: + name: specimen_id title: SPECIMEN_ID range: WhitespaceMinimizedString exact_mappings: - - GRDI:alternative_sample_ID - ISOLATE_ID: - name: ISOLATE_ID + - GRDI:alternative_sample_ID + isolate_id: + name: isolate_id title: ISOLATE_ID range: WhitespaceMinimizedString required: true exact_mappings: - - GRDI:isolate_ID - SAMPLE_ID: - name: SAMPLE_ID + - GRDI:isolate_ID + sample_id: + name: sample_id title: SAMPLE_ID range: WhitespaceMinimizedString required: true exact_mappings: - - GRDI:sample_collector_sample_ID - SENTINEL_SITE: - name: SENTINEL_SITE + - GRDI:sample_collector_sample_ID + sentinel_site: + name: sentinel_site title: SENTINEL_SITE range: WhitespaceMinimizedString - LFZ_ADDITIONAL_SAMPLE_ID: - name: LFZ_ADDITIONAL_SAMPLE_ID + lfz_additional_sample_id: + name: lfz_additional_sample_id title: LFZ_ADDITIONAL_SAMPLE_ID range: WhitespaceMinimizedString - LFZ_ORIGIN_COUNTRY: - name: LFZ_ORIGIN_COUNTRY + lfz_origin_country: + name: lfz_origin_country title: LFZ_ORIGIN_COUNTRY range: WhitespaceMinimizedString - SUBJECT_CODE: - name: SUBJECT_CODE + subject_code: + name: subject_code title: SUBJECT_CODE range: WhitespaceMinimizedString - SUBJECT_DESCRIPTIONS: - name: SUBJECT_DESCRIPTIONS + subject_descriptions: + name: subject_descriptions title: SUBJECT_DESCRIPTIONS - range: SUBJECT_DESCRIPTIONS menu - SUBMITTINGORG_1: - name: SUBMITTINGORG_1 + range: SubjectDescriptionsMenu + submittingorg_1: + name: submittingorg_1 title: SUBMITTINGORG_1 range: WhitespaceMinimizedString exact_mappings: - - GRDI:collected_by - SUBMITTINGLAB_1: - name: SUBMITTINGLAB_1 + - GRDI:collected_by + submittinglab_1: + name: submittinglab_1 title: SUBMITTINGLAB_1 range: WhitespaceMinimizedString exact_mappings: - - GRDI:laboratory_name - PROJECT_1: - name: PROJECT_1 + - GRDI:laboratory_name + project_1: + name: project_1 title: PROJECT_1 range: WhitespaceMinimizedString - COUNTRY_1: - name: COUNTRY_1 + country_1: + name: country_1 title: COUNTRY_1 range: WhitespaceMinimizedString exact_mappings: - - GRDI:geo_loc_name (country) - PROVINCE_1: - name: PROVINCE_1 + - GRDI:geo_loc_name%20%28country%29 + province_1: + name: province_1 title: PROVINCE_1 range: WhitespaceMinimizedString exact_mappings: - - GRDI:geo_loc_name (state/province/region) - CENSUSDIVISION_1: - name: CENSUSDIVISION_1 + - GRDI:geo_loc_name%20%28state/province/region%29 + censusdivision_1: + name: censusdivision_1 title: CENSUSDIVISION_1 range: WhitespaceMinimizedString - REGION: - name: REGION + region: + name: region title: REGION range: WhitespaceMinimizedString - YEAR: - name: YEAR + year: + name: year title: YEAR range: WhitespaceMinimizedString - MONTH: - name: MONTH + month: + name: month title: MONTH range: WhitespaceMinimizedString - QTR: - name: QTR + qtr: + name: qtr title: QTR range: WhitespaceMinimizedString - DATECOLLECTED_1: - name: DATECOLLECTED_1 + datecollected_1: + name: datecollected_1 title: DATECOLLECTED_1 range: date exact_mappings: - - GRDI:sample_collection_date - DATERECEIVED_1: - name: DATERECEIVED_1 + - GRDI:sample_collection_date + datereceived_1: + name: datereceived_1 title: DATERECEIVED_1 range: WhitespaceMinimizedString - DATESHIPPED_1: - name: DATESHIPPED_1 + dateshipped_1: + name: dateshipped_1 title: DATESHIPPED_1 range: WhitespaceMinimizedString - ESTABLISHMENT_1: - name: ESTABLISHMENT_1 + establishment_1: + name: establishment_1 title: ESTABLISHMENT_1 range: WhitespaceMinimizedString - SPECIES: - name: SPECIES + species: + name: species title: SPECIES - range: SPECIES menu + range: SpeciesMenu exact_mappings: - - 'GRDI:host (common name):' - STTYPE: - name: STTYPE + - GRDI:host%20%28common%20name%29%3A + sttype: + name: sttype title: STTYPE - range: STTYPE menu - STYPE: - name: STYPE + range: STTypeMenu + stype: + name: stype title: STYPE - range: STYPE menu - COMMODITY: - name: COMMODITY + range: STypeMenu + commodity: + name: commodity title: COMMODITY - range: COMMODITY menu - SPECIMENSOURCE_1: - name: SPECIMENSOURCE_1 + range: CommodityMenu + specimensource_1: + name: specimensource_1 title: SPECIMENSOURCE_1 - range: SPECIMENSOURCE_1 menu - SPECIMENSUBSOURCE_1: - name: SPECIMENSUBSOURCE_1 + range: SpecimenSource1Menu + specimensubsource_1: + name: specimensubsource_1 title: SPECIMENSUBSOURCE_1 - range: SPECIMENSUBSOURCE_1 menu - SUBJECT_SUBTYPE: - name: SUBJECT_SUBTYPE + range: SpecimenSubsource1Menu + subject_subtype: + name: subject_subtype title: SUBJECT_SUBTYPE - range: SUBJECT_SUBTYPE menu - FIELDSTAFF_1: - name: FIELDSTAFF_1 + range: SubjectSubtypeMenu + fieldstaff_1: + name: fieldstaff_1 title: FIELDSTAFF_1 range: WhitespaceMinimizedString - IN_STORE_PROCESSING: - name: IN_STORE_PROCESSING + in_store_processing: + name: in_store_processing title: IN_STORE_PROCESSING range: WhitespaceMinimizedString - MAYCONTAINFROZENMEAT_1: - name: MAYCONTAINFROZENMEAT_1 + maycontainfrozenmeat_1: + name: maycontainfrozenmeat_1 title: MAYCONTAINFROZENMEAT_1 range: WhitespaceMinimizedString - NOOFCASHREGISTERS_1: - name: NOOFCASHREGISTERS_1 + noofcashregisters_1: + name: noofcashregisters_1 title: NOOFCASHREGISTERS_1 range: WhitespaceMinimizedString - PRICEPERKG_1: - name: PRICEPERKG_1 + priceperkg_1: + name: priceperkg_1 title: PRICEPERKG_1 range: WhitespaceMinimizedString - STORETYPE_SAMPLINGSITE_1: - name: STORETYPE_SAMPLINGSITE_1 + storetype_samplingsite_1: + name: storetype_samplingsite_1 title: STORETYPE_SAMPLINGSITE_1 range: WhitespaceMinimizedString - TEMPERATUREMAX_1: - name: TEMPERATUREMAX_1 + temperaturemax_1: + name: temperaturemax_1 title: TEMPERATUREMAX_1 range: WhitespaceMinimizedString - TEMPERATUREMIN_1: - name: TEMPERATUREMIN_1 + temperaturemin_1: + name: temperaturemin_1 title: TEMPERATUREMIN_1 range: WhitespaceMinimizedString - TEMPERATUREARRIVAL_1: - name: TEMPERATUREARRIVAL_1 + temperaturearrival_1: + name: temperaturearrival_1 title: TEMPERATUREARRIVAL_1 range: WhitespaceMinimizedString - VETID: - name: VETID + vetid: + name: vetid title: VETID range: WhitespaceMinimizedString - ROOMID: - name: ROOMID + roomid: + name: roomid title: ROOMID range: WhitespaceMinimizedString - PENID: - name: PENID + penid: + name: penid title: PENID range: WhitespaceMinimizedString - SAMPLING_TYPE: - name: SAMPLING_TYPE + sampling_type: + name: sampling_type title: SAMPLING_TYPE range: WhitespaceMinimizedString - BARN_ID: - name: BARN_ID + barn_id: + name: barn_id title: BARN_ID range: WhitespaceMinimizedString - DATE_PACKED: - name: DATE_PACKED + date_packed: + name: date_packed title: DATE_PACKED range: WhitespaceMinimizedString - FINAL_ID_GENUS: - name: FINAL_ID_GENUS + final_id_genus: + name: final_id_genus title: FINAL_ID_GENUS range: WhitespaceMinimizedString exact_mappings: - - GRDI:organism - FINAL_ID_SPECIES: - name: FINAL_ID_SPECIES + - GRDI:organism + final_id_species: + name: final_id_species title: FINAL_ID_SPECIES range: WhitespaceMinimizedString exact_mappings: - - GRDI:organism - FINAL_ID_SUBSPECIES: - name: FINAL_ID_SUBSPECIES + - GRDI:organism + final_id_subspecies: + name: final_id_subspecies title: FINAL_ID_SUBSPECIES range: WhitespaceMinimizedString - FINAL_ID_SEROTYPE: - name: FINAL_ID_SEROTYPE + final_id_serotype: + name: final_id_serotype title: FINAL_ID_SEROTYPE range: WhitespaceMinimizedString exact_mappings: - - GRDI:serovar - FINAL_ID_ANTIGEN: - name: FINAL_ID_ANTIGEN + - GRDI:serovar + final_id_antigen: + name: final_id_antigen title: FINAL_ID_ANTIGEN range: WhitespaceMinimizedString - FINAL_ID_PHAGETYPE: - name: FINAL_ID_PHAGETYPE + final_id_phagetype: + name: final_id_phagetype title: FINAL_ID_PHAGETYPE range: WhitespaceMinimizedString exact_mappings: - - GRDI:phagetype - SA_Serotype_Method: - name: SA_Serotype_Method + - GRDI:phagetype + sa_serotype_method: + name: sa_serotype_method title: SA_Serotype_Method range: WhitespaceMinimizedString exact_mappings: - - GRDI:serotyping_method - SEROTYPE_GR: - name: SEROTYPE_GR + - GRDI:serotyping_method + serotype_gr: + name: serotype_gr title: SEROTYPE_GR range: WhitespaceMinimizedString - MIC_AMC: - name: MIC_AMC + mic_amc: + name: mic_amc title: MIC_AMC range: WhitespaceMinimizedString - MIC_AMK: - name: MIC_AMK + mic_amk: + name: mic_amk title: MIC_AMK range: WhitespaceMinimizedString - MIC_AMP: - name: MIC_AMP + mic_amp: + name: mic_amp title: MIC_AMP range: WhitespaceMinimizedString - MIC_AZM: - name: MIC_AZM + mic_azm: + name: mic_azm title: MIC_AZM range: WhitespaceMinimizedString - MIC_CEP: - name: MIC_CEP + mic_cep: + name: mic_cep title: MIC_CEP range: WhitespaceMinimizedString - MIC_CHL: - name: MIC_CHL + mic_chl: + name: mic_chl title: MIC_CHL range: WhitespaceMinimizedString - MIC_CIP: - name: MIC_CIP + mic_cip: + name: mic_cip title: MIC_CIP range: WhitespaceMinimizedString - MIC_CRO: - name: MIC_CRO + mic_cro: + name: mic_cro title: MIC_CRO range: WhitespaceMinimizedString - MIC_FOX: - name: MIC_FOX + mic_fox: + name: mic_fox title: MIC_FOX range: WhitespaceMinimizedString - MIC_GEN: - name: MIC_GEN + mic_gen: + name: mic_gen title: MIC_GEN range: WhitespaceMinimizedString - MIC_KAN: - name: MIC_KAN + mic_kan: + name: mic_kan title: MIC_KAN range: WhitespaceMinimizedString - MIC_MEM: - name: MIC_MEM + mic_mem: + name: mic_mem title: MIC_MEM range: WhitespaceMinimizedString - MIC_NAL: - name: MIC_NAL + mic_nal: + name: mic_nal title: MIC_NAL range: WhitespaceMinimizedString - MIC_SSS: - name: MIC_SSS + mic_sss: + name: mic_sss title: MIC_SSS range: WhitespaceMinimizedString - MIC_STR: - name: MIC_STR + mic_str: + name: mic_str title: MIC_STR range: WhitespaceMinimizedString - MIC_SXT: - name: MIC_SXT + mic_sxt: + name: mic_sxt title: MIC_SXT range: WhitespaceMinimizedString - MIC_TET: - name: MIC_TET + mic_tet: + name: mic_tet title: MIC_TET range: WhitespaceMinimizedString - MIC_TIO: - name: MIC_TIO + mic_tio: + name: mic_tio title: MIC_TIO range: WhitespaceMinimizedString - N_OF_RESISTANCE: - name: N_OF_RESISTANCE + n_of_resistance: + name: n_of_resistance title: N_OF_RESISTANCE range: WhitespaceMinimizedString - NBTESTED: - name: NBTESTED + nbtested: + name: nbtested title: NBTESTED range: WhitespaceMinimizedString - R_PATTERN: - name: R_PATTERN + r_pattern: + name: r_pattern title: R_PATTERN range: WhitespaceMinimizedString - AMR_PA2C: - name: AMR_PA2C + amr_pa2c: + name: amr_pa2c title: AMR_PA2C range: WhitespaceMinimizedString - RLEAST1: - name: RLEAST1 + rleast1: + name: rleast1 title: RLEAST1 range: WhitespaceMinimizedString - RLEAST2: - name: RLEAST2 + rleast2: + name: rleast2 title: RLEAST2 range: WhitespaceMinimizedString - RLEAST3: - name: RLEAST3 + rleast3: + name: rleast3 title: RLEAST3 range: WhitespaceMinimizedString - RLEAST4: - name: RLEAST4 + rleast4: + name: rleast4 title: RLEAST4 range: WhitespaceMinimizedString - RLEAST5: - name: RLEAST5 + rleast5: + name: rleast5 title: RLEAST5 range: WhitespaceMinimizedString - SIR_AMC: - name: SIR_AMC + sir_amc: + name: sir_amc title: SIR_AMC range: WhitespaceMinimizedString - SIR_AMK: - name: SIR_AMK + sir_amk: + name: sir_amk title: SIR_AMK range: WhitespaceMinimizedString - SIR_AMP: - name: SIR_AMP + sir_amp: + name: sir_amp title: SIR_AMP range: WhitespaceMinimizedString - SIR_AZM: - name: SIR_AZM + sir_azm: + name: sir_azm title: SIR_AZM range: WhitespaceMinimizedString - SIR_CEP: - name: SIR_CEP + sir_cep: + name: sir_cep title: SIR_CEP range: WhitespaceMinimizedString - SIR_CHL: - name: SIR_CHL + sir_chl: + name: sir_chl title: SIR_CHL range: WhitespaceMinimizedString - SIR_CIP: - name: SIR_CIP + sir_cip: + name: sir_cip title: SIR_CIP range: WhitespaceMinimizedString - SIR_CRO: - name: SIR_CRO + sir_cro: + name: sir_cro title: SIR_CRO range: WhitespaceMinimizedString - SIR_FOX: - name: SIR_FOX + sir_fox: + name: sir_fox title: SIR_FOX range: WhitespaceMinimizedString - SIR_GEN: - name: SIR_GEN + sir_gen: + name: sir_gen title: SIR_GEN range: WhitespaceMinimizedString - SIR_KAN: - name: SIR_KAN + sir_kan: + name: sir_kan title: SIR_KAN range: WhitespaceMinimizedString - SIR_MEM: - name: SIR_MEM + sir_mem: + name: sir_mem title: SIR_MEM range: WhitespaceMinimizedString - SIR_NAL: - name: SIR_NAL + sir_nal: + name: sir_nal title: SIR_NAL range: WhitespaceMinimizedString - SIR_SSS: - name: SIR_SSS + sir_sss: + name: sir_sss title: SIR_SSS range: WhitespaceMinimizedString - SIR_STR: - name: SIR_STR + sir_str: + name: sir_str title: SIR_STR range: WhitespaceMinimizedString - SIR_SXT: - name: SIR_SXT + sir_sxt: + name: sir_sxt title: SIR_SXT range: WhitespaceMinimizedString - SIR_TET: - name: SIR_TET + sir_tet: + name: sir_tet title: SIR_TET range: WhitespaceMinimizedString - SIR_TIO: - name: SIR_TIO + sir_tio: + name: sir_tio title: SIR_TIO range: WhitespaceMinimizedString - RAMC: - name: RAMC + ramc: + name: ramc title: RAMC range: WhitespaceMinimizedString - RAMK: - name: RAMK + ramk: + name: ramk title: RAMK range: WhitespaceMinimizedString - RAMP: - name: RAMP + ramp: + name: ramp title: RAMP range: WhitespaceMinimizedString - RAZM: - name: RAZM + razm: + name: razm title: RAZM range: WhitespaceMinimizedString - RCEP: - name: RCEP + rcep: + name: rcep title: RCEP range: WhitespaceMinimizedString - RCHL: - name: RCHL + rchl: + name: rchl title: RCHL range: WhitespaceMinimizedString - RCIP: - name: RCIP + rcip: + name: rcip title: RCIP range: WhitespaceMinimizedString - RCRO: - name: RCRO + rcro: + name: rcro title: RCRO range: WhitespaceMinimizedString - RFOX: - name: RFOX + rfox: + name: rfox title: RFOX range: WhitespaceMinimizedString - RGEN: - name: RGEN + rgen: + name: rgen title: RGEN range: WhitespaceMinimizedString - RKAN: - name: RKAN + rkan: + name: rkan title: RKAN range: WhitespaceMinimizedString - RMEM: - name: RMEM + rmem: + name: rmem title: RMEM range: WhitespaceMinimizedString - RNAL: - name: RNAL + rnal: + name: rnal title: RNAL range: WhitespaceMinimizedString - RSSS: - name: RSSS + rsss: + name: rsss title: RSSS range: WhitespaceMinimizedString - RSTR: - name: RSTR + rstr: + name: rstr title: RSTR range: WhitespaceMinimizedString - RSXT: - name: RSXT + rsxt: + name: rsxt title: RSXT range: WhitespaceMinimizedString - RTET: - name: RTET + rtet: + name: rtet title: RTET range: WhitespaceMinimizedString - RTIO: - name: RTIO + rtio: + name: rtio title: RTIO range: WhitespaceMinimizedString - A2C: - name: A2C + a2c: + name: a2c title: A2C range: WhitespaceMinimizedString - CAMC: - name: CAMC + camc: + name: camc title: CAMC range: WhitespaceMinimizedString - CAMK: - name: CAMK + camk: + name: camk title: CAMK range: WhitespaceMinimizedString - CAMP: - name: CAMP + camp: + name: camp title: CAMP range: WhitespaceMinimizedString - CAZM: - name: CAZM + cazm: + name: cazm title: CAZM range: WhitespaceMinimizedString - CCEP: - name: CCEP + ccep: + name: ccep title: CCEP range: WhitespaceMinimizedString - CCHL: - name: CCHL + cchl: + name: cchl title: CCHL range: WhitespaceMinimizedString - CCIP: - name: CCIP + ccip: + name: ccip title: CCIP range: WhitespaceMinimizedString - CCRO: - name: CCRO + ccro: + name: ccro title: CCRO range: WhitespaceMinimizedString - CFOX: - name: CFOX + cfox: + name: cfox title: CFOX range: WhitespaceMinimizedString - CGEN: - name: CGEN + cgen: + name: cgen title: CGEN range: WhitespaceMinimizedString - CKAN: - name: CKAN + ckan: + name: ckan title: CKAN range: WhitespaceMinimizedString - CMEM: - name: CMEM + cmem: + name: cmem title: CMEM range: WhitespaceMinimizedString - CNAL: - name: CNAL + cnal: + name: cnal title: CNAL range: WhitespaceMinimizedString - CSSS: - name: CSSS + csss: + name: csss title: CSSS range: WhitespaceMinimizedString - CSTR: - name: CSTR + cstr: + name: cstr title: CSTR range: WhitespaceMinimizedString - CSXT: - name: CSXT + csxt: + name: csxt title: CSXT range: WhitespaceMinimizedString - CTET: - name: CTET + ctet: + name: ctet title: CTET range: WhitespaceMinimizedString - CTIO: - name: CTIO + ctio: + name: ctio title: CTIO range: WhitespaceMinimizedString - STHY_TESTSRC_ID: - name: STHY_TESTSRC_ID + sthy_testsrc_id: + name: sthy_testsrc_id title: STHY_TESTSRC_ID range: WhitespaceMinimizedString - WINN_TESTSRC_ID: - name: WINN_TESTSRC_ID + winn_testsrc_id: + name: winn_testsrc_id title: WINN_TESTSRC_ID range: WhitespaceMinimizedString - GUEL_TESTSRC_ID: - name: GUEL_TESTSRC_ID + guel_testsrc_id: + name: guel_testsrc_id title: GUEL_TESTSRC_ID range: WhitespaceMinimizedString - RCIP_DANMAP: - name: RCIP_DANMAP + rcip_danmap: + name: rcip_danmap title: RCIP_DANMAP range: WhitespaceMinimizedString - EPIDATESTAMP_1: - name: EPIDATESTAMP_1 + epidatestamp_1: + name: epidatestamp_1 title: EPIDATESTAMP_1 range: WhitespaceMinimizedString - ACSSUT: - name: ACSSUT + acssut: + name: acssut title: ACSSUT range: WhitespaceMinimizedString - AKSSUT: - name: AKSSUT + akssut: + name: akssut title: AKSSUT range: WhitespaceMinimizedString - ACKSSUT: - name: ACKSSUT + ackssut: + name: ackssut title: ACKSSUT range: WhitespaceMinimizedString - MDR_A_SSUT: - name: MDR_A_SSUT + mdr_a_ssut: + name: mdr_a_ssut title: MDR_A_SSUT range: WhitespaceMinimizedString - EXCLUSION: - name: EXCLUSION + exclusion: + name: exclusion title: EXCLUSION range: WhitespaceMinimizedString - RAMINOGLY: - name: RAMINOGLY + raminogly: + name: raminogly title: RAMINOGLY range: WhitespaceMinimizedString - RBETALACTAM: - name: RBETALACTAM + rbetalactam: + name: rbetalactam title: RBETALACTAM range: WhitespaceMinimizedString - RQUINOLONES: - name: RQUINOLONES + rquinolones: + name: rquinolones title: RQUINOLONES range: WhitespaceMinimizedString - RFOLINHIBITOR: - name: RFOLINHIBITOR + rfolinhibitor: + name: rfolinhibitor title: RFOLINHIBITOR range: WhitespaceMinimizedString - MDR: - name: MDR + mdr: + name: mdr title: MDR range: WhitespaceMinimizedString specimen_number: name: specimen_number title: specimen_number range: WhitespaceMinimizedString - EXTERNAL_AGENT: - name: EXTERNAL_AGENT + external_agent: + name: external_agent title: EXTERNAL_AGENT range: WhitespaceMinimizedString - FARM_FLAG: - name: FARM_FLAG + farm_flag: + name: farm_flag title: FARM_FLAG range: WhitespaceMinimizedString - AMIKACINGELET: - name: AMIKACINGELET + amikacingelet: + name: amikacingelet title: AMIKACINGELET range: WhitespaceMinimizedString enums: - SUBJECT_DESCRIPTIONS menu: - name: SUBJECT_DESCRIPTIONS menu + SubjectDescriptionsMenu: + name: SubjectDescriptionsMenu + title: SUBJECT_DESCRIPTIONS menu permissible_values: 1/2 breast: text: 1/2 breast meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Avian Ingredients: text: Avian Ingredients meaning: FOODON:00002616 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Back: text: Back meaning: PATO:0001901 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Balut: text: Balut meaning: FOODON:03302184 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Black Pepper: text: Black Pepper meaning: FOODON:03411191 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Blade Steak: text: Blade Steak exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Blood Meal: text: Blood Meal meaning: FOODON:00001564 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Bone Meal: text: Bone Meal meaning: ENVO:02000054 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Bovine Ingredients: text: Bovine Ingredients meaning: FOODON:03414374 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast: text: Breast meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast back off: text: Breast back off exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast cutlets: text: Breast cutlets exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast Skinless: text: Breast Skinless meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast Skinless Boneless: text: Breast Skinless Boneless meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast with Skin: text: Breast with Skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Brisket: text: Brisket meaning: FOODON:03530020 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Burger: text: Burger meaning: FOODON:00002737 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Calf: text: Calf exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Canola Meal: text: Canola Meal meaning: FOODON:00002694 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Carinata Meal: text: Carinata Meal meaning: FOODON:03316468 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chop: text: Chop exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chops: text: Chops exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A coli: text: coli Complete Feed: text: Complete Feed meaning: FOODON:03309997 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Corn: text: Corn meaning: FOODON:00001765 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Cow: text: Cow meaning: FOODON:03411161 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Cubes: text: Cubes exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Cutlet: text: Cutlet meaning: FOODON:00003001 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Drumstick: text: Drumstick meaning: CURATION:0001378 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Drumstick Skinless: text: Drumstick Skinless meaning: CURATION:0001378 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Drumstick with Skin: text: Drumstick with Skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Drumsticks: text: Drumsticks meaning: CURATION:0001378 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Egg Flour: text: Egg Flour exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Feather Meal: text: Feather Meal meaning: CURATION:0001357 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Feed: text: Feed meaning: FOODON:03309997 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Filet: text: Filet meaning: FOODON:03530144 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Fish Ingredients: text: Fish Ingredients meaning: FOODON:03411222 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Fish Meal: text: Fish Meal meaning: FOODON:03301620 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Grain: text: Grain meaning: FOODON:03311095 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground: text: Ground meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground ( lean): text: Ground ( lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Angus): text: Ground (Angus) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Extra Lean): text: Ground (Extra Lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (extra-lan): text: Ground (extra-lan) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Extra-Lean): text: Ground (Extra-Lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Lean): text: Ground (Lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Medium): text: Ground (Medium) meaning: FOODON:03430117 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Regular): text: Ground (Regular) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (Sirloin): text: Ground (Sirloin) meaning: CURATION:0001614 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground Boneless: text: Ground Boneless meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground extra lean: text: Ground extra lean meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground regular: text: Ground regular meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A ground( extra lean): text: ground( extra lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A ground( medium): text: ground( medium) meaning: FOODON:03430117 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground(Extra lean): text: Ground(Extra lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground(Lean): text: Ground(Lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground(medium): text: Ground(medium) meaning: FOODON:03430117 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A ground(regular): text: ground(regular) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Groundextra lean): text: Groundextra lean) meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground-Lean: text: Ground-Lean meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground-Regular: text: Ground-Regular meaning: FOODON:03430136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Heifer: text: Heifer meaning: FOODON:00002518 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Hummus: text: Hummus meaning: FOODON:00003049 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A In-Shell: text: In-Shell meaning: UBERON:0006612 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Lay Ration: text: Lay Ration exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Leg: text: Leg meaning: UBERON:0000978 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Leg with Skin-Drumstick and Thigh: text: Leg with Skin-Drumstick and Thigh exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Liver: text: Liver meaning: UBERON:0002107 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Loin Center Chop: text: Loin Center Chop meaning: FOODON:03530031 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Meat and Bone Meal: text: Meat and Bone Meal meaning: FOODON:00002738 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Meat Flour/Meal: text: Meat Flour/Meal exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Meat Meal: text: Meat Meal exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mild italian style burger: text: Mild italian style burger exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Necks: text: Necks meaning: UBERON:0000974 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Nuggets: text: Nuggets exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other: text: Other exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Other cut: text: Other cut exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other Cut (Not Ground): text: Other Cut (Not Ground) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other Cut Boneless: text: Other Cut Boneless exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other Cut Boneless (Not Ground): text: Other Cut Boneless (Not Ground) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ovine Ingredients: text: Ovine Ingredients meaning: FOODON:03411183 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pet Food: text: Pet Food meaning: FOODON:00002682 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Porcine Ingredients: text: Porcine Ingredients meaning: FOODON:03411136 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pork Chop (Cut Unknown): text: Pork Chop (Cut Unknown) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Premix: text: Premix exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Premix (Medicated): text: Premix (Medicated) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Processed (Other): text: Processed (Other) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Raw: text: Raw meaning: FOODON:03311126 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Rib Chop: text: Rib Chop meaning: UBERON:0002228 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ribs: text: Ribs meaning: UBERON:0002228 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Roast: text: Roast exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Salami: text: Salami meaning: FOODON:03312067 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sausage: text: Sausage meaning: FOODON:03315904 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sausage (Pepper): text: Sausage (Pepper) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Scallopini: text: Scallopini meaning: FOODON:00003017 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shell on: text: Shell on meaning: UBERON:0006612 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shelled: text: Shelled exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shoulder: text: Shoulder meaning: UBERON:0001467 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shoulder Chop: text: Shoulder Chop meaning: UBERON:0001467 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sirloin Chop: text: Sirloin Chop meaning: FOODON:03530027 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Skim milk powder: text: Skim milk powder meaning: FOODON:03301484 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Soft: text: Soft meaning: PATO:0000387 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Soyabean Meal: text: Soyabean Meal meaning: FOODON:03316468 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Starter Ration: text: Starter Ration exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Steak: text: Steak exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Stew Chunks: text: Stew Chunks meaning: FOODON:00003140 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Supplements: text: Supplements meaning: FOODON:00001874 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A T. high: text: T. high exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Tahini: text: Tahini meaning: FOODON:03304154 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Tender loin: text: Tender loin meaning: FOODON:03530217 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Tenderloin: text: Tenderloin meaning: FOODON:03530217 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Thigh: text: Thigh meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Thigh Skinless: text: Thigh Skinless meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Thigh Skinless Boneless: text: Thigh Skinless Boneless meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Thigh with Skin: text: Thigh with Skin meaning: UBERON:0000014 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Trim: text: Trim meaning: FOODON:00001568 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Unknown Meal: text: Unknown Meal meaning: FOODON:03316468 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Unspecified Feed/Ingredient: text: Unspecified Feed/Ingredient meaning: FOODON:03309997 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Upper Thigh: text: Upper Thigh meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Upper Thigh with Skin: text: Upper Thigh with Skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A upper thight: text: upper thight meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Upperthigh: text: Upperthigh meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A White Pepper: text: White Pepper meaning: FOODON:03304045 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Whole: text: Whole meaning: FOODON:03430131 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Whole Carcass: text: Whole Carcass exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Whole with Skin: text: Whole with Skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Wing: text: Wing meaning: UBERON:0000023 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Wings: text: Wings meaning: UBERON:0000023 exact_mappings: - - 'GRDI:food_product:' - SPECIES menu: - name: SPECIES menu + - GRDI:food_product%3A + SpeciesMenu: + name: SpeciesMenu + title: SPECIES menu permissible_values: '2': text: '2' @@ -2343,8 +2346,9 @@ enums: Zebra: text: Zebra meaning: FOODON:03412097 - STTYPE menu: - name: STTYPE menu + STTypeMenu: + name: STTypeMenu + title: STTYPE menu permissible_values: '0': text: '0' @@ -2354,23 +2358,23 @@ enums: text: ANIMAL meaning: FOODON:00003004 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A ENVIRONMENT: text: ENVIRONMENT meaning: ENVO:01000254 exact_mappings: - - 'GRDI:environmental_material:' - - 'GRDI:environmental_site:' + - GRDI:environmental_material%3A + - GRDI:environmental_site%3A FOOD: text: FOOD meaning: CHEBI:33290 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A HUMAN: text: HUMAN meaning: NCBITAXON:9606 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A PRODUCT: text: PRODUCT QA: @@ -2378,7 +2382,7 @@ enums: UNKNOWN: text: UNKNOWN exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A '2': text: '2' <=8: @@ -2389,339 +2393,340 @@ enums: text: Amphibian meaning: FOODON:03411624 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Aquatic Mammal: text: Aquatic Mammal meaning: FOODON:03411134 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Armadillo: text: Armadillo meaning: FOODON:03411626 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Avian: text: Avian meaning: FOODON:00002616 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Bat: text: Bat meaning: CURATION:0001601 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Biosolids: text: Biosolids meaning: ENVO:00002059 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Bovine: text: Bovine meaning: FOODON:03414374 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Building: text: Building meaning: ENVO:00000073 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Camelid: text: Camelid meaning: FOODON:03412103 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Canine: text: Canine meaning: FOODON:03414847 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Caprine: text: Caprine meaning: FOODON:03411328 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Caprine and Ovine: text: Caprine and Ovine exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Cereal: text: Cereal meaning: FOODON:00001709 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Cereal/Bread/Snack: text: Cereal/Bread/Snack exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Cervid: text: Cervid meaning: FOODON:03411500 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Compost: text: Compost meaning: CURATION:0001527 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Confections/Nuts/Condiments: text: Confections/Nuts/Condiments exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Crocuta: text: Crocuta exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Crustacean: text: Crustacean meaning: FOODON:03411374 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Dairy: text: Dairy meaning: ENVO:00003862 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Dust: text: Dust meaning: ENVO:00002008 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Egg: text: Egg meaning: FOODON:00001274 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Elephant: text: Elephant meaning: FOODON:03412129 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Equine: text: Equine meaning: CURATION:0001431 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Equipment: text: Equipment meaning: CURATION:0000348 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A ERROR: text: ERROR Feed and Ingredients: text: Feed and Ingredients meaning: FOODON:03309997 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Feline: text: Feline meaning: NCIT:C14191 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Ferret: text: Ferret meaning: CURATION:0001411 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Fertilizer: text: Fertilizer meaning: CHEBI:33287 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Fish: text: Fish meaning: FOODON:03411222 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Food: text: Food meaning: CHEBI:33290 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Fruit: text: Fruit meaning: PO:0009001 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Fruits and Vegetables: text: Fruits and Vegetables meaning: FOODON:00002141 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Health (medicine): text: Health (medicine) Herbs and Spices: text: Herbs and Spices exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Herpestidae: text: Herpestidae exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Hippopotamidae: text: Hippopotamidae meaning: NCBITAXON:9831 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Lapine: text: Lapine exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Litter/Manure: text: Litter/Manure meaning: CURATION:0001446 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Manure: text: Manure exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Marsupial: text: Marsupial exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Meat: text: Meat meaning: FOODON:00001006 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mephitida: text: Mephitida exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Mink: text: Mink meaning: FOODON:00002723 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Mixed food: text: Mixed food meaning: CHEBI:33290 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mixed Food/Meat: text: Mixed Food/Meat meaning: FOODON:03315600 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mollusk: text: Mollusk meaning: FOODON:03412112 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Mustelid: text: Mustelid exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A n/a: text: n/a exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Other: text: Other exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Ovine: text: Ovine meaning: FOODON:03411183 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Personnel Clothing: text: Personnel Clothing exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Porcine: text: Porcine meaning: FOODON:03411136 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Primate: text: Primate meaning: NCBITAXON:9443 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Raccoon: text: Raccoon meaning: FOODON:03411461 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Reptile: text: Reptile meaning: FOODON:03411625 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Rodent: text: Rodent meaning: NCBITAXON:9989 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Sewage: text: Sewage meaning: ENVO:00002018 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Soil: text: Soil meaning: ENVO:00001998 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Transportation Supplies: text: Transportation Supplies meaning: ENVO:02000125 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Transportation Vehicles: text: Transportation Vehicles exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Turkey: text: Turkey meaning: FOODON:03414166 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Unknown: text: Unknown exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Unknown Food: text: Unknown Food meaning: CHEBI:33290 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Unspecified: text: Unspecified Unspecified Animal: text: Unspecified Animal meaning: FOODON:00003004 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Unspecified Environmental: text: Unspecified Environmental exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Unspecified Food: text: Unspecified Food meaning: CURATION:0001610 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Unspecified Product: text: Unspecified Product meaning: CHEBI:33290 Ursine: text: Ursine exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Vegetable/Spice: text: Vegetable/Spice exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Water: text: Water meaning: CHEBI:15377 exact_mappings: - - 'GRDI:environmental_material:' - COMMODITY menu: - name: COMMODITY menu + - GRDI:environmental_material%3A + CommodityMenu: + name: CommodityMenu + title: COMMODITY menu permissible_values: <=16: text: <=16 @@ -2729,72 +2734,73 @@ enums: text: Beef meaning: FOODON:00001041 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Broiler: text: Broiler meaning: FOODON:03411198 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Dairy: text: Dairy meaning: ENVO:00003862 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Domestic/Farmed: text: Domestic/Farmed Egg: text: Egg meaning: FOODON:00001274 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Laboratory: text: Laboratory meaning: NCIT:C37984 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Meat: text: Meat meaning: FOODON:00001006 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mutton: text: Mutton meaning: FOODON:00002912 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pet: text: Pet exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Pet/Zoo: text: Pet/Zoo meaning: ENVO:00010625 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Red Veal: text: Red Veal meaning: FOODON:00003083 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Unknown: text: Unknown exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Veal: text: Veal meaning: FOODON:00003083 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A White Veal: text: White Veal meaning: FOODON:00003083 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Wild: text: Wild meaning: FOODON:03530153 - SPECIMENSOURCE_1 menu: - name: SPECIMENSOURCE_1 menu + SpecimenSource1Menu: + name: SpecimenSource1Menu + title: SPECIMENSOURCE_1 menu permissible_values: '2': text: '2' @@ -2807,28 +2813,28 @@ enums: text: Blood meaning: UBERON:0000178 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Blood Meal: text: Blood Meal meaning: FOODON:00001564 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Body Fluid/Excretion: text: Body Fluid/Excretion exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Carcass: text: Carcass meaning: UBERON:0008979 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Check Sample: text: Check Sample meaning: SEP:00042 Contact plate: text: Contact plate exact_mappings: - - 'GRDI:collection_device:' + - GRDI:collection_device%3A Culture: text: Culture meaning: CURATION:0000488 @@ -2836,38 +2842,38 @@ enums: text: Dust meaning: ENVO:00002008 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Egg: text: Egg meaning: FOODON:00001274 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Environment (Animal): text: Environment (Animal) Environmental: text: Environmental meaning: CURATION:0001610 exact_mappings: - - 'GRDI:environmental_material:' - - 'GRDI:environmental_site:' + - GRDI:environmental_material%3A + - GRDI:environmental_site%3A Feces: text: Feces meaning: UBERON:0001988 exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Fetus/Embryo: text: Fetus/Embryo exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Organ: text: Organ meaning: UBERON:0000062 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Organ/Tissue: text: Organ/Tissue exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Proficiency Isolate: text: Proficiency Isolate meaning: NCIT:C53471 @@ -2878,47 +2884,48 @@ enums: text: Rinse meaning: CURATION:0001629 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Septage: text: Septage exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Soya Meal: text: Soya Meal meaning: FOODON:03316468 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Stool: text: Stool meaning: UBERON:0001988 exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Swab: text: Swab meaning: NCIT:C17627 exact_mappings: - - 'GRDI:collection_device:' + - GRDI:collection_device%3A Tissue: text: Tissue meaning: UBERON:0000479 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Unit (Pre-Packaged): text: Unit (Pre-Packaged) meaning: UO:0000000 Unknown: text: Unknown exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Unspecified: text: Unspecified Urine: text: Urine meaning: UBERON:0001088 exact_mappings: - - 'GRDI:body_product:' - SPECIMENSUBSOURCE_1 menu: - name: SPECIMENSUBSOURCE_1 menu + - GRDI:body_product%3A + SpecimenSubsource1Menu: + name: SpecimenSubsource1Menu + title: SPECIMENSUBSOURCE_1 menu permissible_values: '0.25': text: '0.25' @@ -2932,298 +2939,298 @@ enums: text: Abdomen meaning: UBERON:0000916 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Abdominal Muscle: text: Abdominal Muscle meaning: UBERON:0002378 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Abomasum: text: Abomasum meaning: UBERON:0007358 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Abscess: text: Abscess meaning: HP:0025615 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Air Intake: text: Air Intake meaning: ENVO:00002005 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Air Sac: text: Air Sac meaning: UBERON:0009060 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Anal Gland: text: Anal Gland exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Animal Pen: text: Animal Pen meaning: FOODON:00003004 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Balut: text: Balut meaning: FOODON:03302184 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Belt: text: Belt meaning: CURATION:0000406 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Bladder: text: Bladder meaning: CURATION:0000504 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Blood: text: Blood meaning: UBERON:0000178 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Blood vessel: text: Blood vessel meaning: UBERON:0001981 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Bone: text: Bone meaning: UBERON:0001474 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Bone Marrow: text: Bone Marrow meaning: UBERON:0002371 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Bootie: text: Bootie exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Boots: text: Boots meaning: CURATION:0000401 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Brain: text: Brain meaning: UBERON:0000955 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Bursa of Fabricus: text: Bursa of Fabricus meaning: CURATION:0000502 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Cages: text: Cages exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Cavity Fluid (Unspecified): text: Cavity Fluid (Unspecified) meaning: CURATION:0000480 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Cavity fluid unspecified: text: Cavity fluid unspecified meaning: CURATION:0000480 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Cecal Content: text: Cecal Content exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Cecum: text: Cecum meaning: CURATION:0000495 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Chick Boxes: text: Chick Boxes exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Chick Pads: text: Chick Pads exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Cloacae: text: Cloacae meaning: CURATION:0000491 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Cloacal swab: text: Cloacal swab meaning: NCIT:C17627 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Colon: text: Colon meaning: UBERON:0001155 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Confirmation: text: Confirmation exact_mappings: - - GRDI:? + - GRDI:%3F Crates: text: Crates meaning: FOODON:03490213 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Crop: text: Crop meaning: UBERON:0007356 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Culture Plate: text: Culture Plate exact_mappings: - - 'GRDI:collection_device:' + - GRDI:collection_device%3A Digestive System (Unspecified): text: Digestive System (Unspecified) meaning: UBERON:0001007 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Duodenum: text: Duodenum meaning: UBERON:0002114 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Dust: text: Dust meaning: ENVO:00002008 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Ear: text: Ear meaning: UBERON:0001690 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Egg Belt: text: Egg Belt exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Environment Swab: text: Environment Swab exact_mappings: - - 'GRDI:collection_device:' + - GRDI:collection_device%3A Environment Swab (Hatchery): text: Environment Swab (Hatchery) exact_mappings: - - GRDI:environmental_site:hatchery - - GRDI:collection_device:swab + - GRDI:environmental_site%3Ahatchery + - GRDI:collection_device%3Aswab Esophagus: text: Esophagus meaning: UBERON:0001043 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A External Quality Assurance: text: External Quality Assurance meaning: BFO:0000019 exact_mappings: - - GRDI:? + - GRDI:%3F Eye: text: Eye meaning: UBERON:0000970 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Fan: text: Fan meaning: ENVO:00000104 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Fecal Slurry: text: Fecal Slurry meaning: UBERON:0001988 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Feces: text: Feces meaning: UBERON:0001988 exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Feed: text: Feed meaning: FOODON:03309997 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Feeders and Drinkers: text: Feeders and Drinkers meaning: CURATION:0000419 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Fetal Tissue: text: Fetal Tissue exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Final Wash: text: Final Wash meaning: CURATION:0001488 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Floor: text: Floor meaning: CURATION:0000335 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Fluff: text: Fluff exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Fluff (Hatchery): text: Fluff (Hatchery) meaning: ENVO:01001873 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Foot: text: Foot meaning: UO:0010013 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Gall Bladder: text: Gall Bladder meaning: UBERON:0002110 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Gallbladder: text: Gallbladder meaning: UBERON:0002110 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Ganglion: text: Ganglion meaning: UBERON:0000045 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Gizzard: text: Gizzard meaning: UBERON:0005052 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Growth / lesion (unspecified tissue): text: Growth / lesion (unspecified tissue) exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Growth/Lesion (Unspecified Tissue): text: Growth/Lesion (Unspecified Tissue) exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Heart: text: Heart meaning: UBERON:0000948 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Ileum: text: Ileum meaning: UBERON:0002116 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A In-House: text: In-House meaning: ENVO:01000417 @@ -3233,211 +3240,211 @@ enums: Intestinal Contents: text: Intestinal Contents exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Intestine: text: Intestine meaning: UBERON:0000160 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Jejunum: text: Jejunum meaning: UBERON:0002115 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Joint: text: Joint meaning: UBERON:0004905 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Joint Fluid: text: Joint Fluid meaning: UBERON:0001090 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Kidney: text: Kidney meaning: UBERON:0002113 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Levage/peritoneal: text: Levage/peritoneal meaning: CURATION:0000463 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Levage/Tracheal: text: Levage/Tracheal exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Litter: text: Litter meaning: CURATION:0001446 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Litter/Manure: text: Litter/Manure meaning: CURATION:0001446 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Live Haul Truck: text: Live Haul Truck meaning: ENVO:01000602 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Live Haul Truck/Trailer: text: Live Haul Truck/Trailer meaning: ENVO:01000602 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Liver: text: Liver meaning: UBERON:0002107 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Lung: text: Lung meaning: UBERON:0002048 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Lymph Node: text: Lymph Node meaning: UBERON:0000029 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Manure Pit: text: Manure Pit meaning: ENVO:01001872 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Meconium: text: Meconium meaning: UBERON:0007109 exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Mesenteric Lymph Node: text: Mesenteric Lymph Node meaning: UBERON:0002509 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Milk/Colostrum: text: Milk/Colostrum exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Mixed: text: Mixed exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Mixed Organs: text: Mixed Organs meaning: UBERON:0000062 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Mixed Tissues: text: Mixed Tissues meaning: UBERON:0000479 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Mouth: text: Mouth meaning: UBERON:0000165 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Mucous membrane (gut): text: Mucous membrane (gut) exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Mucous membrane (resp): text: Mucous membrane (resp) meaning: UBERON:0000344 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Mucus: text: Mucus meaning: UBERON:0000912 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Muscle: text: Muscle meaning: CURATION:0001428 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Muscle/Meat: text: Muscle/Meat exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Nasal Turbinate: text: Nasal Turbinate meaning: UBERON:0035612 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Nasal/Naries: text: Nasal/Naries meaning: CURATION:0000466 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Organ Unspecified: text: Organ Unspecified meaning: UBERON:0000062 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Ovary: text: Ovary meaning: UBERON:0000992 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Oviduct: text: Oviduct meaning: UBERON:0000993 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Pericardium: text: Pericardium meaning: UBERON:0002407 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Peritoneal Fluid: text: Peritoneal Fluid meaning: UBERON:0001268 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Peritoneum: text: Peritoneum meaning: UBERON:0002358 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Placenta: text: Placenta meaning: UBERON:0001987 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Pleura: text: Pleura meaning: UBERON:0000977 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Plucking Belt: text: Plucking Belt meaning: CURATION:0000406 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Plucking Water: text: Plucking Water meaning: CHEBI:15377 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Pooled Feces: text: Pooled Feces exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Rectal Swab: text: Rectal Swab meaning: CURATION:0000457 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Rectum: text: Rectum meaning: UBERON:0001052 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Research: text: Research meaning: CURATION:0001536 @@ -3445,158 +3452,159 @@ enums: text: Rinse meaning: CURATION:0001629 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Rumen: text: Rumen meaning: UBERON:0007365 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Shell: text: Shell meaning: UBERON:0006612 exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Shell egg: text: Shell egg meaning: UBERON:0005079 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sinus: text: Sinus meaning: CURATION:0000455 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Skin: text: Skin meaning: UBERON:0000014 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Small Intestine: text: Small Intestine meaning: UBERON:0002108 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Soil: text: Soil meaning: ENVO:00001998 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Spinal Cord: text: Spinal Cord meaning: UBERON:0002240 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Spleen: text: Spleen meaning: UBERON:0002106 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Stall: text: Stall exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Stomach: text: Stomach meaning: UBERON:0000945 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Stomach Contents: text: Stomach Contents exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Swab: text: Swab meaning: NCIT:C17627 exact_mappings: - - 'GRDI:collection_device:' + - GRDI:collection_device%3A Swab (Nasal): text: Swab (Nasal) exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Swab (Rectal): text: Swab (Rectal) meaning: CURATION:0000457 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Swab (Tissue Fluid-Unspecified): text: Swab (Tissue Fluid-Unspecified) exact_mappings: - - 'GRDI:anatomical_material:' + - GRDI:anatomical_material%3A Testicle: text: Testicle meaning: UBERON:0000473 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Thorax: text: Thorax meaning: UBERON:0000915 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Trachea: text: Trachea meaning: UBERON:0003126 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Unknown organ: text: Unknown organ meaning: UBERON:0000062 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Unspecified Organ/Tissue: text: Unspecified Organ/Tissue exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Urine: text: Urine meaning: UBERON:0001088 exact_mappings: - - 'GRDI:body_product:' + - GRDI:body_product%3A Uterus: text: Uterus meaning: UBERON:0000995 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Vagina: text: Vagina meaning: UBERON:0000996 exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Walls: text: Walls exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Water: text: Water meaning: CHEBI:15377 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Watering Bowl/Equipment: text: Watering Bowl/Equipment exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Weekly: text: Weekly Weep: text: Weep exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Whole: text: Whole meaning: FOODON:03430131 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Yolk: text: Yolk meaning: UBERON:2000084 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Yolk Sac: text: Yolk Sac meaning: UBERON:0001040 exact_mappings: - - 'GRDI:anatomical_part:' - SUBJECT_SUBTYPE menu: - name: SUBJECT_SUBTYPE menu + - GRDI:anatomical_part%3A + SubjectSubtypeMenu: + name: SubjectSubtypeMenu + title: SUBJECT_SUBTYPE menu permissible_values: <=32: text: <=32 @@ -3608,750 +3616,749 @@ enums: text: Alfalfa Sprouts meaning: FOODON:00002670 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Almond: text: Almond meaning: FOODON:03301355 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Animal pen: text: Animal pen meaning: FOODON:00003004 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Artificial wetland: text: Artificial wetland exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Arugula: text: Arugula meaning: FOODON:00002426 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Basil: text: Basil meaning: FOODON:00003044 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Bean Sprouts: text: Bean Sprouts meaning: FOODON:00002576 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Biosolid: text: Biosolid exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Biosolid/Sludge: text: Biosolid/Sludge meaning: ENVO:00002044 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Bootie: text: Bootie exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Boots: text: Boots meaning: CURATION:0000401 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Breast: text: Breast meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast skinless: text: Breast skinless meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast skinless boneless: text: Breast skinless boneless meaning: UBERON:0000310 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Breast with skin: text: Breast with skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Broom: text: Broom meaning: CURATION:0000397 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Bulk Tank: text: Bulk Tank exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Cantaloupe: text: Cantaloupe meaning: CURATION:0001383 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Carcass (whole): text: Carcass (whole) exact_mappings: - - 'GRDI:anatomical_part:' + - GRDI:anatomical_part%3A Cheese: text: Cheese meaning: FOODON:00001013 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chia Powder: text: Chia Powder exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chia Seeds: text: Chia Seeds meaning: CURATION:0001385 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chia Sprouts: text: Chia Sprouts exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chick Boxes: text: Chick Boxes exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Chick Pads: text: Chick Pads meaning: UBERON:2001977 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Chickpea: text: Chickpea meaning: FOODON:03306811 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chili: text: Chili meaning: FOODON:03301511 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chilli Pepper: text: Chilli Pepper meaning: FOODON:03315873 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chives: text: Chives meaning: FOODON:03311167 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Chops: text: Chops exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Coconut: text: Coconut meaning: FOODON:03303085 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Compost: text: Compost meaning: CURATION:0001527 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Cooler Line: text: Cooler Line meaning: SIO:000511 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Coriander Seeds: text: Coriander Seeds meaning: PO:0009010 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Coriander-Cumin Powder: text: Coriander-Cumin Powder meaning: FOODON:00002976 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Cottage: text: Cottage exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Cucumber: text: Cucumber meaning: FOODON:03301545 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Curry Leaves: text: Curry Leaves meaning: FOODON:03306648 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Curry powder: text: Curry powder meaning: FOODON:03301842 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Cut: text: Cut meaning: ENVO:00000474 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Dead Haul Truck / Trailer: text: Dead Haul Truck / Trailer exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Dill: text: Dill meaning: FOODON:00001811 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Drumstick: text: Drumstick meaning: CURATION:0001378 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Dumpster: text: Dumpster exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Effluent: text: Effluent exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Egg: text: Egg meaning: FOODON:00001274 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Egg Belt: text: Egg Belt exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Fan: text: Fan meaning: ENVO:00000104 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Feed Pans: text: Feed Pans meaning: FOODON:03309997 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Fennel: text: Fennel meaning: FOODON:03309953 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Filet: text: Filet meaning: FOODON:03530144 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Flax and Chia Powder: text: Flax and Chia Powder exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Flax Powder: text: Flax Powder exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Floor: text: Floor meaning: CURATION:0000335 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A For Avian: text: For Avian meaning: FOODON:00002616 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Beef Cattle: text: For Beef Cattle exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Cats: text: For Cats meaning: CURATION:0001354 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Cattle (Beef): text: For Cattle (Beef) exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Cattle (Dairy): text: For Cattle (Dairy) meaning: FOODON:00002505 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Chicken: text: For Chicken meaning: FOODON:03411457 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Dairy Cows: text: For Dairy Cows meaning: FOODON:03411201 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Dogs: text: For Dogs meaning: CURATION:0001351 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Fish: text: For Fish meaning: FOODON:03411222 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Goats: text: For Goats meaning: FOODON:03411328 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Horse: text: For Horse meaning: FOODON:03411229 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Mink: text: For Mink meaning: FOODON:00002723 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Others: text: For Others For Poultry: text: For Poultry meaning: FOODON:00001131 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Swine: text: For Swine meaning: FOODON:03411136 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Turkeys: text: For Turkeys meaning: FOODON:03414166 exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A For Unknown: text: For Unknown For Unspecified: text: For Unspecified exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Garlic Powder: text: Garlic Powder meaning: FOODON:03301844 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ginger: text: Ginger meaning: FOODON:00002718 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Green Onion: text: Green Onion meaning: FOODON:03411478 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground: text: Ground exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (extra lean): text: Ground (extra lean) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (lean): text: Ground (lean) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (medium): text: Ground (medium) meaning: FOODON:03430117 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground (regular): text: Ground (regular) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Ground Water: text: Ground Water meaning: ENVO:00002041 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Ham: text: Ham meaning: FOODON:00002502 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Hazelnut / Filbert: text: Hazelnut / Filbert exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Headcheese: text: Headcheese exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Herb/Spice (Unspecified): text: Herb/Spice (Unspecified) exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Irrigation: text: Irrigation meaning: CURATION:0000309 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Kale: text: Kale meaning: FOODON:03304859 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Kalonji Whole Seed: text: Kalonji Whole Seed exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Lab Surface: text: Lab Surface exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Lake: text: Lake meaning: ENVO:00000020 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Leg: text: Leg meaning: UBERON:0000978 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Lettuce: text: Lettuce meaning: FOODON:00001998 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Liquid whole: text: Liquid whole exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Liver: text: Liver meaning: UBERON:0002107 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Loin center chop non-seasoned: text: Loin center chop non-seasoned exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mango: text: Mango exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Meat: text: Meat meaning: FOODON:00001006 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Milk: text: Milk meaning: UBERON:0001913 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mint: text: Mint meaning: FOODON:00002432 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mixed: text: Mixed exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Mixed Salad/Mixed Greens: text: Mixed Salad/Mixed Greens exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mixed Sprouts: text: Mixed Sprouts meaning: FOODON:03420183 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Mung Bean Sprouts: text: Mung Bean Sprouts exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Oregano: text: Oregano meaning: FOODON:03301482 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other: text: Other exact_mappings: - - 'GRDI:host (common name):' + - GRDI:host%20%28common%20name%29%3A Other chicken: text: Other chicken meaning: FOODON:03411457 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other cut (not ground): text: Other cut (not ground) meaning: ENVO:00000474 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Other variety meats: text: Other variety meats meaning: FOODON:03420218 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Papaya: text: Papaya exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Paprika: text: Paprika meaning: FOODON:03301105 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Parsley: text: Parsley meaning: FOODON:00002942 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pea Sprouts: text: Pea Sprouts exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pepper: text: Pepper meaning: FOODON:00001649 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pepper Powder: text: Pepper Powder exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Pepperoni: text: Pepperoni meaning: FOODON:03311003 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Rasam Powder Spice: text: Rasam Powder Spice exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A River: text: River meaning: ENVO:00000022 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A River Surface: text: River Surface exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Roast: text: Roast exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Rolled: text: Rolled Run Off: text: Run Off meaning: ENVO:00000029 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Sausage: text: Sausage meaning: FOODON:03315904 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Scallopini: text: Scallopini exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sediment: text: Sediment meaning: ENVO:00002007 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Sesame Seed: text: Sesame Seed meaning: FOODON:03310306 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shelf / Sill: text: Shelf / Sill exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Shellfish: text: Shellfish meaning: FOODON:03411433 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shoulder: text: Shoulder meaning: UBERON:0001467 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shoulder Chop: text: Shoulder Chop meaning: UBERON:0001467 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Shoulder chop non-seasoned: text: Shoulder chop non-seasoned exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Soft: text: Soft meaning: PATO:0000387 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Soybean: text: Soybean meaning: FOODON:03301415 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Spinach: text: Spinach meaning: FOODON:03301716 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sprouted Seeds: text: Sprouted Seeds meaning: FOODON:03420102 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Sprouts: text: Sprouts meaning: FOODON:03420183 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Stall: text: Stall exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Steak: text: Steak exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Stew Chunks: text: Stew Chunks meaning: FOODON:00003140 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Surface - Other: text: Surface - Other meaning: CURATION:0000247 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Surface - River: text: Surface - River exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Surface unspecified: text: Surface unspecified meaning: CURATION:0000247 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Surface Water: text: Surface Water meaning: ENVO:00002042 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Tenderloin: text: Tenderloin meaning: FOODON:03530217 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Thigh: text: Thigh meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Thigh with skin: text: Thigh with skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Transformer: text: Transformer exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Truck / Trailer: text: Truck / Trailer meaning: ENVO:01000602 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Truck/Trailer: text: Truck/Trailer meaning: ENVO:01000602 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Turmeric: text: Turmeric meaning: FOODON:03310841 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Unknown: text: Unknown Unknown Surface: text: Unknown Surface meaning: CURATION:0000247 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Unspecified: text: Unspecified Upper Thigh: text: Upper Thigh meaning: UBERON:0000376 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Upper Thigh with Skin: text: Upper Thigh with Skin exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Wall: text: Wall exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Walnut: text: Walnut meaning: FOODON:03315233 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Waste Water: text: Waste Water meaning: ENVO:00002001 exact_mappings: - - 'GRDI:environmental_material:' + - GRDI:environmental_material%3A Watering bowl/equipment: text: Watering bowl/equipment exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Whole: text: Whole meaning: FOODON:03430131 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Wings: text: Wings meaning: UBERON:0000023 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A Working Surface: text: Working Surface meaning: CURATION:0000247 exact_mappings: - - 'GRDI:environmental_site:' + - GRDI:environmental_site%3A Yeast: text: Yeast meaning: FOODON:03411345 exact_mappings: - - 'GRDI:food_product:' + - GRDI:food_product%3A types: WhitespaceMinimizedString: name: WhitespaceMinimizedString typeof: string - description: - 'A string that has all whitespace trimmed off of beginning and end, + description: 'A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).' base: str diff --git a/web/templates/phac_dexa/schema_core.yaml b/web/templates/phac_dexa/schema_core.yaml index 03bc1355..fb48e081 100644 --- a/web/templates/phac_dexa/schema_core.yaml +++ b/web/templates/phac_dexa/schema_core.yaml @@ -12,8 +12,9 @@ classes: name: dh_interface description: 'A DataHarmonizer interface' from_schema: https://example.com/PHAC_Dexa - 'PHAC Dexa': - name: 'PHAC Dexa' + 'PHACDexa': + name: 'PHACDexa' + title: 'PHAC Dexa' description: Specification for PHAC Dexa clinical virus biosample data gathering is_a: dh_interface slots: {} diff --git a/web/templates/phac_dexa/schema_enums.tsv b/web/templates/phac_dexa/schema_enums.tsv index 46ced101..21dc1b69 100644 --- a/web/templates/phac_dexa/schema_enums.tsv +++ b/web/templates/phac_dexa/schema_enums.tsv @@ -1,745 +1,745 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GRDI - -SUBJECT_DESCRIPTIONS menu UBERON:0000310 1/2 breast food_product: - FOODON:00002616 Avian Ingredients food_product: - PATO:0001901 Back food_product: - FOODON:03302184 Balut food_product: - FOODON:03411191 Black Pepper food_product: - Blade Steak food_product: - FOODON:00001564 Blood Meal food_product: - ENVO:02000054 Bone Meal food_product: - FOODON:03414374 Bovine Ingredients food_product: - UBERON:0000310 Breast food_product: - Breast back off food_product: - Breast cutlets food_product: - UBERON:0000310 Breast Skinless food_product: - UBERON:0000310 Breast Skinless Boneless food_product: - Breast with Skin food_product: - FOODON:03530020 Brisket food_product: - FOODON:00002737 Burger food_product: - Calf host (common name): - FOODON:00002694 Canola Meal food_product: - FOODON:03316468 Carinata Meal food_product: - Chop food_product: - Chops food_product: - coli - FOODON:03309997 Complete Feed food_product: - FOODON:00001765 Corn food_product: - FOODON:03411161 Cow host (common name): - Cubes food_product: - FOODON:00003001 Cutlet food_product: - CURATION:0001378 Drumstick food_product: - CURATION:0001378 Drumstick Skinless food_product: - Drumstick with Skin food_product: - CURATION:0001378 Drumsticks food_product: - Egg Flour food_product: - CURATION:0001357 Feather Meal food_product: - FOODON:03309997 Feed food_product: - FOODON:03530144 Filet food_product: - FOODON:03411222 Fish Ingredients food_product: - FOODON:03301620 Fish Meal food_product: - FOODON:03311095 Grain food_product: - FOODON:03430136 Ground food_product: - FOODON:03430136 Ground ( lean) food_product: - FOODON:03430136 Ground (Angus) food_product: - FOODON:03430136 Ground (Extra Lean) food_product: - FOODON:03430136 Ground (extra-lan) food_product: - FOODON:03430136 Ground (Extra-Lean) food_product: - FOODON:03430136 Ground (Lean) food_product: - FOODON:03430117 Ground (Medium) food_product: - FOODON:03430136 Ground (Regular) food_product: - CURATION:0001614 Ground (Sirloin) food_product: - FOODON:03430136 Ground Boneless food_product: - FOODON:03430136 Ground extra lean food_product: - FOODON:03430136 Ground regular food_product: - FOODON:03430136 ground( extra lean) food_product: - FOODON:03430117 ground( medium) food_product: - FOODON:03430136 Ground(Extra lean) food_product: - FOODON:03430136 Ground(Lean) food_product: - FOODON:03430117 Ground(medium) food_product: - FOODON:03430136 ground(regular) food_product: - FOODON:03430136 Groundextra lean) food_product: - FOODON:03430136 Ground-Lean food_product: - FOODON:03430136 Ground-Regular food_product: - FOODON:00002518 Heifer host (common name): - FOODON:00003049 Hummus food_product: - UBERON:0006612 In-Shell food_product: - Lay Ration food_product: - UBERON:0000978 Leg food_product: - Leg with Skin-Drumstick and Thigh food_product: - UBERON:0002107 Liver food_product: - FOODON:03530031 Loin Center Chop food_product: - FOODON:00002738 Meat and Bone Meal food_product: - Meat Flour/Meal food_product: - Meat Meal food_product: - Mild italian style burger food_product: - UBERON:0000974 Necks food_product: - Nuggets food_product: - Other host (common name): - Other cut food_product: - Other Cut (Not Ground) food_product: - Other Cut Boneless food_product: - Other Cut Boneless (Not Ground) food_product: - FOODON:03411183 Ovine Ingredients food_product: - FOODON:00002682 Pet Food food_product: - FOODON:03411136 Porcine Ingredients food_product: - Pork Chop (Cut Unknown) food_product: - Premix food_product: - Premix (Medicated) food_product: - Processed (Other) food_product: - FOODON:03311126 Raw food_product: - UBERON:0002228 Rib Chop food_product: - UBERON:0002228 Ribs food_product: - Roast food_product: - FOODON:03312067 Salami food_product: - FOODON:03315904 Sausage food_product: - Sausage (Pepper) food_product: - FOODON:00003017 Scallopini food_product: - UBERON:0006612 Shell on food_product: - Shelled food_product: - UBERON:0001467 Shoulder food_product: - UBERON:0001467 Shoulder Chop food_product: - FOODON:03530027 Sirloin Chop food_product: - FOODON:03301484 Skim milk powder food_product: - PATO:0000387 Soft food_product: - FOODON:03316468 Soyabean Meal food_product: - Starter Ration food_product: - Steak food_product: - FOODON:00003140 Stew Chunks food_product: - - FOODON:00001874 Supplements food_product: - T. high food_product: - FOODON:03304154 Tahini food_product: - FOODON:03530217 Tender loin food_product: - FOODON:03530217 Tenderloin food_product: - UBERON:0000376 Thigh food_product: - UBERON:0000376 Thigh Skinless food_product: - UBERON:0000376 Thigh Skinless Boneless food_product: - UBERON:0000014 Thigh with Skin food_product: - FOODON:00001568 Trim food_product: - FOODON:03316468 Unknown Meal food_product: - FOODON:03309997 Unspecified Feed/Ingredient food_product: - UBERON:0000376 Upper Thigh food_product: - Upper Thigh with Skin food_product: - UBERON:0000376 upper thight food_product: - UBERON:0000376 Upperthigh food_product: - FOODON:03304045 White Pepper food_product: - FOODON:03430131 Whole food_product: - Whole Carcass food_product: - Whole with Skin food_product: - UBERON:0000023 Wing food_product: - UBERON:0000023 Wings food_product: -SPECIES menu 2 - 4 - <=8 - - FOODON:03411408 Abalone - FOODON:00002670 Alfalfa sprouts - FOODON:00002693 Alpaca - FOODON:03411624 Amphibian - FOODON:00002473 Apple - FOODON:03411134 Aquatic mammal - FOODON:03411626 Armadillo - FOODON:00002616 Avian - FOODON:00003044 Basil - CURATION:0001601 Bat - FOODON:03412406 Bear - NCBITAXON:103695 Bearded Dragon - FOODON:03412098 Bison - Budgie - FOODON:03412103 Camel - FOODON:03412103 Camelid - Canary - FOODON:03414847 Canine - CURATION:0001383 Cantelope - FOODON:03411328 Caprine - Cardemom - Cardinal - FOODON:03411500 Cervid - CURATION:0001646 Chameleon - Cheetah - FOODON:03411457 Chicken - Chimpanzee - Chinchilla - Chinese Water Dragon - FOODON:03411331 Clam - FOODON:00001763 Coriander - Cormorant - Cougar/Mountain Lion - CURATION:0001607 Coyote - FOODON:03411335 Crab - Crane - Crow - FOODON:00003024 Cumin seeds - FOODON:03411644 Cuttlefish - FOODON:03414847 Dog - FOODON:03413363 Dolphin - NCIT:C14191 Domestic Cat - FOODON:03411161 Domestic Cattle - FOODON:03411316 Duck - Dumpster - Eagle - FOODON:03411278 Eel - FOODON:03412129 Elephant - Falcon - NCIT:C14191 Feline - CURATION:0001411 Ferret - Finch - FOODON:03411222 Fish - Flamingo - For Unspecified - CURATION:0001405 Fox - FOODON:03412615 Gecko - FOODON:03411328 Goat - Goat and Sheep - FOODON:03411253 Goose - FOODON:03301123 Grape - FOODON:03411478 Green onions - Grosbeak - FOODON:03301526 ground pepper - FOODON:03413503 Gull - FOODON:03412695 Hare - FOODON:00002933 Hazelnut - FOODON:03414548 Hedgehog - Herb/spice (unspecified) - FOODON:00002890 Heron - NCBITAXON:9831 Hippopotamidae - FOODON:03411229 Horse - FOODON:03412701 Iguana - Jaguar - FOODON:03412092 Kangaroo - Komodo Dragon - Lapine - FOODON:00001998 Lettuce - Lion - FOODON:03412293 Lizard - Marsupial - FOODON:00002723 Mink - FOODON:00002432 Mint - Mixed - Mongoose - NCIT:C14238 Mouse - FOODON:00001287 Mushrooms - FOODON:03411223 Mussel - n/a - Not Available - FOODON:03411514 Octopus - FOODON:03411450 Opossum - FOODON:03301482 Oregano - Other - CURATION:0001394 Otter - FOODON:03411183 Ovine - NCBITAXON:30458 Owl - FOODON:03411224 Oyster - FOODON:00002726 Parrot - FOODON:00002942 Parsley - FOODON:03411382 Partridge - Pea sprouts - FOODON:03306867 Peanut Butter - FOODON:00001649 Pepper - FOODON:03411382 Perdrix - FOODON:03411460 Pheasant - Pickerel - FOODON:03411136 Pig - FOODON:03411304 Pigeon - CURATION:0000439 Pine Siskin - Pony - Porcupine - FOODON:03413364 Porpoise - NCBITAXON:9443 Primate - FOODON:03411346 Quail - FOODON:03411323 Rabbit - FOODON:03411461 Raccoon - FOODON:03414848 Rat - FOODON:03414362 Ratite - Raven - FOODON:03414371 Red Deer - Redpoll - FOODON:03411625 Reptile - FOODON:03414556 Rhea - Robin - NCBITAXON:9989 Rodent - FOODON:00002217 Sage - FOODON:00002220 Salmon - FOODON:03411489 Scallop - CURATION:0000157 Sea Otter - FOODON:03414639 Sea Snail - Seal - FOODON:03310306 Sesame Seed - FOODON:03411183 Sheep - FOODON:03411237 Shrimp - FOODON:03412293 Skink - Skunk - FOODON:03411295 Snake - Sparrow - FOODON:03301716 Spinach - Spotted Hyena - FOODON:03420183 Sprouts - FOODON:03411205 Squid - FOODON:03411389 Squirrel - Stripped Hyena - Swan - FOODON:03412439 Tantalus Monkey - FOODON:03412434 Tilapia - FOODON:03309927 Tomato - FOODON:00000074 Tortoise - FOODON:03411258 Trout - FOODON:03414166 Turkey - FOODON:03411242 Turtle - Unknown - FOODON:00002616 Unspecified Bird - FOODON:03411222 Unspecified Fish - NCBITAXON:9443 Unspecified Primate - FOODON:03411625 Unspecified Reptile - NCBITAXON:9989 Unspecified Rodent - Vulture - Wallnut - CHEBI:15377 Water Dragon - FOODON:00003281 White Fish - FOODON:03530153 Wild Ruminant - Wombat - Woodpecker - FOODON:03412097 Zebra -STTYPE menu 0 - 0.5 - FOODON:00003004 ANIMAL host (common name): - ENVO:01000254 ENVIRONMENT environmental_material:;environmental_site: - CHEBI:33290 FOOD food_product: - NCBITAXON:9606 HUMAN host (common name): - PRODUCT - QA - UNKNOWN host (common name): - 0 - 2 - <=8 - - FOODON:03411624 Amphibian host (common name): - FOODON:03411134 Aquatic Mammal host (common name): - FOODON:03411626 Armadillo host (common name): - FOODON:00002616 Avian host (common name): - CURATION:0001601 Bat host (common name): - ENVO:00002059 Biosolids environmental_material: - FOODON:03414374 Bovine host (common name): - ENVO:00000073 Building environmental_site: - FOODON:03412103 Camelid host (common name): - FOODON:03414847 Canine host (common name): - FOODON:03411328 Caprine host (common name): - Caprine and Ovine host (common name): - FOODON:00001709 Cereal food_product: - Cereal/Bread/Snack food_product: - FOODON:03411500 Cervid host (common name): - CURATION:0001527 Compost environmental_material: - Confections/Nuts/Condiments food_product: - Crocuta host (common name): - FOODON:03411374 Crustacean host (common name): - ENVO:00003862 Dairy environmental_site: - ENVO:00002008 Dust environmental_material: - FOODON:00001274 Egg food_product: - FOODON:03412129 Elephant host (common name): - CURATION:0001431 Equine host (common name): - CURATION:0000348 Equipment environmental_site: - ERROR - FOODON:03309997 Feed and Ingredients food_product: - NCIT:C14191 Feline host (common name): - CURATION:0001411 Ferret host (common name): - CHEBI:33287 Fertilizer environmental_material: - FOODON:03411222 Fish host (common name): - CHEBI:33290 Food food_product: - PO:0009001 Fruit food_product: - FOODON:00002141 Fruits and Vegetables food_product: - Health (medicine) - Herbs and Spices food_product: - Herpestidae host (common name): - NCBITAXON:9831 Hippopotamidae host (common name): - Lapine host (common name): - CURATION:0001446 Litter/Manure environmental_material: - Manure environmental_material: - Marsupial host (common name): - FOODON:00001006 Meat food_product: - Mephitida host (common name): - FOODON:00002723 Mink host (common name): - CHEBI:33290 Mixed food food_product: - FOODON:03315600 Mixed Food/Meat food_product: - FOODON:03412112 Mollusk host (common name): - Mustelid host (common name): - n/a host (common name): - Other host (common name): - FOODON:03411183 Ovine host (common name): - Personnel Clothing environmental_material: - FOODON:03411136 Porcine host (common name): - NCBITAXON:9443 Primate host (common name): - FOODON:03411461 Raccoon host (common name): - FOODON:03411625 Reptile host (common name): - NCBITAXON:9989 Rodent host (common name): - ENVO:00002018 Sewage environmental_material: - ENVO:00001998 Soil environmental_material: - ENVO:02000125 Transportation Supplies environmental_site: - Transportation Vehicles environmental_site: - FOODON:03414166 Turkey host (common name): - Unknown host (common name): - CHEBI:33290 Unknown Food food_product: - Unspecified - FOODON:00003004 Unspecified Animal host (common name): - Unspecified Environmental environmental_site: - CURATION:0001610 Unspecified Food food_product: - CHEBI:33290 Unspecified Product - Ursine host (common name): - Vegetable/Spice food_product: - CHEBI:15377 Water environmental_material: -COMMODITY menu <=16 - FOODON:00001041 Beef food_product: - FOODON:03411198 Broiler host (common name): - ENVO:00003862 Dairy environmental_site: - Domestic/Farmed - FOODON:00001274 Egg food_product: - NCIT:C37984 Laboratory environmental_site: - FOODON:00001006 Meat food_product: - FOODON:00002912 Mutton food_product: - Pet host (common name): - ENVO:00010625 Pet/Zoo environmental_site: - FOODON:00003083 Red Veal food_product: - Unknown host (common name): - FOODON:00003083 Veal food_product: - FOODON:00003083 White Veal food_product: - FOODON:03530153 Wild -SPECIMENSOURCE_1 menu 2 - <=32 - CURATION:0000508 Aliquote / Portion - UBERON:0000178 Blood anatomical_material: - FOODON:00001564 Blood Meal food_product: - Body Fluid/Excretion anatomical_material: - UBERON:0008979 Carcass anatomical_part: - SEP:00042 Check Sample - Contact plate collection_device: - CURATION:0000488 Culture - ENVO:00002008 Dust environmental_material: - FOODON:00001274 Egg food_product: - Environment (Animal) - CURATION:0001610 Environmental environmental_material:;environmental_site: - UBERON:0001988 Feces body_product: - Fetus/Embryo anatomical_part: - UBERON:0000062 Organ anatomical_part: - Organ/Tissue anatomical_material: - NCIT:C53471 Proficiency Isolate - CURATION:0000488 Reference Culture - CURATION:0001629 Rinse environmental_material: - Septage environmental_material: - FOODON:03316468 Soya Meal food_product: - UBERON:0001988 Stool body_product: - NCIT:C17627 Swab collection_device: - UBERON:0000479 Tissue anatomical_material: - UO:0000000 Unit (Pre-Packaged) - Unknown host (common name): - Unspecified - UBERON:0001088 Urine body_product: -SPECIMENSUBSOURCE_1 menu 0.25 - <=0.12 - <=16 - aansarraysubsource - UBERON:0000916 Abdomen anatomical_part: - UBERON:0002378 Abdominal Muscle anatomical_part: - UBERON:0007358 Abomasum anatomical_part: - HP:0025615 Abscess anatomical_material: - ENVO:00002005 Air Intake environmental_site: - UBERON:0009060 Air Sac anatomical_part: - Anal Gland anatomical_part: - FOODON:00003004 Animal Pen environmental_site: - FOODON:03302184 Balut food_product: - CURATION:0000406 Belt environmental_site: - CURATION:0000504 Bladder anatomical_part: - UBERON:0000178 Blood anatomical_material: - UBERON:0001981 Blood vessel anatomical_part: - UBERON:0001474 Bone anatomical_material: - UBERON:0002371 Bone Marrow anatomical_material: - Bootie environmental_material: - CURATION:0000401 Boots environmental_material: - UBERON:0000955 Brain anatomical_part: - CURATION:0000502 Bursa of Fabricus anatomical_part: - Cages environmental_site: - CURATION:0000480 Cavity Fluid (Unspecified) anatomical_material: - CURATION:0000480 Cavity fluid unspecified anatomical_material: - Cecal Content body_product: - CURATION:0000495 Cecum anatomical_part: - Chick Boxes environmental_site: - Chick Pads environmental_material: - CURATION:0000491 Cloacae anatomical_part: - NCIT:C17627 Cloacal swab anatomical_part: - UBERON:0001155 Colon anatomical_part: - Confirmation ? - FOODON:03490213 Crates environmental_site: - UBERON:0007356 Crop environmental_material: - Culture Plate collection_device: - UBERON:0001007 Digestive System (Unspecified) anatomical_part: - UBERON:0002114 Duodenum anatomical_part: - ENVO:00002008 Dust environmental_material: - UBERON:0001690 Ear anatomical_part: - Egg Belt environmental_site: - Environment Swab collection_device: - Environment Swab (Hatchery) environmental_site:hatchery;collection_device:swab - UBERON:0001043 Esophagus anatomical_part: - BFO:0000019 External Quality Assurance ? - UBERON:0000970 Eye anatomical_part: - ENVO:00000104 Fan environmental_site: - UBERON:0001988 Fecal Slurry environmental_material: - UBERON:0001988 Feces body_product: - FOODON:03309997 Feed food_product: - CURATION:0000419 Feeders and Drinkers environmental_site: - Fetal Tissue anatomical_material: - CURATION:0001488 Final Wash environmental_material: - CURATION:0000335 Floor environmental_site: - Fluff environmental_material: - ENVO:01001873 Fluff (Hatchery) environmental_material: - UO:0010013 Foot anatomical_part: - UBERON:0002110 Gall Bladder anatomical_part: - UBERON:0002110 Gallbladder anatomical_part: - UBERON:0000045 Ganglion anatomical_part: - UBERON:0005052 Gizzard anatomical_part: - Growth / lesion (unspecified tissue) anatomical_material: - Growth/Lesion (Unspecified Tissue) anatomical_material: - UBERON:0000948 Heart anatomical_part: - UBERON:0002116 Ileum anatomical_part: - ENVO:01000417 In-House - NCIT:C37984 Inter-Lab Exchange - Intestinal Contents anatomical_material: - UBERON:0000160 Intestine anatomical_part: - UBERON:0002115 Jejunum anatomical_part: - UBERON:0004905 Joint anatomical_part: - UBERON:0001090 Joint Fluid anatomical_material: - UBERON:0002113 Kidney anatomical_part: - CURATION:0000463 Levage/peritoneal anatomical_material: - Levage/Tracheal anatomical_material: - CURATION:0001446 Litter environmental_material: - CURATION:0001446 Litter/Manure environmental_material: - ENVO:01000602 Live Haul Truck environmental_site: - ENVO:01000602 Live Haul Truck/Trailer environmental_site: - UBERON:0002107 Liver food_product: - UBERON:0002048 Lung anatomical_part: - UBERON:0000029 Lymph Node anatomical_part: - ENVO:01001872 Manure Pit environmental_site: - UBERON:0007109 Meconium body_product: - UBERON:0002509 Mesenteric Lymph Node anatomical_part: - Milk/Colostrum body_product: - Mixed host (common name): - UBERON:0000062 Mixed Organs anatomical_part: - UBERON:0000479 Mixed Tissues anatomical_material: - UBERON:0000165 Mouth anatomical_part: - Mucous membrane (gut) anatomical_part: - UBERON:0000344 Mucous membrane (resp) anatomical_part: - UBERON:0000912 Mucus anatomical_material: - CURATION:0001428 Muscle anatomical_part: - Muscle/Meat food_product: - UBERON:0035612 Nasal Turbinate anatomical_part: - CURATION:0000466 Nasal/Naries anatomical_part: - UBERON:0000062 Organ Unspecified anatomical_part: - UBERON:0000992 Ovary anatomical_part: - UBERON:0000993 Oviduct anatomical_part: - UBERON:0002407 Pericardium anatomical_part: - UBERON:0001268 Peritoneal Fluid anatomical_material: - UBERON:0002358 Peritoneum anatomical_part: - UBERON:0001987 Placenta anatomical_part: - UBERON:0000977 Pleura anatomical_part: - CURATION:0000406 Plucking Belt environmental_site: - CHEBI:15377 Plucking Water environmental_material: - Pooled Feces body_product: - CURATION:0000457 Rectal Swab anatomical_part: - UBERON:0001052 Rectum anatomical_part: - CURATION:0001536 Research - CURATION:0001629 Rinse environmental_material: - UBERON:0007365 Rumen anatomical_part: - UBERON:0006612 Shell anatomical_material: - UBERON:0005079 Shell egg food_product: - CURATION:0000455 Sinus anatomical_part: - UBERON:0000014 Skin anatomical_part: - UBERON:0002108 Small Intestine anatomical_part: - ENVO:00001998 Soil environmental_material: - UBERON:0002240 Spinal Cord anatomical_part: - UBERON:0002106 Spleen anatomical_part: - Stall environmental_site: - UBERON:0000945 Stomach anatomical_part: - Stomach Contents body_product: - NCIT:C17627 Swab collection_device: - Swab (Nasal) anatomical_part: - CURATION:0000457 Swab (Rectal) anatomical_part: - Swab (Tissue Fluid-Unspecified) anatomical_material: - UBERON:0000473 Testicle anatomical_part: - UBERON:0000915 Thorax anatomical_part: - UBERON:0003126 Trachea anatomical_part: - UBERON:0000062 Unknown organ anatomical_part: - Unspecified Organ/Tissue anatomical_part: - UBERON:0001088 Urine body_product: - UBERON:0000995 Uterus anatomical_part: - UBERON:0000996 Vagina anatomical_part: - Walls environmental_site: - CHEBI:15377 Water environmental_material: - Watering Bowl/Equipment environmental_site: - Weekly - Weep environmental_material: - FOODON:03430131 Whole food_product: - UBERON:2000084 Yolk food_product: - UBERON:0001040 Yolk Sac anatomical_part: -SUBJECT_SUBTYPE menu <=32 - - >32 - FOODON:00002670 Alfalfa Sprouts food_product: - FOODON:03301355 Almond food_product: - FOODON:00003004 Animal pen environmental_site: - Artificial wetland environmental_site: - FOODON:00002426 Arugula food_product: - FOODON:00003044 Basil food_product: - FOODON:00002576 Bean Sprouts food_product: - Biosolid environmental_material: - ENVO:00002044 Biosolid/Sludge environmental_material: - Bootie environmental_material: - CURATION:0000401 Boots environmental_material: - UBERON:0000310 Breast food_product: - UBERON:0000310 Breast skinless food_product: - UBERON:0000310 Breast skinless boneless food_product: - Breast with skin food_product: - CURATION:0000397 Broom environmental_material: - Bulk Tank environmental_site: - CURATION:0001383 Cantaloupe food_product: - Carcass (whole) anatomical_part: - FOODON:00001013 Cheese food_product: - Chia Powder food_product: - CURATION:0001385 Chia Seeds food_product: - Chia Sprouts food_product: - Chick Boxes environmental_site: - UBERON:2001977 Chick Pads environmental_material: - FOODON:03306811 Chickpea food_product: - FOODON:03301511 Chili food_product: - FOODON:03315873 Chilli Pepper food_product: - FOODON:03311167 Chives food_product: - Chops food_product: - FOODON:03303085 Coconut food_product: - CURATION:0001527 Compost environmental_material: - SIO:000511 Cooler Line environmental_site: - PO:0009010 Coriander Seeds food_product: - FOODON:00002976 Coriander-Cumin Powder food_product: - Cottage environmental_site: - FOODON:03301545 Cucumber food_product: - FOODON:03306648 Curry Leaves food_product: - FOODON:03301842 Curry powder food_product: - ENVO:00000474 Cut food_product: - Dead Haul Truck / Trailer environmental_site: - FOODON:00001811 Dill food_product: - CURATION:0001378 Drumstick food_product: - Dumpster environmental_site: - Effluent environmental_material: - FOODON:00001274 Egg food_product: - Egg Belt environmental_site: - ENVO:00000104 Fan environmental_site: - FOODON:03309997 Feed Pans environmental_site: - FOODON:03309953 Fennel food_product: - FOODON:03530144 Filet food_product: - Flax and Chia Powder food_product: - Flax Powder food_product: - CURATION:0000335 Floor environmental_site: - FOODON:00002616 For Avian host (common name): - For Beef Cattle host (common name): - CURATION:0001354 For Cats host (common name): - For Cattle (Beef) host (common name): - FOODON:00002505 For Cattle (Dairy) host (common name): - FOODON:03411457 For Chicken host (common name): - FOODON:03411201 For Dairy Cows host (common name): - CURATION:0001351 For Dogs host (common name): - FOODON:03411222 For Fish host (common name): - FOODON:03411328 For Goats host (common name): - FOODON:03411229 For Horse host (common name): - FOODON:00002723 For Mink host (common name): - For Others - FOODON:00001131 For Poultry host (common name): - FOODON:03411136 For Swine host (common name): - FOODON:03414166 For Turkeys host (common name): - For Unknown - For Unspecified host (common name): - FOODON:03301844 Garlic Powder food_product: - FOODON:00002718 Ginger food_product: - FOODON:03411478 Green Onion food_product: - Ground food_product: - Ground (extra lean) food_product: - Ground (lean) food_product: - FOODON:03430117 Ground (medium) food_product: - Ground (regular) food_product: - ENVO:00002041 Ground Water environmental_material: - FOODON:00002502 Ham food_product: - Hazelnut / Filbert food_product: - Headcheese food_product: - Herb/Spice (Unspecified) food_product: - CURATION:0000309 Irrigation environmental_site: - FOODON:03304859 Kale food_product: - Kalonji Whole Seed food_product: - Lab Surface environmental_site: - ENVO:00000020 Lake environmental_site: - UBERON:0000978 Leg food_product: - FOODON:00001998 Lettuce food_product: - Liquid whole food_product: - UBERON:0002107 Liver food_product: - Loin center chop non-seasoned food_product: - Mango food_product: - FOODON:00001006 Meat food_product: - UBERON:0001913 Milk food_product: - FOODON:00002432 Mint food_product: - Mixed host (common name): - Mixed Salad/Mixed Greens food_product: - FOODON:03420183 Mixed Sprouts food_product: - Mung Bean Sprouts food_product: - FOODON:03301482 Oregano food_product: - Other host (common name): - FOODON:03411457 Other chicken food_product: - ENVO:00000474 Other cut (not ground) food_product: - FOODON:03420218 Other variety meats food_product: - Papaya food_product: - FOODON:03301105 Paprika food_product: - FOODON:00002942 Parsley food_product: - Pea Sprouts food_product: - FOODON:00001649 Pepper food_product: - Pepper Powder food_product: - FOODON:03311003 Pepperoni food_product: - Rasam Powder Spice food_product: - ENVO:00000022 River environmental_site: - River Surface environmental_site: - Roast food_product: - Rolled - ENVO:00000029 Run Off environmental_material: - FOODON:03315904 Sausage food_product: - Scallopini food_product: - ENVO:00002007 Sediment environmental_material: - FOODON:03310306 Sesame Seed food_product: - Shelf / Sill environmental_site: - FOODON:03411433 Shellfish food_product: - UBERON:0001467 Shoulder food_product: - UBERON:0001467 Shoulder Chop food_product: - Shoulder chop non-seasoned food_product: - PATO:0000387 Soft food_product: - FOODON:03301415 Soybean food_product: - FOODON:03301716 Spinach food_product: - FOODON:03420102 Sprouted Seeds food_product: - FOODON:03420183 Sprouts food_product: - Stall environmental_site: - Steak food_product: - FOODON:00003140 Stew Chunks food_product: - CURATION:0000247 Surface - Other environmental_site: - Surface - River environmental_site: - CURATION:0000247 Surface unspecified environmental_site: - ENVO:00002042 Surface Water environmental_site: - FOODON:03530217 Tenderloin food_product: - UBERON:0000376 Thigh food_product: - Thigh with skin food_product: - Transformer environmental_site: - ENVO:01000602 Truck / Trailer environmental_site: - ENVO:01000602 Truck/Trailer environmental_site: - FOODON:03310841 Turmeric food_product: - Unknown - CURATION:0000247 Unknown Surface environmental_site: - Unspecified - UBERON:0000376 Upper Thigh food_product: - Upper Thigh with Skin food_product: - Wall environmental_site: - FOODON:03315233 Walnut food_product: - ENVO:00002001 Waste Water environmental_material: - Watering bowl/equipment environmental_site: - FOODON:03430131 Whole food_product: - UBERON:0000023 Wings food_product: - CURATION:0000247 Working Surface environmental_site: - FOODON:03411345 Yeast food_product: - \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GRDI + +SUBJECT_DESCRIPTIONS menu SubjectDescriptionsMenu UBERON:0000310 1/2 breast food_product: + FOODON:00002616 Avian Ingredients food_product: + PATO:0001901 Back food_product: + FOODON:03302184 Balut food_product: + FOODON:03411191 Black Pepper food_product: + Blade Steak food_product: + FOODON:00001564 Blood Meal food_product: + ENVO:02000054 Bone Meal food_product: + FOODON:03414374 Bovine Ingredients food_product: + UBERON:0000310 Breast food_product: + Breast back off food_product: + Breast cutlets food_product: + UBERON:0000310 Breast Skinless food_product: + UBERON:0000310 Breast Skinless Boneless food_product: + Breast with Skin food_product: + FOODON:03530020 Brisket food_product: + FOODON:00002737 Burger food_product: + Calf host (common name): + FOODON:00002694 Canola Meal food_product: + FOODON:03316468 Carinata Meal food_product: + Chop food_product: + Chops food_product: + coli + FOODON:03309997 Complete Feed food_product: + FOODON:00001765 Corn food_product: + FOODON:03411161 Cow host (common name): + Cubes food_product: + FOODON:00003001 Cutlet food_product: + CURATION:0001378 Drumstick food_product: + CURATION:0001378 Drumstick Skinless food_product: + Drumstick with Skin food_product: + CURATION:0001378 Drumsticks food_product: + Egg Flour food_product: + CURATION:0001357 Feather Meal food_product: + FOODON:03309997 Feed food_product: + FOODON:03530144 Filet food_product: + FOODON:03411222 Fish Ingredients food_product: + FOODON:03301620 Fish Meal food_product: + FOODON:03311095 Grain food_product: + FOODON:03430136 Ground food_product: + FOODON:03430136 Ground ( lean) food_product: + FOODON:03430136 Ground (Angus) food_product: + FOODON:03430136 Ground (Extra Lean) food_product: + FOODON:03430136 Ground (extra-lan) food_product: + FOODON:03430136 Ground (Extra-Lean) food_product: + FOODON:03430136 Ground (Lean) food_product: + FOODON:03430117 Ground (Medium) food_product: + FOODON:03430136 Ground (Regular) food_product: + CURATION:0001614 Ground (Sirloin) food_product: + FOODON:03430136 Ground Boneless food_product: + FOODON:03430136 Ground extra lean food_product: + FOODON:03430136 Ground regular food_product: + FOODON:03430136 ground( extra lean) food_product: + FOODON:03430117 ground( medium) food_product: + FOODON:03430136 Ground(Extra lean) food_product: + FOODON:03430136 Ground(Lean) food_product: + FOODON:03430117 Ground(medium) food_product: + FOODON:03430136 ground(regular) food_product: + FOODON:03430136 Groundextra lean) food_product: + FOODON:03430136 Ground-Lean food_product: + FOODON:03430136 Ground-Regular food_product: + FOODON:00002518 Heifer host (common name): + FOODON:00003049 Hummus food_product: + UBERON:0006612 In-Shell food_product: + Lay Ration food_product: + UBERON:0000978 Leg food_product: + Leg with Skin-Drumstick and Thigh food_product: + UBERON:0002107 Liver food_product: + FOODON:03530031 Loin Center Chop food_product: + FOODON:00002738 Meat and Bone Meal food_product: + Meat Flour/Meal food_product: + Meat Meal food_product: + Mild italian style burger food_product: + UBERON:0000974 Necks food_product: + Nuggets food_product: + Other host (common name): + Other cut food_product: + Other Cut (Not Ground) food_product: + Other Cut Boneless food_product: + Other Cut Boneless (Not Ground) food_product: + FOODON:03411183 Ovine Ingredients food_product: + FOODON:00002682 Pet Food food_product: + FOODON:03411136 Porcine Ingredients food_product: + Pork Chop (Cut Unknown) food_product: + Premix food_product: + Premix (Medicated) food_product: + Processed (Other) food_product: + FOODON:03311126 Raw food_product: + UBERON:0002228 Rib Chop food_product: + UBERON:0002228 Ribs food_product: + Roast food_product: + FOODON:03312067 Salami food_product: + FOODON:03315904 Sausage food_product: + Sausage (Pepper) food_product: + FOODON:00003017 Scallopini food_product: + UBERON:0006612 Shell on food_product: + Shelled food_product: + UBERON:0001467 Shoulder food_product: + UBERON:0001467 Shoulder Chop food_product: + FOODON:03530027 Sirloin Chop food_product: + FOODON:03301484 Skim milk powder food_product: + PATO:0000387 Soft food_product: + FOODON:03316468 Soyabean Meal food_product: + Starter Ration food_product: + Steak food_product: + FOODON:00003140 Stew Chunks food_product: + + FOODON:00001874 Supplements food_product: + T. high food_product: + FOODON:03304154 Tahini food_product: + FOODON:03530217 Tender loin food_product: + FOODON:03530217 Tenderloin food_product: + UBERON:0000376 Thigh food_product: + UBERON:0000376 Thigh Skinless food_product: + UBERON:0000376 Thigh Skinless Boneless food_product: + UBERON:0000014 Thigh with Skin food_product: + FOODON:00001568 Trim food_product: + FOODON:03316468 Unknown Meal food_product: + FOODON:03309997 Unspecified Feed/Ingredient food_product: + UBERON:0000376 Upper Thigh food_product: + Upper Thigh with Skin food_product: + UBERON:0000376 upper thight food_product: + UBERON:0000376 Upperthigh food_product: + FOODON:03304045 White Pepper food_product: + FOODON:03430131 Whole food_product: + Whole Carcass food_product: + Whole with Skin food_product: + UBERON:0000023 Wing food_product: + UBERON:0000023 Wings food_product: +SPECIES menu SpeciesMenu 2 + 4 + <=8 + + FOODON:03411408 Abalone + FOODON:00002670 Alfalfa sprouts + FOODON:00002693 Alpaca + FOODON:03411624 Amphibian + FOODON:00002473 Apple + FOODON:03411134 Aquatic mammal + FOODON:03411626 Armadillo + FOODON:00002616 Avian + FOODON:00003044 Basil + CURATION:0001601 Bat + FOODON:03412406 Bear + NCBITAXON:103695 Bearded Dragon + FOODON:03412098 Bison + Budgie + FOODON:03412103 Camel + FOODON:03412103 Camelid + Canary + FOODON:03414847 Canine + CURATION:0001383 Cantelope + FOODON:03411328 Caprine + Cardemom + Cardinal + FOODON:03411500 Cervid + CURATION:0001646 Chameleon + Cheetah + FOODON:03411457 Chicken + Chimpanzee + Chinchilla + Chinese Water Dragon + FOODON:03411331 Clam + FOODON:00001763 Coriander + Cormorant + Cougar/Mountain Lion + CURATION:0001607 Coyote + FOODON:03411335 Crab + Crane + Crow + FOODON:00003024 Cumin seeds + FOODON:03411644 Cuttlefish + FOODON:03414847 Dog + FOODON:03413363 Dolphin + NCIT:C14191 Domestic Cat + FOODON:03411161 Domestic Cattle + FOODON:03411316 Duck + Dumpster + Eagle + FOODON:03411278 Eel + FOODON:03412129 Elephant + Falcon + NCIT:C14191 Feline + CURATION:0001411 Ferret + Finch + FOODON:03411222 Fish + Flamingo + For Unspecified + CURATION:0001405 Fox + FOODON:03412615 Gecko + FOODON:03411328 Goat + Goat and Sheep + FOODON:03411253 Goose + FOODON:03301123 Grape + FOODON:03411478 Green onions + Grosbeak + FOODON:03301526 ground pepper + FOODON:03413503 Gull + FOODON:03412695 Hare + FOODON:00002933 Hazelnut + FOODON:03414548 Hedgehog + Herb/spice (unspecified) + FOODON:00002890 Heron + NCBITAXON:9831 Hippopotamidae + FOODON:03411229 Horse + FOODON:03412701 Iguana + Jaguar + FOODON:03412092 Kangaroo + Komodo Dragon + Lapine + FOODON:00001998 Lettuce + Lion + FOODON:03412293 Lizard + Marsupial + FOODON:00002723 Mink + FOODON:00002432 Mint + Mixed + Mongoose + NCIT:C14238 Mouse + FOODON:00001287 Mushrooms + FOODON:03411223 Mussel + n/a + Not Available + FOODON:03411514 Octopus + FOODON:03411450 Opossum + FOODON:03301482 Oregano + Other + CURATION:0001394 Otter + FOODON:03411183 Ovine + NCBITAXON:30458 Owl + FOODON:03411224 Oyster + FOODON:00002726 Parrot + FOODON:00002942 Parsley + FOODON:03411382 Partridge + Pea sprouts + FOODON:03306867 Peanut Butter + FOODON:00001649 Pepper + FOODON:03411382 Perdrix + FOODON:03411460 Pheasant + Pickerel + FOODON:03411136 Pig + FOODON:03411304 Pigeon + CURATION:0000439 Pine Siskin + Pony + Porcupine + FOODON:03413364 Porpoise + NCBITAXON:9443 Primate + FOODON:03411346 Quail + FOODON:03411323 Rabbit + FOODON:03411461 Raccoon + FOODON:03414848 Rat + FOODON:03414362 Ratite + Raven + FOODON:03414371 Red Deer + Redpoll + FOODON:03411625 Reptile + FOODON:03414556 Rhea + Robin + NCBITAXON:9989 Rodent + FOODON:00002217 Sage + FOODON:00002220 Salmon + FOODON:03411489 Scallop + CURATION:0000157 Sea Otter + FOODON:03414639 Sea Snail + Seal + FOODON:03310306 Sesame Seed + FOODON:03411183 Sheep + FOODON:03411237 Shrimp + FOODON:03412293 Skink + Skunk + FOODON:03411295 Snake + Sparrow + FOODON:03301716 Spinach + Spotted Hyena + FOODON:03420183 Sprouts + FOODON:03411205 Squid + FOODON:03411389 Squirrel + Stripped Hyena + Swan + FOODON:03412439 Tantalus Monkey + FOODON:03412434 Tilapia + FOODON:03309927 Tomato + FOODON:00000074 Tortoise + FOODON:03411258 Trout + FOODON:03414166 Turkey + FOODON:03411242 Turtle + Unknown + FOODON:00002616 Unspecified Bird + FOODON:03411222 Unspecified Fish + NCBITAXON:9443 Unspecified Primate + FOODON:03411625 Unspecified Reptile + NCBITAXON:9989 Unspecified Rodent + Vulture + Wallnut + CHEBI:15377 Water Dragon + FOODON:00003281 White Fish + FOODON:03530153 Wild Ruminant + Wombat + Woodpecker + FOODON:03412097 Zebra +STTYPE menu STTypeMenu 0 + 0.5 + FOODON:00003004 ANIMAL host (common name): + ENVO:01000254 ENVIRONMENT environmental_material:;environmental_site: + CHEBI:33290 FOOD food_product: + NCBITAXON:9606 HUMAN host (common name): + PRODUCT + QA + UNKNOWN host (common name): + 0 + 2 + <=8 + + FOODON:03411624 Amphibian host (common name): + FOODON:03411134 Aquatic Mammal host (common name): + FOODON:03411626 Armadillo host (common name): + FOODON:00002616 Avian host (common name): + CURATION:0001601 Bat host (common name): + ENVO:00002059 Biosolids environmental_material: + FOODON:03414374 Bovine host (common name): + ENVO:00000073 Building environmental_site: + FOODON:03412103 Camelid host (common name): + FOODON:03414847 Canine host (common name): + FOODON:03411328 Caprine host (common name): + Caprine and Ovine host (common name): + FOODON:00001709 Cereal food_product: + Cereal/Bread/Snack food_product: + FOODON:03411500 Cervid host (common name): + CURATION:0001527 Compost environmental_material: + Confections/Nuts/Condiments food_product: + Crocuta host (common name): + FOODON:03411374 Crustacean host (common name): + ENVO:00003862 Dairy environmental_site: + ENVO:00002008 Dust environmental_material: + FOODON:00001274 Egg food_product: + FOODON:03412129 Elephant host (common name): + CURATION:0001431 Equine host (common name): + CURATION:0000348 Equipment environmental_site: + ERROR + FOODON:03309997 Feed and Ingredients food_product: + NCIT:C14191 Feline host (common name): + CURATION:0001411 Ferret host (common name): + CHEBI:33287 Fertilizer environmental_material: + FOODON:03411222 Fish host (common name): + CHEBI:33290 Food food_product: + PO:0009001 Fruit food_product: + FOODON:00002141 Fruits and Vegetables food_product: + Health (medicine) + Herbs and Spices food_product: + Herpestidae host (common name): + NCBITAXON:9831 Hippopotamidae host (common name): + Lapine host (common name): + CURATION:0001446 Litter/Manure environmental_material: + Manure environmental_material: + Marsupial host (common name): + FOODON:00001006 Meat food_product: + Mephitida host (common name): + FOODON:00002723 Mink host (common name): + CHEBI:33290 Mixed food food_product: + FOODON:03315600 Mixed Food/Meat food_product: + FOODON:03412112 Mollusk host (common name): + Mustelid host (common name): + n/a host (common name): + Other host (common name): + FOODON:03411183 Ovine host (common name): + Personnel Clothing environmental_material: + FOODON:03411136 Porcine host (common name): + NCBITAXON:9443 Primate host (common name): + FOODON:03411461 Raccoon host (common name): + FOODON:03411625 Reptile host (common name): + NCBITAXON:9989 Rodent host (common name): + ENVO:00002018 Sewage environmental_material: + ENVO:00001998 Soil environmental_material: + ENVO:02000125 Transportation Supplies environmental_site: + Transportation Vehicles environmental_site: + FOODON:03414166 Turkey host (common name): + Unknown host (common name): + CHEBI:33290 Unknown Food food_product: + Unspecified + FOODON:00003004 Unspecified Animal host (common name): + Unspecified Environmental environmental_site: + CURATION:0001610 Unspecified Food food_product: + CHEBI:33290 Unspecified Product + Ursine host (common name): + Vegetable/Spice food_product: + CHEBI:15377 Water environmental_material: +COMMODITY menu CommodityMenu <=16 + FOODON:00001041 Beef food_product: + FOODON:03411198 Broiler host (common name): + ENVO:00003862 Dairy environmental_site: + Domestic/Farmed + FOODON:00001274 Egg food_product: + NCIT:C37984 Laboratory environmental_site: + FOODON:00001006 Meat food_product: + FOODON:00002912 Mutton food_product: + Pet host (common name): + ENVO:00010625 Pet/Zoo environmental_site: + FOODON:00003083 Red Veal food_product: + Unknown host (common name): + FOODON:00003083 Veal food_product: + FOODON:00003083 White Veal food_product: + FOODON:03530153 Wild +SPECIMENSOURCE_1 menu SpecimenSource1Menu 2 + <=32 + CURATION:0000508 Aliquote / Portion + UBERON:0000178 Blood anatomical_material: + FOODON:00001564 Blood Meal food_product: + Body Fluid/Excretion anatomical_material: + UBERON:0008979 Carcass anatomical_part: + SEP:00042 Check Sample + Contact plate collection_device: + CURATION:0000488 Culture + ENVO:00002008 Dust environmental_material: + FOODON:00001274 Egg food_product: + Environment (Animal) + CURATION:0001610 Environmental environmental_material:;environmental_site: + UBERON:0001988 Feces body_product: + Fetus/Embryo anatomical_part: + UBERON:0000062 Organ anatomical_part: + Organ/Tissue anatomical_material: + NCIT:C53471 Proficiency Isolate + CURATION:0000488 Reference Culture + CURATION:0001629 Rinse environmental_material: + Septage environmental_material: + FOODON:03316468 Soya Meal food_product: + UBERON:0001988 Stool body_product: + NCIT:C17627 Swab collection_device: + UBERON:0000479 Tissue anatomical_material: + UO:0000000 Unit (Pre-Packaged) + Unknown host (common name): + Unspecified + UBERON:0001088 Urine body_product: +SPECIMENSUBSOURCE_1 menu SpecimenSubsource1Menu 0.25 + <=0.12 + <=16 + aansarraysubsource + UBERON:0000916 Abdomen anatomical_part: + UBERON:0002378 Abdominal Muscle anatomical_part: + UBERON:0007358 Abomasum anatomical_part: + HP:0025615 Abscess anatomical_material: + ENVO:00002005 Air Intake environmental_site: + UBERON:0009060 Air Sac anatomical_part: + Anal Gland anatomical_part: + FOODON:00003004 Animal Pen environmental_site: + FOODON:03302184 Balut food_product: + CURATION:0000406 Belt environmental_site: + CURATION:0000504 Bladder anatomical_part: + UBERON:0000178 Blood anatomical_material: + UBERON:0001981 Blood vessel anatomical_part: + UBERON:0001474 Bone anatomical_material: + UBERON:0002371 Bone Marrow anatomical_material: + Bootie environmental_material: + CURATION:0000401 Boots environmental_material: + UBERON:0000955 Brain anatomical_part: + CURATION:0000502 Bursa of Fabricus anatomical_part: + Cages environmental_site: + CURATION:0000480 Cavity Fluid (Unspecified) anatomical_material: + CURATION:0000480 Cavity fluid unspecified anatomical_material: + Cecal Content body_product: + CURATION:0000495 Cecum anatomical_part: + Chick Boxes environmental_site: + Chick Pads environmental_material: + CURATION:0000491 Cloacae anatomical_part: + NCIT:C17627 Cloacal swab anatomical_part: + UBERON:0001155 Colon anatomical_part: + Confirmation ? + FOODON:03490213 Crates environmental_site: + UBERON:0007356 Crop environmental_material: + Culture Plate collection_device: + UBERON:0001007 Digestive System (Unspecified) anatomical_part: + UBERON:0002114 Duodenum anatomical_part: + ENVO:00002008 Dust environmental_material: + UBERON:0001690 Ear anatomical_part: + Egg Belt environmental_site: + Environment Swab collection_device: + Environment Swab (Hatchery) environmental_site:hatchery;collection_device:swab + UBERON:0001043 Esophagus anatomical_part: + BFO:0000019 External Quality Assurance ? + UBERON:0000970 Eye anatomical_part: + ENVO:00000104 Fan environmental_site: + UBERON:0001988 Fecal Slurry environmental_material: + UBERON:0001988 Feces body_product: + FOODON:03309997 Feed food_product: + CURATION:0000419 Feeders and Drinkers environmental_site: + Fetal Tissue anatomical_material: + CURATION:0001488 Final Wash environmental_material: + CURATION:0000335 Floor environmental_site: + Fluff environmental_material: + ENVO:01001873 Fluff (Hatchery) environmental_material: + UO:0010013 Foot anatomical_part: + UBERON:0002110 Gall Bladder anatomical_part: + UBERON:0002110 Gallbladder anatomical_part: + UBERON:0000045 Ganglion anatomical_part: + UBERON:0005052 Gizzard anatomical_part: + Growth / lesion (unspecified tissue) anatomical_material: + Growth/Lesion (Unspecified Tissue) anatomical_material: + UBERON:0000948 Heart anatomical_part: + UBERON:0002116 Ileum anatomical_part: + ENVO:01000417 In-House + NCIT:C37984 Inter-Lab Exchange + Intestinal Contents anatomical_material: + UBERON:0000160 Intestine anatomical_part: + UBERON:0002115 Jejunum anatomical_part: + UBERON:0004905 Joint anatomical_part: + UBERON:0001090 Joint Fluid anatomical_material: + UBERON:0002113 Kidney anatomical_part: + CURATION:0000463 Levage/peritoneal anatomical_material: + Levage/Tracheal anatomical_material: + CURATION:0001446 Litter environmental_material: + CURATION:0001446 Litter/Manure environmental_material: + ENVO:01000602 Live Haul Truck environmental_site: + ENVO:01000602 Live Haul Truck/Trailer environmental_site: + UBERON:0002107 Liver food_product: + UBERON:0002048 Lung anatomical_part: + UBERON:0000029 Lymph Node anatomical_part: + ENVO:01001872 Manure Pit environmental_site: + UBERON:0007109 Meconium body_product: + UBERON:0002509 Mesenteric Lymph Node anatomical_part: + Milk/Colostrum body_product: + Mixed host (common name): + UBERON:0000062 Mixed Organs anatomical_part: + UBERON:0000479 Mixed Tissues anatomical_material: + UBERON:0000165 Mouth anatomical_part: + Mucous membrane (gut) anatomical_part: + UBERON:0000344 Mucous membrane (resp) anatomical_part: + UBERON:0000912 Mucus anatomical_material: + CURATION:0001428 Muscle anatomical_part: + Muscle/Meat food_product: + UBERON:0035612 Nasal Turbinate anatomical_part: + CURATION:0000466 Nasal/Naries anatomical_part: + UBERON:0000062 Organ Unspecified anatomical_part: + UBERON:0000992 Ovary anatomical_part: + UBERON:0000993 Oviduct anatomical_part: + UBERON:0002407 Pericardium anatomical_part: + UBERON:0001268 Peritoneal Fluid anatomical_material: + UBERON:0002358 Peritoneum anatomical_part: + UBERON:0001987 Placenta anatomical_part: + UBERON:0000977 Pleura anatomical_part: + CURATION:0000406 Plucking Belt environmental_site: + CHEBI:15377 Plucking Water environmental_material: + Pooled Feces body_product: + CURATION:0000457 Rectal Swab anatomical_part: + UBERON:0001052 Rectum anatomical_part: + CURATION:0001536 Research + CURATION:0001629 Rinse environmental_material: + UBERON:0007365 Rumen anatomical_part: + UBERON:0006612 Shell anatomical_material: + UBERON:0005079 Shell egg food_product: + CURATION:0000455 Sinus anatomical_part: + UBERON:0000014 Skin anatomical_part: + UBERON:0002108 Small Intestine anatomical_part: + ENVO:00001998 Soil environmental_material: + UBERON:0002240 Spinal Cord anatomical_part: + UBERON:0002106 Spleen anatomical_part: + Stall environmental_site: + UBERON:0000945 Stomach anatomical_part: + Stomach Contents body_product: + NCIT:C17627 Swab collection_device: + Swab (Nasal) anatomical_part: + CURATION:0000457 Swab (Rectal) anatomical_part: + Swab (Tissue Fluid-Unspecified) anatomical_material: + UBERON:0000473 Testicle anatomical_part: + UBERON:0000915 Thorax anatomical_part: + UBERON:0003126 Trachea anatomical_part: + UBERON:0000062 Unknown organ anatomical_part: + Unspecified Organ/Tissue anatomical_part: + UBERON:0001088 Urine body_product: + UBERON:0000995 Uterus anatomical_part: + UBERON:0000996 Vagina anatomical_part: + Walls environmental_site: + CHEBI:15377 Water environmental_material: + Watering Bowl/Equipment environmental_site: + Weekly + Weep environmental_material: + FOODON:03430131 Whole food_product: + UBERON:2000084 Yolk food_product: + UBERON:0001040 Yolk Sac anatomical_part: +SUBJECT_SUBTYPE menu SubjectSubtypeMenu <=32 + + >32 + FOODON:00002670 Alfalfa Sprouts food_product: + FOODON:03301355 Almond food_product: + FOODON:00003004 Animal pen environmental_site: + Artificial wetland environmental_site: + FOODON:00002426 Arugula food_product: + FOODON:00003044 Basil food_product: + FOODON:00002576 Bean Sprouts food_product: + Biosolid environmental_material: + ENVO:00002044 Biosolid/Sludge environmental_material: + Bootie environmental_material: + CURATION:0000401 Boots environmental_material: + UBERON:0000310 Breast food_product: + UBERON:0000310 Breast skinless food_product: + UBERON:0000310 Breast skinless boneless food_product: + Breast with skin food_product: + CURATION:0000397 Broom environmental_material: + Bulk Tank environmental_site: + CURATION:0001383 Cantaloupe food_product: + Carcass (whole) anatomical_part: + FOODON:00001013 Cheese food_product: + Chia Powder food_product: + CURATION:0001385 Chia Seeds food_product: + Chia Sprouts food_product: + Chick Boxes environmental_site: + UBERON:2001977 Chick Pads environmental_material: + FOODON:03306811 Chickpea food_product: + FOODON:03301511 Chili food_product: + FOODON:03315873 Chilli Pepper food_product: + FOODON:03311167 Chives food_product: + Chops food_product: + FOODON:03303085 Coconut food_product: + CURATION:0001527 Compost environmental_material: + SIO:000511 Cooler Line environmental_site: + PO:0009010 Coriander Seeds food_product: + FOODON:00002976 Coriander-Cumin Powder food_product: + Cottage environmental_site: + FOODON:03301545 Cucumber food_product: + FOODON:03306648 Curry Leaves food_product: + FOODON:03301842 Curry powder food_product: + ENVO:00000474 Cut food_product: + Dead Haul Truck / Trailer environmental_site: + FOODON:00001811 Dill food_product: + CURATION:0001378 Drumstick food_product: + Dumpster environmental_site: + Effluent environmental_material: + FOODON:00001274 Egg food_product: + Egg Belt environmental_site: + ENVO:00000104 Fan environmental_site: + FOODON:03309997 Feed Pans environmental_site: + FOODON:03309953 Fennel food_product: + FOODON:03530144 Filet food_product: + Flax and Chia Powder food_product: + Flax Powder food_product: + CURATION:0000335 Floor environmental_site: + FOODON:00002616 For Avian host (common name): + For Beef Cattle host (common name): + CURATION:0001354 For Cats host (common name): + For Cattle (Beef) host (common name): + FOODON:00002505 For Cattle (Dairy) host (common name): + FOODON:03411457 For Chicken host (common name): + FOODON:03411201 For Dairy Cows host (common name): + CURATION:0001351 For Dogs host (common name): + FOODON:03411222 For Fish host (common name): + FOODON:03411328 For Goats host (common name): + FOODON:03411229 For Horse host (common name): + FOODON:00002723 For Mink host (common name): + For Others + FOODON:00001131 For Poultry host (common name): + FOODON:03411136 For Swine host (common name): + FOODON:03414166 For Turkeys host (common name): + For Unknown + For Unspecified host (common name): + FOODON:03301844 Garlic Powder food_product: + FOODON:00002718 Ginger food_product: + FOODON:03411478 Green Onion food_product: + Ground food_product: + Ground (extra lean) food_product: + Ground (lean) food_product: + FOODON:03430117 Ground (medium) food_product: + Ground (regular) food_product: + ENVO:00002041 Ground Water environmental_material: + FOODON:00002502 Ham food_product: + Hazelnut / Filbert food_product: + Headcheese food_product: + Herb/Spice (Unspecified) food_product: + CURATION:0000309 Irrigation environmental_site: + FOODON:03304859 Kale food_product: + Kalonji Whole Seed food_product: + Lab Surface environmental_site: + ENVO:00000020 Lake environmental_site: + UBERON:0000978 Leg food_product: + FOODON:00001998 Lettuce food_product: + Liquid whole food_product: + UBERON:0002107 Liver food_product: + Loin center chop non-seasoned food_product: + Mango food_product: + FOODON:00001006 Meat food_product: + UBERON:0001913 Milk food_product: + FOODON:00002432 Mint food_product: + Mixed host (common name): + Mixed Salad/Mixed Greens food_product: + FOODON:03420183 Mixed Sprouts food_product: + Mung Bean Sprouts food_product: + FOODON:03301482 Oregano food_product: + Other host (common name): + FOODON:03411457 Other chicken food_product: + ENVO:00000474 Other cut (not ground) food_product: + FOODON:03420218 Other variety meats food_product: + Papaya food_product: + FOODON:03301105 Paprika food_product: + FOODON:00002942 Parsley food_product: + Pea Sprouts food_product: + FOODON:00001649 Pepper food_product: + Pepper Powder food_product: + FOODON:03311003 Pepperoni food_product: + Rasam Powder Spice food_product: + ENVO:00000022 River environmental_site: + River Surface environmental_site: + Roast food_product: + Rolled + ENVO:00000029 Run Off environmental_material: + FOODON:03315904 Sausage food_product: + Scallopini food_product: + ENVO:00002007 Sediment environmental_material: + FOODON:03310306 Sesame Seed food_product: + Shelf / Sill environmental_site: + FOODON:03411433 Shellfish food_product: + UBERON:0001467 Shoulder food_product: + UBERON:0001467 Shoulder Chop food_product: + Shoulder chop non-seasoned food_product: + PATO:0000387 Soft food_product: + FOODON:03301415 Soybean food_product: + FOODON:03301716 Spinach food_product: + FOODON:03420102 Sprouted Seeds food_product: + FOODON:03420183 Sprouts food_product: + Stall environmental_site: + Steak food_product: + FOODON:00003140 Stew Chunks food_product: + CURATION:0000247 Surface - Other environmental_site: + Surface - River environmental_site: + CURATION:0000247 Surface unspecified environmental_site: + ENVO:00002042 Surface Water environmental_site: + FOODON:03530217 Tenderloin food_product: + UBERON:0000376 Thigh food_product: + Thigh with skin food_product: + Transformer environmental_site: + ENVO:01000602 Truck / Trailer environmental_site: + ENVO:01000602 Truck/Trailer environmental_site: + FOODON:03310841 Turmeric food_product: + Unknown + CURATION:0000247 Unknown Surface environmental_site: + Unspecified + UBERON:0000376 Upper Thigh food_product: + Upper Thigh with Skin food_product: + Wall environmental_site: + FOODON:03315233 Walnut food_product: + ENVO:00002001 Waste Water environmental_material: + Watering bowl/equipment environmental_site: + FOODON:03430131 Whole food_product: + UBERON:0000023 Wings food_product: + CURATION:0000247 Working Surface environmental_site: + FOODON:03411345 Yeast food_product: + \ No newline at end of file diff --git a/web/templates/phac_dexa/schema_slots.tsv b/web/templates/phac_dexa/schema_slots.tsv index f8b7065f..2544c061 100644 --- a/web/templates/phac_dexa/schema_slots.tsv +++ b/web/templates/phac_dexa/schema_slots.tsv @@ -1,157 +1,157 @@ class_name slot_group slot_uri title name range range_2 identifier required recommended multivalued minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GRDI -PHAC Dexa Database Identifiers - Database Identifiers SPECIMEN_ID WhitespaceMinimizedString alternative_sample_ID - Database Identifiers ISOLATE_ID WhitespaceMinimizedString TRUE isolate_ID - Database Identifiers SAMPLE_ID WhitespaceMinimizedString TRUE sample_collector_sample_ID +PHACDexa Database Identifiers + Database Identifiers SPECIMEN_ID specimen_id WhitespaceMinimizedString alternative_sample_ID + Database Identifiers ISOLATE_ID isolate_id WhitespaceMinimizedString TRUE isolate_ID + Database Identifiers SAMPLE_ID sample_id WhitespaceMinimizedString TRUE sample_collector_sample_ID Fields to put in sections - Fields to put in sections SENTINEL_SITE WhitespaceMinimizedString - Fields to put in sections LFZ_ADDITIONAL_SAMPLE_ID WhitespaceMinimizedString - Fields to put in sections LFZ_ORIGIN_COUNTRY WhitespaceMinimizedString - Fields to put in sections SUBJECT_CODE WhitespaceMinimizedString - Fields to put in sections SUBJECT_DESCRIPTIONS SUBJECT_DESCRIPTIONS menu - Fields to put in sections SUBMITTINGORG_1 WhitespaceMinimizedString collected_by - Fields to put in sections SUBMITTINGLAB_1 WhitespaceMinimizedString laboratory_name - Fields to put in sections PROJECT_1 WhitespaceMinimizedString - Fields to put in sections COUNTRY_1 WhitespaceMinimizedString geo_loc_name (country) - Fields to put in sections PROVINCE_1 WhitespaceMinimizedString geo_loc_name (state/province/region) - Fields to put in sections CENSUSDIVISION_1 WhitespaceMinimizedString - Fields to put in sections REGION WhitespaceMinimizedString - Fields to put in sections YEAR WhitespaceMinimizedString - Fields to put in sections MONTH WhitespaceMinimizedString - Fields to put in sections QTR WhitespaceMinimizedString - Fields to put in sections DATECOLLECTED_1 date sample_collection_date - Fields to put in sections DATERECEIVED_1 WhitespaceMinimizedString - Fields to put in sections DATESHIPPED_1 WhitespaceMinimizedString - Fields to put in sections ESTABLISHMENT_1 WhitespaceMinimizedString - Fields to put in sections SPECIES SPECIES menu host (common name): - Fields to put in sections STTYPE STTYPE menu - Fields to put in sections STYPE STYPE menu - Fields to put in sections COMMODITY COMMODITY menu - Fields to put in sections SPECIMENSOURCE_1 SPECIMENSOURCE_1 menu - Fields to put in sections SPECIMENSUBSOURCE_1 SPECIMENSUBSOURCE_1 menu - Fields to put in sections SUBJECT_SUBTYPE SUBJECT_SUBTYPE menu - Fields to put in sections FIELDSTAFF_1 WhitespaceMinimizedString - Fields to put in sections IN_STORE_PROCESSING WhitespaceMinimizedString - Fields to put in sections MAYCONTAINFROZENMEAT_1 WhitespaceMinimizedString - Fields to put in sections NOOFCASHREGISTERS_1 WhitespaceMinimizedString - Fields to put in sections PRICEPERKG_1 WhitespaceMinimizedString - Fields to put in sections STORETYPE_SAMPLINGSITE_1 WhitespaceMinimizedString - Fields to put in sections TEMPERATUREMAX_1 WhitespaceMinimizedString - Fields to put in sections TEMPERATUREMIN_1 WhitespaceMinimizedString - Fields to put in sections TEMPERATUREARRIVAL_1 WhitespaceMinimizedString - Fields to put in sections VETID WhitespaceMinimizedString - Fields to put in sections ROOMID WhitespaceMinimizedString - Fields to put in sections PENID WhitespaceMinimizedString - Fields to put in sections SAMPLING_TYPE WhitespaceMinimizedString - Fields to put in sections BARN_ID WhitespaceMinimizedString - Fields to put in sections DATE_PACKED WhitespaceMinimizedString - Fields to put in sections FINAL_ID_GENUS WhitespaceMinimizedString organism - Fields to put in sections FINAL_ID_SPECIES WhitespaceMinimizedString organism - Fields to put in sections FINAL_ID_SUBSPECIES WhitespaceMinimizedString - Fields to put in sections FINAL_ID_SEROTYPE WhitespaceMinimizedString serovar - Fields to put in sections FINAL_ID_ANTIGEN WhitespaceMinimizedString - Fields to put in sections FINAL_ID_PHAGETYPE WhitespaceMinimizedString phagetype - Fields to put in sections SA_Serotype_Method WhitespaceMinimizedString serotyping_method - Fields to put in sections SEROTYPE_GR WhitespaceMinimizedString - Fields to put in sections MIC_AMC WhitespaceMinimizedString - Fields to put in sections MIC_AMK WhitespaceMinimizedString - Fields to put in sections MIC_AMP WhitespaceMinimizedString - Fields to put in sections MIC_AZM WhitespaceMinimizedString - Fields to put in sections MIC_CEP WhitespaceMinimizedString - Fields to put in sections MIC_CHL WhitespaceMinimizedString - Fields to put in sections MIC_CIP WhitespaceMinimizedString - Fields to put in sections MIC_CRO WhitespaceMinimizedString - Fields to put in sections MIC_FOX WhitespaceMinimizedString - Fields to put in sections MIC_GEN WhitespaceMinimizedString - Fields to put in sections MIC_KAN WhitespaceMinimizedString - Fields to put in sections MIC_MEM WhitespaceMinimizedString - Fields to put in sections MIC_NAL WhitespaceMinimizedString - Fields to put in sections MIC_SSS WhitespaceMinimizedString - Fields to put in sections MIC_STR WhitespaceMinimizedString - Fields to put in sections MIC_SXT WhitespaceMinimizedString - Fields to put in sections MIC_TET WhitespaceMinimizedString - Fields to put in sections MIC_TIO WhitespaceMinimizedString - Fields to put in sections N_OF_RESISTANCE WhitespaceMinimizedString - Fields to put in sections NBTESTED WhitespaceMinimizedString - Fields to put in sections R_PATTERN WhitespaceMinimizedString - Fields to put in sections AMR_PA2C WhitespaceMinimizedString - Fields to put in sections RLEAST1 WhitespaceMinimizedString - Fields to put in sections RLEAST2 WhitespaceMinimizedString - Fields to put in sections RLEAST3 WhitespaceMinimizedString - Fields to put in sections RLEAST4 WhitespaceMinimizedString - Fields to put in sections RLEAST5 WhitespaceMinimizedString - Fields to put in sections SIR_AMC WhitespaceMinimizedString - Fields to put in sections SIR_AMK WhitespaceMinimizedString - Fields to put in sections SIR_AMP WhitespaceMinimizedString - Fields to put in sections SIR_AZM WhitespaceMinimizedString - Fields to put in sections SIR_CEP WhitespaceMinimizedString - Fields to put in sections SIR_CHL WhitespaceMinimizedString - Fields to put in sections SIR_CIP WhitespaceMinimizedString - Fields to put in sections SIR_CRO WhitespaceMinimizedString - Fields to put in sections SIR_FOX WhitespaceMinimizedString - Fields to put in sections SIR_GEN WhitespaceMinimizedString - Fields to put in sections SIR_KAN WhitespaceMinimizedString - Fields to put in sections SIR_MEM WhitespaceMinimizedString - Fields to put in sections SIR_NAL WhitespaceMinimizedString - Fields to put in sections SIR_SSS WhitespaceMinimizedString - Fields to put in sections SIR_STR WhitespaceMinimizedString - Fields to put in sections SIR_SXT WhitespaceMinimizedString - Fields to put in sections SIR_TET WhitespaceMinimizedString - Fields to put in sections SIR_TIO WhitespaceMinimizedString - Fields to put in sections RAMC WhitespaceMinimizedString - Fields to put in sections RAMK WhitespaceMinimizedString - Fields to put in sections RAMP WhitespaceMinimizedString - Fields to put in sections RAZM WhitespaceMinimizedString - Fields to put in sections RCEP WhitespaceMinimizedString - Fields to put in sections RCHL WhitespaceMinimizedString - Fields to put in sections RCIP WhitespaceMinimizedString - Fields to put in sections RCRO WhitespaceMinimizedString - Fields to put in sections RFOX WhitespaceMinimizedString - Fields to put in sections RGEN WhitespaceMinimizedString - Fields to put in sections RKAN WhitespaceMinimizedString - Fields to put in sections RMEM WhitespaceMinimizedString - Fields to put in sections RNAL WhitespaceMinimizedString - Fields to put in sections RSSS WhitespaceMinimizedString - Fields to put in sections RSTR WhitespaceMinimizedString - Fields to put in sections RSXT WhitespaceMinimizedString - Fields to put in sections RTET WhitespaceMinimizedString - Fields to put in sections RTIO WhitespaceMinimizedString - Fields to put in sections A2C WhitespaceMinimizedString - Fields to put in sections CAMC WhitespaceMinimizedString - Fields to put in sections CAMK WhitespaceMinimizedString - Fields to put in sections CAMP WhitespaceMinimizedString - Fields to put in sections CAZM WhitespaceMinimizedString - Fields to put in sections CCEP WhitespaceMinimizedString - Fields to put in sections CCHL WhitespaceMinimizedString - Fields to put in sections CCIP WhitespaceMinimizedString - Fields to put in sections CCRO WhitespaceMinimizedString - Fields to put in sections CFOX WhitespaceMinimizedString - Fields to put in sections CGEN WhitespaceMinimizedString - Fields to put in sections CKAN WhitespaceMinimizedString - Fields to put in sections CMEM WhitespaceMinimizedString - Fields to put in sections CNAL WhitespaceMinimizedString - Fields to put in sections CSSS WhitespaceMinimizedString - Fields to put in sections CSTR WhitespaceMinimizedString - Fields to put in sections CSXT WhitespaceMinimizedString - Fields to put in sections CTET WhitespaceMinimizedString - Fields to put in sections CTIO WhitespaceMinimizedString - Fields to put in sections STHY_TESTSRC_ID WhitespaceMinimizedString - Fields to put in sections WINN_TESTSRC_ID WhitespaceMinimizedString - Fields to put in sections GUEL_TESTSRC_ID WhitespaceMinimizedString - Fields to put in sections RCIP_DANMAP WhitespaceMinimizedString - Fields to put in sections EPIDATESTAMP_1 WhitespaceMinimizedString - Fields to put in sections ACSSUT WhitespaceMinimizedString - Fields to put in sections AKSSUT WhitespaceMinimizedString - Fields to put in sections ACKSSUT WhitespaceMinimizedString - Fields to put in sections MDR_A_SSUT WhitespaceMinimizedString - Fields to put in sections EXCLUSION WhitespaceMinimizedString - Fields to put in sections RAMINOGLY WhitespaceMinimizedString - Fields to put in sections RBETALACTAM WhitespaceMinimizedString - Fields to put in sections RQUINOLONES WhitespaceMinimizedString - Fields to put in sections RFOLINHIBITOR WhitespaceMinimizedString - Fields to put in sections MDR WhitespaceMinimizedString - Fields to put in sections specimen_number WhitespaceMinimizedString - Fields to put in sections EXTERNAL_AGENT WhitespaceMinimizedString - Fields to put in sections FARM_FLAG WhitespaceMinimizedString - Fields to put in sections AMIKACINGELET WhitespaceMinimizedString + Fields to put in sections SENTINEL_SITE sentinel_site WhitespaceMinimizedString + Fields to put in sections LFZ_ADDITIONAL_SAMPLE_ID lfz_additional_sample_id WhitespaceMinimizedString + Fields to put in sections LFZ_ORIGIN_COUNTRY lfz_origin_country WhitespaceMinimizedString + Fields to put in sections SUBJECT_CODE subject_code WhitespaceMinimizedString + Fields to put in sections SUBJECT_DESCRIPTIONS subject_descriptions SubjectDescriptionsMenu + Fields to put in sections SUBMITTINGORG_1 submittingorg_1 WhitespaceMinimizedString collected_by + Fields to put in sections SUBMITTINGLAB_1 submittinglab_1 WhitespaceMinimizedString laboratory_name + Fields to put in sections PROJECT_1 project_1 WhitespaceMinimizedString + Fields to put in sections COUNTRY_1 country_1 WhitespaceMinimizedString geo_loc_name (country) + Fields to put in sections PROVINCE_1 province_1 WhitespaceMinimizedString geo_loc_name (state/province/region) + Fields to put in sections CENSUSDIVISION_1 censusdivision_1 WhitespaceMinimizedString + Fields to put in sections REGION region WhitespaceMinimizedString + Fields to put in sections YEAR year WhitespaceMinimizedString + Fields to put in sections MONTH month WhitespaceMinimizedString + Fields to put in sections QTR qtr WhitespaceMinimizedString + Fields to put in sections DATECOLLECTED_1 datecollected_1 date sample_collection_date + Fields to put in sections DATERECEIVED_1 datereceived_1 WhitespaceMinimizedString + Fields to put in sections DATESHIPPED_1 dateshipped_1 WhitespaceMinimizedString + Fields to put in sections ESTABLISHMENT_1 establishment_1 WhitespaceMinimizedString + Fields to put in sections SPECIES species SpeciesMenu host (common name): + Fields to put in sections STTYPE sttype STTypeMenu + Fields to put in sections STYPE stype STypeMenu + Fields to put in sections COMMODITY commodity CommodityMenu + Fields to put in sections SPECIMENSOURCE_1 specimensource_1 SpecimenSource1Menu + Fields to put in sections SPECIMENSUBSOURCE_1 specimensubsource_1 SpecimenSubsource1Menu + Fields to put in sections SUBJECT_SUBTYPE subject_subtype SubjectSubtypeMenu + Fields to put in sections FIELDSTAFF_1 fieldstaff_1 WhitespaceMinimizedString + Fields to put in sections IN_STORE_PROCESSING in_store_processing WhitespaceMinimizedString + Fields to put in sections MAYCONTAINFROZENMEAT_1 maycontainfrozenmeat_1 WhitespaceMinimizedString + Fields to put in sections NOOFCASHREGISTERS_1 noofcashregisters_1 WhitespaceMinimizedString + Fields to put in sections PRICEPERKG_1 priceperkg_1 WhitespaceMinimizedString + Fields to put in sections STORETYPE_SAMPLINGSITE_1 storetype_samplingsite_1 WhitespaceMinimizedString + Fields to put in sections TEMPERATUREMAX_1 temperaturemax_1 WhitespaceMinimizedString + Fields to put in sections TEMPERATUREMIN_1 temperaturemin_1 WhitespaceMinimizedString + Fields to put in sections TEMPERATUREARRIVAL_1 temperaturearrival_1 WhitespaceMinimizedString + Fields to put in sections VETID vetid WhitespaceMinimizedString + Fields to put in sections ROOMID roomid WhitespaceMinimizedString + Fields to put in sections PENID penid WhitespaceMinimizedString + Fields to put in sections SAMPLING_TYPE sampling_type WhitespaceMinimizedString + Fields to put in sections BARN_ID barn_id WhitespaceMinimizedString + Fields to put in sections DATE_PACKED date_packed WhitespaceMinimizedString + Fields to put in sections FINAL_ID_GENUS final_id_genus WhitespaceMinimizedString organism + Fields to put in sections FINAL_ID_SPECIES final_id_species WhitespaceMinimizedString organism + Fields to put in sections FINAL_ID_SUBSPECIES final_id_subspecies WhitespaceMinimizedString + Fields to put in sections FINAL_ID_SEROTYPE final_id_serotype WhitespaceMinimizedString serovar + Fields to put in sections FINAL_ID_ANTIGEN final_id_antigen WhitespaceMinimizedString + Fields to put in sections FINAL_ID_PHAGETYPE final_id_phagetype WhitespaceMinimizedString phagetype + Fields to put in sections SA_Serotype_Method sa_serotype_method WhitespaceMinimizedString serotyping_method + Fields to put in sections SEROTYPE_GR serotype_gr WhitespaceMinimizedString + Fields to put in sections MIC_AMC mic_amc WhitespaceMinimizedString + Fields to put in sections MIC_AMK mic_amk WhitespaceMinimizedString + Fields to put in sections MIC_AMP mic_amp WhitespaceMinimizedString + Fields to put in sections MIC_AZM mic_azm WhitespaceMinimizedString + Fields to put in sections MIC_CEP mic_cep WhitespaceMinimizedString + Fields to put in sections MIC_CHL mic_chl WhitespaceMinimizedString + Fields to put in sections MIC_CIP mic_cip WhitespaceMinimizedString + Fields to put in sections MIC_CRO mic_cro WhitespaceMinimizedString + Fields to put in sections MIC_FOX mic_fox WhitespaceMinimizedString + Fields to put in sections MIC_GEN mic_gen WhitespaceMinimizedString + Fields to put in sections MIC_KAN mic_kan WhitespaceMinimizedString + Fields to put in sections MIC_MEM mic_mem WhitespaceMinimizedString + Fields to put in sections MIC_NAL mic_nal WhitespaceMinimizedString + Fields to put in sections MIC_SSS mic_sss WhitespaceMinimizedString + Fields to put in sections MIC_STR mic_str WhitespaceMinimizedString + Fields to put in sections MIC_SXT mic_sxt WhitespaceMinimizedString + Fields to put in sections MIC_TET mic_tet WhitespaceMinimizedString + Fields to put in sections MIC_TIO mic_tio WhitespaceMinimizedString + Fields to put in sections N_OF_RESISTANCE n_of_resistance WhitespaceMinimizedString + Fields to put in sections NBTESTED nbtested WhitespaceMinimizedString + Fields to put in sections R_PATTERN r_pattern WhitespaceMinimizedString + Fields to put in sections AMR_PA2C amr_pa2c WhitespaceMinimizedString + Fields to put in sections RLEAST1 rleast1 WhitespaceMinimizedString + Fields to put in sections RLEAST2 rleast2 WhitespaceMinimizedString + Fields to put in sections RLEAST3 rleast3 WhitespaceMinimizedString + Fields to put in sections RLEAST4 rleast4 WhitespaceMinimizedString + Fields to put in sections RLEAST5 rleast5 WhitespaceMinimizedString + Fields to put in sections SIR_AMC sir_amc WhitespaceMinimizedString + Fields to put in sections SIR_AMK sir_amk WhitespaceMinimizedString + Fields to put in sections SIR_AMP sir_amp WhitespaceMinimizedString + Fields to put in sections SIR_AZM sir_azm WhitespaceMinimizedString + Fields to put in sections SIR_CEP sir_cep WhitespaceMinimizedString + Fields to put in sections SIR_CHL sir_chl WhitespaceMinimizedString + Fields to put in sections SIR_CIP sir_cip WhitespaceMinimizedString + Fields to put in sections SIR_CRO sir_cro WhitespaceMinimizedString + Fields to put in sections SIR_FOX sir_fox WhitespaceMinimizedString + Fields to put in sections SIR_GEN sir_gen WhitespaceMinimizedString + Fields to put in sections SIR_KAN sir_kan WhitespaceMinimizedString + Fields to put in sections SIR_MEM sir_mem WhitespaceMinimizedString + Fields to put in sections SIR_NAL sir_nal WhitespaceMinimizedString + Fields to put in sections SIR_SSS sir_sss WhitespaceMinimizedString + Fields to put in sections SIR_STR sir_str WhitespaceMinimizedString + Fields to put in sections SIR_SXT sir_sxt WhitespaceMinimizedString + Fields to put in sections SIR_TET sir_tet WhitespaceMinimizedString + Fields to put in sections SIR_TIO sir_tio WhitespaceMinimizedString + Fields to put in sections RAMC ramc WhitespaceMinimizedString + Fields to put in sections RAMK ramk WhitespaceMinimizedString + Fields to put in sections RAMP ramp WhitespaceMinimizedString + Fields to put in sections RAZM razm WhitespaceMinimizedString + Fields to put in sections RCEP rcep WhitespaceMinimizedString + Fields to put in sections RCHL rchl WhitespaceMinimizedString + Fields to put in sections RCIP rcip WhitespaceMinimizedString + Fields to put in sections RCRO rcro WhitespaceMinimizedString + Fields to put in sections RFOX rfox WhitespaceMinimizedString + Fields to put in sections RGEN rgen WhitespaceMinimizedString + Fields to put in sections RKAN rkan WhitespaceMinimizedString + Fields to put in sections RMEM rmem WhitespaceMinimizedString + Fields to put in sections RNAL rnal WhitespaceMinimizedString + Fields to put in sections RSSS rsss WhitespaceMinimizedString + Fields to put in sections RSTR rstr WhitespaceMinimizedString + Fields to put in sections RSXT rsxt WhitespaceMinimizedString + Fields to put in sections RTET rtet WhitespaceMinimizedString + Fields to put in sections RTIO rtio WhitespaceMinimizedString + Fields to put in sections A2C a2c WhitespaceMinimizedString + Fields to put in sections CAMC camc WhitespaceMinimizedString + Fields to put in sections CAMK camk WhitespaceMinimizedString + Fields to put in sections CAMP camp WhitespaceMinimizedString + Fields to put in sections CAZM cazm WhitespaceMinimizedString + Fields to put in sections CCEP ccep WhitespaceMinimizedString + Fields to put in sections CCHL cchl WhitespaceMinimizedString + Fields to put in sections CCIP ccip WhitespaceMinimizedString + Fields to put in sections CCRO ccro WhitespaceMinimizedString + Fields to put in sections CFOX cfox WhitespaceMinimizedString + Fields to put in sections CGEN cgen WhitespaceMinimizedString + Fields to put in sections CKAN ckan WhitespaceMinimizedString + Fields to put in sections CMEM cmem WhitespaceMinimizedString + Fields to put in sections CNAL cnal WhitespaceMinimizedString + Fields to put in sections CSSS csss WhitespaceMinimizedString + Fields to put in sections CSTR cstr WhitespaceMinimizedString + Fields to put in sections CSXT csxt WhitespaceMinimizedString + Fields to put in sections CTET ctet WhitespaceMinimizedString + Fields to put in sections CTIO ctio WhitespaceMinimizedString + Fields to put in sections STHY_TESTSRC_ID sthy_testsrc_id WhitespaceMinimizedString + Fields to put in sections WINN_TESTSRC_ID winn_testsrc_id WhitespaceMinimizedString + Fields to put in sections GUEL_TESTSRC_ID guel_testsrc_id WhitespaceMinimizedString + Fields to put in sections RCIP_DANMAP rcip_danmap WhitespaceMinimizedString + Fields to put in sections EPIDATESTAMP_1 epidatestamp_1 WhitespaceMinimizedString + Fields to put in sections ACSSUT acssut WhitespaceMinimizedString + Fields to put in sections AKSSUT akssut WhitespaceMinimizedString + Fields to put in sections ACKSSUT ackssut WhitespaceMinimizedString + Fields to put in sections MDR_A_SSUT mdr_a_ssut WhitespaceMinimizedString + Fields to put in sections EXCLUSION exclusion WhitespaceMinimizedString + Fields to put in sections RAMINOGLY raminogly WhitespaceMinimizedString + Fields to put in sections RBETALACTAM rbetalactam WhitespaceMinimizedString + Fields to put in sections RQUINOLONES rquinolones WhitespaceMinimizedString + Fields to put in sections RFOLINHIBITOR rfolinhibitor WhitespaceMinimizedString + Fields to put in sections MDR mdr WhitespaceMinimizedString + Fields to put in sections specimen_number specimen_number WhitespaceMinimizedString + Fields to put in sections EXTERNAL_AGENT external_agent WhitespaceMinimizedString + Fields to put in sections FARM_FLAG farm_flag WhitespaceMinimizedString + Fields to put in sections AMIKACINGELET amikacingelet WhitespaceMinimizedString \ No newline at end of file From bfa561476dfa2f18df2810dfb4bc4a151c760c42 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 9 Oct 2024 14:03:07 -0700 Subject: [PATCH 54/96] phacDexa version bump --- web/templates/phac_dexa/schema.json | 4 ++-- web/templates/phac_dexa/schema.yaml | 4 ++-- web/templates/phac_dexa/schema_core.yaml | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/web/templates/phac_dexa/schema.json b/web/templates/phac_dexa/schema.json index 7d087bd3..5573d6c6 100644 --- a/web/templates/phac_dexa/schema.json +++ b/web/templates/phac_dexa/schema.json @@ -1,8 +1,8 @@ { - "name": "PHAC_Dexa", + "name": "PHACDexa", "description": "", "id": "https://example.com/PHAC_Dexa", - "version": "1.0.0", + "version": "1.1.0", "prefixes": { "linkml": { "prefix_prefix": "linkml", diff --git a/web/templates/phac_dexa/schema.yaml b/web/templates/phac_dexa/schema.yaml index cad62978..b413bb39 100644 --- a/web/templates/phac_dexa/schema.yaml +++ b/web/templates/phac_dexa/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/PHAC_Dexa -name: PHAC_Dexa +name: PHACDexa description: '' -version: 1.0.0 +version: 1.1.0 imports: - linkml:types prefixes: diff --git a/web/templates/phac_dexa/schema_core.yaml b/web/templates/phac_dexa/schema_core.yaml index fb48e081..6c808a00 100644 --- a/web/templates/phac_dexa/schema_core.yaml +++ b/web/templates/phac_dexa/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/PHAC_Dexa -name: "PHAC_Dexa" +name: "PHACDexa" description: "" -version: 1.0.0 +version: 1.1.0 imports: - 'linkml:types' prefixes: From d92284df42943605af1ceef29a31b813cffc81ce Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Wed, 9 Oct 2024 14:04:52 -0700 Subject: [PATCH 55/96] CanCOGeN name field adjustments, and French schema update --- .../canada_covid19/locales/fr/schema.json | 9097 ++++++++--------- .../canada_covid19/locales/fr/schema.yaml | 5773 ++++------- web/templates/canada_covid19/schema.json | 5841 ++++++++--- web/templates/canada_covid19/schema.yaml | 1632 +-- web/templates/canada_covid19/schema_core.yaml | 7 +- web/templates/canada_covid19/schema_enums.tsv | 2425 ++--- web/templates/canada_covid19/schema_slots.tsv | 324 +- 7 files changed, 12722 insertions(+), 12377 deletions(-) diff --git a/web/templates/canada_covid19/locales/fr/schema.json b/web/templates/canada_covid19/locales/fr/schema.json index e2bbe878..1d2a66ed 100644 --- a/web/templates/canada_covid19/locales/fr/schema.json +++ b/web/templates/canada_covid19/locales/fr/schema.json @@ -3,7 +3,7 @@ "description": "", "in_language": "fr", "id": "https://example.com/CanCOGeN_Covid-19", - "version": "2.3.4", + "version": "2.4.0", "imports": [ "linkml:types" ], @@ -37,6326 +37,3853 @@ } }, "enums": { - "umbrella bioproject accession menu": { - "name": "umbrella bioproject accession menu", - "title": "menu d'adhésion au bioprojet parapluie", + "UmbrellaBioprojectAccessionMenu": { + "name": "UmbrellaBioprojectAccessionMenu", + "title": "Menu « Accès au bioprojet cadre »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "PRJNA623807": { - "text": "PRJNA623807", - "title": "PRJNA623807" + "day 1": { + "text": "day 1", + "title": "Jour 1" + }, + "day 8": { + "text": "day 8", + "title": "Jour 8" + }, + "day 10": { + "text": "day 10", + "title": "Jour 10" } } }, - "null value menu": { - "name": "null value menu", - "title": "menu de valeur nulle", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "Menu « Valeur nulle »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Not Applicable": { "text": "Not Applicable", - "meaning": "GENEPIO:0001619", - "title": "Non applicable" + "title": "Sans objet" }, "Missing": { "text": "Missing", - "meaning": "GENEPIO:0001618", - "title": "Manquant" + "title": "Manquante" }, "Not Collected": { "text": "Not Collected", - "meaning": "GENEPIO:0001620", - "title": "Non collecté" + "title": "Non prélevée" }, "Not Provided": { "text": "Not Provided", - "meaning": "GENEPIO:0001668", - "title": "Non fourni" + "title": "Non fournie" }, "Restricted Access": { "text": "Restricted Access", - "meaning": "GENEPIO:0001810", "title": "Accès restreint" } } }, - "geo_loc_name (state/province/territory) menu": { - "name": "geo_loc_name (state/province/territory) menu", - "title": "menu geo_loc_name (état/province/territoire)", + "GeoLocNameStateProvinceTerritoryMenu": { + "name": "GeoLocNameStateProvinceTerritoryMenu", + "title": "Menu « nom_lieu_géo (état/province/territoire) »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Alberta": { - "text": "Alberta", - "meaning": "GAZ:00002566", - "title": "Alberta" - }, "British Columbia": { "text": "British Columbia", - "meaning": "GAZ:00002562", - "title": "Colombie Britannique" - }, - "Manitoba": { - "text": "Manitoba", - "meaning": "GAZ:00002571", - "title": "Manitoba" + "title": "Colombie-Britannique" }, "New Brunswick": { "text": "New Brunswick", - "meaning": "GAZ:00002570", "title": "Nouveau-Brunswick" }, "Newfoundland and Labrador": { "text": "Newfoundland and Labrador", - "meaning": "GAZ:00002567", - "title": "Terre-Neuve et Labrador" + "title": "Terre-Neuve-et-Labrador" }, "Northwest Territories": { "text": "Northwest Territories", - "meaning": "GAZ:00002575", "title": "Territoires du Nord-Ouest" }, "Nova Scotia": { "text": "Nova Scotia", - "meaning": "GAZ:00002565", "title": "Nouvelle-Écosse" }, - "Nunavut": { - "text": "Nunavut", - "meaning": "GAZ:00002574", - "title": "Nunavut" - }, - "Ontario": { - "text": "Ontario", - "meaning": "GAZ:00002563", - "title": "Ontario (en anglais)" - }, "Prince Edward Island": { "text": "Prince Edward Island", - "meaning": "GAZ:00002572", "title": "Île-du-Prince-Édouard" }, "Quebec": { "text": "Quebec", - "meaning": "GAZ:00002569", "title": "Québec" - }, - "Saskatchewan": { - "text": "Saskatchewan", - "meaning": "GAZ:00002564", - "title": "Saskatchewan" - }, - "Yukon": { - "text": "Yukon", - "meaning": "GAZ:00002576", - "title": "Yukon" } } }, - "host age unit menu": { - "name": "host age unit menu", - "title": "menu de l'unité d'âge de l'hôte", + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "Menu « Groupe d’âge de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "month": { "text": "month", - "meaning": "UO:0000035", - "title": "mois" + "title": "Mois" }, "year": { "text": "year", - "meaning": "UO:0000036", - "title": "année" + "title": "Année" } } }, - "sample collection date precision menu": { - "name": "sample collection date precision menu", - "title": "menu de précision de la date de prélèvement des échantillons", + "SampleCollectionDatePrecisionMenu": { + "name": "SampleCollectionDatePrecisionMenu", + "title": "Menu « Précision de la date de prélèvement des échantillons »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "year": { "text": "year", - "meaning": "UO:0000036", - "title": "année" + "title": "Année" }, "month": { "text": "month", - "meaning": "UO:0000035", - "title": "mois" + "title": "Mois" }, "day": { "text": "day", - "meaning": "UO:0000033", - "title": "jour" + "title": "Jour" } } }, - "biomaterial extracted menu": { - "name": "biomaterial extracted menu", - "title": "menu extrait des biomatériaux", + "BiomaterialExtractedMenu": { + "name": "BiomaterialExtractedMenu", + "title": "Menu « Biomatériaux extraits »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "RNA (total)": { "text": "RNA (total)", - "meaning": "OBI:0000895", - "title": "RNA (total)" + "title": "ARN (total)" }, "RNA (poly-A)": { "text": "RNA (poly-A)", - "meaning": "OBI:0000869", - "title": "RNA (poly-A)" + "title": "ARN (poly-A)" }, "RNA (ribo-depleted)": { "text": "RNA (ribo-depleted)", - "meaning": "OBI:0002627", - "title": "RNA (appauvri en ribo)" + "title": "ARN (déplétion ribosomique)" }, "mRNA (messenger RNA)": { "text": "mRNA (messenger RNA)", - "meaning": "GENEPIO:0100104", - "title": "mRNA (messager RNA)" + "title": "ARNm (ARN messager)" }, "mRNA (cDNA)": { "text": "mRNA (cDNA)", - "meaning": "OBI:0002754", - "title": "mRNA (cDNA)" + "title": "ARNm (ADNc)" } } }, - "signs and symptoms menu": { - "name": "signs and symptoms menu", - "title": "menu des signes et symptômes", + "SignsAndSymptomsMenu": { + "name": "SignsAndSymptomsMenu", + "title": "Menu « Signes et symptômes »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Abnormal lung auscultation": { "text": "Abnormal lung auscultation", - "meaning": "HP:0030829", "title": "Auscultation pulmonaire anormale" }, "Abnormality of taste sensation": { "text": "Abnormality of taste sensation", - "meaning": "HP:0000223", "title": "Anomalie de la sensation gustative" }, "Ageusia (complete loss of taste)": { "text": "Ageusia (complete loss of taste)", - "meaning": "HP:0041051", - "is_a": "Abnormality of taste sensation", - "title": "Ageusia (perte totale du goût)" + "title": "Agueusie (perte totale du goût)" }, "Parageusia (distorted sense of taste)": { "text": "Parageusia (distorted sense of taste)", - "meaning": "HP:0031249", - "is_a": "Abnormality of taste sensation", - "title": "Parageusie (déformation du goût)" + "title": "Paragueusie (distorsion du goût)" }, "Hypogeusia (reduced sense of taste)": { "text": "Hypogeusia (reduced sense of taste)", - "meaning": "HP:0000224", - "is_a": "Abnormality of taste sensation", - "title": "Hypogeusie (diminution du sens du goût)" + "title": "Hypogueusie (diminution du goût)" }, "Abnormality of the sense of smell": { "text": "Abnormality of the sense of smell", - "meaning": "HP:0004408", - "title": "Abnormality of the sense of smell" + "title": "Anomalie de l’odorat" }, "Anosmia (lost sense of smell)": { "text": "Anosmia (lost sense of smell)", - "meaning": "HP:0000458", - "is_a": "Abnormality of the sense of smell", - "title": "Anosmie (perte d'odorat)" + "title": "Anosmie (perte de l’odorat)" }, "Hyposmia (reduced sense of smell)": { "text": "Hyposmia (reduced sense of smell)", - "meaning": "HP:0004409", - "is_a": "Abnormality of the sense of smell", - "title": "Hyposmie (diminution de l'odorat)" + "title": "Hyposmie (diminution de l’odorat)" }, "Acute Respiratory Distress Syndrome": { "text": "Acute Respiratory Distress Syndrome", - "meaning": "HP:0033677", - "title": "Syndrome de détresse respiratoire aiguë", - "exact_mappings": [ - "CNPHI:ARDS" - ] + "title": "Syndrome de détresse respiratoire aiguë" }, "Altered mental status": { "text": "Altered mental status", - "meaning": "HP:0011446", - "title": "Altération de l'état mental" + "title": "Altération de l’état mental" }, "Cognitive impairment": { "text": "Cognitive impairment", - "meaning": "HP:0100543", - "is_a": "Altered mental status", - "title": "Troubles cognitifs" - }, - "Coma": { - "text": "Coma", - "meaning": "HP:0001259", - "is_a": "Altered mental status", - "title": "Coma" - }, - "Confusion": { - "text": "Confusion", - "meaning": "HP:0001289", - "is_a": "Altered mental status", - "title": "la confusion" + "title": "Déficit cognitif" }, "Delirium (sudden severe confusion)": { "text": "Delirium (sudden severe confusion)", - "meaning": "HP:0031258", - "is_a": "Confusion", "title": "Délire (confusion grave et soudaine)" }, "Inability to arouse (inability to stay awake)": { "text": "Inability to arouse (inability to stay awake)", - "meaning": "GENEPIO:0100061", - "is_a": "Altered mental status", "title": "Incapacité à se réveiller (incapacité à rester éveillé)" }, "Irritability": { "text": "Irritability", - "meaning": "HP:0000737", - "is_a": "Altered mental status", "title": "Irritabilité" }, "Loss of speech": { "text": "Loss of speech", - "meaning": "HP:0002371", - "is_a": "Altered mental status", "title": "Perte de la parole" }, "Arrhythmia": { "text": "Arrhythmia", - "meaning": "HP:0011675", "title": "Arythmie" }, "Asthenia (generalized weakness)": { "text": "Asthenia (generalized weakness)", - "meaning": "HP:0025406", "title": "Asthénie (faiblesse généralisée)" }, "Chest tightness or pressure": { "text": "Chest tightness or pressure", - "meaning": "HP:0031352", "title": "Oppression ou pression thoracique" }, "Rigors (fever shakes)": { "text": "Rigors (fever shakes)", - "meaning": "HP:0025145", - "is_a": "Chest tightness or pressure", - "title": "Rigidité (tremblements de fièvre)" + "title": "Frissons solennels (tremblements de fièvre)" }, "Chills (sudden cold sensation)": { "text": "Chills (sudden cold sensation)", - "meaning": "HP:0025143", - "title": "Frissons (sensation soudaine de froid)", - "exact_mappings": [ - "CNPHI:Chills" - ] + "title": "Frissons (sensation soudaine de froid)" }, "Conjunctival injection": { "text": "Conjunctival injection", - "meaning": "HP:0030953", "title": "Injection conjonctivale" }, "Conjunctivitis (pink eye)": { "text": "Conjunctivitis (pink eye)", - "meaning": "HP:0000509", - "title": "Conjonctivite (œil rose)", - "exact_mappings": [ - "CNPHI:Conjunctivitis" - ] + "title": "Conjonctivite (yeux rouges)" }, "Coryza (rhinitis)": { "text": "Coryza (rhinitis)", - "meaning": "MP:0001867", "title": "Coryza (rhinite)" }, "Cough": { "text": "Cough", - "meaning": "HP:0012735", "title": "Toux" }, "Nonproductive cough (dry cough)": { "text": "Nonproductive cough (dry cough)", - "meaning": "HP:0031246", - "is_a": "Cough", - "title": "Toux non productive (toux sèche)" + "title": "Toux improductive (toux sèche)" }, "Productive cough (wet cough)": { "text": "Productive cough (wet cough)", - "meaning": "HP:0031245", - "is_a": "Cough", "title": "Toux productive (toux grasse)" }, "Cyanosis (blueish skin discolouration)": { "text": "Cyanosis (blueish skin discolouration)", - "meaning": "HP:0000961", "title": "Cyanose (coloration bleuâtre de la peau)" }, "Acrocyanosis": { "text": "Acrocyanosis", - "meaning": "HP:0001063", - "is_a": "Cyanosis (blueish skin discolouration)", "title": "Acrocyanose" }, "Circumoral cyanosis (bluish around mouth)": { "text": "Circumoral cyanosis (bluish around mouth)", - "meaning": "HP:0032556", - "is_a": "Acrocyanosis", - "title": "Cyanose circulatoire (bleuâtre autour de la bouche)" + "title": "Cyanose péribuccale (bleuâtre autour de la bouche)" }, "Cyanotic face (bluish face)": { "text": "Cyanotic face (bluish face)", - "meaning": "GENEPIO:0100062", - "is_a": "Acrocyanosis", "title": "Visage cyanosé (visage bleuâtre)" }, "Central Cyanosis": { "text": "Central Cyanosis", - "meaning": "GENEPIO:0100063", - "is_a": "Cyanosis (blueish skin discolouration)", "title": "Cyanose centrale" }, "Cyanotic lips (bluish lips)": { "text": "Cyanotic lips (bluish lips)", - "meaning": "GENEPIO:0100064", - "is_a": "Central Cyanosis", "title": "Lèvres cyanosées (lèvres bleutées)" }, "Peripheral Cyanosis": { "text": "Peripheral Cyanosis", - "meaning": "GENEPIO:0100065", - "is_a": "Cyanosis (blueish skin discolouration)", "title": "Cyanose périphérique" }, "Dyspnea (breathing difficulty)": { "text": "Dyspnea (breathing difficulty)", - "meaning": "HP:0002094", "title": "Dyspnée (difficulté à respirer)" }, "Diarrhea (watery stool)": { "text": "Diarrhea (watery stool)", - "meaning": "HP:0002014", - "title": "Diarrhée (selles liquides)", - "exact_mappings": [ - "CNPHI:Diarrhea%2C%20watery" - ] + "title": "Diarrhée (selles aqueuses)" }, "Dry gangrene": { "text": "Dry gangrene", - "meaning": "MP:0031127", "title": "Gangrène sèche" }, "Encephalitis (brain inflammation)": { "text": "Encephalitis (brain inflammation)", - "meaning": "HP:0002383", - "title": "Encéphalite (inflammation du cerveau)", - "exact_mappings": [ - "CNPHI:Encephalitis" - ] + "title": "Encéphalite (inflammation du cerveau)" }, "Encephalopathy": { "text": "Encephalopathy", - "meaning": "HP:0001298", "title": "Encéphalopathie" }, "Fatigue (tiredness)": { "text": "Fatigue (tiredness)", - "meaning": "HP:0012378", - "title": "Fatigue", - "exact_mappings": [ - "CNPHI:Fatigue" - ] + "title": "Fatigue" }, "Fever": { "text": "Fever", - "meaning": "HP:0001945", "title": "Fièvre" }, "Fever (>=38°C)": { "text": "Fever (>=38°C)", - "meaning": "GENEPIO:0100066", - "is_a": "Fever", - "title": "Fièvre (>=38°C)", - "exact_mappings": [ - "CNPHI:Fever" - ] + "title": "Fièvre (>= 38 °C)" }, "Glossitis (inflammation of the tongue)": { "text": "Glossitis (inflammation of the tongue)", - "meaning": "HP:0000206", - "title": "Glossiose (inflammation de la langue)" + "title": "Glossite (inflammation de la langue)" }, "Ground Glass Opacities (GGO)": { "text": "Ground Glass Opacities (GGO)", - "meaning": "GENEPIO:0100067", - "title": "Opacités de verre dépoli" + "title": "Hyperdensité en verre dépoli" }, "Headache": { "text": "Headache", - "meaning": "HP:0002315", - "title": "Maux de tête" + "title": "Mal de tête" }, "Hemoptysis (coughing up blood)": { "text": "Hemoptysis (coughing up blood)", - "meaning": "HP:0002105", - "title": "Hémoptysie (toux de sang)" + "title": "Hémoptysie (toux accompagnée de sang)" }, "Hypocapnia": { "text": "Hypocapnia", - "meaning": "HP:0012417", "title": "Hypocapnie" }, "Hypotension (low blood pressure)": { "text": "Hypotension (low blood pressure)", - "meaning": "HP:0002615", - "title": "Hypotension (baisse de la tension artérielle)" + "title": "Hypotension (tension artérielle basse)" }, "Hypoxemia (low blood oxygen)": { "text": "Hypoxemia (low blood oxygen)", - "meaning": "HP:0012418", - "title": "Hypoxémie (manque d'oxygène dans le sang)" + "title": "Hypoxémie (manque d’oxygène dans le sang)" }, "Silent hypoxemia": { "text": "Silent hypoxemia", - "meaning": "GENEPIO:0100068", - "is_a": "Hypoxemia (low blood oxygen)", "title": "Hypoxémie silencieuse" }, "Internal hemorrhage (internal bleeding)": { "text": "Internal hemorrhage (internal bleeding)", - "meaning": "HP:0011029", - "title": "Hémorragie interne (saignement interne)" + "title": "Hémorragie interne" }, "Loss of Fine Movements": { "text": "Loss of Fine Movements", - "meaning": "NCIT:C121416", "title": "Perte de mouvements fins" }, "Low appetite": { "text": "Low appetite", - "meaning": "HP:0004396", - "title": "Manque d'appétit" + "title": "Perte d’appétit" }, "Malaise (general discomfort/unease)": { "text": "Malaise (general discomfort/unease)", - "meaning": "HP:0033834", "title": "Malaise (malaise général)" }, "Meningismus/nuchal rigidity": { "text": "Meningismus/nuchal rigidity", - "meaning": "HP:0031179", - "title": "Méningisme/rigidité nucale" + "title": "Méningisme/Raideur de la nuque" }, "Muscle weakness": { "text": "Muscle weakness", - "meaning": "HP:0001324", "title": "Faiblesse musculaire" }, "Nasal obstruction (stuffy nose)": { "text": "Nasal obstruction (stuffy nose)", - "meaning": "HP:0001742", "title": "Obstruction nasale (nez bouché)" }, "Nausea": { "text": "Nausea", - "meaning": "HP:0002018", "title": "Nausées" }, "Nose bleed": { "text": "Nose bleed", - "meaning": "HP:0000421", "title": "Saignement de nez" }, "Otitis": { "text": "Otitis", - "meaning": "GENEPIO:0100069", "title": "Otite" }, "Pain": { "text": "Pain", - "meaning": "HP:0012531", "title": "Douleur" }, "Abdominal pain": { "text": "Abdominal pain", - "meaning": "HP:0002027", - "is_a": "Pain", "title": "Douleur abdominale" }, "Arthralgia (painful joints)": { "text": "Arthralgia (painful joints)", - "meaning": "HP:0002829", - "is_a": "Pain", "title": "Arthralgie (articulations douloureuses)" }, "Chest pain": { "text": "Chest pain", - "meaning": "HP:0100749", - "is_a": "Pain", "title": "Douleur thoracique" }, "Pleuritic chest pain": { "text": "Pleuritic chest pain", - "meaning": "HP:0033771", - "is_a": "Chest pain", "title": "Douleur thoracique pleurétique" }, "Myalgia (muscle pain)": { "text": "Myalgia (muscle pain)", - "meaning": "HP:0003326", - "is_a": "Pain", "title": "Myalgie (douleur musculaire)" }, "Pharyngitis (sore throat)": { "text": "Pharyngitis (sore throat)", - "meaning": "HP:0025439", "title": "Pharyngite (mal de gorge)" }, "Pharyngeal exudate": { "text": "Pharyngeal exudate", - "meaning": "GENEPIO:0100070", "title": "Exsudat pharyngé" }, "Pleural effusion": { "text": "Pleural effusion", - "meaning": "HP:0002202", "title": "Épanchement pleural" }, "Pneumonia": { "text": "Pneumonia", - "meaning": "HP:0002090", "title": "Pneumonie" }, "Pseudo-chilblains": { "text": "Pseudo-chilblains", - "meaning": "HP:0033696", - "title": "Pseudo-chilblains" + "title": "Pseudo-engelures" }, "Pseudo-chilblains on fingers (covid fingers)": { "text": "Pseudo-chilblains on fingers (covid fingers)", - "meaning": "GENEPIO:0100072", - "is_a": "Pseudo-chilblains", - "title": "Pseudo-griffes des doigts (doigts covides)" + "title": "Pseudo-engelures sur les doigts (doigts de la COVID)" }, "Pseudo-chilblains on toes (covid toes)": { "text": "Pseudo-chilblains on toes (covid toes)", - "meaning": "GENEPIO:0100073", - "is_a": "Pseudo-chilblains", - "title": "Pseudo-chilblains sur les orteils (covid toes)" + "title": "Pseudo-engelures sur les orteils (orteils de la COVID)" }, "Rash": { "text": "Rash", - "meaning": "HP:0000988", "title": "Éruption cutanée" }, "Rhinorrhea (runny nose)": { "text": "Rhinorrhea (runny nose)", - "meaning": "HP:0031417", "title": "Rhinorrhée (écoulement nasal)" }, "Seizure": { "text": "Seizure", - "meaning": "HP:0001250", - "title": "Crise d'épilepsie" + "title": "Crise d’épilepsie" }, "Motor seizure": { "text": "Motor seizure", - "meaning": "HP:0020219", - "is_a": "Seizure", "title": "Crise motrice" }, "Shivering (involuntary muscle twitching)": { "text": "Shivering (involuntary muscle twitching)", - "meaning": "HP:0025144", - "title": "Frissons (contractions musculaires involontaires)" + "title": "Tremblement (contractions musculaires involontaires)" }, "Slurred speech": { "text": "Slurred speech", - "meaning": "HP:0001350", - "title": "Troubles de l'élocution" + "title": "Troubles de l’élocution" }, "Sneezing": { "text": "Sneezing", - "meaning": "HP:0025095", - "title": "Éternuement" + "title": "Éternuements" }, "Sputum Production": { "text": "Sputum Production", - "meaning": "HP:0033709", - "title": "Production d'expectorations" + "title": "Production d’expectoration" }, "Stroke": { "text": "Stroke", - "meaning": "HP:0001297", "title": "Accident vasculaire cérébral" }, "Swollen Lymph Nodes": { "text": "Swollen Lymph Nodes", - "meaning": "HP:0002716", - "title": "Ganglions lymphatiques gonflés" + "title": "Ganglions lymphatiques enflés" }, "Tachypnea (accelerated respiratory rate)": { "text": "Tachypnea (accelerated respiratory rate)", - "meaning": "HP:0002789", - "title": "Tachypnée (accélération de la fréquence respiratoire)" + "title": "Tachypnée (fréquence respiratoire accélérée)" }, "Vertigo (dizziness)": { "text": "Vertigo (dizziness)", - "meaning": "HP:0002321", "title": "Vertige (étourdissement)" }, "Vomiting (throwing up)": { "text": "Vomiting (throwing up)", - "meaning": "HP:0002013", - "title": "Vomissements (vomissements)" + "title": "Vomissements" } } }, - "host vaccination status menu": { - "name": "host vaccination status menu", - "title": "menu du statut de vaccination de l'hôte", + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "Menu « Statut de vaccination de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Fully Vaccinated": { "text": "Fully Vaccinated", - "meaning": "GENEPIO:0100100", - "title": "Vaccination complète" + "title": "Entièrement vacciné" }, "Partially Vaccinated": { "text": "Partially Vaccinated", - "meaning": "GENEPIO:0100101", "title": "Partiellement vacciné" }, "Not Vaccinated": { "text": "Not Vaccinated", - "meaning": "GENEPIO:0100102", "title": "Non vacciné" } } }, - "prior SARS-CoV-2 antiviral treatment menu": { - "name": "prior SARS-CoV-2 antiviral treatment menu", - "title": "menu de traitement antiviral antérieur contre le SARS-CoV-2", + "PriorSarsCov2AntiviralTreatmentMenu": { + "name": "PriorSarsCov2AntiviralTreatmentMenu", + "title": "Menu « Traitement antiviral contre une infection antérieure par le SRAS-CoV-2 »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Prior antiviral treatment": { "text": "Prior antiviral treatment", - "meaning": "GENEPIO:0100037", "title": "Traitement antiviral antérieur" }, "No prior antiviral treatment": { "text": "No prior antiviral treatment", - "meaning": "GENEPIO:0100233", - "title": "Pas de traitement antiviral antérieur" + "title": "Aucun traitement antiviral antérieur" } } }, - "NML submitted specimen type menu": { - "name": "NML submitted specimen type menu", - "title": "Menu des types d'échantillons soumis au NML", + "NmlSubmittedSpecimenTypeMenu": { + "name": "NmlSubmittedSpecimenTypeMenu", + "title": "Menu « Types d’échantillons soumis au LNM »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Swab": { "text": "Swab", - "meaning": "OBI:0002600", "title": "Écouvillon" }, "RNA": { "text": "RNA", - "meaning": "OBI:0000880", - "title": "RNA" + "title": "ARN" }, "mRNA (cDNA)": { "text": "mRNA (cDNA)", - "meaning": "OBI:0002754", - "title": "mRNA (cDNA)" + "title": "ARNm (ADNc)" }, "Nucleic acid": { "text": "Nucleic acid", - "meaning": "OBI:0001010", "title": "Acide nucléique" }, "Not Applicable": { "text": "Not Applicable", - "meaning": "GENEPIO:0001619", "title": "Sans objet" } } }, - "Related specimen relationship type menu": { - "name": "Related specimen relationship type menu", - "title": "Menu des types de relations entre spécimens associés", + "RelatedSpecimenRelationshipTypeMenu": { + "name": "RelatedSpecimenRelationshipTypeMenu", + "title": "Menu « Types de relations entre spécimens associés »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Acute": { "text": "Acute", - "meaning": "HP:0011009", "title": "Infection aiguë" }, "Chronic (prolonged) infection investigation": { "text": "Chronic (prolonged) infection investigation", - "meaning": "GENEPIO:0101016", - "title": "Enquête sur l'infection chronique (prolongée)" + "title": "Enquête sur l’infection chronique (prolongée)" }, "Convalescent": { "text": "Convalescent", - "title": "Convalescent" + "title": "Phase de convalescence" }, "Familial": { "text": "Familial", - "title": "Familial" + "title": "Forme familiale" }, "Follow-up": { "text": "Follow-up", - "meaning": "EFO:0009642", "title": "Suivi" }, "Reinfection testing": { "text": "Reinfection testing", - "is_a": "Follow-up", "title": "Tests de réinfection" }, "Previously Submitted": { "text": "Previously Submitted", - "title": "Déjà soumis" + "title": "Soumis précédemment" }, "Sequencing/bioinformatics methods development/validation": { "text": "Sequencing/bioinformatics methods development/validation", - "title": "Développement/validation de méthodes de séquençage/bioinformatique" + "title": "Développement et validation de méthodes bioinformatiques ou de séquençage" }, "Specimen sampling methods testing": { "text": "Specimen sampling methods testing", - "title": "Test des méthodes d'échantillonnage des échantillons" + "title": "Essai des méthodes de prélèvement des échantillons" } } }, - "pre-existing conditions and risk factors menu": { - "name": "pre-existing conditions and risk factors menu", - "title": "Menu des conditions préexistantes et des facteurs de risque", + "PreExistingConditionsAndRiskFactorsMenu": { + "name": "PreExistingConditionsAndRiskFactorsMenu", + "title": "Menu « Conditions préexistantes et des facteurs de risque »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Age 60+": { "text": "Age 60+", - "meaning": "VO:0004925", "title": "60 ans et plus" }, "Anemia": { "text": "Anemia", - "meaning": "HP:0001903", "title": "Anémie" }, "Anorexia": { "text": "Anorexia", - "meaning": "HP:0002039", "title": "Anorexie" }, "Birthing labor": { "text": "Birthing labor", - "meaning": "NCIT:C92743", - "title": "Travail d'accouchement" + "title": "Travail ou accouchement" }, "Bone marrow failure": { "text": "Bone marrow failure", - "meaning": "NCIT:C80693", - "title": "Insuffisance de la moelle osseuse" - }, - "Cancer": { - "text": "Cancer", - "meaning": "MONDO:0004992", - "title": "Cancer" + "title": "Insuffisance médullaire" }, "Breast cancer": { "text": "Breast cancer", - "meaning": "MONDO:0007254", - "is_a": "Cancer", "title": "Cancer du sein" }, "Colorectal cancer": { "text": "Colorectal cancer", - "meaning": "MONDO:0005575", - "is_a": "Cancer", "title": "Cancer colorectal" }, "Hematologic malignancy (cancer of the blood)": { "text": "Hematologic malignancy (cancer of the blood)", - "meaning": "DOID:2531", - "is_a": "Cancer", - "title": "Hémopathie maligne (cancer du sang)" + "title": "Hématopathie maligne (cancer du sang)" }, "Lung cancer": { "text": "Lung cancer", - "meaning": "MONDO:0008903", - "is_a": "Cancer", "title": "Cancer du poumon" }, "Metastatic disease": { "text": "Metastatic disease", - "meaning": "MONDO:0024880", - "is_a": "Cancer", "title": "Maladie métastatique" }, "Cancer treatment": { "text": "Cancer treatment", - "meaning": "NCIT:C16212", "title": "Traitement du cancer" }, "Cancer surgery": { "text": "Cancer surgery", - "meaning": "NCIT:C157740", - "is_a": "Cancer treatment", - "title": "Chirurgie du cancer" + "title": "Chirurgie pour un cancer" }, "Chemotherapy": { "text": "Chemotherapy", - "meaning": "NCIT:C15632", - "is_a": "Cancer treatment", "title": "Chimiothérapie" }, "Adjuvant chemotherapy": { "text": "Adjuvant chemotherapy", - "meaning": "NCIT:C15360", - "is_a": "Chemotherapy", "title": "Chimiothérapie adjuvante" }, "Cardiac disorder": { "text": "Cardiac disorder", - "meaning": "NCIT:C3079", - "title": "Troubles cardiaques" + "title": "Trouble cardiaque" }, "Arrhythmia": { "text": "Arrhythmia", - "meaning": "HP:0011675", - "is_a": "Cardiac disorder", "title": "Arythmie" }, "Cardiac disease": { "text": "Cardiac disease", - "meaning": "MONDO:0005267", - "is_a": "Cardiac disorder", "title": "Maladie cardiaque" }, "Cardiomyopathy": { "text": "Cardiomyopathy", - "meaning": "HP:0001638", - "is_a": "Cardiac disorder", - "title": "Cardiomyopathie" + "title": "Myocardiopathie" }, "Cardiac injury": { "text": "Cardiac injury", - "meaning": "GENEPIO:0100074", - "is_a": "Cardiac disorder", "title": "Lésion cardiaque" }, "Hypertension (high blood pressure)": { "text": "Hypertension (high blood pressure)", - "meaning": "HP:0000822", - "is_a": "Cardiac disorder", - "title": "Hypertension (pression artérielle élevée)" + "title": "Hypertension (tension artérielle élevée)" }, "Hypotension (low blood pressure)": { "text": "Hypotension (low blood pressure)", - "meaning": "HP:0002615", - "is_a": "Cardiac disorder", - "title": "Hypotension (pression artérielle basse)" + "title": "Hypotension (tension artérielle basse)" }, "Cesarean section": { "text": "Cesarean section", - "meaning": "HP:0011410", "title": "Césarienne" }, "Chronic cough": { "text": "Chronic cough", - "meaning": "GENEPIO:0100075", "title": "Toux chronique" }, "Chronic gastrointestinal disease": { "text": "Chronic gastrointestinal disease", - "meaning": "GENEPIO:0100076", "title": "Maladie gastro-intestinale chronique" }, "Chronic lung disease": { "text": "Chronic lung disease", - "meaning": "HP:0006528", - "is_a": "Lung disease", "title": "Maladie pulmonaire chronique" }, "Corticosteroids": { "text": "Corticosteroids", - "meaning": "NCIT:C211", "title": "Corticostéroïdes" }, "Diabetes mellitus (diabetes)": { "text": "Diabetes mellitus (diabetes)", - "meaning": "HP:0000819", "title": "Diabète sucré (diabète)" }, "Type I diabetes mellitus (T1D)": { "text": "Type I diabetes mellitus (T1D)", - "meaning": "HP:0100651", - "is_a": "Diabetes mellitus (diabetes)", - "title": "Diabète de type I (T1D)" + "title": "Diabète sucré de type I" }, "Type II diabetes mellitus (T2D)": { "text": "Type II diabetes mellitus (T2D)", - "meaning": "HP:0005978", - "is_a": "Diabetes mellitus (diabetes)", - "title": "Diabète sucré de type II (T2D)" + "title": "Diabète sucré de type II" }, "Eczema": { "text": "Eczema", - "meaning": "HP:0000964", "title": "Eczéma" }, "Electrolyte disturbance": { "text": "Electrolyte disturbance", - "meaning": "HP:0003111", - "title": "Perturbation de l'équilibre électrolytique" + "title": "Perturbation de l’équilibre électrolytique" }, "Hypocalcemia": { "text": "Hypocalcemia", - "meaning": "HP:0002901", - "is_a": "Electrolyte disturbance", "title": "Hypocalcémie" }, "Hypokalemia": { "text": "Hypokalemia", - "meaning": "HP:0002900", - "is_a": "Electrolyte disturbance", "title": "Hypokaliémie" }, "Hypomagnesemia": { "text": "Hypomagnesemia", - "meaning": "HP:0002917", - "is_a": "Electrolyte disturbance", "title": "Hypomagnésémie" }, "Encephalitis (brain inflammation)": { "text": "Encephalitis (brain inflammation)", - "meaning": "HP:0002383", "title": "Encéphalite (inflammation du cerveau)" }, "Epilepsy": { "text": "Epilepsy", - "meaning": "MONDO:0005027", - "title": "Epilepsie" + "title": "Épilepsie" }, "Hemodialysis": { "text": "Hemodialysis", - "meaning": "NCIT:C15248", "title": "Hémodialyse" }, "Hemoglobinopathy": { "text": "Hemoglobinopathy", - "meaning": "MONDO:0044348", "title": "Hémoglobinopathie" }, "Human immunodeficiency virus (HIV)": { "text": "Human immunodeficiency virus (HIV)", - "meaning": "MONDO:0005109", - "title": "Virus de l'immunodéficience humaine" + "title": "Virus de l’immunodéficience humaine (VIH)" }, "Acquired immunodeficiency syndrome (AIDS)": { "text": "Acquired immunodeficiency syndrome (AIDS)", - "meaning": "MONDO:0012268", - "is_a": "Human immunodeficiency virus (HIV)", - "title": "Syndrome d'immunodéficience acquise" + "title": "Syndrome d’immunodéficience acquise (SIDA)" }, "HIV and antiretroviral therapy (ART)": { "text": "HIV and antiretroviral therapy (ART)", - "meaning": "NCIT:C16118", - "is_a": "Human immunodeficiency virus (HIV)", - "title": "HIV et thérapie antirétrovirale" + "title": "VIH et traitement antirétroviral" }, "Immunocompromised": { "text": "Immunocompromised", - "meaning": "NCIT:C14139", - "title": "Immunodéprimés" - }, - "Lupus": { - "text": "Lupus", - "meaning": "MONDO:0004670", - "is_a": "Immunocompromised", - "title": "Lupus" + "title": "Immunodéficience" }, "Inflammatory bowel disease (IBD)": { "text": "Inflammatory bowel disease (IBD)", - "meaning": "MONDO:0005265", - "title": "Maladie inflammatoire de l'intestin (MII)" + "title": "Maladie inflammatoire chronique de l’intestin (MICI)" }, "Colitis": { "text": "Colitis", - "meaning": "HP:0002583", - "is_a": "Inflammatory bowel disease (IBD)", "title": "Colite" }, "Ulcerative colitis": { "text": "Ulcerative colitis", - "meaning": "HP:0100279", - "is_a": "Colitis", "title": "Colite ulcéreuse" }, "Crohn's disease": { "text": "Crohn's disease", - "meaning": "HP:0100280", - "is_a": "Inflammatory bowel disease (IBD)", - "title": "la maladie de Crohn" + "title": "Maladie de Crohn" }, "Renal disorder": { "text": "Renal disorder", - "meaning": "NCIT:C3149", "title": "Trouble rénal" }, "Renal disease": { "text": "Renal disease", - "meaning": "MONDO:0005240", - "is_a": "Renal disorder", "title": "Maladie rénale" }, "Chronic renal disease": { "text": "Chronic renal disease", - "meaning": "HP:0012622", - "is_a": "Renal disease", "title": "Maladie rénale chronique" }, "Renal failure": { "text": "Renal failure", - "meaning": "HP:0000083", - "is_a": "Renal disease", "title": "Insuffisance rénale" }, "Liver disease": { "text": "Liver disease", - "meaning": "MONDO:0005154", "title": "Maladie du foie" }, "Chronic liver disease": { "text": "Chronic liver disease", - "meaning": "NCIT:C113609", - "is_a": "Liver disease", "title": "Maladie chronique du foie" }, + "Fatty liver disease (FLD)": { + "text": "Fatty liver disease (FLD)", + "title": "Stéatose hépatique" + }, "Myalgia (muscle pain)": { "text": "Myalgia (muscle pain)", - "meaning": "HP:0003326", "title": "Myalgie (douleur musculaire)" }, "Myalgic encephalomyelitis (chronic fatigue syndrome)": { "text": "Myalgic encephalomyelitis (chronic fatigue syndrome)", - "meaning": "MONDO:0005404", "title": "Encéphalomyélite myalgique (syndrome de fatigue chronique)" }, "Neurological disorder": { "text": "Neurological disorder", - "meaning": "MONDO:0005071", "title": "Trouble neurologique" }, "Neuromuscular disorder": { "text": "Neuromuscular disorder", - "meaning": "MONDO:0019056", - "is_a": "Neurological disorder", "title": "Trouble neuromusculaire" }, "Obesity": { "text": "Obesity", - "meaning": "HP:0001513", - "title": "L'obésité" + "title": "Obésité" }, "Severe obesity": { "text": "Severe obesity", - "meaning": "MONDO:0005139", - "is_a": "Obesity", "title": "Obésité sévère" }, "Respiratory disorder": { "text": "Respiratory disorder", - "meaning": "MONDO:0005087", - "title": "Troubles respiratoires" + "title": "Trouble respiratoire" }, "Asthma": { "text": "Asthma", - "meaning": "HP:0002099", - "is_a": "Respiratory disorder", "title": "Asthme" }, "Chronic bronchitis": { "text": "Chronic bronchitis", - "meaning": "HP:0004469", - "is_a": "Respiratory disorder", "title": "Bronchite chronique" }, "Chronic obstructive pulmonary disease": { "text": "Chronic obstructive pulmonary disease", - "meaning": "HP:0006510", - "is_a": "Respiratory disorder", "title": "Maladie pulmonaire obstructive chronique" }, "Emphysema": { "text": "Emphysema", - "meaning": "HP:0002097", - "is_a": "Respiratory disorder", "title": "Emphysème" }, "Lung disease": { "text": "Lung disease", - "meaning": "MONDO:0005275", - "is_a": "Respiratory disorder", "title": "Maladie pulmonaire" }, "Pulmonary fibrosis": { "text": "Pulmonary fibrosis", - "meaning": "HP:0002206", - "is_a": "Lung disease", "title": "Fibrose pulmonaire" }, "Pneumonia": { "text": "Pneumonia", - "meaning": "HP:0002090", - "is_a": "Respiratory disorder", "title": "Pneumonie" }, "Respiratory failure": { "text": "Respiratory failure", - "meaning": "HP:0002878", - "is_a": "Respiratory disorder", "title": "Insuffisance respiratoire" }, "Adult respiratory distress syndrome": { "text": "Adult respiratory distress syndrome", - "meaning": "HP:0033677", - "is_a": "Respiratory failure", - "title": "Syndrome de détresse respiratoire de l'adulte" + "title": "Syndrome de détresse respiratoire de l’adulte" }, "Newborn respiratory distress syndrome": { "text": "Newborn respiratory distress syndrome", - "meaning": "MONDO:0009971", - "is_a": "Respiratory failure", "title": "Syndrome de détresse respiratoire du nouveau-né" }, "Tuberculosis": { "text": "Tuberculosis", - "meaning": "MONDO:0018076", - "is_a": "Respiratory disorder", "title": "Tuberculose" }, "Postpartum (≤6 weeks)": { "text": "Postpartum (≤6 weeks)", - "meaning": "GENEPIO:0100077", - "title": "Post-partum (≤6 semaines)" + "title": "Post-partum (≤6 semaines)" }, "Pregnancy": { "text": "Pregnancy", - "meaning": "NCIT:C25742", "title": "Grossesse" }, "Rheumatic disease": { "text": "Rheumatic disease", - "meaning": "MONDO:0005554", "title": "Maladie rhumatismale" }, "Sickle cell disease": { "text": "Sickle cell disease", - "meaning": "MONDO:0011382", "title": "Drépanocytose" }, "Substance use": { "text": "Substance use", - "meaning": "NBO:0001845", - "title": "Consommation de substances psychoactives" + "title": "Consommation de substances" }, "Alcohol abuse": { "text": "Alcohol abuse", - "meaning": "MONDO:0002046", - "is_a": "Substance use", - "title": "Abus d'alcool" + "title": "Consommation abusive d’alcool" }, "Drug abuse": { "text": "Drug abuse", - "meaning": "GENEPIO:0100078", - "is_a": "Substance use", - "title": "Abus de drogues" + "title": "Consommation abusive de drogues" }, "Injection drug abuse": { "text": "Injection drug abuse", - "meaning": "GENEPIO:0100079", - "is_a": "Drug abuse", - "title": "Abus de drogues injectables" + "title": "Consommation abusive de drogues injectables" }, "Smoking": { "text": "Smoking", - "meaning": "NBO:0015005", - "is_a": "Substance use", - "title": "Fumer" + "title": "Tabagisme" }, "Vaping": { "text": "Vaping", - "meaning": "NCIT:C173621", - "is_a": "Substance use", - "title": "Vapoter" + "title": "Vapotage" }, "Tachypnea (accelerated respiratory rate)": { "text": "Tachypnea (accelerated respiratory rate)", - "meaning": "HP:0002789", - "title": "Tachypnée (accélération de la fréquence respiratoire)" + "title": "Tachypnée (fréquence respiratoire accélérée)" }, "Transplant": { "text": "Transplant", - "meaning": "NCIT:C159659", "title": "Transplantation" }, "Hematopoietic stem cell transplant (bone marrow transplant)": { "text": "Hematopoietic stem cell transplant (bone marrow transplant)", - "meaning": "NCIT:C131759", - "is_a": "Transplant", - "title": "Transplantation cardiaque" + "title": "Greffe de cellules souches hématopoïétiques (greffe de moelle osseuse)" }, "Cardiac transplant": { "text": "Cardiac transplant", - "meaning": "GENEPIO:0100080", - "is_a": "Transplant", - "title": "Greffe de cellules souches hématopoïétiques (greffe de moelle osseuse)" + "title": "Transplantation cardiaque" }, "Kidney transplant": { "text": "Kidney transplant", - "meaning": "NCIT:C157332", - "is_a": "Transplant", "title": "Greffe de rein" }, "Liver transplant": { "text": "Liver transplant", - "meaning": "GENEPIO:0100081", - "is_a": "Transplant", "title": "Greffe de foie" } } }, - "variant designation menu": { - "name": "variant designation menu", - "title": "menu de désignation des variantes", + "VariantDesignationMenu": { + "name": "VariantDesignationMenu", + "title": "Menu « Désignation des variants »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Variant of Concern (VOC)": { "text": "Variant of Concern (VOC)", - "meaning": "GENEPIO:0100082", - "title": "Variante d'intérêt (VOI)" + "title": "Variant préoccupant" }, "Variant of Interest (VOI)": { "text": "Variant of Interest (VOI)", - "meaning": "GENEPIO:0100083", - "title": "Variante préoccupante (VOC)" + "title": "Variant d’intérêt" }, "Variant Under Monitoring (VUM)": { "text": "Variant Under Monitoring (VUM)", - "meaning": "GENEPIO:0100279", - "title": "Variante sous surveillance (VUM)" + "title": "Variante sous surveillance" } } }, - "variant evidence menu": { - "name": "variant evidence menu", - "title": "menu de preuves variantes", + "VariantEvidenceMenu": { + "name": "VariantEvidenceMenu", + "title": "Menu « Preuves de variants »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "RT-qPCR": { - "text": "RT-qPCR", - "meaning": "CIDO:0000019", - "title": "RT-qPCR" - }, "Sequencing": { "text": "Sequencing", - "meaning": "CIDO:0000027", "title": "Séquençage" } } }, - "complications menu": { - "name": "complications menu", - "title": "menu des complications", + "ComplicationsMenu": { + "name": "ComplicationsMenu", + "title": "Menu « Complications »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Abnormal blood oxygen level": { "text": "Abnormal blood oxygen level", - "meaning": "HP:0500165", - "title": "Taux d'oxygène anormal dans le sang" + "title": "Taux anormal d’oxygène dans le sang" }, "Acute kidney injury": { "text": "Acute kidney injury", - "meaning": "HP:0001919", "title": "Lésions rénales aiguës" }, "Acute lung injury": { "text": "Acute lung injury", - "meaning": "MONDO:0015796", "title": "Lésions pulmonaires aiguës" }, "Ventilation induced lung injury (VILI)": { "text": "Ventilation induced lung injury (VILI)", - "meaning": "GENEPIO:0100092", - "is_a": "Acute lung injury", - "title": "Lésions pulmonaires induites par la ventilation" + "title": "Lésions pulmonaires causées par la ventilation" }, "Acute respiratory failure": { "text": "Acute respiratory failure", - "meaning": "MONDO:0001208", "title": "Insuffisance respiratoire aiguë" }, "Arrhythmia (complication)": { "text": "Arrhythmia (complication)", - "meaning": "HP:0011675", "title": "Arythmie (complication)" }, "Tachycardia": { "text": "Tachycardia", - "meaning": "HP:0001649", - "is_a": "Arrhythmia (complication)", "title": "Tachycardie" }, "Polymorphic ventricular tachycardia (VT)": { "text": "Polymorphic ventricular tachycardia (VT)", - "meaning": "HP:0031677", - "is_a": "Tachycardia", "title": "Tachycardie ventriculaire polymorphe" }, "Tachyarrhythmia": { "text": "Tachyarrhythmia", - "meaning": "GENEPIO:0100084", - "is_a": "Tachycardia", "title": "Tachyarythmie" }, "Cardiac injury": { "text": "Cardiac injury", - "meaning": "GENEPIO:0100074", "title": "Lésions cardiaques" }, "Cardiac arrest": { "text": "Cardiac arrest", - "meaning": "HP:0001695", "title": "Arrêt cardiaque" }, "Cardiogenic shock": { "text": "Cardiogenic shock", - "meaning": "HP:0030149", "title": "Choc cardiogénique" }, "Blood clot": { "text": "Blood clot", - "meaning": "HP:0001977", - "title": "Caillot de sang" + "title": "Caillot sanguin" }, "Arterial clot": { "text": "Arterial clot", - "meaning": "HP:0004420", - "is_a": "Blood clot", "title": "Caillot artériel" }, "Deep vein thrombosis (DVT)": { "text": "Deep vein thrombosis (DVT)", - "meaning": "HP:0002625", - "is_a": "Blood clot", "title": "Thrombose veineuse profonde" }, "Pulmonary embolism (PE)": { "text": "Pulmonary embolism (PE)", - "meaning": "HP:0002204", - "is_a": "Blood clot", "title": "Embolie pulmonaire" }, "Cardiomyopathy": { "text": "Cardiomyopathy", - "meaning": "HP:0001638", - "title": "Cardiomyopathie" + "title": "Myocardiopathie" }, "Central nervous system invasion": { "text": "Central nervous system invasion", - "meaning": "MONDO:0024619", "title": "Envahissement du système nerveux central" }, "Stroke (complication)": { "text": "Stroke (complication)", - "meaning": "HP:0001297", "title": "Accident vasculaire cérébral (complication)" }, "Central Nervous System Vasculitis": { "text": "Central Nervous System Vasculitis", - "meaning": "MONDO:0003346", - "is_a": "Stroke (complication)", "title": "Vascularite du système nerveux central" }, "Acute ischemic stroke": { "text": "Acute ischemic stroke", - "meaning": "HP:0002140", - "is_a": "Stroke (complication)", "title": "Accident vasculaire cérébral ischémique aigu" }, - "Coma": { - "text": "Coma", - "meaning": "HP:0001259", - "title": "Coma" - }, - "Convulsions": { - "text": "Convulsions", - "meaning": "HP:0011097", - "title": "Les convulsions" - }, "COVID-19 associated coagulopathy (CAC)": { "text": "COVID-19 associated coagulopathy (CAC)", - "meaning": "NCIT:C171562", - "title": "COVID-19 coagulopathie associée (CAC)" + "title": "Coagulopathie associée à la COVID-19 (CAC)" }, "Cystic fibrosis": { "text": "Cystic fibrosis", - "meaning": "MONDO:0009061", - "title": "Mucoviscidose" + "title": "Fibrose kystique" }, "Cytokine release syndrome": { "text": "Cytokine release syndrome", - "meaning": "MONDO:0600008", "title": "Syndrome de libération de cytokines" }, "Disseminated intravascular coagulation (DIC)": { "text": "Disseminated intravascular coagulation (DIC)", - "meaning": "MPATH:108", "title": "Coagulation intravasculaire disséminée" }, "Encephalopathy": { "text": "Encephalopathy", - "meaning": "HP:0001298", "title": "Encéphalopathie" }, "Fulminant myocarditis": { "text": "Fulminant myocarditis", - "meaning": "GENEPIO:0100088", "title": "Myocardite fulminante" }, "Guillain-Barré syndrome": { "text": "Guillain-Barré syndrome", - "meaning": "MONDO:0016218", - "title": "Guillain-Barré syndrome" + "title": "Syndrome de Guillain-Barré" }, "Internal hemorrhage (complication; internal bleeding)": { "text": "Internal hemorrhage (complication; internal bleeding)", - "meaning": "HP:0011029", - "title": "Hémorragie interne (complication ; hémorragie interne)" + "title": "Hémorragie interne (complication)" }, "Intracerebral haemorrhage": { "text": "Intracerebral haemorrhage", - "meaning": "MONDO:0013792", - "is_a": "Internal hemorrhage (complication; internal bleeding)", "title": "Hémorragie intracérébrale" }, "Kawasaki disease": { "text": "Kawasaki disease", - "meaning": "MONDO:0012727", "title": "Maladie de Kawasaki" }, "Complete Kawasaki disease": { "text": "Complete Kawasaki disease", - "meaning": "GENEPIO:0100089", - "is_a": "Kawasaki disease", "title": "Maladie de Kawasaki complète" }, "Incomplete Kawasaki disease": { "text": "Incomplete Kawasaki disease", - "meaning": "GENEPIO:0100090", - "is_a": "Kawasaki disease", "title": "Maladie de Kawasaki incomplète" }, "Liver dysfunction": { "text": "Liver dysfunction", - "meaning": "HP:0001410", - "title": "Dysfonctionnement du foie" + "title": "Trouble hépatique" }, "Acute liver injury": { "text": "Acute liver injury", - "meaning": "GENEPIO:0100091", - "is_a": "Liver dysfunction", "title": "Lésions hépatiques aiguës" }, "Long COVID-19": { "text": "Long COVID-19", - "meaning": "MONDO:0100233", - "title": "Longue COVID-19" + "title": "COVID-19 longue" }, "Meningitis": { "text": "Meningitis", - "meaning": "HP:0001287", "title": "Méningite" }, - "Migraine": { - "text": "Migraine", - "meaning": "HP:0002076", - "title": "Migraine" - }, "Miscarriage": { "text": "Miscarriage", - "meaning": "HP:0005268", "title": "Fausses couches" }, "Multisystem inflammatory syndrome in children (MIS-C)": { "text": "Multisystem inflammatory syndrome in children (MIS-C)", - "meaning": "MONDO:0100163", - "title": "Syndrome inflammatoire multisystémique de l'enfant" + "title": "Syndrome inflammatoire multisystémique chez les enfants" }, "Multisystem inflammatory syndrome in adults (MIS-A)": { "text": "Multisystem inflammatory syndrome in adults (MIS-A)", - "meaning": "MONDO:0100319", - "title": "Syndrome inflammatoire multisystémique chez l'adulte" + "title": "Syndrome inflammatoire multisystémique chez les adultes" }, "Muscle injury": { "text": "Muscle injury", - "meaning": "GENEPIO:0100093", "title": "Lésion musculaire" }, "Myalgic encephalomyelitis (ME)": { "text": "Myalgic encephalomyelitis (ME)", - "meaning": "MONDO:0005404", - "title": "Encéphalomyélite myalgique (syndrome de fatigue chronique)" + "title": "Encéphalomyélite myalgique (EM)" }, "Myocardial infarction (heart attack)": { "text": "Myocardial infarction (heart attack)", - "meaning": "MONDO:0005068", "title": "Infarctus du myocarde (crise cardiaque)" }, "Acute myocardial infarction": { "text": "Acute myocardial infarction", - "meaning": "MONDO:0004781", - "is_a": "Myocardial infarction (heart attack)", "title": "Infarctus aigu du myocarde" }, "ST-segment elevation myocardial infarction": { "text": "ST-segment elevation myocardial infarction", - "meaning": "MONDO:0041656", - "is_a": "Myocardial infarction (heart attack)", "title": "Infarctus du myocarde avec sus-décalage du segment ST" }, "Myocardial injury": { "text": "Myocardial injury", - "meaning": "HP:0001700", "title": "Lésions du myocarde" }, "Neonatal complications": { "text": "Neonatal complications", - "meaning": "NCIT:C168498", "title": "Complications néonatales" }, "Noncardiogenic pulmonary edema": { "text": "Noncardiogenic pulmonary edema", - "meaning": "GENEPIO:0100085", "title": "Œdème pulmonaire non cardiogénique" }, "Acute respiratory distress syndrome (ARDS)": { "text": "Acute respiratory distress syndrome (ARDS)", - "meaning": "HP:0033677", - "is_a": "Noncardiogenic pulmonary edema", - "title": "Syndrome de détresse respiratoire aiguë" + "title": "Syndrome de détresse respiratoire aiguë (SDRA)" }, "COVID-19 associated ARDS (CARDS)": { "text": "COVID-19 associated ARDS (CARDS)", - "meaning": "NCIT:C171551", - "is_a": "Acute respiratory distress syndrome (ARDS)", - "title": "ARDS associé au COVID-19 (CARDS)" + "title": "SDRA associé à la COVID-19 (SDRAC)" }, "Neurogenic pulmonary edema (NPE)": { "text": "Neurogenic pulmonary edema (NPE)", - "meaning": "GENEPIO:0100086", - "is_a": "Acute respiratory distress syndrome (ARDS)", "title": "Œdème pulmonaire neurogène" }, "Organ failure": { "text": "Organ failure", - "meaning": "GENEPIO:0100094", - "title": "Insuffisance organique" + "title": "Défaillance des organes" }, "Heart failure": { "text": "Heart failure", - "meaning": "HP:0001635", - "is_a": "Organ failure", "title": "Insuffisance cardiaque" }, "Liver failure": { "text": "Liver failure", - "meaning": "MONDO:0100192", - "is_a": "Organ failure", "title": "Insuffisance hépatique" }, "Paralysis": { "text": "Paralysis", - "meaning": "HP:0003470", "title": "Paralysie" }, "Pneumothorax (collapsed lung)": { "text": "Pneumothorax (collapsed lung)", - "meaning": "HP:0002107", "title": "Pneumothorax (affaissement du poumon)" }, "Spontaneous pneumothorax": { "text": "Spontaneous pneumothorax", - "meaning": "HP:0002108", - "is_a": "Pneumothorax (collapsed lung)", "title": "Pneumothorax spontané" }, "Spontaneous tension pneumothorax": { "text": "Spontaneous tension pneumothorax", - "meaning": "MONDO:0002075", - "is_a": "Pneumothorax (collapsed lung)", "title": "Pneumothorax spontané sous tension" }, "Pneumonia (complication)": { "text": "Pneumonia (complication)", - "meaning": "HP:0002090", "title": "Pneumonie (complication)" }, "COVID-19 pneumonia": { "text": "COVID-19 pneumonia", - "meaning": "NCIT:C171550", - "is_a": "Pneumonia (complication)", - "title": "Pneumonie COVID-19" + "title": "Pneumonie liée à la COVID-19" }, "Pregancy complications": { "text": "Pregancy complications", - "meaning": "HP:0001197", "title": "Complications de la grossesse" }, "Rhabdomyolysis": { "text": "Rhabdomyolysis", - "meaning": "HP:0003201", "title": "Rhabdomyolyse" }, "Secondary infection": { "text": "Secondary infection", - "meaning": "IDO:0000567", "title": "Infection secondaire" }, "Secondary staph infection": { "text": "Secondary staph infection", - "meaning": "GENEPIO:0100095", - "is_a": "Secondary infection", - "title": "Infection secondaire à staphylocoque" + "title": "Infection staphylococcique secondaire" }, "Secondary strep infection": { "text": "Secondary strep infection", - "meaning": "GENEPIO:0100096", - "is_a": "Secondary infection", - "title": "Infection secondaire à streptocoques" + "title": "Infection streptococcique secondaire" }, "Seizure (complication)": { "text": "Seizure (complication)", - "meaning": "HP:0001250", - "title": "Crise d'épilepsie (complication)" + "title": "Crise d’épilepsie (complication)" }, "Motor seizure": { "text": "Motor seizure", - "meaning": "HP:0020219", - "is_a": "Seizure (complication)", "title": "Crise motrice" }, "Sepsis/Septicemia": { "text": "Sepsis/Septicemia", - "meaning": "HP:0100806", - "title": "Sepsis/Septicémie" + "title": "Sepsie/Septicémie" }, "Sepsis": { "text": "Sepsis", - "meaning": "IDO:0000636", - "is_a": "Sepsis/Septicemia", - "title": "Septicémie (réaction inflammatoire systémique à une infection)" + "title": "Sepsie" }, "Septicemia": { "text": "Septicemia", - "meaning": "NCIT:C3364", - "is_a": "Sepsis/Septicemia", - "title": "Septicémie (infection du sang)" + "title": "Septicémie" }, "Shock": { "text": "Shock", - "meaning": "HP:0031273", "title": "Choc" }, "Hyperinflammatory shock": { "text": "Hyperinflammatory shock", - "meaning": "GENEPIO:0100097", - "is_a": "Shock", "title": "Choc hyperinflammatoire" }, "Refractory cardiogenic shock": { "text": "Refractory cardiogenic shock", - "meaning": "GENEPIO:0100098", - "is_a": "Shock", "title": "Choc cardiogénique réfractaire" }, "Refractory cardiogenic plus vasoplegic shock": { "text": "Refractory cardiogenic plus vasoplegic shock", - "meaning": "GENEPIO:0100099", - "is_a": "Shock", "title": "Choc cardiogénique et vasoplégique réfractaire" }, "Septic shock": { "text": "Septic shock", - "meaning": "NCIT:C35018", - "is_a": "Shock", "title": "Choc septique" }, "Vasculitis": { "text": "Vasculitis", - "meaning": "HP:0002633", "title": "Vascularite" } } }, - "vaccine name menu": { - "name": "vaccine name menu", - "title": "menu nom du vaccin", + "VaccineNameMenu": { + "name": "VaccineNameMenu", + "title": "Menu « Noms de vaccins »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Astrazeneca (Vaxzevria)": { "text": "Astrazeneca (Vaxzevria)", - "meaning": "GENEPIO:0100308", - "title": "Astrazeneca (Vaxzevria)" - }, - "Johnson & Johnson (Janssen)": { - "text": "Johnson & Johnson (Janssen)", - "meaning": "GENEPIO:0100307", - "title": "Johnson & Johnson (Janssen)" - }, - "Moderna (Spikevax)": { - "text": "Moderna (Spikevax)", - "meaning": "GENEPIO:0100304", - "title": "Moderna (Spikevax)" - }, - "Pfizer-BioNTech (Comirnaty)": { - "text": "Pfizer-BioNTech (Comirnaty)", - "meaning": "GENEPIO:0100305", - "title": "Pfizer-BioNTech (Comirnaty)" + "title": "AstraZeneca (Vaxzevria)" }, "Pfizer-BioNTech (Comirnaty Pediatric)": { "text": "Pfizer-BioNTech (Comirnaty Pediatric)", - "meaning": "GENEPIO:0100306", - "title": "Pfizer-BioNTech (Comirnaty Pédiatrique)" + "title": "Pfizer-BioNTech (Comirnaty, formule pédiatrique)" } } }, - "anatomical material menu": { - "name": "anatomical material menu", - "title": "menu de matériel anatomique", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "Menu « Matières anatomiques »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Blood": { "text": "Blood", - "meaning": "UBERON:0000178", "title": "Sang" }, "Fluid": { "text": "Fluid", - "meaning": "UBERON:0006314", - "title": "Fluide" + "title": "Liquide" }, "Saliva": { "text": "Saliva", - "meaning": "UBERON:0001836", - "is_a": "Fluid", "title": "Salive" }, "Fluid (cerebrospinal (CSF))": { "text": "Fluid (cerebrospinal (CSF))", - "meaning": "UBERON:0001359", - "is_a": "Fluid", - "title": "Fluide (cérébrospinal (CSF))" + "title": "Liquide (céphalorachidien)" }, "Fluid (pericardial)": { "text": "Fluid (pericardial)", - "meaning": "UBERON:0002409", - "is_a": "Fluid", - "title": "Fluide (péricardique)" + "title": "Liquide (péricardique)" }, "Fluid (pleural)": { "text": "Fluid (pleural)", - "meaning": "UBERON:0001087", - "is_a": "Fluid", - "title": "Fluide (pleural)" + "title": "Liquide (pleural)" }, "Fluid (vaginal)": { "text": "Fluid (vaginal)", - "meaning": "UBERON:0036243", - "is_a": "Fluid", - "title": "Fluides (vaginaux)" + "title": "Sécrétions (vaginales)" }, "Fluid (amniotic)": { "text": "Fluid (amniotic)", - "meaning": "UBERON:0000173", - "is_a": "Fluid", - "title": "Fluide (amniotique)" + "title": "Liquide (amniotique)" }, "Tissue": { "text": "Tissue", - "meaning": "UBERON:0000479", "title": "Tissu" } } }, - "anatomical part menu": { - "name": "anatomical part menu", - "title": "menu partie anatomique", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "Menu « Parties anatomiques »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Anus": { - "text": "Anus", - "meaning": "UBERON:0001245", - "title": "Anus" - }, "Buccal mucosa": { "text": "Buccal mucosa", - "meaning": "UBERON:0006956", "title": "Muqueuse buccale" }, "Duodenum": { "text": "Duodenum", - "meaning": "UBERON:0002114", "title": "Duodénum" }, "Eye": { "text": "Eye", - "meaning": "UBERON:0000970", - "title": "L'œil" + "title": "Œil" }, "Intestine": { "text": "Intestine", - "meaning": "UBERON:0000160", "title": "Intestin" }, "Lower respiratory tract": { "text": "Lower respiratory tract", - "meaning": "UBERON:0001558", "title": "Voies respiratoires inférieures" }, "Bronchus": { "text": "Bronchus", - "meaning": "UBERON:0002185", - "is_a": "Lower respiratory tract", "title": "Bronches" }, "Lung": { "text": "Lung", - "meaning": "UBERON:0002048", - "is_a": "Lower respiratory tract", "title": "Poumon" }, - "Bronchiole": { - "text": "Bronchiole", - "meaning": "UBERON:0002186", - "is_a": "Lung", - "title": "Bronchiole" - }, "Alveolar sac": { "text": "Alveolar sac", - "meaning": "UBERON:0002169", - "is_a": "Lung", "title": "Sac alvéolaire" }, "Pleural sac": { "text": "Pleural sac", - "meaning": "UBERON:0009778", - "is_a": "Lower respiratory tract", "title": "Sac pleural" }, "Pleural cavity": { "text": "Pleural cavity", - "meaning": "UBERON:0002402", - "is_a": "Pleural sac", "title": "Cavité pleurale" }, "Trachea": { "text": "Trachea", - "meaning": "UBERON:0003126", - "is_a": "Lower respiratory tract", "title": "Trachée" }, - "Rectum": { - "text": "Rectum", - "meaning": "UBERON:0001052", - "title": "Le rectum" - }, "Skin": { "text": "Skin", - "meaning": "UBERON:0001003", "title": "Peau" }, "Stomach": { "text": "Stomach", - "meaning": "UBERON:0000945", "title": "Estomac" }, "Upper respiratory tract": { "text": "Upper respiratory tract", - "meaning": "UBERON:0001557", "title": "Voies respiratoires supérieures" }, "Anterior Nares": { "text": "Anterior Nares", - "meaning": "UBERON:2001427", - "is_a": "Upper respiratory tract", "title": "Narines antérieures" }, "Esophagus": { "text": "Esophagus", - "meaning": "UBERON:0001043", - "is_a": "Upper respiratory tract", "title": "Œsophage" }, "Ethmoid sinus": { "text": "Ethmoid sinus", - "meaning": "UBERON:0002453", - "is_a": "Upper respiratory tract", "title": "Sinus ethmoïdal" }, "Nasal Cavity": { "text": "Nasal Cavity", - "meaning": "UBERON:0001707", - "is_a": "Upper respiratory tract", "title": "Cavité nasale" }, "Middle Nasal Turbinate": { "text": "Middle Nasal Turbinate", - "meaning": "UBERON:0005921", - "is_a": "Nasal Cavity", - "title": "Turbine nasale moyenne" + "title": "Cornet nasal moyen" }, "Inferior Nasal Turbinate": { "text": "Inferior Nasal Turbinate", - "meaning": "UBERON:0005922", - "is_a": "Nasal Cavity", - "title": "Turbine nasale inférieure" + "title": "Cornet nasal inférieur" }, "Nasopharynx (NP)": { "text": "Nasopharynx (NP)", - "meaning": "UBERON:0001728", - "is_a": "Upper respiratory tract", - "title": "Nasopharynx (NP)" + "title": "Nasopharynx" }, "Oropharynx (OP)": { "text": "Oropharynx (OP)", - "meaning": "UBERON:0001729", - "is_a": "Upper respiratory tract", - "title": "Oropharynx (OP)" + "title": "Oropharynx" }, "Pharynx (throat)": { "text": "Pharynx (throat)", - "meaning": "UBERON:0000341", - "is_a": "Upper respiratory tract", - "title": "Le pharynx (gorge)" + "title": "Pharynx (gorge)" } } }, - "body product menu": { - "name": "body product menu", - "title": "menu de produits pour le corps", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "Menu « Produit corporel »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Breast Milk": { "text": "Breast Milk", - "meaning": "UBERON:0001913", - "title": "Le lait maternel" + "title": "Lait maternel" }, "Feces": { "text": "Feces", - "meaning": "UBERON:0001988", "title": "Selles" }, "Fluid (seminal)": { "text": "Fluid (seminal)", - "meaning": "UBERON:0006530", - "title": "Liquide (séminal)" - }, - "Mucus": { - "text": "Mucus", - "meaning": "UBERON:0000912", - "title": "Mucus" + "title": "Sperme" }, "Sputum": { "text": "Sputum", - "meaning": "UBERON:0007311", - "is_a": "Mucus", - "title": "Expectorations" + "title": "Expectoration" }, "Sweat": { "text": "Sweat", - "meaning": "UBERON:0001089", "title": "Sueur" }, "Tear": { "text": "Tear", - "meaning": "UBERON:0001827", "title": "Larme" - }, - "Urine": { - "text": "Urine", - "meaning": "UBERON:0001088", - "title": "Urine" } } }, - "prior SARS-CoV-2 infection menu": { - "name": "prior SARS-CoV-2 infection menu", - "title": "menu d’infection antérieure par le SARS-CoV-2", + "PriorSarsCov2InfectionMenu": { + "name": "PriorSarsCov2InfectionMenu", + "title": "Menu « Infection antérieure par le SRAS-CoV-2 »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Prior infection": { "text": "Prior infection", - "meaning": "GENEPIO:0100037", "title": "Infection antérieure" }, "No prior infection": { "text": "No prior infection", - "meaning": "GENEPIO:0100233", - "title": "Pas d'infection antérieure" + "title": "Aucune infection antérieure" } } }, - "environmental material menu": { - "name": "environmental material menu", - "title": "menu de matériaux environnementaux", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "Menu « Matériel environnemental »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air vent": { "text": "Air vent", - "meaning": "ENVO:03501208", - "title": "Purgeur d'air" + "title": "Évent d’aération" }, "Banknote": { "text": "Banknote", - "meaning": "ENVO:00003896", - "title": "Billets de banque" + "title": "Billet de banque" }, "Bed rail": { "text": "Bed rail", - "meaning": "ENVO:03501209", - "title": "Barre de lit" + "title": "Côté de lit" }, "Building floor": { "text": "Building floor", - "meaning": "ENVO:01000486", "title": "Plancher du bâtiment" }, "Cloth": { "text": "Cloth", - "meaning": "ENVO:02000058", "title": "Tissu" }, "Control panel": { "text": "Control panel", - "meaning": "ENVO:03501210", "title": "Panneau de contrôle" }, "Door": { "text": "Door", - "meaning": "ENVO:03501220", "title": "Porte" }, "Door handle": { "text": "Door handle", - "meaning": "ENVO:03501211", "title": "Poignée de porte" }, "Face mask": { "text": "Face mask", - "meaning": "OBI:0002787", - "title": "Masque facial" + "title": "Masque" }, "Face shield": { "text": "Face shield", - "meaning": "OBI:0002791", - "title": "Masque de protection" + "title": "Écran facial" }, "Food": { "text": "Food", - "meaning": "FOODON:00002403", "title": "Nourriture" }, "Food packaging": { "text": "Food packaging", - "meaning": "FOODON:03490100", "title": "Emballages alimentaires" }, "Glass": { "text": "Glass", - "meaning": "ENVO:01000481", "title": "Verre" }, "Handrail": { "text": "Handrail", - "meaning": "ENVO:03501212", - "title": "Balustrade" + "title": "Main courante" }, "Hospital gown": { "text": "Hospital gown", - "meaning": "OBI:0002796", - "title": "Robe d'hôpital" + "title": "Jaquette d’hôpital" }, "Light switch": { "text": "Light switch", - "meaning": "ENVO:03501213", - "title": "Interrupteur d'éclairage" + "title": "Interrupteur" }, "Locker": { "text": "Locker", - "meaning": "ENVO:03501214", "title": "Casier" }, "N95 mask": { "text": "N95 mask", - "meaning": "OBI:0002790", "title": "Masque N95" }, "Nurse call button": { "text": "Nurse call button", - "meaning": "ENVO:03501215", - "title": "Bouton d'appel infirmière" + "title": "Bouton d’appel de l’infirmière" }, "Paper": { "text": "Paper", - "meaning": "ENVO:03501256", "title": "Papier" }, "Particulate matter": { "text": "Particulate matter", - "meaning": "ENVO:01000060", - "title": "Affaire particulière" + "title": "Matière particulaire" }, "Plastic": { "text": "Plastic", - "meaning": "ENVO:01000404", "title": "Plastique" }, "PPE gown": { "text": "PPE gown", - "meaning": "GENEPIO:0100025", - "title": "Blouse EPI" + "title": "Blouse (EPI)" }, "Sewage": { "text": "Sewage", - "meaning": "ENVO:00002018", "title": "Eaux usées" }, "Sink": { "text": "Sink", - "meaning": "ENVO:01000990", - "title": "Evier" + "title": "Évier" }, "Soil": { "text": "Soil", - "meaning": "ENVO:00001998", "title": "Sol" }, "Stainless steel": { "text": "Stainless steel", - "meaning": "ENVO:03501216", "title": "Acier inoxydable" }, "Tissue paper": { "text": "Tissue paper", - "meaning": "ENVO:03501217", - "title": "Papier de soie" + "title": "Mouchoirs" }, "Toilet bowl": { "text": "Toilet bowl", - "meaning": "ENVO:03501218", - "title": "Cuvette de toilette" + "title": "Cuvette" }, "Water": { "text": "Water", - "meaning": "ENVO:00002006", "title": "Eau" }, "Wastewater": { "text": "Wastewater", - "meaning": "ENVO:00002001", - "is_a": "Water", "title": "Eaux usées" }, "Window": { "text": "Window", - "meaning": "ENVO:03501219", "title": "Fenêtre" }, "Wood": { "text": "Wood", - "meaning": "ENVO:00002040", "title": "Bois" } } }, - "environmental site menu": { - "name": "environmental site menu", - "title": "menu du site environnemental", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "Menu « Site environnemental »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Acute care facility": { "text": "Acute care facility", - "meaning": "ENVO:03501135", - "title": "Établissement de soins aigus" + "title": "Établissement de soins de courte durée" }, "Animal house": { "text": "Animal house", - "meaning": "ENVO:00003040", - "title": "Maison des animaux" + "title": "Refuge pour animaux" }, "Bathroom": { "text": "Bathroom", - "meaning": "ENVO:01000422", "title": "Salle de bain" }, "Clinical assessment centre": { "text": "Clinical assessment centre", - "meaning": "ENVO:03501136", - "title": "Centre d'évaluation clinique" + "title": "Centre d’évaluation clinique" }, "Conference venue": { "text": "Conference venue", - "meaning": "ENVO:03501127", - "title": "Salle de conférence" + "title": "Lieu de la conférence" }, "Corridor": { "text": "Corridor", - "meaning": "ENVO:03501121", "title": "couloir" }, "Daycare": { "text": "Daycare", - "meaning": "ENVO:01000927", "title": "Garderie" }, "Emergency room (ER)": { "text": "Emergency room (ER)", - "meaning": "ENVO:03501145", - "title": "Salle d'urgence" + "title": "Salle d’urgence" }, "Family practice clinic": { "text": "Family practice clinic", - "meaning": "ENVO:03501186", "title": "Clinique de médecine familiale" }, "Group home": { "text": "Group home", - "meaning": "ENVO:03501196", "title": "Foyer de groupe" }, "Homeless shelter": { "text": "Homeless shelter", - "meaning": "ENVO:03501133", - "title": "Foyer pour sans-abri" + "title": "Refuge pour sans-abri" }, "Hospital": { "text": "Hospital", - "meaning": "ENVO:00002173", "title": "Hôpital" }, "Intensive Care Unit (ICU)": { "text": "Intensive Care Unit (ICU)", - "meaning": "ENVO:03501152", "title": "Unité de soins intensifs" }, "Long Term Care Facility": { "text": "Long Term Care Facility", - "meaning": "ENVO:03501194", "title": "Établissement de soins de longue durée" }, "Patient room": { "text": "Patient room", - "meaning": "ENVO:03501180", "title": "Chambre du patient" }, - "Prison": { - "text": "Prison", - "meaning": "ENVO:03501204", - "title": "Prison" - }, "Production Facility": { "text": "Production Facility", - "meaning": "ENVO:01000536", "title": "Installation de production" }, "School": { "text": "School", - "meaning": "ENVO:03501130", "title": "École" }, "Sewage Plant": { "text": "Sewage Plant", - "meaning": "ENVO:00003043", - "title": "Station d'épuration" + "title": "Usine d’épuration des eaux usées" }, "Subway train": { "text": "Subway train", - "meaning": "ENVO:03501109", "title": "Métro" }, "University campus": { "text": "University campus", - "meaning": "ENVO:00000467", - "title": "Campus de l'université" + "title": "Campus de l’université" }, "Wet market": { "text": "Wet market", - "meaning": "ENVO:03501198", - "title": "Marché de l'eau" + "title": "Marché traditionnel de produits frais" } } }, - "collection method menu": { - "name": "collection method menu", - "title": "menu méthode de collecte", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "Menu « Méthode de prélèvement »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Amniocentesis": { "text": "Amniocentesis", - "meaning": "NCIT:C52009", "title": "Amniocentèse" }, - "Aspiration": { - "text": "Aspiration", - "meaning": "NCIT:C15631", - "title": "Aspiration" - }, "Suprapubic Aspiration": { "text": "Suprapubic Aspiration", - "meaning": "GENEPIO:0100028", - "is_a": "Aspiration", - "title": "Aspiration suprapubienne" + "title": "Aspiration sus-pubienne" }, "Tracheal aspiration": { "text": "Tracheal aspiration", - "meaning": "GENEPIO:0100029", - "is_a": "Aspiration", "title": "Aspiration trachéale" }, "Vacuum Aspiration": { "text": "Vacuum Aspiration", - "meaning": "GENEPIO:0100030", - "is_a": "Aspiration", "title": "Aspiration sous vide" }, "Biopsy": { "text": "Biopsy", - "meaning": "OBI:0002650", "title": "Biopsie" }, "Needle Biopsy": { "text": "Needle Biopsy", - "meaning": "OBI:0002651", - "is_a": "Biopsy", - "title": "Biopsie à l'aiguille" - }, - "Filtration": { - "text": "Filtration", - "meaning": "OBI:0302885", - "title": "Filtration" + "title": "Biopsie à l’aiguille" }, "Air filtration": { "text": "Air filtration", - "meaning": "GENEPIO:0100031", - "is_a": "Filtration", - "title": "Filtration de l'air" - }, - "Lavage": { - "text": "Lavage", - "meaning": "OBI:0600044", - "title": "Lavage (lavage médical)" + "title": "Filtration de l’air" }, "Bronchoalveolar lavage (BAL)": { "text": "Bronchoalveolar lavage (BAL)", - "meaning": "GENEPIO:0100032", - "is_a": "Lavage", "title": "Lavage broncho-alvéolaire (LBA)" }, "Gastric Lavage": { "text": "Gastric Lavage", - "meaning": "GENEPIO:0100033", - "is_a": "Lavage", "title": "Lavage gastrique" }, "Lumbar Puncture": { "text": "Lumbar Puncture", - "meaning": "NCIT:C15327", "title": "Ponction lombaire" }, "Necropsy": { "text": "Necropsy", - "meaning": "MMO:0000344", "title": "Nécropsie" }, "Phlebotomy": { "text": "Phlebotomy", - "meaning": "NCIT:C28221", "title": "Phlébotomie" }, "Rinsing": { "text": "Rinsing", - "meaning": "GENEPIO:0002116", - "title": "Rinçage (lavage)" + "title": "Rinçage" }, "Saline gargle (mouth rinse and gargle)": { "text": "Saline gargle (mouth rinse and gargle)", - "meaning": "GENEPIO:0100034", - "is_a": "Rinsing", - "title": "Gargarisme salin (rinçage de la bouche et gargarisme)" + "title": "Gargarisme avec saline (rince-bouche)" }, "Scraping": { "text": "Scraping", - "meaning": "GENEPIO:0100035", - "title": "Raclage" + "title": "Grattage" }, "Swabbing": { "text": "Swabbing", - "meaning": "GENEPIO:0002117", "title": "Écouvillonnage" }, "Finger Prick": { "text": "Finger Prick", - "meaning": "GENEPIO:0100036", - "title": "Piqûre au doigt" + "title": "Piqûre du doigt" }, "Washout Tear Collection": { "text": "Washout Tear Collection", - "meaning": "GENEPIO:0100038", - "title": "Lavage Collecte de larmes" + "title": "Lavage – Collecte de larmes" } } }, - "collection device menu": { - "name": "collection device menu", - "title": "menu du dispositif de collecte", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "Menu « Dispositif de prélèvement »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air filter": { "text": "Air filter", - "meaning": "ENVO:00003968", "title": "Filtre à air" }, "Blood Collection Tube": { "text": "Blood Collection Tube", - "meaning": "OBI:0002859", "title": "Tube de prélèvement sanguin" }, - "Bronchoscope": { - "text": "Bronchoscope", - "meaning": "OBI:0002826", - "title": "Bronchoscope" - }, "Collection Container": { "text": "Collection Container", - "meaning": "OBI:0002088", - "title": "Récipient de collecte" + "title": "Récipient à échantillons" }, "Collection Cup": { "text": "Collection Cup", - "meaning": "GENEPIO:0100026", - "title": "Tasse de collection" + "title": "Godet à échantillons" }, "Fibrobronchoscope Brush": { "text": "Fibrobronchoscope Brush", - "meaning": "OBI:0002825", "title": "Brosse à fibrobronchoscope" }, "Filter": { "text": "Filter", - "meaning": "GENEPIO:0100103", "title": "Filtre" }, "Fine Needle": { "text": "Fine Needle", - "meaning": "OBI:0002827", "title": "Aiguille fine" }, "Microcapillary tube": { "text": "Microcapillary tube", - "meaning": "OBI:0002858", - "title": "Tube microcapillaire" - }, - "Micropipette": { - "text": "Micropipette", - "meaning": "OBI:0001128", - "title": "Micropipette" + "title": "Micropipette de type capillaire" }, "Needle": { "text": "Needle", - "meaning": "OBI:0000436", "title": "Aiguille" }, "Serum Collection Tube": { "text": "Serum Collection Tube", - "meaning": "OBI:0002860", - "title": "Tube de collection de sérum" + "title": "Tube de prélèvement du sérum" }, "Sputum Collection Tube": { "text": "Sputum Collection Tube", - "meaning": "OBI:0002861", "title": "Tube de prélèvement des expectorations" }, "Suction Catheter": { "text": "Suction Catheter", - "meaning": "OBI:0002831", - "title": "Cathéter d'aspiration" + "title": "Cathéter d’aspiration" }, "Swab": { "text": "Swab", - "meaning": "GENEPIO:0100027", "title": "Écouvillon" }, "Urine Collection Tube": { "text": "Urine Collection Tube", - "meaning": "OBI:0002862", - "title": "Tube de prélèvement d'urine" + "title": "Tube de prélèvement d’urine" }, "Virus Transport Medium": { "text": "Virus Transport Medium", - "meaning": "OBI:0002866", - "title": "Milieu de transport des virus" + "title": "Milieu de transport viral" } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", - "title": "menu hôte (nom scientifique)", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "Menu « Hôte (nom scientifique) »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Homo sapiens": { - "text": "Homo sapiens", - "meaning": "NCBITaxon:9606", - "title": "Homo sapiens" - }, "Bos taurus": { "text": "Bos taurus", - "meaning": "NCBITaxon:9913", "title": "Bos taureau" }, - "Canis lupus familiaris": { - "text": "Canis lupus familiaris", - "meaning": "NCBITaxon:9615", - "title": "Canis lupus familier" - }, "Chiroptera": { "text": "Chiroptera", - "meaning": "NCBITaxon:9397", "title": "Chiroptères" }, "Columbidae": { "text": "Columbidae", - "meaning": "NCBITaxon:8930", - "title": "Colombidés" - }, - "Felis catus": { - "text": "Felis catus", - "meaning": "NCBITaxon:9685", - "title": "Felis catus" - }, - "Gallus gallus": { - "text": "Gallus gallus", - "meaning": "NCBITaxon:9031", - "title": "Gallus gallus" - }, - "Manis": { - "text": "Manis", - "meaning": "NCBITaxon:9973", - "title": "Manis" - }, - "Manis javanica": { - "text": "Manis javanica", - "meaning": "NCBITaxon:9974", - "title": "Homme javanais" - }, - "Neovison vison": { - "text": "Neovison vison", - "meaning": "NCBITaxon:452646", - "title": "Vison Neovison" - }, - "Panthera leo": { - "text": "Panthera leo", - "meaning": "NCBITaxon:9689", - "title": "Panthera lion" - }, - "Panthera tigris": { - "text": "Panthera tigris", - "meaning": "NCBITaxon:9694", - "title": "Panthera tigris" + "title": "Columbidés" }, "Rhinolophidae": { "text": "Rhinolophidae", - "meaning": "NCBITaxon:58055", "title": "Rhinolophidés" }, - "Rhinolophus affinis": { - "text": "Rhinolophus affinis", - "meaning": "NCBITaxon:59477", - "title": "Rhinolophus affinis" - }, - "Sus scrofa domesticus": { - "text": "Sus scrofa domesticus", - "meaning": "NCBITaxon:9825", - "title": "Sus scrofa domestique" - }, "Viverridae": { "text": "Viverridae", - "meaning": "NCBITaxon:9673", "title": "Viverridés" } } }, - "host (common name) menu": { - "name": "host (common name) menu", - "title": "menu hôte (nom commun)", + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "Menu « Hôte (nom commun) »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Human": { "text": "Human", - "meaning": "NCBITaxon:9606", "title": "Humain" }, "Bat": { "text": "Bat", - "meaning": "NCBITaxon:9397", - "title": "Chauve souris" + "title": "Chauve-souris" }, "Cat": { "text": "Cat", - "meaning": "NCBITaxon:9685", "title": "Chat" }, "Chicken": { "text": "Chicken", - "meaning": "NCBITaxon:9031", "title": "Poulet" }, "Civets": { "text": "Civets", - "meaning": "NCBITaxon:9673", "title": "Civettes" }, "Cow": { "text": "Cow", - "meaning": "NCBITaxon:9913", - "title": "Vache", - "exact_mappings": [ - "CNPHI:bovine" - ] + "title": "Vache" }, "Dog": { "text": "Dog", - "meaning": "NCBITaxon:9615", "title": "Chien" }, - "Lion": { - "text": "Lion", - "meaning": "NCBITaxon:9689", - "title": "Lion" - }, "Mink": { "text": "Mink", - "meaning": "NCBITaxon:452646", "title": "Vison" }, - "Pangolin": { - "text": "Pangolin", - "meaning": "NCBITaxon:9973", - "title": "Pangolin" - }, "Pig": { "text": "Pig", - "meaning": "NCBITaxon:9825", - "title": "Cochon", - "exact_mappings": [ - "CNPHI:porcine" - ] - }, - "Pigeon": { - "text": "Pigeon", - "meaning": "NCBITaxon:8930", - "title": "Pigeon" + "title": "Cochon" }, "Tiger": { "text": "Tiger", - "meaning": "NCBITaxon:9694", "title": "Tigre" } } }, - "host health state menu": { - "name": "host health state menu", - "title": "menu de l'état de santé de l'hôte", + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "Menu « État de santé de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Asymptomatic": { "text": "Asymptomatic", - "meaning": "NCIT:C3833", "title": "Asymptomatique" }, "Deceased": { "text": "Deceased", - "meaning": "NCIT:C28554", "title": "Décédé" }, "Healthy": { "text": "Healthy", - "meaning": "NCIT:C115935", - "title": "En bonne santé" + "title": "En santé" }, "Recovered": { "text": "Recovered", - "meaning": "NCIT:C49498", "title": "Rétabli" }, "Symptomatic": { "text": "Symptomatic", - "meaning": "NCIT:C25269", "title": "Symptomatique" } } }, - "host health status details menu": { - "name": "host health status details menu", - "title": "Menu détaillé de l'état de santé de l'hôte", + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "Menu « Détails de l’état de santé de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Hospitalized": { "text": "Hospitalized", - "meaning": "NCIT:C25179", "title": "Hospitalisé" }, "Hospitalized (Non-ICU)": { "text": "Hospitalized (Non-ICU)", - "meaning": "GENEPIO:0100045", - "is_a": "Hospitalized", - "title": "Hospitalisé (hors soins intensifs)" + "title": "Hospitalisé (hors USI)" }, "Hospitalized (ICU)": { "text": "Hospitalized (ICU)", - "meaning": "GENEPIO:0100046", - "is_a": "Hospitalized", - "title": "Hospitalisé (ICU)" + "title": "Hospitalisé (USI)" }, "Mechanical Ventilation": { "text": "Mechanical Ventilation", - "meaning": "NCIT:C70909", - "title": "Ventilation mécanique" + "title": "Ventilation artificielle" }, "Medically Isolated": { "text": "Medically Isolated", - "meaning": "GENEPIO:0100047", - "title": "Médicalement isolé" + "title": "Isolement médical" }, "Medically Isolated (Negative Pressure)": { "text": "Medically Isolated (Negative Pressure)", - "meaning": "GENEPIO:0100048", - "is_a": "Medically Isolated", - "title": "Médicalement isolé (pression négative)" + "title": "Isolement médical (pression négative)" }, "Self-quarantining": { "text": "Self-quarantining", - "meaning": "NCIT:C173768", - "title": "Auto-quarantaine" + "title": "Quarantaine volontaire" } } }, - "host health outcome menu": { - "name": "host health outcome menu", - "title": "menu des résultats de santé de l'hôte", + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "Menu « Résultats sanitaires de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Deceased": { "text": "Deceased", - "meaning": "NCIT:C28554", "title": "Décédé" }, "Deteriorating": { "text": "Deteriorating", - "meaning": "NCIT:C25254", - "title": "Se détériorer" + "title": "Détérioration" }, "Recovered": { "text": "Recovered", - "meaning": "NCIT:C49498", "title": "Rétabli" }, "Stable": { "text": "Stable", - "meaning": "NCIT:C30103", - "title": "Écurie" + "title": "Stabilisation" } } }, - "organism menu": { - "name": "organism menu", - "title": "menu de l'organisme", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "Menu « Organisme »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Severe acute respiratory syndrome coronavirus 2": { "text": "Severe acute respiratory syndrome coronavirus 2", - "meaning": "NCBITaxon:2697049", - "title": "Syndrome respiratoire aigu sévère coronavirus 2" - }, - "RaTG13": { - "text": "RaTG13", - "meaning": "NCBITaxon:2709072", - "title": "RaTG13" - }, - "RmYN02": { - "text": "RmYN02", - "meaning": "GENEPIO:0100000", - "title": "RmYN02" + "title": "Coronavirus du syndrome respiratoire aigu sévère 2" } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", - "title": "but du menu d'échantillonnage", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "Menu « Objectif de l’échantillonnage »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Cluster/Outbreak investigation": { "text": "Cluster/Outbreak investigation", - "meaning": "GENEPIO:0100001", - "title": "Enquête sur les grappes et les foyers" + "title": "Enquête sur les grappes et les éclosions" }, "Diagnostic testing": { "text": "Diagnostic testing", - "meaning": "GENEPIO:0100002", "title": "Tests de diagnostic" }, "Research": { "text": "Research", - "meaning": "GENEPIO:0100003", "title": "Recherche" - }, - "Surveillance": { - "text": "Surveillance", - "meaning": "GENEPIO:0100004", - "title": "Surveillance" } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", - "title": "but du menu de séquencement", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "Menu « Objectif du séquençage »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Baseline surveillance (random sampling)": { "text": "Baseline surveillance (random sampling)", - "meaning": "GENEPIO:0100005", "title": "Surveillance de base (échantillonnage aléatoire)" }, "Targeted surveillance (non-random sampling)": { "text": "Targeted surveillance (non-random sampling)", - "meaning": "GENEPIO:0100006", "title": "Surveillance ciblée (échantillonnage non aléatoire)" }, "Priority surveillance project": { "text": "Priority surveillance project", - "meaning": "GENEPIO:0100007", - "is_a": "Targeted surveillance (non-random sampling)", "title": "Projet de surveillance prioritaire" }, "Screening for Variants of Concern (VoC)": { "text": "Screening for Variants of Concern (VoC)", - "meaning": "GENEPIO:0100008", - "is_a": "Priority surveillance project", - "title": "Dépistage des variantes préoccupantes" + "title": "Dépistage des variants préoccupants" }, "Sample has epidemiological link to Variant of Concern (VoC)": { "text": "Sample has epidemiological link to Variant of Concern (VoC)", - "meaning": "GENEPIO:0100273", - "is_a": "Screening for Variants of Concern (VoC)", - "title": "L'échantillon a un lien épidémiologique avec la variante préoccupante" + "title": "Lien épidémiologique entre l’échantillon et le variant préoccupant" }, "Sample has epidemiological link to Omicron Variant": { "text": "Sample has epidemiological link to Omicron Variant", - "meaning": "GENEPIO:0100274", - "is_a": "Sample has epidemiological link to Variant of Concern (VoC)", - "title": "L'échantillon a un lien épidémiologique avec la variante Omicron" + "title": "Lien épidémiologique entre l’échantillon et le variant Omicron" }, "Longitudinal surveillance (repeat sampling of individuals)": { "text": "Longitudinal surveillance (repeat sampling of individuals)", - "meaning": "GENEPIO:0100009", - "is_a": "Priority surveillance project", "title": "Surveillance longitudinale (échantillonnage répété des individus)" }, "Chronic (prolonged) infection surveillance": { "text": "Chronic (prolonged) infection surveillance", - "meaning": "GENEPIO:0100842", - "is_a": "Longitudinal surveillance (repeat sampling of individuals)", "title": "Surveillance des infections chroniques (prolongées)" }, "Re-infection surveillance": { "text": "Re-infection surveillance", - "meaning": "GENEPIO:0100010", - "is_a": "Priority surveillance project", "title": "Surveillance des réinfections" }, "Vaccine escape surveillance": { "text": "Vaccine escape surveillance", - "meaning": "GENEPIO:0100011", - "is_a": "Priority surveillance project", - "title": "Surveillance des fuites de vaccins" + "title": "Surveillance de l’échappement vaccinal" }, "Travel-associated surveillance": { "text": "Travel-associated surveillance", - "meaning": "GENEPIO:0100012", - "is_a": "Priority surveillance project", "title": "Surveillance associée aux voyages" }, "Domestic travel surveillance": { "text": "Domestic travel surveillance", - "meaning": "GENEPIO:0100013", - "is_a": "Travel-associated surveillance", - "title": "Surveillance des voyages nationaux" + "title": "Surveillance des voyages intérieurs" }, "Interstate/ interprovincial travel surveillance": { "text": "Interstate/ interprovincial travel surveillance", - "meaning": "GENEPIO:0100275", - "is_a": "Domestic travel surveillance", - "title": "Surveillance des voyages interétatiques/interprovinciaux" + "title": "Surveillance des voyages entre les États ou les provinces" }, "Intra-state/ intra-provincial travel surveillance": { "text": "Intra-state/ intra-provincial travel surveillance", - "meaning": "GENEPIO:0100276", - "is_a": "Domestic travel surveillance", - "title": "Surveillance des voyages intra-étatiques/intraprovinciaux" + "title": "Surveillance des voyages dans les États ou les provinces" }, "International travel surveillance": { "text": "International travel surveillance", - "meaning": "GENEPIO:0100014", - "is_a": "Travel-associated surveillance", "title": "Surveillance des voyages internationaux" }, "Surveillance of international border crossing by air travel or ground transport": { "text": "Surveillance of international border crossing by air travel or ground transport", - "meaning": "GENEPIO:0100015", - "is_a": "International travel surveillance", - "title": "Surveillance du franchissement des frontières internationales par voie aérienne aérien ou terrestre" + "title": "Surveillance du franchissement des frontières internationales par voie aérienne ou terrestre" }, "Surveillance of international border crossing by air travel": { "text": "Surveillance of international border crossing by air travel", - "meaning": "GENEPIO:0100016", - "is_a": "International travel surveillance", - "title": "Surveillance du franchissement des frontières internationales par voie aérienne aérien" + "title": "Surveillance du franchissement des frontières internationales par voie aérienne" }, "Surveillance of international border crossing by ground transport": { "text": "Surveillance of international border crossing by ground transport", - "meaning": "GENEPIO:0100017", - "is_a": "International travel surveillance", - "title": "Surveillance du franchissement des frontières internationales par transport terrestre" + "title": "Surveillance du franchissement des frontières internationales par voie terrestre" }, "Surveillance from international worker testing": { "text": "Surveillance from international worker testing", - "meaning": "GENEPIO:0100018", - "is_a": "International travel surveillance", - "title": "Surveillance à partir d'essais internationaux sur les travailleurs" + "title": "Surveillance à partir de tests auprès des travailleurs étrangers" }, "Cluster/Outbreak investigation": { "text": "Cluster/Outbreak investigation", - "meaning": "GENEPIO:0100019", - "title": "Enquête sur les grappes et les foyers" + "title": "Enquête sur les grappes et les éclosions" }, "Multi-jurisdictional outbreak investigation": { "text": "Multi-jurisdictional outbreak investigation", - "meaning": "GENEPIO:0100020", - "is_a": "Cluster/Outbreak investigation", - "title": "Enquête sur les foyers multi-juridictionnels" + "title": "Enquête sur les éclosions multijuridictionnelles" }, "Intra-jurisdictional outbreak investigation": { "text": "Intra-jurisdictional outbreak investigation", - "meaning": "GENEPIO:0100021", - "is_a": "Cluster/Outbreak investigation", - "title": "Enquête sur un foyer intra-juridictionnel" + "title": "Enquête sur les éclosions intrajuridictionnelles" }, "Research": { "text": "Research", - "meaning": "GENEPIO:0100022", "title": "Recherche" }, "Viral passage experiment": { "text": "Viral passage experiment", - "meaning": "GENEPIO:0100023", - "is_a": "Research", - "title": "Expérience de passage viral" + "title": "Expérience de transmission virale" }, "Protocol testing experiment": { "text": "Protocol testing experiment", - "meaning": "GENEPIO:0100024", - "is_a": "Research", - "title": "Expérience de test de protocole" + "title": "Expérience du test de protocole" }, "Retrospective sequencing": { "text": "Retrospective sequencing", - "meaning": "GENEPIO:0100356", "title": "Séquençage rétrospectif" } } }, - "specimen processing menu": { - "name": "specimen processing menu", - "title": "menu de traitement des échantillons", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "Menu « Traitement des échantillons »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Virus passage": { "text": "Virus passage", - "meaning": "GENEPIO:0100039", - "title": "Passage du virus" + "title": "Transmission du virus" }, "RNA re-extraction (post RT-PCR)": { "text": "RNA re-extraction (post RT-PCR)", - "meaning": "GENEPIO:0100040", - "title": "Rétablissement de l'extraction de l'RNA (après RT-PCR)" + "title": "Rétablissement de l’extraction de l’ARN (après RT-PCR)" }, "Specimens pooled": { "text": "Specimens pooled", - "meaning": "OBI:0600016", "title": "Échantillons regroupés" } } }, - "lab host menu": { - "name": "lab host menu", - "title": "menu hôte du laboratoire", + "LabHostMenu": { + "name": "LabHostMenu", + "title": "Menu « Laboratoire hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "293/ACE2 cell line": { "text": "293/ACE2 cell line", - "meaning": "GENEPIO:0100041", "title": "Lignée cellulaire 293/ACE2" }, "Caco2 cell line": { "text": "Caco2 cell line", - "meaning": "BTO:0000195", "title": "Lignée cellulaire Caco2" }, "Calu3 cell line": { "text": "Calu3 cell line", - "meaning": "BTO:0002750", "title": "Lignée cellulaire Calu3" }, "EFK3B cell line": { "text": "EFK3B cell line", - "meaning": "GENEPIO:0100042", "title": "Lignée cellulaire EFK3B" }, "HEK293T cell line": { "text": "HEK293T cell line", - "meaning": "BTO:0002181", "title": "Lignée cellulaire HEK293T" }, "HRCE cell line": { "text": "HRCE cell line", - "meaning": "GENEPIO:0100043", "title": "Lignée cellulaire HRCE" }, "Huh7 cell line": { "text": "Huh7 cell line", - "meaning": "BTO:0001950", "title": "Lignée cellulaire Huh7" }, "LLCMk2 cell line": { "text": "LLCMk2 cell line", - "meaning": "CLO:0007330", "title": "Lignée cellulaire LLCMk2" }, "MDBK cell line": { "text": "MDBK cell line", - "meaning": "BTO:0000836", "title": "Lignée cellulaire MDBK" }, "NHBE cell line": { "text": "NHBE cell line", - "meaning": "BTO:0002924", - "title": "lignée cellulaire NHBE" + "title": "Lignée cellulaire NHBE" }, "PK-15 cell line": { "text": "PK-15 cell line", - "meaning": "BTO:0001865", "title": "Lignée cellulaire PK-15" }, "RK-13 cell line": { "text": "RK-13 cell line", - "meaning": "BTO:0002909", "title": "Lignée cellulaire RK-13" }, "U251 cell line": { "text": "U251 cell line", - "meaning": "BTO:0002035", "title": "Lignée cellulaire U251" }, "Vero cell line": { "text": "Vero cell line", - "meaning": "BTO:0001444", "title": "Lignée cellulaire Vero" }, "Vero E6 cell line": { "text": "Vero E6 cell line", - "meaning": "BTO:0004755", - "is_a": "Vero cell line", "title": "Lignée cellulaire Vero E6" }, "VeroE6/TMPRSS2 cell line": { "text": "VeroE6/TMPRSS2 cell line", - "meaning": "GENEPIO:0100044", - "is_a": "Vero E6 cell line", "title": "Lignée cellulaire VeroE6/TMPRSS2" } } }, - "host disease menu": { - "name": "host disease menu", - "title": "menu des maladies hôtes", - "from_schema": "https://example.com/CanCOGeN_Covid-19", - "permissible_values": { - "COVID-19": { - "text": "COVID-19", - "meaning": "MONDO:0100096", - "title": "COVID-19" - } - } - }, - "host age bin menu": { - "name": "host age bin menu", - "title": "menu du bac d'âge de l'hôte", - "from_schema": "https://example.com/CanCOGeN_Covid-19", - "permissible_values": { - "0 - 9": { - "text": "0 - 9", - "meaning": "GENEPIO:0100049", - "title": "0 - 9" - }, - "10 - 19": { - "text": "10 - 19", - "meaning": "GENEPIO:0100050", - "title": "10 - 19" - }, - "20 - 29": { - "text": "20 - 29", - "meaning": "GENEPIO:0100051", - "title": "20 - 29" - }, - "30 - 39": { - "text": "30 - 39", - "meaning": "GENEPIO:0100052", - "title": "30 - 39" - }, - "40 - 49": { - "text": "40 - 49", - "meaning": "GENEPIO:0100053", - "title": "40 - 49" - }, - "50 - 59": { - "text": "50 - 59", - "meaning": "GENEPIO:0100054", - "title": "50 - 59" - }, - "60 - 69": { - "text": "60 - 69", - "meaning": "GENEPIO:0100055", - "title": "60 - 69" - }, - "70 - 79": { - "text": "70 - 79", - "meaning": "GENEPIO:0100056", - "title": "70 - 79" - }, - "80 - 89": { - "text": "80 - 89", - "meaning": "GENEPIO:0100057", - "title": "80 - 89" - }, - "90 - 99": { - "text": "90 - 99", - "meaning": "GENEPIO:0100058", - "title": "90 - 99", - "exact_mappings": [ - "VirusSeq_Portal:90%2B" - ] - }, - "100+": { - "text": "100+", - "meaning": "GENEPIO:0100059", - "title": "100+", - "exact_mappings": [ - "VirusSeq_Portal:90%2B" - ] - } - } + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "Menu « Groupe d’âge de l’hôte »", + "from_schema": "https://example.com/CanCOGeN_Covid-19" }, - "host gender menu": { - "name": "host gender menu", - "title": "menu sexe de l'hôte", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "Menu « Genre de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Female": { "text": "Female", - "meaning": "NCIT:C46110", - "title": "Female" + "title": "Femme" }, "Male": { "text": "Male", - "meaning": "NCIT:C46109", - "title": "Male" + "title": "Homme" }, "Non-binary gender": { "text": "Non-binary gender", - "meaning": "GSSO:000132", - "title": "Non-binary gender" + "title": "Non binaire" }, "Transgender (assigned male at birth)": { "text": "Transgender (assigned male at birth)", - "meaning": "GSSO:004004", - "title": "Transgender (assigned male at birth)" + "title": "Transgenre (sexe masculin à la naissance)" }, "Transgender (assigned female at birth)": { "text": "Transgender (assigned female at birth)", - "meaning": "GSSO:004005", - "title": "Transgender (assigned female at birth)" + "title": "Transgenre (sexe féminin à la naissance)" }, "Undeclared": { "text": "Undeclared", - "meaning": "NCIT:C110959", - "title": "Undeclared" + "title": "Non déclaré" } } }, - "exposure event menu": { - "name": "exposure event menu", - "title": "menu d'événement d'exposition", + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "Menu « Événement d’exposition »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Mass Gathering": { "text": "Mass Gathering", - "meaning": "GENEPIO:0100237", "title": "Rassemblement de masse" }, "Agricultural Event": { "text": "Agricultural Event", - "meaning": "GENEPIO:0100240", - "is_a": "Mass Gathering", "title": "Événement agricole" }, - "Convention": { - "text": "Convention", - "meaning": "GENEPIO:0100238", - "is_a": "Mass Gathering", - "title": "Convention" - }, - "Convocation": { - "text": "Convocation", - "meaning": "GENEPIO:0100239", - "is_a": "Mass Gathering", - "title": "Convocation" - }, "Recreational Event": { "text": "Recreational Event", - "meaning": "GENEPIO:0100417", - "is_a": "Mass Gathering", "title": "Événement récréatif" }, - "Concert": { - "text": "Concert", - "meaning": "GENEPIO:0100418", - "is_a": "Recreational Event", - "title": "Concert" - }, "Sporting Event": { "text": "Sporting Event", - "meaning": "GENEPIO:0100419", - "is_a": "Recreational Event", - "title": "Manifestation sportive" + "title": "Événement sportif" }, "Religious Gathering": { "text": "Religious Gathering", - "meaning": "GENEPIO:0100241", "title": "Rassemblement religieux" }, "Mass": { "text": "Mass", - "meaning": "GENEPIO:0100242", - "is_a": "Religious Gathering", "title": "Messe" }, "Social Gathering": { "text": "Social Gathering", - "meaning": "PCO:0000033", "title": "Rassemblement social" }, "Baby Shower": { "text": "Baby Shower", - "meaning": "PCO:0000039", - "is_a": "Social Gathering", - "title": "Douche de bébé" + "title": "Réception-cadeau pour bébé" }, "Community Event": { "text": "Community Event", - "meaning": "PCO:0000034", - "is_a": "Social Gathering", - "title": "Evénement communautaire" + "title": "Événement communautaire" }, "Family Gathering": { "text": "Family Gathering", - "meaning": "GENEPIO:0100243", - "is_a": "Social Gathering", - "title": "Réunion de famille" + "title": "Rassemblement familial" }, "Family Reunion": { "text": "Family Reunion", - "meaning": "GENEPIO:0100244", - "is_a": "Family Gathering", "title": "Réunion de famille" }, "Funeral": { "text": "Funeral", - "meaning": "GENEPIO:0100245", - "is_a": "Social Gathering", "title": "Funérailles" }, "Party": { "text": "Party", - "meaning": "PCO:0000035", - "is_a": "Social Gathering", - "title": "Faire la fête" + "title": "Fête" }, "Potluck": { "text": "Potluck", - "meaning": "PCO:0000037", - "is_a": "Social Gathering", "title": "Repas-partage" }, "Wedding": { "text": "Wedding", - "meaning": "PCO:0000038", - "is_a": "Social Gathering", "title": "Mariage" }, "Other exposure event": { "text": "Other exposure event", - "title": "Autre événement d'exposition" + "title": "Autre événement d’exposition" } } }, - "exposure contact level menu": { - "name": "exposure contact level menu", - "title": "menu niveau de contact d'exposition", + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "Menu « Niveau de contact de l’exposition »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Contact with infected individual": { "text": "Contact with infected individual", - "meaning": "GENEPIO:0100357", "title": "Contact avec une personne infectée" }, "Direct contact (direct human-to-human contact)": { "text": "Direct contact (direct human-to-human contact)", - "meaning": "TRANS:0000001", - "is_a": "Contact with infected individual", - "title": "Direct (contact interhumain)" + "title": "Contact direct (contact interhumain)" }, "Indirect contact": { "text": "Indirect contact", - "meaning": "GENEPIO:0100246", - "is_a": "Contact with infected individual", "title": "Contact indirect" }, "Close contact (face-to-face, no direct contact)": { "text": "Close contact (face-to-face, no direct contact)", - "meaning": "GENEPIO:0100247", - "is_a": "Indirect contact", - "title": "Contact étroit (face à face)" + "title": "Contact étroit (contact personnel, aucun contact étroit)" }, "Casual contact": { "text": "Casual contact", - "meaning": "GENEPIO:0100248", - "is_a": "Indirect contact", "title": "Contact occasionnel" } } }, - "host role menu": { - "name": "host role menu", - "title": "menu du rôle d'hôte", + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "Menu « Rôle de l’hôte »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Attendee": { "text": "Attendee", - "meaning": "GENEPIO:0100249", "title": "Participant" }, "Student": { "text": "Student", - "meaning": "OMRSE:00000058", - "is_a": "Attendee", "title": "Étudiant" }, - "Patient": { - "text": "Patient", - "meaning": "OMRSE:00000030", - "title": "Patient" - }, "Inpatient": { "text": "Inpatient", - "meaning": "NCIT:C25182", - "is_a": "Patient", "title": "Patient hospitalisé" }, "Outpatient": { "text": "Outpatient", - "meaning": "NCIT:C28293", - "is_a": "Patient", - "title": "Ambulatoire" + "title": "Patient externe" }, "Passenger": { "text": "Passenger", - "meaning": "GENEPIO:0100250", "title": "Passager" }, "Resident": { "text": "Resident", - "meaning": "GENEPIO:0100251", "title": "Résident" }, "Visitor": { "text": "Visitor", - "meaning": "GENEPIO:0100252", "title": "Visiteur" }, "Volunteer": { "text": "Volunteer", - "meaning": "GENEPIO:0100253", "title": "Bénévole" }, "Work": { "text": "Work", - "meaning": "GENEPIO:0100254", "title": "Travail" }, "Administrator": { "text": "Administrator", - "meaning": "GENEPIO:0100255", - "is_a": "Work", "title": "Administrateur" }, "Child Care/Education Worker": { "text": "Child Care/Education Worker", - "is_a": "Work", - "title": "Travailleur en garderie/éducation" + "title": "Travailleur en garderie ou en éducation" }, "Essential Worker": { "text": "Essential Worker", - "is_a": "Work", "title": "Travailleur essentiel" }, "First Responder": { "text": "First Responder", - "meaning": "GENEPIO:0100256", - "is_a": "Work", "title": "Premier intervenant" }, "Firefighter": { "text": "Firefighter", - "meaning": "GENEPIO:0100257", - "is_a": "First Responder", - "title": "Sapeur pompier" + "title": "Pompier" }, "Paramedic": { "text": "Paramedic", - "meaning": "GENEPIO:0100258", - "is_a": "First Responder", - "title": "Paramédical" + "title": "Ambulancier" }, "Police Officer": { "text": "Police Officer", - "meaning": "GENEPIO:0100259", - "is_a": "First Responder", - "title": "Officier de police" + "title": "Policier" }, "Healthcare Worker": { "text": "Healthcare Worker", - "meaning": "GENEPIO:0100334", - "is_a": "Work", "title": "Travailleur de la santé" }, "Community Healthcare Worker": { "text": "Community Healthcare Worker", - "meaning": "GENEPIO:0100420", - "is_a": "Healthcare Worker", "title": "Agent de santé communautaire" }, "Laboratory Worker": { "text": "Laboratory Worker", - "meaning": "GENEPIO:0100262", - "is_a": "Healthcare Worker", - "title": "Ouvrier de laboratoire" + "title": "Travailleur de laboratoire" }, "Nurse": { "text": "Nurse", - "meaning": "OMRSE:00000014", - "is_a": "Healthcare Worker", "title": "Infirmière" }, "Personal Care Aid": { "text": "Personal Care Aid", - "meaning": "GENEPIO:0100263", - "is_a": "Healthcare Worker", "title": "Aide aux soins personnels" }, "Pharmacist": { "text": "Pharmacist", - "meaning": "GENEPIO:0100264", - "is_a": "Healthcare Worker", "title": "Pharmacien" }, "Physician": { "text": "Physician", - "meaning": "OMRSE:00000013", - "is_a": "Healthcare Worker", "title": "Médecin" }, "Housekeeper": { "text": "Housekeeper", - "meaning": "GENEPIO:0100260", - "is_a": "Work", - "title": "Gouvernante" + "title": "Aide-ménagère" }, "International worker": { "text": "International worker", - "is_a": "Work", "title": "Travailleur international" }, "Kitchen Worker": { "text": "Kitchen Worker", - "meaning": "GENEPIO:0100261", - "is_a": "Work", - "title": "Ouvrier de cuisine" + "title": "Aide de cuisine" }, "Rotational Worker": { "text": "Rotational Worker", - "meaning": "GENEPIO:0100354", - "is_a": "Work", "title": "Travailleur en rotation" }, "Seasonal Worker": { "text": "Seasonal Worker", - "meaning": "GENEPIO:0100355", - "is_a": "Work", "title": "Travailleur saisonnier" }, "Transport Worker": { "text": "Transport Worker", - "is_a": "Work", "title": "Ouvrier des transports" }, "Transport Truck Driver": { "text": "Transport Truck Driver", - "is_a": "Transport Worker", "title": "Chauffeur de camion de transport" }, "Veterinarian": { "text": "Veterinarian", - "meaning": "GENEPIO:0100265", - "is_a": "Work", "title": "Vétérinaire" }, "Social role": { "text": "Social role", - "meaning": "OMRSE:00000001", "title": "Rôle social" }, "Acquaintance of case": { "text": "Acquaintance of case", - "meaning": "GENEPIO:0100266", - "is_a": "Social role", - "title": "Connaissance de l'affaire" + "title": "Connaissance du cas" }, "Relative of case": { "text": "Relative of case", - "meaning": "GENEPIO:0100267", - "is_a": "Social role", - "title": "Parent de l'affaire" + "title": "Famille du cas" }, "Child of case": { "text": "Child of case", - "meaning": "GENEPIO:0100268", - "is_a": "Relative of case", - "title": "Enfant de la personne concernée" + "title": "Enfant du cas" }, "Parent of case": { "text": "Parent of case", - "meaning": "GENEPIO:0100269", - "is_a": "Relative of case", - "title": "Parent de l'affaire" + "title": "Parent du cas" }, "Father of case": { "text": "Father of case", - "meaning": "GENEPIO:0100270", - "is_a": "Parent of case", - "title": "Père de l'affaire" + "title": "Père du cas" }, "Mother of case": { "text": "Mother of case", - "meaning": "GENEPIO:0100271", - "is_a": "Parent of case", "title": "Mère du cas" }, "Spouse of case": { "text": "Spouse of case", - "meaning": "GENEPIO:0100272", - "is_a": "Social role", - "title": "Conjoint de l'affaire" + "title": "Conjoint du cas" }, "Other Host Role": { "text": "Other Host Role", - "title": "Autre rôle de l'hôte" + "title": "Autre rôle de l’hôte" } } }, - "exposure setting menu": { - "name": "exposure setting menu", - "title": "menu de réglage de l'exposition", + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "Menu « Contexte de l’exposition »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Human Exposure": { "text": "Human Exposure", - "meaning": "ECTO:3000005", "title": "Exposition humaine" }, "Contact with Known COVID-19 Case": { "text": "Contact with Known COVID-19 Case", - "meaning": "GENEPIO:0100184", - "is_a": "Human Exposure", "title": "Contact avec un cas connu de COVID-19" }, "Contact with Patient": { "text": "Contact with Patient", - "meaning": "GENEPIO:0100185", - "is_a": "Human Exposure", "title": "Contact avec un patient" }, "Contact with Probable COVID-19 Case": { "text": "Contact with Probable COVID-19 Case", - "meaning": "GENEPIO:0100186", - "is_a": "Human Exposure", "title": "Contact avec un cas probable de COVID-19" }, "Contact with Person with Acute Respiratory Illness": { "text": "Contact with Person with Acute Respiratory Illness", - "meaning": "GENEPIO:0100187", - "is_a": "Human Exposure", - "title": "Contact avec une personne atteinte d'une maladie respiratoire aiguë" + "title": "Contact avec une personne atteinte d’une maladie respiratoire aiguë" }, "Contact with Person with Fever and/or Cough": { "text": "Contact with Person with Fever and/or Cough", - "meaning": "GENEPIO:0100188", - "is_a": "Human Exposure", - "title": "Contact avec une personne présentant une fièvre et/ou une toux" + "title": "Contact avec une personne présentant une fièvre ou une toux" }, "Contact with Person who Recently Travelled": { "text": "Contact with Person who Recently Travelled", - "meaning": "GENEPIO:0100189", - "is_a": "Human Exposure", "title": "Contact avec une personne ayant récemment voyagé" }, "Occupational, Residency or Patronage Exposure": { "text": "Occupational, Residency or Patronage Exposure", - "meaning": "GENEPIO:0100190", - "title": "Exposition professionnelle, de résidence ou de patronage" + "title": "Exposition professionnelle ou résidentielle" }, "Abbatoir": { "text": "Abbatoir", - "meaning": "ECTO:1000033", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "Abbatoir" + "title": "Abattoir" }, "Animal Rescue": { "text": "Animal Rescue", - "meaning": "GENEPIO:0100191", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "Sauvetage d'animaux" + "title": "Refuge pour animaux" }, "Childcare": { "text": "Childcare", - "meaning": "GENEPIO:0100192", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "Garde d'enfants" + "title": "Garde d’enfants" }, "Daycare": { "text": "Daycare", - "meaning": "GENEPIO:0100193", - "is_a": "Childcare", "title": "Garderie" }, "Nursery": { "text": "Nursery", - "meaning": "GENEPIO:0100194", - "is_a": "Childcare", - "title": "Crèche" + "title": "Pouponnière" }, "Community Service Centre": { "text": "Community Service Centre", - "meaning": "GENEPIO:0100195", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Centre de services communautaires" }, "Correctional Facility": { "text": "Correctional Facility", - "meaning": "GENEPIO:0100196", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "Établissement pénitentiaire" + "title": "Établissement correctionnel" }, "Dormitory": { "text": "Dormitory", - "meaning": "GENEPIO:0100197", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Dortoir" }, "Farm": { "text": "Farm", - "meaning": "ECTO:1000034", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Ferme" }, "First Nations Reserve": { "text": "First Nations Reserve", - "meaning": "GENEPIO:0100198", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Réserve des Premières Nations" }, "Funeral Home": { "text": "Funeral Home", - "meaning": "GENEPIO:0100199", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "Maison funéraire" + "title": "Salon funéraire" }, "Group Home": { "text": "Group Home", - "meaning": "GENEPIO:0100200", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Foyer de groupe" }, "Healthcare Setting": { "text": "Healthcare Setting", - "meaning": "GENEPIO:0100201", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Établissement de soins de santé" }, - "Ambulance": { - "text": "Ambulance", - "meaning": "GENEPIO:0100202", - "is_a": "Healthcare Setting", - "title": "Ambulance" - }, "Acute Care Facility": { "text": "Acute Care Facility", - "meaning": "GENEPIO:0100203", - "is_a": "Healthcare Setting", - "title": "Établissement de soins aigus" + "title": "Établissement de soins de courte durée" }, "Clinic": { "text": "Clinic", - "meaning": "GENEPIO:0100204", - "is_a": "Healthcare Setting", "title": "Clinique" }, "Community Healthcare (At-Home) Setting": { "text": "Community Healthcare (At-Home) Setting", - "meaning": "GENEPIO:0100415", - "is_a": "Healthcare Setting", "title": "Établissement de soins de santé communautaire (à domicile)" }, "Community Health Centre": { "text": "Community Health Centre", - "meaning": "GENEPIO:0100205", - "is_a": "Healthcare Setting", "title": "Centre de santé communautaire" }, "Hospital": { "text": "Hospital", - "meaning": "ECTO:1000035", - "is_a": "Healthcare Setting", "title": "Hôpital" }, "Emergency Department": { "text": "Emergency Department", - "meaning": "GENEPIO:0100206", - "is_a": "Hospital", "title": "Service des urgences" }, "ICU": { "text": "ICU", - "meaning": "GENEPIO:0100207", - "is_a": "Hospital", - "title": "ICU" + "title": "USI" }, "Ward": { "text": "Ward", - "meaning": "GENEPIO:0100208", - "is_a": "Hospital", - "title": "Salle" + "title": "Service" }, "Laboratory": { "text": "Laboratory", - "meaning": "ECTO:1000036", - "is_a": "Healthcare Setting", "title": "Laboratoire" }, "Long-Term Care Facility": { "text": "Long-Term Care Facility", - "meaning": "GENEPIO:0100209", - "is_a": "Healthcare Setting", "title": "Établissement de soins de longue durée" }, "Pharmacy": { "text": "Pharmacy", - "meaning": "GENEPIO:0100210", - "is_a": "Healthcare Setting", "title": "Pharmacie" }, "Physician's Office": { "text": "Physician's Office", - "meaning": "GENEPIO:0100211", - "is_a": "Healthcare Setting", - "title": "Cabinet du médecin" + "title": "Cabinet de médecin" }, "Household": { "text": "Household", - "meaning": "GENEPIO:0100212", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Ménage" }, "Insecure Housing (Homeless)": { "text": "Insecure Housing (Homeless)", - "meaning": "GENEPIO:0100213", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Logement précaire (sans-abri)" }, "Occupational Exposure": { "text": "Occupational Exposure", - "meaning": "GENEPIO:0100214", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Exposition professionnelle" }, "Worksite": { "text": "Worksite", - "meaning": "GENEPIO:0100215", - "is_a": "Occupational Exposure", - "title": "Chantier" + "title": "Lieu de travail" }, "Office": { "text": "Office", - "meaning": "ECTO:1000037", - "is_a": "Worksite", "title": "Bureau" }, "Outdoors": { "text": "Outdoors", - "meaning": "GENEPIO:0100216", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "En plein air" + "title": "Plein air" }, "Camp/camping": { "text": "Camp/camping", - "meaning": "ECTO:5000009", - "is_a": "Outdoors", - "title": "Camper/camper" + "title": "Camp/Camping" }, "Hiking Trail": { "text": "Hiking Trail", - "meaning": "GENEPIO:0100217", - "is_a": "Outdoors", "title": "Sentier de randonnée" }, "Hunting Ground": { "text": "Hunting Ground", - "meaning": "ECTO:6000030", - "is_a": "Outdoors", - "title": "Terrain de chasse" + "title": "Territoire de chasse" }, "Ski Resort": { "text": "Ski Resort", - "meaning": "GENEPIO:0100218", - "is_a": "Outdoors", "title": "Station de ski" }, "Petting zoo": { "text": "Petting zoo", - "meaning": "ECTO:5000008", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Zoo pour enfants" }, "Place of Worship": { "text": "Place of Worship", - "meaning": "GENEPIO:0100220", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Lieu de culte" }, "Church": { "text": "Church", - "meaning": "GENEPIO:0100221", - "is_a": "Place of Worship", "title": "Église" }, "Mosque": { "text": "Mosque", - "meaning": "GENEPIO:0100222", - "is_a": "Place of Worship", "title": "Mosquée" }, - "Temple": { - "text": "Temple", - "meaning": "GENEPIO:0100223", - "is_a": "Place of Worship", - "title": "Temple" - }, - "Restaurant": { - "text": "Restaurant", - "meaning": "ECTO:1000040", - "is_a": "Occupational, Residency or Patronage Exposure", - "title": "Restaurant" - }, "Retail Store": { "text": "Retail Store", - "meaning": "ECTO:1000041", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Magasin de détail" }, "School": { "text": "School", - "meaning": "GENEPIO:0100224", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "École" }, "Temporary Residence": { "text": "Temporary Residence", - "meaning": "GENEPIO:0100225", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Résidence temporaire" }, "Homeless Shelter": { "text": "Homeless Shelter", - "meaning": "GENEPIO:0100226", - "is_a": "Temporary Residence", "title": "Refuge pour sans-abri" }, "Hotel": { "text": "Hotel", - "meaning": "GENEPIO:0100227", - "is_a": "Temporary Residence", "title": "Hôtel" }, "Veterinary Care Clinic": { "text": "Veterinary Care Clinic", - "meaning": "GENEPIO:0100228", - "is_a": "Occupational, Residency or Patronage Exposure", "title": "Clinique vétérinaire" }, "Travel Exposure": { "text": "Travel Exposure", - "meaning": "GENEPIO:0100229", - "title": "Exposition au voyage" + "title": "Exposition liée au voyage" }, "Travelled on a Cruise Ship": { "text": "Travelled on a Cruise Ship", - "meaning": "GENEPIO:0100230", - "is_a": "Travel Exposure", "title": "Voyage sur un bateau de croisière" }, "Travelled on a Plane": { "text": "Travelled on a Plane", - "meaning": "GENEPIO:0100231", - "is_a": "Travel Exposure", "title": "Voyage en avion" }, "Travelled on Ground Transport": { "text": "Travelled on Ground Transport", - "meaning": "GENEPIO:0100232", - "is_a": "Travel Exposure", - "title": "Transport terrestre" + "title": "Voyage par voie terrestre" }, "Travelled outside Province/Territory": { "text": "Travelled outside Province/Territory", - "meaning": "GENEPIO:0001118", - "is_a": "Travel Exposure", "title": "Voyage en dehors de la province ou du territoire" }, "Travelled outside Canada": { "text": "Travelled outside Canada", - "meaning": "GENEPIO:0001119", - "is_a": "Travel Exposure", "title": "Voyage en dehors du Canada" }, "Other Exposure Setting": { "text": "Other Exposure Setting", - "meaning": "GENEPIO:0100235", - "title": "Autres réglages d'exposition" + "title": "Autres contextes d’exposition" } } }, - "travel point of entry type menu": { - "name": "travel point of entry type menu", - "title": "menu de type de point d'entrée de voyage", + "TravelPointOfEntryTypeMenu": { + "name": "TravelPointOfEntryTypeMenu", + "title": "Menu «  Type de point d’entrée du voyage »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air": { "text": "Air", - "meaning": "GENEPIO:0100408", - "title": "Air" + "title": "Voie aérienne" }, "Land": { "text": "Land", - "meaning": "GENEPIO:0100409", - "title": "Atterrir" - } - } - }, - "border testing test day type menu": { - "name": "border testing test day type menu", - "title": "menu de type jour de test des tests aux frontières", - "from_schema": "https://example.com/CanCOGeN_Covid-19", - "permissible_values": { - "day 1": { - "text": "day 1", - "meaning": "GENEPIO:0100410", - "title": "jour 1" - }, - "day 8": { - "text": "day 8", - "meaning": "GENEPIO:0100411", - "title": "jour 8" - }, - "day 10": { - "text": "day 10", - "meaning": "GENEPIO:0100412", - "title": "jour 10" + "title": "Voie terrestre" } } }, - "travel history availability menu": { - "name": "travel history availability menu", - "title": "menu de disponibilité de l'historique de voyage", + "TravelHistoryAvailabilityMenu": { + "name": "TravelHistoryAvailabilityMenu", + "title": "Menu « Disponibilité des antécédents de voyage »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Travel history available": { "text": "Travel history available", - "meaning": "GENEPIO:0100650", - "title": "Historique de voyage disponible" + "title": "Antécédents de voyage disponibles" }, "Domestic travel history available": { "text": "Domestic travel history available", - "meaning": "GENEPIO:0100651", - "is_a": "Travel history available", - "title": "Historique des voyages intérieurs disponible" + "title": "Antécédents des voyages intérieurs disponibles" }, "International travel history available": { "text": "International travel history available", - "meaning": "GENEPIO:0100652", - "is_a": "Travel history available", - "title": "Historique des voyages internationaux disponible" + "title": "Antécédents des voyages internationaux disponibles" }, "International and domestic travel history available": { "text": "International and domestic travel history available", - "meaning": "GENEPIO:0100653", - "is_a": "Travel history available", - "title": "Historique des voyages internationaux et nationaux disponible" + "title": "Antécédents des voyages intérieurs et internationaux disponibles" }, "No travel history available": { "text": "No travel history available", - "meaning": "GENEPIO:0100654", - "title": "Aucun historique de voyage disponible" + "title": "Aucun antécédent de voyage disponible" } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", - "title": "menu des instruments de séquençage", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "Menu « Instrument de séquençage »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Illumina": { - "text": "Illumina", - "meaning": "GENEPIO:0100105", - "title": "Illumina" - }, "Illumina Genome Analyzer": { "text": "Illumina Genome Analyzer", - "meaning": "GENEPIO:0100106", - "is_a": "Illumina", - "title": "Illumina Genome Analyzer" + "title": "Analyseur de génome Illumina" }, "Illumina Genome Analyzer II": { "text": "Illumina Genome Analyzer II", - "meaning": "GENEPIO:0100107", - "is_a": "Illumina Genome Analyzer", - "title": "Illumina Genome Analyzer II" + "title": "Analyseur de génome Illumina II" }, "Illumina Genome Analyzer IIx": { "text": "Illumina Genome Analyzer IIx", - "meaning": "GENEPIO:0100108", - "is_a": "Illumina Genome Analyzer", - "title": "Illumina Genome Analyzer IIx" - }, - "Illumina HiScanSQ": { - "text": "Illumina HiScanSQ", - "meaning": "GENEPIO:0100109", - "is_a": "Illumina", - "title": "Illumina HiScanSQ" - }, - "Illumina HiSeq": { - "text": "Illumina HiSeq", - "meaning": "GENEPIO:0100110", - "is_a": "Illumina", - "title": "Illumina HiSeq" - }, - "Illumina HiSeq X": { - "text": "Illumina HiSeq X", - "meaning": "GENEPIO:0100111", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq X" - }, - "Illumina HiSeq X Five": { - "text": "Illumina HiSeq X Five", - "meaning": "GENEPIO:0100112", - "is_a": "Illumina HiSeq X", - "title": "Illumina HiSeq X Five" - }, - "Illumina HiSeq X Ten": { - "text": "Illumina HiSeq X Ten", - "meaning": "GENEPIO:0100113", - "is_a": "Illumina HiSeq X", - "title": "Illumina HiSeq X Ten" - }, - "Illumina HiSeq 1000": { - "text": "Illumina HiSeq 1000", - "meaning": "GENEPIO:0100114", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq 1000" - }, - "Illumina HiSeq 1500": { - "text": "Illumina HiSeq 1500", - "meaning": "GENEPIO:0100115", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq 1500" - }, - "Illumina HiSeq 2000": { - "text": "Illumina HiSeq 2000", - "meaning": "GENEPIO:0100116", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq 2000" - }, - "Illumina HiSeq 2500": { - "text": "Illumina HiSeq 2500", - "meaning": "GENEPIO:0100117", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq 2500" - }, - "Illumina HiSeq 3000": { - "text": "Illumina HiSeq 3000", - "meaning": "GENEPIO:0100118", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq 3000" - }, - "Illumina HiSeq 4000": { - "text": "Illumina HiSeq 4000", - "meaning": "GENEPIO:0100119", - "is_a": "Illumina HiSeq", - "title": "Illumina HiSeq 4000" - }, - "Illumina iSeq": { - "text": "Illumina iSeq", - "meaning": "GENEPIO:0100120", - "is_a": "Illumina", - "title": "Illumina iSeq" - }, - "Illumina iSeq 100": { - "text": "Illumina iSeq 100", - "meaning": "GENEPIO:0100121", - "is_a": "Illumina iSeq", - "title": "Illumina iSeq 100" - }, - "Illumina NovaSeq": { - "text": "Illumina NovaSeq", - "meaning": "GENEPIO:0100122", - "is_a": "Illumina", - "title": "Illumina NovaSeq" - }, - "Illumina NovaSeq 6000": { - "text": "Illumina NovaSeq 6000", - "meaning": "GENEPIO:0100123", - "is_a": "Illumina NovaSeq", - "title": "Illumina NovaSeq 6000" - }, - "Illumina MiniSeq": { - "text": "Illumina MiniSeq", - "meaning": "GENEPIO:0100124", - "is_a": "Illumina", - "title": "Illumina MiniSeq" - }, - "Illumina MiSeq": { - "text": "Illumina MiSeq", - "meaning": "GENEPIO:0100125", - "is_a": "Illumina", - "title": "Illumina MiSeq" - }, - "Illumina NextSeq": { - "text": "Illumina NextSeq", - "meaning": "GENEPIO:0100126", - "is_a": "Illumina", - "title": "Illumina NextSeq" - }, - "Illumina NextSeq 500": { - "text": "Illumina NextSeq 500", - "meaning": "GENEPIO:0100127", - "is_a": "Illumina NextSeq", - "title": "Illumina NextSeq 500" - }, - "Illumina NextSeq 550": { - "text": "Illumina NextSeq 550", - "meaning": "GENEPIO:0100128", - "is_a": "Illumina NextSeq", - "title": "Illumina NextSeq 550" - }, - "Illumina NextSeq 2000": { - "text": "Illumina NextSeq 2000", - "meaning": "GENEPIO:0100129", - "is_a": "Illumina NextSeq", - "title": "Illumina NextSeq 2000" - }, - "Pacific Biosciences": { - "text": "Pacific Biosciences", - "meaning": "GENEPIO:0100130", - "title": "Pacific Biosciences" - }, - "PacBio RS": { - "text": "PacBio RS", - "meaning": "GENEPIO:0100131", - "is_a": "Pacific Biosciences", - "title": "PacBio RS" - }, - "PacBio RS II": { - "text": "PacBio RS II", - "meaning": "GENEPIO:0100132", - "is_a": "Pacific Biosciences", - "title": "PacBio RS II" - }, - "PacBio Sequel": { - "text": "PacBio Sequel", - "meaning": "GENEPIO:0100133", - "is_a": "Pacific Biosciences", - "title": "PacBio Sequel" - }, - "PacBio Sequel II": { - "text": "PacBio Sequel II", - "meaning": "GENEPIO:0100134", - "is_a": "Pacific Biosciences", - "title": "PacBio Sequel II" - }, - "Ion Torrent": { - "text": "Ion Torrent", - "meaning": "GENEPIO:0100135", - "title": "Ion Torrent" - }, - "Ion Torrent PGM": { - "text": "Ion Torrent PGM", - "meaning": "GENEPIO:0100136", - "is_a": "Ion Torrent", - "title": "Ion Torrent PGM" - }, - "Ion Torrent Proton": { - "text": "Ion Torrent Proton", - "meaning": "GENEPIO:0100137", - "is_a": "Ion Torrent", - "title": "Ion Torrent Proton" - }, - "Ion Torrent S5 XL": { - "text": "Ion Torrent S5 XL", - "meaning": "GENEPIO:0100138", - "is_a": "Ion Torrent", - "title": "Ion Torrent S5 XL" - }, - "Ion Torrent S5": { - "text": "Ion Torrent S5", - "meaning": "GENEPIO:0100139", - "is_a": "Ion Torrent", - "title": "Ion Torrent S5" - }, - "Oxford Nanopore": { - "text": "Oxford Nanopore", - "meaning": "GENEPIO:0100140", - "title": "Oxford Nanopore" - }, - "Oxford Nanopore GridION": { - "text": "Oxford Nanopore GridION", - "meaning": "GENEPIO:0100141", - "is_a": "Oxford Nanopore", - "title": "Oxford Nanopore GridION" - }, - "Oxford Nanopore MinION": { - "text": "Oxford Nanopore MinION", - "meaning": "GENEPIO:0100142", - "is_a": "Oxford Nanopore", - "title": "Oxford Nanopore MinION" - }, - "Oxford Nanopore PromethION": { - "text": "Oxford Nanopore PromethION", - "meaning": "GENEPIO:0100143", - "is_a": "Oxford Nanopore", - "title": "Oxford Nanopore PromethION" - }, - "BGI Genomics": { - "text": "BGI Genomics", - "meaning": "GENEPIO:0100144", - "title": "BGI Genomics" - }, - "BGI Genomics BGISEQ-500": { - "text": "BGI Genomics BGISEQ-500", - "meaning": "GENEPIO:0100145", - "is_a": "BGI Genomics", - "title": "BGI Genomics BGISEQ-500" - }, - "MGI": { - "text": "MGI", - "meaning": "GENEPIO:0100146", - "title": "MGI" - }, - "MGI DNBSEQ-T7": { - "text": "MGI DNBSEQ-T7", - "meaning": "GENEPIO:0100147", - "is_a": "MGI", - "title": "MGI DNBSEQ-T7" - }, - "MGI DNBSEQ-G400": { - "text": "MGI DNBSEQ-G400", - "meaning": "GENEPIO:0100148", - "is_a": "MGI", - "title": "MGI DNBSEQ-G400" - }, - "MGI DNBSEQ-G400 FAST": { - "text": "MGI DNBSEQ-G400 FAST", - "meaning": "GENEPIO:0100149", - "is_a": "MGI", - "title": "MGI DNBSEQ-G400 FAST" - }, - "MGI DNBSEQ-G50": { - "text": "MGI DNBSEQ-G50", - "meaning": "GENEPIO:0100150", - "is_a": "MGI", - "title": "MGI DNBSEQ-G50" + "title": "Analyseur de génome Illumina IIx" } } }, - "gene name menu": { - "name": "gene name menu", - "title": "menu de nom de gène", + "GeneNameMenu": { + "name": "GeneNameMenu", + "title": "Menu « Nom du gène »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "E gene (orf4)": { "text": "E gene (orf4)", - "meaning": "GENEPIO:0100151", - "title": "E gène (orf4)", - "exact_mappings": [ - "CNPHI:E%20gene", - "BIOSAMPLE:E%20%28orf4%29" - ] + "title": "Gène E (orf4)" }, "M gene (orf5)": { "text": "M gene (orf5)", - "meaning": "GENEPIO:0100152", - "title": "M gène (orf5)", - "exact_mappings": [ - "BIOSAMPLE:M%20%28orf5%29" - ] + "title": "Gène M (orf5)" }, "N gene (orf9)": { "text": "N gene (orf9)", - "meaning": "GENEPIO:0100153", - "title": "N gène (orf9)", - "exact_mappings": [ - "BIOSAMPLE:N%20%28orf9%29" - ] + "title": "Gène N (orf9)" }, "Spike gene (orf2)": { "text": "Spike gene (orf2)", - "meaning": "GENEPIO:0100154", - "title": "Spike gène (orf2)", - "exact_mappings": [ - "BIOSAMPLE:S%20%28orf2%29" - ] - }, - "orf1ab (rep)": { - "text": "orf1ab (rep)", - "meaning": "GENEPIO:0100155", - "title": "orf1ab (rep)", - "exact_mappings": [ - "BIOSAMPLE:orf1ab%20%28rep%29" - ] - }, - "orf1a (pp1a)": { - "text": "orf1a (pp1a)", - "meaning": "GENEPIO:0100156", - "is_a": "orf1ab (rep)", - "title": "orf1a (pp1a)", - "exact_mappings": [ - "BIOSAMPLE:orf1a%20%28pp1a%29" - ] - }, - "nsp11": { - "text": "nsp11", - "meaning": "GENEPIO:0100157", - "is_a": "orf1a (pp1a)", - "title": "nsp11", - "exact_mappings": [ - "BIOSAMPLE:nsp11" - ] - }, - "nsp1": { - "text": "nsp1", - "meaning": "GENEPIO:0100158", - "is_a": "orf1ab (rep)", - "title": "nsp1", - "exact_mappings": [ - "BIOSAMPLE:nsp1" - ] - }, - "nsp2": { - "text": "nsp2", - "meaning": "GENEPIO:0100159", - "is_a": "orf1ab (rep)", - "title": "nsp2", - "exact_mappings": [ - "BIOSAMPLE:nsp2" - ] - }, - "nsp3": { - "text": "nsp3", - "meaning": "GENEPIO:0100160", - "is_a": "orf1ab (rep)", - "title": "nsp3", - "exact_mappings": [ - "BIOSAMPLE:nsp3" - ] - }, - "nsp4": { - "text": "nsp4", - "meaning": "GENEPIO:0100161", - "is_a": "orf1ab (rep)", - "title": "nsp4", - "exact_mappings": [ - "BIOSAMPLE:nsp4" - ] - }, - "nsp5": { - "text": "nsp5", - "meaning": "GENEPIO:0100162", - "is_a": "orf1ab (rep)", - "title": "nsp5", - "exact_mappings": [ - "BIOSAMPLE:nsp5" - ] - }, - "nsp6": { - "text": "nsp6", - "meaning": "GENEPIO:0100163", - "is_a": "orf1ab (rep)", - "title": "nsp6", - "exact_mappings": [ - "BIOSAMPLE:nsp6" - ] - }, - "nsp7": { - "text": "nsp7", - "meaning": "GENEPIO:0100164", - "is_a": "orf1ab (rep)", - "title": "nsp7", - "exact_mappings": [ - "BIOSAMPLE:nsp7" - ] - }, - "nsp8": { - "text": "nsp8", - "meaning": "GENEPIO:0100165", - "is_a": "orf1ab (rep)", - "title": "nsp8", - "exact_mappings": [ - "BIOSAMPLE:nsp8" - ] - }, - "nsp9": { - "text": "nsp9", - "meaning": "GENEPIO:0100166", - "is_a": "orf1ab (rep)", - "title": "nsp9", - "exact_mappings": [ - "BIOSAMPLE:nsp9" - ] - }, - "nsp10": { - "text": "nsp10", - "meaning": "GENEPIO:0100167", - "is_a": "orf1ab (rep)", - "title": "nsp10", - "exact_mappings": [ - "BIOSAMPLE:nsp10" - ] + "title": "Gène de pointe (orf2)" }, "RdRp gene (nsp12)": { "text": "RdRp gene (nsp12)", - "meaning": "GENEPIO:0100168", - "is_a": "orf1ab (rep)", - "title": "RdRp gène (nsp12)", - "exact_mappings": [ - "BIOSAMPLE:nsp12%20%28RdRp%29" - ] + "title": "Gène RdRp (nsp12)" }, "hel gene (nsp13)": { "text": "hel gene (nsp13)", - "meaning": "GENEPIO:0100169", - "is_a": "orf1ab (rep)", - "title": "hel gène (nsp13)", - "exact_mappings": [ - "BIOSAMPLE:nsp13%20%28Hel%29" - ] + "title": "Gène hel (nsp13)" }, "exoN gene (nsp14)": { "text": "exoN gene (nsp14)", - "meaning": "GENEPIO:0100170", - "is_a": "orf1ab (rep)", - "title": "exoN gène (nsp14)", - "exact_mappings": [ - "BIOSAMPLE:nsp14%20%28ExoN%29" - ] - }, - "nsp15": { - "text": "nsp15", - "meaning": "GENEPIO:0100171", - "is_a": "orf1ab (rep)", - "title": "nsp15", - "exact_mappings": [ - "BIOSAMPLE:nsp15" - ] - }, - "nsp16": { - "text": "nsp16", - "meaning": "GENEPIO:0100172", - "is_a": "orf1ab (rep)", - "title": "nsp16", - "exact_mappings": [ - "BIOSAMPLE:nsp16" - ] - }, - "orf3a": { - "text": "orf3a", - "meaning": "GENEPIO:0100173", - "title": "orf3a", - "exact_mappings": [ - "BIOSAMPLE:orf3a" - ] - }, - "orf3b": { - "text": "orf3b", - "meaning": "GENEPIO:0100174", - "title": "orf3b", - "exact_mappings": [ - "BIOSAMPLE:orf3b" - ] - }, - "orf6 (ns6)": { - "text": "orf6 (ns6)", - "meaning": "GENEPIO:0100175", - "title": "orf6 (ns6)", - "exact_mappings": [ - "BIOSAMPLE:orf6%20%28ns6%29" - ] - }, - "orf7a": { - "text": "orf7a", - "meaning": "GENEPIO:0100176", - "title": "orf7a", - "exact_mappings": [ - "BIOSAMPLE:orf7a" - ] - }, - "orf7b (ns7b)": { - "text": "orf7b (ns7b)", - "meaning": "GENEPIO:0100177", - "title": "orf7b (ns7b)", - "exact_mappings": [ - "BIOSAMPLE:orf7b%20%28ns7b%29" - ] - }, - "orf8 (ns8)": { - "text": "orf8 (ns8)", - "meaning": "GENEPIO:0100178", - "title": "orf8 (ns8)", - "exact_mappings": [ - "BIOSAMPLE:orf8%20%28ns8%29" - ] - }, - "orf9b": { - "text": "orf9b", - "meaning": "GENEPIO:0100179", - "title": "orf9b", - "exact_mappings": [ - "BIOSAMPLE:orf9b" - ] - }, - "orf9c": { - "text": "orf9c", - "meaning": "GENEPIO:0100180", - "title": "orf9c", - "exact_mappings": [ - "BIOSAMPLE:orf9c" - ] - }, - "orf10": { - "text": "orf10", - "meaning": "GENEPIO:0100181", - "title": "orf10", - "exact_mappings": [ - "BIOSAMPLE:orf10" - ] - }, - "orf14": { - "text": "orf14", - "meaning": "GENEPIO:0100182", - "title": "orf14", - "exact_mappings": [ - "BIOSAMPLE:orf14" - ] + "title": "Gène exoN (nsp14)" }, "SARS-COV-2 5' UTR": { "text": "SARS-COV-2 5' UTR", - "meaning": "GENEPIO:0100183", - "title": "SARS-COV-2 5' UTR" + "title": "SRAS-COV-2 5' UTR" } } }, - "sequence submitted by menu": { - "name": "sequence submitted by menu", - "title": "séquence soumise par menu", + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", + "title": "Menu « Séquence soumise par »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Alberta Precision Labs (APL)": { - "text": "Alberta Precision Labs (APL)", - "title": "Alberta Precision Labs (APL)" - }, - "Alberta ProvLab North (APLN)": { - "text": "Alberta ProvLab North (APLN)", - "is_a": "Alberta Precision Labs (APL)", - "title": "Alberta ProvLab North (APLN)" - }, - "Alberta ProvLab South (APLS)": { - "text": "Alberta ProvLab South (APLS)", - "is_a": "Alberta Precision Labs (APL)", - "title": "Alberta ProvLab South (APLS)" - }, "BCCDC Public Health Laboratory": { "text": "BCCDC Public Health Laboratory", - "title": "BCCDC Public Health Laboratory" - }, - "Canadore College": { - "text": "Canadore College", - "title": "Canadore College" - }, - "The Centre for Applied Genomics (TCAG)": { - "text": "The Centre for Applied Genomics (TCAG)", - "title": "The Centre for Applied Genomics (TCAG)" - }, - "Dynacare": { - "text": "Dynacare", - "title": "Dynacare" - }, - "Dynacare (Brampton)": { - "text": "Dynacare (Brampton)", - "title": "Dynacare (Brampton)" - }, - "Dynacare (Manitoba)": { - "text": "Dynacare (Manitoba)", - "title": "Dynacare (Manitoba)" - }, - "The Hospital for Sick Children (SickKids)": { - "text": "The Hospital for Sick Children (SickKids)", - "title": "The Hospital for Sick Children (SickKids)" - }, - "Laboratoire de santé publique du Québec (LSPQ)": { - "text": "Laboratoire de santé publique du Québec (LSPQ)", - "title": "Laboratoire de santé publique du Québec (LSPQ)" + "title": "Laboratoire de santé publique du CCMCB" }, "Manitoba Cadham Provincial Laboratory": { "text": "Manitoba Cadham Provincial Laboratory", - "title": "Manitoba Cadham Provincial Laboratory" + "title": "Laboratoire provincial Cadham du Manitoba" }, "McGill University": { "text": "McGill University", - "title": "McGill University" + "title": "Université McGill" }, "McMaster University": { "text": "McMaster University", - "title": "McMaster University" + "title": "Université McMaster" }, "National Microbiology Laboratory (NML)": { "text": "National Microbiology Laboratory (NML)", - "title": "National Microbiology Laboratory (NML)" + "title": "Laboratoire national de microbiologie (LNM)" }, "New Brunswick - Vitalité Health Network": { "text": "New Brunswick - Vitalité Health Network", - "title": "New Brunswick - Vitalité Health Network" + "title": "Nouveau-Brunswick – Réseau de santé Vitalité" }, "Newfoundland and Labrador - Eastern Health": { "text": "Newfoundland and Labrador - Eastern Health", - "title": "Newfoundland and Labrador - Eastern Health" + "title": "Terre-Neuve-et-Labrador – Eastern Health" }, "Newfoundland and Labrador - Newfoundland and Labrador Health Services": { "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services", - "title": "Newfoundland and Labrador - Newfoundland and Labrador Health Services" + "title": "Terre-Neuve-et-Labrador – Newfoundland and Labrador Health Services" }, "Nova Scotia Health Authority": { "text": "Nova Scotia Health Authority", - "title": "Nova Scotia Health Authority" + "title": "Autorité sanitaire de la Nouvelle-Écosse" }, "Ontario Institute for Cancer Research (OICR)": { "text": "Ontario Institute for Cancer Research (OICR)", - "title": "Ontario Institute for Cancer Research (OICR)" + "title": "Institut ontarien de recherche sur le cancer (IORC)" }, "Prince Edward Island - Health PEI": { "text": "Prince Edward Island - Health PEI", - "title": "Prince Edward Island - Health PEI" + "title": "Île-du-Prince-Édouard – Santé Î.-P.-É." }, "Public Health Ontario (PHO)": { "text": "Public Health Ontario (PHO)", - "title": "Public Health Ontario (PHO)" + "title": "Santé publique Ontario (SPO)" }, "Queen's University / Kingston Health Sciences Centre": { "text": "Queen's University / Kingston Health Sciences Centre", - "title": "Queen's University / Kingston Health Sciences Centre" + "title": "Université Queen’s – Centre des sciences de la santé de Kingston" }, "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)": { "text": "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)", - "title": "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)" - }, - "Sunnybrook Health Sciences Centre": { - "text": "Sunnybrook Health Sciences Centre", - "title": "Sunnybrook Health Sciences Centre" + "title": "Saskatchewan – Laboratoire provincial Roy Romanow" }, "Thunder Bay Regional Health Sciences Centre": { "text": "Thunder Bay Regional Health Sciences Centre", - "title": "Thunder Bay Regional Health Sciences Centre" + "title": "Centre régional des sciences\nde la santé de Thunder Bay" } } }, - "sample collected by menu": { - "name": "sample collected by menu", - "title": "échantillon collecté par menu", + "SampleCollectedByMenu": { + "name": "SampleCollectedByMenu", + "title": "Menu « Échantillon prélevé par »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Alberta Precision Labs (APL)": { - "text": "Alberta Precision Labs (APL)", - "title": "Alberta Precision Labs (APL)" - }, - "Alberta ProvLab North (APLN)": { - "text": "Alberta ProvLab North (APLN)", - "is_a": "Alberta Precision Labs (APL)", - "title": "Alberta ProvLab North (APLN)" - }, - "Alberta ProvLab South (APLS)": { - "text": "Alberta ProvLab South (APLS)", - "is_a": "Alberta Precision Labs (APL)", - "title": "Alberta ProvLab South (APLS)" - }, "BCCDC Public Health Laboratory": { "text": "BCCDC Public Health Laboratory", - "title": "BCCDC Public Health Laboratory" - }, - "Dynacare": { - "text": "Dynacare", - "title": "Dynacare" - }, - "Dynacare (Manitoba)": { - "text": "Dynacare (Manitoba)", - "title": "Dynacare (Manitoba)" - }, - "Dynacare (Brampton)": { - "text": "Dynacare (Brampton)", - "title": "Dynacare (Brampton)" + "title": "Laboratoire de santé publique du CCMCB" }, "Eastern Ontario Regional Laboratory Association": { "text": "Eastern Ontario Regional Laboratory Association", - "title": "Eastern Ontario Regional Laboratory Association" - }, - "Hamilton Health Sciences": { - "text": "Hamilton Health Sciences", - "title": "Hamilton Health Sciences" - }, - "The Hospital for Sick Children (SickKids)": { - "text": "The Hospital for Sick Children (SickKids)", - "title": "The Hospital for Sick Children (SickKids)" - }, - "Laboratoire de santé publique du Québec (LSPQ)": { - "text": "Laboratoire de santé publique du Québec (LSPQ)", - "title": "Laboratoire de santé publique du Québec (LSPQ)" + "title": "Association des laboratoires régionaux de l’Est de l’Ontario" }, "Lake of the Woods District Hospital - Ontario": { "text": "Lake of the Woods District Hospital - Ontario", - "title": "Lake of the Woods District Hospital - Ontario" - }, - "LifeLabs": { - "text": "LifeLabs", - "title": "LifeLabs" - }, - "LifeLabs (Ontario)": { - "text": "LifeLabs (Ontario)", - "title": "LifeLabs (Ontario)" + "title": "Lake of the Woods District Hospital – Ontario" }, "Manitoba Cadham Provincial Laboratory": { "text": "Manitoba Cadham Provincial Laboratory", - "title": "Manitoba Cadham Provincial Laboratory" + "title": "Laboratoire provincial Cadham du Manitoba" }, "McMaster University": { "text": "McMaster University", - "title": "McMaster University" - }, - "Mount Sinai Hospital": { - "text": "Mount Sinai Hospital", - "title": "Mount Sinai Hospital" + "title": "Université McMaster" }, "National Microbiology Laboratory (NML)": { "text": "National Microbiology Laboratory (NML)", - "title": "National Microbiology Laboratory (NML)" + "title": "Laboratoire national de microbiologie (LNM)" }, "New Brunswick - Vitalité Health Network": { "text": "New Brunswick - Vitalité Health Network", - "title": "New Brunswick - Vitalité Health Network" + "title": "Nouveau-Brunswick – Réseau de santé Vitalité" }, "Newfoundland and Labrador - Eastern Health": { "text": "Newfoundland and Labrador - Eastern Health", - "title": "Newfoundland and Labrador - Eastern Health" + "title": "Terre-Neuve-et-Labrador – Eastern Health" }, "Newfoundland and Labrador - Newfoundland and Labrador Health Services": { "text": "Newfoundland and Labrador - Newfoundland and Labrador Health Services", - "title": "Newfoundland and Labrador - Newfoundland and Labrador Health Services" + "title": "Terre-Neuve-et-Labrador – Newfoundland and Labrador Health Services" }, "Nova Scotia Health Authority": { "text": "Nova Scotia Health Authority", - "title": "Nova Scotia Health Authority" - }, - "Nunavut": { - "text": "Nunavut", - "title": "Nunavut" + "title": "Autorité sanitaire de la Nouvelle-Écosse" }, "Ontario Institute for Cancer Research (OICR)": { "text": "Ontario Institute for Cancer Research (OICR)", - "title": "Ontario Institute for Cancer Research (OICR)" + "title": "Institut ontarien de recherche sur le cancer (IORC)" }, "Prince Edward Island - Health PEI": { "text": "Prince Edward Island - Health PEI", - "title": "Prince Edward Island - Health PEI" + "title": "Île-du-Prince-Édouard – Santé Î.-P.-É." }, "Public Health Ontario (PHO)": { "text": "Public Health Ontario (PHO)", - "title": "Public Health Ontario (PHO)" + "title": "Santé publique Ontario (SPO)" }, "Queen's University / Kingston Health Sciences Centre": { "text": "Queen's University / Kingston Health Sciences Centre", - "title": "Queen's University / Kingston Health Sciences Centre" + "title": "Université Queen’s – Centre des sciences de la santé de Kingston" }, "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)": { "text": "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)", - "title": "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)" - }, - "Shared Hospital Laboratory": { - "text": "Shared Hospital Laboratory", - "title": "Shared Hospital Laboratory" + "title": "Saskatchewan – Laboratoire provincial Roy Romanow" }, "St. John's Rehab at Sunnybrook Hospital": { "text": "St. John's Rehab at Sunnybrook Hospital", - "title": "St. John's Rehab at Sunnybrook Hospital" - }, - "Switch Health": { - "text": "Switch Health", - "title": "Switch Health" - }, - "Sunnybrook Health Sciences Centre": { - "text": "Sunnybrook Health Sciences Centre", - "title": "Sunnybrook Health Sciences Centre" - }, - "Unity Health Toronto": { - "text": "Unity Health Toronto", - "title": "Unity Health Toronto" - }, - "William Osler Health System": { - "text": "William Osler Health System", - "title": "William Osler Health System" + "title": "St. John’s Rehab à l’hôpital Sunnybrook" } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", - "title": "menu geo_loc_name (pays)", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "Menu « nom_lieu_géo (pays) »", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { - "Afghanistan": { - "text": "Afghanistan", - "meaning": "GAZ:00006882", - "title": "Afghanistan" - }, "Albania": { "text": "Albania", - "meaning": "GAZ:00002953", "title": "Albanie" }, "Algeria": { "text": "Algeria", - "meaning": "GAZ:00000563", "title": "Algérie" }, "American Samoa": { "text": "American Samoa", - "meaning": "GAZ:00003957", "title": "Samoa américaines" }, "Andorra": { "text": "Andorra", - "meaning": "GAZ:00002948", "title": "Andorre" }, - "Angola": { - "text": "Angola", - "meaning": "GAZ:00001095", - "title": "Angola" - }, - "Anguilla": { - "text": "Anguilla", - "meaning": "GAZ:00009159", - "title": "Anguilla" - }, "Antarctica": { "text": "Antarctica", - "meaning": "GAZ:00000462", "title": "Antarctique" }, "Antigua and Barbuda": { "text": "Antigua and Barbuda", - "meaning": "GAZ:00006883", "title": "Antigua-et-Barbuda" }, "Argentina": { "text": "Argentina", - "meaning": "GAZ:00002928", "title": "Argentine" }, "Armenia": { "text": "Armenia", - "meaning": "GAZ:00004094", "title": "Arménie" }, - "Aruba": { - "text": "Aruba", - "meaning": "GAZ:00004025", - "title": "Aruba" - }, "Ashmore and Cartier Islands": { "text": "Ashmore and Cartier Islands", - "meaning": "GAZ:00005901", "title": "Îles Ashmore et Cartier" }, "Australia": { "text": "Australia", - "meaning": "GAZ:00000463", "title": "Australie" }, "Austria": { "text": "Austria", - "meaning": "GAZ:00002942", - "title": "L'Autriche" + "title": "Autriche" }, "Azerbaijan": { "text": "Azerbaijan", - "meaning": "GAZ:00004941", "title": "Azerbaïdjan" }, - "Bahamas": { - "text": "Bahamas", - "meaning": "GAZ:00002733", - "title": "Bahamas" - }, "Bahrain": { "text": "Bahrain", - "meaning": "GAZ:00005281", "title": "Bahreïn" }, "Baker Island": { "text": "Baker Island", - "meaning": "GAZ:00007117", - "title": "Île Boulanger" - }, - "Bangladesh": { - "text": "Bangladesh", - "meaning": "GAZ:00003750", - "title": "Bangladesh" + "title": "Île Baker" }, "Barbados": { "text": "Barbados", - "meaning": "GAZ:00001251", "title": "Barbade" }, "Bassas da India": { "text": "Bassas da India", - "meaning": "GAZ:00005810", - "title": "Bassas de l'Inde" + "title": "Bassas de l’Inde" }, "Belarus": { "text": "Belarus", - "meaning": "GAZ:00006886", - "title": "Biélorussie" + "title": "Bélarus" }, "Belgium": { "text": "Belgium", - "meaning": "GAZ:00002938", "title": "Belgique" }, "Belize": { "text": "Belize", - "meaning": "GAZ:00002934", "title": "Bélize" }, "Benin": { "text": "Benin", - "meaning": "GAZ:00000904", "title": "Bénin" }, "Bermuda": { "text": "Bermuda", - "meaning": "GAZ:00001264", "title": "Bermudes" }, "Bhutan": { "text": "Bhutan", - "meaning": "GAZ:00003920", "title": "Bhoutan" }, "Bolivia": { "text": "Bolivia", - "meaning": "GAZ:00002511", "title": "Bolivie" }, "Borneo": { "text": "Borneo", - "meaning": "GAZ:00025355", "title": "Bornéo" }, "Bosnia and Herzegovina": { "text": "Bosnia and Herzegovina", - "meaning": "GAZ:00006887", - "title": "Bosnie Herzégovine" - }, - "Botswana": { - "text": "Botswana", - "meaning": "GAZ:00001097", - "title": "Botswana" + "title": "Bosnie-Herzégovine" }, "Bouvet Island": { "text": "Bouvet Island", - "meaning": "GAZ:00001453", "title": "Île Bouvet" }, "Brazil": { "text": "Brazil", - "meaning": "GAZ:00002828", "title": "Brésil" }, "British Virgin Islands": { "text": "British Virgin Islands", - "meaning": "GAZ:00003961", "title": "Îles Vierges britanniques" }, - "Brunei": { - "text": "Brunei", - "meaning": "GAZ:00003901", - "title": "Brunéi" - }, "Bulgaria": { "text": "Bulgaria", - "meaning": "GAZ:00002950", "title": "Bulgarie" }, - "Burkina Faso": { - "text": "Burkina Faso", - "meaning": "GAZ:00000905", - "title": "Burkina Faso" - }, - "Burundi": { - "text": "Burundi", - "meaning": "GAZ:00001090", - "title": "Burundi" - }, "Cambodia": { "text": "Cambodia", - "meaning": "GAZ:00006888", "title": "Cambodge" }, "Cameroon": { "text": "Cameroon", - "meaning": "GAZ:00001093", "title": "Cameroun" }, - "Canada": { - "text": "Canada", - "meaning": "GAZ:00002560", - "title": "Canada" - }, "Cape Verde": { "text": "Cape Verde", - "meaning": "GAZ:00001227", "title": "Cap-Vert" }, "Cayman Islands": { "text": "Cayman Islands", - "meaning": "GAZ:00003986", "title": "Îles Caïmans" }, "Central African Republic": { "text": "Central African Republic", - "meaning": "GAZ:00001089", "title": "République centrafricaine" }, "Chad": { "text": "Chad", - "meaning": "GAZ:00000586", "title": "Tchad" }, "Chile": { "text": "Chile", - "meaning": "GAZ:00002825", "title": "Chili" }, "China": { "text": "China", - "meaning": "GAZ:00002845", "title": "Chine" }, "Christmas Island": { "text": "Christmas Island", - "meaning": "GAZ:00005915", - "title": "L'île de noël" + "title": "Île Christmas" }, "Clipperton Island": { "text": "Clipperton Island", - "meaning": "GAZ:00005838", - "title": "Île Clipperton" + "title": "Îlot de Clipperton" }, "Cocos Islands": { "text": "Cocos Islands", - "meaning": "GAZ:00009721", "title": "Îles Cocos" }, "Colombia": { "text": "Colombia", - "meaning": "GAZ:00002929", "title": "Colombie" }, "Comoros": { "text": "Comoros", - "meaning": "GAZ:00005820", "title": "Comores" }, "Cook Islands": { "text": "Cook Islands", - "meaning": "GAZ:00053798", - "title": "les Îles Cook" + "title": "Îles Cook" }, "Coral Sea Islands": { "text": "Coral Sea Islands", - "meaning": "GAZ:00005917", "title": "Îles de la mer de Corail" }, - "Costa Rica": { - "text": "Costa Rica", - "meaning": "GAZ:00002901", - "title": "Costa Rica" - }, "Cote d'Ivoire": { "text": "Cote d'Ivoire", - "meaning": "GAZ:00000906", - "title": "Côte d'Ivoire" + "title": "Côte d’Ivoire" }, "Croatia": { "text": "Croatia", - "meaning": "GAZ:00002719", "title": "Croatie" }, - "Cuba": { - "text": "Cuba", - "meaning": "GAZ:00003762", - "title": "Cuba" - }, "Curacao": { "text": "Curacao", - "meaning": "GAZ:00012582", - "title": "Curacao" + "title": "Curaçao" }, "Cyprus": { "text": "Cyprus", - "meaning": "GAZ:00004006", "title": "Chypre" }, "Czech Republic": { "text": "Czech Republic", - "meaning": "GAZ:00002954", "title": "République tchèque" }, "Democratic Republic of the Congo": { "text": "Democratic Republic of the Congo", - "meaning": "GAZ:00001086", - "title": "République Démocratique du Congo" + "title": "République démocratique du Congo" }, "Denmark": { "text": "Denmark", - "meaning": "GAZ:00005852", "title": "Danemark" }, - "Djibouti": { - "text": "Djibouti", - "meaning": "GAZ:00000582", - "title": "Djibouti" - }, "Dominica": { "text": "Dominica", - "meaning": "GAZ:00006890", "title": "Dominique" }, "Dominican Republic": { "text": "Dominican Republic", - "meaning": "GAZ:00003952", "title": "République dominicaine" }, "Ecuador": { "text": "Ecuador", - "meaning": "GAZ:00002912", "title": "Équateur" }, "Egypt": { "text": "Egypt", - "meaning": "GAZ:00003934", - "title": "Egypte" + "title": "Égypte" }, "El Salvador": { "text": "El Salvador", - "meaning": "GAZ:00002935", - "title": "Le Salvador" + "title": "Salvador" }, "Equatorial Guinea": { "text": "Equatorial Guinea", - "meaning": "GAZ:00001091", - "title": "Guinée Équatoriale" + "title": "Guinée équatoriale" }, "Eritrea": { "text": "Eritrea", - "meaning": "GAZ:00000581", "title": "Érythrée" }, "Estonia": { "text": "Estonia", - "meaning": "GAZ:00002959", "title": "Estonie" }, - "Eswatini": { - "text": "Eswatini", - "meaning": "GAZ:00001099", - "title": "Eswatini" - }, "Ethiopia": { "text": "Ethiopia", - "meaning": "GAZ:00000567", - "title": "Ethiopie" + "title": "Éthiopie" }, "Europa Island": { "text": "Europa Island", - "meaning": "GAZ:00005811", - "title": "Île d'Europe" + "title": "Île Europa" }, "Falkland Islands (Islas Malvinas)": { "text": "Falkland Islands (Islas Malvinas)", - "meaning": "GAZ:00001412", - "title": "Îles Falkland (Islas Malvinas)" + "title": "Îles Falkland (îles Malouines)" }, "Faroe Islands": { "text": "Faroe Islands", - "meaning": "GAZ:00059206", "title": "Îles Féroé" }, "Fiji": { "text": "Fiji", - "meaning": "GAZ:00006891", "title": "Fidji" }, "Finland": { "text": "Finland", - "meaning": "GAZ:00002937", "title": "Finlande" }, - "France": { - "text": "France", - "meaning": "GAZ:00003940", - "title": "France" - }, "French Guiana": { "text": "French Guiana", - "meaning": "GAZ:00002516", - "title": "Guyane Française" + "title": "Guyane française" }, "French Polynesia": { "text": "French Polynesia", - "meaning": "GAZ:00002918", "title": "Polynésie française" }, "French Southern and Antarctic Lands": { "text": "French Southern and Antarctic Lands", - "meaning": "GAZ:00003753", "title": "Terres australes et antarctiques françaises" }, - "Gabon": { - "text": "Gabon", - "meaning": "GAZ:00001092", - "title": "Gabon" - }, "Gambia": { "text": "Gambia", - "meaning": "GAZ:00000907", "title": "Gambie" }, "Gaza Strip": { "text": "Gaza Strip", - "meaning": "GAZ:00009571", - "title": "bande de Gaza" + "title": "Bande de Gaza" }, "Georgia": { "text": "Georgia", - "meaning": "GAZ:00004942", "title": "Géorgie" }, "Germany": { "text": "Germany", - "meaning": "GAZ:00002646", "title": "Allemagne" }, - "Ghana": { - "text": "Ghana", - "meaning": "GAZ:00000908", - "title": "Ghana" - }, - "Gibraltar": { - "text": "Gibraltar", - "meaning": "GAZ:00003987", - "title": "Gibraltar" - }, "Glorioso Islands": { "text": "Glorioso Islands", - "meaning": "GAZ:00005808", "title": "Îles Glorieuses" }, "Greece": { "text": "Greece", - "meaning": "GAZ:00002945", "title": "Grèce" }, "Greenland": { "text": "Greenland", - "meaning": "GAZ:00001507", "title": "Groenland" }, "Grenada": { "text": "Grenada", - "meaning": "GAZ:02000573", "title": "Grenade" }, - "Guadeloupe": { - "text": "Guadeloupe", - "meaning": "GAZ:00067142", - "title": "Guadeloupe" - }, - "Guam": { - "text": "Guam", - "meaning": "GAZ:00003706", - "title": "Guam" - }, - "Guatemala": { - "text": "Guatemala", - "meaning": "GAZ:00002936", - "title": "Guatemala" - }, "Guernsey": { "text": "Guernsey", - "meaning": "GAZ:00001550", "title": "Guernesey" }, "Guinea": { "text": "Guinea", - "meaning": "GAZ:00000909", "title": "Guinée" }, "Guinea-Bissau": { "text": "Guinea-Bissau", - "meaning": "GAZ:00000910", "title": "Guinée-Bissau" }, - "Guyana": { - "text": "Guyana", - "meaning": "GAZ:00002522", - "title": "Guyane" - }, "Haiti": { "text": "Haiti", - "meaning": "GAZ:00003953", "title": "Haïti" }, "Heard Island and McDonald Islands": { "text": "Heard Island and McDonald Islands", - "meaning": "GAZ:00009718", - "title": "Île Heard et îles McDonald" - }, - "Honduras": { - "text": "Honduras", - "meaning": "GAZ:00002894", - "title": "Honduras" - }, - "Hong Kong": { - "text": "Hong Kong", - "meaning": "GAZ:00003203", - "title": "Hong Kong" + "title": "Îles Heard-et-McDonald" }, "Howland Island": { "text": "Howland Island", - "meaning": "GAZ:00007120", "title": "Île Howland" }, "Hungary": { "text": "Hungary", - "meaning": "GAZ:00002952", "title": "Hongrie" }, "Iceland": { "text": "Iceland", - "meaning": "GAZ:00000843", "title": "Islande" }, "India": { "text": "India", - "meaning": "GAZ:00002839", "title": "Inde" }, "Indonesia": { "text": "Indonesia", - "meaning": "GAZ:00003727", "title": "Indonésie" }, - "Iran": { - "text": "Iran", - "meaning": "GAZ:00004474", - "title": "L'Iran" - }, - "Iraq": { - "text": "Iraq", - "meaning": "GAZ:00004483", - "title": "Irak" - }, "Ireland": { "text": "Ireland", - "meaning": "GAZ:00002943", "title": "Irlande" }, "Isle of Man": { "text": "Isle of Man", - "meaning": "GAZ:00052477", "title": "île de Man" }, "Israel": { "text": "Israel", - "meaning": "GAZ:00002476", "title": "Israël" }, "Italy": { "text": "Italy", - "meaning": "GAZ:00002650", "title": "Italie" }, "Jamaica": { "text": "Jamaica", - "meaning": "GAZ:00003781", "title": "Jamaïque" }, - "Jan Mayen": { - "text": "Jan Mayen", - "meaning": "GAZ:00005853", - "title": "Jan Mayen" - }, "Japan": { "text": "Japan", - "meaning": "GAZ:00002747", "title": "Japon" }, "Jarvis Island": { "text": "Jarvis Island", - "meaning": "GAZ:00007118", "title": "Île Jarvis" }, - "Jersey": { - "text": "Jersey", - "meaning": "GAZ:00001551", - "title": "Jersey" - }, "Johnston Atoll": { "text": "Johnston Atoll", - "meaning": "GAZ:00007114", "title": "Atoll Johnston" }, "Jordan": { "text": "Jordan", - "meaning": "GAZ:00002473", - "title": "Jordan" + "title": "Jordanie" }, "Juan de Nova Island": { "text": "Juan de Nova Island", - "meaning": "GAZ:00005809", "title": "Île Juan de Nova" }, - "Kazakhstan": { - "text": "Kazakhstan", - "meaning": "GAZ:00004999", - "title": "Kazakhstan" - }, - "Kenya": { - "text": "Kenya", - "meaning": "GAZ:00001101", - "title": "Kenya" - }, "Kerguelen Archipelago": { "text": "Kerguelen Archipelago", - "meaning": "GAZ:00005682", - "title": "Archipel des Kerguelen" + "title": "Archipel Kerguelen" }, "Kingman Reef": { "text": "Kingman Reef", - "meaning": "GAZ:00007116", - "title": "Récif Kingman" - }, - "Kiribati": { - "text": "Kiribati", - "meaning": "GAZ:00006894", - "title": "Kiribati" - }, - "Kosovo": { - "text": "Kosovo", - "meaning": "GAZ:00011337", - "title": "Kosovo" + "title": "Récif de Kingman" }, "Kuwait": { "text": "Kuwait", - "meaning": "GAZ:00005285", - "title": "Koweit" + "title": "Koweït" }, "Kyrgyzstan": { "text": "Kyrgyzstan", - "meaning": "GAZ:00006893", "title": "Kirghizistan" }, - "Laos": { - "text": "Laos", - "meaning": "GAZ:00006889", - "title": "Laos" - }, "Latvia": { "text": "Latvia", - "meaning": "GAZ:00002958", "title": "Lettonie" }, "Lebanon": { "text": "Lebanon", - "meaning": "GAZ:00002478", "title": "Liban" }, - "Lesotho": { - "text": "Lesotho", - "meaning": "GAZ:00001098", - "title": "Lesotho" - }, "Liberia": { "text": "Liberia", - "meaning": "GAZ:00000911", "title": "Libéria" }, "Libya": { "text": "Libya", - "meaning": "GAZ:00000566", "title": "Libye" }, - "Liechtenstein": { - "text": "Liechtenstein", - "meaning": "GAZ:00003858", - "title": "Liechtenstein" - }, "Line Islands": { "text": "Line Islands", - "meaning": "GAZ:00007144", "title": "Îles de la Ligne" }, "Lithuania": { "text": "Lithuania", - "meaning": "GAZ:00002960", "title": "Lituanie" }, - "Luxembourg": { - "text": "Luxembourg", - "meaning": "GAZ:00002947", - "title": "Luxembourg" - }, "Macau": { "text": "Macau", - "meaning": "GAZ:00003202", "title": "Macao" }, - "Madagascar": { - "text": "Madagascar", - "meaning": "GAZ:00001108", - "title": "Madagascar" - }, - "Malawi": { - "text": "Malawi", - "meaning": "GAZ:00001105", - "title": "Malawi" - }, "Malaysia": { "text": "Malaysia", - "meaning": "GAZ:00003902", "title": "Malaisie" }, - "Maldives": { - "text": "Maldives", - "meaning": "GAZ:00006924", - "title": "Maldives" - }, - "Mali": { - "text": "Mali", - "meaning": "GAZ:00000584", - "title": "Mali" - }, "Malta": { "text": "Malta", - "meaning": "GAZ:00004017", "title": "Malte" }, "Marshall Islands": { "text": "Marshall Islands", - "meaning": "GAZ:00007161", - "title": "Iles Marshall" - }, - "Martinique": { - "text": "Martinique", - "meaning": "GAZ:00067143", - "title": "Martinique" + "title": "Îles Marshall" }, "Mauritania": { "text": "Mauritania", - "meaning": "GAZ:00000583", "title": "Mauritanie" }, "Mauritius": { "text": "Mauritius", - "meaning": "GAZ:00003745", "title": "Maurice" }, - "Mayotte": { - "text": "Mayotte", - "meaning": "GAZ:00003943", - "title": "Mayotte" - }, "Mexico": { "text": "Mexico", - "meaning": "GAZ:00002852", "title": "Mexique" }, "Micronesia": { "text": "Micronesia", - "meaning": "GAZ:00005862", "title": "Micronésie" }, "Midway Islands": { "text": "Midway Islands", - "meaning": "GAZ:00007112", "title": "Îles Midway" }, "Moldova": { "text": "Moldova", - "meaning": "GAZ:00003897", "title": "Moldavie" }, - "Monaco": { - "text": "Monaco", - "meaning": "GAZ:00003857", - "title": "Monaco" - }, "Mongolia": { "text": "Mongolia", - "meaning": "GAZ:00008744", "title": "Mongolie" }, "Montenegro": { "text": "Montenegro", - "meaning": "GAZ:00006898", "title": "Monténégro" }, - "Montserrat": { - "text": "Montserrat", - "meaning": "GAZ:00003988", - "title": "Montserrat" - }, "Morocco": { "text": "Morocco", - "meaning": "GAZ:00000565", "title": "Maroc" }, - "Mozambique": { - "text": "Mozambique", - "meaning": "GAZ:00001100", - "title": "Mozambique" - }, - "Myanmar": { - "text": "Myanmar", - "meaning": "GAZ:00006899", - "title": "Birmanie" - }, "Namibia": { "text": "Namibia", - "meaning": "GAZ:00001096", "title": "Namibie" }, - "Nauru": { - "text": "Nauru", - "meaning": "GAZ:00006900", - "title": "Nauru" - }, "Navassa Island": { "text": "Navassa Island", - "meaning": "GAZ:00007119", - "title": "Île Navasse" + "title": "Île Navassa" }, "Nepal": { "text": "Nepal", - "meaning": "GAZ:00004399", "title": "Népal" }, "Netherlands": { "text": "Netherlands", - "meaning": "GAZ:00002946", "title": "Pays-Bas" }, "New Caledonia": { "text": "New Caledonia", - "meaning": "GAZ:00005206", - "title": "Nouvelle Calédonie" + "title": "Nouvelle-Calédonie" }, "New Zealand": { "text": "New Zealand", - "meaning": "GAZ:00000469", "title": "Nouvelle-Zélande" }, - "Nicaragua": { - "text": "Nicaragua", - "meaning": "GAZ:00002978", - "title": "Nicaragua" - }, - "Niger": { - "text": "Niger", - "meaning": "GAZ:00000585", - "title": "Niger" - }, "Nigeria": { "text": "Nigeria", - "meaning": "GAZ:00000912", - "title": "Nigeria" + "title": "Nigéria" }, "Niue": { "text": "Niue", - "meaning": "GAZ:00006902", "title": "Nioué" }, "Norfolk Island": { "text": "Norfolk Island", - "meaning": "GAZ:00005908", - "title": "l'ile de Norfolk" + "title": "Île Norfolk" }, "North Korea": { "text": "North Korea", - "meaning": "GAZ:00002801", "title": "Corée du Nord" }, "North Macedonia": { "text": "North Macedonia", - "meaning": "GAZ:00006895", "title": "Macédoine du Nord" }, "North Sea": { "text": "North Sea", - "meaning": "GAZ:00002284", - "title": "la mer du Nord" + "title": "Mer du Nord" }, "Northern Mariana Islands": { "text": "Northern Mariana Islands", - "meaning": "GAZ:00003958", "title": "Îles Mariannes du Nord" }, "Norway": { "text": "Norway", - "meaning": "GAZ:00002699", "title": "Norvège" }, - "Oman": { - "text": "Oman", - "meaning": "GAZ:00005283", - "title": "Oman" - }, - "Pakistan": { - "text": "Pakistan", - "meaning": "GAZ:00005246", - "title": "Pakistan" - }, "Palau": { "text": "Palau", - "meaning": "GAZ:00006905", "title": "Palaos" }, - "Panama": { - "text": "Panama", - "meaning": "GAZ:00002892", - "title": "Panama" - }, "Papua New Guinea": { "text": "Papua New Guinea", - "meaning": "GAZ:00003922", - "title": "Papouasie Nouvelle Guinée" + "title": "Papouasie-Nouvelle-Guinée" }, "Paracel Islands": { "text": "Paracel Islands", - "meaning": "GAZ:00010832", - "title": "Iles Paracel" - }, - "Paraguay": { - "text": "Paraguay", - "meaning": "GAZ:00002933", - "title": "Paraguay" + "title": "Îles Paracel" }, "Peru": { "text": "Peru", - "meaning": "GAZ:00002932", "title": "Pérou" }, - "Philippines": { - "text": "Philippines", - "meaning": "GAZ:00004525", - "title": "Philippines" - }, "Pitcairn Islands": { "text": "Pitcairn Islands", - "meaning": "GAZ:00005867", - "title": "Îles Pitcairn" + "title": "Île Pitcairn" }, "Poland": { "text": "Poland", - "meaning": "GAZ:00002939", "title": "Pologne" }, - "Portugal": { - "text": "Portugal", - "meaning": "GAZ:00004126", - "title": "le Portugal" - }, "Puerto Rico": { "text": "Puerto Rico", - "meaning": "GAZ:00006935", "title": "Porto Rico" }, - "Qatar": { - "text": "Qatar", - "meaning": "GAZ:00005286", - "title": "Qatar" - }, "Republic of the Congo": { "text": "Republic of the Congo", - "meaning": "GAZ:00001088", "title": "République du Congo" }, "Reunion": { "text": "Reunion", - "meaning": "GAZ:00003945", "title": "Réunion" }, "Romania": { "text": "Romania", - "meaning": "GAZ:00002951", "title": "Roumanie" }, "Ross Sea": { "text": "Ross Sea", - "meaning": "GAZ:00023304", "title": "Mer de Ross" }, "Russia": { "text": "Russia", - "meaning": "GAZ:00002721", "title": "Russie" }, - "Rwanda": { - "text": "Rwanda", - "meaning": "GAZ:00001087", - "title": "Rwanda" - }, "Saint Helena": { "text": "Saint Helena", - "meaning": "GAZ:00000849", "title": "Sainte-Hélène" }, "Saint Kitts and Nevis": { "text": "Saint Kitts and Nevis", - "meaning": "GAZ:00006906", - "title": "Saint-Christophe-et-Niévès" + "title": "Saint-Kitts-et-Nevis" }, "Saint Lucia": { "text": "Saint Lucia", - "meaning": "GAZ:00006909", "title": "Sainte-Lucie" }, "Saint Pierre and Miquelon": { "text": "Saint Pierre and Miquelon", - "meaning": "GAZ:00003942", "title": "Saint-Pierre-et-Miquelon" }, "Saint Martin": { "text": "Saint Martin", - "meaning": "GAZ:00005841", - "title": "Saint Martin" + "title": "Saint-Martin" }, "Saint Vincent and the Grenadines": { "text": "Saint Vincent and the Grenadines", - "meaning": "GAZ:02000565", "title": "Saint-Vincent-et-les-Grenadines" }, - "Samoa": { - "text": "Samoa", - "meaning": "GAZ:00006910", - "title": "Samoa" - }, "San Marino": { "text": "San Marino", - "meaning": "GAZ:00003102", - "title": "Saint Marin" + "title": "Saint-Marin" }, "Sao Tome and Principe": { "text": "Sao Tome and Principe", - "meaning": "GAZ:00006927", - "title": "Sao Tomé et Principe" + "title": "Sao Tomé-et-Principe" }, "Saudi Arabia": { "text": "Saudi Arabia", - "meaning": "GAZ:00005279", - "title": "Arabie Saoudite" + "title": "Arabie saoudite" }, "Senegal": { "text": "Senegal", - "meaning": "GAZ:00000913", "title": "Sénégal" }, "Serbia": { "text": "Serbia", - "meaning": "GAZ:00002957", "title": "Serbie" }, - "Seychelles": { - "text": "Seychelles", - "meaning": "GAZ:00006922", - "title": "les Seychelles" - }, - "Sierra Leone": { - "text": "Sierra Leone", - "meaning": "GAZ:00000914", - "title": "Sierra Leone" - }, "Singapore": { "text": "Singapore", - "meaning": "GAZ:00003923", "title": "Singapour" }, "Sint Maarten": { "text": "Sint Maarten", - "meaning": "GAZ:00012579", "title": "Saint-Martin" }, "Slovakia": { "text": "Slovakia", - "meaning": "GAZ:00002956", "title": "Slovaquie" }, "Slovenia": { "text": "Slovenia", - "meaning": "GAZ:00002955", "title": "Slovénie" }, "Solomon Islands": { "text": "Solomon Islands", - "meaning": "GAZ:00005275", - "title": "Les îles Salomon" + "title": "Îles Salomon" }, "Somalia": { "text": "Somalia", - "meaning": "GAZ:00001104", "title": "Somalie" }, "South Africa": { "text": "South Africa", - "meaning": "GAZ:00001094", "title": "Afrique du Sud" }, "South Georgia and the South Sandwich Islands": { "text": "South Georgia and the South Sandwich Islands", - "meaning": "GAZ:00003990", "title": "Géorgie du Sud et îles Sandwich du Sud" }, "South Korea": { "text": "South Korea", - "meaning": "GAZ:00002802", "title": "Corée du Sud" }, "South Sudan": { "text": "South Sudan", - "meaning": "GAZ:00233439", - "title": "Soudan du sud" + "title": "Soudan du Sud" }, "Spain": { "text": "Spain", - "meaning": "GAZ:00000591", "title": "Espagne" }, "Spratly Islands": { "text": "Spratly Islands", - "meaning": "GAZ:00010831", "title": "Îles Spratly" }, - "Sri Lanka": { - "text": "Sri Lanka", - "meaning": "GAZ:00003924", - "title": "Sri Lanka" - }, "State of Palestine": { "text": "State of Palestine", - "meaning": "GAZ:00002475", "title": "État de Palestine" }, "Sudan": { "text": "Sudan", - "meaning": "GAZ:00000560", "title": "Soudan" }, - "Suriname": { - "text": "Suriname", - "meaning": "GAZ:00002525", - "title": "Surinam" - }, - "Svalbard": { - "text": "Svalbard", - "meaning": "GAZ:00005396", - "title": "Svalbard" - }, - "Swaziland": { - "text": "Swaziland", - "meaning": "GAZ:00001099", - "title": "Swaziland" - }, "Sweden": { "text": "Sweden", - "meaning": "GAZ:00002729", "title": "Suède" }, "Switzerland": { "text": "Switzerland", - "meaning": "GAZ:00002941", "title": "Suisse" }, "Syria": { "text": "Syria", - "meaning": "GAZ:00002474", "title": "Syrie" }, "Taiwan": { "text": "Taiwan", - "meaning": "GAZ:00005341", "title": "Taïwan" }, "Tajikistan": { "text": "Tajikistan", - "meaning": "GAZ:00006912", "title": "Tadjikistan" }, "Tanzania": { "text": "Tanzania", - "meaning": "GAZ:00001103", "title": "Tanzanie" }, "Thailand": { "text": "Thailand", - "meaning": "GAZ:00003744", "title": "Thaïlande" }, - "Timor-Leste": { - "text": "Timor-Leste", - "meaning": "GAZ:00006913", - "title": "Timor-Leste" - }, - "Togo": { - "text": "Togo", - "meaning": "GAZ:00000915", - "title": "Aller" - }, "Tokelau": { "text": "Tokelau", - "meaning": "GAZ:00260188", - "title": "Tokélaou" - }, - "Tonga": { - "text": "Tonga", - "meaning": "GAZ:00006916", - "title": "Tonga" + "title": "Tokelaou" }, "Trinidad and Tobago": { "text": "Trinidad and Tobago", - "meaning": "GAZ:00003767", "title": "Trinité-et-Tobago" }, "Tromelin Island": { "text": "Tromelin Island", - "meaning": "GAZ:00005812", "title": "Île Tromelin" }, "Tunisia": { "text": "Tunisia", - "meaning": "GAZ:00000562", "title": "Tunisie" }, "Turkey": { "text": "Turkey", - "meaning": "GAZ:00000558", "title": "Turquie" }, "Turkmenistan": { "text": "Turkmenistan", - "meaning": "GAZ:00005018", "title": "Turkménistan" }, "Turks and Caicos Islands": { "text": "Turks and Caicos Islands", - "meaning": "GAZ:00003955", - "title": "îles Turques-et-Caïques" - }, - "Tuvalu": { - "text": "Tuvalu", - "meaning": "GAZ:00009715", - "title": "Tuvalu" + "title": "Îles Turks et Caicos" }, "United States of America": { "text": "United States of America", - "meaning": "GAZ:00002459", - "title": "les états-unis d'Amérique" + "title": "États-Unis" }, "Uganda": { "text": "Uganda", - "meaning": "GAZ:00001102", "title": "Ouganda" }, - "Ukraine": { - "text": "Ukraine", - "meaning": "GAZ:00002724", - "title": "Ukraine" - }, "United Arab Emirates": { "text": "United Arab Emirates", - "meaning": "GAZ:00005282", - "title": "Emirats Arabes Unis" + "title": "Émirats arabes unis" }, "United Kingdom": { "text": "United Kingdom", - "meaning": "GAZ:00002637", "title": "Royaume-Uni" }, - "Uruguay": { - "text": "Uruguay", - "meaning": "GAZ:00002930", - "title": "Uruguay" - }, "Uzbekistan": { "text": "Uzbekistan", - "meaning": "GAZ:00004979", "title": "Ouzbékistan" }, - "Vanuatu": { - "text": "Vanuatu", - "meaning": "GAZ:00006918", - "title": "Vanuatu" - }, - "Venezuela": { - "text": "Venezuela", - "meaning": "GAZ:00002931", - "title": "Venezuela" - }, "Viet Nam": { "text": "Viet Nam", - "meaning": "GAZ:00003756", - "title": "Viet Nam" + "title": "Vietnam" }, "Virgin Islands": { "text": "Virgin Islands", - "meaning": "GAZ:00003959", - "title": "Les iles vierges" + "title": "Îles vierges" }, "Wake Island": { "text": "Wake Island", - "meaning": "GAZ:00007111", "title": "Île de Wake" }, "Wallis and Futuna": { "text": "Wallis and Futuna", - "meaning": "GAZ:00007191", - "title": "Wallis et Futuna" + "title": "Wallis-et-Futuna" }, "West Bank": { "text": "West Bank", - "meaning": "GAZ:00009572", - "title": "banque de l'Ouest" + "title": "Cisjordanie" }, "Western Sahara": { "text": "Western Sahara", - "meaning": "GAZ:00000564", - "title": "Sahara occidental" + "title": "République arabe sahraouie démocratique" }, "Yemen": { "text": "Yemen", - "meaning": "GAZ:00005284", "title": "Yémen" }, "Zambia": { "text": "Zambia", - "meaning": "GAZ:00001107", "title": "Zambie" - }, - "Zimbabwe": { - "text": "Zimbabwe", - "meaning": "GAZ:00001106", - "title": "Zimbabwe" } } } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "Le nom défini par l'utilisateur pour l'échantillon.", - "title": "Collecteur d'échantillons ID de l'échantillon", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "Nom défini par l’utilisateur pour l’échantillon", + "title": "ID du collecteur d’échantillons", "comments": [ - "Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de stocker la clé qui correspond aux identifiants d'origine et alternatifs pour la traçabilité et le suivi si nécessaire. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n'importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire." + "Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de conserver la clé qui correspond aux identifiants d’origine et alternatifs aux fins de traçabilité et de suivi, au besoin. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n’importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire." ], "examples": [ { @@ -6364,223 +3891,413 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Identificateurs de base de données" }, - "third party lab service provider name": { - "name": "third party lab service provider name", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "third party lab sample ID": { - "name": "third party lab sample ID", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "case ID": { - "name": "case ID", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "IRIDA sample name": { - "name": "IRIDA sample name", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "bioproject accession": { - "name": "bioproject accession", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "biosample accession": { - "name": "biosample accession", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "SRA accession": { - "name": "SRA accession", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "GenBank accession": { - "name": "GenBank accession", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "GISAID accession": { - "name": "GISAID accession", - "from_schema": "https://example.com/CanCOGeN_Covid-19" - }, - "sample collected by": { - "name": "sample collected by", - "description": "Le nom de l’organisation à laquelle le collecteur d’échantillons est affilié.", - "title": "échantillon collecté par", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", + "description": "Nom de la société ou du laboratoire tiers qui fournit les services", + "title": "Nom du fournisseur de services de laboratoire tiers", "comments": [ - "Le nom de l’agence doit être écrit au complet (à quelques exceptions près) et être cohérent dans plusieurs soumissions." + "Indiquez le nom complet et non abrégé de l’entreprise ou du laboratoire." ], "examples": [ { - "value": "Laboratoire de santé publique du BCCDC" + "value": "Switch Health" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sample collector contact email": { - "name": "sample collector contact email", - "description": "L'adresse email du contact responsable du suivi concernant l'échantillon.", - "title": "Courriel de contact du collecteur d'échantillons", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", + "description": "Identifiant attribué à un échantillon par un prestataire de services tiers", + "title": "ID de l’échantillon de laboratoire tiers", "comments": [ - "L'adresse e-mail peut représenter une personne ou un laboratoire spécifique." + "Conservez l’identifiant de l’échantillon fourni par le prestataire de services tiers." ], "examples": [ { - "value": "RespLab@lab.ca" + "value": "SHK123456" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sample collector contact address": { - "name": "sample collector contact address", - "description": "L'adresse postale de l'agence qui soumet l'échantillon.", - "title": "adresse de contact du collecteur d'échantillons", + "case_id": { + "name": "case_id", + "description": "Identifiant utilisé pour désigner un cas de maladie détecté sur le plan épidémiologique", + "title": "ID du dossier", "comments": [ - "L'adresse postale doit être au format : numéro et nom de la rue, ville, état/province/région, pays, code postal/code postal." + "Fournissez l’identifiant du cas, lequel facilite grandement le lien entre les données de laboratoire et les données épidémiologiques. Il peut être considéré comme une information identifiable. Consultez l’intendant des données avant de le transmettre." ], "examples": [ { - "value": "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + "value": "ABCD1234" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "Le nom de l'agence qui a généré la séquence.", - "title": "séquence soumise par", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", + "description": "Identifiant principal d’un échantillon associé précédemment soumis au dépôt", + "title": "ID principal de l’échantillon associé", "comments": [ - "Le nom de l’agence doit être écrit au complet (à quelques exceptions près) et être cohérent dans plusieurs soumissions." + "Conservez l’identifiant primaire de l’échantillon correspondant précédemment soumis au Laboratoire national de microbiologie afin que les échantillons puissent être liés et suivis dans le système." ], "examples": [ { - "value": "Santé publique Ontario (SPO)" + "value": "SR20-12345" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "description": "L'adresse email du contact responsable du suivi de la séquence.", - "title": "séquence courriel de contact du déposant", + "irida_sample_name": { + "name": "irida_sample_name", + "description": "Identifiant attribué à un isolat séquencé dans IRIDA", + "title": "Nom de l’échantillon IRIDA", "comments": [ - "L'adresse e-mail peut représenter une personne ou un laboratoire spécifique." + "Enregistrez le nom de l’échantillon IRIDA, lequel sera créé par la personne saisissant les données dans la plateforme connexe. Les échantillons IRIDA peuvent être liés à des métadonnées et à des données de séquence, ou simplement à des métadonnées. Il est recommandé que le nom de l’échantillon IRIDA soit identique ou contienne l’ID de l’échantillon du collecteur pour assurer une meilleure traçabilité. Il est également recommandé que le nom de l’échantillon IRIDA reflète l’accès à GISAID. Les noms d’échantillons IRIDA ne peuvent pas contenir de barres obliques. Celles-ci doivent être remplacées par des traits de soulignement. Consultez la documentation IRIDA pour en savoir plus sur les caractères spéciaux (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)." ], "examples": [ { - "value": "RespLab@lab.ca" + "value": "prov_rona_99" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "description": "L'adresse postale de l'agence soumettant la séquence.", - "title": "adresse de contact de l'auteur de la séquence", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", + "description": "Numéro d’accès à INSDC attribué au bioprojet cadre pour l’effort canadien de séquençage du SRAS-CoV-2", + "title": "Numéro d’accès au bioprojet cadre", "comments": [ - "L'adresse postale doit être au format : numéro et nom de la rue, ville, état/province/région, pays, code postal/code postal." + "Enregistrez le numéro d’accès au bioprojet cadre en le sélectionnant à partir de la liste déroulante du modèle. Ce numéro sera identique pour tous les soumissionnaires du RCanGéCO. Différentes provinces auront leurs propres bioprojets, mais ces derniers seront liés sous un seul bioprojet cadre." ], "examples": [ { - "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + "value": "PRJNA623807" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sample collection date": { - "name": "sample collection date", - "description": "La date à laquelle l'échantillon a été prélevé.", - "title": "date de collecte de l'échantillon", + "bioproject_accession": { + "name": "bioproject_accession", + "description": "Numéro d’accès à INSDC du bioprojet auquel appartient un échantillon biologique", + "title": "Numéro d’accès au bioprojet", "comments": [ - "Enregistrez avec précision la date de collecte dans le modèle. La granularité requise inclut l’année, le mois et le jour. Avant de partager ces données, assurez-vous que cette date n’est pas considérée comme une information identifiable. Si cette date est considérée comme identifiable, il est acceptable d'ajouter du « jitter » à la date de collecte en ajoutant ou en soustrayant des jours calendaires. Ne modifiez pas la date de collecte dans vos dossiers originaux. Alternativement, la « date de réception » peut être utilisée comme substitut dans les données que vous partagez. La date doit être fournie au format standard ISO 8601 « YYYY-MM-DD »." + "Enregistrez le numéro d’accès au bioprojet. Les bioprojets sont un outil d’organisation qui relie les données de séquence brutes, les assemblages et leurs métadonnées associées. Chaque province se verra attribuer un numéro d’accès différent au bioprojet par le Laboratoire national de microbiologie. Un numéro d’accès valide au bioprojet du NCBI contient le préfixe PRJN (p. ex., PRJNA12345); il est créé une fois au début d’un nouveau projet de séquençage." ], "examples": [ { - "value": "2020-03-16" + "value": "PRJNA608651" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sample collection date precision": { - "name": "sample collection date precision", - "description": "La précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie.", - "title": "date de collecte de l'échantillon précision", + "biosample_accession": { + "name": "biosample_accession", + "description": "Identifiant attribué à un échantillon biologique dans les archives INSDC", + "title": "Numéro d’accès à un échantillon biologique", "comments": [ - "Fournissez la précision de la granularité au « jour », au « mois » ou à « l'année » pour la date fournie dans le champ « date de prélèvement de l'échantillon ». La « date de prélèvement de l'échantillon » sera tronquée à la précision spécifiée lors de l'exportation ; « jour » pour «YYYY-MM-DD », « mois » pour « YYYY-MM » ou « année » pour « YYYY »." + "Conservez le numéro d’accès renvoyé avec la soumission d’un échantillon biologique. Les échantillons biologiques de NCBI seront assortis du SAMN." ], "examples": [ { - "value": "année" + "value": "SAMN14180202" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sample received date": { - "name": "sample received date", - "description": "La date à laquelle l'échantillon a été reçu.", - "title": "date de réception de l'échantillon", + "sra_accession": { + "name": "sra_accession", + "description": "Identifiant de l’archive des séquences reliant les données de séquences brutes de lecture, les métadonnées méthodologiques et les mesures de contrôle de la qualité soumises à INSDC", + "title": "Numéro d’accès à l’archive des séquences", "comments": [ - "La date à laquelle l'échantillon a été reçu par un laboratoire qui n'était pas le point de prélèvement. Norme ISO 8601 « YYYY-MM-DD»." + "Conservez le numéro d’accès attribué au « cycle » soumis. Les accès NCBI-SRA commencent par SRR." ], "examples": [ { - "value": "2020-03-20" + "value": "SRR11177792" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "description": "Le pays d'origine de l'échantillon.", - "title": "nom du geo_loc (pays)", + "genbank_accession": { + "name": "genbank_accession", + "description": "Identifiant GenBank attribué à la séquence dans les archives INSDC", + "title": "Numéro d’accès à GenBank", "comments": [ - "Fournissez le nom du pays dans la liste de sélection du modèle" + "Conservez le numéro d’accès renvoyé avec la soumission de GenBank (assemblage du génome viral)." ], "examples": [ { - "value": "Canada" + "value": "MN908947.3" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", - "description": "L'État/la province/le territoire d'origine de l'échantillon.", - "title": "nom du geo_loc (état/province/territoire)", + "gisaid_accession": { + "name": "gisaid_accession", + "description": "Numéro d’accès à la GISAID attribué à la séquence", + "title": "Numéro d’accès à la GISAID", "comments": [ - "Fournissez le nom de l’État/de la province/du territoire à partir de l’ontologie géographique GAZ. Recherchez des termes géographiques ici : https://www.ebi.ac.uk/ols/ontologies/gaz" + "Conservez le numéro d’accès renvoyé avec la soumission de la GISAID." ], "examples": [ { - "value": "Saskatchewan" + "value": "EPI_ISL_436489" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_group": "Collecte et traitement des échantillons" + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", - "description": "La ville d'origine de l'échantillon.", - "title": "nom du geo_loc (ville)", + "sample_collected_by": { + "name": "sample_collected_by", + "description": "Nom de l’organisme ayant prélevé l’échantillon original", + "title": "Échantillon prélevé par", "comments": [ - "Fournissez le nom de la ville à partir de l’ontologie géographique GAZ. Recherchez des termes géographiques ici : https://www.ebi.ac.uk/ols/ontologies/gaz" + "Le nom du collecteur d’échantillons doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions, par exemple Agence de la santé publique du Canada, Santé publique Ontario, Centre de contrôle des maladies de la Colombie-Britannique." + ], + "examples": [ + { + "value": "Centre de contrôle des maladies de la Colombie-Britannique" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon", + "title": "Adresse courriel du collecteur d’échantillons", + "comments": [ + "L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca)." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", + "description": "Adresse postale de l’organisme soumettant l’échantillon", + "title": "Adresse du collecteur d’échantillons", + "comments": [ + "Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays." + ], + "examples": [ + { + "value": "655, rue Lab, Vancouver (Colombie-Britannique) V5N 2A2 Canada" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "Nom de l’organisme ayant généré la séquence", + "title": "Séquence soumise par", + "comments": [ + "Le nom de l’agence doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions. Si vous soumettez des échantillons plutôt que des données de séquençage, veuillez inscrire « Laboratoire national de microbiologie (LNM) »." + ], + "examples": [ + { + "value": "Santé publique Ontario (SPO)" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon", + "title": "Adresse courriel du soumissionnaire de séquence", + "comments": [ + "L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca)." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", + "description": "Adresse postale de l’organisme soumettant l’échantillon", + "title": "Adresse du soumissionnaire de séquence", + "comments": [ + "Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays." + ], + "examples": [ + { + "value": "123, rue Sunnybrooke, Toronto (Ontario) M4P 1L6 Canada" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sample_collection_date": { + "name": "sample_collection_date", + "description": "Date à laquelle l’échantillon a été prélevé", + "title": "Date de prélèvement de l’échantillon", + "comments": [ + "La date de prélèvement des échantillons est essentielle pour la surveillance et de nombreux types d’analyses. La granularité requise comprend l’année, le mois et le jour. Si cette date est considérée comme un renseignement identifiable, il est acceptable d’y ajouter une « gigue » en ajoutant ou en soustrayant un jour civil. La « date de réception » peut également servir de date de rechange. La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", + "description": "Précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie", + "title": "Précision de la date de prélèvement de l’échantillon", + "comments": [ + "Fournissez la précision de la granularité au « jour », au « mois » ou à « l’année » pour la date fournie dans le champ « Date de prélèvement de l’échantillon ». Cette date sera tronquée selon la précision spécifiée lors de l’exportation : « jour » pour « AAAA-MM-JJ », « mois » pour « AAAA-MM » ou « année » pour « AAAA »." + ], + "examples": [ + { + "value": "année" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "sample_received_date": { + "name": "sample_received_date", + "description": "Date à laquelle l’échantillon a été reçu", + "title": "Date de réception de l’échantillon", + "comments": [ + "La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "Pays d’origine de l’échantillon", + "title": "nom_lieu_géo (pays)", + "comments": [ + "Fournissez le nom du pays à partir du vocabulaire contrôlé fourni." + ], + "examples": [ + { + "value": "Canada" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "Province ou territoire où l’échantillon a été prélevé", + "title": "nom_lieu_géo (état/province/territoire)", + "comments": [ + "Fournissez le nom de la province ou du territoire à partir du vocabulaire contrôlé fourni." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], + "slot_group": "Collecte et traitement des échantillons" + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "Ville où l’échantillon a été prélevé", + "title": "nom_géo_loc (ville)", + "comments": [ + "Fournissez le nom de la ville. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." ], "examples": [ { @@ -6588,29 +4305,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, "organism": { "name": "organism", - "description": "Nom taxonomique de l'organisme.", - "title": "organisme", + "description": "Nom taxonomique de l’organisme", + "title": "Organisme", "comments": [ - "Sélectionnez « Coronavirus 2 du syndrome respiratoire aigu sévère » si vous séquencez le SRAS-CoV-2. Si un autre Coronaviridae est en cours de séquençage, fournissez le nom taxonomique de NCBITaxon. Recherchez des termes de taxonomie sur https://www.ebi.ac.uk/ols/ontologies/ncbitaxon." + "Utilisez « coronavirus du syndrome respiratoire aigu sévère 2 ». Cette valeur est fournie dans le modèle." ], "examples": [ { - "value": "Syndrome respiratoire aigu sévère coronavirus 2" + "value": "Coronavirus du syndrome respiratoire aigu sévère 2" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, "isolate": { "name": "isolate", - "description": "Identifiant de l'isolat spécifique.", - "title": "isolat", + "description": "Identifiant de l’isolat spécifique", + "title": "Isolat", "comments": [ - "Cet identifiant doit être un identifiant alphanumérique unique, indexé au sein de votre laboratoire. S'il est soumis à l'INSDC, le nom « isoler » est propagé dans différentes bases de données. En tant que tel, structurez le nom « isolat » pour qu'il soit conforme à ICTV/INSDC dans le format suivant : « SARS-CoV-2/host/country/sampleID/date »." + "Fournissez le nom du virus de la GISAID, qui doit être écrit dans le format « hCov-19/CANADA/code ISO provincial à 2 chiffres-xxxxx/année »." ], "examples": [ { @@ -6618,44 +4341,53 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "purpose of sampling": { - "name": "purpose of sampling", - "description": "La raison pour laquelle l’échantillon a été collecté.", - "title": "Objectif de l'échantillonnage", + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "Motif de prélèvement de l’échantillon", + "title": "Objectif de l’échantillonnage", "comments": [ - "Sélectionnez une valeur dans la liste de sélection du modèle." + "La raison pour laquelle un échantillon a été prélevé peut fournir des renseignements sur les biais potentiels de la stratégie d’échantillonnage. Choisissez l’objectif de l’échantillonnage à partir de la liste déroulante du modèle. Il est très probable que l’échantillon ait été prélevé en vue d’un test diagnostique. La raison pour laquelle un échantillon a été prélevé à l’origine peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage, ce qui doit être indiqué dans le champ « Objectif du séquençage »." ], "examples": [ { - "value": "Tests de diagnostic" + "value": "Tests diagnostiques" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "description": "Plus de détails concernant la raison pour laquelle l’échantillon a été collecté.", - "title": "détails de l'objectif de l'échantillonnage", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", + "description": "Détails précis concernant le motif de prélèvement de l’échantillon", + "title": "Détails de l’objectif de l’échantillonnage", "comments": [ - "Fournissez une description en texte libre de la stratégie d’échantillonnage ou des échantillons collectés." + "Fournissez une description détaillée de la raison pour laquelle l’échantillon a été prélevé en utilisant du texte libre. La description peut inclure l’importance de l’échantillon pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Si les détails ne sont pas disponibles, fournissez une valeur nulle." ], "examples": [ { - "value": "L'échantillon a été collecté pour étudier la prévalence des variantes associées à la transmission du vison à l'homme au Canada." + "value": "L’échantillon a été prélevé pour étudier la prévalence des variants associés à la transmission du vison à l’homme au Canada." } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", - "description": "Le type d'échantillon soumis au Laboratoire national de microbiologie (NML) pour analyse.", - "title": "Type de spécimen soumis au NML", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", + "description": "Type d’échantillon soumis au Laboratoire national de microbiologie (LNM) aux fins d’analyse", + "title": "Type d’échantillon soumis au LNM", "comments": [ - "Ces informations sont requises pour le téléchargement via le système CNPHI LaSER. Sélectionnez le type d’échantillon dans la liste de sélection fournie. Si des données de séquence sont soumises plutôt qu'un échantillon à tester, sélectionnez « Non applicable »." + "Ces renseignements sont requis pour le téléchargement à l’aide du système LaSER du RCRSP. Choisissez le type d’échantillon à partir de la liste de sélection fournie. Si les données de séquences sont soumises plutôt qu’un échantillon aux fins d’analyse, sélectionnez « Sans objet »." ], "examples": [ { @@ -6663,29 +4395,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", - "description": "La relation entre le spécimen actuel et le spécimen/échantillon précédemment soumis au référentiel.", - "title": "Type de relation du spécimen apparenté", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", + "description": "Relation entre l’échantillon actuel et celui précédemment soumis au dépôt", + "title": "Type de relation de l’échantillon lié", "comments": [ - "Fournissez l'étiquette qui décrit comment l'échantillon précédent est lié à l'échantillon actuel soumis à partir de la liste de sélection fournie, afin que les échantillons puissent être liés et suivis dans le système." + "Fournissez l’étiquette qui décrit comment l’échantillon précédent est lié à l’échantillon actuel soumis à partir de la liste de sélection fournie afin que les échantillons puissent être liés et suivis dans le système." ], "examples": [ { - "value": "Test des méthodes d’échantillonnage des échantillons" + "value": "Test des méthodes de prélèvement des échantillons" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "anatomical material": { - "name": "anatomical material", - "description": "Une substance obtenue à partir d'une partie anatomique d'un organisme, par ex. tissu, sang.", - "title": "matière anatomique", + "anatomical_material": { + "name": "anatomical_material", + "description": "Substance obtenue à partir d’une partie anatomique d’un organisme (p. ex., tissu, sang)", + "title": "Matière anatomique", "comments": [ - "Fournissez un descripteur si un matériau anatomique a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/uberon. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si une matière anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { @@ -6693,14 +4431,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "anatomical part": { - "name": "anatomical part", - "description": "Une partie anatomique d'un organisme, par ex. oropharynx.", - "title": "partie anatomique", + "anatomical_part": { + "name": "anatomical_part", + "description": "Partie anatomique d’un organisme (p. ex., oropharynx)", + "title": "Partie anatomique", "comments": [ - "Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/uberon. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { @@ -6708,14 +4449,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "body product": { - "name": "body product", - "description": "Une substance excrétée/sécrétée par un organisme, par ex. selles, urine, sueur.", - "title": "produit corporel", + "body_product": { + "name": "body_product", + "description": "Substance excrétée ou sécrétée par un organisme (p. ex., selles, urine, sueur)", + "title": "Produit corporel", "comments": [ - "Fournissez une description si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/uberon. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { @@ -6723,29 +4467,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "environmental material": { - "name": "environmental material", - "description": "Une substance obtenue à partir de l'environnement naturel ou artificiel, par ex. sol, eau, eaux usées, poignée de porte, rampe de lit, masque facial.", - "title": "matériau environnemental", + "environmental_material": { + "name": "environmental_material", + "description": "Substance obtenue à partir de l’environnement naturel ou artificiel (p. ex., sol, eau, eaux usées)", + "title": "Matériel environnemental", "comments": [ - "Fournissez un descripteur si un matériau environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/envo. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si une matière environnementale a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { - "value": "Masque facial" + "value": "Masque" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "environmental site": { - "name": "environmental site", - "description": "Un emplacement environnemental peut décrire un site dans l'environnement naturel ou bâti, par ex. hôpital, marché humide, grotte aux chauves-souris.", - "title": "site environnemental", + "environmental_site": { + "name": "environmental_site", + "description": "Emplacement environnemental pouvant décrire un site dans l’environnement naturel ou artificiel (p. ex., surface de contact, boîte métallique, hôpital, marché traditionnel de produits frais, grotte de chauves-souris)", + "title": "Site environnemental", "comments": [ - "Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/envo. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { @@ -6753,14 +4503,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "collection device": { - "name": "collection device", - "description": "L'instrument ou le récipient utilisé pour collecter l'échantillon, par ex. écouvillon.", - "title": "dispositif de collecte", + "collection_device": { + "name": "collection_device", + "description": "Instrument ou contenant utilisé pour prélever l’échantillon (p. ex., écouvillon)", + "title": "Dispositif de prélèvement", "comments": [ - "Fournissez une description si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/obi. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { @@ -6768,57 +4521,69 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "collection method": { - "name": "collection method", - "description": "Le processus utilisé pour collecter l'échantillon, par ex. phlébotomie, autopsie.", - "title": "méthode de collecte", + "collection_method": { + "name": "collection_method", + "description": "Processus utilisé pour prélever l’échantillon (p. ex., phlébotomie, autopsie)", + "title": "Méthode de prélèvement", "comments": [ - "Fournissez une description si une méthode de collecte a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/obi. Si cela ne s’applique pas, laissez vide." + "Fournissez un descripteur si une méthode de prélèvement a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." ], "examples": [ { - "value": "Lavage broncho-alvéolaire (LBA)" + "value": "Lavage bronchoalvéolaire (LBA)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "collection protocol": { - "name": "collection protocol", - "description": "Le nom et la version d'un protocole particulier utilisé pour l'échantillonnage.", - "title": "protocole de collecte", + "collection_protocol": { + "name": "collection_protocol", + "description": "Nom et version d’un protocole particulier utilisé pour l’échantillonnage", + "title": "Protocole de prélèvement", "comments": [ - "Fournissez le nom et la version du protocole utilisé pour collecter les échantillons." + "Texte libre." ], "examples": [ { - "value": "BCRonaSamplingProtocol v. 1.2" + "value": "CBRonaProtocoleÉchantillonnage v. 1.2" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "specimen processing": { - "name": "specimen processing", - "description": "Tout traitement appliqué à l’échantillon pendant ou après la réception de l’échantillon.", - "title": "processus de traitement des spécimens", + "specimen_processing": { + "name": "specimen_processing", + "description": "Tout traitement appliqué à l’échantillon pendant ou après sa réception", + "title": "Traitement des échantillons", "comments": [ - "Critique pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, incluez les informations dans les champs « hôte du laboratoire », « numéro de passage » et « méthode de passage ». Si aucun des processus de la liste de sélection ne s'applique, inscrivez « non applicable »." + "Essentiel pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, ajoutez les renseignements dans les champs « Laboratoire hôte », « Nombre de transmissions » et « Méthode de transmission ». Si aucun des processus de la liste de sélection ne s’applique, inscrivez « Sans objet »." ], "examples": [ { - "value": "Passage du virus" + "value": "Transmission du virus" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "specimen processing details": { - "name": "specimen processing details", - "description": "Informations détaillées concernant le traitement appliqué à un échantillon pendant ou après la réception de l'échantillon.", - "title": "détails du processus des échantillons", + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "Renseignements détaillés concernant le traitement appliqué à un échantillon pendant ou après sa réception", + "title": "Détails du traitement des échantillons", "comments": [ "Fournissez une description en texte libre de tous les détails du traitement appliqués à un échantillon." ], @@ -6828,14 +4593,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "lab host": { - "name": "lab host", - "description": "Nom et description de l'hôte de laboratoire utilisé pour propager l'organisme source ou le matériel à partir duquel l'échantillon a été obtenu.", - "title": "hôte du laboratoire", + "lab_host": { + "name": "lab_host", + "description": "Nom et description du laboratoire hôte utilisé pour propager l’organisme source ou le matériel à partir duquel l’échantillon a été obtenu", + "title": "Laboratoire hôte", "comments": [ - "Type de lignée cellulaire utilisée pour la propagation. Sélectionnez une valeur dans la liste de sélection. S'il n'est pas adopté, mettez \"sans objet\"." + "Type de lignée cellulaire utilisée pour la propagation. Choisissez le nom de cette lignée à partir de la liste de sélection dans le modèle. Si le virus n’a pas été transmis, indiquez « Sans objet »." ], "examples": [ { @@ -6843,14 +4611,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "passage number": { - "name": "passage number", - "description": "Nombre de passages.", - "title": "numéro de passage", + "passage_number": { + "name": "passage_number", + "description": "Nombre de transmissions", + "title": "Nombre de transmission", "comments": [ - "Indiquez le nombre de passages connus. S'il n'est pas adopté, mettre \"sans objet\"" + "Indiquez le nombre de transmissions connues. Si le virus n’a pas été transmis, indiquez « Sans objet »." ], "examples": [ { @@ -6858,44 +4629,53 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "passage method": { - "name": "passage method", - "description": "Description de la façon dont l'organisme a été transmis.", - "title": "méthode de passage", + "passage_method": { + "name": "passage_method", + "description": "Description de la façon dont l’organisme a été transmis", + "title": "Méthode de transmission", "comments": [ - "Texte libre. Fournissez une brève description. S'il n'est pas adopté, mettez \"sans objet\"." + "Texte libre. Fournissez une brève description (<10 mots). Si le virus n’a pas été transmis, indiquez « Sans objet »." ], "examples": [ { - "value": "0.25% trypsin + 0.02% EDTA" + "value": "0,25 % de trypsine + 0,02 % d’EDTA" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "biomaterial extracted": { - "name": "biomaterial extracted", - "description": "Biomatériau extrait d’échantillons à des fins de séquençage.", - "title": "biomatériau extrait", + "biomaterial_extracted": { + "name": "biomaterial_extracted", + "description": "Biomatériau extrait d’échantillons aux fins de séquençage", + "title": "Biomatériau extrait", "comments": [ - "Fournissez le biomatériau extrait de la liste de sélection dans le modèle." + "Fournissez le biomatériau extrait à partir de la liste de sélection dans le modèle." ], "examples": [ { - "value": "RNA (total)" + "value": "ARN (total)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Collecte et traitement des échantillons" }, - "host (common name)": { - "name": "host (common name)", - "description": "Le nom couramment utilisé de l'hôte.", - "title": "hôte (nom commun)", + "host_common_name": { + "name": "host_common_name", + "description": "Nom couramment utilisé pour l’hôte", + "title": "Hôte (nom commun)", "comments": [ - "Le nom commun ou le nom scientifique sont requis s’il y avait un hôte. Exemples de noms communs, par ex. humain, chauve-souris. Sélectionnez une valeur dans la liste de sélection. Si l'échantillon était environnemental, inscrivez « sans objet »." + "Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Des exemples de noms communs sont « humain » et « chauve-souris ». Si l’échantillon était environnemental, inscrivez « Sans objet »." ], "examples": [ { @@ -6903,14 +4683,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "Le nom taxonomique ou scientifique de l’hôte.", - "title": "hôte (nom scientifique)", + "host_scientific_name": { + "name": "host_scientific_name", + "description": "Nom taxonomique ou scientifique de l’hôte", + "title": "Hôte (nom scientifique)", "comments": [ - "Le nom commun ou le nom scientifique sont requis s’il y avait un hôte. Exemples de noms scientifiques, par ex. Homo sapiens. Sélectionnez une valeur dans la liste de sélection. Si l'échantillon était environnemental, inscrivez « sans objet »." + "Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Un exemple de nom scientifique est « homo sapiens ». Si l’échantillon était environnemental, inscrivez « Sans objet »." ], "examples": [ { @@ -6918,14 +4701,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host health state": { - "name": "host health state", - "description": "État de santé de l'hôte au moment du prélèvement de l'échantillon.", - "title": "état de santé de l'hôte", + "host_health_state": { + "name": "host_health_state", + "description": "État de santé de l’hôte au moment du prélèvement d’échantillons", + "title": "État de santé de l’hôte", "comments": [ - "Si vous le connaissez, sélectionnez une valeur dans la liste de sélection." + "Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { @@ -6933,29 +4719,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host health status details": { - "name": "host health status details", - "description": "Plus de détails concernant l'état de santé ou de maladie de l'hôte au moment de la collecte.", - "title": "détails de l'état de santé de l'hôte", + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Plus de détails concernant l’état de santé ou de maladie de l’hôte au moment du prélèvement", + "title": "Détails de l’état de santé de l’hôte", "comments": [ - "Si vous le connaissez, sélectionnez une valeur dans la liste de sélection." + "Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { - "value": "Hospitalisé (ICU)" + "value": "Hospitalisé (USI)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host health outcome": { - "name": "host health outcome", - "description": "Résultat de la maladie chez l’hôte.", - "title": "résultat sanitaire de l'hôte", + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Résultats de la maladie chez l’hôte", + "title": "Résultats sanitaires de l’hôte", "comments": [ - "Si vous le connaissez, sélectionnez une valeur dans la liste de sélection." + "Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { @@ -6963,14 +4755,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host disease": { - "name": "host disease", - "description": "Le nom de la maladie vécue par l'hôte.", - "title": "maladie de l'hôte", + "host_disease": { + "name": "host_disease", + "description": "Nom de la maladie vécue par l’hôte", + "title": "Maladie de l’hôte", "comments": [ - "Ce champ n'est obligatoire que s'il y avait un hôte. Si l’hôte était un humain, sélectionnez COVID-19 dans la liste de sélection. Si l’hôte était asymptomatique, cela peut être enregistré sous « détails sur l’état de santé de l’hôte ». « COVID-19 » doit toujours être fourni si le patient est asymptomatique. Si l’hôte n’est pas humain et que l’état pathologique n’est pas connu ou que l’hôte semble en bonne santé, inscrivez « sans objet »." + "Sélectionnez « COVID-19 » à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { @@ -6978,14 +4773,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host age": { - "name": "host age", - "description": "Âge de l'hôte au moment de l'échantillonnage.", - "title": "âge de l'hôte", + "host_age": { + "name": "host_age", + "description": "Âge de l’hôte au moment du prélèvement d’échantillons", + "title": "Âge de l’hôte", "comments": [ - "Si connu, indiquez l’âge. Le regroupement par âge est également acceptable." + "Entrez l’âge de l’hôte en années. S’il n’est pas disponible, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet »." ], "examples": [ { @@ -6993,14 +4791,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host age unit": { - "name": "host age unit", - "description": "Les unités utilisées pour mesurer l'âge de l'hôte.", - "title": "unité d'âge de l'hôte", + "host_age_unit": { + "name": "host_age_unit", + "description": "Unité utilisée pour mesurer l’âge de l’hôte (mois ou année)", + "title": "Catégorie d’âge de l’hôte", "comments": [ - "Si vous le savez, indiquez les unités d'âge utilisées pour mesurer l'âge de l'hôte à partir de la liste de sélection." + "Indiquez si l’âge de l’hôte est en mois ou en années. L’âge indiqué en mois sera classé dans la tranche d’âge de 0 à 9 ans." ], "examples": [ { @@ -7008,14 +4809,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host age bin": { - "name": "host age bin", - "description": "La catégorie d'âge de l'hôte au moment de l'échantillonnage.", - "title": "âge de l'hôte bin", + "host_age_bin": { + "name": "host_age_bin", + "description": "Âge de l’hôte au moment du prélèvement d’échantillons (groupe d’âge)", + "title": "Groupe d’âge de l’hôte", "comments": [ - "Des tranches d'âge ont été fournies tous les 10 ans. Si l'âge d'un hôte ne peut pas être spécifié en raison de problèmes de confidentialité, une catégorie d'âge peut être utilisée comme alternative." + "Sélectionnez la tranche d’âge correspondante de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne la connaissez pas, fournissez une valeur nulle." ], "examples": [ { @@ -7023,14 +4827,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host gender": { - "name": "host gender", - "description": "Le sexe de l’hôte au moment du prélèvement de l’échantillon.", - "title": "sexe de l'hôte", + "host_gender": { + "name": "host_gender", + "description": "Genre de l’hôte au moment du prélèvement d’échantillons", + "title": "Genre de l’hôte", "comments": [ - "Si vous le connaissez, sélectionnez une valeur dans la liste de sélection." + "Sélectionnez le genre correspondant de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne le connaissez pas, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet »." ], "examples": [ { @@ -7038,14 +4845,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", - "description": "Le pays où réside l'hôte.", - "title": "résidence de l'hôte nom du geo_loc (pays)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", + "description": "Pays de résidence de l’hôte", + "title": "Résidence de l’hôte – Nom de géo_loc (pays)", "comments": [ - "Si vous le connaissez, sélectionnez une valeur dans la liste de sélection." + "Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { @@ -7053,29 +4863,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", - "description": "L'état/province/territoire de résidence de l'hôte.", - "title": "nom du geo_loc de la résidence de l'hôte (état/province/territoire)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", + "description": "État, province ou territoire de résidence de l’hôte", + "title": "Résidence de l’hôte – Nom de géo_loc (état/province/territoire)", "comments": [ - "Sélectionnez le nom de la province/du territoire dans la liste de sélection fournie dans le modèle." + "Sélectionnez le nom de la province ou du territoire à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { - "value": "Quebec" + "value": "Québec" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host subject ID": { - "name": "host subject ID", - "description": "Un identifiant unique par lequel chaque hôte peut être référencé, par ex. #131", - "title": "ID du sujet de l'hôte", + "host_subject_id": { + "name": "host_subject_id", + "description": "Identifiant unique permettant de désigner chaque hôte (p. ex., 131)", + "title": "ID du sujet de l’hôte", "comments": [ - "Doit être un identifiant unique défini par l'utilisateur. Cet identifiant peut aider à relier les données de laboratoire aux données épidémiologiques, mais il s’agit probablement d’informations sensibles. Consultez le gestionnaire de données." + "Fournissez l’identifiant de l’hôte. Il doit s’agir d’un identifiant unique défini par l’utilisateur." ], "examples": [ { @@ -7083,14 +4899,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "symptom onset date": { - "name": "symptom onset date", - "description": "La date à laquelle les symptômes ont commencé ou ont été observés pour la première fois.", - "title": "date d'apparition des symptômes", + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "Date à laquelle les symptômes ont commencé ou ont été observés pour la première fois", + "title": "Date d’apparition des symptômes", "comments": [ - "Si connue, indiquez la date d'apparition des symptômes au format standard ISO 8601 «YYYY-MM-DD »." + "La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." ], "examples": [ { @@ -7098,77 +4917,89 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "signs and symptoms": { - "name": "signs and symptoms", - "description": "Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélateur d'une maladie, rapporté par un patient.", - "title": "signes et symptômes", + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélant une maladie, qui est signalé par un patient ou un clinicien", + "title": "Signes et symptômes", "comments": [ - "Sélectionnez tous les symptômes ressentis par l'hôte dans la liste de sélection." + "Sélectionnez tous les symptômes ressentis par l’hôte à partir de la liste de sélection." ], "examples": [ { "value": "Frissons (sensation soudaine de froid)" }, { - "value": "Toux" + "value": "toux" }, { - "value": "Fièvre" + "value": "fièvre" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "description": "Conditions préexistantes du patient et facteurs de risque.
  • Condition préexistante : condition médicale qui existait avant l’infection actuelle.
  • Facteur de risque : variable associée à un risque accru de maladie ou d’infection.", - "title": "les conditions préexistantes et les facteurs de risque", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Conditions préexistantes et facteurs de risque du patient
  • Condition préexistante : Condition médicale qui existait avant l’infection actuelle
  • Facteur de risque : Variable associée à un risque accru de maladie ou d’infection", + "title": "Conditions préexistantes et facteurs de risque", "comments": [ - "Sélectionnez toutes les conditions préexistantes et les facteurs de risque rencontrés par l'hôte dans la liste de sélection. S'il manque le terme souhaité, contactez l'équipe de curation." + "Sélectionnez toutes les conditions préexistantes et tous les facteurs de risque de l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." ], "examples": [ { "value": "Asthme" }, { - "value": "Grossesse" + "value": "grossesse" }, { - "value": "Fumeur" + "value": "tabagisme" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, "complications": { "name": "complications", - "description": "Complications médicales du patient qui seraient dues à une maladie de l’hôte.", - "title": "les complications", + "description": "Complications médicales du patient qui seraient dues à une maladie de l’hôte", + "title": "Complications", "comments": [ - "Sélectionnez toutes les complications rencontrées par l'hôte dans la liste de sélection." + "Sélectionnez toutes les complications éprouvées par l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." ], "examples": [ { "value": "Insuffisance respiratoire aiguë" }, { - "value": "Coma" + "value": "coma" }, { - "value": "Septicémie" + "value": "septicémie" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'hôte" }, - "host vaccination status": { - "name": "host vaccination status", - "description": "Le statut vaccinal de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné).", - "title": "le statut vaccinal de l'hôte", + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "Statut de vaccination de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné)", + "title": "Statut de vaccination de l’hôte", "comments": [ - "Sélectionnez le statut vaccinal de l'hôte dans la liste de sélection." + "Sélectionnez le statut de vaccination de l’hôte à partir de la liste de sélection." ], "examples": [ { @@ -7176,14 +5007,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", - "description": "Le nombre de doses de vaccin reçues par l’hôte.", - "title": "nombre de doses de vaccin reçues", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "Nombre de doses du vaccin reçues par l’hôte", + "title": "Nombre de doses du vaccin reçues", "comments": [ - "Enregistrez le nombre de doses de vaccin que l’hôte a reçues." + "Enregistrez le nombre de doses du vaccin que l’hôte a reçues." ], "examples": [ { @@ -7191,14 +5025,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", - "description": "Nom du vaccin administré comme première dose d'un schéma vaccinal.", - "title": "dose de vaccination 1 nom du vaccin", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "Nom du vaccin administré comme première dose d’un schéma vaccinal", + "title": "Dose du vaccin 1 – Nom du vaccin", "comments": [ - "Indiquez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur dans la liste de sélection." + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur à partir de la liste de sélection." ], "examples": [ { @@ -7206,14 +5043,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", - "description": "La date à laquelle la première dose d’un vaccin a été administrée.", - "title": "dose de vaccination 1 date de vaccination", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "Date à laquelle la première dose d’un vaccin a été administrée", + "title": "Dose du vaccin 1 – Date du vaccin", "comments": [ - "Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 «YYYY-MM-DD »." + "Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." ], "examples": [ { @@ -7221,14 +5061,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", - "description": "Nom du vaccin administré comme deuxième dose d'un schéma vaccinal.", - "title": "dose de vaccination 2 nom du vaccin", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "Nom du vaccin administré comme deuxième dose d’un schéma vaccinal", + "title": "Dose du vaccin 2 – Nom du vaccin", "comments": [ - "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur dans la liste de sélection." + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur à partir de la liste de sélection." ], "examples": [ { @@ -7236,14 +5079,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", - "description": "La date à laquelle la deuxième dose d’un vaccin a été administrée.", - "title": "dose de vaccination 2 date de vaccination", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "Date à laquelle la deuxième dose d’un vaccin a été administrée", + "title": "Dose du vaccin 2 – Date du vaccin", "comments": [ - "Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 « YYYY-MM-DD »." + "Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." ], "examples": [ { @@ -7251,14 +5097,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", - "description": "Nom du vaccin administré comme troisième dose d'un schéma vaccinal.", - "title": "dose de vaccination 3 nom du vaccin", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", + "description": "Nom du vaccin administré comme troisième dose d’un schéma vaccinal", + "title": "Dose du vaccin 3 – Nom du vaccin", "comments": [ - "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur dans la liste de sélection." + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur à partir de la liste de sélection." ], "examples": [ { @@ -7266,14 +5115,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", - "description": "La date à laquelle la troisième dose d’un vaccin a été administrée.", - "title": "dose de vaccination 3 date de vaccination", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", + "description": "Date à laquelle la troisième dose d’un vaccin a été administrée", + "title": "Dose du vaccin 3 – Date du vaccin", "comments": [ - "Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 «YYYY-MM-DD »." + "Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." ], "examples": [ { @@ -7281,14 +5133,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", - "description": "Nom du vaccin administré comme quatrième dose d'un schéma vaccinal.", - "title": "dose de vaccination 4 nom du vaccin", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", + "description": "Nom du vaccin administré comme quatrième dose d’un schéma vaccinal", + "title": "Dose du vaccin 4 – Nom du vaccin", "comments": [ - "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur dans la liste de sélection." + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur à partir de la liste de sélection." ], "examples": [ { @@ -7296,14 +5151,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", - "description": "La date à laquelle la quatrième dose d’un vaccin a été administrée.", - "title": "dose de vaccination 4 date de vaccination", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", + "description": "Date à laquelle la quatrième dose d’un vaccin a été administrée", + "title": "Dose du vaccin 4 – Date du vaccin", "comments": [ - "Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 « YYYY-MM-DD »." + "Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." ], "examples": [ { @@ -7311,14 +5169,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination history": { - "name": "vaccination history", - "description": "Une description des vaccins reçus et les dates d'administration d'une série de vaccinations contre une maladie spécifique ou un ensemble de maladies.", - "title": "les antécédents de vaccination", + "vaccination_history": { + "name": "vaccination_history", + "description": "Description des vaccins reçus et dates d’administration d’une série de vaccins contre une maladie spécifique ou un ensemble de maladies", + "title": "Antécédents de vaccination", "comments": [ - "Description en texte libre des dates et des vaccins administrés contre une maladie/un ensemble de maladies particulier. Il est également acceptable de concaténer les informations sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules." + "Description en texte libre des dates et des vaccins administrés contre une maladie précise ou un ensemble de maladies. Il est également acceptable de concaténer les renseignements sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules." ], "examples": [ { @@ -7335,14 +5196,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", - "description": "Le pays où l'hôte a probablement été exposé à l'agent causal de la maladie.", - "title": "lieu d'exposition geo_loc nom (pays)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", + "description": "Pays où l’hôte a probablement été exposé à l’agent causal de la maladie", + "title": "Lieu de l’exposition – Nom de géo_loc (pays)", "comments": [ - "Cet emplacement concerne le pays dans lequel l'hôte est censé être exposé et peut ne pas être le même que le pays de résidence de l'hôte. Si vous le connaissez, indiquez le nom du pays dans la liste de sélection." + "Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle." ], "examples": [ { @@ -7350,29 +5214,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", - "description": "Le nom de la ville de destination du voyage le plus récent.", - "title": "destination du dernier voyage (ville)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", + "description": "Nom de la ville de destination du voyage le plus récent", + "title": "Destination du dernier voyage (ville)", "comments": [ - "Indiquez le nom de la ville dans laquelle l'hôte s'est rendu. Utilisez ce service de recherche pour identifier le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz" + "Indiquez le nom de la ville dans laquelle l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." ], "examples": [ { - "value": "La ville de New York" + "value": "New York City" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", - "description": "Le nom de la province de destination du voyage le plus récent.", - "title": "destination du dernier voyage (état/province/territoire)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", + "description": "Nom de la province de destination du voyage le plus récent", + "title": "Destination du dernier voyage (état/province/territoire)", "comments": [ - "Indiquez le nom de l'État/de la province/du territoire où l'hôte s'est rendu. Utilisez ce service de recherche pour identifier le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz" + "Indiquez le nom de l’État, de la province ou du territoire où l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." ], "examples": [ { @@ -7380,14 +5250,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", - "description": "Le nom du pays de destination du voyage le plus récent.", - "title": "destination du dernier voyage (pays)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", + "description": "Nom du pays de destination du voyage le plus récent", + "title": "Destination du dernier voyage (pays)", "comments": [ - "Indiquez le nom du pays dans lequel l'hôte s'est rendu. Utilisez ce service de recherche pour identifier le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz" + "Indiquez le nom du pays dans lequel l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." ], "examples": [ { @@ -7395,14 +5268,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "most recent travel departure date": { - "name": "most recent travel departure date", - "description": "Date du départ le plus récent d'une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits.", - "title": "date de départ du voyage la plus récente", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", + "description": "Date du départ le plus récent d’une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits", + "title": "Date de départ de voyage la plus récente", "comments": [ - "Indiquez la date de départ du voyage au format standard ISO 8601 « YYYY-MM-DD »." + "Indiquez la date de départ du voyage." ], "examples": [ { @@ -7410,14 +5286,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "most recent travel return date": { - "name": "most recent travel return date", - "description": "Date du retour le plus récent d'une personne à une résidence après un voyage au départ de cette résidence.", - "title": "date de retour la plus récente", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", + "description": "Date du retour le plus récent d’une personne à une résidence après un voyage au départ de cette résidence", + "title": "Date de retour de voyage la plus récente", "comments": [ - "Indiquez la date de retour du voyage au format standard ISO 8601 « YYYY-MM-DD»." + "Indiquez la date de retour du voyage." ], "examples": [ { @@ -7425,12 +5304,15 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel point of entry type": { - "name": "travel point of entry type", - "description": "Le type de point d’entrée par lequel un voyageur arrive.", - "title": "voyage type de point d'entrée", + "travel_point_of_entry_type": { + "name": "travel_point_of_entry_type", + "description": "Type de point d’entrée par lequel un voyageur arrive", + "title": "Type de point d’entrée du voyage", "comments": [ "Sélectionnez le type de point d’entrée." ], @@ -7440,12 +5322,15 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "border testing test day type": { - "name": "border testing test day type", - "description": "Le jour où un voyageur a été testé à son arrivée ou après son point d’entrée.", - "title": "test aux frontières jour du test type", + "border_testing_test_day_type": { + "name": "border_testing_test_day_type", + "description": "Jour où un voyageur a été testé à son point d’entrée ou après cette date", + "title": "Jour du dépistage à la frontière", "comments": [ "Sélectionnez le jour du test." ], @@ -7455,50 +5340,59 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel history": { - "name": "travel history", - "description": "Historique de voyage au cours des six derniers mois.", - "title": "histoire du voyage", + "travel_history": { + "name": "travel_history", + "description": "Historique de voyage au cours des six derniers mois", + "title": "Antécédents de voyage", "comments": [ - "Précisez les pays (et les emplacements plus précis si connus) parcourus au cours des six derniers mois ; peut inclure plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Fournir sous forme de texte libre." + "Précisez les pays (et les emplacements plus précis, si vous les connaissez) visités au cours des six derniers mois, ce qui peut comprendre plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Commencez par le voyage le plus récent." ], "examples": [ { "value": "Canada, Vancouver" }, { - "value": "USA, Seattle" + "value": "États-Unis, Seattle" }, { "value": "Italie, Milan" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel history availability": { - "name": "travel history availability", - "description": "La disponibilité de différents types d’historiques de voyages au cours des 6 derniers mois (par exemple internationaux, nationaux).", - "title": "disponibilité de l'historique de voyage", + "travel_history_availability": { + "name": "travel_history_availability", + "description": "Disponibilité de différents types d’historiques de voyages au cours des six derniers mois (p. ex., internationaux, nationaux)", + "title": "Disponibilité des antécédents de voyage", "comments": [ - "Si l'historique de voyage est disponible, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d'historique de voyage disponible en sélectionnant une valeur dans la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu'un échantillon est associé à un voyage lorsque le « but du séquençage » n'est pas associé à un voyage." + "Si les antécédents de voyage sont disponibles, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d’antécédents disponibles en sélectionnant une valeur à partir de la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu’un échantillon est associé à un voyage lorsque le « but du séquençage » n’est pas associé à un voyage." ], "examples": [ { - "value": "Historique des voyages internationaux disponible" + "value": "Antécédents de voyage à l’étranger disponible" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure event": { - "name": "exposure event", - "description": "Événement conduisant à une exposition.", - "title": "exposition événement", + "exposure_event": { + "name": "exposure_event", + "description": "Événement conduisant à une exposition", + "title": "Événement d’exposition", "comments": [ - "S'il est connu, sélectionnez l'événement d'exposition dans la liste de sélection." + "Sélectionnez un événement conduisant à une exposition à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." ], "examples": [ { @@ -7506,14 +5400,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure contact level": { - "name": "exposure contact level", - "description": "Le type de contact de transmission d’exposition.", - "title": "exposition niveau de contact", + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "Type de contact de transmission d’exposition", + "title": "Niveau de contact de l’exposition", "comments": [ - "Sélectionnez une exposition directe ou indirecte dans la liste de sélection." + "Sélectionnez une exposition directe ou indirecte à partir de la liste de sélection." ], "examples": [ { @@ -7521,14 +5418,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "host role": { - "name": "host role", - "description": "Le rôle de l'hôte par rapport au paramètre d'exposition.", - "title": "rôle d'hôte", + "host_role": { + "name": "host_role", + "description": "Rôle de l’hôte par rapport au paramètre d’exposition", + "title": "Rôle de l’hôte", "comments": [ - "Sélectionnez le(s) rôle(s) personnel(s) de l'hôte dans la liste de sélection fournie dans le modèle. S'il manque le terme souhaité, contactez l'équipe de curation." + "Sélectionnez les rôles personnels de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." ], "examples": [ { @@ -7536,44 +5436,53 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure setting": { - "name": "exposure setting", - "description": "Le cadre menant à l’exposition.", - "title": "réglage de l'exposition", + "exposure_setting": { + "name": "exposure_setting", + "description": "Contexte menant à l’exposition", + "title": "Contexte de l’exposition", "comments": [ - "Sélectionnez le(s) paramètre(s) d'exposition de l'hôte dans la liste de sélection fournie dans le modèle. S’il manque un terme souhaité, contactez l’équipe de curation." + "Sélectionnez les contextes menant à l’exposition de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." ], "examples": [ { - "value": "Cadre de soins de santé" + "value": "Milieu de soins de santé" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure details": { - "name": "exposure details", - "description": "Informations supplémentaires sur l’exposition de l’hôte.", - "title": "détails de l'exposition", + "exposure_details": { + "name": "exposure_details", + "description": "Renseignements supplémentaires sur l’exposition de l’hôte", + "title": "Détails de l’exposition", "comments": [ - "Description en texte libre de l'exposition." + "Description en texte libre de l’exposition." ], "examples": [ { - "value": "Rôle d'hôte - Autre : Chauffeur de bus" + "value": "Rôle d’hôte - Autre : Conducteur d’autobus" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", - "description": "S'il y a eu une infection antérieure par le SARS-CoV-2.", - "title": "infection antérieure par le SARS-CoV-2", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", + "description": "Infection antérieure par le SRAS-CoV-2 ou non", + "title": "Infection antérieure par le SRAS-CoV-2", "comments": [ - "Si vous le savez, fournissez des informations indiquant si la personne a déjà eu une infection par le SARS-CoV-2. Sélectionnez une valeur dans la liste de sélection." + "Si vous le savez, fournissez des renseignements indiquant si la personne a déjà eu une infection par le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection." ], "examples": [ { @@ -7581,14 +5490,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", - "description": "L’identifiant de l’isolat trouvé lors de l’infection antérieure par le SARS-CoV-2.", - "title": "isolat d'une infection antérieure par le SARS-CoV-2", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", + "description": "Identifiant de l’isolat trouvé lors de l’infection antérieure par le SRAS-CoV-2", + "title": "Isolat d’une infection antérieure par le SRAS-CoV-2", "comments": [ - "Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom « isolat » pour qu'il soit conforme à la norme ICTV/INSDC au format suivant : « SARS-CoV-2/host/country/sampleID/date »." + "Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom de « l’isolat » pour qu’il soit conforme à la norme ICTV/INSDC dans le format suivant : « SRAS-CoV-2/hôte/pays/IDéchantillon/date »." ], "examples": [ { @@ -7596,14 +5508,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", - "description": "La date du diagnostic de l’infection antérieure par le SARS-CoV-2.", - "title": "date d'une infection antérieure par le SARS-CoV-2", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", + "description": "Date du diagnostic de l’infection antérieure par le SRAS-CoV-2", + "title": "Date d’une infection antérieure par le SRAS-CoV-2", "comments": [ - "Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d'infection antérieure par le SARS-CoV-2 au format standard ISO 8601 « YYYY-MM-DD »." + "Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d’infection antérieure par le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD »." ], "examples": [ { @@ -7611,29 +5526,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", - "description": "S'il y a eu un traitement antérieur contre le SARS-CoV-2 avec un agent antiviral.", - "title": "traitement antiviral antérieur contre le SARS-CoV-2", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", + "description": "Traitement contre une infection antérieure par le SRAS-CoV-2 avec un agent antiviral ou non", + "title": "Traitement antiviral contre une infection antérieure par le SRAS-CoV-2", "comments": [ - "Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SARS-CoV-2. Sélectionnez une valeur dans la liste de sélection." + "Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection." ], "examples": [ { - "value": "Aucun traitement antiviral préalable" + "value": "Aucun traitement antiviral antérieur" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", - "description": "Le nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SARS-CoV-2.", - "title": "agent du traitement antiviral antérieur contre le SARS-CoV-2", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", + "description": "Nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SRAS-CoV-2", + "title": "Agent du traitement antiviral contre une infection antérieure par le SRAS-CoV-2", "comments": [ - "Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous séparés par des virgules." + "Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous, séparés par des virgules." ], "examples": [ { @@ -7641,14 +5562,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", - "description": "Le traitement a été administré pour la première fois lors de l’infection antérieure par le SARS-CoV-2.", - "title": "date du traitement antiviral antérieur contre le SARS-CoV-2", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", + "description": "Date à laquelle le traitement a été administré pour la première fois lors de l’infection antérieure par le SRAS-CoV-2", + "title": "Date du traitement antiviral contre une infection antérieure par le SRAS-CoV-2", "comments": [ - "Indiquez la date à laquelle l'agent de traitement antiviral a été administré pour la première fois lors de l'infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SARS-CoV-2 au format standard ISO 8601 « YYYY-MM-DD »." + "Indiquez la date à laquelle l’agent de traitement antiviral a été administré pour la première fois lors de l’infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD »." ], "examples": [ { @@ -7656,14 +5580,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "purpose of sequencing": { - "name": "purpose of sequencing", - "description": "La raison pour laquelle l’échantillon a été séquencé.", - "title": "objectif du séquençage", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "Raison pour laquelle l’échantillon a été séquencé", + "title": "Objectif du séquençage", "comments": [ - "La raison pour laquelle un échantillon a été initialement collecté peut différer de la raison pour laquelle il a été sélectionné pour le séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des informations sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. La raison du prélèvement de l’échantillon doit être indiquée dans le champ « objectif de l’échantillonnage »." + "La raison pour laquelle un échantillon a été initialement prélevé peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des renseignements sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. Le motif de prélèvement de l’échantillon doit être indiqué dans le champ « Objectif de l’échantillonnage »." ], "examples": [ { @@ -7671,29 +5598,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "description": "La description de la raison pour laquelle l'échantillon a été séquencé, fournissant des détails spécifiques.", - "title": "objectif du séquençage détails", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "Description de la raison pour laquelle l’échantillon a été séquencé, fournissant des détails spécifiques", + "title": "Détails de l’objectif du séquençage", "comments": [ - "Fournissez une description détaillée de la raison pour laquelle l'échantillon a été séquencé à l'aide d'une liste de sélection. La description peut inclure l’importance des séquences pour une enquête/activité de surveillance/question de recherche particulière en santé publique. Les descriptions standardisées suggérées comprennent : Dépisté pour l'échec de la cible du gène S (abandon S), Dépisté pour les variantes de vison, Dépisté pour la variante B.1.1.7, Dépisté pour la variante B.1.135, Dépisté pour la variante P.1, Dépisté en raison des antécédents de voyage, Dépisté en raison d'un contact étroit avec une personne infectée, Évaluation des mesures de contrôle de la santé publique, Détermination des introductions et de la propagation précoces, Enquête sur les expositions liées aux compagnies aériennes, Enquête sur les travailleurs étrangers temporaires, Enquête sur les régions éloignées, Enquête sur les travailleurs de la santé, Enquête sur les écoles/universités, Enquête sur la réinfection." + "Fournissez une description détaillée de la raison pour laquelle l’échantillon a été séquencé en utilisant du texte libre. La description peut inclure l’importance des séquences pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Les descriptions normalisées suggérées sont les suivantes : Dépistage de l’absence de détection du gène S (abandon du gène S), dépistage de variants associés aux visons, dépistage du variant B.1.1.7, dépistage du variant B.1.135, dépistage du variant P.1, dépistage en raison des antécédents de voyage, dépistage en raison d’un contact étroit avec une personne infectée, évaluation des mesures de contrôle de la santé publique, détermination des introductions et de la propagation précoces, enquête sur les expositions liées aux voyages aériens, enquête sur les travailleurs étrangers temporaires, enquête sur les régions éloignées, enquête sur les travailleurs de la santé, enquête sur les écoles et les universités, enquête sur la réinfection." ], "examples": [ { - "value": "Dépisté pour échec de la cible du gène S (abandon S)" + "value": "Dépistage de l’absence de détection du gène S (abandon du gène S)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "sequencing date": { - "name": "sequencing date", - "description": "La date à laquelle l’échantillon a été séquencé.", - "title": "date de séquençage", + "sequencing_date": { + "name": "sequencing_date", + "description": "Date à laquelle l’échantillon a été séquencé", + "title": "Date de séquençage", "comments": [ - "Fournissez la date de séquençage au format standard ISO 8601 « YYYY-MM-DD »." + "La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." ], "examples": [ { @@ -7701,14 +5634,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "library ID": { - "name": "library ID", - "description": "L’identifiant spécifié par l’utilisateur pour la bibliothèque préparée pour le séquençage.", + "library_id": { + "name": "library_id", + "description": "Identifiant spécifié par l’utilisateur pour la bibliothèque faisant l’objet du séquençage", "title": "ID de la bibliothèque", "comments": [ - "Le nom de la bibliothèque doit être unique et peut être un identifiant généré automatiquement à partir de votre LIMS ou une modification de l'ID d'isolat." + "Le nom de la bibliothèque doit être unique et peut être un ID généré automatiquement à partir de votre système de gestion de l’information des laboratoires, ou une modification de l’ID de l’isolat." ], "examples": [ { @@ -7716,29 +5652,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "amplicon size": { - "name": "amplicon size", - "description": "La longueur de l'amplicon généré par l'amplification PCR.", - "title": "taille de l'amplicon", + "amplicon_size": { + "name": "amplicon_size", + "description": "Longueur de l’amplicon généré par l’amplification de la réaction de polymérisation en chaîne", + "title": "Taille de l’amplicon", "comments": [ "Fournissez la taille de l’amplicon, y compris les unités." ], "examples": [ { - "value": "300bp" + "value": "300 pb" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "library preparation kit": { - "name": "library preparation kit", - "description": "Nom du kit de préparation de la bibliothèque DNA utilisé pour générer la bibliothèque en cours de séquençage.", - "title": "kit de préparation de librairie", + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "Nom de la trousse de préparation de la banque d’ADN utilisée pour générer la bibliothèque faisant l’objet du séquençage", + "title": "Trousse de préparation de la bibliothèque", "comments": [ - "Indiquez le nom du kit de préparation de bibliothèque utilisé." + "Indiquez le nom de la trousse de préparation de la bibliothèque utilisée." ], "examples": [ { @@ -7746,14 +5688,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "flow cell barcode": { - "name": "flow cell barcode", - "description": "Le code-barres de la Flow Cell utilisée pour le séquençage.", - "title": "code-barres de la cellule d'écoulement", + "flow_cell_barcode": { + "name": "flow_cell_barcode", + "description": "Code-barres de la cuve à circulation utilisée aux fins de séquençage", + "title": "Code-barres de la cuve à circulation", "comments": [ - "Fournissez le code-barres de la Flow Cell utilisée pour séquencer l’échantillon." + "Fournissez le code-barres de la cuve à circulation utilisée pour séquencer l’échantillon." ], "examples": [ { @@ -7761,14 +5706,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "sequencing instrument": { - "name": "sequencing instrument", - "description": "Le modèle de l’instrument de séquençage utilisé.", - "title": "instrument de séquençage", + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "Modèle de l’instrument de séquençage utilisé", + "title": "Instrument de séquençage", "comments": [ - "Sélectionnez l’instrument de séquençage dans la liste de sélection." + "Sélectionnez l’instrument de séquençage à partir de la liste de sélection." ], "examples": [ { @@ -7776,14 +5724,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "sequencing protocol name": { - "name": "sequencing protocol name", - "description": "Le nom et le numéro de version du protocole de séquençage utilisé.", - "title": "nom du protocole de séquençage", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", + "description": "Nom et numéro de version du protocole de séquençage utilisé", + "title": "Nom du protocole de séquençage", "comments": [ - "Fournissez le nom et la version du protocole de séquençage." + "Fournissez le nom et la version du protocole de séquençage (p. ex., 1D_DNA_MinION)." ], "examples": [ { @@ -7791,27 +5742,33 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "sequencing protocol": { - "name": "sequencing protocol", - "description": "Le protocole utilisé pour générer la séquence.", - "title": "protocole de séquençage", + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "Protocole utilisé pour générer la séquence", + "title": "Protocole de séquençage", "comments": [ - "Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Texte suggéré, complétez les informations là où elles sont indiquées. : \"Le séquençage viral a été effectué selon une stratégie d'amplicon en mosaïque en utilisant le schéma d'amorce . Le séquençage a été effectué à l'aide d'un instrument de séquençage . Les bibliothèques ont été préparées à l'aide de la bibliothèque . trousse.\"" + "Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Voici le texte suggéré (insérez les renseignements manquants) : « Le séquençage viral a été effectué selon une stratégie d’amplicon en mosaïque en utilisant le schéma d’amorce <à remplir>. Le séquençage a été effectué à l’aide d’un instrument de séquençage <à remplir>. Les bibliothèques ont été préparées à l’aide de la trousse <à remplir>. »" ], "examples": [ { - "value": "Les génomes ont été générés par séquençage d'amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l'aide des kits Illumina DNA Prep et les données de séquence ont été produites à l'aide des kits de séquençage Miseq Micro v2 (500 cycles)." + "value": "Les génomes ont été générés par séquençage d’amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l’aide des trousses de préparation de l’ADN Illumina et les données de séquence ont été produites à l’aide des trousses de séquençage Miseq Micro v2 (500 cycles)." } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "sequencing kit number": { - "name": "sequencing kit number", - "description": "Le numéro de kit du fabricant.", - "title": "numéro du kit de séquençage", + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "description": "Numéro de la trousse du fabricant", + "title": "Numéro de la trousse de séquençage", "comments": [ "Valeur alphanumérique." ], @@ -7821,14 +5778,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "description": "Les spécifications des amorces (séquences d'amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer.", - "title": "de la liste des amorces pcr de l'amplicon", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "Spécifications liées aux amorces (séquences d’amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer", + "title": "Schéma d’amorce pour la réaction de polymérisation en chaîne de l’amplicon", "comments": [ - "Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons pour le séquençage." + "Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons aux fins de séquençage." ], "examples": [ { @@ -7836,14 +5796,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Séquençage" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "La méthode utilisée pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l'adaptateur, le filtrage, etc.", - "title": "méthode de traitement des données de séquences brutes", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "Nom et numéro de version du logiciel utilisé pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l’adaptateur, le filtrage, etc.", + "title": "Méthode de traitement des données de séquences brutes", "comments": [ - "Fournissez le nom et les numéros de version du logiciel utilisé pour traiter les données brutes." + "Fournissez le nom du logiciel, suivi de la version (p. ex., Trimmomatic v. 0.38, Porechop v. 0.2.03)." ], "examples": [ { @@ -7851,14 +5814,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "dehosting method": { - "name": "dehosting method", - "description": "Méthode utilisée pour supprimer les lectures de l'hôte de la séquence de l'agent pathogène.", - "title": "méthode de déshostage", + "dehosting_method": { + "name": "dehosting_method", + "description": "Méthode utilisée pour supprimer les lectures de l’hôte de la séquence de l’agent pathogène", + "title": "Méthode de retrait de l’hôte", "comments": [ - "Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l'hôte." + "Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l’hôte." ], "examples": [ { @@ -7866,14 +5832,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "Le nom de la séquence consensus.", - "title": "nom de la séquence consensus", + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "description": "Nom de la séquence de consensus", + "title": "Nom de la séquence de consensus", "comments": [ - "Fournissez le nom et le numéro de version de la séquence consensus." + "Fournissez le nom et le numéro de version de la séquence de consensus." ], "examples": [ { @@ -7881,14 +5850,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "Le nom du fichier de séquence consensus.", - "title": "nom de fichier de la séquence consensus", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", + "description": "Nom du fichier de la séquence de consensus", + "title": "Nom du fichier de la séquence de consensus", "comments": [ - "Fournissez le nom et le numéro de version du fichier FASTA de séquence consensus." + "Fournissez le nom et le numéro de version du fichier FASTA de la séquence de consensus." ], "examples": [ { @@ -7896,14 +5868,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "Le chemin d’accès du fichier de séquence consensus.", - "title": "chemin de fichier de la séquence consensus", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "description": "Chemin d’accès au fichier de la séquence de consensus", + "title": "Chemin d’accès au fichier de la séquence de consensus", "comments": [ - "Fournissez le chemin d’accès du fichier FASTA de séquence consensus." + "Fournissez le chemin d’accès au fichier FASTA de la séquence de consensus." ], "examples": [ { @@ -7911,14 +5886,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "Le nom du logiciel utilisé pour générer la séquence consensus.", - "title": "nom du logiciel de séquençage du consensus", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "Nom du logiciel utilisé pour générer la séquence de consensus", + "title": "Nom du logiciel de la séquence de consensus", "comments": [ - "Fournissez le nom du logiciel utilisé pour générer la séquence consensus." + "Fournissez le nom du logiciel utilisé pour générer la séquence de consensus." ], "examples": [ { @@ -7926,14 +5904,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "La version du logiciel utilisé pour générer la séquence consensus.", - "title": "version du logiciel de la séquence consensus", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "Version du logiciel utilisé pour générer la séquence de consensus", + "title": "Version du logiciel de la séquence de consensus", "comments": [ - "Fournir la version du logiciel utilisé pour générer la séquence consensus." + "Fournir la version du logiciel utilisé pour générer la séquence de consensus." ], "examples": [ { @@ -7941,29 +5922,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "Le pourcentage du génome de référence couvert par les données séquencées, jusqu'à une profondeur prescrite.", - "title": "valeur de l'étendue de la couverture", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "Pourcentage du génome de référence couvert par les données séquencées, jusqu’à une profondeur prescrite", + "title": "Valeur de l’étendue de la couverture", "comments": [ "Fournissez la valeur en pourcentage." ], "examples": [ { - "value": "95%" + "value": "95 %" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "Le nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite.", - "title": "valeur de la profondeur de couverture", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "Nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite", + "title": "Valeur de l’ampleur de la couverture", "comments": [ - "Apporter de la valeur sous forme de pli de couverture." + "Fournissez la valeur sous forme de couverture amplifiée." ], "examples": [ { @@ -7971,14 +5958,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "Seuil utilisé comme seuil pour la profondeur de couverture.", - "title": "seuil de profondeur de couverture", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "Seuil utilisé comme limite pour l’ampleur de la couverture", + "title": "Seuil de l’ampleur de la couverture", "comments": [ - "Fournit la couverture de pli de seuil." + "Fournissez la couverture amplifiée." ], "examples": [ { @@ -7986,14 +5976,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "Le nom de fichier spécifié par l'utilisateur du fichier r1 FASTQ.", - "title": "r1 nom de fichier fastq", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "description": "Nom du fichier R1 FASTQ spécifié par l’utilisateur", + "title": "Nom de fichier R1 FASTQ", "comments": [ - "Fournissez le nom du fichier r1 FASTQ." + "Fournissez le nom du fichier R1 FASTQ." ], "examples": [ { @@ -8001,14 +5994,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "Le nom de fichier spécifié par l'utilisateur du fichier r2 FASTQ.", - "title": "r2 nom de fichier fastq", + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "Nom du fichier R2 FASTQ spécifié par l’utilisateur", + "title": "Nom de fichier R2 FASTQ", "comments": [ - "Fournissez le nom du fichier r2 FASTQ." + "Fournissez le nom du fichier R2 FASTQ." ], "examples": [ { @@ -8016,14 +6012,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "Le chemin du fichier r1 FASTQ.", - "title": "chemin de fichier r1 fastq", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "description": "Emplacement du fichier R1 FASTQ dans le système de l’utilisateur", + "title": "Chemin d’accès au fichier R1 FASTQ", "comments": [ - "Fournissez le chemin du fichier r1 FASTQ." + "Fournissez le chemin d’accès au fichier R1 FASTQ." ], "examples": [ { @@ -8031,14 +6030,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "Le chemin d'accès du fichier r2 FASTQ.", - "title": "chemin du fichier r2 fastq", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "description": "Emplacement du fichier R2 FASTQ dans le système de l’utilisateur", + "title": "Chemin d’accès au fichier R2 FASTQ", "comments": [ - "Fournissez le chemin d'accès du fichier r2 FASTQ." + "Fournissez le chemin d’accès au fichier R2 FASTQ." ], "examples": [ { @@ -8046,14 +6048,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "fast5 filename": { - "name": "fast5 filename", - "description": "Le nom de fichier spécifié par l'utilisateur du fichier FAST5.", - "title": "nom de fichier fast5", + "fast5_filename": { + "name": "fast5_filename", + "description": "Nom du fichier FAST5 spécifié par l’utilisateur", + "title": "Nom de fichier FAST5", "comments": [ - "Fournissez le nom du fichier FAST5." + "Fournissez le nom du fichier FAST5." ], "examples": [ { @@ -8061,14 +6066,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "Le chemin du fichier FAST5.", - "title": "chemin de fichier fast5", + "fast5_filepath": { + "name": "fast5_filepath", + "description": "Emplacement du fichier FAST5 dans le système de l’utilisateur", + "title": "Chemin d’accès au fichier FAST5", "comments": [ - "Fournissez le chemin du fichier FAST5." + "Fournissez le chemin d’accès au fichier FAST5." ], "examples": [ { @@ -8076,42 +6084,51 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "Le nombre total de paires de bases générées par le processus de séquençage.", - "title": "nombre de paires de bases séquencées", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "Nombre total de paires de bases générées par le processus de séquençage", + "title": "Nombre de paires de bases séquencées", "comments": [ "Fournissez une valeur numérique (pas besoin d’inclure des unités)." ], "examples": [ { - "value": "387566" + "value": "387 566" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Taille du génome assemblé décrite comme le nombre de paires de bases.", - "title": "longueur consensuelle du génome", + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "Taille du génome reconstitué décrite comme étant le nombre de paires de bases", + "title": "Longueur consensuelle du génome", "comments": [ "Fournissez une valeur numérique (pas besoin d’inclure des unités)." ], "examples": [ { - "value": "38677" + "value": "38 677" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", - "description": "Le nombre de N symboles présents dans la séquence fasta consensus, pour 100 kbp de séquence.", - "title": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "Nombre de symboles N présents dans la séquence fasta de consensus, par 100 kbp de séquence", + "title": "N par 100 kbp", "comments": [ "Fournissez une valeur numérique (pas besoin d’inclure des unités)." ], @@ -8121,14 +6138,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "reference genome accession": { - "name": "reference genome accession", - "description": "Un identifiant persistant et unique d’une entrée de base de données génomique.", - "title": "accession au génome de référence", + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "Identifiant persistant et unique d’une entrée dans une base de données génomique", + "title": "Accès au génome de référence", "comments": [ - "Fournissez le numéro d’accès du génome de référence." + "Fournissez le numéro d’accès au génome de référence." ], "examples": [ { @@ -8136,14 +6156,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "Le nom et le numéro de version du protocole bioinformatique utilisé.", - "title": "protocole bioinformatique", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "Description de la stratégie bioinformatique globale utilisée", + "title": "Protocole bioinformatique", "comments": [ - "Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes et/ou générer des assemblages et/ou générer des séquences consensus peuvent être fournis dans une SOP ou un protocole. Fournissez le nom et le numéro de version du protocole, ou un lien s'il est déposé dans un référentiel de protocoles." + "Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes, générer des assemblages ou générer des séquences de consensus peuvent être fournis dans une PON, un protocole, un pipeline ou un flux de travail. Fournissez le nom et le numéro de version du protocole, ou un lien GitHub vers un pipeline ou un flux de travail." ], "examples": [ { @@ -8151,14 +6174,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "lineage/clade name": { - "name": "lineage/clade name", - "description": "Le nom de la lignée ou du clade.", - "title": "nom du lineage/clade", + "lineage_clade_name": { + "name": "lineage_clade_name", + "description": "Nom de la lignée ou du clade", + "title": "Nom de la lignée ou du clade", "comments": [ - "Fournissez le nom de la lignée/clade Pangolin ou Nextstrain." + "Fournissez le nom de la lignée ou du clade Pangolin ou Nextstrain." ], "examples": [ { @@ -8166,14 +6192,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur les lignées et les variantes" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", - "description": "Le nom du logiciel utilisé pour déterminer la lignée/clade.", - "title": "nom du logiciel d'analyse de linéage/clade", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", + "description": "Nom du logiciel utilisé pour déterminer la lignée ou le clade", + "title": "Nom du logiciel d’analyse de la lignée ou du clade", "comments": [ - "Fournissez le nom du logiciel utilisé pour déterminer la lignée/clade." + "Fournissez le nom du logiciel utilisé pour déterminer la lignée ou le clade." ], "examples": [ { @@ -8181,14 +6210,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur les lignées et les variantes" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", - "description": "La version du logiciel utilisé pour déterminer la lignée/clade.", - "title": "version du logiciel d'analyse de linéage/clade", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", + "description": "Version du logiciel utilisé pour déterminer la lignée ou le clade", + "title": "Version du logiciel d’analyse de la lignée ou du clade", "comments": [ - "Fournissez la version du logiciel utilisé pour déterminer la lignée/clade." + "Fournissez la version du logiciel utilisé pour déterminer la lignée ou le clade." ], "examples": [ { @@ -8196,29 +6228,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur les lignées et les variantes" }, - "variant designation": { - "name": "variant designation", - "description": "La classification des variantes de la lignée/clade, c'est-à-dire variante, variante préoccupante.", - "title": "désignation de la variante", + "variant_designation": { + "name": "variant_designation", + "description": "Classification des variants de la lignée ou du clade (c.-à-d. le variant, le variant préoccupant)", + "title": "Désignation du variant", "comments": [ - "Si la lignée/clade est considérée comme une variante préoccupante, sélectionnez Variante préoccupante dans la liste de sélection. Si la lignée/clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques) mais qu’il ne s’agit pas d’une variante préoccupante globale, sélectionnez Variante. Si la lignée/clade ne contient pas de mutations préoccupantes, laissez ce champ vide." + "Si la lignée ou le clade est considéré comme étant un variant préoccupant, sélectionnez l’option connexe à partir de la liste de sélection. Si la lignée ou le clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques), mais qu’il ne s’agit pas d’un variant préoccupant global, sélectionnez « Variante ». Si la lignée ou le clade ne contient pas de mutations préoccupantes, laissez ce champ vide." ], "examples": [ { - "value": "Variante préoccupante (VOC)" + "value": "Variant préoccupant" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur les lignées et les variantes" }, - "variant evidence": { - "name": "variant evidence", - "description": "Preuve utilisée pour déterminer la variante.", - "title": "preuve de la variante", + "variant_evidence": { + "name": "variant_evidence", + "description": "Données probantes utilisées pour déterminer le variant", + "title": "Données probantes du variant", "comments": [ - "Sélectionnez si l’échantillon a été dépisté à l’aide de RT-qPCR ou par séquençage dans la liste de sélection." + "Indiquez si l’échantillon a fait l’objet d’un dépistage RT-qPCR ou par séquençage à partir de la liste de sélection." ], "examples": [ { @@ -8226,44 +6264,53 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur les lignées et les variantes" }, - "variant evidence details": { - "name": "variant evidence details", - "description": "Détails sur les preuves utilisées pour déterminer la variante.", - "title": "détails de la preuve de la variante", + "variant_evidence_details": { + "name": "variant_evidence_details", + "description": "Détails sur les données probantes utilisées pour déterminer le variant", + "title": "Détails liés aux données probantes du variant", "comments": [ - "Fournissez le test et répertoriez l’ensemble des mutations définissant la lignée utilisées pour effectuer la détermination des variantes. Si des mutations intéressantes/préoccupantes ont été observées en plus des mutations définissant la lignée, décrivez-les ici." + "Fournissez l’essai biologique et répertoriez l’ensemble des mutations définissant la lignée qui sont utilisées pour effectuer la détermination des variants. Si des mutations d’intérêt ou de préoccupation ont été observées en plus des mutations définissant la lignée, décrivez-les ici." ], "examples": [ { - "value": "Mutations définissant la lignée: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)." + "value": "Mutations définissant la lignée : ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)." } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Informations sur les lignées et les variantes" }, - "gene name 1": { - "name": "gene name 1", - "description": "Le nom du gène utilisé dans le test diagnostique RT-PCR.", - "title": "nom du gène 1", + "gene_name_1": { + "name": "gene_name_1", + "description": "Nom du gène utilisé dans le test diagnostique RT-PCR", + "title": "Nom du gène 1", "comments": [ - "Sélectionnez un gène dans la liste de sélection. Si le gène qui vous intéresse ne figure pas dans la liste, indiquez le nom complet du gène ou le symbole du gène (forme abrégée du nom du gène). Les noms et symboles de gènes standardisés peuvent être trouvés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI" + "Indiquez le nom complet du gène soumis au dépistage. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI." ], "examples": [ { - "value": "E gene (orf4)" + "value": "Gène E (orf4)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", - "description": "Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic.", - "title": "protocole de diagnostic pcr 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", + "description": "Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques", + "title": "Protocole de diagnostic de polymérase en chaîne 1", "comments": [ - "Le nom et le numéro de version du protocole utilisé pour réaliser un test PCR diagnostique. Ces informations peuvent être comparées aux données de séquence pour l’évaluation des performances et le contrôle qualité." + "Le nom et le numéro de version du protocole utilisé pour réaliser un test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité." ], "examples": [ { @@ -8271,14 +6318,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "description": "La valeur du seuil de cycle (Ct) résulte d’un test de diagnostic RT-PCR du SARS-CoV-2.", - "title": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", + "description": "Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2", + "title": "Valeur de diagnostic de polymérase en chaîne 1", "comments": [ - "Fournissez la valeur du seuil de cycle (Ct) de l’échantillon issu du test de diagnostic RT-PCR." + "Fournissez la valeur Ct de l’échantillon issu du test diagnostique RT-PCR." ], "examples": [ { @@ -8286,29 +6336,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "gene name 2": { - "name": "gene name 2", - "description": "Le nom du gène utilisé dans le test diagnostique RT-PCR.", - "title": "nom du gène 2", + "gene_name_2": { + "name": "gene_name_2", + "description": "Nom du gène utilisé dans le test diagnostique RT-PCR", + "title": "Nom du gène 2", "comments": [ - "Sélectionnez un gène dans la liste de sélection. Si le gène qui vous intéresse ne figure pas dans la liste, indiquez le nom complet du gène ou le symbole du gène (forme abrégée du nom du gène). Les noms et symboles de gènes standardisés peuvent être trouvés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI" + "Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI." ], "examples": [ { - "value": "RdRp gene (nsp12)" + "value": "Gène RdRp (nsp12)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", - "description": "Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic.", - "title": "protocole de diagnostic pcr 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", + "description": "Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques", + "title": "Protocole de diagnostic de polymérase en chaîne 2", "comments": [ - "Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test de diagnostic PCR. Ces informations peuvent être comparées aux données de séquence pour l’évaluation des performances et le contrôle qualité." + "Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité." ], "examples": [ { @@ -8316,14 +6372,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "description": "La valeur du seuil de cycle (Ct) résulte d’un test de diagnostic RT-PCR du SARS-CoV-2.", - "title": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", + "description": "Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2", + "title": "Valeur de diagnostic de polymérase en chaîne 2", "comments": [ - "Fournissez la valeur du seuil de cycle (Ct) de l’échantillon issu du deuxième test de diagnostic RT-PCR." + "Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR." ], "examples": [ { @@ -8331,29 +6390,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "gene name 3": { - "name": "gene name 3", - "description": "Le nom du gène utilisé dans le test diagnostique RT-PCR.", - "title": "nom du gène 3", + "gene_name_3": { + "name": "gene_name_3", + "description": "Nom du gène utilisé dans le test diagnostique RT-PCR", + "title": "Nom du gène 3", "comments": [ - "Fournissez le nom complet d’un autre gène utilisé dans un test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Les noms et symboles de gènes standardisés peuvent être trouvés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI" + "Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI." ], "examples": [ { - "value": "RdRp gene (nsp12)" + "value": "Gène RdRp (nsp12)" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 3": { - "name": "diagnostic pcr protocol 3", - "description": "Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic.", - "title": "protocole de diagnostic pcr 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", + "description": "Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques", + "title": "Protocole de diagnostic de polymérase en chaîne 3", "comments": [ - "Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test de diagnostic PCR. Ces informations peuvent être comparées aux données de séquence pour l’évaluation des performances et le contrôle qualité." + "Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité." ], "examples": [ { @@ -8361,14 +6426,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "description": "La valeur Ct résulte d’un test de diagnostic SARS-CoV-2 RT-PCR.", - "title": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", + "description": "Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2", + "title": "Valeur de diagnostic de polymérase en chaîne 3", "comments": [ - "Fournissez la valeur CT de l’échantillon du deuxième test de diagnostic RT-PCR." + "Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR." ], "examples": [ { @@ -8376,29 +6444,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Tests de diagnostic des agents pathogènes" }, "authors": { "name": "authors", - "description": "Noms des personnes contribuant aux processus de collecte d’échantillons, de génération de séquences, d’analyse et de soumission de données.", - "title": "auteurs", + "description": "Noms des personnes contribuant aux processus de prélèvement d’échantillons, de génération de séquences, d’analyse et de soumission de données", + "title": "Auteurs", "comments": [ - "Incluez le prénom et le nom de toutes les personnes qui doivent être attribuées, séparés par une virgule." + "Incluez le prénom et le nom de toutes les personnes qui doivent être affectées, séparés par une virgule." ], "examples": [ { - "value": "Tejinder Singh, Fei Hu, Joe Blogs" + "value": "Tejinder Singh, Fei Hu, Joe Blogs" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Reconnaissance des contributeurs" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "Provenance du logiciel DataHarmonizer et de la version du modèle.", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "Provenance du logiciel DataHarmonizer et de la version du modèle", "title": "Provenance de DataHarmonizer", "comments": [ - "Les informations actuelles sur la version du logiciel et du modèle seront automatiquement générées dans ce champ une fois que l'utilisateur aura utilisé la fonction « valider ». Ces informations seront générées indépendamment du fait que la ligne soit valide ou non." + "Les renseignements actuels sur la version du logiciel et du modèle seront automatiquement générés dans ce champ une fois que l’utilisateur aura utilisé la fonction « Valider ». Ces renseignements seront générés indépendamment du fait que la ligne soit valide ou non." ], "examples": [ { @@ -8406,6 +6480,9 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "domain_of": [ + "CanCOGeNCovid19" + ], "slot_group": "Reconnaissance des contributeurs" } }, @@ -8415,121 +6492,133 @@ "description": "A DataHarmonizer interface", "from_schema": "https://example.com/CanCOGeN_Covid-19" }, - "CanCOGeN Covid-19": { - "name": "CanCOGeN Covid-19", + "CanCOGeNCovid19": { + "name": "CanCOGeNCovid19", "description": "Canadian specification for Covid-19 clinical virus biosample data gathering", + "title": "CanCOGeN Covid-19", "from_schema": "https://example.com/CanCOGeN_Covid-19", "see_also": [ "templates/canada_covid19/SOP.pdf" ], "is_a": "dh_interface", "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 1, "slot_group": "Identificateurs de base de données" }, - "third party lab service provider name": { - "name": "third party lab service provider name", - "rank": 2 + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", + "rank": 2, + "slot_group": "Identificateurs de base de données" }, - "third party lab sample ID": { - "name": "third party lab sample ID", - "rank": 3 + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", + "rank": 3, + "slot_group": "Identificateurs de base de données" }, - "case ID": { - "name": "case ID", - "rank": 4 + "case_id": { + "name": "case_id", + "rank": 4, + "slot_group": "Identificateurs de base de données" }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", - "rank": 5 + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", + "rank": 5, + "slot_group": "Identificateurs de base de données" }, - "IRIDA sample name": { - "name": "IRIDA sample name", - "rank": 6 + "irida_sample_name": { + "name": "irida_sample_name", + "rank": 6, + "slot_group": "Identificateurs de base de données" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", - "rank": 7 + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", + "rank": 7, + "slot_group": "Identificateurs de base de données" }, - "bioproject accession": { - "name": "bioproject accession", - "rank": 8 + "bioproject_accession": { + "name": "bioproject_accession", + "rank": 8, + "slot_group": "Identificateurs de base de données" }, - "biosample accession": { - "name": "biosample accession", - "rank": 9 + "biosample_accession": { + "name": "biosample_accession", + "rank": 9, + "slot_group": "Identificateurs de base de données" }, - "SRA accession": { - "name": "SRA accession", - "rank": 10 + "sra_accession": { + "name": "sra_accession", + "rank": 10, + "slot_group": "Identificateurs de base de données" }, - "GenBank accession": { - "name": "GenBank accession", - "rank": 11 + "genbank_accession": { + "name": "genbank_accession", + "rank": 11, + "slot_group": "Identificateurs de base de données" }, - "GISAID accession": { - "name": "GISAID accession", - "rank": 12 + "gisaid_accession": { + "name": "gisaid_accession", + "rank": 12, + "slot_group": "Identificateurs de base de données" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 13, "slot_group": "Collecte et traitement des échantillons" }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "rank": 14, "slot_group": "Collecte et traitement des échantillons" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "rank": 15, "slot_group": "Collecte et traitement des échantillons" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 16, "slot_group": "Collecte et traitement des échantillons" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "rank": 17, "slot_group": "Collecte et traitement des échantillons" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "rank": 18, "slot_group": "Collecte et traitement des échantillons" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "rank": 19, "slot_group": "Collecte et traitement des échantillons" }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "rank": 20, "slot_group": "Collecte et traitement des échantillons" }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "rank": 21, "slot_group": "Collecte et traitement des échantillons" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 22, "slot_group": "Collecte et traitement des échantillons" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 23, "slot_group": "Collecte et traitement des échantillons" }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "rank": 24, "slot_group": "Collecte et traitement des échantillons" }, @@ -8543,173 +6632,173 @@ "rank": 26, "slot_group": "Collecte et traitement des échantillons" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "rank": 27, "slot_group": "Collecte et traitement des échantillons" }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "rank": 28, "slot_group": "Collecte et traitement des échantillons" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "rank": 29, "slot_group": "Collecte et traitement des échantillons" }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "rank": 30, "slot_group": "Collecte et traitement des échantillons" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "rank": 31, "slot_group": "Collecte et traitement des échantillons" }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "rank": 32, "slot_group": "Collecte et traitement des échantillons" }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "rank": 33, "slot_group": "Collecte et traitement des échantillons" }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "rank": 34, "slot_group": "Collecte et traitement des échantillons" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "rank": 35, "slot_group": "Collecte et traitement des échantillons" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 36, "slot_group": "Collecte et traitement des échantillons" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 37, "slot_group": "Collecte et traitement des échantillons" }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "rank": 38, "slot_group": "Collecte et traitement des échantillons" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "rank": 39, "slot_group": "Collecte et traitement des échantillons" }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "rank": 40, "slot_group": "Collecte et traitement des échantillons" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "rank": 41, "slot_group": "Collecte et traitement des échantillons" }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "rank": 42, "slot_group": "Collecte et traitement des échantillons" }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "rank": 43, "slot_group": "Collecte et traitement des échantillons" }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "rank": 44, "slot_group": "Collecte et traitement des échantillons" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "rank": 45, "slot_group": "Informations sur l'hôte" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 46, "slot_group": "Informations sur l'hôte" }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "rank": 47, "slot_group": "Informations sur l'hôte" }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "rank": 48, "slot_group": "Informations sur l'hôte" }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "rank": 49, "slot_group": "Informations sur l'hôte" }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "rank": 50, "slot_group": "Informations sur l'hôte" }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "rank": 51, "slot_group": "Informations sur l'hôte" }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "rank": 52, "slot_group": "Informations sur l'hôte" }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "rank": 53, "slot_group": "Informations sur l'hôte" }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "rank": 54, "slot_group": "Informations sur l'hôte" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "rank": 55, "slot_group": "Informations sur l'hôte" }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", "rank": 56, "slot_group": "Informations sur l'hôte" }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "rank": 57, "slot_group": "Informations sur l'hôte" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "rank": 58, "slot_group": "Informations sur l'hôte" }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "rank": 59, "slot_group": "Informations sur l'hôte" }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "rank": 60, "slot_group": "Informations sur l'hôte" }, @@ -8718,403 +6807,403 @@ "rank": 61, "slot_group": "Informations sur l'hôte" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "rank": 62, "slot_group": "Informations sur la vaccination de l'hôte" }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "rank": 63, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "rank": 64, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "rank": 65, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "rank": 66, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "rank": 67, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "rank": 68, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "rank": 69, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "rank": 70, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "rank": 71, "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "rank": 72, "slot_group": "Informations sur la vaccination de l'hôte" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "rank": 73, "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "rank": 74, "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "rank": 75, "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "rank": 76, "slot_group": "Informations sur l'exposition de l'hôte" }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "rank": 77, "slot_group": "Informations sur l'exposition de l'hôte" }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "rank": 78, "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel point of entry type": { - "name": "travel point of entry type", + "travel_point_of_entry_type": { + "name": "travel_point_of_entry_type", "rank": 79, "slot_group": "Informations sur l'exposition de l'hôte" }, - "border testing test day type": { - "name": "border testing test day type", + "border_testing_test_day_type": { + "name": "border_testing_test_day_type", "rank": 80, "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "rank": 81, "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel history availability": { - "name": "travel history availability", + "travel_history_availability": { + "name": "travel_history_availability", "rank": 82, "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "rank": 83, "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "rank": 84, "slot_group": "Informations sur l'exposition de l'hôte" }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "rank": 85, "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "rank": 86, "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "rank": 87, "slot_group": "Informations sur l'exposition de l'hôte" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "rank": 88, "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "rank": 89, "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "rank": 90, "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "rank": 91, "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "rank": 92, "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "rank": 93, "slot_group": "Informations sur la réinfection de l'hôte" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 94, "slot_group": "Séquençage" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 95, "slot_group": "Séquençage" }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "rank": 96, "slot_group": "Séquençage" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "rank": 97, "slot_group": "Séquençage" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "rank": 98, "slot_group": "Séquençage" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 99, "slot_group": "Séquençage" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "rank": 100, "slot_group": "Séquençage" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 101, "slot_group": "Séquençage" }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "rank": 102, "slot_group": "Séquençage" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 103, "slot_group": "Séquençage" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "rank": 104, "slot_group": "Séquençage" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 105, "slot_group": "Séquençage" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 106, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "rank": 107, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence name": { - "name": "consensus sequence name", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "rank": 108, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence filename": { - "name": "consensus sequence filename", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "rank": 109, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", "rank": 110, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 111, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 112, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 113, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 114, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 115, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1 fastq filename": { - "name": "r1 fastq filename", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", "rank": 116, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r2 fastq filename": { - "name": "r2 fastq filename", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "rank": 117, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "rank": 118, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "rank": 119, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "fast5 filename": { - "name": "fast5 filename", + "fast5_filename": { + "name": "fast5_filename", "rank": 120, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "fast5 filepath": { - "name": "fast5 filepath", + "fast5_filepath": { + "name": "fast5_filepath", "rank": 121, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 122, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "rank": 123, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "rank": 124, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 125, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 126, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "rank": 127, "slot_group": "Informations sur les lignées et les variantes" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "rank": 128, "slot_group": "Informations sur les lignées et les variantes" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "rank": 129, "slot_group": "Informations sur les lignées et les variantes" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "rank": 130, "slot_group": "Informations sur les lignées et les variantes" }, - "variant evidence": { - "name": "variant evidence", + "variant_evidence": { + "name": "variant_evidence", "rank": 131, "slot_group": "Informations sur les lignées et les variantes" }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "rank": 132, "slot_group": "Informations sur les lignées et les variantes" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "rank": 133, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "rank": 134, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "rank": 135, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "rank": 136, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "rank": 137, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "rank": 138, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "rank": 139, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 3": { - "name": "diagnostic pcr protocol 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", "rank": 140, "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "rank": 141, "slot_group": "Tests de diagnostic des agents pathogènes" }, @@ -9123,1836 +7212,3046 @@ "rank": 142, "slot_group": "Reconnaissance des contributeurs" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 143, "slot_group": "Reconnaissance des contributeurs" } }, "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", - "description": "Le nom défini par l'utilisateur pour l'échantillon.", - "title": "Collecteur d'échantillons ID de l'échantillon", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "Nom défini par l’utilisateur pour l’échantillon", + "title": "ID du collecteur d’échantillons", + "comments": [ + "Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de conserver la clé qui correspond aux identifiants d’origine et alternatifs aux fins de traçabilité et de suivi, au besoin. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n’importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 1, - "alias": "specimen_collector_sample_ID", - "owner": "CanCOGeN Covid-19", + "alias": "specimen_collector_sample_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Identificateurs de base de données" }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", + "description": "Nom de la société ou du laboratoire tiers qui fournit les services", + "title": "Nom du fournisseur de services de laboratoire tiers", + "comments": [ + "Indiquez le nom complet et non abrégé de l’entreprise ou du laboratoire." + ], + "examples": [ + { + "value": "Switch Health" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 2, "alias": "third_party_lab_service_provider_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", + "description": "Identifiant attribué à un échantillon par un prestataire de services tiers", + "title": "ID de l’échantillon de laboratoire tiers", + "comments": [ + "Conservez l’identifiant de l’échantillon fourni par le prestataire de services tiers." + ], + "examples": [ + { + "value": "SHK123456" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 3, - "alias": "third_party_lab_sample_ID", - "owner": "CanCOGeN Covid-19", + "alias": "third_party_lab_sample_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", + "description": "Identifiant utilisé pour désigner un cas de maladie détecté sur le plan épidémiologique", + "title": "ID du dossier", + "comments": [ + "Fournissez l’identifiant du cas, lequel facilite grandement le lien entre les données de laboratoire et les données épidémiologiques. Il peut être considéré comme une information identifiable. Consultez l’intendant des données avant de le transmettre." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 4, - "alias": "case_ID", - "owner": "CanCOGeN Covid-19", + "alias": "case_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", + "description": "Identifiant principal d’un échantillon associé précédemment soumis au dépôt", + "title": "ID principal de l’échantillon associé", + "comments": [ + "Conservez l’identifiant primaire de l’échantillon correspondant précédemment soumis au Laboratoire national de microbiologie afin que les échantillons puissent être liés et suivis dans le système." + ], + "examples": [ + { + "value": "SR20-12345" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 5, - "alias": "Related_specimen_primary_ID", - "owner": "CanCOGeN Covid-19", + "alias": "related_specimen_primary_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", + "description": "Identifiant attribué à un isolat séquencé dans IRIDA", + "title": "Nom de l’échantillon IRIDA", + "comments": [ + "Enregistrez le nom de l’échantillon IRIDA, lequel sera créé par la personne saisissant les données dans la plateforme connexe. Les échantillons IRIDA peuvent être liés à des métadonnées et à des données de séquence, ou simplement à des métadonnées. Il est recommandé que le nom de l’échantillon IRIDA soit identique ou contienne l’ID de l’échantillon du collecteur pour assurer une meilleure traçabilité. Il est également recommandé que le nom de l’échantillon IRIDA reflète l’accès à GISAID. Les noms d’échantillons IRIDA ne peuvent pas contenir de barres obliques. Celles-ci doivent être remplacées par des traits de soulignement. Consultez la documentation IRIDA pour en savoir plus sur les caractères spéciaux (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 6, - "alias": "IRIDA_sample_name", - "owner": "CanCOGeN Covid-19", + "alias": "irida_sample_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", + "description": "Numéro d’accès à INSDC attribué au bioprojet cadre pour l’effort canadien de séquençage du SRAS-CoV-2", + "title": "Numéro d’accès au bioprojet cadre", + "comments": [ + "Enregistrez le numéro d’accès au bioprojet cadre en le sélectionnant à partir de la liste déroulante du modèle. Ce numéro sera identique pour tous les soumissionnaires du RCanGéCO. Différentes provinces auront leurs propres bioprojets, mais ces derniers seront liés sous un seul bioprojet cadre." + ], + "examples": [ + { + "value": "PRJNA623807" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 7, "alias": "umbrella_bioproject_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", + "description": "Numéro d’accès à INSDC du bioprojet auquel appartient un échantillon biologique", + "title": "Numéro d’accès au bioprojet", + "comments": [ + "Enregistrez le numéro d’accès au bioprojet. Les bioprojets sont un outil d’organisation qui relie les données de séquence brutes, les assemblages et leurs métadonnées associées. Chaque province se verra attribuer un numéro d’accès différent au bioprojet par le Laboratoire national de microbiologie. Un numéro d’accès valide au bioprojet du NCBI contient le préfixe PRJN (p. ex., PRJNA12345); il est créé une fois au début d’un nouveau projet de séquençage." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 8, "alias": "bioproject_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", + "description": "Identifiant attribué à un échantillon biologique dans les archives INSDC", + "title": "Numéro d’accès à un échantillon biologique", + "comments": [ + "Conservez le numéro d’accès renvoyé avec la soumission d’un échantillon biologique. Les échantillons biologiques de NCBI seront assortis du SAMN." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 9, "alias": "biosample_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", + "description": "Identifiant de l’archive des séquences reliant les données de séquences brutes de lecture, les métadonnées méthodologiques et les mesures de contrôle de la qualité soumises à INSDC", + "title": "Numéro d’accès à l’archive des séquences", + "comments": [ + "Conservez le numéro d’accès attribué au « cycle » soumis. Les accès NCBI-SRA commencent par SRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 10, - "alias": "SRA_accession", - "owner": "CanCOGeN Covid-19", + "alias": "sra_accession", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", + "description": "Identifiant GenBank attribué à la séquence dans les archives INSDC", + "title": "Numéro d’accès à GenBank", + "comments": [ + "Conservez le numéro d’accès renvoyé avec la soumission de GenBank (assemblage du génome viral)." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 11, - "alias": "GenBank_accession", - "owner": "CanCOGeN Covid-19", + "alias": "genbank_accession", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", + "description": "Numéro d’accès à la GISAID attribué à la séquence", + "title": "Numéro d’accès à la GISAID", + "comments": [ + "Conservez le numéro d’accès renvoyé avec la soumission de la GISAID." + ], + "examples": [ + { + "value": "EPI_ISL_436489" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 12, - "alias": "GISAID_accession", - "owner": "CanCOGeN Covid-19", + "alias": "gisaid_accession", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" - ] + "CanCOGeNCovid19" + ], + "slot_group": "Identificateurs de base de données" }, - "sample collected by": { - "name": "sample collected by", - "description": "Le nom de l’organisation à laquelle le collecteur d’échantillons est affilié.", - "title": "échantillon collecté par", + "sample_collected_by": { + "name": "sample_collected_by", + "description": "Nom de l’organisme ayant prélevé l’échantillon original", + "title": "Échantillon prélevé par", + "comments": [ + "Le nom du collecteur d’échantillons doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions, par exemple Agence de la santé publique du Canada, Santé publique Ontario, Centre de contrôle des maladies de la Colombie-Britannique." + ], + "examples": [ + { + "value": "Centre de contrôle des maladies de la Colombie-Britannique" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 13, "alias": "sample_collected_by", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sample collector contact email": { - "name": "sample collector contact email", - "description": "L'adresse email du contact responsable du suivi concernant l'échantillon.", - "title": "Courriel de contact du collecteur d'échantillons", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", + "description": "Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon", + "title": "Adresse courriel du collecteur d’échantillons", + "comments": [ + "L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca)." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 14, "alias": "sample_collector_contact_email", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sample collector contact address": { - "name": "sample collector contact address", - "description": "L'adresse postale de l'agence qui soumet l'échantillon.", - "title": "adresse de contact du collecteur d'échantillons", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", + "description": "Adresse postale de l’organisme soumettant l’échantillon", + "title": "Adresse du collecteur d’échantillons", + "comments": [ + "Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays." + ], + "examples": [ + { + "value": "655, rue Lab, Vancouver (Colombie-Britannique) V5N 2A2 Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 15, "alias": "sample_collector_contact_address", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sequence submitted by": { - "name": "sequence submitted by", - "description": "Le nom de l'agence qui a généré la séquence.", - "title": "séquence soumise par", + "sequence_submitted_by": { + "name": "sequence_submitted_by", + "description": "Nom de l’organisme ayant généré la séquence", + "title": "Séquence soumise par", + "comments": [ + "Le nom de l’agence doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions. Si vous soumettez des échantillons plutôt que des données de séquençage, veuillez inscrire « Laboratoire national de microbiologie (LNM) »." + ], + "examples": [ + { + "value": "Santé publique Ontario (SPO)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 16, "alias": "sequence_submitted_by", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", - "description": "L'adresse email du contact responsable du suivi de la séquence.", - "title": "séquence courriel de contact du déposant", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", + "description": "Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon", + "title": "Adresse courriel du soumissionnaire de séquence", + "comments": [ + "L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca)." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 17, "alias": "sequence_submitter_contact_email", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", - "description": "L'adresse postale de l'agence soumettant la séquence.", - "title": "adresse de contact de l'auteur de la séquence", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", + "description": "Adresse postale de l’organisme soumettant l’échantillon", + "title": "Adresse du soumissionnaire de séquence", + "comments": [ + "Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays." + ], + "examples": [ + { + "value": "123, rue Sunnybrooke, Toronto (Ontario) M4P 1L6 Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 18, "alias": "sequence_submitter_contact_address", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sample collection date": { - "name": "sample collection date", - "description": "La date à laquelle l'échantillon a été prélevé.", - "title": "date de collecte de l'échantillon", + "sample_collection_date": { + "name": "sample_collection_date", + "description": "Date à laquelle l’échantillon a été prélevé", + "title": "Date de prélèvement de l’échantillon", + "comments": [ + "La date de prélèvement des échantillons est essentielle pour la surveillance et de nombreux types d’analyses. La granularité requise comprend l’année, le mois et le jour. Si cette date est considérée comme un renseignement identifiable, il est acceptable d’y ajouter une « gigue » en ajoutant ou en soustrayant un jour civil. La « date de réception » peut également servir de date de rechange. La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 19, "alias": "sample_collection_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sample collection date precision": { - "name": "sample collection date precision", - "description": "La précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie.", - "title": "date de collecte de l'échantillon précision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", + "description": "Précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie", + "title": "Précision de la date de prélèvement de l’échantillon", + "comments": [ + "Fournissez la précision de la granularité au « jour », au « mois » ou à « l’année » pour la date fournie dans le champ « Date de prélèvement de l’échantillon ». Cette date sera tronquée selon la précision spécifiée lors de l’exportation : « jour » pour « AAAA-MM-JJ », « mois » pour « AAAA-MM » ou « année » pour « AAAA »." + ], + "examples": [ + { + "value": "année" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 20, "alias": "sample_collection_date_precision", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "sample received date": { - "name": "sample received date", - "description": "La date à laquelle l'échantillon a été reçu.", - "title": "date de réception de l'échantillon", + "sample_received_date": { + "name": "sample_received_date", + "description": "Date à laquelle l’échantillon a été reçu", + "title": "Date de réception de l’échantillon", + "comments": [ + "La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 21, "alias": "sample_received_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", - "description": "Le pays d'origine de l'échantillon.", - "title": "nom du geo_loc (pays)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", + "description": "Pays d’origine de l’échantillon", + "title": "nom_lieu_géo (pays)", + "comments": [ + "Fournissez le nom du pays à partir du vocabulaire contrôlé fourni." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 22, - "alias": "geo_loc_name_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "geo_loc_name_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", - "description": "L'État/la province/le territoire d'origine de l'échantillon.", - "title": "nom du geo_loc (état/province/territoire)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", + "description": "Province ou territoire où l’échantillon a été prélevé", + "title": "nom_lieu_géo (état/province/territoire)", + "comments": [ + "Fournissez le nom de la province ou du territoire à partir du vocabulaire contrôlé fourni." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 23, - "alias": "geo_loc_name_(state/province/territory)", - "owner": "CanCOGeN Covid-19", + "alias": "geo_loc_name_state_province_territory", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", - "description": "La ville d'origine de l'échantillon.", - "title": "nom du geo_loc (ville)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", + "description": "Ville où l’échantillon a été prélevé", + "title": "nom_géo_loc (ville)", + "comments": [ + "Fournissez le nom de la ville. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." + ], + "examples": [ + { + "value": "Medicine Hat" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 24, - "alias": "geo_loc_name_(city)", - "owner": "CanCOGeN Covid-19", + "alias": "geo_loc_name_city", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, "organism": { "name": "organism", - "description": "Nom taxonomique de l'organisme.", - "title": "organisme", + "description": "Nom taxonomique de l’organisme", + "title": "Organisme", + "comments": [ + "Utilisez « coronavirus du syndrome respiratoire aigu sévère 2 ». Cette valeur est fournie dans le modèle." + ], + "examples": [ + { + "value": "Coronavirus du syndrome respiratoire aigu sévère 2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 25, "alias": "organism", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, "isolate": { "name": "isolate", - "description": "Identifiant de l'isolat spécifique.", - "title": "isolat", + "description": "Identifiant de l’isolat spécifique", + "title": "Isolat", + "comments": [ + "Fournissez le nom du virus de la GISAID, qui doit être écrit dans le format « hCov-19/CANADA/code ISO provincial à 2 chiffres-xxxxx/année »." + ], + "examples": [ + { + "value": "hCov-19/CANADA/BC-prov_rona_99/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 26, "alias": "isolate", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "purpose of sampling": { - "name": "purpose of sampling", - "description": "La raison pour laquelle l’échantillon a été collecté.", - "title": "Objectif de l'échantillonnage", + "purpose_of_sampling": { + "name": "purpose_of_sampling", + "description": "Motif de prélèvement de l’échantillon", + "title": "Objectif de l’échantillonnage", + "comments": [ + "La raison pour laquelle un échantillon a été prélevé peut fournir des renseignements sur les biais potentiels de la stratégie d’échantillonnage. Choisissez l’objectif de l’échantillonnage à partir de la liste déroulante du modèle. Il est très probable que l’échantillon ait été prélevé en vue d’un test diagnostique. La raison pour laquelle un échantillon a été prélevé à l’origine peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage, ce qui doit être indiqué dans le champ « Objectif du séquençage »." + ], + "examples": [ + { + "value": "Tests diagnostiques" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 27, "alias": "purpose_of_sampling", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "purpose of sampling details": { - "name": "purpose of sampling details", - "description": "Plus de détails concernant la raison pour laquelle l’échantillon a été collecté.", - "title": "détails de l'objectif de l'échantillonnage", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", + "description": "Détails précis concernant le motif de prélèvement de l’échantillon", + "title": "Détails de l’objectif de l’échantillonnage", + "comments": [ + "Fournissez une description détaillée de la raison pour laquelle l’échantillon a été prélevé en utilisant du texte libre. La description peut inclure l’importance de l’échantillon pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Si les détails ne sont pas disponibles, fournissez une valeur nulle." + ], + "examples": [ + { + "value": "L’échantillon a été prélevé pour étudier la prévalence des variants associés à la transmission du vison à l’homme au Canada." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 28, "alias": "purpose_of_sampling_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", - "description": "Le type d'échantillon soumis au Laboratoire national de microbiologie (NML) pour analyse.", - "title": "Type de spécimen soumis au NML", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", + "description": "Type d’échantillon soumis au Laboratoire national de microbiologie (LNM) aux fins d’analyse", + "title": "Type d’échantillon soumis au LNM", + "comments": [ + "Ces renseignements sont requis pour le téléchargement à l’aide du système LaSER du RCRSP. Choisissez le type d’échantillon à partir de la liste de sélection fournie. Si les données de séquences sont soumises plutôt qu’un échantillon aux fins d’analyse, sélectionnez « Sans objet »." + ], + "examples": [ + { + "value": "Écouvillon" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 29, - "alias": "NML_submitted_specimen_type", - "owner": "CanCOGeN Covid-19", + "alias": "nml_submitted_specimen_type", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", - "description": "La relation entre le spécimen actuel et le spécimen/échantillon précédemment soumis au référentiel.", - "title": "Type de relation du spécimen apparenté", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", + "description": "Relation entre l’échantillon actuel et celui précédemment soumis au dépôt", + "title": "Type de relation de l’échantillon lié", + "comments": [ + "Fournissez l’étiquette qui décrit comment l’échantillon précédent est lié à l’échantillon actuel soumis à partir de la liste de sélection fournie afin que les échantillons puissent être liés et suivis dans le système." + ], + "examples": [ + { + "value": "Test des méthodes de prélèvement des échantillons" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 30, - "alias": "Related_specimen_relationship_type", - "owner": "CanCOGeN Covid-19", + "alias": "related_specimen_relationship_type", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "anatomical material": { - "name": "anatomical material", - "description": "Une substance obtenue à partir d'une partie anatomique d'un organisme, par ex. tissu, sang.", - "title": "matière anatomique", + "anatomical_material": { + "name": "anatomical_material", + "description": "Substance obtenue à partir d’une partie anatomique d’un organisme (p. ex., tissu, sang)", + "title": "Matière anatomique", + "comments": [ + "Fournissez un descripteur si une matière anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Sang" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 31, "alias": "anatomical_material", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "anatomical part": { - "name": "anatomical part", - "description": "Une partie anatomique d'un organisme, par ex. oropharynx.", - "title": "partie anatomique", + "anatomical_part": { + "name": "anatomical_part", + "description": "Partie anatomique d’un organisme (p. ex., oropharynx)", + "title": "Partie anatomique", + "comments": [ + "Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Nasopharynx (NP)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 32, "alias": "anatomical_part", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "body product": { - "name": "body product", - "description": "Une substance excrétée/sécrétée par un organisme, par ex. selles, urine, sueur.", - "title": "produit corporel", + "body_product": { + "name": "body_product", + "description": "Substance excrétée ou sécrétée par un organisme (p. ex., selles, urine, sueur)", + "title": "Produit corporel", + "comments": [ + "Fournissez un descripteur si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Selles" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 33, "alias": "body_product", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "environmental material": { - "name": "environmental material", - "description": "Une substance obtenue à partir de l'environnement naturel ou artificiel, par ex. sol, eau, eaux usées, poignée de porte, rampe de lit, masque facial.", - "title": "matériau environnemental", + "environmental_material": { + "name": "environmental_material", + "description": "Substance obtenue à partir de l’environnement naturel ou artificiel (p. ex., sol, eau, eaux usées)", + "title": "Matériel environnemental", + "comments": [ + "Fournissez un descripteur si une matière environnementale a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Masque" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 34, "alias": "environmental_material", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "environmental site": { - "name": "environmental site", - "description": "Un emplacement environnemental peut décrire un site dans l'environnement naturel ou bâti, par ex. hôpital, marché humide, grotte aux chauves-souris.", - "title": "site environnemental", + "environmental_site": { + "name": "environmental_site", + "description": "Emplacement environnemental pouvant décrire un site dans l’environnement naturel ou artificiel (p. ex., surface de contact, boîte métallique, hôpital, marché traditionnel de produits frais, grotte de chauves-souris)", + "title": "Site environnemental", + "comments": [ + "Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Installation de production" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 35, "alias": "environmental_site", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "collection device": { - "name": "collection device", - "description": "L'instrument ou le récipient utilisé pour collecter l'échantillon, par ex. écouvillon.", - "title": "dispositif de collecte", + "collection_device": { + "name": "collection_device", + "description": "Instrument ou contenant utilisé pour prélever l’échantillon (p. ex., écouvillon)", + "title": "Dispositif de prélèvement", + "comments": [ + "Fournissez un descripteur si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Écouvillon" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 36, "alias": "collection_device", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "collection method": { - "name": "collection method", - "description": "Le processus utilisé pour collecter l'échantillon, par ex. phlébotomie, autopsie.", - "title": "méthode de collecte", + "collection_method": { + "name": "collection_method", + "description": "Processus utilisé pour prélever l’échantillon (p. ex., phlébotomie, autopsie)", + "title": "Méthode de prélèvement", + "comments": [ + "Fournissez un descripteur si une méthode de prélèvement a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." + ], + "examples": [ + { + "value": "Lavage bronchoalvéolaire (LBA)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 37, "alias": "collection_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "collection protocol": { - "name": "collection protocol", - "description": "Le nom et la version d'un protocole particulier utilisé pour l'échantillonnage.", - "title": "protocole de collecte", + "collection_protocol": { + "name": "collection_protocol", + "description": "Nom et version d’un protocole particulier utilisé pour l’échantillonnage", + "title": "Protocole de prélèvement", + "comments": [ + "Texte libre." + ], + "examples": [ + { + "value": "CBRonaProtocoleÉchantillonnage v. 1.2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 38, "alias": "collection_protocol", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "specimen processing": { - "name": "specimen processing", - "description": "Tout traitement appliqué à l’échantillon pendant ou après la réception de l’échantillon.", - "title": "processus de traitement des spécimens", + "specimen_processing": { + "name": "specimen_processing", + "description": "Tout traitement appliqué à l’échantillon pendant ou après sa réception", + "title": "Traitement des échantillons", + "comments": [ + "Essentiel pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, ajoutez les renseignements dans les champs « Laboratoire hôte », « Nombre de transmissions » et « Méthode de transmission ». Si aucun des processus de la liste de sélection ne s’applique, inscrivez « Sans objet »." + ], + "examples": [ + { + "value": "Transmission du virus" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 39, "alias": "specimen_processing", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "specimen processing details": { - "name": "specimen processing details", - "description": "Informations détaillées concernant le traitement appliqué à un échantillon pendant ou après la réception de l'échantillon.", - "title": "détails du processus des échantillons", + "specimen_processing_details": { + "name": "specimen_processing_details", + "description": "Renseignements détaillés concernant le traitement appliqué à un échantillon pendant ou après sa réception", + "title": "Détails du traitement des échantillons", + "comments": [ + "Fournissez une description en texte libre de tous les détails du traitement appliqués à un échantillon." + ], + "examples": [ + { + "value": "25 écouvillons ont été regroupés et préparés en tant qu’échantillon unique lors de la préparation de la bibliothèque." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 40, "alias": "specimen_processing_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "lab host": { - "name": "lab host", - "description": "Nom et description de l'hôte de laboratoire utilisé pour propager l'organisme source ou le matériel à partir duquel l'échantillon a été obtenu.", - "title": "hôte du laboratoire", + "lab_host": { + "name": "lab_host", + "description": "Nom et description du laboratoire hôte utilisé pour propager l’organisme source ou le matériel à partir duquel l’échantillon a été obtenu", + "title": "Laboratoire hôte", + "comments": [ + "Type de lignée cellulaire utilisée pour la propagation. Choisissez le nom de cette lignée à partir de la liste de sélection dans le modèle. Si le virus n’a pas été transmis, indiquez « Sans objet »." + ], + "examples": [ + { + "value": "Lignée cellulaire Vero E6" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 41, "alias": "lab_host", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "passage number": { - "name": "passage number", - "description": "Nombre de passages.", - "title": "numéro de passage", + "passage_number": { + "name": "passage_number", + "description": "Nombre de transmissions", + "title": "Nombre de transmission", + "comments": [ + "Indiquez le nombre de transmissions connues. Si le virus n’a pas été transmis, indiquez « Sans objet »." + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 42, "alias": "passage_number", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "passage method": { - "name": "passage method", - "description": "Description de la façon dont l'organisme a été transmis.", - "title": "méthode de passage", + "passage_method": { + "name": "passage_method", + "description": "Description de la façon dont l’organisme a été transmis", + "title": "Méthode de transmission", + "comments": [ + "Texte libre. Fournissez une brève description (<10 mots). Si le virus n’a pas été transmis, indiquez « Sans objet »." + ], + "examples": [ + { + "value": "0,25 % de trypsine + 0,02 % d’EDTA" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 43, "alias": "passage_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "biomaterial extracted": { - "name": "biomaterial extracted", - "description": "Biomatériau extrait d’échantillons à des fins de séquençage.", - "title": "biomatériau extrait", + "biomaterial_extracted": { + "name": "biomaterial_extracted", + "description": "Biomatériau extrait d’échantillons aux fins de séquençage", + "title": "Biomatériau extrait", + "comments": [ + "Fournissez le biomatériau extrait à partir de la liste de sélection dans le modèle." + ], + "examples": [ + { + "value": "ARN (total)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 44, "alias": "biomaterial_extracted", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Collecte et traitement des échantillons" }, - "host (common name)": { - "name": "host (common name)", - "description": "Le nom couramment utilisé de l'hôte.", - "title": "hôte (nom commun)", + "host_common_name": { + "name": "host_common_name", + "description": "Nom couramment utilisé pour l’hôte", + "title": "Hôte (nom commun)", + "comments": [ + "Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Des exemples de noms communs sont « humain » et « chauve-souris ». Si l’échantillon était environnemental, inscrivez « Sans objet »." + ], + "examples": [ + { + "value": "Humain" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 45, - "alias": "host_(common_name)", - "owner": "CanCOGeN Covid-19", + "alias": "host_common_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host (scientific name)": { - "name": "host (scientific name)", - "description": "Le nom taxonomique ou scientifique de l’hôte.", - "title": "hôte (nom scientifique)", + "host_scientific_name": { + "name": "host_scientific_name", + "description": "Nom taxonomique ou scientifique de l’hôte", + "title": "Hôte (nom scientifique)", + "comments": [ + "Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Un exemple de nom scientifique est « homo sapiens ». Si l’échantillon était environnemental, inscrivez « Sans objet »." + ], + "examples": [ + { + "value": "Homo sapiens" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 46, - "alias": "host_(scientific_name)", - "owner": "CanCOGeN Covid-19", + "alias": "host_scientific_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host health state": { - "name": "host health state", - "description": "État de santé de l'hôte au moment du prélèvement de l'échantillon.", - "title": "état de santé de l'hôte", + "host_health_state": { + "name": "host_health_state", + "description": "État de santé de l’hôte au moment du prélèvement d’échantillons", + "title": "État de santé de l’hôte", + "comments": [ + "Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "Symptomatique" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 47, "alias": "host_health_state", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host health status details": { - "name": "host health status details", - "description": "Plus de détails concernant l'état de santé ou de maladie de l'hôte au moment de la collecte.", - "title": "détails de l'état de santé de l'hôte", + "host_health_status_details": { + "name": "host_health_status_details", + "description": "Plus de détails concernant l’état de santé ou de maladie de l’hôte au moment du prélèvement", + "title": "Détails de l’état de santé de l’hôte", + "comments": [ + "Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "Hospitalisé (USI)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 48, "alias": "host_health_status_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host health outcome": { - "name": "host health outcome", - "description": "Résultat de la maladie chez l’hôte.", - "title": "résultat sanitaire de l'hôte", + "host_health_outcome": { + "name": "host_health_outcome", + "description": "Résultats de la maladie chez l’hôte", + "title": "Résultats sanitaires de l’hôte", + "comments": [ + "Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "Rétabli" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 49, "alias": "host_health_outcome", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host disease": { - "name": "host disease", - "description": "Le nom de la maladie vécue par l'hôte.", - "title": "maladie de l'hôte", + "host_disease": { + "name": "host_disease", + "description": "Nom de la maladie vécue par l’hôte", + "title": "Maladie de l’hôte", + "comments": [ + "Sélectionnez « COVID-19 » à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "COVID-19" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 50, "alias": "host_disease", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host age": { - "name": "host age", - "description": "Âge de l'hôte au moment de l'échantillonnage.", - "title": "âge de l'hôte", + "host_age": { + "name": "host_age", + "description": "Âge de l’hôte au moment du prélèvement d’échantillons", + "title": "Âge de l’hôte", + "comments": [ + "Entrez l’âge de l’hôte en années. S’il n’est pas disponible, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet »." + ], + "examples": [ + { + "value": "79" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 51, "alias": "host_age", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host age unit": { - "name": "host age unit", - "description": "Les unités utilisées pour mesurer l'âge de l'hôte.", - "title": "unité d'âge de l'hôte", + "host_age_unit": { + "name": "host_age_unit", + "description": "Unité utilisée pour mesurer l’âge de l’hôte (mois ou année)", + "title": "Catégorie d’âge de l’hôte", + "comments": [ + "Indiquez si l’âge de l’hôte est en mois ou en années. L’âge indiqué en mois sera classé dans la tranche d’âge de 0 à 9 ans." + ], + "examples": [ + { + "value": "année" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 52, "alias": "host_age_unit", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host age bin": { - "name": "host age bin", - "description": "La catégorie d'âge de l'hôte au moment de l'échantillonnage.", - "title": "âge de l'hôte bin", + "host_age_bin": { + "name": "host_age_bin", + "description": "Âge de l’hôte au moment du prélèvement d’échantillons (groupe d’âge)", + "title": "Groupe d’âge de l’hôte", + "comments": [ + "Sélectionnez la tranche d’âge correspondante de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne la connaissez pas, fournissez une valeur nulle." + ], + "examples": [ + { + "value": "60 - 69" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 53, "alias": "host_age_bin", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host gender": { - "name": "host gender", - "description": "Le sexe de l’hôte au moment du prélèvement de l’échantillon.", - "title": "sexe de l'hôte", + "host_gender": { + "name": "host_gender", + "description": "Genre de l’hôte au moment du prélèvement d’échantillons", + "title": "Genre de l’hôte", + "comments": [ + "Sélectionnez le genre correspondant de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne le connaissez pas, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet »." + ], + "examples": [ + { + "value": "Homme" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 54, "alias": "host_gender", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", - "description": "Le pays où réside l'hôte.", - "title": "résidence de l'hôte nom du geo_loc (pays)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", + "description": "Pays de résidence de l’hôte", + "title": "Résidence de l’hôte – Nom de géo_loc (pays)", + "comments": [ + "Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 55, - "alias": "host_residence_geo_loc_name_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "host_residence_geo_loc_name_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", - "description": "L'état/province/territoire de résidence de l'hôte.", - "title": "nom du geo_loc de la résidence de l'hôte (état/province/territoire)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", + "description": "État, province ou territoire de résidence de l’hôte", + "title": "Résidence de l’hôte – Nom de géo_loc (état/province/territoire)", + "comments": [ + "Sélectionnez le nom de la province ou du territoire à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "Québec" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 56, - "alias": "host_residence_geo_loc_name_(state/province/territory)", - "owner": "CanCOGeN Covid-19", + "alias": "host_residence_geo_loc_name_state_province_territory", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host subject ID": { - "name": "host subject ID", - "description": "Un identifiant unique par lequel chaque hôte peut être référencé, par ex. #131", - "title": "ID du sujet de l'hôte", + "host_subject_id": { + "name": "host_subject_id", + "description": "Identifiant unique permettant de désigner chaque hôte (p. ex., 131)", + "title": "ID du sujet de l’hôte", + "comments": [ + "Fournissez l’identifiant de l’hôte. Il doit s’agir d’un identifiant unique défini par l’utilisateur." + ], + "examples": [ + { + "value": "BCxy123" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 57, - "alias": "host_subject_ID", - "owner": "CanCOGeN Covid-19", + "alias": "host_subject_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "symptom onset date": { - "name": "symptom onset date", - "description": "La date à laquelle les symptômes ont commencé ou ont été observés pour la première fois.", - "title": "date d'apparition des symptômes", + "symptom_onset_date": { + "name": "symptom_onset_date", + "description": "Date à laquelle les symptômes ont commencé ou ont été observés pour la première fois", + "title": "Date d’apparition des symptômes", + "comments": [ + "La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 58, "alias": "symptom_onset_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "signs and symptoms": { - "name": "signs and symptoms", - "description": "Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélateur d'une maladie, rapporté par un patient.", - "title": "signes et symptômes", + "signs_and_symptoms": { + "name": "signs_and_symptoms", + "description": "Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélant une maladie, qui est signalé par un patient ou un clinicien", + "title": "Signes et symptômes", + "comments": [ + "Sélectionnez tous les symptômes ressentis par l’hôte à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Frissons (sensation soudaine de froid)" + }, + { + "value": "toux" + }, + { + "value": "fièvre" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 59, "alias": "signs_and_symptoms", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", - "description": "Conditions préexistantes du patient et facteurs de risque.
  • Condition préexistante : condition médicale qui existait avant l’infection actuelle.
  • Facteur de risque : variable associée à un risque accru de maladie ou d’infection.", - "title": "les conditions préexistantes et les facteurs de risque", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", + "description": "Conditions préexistantes et facteurs de risque du patient
  • Condition préexistante : Condition médicale qui existait avant l’infection actuelle
  • Facteur de risque : Variable associée à un risque accru de maladie ou d’infection", + "title": "Conditions préexistantes et facteurs de risque", + "comments": [ + "Sélectionnez toutes les conditions préexistantes et tous les facteurs de risque de l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." + ], + "examples": [ + { + "value": "Asthme" + }, + { + "value": "grossesse" + }, + { + "value": "tabagisme" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 60, - "alias": "pre_existing_conditions_and_risk_factors", - "owner": "CanCOGeN Covid-19", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, "complications": { "name": "complications", - "description": "Complications médicales du patient qui seraient dues à une maladie de l’hôte.", - "title": "les complications", + "description": "Complications médicales du patient qui seraient dues à une maladie de l’hôte", + "title": "Complications", + "comments": [ + "Sélectionnez toutes les complications éprouvées par l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." + ], + "examples": [ + { + "value": "Insuffisance respiratoire aiguë" + }, + { + "value": "coma" + }, + { + "value": "septicémie" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 61, "alias": "complications", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'hôte" }, - "host vaccination status": { - "name": "host vaccination status", - "description": "Le statut vaccinal de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné).", - "title": "le statut vaccinal de l'hôte", + "host_vaccination_status": { + "name": "host_vaccination_status", + "description": "Statut de vaccination de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné)", + "title": "Statut de vaccination de l’hôte", + "comments": [ + "Sélectionnez le statut de vaccination de l’hôte à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Entièrement vacciné" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 62, "alias": "host_vaccination_status", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", - "description": "Le nombre de doses de vaccin reçues par l’hôte.", - "title": "nombre de doses de vaccin reçues", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", + "description": "Nombre de doses du vaccin reçues par l’hôte", + "title": "Nombre de doses du vaccin reçues", + "comments": [ + "Enregistrez le nombre de doses du vaccin que l’hôte a reçues." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 63, "alias": "number_of_vaccine_doses_received", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", - "description": "Nom du vaccin administré comme première dose d'un schéma vaccinal.", - "title": "dose de vaccination 1 nom du vaccin", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", + "description": "Nom du vaccin administré comme première dose d’un schéma vaccinal", + "title": "Dose du vaccin 1 – Nom du vaccin", + "comments": [ + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 64, "alias": "vaccination_dose_1_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", - "description": "La date à laquelle la première dose d’un vaccin a été administrée.", - "title": "dose de vaccination 1 date de vaccination", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", + "description": "Date à laquelle la première dose d’un vaccin a été administrée", + "title": "Dose du vaccin 1 – Date du vaccin", + "comments": [ + "Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 65, "alias": "vaccination_dose_1_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", - "description": "Nom du vaccin administré comme deuxième dose d'un schéma vaccinal.", - "title": "dose de vaccination 2 nom du vaccin", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", + "description": "Nom du vaccin administré comme deuxième dose d’un schéma vaccinal", + "title": "Dose du vaccin 2 – Nom du vaccin", + "comments": [ + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 66, "alias": "vaccination_dose_2_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", - "description": "La date à laquelle la deuxième dose d’un vaccin a été administrée.", - "title": "dose de vaccination 2 date de vaccination", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", + "description": "Date à laquelle la deuxième dose d’un vaccin a été administrée", + "title": "Dose du vaccin 2 – Date du vaccin", + "comments": [ + "Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 67, "alias": "vaccination_dose_2_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", - "description": "Nom du vaccin administré comme troisième dose d'un schéma vaccinal.", - "title": "dose de vaccination 3 nom du vaccin", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", + "description": "Nom du vaccin administré comme troisième dose d’un schéma vaccinal", + "title": "Dose du vaccin 3 – Nom du vaccin", + "comments": [ + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 68, "alias": "vaccination_dose_3_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", - "description": "La date à laquelle la troisième dose d’un vaccin a été administrée.", - "title": "dose de vaccination 3 date de vaccination", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", + "description": "Date à laquelle la troisième dose d’un vaccin a été administrée", + "title": "Dose du vaccin 3 – Date du vaccin", + "comments": [ + "Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." + ], + "examples": [ + { + "value": "2021-12-30" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 69, "alias": "vaccination_dose_3_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", - "description": "Nom du vaccin administré comme quatrième dose d'un schéma vaccinal.", - "title": "dose de vaccination 4 nom du vaccin", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", + "description": "Nom du vaccin administré comme quatrième dose d’un schéma vaccinal", + "title": "Dose du vaccin 4 – Nom du vaccin", + "comments": [ + "Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 70, "alias": "vaccination_dose_4_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", - "description": "La date à laquelle la quatrième dose d’un vaccin a été administrée.", - "title": "dose de vaccination 4 date de vaccination", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", + "description": "Date à laquelle la quatrième dose d’un vaccin a été administrée", + "title": "Dose du vaccin 4 – Date du vaccin", + "comments": [ + "Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD »." + ], + "examples": [ + { + "value": "2022-01-15" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 71, "alias": "vaccination_dose_4_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "vaccination history": { - "name": "vaccination history", - "description": "Une description des vaccins reçus et les dates d'administration d'une série de vaccinations contre une maladie spécifique ou un ensemble de maladies.", - "title": "les antécédents de vaccination", + "vaccination_history": { + "name": "vaccination_history", + "description": "Description des vaccins reçus et dates d’administration d’une série de vaccins contre une maladie spécifique ou un ensemble de maladies", + "title": "Antécédents de vaccination", + "comments": [ + "Description en texte libre des dates et des vaccins administrés contre une maladie précise ou un ensemble de maladies. Il est également acceptable de concaténer les renseignements sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 72, "alias": "vaccination_history", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la vaccination de l'hôte" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", - "description": "Le pays où l'hôte a probablement été exposé à l'agent causal de la maladie.", - "title": "lieu d'exposition geo_loc nom (pays)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", + "description": "Pays où l’hôte a probablement été exposé à l’agent causal de la maladie", + "title": "Lieu de l’exposition – Nom de géo_loc (pays)", + "comments": [ + "Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 73, - "alias": "location_of_exposure_geo_loc_name_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "location_of_exposure_geo_loc_name_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", - "description": "Le nom de la ville de destination du voyage le plus récent.", - "title": "destination du dernier voyage (ville)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", + "description": "Nom de la ville de destination du voyage le plus récent", + "title": "Destination du dernier voyage (ville)", + "comments": [ + "Indiquez le nom de la ville dans laquelle l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." + ], + "examples": [ + { + "value": "New York City" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 74, - "alias": "destination_of_most_recent_travel_(city)", - "owner": "CanCOGeN Covid-19", + "alias": "destination_of_most_recent_travel_city", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", - "description": "Le nom de la province de destination du voyage le plus récent.", - "title": "destination du dernier voyage (état/province/territoire)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", + "description": "Nom de la province de destination du voyage le plus récent", + "title": "Destination du dernier voyage (état/province/territoire)", + "comments": [ + "Indiquez le nom de l’État, de la province ou du territoire où l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." + ], + "examples": [ + { + "value": "Californie" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 75, - "alias": "destination_of_most_recent_travel_(state/province/territory)", - "owner": "CanCOGeN Covid-19", + "alias": "destination_of_most_recent_travel_state_province_territory", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", - "description": "Le nom du pays de destination du voyage le plus récent.", - "title": "destination du dernier voyage (pays)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", + "description": "Nom du pays de destination du voyage le plus récent", + "title": "Destination du dernier voyage (pays)", + "comments": [ + "Indiquez le nom du pays dans lequel l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz." + ], + "examples": [ + { + "value": "Royaume-Uni" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 76, - "alias": "destination_of_most_recent_travel_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "destination_of_most_recent_travel_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "most recent travel departure date": { - "name": "most recent travel departure date", - "description": "Date du départ le plus récent d'une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits.", - "title": "date de départ du voyage la plus récente", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", + "description": "Date du départ le plus récent d’une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits", + "title": "Date de départ de voyage la plus récente", + "comments": [ + "Indiquez la date de départ du voyage." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 77, "alias": "most_recent_travel_departure_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "most recent travel return date": { - "name": "most recent travel return date", - "description": "Date du retour le plus récent d'une personne à une résidence après un voyage au départ de cette résidence.", - "title": "date de retour la plus récente", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", + "description": "Date du retour le plus récent d’une personne à une résidence après un voyage au départ de cette résidence", + "title": "Date de retour de voyage la plus récente", + "comments": [ + "Indiquez la date de retour du voyage." + ], + "examples": [ + { + "value": "2020-04-26" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 78, "alias": "most_recent_travel_return_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel point of entry type": { - "name": "travel point of entry type", - "description": "Le type de point d’entrée par lequel un voyageur arrive.", - "title": "voyage type de point d'entrée", + "travel_point_of_entry_type": { + "name": "travel_point_of_entry_type", + "description": "Type de point d’entrée par lequel un voyageur arrive", + "title": "Type de point d’entrée du voyage", + "comments": [ + "Sélectionnez le type de point d’entrée." + ], + "examples": [ + { + "value": "Air" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 79, "alias": "travel_point_of_entry_type", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "border testing test day type": { - "name": "border testing test day type", - "description": "Le jour où un voyageur a été testé à son arrivée ou après son point d’entrée.", - "title": "test aux frontières jour du test type", + "border_testing_test_day_type": { + "name": "border_testing_test_day_type", + "description": "Jour où un voyageur a été testé à son point d’entrée ou après cette date", + "title": "Jour du dépistage à la frontière", + "comments": [ + "Sélectionnez le jour du test." + ], + "examples": [ + { + "value": "Jour 1" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 80, "alias": "border_testing_test_day_type", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel history": { - "name": "travel history", - "description": "Historique de voyage au cours des six derniers mois.", - "title": "histoire du voyage", + "travel_history": { + "name": "travel_history", + "description": "Historique de voyage au cours des six derniers mois", + "title": "Antécédents de voyage", + "comments": [ + "Précisez les pays (et les emplacements plus précis, si vous les connaissez) visités au cours des six derniers mois, ce qui peut comprendre plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Commencez par le voyage le plus récent." + ], + "examples": [ + { + "value": "Canada, Vancouver" + }, + { + "value": "États-Unis, Seattle" + }, + { + "value": "Italie, Milan" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 81, "alias": "travel_history", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "travel history availability": { - "name": "travel history availability", - "description": "La disponibilité de différents types d’historiques de voyages au cours des 6 derniers mois (par exemple internationaux, nationaux).", - "title": "disponibilité de l'historique de voyage", + "travel_history_availability": { + "name": "travel_history_availability", + "description": "Disponibilité de différents types d’historiques de voyages au cours des six derniers mois (p. ex., internationaux, nationaux)", + "title": "Disponibilité des antécédents de voyage", + "comments": [ + "Si les antécédents de voyage sont disponibles, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d’antécédents disponibles en sélectionnant une valeur à partir de la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu’un échantillon est associé à un voyage lorsque le « but du séquençage » n’est pas associé à un voyage." + ], + "examples": [ + { + "value": "Antécédents de voyage à l’étranger disponible" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 82, "alias": "travel_history_availability", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure event": { - "name": "exposure event", - "description": "Événement conduisant à une exposition.", - "title": "exposition événement", + "exposure_event": { + "name": "exposure_event", + "description": "Événement conduisant à une exposition", + "title": "Événement d’exposition", + "comments": [ + "Sélectionnez un événement conduisant à une exposition à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." + ], + "examples": [ + { + "value": "Convention" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 83, "alias": "exposure_event", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure contact level": { - "name": "exposure contact level", - "description": "Le type de contact de transmission d’exposition.", - "title": "exposition niveau de contact", + "exposure_contact_level": { + "name": "exposure_contact_level", + "description": "Type de contact de transmission d’exposition", + "title": "Niveau de contact de l’exposition", + "comments": [ + "Sélectionnez une exposition directe ou indirecte à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Direct" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 84, "alias": "exposure_contact_level", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "host role": { - "name": "host role", - "description": "Le rôle de l'hôte par rapport au paramètre d'exposition.", - "title": "rôle d'hôte", + "host_role": { + "name": "host_role", + "description": "Rôle de l’hôte par rapport au paramètre d’exposition", + "title": "Rôle de l’hôte", + "comments": [ + "Sélectionnez les rôles personnels de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." + ], + "examples": [ + { + "value": "Patient" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 85, "alias": "host_role", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure setting": { - "name": "exposure setting", - "description": "Le cadre menant à l’exposition.", - "title": "réglage de l'exposition", + "exposure_setting": { + "name": "exposure_setting", + "description": "Contexte menant à l’exposition", + "title": "Contexte de l’exposition", + "comments": [ + "Sélectionnez les contextes menant à l’exposition de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données." + ], + "examples": [ + { + "value": "Milieu de soins de santé" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 86, "alias": "exposure_setting", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "exposure details": { - "name": "exposure details", - "description": "Informations supplémentaires sur l’exposition de l’hôte.", - "title": "détails de l'exposition", + "exposure_details": { + "name": "exposure_details", + "description": "Renseignements supplémentaires sur l’exposition de l’hôte", + "title": "Détails de l’exposition", + "comments": [ + "Description en texte libre de l’exposition." + ], + "examples": [ + { + "value": "Rôle d’hôte - Autre : Conducteur d’autobus" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 87, "alias": "exposure_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur l'exposition de l'hôte" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", - "description": "S'il y a eu une infection antérieure par le SARS-CoV-2.", - "title": "infection antérieure par le SARS-CoV-2", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", + "description": "Infection antérieure par le SRAS-CoV-2 ou non", + "title": "Infection antérieure par le SRAS-CoV-2", + "comments": [ + "Si vous le savez, fournissez des renseignements indiquant si la personne a déjà eu une infection par le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Oui" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 88, - "alias": "prior_SARS_CoV_2_infection", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_infection", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", - "description": "L’identifiant de l’isolat trouvé lors de l’infection antérieure par le SARS-CoV-2.", - "title": "isolat d'une infection antérieure par le SARS-CoV-2", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", + "description": "Identifiant de l’isolat trouvé lors de l’infection antérieure par le SRAS-CoV-2", + "title": "Isolat d’une infection antérieure par le SRAS-CoV-2", + "comments": [ + "Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom de « l’isolat » pour qu’il soit conforme à la norme ICTV/INSDC dans le format suivant : « SRAS-CoV-2/hôte/pays/IDéchantillon/date »." + ], + "examples": [ + { + "value": "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 89, - "alias": "prior_SARS_CoV_2_infection_isolate", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_infection_isolate", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", - "description": "La date du diagnostic de l’infection antérieure par le SARS-CoV-2.", - "title": "date d'une infection antérieure par le SARS-CoV-2", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", + "description": "Date du diagnostic de l’infection antérieure par le SRAS-CoV-2", + "title": "Date d’une infection antérieure par le SRAS-CoV-2", + "comments": [ + "Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d’infection antérieure par le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD »." + ], + "examples": [ + { + "value": "2021-01-23" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 90, - "alias": "prior_SARS_CoV_2_infection_date", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_infection_date", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", - "description": "S'il y a eu un traitement antérieur contre le SARS-CoV-2 avec un agent antiviral.", - "title": "traitement antiviral antérieur contre le SARS-CoV-2", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", + "description": "Traitement contre une infection antérieure par le SRAS-CoV-2 avec un agent antiviral ou non", + "title": "Traitement antiviral contre une infection antérieure par le SRAS-CoV-2", + "comments": [ + "Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Aucun traitement antiviral antérieur" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 91, - "alias": "prior_SARS_CoV_2_antiviral_treatment", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_antiviral_treatment", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", - "description": "Le nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SARS-CoV-2.", - "title": "agent du traitement antiviral antérieur contre le SARS-CoV-2", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", + "description": "Nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SRAS-CoV-2", + "title": "Agent du traitement antiviral contre une infection antérieure par le SRAS-CoV-2", + "comments": [ + "Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous, séparés par des virgules." + ], + "examples": [ + { + "value": "Remdesivir" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 92, - "alias": "prior_SARS_CoV_2_antiviral_treatment_agent", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_antiviral_treatment_agent", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", - "description": "Le traitement a été administré pour la première fois lors de l’infection antérieure par le SARS-CoV-2.", - "title": "date du traitement antiviral antérieur contre le SARS-CoV-2", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", + "description": "Date à laquelle le traitement a été administré pour la première fois lors de l’infection antérieure par le SRAS-CoV-2", + "title": "Date du traitement antiviral contre une infection antérieure par le SRAS-CoV-2", + "comments": [ + "Indiquez la date à laquelle l’agent de traitement antiviral a été administré pour la première fois lors de l’infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD »." + ], + "examples": [ + { + "value": "2021-01-28" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 93, - "alias": "prior_SARS_CoV_2_antiviral_treatment_date", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_antiviral_treatment_date", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur la réinfection de l'hôte" }, - "purpose of sequencing": { - "name": "purpose of sequencing", - "description": "La raison pour laquelle l’échantillon a été séquencé.", - "title": "objectif du séquençage", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", + "description": "Raison pour laquelle l’échantillon a été séquencé", + "title": "Objectif du séquençage", + "comments": [ + "La raison pour laquelle un échantillon a été initialement prélevé peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des renseignements sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. Le motif de prélèvement de l’échantillon doit être indiqué dans le champ « Objectif de l’échantillonnage »." + ], + "examples": [ + { + "value": "Surveillance de base (échantillonnage aléatoire)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 94, "alias": "purpose_of_sequencing", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", - "description": "La description de la raison pour laquelle l'échantillon a été séquencé, fournissant des détails spécifiques.", - "title": "objectif du séquençage détails", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", + "description": "Description de la raison pour laquelle l’échantillon a été séquencé, fournissant des détails spécifiques", + "title": "Détails de l’objectif du séquençage", + "comments": [ + "Fournissez une description détaillée de la raison pour laquelle l’échantillon a été séquencé en utilisant du texte libre. La description peut inclure l’importance des séquences pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Les descriptions normalisées suggérées sont les suivantes : Dépistage de l’absence de détection du gène S (abandon du gène S), dépistage de variants associés aux visons, dépistage du variant B.1.1.7, dépistage du variant B.1.135, dépistage du variant P.1, dépistage en raison des antécédents de voyage, dépistage en raison d’un contact étroit avec une personne infectée, évaluation des mesures de contrôle de la santé publique, détermination des introductions et de la propagation précoces, enquête sur les expositions liées aux voyages aériens, enquête sur les travailleurs étrangers temporaires, enquête sur les régions éloignées, enquête sur les travailleurs de la santé, enquête sur les écoles et les universités, enquête sur la réinfection." + ], + "examples": [ + { + "value": "Dépistage de l’absence de détection du gène S (abandon du gène S)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 95, "alias": "purpose_of_sequencing_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "sequencing date": { - "name": "sequencing date", - "description": "La date à laquelle l’échantillon a été séquencé.", - "title": "date de séquençage", + "sequencing_date": { + "name": "sequencing_date", + "description": "Date à laquelle l’échantillon a été séquencé", + "title": "Date de séquençage", + "comments": [ + "La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ »." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 96, "alias": "sequencing_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "library ID": { - "name": "library ID", - "description": "L’identifiant spécifié par l’utilisateur pour la bibliothèque préparée pour le séquençage.", + "library_id": { + "name": "library_id", + "description": "Identifiant spécifié par l’utilisateur pour la bibliothèque faisant l’objet du séquençage", "title": "ID de la bibliothèque", + "comments": [ + "Le nom de la bibliothèque doit être unique et peut être un ID généré automatiquement à partir de votre système de gestion de l’information des laboratoires, ou une modification de l’ID de l’isolat." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 97, - "alias": "library_ID", - "owner": "CanCOGeN Covid-19", + "alias": "library_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "amplicon size": { - "name": "amplicon size", - "description": "La longueur de l'amplicon généré par l'amplification PCR.", - "title": "taille de l'amplicon", + "amplicon_size": { + "name": "amplicon_size", + "description": "Longueur de l’amplicon généré par l’amplification de la réaction de polymérisation en chaîne", + "title": "Taille de l’amplicon", + "comments": [ + "Fournissez la taille de l’amplicon, y compris les unités." + ], + "examples": [ + { + "value": "300 pb" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 98, "alias": "amplicon_size", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "library preparation kit": { - "name": "library preparation kit", - "description": "Nom du kit de préparation de la bibliothèque DNA utilisé pour générer la bibliothèque en cours de séquençage.", - "title": "kit de préparation de librairie", + "library_preparation_kit": { + "name": "library_preparation_kit", + "description": "Nom de la trousse de préparation de la banque d’ADN utilisée pour générer la bibliothèque faisant l’objet du séquençage", + "title": "Trousse de préparation de la bibliothèque", + "comments": [ + "Indiquez le nom de la trousse de préparation de la bibliothèque utilisée." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 99, "alias": "library_preparation_kit", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "flow cell barcode": { - "name": "flow cell barcode", - "description": "Le code-barres de la Flow Cell utilisée pour le séquençage.", - "title": "code-barres de la cellule d'écoulement", + "flow_cell_barcode": { + "name": "flow_cell_barcode", + "description": "Code-barres de la cuve à circulation utilisée aux fins de séquençage", + "title": "Code-barres de la cuve à circulation", + "comments": [ + "Fournissez le code-barres de la cuve à circulation utilisée pour séquencer l’échantillon." + ], + "examples": [ + { + "value": "FAB06069" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 100, "alias": "flow_cell_barcode", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "sequencing instrument": { - "name": "sequencing instrument", - "description": "Le modèle de l’instrument de séquençage utilisé.", - "title": "instrument de séquençage", + "sequencing_instrument": { + "name": "sequencing_instrument", + "description": "Modèle de l’instrument de séquençage utilisé", + "title": "Instrument de séquençage", + "comments": [ + "Sélectionnez l’instrument de séquençage à partir de la liste de sélection." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 101, "alias": "sequencing_instrument", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "sequencing protocol name": { - "name": "sequencing protocol name", - "description": "Le nom et le numéro de version du protocole de séquençage utilisé.", - "title": "nom du protocole de séquençage", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", + "description": "Nom et numéro de version du protocole de séquençage utilisé", + "title": "Nom du protocole de séquençage", + "comments": [ + "Fournissez le nom et la version du protocole de séquençage (p. ex., 1D_DNA_MinION)." + ], + "examples": [ + { + "value": "https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 102, "alias": "sequencing_protocol_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "sequencing protocol": { - "name": "sequencing protocol", - "description": "Le protocole utilisé pour générer la séquence.", - "title": "protocole de séquençage", + "sequencing_protocol": { + "name": "sequencing_protocol", + "description": "Protocole utilisé pour générer la séquence", + "title": "Protocole de séquençage", + "comments": [ + "Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Voici le texte suggéré (insérez les renseignements manquants) : « Le séquençage viral a été effectué selon une stratégie d’amplicon en mosaïque en utilisant le schéma d’amorce <à remplir>. Le séquençage a été effectué à l’aide d’un instrument de séquençage <à remplir>. Les bibliothèques ont été préparées à l’aide de la trousse <à remplir>. »" + ], + "examples": [ + { + "value": "Les génomes ont été générés par séquençage d’amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l’aide des trousses de préparation de l’ADN Illumina et les données de séquence ont été produites à l’aide des trousses de séquençage Miseq Micro v2 (500 cycles)." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 103, "alias": "sequencing_protocol", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "sequencing kit number": { - "name": "sequencing kit number", - "description": "Le numéro de kit du fabricant.", - "title": "numéro du kit de séquençage", + "sequencing_kit_number": { + "name": "sequencing_kit_number", + "description": "Numéro de la trousse du fabricant", + "title": "Numéro de la trousse de séquençage", + "comments": [ + "Valeur alphanumérique." + ], + "examples": [ + { + "value": "AB456XYZ789" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 104, "alias": "sequencing_kit_number", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", - "description": "Les spécifications des amorces (séquences d'amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer.", - "title": "de la liste des amorces pcr de l'amplicon", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "Spécifications liées aux amorces (séquences d’amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer", + "title": "Schéma d’amorce pour la réaction de polymérisation en chaîne de l’amplicon", + "comments": [ + "Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons aux fins de séquençage." + ], + "examples": [ + { + "value": "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 105, "alias": "amplicon_pcr_primer_scheme", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Séquençage" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "La méthode utilisée pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l'adaptateur, le filtrage, etc.", - "title": "méthode de traitement des données de séquences brutes", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "Nom et numéro de version du logiciel utilisé pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l’adaptateur, le filtrage, etc.", + "title": "Méthode de traitement des données de séquences brutes", + "comments": [ + "Fournissez le nom du logiciel, suivi de la version (p. ex., Trimmomatic v. 0.38, Porechop v. 0.2.03)." + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 106, "alias": "raw_sequence_data_processing_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "dehosting method": { - "name": "dehosting method", - "description": "Méthode utilisée pour supprimer les lectures de l'hôte de la séquence de l'agent pathogène.", - "title": "méthode de déshostage", + "dehosting_method": { + "name": "dehosting_method", + "description": "Méthode utilisée pour supprimer les lectures de l’hôte de la séquence de l’agent pathogène", + "title": "Méthode de retrait de l’hôte", + "comments": [ + "Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l’hôte." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 107, "alias": "dehosting_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "Le nom de la séquence consensus.", - "title": "nom de la séquence consensus", + "consensus_sequence_name": { + "name": "consensus_sequence_name", + "description": "Nom de la séquence de consensus", + "title": "Nom de la séquence de consensus", + "comments": [ + "Fournissez le nom et le numéro de version de la séquence de consensus." + ], + "examples": [ + { + "value": "ncov123assembly3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 108, "alias": "consensus_sequence_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "Le nom du fichier de séquence consensus.", - "title": "nom de fichier de la séquence consensus", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", + "description": "Nom du fichier de la séquence de consensus", + "title": "Nom du fichier de la séquence de consensus", + "comments": [ + "Fournissez le nom et le numéro de version du fichier FASTA de la séquence de consensus." + ], + "examples": [ + { + "value": "ncov123assembly.fasta" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 109, "alias": "consensus_sequence_filename", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "Le chemin d’accès du fichier de séquence consensus.", - "title": "chemin de fichier de la séquence consensus", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "description": "Chemin d’accès au fichier de la séquence de consensus", + "title": "Chemin d’accès au fichier de la séquence de consensus", + "comments": [ + "Fournissez le chemin d’accès au fichier FASTA de la séquence de consensus." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/ncov123assembly.fasta" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 110, "alias": "consensus_sequence_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "Le nom du logiciel utilisé pour générer la séquence consensus.", - "title": "nom du logiciel de séquençage du consensus", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "Nom du logiciel utilisé pour générer la séquence de consensus", + "title": "Nom du logiciel de la séquence de consensus", + "comments": [ + "Fournissez le nom du logiciel utilisé pour générer la séquence de consensus." + ], + "examples": [ + { + "value": "iVar" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 111, "alias": "consensus_sequence_software_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "La version du logiciel utilisé pour générer la séquence consensus.", - "title": "version du logiciel de la séquence consensus", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "Version du logiciel utilisé pour générer la séquence de consensus", + "title": "Version du logiciel de la séquence de consensus", + "comments": [ + "Fournir la version du logiciel utilisé pour générer la séquence de consensus." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 112, "alias": "consensus_sequence_software_version", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "Le pourcentage du génome de référence couvert par les données séquencées, jusqu'à une profondeur prescrite.", - "title": "valeur de l'étendue de la couverture", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", + "description": "Pourcentage du génome de référence couvert par les données séquencées, jusqu’à une profondeur prescrite", + "title": "Valeur de l’étendue de la couverture", + "comments": [ + "Fournissez la valeur en pourcentage." + ], + "examples": [ + { + "value": "95 %" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 113, "alias": "breadth_of_coverage_value", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "Le nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite.", - "title": "valeur de la profondeur de couverture", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", + "description": "Nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite", + "title": "Valeur de l’ampleur de la couverture", + "comments": [ + "Fournissez la valeur sous forme de couverture amplifiée." + ], + "examples": [ + { + "value": "400x" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 114, "alias": "depth_of_coverage_value", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "Seuil utilisé comme seuil pour la profondeur de couverture.", - "title": "seuil de profondeur de couverture", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", + "description": "Seuil utilisé comme limite pour l’ampleur de la couverture", + "title": "Seuil de l’ampleur de la couverture", + "comments": [ + "Fournissez la couverture amplifiée." + ], + "examples": [ + { + "value": "100x" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 115, "alias": "depth_of_coverage_threshold", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "Le nom de fichier spécifié par l'utilisateur du fichier r1 FASTQ.", - "title": "r1 nom de fichier fastq", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", + "description": "Nom du fichier R1 FASTQ spécifié par l’utilisateur", + "title": "Nom de fichier R1 FASTQ", + "comments": [ + "Fournissez le nom du fichier R1 FASTQ." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 116, - "alias": "r1_fastq_filename", - "owner": "CanCOGeN Covid-19", + "alias": "r1_fastq_filename________", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "Le nom de fichier spécifié par l'utilisateur du fichier r2 FASTQ.", - "title": "r2 nom de fichier fastq", + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "Nom du fichier R2 FASTQ spécifié par l’utilisateur", + "title": "Nom de fichier R2 FASTQ", + "comments": [ + "Fournissez le nom du fichier R2 FASTQ." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 117, "alias": "r2_fastq_filename", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "Le chemin du fichier r1 FASTQ.", - "title": "chemin de fichier r1 fastq", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "description": "Emplacement du fichier R1 FASTQ dans le système de l’utilisateur", + "title": "Chemin d’accès au fichier R1 FASTQ", + "comments": [ + "Fournissez le chemin d’accès au fichier R1 FASTQ." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 118, "alias": "r1_fastq_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "Le chemin d'accès du fichier r2 FASTQ.", - "title": "chemin du fichier r2 fastq", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "description": "Emplacement du fichier R2 FASTQ dans le système de l’utilisateur", + "title": "Chemin d’accès au fichier R2 FASTQ", + "comments": [ + "Fournissez le chemin d’accès au fichier R2 FASTQ." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 119, "alias": "r2_fastq_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "fast5 filename": { - "name": "fast5 filename", - "description": "Le nom de fichier spécifié par l'utilisateur du fichier FAST5.", - "title": "nom de fichier fast5", + "fast5_filename": { + "name": "fast5_filename", + "description": "Nom du fichier FAST5 spécifié par l’utilisateur", + "title": "Nom de fichier FAST5", + "comments": [ + "Fournissez le nom du fichier FAST5." + ], + "examples": [ + { + "value": "rona123assembly.fast5" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 120, "alias": "fast5_filename", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "Le chemin du fichier FAST5.", - "title": "chemin de fichier fast5", + "fast5_filepath": { + "name": "fast5_filepath", + "description": "Emplacement du fichier FAST5 dans le système de l’utilisateur", + "title": "Chemin d’accès au fichier FAST5", + "comments": [ + "Fournissez le chemin d’accès au fichier FAST5." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/rona123assembly.fast5" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 121, "alias": "fast5_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "Le nombre total de paires de bases générées par le processus de séquençage.", - "title": "nombre de paires de bases séquencées", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "Nombre total de paires de bases générées par le processus de séquençage", + "title": "Nombre de paires de bases séquencées", + "comments": [ + "Fournissez une valeur numérique (pas besoin d’inclure des unités)." + ], + "examples": [ + { + "value": "387 566" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 122, "alias": "number_of_base_pairs_sequenced", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Taille du génome assemblé décrite comme le nombre de paires de bases.", - "title": "longueur consensuelle du génome", + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "Taille du génome reconstitué décrite comme étant le nombre de paires de bases", + "title": "Longueur consensuelle du génome", + "comments": [ + "Fournissez une valeur numérique (pas besoin d’inclure des unités)." + ], + "examples": [ + { + "value": "38 677" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 123, "alias": "consensus_genome_length", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", - "description": "Le nombre de N symboles présents dans la séquence fasta consensus, pour 100 kbp de séquence.", - "title": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", + "description": "Nombre de symboles N présents dans la séquence fasta de consensus, par 100 kbp de séquence", + "title": "N par 100 kbp", + "comments": [ + "Fournissez une valeur numérique (pas besoin d’inclure des unités)." + ], + "examples": [ + { + "value": "330" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 124, - "alias": "Ns_per_100_kbp", - "owner": "CanCOGeN Covid-19", + "alias": "ns_per_100_kbp", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "reference genome accession": { - "name": "reference genome accession", - "description": "Un identifiant persistant et unique d’une entrée de base de données génomique.", - "title": "accession au génome de référence", + "reference_genome_accession": { + "name": "reference_genome_accession", + "description": "Identifiant persistant et unique d’une entrée dans une base de données génomique", + "title": "Accès au génome de référence", + "comments": [ + "Fournissez le numéro d’accès au génome de référence." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 125, "alias": "reference_genome_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "Le nom et le numéro de version du protocole bioinformatique utilisé.", - "title": "protocole bioinformatique", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", + "description": "Description de la stratégie bioinformatique globale utilisée", + "title": "Protocole bioinformatique", + "comments": [ + "Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes, générer des assemblages ou générer des séquences de consensus peuvent être fournis dans une PON, un protocole, un pipeline ou un flux de travail. Fournissez le nom et le numéro de version du protocole, ou un lien GitHub vers un pipeline ou un flux de travail." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 126, "alias": "bioinformatics_protocol", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "lineage/clade name": { - "name": "lineage/clade name", - "description": "Le nom de la lignée ou du clade.", - "title": "nom du lineage/clade", + "lineage_clade_name": { + "name": "lineage_clade_name", + "description": "Nom de la lignée ou du clade", + "title": "Nom de la lignée ou du clade", + "comments": [ + "Fournissez le nom de la lignée ou du clade Pangolin ou Nextstrain." + ], + "examples": [ + { + "value": "B.1.1.7" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 127, - "alias": "lineage/clade_name", - "owner": "CanCOGeN Covid-19", + "alias": "lineage_clade_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur les lignées et les variantes" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", - "description": "Le nom du logiciel utilisé pour déterminer la lignée/clade.", - "title": "nom du logiciel d'analyse de linéage/clade", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", + "description": "Nom du logiciel utilisé pour déterminer la lignée ou le clade", + "title": "Nom du logiciel d’analyse de la lignée ou du clade", + "comments": [ + "Fournissez le nom du logiciel utilisé pour déterminer la lignée ou le clade." + ], + "examples": [ + { + "value": "Pangolin" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 128, - "alias": "lineage/clade_analysis_software_name", - "owner": "CanCOGeN Covid-19", + "alias": "lineage_clade_analysis_software_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur les lignées et les variantes" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", - "description": "La version du logiciel utilisé pour déterminer la lignée/clade.", - "title": "version du logiciel d'analyse de linéage/clade", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", + "description": "Version du logiciel utilisé pour déterminer la lignée ou le clade", + "title": "Version du logiciel d’analyse de la lignée ou du clade", + "comments": [ + "Fournissez la version du logiciel utilisé pour déterminer la lignée ou le clade." + ], + "examples": [ + { + "value": "2.1.10" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 129, - "alias": "lineage/clade_analysis_software_version", - "owner": "CanCOGeN Covid-19", + "alias": "lineage_clade_analysis_software_version", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur les lignées et les variantes" }, - "variant designation": { - "name": "variant designation", - "description": "La classification des variantes de la lignée/clade, c'est-à-dire variante, variante préoccupante.", - "title": "désignation de la variante", + "variant_designation": { + "name": "variant_designation", + "description": "Classification des variants de la lignée ou du clade (c.-à-d. le variant, le variant préoccupant)", + "title": "Désignation du variant", + "comments": [ + "Si la lignée ou le clade est considéré comme étant un variant préoccupant, sélectionnez l’option connexe à partir de la liste de sélection. Si la lignée ou le clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques), mais qu’il ne s’agit pas d’un variant préoccupant global, sélectionnez « Variante ». Si la lignée ou le clade ne contient pas de mutations préoccupantes, laissez ce champ vide." + ], + "examples": [ + { + "value": "Variant préoccupant" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 130, "alias": "variant_designation", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur les lignées et les variantes" }, - "variant evidence": { - "name": "variant evidence", - "description": "Preuve utilisée pour déterminer la variante.", - "title": "preuve de la variante", + "variant_evidence": { + "name": "variant_evidence", + "description": "Données probantes utilisées pour déterminer le variant", + "title": "Données probantes du variant", + "comments": [ + "Indiquez si l’échantillon a fait l’objet d’un dépistage RT-qPCR ou par séquençage à partir de la liste de sélection." + ], + "examples": [ + { + "value": "RT-qPCR" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 131, "alias": "variant_evidence", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur les lignées et les variantes" }, - "variant evidence details": { - "name": "variant evidence details", - "description": "Détails sur les preuves utilisées pour déterminer la variante.", - "title": "détails de la preuve de la variante", + "variant_evidence_details": { + "name": "variant_evidence_details", + "description": "Détails sur les données probantes utilisées pour déterminer le variant", + "title": "Détails liés aux données probantes du variant", + "comments": [ + "Fournissez l’essai biologique et répertoriez l’ensemble des mutations définissant la lignée qui sont utilisées pour effectuer la détermination des variants. Si des mutations d’intérêt ou de préoccupation ont été observées en plus des mutations définissant la lignée, décrivez-les ici." + ], + "examples": [ + { + "value": "Mutations définissant la lignée : ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 132, "alias": "variant_evidence_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Informations sur les lignées et les variantes" }, - "gene name 1": { - "name": "gene name 1", - "description": "Le nom du gène utilisé dans le test diagnostique RT-PCR.", - "title": "nom du gène 1", + "gene_name_1": { + "name": "gene_name_1", + "description": "Nom du gène utilisé dans le test diagnostique RT-PCR", + "title": "Nom du gène 1", + "comments": [ + "Indiquez le nom complet du gène soumis au dépistage. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI." + ], + "examples": [ + { + "value": "Gène E (orf4)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 133, "alias": "gene_name_1", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", - "description": "Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic.", - "title": "protocole de diagnostic pcr 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", + "description": "Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques", + "title": "Protocole de diagnostic de polymérase en chaîne 1", + "comments": [ + "Le nom et le numéro de version du protocole utilisé pour réaliser un test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité." + ], + "examples": [ + { + "value": "EGenePCRTest 2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 134, "alias": "diagnostic_pcr_protocol_1", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", - "description": "La valeur du seuil de cycle (Ct) résulte d’un test de diagnostic RT-PCR du SARS-CoV-2.", - "title": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", + "description": "Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2", + "title": "Valeur de diagnostic de polymérase en chaîne 1", + "comments": [ + "Fournissez la valeur Ct de l’échantillon issu du test diagnostique RT-PCR." + ], + "examples": [ + { + "value": "21" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 135, - "alias": "diagnostic_pcr_Ct_value_1", - "owner": "CanCOGeN Covid-19", + "alias": "diagnostic_pcr_ct_value_1", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "gene name 2": { - "name": "gene name 2", - "description": "Le nom du gène utilisé dans le test diagnostique RT-PCR.", - "title": "nom du gène 2", + "gene_name_2": { + "name": "gene_name_2", + "description": "Nom du gène utilisé dans le test diagnostique RT-PCR", + "title": "Nom du gène 2", + "comments": [ + "Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI." + ], + "examples": [ + { + "value": "Gène RdRp (nsp12)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 136, "alias": "gene_name_2", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", - "description": "Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic.", - "title": "protocole de diagnostic pcr 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", + "description": "Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques", + "title": "Protocole de diagnostic de polymérase en chaîne 2", + "comments": [ + "Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité." + ], + "examples": [ + { + "value": "RdRpGenePCRTest 3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 137, "alias": "diagnostic_pcr_protocol_2", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", - "description": "La valeur du seuil de cycle (Ct) résulte d’un test de diagnostic RT-PCR du SARS-CoV-2.", - "title": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", + "description": "Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2", + "title": "Valeur de diagnostic de polymérase en chaîne 2", + "comments": [ + "Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR." + ], + "examples": [ + { + "value": "36" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 138, - "alias": "diagnostic_pcr_Ct_value_2", - "owner": "CanCOGeN Covid-19", + "alias": "diagnostic_pcr_ct_value_2", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "gene name 3": { - "name": "gene name 3", - "description": "Le nom du gène utilisé dans le test diagnostique RT-PCR.", - "title": "nom du gène 3", + "gene_name_3": { + "name": "gene_name_3", + "description": "Nom du gène utilisé dans le test diagnostique RT-PCR", + "title": "Nom du gène 3", + "comments": [ + "Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI." + ], + "examples": [ + { + "value": "Gène RdRp (nsp12)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 139, "alias": "gene_name_3", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr protocol 3": { - "name": "diagnostic pcr protocol 3", - "description": "Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic.", - "title": "protocole de diagnostic pcr 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", + "description": "Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques", + "title": "Protocole de diagnostic de polymérase en chaîne 3", + "comments": [ + "Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité." + ], + "examples": [ + { + "value": "RdRpGenePCRTest 3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 140, "alias": "diagnostic_pcr_protocol_3", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", - "description": "La valeur Ct résulte d’un test de diagnostic SARS-CoV-2 RT-PCR.", - "title": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", + "description": "Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2", + "title": "Valeur de diagnostic de polymérase en chaîne 3", + "comments": [ + "Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR." + ], + "examples": [ + { + "value": "30" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 141, - "alias": "diagnostic_pcr_Ct_value_3", - "owner": "CanCOGeN Covid-19", + "alias": "diagnostic_pcr_ct_value_3", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Tests de diagnostic des agents pathogènes" }, "authors": { "name": "authors", - "description": "Noms des personnes contribuant aux processus de collecte d’échantillons, de génération de séquences, d’analyse et de soumission de données.", - "title": "auteurs", + "description": "Noms des personnes contribuant aux processus de prélèvement d’échantillons, de génération de séquences, d’analyse et de soumission de données", + "title": "Auteurs", + "comments": [ + "Incluez le prénom et le nom de toutes les personnes qui doivent être affectées, séparés par une virgule." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 142, "alias": "authors", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Reconnaissance des contributeurs" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "Provenance du logiciel DataHarmonizer et de la version du modèle.", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "Provenance du logiciel DataHarmonizer et de la version du modèle", "title": "Provenance de DataHarmonizer", + "comments": [ + "Les renseignements actuels sur la version du logiciel et du modèle seront automatiquement générés dans ce champ une fois que l’utilisateur aura utilisé la fonction « Valider ». Ces renseignements seront générés indépendamment du fait que la ligne soit valide ou non." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 143, - "alias": "DataHarmonizer_provenance", - "owner": "CanCOGeN Covid-19", + "alias": "dataharmonizer_provenance", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Reconnaissance des contributeurs" } diff --git a/web/templates/canada_covid19/locales/fr/schema.yaml b/web/templates/canada_covid19/locales/fr/schema.yaml index 840c074e..03f8f725 100644 --- a/web/templates/canada_covid19/locales/fr/schema.yaml +++ b/web/templates/canada_covid19/locales/fr/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/CanCOGeN_Covid-19 name: CanCOGeN_Covid-19 description: '' -version: 2.3.4 +version: 2.4.0 in_language: fr imports: - linkml:types @@ -13,216 +13,228 @@ classes: name: dh_interface description: A DataHarmonizer interface from_schema: https://example.com/CanCOGeN_Covid-19 - CanCOGeN Covid-19: - name: CanCOGeN Covid-19 + CanCOGeNCovid19: + name: CanCOGeNCovid19 + title: CanCOGeN Covid-19 description: Canadian specification for Covid-19 clinical virus biosample data gathering is_a: dh_interface see_also: templates/canada_covid19/SOP.pdf slots: - - specimen collector sample ID - - third party lab service provider name - - third party lab sample ID - - case ID - - Related specimen primary ID - - IRIDA sample name - - umbrella bioproject accession - - bioproject accession - - biosample accession - - SRA accession - - GenBank accession - - GISAID accession - - sample collected by - - sample collector contact email - - sample collector contact address - - sequence submitted by - - sequence submitter contact email - - sequence submitter contact address - - sample collection date - - sample collection date precision - - sample received date - - geo_loc_name (country) - - geo_loc_name (state/province/territory) - - geo_loc_name (city) + - specimen_collector_sample_id + - third_party_lab_service_provider_name + - third_party_lab_sample_id + - case_id + - related_specimen_primary_id + - irida_sample_name + - umbrella_bioproject_accession + - bioproject_accession + - biosample_accession + - sra_accession + - genbank_accession + - gisaid_accession + - sample_collected_by + - sample_collector_contact_email + - sample_collector_contact_address + - sequence_submitted_by + - sequence_submitter_contact_email + - sequence_submitter_contact_address + - sample_collection_date + - sample_collection_date_precision + - sample_received_date + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_city - organism - isolate - - purpose of sampling - - purpose of sampling details - - NML submitted specimen type - - Related specimen relationship type - - anatomical material - - anatomical part - - body product - - environmental material - - environmental site - - collection device - - collection method - - collection protocol - - specimen processing - - specimen processing details - - lab host - - passage number - - passage method - - biomaterial extracted - - host (common name) - - host (scientific name) - - host health state - - host health status details - - host health outcome - - host disease - - host age - - host age unit - - host age bin - - host gender - - host residence geo_loc name (country) - - host residence geo_loc name (state/province/territory) - - host subject ID - - symptom onset date - - signs and symptoms - - pre-existing conditions and risk factors + - purpose_of_sampling + - purpose_of_sampling_details + - nml_submitted_specimen_type + - related_specimen_relationship_type + - anatomical_material + - anatomical_part + - body_product + - environmental_material + - environmental_site + - collection_device + - collection_method + - collection_protocol + - specimen_processing + - specimen_processing_details + - lab_host + - passage_number + - passage_method + - biomaterial_extracted + - host_common_name + - host_scientific_name + - host_health_state + - host_health_status_details + - host_health_outcome + - host_disease + - host_age + - host_age_unit + - host_age_bin + - host_gender + - host_residence_geo_loc_name_country + - host_residence_geo_loc_name_state_province_territory + - host_subject_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors - complications - - host vaccination status - - number of vaccine doses received - - vaccination dose 1 vaccine name - - vaccination dose 1 vaccination date - - vaccination dose 2 vaccine name - - vaccination dose 2 vaccination date - - vaccination dose 3 vaccine name - - vaccination dose 3 vaccination date - - vaccination dose 4 vaccine name - - vaccination dose 4 vaccination date - - vaccination history - - location of exposure geo_loc name (country) - - destination of most recent travel (city) - - destination of most recent travel (state/province/territory) - - destination of most recent travel (country) - - most recent travel departure date - - most recent travel return date - - travel point of entry type - - border testing test day type - - travel history - - travel history availability - - exposure event - - exposure contact level - - host role - - exposure setting - - exposure details - - prior SARS-CoV-2 infection - - prior SARS-CoV-2 infection isolate - - prior SARS-CoV-2 infection date - - prior SARS-CoV-2 antiviral treatment - - prior SARS-CoV-2 antiviral treatment agent - - prior SARS-CoV-2 antiviral treatment date - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library ID - - amplicon size - - library preparation kit - - flow cell barcode - - sequencing instrument - - sequencing protocol name - - sequencing protocol - - sequencing kit number - - amplicon pcr primer scheme - - raw sequence data processing method - - dehosting method - - consensus sequence name - - consensus sequence filename - - consensus sequence filepath - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - r1 fastq filename - - r2 fastq filename - - r1 fastq filepath - - r2 fastq filepath - - fast5 filename - - fast5 filepath - - number of base pairs sequenced - - consensus genome length - - Ns per 100 kbp - - reference genome accession - - bioinformatics protocol - - lineage/clade name - - lineage/clade analysis software name - - lineage/clade analysis software version - - variant designation - - variant evidence - - variant evidence details - - gene name 1 - - diagnostic pcr protocol 1 - - diagnostic pcr Ct value 1 - - gene name 2 - - diagnostic pcr protocol 2 - - diagnostic pcr Ct value 2 - - gene name 3 - - diagnostic pcr protocol 3 - - diagnostic pcr Ct value 3 + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_dose_3_vaccine_name + - vaccination_dose_3_vaccination_date + - vaccination_dose_4_vaccine_name + - vaccination_dose_4_vaccination_date + - vaccination_history + - location_of_exposure_geo_loc_name_country + - destination_of_most_recent_travel_city + - destination_of_most_recent_travel_state_province_territory + - destination_of_most_recent_travel_country + - most_recent_travel_departure_date + - most_recent_travel_return_date + - travel_point_of_entry_type + - border_testing_test_day_type + - travel_history + - travel_history_availability + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - prior_sarscov2_infection + - prior_sarscov2_infection_isolate + - prior_sarscov2_infection_date + - prior_sarscov2_antiviral_treatment + - prior_sarscov2_antiviral_treatment_agent + - prior_sarscov2_antiviral_treatment_date + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_id + - amplicon_size + - library_preparation_kit + - flow_cell_barcode + - sequencing_instrument + - sequencing_protocol_name + - sequencing_protocol + - sequencing_kit_number + - amplicon_pcr_primer_scheme + - raw_sequence_data_processing_method + - dehosting_method + - consensus_sequence_name + - consensus_sequence_filename + - consensus_sequence_filepath + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - r1_fastq_filename________ + - r2_fastq_filename + - r1_fastq_filepath + - r2_fastq_filepath + - fast5_filename + - fast5_filepath + - number_of_base_pairs_sequenced + - consensus_genome_length + - ns_per_100_kbp + - reference_genome_accession + - bioinformatics_protocol + - lineage_clade_name + - lineage_clade_analysis_software_name + - lineage_clade_analysis_software_version + - variant_designation + - variant_evidence + - variant_evidence_details + - gene_name_1 + - diagnostic_pcr_protocol_1 + - diagnostic_pcr_ct_value_1 + - gene_name_2 + - diagnostic_pcr_protocol_2 + - diagnostic_pcr_ct_value_2 + - gene_name_3 + - diagnostic_pcr_protocol_3 + - diagnostic_pcr_ct_value_3 - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: "Identificateurs de base de donn\xE9es" - third party lab service provider name: + third_party_lab_service_provider_name: rank: 2 - third party lab sample ID: + slot_group: "Identificateurs de base de donn\xE9es" + third_party_lab_sample_id: rank: 3 - case ID: + slot_group: "Identificateurs de base de donn\xE9es" + case_id: rank: 4 - Related specimen primary ID: + slot_group: "Identificateurs de base de donn\xE9es" + related_specimen_primary_id: rank: 5 - IRIDA sample name: + slot_group: "Identificateurs de base de donn\xE9es" + irida_sample_name: rank: 6 - umbrella bioproject accession: + slot_group: "Identificateurs de base de donn\xE9es" + umbrella_bioproject_accession: rank: 7 - bioproject accession: + slot_group: "Identificateurs de base de donn\xE9es" + bioproject_accession: rank: 8 - biosample accession: + slot_group: "Identificateurs de base de donn\xE9es" + biosample_accession: rank: 9 - SRA accession: + slot_group: "Identificateurs de base de donn\xE9es" + sra_accession: rank: 10 - GenBank accession: + slot_group: "Identificateurs de base de donn\xE9es" + genbank_accession: rank: 11 - GISAID accession: + slot_group: "Identificateurs de base de donn\xE9es" + gisaid_accession: rank: 12 - sample collected by: + slot_group: "Identificateurs de base de donn\xE9es" + sample_collected_by: rank: 13 slot_group: "Collecte et traitement des \xE9chantillons" - sample collector contact email: + sample_collector_contact_email: rank: 14 slot_group: "Collecte et traitement des \xE9chantillons" - sample collector contact address: + sample_collector_contact_address: rank: 15 slot_group: "Collecte et traitement des \xE9chantillons" - sequence submitted by: + sequence_submitted_by: rank: 16 slot_group: "Collecte et traitement des \xE9chantillons" - sequence submitter contact email: + sequence_submitter_contact_email: rank: 17 slot_group: "Collecte et traitement des \xE9chantillons" - sequence submitter contact address: + sequence_submitter_contact_address: rank: 18 slot_group: "Collecte et traitement des \xE9chantillons" - sample collection date: + sample_collection_date: rank: 19 slot_group: "Collecte et traitement des \xE9chantillons" - sample collection date precision: + sample_collection_date_precision: rank: 20 slot_group: "Collecte et traitement des \xE9chantillons" - sample received date: + sample_received_date: rank: 21 slot_group: "Collecte et traitement des \xE9chantillons" - geo_loc_name (country): + geo_loc_name_country: rank: 22 slot_group: "Collecte et traitement des \xE9chantillons" - geo_loc_name (state/province/territory): + geo_loc_name_state_province_territory: rank: 23 slot_group: "Collecte et traitement des \xE9chantillons" - geo_loc_name (city): + geo_loc_name_city: rank: 24 slot_group: "Collecte et traitement des \xE9chantillons" organism: @@ -231,714 +243,833 @@ classes: isolate: rank: 26 slot_group: "Collecte et traitement des \xE9chantillons" - purpose of sampling: + purpose_of_sampling: rank: 27 slot_group: "Collecte et traitement des \xE9chantillons" - purpose of sampling details: + purpose_of_sampling_details: rank: 28 slot_group: "Collecte et traitement des \xE9chantillons" - NML submitted specimen type: + nml_submitted_specimen_type: rank: 29 slot_group: "Collecte et traitement des \xE9chantillons" - Related specimen relationship type: + related_specimen_relationship_type: rank: 30 slot_group: "Collecte et traitement des \xE9chantillons" - anatomical material: + anatomical_material: rank: 31 slot_group: "Collecte et traitement des \xE9chantillons" - anatomical part: + anatomical_part: rank: 32 slot_group: "Collecte et traitement des \xE9chantillons" - body product: + body_product: rank: 33 slot_group: "Collecte et traitement des \xE9chantillons" - environmental material: + environmental_material: rank: 34 slot_group: "Collecte et traitement des \xE9chantillons" - environmental site: + environmental_site: rank: 35 slot_group: "Collecte et traitement des \xE9chantillons" - collection device: + collection_device: rank: 36 slot_group: "Collecte et traitement des \xE9chantillons" - collection method: + collection_method: rank: 37 slot_group: "Collecte et traitement des \xE9chantillons" - collection protocol: + collection_protocol: rank: 38 slot_group: "Collecte et traitement des \xE9chantillons" - specimen processing: + specimen_processing: rank: 39 slot_group: "Collecte et traitement des \xE9chantillons" - specimen processing details: + specimen_processing_details: rank: 40 slot_group: "Collecte et traitement des \xE9chantillons" - lab host: + lab_host: rank: 41 slot_group: "Collecte et traitement des \xE9chantillons" - passage number: + passage_number: rank: 42 slot_group: "Collecte et traitement des \xE9chantillons" - passage method: + passage_method: rank: 43 slot_group: "Collecte et traitement des \xE9chantillons" - biomaterial extracted: + biomaterial_extracted: rank: 44 slot_group: "Collecte et traitement des \xE9chantillons" - host (common name): + host_common_name: rank: 45 slot_group: "Informations sur l'h\xF4te" - host (scientific name): + host_scientific_name: rank: 46 slot_group: "Informations sur l'h\xF4te" - host health state: + host_health_state: rank: 47 slot_group: "Informations sur l'h\xF4te" - host health status details: + host_health_status_details: rank: 48 slot_group: "Informations sur l'h\xF4te" - host health outcome: + host_health_outcome: rank: 49 slot_group: "Informations sur l'h\xF4te" - host disease: + host_disease: rank: 50 slot_group: "Informations sur l'h\xF4te" - host age: + host_age: rank: 51 slot_group: "Informations sur l'h\xF4te" - host age unit: + host_age_unit: rank: 52 slot_group: "Informations sur l'h\xF4te" - host age bin: + host_age_bin: rank: 53 slot_group: "Informations sur l'h\xF4te" - host gender: + host_gender: rank: 54 slot_group: "Informations sur l'h\xF4te" - host residence geo_loc name (country): + host_residence_geo_loc_name_country: rank: 55 slot_group: "Informations sur l'h\xF4te" - host residence geo_loc name (state/province/territory): + host_residence_geo_loc_name_state_province_territory: rank: 56 slot_group: "Informations sur l'h\xF4te" - host subject ID: + host_subject_id: rank: 57 slot_group: "Informations sur l'h\xF4te" - symptom onset date: + symptom_onset_date: rank: 58 slot_group: "Informations sur l'h\xF4te" - signs and symptoms: + signs_and_symptoms: rank: 59 slot_group: "Informations sur l'h\xF4te" - pre-existing conditions and risk factors: + preexisting_conditions_and_risk_factors: rank: 60 slot_group: "Informations sur l'h\xF4te" complications: rank: 61 slot_group: "Informations sur l'h\xF4te" - host vaccination status: + host_vaccination_status: rank: 62 slot_group: "Informations sur la vaccination de l'h\xF4te" - number of vaccine doses received: + number_of_vaccine_doses_received: rank: 63 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 1 vaccine name: + vaccination_dose_1_vaccine_name: rank: 64 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 1 vaccination date: + vaccination_dose_1_vaccination_date: rank: 65 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 2 vaccine name: + vaccination_dose_2_vaccine_name: rank: 66 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 2 vaccination date: + vaccination_dose_2_vaccination_date: rank: 67 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 3 vaccine name: + vaccination_dose_3_vaccine_name: rank: 68 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 3 vaccination date: + vaccination_dose_3_vaccination_date: rank: 69 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 4 vaccine name: + vaccination_dose_4_vaccine_name: rank: 70 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination dose 4 vaccination date: + vaccination_dose_4_vaccination_date: rank: 71 slot_group: "Informations sur la vaccination de l'h\xF4te" - vaccination history: + vaccination_history: rank: 72 slot_group: "Informations sur la vaccination de l'h\xF4te" - location of exposure geo_loc name (country): + location_of_exposure_geo_loc_name_country: rank: 73 slot_group: "Informations sur l'exposition de l'h\xF4te" - destination of most recent travel (city): + destination_of_most_recent_travel_city: rank: 74 slot_group: "Informations sur l'exposition de l'h\xF4te" - destination of most recent travel (state/province/territory): + destination_of_most_recent_travel_state_province_territory: rank: 75 slot_group: "Informations sur l'exposition de l'h\xF4te" - destination of most recent travel (country): + destination_of_most_recent_travel_country: rank: 76 slot_group: "Informations sur l'exposition de l'h\xF4te" - most recent travel departure date: + most_recent_travel_departure_date: rank: 77 slot_group: "Informations sur l'exposition de l'h\xF4te" - most recent travel return date: + most_recent_travel_return_date: rank: 78 slot_group: "Informations sur l'exposition de l'h\xF4te" - travel point of entry type: + travel_point_of_entry_type: rank: 79 slot_group: "Informations sur l'exposition de l'h\xF4te" - border testing test day type: + border_testing_test_day_type: rank: 80 slot_group: "Informations sur l'exposition de l'h\xF4te" - travel history: + travel_history: rank: 81 slot_group: "Informations sur l'exposition de l'h\xF4te" - travel history availability: + travel_history_availability: rank: 82 slot_group: "Informations sur l'exposition de l'h\xF4te" - exposure event: + exposure_event: rank: 83 slot_group: "Informations sur l'exposition de l'h\xF4te" - exposure contact level: + exposure_contact_level: rank: 84 slot_group: "Informations sur l'exposition de l'h\xF4te" - host role: + host_role: rank: 85 slot_group: "Informations sur l'exposition de l'h\xF4te" - exposure setting: + exposure_setting: rank: 86 slot_group: "Informations sur l'exposition de l'h\xF4te" - exposure details: + exposure_details: rank: 87 slot_group: "Informations sur l'exposition de l'h\xF4te" - prior SARS-CoV-2 infection: + prior_sarscov2_infection: rank: 88 slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - prior SARS-CoV-2 infection isolate: + prior_sarscov2_infection_isolate: rank: 89 slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - prior SARS-CoV-2 infection date: + prior_sarscov2_infection_date: rank: 90 slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - prior SARS-CoV-2 antiviral treatment: + prior_sarscov2_antiviral_treatment: rank: 91 slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - prior SARS-CoV-2 antiviral treatment agent: + prior_sarscov2_antiviral_treatment_agent: rank: 92 slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - prior SARS-CoV-2 antiviral treatment date: + prior_sarscov2_antiviral_treatment_date: rank: 93 slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - purpose of sequencing: + purpose_of_sequencing: rank: 94 slot_group: "S\xE9quen\xE7age" - purpose of sequencing details: + purpose_of_sequencing_details: rank: 95 slot_group: "S\xE9quen\xE7age" - sequencing date: + sequencing_date: rank: 96 slot_group: "S\xE9quen\xE7age" - library ID: + library_id: rank: 97 slot_group: "S\xE9quen\xE7age" - amplicon size: + amplicon_size: rank: 98 slot_group: "S\xE9quen\xE7age" - library preparation kit: + library_preparation_kit: rank: 99 slot_group: "S\xE9quen\xE7age" - flow cell barcode: + flow_cell_barcode: rank: 100 slot_group: "S\xE9quen\xE7age" - sequencing instrument: + sequencing_instrument: rank: 101 slot_group: "S\xE9quen\xE7age" - sequencing protocol name: + sequencing_protocol_name: rank: 102 slot_group: "S\xE9quen\xE7age" - sequencing protocol: + sequencing_protocol: rank: 103 slot_group: "S\xE9quen\xE7age" - sequencing kit number: + sequencing_kit_number: rank: 104 slot_group: "S\xE9quen\xE7age" - amplicon pcr primer scheme: + amplicon_pcr_primer_scheme: rank: 105 slot_group: "S\xE9quen\xE7age" - raw sequence data processing method: + raw_sequence_data_processing_method: rank: 106 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - dehosting method: + dehosting_method: rank: 107 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - consensus sequence name: + consensus_sequence_name: rank: 108 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - consensus sequence filename: + consensus_sequence_filename: rank: 109 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - consensus sequence filepath: + consensus_sequence_filepath: rank: 110 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - consensus sequence software name: + consensus_sequence_software_name: rank: 111 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - consensus sequence software version: + consensus_sequence_software_version: rank: 112 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - breadth of coverage value: + breadth_of_coverage_value: rank: 113 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - depth of coverage value: + depth_of_coverage_value: rank: 114 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - depth of coverage threshold: + depth_of_coverage_threshold: rank: 115 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - r1 fastq filename: + r1_fastq_filename________: rank: 116 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - r2 fastq filename: + r2_fastq_filename: rank: 117 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - r1 fastq filepath: + r1_fastq_filepath: rank: 118 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - r2 fastq filepath: + r2_fastq_filepath: rank: 119 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - fast5 filename: + fast5_filename: rank: 120 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - fast5 filepath: + fast5_filepath: rank: 121 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - number of base pairs sequenced: + number_of_base_pairs_sequenced: rank: 122 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - consensus genome length: + consensus_genome_length: rank: 123 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - Ns per 100 kbp: + ns_per_100_kbp: rank: 124 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - reference genome accession: + reference_genome_accession: rank: 125 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - bioinformatics protocol: + bioinformatics_protocol: rank: 126 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - lineage/clade name: + lineage_clade_name: rank: 127 slot_group: "Informations sur les lign\xE9es et les variantes" - lineage/clade analysis software name: + lineage_clade_analysis_software_name: rank: 128 slot_group: "Informations sur les lign\xE9es et les variantes" - lineage/clade analysis software version: + lineage_clade_analysis_software_version: rank: 129 slot_group: "Informations sur les lign\xE9es et les variantes" - variant designation: + variant_designation: rank: 130 slot_group: "Informations sur les lign\xE9es et les variantes" - variant evidence: + variant_evidence: rank: 131 slot_group: "Informations sur les lign\xE9es et les variantes" - variant evidence details: + variant_evidence_details: rank: 132 slot_group: "Informations sur les lign\xE9es et les variantes" - gene name 1: + gene_name_1: rank: 133 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - diagnostic pcr protocol 1: + diagnostic_pcr_protocol_1: rank: 134 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - diagnostic pcr Ct value 1: + diagnostic_pcr_ct_value_1: rank: 135 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - gene name 2: + gene_name_2: rank: 136 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - diagnostic pcr protocol 2: + diagnostic_pcr_protocol_2: rank: 137 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - diagnostic pcr Ct value 2: + diagnostic_pcr_ct_value_2: rank: 138 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - gene name 3: + gene_name_3: rank: 139 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - diagnostic pcr protocol 3: + diagnostic_pcr_protocol_3: rank: 140 slot_group: "Tests de diagnostic des agents pathog\xE8nes" - diagnostic pcr Ct value 3: + diagnostic_pcr_ct_value_3: rank: 141 slot_group: "Tests de diagnostic des agents pathog\xE8nes" authors: rank: 142 slot_group: Reconnaissance des contributeurs - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 143 slot_group: Reconnaissance des contributeurs slots: - specimen collector sample ID: - name: specimen collector sample ID - title: "Collecteur d'\xE9chantillons ID de l'\xE9chantillon" - description: "Le nom d\xE9fini par l'utilisateur pour l'\xE9chantillon." + specimen_collector_sample_id: + name: specimen_collector_sample_id + title: "ID du collecteur d\u2019\xE9chantillons" + description: "Nom d\xE9fini par l\u2019utilisateur pour l\u2019\xE9chantillon" slot_group: "Identificateurs de base de donn\xE9es" comments: "Conservez l\u2019ID de l\u2019\xE9chantillon du collecteur. Si ce num\xE9\ ro est consid\xE9r\xE9 comme une information identifiable, fournissez un autre\ - \ identifiant. Assurez-vous de stocker la cl\xE9 qui correspond aux identifiants\ - \ d'origine et alternatifs pour la tra\xE7abilit\xE9 et le suivi si n\xE9cessaire.\ - \ Chaque ID d\u2019\xE9chantillon de collecteur provenant d\u2019un seul demandeur\ - \ doit \xEAtre unique. Il peut avoir n'importe quel format, mais nous vous sugg\xE9\ - rons de le rendre concis, unique et coh\xE9rent au sein de votre laboratoire." + \ identifiant. Assurez-vous de conserver la cl\xE9 qui correspond aux identifiants\ + \ d\u2019origine et alternatifs aux fins de tra\xE7abilit\xE9 et de suivi, au\ + \ besoin. Chaque ID d\u2019\xE9chantillon de collecteur provenant d\u2019un\ + \ seul demandeur doit \xEAtre unique. Il peut avoir n\u2019importe quel format,\ + \ mais nous vous sugg\xE9rons de le rendre concis, unique et coh\xE9rent au\ + \ sein de votre laboratoire." examples: - value: prov_rona_99 - third party lab service provider name: - name: third party lab service provider name - third party lab sample ID: - name: third party lab sample ID - case ID: - name: case ID - Related specimen primary ID: - name: Related specimen primary ID - IRIDA sample name: - name: IRIDA sample name - umbrella bioproject accession: - name: umbrella bioproject accession - bioproject accession: - name: bioproject accession - biosample accession: - name: biosample accession - SRA accession: - name: SRA accession - GenBank accession: - name: GenBank accession - GISAID accession: - name: GISAID accession - sample collected by: - name: sample collected by - title: "\xE9chantillon collect\xE9 par" - description: "Le nom de l\u2019organisation \xE0 laquelle le collecteur d\u2019\ - \xE9chantillons est affili\xE9." + third_party_lab_service_provider_name: + name: third_party_lab_service_provider_name + title: Nom du fournisseur de services de laboratoire tiers + description: "Nom de la soci\xE9t\xE9 ou du laboratoire tiers qui fournit les\ + \ services" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Indiquez le nom complet et non abr\xE9g\xE9 de l\u2019entreprise ou\ + \ du laboratoire." + examples: + - value: Switch Health + third_party_lab_sample_id: + name: third_party_lab_sample_id + title: "ID de l\u2019\xE9chantillon de laboratoire tiers" + description: "Identifiant attribu\xE9 \xE0 un \xE9chantillon par un prestataire\ + \ de services tiers" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Conservez l\u2019identifiant de l\u2019\xE9chantillon fourni par le\ + \ prestataire de services tiers." + examples: + - value: SHK123456 + case_id: + name: case_id + title: ID du dossier + description: "Identifiant utilis\xE9 pour d\xE9signer un cas de maladie d\xE9\ + tect\xE9 sur le plan \xE9pid\xE9miologique" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Fournissez l\u2019identifiant du cas, lequel facilite grandement le\ + \ lien entre les donn\xE9es de laboratoire et les donn\xE9es \xE9pid\xE9miologiques.\ + \ Il peut \xEAtre consid\xE9r\xE9 comme une information identifiable. Consultez\ + \ l\u2019intendant des donn\xE9es avant de le transmettre." + examples: + - value: ABCD1234 + related_specimen_primary_id: + name: related_specimen_primary_id + title: "ID principal de l\u2019\xE9chantillon associ\xE9" + description: "Identifiant principal d\u2019un \xE9chantillon associ\xE9 pr\xE9\ + c\xE9demment soumis au d\xE9p\xF4t" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Conservez l\u2019identifiant primaire de l\u2019\xE9chantillon correspondant\ + \ pr\xE9c\xE9demment soumis au Laboratoire national de microbiologie afin que\ + \ les \xE9chantillons puissent \xEAtre li\xE9s et suivis dans le syst\xE8me." + examples: + - value: SR20-12345 + irida_sample_name: + name: irida_sample_name + title: "Nom de l\u2019\xE9chantillon IRIDA" + description: "Identifiant attribu\xE9 \xE0 un isolat s\xE9quenc\xE9 dans IRIDA" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Enregistrez le nom de l\u2019\xE9chantillon IRIDA, lequel sera cr\xE9\ + \xE9 par la personne saisissant les donn\xE9es dans la plateforme connexe. Les\ + \ \xE9chantillons IRIDA peuvent \xEAtre li\xE9s \xE0 des m\xE9tadonn\xE9es et\ + \ \xE0 des donn\xE9es de s\xE9quence, ou simplement \xE0 des m\xE9tadonn\xE9\ + es. Il est recommand\xE9 que le nom de l\u2019\xE9chantillon IRIDA soit identique\ + \ ou contienne l\u2019ID de l\u2019\xE9chantillon du collecteur pour assurer\ + \ une meilleure tra\xE7abilit\xE9. Il est \xE9galement recommand\xE9 que le\ + \ nom de l\u2019\xE9chantillon IRIDA refl\xE8te l\u2019acc\xE8s \xE0 GISAID.\ + \ Les noms d\u2019\xE9chantillons IRIDA ne peuvent pas contenir de barres obliques.\ + \ Celles-ci doivent \xEAtre remplac\xE9es par des traits de soulignement. Consultez\ + \ la documentation IRIDA pour en savoir plus sur les caract\xE8res sp\xE9ciaux\ + \ (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)." + examples: + - value: prov_rona_99 + umbrella_bioproject_accession: + name: umbrella_bioproject_accession + title: "Num\xE9ro d\u2019acc\xE8s au bioprojet cadre" + description: "Num\xE9ro d\u2019acc\xE8s \xE0 INSDC attribu\xE9 au bioprojet cadre\ + \ pour l\u2019effort canadien de s\xE9quen\xE7age du SRAS-CoV-2" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Enregistrez le num\xE9ro d\u2019acc\xE8s au bioprojet cadre en le s\xE9\ + lectionnant \xE0 partir de la liste d\xE9roulante du mod\xE8le. Ce num\xE9ro\ + \ sera identique pour tous les soumissionnaires du RCanG\xE9CO. Diff\xE9rentes\ + \ provinces auront leurs propres bioprojets, mais ces derniers seront li\xE9\ + s sous un seul bioprojet cadre." + examples: + - value: PRJNA623807 + bioproject_accession: + name: bioproject_accession + title: "Num\xE9ro d\u2019acc\xE8s au bioprojet" + description: "Num\xE9ro d\u2019acc\xE8s \xE0 INSDC du bioprojet auquel appartient\ + \ un \xE9chantillon biologique" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Enregistrez le num\xE9ro d\u2019acc\xE8s au bioprojet. Les bioprojets\ + \ sont un outil d\u2019organisation qui relie les donn\xE9es de s\xE9quence\ + \ brutes, les assemblages et leurs m\xE9tadonn\xE9es associ\xE9es. Chaque province\ + \ se verra attribuer un num\xE9ro d\u2019acc\xE8s diff\xE9rent au bioprojet\ + \ par le Laboratoire national de microbiologie. Un num\xE9ro d\u2019acc\xE8\ + s valide au bioprojet du NCBI contient le pr\xE9fixe PRJN (p.\_ex., PRJNA12345);\ + \ il est cr\xE9\xE9 une fois au d\xE9but d\u2019un nouveau projet de s\xE9quen\xE7\ + age." + examples: + - value: PRJNA608651 + biosample_accession: + name: biosample_accession + title: "Num\xE9ro d\u2019acc\xE8s \xE0 un \xE9chantillon biologique" + description: "Identifiant attribu\xE9 \xE0 un \xE9chantillon biologique dans les\ + \ archives INSDC" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Conservez le num\xE9ro d\u2019acc\xE8s renvoy\xE9 avec la soumission\ + \ d\u2019un \xE9chantillon biologique. Les \xE9chantillons biologiques de NCBI\ + \ seront assortis du SAMN." + examples: + - value: SAMN14180202 + sra_accession: + name: sra_accession + title: "Num\xE9ro d\u2019acc\xE8s \xE0 l\u2019archive des s\xE9quences" + description: "Identifiant de l\u2019archive des s\xE9quences reliant les donn\xE9\ + es de s\xE9quences brutes de lecture, les m\xE9tadonn\xE9es m\xE9thodologiques\ + \ et les mesures de contr\xF4le de la qualit\xE9 soumises \xE0 INSDC" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Conservez le num\xE9ro d\u2019acc\xE8s attribu\xE9 au \xAB cycle \xBB\ + \ soumis. Les acc\xE8s NCBI-SRA commencent par SRR." + examples: + - value: SRR11177792 + genbank_accession: + name: genbank_accession + title: "Num\xE9ro d\u2019acc\xE8s \xE0 GenBank" + description: "Identifiant GenBank attribu\xE9 \xE0 la s\xE9quence dans les archives\ + \ INSDC" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Conservez le num\xE9ro d\u2019acc\xE8s renvoy\xE9 avec la soumission\ + \ de GenBank (assemblage du g\xE9nome viral)." + examples: + - value: MN908947.3 + gisaid_accession: + name: gisaid_accession + title: "Num\xE9ro d\u2019acc\xE8s \xE0 la GISAID" + description: "Num\xE9ro d\u2019acc\xE8s \xE0 la GISAID attribu\xE9 \xE0 la s\xE9\ + quence" + slot_group: "Identificateurs de base de donn\xE9es" + comments: "Conservez le num\xE9ro d\u2019acc\xE8s renvoy\xE9 avec la soumission\ + \ de la GISAID." + examples: + - value: EPI_ISL_436489 + sample_collected_by: + name: sample_collected_by + title: "\xC9chantillon pr\xE9lev\xE9 par" + description: "Nom de l\u2019organisme ayant pr\xE9lev\xE9 l\u2019\xE9chantillon\ + \ original" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Le nom de l\u2019agence doit \xEAtre \xE9crit au complet (\xE0 quelques\ - \ exceptions pr\xE8s) et \xEAtre coh\xE9rent dans plusieurs soumissions." - examples: - - value: "Laboratoire de sant\xE9 publique du BCCDC" - sample collector contact email: - name: sample collector contact email - title: "Courriel de contact du collecteur d'\xE9chantillons" - description: "L'adresse email du contact responsable du suivi concernant l'\xE9\ - chantillon." + comments: "Le nom du collecteur d\u2019\xE9chantillons doit \xEAtre \xE9crit au\ + \ long (\xE0 quelques exceptions pr\xE8s) et \xEAtre coh\xE9rent dans plusieurs\ + \ soumissions, par exemple Agence de la sant\xE9 publique du Canada, Sant\xE9\ + \ publique Ontario, Centre de contr\xF4le des maladies de la Colombie-Britannique." + examples: + - value: "Centre de contr\xF4le des maladies de la Colombie-Britannique" + sample_collector_contact_email: + name: sample_collector_contact_email + title: "Adresse courriel du collecteur d\u2019\xE9chantillons" + description: "Adresse courriel de la personne-ressource responsable du suivi concernant\ + \ l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "L'adresse e-mail peut repr\xE9senter une personne ou un laboratoire\ - \ sp\xE9cifique." + comments: "L\u2019adresse courriel peut repr\xE9senter une personne ou un laboratoire\ + \ sp\xE9cifique (p.\_ex., johnnyblogs@lab.ca, or RespLab@lab.ca)." examples: - value: RespLab@lab.ca - sample collector contact address: - name: sample collector contact address - title: "adresse de contact du collecteur d'\xE9chantillons" - description: "L'adresse postale de l'agence qui soumet l'\xE9chantillon." + sample_collector_contact_address: + name: sample_collector_contact_address + title: "Adresse du collecteur d\u2019\xE9chantillons" + description: "Adresse postale de l\u2019organisme soumettant l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "L'adresse postale doit \xEAtre au format\_: num\xE9ro et nom de la\ - \ rue, ville, \xE9tat/province/r\xE9gion, pays, code postal/code postal." - examples: - - value: 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada - sequence submitted by: - name: sequence submitted by - title: "s\xE9quence soumise par" - description: "Le nom de l'agence qui a g\xE9n\xE9r\xE9 la s\xE9quence." + comments: "Le format de l\u2019adresse postale doit \xEAtre le suivant\_: Num\xE9\ + ro et nom de la rue, ville, province/territoire, code postal et pays." + examples: + - value: "655, rue\_Lab, Vancouver (Colombie-Britannique) V5N\_2A2 Canada" + sequence_submitted_by: + name: sequence_submitted_by + title: "S\xE9quence soumise par" + description: "Nom de l\u2019organisme ayant g\xE9n\xE9r\xE9 la s\xE9quence" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Le nom de l\u2019agence doit \xEAtre \xE9crit au complet (\xE0 quelques\ - \ exceptions pr\xE8s) et \xEAtre coh\xE9rent dans plusieurs soumissions." + comments: "Le nom de l\u2019agence doit \xEAtre \xE9crit au long (\xE0 quelques\ + \ exceptions pr\xE8s) et \xEAtre coh\xE9rent dans plusieurs soumissions. Si\ + \ vous soumettez des \xE9chantillons plut\xF4t que des donn\xE9es de s\xE9quen\xE7\ + age, veuillez inscrire \xAB\_Laboratoire national de microbiologie (LNM)\_\xBB\ + ." examples: - value: "Sant\xE9 publique Ontario (SPO)" - sequence submitter contact email: - name: sequence submitter contact email - title: "s\xE9quence courriel de contact du d\xE9posant" - description: "L'adresse email du contact responsable du suivi de la s\xE9quence." + sequence_submitter_contact_email: + name: sequence_submitter_contact_email + title: "Adresse courriel du soumissionnaire de s\xE9quence" + description: "Adresse courriel de la personne-ressource responsable du suivi concernant\ + \ l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "L'adresse e-mail peut repr\xE9senter une personne ou un laboratoire\ - \ sp\xE9cifique." + comments: "L\u2019adresse courriel peut repr\xE9senter une personne ou un laboratoire\ + \ sp\xE9cifique (p.\_ex., johnnyblogs@lab.ca, or RespLab@lab.ca)." examples: - value: RespLab@lab.ca - sequence submitter contact address: - name: sequence submitter contact address - title: "adresse de contact de l'auteur de la s\xE9quence" - description: "L'adresse postale de l'agence soumettant la s\xE9quence." + sequence_submitter_contact_address: + name: sequence_submitter_contact_address + title: "Adresse du soumissionnaire de s\xE9quence" + description: "Adresse postale de l\u2019organisme soumettant l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "L'adresse postale doit \xEAtre au format\_: num\xE9ro et nom de la\ - \ rue, ville, \xE9tat/province/r\xE9gion, pays, code postal/code postal." - examples: - - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada - sample collection date: - name: sample collection date - title: "date de collecte de l'\xE9chantillon" - description: "La date \xE0 laquelle l'\xE9chantillon a \xE9t\xE9 pr\xE9lev\xE9\ - ." + comments: "Le format de l\u2019adresse postale doit \xEAtre le suivant\_: Num\xE9\ + ro et nom de la rue, ville, province/territoire, code postal et pays." + examples: + - value: "123, rue\_Sunnybrooke, Toronto (Ontario) M4P\_1L6 Canada" + sample_collection_date: + name: sample_collection_date + title: "Date de pr\xE9l\xE8vement de l\u2019\xE9chantillon" + description: "Date \xE0 laquelle l\u2019\xE9chantillon a \xE9t\xE9 pr\xE9lev\xE9" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Enregistrez avec pr\xE9cision la date de collecte dans le mod\xE8le.\ - \ La granularit\xE9 requise inclut l\u2019ann\xE9e, le mois et le jour. Avant\ - \ de partager ces donn\xE9es, assurez-vous que cette date n\u2019est pas consid\xE9\ - r\xE9e comme une information identifiable. Si cette date est consid\xE9r\xE9\ - e comme identifiable, il est acceptable d'ajouter du \xAB jitter \xBB \xE0 la\ - \ date de collecte en ajoutant ou en soustrayant des jours calendaires. Ne modifiez\ - \ pas la date de collecte dans vos dossiers originaux. Alternativement, la \xAB\ - \ date de r\xE9ception \xBB peut \xEAtre utilis\xE9e comme substitut dans les\ - \ donn\xE9es que vous partagez. La date doit \xEAtre fournie au format standard\ - \ ISO 8601 \xAB YYYY-MM-DD \xBB." + comments: "La date de pr\xE9l\xE8vement des \xE9chantillons est essentielle pour\ + \ la surveillance et de nombreux types d\u2019analyses. La granularit\xE9 requise\ + \ comprend l\u2019ann\xE9e, le mois et le jour. Si cette date est consid\xE9\ + r\xE9e comme un renseignement identifiable, il est acceptable d\u2019y ajouter\ + \ une \xAB\_gigue\_\xBB en ajoutant ou en soustrayant un jour civil. La \xAB\ + \_date de r\xE9ception\_\xBB peut \xE9galement servir de date de rechange. La\ + \ date doit \xEAtre fournie selon le format standard ISO\_8601\_: \xAB\_AAAA-MM-JJ\_\ + \xBB." examples: - value: '2020-03-16' - sample collection date precision: - name: sample collection date precision - title: "date de collecte de l'\xE9chantillon pr\xE9cision" - description: "La pr\xE9cision avec laquelle la \xAB date de pr\xE9l\xE8vement\ - \ de l\u2019\xE9chantillon \xBB a \xE9t\xE9 fournie." + sample_collection_date_precision: + name: sample_collection_date_precision + title: "Pr\xE9cision de la date de pr\xE9l\xE8vement de l\u2019\xE9chantillon" + description: "Pr\xE9cision avec laquelle la \xAB\_date de pr\xE9l\xE8vement de\ + \ l\u2019\xE9chantillon\_\xBB a \xE9t\xE9 fournie" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez la pr\xE9cision de la granularit\xE9 au \xAB jour \xBB,\ - \ au \xAB mois \xBB ou \xE0 \xAB l'ann\xE9e \xBB pour la date fournie dans le\ - \ champ \xAB date de pr\xE9l\xE8vement de l'\xE9chantillon \xBB. La \xAB date\ - \ de pr\xE9l\xE8vement de l'\xE9chantillon \xBB sera tronqu\xE9e \xE0 la pr\xE9\ - cision sp\xE9cifi\xE9e lors de l'exportation\_; \xAB jour \xBB pour \xABYYYY-MM-DD\ - \ \xBB, \xAB mois \xBB pour \xAB YYYY-MM \xBB ou \xAB ann\xE9e \xBB pour \xAB\ - \ YYYY \xBB." + comments: "Fournissez la pr\xE9cision de la granularit\xE9 au \xAB\_jour\_\xBB\ + , au \xAB\_mois\_\xBB ou \xE0 \xAB\_l\u2019ann\xE9e\_\xBB pour la date fournie\ + \ dans le champ \xAB\_Date de pr\xE9l\xE8vement de l\u2019\xE9chantillon\_\xBB\ + . Cette date sera tronqu\xE9e selon la pr\xE9cision sp\xE9cifi\xE9e lors de\ + \ l\u2019exportation\_: \xAB\_jour\_\xBB pour \xAB\_AAAA-MM-JJ\_\xBB, \xAB\_\ + mois\_\xBB pour \xAB\_AAAA-MM\_\xBB ou \xAB\_ann\xE9e\_\xBB pour \xAB\_AAAA\_\ + \xBB." examples: - value: "ann\xE9e" - sample received date: - name: sample received date - title: "date de r\xE9ception de l'\xE9chantillon" - description: "La date \xE0 laquelle l'\xE9chantillon a \xE9t\xE9 re\xE7u." + sample_received_date: + name: sample_received_date + title: "Date de r\xE9ception de l\u2019\xE9chantillon" + description: "Date \xE0 laquelle l\u2019\xE9chantillon a \xE9t\xE9 re\xE7u" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "La date \xE0 laquelle l'\xE9chantillon a \xE9t\xE9 re\xE7u par un laboratoire\ - \ qui n'\xE9tait pas le point de pr\xE9l\xE8vement. Norme ISO 8601 \xAB YYYY-MM-DD\xBB\ - ." + comments: "La date doit \xEAtre fournie selon le format standard ISO\_8601\_:\ + \ \xAB\_AAAA-MM-JJ\_\xBB." examples: - value: '2020-03-20' - geo_loc_name (country): - name: geo_loc_name (country) - title: nom du geo_loc (pays) - description: "Le pays d'origine de l'\xE9chantillon." + geo_loc_name_country: + name: geo_loc_name_country + title: "nom_lieu_g\xE9o (pays)" + description: "Pays d\u2019origine de l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez le nom du pays dans la liste de s\xE9lection du mod\xE8\ - le" + comments: "Fournissez le nom du pays \xE0 partir du vocabulaire contr\xF4l\xE9\ + \ fourni." examples: - value: Canada - geo_loc_name (state/province/territory): - name: geo_loc_name (state/province/territory) - title: "nom du geo_loc (\xE9tat/province/territoire)" - description: "L'\xC9tat/la province/le territoire d'origine de l'\xE9chantillon." + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory + title: "nom_lieu_g\xE9o (\xE9tat/province/territoire)" + description: "Province ou territoire o\xF9 l\u2019\xE9chantillon a \xE9t\xE9 pr\xE9\ + lev\xE9" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez le nom de l\u2019\xC9tat/de la province/du territoire \xE0\ - \ partir de l\u2019ontologie g\xE9ographique GAZ. Recherchez des termes g\xE9\ - ographiques ici\_: https://www.ebi.ac.uk/ols/ontologies/gaz" + comments: "Fournissez le nom de la province ou du territoire \xE0 partir du vocabulaire\ + \ contr\xF4l\xE9 fourni." examples: - value: Saskatchewan - geo_loc_name (city): - name: geo_loc_name (city) - title: nom du geo_loc (ville) - description: "La ville d'origine de l'\xE9chantillon." + geo_loc_name_city: + name: geo_loc_name_city + title: "nom_g\xE9o_loc (ville)" + description: "Ville o\xF9 l\u2019\xE9chantillon a \xE9t\xE9 pr\xE9lev\xE9" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez le nom de la ville \xE0 partir de l\u2019ontologie g\xE9\ - ographique GAZ. Recherchez des termes g\xE9ographiques ici\_: https://www.ebi.ac.uk/ols/ontologies/gaz" + comments: "Fournissez le nom de la ville. Utilisez ce service de recherche pour\ + \ trouver le terme normalis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/gaz." examples: - value: Medicine Hat organism: name: organism - title: organisme - description: Nom taxonomique de l'organisme. + title: Organisme + description: "Nom taxonomique de l\u2019organisme" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "S\xE9lectionnez \xAB\_Coronavirus 2 du syndrome respiratoire aigu s\xE9\ - v\xE8re\_\xBB si vous s\xE9quencez le SRAS-CoV-2. Si un autre Coronaviridae\ - \ est en cours de s\xE9quen\xE7age, fournissez le nom taxonomique de NCBITaxon.\ - \ Recherchez des termes de taxonomie sur https://www.ebi.ac.uk/ols/ontologies/ncbitaxon." + comments: "Utilisez \xAB\_coronavirus du syndrome respiratoire aigu s\xE9v\xE8\ + re\_2\_\xBB. Cette valeur est fournie dans le mod\xE8le." examples: - - value: "Syndrome respiratoire aigu s\xE9v\xE8re coronavirus 2" + - value: "Coronavirus du syndrome respiratoire aigu s\xE9v\xE8re\_2" isolate: name: isolate - title: isolat - description: "Identifiant de l'isolat sp\xE9cifique." + title: Isolat + description: "Identifiant de l\u2019isolat sp\xE9cifique" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Cet identifiant doit \xEAtre un identifiant alphanum\xE9rique unique,\ - \ index\xE9 au sein de votre laboratoire. S'il est soumis \xE0 l'INSDC, le nom\ - \ \xAB isoler \xBB est propag\xE9 dans diff\xE9rentes bases de donn\xE9es. En\ - \ tant que tel, structurez le nom \xAB\_isolat\_\xBB pour qu'il soit conforme\ - \ \xE0 ICTV/INSDC dans le format suivant\_: \xAB\_SARS-CoV-2/host/country/sampleID/date\_\ - \xBB." + comments: "Fournissez le nom du virus de la GISAID, qui doit \xEAtre \xE9crit\ + \ dans le format \xAB\_hCov-19/CANADA/code ISO provincial \xE0 2\_chiffres-xxxxx/ann\xE9\ + e\_\xBB." examples: - value: hCov-19/CANADA/BC-prov_rona_99/2020 - purpose of sampling: - name: purpose of sampling - title: "Objectif de l'\xE9chantillonnage" - description: "La raison pour laquelle l\u2019\xE9chantillon a \xE9t\xE9 collect\xE9\ - ." + purpose_of_sampling: + name: purpose_of_sampling + title: "Objectif de l\u2019\xE9chantillonnage" + description: "Motif de pr\xE9l\xE8vement de l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "S\xE9lectionnez une valeur dans la liste de s\xE9lection du mod\xE8\ - le." - examples: - - value: Tests de diagnostic - purpose of sampling details: - name: purpose of sampling details - title: "d\xE9tails de l'objectif de l'\xE9chantillonnage" - description: "Plus de d\xE9tails concernant la raison pour laquelle l\u2019\xE9\ - chantillon a \xE9t\xE9 collect\xE9." + comments: "La raison pour laquelle un \xE9chantillon a \xE9t\xE9 pr\xE9lev\xE9\ + \ peut fournir des renseignements sur les biais potentiels de la strat\xE9gie\ + \ d\u2019\xE9chantillonnage. Choisissez l\u2019objectif de l\u2019\xE9chantillonnage\ + \ \xE0 partir de la liste d\xE9roulante du mod\xE8le. Il est tr\xE8s probable\ + \ que l\u2019\xE9chantillon ait \xE9t\xE9 pr\xE9lev\xE9 en vue d\u2019un test\ + \ diagnostique. La raison pour laquelle un \xE9chantillon a \xE9t\xE9 pr\xE9\ + lev\xE9 \xE0 l\u2019origine peut diff\xE9rer de la raison pour laquelle il a\ + \ \xE9t\xE9 s\xE9lectionn\xE9 aux fins de s\xE9quen\xE7age, ce qui doit \xEA\ + tre indiqu\xE9 dans le champ \xAB\_Objectif du s\xE9quen\xE7age\_\xBB." + examples: + - value: Tests diagnostiques + purpose_of_sampling_details: + name: purpose_of_sampling_details + title: "D\xE9tails de l\u2019objectif de l\u2019\xE9chantillonnage" + description: "D\xE9tails pr\xE9cis concernant le motif de pr\xE9l\xE8vement de\ + \ l\u2019\xE9chantillon" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez une description en texte libre de la strat\xE9gie d\u2019\ - \xE9chantillonnage ou des \xE9chantillons collect\xE9s." - examples: - - value: "L'\xE9chantillon a \xE9t\xE9 collect\xE9 pour \xE9tudier la pr\xE9valence\ - \ des variantes associ\xE9es \xE0 la transmission du vison \xE0 l'homme au\ - \ Canada." - NML submitted specimen type: - name: NML submitted specimen type - title: "Type de sp\xE9cimen soumis au NML" - description: "Le type d'\xE9chantillon soumis au Laboratoire national de microbiologie\ - \ (NML) pour analyse." + comments: "Fournissez une description d\xE9taill\xE9e de la raison pour laquelle\ + \ l\u2019\xE9chantillon a \xE9t\xE9 pr\xE9lev\xE9 en utilisant du texte libre.\ + \ La description peut inclure l\u2019importance de l\u2019\xE9chantillon pour\ + \ une enqu\xEAte, une activit\xE9 de surveillance ou une question de recherche\ + \ particuli\xE8re dans le domaine de la sant\xE9 publique. Si les d\xE9tails\ + \ ne sont pas disponibles, fournissez une valeur nulle." + examples: + - value: "L\u2019\xE9chantillon a \xE9t\xE9 pr\xE9lev\xE9 pour \xE9tudier la pr\xE9\ + valence des variants associ\xE9s \xE0 la transmission du vison \xE0 l\u2019\ + homme au Canada." + nml_submitted_specimen_type: + name: nml_submitted_specimen_type + title: "Type d\u2019\xE9chantillon soumis au LNM" + description: "Type d\u2019\xE9chantillon soumis au Laboratoire national de microbiologie\ + \ (LNM) aux fins d\u2019analyse" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Ces informations sont requises pour le t\xE9l\xE9chargement via le\ - \ syst\xE8me CNPHI LaSER. S\xE9lectionnez le type d\u2019\xE9chantillon dans\ - \ la liste de s\xE9lection fournie. Si des donn\xE9es de s\xE9quence sont soumises\ - \ plut\xF4t qu'un \xE9chantillon \xE0 tester, s\xE9lectionnez \xAB\_Non applicable\_\ - \xBB." + comments: "Ces renseignements sont requis pour le t\xE9l\xE9chargement \xE0 l\u2019\ + aide du syst\xE8me LaSER du RCRSP. Choisissez le type d\u2019\xE9chantillon\ + \ \xE0 partir de la liste de s\xE9lection fournie. Si les donn\xE9es de s\xE9\ + quences sont soumises plut\xF4t qu\u2019un \xE9chantillon aux fins d\u2019analyse,\ + \ s\xE9lectionnez \xAB\_Sans objet\_\xBB." examples: - value: "\xC9couvillon" - Related specimen relationship type: - name: Related specimen relationship type - title: "Type de relation du sp\xE9cimen apparent\xE9" - description: "La relation entre le sp\xE9cimen actuel et le sp\xE9cimen/\xE9chantillon\ - \ pr\xE9c\xE9demment soumis au r\xE9f\xE9rentiel." + related_specimen_relationship_type: + name: related_specimen_relationship_type + title: "Type de relation de l\u2019\xE9chantillon li\xE9" + description: "Relation entre l\u2019\xE9chantillon actuel et celui pr\xE9c\xE9\ + demment soumis au d\xE9p\xF4t" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez l'\xE9tiquette qui d\xE9crit comment l'\xE9chantillon pr\xE9\ - c\xE9dent est li\xE9 \xE0 l'\xE9chantillon actuel soumis \xE0 partir de la liste\ - \ de s\xE9lection fournie, afin que les \xE9chantillons puissent \xEAtre li\xE9\ - s et suivis dans le syst\xE8me." - examples: - - value: "Test des m\xE9thodes d\u2019\xE9chantillonnage des \xE9chantillons" - anatomical material: - name: anatomical material - title: "mati\xE8re anatomique" - description: "Une substance obtenue \xE0 partir d'une partie anatomique d'un organisme,\ - \ par ex. tissu, sang." + comments: "Fournissez l\u2019\xE9tiquette qui d\xE9crit comment l\u2019\xE9chantillon\ + \ pr\xE9c\xE9dent est li\xE9 \xE0 l\u2019\xE9chantillon actuel soumis \xE0 partir\ + \ de la liste de s\xE9lection fournie afin que les \xE9chantillons puissent\ + \ \xEAtre li\xE9s et suivis dans le syst\xE8me." + examples: + - value: "Test des m\xE9thodes de pr\xE9l\xE8vement des \xE9chantillons" + anatomical_material: + name: anatomical_material + title: "Mati\xE8re anatomique" + description: "Substance obtenue \xE0 partir d\u2019une partie anatomique d\u2019\ + un organisme (p.\_ex., tissu, sang)" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez un descripteur si un mat\xE9riau anatomique a \xE9t\xE9\ - \ \xE9chantillonn\xE9. Utilisez la liste de s\xE9lection fournie dans le mod\xE8\ - le. Si un terme souhait\xE9 manque dans la liste de s\xE9lection, utilisez ce\ - \ service de recherche pour identifier un terme standardis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/uberon.\ - \ Si cela ne s\u2019applique pas, laissez vide." + comments: "Fournissez un descripteur si une mati\xE8re anatomique a \xE9t\xE9\ + \ \xE9chantillonn\xE9e. Utilisez la liste de s\xE9lection fournie dans le mod\xE8\ + le. Si un terme souhait\xE9 ne figure pas dans la liste de s\xE9lection, veuillez\ + \ envoyer un courriel \xE0 l\u2019adresse emma_griffiths@sfu.ca. Si ce n\u2019\ + est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." examples: - value: Sang - anatomical part: - name: anatomical part - title: partie anatomique - description: Une partie anatomique d'un organisme, par ex. oropharynx. + anatomical_part: + name: anatomical_part + title: Partie anatomique + description: "Partie anatomique d\u2019un organisme (p.\_ex., oropharynx)" slot_group: "Collecte et traitement des \xE9chantillons" comments: "Fournissez un descripteur si une partie anatomique a \xE9t\xE9 \xE9\ chantillonn\xE9e. Utilisez la liste de s\xE9lection fournie dans le mod\xE8\ - le. Si un terme souhait\xE9 manque dans la liste de s\xE9lection, utilisez ce\ - \ service de recherche pour identifier un terme standardis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/uberon.\ - \ Si cela ne s\u2019applique pas, laissez vide." + le. Si un terme souhait\xE9 ne figure pas dans la liste de s\xE9lection, veuillez\ + \ envoyer un courriel \xE0 l\u2019adresse emma_griffiths@sfu.ca. Si ce n\u2019\ + est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." examples: - value: Nasopharynx (NP) - body product: - name: body product - title: produit corporel - description: "Une substance excr\xE9t\xE9e/s\xE9cr\xE9t\xE9e par un organisme,\ - \ par ex. selles, urine, sueur." + body_product: + name: body_product + title: Produit corporel + description: "Substance excr\xE9t\xE9e ou s\xE9cr\xE9t\xE9e par un organisme (p.\_\ + ex., selles, urine, sueur)" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez une description si un produit corporel a \xE9t\xE9 \xE9\ - chantillonn\xE9. Utilisez la liste de s\xE9lection fournie dans le mod\xE8le.\ - \ Si un terme souhait\xE9 manque dans la liste de s\xE9lection, utilisez ce\ - \ service de recherche pour identifier un terme standardis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/uberon.\ - \ Si cela ne s\u2019applique pas, laissez vide." + comments: "Fournissez un descripteur si un produit corporel a \xE9t\xE9 \xE9chantillonn\xE9\ + . Utilisez la liste de s\xE9lection fournie dans le mod\xE8le. Si un terme souhait\xE9\ + \ ne figure pas dans la liste de s\xE9lection, veuillez envoyer un courriel\ + \ \xE0 l\u2019adresse emma_griffiths@sfu.ca. Si ce n\u2019est pas le cas, ne\ + \ laissez pas le champ vide. Choisissez une valeur nulle." examples: - value: Selles - environmental material: - name: environmental material - title: "mat\xE9riau environnemental" - description: "Une substance obtenue \xE0 partir de l'environnement naturel ou\ - \ artificiel, par ex. sol, eau, eaux us\xE9es, poign\xE9e de porte, rampe de\ - \ lit, masque facial." + environmental_material: + name: environmental_material + title: "Mat\xE9riel environnemental" + description: "Substance obtenue \xE0 partir de l\u2019environnement naturel ou\ + \ artificiel (p.\_ex., sol, eau, eaux us\xE9es)" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez un descripteur si un mat\xE9riau environnemental a \xE9\ - t\xE9 \xE9chantillonn\xE9. Utilisez la liste de s\xE9lection fournie dans le\ - \ mod\xE8le. Si un terme souhait\xE9 manque dans la liste de s\xE9lection, utilisez\ - \ ce service de recherche pour identifier un terme standardis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/envo.\ - \ Si cela ne s\u2019applique pas, laissez vide." - examples: - - value: Masque facial - environmental site: - name: environmental site - title: site environnemental - description: "Un emplacement environnemental peut d\xE9crire un site dans l'environnement\ - \ naturel ou b\xE2ti, par ex. h\xF4pital, march\xE9 humide, grotte aux chauves-souris." + comments: "Fournissez un descripteur si une mati\xE8re environnementale a \xE9\ + t\xE9 \xE9chantillonn\xE9e. Utilisez la liste de s\xE9lection fournie dans le\ + \ mod\xE8le. Si un terme souhait\xE9 ne figure pas dans la liste de s\xE9lection,\ + \ veuillez envoyer un courriel \xE0 l\u2019adresse emma_griffiths@sfu.ca. Si\ + \ ce n\u2019est pas le cas, ne laissez pas le champ vide. Choisissez une valeur\ + \ nulle." + examples: + - value: Masque + environmental_site: + name: environmental_site + title: Site environnemental + description: "Emplacement environnemental pouvant d\xE9crire un site dans l\u2019\ + environnement naturel ou artificiel (p.\_ex., surface de contact, bo\xEEte m\xE9\ + tallique, h\xF4pital, march\xE9 traditionnel de produits frais, grotte de chauves-souris)" slot_group: "Collecte et traitement des \xE9chantillons" comments: "Fournissez un descripteur si un site environnemental a \xE9t\xE9 \xE9\ chantillonn\xE9. Utilisez la liste de s\xE9lection fournie dans le mod\xE8le.\ - \ Si un terme souhait\xE9 manque dans la liste de s\xE9lection, utilisez ce\ - \ service de recherche pour identifier un terme standardis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/envo.\ - \ Si cela ne s\u2019applique pas, laissez vide." + \ Si un terme souhait\xE9 ne figure pas dans la liste de s\xE9lection, veuillez\ + \ envoyer un courriel \xE0 l\u2019adresse emma_griffiths@sfu.ca. Si ce n\u2019\ + est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle." examples: - value: Installation de production - collection device: - name: collection device - title: dispositif de collecte - description: "L'instrument ou le r\xE9cipient utilis\xE9 pour collecter l'\xE9\ - chantillon, par ex. \xE9couvillon." + collection_device: + name: collection_device + title: "Dispositif de pr\xE9l\xE8vement" + description: "Instrument ou contenant utilis\xE9 pour pr\xE9lever l\u2019\xE9\ + chantillon (p.\_ex., \xE9couvillon)" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez une description si un dispositif de pr\xE9l\xE8vement a\ - \ \xE9t\xE9 utilis\xE9 pour l\u2019\xE9chantillonnage. Utilisez la liste de\ - \ s\xE9lection fournie dans le mod\xE8le. Si un terme souhait\xE9 manque dans\ - \ la liste de s\xE9lection, utilisez ce service de recherche pour identifier\ - \ un terme standardis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/obi. Si cela\ - \ ne s\u2019applique pas, laissez vide." + comments: "Fournissez un descripteur si un dispositif de pr\xE9l\xE8vement a \xE9\ + t\xE9 utilis\xE9 pour l\u2019\xE9chantillonnage. Utilisez la liste de s\xE9\ + lection fournie dans le mod\xE8le. Si un terme souhait\xE9 ne figure pas dans\ + \ la liste de s\xE9lection, veuillez envoyer un courriel \xE0 l\u2019adresse\ + \ emma_griffiths@sfu.ca. Si ce n\u2019est pas le cas, ne laissez pas le champ\ + \ vide. Choisissez une valeur nulle." examples: - value: "\xC9couvillon" - collection method: - name: collection method - title: "m\xE9thode de collecte" - description: "Le processus utilis\xE9 pour collecter l'\xE9chantillon, par ex.\ - \ phl\xE9botomie, autopsie." + collection_method: + name: collection_method + title: "M\xE9thode de pr\xE9l\xE8vement" + description: "Processus utilis\xE9 pour pr\xE9lever l\u2019\xE9chantillon (p.\_\ + ex., phl\xE9botomie, autopsie)" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez une description si une m\xE9thode de collecte a \xE9t\xE9\ - \ utilis\xE9e pour l\u2019\xE9chantillonnage. Utilisez la liste de s\xE9lection\ - \ fournie dans le mod\xE8le. Si un terme souhait\xE9 manque dans la liste de\ - \ s\xE9lection, utilisez ce service de recherche pour identifier un terme standardis\xE9\ - \_: https://www.ebi.ac.uk/ols/ontologies/obi. Si cela ne s\u2019applique pas,\ - \ laissez vide." - examples: - - value: "Lavage broncho-alv\xE9olaire (LBA)" - collection protocol: - name: collection protocol - title: protocole de collecte - description: "Le nom et la version d'un protocole particulier utilis\xE9 pour\ - \ l'\xE9chantillonnage." + comments: "Fournissez un descripteur si une m\xE9thode de pr\xE9l\xE8vement a\ + \ \xE9t\xE9 utilis\xE9e pour l\u2019\xE9chantillonnage. Utilisez la liste de\ + \ s\xE9lection fournie dans le mod\xE8le. Si un terme souhait\xE9 ne figure\ + \ pas dans la liste de s\xE9lection, veuillez envoyer un courriel \xE0 l\u2019\ + adresse emma_griffiths@sfu.ca. Si ce n\u2019est pas le cas, ne laissez pas le\ + \ champ vide. Choisissez une valeur nulle." + examples: + - value: "Lavage bronchoalv\xE9olaire (LBA)" + collection_protocol: + name: collection_protocol + title: "Protocole de pr\xE9l\xE8vement" + description: "Nom et version d\u2019un protocole particulier utilis\xE9 pour l\u2019\ + \xE9chantillonnage" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez le nom et la version du protocole utilis\xE9 pour collecter\ - \ les \xE9chantillons." + comments: Texte libre. examples: - - value: BCRonaSamplingProtocol v. 1.2 - specimen processing: - name: specimen processing - title: "processus de traitement des sp\xE9cimens" + - value: "CBRonaProtocole\xC9chantillonnage v.\_1.2" + specimen_processing: + name: specimen_processing + title: "Traitement des \xE9chantillons" description: "Tout traitement appliqu\xE9 \xE0 l\u2019\xE9chantillon pendant ou\ - \ apr\xE8s la r\xE9ception de l\u2019\xE9chantillon." + \ apr\xE8s sa r\xE9ception" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Critique pour l\u2019interpr\xE9tation des donn\xE9es. S\xE9lectionnez\ + comments: "Essentiel pour l\u2019interpr\xE9tation des donn\xE9es. S\xE9lectionnez\ \ tous les processus applicables dans la liste de s\xE9lection. Si le virus\ - \ a \xE9t\xE9 transmis, incluez les informations dans les champs \xAB h\xF4\ - te du laboratoire \xBB, \xAB num\xE9ro de passage \xBB et \xAB m\xE9thode de\ - \ passage \xBB. Si aucun des processus de la liste de s\xE9lection ne s'applique,\ - \ inscrivez \xAB\_non applicable\_\xBB." - examples: - - value: Passage du virus - specimen processing details: - name: specimen processing details - title: "d\xE9tails du processus des \xE9chantillons" - description: "Informations d\xE9taill\xE9es concernant le traitement appliqu\xE9\ - \ \xE0 un \xE9chantillon pendant ou apr\xE8s la r\xE9ception de l'\xE9chantillon." + \ a \xE9t\xE9 transmis, ajoutez les renseignements dans les champs \xAB Laboratoire\ + \ h\xF4te \xBB, \xAB Nombre de transmissions \xBB et \xAB M\xE9thode de transmission\ + \ \xBB. Si aucun des processus de la liste de s\xE9lection ne s\u2019applique,\ + \ inscrivez \xAB\_Sans objet\_\xBB." + examples: + - value: Transmission du virus + specimen_processing_details: + name: specimen_processing_details + title: "D\xE9tails du traitement des \xE9chantillons" + description: "Renseignements d\xE9taill\xE9s concernant le traitement appliqu\xE9\ + \ \xE0 un \xE9chantillon pendant ou apr\xE8s sa r\xE9ception" slot_group: "Collecte et traitement des \xE9chantillons" comments: "Fournissez une description en texte libre de tous les d\xE9tails du\ \ traitement appliqu\xE9s \xE0 un \xE9chantillon." @@ -946,5010 +1077,3086 @@ slots: - value: "25 \xE9couvillons ont \xE9t\xE9 regroup\xE9s et pr\xE9par\xE9s en tant\ \ qu\u2019\xE9chantillon unique lors de la pr\xE9paration de la biblioth\xE8\ que." - lab host: - name: lab host - title: "h\xF4te du laboratoire" - description: "Nom et description de l'h\xF4te de laboratoire utilis\xE9 pour propager\ - \ l'organisme source ou le mat\xE9riel \xE0 partir duquel l'\xE9chantillon a\ - \ \xE9t\xE9 obtenu." + lab_host: + name: lab_host + title: "Laboratoire h\xF4te" + description: "Nom et description du laboratoire h\xF4te utilis\xE9 pour propager\ + \ l\u2019organisme source ou le mat\xE9riel \xE0 partir duquel l\u2019\xE9chantillon\ + \ a \xE9t\xE9 obtenu" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Type de lign\xE9e cellulaire utilis\xE9e pour la propagation. S\xE9\ - lectionnez une valeur dans la liste de s\xE9lection. S'il n'est pas adopt\xE9\ - , mettez \"sans objet\"." + comments: "Type de lign\xE9e cellulaire utilis\xE9e pour la propagation. Choisissez\ + \ le nom de cette lign\xE9e \xE0 partir de la liste de s\xE9lection dans le\ + \ mod\xE8le. Si le virus n\u2019a pas \xE9t\xE9 transmis, indiquez \xAB\_Sans\ + \ objet\_\xBB." examples: - value: "Lign\xE9e cellulaire Vero E6" - passage number: - name: passage number - title: "num\xE9ro de passage" - description: Nombre de passages. + passage_number: + name: passage_number + title: Nombre de transmission + description: Nombre de transmissions slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Indiquez le nombre de passages connus. S'il n'est pas adopt\xE9, mettre\ - \ \"sans objet\"" + comments: "Indiquez le nombre de transmissions connues. Si le virus n\u2019a pas\ + \ \xE9t\xE9 transmis, indiquez \xAB\_Sans objet\_\xBB." examples: - value: '3' - passage method: - name: passage method - title: "m\xE9thode de passage" - description: "Description de la fa\xE7on dont l'organisme a \xE9t\xE9 transmis." + passage_method: + name: passage_method + title: "M\xE9thode de transmission" + description: "Description de la fa\xE7on dont l\u2019organisme a \xE9t\xE9 transmis" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Texte libre. Fournissez une br\xE8ve description. S'il n'est pas adopt\xE9\ - , mettez \"sans objet\"." - examples: - - value: 0.25% trypsin + 0.02% EDTA - biomaterial extracted: - name: biomaterial extracted - title: "biomat\xE9riau extrait" - description: "Biomat\xE9riau extrait d\u2019\xE9chantillons \xE0 des fins de s\xE9\ - quen\xE7age." + comments: "Texte libre. Fournissez une br\xE8ve description (<10\_mots). Si le\ + \ virus n\u2019a pas \xE9t\xE9 transmis, indiquez \xAB\_Sans objet\_\xBB." + examples: + - value: "0,25\_% de trypsine + 0,02\_% d\u2019EDTA" + biomaterial_extracted: + name: biomaterial_extracted + title: "Biomat\xE9riau extrait" + description: "Biomat\xE9riau extrait d\u2019\xE9chantillons aux fins de s\xE9\ + quen\xE7age" slot_group: "Collecte et traitement des \xE9chantillons" - comments: "Fournissez le biomat\xE9riau extrait de la liste de s\xE9lection dans\ - \ le mod\xE8le." - examples: - - value: RNA (total) - host (common name): - name: host (common name) - title: "h\xF4te (nom commun)" - description: "Le nom couramment utilis\xE9 de l'h\xF4te." + comments: "Fournissez le biomat\xE9riau extrait \xE0 partir de la liste de s\xE9\ + lection dans le mod\xE8le." + examples: + - value: ARN (total) + host_common_name: + name: host_common_name + title: "H\xF4te (nom commun)" + description: "Nom couramment utilis\xE9 pour l\u2019h\xF4te" slot_group: "Informations sur l'h\xF4te" - comments: "Le nom commun ou le nom scientifique sont requis s\u2019il y avait\ - \ un h\xF4te. Exemples de noms communs, par ex. humain, chauve-souris. S\xE9\ - lectionnez une valeur dans la liste de s\xE9lection. Si l'\xE9chantillon \xE9\ - tait environnemental, inscrivez \xAB sans objet \xBB." + comments: "Le nom commun ou scientifique est requis s\u2019il y avait un h\xF4\ + te. Les deux peuvent \xEAtre fournis s\u2019ils sont connus. Utilisez les termes\ + \ figurant dans les listes de s\xE9lection du mod\xE8le. Des exemples de noms\ + \ communs sont \xAB\_humain\_\xBB et \xAB\_chauve-souris\_\xBB. Si l\u2019\xE9\ + chantillon \xE9tait environnemental, inscrivez \xAB Sans objet \xBB." examples: - value: Humain - host (scientific name): - name: host (scientific name) - title: "h\xF4te (nom scientifique)" - description: "Le nom taxonomique ou scientifique de l\u2019h\xF4te." + host_scientific_name: + name: host_scientific_name + title: "H\xF4te (nom scientifique)" + description: "Nom taxonomique ou scientifique de l\u2019h\xF4te" slot_group: "Informations sur l'h\xF4te" - comments: "Le nom commun ou le nom scientifique sont requis s\u2019il y avait\ - \ un h\xF4te. Exemples de noms scientifiques, par ex. Homo sapiens. S\xE9lectionnez\ - \ une valeur dans la liste de s\xE9lection. Si l'\xE9chantillon \xE9tait environnemental,\ - \ inscrivez \xAB sans objet \xBB." + comments: "Le nom commun ou scientifique est requis s\u2019il y avait un h\xF4\ + te. Les deux peuvent \xEAtre fournis s\u2019ils sont connus. Utilisez les termes\ + \ figurant dans les listes de s\xE9lection du mod\xE8le. Un exemple de nom scientifique\ + \ est \xAB\_homo sapiens\_\xBB. Si l\u2019\xE9chantillon \xE9tait environnemental,\ + \ inscrivez \xAB Sans objet \xBB." examples: - value: Homo sapiens - host health state: - name: host health state - title: "\xE9tat de sant\xE9 de l'h\xF4te" - description: "\xC9tat de sant\xE9 de l'h\xF4te au moment du pr\xE9l\xE8vement\ - \ de l'\xE9chantillon." + host_health_state: + name: host_health_state + title: "\xC9tat de sant\xE9 de l\u2019h\xF4te" + description: "\xC9tat de sant\xE9 de l\u2019h\xF4te au moment du pr\xE9l\xE8vement\ + \ d\u2019\xE9chantillons" slot_group: "Informations sur l'h\xF4te" - comments: "Si vous le connaissez, s\xE9lectionnez une valeur dans la liste de\ - \ s\xE9lection." + comments: "Si vous le connaissez, s\xE9lectionnez un descripteur \xE0 partir de\ + \ la liste de s\xE9lection fournie dans le mod\xE8le." examples: - value: Symptomatique - host health status details: - name: host health status details - title: "d\xE9tails de l'\xE9tat de sant\xE9 de l'h\xF4te" - description: "Plus de d\xE9tails concernant l'\xE9tat de sant\xE9 ou de maladie\ - \ de l'h\xF4te au moment de la collecte." + host_health_status_details: + name: host_health_status_details + title: "D\xE9tails de l\u2019\xE9tat de sant\xE9 de l\u2019h\xF4te" + description: "Plus de d\xE9tails concernant l\u2019\xE9tat de sant\xE9 ou de maladie\ + \ de l\u2019h\xF4te au moment du pr\xE9l\xE8vement" slot_group: "Informations sur l'h\xF4te" - comments: "Si vous le connaissez, s\xE9lectionnez une valeur dans la liste de\ - \ s\xE9lection." - examples: - - value: "Hospitalis\xE9 (ICU)" - host health outcome: - name: host health outcome - title: "r\xE9sultat sanitaire de l'h\xF4te" - description: "R\xE9sultat de la maladie chez l\u2019h\xF4te." + comments: "Si vous le connaissez, s\xE9lectionnez un descripteur \xE0 partir de\ + \ la liste de s\xE9lection fournie dans le mod\xE8le." + examples: + - value: "Hospitalis\xE9 (USI)" + host_health_outcome: + name: host_health_outcome + title: "R\xE9sultats sanitaires de l\u2019h\xF4te" + description: "R\xE9sultats de la maladie chez l\u2019h\xF4te" slot_group: "Informations sur l'h\xF4te" - comments: "Si vous le connaissez, s\xE9lectionnez une valeur dans la liste de\ - \ s\xE9lection." + comments: "Si vous le connaissez, s\xE9lectionnez un descripteur \xE0 partir de\ + \ la liste de s\xE9lection fournie dans le mod\xE8le." examples: - value: "R\xE9tabli" - host disease: - name: host disease - title: "maladie de l'h\xF4te" - description: "Le nom de la maladie v\xE9cue par l'h\xF4te." + host_disease: + name: host_disease + title: "Maladie de l\u2019h\xF4te" + description: "Nom de la maladie v\xE9cue par l\u2019h\xF4te" slot_group: "Informations sur l'h\xF4te" - comments: "Ce champ n'est obligatoire que s'il y avait un h\xF4te. Si l\u2019\ - h\xF4te \xE9tait un humain, s\xE9lectionnez COVID-19 dans la liste de s\xE9\ - lection. Si l\u2019h\xF4te \xE9tait asymptomatique, cela peut \xEAtre enregistr\xE9\ - \ sous \xAB\_d\xE9tails sur l\u2019\xE9tat de sant\xE9 de l\u2019h\xF4te\_\xBB\ - . \xAB\_COVID-19\_\xBB doit toujours \xEAtre fourni si le patient est asymptomatique.\ - \ Si l\u2019h\xF4te n\u2019est pas humain et que l\u2019\xE9tat pathologique\ - \ n\u2019est pas connu ou que l\u2019h\xF4te semble en bonne sant\xE9, inscrivez\ - \ \xAB sans objet \xBB." + comments: "S\xE9lectionnez \xAB\_COVID-19\_\xBB \xE0 partir de la liste de s\xE9\ + lection fournie dans le mod\xE8le." examples: - value: COVID-19 - host age: - name: host age - title: "\xE2ge de l'h\xF4te" - description: "\xC2ge de l'h\xF4te au moment de l'\xE9chantillonnage." + host_age: + name: host_age + title: "\xC2ge de l\u2019h\xF4te" + description: "\xC2ge de l\u2019h\xF4te au moment du pr\xE9l\xE8vement d\u2019\xE9\ + chantillons" slot_group: "Informations sur l'h\xF4te" - comments: "Si connu, indiquez l\u2019\xE2ge. Le regroupement par \xE2ge est \xE9\ - galement acceptable." + comments: "Entrez l\u2019\xE2ge de l\u2019h\xF4te en ann\xE9es. S\u2019il n\u2019\ + est pas disponible, fournissez une valeur nulle. S\u2019il n\u2019y a pas d\u2019\ + h\xF4te, inscrivez \xAB\_Sans objet\_\xBB." examples: - value: '79' - host age unit: - name: host age unit - title: "unit\xE9 d'\xE2ge de l'h\xF4te" - description: "Les unit\xE9s utilis\xE9es pour mesurer l'\xE2ge de l'h\xF4te." + host_age_unit: + name: host_age_unit + title: "Cat\xE9gorie d\u2019\xE2ge de l\u2019h\xF4te" + description: "Unit\xE9 utilis\xE9e pour mesurer l\u2019\xE2ge de l\u2019h\xF4\ + te (mois ou ann\xE9e)" slot_group: "Informations sur l'h\xF4te" - comments: "Si vous le savez, indiquez les unit\xE9s d'\xE2ge utilis\xE9es pour\ - \ mesurer l'\xE2ge de l'h\xF4te \xE0 partir de la liste de s\xE9lection." + comments: "Indiquez si l\u2019\xE2ge de l\u2019h\xF4te est en mois ou en ann\xE9\ + es. L\u2019\xE2ge indiqu\xE9 en mois sera class\xE9 dans la tranche d\u2019\xE2\ + ge de 0 \xE0 9\_ans." examples: - value: "ann\xE9e" - host age bin: - name: host age bin - title: "\xE2ge de l'h\xF4te bin" - description: "La cat\xE9gorie d'\xE2ge de l'h\xF4te au moment de l'\xE9chantillonnage." + host_age_bin: + name: host_age_bin + title: "Groupe d\u2019\xE2ge de l\u2019h\xF4te" + description: "\xC2ge de l\u2019h\xF4te au moment du pr\xE9l\xE8vement d\u2019\xE9\ + chantillons (groupe d\u2019\xE2ge)" slot_group: "Informations sur l'h\xF4te" - comments: "Des tranches d'\xE2ge ont \xE9t\xE9 fournies tous les 10 ans. Si l'\xE2\ - ge d'un h\xF4te ne peut pas \xEAtre sp\xE9cifi\xE9 en raison de probl\xE8mes\ - \ de confidentialit\xE9, une cat\xE9gorie d'\xE2ge peut \xEAtre utilis\xE9e\ - \ comme alternative." + comments: "S\xE9lectionnez la tranche d\u2019\xE2ge correspondante de l\u2019\ + h\xF4te \xE0 partir de la liste de s\xE9lection fournie dans le mod\xE8le. Si\ + \ vous ne la connaissez pas, fournissez une valeur nulle." examples: - value: 60 - 69 - host gender: - name: host gender - title: "sexe de l'h\xF4te" - description: "Le sexe de l\u2019h\xF4te au moment du pr\xE9l\xE8vement de l\u2019\ - \xE9chantillon." + host_gender: + name: host_gender + title: "Genre de l\u2019h\xF4te" + description: "Genre de l\u2019h\xF4te au moment du pr\xE9l\xE8vement d\u2019\xE9\ + chantillons" slot_group: "Informations sur l'h\xF4te" - comments: "Si vous le connaissez, s\xE9lectionnez une valeur dans la liste de\ - \ s\xE9lection." + comments: "S\xE9lectionnez le genre correspondant de l\u2019h\xF4te \xE0 partir\ + \ de la liste de s\xE9lection fournie dans le mod\xE8le. Si vous ne le connaissez\ + \ pas, fournissez une valeur nulle. S\u2019il n\u2019y a pas d\u2019h\xF4te,\ + \ inscrivez \xAB\_Sans objet\_\xBB." examples: - value: Homme - host residence geo_loc name (country): - name: host residence geo_loc name (country) - title: "r\xE9sidence de l'h\xF4te nom du geo_loc (pays)" - description: "Le pays o\xF9 r\xE9side l'h\xF4te." + host_residence_geo_loc_name_country: + name: host_residence_geo_loc_name_country + title: "R\xE9sidence de l\u2019h\xF4te\_\u2013 Nom de g\xE9o_loc (pays)" + description: "Pays de r\xE9sidence de l\u2019h\xF4te" slot_group: "Informations sur l'h\xF4te" - comments: "Si vous le connaissez, s\xE9lectionnez une valeur dans la liste de\ - \ s\xE9lection." + comments: "S\xE9lectionnez le nom du pays \xE0 partir de la liste de s\xE9lection\ + \ fournie dans le mod\xE8le." examples: - value: Canada - host residence geo_loc name (state/province/territory): - name: host residence geo_loc name (state/province/territory) - title: "nom du geo_loc de la r\xE9sidence de l'h\xF4te (\xE9tat/province/territoire)" - description: "L'\xE9tat/province/territoire de r\xE9sidence de l'h\xF4te." + host_residence_geo_loc_name_state_province_territory: + name: host_residence_geo_loc_name_state_province_territory + title: "R\xE9sidence de l\u2019h\xF4te\_\u2013 Nom de g\xE9o_loc (\xE9tat/province/territoire)" + description: "\xC9tat, province ou territoire de r\xE9sidence de l\u2019h\xF4\ + te" slot_group: "Informations sur l'h\xF4te" - comments: "S\xE9lectionnez le nom de la province/du territoire dans la liste de\ - \ s\xE9lection fournie dans le mod\xE8le." - examples: - - value: Quebec - host subject ID: - name: host subject ID - title: "ID du sujet de l'h\xF4te" - description: "Un identifiant unique par lequel chaque h\xF4te peut \xEAtre r\xE9\ - f\xE9renc\xE9, par ex. #131" + comments: "S\xE9lectionnez le nom de la province ou du territoire \xE0 partir\ + \ de la liste de s\xE9lection fournie dans le mod\xE8le." + examples: + - value: "Qu\xE9bec" + host_subject_id: + name: host_subject_id + title: "ID du sujet de l\u2019h\xF4te" + description: "Identifiant unique permettant de d\xE9signer chaque h\xF4te (p.\_\ + ex., 131)" slot_group: "Informations sur l'h\xF4te" - comments: "Doit \xEAtre un identifiant unique d\xE9fini par l'utilisateur. Cet\ - \ identifiant peut aider \xE0 relier les donn\xE9es de laboratoire aux donn\xE9\ - es \xE9pid\xE9miologiques, mais il s\u2019agit probablement d\u2019informations\ - \ sensibles. Consultez le gestionnaire de donn\xE9es." + comments: "Fournissez l\u2019identifiant de l\u2019h\xF4te. Il doit s\u2019agir\ + \ d\u2019un identifiant unique d\xE9fini par l\u2019utilisateur." examples: - value: BCxy123 - symptom onset date: - name: symptom onset date - title: "date d'apparition des sympt\xF4mes" - description: "La date \xE0 laquelle les sympt\xF4mes ont commenc\xE9 ou ont \xE9\ - t\xE9 observ\xE9s pour la premi\xE8re fois." + symptom_onset_date: + name: symptom_onset_date + title: "Date d\u2019apparition des sympt\xF4mes" + description: "Date \xE0 laquelle les sympt\xF4mes ont commenc\xE9 ou ont \xE9\ + t\xE9 observ\xE9s pour la premi\xE8re\_fois" slot_group: "Informations sur l'h\xF4te" - comments: "Si connue, indiquez la date d'apparition des sympt\xF4mes au format\ - \ standard ISO 8601 \xABYYYY-MM-DD \xBB." + comments: "La date doit \xEAtre fournie selon le format standard ISO\_8601\_:\ + \ \xAB\_AAAA-MM-JJ\_\xBB." examples: - value: '2020-03-16' - signs and symptoms: - name: signs and symptoms - title: "signes et sympt\xF4mes" + signs_and_symptoms: + name: signs_and_symptoms + title: "Signes et sympt\xF4mes" description: "Changement per\xE7u dans la fonction ou la sensation (perte, perturbation\ - \ ou apparence) r\xE9v\xE9lateur d'une maladie, rapport\xE9 par un patient." + \ ou apparence) r\xE9v\xE9lant une maladie, qui est signal\xE9 par un patient\ + \ ou un clinicien" slot_group: "Informations sur l'h\xF4te" - comments: "S\xE9lectionnez tous les sympt\xF4mes ressentis par l'h\xF4te dans\ - \ la liste de s\xE9lection." + comments: "S\xE9lectionnez tous les sympt\xF4mes ressentis par l\u2019h\xF4te\ + \ \xE0 partir de la liste de s\xE9lection." examples: - value: Frissons (sensation soudaine de froid) - - value: Toux - - value: "Fi\xE8vre" - pre-existing conditions and risk factors: - name: pre-existing conditions and risk factors - title: "les conditions pr\xE9existantes et les facteurs de risque" - description: "Conditions pr\xE9existantes du patient et facteurs de risque.
  • Condition\ - \ pr\xE9existante\_: condition m\xE9dicale qui existait avant l\u2019infection\ - \ actuelle.
  • Facteur de risque\_: variable associ\xE9e \xE0 un risque accru\ - \ de maladie ou d\u2019infection." + - value: toux + - value: "fi\xE8vre" + preexisting_conditions_and_risk_factors: + name: preexisting_conditions_and_risk_factors + title: "Conditions pr\xE9existantes et facteurs de risque" + description: "Conditions pr\xE9existantes et facteurs de risque du patient
  • Condition\ + \ pr\xE9existante\_: Condition m\xE9dicale qui existait avant l\u2019infection\ + \ actuelle
  • Facteur de risque\_: Variable associ\xE9e \xE0 un risque accru\ + \ de maladie ou d\u2019infection" slot_group: "Informations sur l'h\xF4te" - comments: "S\xE9lectionnez toutes les conditions pr\xE9existantes et les facteurs\ - \ de risque rencontr\xE9s par l'h\xF4te dans la liste de s\xE9lection. S'il\ - \ manque le terme souhait\xE9, contactez l'\xE9quipe de curation." + comments: "S\xE9lectionnez toutes les conditions pr\xE9existantes et tous les\ + \ facteurs de risque de l\u2019h\xF4te \xE0 partir de la liste de s\xE9lection.\ + \ S\u2019il manque le terme souhait\xE9, veuillez communiquer avec l\u2019\xE9\ + quipe de conservation des donn\xE9es." examples: - value: Asthme - - value: Grossesse - - value: Fumeur + - value: grossesse + - value: tabagisme complications: name: complications - title: les complications + title: Complications description: "Complications m\xE9dicales du patient qui seraient dues \xE0 une\ - \ maladie de l\u2019h\xF4te." + \ maladie de l\u2019h\xF4te" slot_group: "Informations sur l'h\xF4te" - comments: "S\xE9lectionnez toutes les complications rencontr\xE9es par l'h\xF4\ - te dans la liste de s\xE9lection." + comments: "S\xE9lectionnez toutes les complications \xE9prouv\xE9es par l\u2019\ + h\xF4te \xE0 partir de la liste de s\xE9lection. S\u2019il manque le terme souhait\xE9\ + , veuillez communiquer avec l\u2019\xE9quipe de conservation des donn\xE9es." examples: - value: "Insuffisance respiratoire aigu\xEB" - - value: Coma - - value: "Septic\xE9mie" - host vaccination status: - name: host vaccination status - title: "le statut vaccinal de l'h\xF4te" - description: "Le statut vaccinal de l\u2019h\xF4te (enti\xE8rement vaccin\xE9\ - , partiellement vaccin\xE9 ou non vaccin\xE9)." + - value: coma + - value: "septic\xE9mie" + host_vaccination_status: + name: host_vaccination_status + title: "Statut de vaccination de l\u2019h\xF4te" + description: "Statut de vaccination de l\u2019h\xF4te (enti\xE8rement vaccin\xE9\ + , partiellement vaccin\xE9 ou non vaccin\xE9)" slot_group: "Informations sur la vaccination de l'h\xF4te" - comments: "S\xE9lectionnez le statut vaccinal de l'h\xF4te dans la liste de s\xE9\ - lection." + comments: "S\xE9lectionnez le statut de vaccination de l\u2019h\xF4te \xE0 partir\ + \ de la liste de s\xE9lection." examples: - value: "Enti\xE8rement vaccin\xE9" - number of vaccine doses received: - name: number of vaccine doses received - title: "nombre de doses de vaccin re\xE7ues" - description: "Le nombre de doses de vaccin re\xE7ues par l\u2019h\xF4te." + number_of_vaccine_doses_received: + name: number_of_vaccine_doses_received + title: "Nombre de doses du vaccin re\xE7ues" + description: "Nombre de doses du vaccin re\xE7ues par l\u2019h\xF4te" slot_group: "Informations sur la vaccination de l'h\xF4te" - comments: "Enregistrez le nombre de doses de vaccin que l\u2019h\xF4te a re\xE7\ + comments: "Enregistrez le nombre de doses du vaccin que l\u2019h\xF4te a re\xE7\ ues." examples: - value: '2' - vaccination dose 1 vaccine name: - name: vaccination dose 1 vaccine name - title: dose de vaccination 1 nom du vaccin - description: "Nom du vaccin administr\xE9 comme premi\xE8re dose d'un sch\xE9\ - ma vaccinal." + vaccination_dose_1_vaccine_name: + name: vaccination_dose_1_vaccine_name + title: "Dose du vaccin\_1\_\u2013 Nom du vaccin" + description: "Nom du vaccin administr\xE9 comme premi\xE8re\_dose d\u2019un sch\xE9\ + ma vaccinal" slot_group: "Informations sur la vaccination de l'h\xF4te" - comments: "Indiquez le nom et le fabricant correspondant du vaccin contre la COVID-19\ - \ administr\xE9 comme premi\xE8re dose en s\xE9lectionnant une valeur dans la\ - \ liste de s\xE9lection." + comments: "Fournissez le nom et le fabricant correspondant du vaccin contre la\ + \ COVID-19 administr\xE9 comme premi\xE8re dose en s\xE9lectionnant une valeur\ + \ \xE0 partir de la liste de s\xE9lection." examples: - value: Pfizer-BioNTech (Comirnaty) - vaccination dose 1 vaccination date: - name: vaccination dose 1 vaccination date - title: dose de vaccination 1 date de vaccination - description: "La date \xE0 laquelle la premi\xE8re dose d\u2019un vaccin a \xE9\ - t\xE9 administr\xE9e." + vaccination_dose_1_vaccination_date: + name: vaccination_dose_1_vaccination_date + title: "Dose du vaccin\_1\_\u2013 Date du vaccin" + description: "Date \xE0 laquelle la premi\xE8re\_dose d\u2019un vaccin a \xE9\ + t\xE9 administr\xE9e" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Indiquez la date \xE0 laquelle la premi\xE8re dose du vaccin contre\ - \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie au format\ - \ standard ISO 8601 \xABYYYY-MM-DD \xBB." + \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie selon\ + \ le format standard ISO\_8601 \xAB\_AAAA-MM-DD\_\xBB." examples: - value: '2021-03-01' - vaccination dose 2 vaccine name: - name: vaccination dose 2 vaccine name - title: dose de vaccination 2 nom du vaccin - description: "Nom du vaccin administr\xE9 comme deuxi\xE8me dose d'un sch\xE9\ - ma vaccinal." + vaccination_dose_2_vaccine_name: + name: vaccination_dose_2_vaccine_name + title: "Dose du vaccin\_2\_\u2013 Nom du vaccin" + description: "Nom du vaccin administr\xE9 comme deuxi\xE8me\_dose d\u2019un sch\xE9\ + ma vaccinal" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Fournissez le nom et le fabricant correspondant du vaccin contre la\ - \ COVID-19 administr\xE9 comme deuxi\xE8me dose en s\xE9lectionnant une valeur\ - \ dans la liste de s\xE9lection." + \ COVID-19 administr\xE9 comme deuxi\xE8me\_dose en s\xE9lectionnant une valeur\ + \ \xE0 partir de la liste de s\xE9lection." examples: - value: Pfizer-BioNTech (Comirnaty) - vaccination dose 2 vaccination date: - name: vaccination dose 2 vaccination date - title: dose de vaccination 2 date de vaccination - description: "La date \xE0 laquelle la deuxi\xE8me dose d\u2019un vaccin a \xE9\ - t\xE9 administr\xE9e." + vaccination_dose_2_vaccination_date: + name: vaccination_dose_2_vaccination_date + title: "Dose du vaccin\_2\_\u2013 Date du vaccin" + description: "Date \xE0 laquelle la deuxi\xE8me\_dose d\u2019un vaccin a \xE9\ + t\xE9 administr\xE9e" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Indiquez la date \xE0 laquelle la deuxi\xE8me dose du vaccin contre\ - \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie au format\ - \ standard ISO 8601 \xAB YYYY-MM-DD \xBB." + \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie selon\ + \ le format standard ISO\_8601 \xAB\_AAAA-MM-DD\_\xBB." examples: - value: '2021-09-01' - vaccination dose 3 vaccine name: - name: vaccination dose 3 vaccine name - title: dose de vaccination 3 nom du vaccin - description: "Nom du vaccin administr\xE9 comme troisi\xE8me dose d'un sch\xE9\ - ma vaccinal." + vaccination_dose_3_vaccine_name: + name: vaccination_dose_3_vaccine_name + title: "Dose du vaccin\_3\_\u2013 Nom du vaccin" + description: "Nom du vaccin administr\xE9 comme troisi\xE8me\_dose d\u2019un sch\xE9\ + ma vaccinal" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Fournissez le nom et le fabricant correspondant du vaccin contre la\ - \ COVID-19 administr\xE9 comme troisi\xE8me dose en s\xE9lectionnant une valeur\ - \ dans la liste de s\xE9lection." + \ COVID-19 administr\xE9 comme troisi\xE8me\_dose en s\xE9lectionnant une valeur\ + \ \xE0 partir de la liste de s\xE9lection." examples: - value: Pfizer-BioNTech (Comirnaty) - vaccination dose 3 vaccination date: - name: vaccination dose 3 vaccination date - title: dose de vaccination 3 date de vaccination - description: "La date \xE0 laquelle la troisi\xE8me dose d\u2019un vaccin a \xE9\ - t\xE9 administr\xE9e." + vaccination_dose_3_vaccination_date: + name: vaccination_dose_3_vaccination_date + title: "Dose du vaccin\_3\_\u2013 Date du vaccin" + description: "Date \xE0 laquelle la troisi\xE8me\_dose d\u2019un vaccin a \xE9\ + t\xE9 administr\xE9e" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Indiquez la date \xE0 laquelle la troisi\xE8me dose du vaccin contre\ - \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie au format\ - \ standard ISO 8601 \xABYYYY-MM-DD \xBB." + \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie selon\ + \ le format standard ISO\_8601 \xAB\_AAAA-MM-DD\_\xBB." examples: - value: '2021-12-30' - vaccination dose 4 vaccine name: - name: vaccination dose 4 vaccine name - title: dose de vaccination 4 nom du vaccin - description: "Nom du vaccin administr\xE9 comme quatri\xE8me dose d'un sch\xE9\ - ma vaccinal." + vaccination_dose_4_vaccine_name: + name: vaccination_dose_4_vaccine_name + title: "Dose du vaccin\_4\_\u2013 Nom du vaccin" + description: "Nom du vaccin administr\xE9 comme quatri\xE8me dose d\u2019un sch\xE9\ + ma vaccinal" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Fournissez le nom et le fabricant correspondant du vaccin contre la\ - \ COVID-19 administr\xE9 comme quatri\xE8me dose en s\xE9lectionnant une valeur\ - \ dans la liste de s\xE9lection." + \ COVID-19 administr\xE9 comme quatri\xE8me\_dose en s\xE9lectionnant une valeur\ + \ \xE0 partir de la liste de s\xE9lection." examples: - value: Pfizer-BioNTech (Comirnaty) - vaccination dose 4 vaccination date: - name: vaccination dose 4 vaccination date - title: dose de vaccination 4 date de vaccination - description: "La date \xE0 laquelle la quatri\xE8me dose d\u2019un vaccin a \xE9\ - t\xE9 administr\xE9e." + vaccination_dose_4_vaccination_date: + name: vaccination_dose_4_vaccination_date + title: "Dose du vaccin\_4\_\u2013 Date du vaccin" + description: "Date \xE0 laquelle la quatri\xE8me\_dose d\u2019un vaccin a \xE9\ + t\xE9 administr\xE9e" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Indiquez la date \xE0 laquelle la quatri\xE8me dose du vaccin contre\ - \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie au format\ - \ standard ISO 8601 \xAB YYYY-MM-DD \xBB." + \ la COVID-19 a \xE9t\xE9 administr\xE9e. La date doit \xEAtre fournie selon\ + \ le format standard ISO\_8601 \xAB\_AAAA-MM-DD\_\xBB." examples: - value: '2022-01-15' - vaccination history: - name: vaccination history - title: "les ant\xE9c\xE9dents de vaccination" - description: "Une description des vaccins re\xE7us et les dates d'administration\ - \ d'une s\xE9rie de vaccinations contre une maladie sp\xE9cifique ou un ensemble\ - \ de maladies." + vaccination_history: + name: vaccination_history + title: "Ant\xE9c\xE9dents de vaccination" + description: "Description des vaccins re\xE7us et dates d\u2019administration\ + \ d\u2019une s\xE9rie de vaccins contre une maladie sp\xE9cifique ou un ensemble\ + \ de maladies" slot_group: "Informations sur la vaccination de l'h\xF4te" comments: "Description en texte libre des dates et des vaccins administr\xE9s\ - \ contre une maladie/un ensemble de maladies particulier. Il est \xE9galement\ - \ acceptable de concat\xE9ner les informations sur les doses individuelles (nom\ - \ du vaccin, date de vaccination) s\xE9par\xE9es par des points-virgules." + \ contre une maladie pr\xE9cise ou un ensemble de maladies. Il est \xE9galement\ + \ acceptable de concat\xE9ner les renseignements sur les doses individuelles\ + \ (nom du vaccin, date de vaccination) s\xE9par\xE9es par des points-virgules." examples: - value: Pfizer-BioNTech (Comirnaty) - value: '2021-03-01' - value: Pfizer-BioNTech (Comirnaty) - value: '2022-01-15' - location of exposure geo_loc name (country): - name: location of exposure geo_loc name (country) - title: lieu d'exposition geo_loc nom (pays) - description: "Le pays o\xF9 l'h\xF4te a probablement \xE9t\xE9 expos\xE9 \xE0\ - \ l'agent causal de la maladie." + location_of_exposure_geo_loc_name_country: + name: location_of_exposure_geo_loc_name_country + title: "Lieu de l\u2019exposition\_\u2013 Nom de g\xE9o_loc (pays)" + description: "Pays o\xF9 l\u2019h\xF4te a probablement \xE9t\xE9 expos\xE9 \xE0\ + \ l\u2019agent causal de la maladie" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Cet emplacement concerne le pays dans lequel l'h\xF4te est cens\xE9\ - \ \xEAtre expos\xE9 et peut ne pas \xEAtre le m\xEAme que le pays de r\xE9sidence\ - \ de l'h\xF4te. Si vous le connaissez, indiquez le nom du pays dans la liste\ - \ de s\xE9lection." + comments: "S\xE9lectionnez le nom du pays \xE0 partir de la liste de s\xE9lection\ + \ fournie dans le mod\xE8le." examples: - value: Canada - destination of most recent travel (city): - name: destination of most recent travel (city) - title: destination du dernier voyage (ville) - description: "Le nom de la ville de destination du voyage le plus r\xE9cent." + destination_of_most_recent_travel_city: + name: destination_of_most_recent_travel_city + title: Destination du dernier voyage (ville) + description: "Nom de la ville de destination du voyage le plus r\xE9cent" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Indiquez le nom de la ville dans laquelle l'h\xF4te s'est rendu. Utilisez\ - \ ce service de recherche pour identifier le terme normalis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/gaz" - examples: - - value: La ville de New York - destination of most recent travel (state/province/territory): - name: destination of most recent travel (state/province/territory) - title: "destination du dernier voyage (\xE9tat/province/territoire)" - description: "Le nom de la province de destination du voyage le plus r\xE9cent." + comments: "Indiquez le nom de la ville dans laquelle l\u2019h\xF4te s\u2019est\ + \ rendu. Utilisez ce service de recherche pour trouver le terme normalis\xE9\ + \_: https://www.ebi.ac.uk/ols/ontologies/gaz." + examples: + - value: New York City + destination_of_most_recent_travel_state_province_territory: + name: destination_of_most_recent_travel_state_province_territory + title: "Destination du dernier voyage (\xE9tat/province/territoire)" + description: "Nom de la province de destination du voyage le plus r\xE9cent" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Indiquez le nom de l'\xC9tat/de la province/du territoire o\xF9 l'h\xF4\ - te s'est rendu. Utilisez ce service de recherche pour identifier le terme normalis\xE9\ - \_: https://www.ebi.ac.uk/ols/ontologies/gaz" + comments: "Indiquez le nom de l\u2019\xC9tat, de la province ou du territoire\ + \ o\xF9 l\u2019h\xF4te s\u2019est rendu. Utilisez ce service de recherche pour\ + \ trouver le terme normalis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/gaz." examples: - value: Californie - destination of most recent travel (country): - name: destination of most recent travel (country) - title: destination du dernier voyage (pays) - description: "Le nom du pays de destination du voyage le plus r\xE9cent." + destination_of_most_recent_travel_country: + name: destination_of_most_recent_travel_country + title: Destination du dernier voyage (pays) + description: "Nom du pays de destination du voyage le plus r\xE9cent" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Indiquez le nom du pays dans lequel l'h\xF4te s'est rendu. Utilisez\ - \ ce service de recherche pour identifier le terme normalis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/gaz" + comments: "Indiquez le nom du pays dans lequel l\u2019h\xF4te s\u2019est rendu.\ + \ Utilisez ce service de recherche pour trouver le terme normalis\xE9\_: https://www.ebi.ac.uk/ols/ontologies/gaz." examples: - value: Royaume-Uni - most recent travel departure date: - name: most recent travel departure date - title: "date de d\xE9part du voyage la plus r\xE9cente" - description: "Date du d\xE9part le plus r\xE9cent d'une personne de sa r\xE9sidence\ - \ principale (\xE0 ce moment-l\xE0) pour un voyage vers un ou plusieurs autres\ - \ endroits." + most_recent_travel_departure_date: + name: most_recent_travel_departure_date + title: "Date de d\xE9part de voyage la plus r\xE9cente" + description: "Date du d\xE9part le plus r\xE9cent d\u2019une personne de sa r\xE9\ + sidence principale (\xE0 ce moment-l\xE0) pour un voyage vers un ou plusieurs\ + \ autres endroits" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Indiquez la date de d\xE9part du voyage au format standard ISO 8601\ - \ \xAB YYYY-MM-DD \xBB." + comments: "Indiquez la date de d\xE9part du voyage." examples: - value: '2020-03-16' - most recent travel return date: - name: most recent travel return date - title: "date de retour la plus r\xE9cente" - description: "Date du retour le plus r\xE9cent d'une personne \xE0 une r\xE9sidence\ - \ apr\xE8s un voyage au d\xE9part de cette r\xE9sidence." + most_recent_travel_return_date: + name: most_recent_travel_return_date + title: "Date de retour de voyage la plus r\xE9cente" + description: "Date du retour le plus r\xE9cent d\u2019une personne \xE0 une r\xE9\ + sidence apr\xE8s un voyage au d\xE9part de cette r\xE9sidence" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Indiquez la date de retour du voyage au format standard ISO 8601 \xAB\ - \ YYYY-MM-DD\xBB." + comments: Indiquez la date de retour du voyage. examples: - value: '2020-04-26' - travel point of entry type: - name: travel point of entry type - title: "voyage type de point d'entr\xE9e" - description: "Le type de point d\u2019entr\xE9e par lequel un voyageur arrive." + travel_point_of_entry_type: + name: travel_point_of_entry_type + title: "Type de point d\u2019entr\xE9e du voyage" + description: "Type de point d\u2019entr\xE9e par lequel un voyageur arrive" slot_group: "Informations sur l'exposition de l'h\xF4te" comments: "S\xE9lectionnez le type de point d\u2019entr\xE9e." examples: - value: Air - border testing test day type: - name: border testing test day type - title: "test aux fronti\xE8res jour du test type" - description: "Le jour o\xF9 un voyageur a \xE9t\xE9 test\xE9 \xE0 son arriv\xE9\ - e ou apr\xE8s son point d\u2019entr\xE9e." + border_testing_test_day_type: + name: border_testing_test_day_type + title: "Jour du d\xE9pistage \xE0 la fronti\xE8re" + description: "Jour o\xF9 un voyageur a \xE9t\xE9 test\xE9 \xE0 son point d\u2019\ + entr\xE9e ou apr\xE8s cette date" slot_group: "Informations sur l'exposition de l'h\xF4te" comments: "S\xE9lectionnez le jour du test." examples: - value: Jour 1 - travel history: - name: travel history - title: histoire du voyage - description: Historique de voyage au cours des six derniers mois. + travel_history: + name: travel_history + title: "Ant\xE9c\xE9dents de voyage" + description: "Historique de voyage au cours des six\_derniers mois" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Pr\xE9cisez les pays (et les emplacements plus pr\xE9cis si connus)\ - \ parcourus au cours des six derniers mois\_; peut inclure plusieurs voyages.\ - \ S\xE9parez plusieurs \xE9v\xE9nements de voyage par un point-virgule. Fournir\ - \ sous forme de texte libre." + comments: "Pr\xE9cisez les pays (et les emplacements plus pr\xE9cis, si vous les\ + \ connaissez) visit\xE9s au cours des six\_derniers mois, ce qui peut comprendre\ + \ plusieurs voyages. S\xE9parez plusieurs \xE9v\xE9nements de voyage par un\ + \ point-virgule. Commencez par le voyage le plus r\xE9cent." examples: - value: Canada, Vancouver - - value: USA, Seattle + - value: "\xC9tats-Unis, Seattle" - value: Italie, Milan - travel history availability: - name: travel history availability - title: "disponibilit\xE9 de l'historique de voyage" - description: "La disponibilit\xE9 de diff\xE9rents types d\u2019historiques de\ - \ voyages au cours des 6 derniers mois (par exemple internationaux, nationaux)." + travel_history_availability: + name: travel_history_availability + title: "Disponibilit\xE9 des ant\xE9c\xE9dents de voyage" + description: "Disponibilit\xE9 de diff\xE9rents types d\u2019historiques de voyages\ + \ au cours des six\_derniers mois (p.\_ex., internationaux, nationaux)" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "Si l'historique de voyage est disponible, mais que les d\xE9tails du\ - \ voyage ne peuvent pas \xEAtre fournis, indiquez-le ainsi que le type d'historique\ - \ de voyage disponible en s\xE9lectionnant une valeur dans la liste de s\xE9\ - lection. Les valeurs de ce champ peuvent \xEAtre utilis\xE9es pour indiquer\ - \ qu'un \xE9chantillon est associ\xE9 \xE0 un voyage lorsque le \xAB but du\ - \ s\xE9quen\xE7age \xBB n'est pas associ\xE9 \xE0 un voyage." - examples: - - value: Historique des voyages internationaux disponible - exposure event: - name: exposure event - title: "exposition \xE9v\xE9nement" - description: "\xC9v\xE9nement conduisant \xE0 une exposition." + comments: "Si les ant\xE9c\xE9dents de voyage sont disponibles, mais que les d\xE9\ + tails du voyage ne peuvent pas \xEAtre fournis, indiquez-le ainsi que le type\ + \ d\u2019ant\xE9c\xE9dents disponibles en s\xE9lectionnant une valeur \xE0 partir\ + \ de la liste de s\xE9lection. Les valeurs de ce champ peuvent \xEAtre utilis\xE9\ + es pour indiquer qu\u2019un \xE9chantillon est associ\xE9 \xE0 un voyage lorsque\ + \ le \xAB but du s\xE9quen\xE7age \xBB n\u2019est pas associ\xE9 \xE0 un voyage." + examples: + - value: "Ant\xE9c\xE9dents de voyage \xE0 l\u2019\xE9tranger disponible" + exposure_event: + name: exposure_event + title: "\xC9v\xE9nement d\u2019exposition" + description: "\xC9v\xE9nement conduisant \xE0 une exposition" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "S'il est connu, s\xE9lectionnez l'\xE9v\xE9nement d'exposition dans\ - \ la liste de s\xE9lection." + comments: "S\xE9lectionnez un \xE9v\xE9nement conduisant \xE0 une exposition \xE0\ + \ partir de la liste de s\xE9lection fournie dans le mod\xE8le. S\u2019il manque\ + \ le terme souhait\xE9, veuillez communiquer avec l\u2019\xE9quipe de conservation\ + \ des donn\xE9es." examples: - value: Convention - exposure contact level: - name: exposure contact level - title: exposition niveau de contact - description: "Le type de contact de transmission d\u2019exposition." + exposure_contact_level: + name: exposure_contact_level + title: "Niveau de contact de l\u2019exposition" + description: "Type de contact de transmission d\u2019exposition" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "S\xE9lectionnez une exposition directe ou indirecte dans la liste de\ - \ s\xE9lection." + comments: "S\xE9lectionnez une exposition directe ou indirecte \xE0 partir de\ + \ la liste de s\xE9lection." examples: - value: Direct - host role: - name: host role - title: "r\xF4le d'h\xF4te" - description: "Le r\xF4le de l'h\xF4te par rapport au param\xE8tre d'exposition." + host_role: + name: host_role + title: "R\xF4le de l\u2019h\xF4te" + description: "R\xF4le de l\u2019h\xF4te par rapport au param\xE8tre d\u2019exposition" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "S\xE9lectionnez le(s) r\xF4le(s) personnel(s) de l'h\xF4te dans la\ - \ liste de s\xE9lection fournie dans le mod\xE8le. S'il manque le terme souhait\xE9\ - , contactez l'\xE9quipe de curation." + comments: "S\xE9lectionnez les r\xF4les personnels de l\u2019h\xF4te \xE0 partir\ + \ de la liste de s\xE9lection fournie dans le mod\xE8le. S\u2019il manque le\ + \ terme souhait\xE9, veuillez communiquer avec l\u2019\xE9quipe de conservation\ + \ des donn\xE9es." examples: - value: Patient - exposure setting: - name: exposure setting - title: "r\xE9glage de l'exposition" - description: "Le cadre menant \xE0 l\u2019exposition." + exposure_setting: + name: exposure_setting + title: "Contexte de l\u2019exposition" + description: "Contexte menant \xE0 l\u2019exposition" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: "S\xE9lectionnez le(s) param\xE8tre(s) d'exposition de l'h\xF4te dans\ - \ la liste de s\xE9lection fournie dans le mod\xE8le. S\u2019il manque un terme\ - \ souhait\xE9, contactez l\u2019\xE9quipe de curation." - examples: - - value: "Cadre de soins de sant\xE9" - exposure details: - name: exposure details - title: "d\xE9tails de l'exposition" - description: "Informations suppl\xE9mentaires sur l\u2019exposition de l\u2019\ - h\xF4te." + comments: "S\xE9lectionnez les contextes menant \xE0 l\u2019exposition de l\u2019\ + h\xF4te \xE0 partir de la liste de s\xE9lection fournie dans le mod\xE8le. S\u2019\ + il manque le terme souhait\xE9, veuillez communiquer avec l\u2019\xE9quipe de\ + \ conservation des donn\xE9es." + examples: + - value: "Milieu de soins de sant\xE9" + exposure_details: + name: exposure_details + title: "D\xE9tails de l\u2019exposition" + description: "Renseignements suppl\xE9mentaires sur l\u2019exposition de l\u2019\ + h\xF4te" slot_group: "Informations sur l'exposition de l'h\xF4te" - comments: Description en texte libre de l'exposition. + comments: "Description en texte libre de l\u2019exposition." examples: - - value: "R\xF4le d'h\xF4te - Autre\_: Chauffeur de bus" - prior SARS-CoV-2 infection: - name: prior SARS-CoV-2 infection - title: "infection ant\xE9rieure par le SARS-CoV-2" - description: "S'il y a eu une infection ant\xE9rieure par le SARS-CoV-2." + - value: "R\xF4le d\u2019h\xF4te - Autre\_: Conducteur d\u2019autobus" + prior_sarscov2_infection: + name: prior_sarscov2_infection + title: "Infection ant\xE9rieure par le SRAS-CoV-2" + description: "Infection ant\xE9rieure par le SRAS-CoV-2 ou non" slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - comments: "Si vous le savez, fournissez des informations indiquant si la personne\ - \ a d\xE9j\xE0 eu une infection par le SARS-CoV-2. S\xE9lectionnez une valeur\ - \ dans la liste de s\xE9lection." + comments: "Si vous le savez, fournissez des renseignements indiquant si la personne\ + \ a d\xE9j\xE0 eu une infection par le SRAS-CoV-2. S\xE9lectionnez une valeur\ + \ \xE0 partir de la liste de s\xE9lection." examples: - value: Oui - prior SARS-CoV-2 infection isolate: - name: prior SARS-CoV-2 infection isolate - title: "isolat d'une infection ant\xE9rieure par le SARS-CoV-2" - description: "L\u2019identifiant de l\u2019isolat trouv\xE9 lors de l\u2019infection\ - \ ant\xE9rieure par le SARS-CoV-2." + prior_sarscov2_infection_isolate: + name: prior_sarscov2_infection_isolate + title: "Isolat d\u2019une infection ant\xE9rieure par le SRAS-CoV-2" + description: "Identifiant de l\u2019isolat trouv\xE9 lors de l\u2019infection\ + \ ant\xE9rieure par le SRAS-CoV-2" slot_group: "Informations sur la r\xE9infection de l'h\xF4te" comments: "Indiquez le nom de l\u2019isolat de l\u2019infection ant\xE9rieure\ - \ la plus r\xE9cente. Structurez le nom \xAB\_isolat\_\xBB pour qu'il soit conforme\ - \ \xE0 la norme ICTV/INSDC au format suivant\_: \xAB\_SARS-CoV-2/host/country/sampleID/date\_\ - \xBB." + \ la plus r\xE9cente. Structurez le nom de \xAB\_l\u2019isolat\_\xBB pour qu\u2019\ + il soit conforme \xE0 la norme ICTV/INSDC dans le format suivant\_: \xAB\_SRAS-CoV-2/h\xF4\ + te/pays/ID\xE9chantillon/date\_\xBB." examples: - value: SARS-CoV-2/human/USA/CA-CDPH-001/2020 - prior SARS-CoV-2 infection date: - name: prior SARS-CoV-2 infection date - title: "date d'une infection ant\xE9rieure par le SARS-CoV-2" - description: "La date du diagnostic de l\u2019infection ant\xE9rieure par le SARS-CoV-2." + prior_sarscov2_infection_date: + name: prior_sarscov2_infection_date + title: "Date d\u2019une infection ant\xE9rieure par le SRAS-CoV-2" + description: "Date du diagnostic de l\u2019infection ant\xE9rieure par le SRAS-CoV-2" slot_group: "Informations sur la r\xE9infection de l'h\xF4te" comments: "Indiquez la date \xE0 laquelle l\u2019infection ant\xE9rieure la plus\ - \ r\xE9cente a \xE9t\xE9 diagnostiqu\xE9e. Fournissez la date d'infection ant\xE9\ - rieure par le SARS-CoV-2 au format standard ISO 8601 \xAB YYYY-MM-DD \xBB." + \ r\xE9cente a \xE9t\xE9 diagnostiqu\xE9e. Fournissez la date d\u2019infection\ + \ ant\xE9rieure par le SRAS-CoV-2 selon le format standard ISO\_8601 \xAB AAAA-MM-DD\ + \ \xBB." examples: - value: '2021-01-23' - prior SARS-CoV-2 antiviral treatment: - name: prior SARS-CoV-2 antiviral treatment - title: "traitement antiviral ant\xE9rieur contre le SARS-CoV-2" - description: "S'il y a eu un traitement ant\xE9rieur contre le SARS-CoV-2 avec\ - \ un agent antiviral." + prior_sarscov2_antiviral_treatment: + name: prior_sarscov2_antiviral_treatment + title: "Traitement antiviral contre une infection ant\xE9rieure par le SRAS-CoV-2" + description: "Traitement contre une infection ant\xE9rieure par le SRAS-CoV-2\ + \ avec un agent antiviral ou non" slot_group: "Informations sur la r\xE9infection de l'h\xF4te" comments: "Si vous le savez, indiquez si la personne a d\xE9j\xE0 re\xE7u un traitement\ - \ antiviral contre le SARS-CoV-2. S\xE9lectionnez une valeur dans la liste de\ - \ s\xE9lection." - examples: - - value: "Aucun traitement antiviral pr\xE9alable" - prior SARS-CoV-2 antiviral treatment agent: - name: prior SARS-CoV-2 antiviral treatment agent - title: "agent du traitement antiviral ant\xE9rieur contre le SARS-CoV-2" - description: "Le nom de l\u2019agent de traitement antiviral administr\xE9 lors\ - \ de l\u2019infection ant\xE9rieure par le SARS-CoV-2." + \ antiviral contre le SRAS-CoV-2. S\xE9lectionnez une valeur \xE0 partir de\ + \ la liste de s\xE9lection." + examples: + - value: "Aucun traitement antiviral ant\xE9rieur" + prior_sarscov2_antiviral_treatment_agent: + name: prior_sarscov2_antiviral_treatment_agent + title: "Agent du traitement antiviral contre une infection ant\xE9rieure par le\ + \ SRAS-CoV-2" + description: "Nom de l\u2019agent de traitement antiviral administr\xE9 lors de\ + \ l\u2019infection ant\xE9rieure par le SRAS-CoV-2" slot_group: "Informations sur la r\xE9infection de l'h\xF4te" comments: "Indiquez le nom de l\u2019agent de traitement antiviral administr\xE9\ \ lors de l\u2019infection ant\xE9rieure la plus r\xE9cente. Si aucun traitement\ \ n\u2019a \xE9t\xE9 administr\xE9, inscrivez \xAB Aucun traitement \xBB. Si\ \ plusieurs agents antiviraux ont \xE9t\xE9 administr\xE9s, \xE9num\xE9rez-les\ - \ tous s\xE9par\xE9s par des virgules." + \ tous, s\xE9par\xE9s par des virgules." examples: - value: Remdesivir - prior SARS-CoV-2 antiviral treatment date: - name: prior SARS-CoV-2 antiviral treatment date - title: "date du traitement antiviral ant\xE9rieur contre le SARS-CoV-2" - description: "Le traitement a \xE9t\xE9 administr\xE9 pour la premi\xE8re fois\ - \ lors de l\u2019infection ant\xE9rieure par le SARS-CoV-2." + prior_sarscov2_antiviral_treatment_date: + name: prior_sarscov2_antiviral_treatment_date + title: "Date du traitement antiviral contre une infection ant\xE9rieure par le\ + \ SRAS-CoV-2" + description: "Date \xE0 laquelle le traitement a \xE9t\xE9 administr\xE9 pour\ + \ la premi\xE8re\_fois lors de l\u2019infection ant\xE9rieure par le SRAS-CoV-2" slot_group: "Informations sur la r\xE9infection de l'h\xF4te" - comments: "Indiquez la date \xE0 laquelle l'agent de traitement antiviral a \xE9\ - t\xE9 administr\xE9 pour la premi\xE8re fois lors de l'infection ant\xE9rieure\ - \ la plus r\xE9cente. Fournissez la date du traitement ant\xE9rieur contre le\ - \ SARS-CoV-2 au format standard ISO 8601 \xAB YYYY-MM-DD \xBB." + comments: "Indiquez la date \xE0 laquelle l\u2019agent de traitement antiviral\ + \ a \xE9t\xE9 administr\xE9 pour la premi\xE8re fois lors de l\u2019infection\ + \ ant\xE9rieure la plus r\xE9cente. Fournissez la date du traitement ant\xE9\ + rieur contre le SRAS-CoV-2 selon le format standard ISO\_8601 \xAB AAAA-MM-DD\ + \ \xBB." examples: - value: '2021-01-28' - purpose of sequencing: - name: purpose of sequencing - title: "objectif du s\xE9quen\xE7age" - description: "La raison pour laquelle l\u2019\xE9chantillon a \xE9t\xE9 s\xE9\ - quenc\xE9." + purpose_of_sequencing: + name: purpose_of_sequencing + title: "Objectif du s\xE9quen\xE7age" + description: "Raison pour laquelle l\u2019\xE9chantillon a \xE9t\xE9 s\xE9quenc\xE9" slot_group: "S\xE9quen\xE7age" comments: "La raison pour laquelle un \xE9chantillon a \xE9t\xE9 initialement\ - \ collect\xE9 peut diff\xE9rer de la raison pour laquelle il a \xE9t\xE9 s\xE9\ - lectionn\xE9 pour le s\xE9quen\xE7age. La raison pour laquelle un \xE9chantillon\ - \ a \xE9t\xE9 s\xE9quenc\xE9 peut fournir des informations sur les biais potentiels\ + \ pr\xE9lev\xE9 peut diff\xE9rer de la raison pour laquelle il a \xE9t\xE9 s\xE9\ + lectionn\xE9 aux fins de s\xE9quen\xE7age. La raison pour laquelle un \xE9chantillon\ + \ a \xE9t\xE9 s\xE9quenc\xE9 peut fournir des renseignements sur les biais potentiels\ \ dans la strat\xE9gie de s\xE9quen\xE7age. Fournissez le but du s\xE9quen\xE7\ - age \xE0 partir de la liste de s\xE9lection dans le mod\xE8le. La raison du\ - \ pr\xE9l\xE8vement de l\u2019\xE9chantillon doit \xEAtre indiqu\xE9e dans le\ - \ champ \xAB\_objectif de l\u2019\xE9chantillonnage\_\xBB." + age \xE0 partir de la liste de s\xE9lection dans le mod\xE8le. Le motif de pr\xE9\ + l\xE8vement de l\u2019\xE9chantillon doit \xEAtre indiqu\xE9 dans le champ \xAB\ + \_Objectif de l\u2019\xE9chantillonnage\_\xBB." examples: - value: "Surveillance de base (\xE9chantillonnage al\xE9atoire)" - purpose of sequencing details: - name: purpose of sequencing details - title: "objectif du s\xE9quen\xE7age d\xE9tails" - description: "La description de la raison pour laquelle l'\xE9chantillon a \xE9\ - t\xE9 s\xE9quenc\xE9, fournissant des d\xE9tails sp\xE9cifiques." + purpose_of_sequencing_details: + name: purpose_of_sequencing_details + title: "D\xE9tails de l\u2019objectif du s\xE9quen\xE7age" + description: "Description de la raison pour laquelle l\u2019\xE9chantillon a \xE9\ + t\xE9 s\xE9quenc\xE9, fournissant des d\xE9tails sp\xE9cifiques" slot_group: "S\xE9quen\xE7age" comments: "Fournissez une description d\xE9taill\xE9e de la raison pour laquelle\ - \ l'\xE9chantillon a \xE9t\xE9 s\xE9quenc\xE9 \xE0 l'aide d'une liste de s\xE9\ - lection. La description peut inclure l\u2019importance des s\xE9quences pour\ - \ une enqu\xEAte/activit\xE9 de surveillance/question de recherche particuli\xE8\ - re en sant\xE9 publique. Les descriptions standardis\xE9es sugg\xE9r\xE9es comprennent\_\ - : D\xE9pist\xE9 pour l'\xE9chec de la cible du g\xE8ne S (abandon S), D\xE9\ - pist\xE9 pour les variantes de vison, D\xE9pist\xE9 pour la variante B.1.1.7,\ - \ D\xE9pist\xE9 pour la variante B.1.135, D\xE9pist\xE9 pour la variante P.1,\ - \ D\xE9pist\xE9 en raison des ant\xE9c\xE9dents de voyage, D\xE9pist\xE9 en\ - \ raison d'un contact \xE9troit avec une personne infect\xE9e, \xC9valuation\ - \ des mesures de contr\xF4le de la sant\xE9 publique, D\xE9termination des introductions\ - \ et de la propagation pr\xE9coces, Enqu\xEAte sur les expositions li\xE9es\ - \ aux compagnies a\xE9riennes, Enqu\xEAte sur les travailleurs \xE9trangers\ - \ temporaires, Enqu\xEAte sur les r\xE9gions \xE9loign\xE9es, Enqu\xEAte sur\ - \ les travailleurs de la sant\xE9, Enqu\xEAte sur les \xE9coles/universit\xE9\ - s, Enqu\xEAte sur la r\xE9infection." - examples: - - value: "D\xE9pist\xE9 pour \xE9chec de la cible du g\xE8ne S (abandon S)" - sequencing date: - name: sequencing date - title: "date de s\xE9quen\xE7age" - description: "La date \xE0 laquelle l\u2019\xE9chantillon a \xE9t\xE9 s\xE9quenc\xE9\ - ." + \ l\u2019\xE9chantillon a \xE9t\xE9 s\xE9quenc\xE9 en utilisant du texte libre.\ + \ La description peut inclure l\u2019importance des s\xE9quences pour une enqu\xEA\ + te, une activit\xE9 de surveillance ou une question de recherche particuli\xE8\ + re dans le domaine de la sant\xE9 publique. Les descriptions normalis\xE9es\ + \ sugg\xE9r\xE9es sont les suivantes\_: D\xE9pistage de l\u2019absence de d\xE9\ + tection du g\xE8ne\_S (abandon du g\xE8ne\_S), d\xE9pistage de variants associ\xE9\ + s aux visons, d\xE9pistage du variant\_B.1.1.7, d\xE9pistage du variant\_B.1.135,\ + \ d\xE9pistage du variant\_P.1, d\xE9pistage en raison des ant\xE9c\xE9dents\ + \ de voyage, d\xE9pistage en raison d\u2019un contact \xE9troit avec une personne\ + \ infect\xE9e, \xE9valuation des mesures de contr\xF4le de la sant\xE9 publique,\ + \ d\xE9termination des introductions et de la propagation pr\xE9coces, enqu\xEA\ + te sur les expositions li\xE9es aux voyages a\xE9riens, enqu\xEAte sur les travailleurs\ + \ \xE9trangers temporaires, enqu\xEAte sur les r\xE9gions \xE9loign\xE9es, enqu\xEA\ + te sur les travailleurs de la sant\xE9, enqu\xEAte sur les \xE9coles et les\ + \ universit\xE9s, enqu\xEAte sur la r\xE9infection." + examples: + - value: "D\xE9pistage de l\u2019absence de d\xE9tection du g\xE8ne\_S (abandon\ + \ du g\xE8ne\_S)" + sequencing_date: + name: sequencing_date + title: "Date de s\xE9quen\xE7age" + description: "Date \xE0 laquelle l\u2019\xE9chantillon a \xE9t\xE9 s\xE9quenc\xE9" slot_group: "S\xE9quen\xE7age" - comments: "Fournissez la date de s\xE9quen\xE7age au format standard ISO 8601\ - \ \xAB YYYY-MM-DD \xBB." + comments: "La date doit \xEAtre fournie selon le format standard ISO\_8601\_:\ + \ \xAB\_AAAA-MM-JJ\_\xBB." examples: - value: '2020-06-22' - library ID: - name: library ID + library_id: + name: library_id title: "ID de la biblioth\xE8que" - description: "L\u2019identifiant sp\xE9cifi\xE9 par l\u2019utilisateur pour la\ - \ biblioth\xE8que pr\xE9par\xE9e pour le s\xE9quen\xE7age." + description: "Identifiant sp\xE9cifi\xE9 par l\u2019utilisateur pour la biblioth\xE8\ + que faisant l\u2019objet du s\xE9quen\xE7age" slot_group: "S\xE9quen\xE7age" comments: "Le nom de la biblioth\xE8que doit \xEAtre unique et peut \xEAtre un\ - \ identifiant g\xE9n\xE9r\xE9 automatiquement \xE0 partir de votre LIMS ou une\ - \ modification de l'ID d'isolat." + \ ID g\xE9n\xE9r\xE9 automatiquement \xE0 partir de votre syst\xE8me de gestion\ + \ de l\u2019information des laboratoires, ou une modification de l\u2019ID de\ + \ l\u2019isolat." examples: - value: XYZ_123345 - amplicon size: - name: amplicon size - title: taille de l'amplicon - description: "La longueur de l'amplicon g\xE9n\xE9r\xE9 par l'amplification PCR." + amplicon_size: + name: amplicon_size + title: "Taille de l\u2019amplicon" + description: "Longueur de l\u2019amplicon g\xE9n\xE9r\xE9 par l\u2019amplification\ + \ de la r\xE9action de polym\xE9risation en cha\xEEne" slot_group: "S\xE9quen\xE7age" comments: "Fournissez la taille de l\u2019amplicon, y compris les unit\xE9s." examples: - - value: 300bp - library preparation kit: - name: library preparation kit - title: "kit de pr\xE9paration de librairie" - description: "Nom du kit de pr\xE9paration de la biblioth\xE8que DNA utilis\xE9\ - \ pour g\xE9n\xE9rer la biblioth\xE8que en cours de s\xE9quen\xE7age." + - value: "300\_pb" + library_preparation_kit: + name: library_preparation_kit + title: "Trousse de pr\xE9paration de la biblioth\xE8que" + description: "Nom de la trousse de pr\xE9paration de la banque d\u2019ADN utilis\xE9\ + e pour g\xE9n\xE9rer la biblioth\xE8que faisant l\u2019objet du s\xE9quen\xE7\ + age" slot_group: "S\xE9quen\xE7age" - comments: "Indiquez le nom du kit de pr\xE9paration de biblioth\xE8que utilis\xE9\ - ." + comments: "Indiquez le nom de la trousse de pr\xE9paration de la biblioth\xE8\ + que utilis\xE9e." examples: - value: Nextera XT - flow cell barcode: - name: flow cell barcode - title: "code-barres de la cellule d'\xE9coulement" - description: "Le code-barres de la Flow Cell utilis\xE9e pour le s\xE9quen\xE7\ - age." + flow_cell_barcode: + name: flow_cell_barcode + title: "Code-barres de la cuve \xE0 circulation" + description: "Code-barres de la cuve \xE0 circulation utilis\xE9e aux fins de\ + \ s\xE9quen\xE7age" slot_group: "S\xE9quen\xE7age" - comments: "Fournissez le code-barres de la Flow Cell utilis\xE9e pour s\xE9quencer\ - \ l\u2019\xE9chantillon." + comments: "Fournissez le code-barres de la cuve \xE0 circulation utilis\xE9e pour\ + \ s\xE9quencer l\u2019\xE9chantillon." examples: - value: FAB06069 - sequencing instrument: - name: sequencing instrument - title: "instrument de s\xE9quen\xE7age" - description: "Le mod\xE8le de l\u2019instrument de s\xE9quen\xE7age utilis\xE9\ - ." + sequencing_instrument: + name: sequencing_instrument + title: "Instrument de s\xE9quen\xE7age" + description: "Mod\xE8le de l\u2019instrument de s\xE9quen\xE7age utilis\xE9" slot_group: "S\xE9quen\xE7age" - comments: "S\xE9lectionnez l\u2019instrument de s\xE9quen\xE7age dans la liste\ - \ de s\xE9lection." + comments: "S\xE9lectionnez l\u2019instrument de s\xE9quen\xE7age \xE0 partir de\ + \ la liste de s\xE9lection." examples: - value: Oxford Nanopore MinION - sequencing protocol name: - name: sequencing protocol name - title: "nom du protocole de s\xE9quen\xE7age" - description: "Le nom et le num\xE9ro de version du protocole de s\xE9quen\xE7\ - age utilis\xE9." + sequencing_protocol_name: + name: sequencing_protocol_name + title: "Nom du protocole de s\xE9quen\xE7age" + description: "Nom et num\xE9ro de version du protocole de s\xE9quen\xE7age utilis\xE9" slot_group: "S\xE9quen\xE7age" - comments: "Fournissez le nom et la version du protocole de s\xE9quen\xE7age." + comments: "Fournissez le nom et la version du protocole de s\xE9quen\xE7age (p.\_\ + ex., 1D_DNA_MinION)." examples: - value: https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann - sequencing protocol: - name: sequencing protocol - title: "protocole de s\xE9quen\xE7age" - description: "Le protocole utilis\xE9 pour g\xE9n\xE9rer la s\xE9quence." + sequencing_protocol: + name: sequencing_protocol + title: "Protocole de s\xE9quen\xE7age" + description: "Protocole utilis\xE9 pour g\xE9n\xE9rer la s\xE9quence" slot_group: "S\xE9quen\xE7age" comments: "Fournissez une description en texte libre des m\xE9thodes et du mat\xE9\ - riel utilis\xE9s pour g\xE9n\xE9rer la s\xE9quence. Texte sugg\xE9r\xE9, compl\xE9\ - tez les informations l\xE0 o\xF9 elles sont indiqu\xE9es.\_: \"Le s\xE9quen\xE7\ - age viral a \xE9t\xE9 effectu\xE9 selon une strat\xE9gie d'amplicon en mosa\xEF\ - que en utilisant le sch\xE9ma d'amorce . Le s\xE9quen\xE7age a \xE9\ - t\xE9 effectu\xE9 \xE0 l'aide d'un instrument de s\xE9quen\xE7age .\ - \ Les biblioth\xE8ques ont \xE9t\xE9 pr\xE9par\xE9es \xE0 l'aide de la biblioth\xE8\ - que . trousse.\"" - examples: - - value: "Les g\xE9nomes ont \xE9t\xE9 g\xE9n\xE9r\xE9s par s\xE9quen\xE7age d'amplicons\ - \ de 1 200 pb avec des amorces de sch\xE9ma Freed. Les biblioth\xE8ques ont\ - \ \xE9t\xE9 cr\xE9\xE9es \xE0 l'aide des kits Illumina DNA Prep et les donn\xE9\ - es de s\xE9quence ont \xE9t\xE9 produites \xE0 l'aide des kits de s\xE9quen\xE7\ - age Miseq Micro v2 (500 cycles)." - sequencing kit number: - name: sequencing kit number - title: "num\xE9ro du kit de s\xE9quen\xE7age" - description: "Le num\xE9ro de kit du fabricant." + riel utilis\xE9s pour g\xE9n\xE9rer la s\xE9quence. Voici le texte sugg\xE9\ + r\xE9 (ins\xE9rez les renseignements manquants)\_: \xAB\_Le s\xE9quen\xE7age\ + \ viral a \xE9t\xE9 effectu\xE9 selon une strat\xE9gie d\u2019amplicon en mosa\xEF\ + que en utilisant le sch\xE9ma d\u2019amorce <\xE0 remplir>. Le s\xE9quen\xE7\ + age a \xE9t\xE9 effectu\xE9 \xE0 l\u2019aide d\u2019un instrument de s\xE9quen\xE7\ + age <\xE0 remplir>. Les biblioth\xE8ques ont \xE9t\xE9 pr\xE9par\xE9es \xE0\ + \ l\u2019aide de la trousse <\xE0 remplir>.\_\xBB" + examples: + - value: "Les g\xE9nomes ont \xE9t\xE9 g\xE9n\xE9r\xE9s par s\xE9quen\xE7age d\u2019\ + amplicons de 1 200 pb avec des amorces de sch\xE9ma Freed. Les biblioth\xE8\ + ques ont \xE9t\xE9 cr\xE9\xE9es \xE0 l\u2019aide des trousses de pr\xE9paration\ + \ de l\u2019ADN Illumina et les donn\xE9es de s\xE9quence ont \xE9t\xE9 produites\ + \ \xE0 l\u2019aide des trousses de s\xE9quen\xE7age Miseq Micro v2 (500\_\ + cycles)." + sequencing_kit_number: + name: sequencing_kit_number + title: "Num\xE9ro de la trousse de s\xE9quen\xE7age" + description: "Num\xE9ro de la trousse du fabricant" slot_group: "S\xE9quen\xE7age" comments: "Valeur alphanum\xE9rique." examples: - value: AB456XYZ789 - amplicon pcr primer scheme: - name: amplicon pcr primer scheme - title: de la liste des amorces pcr de l'amplicon - description: "Les sp\xE9cifications des amorces (s\xE9quences d'amorces, positions\ - \ de liaison, taille des fragments g\xE9n\xE9r\xE9s, etc.) utilis\xE9es pour\ - \ g\xE9n\xE9rer les amplicons \xE0 s\xE9quencer." + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme + title: "Sch\xE9ma d\u2019amorce pour la r\xE9action de polym\xE9risation en cha\xEE\ + ne de l\u2019amplicon" + description: "Sp\xE9cifications li\xE9es aux amorces (s\xE9quences d\u2019amorces,\ + \ positions de liaison, taille des fragments g\xE9n\xE9r\xE9s, etc.) utilis\xE9\ + es pour g\xE9n\xE9rer les amplicons \xE0 s\xE9quencer" slot_group: "S\xE9quen\xE7age" comments: "Fournissez le nom et la version du sch\xE9ma d\u2019amorce utilis\xE9\ - \ pour g\xE9n\xE9rer les amplicons pour le s\xE9quen\xE7age." + \ pour g\xE9n\xE9rer les amplicons aux fins de s\xE9quen\xE7age." examples: - value: https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv - raw sequence data processing method: - name: raw sequence data processing method - title: "m\xE9thode de traitement des donn\xE9es de s\xE9quences brutes" - description: "La m\xE9thode utilis\xE9e pour le traitement des donn\xE9es brutes,\ - \ comme la suppression des codes-barres, le d\xE9coupage de l'adaptateur, le\ - \ filtrage, etc." + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method + title: "M\xE9thode de traitement des donn\xE9es de s\xE9quences brutes" + description: "Nom et num\xE9ro de version du logiciel utilis\xE9 pour le traitement\ + \ des donn\xE9es brutes, comme la suppression des codes-barres, le d\xE9coupage\ + \ de l\u2019adaptateur, le filtrage, etc." slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: "Fournissez le nom et les num\xE9ros de version du logiciel utilis\xE9\ - \ pour traiter les donn\xE9es brutes." + comments: "Fournissez le nom du logiciel, suivi de la version (p.\_ex., Trimmomatic\_\ + v.\_0.38, Porechop\_v.\_0.2.03)." examples: - value: Porechop 0.2.3 - dehosting method: - name: dehosting method - title: "m\xE9thode de d\xE9shostage" - description: "M\xE9thode utilis\xE9e pour supprimer les lectures de l'h\xF4te\ - \ de la s\xE9quence de l'agent pathog\xE8ne." + dehosting_method: + name: dehosting_method + title: "M\xE9thode de retrait de l\u2019h\xF4te" + description: "M\xE9thode utilis\xE9e pour supprimer les lectures de l\u2019h\xF4\ + te de la s\xE9quence de l\u2019agent pathog\xE8ne" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Fournissez le nom et le num\xE9ro de version du logiciel utilis\xE9\ - \ pour supprimer les lectures de l'h\xF4te." + \ pour supprimer les lectures de l\u2019h\xF4te." examples: - value: Nanostripper - consensus sequence name: - name: consensus sequence name - title: "nom de la s\xE9quence consensus" - description: "Le nom de la s\xE9quence consensus." + consensus_sequence_name: + name: consensus_sequence_name + title: "Nom de la s\xE9quence de consensus" + description: "Nom de la s\xE9quence de consensus" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: "Fournissez le nom et le num\xE9ro de version de la s\xE9quence consensus." + comments: "Fournissez le nom et le num\xE9ro de version de la s\xE9quence de consensus." examples: - value: ncov123assembly3 - consensus sequence filename: - name: consensus sequence filename - title: "nom de fichier de la s\xE9quence consensus" - description: "Le nom du fichier de s\xE9quence consensus." + consensus_sequence_filename: + name: consensus_sequence_filename + title: "Nom du fichier de la s\xE9quence de consensus" + description: "Nom du fichier de la s\xE9quence de consensus" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: "Fournissez le nom et le num\xE9ro de version du fichier FASTA de s\xE9\ - quence consensus." + comments: "Fournissez le nom et le num\xE9ro de version du fichier FASTA de la\ + \ s\xE9quence de consensus." examples: - value: ncov123assembly.fasta - consensus sequence filepath: - name: consensus sequence filepath - title: "chemin de fichier de la s\xE9quence consensus" - description: "Le chemin d\u2019acc\xE8s du fichier de s\xE9quence consensus." + consensus_sequence_filepath: + name: consensus_sequence_filepath + title: "Chemin d\u2019acc\xE8s au fichier de la s\xE9quence de consensus" + description: "Chemin d\u2019acc\xE8s au fichier de la s\xE9quence de consensus" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: "Fournissez le chemin d\u2019acc\xE8s du fichier FASTA de s\xE9quence\ - \ consensus." + comments: "Fournissez le chemin d\u2019acc\xE8s au fichier FASTA de la s\xE9quence\ + \ de consensus." examples: - value: /User/Documents/RespLab/Data/ncov123assembly.fasta - consensus sequence software name: - name: consensus sequence software name - title: "nom du logiciel de s\xE9quen\xE7age du consensus" - description: "Le nom du logiciel utilis\xE9 pour g\xE9n\xE9rer la s\xE9quence\ - \ consensus." + consensus_sequence_software_name: + name: consensus_sequence_software_name + title: "Nom du logiciel de la s\xE9quence de consensus" + description: "Nom du logiciel utilis\xE9 pour g\xE9n\xE9rer la s\xE9quence de\ + \ consensus" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Fournissez le nom du logiciel utilis\xE9 pour g\xE9n\xE9rer la s\xE9\ - quence consensus." + quence de consensus." examples: - value: iVar - consensus sequence software version: - name: consensus sequence software version - title: "version du logiciel de la s\xE9quence consensus" - description: "La version du logiciel utilis\xE9 pour g\xE9n\xE9rer la s\xE9quence\ - \ consensus." + consensus_sequence_software_version: + name: consensus_sequence_software_version + title: "Version du logiciel de la s\xE9quence de consensus" + description: "Version du logiciel utilis\xE9 pour g\xE9n\xE9rer la s\xE9quence\ + \ de consensus" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Fournir la version du logiciel utilis\xE9 pour g\xE9n\xE9rer la s\xE9\ - quence consensus." + quence de consensus." examples: - value: '1.3' - breadth of coverage value: - name: breadth of coverage value - title: "valeur de l'\xE9tendue de la couverture" - description: "Le pourcentage du g\xE9nome de r\xE9f\xE9rence couvert par les donn\xE9\ - es s\xE9quenc\xE9es, jusqu'\xE0 une profondeur prescrite." + breadth_of_coverage_value: + name: breadth_of_coverage_value + title: "Valeur de l\u2019\xE9tendue de la couverture" + description: "Pourcentage du g\xE9nome de r\xE9f\xE9rence couvert par les donn\xE9\ + es s\xE9quenc\xE9es, jusqu\u2019\xE0 une profondeur prescrite" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: Fournissez la valeur en pourcentage. examples: - - value: 95% - depth of coverage value: - name: depth of coverage value - title: valeur de la profondeur de couverture - description: "Le nombre moyen de lectures repr\xE9sentant un nucl\xE9otide donn\xE9\ - \ dans la s\xE9quence reconstruite." + - value: "95\_%" + depth_of_coverage_value: + name: depth_of_coverage_value + title: "Valeur de l\u2019ampleur de la couverture" + description: "Nombre moyen de lectures repr\xE9sentant un nucl\xE9otide donn\xE9\ + \ dans la s\xE9quence reconstruite" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Apporter de la valeur sous forme de pli de couverture. + comments: "Fournissez la valeur sous forme de couverture amplifi\xE9e." examples: - value: 400x - depth of coverage threshold: - name: depth of coverage threshold - title: seuil de profondeur de couverture - description: "Seuil utilis\xE9 comme seuil pour la profondeur de couverture." + depth_of_coverage_threshold: + name: depth_of_coverage_threshold + title: "Seuil de l\u2019ampleur de la couverture" + description: "Seuil utilis\xE9 comme limite pour l\u2019ampleur de la couverture" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Fournit la couverture de pli de seuil. + comments: "Fournissez la couverture amplifi\xE9e." examples: - value: 100x - r1 fastq filename: - name: r1 fastq filename - title: r1 nom de fichier fastq - description: "Le nom de fichier sp\xE9cifi\xE9 par l'utilisateur du fichier r1\ - \ FASTQ." + r1_fastq_filename________: + name: r1_fastq_filename________ + title: "Nom de fichier\_R1\_FASTQ" + description: "Nom du fichier\_R1\_FASTQ sp\xE9cifi\xE9 par l\u2019utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Fournissez le nom du fichier r1 FASTQ. + comments: "Fournissez le nom du fichier\_R1 FASTQ." examples: - value: ABC123_S1_L001_R1_001.fastq.gz - r2 fastq filename: - name: r2 fastq filename - title: r2 nom de fichier fastq - description: "Le nom de fichier sp\xE9cifi\xE9 par l'utilisateur du fichier r2\ - \ FASTQ." + r2_fastq_filename: + name: r2_fastq_filename + title: "Nom de fichier\_R2\_FASTQ" + description: "Nom du fichier\_R2\_FASTQ sp\xE9cifi\xE9 par l\u2019utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Fournissez le nom du fichier r2 FASTQ. + comments: "Fournissez le nom du fichier\_R2 FASTQ." examples: - value: ABC123_S1_L001_R2_001.fastq.gz - r1 fastq filepath: - name: r1 fastq filepath - title: chemin de fichier r1 fastq - description: Le chemin du fichier r1 FASTQ. + r1_fastq_filepath: + name: r1_fastq_filepath + title: "Chemin d\u2019acc\xE8s au fichier\_R1\_FASTQ" + description: "Emplacement du fichier\_R1\_FASTQ dans le syst\xE8me de l\u2019\ + utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Fournissez le chemin du fichier r1 FASTQ. + comments: "Fournissez le chemin d\u2019acc\xE8s au fichier\_R1 FASTQ." examples: - value: /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz - r2 fastq filepath: - name: r2 fastq filepath - title: chemin du fichier r2 fastq - description: "Le chemin d'acc\xE8s du fichier r2 FASTQ." + r2_fastq_filepath: + name: r2_fastq_filepath + title: "Chemin d\u2019acc\xE8s au fichier\_R2\_FASTQ" + description: "Emplacement du fichier\_R2\_FASTQ dans le syst\xE8me de l\u2019\ + utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: "Fournissez le chemin d'acc\xE8s du fichier r2 FASTQ." + comments: "Fournissez le chemin d\u2019acc\xE8s au fichier\_R2 FASTQ." examples: - value: /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz - fast5 filename: - name: fast5 filename - title: nom de fichier fast5 - description: "Le nom de fichier sp\xE9cifi\xE9 par l'utilisateur du fichier FAST5." + fast5_filename: + name: fast5_filename + title: "Nom de fichier\_FAST5" + description: "Nom du fichier\_FAST5 sp\xE9cifi\xE9 par l\u2019utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Fournissez le nom du fichier FAST5. + comments: "Fournissez le nom du fichier\_FAST5." examples: - value: rona123assembly.fast5 - fast5 filepath: - name: fast5 filepath - title: chemin de fichier fast5 - description: Le chemin du fichier FAST5. + fast5_filepath: + name: fast5_filepath + title: "Chemin d\u2019acc\xE8s au fichier\_FAST5" + description: "Emplacement du fichier\_FAST5 dans le syst\xE8me de l\u2019utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: Fournissez le chemin du fichier FAST5. + comments: "Fournissez le chemin d\u2019acc\xE8s au fichier\_FAST5." examples: - value: /User/Documents/RespLab/Data/rona123assembly.fast5 - number of base pairs sequenced: - name: number of base pairs sequenced - title: "nombre de paires de bases s\xE9quenc\xE9es" - description: "Le nombre total de paires de bases g\xE9n\xE9r\xE9es par le processus\ - \ de s\xE9quen\xE7age." + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced + title: "Nombre de paires de bases s\xE9quenc\xE9es" + description: "Nombre total de paires de bases g\xE9n\xE9r\xE9es par le processus\ + \ de s\xE9quen\xE7age" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Fournissez une valeur num\xE9rique (pas besoin d\u2019inclure des unit\xE9\ s)." examples: - - value: '387566' - consensus genome length: - name: consensus genome length - title: "longueur consensuelle du g\xE9nome" - description: "Taille du g\xE9nome assembl\xE9 d\xE9crite comme le nombre de paires\ - \ de bases." + - value: "387\_566" + consensus_genome_length: + name: consensus_genome_length + title: "Longueur consensuelle du g\xE9nome" + description: "Taille du g\xE9nome reconstitu\xE9 d\xE9crite comme \xE9tant le\ + \ nombre de paires de bases" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Fournissez une valeur num\xE9rique (pas besoin d\u2019inclure des unit\xE9\ s)." examples: - - value: '38677' - Ns per 100 kbp: - name: Ns per 100 kbp - title: Ns per 100 kbp - description: "Le nombre de N symboles pr\xE9sents dans la s\xE9quence fasta consensus,\ - \ pour 100\_kbp de s\xE9quence." + - value: "38\_677" + ns_per_100_kbp: + name: ns_per_100_kbp + title: "N par 100\_kbp" + description: "Nombre de symboles N pr\xE9sents dans la s\xE9quence fasta de consensus,\ + \ par 100\_kbp de s\xE9quence" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Fournissez une valeur num\xE9rique (pas besoin d\u2019inclure des unit\xE9\ s)." examples: - value: '330' - reference genome accession: - name: reference genome accession - title: "accession au g\xE9nome de r\xE9f\xE9rence" - description: "Un identifiant persistant et unique d\u2019une entr\xE9e de base\ - \ de donn\xE9es g\xE9nomique." + reference_genome_accession: + name: reference_genome_accession + title: "Acc\xE8s au g\xE9nome de r\xE9f\xE9rence" + description: "Identifiant persistant et unique d\u2019une entr\xE9e dans une base\ + \ de donn\xE9es g\xE9nomique" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - comments: "Fournissez le num\xE9ro d\u2019acc\xE8s du g\xE9nome de r\xE9f\xE9\ + comments: "Fournissez le num\xE9ro d\u2019acc\xE8s au g\xE9nome de r\xE9f\xE9\ rence." examples: - value: NC_045512.2 - bioinformatics protocol: - name: bioinformatics protocol - title: protocole bioinformatique - description: "Le nom et le num\xE9ro de version du protocole bioinformatique utilis\xE9\ - ." + bioinformatics_protocol: + name: bioinformatics_protocol + title: Protocole bioinformatique + description: "Description de la strat\xE9gie bioinformatique globale utilis\xE9\ + e" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" comments: "Des d\xE9tails suppl\xE9mentaires concernant les m\xE9thodes utilis\xE9\ - es pour traiter les donn\xE9es brutes et/ou g\xE9n\xE9rer des assemblages et/ou\ - \ g\xE9n\xE9rer des s\xE9quences consensus peuvent \xEAtre fournis dans une\ - \ SOP ou un protocole. Fournissez le nom et le num\xE9ro de version du protocole,\ - \ ou un lien s'il est d\xE9pos\xE9 dans un r\xE9f\xE9rentiel de protocoles." + es pour traiter les donn\xE9es brutes, g\xE9n\xE9rer des assemblages ou g\xE9\ + n\xE9rer des s\xE9quences de consensus peuvent \xEAtre fournis dans une PON,\ + \ un protocole, un pipeline ou un flux de travail. Fournissez le nom et le num\xE9\ + ro de version du protocole, ou un lien GitHub vers un pipeline ou un flux de\ + \ travail." examples: - value: https://github.com/phac-nml/ncov2019-artic-nf - lineage/clade name: - name: lineage/clade name - title: nom du lineage/clade - description: "Le nom de la lign\xE9e ou du clade." + lineage_clade_name: + name: lineage_clade_name + title: "Nom de la lign\xE9e ou du clade" + description: "Nom de la lign\xE9e ou du clade" slot_group: "Informations sur les lign\xE9es et les variantes" - comments: "Fournissez le nom de la lign\xE9e/clade Pangolin ou Nextstrain." + comments: "Fournissez le nom de la lign\xE9e ou du clade Pangolin ou Nextstrain." examples: - value: B.1.1.7 - lineage/clade analysis software name: - name: lineage/clade analysis software name - title: "nom du logiciel d'analyse de lin\xE9age/clade" - description: "Le nom du logiciel utilis\xE9 pour d\xE9terminer la lign\xE9e/clade." + lineage_clade_analysis_software_name: + name: lineage_clade_analysis_software_name + title: "Nom du logiciel d\u2019analyse de la lign\xE9e ou du clade" + description: "Nom du logiciel utilis\xE9 pour d\xE9terminer la lign\xE9e ou le\ + \ clade" slot_group: "Informations sur les lign\xE9es et les variantes" comments: "Fournissez le nom du logiciel utilis\xE9 pour d\xE9terminer la lign\xE9\ - e/clade." + e ou le clade." examples: - value: Pangolin - lineage/clade analysis software version: - name: lineage/clade analysis software version - title: "version du logiciel d'analyse de lin\xE9age/clade" - description: "La version du logiciel utilis\xE9 pour d\xE9terminer la lign\xE9\ - e/clade." + lineage_clade_analysis_software_version: + name: lineage_clade_analysis_software_version + title: "Version du logiciel d\u2019analyse de la lign\xE9e ou du clade" + description: "Version du logiciel utilis\xE9 pour d\xE9terminer la lign\xE9e ou\ + \ le clade" slot_group: "Informations sur les lign\xE9es et les variantes" comments: "Fournissez la version du logiciel utilis\xE9 pour d\xE9terminer la\ - \ lign\xE9e/clade." + \ lign\xE9e ou le clade." examples: - value: 2.1.10 - variant designation: - name: variant designation - title: "d\xE9signation de la variante" - description: "La classification des variantes de la lign\xE9e/clade, c'est-\xE0\ - -dire variante, variante pr\xE9occupante." + variant_designation: + name: variant_designation + title: "D\xE9signation du variant" + description: "Classification des variants de la lign\xE9e ou du clade (c.-\xE0\ + -d. le variant, le variant pr\xE9occupant)" slot_group: "Informations sur les lign\xE9es et les variantes" - comments: "Si la lign\xE9e/clade est consid\xE9r\xE9e comme une variante pr\xE9\ - occupante, s\xE9lectionnez Variante pr\xE9occupante dans la liste de s\xE9lection.\ - \ Si la lign\xE9e/clade contient des mutations pr\xE9occupantes (mutations qui\ - \ augmentent la transmission, la gravit\xE9 clinique ou d\u2019autres facteurs\ - \ \xE9pid\xE9miologiques) mais qu\u2019il ne s\u2019agit pas d\u2019une variante\ - \ pr\xE9occupante globale, s\xE9lectionnez Variante. Si la lign\xE9e/clade ne\ - \ contient pas de mutations pr\xE9occupantes, laissez ce champ vide." - examples: - - value: "Variante pr\xE9occupante (VOC)" - variant evidence: - name: variant evidence - title: preuve de la variante - description: "Preuve utilis\xE9e pour d\xE9terminer la variante." + comments: "Si la lign\xE9e ou le clade est consid\xE9r\xE9 comme \xE9tant un variant\ + \ pr\xE9occupant, s\xE9lectionnez l\u2019option connexe \xE0 partir de la liste\ + \ de s\xE9lection. Si la lign\xE9e ou le clade contient des mutations pr\xE9\ + occupantes (mutations qui augmentent la transmission, la gravit\xE9 clinique\ + \ ou d\u2019autres facteurs \xE9pid\xE9miologiques), mais qu\u2019il ne s\u2019\ + agit pas d\u2019un variant pr\xE9occupant global, s\xE9lectionnez \xAB\_Variante\_\ + \xBB. Si la lign\xE9e ou le clade ne contient pas de mutations pr\xE9occupantes,\ + \ laissez ce champ vide." + examples: + - value: "Variant pr\xE9occupant" + variant_evidence: + name: variant_evidence + title: "Donn\xE9es probantes du variant" + description: "Donn\xE9es probantes utilis\xE9es pour d\xE9terminer le variant" slot_group: "Informations sur les lign\xE9es et les variantes" - comments: "S\xE9lectionnez si l\u2019\xE9chantillon a \xE9t\xE9 d\xE9pist\xE9\ - \ \xE0 l\u2019aide de RT-qPCR ou par s\xE9quen\xE7age dans la liste de s\xE9\ - lection." + comments: "Indiquez si l\u2019\xE9chantillon a fait l\u2019objet d\u2019un d\xE9\ + pistage RT-qPCR ou par s\xE9quen\xE7age \xE0 partir de la liste de s\xE9lection." examples: - value: RT-qPCR - variant evidence details: - name: variant evidence details - title: "d\xE9tails de la preuve de la variante" - description: "D\xE9tails sur les preuves utilis\xE9es pour d\xE9terminer la variante." + variant_evidence_details: + name: variant_evidence_details + title: "D\xE9tails li\xE9s aux donn\xE9es probantes du variant" + description: "D\xE9tails sur les donn\xE9es probantes utilis\xE9es pour d\xE9\ + terminer le variant" slot_group: "Informations sur les lign\xE9es et les variantes" - comments: "Fournissez le test et r\xE9pertoriez l\u2019ensemble des mutations\ - \ d\xE9finissant la lign\xE9e utilis\xE9es pour effectuer la d\xE9termination\ - \ des variantes. Si des mutations int\xE9ressantes/pr\xE9occupantes ont \xE9\ - t\xE9 observ\xE9es en plus des mutations d\xE9finissant la lign\xE9e, d\xE9\ - crivez-les ici." + comments: "Fournissez l\u2019essai biologique et r\xE9pertoriez l\u2019ensemble\ + \ des mutations d\xE9finissant la lign\xE9e qui sont utilis\xE9es pour effectuer\ + \ la d\xE9termination des variants. Si des mutations d\u2019int\xE9r\xEAt ou\ + \ de pr\xE9occupation ont \xE9t\xE9 observ\xE9es en plus des mutations d\xE9\ + finissant la lign\xE9e, d\xE9crivez-les ici." examples: - - value: "Mutations d\xE9finissant la lign\xE9e: ORF1ab (K1655N), Spike (K417N,\ + - value: "Mutations d\xE9finissant la lign\xE9e\_: ORF1ab (K1655N), Spike (K417N,\ \ E484K, N501Y, D614G, A701V), N (T205I), E (P71L)." - gene name 1: - name: gene name 1 - title: "nom du g\xE8ne 1" - description: "Le nom du g\xE8ne utilis\xE9 dans le test diagnostique RT-PCR." + gene_name_1: + name: gene_name_1 + title: "Nom du g\xE8ne\_1" + description: "Nom du g\xE8ne utilis\xE9 dans le test diagnostique RT-PCR" slot_group: "Tests de diagnostic des agents pathog\xE8nes" - comments: "S\xE9lectionnez un g\xE8ne dans la liste de s\xE9lection. Si le g\xE8\ - ne qui vous int\xE9resse ne figure pas dans la liste, indiquez le nom complet\ - \ du g\xE8ne ou le symbole du g\xE8ne (forme abr\xE9g\xE9e du nom du g\xE8ne).\ - \ Les noms et symboles de g\xE8nes standardis\xE9s peuvent \xEAtre trouv\xE9\ - s dans Gene Ontology en utilisant ce service de recherche\_: https://bit.ly/2Sq1LbI" - examples: - - value: E gene (orf4) - diagnostic pcr protocol 1: - name: diagnostic pcr protocol 1 - title: protocole de diagnostic pcr 1 - description: "Le nom et le num\xE9ro de version du protocole utilis\xE9 pour l\u2019\ - amplification des marqueurs de diagnostic." + comments: "Indiquez le nom complet du g\xE8ne soumis au d\xE9pistage. Le symbole\ + \ du g\xE8ne (forme abr\xE9g\xE9e du nom du g\xE8ne) peut \xE9galement \xEA\ + tre fourni. Il est possible de trouver les noms et les symboles de g\xE8nes\ + \ normalis\xE9s dans Gene Ontology en utilisant ce service de recherche\_: https://bit.ly/2Sq1LbI." + examples: + - value: "G\xE8ne\_E (orf4)" + diagnostic_pcr_protocol_1: + name: diagnostic_pcr_protocol_1 + title: "Protocole de diagnostic de polym\xE9rase en cha\xEEne\_1" + description: "Nom et num\xE9ro de version du protocole utilis\xE9 pour l\u2019\ + amplification des marqueurs diagnostiques" slot_group: "Tests de diagnostic des agents pathog\xE8nes" comments: "Le nom et le num\xE9ro de version du protocole utilis\xE9 pour r\xE9\ - aliser un test PCR diagnostique. Ces informations peuvent \xEAtre compar\xE9\ - es aux donn\xE9es de s\xE9quence pour l\u2019\xE9valuation des performances\ - \ et le contr\xF4le qualit\xE9." + aliser un test diagnostique bas\xE9 sur la r\xE9action en cha\xEEne de la polym\xE9\ + rase. Ces renseignements peuvent \xEAtre compar\xE9s aux donn\xE9es de s\xE9\ + quence pour l\u2019\xE9valuation du rendement et le contr\xF4le de la qualit\xE9\ + ." examples: - value: EGenePCRTest 2 - diagnostic pcr Ct value 1: - name: diagnostic pcr Ct value 1 - title: diagnostic pcr Ct value 1 - description: "La valeur du seuil de cycle (Ct) r\xE9sulte d\u2019un test de diagnostic\ - \ RT-PCR du SARS-CoV-2." + diagnostic_pcr_ct_value_1: + name: diagnostic_pcr_ct_value_1 + title: "Valeur de diagnostic de polym\xE9rase en cha\xEEne\_1" + description: "Valeur Ct obtenue \xE0 la suite d\u2019un test de diagnostic RT-PCR\ + \ du SRAS-CoV-2" slot_group: "Tests de diagnostic des agents pathog\xE8nes" - comments: "Fournissez la valeur du seuil de cycle (Ct) de l\u2019\xE9chantillon\ - \ issu du test de diagnostic RT-PCR." + comments: "Fournissez la valeur Ct de l\u2019\xE9chantillon issu du test diagnostique\ + \ RT-PCR." examples: - value: '21' - gene name 2: - name: gene name 2 - title: "nom du g\xE8ne 2" - description: "Le nom du g\xE8ne utilis\xE9 dans le test diagnostique RT-PCR." + gene_name_2: + name: gene_name_2 + title: "Nom du g\xE8ne\_2" + description: "Nom du g\xE8ne utilis\xE9 dans le test diagnostique RT-PCR" slot_group: "Tests de diagnostic des agents pathog\xE8nes" - comments: "S\xE9lectionnez un g\xE8ne dans la liste de s\xE9lection. Si le g\xE8\ - ne qui vous int\xE9resse ne figure pas dans la liste, indiquez le nom complet\ - \ du g\xE8ne ou le symbole du g\xE8ne (forme abr\xE9g\xE9e du nom du g\xE8ne).\ - \ Les noms et symboles de g\xE8nes standardis\xE9s peuvent \xEAtre trouv\xE9\ - s dans Gene Ontology en utilisant ce service de recherche\_: https://bit.ly/2Sq1LbI" - examples: - - value: RdRp gene (nsp12) - diagnostic pcr protocol 2: - name: diagnostic pcr protocol 2 - title: protocole de diagnostic pcr 2 - description: "Le nom et le num\xE9ro de version du protocole utilis\xE9 pour l\u2019\ - amplification des marqueurs de diagnostic." + comments: "Indiquez le nom complet d\u2019un autre g\xE8ne utilis\xE9 dans le\ + \ test\_RT-PCR. Le symbole du g\xE8ne (forme abr\xE9g\xE9e du nom du g\xE8ne)\ + \ peut \xE9galement \xEAtre fourni. Il est possible de trouver les noms et les\ + \ symboles de g\xE8nes normalis\xE9s dans Gene Ontology en utilisant ce service\ + \ de recherche\_: https://bit.ly/2Sq1LbI." + examples: + - value: "G\xE8ne RdRp (nsp12)" + diagnostic_pcr_protocol_2: + name: diagnostic_pcr_protocol_2 + title: "Protocole de diagnostic de polym\xE9rase en cha\xEEne\_2" + description: "Nom et num\xE9ro de version du protocole utilis\xE9 pour l\u2019\ + amplification des marqueurs diagnostiques" slot_group: "Tests de diagnostic des agents pathog\xE8nes" comments: "Le nom et le num\xE9ro de version du protocole utilis\xE9 pour r\xE9\ - aliser un deuxi\xE8me test de diagnostic PCR. Ces informations peuvent \xEA\ - tre compar\xE9es aux donn\xE9es de s\xE9quence pour l\u2019\xE9valuation des\ - \ performances et le contr\xF4le qualit\xE9." + aliser un deuxi\xE8me test diagnostique bas\xE9 sur la r\xE9action en cha\xEE\ + ne de la polym\xE9rase. Ces renseignements peuvent \xEAtre compar\xE9s aux donn\xE9\ + es de s\xE9quence pour l\u2019\xE9valuation du rendement et le contr\xF4le de\ + \ la qualit\xE9." examples: - value: RdRpGenePCRTest 3 - diagnostic pcr Ct value 2: - name: diagnostic pcr Ct value 2 - title: diagnostic pcr Ct value 2 - description: "La valeur du seuil de cycle (Ct) r\xE9sulte d\u2019un test de diagnostic\ - \ RT-PCR du SARS-CoV-2." + diagnostic_pcr_ct_value_2: + name: diagnostic_pcr_ct_value_2 + title: "Valeur de diagnostic de polym\xE9rase en cha\xEEne\_2" + description: "Valeur Ct obtenue \xE0 la suite d\u2019un test de diagnostic RT-PCR\ + \ du SRAS-CoV-2" slot_group: "Tests de diagnostic des agents pathog\xE8nes" - comments: "Fournissez la valeur du seuil de cycle (Ct) de l\u2019\xE9chantillon\ - \ issu du deuxi\xE8me test de diagnostic RT-PCR." + comments: "Fournissez la valeur Ct du deuxi\xE8me \xE9chantillon issu du deuxi\xE8\ + me test diagnostique RT-PCR." examples: - value: '36' - gene name 3: - name: gene name 3 - title: "nom du g\xE8ne 3" - description: "Le nom du g\xE8ne utilis\xE9 dans le test diagnostique RT-PCR." + gene_name_3: + name: gene_name_3 + title: "Nom du g\xE8ne\_3" + description: "Nom du g\xE8ne utilis\xE9 dans le test diagnostique RT-PCR" slot_group: "Tests de diagnostic des agents pathog\xE8nes" - comments: "Fournissez le nom complet d\u2019un autre g\xE8ne utilis\xE9 dans un\ - \ test RT-PCR. Le symbole du g\xE8ne (forme abr\xE9g\xE9e du nom du g\xE8ne)\ - \ peut \xE9galement \xEAtre fourni. Les noms et symboles de g\xE8nes standardis\xE9\ - s peuvent \xEAtre trouv\xE9s dans Gene Ontology en utilisant ce service de recherche\_\ - : https://bit.ly/2Sq1LbI" - examples: - - value: RdRp gene (nsp12) - diagnostic pcr protocol 3: - name: diagnostic pcr protocol 3 - title: protocole de diagnostic pcr 3 - description: "Le nom et le num\xE9ro de version du protocole utilis\xE9 pour l\u2019\ - amplification des marqueurs de diagnostic." + comments: "Indiquez le nom complet d\u2019un autre g\xE8ne utilis\xE9 dans le\ + \ test\_RT-PCR. Le symbole du g\xE8ne (forme abr\xE9g\xE9e du nom du g\xE8ne)\ + \ peut \xE9galement \xEAtre fourni. Il est possible de trouver les noms et les\ + \ symboles de g\xE8nes normalis\xE9s dans Gene Ontology en utilisant ce service\ + \ de recherche\_: https://bit.ly/2Sq1LbI." + examples: + - value: "G\xE8ne RdRp (nsp12)" + diagnostic_pcr_protocol_3: + name: diagnostic_pcr_protocol_3 + title: "Protocole de diagnostic de polym\xE9rase en cha\xEEne\_3" + description: "Nom et num\xE9ro de version du protocole utilis\xE9 pour l\u2019\ + amplification des marqueurs diagnostiques" slot_group: "Tests de diagnostic des agents pathog\xE8nes" comments: "Le nom et le num\xE9ro de version du protocole utilis\xE9 pour r\xE9\ - aliser un deuxi\xE8me test de diagnostic PCR. Ces informations peuvent \xEA\ - tre compar\xE9es aux donn\xE9es de s\xE9quence pour l\u2019\xE9valuation des\ - \ performances et le contr\xF4le qualit\xE9." + aliser un deuxi\xE8me test diagnostique bas\xE9 sur la r\xE9action en cha\xEE\ + ne de la polym\xE9rase. Ces renseignements peuvent \xEAtre compar\xE9s aux donn\xE9\ + es de s\xE9quence pour l\u2019\xE9valuation du rendement et le contr\xF4le de\ + \ la qualit\xE9." examples: - value: RdRpGenePCRTest 3 - diagnostic pcr Ct value 3: - name: diagnostic pcr Ct value 3 - title: diagnostic pcr Ct value 3 - description: "La valeur Ct r\xE9sulte d\u2019un test de diagnostic SARS-CoV-2\ - \ RT-PCR." + diagnostic_pcr_ct_value_3: + name: diagnostic_pcr_ct_value_3 + title: "Valeur de diagnostic de polym\xE9rase en cha\xEEne\_3" + description: "Valeur Ct obtenue \xE0 la suite d\u2019un test de diagnostic RT-PCR\ + \ du SRAS-CoV-2" slot_group: "Tests de diagnostic des agents pathog\xE8nes" - comments: "Fournissez la valeur CT de l\u2019\xE9chantillon du deuxi\xE8me test\ - \ de diagnostic RT-PCR." + comments: "Fournissez la valeur Ct du deuxi\xE8me \xE9chantillon issu du deuxi\xE8\ + me test diagnostique RT-PCR." examples: - value: '30' authors: name: authors - title: auteurs - description: "Noms des personnes contribuant aux processus de collecte d\u2019\ - \xE9chantillons, de g\xE9n\xE9ration de s\xE9quences, d\u2019analyse et de soumission\ - \ de donn\xE9es." + title: Auteurs + description: "Noms des personnes contribuant aux processus de pr\xE9l\xE8vement\ + \ d\u2019\xE9chantillons, de g\xE9n\xE9ration de s\xE9quences, d\u2019analyse\ + \ et de soumission de donn\xE9es" slot_group: Reconnaissance des contributeurs comments: "Incluez le pr\xE9nom et le nom de toutes les personnes qui doivent\ - \ \xEAtre attribu\xE9es, s\xE9par\xE9s par une virgule." + \ \xEAtre affect\xE9es, s\xE9par\xE9s par une virgule." examples: - - value: Tejinder Singh, Fei Hu, Joe Blogs - DataHarmonizer provenance: - name: DataHarmonizer provenance + - value: "Tejinder\_Singh, Fei\_Hu, Joe\_Blogs" + dataharmonizer_provenance: + name: dataharmonizer_provenance title: Provenance de DataHarmonizer description: "Provenance du logiciel DataHarmonizer et de la version du mod\xE8\ - le." + le" slot_group: Reconnaissance des contributeurs - comments: "Les informations actuelles sur la version du logiciel et du mod\xE8\ - le seront automatiquement g\xE9n\xE9r\xE9es dans ce champ une fois que l'utilisateur\ - \ aura utilis\xE9 la fonction \xAB valider \xBB. Ces informations seront g\xE9\ - n\xE9r\xE9es ind\xE9pendamment du fait que la ligne soit valide ou non." + comments: "Les renseignements actuels sur la version du logiciel et du mod\xE8\ + le seront automatiquement g\xE9n\xE9r\xE9s dans ce champ une fois que l\u2019\ + utilisateur aura utilis\xE9 la fonction \xAB Valider \xBB. Ces renseignements\ + \ seront g\xE9n\xE9r\xE9s ind\xE9pendamment du fait que la ligne soit valide\ + \ ou non." examples: - value: DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 enums: - umbrella bioproject accession menu: - name: umbrella bioproject accession menu + UmbrellaBioprojectAccessionMenu: + name: UmbrellaBioprojectAccessionMenu permissible_values: - PRJNA623807: - title: PRJNA623807 - title: "menu d'adh\xE9sion au bioprojet parapluie" - null value menu: - name: null value menu + day 1: + title: Jour 1 + day 8: + title: Jour 8 + day 10: + title: Jour 10 + title: "Menu \xAB\_Acc\xE8s au bioprojet cadre\_\xBB" + NullValueMenu: + name: NullValueMenu permissible_values: Not Applicable: - meaning: GENEPIO:0001619 - title: Non applicable + title: Sans objet Missing: - meaning: GENEPIO:0001618 - title: Manquant + title: Manquante Not Collected: - meaning: GENEPIO:0001620 - title: "Non collect\xE9" + title: "Non pr\xE9lev\xE9e" Not Provided: - meaning: GENEPIO:0001668 - title: Non fourni + title: Non fournie Restricted Access: - meaning: GENEPIO:0001810 title: "Acc\xE8s restreint" - title: menu de valeur nulle - geo_loc_name (state/province/territory) menu: - name: geo_loc_name (state/province/territory) menu + title: "Menu \xAB\_Valeur nulle\_\xBB" + GeoLocNameStateProvinceTerritoryMenu: + name: GeoLocNameStateProvinceTerritoryMenu permissible_values: - Alberta: - meaning: GAZ:00002566 - title: Alberta British Columbia: - meaning: GAZ:00002562 - title: Colombie Britannique - Manitoba: - meaning: GAZ:00002571 - title: Manitoba + title: Colombie-Britannique New Brunswick: - meaning: GAZ:00002570 title: Nouveau-Brunswick Newfoundland and Labrador: - meaning: GAZ:00002567 - title: Terre-Neuve et Labrador + title: Terre-Neuve-et-Labrador Northwest Territories: - meaning: GAZ:00002575 title: Territoires du Nord-Ouest Nova Scotia: - meaning: GAZ:00002565 title: "Nouvelle-\xC9cosse" - Nunavut: - meaning: GAZ:00002574 - title: Nunavut - Ontario: - meaning: GAZ:00002563 - title: Ontario (en anglais) Prince Edward Island: - meaning: GAZ:00002572 title: "\xCEle-du-Prince-\xC9douard" Quebec: - meaning: GAZ:00002569 title: "Qu\xE9bec" - Saskatchewan: - meaning: GAZ:00002564 - title: Saskatchewan - Yukon: - meaning: GAZ:00002576 - title: Yukon - title: "menu geo_loc_name (\xE9tat/province/territoire)" - host age unit menu: - name: host age unit menu + title: "Menu \xAB\_nom_lieu_g\xE9o (\xE9tat/province/territoire)\_\xBB" + HostAgeUnitMenu: + name: HostAgeUnitMenu permissible_values: month: - meaning: UO:0000035 - title: mois + title: Mois year: - meaning: UO:0000036 - title: "ann\xE9e" - title: "menu de l'unit\xE9 d'\xE2ge de l'h\xF4te" - sample collection date precision menu: - name: sample collection date precision menu + title: "Ann\xE9e" + title: "Menu \xAB\_Groupe d\u2019\xE2ge de l\u2019h\xF4te\_\xBB" + SampleCollectionDatePrecisionMenu: + name: SampleCollectionDatePrecisionMenu permissible_values: year: - meaning: UO:0000036 - title: "ann\xE9e" + title: "Ann\xE9e" month: - meaning: UO:0000035 - title: mois + title: Mois day: - meaning: UO:0000033 - title: jour - title: "menu de pr\xE9cision de la date de pr\xE9l\xE8vement des \xE9chantillons" - biomaterial extracted menu: - name: biomaterial extracted menu + title: Jour + title: "Menu \xAB\_Pr\xE9cision de la date de pr\xE9l\xE8vement des \xE9chantillons\_\ + \xBB" + BiomaterialExtractedMenu: + name: BiomaterialExtractedMenu permissible_values: RNA (total): - meaning: OBI:0000895 - title: RNA (total) + title: ARN (total) RNA (poly-A): - meaning: OBI:0000869 - title: RNA (poly-A) + title: ARN (poly-A) RNA (ribo-depleted): - meaning: OBI:0002627 - title: RNA (appauvri en ribo) + title: "ARN (d\xE9pl\xE9tion ribosomique)" mRNA (messenger RNA): - meaning: GENEPIO:0100104 - title: mRNA (messager RNA) + title: ARNm (ARN messager) mRNA (cDNA): - meaning: OBI:0002754 - title: mRNA (cDNA) - title: "menu extrait des biomat\xE9riaux" - signs and symptoms menu: - name: signs and symptoms menu + title: ARNm (ADNc) + title: "Menu \xAB\_Biomat\xE9riaux extraits\_\xBB" + SignsAndSymptomsMenu: + name: SignsAndSymptomsMenu permissible_values: Abnormal lung auscultation: - meaning: HP:0030829 title: Auscultation pulmonaire anormale Abnormality of taste sensation: - meaning: HP:0000223 title: Anomalie de la sensation gustative Ageusia (complete loss of taste): - meaning: HP:0041051 - is_a: Abnormality of taste sensation - title: "Ageusia (perte totale du go\xFBt)" + title: "Agueusie (perte totale du go\xFBt)" Parageusia (distorted sense of taste): - meaning: HP:0031249 - is_a: Abnormality of taste sensation - title: "Parageusie (d\xE9formation du go\xFBt)" + title: "Paragueusie (distorsion du go\xFBt)" Hypogeusia (reduced sense of taste): - meaning: HP:0000224 - is_a: Abnormality of taste sensation - title: "Hypogeusie (diminution du sens du go\xFBt)" + title: "Hypogueusie (diminution du go\xFBt)" Abnormality of the sense of smell: - meaning: HP:0004408 - title: Abnormality of the sense of smell + title: "Anomalie de l\u2019odorat" Anosmia (lost sense of smell): - meaning: HP:0000458 - is_a: Abnormality of the sense of smell - title: Anosmie (perte d'odorat) + title: "Anosmie (perte de l\u2019odorat)" Hyposmia (reduced sense of smell): - meaning: HP:0004409 - is_a: Abnormality of the sense of smell - title: Hyposmie (diminution de l'odorat) + title: "Hyposmie (diminution de l\u2019odorat)" Acute Respiratory Distress Syndrome: - meaning: HP:0033677 - exact_mappings: - - CNPHI:ARDS title: "Syndrome de d\xE9tresse respiratoire aigu\xEB" Altered mental status: - meaning: HP:0011446 - title: "Alt\xE9ration de l'\xE9tat mental" + title: "Alt\xE9ration de l\u2019\xE9tat mental" Cognitive impairment: - meaning: HP:0100543 - is_a: Altered mental status - title: Troubles cognitifs - Coma: - meaning: HP:0001259 - is_a: Altered mental status - title: Coma - Confusion: - meaning: HP:0001289 - is_a: Altered mental status - title: la confusion + title: "D\xE9ficit cognitif" Delirium (sudden severe confusion): - meaning: HP:0031258 - is_a: Confusion title: "D\xE9lire (confusion grave et soudaine)" Inability to arouse (inability to stay awake): - meaning: GENEPIO:0100061 - is_a: Altered mental status title: "Incapacit\xE9 \xE0 se r\xE9veiller (incapacit\xE9 \xE0 rester \xE9\ veill\xE9)" Irritability: - meaning: HP:0000737 - is_a: Altered mental status title: "Irritabilit\xE9" Loss of speech: - meaning: HP:0002371 - is_a: Altered mental status title: Perte de la parole Arrhythmia: - meaning: HP:0011675 title: Arythmie Asthenia (generalized weakness): - meaning: HP:0025406 title: "Asth\xE9nie (faiblesse g\xE9n\xE9ralis\xE9e)" Chest tightness or pressure: - meaning: HP:0031352 title: Oppression ou pression thoracique Rigors (fever shakes): - meaning: HP:0025145 - is_a: Chest tightness or pressure - title: "Rigidit\xE9 (tremblements de fi\xE8vre)" + title: "Frissons solennels (tremblements de fi\xE8vre)" Chills (sudden cold sensation): - meaning: HP:0025143 - exact_mappings: - - CNPHI:Chills title: Frissons (sensation soudaine de froid) Conjunctival injection: - meaning: HP:0030953 title: Injection conjonctivale Conjunctivitis (pink eye): - meaning: HP:0000509 - exact_mappings: - - CNPHI:Conjunctivitis - title: "Conjonctivite (\u0153il rose)" + title: Conjonctivite (yeux rouges) Coryza (rhinitis): - meaning: MP:0001867 title: Coryza (rhinite) Cough: - meaning: HP:0012735 title: Toux Nonproductive cough (dry cough): - meaning: HP:0031246 - is_a: Cough - title: "Toux non productive (toux s\xE8che)" + title: "Toux improductive (toux s\xE8che)" Productive cough (wet cough): - meaning: HP:0031245 - is_a: Cough title: Toux productive (toux grasse) Cyanosis (blueish skin discolouration): - meaning: HP:0000961 title: "Cyanose (coloration bleu\xE2tre de la peau)" Acrocyanosis: - meaning: HP:0001063 - is_a: Cyanosis (blueish skin discolouration) title: Acrocyanose Circumoral cyanosis (bluish around mouth): - meaning: HP:0032556 - is_a: Acrocyanosis - title: "Cyanose circulatoire (bleu\xE2tre autour de la bouche)" + title: "Cyanose p\xE9ribuccale (bleu\xE2tre autour de la bouche)" Cyanotic face (bluish face): - meaning: GENEPIO:0100062 - is_a: Acrocyanosis title: "Visage cyanos\xE9 (visage bleu\xE2tre)" Central Cyanosis: - meaning: GENEPIO:0100063 - is_a: Cyanosis (blueish skin discolouration) title: Cyanose centrale Cyanotic lips (bluish lips): - meaning: GENEPIO:0100064 - is_a: Central Cyanosis title: "L\xE8vres cyanos\xE9es (l\xE8vres bleut\xE9es)" Peripheral Cyanosis: - meaning: GENEPIO:0100065 - is_a: Cyanosis (blueish skin discolouration) title: "Cyanose p\xE9riph\xE9rique" Dyspnea (breathing difficulty): - meaning: HP:0002094 title: "Dyspn\xE9e (difficult\xE9 \xE0 respirer)" Diarrhea (watery stool): - meaning: HP:0002014 - exact_mappings: - - CNPHI:Diarrhea%2C%20watery - title: "Diarrh\xE9e (selles liquides)" + title: "Diarrh\xE9e (selles aqueuses)" Dry gangrene: - meaning: MP:0031127 title: "Gangr\xE8ne s\xE8che" Encephalitis (brain inflammation): - meaning: HP:0002383 - exact_mappings: - - CNPHI:Encephalitis title: "Enc\xE9phalite (inflammation du cerveau)" Encephalopathy: - meaning: HP:0001298 title: "Enc\xE9phalopathie" Fatigue (tiredness): - meaning: HP:0012378 - exact_mappings: - - CNPHI:Fatigue title: Fatigue Fever: - meaning: HP:0001945 title: "Fi\xE8vre" "Fever (>=38\xB0C)": - meaning: GENEPIO:0100066 - exact_mappings: - - CNPHI:Fever - is_a: Fever - title: "Fi\xE8vre (>=38\xB0C)" + title: "Fi\xE8vre (>= 38\_\xB0C)" Glossitis (inflammation of the tongue): - meaning: HP:0000206 - title: Glossiose (inflammation de la langue) + title: Glossite (inflammation de la langue) Ground Glass Opacities (GGO): - meaning: GENEPIO:0100067 - title: "Opacit\xE9s de verre d\xE9poli" + title: "Hyperdensit\xE9 en verre d\xE9poli" Headache: - meaning: HP:0002315 - title: "Maux de t\xEAte" + title: "Mal de t\xEAte" Hemoptysis (coughing up blood): - meaning: HP:0002105 - title: "H\xE9moptysie (toux de sang)" + title: "H\xE9moptysie (toux accompagn\xE9e de sang)" Hypocapnia: - meaning: HP:0012417 title: Hypocapnie Hypotension (low blood pressure): - meaning: HP:0002615 - title: "Hypotension (baisse de la tension art\xE9rielle)" + title: "Hypotension (tension art\xE9rielle basse)" Hypoxemia (low blood oxygen): - meaning: HP:0012418 - title: "Hypox\xE9mie (manque d'oxyg\xE8ne dans le sang)" + title: "Hypox\xE9mie (manque d\u2019oxyg\xE8ne dans le sang)" Silent hypoxemia: - meaning: GENEPIO:0100068 - is_a: Hypoxemia (low blood oxygen) title: "Hypox\xE9mie silencieuse" Internal hemorrhage (internal bleeding): - meaning: HP:0011029 - title: "H\xE9morragie interne (saignement interne)" + title: "H\xE9morragie interne" Loss of Fine Movements: - meaning: NCIT:C121416 title: Perte de mouvements fins Low appetite: - meaning: HP:0004396 - title: "Manque d'app\xE9tit" + title: "Perte d\u2019app\xE9tit" Malaise (general discomfort/unease): - meaning: HP:0033834 title: "Malaise (malaise g\xE9n\xE9ral)" Meningismus/nuchal rigidity: - meaning: HP:0031179 - title: "M\xE9ningisme/rigidit\xE9 nucale" + title: "M\xE9ningisme/Raideur de la nuque" Muscle weakness: - meaning: HP:0001324 title: Faiblesse musculaire Nasal obstruction (stuffy nose): - meaning: HP:0001742 title: "Obstruction nasale (nez bouch\xE9)" Nausea: - meaning: HP:0002018 title: "Naus\xE9es" Nose bleed: - meaning: HP:0000421 title: Saignement de nez Otitis: - meaning: GENEPIO:0100069 title: Otite Pain: - meaning: HP:0012531 title: Douleur Abdominal pain: - meaning: HP:0002027 - is_a: Pain title: Douleur abdominale Arthralgia (painful joints): - meaning: HP:0002829 - is_a: Pain title: Arthralgie (articulations douloureuses) Chest pain: - meaning: HP:0100749 - is_a: Pain title: Douleur thoracique Pleuritic chest pain: - meaning: HP:0033771 - is_a: Chest pain title: "Douleur thoracique pleur\xE9tique" Myalgia (muscle pain): - meaning: HP:0003326 - is_a: Pain title: Myalgie (douleur musculaire) Pharyngitis (sore throat): - meaning: HP:0025439 title: Pharyngite (mal de gorge) Pharyngeal exudate: - meaning: GENEPIO:0100070 title: "Exsudat pharyng\xE9" Pleural effusion: - meaning: HP:0002202 title: "\xC9panchement pleural" Pneumonia: - meaning: HP:0002090 title: Pneumonie Pseudo-chilblains: - meaning: HP:0033696 - title: Pseudo-chilblains + title: Pseudo-engelures Pseudo-chilblains on fingers (covid fingers): - meaning: GENEPIO:0100072 - is_a: Pseudo-chilblains - title: Pseudo-griffes des doigts (doigts covides) + title: Pseudo-engelures sur les doigts (doigts de la COVID) Pseudo-chilblains on toes (covid toes): - meaning: GENEPIO:0100073 - is_a: Pseudo-chilblains - title: Pseudo-chilblains sur les orteils (covid toes) + title: Pseudo-engelures sur les orteils (orteils de la COVID) Rash: - meaning: HP:0000988 title: "\xC9ruption cutan\xE9e" Rhinorrhea (runny nose): - meaning: HP:0031417 title: "Rhinorrh\xE9e (\xE9coulement nasal)" Seizure: - meaning: HP:0001250 - title: "Crise d'\xE9pilepsie" + title: "Crise d\u2019\xE9pilepsie" Motor seizure: - meaning: HP:0020219 - is_a: Seizure title: Crise motrice Shivering (involuntary muscle twitching): - meaning: HP:0025144 - title: Frissons (contractions musculaires involontaires) + title: Tremblement (contractions musculaires involontaires) Slurred speech: - meaning: HP:0001350 - title: "Troubles de l'\xE9locution" + title: "Troubles de l\u2019\xE9locution" Sneezing: - meaning: HP:0025095 - title: "\xC9ternuement" + title: "\xC9ternuements" Sputum Production: - meaning: HP:0033709 - title: Production d'expectorations + title: "Production d\u2019expectoration" Stroke: - meaning: HP:0001297 title: "Accident vasculaire c\xE9r\xE9bral" Swollen Lymph Nodes: - meaning: HP:0002716 - title: "Ganglions lymphatiques gonfl\xE9s" + title: "Ganglions lymphatiques enfl\xE9s" Tachypnea (accelerated respiratory rate): - meaning: HP:0002789 - title: "Tachypn\xE9e (acc\xE9l\xE9ration de la fr\xE9quence respiratoire)" + title: "Tachypn\xE9e (fr\xE9quence respiratoire acc\xE9l\xE9r\xE9e)" Vertigo (dizziness): - meaning: HP:0002321 title: "Vertige (\xE9tourdissement)" Vomiting (throwing up): - meaning: HP:0002013 - title: Vomissements (vomissements) - title: "menu des signes et sympt\xF4mes" - host vaccination status menu: - name: host vaccination status menu + title: Vomissements + title: "Menu \xAB\_Signes et sympt\xF4mes\_\xBB" + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu permissible_values: Fully Vaccinated: - meaning: GENEPIO:0100100 - title: "Vaccination compl\xE8te" + title: "Enti\xE8rement vaccin\xE9" Partially Vaccinated: - meaning: GENEPIO:0100101 title: "Partiellement vaccin\xE9" Not Vaccinated: - meaning: GENEPIO:0100102 title: "Non vaccin\xE9" - title: "menu du statut de vaccination de l'h\xF4te" - prior SARS-CoV-2 antiviral treatment menu: - name: prior SARS-CoV-2 antiviral treatment menu + title: "Menu \xAB\_Statut de vaccination de l\u2019h\xF4te\_\xBB" + PriorSarsCov2AntiviralTreatmentMenu: + name: PriorSarsCov2AntiviralTreatmentMenu permissible_values: Prior antiviral treatment: - meaning: GENEPIO:0100037 title: "Traitement antiviral ant\xE9rieur" No prior antiviral treatment: - meaning: GENEPIO:0100233 - title: "Pas de traitement antiviral ant\xE9rieur" - title: "menu de traitement antiviral ant\xE9rieur contre le SARS-CoV-2" - NML submitted specimen type menu: - name: NML submitted specimen type menu + title: "Aucun traitement antiviral ant\xE9rieur" + title: "Menu \xAB\_Traitement antiviral contre une infection ant\xE9rieure par\ + \ le SRAS-CoV-2\_\xBB" + NmlSubmittedSpecimenTypeMenu: + name: NmlSubmittedSpecimenTypeMenu permissible_values: Swab: - meaning: OBI:0002600 title: "\xC9couvillon" RNA: - meaning: OBI:0000880 - title: RNA + title: ARN mRNA (cDNA): - meaning: OBI:0002754 - title: mRNA (cDNA) + title: ARNm (ADNc) Nucleic acid: - meaning: OBI:0001010 title: "Acide nucl\xE9ique" Not Applicable: - meaning: GENEPIO:0001619 title: Sans objet - title: "Menu des types d'\xE9chantillons soumis au NML" - Related specimen relationship type menu: - name: Related specimen relationship type menu + title: "Menu \xAB\_Types d\u2019\xE9chantillons soumis au LNM\_\xBB" + RelatedSpecimenRelationshipTypeMenu: + name: RelatedSpecimenRelationshipTypeMenu permissible_values: Acute: - meaning: HP:0011009 title: "Infection aigu\xEB" Chronic (prolonged) infection investigation: - meaning: GENEPIO:0101016 - title: "Enqu\xEAte sur l'infection chronique (prolong\xE9e)" + title: "Enqu\xEAte sur l\u2019infection chronique (prolong\xE9e)" Convalescent: - title: Convalescent + title: Phase de convalescence Familial: - title: Familial + title: Forme familiale Follow-up: - meaning: EFO:0009642 title: Suivi Reinfection testing: - is_a: Follow-up title: "Tests de r\xE9infection" Previously Submitted: - title: "D\xE9j\xE0 soumis" + title: "Soumis pr\xE9c\xE9demment" Sequencing/bioinformatics methods development/validation: - title: "D\xE9veloppement/validation de m\xE9thodes de s\xE9quen\xE7age/bioinformatique" + title: "D\xE9veloppement et validation de m\xE9thodes bioinformatiques ou\ + \ de s\xE9quen\xE7age" Specimen sampling methods testing: - title: "Test des m\xE9thodes d'\xE9chantillonnage des \xE9chantillons" - title: "Menu des types de relations entre sp\xE9cimens associ\xE9s" - pre-existing conditions and risk factors menu: - name: pre-existing conditions and risk factors menu + title: "Essai des m\xE9thodes de pr\xE9l\xE8vement des \xE9chantillons" + title: "Menu \xAB\_Types de relations entre sp\xE9cimens associ\xE9s\_\xBB" + PreExistingConditionsAndRiskFactorsMenu: + name: PreExistingConditionsAndRiskFactorsMenu permissible_values: Age 60+: - meaning: VO:0004925 title: 60 ans et plus Anemia: - meaning: HP:0001903 title: "An\xE9mie" Anorexia: - meaning: HP:0002039 title: Anorexie Birthing labor: - meaning: NCIT:C92743 - title: Travail d'accouchement + title: Travail ou accouchement Bone marrow failure: - meaning: NCIT:C80693 - title: Insuffisance de la moelle osseuse - Cancer: - meaning: MONDO:0004992 - title: Cancer + title: "Insuffisance m\xE9dullaire" Breast cancer: - meaning: MONDO:0007254 - is_a: Cancer title: Cancer du sein Colorectal cancer: - meaning: MONDO:0005575 - is_a: Cancer title: Cancer colorectal Hematologic malignancy (cancer of the blood): - meaning: DOID:2531 - is_a: Cancer - title: "H\xE9mopathie maligne (cancer du sang)" + title: "H\xE9matopathie maligne (cancer du sang)" Lung cancer: - meaning: MONDO:0008903 - is_a: Cancer title: Cancer du poumon Metastatic disease: - meaning: MONDO:0024880 - is_a: Cancer title: "Maladie m\xE9tastatique" Cancer treatment: - meaning: NCIT:C16212 title: Traitement du cancer Cancer surgery: - meaning: NCIT:C157740 - is_a: Cancer treatment - title: Chirurgie du cancer + title: Chirurgie pour un cancer Chemotherapy: - meaning: NCIT:C15632 - is_a: Cancer treatment title: "Chimioth\xE9rapie" Adjuvant chemotherapy: - meaning: NCIT:C15360 - is_a: Chemotherapy title: "Chimioth\xE9rapie adjuvante" Cardiac disorder: - meaning: NCIT:C3079 - title: Troubles cardiaques + title: Trouble cardiaque Arrhythmia: - meaning: HP:0011675 - is_a: Cardiac disorder title: Arythmie Cardiac disease: - meaning: MONDO:0005267 - is_a: Cardiac disorder title: Maladie cardiaque Cardiomyopathy: - meaning: HP:0001638 - is_a: Cardiac disorder - title: Cardiomyopathie + title: Myocardiopathie Cardiac injury: - meaning: GENEPIO:0100074 - is_a: Cardiac disorder title: "L\xE9sion cardiaque" Hypertension (high blood pressure): - meaning: HP:0000822 - is_a: Cardiac disorder - title: "Hypertension (pression art\xE9rielle \xE9lev\xE9e)" + title: "Hypertension (tension art\xE9rielle \xE9lev\xE9e)" Hypotension (low blood pressure): - meaning: HP:0002615 - is_a: Cardiac disorder - title: "Hypotension (pression art\xE9rielle basse)" + title: "Hypotension (tension art\xE9rielle basse)" Cesarean section: - meaning: HP:0011410 title: "C\xE9sarienne" Chronic cough: - meaning: GENEPIO:0100075 title: Toux chronique Chronic gastrointestinal disease: - meaning: GENEPIO:0100076 title: Maladie gastro-intestinale chronique Chronic lung disease: - meaning: HP:0006528 - is_a: Lung disease title: Maladie pulmonaire chronique Corticosteroids: - meaning: NCIT:C211 title: "Corticost\xE9ro\xEFdes" Diabetes mellitus (diabetes): - meaning: HP:0000819 title: "Diab\xE8te sucr\xE9 (diab\xE8te)" Type I diabetes mellitus (T1D): - meaning: HP:0100651 - is_a: Diabetes mellitus (diabetes) - title: "Diab\xE8te de type I (T1D)" + title: "Diab\xE8te sucr\xE9 de type I" Type II diabetes mellitus (T2D): - meaning: HP:0005978 - is_a: Diabetes mellitus (diabetes) - title: "Diab\xE8te sucr\xE9 de type II (T2D)" + title: "Diab\xE8te sucr\xE9 de type II" Eczema: - meaning: HP:0000964 title: "Ecz\xE9ma" Electrolyte disturbance: - meaning: HP:0003111 - title: "Perturbation de l'\xE9quilibre \xE9lectrolytique" + title: "Perturbation de l\u2019\xE9quilibre \xE9lectrolytique" Hypocalcemia: - meaning: HP:0002901 - is_a: Electrolyte disturbance title: "Hypocalc\xE9mie" Hypokalemia: - meaning: HP:0002900 - is_a: Electrolyte disturbance title: "Hypokali\xE9mie" Hypomagnesemia: - meaning: HP:0002917 - is_a: Electrolyte disturbance title: "Hypomagn\xE9s\xE9mie" Encephalitis (brain inflammation): - meaning: HP:0002383 title: "Enc\xE9phalite (inflammation du cerveau)" Epilepsy: - meaning: MONDO:0005027 - title: Epilepsie + title: "\xC9pilepsie" Hemodialysis: - meaning: NCIT:C15248 title: "H\xE9modialyse" Hemoglobinopathy: - meaning: MONDO:0044348 title: "H\xE9moglobinopathie" Human immunodeficiency virus (HIV): - meaning: MONDO:0005109 - title: "Virus de l'immunod\xE9ficience humaine" + title: "Virus de l\u2019immunod\xE9ficience humaine (VIH)" Acquired immunodeficiency syndrome (AIDS): - meaning: MONDO:0012268 - is_a: Human immunodeficiency virus (HIV) - title: "Syndrome d'immunod\xE9ficience acquise" + title: "Syndrome d\u2019immunod\xE9ficience acquise (SIDA)" HIV and antiretroviral therapy (ART): - meaning: NCIT:C16118 - is_a: Human immunodeficiency virus (HIV) - title: "HIV et th\xE9rapie antir\xE9trovirale" + title: "VIH et traitement antir\xE9troviral" Immunocompromised: - meaning: NCIT:C14139 - title: "Immunod\xE9prim\xE9s" - Lupus: - meaning: MONDO:0004670 - is_a: Immunocompromised - title: Lupus + title: "Immunod\xE9ficience" Inflammatory bowel disease (IBD): - meaning: MONDO:0005265 - title: Maladie inflammatoire de l'intestin (MII) + title: "Maladie inflammatoire chronique de l\u2019intestin (MICI)" Colitis: - meaning: HP:0002583 - is_a: Inflammatory bowel disease (IBD) title: Colite Ulcerative colitis: - meaning: HP:0100279 - is_a: Colitis title: "Colite ulc\xE9reuse" Crohn's disease: - meaning: HP:0100280 - is_a: Inflammatory bowel disease (IBD) - title: la maladie de Crohn + title: Maladie de Crohn Renal disorder: - meaning: NCIT:C3149 title: "Trouble r\xE9nal" Renal disease: - meaning: MONDO:0005240 - is_a: Renal disorder title: "Maladie r\xE9nale" Chronic renal disease: - meaning: HP:0012622 - is_a: Renal disease title: "Maladie r\xE9nale chronique" Renal failure: - meaning: HP:0000083 - is_a: Renal disease title: "Insuffisance r\xE9nale" Liver disease: - meaning: MONDO:0005154 title: Maladie du foie Chronic liver disease: - meaning: NCIT:C113609 - is_a: Liver disease title: Maladie chronique du foie + Fatty liver disease (FLD): + title: "St\xE9atose h\xE9patique" Myalgia (muscle pain): - meaning: HP:0003326 title: Myalgie (douleur musculaire) Myalgic encephalomyelitis (chronic fatigue syndrome): - meaning: MONDO:0005404 title: "Enc\xE9phalomy\xE9lite myalgique (syndrome de fatigue chronique)" Neurological disorder: - meaning: MONDO:0005071 title: Trouble neurologique Neuromuscular disorder: - meaning: MONDO:0019056 - is_a: Neurological disorder title: Trouble neuromusculaire Obesity: - meaning: HP:0001513 - title: "L'ob\xE9sit\xE9" + title: "Ob\xE9sit\xE9" Severe obesity: - meaning: MONDO:0005139 - is_a: Obesity title: "Ob\xE9sit\xE9 s\xE9v\xE8re" Respiratory disorder: - meaning: MONDO:0005087 - title: Troubles respiratoires + title: Trouble respiratoire Asthma: - meaning: HP:0002099 - is_a: Respiratory disorder title: Asthme Chronic bronchitis: - meaning: HP:0004469 - is_a: Respiratory disorder title: Bronchite chronique Chronic obstructive pulmonary disease: - meaning: HP:0006510 - is_a: Respiratory disorder title: Maladie pulmonaire obstructive chronique Emphysema: - meaning: HP:0002097 - is_a: Respiratory disorder title: "Emphys\xE8me" Lung disease: - meaning: MONDO:0005275 - is_a: Respiratory disorder title: Maladie pulmonaire Pulmonary fibrosis: - meaning: HP:0002206 - is_a: Lung disease title: Fibrose pulmonaire Pneumonia: - meaning: HP:0002090 - is_a: Respiratory disorder title: Pneumonie Respiratory failure: - meaning: HP:0002878 - is_a: Respiratory disorder title: Insuffisance respiratoire Adult respiratory distress syndrome: - meaning: HP:0033677 - is_a: Respiratory failure - title: "Syndrome de d\xE9tresse respiratoire de l'adulte" + title: "Syndrome de d\xE9tresse respiratoire de l\u2019adulte" Newborn respiratory distress syndrome: - meaning: MONDO:0009971 - is_a: Respiratory failure title: "Syndrome de d\xE9tresse respiratoire du nouveau-n\xE9" Tuberculosis: - meaning: MONDO:0018076 - is_a: Respiratory disorder title: Tuberculose "Postpartum (\u22646 weeks)": - meaning: GENEPIO:0100077 - title: "Post-partum (\u22646 semaines)" + title: "Post-partum (\u22646\_semaines)" Pregnancy: - meaning: NCIT:C25742 title: Grossesse Rheumatic disease: - meaning: MONDO:0005554 title: Maladie rhumatismale Sickle cell disease: - meaning: MONDO:0011382 title: "Dr\xE9panocytose" Substance use: - meaning: NBO:0001845 - title: Consommation de substances psychoactives + title: Consommation de substances Alcohol abuse: - meaning: MONDO:0002046 - is_a: Substance use - title: Abus d'alcool + title: "Consommation abusive d\u2019alcool" Drug abuse: - meaning: GENEPIO:0100078 - is_a: Substance use - title: Abus de drogues + title: Consommation abusive de drogues Injection drug abuse: - meaning: GENEPIO:0100079 - is_a: Drug abuse - title: Abus de drogues injectables + title: Consommation abusive de drogues injectables Smoking: - meaning: NBO:0015005 - is_a: Substance use - title: Fumer + title: Tabagisme Vaping: - meaning: NCIT:C173621 - is_a: Substance use - title: Vapoter + title: Vapotage Tachypnea (accelerated respiratory rate): - meaning: HP:0002789 - title: "Tachypn\xE9e (acc\xE9l\xE9ration de la fr\xE9quence respiratoire)" + title: "Tachypn\xE9e (fr\xE9quence respiratoire acc\xE9l\xE9r\xE9e)" Transplant: - meaning: NCIT:C159659 title: Transplantation Hematopoietic stem cell transplant (bone marrow transplant): - meaning: NCIT:C131759 - is_a: Transplant - title: Transplantation cardiaque - Cardiac transplant: - meaning: GENEPIO:0100080 - is_a: Transplant title: "Greffe de cellules souches h\xE9matopo\xEF\xE9tiques (greffe de moelle\ \ osseuse)" + Cardiac transplant: + title: Transplantation cardiaque Kidney transplant: - meaning: NCIT:C157332 - is_a: Transplant title: Greffe de rein Liver transplant: - meaning: GENEPIO:0100081 - is_a: Transplant title: Greffe de foie - title: "Menu des conditions pr\xE9existantes et des facteurs de risque" - variant designation menu: - name: variant designation menu + title: "Menu \xAB\_Conditions pr\xE9existantes et des facteurs de risque\_\xBB" + VariantDesignationMenu: + name: VariantDesignationMenu permissible_values: Variant of Concern (VOC): - meaning: GENEPIO:0100082 - title: "Variante d'int\xE9r\xEAt (VOI)" + title: "Variant pr\xE9occupant" Variant of Interest (VOI): - meaning: GENEPIO:0100083 - title: "Variante pr\xE9occupante (VOC)" + title: "Variant d\u2019int\xE9r\xEAt" Variant Under Monitoring (VUM): - meaning: GENEPIO:0100279 - title: Variante sous surveillance (VUM) - title: "menu de d\xE9signation des variantes" - variant evidence menu: - name: variant evidence menu + title: Variante sous surveillance + title: "Menu \xAB\_D\xE9signation des variants\_\xBB" + VariantEvidenceMenu: + name: VariantEvidenceMenu permissible_values: - RT-qPCR: - meaning: CIDO:0000019 - title: RT-qPCR Sequencing: - meaning: CIDO:0000027 title: "S\xE9quen\xE7age" - title: menu de preuves variantes - complications menu: - name: complications menu + title: "Menu \xAB\_Preuves de variants\_\xBB" + ComplicationsMenu: + name: ComplicationsMenu permissible_values: Abnormal blood oxygen level: - meaning: HP:0500165 - title: "Taux d'oxyg\xE8ne anormal dans le sang" + title: "Taux anormal d\u2019oxyg\xE8ne dans le sang" Acute kidney injury: - meaning: HP:0001919 title: "L\xE9sions r\xE9nales aigu\xEBs" Acute lung injury: - meaning: MONDO:0015796 title: "L\xE9sions pulmonaires aigu\xEBs" Ventilation induced lung injury (VILI): - meaning: GENEPIO:0100092 - is_a: Acute lung injury - title: "L\xE9sions pulmonaires induites par la ventilation" + title: "L\xE9sions pulmonaires caus\xE9es par la ventilation" Acute respiratory failure: - meaning: MONDO:0001208 title: "Insuffisance respiratoire aigu\xEB" Arrhythmia (complication): - meaning: HP:0011675 title: Arythmie (complication) Tachycardia: - meaning: HP:0001649 - is_a: Arrhythmia (complication) title: Tachycardie Polymorphic ventricular tachycardia (VT): - meaning: HP:0031677 - is_a: Tachycardia title: Tachycardie ventriculaire polymorphe Tachyarrhythmia: - meaning: GENEPIO:0100084 - is_a: Tachycardia title: Tachyarythmie Cardiac injury: - meaning: GENEPIO:0100074 title: "L\xE9sions cardiaques" Cardiac arrest: - meaning: HP:0001695 title: "Arr\xEAt cardiaque" Cardiogenic shock: - meaning: HP:0030149 title: "Choc cardiog\xE9nique" Blood clot: - meaning: HP:0001977 - title: Caillot de sang + title: Caillot sanguin Arterial clot: - meaning: HP:0004420 - is_a: Blood clot title: "Caillot art\xE9riel" Deep vein thrombosis (DVT): - meaning: HP:0002625 - is_a: Blood clot title: Thrombose veineuse profonde Pulmonary embolism (PE): - meaning: HP:0002204 - is_a: Blood clot title: Embolie pulmonaire Cardiomyopathy: - meaning: HP:0001638 - title: Cardiomyopathie + title: Myocardiopathie Central nervous system invasion: - meaning: MONDO:0024619 title: "Envahissement du syst\xE8me nerveux central" Stroke (complication): - meaning: HP:0001297 title: "Accident vasculaire c\xE9r\xE9bral (complication)" Central Nervous System Vasculitis: - meaning: MONDO:0003346 - is_a: Stroke (complication) title: "Vascularite du syst\xE8me nerveux central" Acute ischemic stroke: - meaning: HP:0002140 - is_a: Stroke (complication) title: "Accident vasculaire c\xE9r\xE9bral isch\xE9mique aigu" - Coma: - meaning: HP:0001259 - title: Coma - Convulsions: - meaning: HP:0011097 - title: Les convulsions COVID-19 associated coagulopathy (CAC): - meaning: NCIT:C171562 - title: "COVID-19 coagulopathie associ\xE9e (CAC)" + title: "Coagulopathie associ\xE9e \xE0 la COVID-19 (CAC)" Cystic fibrosis: - meaning: MONDO:0009061 - title: Mucoviscidose + title: Fibrose kystique Cytokine release syndrome: - meaning: MONDO:0600008 title: "Syndrome de lib\xE9ration de cytokines" Disseminated intravascular coagulation (DIC): - meaning: MPATH:108 title: "Coagulation intravasculaire diss\xE9min\xE9e" Encephalopathy: - meaning: HP:0001298 title: "Enc\xE9phalopathie" Fulminant myocarditis: - meaning: GENEPIO:0100088 title: Myocardite fulminante "Guillain-Barr\xE9 syndrome": - meaning: MONDO:0016218 - title: "Guillain-Barr\xE9 syndrome" + title: "Syndrome de Guillain-Barr\xE9" Internal hemorrhage (complication; internal bleeding): - meaning: HP:0011029 - title: "H\xE9morragie interne (complication ; h\xE9morragie interne)" + title: "H\xE9morragie interne (complication)" Intracerebral haemorrhage: - meaning: MONDO:0013792 - is_a: Internal hemorrhage (complication; internal bleeding) title: "H\xE9morragie intrac\xE9r\xE9brale" Kawasaki disease: - meaning: MONDO:0012727 title: Maladie de Kawasaki Complete Kawasaki disease: - meaning: GENEPIO:0100089 - is_a: Kawasaki disease title: "Maladie de Kawasaki compl\xE8te" Incomplete Kawasaki disease: - meaning: GENEPIO:0100090 - is_a: Kawasaki disease title: "Maladie de Kawasaki incompl\xE8te" Liver dysfunction: - meaning: HP:0001410 - title: Dysfonctionnement du foie + title: "Trouble h\xE9patique" Acute liver injury: - meaning: GENEPIO:0100091 - is_a: Liver dysfunction title: "L\xE9sions h\xE9patiques aigu\xEBs" Long COVID-19: - meaning: MONDO:0100233 - title: Longue COVID-19 + title: COVID-19 longue Meningitis: - meaning: HP:0001287 title: "M\xE9ningite" - Migraine: - meaning: HP:0002076 - title: Migraine Miscarriage: - meaning: HP:0005268 title: Fausses couches Multisystem inflammatory syndrome in children (MIS-C): - meaning: MONDO:0100163 - title: "Syndrome inflammatoire multisyst\xE9mique de l'enfant" + title: "Syndrome inflammatoire multisyst\xE9mique chez les enfants" Multisystem inflammatory syndrome in adults (MIS-A): - meaning: MONDO:0100319 - title: "Syndrome inflammatoire multisyst\xE9mique chez l'adulte" + title: "Syndrome inflammatoire multisyst\xE9mique chez les adultes" Muscle injury: - meaning: GENEPIO:0100093 title: "L\xE9sion musculaire" Myalgic encephalomyelitis (ME): - meaning: MONDO:0005404 - title: "Enc\xE9phalomy\xE9lite myalgique (syndrome de fatigue chronique)" + title: "Enc\xE9phalomy\xE9lite myalgique (EM)" Myocardial infarction (heart attack): - meaning: MONDO:0005068 title: Infarctus du myocarde (crise cardiaque) Acute myocardial infarction: - meaning: MONDO:0004781 - is_a: Myocardial infarction (heart attack) title: Infarctus aigu du myocarde ST-segment elevation myocardial infarction: - meaning: MONDO:0041656 - is_a: Myocardial infarction (heart attack) title: "Infarctus du myocarde avec sus-d\xE9calage du segment ST" Myocardial injury: - meaning: HP:0001700 title: "L\xE9sions du myocarde" Neonatal complications: - meaning: NCIT:C168498 title: "Complications n\xE9onatales" Noncardiogenic pulmonary edema: - meaning: GENEPIO:0100085 title: "\u0152d\xE8me pulmonaire non cardiog\xE9nique" Acute respiratory distress syndrome (ARDS): - meaning: HP:0033677 - is_a: Noncardiogenic pulmonary edema - title: "Syndrome de d\xE9tresse respiratoire aigu\xEB" + title: "Syndrome de d\xE9tresse respiratoire aigu\xEB (SDRA)" COVID-19 associated ARDS (CARDS): - meaning: NCIT:C171551 - is_a: Acute respiratory distress syndrome (ARDS) - title: "ARDS associ\xE9 au COVID-19 (CARDS)" + title: "SDRA associ\xE9 \xE0 la COVID-19 (SDRAC)" Neurogenic pulmonary edema (NPE): - meaning: GENEPIO:0100086 - is_a: Acute respiratory distress syndrome (ARDS) title: "\u0152d\xE8me pulmonaire neurog\xE8ne" Organ failure: - meaning: GENEPIO:0100094 - title: Insuffisance organique + title: "D\xE9faillance des organes" Heart failure: - meaning: HP:0001635 - is_a: Organ failure title: Insuffisance cardiaque Liver failure: - meaning: MONDO:0100192 - is_a: Organ failure title: "Insuffisance h\xE9patique" Paralysis: - meaning: HP:0003470 title: Paralysie Pneumothorax (collapsed lung): - meaning: HP:0002107 title: Pneumothorax (affaissement du poumon) Spontaneous pneumothorax: - meaning: HP:0002108 - is_a: Pneumothorax (collapsed lung) title: "Pneumothorax spontan\xE9" Spontaneous tension pneumothorax: - meaning: MONDO:0002075 - is_a: Pneumothorax (collapsed lung) title: "Pneumothorax spontan\xE9 sous tension" Pneumonia (complication): - meaning: HP:0002090 title: Pneumonie (complication) COVID-19 pneumonia: - meaning: NCIT:C171550 - is_a: Pneumonia (complication) - title: Pneumonie COVID-19 + title: "Pneumonie li\xE9e \xE0 la COVID-19" Pregancy complications: - meaning: HP:0001197 title: Complications de la grossesse Rhabdomyolysis: - meaning: HP:0003201 title: Rhabdomyolyse Secondary infection: - meaning: IDO:0000567 title: Infection secondaire Secondary staph infection: - meaning: GENEPIO:0100095 - is_a: Secondary infection - title: "Infection secondaire \xE0 staphylocoque" + title: Infection staphylococcique secondaire Secondary strep infection: - meaning: GENEPIO:0100096 - is_a: Secondary infection - title: "Infection secondaire \xE0 streptocoques" + title: Infection streptococcique secondaire Seizure (complication): - meaning: HP:0001250 - title: "Crise d'\xE9pilepsie (complication)" + title: "Crise d\u2019\xE9pilepsie (complication)" Motor seizure: - meaning: HP:0020219 - is_a: Seizure (complication) title: Crise motrice Sepsis/Septicemia: - meaning: HP:0100806 - title: "Sepsis/Septic\xE9mie" + title: "Sepsie/Septic\xE9mie" Sepsis: - meaning: IDO:0000636 - is_a: Sepsis/Septicemia - title: "Septic\xE9mie (r\xE9action inflammatoire syst\xE9mique \xE0 une infection)" + title: Sepsie Septicemia: - meaning: NCIT:C3364 - is_a: Sepsis/Septicemia - title: "Septic\xE9mie (infection du sang)" + title: "Septic\xE9mie" Shock: - meaning: HP:0031273 title: Choc Hyperinflammatory shock: - meaning: GENEPIO:0100097 - is_a: Shock title: Choc hyperinflammatoire Refractory cardiogenic shock: - meaning: GENEPIO:0100098 - is_a: Shock title: "Choc cardiog\xE9nique r\xE9fractaire" Refractory cardiogenic plus vasoplegic shock: - meaning: GENEPIO:0100099 - is_a: Shock title: "Choc cardiog\xE9nique et vasopl\xE9gique r\xE9fractaire" Septic shock: - meaning: NCIT:C35018 - is_a: Shock title: Choc septique Vasculitis: - meaning: HP:0002633 title: Vascularite - title: menu des complications - vaccine name menu: - name: vaccine name menu + title: "Menu \xAB\_Complications\_\xBB" + VaccineNameMenu: + name: VaccineNameMenu permissible_values: Astrazeneca (Vaxzevria): - meaning: GENEPIO:0100308 - title: Astrazeneca (Vaxzevria) - Johnson & Johnson (Janssen): - meaning: GENEPIO:0100307 - title: Johnson & Johnson (Janssen) - Moderna (Spikevax): - meaning: GENEPIO:0100304 - title: Moderna (Spikevax) - Pfizer-BioNTech (Comirnaty): - meaning: GENEPIO:0100305 - title: Pfizer-BioNTech (Comirnaty) + title: AstraZeneca (Vaxzevria) Pfizer-BioNTech (Comirnaty Pediatric): - meaning: GENEPIO:0100306 - title: "Pfizer-BioNTech (Comirnaty P\xE9diatrique)" - title: menu nom du vaccin - anatomical material menu: - name: anatomical material menu + title: "Pfizer-BioNTech (Comirnaty, formule p\xE9diatrique)" + title: "Menu \xAB\_Noms de vaccins\_\xBB" + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu permissible_values: Blood: - meaning: UBERON:0000178 title: Sang Fluid: - meaning: UBERON:0006314 - title: Fluide + title: Liquide Saliva: - meaning: UBERON:0001836 - is_a: Fluid title: Salive Fluid (cerebrospinal (CSF)): - meaning: UBERON:0001359 - is_a: Fluid - title: "Fluide (c\xE9r\xE9brospinal (CSF))" + title: "Liquide (c\xE9phalorachidien)" Fluid (pericardial): - meaning: UBERON:0002409 - is_a: Fluid - title: "Fluide (p\xE9ricardique)" + title: "Liquide (p\xE9ricardique)" Fluid (pleural): - meaning: UBERON:0001087 - is_a: Fluid - title: Fluide (pleural) + title: Liquide (pleural) Fluid (vaginal): - meaning: UBERON:0036243 - is_a: Fluid - title: Fluides (vaginaux) + title: "S\xE9cr\xE9tions (vaginales)" Fluid (amniotic): - meaning: UBERON:0000173 - is_a: Fluid - title: Fluide (amniotique) + title: Liquide (amniotique) Tissue: - meaning: UBERON:0000479 title: Tissu - title: "menu de mat\xE9riel anatomique" - anatomical part menu: - name: anatomical part menu + title: "Menu \xAB\_Mati\xE8res anatomiques\_\xBB" + AnatomicalPartMenu: + name: AnatomicalPartMenu permissible_values: - Anus: - meaning: UBERON:0001245 - title: Anus Buccal mucosa: - meaning: UBERON:0006956 title: Muqueuse buccale Duodenum: - meaning: UBERON:0002114 title: "Duod\xE9num" Eye: - meaning: UBERON:0000970 - title: "L'\u0153il" + title: "\u0152il" Intestine: - meaning: UBERON:0000160 title: Intestin Lower respiratory tract: - meaning: UBERON:0001558 title: "Voies respiratoires inf\xE9rieures" Bronchus: - meaning: UBERON:0002185 - is_a: Lower respiratory tract title: Bronches Lung: - meaning: UBERON:0002048 - is_a: Lower respiratory tract title: Poumon - Bronchiole: - meaning: UBERON:0002186 - is_a: Lung - title: Bronchiole Alveolar sac: - meaning: UBERON:0002169 - is_a: Lung title: "Sac alv\xE9olaire" Pleural sac: - meaning: UBERON:0009778 - is_a: Lower respiratory tract title: Sac pleural Pleural cavity: - meaning: UBERON:0002402 - is_a: Pleural sac title: "Cavit\xE9 pleurale" Trachea: - meaning: UBERON:0003126 - is_a: Lower respiratory tract title: "Trach\xE9e" - Rectum: - meaning: UBERON:0001052 - title: Le rectum Skin: - meaning: UBERON:0001003 title: Peau Stomach: - meaning: UBERON:0000945 title: Estomac Upper respiratory tract: - meaning: UBERON:0001557 title: "Voies respiratoires sup\xE9rieures" Anterior Nares: - meaning: UBERON:2001427 - is_a: Upper respiratory tract title: "Narines ant\xE9rieures" Esophagus: - meaning: UBERON:0001043 - is_a: Upper respiratory tract title: "\u0152sophage" Ethmoid sinus: - meaning: UBERON:0002453 - is_a: Upper respiratory tract title: "Sinus ethmo\xEFdal" Nasal Cavity: - meaning: UBERON:0001707 - is_a: Upper respiratory tract title: "Cavit\xE9 nasale" Middle Nasal Turbinate: - meaning: UBERON:0005921 - is_a: Nasal Cavity - title: Turbine nasale moyenne + title: Cornet nasal moyen Inferior Nasal Turbinate: - meaning: UBERON:0005922 - is_a: Nasal Cavity - title: "Turbine nasale inf\xE9rieure" + title: "Cornet nasal inf\xE9rieur" Nasopharynx (NP): - meaning: UBERON:0001728 - is_a: Upper respiratory tract - title: Nasopharynx (NP) + title: Nasopharynx Oropharynx (OP): - meaning: UBERON:0001729 - is_a: Upper respiratory tract - title: Oropharynx (OP) + title: Oropharynx Pharynx (throat): - meaning: UBERON:0000341 - is_a: Upper respiratory tract - title: Le pharynx (gorge) - title: menu partie anatomique - body product menu: - name: body product menu + title: Pharynx (gorge) + title: "Menu \xAB\_Parties anatomiques\_\xBB" + BodyProductMenu: + name: BodyProductMenu permissible_values: Breast Milk: - meaning: UBERON:0001913 - title: Le lait maternel + title: Lait maternel Feces: - meaning: UBERON:0001988 title: Selles Fluid (seminal): - meaning: UBERON:0006530 - title: "Liquide (s\xE9minal)" - Mucus: - meaning: UBERON:0000912 - title: Mucus + title: Sperme Sputum: - meaning: UBERON:0007311 - is_a: Mucus - title: Expectorations + title: Expectoration Sweat: - meaning: UBERON:0001089 title: Sueur Tear: - meaning: UBERON:0001827 title: Larme - Urine: - meaning: UBERON:0001088 - title: Urine - title: menu de produits pour le corps - prior SARS-CoV-2 infection menu: - name: prior SARS-CoV-2 infection menu + title: "Menu \xAB\_Produit corporel\_\xBB" + PriorSarsCov2InfectionMenu: + name: PriorSarsCov2InfectionMenu permissible_values: Prior infection: - meaning: GENEPIO:0100037 title: "Infection ant\xE9rieure" No prior infection: - meaning: GENEPIO:0100233 - title: "Pas d'infection ant\xE9rieure" - title: "menu d\u2019infection ant\xE9rieure par le SARS-CoV-2" - environmental material menu: - name: environmental material menu + title: "Aucune infection ant\xE9rieure" + title: "Menu \xAB\_Infection ant\xE9rieure par le SRAS-CoV-2\_\xBB" + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu permissible_values: Air vent: - meaning: ENVO:03501208 - title: Purgeur d'air + title: "\xC9vent d\u2019a\xE9ration" Banknote: - meaning: ENVO:00003896 - title: Billets de banque + title: Billet de banque Bed rail: - meaning: ENVO:03501209 - title: Barre de lit + title: "C\xF4t\xE9 de lit" Building floor: - meaning: ENVO:01000486 title: "Plancher du b\xE2timent" Cloth: - meaning: ENVO:02000058 title: Tissu Control panel: - meaning: ENVO:03501210 title: "Panneau de contr\xF4le" Door: - meaning: ENVO:03501220 title: Porte Door handle: - meaning: ENVO:03501211 title: "Poign\xE9e de porte" Face mask: - meaning: OBI:0002787 - title: Masque facial + title: Masque Face shield: - meaning: OBI:0002791 - title: Masque de protection + title: "\xC9cran facial" Food: - meaning: FOODON:00002403 title: Nourriture Food packaging: - meaning: FOODON:03490100 title: Emballages alimentaires Glass: - meaning: ENVO:01000481 title: Verre Handrail: - meaning: ENVO:03501212 - title: Balustrade + title: Main courante Hospital gown: - meaning: OBI:0002796 - title: "Robe d'h\xF4pital" + title: "Jaquette d\u2019h\xF4pital" Light switch: - meaning: ENVO:03501213 - title: "Interrupteur d'\xE9clairage" + title: Interrupteur Locker: - meaning: ENVO:03501214 title: Casier N95 mask: - meaning: OBI:0002790 title: Masque N95 Nurse call button: - meaning: ENVO:03501215 - title: "Bouton d'appel infirmi\xE8re" + title: "Bouton d\u2019appel de l\u2019infirmi\xE8re" Paper: - meaning: ENVO:03501256 title: Papier Particulate matter: - meaning: ENVO:01000060 - title: "Affaire particuli\xE8re" + title: "Mati\xE8re particulaire" Plastic: - meaning: ENVO:01000404 title: Plastique PPE gown: - meaning: GENEPIO:0100025 - title: Blouse EPI + title: Blouse (EPI) Sewage: - meaning: ENVO:00002018 title: "Eaux us\xE9es" Sink: - meaning: ENVO:01000990 - title: Evier + title: "\xC9vier" Soil: - meaning: ENVO:00001998 title: Sol Stainless steel: - meaning: ENVO:03501216 title: Acier inoxydable Tissue paper: - meaning: ENVO:03501217 - title: Papier de soie + title: Mouchoirs Toilet bowl: - meaning: ENVO:03501218 - title: Cuvette de toilette + title: Cuvette Water: - meaning: ENVO:00002006 title: Eau Wastewater: - meaning: ENVO:00002001 - is_a: Water title: "Eaux us\xE9es" Window: - meaning: ENVO:03501219 title: "Fen\xEAtre" Wood: - meaning: ENVO:00002040 title: Bois - title: "menu de mat\xE9riaux environnementaux" - environmental site menu: - name: environmental site menu + title: "Menu \xAB\_Mat\xE9riel environnemental\_\xBB" + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu permissible_values: Acute care facility: - meaning: ENVO:03501135 - title: "\xC9tablissement de soins aigus" + title: "\xC9tablissement de soins de courte dur\xE9e" Animal house: - meaning: ENVO:00003040 - title: Maison des animaux + title: Refuge pour animaux Bathroom: - meaning: ENVO:01000422 title: Salle de bain Clinical assessment centre: - meaning: ENVO:03501136 - title: "Centre d'\xE9valuation clinique" + title: "Centre d\u2019\xE9valuation clinique" Conference venue: - meaning: ENVO:03501127 - title: "Salle de conf\xE9rence" + title: "Lieu de la conf\xE9rence" Corridor: - meaning: ENVO:03501121 title: couloir Daycare: - meaning: ENVO:01000927 title: Garderie Emergency room (ER): - meaning: ENVO:03501145 - title: Salle d'urgence + title: "Salle d\u2019urgence" Family practice clinic: - meaning: ENVO:03501186 title: "Clinique de m\xE9decine familiale" Group home: - meaning: ENVO:03501196 title: Foyer de groupe Homeless shelter: - meaning: ENVO:03501133 - title: Foyer pour sans-abri + title: Refuge pour sans-abri Hospital: - meaning: ENVO:00002173 title: "H\xF4pital" Intensive Care Unit (ICU): - meaning: ENVO:03501152 title: "Unit\xE9 de soins intensifs" Long Term Care Facility: - meaning: ENVO:03501194 title: "\xC9tablissement de soins de longue dur\xE9e" Patient room: - meaning: ENVO:03501180 title: Chambre du patient - Prison: - meaning: ENVO:03501204 - title: Prison Production Facility: - meaning: ENVO:01000536 title: Installation de production School: - meaning: ENVO:03501130 title: "\xC9cole" Sewage Plant: - meaning: ENVO:00003043 - title: "Station d'\xE9puration" + title: "Usine d\u2019\xE9puration des eaux us\xE9es" Subway train: - meaning: ENVO:03501109 title: "M\xE9tro" University campus: - meaning: ENVO:00000467 - title: "Campus de l'universit\xE9" + title: "Campus de l\u2019universit\xE9" Wet market: - meaning: ENVO:03501198 - title: "March\xE9 de l'eau" - title: menu du site environnemental - collection method menu: - name: collection method menu + title: "March\xE9 traditionnel de produits frais" + title: "Menu \xAB\_Site environnemental\_\xBB" + CollectionMethodMenu: + name: CollectionMethodMenu permissible_values: Amniocentesis: - meaning: NCIT:C52009 title: "Amniocent\xE8se" - Aspiration: - meaning: NCIT:C15631 - title: Aspiration Suprapubic Aspiration: - meaning: GENEPIO:0100028 - is_a: Aspiration - title: Aspiration suprapubienne + title: Aspiration sus-pubienne Tracheal aspiration: - meaning: GENEPIO:0100029 - is_a: Aspiration title: "Aspiration trach\xE9ale" Vacuum Aspiration: - meaning: GENEPIO:0100030 - is_a: Aspiration title: Aspiration sous vide Biopsy: - meaning: OBI:0002650 title: Biopsie Needle Biopsy: - meaning: OBI:0002651 - is_a: Biopsy - title: "Biopsie \xE0 l'aiguille" - Filtration: - meaning: OBI:0302885 - title: Filtration + title: "Biopsie \xE0 l\u2019aiguille" Air filtration: - meaning: GENEPIO:0100031 - is_a: Filtration - title: Filtration de l'air - Lavage: - meaning: OBI:0600044 - title: "Lavage (lavage m\xE9dical)" + title: "Filtration de l\u2019air" Bronchoalveolar lavage (BAL): - meaning: GENEPIO:0100032 - is_a: Lavage title: "Lavage broncho-alv\xE9olaire (LBA)" Gastric Lavage: - meaning: GENEPIO:0100033 - is_a: Lavage title: Lavage gastrique Lumbar Puncture: - meaning: NCIT:C15327 title: Ponction lombaire Necropsy: - meaning: MMO:0000344 title: "N\xE9cropsie" Phlebotomy: - meaning: NCIT:C28221 title: "Phl\xE9botomie" Rinsing: - meaning: GENEPIO:0002116 - title: "Rin\xE7age (lavage)" + title: "Rin\xE7age" Saline gargle (mouth rinse and gargle): - meaning: GENEPIO:0100034 - is_a: Rinsing - title: "Gargarisme salin (rin\xE7age de la bouche et gargarisme)" + title: Gargarisme avec saline (rince-bouche) Scraping: - meaning: GENEPIO:0100035 - title: Raclage + title: Grattage Swabbing: - meaning: GENEPIO:0002117 title: "\xC9couvillonnage" Finger Prick: - meaning: GENEPIO:0100036 - title: "Piq\xFBre au doigt" + title: "Piq\xFBre du doigt" Washout Tear Collection: - meaning: GENEPIO:0100038 - title: Lavage Collecte de larmes - title: "menu m\xE9thode de collecte" - collection device menu: - name: collection device menu + title: "Lavage\_\u2013 Collecte de larmes" + title: "Menu \xAB\_M\xE9thode de pr\xE9l\xE8vement\_\xBB" + CollectionDeviceMenu: + name: CollectionDeviceMenu permissible_values: Air filter: - meaning: ENVO:00003968 title: "Filtre \xE0 air" Blood Collection Tube: - meaning: OBI:0002859 title: "Tube de pr\xE9l\xE8vement sanguin" - Bronchoscope: - meaning: OBI:0002826 - title: Bronchoscope Collection Container: - meaning: OBI:0002088 - title: "R\xE9cipient de collecte" + title: "R\xE9cipient \xE0 \xE9chantillons" Collection Cup: - meaning: GENEPIO:0100026 - title: Tasse de collection + title: "Godet \xE0 \xE9chantillons" Fibrobronchoscope Brush: - meaning: OBI:0002825 title: "Brosse \xE0 fibrobronchoscope" Filter: - meaning: GENEPIO:0100103 title: Filtre Fine Needle: - meaning: OBI:0002827 title: Aiguille fine Microcapillary tube: - meaning: OBI:0002858 - title: Tube microcapillaire - Micropipette: - meaning: OBI:0001128 - title: Micropipette + title: Micropipette de type capillaire Needle: - meaning: OBI:0000436 title: Aiguille Serum Collection Tube: - meaning: OBI:0002860 - title: "Tube de collection de s\xE9rum" + title: "Tube de pr\xE9l\xE8vement du s\xE9rum" Sputum Collection Tube: - meaning: OBI:0002861 title: "Tube de pr\xE9l\xE8vement des expectorations" Suction Catheter: - meaning: OBI:0002831 - title: "Cath\xE9ter d'aspiration" + title: "Cath\xE9ter d\u2019aspiration" Swab: - meaning: GENEPIO:0100027 title: "\xC9couvillon" Urine Collection Tube: - meaning: OBI:0002862 - title: "Tube de pr\xE9l\xE8vement d'urine" + title: "Tube de pr\xE9l\xE8vement d\u2019urine" Virus Transport Medium: - meaning: OBI:0002866 - title: Milieu de transport des virus - title: menu du dispositif de collecte - host (scientific name) menu: - name: host (scientific name) menu + title: Milieu de transport viral + title: "Menu \xAB\_Dispositif de pr\xE9l\xE8vement\_\xBB" + HostScientificNameMenu: + name: HostScientificNameMenu permissible_values: - Homo sapiens: - meaning: NCBITaxon:9606 - title: Homo sapiens Bos taurus: - meaning: NCBITaxon:9913 title: Bos taureau - Canis lupus familiaris: - meaning: NCBITaxon:9615 - title: Canis lupus familier Chiroptera: - meaning: NCBITaxon:9397 title: "Chiropt\xE8res" Columbidae: - meaning: NCBITaxon:8930 - title: "Colombid\xE9s" - Felis catus: - meaning: NCBITaxon:9685 - title: Felis catus - Gallus gallus: - meaning: NCBITaxon:9031 - title: Gallus gallus - Manis: - meaning: NCBITaxon:9973 - title: Manis - Manis javanica: - meaning: NCBITaxon:9974 - title: Homme javanais - Neovison vison: - meaning: NCBITaxon:452646 - title: Vison Neovison - Panthera leo: - meaning: NCBITaxon:9689 - title: Panthera lion - Panthera tigris: - meaning: NCBITaxon:9694 - title: Panthera tigris + title: "Columbid\xE9s" Rhinolophidae: - meaning: NCBITaxon:58055 title: "Rhinolophid\xE9s" - Rhinolophus affinis: - meaning: NCBITaxon:59477 - title: Rhinolophus affinis - Sus scrofa domesticus: - meaning: NCBITaxon:9825 - title: Sus scrofa domestique Viverridae: - meaning: NCBITaxon:9673 title: "Viverrid\xE9s" - title: "menu h\xF4te (nom scientifique)" - host (common name) menu: - name: host (common name) menu + title: "Menu \xAB\_H\xF4te (nom scientifique)\_\xBB" + HostCommonNameMenu: + name: HostCommonNameMenu permissible_values: Human: - meaning: NCBITaxon:9606 title: Humain Bat: - meaning: NCBITaxon:9397 - title: Chauve souris + title: Chauve-souris Cat: - meaning: NCBITaxon:9685 title: Chat Chicken: - meaning: NCBITaxon:9031 title: Poulet Civets: - meaning: NCBITaxon:9673 title: Civettes Cow: - meaning: NCBITaxon:9913 - exact_mappings: - - CNPHI:bovine title: Vache Dog: - meaning: NCBITaxon:9615 title: Chien - Lion: - meaning: NCBITaxon:9689 - title: Lion Mink: - meaning: NCBITaxon:452646 title: Vison - Pangolin: - meaning: NCBITaxon:9973 - title: Pangolin Pig: - meaning: NCBITaxon:9825 - exact_mappings: - - CNPHI:porcine title: Cochon - Pigeon: - meaning: NCBITaxon:8930 - title: Pigeon Tiger: - meaning: NCBITaxon:9694 title: Tigre - title: "menu h\xF4te (nom commun)" - host health state menu: - name: host health state menu + title: "Menu \xAB\_H\xF4te (nom commun)\_\xBB" + HostHealthStateMenu: + name: HostHealthStateMenu permissible_values: Asymptomatic: - meaning: NCIT:C3833 title: Asymptomatique Deceased: - meaning: NCIT:C28554 title: "D\xE9c\xE9d\xE9" Healthy: - meaning: NCIT:C115935 - title: "En bonne sant\xE9" + title: "En sant\xE9" Recovered: - meaning: NCIT:C49498 title: "R\xE9tabli" Symptomatic: - meaning: NCIT:C25269 title: Symptomatique - title: "menu de l'\xE9tat de sant\xE9 de l'h\xF4te" - host health status details menu: - name: host health status details menu + title: "Menu \xAB\_\xC9tat de sant\xE9 de l\u2019h\xF4te\_\xBB" + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu permissible_values: Hospitalized: - meaning: NCIT:C25179 title: "Hospitalis\xE9" Hospitalized (Non-ICU): - meaning: GENEPIO:0100045 - is_a: Hospitalized - title: "Hospitalis\xE9 (hors soins intensifs)" + title: "Hospitalis\xE9 (hors USI)" Hospitalized (ICU): - meaning: GENEPIO:0100046 - is_a: Hospitalized - title: "Hospitalis\xE9 (ICU)" + title: "Hospitalis\xE9 (USI)" Mechanical Ventilation: - meaning: NCIT:C70909 - title: "Ventilation m\xE9canique" + title: Ventilation artificielle Medically Isolated: - meaning: GENEPIO:0100047 - title: "M\xE9dicalement isol\xE9" + title: "Isolement m\xE9dical" Medically Isolated (Negative Pressure): - meaning: GENEPIO:0100048 - is_a: Medically Isolated - title: "M\xE9dicalement isol\xE9 (pression n\xE9gative)" + title: "Isolement m\xE9dical (pression n\xE9gative)" Self-quarantining: - meaning: NCIT:C173768 - title: Auto-quarantaine - title: "Menu d\xE9taill\xE9 de l'\xE9tat de sant\xE9 de l'h\xF4te" - host health outcome menu: - name: host health outcome menu + title: Quarantaine volontaire + title: "Menu \xAB\_D\xE9tails de l\u2019\xE9tat de sant\xE9 de l\u2019h\xF4te\_\ + \xBB" + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu permissible_values: Deceased: - meaning: NCIT:C28554 title: "D\xE9c\xE9d\xE9" Deteriorating: - meaning: NCIT:C25254 - title: "Se d\xE9t\xE9riorer" + title: "D\xE9t\xE9rioration" Recovered: - meaning: NCIT:C49498 title: "R\xE9tabli" Stable: - meaning: NCIT:C30103 - title: "\xC9curie" - title: "menu des r\xE9sultats de sant\xE9 de l'h\xF4te" - organism menu: - name: organism menu + title: Stabilisation + title: "Menu \xAB\_R\xE9sultats sanitaires de l\u2019h\xF4te\_\xBB" + OrganismMenu: + name: OrganismMenu permissible_values: Severe acute respiratory syndrome coronavirus 2: - meaning: NCBITaxon:2697049 - title: "Syndrome respiratoire aigu s\xE9v\xE8re coronavirus 2" - RaTG13: - meaning: NCBITaxon:2709072 - title: RaTG13 - RmYN02: - meaning: GENEPIO:0100000 - title: RmYN02 - title: menu de l'organisme - purpose of sampling menu: - name: purpose of sampling menu + title: "Coronavirus du syndrome respiratoire aigu s\xE9v\xE8re\_2" + title: "Menu \xAB\_Organisme\_\xBB" + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu permissible_values: Cluster/Outbreak investigation: - meaning: GENEPIO:0100001 - title: "Enqu\xEAte sur les grappes et les foyers" + title: "Enqu\xEAte sur les grappes et les \xE9closions" Diagnostic testing: - meaning: GENEPIO:0100002 title: Tests de diagnostic Research: - meaning: GENEPIO:0100003 title: Recherche - Surveillance: - meaning: GENEPIO:0100004 - title: Surveillance - title: "but du menu d'\xE9chantillonnage" - purpose of sequencing menu: - name: purpose of sequencing menu + title: "Menu \xAB\_Objectif de l\u2019\xE9chantillonnage\_\xBB" + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu permissible_values: Baseline surveillance (random sampling): - meaning: GENEPIO:0100005 title: "Surveillance de base (\xE9chantillonnage al\xE9atoire)" Targeted surveillance (non-random sampling): - meaning: GENEPIO:0100006 title: "Surveillance cibl\xE9e (\xE9chantillonnage non al\xE9atoire)" Priority surveillance project: - meaning: GENEPIO:0100007 - is_a: Targeted surveillance (non-random sampling) title: Projet de surveillance prioritaire Screening for Variants of Concern (VoC): - meaning: GENEPIO:0100008 - is_a: Priority surveillance project - title: "D\xE9pistage des variantes pr\xE9occupantes" + title: "D\xE9pistage des variants pr\xE9occupants" Sample has epidemiological link to Variant of Concern (VoC): - meaning: GENEPIO:0100273 - is_a: Screening for Variants of Concern (VoC) - title: "L'\xE9chantillon a un lien \xE9pid\xE9miologique avec la variante\ - \ pr\xE9occupante" + title: "Lien \xE9pid\xE9miologique entre l\u2019\xE9chantillon et le variant\ + \ pr\xE9occupant" Sample has epidemiological link to Omicron Variant: - meaning: GENEPIO:0100274 - is_a: Sample has epidemiological link to Variant of Concern (VoC) - title: "L'\xE9chantillon a un lien \xE9pid\xE9miologique avec la variante\ + title: "Lien \xE9pid\xE9miologique entre l\u2019\xE9chantillon et le variant\ \ Omicron" Longitudinal surveillance (repeat sampling of individuals): - meaning: GENEPIO:0100009 - is_a: Priority surveillance project title: "Surveillance longitudinale (\xE9chantillonnage r\xE9p\xE9t\xE9 des\ \ individus)" Chronic (prolonged) infection surveillance: - meaning: GENEPIO:0100842 - is_a: Longitudinal surveillance (repeat sampling of individuals) title: "Surveillance des infections chroniques (prolong\xE9es)" Re-infection surveillance: - meaning: GENEPIO:0100010 - is_a: Priority surveillance project title: "Surveillance des r\xE9infections" Vaccine escape surveillance: - meaning: GENEPIO:0100011 - is_a: Priority surveillance project - title: Surveillance des fuites de vaccins + title: "Surveillance de l\u2019\xE9chappement vaccinal" Travel-associated surveillance: - meaning: GENEPIO:0100012 - is_a: Priority surveillance project title: "Surveillance associ\xE9e aux voyages" Domestic travel surveillance: - meaning: GENEPIO:0100013 - is_a: Travel-associated surveillance - title: Surveillance des voyages nationaux + title: "Surveillance des voyages int\xE9rieurs" Interstate/ interprovincial travel surveillance: - meaning: GENEPIO:0100275 - is_a: Domestic travel surveillance - title: "Surveillance des voyages inter\xE9tatiques/interprovinciaux" + title: "Surveillance des voyages entre les \xC9tats ou les provinces" Intra-state/ intra-provincial travel surveillance: - meaning: GENEPIO:0100276 - is_a: Domestic travel surveillance - title: "Surveillance des voyages intra-\xE9tatiques/intraprovinciaux" + title: "Surveillance des voyages dans les \xC9tats ou les provinces" International travel surveillance: - meaning: GENEPIO:0100014 - is_a: Travel-associated surveillance title: Surveillance des voyages internationaux Surveillance of international border crossing by air travel or ground transport: - meaning: GENEPIO:0100015 - is_a: International travel surveillance title: "Surveillance du franchissement des fronti\xE8res internationales par\ - \ voie a\xE9rienne a\xE9rien ou terrestre" + \ voie a\xE9rienne ou terrestre" Surveillance of international border crossing by air travel: - meaning: GENEPIO:0100016 - is_a: International travel surveillance title: "Surveillance du franchissement des fronti\xE8res internationales par\ - \ voie a\xE9rienne a\xE9rien" + \ voie a\xE9rienne" Surveillance of international border crossing by ground transport: - meaning: GENEPIO:0100017 - is_a: International travel surveillance title: "Surveillance du franchissement des fronti\xE8res internationales par\ - \ transport terrestre" + \ voie terrestre" Surveillance from international worker testing: - meaning: GENEPIO:0100018 - is_a: International travel surveillance - title: "Surveillance \xE0 partir d'essais internationaux sur les travailleurs" + title: "Surveillance \xE0 partir de tests aupr\xE8s des travailleurs \xE9\ + trangers" Cluster/Outbreak investigation: - meaning: GENEPIO:0100019 - title: "Enqu\xEAte sur les grappes et les foyers" + title: "Enqu\xEAte sur les grappes et les \xE9closions" Multi-jurisdictional outbreak investigation: - meaning: GENEPIO:0100020 - is_a: Cluster/Outbreak investigation - title: "Enqu\xEAte sur les foyers multi-juridictionnels" + title: "Enqu\xEAte sur les \xE9closions multijuridictionnelles" Intra-jurisdictional outbreak investigation: - meaning: GENEPIO:0100021 - is_a: Cluster/Outbreak investigation - title: "Enqu\xEAte sur un foyer intra-juridictionnel" + title: "Enqu\xEAte sur les \xE9closions intrajuridictionnelles" Research: - meaning: GENEPIO:0100022 title: Recherche Viral passage experiment: - meaning: GENEPIO:0100023 - is_a: Research - title: "Exp\xE9rience de passage viral" + title: "Exp\xE9rience de transmission virale" Protocol testing experiment: - meaning: GENEPIO:0100024 - is_a: Research - title: "Exp\xE9rience de test de protocole" + title: "Exp\xE9rience du test de protocole" Retrospective sequencing: - meaning: GENEPIO:0100356 title: "S\xE9quen\xE7age r\xE9trospectif" - title: "but du menu de s\xE9quencement" - specimen processing menu: - name: specimen processing menu + title: "Menu \xAB\_Objectif du s\xE9quen\xE7age\_\xBB" + SpecimenProcessingMenu: + name: SpecimenProcessingMenu permissible_values: Virus passage: - meaning: GENEPIO:0100039 - title: Passage du virus + title: Transmission du virus RNA re-extraction (post RT-PCR): - meaning: GENEPIO:0100040 - title: "R\xE9tablissement de l'extraction de l'RNA (apr\xE8s RT-PCR)" + title: "R\xE9tablissement de l\u2019extraction de l\u2019ARN (apr\xE8s RT-PCR)" Specimens pooled: - meaning: OBI:0600016 title: "\xC9chantillons regroup\xE9s" - title: "menu de traitement des \xE9chantillons" - lab host menu: - name: lab host menu + title: "Menu \xAB\_Traitement des \xE9chantillons\_\xBB" + LabHostMenu: + name: LabHostMenu permissible_values: 293/ACE2 cell line: - meaning: GENEPIO:0100041 title: "Lign\xE9e cellulaire 293/ACE2" Caco2 cell line: - meaning: BTO:0000195 title: "Lign\xE9e cellulaire Caco2" Calu3 cell line: - meaning: BTO:0002750 title: "Lign\xE9e cellulaire Calu3" EFK3B cell line: - meaning: GENEPIO:0100042 title: "Lign\xE9e cellulaire EFK3B" HEK293T cell line: - meaning: BTO:0002181 title: "Lign\xE9e cellulaire HEK293T" HRCE cell line: - meaning: GENEPIO:0100043 title: "Lign\xE9e cellulaire HRCE" Huh7 cell line: - meaning: BTO:0001950 title: "Lign\xE9e cellulaire Huh7" LLCMk2 cell line: - meaning: CLO:0007330 title: "Lign\xE9e cellulaire LLCMk2" MDBK cell line: - meaning: BTO:0000836 title: "Lign\xE9e cellulaire MDBK" NHBE cell line: - meaning: BTO:0002924 - title: "lign\xE9e cellulaire NHBE" + title: "Lign\xE9e cellulaire NHBE" PK-15 cell line: - meaning: BTO:0001865 title: "Lign\xE9e cellulaire PK-15" RK-13 cell line: - meaning: BTO:0002909 title: "Lign\xE9e cellulaire RK-13" U251 cell line: - meaning: BTO:0002035 title: "Lign\xE9e cellulaire U251" Vero cell line: - meaning: BTO:0001444 title: "Lign\xE9e cellulaire Vero" Vero E6 cell line: - meaning: BTO:0004755 - is_a: Vero cell line title: "Lign\xE9e cellulaire Vero E6" VeroE6/TMPRSS2 cell line: - meaning: GENEPIO:0100044 - is_a: Vero E6 cell line title: "Lign\xE9e cellulaire VeroE6/TMPRSS2" - title: "menu h\xF4te du laboratoire" - host disease menu: - name: host disease menu - permissible_values: - COVID-19: - meaning: MONDO:0100096 - title: COVID-19 - title: "menu des maladies h\xF4tes" - host age bin menu: - name: host age bin menu - permissible_values: - 0 - 9: - meaning: GENEPIO:0100049 - title: 0 - 9 - 10 - 19: - meaning: GENEPIO:0100050 - title: 10 - 19 - 20 - 29: - meaning: GENEPIO:0100051 - title: 20 - 29 - 30 - 39: - meaning: GENEPIO:0100052 - title: 30 - 39 - 40 - 49: - meaning: GENEPIO:0100053 - title: 40 - 49 - 50 - 59: - meaning: GENEPIO:0100054 - title: 50 - 59 - 60 - 69: - meaning: GENEPIO:0100055 - title: 60 - 69 - 70 - 79: - meaning: GENEPIO:0100056 - title: 70 - 79 - 80 - 89: - meaning: GENEPIO:0100057 - title: 80 - 89 - 90 - 99: - meaning: GENEPIO:0100058 - exact_mappings: - - VirusSeq_Portal:90%2B - title: 90 - 99 - 100+: - meaning: GENEPIO:0100059 - exact_mappings: - - VirusSeq_Portal:90%2B - title: 100+ - title: "menu du bac d'\xE2ge de l'h\xF4te" - host gender menu: - name: host gender menu + title: "Menu \xAB\_Laboratoire h\xF4te\_\xBB" + HostAgeBinMenu: + name: HostAgeBinMenu + permissible_values: {} + title: "Menu \xAB\_Groupe d\u2019\xE2ge de l\u2019h\xF4te\_\xBB" + HostGenderMenu: + name: HostGenderMenu permissible_values: Female: - meaning: NCIT:C46110 - title: Female + title: Femme Male: - meaning: NCIT:C46109 - title: Male + title: Homme Non-binary gender: - meaning: GSSO:000132 - title: Non-binary gender + title: Non binaire Transgender (assigned male at birth): - meaning: GSSO:004004 - title: Transgender (assigned male at birth) + title: "Transgenre (sexe masculin \xE0 la naissance)" Transgender (assigned female at birth): - meaning: GSSO:004005 - title: Transgender (assigned female at birth) + title: "Transgenre (sexe f\xE9minin \xE0 la naissance)" Undeclared: - meaning: NCIT:C110959 - title: Undeclared - title: "menu sexe de l'h\xF4te" - exposure event menu: - name: exposure event menu + title: "Non d\xE9clar\xE9" + title: "Menu \xAB\_Genre de l\u2019h\xF4te\_\xBB" + ExposureEventMenu: + name: ExposureEventMenu permissible_values: Mass Gathering: - meaning: GENEPIO:0100237 title: Rassemblement de masse Agricultural Event: - meaning: GENEPIO:0100240 - is_a: Mass Gathering title: "\xC9v\xE9nement agricole" - Convention: - meaning: GENEPIO:0100238 - is_a: Mass Gathering - title: Convention - Convocation: - meaning: GENEPIO:0100239 - is_a: Mass Gathering - title: Convocation Recreational Event: - meaning: GENEPIO:0100417 - is_a: Mass Gathering title: "\xC9v\xE9nement r\xE9cr\xE9atif" - Concert: - meaning: GENEPIO:0100418 - is_a: Recreational Event - title: Concert Sporting Event: - meaning: GENEPIO:0100419 - is_a: Recreational Event - title: Manifestation sportive + title: "\xC9v\xE9nement sportif" Religious Gathering: - meaning: GENEPIO:0100241 title: Rassemblement religieux Mass: - meaning: GENEPIO:0100242 - is_a: Religious Gathering title: Messe Social Gathering: - meaning: PCO:0000033 title: Rassemblement social Baby Shower: - meaning: PCO:0000039 - is_a: Social Gathering - title: "Douche de b\xE9b\xE9" + title: "R\xE9ception-cadeau pour b\xE9b\xE9" Community Event: - meaning: PCO:0000034 - is_a: Social Gathering - title: "Ev\xE9nement communautaire" + title: "\xC9v\xE9nement communautaire" Family Gathering: - meaning: GENEPIO:0100243 - is_a: Social Gathering - title: "R\xE9union de famille" + title: Rassemblement familial Family Reunion: - meaning: GENEPIO:0100244 - is_a: Family Gathering title: "R\xE9union de famille" Funeral: - meaning: GENEPIO:0100245 - is_a: Social Gathering title: "Fun\xE9railles" Party: - meaning: PCO:0000035 - is_a: Social Gathering - title: "Faire la f\xEAte" + title: "F\xEAte" Potluck: - meaning: PCO:0000037 - is_a: Social Gathering title: Repas-partage Wedding: - meaning: PCO:0000038 - is_a: Social Gathering title: Mariage Other exposure event: - title: "Autre \xE9v\xE9nement d'exposition" - title: "menu d'\xE9v\xE9nement d'exposition" - exposure contact level menu: - name: exposure contact level menu + title: "Autre \xE9v\xE9nement d\u2019exposition" + title: "Menu \xAB\_\xC9v\xE9nement d\u2019exposition\_\xBB" + ExposureContactLevelMenu: + name: ExposureContactLevelMenu permissible_values: Contact with infected individual: - meaning: GENEPIO:0100357 title: "Contact avec une personne infect\xE9e" Direct contact (direct human-to-human contact): - meaning: TRANS:0000001 - is_a: Contact with infected individual - title: Direct (contact interhumain) + title: Contact direct (contact interhumain) Indirect contact: - meaning: GENEPIO:0100246 - is_a: Contact with infected individual title: Contact indirect Close contact (face-to-face, no direct contact): - meaning: GENEPIO:0100247 - is_a: Indirect contact - title: "Contact \xE9troit (face \xE0 face)" + title: "Contact \xE9troit (contact personnel, aucun contact \xE9troit)" Casual contact: - meaning: GENEPIO:0100248 - is_a: Indirect contact title: Contact occasionnel - title: menu niveau de contact d'exposition - host role menu: - name: host role menu + title: "Menu \xAB\_Niveau de contact de l\u2019exposition\_\xBB" + HostRoleMenu: + name: HostRoleMenu permissible_values: Attendee: - meaning: GENEPIO:0100249 title: Participant Student: - meaning: OMRSE:00000058 - is_a: Attendee title: "\xC9tudiant" - Patient: - meaning: OMRSE:00000030 - title: Patient Inpatient: - meaning: NCIT:C25182 - is_a: Patient title: "Patient hospitalis\xE9" Outpatient: - meaning: NCIT:C28293 - is_a: Patient - title: Ambulatoire + title: Patient externe Passenger: - meaning: GENEPIO:0100250 title: Passager Resident: - meaning: GENEPIO:0100251 title: "R\xE9sident" Visitor: - meaning: GENEPIO:0100252 title: Visiteur Volunteer: - meaning: GENEPIO:0100253 title: "B\xE9n\xE9vole" Work: - meaning: GENEPIO:0100254 title: Travail Administrator: - meaning: GENEPIO:0100255 - is_a: Work title: Administrateur Child Care/Education Worker: - is_a: Work - title: "Travailleur en garderie/\xE9ducation" + title: "Travailleur en garderie ou en \xE9ducation" Essential Worker: - is_a: Work title: Travailleur essentiel First Responder: - meaning: GENEPIO:0100256 - is_a: Work title: Premier intervenant Firefighter: - meaning: GENEPIO:0100257 - is_a: First Responder - title: Sapeur pompier + title: Pompier Paramedic: - meaning: GENEPIO:0100258 - is_a: First Responder - title: "Param\xE9dical" + title: Ambulancier Police Officer: - meaning: GENEPIO:0100259 - is_a: First Responder - title: Officier de police + title: Policier Healthcare Worker: - meaning: GENEPIO:0100334 - is_a: Work title: "Travailleur de la sant\xE9" Community Healthcare Worker: - meaning: GENEPIO:0100420 - is_a: Healthcare Worker title: "Agent de sant\xE9 communautaire" Laboratory Worker: - meaning: GENEPIO:0100262 - is_a: Healthcare Worker - title: Ouvrier de laboratoire + title: Travailleur de laboratoire Nurse: - meaning: OMRSE:00000014 - is_a: Healthcare Worker title: "Infirmi\xE8re" Personal Care Aid: - meaning: GENEPIO:0100263 - is_a: Healthcare Worker title: Aide aux soins personnels Pharmacist: - meaning: GENEPIO:0100264 - is_a: Healthcare Worker title: Pharmacien Physician: - meaning: OMRSE:00000013 - is_a: Healthcare Worker title: "M\xE9decin" Housekeeper: - meaning: GENEPIO:0100260 - is_a: Work - title: Gouvernante + title: "Aide-m\xE9nag\xE8re" International worker: - is_a: Work title: Travailleur international Kitchen Worker: - meaning: GENEPIO:0100261 - is_a: Work - title: Ouvrier de cuisine + title: Aide de cuisine Rotational Worker: - meaning: GENEPIO:0100354 - is_a: Work title: Travailleur en rotation Seasonal Worker: - meaning: GENEPIO:0100355 - is_a: Work title: Travailleur saisonnier Transport Worker: - is_a: Work title: Ouvrier des transports Transport Truck Driver: - is_a: Transport Worker title: Chauffeur de camion de transport Veterinarian: - meaning: GENEPIO:0100265 - is_a: Work title: "V\xE9t\xE9rinaire" Social role: - meaning: OMRSE:00000001 title: "R\xF4le social" Acquaintance of case: - meaning: GENEPIO:0100266 - is_a: Social role - title: Connaissance de l'affaire + title: Connaissance du cas Relative of case: - meaning: GENEPIO:0100267 - is_a: Social role - title: Parent de l'affaire + title: Famille du cas Child of case: - meaning: GENEPIO:0100268 - is_a: Relative of case - title: "Enfant de la personne concern\xE9e" + title: Enfant du cas Parent of case: - meaning: GENEPIO:0100269 - is_a: Relative of case - title: Parent de l'affaire + title: Parent du cas Father of case: - meaning: GENEPIO:0100270 - is_a: Parent of case - title: "P\xE8re de l'affaire" + title: "P\xE8re du cas" Mother of case: - meaning: GENEPIO:0100271 - is_a: Parent of case title: "M\xE8re du cas" Spouse of case: - meaning: GENEPIO:0100272 - is_a: Social role - title: Conjoint de l'affaire + title: Conjoint du cas Other Host Role: - title: "Autre r\xF4le de l'h\xF4te" - title: "menu du r\xF4le d'h\xF4te" - exposure setting menu: - name: exposure setting menu + title: "Autre r\xF4le de l\u2019h\xF4te" + title: "Menu \xAB\_R\xF4le de l\u2019h\xF4te\_\xBB" + ExposureSettingMenu: + name: ExposureSettingMenu permissible_values: Human Exposure: - meaning: ECTO:3000005 title: Exposition humaine Contact with Known COVID-19 Case: - meaning: GENEPIO:0100184 - is_a: Human Exposure title: Contact avec un cas connu de COVID-19 Contact with Patient: - meaning: GENEPIO:0100185 - is_a: Human Exposure title: Contact avec un patient Contact with Probable COVID-19 Case: - meaning: GENEPIO:0100186 - is_a: Human Exposure title: Contact avec un cas probable de COVID-19 Contact with Person with Acute Respiratory Illness: - meaning: GENEPIO:0100187 - is_a: Human Exposure - title: "Contact avec une personne atteinte d'une maladie respiratoire aigu\xEB" + title: "Contact avec une personne atteinte d\u2019une maladie respiratoire\ + \ aigu\xEB" Contact with Person with Fever and/or Cough: - meaning: GENEPIO:0100188 - is_a: Human Exposure - title: "Contact avec une personne pr\xE9sentant une fi\xE8vre et/ou une toux" + title: "Contact avec une personne pr\xE9sentant une fi\xE8vre ou une toux" Contact with Person who Recently Travelled: - meaning: GENEPIO:0100189 - is_a: Human Exposure title: "Contact avec une personne ayant r\xE9cemment voyag\xE9" Occupational, Residency or Patronage Exposure: - meaning: GENEPIO:0100190 - title: "Exposition professionnelle, de r\xE9sidence ou de patronage" + title: "Exposition professionnelle ou r\xE9sidentielle" Abbatoir: - meaning: ECTO:1000033 - is_a: Occupational, Residency or Patronage Exposure - title: Abbatoir + title: Abattoir Animal Rescue: - meaning: GENEPIO:0100191 - is_a: Occupational, Residency or Patronage Exposure - title: Sauvetage d'animaux + title: Refuge pour animaux Childcare: - meaning: GENEPIO:0100192 - is_a: Occupational, Residency or Patronage Exposure - title: Garde d'enfants + title: "Garde d\u2019enfants" Daycare: - meaning: GENEPIO:0100193 - is_a: Childcare title: Garderie Nursery: - meaning: GENEPIO:0100194 - is_a: Childcare - title: "Cr\xE8che" + title: "Pouponni\xE8re" Community Service Centre: - meaning: GENEPIO:0100195 - is_a: Occupational, Residency or Patronage Exposure title: Centre de services communautaires Correctional Facility: - meaning: GENEPIO:0100196 - is_a: Occupational, Residency or Patronage Exposure - title: "\xC9tablissement p\xE9nitentiaire" + title: "\xC9tablissement correctionnel" Dormitory: - meaning: GENEPIO:0100197 - is_a: Occupational, Residency or Patronage Exposure title: Dortoir Farm: - meaning: ECTO:1000034 - is_a: Occupational, Residency or Patronage Exposure title: Ferme First Nations Reserve: - meaning: GENEPIO:0100198 - is_a: Occupational, Residency or Patronage Exposure title: "R\xE9serve des Premi\xE8res Nations" Funeral Home: - meaning: GENEPIO:0100199 - is_a: Occupational, Residency or Patronage Exposure - title: "Maison fun\xE9raire" + title: "Salon fun\xE9raire" Group Home: - meaning: GENEPIO:0100200 - is_a: Occupational, Residency or Patronage Exposure title: Foyer de groupe Healthcare Setting: - meaning: GENEPIO:0100201 - is_a: Occupational, Residency or Patronage Exposure title: "\xC9tablissement de soins de sant\xE9" - Ambulance: - meaning: GENEPIO:0100202 - is_a: Healthcare Setting - title: Ambulance Acute Care Facility: - meaning: GENEPIO:0100203 - is_a: Healthcare Setting - title: "\xC9tablissement de soins aigus" + title: "\xC9tablissement de soins de courte dur\xE9e" Clinic: - meaning: GENEPIO:0100204 - is_a: Healthcare Setting title: Clinique Community Healthcare (At-Home) Setting: - meaning: GENEPIO:0100415 - is_a: Healthcare Setting title: "\xC9tablissement de soins de sant\xE9 communautaire (\xE0 domicile)" Community Health Centre: - meaning: GENEPIO:0100205 - is_a: Healthcare Setting title: "Centre de sant\xE9 communautaire" Hospital: - meaning: ECTO:1000035 - is_a: Healthcare Setting title: "H\xF4pital" Emergency Department: - meaning: GENEPIO:0100206 - is_a: Hospital title: Service des urgences ICU: - meaning: GENEPIO:0100207 - is_a: Hospital - title: ICU + title: USI Ward: - meaning: GENEPIO:0100208 - is_a: Hospital - title: Salle + title: Service Laboratory: - meaning: ECTO:1000036 - is_a: Healthcare Setting title: Laboratoire Long-Term Care Facility: - meaning: GENEPIO:0100209 - is_a: Healthcare Setting title: "\xC9tablissement de soins de longue dur\xE9e" Pharmacy: - meaning: GENEPIO:0100210 - is_a: Healthcare Setting title: Pharmacie Physician's Office: - meaning: GENEPIO:0100211 - is_a: Healthcare Setting - title: "Cabinet du m\xE9decin" + title: "Cabinet de m\xE9decin" Household: - meaning: GENEPIO:0100212 - is_a: Occupational, Residency or Patronage Exposure title: "M\xE9nage" Insecure Housing (Homeless): - meaning: GENEPIO:0100213 - is_a: Occupational, Residency or Patronage Exposure title: "Logement pr\xE9caire (sans-abri)" Occupational Exposure: - meaning: GENEPIO:0100214 - is_a: Occupational, Residency or Patronage Exposure title: Exposition professionnelle Worksite: - meaning: GENEPIO:0100215 - is_a: Occupational Exposure - title: Chantier + title: Lieu de travail Office: - meaning: ECTO:1000037 - is_a: Worksite title: Bureau Outdoors: - meaning: GENEPIO:0100216 - is_a: Occupational, Residency or Patronage Exposure - title: En plein air + title: Plein air Camp/camping: - meaning: ECTO:5000009 - is_a: Outdoors - title: Camper/camper + title: Camp/Camping Hiking Trail: - meaning: GENEPIO:0100217 - is_a: Outdoors title: "Sentier de randonn\xE9e" Hunting Ground: - meaning: ECTO:6000030 - is_a: Outdoors - title: Terrain de chasse + title: Territoire de chasse Ski Resort: - meaning: GENEPIO:0100218 - is_a: Outdoors title: Station de ski Petting zoo: - meaning: ECTO:5000008 - is_a: Occupational, Residency or Patronage Exposure title: Zoo pour enfants Place of Worship: - meaning: GENEPIO:0100220 - is_a: Occupational, Residency or Patronage Exposure title: Lieu de culte Church: - meaning: GENEPIO:0100221 - is_a: Place of Worship title: "\xC9glise" Mosque: - meaning: GENEPIO:0100222 - is_a: Place of Worship title: "Mosqu\xE9e" - Temple: - meaning: GENEPIO:0100223 - is_a: Place of Worship - title: Temple - Restaurant: - meaning: ECTO:1000040 - is_a: Occupational, Residency or Patronage Exposure - title: Restaurant Retail Store: - meaning: ECTO:1000041 - is_a: Occupational, Residency or Patronage Exposure title: "Magasin de d\xE9tail" School: - meaning: GENEPIO:0100224 - is_a: Occupational, Residency or Patronage Exposure title: "\xC9cole" Temporary Residence: - meaning: GENEPIO:0100225 - is_a: Occupational, Residency or Patronage Exposure title: "R\xE9sidence temporaire" Homeless Shelter: - meaning: GENEPIO:0100226 - is_a: Temporary Residence title: Refuge pour sans-abri Hotel: - meaning: GENEPIO:0100227 - is_a: Temporary Residence title: "H\xF4tel" Veterinary Care Clinic: - meaning: GENEPIO:0100228 - is_a: Occupational, Residency or Patronage Exposure title: "Clinique v\xE9t\xE9rinaire" Travel Exposure: - meaning: GENEPIO:0100229 - title: Exposition au voyage + title: "Exposition li\xE9e au voyage" Travelled on a Cruise Ship: - meaning: GENEPIO:0100230 - is_a: Travel Exposure title: "Voyage sur un bateau de croisi\xE8re" Travelled on a Plane: - meaning: GENEPIO:0100231 - is_a: Travel Exposure title: Voyage en avion Travelled on Ground Transport: - meaning: GENEPIO:0100232 - is_a: Travel Exposure - title: Transport terrestre + title: Voyage par voie terrestre Travelled outside Province/Territory: - meaning: GENEPIO:0001118 - is_a: Travel Exposure title: Voyage en dehors de la province ou du territoire Travelled outside Canada: - meaning: GENEPIO:0001119 - is_a: Travel Exposure title: Voyage en dehors du Canada Other Exposure Setting: - meaning: GENEPIO:0100235 - title: "Autres r\xE9glages d'exposition" - title: "menu de r\xE9glage de l'exposition" - travel point of entry type menu: - name: travel point of entry type menu + title: "Autres contextes d\u2019exposition" + title: "Menu \xAB\_Contexte de l\u2019exposition\_\xBB" + TravelPointOfEntryTypeMenu: + name: TravelPointOfEntryTypeMenu permissible_values: Air: - meaning: GENEPIO:0100408 - title: Air + title: "Voie a\xE9rienne" Land: - meaning: GENEPIO:0100409 - title: Atterrir - title: "menu de type de point d'entr\xE9e de voyage" - border testing test day type menu: - name: border testing test day type menu - permissible_values: - day 1: - meaning: GENEPIO:0100410 - title: jour 1 - day 8: - meaning: GENEPIO:0100411 - title: jour 8 - day 10: - meaning: GENEPIO:0100412 - title: jour 10 - title: "menu de type jour de test des tests aux fronti\xE8res" - travel history availability menu: - name: travel history availability menu + title: Voie terrestre + title: "Menu \xAB\_ Type de point d\u2019entr\xE9e du voyage\_\xBB" + TravelHistoryAvailabilityMenu: + name: TravelHistoryAvailabilityMenu permissible_values: Travel history available: - meaning: GENEPIO:0100650 - title: Historique de voyage disponible + title: "Ant\xE9c\xE9dents de voyage disponibles" Domestic travel history available: - meaning: GENEPIO:0100651 - is_a: Travel history available - title: "Historique des voyages int\xE9rieurs disponible" + title: "Ant\xE9c\xE9dents des voyages int\xE9rieurs disponibles" International travel history available: - meaning: GENEPIO:0100652 - is_a: Travel history available - title: Historique des voyages internationaux disponible + title: "Ant\xE9c\xE9dents des voyages internationaux disponibles" International and domestic travel history available: - meaning: GENEPIO:0100653 - is_a: Travel history available - title: Historique des voyages internationaux et nationaux disponible + title: "Ant\xE9c\xE9dents des voyages int\xE9rieurs et internationaux disponibles" No travel history available: - meaning: GENEPIO:0100654 - title: Aucun historique de voyage disponible - title: "menu de disponibilit\xE9 de l'historique de voyage" - sequencing instrument menu: - name: sequencing instrument menu + title: "Aucun ant\xE9c\xE9dent de voyage disponible" + title: "Menu \xAB\_Disponibilit\xE9 des ant\xE9c\xE9dents de voyage\_\xBB" + SequencingInstrumentMenu: + name: SequencingInstrumentMenu permissible_values: - Illumina: - meaning: GENEPIO:0100105 - title: Illumina Illumina Genome Analyzer: - meaning: GENEPIO:0100106 - is_a: Illumina - title: Illumina Genome Analyzer + title: "Analyseur de g\xE9nome Illumina" Illumina Genome Analyzer II: - meaning: GENEPIO:0100107 - is_a: Illumina Genome Analyzer - title: Illumina Genome Analyzer II + title: "Analyseur de g\xE9nome Illumina II" Illumina Genome Analyzer IIx: - meaning: GENEPIO:0100108 - is_a: Illumina Genome Analyzer - title: Illumina Genome Analyzer IIx - Illumina HiScanSQ: - meaning: GENEPIO:0100109 - is_a: Illumina - title: Illumina HiScanSQ - Illumina HiSeq: - meaning: GENEPIO:0100110 - is_a: Illumina - title: Illumina HiSeq - Illumina HiSeq X: - meaning: GENEPIO:0100111 - is_a: Illumina HiSeq - title: Illumina HiSeq X - Illumina HiSeq X Five: - meaning: GENEPIO:0100112 - is_a: Illumina HiSeq X - title: Illumina HiSeq X Five - Illumina HiSeq X Ten: - meaning: GENEPIO:0100113 - is_a: Illumina HiSeq X - title: Illumina HiSeq X Ten - Illumina HiSeq 1000: - meaning: GENEPIO:0100114 - is_a: Illumina HiSeq - title: Illumina HiSeq 1000 - Illumina HiSeq 1500: - meaning: GENEPIO:0100115 - is_a: Illumina HiSeq - title: Illumina HiSeq 1500 - Illumina HiSeq 2000: - meaning: GENEPIO:0100116 - is_a: Illumina HiSeq - title: Illumina HiSeq 2000 - Illumina HiSeq 2500: - meaning: GENEPIO:0100117 - is_a: Illumina HiSeq - title: Illumina HiSeq 2500 - Illumina HiSeq 3000: - meaning: GENEPIO:0100118 - is_a: Illumina HiSeq - title: Illumina HiSeq 3000 - Illumina HiSeq 4000: - meaning: GENEPIO:0100119 - is_a: Illumina HiSeq - title: Illumina HiSeq 4000 - Illumina iSeq: - meaning: GENEPIO:0100120 - is_a: Illumina - title: Illumina iSeq - Illumina iSeq 100: - meaning: GENEPIO:0100121 - is_a: Illumina iSeq - title: Illumina iSeq 100 - Illumina NovaSeq: - meaning: GENEPIO:0100122 - is_a: Illumina - title: Illumina NovaSeq - Illumina NovaSeq 6000: - meaning: GENEPIO:0100123 - is_a: Illumina NovaSeq - title: Illumina NovaSeq 6000 - Illumina MiniSeq: - meaning: GENEPIO:0100124 - is_a: Illumina - title: Illumina MiniSeq - Illumina MiSeq: - meaning: GENEPIO:0100125 - is_a: Illumina - title: Illumina MiSeq - Illumina NextSeq: - meaning: GENEPIO:0100126 - is_a: Illumina - title: Illumina NextSeq - Illumina NextSeq 500: - meaning: GENEPIO:0100127 - is_a: Illumina NextSeq - title: Illumina NextSeq 500 - Illumina NextSeq 550: - meaning: GENEPIO:0100128 - is_a: Illumina NextSeq - title: Illumina NextSeq 550 - Illumina NextSeq 2000: - meaning: GENEPIO:0100129 - is_a: Illumina NextSeq - title: Illumina NextSeq 2000 - Pacific Biosciences: - meaning: GENEPIO:0100130 - title: Pacific Biosciences - PacBio RS: - meaning: GENEPIO:0100131 - is_a: Pacific Biosciences - title: PacBio RS - PacBio RS II: - meaning: GENEPIO:0100132 - is_a: Pacific Biosciences - title: PacBio RS II - PacBio Sequel: - meaning: GENEPIO:0100133 - is_a: Pacific Biosciences - title: PacBio Sequel - PacBio Sequel II: - meaning: GENEPIO:0100134 - is_a: Pacific Biosciences - title: PacBio Sequel II - Ion Torrent: - meaning: GENEPIO:0100135 - title: Ion Torrent - Ion Torrent PGM: - meaning: GENEPIO:0100136 - is_a: Ion Torrent - title: Ion Torrent PGM - Ion Torrent Proton: - meaning: GENEPIO:0100137 - is_a: Ion Torrent - title: Ion Torrent Proton - Ion Torrent S5 XL: - meaning: GENEPIO:0100138 - is_a: Ion Torrent - title: Ion Torrent S5 XL - Ion Torrent S5: - meaning: GENEPIO:0100139 - is_a: Ion Torrent - title: Ion Torrent S5 - Oxford Nanopore: - meaning: GENEPIO:0100140 - title: Oxford Nanopore - Oxford Nanopore GridION: - meaning: GENEPIO:0100141 - is_a: Oxford Nanopore - title: Oxford Nanopore GridION - Oxford Nanopore MinION: - meaning: GENEPIO:0100142 - is_a: Oxford Nanopore - title: Oxford Nanopore MinION - Oxford Nanopore PromethION: - meaning: GENEPIO:0100143 - is_a: Oxford Nanopore - title: Oxford Nanopore PromethION - BGI Genomics: - meaning: GENEPIO:0100144 - title: BGI Genomics - BGI Genomics BGISEQ-500: - meaning: GENEPIO:0100145 - is_a: BGI Genomics - title: BGI Genomics BGISEQ-500 - MGI: - meaning: GENEPIO:0100146 - title: MGI - MGI DNBSEQ-T7: - meaning: GENEPIO:0100147 - is_a: MGI - title: MGI DNBSEQ-T7 - MGI DNBSEQ-G400: - meaning: GENEPIO:0100148 - is_a: MGI - title: MGI DNBSEQ-G400 - MGI DNBSEQ-G400 FAST: - meaning: GENEPIO:0100149 - is_a: MGI - title: MGI DNBSEQ-G400 FAST - MGI DNBSEQ-G50: - meaning: GENEPIO:0100150 - is_a: MGI - title: MGI DNBSEQ-G50 - title: "menu des instruments de s\xE9quen\xE7age" - gene name menu: - name: gene name menu + title: "Analyseur de g\xE9nome Illumina IIx" + title: "Menu \xAB\_Instrument de s\xE9quen\xE7age\_\xBB" + GeneNameMenu: + name: GeneNameMenu permissible_values: E gene (orf4): - meaning: GENEPIO:0100151 - exact_mappings: - - CNPHI:E%20gene - - BIOSAMPLE:E%20%28orf4%29 - title: "E g\xE8ne (orf4)" + title: "G\xE8ne E (orf4)" M gene (orf5): - meaning: GENEPIO:0100152 - exact_mappings: - - BIOSAMPLE:M%20%28orf5%29 - title: "M g\xE8ne (orf5)" + title: "G\xE8ne M (orf5)" N gene (orf9): - meaning: GENEPIO:0100153 - exact_mappings: - - BIOSAMPLE:N%20%28orf9%29 - title: "N g\xE8ne (orf9)" + title: "G\xE8ne N (orf9)" Spike gene (orf2): - meaning: GENEPIO:0100154 - exact_mappings: - - BIOSAMPLE:S%20%28orf2%29 - title: "Spike g\xE8ne (orf2)" - orf1ab (rep): - meaning: GENEPIO:0100155 - exact_mappings: - - BIOSAMPLE:orf1ab%20%28rep%29 - title: orf1ab (rep) - orf1a (pp1a): - meaning: GENEPIO:0100156 - exact_mappings: - - BIOSAMPLE:orf1a%20%28pp1a%29 - is_a: orf1ab (rep) - title: orf1a (pp1a) - nsp11: - meaning: GENEPIO:0100157 - exact_mappings: - - BIOSAMPLE:nsp11 - is_a: orf1a (pp1a) - title: nsp11 - nsp1: - meaning: GENEPIO:0100158 - exact_mappings: - - BIOSAMPLE:nsp1 - is_a: orf1ab (rep) - title: nsp1 - nsp2: - meaning: GENEPIO:0100159 - exact_mappings: - - BIOSAMPLE:nsp2 - is_a: orf1ab (rep) - title: nsp2 - nsp3: - meaning: GENEPIO:0100160 - exact_mappings: - - BIOSAMPLE:nsp3 - is_a: orf1ab (rep) - title: nsp3 - nsp4: - meaning: GENEPIO:0100161 - exact_mappings: - - BIOSAMPLE:nsp4 - is_a: orf1ab (rep) - title: nsp4 - nsp5: - meaning: GENEPIO:0100162 - exact_mappings: - - BIOSAMPLE:nsp5 - is_a: orf1ab (rep) - title: nsp5 - nsp6: - meaning: GENEPIO:0100163 - exact_mappings: - - BIOSAMPLE:nsp6 - is_a: orf1ab (rep) - title: nsp6 - nsp7: - meaning: GENEPIO:0100164 - exact_mappings: - - BIOSAMPLE:nsp7 - is_a: orf1ab (rep) - title: nsp7 - nsp8: - meaning: GENEPIO:0100165 - exact_mappings: - - BIOSAMPLE:nsp8 - is_a: orf1ab (rep) - title: nsp8 - nsp9: - meaning: GENEPIO:0100166 - exact_mappings: - - BIOSAMPLE:nsp9 - is_a: orf1ab (rep) - title: nsp9 - nsp10: - meaning: GENEPIO:0100167 - exact_mappings: - - BIOSAMPLE:nsp10 - is_a: orf1ab (rep) - title: nsp10 + title: "G\xE8ne de pointe (orf2)" RdRp gene (nsp12): - meaning: GENEPIO:0100168 - exact_mappings: - - BIOSAMPLE:nsp12%20%28RdRp%29 - is_a: orf1ab (rep) - title: "RdRp g\xE8ne (nsp12)" + title: "G\xE8ne RdRp (nsp12)" hel gene (nsp13): - meaning: GENEPIO:0100169 - exact_mappings: - - BIOSAMPLE:nsp13%20%28Hel%29 - is_a: orf1ab (rep) - title: "hel g\xE8ne (nsp13)" + title: "G\xE8ne hel (nsp13)" exoN gene (nsp14): - meaning: GENEPIO:0100170 - exact_mappings: - - BIOSAMPLE:nsp14%20%28ExoN%29 - is_a: orf1ab (rep) - title: "exoN g\xE8ne (nsp14)" - nsp15: - meaning: GENEPIO:0100171 - exact_mappings: - - BIOSAMPLE:nsp15 - is_a: orf1ab (rep) - title: nsp15 - nsp16: - meaning: GENEPIO:0100172 - exact_mappings: - - BIOSAMPLE:nsp16 - is_a: orf1ab (rep) - title: nsp16 - orf3a: - meaning: GENEPIO:0100173 - exact_mappings: - - BIOSAMPLE:orf3a - title: orf3a - orf3b: - meaning: GENEPIO:0100174 - exact_mappings: - - BIOSAMPLE:orf3b - title: orf3b - orf6 (ns6): - meaning: GENEPIO:0100175 - exact_mappings: - - BIOSAMPLE:orf6%20%28ns6%29 - title: orf6 (ns6) - orf7a: - meaning: GENEPIO:0100176 - exact_mappings: - - BIOSAMPLE:orf7a - title: orf7a - orf7b (ns7b): - meaning: GENEPIO:0100177 - exact_mappings: - - BIOSAMPLE:orf7b%20%28ns7b%29 - title: orf7b (ns7b) - orf8 (ns8): - meaning: GENEPIO:0100178 - exact_mappings: - - BIOSAMPLE:orf8%20%28ns8%29 - title: orf8 (ns8) - orf9b: - meaning: GENEPIO:0100179 - exact_mappings: - - BIOSAMPLE:orf9b - title: orf9b - orf9c: - meaning: GENEPIO:0100180 - exact_mappings: - - BIOSAMPLE:orf9c - title: orf9c - orf10: - meaning: GENEPIO:0100181 - exact_mappings: - - BIOSAMPLE:orf10 - title: orf10 - orf14: - meaning: GENEPIO:0100182 - exact_mappings: - - BIOSAMPLE:orf14 - title: orf14 + title: "G\xE8ne exoN (nsp14)" SARS-COV-2 5' UTR: - meaning: GENEPIO:0100183 - title: SARS-COV-2 5' UTR - title: "menu de nom de g\xE8ne" - sequence submitted by menu: - name: sequence submitted by menu + title: SRAS-COV-2 5' UTR + title: "Menu \xAB\_Nom du g\xE8ne\_\xBB" + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu permissible_values: - Alberta Precision Labs (APL): - title: Alberta Precision Labs (APL) - Alberta ProvLab North (APLN): - is_a: Alberta Precision Labs (APL) - title: Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS): - is_a: Alberta Precision Labs (APL) - title: Alberta ProvLab South (APLS) BCCDC Public Health Laboratory: - title: BCCDC Public Health Laboratory - Canadore College: - title: Canadore College - The Centre for Applied Genomics (TCAG): - title: The Centre for Applied Genomics (TCAG) - Dynacare: - title: Dynacare - Dynacare (Brampton): - title: Dynacare (Brampton) - Dynacare (Manitoba): - title: Dynacare (Manitoba) - The Hospital for Sick Children (SickKids): - title: The Hospital for Sick Children (SickKids) - "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ)": - title: "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ)" + title: "Laboratoire de sant\xE9 publique du CCMCB" Manitoba Cadham Provincial Laboratory: - title: Manitoba Cadham Provincial Laboratory + title: Laboratoire provincial Cadham du Manitoba McGill University: - title: McGill University + title: "Universit\xE9 McGill" McMaster University: - title: McMaster University + title: "Universit\xE9 McMaster" National Microbiology Laboratory (NML): - title: National Microbiology Laboratory (NML) + title: Laboratoire national de microbiologie (LNM) "New Brunswick - Vitalit\xE9 Health Network": - title: "New Brunswick - Vitalit\xE9 Health Network" + title: "Nouveau-Brunswick\_\u2013 R\xE9seau de sant\xE9 Vitalit\xE9" Newfoundland and Labrador - Eastern Health: - title: Newfoundland and Labrador - Eastern Health + title: "Terre-Neuve-et-Labrador\_\u2013 Eastern Health" Newfoundland and Labrador - Newfoundland and Labrador Health Services: - title: Newfoundland and Labrador - Newfoundland and Labrador Health Services + title: "Terre-Neuve-et-Labrador\_\u2013 Newfoundland and Labrador Health Services" Nova Scotia Health Authority: - title: Nova Scotia Health Authority + title: "Autorit\xE9 sanitaire de la Nouvelle-\xC9cosse" Ontario Institute for Cancer Research (OICR): - title: Ontario Institute for Cancer Research (OICR) + title: Institut ontarien de recherche sur le cancer (IORC) Prince Edward Island - Health PEI: - title: Prince Edward Island - Health PEI + title: "\xCEle-du-Prince-\xC9douard\_\u2013 Sant\xE9 \xCE.-P.-\xC9." Public Health Ontario (PHO): - title: Public Health Ontario (PHO) + title: "Sant\xE9 publique Ontario (SPO)" Queen's University / Kingston Health Sciences Centre: - title: Queen's University / Kingston Health Sciences Centre + title: "Universit\xE9 Queen\u2019s\_\u2013 Centre des sciences de la sant\xE9\ + \ de Kingston" Saskatchewan - Roy Romanow Provincial Laboratory (RRPL): - title: Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Sunnybrook Health Sciences Centre: - title: Sunnybrook Health Sciences Centre + title: "Saskatchewan\_\u2013 Laboratoire provincial Roy\_Romanow" Thunder Bay Regional Health Sciences Centre: - title: Thunder Bay Regional Health Sciences Centre - title: "s\xE9quence soumise par menu" - sample collected by menu: - name: sample collected by menu + title: "Centre r\xE9gional des sciences\nde la sant\xE9 de Thunder\_Bay" + title: "Menu \xAB\_S\xE9quence soumise par\_\xBB" + SampleCollectedByMenu: + name: SampleCollectedByMenu permissible_values: - Alberta Precision Labs (APL): - title: Alberta Precision Labs (APL) - Alberta ProvLab North (APLN): - is_a: Alberta Precision Labs (APL) - title: Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS): - is_a: Alberta Precision Labs (APL) - title: Alberta ProvLab South (APLS) BCCDC Public Health Laboratory: - title: BCCDC Public Health Laboratory - Dynacare: - title: Dynacare - Dynacare (Manitoba): - title: Dynacare (Manitoba) - Dynacare (Brampton): - title: Dynacare (Brampton) + title: "Laboratoire de sant\xE9 publique du CCMCB" Eastern Ontario Regional Laboratory Association: - title: Eastern Ontario Regional Laboratory Association - Hamilton Health Sciences: - title: Hamilton Health Sciences - The Hospital for Sick Children (SickKids): - title: The Hospital for Sick Children (SickKids) - "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ)": - title: "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ)" + title: "Association des laboratoires r\xE9gionaux de l\u2019Est de l\u2019\ + Ontario" Lake of the Woods District Hospital - Ontario: - title: Lake of the Woods District Hospital - Ontario - LifeLabs: - title: LifeLabs - LifeLabs (Ontario): - title: LifeLabs (Ontario) + title: "Lake of the Woods District Hospital\_\u2013 Ontario" Manitoba Cadham Provincial Laboratory: - title: Manitoba Cadham Provincial Laboratory + title: Laboratoire provincial Cadham du Manitoba McMaster University: - title: McMaster University - Mount Sinai Hospital: - title: Mount Sinai Hospital + title: "Universit\xE9 McMaster" National Microbiology Laboratory (NML): - title: National Microbiology Laboratory (NML) + title: Laboratoire national de microbiologie (LNM) "New Brunswick - Vitalit\xE9 Health Network": - title: "New Brunswick - Vitalit\xE9 Health Network" + title: "Nouveau-Brunswick\_\u2013 R\xE9seau de sant\xE9 Vitalit\xE9" Newfoundland and Labrador - Eastern Health: - title: Newfoundland and Labrador - Eastern Health + title: "Terre-Neuve-et-Labrador\_\u2013 Eastern Health" Newfoundland and Labrador - Newfoundland and Labrador Health Services: - title: Newfoundland and Labrador - Newfoundland and Labrador Health Services + title: "Terre-Neuve-et-Labrador\_\u2013 Newfoundland and Labrador Health Services" Nova Scotia Health Authority: - title: Nova Scotia Health Authority - Nunavut: - title: Nunavut + title: "Autorit\xE9 sanitaire de la Nouvelle-\xC9cosse" Ontario Institute for Cancer Research (OICR): - title: Ontario Institute for Cancer Research (OICR) + title: Institut ontarien de recherche sur le cancer (IORC) Prince Edward Island - Health PEI: - title: Prince Edward Island - Health PEI + title: "\xCEle-du-Prince-\xC9douard\_\u2013 Sant\xE9 \xCE.-P.-\xC9." Public Health Ontario (PHO): - title: Public Health Ontario (PHO) + title: "Sant\xE9 publique Ontario (SPO)" Queen's University / Kingston Health Sciences Centre: - title: Queen's University / Kingston Health Sciences Centre + title: "Universit\xE9 Queen\u2019s\_\u2013 Centre des sciences de la sant\xE9\ + \ de Kingston" Saskatchewan - Roy Romanow Provincial Laboratory (RRPL): - title: Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Shared Hospital Laboratory: - title: Shared Hospital Laboratory + title: "Saskatchewan\_\u2013 Laboratoire provincial Roy\_Romanow" St. John's Rehab at Sunnybrook Hospital: - title: St. John's Rehab at Sunnybrook Hospital - Switch Health: - title: Switch Health - Sunnybrook Health Sciences Centre: - title: Sunnybrook Health Sciences Centre - Unity Health Toronto: - title: Unity Health Toronto - William Osler Health System: - title: William Osler Health System - title: "\xE9chantillon collect\xE9 par menu" - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + title: "St. John\u2019s Rehab \xE0 l\u2019h\xF4pital Sunnybrook" + title: "Menu \xAB\_\xC9chantillon pr\xE9lev\xE9 par\_\xBB" + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu permissible_values: - Afghanistan: - meaning: GAZ:00006882 - title: Afghanistan Albania: - meaning: GAZ:00002953 title: Albanie Algeria: - meaning: GAZ:00000563 title: "Alg\xE9rie" American Samoa: - meaning: GAZ:00003957 title: "Samoa am\xE9ricaines" Andorra: - meaning: GAZ:00002948 title: Andorre - Angola: - meaning: GAZ:00001095 - title: Angola - Anguilla: - meaning: GAZ:00009159 - title: Anguilla Antarctica: - meaning: GAZ:00000462 title: Antarctique Antigua and Barbuda: - meaning: GAZ:00006883 title: Antigua-et-Barbuda Argentina: - meaning: GAZ:00002928 title: Argentine Armenia: - meaning: GAZ:00004094 title: "Arm\xE9nie" - Aruba: - meaning: GAZ:00004025 - title: Aruba Ashmore and Cartier Islands: - meaning: GAZ:00005901 title: "\xCEles Ashmore et Cartier" Australia: - meaning: GAZ:00000463 title: Australie Austria: - meaning: GAZ:00002942 - title: L'Autriche + title: Autriche Azerbaijan: - meaning: GAZ:00004941 title: "Azerba\xEFdjan" - Bahamas: - meaning: GAZ:00002733 - title: Bahamas Bahrain: - meaning: GAZ:00005281 title: "Bahre\xEFn" Baker Island: - meaning: GAZ:00007117 - title: "\xCEle Boulanger" - Bangladesh: - meaning: GAZ:00003750 - title: Bangladesh + title: "\xCEle Baker" Barbados: - meaning: GAZ:00001251 title: Barbade Bassas da India: - meaning: GAZ:00005810 - title: Bassas de l'Inde + title: "Bassas de l\u2019Inde" Belarus: - meaning: GAZ:00006886 - title: "Bi\xE9lorussie" + title: "B\xE9larus" Belgium: - meaning: GAZ:00002938 title: Belgique Belize: - meaning: GAZ:00002934 title: "B\xE9lize" Benin: - meaning: GAZ:00000904 title: "B\xE9nin" Bermuda: - meaning: GAZ:00001264 title: Bermudes Bhutan: - meaning: GAZ:00003920 title: Bhoutan Bolivia: - meaning: GAZ:00002511 title: Bolivie Borneo: - meaning: GAZ:00025355 title: "Born\xE9o" Bosnia and Herzegovina: - meaning: GAZ:00006887 - title: "Bosnie Herz\xE9govine" - Botswana: - meaning: GAZ:00001097 - title: Botswana + title: "Bosnie-Herz\xE9govine" Bouvet Island: - meaning: GAZ:00001453 title: "\xCEle Bouvet" Brazil: - meaning: GAZ:00002828 title: "Br\xE9sil" British Virgin Islands: - meaning: GAZ:00003961 title: "\xCEles Vierges britanniques" - Brunei: - meaning: GAZ:00003901 - title: "Brun\xE9i" Bulgaria: - meaning: GAZ:00002950 title: Bulgarie - Burkina Faso: - meaning: GAZ:00000905 - title: Burkina Faso - Burundi: - meaning: GAZ:00001090 - title: Burundi Cambodia: - meaning: GAZ:00006888 title: Cambodge Cameroon: - meaning: GAZ:00001093 title: Cameroun - Canada: - meaning: GAZ:00002560 - title: Canada Cape Verde: - meaning: GAZ:00001227 title: Cap-Vert Cayman Islands: - meaning: GAZ:00003986 title: "\xCEles Ca\xEFmans" Central African Republic: - meaning: GAZ:00001089 title: "R\xE9publique centrafricaine" Chad: - meaning: GAZ:00000586 title: Tchad Chile: - meaning: GAZ:00002825 title: Chili China: - meaning: GAZ:00002845 title: Chine Christmas Island: - meaning: GAZ:00005915 - title: "L'\xEEle de no\xEBl" + title: "\xCEle Christmas" Clipperton Island: - meaning: GAZ:00005838 - title: "\xCEle Clipperton" + title: "\xCElot de Clipperton" Cocos Islands: - meaning: GAZ:00009721 title: "\xCEles Cocos" Colombia: - meaning: GAZ:00002929 title: Colombie Comoros: - meaning: GAZ:00005820 title: Comores Cook Islands: - meaning: GAZ:00053798 - title: "les \xCEles Cook" + title: "\xCEles Cook" Coral Sea Islands: - meaning: GAZ:00005917 title: "\xCEles de la mer de Corail" - Costa Rica: - meaning: GAZ:00002901 - title: Costa Rica Cote d'Ivoire: - meaning: GAZ:00000906 - title: "C\xF4te d'Ivoire" + title: "C\xF4te d\u2019Ivoire" Croatia: - meaning: GAZ:00002719 title: Croatie - Cuba: - meaning: GAZ:00003762 - title: Cuba Curacao: - meaning: GAZ:00012582 - title: Curacao + title: "Cura\xE7ao" Cyprus: - meaning: GAZ:00004006 title: Chypre Czech Republic: - meaning: GAZ:00002954 title: "R\xE9publique tch\xE8que" Democratic Republic of the Congo: - meaning: GAZ:00001086 - title: "R\xE9publique D\xE9mocratique du Congo" + title: "R\xE9publique d\xE9mocratique du Congo" Denmark: - meaning: GAZ:00005852 title: Danemark - Djibouti: - meaning: GAZ:00000582 - title: Djibouti Dominica: - meaning: GAZ:00006890 title: Dominique Dominican Republic: - meaning: GAZ:00003952 title: "R\xE9publique dominicaine" Ecuador: - meaning: GAZ:00002912 title: "\xC9quateur" Egypt: - meaning: GAZ:00003934 - title: Egypte + title: "\xC9gypte" El Salvador: - meaning: GAZ:00002935 - title: Le Salvador + title: Salvador Equatorial Guinea: - meaning: GAZ:00001091 - title: "Guin\xE9e \xC9quatoriale" + title: "Guin\xE9e \xE9quatoriale" Eritrea: - meaning: GAZ:00000581 title: "\xC9rythr\xE9e" Estonia: - meaning: GAZ:00002959 title: Estonie - Eswatini: - meaning: GAZ:00001099 - title: Eswatini Ethiopia: - meaning: GAZ:00000567 - title: Ethiopie + title: "\xC9thiopie" Europa Island: - meaning: GAZ:00005811 - title: "\xCEle d'Europe" + title: "\xCEle Europa" Falkland Islands (Islas Malvinas): - meaning: GAZ:00001412 - title: "\xCEles Falkland (Islas Malvinas)" + title: "\xCEles Falkland (\xEEles Malouines)" Faroe Islands: - meaning: GAZ:00059206 title: "\xCEles F\xE9ro\xE9" Fiji: - meaning: GAZ:00006891 title: Fidji Finland: - meaning: GAZ:00002937 title: Finlande - France: - meaning: GAZ:00003940 - title: France French Guiana: - meaning: GAZ:00002516 - title: "Guyane Fran\xE7aise" + title: "Guyane fran\xE7aise" French Polynesia: - meaning: GAZ:00002918 title: "Polyn\xE9sie fran\xE7aise" French Southern and Antarctic Lands: - meaning: GAZ:00003753 title: "Terres australes et antarctiques fran\xE7aises" - Gabon: - meaning: GAZ:00001092 - title: Gabon Gambia: - meaning: GAZ:00000907 title: Gambie Gaza Strip: - meaning: GAZ:00009571 - title: bande de Gaza + title: Bande de Gaza Georgia: - meaning: GAZ:00004942 title: "G\xE9orgie" Germany: - meaning: GAZ:00002646 title: Allemagne - Ghana: - meaning: GAZ:00000908 - title: Ghana - Gibraltar: - meaning: GAZ:00003987 - title: Gibraltar Glorioso Islands: - meaning: GAZ:00005808 title: "\xCEles Glorieuses" Greece: - meaning: GAZ:00002945 title: "Gr\xE8ce" Greenland: - meaning: GAZ:00001507 title: Groenland Grenada: - meaning: GAZ:02000573 title: Grenade - Guadeloupe: - meaning: GAZ:00067142 - title: Guadeloupe - Guam: - meaning: GAZ:00003706 - title: Guam - Guatemala: - meaning: GAZ:00002936 - title: Guatemala Guernsey: - meaning: GAZ:00001550 title: Guernesey Guinea: - meaning: GAZ:00000909 title: "Guin\xE9e" Guinea-Bissau: - meaning: GAZ:00000910 title: "Guin\xE9e-Bissau" - Guyana: - meaning: GAZ:00002522 - title: Guyane Haiti: - meaning: GAZ:00003953 title: "Ha\xEFti" Heard Island and McDonald Islands: - meaning: GAZ:00009718 - title: "\xCEle Heard et \xEEles McDonald" - Honduras: - meaning: GAZ:00002894 - title: Honduras - Hong Kong: - meaning: GAZ:00003203 - title: Hong Kong + title: "\xCEles Heard-et-McDonald" Howland Island: - meaning: GAZ:00007120 title: "\xCEle Howland" Hungary: - meaning: GAZ:00002952 title: Hongrie Iceland: - meaning: GAZ:00000843 title: Islande India: - meaning: GAZ:00002839 title: Inde Indonesia: - meaning: GAZ:00003727 title: "Indon\xE9sie" - Iran: - meaning: GAZ:00004474 - title: L'Iran - Iraq: - meaning: GAZ:00004483 - title: Irak Ireland: - meaning: GAZ:00002943 title: Irlande Isle of Man: - meaning: GAZ:00052477 title: "\xEEle de Man" Israel: - meaning: GAZ:00002476 title: "Isra\xEBl" Italy: - meaning: GAZ:00002650 title: Italie Jamaica: - meaning: GAZ:00003781 title: "Jama\xEFque" - Jan Mayen: - meaning: GAZ:00005853 - title: Jan Mayen Japan: - meaning: GAZ:00002747 title: Japon Jarvis Island: - meaning: GAZ:00007118 title: "\xCEle Jarvis" - Jersey: - meaning: GAZ:00001551 - title: Jersey Johnston Atoll: - meaning: GAZ:00007114 title: Atoll Johnston Jordan: - meaning: GAZ:00002473 - title: Jordan + title: Jordanie Juan de Nova Island: - meaning: GAZ:00005809 title: "\xCEle Juan de Nova" - Kazakhstan: - meaning: GAZ:00004999 - title: Kazakhstan - Kenya: - meaning: GAZ:00001101 - title: Kenya Kerguelen Archipelago: - meaning: GAZ:00005682 - title: Archipel des Kerguelen + title: Archipel Kerguelen Kingman Reef: - meaning: GAZ:00007116 - title: "R\xE9cif Kingman" - Kiribati: - meaning: GAZ:00006894 - title: Kiribati - Kosovo: - meaning: GAZ:00011337 - title: Kosovo + title: "R\xE9cif de Kingman" Kuwait: - meaning: GAZ:00005285 - title: Koweit + title: "Kowe\xEFt" Kyrgyzstan: - meaning: GAZ:00006893 title: Kirghizistan - Laos: - meaning: GAZ:00006889 - title: Laos Latvia: - meaning: GAZ:00002958 title: Lettonie Lebanon: - meaning: GAZ:00002478 title: Liban - Lesotho: - meaning: GAZ:00001098 - title: Lesotho Liberia: - meaning: GAZ:00000911 title: "Lib\xE9ria" Libya: - meaning: GAZ:00000566 title: Libye - Liechtenstein: - meaning: GAZ:00003858 - title: Liechtenstein Line Islands: - meaning: GAZ:00007144 title: "\xCEles de la Ligne" Lithuania: - meaning: GAZ:00002960 title: Lituanie - Luxembourg: - meaning: GAZ:00002947 - title: Luxembourg Macau: - meaning: GAZ:00003202 title: Macao - Madagascar: - meaning: GAZ:00001108 - title: Madagascar - Malawi: - meaning: GAZ:00001105 - title: Malawi Malaysia: - meaning: GAZ:00003902 title: Malaisie - Maldives: - meaning: GAZ:00006924 - title: Maldives - Mali: - meaning: GAZ:00000584 - title: Mali Malta: - meaning: GAZ:00004017 title: Malte Marshall Islands: - meaning: GAZ:00007161 - title: Iles Marshall - Martinique: - meaning: GAZ:00067143 - title: Martinique + title: "\xCEles Marshall" Mauritania: - meaning: GAZ:00000583 title: Mauritanie Mauritius: - meaning: GAZ:00003745 title: Maurice - Mayotte: - meaning: GAZ:00003943 - title: Mayotte Mexico: - meaning: GAZ:00002852 title: Mexique Micronesia: - meaning: GAZ:00005862 title: "Micron\xE9sie" Midway Islands: - meaning: GAZ:00007112 title: "\xCEles Midway" Moldova: - meaning: GAZ:00003897 title: Moldavie - Monaco: - meaning: GAZ:00003857 - title: Monaco Mongolia: - meaning: GAZ:00008744 title: Mongolie Montenegro: - meaning: GAZ:00006898 title: "Mont\xE9n\xE9gro" - Montserrat: - meaning: GAZ:00003988 - title: Montserrat Morocco: - meaning: GAZ:00000565 title: Maroc - Mozambique: - meaning: GAZ:00001100 - title: Mozambique - Myanmar: - meaning: GAZ:00006899 - title: Birmanie Namibia: - meaning: GAZ:00001096 title: Namibie - Nauru: - meaning: GAZ:00006900 - title: Nauru Navassa Island: - meaning: GAZ:00007119 - title: "\xCEle Navasse" + title: "\xCEle Navassa" Nepal: - meaning: GAZ:00004399 title: "N\xE9pal" Netherlands: - meaning: GAZ:00002946 title: Pays-Bas New Caledonia: - meaning: GAZ:00005206 - title: "Nouvelle Cal\xE9donie" + title: "Nouvelle-Cal\xE9donie" New Zealand: - meaning: GAZ:00000469 title: "Nouvelle-Z\xE9lande" - Nicaragua: - meaning: GAZ:00002978 - title: Nicaragua - Niger: - meaning: GAZ:00000585 - title: Niger Nigeria: - meaning: GAZ:00000912 - title: Nigeria + title: "Nig\xE9ria" Niue: - meaning: GAZ:00006902 title: "Niou\xE9" Norfolk Island: - meaning: GAZ:00005908 - title: l'ile de Norfolk + title: "\xCEle Norfolk" North Korea: - meaning: GAZ:00002801 title: "Cor\xE9e du Nord" North Macedonia: - meaning: GAZ:00006895 title: "Mac\xE9doine du Nord" North Sea: - meaning: GAZ:00002284 - title: la mer du Nord + title: Mer du Nord Northern Mariana Islands: - meaning: GAZ:00003958 title: "\xCEles Mariannes du Nord" Norway: - meaning: GAZ:00002699 title: "Norv\xE8ge" - Oman: - meaning: GAZ:00005283 - title: Oman - Pakistan: - meaning: GAZ:00005246 - title: Pakistan Palau: - meaning: GAZ:00006905 title: Palaos - Panama: - meaning: GAZ:00002892 - title: Panama Papua New Guinea: - meaning: GAZ:00003922 - title: "Papouasie Nouvelle Guin\xE9e" + title: "Papouasie-Nouvelle-Guin\xE9e" Paracel Islands: - meaning: GAZ:00010832 - title: Iles Paracel - Paraguay: - meaning: GAZ:00002933 - title: Paraguay + title: "\xCEles Paracel" Peru: - meaning: GAZ:00002932 title: "P\xE9rou" - Philippines: - meaning: GAZ:00004525 - title: Philippines Pitcairn Islands: - meaning: GAZ:00005867 - title: "\xCEles Pitcairn" + title: "\xCEle Pitcairn" Poland: - meaning: GAZ:00002939 title: Pologne - Portugal: - meaning: GAZ:00004126 - title: le Portugal Puerto Rico: - meaning: GAZ:00006935 title: Porto Rico - Qatar: - meaning: GAZ:00005286 - title: Qatar Republic of the Congo: - meaning: GAZ:00001088 title: "R\xE9publique du Congo" Reunion: - meaning: GAZ:00003945 title: "R\xE9union" Romania: - meaning: GAZ:00002951 title: Roumanie Ross Sea: - meaning: GAZ:00023304 title: Mer de Ross Russia: - meaning: GAZ:00002721 title: Russie - Rwanda: - meaning: GAZ:00001087 - title: Rwanda Saint Helena: - meaning: GAZ:00000849 title: "Sainte-H\xE9l\xE8ne" Saint Kitts and Nevis: - meaning: GAZ:00006906 - title: "Saint-Christophe-et-Ni\xE9v\xE8s" + title: Saint-Kitts-et-Nevis Saint Lucia: - meaning: GAZ:00006909 title: Sainte-Lucie Saint Pierre and Miquelon: - meaning: GAZ:00003942 title: Saint-Pierre-et-Miquelon Saint Martin: - meaning: GAZ:00005841 - title: Saint Martin + title: Saint-Martin Saint Vincent and the Grenadines: - meaning: GAZ:02000565 title: Saint-Vincent-et-les-Grenadines - Samoa: - meaning: GAZ:00006910 - title: Samoa San Marino: - meaning: GAZ:00003102 - title: Saint Marin + title: Saint-Marin Sao Tome and Principe: - meaning: GAZ:00006927 - title: "Sao Tom\xE9 et Principe" + title: "Sao Tom\xE9-et-Principe" Saudi Arabia: - meaning: GAZ:00005279 - title: Arabie Saoudite + title: Arabie saoudite Senegal: - meaning: GAZ:00000913 title: "S\xE9n\xE9gal" Serbia: - meaning: GAZ:00002957 title: Serbie - Seychelles: - meaning: GAZ:00006922 - title: les Seychelles - Sierra Leone: - meaning: GAZ:00000914 - title: Sierra Leone Singapore: - meaning: GAZ:00003923 title: Singapour Sint Maarten: - meaning: GAZ:00012579 title: Saint-Martin Slovakia: - meaning: GAZ:00002956 title: Slovaquie Slovenia: - meaning: GAZ:00002955 title: "Slov\xE9nie" Solomon Islands: - meaning: GAZ:00005275 - title: "Les \xEEles Salomon" + title: "\xCEles Salomon" Somalia: - meaning: GAZ:00001104 title: Somalie South Africa: - meaning: GAZ:00001094 title: Afrique du Sud South Georgia and the South Sandwich Islands: - meaning: GAZ:00003990 title: "G\xE9orgie du Sud et \xEEles Sandwich du Sud" South Korea: - meaning: GAZ:00002802 title: "Cor\xE9e du Sud" South Sudan: - meaning: GAZ:00233439 - title: Soudan du sud + title: Soudan du Sud Spain: - meaning: GAZ:00000591 title: Espagne Spratly Islands: - meaning: GAZ:00010831 title: "\xCEles Spratly" - Sri Lanka: - meaning: GAZ:00003924 - title: Sri Lanka State of Palestine: - meaning: GAZ:00002475 title: "\xC9tat de Palestine" Sudan: - meaning: GAZ:00000560 title: Soudan - Suriname: - meaning: GAZ:00002525 - title: Surinam - Svalbard: - meaning: GAZ:00005396 - title: Svalbard - Swaziland: - meaning: GAZ:00001099 - title: Swaziland Sweden: - meaning: GAZ:00002729 title: "Su\xE8de" Switzerland: - meaning: GAZ:00002941 title: Suisse Syria: - meaning: GAZ:00002474 title: Syrie Taiwan: - meaning: GAZ:00005341 title: "Ta\xEFwan" Tajikistan: - meaning: GAZ:00006912 title: Tadjikistan Tanzania: - meaning: GAZ:00001103 title: Tanzanie Thailand: - meaning: GAZ:00003744 title: "Tha\xEFlande" - Timor-Leste: - meaning: GAZ:00006913 - title: Timor-Leste - Togo: - meaning: GAZ:00000915 - title: Aller Tokelau: - meaning: GAZ:00260188 - title: "Tok\xE9laou" - Tonga: - meaning: GAZ:00006916 - title: Tonga + title: Tokelaou Trinidad and Tobago: - meaning: GAZ:00003767 title: "Trinit\xE9-et-Tobago" Tromelin Island: - meaning: GAZ:00005812 title: "\xCEle Tromelin" Tunisia: - meaning: GAZ:00000562 title: Tunisie Turkey: - meaning: GAZ:00000558 title: Turquie Turkmenistan: - meaning: GAZ:00005018 title: "Turkm\xE9nistan" Turks and Caicos Islands: - meaning: GAZ:00003955 - title: "\xEEles Turques-et-Ca\xEFques" - Tuvalu: - meaning: GAZ:00009715 - title: Tuvalu + title: "\xCEles Turks et Caicos" United States of America: - meaning: GAZ:00002459 - title: "les \xE9tats-unis d'Am\xE9rique" + title: "\xC9tats-Unis" Uganda: - meaning: GAZ:00001102 title: Ouganda - Ukraine: - meaning: GAZ:00002724 - title: Ukraine United Arab Emirates: - meaning: GAZ:00005282 - title: Emirats Arabes Unis + title: "\xC9mirats arabes unis" United Kingdom: - meaning: GAZ:00002637 title: Royaume-Uni - Uruguay: - meaning: GAZ:00002930 - title: Uruguay Uzbekistan: - meaning: GAZ:00004979 title: "Ouzb\xE9kistan" - Vanuatu: - meaning: GAZ:00006918 - title: Vanuatu - Venezuela: - meaning: GAZ:00002931 - title: Venezuela Viet Nam: - meaning: GAZ:00003756 - title: Viet Nam + title: Vietnam Virgin Islands: - meaning: GAZ:00003959 - title: Les iles vierges + title: "\xCEles vierges" Wake Island: - meaning: GAZ:00007111 title: "\xCEle de Wake" Wallis and Futuna: - meaning: GAZ:00007191 - title: Wallis et Futuna + title: Wallis-et-Futuna West Bank: - meaning: GAZ:00009572 - title: banque de l'Ouest + title: Cisjordanie Western Sahara: - meaning: GAZ:00000564 - title: Sahara occidental + title: "R\xE9publique arabe sahraouie d\xE9mocratique" Yemen: - meaning: GAZ:00005284 title: "Y\xE9men" Zambia: - meaning: GAZ:00001107 title: Zambie - Zimbabwe: - meaning: GAZ:00001106 - title: Zimbabwe - title: menu geo_loc_name (pays) + title: "Menu \xAB\_nom_lieu_g\xE9o (pays)\_\xBB" types: WhitespaceMinimizedString: name: WhitespaceMinimizedString diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json index 2d5b7031..44080e1b 100644 --- a/web/templates/canada_covid19/schema.json +++ b/web/templates/canada_covid19/schema.json @@ -3,7 +3,7 @@ "description": "", "in_language": "['en', 'fr']", "id": "https://example.com/CanCOGeN_Covid-19", - "version": "2.3.4", + "version": "2.4.0", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -297,8 +297,9 @@ } }, "enums": { - "umbrella bioproject accession menu": { - "name": "umbrella bioproject accession menu", + "UmbrellaBioprojectAccessionMenu": { + "name": "UmbrellaBioprojectAccessionMenu", + "title": "umbrella bioproject accession menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "PRJNA623807": { @@ -306,8 +307,9 @@ } } }, - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "null value menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Not Applicable": { @@ -332,8 +334,9 @@ } } }, - "geo_loc_name (state/province/territory) menu": { - "name": "geo_loc_name (state/province/territory) menu", + "GeoLocNameStateProvinceTerritoryMenu": { + "name": "GeoLocNameStateProvinceTerritoryMenu", + "title": "geo_loc_name (state/province/territory) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Alberta": { @@ -390,8 +393,9 @@ } } }, - "host age unit menu": { - "name": "host age unit menu", + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host age unit menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "month": { @@ -404,8 +408,9 @@ } } }, - "sample collection date precision menu": { - "name": "sample collection date precision menu", + "SampleCollectionDatePrecisionMenu": { + "name": "SampleCollectionDatePrecisionMenu", + "title": "sample collection date precision menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "year": { @@ -422,8 +427,9 @@ } } }, - "biomaterial extracted menu": { - "name": "biomaterial extracted menu", + "BiomaterialExtractedMenu": { + "name": "BiomaterialExtractedMenu", + "title": "biomaterial extracted menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "RNA (total)": { @@ -448,8 +454,9 @@ } } }, - "signs and symptoms menu": { - "name": "signs and symptoms menu", + "SignsAndSymptomsMenu": { + "name": "SignsAndSymptomsMenu", + "title": "signs and symptoms menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Abnormal lung auscultation": { @@ -854,8 +861,9 @@ } } }, - "host vaccination status menu": { - "name": "host vaccination status menu", + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "host vaccination status menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Fully Vaccinated": { @@ -872,8 +880,9 @@ } } }, - "prior SARS-CoV-2 antiviral treatment menu": { - "name": "prior SARS-CoV-2 antiviral treatment menu", + "PriorSarsCov2AntiviralTreatmentMenu": { + "name": "PriorSarsCov2AntiviralTreatmentMenu", + "title": "prior SARS-CoV-2 antiviral treatment menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Prior antiviral treatment": { @@ -886,8 +895,9 @@ } } }, - "NML submitted specimen type menu": { - "name": "NML submitted specimen type menu", + "NmlSubmittedSpecimenTypeMenu": { + "name": "NmlSubmittedSpecimenTypeMenu", + "title": "NML submitted specimen type menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Swab": { @@ -912,8 +922,9 @@ } } }, - "Related specimen relationship type menu": { - "name": "Related specimen relationship type menu", + "RelatedSpecimenRelationshipTypeMenu": { + "name": "RelatedSpecimenRelationshipTypeMenu", + "title": "Related specimen relationship type menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Acute": { @@ -949,8 +960,9 @@ } } }, - "pre-existing conditions and risk factors menu": { - "name": "pre-existing conditions and risk factors menu", + "PreExistingConditionsAndRiskFactorsMenu": { + "name": "PreExistingConditionsAndRiskFactorsMenu", + "title": "pre-existing conditions and risk factors menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Age 60+": { @@ -1364,8 +1376,9 @@ } } }, - "variant designation menu": { - "name": "variant designation menu", + "VariantDesignationMenu": { + "name": "VariantDesignationMenu", + "title": "variant designation menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Variant of Concern (VOC)": { @@ -1382,8 +1395,9 @@ } } }, - "variant evidence menu": { - "name": "variant evidence menu", + "VariantEvidenceMenu": { + "name": "VariantEvidenceMenu", + "title": "variant evidence menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "RT-qPCR": { @@ -1396,8 +1410,9 @@ } } }, - "complications menu": { - "name": "complications menu", + "ComplicationsMenu": { + "name": "ComplicationsMenu", + "title": "complications menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Abnormal blood oxygen level": { @@ -1750,8 +1765,9 @@ } } }, - "vaccine name menu": { - "name": "vaccine name menu", + "VaccineNameMenu": { + "name": "VaccineNameMenu", + "title": "vaccine name menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Astrazeneca (Vaxzevria)": { @@ -1776,8 +1792,9 @@ } } }, - "anatomical material menu": { - "name": "anatomical material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical material menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Blood": { @@ -1824,8 +1841,9 @@ } } }, - "anatomical part menu": { - "name": "anatomical part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical part menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Anus": { @@ -1950,8 +1968,9 @@ } } }, - "body product menu": { - "name": "body product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body product menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Breast Milk": { @@ -1989,8 +2008,9 @@ } } }, - "prior SARS-CoV-2 infection menu": { - "name": "prior SARS-CoV-2 infection menu", + "PriorSarsCov2InfectionMenu": { + "name": "PriorSarsCov2InfectionMenu", + "title": "prior SARS-CoV-2 infection menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Prior infection": { @@ -2003,8 +2023,9 @@ } } }, - "environmental material menu": { - "name": "environmental material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "environmental material menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air vent": { @@ -2142,8 +2163,9 @@ } } }, - "environmental site menu": { - "name": "environmental site menu", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental site menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Acute care facility": { @@ -2236,8 +2258,9 @@ } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Amniocentesis": { @@ -2334,8 +2357,9 @@ } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air filter": { @@ -2408,8 +2432,9 @@ } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Homo sapiens": { @@ -2478,8 +2503,9 @@ } } }, - "host (common name) menu": { - "name": "host (common name) menu", + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Human": { @@ -2542,8 +2568,9 @@ } } }, - "host health state menu": { - "name": "host health state menu", + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "host health state menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Asymptomatic": { @@ -2568,8 +2595,9 @@ } } }, - "host health status details menu": { - "name": "host health status details menu", + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "host health status details menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Hospitalized": { @@ -2605,8 +2633,9 @@ } } }, - "host health outcome menu": { - "name": "host health outcome menu", + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "host health outcome menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Deceased": { @@ -2627,8 +2656,9 @@ } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Severe acute respiratory syndrome coronavirus 2": { @@ -2645,8 +2675,9 @@ } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Cluster/Outbreak investigation": { @@ -2667,8 +2698,9 @@ } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose of sequencing menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Baseline surveillance (random sampling)": { @@ -2798,8 +2830,9 @@ } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Virus passage": { @@ -2816,8 +2849,9 @@ } } }, - "lab host menu": { - "name": "lab host menu", + "LabHostMenu": { + "name": "LabHostMenu", + "title": "lab host menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "293/ACE2 cell line": { @@ -2885,21 +2919,16 @@ "text": "VeroE6/TMPRSS2 cell line", "meaning": "GENEPIO:0100044", "is_a": "Vero E6 cell line" - } - } - }, - "host disease menu": { - "name": "host disease menu", - "from_schema": "https://example.com/CanCOGeN_Covid-19", - "permissible_values": { + }, "COVID-19": { "text": "COVID-19", "meaning": "MONDO:0100096" } } }, - "host age bin menu": { - "name": "host age bin menu", + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host age bin menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "0 - 9": { @@ -2954,8 +2983,9 @@ } } }, - "host gender menu": { - "name": "host gender menu", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host gender menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Female": { @@ -2984,8 +3014,9 @@ } } }, - "exposure event menu": { - "name": "exposure event menu", + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "exposure event menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Mass Gathering": { @@ -3080,8 +3111,9 @@ } } }, - "exposure contact level menu": { - "name": "exposure contact level menu", + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "exposure contact level menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Contact with infected individual": { @@ -3110,8 +3142,9 @@ } } }, - "host role menu": { - "name": "host role menu", + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "host role menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Attendee": { @@ -3306,8 +3339,9 @@ } } }, - "exposure setting menu": { - "name": "exposure setting menu", + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "exposure setting menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Human Exposure": { @@ -3623,8 +3657,9 @@ } } }, - "travel point of entry type menu": { - "name": "travel point of entry type menu", + "TravelPointOfEntryTypeMenu": { + "name": "TravelPointOfEntryTypeMenu", + "title": "travel point of entry type menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air": { @@ -3634,13 +3669,7 @@ "Land": { "text": "Land", "meaning": "GENEPIO:0100409" - } - } - }, - "border testing test day type menu": { - "name": "border testing test day type menu", - "from_schema": "https://example.com/CanCOGeN_Covid-19", - "permissible_values": { + }, "day 1": { "text": "day 1", "meaning": "GENEPIO:0100410" @@ -3655,8 +3684,9 @@ } } }, - "travel history availability menu": { - "name": "travel history availability menu", + "TravelHistoryAvailabilityMenu": { + "name": "TravelHistoryAvailabilityMenu", + "title": "travel history availability menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Travel history available": { @@ -3684,8 +3714,9 @@ } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Illumina": { @@ -3914,8 +3945,9 @@ } } }, - "gene name menu": { - "name": "gene name menu", + "GeneNameMenu": { + "name": "GeneNameMenu", + "title": "gene name menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "E gene (orf4)": { @@ -4166,8 +4198,9 @@ } } }, - "sequence submitted by menu": { - "name": "sequence submitted by menu", + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", + "title": "sequence submitted by menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -4252,8 +4285,9 @@ } } }, - "sample collected by menu": { - "name": "sample collected by menu", + "SampleCollectedByMenu": { + "name": "SampleCollectedByMenu", + "title": "sample collected by menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -4362,8 +4396,9 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Afghanistan": { @@ -5454,8 +5489,8 @@ } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -5476,11 +5511,14 @@ ], "slot_uri": "GENEPIO:0001123", "identifier": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "required": true }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "description": "The name of the third party company or laboratory that provided services.", "title": "third party lab service provider name", "comments": [ @@ -5496,10 +5534,13 @@ "NML_LIMS:HC_TEXT5" ], "slot_uri": "GENEPIO:0001202", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "description": "The identifier assigned to a sample by a third party service provider.", "title": "third party lab sample ID", "comments": [ @@ -5515,10 +5556,13 @@ "NML_LIMS:PH_ID_NUMBER_PRIMARY" ], "slot_uri": "GENEPIO:0001149", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", "comments": [ @@ -5534,11 +5578,14 @@ "NML_LIMS:PH_CASE_ID" ], "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", "comments": [ @@ -5556,17 +5603,20 @@ "NML_LIMS:PH_RELATED_PRIMARY_ID" ], "slot_uri": "GENEPIO:0001128", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "description": "The identifier assigned to a sequenced isolate in IRIDA.", "title": "IRIDA sample name", "comments": [ @@ -5582,10 +5632,13 @@ "NML_LIMS:IRIDA%20sample%20name" ], "slot_uri": "GENEPIO:0001131", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort.", "title": "umbrella bioproject accession", "comments": [ @@ -5601,15 +5654,18 @@ "NML_LIMS:umbrella%20bioproject%20accession" ], "slot_uri": "GENEPIO:0001133", - "range": "umbrella bioproject accession menu", + "domain_of": [ + "CanCOGeNCovid19" + ], + "range": "UmbrellaBioprojectAccessionMenu", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", "comments": [ @@ -5627,6 +5683,9 @@ "BIOSAMPLE:bioproject_accession" ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5634,8 +5693,8 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", "comments": [ @@ -5652,6 +5711,9 @@ "NML_LIMS:PH_BIOSAMPLE_ACCESSION" ], "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5659,8 +5721,8 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", "comments": [ @@ -5677,6 +5739,9 @@ "NML_LIMS:PH_SRA_ACCESSION" ], "slot_uri": "GENEPIO:0001142", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5684,8 +5749,8 @@ "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", "comments": [ @@ -5702,6 +5767,9 @@ "NML_LIMS:GenBank%20accession" ], "slot_uri": "GENEPIO:0001145", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5709,8 +5777,8 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "comments": [ @@ -5729,6 +5797,9 @@ "VirusSeq_Portal:GISAID%20accession" ], "slot_uri": "GENEPIO:0001147", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5736,8 +5807,8 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", "comments": [ @@ -5757,18 +5828,21 @@ "VirusSeq_Portal:sample%20collected%20by" ], "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "sample collected by menu" + "range": "SampleCollectedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "comments": [ @@ -5784,11 +5858,14 @@ "NML_LIMS:sample%20collector%20contact%20email" ], "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "comments": [ @@ -5805,10 +5882,13 @@ "NML_LIMS:sample%20collector%20contact%20address" ], "slot_uri": "GENEPIO:0001158", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", "comments": [ @@ -5828,18 +5908,21 @@ "VirusSeq_Portal:sequence%20submitted%20by" ], "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "SequenceSubmittedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", "comments": [ @@ -5855,10 +5938,13 @@ "NML_LIMS:sequence%20submitter%20contact%20email" ], "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "description": "The mailing address of the agency submitting the sequence.", "title": "sequence submitter contact address", "comments": [ @@ -5875,10 +5961,13 @@ "NML_LIMS:sequence%20submitter%20contact%20address" ], "slot_uri": "GENEPIO:0001167", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", "todos": [ @@ -5902,18 +5991,21 @@ "VirusSeq_Portal:sample%20collection%20date" ], "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", "comments": [ @@ -5930,18 +6022,21 @@ "NML_LIMS:HC_TEXT2" ], "slot_uri": "GENEPIO:0001177", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "sample collection date precision menu" + "range": "SampleCollectionDatePrecisionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", "comments": [ @@ -5957,17 +6052,20 @@ "NML_LIMS:sample%20received%20date" ], "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", "comments": [ @@ -5987,18 +6085,21 @@ "VirusSeq_Portal:geo_loc_name%20%28country%29" ], "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", "comments": [ @@ -6017,18 +6118,21 @@ "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" ], "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "GeoLocNameStateProvinceTerritoryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city where the sample was collected.", "title": "geo_loc_name (city)", "comments": [ @@ -6045,6 +6149,9 @@ "NML_LIMS:geo_loc_name%20%28city%29" ], "slot_uri": "GENEPIO:0001189", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, "organism": { @@ -6067,13 +6174,16 @@ "VirusSeq_Portal:organism" ], "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6100,18 +6210,21 @@ "VirusSeq_Portal:fasta%20header%20name" ], "slot_uri": "GENEPIO:0001195", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", "comments": [ @@ -6130,18 +6243,21 @@ "VirusSeq_Portal:purpose%20of%20sampling" ], "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "comments": [ @@ -6160,18 +6276,21 @@ "VirusSeq_Portal:purpose%20of%20sampling%20details" ], "slot_uri": "GENEPIO:0001200", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", "comments": [ @@ -6188,11 +6307,14 @@ "NML_LIMS:PH_SPECIMEN_TYPE" ], "slot_uri": "GENEPIO:0001204", - "range": "NML submitted specimen type menu", + "domain_of": [ + "CanCOGeNCovid19" + ], + "range": "NmlSubmittedSpecimenTypeMenu", "required": true }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", "title": "Related specimen relationship type", "comments": [ @@ -6210,10 +6332,13 @@ "NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE" ], "slot_uri": "GENEPIO:0001209", - "range": "Related specimen relationship type menu" + "domain_of": [ + "CanCOGeNCovid19" + ], + "range": "RelatedSpecimenRelationshipTypeMenu" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", "comments": [ @@ -6234,19 +6359,22 @@ "VirusSeq_Portal:anatomical%20material" ], "slot_uri": "GENEPIO:0001211", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "anatomical material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", "comments": [ @@ -6267,19 +6395,22 @@ "VirusSeq_Portal:anatomical%20part" ], "slot_uri": "GENEPIO:0001214", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "anatomical part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", "comments": [ @@ -6300,19 +6431,22 @@ "VirusSeq_Portal:body%20product" ], "slot_uri": "GENEPIO:0001216", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "body product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", "comments": [ @@ -6333,19 +6467,22 @@ "VirusSeq_Portal:environmental%20material" ], "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "environmental material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", "comments": [ @@ -6366,19 +6503,22 @@ "VirusSeq_Portal:environmental%20site" ], "slot_uri": "GENEPIO:0001232", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "environmental site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", "comments": [ @@ -6399,19 +6539,22 @@ "VirusSeq_Portal:collection%20device" ], "slot_uri": "GENEPIO:0001234", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", "comments": [ @@ -6432,19 +6575,22 @@ "VirusSeq_Portal:collection%20method" ], "slot_uri": "GENEPIO:0001241", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "collection method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", "comments": [ @@ -6460,10 +6606,13 @@ "NML_LIMS:collection%20protocol" ], "slot_uri": "GENEPIO:0001243", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -6480,19 +6629,22 @@ "NML_LIMS:specimen%20processing" ], "slot_uri": "GENEPIO:0001253", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "specimen processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -6505,10 +6657,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", "title": "lab host", "comments": [ @@ -6526,18 +6681,21 @@ "BIOSAMPLE:lab_host" ], "slot_uri": "GENEPIO:0001255", + "domain_of": [ + "CanCOGeNCovid19" + ], "recommended": true, "any_of": [ { - "range": "lab host menu" + "range": "LabHostMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "description": "Number of passages.", "title": "passage number", "comments": [ @@ -6555,19 +6713,22 @@ "BIOSAMPLE:passage_history" ], "slot_uri": "GENEPIO:0001261", + "domain_of": [ + "CanCOGeNCovid19" + ], "recommended": true, - "minimum_value": "0", + "minimum_value": 0, "any_of": [ { "range": "integer" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "description": "Description of how organism was passaged.", "title": "passage method", "comments": [ @@ -6585,18 +6746,21 @@ "BIOSAMPLE:passage_method" ], "slot_uri": "GENEPIO:0001264", + "domain_of": [ + "CanCOGeNCovid19" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "title": "biomaterial extracted", "comments": [ @@ -6612,17 +6776,20 @@ "NML_LIMS:biomaterial%20extracted" ], "slot_uri": "GENEPIO:0001266", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "biomaterial extracted menu" + "range": "BiomaterialExtractedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", "comments": [ @@ -6639,17 +6806,20 @@ "NML_LIMS:PH_ANIMAL_TYPE" ], "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", "comments": [ @@ -6668,18 +6838,21 @@ "VirusSeq_Portal:host%20%28scientific%20name%29" ], "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "description": "Health status of the host at the time of sample collection.", "title": "host health state", "comments": [ @@ -6698,17 +6871,20 @@ "BIOSAMPLE:host_health_state" ], "slot_uri": "GENEPIO:0001388", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "host health state menu" + "range": "HostHealthStateMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "description": "Further details pertaining to the health or disease status of the host at time of collection.", "title": "host health status details", "comments": [ @@ -6725,17 +6901,20 @@ "NML_LIMS:PH_HOST_HEALTH_DETAILS" ], "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "host health status details menu" + "range": "HostHealthStatusDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", "comments": [ @@ -6752,17 +6931,20 @@ "BIOSAMPLE:host_disease_outcome" ], "slot_uri": "GENEPIO:0001390", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "host health outcome menu" + "range": "HostHealthOutcomeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", "comments": [ @@ -6781,18 +6963,21 @@ "VirusSeq_Portal:host%20disease" ], "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "host disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", "comments": [ @@ -6812,20 +6997,23 @@ "VirusSeq_Portal:host%20age" ], "slot_uri": "GENEPIO:0001392", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, - "minimum_value": "0", - "maximum_value": "130", + "minimum_value": 0, + "maximum_value": 130, "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The unit used to measure the host age, in either months or years.", "title": "host age unit", "comments": [ @@ -6843,18 +7031,21 @@ "VirusSeq_Portal:host%20age%20unit" ], "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "host age unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host age bin", "comments": [ @@ -6872,18 +7063,21 @@ "VirusSeq_Portal:host%20age%20bin" ], "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { - "range": "host age bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", "comments": [ @@ -6903,23 +7097,21 @@ "VirusSeq_Portal:host%20gender" ], "slot_uri": "GENEPIO:0001395", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, - "structured_pattern": { - "syntax": "{Title_Case}", - "interpolated": true, - "partial_match": false - }, "any_of": [ { - "range": "host gender menu" + "range": "HostGenderMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "description": "The country of residence of the host.", "title": "host residence geo_loc name (country)", "comments": [ @@ -6935,17 +7127,20 @@ "NML_LIMS:PH_HOST_COUNTRY" ], "slot_uri": "GENEPIO:0001396", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", "description": "The state/province/territory of residence of the host.", "title": "host residence geo_loc name (state/province/territory)", "comments": [ @@ -6961,17 +7156,20 @@ "NML_LIMS:PH_HOST_PROVINCE" ], "slot_uri": "GENEPIO:0001397", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "GeoLocNameStateProvinceTerritoryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to e.g. #131", "title": "host subject ID", "comments": [ @@ -6988,10 +7186,13 @@ "BIOSAMPLE:host_subject_id" ], "slot_uri": "GENEPIO:0001398", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", "comments": [ @@ -7008,17 +7209,20 @@ "NML_LIMS:HC_ONSET_DATE" ], "slot_uri": "GENEPIO:0001399", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician.", "title": "signs and symptoms", "comments": [ @@ -7041,18 +7245,21 @@ "NML_LIMS:HC_SYMPTOMS" ], "slot_uri": "GENEPIO:0001400", + "domain_of": [ + "CanCOGeNCovid19" + ], "multivalued": true, "any_of": [ { - "range": "signs and symptoms menu" + "range": "SignsAndSymptomsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", "title": "pre-existing conditions and risk factors", "comments": [ @@ -7074,13 +7281,16 @@ "NML_LIMS:pre-existing%20conditions%20and%20risk%20factors" ], "slot_uri": "GENEPIO:0001401", + "domain_of": [ + "CanCOGeNCovid19" + ], "multivalued": true, "any_of": [ { - "range": "pre-existing conditions and risk factors menu" + "range": "PreExistingConditionsAndRiskFactorsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -7107,18 +7317,21 @@ "NML_LIMS:complications" ], "slot_uri": "GENEPIO:0001402", + "domain_of": [ + "CanCOGeNCovid19" + ], "multivalued": true, "any_of": [ { - "range": "complications menu" + "range": "ComplicationsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", "comments": [ @@ -7134,17 +7347,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0001404", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "host vaccination status menu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "description": "The number of doses of the vaccine recived by the host.", "title": "number of vaccine doses received", "comments": [ @@ -7157,10 +7373,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001406", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "integer" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", "title": "vaccination dose 1 vaccine name", "comments": [ @@ -7176,17 +7395,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100313", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "vaccine name menu" + "range": "VaccineNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", "comments": [ @@ -7202,17 +7424,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100314", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", "title": "vaccination dose 2 vaccine name", "comments": [ @@ -7228,17 +7453,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100315", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "vaccine name menu" + "range": "VaccineNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination dose 2 vaccination date", "comments": [ @@ -7254,17 +7482,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100316", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "description": "The name of the vaccine administered as the third dose of a vaccine regimen.", "title": "vaccination dose 3 vaccine name", "comments": [ @@ -7280,17 +7511,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100317", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "vaccine name menu" + "range": "VaccineNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "description": "The date the third dose of a vaccine was administered.", "title": "vaccination dose 3 vaccination date", "comments": [ @@ -7306,17 +7540,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100318", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "description": "The name of the vaccine administered as the fourth dose of a vaccine regimen.", "title": "vaccination dose 4 vaccine name", "comments": [ @@ -7332,17 +7569,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100319", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "vaccine name menu" + "range": "VaccineNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "description": "The date the fourth dose of a vaccine was administered.", "title": "vaccination dose 4 vaccination date", "comments": [ @@ -7358,17 +7598,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100320", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", "comments": [ @@ -7393,10 +7636,13 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100321", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "description": "The country where the host was likely exposed to the causative agent of the illness.", "title": "location of exposure geo_loc name (country)", "comments": [ @@ -7412,17 +7658,20 @@ "NML_LIMS:PH_EXPOSURE_COUNTRY" ], "slot_uri": "GENEPIO:0001410", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "description": "The name of the city that was the destination of most recent travel.", "title": "destination of most recent travel (city)", "comments": [ @@ -7439,10 +7688,13 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001411", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "description": "The name of the province that was the destination of most recent travel.", "title": "destination of most recent travel (state/province/territory)", "comments": [ @@ -7459,10 +7711,13 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001412", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "description": "The name of the country that was the destination of most recent travel.", "title": "destination of most recent travel (country)", "comments": [ @@ -7479,17 +7734,20 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001413", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", "title": "most recent travel departure date", "comments": [ @@ -7506,17 +7764,20 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001414", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", "title": "most recent travel return date", "comments": [ @@ -7533,17 +7794,20 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001415", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "travel point of entry type": { - "name": "travel point of entry type", + "travel_point_of_entry_type": { + "name": "travel_point_of_entry_type", "description": "The type of entry point a traveler arrives through.", "title": "travel point of entry type", "comments": [ @@ -7559,18 +7823,21 @@ "NML_LIMS:PH_POINT_OF_ENTRY" ], "slot_uri": "GENEPIO:0100413", + "domain_of": [ + "CanCOGeNCovid19" + ], "recommended": true, "any_of": [ { - "range": "travel point of entry type menu" + "range": "TravelPointOfEntryTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "border testing test day type": { - "name": "border testing test day type", + "border_testing_test_day_type": { + "name": "border_testing_test_day_type", "description": "The day a traveller was tested on or after arrival at their point of entry.", "title": "border testing test day type", "comments": [ @@ -7586,18 +7853,21 @@ "NML_LIMS:PH_DAY" ], "slot_uri": "GENEPIO:0100414", + "domain_of": [ + "CanCOGeNCovid19" + ], "recommended": true, "any_of": [ { - "range": "border testing test day type menu" + "range": "BorderTestingTestDayTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "description": "Travel history in last six months.", "title": "travel history", "comments": [ @@ -7619,10 +7889,13 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0001416", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "travel history availability": { - "name": "travel history availability", + "travel_history_availability": { + "name": "travel_history_availability", "description": "The availability of different types of travel history in the last 6 months (e.g. international, domestic).", "title": "travel history availability", "comments": [ @@ -7638,17 +7911,20 @@ "NML_LIMS:PH_TRAVEL" ], "slot_uri": "GENEPIO:0100649", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "travel history availability menu" + "range": "TravelHistoryAvailabilityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", "comments": [ @@ -7666,17 +7942,20 @@ "NML_LIMS:PH_EXPOSURE" ], "slot_uri": "GENEPIO:0001417", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", "comments": [ @@ -7692,17 +7971,20 @@ "NML_LIMS:exposure%20contact%20level" ], "slot_uri": "GENEPIO:0001418", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", "comments": [ @@ -7718,11 +8000,14 @@ "NML_LIMS:PH_HOST_ROLE" ], "slot_uri": "GENEPIO:0001419", - "multivalued": true, - "range": "host role menu" + "domain_of": [ + "CanCOGeNCovid19" + ], + "range": "HostRoleMenu", + "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", "comments": [ @@ -7738,11 +8023,14 @@ "NML_LIMS:PH_EXPOSURE" ], "slot_uri": "GENEPIO:0001428", - "multivalued": true, - "range": "exposure setting menu" + "domain_of": [ + "CanCOGeNCovid19" + ], + "range": "ExposureSettingMenu", + "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", "comments": [ @@ -7758,10 +8046,13 @@ "NML_LIMS:PH_EXPOSURE_DETAILS" ], "slot_uri": "GENEPIO:0001431", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "description": "Whether there was prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection", "comments": [ @@ -7777,17 +8068,20 @@ "NML_LIMS:prior%20SARS-CoV-2%20infection" ], "slot_uri": "GENEPIO:0001435", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "prior SARS-CoV-2 infection menu" + "range": "PriorSarsCov2InfectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "description": "The identifier of the isolate found in the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection isolate", "comments": [ @@ -7803,10 +8097,13 @@ "NML_LIMS:prior%20SARS-CoV-2%20infection%20isolate" ], "slot_uri": "GENEPIO:0001436", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection date", "comments": [ @@ -7822,10 +8119,13 @@ "NML_LIMS:prior%20SARS-CoV-2%20infection%20date" ], "slot_uri": "GENEPIO:0001437", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "date" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", "title": "prior SARS-CoV-2 antiviral treatment", "comments": [ @@ -7841,17 +8141,20 @@ "NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment" ], "slot_uri": "GENEPIO:0001438", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "prior SARS-CoV-2 antiviral treatment menu" + "range": "PriorSarsCov2AntiviralTreatmentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment agent", "comments": [ @@ -7867,10 +8170,13 @@ "NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment%20agent" ], "slot_uri": "GENEPIO:0001439", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "description": "The date treatment was first administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment date", "comments": [ @@ -7886,10 +8192,13 @@ "NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment%20date" ], "slot_uri": "GENEPIO:0001440", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "date" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", "comments": [ @@ -7908,19 +8217,22 @@ "VirusSeq_Portal:purpose%20of%20sequencing" ], "slot_uri": "GENEPIO:0001445", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "purpose of sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "comments": [ @@ -7938,18 +8250,21 @@ "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ @@ -7968,18 +8283,21 @@ "NML_LIMS:PH_SEQUENCING_DATE" ], "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", "comments": [ @@ -7995,11 +8313,14 @@ "NML_LIMS:library%20ID" ], "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", "comments": [ @@ -8015,10 +8336,13 @@ "NML_LIMS:amplicon%20size" ], "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", "comments": [ @@ -8034,10 +8358,13 @@ "NML_LIMS:PH_LIBRARY_PREP_KIT" ], "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "description": "The barcode of the flow cell used for sequencing.", "title": "flow cell barcode", "comments": [ @@ -8053,10 +8380,13 @@ "NML_LIMS:flow%20cell%20barcode" ], "slot_uri": "GENEPIO:0001451", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", "comments": [ @@ -8075,19 +8405,22 @@ "VirusSeq_Portal:sequencing%20instrument" ], "slot_uri": "GENEPIO:0001452", - "multivalued": true, + "domain_of": [ + "CanCOGeNCovid19" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "sequencing instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "description": "The name and version number of the sequencing protocol used.", "title": "sequencing protocol name", "comments": [ @@ -8104,11 +8437,14 @@ "NML_LIMS:PH_SEQ_PROTOCOL_NAME" ], "slot_uri": "GENEPIO:0001453", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -8125,10 +8461,13 @@ "VirusSeq_Portal:sequencing%20protocol" ], "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "description": "The manufacturer's kit number.", "title": "sequencing kit number", "comments": [ @@ -8144,10 +8483,13 @@ "NML_LIMS:sequencing%20kit%20number" ], "slot_uri": "GENEPIO:0001455", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", "comments": [ @@ -8163,10 +8505,13 @@ "NML_LIMS:amplicon%20pcr%20primer%20scheme" ], "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "comments": [ @@ -8183,11 +8528,14 @@ "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" ], "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "required": true }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "comments": [ @@ -8204,11 +8552,14 @@ "VirusSeq_Portal:dehosting%20method" ], "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence name": { - "name": "consensus sequence name", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "description": "The name of the consensus sequence.", "title": "consensus sequence name", "comments": [ @@ -8224,10 +8575,13 @@ "NML_LIMS:consensus%20sequence%20name" ], "slot_uri": "GENEPIO:0001460", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "consensus sequence filename": { - "name": "consensus sequence filename", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "description": "The name of the consensus sequence file.", "title": "consensus sequence filename", "comments": [ @@ -8243,10 +8597,13 @@ "NML_LIMS:consensus%20sequence%20filename" ], "slot_uri": "GENEPIO:0001461", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", "description": "The filepath of the consensus sequence file.", "title": "consensus sequence filepath", "comments": [ @@ -8262,10 +8619,13 @@ "NML_LIMS:consensus%20sequence%20filepath" ], "slot_uri": "GENEPIO:0001462", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "comments": [ @@ -8284,11 +8644,14 @@ "VirusSeq_Portal:consensus%20sequence%20software%20name" ], "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "comments": [ @@ -8306,11 +8669,14 @@ "VirusSeq_Portal:consensus%20sequence%20software%20version" ], "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "required": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", "comments": [ @@ -8327,10 +8693,13 @@ "VirusSeq_Portal:breadth%20of%20coverage%20value" ], "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", "comments": [ @@ -8348,10 +8717,13 @@ "VirusSeq_Portal:depth%20of%20coverage%20value" ], "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", "comments": [ @@ -8367,10 +8739,13 @@ "NML_LIMS:depth%20of%20coverage%20threshold" ], "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "r1 fastq filename": { - "name": "r1 fastq filename", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", "comments": [ @@ -8386,11 +8761,14 @@ "NML_LIMS:r1%20fastq%20filename" ], "slot_uri": "GENEPIO:0001476", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "r2 fastq filename": { - "name": "r2 fastq filename", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "description": "The user-specified filename of the r2 FASTQ file.", "title": "r2 fastq filename", "comments": [ @@ -8406,11 +8784,14 @@ "NML_LIMS:r2%20fastq%20filename" ], "slot_uri": "GENEPIO:0001477", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "description": "The location of the r1 FASTQ file within a user's file system.", "title": "r1 fastq filepath", "comments": [ @@ -8426,10 +8807,13 @@ "NML_LIMS:r1%20fastq%20filepath" ], "slot_uri": "GENEPIO:0001478", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "description": "The location of the r2 FASTQ file within a user's file system.", "title": "r2 fastq filepath", "comments": [ @@ -8445,10 +8829,13 @@ "NML_LIMS:r2%20fastq%20filepath" ], "slot_uri": "GENEPIO:0001479", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "fast5 filename": { - "name": "fast5 filename", + "fast5_filename": { + "name": "fast5_filename", "description": "The user-specified filename of the FAST5 file.", "title": "fast5 filename", "comments": [ @@ -8464,10 +8851,13 @@ "NML_LIMS:fast5%20filename" ], "slot_uri": "GENEPIO:0001480", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "fast5 filepath": { - "name": "fast5 filepath", + "fast5_filepath": { + "name": "fast5_filepath", "description": "The location of the FAST5 file within a user's file system.", "title": "fast5 filepath", "comments": [ @@ -8483,10 +8873,13 @@ "NML_LIMS:fast5%20filepath" ], "slot_uri": "GENEPIO:0001481", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", "comments": [ @@ -8502,11 +8895,14 @@ "NML_LIMS:number%20of%20base%20pairs%20sequenced" ], "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "integer", - "minimum_value": "0" + "minimum_value": 0 }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "Size of the reconstructed genome described as the number of base pairs.", "title": "consensus genome length", "comments": [ @@ -8522,11 +8918,14 @@ "NML_LIMS:consensus%20genome%20length" ], "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "integer", - "minimum_value": "0" + "minimum_value": 0 }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", "title": "Ns per 100 kbp", "comments": [ @@ -8542,11 +8941,14 @@ "NML_LIMS:Ns%20per%20100%20kbp" ], "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "decimal", - "minimum_value": "0" + "minimum_value": 0 }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", "comments": [ @@ -8563,10 +8965,13 @@ "VirusSeq_Portal:reference%20genome%20accession" ], "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "comments": [ @@ -8584,11 +8989,14 @@ "VirusSeq_Portal:bioinformatics%20protocol" ], "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "required": true }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "description": "The name of the lineage or clade.", "title": "lineage/clade name", "comments": [ @@ -8604,10 +9012,13 @@ "NML_LIMS:PH_LINEAGE_CLADE_NAME" ], "slot_uri": "GENEPIO:0001500", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "description": "The name of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software name", "comments": [ @@ -8623,10 +9034,13 @@ "NML_LIMS:PH_LINEAGE_CLADE_SOFTWARE" ], "slot_uri": "GENEPIO:0001501", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "description": "The version of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software version", "comments": [ @@ -8642,10 +9056,13 @@ "NML_LIMS:PH_LINEAGE_CLADE_VERSION" ], "slot_uri": "GENEPIO:0001502", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", "title": "variant designation", "comments": [ @@ -8661,17 +9078,20 @@ "NML_LIMS:PH_VARIANT_DESIGNATION" ], "slot_uri": "GENEPIO:0001503", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "variant designation menu" + "range": "VariantDesignationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "variant evidence": { - "name": "variant evidence", + "variant_evidence": { + "name": "variant_evidence", "description": "The evidence used to make the variant determination.", "title": "variant evidence", "comments": [ @@ -8687,17 +9107,20 @@ "NML_LIMS:PH_VARIANT_EVIDENCE" ], "slot_uri": "GENEPIO:0001504", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "variant evidence menu" + "range": "VariantEvidenceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "description": "Details about the evidence used to make the variant determination.", "title": "variant evidence details", "comments": [ @@ -8713,10 +9136,13 @@ "NML_LIMS:PH_VARIANT_EVIDENCE_DETAILS" ], "slot_uri": "GENEPIO:0001505", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 1", "comments": [ @@ -8735,17 +9161,20 @@ "VirusSeq_Portal:gene%20name" ], "slot_uri": "GENEPIO:0001507", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 1", "comments": [ @@ -8758,10 +9187,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001508", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", "comments": [ @@ -8780,17 +9212,20 @@ "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" ], "slot_uri": "GENEPIO:0001509", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 2", "comments": [ @@ -8808,17 +9243,20 @@ "BIOSAMPLE:gene_name_2" ], "slot_uri": "GENEPIO:0001510", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 2", "comments": [ @@ -8831,10 +9269,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001511", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", "comments": [ @@ -8852,17 +9293,20 @@ "BIOSAMPLE:diagnostic_PCR_CT_value_2" ], "slot_uri": "GENEPIO:0001512", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 3", "comments": [ @@ -8879,17 +9323,20 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233" ], "slot_uri": "GENEPIO:0001513", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr protocol 3": { - "name": "diagnostic pcr protocol 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 3", "comments": [ @@ -8902,10 +9349,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001514", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", "comments": [ @@ -8922,12 +9372,15 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value" ], "slot_uri": "GENEPIO:0001515", + "domain_of": [ + "CanCOGeNCovid19" + ], "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -8950,11 +9403,14 @@ "NML_LIMS:PH_CANCOGEN_AUTHORS" ], "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", "comments": [ @@ -8972,6 +9428,9 @@ "NML_LIMS:HC_COMMENTS" ], "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "CanCOGeNCovid19" + ], "range": "Provenance" } }, @@ -8981,132 +9440,133 @@ "description": "A DataHarmonizer interface", "from_schema": "https://example.com/CanCOGeN_Covid-19" }, - "CanCOGeN Covid-19": { - "name": "CanCOGeN Covid-19", + "CanCOGeNCovid19": { + "name": "CanCOGeNCovid19", "description": "Canadian specification for Covid-19 clinical virus biosample data gathering", + "title": "CanCOGeN Covid-19", "from_schema": "https://example.com/CanCOGeN_Covid-19", "see_also": [ "templates/canada_covid19/SOP.pdf" ], "is_a": "dh_interface", "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 1, "slot_group": "Database Identifiers" }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "rank": 2, "slot_group": "Database Identifiers" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "rank": 3, "slot_group": "Database Identifiers" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "rank": 4, "slot_group": "Database Identifiers" }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "rank": 5, "slot_group": "Database Identifiers" }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "rank": 6, "slot_group": "Database Identifiers" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "rank": 7, "slot_group": "Database Identifiers" }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "rank": 8, "slot_group": "Database Identifiers" }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "rank": 9, "slot_group": "Database Identifiers" }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "rank": 10, "slot_group": "Database Identifiers" }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "rank": 11, "slot_group": "Database Identifiers" }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "rank": 12, "slot_group": "Database Identifiers" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 13, "slot_group": "Sample collection and processing" }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "rank": 14, "slot_group": "Sample collection and processing" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "rank": 15, "slot_group": "Sample collection and processing" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 16, "slot_group": "Sample collection and processing" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "rank": 17, "slot_group": "Sample collection and processing" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "rank": 18, "slot_group": "Sample collection and processing" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "rank": 19, "slot_group": "Sample collection and processing" }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "rank": 20, "slot_group": "Sample collection and processing" }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "rank": 21, "slot_group": "Sample collection and processing" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 22, "slot_group": "Sample collection and processing" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 23, "slot_group": "Sample collection and processing" }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "rank": 24, "slot_group": "Sample collection and processing" }, @@ -9120,173 +9580,173 @@ "rank": 26, "slot_group": "Sample collection and processing" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "rank": 27, "slot_group": "Sample collection and processing" }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "rank": 28, "slot_group": "Sample collection and processing" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "rank": 29, "slot_group": "Sample collection and processing" }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "rank": 30, "slot_group": "Sample collection and processing" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "rank": 31, "slot_group": "Sample collection and processing" }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "rank": 32, "slot_group": "Sample collection and processing" }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "rank": 33, "slot_group": "Sample collection and processing" }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "rank": 34, "slot_group": "Sample collection and processing" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "rank": 35, "slot_group": "Sample collection and processing" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 36, "slot_group": "Sample collection and processing" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 37, "slot_group": "Sample collection and processing" }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "rank": 38, "slot_group": "Sample collection and processing" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "rank": 39, "slot_group": "Sample collection and processing" }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "rank": 40, "slot_group": "Sample collection and processing" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "rank": 41, "slot_group": "Sample collection and processing" }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "rank": 42, "slot_group": "Sample collection and processing" }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "rank": 43, "slot_group": "Sample collection and processing" }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "rank": 44, "slot_group": "Sample collection and processing" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "rank": 45, "slot_group": "Host Information" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 46, "slot_group": "Host Information" }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "rank": 47, "slot_group": "Host Information" }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "rank": 48, "slot_group": "Host Information" }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "rank": 49, "slot_group": "Host Information" }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "rank": 50, "slot_group": "Host Information" }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "rank": 51, "slot_group": "Host Information" }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "rank": 52, "slot_group": "Host Information" }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "rank": 53, "slot_group": "Host Information" }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "rank": 54, "slot_group": "Host Information" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "rank": 55, "slot_group": "Host Information" }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", "rank": 56, "slot_group": "Host Information" }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "rank": 57, "slot_group": "Host Information" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "rank": 58, "slot_group": "Host Information" }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "rank": 59, "slot_group": "Host Information" }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "rank": 60, "slot_group": "Host Information" }, @@ -9295,403 +9755,403 @@ "rank": 61, "slot_group": "Host Information" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "rank": 62, "slot_group": "Host vaccination information" }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "rank": 63, "slot_group": "Host vaccination information" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "rank": 64, "slot_group": "Host vaccination information" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "rank": 65, "slot_group": "Host vaccination information" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "rank": 66, "slot_group": "Host vaccination information" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "rank": 67, "slot_group": "Host vaccination information" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "rank": 68, "slot_group": "Host vaccination information" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "rank": 69, "slot_group": "Host vaccination information" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "rank": 70, "slot_group": "Host vaccination information" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "rank": 71, "slot_group": "Host vaccination information" }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "rank": 72, "slot_group": "Host vaccination information" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "rank": 73, "slot_group": "Host exposure information" }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "rank": 74, "slot_group": "Host exposure information" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "rank": 75, "slot_group": "Host exposure information" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "rank": 76, "slot_group": "Host exposure information" }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "rank": 77, "slot_group": "Host exposure information" }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "rank": 78, "slot_group": "Host exposure information" }, - "travel point of entry type": { - "name": "travel point of entry type", + "travel_point_of_entry_type": { + "name": "travel_point_of_entry_type", "rank": 79, "slot_group": "Host exposure information" }, - "border testing test day type": { - "name": "border testing test day type", + "border_testing_test_day_type": { + "name": "border_testing_test_day_type", "rank": 80, "slot_group": "Host exposure information" }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "rank": 81, "slot_group": "Host exposure information" }, - "travel history availability": { - "name": "travel history availability", + "travel_history_availability": { + "name": "travel_history_availability", "rank": 82, "slot_group": "Host exposure information" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "rank": 83, "slot_group": "Host exposure information" }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "rank": 84, "slot_group": "Host exposure information" }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "rank": 85, "slot_group": "Host exposure information" }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "rank": 86, "slot_group": "Host exposure information" }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "rank": 87, "slot_group": "Host exposure information" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "rank": 88, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "rank": 89, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "rank": 90, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "rank": 91, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "rank": 92, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "rank": 93, "slot_group": "Host reinfection information" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 94, "slot_group": "Sequencing" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 95, "slot_group": "Sequencing" }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "rank": 96, "slot_group": "Sequencing" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "rank": 97, "slot_group": "Sequencing" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "rank": 98, "slot_group": "Sequencing" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 99, "slot_group": "Sequencing" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "rank": 100, "slot_group": "Sequencing" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 101, "slot_group": "Sequencing" }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "rank": 102, "slot_group": "Sequencing" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 103, "slot_group": "Sequencing" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "rank": 104, "slot_group": "Sequencing" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 105, "slot_group": "Sequencing" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 106, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "rank": 107, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence name": { - "name": "consensus sequence name", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "rank": 108, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence filename": { - "name": "consensus sequence filename", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "rank": 109, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", "rank": 110, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 111, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 112, "slot_group": "Bioinformatics and QC metrics" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 113, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 114, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 115, "slot_group": "Bioinformatics and QC metrics" }, - "r1 fastq filename": { - "name": "r1 fastq filename", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", "rank": 116, "slot_group": "Bioinformatics and QC metrics" }, - "r2 fastq filename": { - "name": "r2 fastq filename", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "rank": 117, "slot_group": "Bioinformatics and QC metrics" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "rank": 118, "slot_group": "Bioinformatics and QC metrics" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "rank": 119, "slot_group": "Bioinformatics and QC metrics" }, - "fast5 filename": { - "name": "fast5 filename", + "fast5_filename": { + "name": "fast5_filename", "rank": 120, "slot_group": "Bioinformatics and QC metrics" }, - "fast5 filepath": { - "name": "fast5 filepath", + "fast5_filepath": { + "name": "fast5_filepath", "rank": 121, "slot_group": "Bioinformatics and QC metrics" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 122, "slot_group": "Bioinformatics and QC metrics" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "rank": 123, "slot_group": "Bioinformatics and QC metrics" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "rank": 124, "slot_group": "Bioinformatics and QC metrics" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 125, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 126, "slot_group": "Bioinformatics and QC metrics" }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "rank": 127, "slot_group": "Lineage and Variant information" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "rank": 128, "slot_group": "Lineage and Variant information" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "rank": 129, "slot_group": "Lineage and Variant information" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "rank": 130, "slot_group": "Lineage and Variant information" }, - "variant evidence": { - "name": "variant evidence", + "variant_evidence": { + "name": "variant_evidence", "rank": 131, "slot_group": "Lineage and Variant information" }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "rank": 132, "slot_group": "Lineage and Variant information" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "rank": 133, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "rank": 134, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "rank": 135, "slot_group": "Pathogen diagnostic testing" }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "rank": 136, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "rank": 137, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "rank": 138, "slot_group": "Pathogen diagnostic testing" }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "rank": 139, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr protocol 3": { - "name": "diagnostic pcr protocol 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", "rank": 140, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "rank": 141, "slot_group": "Pathogen diagnostic testing" }, @@ -9700,136 +10160,240 @@ "rank": 142, "slot_group": "Contributor acknowledgement" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 143, "slot_group": "Contributor acknowledgement" } }, "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", + "NML_LIMS:TEXT_ID", + "BIOSAMPLE:sample_name", + "VirusSeq_Portal:specimen%20collector%20sample%20ID" + ], "rank": 1, "slot_uri": "GENEPIO:0001123", "identifier": true, - "alias": "specimen_collector_sample_ID", - "owner": "CanCOGeN Covid-19", + "alias": "specimen_collector_sample_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "description": "The name of the third party company or laboratory that provided services.", "title": "third party lab service provider name", + "comments": [ + "Provide the full, unabbreviated name of the company or laboratory." + ], + "examples": [ + { + "value": "Switch Health" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:HC_TEXT5" + ], "rank": 2, "slot_uri": "GENEPIO:0001202", "alias": "third_party_lab_service_provider_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "description": "The identifier assigned to a sample by a third party service provider.", "title": "third party lab sample ID", + "comments": [ + "Store the sample identifier supplied by the third party services provider." + ], + "examples": [ + { + "value": "SHK123456" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_ID_NUMBER_PRIMARY" + ], "rank": 3, "slot_uri": "GENEPIO:0001149", - "alias": "third_party_lab_sample_ID", - "owner": "CanCOGeN Covid-19", + "alias": "third_party_lab_sample_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_CASE_ID" + ], "rank": 4, "slot_uri": "GENEPIO:0100281", - "alias": "case_ID", - "owner": "CanCOGeN Covid-19", + "alias": "case_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "recommended": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", + "comments": [ + "Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system." + ], + "examples": [ + { + "value": "SR20-12345" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_PRIMARY_ID" + ], "rank": 5, "slot_uri": "GENEPIO:0001128", - "alias": "Related_specimen_primary_ID", - "owner": "CanCOGeN Covid-19", + "alias": "related_specimen_primary_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Database Identifiers" + "slot_group": "Database Identifiers", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "description": "The identifier assigned to a sequenced isolate in IRIDA.", "title": "IRIDA sample name", + "comments": [ + "Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:IRIDA%20sample%20name" + ], "rank": 6, "slot_uri": "GENEPIO:0001131", - "alias": "IRIDA_sample_name", - "owner": "CanCOGeN Covid-19", + "alias": "irida_sample_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort.", "title": "umbrella bioproject accession", + "comments": [ + "Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject." + ], + "examples": [ + { + "value": "PRJNA623807" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:umbrella%20bioproject%20accession" + ], "rank": 7, "slot_uri": "GENEPIO:0001133", "alias": "umbrella_bioproject_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", - "range": "umbrella bioproject accession menu", + "range": "UmbrellaBioprojectAccessionMenu", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:BioProject%20Accession", + "NML_LIMS:PH_BIOPROJECT_ACCESSION", + "BIOSAMPLE:bioproject_accession" + ], "rank": 8, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -9839,17 +10403,29 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:BioSample%20Accession", + "NML_LIMS:PH_BIOSAMPLE_ACCESSION" + ], "rank": 9, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -9859,17 +10435,29 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", + "comments": [ + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:SRA%20Accession", + "NML_LIMS:PH_SRA_ACCESSION" + ], "rank": 10, "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", - "owner": "CanCOGeN Covid-19", + "alias": "sra_accession", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -9879,17 +10467,29 @@ "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", + "comments": [ + "Store the accession returned from a GenBank submission (viral genome assembly)." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" + ], "rank": 11, "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", - "owner": "CanCOGeN Covid-19", + "alias": "genbank_accession", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -9899,17 +10499,31 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", + "comments": [ + "Store the accession returned from the GISAID submission." + ], + "examples": [ + { + "value": "EPI_ISL_436489" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID", + "BIOSAMPLE:GISAID_accession", + "VirusSeq_Portal:GISAID%20accession" + ], "rank": 12, "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", - "owner": "CanCOGeN Covid-19", + "alias": "gisaid_accession", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -9919,182 +10533,397 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", + "comments": [ + "The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)." + ], + "examples": [ + { + "value": "BC Centre for Disease Control" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", + "NML_LIMS:CUSTOMER", + "BIOSAMPLE:collected_by", + "VirusSeq_Portal:sample%20collected%20by" + ], "rank": 13, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SampleCollectedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:sample%20collector%20contact%20email" + ], "rank": 14, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ + { + "value": "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Address", + "NML_LIMS:sample%20collector%20contact%20address" + ], "rank": 15, "slot_uri": "GENEPIO:0001158", "alias": "sample_collector_contact_address", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by", + "VirusSeq_Portal:sequence%20submitted%20by" + ], "rank": 16, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:sequence%20submitter%20contact%20email" + ], "rank": 17, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "description": "The mailing address of the agency submitting the sequence.", "title": "sequence submitter contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ + { + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Address", + "NML_LIMS:sequence%20submitter%20contact%20address" + ], "rank": 18, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add \"jitter\" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", + "NML_LIMS:HC_COLLECT_DATE", + "BIOSAMPLE:sample%20collection%20date", + "VirusSeq_Portal:sample%20collection%20date" + ], "rank": 19, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", + "comments": [ + "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + ], + "examples": [ + { + "value": "year" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Precision%20of%20date%20collected", + "NML_LIMS:HC_TEXT2" + ], "rank": 20, "slot_uri": "GENEPIO:0001177", "alias": "sample_collection_date_precision", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SampleCollectionDatePrecisionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:sample%20received%20date" + ], "rank": 21, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", + "comments": [ + "Provide the country name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Location", + "CNPHI:Patient%20Country", + "NML_LIMS:HC_COUNTRY", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28country%29" + ], "rank": 22, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "geo_loc_name_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Patient%20Province", + "NML_LIMS:HC_PROVINCE", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" + ], "rank": 23, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", - "owner": "CanCOGeN Covid-19", + "alias": "geo_loc_name_state_province_territory", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city where the sample was collected.", "title": "geo_loc_name (city)", + "comments": [ + "Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Medicine Hat" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Patient%20City", + "NML_LIMS:geo_loc_name%20%28city%29" + ], "rank": 24, "slot_uri": "GENEPIO:0001189", - "alias": "geo_loc_name_(city)", - "owner": "CanCOGeN Covid-19", + "alias": "geo_loc_name_city", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" @@ -10103,1783 +10932,3753 @@ "name": "organism", "description": "Taxonomic name of the organism.", "title": "organism", + "comments": [ + "Use \"Severe acute respiratory syndrome coronavirus 2\". This value is provided in the template." + ], + "examples": [ + { + "value": "Severe acute respiratory syndrome coronavirus 2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Pathogen", + "NML_LIMS:HC_CURRENT_ID", + "BIOSAMPLE:organism", + "VirusSeq_Portal:organism" + ], "rank": 25, "slot_uri": "GENEPIO:0001191", "alias": "organism", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "OrganismMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "isolate": { "name": "isolate", "description": "Identifier of the specific isolate.", "title": "isolate", + "comments": [ + "Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”." + ], + "examples": [ + { + "value": "hCov-19/CANADA/BC-prov_rona_99/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS", + "BIOSAMPLE:isolate", + "BIOSAMPLE:GISAID_virus_name", + "VirusSeq_Portal:isolate", + "VirusSeq_Portal:fasta%20header%20name" + ], "rank": 26, "slot_uri": "GENEPIO:0001195", "alias": "isolate", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Diagnostic testing" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sampling", + "NML_LIMS:HC_SAMPLE_CATEGORY", + "BIOSAMPLE:purpose_of_sampling", + "VirusSeq_Portal:purpose%20of%20sampling" + ], "rank": 27, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", + "comments": [ + "Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value." + ], + "examples": [ + { + "value": "The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", + "NML_LIMS:PH_SAMPLING_DETAILS", + "BIOSAMPLE:description", + "VirusSeq_Portal:purpose%20of%20sampling%20details" + ], "rank": 28, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", + "comments": [ + "This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”." + ], + "examples": [ + { + "value": "swab" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Specimen%20Type", + "NML_LIMS:PH_SPECIMEN_TYPE" + ], "rank": 29, "slot_uri": "GENEPIO:0001204", - "alias": "NML_submitted_specimen_type", - "owner": "CanCOGeN Covid-19", + "alias": "nml_submitted_specimen_type", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "range": "NML submitted specimen type menu", + "range": "NmlSubmittedSpecimenTypeMenu", "required": true }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", "title": "Related specimen relationship type", + "comments": [ + "Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system." + ], + "examples": [ + { + "value": "Specimen sampling methods testing" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE" + ], "rank": 30, "slot_uri": "GENEPIO:0001209", - "alias": "Related_specimen_relationship_type", - "owner": "CanCOGeN Covid-19", + "alias": "related_specimen_relationship_type", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "range": "Related specimen relationship type menu" + "range": "RelatedSpecimenRelationshipTypeMenu" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Blood" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", + "NML_LIMS:PH_ISOLATION_SITE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "VirusSeq_Portal:anatomical%20material" + ], "rank": 31, "slot_uri": "GENEPIO:0001211", - "multivalued": true, "alias": "anatomical_material", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Nasopharynx (NP)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", + "NML_LIMS:PH_ISOLATION_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "VirusSeq_Portal:anatomical%20part" + ], "rank": 32, "slot_uri": "GENEPIO:0001214", - "multivalued": true, "alias": "anatomical_part", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Feces" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", + "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "VirusSeq_Portal:body%20product" + ], "rank": 33, "slot_uri": "GENEPIO:0001216", - "multivalued": true, "alias": "body_product", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", + "comments": [ + "Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Face mask" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Environmental%20Material", + "NML_LIMS:PH_ENVIRONMENTAL_MATERIAL", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_material", + "VirusSeq_Portal:environmental%20material" + ], "rank": 34, "slot_uri": "GENEPIO:0001223", - "multivalued": true, "alias": "environmental_material", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", + "comments": [ + "Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Production Facility" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Environmental%20Site", + "NML_LIMS:PH_ENVIRONMENTAL_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_site", + "VirusSeq_Portal:environmental%20site" + ], "rank": 35, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", + "comments": [ + "Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Swab" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", + "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "VirusSeq_Portal:collection%20device" + ], "rank": 36, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Bronchoalveolar lavage (BAL)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", + "NML_LIMS:COLLECTION_METHOD", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "VirusSeq_Portal:collection%20method" + ], "rank": 37, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", + "comments": [ + "Free text." + ], + "examples": [ + { + "value": "BCRonaSamplingProtocol v. 1.2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:collection%20protocol" + ], "rank": 38, "slot_uri": "GENEPIO:0001243", "alias": "collection_protocol", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." + ], + "examples": [ + { + "value": "Virus passage" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Passage%20details/history", + "NML_LIMS:specimen%20processing" + ], "rank": 39, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample." + ], + "examples": [ + { + "value": "25 swabs were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 40, "slot_uri": "GENEPIO:0100311", "alias": "specimen_processing_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", "title": "lab host", + "comments": [ + "Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put \"not applicable\"." + ], + "examples": [ + { + "value": "Vero E6 cell line" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Passage%20details/history", + "NML_LIMS:lab%20host", + "BIOSAMPLE:lab_host" + ], "rank": 41, "slot_uri": "GENEPIO:0001255", "alias": "lab_host", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "LabHostMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "description": "Number of passages.", "title": "passage number", + "comments": [ + "Provide number of known passages. If not passaged, put \"not applicable\"" + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Passage%20details/history", + "NML_LIMS:passage%20number", + "BIOSAMPLE:passage_history" + ], "rank": 42, "slot_uri": "GENEPIO:0001261", "alias": "passage_number", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", "recommended": true, - "minimum_value": "0" + "minimum_value": 0, + "any_of": [ + { + "range": "integer" + }, + { + "range": "NullValueMenu" + } + ] }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "description": "Description of how organism was passaged.", "title": "passage method", + "comments": [ + "Free text. Provide a very short description (<10 words). If not passaged, put \"not applicable\"." + ], + "examples": [ + { + "value": "0.25% trypsin + 0.02% EDTA" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Passage%20details/history", + "NML_LIMS:passage%20method", + "BIOSAMPLE:passage_method" + ], "rank": 43, "slot_uri": "GENEPIO:0001264", "alias": "passage_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "title": "biomaterial extracted", + "comments": [ + "Provide the biomaterial extracted from the picklist in the template." + ], + "examples": [ + { + "value": "RNA (total)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:biomaterial%20extracted" + ], "rank": 44, "slot_uri": "GENEPIO:0001266", "alias": "biomaterial_extracted", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "BiomaterialExtractedMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put \"not applicable." + ], + "examples": [ + { + "value": "Human" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Animal%20Type", + "NML_LIMS:PH_ANIMAL_TYPE" + ], "rank": 45, "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", - "owner": "CanCOGeN Covid-19", + "alias": "host_common_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostCommonNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], + "examples": [ + { + "value": "Homo sapiens" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host%20%28scientific%20name%29", + "BIOSAMPLE:host", + "VirusSeq_Portal:host%20%28scientific%20name%29" + ], "rank": 46, "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", - "owner": "CanCOGeN Covid-19", + "alias": "host_scientific_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "description": "Health status of the host at the time of sample collection.", "title": "host health state", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Symptomatic" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:Host%20Health%20State", + "NML_LIMS:PH_HOST_HEALTH", + "BIOSAMPLE:host_health_state" + ], "rank": 47, "slot_uri": "GENEPIO:0001388", "alias": "host_health_state", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStateMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "description": "Further details pertaining to the health or disease status of the host at time of collection.", "title": "host health status details", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Hospitalized (ICU)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Host%20Health%20State%20Details", + "NML_LIMS:PH_HOST_HEALTH_DETAILS" + ], "rank": 48, "slot_uri": "GENEPIO:0001389", "alias": "host_health_status_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStatusDetailsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Recovered" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_OUTCOME", + "BIOSAMPLE:host_disease_outcome" + ], "rank": 49, "slot_uri": "GENEPIO:0001390", "alias": "host_health_outcome", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthOutcomeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", + "comments": [ + "Select \"COVID-19\" from the pick list provided in the template." + ], + "examples": [ + { + "value": "COVID-19" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Host%20Disease", + "NML_LIMS:PH_HOST_DISEASE", + "BIOSAMPLE:host_disease", + "VirusSeq_Portal:host%20disease" + ], "rank": 50, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", + "comments": [ + "Enter the age of the host in years. If not available, provide a null value. If there is not host, put \"Not Applicable\"." + ], + "examples": [ + { + "value": "79" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:Patient%20Age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age", + "VirusSeq_Portal:host%20age" + ], "rank": 51, "slot_uri": "GENEPIO:0001392", "alias": "host_age", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", "required": true, - "minimum_value": "0", - "maximum_value": "130" + "minimum_value": 0, + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The unit used to measure the host age, in either months or years.", "title": "host age unit", + "comments": [ + "Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin." + ], + "examples": [ + { + "value": "year" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Age%20Units", + "NML_LIMS:PH_AGE_UNIT", + "VirusSeq_Portal:host%20age%20unit" + ], "rank": 52, "slot_uri": "GENEPIO:0001393", "alias": "host_age_unit", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostAgeUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host age bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value." + ], + "examples": [ + { + "value": "60 - 69" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Host%20Age%20Category", + "NML_LIMS:PH_AGE_GROUP", + "VirusSeq_Portal:host%20age%20bin" + ], "rank": 53, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", + "comments": [ + "Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put \"Not Applicable\"." + ], + "examples": [ + { + "value": "Male" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Gender", + "CNPHI:Patient%20Sex", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex", + "VirusSeq_Portal:host%20gender" + ], "rank": 54, "slot_uri": "GENEPIO:0001395", "alias": "host_gender", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", "required": true, - "structured_pattern": { - "syntax": "{Title_Case}", - "interpolated": true, - "partial_match": false - } + "any_of": [ + { + "range": "HostGenderMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "description": "The country of residence of the host.", "title": "host residence geo_loc name (country)", + "comments": [ + "Select the country name from pick list provided in the template." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_HOST_COUNTRY" + ], "rank": 55, "slot_uri": "GENEPIO:0001396", - "alias": "host_residence_geo_loc_name_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "host_residence_geo_loc_name_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host residence geo_loc name (state/province/territory)": { - "name": "host residence geo_loc name (state/province/territory)", + "host_residence_geo_loc_name_state_province_territory": { + "name": "host_residence_geo_loc_name_state_province_territory", "description": "The state/province/territory of residence of the host.", "title": "host residence geo_loc name (state/province/territory)", + "comments": [ + "Select the province/territory name from pick list provided in the template." + ], + "examples": [ + { + "value": "Quebec" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_HOST_PROVINCE" + ], "rank": 56, "slot_uri": "GENEPIO:0001397", - "alias": "host_residence_geo_loc_name_(state/province/territory)", - "owner": "CanCOGeN Covid-19", + "alias": "host_residence_geo_loc_name_state_province_territory", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to e.g. #131", "title": "host subject ID", + "comments": [ + "Provide the host identifier. Should be a unique, user-defined identifier." + ], + "examples": [ + { + "value": "BCxy123" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:host%20subject%20ID", + "BIOSAMPLE:host_subject_id" + ], "rank": 57, "slot_uri": "GENEPIO:0001398", - "alias": "host_subject_ID", - "owner": "CanCOGeN Covid-19", + "alias": "host_subject_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Symptoms%20Onset%20Date", + "NML_LIMS:HC_ONSET_DATE" + ], "rank": 58, "slot_uri": "GENEPIO:0001399", "alias": "symptom_onset_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician.", "title": "signs and symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Chills (sudden cold sensation)" + }, + { + "value": "Cough" + }, + { + "value": "Fever" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Symptoms", + "NML_LIMS:HC_SYMPTOMS" + ], "rank": 59, "slot_uri": "GENEPIO:0001400", - "multivalued": true, "alias": "signs_and_symptoms", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "SignsAndSymptomsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "description": "Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection.", "title": "pre-existing conditions and risk factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma" + }, + { + "value": "Pregnancy" + }, + { + "value": "Smoking" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:pre-existing%20conditions%20and%20risk%20factors" + ], "rank": 60, "slot_uri": "GENEPIO:0001401", - "multivalued": true, - "alias": "pre_existing_conditions_and_risk_factors", - "owner": "CanCOGeN Covid-19", + "alias": "preexisting_conditions_and_risk_factors", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "PreExistingConditionsAndRiskFactorsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "complications": { "name": "complications", "description": "Patient medical complications that are believed to have occurred as a result of host disease.", "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Acute Respiratory Failure" + }, + { + "value": "Coma" + }, + { + "value": "Septicemia" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:complications" + ], "rank": 61, "slot_uri": "GENEPIO:0001402", - "multivalued": true, "alias": "complications", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "ComplicationsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 62, "slot_uri": "GENEPIO:0001404", "alias": "host_vaccination_status", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "host vaccination status menu" + }, + { + "range": "NullValueMenu" + } + ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "description": "The number of doses of the vaccine recived by the host.", "title": "number of vaccine doses received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 63, "slot_uri": "GENEPIO:0001406", "alias": "number_of_vaccine_doses_received", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host vaccination information", "range": "integer" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", "title": "vaccination dose 1 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 64, "slot_uri": "GENEPIO:0100313", "alias": "vaccination_dose_1_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "VaccineNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 65, "slot_uri": "GENEPIO:0100314", "alias": "vaccination_dose_1_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", "title": "vaccination dose 2 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 66, "slot_uri": "GENEPIO:0100315", "alias": "vaccination_dose_2_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "VaccineNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination dose 2 vaccination date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 67, "slot_uri": "GENEPIO:0100316", "alias": "vaccination_dose_2_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "description": "The name of the vaccine administered as the third dose of a vaccine regimen.", "title": "vaccination dose 3 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 68, "slot_uri": "GENEPIO:0100317", "alias": "vaccination_dose_3_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "VaccineNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "description": "The date the third dose of a vaccine was administered.", "title": "vaccination dose 3 vaccination date", + "comments": [ + "Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-12-30" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 69, "slot_uri": "GENEPIO:0100318", "alias": "vaccination_dose_3_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "description": "The name of the vaccine administered as the fourth dose of a vaccine regimen.", "title": "vaccination dose 4 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 70, "slot_uri": "GENEPIO:0100319", "alias": "vaccination_dose_4_vaccine_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "VaccineNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "description": "The date the fourth dose of a vaccine was administered.", "title": "vaccination dose 4 vaccination date", + "comments": [ + "Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-01-15" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 71, "slot_uri": "GENEPIO:0100320", "alias": "vaccination_dose_4_vaccination_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 72, "slot_uri": "GENEPIO:0100321", "alias": "vaccination_history", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "description": "The country where the host was likely exposed to the causative agent of the illness.", "title": "location of exposure geo_loc name (country)", + "comments": [ + "Select the country name from pick list provided in the template." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_COUNTRY" + ], "rank": 73, "slot_uri": "GENEPIO:0001410", - "alias": "location_of_exposure_geo_loc_name_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "location_of_exposure_geo_loc_name_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "description": "The name of the city that was the destination of most recent travel.", "title": "destination of most recent travel (city)", + "comments": [ + "Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "New York City" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date", + "NML_LIMS:PH_TRAVEL" + ], "rank": 74, "slot_uri": "GENEPIO:0001411", - "alias": "destination_of_most_recent_travel_(city)", - "owner": "CanCOGeN Covid-19", + "alias": "destination_of_most_recent_travel_city", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "description": "The name of the province that was the destination of most recent travel.", "title": "destination of most recent travel (state/province/territory)", + "comments": [ + "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "California" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date", + "NML_LIMS:PH_TRAVEL" + ], "rank": 75, "slot_uri": "GENEPIO:0001412", - "alias": "destination_of_most_recent_travel_(state/province/territory)", - "owner": "CanCOGeN Covid-19", + "alias": "destination_of_most_recent_travel_state_province_territory", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "description": "The name of the country that was the destination of most recent travel.", "title": "destination of most recent travel (country)", + "comments": [ + "Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "United Kingdom" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date", + "NML_LIMS:PH_TRAVEL" + ], "rank": 76, "slot_uri": "GENEPIO:0001413", - "alias": "destination_of_most_recent_travel_(country)", - "owner": "CanCOGeN Covid-19", + "alias": "destination_of_most_recent_travel_country", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", "title": "most recent travel departure date", + "comments": [ + "Provide the travel departure date." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date", + "NML_LIMS:PH_TRAVEL" + ], "rank": 77, "slot_uri": "GENEPIO:0001414", "alias": "most_recent_travel_departure_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", "title": "most recent travel return date", + "comments": [ + "Provide the travel return date." + ], + "examples": [ + { + "value": "2020-04-26" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date", + "NML_LIMS:PH_TRAVEL" + ], "rank": 78, "slot_uri": "GENEPIO:0001415", "alias": "most_recent_travel_return_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "travel point of entry type": { - "name": "travel point of entry type", + "travel_point_of_entry_type": { + "name": "travel_point_of_entry_type", "description": "The type of entry point a traveler arrives through.", "title": "travel point of entry type", + "comments": [ + "Select the point of entry type." + ], + "examples": [ + { + "value": "Air" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_POINT_OF_ENTRY" + ], "rank": 79, "slot_uri": "GENEPIO:0100413", "alias": "travel_point_of_entry_type", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "TravelPointOfEntryTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "border testing test day type": { - "name": "border testing test day type", + "border_testing_test_day_type": { + "name": "border_testing_test_day_type", "description": "The day a traveller was tested on or after arrival at their point of entry.", "title": "border testing test day type", + "comments": [ + "Select the test day." + ], + "examples": [ + { + "value": "day 1" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_DAY" + ], "rank": 80, "slot_uri": "GENEPIO:0100414", "alias": "border_testing_test_day_type", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "BorderTestingTestDayTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "description": "Travel history in last six months.", "title": "travel history", + "comments": [ + "Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first." + ], + "examples": [ + { + "value": "Canada, Vancouver" + }, + { + "value": "USA, Seattle" + }, + { + "value": "Italy, Milan" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], "rank": 81, "slot_uri": "GENEPIO:0001416", "alias": "travel_history", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "travel history availability": { - "name": "travel history availability", + "travel_history_availability": { + "name": "travel_history_availability", "description": "The availability of different types of travel history in the last 6 months (e.g. international, domestic).", "title": "travel history availability", + "comments": [ + "If travel history is available, but the details of travel cannot be provided, indicate this and the type of travel history availble by selecting a value from the picklist. The values in this field can be used to indicate a sample is associated with a travel when the \"purpose of sequencing\" is not travel-associated." + ], + "examples": [ + { + "value": "International travel history available" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_TRAVEL" + ], "rank": 82, "slot_uri": "GENEPIO:0100649", "alias": "travel_history_availability", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "TravelHistoryAvailabilityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Convention" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], "rank": 83, "slot_uri": "GENEPIO:0001417", "alias": "exposure_event", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureEventMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], "rank": 84, "slot_uri": "GENEPIO:0001418", "alias": "exposure_contact_level", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureContactLevelMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Patient" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], "rank": 85, "slot_uri": "GENEPIO:0001419", - "multivalued": true, "alias": "host_role", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", - "range": "host role menu" + "range": "HostRoleMenu", + "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], "rank": 86, "slot_uri": "GENEPIO:0001428", - "multivalued": true, "alias": "exposure_setting", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", - "range": "exposure setting menu" + "range": "ExposureSettingMenu", + "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Host role - Other: Bus Driver" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], "rank": 87, "slot_uri": "GENEPIO:0001431", "alias": "exposure_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "description": "Whether there was prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection", + "comments": [ + "If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list." + ], + "examples": [ + { + "value": "Yes" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:prior%20SARS-CoV-2%20infection" + ], "rank": 88, "slot_uri": "GENEPIO:0001435", - "alias": "prior_SARS_CoV_2_infection", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_infection", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host reinfection information" + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorSarsCov2InfectionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "description": "The identifier of the isolate found in the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection isolate", + "comments": [ + "Provide the isolate name of the most recent prior infection. Structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"SARS-CoV-2/host/country/sampleID/date\"." + ], + "examples": [ + { + "value": "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:prior%20SARS-CoV-2%20infection%20isolate" + ], "rank": 89, "slot_uri": "GENEPIO:0001436", - "alias": "prior_SARS_CoV_2_infection_isolate", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_infection_isolate", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host reinfection information", "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection date", + "comments": [ + "Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-01-23" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:prior%20SARS-CoV-2%20infection%20date" + ], "rank": 90, "slot_uri": "GENEPIO:0001437", - "alias": "prior_SARS_CoV_2_infection_date", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_infection_date", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host reinfection information", "range": "date" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", "title": "prior SARS-CoV-2 antiviral treatment", + "comments": [ + "If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list." + ], + "examples": [ + { + "value": "No prior antiviral treatment" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment" + ], "rank": 91, "slot_uri": "GENEPIO:0001438", - "alias": "prior_SARS_CoV_2_antiviral_treatment", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_antiviral_treatment", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Host reinfection information" + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorSarsCov2AntiviralTreatmentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment agent", + "comments": [ + "Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put \"No treatment\". If multiple antiviral agents were administered, list them all separated by commas." + ], + "examples": [ + { + "value": "Remdesivir" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment%20agent" + ], "rank": 92, "slot_uri": "GENEPIO:0001439", - "alias": "prior_SARS_CoV_2_antiviral_treatment_agent", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_antiviral_treatment_agent", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host reinfection information", "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "description": "The date treatment was first administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment date", + "comments": [ + "Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-01-28" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment%20date" + ], "rank": 93, "slot_uri": "GENEPIO:0001440", - "alias": "prior_SARS_CoV_2_antiviral_treatment_date", - "owner": "CanCOGeN Covid-19", + "alias": "prior_sarscov2_antiviral_treatment_date", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Host reinfection information", "range": "date" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Baseline surveillance (random sampling)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING", + "BIOSAMPLE:purpose_of_sequencing", + "VirusSeq_Portal:purpose%20of%20sequencing" + ], "rank": 94, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection." + ], + "examples": [ + { + "value": "Screened for S gene target failure (S dropout)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", + "VirusSeq_Portal:purpose%20of%20sequencing%20details" + ], "rank": 95, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_DATE" + ], "rank": 96, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:library%20ID" + ], "rank": 97, "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", - "owner": "CanCOGeN Covid-19", + "alias": "library_id", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", + "comments": [ + "Provide the amplicon size, including the units." + ], + "examples": [ + { + "value": "300bp" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:amplicon%20size" + ], "rank": 98, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_LIBRARY_PREP_KIT" + ], "rank": 99, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "description": "The barcode of the flow cell used for sequencing.", "title": "flow cell barcode", + "comments": [ + "Provide the barcode of the flow cell used for sequencing the sample." + ], + "examples": [ + { + "value": "FAB06069" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:flow%20cell%20barcode" + ], "rank": 100, "slot_uri": "GENEPIO:0001451", "alias": "flow_cell_barcode", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", + "NML_LIMS:PH_INSTRUMENT_CGN", + "VirusSeq_Portal:sequencing%20instrument" + ], "rank": 101, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "description": "The name and version number of the sequencing protocol used.", "title": "sequencing protocol name", + "comments": [ + "Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION" + ], + "examples": [ + { + "value": "https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Sequencing%20Protocol%20Name", + "NML_LIMS:PH_SEQ_PROTOCOL_NAME" + ], "rank": 102, "slot_uri": "GENEPIO:0001453", "alias": "sequencing_protocol_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString", "recommended": true }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", + "comments": [ + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + ], + "examples": [ + { + "value": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_TESTING_PROTOCOL", + "VirusSeq_Portal:sequencing%20protocol" + ], "rank": 103, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "description": "The manufacturer's kit number.", "title": "sequencing kit number", + "comments": [ + "Alphanumeric value." + ], + "examples": [ + { + "value": "AB456XYZ789" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:sequencing%20kit%20number" + ], "rank": 104, "slot_uri": "GENEPIO:0001455", "alias": "sequencing_kit_number", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:amplicon%20pcr%20primer%20scheme" + ], "rank": 105, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_RAW_SEQUENCE_METHOD", + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" + ], "rank": 106, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_DEHOSTING_METHOD", + "VirusSeq_Portal:dehosting%20method" + ], "rank": 107, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence name": { - "name": "consensus sequence name", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "description": "The name of the consensus sequence.", "title": "consensus sequence name", + "comments": [ + "Provide the name and version number of the consensus sequence." + ], + "examples": [ + { + "value": "ncov123assembly3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20name" + ], "rank": 108, "slot_uri": "GENEPIO:0001460", "alias": "consensus_sequence_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence filename": { - "name": "consensus sequence filename", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "description": "The name of the consensus sequence file.", "title": "consensus sequence filename", + "comments": [ + "Provide the name and version number of the consensus sequence FASTA file." + ], + "examples": [ + { + "value": "ncov123assembly.fasta" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filename" + ], "rank": 109, "slot_uri": "GENEPIO:0001461", "alias": "consensus_sequence_filename", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", "description": "The filepath of the consensus sequence file.", "title": "consensus sequence filepath", + "comments": [ + "Provide the filepath of the consensus sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/ncov123assembly.fasta" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filepath" + ], "rank": 110, "slot_uri": "GENEPIO:0001462", "alias": "consensus_sequence_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" + ], "rank": 111, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" + ], "rank": 112, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95%" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:breadth%20of%20coverage%20value", + "VirusSeq_Portal:breadth%20of%20coverage%20value" + ], "rank": 113, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400x" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Coverage", + "NML_LIMS:depth%20of%20coverage%20value", + "VirusSeq_Portal:depth%20of%20coverage%20value" + ], "rank": 114, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100x" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:depth%20of%20coverage%20threshold" + ], "rank": 115, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r1 fastq filename": { - "name": "r1 fastq filename", + "r1_fastq_filename________": { + "name": "r1_fastq_filename________", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", + "comments": [ + "Provide the r1 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R1_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:r1%20fastq%20filename" + ], "rank": 116, "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename", - "owner": "CanCOGeN Covid-19", + "alias": "r1_fastq_filename________", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "r2 fastq filename": { - "name": "r2 fastq filename", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "description": "The user-specified filename of the r2 FASTQ file.", "title": "r2 fastq filename", + "comments": [ + "Provide the r2 FASTQ filename." + ], + "examples": [ + { + "value": "ABC123_S1_L001_R2_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:r2%20fastq%20filename" + ], "rank": 117, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "description": "The location of the r1 FASTQ file within a user's file system.", "title": "r1 fastq filepath", + "comments": [ + "Provide the filepath for the r1 FASTQ file. This information aids in data management." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:r1%20fastq%20filepath" + ], "rank": 118, "slot_uri": "GENEPIO:0001478", "alias": "r1_fastq_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "description": "The location of the r2 FASTQ file within a user's file system.", "title": "r2 fastq filepath", + "comments": [ + "Provide the filepath for the r2 FASTQ file. This information aids in data management." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:r2%20fastq%20filepath" + ], "rank": 119, "slot_uri": "GENEPIO:0001479", "alias": "r2_fastq_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "fast5 filename": { - "name": "fast5 filename", + "fast5_filename": { + "name": "fast5_filename", "description": "The user-specified filename of the FAST5 file.", "title": "fast5 filename", + "comments": [ + "Provide the FAST5 filename." + ], + "examples": [ + { + "value": "rona123assembly.fast5" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:fast5%20filename" + ], "rank": 120, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "fast5 filepath": { - "name": "fast5 filepath", + "fast5_filepath": { + "name": "fast5_filepath", "description": "The location of the FAST5 file within a user's file system.", "title": "fast5 filepath", + "comments": [ + "Provide the filepath for the FAST5 file. This information aids in data management." + ], + "examples": [ + { + "value": "/User/Documents/RespLab/Data/rona123assembly.fast5" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:fast5%20filepath" + ], "rank": 121, "slot_uri": "GENEPIO:0001481", "alias": "fast5_filepath", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "387566" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:number%20of%20base%20pairs%20sequenced" + ], "rank": 122, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "integer", - "minimum_value": "0" + "minimum_value": 0 }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "Size of the reconstructed genome described as the number of base pairs.", "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "38677" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:consensus%20genome%20length" + ], "rank": 123, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "integer", - "minimum_value": "0" + "minimum_value": 0 }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", "title": "Ns per 100 kbp", + "comments": [ + "Provide a numerical value (no need to include units)." + ], + "examples": [ + { + "value": "330" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:Ns%20per%20100%20kbp" + ], "rank": 124, "slot_uri": "GENEPIO:0001484", - "alias": "Ns_per_100_kbp", - "owner": "CanCOGeN Covid-19", + "alias": "ns_per_100_kbp", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "decimal", - "minimum_value": "0" + "minimum_value": 0 }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], + "examples": [ + { + "value": "NC_045512.2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:reference%20genome%20accession", + "VirusSeq_Portal:reference%20genome%20accession" + ], "rank": 125, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Bioinformatics%20Protocol", + "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", + "VirusSeq_Portal:bioinformatics%20protocol" + ], "rank": 126, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "description": "The name of the lineage or clade.", "title": "lineage/clade name", + "comments": [ + "Provide the Pangolin or Nextstrain lineage/clade name." + ], + "examples": [ + { + "value": "B.1.1.7" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_LINEAGE_CLADE_NAME" + ], "rank": 127, "slot_uri": "GENEPIO:0001500", - "alias": "lineage/clade_name", - "owner": "CanCOGeN Covid-19", + "alias": "lineage_clade_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "description": "The name of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software name", + "comments": [ + "Provide the name of the software used to determine the lineage/clade." + ], + "examples": [ + { + "value": "Pangolin" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_LINEAGE_CLADE_SOFTWARE" + ], "rank": 128, "slot_uri": "GENEPIO:0001501", - "alias": "lineage/clade_analysis_software_name", - "owner": "CanCOGeN Covid-19", + "alias": "lineage_clade_analysis_software_name", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "description": "The version of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software version", + "comments": [ + "Provide the version of the software used ot determine the lineage/clade." + ], + "examples": [ + { + "value": "2.1.10" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_LINEAGE_CLADE_VERSION" + ], "rank": 129, "slot_uri": "GENEPIO:0001502", - "alias": "lineage/clade_analysis_software_version", - "owner": "CanCOGeN Covid-19", + "alias": "lineage_clade_analysis_software_version", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", "title": "variant designation", + "comments": [ + "If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank." + ], + "examples": [ + { + "value": "Variant of Concern" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VARIANT_DESIGNATION" + ], "rank": 130, "slot_uri": "GENEPIO:0001503", "alias": "variant_designation", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Lineage and Variant information" + "slot_group": "Lineage and Variant information", + "any_of": [ + { + "range": "VariantDesignationMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "variant evidence": { - "name": "variant evidence", + "variant_evidence": { + "name": "variant_evidence", "description": "The evidence used to make the variant determination.", "title": "variant evidence", + "comments": [ + "Select whether the sample was screened using RT-qPCR or by sequencing from the pick list." + ], + "examples": [ + { + "value": "RT-qPCR" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VARIANT_EVIDENCE" + ], "rank": 131, "slot_uri": "GENEPIO:0001504", "alias": "variant_evidence", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Lineage and Variant information" + "slot_group": "Lineage and Variant information", + "any_of": [ + { + "range": "VariantEvidenceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "description": "Details about the evidence used to make the variant determination.", "title": "variant evidence details", + "comments": [ + "Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here." + ], + "examples": [ + { + "value": "Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L)." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NML_LIMS:PH_VARIANT_EVIDENCE_DETAILS" + ], "rank": 132, "slot_uri": "GENEPIO:0001505", "alias": "variant_evidence_details", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 1", + "comments": [ + "Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "E gene (orf4)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", + "BIOSAMPLE:gene_name_1", + "VirusSeq_Portal:gene%20name" + ], "rank": 133, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 1", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "EGenePCRTest 2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 134, "slot_uri": "GENEPIO:0001508", "alias": "diagnostic_pcr_protocol_1", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", + "comments": [ + "Provide the CT value of the sample from the diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "21" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Gene%20Target%201%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_1", + "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" + ], "rank": 135, "slot_uri": "GENEPIO:0001509", - "alias": "diagnostic_pcr_Ct_value_1", - "owner": "CanCOGeN Covid-19", + "alias": "diagnostic_pcr_ct_value_1", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 2", + "comments": [ + "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "RdRp gene (nsp12)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", + "BIOSAMPLE:gene_name_2" + ], "rank": 136, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 2", + "comments": [ + "The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "RdRpGenePCRTest 3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 137, "slot_uri": "GENEPIO:0001511", "alias": "diagnostic_pcr_protocol_2", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "36" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Gene%20Target%202%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_2" + ], "rank": 138, "slot_uri": "GENEPIO:0001512", - "alias": "diagnostic_pcr_Ct_value_2", - "owner": "CanCOGeN Covid-19", + "alias": "diagnostic_pcr_ct_value_2", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 3", + "comments": [ + "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "RdRp gene (nsp12)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233" + ], "rank": 139, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr protocol 3": { - "name": "diagnostic pcr protocol 3", + "diagnostic_pcr_protocol_3": { + "name": "diagnostic_pcr_protocol_3", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 3", + "comments": [ + "The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "RdRpGenePCRTest 3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 140, "slot_uri": "GENEPIO:0001514", "alias": "diagnostic_pcr_protocol_3", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "30" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "CNPHI:Gene%20Target%203%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value" + ], "rank": 141, "slot_uri": "GENEPIO:0001515", - "alias": "diagnostic_pcr_Ct_value_3", - "owner": "CanCOGeN Covid-19", + "alias": "diagnostic_pcr_ct_value_3", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, "authors": { "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Authors", + "CNPHI:Authors", + "NML_LIMS:PH_CANCOGEN_AUTHORS" + ], "rank": 142, "slot_uri": "GENEPIO:0001517", "alias": "authors", - "owner": "CanCOGeN Covid-19", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Contributor acknowledgement", "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:DataHarmonizer%20provenance", + "CNPHI:Additional%20Comments", + "NML_LIMS:HC_COMMENTS" + ], "rank": 143, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", - "owner": "CanCOGeN Covid-19", + "alias": "dataharmonizer_provenance", + "owner": "CanCOGeNCovid19", "domain_of": [ - "CanCOGeN Covid-19" + "CanCOGeNCovid19" ], "slot_group": "Contributor acknowledgement", "range": "Provenance" diff --git a/web/templates/canada_covid19/schema.yaml b/web/templates/canada_covid19/schema.yaml index d9983257..37aa58ce 100644 --- a/web/templates/canada_covid19/schema.yaml +++ b/web/templates/canada_covid19/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/CanCOGeN_Covid-19 name: CanCOGeN_Covid-19 description: '' -version: 2.3.4 +version: 2.4.0 in_language: - en - fr @@ -15,227 +15,228 @@ classes: name: dh_interface description: A DataHarmonizer interface from_schema: https://example.com/CanCOGeN_Covid-19 - CanCOGeN Covid-19: - name: CanCOGeN Covid-19 + CanCOGeNCovid19: + name: CanCOGeNCovid19 + title: CanCOGeN Covid-19 description: Canadian specification for Covid-19 clinical virus biosample data gathering is_a: dh_interface see_also: templates/canada_covid19/SOP.pdf slots: - - specimen collector sample ID - - third party lab service provider name - - third party lab sample ID - - case ID - - Related specimen primary ID - - IRIDA sample name - - umbrella bioproject accession - - bioproject accession - - biosample accession - - SRA accession - - GenBank accession - - GISAID accession - - sample collected by - - sample collector contact email - - sample collector contact address - - sequence submitted by - - sequence submitter contact email - - sequence submitter contact address - - sample collection date - - sample collection date precision - - sample received date - - geo_loc_name (country) - - geo_loc_name (state/province/territory) - - geo_loc_name (city) + - specimen_collector_sample_id + - third_party_lab_service_provider_name + - third_party_lab_sample_id + - case_id + - related_specimen_primary_id + - irida_sample_name + - umbrella_bioproject_accession + - bioproject_accession + - biosample_accession + - sra_accession + - genbank_accession + - gisaid_accession + - sample_collected_by + - sample_collector_contact_email + - sample_collector_contact_address + - sequence_submitted_by + - sequence_submitter_contact_email + - sequence_submitter_contact_address + - sample_collection_date + - sample_collection_date_precision + - sample_received_date + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_city - organism - isolate - - purpose of sampling - - purpose of sampling details - - NML submitted specimen type - - Related specimen relationship type - - anatomical material - - anatomical part - - body product - - environmental material - - environmental site - - collection device - - collection method - - collection protocol - - specimen processing - - specimen processing details - - lab host - - passage number - - passage method - - biomaterial extracted - - host (common name) - - host (scientific name) - - host health state - - host health status details - - host health outcome - - host disease - - host age - - host age unit - - host age bin - - host gender - - host residence geo_loc name (country) - - host residence geo_loc name (state/province/territory) - - host subject ID - - symptom onset date - - signs and symptoms - - pre-existing conditions and risk factors + - purpose_of_sampling + - purpose_of_sampling_details + - nml_submitted_specimen_type + - related_specimen_relationship_type + - anatomical_material + - anatomical_part + - body_product + - environmental_material + - environmental_site + - collection_device + - collection_method + - collection_protocol + - specimen_processing + - specimen_processing_details + - lab_host + - passage_number + - passage_method + - biomaterial_extracted + - host_common_name + - host_scientific_name + - host_health_state + - host_health_status_details + - host_health_outcome + - host_disease + - host_age + - host_age_unit + - host_age_bin + - host_gender + - host_residence_geo_loc_name_country + - host_residence_geo_loc_name_state_province_territory + - host_subject_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors - complications - - host vaccination status - - number of vaccine doses received - - vaccination dose 1 vaccine name - - vaccination dose 1 vaccination date - - vaccination dose 2 vaccine name - - vaccination dose 2 vaccination date - - vaccination dose 3 vaccine name - - vaccination dose 3 vaccination date - - vaccination dose 4 vaccine name - - vaccination dose 4 vaccination date - - vaccination history - - location of exposure geo_loc name (country) - - destination of most recent travel (city) - - destination of most recent travel (state/province/territory) - - destination of most recent travel (country) - - most recent travel departure date - - most recent travel return date - - travel point of entry type - - border testing test day type - - travel history - - travel history availability - - exposure event - - exposure contact level - - host role - - exposure setting - - exposure details - - prior SARS-CoV-2 infection - - prior SARS-CoV-2 infection isolate - - prior SARS-CoV-2 infection date - - prior SARS-CoV-2 antiviral treatment - - prior SARS-CoV-2 antiviral treatment agent - - prior SARS-CoV-2 antiviral treatment date - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library ID - - amplicon size - - library preparation kit - - flow cell barcode - - sequencing instrument - - sequencing protocol name - - sequencing protocol - - sequencing kit number - - amplicon pcr primer scheme - - raw sequence data processing method - - dehosting method - - consensus sequence name - - consensus sequence filename - - consensus sequence filepath - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - r1 fastq filename - - r2 fastq filename - - r1 fastq filepath - - r2 fastq filepath - - fast5 filename - - fast5 filepath - - number of base pairs sequenced - - consensus genome length - - Ns per 100 kbp - - reference genome accession - - bioinformatics protocol - - lineage/clade name - - lineage/clade analysis software name - - lineage/clade analysis software version - - variant designation - - variant evidence - - variant evidence details - - gene name 1 - - diagnostic pcr protocol 1 - - diagnostic pcr Ct value 1 - - gene name 2 - - diagnostic pcr protocol 2 - - diagnostic pcr Ct value 2 - - gene name 3 - - diagnostic pcr protocol 3 - - diagnostic pcr Ct value 3 + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_dose_3_vaccine_name + - vaccination_dose_3_vaccination_date + - vaccination_dose_4_vaccine_name + - vaccination_dose_4_vaccination_date + - vaccination_history + - location_of_exposure_geo_loc_name_country + - destination_of_most_recent_travel_city + - destination_of_most_recent_travel_state_province_territory + - destination_of_most_recent_travel_country + - most_recent_travel_departure_date + - most_recent_travel_return_date + - travel_point_of_entry_type + - border_testing_test_day_type + - travel_history + - travel_history_availability + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - prior_sarscov2_infection + - prior_sarscov2_infection_isolate + - prior_sarscov2_infection_date + - prior_sarscov2_antiviral_treatment + - prior_sarscov2_antiviral_treatment_agent + - prior_sarscov2_antiviral_treatment_date + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_id + - amplicon_size + - library_preparation_kit + - flow_cell_barcode + - sequencing_instrument + - sequencing_protocol_name + - sequencing_protocol + - sequencing_kit_number + - amplicon_pcr_primer_scheme + - raw_sequence_data_processing_method + - dehosting_method + - consensus_sequence_name + - consensus_sequence_filename + - consensus_sequence_filepath + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - r1_fastq_filename________ + - r2_fastq_filename + - r1_fastq_filepath + - r2_fastq_filepath + - fast5_filename + - fast5_filepath + - number_of_base_pairs_sequenced + - consensus_genome_length + - ns_per_100_kbp + - reference_genome_accession + - bioinformatics_protocol + - lineage_clade_name + - lineage_clade_analysis_software_name + - lineage_clade_analysis_software_version + - variant_designation + - variant_evidence + - variant_evidence_details + - gene_name_1 + - diagnostic_pcr_protocol_1 + - diagnostic_pcr_ct_value_1 + - gene_name_2 + - diagnostic_pcr_protocol_2 + - diagnostic_pcr_ct_value_2 + - gene_name_3 + - diagnostic_pcr_protocol_3 + - diagnostic_pcr_ct_value_3 - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database Identifiers - third party lab service provider name: + third_party_lab_service_provider_name: rank: 2 slot_group: Database Identifiers - third party lab sample ID: + third_party_lab_sample_id: rank: 3 slot_group: Database Identifiers - case ID: + case_id: rank: 4 slot_group: Database Identifiers - Related specimen primary ID: + related_specimen_primary_id: rank: 5 slot_group: Database Identifiers - IRIDA sample name: + irida_sample_name: rank: 6 slot_group: Database Identifiers - umbrella bioproject accession: + umbrella_bioproject_accession: rank: 7 slot_group: Database Identifiers - bioproject accession: + bioproject_accession: rank: 8 slot_group: Database Identifiers - biosample accession: + biosample_accession: rank: 9 slot_group: Database Identifiers - SRA accession: + sra_accession: rank: 10 slot_group: Database Identifiers - GenBank accession: + genbank_accession: rank: 11 slot_group: Database Identifiers - GISAID accession: + gisaid_accession: rank: 12 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 13 slot_group: Sample collection and processing - sample collector contact email: + sample_collector_contact_email: rank: 14 slot_group: Sample collection and processing - sample collector contact address: + sample_collector_contact_address: rank: 15 slot_group: Sample collection and processing - sequence submitted by: + sequence_submitted_by: rank: 16 slot_group: Sample collection and processing - sequence submitter contact email: + sequence_submitter_contact_email: rank: 17 slot_group: Sample collection and processing - sequence submitter contact address: + sequence_submitter_contact_address: rank: 18 slot_group: Sample collection and processing - sample collection date: + sample_collection_date: rank: 19 slot_group: Sample collection and processing - sample collection date precision: + sample_collection_date_precision: rank: 20 slot_group: Sample collection and processing - sample received date: + sample_received_date: rank: 21 slot_group: Sample collection and processing - geo_loc_name (country): + geo_loc_name_country: rank: 22 slot_group: Sample collection and processing - geo_loc_name (state/province/territory): + geo_loc_name_state_province_territory: rank: 23 slot_group: Sample collection and processing - geo_loc_name (city): + geo_loc_name_city: rank: 24 slot_group: Sample collection and processing organism: @@ -244,360 +245,360 @@ classes: isolate: rank: 26 slot_group: Sample collection and processing - purpose of sampling: + purpose_of_sampling: rank: 27 slot_group: Sample collection and processing - purpose of sampling details: + purpose_of_sampling_details: rank: 28 slot_group: Sample collection and processing - NML submitted specimen type: + nml_submitted_specimen_type: rank: 29 slot_group: Sample collection and processing - Related specimen relationship type: + related_specimen_relationship_type: rank: 30 slot_group: Sample collection and processing - anatomical material: + anatomical_material: rank: 31 slot_group: Sample collection and processing - anatomical part: + anatomical_part: rank: 32 slot_group: Sample collection and processing - body product: + body_product: rank: 33 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 34 slot_group: Sample collection and processing - environmental site: + environmental_site: rank: 35 slot_group: Sample collection and processing - collection device: + collection_device: rank: 36 slot_group: Sample collection and processing - collection method: + collection_method: rank: 37 slot_group: Sample collection and processing - collection protocol: + collection_protocol: rank: 38 slot_group: Sample collection and processing - specimen processing: + specimen_processing: rank: 39 slot_group: Sample collection and processing - specimen processing details: + specimen_processing_details: rank: 40 slot_group: Sample collection and processing - lab host: + lab_host: rank: 41 slot_group: Sample collection and processing - passage number: + passage_number: rank: 42 slot_group: Sample collection and processing - passage method: + passage_method: rank: 43 slot_group: Sample collection and processing - biomaterial extracted: + biomaterial_extracted: rank: 44 slot_group: Sample collection and processing - host (common name): + host_common_name: rank: 45 slot_group: Host Information - host (scientific name): + host_scientific_name: rank: 46 slot_group: Host Information - host health state: + host_health_state: rank: 47 slot_group: Host Information - host health status details: + host_health_status_details: rank: 48 slot_group: Host Information - host health outcome: + host_health_outcome: rank: 49 slot_group: Host Information - host disease: + host_disease: rank: 50 slot_group: Host Information - host age: + host_age: rank: 51 slot_group: Host Information - host age unit: + host_age_unit: rank: 52 slot_group: Host Information - host age bin: + host_age_bin: rank: 53 slot_group: Host Information - host gender: + host_gender: rank: 54 slot_group: Host Information - host residence geo_loc name (country): + host_residence_geo_loc_name_country: rank: 55 slot_group: Host Information - host residence geo_loc name (state/province/territory): + host_residence_geo_loc_name_state_province_territory: rank: 56 slot_group: Host Information - host subject ID: + host_subject_id: rank: 57 slot_group: Host Information - symptom onset date: + symptom_onset_date: rank: 58 slot_group: Host Information - signs and symptoms: + signs_and_symptoms: rank: 59 slot_group: Host Information - pre-existing conditions and risk factors: + preexisting_conditions_and_risk_factors: rank: 60 slot_group: Host Information complications: rank: 61 slot_group: Host Information - host vaccination status: + host_vaccination_status: rank: 62 slot_group: Host vaccination information - number of vaccine doses received: + number_of_vaccine_doses_received: rank: 63 slot_group: Host vaccination information - vaccination dose 1 vaccine name: + vaccination_dose_1_vaccine_name: rank: 64 slot_group: Host vaccination information - vaccination dose 1 vaccination date: + vaccination_dose_1_vaccination_date: rank: 65 slot_group: Host vaccination information - vaccination dose 2 vaccine name: + vaccination_dose_2_vaccine_name: rank: 66 slot_group: Host vaccination information - vaccination dose 2 vaccination date: + vaccination_dose_2_vaccination_date: rank: 67 slot_group: Host vaccination information - vaccination dose 3 vaccine name: + vaccination_dose_3_vaccine_name: rank: 68 slot_group: Host vaccination information - vaccination dose 3 vaccination date: + vaccination_dose_3_vaccination_date: rank: 69 slot_group: Host vaccination information - vaccination dose 4 vaccine name: + vaccination_dose_4_vaccine_name: rank: 70 slot_group: Host vaccination information - vaccination dose 4 vaccination date: + vaccination_dose_4_vaccination_date: rank: 71 slot_group: Host vaccination information - vaccination history: + vaccination_history: rank: 72 slot_group: Host vaccination information - location of exposure geo_loc name (country): + location_of_exposure_geo_loc_name_country: rank: 73 slot_group: Host exposure information - destination of most recent travel (city): + destination_of_most_recent_travel_city: rank: 74 slot_group: Host exposure information - destination of most recent travel (state/province/territory): + destination_of_most_recent_travel_state_province_territory: rank: 75 slot_group: Host exposure information - destination of most recent travel (country): + destination_of_most_recent_travel_country: rank: 76 slot_group: Host exposure information - most recent travel departure date: + most_recent_travel_departure_date: rank: 77 slot_group: Host exposure information - most recent travel return date: + most_recent_travel_return_date: rank: 78 slot_group: Host exposure information - travel point of entry type: + travel_point_of_entry_type: rank: 79 slot_group: Host exposure information - border testing test day type: + border_testing_test_day_type: rank: 80 slot_group: Host exposure information - travel history: + travel_history: rank: 81 slot_group: Host exposure information - travel history availability: + travel_history_availability: rank: 82 slot_group: Host exposure information - exposure event: + exposure_event: rank: 83 slot_group: Host exposure information - exposure contact level: + exposure_contact_level: rank: 84 slot_group: Host exposure information - host role: + host_role: rank: 85 slot_group: Host exposure information - exposure setting: + exposure_setting: rank: 86 slot_group: Host exposure information - exposure details: + exposure_details: rank: 87 slot_group: Host exposure information - prior SARS-CoV-2 infection: + prior_sarscov2_infection: rank: 88 slot_group: Host reinfection information - prior SARS-CoV-2 infection isolate: + prior_sarscov2_infection_isolate: rank: 89 slot_group: Host reinfection information - prior SARS-CoV-2 infection date: + prior_sarscov2_infection_date: rank: 90 slot_group: Host reinfection information - prior SARS-CoV-2 antiviral treatment: + prior_sarscov2_antiviral_treatment: rank: 91 slot_group: Host reinfection information - prior SARS-CoV-2 antiviral treatment agent: + prior_sarscov2_antiviral_treatment_agent: rank: 92 slot_group: Host reinfection information - prior SARS-CoV-2 antiviral treatment date: + prior_sarscov2_antiviral_treatment_date: rank: 93 slot_group: Host reinfection information - purpose of sequencing: + purpose_of_sequencing: rank: 94 slot_group: Sequencing - purpose of sequencing details: + purpose_of_sequencing_details: rank: 95 slot_group: Sequencing - sequencing date: + sequencing_date: rank: 96 slot_group: Sequencing - library ID: + library_id: rank: 97 slot_group: Sequencing - amplicon size: + amplicon_size: rank: 98 slot_group: Sequencing - library preparation kit: + library_preparation_kit: rank: 99 slot_group: Sequencing - flow cell barcode: + flow_cell_barcode: rank: 100 slot_group: Sequencing - sequencing instrument: + sequencing_instrument: rank: 101 slot_group: Sequencing - sequencing protocol name: + sequencing_protocol_name: rank: 102 slot_group: Sequencing - sequencing protocol: + sequencing_protocol: rank: 103 slot_group: Sequencing - sequencing kit number: + sequencing_kit_number: rank: 104 slot_group: Sequencing - amplicon pcr primer scheme: + amplicon_pcr_primer_scheme: rank: 105 slot_group: Sequencing - raw sequence data processing method: + raw_sequence_data_processing_method: rank: 106 slot_group: Bioinformatics and QC metrics - dehosting method: + dehosting_method: rank: 107 slot_group: Bioinformatics and QC metrics - consensus sequence name: + consensus_sequence_name: rank: 108 slot_group: Bioinformatics and QC metrics - consensus sequence filename: + consensus_sequence_filename: rank: 109 slot_group: Bioinformatics and QC metrics - consensus sequence filepath: + consensus_sequence_filepath: rank: 110 slot_group: Bioinformatics and QC metrics - consensus sequence software name: + consensus_sequence_software_name: rank: 111 slot_group: Bioinformatics and QC metrics - consensus sequence software version: + consensus_sequence_software_version: rank: 112 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + breadth_of_coverage_value: rank: 113 slot_group: Bioinformatics and QC metrics - depth of coverage value: + depth_of_coverage_value: rank: 114 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + depth_of_coverage_threshold: rank: 115 slot_group: Bioinformatics and QC metrics - r1 fastq filename: + r1_fastq_filename________: rank: 116 slot_group: Bioinformatics and QC metrics - r2 fastq filename: + r2_fastq_filename: rank: 117 slot_group: Bioinformatics and QC metrics - r1 fastq filepath: + r1_fastq_filepath: rank: 118 slot_group: Bioinformatics and QC metrics - r2 fastq filepath: + r2_fastq_filepath: rank: 119 slot_group: Bioinformatics and QC metrics - fast5 filename: + fast5_filename: rank: 120 slot_group: Bioinformatics and QC metrics - fast5 filepath: + fast5_filepath: rank: 121 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + number_of_base_pairs_sequenced: rank: 122 slot_group: Bioinformatics and QC metrics - consensus genome length: + consensus_genome_length: rank: 123 slot_group: Bioinformatics and QC metrics - Ns per 100 kbp: + ns_per_100_kbp: rank: 124 slot_group: Bioinformatics and QC metrics - reference genome accession: + reference_genome_accession: rank: 125 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + bioinformatics_protocol: rank: 126 slot_group: Bioinformatics and QC metrics - lineage/clade name: + lineage_clade_name: rank: 127 slot_group: Lineage and Variant information - lineage/clade analysis software name: + lineage_clade_analysis_software_name: rank: 128 slot_group: Lineage and Variant information - lineage/clade analysis software version: + lineage_clade_analysis_software_version: rank: 129 slot_group: Lineage and Variant information - variant designation: + variant_designation: rank: 130 slot_group: Lineage and Variant information - variant evidence: + variant_evidence: rank: 131 slot_group: Lineage and Variant information - variant evidence details: + variant_evidence_details: rank: 132 slot_group: Lineage and Variant information - gene name 1: + gene_name_1: rank: 133 slot_group: Pathogen diagnostic testing - diagnostic pcr protocol 1: + diagnostic_pcr_protocol_1: rank: 134 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 1: + diagnostic_pcr_ct_value_1: rank: 135 slot_group: Pathogen diagnostic testing - gene name 2: + gene_name_2: rank: 136 slot_group: Pathogen diagnostic testing - diagnostic pcr protocol 2: + diagnostic_pcr_protocol_2: rank: 137 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 2: + diagnostic_pcr_ct_value_2: rank: 138 slot_group: Pathogen diagnostic testing - gene name 3: + gene_name_3: rank: 139 slot_group: Pathogen diagnostic testing - diagnostic pcr protocol 3: + diagnostic_pcr_protocol_3: rank: 140 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 3: + diagnostic_pcr_ct_value_3: rank: 141 slot_group: Pathogen diagnostic testing authors: rank: 142 slot_group: Contributor acknowledgement - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 143 slot_group: Contributor acknowledgement slots: - specimen collector sample ID: - name: specimen collector sample ID + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. comments: Store the collector sample ID. If this number is considered identifiable @@ -618,8 +619,8 @@ slots: - NML_LIMS:TEXT_ID - BIOSAMPLE:sample_name - VirusSeq_Portal:specimen%20collector%20sample%20ID - third party lab service provider name: - name: third party lab service provider name + third_party_lab_service_provider_name: + name: third_party_lab_service_provider_name title: third party lab service provider name description: The name of the third party company or laboratory that provided services. comments: Provide the full, unabbreviated name of the company or laboratory. @@ -629,8 +630,8 @@ slots: - value: Switch Health exact_mappings: - NML_LIMS:HC_TEXT5 - third party lab sample ID: - name: third party lab sample ID + third_party_lab_sample_id: + name: third_party_lab_sample_id title: third party lab sample ID description: The identifier assigned to a sample by a third party service provider. comments: Store the sample identifier supplied by the third party services provider. @@ -640,8 +641,8 @@ slots: - value: SHK123456 exact_mappings: - NML_LIMS:PH_ID_NUMBER_PRIMARY - case ID: - name: case ID + case_id: + name: case_id title: case ID description: The identifier used to specify an epidemiologically detected case of disease. @@ -655,8 +656,8 @@ slots: - value: ABCD1234 exact_mappings: - NML_LIMS:PH_CASE_ID - Related specimen primary ID: - name: Related specimen primary ID + related_specimen_primary_id: + name: related_specimen_primary_id title: Related specimen primary ID description: The primary ID of a related specimen previously submitted to the repository. @@ -666,15 +667,15 @@ slots: slot_uri: GENEPIO:0001128 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu examples: - value: SR20-12345 exact_mappings: - CNPHI:Related%20Specimen%20ID - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_PRIMARY_ID - IRIDA sample name: - name: IRIDA sample name + irida_sample_name: + name: irida_sample_name title: IRIDA sample name description: The identifier assigned to a sequenced isolate in IRIDA. comments: Store the IRIDA sample name. The IRIDA sample name will be created by @@ -691,8 +692,8 @@ slots: - value: prov_rona_99 exact_mappings: - NML_LIMS:IRIDA%20sample%20name - umbrella bioproject accession: - name: umbrella bioproject accession + umbrella_bioproject_accession: + name: umbrella_bioproject_accession title: umbrella bioproject accession description: The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. @@ -701,7 +702,7 @@ slots: CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. slot_uri: GENEPIO:0001133 - range: umbrella bioproject accession menu + range: UmbrellaBioprojectAccessionMenu structured_pattern: syntax: '{UPPER_CASE}' partial_match: false @@ -710,8 +711,8 @@ slots: - value: PRJNA623807 exact_mappings: - NML_LIMS:umbrella%20bioproject%20accession - bioproject accession: - name: bioproject accession + bioproject_accession: + name: bioproject_accession title: bioproject accession description: The INSDC accession number of the BioProject(s) to which the BioSample belongs. @@ -733,8 +734,8 @@ slots: - CNPHI:BioProject%20Accession - NML_LIMS:PH_BIOPROJECT_ACCESSION - BIOSAMPLE:bioproject_accession - biosample accession: - name: biosample accession + biosample_accession: + name: biosample_accession title: biosample accession description: The identifier assigned to a BioSample in INSDC archives. comments: Store the accession returned from the BioSample submission. NCBI BioSamples @@ -750,8 +751,8 @@ slots: exact_mappings: - CNPHI:BioSample%20Accession - NML_LIMS:PH_BIOSAMPLE_ACCESSION - SRA accession: - name: SRA accession + sra_accession: + name: sra_accession title: SRA accession description: The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. @@ -768,8 +769,8 @@ slots: exact_mappings: - CNPHI:SRA%20Accession - NML_LIMS:PH_SRA_ACCESSION - GenBank accession: - name: GenBank accession + genbank_accession: + name: genbank_accession title: GenBank accession description: The GenBank identifier assigned to the sequence in the INSDC archives. comments: Store the accession returned from a GenBank submission (viral genome @@ -785,8 +786,8 @@ slots: exact_mappings: - CNPHI:GenBank%20Accession - NML_LIMS:GenBank%20accession - GISAID accession: - name: GISAID accession + gisaid_accession: + name: gisaid_accession title: GISAID accession description: The GISAID accession number assigned to the sequence. comments: Store the accession returned from the GISAID submission. @@ -803,8 +804,8 @@ slots: - NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID - BIOSAMPLE:GISAID_accession - VirusSeq_Portal:GISAID%20accession - sample collected by: - name: sample collected by + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the agency that collected the original sample. comments: The name of the sample collector should be written out in full, (with @@ -814,8 +815,8 @@ slots: be hospital, provincial public health lab, or other). slot_uri: GENEPIO:0001153 any_of: - - range: sample collected by menu - - range: null value menu + - range: SampleCollectedByMenu + - range: NullValueMenu required: true examples: - value: BC Centre for Disease Control @@ -825,8 +826,8 @@ slots: - NML_LIMS:CUSTOMER - BIOSAMPLE:collected_by - VirusSeq_Portal:sample%20collected%20by - sample collector contact email: - name: sample collector contact email + sample_collector_contact_email: + name: sample_collector_contact_email title: sample collector contact email description: The email address of the contact responsible for follow-up regarding the sample. @@ -839,8 +840,8 @@ slots: - value: RespLab@lab.ca exact_mappings: - NML_LIMS:sample%20collector%20contact%20email - sample collector contact address: - name: sample collector contact address + sample_collector_contact_address: + name: sample_collector_contact_address title: sample collector contact address description: The mailing address of the agency submitting the sample. comments: 'The mailing address should be in the format: Street number and name, @@ -852,8 +853,8 @@ slots: exact_mappings: - GISAID:Address - NML_LIMS:sample%20collector%20contact%20address - sequence submitted by: - name: sequence submitted by + sequence_submitted_by: + name: sequence_submitted_by title: sequence submitted by description: The name of the agency that generated the sequence. comments: The name of the agency should be written out in full, (with minor exceptions) @@ -861,8 +862,8 @@ slots: than sequencing data, please put the "National Microbiology Laboratory (NML)". slot_uri: GENEPIO:0001159 any_of: - - range: sequence submitted by menu - - range: null value menu + - range: SequenceSubmittedByMenu + - range: NullValueMenu required: true examples: - value: Public Health Ontario (PHO) @@ -872,8 +873,8 @@ slots: - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by - VirusSeq_Portal:sequence%20submitted%20by - sequence submitter contact email: - name: sequence submitter contact email + sequence_submitter_contact_email: + name: sequence_submitter_contact_email title: sequence submitter contact email description: The email address of the contact responsible for follow-up regarding the sequence. @@ -885,8 +886,8 @@ slots: - value: RespLab@lab.ca exact_mappings: - NML_LIMS:sequence%20submitter%20contact%20email - sequence submitter contact address: - name: sequence submitter contact address + sequence_submitter_contact_address: + name: sequence_submitter_contact_address title: sequence submitter contact address description: The mailing address of the agency submitting the sequence. comments: 'The mailing address should be in the format: Street number and name, @@ -898,8 +899,8 @@ slots: exact_mappings: - GISAID:Address - NML_LIMS:sequence%20submitter%20contact%20address - sample collection date: - name: sample collection date + sample_collection_date: + name: sample_collection_date title: sample collection date description: The date on which the sample was collected. comments: "Sample collection date is critical for surveillance and many types\ @@ -911,7 +912,7 @@ slots: slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} @@ -924,8 +925,8 @@ slots: - NML_LIMS:HC_COLLECT_DATE - BIOSAMPLE:sample%20collection%20date - VirusSeq_Portal:sample%20collection%20date - sample collection date precision: - name: sample collection date precision + sample_collection_date_precision: + name: sample_collection_date_precision title: sample collection date precision description: The precision to which the "sample collection date" was provided. comments: Provide the precision of granularity to the "day", "month", or "year" @@ -934,36 +935,36 @@ slots: "month" for "YYYY-MM", or "year" for "YYYY". slot_uri: GENEPIO:0001177 any_of: - - range: sample collection date precision menu - - range: null value menu + - range: SampleCollectionDatePrecisionMenu + - range: NullValueMenu required: true examples: - value: year exact_mappings: - CNPHI:Precision%20of%20date%20collected - NML_LIMS:HC_TEXT2 - sample received date: - name: sample received date + sample_received_date: + name: sample_received_date title: sample received date description: The date on which the sample was received. comments: ISO 8601 standard "YYYY-MM-DD". slot_uri: GENEPIO:0001179 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-20' exact_mappings: - NML_LIMS:sample%20received%20date - geo_loc_name (country): - name: geo_loc_name (country) + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc_name (country) description: The country where the sample was collected. comments: Provide the country name from the controlled vocabulary provided. slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true examples: - value: Canada @@ -973,15 +974,15 @@ slots: - NML_LIMS:HC_COUNTRY - BIOSAMPLE:geo_loc_name - VirusSeq_Portal:geo_loc_name%20%28country%29 - geo_loc_name (state/province/territory): - name: geo_loc_name (state/province/territory) + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo_loc_name (state/province/territory) description: The province/territory where the sample was collected. comments: Provide the province/territory name from the controlled vocabulary provided. slot_uri: GENEPIO:0001185 any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu required: true examples: - value: Saskatchewan @@ -990,8 +991,8 @@ slots: - NML_LIMS:HC_PROVINCE - BIOSAMPLE:geo_loc_name - VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29 - geo_loc_name (city): - name: geo_loc_name (city) + geo_loc_name_city: + name: geo_loc_name_city title: geo_loc_name (city) description: The city where the sample was collected. comments: 'Provide the city name. Use this look-up service to identify the standardized @@ -1011,8 +1012,8 @@ slots: provided in the template. slot_uri: GENEPIO:0001191 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu required: true examples: - value: Severe acute respiratory syndrome coronavirus 2 @@ -1030,7 +1031,7 @@ slots: slot_uri: GENEPIO:0001195 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: hCov-19/CANADA/BC-prov_rona_99/2020 @@ -1042,8 +1043,8 @@ slots: - BIOSAMPLE:GISAID_virus_name - VirusSeq_Portal:isolate - VirusSeq_Portal:fasta%20header%20name - purpose of sampling: - name: purpose of sampling + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: The reason a sample was collected may provide information about potential @@ -1054,8 +1055,8 @@ slots: of sequencing" field. slot_uri: GENEPIO:0001198 any_of: - - range: purpose of sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu required: true examples: - value: Diagnostic testing @@ -1064,8 +1065,8 @@ slots: - NML_LIMS:HC_SAMPLE_CATEGORY - BIOSAMPLE:purpose_of_sampling - VirusSeq_Portal:purpose%20of%20sampling - purpose of sampling details: - name: purpose of sampling details + purpose_of_sampling_details: + name: purpose_of_sampling_details title: purpose of sampling details description: The description of why the sample was collected, providing specific details. @@ -1076,7 +1077,7 @@ slots: slot_uri: GENEPIO:0001200 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: The sample was collected to investigate the prevalence of variants associated @@ -1086,8 +1087,8 @@ slots: - NML_LIMS:PH_SAMPLING_DETAILS - BIOSAMPLE:description - VirusSeq_Portal:purpose%20of%20sampling%20details - NML submitted specimen type: - name: NML submitted specimen type + nml_submitted_specimen_type: + name: nml_submitted_specimen_type title: NML submitted specimen type description: The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. @@ -1096,15 +1097,15 @@ slots: \ being submitted rather than a specimen for testing, select \u201CNot Applicable\u201D\ ." slot_uri: GENEPIO:0001204 - range: NML submitted specimen type menu + range: NmlSubmittedSpecimenTypeMenu required: true examples: - value: swab exact_mappings: - CNPHI:Specimen%20Type - NML_LIMS:PH_SPECIMEN_TYPE - Related specimen relationship type: - name: Related specimen relationship type + related_specimen_relationship_type: + name: related_specimen_relationship_type title: Related specimen relationship type description: The relationship of the current specimen to the specimen/sample previously submitted to the repository. @@ -1112,15 +1113,15 @@ slots: the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. slot_uri: GENEPIO:0001209 - range: Related specimen relationship type menu + range: RelatedSpecimenRelationshipTypeMenu examples: - value: Specimen sampling methods testing exact_mappings: - CNPHI:Related%20Specimen%20ID - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE - anatomical material: - name: anatomical material + anatomical_material: + name: anatomical_material title: anatomical material description: A substance obtained from an anatomical part of an organism e.g. tissue, blood. @@ -1130,8 +1131,8 @@ slots: a null value. slot_uri: GENEPIO:0001211 any_of: - - range: anatomical material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1143,8 +1144,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_material - VirusSeq_Portal:anatomical%20material - anatomical part: - name: anatomical part + anatomical_part: + name: anatomical_part title: anatomical part description: An anatomical part of an organism e.g. oropharynx. comments: Provide a descriptor if an anatomical part was sampled. Use the picklist @@ -1153,8 +1154,8 @@ slots: value. slot_uri: GENEPIO:0001214 any_of: - - range: anatomical part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1166,8 +1167,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_part - VirusSeq_Portal:anatomical%20part - body product: - name: body product + body_product: + name: body_product title: body product description: A substance excreted/secreted from an organism e.g. feces, urine, sweat. @@ -1177,8 +1178,8 @@ slots: value. slot_uri: GENEPIO:0001216 any_of: - - range: body product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1190,8 +1191,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:body_product - VirusSeq_Portal:body%20product - environmental material: - name: environmental material + environmental_material: + name: environmental_material title: environmental material description: A substance obtained from the natural or man-made environment e.g. soil, water, sewage. @@ -1201,8 +1202,8 @@ slots: a null value. slot_uri: GENEPIO:0001223 any_of: - - range: environmental material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1214,8 +1215,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_material - VirusSeq_Portal:environmental%20material - environmental site: - name: environmental site + environmental_site: + name: environmental_site title: environmental site description: An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. @@ -1225,8 +1226,8 @@ slots: value. slot_uri: GENEPIO:0001232 any_of: - - range: environmental site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1238,8 +1239,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_site - VirusSeq_Portal:environmental%20site - collection device: - name: collection device + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. swab. comments: Provide a descriptor if a device was used for sampling. Use the picklist @@ -1248,8 +1249,8 @@ slots: value. slot_uri: GENEPIO:0001234 any_of: - - range: collection device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1261,8 +1262,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_device - VirusSeq_Portal:collection%20device - collection method: - name: collection method + collection_method: + name: collection_method title: collection method description: The process used to collect the sample e.g. phlebotamy, necropsy. comments: Provide a descriptor if a collection method was used for sampling. Use @@ -1271,8 +1272,8 @@ slots: Choose a null value. slot_uri: GENEPIO:0001241 any_of: - - range: collection method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -1284,8 +1285,8 @@ slots: - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method - VirusSeq_Portal:collection%20method - collection protocol: - name: collection protocol + collection_protocol: + name: collection_protocol title: collection protocol description: The name and version of a particular protocol used for sampling. comments: Free text. @@ -1295,8 +1296,8 @@ slots: - value: BCRonaSamplingProtocol v. 1.2 exact_mappings: - NML_LIMS:collection%20protocol - specimen processing: - name: specimen processing + specimen_processing: + name: specimen_processing title: specimen processing description: Any processing applied to the sample during or after receiving the sample. @@ -1306,8 +1307,8 @@ slots: pick list apply, put "not applicable". slot_uri: GENEPIO:0001253 any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -1315,8 +1316,8 @@ slots: exact_mappings: - GISAID:Passage%20details/history - NML_LIMS:specimen%20processing - specimen processing details: - name: specimen processing details + specimen_processing_details: + name: specimen_processing_details title: specimen processing details description: Detailed information regarding the processing applied to a sample during or after receiving the sample. @@ -1327,8 +1328,8 @@ slots: examples: - value: 25 swabs were pooled and further prepared as a single sample during library prep. - lab host: - name: lab host + lab_host: + name: lab_host title: lab host description: Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. @@ -1336,8 +1337,8 @@ slots: line using the picklist in the template. If not passaged, put "not applicable". slot_uri: GENEPIO:0001255 any_of: - - range: lab host menu - - range: null value menu + - range: LabHostMenu + - range: NullValueMenu recommended: true examples: - value: Vero E6 cell line @@ -1345,16 +1346,16 @@ slots: - GISAID:Passage%20details/history - NML_LIMS:lab%20host - BIOSAMPLE:lab_host - passage number: - name: passage number + passage_number: + name: passage_number title: passage number description: Number of passages. comments: Provide number of known passages. If not passaged, put "not applicable" slot_uri: GENEPIO:0001261 any_of: - range: integer - - range: null value menu - minimum_value: '0' + - range: NullValueMenu + minimum_value: 0 recommended: true examples: - value: '3' @@ -1362,8 +1363,8 @@ slots: - GISAID:Passage%20details/history - NML_LIMS:passage%20number - BIOSAMPLE:passage_history - passage method: - name: passage method + passage_method: + name: passage_method title: passage method description: Description of how organism was passaged. comments: Free text. Provide a very short description (<10 words). If not passaged, @@ -1371,7 +1372,7 @@ slots: slot_uri: GENEPIO:0001264 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true examples: - value: 0.25% trypsin + 0.02% EDTA @@ -1379,21 +1380,21 @@ slots: - GISAID:Passage%20details/history - NML_LIMS:passage%20method - BIOSAMPLE:passage_method - biomaterial extracted: - name: biomaterial extracted + biomaterial_extracted: + name: biomaterial_extracted title: biomaterial extracted description: The biomaterial extracted from samples for the purpose of sequencing. comments: Provide the biomaterial extracted from the picklist in the template. slot_uri: GENEPIO:0001266 any_of: - - range: biomaterial extracted menu - - range: null value menu + - range: BiomaterialExtractedMenu + - range: NullValueMenu examples: - value: RNA (total) exact_mappings: - NML_LIMS:biomaterial%20extracted - host (common name): - name: host (common name) + host_common_name: + name: host_common_name title: host (common name) description: The commonly used name of the host. comments: Common name or scientific name are required if there was a host. Both @@ -1401,15 +1402,15 @@ slots: name e.g. human, bat. If the sample was environmental, put "not applicable. slot_uri: GENEPIO:0001386 any_of: - - range: host (common name) menu - - range: null value menu + - range: HostCommonNameMenu + - range: NullValueMenu examples: - value: Human exact_mappings: - CNPHI:Animal%20Type - NML_LIMS:PH_ANIMAL_TYPE - host (scientific name): - name: host (scientific name) + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. comments: Common name or scientific name are required if there was a host. Both @@ -1417,8 +1418,8 @@ slots: name e.g. Homo sapiens, If the sample was environmental, put "not applicable slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu + - range: HostScientificNameMenu + - range: NullValueMenu required: true examples: - value: Homo sapiens @@ -1427,15 +1428,15 @@ slots: - NML_LIMS:host%20%28scientific%20name%29 - BIOSAMPLE:host - VirusSeq_Portal:host%20%28scientific%20name%29 - host health state: - name: host health state + host_health_state: + name: host_health_state title: host health state description: Health status of the host at the time of sample collection. comments: If known, select a descriptor from the pick list provided in the template. slot_uri: GENEPIO:0001388 any_of: - - range: host health state menu - - range: null value menu + - range: HostHealthStateMenu + - range: NullValueMenu examples: - value: Symptomatic exact_mappings: @@ -1443,44 +1444,44 @@ slots: - CNPHI:Host%20Health%20State - NML_LIMS:PH_HOST_HEALTH - BIOSAMPLE:host_health_state - host health status details: - name: host health status details + host_health_status_details: + name: host_health_status_details title: host health status details description: Further details pertaining to the health or disease status of the host at time of collection. comments: If known, select a descriptor from the pick list provided in the template. slot_uri: GENEPIO:0001389 any_of: - - range: host health status details menu - - range: null value menu + - range: HostHealthStatusDetailsMenu + - range: NullValueMenu examples: - value: Hospitalized (ICU) exact_mappings: - CNPHI:Host%20Health%20State%20Details - NML_LIMS:PH_HOST_HEALTH_DETAILS - host health outcome: - name: host health outcome + host_health_outcome: + name: host_health_outcome title: host health outcome description: Disease outcome in the host. comments: If known, select a descriptor from the pick list provided in the template. slot_uri: GENEPIO:0001390 any_of: - - range: host health outcome menu - - range: null value menu + - range: HostHealthOutcomeMenu + - range: NullValueMenu examples: - value: Recovered exact_mappings: - NML_LIMS:PH_HOST_HEALTH_OUTCOME - BIOSAMPLE:host_disease_outcome - host disease: - name: host disease + host_disease: + name: host_disease title: host disease description: The name of the disease experienced by the host. comments: Select "COVID-19" from the pick list provided in the template. slot_uri: GENEPIO:0001391 any_of: - - range: host disease menu - - range: null value menu + - range: HostDiseaseMenu + - range: NullValueMenu required: true examples: - value: COVID-19 @@ -1489,8 +1490,8 @@ slots: - NML_LIMS:PH_HOST_DISEASE - BIOSAMPLE:host_disease - VirusSeq_Portal:host%20disease - host age: - name: host age + host_age: + name: host_age title: host age description: Age of host at the time of sampling. comments: Enter the age of the host in years. If not available, provide a null @@ -1498,9 +1499,9 @@ slots: slot_uri: GENEPIO:0001392 any_of: - range: decimal - - range: null value menu - minimum_value: '0' - maximum_value: '130' + - range: NullValueMenu + minimum_value: 0 + maximum_value: 130 required: true examples: - value: '79' @@ -1510,16 +1511,16 @@ slots: - NML_LIMS:PH_AGE - BIOSAMPLE:host_age - VirusSeq_Portal:host%20age - host age unit: - name: host age unit + host_age_unit: + name: host_age_unit title: host age unit description: The unit used to measure the host age, in either months or years. comments: Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. slot_uri: GENEPIO:0001393 any_of: - - range: host age unit menu - - range: null value menu + - range: HostAgeUnitMenu + - range: NullValueMenu required: true examples: - value: year @@ -1527,16 +1528,16 @@ slots: - CNPHI:Age%20Units - NML_LIMS:PH_AGE_UNIT - VirusSeq_Portal:host%20age%20unit - host age bin: - name: host age bin + host_age_bin: + name: host_age_bin title: host age bin description: Age of host at the time of sampling, expressed as an age group. comments: Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. slot_uri: GENEPIO:0001394 any_of: - - range: host age bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu required: true examples: - value: 60 - 69 @@ -1544,8 +1545,8 @@ slots: - CNPHI:Host%20Age%20Category - NML_LIMS:PH_AGE_GROUP - VirusSeq_Portal:host%20age%20bin - host gender: - name: host gender + host_gender: + name: host_gender title: host gender description: The gender of the host at the time of sample collection. comments: Select the corresponding host gender from the pick list provided in @@ -1553,13 +1554,9 @@ slots: "Not Applicable". slot_uri: GENEPIO:0001395 any_of: - - range: host gender menu - - range: null value menu + - range: HostGenderMenu + - range: NullValueMenu required: true - structured_pattern: - syntax: '{Title_Case}' - partial_match: false - interpolated: true examples: - value: Male exact_mappings: @@ -1568,34 +1565,34 @@ slots: - NML_LIMS:VD_SEX - BIOSAMPLE:host_sex - VirusSeq_Portal:host%20gender - host residence geo_loc name (country): - name: host residence geo_loc name (country) + host_residence_geo_loc_name_country: + name: host_residence_geo_loc_name_country title: host residence geo_loc name (country) description: The country of residence of the host. comments: Select the country name from pick list provided in the template. slot_uri: GENEPIO:0001396 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: Canada exact_mappings: - NML_LIMS:PH_HOST_COUNTRY - host residence geo_loc name (state/province/territory): - name: host residence geo_loc name (state/province/territory) + host_residence_geo_loc_name_state_province_territory: + name: host_residence_geo_loc_name_state_province_territory title: host residence geo_loc name (state/province/territory) description: The state/province/territory of residence of the host. comments: Select the province/territory name from pick list provided in the template. slot_uri: GENEPIO:0001397 any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu examples: - value: Quebec exact_mappings: - NML_LIMS:PH_HOST_PROVINCE - host subject ID: - name: host subject ID + host_subject_id: + name: host_subject_id title: host subject ID description: 'A unique identifier by which each host can be referred to e.g. #131' comments: Provide the host identifier. Should be a unique, user-defined identifier. @@ -1606,30 +1603,30 @@ slots: exact_mappings: - NML_LIMS:host%20subject%20ID - BIOSAMPLE:host_subject_id - symptom onset date: - name: symptom onset date + symptom_onset_date: + name: symptom_onset_date title: symptom onset date description: The date on which the symptoms began or were first noted. comments: ISO 8601 standard "YYYY-MM-DD". slot_uri: GENEPIO:0001399 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-16' exact_mappings: - CNPHI:Symptoms%20Onset%20Date - NML_LIMS:HC_ONSET_DATE - signs and symptoms: - name: signs and symptoms + signs_and_symptoms: + name: signs_and_symptoms title: signs and symptoms description: A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. comments: Select all of the symptoms experienced by the host from the pick list. slot_uri: GENEPIO:0001400 any_of: - - range: signs and symptoms menu - - range: null value menu + - range: SignsAndSymptomsMenu + - range: NullValueMenu multivalued: true examples: - value: Chills (sudden cold sensation) @@ -1638,8 +1635,8 @@ slots: exact_mappings: - CNPHI:Symptoms - NML_LIMS:HC_SYMPTOMS - pre-existing conditions and risk factors: - name: pre-existing conditions and risk factors + preexisting_conditions_and_risk_factors: + name: preexisting_conditions_and_risk_factors title: pre-existing conditions and risk factors description: 'Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection. @@ -1650,8 +1647,8 @@ slots: curation team. slot_uri: GENEPIO:0001401 any_of: - - range: pre-existing conditions and risk factors menu - - range: null value menu + - range: PreExistingConditionsAndRiskFactorsMenu + - range: NullValueMenu multivalued: true examples: - value: Asthma @@ -1668,8 +1665,8 @@ slots: list. If the desired term is missing, contact the curation team. slot_uri: GENEPIO:0001402 any_of: - - range: complications menu - - range: null value menu + - range: ComplicationsMenu + - range: NullValueMenu multivalued: true examples: - value: Acute Respiratory Failure @@ -1677,8 +1674,8 @@ slots: - value: Septicemia exact_mappings: - NML_LIMS:complications - host vaccination status: - name: host vaccination status + host_vaccination_status: + name: host_vaccination_status title: host vaccination status description: The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). @@ -1686,13 +1683,13 @@ slots: slot_uri: GENEPIO:0001404 any_of: - range: host vaccination status menu - - range: null value menu + - range: NullValueMenu examples: - value: Fully Vaccinated exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - number of vaccine doses received: - name: number of vaccine doses received + number_of_vaccine_doses_received: + name: number_of_vaccine_doses_received title: number of vaccine doses received description: The number of doses of the vaccine recived by the host. comments: Record how many doses of the vaccine the host has received. @@ -1700,8 +1697,8 @@ slots: range: integer examples: - value: '2' - vaccination dose 1 vaccine name: - name: vaccination dose 1 vaccine name + vaccination_dose_1_vaccine_name: + name: vaccination_dose_1_vaccine_name title: vaccination dose 1 vaccine name description: The name of the vaccine administered as the first dose of a vaccine regimen. @@ -1709,14 +1706,14 @@ slots: vaccine administered as the first dose by selecting a value from the pick list slot_uri: GENEPIO:0100313 any_of: - - range: vaccine name menu - - range: null value menu + - range: VaccineNameMenu + - range: NullValueMenu examples: - value: Pfizer-BioNTech (Comirnaty) exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 1 vaccination date: - name: vaccination dose 1 vaccination date + vaccination_dose_1_vaccination_date: + name: vaccination_dose_1_vaccination_date title: vaccination dose 1 vaccination date description: The date the first dose of a vaccine was administered. comments: Provide the date the first dose of COVID-19 vaccine was administered. @@ -1724,13 +1721,13 @@ slots: slot_uri: GENEPIO:0100314 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2021-03-01' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 2 vaccine name: - name: vaccination dose 2 vaccine name + vaccination_dose_2_vaccine_name: + name: vaccination_dose_2_vaccine_name title: vaccination dose 2 vaccine name description: The name of the vaccine administered as the second dose of a vaccine regimen. @@ -1738,14 +1735,14 @@ slots: vaccine administered as the second dose by selecting a value from the pick list slot_uri: GENEPIO:0100315 any_of: - - range: vaccine name menu - - range: null value menu + - range: VaccineNameMenu + - range: NullValueMenu examples: - value: Pfizer-BioNTech (Comirnaty) exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 2 vaccination date: - name: vaccination dose 2 vaccination date + vaccination_dose_2_vaccination_date: + name: vaccination_dose_2_vaccination_date title: vaccination dose 2 vaccination date description: The date the second dose of a vaccine was administered. comments: Provide the date the second dose of COVID-19 vaccine was administered. @@ -1753,13 +1750,13 @@ slots: slot_uri: GENEPIO:0100316 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2021-09-01' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 3 vaccine name: - name: vaccination dose 3 vaccine name + vaccination_dose_3_vaccine_name: + name: vaccination_dose_3_vaccine_name title: vaccination dose 3 vaccine name description: The name of the vaccine administered as the third dose of a vaccine regimen. @@ -1767,14 +1764,14 @@ slots: vaccine administered as the third dose by selecting a value from the pick list slot_uri: GENEPIO:0100317 any_of: - - range: vaccine name menu - - range: null value menu + - range: VaccineNameMenu + - range: NullValueMenu examples: - value: Pfizer-BioNTech (Comirnaty) exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 3 vaccination date: - name: vaccination dose 3 vaccination date + vaccination_dose_3_vaccination_date: + name: vaccination_dose_3_vaccination_date title: vaccination dose 3 vaccination date description: The date the third dose of a vaccine was administered. comments: Provide the date the third dose of COVID-19 vaccine was administered. @@ -1782,13 +1779,13 @@ slots: slot_uri: GENEPIO:0100318 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2021-12-30' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 4 vaccine name: - name: vaccination dose 4 vaccine name + vaccination_dose_4_vaccine_name: + name: vaccination_dose_4_vaccine_name title: vaccination dose 4 vaccine name description: The name of the vaccine administered as the fourth dose of a vaccine regimen. @@ -1796,14 +1793,14 @@ slots: vaccine administered as the fourth dose by selecting a value from the pick list slot_uri: GENEPIO:0100319 any_of: - - range: vaccine name menu - - range: null value menu + - range: VaccineNameMenu + - range: NullValueMenu examples: - value: Pfizer-BioNTech (Comirnaty) exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination dose 4 vaccination date: - name: vaccination dose 4 vaccination date + vaccination_dose_4_vaccination_date: + name: vaccination_dose_4_vaccination_date title: vaccination dose 4 vaccination date description: The date the fourth dose of a vaccine was administered. comments: Provide the date the fourth dose of COVID-19 vaccine was administered. @@ -1811,13 +1808,13 @@ slots: slot_uri: GENEPIO:0100320 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2022-01-15' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination history: - name: vaccination history + vaccination_history: + name: vaccination_history title: vaccination history description: A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. @@ -1833,22 +1830,22 @@ slots: - value: '2022-01-15' exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - location of exposure geo_loc name (country): - name: location of exposure geo_loc name (country) + location_of_exposure_geo_loc_name_country: + name: location_of_exposure_geo_loc_name_country title: location of exposure geo_loc name (country) description: The country where the host was likely exposed to the causative agent of the illness. comments: Select the country name from pick list provided in the template. slot_uri: GENEPIO:0001410 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: Canada exact_mappings: - NML_LIMS:PH_EXPOSURE_COUNTRY - destination of most recent travel (city): - name: destination of most recent travel (city) + destination_of_most_recent_travel_city: + name: destination_of_most_recent_travel_city title: destination of most recent travel (city) description: The name of the city that was the destination of most recent travel. comments: 'Provide the name of the city that the host travelled to. Use this look-up @@ -1860,8 +1857,8 @@ slots: exact_mappings: - CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date - NML_LIMS:PH_TRAVEL - destination of most recent travel (state/province/territory): - name: destination of most recent travel (state/province/territory) + destination_of_most_recent_travel_state_province_territory: + name: destination_of_most_recent_travel_state_province_territory title: destination of most recent travel (state/province/territory) description: The name of the province that was the destination of most recent travel. @@ -1874,23 +1871,23 @@ slots: exact_mappings: - CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date - NML_LIMS:PH_TRAVEL - destination of most recent travel (country): - name: destination of most recent travel (country) + destination_of_most_recent_travel_country: + name: destination_of_most_recent_travel_country title: destination of most recent travel (country) description: The name of the country that was the destination of most recent travel. comments: 'Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz' slot_uri: GENEPIO:0001413 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu examples: - value: United Kingdom exact_mappings: - CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date - NML_LIMS:PH_TRAVEL - most recent travel departure date: - name: most recent travel departure date + most_recent_travel_departure_date: + name: most_recent_travel_departure_date title: most recent travel departure date description: The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. @@ -1898,14 +1895,14 @@ slots: slot_uri: GENEPIO:0001414 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-03-16' exact_mappings: - CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date - NML_LIMS:PH_TRAVEL - most recent travel return date: - name: most recent travel return date + most_recent_travel_return_date: + name: most_recent_travel_return_date title: most recent travel return date description: The date of a person's most recent return to some residence from a journey originating at that residence. @@ -1913,43 +1910,43 @@ slots: slot_uri: GENEPIO:0001415 any_of: - range: date - - range: null value menu + - range: NullValueMenu examples: - value: '2020-04-26' exact_mappings: - CNPHI:Country%20of%20Travel%7CProvince%20of%20Travel%7CCity%20of%20Travel%7CTravel%20start%20date%7CTravel%20End%20Date - NML_LIMS:PH_TRAVEL - travel point of entry type: - name: travel point of entry type + travel_point_of_entry_type: + name: travel_point_of_entry_type title: travel point of entry type description: The type of entry point a traveler arrives through. comments: Select the point of entry type. slot_uri: GENEPIO:0100413 any_of: - - range: travel point of entry type menu - - range: null value menu + - range: TravelPointOfEntryTypeMenu + - range: NullValueMenu recommended: true examples: - value: Air exact_mappings: - NML_LIMS:PH_POINT_OF_ENTRY - border testing test day type: - name: border testing test day type + border_testing_test_day_type: + name: border_testing_test_day_type title: border testing test day type description: The day a traveller was tested on or after arrival at their point of entry. comments: Select the test day. slot_uri: GENEPIO:0100414 any_of: - - range: border testing test day type menu - - range: null value menu + - range: BorderTestingTestDayTypeMenu + - range: NullValueMenu recommended: true examples: - value: day 1 exact_mappings: - NML_LIMS:PH_DAY - travel history: - name: travel history + travel_history: + name: travel_history title: travel history description: Travel history in last six months. comments: Specify the countries (and more granular locations if known, separated @@ -1963,8 +1960,8 @@ slots: - value: Italy, Milan exact_mappings: - NML_LIMS:PH_TRAVEL - travel history availability: - name: travel history availability + travel_history_availability: + name: travel_history_availability title: travel history availability description: The availability of different types of travel history in the last 6 months (e.g. international, domestic). @@ -1975,69 +1972,69 @@ slots: travel-associated. slot_uri: GENEPIO:0100649 any_of: - - range: travel history availability menu - - range: null value menu + - range: TravelHistoryAvailabilityMenu + - range: NullValueMenu examples: - value: International travel history available exact_mappings: - NML_LIMS:PH_TRAVEL - exposure event: - name: exposure event + exposure_event: + name: exposure_event title: exposure event description: Event leading to exposure. comments: Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. slot_uri: GENEPIO:0001417 any_of: - - range: exposure event menu - - range: null value menu + - range: ExposureEventMenu + - range: NullValueMenu examples: - value: Convention exact_mappings: - GISAID:Additional%20location%20information - CNPHI:Exposure%20Event - NML_LIMS:PH_EXPOSURE - exposure contact level: - name: exposure contact level + exposure_contact_level: + name: exposure_contact_level title: exposure contact level description: The exposure transmission contact type. comments: Select direct or indirect exposure from the pick-list. slot_uri: GENEPIO:0001418 any_of: - - range: exposure contact level menu - - range: null value menu + - range: ExposureContactLevelMenu + - range: NullValueMenu examples: - value: Direct exact_mappings: - NML_LIMS:exposure%20contact%20level - host role: - name: host role + host_role: + name: host_role title: host role description: The role of the host in relation to the exposure setting. comments: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. slot_uri: GENEPIO:0001419 - range: host role menu + range: HostRoleMenu multivalued: true examples: - value: Patient exact_mappings: - NML_LIMS:PH_HOST_ROLE - exposure setting: - name: exposure setting + exposure_setting: + name: exposure_setting title: exposure setting description: The setting leading to exposure. comments: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. slot_uri: GENEPIO:0001428 - range: exposure setting menu + range: ExposureSettingMenu multivalued: true examples: - value: Healthcare Setting exact_mappings: - NML_LIMS:PH_EXPOSURE - exposure details: - name: exposure details + exposure_details: + name: exposure_details title: exposure details description: Additional host exposure information. comments: Free text description of the exposure. @@ -2047,22 +2044,22 @@ slots: - value: 'Host role - Other: Bus Driver' exact_mappings: - NML_LIMS:PH_EXPOSURE_DETAILS - prior SARS-CoV-2 infection: - name: prior SARS-CoV-2 infection + prior_sarscov2_infection: + name: prior_sarscov2_infection title: prior SARS-CoV-2 infection description: Whether there was prior SARS-CoV-2 infection. comments: If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. slot_uri: GENEPIO:0001435 any_of: - - range: prior SARS-CoV-2 infection menu - - range: null value menu + - range: PriorSarsCov2InfectionMenu + - range: NullValueMenu examples: - value: 'Yes' exact_mappings: - NML_LIMS:prior%20SARS-CoV-2%20infection - prior SARS-CoV-2 infection isolate: - name: prior SARS-CoV-2 infection isolate + prior_sarscov2_infection_isolate: + name: prior_sarscov2_infection_isolate title: prior SARS-CoV-2 infection isolate description: The identifier of the isolate found in the prior SARS-CoV-2 infection. comments: 'Provide the isolate name of the most recent prior infection. Structure @@ -2073,8 +2070,8 @@ slots: - value: SARS-CoV-2/human/USA/CA-CDPH-001/2020 exact_mappings: - NML_LIMS:prior%20SARS-CoV-2%20infection%20isolate - prior SARS-CoV-2 infection date: - name: prior SARS-CoV-2 infection date + prior_sarscov2_infection_date: + name: prior_sarscov2_infection_date title: prior SARS-CoV-2 infection date description: The date of diagnosis of the prior SARS-CoV-2 infection. comments: Provide the date that the most recent prior infection was diagnosed. @@ -2085,22 +2082,22 @@ slots: - value: '2021-01-23' exact_mappings: - NML_LIMS:prior%20SARS-CoV-2%20infection%20date - prior SARS-CoV-2 antiviral treatment: - name: prior SARS-CoV-2 antiviral treatment + prior_sarscov2_antiviral_treatment: + name: prior_sarscov2_antiviral_treatment title: prior SARS-CoV-2 antiviral treatment description: Whether there was prior SARS-CoV-2 treatment with an antiviral agent. comments: If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. slot_uri: GENEPIO:0001438 any_of: - - range: prior SARS-CoV-2 antiviral treatment menu - - range: null value menu + - range: PriorSarsCov2AntiviralTreatmentMenu + - range: NullValueMenu examples: - value: No prior antiviral treatment exact_mappings: - NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment - prior SARS-CoV-2 antiviral treatment agent: - name: prior SARS-CoV-2 antiviral treatment agent + prior_sarscov2_antiviral_treatment_agent: + name: prior_sarscov2_antiviral_treatment_agent title: prior SARS-CoV-2 antiviral treatment agent description: The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. @@ -2113,8 +2110,8 @@ slots: - value: Remdesivir exact_mappings: - NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment%20agent - prior SARS-CoV-2 antiviral treatment date: - name: prior SARS-CoV-2 antiviral treatment date + prior_sarscov2_antiviral_treatment_date: + name: prior_sarscov2_antiviral_treatment_date title: prior SARS-CoV-2 antiviral treatment date description: The date treatment was first administered during the prior SARS-CoV-2 infection. @@ -2127,8 +2124,8 @@ slots: - value: '2021-01-28' exact_mappings: - NML_LIMS:prior%20SARS-CoV-2%20antiviral%20treatment%20date - purpose of sequencing: - name: purpose of sequencing + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the @@ -2138,8 +2135,8 @@ slots: sample collection should be indicated in the "purpose of sampling" field. slot_uri: GENEPIO:0001445 any_of: - - range: purpose of sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -2149,8 +2146,8 @@ slots: - NML_LIMS:PH_REASON_FOR_SEQUENCING - BIOSAMPLE:purpose_of_sequencing - VirusSeq_Portal:purpose%20of%20sequencing - purpose of sequencing details: - name: purpose of sequencing details + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details description: The description of why the sample was sequenced providing specific details. @@ -2168,7 +2165,7 @@ slots: slot_uri: GENEPIO:0001446 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true examples: - value: Screened for S gene target failure (S dropout) @@ -2176,15 +2173,15 @@ slots: - CNPHI:Details%20on%20the%20Reason%20for%20Sequencing - NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS - VirusSeq_Portal:purpose%20of%20sequencing%20details - sequencing date: - name: sequencing date + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: ISO 8601 standard "YYYY-MM-DD". slot_uri: GENEPIO:0001447 any_of: - range: date - - range: null value menu + - range: NullValueMenu todos: - '>={sample collection date}' required: true @@ -2192,8 +2189,8 @@ slots: - value: '2020-06-22' exact_mappings: - NML_LIMS:PH_SEQUENCING_DATE - library ID: - name: library ID + library_id: + name: library_id title: library ID description: The user-specified identifier for the library prepared for sequencing. comments: The library name should be unique, and can be an autogenerated ID from @@ -2205,8 +2202,8 @@ slots: - value: XYZ_123345 exact_mappings: - NML_LIMS:library%20ID - amplicon size: - name: amplicon size + amplicon_size: + name: amplicon_size title: amplicon size description: The length of the amplicon generated by PCR amplification. comments: Provide the amplicon size, including the units. @@ -2216,8 +2213,8 @@ slots: - value: 300bp exact_mappings: - NML_LIMS:amplicon%20size - library preparation kit: - name: library preparation kit + library_preparation_kit: + name: library_preparation_kit title: library preparation kit description: The name of the DNA library preparation kit used to generate the library being sequenced. @@ -2228,8 +2225,8 @@ slots: - value: Nextera XT exact_mappings: - NML_LIMS:PH_LIBRARY_PREP_KIT - flow cell barcode: - name: flow cell barcode + flow_cell_barcode: + name: flow_cell_barcode title: flow cell barcode description: The barcode of the flow cell used for sequencing. comments: Provide the barcode of the flow cell used for sequencing the sample. @@ -2239,15 +2236,15 @@ slots: - value: FAB06069 exact_mappings: - NML_LIMS:flow%20cell%20barcode - sequencing instrument: - name: sequencing instrument + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Select a sequencing instrument from the picklist provided in the template. slot_uri: GENEPIO:0001452 any_of: - - range: sequencing instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu multivalued: true required: true examples: @@ -2257,8 +2254,8 @@ slots: - CNPHI:Sequencing%20Instrument - NML_LIMS:PH_INSTRUMENT_CGN - VirusSeq_Portal:sequencing%20instrument - sequencing protocol name: - name: sequencing protocol name + sequencing_protocol_name: + name: sequencing_protocol_name title: sequencing protocol name description: The name and version number of the sequencing protocol used. comments: Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION @@ -2270,8 +2267,8 @@ slots: exact_mappings: - CNPHI:Sequencing%20Protocol%20Name - NML_LIMS:PH_SEQ_PROTOCOL_NAME - sequencing protocol: - name: sequencing protocol + sequencing_protocol: + name: sequencing_protocol title: sequencing protocol description: The protocol used to generate the sequence. comments: 'Provide a free text description of the methods and materials used to @@ -2289,8 +2286,8 @@ slots: exact_mappings: - NML_LIMS:PH_TESTING_PROTOCOL - VirusSeq_Portal:sequencing%20protocol - sequencing kit number: - name: sequencing kit number + sequencing_kit_number: + name: sequencing_kit_number title: sequencing kit number description: The manufacturer's kit number. comments: Alphanumeric value. @@ -2300,8 +2297,8 @@ slots: - value: AB456XYZ789 exact_mappings: - NML_LIMS:sequencing%20kit%20number - amplicon pcr primer scheme: - name: amplicon pcr primer scheme + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme title: amplicon pcr primer scheme description: The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. @@ -2313,8 +2310,8 @@ slots: - value: https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv exact_mappings: - NML_LIMS:amplicon%20pcr%20primer%20scheme - raw sequence data processing method: - name: raw sequence data processing method + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method description: The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. @@ -2328,8 +2325,8 @@ slots: exact_mappings: - NML_LIMS:PH_RAW_SEQUENCE_METHOD - VirusSeq_Portal:raw%20sequence%20data%20processing%20method - dehosting method: - name: dehosting method + dehosting_method: + name: dehosting_method title: dehosting method description: The method used to remove host reads from the pathogen sequence. comments: Provide the name and version number of the software used to remove host @@ -2342,8 +2339,8 @@ slots: exact_mappings: - NML_LIMS:PH_DEHOSTING_METHOD - VirusSeq_Portal:dehosting%20method - consensus sequence name: - name: consensus sequence name + consensus_sequence_name: + name: consensus_sequence_name title: consensus sequence name description: The name of the consensus sequence. comments: Provide the name and version number of the consensus sequence. @@ -2353,8 +2350,8 @@ slots: - value: ncov123assembly3 exact_mappings: - NML_LIMS:consensus%20sequence%20name - consensus sequence filename: - name: consensus sequence filename + consensus_sequence_filename: + name: consensus_sequence_filename title: consensus sequence filename description: The name of the consensus sequence file. comments: Provide the name and version number of the consensus sequence FASTA @@ -2365,8 +2362,8 @@ slots: - value: ncov123assembly.fasta exact_mappings: - NML_LIMS:consensus%20sequence%20filename - consensus sequence filepath: - name: consensus sequence filepath + consensus_sequence_filepath: + name: consensus_sequence_filepath title: consensus sequence filepath description: The filepath of the consensus sequence file. comments: Provide the filepath of the consensus sequence FASTA file. @@ -2376,8 +2373,8 @@ slots: - value: /User/Documents/RespLab/Data/ncov123assembly.fasta exact_mappings: - NML_LIMS:consensus%20sequence%20filepath - consensus sequence software name: - name: consensus sequence software name + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name description: The name of software used to generate the consensus sequence. comments: Provide the name of the software used to generate the consensus sequence. @@ -2391,8 +2388,8 @@ slots: - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE - VirusSeq_Portal:consensus%20sequence%20software%20name - consensus sequence software version: - name: consensus sequence software version + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version description: The version of the software used to generate the consensus sequence. comments: Provide the version of the software used to generate the consensus sequence. @@ -2405,8 +2402,8 @@ slots: - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION - VirusSeq_Portal:consensus%20sequence%20software%20version - breadth of coverage value: - name: breadth of coverage value + breadth_of_coverage_value: + name: breadth_of_coverage_value title: breadth of coverage value description: The percentage of the reference genome covered by the sequenced data, to a prescribed depth. @@ -2418,8 +2415,8 @@ slots: exact_mappings: - NML_LIMS:breadth%20of%20coverage%20value - VirusSeq_Portal:breadth%20of%20coverage%20value - depth of coverage value: - name: depth of coverage value + depth_of_coverage_value: + name: depth_of_coverage_value title: depth of coverage value description: The average number of reads representing a given nucleotide in the reconstructed sequence. @@ -2432,8 +2429,8 @@ slots: - GISAID:Coverage - NML_LIMS:depth%20of%20coverage%20value - VirusSeq_Portal:depth%20of%20coverage%20value - depth of coverage threshold: - name: depth of coverage threshold + depth_of_coverage_threshold: + name: depth_of_coverage_threshold title: depth of coverage threshold description: The threshold used as a cut-off for the depth of coverage. comments: Provide the threshold fold coverage. @@ -2443,8 +2440,8 @@ slots: - value: 100x exact_mappings: - NML_LIMS:depth%20of%20coverage%20threshold - r1 fastq filename: - name: r1 fastq filename + r1_fastq_filename________: + name: r1_fastq_filename________ title: r1 fastq filename description: The user-specified filename of the r1 FASTQ file. comments: Provide the r1 FASTQ filename. @@ -2455,8 +2452,8 @@ slots: - value: ABC123_S1_L001_R1_001.fastq.gz exact_mappings: - NML_LIMS:r1%20fastq%20filename - r2 fastq filename: - name: r2 fastq filename + r2_fastq_filename: + name: r2_fastq_filename title: r2 fastq filename description: The user-specified filename of the r2 FASTQ file. comments: Provide the r2 FASTQ filename. @@ -2467,8 +2464,8 @@ slots: - value: ABC123_S1_L001_R2_001.fastq.gz exact_mappings: - NML_LIMS:r2%20fastq%20filename - r1 fastq filepath: - name: r1 fastq filepath + r1_fastq_filepath: + name: r1_fastq_filepath title: r1 fastq filepath description: The location of the r1 FASTQ file within a user's file system. comments: Provide the filepath for the r1 FASTQ file. This information aids in @@ -2479,8 +2476,8 @@ slots: - value: /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz exact_mappings: - NML_LIMS:r1%20fastq%20filepath - r2 fastq filepath: - name: r2 fastq filepath + r2_fastq_filepath: + name: r2_fastq_filepath title: r2 fastq filepath description: The location of the r2 FASTQ file within a user's file system. comments: Provide the filepath for the r2 FASTQ file. This information aids in @@ -2491,8 +2488,8 @@ slots: - value: /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz exact_mappings: - NML_LIMS:r2%20fastq%20filepath - fast5 filename: - name: fast5 filename + fast5_filename: + name: fast5_filename title: fast5 filename description: The user-specified filename of the FAST5 file. comments: Provide the FAST5 filename. @@ -2502,8 +2499,8 @@ slots: - value: rona123assembly.fast5 exact_mappings: - NML_LIMS:fast5%20filename - fast5 filepath: - name: fast5 filepath + fast5_filepath: + name: fast5_filepath title: fast5 filepath description: The location of the FAST5 file within a user's file system. comments: Provide the filepath for the FAST5 file. This information aids in data @@ -2514,46 +2511,46 @@ slots: - value: /User/Documents/RespLab/Data/rona123assembly.fast5 exact_mappings: - NML_LIMS:fast5%20filepath - number of base pairs sequenced: - name: number of base pairs sequenced + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced title: number of base pairs sequenced description: The number of total base pairs generated by the sequencing process. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001482 range: integer - minimum_value: '0' + minimum_value: 0 examples: - value: '387566' exact_mappings: - NML_LIMS:number%20of%20base%20pairs%20sequenced - consensus genome length: - name: consensus genome length + consensus_genome_length: + name: consensus_genome_length title: consensus genome length description: Size of the reconstructed genome described as the number of base pairs. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001483 range: integer - minimum_value: '0' + minimum_value: 0 examples: - value: '38677' exact_mappings: - NML_LIMS:consensus%20genome%20length - Ns per 100 kbp: - name: Ns per 100 kbp + ns_per_100_kbp: + name: ns_per_100_kbp title: Ns per 100 kbp description: The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001484 range: decimal - minimum_value: '0' + minimum_value: 0 examples: - value: '330' exact_mappings: - NML_LIMS:Ns%20per%20100%20kbp - reference genome accession: - name: reference genome accession + reference_genome_accession: + name: reference_genome_accession title: reference genome accession description: A persistent, unique identifier of a genome database entry. comments: Provide the accession number of the reference genome. @@ -2564,8 +2561,8 @@ slots: exact_mappings: - NML_LIMS:reference%20genome%20accession - VirusSeq_Portal:reference%20genome%20accession - bioinformatics protocol: - name: bioinformatics protocol + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Further details regarding the methods used to process raw data, and/or @@ -2581,8 +2578,8 @@ slots: - CNPHI:Bioinformatics%20Protocol - NML_LIMS:PH_BIOINFORMATICS_PROTOCOL - VirusSeq_Portal:bioinformatics%20protocol - lineage/clade name: - name: lineage/clade name + lineage_clade_name: + name: lineage_clade_name title: lineage/clade name description: The name of the lineage or clade. comments: Provide the Pangolin or Nextstrain lineage/clade name. @@ -2592,8 +2589,8 @@ slots: - value: B.1.1.7 exact_mappings: - NML_LIMS:PH_LINEAGE_CLADE_NAME - lineage/clade analysis software name: - name: lineage/clade analysis software name + lineage_clade_analysis_software_name: + name: lineage_clade_analysis_software_name title: lineage/clade analysis software name description: The name of the software used to determine the lineage/clade. comments: Provide the name of the software used to determine the lineage/clade. @@ -2603,8 +2600,8 @@ slots: - value: Pangolin exact_mappings: - NML_LIMS:PH_LINEAGE_CLADE_SOFTWARE - lineage/clade analysis software version: - name: lineage/clade analysis software version + lineage_clade_analysis_software_version: + name: lineage_clade_analysis_software_version title: lineage/clade analysis software version description: The version of the software used to determine the lineage/clade. comments: Provide the version of the software used ot determine the lineage/clade. @@ -2614,8 +2611,8 @@ slots: - value: 2.1.10 exact_mappings: - NML_LIMS:PH_LINEAGE_CLADE_VERSION - variant designation: - name: variant designation + variant_designation: + name: variant_designation title: variant designation description: The variant classification of the lineage/clade i.e. variant, variant of concern. @@ -2626,28 +2623,28 @@ slots: does not contain mutations of concern, leave blank. slot_uri: GENEPIO:0001503 any_of: - - range: variant designation menu - - range: null value menu + - range: VariantDesignationMenu + - range: NullValueMenu examples: - value: Variant of Concern exact_mappings: - NML_LIMS:PH_VARIANT_DESIGNATION - variant evidence: - name: variant evidence + variant_evidence: + name: variant_evidence title: variant evidence description: The evidence used to make the variant determination. comments: Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. slot_uri: GENEPIO:0001504 any_of: - - range: variant evidence menu - - range: null value menu + - range: VariantEvidenceMenu + - range: NullValueMenu examples: - value: RT-qPCR exact_mappings: - NML_LIMS:PH_VARIANT_EVIDENCE - variant evidence details: - name: variant evidence details + variant_evidence_details: + name: variant_evidence_details title: variant evidence details description: Details about the evidence used to make the variant determination. comments: Provide the assay and list the set of lineage-defining mutations used @@ -2660,8 +2657,8 @@ slots: D614G, A701V), N (T205I), E (P71L).' exact_mappings: - NML_LIMS:PH_VARIANT_EVIDENCE_DETAILS - gene name 1: - name: gene name 1 + gene_name_1: + name: gene_name_1 title: gene name 1 description: The name of the gene used in the diagnostic RT-PCR test. comments: 'Provide the full name of the gene used in the test. The gene symbol @@ -2669,8 +2666,8 @@ slots: symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' slot_uri: GENEPIO:0001507 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu examples: - value: E gene (orf4) exact_mappings: @@ -2678,8 +2675,8 @@ slots: - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231 - BIOSAMPLE:gene_name_1 - VirusSeq_Portal:gene%20name - diagnostic pcr protocol 1: - name: diagnostic pcr protocol 1 + diagnostic_pcr_protocol_1: + name: diagnostic_pcr_protocol_1 title: diagnostic pcr protocol 1 description: The name and version number of the protocol used for diagnostic marker amplification. @@ -2690,15 +2687,15 @@ slots: range: WhitespaceMinimizedString examples: - value: EGenePCRTest 2 - diagnostic pcr Ct value 1: - name: diagnostic pcr Ct value 1 + diagnostic_pcr_ct_value_1: + name: diagnostic_pcr_ct_value_1 title: diagnostic pcr Ct value 1 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the diagnostic RT-PCR test. slot_uri: GENEPIO:0001509 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '21' exact_mappings: @@ -2706,8 +2703,8 @@ slots: - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_1 - VirusSeq_Portal:diagnostic%20pcr%20Ct%20value - gene name 2: - name: gene name 2 + gene_name_2: + name: gene_name_2 title: gene name 2 description: The name of the gene used in the diagnostic RT-PCR test. comments: 'Provide the full name of another gene used in an RT-PCR test. The gene @@ -2715,16 +2712,16 @@ slots: and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' slot_uri: GENEPIO:0001510 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu examples: - value: RdRp gene (nsp12) exact_mappings: - CNPHI:Gene%20Target%202 - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232 - BIOSAMPLE:gene_name_2 - diagnostic pcr protocol 2: - name: diagnostic pcr protocol 2 + diagnostic_pcr_protocol_2: + name: diagnostic_pcr_protocol_2 title: diagnostic pcr protocol 2 description: The name and version number of the protocol used for diagnostic marker amplification. @@ -2735,8 +2732,8 @@ slots: range: WhitespaceMinimizedString examples: - value: RdRpGenePCRTest 3 - diagnostic pcr Ct value 2: - name: diagnostic pcr Ct value 2 + diagnostic_pcr_ct_value_2: + name: diagnostic_pcr_ct_value_2 title: diagnostic pcr Ct value 2 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR @@ -2744,15 +2741,15 @@ slots: slot_uri: GENEPIO:0001512 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '36' exact_mappings: - CNPHI:Gene%20Target%202%20CT%20Value - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_2 - gene name 3: - name: gene name 3 + gene_name_3: + name: gene_name_3 title: gene name 3 description: The name of the gene used in the diagnostic RT-PCR test. comments: 'Provide the full name of another gene used in an RT-PCR test. The gene @@ -2760,15 +2757,15 @@ slots: and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' slot_uri: GENEPIO:0001513 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu examples: - value: RdRp gene (nsp12) exact_mappings: - CNPHI:Gene%20Target%203 - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233 - diagnostic pcr protocol 3: - name: diagnostic pcr protocol 3 + diagnostic_pcr_protocol_3: + name: diagnostic_pcr_protocol_3 title: diagnostic pcr protocol 3 description: The name and version number of the protocol used for diagnostic marker amplification. @@ -2779,8 +2776,8 @@ slots: range: WhitespaceMinimizedString examples: - value: RdRpGenePCRTest 3 - diagnostic pcr Ct value 3: - name: diagnostic pcr Ct value 3 + diagnostic_pcr_ct_value_3: + name: diagnostic_pcr_ct_value_3 title: diagnostic pcr Ct value 3 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR @@ -2788,7 +2785,7 @@ slots: slot_uri: GENEPIO:0001515 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu examples: - value: '30' exact_mappings: @@ -2810,8 +2807,8 @@ slots: - GISAID:Authors - CNPHI:Authors - NML_LIMS:PH_CANCOGEN_AUTHORS - DataHarmonizer provenance: - name: DataHarmonizer provenance + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance description: The DataHarmonizer software and template version provenance. comments: The current software and template version information will be automatically @@ -2826,13 +2823,15 @@ slots: - CNPHI:Additional%20Comments - NML_LIMS:HC_COMMENTS enums: - umbrella bioproject accession menu: - name: umbrella bioproject accession menu + UmbrellaBioprojectAccessionMenu: + name: UmbrellaBioprojectAccessionMenu + title: umbrella bioproject accession menu permissible_values: PRJNA623807: text: PRJNA623807 - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu + title: null value menu permissible_values: Not Applicable: text: Not Applicable @@ -2849,8 +2848,9 @@ enums: Restricted Access: text: Restricted Access meaning: GENEPIO:0001810 - geo_loc_name (state/province/territory) menu: - name: geo_loc_name (state/province/territory) menu + GeoLocNameStateProvinceTerritoryMenu: + name: GeoLocNameStateProvinceTerritoryMenu + title: geo_loc_name (state/province/territory) menu permissible_values: Alberta: text: Alberta @@ -2891,8 +2891,9 @@ enums: Yukon: text: Yukon meaning: GAZ:00002576 - host age unit menu: - name: host age unit menu + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host age unit menu permissible_values: month: text: month @@ -2900,8 +2901,9 @@ enums: year: text: year meaning: UO:0000036 - sample collection date precision menu: - name: sample collection date precision menu + SampleCollectionDatePrecisionMenu: + name: SampleCollectionDatePrecisionMenu + title: sample collection date precision menu permissible_values: year: text: year @@ -2912,8 +2914,9 @@ enums: day: text: day meaning: UO:0000033 - biomaterial extracted menu: - name: biomaterial extracted menu + BiomaterialExtractedMenu: + name: BiomaterialExtractedMenu + title: biomaterial extracted menu permissible_values: RNA (total): text: RNA (total) @@ -2930,8 +2933,9 @@ enums: mRNA (cDNA): text: mRNA (cDNA) meaning: OBI:0002754 - signs and symptoms menu: - name: signs and symptoms menu + SignsAndSymptomsMenu: + name: SignsAndSymptomsMenu + title: signs and symptoms menu permissible_values: Abnormal lung auscultation: text: Abnormal lung auscultation @@ -3239,8 +3243,9 @@ enums: Vomiting (throwing up): text: Vomiting (throwing up) meaning: HP:0002013 - host vaccination status menu: - name: host vaccination status menu + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu + title: host vaccination status menu permissible_values: Fully Vaccinated: text: Fully Vaccinated @@ -3251,8 +3256,9 @@ enums: Not Vaccinated: text: Not Vaccinated meaning: GENEPIO:0100102 - prior SARS-CoV-2 antiviral treatment menu: - name: prior SARS-CoV-2 antiviral treatment menu + PriorSarsCov2AntiviralTreatmentMenu: + name: PriorSarsCov2AntiviralTreatmentMenu + title: prior SARS-CoV-2 antiviral treatment menu permissible_values: Prior antiviral treatment: text: Prior antiviral treatment @@ -3260,8 +3266,9 @@ enums: No prior antiviral treatment: text: No prior antiviral treatment meaning: GENEPIO:0100233 - NML submitted specimen type menu: - name: NML submitted specimen type menu + NmlSubmittedSpecimenTypeMenu: + name: NmlSubmittedSpecimenTypeMenu + title: NML submitted specimen type menu permissible_values: Swab: text: Swab @@ -3278,8 +3285,9 @@ enums: Not Applicable: text: Not Applicable meaning: GENEPIO:0001619 - Related specimen relationship type menu: - name: Related specimen relationship type menu + RelatedSpecimenRelationshipTypeMenu: + name: RelatedSpecimenRelationshipTypeMenu + title: Related specimen relationship type menu permissible_values: Acute: text: Acute @@ -3303,8 +3311,9 @@ enums: text: Sequencing/bioinformatics methods development/validation Specimen sampling methods testing: text: Specimen sampling methods testing - pre-existing conditions and risk factors menu: - name: pre-existing conditions and risk factors menu + PreExistingConditionsAndRiskFactorsMenu: + name: PreExistingConditionsAndRiskFactorsMenu + title: pre-existing conditions and risk factors menu permissible_values: Age 60+: text: Age 60+ @@ -3626,8 +3635,9 @@ enums: text: Liver transplant meaning: GENEPIO:0100081 is_a: Transplant - variant designation menu: - name: variant designation menu + VariantDesignationMenu: + name: VariantDesignationMenu + title: variant designation menu permissible_values: Variant of Concern (VOC): text: Variant of Concern (VOC) @@ -3638,8 +3648,9 @@ enums: Variant Under Monitoring (VUM): text: Variant Under Monitoring (VUM) meaning: GENEPIO:0100279 - variant evidence menu: - name: variant evidence menu + VariantEvidenceMenu: + name: VariantEvidenceMenu + title: variant evidence menu permissible_values: RT-qPCR: text: RT-qPCR @@ -3647,8 +3658,9 @@ enums: Sequencing: text: Sequencing meaning: CIDO:0000027 - complications menu: - name: complications menu + ComplicationsMenu: + name: ComplicationsMenu + title: complications menu permissible_values: Abnormal blood oxygen level: text: Abnormal blood oxygen level @@ -3919,8 +3931,9 @@ enums: Vasculitis: text: Vasculitis meaning: HP:0002633 - vaccine name menu: - name: vaccine name menu + VaccineNameMenu: + name: VaccineNameMenu + title: vaccine name menu permissible_values: Astrazeneca (Vaxzevria): text: Astrazeneca (Vaxzevria) @@ -3937,8 +3950,9 @@ enums: Pfizer-BioNTech (Comirnaty Pediatric): text: Pfizer-BioNTech (Comirnaty Pediatric) meaning: GENEPIO:0100306 - anatomical material menu: - name: anatomical material menu + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical material menu permissible_values: Blood: text: Blood @@ -3973,8 +3987,9 @@ enums: Tissue: text: Tissue meaning: UBERON:0000479 - anatomical part menu: - name: anatomical part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical part menu permissible_values: Anus: text: Anus @@ -4070,8 +4085,9 @@ enums: text: Pharynx (throat) meaning: UBERON:0000341 is_a: Upper respiratory tract - body product menu: - name: body product menu + BodyProductMenu: + name: BodyProductMenu + title: body product menu permissible_values: Breast Milk: text: Breast Milk @@ -4098,8 +4114,9 @@ enums: Urine: text: Urine meaning: UBERON:0001088 - prior SARS-CoV-2 infection menu: - name: prior SARS-CoV-2 infection menu + PriorSarsCov2InfectionMenu: + name: PriorSarsCov2InfectionMenu + title: prior SARS-CoV-2 infection menu permissible_values: Prior infection: text: Prior infection @@ -4107,8 +4124,9 @@ enums: No prior infection: text: No prior infection meaning: GENEPIO:0100233 - environmental material menu: - name: environmental material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu + title: environmental material menu permissible_values: Air vent: text: Air vent @@ -4210,8 +4228,9 @@ enums: Wood: text: Wood meaning: ENVO:00002040 - environmental site menu: - name: environmental site menu + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental site menu permissible_values: Acute care facility: text: Acute care facility @@ -4279,8 +4298,9 @@ enums: Wet market: text: Wet market meaning: ENVO:03501198 - collection method menu: - name: collection method menu + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: Amniocentesis: text: Amniocentesis @@ -4353,8 +4373,9 @@ enums: Washout Tear Collection: text: Washout Tear Collection meaning: GENEPIO:0100038 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: Air filter: text: Air filter @@ -4407,8 +4428,9 @@ enums: Virus Transport Medium: text: Virus Transport Medium meaning: OBI:0002866 - host (scientific name) menu: - name: host (scientific name) menu + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu permissible_values: Homo sapiens: text: Homo sapiens @@ -4458,8 +4480,9 @@ enums: Viverridae: text: Viverridae meaning: NCBITaxon:9673 - host (common name) menu: - name: host (common name) menu + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu permissible_values: Human: text: Human @@ -4504,8 +4527,9 @@ enums: Tiger: text: Tiger meaning: NCBITaxon:9694 - host health state menu: - name: host health state menu + HostHealthStateMenu: + name: HostHealthStateMenu + title: host health state menu permissible_values: Asymptomatic: text: Asymptomatic @@ -4522,8 +4546,9 @@ enums: Symptomatic: text: Symptomatic meaning: NCIT:C25269 - host health status details menu: - name: host health status details menu + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu + title: host health status details menu permissible_values: Hospitalized: text: Hospitalized @@ -4549,8 +4574,9 @@ enums: Self-quarantining: text: Self-quarantining meaning: NCIT:C173768 - host health outcome menu: - name: host health outcome menu + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu + title: host health outcome menu permissible_values: Deceased: text: Deceased @@ -4564,8 +4590,9 @@ enums: Stable: text: Stable meaning: NCIT:C30103 - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu + title: organism menu permissible_values: Severe acute respiratory syndrome coronavirus 2: text: Severe acute respiratory syndrome coronavirus 2 @@ -4576,8 +4603,9 @@ enums: RmYN02: text: RmYN02 meaning: GENEPIO:0100000 - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation: text: Cluster/Outbreak investigation @@ -4591,8 +4619,9 @@ enums: Surveillance: text: Surveillance meaning: GENEPIO:0100004 - purpose of sequencing menu: - name: purpose of sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose of sequencing menu permissible_values: Baseline surveillance (random sampling): text: Baseline surveillance (random sampling) @@ -4694,8 +4723,9 @@ enums: Retrospective sequencing: text: Retrospective sequencing meaning: GENEPIO:0100356 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Virus passage: text: Virus passage @@ -4706,8 +4736,9 @@ enums: Specimens pooled: text: Specimens pooled meaning: OBI:0600016 - lab host menu: - name: lab host menu + LabHostMenu: + name: LabHostMenu + title: lab host menu permissible_values: 293/ACE2 cell line: text: 293/ACE2 cell line @@ -4759,14 +4790,12 @@ enums: text: VeroE6/TMPRSS2 cell line meaning: GENEPIO:0100044 is_a: Vero E6 cell line - host disease menu: - name: host disease menu - permissible_values: COVID-19: text: COVID-19 meaning: MONDO:0100096 - host age bin menu: - name: host age bin menu + HostAgeBinMenu: + name: HostAgeBinMenu + title: host age bin menu permissible_values: 0 - 9: text: 0 - 9 @@ -4805,8 +4834,9 @@ enums: meaning: GENEPIO:0100059 exact_mappings: - VirusSeq_Portal:90%2B - host gender menu: - name: host gender menu + HostGenderMenu: + name: HostGenderMenu + title: host gender menu permissible_values: Female: text: Female @@ -4826,8 +4856,9 @@ enums: Undeclared: text: Undeclared meaning: NCIT:C110959 - exposure event menu: - name: exposure event menu + ExposureEventMenu: + name: ExposureEventMenu + title: exposure event menu permissible_values: Mass Gathering: text: Mass Gathering @@ -4900,8 +4931,9 @@ enums: is_a: Social Gathering Other exposure event: text: Other exposure event - exposure contact level menu: - name: exposure contact level menu + ExposureContactLevelMenu: + name: ExposureContactLevelMenu + title: exposure contact level menu permissible_values: Contact with infected individual: text: Contact with infected individual @@ -4922,8 +4954,9 @@ enums: text: Casual contact meaning: GENEPIO:0100248 is_a: Indirect contact - host role menu: - name: host role menu + HostRoleMenu: + name: HostRoleMenu + title: host role menu permissible_values: Attendee: text: Attendee @@ -5074,8 +5107,9 @@ enums: is_a: Social role Other Host Role: text: Other Host Role - exposure setting menu: - name: exposure setting menu + ExposureSettingMenu: + name: ExposureSettingMenu + title: exposure setting menu permissible_values: Human Exposure: text: Human Exposure @@ -5325,8 +5359,9 @@ enums: Other Exposure Setting: text: Other Exposure Setting meaning: GENEPIO:0100235 - travel point of entry type menu: - name: travel point of entry type menu + TravelPointOfEntryTypeMenu: + name: TravelPointOfEntryTypeMenu + title: travel point of entry type menu permissible_values: Air: text: Air @@ -5334,9 +5369,6 @@ enums: Land: text: Land meaning: GENEPIO:0100409 - border testing test day type menu: - name: border testing test day type menu - permissible_values: day 1: text: day 1 meaning: GENEPIO:0100410 @@ -5346,8 +5378,9 @@ enums: day 10: text: day 10 meaning: GENEPIO:0100412 - travel history availability menu: - name: travel history availability menu + TravelHistoryAvailabilityMenu: + name: TravelHistoryAvailabilityMenu + title: travel history availability menu permissible_values: Travel history available: text: Travel history available @@ -5367,8 +5400,9 @@ enums: No travel history available: text: No travel history available meaning: GENEPIO:0100654 - sequencing instrument menu: - name: sequencing instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: Illumina: text: Illumina @@ -5548,8 +5582,9 @@ enums: text: MGI DNBSEQ-G50 meaning: GENEPIO:0100150 is_a: MGI - gene name menu: - name: gene name menu + GeneNameMenu: + name: GeneNameMenu + title: gene name menu permissible_values: E gene (orf4): text: E gene (orf4) @@ -5732,8 +5767,9 @@ enums: SARS-COV-2 5' UTR: text: SARS-COV-2 5' UTR meaning: GENEPIO:0100183 - sequence submitted by menu: - name: sequence submitted by menu + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu + title: sequence submitted by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -5789,8 +5825,9 @@ enums: text: Sunnybrook Health Sciences Centre Thunder Bay Regional Health Sciences Centre: text: Thunder Bay Regional Health Sciences Centre - sample collected by menu: - name: sample collected by menu + SampleCollectedByMenu: + name: SampleCollectedByMenu + title: sample collected by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -5862,8 +5899,9 @@ enums: text: Unity Health Toronto William Osler Health System: text: William Osler Health System - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: Afghanistan: text: Afghanistan diff --git a/web/templates/canada_covid19/schema_core.yaml b/web/templates/canada_covid19/schema_core.yaml index b3083a9d..e0b7cf71 100644 --- a/web/templates/canada_covid19/schema_core.yaml +++ b/web/templates/canada_covid19/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/CanCOGeN_Covid-19 name: CanCOGeN_Covid-19 description: "" -version: 2.3.4 +version: 2.4.0 in_language: - 'en' - 'fr' @@ -15,8 +15,9 @@ classes: name: dh_interface description: 'A DataHarmonizer interface' from_schema: https://example.com/CanCOGeN_Covid-19 - 'CanCOGeN Covid-19': - name: 'CanCOGeN Covid-19' + 'CanCOGeNCovid19': + name: 'CanCOGeNCovid19' + title: 'CanCOGeN Covid-19' description: Canadian specification for Covid-19 clinical virus biosample data gathering is_a: dh_interface see_also: templates/canada_covid19/SOP.pdf diff --git a/web/templates/canada_covid19/schema_enums.tsv b/web/templates/canada_covid19/schema_enums.tsv index cfa4d6f0..37e0bf27 100644 --- a/web/templates/canada_covid19/schema_enums.tsv +++ b/web/templates/canada_covid19/schema_enums.tsv @@ -1,1212 +1,1213 @@ -title title_fr meaning menu_1 menu_2 menu_3 menu_4 menu_5 menu_1_fr menu_2_fr menu_3_fr menu_4_fr menu_5_fr description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal - -umbrella bioproject accession menu menu d'adhésion au bioprojet parapluie PRJNA623807 PRJNA623807 - -null value menu menu de valeur nulle GENEPIO:0001619 Not Applicable Non applicable - GENEPIO:0001618 Missing Manquant - GENEPIO:0001620 Not Collected Non collecté - GENEPIO:0001668 Not Provided Non fourni - GENEPIO:0001810 Restricted Access Accès restreint - -geo_loc_name (state/province/territory) menu menu geo_loc_name (état/province/territoire) GAZ:00002566 Alberta Alberta - GAZ:00002562 British Columbia Colombie Britannique - GAZ:00002571 Manitoba Manitoba - GAZ:00002570 New Brunswick Nouveau-Brunswick - GAZ:00002567 Newfoundland and Labrador Terre-Neuve et Labrador - GAZ:00002575 Northwest Territories Territoires du Nord-Ouest - GAZ:00002565 Nova Scotia Nouvelle-Écosse - GAZ:00002574 Nunavut Nunavut - GAZ:00002563 Ontario Ontario (en anglais) - GAZ:00002572 Prince Edward Island Île-du-Prince-Édouard - GAZ:00002569 Quebec Québec - GAZ:00002564 Saskatchewan Saskatchewan - GAZ:00002576 Yukon Yukon - - -host age unit menu menu de l'unité d'âge de l'hôte UO:0000035 month mois - UO:0000036 year année - - -sample collection date precision menu menu de précision de la date de prélèvement des échantillons UO:0000036 year année - UO:0000035 month mois - UO:0000033 day jour - - -biomaterial extracted menu menu extrait des biomatériaux OBI:0000895 RNA (total) RNA (total) - OBI:0000869 RNA (poly-A) RNA (poly-A) - OBI:0002627 RNA (ribo-depleted) RNA (appauvri en ribo) - GENEPIO:0100104 mRNA (messenger RNA) mRNA (messager RNA) - OBI:0002754 mRNA (cDNA) mRNA (cDNA) - - -signs and symptoms menu menu des signes et symptômes HP:0030829 Abnormal lung auscultation Auscultation pulmonaire anormale - HP:0000223 Abnormality of taste sensation Anomalie de la sensation gustative - HP:0041051 Ageusia (complete loss of taste) Ageusia (perte totale du goût) - HP:0031249 Parageusia (distorted sense of taste) Parageusie (déformation du goût) - HP:0000224 Hypogeusia (reduced sense of taste) Hypogeusie (diminution du sens du goût) - HP:0004408 Abnormality of the sense of smell Abnormality of the sense of smell - HP:0000458 Anosmia (lost sense of smell) Anosmie (perte d'odorat) - HP:0004409 Hyposmia (reduced sense of smell) Hyposmie (diminution de l'odorat) - HP:0033677 Acute Respiratory Distress Syndrome Syndrome de détresse respiratoire aiguë ARDS - HP:0011446 Altered mental status Altération de l'état mental - HP:0100543 Cognitive impairment Troubles cognitifs - HP:0001259 Coma Coma - HP:0001289 Confusion la confusion - HP:0031258 Delirium (sudden severe confusion) Délire (confusion grave et soudaine) - GENEPIO:0100061 Inability to arouse (inability to stay awake) Incapacité à se réveiller (incapacité à rester éveillé) - HP:0000737 Irritability Irritabilité - HP:0002371 Loss of speech Perte de la parole - HP:0011675 Arrhythmia Arythmie - HP:0025406 Asthenia (generalized weakness) Asthénie (faiblesse généralisée) - HP:0031352 Chest tightness or pressure Oppression ou pression thoracique - HP:0025145 Rigors (fever shakes) Rigidité (tremblements de fièvre) - HP:0025143 Chills (sudden cold sensation) Frissons (sensation soudaine de froid) Chills - HP:0030953 Conjunctival injection Injection conjonctivale - HP:0000509 Conjunctivitis (pink eye) Conjonctivite (œil rose) Conjunctivitis - MP:0001867 Coryza (rhinitis) Coryza (rhinite) - HP:0012735 Cough Toux - HP:0031246 Nonproductive cough (dry cough) Toux non productive (toux sèche) - HP:0031245 Productive cough (wet cough) Toux productive (toux grasse) - HP:0000961 Cyanosis (blueish skin discolouration) Cyanose (coloration bleuâtre de la peau) - HP:0001063 Acrocyanosis Acrocyanose - HP:0032556 Circumoral cyanosis (bluish around mouth) Cyanose circulatoire (bleuâtre autour de la bouche) - GENEPIO:0100062 Cyanotic face (bluish face) Visage cyanosé (visage bleuâtre) - GENEPIO:0100063 Central Cyanosis Cyanose centrale - GENEPIO:0100064 Cyanotic lips (bluish lips) Lèvres cyanosées (lèvres bleutées) - GENEPIO:0100065 Peripheral Cyanosis Cyanose périphérique - HP:0002094 Dyspnea (breathing difficulty) Dyspnée (difficulté à respirer) - HP:0002014 Diarrhea (watery stool) Diarrhée (selles liquides) Diarrhea, watery - MP:0031127 Dry gangrene Gangrène sèche - HP:0002383 Encephalitis (brain inflammation) Encéphalite (inflammation du cerveau) Encephalitis - HP:0001298 Encephalopathy Encéphalopathie - HP:0012378 Fatigue (tiredness) Fatigue Fatigue - HP:0001945 Fever Fièvre - GENEPIO:0100066 Fever (>=38°C) Fièvre (>=38°C) Fever - HP:0000206 Glossitis (inflammation of the tongue) Glossiose (inflammation de la langue) - GENEPIO:0100067 Ground Glass Opacities (GGO) Opacités de verre dépoli - HP:0002315 Headache Maux de tête - HP:0002105 Hemoptysis (coughing up blood) Hémoptysie (toux de sang) - HP:0012417 Hypocapnia Hypocapnie - HP:0002615 Hypotension (low blood pressure) Hypotension (baisse de la tension artérielle) - HP:0012418 Hypoxemia (low blood oxygen) Hypoxémie (manque d'oxygène dans le sang) - GENEPIO:0100068 Silent hypoxemia Hypoxémie silencieuse - HP:0011029 Internal hemorrhage (internal bleeding) Hémorragie interne (saignement interne) - NCIT:C121416 Loss of Fine Movements Perte de mouvements fins - HP:0004396 Low appetite Manque d'appétit - HP:0033834 Malaise (general discomfort/unease) Malaise (malaise général) - HP:0031179 Meningismus/nuchal rigidity Méningisme/rigidité nucale - HP:0001324 Muscle weakness Faiblesse musculaire - HP:0001742 Nasal obstruction (stuffy nose) Obstruction nasale (nez bouché) - HP:0002018 Nausea Nausées - HP:0000421 Nose bleed Saignement de nez - GENEPIO:0100069 Otitis Otite - HP:0012531 Pain Douleur - HP:0002027 Abdominal pain Douleur abdominale - HP:0002829 Arthralgia (painful joints) Arthralgie (articulations douloureuses) - HP:0100749 Chest pain Douleur thoracique - HP:0033771 Pleuritic chest pain Douleur thoracique pleurétique - HP:0003326 Myalgia (muscle pain) Myalgie (douleur musculaire) - HP:0025439 Pharyngitis (sore throat) Pharyngite (mal de gorge) - GENEPIO:0100070 Pharyngeal exudate Exsudat pharyngé - HP:0002202 Pleural effusion Épanchement pleural - HP:0002090 Pneumonia Pneumonie - HP:0033696 Pseudo-chilblains Pseudo-chilblains - GENEPIO:0100072 Pseudo-chilblains on fingers (covid fingers) Pseudo-griffes des doigts (doigts covides) - GENEPIO:0100073 Pseudo-chilblains on toes (covid toes) Pseudo-chilblains sur les orteils (covid toes) - HP:0000988 Rash Éruption cutanée - HP:0031417 Rhinorrhea (runny nose) Rhinorrhée (écoulement nasal) - HP:0001250 Seizure Crise d'épilepsie - HP:0020219 Motor seizure Crise motrice - HP:0025144 Shivering (involuntary muscle twitching) Frissons (contractions musculaires involontaires) - HP:0001350 Slurred speech Troubles de l'élocution - HP:0025095 Sneezing Éternuement - HP:0033709 Sputum Production Production d'expectorations - HP:0001297 Stroke Accident vasculaire cérébral - HP:0002716 Swollen Lymph Nodes Ganglions lymphatiques gonflés - HP:0002789 Tachypnea (accelerated respiratory rate) Tachypnée (accélération de la fréquence respiratoire) - HP:0002321 Vertigo (dizziness) Vertige (étourdissement) - HP:0002013 Vomiting (throwing up) Vomissements (vomissements) - - -host vaccination status menu menu du statut de vaccination de l'hôte GENEPIO:0100100 Fully Vaccinated Vaccination complète - GENEPIO:0100101 Partially Vaccinated Partiellement vacciné - GENEPIO:0100102 Not Vaccinated Non vacciné - - -prior SARS-CoV-2 antiviral treatment menu menu de traitement antiviral antérieur contre le SARS-CoV-2 GENEPIO:0100037 Prior antiviral treatment Traitement antiviral antérieur - GENEPIO:0100233 No prior antiviral treatment Pas de traitement antiviral antérieur - - -NML submitted specimen type menu Menu des types d'échantillons soumis au NML OBI:0002600 Swab Écouvillon - OBI:0000880 RNA RNA - OBI:0002754 mRNA (cDNA) mRNA (cDNA) - OBI:0001010 Nucleic acid Acide nucléique - GENEPIO:0001619 Not Applicable Sans objet - - -Related specimen relationship type menu Menu des types de relations entre spécimens associés HP:0011009 Acute Infection aiguë - GENEPIO:0101016 Chronic (prolonged) infection investigation Enquête sur l'infection chronique (prolongée) - Convalescent Convalescent - Familial Familial - EFO:0009642 Follow-up Suivi - Reinfection testing Tests de réinfection - Previously Submitted Déjà soumis - Sequencing/bioinformatics methods development/validation Développement/validation de méthodes de séquençage/bioinformatique - Specimen sampling methods testing Test des méthodes d'échantillonnage des échantillons - - -pre-existing conditions and risk factors menu Menu des conditions préexistantes et des facteurs de risque VO:0004925 Age 60+ 60 ans et plus - HP:0001903 Anemia Anémie - HP:0002039 Anorexia Anorexie - NCIT:C92743 Birthing labor Travail d'accouchement - NCIT:C80693 Bone marrow failure Insuffisance de la moelle osseuse - MONDO:0004992 Cancer Cancer - MONDO:0007254 Breast cancer Cancer du sein - MONDO:0005575 Colorectal cancer Cancer colorectal - DOID:2531 Hematologic malignancy (cancer of the blood) Hémopathie maligne (cancer du sang) - MONDO:0008903 Lung cancer Cancer du poumon - MONDO:0024880 Metastatic disease Maladie métastatique - NCIT:C16212 Cancer treatment Traitement du cancer - NCIT:C157740 Cancer surgery Chirurgie du cancer - NCIT:C15632 Chemotherapy Chimiothérapie - NCIT:C15360 Adjuvant chemotherapy Chimiothérapie adjuvante - NCIT:C3079 Cardiac disorder Troubles cardiaques - HP:0011675 Arrhythmia Arythmie - MONDO:0005267 Cardiac disease Maladie cardiaque - HP:0001638 Cardiomyopathy Cardiomyopathie - GENEPIO:0100074 Cardiac injury Lésion cardiaque - HP:0000822 Hypertension (high blood pressure) Hypertension (pression artérielle élevée) - HP:0002615 Hypotension (low blood pressure) Hypotension (pression artérielle basse) - HP:0011410 Cesarean section Césarienne - GENEPIO:0100075 Chronic cough Toux chronique - GENEPIO:0100076 Chronic gastrointestinal disease Maladie gastro-intestinale chronique - HP:0006528 Chronic lung disease Maladie pulmonaire chronique - NCIT:C211 Corticosteroids Corticostéroïdes - HP:0000819 Diabetes mellitus (diabetes) Diabète sucré (diabète) - HP:0100651 Type I diabetes mellitus (T1D) Diabète de type I (T1D) - HP:0005978 Type II diabetes mellitus (T2D) Diabète sucré de type II (T2D) - HP:0000964 Eczema Eczéma - HP:0003111 Electrolyte disturbance Perturbation de l'équilibre électrolytique - HP:0002901 Hypocalcemia Hypocalcémie - HP:0002900 Hypokalemia Hypokaliémie - HP:0002917 Hypomagnesemia Hypomagnésémie - HP:0002383 Encephalitis (brain inflammation) Encéphalite (inflammation du cerveau) - MONDO:0005027 Epilepsy Epilepsie - NCIT:C15248 Hemodialysis Hémodialyse - MONDO:0044348 Hemoglobinopathy Hémoglobinopathie - MONDO:0005109 Human immunodeficiency virus (HIV) Virus de l'immunodéficience humaine - MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) Syndrome d'immunodéficience acquise - NCIT:C16118 HIV and antiretroviral therapy (ART) HIV et thérapie antirétrovirale - NCIT:C14139 Immunocompromised Immunodéprimés - MONDO:0004670 Lupus Lupus - MONDO:0005265 Inflammatory bowel disease (IBD) Maladie inflammatoire de l'intestin (MII) - HP:0002583 Colitis Colite - HP:0100279 Ulcerative colitis Colite ulcéreuse - HP:0100280 Crohn's disease la maladie de Crohn - NCIT:C3149 Renal disorder Trouble rénal - MONDO:0005240 Renal disease Maladie rénale - HP:0012622 Chronic renal disease Maladie rénale chronique - HP:0000083 Renal failure Insuffisance rénale - MONDO:0005154 Liver disease Maladie du foie - NCIT:C113609 Chronic liver disease Maladie chronique du foie - HP:0001397 Fatty liver disease (FLD) - HP:0003326 Myalgia (muscle pain) Myalgie (douleur musculaire) - MONDO:0005404 Myalgic encephalomyelitis (chronic fatigue syndrome) Encéphalomyélite myalgique (syndrome de fatigue chronique) - MONDO:0005071 Neurological disorder Trouble neurologique - MONDO:0019056 Neuromuscular disorder Trouble neuromusculaire - HP:0001513 Obesity L'obésité - MONDO:0005139 Severe obesity Obésité sévère - MONDO:0005087 Respiratory disorder Troubles respiratoires - HP:0002099 Asthma Asthme - HP:0004469 Chronic bronchitis Bronchite chronique - HP:0006510 Chronic obstructive pulmonary disease Maladie pulmonaire obstructive chronique - HP:0002097 Emphysema Emphysème - MONDO:0005275 Lung disease Maladie pulmonaire - HP:0006528 Chronic lung disease Maladie pulmonaire chronique - HP:0002206 Pulmonary fibrosis Fibrose pulmonaire - HP:0002090 Pneumonia Pneumonie - HP:0002878 Respiratory failure Insuffisance respiratoire - HP:0033677 Adult respiratory distress syndrome Syndrome de détresse respiratoire de l'adulte - MONDO:0009971 Newborn respiratory distress syndrome Syndrome de détresse respiratoire du nouveau-né - MONDO:0018076 Tuberculosis Tuberculose - GENEPIO:0100077 Postpartum (≤6 weeks) Post-partum (≤6 semaines) - NCIT:C25742 Pregnancy Grossesse - MONDO:0005554 Rheumatic disease Maladie rhumatismale - MONDO:0011382 Sickle cell disease Drépanocytose - NBO:0001845 Substance use Consommation de substances psychoactives - MONDO:0002046 Alcohol abuse Abus d'alcool - GENEPIO:0100078 Drug abuse Abus de drogues - GENEPIO:0100079 Injection drug abuse Abus de drogues injectables - NBO:0015005 Smoking Fumer - NCIT:C173621 Vaping Vapoter - HP:0002789 Tachypnea (accelerated respiratory rate) Tachypnée (accélération de la fréquence respiratoire) - NCIT:C159659 Transplant Transplantation - NCIT:C131759 Hematopoietic stem cell transplant (bone marrow transplant) Transplantation cardiaque - GENEPIO:0100080 Cardiac transplant Greffe de cellules souches hématopoïétiques (greffe de moelle osseuse) - NCIT:C157332 Kidney transplant Greffe de rein - GENEPIO:0100081 Liver transplant Greffe de foie - - -variant designation menu menu de désignation des variantes GENEPIO:0100082 Variant of Concern (VOC) Variante d'intérêt (VOI) - GENEPIO:0100083 Variant of Interest (VOI) Variante préoccupante (VOC) - GENEPIO:0100279 Variant Under Monitoring (VUM) Variante sous surveillance (VUM) - - -variant evidence menu menu de preuves variantes CIDO:0000019 RT-qPCR RT-qPCR - CIDO:0000027 Sequencing Séquençage - - -complications menu menu des complications HP:0500165 Abnormal blood oxygen level Taux d'oxygène anormal dans le sang - HP:0001919 Acute kidney injury Lésions rénales aiguës - MONDO:0015796 Acute lung injury Lésions pulmonaires aiguës - GENEPIO:0100092 Ventilation induced lung injury (VILI) Lésions pulmonaires induites par la ventilation - MONDO:0001208 Acute respiratory failure Insuffisance respiratoire aiguë - HP:0011675 Arrhythmia (complication) Arythmie (complication) - HP:0001649 Tachycardia Tachycardie - HP:0031677 Polymorphic ventricular tachycardia (VT) Tachycardie ventriculaire polymorphe - GENEPIO:0100084 Tachyarrhythmia Tachyarythmie - GENEPIO:0100074 Cardiac injury Lésions cardiaques - HP:0001695 Cardiac arrest Arrêt cardiaque - HP:0030149 Cardiogenic shock Choc cardiogénique - HP:0001977 Blood clot Caillot de sang - HP:0004420 Arterial clot Caillot artériel - HP:0002625 Deep vein thrombosis (DVT) Thrombose veineuse profonde - HP:0002204 Pulmonary embolism (PE) Embolie pulmonaire - HP:0001638 Cardiomyopathy Cardiomyopathie - MONDO:0024619 Central nervous system invasion Envahissement du système nerveux central - HP:0001297 Stroke (complication) Accident vasculaire cérébral (complication) - MONDO:0003346 Central Nervous System Vasculitis Vascularite du système nerveux central - HP:0002140 Acute ischemic stroke Accident vasculaire cérébral ischémique aigu - HP:0001259 Coma Coma - HP:0011097 Convulsions Les convulsions - NCIT:C171562 COVID-19 associated coagulopathy (CAC) COVID-19 coagulopathie associée (CAC) - MONDO:0009061 Cystic fibrosis Mucoviscidose - MONDO:0600008 Cytokine release syndrome Syndrome de libération de cytokines - MPATH:108 Disseminated intravascular coagulation (DIC) Coagulation intravasculaire disséminée - HP:0001298 Encephalopathy Encéphalopathie - GENEPIO:0100088 Fulminant myocarditis Myocardite fulminante - MONDO:0016218 Guillain-Barré syndrome Guillain-Barré syndrome - HP:0011029 Internal hemorrhage (complication; internal bleeding) Hémorragie interne (complication ; hémorragie interne) - MONDO:0013792 Intracerebral haemorrhage Hémorragie intracérébrale - MONDO:0012727 Kawasaki disease Maladie de Kawasaki - GENEPIO:0100089 Complete Kawasaki disease Maladie de Kawasaki complète - GENEPIO:0100090 Incomplete Kawasaki disease Maladie de Kawasaki incomplète - HP:0001410 Liver dysfunction Dysfonctionnement du foie - GENEPIO:0100091 Acute liver injury Lésions hépatiques aiguës - MONDO:0100233 Long COVID-19 Longue COVID-19 - HP:0001287 Meningitis Méningite - HP:0002076 Migraine Migraine - HP:0005268 Miscarriage Fausses couches - MONDO:0100163 Multisystem inflammatory syndrome in children (MIS-C) Syndrome inflammatoire multisystémique de l'enfant - MONDO:0100319 Multisystem inflammatory syndrome in adults (MIS-A) Syndrome inflammatoire multisystémique chez l'adulte - GENEPIO:0100093 Muscle injury Lésion musculaire - MONDO:0005404 Myalgic encephalomyelitis (ME) Encéphalomyélite myalgique (syndrome de fatigue chronique) - MONDO:0005068 Myocardial infarction (heart attack) Infarctus du myocarde (crise cardiaque) - MONDO:0004781 Acute myocardial infarction Infarctus aigu du myocarde - MONDO:0041656 ST-segment elevation myocardial infarction Infarctus du myocarde avec sus-décalage du segment ST - HP:0001700 Myocardial injury Lésions du myocarde - NCIT:C168498 Neonatal complications Complications néonatales - GENEPIO:0100085 Noncardiogenic pulmonary edema Œdème pulmonaire non cardiogénique - HP:0033677 Acute respiratory distress syndrome (ARDS) Syndrome de détresse respiratoire aiguë - NCIT:C171551 COVID-19 associated ARDS (CARDS) ARDS associé au COVID-19 (CARDS) - GENEPIO:0100086 Neurogenic pulmonary edema (NPE) Œdème pulmonaire neurogène - GENEPIO:0100094 Organ failure Insuffisance organique - HP:0001635 Heart failure Insuffisance cardiaque - MONDO:0100192 Liver failure Insuffisance hépatique - HP:0003470 Paralysis Paralysie - HP:0002107 Pneumothorax (collapsed lung) Pneumothorax (affaissement du poumon) - HP:0002108 Spontaneous pneumothorax Pneumothorax spontané - MONDO:0002075 Spontaneous tension pneumothorax Pneumothorax spontané sous tension - HP:0002090 Pneumonia (complication) Pneumonie (complication) - NCIT:C171550 COVID-19 pneumonia Pneumonie COVID-19 - HP:0001197 Pregancy complications Complications de la grossesse - HP:0003201 Rhabdomyolysis Rhabdomyolyse - IDO:0000567 Secondary infection Infection secondaire - GENEPIO:0100095 Secondary staph infection Infection secondaire à staphylocoque - GENEPIO:0100096 Secondary strep infection Infection secondaire à streptocoques - HP:0001250 Seizure (complication) Crise d'épilepsie (complication) - HP:0020219 Motor seizure Crise motrice - HP:0100806 Sepsis/Septicemia Sepsis/Septicémie - IDO:0000636 Sepsis Septicémie (réaction inflammatoire systémique à une infection) - NCIT:C3364 Septicemia Septicémie (infection du sang) - HP:0031273 Shock Choc - GENEPIO:0100097 Hyperinflammatory shock Choc hyperinflammatoire - GENEPIO:0100098 Refractory cardiogenic shock Choc cardiogénique réfractaire - GENEPIO:0100099 Refractory cardiogenic plus vasoplegic shock Choc cardiogénique et vasoplégique réfractaire - NCIT:C35018 Septic shock Choc septique - HP:0002633 Vasculitis Vascularite - - -vaccine name menu menu nom du vaccin GENEPIO:0100308 Astrazeneca (Vaxzevria) Astrazeneca (Vaxzevria) - GENEPIO:0100307 Johnson & Johnson (Janssen) Johnson & Johnson (Janssen) - GENEPIO:0100304 Moderna (Spikevax) Moderna (Spikevax) - GENEPIO:0100305 Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) - GENEPIO:0100306 Pfizer-BioNTech (Comirnaty Pediatric) Pfizer-BioNTech (Comirnaty Pédiatrique) - - -anatomical material menu menu de matériel anatomique UBERON:0000178 Blood Sang - UBERON:0006314 Fluid Fluide - UBERON:0001836 Saliva Salive - UBERON:0001359 Fluid (cerebrospinal (CSF)) Fluide (cérébrospinal (CSF)) - UBERON:0002409 Fluid (pericardial) Fluide (péricardique) - UBERON:0001087 Fluid (pleural) Fluide (pleural) - UBERON:0036243 Fluid (vaginal) Fluides (vaginaux) - UBERON:0000173 Fluid (amniotic) Fluide (amniotique) - UBERON:0000479 Tissue Tissu - - -anatomical part menu menu partie anatomique UBERON:0001245 Anus Anus - UBERON:0006956 Buccal mucosa Muqueuse buccale - UBERON:0002114 Duodenum Duodénum - UBERON:0000970 Eye L'œil - UBERON:0000160 Intestine Intestin - UBERON:0001558 Lower respiratory tract Voies respiratoires inférieures - UBERON:0002185 Bronchus Bronches - UBERON:0002048 Lung Poumon - UBERON:0002186 Bronchiole Bronchiole - UBERON:0002169 Alveolar sac Sac alvéolaire - UBERON:0009778 Pleural sac Sac pleural - UBERON:0002402 Pleural cavity Cavité pleurale - UBERON:0003126 Trachea Trachée - UBERON:0001052 Rectum Le rectum - UBERON:0001003 Skin Peau - UBERON:0000945 Stomach Estomac - UBERON:0001557 Upper respiratory tract Voies respiratoires supérieures - UBERON:2001427 Anterior Nares Narines antérieures - UBERON:0001043 Esophagus Œsophage - UBERON:0002453 Ethmoid sinus Sinus ethmoïdal - UBERON:0001707 Nasal Cavity Cavité nasale - UBERON:0005921 Middle Nasal Turbinate Turbine nasale moyenne - UBERON:0005922 Inferior Nasal Turbinate Turbine nasale inférieure - UBERON:0001728 Nasopharynx (NP) Nasopharynx (NP) - UBERON:0001729 Oropharynx (OP) Oropharynx (OP) - UBERON:0000341 Pharynx (throat) Le pharynx (gorge) - - -body product menu menu de produits pour le corps UBERON:0001913 Breast Milk Le lait maternel - UBERON:0001988 Feces Selles - UBERON:0006530 Fluid (seminal) Liquide (séminal) - UBERON:0000912 Mucus Mucus - UBERON:0007311 Sputum Expectorations - UBERON:0001089 Sweat Sueur - UBERON:0001827 Tear Larme - UBERON:0001088 Urine Urine - - -prior SARS-CoV-2 infection menu menu d’infection antérieure par le SARS-CoV-2 GENEPIO:0100037 Prior infection Infection antérieure - GENEPIO:0100233 No prior infection Pas d'infection antérieure - - -environmental material menu menu de matériaux environnementaux ENVO:03501208 Air vent Purgeur d'air - ENVO:00003896 Banknote Billets de banque - ENVO:03501209 Bed rail Barre de lit - ENVO:01000486 Building floor Plancher du bâtiment - ENVO:02000058 Cloth Tissu - ENVO:03501210 Control panel Panneau de contrôle - ENVO:03501220 Door Porte - ENVO:03501211 Door handle Poignée de porte - OBI:0002787 Face mask Masque facial - OBI:0002791 Face shield Masque de protection - FOODON:00002403 Food Nourriture - FOODON:03490100 Food packaging Emballages alimentaires - ENVO:01000481 Glass Verre - ENVO:03501212 Handrail Balustrade - OBI:0002796 Hospital gown Robe d'hôpital - ENVO:03501213 Light switch Interrupteur d'éclairage - ENVO:03501214 Locker Casier - OBI:0002790 N95 mask Masque N95 - ENVO:03501215 Nurse call button Bouton d'appel infirmière - ENVO:03501256 Paper Papier - ENVO:01000060 Particulate matter Affaire particulière - ENVO:01000404 Plastic Plastique - GENEPIO:0100025 PPE gown Blouse EPI - ENVO:00002018 Sewage Eaux usées - ENVO:01000990 Sink Evier - ENVO:00001998 Soil Sol - ENVO:03501216 Stainless steel Acier inoxydable - ENVO:03501217 Tissue paper Papier de soie - ENVO:03501218 Toilet bowl Cuvette de toilette - ENVO:00002006 Water Eau - ENVO:00002001 Wastewater Eaux usées - ENVO:03501219 Window Fenêtre - ENVO:00002040 Wood Bois - - -environmental site menu menu du site environnemental ENVO:03501135 Acute care facility Établissement de soins aigus - ENVO:00003040 Animal house Maison des animaux - ENVO:01000422 Bathroom Salle de bain - ENVO:03501136 Clinical assessment centre Centre d'évaluation clinique - ENVO:03501127 Conference venue Salle de conférence - ENVO:03501121 Corridor couloir - ENVO:01000927 Daycare Garderie - ENVO:03501145 Emergency room (ER) Salle d'urgence - ENVO:03501186 Family practice clinic Clinique de médecine familiale - ENVO:03501196 Group home Foyer de groupe - ENVO:03501133 Homeless shelter Foyer pour sans-abri - ENVO:00002173 Hospital Hôpital - ENVO:03501152 Intensive Care Unit (ICU) Unité de soins intensifs - ENVO:03501194 Long Term Care Facility Établissement de soins de longue durée - ENVO:03501180 Patient room Chambre du patient - ENVO:03501204 Prison Prison - ENVO:01000536 Production Facility Installation de production - ENVO:03501130 School École - ENVO:00003043 Sewage Plant Station d'épuration - ENVO:03501109 Subway train Métro - ENVO:00000467 University campus Campus de l'université - ENVO:03501198 Wet market Marché de l'eau - - -collection method menu menu méthode de collecte NCIT:C52009 Amniocentesis Amniocentèse - NCIT:C15631 Aspiration Aspiration - GENEPIO:0100028 Suprapubic Aspiration Aspiration suprapubienne - GENEPIO:0100029 Tracheal aspiration Aspiration trachéale - GENEPIO:0100030 Vacuum Aspiration Aspiration sous vide - OBI:0002650 Biopsy Biopsie - OBI:0002651 Needle Biopsy Biopsie à l'aiguille - OBI:0302885 Filtration Filtration - GENEPIO:0100031 Air filtration Filtration de l'air - OBI:0600044 Lavage Lavage (lavage médical) - GENEPIO:0100032 Bronchoalveolar lavage (BAL) Lavage broncho-alvéolaire (LBA) - GENEPIO:0100033 Gastric Lavage Lavage gastrique - NCIT:C15327 Lumbar Puncture Ponction lombaire - MMO:0000344 Necropsy Nécropsie - NCIT:C28221 Phlebotomy Phlébotomie - GENEPIO:0002116 Rinsing Rinçage (lavage) - GENEPIO:0100034 Saline gargle (mouth rinse and gargle) Gargarisme salin (rinçage de la bouche et gargarisme) - GENEPIO:0100035 Scraping Raclage - GENEPIO:0002117 Swabbing Écouvillonnage - GENEPIO:0100036 Finger Prick Piqûre au doigt - GENEPIO:0100038 Washout Tear Collection Lavage Collecte de larmes - - -collection device menu menu du dispositif de collecte ENVO:00003968 Air filter Filtre à air - OBI:0002859 Blood Collection Tube Tube de prélèvement sanguin - OBI:0002826 Bronchoscope Bronchoscope - OBI:0002088 Collection Container Récipient de collecte - GENEPIO:0100026 Collection Cup Tasse de collection - OBI:0002825 Fibrobronchoscope Brush Brosse à fibrobronchoscope - GENEPIO:0100103 Filter Filtre - OBI:0002827 Fine Needle Aiguille fine - OBI:0002858 Microcapillary tube Tube microcapillaire - OBI:0001128 Micropipette Micropipette - OBI:0000436 Needle Aiguille - OBI:0002860 Serum Collection Tube Tube de collection de sérum - OBI:0002861 Sputum Collection Tube Tube de prélèvement des expectorations - OBI:0002831 Suction Catheter Cathéter d'aspiration - GENEPIO:0100027 Swab Écouvillon - OBI:0002862 Urine Collection Tube Tube de prélèvement d'urine - OBI:0002866 Virus Transport Medium Milieu de transport des virus - - -host (scientific name) menu menu hôte (nom scientifique) NCBITaxon:9606 Homo sapiens Homo sapiens - NCBITaxon:9913 Bos taurus Bos taureau - NCBITaxon:9615 Canis lupus familiaris Canis lupus familier - NCBITaxon:9397 Chiroptera Chiroptères - NCBITaxon:8930 Columbidae Colombidés - NCBITaxon:9685 Felis catus Felis catus - NCBITaxon:9031 Gallus gallus Gallus gallus - NCBITaxon:9973 Manis Manis - NCBITaxon:9974 Manis javanica Homme javanais - NCBITaxon:452646 Neovison vison Vison Neovison - NCBITaxon:9689 Panthera leo Panthera lion - NCBITaxon:9694 Panthera tigris Panthera tigris - NCBITaxon:58055 Rhinolophidae Rhinolophidés - NCBITaxon:59477 Rhinolophus affinis Rhinolophus affinis - NCBITaxon:9825 Sus scrofa domesticus Sus scrofa domestique - NCBITaxon:9673 Viverridae Viverridés - -host (common name) menu menu hôte (nom commun) NCBITaxon:9606 Human Humain - NCBITaxon:9397 Bat Chauve souris - NCBITaxon:9685 Cat Chat - NCBITaxon:9031 Chicken Poulet - NCBITaxon:9673 Civets Civettes - NCBITaxon:9913 Cow Vache bovine - NCBITaxon:9615 Dog Chien - NCBITaxon:9689 Lion Lion - NCBITaxon:452646 Mink Vison - NCBITaxon:9973 Pangolin Pangolin - NCBITaxon:9825 Pig Cochon porcine - NCBITaxon:8930 Pigeon Pigeon - NCBITaxon:9694 Tiger Tigre - - -host health state menu menu de l'état de santé de l'hôte NCIT:C3833 Asymptomatic Asymptomatique - NCIT:C28554 Deceased Décédé - NCIT:C115935 Healthy En bonne santé - NCIT:C49498 Recovered Rétabli - NCIT:C25269 Symptomatic Symptomatique - - -host health status details menu Menu détaillé de l'état de santé de l'hôte NCIT:C25179 Hospitalized Hospitalisé - GENEPIO:0100045 Hospitalized (Non-ICU) Hospitalisé (hors soins intensifs) - GENEPIO:0100046 Hospitalized (ICU) Hospitalisé (ICU) - NCIT:C70909 Mechanical Ventilation Ventilation mécanique - GENEPIO:0100047 Medically Isolated Médicalement isolé - GENEPIO:0100048 Medically Isolated (Negative Pressure) Médicalement isolé (pression négative) - NCIT:C173768 Self-quarantining Auto-quarantaine - - -host health outcome menu menu des résultats de santé de l'hôte NCIT:C28554 Deceased Décédé - NCIT:C25254 Deteriorating Se détériorer - NCIT:C49498 Recovered Rétabli - NCIT:C30103 Stable Écurie - - -organism menu menu de l'organisme NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 Syndrome respiratoire aigu sévère coronavirus 2 - NCBITaxon:2709072 RaTG13 RaTG13 - GENEPIO:0100000 RmYN02 RmYN02 - - -purpose of sampling menu but du menu d'échantillonnage GENEPIO:0100001 Cluster/Outbreak investigation Enquête sur les grappes et les foyers - GENEPIO:0100002 Diagnostic testing Tests de diagnostic - GENEPIO:0100003 Research Recherche - GENEPIO:0100004 Surveillance Surveillance - - -purpose of sequencing menu but du menu de séquencement GENEPIO:0100005 Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) - GENEPIO:0100006 Targeted surveillance (non-random sampling) Surveillance ciblée (échantillonnage non aléatoire) - GENEPIO:0100007 Priority surveillance project Projet de surveillance prioritaire - GENEPIO:0100008 Screening for Variants of Concern (VoC) Dépistage des variantes préoccupantes - GENEPIO:0100273 Sample has epidemiological link to Variant of Concern (VoC) L'échantillon a un lien épidémiologique avec la variante préoccupante - GENEPIO:0100274 Sample has epidemiological link to Omicron Variant L'échantillon a un lien épidémiologique avec la variante Omicron - GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) Surveillance longitudinale (échantillonnage répété des individus) - GENEPIO:0100842 Chronic (prolonged) infection surveillance Surveillance des infections chroniques (prolongées) - GENEPIO:0100010 Re-infection surveillance Surveillance des réinfections - GENEPIO:0100011 Vaccine escape surveillance Surveillance des fuites de vaccins - GENEPIO:0100012 Travel-associated surveillance Surveillance associée aux voyages - GENEPIO:0100013 Domestic travel surveillance Surveillance des voyages nationaux - GENEPIO:0100275 Interstate/ interprovincial travel surveillance Surveillance des voyages interétatiques/interprovinciaux - GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance Surveillance des voyages intra-étatiques/intraprovinciaux - GENEPIO:0100014 International travel surveillance Surveillance des voyages internationaux - GENEPIO:0100015 Surveillance of international border crossing by air travel or ground transport Surveillance du franchissement des frontières internationales par voie aérienne aérien ou terrestre - GENEPIO:0100016 Surveillance of international border crossing by air travel Surveillance du franchissement des frontières internationales par voie aérienne aérien - GENEPIO:0100017 Surveillance of international border crossing by ground transport Surveillance du franchissement des frontières internationales par transport terrestre - GENEPIO:0100018 Surveillance from international worker testing Surveillance à partir d'essais internationaux sur les travailleurs - GENEPIO:0100019 Cluster/Outbreak investigation Enquête sur les grappes et les foyers - GENEPIO:0100020 Multi-jurisdictional outbreak investigation Enquête sur les foyers multi-juridictionnels - GENEPIO:0100021 Intra-jurisdictional outbreak investigation Enquête sur un foyer intra-juridictionnel - GENEPIO:0100022 Research Recherche - GENEPIO:0100023 Viral passage experiment Expérience de passage viral - GENEPIO:0100024 Protocol testing experiment Expérience de test de protocole - GENEPIO:0100356 Retrospective sequencing Séquençage rétrospectif - - -specimen processing menu menu de traitement des échantillons GENEPIO:0100039 Virus passage Passage du virus - GENEPIO:0100040 RNA re-extraction (post RT-PCR) Rétablissement de l'extraction de l'RNA (après RT-PCR) - OBI:0600016 Specimens pooled Échantillons regroupés - - -lab host menu menu hôte du laboratoire GENEPIO:0100041 293/ACE2 cell line Lignée cellulaire 293/ACE2 - BTO:0000195 Caco2 cell line Lignée cellulaire Caco2 - BTO:0002750 Calu3 cell line Lignée cellulaire Calu3 - GENEPIO:0100042 EFK3B cell line Lignée cellulaire EFK3B - BTO:0002181 HEK293T cell line Lignée cellulaire HEK293T - GENEPIO:0100043 HRCE cell line Lignée cellulaire HRCE - BTO:0001950 Huh7 cell line Lignée cellulaire Huh7 - CLO:0007330 LLCMk2 cell line Lignée cellulaire LLCMk2 - BTO:0000836 MDBK cell line Lignée cellulaire MDBK - BTO:0002924 NHBE cell line lignée cellulaire NHBE - BTO:0001865 PK-15 cell line Lignée cellulaire PK-15 - BTO:0002909 RK-13 cell line Lignée cellulaire RK-13 - BTO:0002035 U251 cell line Lignée cellulaire U251 - BTO:0001444 Vero cell line Lignée cellulaire Vero - BTO:0004755 Vero E6 cell line Lignée cellulaire Vero E6 - GENEPIO:0100044 VeroE6/TMPRSS2 cell line Lignée cellulaire VeroE6/TMPRSS2 - - -host disease menu menu des maladies hôtes MONDO:0100096 COVID-19 COVID-19 - - -host age bin menu menu du bac d'âge de l'hôte GENEPIO:0100049 0 - 9 0 - 9 - GENEPIO:0100050 10 - 19 10 - 19 - GENEPIO:0100051 20 - 29 20 - 29 - GENEPIO:0100052 30 - 39 30 - 39 - GENEPIO:0100053 40 - 49 40 - 49 - GENEPIO:0100054 50 - 59 50 - 59 - GENEPIO:0100055 60 - 69 60 - 69 - GENEPIO:0100056 70 - 79 70 - 79 - GENEPIO:0100057 80 - 89 80 - 89 - GENEPIO:0100058 90 - 99 90 - 99 90+ - GENEPIO:0100059 100+ 100+ 90+ - - -host gender menu menu sexe de l'hôte NCIT:C46110 Female Female - NCIT:C46109 Male Male - GSSO:000132 Non-binary gender Non-binary gender - GSSO:004004 Transgender (assigned male at birth) Transgender (assigned male at birth) - GSSO:004005 Transgender (assigned female at birth) Transgender (assigned female at birth) - NCIT:C110959 Undeclared Undeclared - - -exposure event menu menu d'événement d'exposition GENEPIO:0100237 Mass Gathering Rassemblement de masse - GENEPIO:0100240 Agricultural Event Événement agricole - GENEPIO:0100238 Convention Convention - GENEPIO:0100239 Convocation Convocation - GENEPIO:0100417 Recreational Event Événement récréatif - GENEPIO:0100418 Concert Concert - GENEPIO:0100419 Sporting Event Manifestation sportive - GENEPIO:0100241 Religious Gathering Rassemblement religieux - GENEPIO:0100242 Mass Messe - PCO:0000033 Social Gathering Rassemblement social - PCO:0000039 Baby Shower Douche de bébé - PCO:0000034 Community Event Evénement communautaire - GENEPIO:0100243 Family Gathering Réunion de famille - GENEPIO:0100244 Family Reunion Réunion de famille - GENEPIO:0100245 Funeral Funérailles - PCO:0000035 Party Faire la fête - PCO:0000037 Potluck Repas-partage - PCO:0000038 Wedding Mariage - Other exposure event Autre événement d'exposition - - -exposure contact level menu menu niveau de contact d'exposition GENEPIO:0100357 Contact with infected individual Contact avec une personne infectée - TRANS:0000001 Direct contact (direct human-to-human contact) Direct (contact interhumain) - GENEPIO:0100246 Indirect contact Contact indirect - GENEPIO:0100247 Close contact (face-to-face, no direct contact) Contact étroit (face à face) - GENEPIO:0100248 Casual contact Contact occasionnel - - -host role menu menu du rôle d'hôte GENEPIO:0100249 Attendee Participant - OMRSE:00000058 Student Étudiant - OMRSE:00000030 Patient Patient - NCIT:C25182 Inpatient Patient hospitalisé - NCIT:C28293 Outpatient Ambulatoire - GENEPIO:0100250 Passenger Passager - GENEPIO:0100251 Resident Résident - GENEPIO:0100252 Visitor Visiteur - GENEPIO:0100253 Volunteer Bénévole - GENEPIO:0100254 Work Travail - GENEPIO:0100255 Administrator Administrateur - Child Care/Education Worker Travailleur en garderie/éducation - Essential Worker Travailleur essentiel - GENEPIO:0100256 First Responder Premier intervenant - GENEPIO:0100257 Firefighter Sapeur pompier - GENEPIO:0100258 Paramedic Paramédical - GENEPIO:0100259 Police Officer Officier de police - GENEPIO:0100334 Healthcare Worker Travailleur de la santé - GENEPIO:0100420 Community Healthcare Worker Agent de santé communautaire - GENEPIO:0100262 Laboratory Worker Ouvrier de laboratoire - OMRSE:00000014 Nurse Infirmière - GENEPIO:0100263 Personal Care Aid Aide aux soins personnels - GENEPIO:0100264 Pharmacist Pharmacien - OMRSE:00000013 Physician Médecin - GENEPIO:0100260 Housekeeper Gouvernante - International worker Travailleur international - GENEPIO:0100261 Kitchen Worker Ouvrier de cuisine - GENEPIO:0100354 Rotational Worker Travailleur en rotation - GENEPIO:0100355 Seasonal Worker Travailleur saisonnier - Transport Worker Ouvrier des transports - Transport Truck Driver Chauffeur de camion de transport - GENEPIO:0100265 Veterinarian Vétérinaire - OMRSE:00000001 Social role Rôle social - GENEPIO:0100266 Acquaintance of case Connaissance de l'affaire - GENEPIO:0100267 Relative of case Parent de l'affaire - GENEPIO:0100268 Child of case Enfant de la personne concernée - GENEPIO:0100269 Parent of case Parent de l'affaire - GENEPIO:0100270 Father of case Père de l'affaire - GENEPIO:0100271 Mother of case Mère du cas - GENEPIO:0100272 Spouse of case Conjoint de l'affaire - Other Host Role Autre rôle de l'hôte - - -exposure setting menu menu de réglage de l'exposition ECTO:3000005 Human Exposure Exposition humaine - GENEPIO:0100184 Contact with Known COVID-19 Case Contact avec un cas connu de COVID-19 - GENEPIO:0100185 Contact with Patient Contact avec un patient - GENEPIO:0100186 Contact with Probable COVID-19 Case Contact avec un cas probable de COVID-19 - GENEPIO:0100187 Contact with Person with Acute Respiratory Illness Contact avec une personne atteinte d'une maladie respiratoire aiguë - GENEPIO:0100188 Contact with Person with Fever and/or Cough Contact avec une personne présentant une fièvre et/ou une toux - GENEPIO:0100189 Contact with Person who Recently Travelled Contact avec une personne ayant récemment voyagé - GENEPIO:0100190 Occupational, Residency or Patronage Exposure Exposition professionnelle, de résidence ou de patronage - ECTO:1000033 Abbatoir Abbatoir - GENEPIO:0100191 Animal Rescue Sauvetage d'animaux - GENEPIO:0100192 Childcare Garde d'enfants - GENEPIO:0100193 Daycare Garderie - GENEPIO:0100194 Nursery Crèche - GENEPIO:0100195 Community Service Centre Centre de services communautaires - GENEPIO:0100196 Correctional Facility Établissement pénitentiaire - GENEPIO:0100197 Dormitory Dortoir - ECTO:1000034 Farm Ferme - GENEPIO:0100198 First Nations Reserve Réserve des Premières Nations - GENEPIO:0100199 Funeral Home Maison funéraire - GENEPIO:0100200 Group Home Foyer de groupe - GENEPIO:0100201 Healthcare Setting Établissement de soins de santé - GENEPIO:0100202 Ambulance Ambulance - GENEPIO:0100203 Acute Care Facility Établissement de soins aigus - GENEPIO:0100204 Clinic Clinique - GENEPIO:0100415 Community Healthcare (At-Home) Setting Établissement de soins de santé communautaire (à domicile) - GENEPIO:0100205 Community Health Centre Centre de santé communautaire - ECTO:1000035 Hospital Hôpital - GENEPIO:0100206 Emergency Department Service des urgences - GENEPIO:0100207 ICU ICU - GENEPIO:0100208 Ward Salle - ECTO:1000036 Laboratory Laboratoire - GENEPIO:0100209 Long-Term Care Facility Établissement de soins de longue durée - GENEPIO:0100210 Pharmacy Pharmacie - GENEPIO:0100211 Physician's Office Cabinet du médecin - GENEPIO:0100212 Household Ménage - GENEPIO:0100213 Insecure Housing (Homeless) Logement précaire (sans-abri) - GENEPIO:0100214 Occupational Exposure Exposition professionnelle - GENEPIO:0100215 Worksite Chantier - ECTO:1000037 Office Bureau - GENEPIO:0100216 Outdoors En plein air - ECTO:5000009 Camp/camping Camper/camper - GENEPIO:0100217 Hiking Trail Sentier de randonnée - ECTO:6000030 Hunting Ground Terrain de chasse - GENEPIO:0100218 Ski Resort Station de ski - ECTO:5000008 Petting zoo Zoo pour enfants - GENEPIO:0100220 Place of Worship Lieu de culte - GENEPIO:0100221 Church Église - GENEPIO:0100222 Mosque Mosquée - GENEPIO:0100223 Temple Temple - ECTO:1000040 Restaurant Restaurant - ECTO:1000041 Retail Store Magasin de détail - GENEPIO:0100224 School École - GENEPIO:0100225 Temporary Residence Résidence temporaire - GENEPIO:0100226 Homeless Shelter Refuge pour sans-abri - GENEPIO:0100227 Hotel Hôtel - GENEPIO:0100228 Veterinary Care Clinic Clinique vétérinaire - GENEPIO:0100229 Travel Exposure Exposition au voyage - GENEPIO:0100230 Travelled on a Cruise Ship Voyage sur un bateau de croisière - GENEPIO:0100231 Travelled on a Plane Voyage en avion - GENEPIO:0100232 Travelled on Ground Transport Transport terrestre - GENEPIO:0001118 Travelled outside Province/Territory Voyage en dehors de la province ou du territoire - GENEPIO:0001119 Travelled outside Canada Voyage en dehors du Canada - GENEPIO:0100235 Other Exposure Setting Autres réglages d'exposition - - -travel point of entry type menu menu de type de point d'entrée de voyage GENEPIO:0100408 Air Air - GENEPIO:0100409 Land Atterrir - - -border testing test day type menu menu de type jour de test des tests aux frontières GENEPIO:0100410 day 1 jour 1 - GENEPIO:0100411 day 8 jour 8 - GENEPIO:0100412 day 10 jour 10 - - -travel history availability menu menu de disponibilité de l'historique de voyage GENEPIO:0100650 Travel history available Historique de voyage disponible - GENEPIO:0100651 Domestic travel history available Historique des voyages intérieurs disponible - GENEPIO:0100652 International travel history available Historique des voyages internationaux disponible - GENEPIO:0100653 International and domestic travel history available Historique des voyages internationaux et nationaux disponible - GENEPIO:0100654 No travel history available Aucun historique de voyage disponible - - -sequencing instrument menu menu des instruments de séquençage GENEPIO:0100105 Illumina Illumina - GENEPIO:0100106 Illumina Genome Analyzer Illumina Genome Analyzer - GENEPIO:0100107 Illumina Genome Analyzer II Illumina Genome Analyzer II - GENEPIO:0100108 Illumina Genome Analyzer IIx Illumina Genome Analyzer IIx - GENEPIO:0100109 Illumina HiScanSQ Illumina HiScanSQ - GENEPIO:0100110 Illumina HiSeq Illumina HiSeq - GENEPIO:0100111 Illumina HiSeq X Illumina HiSeq X - GENEPIO:0100112 Illumina HiSeq X Five Illumina HiSeq X Five - GENEPIO:0100113 Illumina HiSeq X Ten Illumina HiSeq X Ten - GENEPIO:0100114 Illumina HiSeq 1000 Illumina HiSeq 1000 - GENEPIO:0100115 Illumina HiSeq 1500 Illumina HiSeq 1500 - GENEPIO:0100116 Illumina HiSeq 2000 Illumina HiSeq 2000 - GENEPIO:0100117 Illumina HiSeq 2500 Illumina HiSeq 2500 - GENEPIO:0100118 Illumina HiSeq 3000 Illumina HiSeq 3000 - GENEPIO:0100119 Illumina HiSeq 4000 Illumina HiSeq 4000 - GENEPIO:0100120 Illumina iSeq Illumina iSeq - GENEPIO:0100121 Illumina iSeq 100 Illumina iSeq 100 - GENEPIO:0100122 Illumina NovaSeq Illumina NovaSeq - GENEPIO:0100123 Illumina NovaSeq 6000 Illumina NovaSeq 6000 - GENEPIO:0100124 Illumina MiniSeq Illumina MiniSeq - GENEPIO:0100125 Illumina MiSeq Illumina MiSeq - GENEPIO:0100126 Illumina NextSeq Illumina NextSeq - GENEPIO:0100127 Illumina NextSeq 500 Illumina NextSeq 500 - GENEPIO:0100128 Illumina NextSeq 550 Illumina NextSeq 550 - GENEPIO:0100129 Illumina NextSeq 2000 Illumina NextSeq 2000 - GENEPIO:0100130 Pacific Biosciences Pacific Biosciences - GENEPIO:0100131 PacBio RS PacBio RS - GENEPIO:0100132 PacBio RS II PacBio RS II - GENEPIO:0100133 PacBio Sequel PacBio Sequel - GENEPIO:0100134 PacBio Sequel II PacBio Sequel II - GENEPIO:0100135 Ion Torrent Ion Torrent - GENEPIO:0100136 Ion Torrent PGM Ion Torrent PGM - GENEPIO:0100137 Ion Torrent Proton Ion Torrent Proton - GENEPIO:0100138 Ion Torrent S5 XL Ion Torrent S5 XL - GENEPIO:0100139 Ion Torrent S5 Ion Torrent S5 - GENEPIO:0100140 Oxford Nanopore Oxford Nanopore - GENEPIO:0100141 Oxford Nanopore GridION Oxford Nanopore GridION - GENEPIO:0100142 Oxford Nanopore MinION Oxford Nanopore MinION - GENEPIO:0100143 Oxford Nanopore PromethION Oxford Nanopore PromethION - GENEPIO:0100144 BGI Genomics BGI Genomics - GENEPIO:0100145 BGI Genomics BGISEQ-500 BGI Genomics BGISEQ-500 - GENEPIO:0100146 MGI MGI - GENEPIO:0100147 MGI DNBSEQ-T7 MGI DNBSEQ-T7 - GENEPIO:0100148 MGI DNBSEQ-G400 MGI DNBSEQ-G400 - GENEPIO:0100149 MGI DNBSEQ-G400 FAST MGI DNBSEQ-G400 FAST - GENEPIO:0100150 MGI DNBSEQ-G50 MGI DNBSEQ-G50 - - -gene name menu menu de nom de gène GENEPIO:0100151 E gene (orf4) E gène (orf4) E gene E (orf4) - GENEPIO:0100152 M gene (orf5) M gène (orf5) M (orf5) - GENEPIO:0100153 N gene (orf9) N gène (orf9) N (orf9) - GENEPIO:0100154 Spike gene (orf2) Spike gène (orf2) S (orf2) - GENEPIO:0100155 orf1ab (rep) orf1ab (rep) orf1ab (rep) - GENEPIO:0100156 orf1a (pp1a) orf1a (pp1a) orf1a (pp1a) - GENEPIO:0100157 nsp11 nsp11 nsp11 - GENEPIO:0100158 nsp1 nsp1 nsp1 - GENEPIO:0100159 nsp2 nsp2 nsp2 - GENEPIO:0100160 nsp3 nsp3 nsp3 - GENEPIO:0100161 nsp4 nsp4 nsp4 - GENEPIO:0100162 nsp5 nsp5 nsp5 - GENEPIO:0100163 nsp6 nsp6 nsp6 - GENEPIO:0100164 nsp7 nsp7 nsp7 - GENEPIO:0100165 nsp8 nsp8 nsp8 - GENEPIO:0100166 nsp9 nsp9 nsp9 - GENEPIO:0100167 nsp10 nsp10 nsp10 - GENEPIO:0100168 RdRp gene (nsp12) RdRp gène (nsp12) nsp12 (RdRp) - GENEPIO:0100169 hel gene (nsp13) hel gène (nsp13) nsp13 (Hel) - GENEPIO:0100170 exoN gene (nsp14) exoN gène (nsp14) nsp14 (ExoN) - GENEPIO:0100171 nsp15 nsp15 nsp15 - GENEPIO:0100172 nsp16 nsp16 nsp16 - GENEPIO:0100173 orf3a orf3a orf3a - GENEPIO:0100174 orf3b orf3b orf3b - GENEPIO:0100175 orf6 (ns6) orf6 (ns6) orf6 (ns6) - GENEPIO:0100176 orf7a orf7a orf7a - GENEPIO:0100177 orf7b (ns7b) orf7b (ns7b) orf7b (ns7b) - GENEPIO:0100178 orf8 (ns8) orf8 (ns8) orf8 (ns8) - GENEPIO:0100179 orf9b orf9b orf9b - GENEPIO:0100180 orf9c orf9c orf9c - GENEPIO:0100181 orf10 orf10 orf10 - GENEPIO:0100182 orf14 orf14 orf14 - GENEPIO:0100183 SARS-COV-2 5' UTR SARS-COV-2 5' UTR - - -sequence submitted by menu séquence soumise par menu Alberta Precision Labs (APL) Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory BCCDC Public Health Laboratory - Canadore College Canadore College - The Centre for Applied Genomics (TCAG) The Centre for Applied Genomics (TCAG) - Dynacare Dynacare - Dynacare (Brampton) Dynacare (Brampton) - Dynacare (Manitoba) Dynacare (Manitoba) - The Hospital for Sick Children (SickKids) The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) Laboratoire de santé publique du Québec (LSPQ) - Manitoba Cadham Provincial Laboratory Manitoba Cadham Provincial Laboratory - McGill University McGill University - McMaster University McMaster University - National Microbiology Laboratory (NML) National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health Newfoundland and Labrador - Eastern Health - Newfoundland and Labrador - Newfoundland and Labrador Health Services Newfoundland and Labrador - Newfoundland and Labrador Health Services - Nova Scotia Health Authority Nova Scotia Health Authority - Ontario Institute for Cancer Research (OICR) Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI Prince Edward Island - Health PEI - Public Health Ontario (PHO) Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Sunnybrook Health Sciences Centre Sunnybrook Health Sciences Centre - Thunder Bay Regional Health Sciences Centre Thunder Bay Regional Health Sciences Centre - - -sample collected by menu échantillon collecté par menu Alberta Precision Labs (APL) Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory BCCDC Public Health Laboratory - Dynacare Dynacare - Dynacare (Manitoba) Dynacare (Manitoba) - Dynacare (Brampton) Dynacare (Brampton) - Eastern Ontario Regional Laboratory Association Eastern Ontario Regional Laboratory Association - Hamilton Health Sciences Hamilton Health Sciences - The Hospital for Sick Children (SickKids) The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) Laboratoire de santé publique du Québec (LSPQ) - Lake of the Woods District Hospital - Ontario Lake of the Woods District Hospital - Ontario - LifeLabs LifeLabs - LifeLabs (Ontario) LifeLabs (Ontario) - Manitoba Cadham Provincial Laboratory Manitoba Cadham Provincial Laboratory - McMaster University McMaster University - Mount Sinai Hospital Mount Sinai Hospital - National Microbiology Laboratory (NML) National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health Newfoundland and Labrador - Eastern Health - Newfoundland and Labrador - Newfoundland and Labrador Health Services Newfoundland and Labrador - Newfoundland and Labrador Health Services - Nova Scotia Health Authority Nova Scotia Health Authority - Nunavut Nunavut - Ontario Institute for Cancer Research (OICR) Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI Prince Edward Island - Health PEI - Public Health Ontario (PHO) Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Shared Hospital Laboratory Shared Hospital Laboratory - St. John's Rehab at Sunnybrook Hospital St. John's Rehab at Sunnybrook Hospital - Switch Health Switch Health - Sunnybrook Health Sciences Centre Sunnybrook Health Sciences Centre - Unity Health Toronto Unity Health Toronto - William Osler Health System William Osler Health System - - -geo_loc_name (country) menu menu geo_loc_name (pays) GAZ:00006882 Afghanistan Afghanistan - GAZ:00002953 Albania Albanie - GAZ:00000563 Algeria Algérie - GAZ:00003957 American Samoa Samoa américaines - GAZ:00002948 Andorra Andorre - GAZ:00001095 Angola Angola - GAZ:00009159 Anguilla Anguilla - GAZ:00000462 Antarctica Antarctique - GAZ:00006883 Antigua and Barbuda Antigua-et-Barbuda - GAZ:00002928 Argentina Argentine - GAZ:00004094 Armenia Arménie - GAZ:00004025 Aruba Aruba - GAZ:00005901 Ashmore and Cartier Islands Îles Ashmore et Cartier - GAZ:00000463 Australia Australie - GAZ:00002942 Austria L'Autriche - GAZ:00004941 Azerbaijan Azerbaïdjan - GAZ:00002733 Bahamas Bahamas - GAZ:00005281 Bahrain Bahreïn - GAZ:00007117 Baker Island Île Boulanger - GAZ:00003750 Bangladesh Bangladesh - GAZ:00001251 Barbados Barbade - GAZ:00005810 Bassas da India Bassas de l'Inde - GAZ:00006886 Belarus Biélorussie - GAZ:00002938 Belgium Belgique - GAZ:00002934 Belize Bélize - GAZ:00000904 Benin Bénin - GAZ:00001264 Bermuda Bermudes - GAZ:00003920 Bhutan Bhoutan - GAZ:00002511 Bolivia Bolivie - GAZ:00025355 Borneo Bornéo - GAZ:00006887 Bosnia and Herzegovina Bosnie Herzégovine - GAZ:00001097 Botswana Botswana - GAZ:00001453 Bouvet Island Île Bouvet - GAZ:00002828 Brazil Brésil - GAZ:00003961 British Virgin Islands Îles Vierges britanniques - GAZ:00003901 Brunei Brunéi - GAZ:00002950 Bulgaria Bulgarie - GAZ:00000905 Burkina Faso Burkina Faso - GAZ:00001090 Burundi Burundi - GAZ:00006888 Cambodia Cambodge - GAZ:00001093 Cameroon Cameroun - GAZ:00002560 Canada Canada - GAZ:00001227 Cape Verde Cap-Vert - GAZ:00003986 Cayman Islands Îles Caïmans - GAZ:00001089 Central African Republic République centrafricaine - GAZ:00000586 Chad Tchad - GAZ:00002825 Chile Chili - GAZ:00002845 China Chine - GAZ:00005915 Christmas Island L'île de noël - GAZ:00005838 Clipperton Island Île Clipperton - GAZ:00009721 Cocos Islands Îles Cocos - GAZ:00002929 Colombia Colombie - GAZ:00005820 Comoros Comores - GAZ:00053798 Cook Islands les Îles Cook - GAZ:00005917 Coral Sea Islands Îles de la mer de Corail - GAZ:00002901 Costa Rica Costa Rica - GAZ:00000906 Cote d'Ivoire Côte d'Ivoire - GAZ:00002719 Croatia Croatie - GAZ:00003762 Cuba Cuba - GAZ:00012582 Curacao Curacao - GAZ:00004006 Cyprus Chypre - GAZ:00002954 Czech Republic République tchèque - GAZ:00001086 Democratic Republic of the Congo République Démocratique du Congo - GAZ:00005852 Denmark Danemark - GAZ:00000582 Djibouti Djibouti - GAZ:00006890 Dominica Dominique - GAZ:00003952 Dominican Republic République dominicaine - GAZ:00002912 Ecuador Équateur - GAZ:00003934 Egypt Egypte - GAZ:00002935 El Salvador Le Salvador - GAZ:00001091 Equatorial Guinea Guinée Équatoriale - GAZ:00000581 Eritrea Érythrée - GAZ:00002959 Estonia Estonie - GAZ:00001099 Eswatini Eswatini - GAZ:00000567 Ethiopia Ethiopie - GAZ:00005811 Europa Island Île d'Europe - GAZ:00001412 Falkland Islands (Islas Malvinas) Îles Falkland (Islas Malvinas) - GAZ:00059206 Faroe Islands Îles Féroé - GAZ:00006891 Fiji Fidji - GAZ:00002937 Finland Finlande - GAZ:00003940 France France - GAZ:00002516 French Guiana Guyane Française - GAZ:00002918 French Polynesia Polynésie française - GAZ:00003753 French Southern and Antarctic Lands Terres australes et antarctiques françaises - GAZ:00001092 Gabon Gabon - GAZ:00000907 Gambia Gambie - GAZ:00009571 Gaza Strip bande de Gaza - GAZ:00004942 Georgia Géorgie - GAZ:00002646 Germany Allemagne - GAZ:00000908 Ghana Ghana - GAZ:00003987 Gibraltar Gibraltar - GAZ:00005808 Glorioso Islands Îles Glorieuses - GAZ:00002945 Greece Grèce - GAZ:00001507 Greenland Groenland - GAZ:02000573 Grenada Grenade - GAZ:00067142 Guadeloupe Guadeloupe - GAZ:00003706 Guam Guam - GAZ:00002936 Guatemala Guatemala - GAZ:00001550 Guernsey Guernesey - GAZ:00000909 Guinea Guinée - GAZ:00000910 Guinea-Bissau Guinée-Bissau - GAZ:00002522 Guyana Guyane - GAZ:00003953 Haiti Haïti - GAZ:00009718 Heard Island and McDonald Islands Île Heard et îles McDonald - GAZ:00002894 Honduras Honduras - GAZ:00003203 Hong Kong Hong Kong - GAZ:00007120 Howland Island Île Howland - GAZ:00002952 Hungary Hongrie - GAZ:00000843 Iceland Islande - GAZ:00002839 India Inde - GAZ:00003727 Indonesia Indonésie - GAZ:00004474 Iran L'Iran - GAZ:00004483 Iraq Irak - GAZ:00002943 Ireland Irlande - GAZ:00052477 Isle of Man île de Man - GAZ:00002476 Israel Israël - GAZ:00002650 Italy Italie - GAZ:00003781 Jamaica Jamaïque - GAZ:00005853 Jan Mayen Jan Mayen - GAZ:00002747 Japan Japon - GAZ:00007118 Jarvis Island Île Jarvis - GAZ:00001551 Jersey Jersey - GAZ:00007114 Johnston Atoll Atoll Johnston - GAZ:00002473 Jordan Jordan - GAZ:00005809 Juan de Nova Island Île Juan de Nova - GAZ:00004999 Kazakhstan Kazakhstan - GAZ:00001101 Kenya Kenya - GAZ:00005682 Kerguelen Archipelago Archipel des Kerguelen - GAZ:00007116 Kingman Reef Récif Kingman - GAZ:00006894 Kiribati Kiribati - GAZ:00011337 Kosovo Kosovo - GAZ:00005285 Kuwait Koweit - GAZ:00006893 Kyrgyzstan Kirghizistan - GAZ:00006889 Laos Laos - GAZ:00002958 Latvia Lettonie - GAZ:00002478 Lebanon Liban - GAZ:00001098 Lesotho Lesotho - GAZ:00000911 Liberia Libéria - GAZ:00000566 Libya Libye - GAZ:00003858 Liechtenstein Liechtenstein - GAZ:00007144 Line Islands Îles de la Ligne - GAZ:00002960 Lithuania Lituanie - GAZ:00002947 Luxembourg Luxembourg - GAZ:00003202 Macau Macao - GAZ:00001108 Madagascar Madagascar - GAZ:00001105 Malawi Malawi - GAZ:00003902 Malaysia Malaisie - GAZ:00006924 Maldives Maldives - GAZ:00000584 Mali Mali - GAZ:00004017 Malta Malte - GAZ:00007161 Marshall Islands Iles Marshall - GAZ:00067143 Martinique Martinique - GAZ:00000583 Mauritania Mauritanie - GAZ:00003745 Mauritius Maurice - GAZ:00003943 Mayotte Mayotte - GAZ:00002852 Mexico Mexique - GAZ:00005862 Micronesia Micronésie - GAZ:00007112 Midway Islands Îles Midway - GAZ:00003897 Moldova Moldavie - GAZ:00003857 Monaco Monaco - GAZ:00008744 Mongolia Mongolie - GAZ:00006898 Montenegro Monténégro - GAZ:00003988 Montserrat Montserrat - GAZ:00000565 Morocco Maroc - GAZ:00001100 Mozambique Mozambique - GAZ:00006899 Myanmar Birmanie - GAZ:00001096 Namibia Namibie - GAZ:00006900 Nauru Nauru - GAZ:00007119 Navassa Island Île Navasse - GAZ:00004399 Nepal Népal - GAZ:00002946 Netherlands Pays-Bas - GAZ:00005206 New Caledonia Nouvelle Calédonie - GAZ:00000469 New Zealand Nouvelle-Zélande - GAZ:00002978 Nicaragua Nicaragua - GAZ:00000585 Niger Niger - GAZ:00000912 Nigeria Nigeria - GAZ:00006902 Niue Nioué - GAZ:00005908 Norfolk Island l'ile de Norfolk - GAZ:00002801 North Korea Corée du Nord - GAZ:00006895 North Macedonia Macédoine du Nord - GAZ:00002284 North Sea la mer du Nord - GAZ:00003958 Northern Mariana Islands Îles Mariannes du Nord - GAZ:00002699 Norway Norvège - GAZ:00005283 Oman Oman - GAZ:00005246 Pakistan Pakistan - GAZ:00006905 Palau Palaos - GAZ:00002892 Panama Panama - GAZ:00003922 Papua New Guinea Papouasie Nouvelle Guinée - GAZ:00010832 Paracel Islands Iles Paracel - GAZ:00002933 Paraguay Paraguay - GAZ:00002932 Peru Pérou - GAZ:00004525 Philippines Philippines - GAZ:00005867 Pitcairn Islands Îles Pitcairn - GAZ:00002939 Poland Pologne - GAZ:00004126 Portugal le Portugal - GAZ:00006935 Puerto Rico Porto Rico - GAZ:00005286 Qatar Qatar - GAZ:00001088 Republic of the Congo République du Congo - GAZ:00003945 Reunion Réunion - GAZ:00002951 Romania Roumanie - GAZ:00023304 Ross Sea Mer de Ross - GAZ:00002721 Russia Russie - GAZ:00001087 Rwanda Rwanda - GAZ:00000849 Saint Helena Sainte-Hélène - GAZ:00006906 Saint Kitts and Nevis Saint-Christophe-et-Niévès - GAZ:00006909 Saint Lucia Sainte-Lucie - GAZ:00003942 Saint Pierre and Miquelon Saint-Pierre-et-Miquelon - GAZ:00005841 Saint Martin Saint Martin - GAZ:02000565 Saint Vincent and the Grenadines Saint-Vincent-et-les-Grenadines - GAZ:00006910 Samoa Samoa - GAZ:00003102 San Marino Saint Marin - GAZ:00006927 Sao Tome and Principe Sao Tomé et Principe - GAZ:00005279 Saudi Arabia Arabie Saoudite - GAZ:00000913 Senegal Sénégal - GAZ:00002957 Serbia Serbie - GAZ:00006922 Seychelles les Seychelles - GAZ:00000914 Sierra Leone Sierra Leone - GAZ:00003923 Singapore Singapour - GAZ:00012579 Sint Maarten Saint-Martin - GAZ:00002956 Slovakia Slovaquie - GAZ:00002955 Slovenia Slovénie - GAZ:00005275 Solomon Islands Les îles Salomon - GAZ:00001104 Somalia Somalie - GAZ:00001094 South Africa Afrique du Sud - GAZ:00003990 South Georgia and the South Sandwich Islands Géorgie du Sud et îles Sandwich du Sud - GAZ:00002802 South Korea Corée du Sud - GAZ:00233439 South Sudan Soudan du sud - GAZ:00000591 Spain Espagne - GAZ:00010831 Spratly Islands Îles Spratly - GAZ:00003924 Sri Lanka Sri Lanka - GAZ:00002475 State of Palestine État de Palestine - GAZ:00000560 Sudan Soudan - GAZ:00002525 Suriname Surinam - GAZ:00005396 Svalbard Svalbard - GAZ:00001099 Swaziland Swaziland - GAZ:00002729 Sweden Suède - GAZ:00002941 Switzerland Suisse - GAZ:00002474 Syria Syrie - GAZ:00005341 Taiwan Taïwan - GAZ:00006912 Tajikistan Tadjikistan - GAZ:00001103 Tanzania Tanzanie - GAZ:00003744 Thailand Thaïlande - GAZ:00006913 Timor-Leste Timor-Leste - GAZ:00000915 Togo Aller - GAZ:00260188 Tokelau Tokélaou - GAZ:00006916 Tonga Tonga - GAZ:00003767 Trinidad and Tobago Trinité-et-Tobago - GAZ:00005812 Tromelin Island Île Tromelin - GAZ:00000562 Tunisia Tunisie - GAZ:00000558 Turkey Turquie - GAZ:00005018 Turkmenistan Turkménistan - GAZ:00003955 Turks and Caicos Islands îles Turques-et-Caïques - GAZ:00009715 Tuvalu Tuvalu - GAZ:00002459 United States of America les états-unis d'Amérique - GAZ:00001102 Uganda Ouganda - GAZ:00002724 Ukraine Ukraine - GAZ:00005282 United Arab Emirates Emirats Arabes Unis - GAZ:00002637 United Kingdom Royaume-Uni - GAZ:00002930 Uruguay Uruguay - GAZ:00004979 Uzbekistan Ouzbékistan - GAZ:00006918 Vanuatu Vanuatu - GAZ:00002931 Venezuela Venezuela - GAZ:00003756 Viet Nam Viet Nam - GAZ:00003959 Virgin Islands Les iles vierges - GAZ:00007111 Wake Island Île de Wake - GAZ:00007191 Wallis and Futuna Wallis et Futuna - GAZ:00009572 West Bank banque de l'Ouest - GAZ:00000564 Western Sahara Sahara occidental - GAZ:00005284 Yemen Yémen - GAZ:00001107 Zambia Zambie - GAZ:00001106 Zimbabwe Zimbabwe - - \ No newline at end of file +title name title_fr meaning menu_1 menu_2 menu_3 menu_4 menu_5 menu_1_fr menu_2_fr menu_3_fr menu_4_fr menu_5_fr description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal + +umbrella bioproject accession menu UmbrellaBioprojectAccessionMenu Menu « Accès au bioprojet cadre » PRJNA623807 PRJNA623807 + +null value menu NullValueMenu Menu « Valeur nulle » GENEPIO:0001619 Not Applicable Sans objet + GENEPIO:0001618 Missing Manquante + GENEPIO:0001620 Not Collected Non prélevée + GENEPIO:0001668 Not Provided Non fournie + GENEPIO:0001810 Restricted Access Accès restreint + +geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu Menu « nom_lieu_géo (état/province/territoire) » GAZ:00002566 Alberta Alberta + GAZ:00002562 British Columbia Colombie-Britannique + GAZ:00002571 Manitoba Manitoba + GAZ:00002570 New Brunswick Nouveau-Brunswick + GAZ:00002567 Newfoundland and Labrador Terre-Neuve-et-Labrador + GAZ:00002575 Northwest Territories Territoires du Nord-Ouest + GAZ:00002565 Nova Scotia Nouvelle-Écosse + GAZ:00002574 Nunavut Nunavut + GAZ:00002563 Ontario Ontario + GAZ:00002572 Prince Edward Island Île-du-Prince-Édouard + GAZ:00002569 Quebec Québec + GAZ:00002564 Saskatchewan Saskatchewan + GAZ:00002576 Yukon Yukon + + +host age unit menu HostAgeUnitMenu Menu « Groupe d’âge de l’hôte » UO:0000035 month Mois + UO:0000036 year Année + + +sample collection date precision menu SampleCollectionDatePrecisionMenu Menu « Précision de la date de prélèvement des échantillons » UO:0000036 year Année + UO:0000035 month Mois + UO:0000033 day Jour + + +biomaterial extracted menu BiomaterialExtractedMenu Menu « Biomatériaux extraits » OBI:0000895 RNA (total) ARN (total) + OBI:0000869 RNA (poly-A) ARN (poly-A) + OBI:0002627 RNA (ribo-depleted) ARN (déplétion ribosomique) + GENEPIO:0100104 mRNA (messenger RNA) ARNm (ARN messager) + OBI:0002754 mRNA (cDNA) ARNm (ADNc) + + +signs and symptoms menu SignsAndSymptomsMenu Menu « Signes et symptômes » HP:0030829 Abnormal lung auscultation Auscultation pulmonaire anormale + HP:0000223 Abnormality of taste sensation Anomalie de la sensation gustative + HP:0041051 Ageusia (complete loss of taste) Agueusie (perte totale du goût) + HP:0031249 Parageusia (distorted sense of taste) Paragueusie (distorsion du goût) + HP:0000224 Hypogeusia (reduced sense of taste) Hypogueusie (diminution du goût) + HP:0004408 Abnormality of the sense of smell Anomalie de l’odorat + HP:0000458 Anosmia (lost sense of smell) Anosmie (perte de l’odorat) + HP:0004409 Hyposmia (reduced sense of smell) Hyposmie (diminution de l’odorat) + HP:0033677 Acute Respiratory Distress Syndrome Syndrome de détresse respiratoire aiguë ARDS + HP:0011446 Altered mental status Altération de l’état mental + HP:0100543 Cognitive impairment Déficit cognitif + HP:0001259 Coma Coma + HP:0001289 Confusion Confusion + HP:0031258 Delirium (sudden severe confusion) Délire (confusion grave et soudaine) + GENEPIO:0100061 Inability to arouse (inability to stay awake) Incapacité à se réveiller (incapacité à rester éveillé) + HP:0000737 Irritability Irritabilité + HP:0002371 Loss of speech Perte de la parole + HP:0011675 Arrhythmia Arythmie + HP:0025406 Asthenia (generalized weakness) Asthénie (faiblesse généralisée) + HP:0031352 Chest tightness or pressure Oppression ou pression thoracique + HP:0025145 Rigors (fever shakes) Frissons solennels (tremblements de fièvre) + HP:0025143 Chills (sudden cold sensation) Frissons (sensation soudaine de froid) Chills + HP:0030953 Conjunctival injection Injection conjonctivale + HP:0000509 Conjunctivitis (pink eye) Conjonctivite (yeux rouges) Conjunctivitis + MP:0001867 Coryza (rhinitis) Coryza (rhinite) + HP:0012735 Cough Toux + HP:0031246 Nonproductive cough (dry cough) Toux improductive (toux sèche) + HP:0031245 Productive cough (wet cough) Toux productive (toux grasse) + HP:0000961 Cyanosis (blueish skin discolouration) Cyanose (coloration bleuâtre de la peau) + HP:0001063 Acrocyanosis Acrocyanose + HP:0032556 Circumoral cyanosis (bluish around mouth) Cyanose péribuccale (bleuâtre autour de la bouche) + GENEPIO:0100062 Cyanotic face (bluish face) Visage cyanosé (visage bleuâtre) + GENEPIO:0100063 Central Cyanosis Cyanose centrale + GENEPIO:0100064 Cyanotic lips (bluish lips) Lèvres cyanosées (lèvres bleutées) + GENEPIO:0100065 Peripheral Cyanosis Cyanose périphérique + HP:0002094 Dyspnea (breathing difficulty) Dyspnée (difficulté à respirer) + HP:0002014 Diarrhea (watery stool) Diarrhée (selles aqueuses) Diarrhea, watery + MP:0031127 Dry gangrene Gangrène sèche + HP:0002383 Encephalitis (brain inflammation) Encéphalite (inflammation du cerveau) Encephalitis + HP:0001298 Encephalopathy Encéphalopathie + HP:0012378 Fatigue (tiredness) Fatigue Fatigue + HP:0001945 Fever Fièvre + GENEPIO:0100066 Fever (>=38°C) Fièvre (>= 38 °C) Fever + HP:0000206 Glossitis (inflammation of the tongue) Glossite (inflammation de la langue) + GENEPIO:0100067 Ground Glass Opacities (GGO) Hyperdensité en verre dépoli + HP:0002315 Headache Mal de tête + HP:0002105 Hemoptysis (coughing up blood) Hémoptysie (toux accompagnée de sang) + HP:0012417 Hypocapnia Hypocapnie + HP:0002615 Hypotension (low blood pressure) Hypotension (tension artérielle basse) + HP:0012418 Hypoxemia (low blood oxygen) Hypoxémie (manque d’oxygène dans le sang) + GENEPIO:0100068 Silent hypoxemia Hypoxémie silencieuse + HP:0011029 Internal hemorrhage (internal bleeding) Hémorragie interne + NCIT:C121416 Loss of Fine Movements Perte de mouvements fins + HP:0004396 Low appetite Perte d’appétit + HP:0033834 Malaise (general discomfort/unease) Malaise (malaise général) + HP:0031179 Meningismus/nuchal rigidity Méningisme/Raideur de la nuque + HP:0001324 Muscle weakness Faiblesse musculaire + HP:0001742 Nasal obstruction (stuffy nose) Obstruction nasale (nez bouché) + HP:0002018 Nausea Nausées + HP:0000421 Nose bleed Saignement de nez + GENEPIO:0100069 Otitis Otite + HP:0012531 Pain Douleur + HP:0002027 Abdominal pain Douleur abdominale + HP:0002829 Arthralgia (painful joints) Arthralgie (articulations douloureuses) + HP:0100749 Chest pain Douleur thoracique + HP:0033771 Pleuritic chest pain Douleur thoracique pleurétique + HP:0003326 Myalgia (muscle pain) Myalgie (douleur musculaire) + HP:0025439 Pharyngitis (sore throat) Pharyngite (mal de gorge) + GENEPIO:0100070 Pharyngeal exudate Exsudat pharyngé + HP:0002202 Pleural effusion Épanchement pleural + HP:0002090 Pneumonia Pneumonie + HP:0033696 Pseudo-chilblains Pseudo-engelures + GENEPIO:0100072 Pseudo-chilblains on fingers (covid fingers) Pseudo-engelures sur les doigts (doigts de la COVID) + GENEPIO:0100073 Pseudo-chilblains on toes (covid toes) Pseudo-engelures sur les orteils (orteils de la COVID) + HP:0000988 Rash Éruption cutanée + HP:0031417 Rhinorrhea (runny nose) Rhinorrhée (écoulement nasal) + HP:0001250 Seizure Crise d’épilepsie + HP:0020219 Motor seizure Crise motrice + HP:0025144 Shivering (involuntary muscle twitching) Tremblement (contractions musculaires involontaires) + HP:0001350 Slurred speech Troubles de l’élocution + HP:0025095 Sneezing Éternuements + HP:0033709 Sputum Production Production d’expectoration + HP:0001297 Stroke Accident vasculaire cérébral + HP:0002716 Swollen Lymph Nodes Ganglions lymphatiques enflés + HP:0002789 Tachypnea (accelerated respiratory rate) Tachypnée (fréquence respiratoire accélérée) + HP:0002321 Vertigo (dizziness) Vertige (étourdissement) + HP:0002013 Vomiting (throwing up) Vomissements + + +host vaccination status menu HostVaccinationStatusMenu Menu « Statut de vaccination de l’hôte » GENEPIO:0100100 Fully Vaccinated Entièrement vacciné + GENEPIO:0100101 Partially Vaccinated Partiellement vacciné + GENEPIO:0100102 Not Vaccinated Non vacciné + + +prior SARS-CoV-2 antiviral treatment menu PriorSarsCov2AntiviralTreatmentMenu Menu « Traitement antiviral contre une infection antérieure par le SRAS-CoV-2 » GENEPIO:0100037 Prior antiviral treatment Traitement antiviral antérieur + GENEPIO:0100233 No prior antiviral treatment Aucun traitement antiviral antérieur + + +NML submitted specimen type menu NmlSubmittedSpecimenTypeMenu Menu « Types d’échantillons soumis au LNM » OBI:0002600 Swab Écouvillon + OBI:0000880 RNA ARN + OBI:0002754 mRNA (cDNA) ARNm (ADNc) + OBI:0001010 Nucleic acid Acide nucléique + GENEPIO:0001619 Not Applicable Sans objet + + +Related specimen relationship type menu RelatedSpecimenRelationshipTypeMenu Menu « Types de relations entre spécimens associés » HP:0011009 Acute Infection aiguë + GENEPIO:0101016 Chronic (prolonged) infection investigation Enquête sur l’infection chronique (prolongée) + Convalescent Phase de convalescence + Familial Forme familiale + EFO:0009642 Follow-up Suivi + Reinfection testing Tests de réinfection + Previously Submitted Soumis précédemment + Sequencing/bioinformatics methods development/validation Développement et validation de méthodes bioinformatiques ou de séquençage + Specimen sampling methods testing Essai des méthodes de prélèvement des échantillons + + +pre-existing conditions and risk factors menu PreExistingConditionsAndRiskFactorsMenu Menu « Conditions préexistantes et des facteurs de risque » VO:0004925 Age 60+ 60 ans et plus + HP:0001903 Anemia Anémie + HP:0002039 Anorexia Anorexie + NCIT:C92743 Birthing labor Travail ou accouchement + NCIT:C80693 Bone marrow failure Insuffisance médullaire + MONDO:0004992 Cancer Cancer + MONDO:0007254 Breast cancer Cancer du sein + MONDO:0005575 Colorectal cancer Cancer colorectal + DOID:2531 Hematologic malignancy (cancer of the blood) Hématopathie maligne (cancer du sang) + MONDO:0008903 Lung cancer Cancer du poumon + MONDO:0024880 Metastatic disease Maladie métastatique + NCIT:C16212 Cancer treatment Traitement du cancer + NCIT:C157740 Cancer surgery Chirurgie pour un cancer + NCIT:C15632 Chemotherapy Chimiothérapie + NCIT:C15360 Adjuvant chemotherapy Chimiothérapie adjuvante + NCIT:C3079 Cardiac disorder Trouble cardiaque + HP:0011675 Arrhythmia Arythmie + MONDO:0005267 Cardiac disease Maladie cardiaque + HP:0001638 Cardiomyopathy Myocardiopathie + GENEPIO:0100074 Cardiac injury Lésion cardiaque + HP:0000822 Hypertension (high blood pressure) Hypertension (tension artérielle élevée) + HP:0002615 Hypotension (low blood pressure) Hypotension (tension artérielle basse) + HP:0011410 Cesarean section Césarienne + GENEPIO:0100075 Chronic cough Toux chronique + GENEPIO:0100076 Chronic gastrointestinal disease Maladie gastro-intestinale chronique + HP:0006528 Chronic lung disease Maladie pulmonaire chronique + NCIT:C211 Corticosteroids Corticostéroïdes + HP:0000819 Diabetes mellitus (diabetes) Diabète sucré (diabète) + HP:0100651 Type I diabetes mellitus (T1D) Diabète sucré de type I + HP:0005978 Type II diabetes mellitus (T2D) Diabète sucré de type II + HP:0000964 Eczema Eczéma + HP:0003111 Electrolyte disturbance Perturbation de l’équilibre électrolytique + HP:0002901 Hypocalcemia Hypocalcémie + HP:0002900 Hypokalemia Hypokaliémie + HP:0002917 Hypomagnesemia Hypomagnésémie + HP:0002383 Encephalitis (brain inflammation) Encéphalite (inflammation du cerveau) + MONDO:0005027 Epilepsy Épilepsie + NCIT:C15248 Hemodialysis Hémodialyse + MONDO:0044348 Hemoglobinopathy Hémoglobinopathie + MONDO:0005109 Human immunodeficiency virus (HIV) Virus de l’immunodéficience humaine (VIH) + MONDO:0012268 Acquired immunodeficiency syndrome (AIDS) Syndrome d’immunodéficience acquise (SIDA) + NCIT:C16118 HIV and antiretroviral therapy (ART) VIH et traitement antirétroviral + NCIT:C14139 Immunocompromised Immunodéficience + MONDO:0004670 Lupus Lupus + MONDO:0005265 Inflammatory bowel disease (IBD) Maladie inflammatoire chronique de l’intestin (MICI) + HP:0002583 Colitis Colite + HP:0100279 Ulcerative colitis Colite ulcéreuse + HP:0100280 Crohn's disease Maladie de Crohn + NCIT:C3149 Renal disorder Trouble rénal + MONDO:0005240 Renal disease Maladie rénale + HP:0012622 Chronic renal disease Maladie rénale chronique + HP:0000083 Renal failure Insuffisance rénale + MONDO:0005154 Liver disease Maladie du foie + NCIT:C113609 Chronic liver disease Maladie chronique du foie + HP:0001397 Fatty liver disease (FLD) Stéatose hépatique + HP:0003326 Myalgia (muscle pain) Myalgie (douleur musculaire) + MONDO:0005404 Myalgic encephalomyelitis (chronic fatigue syndrome) Encéphalomyélite myalgique (syndrome de fatigue chronique) + MONDO:0005071 Neurological disorder Trouble neurologique + MONDO:0019056 Neuromuscular disorder Trouble neuromusculaire + HP:0001513 Obesity Obésité + MONDO:0005139 Severe obesity Obésité sévère + MONDO:0005087 Respiratory disorder Trouble respiratoire + HP:0002099 Asthma Asthme + HP:0004469 Chronic bronchitis Bronchite chronique + HP:0006510 Chronic obstructive pulmonary disease Maladie pulmonaire obstructive chronique + HP:0002097 Emphysema Emphysème + MONDO:0005275 Lung disease Maladie pulmonaire + HP:0006528 Chronic lung disease Maladie pulmonaire chronique + HP:0002206 Pulmonary fibrosis Fibrose pulmonaire + HP:0002090 Pneumonia Pneumonie + HP:0002878 Respiratory failure Insuffisance respiratoire + HP:0033677 Adult respiratory distress syndrome Syndrome de détresse respiratoire de l’adulte + MONDO:0009971 Newborn respiratory distress syndrome Syndrome de détresse respiratoire du nouveau-né + MONDO:0018076 Tuberculosis Tuberculose + GENEPIO:0100077 Postpartum (≤6 weeks) Post-partum (≤6 semaines) + NCIT:C25742 Pregnancy Grossesse + MONDO:0005554 Rheumatic disease Maladie rhumatismale + MONDO:0011382 Sickle cell disease Drépanocytose + NBO:0001845 Substance use Consommation de substances + MONDO:0002046 Alcohol abuse Consommation abusive d’alcool + GENEPIO:0100078 Drug abuse Consommation abusive de drogues + GENEPIO:0100079 Injection drug abuse Consommation abusive de drogues injectables + NBO:0015005 Smoking Tabagisme + NCIT:C173621 Vaping Vapotage + HP:0002789 Tachypnea (accelerated respiratory rate) Tachypnée (fréquence respiratoire accélérée) + NCIT:C159659 Transplant Transplantation + NCIT:C131759 Hematopoietic stem cell transplant (bone marrow transplant) Greffe de cellules souches hématopoïétiques (greffe de moelle osseuse) + GENEPIO:0100080 Cardiac transplant Transplantation cardiaque + NCIT:C157332 Kidney transplant Greffe de rein + GENEPIO:0100081 Liver transplant Greffe de foie + + +variant designation menu VariantDesignationMenu Menu « Désignation des variants » GENEPIO:0100082 Variant of Concern (VOC) Variant préoccupant + GENEPIO:0100083 Variant of Interest (VOI) Variant d’intérêt + GENEPIO:0100279 Variant Under Monitoring (VUM) Variante sous surveillance + + +variant evidence menu VariantEvidenceMenu Menu « Preuves de variants » CIDO:0000019 RT-qPCR RT-qPCR + CIDO:0000027 Sequencing Séquençage + + +complications menu ComplicationsMenu Menu « Complications » HP:0500165 Abnormal blood oxygen level Taux anormal d’oxygène dans le sang + HP:0001919 Acute kidney injury Lésions rénales aiguës + MONDO:0015796 Acute lung injury Lésions pulmonaires aiguës + GENEPIO:0100092 Ventilation induced lung injury (VILI) Lésions pulmonaires causées par la ventilation + MONDO:0001208 Acute respiratory failure Insuffisance respiratoire aiguë + HP:0011675 Arrhythmia (complication) Arythmie (complication) + HP:0001649 Tachycardia Tachycardie + HP:0031677 Polymorphic ventricular tachycardia (VT) Tachycardie ventriculaire polymorphe + GENEPIO:0100084 Tachyarrhythmia Tachyarythmie + GENEPIO:0100074 Cardiac injury Lésions cardiaques + HP:0001695 Cardiac arrest Arrêt cardiaque + HP:0030149 Cardiogenic shock Choc cardiogénique + HP:0001977 Blood clot Caillot sanguin + HP:0004420 Arterial clot Caillot artériel + HP:0002625 Deep vein thrombosis (DVT) Thrombose veineuse profonde + HP:0002204 Pulmonary embolism (PE) Embolie pulmonaire + HP:0001638 Cardiomyopathy Myocardiopathie + MONDO:0024619 Central nervous system invasion Envahissement du système nerveux central + HP:0001297 Stroke (complication) Accident vasculaire cérébral (complication) + MONDO:0003346 Central Nervous System Vasculitis Vascularite du système nerveux central + HP:0002140 Acute ischemic stroke Accident vasculaire cérébral ischémique aigu + HP:0001259 Coma Coma + HP:0011097 Convulsions Convulsions + NCIT:C171562 COVID-19 associated coagulopathy (CAC) Coagulopathie associée à la COVID-19 (CAC) + MONDO:0009061 Cystic fibrosis Fibrose kystique + MONDO:0600008 Cytokine release syndrome Syndrome de libération de cytokines + MPATH:108 Disseminated intravascular coagulation (DIC) Coagulation intravasculaire disséminée + HP:0001298 Encephalopathy Encéphalopathie + GENEPIO:0100088 Fulminant myocarditis Myocardite fulminante + MONDO:0016218 Guillain-Barré syndrome Syndrome de Guillain-Barré + HP:0011029 Internal hemorrhage (complication; internal bleeding) Hémorragie interne (complication) + MONDO:0013792 Intracerebral haemorrhage Hémorragie intracérébrale + MONDO:0012727 Kawasaki disease Maladie de Kawasaki + GENEPIO:0100089 Complete Kawasaki disease Maladie de Kawasaki complète + GENEPIO:0100090 Incomplete Kawasaki disease Maladie de Kawasaki incomplète + HP:0001410 Liver dysfunction Trouble hépatique + GENEPIO:0100091 Acute liver injury Lésions hépatiques aiguës + MONDO:0100233 Long COVID-19 COVID-19 longue + HP:0001287 Meningitis Méningite + HP:0002076 Migraine Migraine + HP:0005268 Miscarriage Fausses couches + MONDO:0100163 Multisystem inflammatory syndrome in children (MIS-C) Syndrome inflammatoire multisystémique chez les enfants + MONDO:0100319 Multisystem inflammatory syndrome in adults (MIS-A) Syndrome inflammatoire multisystémique chez les adultes + GENEPIO:0100093 Muscle injury Lésion musculaire + MONDO:0005404 Myalgic encephalomyelitis (ME) Encéphalomyélite myalgique (EM) + MONDO:0005068 Myocardial infarction (heart attack) Infarctus du myocarde (crise cardiaque) + MONDO:0004781 Acute myocardial infarction Infarctus aigu du myocarde + MONDO:0041656 ST-segment elevation myocardial infarction Infarctus du myocarde avec sus-décalage du segment ST + HP:0001700 Myocardial injury Lésions du myocarde + NCIT:C168498 Neonatal complications Complications néonatales + GENEPIO:0100085 Noncardiogenic pulmonary edema Œdème pulmonaire non cardiogénique + HP:0033677 Acute respiratory distress syndrome (ARDS) Syndrome de détresse respiratoire aiguë (SDRA) + NCIT:C171551 COVID-19 associated ARDS (CARDS) SDRA associé à la COVID-19 (SDRAC) + GENEPIO:0100086 Neurogenic pulmonary edema (NPE) Œdème pulmonaire neurogène + GENEPIO:0100094 Organ failure Défaillance des organes + HP:0001635 Heart failure Insuffisance cardiaque + MONDO:0100192 Liver failure Insuffisance hépatique + HP:0003470 Paralysis Paralysie + HP:0002107 Pneumothorax (collapsed lung) Pneumothorax (affaissement du poumon) + HP:0002108 Spontaneous pneumothorax Pneumothorax spontané + MONDO:0002075 Spontaneous tension pneumothorax Pneumothorax spontané sous tension + HP:0002090 Pneumonia (complication) Pneumonie (complication) + NCIT:C171550 COVID-19 pneumonia Pneumonie liée à la COVID-19 + HP:0001197 Pregancy complications Complications de la grossesse + HP:0003201 Rhabdomyolysis Rhabdomyolyse + IDO:0000567 Secondary infection Infection secondaire + GENEPIO:0100095 Secondary staph infection Infection staphylococcique secondaire + GENEPIO:0100096 Secondary strep infection Infection streptococcique secondaire + HP:0001250 Seizure (complication) Crise d’épilepsie (complication) + HP:0020219 Motor seizure Crise motrice + HP:0100806 Sepsis/Septicemia Sepsie/Septicémie + IDO:0000636 Sepsis Sepsie + NCIT:C3364 Septicemia Septicémie + HP:0031273 Shock Choc + GENEPIO:0100097 Hyperinflammatory shock Choc hyperinflammatoire + GENEPIO:0100098 Refractory cardiogenic shock Choc cardiogénique réfractaire + GENEPIO:0100099 Refractory cardiogenic plus vasoplegic shock Choc cardiogénique et vasoplégique réfractaire + NCIT:C35018 Septic shock Choc septique + HP:0002633 Vasculitis Vascularite + + +vaccine name menu VaccineNameMenu Menu « Noms de vaccins » GENEPIO:0100308 Astrazeneca (Vaxzevria) AstraZeneca (Vaxzevria) + GENEPIO:0100307 Johnson & Johnson (Janssen) Johnson & Johnson (Janssen) + GENEPIO:0100304 Moderna (Spikevax) Moderna (Spikevax) + GENEPIO:0100305 Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) + GENEPIO:0100306 Pfizer-BioNTech (Comirnaty Pediatric) Pfizer-BioNTech (Comirnaty, formule pédiatrique) + + +anatomical material menu AnatomicalMaterialMenu Menu « Matières anatomiques » UBERON:0000178 Blood Sang + UBERON:0006314 Fluid Liquide + UBERON:0001836 Saliva Salive + UBERON:0001359 Fluid (cerebrospinal (CSF)) Liquide (céphalorachidien) + UBERON:0002409 Fluid (pericardial) Liquide (péricardique) + UBERON:0001087 Fluid (pleural) Liquide (pleural) + UBERON:0036243 Fluid (vaginal) Sécrétions (vaginales) + UBERON:0000173 Fluid (amniotic) Liquide (amniotique) + UBERON:0000479 Tissue Tissu + + +anatomical part menu AnatomicalPartMenu Menu « Parties anatomiques » UBERON:0001245 Anus Anus + UBERON:0006956 Buccal mucosa Muqueuse buccale + UBERON:0002114 Duodenum Duodénum + UBERON:0000970 Eye Œil + UBERON:0000160 Intestine Intestin + UBERON:0001558 Lower respiratory tract Voies respiratoires inférieures + UBERON:0002185 Bronchus Bronches + UBERON:0002048 Lung Poumon + UBERON:0002186 Bronchiole Bronchiole + UBERON:0002169 Alveolar sac Sac alvéolaire + UBERON:0009778 Pleural sac Sac pleural + UBERON:0002402 Pleural cavity Cavité pleurale + UBERON:0003126 Trachea Trachée + UBERON:0001052 Rectum Rectum + UBERON:0001003 Skin Peau + UBERON:0000945 Stomach Estomac + UBERON:0001557 Upper respiratory tract Voies respiratoires supérieures + UBERON:2001427 Anterior Nares Narines antérieures + UBERON:0001043 Esophagus Œsophage + UBERON:0002453 Ethmoid sinus Sinus ethmoïdal + UBERON:0001707 Nasal Cavity Cavité nasale + UBERON:0005921 Middle Nasal Turbinate Cornet nasal moyen + UBERON:0005922 Inferior Nasal Turbinate Cornet nasal inférieur + UBERON:0001728 Nasopharynx (NP) Nasopharynx + UBERON:0001729 Oropharynx (OP) Oropharynx + UBERON:0000341 Pharynx (throat) Pharynx (gorge) + + +body product menu BodyProductMenu Menu « Produit corporel » UBERON:0001913 Breast Milk Lait maternel + UBERON:0001988 Feces Selles + UBERON:0006530 Fluid (seminal) Sperme + UBERON:0000912 Mucus Mucus + UBERON:0007311 Sputum Expectoration + UBERON:0001089 Sweat Sueur + UBERON:0001827 Tear Larme + UBERON:0001088 Urine Urine + + +prior SARS-CoV-2 infection menu PriorSarsCov2InfectionMenu Menu « Infection antérieure par le SRAS-CoV-2 » GENEPIO:0100037 Prior infection Infection antérieure + GENEPIO:0100233 No prior infection Aucune infection antérieure + + +environmental material menu EnvironmentalMaterialMenu Menu « Matériel environnemental » ENVO:03501208 Air vent Évent d’aération + ENVO:00003896 Banknote Billet de banque + ENVO:03501209 Bed rail Côté de lit + ENVO:01000486 Building floor Plancher du bâtiment + ENVO:02000058 Cloth Tissu + ENVO:03501210 Control panel Panneau de contrôle + ENVO:03501220 Door Porte + ENVO:03501211 Door handle Poignée de porte + OBI:0002787 Face mask Masque + OBI:0002791 Face shield Écran facial + FOODON:00002403 Food Nourriture + FOODON:03490100 Food packaging Emballages alimentaires + ENVO:01000481 Glass Verre + ENVO:03501212 Handrail Main courante + OBI:0002796 Hospital gown Jaquette d’hôpital + ENVO:03501213 Light switch Interrupteur + ENVO:03501214 Locker Casier + OBI:0002790 N95 mask Masque N95 + ENVO:03501215 Nurse call button Bouton d’appel de l’infirmière + ENVO:03501256 Paper Papier + ENVO:01000060 Particulate matter Matière particulaire + ENVO:01000404 Plastic Plastique + GENEPIO:0100025 PPE gown Blouse (EPI) + ENVO:00002018 Sewage Eaux usées + ENVO:01000990 Sink Évier + ENVO:00001998 Soil Sol + ENVO:03501216 Stainless steel Acier inoxydable + ENVO:03501217 Tissue paper Mouchoirs + ENVO:03501218 Toilet bowl Cuvette + ENVO:00002006 Water Eau + ENVO:00002001 Wastewater Eaux usées + ENVO:03501219 Window Fenêtre + ENVO:00002040 Wood Bois + + +environmental site menu EnvironmentalSiteMenu Menu « Site environnemental » ENVO:03501135 Acute care facility Établissement de soins de courte durée + ENVO:00003040 Animal house Refuge pour animaux + ENVO:01000422 Bathroom Salle de bain + ENVO:03501136 Clinical assessment centre Centre d’évaluation clinique + ENVO:03501127 Conference venue Lieu de la conférence + ENVO:03501121 Corridor couloir + ENVO:01000927 Daycare Garderie + ENVO:03501145 Emergency room (ER) Salle d’urgence + ENVO:03501186 Family practice clinic Clinique de médecine familiale + ENVO:03501196 Group home Foyer de groupe + ENVO:03501133 Homeless shelter Refuge pour sans-abri + ENVO:00002173 Hospital Hôpital + ENVO:03501152 Intensive Care Unit (ICU) Unité de soins intensifs + ENVO:03501194 Long Term Care Facility Établissement de soins de longue durée + ENVO:03501180 Patient room Chambre du patient + ENVO:03501204 Prison Prison + ENVO:01000536 Production Facility Installation de production + ENVO:03501130 School École + ENVO:00003043 Sewage Plant Usine d’épuration des eaux usées + ENVO:03501109 Subway train Métro + ENVO:00000467 University campus Campus de l’université + ENVO:03501198 Wet market Marché traditionnel de produits frais + + +collection method menu CollectionMethodMenu Menu « Méthode de prélèvement » NCIT:C52009 Amniocentesis Amniocentèse + NCIT:C15631 Aspiration Aspiration + GENEPIO:0100028 Suprapubic Aspiration Aspiration sus-pubienne + GENEPIO:0100029 Tracheal aspiration Aspiration trachéale + GENEPIO:0100030 Vacuum Aspiration Aspiration sous vide + OBI:0002650 Biopsy Biopsie + OBI:0002651 Needle Biopsy Biopsie à l’aiguille + OBI:0302885 Filtration Filtration + GENEPIO:0100031 Air filtration Filtration de l’air + OBI:0600044 Lavage Lavage + GENEPIO:0100032 Bronchoalveolar lavage (BAL) Lavage broncho-alvéolaire (LBA) + GENEPIO:0100033 Gastric Lavage Lavage gastrique + NCIT:C15327 Lumbar Puncture Ponction lombaire + MMO:0000344 Necropsy Nécropsie + NCIT:C28221 Phlebotomy Phlébotomie + GENEPIO:0002116 Rinsing Rinçage + GENEPIO:0100034 Saline gargle (mouth rinse and gargle) Gargarisme avec saline (rince-bouche) + GENEPIO:0100035 Scraping Grattage + GENEPIO:0002117 Swabbing Écouvillonnage + GENEPIO:0100036 Finger Prick Piqûre du doigt + GENEPIO:0100038 Washout Tear Collection Lavage – Collecte de larmes + + +collection device menu CollectionDeviceMenu Menu « Dispositif de prélèvement » ENVO:00003968 Air filter Filtre à air + OBI:0002859 Blood Collection Tube Tube de prélèvement sanguin + OBI:0002826 Bronchoscope Bronchoscope + OBI:0002088 Collection Container Récipient à échantillons + GENEPIO:0100026 Collection Cup Godet à échantillons + OBI:0002825 Fibrobronchoscope Brush Brosse à fibrobronchoscope + GENEPIO:0100103 Filter Filtre + OBI:0002827 Fine Needle Aiguille fine + OBI:0002858 Microcapillary tube Micropipette de type capillaire + OBI:0001128 Micropipette Micropipette + OBI:0000436 Needle Aiguille + OBI:0002860 Serum Collection Tube Tube de prélèvement du sérum + OBI:0002861 Sputum Collection Tube Tube de prélèvement des expectorations + OBI:0002831 Suction Catheter Cathéter d’aspiration + GENEPIO:0100027 Swab Écouvillon + OBI:0002862 Urine Collection Tube Tube de prélèvement d’urine + OBI:0002866 Virus Transport Medium Milieu de transport viral + + +host (scientific name) menu HostScientificNameMenu Menu « Hôte (nom scientifique) » NCBITaxon:9606 Homo sapiens Homo sapiens + NCBITaxon:9913 Bos taurus Bos taureau + NCBITaxon:9615 Canis lupus familiaris Canis lupus familiaris + NCBITaxon:9397 Chiroptera Chiroptères + NCBITaxon:8930 Columbidae Columbidés + NCBITaxon:9685 Felis catus Felis catus + NCBITaxon:9031 Gallus gallus Gallus gallus + NCBITaxon:9973 Manis Manis + NCBITaxon:9974 Manis javanica Manis javanica + NCBITaxon:452646 Neovison vison Neovison vison + NCBITaxon:9689 Panthera leo Panthera leo + NCBITaxon:9694 Panthera tigris Panthera tigris + NCBITaxon:58055 Rhinolophidae Rhinolophidés + NCBITaxon:59477 Rhinolophus affinis Rhinolophus affinis + NCBITaxon:9825 Sus scrofa domesticus Sus scrofa domesticus + NCBITaxon:9673 Viverridae Viverridés + +host (common name) menu HostCommonNameMenu Menu « Hôte (nom commun) » NCBITaxon:9606 Human Humain + NCBITaxon:9397 Bat Chauve-souris + NCBITaxon:9685 Cat Chat + NCBITaxon:9031 Chicken Poulet + NCBITaxon:9673 Civets Civettes + NCBITaxon:9913 Cow Vache bovine + NCBITaxon:9615 Dog Chien + NCBITaxon:9689 Lion Lion + NCBITaxon:452646 Mink Vison + NCBITaxon:9973 Pangolin Pangolin + NCBITaxon:9825 Pig Cochon porcine + NCBITaxon:8930 Pigeon Pigeon + NCBITaxon:9694 Tiger Tigre + + +host health state menu HostHealthStateMenu Menu « État de santé de l’hôte » NCIT:C3833 Asymptomatic Asymptomatique + NCIT:C28554 Deceased Décédé + NCIT:C115935 Healthy En santé + NCIT:C49498 Recovered Rétabli + NCIT:C25269 Symptomatic Symptomatique + + +host health status details menu HostHealthStatusDetailsMenu Menu « Détails de l’état de santé de l’hôte » NCIT:C25179 Hospitalized Hospitalisé + GENEPIO:0100045 Hospitalized (Non-ICU) Hospitalisé (hors USI) + GENEPIO:0100046 Hospitalized (ICU) Hospitalisé (USI) + NCIT:C70909 Mechanical Ventilation Ventilation artificielle + GENEPIO:0100047 Medically Isolated Isolement médical + GENEPIO:0100048 Medically Isolated (Negative Pressure) Isolement médical (pression négative) + NCIT:C173768 Self-quarantining Quarantaine volontaire + + +host health outcome menu HostHealthOutcomeMenu Menu « Résultats sanitaires de l’hôte » NCIT:C28554 Deceased Décédé + NCIT:C25254 Deteriorating Détérioration + NCIT:C49498 Recovered Rétabli + NCIT:C30103 Stable Stabilisation + + +organism menu OrganismMenu Menu « Organisme » NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 Coronavirus du syndrome respiratoire aigu sévère 2 + NCBITaxon:2709072 RaTG13 RaTG13 + GENEPIO:0100000 RmYN02 RmYN02 + + +purpose of sampling menu PurposeOfSamplingMenu Menu « Objectif de l’échantillonnage » GENEPIO:0100001 Cluster/Outbreak investigation Enquête sur les grappes et les éclosions + GENEPIO:0100002 Diagnostic testing Tests de diagnostic + GENEPIO:0100003 Research Recherche + GENEPIO:0100004 Surveillance Surveillance + + +purpose of sequencing menu PurposeOfSequencingMenu Menu « Objectif du séquençage » GENEPIO:0100005 Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) + GENEPIO:0100006 Targeted surveillance (non-random sampling) Surveillance ciblée (échantillonnage non aléatoire) + GENEPIO:0100007 Priority surveillance project Projet de surveillance prioritaire + GENEPIO:0100008 Screening for Variants of Concern (VoC) Dépistage des variants préoccupants + GENEPIO:0100273 Sample has epidemiological link to Variant of Concern (VoC) Lien épidémiologique entre l’échantillon et le variant préoccupant + GENEPIO:0100274 Sample has epidemiological link to Omicron Variant Lien épidémiologique entre l’échantillon et le variant Omicron + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) Surveillance longitudinale (échantillonnage répété des individus) + GENEPIO:0100842 Chronic (prolonged) infection surveillance Surveillance des infections chroniques (prolongées) + GENEPIO:0100010 Re-infection surveillance Surveillance des réinfections + GENEPIO:0100011 Vaccine escape surveillance Surveillance de l’échappement vaccinal + GENEPIO:0100012 Travel-associated surveillance Surveillance associée aux voyages + GENEPIO:0100013 Domestic travel surveillance Surveillance des voyages intérieurs + GENEPIO:0100275 Interstate/ interprovincial travel surveillance Surveillance des voyages entre les États ou les provinces + GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance Surveillance des voyages dans les États ou les provinces + GENEPIO:0100014 International travel surveillance Surveillance des voyages internationaux + GENEPIO:0100015 Surveillance of international border crossing by air travel or ground transport Surveillance du franchissement des frontières internationales par voie aérienne ou terrestre + GENEPIO:0100016 Surveillance of international border crossing by air travel Surveillance du franchissement des frontières internationales par voie aérienne + GENEPIO:0100017 Surveillance of international border crossing by ground transport Surveillance du franchissement des frontières internationales par voie terrestre + GENEPIO:0100018 Surveillance from international worker testing Surveillance à partir de tests auprès des travailleurs étrangers + GENEPIO:0100019 Cluster/Outbreak investigation Enquête sur les grappes et les éclosions + GENEPIO:0100020 Multi-jurisdictional outbreak investigation Enquête sur les éclosions multijuridictionnelles + GENEPIO:0100021 Intra-jurisdictional outbreak investigation Enquête sur les éclosions intrajuridictionnelles + GENEPIO:0100022 Research Recherche + GENEPIO:0100023 Viral passage experiment Expérience de transmission virale + GENEPIO:0100024 Protocol testing experiment Expérience du test de protocole + GENEPIO:0100356 Retrospective sequencing Séquençage rétrospectif + + +specimen processing menu SpecimenProcessingMenu Menu « Traitement des échantillons » GENEPIO:0100039 Virus passage Transmission du virus + GENEPIO:0100040 RNA re-extraction (post RT-PCR) Rétablissement de l’extraction de l’ARN (après RT-PCR) + OBI:0600016 Specimens pooled Échantillons regroupés + + +lab host menu LabHostMenu Menu « Laboratoire hôte » GENEPIO:0100041 293/ACE2 cell line Lignée cellulaire 293/ACE2 + BTO:0000195 Caco2 cell line Lignée cellulaire Caco2 + BTO:0002750 Calu3 cell line Lignée cellulaire Calu3 + GENEPIO:0100042 EFK3B cell line Lignée cellulaire EFK3B + BTO:0002181 HEK293T cell line Lignée cellulaire HEK293T + GENEPIO:0100043 HRCE cell line Lignée cellulaire HRCE + BTO:0001950 Huh7 cell line Lignée cellulaire Huh7 + CLO:0007330 LLCMk2 cell line Lignée cellulaire LLCMk2 + BTO:0000836 MDBK cell line Lignée cellulaire MDBK + BTO:0002924 NHBE cell line Lignée cellulaire NHBE + BTO:0001865 PK-15 cell line Lignée cellulaire PK-15 + BTO:0002909 RK-13 cell line Lignée cellulaire RK-13 + BTO:0002035 U251 cell line Lignée cellulaire U251 + BTO:0001444 Vero cell line Lignée cellulaire Vero + BTO:0004755 Vero E6 cell line Lignée cellulaire Vero E6 + GENEPIO:0100044 VeroE6/TMPRSS2 cell line Lignée cellulaire VeroE6/TMPRSS2 + + +host disease menu UmbrellaBioprojectAccessionMenu Menu « Maladie de l’hôte » MONDO:0100096 COVID-19 COVID-19 + + +host age bin menu HostAgeBinMenu Menu « Groupe d’âge de l’hôte » GENEPIO:0100049 0 - 9 0 - 9 + GENEPIO:0100050 10 - 19 10 - 19 + GENEPIO:0100051 20 - 29 20 - 29 + GENEPIO:0100052 30 - 39 30 - 39 + GENEPIO:0100053 40 - 49 40 - 49 + GENEPIO:0100054 50 - 59 50 - 59 + GENEPIO:0100055 60 - 69 60 - 69 + GENEPIO:0100056 70 - 79 70 - 79 + GENEPIO:0100057 80 - 89 80 - 89 + GENEPIO:0100058 90 - 99 90 - 99 90+ + GENEPIO:0100059 100+ 100+ 90+ + + +host gender menu HostGenderMenu Menu « Genre de l’hôte » NCIT:C46110 Female Femme + NCIT:C46109 Male Homme + GSSO:000132 Non-binary gender Non binaire + GSSO:004004 Transgender (assigned male at birth) Transgenre (sexe masculin à la naissance) + GSSO:004005 Transgender (assigned female at birth) Transgenre (sexe féminin à la naissance) + NCIT:C110959 Undeclared Non déclaré + + +exposure event menu ExposureEventMenu Menu « Événement d’exposition » GENEPIO:0100237 Mass Gathering Rassemblement de masse + GENEPIO:0100240 Agricultural Event Événement agricole + GENEPIO:0100238 Convention Convention + GENEPIO:0100239 Convocation Convocation + GENEPIO:0100417 Recreational Event Événement récréatif + GENEPIO:0100418 Concert Concert + GENEPIO:0100419 Sporting Event Événement sportif + GENEPIO:0100241 Religious Gathering Rassemblement religieux + GENEPIO:0100242 Mass Messe + PCO:0000033 Social Gathering Rassemblement social + PCO:0000039 Baby Shower Réception-cadeau pour bébé + PCO:0000034 Community Event Événement communautaire + GENEPIO:0100243 Family Gathering Rassemblement familial + GENEPIO:0100244 Family Reunion Réunion de famille + GENEPIO:0100245 Funeral Funérailles + PCO:0000035 Party Fête + PCO:0000037 Potluck Repas-partage + PCO:0000038 Wedding Mariage + Other exposure event Autre événement d’exposition + + +exposure contact level menu ExposureContactLevelMenu Menu « Niveau de contact de l’exposition » GENEPIO:0100357 Contact with infected individual Contact avec une personne infectée + TRANS:0000001 Direct contact (direct human-to-human contact) Contact direct (contact interhumain) + GENEPIO:0100246 Indirect contact Contact indirect + GENEPIO:0100247 Close contact (face-to-face, no direct contact) Contact étroit (contact personnel, aucun contact étroit) + GENEPIO:0100248 Casual contact Contact occasionnel + + +host role menu HostRoleMenu Menu « Rôle de l’hôte » GENEPIO:0100249 Attendee Participant + OMRSE:00000058 Student Étudiant + OMRSE:00000030 Patient Patient + NCIT:C25182 Inpatient Patient hospitalisé + NCIT:C28293 Outpatient Patient externe + GENEPIO:0100250 Passenger Passager + GENEPIO:0100251 Resident Résident + GENEPIO:0100252 Visitor Visiteur + GENEPIO:0100253 Volunteer Bénévole + GENEPIO:0100254 Work Travail + GENEPIO:0100255 Administrator Administrateur + Child Care/Education Worker Travailleur en garderie ou en éducation + Essential Worker Travailleur essentiel + GENEPIO:0100256 First Responder Premier intervenant + GENEPIO:0100257 Firefighter Pompier + GENEPIO:0100258 Paramedic Ambulancier + GENEPIO:0100259 Police Officer Policier + GENEPIO:0100334 Healthcare Worker Travailleur de la santé + GENEPIO:0100420 Community Healthcare Worker Agent de santé communautaire + GENEPIO:0100262 Laboratory Worker Travailleur de laboratoire + OMRSE:00000014 Nurse Infirmière + GENEPIO:0100263 Personal Care Aid Aide aux soins personnels + GENEPIO:0100264 Pharmacist Pharmacien + OMRSE:00000013 Physician Médecin + GENEPIO:0100260 Housekeeper Aide-ménagère + International worker Travailleur international + GENEPIO:0100261 Kitchen Worker Aide de cuisine + GENEPIO:0100354 Rotational Worker Travailleur en rotation + GENEPIO:0100355 Seasonal Worker Travailleur saisonnier + Transport Worker Ouvrier des transports + Transport Truck Driver Chauffeur de camion de transport + GENEPIO:0100265 Veterinarian Vétérinaire + OMRSE:00000001 Social role Rôle social + GENEPIO:0100266 Acquaintance of case Connaissance du cas + GENEPIO:0100267 Relative of case Famille du cas + GENEPIO:0100268 Child of case Enfant du cas + GENEPIO:0100269 Parent of case Parent du cas + GENEPIO:0100270 Father of case Père du cas + GENEPIO:0100271 Mother of case Mère du cas + GENEPIO:0100272 Spouse of case Conjoint du cas + Other Host Role Autre rôle de l’hôte + + +exposure setting menu ExposureSettingMenu Menu « Contexte de l’exposition » ECTO:3000005 Human Exposure Exposition humaine + GENEPIO:0100184 Contact with Known COVID-19 Case Contact avec un cas connu de COVID-19 + GENEPIO:0100185 Contact with Patient Contact avec un patient + GENEPIO:0100186 Contact with Probable COVID-19 Case Contact avec un cas probable de COVID-19 + GENEPIO:0100187 Contact with Person with Acute Respiratory Illness Contact avec une personne atteinte d’une maladie respiratoire aiguë + GENEPIO:0100188 Contact with Person with Fever and/or Cough Contact avec une personne présentant une fièvre ou une toux + GENEPIO:0100189 Contact with Person who Recently Travelled Contact avec une personne ayant récemment voyagé + GENEPIO:0100190 Occupational, Residency or Patronage Exposure Exposition professionnelle ou résidentielle + ECTO:1000033 Abbatoir Abattoir + GENEPIO:0100191 Animal Rescue Refuge pour animaux + GENEPIO:0100192 Childcare Garde d’enfants + GENEPIO:0100193 Daycare Garderie + GENEPIO:0100194 Nursery Pouponnière + GENEPIO:0100195 Community Service Centre Centre de services communautaires + GENEPIO:0100196 Correctional Facility Établissement correctionnel + GENEPIO:0100197 Dormitory Dortoir + ECTO:1000034 Farm Ferme + GENEPIO:0100198 First Nations Reserve Réserve des Premières Nations + GENEPIO:0100199 Funeral Home Salon funéraire + GENEPIO:0100200 Group Home Foyer de groupe + GENEPIO:0100201 Healthcare Setting Établissement de soins de santé + GENEPIO:0100202 Ambulance Ambulance + GENEPIO:0100203 Acute Care Facility Établissement de soins de courte durée + GENEPIO:0100204 Clinic Clinique + GENEPIO:0100415 Community Healthcare (At-Home) Setting Établissement de soins de santé communautaire (à domicile) + GENEPIO:0100205 Community Health Centre Centre de santé communautaire + ECTO:1000035 Hospital Hôpital + GENEPIO:0100206 Emergency Department Service des urgences + GENEPIO:0100207 ICU USI + GENEPIO:0100208 Ward Service + ECTO:1000036 Laboratory Laboratoire + GENEPIO:0100209 Long-Term Care Facility Établissement de soins de longue durée + GENEPIO:0100210 Pharmacy Pharmacie + GENEPIO:0100211 Physician's Office Cabinet de médecin + GENEPIO:0100212 Household Ménage + GENEPIO:0100213 Insecure Housing (Homeless) Logement précaire (sans-abri) + GENEPIO:0100214 Occupational Exposure Exposition professionnelle + GENEPIO:0100215 Worksite Lieu de travail + ECTO:1000037 Office Bureau + GENEPIO:0100216 Outdoors Plein air + ECTO:5000009 Camp/camping Camp/Camping + GENEPIO:0100217 Hiking Trail Sentier de randonnée + ECTO:6000030 Hunting Ground Territoire de chasse + GENEPIO:0100218 Ski Resort Station de ski + ECTO:5000008 Petting zoo Zoo pour enfants + GENEPIO:0100220 Place of Worship Lieu de culte + GENEPIO:0100221 Church Église + GENEPIO:0100222 Mosque Mosquée + GENEPIO:0100223 Temple Temple + ECTO:1000040 Restaurant Restaurant + ECTO:1000041 Retail Store Magasin de détail + GENEPIO:0100224 School École + GENEPIO:0100225 Temporary Residence Résidence temporaire + GENEPIO:0100226 Homeless Shelter Refuge pour sans-abri + GENEPIO:0100227 Hotel Hôtel + GENEPIO:0100228 Veterinary Care Clinic Clinique vétérinaire + GENEPIO:0100229 Travel Exposure Exposition liée au voyage + GENEPIO:0100230 Travelled on a Cruise Ship Voyage sur un bateau de croisière + GENEPIO:0100231 Travelled on a Plane Voyage en avion + GENEPIO:0100232 Travelled on Ground Transport Voyage par voie terrestre + GENEPIO:0001118 Travelled outside Province/Territory Voyage en dehors de la province ou du territoire + GENEPIO:0001119 Travelled outside Canada Voyage en dehors du Canada + GENEPIO:0100235 Other Exposure Setting Autres contextes d’exposition + + +travel point of entry type menu TravelPointOfEntryTypeMenu Menu «  Type de point d’entrée du voyage » GENEPIO:0100408 Air Voie aérienne + GENEPIO:0100409 Land Voie terrestre + + +border testing test day type menu UmbrellaBioprojectAccessionMenu Menu « Jour du dépistage à la frontière » GENEPIO:0100410 day 1 Jour 1 + GENEPIO:0100411 day 8 Jour 8 + GENEPIO:0100412 day 10 Jour 10 + + +travel history availability menu TravelHistoryAvailabilityMenu Menu « Disponibilité des antécédents de voyage » GENEPIO:0100650 Travel history available Antécédents de voyage disponibles + GENEPIO:0100651 Domestic travel history available Antécédents des voyages intérieurs disponibles + GENEPIO:0100652 International travel history available Antécédents des voyages internationaux disponibles + GENEPIO:0100653 International and domestic travel history available Antécédents des voyages intérieurs et internationaux disponibles + GENEPIO:0100654 No travel history available Aucun antécédent de voyage disponible + + +sequencing instrument menu SequencingInstrumentMenu Menu « Instrument de séquençage » GENEPIO:0100105 Illumina Illumina + GENEPIO:0100106 Illumina Genome Analyzer Analyseur de génome Illumina + GENEPIO:0100107 Illumina Genome Analyzer II Analyseur de génome Illumina II + GENEPIO:0100108 Illumina Genome Analyzer IIx Analyseur de génome Illumina IIx + GENEPIO:0100109 Illumina HiScanSQ Illumina HiScanSQ + GENEPIO:0100110 Illumina HiSeq Illumina HiSeq + GENEPIO:0100111 Illumina HiSeq X Illumina HiSeq X + GENEPIO:0100112 Illumina HiSeq X Five Illumina HiSeq X Five + GENEPIO:0100113 Illumina HiSeq X Ten Illumina HiSeq X Ten + GENEPIO:0100114 Illumina HiSeq 1000 Illumina HiSeq 1000 + GENEPIO:0100115 Illumina HiSeq 1500 Illumina HiSeq 1500 + GENEPIO:0100116 Illumina HiSeq 2000 Illumina HiSeq 2000 + GENEPIO:0100117 Illumina HiSeq 2500 Illumina HiSeq 2500 + GENEPIO:0100118 Illumina HiSeq 3000 Illumina HiSeq 3000 + GENEPIO:0100119 Illumina HiSeq 4000 Illumina HiSeq 4000 + GENEPIO:0100120 Illumina iSeq Illumina iSeq + GENEPIO:0100121 Illumina iSeq 100 Illumina iSeq 100 + GENEPIO:0100122 Illumina NovaSeq Illumina NovaSeq + GENEPIO:0100123 Illumina NovaSeq 6000 Illumina NovaSeq 6000 + GENEPIO:0100124 Illumina MiniSeq Illumina MiniSeq + GENEPIO:0100125 Illumina MiSeq Illumina MiSeq + GENEPIO:0100126 Illumina NextSeq Illumina NextSeq + GENEPIO:0100127 Illumina NextSeq 500 Illumina NextSeq 500 + GENEPIO:0100128 Illumina NextSeq 550 Illumina NextSeq 550 + GENEPIO:0100129 Illumina NextSeq 2000 Illumina NextSeq 2000 + GENEPIO:0100130 Pacific Biosciences Pacific Biosciences + GENEPIO:0100131 PacBio RS PacBio RS + GENEPIO:0100132 PacBio RS II PacBio RS II + GENEPIO:0100133 PacBio Sequel PacBio Sequel + GENEPIO:0100134 PacBio Sequel II PacBio Sequel II + GENEPIO:0100135 Ion Torrent Ion Torrent + GENEPIO:0100136 Ion Torrent PGM Ion Torrent PGM + GENEPIO:0100137 Ion Torrent Proton Ion Torrent Proton + GENEPIO:0100138 Ion Torrent S5 XL Ion Torrent S5 XL + GENEPIO:0100139 Ion Torrent S5 Ion Torrent S5 + GENEPIO:0100140 Oxford Nanopore Oxford Nanopore + GENEPIO:0100141 Oxford Nanopore GridION Oxford Nanopore GridION + GENEPIO:0100142 Oxford Nanopore MinION Oxford Nanopore MinION + GENEPIO:0100143 Oxford Nanopore PromethION Oxford Nanopore PromethION + GENEPIO:0100144 BGI Genomics BGI Genomics + GENEPIO:0100145 BGI Genomics BGISEQ-500 BGI Genomics BGISEQ-500 + GENEPIO:0100146 MGI MGI + GENEPIO:0100147 MGI DNBSEQ-T7 MGI DNBSEQ-T7 + GENEPIO:0100148 MGI DNBSEQ-G400 MGI DNBSEQ-G400 + GENEPIO:0100149 MGI DNBSEQ-G400 FAST MGI DNBSEQ-G400 FAST + GENEPIO:0100150 MGI DNBSEQ-G50 MGI DNBSEQ-G50 + + +gene name menu GeneNameMenu Menu « Nom du gène » GENEPIO:0100151 E gene (orf4) Gène E (orf4) E gene E (orf4) + GENEPIO:0100152 M gene (orf5) Gène M (orf5) M (orf5) + GENEPIO:0100153 N gene (orf9) Gène N (orf9) N (orf9) + GENEPIO:0100154 Spike gene (orf2) Gène de pointe (orf2) S (orf2) + GENEPIO:0100155 orf1ab (rep) orf1ab (rep) orf1ab (rep) + GENEPIO:0100156 orf1a (pp1a) orf1a (pp1a) orf1a (pp1a) + GENEPIO:0100157 nsp11 nsp11 nsp11 + GENEPIO:0100158 nsp1 nsp1 nsp1 + GENEPIO:0100159 nsp2 nsp2 nsp2 + GENEPIO:0100160 nsp3 nsp3 nsp3 + GENEPIO:0100161 nsp4 nsp4 nsp4 + GENEPIO:0100162 nsp5 nsp5 nsp5 + GENEPIO:0100163 nsp6 nsp6 nsp6 + GENEPIO:0100164 nsp7 nsp7 nsp7 + GENEPIO:0100165 nsp8 nsp8 nsp8 + GENEPIO:0100166 nsp9 nsp9 nsp9 + GENEPIO:0100167 nsp10 nsp10 nsp10 + GENEPIO:0100168 RdRp gene (nsp12) Gène RdRp (nsp12) nsp12 (RdRp) + GENEPIO:0100169 hel gene (nsp13) Gène hel (nsp13) nsp13 (Hel) + GENEPIO:0100170 exoN gene (nsp14) Gène exoN (nsp14) nsp14 (ExoN) + GENEPIO:0100171 nsp15 nsp15 nsp15 + GENEPIO:0100172 nsp16 nsp16 nsp16 + GENEPIO:0100173 orf3a orf3a orf3a + GENEPIO:0100174 orf3b orf3b orf3b + GENEPIO:0100175 orf6 (ns6) orf6 (ns6) orf6 (ns6) + GENEPIO:0100176 orf7a orf7a orf7a + GENEPIO:0100177 orf7b (ns7b) orf7b (ns7b) orf7b (ns7b) + GENEPIO:0100178 orf8 (ns8) orf8 (ns8) orf8 (ns8) + GENEPIO:0100179 orf9b orf9b orf9b + GENEPIO:0100180 orf9c orf9c orf9c + GENEPIO:0100181 orf10 orf10 orf10 + GENEPIO:0100182 orf14 orf14 orf14 + GENEPIO:0100183 SARS-COV-2 5' UTR SRAS-COV-2 5' UTR + + +sequence submitted by menu SequenceSubmittedByMenu Menu « Séquence soumise par » Alberta Precision Labs (APL) Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory Laboratoire de santé publique du CCMCB + Canadore College Canadore College + The Centre for Applied Genomics (TCAG) The Centre for Applied Genomics (TCAG) + Dynacare Dynacare + Dynacare (Brampton) Dynacare (Brampton) + Dynacare (Manitoba) Dynacare (Manitoba) + The Hospital for Sick Children (SickKids) The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) Laboratoire de santé publique du Québec (LSPQ) + Manitoba Cadham Provincial Laboratory Laboratoire provincial Cadham du Manitoba + McGill University Université McGill + McMaster University Université McMaster + National Microbiology Laboratory (NML) Laboratoire national de microbiologie (LNM) + New Brunswick - Vitalité Health Network Nouveau-Brunswick – Réseau de santé Vitalité + Newfoundland and Labrador - Eastern Health Terre-Neuve-et-Labrador – Eastern Health + Newfoundland and Labrador - Newfoundland and Labrador Health Services Terre-Neuve-et-Labrador – Newfoundland and Labrador Health Services + Nova Scotia Health Authority Autorité sanitaire de la Nouvelle-Écosse + Ontario Institute for Cancer Research (OICR) Institut ontarien de recherche sur le cancer (IORC) + Prince Edward Island - Health PEI Île-du-Prince-Édouard – Santé Î.-P.-É. + Public Health Ontario (PHO) Santé publique Ontario (SPO) + Queen's University / Kingston Health Sciences Centre Université Queen’s – Centre des sciences de la santé de Kingston + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) Saskatchewan – Laboratoire provincial Roy Romanow + Sunnybrook Health Sciences Centre Sunnybrook Health Sciences Centre + Thunder Bay Regional Health Sciences Centre "Centre régional des sciences +de la santé de Thunder Bay" + + +sample collected by menu SampleCollectedByMenu Menu « Échantillon prélevé par » Alberta Precision Labs (APL) Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory Laboratoire de santé publique du CCMCB + Dynacare Dynacare + Dynacare (Manitoba) Dynacare (Manitoba) + Dynacare (Brampton) Dynacare (Brampton) + Eastern Ontario Regional Laboratory Association Association des laboratoires régionaux de l’Est de l’Ontario + Hamilton Health Sciences Hamilton Health Sciences + The Hospital for Sick Children (SickKids) The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) Laboratoire de santé publique du Québec (LSPQ) + Lake of the Woods District Hospital - Ontario Lake of the Woods District Hospital – Ontario + LifeLabs LifeLabs + LifeLabs (Ontario) LifeLabs (Ontario) + Manitoba Cadham Provincial Laboratory Laboratoire provincial Cadham du Manitoba + McMaster University Université McMaster + Mount Sinai Hospital Mount Sinai Hospital + National Microbiology Laboratory (NML) Laboratoire national de microbiologie (LNM) + New Brunswick - Vitalité Health Network Nouveau-Brunswick – Réseau de santé Vitalité + Newfoundland and Labrador - Eastern Health Terre-Neuve-et-Labrador – Eastern Health + Newfoundland and Labrador - Newfoundland and Labrador Health Services Terre-Neuve-et-Labrador – Newfoundland and Labrador Health Services + Nova Scotia Health Authority Autorité sanitaire de la Nouvelle-Écosse + Nunavut Nunavut + Ontario Institute for Cancer Research (OICR) Institut ontarien de recherche sur le cancer (IORC) + Prince Edward Island - Health PEI Île-du-Prince-Édouard – Santé Î.-P.-É. + Public Health Ontario (PHO) Santé publique Ontario (SPO) + Queen's University / Kingston Health Sciences Centre Université Queen’s – Centre des sciences de la santé de Kingston + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) Saskatchewan – Laboratoire provincial Roy Romanow + Shared Hospital Laboratory Shared Hospital Laboratory + St. John's Rehab at Sunnybrook Hospital St. John’s Rehab à l’hôpital Sunnybrook + Switch Health Switch Health + Sunnybrook Health Sciences Centre Sunnybrook Health Sciences Centre + Unity Health Toronto Unity Health Toronto + William Osler Health System William Osler Health System + + +geo_loc_name (country) menu GeoLocNameCountryMenu Menu « nom_lieu_géo (pays) » GAZ:00006882 Afghanistan Afghanistan + GAZ:00002953 Albania Albanie + GAZ:00000563 Algeria Algérie + GAZ:00003957 American Samoa Samoa américaines + GAZ:00002948 Andorra Andorre + GAZ:00001095 Angola Angola + GAZ:00009159 Anguilla Anguilla + GAZ:00000462 Antarctica Antarctique + GAZ:00006883 Antigua and Barbuda Antigua-et-Barbuda + GAZ:00002928 Argentina Argentine + GAZ:00004094 Armenia Arménie + GAZ:00004025 Aruba Aruba + GAZ:00005901 Ashmore and Cartier Islands Îles Ashmore et Cartier + GAZ:00000463 Australia Australie + GAZ:00002942 Austria Autriche + GAZ:00004941 Azerbaijan Azerbaïdjan + GAZ:00002733 Bahamas Bahamas + GAZ:00005281 Bahrain Bahreïn + GAZ:00007117 Baker Island Île Baker + GAZ:00003750 Bangladesh Bangladesh + GAZ:00001251 Barbados Barbade + GAZ:00005810 Bassas da India Bassas de l’Inde + GAZ:00006886 Belarus Bélarus + GAZ:00002938 Belgium Belgique + GAZ:00002934 Belize Bélize + GAZ:00000904 Benin Bénin + GAZ:00001264 Bermuda Bermudes + GAZ:00003920 Bhutan Bhoutan + GAZ:00002511 Bolivia Bolivie + GAZ:00025355 Borneo Bornéo + GAZ:00006887 Bosnia and Herzegovina Bosnie-Herzégovine + GAZ:00001097 Botswana Botswana + GAZ:00001453 Bouvet Island Île Bouvet + GAZ:00002828 Brazil Brésil + GAZ:00003961 British Virgin Islands Îles Vierges britanniques + GAZ:00003901 Brunei Brunei + GAZ:00002950 Bulgaria Bulgarie + GAZ:00000905 Burkina Faso Burkina Faso + GAZ:00001090 Burundi Burundi + GAZ:00006888 Cambodia Cambodge + GAZ:00001093 Cameroon Cameroun + GAZ:00002560 Canada Canada + GAZ:00001227 Cape Verde Cap-Vert + GAZ:00003986 Cayman Islands Îles Caïmans + GAZ:00001089 Central African Republic République centrafricaine + GAZ:00000586 Chad Tchad + GAZ:00002825 Chile Chili + GAZ:00002845 China Chine + GAZ:00005915 Christmas Island Île Christmas + GAZ:00005838 Clipperton Island Îlot de Clipperton + GAZ:00009721 Cocos Islands Îles Cocos + GAZ:00002929 Colombia Colombie + GAZ:00005820 Comoros Comores + GAZ:00053798 Cook Islands Îles Cook + GAZ:00005917 Coral Sea Islands Îles de la mer de Corail + GAZ:00002901 Costa Rica Costa Rica + GAZ:00000906 Cote d'Ivoire Côte d’Ivoire + GAZ:00002719 Croatia Croatie + GAZ:00003762 Cuba Cuba + GAZ:00012582 Curacao Curaçao + GAZ:00004006 Cyprus Chypre + GAZ:00002954 Czech Republic République tchèque + GAZ:00001086 Democratic Republic of the Congo République démocratique du Congo + GAZ:00005852 Denmark Danemark + GAZ:00000582 Djibouti Djibouti + GAZ:00006890 Dominica Dominique + GAZ:00003952 Dominican Republic République dominicaine + GAZ:00002912 Ecuador Équateur + GAZ:00003934 Egypt Égypte + GAZ:00002935 El Salvador Salvador + GAZ:00001091 Equatorial Guinea Guinée équatoriale + GAZ:00000581 Eritrea Érythrée + GAZ:00002959 Estonia Estonie + GAZ:00001099 Eswatini Eswatini + GAZ:00000567 Ethiopia Éthiopie + GAZ:00005811 Europa Island Île Europa + GAZ:00001412 Falkland Islands (Islas Malvinas) Îles Falkland (îles Malouines) + GAZ:00059206 Faroe Islands Îles Féroé + GAZ:00006891 Fiji Fidji + GAZ:00002937 Finland Finlande + GAZ:00003940 France France + GAZ:00002516 French Guiana Guyane française + GAZ:00002918 French Polynesia Polynésie française + GAZ:00003753 French Southern and Antarctic Lands Terres australes et antarctiques françaises + GAZ:00001092 Gabon Gabon + GAZ:00000907 Gambia Gambie + GAZ:00009571 Gaza Strip Bande de Gaza + GAZ:00004942 Georgia Géorgie + GAZ:00002646 Germany Allemagne + GAZ:00000908 Ghana Ghana + GAZ:00003987 Gibraltar Gibraltar + GAZ:00005808 Glorioso Islands Îles Glorieuses + GAZ:00002945 Greece Grèce + GAZ:00001507 Greenland Groenland + GAZ:02000573 Grenada Grenade + GAZ:00067142 Guadeloupe Guadeloupe + GAZ:00003706 Guam Guam + GAZ:00002936 Guatemala Guatemala + GAZ:00001550 Guernsey Guernesey + GAZ:00000909 Guinea Guinée + GAZ:00000910 Guinea-Bissau Guinée-Bissau + GAZ:00002522 Guyana Guyana + GAZ:00003953 Haiti Haïti + GAZ:00009718 Heard Island and McDonald Islands Îles Heard-et-McDonald + GAZ:00002894 Honduras Honduras + GAZ:00003203 Hong Kong Hong Kong + GAZ:00007120 Howland Island Île Howland + GAZ:00002952 Hungary Hongrie + GAZ:00000843 Iceland Islande + GAZ:00002839 India Inde + GAZ:00003727 Indonesia Indonésie + GAZ:00004474 Iran Iran + GAZ:00004483 Iraq Iraq + GAZ:00002943 Ireland Irlande + GAZ:00052477 Isle of Man île de Man + GAZ:00002476 Israel Israël + GAZ:00002650 Italy Italie + GAZ:00003781 Jamaica Jamaïque + GAZ:00005853 Jan Mayen Jan Mayen + GAZ:00002747 Japan Japon + GAZ:00007118 Jarvis Island Île Jarvis + GAZ:00001551 Jersey Jersey + GAZ:00007114 Johnston Atoll Atoll Johnston + GAZ:00002473 Jordan Jordanie + GAZ:00005809 Juan de Nova Island Île Juan de Nova + GAZ:00004999 Kazakhstan Kazakhstan + GAZ:00001101 Kenya Kenya + GAZ:00005682 Kerguelen Archipelago Archipel Kerguelen + GAZ:00007116 Kingman Reef Récif de Kingman + GAZ:00006894 Kiribati Kiribati + GAZ:00011337 Kosovo Kosovo + GAZ:00005285 Kuwait Koweït + GAZ:00006893 Kyrgyzstan Kirghizistan + GAZ:00006889 Laos Laos + GAZ:00002958 Latvia Lettonie + GAZ:00002478 Lebanon Liban + GAZ:00001098 Lesotho Lesotho + GAZ:00000911 Liberia Libéria + GAZ:00000566 Libya Libye + GAZ:00003858 Liechtenstein Liechtenstein + GAZ:00007144 Line Islands Îles de la Ligne + GAZ:00002960 Lithuania Lituanie + GAZ:00002947 Luxembourg Luxembourg + GAZ:00003202 Macau Macao + GAZ:00001108 Madagascar Madagascar + GAZ:00001105 Malawi Malawi + GAZ:00003902 Malaysia Malaisie + GAZ:00006924 Maldives Maldives + GAZ:00000584 Mali Mali + GAZ:00004017 Malta Malte + GAZ:00007161 Marshall Islands Îles Marshall + GAZ:00067143 Martinique Martinique + GAZ:00000583 Mauritania Mauritanie + GAZ:00003745 Mauritius Maurice + GAZ:00003943 Mayotte Mayotte + GAZ:00002852 Mexico Mexique + GAZ:00005862 Micronesia Micronésie + GAZ:00007112 Midway Islands Îles Midway + GAZ:00003897 Moldova Moldavie + GAZ:00003857 Monaco Monaco + GAZ:00008744 Mongolia Mongolie + GAZ:00006898 Montenegro Monténégro + GAZ:00003988 Montserrat Montserrat + GAZ:00000565 Morocco Maroc + GAZ:00001100 Mozambique Mozambique + GAZ:00006899 Myanmar Myanmar + GAZ:00001096 Namibia Namibie + GAZ:00006900 Nauru Nauru + GAZ:00007119 Navassa Island Île Navassa + GAZ:00004399 Nepal Népal + GAZ:00002946 Netherlands Pays-Bas + GAZ:00005206 New Caledonia Nouvelle-Calédonie + GAZ:00000469 New Zealand Nouvelle-Zélande + GAZ:00002978 Nicaragua Nicaragua + GAZ:00000585 Niger Niger + GAZ:00000912 Nigeria Nigéria + GAZ:00006902 Niue Nioué + GAZ:00005908 Norfolk Island Île Norfolk + GAZ:00002801 North Korea Corée du Nord + GAZ:00006895 North Macedonia Macédoine du Nord + GAZ:00002284 North Sea Mer du Nord + GAZ:00003958 Northern Mariana Islands Îles Mariannes du Nord + GAZ:00002699 Norway Norvège + GAZ:00005283 Oman Oman + GAZ:00005246 Pakistan Pakistan + GAZ:00006905 Palau Palaos + GAZ:00002892 Panama Panama + GAZ:00003922 Papua New Guinea Papouasie-Nouvelle-Guinée + GAZ:00010832 Paracel Islands Îles Paracel + GAZ:00002933 Paraguay Paraguay + GAZ:00002932 Peru Pérou + GAZ:00004525 Philippines Philippines + GAZ:00005867 Pitcairn Islands Île Pitcairn + GAZ:00002939 Poland Pologne + GAZ:00004126 Portugal Portugal + GAZ:00006935 Puerto Rico Porto Rico + GAZ:00005286 Qatar Qatar + GAZ:00001088 Republic of the Congo République du Congo + GAZ:00003945 Reunion Réunion + GAZ:00002951 Romania Roumanie + GAZ:00023304 Ross Sea Mer de Ross + GAZ:00002721 Russia Russie + GAZ:00001087 Rwanda Rwanda + GAZ:00000849 Saint Helena Sainte-Hélène + GAZ:00006906 Saint Kitts and Nevis Saint-Kitts-et-Nevis + GAZ:00006909 Saint Lucia Sainte-Lucie + GAZ:00003942 Saint Pierre and Miquelon Saint-Pierre-et-Miquelon + GAZ:00005841 Saint Martin Saint-Martin + GAZ:02000565 Saint Vincent and the Grenadines Saint-Vincent-et-les-Grenadines + GAZ:00006910 Samoa Samoa + GAZ:00003102 San Marino Saint-Marin + GAZ:00006927 Sao Tome and Principe Sao Tomé-et-Principe + GAZ:00005279 Saudi Arabia Arabie saoudite + GAZ:00000913 Senegal Sénégal + GAZ:00002957 Serbia Serbie + GAZ:00006922 Seychelles Seychelles + GAZ:00000914 Sierra Leone Sierra Leone + GAZ:00003923 Singapore Singapour + GAZ:00012579 Sint Maarten Saint-Martin + GAZ:00002956 Slovakia Slovaquie + GAZ:00002955 Slovenia Slovénie + GAZ:00005275 Solomon Islands Îles Salomon + GAZ:00001104 Somalia Somalie + GAZ:00001094 South Africa Afrique du Sud + GAZ:00003990 South Georgia and the South Sandwich Islands Géorgie du Sud et îles Sandwich du Sud + GAZ:00002802 South Korea Corée du Sud + GAZ:00233439 South Sudan Soudan du Sud + GAZ:00000591 Spain Espagne + GAZ:00010831 Spratly Islands Îles Spratly + GAZ:00003924 Sri Lanka Sri Lanka + GAZ:00002475 State of Palestine État de Palestine + GAZ:00000560 Sudan Soudan + GAZ:00002525 Suriname Suriname + GAZ:00005396 Svalbard Svalbard + GAZ:00001099 Swaziland Swaziland + GAZ:00002729 Sweden Suède + GAZ:00002941 Switzerland Suisse + GAZ:00002474 Syria Syrie + GAZ:00005341 Taiwan Taïwan + GAZ:00006912 Tajikistan Tadjikistan + GAZ:00001103 Tanzania Tanzanie + GAZ:00003744 Thailand Thaïlande + GAZ:00006913 Timor-Leste Timor-Leste + GAZ:00000915 Togo Togo + GAZ:00260188 Tokelau Tokelaou + GAZ:00006916 Tonga Tonga + GAZ:00003767 Trinidad and Tobago Trinité-et-Tobago + GAZ:00005812 Tromelin Island Île Tromelin + GAZ:00000562 Tunisia Tunisie + GAZ:00000558 Turkey Turquie + GAZ:00005018 Turkmenistan Turkménistan + GAZ:00003955 Turks and Caicos Islands Îles Turks et Caicos + GAZ:00009715 Tuvalu Tuvalu + GAZ:00002459 United States of America États-Unis + GAZ:00001102 Uganda Ouganda + GAZ:00002724 Ukraine Ukraine + GAZ:00005282 United Arab Emirates Émirats arabes unis + GAZ:00002637 United Kingdom Royaume-Uni + GAZ:00002930 Uruguay Uruguay + GAZ:00004979 Uzbekistan Ouzbékistan + GAZ:00006918 Vanuatu Vanuatu + GAZ:00002931 Venezuela Venezuela + GAZ:00003756 Viet Nam Vietnam + GAZ:00003959 Virgin Islands Îles vierges + GAZ:00007111 Wake Island Île de Wake + GAZ:00007191 Wallis and Futuna Wallis-et-Futuna + GAZ:00009572 West Bank Cisjordanie + GAZ:00000564 Western Sahara République arabe sahraouie démocratique + GAZ:00005284 Yemen Yémen + GAZ:00001107 Zambia Zambie + GAZ:00001106 Zimbabwe Zimbabwe + + \ No newline at end of file diff --git a/web/templates/canada_covid19/schema_slots.tsv b/web/templates/canada_covid19/schema_slots.tsv index 9fcda587..72a06d58 100644 --- a/web/templates/canada_covid19/schema_slots.tsv +++ b/web/templates/canada_covid19/schema_slots.tsv @@ -1,162 +1,162 @@ -class_name slot_group slot_group_fr slot_uri title title_fr name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description description_fr comments comments_fr examples examples_fr EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -CanCOGeN Covid-19 GENEPIO:0001122 Database Identifiers - Database Identifiers Identificateurs de base de données GENEPIO:0001123 specimen collector sample ID Collecteur d'échantillons ID de l'échantillon WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Le nom défini par l'utilisateur pour l'échantillon. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de stocker la clé qui correspond aux identifiants d'origine et alternatifs pour la traçabilité et le suivi si nécessaire. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n'importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire. prov_rona_99 prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID - Database Identifiers GENEPIO:0001202 third party lab service provider name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 - Database Identifiers GENEPIO:0001149 third party lab sample ID WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY - Database Identifiers GENEPIO:0100281 case ID WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID - Database Identifiers GENEPIO:0001128 Related specimen primary ID WhitespaceMinimizedString null value menu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID - Database Identifiers GENEPIO:0001131 IRIDA sample name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name - Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella bioproject accession menu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession - Database Identifiers GENEPIO:0001136 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession - Database Identifiers GENEPIO:0001139 biosample accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers GENEPIO:0001142 SRA accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers GENEPIO:0001145 GenBank accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession - Database Identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession - GENEPIO:0001150 Sample collection and processing - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001153 sample collected by échantillon collecté par sample collected by menu null value menu TRUE The name of the agency that collected the original sample. Le nom de l’organisation à laquelle le collecteur d’échantillons est affilié. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). Le nom de l’agence doit être écrit au complet (à quelques exceptions près) et être cohérent dans plusieurs soumissions. BC Centre for Disease Control Laboratoire de santé publique du BCCDC Originating lab Lab Name CUSTOMER collected_by sample collected by - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001156 sample collector contact email Courriel de contact du collecteur d'échantillons WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. L'adresse email du contact responsable du suivi concernant l'échantillon. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L'adresse e-mail peut représenter une personne ou un laboratoire spécifique. RespLab@lab.ca RespLab@lab.ca sample collector contact email - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001158 sample collector contact address adresse de contact du collecteur d'échantillons WhitespaceMinimizedString The mailing address of the agency submitting the sample. L'adresse postale de l'agence qui soumet l'échantillon. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country L'adresse postale doit être au format : numéro et nom de la rue, ville, état/province/région, pays, code postal/code postal. 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001159 sequence submitted by séquence soumise par sequence submitted by menu null value menu TRUE The name of the agency that generated the sequence. Le nom de l'agence qui a généré la séquence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Le nom de l’agence doit être écrit au complet (à quelques exceptions près) et être cohérent dans plusieurs soumissions. Public Health Ontario (PHO) Santé publique Ontario (SPO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001165 sequence submitter contact email séquence courriel de contact du déposant WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. L'adresse email du contact responsable du suivi de la séquence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L'adresse e-mail peut représenter une personne ou un laboratoire spécifique. RespLab@lab.ca RespLab@lab.ca sequence submitter contact email - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001167 sequence submitter contact address adresse de contact de l'auteur de la séquence WhitespaceMinimizedString The mailing address of the agency submitting the sequence. L'adresse postale de l'agence soumettant la séquence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country L'adresse postale doit être au format : numéro et nom de la rue, ville, état/province/région, pays, code postal/code postal. 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001174 sample collection date date de collecte de l'échantillon date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. La date à laquelle l'échantillon a été prélevé. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Enregistrez avec précision la date de collecte dans le modèle. La granularité requise inclut l’année, le mois et le jour. Avant de partager ces données, assurez-vous que cette date n’est pas considérée comme une information identifiable. Si cette date est considérée comme identifiable, il est acceptable d'ajouter du « jitter » à la date de collecte en ajoutant ou en soustrayant des jours calendaires. Ne modifiez pas la date de collecte dans vos dossiers originaux. Alternativement, la « date de réception » peut être utilisée comme substitut dans les données que vous partagez. La date doit être fournie au format standard ISO 8601 « YYYY-MM-DD ». 2020-03-16 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001177 sample collection date precision date de collecte de l'échantillon précision sample collection date precision menu null value menu TRUE The precision to which the "sample collection date" was provided. La précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". Fournissez la précision de la granularité au « jour », au « mois » ou à « l'année » pour la date fournie dans le champ « date de prélèvement de l'échantillon ». La « date de prélèvement de l'échantillon » sera tronquée à la précision spécifiée lors de l'exportation ; « jour » pour «YYYY-MM-DD », « mois » pour « YYYY-MM » ou « année » pour « YYYY ». year année Precision of date collected HC_TEXT2 - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001179 sample received date date de réception de l'échantillon date null value menu The date on which the sample was received. La date à laquelle l'échantillon a été reçu. ISO 8601 standard "YYYY-MM-DD". La date à laquelle l'échantillon a été reçu par un laboratoire qui n'était pas le point de prélèvement. Norme ISO 8601 « YYYY-MM-DD». 2020-03-20 2020-03-20 sample received date - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001181 geo_loc_name (country) nom du geo_loc (pays) geo_loc_name (country) menu null value menu TRUE The country where the sample was collected. Le pays d'origine de l'échantillon. Provide the country name from the controlled vocabulary provided. Fournissez le nom du pays dans la liste de sélection du modèle Canada Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001185 geo_loc_name (state/province/territory) nom du geo_loc (état/province/territoire) geo_loc_name (state/province/territory) menu null value menu TRUE The province/territory where the sample was collected. L'État/la province/le territoire d'origine de l'échantillon. Provide the province/territory name from the controlled vocabulary provided. Fournissez le nom de l’État/de la province/du territoire à partir de l’ontologie géographique GAZ. Recherchez des termes géographiques ici : https://www.ebi.ac.uk/ols/ontologies/gaz Saskatchewan Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001189 geo_loc_name (city) nom du geo_loc (ville) WhitespaceMinimizedString The city where the sample was collected. La ville d'origine de l'échantillon. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Fournissez le nom de la ville à partir de l’ontologie géographique GAZ. Recherchez des termes géographiques ici : https://www.ebi.ac.uk/ols/ontologies/gaz Medicine Hat Medicine Hat Patient City geo_loc_name (city) - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001191 organism organisme organism menu null value menu TRUE Taxonomic name of the organism. Nom taxonomique de l'organisme. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Sélectionnez « Coronavirus 2 du syndrome respiratoire aigu sévère » si vous séquencez le SRAS-CoV-2. Si un autre Coronaviridae est en cours de séquençage, fournissez le nom taxonomique de NCBITaxon. Recherchez des termes de taxonomie sur https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Severe acute respiratory syndrome coronavirus 2 Syndrome respiratoire aigu sévère coronavirus 2 Pathogen HC_CURRENT_ID organism organism - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001195 isolate isolat WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. Identifiant de l'isolat spécifique. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. Cet identifiant doit être un identifiant alphanumérique unique, indexé au sein de votre laboratoire. S'il est soumis à l'INSDC, le nom « isoler » est propagé dans différentes bases de données. En tant que tel, structurez le nom « isolat » pour qu'il soit conforme à ICTV/INSDC dans le format suivant : « SARS-CoV-2/host/country/sampleID/date ». hCov-19/CANADA/BC-prov_rona_99/2020 hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001198 purpose of sampling Objectif de l'échantillonnage purpose of sampling menu null value menu TRUE The reason that the sample was collected. La raison pour laquelle l’échantillon a été collecté. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Sélectionnez une valeur dans la liste de sélection du modèle. Diagnostic testing Tests de diagnostic Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001200 purpose of sampling details détails de l'objectif de l'échantillonnage WhitespaceMinimizedString null value menu TRUE The description of why the sample was collected, providing specific details. Plus de détails concernant la raison pour laquelle l’échantillon a été collecté. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Fournissez une description en texte libre de la stratégie d’échantillonnage ou des échantillons collectés. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. L'échantillon a été collecté pour étudier la prévalence des variantes associées à la transmission du vison à l'homme au Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001204 NML submitted specimen type Type de spécimen soumis au NML NML submitted specimen type menu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. Le type d'échantillon soumis au Laboratoire national de microbiologie (NML) pour analyse. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Ces informations sont requises pour le téléchargement via le système CNPHI LaSER. Sélectionnez le type d’échantillon dans la liste de sélection fournie. Si des données de séquence sont soumises plutôt qu'un échantillon à tester, sélectionnez « Non applicable ». swab Écouvillon Specimen Type PH_SPECIMEN_TYPE - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001209 Related specimen relationship type Type de relation du spécimen apparenté Related specimen relationship type menu The relationship of the current specimen to the specimen/sample previously submitted to the repository. La relation entre le spécimen actuel et le spécimen/échantillon précédemment soumis au référentiel. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Fournissez l'étiquette qui décrit comment l'échantillon précédent est lié à l'échantillon actuel soumis à partir de la liste de sélection fournie, afin que les échantillons puissent être liés et suivis dans le système. Specimen sampling methods testing Test des méthodes d’échantillonnage des échantillons Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001211 anatomical material matière anatomique anatomical material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Une substance obtenue à partir d'une partie anatomique d'un organisme, par ex. tissu, sang. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un matériau anatomique a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/uberon. Si cela ne s’applique pas, laissez vide. Blood Sang Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001214 anatomical part partie anatomique anatomical part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Une partie anatomique d'un organisme, par ex. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/uberon. Si cela ne s’applique pas, laissez vide. Nasopharynx (NP) Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001216 body product produit corporel body product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Une substance excrétée/sécrétée par un organisme, par ex. selles, urine, sueur. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez une description si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/uberon. Si cela ne s’applique pas, laissez vide. Feces Selles Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001223 environmental material matériau environnemental environmental material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Une substance obtenue à partir de l'environnement naturel ou artificiel, par ex. sol, eau, eaux usées, poignée de porte, rampe de lit, masque facial. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un matériau environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/envo. Si cela ne s’applique pas, laissez vide. Face mask Masque facial Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001232 environmental site site environnemental environmental site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Un emplacement environnemental peut décrire un site dans l'environnement naturel ou bâti, par ex. hôpital, marché humide, grotte aux chauves-souris. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/envo. Si cela ne s’applique pas, laissez vide. Production Facility Installation de production Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001234 collection device dispositif de collecte collection device menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. L'instrument ou le récipient utilisé pour collecter l'échantillon, par ex. écouvillon. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez une description si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/obi. Si cela ne s’applique pas, laissez vide. Swab Écouvillon Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001241 collection method méthode de collecte collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Le processus utilisé pour collecter l'échantillon, par ex. phlébotomie, autopsie. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez une description si une méthode de collecte a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité manque dans la liste de sélection, utilisez ce service de recherche pour identifier un terme standardisé : https://www.ebi.ac.uk/ols/ontologies/obi. Si cela ne s’applique pas, laissez vide. Bronchoalveolar lavage (BAL) Lavage broncho-alvéolaire (LBA) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001243 collection protocol protocole de collecte WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Le nom et la version d'un protocole particulier utilisé pour l'échantillonnage. Free text. Fournissez le nom et la version du protocole utilisé pour collecter les échantillons. BCRonaSamplingProtocol v. 1.2 BCRonaSamplingProtocol v. 1.2 collection protocol - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001253 specimen processing processus de traitement des spécimens specimen processing menu null value menu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Tout traitement appliqué à l’échantillon pendant ou après la réception de l’échantillon. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Critique pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, incluez les informations dans les champs « hôte du laboratoire », « numéro de passage » et « méthode de passage ». Si aucun des processus de la liste de sélection ne s'applique, inscrivez « non applicable ». Virus passage Passage du virus Passage details/history specimen processing - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0100311 specimen processing details détails du processus des échantillons WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Informations détaillées concernant le traitement appliqué à un échantillon pendant ou après la réception de l'échantillon. Provide a free text description of any processing details applied to a sample. Fournissez une description en texte libre de tous les détails du traitement appliqués à un échantillon. 25 swabs were pooled and further prepared as a single sample during library prep. 25 écouvillons ont été regroupés et préparés en tant qu’échantillon unique lors de la préparation de la bibliothèque. - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001255 lab host hôte du laboratoire lab host menu null value menu TRUE Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Nom et description de l'hôte de laboratoire utilisé pour propager l'organisme source ou le matériel à partir duquel l'échantillon a été obtenu. Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Type de lignée cellulaire utilisée pour la propagation. Sélectionnez une valeur dans la liste de sélection. S'il n'est pas adopté, mettez "sans objet". Vero E6 cell line Lignée cellulaire Vero E6 Passage details/history lab host lab_host - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001261 passage number numéro de passage integer null value menu TRUE 0 Number of passages. Nombre de passages. Provide number of known passages. If not passaged, put "not applicable" Indiquez le nombre de passages connus. S'il n'est pas adopté, mettre "sans objet" 3 3 Passage details/history passage number passage_history - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001264 passage method méthode de passage WhitespaceMinimizedString null value menu TRUE Description of how organism was passaged. Description de la façon dont l'organisme a été transmis. Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". Texte libre. Fournissez une brève description. S'il n'est pas adopté, mettez "sans objet". 0.25% trypsin + 0.02% EDTA 0.25% trypsin + 0.02% EDTA Passage details/history passage method passage_method - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001266 biomaterial extracted biomatériau extrait biomaterial extracted menu null value menu The biomaterial extracted from samples for the purpose of sequencing. Biomatériau extrait d’échantillons à des fins de séquençage. Provide the biomaterial extracted from the picklist in the template. Fournissez le biomatériau extrait de la liste de sélection dans le modèle. RNA (total) RNA (total) biomaterial extracted - GENEPIO:0001268 Host Information - Host Information Informations sur l'hôte GENEPIO:0001386 host (common name) hôte (nom commun) host (common name) menu null value menu The commonly used name of the host. Le nom couramment utilisé de l'hôte. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Le nom commun ou le nom scientifique sont requis s’il y avait un hôte. Exemples de noms communs, par ex. humain, chauve-souris. Sélectionnez une valeur dans la liste de sélection. Si l'échantillon était environnemental, inscrivez « sans objet ». Human Humain Animal Type PH_ANIMAL_TYPE - Host Information Informations sur l'hôte GENEPIO:0001387 host (scientific name) hôte (nom scientifique) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. Le nom taxonomique ou scientifique de l’hôte. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Le nom commun ou le nom scientifique sont requis s’il y avait un hôte. Exemples de noms scientifiques, par ex. Homo sapiens. Sélectionnez une valeur dans la liste de sélection. Si l'échantillon était environnemental, inscrivez « sans objet ». Homo sapiens Homo sapiens Host host (scientific name) host host (scientific name) - Host Information Informations sur l'hôte GENEPIO:0001388 host health state état de santé de l'hôte host health state menu null value menu Health status of the host at the time of sample collection. État de santé de l'hôte au moment du prélèvement de l'échantillon. If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez une valeur dans la liste de sélection. Symptomatic Symptomatique Patient status Host Health State PH_HOST_HEALTH host_health_state - Host Information Informations sur l'hôte GENEPIO:0001389 host health status details détails de l'état de santé de l'hôte host health status details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. Plus de détails concernant l'état de santé ou de maladie de l'hôte au moment de la collecte. If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez une valeur dans la liste de sélection. Hospitalized (ICU) Hospitalisé (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS - Host Information Informations sur l'hôte GENEPIO:0001390 host health outcome résultat sanitaire de l'hôte host health outcome menu null value menu Disease outcome in the host. Résultat de la maladie chez l’hôte. If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez une valeur dans la liste de sélection. Recovered Rétabli PH_HOST_HEALTH_OUTCOME host_disease_outcome - Host Information Informations sur l'hôte GENEPIO:0001391 host disease maladie de l'hôte host disease menu null value menu TRUE The name of the disease experienced by the host. Le nom de la maladie vécue par l'hôte. Select "COVID-19" from the pick list provided in the template. Ce champ n'est obligatoire que s'il y avait un hôte. Si l’hôte était un humain, sélectionnez COVID-19 dans la liste de sélection. Si l’hôte était asymptomatique, cela peut être enregistré sous « détails sur l’état de santé de l’hôte ». « COVID-19 » doit toujours être fourni si le patient est asymptomatique. Si l’hôte n’est pas humain et que l’état pathologique n’est pas connu ou que l’hôte semble en bonne santé, inscrivez « sans objet ». COVID-19 COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease - Host Information Informations sur l'hôte GENEPIO:0001392 host age âge de l'hôte decimal null value menu TRUE 0 130 Age of host at the time of sampling. Âge de l'hôte au moment de l'échantillonnage. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". Si connu, indiquez l’âge. Le regroupement par âge est également acceptable. 79 79 Patient age Patient Age PH_AGE host_age host age - Host Information Informations sur l'hôte GENEPIO:0001393 host age unit unité d'âge de l'hôte host age unit menu null value menu TRUE The unit used to measure the host age, in either months or years. Les unités utilisées pour mesurer l'âge de l'hôte. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. Si vous le savez, indiquez les unités d'âge utilisées pour mesurer l'âge de l'hôte à partir de la liste de sélection. year année Age Units PH_AGE_UNIT host age unit - Host Information Informations sur l'hôte GENEPIO:0001394 host age bin âge de l'hôte bin host age bin menu null value menu TRUE Age of host at the time of sampling, expressed as an age group. La catégorie d'âge de l'hôte au moment de l'échantillonnage. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. Des tranches d'âge ont été fournies tous les 10 ans. Si l'âge d'un hôte ne peut pas être spécifié en raison de problèmes de confidentialité, une catégorie d'âge peut être utilisée comme alternative. 60 - 69 60 - 69 Host Age Category PH_AGE_GROUP host age bin - Host Information Informations sur l'hôte GENEPIO:0001395 host gender sexe de l'hôte host gender menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. Le sexe de l’hôte au moment du prélèvement de l’échantillon. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Si vous le connaissez, sélectionnez une valeur dans la liste de sélection. Male Homme Gender Patient Sex VD_SEX host_sex host gender - Host Information Informations sur l'hôte GENEPIO:0001396 host residence geo_loc name (country) résidence de l'hôte nom du geo_loc (pays) geo_loc_name (country) menu null value menu The country of residence of the host. Le pays où réside l'hôte. Select the country name from pick list provided in the template. Si vous le connaissez, sélectionnez une valeur dans la liste de sélection. Canada Canada PH_HOST_COUNTRY - Host Information Informations sur l'hôte GENEPIO:0001397 host residence geo_loc name (state/province/territory) nom du geo_loc de la résidence de l'hôte (état/province/territoire) geo_loc_name (state/province/territory) menu null value menu The state/province/territory of residence of the host. L'état/province/territoire de résidence de l'hôte. Select the province/territory name from pick list provided in the template. Sélectionnez le nom de la province/du territoire dans la liste de sélection fournie dans le modèle. Quebec Quebec PH_HOST_PROVINCE - Host Information Informations sur l'hôte GENEPIO:0001398 host subject ID ID du sujet de l'hôte WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Un identifiant unique par lequel chaque hôte peut être référencé, par ex. #131 Provide the host identifier. Should be a unique, user-defined identifier. Doit être un identifiant unique défini par l'utilisateur. Cet identifiant peut aider à relier les données de laboratoire aux données épidémiologiques, mais il s’agit probablement d’informations sensibles. Consultez le gestionnaire de données. BCxy123 BCxy123 host subject ID host_subject_id - Host Information Informations sur l'hôte GENEPIO:0001399 symptom onset date date d'apparition des symptômes date null value menu The date on which the symptoms began or were first noted. La date à laquelle les symptômes ont commencé ou ont été observés pour la première fois. ISO 8601 standard "YYYY-MM-DD". Si connue, indiquez la date d'apparition des symptômes au format standard ISO 8601 «YYYY-MM-DD ». 2020-03-16 2020-03-16 Symptoms Onset Date HC_ONSET_DATE - Host Information Informations sur l'hôte GENEPIO:0001400 signs and symptoms signes et symptômes signs and symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélateur d'une maladie, rapporté par un patient. Select all of the symptoms experienced by the host from the pick list. Sélectionnez tous les symptômes ressentis par l'hôte dans la liste de sélection. Chills (sudden cold sensation); Cough; Fever Frissons (sensation soudaine de froid) ; Toux; Fièvre Symptoms HC_SYMPTOMS - Host Information Informations sur l'hôte GENEPIO:0001401 pre-existing conditions and risk factors les conditions préexistantes et les facteurs de risque pre-existing conditions and risk factors menu null value menu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Conditions préexistantes du patient et facteurs de risque.
  • Condition préexistante : condition médicale qui existait avant l’infection actuelle.
  • Facteur de risque : variable associée à un risque accru de maladie ou d’infection.  Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les conditions préexistantes et les facteurs de risque rencontrés par l'hôte dans la liste de sélection. S'il manque le terme souhaité, contactez l'équipe de curation. Asthma; Pregnancy; Smoking Asthme; Grossesse; Fumeur pre-existing conditions and risk factors - Host Information Informations sur l'hôte GENEPIO:0001402 complications les complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Complications médicales du patient qui seraient dues à une maladie de l’hôte. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les complications rencontrées par l'hôte dans la liste de sélection. Acute Respiratory Failure; Coma; Septicemia Insuffisance respiratoire aiguë; Coma; Septicémie complications - GENEPIO:0001403 Host vaccination information - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001404 host vaccination status le statut vaccinal de l'hôte host vaccination status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Le statut vaccinal de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné). Select the vaccination status of the host from the pick list. Sélectionnez le statut vaccinal de l'hôte dans la liste de sélection. Fully Vaccinated Entièrement vacciné PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001406 number of vaccine doses received nombre de doses de vaccin reçues integer The number of doses of the vaccine recived by the host. Le nombre de doses de vaccin reçues par l’hôte. Record how many doses of the vaccine the host has received. Enregistrez le nombre de doses de vaccin que l’hôte a reçues. 2 2 - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100313 vaccination dose 1 vaccine name dose de vaccination 1 nom du vaccin vaccine name menu null value menu The name of the vaccine administered as the first dose of a vaccine regimen. Nom du vaccin administré comme première dose d'un schéma vaccinal. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Indiquez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur dans la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100314 vaccination dose 1 vaccination date dose de vaccination 1 date de vaccination date null value menu The date the first dose of a vaccine was administered. La date à laquelle la première dose d’un vaccin a été administrée. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 «YYYY-MM-DD ». 2021-03-01 2021-03-01 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100315 vaccination dose 2 vaccine name dose de vaccination 2 nom du vaccin vaccine name menu null value menu The name of the vaccine administered as the second dose of a vaccine regimen. Nom du vaccin administré comme deuxième dose d'un schéma vaccinal. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur dans la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100316 vaccination dose 2 vaccination date dose de vaccination 2 date de vaccination date null value menu The date the second dose of a vaccine was administered. La date à laquelle la deuxième dose d’un vaccin a été administrée. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 « YYYY-MM-DD ». 2021-09-01 2021-09-01 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100317 vaccination dose 3 vaccine name dose de vaccination 3 nom du vaccin vaccine name menu null value menu The name of the vaccine administered as the third dose of a vaccine regimen. Nom du vaccin administré comme troisième dose d'un schéma vaccinal. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur dans la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100318 vaccination dose 3 vaccination date dose de vaccination 3 date de vaccination date null value menu The date the third dose of a vaccine was administered. La date à laquelle la troisième dose d’un vaccin a été administrée. Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 «YYYY-MM-DD ». 2021-12-30 2021-12-30 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100319 vaccination dose 4 vaccine name dose de vaccination 4 nom du vaccin vaccine name menu null value menu The name of the vaccine administered as the fourth dose of a vaccine regimen. Nom du vaccin administré comme quatrième dose d'un schéma vaccinal. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur dans la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100320 vaccination dose 4 vaccination date dose de vaccination 4 date de vaccination date null value menu The date the fourth dose of a vaccine was administered. La date à laquelle la quatrième dose d’un vaccin a été administrée. Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie au format standard ISO 8601 « YYYY-MM-DD ». 2022-01-15 2022-01-15 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100321 vaccination history les antécédents de vaccination WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Une description des vaccins reçus et les dates d'administration d'une série de vaccinations contre une maladie spécifique ou un ensemble de maladies. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Description en texte libre des dates et des vaccins administrés contre une maladie/un ensemble de maladies particulier. Il est également acceptable de concaténer les informations sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 PH_VACCINATION_HISTORY - GENEPIO:0001409 Host exposure information - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001410 location of exposure geo_loc name (country) lieu d'exposition geo_loc nom (pays) geo_loc_name (country) menu null value menu The country where the host was likely exposed to the causative agent of the illness. Le pays où l'hôte a probablement été exposé à l'agent causal de la maladie. Select the country name from pick list provided in the template. Cet emplacement concerne le pays dans lequel l'hôte est censé être exposé et peut ne pas être le même que le pays de résidence de l'hôte. Si vous le connaissez, indiquez le nom du pays dans la liste de sélection. Canada Canada PH_EXPOSURE_COUNTRY - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001411 destination of most recent travel (city) destination du dernier voyage (ville) WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Le nom de la ville de destination du voyage le plus récent. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de la ville dans laquelle l'hôte s'est rendu. Utilisez ce service de recherche pour identifier le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz New York City La ville de New York Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001412 destination of most recent travel (state/province/territory) destination du dernier voyage (état/province/territoire) WhitespaceMinimizedString The name of the province that was the destination of most recent travel. Le nom de la province de destination du voyage le plus récent. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de l'État/de la province/du territoire où l'hôte s'est rendu. Utilisez ce service de recherche pour identifier le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz California Californie Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001413 destination of most recent travel (country) destination du dernier voyage (pays) geo_loc_name (country) menu null value menu The name of the country that was the destination of most recent travel. Le nom du pays de destination du voyage le plus récent. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom du pays dans lequel l'hôte s'est rendu. Utilisez ce service de recherche pour identifier le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom Royaume-Uni Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001414 most recent travel departure date date de départ du voyage la plus récente date null value menu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Date du départ le plus récent d'une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits. Provide the travel departure date. Indiquez la date de départ du voyage au format standard ISO 8601 « YYYY-MM-DD ». 2020-03-16 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001415 most recent travel return date date de retour la plus récente date null value menu The date of a person's most recent return to some residence from a journey originating at that residence. Date du retour le plus récent d'une personne à une résidence après un voyage au départ de cette résidence. Provide the travel return date. Indiquez la date de retour du voyage au format standard ISO 8601 « YYYY-MM-DD». 2020-04-26 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100413 travel point of entry type voyage type de point d'entrée travel point of entry type menu null value menu TRUE The type of entry point a traveler arrives through. Le type de point d’entrée par lequel un voyageur arrive. Select the point of entry type. Sélectionnez le type de point d’entrée. Air Air PH_POINT_OF_ENTRY - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100414 border testing test day type test aux frontières jour du test type border testing test day type menu null value menu TRUE The day a traveller was tested on or after arrival at their point of entry. Le jour où un voyageur a été testé à son arrivée ou après son point d’entrée. Select the test day. Sélectionnez le jour du test. day 1 Jour 1 PH_DAY - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001416 travel history histoire du voyage WhitespaceMinimizedString Travel history in last six months. Historique de voyage au cours des six derniers mois. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Précisez les pays (et les emplacements plus précis si connus) parcourus au cours des six derniers mois ; peut inclure plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Fournir sous forme de texte libre. Canada, Vancouver; USA, Seattle; Italy, Milan Canada, Vancouver; USA, Seattle ; Italie, Milan PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100649 travel history availability disponibilité de l'historique de voyage travel history availability menu null value menu The availability of different types of travel history in the last 6 months (e.g. international, domestic). La disponibilité de différents types d’historiques de voyages au cours des 6 derniers mois (par exemple internationaux, nationaux). If travel history is available, but the details of travel cannot be provided, indicate this and the type of travel history availble by selecting a value from the picklist. The values in this field can be used to indicate a sample is associated with a travel when the "purpose of sequencing" is not travel-associated. Si l'historique de voyage est disponible, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d'historique de voyage disponible en sélectionnant une valeur dans la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu'un échantillon est associé à un voyage lorsque le « but du séquençage » n'est pas associé à un voyage. International travel history available Historique des voyages internationaux disponible PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001417 exposure event exposition événement exposure event menu null value menu Event leading to exposure. Événement conduisant à une exposition. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. S'il est connu, sélectionnez l'événement d'exposition dans la liste de sélection. Convention Convention Additional location information Exposure Event PH_EXPOSURE - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001418 exposure contact level exposition niveau de contact exposure contact level menu null value menu The exposure transmission contact type. Le type de contact de transmission d’exposition. Select direct or indirect exposure from the pick-list. Sélectionnez une exposition directe ou indirecte dans la liste de sélection. Direct Direct exposure contact level - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001419 host role rôle d'hôte host role menu TRUE The role of the host in relation to the exposure setting. Le rôle de l'hôte par rapport au paramètre d'exposition. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez le(s) rôle(s) personnel(s) de l'hôte dans la liste de sélection fournie dans le modèle. S'il manque le terme souhaité, contactez l'équipe de curation. Patient Patient PH_HOST_ROLE - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001428 exposure setting réglage de l'exposition exposure setting menu TRUE The setting leading to exposure. Le cadre menant à l’exposition. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Sélectionnez le(s) paramètre(s) d'exposition de l'hôte dans la liste de sélection fournie dans le modèle. S’il manque un terme souhaité, contactez l’équipe de curation. Healthcare Setting Cadre de soins de santé PH_EXPOSURE - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001431 exposure details détails de l'exposition WhitespaceMinimizedString Additional host exposure information. Informations supplémentaires sur l’exposition de l’hôte. Free text description of the exposure. Description en texte libre de l'exposition. Host role - Other: Bus Driver Rôle d'hôte - Autre : Chauffeur de bus PH_EXPOSURE_DETAILS - - - GENEPIO:0001434 Host reinfection information - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001435 prior SARS-CoV-2 infection infection antérieure par le SARS-CoV-2 prior SARS-CoV-2 infection menu null value menu Whether there was prior SARS-CoV-2 infection. S'il y a eu une infection antérieure par le SARS-CoV-2. If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Si vous le savez, fournissez des informations indiquant si la personne a déjà eu une infection par le SARS-CoV-2. Sélectionnez une valeur dans la liste de sélection. Yes Oui prior SARS-CoV-2 infection - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001436 prior SARS-CoV-2 infection isolate isolat d'une infection antérieure par le SARS-CoV-2 WhitespaceMinimizedString The identifier of the isolate found in the prior SARS-CoV-2 infection. L’identifiant de l’isolat trouvé lors de l’infection antérieure par le SARS-CoV-2. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom « isolat » pour qu'il soit conforme à la norme ICTV/INSDC au format suivant : « SARS-CoV-2/host/country/sampleID/date ». SARS-CoV-2/human/USA/CA-CDPH-001/2020 SARS-CoV-2/human/USA/CA-CDPH-001/2020 prior SARS-CoV-2 infection isolate - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001437 prior SARS-CoV-2 infection date date d'une infection antérieure par le SARS-CoV-2 date The date of diagnosis of the prior SARS-CoV-2 infection. La date du diagnostic de l’infection antérieure par le SARS-CoV-2. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d'infection antérieure par le SARS-CoV-2 au format standard ISO 8601 « YYYY-MM-DD ». 2021-01-23 2021-01-23 prior SARS-CoV-2 infection date - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001438 prior SARS-CoV-2 antiviral treatment traitement antiviral antérieur contre le SARS-CoV-2 prior SARS-CoV-2 antiviral treatment menu null value menu Whether there was prior SARS-CoV-2 treatment with an antiviral agent. S'il y a eu un traitement antérieur contre le SARS-CoV-2 avec un agent antiviral. If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SARS-CoV-2. Sélectionnez une valeur dans la liste de sélection. No prior antiviral treatment Aucun traitement antiviral préalable prior SARS-CoV-2 antiviral treatment - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001439 prior SARS-CoV-2 antiviral treatment agent agent du traitement antiviral antérieur contre le SARS-CoV-2 WhitespaceMinimizedString The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Le nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SARS-CoV-2. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous séparés par des virgules. Remdesivir Remdesivir prior SARS-CoV-2 antiviral treatment agent - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001440 prior SARS-CoV-2 antiviral treatment date date du traitement antiviral antérieur contre le SARS-CoV-2 date The date treatment was first administered during the prior SARS-CoV-2 infection. Le traitement a été administré pour la première fois lors de l’infection antérieure par le SARS-CoV-2. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l'agent de traitement antiviral a été administré pour la première fois lors de l'infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SARS-CoV-2 au format standard ISO 8601 « YYYY-MM-DD ». 2021-01-28 2021-01-28 prior SARS-CoV-2 antiviral treatment date - - - GENEPIO:0001441 Sequencing - Sequencing Séquençage GENEPIO:0001445 purpose of sequencing objectif du séquençage purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. La raison pour laquelle l’échantillon a été séquencé. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. La raison pour laquelle un échantillon a été initialement collecté peut différer de la raison pour laquelle il a été sélectionné pour le séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des informations sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. La raison du prélèvement de l’échantillon doit être indiquée dans le champ « objectif de l’échantillonnage ». Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing - Sequencing Séquençage GENEPIO:0001446 purpose of sequencing details objectif du séquençage détails WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. La description de la raison pour laquelle l'échantillon a été séquencé, fournissant des détails spécifiques. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Fournissez une description détaillée de la raison pour laquelle l'échantillon a été séquencé à l'aide d'une liste de sélection. La description peut inclure l’importance des séquences pour une enquête/activité de surveillance/question de recherche particulière en santé publique. Les descriptions standardisées suggérées comprennent : Dépisté pour l'échec de la cible du gène S (abandon S), Dépisté pour les variantes de vison, Dépisté pour la variante B.1.1.7, Dépisté pour la variante B.1.135, Dépisté pour la variante P.1, Dépisté en raison des antécédents de voyage, Dépisté en raison d'un contact étroit avec une personne infectée, Évaluation des mesures de contrôle de la santé publique, Détermination des introductions et de la propagation précoces, Enquête sur les expositions liées aux compagnies aériennes, Enquête sur les travailleurs étrangers temporaires, Enquête sur les régions éloignées, Enquête sur les travailleurs de la santé, Enquête sur les écoles/universités, Enquête sur la réinfection. Screened for S gene target failure (S dropout) Dépisté pour échec de la cible du gène S (abandon S) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing Séquençage GENEPIO:0001447 sequencing date date de séquençage date null value menu TRUE {sample collection date} The date the sample was sequenced. La date à laquelle l’échantillon a été séquencé. ISO 8601 standard "YYYY-MM-DD". Fournissez la date de séquençage au format standard ISO 8601 « YYYY-MM-DD ». 2020-06-22 2020-06-22 PH_SEQUENCING_DATE - Sequencing Séquençage GENEPIO:0001448 library ID ID de la bibliothèque WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. L’identifiant spécifié par l’utilisateur pour la bibliothèque préparée pour le séquençage. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. Le nom de la bibliothèque doit être unique et peut être un identifiant généré automatiquement à partir de votre LIMS ou une modification de l'ID d'isolat. XYZ_123345 XYZ_123345 library ID - Sequencing Séquençage GENEPIO:0001449 amplicon size taille de l'amplicon WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. La longueur de l'amplicon généré par l'amplification PCR. Provide the amplicon size, including the units. Fournissez la taille de l’amplicon, y compris les unités. 300bp 300bp amplicon size - Sequencing Séquençage GENEPIO:0001450 library preparation kit kit de préparation de librairie WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Nom du kit de préparation de la bibliothèque DNA utilisé pour générer la bibliothèque en cours de séquençage. Provide the name of the library preparation kit used. Indiquez le nom du kit de préparation de bibliothèque utilisé. Nextera XT Nextera XT PH_LIBRARY_PREP_KIT - Sequencing Séquençage GENEPIO:0001451 flow cell barcode code-barres de la cellule d'écoulement WhitespaceMinimizedString The barcode of the flow cell used for sequencing. Le code-barres de la Flow Cell utilisée pour le séquençage. Provide the barcode of the flow cell used for sequencing the sample. Fournissez le code-barres de la Flow Cell utilisée pour séquencer l’échantillon. FAB06069 FAB06069 flow cell barcode - Sequencing Séquençage GENEPIO:0001452 sequencing instrument instrument de séquençage sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Le modèle de l’instrument de séquençage utilisé. Select a sequencing instrument from the picklist provided in the template. Sélectionnez l’instrument de séquençage dans la liste de sélection. Oxford Nanopore MinION Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument - Sequencing Séquençage GENEPIO:0001453 sequencing protocol name nom du protocole de séquençage WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Le nom et le numéro de version du protocole de séquençage utilisé. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION Fournissez le nom et la version du protocole de séquençage. https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name PH_SEQ_PROTOCOL_NAME - Sequencing Séquençage GENEPIO:0001454 sequencing protocol protocole de séquençage WhitespaceMinimizedString The protocol used to generate the sequence. Le protocole utilisé pour générer la séquence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Texte suggéré, complétez les informations là où elles sont indiquées. : "Le séquençage viral a été effectué selon une stratégie d'amplicon en mosaïque en utilisant le schéma d'amorce . Le séquençage a été effectué à l'aide d'un instrument de séquençage . Les bibliothèques ont été préparées à l'aide de la bibliothèque . trousse." Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Les génomes ont été générés par séquençage d'amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l'aide des kits Illumina DNA Prep et les données de séquence ont été produites à l'aide des kits de séquençage Miseq Micro v2 (500 cycles). PH_TESTING_PROTOCOL sequencing protocol - Sequencing Séquençage GENEPIO:0001455 sequencing kit number numéro du kit de séquençage WhitespaceMinimizedString The manufacturer's kit number. Le numéro de kit du fabricant. Alphanumeric value. Valeur alphanumérique. AB456XYZ789 AB456XYZ789 sequencing kit number - Sequencing Séquençage GENEPIO:0001456 amplicon pcr primer scheme de la liste des amorces pcr de l'amplicon WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Les spécifications des amorces (séquences d'amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons pour le séquençage. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon pcr primer scheme - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001458 raw sequence data processing method méthode de traitement des données de séquences brutes WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. La méthode utilisée pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l'adaptateur, le filtrage, etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Fournissez le nom et les numéros de version du logiciel utilisé pour traiter les données brutes. Porechop 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001459 dehosting method méthode de déshostage WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Méthode utilisée pour supprimer les lectures de l'hôte de la séquence de l'agent pathogène. Provide the name and version number of the software used to remove host reads. Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l'hôte. Nanostripper Nanostripper PH_DEHOSTING_METHOD dehosting method - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001460 consensus sequence name nom de la séquence consensus WhitespaceMinimizedString The name of the consensus sequence. Le nom de la séquence consensus. Provide the name and version number of the consensus sequence. Fournissez le nom et le numéro de version de la séquence consensus. ncov123assembly3 ncov123assembly3 consensus sequence name - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001461 consensus sequence filename nom de fichier de la séquence consensus WhitespaceMinimizedString The name of the consensus sequence file. Le nom du fichier de séquence consensus. Provide the name and version number of the consensus sequence FASTA file. Fournissez le nom et le numéro de version du fichier FASTA de séquence consensus. ncov123assembly.fasta ncov123assembly.fasta consensus sequence filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001462 consensus sequence filepath chemin de fichier de la séquence consensus WhitespaceMinimizedString The filepath of the consensus sequence file. Le chemin d’accès du fichier de séquence consensus. Provide the filepath of the consensus sequence FASTA file. Fournissez le chemin d’accès du fichier FASTA de séquence consensus. /User/Documents/RespLab/Data/ncov123assembly.fasta /User/Documents/RespLab/Data/ncov123assembly.fasta consensus sequence filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001463 consensus sequence software name nom du logiciel de séquençage du consensus WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Le nom du logiciel utilisé pour générer la séquence consensus. Provide the name of the software used to generate the consensus sequence. Fournissez le nom du logiciel utilisé pour générer la séquence consensus. iVar iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001469 consensus sequence software version version du logiciel de la séquence consensus WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. La version du logiciel utilisé pour générer la séquence consensus. Provide the version of the software used to generate the consensus sequence. Fournir la version du logiciel utilisé pour générer la séquence consensus. 1.3 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001472 breadth of coverage value valeur de l'étendue de la couverture WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Le pourcentage du génome de référence couvert par les données séquencées, jusqu'à une profondeur prescrite. Provide value as a percent. Fournissez la valeur en pourcentage. 95% 95% breadth of coverage value breadth of coverage value - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001474 depth of coverage value valeur de la profondeur de couverture WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Le nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite. Provide value as a fold of coverage. Apporter de la valeur sous forme de pli de couverture. 400x 400x Coverage depth of coverage value depth of coverage value - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001475 depth of coverage threshold seuil de profondeur de couverture WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Seuil utilisé comme seuil pour la profondeur de couverture. Provide the threshold fold coverage. Fournit la couverture de pli de seuil. 100x 100x depth of coverage threshold - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001476 r1 fastq filename r1 nom de fichier fastq WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Le nom de fichier spécifié par l'utilisateur du fichier r1 FASTQ. Provide the r1 FASTQ filename. Fournissez le nom du fichier r1 FASTQ. ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001477 r2 fastq filename r2 nom de fichier fastq WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Le nom de fichier spécifié par l'utilisateur du fichier r2 FASTQ. Provide the r2 FASTQ filename. Fournissez le nom du fichier r2 FASTQ. ABC123_S1_L001_R2_001.fastq.gz ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001478 r1 fastq filepath chemin de fichier r1 fastq WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Le chemin du fichier r1 FASTQ. Provide the filepath for the r1 FASTQ file. This information aids in data management. Fournissez le chemin du fichier r1 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001479 r2 fastq filepath chemin du fichier r2 fastq WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Le chemin d'accès du fichier r2 FASTQ. Provide the filepath for the r2 FASTQ file. This information aids in data management. Fournissez le chemin d'accès du fichier r2 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001480 fast5 filename nom de fichier fast5 WhitespaceMinimizedString The user-specified filename of the FAST5 file. Le nom de fichier spécifié par l'utilisateur du fichier FAST5. Provide the FAST5 filename. Fournissez le nom du fichier FAST5. rona123assembly.fast5 rona123assembly.fast5 fast5 filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001481 fast5 filepath chemin de fichier fast5 WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Le chemin du fichier FAST5. Provide the filepath for the FAST5 file. This information aids in data management. Fournissez le chemin du fichier FAST5. /User/Documents/RespLab/Data/rona123assembly.fast5 /User/Documents/RespLab/Data/rona123assembly.fast5 fast5 filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001482 number of base pairs sequenced nombre de paires de bases séquencées integer 0 The number of total base pairs generated by the sequencing process. Le nombre total de paires de bases générées par le processus de séquençage. Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 387566 387566 number of base pairs sequenced - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001483 consensus genome length longueur consensuelle du génome integer 0 Size of the reconstructed genome described as the number of base pairs. Taille du génome assemblé décrite comme le nombre de paires de bases. Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 38677 38677 consensus genome length - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001484 Ns per 100 kbp Ns per 100 kbp decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Le nombre de N symboles présents dans la séquence fasta consensus, pour 100 kbp de séquence. Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 330 330 Ns per 100 kbp - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001485 reference genome accession accession au génome de référence WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Un identifiant persistant et unique d’une entrée de base de données génomique. Provide the accession number of the reference genome. Fournissez le numéro d’accès du génome de référence. NC_045512.2 NC_045512.2 reference genome accession reference genome accession - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001489 bioinformatics protocol protocole bioinformatique WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Le nom et le numéro de version du protocole bioinformatique utilisé. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes et/ou générer des assemblages et/ou générer des séquences consensus peuvent être fournis dans une SOP ou un protocole. Fournissez le nom et le numéro de version du protocole, ou un lien s'il est déposé dans un référentiel de protocoles. https://github.com/phac-nml/ncov2019-artic-nf https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol - GENEPIO:0001498 Lineage and Variant information - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001500 lineage/clade name nom du lineage/clade WhitespaceMinimizedString The name of the lineage or clade. Le nom de la lignée ou du clade. Provide the Pangolin or Nextstrain lineage/clade name. Fournissez le nom de la lignée/clade Pangolin ou Nextstrain. B.1.1.7 B.1.1.7 PH_LINEAGE_CLADE_NAME - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001501 lineage/clade analysis software name nom du logiciel d'analyse de linéage/clade WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Le nom du logiciel utilisé pour déterminer la lignée/clade. Provide the name of the software used to determine the lineage/clade. Fournissez le nom du logiciel utilisé pour déterminer la lignée/clade. Pangolin Pangolin PH_LINEAGE_CLADE_SOFTWARE - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001502 lineage/clade analysis software version version du logiciel d'analyse de linéage/clade WhitespaceMinimizedString The version of the software used to determine the lineage/clade. La version du logiciel utilisé pour déterminer la lignée/clade. Provide the version of the software used ot determine the lineage/clade. Fournissez la version du logiciel utilisé pour déterminer la lignée/clade. 2.1.10 2.1.10 PH_LINEAGE_CLADE_VERSION - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001503 variant designation désignation de la variante variant designation menu null value menu The variant classification of the lineage/clade i.e. variant, variant of concern. La classification des variantes de la lignée/clade, c'est-à-dire variante, variante préoccupante. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Si la lignée/clade est considérée comme une variante préoccupante, sélectionnez Variante préoccupante dans la liste de sélection. Si la lignée/clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques) mais qu’il ne s’agit pas d’une variante préoccupante globale, sélectionnez Variante. Si la lignée/clade ne contient pas de mutations préoccupantes, laissez ce champ vide. Variant of Concern Variante préoccupante (VOC) PH_VARIANT_DESIGNATION - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001504 variant evidence preuve de la variante variant evidence menu null value menu The evidence used to make the variant determination. Preuve utilisée pour déterminer la variante. Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. Sélectionnez si l’échantillon a été dépisté à l’aide de RT-qPCR ou par séquençage dans la liste de sélection. RT-qPCR RT-qPCR PH_VARIANT_EVIDENCE - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001505 variant evidence details détails de la preuve de la variante WhitespaceMinimizedString Details about the evidence used to make the variant determination. Détails sur les preuves utilisées pour déterminer la variante. Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Fournissez le test et répertoriez l’ensemble des mutations définissant la lignée utilisées pour effectuer la détermination des variantes. Si des mutations intéressantes/préoccupantes ont été observées en plus des mutations définissant la lignée, décrivez-les ici. Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). Mutations définissant la lignée: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). PH_VARIANT_EVIDENCE_DETAILS - GENEPIO:0001506 Pathogen diagnostic testing - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001507 gene name 1 nom du gène 1 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Le nom du gène utilisé dans le test diagnostique RT-PCR. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Sélectionnez un gène dans la liste de sélection. Si le gène qui vous intéresse ne figure pas dans la liste, indiquez le nom complet du gène ou le symbole du gène (forme abrégée du nom du gène). Les noms et symboles de gènes standardisés peuvent être trouvés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI E gene (orf4) E gene (orf4) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001508 diagnostic pcr protocol 1 protocole de diagnostic pcr 1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un test PCR diagnostique. Ces informations peuvent être comparées aux données de séquence pour l’évaluation des performances et le contrôle qualité. EGenePCRTest 2 EGenePCRTest 2 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic pcr Ct value 1 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. La valeur du seuil de cycle (Ct) résulte d’un test de diagnostic RT-PCR du SARS-CoV-2. Provide the CT value of the sample from the diagnostic RT-PCR test. Fournissez la valeur du seuil de cycle (Ct) de l’échantillon issu du test de diagnostic RT-PCR. 21 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001510 gene name 2 nom du gène 2 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Le nom du gène utilisé dans le test diagnostique RT-PCR. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Sélectionnez un gène dans la liste de sélection. Si le gène qui vous intéresse ne figure pas dans la liste, indiquez le nom complet du gène ou le symbole du gène (forme abrégée du nom du gène). Les noms et symboles de gènes standardisés peuvent être trouvés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI RdRp gene (nsp12) RdRp gene (nsp12) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001511 diagnostic pcr protocol 2 protocole de diagnostic pcr 2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test de diagnostic PCR. Ces informations peuvent être comparées aux données de séquence pour l’évaluation des performances et le contrôle qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic pcr Ct value 2 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. La valeur du seuil de cycle (Ct) résulte d’un test de diagnostic RT-PCR du SARS-CoV-2. Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur du seuil de cycle (Ct) de l’échantillon issu du deuxième test de diagnostic RT-PCR. 36 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001513 gene name 3 nom du gène 3 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Le nom du gène utilisé dans le test diagnostique RT-PCR. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Fournissez le nom complet d’un autre gène utilisé dans un test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Les noms et symboles de gènes standardisés peuvent être trouvés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI RdRp gene (nsp12) RdRp gene (nsp12) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001514 diagnostic pcr protocol 3 protocole de diagnostic pcr 3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Le nom et le numéro de version du protocole utilisé pour l’amplification des marqueurs de diagnostic. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test de diagnostic PCR. Ces informations peuvent être comparées aux données de séquence pour l’évaluation des performances et le contrôle qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic pcr Ct value 3 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. La valeur Ct résulte d’un test de diagnostic SARS-CoV-2 RT-PCR. Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur CT de l’échantillon du deuxième test de diagnostic RT-PCR. 30 30 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value - - - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001517 authors auteurs WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Noms des personnes contribuant aux processus de collecte d’échantillons, de génération de séquences, d’analyse et de soumission de données. Include the first and last names of all individuals that should be attributed, separated by a comma. Incluez le prénom et le nom de toutes les personnes qui doivent être attribuées, séparés par une virgule. Tejinder Singh, Fei Hu, Joe Blogs Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS - Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001518 DataHarmonizer provenance Provenance de DataHarmonizer Provenance The DataHarmonizer software and template version provenance. Provenance du logiciel DataHarmonizer et de la version du modèle. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. Les informations actuelles sur la version du logiciel et du modèle seront automatiquement générées dans ce champ une fois que l'utilisateur aura utilisé la fonction « valider ». Ces informations seront générées indépendamment du fait que la ligne soit valide ou non. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS - \ No newline at end of file +class_name slot_group slot_group_fr slot_uri title name title_fr rangeOld range range_2_Old range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description description_fr comments comments_fr examples examples_fr EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +CanCOGeNCovid19 GENEPIO:0001122 Database Identifiers + Database Identifiers Identificateurs de base de données GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id ID du collecteur d’échantillons WhitespaceMinimizedString WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Nom défini par l’utilisateur pour l’échantillon Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de conserver la clé qui correspond aux identifiants d’origine et alternatifs aux fins de traçabilité et de suivi, au besoin. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n’importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire. prov_rona_99 prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID + Database Identifiers Identificateurs de base de données GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name Nom du fournisseur de services de laboratoire tiers WhitespaceMinimizedString WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Nom de la société ou du laboratoire tiers qui fournit les services Provide the full, unabbreviated name of the company or laboratory. Indiquez le nom complet et non abrégé de l’entreprise ou du laboratoire. Switch Health Switch Health HC_TEXT5 + Database Identifiers Identificateurs de base de données GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id ID de l’échantillon de laboratoire tiers WhitespaceMinimizedString WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Identifiant attribué à un échantillon par un prestataire de services tiers Store the sample identifier supplied by the third party services provider. Conservez l’identifiant de l’échantillon fourni par le prestataire de services tiers. SHK123456 SHK123456 PH_ID_NUMBER_PRIMARY + Database Identifiers Identificateurs de base de données GENEPIO:0100281 case ID case_id ID du dossier WhitespaceMinimizedString WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Identifiant utilisé pour désigner un cas de maladie détecté sur le plan épidémiologique Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. Fournissez l’identifiant du cas, lequel facilite grandement le lien entre les données de laboratoire et les données épidémiologiques. Il peut être considéré comme une information identifiable. Consultez l’intendant des données avant de le transmettre. ABCD1234 ABCD1234 PH_CASE_ID + Database Identifiers Identificateurs de base de données GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id ID principal de l’échantillon associé WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu The primary ID of a related specimen previously submitted to the repository. Identifiant principal d’un échantillon associé précédemment soumis au dépôt Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. Conservez l’identifiant primaire de l’échantillon correspondant précédemment soumis au Laboratoire national de microbiologie afin que les échantillons puissent être liés et suivis dans le système. SR20-12345 SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID + Database Identifiers Identificateurs de base de données GENEPIO:0001131 IRIDA sample name irida_sample_name Nom de l’échantillon IRIDA WhitespaceMinimizedString WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Identifiant attribué à un isolat séquencé dans IRIDA Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). Enregistrez le nom de l’échantillon IRIDA, lequel sera créé par la personne saisissant les données dans la plateforme connexe. Les échantillons IRIDA peuvent être liés à des métadonnées et à des données de séquence, ou simplement à des métadonnées. Il est recommandé que le nom de l’échantillon IRIDA soit identique ou contienne l’ID de l’échantillon du collecteur pour assurer une meilleure traçabilité. Il est également recommandé que le nom de l’échantillon IRIDA reflète l’accès à GISAID. Les noms d’échantillons IRIDA ne peuvent pas contenir de barres obliques. Celles-ci doivent être remplacées par des traits de soulignement. Consultez la documentation IRIDA pour en savoir plus sur les caractères spéciaux (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 prov_rona_99 IRIDA sample name + Database Identifiers Identificateurs de base de données GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession Numéro d’accès au bioprojet cadre umbrella bioproject accession menu UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Numéro d’accès à INSDC attribué au bioprojet cadre pour l’effort canadien de séquençage du SRAS-CoV-2 Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. Enregistrez le numéro d’accès au bioprojet cadre en le sélectionnant à partir de la liste déroulante du modèle. Ce numéro sera identique pour tous les soumissionnaires du RCanGéCO. Différentes provinces auront leurs propres bioprojets, mais ces derniers seront liés sous un seul bioprojet cadre. PRJNA623807 PRJNA623807 umbrella bioproject accession + Database Identifiers Identificateurs de base de données GENEPIO:0001136 bioproject accession bioproject_accession Numéro d’accès au bioprojet WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Numéro d’accès à INSDC du bioprojet auquel appartient un échantillon biologique Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. Enregistrez le numéro d’accès au bioprojet. Les bioprojets sont un outil d’organisation qui relie les données de séquence brutes, les assemblages et leurs métadonnées associées. Chaque province se verra attribuer un numéro d’accès différent au bioprojet par le Laboratoire national de microbiologie. Un numéro d’accès valide au bioprojet du NCBI contient le préfixe PRJN (p. ex., PRJNA12345); il est créé une fois au début d’un nouveau projet de séquençage. PRJNA608651 PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession + Database Identifiers Identificateurs de base de données GENEPIO:0001139 biosample accession biosample_accession Numéro d’accès à un échantillon biologique WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Identifiant attribué à un échantillon biologique dans les archives INSDC Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. Conservez le numéro d’accès renvoyé avec la soumission d’un échantillon biologique. Les échantillons biologiques de NCBI seront assortis du SAMN. SAMN14180202 SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION + Database Identifiers Identificateurs de base de données GENEPIO:0001142 SRA accession sra_accession Numéro d’accès à l’archive des séquences WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Identifiant de l’archive des séquences reliant les données de séquences brutes de lecture, les métadonnées méthodologiques et les mesures de contrôle de la qualité soumises à INSDC Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. Conservez le numéro d’accès attribué au « cycle » soumis. Les accès NCBI-SRA commencent par SRR. SRR11177792 SRR11177792 SRA Accession PH_SRA_ACCESSION + Database Identifiers Identificateurs de base de données GENEPIO:0001145 GenBank accession genbank_accession Numéro d’accès à GenBank WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Identifiant GenBank attribué à la séquence dans les archives INSDC Store the accession returned from a GenBank submission (viral genome assembly). Conservez le numéro d’accès renvoyé avec la soumission de GenBank (assemblage du génome viral). MN908947.3 MN908947.3 GenBank Accession GenBank accession + Database Identifiers Identificateurs de base de données GENEPIO:0001147 GISAID accession gisaid_accession Numéro d’accès à la GISAID WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Numéro d’accès à la GISAID attribué à la séquence Store the accession returned from the GISAID submission. Conservez le numéro d’accès renvoyé avec la soumission de la GISAID. EPI_ISL_436489 EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession + GENEPIO:0001150 Sample collection and processing + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001153 sample collected by sample_collected_by Échantillon prélevé par sample collected by menu SampleCollectedByMenu null value menu NullValueMenu TRUE The name of the agency that collected the original sample. Nom de l’organisme ayant prélevé l’échantillon original The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). Le nom du collecteur d’échantillons doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions, par exemple Agence de la santé publique du Canada, Santé publique Ontario, Centre de contrôle des maladies de la Colombie-Britannique. BC Centre for Disease Control Centre de contrôle des maladies de la Colombie-Britannique Originating lab Lab Name CUSTOMER collected_by sample collected by + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001156 sample collector contact email sample_collector_contact_email Adresse courriel du collecteur d’échantillons WhitespaceMinimizedString WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca). RespLab@lab.ca RespLab@lab.ca sample collector contact email + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001158 sample collector contact address sample_collector_contact_address Adresse du collecteur d’échantillons WhitespaceMinimizedString WhitespaceMinimizedString The mailing address of the agency submitting the sample. Adresse postale de l’organisme soumettant l’échantillon The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays. 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada 655, rue Lab, Vancouver (Colombie-Britannique) V5N 2A2 Canada Address sample collector contact address + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001159 sequence submitted by sequence_submitted_by Séquence soumise par sequence submitted by menu SequenceSubmittedByMenu null value menu NullValueMenu TRUE The name of the agency that generated the sequence. Nom de l’organisme ayant généré la séquence The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Le nom de l’agence doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions. Si vous soumettez des échantillons plutôt que des données de séquençage, veuillez inscrire « Laboratoire national de microbiologie (LNM) ». Public Health Ontario (PHO) Santé publique Ontario (SPO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email Adresse courriel du soumissionnaire de séquence WhitespaceMinimizedString WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca). RespLab@lab.ca RespLab@lab.ca sequence submitter contact email + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address Adresse du soumissionnaire de séquence WhitespaceMinimizedString WhitespaceMinimizedString The mailing address of the agency submitting the sequence. Adresse postale de l’organisme soumettant l’échantillon The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays. 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada 123, rue Sunnybrooke, Toronto (Ontario) M4P 1L6 Canada Address sequence submitter contact address + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001174 sample collection date sample_collection_date Date de prélèvement de l’échantillon date date null value menu NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Date à laquelle l’échantillon a été prélevé Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". La date de prélèvement des échantillons est essentielle pour la surveillance et de nombreux types d’analyses. La granularité requise comprend l’année, le mois et le jour. Si cette date est considérée comme un renseignement identifiable, il est acceptable d’y ajouter une « gigue » en ajoutant ou en soustrayant un jour civil. La « date de réception » peut également servir de date de rechange. La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-16 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001177 sample collection date precision sample_collection_date_precision Précision de la date de prélèvement de l’échantillon sample collection date precision menu SampleCollectionDatePrecisionMenu null value menu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". Fournissez la précision de la granularité au « jour », au « mois » ou à « l’année » pour la date fournie dans le champ « Date de prélèvement de l’échantillon ». Cette date sera tronquée selon la précision spécifiée lors de l’exportation : « jour » pour « AAAA-MM-JJ », « mois » pour « AAAA-MM » ou « année » pour « AAAA ». year année Precision of date collected HC_TEXT2 + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001179 sample received date sample_received_date Date de réception de l’échantillon date date null value menu NullValueMenu The date on which the sample was received. Date à laquelle l’échantillon a été reçu ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-20 2020-03-20 sample received date + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country nom_lieu_géo (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu TRUE The country where the sample was collected. Pays d’origine de l’échantillon Provide the country name from the controlled vocabulary provided. Fournissez le nom du pays à partir du vocabulaire contrôlé fourni. Canada Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory nom_lieu_géo (état/province/territoire) geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu null value menu NullValueMenu TRUE The province/territory where the sample was collected. Province ou territoire où l’échantillon a été prélevé Provide the province/territory name from the controlled vocabulary provided. Fournissez le nom de la province ou du territoire à partir du vocabulaire contrôlé fourni. Saskatchewan Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001189 geo_loc_name (city) geo_loc_name_city nom_géo_loc (ville) WhitespaceMinimizedString WhitespaceMinimizedString The city where the sample was collected. Ville où l’échantillon a été prélevé Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Fournissez le nom de la ville. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. Medicine Hat Medicine Hat Patient City geo_loc_name (city) + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001191 organism organism Organisme organism menu OrganismMenu null value menu NullValueMenu TRUE Taxonomic name of the organism. Nom taxonomique de l’organisme Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Utilisez « coronavirus du syndrome respiratoire aigu sévère 2 ». Cette valeur est fournie dans le modèle. Severe acute respiratory syndrome coronavirus 2 Coronavirus du syndrome respiratoire aigu sévère 2 Pathogen HC_CURRENT_ID organism organism + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001195 isolate isolate Isolat WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE Identifier of the specific isolate. Identifiant de l’isolat spécifique Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. Fournissez le nom du virus de la GISAID, qui doit être écrit dans le format « hCov-19/CANADA/code ISO provincial à 2 chiffres-xxxxx/année ». hCov-19/CANADA/BC-prov_rona_99/2020 hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001198 purpose of sampling purpose_of_sampling Objectif de l’échantillonnage purpose of sampling menu PurposeOfSamplingMenu null value menu NullValueMenu TRUE The reason that the sample was collected. Motif de prélèvement de l’échantillon The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. La raison pour laquelle un échantillon a été prélevé peut fournir des renseignements sur les biais potentiels de la stratégie d’échantillonnage. Choisissez l’objectif de l’échantillonnage à partir de la liste déroulante du modèle. Il est très probable que l’échantillon ait été prélevé en vue d’un test diagnostique. La raison pour laquelle un échantillon a été prélevé à l’origine peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage, ce qui doit être indiqué dans le champ « Objectif du séquençage ». Diagnostic testing Tests diagnostiques Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details Détails de l’objectif de l’échantillonnage WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE The description of why the sample was collected, providing specific details. Détails précis concernant le motif de prélèvement de l’échantillon Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été prélevé en utilisant du texte libre. La description peut inclure l’importance de l’échantillon pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Si les détails ne sont pas disponibles, fournissez une valeur nulle. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. L’échantillon a été prélevé pour étudier la prévalence des variants associés à la transmission du vison à l’homme au Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type Type d’échantillon soumis au LNM NML submitted specimen type menu NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. Type d’échantillon soumis au Laboratoire national de microbiologie (LNM) aux fins d’analyse This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Ces renseignements sont requis pour le téléchargement à l’aide du système LaSER du RCRSP. Choisissez le type d’échantillon à partir de la liste de sélection fournie. Si les données de séquences sont soumises plutôt qu’un échantillon aux fins d’analyse, sélectionnez « Sans objet ». swab Écouvillon Specimen Type PH_SPECIMEN_TYPE + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type Type de relation de l’échantillon lié Related specimen relationship type menu RelatedSpecimenRelationshipTypeMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Relation entre l’échantillon actuel et celui précédemment soumis au dépôt Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Fournissez l’étiquette qui décrit comment l’échantillon précédent est lié à l’échantillon actuel soumis à partir de la liste de sélection fournie afin que les échantillons puissent être liés et suivis dans le système. Specimen sampling methods testing Test des méthodes de prélèvement des échantillons Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001211 anatomical material anatomical_material Matière anatomique anatomical material menu AnatomicalMaterialMenu null value menu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Substance obtenue à partir d’une partie anatomique d’un organisme (p. ex., tissu, sang) Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une matière anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Blood Sang Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001214 anatomical part anatomical_part Partie anatomique anatomical part menu AnatomicalPartMenu null value menu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Partie anatomique d’un organisme (p. ex., oropharynx) Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Nasopharynx (NP) Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001216 body product body_product Produit corporel body product menu BodyProductMenu null value menu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Substance excrétée ou sécrétée par un organisme (p. ex., selles, urine, sueur) Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Feces Selles Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001223 environmental material environmental_material Matériel environnemental environmental material menu EnvironmentalMaterialMenu null value menu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Substance obtenue à partir de l’environnement naturel ou artificiel (p. ex., sol, eau, eaux usées) Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une matière environnementale a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Face mask Masque Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001232 environmental site environmental_site Site environnemental environmental site menu EnvironmentalSiteMenu null value menu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Emplacement environnemental pouvant décrire un site dans l’environnement naturel ou artificiel (p. ex., surface de contact, boîte métallique, hôpital, marché traditionnel de produits frais, grotte de chauves-souris) Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Production Facility Installation de production Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001234 collection device collection_device Dispositif de prélèvement collection device menu CollectionDeviceMenu null value menu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Instrument ou contenant utilisé pour prélever l’échantillon (p. ex., écouvillon) Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Swab Écouvillon Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001241 collection method collection_method Méthode de prélèvement collection method menu CollectionMethodMenu null value menu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Processus utilisé pour prélever l’échantillon (p. ex., phlébotomie, autopsie) Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une méthode de prélèvement a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Bronchoalveolar lavage (BAL) Lavage bronchoalvéolaire (LBA) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001243 collection protocol collection_protocol Protocole de prélèvement WhitespaceMinimizedString WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Nom et version d’un protocole particulier utilisé pour l’échantillonnage Free text. Texte libre. BCRonaSamplingProtocol v. 1.2 CBRonaProtocoleÉchantillonnage v. 1.2 collection protocol + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001253 specimen processing specimen_processing Traitement des échantillons specimen processing menu SpecimenProcessingMenu null value menu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Tout traitement appliqué à l’échantillon pendant ou après sa réception Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Essentiel pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, ajoutez les renseignements dans les champs « Laboratoire hôte », « Nombre de transmissions » et « Méthode de transmission ». Si aucun des processus de la liste de sélection ne s’applique, inscrivez « Sans objet ». Virus passage Transmission du virus Passage details/history specimen processing + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0100311 specimen processing details specimen_processing_details Détails du traitement des échantillons WhitespaceMinimizedString WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Renseignements détaillés concernant le traitement appliqué à un échantillon pendant ou après sa réception Provide a free text description of any processing details applied to a sample. Fournissez une description en texte libre de tous les détails du traitement appliqués à un échantillon. 25 swabs were pooled and further prepared as a single sample during library prep. 25 écouvillons ont été regroupés et préparés en tant qu’échantillon unique lors de la préparation de la bibliothèque. + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001255 lab host lab_host Laboratoire hôte lab host menu LabHostMenu null value menu NullValueMenu TRUE Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Nom et description du laboratoire hôte utilisé pour propager l’organisme source ou le matériel à partir duquel l’échantillon a été obtenu Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Type de lignée cellulaire utilisée pour la propagation. Choisissez le nom de cette lignée à partir de la liste de sélection dans le modèle. Si le virus n’a pas été transmis, indiquez « Sans objet ». Vero E6 cell line Lignée cellulaire Vero E6 Passage details/history lab host lab_host + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001261 passage number passage_number Nombre de transmission integer integer null value menu NullValueMenu TRUE 0 Number of passages. Nombre de transmissions Provide number of known passages. If not passaged, put "not applicable" Indiquez le nombre de transmissions connues. Si le virus n’a pas été transmis, indiquez « Sans objet ». 3 3 Passage details/history passage number passage_history + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001264 passage method passage_method Méthode de transmission WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE Description of how organism was passaged. Description de la façon dont l’organisme a été transmis Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". Texte libre. Fournissez une brève description (<10 mots). Si le virus n’a pas été transmis, indiquez « Sans objet ». 0.25% trypsin + 0.02% EDTA 0,25 % de trypsine + 0,02 % d’EDTA Passage details/history passage method passage_method + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001266 biomaterial extracted biomaterial_extracted Biomatériau extrait biomaterial extracted menu BiomaterialExtractedMenu null value menu NullValueMenu The biomaterial extracted from samples for the purpose of sequencing. Biomatériau extrait d’échantillons aux fins de séquençage Provide the biomaterial extracted from the picklist in the template. Fournissez le biomatériau extrait à partir de la liste de sélection dans le modèle. RNA (total) ARN (total) biomaterial extracted + GENEPIO:0001268 Host Information + Host Information Informations sur l'hôte GENEPIO:0001386 host (common name) host_common_name Hôte (nom commun) host (common name) menu HostCommonNameMenu null value menu NullValueMenu The commonly used name of the host. Nom couramment utilisé pour l’hôte Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Des exemples de noms communs sont « humain » et « chauve-souris ». Si l’échantillon était environnemental, inscrivez « Sans objet ». Human Humain Animal Type PH_ANIMAL_TYPE + Host Information Informations sur l'hôte GENEPIO:0001387 host (scientific name) host_scientific_name Hôte (nom scientifique) host (scientific name) menu HostScientificNameMenu null value menu NullValueMenu TRUE The taxonomic, or scientific name of the host. Nom taxonomique ou scientifique de l’hôte Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Un exemple de nom scientifique est « homo sapiens ». Si l’échantillon était environnemental, inscrivez « Sans objet ». Homo sapiens Homo sapiens Host host (scientific name) host host (scientific name) + Host Information Informations sur l'hôte GENEPIO:0001388 host health state host_health_state État de santé de l’hôte host health state menu HostHealthStateMenu null value menu NullValueMenu Health status of the host at the time of sample collection. État de santé de l’hôte au moment du prélèvement d’échantillons If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Symptomatic Symptomatique Patient status Host Health State PH_HOST_HEALTH host_health_state + Host Information Informations sur l'hôte GENEPIO:0001389 host health status details host_health_status_details Détails de l’état de santé de l’hôte host health status details menu HostHealthStatusDetailsMenu null value menu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. Plus de détails concernant l’état de santé ou de maladie de l’hôte au moment du prélèvement If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Hospitalized (ICU) Hospitalisé (USI) Host Health State Details PH_HOST_HEALTH_DETAILS + Host Information Informations sur l'hôte GENEPIO:0001390 host health outcome host_health_outcome Résultats sanitaires de l’hôte host health outcome menu HostHealthOutcomeMenu null value menu NullValueMenu Disease outcome in the host. Résultats de la maladie chez l’hôte If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Recovered Rétabli PH_HOST_HEALTH_OUTCOME host_disease_outcome + Host Information Informations sur l'hôte GENEPIO:0001391 host disease host_disease Maladie de l’hôte host disease menu HostDiseaseMenu null value menu NullValueMenu TRUE The name of the disease experienced by the host. Nom de la maladie vécue par l’hôte Select "COVID-19" from the pick list provided in the template. Sélectionnez « COVID-19 » à partir de la liste de sélection fournie dans le modèle. COVID-19 COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease + Host Information Informations sur l'hôte GENEPIO:0001392 host age host_age Âge de l’hôte decimal decimal null value menu NullValueMenu TRUE 0 130 Age of host at the time of sampling. Âge de l’hôte au moment du prélèvement d’échantillons Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". Entrez l’âge de l’hôte en années. S’il n’est pas disponible, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet ». 79 79 Patient age Patient Age PH_AGE host_age host age + Host Information Informations sur l'hôte GENEPIO:0001393 host age unit host_age_unit Catégorie d’âge de l’hôte host age unit menu HostAgeUnitMenu null value menu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Unité utilisée pour mesurer l’âge de l’hôte (mois ou année) Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. Indiquez si l’âge de l’hôte est en mois ou en années. L’âge indiqué en mois sera classé dans la tranche d’âge de 0 à 9 ans. year année Age Units PH_AGE_UNIT host age unit + Host Information Informations sur l'hôte GENEPIO:0001394 host age bin host_age_bin Groupe d’âge de l’hôte host age bin menu HostAgeBinMenu null value menu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Âge de l’hôte au moment du prélèvement d’échantillons (groupe d’âge) Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. Sélectionnez la tranche d’âge correspondante de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne la connaissez pas, fournissez une valeur nulle. 60 - 69 60 - 69 Host Age Category PH_AGE_GROUP host age bin + Host Information Informations sur l'hôte GENEPIO:0001395 host gender host_gender Genre de l’hôte host gender menu HostGenderMenu null value menu NullValueMenu TRUE The gender of the host at the time of sample collection. Genre de l’hôte au moment du prélèvement d’échantillons Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Sélectionnez le genre correspondant de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne le connaissez pas, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet ». Male Homme Gender Patient Sex VD_SEX host_sex host gender + Host Information Informations sur l'hôte GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country Résidence de l’hôte – Nom de géo_loc (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu The country of residence of the host. Pays de résidence de l’hôte Select the country name from pick list provided in the template. Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle. Canada Canada PH_HOST_COUNTRY + Host Information Informations sur l'hôte GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory Résidence de l’hôte – Nom de géo_loc (état/province/territoire) geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu null value menu NullValueMenu The state/province/territory of residence of the host. État, province ou territoire de résidence de l’hôte Select the province/territory name from pick list provided in the template. Sélectionnez le nom de la province ou du territoire à partir de la liste de sélection fournie dans le modèle. Quebec Québec PH_HOST_PROVINCE + Host Information Informations sur l'hôte GENEPIO:0001398 host subject ID host_subject_id ID du sujet de l’hôte WhitespaceMinimizedString WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Identifiant unique permettant de désigner chaque hôte (p. ex., 131) Provide the host identifier. Should be a unique, user-defined identifier. Fournissez l’identifiant de l’hôte. Il doit s’agir d’un identifiant unique défini par l’utilisateur. BCxy123 BCxy123 host subject ID host_subject_id + Host Information Informations sur l'hôte GENEPIO:0001399 symptom onset date symptom_onset_date Date d’apparition des symptômes date date null value menu NullValueMenu The date on which the symptoms began or were first noted. Date à laquelle les symptômes ont commencé ou ont été observés pour la première fois ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-16 2020-03-16 Symptoms Onset Date HC_ONSET_DATE + Host Information Informations sur l'hôte GENEPIO:0001400 signs and symptoms signs_and_symptoms Signes et symptômes signs and symptoms menu SignsAndSymptomsMenu null value menu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélant une maladie, qui est signalé par un patient ou un clinicien Select all of the symptoms experienced by the host from the pick list. Sélectionnez tous les symptômes ressentis par l’hôte à partir de la liste de sélection. Chills (sudden cold sensation); Cough; Fever Frissons (sensation soudaine de froid); toux; fièvre Symptoms HC_SYMPTOMS + Host Information Informations sur l'hôte GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors Conditions préexistantes et facteurs de risque pre-existing conditions and risk factors menu PreExistingConditionsAndRiskFactorsMenu null value menu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Conditions préexistantes et facteurs de risque du patient
  • Condition préexistante : Condition médicale qui existait avant l’infection actuelle
  • Facteur de risque : Variable associée à un risque accru de maladie ou d’infection  Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les conditions préexistantes et tous les facteurs de risque de l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Asthma; Pregnancy; Smoking Asthme; grossesse; tabagisme pre-existing conditions and risk factors + Host Information Informations sur l'hôte GENEPIO:0001402 complications complications Complications complications menu ComplicationsMenu null value menu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Complications médicales du patient qui seraient dues à une maladie de l’hôte Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les complications éprouvées par l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Acute Respiratory Failure; Coma; Septicemia Insuffisance respiratoire aiguë; coma; septicémie complications + GENEPIO:0001403 Host vaccination information + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001404 host vaccination status host_vaccination_status Statut de vaccination de l’hôte host vaccination status menu host vaccination status menu null value menu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Statut de vaccination de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné) Select the vaccination status of the host from the pick list. Sélectionnez le statut de vaccination de l’hôte à partir de la liste de sélection. Fully Vaccinated Entièrement vacciné PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received Nombre de doses du vaccin reçues integer integer The number of doses of the vaccine recived by the host. Nombre de doses du vaccin reçues par l’hôte Record how many doses of the vaccine the host has received. Enregistrez le nombre de doses du vaccin que l’hôte a reçues. 2 2 + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name Dose du vaccin 1 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Nom du vaccin administré comme première dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date Dose du vaccin 1 – Date du vaccin date date null value menu NullValueMenu The date the first dose of a vaccine was administered. Date à laquelle la première dose d’un vaccin a été administrée Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-03-01 2021-03-01 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100315 vaccination dose 2 vaccine name vaccination_dose_2_vaccine_name Dose du vaccin 2 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the second dose of a vaccine regimen. Nom du vaccin administré comme deuxième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100316 vaccination dose 2 vaccination date vaccination_dose_2_vaccination_date Dose du vaccin 2 – Date du vaccin date date null value menu NullValueMenu The date the second dose of a vaccine was administered. Date à laquelle la deuxième dose d’un vaccin a été administrée Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-09-01 2021-09-01 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100317 vaccination dose 3 vaccine name vaccination_dose_3_vaccine_name Dose du vaccin 3 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the third dose of a vaccine regimen. Nom du vaccin administré comme troisième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100318 vaccination dose 3 vaccination date vaccination_dose_3_vaccination_date Dose du vaccin 3 – Date du vaccin date date null value menu NullValueMenu The date the third dose of a vaccine was administered. Date à laquelle la troisième dose d’un vaccin a été administrée Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-12-30 2021-12-30 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100319 vaccination dose 4 vaccine name vaccination_dose_4_vaccine_name Dose du vaccin 4 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the fourth dose of a vaccine regimen. Nom du vaccin administré comme quatrième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100320 vaccination dose 4 vaccination date vaccination_dose_4_vaccination_date Dose du vaccin 4 – Date du vaccin date date null value menu NullValueMenu The date the fourth dose of a vaccine was administered. Date à laquelle la quatrième dose d’un vaccin a été administrée Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2022-01-15 2022-01-15 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100321 vaccination history vaccination_history Antécédents de vaccination WhitespaceMinimizedString WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Description des vaccins reçus et dates d’administration d’une série de vaccins contre une maladie spécifique ou un ensemble de maladies Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Description en texte libre des dates et des vaccins administrés contre une maladie précise ou un ensemble de maladies. Il est également acceptable de concaténer les renseignements sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 PH_VACCINATION_HISTORY + GENEPIO:0001409 Host exposure information + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country Lieu de l’exposition – Nom de géo_loc (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Pays où l’hôte a probablement été exposé à l’agent causal de la maladie Select the country name from pick list provided in the template. Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle. Canada Canada PH_EXPOSURE_COUNTRY + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city Destination du dernier voyage (ville) WhitespaceMinimizedString WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Nom de la ville de destination du voyage le plus récent Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de la ville dans laquelle l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. New York City New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory Destination du dernier voyage (état/province/territoire) WhitespaceMinimizedString WhitespaceMinimizedString The name of the province that was the destination of most recent travel. Nom de la province de destination du voyage le plus récent Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de l’État, de la province ou du territoire où l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. California Californie Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country Destination du dernier voyage (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu The name of the country that was the destination of most recent travel. Nom du pays de destination du voyage le plus récent Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom du pays dans lequel l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. United Kingdom Royaume-Uni Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date Date de départ de voyage la plus récente date date null value menu NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Date du départ le plus récent d’une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits Provide the travel departure date. Indiquez la date de départ du voyage. 2020-03-16 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001415 most recent travel return date most_recent_travel_return_date Date de retour de voyage la plus récente date date null value menu NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Date du retour le plus récent d’une personne à une résidence après un voyage au départ de cette résidence Provide the travel return date. Indiquez la date de retour du voyage. 2020-04-26 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100413 travel point of entry type travel_point_of_entry_type Type de point d’entrée du voyage travel point of entry type menu TravelPointOfEntryTypeMenu null value menu NullValueMenu TRUE The type of entry point a traveler arrives through. Type de point d’entrée par lequel un voyageur arrive Select the point of entry type. Sélectionnez le type de point d’entrée. Air Air PH_POINT_OF_ENTRY + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100414 border testing test day type border_testing_test_day_type Jour du dépistage à la frontière border testing test day type menu BorderTestingTestDayTypeMenu null value menu NullValueMenu TRUE The day a traveller was tested on or after arrival at their point of entry. Jour où un voyageur a été testé à son point d’entrée ou après cette date Select the test day. Sélectionnez le jour du test. day 1 Jour 1 PH_DAY + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001416 travel history travel_history Antécédents de voyage WhitespaceMinimizedString WhitespaceMinimizedString Travel history in last six months. Historique de voyage au cours des six derniers mois Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Précisez les pays (et les emplacements plus précis, si vous les connaissez) visités au cours des six derniers mois, ce qui peut comprendre plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Commencez par le voyage le plus récent. Canada, Vancouver; USA, Seattle; Italy, Milan Canada, Vancouver; États-Unis, Seattle; Italie, Milan PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100649 travel history availability travel_history_availability Disponibilité des antécédents de voyage travel history availability menu TravelHistoryAvailabilityMenu null value menu NullValueMenu The availability of different types of travel history in the last 6 months (e.g. international, domestic). Disponibilité de différents types d’historiques de voyages au cours des six derniers mois (p. ex., internationaux, nationaux) If travel history is available, but the details of travel cannot be provided, indicate this and the type of travel history availble by selecting a value from the picklist. The values in this field can be used to indicate a sample is associated with a travel when the "purpose of sequencing" is not travel-associated. Si les antécédents de voyage sont disponibles, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d’antécédents disponibles en sélectionnant une valeur à partir de la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu’un échantillon est associé à un voyage lorsque le « but du séquençage » n’est pas associé à un voyage. International travel history available Antécédents de voyage à l’étranger disponible PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001417 exposure event exposure_event Événement d’exposition exposure event menu ExposureEventMenu null value menu NullValueMenu Event leading to exposure. Événement conduisant à une exposition Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez un événement conduisant à une exposition à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Convention Convention Additional location information Exposure Event PH_EXPOSURE + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001418 exposure contact level exposure_contact_level Niveau de contact de l’exposition exposure contact level menu ExposureContactLevelMenu null value menu NullValueMenu The exposure transmission contact type. Type de contact de transmission d’exposition Select direct or indirect exposure from the pick-list. Sélectionnez une exposition directe ou indirecte à partir de la liste de sélection. Direct Direct exposure contact level + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001419 host role host_role Rôle de l’hôte host role menu HostRoleMenu TRUE The role of the host in relation to the exposure setting. Rôle de l’hôte par rapport au paramètre d’exposition Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez les rôles personnels de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Patient Patient PH_HOST_ROLE + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001428 exposure setting exposure_setting Contexte de l’exposition exposure setting menu ExposureSettingMenu TRUE The setting leading to exposure. Contexte menant à l’exposition Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Sélectionnez les contextes menant à l’exposition de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Healthcare Setting Milieu de soins de santé PH_EXPOSURE + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001431 exposure details exposure_details Détails de l’exposition WhitespaceMinimizedString WhitespaceMinimizedString Additional host exposure information. Renseignements supplémentaires sur l’exposition de l’hôte Free text description of the exposure. Description en texte libre de l’exposition. Host role - Other: Bus Driver Rôle d’hôte - Autre : Conducteur d’autobus PH_EXPOSURE_DETAILS + + + GENEPIO:0001434 Host reinfection information + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001435 prior SARS-CoV-2 infection prior_sarscov2_infection Infection antérieure par le SRAS-CoV-2 prior SARS-CoV-2 infection menu PriorSarsCov2InfectionMenu null value menu NullValueMenu Whether there was prior SARS-CoV-2 infection. Infection antérieure par le SRAS-CoV-2 ou non If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Si vous le savez, fournissez des renseignements indiquant si la personne a déjà eu une infection par le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection. Yes Oui prior SARS-CoV-2 infection + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001436 prior SARS-CoV-2 infection isolate prior_sarscov2_infection_isolate Isolat d’une infection antérieure par le SRAS-CoV-2 WhitespaceMinimizedString WhitespaceMinimizedString The identifier of the isolate found in the prior SARS-CoV-2 infection. Identifiant de l’isolat trouvé lors de l’infection antérieure par le SRAS-CoV-2 Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom de « l’isolat » pour qu’il soit conforme à la norme ICTV/INSDC dans le format suivant : « SRAS-CoV-2/hôte/pays/IDéchantillon/date ». SARS-CoV-2/human/USA/CA-CDPH-001/2020 SARS-CoV-2/human/USA/CA-CDPH-001/2020 prior SARS-CoV-2 infection isolate + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001437 prior SARS-CoV-2 infection date prior_sarscov2_infection_date Date d’une infection antérieure par le SRAS-CoV-2 date date The date of diagnosis of the prior SARS-CoV-2 infection. Date du diagnostic de l’infection antérieure par le SRAS-CoV-2 Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d’infection antérieure par le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-01-23 2021-01-23 prior SARS-CoV-2 infection date + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001438 prior SARS-CoV-2 antiviral treatment prior_sarscov2_antiviral_treatment Traitement antiviral contre une infection antérieure par le SRAS-CoV-2 prior SARS-CoV-2 antiviral treatment menu PriorSarsCov2AntiviralTreatmentMenu null value menu NullValueMenu Whether there was prior SARS-CoV-2 treatment with an antiviral agent. Traitement contre une infection antérieure par le SRAS-CoV-2 avec un agent antiviral ou non If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection. No prior antiviral treatment Aucun traitement antiviral antérieur prior SARS-CoV-2 antiviral treatment + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001439 prior SARS-CoV-2 antiviral treatment agent prior_sarscov2_antiviral_treatment_agent Agent du traitement antiviral contre une infection antérieure par le SRAS-CoV-2 WhitespaceMinimizedString WhitespaceMinimizedString The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SRAS-CoV-2 Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous, séparés par des virgules. Remdesivir Remdesivir prior SARS-CoV-2 antiviral treatment agent + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001440 prior SARS-CoV-2 antiviral treatment date prior_sarscov2_antiviral_treatment_date Date du traitement antiviral contre une infection antérieure par le SRAS-CoV-2 date date The date treatment was first administered during the prior SARS-CoV-2 infection. Date à laquelle le traitement a été administré pour la première fois lors de l’infection antérieure par le SRAS-CoV-2 Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’agent de traitement antiviral a été administré pour la première fois lors de l’infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-01-28 2021-01-28 prior SARS-CoV-2 antiviral treatment date + + + GENEPIO:0001441 Sequencing + Sequencing Séquençage GENEPIO:0001445 purpose of sequencing purpose_of_sequencing Objectif du séquençage purpose of sequencing menu PurposeOfSequencingMenu null value menu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Raison pour laquelle l’échantillon a été séquencé The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. La raison pour laquelle un échantillon a été initialement prélevé peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des renseignements sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. Le motif de prélèvement de l’échantillon doit être indiqué dans le champ « Objectif de l’échantillonnage ». Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing + Sequencing Séquençage GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details Détails de l’objectif du séquençage WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Description de la raison pour laquelle l’échantillon a été séquencé, fournissant des détails spécifiques Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été séquencé en utilisant du texte libre. La description peut inclure l’importance des séquences pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Les descriptions normalisées suggérées sont les suivantes : Dépistage de l’absence de détection du gène S (abandon du gène S), dépistage de variants associés aux visons, dépistage du variant B.1.1.7, dépistage du variant B.1.135, dépistage du variant P.1, dépistage en raison des antécédents de voyage, dépistage en raison d’un contact étroit avec une personne infectée, évaluation des mesures de contrôle de la santé publique, détermination des introductions et de la propagation précoces, enquête sur les expositions liées aux voyages aériens, enquête sur les travailleurs étrangers temporaires, enquête sur les régions éloignées, enquête sur les travailleurs de la santé, enquête sur les écoles et les universités, enquête sur la réinfection. Screened for S gene target failure (S dropout) Dépistage de l’absence de détection du gène S (abandon du gène S) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details + Sequencing Séquençage GENEPIO:0001447 sequencing date sequencing_date Date de séquençage date date null value menu NullValueMenu TRUE {sample collection date} The date the sample was sequenced. Date à laquelle l’échantillon a été séquencé ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-06-22 2020-06-22 PH_SEQUENCING_DATE + Sequencing Séquençage GENEPIO:0001448 library ID library_id ID de la bibliothèque WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. Identifiant spécifié par l’utilisateur pour la bibliothèque faisant l’objet du séquençage The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. Le nom de la bibliothèque doit être unique et peut être un ID généré automatiquement à partir de votre système de gestion de l’information des laboratoires, ou une modification de l’ID de l’isolat. XYZ_123345 XYZ_123345 library ID + Sequencing Séquençage GENEPIO:0001449 amplicon size amplicon_size Taille de l’amplicon WhitespaceMinimizedString WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Longueur de l’amplicon généré par l’amplification de la réaction de polymérisation en chaîne Provide the amplicon size, including the units. Fournissez la taille de l’amplicon, y compris les unités. 300bp 300 pb amplicon size + Sequencing Séquençage GENEPIO:0001450 library preparation kit library_preparation_kit Trousse de préparation de la bibliothèque WhitespaceMinimizedString WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Nom de la trousse de préparation de la banque d’ADN utilisée pour générer la bibliothèque faisant l’objet du séquençage Provide the name of the library preparation kit used. Indiquez le nom de la trousse de préparation de la bibliothèque utilisée. Nextera XT Nextera XT PH_LIBRARY_PREP_KIT + Sequencing Séquençage GENEPIO:0001451 flow cell barcode flow_cell_barcode Code-barres de la cuve à circulation WhitespaceMinimizedString WhitespaceMinimizedString The barcode of the flow cell used for sequencing. Code-barres de la cuve à circulation utilisée aux fins de séquençage Provide the barcode of the flow cell used for sequencing the sample. Fournissez le code-barres de la cuve à circulation utilisée pour séquencer l’échantillon. FAB06069 FAB06069 flow cell barcode + Sequencing Séquençage GENEPIO:0001452 sequencing instrument sequencing_instrument Instrument de séquençage sequencing instrument menu SequencingInstrumentMenu null value menu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Modèle de l’instrument de séquençage utilisé Select a sequencing instrument from the picklist provided in the template. Sélectionnez l’instrument de séquençage à partir de la liste de sélection. Oxford Nanopore MinION Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument + Sequencing Séquençage GENEPIO:0001453 sequencing protocol name sequencing_protocol_name Nom du protocole de séquençage WhitespaceMinimizedString WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Nom et numéro de version du protocole de séquençage utilisé Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION Fournissez le nom et la version du protocole de séquençage (p. ex., 1D_DNA_MinION). https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name PH_SEQ_PROTOCOL_NAME + Sequencing Séquençage GENEPIO:0001454 sequencing protocol sequencing_protocol Protocole de séquençage WhitespaceMinimizedString WhitespaceMinimizedString The protocol used to generate the sequence. Protocole utilisé pour générer la séquence Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Voici le texte suggéré (insérez les renseignements manquants) : « Le séquençage viral a été effectué selon une stratégie d’amplicon en mosaïque en utilisant le schéma d’amorce <à remplir>. Le séquençage a été effectué à l’aide d’un instrument de séquençage <à remplir>. Les bibliothèques ont été préparées à l’aide de la trousse <à remplir>. » Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Les génomes ont été générés par séquençage d’amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l’aide des trousses de préparation de l’ADN Illumina et les données de séquence ont été produites à l’aide des trousses de séquençage Miseq Micro v2 (500 cycles). PH_TESTING_PROTOCOL sequencing protocol + Sequencing Séquençage GENEPIO:0001455 sequencing kit number sequencing_kit_number Numéro de la trousse de séquençage WhitespaceMinimizedString WhitespaceMinimizedString The manufacturer's kit number. Numéro de la trousse du fabricant Alphanumeric value. Valeur alphanumérique. AB456XYZ789 AB456XYZ789 sequencing kit number + Sequencing Séquençage GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme Schéma d’amorce pour la réaction de polymérisation en chaîne de l’amplicon WhitespaceMinimizedString WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Spécifications liées aux amorces (séquences d’amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer Provide the name and version of the primer scheme used to generate the amplicons for sequencing. Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons aux fins de séquençage. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon pcr primer scheme + GENEPIO:0001457 Bioinformatics and QC metrics + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method Méthode de traitement des données de séquences brutes WhitespaceMinimizedString WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Nom et numéro de version du logiciel utilisé pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l’adaptateur, le filtrage, etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Fournissez le nom du logiciel, suivi de la version (p. ex., Trimmomatic v. 0.38, Porechop v. 0.2.03). Porechop 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001459 dehosting method dehosting_method Méthode de retrait de l’hôte WhitespaceMinimizedString WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Méthode utilisée pour supprimer les lectures de l’hôte de la séquence de l’agent pathogène Provide the name and version number of the software used to remove host reads. Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l’hôte. Nanostripper Nanostripper PH_DEHOSTING_METHOD dehosting method + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001460 consensus sequence name consensus_sequence_name Nom de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString The name of the consensus sequence. Nom de la séquence de consensus Provide the name and version number of the consensus sequence. Fournissez le nom et le numéro de version de la séquence de consensus. ncov123assembly3 ncov123assembly3 consensus sequence name + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001461 consensus sequence filename consensus_sequence_filename Nom du fichier de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString The name of the consensus sequence file. Nom du fichier de la séquence de consensus Provide the name and version number of the consensus sequence FASTA file. Fournissez le nom et le numéro de version du fichier FASTA de la séquence de consensus. ncov123assembly.fasta ncov123assembly.fasta consensus sequence filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001462 consensus sequence filepath consensus_sequence_filepath Chemin d’accès au fichier de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString The filepath of the consensus sequence file. Chemin d’accès au fichier de la séquence de consensus Provide the filepath of the consensus sequence FASTA file. Fournissez le chemin d’accès au fichier FASTA de la séquence de consensus. /User/Documents/RespLab/Data/ncov123assembly.fasta /User/Documents/RespLab/Data/ncov123assembly.fasta consensus sequence filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name Nom du logiciel de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Nom du logiciel utilisé pour générer la séquence de consensus Provide the name of the software used to generate the consensus sequence. Fournissez le nom du logiciel utilisé pour générer la séquence de consensus. iVar iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version Version du logiciel de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Version du logiciel utilisé pour générer la séquence de consensus Provide the version of the software used to generate the consensus sequence. Fournir la version du logiciel utilisé pour générer la séquence de consensus. 1.3 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value Valeur de l’étendue de la couverture WhitespaceMinimizedString WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Pourcentage du génome de référence couvert par les données séquencées, jusqu’à une profondeur prescrite Provide value as a percent. Fournissez la valeur en pourcentage. 95% 95 % breadth of coverage value breadth of coverage value + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001474 depth of coverage value depth_of_coverage_value Valeur de l’ampleur de la couverture WhitespaceMinimizedString WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite Provide value as a fold of coverage. Fournissez la valeur sous forme de couverture amplifiée. 400x 400x Coverage depth of coverage value depth of coverage value + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold Seuil de l’ampleur de la couverture WhitespaceMinimizedString WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Seuil utilisé comme limite pour l’ampleur de la couverture Provide the threshold fold coverage. Fournissez la couverture amplifiée. 100x 100x depth of coverage threshold + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001476 r1 fastq filename r1_fastq_filename________ Nom de fichier R1 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Nom du fichier R1 FASTQ spécifié par l’utilisateur Provide the r1 FASTQ filename. Fournissez le nom du fichier R1 FASTQ. ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001477 r2 fastq filename r2_fastq_filename Nom de fichier R2 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Nom du fichier R2 FASTQ spécifié par l’utilisateur Provide the r2 FASTQ filename. Fournissez le nom du fichier R2 FASTQ. ABC123_S1_L001_R2_001.fastq.gz ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath Chemin d’accès au fichier R1 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Emplacement du fichier R1 FASTQ dans le système de l’utilisateur Provide the filepath for the r1 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R1 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath Chemin d’accès au fichier R2 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Emplacement du fichier R2 FASTQ dans le système de l’utilisateur Provide the filepath for the r2 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R2 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001480 fast5 filename fast5_filename Nom de fichier FAST5 WhitespaceMinimizedString WhitespaceMinimizedString The user-specified filename of the FAST5 file. Nom du fichier FAST5 spécifié par l’utilisateur Provide the FAST5 filename. Fournissez le nom du fichier FAST5. rona123assembly.fast5 rona123assembly.fast5 fast5 filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001481 fast5 filepath fast5_filepath Chemin d’accès au fichier FAST5 WhitespaceMinimizedString WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Emplacement du fichier FAST5 dans le système de l’utilisateur Provide the filepath for the FAST5 file. This information aids in data management. Fournissez le chemin d’accès au fichier FAST5. /User/Documents/RespLab/Data/rona123assembly.fast5 /User/Documents/RespLab/Data/rona123assembly.fast5 fast5 filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Nombre de paires de bases séquencées integer integer 0 The number of total base pairs generated by the sequencing process. Nombre total de paires de bases générées par le processus de séquençage Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 387566 387 566 number of base pairs sequenced + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001483 consensus genome length consensus_genome_length Longueur consensuelle du génome integer integer 0 Size of the reconstructed genome described as the number of base pairs. Taille du génome reconstitué décrite comme étant le nombre de paires de bases Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 38677 38 677 consensus genome length + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp N par 100 kbp decimal decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Nombre de symboles N présents dans la séquence fasta de consensus, par 100 kbp de séquence Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 330 330 Ns per 100 kbp + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001485 reference genome accession reference_genome_accession Accès au génome de référence WhitespaceMinimizedString WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Identifiant persistant et unique d’une entrée dans une base de données génomique Provide the accession number of the reference genome. Fournissez le numéro d’accès au génome de référence. NC_045512.2 NC_045512.2 reference genome accession reference genome accession + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol Protocole bioinformatique WhitespaceMinimizedString WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Description de la stratégie bioinformatique globale utilisée Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes, générer des assemblages ou générer des séquences de consensus peuvent être fournis dans une PON, un protocole, un pipeline ou un flux de travail. Fournissez le nom et le numéro de version du protocole, ou un lien GitHub vers un pipeline ou un flux de travail. https://github.com/phac-nml/ncov2019-artic-nf https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol + GENEPIO:0001498 Lineage and Variant information + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001500 lineage/clade name lineage_clade_name Nom de la lignée ou du clade WhitespaceMinimizedString WhitespaceMinimizedString The name of the lineage or clade. Nom de la lignée ou du clade Provide the Pangolin or Nextstrain lineage/clade name. Fournissez le nom de la lignée ou du clade Pangolin ou Nextstrain. B.1.1.7 B.1.1.7 PH_LINEAGE_CLADE_NAME + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name Nom du logiciel d’analyse de la lignée ou du clade WhitespaceMinimizedString WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Nom du logiciel utilisé pour déterminer la lignée ou le clade Provide the name of the software used to determine the lineage/clade. Fournissez le nom du logiciel utilisé pour déterminer la lignée ou le clade. Pangolin Pangolin PH_LINEAGE_CLADE_SOFTWARE + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version Version du logiciel d’analyse de la lignée ou du clade WhitespaceMinimizedString WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Version du logiciel utilisé pour déterminer la lignée ou le clade Provide the version of the software used ot determine the lineage/clade. Fournissez la version du logiciel utilisé pour déterminer la lignée ou le clade. 2.1.10 2.1.10 PH_LINEAGE_CLADE_VERSION + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001503 variant designation variant_designation Désignation du variant variant designation menu VariantDesignationMenu null value menu NullValueMenu The variant classification of the lineage/clade i.e. variant, variant of concern. Classification des variants de la lignée ou du clade (c.-à-d. le variant, le variant préoccupant) If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Si la lignée ou le clade est considéré comme étant un variant préoccupant, sélectionnez l’option connexe à partir de la liste de sélection. Si la lignée ou le clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques), mais qu’il ne s’agit pas d’un variant préoccupant global, sélectionnez « Variante ». Si la lignée ou le clade ne contient pas de mutations préoccupantes, laissez ce champ vide. Variant of Concern Variant préoccupant PH_VARIANT_DESIGNATION + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001504 variant evidence variant_evidence Données probantes du variant variant evidence menu VariantEvidenceMenu null value menu NullValueMenu The evidence used to make the variant determination. Données probantes utilisées pour déterminer le variant Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. Indiquez si l’échantillon a fait l’objet d’un dépistage RT-qPCR ou par séquençage à partir de la liste de sélection. RT-qPCR RT-qPCR PH_VARIANT_EVIDENCE + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001505 variant evidence details variant_evidence_details Détails liés aux données probantes du variant WhitespaceMinimizedString WhitespaceMinimizedString Details about the evidence used to make the variant determination. Détails sur les données probantes utilisées pour déterminer le variant Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Fournissez l’essai biologique et répertoriez l’ensemble des mutations définissant la lignée qui sont utilisées pour effectuer la détermination des variants. Si des mutations d’intérêt ou de préoccupation ont été observées en plus des mutations définissant la lignée, décrivez-les ici. Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). Mutations définissant la lignée : ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). PH_VARIANT_EVIDENCE_DETAILS + GENEPIO:0001506 Pathogen diagnostic testing + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001507 gene name 1 gene_name_1 Nom du gène 1 gene name menu GeneNameMenu null value menu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet du gène soumis au dépistage. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. E gene (orf4) Gène E (orf4) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 Protocole de diagnostic de polymérase en chaîne 1 WhitespaceMinimizedString WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. EGenePCRTest 2 EGenePCRTest 2 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 Valeur de diagnostic de polymérase en chaîne 1 decimal decimal null value menu NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the diagnostic RT-PCR test. Fournissez la valeur Ct de l’échantillon issu du test diagnostique RT-PCR. 21 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001510 gene name 2 gene_name_2 Nom du gène 2 gene name menu GeneNameMenu null value menu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. RdRp gene (nsp12) Gène RdRp (nsp12) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 Protocole de diagnostic de polymérase en chaîne 2 WhitespaceMinimizedString WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 Valeur de diagnostic de polymérase en chaîne 2 decimal decimal null value menu NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR. 36 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001513 gene name 3 gene_name_3 Nom du gène 3 gene name menu GeneNameMenu null value menu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. RdRp gene (nsp12) Gène RdRp (nsp12) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 Protocole de diagnostic de polymérase en chaîne 3 WhitespaceMinimizedString WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 Valeur de diagnostic de polymérase en chaîne 3 decimal decimal null value menu NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR. 30 30 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value + + + GENEPIO:0001516 Contributor acknowledgement + Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001517 authors authors Auteurs WhitespaceMinimizedString WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Noms des personnes contribuant aux processus de prélèvement d’échantillons, de génération de séquences, d’analyse et de soumission de données Include the first and last names of all individuals that should be attributed, separated by a comma. Incluez le prénom et le nom de toutes les personnes qui doivent être affectées, séparés par une virgule. Tejinder Singh, Fei Hu, Joe Blogs Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS + Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance de DataHarmonizer Provenance Provenance The DataHarmonizer software and template version provenance. Provenance du logiciel DataHarmonizer et de la version du modèle The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. Les renseignements actuels sur la version du logiciel et du modèle seront automatiquement générés dans ce champ une fois que l’utilisateur aura utilisé la fonction « Valider ». Ces renseignements seront générés indépendamment du fait que la ligne soit valide ou non. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS + \ No newline at end of file From 5866b2520c5e282e2ec1c8a9554a893b97d0dce3 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 10 Oct 2024 12:50:28 -0700 Subject: [PATCH 56/96] Should prevent clipping of cell content at 255 characters. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 5850c9f5..0e0f29cb 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "data-harmonizer", - "version": "1.7.0", + "version": "1.7.1", "description": "A standardized spreadsheet editor and validator that can be run offline and locally", "repository": "git@github.com:cidgoh/DataHarmonizer.git", "license": "MIT", From 9024ac55f053b1eebd0d4c41a8538eafe5fdbd08 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Fri, 11 Oct 2024 12:11:45 +0100 Subject: [PATCH 57/96] SDRF Scheme enum and slot changes Made changes to schema enums and schema slots --- web/templates/SDRF/schema_enums.tsv | 102 ++++++++++++++++++++++++++++ web/templates/SDRF/schema_slots.tsv | 23 +++++++ 2 files changed, 125 insertions(+) create mode 100644 web/templates/SDRF/schema_enums.tsv create mode 100644 web/templates/SDRF/schema_slots.tsv diff --git a/web/templates/SDRF/schema_enums.tsv b/web/templates/SDRF/schema_enums.tsv new file mode 100644 index 00000000..ad76626b --- /dev/null +++ b/web/templates/SDRF/schema_enums.tsv @@ -0,0 +1,102 @@ +name title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_SDRF +NullValueMenu null value menu A menu of data collection status options for this field. + NCIT:C48660 not applicable Determination of a value is not relevant in the current context. not applicable + NCIT:C126101 not available The desired information is not available. not available +CharacteristicsOrganismMenu characteristics organism menu NCBITaxon:9606 homo sapiens Homo sapiens +CharacteristicsSexMenu characteristics sex menu PATO:0000384 male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male + PATO:0000383 female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female +TechnologyTypeMenu technology type menu EFO:0002766 proteomic profiling by mass spectrometry An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry proteomic profiling by mass spectrometry +CommentProteomicsDataAcquisitionMethodMenu comment[proteomics data acquisition method] Menu PRIDE:0000627 Data-dependent acquisition Data-dependent acquisition + PRIDE:0000450 Data-independent acquisition Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846. Data-independent acquisition +CommentLabelMenu comment[label] Menu PRIDE:0000541 ICAT heavy AC=PRIDE:0000541;NT=ICAT heavy + PRIDE:0000542 ICAT light AC=PRIDE:0000542;NT=ICAT light + PRIDE:0000531 ITRAQ113 AC=PRIDE:0000531;NT=ITRAQ113 + PRIDE:0000532 ITRAQ114 AC=PRIDE:0000532;NT=ITRAQ114 + PRIDE:0000533 ITRAQ115 AC=PRIDE:0000533;NT=ITRAQ115 + PRIDE:0000534 ITRAQ116 AC=PRIDE:0000534;NT=ITRAQ116 + PRIDE:0000535 ITRAQ117 AC=PRIDE:0000535;NT=ITRAQ117 + PRIDE:0000536 ITRAQ118 AC=PRIDE:0000536;NT=ITRAQ118 + PRIDE:0000537 ITRAQ119 AC=PRIDE:0000537;NT=ITRAQ119 + PRIDE:0000538 ITRAQ121 AC=PRIDE:0000538;NT=ITRAQ121 + MS:1002038 label free sample AC=MS:1002038;NT=label free sample + PRIDE:0000621 13C Metabolic label 13C AC=PRIDE::0000621;NT=13C + PRIDE:0000620 15N Metabolic label 15N AC=PRIDE::0000620;NT=15N + PRIDE:0000622 18O Metabolic label 18O AC=PRIDE:0000622;NT=18O + PRIDE:0000516 TMT126 AC=PRIDE:0000516;NT=TMT126 + PRIDE:0000517 TMT127 AC=PRIDE:0000517;NT=TMT127 + PRIDE:0000518 TMT127C AC=PRIDE:0000518;NT=TMT127C + PRIDE:0000519 TMT127N AC=PRIDE:0000519;NT=TMT127N + PRIDE:0000520 TMT128 AC=PRIDE:0000520;NT=TMT128 + PRIDE:0000521 TMT128C AC=PRIDE:0000521;NT=TMT128C + PRIDE:0000522 TMT128N AC=PRIDE:0000522;NT=TMT128N + PRIDE:0000523 TMT129 AC=PRIDE:0000523;NT=TMT129 + PRIDE:0000524 TMT129C AC=PRIDE:0000524;NT=TMT129C + PRIDE:0000525 TMT129N AC=PRIDE:0000525;NT=TMT129N + PRIDE:0000526 TMT130 AC=PRIDE:0000526;NT=TMT130 + PRIDE:0000527 TMT130C AC=PRIDE:0000527;NT=TMT130C + PRIDE:0000528 TMT130N AC=PRIDE:0000528;NT=TMT130N + PRIDE:0000529 TMT131 AC=PRIDE:0000529;NT=TMT131 + PRIDE:0000581 TMT131C AC=PRIDE:0000581;NT=TMT131C + PRIDE:0000580 TMT131N AC=PRIDE:0000580;NT=TMT131N + PRIDE:0000583 TMT132C AC=PRIDE:0000583;NT=TMT132C + PRIDE:0000582 TMT132N AC=PRIDE:0000582;NT=TMT132N + PRIDE:0000633 TMT133C AC=PRIDE:0000633;NT=TMT133C + PRIDE:0000632 TMT133N AC=PRIDE:0000632;NT=TMT133N + PRIDE:0000642 TMT134C AC=PRIDE:0000642;NT=TMT134C + PRIDE:0000634 TMT134N AC=PRIDE:0000634;NT=TMT134N + PRIDE:0000643 TMT135N AC=PRIDE:0000643;NT=TMT135N +CommentInstrumentMenu comment[instrument] Menu MS:1003095 Orbitrap Exploris 120 Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS. NT=Orbitrap Exploris 120;AC=MS:1003095 + MS:1003094 Orbitrap Exploris 240 Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS. NT=Orbitrap Exploris 240;AC=MS:1003094 + MS:1003028 Orbitrap Exploris 480 Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS. NT=Orbitrap Exploris 480;AC=MS:1003028 + MS:1003356 Orbitrap Ascend Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. NT=Orbitrap Ascend;AC=MS:1003356 + MS:1003378 Orbitrap Astral Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer. NT=Orbitrap Astral;AC=MS:1003378 + MS:1003029 Orbitrap Eclipse Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. NT=Orbitrap Eclipse;AC=MS:1003029 + MS:1002416 Orbitrap Fusion Thermo Scientific Orbitrap Fusion. NT=Orbitrap Fusion;AC=MS:1002416 + MS:1002417 Orbitrap Fusion ETD Thermo Scientific Orbitrap Fusion with ETD. NT=Orbitrap Fusion ETD;AC=MS:1002417 + MS:1002732 Orbitrap Fusion Lumos Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. NT=Orbitrap Fusion Lumos;AC=MS:1002732 + MS:1003112 Orbitrap ID-X Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. NT=Orbitrap ID-X;AC=MS:1003112 + MS:1003411 Orbitrap IQ-X Thermo Scientific Orbitrap IQ-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. NT=Orbitrap IQ-X;AC=MS:1003411 + MS:1000449 LTQ Orbitrap Finnigan LTQ Orbitrap MS. NT=LTQ Orbitrap;AC=MS:1000449 + MS:1002835 LTQ Orbitrap Classic Thermo Fisher Scientific LTQ Orbitrap Classic. NT=LTQ Orbitrap Classic;AC=MS:1002835 + MS:1000555 LTQ Orbitrap Discovery LTQ Orbitrap Discovery. NT=LTQ Orbitrap Discovery;AC=MS:1000555 + MS:1001910 LTQ Orbitrap Elite Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite. NT=LTQ Orbitrap Elite;AC=MS:1001910 + MS:1001742 LTQ Orbitrap Velos Finnigan LTQ Orbitrap Velos MS NT=LTQ Orbitrap Velos;AC=MS:1001742 + MS:1003096 LTQ Orbitrap Velos Pro Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro. NT=LTQ Orbitrap Velos Pro;AC=MS:1003096 + MS:1000556 LTQ Orbitrap XL LTQ Orbitrap XL. NT=LTQ Orbitrap XL;AC=MS:1000556 + MS:1000639 LTQ Orbitrap XL ETD Thermo Scientific LTQ Orbitrap XL MS with ETD. NT=LTQ Orbitrap XL ETD;AC=MS:1000639 + MS:1000643 MALDI LTQ Orbitrap Thermo Scientific MALDI LTQ Orbitrap MS. NT=MALDI LTQ Orbitrap;AC=MS:1000643 + MS:1003395 Q Exactive GC Orbitrap Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer. NT=Q Exactive GC Orbitrap;AC=MS:1003395 + MS:1002877 Q Exactive HF-X Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS. NT=Q Exactive HF-X;AC=MS:1002877 + MS:1003245 Q Exactive UHMR Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS. NT=Q Exactive UHMR;AC=MS:1003245 + MS:1003123 Bruker Daltonics timsTOF series Bruker Daltonics timsTOF series NT=Bruker Daltonics timsTOF series;AC=MS:1003123 + MS:1003229 timsTOF Bruker Daltonics' timsTOF. NT=timsTOF;AC=MS:1003229 + MS:1003124 timsTOF fleX Bruker Daltonics' timsTOF fleX NT=timsTOF fleX;AC=MS:1003124 + MS:1003397 timsTOF fleX MALDI-2 Bruker Daltonics' timsTOF fleX MALDI-2. NT=timsTOF fleX MALDI-2;AC=MS:1003397 + MS:1003404 timsTOF HT Bruker Daltonics' timsTOF HT. NT=timsTOF HT;AC=MS:1003404 + MS:1003005 timsTOF Pro Bruker Daltonics' timsTOF Pro. NT=timsTOF Pro;AC=MS:1003005 + MS:1003230 timsTOF Pro 2 Bruker Daltonics' timsTOF Pro 2. NT=timsTOF Pro 2;AC=MS:1003230 + MS:1003231 timsTOF SCP Bruker Daltonics' timsTOF SCP. NT=timsTOF SCP;AC=MS:1003231 + MS:1003383 timsTOF Ultra Bruker Daltonics' timsTOF Ultra. NT=timsTOF Ultra;AC=MS:1003383 + MS:1003412 timsTOF Ultra 2 Bruker Daltonics timsTOF Ultra 2. NT=timsTOF Ultra 2;AC=MS:1003412 +CommentCleavageAgentDetailsMenu comment[cleavage agent details] Menu MS:1001918 2-iodobenzoate Chemical iodobenzoate. Cleaves after W. AC=MS:1001918;NT=2-iodobenzoate + MS:1001303 Arg-C Endoproteinase Arg-C. AC=MS:1001303;NT=Arg-C + MS:1001304 Asp-N Endoproteinase Asp-N. AC=MS:1001304;NT=Asp-N + MS:1001305 Asp-N_ambic Enzyme Asp-N, Ammonium Bicarbonate (AmBic). AC=MS:1001305;NT=Asp-N_ambic + MS:1001306 Chymotrypsin Enzyme chymotrypsin. AC=MS:1001306;NT=Chymotrypsin + MS:1001307 CNBr Cyanogen bromide. AC=MS:1001307;NT=CNBr + MS:1001308 Formic_acid Formic acid AC=MS:1001308;NT=Formic_acid + MS:1001917 glutamyl endopeptidase Enzyme glutamyl endopeptidase (EC 3.4.21.19). AC=MS:1001917;NT=glutamyl endopeptidase + MS:1001915 leukocyte elastase Enzyme leukocyte elastase (EC 3.4.21.37). AC=MS:1001915;NT=leukocyte elastase + MS:1001309 Lys-C Endoproteinase Lys-C. AC=MS:1001309;NT=Lys-C + MS:1001310 Lys-C/P Proteinase Lys-C/P. AC=MS:1001310;NT=Lys-C/P + MS:1003093 Lys-N Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues AC=MS:1003093;NT=Lys-N + MS:1002708 LysargiNase Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues. AC=MS:1002708;NT=LysargiNase + MS:1001955 no cleavage AC=MS:1001955;NT=no cleavage + MS:1001311 PepsinA PepsinA proteinase. AC=MS:1001311;NT=PepsinA + MS:1001916 proline endopeptidase Enzyme proline endopeptidase (EC 3.4.21.26). AC=MS:1001916;NT=proline endopeptidase + MS:1001312 TrypChymo Cleavage agent TrypChymo. AC=MS:1001312;NT=TrypChymo + MS:1001251 Trypsin Enzyme trypsin. AC=MS:1001251;NT=Trypsin + MS:1001313 Trypsin/P Cleavage agent Trypsin/P. AC=MS:1001313;NT=Trypsin/P + MS:1001956 unspecific cleavage Unspecific cleavage. AC=MS:1001956;NT=unspecific cleavage + MS:1001314 V8-DE Cleavage agent V8-DE AC=MS:1001314;NT=V8-DE + MS:1001315 V8-E Cleavage agent V8-E. AC=MS:1001315;NT=V8-E \ No newline at end of file diff --git a/web/templates/SDRF/schema_slots.tsv b/web/templates/SDRF/schema_slots.tsv new file mode 100644 index 00000000..cf3b9ef9 --- /dev/null +++ b/web/templates/SDRF/schema_slots.tsv @@ -0,0 +1,23 @@ +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_SDRF +SDRF SDRF form PRIDE:0000623 source name source_name WhitespaceMinimizedString TRUE TRUE Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics Sample 1 source name + SDRF form OBI:0100026 organism organism CharacteristicsOrganismMenu NullValueMenu TRUE A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. Homo sapiens characteristics[organism] + SDRF form EFO:0000635 organism part organism_part WhitespaceMinimizedString NullValueMenu TRUE The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. Check the organism part ontology on https://www.ebi.ac.uk/ols4/ and fill the column tissue, organ, system, sperm, blood or body location (arm). characteristics[organism part] + SDRF form EFO:0000324 cell type cell_type WhitespaceMinimizedString NullValueMenu TRUE A cell type is a distinct morphological or functional form of cell. Check the cell type ontology with EFO on https://www.ebi.ac.uk/ols4/ and fill the column adipocyte characteristics[cell type] + SDRF form HANCESTRO:0004 ancestry category ancestry_category WhitespaceMinimizedString NullValueMenu TRUE Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data Asian, European characteristics[ancestry category] + SDRF form EFO:0000246 age age WhitespaceMinimizedString NullValueMenu TRUE A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). 12Y characteristics[age] + SDRF form PATO:0000047 sex sex CharacteristicsSexMenu NullValueMenu TRUE An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny. The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. Male, Female characteristics[sex] + SDRF form MONDO:0000001 disease disease WhitespaceMinimizedString NullValueMenu TRUE A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. Check the disease ontology with MONDO on https://www.ebi.ac.uk/ols4/ and fill the column Sickle cell anemia characteristics[disease] + SDRF form EFO:0000542 individual individual WhitespaceMinimizedString NullValueMenu TRUE An individual used as a specimen in an experiment, from which a material sample was derived. ADE1 characteristics[individual] + SDRF form MS:1001809 biological replicate biological_replicate WhitespaceMinimizedString TRUE The study variable is 'biological replicate'. This means, the run was generated from another individual or sample. 1, 2 characteristics[biological replicate] + SDRF form assay name assay_name WhitespaceMinimizedString TRUE assay name for the MS run run 1 assay name + SDRF form EFO:0005521 technology type technology_type TechnologyTypeMenu TRUE The technology type or platform of the reporters on the array. Proteomic profiling by mass spectrometry technology type + SDRF form PRIDE:0000659 proteomics data acquisition method proteomics_data_acquisition_method CommentProteomicsDataAcquisitionMethodMenu TRUE proteomics data acquisition method Data-dependent acquisition comment[proteomics data acquisition method] + SDRF form MS:1001808 technical replicate technical_replicate WhitespaceMinimizedString TRUE The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'. 1, 2 comment[technical replicate] + SDRF form EFO:0004095 data file data_file WhitespaceMinimizedString TRUE A file stored for use on a computer containing data. test.raw comment[data file] + SDRF form MS:1000858 fraction identifier fraction_identifier WhitespaceMinimizedString TRUE Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information. 1 comment[fraction identifier] + SDRF form PRIDE:0000514 label label CommentLabelMenu TRUE Quantification channel label ICAT heavy comment[label] + SDRF form MS:1000463 instrument instrument CommentInstrumentMenu TRUE Description of the instrument or the mass spectrometer. Orbitrap Exploris 120 comment[instrument] + SDRF form MS:1001044 cleavage agent details cleavage_agent_details CommentCleavageAgentDetailsMenu TRUE Details of cleavage agent (enzyme) 2-iodobenzoate comment[cleavage agent details] + SDRF form MS:1001055 modification parameters modification_parameters WhitespaceMinimizedString Modification parameters for the search engine run. Carbamidomethyl comment[modification parameters] + SDRF form PRIDE:0000575 precursor mass tolerance precursor_mass_tolerance WhitespaceMinimizedString Threshold at precursor level to compare experimental mass with theoretical mass 10 ppm comment[precursor mass tolerance] + SDRF form PRIDE:0000576 fragment mass tolerance fragment_mass_tolerance WhitespaceMinimizedString TRUE Threshold at fragment level to compare experimental mass with theoretical mass 0.05 Da comment[fragment mass tolerance] \ No newline at end of file From 5e0d95d29a5ecdb93eea8d9aaf1140d9feef825e Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Fri, 11 Oct 2024 12:40:06 +0100 Subject: [PATCH 58/96] schema_core.yaml --- web/templates/SDRF/schema_core.yaml | 40 +++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 web/templates/SDRF/schema_core.yaml diff --git a/web/templates/SDRF/schema_core.yaml b/web/templates/SDRF/schema_core.yaml new file mode 100644 index 00000000..909c35b2 --- /dev/null +++ b/web/templates/SDRF/schema_core.yaml @@ -0,0 +1,40 @@ +id: https://example.com/SDRF +name: "SDRF" +description: "" +version: 1.0.0 +in_language: +- 'en' +imports: +- 'linkml:types' +prefixes: + linkml: 'https://w3id.org/linkml/' + PRIDE: 'http://purl.obolibrary.org/obo/PRIDE' +classes: + dh_interface: + name: dh_interface + description: 'A DataHarmonizer interface' + 'SDRF': + name: 'SDRF' + title: 'Template Name' + description: "Specification for PRIDE samples data gathering" + is_a: dh_interface + see_also: templates/TEMPLATE_FOLDER/SOP.pdf +slots: {} +enums: {} +types: + WhitespaceMinimizedString: + name: 'WhitespaceMinimizedString' + typeof: string + description: 'A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).' + base: str + uri: xsd:token + Provenance: + name: 'Provenance' + typeof: string + description: 'A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.' + base: str + uri: xsd:token +settings: + Title_Case: "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" + UPPER_CASE: "[A-Z\\W\\d_]*" + lower_case: "[a-z\\W\\d_]*" From 323eaa34e318099bff13e07d7a4f8c395b730cf3 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Sat, 12 Oct 2024 18:18:20 +0100 Subject: [PATCH 59/96] schema, export --- web/templates/SDRF/export.js | 2 + web/templates/SDRF/schema.json | 531 +++++++++++++++++++++++++++++++++ web/templates/SDRF/schema.yaml | 152 ++++++++++ 3 files changed, 685 insertions(+) create mode 100644 web/templates/SDRF/export.js create mode 100644 web/templates/SDRF/schema.json create mode 100644 web/templates/SDRF/schema.yaml diff --git a/web/templates/SDRF/export.js b/web/templates/SDRF/export.js new file mode 100644 index 00000000..592ad2d1 --- /dev/null +++ b/web/templates/SDRF/export.js @@ -0,0 +1,2 @@ +// A dictionary of possible export formats +export default {}; diff --git a/web/templates/SDRF/schema.json b/web/templates/SDRF/schema.json new file mode 100644 index 00000000..e6734bc5 --- /dev/null +++ b/web/templates/SDRF/schema.json @@ -0,0 +1,531 @@ +{ + "name": "YOUR_SCHEMA_NAME", + "description": "A description of the schema containing one or more templates.", + "in_language": "['en']", + "id": "https://example.com/CanCOGeN_Covid-19", + "version": "1.0.0", + "prefixes": { + "linkml": { + "prefix_prefix": "linkml", + "prefix_reference": "https://w3id.org/linkml/" + }, + "ONTOLOGY1": { + "prefix_prefix": "ONTOLOGY1", + "prefix_reference": "http://purl.obolibrary.org/obo/ONTOLOGY1_" + }, + "xsd": { + "prefix_prefix": "xsd", + "prefix_reference": "http://www.w3.org/2001/XMLSchema#" + }, + "shex": { + "prefix_prefix": "shex", + "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" + } + }, + "default_prefix": "https://example.com/CanCOGeN_Covid-19/", + "types": { + "WhitespaceMinimizedString": { + "name": "WhitespaceMinimizedString", + "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "typeof": "string", + "base": "str", + "uri": "xsd:token" + }, + "Provenance": { + "name": "Provenance", + "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "typeof": "string", + "base": "str", + "uri": "xsd:token" + }, + "string": { + "name": "string", + "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Text" + ], + "base": "str", + "uri": "xsd:string" + }, + "integer": { + "name": "integer", + "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Integer" + ], + "base": "int", + "uri": "xsd:integer" + }, + "boolean": { + "name": "boolean", + "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Boolean" + ], + "base": "Bool", + "uri": "xsd:boolean", + "repr": "bool" + }, + "float": { + "name": "float", + "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:float" + }, + "double": { + "name": "double", + "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "close_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "xsd:double" + }, + "decimal": { + "name": "decimal", + "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "broad_mappings": [ + "schema:Number" + ], + "base": "Decimal", + "uri": "xsd:decimal" + }, + "time": { + "name": "time", + "description": "A time object represents a (local) time of day, independent of any particular day", + "notes": [ + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Time" + ], + "base": "XSDTime", + "uri": "xsd:time", + "repr": "str" + }, + "date": { + "name": "date", + "description": "a date (year, month and day) in an idealized calendar", + "notes": [ + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Date" + ], + "base": "XSDDate", + "uri": "xsd:date", + "repr": "str" + }, + "datetime": { + "name": "datetime", + "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:DateTime" + ], + "base": "XSDDateTime", + "uri": "xsd:dateTime", + "repr": "str" + }, + "date_or_datetime": { + "name": "date_or_datetime", + "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "linkml:DateOrDatetime", + "repr": "str" + }, + "uriorcurie": { + "name": "uriorcurie", + "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "URIorCURIE", + "uri": "xsd:anyURI", + "repr": "str" + }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, + "uri": { + "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", + "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "close_mappings": [ + "schema:URL" + ], + "base": "URI", + "uri": "xsd:anyURI", + "repr": "str" + }, + "ncname": { + "name": "ncname", + "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "NCName", + "uri": "xsd:string", + "repr": "str" + }, + "objectidentifier": { + "name": "objectidentifier", + "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "ElementIdentifier", + "uri": "shex:iri", + "repr": "str" + }, + "nodeidentifier": { + "name": "nodeidentifier", + "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "NodeIdentifier", + "uri": "shex:nonLiteral", + "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "xsd:string", + "repr": "str" + } + }, + "enums": { + "NullValueMenu": { + "name": "NullValueMenu", + "description": "A menu of data collection status options for this field.", + "title": "null value menu", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "permissible_values": { + "Not Applicable": { + "text": "Not Applicable", + "meaning": "GENEPIO:0001619" + }, + "Missing": { + "text": "Missing", + "meaning": "GENEPIO:0001618" + }, + "Not Collected": { + "text": "Not Collected", + "meaning": "GENEPIO:0001620" + }, + "Not Provided": { + "text": "Not Provided", + "meaning": "GENEPIO:0001668" + }, + "Restricted Access": { + "text": "Restricted Access", + "meaning": "GENEPIO:0001810" + } + } + }, + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", + "description": "A menu of analytic laboratories.", + "title": "sequence submitted by menu", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "permissible_values": { + "Alberta Precision Labs (APL)": { + "text": "Alberta Precision Labs (APL)" + }, + "Alberta ProvLab North (APLN)": { + "text": "Alberta ProvLab North (APLN)", + "is_a": "Alberta Precision Labs (APL)" + }, + "Alberta ProvLab South (APLS)": { + "text": "Alberta ProvLab South (APLS)", + "is_a": "Alberta Precision Labs (APL)" + }, + "BCCDC Public Health Laboratory": { + "text": "BCCDC Public Health Laboratory" + }, + "Canadore College": { + "text": "Canadore College" + }, + "The Centre for Applied Genomics (TCAG)": { + "text": "The Centre for Applied Genomics (TCAG)" + }, + "Dynacare": { + "text": "Dynacare" + }, + "Dynacare (Brampton)": { + "text": "Dynacare (Brampton)" + }, + "Dynacare (Manitoba)": { + "text": "Dynacare (Manitoba)" + }, + "The Hospital for Sick Children (SickKids)": { + "text": "The Hospital for Sick Children (SickKids)" + }, + "Laboratoire de santé publique du Québec (LSPQ)": { + "text": "Laboratoire de santé publique du Québec (LSPQ)" + }, + "Manitoba Cadham Provincial Laboratory": { + "text": "Manitoba Cadham Provincial Laboratory" + }, + "McGill University": { + "text": "McGill University" + }, + "McMaster University": { + "text": "McMaster University" + }, + "National Microbiology Laboratory (NML)": { + "text": "National Microbiology Laboratory (NML)" + }, + "New Brunswick - Vitalité Health Network": { + "text": "New Brunswick - Vitalité Health Network" + }, + "Newfoundland and Labrador - Eastern Health": { + "text": "Newfoundland and Labrador - Eastern Health" + }, + "Nova Scotia Health Authority": { + "text": "Nova Scotia Health Authority" + }, + "Ontario Institute for Cancer Research (OICR)": { + "text": "Ontario Institute for Cancer Research (OICR)" + }, + "Prince Edward Island - Health PEI": { + "text": "Prince Edward Island - Health PEI" + }, + "Public Health Ontario (PHO)": { + "text": "Public Health Ontario (PHO)" + }, + "Queen's University / Kingston Health Sciences Centre": { + "text": "Queen's University / Kingston Health Sciences Centre" + }, + "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)": { + "text": "Saskatchewan - Roy Romanow Provincial Laboratory (RRPL)" + }, + "Sunnybrook Health Sciences Centre": { + "text": "Sunnybrook Health Sciences Centre" + }, + "Thunder Bay Regional Health Sciences Centre": { + "text": "Thunder Bay Regional Health Sciences Centre" + } + } + } + }, + "slots": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "examples": [ + { + "value": "prov_mpox_1234" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "SOMEWHERE:Sample%20ID%20given%20by%20the%20sample%20provider" + ], + "identifier": true, + "range": "WhitespaceMinimizedString", + "required": true + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency that generated the sequence.", + "title": "sequenced by", + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "slot_uri": "GENEPIO:0100416", + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + } + }, + "classes": { + "dh_interface": { + "name": "dh_interface", + "description": "A DataHarmonizer interface", + "from_schema": "https://example.com/CanCOGeN_Covid-19" + }, + "TemplateName": { + "name": "TemplateName", + "description": "A description of the template.", + "title": "Template Name", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "see_also": [ + "templates/TEMPLATE_FOLDER/SOP.pdf" + ], + "is_a": "dh_interface", + "slot_usage": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "rank": 1, + "slot_group": "Database Identifiers" + }, + "sequenced_by": { + "name": "sequenced_by", + "rank": 2, + "slot_group": "Sample collection and processing" + } + }, + "attributes": { + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", + "description": "The user-defined name for the sample.", + "title": "specimen collector sample ID", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "rank": 1, + "identifier": true, + "alias": "specimen_collector_sample_id", + "owner": "TemplateName", + "domain_of": [ + "TemplateName" + ], + "slot_group": "Database Identifiers", + "range": "WhitespaceMinimizedString", + "required": true + }, + "sequenced_by": { + "name": "sequenced_by", + "description": "The name of the agency that generated the sequence.", + "title": "sequenced by", + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "rank": 2, + "slot_uri": "GENEPIO:0100416", + "alias": "sequenced_by", + "owner": "TemplateName", + "domain_of": [ + "TemplateName" + ], + "slot_group": "Sample collection and processing", + "required": true + } + } + } + }, + "settings": { + "Title_Case": { + "setting_key": "Title_Case", + "setting_value": "(((?<=\\b)[^a-z\\W]\\w*?|[\\W])+)" + }, + "UPPER_CASE": { + "setting_key": "UPPER_CASE", + "setting_value": "[A-Z\\W\\d_]*" + }, + "lower_case": { + "setting_key": "lower_case", + "setting_value": "[a-z\\W\\d_]*" + } + }, + "@type": "SchemaDefinition" +} \ No newline at end of file diff --git a/web/templates/SDRF/schema.yaml b/web/templates/SDRF/schema.yaml new file mode 100644 index 00000000..d4815e26 --- /dev/null +++ b/web/templates/SDRF/schema.yaml @@ -0,0 +1,152 @@ +id: https://example.com/CanCOGeN_Covid-19 +name: YOUR_SCHEMA_NAME +description: A description of the schema containing one or more templates. +version: 1.0.0 +in_language: +- en +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + ONTOLOGY1: http://purl.obolibrary.org/obo/ONTOLOGY1_ +classes: + dh_interface: + name: dh_interface + description: A DataHarmonizer interface + TemplateName: + name: TemplateName + title: Template Name + description: A description of the template. + is_a: dh_interface + see_also: templates/TEMPLATE_FOLDER/SOP.pdf + slots: + - specimen_collector_sample_id + - sequenced_by + slot_usage: + specimen_collector_sample_id: + rank: 1 + slot_group: Database Identifiers + sequenced_by: + rank: 2 + slot_group: Sample collection and processing +slots: + specimen_collector_sample_id: + name: specimen_collector_sample_id + title: specimen collector sample ID + description: The user-defined name for the sample. + identifier: true + range: WhitespaceMinimizedString + required: true + examples: + - value: prov_mpox_1234 + exact_mappings: + - SOMEWHERE:Sample%20ID%20given%20by%20the%20sample%20provider + sequenced_by: + name: sequenced_by + title: sequenced by + description: The name of the agency that generated the sequence. + slot_uri: GENEPIO:0100416 + any_of: + - range: SequenceSubmittedByMenu + - range: NullValueMenu + required: true + examples: + - value: Public Health Ontario (PHO) +enums: + NullValueMenu: + name: NullValueMenu + title: null value menu + description: A menu of data collection status options for this field. + permissible_values: + Not Applicable: + text: Not Applicable + meaning: GENEPIO:0001619 + Missing: + text: Missing + meaning: GENEPIO:0001618 + Not Collected: + text: Not Collected + meaning: GENEPIO:0001620 + Not Provided: + text: Not Provided + meaning: GENEPIO:0001668 + Restricted Access: + text: Restricted Access + meaning: GENEPIO:0001810 + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu + title: sequence submitted by menu + description: A menu of analytic laboratories. + permissible_values: + Alberta Precision Labs (APL): + text: Alberta Precision Labs (APL) + Alberta ProvLab North (APLN): + text: Alberta ProvLab North (APLN) + is_a: Alberta Precision Labs (APL) + Alberta ProvLab South (APLS): + text: Alberta ProvLab South (APLS) + is_a: Alberta Precision Labs (APL) + BCCDC Public Health Laboratory: + text: BCCDC Public Health Laboratory + Canadore College: + text: Canadore College + The Centre for Applied Genomics (TCAG): + text: The Centre for Applied Genomics (TCAG) + Dynacare: + text: Dynacare + Dynacare (Brampton): + text: Dynacare (Brampton) + Dynacare (Manitoba): + text: Dynacare (Manitoba) + The Hospital for Sick Children (SickKids): + text: The Hospital for Sick Children (SickKids) + "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ)": + text: "Laboratoire de sant\xE9 publique du Qu\xE9bec (LSPQ)" + Manitoba Cadham Provincial Laboratory: + text: Manitoba Cadham Provincial Laboratory + McGill University: + text: McGill University + McMaster University: + text: McMaster University + National Microbiology Laboratory (NML): + text: National Microbiology Laboratory (NML) + "New Brunswick - Vitalit\xE9 Health Network": + text: "New Brunswick - Vitalit\xE9 Health Network" + Newfoundland and Labrador - Eastern Health: + text: Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority: + text: Nova Scotia Health Authority + Ontario Institute for Cancer Research (OICR): + text: Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI: + text: Prince Edward Island - Health PEI + Public Health Ontario (PHO): + text: Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre: + text: Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL): + text: Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Sunnybrook Health Sciences Centre: + text: Sunnybrook Health Sciences Centre + Thunder Bay Regional Health Sciences Centre: + text: Thunder Bay Regional Health Sciences Centre +types: + WhitespaceMinimizedString: + name: WhitespaceMinimizedString + typeof: string + description: 'A string that has all whitespace trimmed off of beginning and end, + and all internal whitespace segments reduced to single spaces. Whitespace includes + #x9 (tab), #xA (linefeed), and #xD (carriage return).' + base: str + uri: xsd:token + Provenance: + name: Provenance + typeof: string + description: A field containing a DataHarmonizer versioning marker. It is issued + by DataHarmonizer when validation is applied to a given row of data. + base: str + uri: xsd:token +settings: + Title_Case: (((?<=\b)[^a-z\W]\w*?|[\W])+) + UPPER_CASE: '[A-Z\W\d_]*' + lower_case: '[a-z\W\d_]*' From 9201f9151318958497f97ac5c50614a04c912265 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Mon, 14 Oct 2024 10:08:01 +0100 Subject: [PATCH 60/96] Update schema.json --- web/templates/SDRF/schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/templates/SDRF/schema.json b/web/templates/SDRF/schema.json index e6734bc5..5a47bb64 100644 --- a/web/templates/SDRF/schema.json +++ b/web/templates/SDRF/schema.json @@ -1,5 +1,5 @@ { - "name": "YOUR_SCHEMA_NAME", + "name": "SDRF", "description": "A description of the schema containing one or more templates.", "in_language": "['en']", "id": "https://example.com/CanCOGeN_Covid-19", From a7b68ca9a18d001783581c13b928b4276d1edb22 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 15 Oct 2024 20:04:33 -0700 Subject: [PATCH 61/96] Update menu to match CanCOGeN Template class name --- web/templates/menu.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/templates/menu.json b/web/templates/menu.json index ac7bc408..491020d6 100644 --- a/web/templates/menu.json +++ b/web/templates/menu.json @@ -1,6 +1,6 @@ { "canada_covid19": { - "CanCOGeN Covid-19": { + "CanCOGeNCovid19": { "name": "CanCOGeN Covid-19", "status": "published", "display": true From fdd21661049545e1abf5f3f5b634d580b3f3de44 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 18 Oct 2024 23:50:57 -0700 Subject: [PATCH 62/96] pathogen agnostic template tweak --- web/templates/menu.json | 2 +- web/templates/pathogen/schema.json | 2581 +++++++++++++++++------ web/templates/pathogen/schema.yaml | 1060 +++++----- web/templates/pathogen/schema_core.yaml | 7 +- web/templates/pathogen/schema_enums.tsv | 1352 ++++++------ web/templates/pathogen/schema_slots.tsv | 131 +- 6 files changed, 3192 insertions(+), 1941 deletions(-) diff --git a/web/templates/menu.json b/web/templates/menu.json index 491020d6..0dd4b463 100644 --- a/web/templates/menu.json +++ b/web/templates/menu.json @@ -42,7 +42,7 @@ } }, "pathogen": { - "Pathogen Agnostic": { + "PathogenAgnostic": { "name": "Pathogen Agnostic", "status": "published", "display": true diff --git a/web/templates/pathogen/schema.json b/web/templates/pathogen/schema.json index acc413c8..883fd4a5 100644 --- a/web/templates/pathogen/schema.json +++ b/web/templates/pathogen/schema.json @@ -1,5 +1,5 @@ { - "name": "Pathogen_Agnostic", + "name": "PathogenAgnostic", "description": "", "id": "https://example.com/Pathogen_Agnostic", "version": "1.0.0", @@ -46,6 +46,9 @@ "string": { "name": "string", "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "schema:Text" @@ -56,6 +59,9 @@ "integer": { "name": "integer", "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "schema:Integer" @@ -66,6 +72,9 @@ "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "schema:Boolean" @@ -77,6 +86,9 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "schema:Float" @@ -87,6 +99,9 @@ "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "close_mappings": [ "schema:Float" @@ -97,6 +112,9 @@ "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "broad_mappings": [ "schema:Number" @@ -108,21 +126,23 @@ "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "schema:Time" ], "base": "XSDTime", - "uri": "xsd:dateTime", + "uri": "xsd:time", "repr": "str" }, "date": { "name": "date", "description": "a date (year, month and day) in an idealized calendar", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ @@ -135,6 +155,9 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "schema:DateTime" @@ -146,6 +169,9 @@ "date_or_datetime": { "name": "date_or_datetime", "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "base": "str", "uri": "linkml:DateOrDatetime", @@ -154,6 +180,9 @@ "uriorcurie": { "name": "uriorcurie", "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "base": "URIorCURIE", "uri": "xsd:anyURI", @@ -163,6 +192,9 @@ "name": "curie", "conforms_to": "https://www.w3.org/TR/curie/", "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], "comments": [ "in RDF serializations this MUST be expanded to a URI", "in non-RDF serializations MAY be serialized as the compact representation" @@ -176,6 +208,9 @@ "name": "uri", "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], "comments": [ "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" ], @@ -190,6 +225,9 @@ "ncname": { "name": "ncname", "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "base": "NCName", "uri": "xsd:string", @@ -198,8 +236,11 @@ "objectidentifier": { "name": "objectidentifier", "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], "comments": [ - "Used for inheritence and type checking" + "Used for inheritance and type checking" ], "from_schema": "https://example.com/Pathogen_Agnostic", "base": "ElementIdentifier", @@ -209,15 +250,55 @@ "nodeidentifier": { "name": "nodeidentifier", "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], "from_schema": "https://example.com/Pathogen_Agnostic", "base": "NodeIdentifier", "uri": "shex:nonLiteral", "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/Pathogen_Agnostic", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/Pathogen_Agnostic", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/Pathogen_Agnostic", + "base": "str", + "uri": "xsd:string", + "repr": "str" } }, "enums": { - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "null value menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Not Applicable": { @@ -242,8 +323,9 @@ } } }, - "geo_loc_name (state/province/territory) menu": { - "name": "geo_loc_name (state/province/territory) menu", + "GeoLocNameStateProvinceTerritoryMenu": { + "name": "GeoLocNameStateProvinceTerritoryMenu", + "title": "geo_loc_name (state/province/territory) menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Alberta": { @@ -300,8 +382,9 @@ } } }, - "host age unit menu": { - "name": "host age unit menu", + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host age unit menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "month": { @@ -314,8 +397,9 @@ } } }, - "sample collection date precision menu": { - "name": "sample collection date precision menu", + "SampleCollectionDatePrecisionMenu": { + "name": "SampleCollectionDatePrecisionMenu", + "title": "sample collection date precision menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "year": { @@ -332,8 +416,9 @@ } } }, - "NML submitted specimen type menu": { - "name": "NML submitted specimen type menu", + "NmlSubmittedSpecimenTypeMenu": { + "name": "NmlSubmittedSpecimenTypeMenu", + "title": "NML submitted specimen type menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Swab": { @@ -358,8 +443,9 @@ } } }, - "anatomical material menu": { - "name": "anatomical material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical material menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Blood": { @@ -406,8 +492,9 @@ } } }, - "anatomical part menu": { - "name": "anatomical part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical part menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Anus": { @@ -527,8 +614,9 @@ } } }, - "body product menu": { - "name": "body product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body product menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Breast Milk": { @@ -566,8 +654,9 @@ } } }, - "environmental material menu": { - "name": "environmental material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "environmental material menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Air vent": { @@ -705,8 +794,9 @@ } } }, - "environmental site menu": { - "name": "environmental site menu", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental site menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Acute care facility": { @@ -799,8 +889,9 @@ } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Amniocentesis": { @@ -897,8 +988,9 @@ } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Air filter": { @@ -971,8 +1063,9 @@ } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Homo sapiens": { @@ -1041,8 +1134,9 @@ } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Severe acute respiratory syndrome coronavirus 2": { @@ -1068,8 +1162,9 @@ } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Cluster/Outbreak investigation": { @@ -1090,8 +1185,9 @@ } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose of sequencing menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Baseline surveillance (random sampling)": { @@ -1211,8 +1307,9 @@ } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Virus passage": { @@ -1229,8 +1326,9 @@ } } }, - "host disease menu": { - "name": "host disease menu", + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host disease menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "COVID-19": { @@ -1242,8 +1340,9 @@ } } }, - "host age bin menu": { - "name": "host age bin menu", + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host age bin menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "0 - 9": { @@ -1286,20 +1385,21 @@ "text": "90 - 99", "meaning": "GENEPIO:0100058", "exact_mappings": [ - "VirusSeq_Portal:90+" + "VirusSeq_Portal:90%2B" ] }, "100+": { "text": "100+", "meaning": "GENEPIO:0100059", "exact_mappings": [ - "VirusSeq_Portal:90+" + "VirusSeq_Portal:90%2B" ] } } }, - "host gender menu": { - "name": "host gender menu", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host gender menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Female": { @@ -1328,8 +1428,9 @@ } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Illumina": { @@ -1558,8 +1659,9 @@ } } }, - "sequenced by menu": { - "name": "sequenced by menu", + "SequencedByMenu": { + "name": "SequencedByMenu", + "title": "sequenced by menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -1608,8 +1710,9 @@ } } }, - "sequence submitted by menu": { - "name": "sequence submitted by menu", + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", + "title": "sequence submitted by menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -1691,8 +1794,9 @@ } } }, - "sample collected by menu": { - "name": "sample collected by menu", + "SampleCollectedByMenu": { + "name": "SampleCollectedByMenu", + "title": "sample collected by menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -1798,8 +1902,9 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/Pathogen_Agnostic", "permissible_values": { "Afghanistan": { @@ -2890,8 +2995,8 @@ } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -2904,19 +3009,22 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Sample ID given by the sample provider", - "CNPHI:Primary Specimen ID", + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", "NML_LIMS:TEXT_ID", "BIOSAMPLE:sample_name", - "VirusSeq_Portal:specimen collector sample ID" + "VirusSeq_Portal:specimen%20collector%20sample%20ID" ], "slot_uri": "GENEPIO:0001123", "identifier": true, + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "required": true }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "description": "The name of the third party company or laboratory that provided services.", "title": "third party lab service provider name", "comments": [ @@ -2932,10 +3040,13 @@ "NML_LIMS:HC_TEXT5" ], "slot_uri": "GENEPIO:0001202", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "description": "The identifier assigned to a sample by a third party service provider.", "title": "third party lab sample ID", "comments": [ @@ -2951,10 +3062,13 @@ "NML_LIMS:PH_ID_NUMBER_PRIMARY" ], "slot_uri": "GENEPIO:0001149", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", "comments": [ @@ -2970,11 +3084,14 @@ "NML_LIMS:PH_CASE_ID" ], "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", "comments": [ @@ -2987,22 +3104,25 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Related Specimen ID", - "CNPHI:Related Specimen Relationship Type", + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", "NML_LIMS:PH_RELATED_PRIMARY_ID" ], "slot_uri": "GENEPIO:0001128", + "domain_of": [ + "PathogenAgnostic" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "description": "The identifier assigned to a sequenced isolate in IRIDA.", "title": "IRIDA sample name", "comments": [ @@ -3015,13 +3135,16 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "NML_LIMS:IRIDA sample name" + "NML_LIMS:IRIDA%20sample%20name" ], "slot_uri": "GENEPIO:0001131", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort.", "title": "umbrella bioproject accession", "comments": [ @@ -3034,18 +3157,21 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "NML_LIMS:umbrella bioproject accession" + "NML_LIMS:umbrella%20bioproject%20accession" ], "slot_uri": "GENEPIO:0001133", - "range": "umbrella bioproject accession menu", + "domain_of": [ + "PathogenAgnostic" + ], + "range": "UmbrellaBioprojectAccessionMenu", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", "comments": [ @@ -3058,11 +3184,14 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:BioProject Accession", + "CNPHI:BioProject%20Accession", "NML_LIMS:PH_BIOPROJECT_ACCESSION", "BIOSAMPLE:bioproject_accession" ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3070,8 +3199,8 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", "comments": [ @@ -3084,10 +3213,13 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:BioSample Accession", + "CNPHI:BioSample%20Accession", "NML_LIMS:PH_BIOSAMPLE_ACCESSION" ], "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3095,8 +3227,8 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", "comments": [ @@ -3109,10 +3241,13 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:SRA Accession", + "CNPHI:SRA%20Accession", "NML_LIMS:PH_SRA_ACCESSION" ], "slot_uri": "GENEPIO:0001142", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3120,8 +3255,8 @@ "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", "comments": [ @@ -3134,10 +3269,13 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:GenBank Accession", - "NML_LIMS:GenBank accession" + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" ], "slot_uri": "GENEPIO:0001145", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3145,8 +3283,8 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "comments": [ @@ -3159,12 +3297,15 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:GISAID Accession (if known)", - "NML_LIMS:SUBMISSIONS - GISAID Accession ID", + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID", "BIOSAMPLE:GISAID_accession", - "VirusSeq_Portal:GISAID accession" + "VirusSeq_Portal:GISAID%20accession" ], "slot_uri": "GENEPIO:0001147", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3172,8 +3313,8 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", "comments": [ @@ -3186,25 +3327,28 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Originating lab", - "CNPHI:Lab Name", + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", "NML_LIMS:CUSTOMER", "BIOSAMPLE:collected_by", - "VirusSeq_Portal:sample collected by" + "VirusSeq_Portal:sample%20collected%20by" ], "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "sample collected by menu" + "range": "SampleCollectedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency that generated the sequence.", "title": "sequenced by", "comments": [ @@ -3221,18 +3365,21 @@ "BIOSAMPLE:sequenced_by" ], "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "SequenceSubmittedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", "comments": [ @@ -3245,25 +3392,28 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Submitting lab", - "CNPHI:Sequencing Centre", + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by", - "VirusSeq_Portal:sequence submitted by" + "VirusSeq_Portal:sequence%20submitted%20by" ], "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "SequenceSubmittedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", "todos": [ @@ -3280,25 +3430,28 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Collection date", - "CNPHI:Patient Sample Collected Date", + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", "NML_LIMS:HC_COLLECT_DATE", - "BIOSAMPLE:sample collection date", - "VirusSeq_Portal:sample collection date" + "BIOSAMPLE:sample%20collection%20date", + "VirusSeq_Portal:sample%20collection%20date" ], "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", "comments": [ @@ -3311,22 +3464,25 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Precision of date collected", + "CNPHI:Precision%20of%20date%20collected", "NML_LIMS:HC_TEXT2" ], "slot_uri": "GENEPIO:0001177", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "sample collection date precision menu" + "range": "SampleCollectionDatePrecisionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", "comments": [ @@ -3340,24 +3496,27 @@ "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "GISAID:Location", - "CNPHI:Patient Country", + "CNPHI:Patient%20Country", "NML_LIMS:HC_COUNTRY", "BIOSAMPLE:geo_loc_name", - "VirusSeq_Portal:geo_loc_name (country)" + "VirusSeq_Portal:geo_loc_name%20%28country%29" ], "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", "comments": [ @@ -3370,19 +3529,22 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Patient Province", + "CNPHI:Patient%20Province", "NML_LIMS:HC_PROVINCE", "BIOSAMPLE:geo_loc_name", - "VirusSeq_Portal:geo_loc_name (state/province/territory)" + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" ], "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "GeoLocNameStateProvinceTerritoryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -3406,13 +3568,16 @@ "VirusSeq_Portal:organism" ], "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -3430,27 +3595,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Virus name", - "CNPHI:GISAID Virus Name", - "NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS", + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS", "BIOSAMPLE:isolate", "BIOSAMPLE:GISAID_virus_name", "VirusSeq_Portal:isolate", - "VirusSeq_Portal:fasta header name" + "VirusSeq_Portal:fasta%20header%20name" ], "slot_uri": "GENEPIO:0001195", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", "comments": [ @@ -3463,24 +3631,27 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Reason for Sampling", + "CNPHI:Reason%20for%20Sampling", "NML_LIMS:HC_SAMPLE_CATEGORY", "BIOSAMPLE:purpose_of_sampling", - "VirusSeq_Portal:purpose of sampling" + "VirusSeq_Portal:purpose%20of%20sampling" ], "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "comments": [ @@ -3493,24 +3664,27 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Details on the Reason for Sampling", + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", "NML_LIMS:PH_SAMPLING_DETAILS", "BIOSAMPLE:description", - "VirusSeq_Portal:purpose of sampling details" + "VirusSeq_Portal:purpose%20of%20sampling%20details" ], "slot_uri": "GENEPIO:0001200", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", "comments": [ @@ -3523,15 +3697,18 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Specimen Type", + "CNPHI:Specimen%20Type", "NML_LIMS:PH_SPECIMEN_TYPE" ], "slot_uri": "GENEPIO:0001204", - "range": "NML submitted specimen type menu", + "domain_of": [ + "PathogenAgnostic" + ], + "range": "NMLSubmittedSpecimenTypeMenu", "recommended": true }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", "comments": [ @@ -3544,27 +3721,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Anatomical Material", + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", "NML_LIMS:PH_ISOLATION_SITE_DESC", "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_material", - "VirusSeq_Portal:anatomical material" + "VirusSeq_Portal:anatomical%20material" ], "slot_uri": "GENEPIO:0001211", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "anatomical material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", "comments": [ @@ -3577,27 +3757,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Anatomical Site", + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", "NML_LIMS:PH_ISOLATION_SITE", "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_part", - "VirusSeq_Portal:anatomical part" + "VirusSeq_Portal:anatomical%20part" ], "slot_uri": "GENEPIO:0001214", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "anatomical part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", "comments": [ @@ -3610,27 +3793,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Body Product", + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", "BIOSAMPLE:isolation_source", "BIOSAMPLE:body_product", - "VirusSeq_Portal:body product" + "VirusSeq_Portal:body%20product" ], "slot_uri": "GENEPIO:0001216", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "body product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", "comments": [ @@ -3643,27 +3829,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Environmental Material", + "GISAID:Specimen%20source", + "CNPHI:Environmental%20Material", "NML_LIMS:PH_ENVIRONMENTAL_MATERIAL", "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_material", - "VirusSeq_Portal:environmental material" + "VirusSeq_Portal:environmental%20material" ], "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "environmental material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", "comments": [ @@ -3676,27 +3865,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Environmental Site", + "GISAID:Specimen%20source", + "CNPHI:Environmental%20Site", "NML_LIMS:PH_ENVIRONMENTAL_SITE", "BIOSAMPLE:isolation_source", "BIOSAMPLE:environmental_site", - "VirusSeq_Portal:environmental site" + "VirusSeq_Portal:environmental%20site" ], "slot_uri": "GENEPIO:0001232", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "environmental site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", "comments": [ @@ -3709,27 +3901,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Specimen Collection Matrix", + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_device", - "VirusSeq_Portal:collection device" + "VirusSeq_Portal:collection%20device" ], "slot_uri": "GENEPIO:0001234", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", "comments": [ @@ -3742,27 +3937,30 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Collection Method", + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", "NML_LIMS:COLLECTION_METHOD", "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_method", - "VirusSeq_Portal:collection method" + "VirusSeq_Portal:collection%20method" ], "slot_uri": "GENEPIO:0001241", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "collection method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -3775,23 +3973,26 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Passage details/history", - "NML_LIMS:specimen processing" + "GISAID:Passage%20details/history", + "NML_LIMS:specimen%20processing" ], "slot_uri": "GENEPIO:0001253", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "specimen processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -3804,10 +4005,13 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", "comments": [ @@ -3821,23 +4025,26 @@ "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "GISAID:Host", - "NML_LIMS:host (scientific name)", + "NML_LIMS:host%20%28scientific%20name%29", "BIOSAMPLE:host", - "VirusSeq_Portal:host (scientific name)" + "VirusSeq_Portal:host%20%28scientific%20name%29" ], "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", "comments": [ @@ -3850,24 +4057,27 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Host Disease", + "CNPHI:Host%20Disease", "NML_LIMS:PH_HOST_DISEASE", "BIOSAMPLE:host_disease", - "VirusSeq_Portal:host disease" + "VirusSeq_Portal:host%20disease" ], "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "host disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", "comments": [ @@ -3880,13 +4090,16 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Patient age", - "CNPHI:Patient Age", + "GISAID:Patient%20age", + "CNPHI:Patient%20Age", "NML_LIMS:PH_AGE", "BIOSAMPLE:host_age", - "VirusSeq_Portal:host age" + "VirusSeq_Portal:host%20age" ], "slot_uri": "GENEPIO:0001392", + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, "minimum_value": 0, "maximum_value": 130, @@ -3895,12 +4108,12 @@ "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The unit used to measure the host age, in either months or years.", "title": "host age unit", "comments": [ @@ -3913,23 +4126,26 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Age Units", + "CNPHI:Age%20Units", "NML_LIMS:PH_AGE_UNIT", - "VirusSeq_Portal:host age unit" + "VirusSeq_Portal:host%20age%20unit" ], "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "host age unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host age bin", "comments": [ @@ -3942,23 +4158,26 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Host Age Category", + "CNPHI:Host%20Age%20Category", "NML_LIMS:PH_AGE_GROUP", - "VirusSeq_Portal:host age bin" + "VirusSeq_Portal:host%20age%20bin" ], "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, "any_of": [ { - "range": "host age bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", "comments": [ @@ -3972,12 +4191,15 @@ "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "GISAID:Gender", - "CNPHI:Patient Sex", + "CNPHI:Patient%20Sex", "NML_LIMS:VD_SEX", "BIOSAMPLE:host_sex", - "VirusSeq_Portal:host gender" + "VirusSeq_Portal:host%20gender" ], "slot_uri": "GENEPIO:0001395", + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, "structured_pattern": { "syntax": "{Title_Case}", @@ -3986,15 +4208,15 @@ }, "any_of": [ { - "range": "host gender menu" + "range": "HostGenderMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", "comments": [ @@ -4007,25 +4229,28 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Reason for Sequencing", + "CNPHI:Reason%20for%20Sequencing", "NML_LIMS:PH_REASON_FOR_SEQUENCING", "BIOSAMPLE:purpose_of_sequencing", - "VirusSeq_Portal:purpose of sequencing" + "VirusSeq_Portal:purpose%20of%20sequencing" ], "slot_uri": "GENEPIO:0001445", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "purpose of sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "comments": [ @@ -4038,23 +4263,26 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Details on the Reason for Sequencing", + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", - "VirusSeq_Portal:purpose of sequencing details" + "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "PathogenAgnostic" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ @@ -4073,18 +4301,21 @@ "NML_LIMS:PH_SEQUENCING_DATE" ], "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "PathogenAgnostic" + ], "recommended": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", "comments": [ @@ -4100,11 +4331,14 @@ "NML_LIMS:PH_LIBRARY_PREP_KIT" ], "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", "comments": [ @@ -4117,25 +4351,28 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Sequencing technology", - "CNPHI:Sequencing Instrument", + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", "NML_LIMS:PH_INSTRUMENT_CGN", - "VirusSeq_Portal:sequencing instrument" + "VirusSeq_Portal:sequencing%20instrument" ], "slot_uri": "GENEPIO:0001452", - "multivalued": true, + "domain_of": [ + "PathogenAgnostic" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "sequencing instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "comments": [ @@ -4149,14 +4386,17 @@ "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "NML_LIMS:PH_RAW_SEQUENCE_METHOD", - "VirusSeq_Portal:raw sequence data processing method" + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" ], "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "required": true }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "comments": [ @@ -4170,16 +4410,19 @@ "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ "NML_LIMS:PH_DEHOSTING_METHOD", - "VirusSeq_Portal:dehosting method" + "VirusSeq_Portal:dehosting%20method" ], "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "required": true }, - "assembly sequence software name": { - "name": "assembly sequence software name", + "assembly_software_name": { + "name": "assembly_software_name", "description": "The name of software used to generate the assembled sequence.", - "title": "assembly sequence software name", + "title": "assembly software name", "comments": [ "Provide the name of the software used to generate the assembled sequence." ], @@ -4189,13 +4432,16 @@ } ], "from_schema": "https://example.com/Pathogen_Agnostic", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "assembly sequence software version": { - "name": "assembly sequence software version", + "assembly_software_version": { + "name": "assembly_software_version", "description": "The version of the software used to generate the assembled sequence.", - "title": "assembly sequence software version", + "title": "assembly software version", "comments": [ "Provide the version of the software used to generate the assembled sequence." ], @@ -4205,11 +4451,14 @@ } ], "from_schema": "https://example.com/Pathogen_Agnostic", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "comments": [ @@ -4222,17 +4471,20 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:Assembly method", - "CNPHI:consensus sequence", + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", "NML_LIMS:PH_CONSENSUS_SEQUENCE", - "VirusSeq_Portal:consensus sequence software name" + "VirusSeq_Portal:consensus%20sequence%20software%20name" ], "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "comments": [ @@ -4245,16 +4497,19 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:consensus sequence", + "CNPHI:consensus%20sequence", "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", - "VirusSeq_Portal:consensus sequence software version" + "VirusSeq_Portal:consensus%20sequence%20software%20version" ], "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "comments": [ @@ -4267,11 +4522,14 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "CNPHI:Bioinformatics Protocol", + "CNPHI:Bioinformatics%20Protocol", "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", - "VirusSeq_Portal:bioinformatics protocol" + "VirusSeq_Portal:bioinformatics%20protocol" ], "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "required": true }, @@ -4294,11 +4552,14 @@ "NML_LIMS:PH_CANCOGEN_AUTHORS" ], "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "PathogenAgnostic" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", "comments": [ @@ -4311,11 +4572,14 @@ ], "from_schema": "https://example.com/Pathogen_Agnostic", "exact_mappings": [ - "GISAID:DataHarmonizer provenance", - "CNPHI:Additional Comments", + "GISAID:DataHarmonizer%20provenance", + "CNPHI:Additional%20Comments", "NML_LIMS:HC_COMMENTS" ], "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "PathogenAgnostic" + ], "range": "Provenance" } }, @@ -4325,103 +4589,104 @@ "description": "A DataHarmonizer interface", "from_schema": "https://example.com/Pathogen_Agnostic" }, - "Pathogen Agnostic": { - "name": "Pathogen Agnostic", + "PathogenAgnostic": { + "name": "PathogenAgnostic", + "title": "Pathogen Agnostic", "from_schema": "https://example.com/Pathogen_Agnostic", "is_a": "dh_interface", "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 1, "slot_group": "Database Identifiers" }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "rank": 2, "slot_group": "Database Identifiers" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "rank": 3, "slot_group": "Database Identifiers" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "rank": 4, "slot_group": "Database Identifiers" }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "rank": 5, "slot_group": "Database Identifiers" }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "rank": 6, "slot_group": "Database Identifiers" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "rank": 7, "slot_group": "Database Identifiers" }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "rank": 8, "slot_group": "Database Identifiers" }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "rank": 9, "slot_group": "Database Identifiers" }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "rank": 10, "slot_group": "Database Identifiers" }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "rank": 11, "slot_group": "Database Identifiers" }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "rank": 12, "slot_group": "Database Identifiers" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 13, "slot_group": "Sample collection and processing" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "rank": 14, "slot_group": "Sample collection and processing" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 15, "slot_group": "Sample collection and processing" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "rank": 16, "slot_group": "Sample collection and processing" }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 18, "slot_group": "Sample collection and processing" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 19, "slot_group": "Sample collection and processing" }, @@ -4435,153 +4700,153 @@ "rank": 21, "slot_group": "Sample collection and processing" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "rank": 22, "slot_group": "Sample collection and processing" }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "rank": 23, "slot_group": "Sample collection and processing" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "rank": 24, "slot_group": "Sample collection and processing" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "rank": 25, "slot_group": "Sample collection and processing" }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "rank": 26, "slot_group": "Sample collection and processing" }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "rank": 27, "slot_group": "Sample collection and processing" }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "rank": 28, "slot_group": "Sample collection and processing" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "rank": 29, "slot_group": "Sample collection and processing" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 30, "slot_group": "Sample collection and processing" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 31, "slot_group": "Sample collection and processing" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "rank": 32, "slot_group": "Sample collection and processing" }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "rank": 33, "slot_group": "Sample collection and processing" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 34, "slot_group": "Host Information" }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "rank": 35, "slot_group": "Host Information" }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "rank": 36, "slot_group": "Host Information" }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "rank": 37, "slot_group": "Host Information" }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "rank": 38, "slot_group": "Host Information" }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "rank": 39, "slot_group": "Host Information" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 40, "slot_group": "Sequencing" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 41, "slot_group": "Sequencing" }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "rank": 42, "slot_group": "Sequencing" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 43, "slot_group": "Sequencing" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 44, "slot_group": "Sequencing" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 45, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "rank": 46, "slot_group": "Bioinformatics and QC metrics" }, - "assembly sequence software name": { - "name": "assembly sequence software name", + "assembly_software_name": { + "name": "assembly_software_name", "rank": 47, "slot_group": "Bioinformatics and QC metrics" }, - "assembly sequence software version": { - "name": "assembly sequence software version", + "assembly_software_version": { + "name": "assembly_software_version", "rank": 48, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 49, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 50, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 51, "slot_group": "Bioinformatics and QC metrics" }, @@ -4590,136 +4855,240 @@ "rank": 52, "slot_group": "Contributor acknowledgement" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 53, "slot_group": "Contributor acknowledgement" } }, "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", + "NML_LIMS:TEXT_ID", + "BIOSAMPLE:sample_name", + "VirusSeq_Portal:specimen%20collector%20sample%20ID" + ], "rank": 1, "slot_uri": "GENEPIO:0001123", "identifier": true, - "alias": "specimen_collector_sample_ID", - "owner": "Pathogen Agnostic", + "alias": "specimen_collector_sample_id", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "description": "The name of the third party company or laboratory that provided services.", "title": "third party lab service provider name", + "comments": [ + "Provide the full, unabbreviated name of the company or laboratory." + ], + "examples": [ + { + "value": "Switch Health" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:HC_TEXT5" + ], "rank": 2, "slot_uri": "GENEPIO:0001202", "alias": "third_party_lab_service_provider_name", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "description": "The identifier assigned to a sample by a third party service provider.", "title": "third party lab sample ID", + "comments": [ + "Store the sample identifier supplied by the third party services provider." + ], + "examples": [ + { + "value": "SHK123456" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_ID_NUMBER_PRIMARY" + ], "rank": 3, "slot_uri": "GENEPIO:0001149", - "alias": "third_party_lab_sample_ID", - "owner": "Pathogen Agnostic", + "alias": "third_party_lab_sample_id", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_CASE_ID" + ], "rank": 4, "slot_uri": "GENEPIO:0100281", - "alias": "case_ID", - "owner": "Pathogen Agnostic", + "alias": "case_id", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "recommended": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", + "comments": [ + "Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system." + ], + "examples": [ + { + "value": "SR20-12345" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_PRIMARY_ID" + ], "rank": 5, "slot_uri": "GENEPIO:0001128", - "alias": "Related_specimen_primary_ID", - "owner": "Pathogen Agnostic", + "alias": "related_specimen_primary_id", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], - "slot_group": "Database Identifiers" + "slot_group": "Database Identifiers", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "description": "The identifier assigned to a sequenced isolate in IRIDA.", "title": "IRIDA sample name", + "comments": [ + "Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:IRIDA%20sample%20name" + ], "rank": 6, "slot_uri": "GENEPIO:0001131", - "alias": "IRIDA_sample_name", - "owner": "Pathogen Agnostic", + "alias": "irida_sample_name", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort.", "title": "umbrella bioproject accession", + "comments": [ + "Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject." + ], + "examples": [ + { + "value": "PRJNA623807" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:umbrella%20bioproject%20accession" + ], "rank": 7, "slot_uri": "GENEPIO:0001133", "alias": "umbrella_bioproject_accession", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", - "range": "umbrella bioproject accession menu", + "range": "UmbrellaBioprojectAccessionMenu", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:BioProject%20Accession", + "NML_LIMS:PH_BIOPROJECT_ACCESSION", + "BIOSAMPLE:bioproject_accession" + ], "rank": 8, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -4729,17 +5098,29 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:BioSample%20Accession", + "NML_LIMS:PH_BIOSAMPLE_ACCESSION" + ], "rank": 9, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -4749,17 +5130,29 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", + "comments": [ + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:SRA%20Accession", + "NML_LIMS:PH_SRA_ACCESSION" + ], "rank": 10, "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", - "owner": "Pathogen Agnostic", + "alias": "sra_accession", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -4769,17 +5162,29 @@ "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", + "comments": [ + "Store the accession returned from a GenBank submission (viral genome assembly)." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" + ], "rank": 11, "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", - "owner": "Pathogen Agnostic", + "alias": "genbank_accession", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -4789,17 +5194,31 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", + "comments": [ + "Store the accession returned from the GISAID submission." + ], + "examples": [ + { + "value": "EPI_ISL_436489" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID", + "BIOSAMPLE:GISAID_accession", + "VirusSeq_Portal:GISAID%20accession" + ], "rank": 12, "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", - "owner": "Pathogen Agnostic", + "alias": "gisaid_accession", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", @@ -4809,418 +5228,999 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", + "comments": [ + "The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)." + ], + "examples": [ + { + "value": "BC Centre for Disease Control" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", + "NML_LIMS:CUSTOMER", + "BIOSAMPLE:collected_by", + "VirusSeq_Portal:sample%20collected%20by" + ], "rank": 13, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SampleCollectedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency that generated the sequence.", "title": "sequenced by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by" + ], "rank": 14, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by", + "VirusSeq_Portal:sequence%20submitted%20by" + ], "rank": 15, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add \"jitter\" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", + "NML_LIMS:HC_COLLECT_DATE", + "BIOSAMPLE:sample%20collection%20date", + "VirusSeq_Portal:sample%20collection%20date" + ], "rank": 16, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", + "comments": [ + "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + ], + "examples": [ + { + "value": "year" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Precision%20of%20date%20collected", + "NML_LIMS:HC_TEXT2" + ], "rank": 17, "slot_uri": "GENEPIO:0001177", "alias": "sample_collection_date_precision", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SampleCollectionDatePrecisionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", + "comments": [ + "Provide the country name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Location", + "CNPHI:Patient%20Country", + "NML_LIMS:HC_COUNTRY", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28country%29" + ], "rank": 18, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", - "owner": "Pathogen Agnostic", + "alias": "geo_loc_name_country", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Patient%20Province", + "NML_LIMS:HC_PROVINCE", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" + ], "rank": 19, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", - "owner": "Pathogen Agnostic", + "alias": "geo_loc_name_state_province_territory", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "organism": { "name": "organism", "description": "Taxonomic name of the organism.", "title": "organism", + "comments": [ + "Use \"Severe acute respiratory syndrome coronavirus 2\". This value is provided in the template." + ], + "examples": [ + { + "value": "Severe acute respiratory syndrome coronavirus 2" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Pathogen", + "NML_LIMS:HC_CURRENT_ID", + "BIOSAMPLE:organism", + "VirusSeq_Portal:organism" + ], "rank": 20, "slot_uri": "GENEPIO:0001191", "alias": "organism", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "OrganismMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "isolate": { "name": "isolate", "description": "Identifier of the specific isolate.", "title": "isolate", + "comments": [ + "Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”." + ], + "examples": [ + { + "value": "hCov-19/CANADA/BC-prov_rona_99/2020" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS", + "BIOSAMPLE:isolate", + "BIOSAMPLE:GISAID_virus_name", + "VirusSeq_Portal:isolate", + "VirusSeq_Portal:fasta%20header%20name" + ], "rank": 21, "slot_uri": "GENEPIO:0001195", "alias": "isolate", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Diagnostic testing" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sampling", + "NML_LIMS:HC_SAMPLE_CATEGORY", + "BIOSAMPLE:purpose_of_sampling", + "VirusSeq_Portal:purpose%20of%20sampling" + ], "rank": 22, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", + "comments": [ + "Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value." + ], + "examples": [ + { + "value": "The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada." + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", + "NML_LIMS:PH_SAMPLING_DETAILS", + "BIOSAMPLE:description", + "VirusSeq_Portal:purpose%20of%20sampling%20details" + ], "rank": 23, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", + "comments": [ + "This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”." + ], + "examples": [ + { + "value": "swab" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Specimen%20Type", + "NML_LIMS:PH_SPECIMEN_TYPE" + ], "rank": 24, "slot_uri": "GENEPIO:0001204", - "alias": "NML_submitted_specimen_type", - "owner": "Pathogen Agnostic", + "alias": "nml_submitted_specimen_type", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "range": "NML submitted specimen type menu", + "range": "NMLSubmittedSpecimenTypeMenu", "recommended": true }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Blood" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", + "NML_LIMS:PH_ISOLATION_SITE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "VirusSeq_Portal:anatomical%20material" + ], "rank": 25, "slot_uri": "GENEPIO:0001211", - "multivalued": true, "alias": "anatomical_material", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Nasopharynx (NP)" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", + "NML_LIMS:PH_ISOLATION_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "VirusSeq_Portal:anatomical%20part" + ], "rank": 26, "slot_uri": "GENEPIO:0001214", - "multivalued": true, "alias": "anatomical_part", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Feces" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", + "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "VirusSeq_Portal:body%20product" + ], "rank": 27, "slot_uri": "GENEPIO:0001216", - "multivalued": true, "alias": "body_product", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", + "comments": [ + "Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Face mask" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Environmental%20Material", + "NML_LIMS:PH_ENVIRONMENTAL_MATERIAL", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_material", + "VirusSeq_Portal:environmental%20material" + ], "rank": 28, "slot_uri": "GENEPIO:0001223", - "multivalued": true, "alias": "environmental_material", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", + "comments": [ + "Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Production Facility" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Environmental%20Site", + "NML_LIMS:PH_ENVIRONMENTAL_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:environmental_site", + "VirusSeq_Portal:environmental%20site" + ], "rank": 29, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", + "comments": [ + "Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Swab" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", + "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "VirusSeq_Portal:collection%20device" + ], "rank": 30, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Bronchoalveolar lavage (BAL)" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", + "NML_LIMS:COLLECTION_METHOD", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "VirusSeq_Portal:collection%20method" + ], "rank": 31, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." + ], + "examples": [ + { + "value": "Specimens pooled" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Passage%20details/history", + "NML_LIMS:specimen%20processing" + ], "rank": 32, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample." + ], + "examples": [ + { + "value": "25 swabs were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", "rank": 33, "slot_uri": "GENEPIO:0100311", "alias": "specimen_processing_details", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], + "examples": [ + { + "value": "Homo sapiens" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host%20%28scientific%20name%29", + "BIOSAMPLE:host", + "VirusSeq_Portal:host%20%28scientific%20name%29" + ], "rank": 34, "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", - "owner": "Pathogen Agnostic", + "alias": "host_scientific_name", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", + "comments": [ + "Select \"COVID-19\" from the pick list provided in the template." + ], + "examples": [ + { + "value": "COVID-19" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Host%20Disease", + "NML_LIMS:PH_HOST_DISEASE", + "BIOSAMPLE:host_disease", + "VirusSeq_Portal:host%20disease" + ], "rank": 35, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", + "comments": [ + "Enter the age of the host in years. If not available, provide a null value. If there is not host, put \"Not Applicable\"." + ], + "examples": [ + { + "value": "79" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:Patient%20Age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age", + "VirusSeq_Portal:host%20age" + ], "rank": 36, "slot_uri": "GENEPIO:0001392", "alias": "host_age", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Host Information", "recommended": true, "minimum_value": 0, - "maximum_value": 130 + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The unit used to measure the host age, in either months or years.", "title": "host age unit", + "comments": [ + "Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin." + ], + "examples": [ + { + "value": "years" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Age%20Units", + "NML_LIMS:PH_AGE_UNIT", + "VirusSeq_Portal:host%20age%20unit" + ], "rank": 37, "slot_uri": "GENEPIO:0001393", "alias": "host_age_unit", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "HostAgeUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host age bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value." + ], + "examples": [ + { + "value": "60 - 69" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Host%20Age%20Category", + "NML_LIMS:PH_AGE_GROUP", + "VirusSeq_Portal:host%20age%20bin" + ], "rank": 38, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", + "comments": [ + "Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put \"Not Applicable\"." + ], + "examples": [ + { + "value": "Male" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Gender", + "CNPHI:Patient%20Sex", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex", + "VirusSeq_Portal:host%20gender" + ], "rank": 39, "slot_uri": "GENEPIO:0001395", "alias": "host_gender", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Host Information", "recommended": true, @@ -5228,191 +6228,377 @@ "syntax": "{Title_Case}", "interpolated": true, "partial_match": false - } + }, + "any_of": [ + { + "range": "HostGenderMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Baseline surveillance (random sampling)" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING", + "BIOSAMPLE:purpose_of_sequencing", + "VirusSeq_Portal:purpose%20of%20sequencing" + ], "rank": 40, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection." + ], + "examples": [ + { + "value": "Screened for S gene target failure (S dropout)" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", + "VirusSeq_Portal:purpose%20of%20sequencing%20details" + ], "rank": 41, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sequencing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "todos": [ + ">={sample collection date}" + ], + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_DATE" + ], "rank": 42, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sequencing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_LIBRARY_PREP_KIT" + ], "rank": 43, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString", "recommended": true }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", + "NML_LIMS:PH_INSTRUMENT_CGN", + "VirusSeq_Portal:sequencing%20instrument" + ], "rank": 44, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_RAW_SEQUENCE_METHOD", + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" + ], "rank": 45, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "NML_LIMS:PH_DEHOSTING_METHOD", + "VirusSeq_Portal:dehosting%20method" + ], "rank": 46, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "assembly sequence software name": { - "name": "assembly sequence software name", + "assembly_software_name": { + "name": "assembly_software_name", "description": "The name of software used to generate the assembled sequence.", - "title": "assembly sequence software name", + "title": "assembly software name", + "comments": [ + "Provide the name of the software used to generate the assembled sequence." + ], + "examples": [ + { + "value": "Shovill" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", "rank": 47, - "alias": "assembly_sequence_software_name", - "owner": "Pathogen Agnostic", + "alias": "assembly_software_name", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "assembly sequence software version": { - "name": "assembly sequence software version", + "assembly_software_version": { + "name": "assembly_software_version", "description": "The version of the software used to generate the assembled sequence.", - "title": "assembly sequence software version", + "title": "assembly software version", + "comments": [ + "Provide the version of the software used to generate the assembled sequence." + ], + "examples": [ + { + "value": "1.2.3" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", "rank": 48, - "alias": "assembly_sequence_software_version", - "owner": "Pathogen Agnostic", + "alias": "assembly_software_version", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" + ], "rank": 49, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" + ], "rank": 50, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], + "examples": [ + { + "value": "https://github.com/phac-nml/ncov2019-artic-nf" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "CNPHI:Bioinformatics%20Protocol", + "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", + "VirusSeq_Portal:bioinformatics%20protocol" + ], "rank": 51, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", @@ -5422,29 +6608,55 @@ "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:Authors", + "CNPHI:Authors", + "NML_LIMS:PH_CANCOGEN_AUTHORS" + ], "rank": 52, "slot_uri": "GENEPIO:0001517", "alias": "authors", - "owner": "Pathogen Agnostic", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Contributor acknowledgement", "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0" + } + ], "from_schema": "https://example.com/Pathogen_Agnostic", + "exact_mappings": [ + "GISAID:DataHarmonizer%20provenance", + "CNPHI:Additional%20Comments", + "NML_LIMS:HC_COMMENTS" + ], "rank": 53, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", - "owner": "Pathogen Agnostic", + "alias": "dataharmonizer_provenance", + "owner": "PathogenAgnostic", "domain_of": [ - "Pathogen Agnostic" + "PathogenAgnostic" ], "slot_group": "Contributor acknowledgement", "range": "Provenance" @@ -5452,7 +6664,6 @@ } } }, - "source_file": "schema.yaml", "settings": { "Title_Case": { "setting_key": "Title_Case", diff --git a/web/templates/pathogen/schema.yaml b/web/templates/pathogen/schema.yaml index f518e433..623b739e 100644 --- a/web/templates/pathogen/schema.yaml +++ b/web/templates/pathogen/schema.yaml @@ -1,5 +1,5 @@ id: https://example.com/Pathogen_Agnostic -name: Pathogen_Agnostic +name: PathogenAgnostic description: '' version: 1.0.0 imports: @@ -12,120 +12,121 @@ classes: name: dh_interface description: A DataHarmonizer interface from_schema: https://example.com/Pathogen_Agnostic - Pathogen Agnostic: - name: Pathogen Agnostic + PathogenAgnostic: + name: PathogenAgnostic + title: Pathogen Agnostic description: null is_a: dh_interface slots: - - specimen collector sample ID - - third party lab service provider name - - third party lab sample ID - - case ID - - Related specimen primary ID - - IRIDA sample name - - umbrella bioproject accession - - bioproject accession - - biosample accession - - SRA accession - - GenBank accession - - GISAID accession - - sample collected by - - sequenced by - - sequence submitted by - - sample collection date - - sample collection date precision - - geo_loc_name (country) - - geo_loc_name (state/province/territory) + - specimen_collector_sample_id + - third_party_lab_service_provider_name + - third_party_lab_sample_id + - case_id + - related_specimen_primary_id + - irida_sample_name + - umbrella_bioproject_accession + - bioproject_accession + - biosample_accession + - sra_accession + - genbank_accession + - gisaid_accession + - sample_collected_by + - sequenced_by + - sequence_submitted_by + - sample_collection_date + - sample_collection_date_precision + - geo_loc_name_country + - geo_loc_name_state_province_territory - organism - isolate - - purpose of sampling - - purpose of sampling details - - NML submitted specimen type - - anatomical material - - anatomical part - - body product - - environmental material - - environmental site - - collection device - - collection method - - specimen processing - - specimen processing details - - host (scientific name) - - host disease - - host age - - host age unit - - host age bin - - host gender - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library preparation kit - - sequencing instrument - - raw sequence data processing method - - dehosting method - - assembly sequence software name - - assembly sequence software version - - consensus sequence software name - - consensus sequence software version - - bioinformatics protocol + - purpose_of_sampling + - purpose_of_sampling_details + - nml_submitted_specimen_type + - anatomical_material + - anatomical_part + - body_product + - environmental_material + - environmental_site + - collection_device + - collection_method + - specimen_processing + - specimen_processing_details + - host_scientific_name + - host_disease + - host_age + - host_age_unit + - host_age_bin + - host_gender + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_preparation_kit + - sequencing_instrument + - raw_sequence_data_processing_method + - dehosting_method + - assembly_software_name + - assembly_software_version + - consensus_sequence_software_name + - consensus_sequence_software_version + - bioinformatics_protocol - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database Identifiers - third party lab service provider name: + third_party_lab_service_provider_name: rank: 2 slot_group: Database Identifiers - third party lab sample ID: + third_party_lab_sample_id: rank: 3 slot_group: Database Identifiers - case ID: + case_id: rank: 4 slot_group: Database Identifiers - Related specimen primary ID: + related_specimen_primary_id: rank: 5 slot_group: Database Identifiers - IRIDA sample name: + irida_sample_name: rank: 6 slot_group: Database Identifiers - umbrella bioproject accession: + umbrella_bioproject_accession: rank: 7 slot_group: Database Identifiers - bioproject accession: + bioproject_accession: rank: 8 slot_group: Database Identifiers - biosample accession: + biosample_accession: rank: 9 slot_group: Database Identifiers - SRA accession: + sra_accession: rank: 10 slot_group: Database Identifiers - GenBank accession: + genbank_accession: rank: 11 slot_group: Database Identifiers - GISAID accession: + gisaid_accession: rank: 12 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 13 slot_group: Sample collection and processing - sequenced by: + sequenced_by: rank: 14 slot_group: Sample collection and processing - sequence submitted by: + sequence_submitted_by: rank: 15 slot_group: Sample collection and processing - sample collection date: + sample_collection_date: rank: 16 slot_group: Sample collection and processing - sample collection date precision: + sample_collection_date_precision: rank: 17 slot_group: Sample collection and processing - geo_loc_name (country): + geo_loc_name_country: rank: 18 slot_group: Sample collection and processing - geo_loc_name (state/province/territory): + geo_loc_name_state_province_territory: rank: 19 slot_group: Sample collection and processing organism: @@ -134,105 +135,105 @@ classes: isolate: rank: 21 slot_group: Sample collection and processing - purpose of sampling: + purpose_of_sampling: rank: 22 slot_group: Sample collection and processing - purpose of sampling details: + purpose_of_sampling_details: rank: 23 slot_group: Sample collection and processing - NML submitted specimen type: + nml_submitted_specimen_type: rank: 24 slot_group: Sample collection and processing - anatomical material: + anatomical_material: rank: 25 slot_group: Sample collection and processing - anatomical part: + anatomical_part: rank: 26 slot_group: Sample collection and processing - body product: + body_product: rank: 27 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 28 slot_group: Sample collection and processing - environmental site: + environmental_site: rank: 29 slot_group: Sample collection and processing - collection device: + collection_device: rank: 30 slot_group: Sample collection and processing - collection method: + collection_method: rank: 31 slot_group: Sample collection and processing - specimen processing: + specimen_processing: rank: 32 slot_group: Sample collection and processing - specimen processing details: + specimen_processing_details: rank: 33 slot_group: Sample collection and processing - host (scientific name): + host_scientific_name: rank: 34 slot_group: Host Information - host disease: + host_disease: rank: 35 slot_group: Host Information - host age: + host_age: rank: 36 slot_group: Host Information - host age unit: + host_age_unit: rank: 37 slot_group: Host Information - host age bin: + host_age_bin: rank: 38 slot_group: Host Information - host gender: + host_gender: rank: 39 slot_group: Host Information - purpose of sequencing: + purpose_of_sequencing: rank: 40 slot_group: Sequencing - purpose of sequencing details: + purpose_of_sequencing_details: rank: 41 slot_group: Sequencing - sequencing date: + sequencing_date: rank: 42 slot_group: Sequencing - library preparation kit: + library_preparation_kit: rank: 43 slot_group: Sequencing - sequencing instrument: + sequencing_instrument: rank: 44 slot_group: Sequencing - raw sequence data processing method: + raw_sequence_data_processing_method: rank: 45 slot_group: Bioinformatics and QC metrics - dehosting method: + dehosting_method: rank: 46 slot_group: Bioinformatics and QC metrics - assembly sequence software name: + assembly_software_name: rank: 47 slot_group: Bioinformatics and QC metrics - assembly sequence software version: + assembly_software_version: rank: 48 slot_group: Bioinformatics and QC metrics - consensus sequence software name: + consensus_sequence_software_name: rank: 49 slot_group: Bioinformatics and QC metrics - consensus sequence software version: + consensus_sequence_software_version: rank: 50 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + bioinformatics_protocol: rank: 51 slot_group: Bioinformatics and QC metrics authors: rank: 52 slot_group: Contributor acknowledgement - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 53 slot_group: Contributor acknowledgement slots: - specimen collector sample ID: - name: specimen collector sample ID + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. comments: Store the collector sample ID. If this number is considered identifiable @@ -241,75 +242,75 @@ slots: Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. - examples: - - value: prov_rona_99 slot_uri: GENEPIO:0001123 - range: WhitespaceMinimizedString identifier: true + range: WhitespaceMinimizedString required: true + examples: + - value: prov_rona_99 exact_mappings: - - GISAID:Sample ID given by the sample provider - - CNPHI:Primary Specimen ID + - GISAID:Sample%20ID%20given%20by%20the%20sample%20provider + - CNPHI:Primary%20Specimen%20ID - NML_LIMS:TEXT_ID - BIOSAMPLE:sample_name - - VirusSeq_Portal:specimen collector sample ID - third party lab service provider name: - name: third party lab service provider name + - VirusSeq_Portal:specimen%20collector%20sample%20ID + third_party_lab_service_provider_name: + name: third_party_lab_service_provider_name title: third party lab service provider name description: The name of the third party company or laboratory that provided services. comments: Provide the full, unabbreviated name of the company or laboratory. - examples: - - value: Switch Health slot_uri: GENEPIO:0001202 range: WhitespaceMinimizedString + examples: + - value: Switch Health exact_mappings: - NML_LIMS:HC_TEXT5 - third party lab sample ID: - name: third party lab sample ID + third_party_lab_sample_id: + name: third_party_lab_sample_id title: third party lab sample ID description: The identifier assigned to a sample by a third party service provider. comments: Store the sample identifier supplied by the third party services provider. - examples: - - value: SHK123456 slot_uri: GENEPIO:0001149 range: WhitespaceMinimizedString + examples: + - value: SHK123456 exact_mappings: - NML_LIMS:PH_ID_NUMBER_PRIMARY - case ID: - name: case ID + case_id: + name: case_id title: case ID description: The identifier used to specify an epidemiologically detected case of disease. comments: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. - examples: - - value: ABCD1234 slot_uri: GENEPIO:0100281 range: WhitespaceMinimizedString recommended: true + examples: + - value: ABCD1234 exact_mappings: - NML_LIMS:PH_CASE_ID - Related specimen primary ID: - name: Related specimen primary ID + related_specimen_primary_id: + name: related_specimen_primary_id title: Related specimen primary ID description: The primary ID of a related specimen previously submitted to the repository. comments: Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. - examples: - - value: SR20-12345 slot_uri: GENEPIO:0001128 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu + examples: + - value: SR20-12345 exact_mappings: - - CNPHI:Related Specimen ID - - CNPHI:Related Specimen Relationship Type + - CNPHI:Related%20Specimen%20ID + - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_PRIMARY_ID - IRIDA sample name: - name: IRIDA sample name + irida_sample_name: + name: irida_sample_name title: IRIDA sample name description: The identifier assigned to a sequenced isolate in IRIDA. comments: Store the IRIDA sample name. The IRIDA sample name will be created by @@ -320,14 +321,14 @@ slots: mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). - examples: - - value: prov_rona_99 slot_uri: GENEPIO:0001131 range: WhitespaceMinimizedString + examples: + - value: prov_rona_99 exact_mappings: - - NML_LIMS:IRIDA sample name - umbrella bioproject accession: - name: umbrella bioproject accession + - NML_LIMS:IRIDA%20sample%20name + umbrella_bioproject_accession: + name: umbrella_bioproject_accession title: umbrella bioproject accession description: The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. @@ -335,18 +336,18 @@ slots: in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. - examples: - - value: PRJNA623807 slot_uri: GENEPIO:0001133 - range: umbrella bioproject accession menu + range: UmbrellaBioprojectAccessionMenu structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: PRJNA623807 exact_mappings: - - NML_LIMS:umbrella bioproject accession - bioproject accession: - name: bioproject accession + - NML_LIMS:umbrella%20bioproject%20accession + bioproject_accession: + name: bioproject_accession title: bioproject accession description: The INSDC accession number of the BioProject(s) to which the BioSample belongs. @@ -356,90 +357,90 @@ slots: by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. - examples: - - value: PRJNA608651 slot_uri: GENEPIO:0001136 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: PRJNA608651 exact_mappings: - - CNPHI:BioProject Accession + - CNPHI:BioProject%20Accession - NML_LIMS:PH_BIOPROJECT_ACCESSION - BIOSAMPLE:bioproject_accession - biosample accession: - name: biosample accession + biosample_accession: + name: biosample_accession title: biosample accession description: The identifier assigned to a BioSample in INSDC archives. comments: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. - examples: - - value: SAMN14180202 slot_uri: GENEPIO:0001139 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: SAMN14180202 exact_mappings: - - CNPHI:BioSample Accession + - CNPHI:BioSample%20Accession - NML_LIMS:PH_BIOSAMPLE_ACCESSION - SRA accession: - name: SRA accession + sra_accession: + name: sra_accession title: SRA accession description: The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. comments: Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. - examples: - - value: SRR11177792 slot_uri: GENEPIO:0001142 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: SRR11177792 exact_mappings: - - CNPHI:SRA Accession + - CNPHI:SRA%20Accession - NML_LIMS:PH_SRA_ACCESSION - GenBank accession: - name: GenBank accession + genbank_accession: + name: genbank_accession title: GenBank accession description: The GenBank identifier assigned to the sequence in the INSDC archives. comments: Store the accession returned from a GenBank submission (viral genome assembly). - examples: - - value: MN908947.3 slot_uri: GENEPIO:0001145 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: MN908947.3 exact_mappings: - - CNPHI:GenBank Accession - - NML_LIMS:GenBank accession - GISAID accession: - name: GISAID accession + - CNPHI:GenBank%20Accession + - NML_LIMS:GenBank%20accession + gisaid_accession: + name: gisaid_accession title: GISAID accession description: The GISAID accession number assigned to the sequence. comments: Store the accession returned from the GISAID submission. - examples: - - value: EPI_ISL_436489 slot_uri: GENEPIO:0001147 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: EPI_ISL_436489 exact_mappings: - - CNPHI:GISAID Accession (if known) - - NML_LIMS:SUBMISSIONS - GISAID Accession ID + - CNPHI:GISAID%20Accession%20%28if%20known%29 + - NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID - BIOSAMPLE:GISAID_accession - - VirusSeq_Portal:GISAID accession - sample collected by: - name: sample collected by + - VirusSeq_Portal:GISAID%20accession + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the agency that collected the original sample. comments: The name of the sample collector should be written out in full, (with @@ -447,58 +448,58 @@ slots: Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). - examples: - - value: BC Centre for Disease Control slot_uri: GENEPIO:0001153 any_of: - - range: sample collected by menu - - range: null value menu + - range: SampleCollectedByMenu + - range: NullValueMenu required: true + examples: + - value: BC Centre for Disease Control exact_mappings: - - GISAID:Originating lab - - CNPHI:Lab Name + - GISAID:Originating%20lab + - CNPHI:Lab%20Name - NML_LIMS:CUSTOMER - BIOSAMPLE:collected_by - - VirusSeq_Portal:sample collected by - sequenced by: - name: sequenced by + - VirusSeq_Portal:sample%20collected%20by + sequenced_by: + name: sequenced_by title: sequenced by description: The name of the agency that generated the sequence. comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". - examples: - - value: Public Health Ontario (PHO) slot_uri: GENEPIO:0100416 any_of: - - range: sequence submitted by menu - - range: null value menu + - range: SequenceSubmittedByMenu + - range: NullValueMenu required: true + examples: + - value: Public Health Ontario (PHO) exact_mappings: - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by - sequence submitted by: - name: sequence submitted by + sequence_submitted_by: + name: sequence_submitted_by title: sequence submitted by description: The name of the agency that generated the sequence. comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". - examples: - - value: Public Health Ontario (PHO) slot_uri: GENEPIO:0001159 any_of: - - range: sequence submitted by menu - - range: null value menu + - range: SequenceSubmittedByMenu + - range: NullValueMenu required: true + examples: + - value: Public Health Ontario (PHO) exact_mappings: - - GISAID:Submitting lab - - CNPHI:Sequencing Centre + - GISAID:Submitting%20lab + - CNPHI:Sequencing%20Centre - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by - - VirusSeq_Portal:sequence submitted by - sample collection date: - name: sample collection date + - VirusSeq_Portal:sequence%20submitted%20by + sample_collection_date: + name: sample_collection_date title: sample collection date description: The date on which the sample was collected. comments: "Sample collection date is critical for surveillance and many types\ @@ -507,88 +508,88 @@ slots: \ by adding or subtracting a calendar day (acceptable by GISAID). Alternatively,\ \ \u201Dreceived date\u201D may be used as a substitute. The date should be\ \ provided in ISO 8601 standard format \"YYYY-MM-DD\"." - examples: - - value: '2020-03-16' slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu - required: true + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} + required: true + examples: + - value: '2020-03-16' exact_mappings: - - GISAID:Collection date - - CNPHI:Patient Sample Collected Date + - GISAID:Collection%20date + - CNPHI:Patient%20Sample%20Collected%20Date - NML_LIMS:HC_COLLECT_DATE - - BIOSAMPLE:sample collection date - - VirusSeq_Portal:sample collection date - sample collection date precision: - name: sample collection date precision + - BIOSAMPLE:sample%20collection%20date + - VirusSeq_Portal:sample%20collection%20date + sample_collection_date_precision: + name: sample_collection_date_precision title: sample collection date precision description: The precision to which the "sample collection date" was provided. comments: Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". - examples: - - value: year slot_uri: GENEPIO:0001177 any_of: - - range: sample collection date precision menu - - range: null value menu + - range: SampleCollectionDatePrecisionMenu + - range: NullValueMenu required: true + examples: + - value: year exact_mappings: - - CNPHI:Precision of date collected + - CNPHI:Precision%20of%20date%20collected - NML_LIMS:HC_TEXT2 - geo_loc_name (country): - name: geo_loc_name (country) + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc_name (country) description: The country where the sample was collected. comments: Provide the country name from the controlled vocabulary provided. - examples: - - value: Canada slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true + examples: + - value: Canada exact_mappings: - GISAID:Location - - CNPHI:Patient Country + - CNPHI:Patient%20Country - NML_LIMS:HC_COUNTRY - BIOSAMPLE:geo_loc_name - - VirusSeq_Portal:geo_loc_name (country) - geo_loc_name (state/province/territory): - name: geo_loc_name (state/province/territory) + - VirusSeq_Portal:geo_loc_name%20%28country%29 + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo_loc_name (state/province/territory) description: The province/territory where the sample was collected. comments: Provide the province/territory name from the controlled vocabulary provided. - examples: - - value: Saskatchewan slot_uri: GENEPIO:0001185 any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu required: true + examples: + - value: Saskatchewan exact_mappings: - - CNPHI:Patient Province + - CNPHI:Patient%20Province - NML_LIMS:HC_PROVINCE - BIOSAMPLE:geo_loc_name - - VirusSeq_Portal:geo_loc_name (state/province/territory) + - VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29 organism: name: organism title: organism description: Taxonomic name of the organism. comments: Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. - examples: - - value: Severe acute respiratory syndrome coronavirus 2 slot_uri: GENEPIO:0001191 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu required: true + examples: + - value: Severe acute respiratory syndrome coronavirus 2 exact_mappings: - CNPHI:Pathogen - NML_LIMS:HC_CURRENT_ID @@ -600,23 +601,23 @@ slots: description: Identifier of the specific isolate. comments: "Provide the GISAID virus name, which should be written in the format\ \ \u201ChCov-19/CANADA/2 digit provincial ISO code-xxxxx/year\u201D." - examples: - - value: hCov-19/CANADA/BC-prov_rona_99/2020 slot_uri: GENEPIO:0001195 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true + examples: + - value: hCov-19/CANADA/BC-prov_rona_99/2020 exact_mappings: - - GISAID:Virus name - - CNPHI:GISAID Virus Name - - NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS + - GISAID:Virus%20name + - CNPHI:GISAID%20Virus%20Name + - NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS - BIOSAMPLE:isolate - BIOSAMPLE:GISAID_virus_name - VirusSeq_Portal:isolate - - VirusSeq_Portal:fasta header name - purpose of sampling: - name: purpose of sampling + - VirusSeq_Portal:fasta%20header%20name + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: The reason a sample was collected may provide information about potential @@ -625,20 +626,20 @@ slots: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. - examples: - - value: Diagnostic testing slot_uri: GENEPIO:0001198 any_of: - - range: purpose of sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu required: true + examples: + - value: Diagnostic testing exact_mappings: - - CNPHI:Reason for Sampling + - CNPHI:Reason%20for%20Sampling - NML_LIMS:HC_SAMPLE_CATEGORY - BIOSAMPLE:purpose_of_sampling - - VirusSeq_Portal:purpose of sampling - purpose of sampling details: - name: purpose of sampling details + - VirusSeq_Portal:purpose%20of%20sampling + purpose_of_sampling_details: + name: purpose_of_sampling_details title: purpose of sampling details description: The description of why the sample was collected, providing specific details. @@ -646,21 +647,21 @@ slots: free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. - examples: - - value: The sample was collected to investigate the prevalence of variants associated - with mink-to-human transmission in Canada. slot_uri: GENEPIO:0001200 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true + examples: + - value: The sample was collected to investigate the prevalence of variants associated + with mink-to-human transmission in Canada. exact_mappings: - - CNPHI:Details on the Reason for Sampling + - CNPHI:Details%20on%20the%20Reason%20for%20Sampling - NML_LIMS:PH_SAMPLING_DETAILS - BIOSAMPLE:description - - VirusSeq_Portal:purpose of sampling details - NML submitted specimen type: - name: NML submitted specimen type + - VirusSeq_Portal:purpose%20of%20sampling%20details + nml_submitted_specimen_type: + name: nml_submitted_specimen_type title: NML submitted specimen type description: The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. @@ -668,16 +669,16 @@ slots: \ Select the specimen type from the pick list provided. If sequence data is\ \ being submitted rather than a specimen for testing, select \u201CNot Applicable\u201D\ ." - examples: - - value: swab slot_uri: GENEPIO:0001204 - range: NML submitted specimen type menu + range: NMLSubmittedSpecimenTypeMenu recommended: true + examples: + - value: swab exact_mappings: - - CNPHI:Specimen Type + - CNPHI:Specimen%20Type - NML_LIMS:PH_SPECIMEN_TYPE - anatomical material: - name: anatomical material + anatomical_material: + name: anatomical_material title: anatomical material description: A substance obtained from an anatomical part of an organism e.g. tissue, blood. @@ -685,46 +686,46 @@ slots: picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Blood slot_uri: GENEPIO:0001211 any_of: - - range: anatomical material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Blood exact_mappings: - - GISAID:Specimen source - - CNPHI:Anatomical Material + - GISAID:Specimen%20source + - CNPHI:Anatomical%20Material - NML_LIMS:PH_ISOLATION_SITE_DESC - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_material - - VirusSeq_Portal:anatomical material - anatomical part: - name: anatomical part + - VirusSeq_Portal:anatomical%20material + anatomical_part: + name: anatomical_part title: anatomical part description: An anatomical part of an organism e.g. oropharynx. comments: Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Nasopharynx (NP) slot_uri: GENEPIO:0001214 any_of: - - range: anatomical part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Nasopharynx (NP) exact_mappings: - - GISAID:Specimen source - - CNPHI:Anatomical Site + - GISAID:Specimen%20source + - CNPHI:Anatomical%20Site - NML_LIMS:PH_ISOLATION_SITE - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_part - - VirusSeq_Portal:anatomical part - body product: - name: body product + - VirusSeq_Portal:anatomical%20part + body_product: + name: body_product title: body product description: A substance excreted/secreted from an organism e.g. feces, urine, sweat. @@ -732,23 +733,23 @@ slots: provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Feces slot_uri: GENEPIO:0001216 any_of: - - range: body product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Feces exact_mappings: - - GISAID:Specimen source - - CNPHI:Body Product + - GISAID:Specimen%20source + - CNPHI:Body%20Product - NML_LIMS:PH_SPECIMEN_SOURCE_DESC - BIOSAMPLE:isolation_source - BIOSAMPLE:body_product - - VirusSeq_Portal:body product - environmental material: - name: environmental material + - VirusSeq_Portal:body%20product + environmental_material: + name: environmental_material title: environmental material description: A substance obtained from the natural or man-made environment e.g. soil, water, sewage. @@ -756,23 +757,23 @@ slots: picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Face mask slot_uri: GENEPIO:0001223 any_of: - - range: environmental material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Face mask exact_mappings: - - GISAID:Specimen source - - CNPHI:Environmental Material + - GISAID:Specimen%20source + - CNPHI:Environmental%20Material - NML_LIMS:PH_ENVIRONMENTAL_MATERIAL - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_material - - VirusSeq_Portal:environmental material - environmental site: - name: environmental site + - VirusSeq_Portal:environmental%20material + environmental_site: + name: environmental_site title: environmental site description: An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. @@ -780,69 +781,69 @@ slots: provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Production Facility slot_uri: GENEPIO:0001232 any_of: - - range: environmental site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Production Facility exact_mappings: - - GISAID:Specimen source - - CNPHI:Environmental Site + - GISAID:Specimen%20source + - CNPHI:Environmental%20Site - NML_LIMS:PH_ENVIRONMENTAL_SITE - BIOSAMPLE:isolation_source - BIOSAMPLE:environmental_site - - VirusSeq_Portal:environmental site - collection device: - name: collection device + - VirusSeq_Portal:environmental%20site + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. swab. comments: Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Swab slot_uri: GENEPIO:0001234 any_of: - - range: collection device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Swab exact_mappings: - - GISAID:Specimen source - - CNPHI:Specimen Collection Matrix + - GISAID:Specimen%20source + - CNPHI:Specimen%20Collection%20Matrix - NML_LIMS:PH_SPECIMEN_TYPE_ORIG - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_device - - VirusSeq_Portal:collection device - collection method: - name: collection method + - VirusSeq_Portal:collection%20device + collection_method: + name: collection_method title: collection method description: The process used to collect the sample e.g. phlebotamy, necropsy. comments: Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Bronchoalveolar lavage (BAL) slot_uri: GENEPIO:0001241 any_of: - - range: collection method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Bronchoalveolar lavage (BAL) exact_mappings: - - GISAID:Specimen source - - CNPHI:Collection Method + - GISAID:Specimen%20source + - CNPHI:Collection%20Method - NML_LIMS:COLLECTION_METHOD - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method - - VirusSeq_Portal:collection method - specimen processing: - name: specimen processing + - VirusSeq_Portal:collection%20method + specimen_processing: + name: specimen_processing title: specimen processing description: Any processing applied to the sample during or after receiving the sample. @@ -850,146 +851,146 @@ slots: from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". - examples: - - value: Specimens pooled slot_uri: GENEPIO:0001253 any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Specimens pooled exact_mappings: - - GISAID:Passage details/history - - NML_LIMS:specimen processing - specimen processing details: - name: specimen processing details + - GISAID:Passage%20details/history + - NML_LIMS:specimen%20processing + specimen_processing_details: + name: specimen_processing_details title: specimen processing details description: Detailed information regarding the processing applied to a sample during or after receiving the sample. comments: Provide a free text description of any processing details applied to a sample. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString examples: - value: 25 swabs were pooled and further prepared as a single sample during library prep. - slot_uri: GENEPIO:0100311 - range: WhitespaceMinimizedString - host (scientific name): - name: host (scientific name) + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. comments: Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable - examples: - - value: Homo sapiens slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu + - range: HostScientificNameMenu + - range: NullValueMenu required: true + examples: + - value: Homo sapiens exact_mappings: - GISAID:Host - - NML_LIMS:host (scientific name) + - NML_LIMS:host%20%28scientific%20name%29 - BIOSAMPLE:host - - VirusSeq_Portal:host (scientific name) - host disease: - name: host disease + - VirusSeq_Portal:host%20%28scientific%20name%29 + host_disease: + name: host_disease title: host disease description: The name of the disease experienced by the host. comments: Select "COVID-19" from the pick list provided in the template. - examples: - - value: COVID-19 slot_uri: GENEPIO:0001391 any_of: - - range: host disease menu - - range: null value menu + - range: HostDiseaseMenu + - range: NullValueMenu recommended: true + examples: + - value: COVID-19 exact_mappings: - - CNPHI:Host Disease + - CNPHI:Host%20Disease - NML_LIMS:PH_HOST_DISEASE - BIOSAMPLE:host_disease - - VirusSeq_Portal:host disease - host age: - name: host age + - VirusSeq_Portal:host%20disease + host_age: + name: host_age title: host age description: Age of host at the time of sampling. comments: Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". - examples: - - value: '79' slot_uri: GENEPIO:0001392 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu + minimum_value: 0 + maximum_value: 130 recommended: true - minimum_value: '0' - maximum_value: '130' + examples: + - value: '79' exact_mappings: - - GISAID:Patient age - - CNPHI:Patient Age + - GISAID:Patient%20age + - CNPHI:Patient%20Age - NML_LIMS:PH_AGE - BIOSAMPLE:host_age - - VirusSeq_Portal:host age - host age unit: - name: host age unit + - VirusSeq_Portal:host%20age + host_age_unit: + name: host_age_unit title: host age unit description: The unit used to measure the host age, in either months or years. comments: Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. - examples: - - value: years slot_uri: GENEPIO:0001393 any_of: - - range: host age unit menu - - range: null value menu + - range: HostAgeUnitMenu + - range: NullValueMenu recommended: true + examples: + - value: years exact_mappings: - - CNPHI:Age Units + - CNPHI:Age%20Units - NML_LIMS:PH_AGE_UNIT - - VirusSeq_Portal:host age unit - host age bin: - name: host age bin + - VirusSeq_Portal:host%20age%20unit + host_age_bin: + name: host_age_bin title: host age bin description: Age of host at the time of sampling, expressed as an age group. comments: Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. - examples: - - value: 60 - 69 slot_uri: GENEPIO:0001394 any_of: - - range: host age bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu recommended: true + examples: + - value: 60 - 69 exact_mappings: - - CNPHI:Host Age Category + - CNPHI:Host%20Age%20Category - NML_LIMS:PH_AGE_GROUP - - VirusSeq_Portal:host age bin - host gender: - name: host gender + - VirusSeq_Portal:host%20age%20bin + host_gender: + name: host_gender title: host gender description: The gender of the host at the time of sample collection. comments: Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". - examples: - - value: Male slot_uri: GENEPIO:0001395 any_of: - - range: host gender menu - - range: null value menu + - range: HostGenderMenu + - range: NullValueMenu recommended: true structured_pattern: syntax: '{Title_Case}' partial_match: false interpolated: true + examples: + - value: Male exact_mappings: - GISAID:Gender - - CNPHI:Patient Sex + - CNPHI:Patient%20Sex - NML_LIMS:VD_SEX - BIOSAMPLE:host_sex - - VirusSeq_Portal:host gender - purpose of sequencing: - name: purpose of sequencing + - VirusSeq_Portal:host%20gender + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the @@ -997,21 +998,21 @@ slots: may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. - examples: - - value: Baseline surveillance (random sampling) slot_uri: GENEPIO:0001445 any_of: - - range: purpose of sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Baseline surveillance (random sampling) exact_mappings: - - CNPHI:Reason for Sequencing + - CNPHI:Reason%20for%20Sequencing - NML_LIMS:PH_REASON_FOR_SEQUENCING - BIOSAMPLE:purpose_of_sequencing - - VirusSeq_Portal:purpose of sequencing - purpose of sequencing details: - name: purpose of sequencing details + - VirusSeq_Portal:purpose%20of%20sequencing + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details description: The description of why the sample was sequenced providing specific details. @@ -1026,157 +1027,157 @@ slots: airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection.' - examples: - - value: Screened for S gene target failure (S dropout) slot_uri: GENEPIO:0001446 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true + examples: + - value: Screened for S gene target failure (S dropout) exact_mappings: - - CNPHI:Details on the Reason for Sequencing + - CNPHI:Details%20on%20the%20Reason%20for%20Sequencing - NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS - - VirusSeq_Portal:purpose of sequencing details - sequencing date: - name: sequencing date + - VirusSeq_Portal:purpose%20of%20sequencing%20details + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: ISO 8601 standard "YYYY-MM-DD". - examples: - - value: '2020-06-22' slot_uri: GENEPIO:0001447 any_of: - range: date - - range: null value menu - recommended: true + - range: NullValueMenu todos: - '>={sample collection date}' + recommended: true + examples: + - value: '2020-06-22' exact_mappings: - NML_LIMS:PH_SEQUENCING_DATE - library preparation kit: - name: library preparation kit + library_preparation_kit: + name: library_preparation_kit title: library preparation kit description: The name of the DNA library preparation kit used to generate the library being sequenced. comments: Provide the name of the library preparation kit used. - examples: - - value: Nextera XT slot_uri: GENEPIO:0001450 range: WhitespaceMinimizedString recommended: true + examples: + - value: Nextera XT exact_mappings: - NML_LIMS:PH_LIBRARY_PREP_KIT - sequencing instrument: - name: sequencing instrument + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Select a sequencing instrument from the picklist provided in the template. - examples: - - value: Oxford Nanopore MinION slot_uri: GENEPIO:0001452 any_of: - - range: sequencing instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Oxford Nanopore MinION exact_mappings: - - GISAID:Sequencing technology - - CNPHI:Sequencing Instrument + - GISAID:Sequencing%20technology + - CNPHI:Sequencing%20Instrument - NML_LIMS:PH_INSTRUMENT_CGN - - VirusSeq_Portal:sequencing instrument - raw sequence data processing method: - name: raw sequence data processing method + - VirusSeq_Portal:sequencing%20instrument + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method description: The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. comments: Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 - examples: - - value: Porechop 0.2.3 slot_uri: GENEPIO:0001458 range: WhitespaceMinimizedString required: true + examples: + - value: Porechop 0.2.3 exact_mappings: - NML_LIMS:PH_RAW_SEQUENCE_METHOD - - VirusSeq_Portal:raw sequence data processing method - dehosting method: - name: dehosting method + - VirusSeq_Portal:raw%20sequence%20data%20processing%20method + dehosting_method: + name: dehosting_method title: dehosting method description: The method used to remove host reads from the pathogen sequence. comments: Provide the name and version number of the software used to remove host reads. - examples: - - value: Nanostripper slot_uri: GENEPIO:0001459 range: WhitespaceMinimizedString required: true + examples: + - value: Nanostripper exact_mappings: - NML_LIMS:PH_DEHOSTING_METHOD - - VirusSeq_Portal:dehosting method - assembly sequence software name: - name: assembly sequence software name - title: assembly sequence software name + - VirusSeq_Portal:dehosting%20method + assembly_software_name: + name: assembly_software_name + title: assembly software name description: The name of software used to generate the assembled sequence. comments: Provide the name of the software used to generate the assembled sequence. - examples: - - value: Shovill range: WhitespaceMinimizedString recommended: true - assembly sequence software version: - name: assembly sequence software version - title: assembly sequence software version + examples: + - value: Shovill + assembly_software_version: + name: assembly_software_version + title: assembly software version description: The version of the software used to generate the assembled sequence. comments: Provide the version of the software used to generate the assembled sequence. - examples: - - value: 1.2.3 range: WhitespaceMinimizedString recommended: true - consensus sequence software name: - name: consensus sequence software name + examples: + - value: 1.2.3 + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name description: The name of software used to generate the consensus sequence. comments: Provide the name of the software used to generate the consensus sequence. - examples: - - value: iVar slot_uri: GENEPIO:0001463 range: WhitespaceMinimizedString recommended: true + examples: + - value: iVar exact_mappings: - - GISAID:Assembly method - - CNPHI:consensus sequence + - GISAID:Assembly%20method + - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE - - VirusSeq_Portal:consensus sequence software name - consensus sequence software version: - name: consensus sequence software version + - VirusSeq_Portal:consensus%20sequence%20software%20name + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version description: The version of the software used to generate the consensus sequence. comments: Provide the version of the software used to generate the consensus sequence. - examples: - - value: '1.3' slot_uri: GENEPIO:0001469 range: WhitespaceMinimizedString recommended: true + examples: + - value: '1.3' exact_mappings: - - CNPHI:consensus sequence + - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION - - VirusSeq_Portal:consensus sequence software version - bioinformatics protocol: - name: bioinformatics protocol + - VirusSeq_Portal:consensus%20sequence%20software%20version + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. - examples: - - value: https://github.com/phac-nml/ncov2019-artic-nf slot_uri: GENEPIO:0001489 range: WhitespaceMinimizedString required: true + examples: + - value: https://github.com/phac-nml/ncov2019-artic-nf exact_mappings: - - CNPHI:Bioinformatics Protocol + - CNPHI:Bioinformatics%20Protocol - NML_LIMS:PH_BIOINFORMATICS_PROTOCOL - - VirusSeq_Portal:bioinformatics protocol + - VirusSeq_Portal:bioinformatics%20protocol authors: name: authors title: authors @@ -1184,33 +1185,34 @@ slots: sequence generation, analysis, and data submission. comments: Include the first and last names of all individuals that should be attributed, separated by a comma. - examples: - - value: Tejinder Singh, Fei Hu, Joe Blogs slot_uri: GENEPIO:0001517 range: WhitespaceMinimizedString recommended: true + examples: + - value: Tejinder Singh, Fei Hu, Joe Blogs exact_mappings: - GISAID:Authors - CNPHI:Authors - NML_LIMS:PH_CANCOGEN_AUTHORS - DataHarmonizer provenance: - name: DataHarmonizer provenance + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance description: The DataHarmonizer software and template version provenance. comments: The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. - examples: - - value: DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 slot_uri: GENEPIO:0001518 range: Provenance + examples: + - value: DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 exact_mappings: - - GISAID:DataHarmonizer provenance - - CNPHI:Additional Comments + - GISAID:DataHarmonizer%20provenance + - CNPHI:Additional%20Comments - NML_LIMS:HC_COMMENTS enums: - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu + title: null value menu permissible_values: Not Applicable: text: Not Applicable @@ -1227,8 +1229,9 @@ enums: Restricted Access: text: Restricted Access meaning: GENEPIO:0001810 - geo_loc_name (state/province/territory) menu: - name: geo_loc_name (state/province/territory) menu + GeoLocNameStateProvinceTerritoryMenu: + name: GeoLocNameStateProvinceTerritoryMenu + title: geo_loc_name (state/province/territory) menu permissible_values: Alberta: text: Alberta @@ -1269,8 +1272,9 @@ enums: Yukon: text: Yukon meaning: GAZ:00002576 - host age unit menu: - name: host age unit menu + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host age unit menu permissible_values: month: text: month @@ -1278,8 +1282,9 @@ enums: year: text: year meaning: UO:0000036 - sample collection date precision menu: - name: sample collection date precision menu + SampleCollectionDatePrecisionMenu: + name: SampleCollectionDatePrecisionMenu + title: sample collection date precision menu permissible_values: year: text: year @@ -1290,8 +1295,9 @@ enums: day: text: day meaning: UO:0000033 - NML submitted specimen type menu: - name: NML submitted specimen type menu + NmlSubmittedSpecimenTypeMenu: + name: NmlSubmittedSpecimenTypeMenu + title: NML submitted specimen type menu permissible_values: Swab: text: Swab @@ -1308,8 +1314,9 @@ enums: Not Applicable: text: Not Applicable meaning: GENEPIO:0001619 - anatomical material menu: - name: anatomical material menu + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical material menu permissible_values: Blood: text: Blood @@ -1344,8 +1351,9 @@ enums: Tissue: text: Tissue meaning: UBERON:0000479 - anatomical part menu: - name: anatomical part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical part menu permissible_values: Anus: text: Anus @@ -1437,8 +1445,9 @@ enums: text: Oropharynx (OP) meaning: UBERON:0001729 is_a: Upper respiratory tract - body product menu: - name: body product menu + BodyProductMenu: + name: BodyProductMenu + title: body product menu permissible_values: Breast Milk: text: Breast Milk @@ -1465,8 +1474,9 @@ enums: Urine: text: Urine meaning: UBERON:0001088 - environmental material menu: - name: environmental material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu + title: environmental material menu permissible_values: Air vent: text: Air vent @@ -1568,8 +1578,9 @@ enums: Wood: text: Wood meaning: ENVO:00002040 - environmental site menu: - name: environmental site menu + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental site menu permissible_values: Acute care facility: text: Acute care facility @@ -1637,8 +1648,9 @@ enums: Wet market: text: Wet market meaning: ENVO:03501198 - collection method menu: - name: collection method menu + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: Amniocentesis: text: Amniocentesis @@ -1711,8 +1723,9 @@ enums: Washout Tear Collection: text: Washout Tear Collection meaning: GENEPIO:0100038 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: Air filter: text: Air filter @@ -1765,8 +1778,9 @@ enums: Virus Transport Medium: text: Virus Transport Medium meaning: OBI:0002866 - host (scientific name) menu: - name: host (scientific name) menu + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu permissible_values: Homo sapiens: text: Homo sapiens @@ -1816,8 +1830,9 @@ enums: Viverridae: text: Viverridae meaning: NCBITaxon:9673 - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu + title: organism menu permissible_values: Severe acute respiratory syndrome coronavirus 2: text: Severe acute respiratory syndrome coronavirus 2 @@ -1834,8 +1849,9 @@ enums: Norovirus: text: Norovirus is_a: Enteric virus - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation: text: Cluster/Outbreak investigation @@ -1849,8 +1865,9 @@ enums: Surveillance: text: Surveillance meaning: GENEPIO:0100004 - purpose of sequencing menu: - name: purpose of sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose of sequencing menu permissible_values: Baseline surveillance (random sampling): text: Baseline surveillance (random sampling) @@ -1944,8 +1961,9 @@ enums: Retrospective sequencing: text: Retrospective sequencing meaning: GENEPIO:0100356 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Virus passage: text: Virus passage @@ -1956,16 +1974,18 @@ enums: Specimens pooled: text: Specimens pooled meaning: OBI:0600016 - host disease menu: - name: host disease menu + HostDiseaseMenu: + name: HostDiseaseMenu + title: host disease menu permissible_values: COVID-19: text: COVID-19 meaning: MONDO:0100096 Gastrointestinal disease: text: Gastrointestinal disease - host age bin menu: - name: host age bin menu + HostAgeBinMenu: + name: HostAgeBinMenu + title: host age bin menu permissible_values: 0 - 9: text: 0 - 9 @@ -1998,14 +2018,15 @@ enums: text: 90 - 99 meaning: GENEPIO:0100058 exact_mappings: - - VirusSeq_Portal:90+ + - VirusSeq_Portal:90%2B 100+: text: 100+ meaning: GENEPIO:0100059 exact_mappings: - - VirusSeq_Portal:90+ - host gender menu: - name: host gender menu + - VirusSeq_Portal:90%2B + HostGenderMenu: + name: HostGenderMenu + title: host gender menu permissible_values: Female: text: Female @@ -2025,8 +2046,9 @@ enums: Undeclared: text: Undeclared meaning: NCIT:C110959 - sequencing instrument menu: - name: sequencing instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: Illumina: text: Illumina @@ -2206,8 +2228,9 @@ enums: text: MGI DNBSEQ-G50 meaning: GENEPIO:0100150 is_a: MGI - sequenced by menu: - name: sequenced by menu + SequencedByMenu: + name: SequencedByMenu + title: sequenced by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -2239,8 +2262,9 @@ enums: text: Public Health Ontario (PHO) Saskatchewan - Roy Romanow Provincial Laboratory (RRPL): text: Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - sequence submitted by menu: - name: sequence submitted by menu + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu + title: sequence submitted by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -2294,8 +2318,9 @@ enums: text: Sunnybrook Health Sciences Centre Thunder Bay Regional Health Sciences Centre: text: Thunder Bay Regional Health Sciences Centre - sample collected by menu: - name: sample collected by menu + SampleCollectedByMenu: + name: SampleCollectedByMenu + title: sample collected by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -2365,8 +2390,9 @@ enums: text: Unity Health Toronto William Osler Health System: text: William Osler Health System - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: Afghanistan: text: Afghanistan diff --git a/web/templates/pathogen/schema_core.yaml b/web/templates/pathogen/schema_core.yaml index 356219b0..53dac5dc 100644 --- a/web/templates/pathogen/schema_core.yaml +++ b/web/templates/pathogen/schema_core.yaml @@ -1,5 +1,5 @@ id: https://example.com/Pathogen_Agnostic -name: Pathogen_Agnostic +name: PathogenAgnostic description: "" version: 1.0.0 imports: @@ -12,8 +12,9 @@ classes: name: dh_interface description: 'A DataHarmonizer interface' from_schema: https://example.com/Pathogen_Agnostic - "Pathogen Agnostic": - name: 'Pathogen Agnostic' + "PathogenAgnostic": + name: 'PathogenAgnostic' + title: 'Pathogen Agnostic' description: is_a: dh_interface slots: {} diff --git a/web/templates/pathogen/schema_enums.tsv b/web/templates/pathogen/schema_enums.tsv index 64559d50..ff25065f 100644 --- a/web/templates/pathogen/schema_enums.tsv +++ b/web/templates/pathogen/schema_enums.tsv @@ -1,676 +1,676 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal - -null value menu GENEPIO:0001619 Not Applicable - GENEPIO:0001618 Missing - GENEPIO:0001620 Not Collected - GENEPIO:0001668 Not Provided - GENEPIO:0001810 Restricted Access - -geo_loc_name (state/province/territory) menu GAZ:00002566 Alberta - GAZ:00002562 British Columbia - GAZ:00002571 Manitoba - GAZ:00002570 New Brunswick - GAZ:00002567 Newfoundland and Labrador - GAZ:00002575 Northwest Territories - GAZ:00002565 Nova Scotia - GAZ:00002574 Nunavut - GAZ:00002563 Ontario - GAZ:00002572 Prince Edward Island - GAZ:00002569 Quebec - GAZ:00002564 Saskatchewan - GAZ:00002576 Yukon - - -host age unit menu UO:0000035 month - UO:0000036 year - - -sample collection date precision menu UO:0000036 year - UO:0000035 month - UO:0000033 day - - -NML submitted specimen type menu OBI:0002600 Swab - OBI:0000880 RNA - OBI:0002754 mRNA (cDNA) - OBI:0001010 Nucleic acid - GENEPIO:0001619 Not Applicable - - -anatomical material menu UBERON:0000178 Blood - UBERON:0006314 Fluid - UBERON:0001836 Saliva - UBERON:0001359 Fluid (cerebrospinal (CSF)) - UBERON:0002409 Fluid (pericardial) - UBERON:0001087 Fluid (pleural) - UBERON:0036243 Fluid (vaginal) - UBERON:0000173 Fluid (amniotic) - UBERON:0000479 Tissue - - -anatomical part menu UBERON:0001245 Anus - UBERON:0006956 Buccal mucosa - UBERON:0002114 Duodenum - UBERON:0000970 Eye - UBERON:0000160 Intestine - UBERON:0001558 Lower respiratory tract - UBERON:0002185 Bronchus - UBERON:0002048 Lung - UBERON:0002186 Bronchiole - UBERON:0002169 Alveolar sac - UBERON:0009778 Pleural sac - UBERON:0002402 Pleural cavity - UBERON:0003126 Trachea - UBERON:0001052 Rectum - UBERON:0001003 Skin - UBERON:0000945 Stomach - UBERON:0001557 Upper respiratory tract - UBERON:2001427 Anterior Nares - UBERON:0001043 Esophagus - UBERON:0002453 Ethmoid sinus - UBERON:0001707 Nasal Cavity - UBERON:0005921 Middle Nasal Turbinate - UBERON:0005922 Inferior Nasal Turbinate - UBERON:0001728 Nasopharynx (NP) - UBERON:0001729 Oropharynx (OP) - - -body product menu UBERON:0001913 Breast Milk - UBERON:0001988 Feces - UBERON:0006530 Fluid (seminal) - UBERON:0000912 Mucus - UBERON:0007311 Sputum - UBERON:0001089 Sweat - UBERON:0001827 Tear - UBERON:0001088 Urine - - -environmental material menu ENVO:03501208 Air vent - ENVO:00003896 Banknote - ENVO:03501209 Bed rail - ENVO:01000486 Building floor - ENVO:02000058 Cloth - ENVO:03501210 Control panel - ENVO:03501220 Door - ENVO:03501211 Door handle - OBI:0002787 Face mask - OBI:0002791 Face shield - FOODON:00002403 Food - FOODON:03490100 Food packaging - ENVO:01000481 Glass - ENVO:03501212 Handrail - OBI:0002796 Hospital gown - ENVO:03501213 Light switch - ENVO:03501214 Locker - OBI:0002790 N95 mask - ENVO:03501215 Nurse call button - ENVO:03501256 Paper - ENVO:01000060 Particulate matter - ENVO:01000404 Plastic - GENEPIO:0100025 PPE gown - ENVO:00002018 Sewage - ENVO:01000990 Sink - ENVO:00001998 Soil - ENVO:03501216 Stainless steel - ENVO:03501217 Tissue paper - ENVO:03501218 Toilet bowl - ENVO:00002006 Water - ENVO:00002001 Wastewater - ENVO:03501219 Window - ENVO:00002040 Wood - - -environmental site menu ENVO:03501135 Acute care facility - ENVO:00003040 Animal house - ENVO:01000422 Bathroom - ENVO:03501136 Clinical assessment centre - ENVO:03501127 Conference venue - ENVO:03501121 Corridor - ENVO:01000927 Daycare - ENVO:03501145 Emergency room (ER) - ENVO:03501186 Family practice clinic - ENVO:03501196 Group home - ENVO:03501133 Homeless shelter - ENVO:00002173 Hospital - ENVO:03501152 Intensive Care Unit (ICU) - ENVO:03501194 Long Term Care Facility - ENVO:03501180 Patient room - ENVO:03501204 Prison - ENVO:01000536 Production Facility - ENVO:03501130 School - ENVO:00003043 Sewage Plant - ENVO:03501109 Subway train - ENVO:00000467 University campus - ENVO:03501198 Wet market - - -collection method menu NCIT:C52009 Amniocentesis - NCIT:C15631 Aspiration - GENEPIO:0100028 Suprapubic Aspiration - GENEPIO:0100029 Tracheal aspiration - GENEPIO:0100030 Vacuum Aspiration - OBI:0002650 Biopsy - OBI:0002651 Needle Biopsy - OBI:0302885 Filtration - GENEPIO:0100031 Air filtration - OBI:0600044 Lavage - GENEPIO:0100032 Bronchoalveolar lavage (BAL) - GENEPIO:0100033 Gastric Lavage - NCIT:C15327 Lumbar Puncture - MMO:0000344 Necropsy - NCIT:C28221 Phlebotomy - GENEPIO:0002116 Rinsing - GENEPIO:0100034 Saline gargle (mouth rinse and gargle) - GENEPIO:0100035 Scraping - GENEPIO:0002117 Swabbing - GENEPIO:0100036 Finger Prick - GENEPIO:0100038 Washout Tear Collection - - -collection device menu ENVO:00003968 Air filter - OBI:0002859 Blood Collection Tube - OBI:0002826 Bronchoscope - OBI:0002088 Collection Container - GENEPIO:0100026 Collection Cup - OBI:0002825 Fibrobronchoscope Brush - GENEPIO:0100103 Filter - OBI:0002827 Fine Needle - OBI:0002858 Microcapillary tube - OBI:0001128 Micropipette - OBI:0000436 Needle - OBI:0002860 Serum Collection Tube - OBI:0002861 Sputum Collection Tube - OBI:0002831 Suction Catheter - GENEPIO:0100027 Swab - OBI:0002862 Urine Collection Tube - OBI:0002866 Virus Transport Medium - - -host (scientific name) menu NCBITaxon:9606 Homo sapiens - NCBITaxon:9913 Bos taurus - NCBITaxon:9615 Canis lupus familiaris - NCBITaxon:9397 Chiroptera - NCBITaxon:8930 Columbidae - NCBITaxon:9685 Felis catus - NCBITaxon:9031 Gallus gallus - NCBITaxon:9973 Manis - NCBITaxon:9974 Manis javanica - NCBITaxon:452646 Neovison vison - NCBITaxon:9689 Panthera leo - NCBITaxon:9694 Panthera tigris - NCBITaxon:58055 Rhinolophidae - NCBITaxon:59477 Rhinolophus affinis - NCBITaxon:9825 Sus scrofa domesticus - NCBITaxon:9673 Viverridae - - - -organism menu NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 - Monkeypox virus - Enteric bacteria - Escherichia coli - Enteric virus - Norovirus - - -purpose of sampling menu GENEPIO:0100001 Cluster/Outbreak investigation - GENEPIO:0100002 Diagnostic testing - GENEPIO:0100003 Research - GENEPIO:0100004 Surveillance - - -purpose of sequencing menu GENEPIO:0100005 Baseline surveillance (random sampling) - GENEPIO:0100006 Targeted surveillance (non-random sampling) - GENEPIO:0100007 Priority surveillance project - GENEPIO:0100008 Screening for Variants of Concern (VoC) - GENEPIO:0100273 Sample has epidemiological link to Variant of Concern (VoC) - GENEPIO:0100274 Sample has epidemiological link to Omicron Variant - GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) - GENEPIO:0100010 Re-infection surveillance - GENEPIO:0100011 Vaccine escape surveillance - GENEPIO:0100012 Travel-associated surveillance - GENEPIO:0100013 Domestic travel surveillance - GENEPIO:0100275 Interstate/ interprovincial travel surveillance - GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance - GENEPIO:0100014 International travel surveillance - GENEPIO:0100015 Surveillance of international border crossing by air travel or ground transport - GENEPIO:0100016 Surveillance of international border crossing by air travel - GENEPIO:0100017 Surveillance of international border crossing by ground transport - GENEPIO:0100018 Surveillance from international worker testing - GENEPIO:0100019 Cluster/Outbreak investigation - GENEPIO:0100020 Multi-jurisdictional outbreak investigation - GENEPIO:0100021 Intra-jurisdictional outbreak investigation - GENEPIO:0100022 Research - GENEPIO:0100024 Protocol testing experiment - GENEPIO:0100356 Retrospective sequencing - - -specimen processing menu GENEPIO:0100039 Virus passage - GENEPIO:0100040 RNA re-extraction (post RT-PCR) - OBI:0600016 Specimens pooled - - -host disease menu MONDO:0100096 COVID-19 - Gastrointestinal disease - - -host age bin menu GENEPIO:0100049 0 - 9 - GENEPIO:0100050 10 - 19 - GENEPIO:0100051 20 - 29 - GENEPIO:0100052 30 - 39 - GENEPIO:0100053 40 - 49 - GENEPIO:0100054 50 - 59 - GENEPIO:0100055 60 - 69 - GENEPIO:0100056 70 - 79 - GENEPIO:0100057 80 - 89 - GENEPIO:0100058 90 - 99 90+ - GENEPIO:0100059 100+ 90+ - - -host gender menu NCIT:C46110 Female - NCIT:C46109 Male - GSSO:000132 Non-binary gender - GSSO:004004 Transgender (assigned male at birth) - GSSO:004005 Transgender (assigned female at birth) - NCIT:C110959 Undeclared - - -sequencing instrument menu GENEPIO:0100105 Illumina - GENEPIO:0100106 Illumina Genome Analyzer - GENEPIO:0100107 Illumina Genome Analyzer II - GENEPIO:0100108 Illumina Genome Analyzer IIx - GENEPIO:0100109 Illumina HiScanSQ - GENEPIO:0100110 Illumina HiSeq - GENEPIO:0100111 Illumina HiSeq X - GENEPIO:0100112 Illumina HiSeq X Five - GENEPIO:0100113 Illumina HiSeq X Ten - GENEPIO:0100114 Illumina HiSeq 1000 - GENEPIO:0100115 Illumina HiSeq 1500 - GENEPIO:0100116 Illumina HiSeq 2000 - GENEPIO:0100117 Illumina HiSeq 2500 - GENEPIO:0100118 Illumina HiSeq 3000 - GENEPIO:0100119 Illumina HiSeq 4000 - GENEPIO:0100120 Illumina iSeq - GENEPIO:0100121 Illumina iSeq 100 - GENEPIO:0100122 Illumina NovaSeq - GENEPIO:0100123 Illumina NovaSeq 6000 - GENEPIO:0100124 Illumina MiniSeq - GENEPIO:0100125 Illumina MiSeq - GENEPIO:0100126 Illumina NextSeq - GENEPIO:0100127 Illumina NextSeq 500 - GENEPIO:0100128 Illumina NextSeq 550 - GENEPIO:0100129 Illumina NextSeq 2000 - GENEPIO:0100130 Pacific Biosciences - GENEPIO:0100131 PacBio RS - GENEPIO:0100132 PacBio RS II - GENEPIO:0100133 PacBio Sequel - GENEPIO:0100134 PacBio Sequel II - GENEPIO:0100135 Ion Torrent - GENEPIO:0100136 Ion Torrent PGM - GENEPIO:0100137 Ion Torrent Proton - GENEPIO:0100138 Ion Torrent S5 XL - GENEPIO:0100139 Ion Torrent S5 - GENEPIO:0100140 Oxford Nanopore - GENEPIO:0100141 Oxford Nanopore GridION - GENEPIO:0100142 Oxford Nanopore MinION - GENEPIO:0100143 Oxford Nanopore PromethION - GENEPIO:0100144 BGI Genomics - GENEPIO:0100145 BGI Genomics BGISEQ-500 - GENEPIO:0100146 MGI - GENEPIO:0100147 MGI DNBSEQ-T7 - GENEPIO:0100148 MGI DNBSEQ-G400 - GENEPIO:0100149 MGI DNBSEQ-G400 FAST - GENEPIO:0100150 MGI DNBSEQ-G50 - - -sequenced by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Laboratoire de santé publique du Québec (LSPQ) - Manitoba Cadham Provincial Laboratory - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - - -sequence submitted by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Canadore College - The Centre for Applied Genomics (TCAG) - Dynacare - Dynacare (Brampton) - Dynacare (Manitoba) - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Manitoba Cadham Provincial Laboratory - McGill University - McMaster University - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Sunnybrook Health Sciences Centre - Thunder Bay Regional Health Sciences Centre - - - sample collected by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Dynacare - Dynacare (Manitoba) - Dynacare (Brampton) - Eastern Ontario Regional Laboratory Association - Hamilton Health Sciences - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Lake of the Woods District Hospital - Ontario - LifeLabs - LifeLabs (Ontario) - Manitoba Cadham Provincial Laboratory - McMaster University - Mount Sinai Hospital - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Nunavut - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Shared Hospital Laboratory - St. John's Rehab at Sunnybrook Hospital - Switch Health - Sunnybrook Health Sciences Centre - Unity Health Toronto - William Osler Health System - - -geo_loc_name (country) menu GAZ:00006882 Afghanistan - GAZ:00002953 Albania - GAZ:00000563 Algeria - GAZ:00003957 American Samoa - GAZ:00002948 Andorra - GAZ:00001095 Angola - GAZ:00009159 Anguilla - GAZ:00000462 Antarctica - GAZ:00006883 Antigua and Barbuda - GAZ:00002928 Argentina - GAZ:00004094 Armenia - GAZ:00004025 Aruba - GAZ:00005901 Ashmore and Cartier Islands - GAZ:00000463 Australia - GAZ:00002942 Austria - GAZ:00004941 Azerbaijan - GAZ:00002733 Bahamas - GAZ:00005281 Bahrain - GAZ:00007117 Baker Island - GAZ:00003750 Bangladesh - GAZ:00001251 Barbados - GAZ:00005810 Bassas da India - GAZ:00006886 Belarus - GAZ:00002938 Belgium - GAZ:00002934 Belize - GAZ:00000904 Benin - GAZ:00001264 Bermuda - GAZ:00003920 Bhutan - GAZ:00002511 Bolivia - GAZ:00025355 Borneo - GAZ:00006887 Bosnia and Herzegovina - GAZ:00001097 Botswana - GAZ:00001453 Bouvet Island - GAZ:00002828 Brazil - GAZ:00003961 British Virgin Islands - GAZ:00003901 Brunei - GAZ:00002950 Bulgaria - GAZ:00000905 Burkina Faso - GAZ:00001090 Burundi - GAZ:00006888 Cambodia - GAZ:00001093 Cameroon - GAZ:00002560 Canada - GAZ:00001227 Cape Verde - GAZ:00003986 Cayman Islands - GAZ:00001089 Central African Republic - GAZ:00000586 Chad - GAZ:00002825 Chile - GAZ:00002845 China - GAZ:00005915 Christmas Island - GAZ:00005838 Clipperton Island - GAZ:00009721 Cocos Islands - GAZ:00002929 Colombia - GAZ:00005820 Comoros - GAZ:00053798 Cook Islands - GAZ:00005917 Coral Sea Islands - GAZ:00002901 Costa Rica - GAZ:00000906 Cote d'Ivoire - GAZ:00002719 Croatia - GAZ:00003762 Cuba - GAZ:00012582 Curacao - GAZ:00004006 Cyprus - GAZ:00002954 Czech Republic - GAZ:00001086 Democratic Republic of the Congo - GAZ:00005852 Denmark - GAZ:00000582 Djibouti - GAZ:00006890 Dominica - GAZ:00003952 Dominican Republic - GAZ:00002912 Ecuador - GAZ:00003934 Egypt - GAZ:00002935 El Salvador - GAZ:00001091 Equatorial Guinea - GAZ:00000581 Eritrea - GAZ:00002959 Estonia - GAZ:00001099 Eswatini - GAZ:00000567 Ethiopia - GAZ:00005811 Europa Island - GAZ:00001412 Falkland Islands (Islas Malvinas) - GAZ:00059206 Faroe Islands - GAZ:00006891 Fiji - GAZ:00002937 Finland - GAZ:00003940 France - GAZ:00002516 French Guiana - GAZ:00002918 French Polynesia - GAZ:00003753 French Southern and Antarctic Lands - GAZ:00001092 Gabon - GAZ:00000907 Gambia - GAZ:00009571 Gaza Strip - GAZ:00004942 Georgia - GAZ:00002646 Germany - GAZ:00000908 Ghana - GAZ:00003987 Gibraltar - GAZ:00005808 Glorioso Islands - GAZ:00002945 Greece - GAZ:00001507 Greenland - GAZ:02000573 Grenada - GAZ:00067142 Guadeloupe - GAZ:00003706 Guam - GAZ:00002936 Guatemala - GAZ:00001550 Guernsey - GAZ:00000909 Guinea - GAZ:00000910 Guinea-Bissau - GAZ:00002522 Guyana - GAZ:00003953 Haiti - GAZ:00009718 Heard Island and McDonald Islands - GAZ:00002894 Honduras - GAZ:00003203 Hong Kong - GAZ:00007120 Howland Island - GAZ:00002952 Hungary - GAZ:00000843 Iceland - GAZ:00002839 India - GAZ:00003727 Indonesia - GAZ:00004474 Iran - GAZ:00004483 Iraq - GAZ:00002943 Ireland - GAZ:00052477 Isle of Man - GAZ:00002476 Israel - GAZ:00002650 Italy - GAZ:00003781 Jamaica - GAZ:00005853 Jan Mayen - GAZ:00002747 Japan - GAZ:00007118 Jarvis Island - GAZ:00001551 Jersey - GAZ:00007114 Johnston Atoll - GAZ:00002473 Jordan - GAZ:00005809 Juan de Nova Island - GAZ:00004999 Kazakhstan - GAZ:00001101 Kenya - GAZ:00005682 Kerguelen Archipelago - GAZ:00007116 Kingman Reef - GAZ:00006894 Kiribati - GAZ:00011337 Kosovo - GAZ:00005285 Kuwait - GAZ:00006893 Kyrgyzstan - GAZ:00006889 Laos - GAZ:00002958 Latvia - GAZ:00002478 Lebanon - GAZ:00001098 Lesotho - GAZ:00000911 Liberia - GAZ:00000566 Libya - GAZ:00003858 Liechtenstein - GAZ:00007144 Line Islands - GAZ:00002960 Lithuania - GAZ:00002947 Luxembourg - GAZ:00003202 Macau - GAZ:00001108 Madagascar - GAZ:00001105 Malawi - GAZ:00003902 Malaysia - GAZ:00006924 Maldives - GAZ:00000584 Mali - GAZ:00004017 Malta - GAZ:00007161 Marshall Islands - GAZ:00067143 Martinique - GAZ:00000583 Mauritania - GAZ:00003745 Mauritius - GAZ:00003943 Mayotte - GAZ:00002852 Mexico - GAZ:00005862 Micronesia - GAZ:00007112 Midway Islands - GAZ:00003897 Moldova - GAZ:00003857 Monaco - GAZ:00008744 Mongolia - GAZ:00006898 Montenegro - GAZ:00003988 Montserrat - GAZ:00000565 Morocco - GAZ:00001100 Mozambique - GAZ:00006899 Myanmar - GAZ:00001096 Namibia - GAZ:00006900 Nauru - GAZ:00007119 Navassa Island - GAZ:00004399 Nepal - GAZ:00002946 Netherlands - GAZ:00005206 New Caledonia - GAZ:00000469 New Zealand - GAZ:00002978 Nicaragua - GAZ:00000585 Niger - GAZ:00000912 Nigeria - GAZ:00006902 Niue - GAZ:00005908 Norfolk Island - GAZ:00002801 North Korea - GAZ:00006895 North Macedonia - GAZ:00002284 North Sea - GAZ:00003958 Northern Mariana Islands - GAZ:00002699 Norway - GAZ:00005283 Oman - GAZ:00005246 Pakistan - GAZ:00006905 Palau - GAZ:00002892 Panama - GAZ:00003922 Papua New Guinea - GAZ:00010832 Paracel Islands - GAZ:00002933 Paraguay - GAZ:00002932 Peru - GAZ:00004525 Philippines - GAZ:00005867 Pitcairn Islands - GAZ:00002939 Poland - GAZ:00004126 Portugal - GAZ:00006935 Puerto Rico - GAZ:00005286 Qatar - GAZ:00001088 Republic of the Congo - GAZ:00003945 Reunion - GAZ:00002951 Romania - GAZ:00023304 Ross Sea - GAZ:00002721 Russia - GAZ:00001087 Rwanda - GAZ:00000849 Saint Helena - GAZ:00006906 Saint Kitts and Nevis - GAZ:00006909 Saint Lucia - GAZ:00003942 Saint Pierre and Miquelon - GAZ:00005841 Saint Martin - GAZ:02000565 Saint Vincent and the Grenadines - GAZ:00006910 Samoa - GAZ:00003102 San Marino - GAZ:00006927 Sao Tome and Principe - GAZ:00005279 Saudi Arabia - GAZ:00000913 Senegal - GAZ:00002957 Serbia - GAZ:00006922 Seychelles - GAZ:00000914 Sierra Leone - GAZ:00003923 Singapore - GAZ:00012579 Sint Maarten - GAZ:00002956 Slovakia - GAZ:00002955 Slovenia - GAZ:00005275 Solomon Islands - GAZ:00001104 Somalia - GAZ:00001094 South Africa - GAZ:00003990 South Georgia and the South Sandwich Islands - GAZ:00002802 South Korea - GAZ:00233439 South Sudan - GAZ:00000591 Spain - GAZ:00010831 Spratly Islands - GAZ:00003924 Sri Lanka - GAZ:00002475 State of Palestine - GAZ:00000560 Sudan - GAZ:00002525 Suriname - GAZ:00005396 Svalbard - GAZ:00001099 Swaziland - GAZ:00002729 Sweden - GAZ:00002941 Switzerland - GAZ:00002474 Syria - GAZ:00005341 Taiwan - GAZ:00006912 Tajikistan - GAZ:00001103 Tanzania - GAZ:00003744 Thailand - GAZ:00006913 Timor-Leste - GAZ:00000915 Togo - GAZ:00260188 Tokelau - GAZ:00006916 Tonga - GAZ:00003767 Trinidad and Tobago - GAZ:00005812 Tromelin Island - GAZ:00000562 Tunisia - GAZ:00000558 Turkey - GAZ:00005018 Turkmenistan - GAZ:00003955 Turks and Caicos Islands - GAZ:00009715 Tuvalu - GAZ:00002459 United States of America - GAZ:00001102 Uganda - GAZ:00002724 Ukraine - GAZ:00005282 United Arab Emirates - GAZ:00002637 United Kingdom - GAZ:00002930 Uruguay - GAZ:00004979 Uzbekistan - GAZ:00006918 Vanuatu - GAZ:00002931 Venezuela - GAZ:00003756 Viet Nam - GAZ:00003959 Virgin Islands - GAZ:00007111 Wake Island - GAZ:00007191 Wallis and Futuna - GAZ:00009572 West Bank - GAZ:00000564 Western Sahara - GAZ:00005284 Yemen - GAZ:00001107 Zambia - GAZ:00001106 Zimbabwe - - \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal + +null value menu NullValueMenu GENEPIO:0001619 Not Applicable + GENEPIO:0001618 Missing + GENEPIO:0001620 Not Collected + GENEPIO:0001668 Not Provided + GENEPIO:0001810 Restricted Access + +geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu GAZ:00002566 Alberta + GAZ:00002562 British Columbia + GAZ:00002571 Manitoba + GAZ:00002570 New Brunswick + GAZ:00002567 Newfoundland and Labrador + GAZ:00002575 Northwest Territories + GAZ:00002565 Nova Scotia + GAZ:00002574 Nunavut + GAZ:00002563 Ontario + GAZ:00002572 Prince Edward Island + GAZ:00002569 Quebec + GAZ:00002564 Saskatchewan + GAZ:00002576 Yukon + + +host age unit menu HostAgeUnitMenu UO:0000035 month + UO:0000036 year + + +sample collection date precision menu SampleCollectionDatePrecisionMenu UO:0000036 year + UO:0000035 month + UO:0000033 day + + +NML submitted specimen type menu NmlSubmittedSpecimenTypeMenu OBI:0002600 Swab + OBI:0000880 RNA + OBI:0002754 mRNA (cDNA) + OBI:0001010 Nucleic acid + GENEPIO:0001619 Not Applicable + + +anatomical material menu AnatomicalMaterialMenu UBERON:0000178 Blood + UBERON:0006314 Fluid + UBERON:0001836 Saliva + UBERON:0001359 Fluid (cerebrospinal (CSF)) + UBERON:0002409 Fluid (pericardial) + UBERON:0001087 Fluid (pleural) + UBERON:0036243 Fluid (vaginal) + UBERON:0000173 Fluid (amniotic) + UBERON:0000479 Tissue + + +anatomical part menu AnatomicalPartMenu UBERON:0001245 Anus + UBERON:0006956 Buccal mucosa + UBERON:0002114 Duodenum + UBERON:0000970 Eye + UBERON:0000160 Intestine + UBERON:0001558 Lower respiratory tract + UBERON:0002185 Bronchus + UBERON:0002048 Lung + UBERON:0002186 Bronchiole + UBERON:0002169 Alveolar sac + UBERON:0009778 Pleural sac + UBERON:0002402 Pleural cavity + UBERON:0003126 Trachea + UBERON:0001052 Rectum + UBERON:0001003 Skin + UBERON:0000945 Stomach + UBERON:0001557 Upper respiratory tract + UBERON:2001427 Anterior Nares + UBERON:0001043 Esophagus + UBERON:0002453 Ethmoid sinus + UBERON:0001707 Nasal Cavity + UBERON:0005921 Middle Nasal Turbinate + UBERON:0005922 Inferior Nasal Turbinate + UBERON:0001728 Nasopharynx (NP) + UBERON:0001729 Oropharynx (OP) + + +body product menu BodyProductMenu UBERON:0001913 Breast Milk + UBERON:0001988 Feces + UBERON:0006530 Fluid (seminal) + UBERON:0000912 Mucus + UBERON:0007311 Sputum + UBERON:0001089 Sweat + UBERON:0001827 Tear + UBERON:0001088 Urine + + +environmental material menu EnvironmentalMaterialMenu ENVO:03501208 Air vent + ENVO:00003896 Banknote + ENVO:03501209 Bed rail + ENVO:01000486 Building floor + ENVO:02000058 Cloth + ENVO:03501210 Control panel + ENVO:03501220 Door + ENVO:03501211 Door handle + OBI:0002787 Face mask + OBI:0002791 Face shield + FOODON:00002403 Food + FOODON:03490100 Food packaging + ENVO:01000481 Glass + ENVO:03501212 Handrail + OBI:0002796 Hospital gown + ENVO:03501213 Light switch + ENVO:03501214 Locker + OBI:0002790 N95 mask + ENVO:03501215 Nurse call button + ENVO:03501256 Paper + ENVO:01000060 Particulate matter + ENVO:01000404 Plastic + GENEPIO:0100025 PPE gown + ENVO:00002018 Sewage + ENVO:01000990 Sink + ENVO:00001998 Soil + ENVO:03501216 Stainless steel + ENVO:03501217 Tissue paper + ENVO:03501218 Toilet bowl + ENVO:00002006 Water + ENVO:00002001 Wastewater + ENVO:03501219 Window + ENVO:00002040 Wood + + +environmental site menu EnvironmentalSiteMenu ENVO:03501135 Acute care facility + ENVO:00003040 Animal house + ENVO:01000422 Bathroom + ENVO:03501136 Clinical assessment centre + ENVO:03501127 Conference venue + ENVO:03501121 Corridor + ENVO:01000927 Daycare + ENVO:03501145 Emergency room (ER) + ENVO:03501186 Family practice clinic + ENVO:03501196 Group home + ENVO:03501133 Homeless shelter + ENVO:00002173 Hospital + ENVO:03501152 Intensive Care Unit (ICU) + ENVO:03501194 Long Term Care Facility + ENVO:03501180 Patient room + ENVO:03501204 Prison + ENVO:01000536 Production Facility + ENVO:03501130 School + ENVO:00003043 Sewage Plant + ENVO:03501109 Subway train + ENVO:00000467 University campus + ENVO:03501198 Wet market + + +collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis + NCIT:C15631 Aspiration + GENEPIO:0100028 Suprapubic Aspiration + GENEPIO:0100029 Tracheal aspiration + GENEPIO:0100030 Vacuum Aspiration + OBI:0002650 Biopsy + OBI:0002651 Needle Biopsy + OBI:0302885 Filtration + GENEPIO:0100031 Air filtration + OBI:0600044 Lavage + GENEPIO:0100032 Bronchoalveolar lavage (BAL) + GENEPIO:0100033 Gastric Lavage + NCIT:C15327 Lumbar Puncture + MMO:0000344 Necropsy + NCIT:C28221 Phlebotomy + GENEPIO:0002116 Rinsing + GENEPIO:0100034 Saline gargle (mouth rinse and gargle) + GENEPIO:0100035 Scraping + GENEPIO:0002117 Swabbing + GENEPIO:0100036 Finger Prick + GENEPIO:0100038 Washout Tear Collection + + +collection device menu CollectionDeviceMenu ENVO:00003968 Air filter + OBI:0002859 Blood Collection Tube + OBI:0002826 Bronchoscope + OBI:0002088 Collection Container + GENEPIO:0100026 Collection Cup + OBI:0002825 Fibrobronchoscope Brush + GENEPIO:0100103 Filter + OBI:0002827 Fine Needle + OBI:0002858 Microcapillary tube + OBI:0001128 Micropipette + OBI:0000436 Needle + OBI:0002860 Serum Collection Tube + OBI:0002861 Sputum Collection Tube + OBI:0002831 Suction Catheter + GENEPIO:0100027 Swab + OBI:0002862 Urine Collection Tube + OBI:0002866 Virus Transport Medium + + +host (scientific name) menu HostScientificNameMenu NCBITaxon:9606 Homo sapiens + NCBITaxon:9913 Bos taurus + NCBITaxon:9615 Canis lupus familiaris + NCBITaxon:9397 Chiroptera + NCBITaxon:8930 Columbidae + NCBITaxon:9685 Felis catus + NCBITaxon:9031 Gallus gallus + NCBITaxon:9973 Manis + NCBITaxon:9974 Manis javanica + NCBITaxon:452646 Neovison vison + NCBITaxon:9689 Panthera leo + NCBITaxon:9694 Panthera tigris + NCBITaxon:58055 Rhinolophidae + NCBITaxon:59477 Rhinolophus affinis + NCBITaxon:9825 Sus scrofa domesticus + NCBITaxon:9673 Viverridae + + + +organism menu OrganismMenu NCBITaxon:2697049 Severe acute respiratory syndrome coronavirus 2 + Monkeypox virus + Enteric bacteria + Escherichia coli + Enteric virus + Norovirus + + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 Cluster/Outbreak investigation + GENEPIO:0100002 Diagnostic testing + GENEPIO:0100003 Research + GENEPIO:0100004 Surveillance + + +purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) + GENEPIO:0100006 Targeted surveillance (non-random sampling) + GENEPIO:0100007 Priority surveillance project + GENEPIO:0100008 Screening for Variants of Concern (VoC) + GENEPIO:0100273 Sample has epidemiological link to Variant of Concern (VoC) + GENEPIO:0100274 Sample has epidemiological link to Omicron Variant + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) + GENEPIO:0100010 Re-infection surveillance + GENEPIO:0100011 Vaccine escape surveillance + GENEPIO:0100012 Travel-associated surveillance + GENEPIO:0100013 Domestic travel surveillance + GENEPIO:0100275 Interstate/ interprovincial travel surveillance + GENEPIO:0100276 Intra-state/ intra-provincial travel surveillance + GENEPIO:0100014 International travel surveillance + GENEPIO:0100015 Surveillance of international border crossing by air travel or ground transport + GENEPIO:0100016 Surveillance of international border crossing by air travel + GENEPIO:0100017 Surveillance of international border crossing by ground transport + GENEPIO:0100018 Surveillance from international worker testing + GENEPIO:0100019 Cluster/Outbreak investigation + GENEPIO:0100020 Multi-jurisdictional outbreak investigation + GENEPIO:0100021 Intra-jurisdictional outbreak investigation + GENEPIO:0100022 Research + GENEPIO:0100024 Protocol testing experiment + GENEPIO:0100356 Retrospective sequencing + + +specimen processing menu SpecimenProcessingMenu GENEPIO:0100039 Virus passage + GENEPIO:0100040 RNA re-extraction (post RT-PCR) + OBI:0600016 Specimens pooled + + +host disease menu HostDiseaseMenu MONDO:0100096 COVID-19 + Gastrointestinal disease + + +host age bin menu HostAgeBinMenu GENEPIO:0100049 0 - 9 + GENEPIO:0100050 10 - 19 + GENEPIO:0100051 20 - 29 + GENEPIO:0100052 30 - 39 + GENEPIO:0100053 40 - 49 + GENEPIO:0100054 50 - 59 + GENEPIO:0100055 60 - 69 + GENEPIO:0100056 70 - 79 + GENEPIO:0100057 80 - 89 + GENEPIO:0100058 90 - 99 90+ + GENEPIO:0100059 100+ 90+ + + +host gender menu HostGenderMenu NCIT:C46110 Female + NCIT:C46109 Male + GSSO:000132 Non-binary gender + GSSO:004004 Transgender (assigned male at birth) + GSSO:004005 Transgender (assigned female at birth) + NCIT:C110959 Undeclared + + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina + GENEPIO:0100106 Illumina Genome Analyzer + GENEPIO:0100107 Illumina Genome Analyzer II + GENEPIO:0100108 Illumina Genome Analyzer IIx + GENEPIO:0100109 Illumina HiScanSQ + GENEPIO:0100110 Illumina HiSeq + GENEPIO:0100111 Illumina HiSeq X + GENEPIO:0100112 Illumina HiSeq X Five + GENEPIO:0100113 Illumina HiSeq X Ten + GENEPIO:0100114 Illumina HiSeq 1000 + GENEPIO:0100115 Illumina HiSeq 1500 + GENEPIO:0100116 Illumina HiSeq 2000 + GENEPIO:0100117 Illumina HiSeq 2500 + GENEPIO:0100118 Illumina HiSeq 3000 + GENEPIO:0100119 Illumina HiSeq 4000 + GENEPIO:0100120 Illumina iSeq + GENEPIO:0100121 Illumina iSeq 100 + GENEPIO:0100122 Illumina NovaSeq + GENEPIO:0100123 Illumina NovaSeq 6000 + GENEPIO:0100124 Illumina MiniSeq + GENEPIO:0100125 Illumina MiSeq + GENEPIO:0100126 Illumina NextSeq + GENEPIO:0100127 Illumina NextSeq 500 + GENEPIO:0100128 Illumina NextSeq 550 + GENEPIO:0100129 Illumina NextSeq 2000 + GENEPIO:0100130 Pacific Biosciences + GENEPIO:0100131 PacBio RS + GENEPIO:0100132 PacBio RS II + GENEPIO:0100133 PacBio Sequel + GENEPIO:0100134 PacBio Sequel II + GENEPIO:0100135 Ion Torrent + GENEPIO:0100136 Ion Torrent PGM + GENEPIO:0100137 Ion Torrent Proton + GENEPIO:0100138 Ion Torrent S5 XL + GENEPIO:0100139 Ion Torrent S5 + GENEPIO:0100140 Oxford Nanopore + GENEPIO:0100141 Oxford Nanopore GridION + GENEPIO:0100142 Oxford Nanopore MinION + GENEPIO:0100143 Oxford Nanopore PromethION + GENEPIO:0100144 BGI Genomics + GENEPIO:0100145 BGI Genomics BGISEQ-500 + GENEPIO:0100146 MGI + GENEPIO:0100147 MGI DNBSEQ-T7 + GENEPIO:0100148 MGI DNBSEQ-G400 + GENEPIO:0100149 MGI DNBSEQ-G400 FAST + GENEPIO:0100150 MGI DNBSEQ-G50 + + +sequenced by menu SequencedByMenu Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Laboratoire de santé publique du Québec (LSPQ) + Manitoba Cadham Provincial Laboratory + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + + +sequence submitted by menu SequenceSubmittedByMenu Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Canadore College + The Centre for Applied Genomics (TCAG) + Dynacare + Dynacare (Brampton) + Dynacare (Manitoba) + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Manitoba Cadham Provincial Laboratory + McGill University + McMaster University + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Sunnybrook Health Sciences Centre + Thunder Bay Regional Health Sciences Centre + + + sample collected by menu SampleCollectedByMenu Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Dynacare + Dynacare (Manitoba) + Dynacare (Brampton) + Eastern Ontario Regional Laboratory Association + Hamilton Health Sciences + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Lake of the Woods District Hospital - Ontario + LifeLabs + LifeLabs (Ontario) + Manitoba Cadham Provincial Laboratory + McMaster University + Mount Sinai Hospital + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Nunavut + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Shared Hospital Laboratory + St. John's Rehab at Sunnybrook Hospital + Switch Health + Sunnybrook Health Sciences Centre + Unity Health Toronto + William Osler Health System + + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan + GAZ:00002953 Albania + GAZ:00000563 Algeria + GAZ:00003957 American Samoa + GAZ:00002948 Andorra + GAZ:00001095 Angola + GAZ:00009159 Anguilla + GAZ:00000462 Antarctica + GAZ:00006883 Antigua and Barbuda + GAZ:00002928 Argentina + GAZ:00004094 Armenia + GAZ:00004025 Aruba + GAZ:00005901 Ashmore and Cartier Islands + GAZ:00000463 Australia + GAZ:00002942 Austria + GAZ:00004941 Azerbaijan + GAZ:00002733 Bahamas + GAZ:00005281 Bahrain + GAZ:00007117 Baker Island + GAZ:00003750 Bangladesh + GAZ:00001251 Barbados + GAZ:00005810 Bassas da India + GAZ:00006886 Belarus + GAZ:00002938 Belgium + GAZ:00002934 Belize + GAZ:00000904 Benin + GAZ:00001264 Bermuda + GAZ:00003920 Bhutan + GAZ:00002511 Bolivia + GAZ:00025355 Borneo + GAZ:00006887 Bosnia and Herzegovina + GAZ:00001097 Botswana + GAZ:00001453 Bouvet Island + GAZ:00002828 Brazil + GAZ:00003961 British Virgin Islands + GAZ:00003901 Brunei + GAZ:00002950 Bulgaria + GAZ:00000905 Burkina Faso + GAZ:00001090 Burundi + GAZ:00006888 Cambodia + GAZ:00001093 Cameroon + GAZ:00002560 Canada + GAZ:00001227 Cape Verde + GAZ:00003986 Cayman Islands + GAZ:00001089 Central African Republic + GAZ:00000586 Chad + GAZ:00002825 Chile + GAZ:00002845 China + GAZ:00005915 Christmas Island + GAZ:00005838 Clipperton Island + GAZ:00009721 Cocos Islands + GAZ:00002929 Colombia + GAZ:00005820 Comoros + GAZ:00053798 Cook Islands + GAZ:00005917 Coral Sea Islands + GAZ:00002901 Costa Rica + GAZ:00000906 Cote d'Ivoire + GAZ:00002719 Croatia + GAZ:00003762 Cuba + GAZ:00012582 Curacao + GAZ:00004006 Cyprus + GAZ:00002954 Czech Republic + GAZ:00001086 Democratic Republic of the Congo + GAZ:00005852 Denmark + GAZ:00000582 Djibouti + GAZ:00006890 Dominica + GAZ:00003952 Dominican Republic + GAZ:00002912 Ecuador + GAZ:00003934 Egypt + GAZ:00002935 El Salvador + GAZ:00001091 Equatorial Guinea + GAZ:00000581 Eritrea + GAZ:00002959 Estonia + GAZ:00001099 Eswatini + GAZ:00000567 Ethiopia + GAZ:00005811 Europa Island + GAZ:00001412 Falkland Islands (Islas Malvinas) + GAZ:00059206 Faroe Islands + GAZ:00006891 Fiji + GAZ:00002937 Finland + GAZ:00003940 France + GAZ:00002516 French Guiana + GAZ:00002918 French Polynesia + GAZ:00003753 French Southern and Antarctic Lands + GAZ:00001092 Gabon + GAZ:00000907 Gambia + GAZ:00009571 Gaza Strip + GAZ:00004942 Georgia + GAZ:00002646 Germany + GAZ:00000908 Ghana + GAZ:00003987 Gibraltar + GAZ:00005808 Glorioso Islands + GAZ:00002945 Greece + GAZ:00001507 Greenland + GAZ:02000573 Grenada + GAZ:00067142 Guadeloupe + GAZ:00003706 Guam + GAZ:00002936 Guatemala + GAZ:00001550 Guernsey + GAZ:00000909 Guinea + GAZ:00000910 Guinea-Bissau + GAZ:00002522 Guyana + GAZ:00003953 Haiti + GAZ:00009718 Heard Island and McDonald Islands + GAZ:00002894 Honduras + GAZ:00003203 Hong Kong + GAZ:00007120 Howland Island + GAZ:00002952 Hungary + GAZ:00000843 Iceland + GAZ:00002839 India + GAZ:00003727 Indonesia + GAZ:00004474 Iran + GAZ:00004483 Iraq + GAZ:00002943 Ireland + GAZ:00052477 Isle of Man + GAZ:00002476 Israel + GAZ:00002650 Italy + GAZ:00003781 Jamaica + GAZ:00005853 Jan Mayen + GAZ:00002747 Japan + GAZ:00007118 Jarvis Island + GAZ:00001551 Jersey + GAZ:00007114 Johnston Atoll + GAZ:00002473 Jordan + GAZ:00005809 Juan de Nova Island + GAZ:00004999 Kazakhstan + GAZ:00001101 Kenya + GAZ:00005682 Kerguelen Archipelago + GAZ:00007116 Kingman Reef + GAZ:00006894 Kiribati + GAZ:00011337 Kosovo + GAZ:00005285 Kuwait + GAZ:00006893 Kyrgyzstan + GAZ:00006889 Laos + GAZ:00002958 Latvia + GAZ:00002478 Lebanon + GAZ:00001098 Lesotho + GAZ:00000911 Liberia + GAZ:00000566 Libya + GAZ:00003858 Liechtenstein + GAZ:00007144 Line Islands + GAZ:00002960 Lithuania + GAZ:00002947 Luxembourg + GAZ:00003202 Macau + GAZ:00001108 Madagascar + GAZ:00001105 Malawi + GAZ:00003902 Malaysia + GAZ:00006924 Maldives + GAZ:00000584 Mali + GAZ:00004017 Malta + GAZ:00007161 Marshall Islands + GAZ:00067143 Martinique + GAZ:00000583 Mauritania + GAZ:00003745 Mauritius + GAZ:00003943 Mayotte + GAZ:00002852 Mexico + GAZ:00005862 Micronesia + GAZ:00007112 Midway Islands + GAZ:00003897 Moldova + GAZ:00003857 Monaco + GAZ:00008744 Mongolia + GAZ:00006898 Montenegro + GAZ:00003988 Montserrat + GAZ:00000565 Morocco + GAZ:00001100 Mozambique + GAZ:00006899 Myanmar + GAZ:00001096 Namibia + GAZ:00006900 Nauru + GAZ:00007119 Navassa Island + GAZ:00004399 Nepal + GAZ:00002946 Netherlands + GAZ:00005206 New Caledonia + GAZ:00000469 New Zealand + GAZ:00002978 Nicaragua + GAZ:00000585 Niger + GAZ:00000912 Nigeria + GAZ:00006902 Niue + GAZ:00005908 Norfolk Island + GAZ:00002801 North Korea + GAZ:00006895 North Macedonia + GAZ:00002284 North Sea + GAZ:00003958 Northern Mariana Islands + GAZ:00002699 Norway + GAZ:00005283 Oman + GAZ:00005246 Pakistan + GAZ:00006905 Palau + GAZ:00002892 Panama + GAZ:00003922 Papua New Guinea + GAZ:00010832 Paracel Islands + GAZ:00002933 Paraguay + GAZ:00002932 Peru + GAZ:00004525 Philippines + GAZ:00005867 Pitcairn Islands + GAZ:00002939 Poland + GAZ:00004126 Portugal + GAZ:00006935 Puerto Rico + GAZ:00005286 Qatar + GAZ:00001088 Republic of the Congo + GAZ:00003945 Reunion + GAZ:00002951 Romania + GAZ:00023304 Ross Sea + GAZ:00002721 Russia + GAZ:00001087 Rwanda + GAZ:00000849 Saint Helena + GAZ:00006906 Saint Kitts and Nevis + GAZ:00006909 Saint Lucia + GAZ:00003942 Saint Pierre and Miquelon + GAZ:00005841 Saint Martin + GAZ:02000565 Saint Vincent and the Grenadines + GAZ:00006910 Samoa + GAZ:00003102 San Marino + GAZ:00006927 Sao Tome and Principe + GAZ:00005279 Saudi Arabia + GAZ:00000913 Senegal + GAZ:00002957 Serbia + GAZ:00006922 Seychelles + GAZ:00000914 Sierra Leone + GAZ:00003923 Singapore + GAZ:00012579 Sint Maarten + GAZ:00002956 Slovakia + GAZ:00002955 Slovenia + GAZ:00005275 Solomon Islands + GAZ:00001104 Somalia + GAZ:00001094 South Africa + GAZ:00003990 South Georgia and the South Sandwich Islands + GAZ:00002802 South Korea + GAZ:00233439 South Sudan + GAZ:00000591 Spain + GAZ:00010831 Spratly Islands + GAZ:00003924 Sri Lanka + GAZ:00002475 State of Palestine + GAZ:00000560 Sudan + GAZ:00002525 Suriname + GAZ:00005396 Svalbard + GAZ:00001099 Swaziland + GAZ:00002729 Sweden + GAZ:00002941 Switzerland + GAZ:00002474 Syria + GAZ:00005341 Taiwan + GAZ:00006912 Tajikistan + GAZ:00001103 Tanzania + GAZ:00003744 Thailand + GAZ:00006913 Timor-Leste + GAZ:00000915 Togo + GAZ:00260188 Tokelau + GAZ:00006916 Tonga + GAZ:00003767 Trinidad and Tobago + GAZ:00005812 Tromelin Island + GAZ:00000562 Tunisia + GAZ:00000558 Turkey + GAZ:00005018 Turkmenistan + GAZ:00003955 Turks and Caicos Islands + GAZ:00009715 Tuvalu + GAZ:00002459 United States of America + GAZ:00001102 Uganda + GAZ:00002724 Ukraine + GAZ:00005282 United Arab Emirates + GAZ:00002637 United Kingdom + GAZ:00002930 Uruguay + GAZ:00004979 Uzbekistan + GAZ:00006918 Vanuatu + GAZ:00002931 Venezuela + GAZ:00003756 Viet Nam + GAZ:00003959 Virgin Islands + GAZ:00007111 Wake Island + GAZ:00007191 Wallis and Futuna + GAZ:00009572 West Bank + GAZ:00000564 Western Sahara + GAZ:00005284 Yemen + GAZ:00001107 Zambia + GAZ:00001106 Zimbabwe + + \ No newline at end of file diff --git a/web/templates/pathogen/schema_slots.tsv b/web/templates/pathogen/schema_slots.tsv index 353fc07e..7e15d397 100644 --- a/web/templates/pathogen/schema_slots.tsv +++ b/web/templates/pathogen/schema_slots.tsv @@ -1,61 +1,74 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -Pathogen Agnostic GENEPIO:0001122 Database Identifiers - Database Identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID - Database Identifiers GENEPIO:0001202 third party lab service provider name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 - Database Identifiers GENEPIO:0001149 third party lab sample ID WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY - Database Identifiers GENEPIO:0100281 case ID WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID - Database Identifiers GENEPIO:0001128 Related specimen primary ID WhitespaceMinimizedString null value menu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID - Database Identifiers GENEPIO:0001131 IRIDA sample name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name - Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella bioproject accession menu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession - Database Identifiers GENEPIO:0001136 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession - Database Identifiers GENEPIO:0001139 biosample accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers GENEPIO:0001142 SRA accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers GENEPIO:0001145 GenBank accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession - Database Identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession - GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001153 sample collected by sample collected by menu null value menu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by - Sample collection and processing GENEPIO:0100416 sequenced by sequence submitted by menu null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by - Sample collection and processing GENEPIO:0001159 sequence submitted by sequence submitted by menu null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by - Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date - Sample collection and processing GENEPIO:0001177 sample collection date precision sample collection date precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name (state/province/territory) menu null value menu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) - Sample collection and processing GENEPIO:0001191 organism organism menu null value menu TRUE Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 Pathogen HC_CURRENT_ID organism organism - Sample collection and processing GENEPIO:0001195 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name - Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling menu null value menu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling - Sample collection and processing GENEPIO:0001200 purpose of sampling details WhitespaceMinimizedString null value menu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details - Sample collection and processing GENEPIO:0001204 NML submitted specimen type NML submitted specimen type menu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE - Sample collection and processing GENEPIO:0001211 anatomical material anatomical material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material - Sample collection and processing GENEPIO:0001214 anatomical part anatomical part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part - Sample collection and processing GENEPIO:0001216 body product body product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product - Sample collection and processing GENEPIO:0001223 environmental material environmental material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material - Sample collection and processing GENEPIO:0001232 environmental site environmental site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site - Sample collection and processing GENEPIO:0001234 collection device collection device menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device - Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method - Sample collection and processing GENEPIO:0001253 specimen processing specimen processing menu null value menu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled Passage details/history specimen processing - Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. - GENEPIO:0001268 Host Information - Host Information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) - Host Information GENEPIO:0001391 host disease host disease menu null value menu TRUE The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease - Host Information GENEPIO:0001392 host age decimal null value menu TRUE 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age - Host Information GENEPIO:0001393 host age unit host age unit menu null value menu TRUE The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit - Host Information GENEPIO:0001394 host age bin host age bin menu null value menu TRUE Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin - Host Information GENEPIO:0001395 host gender host gender menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Male Gender Patient Sex VD_SEX host_sex host gender - GENEPIO:0001441 Sequencing - Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing - Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing GENEPIO:0001447 sequencing date date null value menu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE - Sequencing GENEPIO:0001450 library preparation kit WhitespaceMinimizedString TRUE The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT - Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method - Bioinformatics and QC metrics assembly sequence software name WhitespaceMinimizedString TRUE The name of software used to generate the assembled sequence. Provide the name of the software used to generate the assembled sequence. Shovill - Bioinformatics and QC metrics assembly sequence software version WhitespaceMinimizedString TRUE The version of the software used to generate the assembled sequence. Provide the version of the software used to generate the assembled sequence. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS +PathogenAgnostic GENEPIO:0001122 Database Identifiers database_identifiers + Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID + Database Identifiers GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 + Database Identifiers GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY + Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID + Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID + Database Identifiers GENEPIO:0001131 IRIDA sample name irida_sample_name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name + Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession + Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession + Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION + Database Identifiers GENEPIO:0001142 SRA accession sra_accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION + Database Identifiers GENEPIO:0001145 GenBank accession genbank_accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession + Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession + GENEPIO:0001150 Sample collection and processing sample_collection_and_processing + Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by + Sample collection and processing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by + Sample collection and processing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by + Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date + Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) + Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 Pathogen HC_CURRENT_ID organism organism + Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name + Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling + Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details + Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NMLSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE + Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material + Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part + Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product + Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material + Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site + Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device + Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method + Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled Passage details/history specimen processing + Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. + GENEPIO:0001268 Host Information host_information + Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) + Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease + Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age + Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit + Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin + Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Male Gender Patient Sex VD_SEX host_sex host gender + GENEPIO:0001441 Sequencing sequencing + Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing + Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details + Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE + Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString TRUE The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT + Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument + GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method + Bioinformatics and QC metrics assembly software name assembly_software_name WhitespaceMinimizedString TRUE The name of software used to generate the assembled sequence. Provide the name of the software used to generate the assembled sequence. Shovill + Bioinformatics and QC metrics assembly software version assembly_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the assembled sequence. Provide the version of the software used to generate the assembled sequence. 1.2.3 + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS + + + + + + + + + + + + + \ No newline at end of file From beedd5780ded1a34260fe5d40315f9d4ca54d7ec Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 22 Oct 2024 08:45:28 -0700 Subject: [PATCH 63/96] template vocabulary update --- web/templates/hpai/schema.json | 3643 +++++++++++++-------- web/templates/hpai/schema.yaml | 2051 ++++++++---- web/templates/hpai/schema_enums.tsv | 249 +- web/templates/hpai/schema_slots.tsv | 33 +- web/templates/mpox/schema.json | 27 +- web/templates/mpox/schema.yaml | 21 +- web/templates/mpox/schema_enums.tsv | 2 +- web/templates/mpox/schema_slots.tsv | 9 +- web/templates/wastewater/schema.json | 315 +- web/templates/wastewater/schema.yaml | 128 +- web/templates/wastewater/schema_enums.tsv | 130 +- web/templates/wastewater/schema_slots.tsv | 526 +-- 12 files changed, 4634 insertions(+), 2500 deletions(-) diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index 08b813be..58fd8481 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -2638,9 +2638,9 @@ } } }, - "PurposeOfSampling": { - "name": "PurposeOfSampling", - "title": "purpose of sampling", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Cluster/Outbreak investigation [GENEPIO:0100001]": { @@ -2688,9 +2688,9 @@ } } }, - "PresamplingActivity": { - "name": "PresamplingActivity", - "title": "presampling activity", + "PresamplingActivityMenu": { + "name": "PresamplingActivityMenu", + "title": "presampling activity menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Addition of substances to food/water [GENEPIO:0100536]": { @@ -2756,9 +2756,9 @@ } } }, - "SampleStorageDurationUnit": { - "name": "SampleStorageDurationUnit", - "title": "sample storage duration unit", + "SampleStorageDurationUnitMenu": { + "name": "SampleStorageDurationUnitMenu", + "title": "sample storage duration unit menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Second [UO:0000010]": { @@ -2798,9 +2798,9 @@ } } }, - "SpecimenProcessing": { - "name": "SpecimenProcessing", - "title": "specimen processing", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Concentration [OBI:0600041]": { @@ -2825,9 +2825,9 @@ } } }, - "ExperimentalSpecimenRoleType": { - "name": "ExperimentalSpecimenRoleType", - "title": "experimental specimen role type", + "ExperimentalSpecimenRoleTypeMenu": { + "name": "ExperimentalSpecimenRoleTypeMenu", + "title": "experimental specimen role type menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Positive experimental control [GENEPIO:0101018]": { @@ -3771,9 +3771,9 @@ } } }, - "HostGender": { - "name": "HostGender", - "title": "host_gender", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host_gender menu", "from_schema": "https://example.com/hpai", "permissible_values": { "Female [NCIT:C46110]": { @@ -5585,25 +5585,32 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "<10 people": { - "text": "<10 people" + "text": "<10 people", + "description": "An estimation of population size for a group smaller than 10 people." }, "10 - 100 people": { - "text": "10 - 100 people" + "text": "10 - 100 people", + "description": "An estimation of population size for a group smaller than 100 people and larger than 10 people." }, "100 - 1,000 people": { - "text": "100 - 1,000 people" + "text": "100 - 1,000 people", + "description": "An estimation of population size for a group smaller than 1,000 people and larger than 100 people." }, "1,000 - 10,000 people": { - "text": "1,000 - 10,000 people" + "text": "1,000 - 10,000 people", + "description": "An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people." }, "10,000 - 100,000 people": { - "text": "10,000 - 100,000 people" + "text": "10,000 - 100,000 people", + "description": "An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people." }, "100,000 - 1,000,000 people": { - "text": "100,000 - 1,000,000 people" + "text": "100,000 - 1,000,000 people", + "description": "An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people." }, "1,000,000+ people": { - "text": "1,000,000+ people" + "text": "1,000,000+ people", + "description": "An estimation of population size for a group larger than 1,000,000 people." } } }, @@ -5784,6 +5791,861 @@ } } }, + "WaterDepthUnitsMenu": { + "name": "WaterDepthUnitsMenu", + "title": "water_depth_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", + "meaning": "UO:0000015" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", + "meaning": "UO:0000008" + }, + "kilometer (km) [UO:0010066]": { + "text": "kilometer (km) [UO:0010066]", + "description": "A length unit which is equal to one thousand meters.", + "meaning": "UO:0010066" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", + "meaning": "UO:0010011" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", + "meaning": "UO:0010013" + } + } + }, + "SedimentDepthUnitsMenu": { + "name": "SedimentDepthUnitsMenu", + "title": "sediment_depth_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "centimeter (cm) [UO:0000015]": { + "text": "centimeter (cm) [UO:0000015]", + "description": "A length unit which is equal to one hundredth of a meter or 10^[-2] m", + "meaning": "UO:0000015" + }, + "meter (m) [UO:0000008]": { + "text": "meter (m) [UO:0000008]", + "description": "An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second.", + "meaning": "UO:0000008" + }, + "kilometer (km) [UO:0010066]": { + "text": "kilometer (km) [UO:0010066]", + "description": "A length unit which is equal to one thousand meters.", + "meaning": "UO:0010066" + }, + "inch (in) [UO:0010011]": { + "text": "inch (in) [UO:0010011]", + "description": "A non-SI unit of length defined as one twelfth of a foot.", + "meaning": "UO:0010011" + }, + "foot (ft) [UO:0010013]": { + "text": "foot (ft) [UO:0010013]", + "description": "A non-SI unit of length which is approximately 0.3048 meters.", + "meaning": "UO:0010013" + } + } + }, + "AirTemperatureUnitsMenu": { + "name": "AirTemperatureUnitsMenu", + "title": "air_temperature_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "WaterTemperatureUnitsMenu": { + "name": "WaterTemperatureUnitsMenu", + "title": "water_temperature_units menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "degree Fahrenheit (F) [UO:0000195]": { + "text": "degree Fahrenheit (F) [UO:0000195]", + "description": "A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions.", + "meaning": "UO:0000195" + }, + "degree Celsius (C) [UO:0000027]": { + "text": "degree Celsius (C) [UO:0000027]", + "description": "A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions.", + "meaning": "UO:0000027" + } + } + }, + "SequencingPlatformMenu": { + "name": "SequencingPlatformMenu", + "title": "sequencing_platform menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Illumina [GENEPIO:0001923]": { + "text": "Illumina [GENEPIO:0001923]", + "description": "A sequencing platform provided by the Illumina company.", + "meaning": "GENEPIO:0001923" + }, + "Pacific Biosciences [GENEPIO:0001927]": { + "text": "Pacific Biosciences [GENEPIO:0001927]", + "description": "A sequencing platform provided by the Pacific Biosciences company.", + "meaning": "GENEPIO:0001927" + }, + "Ion Torrent [GENEPIO:0002683]": { + "text": "Ion Torrent [GENEPIO:0002683]", + "description": "A sequencing platform provided by the Ion Torrent company.", + "meaning": "GENEPIO:0002683" + }, + "Oxford Nanopore Technologies [GENEPIO:0100986]": { + "text": "Oxford Nanopore Technologies [GENEPIO:0100986]", + "description": "An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK.", + "meaning": "GENEPIO:0100986" + }, + "BGI Genomics [GENEPIO:0004324]": { + "text": "BGI Genomics [GENEPIO:0004324]", + "description": "A sequencing platform provided by the BGI Genomics company.", + "meaning": "GENEPIO:0004324" + }, + "MGI [GENEPIO:0004325]": { + "text": "MGI [GENEPIO:0004325]", + "description": "A sequencing platform provided by the MGI company.", + "meaning": "GENEPIO:0004325" + }, + "Roche LS454 [GENEPIO:0001926]": { + "text": "Roche LS454 [GENEPIO:0001926]", + "description": "A sequencing platform provided by the 454 Life Sciences company.", + "meaning": "GENEPIO:0001926" + }, + "SOLiD sequencing [GENEPIO:0002684]": { + "text": "SOLiD sequencing [GENEPIO:0002684]", + "description": "A sequencing platform provided by Life Technologies Corporation.", + "meaning": "GENEPIO:0002684" + }, + "Complete Genomics [GENEPIO:0001924]": { + "text": "Complete Genomics [GENEPIO:0001924]", + "description": "An in-house sequencing platform provided by Complete Genomics.", + "meaning": "GENEPIO:0001924" + }, + "Helicos [GENEPIO:0002682]": { + "text": "Helicos [GENEPIO:0002682]", + "description": "A sequencing platform brand provided by Helicos corporation (now defunct).", + "meaning": "GENEPIO:0002682" + }, + "Applied Biosystems [GENEPIO:0100985]": { + "text": "Applied Biosystems [GENEPIO:0100985]", + "description": "A sequencing platform provided by ThermoFisher.", + "meaning": "GENEPIO:0100985" + } + } + }, + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing_instrument menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Illumina [GENEPIO:0100105]": { + "text": "Illumina [GENEPIO:0100105]", + "description": "A DNA sequencer manufactured by the Illumina corporation.", + "meaning": "GENEPIO:0100105" + }, + "Illumina Genome Analyzer [GENEPIO:0100106]": { + "text": "Illumina Genome Analyzer [GENEPIO:0100106]", + "description": "A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.", + "meaning": "GENEPIO:0100106", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina Genome Analyzer II [OBI:0000703]": { + "text": "Illumina Genome Analyzer II [OBI:0000703]", + "description": "A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0000703", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina Genome Analyzer IIx [OBI:0002000]": { + "text": "Illumina Genome Analyzer IIx [OBI:0002000]", + "description": "An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.", + "meaning": "OBI:0002000", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina HiScanSQ [GENEPIO:0100109]": { + "text": "Illumina HiScanSQ [GENEPIO:0100109]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an \"SQ Module\" to support microfluidics.", + "meaning": "GENEPIO:0100109", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina HiSeq [GENEPIO:0100110]": { + "text": "Illumina HiSeq [GENEPIO:0100110]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield.", + "meaning": "GENEPIO:0100110", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina HiSeq X [GENEPIO:0100111]": { + "text": "Illumina HiSeq X [GENEPIO:0100111]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000.", + "meaning": "GENEPIO:0100111", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq X Five [GENEPIO:0100112]": { + "text": "Illumina HiSeq X Five [GENEPIO:0100112]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems.", + "meaning": "GENEPIO:0100112", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq X Ten [GENEPIO:0100113]": { + "text": "Illumina HiSeq X Ten [GENEPIO:0100113]", + "description": "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.", + "meaning": "GENEPIO:0100113", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 1000 [OBI:0002022]": { + "text": "Illumina HiSeq 1000 [OBI:0002022]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002022", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 1500 [GENEPIO:0100115]": { + "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day.", + "meaning": "GENEPIO:0100115", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 2000 [OBI:0002001]": { + "text": "Illumina HiSeq 2000 [OBI:0002001]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run.", + "meaning": "OBI:0002001", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 2500 [OBI:0002002]": { + "text": "Illumina HiSeq 2500 [OBI:0002002]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples.", + "meaning": "OBI:0002002", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 3000 [OBI:0002048]": { + "text": "Illumina HiSeq 3000 [OBI:0002048]", + "description": "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day.", + "meaning": "OBI:0002048", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina HiSeq 4000 [OBI:0002049]": { + "text": "Illumina HiSeq 4000 [OBI:0002049]", + "description": "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day.", + "meaning": "OBI:0002049", + "is_a": "Illumina HiSeq [GENEPIO:0100110]" + }, + "Illumina iSeq [GENEPIO:0100120]": { + "text": "Illumina iSeq [GENEPIO:0100120]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight.", + "meaning": "GENEPIO:0100120", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina iSeq 100 [GENEPIO:0100121]": { + "text": "Illumina iSeq 100 [GENEPIO:0100121]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB.", + "meaning": "GENEPIO:0100121", + "is_a": "Illumina iSeq [GENEPIO:0100120]" + }, + "Illumina NovaSeq [GENEPIO:0100122]": { + "text": "Illumina NovaSeq [GENEPIO:0100122]", + "description": "A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode.", + "meaning": "GENEPIO:0100122", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina NovaSeq 6000 [GENEPIO:0100123]": { + "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters.", + "meaning": "GENEPIO:0100123", + "is_a": "Illumina NovaSeq [GENEPIO:0100122]" + }, + "Illumina MiniSeq [GENEPIO:0100124]": { + "text": "Illumina MiniSeq [GENEPIO:0100124]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", + "meaning": "GENEPIO:0100124", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina MiSeq [OBI:0002003]": { + "text": "Illumina MiSeq [OBI:0002003]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.", + "meaning": "OBI:0002003", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina NextSeq [GENEPIO:0100126]": { + "text": "Illumina NextSeq [GENEPIO:0100126]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb.", + "meaning": "GENEPIO:0100126", + "is_a": "Illumina [GENEPIO:0100105]" + }, + "Illumina NextSeq 500 [OBI:0002021]": { + "text": "Illumina NextSeq 500 [OBI:0002021]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.", + "meaning": "OBI:0002021", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "Illumina NextSeq 550 [GENEPIO:0100128]": { + "text": "Illumina NextSeq 550 [GENEPIO:0100128]", + "description": "A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model.", + "meaning": "GENEPIO:0100128", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "Illumina NextSeq 1000 [GENEPIO:0004432]": { + "text": "Illumina NextSeq 1000 [GENEPIO:0004432]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells.", + "meaning": "GENEPIO:0004432", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "Illumina NextSeq 2000 [GENEPIO:0100129]": { + "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", + "description": "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb.", + "meaning": "GENEPIO:0100129", + "is_a": "Illumina NextSeq [GENEPIO:0100126]" + }, + "PacBio [GENEPIO:0100130]": { + "text": "PacBio [GENEPIO:0100130]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation.", + "meaning": "GENEPIO:0100130" + }, + "PacBio RS [GENEPIO:0100131]": { + "text": "PacBio RS [GENEPIO:0100131]", + "description": "A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company.", + "meaning": "GENEPIO:0100131", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "PacBio RS II [OBI:0002012]": { + "text": "PacBio RS II [OBI:0002012]", + "description": "A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy.", + "meaning": "OBI:0002012", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "PacBio Sequel [GENEPIO:0100133]": { + "text": "PacBio Sequel [GENEPIO:0100133]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation", + "meaning": "GENEPIO:0100133", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "PacBio Sequel II [GENEPIO:0100134]": { + "text": "PacBio Sequel II [GENEPIO:0100134]", + "description": "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation.", + "meaning": "GENEPIO:0100134", + "is_a": "PacBio [GENEPIO:0100130]" + }, + "Ion Torrent [GENEPIO:0100135]": { + "text": "Ion Torrent [GENEPIO:0100135]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation.", + "meaning": "GENEPIO:0100135" + }, + "Ion Torrent PGM [GENEPIO:0100136]": { + "text": "Ion Torrent PGM [GENEPIO:0100136]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB.", + "meaning": "GENEPIO:0100136", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Ion Torrent Proton [GENEPIO:0100137]": { + "text": "Ion Torrent Proton [GENEPIO:0100137]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb.", + "meaning": "GENEPIO:0100137", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Ion Torrent S5 XL [GENEPIO:0100138]": { + "text": "Ion Torrent S5 XL [GENEPIO:0100138]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model.", + "meaning": "GENEPIO:0100138", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Ion Torrent S5 [GENEPIO:0100139]": { + "text": "Ion Torrent S5 [GENEPIO:0100139]", + "description": "A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material.", + "meaning": "GENEPIO:0100139", + "is_a": "Ion Torrent [GENEPIO:0100135]" + }, + "Oxford Nanopore [GENEPIO:0100140]": { + "text": "Oxford Nanopore [GENEPIO:0100140]", + "description": "A DNA sequencer manufactured by the Oxford Nanopore corporation.", + "meaning": "GENEPIO:0100140" + }, + "Oxford Nanopore Flongle [GENEPIO:0004433]": { + "text": "Oxford Nanopore Flongle [GENEPIO:0004433]", + "description": "An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells.", + "meaning": "GENEPIO:0004433", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore GridION [GENEPIO:0100141]": { + "text": "Oxford Nanopore GridION [GENEPIO:0100141]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual", + "meaning": "GENEPIO:0100141", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore MinION [GENEPIO:0100142]": { + "text": "Oxford Nanopore MinION [GENEPIO:0100142]", + "description": "A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array.", + "meaning": "GENEPIO:0100142", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "Oxford Nanopore PromethION [GENEPIO:0100143]": { + "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", + "description": "A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously.", + "meaning": "GENEPIO:0100143", + "is_a": "Oxford Nanopore [GENEPIO:0100140]" + }, + "BGI Genomics sequencing instrument [GENEPIO:0100144]": { + "text": "BGI Genomics sequencing instrument [GENEPIO:0100144]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation.", + "meaning": "GENEPIO:0100144" + }, + "BGISEQ-500 [GENEPIO:0100145]": { + "text": "BGISEQ-500 [GENEPIO:0100145]", + "description": "A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and \"DNA Nanoballs\".", + "meaning": "GENEPIO:0100145", + "is_a": "BGI Genomics sequencing instrument [GENEPIO:0100144]" + }, + "MGI sequencing instrument [GENEPIO:0100146]": { + "text": "MGI sequencing instrument [GENEPIO:0100146]", + "description": "A DNA sequencer manufactured by the MGI corporation.", + "meaning": "GENEPIO:0100146" + }, + "MGISEQ-2000RS [GENEPIO:0100971]": { + "text": "MGISEQ-2000RS [GENEPIO:0100971]", + "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing.", + "meaning": "GENEPIO:0100971", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G99 [GENEPIO:0100972]": { + "text": "MGI DNBSEQ-G99 [GENEPIO:0100972]", + "description": "An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds.", + "meaning": "GENEPIO:0100972", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G400 [GENEPIO:0100148]": { + "text": "MGI DNBSEQ-G400 [GENEPIO:0100148]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run.", + "meaning": "GENEPIO:0100148", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]": { + "text": "MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400.", + "meaning": "GENEPIO:0100149", + "is_a": "MGI DNBSEQ-G400 [GENEPIO:0100148]" + }, + "MGI DNBSEQ-T7 [GENEPIO:0100147]": { + "text": "MGI DNBSEQ-T7 [GENEPIO:0100147]", + "description": "A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day.", + "meaning": "GENEPIO:0100147", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-E25 [GENEPIO:0100973]": { + "text": "MGI DNBSEQ-E25 [GENEPIO:0100973]", + "description": "An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab.", + "meaning": "GENEPIO:0100973", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "MGI DNBSEQ-G50 [GENEPIO:0100150]": { + "text": "MGI DNBSEQ-G50 [GENEPIO:0100150]", + "description": "A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths.", + "meaning": "GENEPIO:0100150", + "is_a": "MGI sequencing instrument [GENEPIO:0100146]" + }, + "454 Genome Sequencer [GENEPIO:0001937]": { + "text": "454 Genome Sequencer [GENEPIO:0001937]", + "description": "A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing.", + "meaning": "GENEPIO:0001937" + }, + "454 Genome Sequencer 20 [OBI:0000689]": { + "text": "454 Genome Sequencer 20 [OBI:0000689]", + "description": "A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem.", + "meaning": "OBI:0000689", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer FLX [OBI:0000702]": { + "text": "454 Genome Sequencer FLX [OBI:0000702]", + "description": "A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths.", + "meaning": "OBI:0000702", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer FLX+ [GENEPIO:0100982]": { + "text": "454 Genome Sequencer FLX+ [GENEPIO:0100982]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+.", + "meaning": "GENEPIO:0100982", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]": { + "text": "454 Genome Sequencer FLX Titanium [GENEPIO:0001936]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads.", + "meaning": "GENEPIO:0001936", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "454 Genome Sequencer Junior [GENEPIO:0001938]": { + "text": "454 Genome Sequencer Junior [GENEPIO:0001938]", + "description": "A 454 Genome Sequencer that performs pyrosequencing and is more compact.", + "meaning": "GENEPIO:0001938", + "is_a": "454 Genome Sequencer [GENEPIO:0001937]" + }, + "SOLiD System [OBI:0000696]": { + "text": "SOLiD System [OBI:0000696]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation.", + "meaning": "OBI:0000696" + }, + "SOLiD 5500 [GENEPIO:0001929]": { + "text": "SOLiD 5500 [GENEPIO:0001929]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series.", + "meaning": "GENEPIO:0001929", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]": { + "text": "SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]", + "description": "A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model.", + "meaning": "GENEPIO:0001930", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]": { + "text": "SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer.", + "meaning": "GENEPIO:0100984", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 3 Plus System [OBI:0002007]": { + "text": "SOLiD 3 Plus System [OBI:0002007]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run.", + "meaning": "OBI:0002007", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 4 System [OBI:0002024]": { + "text": "SOLiD 4 System [OBI:0002024]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput.", + "meaning": "OBI:0002024", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD 4hq System [GENEPIO:0001928]": { + "text": "SOLiD 4hq System [GENEPIO:0001928]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput.", + "meaning": "GENEPIO:0001928", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD PI System [GENEPIO:0001931]": { + "text": "SOLiD PI System [GENEPIO:0001931]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput.", + "meaning": "GENEPIO:0001931", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD System 2.0 [GENEPIO:0001932]": { + "text": "SOLiD System 2.0 [GENEPIO:0001932]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", + "meaning": "GENEPIO:0001932", + "is_a": "SOLiD System [OBI:0000696]" + }, + "SOLiD System 3.0 [GENEPIO:0001933]": { + "text": "SOLiD System 3.0 [GENEPIO:0001933]", + "description": "A DNA sequencer which is manufactured by the Applied Biosystems corporation.", + "meaning": "GENEPIO:0001933", + "is_a": "SOLiD System [OBI:0000696]" + }, + "HeliScope Single Molecule Sequencer [OBI:0000717]": { + "text": "HeliScope Single Molecule Sequencer [OBI:0000717]", + "description": "A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry.", + "meaning": "OBI:0000717" + }, + "Applied Biosystems sequencing instrument model [GENEPIO:0100974]": { + "text": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]", + "description": "A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis.", + "meaning": "GENEPIO:0100974" + }, + "AB 310 Genetic Analyzer [GENEPIO:0100975]": { + "text": "AB 310 Genetic Analyzer [GENEPIO:0100975]", + "description": "An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated.", + "meaning": "GENEPIO:0100975", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3130 Genetic Analyzer [GENEPIO:0100976]": { + "text": "AB 3130 Genetic Analyzer [GENEPIO:0100976]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries.", + "meaning": "GENEPIO:0100976", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3130xL Genetic Analyzer [GENEPIO:0100977]": { + "text": "AB 3130xL Genetic Analyzer [GENEPIO:0100977]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries.", + "meaning": "GENEPIO:0100977", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3500 Genetic Analyzer [GENEPIO:0100978]": { + "text": "AB 3500 Genetic Analyzer [GENEPIO:0100978]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates.", + "meaning": "GENEPIO:0100978", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3500xL Genetic Analyzer [GENEPIO:0100979]": { + "text": "AB 3500xL Genetic Analyzer [GENEPIO:0100979]", + "description": "An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates.", + "meaning": "GENEPIO:0100979", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3730 Genetic Analyzer [GENEPIO:0100980]": { + "text": "AB 3730 Genetic Analyzer [GENEPIO:0100980]", + "description": "An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing.", + "meaning": "GENEPIO:0100980", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + }, + "AB 3730xL Genetic Analyzer [GENEPIO:0100981]": { + "text": "AB 3730xL Genetic Analyzer [GENEPIO:0100981]", + "description": "An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing.", + "meaning": "GENEPIO:0100981", + "is_a": "Applied Biosystems sequencing instrument model [GENEPIO:0100974]" + } + } + }, + "GenomicTargetEnrichmentMethodMenu": { + "name": "GenomicTargetEnrichmentMethodMenu", + "title": "genomic_target_enrichment_method menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Hybrid selection method (bait-capture) [GENEPIO:0001950]": { + "text": "Hybrid selection method (bait-capture) [GENEPIO:0001950]", + "description": "Selection by hybridization in array or solution.", + "meaning": "GENEPIO:0001950" + }, + "rRNA depletion method [GENEPIO:0101020]": { + "text": "rRNA depletion method [GENEPIO:0101020]", + "description": "Removal of background RNA for the purposes of enriching the genomic target.", + "meaning": "GENEPIO:0101020" + } + } + }, + "QualityControlDeterminationMenu": { + "name": "QualityControlDeterminationMenu", + "title": "quality_control_determination menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "No quality control issues identified [GENEPIO:0100562]": { + "text": "No quality control issues identified [GENEPIO:0100562]", + "description": "A statement confirming that quality control processes were carried out and no quality issues were detected.", + "meaning": "GENEPIO:0100562" + }, + "Sequence passed quality control [GENEPIO:0100563]": { + "text": "Sequence passed quality control [GENEPIO:0100563]", + "description": "A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", + "meaning": "GENEPIO:0100563" + }, + "Sequence failed quality control [GENEPIO:0100564]": { + "text": "Sequence failed quality control [GENEPIO:0100564]", + "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", + "meaning": "GENEPIO:0100564" + }, + "Minor quality control issues identified [GENEPIO:0100565]": { + "text": "Minor quality control issues identified [GENEPIO:0100565]", + "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", + "meaning": "GENEPIO:0100565" + }, + "Sequence flagged for potential quality control issues [GENEPIO:0100566]": { + "text": "Sequence flagged for potential quality control issues [GENEPIO:0100566]", + "description": "A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", + "meaning": "GENEPIO:0100566" + }, + "Quality control not performed [GENEPIO:0100567]": { + "text": "Quality control not performed [GENEPIO:0100567]", + "description": "A statement confirming that quality control processes have not been carried out.", + "meaning": "GENEPIO:0100567" + } + } + }, + "QualityControlIssuesMenu": { + "name": "QualityControlIssuesMenu", + "title": "quality_control_issues menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Low quality sequence [GENEPIO:0100568]": { + "text": "Low quality sequence [GENEPIO:0100568]", + "description": "Sequence data that does not meet quality control thresholds.", + "meaning": "GENEPIO:0100568" + }, + "Sequence contaminated [GENEPIO:0100569]": { + "text": "Sequence contaminated [GENEPIO:0100569]", + "description": "Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", + "meaning": "GENEPIO:0100569" + }, + "Low average genome coverage [GENEPIO:0100570]": { + "text": "Low average genome coverage [GENEPIO:0100570]", + "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", + "meaning": "GENEPIO:0100570" + }, + "Low percent genome captured [GENEPIO:0100571]": { + "text": "Low percent genome captured [GENEPIO:0100571]", + "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", + "meaning": "GENEPIO:0100571" + }, + "Read lengths shorter than expected [GENEPIO:0100572]": { + "text": "Read lengths shorter than expected [GENEPIO:0100572]", + "description": "Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", + "meaning": "GENEPIO:0100572" + }, + "Sequence amplification artifacts [GENEPIO:0100573]": { + "text": "Sequence amplification artifacts [GENEPIO:0100573]", + "description": "Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", + "meaning": "GENEPIO:0100573" + }, + "Low signal to noise ratio [GENEPIO:0100574]": { + "text": "Low signal to noise ratio [GENEPIO:0100574]", + "description": "Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", + "meaning": "GENEPIO:0100574" + }, + "Low coverage of characteristic mutations [GENEPIO:0100575]": { + "text": "Low coverage of characteristic mutations [GENEPIO:0100575]", + "description": "Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", + "meaning": "GENEPIO:0100575" + } + } + }, + "DiagnosticTargetPresenceMenu": { + "name": "DiagnosticTargetPresenceMenu", + "title": "diagnostic target presence menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "diagnostic target present [GENEPIO:0100987]": { + "text": "diagnostic target present [GENEPIO:0100987]", + "description": "A quality inhering in a bearer by virtue of the bearer's existence.", + "meaning": "GENEPIO:0100987" + }, + "diagnostic target absent [GENEPIO:0100988]": { + "text": "diagnostic target absent [GENEPIO:0100988]", + "description": "Aquality denoting the lack of an entity.", + "meaning": "GENEPIO:0100988" + } + } + }, + "DiagnosticMeasurementUnitMenu": { + "name": "DiagnosticMeasurementUnitMenu", + "title": "diagnostic measurement unit menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "gene copies per liter (GC/L)": { + "text": "gene copies per liter (GC/L)", + "description": "A unit that measures the number of copies of a given gene within a liter of a biological material." + }, + "cycle threshold (Ct) [GENEPIO:0100657]": { + "text": "cycle threshold (Ct) [GENEPIO:0100657]", + "description": "A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test.", + "meaning": "GENEPIO:0100657" + }, + "colony forming units per milliliter (CFU/mL) [UO:0000213]": { + "text": "colony forming units per milliliter (CFU/mL) [UO:0000213]", + "description": "A unit of microbial density that describes the number of colony forming units within a milliliter of material.", + "meaning": "UO:0000213" + }, + "colony forming units per 100 milliliter (CFU/100 mL)": { + "text": "colony forming units per 100 milliliter (CFU/100 mL)", + "description": "A unit of microbial density that describes the number of colony forming units within 100 milliliters of material." + }, + "colony forming units per grams total solids (CFU/gTS)": { + "text": "colony forming units per grams total solids (CFU/gTS)", + "description": "A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material." + }, + "most probable number per milliliter (MPN/mL)": { + "text": "most probable number per milliliter (MPN/mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within one milliliter of material." + }, + "most probable number per 100 milliliter (MPN/100 mL)": { + "text": "most probable number per 100 milliliter (MPN/100 mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material." + } + } + }, + "DiagnosticMeasurementMethodMenu": { + "name": "DiagnosticMeasurementMethodMenu", + "title": "diagnostic measurement method menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]": { + "text": "Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]", + "description": "An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.", + "meaning": "OBI:0000893" + }, + "Digital real time polymerase chain reaction (dPCR)": { + "text": "Digital real time polymerase chain reaction (dPCR)", + "description": "A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction" + }, + "Bacteria culture test": { + "text": "Bacteria culture test", + "description": "An assay to identify the presence of bacteria" + } + } + }, + "ExperimentalInterventionMenu": { + "name": "ExperimentalInterventionMenu", + "title": "experimental_intervention menu", + "from_schema": "https://example.com/hpai", + "permissible_values": { + "Addition of substances to food/water [GENEPIO:0100536]": { + "text": "Addition of substances to food/water [GENEPIO:0100536]", + "description": "The addition of substances to food or water administered to an individual or group of individuals.", + "meaning": "GENEPIO:0100536" + }, + "Antimicrobial pre-treatment [GENEPIO:0100537]": { + "text": "Antimicrobial pre-treatment [GENEPIO:0100537]", + "description": "The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity.", + "meaning": "GENEPIO:0100537" + }, + "Certified animal husbandry practices [GENEPIO:0100538]": { + "text": "Certified animal husbandry practices [GENEPIO:0100538]", + "description": "The implementation of animal husbandy practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100538" + }, + "Certified organic farming practices [GENEPIO:0100539]": { + "text": "Certified organic farming practices [GENEPIO:0100539]", + "description": "The implementation of organic farming practices that have been certified by an authorized organization.", + "meaning": "GENEPIO:0100539" + }, + "Change in storage conditions [GENEPIO:0100540]": { + "text": "Change in storage conditions [GENEPIO:0100540]", + "description": "A change in the storage conditions of a material or a substance.", + "meaning": "GENEPIO:0100540" + }, + "Cleaning/disinfection [GENEPIO:0100541]": { + "text": "Cleaning/disinfection [GENEPIO:0100541]", + "description": "A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment.", + "meaning": "GENEPIO:0100541" + }, + "Extended downtime between activities [GENEPIO:0100542]": { + "text": "Extended downtime between activities [GENEPIO:0100542]", + "description": "A prolonged period of inactivity between processes or events.", + "meaning": "GENEPIO:0100542" + }, + "Fertilizer pre-treatment [GENEPIO:0100543]": { + "text": "Fertilizer pre-treatment [GENEPIO:0100543]", + "description": "The addition of fertilizer to a material or environment prior to some other event or activity.", + "meaning": "GENEPIO:0100543" + }, + "Logistic slaughter [GENEPIO:0100545]": { + "text": "Logistic slaughter [GENEPIO:0100545]", + "description": "The logistical planning of events and processes upstream of the immediate slaughter of an animal (which may include controlling transport climate; traffic conditions, number of pick-up farms, as well as time and distance during transport; queuing at the abattoir etc) that optimize operations and reduce stress on the animal.", + "meaning": "GENEPIO:0100545" + }, + "Microbial pre-treatment [GENEPIO:0100546]": { + "text": "Microbial pre-treatment [GENEPIO:0100546]", + "description": "The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity.", + "meaning": "GENEPIO:0100546" + }, + "Probiotic pre-treatment [GENEPIO:0100547]": { + "text": "Probiotic pre-treatment [GENEPIO:0100547]", + "description": "The addition of a probiotic substance to an individual or material prior to some other event or activity.", + "meaning": "GENEPIO:0100547" + }, + "Vaccination [NCIT:C15346]": { + "text": "Vaccination [NCIT:C15346]", + "description": "Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment.", + "meaning": "NCIT:C15346" + } + } + }, "AirPressureMeasurementUnitMenu": { "name": "AirPressureMeasurementUnitMenu", "title": "air_pressure_measurement_unit menu", @@ -5827,28 +6689,36 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "cubic meter per second (m^3/s)": { - "text": "cubic meter per second (m^3/s)" + "text": "cubic meter per second (m^3/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second." }, "cubic meter per minute (m^3/min)": { - "text": "cubic meter per minute (m^3/min)" + "text": "cubic meter per minute (m^3/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute." }, "cubic meter per hour (m^3/h)": { - "text": "cubic meter per hour (m^3/h)" + "text": "cubic meter per hour (m^3/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour." }, "liter per second (L/s)": { - "text": "liter per second (L/s)" + "text": "liter per second (L/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second." }, "liter per minute (L/min)": { - "text": "liter per minute (L/min)" + "text": "liter per minute (L/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute." }, "liter per hour (L/h)": { - "text": "liter per hour (L/h)" + "text": "liter per hour (L/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour." }, "liter per day (L/day)": { - "text": "liter per day (L/day)" + "text": "liter per day (L/day)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day." }, "million gallons per day (MGD)": { - "text": "million gallons per day (MGD)" + "text": "million gallons per day (MGD)", + "description": "A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day." } } }, @@ -5858,28 +6728,36 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "cubic meter per second (m^3/s)": { - "text": "cubic meter per second (m^3/s)" + "text": "cubic meter per second (m^3/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second." }, "cubic meter per minute (m^3/min)": { - "text": "cubic meter per minute (m^3/min)" + "text": "cubic meter per minute (m^3/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute." }, "cubic meter per hour (m^3/h)": { - "text": "cubic meter per hour (m^3/h)" + "text": "cubic meter per hour (m^3/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour." }, "liter per second (L/s)": { - "text": "liter per second (L/s)" + "text": "liter per second (L/s)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second." }, "liter per minute (L/min)": { - "text": "liter per minute (L/min)" + "text": "liter per minute (L/min)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute." }, "liter per hour (L/h)": { - "text": "liter per hour (L/h)" + "text": "liter per hour (L/h)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour." }, "liter per day (L/day)": { - "text": "liter per day (L/day)" + "text": "liter per day (L/day)", + "description": "A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day." }, "million gallons per day (MGD)": { - "text": "million gallons per day (MGD)" + "text": "million gallons per day (MGD)", + "description": "A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day." } } }, @@ -5889,7 +6767,8 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "nephelometric turbidity unit (NTU)": { - "text": "nephelometric turbidity unit (NTU)" + "text": "nephelometric turbidity unit (NTU)", + "description": "A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample." }, "formazin nephelometric unit (FNU) [UO:0000318]": { "text": "formazin nephelometric unit (FNU) [UO:0000318]", @@ -6013,7 +6892,8 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "milliequivalent per liter (meq/L)": { - "text": "milliequivalent per liter (meq/L)" + "text": "milliequivalent per liter (meq/L)", + "description": "A unit of ion concentration that represents chemical activity per volume." }, "milligram per liter (mg/L) [UO:0000273]": { "text": "milligram per liter (mg/L) [UO:0000273]", @@ -6033,13 +6913,16 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "milliSiemen per centimeter (mS/cm)": { - "text": "milliSiemen per centimeter (mS/cm)" + "text": "milliSiemen per centimeter (mS/cm)", + "description": "A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m)." }, "microSiemen per centimeter (μS/cm)": { - "text": "microSiemen per centimeter (μS/cm)" + "text": "microSiemen per centimeter (μS/cm)", + "description": "A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m)." }, "Siemen per meter (S/m)": { - "text": "Siemen per meter (S/m)" + "text": "Siemen per meter (S/m)", + "description": "An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m)." } } }, @@ -6049,10 +6932,12 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "practical salinity unit (PSU)": { - "text": "practical salinity unit (PSU)" + "text": "practical salinity unit (PSU)", + "description": "A unitless measure of salinity that is equivalent to per thousand." }, "weight for weight (% w/w)": { - "text": "weight for weight (% w/w)" + "text": "weight for weight (% w/w)", + "description": "A unitless comparison based on weight rather than volume, which is equivalent to per hundred." }, "parts per thousand [UO:0000168]": { "text": "parts per thousand [UO:0000168]", @@ -6082,7 +6967,8 @@ "meaning": "UO:0000175" }, "gram per total solids (g/gTS)": { - "text": "gram per total solids (g/gTS)" + "text": "gram per total solids (g/gTS)", + "description": "A unitless comparison of the weight of a substance as a proportion to the weight of total solids." } } }, @@ -6092,7 +6978,8 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "gram per total solids (g/gTS)": { - "text": "gram per total solids (g/gTS)" + "text": "gram per total solids (g/gTS)", + "description": "A unitless comparison of the weight of a substance as a proportion to the weight of total solids." }, "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]": { "text": "orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]", @@ -6154,10 +7041,12 @@ "from_schema": "https://example.com/hpai", "permissible_values": { "log10 gene copies per 100 milliliter (log10 GC/100 mL)": { - "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)" + "text": "log10 gene copies per 100 milliliter (log10 GC/100 mL)", + "description": "A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material." }, "gene copies per liter (GC/L)": { - "text": "gene copies per liter (GC/L)" + "text": "gene copies per liter (GC/L)", + "description": "A unit that measures the number of copies of a given gene within a liter of a biological material." }, "PCR quantification cycle [UO:0010077]": { "text": "PCR quantification cycle [UO:0010077]", @@ -6165,7 +7054,8 @@ "meaning": "UO:0010077" }, "log10 gene copies per nanogram total DNA": { - "text": "log10 gene copies per nanogram total DNA" + "text": "log10 gene copies per nanogram total DNA", + "description": "A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material." } } }, @@ -6204,16 +7094,20 @@ "meaning": "UO:0000213" }, "colony forming units per 100 milliliter (CFU/100 mL)": { - "text": "colony forming units per 100 milliliter (CFU/100 mL)" + "text": "colony forming units per 100 milliliter (CFU/100 mL)", + "description": "A unit of microbial density that describes the number of colony forming units within 100 milliliters of material." }, "colony forming units per grams total solids (CFU/gTS)": { - "text": "colony forming units per grams total solids (CFU/gTS)" + "text": "colony forming units per grams total solids (CFU/gTS)", + "description": "A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material." }, "most probable number per milliliter (MPN/mL)": { - "text": "most probable number per milliliter (MPN/mL)" + "text": "most probable number per milliliter (MPN/mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within one milliliter of material." }, "most probable number per 100 milliliter (MPN/100 mL)": { - "text": "most probable number per 100 milliliter (MPN/100 mL)" + "text": "most probable number per 100 milliliter (MPN/100 mL)", + "description": "A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material." } } }, @@ -8309,7 +9203,7 @@ "HPAIEnviro", "HPAIHost" ], - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -10548,7 +11442,7 @@ ], "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -10613,6 +11507,202 @@ } ] }, + "water_depth": { + "name": "water_depth", + "description": "The depth of some water.", + "title": "water_depth", + "comments": [ + "Provide the numerical depth only of water only (without units)." + ], + "examples": [ + { + "value": "5" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100440", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_depth_units": { + "name": "water_depth_units", + "description": "The units of measurement for water depth.", + "title": "water_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101025", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "WaterDepthUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sediment_depth": { + "name": "sediment_depth", + "description": "The depth of some sediment.", + "title": "sediment_depth", + "comments": [ + "Provide the numerical depth only of the sediment (without units)." + ], + "examples": [ + { + "value": "2" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100697", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "sediment_depth_units": { + "name": "sediment_depth_units", + "description": "The units of measurement for sediment depth.", + "title": "sediment_depth_units", + "comments": [ + "Provide the units of measurement for which the depth was recorded." + ], + "examples": [ + { + "value": "meter (m) [UO:0000008]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101026", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "SedimentDepthUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "air_temperature": { + "name": "air_temperature", + "description": "The temperature of some air.", + "title": "air_temperature", + "comments": [ + "Provide the numerical value for the temperature of the air (without units)." + ], + "examples": [ + { + "value": "25" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100441", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "air_temperature_units": { + "name": "air_temperature_units", + "description": "The units of measurement for air temperature.", + "title": "air_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101027", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "AirTemperatureUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "water_temperature": { + "name": "water_temperature", + "description": "The temperature of some water.", + "title": "water_temperature", + "comments": [ + "Provide the numerical value for the temperature of the water (without units)." + ], + "examples": [ + { + "value": "4" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0100698", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "range": "WhitespaceMinimizedString" + }, + "water_temperature_units": { + "name": "water_temperature_units", + "description": "The units of measurement for water temperature.", + "title": "water_temperature_units", + "comments": [ + "Provide the units of measurement for which the temperature was recorded." + ], + "examples": [ + { + "value": "degree Celsius (C) [UO:0000027]" + } + ], + "from_schema": "https://example.com/hpai", + "slot_uri": "GENEPIO:0101028", + "domain_of": [ + "HPAI", + "HPAIWW", + "HPAIEnviro" + ], + "any_of": [ + { + "range": "WaterTemperatureUnitsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, "precipitation_measurement_value": { "name": "precipitation_measurement_value", "description": "The amount of water which has fallen during a precipitation process.", @@ -10642,231 +11732,6 @@ } ] }, - "water_depth": { - "name": "water_depth", - "description": "The depth of some water.", - "title": "water_depth", - "comments": [ - "Provide the numerical depth only of water only (without units)." - ], - "examples": [ - { - "value": "5" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100440", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "water_depth_units": { - "name": "water_depth_units", - "description": "The units of measurement for water depth.", - "title": "water_depth_units", - "comments": [ - "Provide the units of measurement for which the depth was recorded." - ], - "examples": [ - { - "value": "meter (m) [UO:0000008]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101025", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "WaterDepthUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "sediment_depth": { - "name": "sediment_depth", - "description": "The depth of some sediment.", - "title": "sediment_depth", - "comments": [ - "Provide the numerical depth only of the sediment (without units)." - ], - "examples": [ - { - "value": "2" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100697", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "sediment_depth_units": { - "name": "sediment_depth_units", - "description": "The units of measurement for sediment depth.", - "title": "sediment_depth_units", - "comments": [ - "Provide the units of measurement for which the depth was recorded." - ], - "examples": [ - { - "value": "meter (m) [UO:0000008]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101026", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "SedimentDepthUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "air_temperature": { - "name": "air_temperature", - "description": "The temperature of some air.", - "title": "air_temperature", - "comments": [ - "Provide the numerical value for the temperature of the air (without units)." - ], - "examples": [ - { - "value": "25" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100441", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "air_temperature_units": { - "name": "air_temperature_units", - "description": "The units of measurement for air temperature.", - "title": "air_temperature_units", - "comments": [ - "Provide the units of measurement for which the temperature was recorded." - ], - "examples": [ - { - "value": "degree Celsius (C) [UO:0000027]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101027", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "AirTemperatureUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "water_temperature": { - "name": "water_temperature", - "description": "The temperature of some water.", - "title": "water_temperature", - "comments": [ - "Provide the numerical value for the temperature of the water (without units)." - ], - "examples": [ - { - "value": "4" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100698", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "range": "WhitespaceMinimizedString" - }, - "water_temperature_units": { - "name": "water_temperature_units", - "description": "The units of measurement for water temperature.", - "title": "water_temperature_units", - "comments": [ - "Provide the units of measurement for which the temperature was recorded." - ], - "examples": [ - { - "value": "degree Celsius (C) [UO:0000027]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0101028", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "any_of": [ - { - "range": "WaterTemperatureUnitsMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", - "comments": [ - "Provide the weather conditions at the time of sample collection." - ], - "examples": [ - { - "value": "Rain [ENVO:01001564]" - } - ], - "from_schema": "https://example.com/hpai", - "slot_uri": "GENEPIO:0100442", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "multivalued": true, - "any_of": [ - { - "range": "WeatherTypeMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", @@ -12032,7 +12897,7 @@ ], "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -14362,7 +15227,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -14777,27 +15642,27 @@ "host_common_name": { "name": "host_common_name", "rank": 67, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_scientific_name": { "name": "host_scientific_name", "rank": 68, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_ecotype": { "name": "host_ecotype", "rank": 69, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_breed": { "name": "host_breed", "rank": 70, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_food_production_name": { "name": "host_food_production_name", "rank": 71, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_age": { "name": "host_age", @@ -14812,12 +15677,12 @@ "host_age_bin": { "name": "host_age_bin", "rank": 74, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_disease": { "name": "host_disease", "rank": 75, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_health_state": { "name": "host_health_state", @@ -14979,789 +15844,784 @@ "rank": 107, "slot_group": "Environmental conditions and measurements" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "rank": 108, - "slot_group": "Environmental conditions and measurements" - }, "water_depth": { "name": "water_depth", - "rank": 109, + "rank": 108, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 110, + "rank": 109, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 111, + "rank": 110, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 112, + "rank": 111, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 113, + "rank": 112, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 114, + "rank": 113, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 115, + "rank": 114, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 116, + "rank": 115, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 117, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 116, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", - "rank": 118, + "rank": 117, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", - "rank": 119, + "rank": 118, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_value": { "name": "ambient_temperature_measurement_value", - "rank": 120, + "rank": 119, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_unit": { "name": "ambient_temperature_measurement_unit", - "rank": 121, + "rank": 120, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_value": { "name": "ph_measurement_value", - "rank": 122, + "rank": 121, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_method": { "name": "ph_measurement_method", - "rank": 123, + "rank": 122, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_value": { "name": "total_daily_flow_rate_measurement_value", - "rank": 124, + "rank": 123, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_unit": { "name": "total_daily_flow_rate_measurement_unit", - "rank": 125, + "rank": 124, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_method": { "name": "total_daily_flow_rate_measurement_method", - "rank": 126, + "rank": 125, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_value": { "name": "instantaneous_flow_rate_measurement_value", - "rank": 127, + "rank": 126, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_unit": { "name": "instantaneous_flow_rate_measurement_unit", - "rank": 128, + "rank": 127, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_method": { "name": "instantaneous_flow_rate_measurement_method", - "rank": 129, + "rank": 128, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_value": { "name": "turbidity_measurement_value", - "rank": 130, + "rank": 129, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_unit": { "name": "turbidity_measurement_unit", - "rank": 131, + "rank": 130, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_method": { "name": "turbidity_measurement_method", - "rank": 132, + "rank": 131, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_value": { "name": "dissolved_oxygen_measurement_value", - "rank": 133, + "rank": 132, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_unit": { "name": "dissolved_oxygen_measurement_unit", - "rank": 134, + "rank": 133, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_method": { "name": "dissolved_oxygen_measurement_method", - "rank": 135, + "rank": 134, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_value": { "name": "oxygen_reduction_potential_orp_measurement_value", - "rank": 136, + "rank": 135, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_unit": { "name": "oxygen_reduction_potential_orp_measurement_unit", - "rank": 137, + "rank": 136, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_method": { "name": "oxygen_reduction_potential_orp_measurement_method", - "rank": 138, + "rank": 137, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_value": { "name": "chemical_oxygen_demand_cod_measurement_value", - "rank": 139, + "rank": 138, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_unit": { "name": "chemical_oxygen_demand_cod_measurement_unit", - "rank": 140, + "rank": 139, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_method": { "name": "chemical_oxygen_demand_cod_measurement_method", - "rank": 141, + "rank": 140, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", - "rank": 142, + "rank": 141, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", - "rank": 143, + "rank": 142, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", - "rank": 144, + "rank": 143, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_value": { "name": "total_suspended_solids_tss_measurement_value", - "rank": 145, + "rank": 144, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_unit": { "name": "total_suspended_solids_tss_measurement_unit", - "rank": 146, + "rank": 145, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_method": { "name": "total_suspended_solids_tss_measurement_method", - "rank": 147, + "rank": 146, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_value": { "name": "total_dissolved_solids_tds_measurement_value", - "rank": 148, + "rank": 147, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_unit": { "name": "total_dissolved_solids_tds_measurement_unit", - "rank": 149, + "rank": 148, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_method": { "name": "total_dissolved_solids_tds_measurement_method", - "rank": 150, + "rank": 149, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_value": { "name": "total_solids_ts_measurement_value", - "rank": 151, + "rank": 150, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_unit": { "name": "total_solids_ts_measurement_unit", - "rank": 152, + "rank": 151, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_method": { "name": "total_solids_ts_measurement_method", - "rank": 153, + "rank": 152, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_value": { "name": "alkalinity_measurement_value", - "rank": 154, + "rank": 153, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_unit": { "name": "alkalinity_measurement_unit", - "rank": 155, + "rank": 154, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_method": { "name": "alkalinity_measurement_method", - "rank": 156, + "rank": 155, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_value": { "name": "conductivity_measurement_value", - "rank": 157, + "rank": 156, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_unit": { "name": "conductivity_measurement_unit", - "rank": 158, + "rank": 157, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_method": { "name": "conductivity_measurement_method", - "rank": 159, + "rank": 158, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_value": { "name": "salinity_measurement_value", - "rank": 160, + "rank": 159, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_unit": { "name": "salinity_measurement_unit", - "rank": 161, + "rank": 160, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_method": { "name": "salinity_measurement_method", - "rank": 162, + "rank": 161, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_value": { "name": "total_nitrogen_tn_measurement_value", - "rank": 163, + "rank": 162, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_unit": { "name": "total_nitrogen_tn_measurement_unit", - "rank": 164, + "rank": 163, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_method": { "name": "total_nitrogen_tn_measurement_method", - "rank": 165, + "rank": 164, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_value": { "name": "total_phosphorus_tp_measurement_value", - "rank": 166, + "rank": 165, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_unit": { "name": "total_phosphorus_tp_measurement_unit", - 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"rank": 202, + "rank": 201, "slot_group": "Sequence information" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 203, + "rank": 202, "slot_group": "Sequence information" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 204, + "rank": 203, "slot_group": "Sequence information" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 205, + "rank": 204, "slot_group": "Sequence information" }, "amplicon_size": { "name": "amplicon_size", - "rank": 206, + "rank": 205, "slot_group": "Sequence information" }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 207, + "rank": 206, "slot_group": "Sequence information" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 208, + "rank": 207, "slot_group": "Sequence information" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 209, + "rank": 208, "slot_group": "Sequence information" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - 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"rank": 218, + "rank": 217, "slot_group": "Bioinformatics and QC metrics" }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", - "rank": 219, + "rank": 218, "slot_group": "Bioinformatics and QC metrics" }, "dehosting_method": { "name": "dehosting_method", - "rank": 220, + "rank": 219, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_name": { "name": "sequence_assembly_software_name", - "rank": 221, + "rank": 220, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_version": { "name": "sequence_assembly_software_version", - "rank": 222, + "rank": 221, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "name": "consensus_sequence_software_name", - "rank": 223, + "rank": 222, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "name": "consensus_sequence_software_version", - "rank": 224, + "rank": 223, "slot_group": "Bioinformatics and QC metrics" }, "breadth_of_coverage_value": { "name": "breadth_of_coverage_value", - "rank": 225, + "rank": 224, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_value": { "name": "depth_of_coverage_value", - "rank": 226, + "rank": 225, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_threshold": { "name": "depth_of_coverage_threshold", - "rank": 227, + "rank": 226, "slot_group": "Bioinformatics and QC metrics" }, "genome_completeness": { "name": "genome_completeness", - "rank": 228, + "rank": 227, "slot_group": "Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "name": "number_of_base_pairs_sequenced", - "rank": 229, + "rank": 228, "slot_group": "Bioinformatics and QC metrics" }, "number_of_total_reads": { "name": "number_of_total_reads", - "rank": 230, + "rank": 229, "slot_group": "Bioinformatics and QC metrics" }, "number_of_unique_reads": { "name": "number_of_unique_reads", - "rank": 231, + "rank": 230, "slot_group": "Bioinformatics and QC metrics" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", - "rank": 232, + "rank": 231, "slot_group": "Bioinformatics and QC metrics" }, "number_of_contigs": { "name": "number_of_contigs", - "rank": 233, + "rank": 232, "slot_group": "Bioinformatics and QC metrics" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", - "rank": 234, + "rank": 233, "slot_group": "Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", - "rank": 235, + "rank": 234, "slot_group": "Bioinformatics and QC metrics" }, "n50": { "name": "n50", - "rank": 236, + "rank": 235, "slot_group": "Bioinformatics and QC metrics" }, "percent_read_contamination_": { "name": "percent_read_contamination_", - "rank": 237, + "rank": 236, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_length": { "name": "sequence_assembly_length", - "rank": 238, + "rank": 237, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 239, + "rank": 238, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 240, + "rank": 239, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 241, + "rank": 240, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 242, + "rank": 241, "slot_group": "Bioinformatics and QC metrics" }, "read_mapping_software_name": { "name": "read_mapping_software_name", - "rank": 243, + "rank": 242, "slot_group": "Taxonomic identification information" }, "read_mapping_software_version": { "name": "read_mapping_software_version", - "rank": 244, + "rank": 243, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_name": { "name": "taxonomic_reference_database_name", - "rank": 245, + "rank": 244, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_version": { "name": "taxonomic_reference_database_version", - "rank": 246, + "rank": 245, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_report_filename": { "name": "taxonomic_analysis_report_filename", - "rank": 247, + "rank": 246, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_date": { "name": "taxonomic_analysis_date", - "rank": 248, + "rank": 247, "slot_group": "Taxonomic identification information" }, "read_mapping_criteria": { "name": "read_mapping_criteria", - "rank": 249, + "rank": 248, "slot_group": "Taxonomic identification information" }, "genetic_target_name": { "name": "genetic_target_name", - "rank": 250, + "rank": 249, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region": { "name": "genetic_target_region", - "rank": 251, + "rank": 250, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region_reference_genome": { "name": "genetic_target_region_reference_genome", - "rank": 252, + "rank": 251, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_target_presence": { "name": "diagnostic_target_presence", - "rank": 253, + "rank": 252, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_value": { "name": "diagnostic_measurement_value", - "rank": 254, + "rank": 253, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_unit": { "name": "diagnostic_measurement_unit", - "rank": 255, + "rank": 254, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_method": { "name": "diagnostic_measurement_method", - "rank": 256, + "rank": 255, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_value": { "name": "diagnostic_testing_threshold_value", - "rank": 257, + "rank": 256, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_units": { "name": "diagnostic_testing_threshold_units", - "rank": 258, + "rank": 257, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_details": { "name": "diagnostic_testing_details", - "rank": 259, + "rank": 258, "slot_group": "Pathogen diagnostic testing" }, "prevalence_metrics": { "name": "prevalence_metrics", - "rank": 260, + "rank": 259, "slot_group": "Risk assessment information" }, "prevalence_metrics_details": { "name": "prevalence_metrics_details", - "rank": 261, + "rank": 260, "slot_group": "Risk assessment information" }, "stage_of_production": { "name": "stage_of_production", - "rank": 262, + "rank": 261, "slot_group": "Risk assessment information" }, "experimental_intervention": { "name": "experimental_intervention", - "rank": 263, + "rank": 262, "slot_group": "Risk assessment information" }, "experiment_intervention_details": { "name": "experiment_intervention_details", - "rank": 264, + "rank": 263, "slot_group": "Risk assessment information" } }, @@ -16436,7 +17296,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -17878,7 +18738,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -17918,7 +18778,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -17953,7 +18813,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_breed": { @@ -17981,7 +18841,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_food_production_name": { @@ -18008,7 +18868,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostFoodProductionNameMenu" @@ -18106,7 +18966,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostAgeBinMenu" @@ -18140,7 +19000,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostDiseaseMenu" @@ -19007,7 +19867,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -19080,39 +19940,6 @@ } ] }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", - "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." - ], - "examples": [ - { - "value": "12" - } - ], - "from_schema": "https://example.com/hpai", - "rank": 108, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", - "owner": "HPAI", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "slot_group": "Environmental conditions and measurements", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "water_depth": { "name": "water_depth", "description": "The depth of some water.", @@ -19126,7 +19953,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 109, + "rank": 108, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "HPAI", @@ -19151,7 +19978,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 110, + "rank": 109, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "HPAI", @@ -19183,7 +20010,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 111, + "rank": 110, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "HPAI", @@ -19208,7 +20035,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 112, + "rank": 111, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "HPAI", @@ -19240,7 +20067,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 113, + "rank": 112, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "HPAI", @@ -19265,7 +20092,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 114, + "rank": 113, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "HPAI", @@ -19297,7 +20124,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 115, + "rank": 114, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "HPAI", @@ -19322,7 +20149,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 116, + "rank": 115, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "HPAI", @@ -19341,22 +20168,22 @@ } ] }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "12" } ], "from_schema": "https://example.com/hpai", - "rank": 117, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 116, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "HPAI", "domain_of": [ "HPAI", @@ -19364,10 +20191,10 @@ "HPAIEnviro" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "recommended": true, "any_of": [ { - "range": "WeatherTypeMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -19387,7 +20214,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 118, + "rank": 117, "slot_uri": "GENEPIO:0100912", "alias": "precipitation_measurement_unit", "owner": "HPAI", @@ -19420,7 +20247,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 119, + "rank": 118, "slot_uri": "GENEPIO:0100913", "alias": "precipitation_measurement_method", "owner": "HPAI", @@ -19445,7 +20272,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 120, + "rank": 119, "slot_uri": "GENEPIO:0100935", "alias": "ambient_temperature_measurement_value", "owner": "HPAI", @@ -19470,7 +20297,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 121, + "rank": 120, "slot_uri": "GENEPIO:0100936", "alias": "ambient_temperature_measurement_unit", "owner": "HPAI", @@ -19502,7 +20329,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 122, + "rank": 121, "slot_uri": "GENEPIO:0001736", "alias": "ph_measurement_value", "owner": "HPAI", @@ -19527,7 +20354,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 123, + "rank": 122, "slot_uri": "GENEPIO:0100781", "alias": "ph_measurement_method", "owner": "HPAI", @@ -19552,7 +20379,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 124, + "rank": 123, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", "owner": "HPAI", @@ -19577,7 +20404,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 125, + "rank": 124, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", "owner": "HPAI", @@ -19609,7 +20436,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 126, + "rank": 125, "slot_uri": "GENEPIO:0100907", "alias": "total_daily_flow_rate_measurement_method", "owner": "HPAI", @@ -19634,7 +20461,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 127, + "rank": 126, "slot_uri": "GENEPIO:0100908", "alias": "instantaneous_flow_rate_measurement_value", "owner": "HPAI", @@ -19659,7 +20486,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 128, + "rank": 127, "slot_uri": "GENEPIO:0100909", "alias": "instantaneous_flow_rate_measurement_unit", "owner": "HPAI", @@ -19691,7 +20518,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 129, + "rank": 128, "slot_uri": "GENEPIO:0100910", "alias": "instantaneous_flow_rate_measurement_method", "owner": "HPAI", @@ -19716,7 +20543,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 130, + "rank": 129, "slot_uri": "GENEPIO:0100783", "alias": "turbidity_measurement_value", "owner": "HPAI", @@ -19742,7 +20569,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 131, + "rank": 130, "slot_uri": "GENEPIO:0100914", "alias": "turbidity_measurement_unit", "owner": "HPAI", @@ -19775,7 +20602,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 132, + "rank": 131, "slot_uri": "GENEPIO:0101013", "alias": "turbidity_measurement_method", "owner": "HPAI", @@ -19800,7 +20627,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 133, + "rank": 132, "slot_uri": "GENEPIO:0100915", "alias": "dissolved_oxygen_measurement_value", "owner": "HPAI", @@ -19825,7 +20652,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 134, + "rank": 133, "slot_uri": "GENEPIO:0100784", "alias": "dissolved_oxygen_measurement_unit", "owner": "HPAI", @@ -19857,7 +20684,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 135, + "rank": 134, "slot_uri": "GENEPIO:0100785", "alias": "dissolved_oxygen_measurement_method", "owner": "HPAI", @@ -19882,7 +20709,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 136, + "rank": 135, "slot_uri": "GENEPIO:0100917", "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "HPAI", @@ -19907,7 +20734,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 137, + "rank": 136, "slot_uri": "GENEPIO:0100786", "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "HPAI", @@ -19939,7 +20766,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 138, + "rank": 137, "slot_uri": "GENEPIO:0100787", "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "HPAI", @@ -19964,7 +20791,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 139, + "rank": 138, "slot_uri": "GENEPIO:0100788", "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "HPAI", @@ -19989,7 +20816,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 140, + "rank": 139, "slot_uri": "GENEPIO:0100789", "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "HPAI", @@ -20021,7 +20848,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 141, + "rank": 140, "slot_uri": "GENEPIO:0100790", "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "HPAI", @@ -20046,7 +20873,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 142, + "rank": 141, "slot_uri": "GENEPIO:0100791", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "HPAI", @@ -20071,7 +20898,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 143, + "rank": 142, "slot_uri": "GENEPIO:0100792", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "HPAI", @@ -20103,7 +20930,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 144, + "rank": 143, "slot_uri": "GENEPIO:0100793", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "HPAI", @@ -20128,7 +20955,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 145, + "rank": 144, "slot_uri": "GENEPIO:0100794", "alias": "total_suspended_solids_tss_measurement_value", "owner": "HPAI", @@ -20153,7 +20980,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 146, + "rank": 145, "slot_uri": "GENEPIO:0100795", "alias": "total_suspended_solids_tss_measurement_unit", "owner": "HPAI", @@ -20185,7 +21012,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 147, + "rank": 146, "slot_uri": "GENEPIO:0100796", "alias": "total_suspended_solids_tss_measurement_method", "owner": "HPAI", @@ -20210,7 +21037,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 148, + "rank": 147, "slot_uri": "GENEPIO:0100797", "alias": "total_dissolved_solids_tds_measurement_value", "owner": "HPAI", @@ -20235,7 +21062,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 149, + "rank": 148, "slot_uri": "GENEPIO:0100798", "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "HPAI", @@ -20267,7 +21094,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 150, + "rank": 149, "slot_uri": "GENEPIO:0100799", "alias": "total_dissolved_solids_tds_measurement_method", "owner": "HPAI", @@ -20292,7 +21119,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 151, + "rank": 150, "slot_uri": "GENEPIO:0100800", "alias": "total_solids_ts_measurement_value", "owner": "HPAI", @@ -20317,7 +21144,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 152, + "rank": 151, "slot_uri": "GENEPIO:0100801", "alias": "total_solids_ts_measurement_unit", "owner": "HPAI", @@ -20349,7 +21176,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 153, + "rank": 152, "slot_uri": "GENEPIO:0100802", "alias": "total_solids_ts_measurement_method", "owner": "HPAI", @@ -20374,7 +21201,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 154, + "rank": 153, "slot_uri": "GENEPIO:0100878", "alias": "alkalinity_measurement_value", "owner": "HPAI", @@ -20399,7 +21226,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 155, + "rank": 154, "slot_uri": "GENEPIO:0100879", "alias": "alkalinity_measurement_unit", "owner": "HPAI", @@ -20431,7 +21258,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 156, + "rank": 155, "slot_uri": "GENEPIO:0100880", "alias": "alkalinity_measurement_method", "owner": "HPAI", @@ -20456,7 +21283,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 157, + "rank": 156, "slot_uri": "GENEPIO:0100916", "alias": "conductivity_measurement_value", "owner": "HPAI", @@ -20481,7 +21308,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 158, + "rank": 157, "slot_uri": "GENEPIO:0100803", "alias": "conductivity_measurement_unit", "owner": "HPAI", @@ -20513,7 +21340,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 159, + "rank": 158, "slot_uri": "GENEPIO:0100804", "alias": "conductivity_measurement_method", "owner": "HPAI", @@ -20538,7 +21365,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 160, + "rank": 159, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", "owner": "HPAI", @@ -20563,7 +21390,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 161, + "rank": 160, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", "owner": "HPAI", @@ -20595,7 +21422,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 162, + "rank": 161, "slot_uri": "GENEPIO:0100807", "alias": "salinity_measurement_method", "owner": "HPAI", @@ -20620,7 +21447,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 163, + "rank": 162, "slot_uri": "GENEPIO:0100808", "alias": "total_nitrogen_tn_measurement_value", "owner": "HPAI", @@ -20645,7 +21472,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 164, + "rank": 163, "slot_uri": "GENEPIO:0100809", "alias": "total_nitrogen_tn_measurement_unit", "owner": "HPAI", @@ -20677,7 +21504,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 165, + "rank": 164, "slot_uri": "GENEPIO:0100810", "alias": "total_nitrogen_tn_measurement_method", "owner": "HPAI", @@ -20702,7 +21529,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 166, + "rank": 165, "slot_uri": "GENEPIO:0100811", "alias": "total_phosphorus_tp_measurement_value", "owner": "HPAI", @@ -20727,7 +21554,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 167, + "rank": 166, "slot_uri": "GENEPIO:0100812", "alias": "total_phosphorus_tp_measurement_unit", "owner": "HPAI", @@ -20739,7 +21566,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -20759,7 +21586,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 168, + "rank": 167, "slot_uri": "GENEPIO:0100813", "alias": "total_phosphorus_tp_measurement_method", "owner": "HPAI", @@ -20784,7 +21611,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 169, + "rank": 168, "slot_uri": "GENEPIO:0100814", "alias": "fecal_contamination_indicator_", "owner": "HPAI", @@ -20817,7 +21644,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 170, + "rank": 169, "slot_uri": "GENEPIO:0100815", "alias": "fecal_contamination_value", "owner": "HPAI", @@ -20843,7 +21670,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 171, + "rank": 170, "slot_uri": "GENEPIO:0100816", "alias": "fecal_contamination_unit", "owner": "HPAI", @@ -20876,7 +21703,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 172, + "rank": 171, "slot_uri": "GENEPIO:0100817", "alias": "fecal_contamination_method", "owner": "HPAI", @@ -20901,7 +21728,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 173, + "rank": 172, "slot_uri": "GENEPIO:0100818", "alias": "fecal_coliform_count_value", "owner": "HPAI", @@ -20926,7 +21753,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 174, + "rank": 173, "slot_uri": "GENEPIO:0100819", "alias": "fecal_coliform_count_unit", "owner": "HPAI", @@ -20958,7 +21785,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 175, + "rank": 174, "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "HPAI", @@ -20983,7 +21810,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 176, + "rank": 175, "slot_uri": "GENEPIO:0100837", "alias": "urinary_contamination_indicator", "owner": "HPAI", @@ -21015,7 +21842,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 177, + "rank": 176, "slot_uri": "GENEPIO:0100838", "alias": "urinary_contamination_value", "owner": "HPAI", @@ -21040,7 +21867,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 178, + "rank": 177, "slot_uri": "GENEPIO:0100839", "alias": "urinary_contamination_unit", "owner": "HPAI", @@ -21072,7 +21899,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 179, + "rank": 178, "slot_uri": "GENEPIO:0100840", "alias": "urinary_contamination_method", "owner": "HPAI", @@ -21097,7 +21924,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 180, + "rank": 179, "slot_uri": "GENEPIO:0100821", "alias": "sample_temperature_value_at_collection", "owner": "HPAI", @@ -21122,7 +21949,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 181, + "rank": 180, "slot_uri": "GENEPIO:0100822", "alias": "sample_temperature_unit_at_collection", "owner": "HPAI", @@ -21154,7 +21981,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 182, + "rank": 181, "slot_uri": "GENEPIO:0100823", "alias": "sample_temperature_value_when_received", "owner": "HPAI", @@ -21179,7 +22006,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 183, + "rank": 182, "slot_uri": "GENEPIO:0100824", "alias": "sample_temperature_unit_when_received", "owner": "HPAI", @@ -21211,7 +22038,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 184, + "rank": 183, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "HPAI", @@ -21238,7 +22065,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 185, + "rank": 184, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "HPAI", @@ -21268,7 +22095,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 186, + "rank": 185, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "HPAI", @@ -21295,7 +22122,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 187, + "rank": 186, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing__", "owner": "HPAI", @@ -21331,7 +22158,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 188, + "rank": 187, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "HPAI", @@ -21362,7 +22189,7 @@ "GISAID:sequenced_by", "BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 189, + "rank": 188, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "HPAI", @@ -21397,7 +22224,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 190, + "rank": 189, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "HPAI", @@ -21424,7 +22251,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 191, + "rank": 190, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "HPAI", @@ -21459,7 +22286,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 192, + "rank": 191, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "HPAI", @@ -21494,7 +22321,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 193, + "rank": 192, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "HPAI", @@ -21529,7 +22356,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 194, + "rank": 193, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "HPAI", @@ -21565,7 +22392,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 195, + "rank": 194, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "HPAI", @@ -21576,7 +22403,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -21592,7 +22419,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 196, + "rank": 195, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "HPAI", @@ -21603,7 +22430,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -21614,7 +22441,7 @@ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/hpai", - "rank": 197, + "rank": 196, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", "owner": "HPAI", @@ -21625,7 +22452,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -21642,7 +22469,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 198, + "rank": 197, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "HPAI", @@ -21669,7 +22496,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 199, + "rank": 198, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "HPAI", @@ -21703,7 +22530,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 200, + "rank": 199, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "HPAI", @@ -21737,7 +22564,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 201, + "rank": 200, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "HPAI", @@ -21764,7 +22591,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 202, + "rank": 201, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "HPAI", @@ -21791,7 +22618,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 203, + "rank": 202, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "HPAI", @@ -21818,7 +22645,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 204, + "rank": 203, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "HPAI", @@ -21845,7 +22672,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 205, + "rank": 204, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "HPAI", @@ -21872,7 +22699,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 206, + "rank": 205, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "HPAI", @@ -21899,7 +22726,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 207, + "rank": 206, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "HPAI", @@ -21926,7 +22753,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 208, + "rank": 207, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "HPAI", @@ -21953,7 +22780,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 209, + "rank": 208, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "HPAI", @@ -21980,7 +22807,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 210, + "rank": 209, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "HPAI", @@ -22007,7 +22834,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 211, + "rank": 210, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "HPAI", @@ -22034,7 +22861,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 212, + "rank": 211, "slot_uri": "GENEPIO:0101715", "alias": "genome_sequence_file_name", "owner": "HPAI", @@ -22061,7 +22888,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 213, + "rank": 212, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "HPAI", @@ -22088,7 +22915,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 214, + "rank": 213, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "HPAI", @@ -22115,7 +22942,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 215, + "rank": 214, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "HPAI", @@ -22142,7 +22969,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 216, + "rank": 215, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "HPAI", @@ -22177,7 +23004,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 217, + "rank": 216, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "HPAI", @@ -22212,7 +23039,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 218, + "rank": 217, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "HPAI", @@ -22239,7 +23066,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 219, + "rank": 218, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "HPAI", @@ -22274,7 +23101,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 220, + "rank": 219, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "HPAI", @@ -22309,7 +23136,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 221, + "rank": 220, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "HPAI", @@ -22343,7 +23170,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 222, + "rank": 221, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "HPAI", @@ -22377,7 +23204,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 223, + "rank": 222, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "HPAI", @@ -22411,7 +23238,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 224, + "rank": 223, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "HPAI", @@ -22445,7 +23272,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 225, + "rank": 224, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "HPAI", @@ -22472,7 +23299,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 226, + "rank": 225, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "HPAI", @@ -22499,7 +23326,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 227, + "rank": 226, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "HPAI", @@ -22526,7 +23353,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 228, + "rank": 227, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "HPAI", @@ -22553,7 +23380,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 229, + "rank": 228, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "HPAI", @@ -22580,7 +23407,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 230, + "rank": 229, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "HPAI", @@ -22607,7 +23434,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 231, + "rank": 230, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "HPAI", @@ -22634,7 +23461,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 232, + "rank": 231, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "HPAI", @@ -22661,7 +23488,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 233, + "rank": 232, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "HPAI", @@ -22688,7 +23515,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 234, + "rank": 233, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "HPAI", @@ -22715,7 +23542,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 235, + "rank": 234, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "HPAI", @@ -22742,7 +23569,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 236, + "rank": 235, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "HPAI", @@ -22769,7 +23596,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 237, + "rank": 236, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "HPAI", @@ -22796,7 +23623,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 238, + "rank": 237, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "HPAI", @@ -22823,7 +23650,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 239, + "rank": 238, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "HPAI", @@ -22850,7 +23677,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 240, + "rank": 239, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "HPAI", @@ -22877,7 +23704,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 241, + "rank": 240, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "HPAI", @@ -22904,7 +23731,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 242, + "rank": 241, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "HPAI", @@ -22931,7 +23758,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 243, + "rank": 242, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "HPAI", @@ -22958,7 +23785,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 244, + "rank": 243, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "HPAI", @@ -22985,7 +23812,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 245, + "rank": 244, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "HPAI", @@ -23012,7 +23839,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 246, + "rank": 245, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "HPAI", @@ -23039,7 +23866,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 247, + "rank": 246, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "HPAI", @@ -23066,7 +23893,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 248, + "rank": 247, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "HPAI", @@ -23093,7 +23920,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 249, + "rank": 248, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "HPAI", @@ -23120,7 +23947,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 250, + "rank": 249, "slot_uri": "GENEPIO:0101116", "alias": "genetic_target_name", "owner": "HPAI", @@ -23146,7 +23973,7 @@ "description": "The specific region or segment of a genetic sequence used for testing or analysis.", "title": "genetic target region", "from_schema": "https://example.com/hpai", - "rank": 251, + "rank": 250, "slot_uri": "GENEPIO:0101117", "alias": "genetic_target_region", "owner": "HPAI", @@ -23165,7 +23992,7 @@ "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", "title": "genetic target region reference genome", "from_schema": "https://example.com/hpai", - "rank": 252, + "rank": 251, "slot_uri": "GENEPIO:0101118", "alias": "genetic_target_region_reference_genome", "owner": "HPAI", @@ -23192,7 +24019,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 253, + "rank": 252, "slot_uri": "GENEPIO:0100962", "alias": "diagnostic_target_presence", "owner": "HPAI", @@ -23226,7 +24053,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 254, + "rank": 253, "slot_uri": "GENEPIO:0100963", "alias": "diagnostic_measurement_value", "owner": "HPAI", @@ -23253,7 +24080,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 255, + "rank": 254, "slot_uri": "GENEPIO:0100964", "alias": "diagnostic_measurement_unit", "owner": "HPAI", @@ -23287,7 +24114,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 256, + "rank": 255, "slot_uri": "GENEPIO:0100965", "alias": "diagnostic_measurement_method", "owner": "HPAI", @@ -23313,7 +24140,7 @@ "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold value", "from_schema": "https://example.com/hpai", - "rank": 257, + "rank": 256, "slot_uri": "GENEPIO:0101104", "alias": "diagnostic_testing_threshold_value", "owner": "HPAI", @@ -23332,7 +24159,7 @@ "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold units", "from_schema": "https://example.com/hpai", - "rank": 258, + "rank": 257, "slot_uri": "GENEPIO:0101105", "alias": "diagnostic_testing_threshold_units", "owner": "HPAI", @@ -23351,7 +24178,7 @@ "description": "Describe any details of the diagnsotic testing.", "title": "diagnostic testing details", "from_schema": "https://example.com/hpai", - "rank": 259, + "rank": 258, "slot_uri": "GENEPIO:0101106", "alias": "diagnostic_testing_details", "owner": "HPAI", @@ -23378,7 +24205,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 260, + "rank": 259, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "HPAI", @@ -23406,7 +24233,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 261, + "rank": 260, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "HPAI", @@ -23434,7 +24261,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 262, + "rank": 261, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "HPAI", @@ -23449,7 +24276,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -23469,7 +24296,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 263, + "rank": 262, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "HPAI", @@ -23505,7 +24332,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 264, + "rank": 263, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "HPAI", @@ -23872,17 +24699,17 @@ "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", "rank": 68, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", "rank": 69, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", "rank": 70, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", @@ -24891,7 +25718,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -26334,7 +27161,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -26361,7 +27188,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -26383,7 +27210,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -28207,7 +29034,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -28612,789 +29439,784 @@ "rank": 64, "slot_group": "Environmental conditions and measurements" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "rank": 65, - "slot_group": "Environmental conditions and measurements" - }, "water_depth": { "name": "water_depth", - "rank": 66, + "rank": 65, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 67, + "rank": 66, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 68, + "rank": 67, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 69, + "rank": 68, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 70, + "rank": 69, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 71, + "rank": 70, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 72, + "rank": 71, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 73, + "rank": 72, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 74, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 73, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", - "rank": 75, + "rank": 74, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", - "rank": 76, + "rank": 75, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_value": { "name": "ambient_temperature_measurement_value", - "rank": 77, + "rank": 76, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_unit": { "name": "ambient_temperature_measurement_unit", - "rank": 78, + "rank": 77, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_value": { "name": "ph_measurement_value", - "rank": 79, + "rank": 78, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_method": { "name": "ph_measurement_method", - "rank": 80, + "rank": 79, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_value": { "name": "total_daily_flow_rate_measurement_value", - "rank": 81, + "rank": 80, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_unit": { "name": "total_daily_flow_rate_measurement_unit", - "rank": 82, + "rank": 81, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_method": { "name": "total_daily_flow_rate_measurement_method", - "rank": 83, + "rank": 82, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_value": { "name": "instantaneous_flow_rate_measurement_value", - "rank": 84, + "rank": 83, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_unit": { "name": "instantaneous_flow_rate_measurement_unit", - "rank": 85, + "rank": 84, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_method": { "name": "instantaneous_flow_rate_measurement_method", - "rank": 86, + "rank": 85, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_value": { "name": "turbidity_measurement_value", - "rank": 87, + "rank": 86, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_unit": { "name": "turbidity_measurement_unit", - "rank": 88, + "rank": 87, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_method": { "name": "turbidity_measurement_method", - "rank": 89, + "rank": 88, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_value": { "name": "dissolved_oxygen_measurement_value", - "rank": 90, + "rank": 89, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_unit": { "name": "dissolved_oxygen_measurement_unit", - "rank": 91, + "rank": 90, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_method": { "name": "dissolved_oxygen_measurement_method", - "rank": 92, + "rank": 91, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_value": { "name": "oxygen_reduction_potential_orp_measurement_value", - "rank": 93, + "rank": 92, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_unit": { "name": "oxygen_reduction_potential_orp_measurement_unit", - "rank": 94, + "rank": 93, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_method": { "name": "oxygen_reduction_potential_orp_measurement_method", - "rank": 95, + "rank": 94, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_value": { "name": "chemical_oxygen_demand_cod_measurement_value", - "rank": 96, + "rank": 95, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_unit": { "name": "chemical_oxygen_demand_cod_measurement_unit", - "rank": 97, + "rank": 96, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_method": { "name": "chemical_oxygen_demand_cod_measurement_method", - "rank": 98, + "rank": 97, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", - "rank": 99, + "rank": 98, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", - "rank": 100, + "rank": 99, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", - "rank": 101, + "rank": 100, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_value": { "name": "total_suspended_solids_tss_measurement_value", - "rank": 102, + "rank": 101, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_unit": { "name": "total_suspended_solids_tss_measurement_unit", - "rank": 103, + "rank": 102, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_method": { "name": "total_suspended_solids_tss_measurement_method", - "rank": 104, + "rank": 103, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_value": { "name": "total_dissolved_solids_tds_measurement_value", - "rank": 105, + "rank": 104, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_unit": { "name": "total_dissolved_solids_tds_measurement_unit", - "rank": 106, + "rank": 105, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_method": { "name": "total_dissolved_solids_tds_measurement_method", - "rank": 107, + "rank": 106, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_value": { "name": "total_solids_ts_measurement_value", - "rank": 108, + "rank": 107, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_unit": { "name": "total_solids_ts_measurement_unit", - "rank": 109, + "rank": 108, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_method": { "name": "total_solids_ts_measurement_method", - "rank": 110, + "rank": 109, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_value": { "name": "alkalinity_measurement_value", - "rank": 111, + "rank": 110, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_unit": { "name": "alkalinity_measurement_unit", - "rank": 112, + "rank": 111, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_method": { "name": "alkalinity_measurement_method", - "rank": 113, + "rank": 112, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_value": { "name": "conductivity_measurement_value", - "rank": 114, + "rank": 113, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_unit": { "name": "conductivity_measurement_unit", - "rank": 115, + "rank": 114, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_method": { "name": "conductivity_measurement_method", - "rank": 116, + "rank": 115, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_value": { "name": "salinity_measurement_value", - "rank": 117, + "rank": 116, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_unit": { "name": "salinity_measurement_unit", - "rank": 118, + "rank": 117, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_method": { "name": "salinity_measurement_method", - "rank": 119, + "rank": 118, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_value": { "name": "total_nitrogen_tn_measurement_value", - 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"rank": 190, + "rank": 189, "slot_group": "Bioinformatics and QC metrics" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", - "rank": 191, + "rank": 190, "slot_group": "Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", - "rank": 192, + "rank": 191, "slot_group": "Bioinformatics and QC metrics" }, "n50": { "name": "n50", - "rank": 193, + "rank": 192, "slot_group": "Bioinformatics and QC metrics" }, "percent_read_contamination_": { "name": "percent_read_contamination_", - "rank": 194, + "rank": 193, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_length": { "name": "sequence_assembly_length", - "rank": 195, + "rank": 194, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 196, + "rank": 195, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 197, + "rank": 196, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 198, + "rank": 197, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 199, + "rank": 198, "slot_group": "Bioinformatics and QC metrics" }, "read_mapping_software_name": { "name": "read_mapping_software_name", - "rank": 200, + "rank": 199, "slot_group": "Taxonomic identification information" }, "read_mapping_software_version": { "name": "read_mapping_software_version", - "rank": 201, + "rank": 200, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_name": { "name": "taxonomic_reference_database_name", - "rank": 202, + "rank": 201, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_version": { "name": "taxonomic_reference_database_version", - "rank": 203, + "rank": 202, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_report_filename": { "name": "taxonomic_analysis_report_filename", - "rank": 204, + "rank": 203, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_date": { "name": "taxonomic_analysis_date", - "rank": 205, + "rank": 204, "slot_group": "Taxonomic identification information" }, "read_mapping_criteria": { "name": "read_mapping_criteria", - "rank": 206, + "rank": 205, "slot_group": "Taxonomic identification information" }, "genetic_target_name": { "name": "genetic_target_name", - "rank": 207, + "rank": 206, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region": { "name": "genetic_target_region", - "rank": 208, + "rank": 207, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region_reference_genome": { "name": "genetic_target_region_reference_genome", - "rank": 209, + "rank": 208, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_target_presence": { "name": "diagnostic_target_presence", - "rank": 210, + "rank": 209, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_value": { "name": "diagnostic_measurement_value", - "rank": 211, + "rank": 210, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_unit": { "name": "diagnostic_measurement_unit", - "rank": 212, + "rank": 211, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_method": { "name": "diagnostic_measurement_method", - "rank": 213, + "rank": 212, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_value": { "name": "diagnostic_testing_threshold_value", - "rank": 214, + "rank": 213, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_units": { "name": "diagnostic_testing_threshold_units", - "rank": 215, + "rank": 214, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_details": { "name": "diagnostic_testing_details", - "rank": 216, + "rank": 215, "slot_group": "Pathogen diagnostic testing" }, "prevalence_metrics": { "name": "prevalence_metrics", - "rank": 217, + "rank": 216, "slot_group": "Risk assessment information" }, "prevalence_metrics_details": { "name": "prevalence_metrics_details", - "rank": 218, + "rank": 217, "slot_group": "Risk assessment information" }, "stage_of_production": { "name": "stage_of_production", - "rank": 219, + "rank": 218, "slot_group": "Risk assessment information" }, "experimental_intervention": { "name": "experimental_intervention", - "rank": 220, + "rank": 219, "slot_group": "Risk assessment information" }, "experiment_intervention_details": { "name": "experiment_intervention_details", - "rank": 221, + "rank": 220, "slot_group": "Risk assessment information" } }, @@ -30069,7 +30891,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -31294,7 +32116,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -31367,39 +32189,6 @@ } ] }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", - "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." - ], - "examples": [ - { - "value": "12" - } - ], - "from_schema": "https://example.com/hpai", - "rank": 65, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", - "owner": "HPAIWW", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "slot_group": "Environmental conditions and measurements", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "water_depth": { "name": "water_depth", "description": "The depth of some water.", @@ -31413,7 +32202,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 66, + "rank": 65, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "HPAIWW", @@ -31438,7 +32227,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 67, + "rank": 66, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "HPAIWW", @@ -31470,7 +32259,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 68, + "rank": 67, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "HPAIWW", @@ -31495,7 +32284,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 69, + "rank": 68, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "HPAIWW", @@ -31527,7 +32316,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 70, + "rank": 69, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "HPAIWW", @@ -31552,7 +32341,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 71, + "rank": 70, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "HPAIWW", @@ -31584,7 +32373,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 72, + "rank": 71, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "HPAIWW", @@ -31609,7 +32398,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 73, + "rank": 72, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "HPAIWW", @@ -31628,22 +32417,22 @@ } ] }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "12" } ], "from_schema": "https://example.com/hpai", - "rank": 74, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 73, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "HPAIWW", "domain_of": [ "HPAI", @@ -31651,10 +32440,10 @@ "HPAIEnviro" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "recommended": true, "any_of": [ { - "range": "WeatherTypeMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -31674,7 +32463,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 75, + "rank": 74, "slot_uri": "GENEPIO:0100912", "alias": "precipitation_measurement_unit", "owner": "HPAIWW", @@ -31707,7 +32496,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 76, + "rank": 75, "slot_uri": "GENEPIO:0100913", "alias": "precipitation_measurement_method", "owner": "HPAIWW", @@ -31732,7 +32521,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 77, + "rank": 76, "slot_uri": "GENEPIO:0100935", "alias": "ambient_temperature_measurement_value", "owner": "HPAIWW", @@ -31757,7 +32546,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 78, + "rank": 77, "slot_uri": "GENEPIO:0100936", "alias": "ambient_temperature_measurement_unit", "owner": "HPAIWW", @@ -31789,7 +32578,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 79, + "rank": 78, "slot_uri": "GENEPIO:0001736", "alias": "ph_measurement_value", "owner": "HPAIWW", @@ -31814,7 +32603,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 80, + "rank": 79, "slot_uri": "GENEPIO:0100781", "alias": "ph_measurement_method", "owner": "HPAIWW", @@ -31839,7 +32628,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 81, + "rank": 80, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", "owner": "HPAIWW", @@ -31864,7 +32653,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 82, + "rank": 81, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", "owner": "HPAIWW", @@ -31896,7 +32685,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 83, + "rank": 82, "slot_uri": "GENEPIO:0100907", "alias": "total_daily_flow_rate_measurement_method", "owner": "HPAIWW", @@ -31921,7 +32710,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 84, + "rank": 83, "slot_uri": "GENEPIO:0100908", "alias": "instantaneous_flow_rate_measurement_value", "owner": "HPAIWW", @@ -31946,7 +32735,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 85, + "rank": 84, "slot_uri": "GENEPIO:0100909", "alias": "instantaneous_flow_rate_measurement_unit", "owner": "HPAIWW", @@ -31978,7 +32767,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 86, + "rank": 85, "slot_uri": "GENEPIO:0100910", "alias": "instantaneous_flow_rate_measurement_method", "owner": "HPAIWW", @@ -32003,7 +32792,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 87, + "rank": 86, "slot_uri": "GENEPIO:0100783", "alias": "turbidity_measurement_value", "owner": "HPAIWW", @@ -32029,7 +32818,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 88, + "rank": 87, "slot_uri": "GENEPIO:0100914", "alias": "turbidity_measurement_unit", "owner": "HPAIWW", @@ -32062,7 +32851,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 89, + "rank": 88, "slot_uri": "GENEPIO:0101013", "alias": "turbidity_measurement_method", "owner": "HPAIWW", @@ -32087,7 +32876,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 90, + "rank": 89, "slot_uri": "GENEPIO:0100915", "alias": "dissolved_oxygen_measurement_value", "owner": "HPAIWW", @@ -32112,7 +32901,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 91, + "rank": 90, "slot_uri": "GENEPIO:0100784", "alias": "dissolved_oxygen_measurement_unit", "owner": "HPAIWW", @@ -32144,7 +32933,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 92, + "rank": 91, "slot_uri": "GENEPIO:0100785", "alias": "dissolved_oxygen_measurement_method", "owner": "HPAIWW", @@ -32169,7 +32958,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 93, + "rank": 92, "slot_uri": "GENEPIO:0100917", "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "HPAIWW", @@ -32194,7 +32983,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 94, + "rank": 93, "slot_uri": "GENEPIO:0100786", "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "HPAIWW", @@ -32226,7 +33015,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 95, + "rank": 94, "slot_uri": "GENEPIO:0100787", "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "HPAIWW", @@ -32251,7 +33040,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 96, + "rank": 95, "slot_uri": "GENEPIO:0100788", "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "HPAIWW", @@ -32276,7 +33065,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 97, + "rank": 96, "slot_uri": "GENEPIO:0100789", "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "HPAIWW", @@ -32308,7 +33097,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 98, + "rank": 97, "slot_uri": "GENEPIO:0100790", "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "HPAIWW", @@ -32333,7 +33122,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 99, + "rank": 98, "slot_uri": "GENEPIO:0100791", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "HPAIWW", @@ -32358,7 +33147,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 100, + "rank": 99, "slot_uri": "GENEPIO:0100792", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "HPAIWW", @@ -32390,7 +33179,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 101, + "rank": 100, "slot_uri": "GENEPIO:0100793", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "HPAIWW", @@ -32415,7 +33204,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 102, + "rank": 101, "slot_uri": "GENEPIO:0100794", "alias": "total_suspended_solids_tss_measurement_value", "owner": "HPAIWW", @@ -32440,7 +33229,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 103, + "rank": 102, "slot_uri": "GENEPIO:0100795", "alias": "total_suspended_solids_tss_measurement_unit", "owner": "HPAIWW", @@ -32472,7 +33261,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 104, + "rank": 103, "slot_uri": "GENEPIO:0100796", "alias": "total_suspended_solids_tss_measurement_method", "owner": "HPAIWW", @@ -32497,7 +33286,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 105, + "rank": 104, "slot_uri": "GENEPIO:0100797", "alias": "total_dissolved_solids_tds_measurement_value", "owner": "HPAIWW", @@ -32522,7 +33311,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 106, + "rank": 105, "slot_uri": "GENEPIO:0100798", "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "HPAIWW", @@ -32554,7 +33343,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 107, + "rank": 106, "slot_uri": "GENEPIO:0100799", "alias": "total_dissolved_solids_tds_measurement_method", "owner": "HPAIWW", @@ -32579,7 +33368,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 108, + "rank": 107, "slot_uri": "GENEPIO:0100800", "alias": "total_solids_ts_measurement_value", "owner": "HPAIWW", @@ -32604,7 +33393,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 109, + "rank": 108, "slot_uri": "GENEPIO:0100801", "alias": "total_solids_ts_measurement_unit", "owner": "HPAIWW", @@ -32636,7 +33425,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 110, + "rank": 109, "slot_uri": "GENEPIO:0100802", "alias": "total_solids_ts_measurement_method", "owner": "HPAIWW", @@ -32661,7 +33450,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 111, + "rank": 110, "slot_uri": "GENEPIO:0100878", "alias": "alkalinity_measurement_value", "owner": "HPAIWW", @@ -32686,7 +33475,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 112, + "rank": 111, "slot_uri": "GENEPIO:0100879", "alias": "alkalinity_measurement_unit", "owner": "HPAIWW", @@ -32718,7 +33507,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 113, + "rank": 112, "slot_uri": "GENEPIO:0100880", "alias": "alkalinity_measurement_method", "owner": "HPAIWW", @@ -32743,7 +33532,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 114, + "rank": 113, "slot_uri": "GENEPIO:0100916", "alias": "conductivity_measurement_value", "owner": "HPAIWW", @@ -32768,7 +33557,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 115, + "rank": 114, "slot_uri": "GENEPIO:0100803", "alias": "conductivity_measurement_unit", "owner": "HPAIWW", @@ -32800,7 +33589,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 116, + "rank": 115, "slot_uri": "GENEPIO:0100804", "alias": "conductivity_measurement_method", "owner": "HPAIWW", @@ -32825,7 +33614,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 117, + "rank": 116, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", "owner": "HPAIWW", @@ -32850,7 +33639,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 118, + "rank": 117, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", "owner": "HPAIWW", @@ -32882,7 +33671,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 119, + "rank": 118, "slot_uri": "GENEPIO:0100807", "alias": "salinity_measurement_method", "owner": "HPAIWW", @@ -32907,7 +33696,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 120, + "rank": 119, "slot_uri": "GENEPIO:0100808", "alias": "total_nitrogen_tn_measurement_value", "owner": "HPAIWW", @@ -32932,7 +33721,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 121, + "rank": 120, "slot_uri": "GENEPIO:0100809", "alias": "total_nitrogen_tn_measurement_unit", "owner": "HPAIWW", @@ -32964,7 +33753,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 122, + "rank": 121, "slot_uri": "GENEPIO:0100810", "alias": "total_nitrogen_tn_measurement_method", "owner": "HPAIWW", @@ -32989,7 +33778,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 123, + "rank": 122, "slot_uri": "GENEPIO:0100811", "alias": "total_phosphorus_tp_measurement_value", "owner": "HPAIWW", @@ -33014,7 +33803,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 124, + "rank": 123, "slot_uri": "GENEPIO:0100812", "alias": "total_phosphorus_tp_measurement_unit", "owner": "HPAIWW", @@ -33026,7 +33815,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -33046,7 +33835,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 125, + "rank": 124, "slot_uri": "GENEPIO:0100813", "alias": "total_phosphorus_tp_measurement_method", "owner": "HPAIWW", @@ -33071,7 +33860,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 126, + "rank": 125, "slot_uri": "GENEPIO:0100814", "alias": "fecal_contamination_indicator_", "owner": "HPAIWW", @@ -33104,7 +33893,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 127, + "rank": 126, "slot_uri": "GENEPIO:0100815", "alias": "fecal_contamination_value", "owner": "HPAIWW", @@ -33130,7 +33919,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 128, + "rank": 127, "slot_uri": "GENEPIO:0100816", "alias": "fecal_contamination_unit", "owner": "HPAIWW", @@ -33163,7 +33952,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 129, + "rank": 128, "slot_uri": "GENEPIO:0100817", "alias": "fecal_contamination_method", "owner": "HPAIWW", @@ -33188,7 +33977,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 130, + "rank": 129, "slot_uri": "GENEPIO:0100818", "alias": "fecal_coliform_count_value", "owner": "HPAIWW", @@ -33213,7 +34002,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 131, + "rank": 130, "slot_uri": "GENEPIO:0100819", "alias": "fecal_coliform_count_unit", "owner": "HPAIWW", @@ -33245,7 +34034,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 132, + "rank": 131, "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "HPAIWW", @@ -33270,7 +34059,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 133, + "rank": 132, "slot_uri": "GENEPIO:0100837", "alias": "urinary_contamination_indicator", "owner": "HPAIWW", @@ -33302,7 +34091,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 134, + "rank": 133, "slot_uri": "GENEPIO:0100838", "alias": "urinary_contamination_value", "owner": "HPAIWW", @@ -33327,7 +34116,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 135, + "rank": 134, "slot_uri": "GENEPIO:0100839", "alias": "urinary_contamination_unit", "owner": "HPAIWW", @@ -33359,7 +34148,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 136, + "rank": 135, "slot_uri": "GENEPIO:0100840", "alias": "urinary_contamination_method", "owner": "HPAIWW", @@ -33384,7 +34173,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 137, + "rank": 136, "slot_uri": "GENEPIO:0100821", "alias": "sample_temperature_value_at_collection", "owner": "HPAIWW", @@ -33409,7 +34198,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 138, + "rank": 137, "slot_uri": "GENEPIO:0100822", "alias": "sample_temperature_unit_at_collection", "owner": "HPAIWW", @@ -33441,7 +34230,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 139, + "rank": 138, "slot_uri": "GENEPIO:0100823", "alias": "sample_temperature_value_when_received", "owner": "HPAIWW", @@ -33466,7 +34255,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 140, + "rank": 139, "slot_uri": "GENEPIO:0100824", "alias": "sample_temperature_unit_when_received", "owner": "HPAIWW", @@ -33498,7 +34287,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 141, + "rank": 140, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "HPAIWW", @@ -33525,7 +34314,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 142, + "rank": 141, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "HPAIWW", @@ -33555,7 +34344,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 143, + "rank": 142, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "HPAIWW", @@ -33582,7 +34371,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 144, + "rank": 143, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing__", "owner": "HPAIWW", @@ -33618,7 +34407,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 145, + "rank": 144, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "HPAIWW", @@ -33649,7 +34438,7 @@ "GISAID:sequenced_by", "BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 146, + "rank": 145, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "HPAIWW", @@ -33684,7 +34473,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 147, + "rank": 146, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "HPAIWW", @@ -33711,7 +34500,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 148, + "rank": 147, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "HPAIWW", @@ -33746,7 +34535,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 149, + "rank": 148, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "HPAIWW", @@ -33781,7 +34570,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 150, + "rank": 149, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "HPAIWW", @@ -33816,7 +34605,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 151, + "rank": 150, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "HPAIWW", @@ -33852,7 +34641,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 152, + "rank": 151, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "HPAIWW", @@ -33863,7 +34652,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -33879,7 +34668,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 153, + "rank": 152, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "HPAIWW", @@ -33890,7 +34679,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -33901,7 +34690,7 @@ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/hpai", - "rank": 154, + "rank": 153, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", "owner": "HPAIWW", @@ -33912,7 +34701,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -33929,7 +34718,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 155, + "rank": 154, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "HPAIWW", @@ -33956,7 +34745,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 156, + "rank": 155, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "HPAIWW", @@ -33990,7 +34779,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 157, + "rank": 156, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "HPAIWW", @@ -34024,7 +34813,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 158, + "rank": 157, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "HPAIWW", @@ -34051,7 +34840,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 159, + "rank": 158, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "HPAIWW", @@ -34078,7 +34867,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 160, + "rank": 159, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "HPAIWW", @@ -34105,7 +34894,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 161, + "rank": 160, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "HPAIWW", @@ -34132,7 +34921,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 162, + "rank": 161, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "HPAIWW", @@ -34159,7 +34948,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 163, + "rank": 162, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "HPAIWW", @@ -34186,7 +34975,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 164, + "rank": 163, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "HPAIWW", @@ -34213,7 +35002,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 165, + "rank": 164, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "HPAIWW", @@ -34240,7 +35029,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 166, + "rank": 165, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "HPAIWW", @@ -34267,7 +35056,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 167, + "rank": 166, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "HPAIWW", @@ -34294,7 +35083,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 168, + "rank": 167, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "HPAIWW", @@ -34321,7 +35110,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 169, + "rank": 168, "slot_uri": "GENEPIO:0101715", "alias": "genome_sequence_file_name", "owner": "HPAIWW", @@ -34348,7 +35137,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 170, + "rank": 169, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "HPAIWW", @@ -34375,7 +35164,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 171, + "rank": 170, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "HPAIWW", @@ -34402,7 +35191,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 172, + "rank": 171, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "HPAIWW", @@ -34429,7 +35218,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 173, + "rank": 172, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "HPAIWW", @@ -34464,7 +35253,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 174, + "rank": 173, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "HPAIWW", @@ -34499,7 +35288,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 175, + "rank": 174, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "HPAIWW", @@ -34526,7 +35315,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 176, + "rank": 175, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "HPAIWW", @@ -34561,7 +35350,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 177, + "rank": 176, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "HPAIWW", @@ -34596,7 +35385,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 178, + "rank": 177, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "HPAIWW", @@ -34630,7 +35419,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 179, + "rank": 178, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "HPAIWW", @@ -34664,7 +35453,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 180, + "rank": 179, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "HPAIWW", @@ -34698,7 +35487,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 181, + "rank": 180, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "HPAIWW", @@ -34732,7 +35521,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 182, + "rank": 181, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "HPAIWW", @@ -34759,7 +35548,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 183, + "rank": 182, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "HPAIWW", @@ -34786,7 +35575,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 184, + "rank": 183, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "HPAIWW", @@ -34813,7 +35602,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 185, + "rank": 184, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "HPAIWW", @@ -34840,7 +35629,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 186, + "rank": 185, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "HPAIWW", @@ -34867,7 +35656,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 187, + "rank": 186, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "HPAIWW", @@ -34894,7 +35683,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 188, + "rank": 187, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "HPAIWW", @@ -34921,7 +35710,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 189, + "rank": 188, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "HPAIWW", @@ -34948,7 +35737,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 190, + "rank": 189, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "HPAIWW", @@ -34975,7 +35764,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 191, + "rank": 190, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "HPAIWW", @@ -35002,7 +35791,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 192, + "rank": 191, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "HPAIWW", @@ -35029,7 +35818,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 193, + "rank": 192, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "HPAIWW", @@ -35056,7 +35845,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 194, + "rank": 193, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "HPAIWW", @@ -35083,7 +35872,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 195, + "rank": 194, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "HPAIWW", @@ -35110,7 +35899,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 196, + "rank": 195, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "HPAIWW", @@ -35137,7 +35926,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 197, + "rank": 196, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "HPAIWW", @@ -35164,7 +35953,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 198, + "rank": 197, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "HPAIWW", @@ -35191,7 +35980,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 199, + "rank": 198, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "HPAIWW", @@ -35218,7 +36007,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 200, + "rank": 199, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "HPAIWW", @@ -35245,7 +36034,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 201, + "rank": 200, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "HPAIWW", @@ -35272,7 +36061,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 202, + "rank": 201, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "HPAIWW", @@ -35299,7 +36088,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 203, + "rank": 202, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "HPAIWW", @@ -35326,7 +36115,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 204, + "rank": 203, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "HPAIWW", @@ -35353,7 +36142,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 205, + "rank": 204, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "HPAIWW", @@ -35380,7 +36169,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 206, + "rank": 205, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "HPAIWW", @@ -35407,7 +36196,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 207, + "rank": 206, "slot_uri": "GENEPIO:0101116", "alias": "genetic_target_name", "owner": "HPAIWW", @@ -35433,7 +36222,7 @@ "description": "The specific region or segment of a genetic sequence used for testing or analysis.", "title": "genetic target region", "from_schema": "https://example.com/hpai", - "rank": 208, + "rank": 207, "slot_uri": "GENEPIO:0101117", "alias": "genetic_target_region", "owner": "HPAIWW", @@ -35452,7 +36241,7 @@ "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", "title": "genetic target region reference genome", "from_schema": "https://example.com/hpai", - "rank": 209, + "rank": 208, "slot_uri": "GENEPIO:0101118", "alias": "genetic_target_region_reference_genome", "owner": "HPAIWW", @@ -35479,7 +36268,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 210, + "rank": 209, "slot_uri": "GENEPIO:0100962", "alias": "diagnostic_target_presence", "owner": "HPAIWW", @@ -35513,7 +36302,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 211, + "rank": 210, "slot_uri": "GENEPIO:0100963", "alias": "diagnostic_measurement_value", "owner": "HPAIWW", @@ -35540,7 +36329,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 212, + "rank": 211, "slot_uri": "GENEPIO:0100964", "alias": "diagnostic_measurement_unit", "owner": "HPAIWW", @@ -35574,7 +36363,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 213, + "rank": 212, "slot_uri": "GENEPIO:0100965", "alias": "diagnostic_measurement_method", "owner": "HPAIWW", @@ -35600,7 +36389,7 @@ "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold value", "from_schema": "https://example.com/hpai", - "rank": 214, + "rank": 213, "slot_uri": "GENEPIO:0101104", "alias": "diagnostic_testing_threshold_value", "owner": "HPAIWW", @@ -35619,7 +36408,7 @@ "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold units", "from_schema": "https://example.com/hpai", - "rank": 215, + "rank": 214, "slot_uri": "GENEPIO:0101105", "alias": "diagnostic_testing_threshold_units", "owner": "HPAIWW", @@ -35638,7 +36427,7 @@ "description": "Describe any details of the diagnsotic testing.", "title": "diagnostic testing details", "from_schema": "https://example.com/hpai", - "rank": 216, + "rank": 215, "slot_uri": "GENEPIO:0101106", "alias": "diagnostic_testing_details", "owner": "HPAIWW", @@ -35665,7 +36454,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 217, + "rank": 216, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "HPAIWW", @@ -35693,7 +36482,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 218, + "rank": 217, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "HPAIWW", @@ -35721,7 +36510,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 219, + "rank": 218, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "HPAIWW", @@ -35736,7 +36525,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -35756,7 +36545,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 220, + "rank": 219, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "HPAIWW", @@ -35792,7 +36581,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 221, + "rank": 220, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "HPAIWW", @@ -36141,789 +36930,784 @@ "rank": 64, "slot_group": "Environmental conditions and measurements" }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "rank": 65, - "slot_group": "Environmental conditions and measurements" - }, "water_depth": { "name": "water_depth", - "rank": 66, + "rank": 65, "slot_group": "Environmental conditions and measurements" }, "water_depth_units": { "name": "water_depth_units", - "rank": 67, + "rank": 66, "slot_group": "Environmental conditions and measurements" }, "sediment_depth": { "name": "sediment_depth", - "rank": 68, + "rank": 67, "slot_group": "Environmental conditions and measurements" }, "sediment_depth_units": { "name": "sediment_depth_units", - "rank": 69, + "rank": 68, "slot_group": "Environmental conditions and measurements" }, "air_temperature": { "name": "air_temperature", - "rank": 70, + "rank": 69, "slot_group": "Environmental conditions and measurements" }, "air_temperature_units": { "name": "air_temperature_units", - "rank": 71, + "rank": 70, "slot_group": "Environmental conditions and measurements" }, "water_temperature": { "name": "water_temperature", - "rank": 72, + "rank": 71, "slot_group": "Environmental conditions and measurements" }, "water_temperature_units": { "name": "water_temperature_units", - "rank": 73, + "rank": 72, "slot_group": "Environmental conditions and measurements" }, - "weather_type": { - "name": "weather_type", - "rank": 74, + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "rank": 73, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", - "rank": 75, + "rank": 74, "slot_group": "Environmental conditions and measurements" }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", - "rank": 76, + "rank": 75, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_value": { "name": "ambient_temperature_measurement_value", - "rank": 77, + "rank": 76, "slot_group": "Environmental conditions and measurements" }, "ambient_temperature_measurement_unit": { "name": "ambient_temperature_measurement_unit", - "rank": 78, + "rank": 77, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_value": { "name": "ph_measurement_value", - "rank": 79, + "rank": 78, "slot_group": "Environmental conditions and measurements" }, "ph_measurement_method": { "name": "ph_measurement_method", - "rank": 80, + "rank": 79, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_value": { "name": "total_daily_flow_rate_measurement_value", - "rank": 81, + "rank": 80, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_unit": { "name": "total_daily_flow_rate_measurement_unit", - "rank": 82, + "rank": 81, "slot_group": "Environmental conditions and measurements" }, "total_daily_flow_rate_measurement_method": { "name": "total_daily_flow_rate_measurement_method", - "rank": 83, + "rank": 82, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_value": { "name": "instantaneous_flow_rate_measurement_value", - "rank": 84, + "rank": 83, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_unit": { "name": "instantaneous_flow_rate_measurement_unit", - "rank": 85, + "rank": 84, "slot_group": "Environmental conditions and measurements" }, "instantaneous_flow_rate_measurement_method": { "name": "instantaneous_flow_rate_measurement_method", - "rank": 86, + "rank": 85, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_value": { "name": "turbidity_measurement_value", - "rank": 87, + "rank": 86, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_unit": { "name": "turbidity_measurement_unit", - "rank": 88, + "rank": 87, "slot_group": "Environmental conditions and measurements" }, "turbidity_measurement_method": { "name": "turbidity_measurement_method", - "rank": 89, + "rank": 88, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_value": { "name": "dissolved_oxygen_measurement_value", - "rank": 90, + "rank": 89, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_unit": { "name": "dissolved_oxygen_measurement_unit", - "rank": 91, + "rank": 90, "slot_group": "Environmental conditions and measurements" }, "dissolved_oxygen_measurement_method": { "name": "dissolved_oxygen_measurement_method", - "rank": 92, + "rank": 91, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_value": { "name": "oxygen_reduction_potential_orp_measurement_value", - "rank": 93, + "rank": 92, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_unit": { "name": "oxygen_reduction_potential_orp_measurement_unit", - "rank": 94, + "rank": 93, "slot_group": "Environmental conditions and measurements" }, "oxygen_reduction_potential_orp_measurement_method": { "name": "oxygen_reduction_potential_orp_measurement_method", - "rank": 95, + "rank": 94, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_value": { "name": "chemical_oxygen_demand_cod_measurement_value", - "rank": 96, + "rank": 95, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_unit": { "name": "chemical_oxygen_demand_cod_measurement_unit", - "rank": 97, + "rank": 96, "slot_group": "Environmental conditions and measurements" }, "chemical_oxygen_demand_cod_measurement_method": { "name": "chemical_oxygen_demand_cod_measurement_method", - "rank": 98, + "rank": 97, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", - "rank": 99, + "rank": 98, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", - "rank": 100, + "rank": 99, "slot_group": "Environmental conditions and measurements" }, "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method": { "name": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", - "rank": 101, + "rank": 100, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_value": { "name": "total_suspended_solids_tss_measurement_value", - "rank": 102, + "rank": 101, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_unit": { "name": "total_suspended_solids_tss_measurement_unit", - "rank": 103, + "rank": 102, "slot_group": "Environmental conditions and measurements" }, "total_suspended_solids_tss_measurement_method": { "name": "total_suspended_solids_tss_measurement_method", - "rank": 104, + "rank": 103, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_value": { "name": "total_dissolved_solids_tds_measurement_value", - "rank": 105, + "rank": 104, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_unit": { "name": "total_dissolved_solids_tds_measurement_unit", - "rank": 106, + "rank": 105, "slot_group": "Environmental conditions and measurements" }, "total_dissolved_solids_tds_measurement_method": { "name": "total_dissolved_solids_tds_measurement_method", - "rank": 107, + "rank": 106, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_value": { "name": "total_solids_ts_measurement_value", - "rank": 108, + "rank": 107, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_unit": { "name": "total_solids_ts_measurement_unit", - "rank": 109, + "rank": 108, "slot_group": "Environmental conditions and measurements" }, "total_solids_ts_measurement_method": { "name": "total_solids_ts_measurement_method", - "rank": 110, + "rank": 109, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_value": { "name": "alkalinity_measurement_value", - "rank": 111, + "rank": 110, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_unit": { "name": "alkalinity_measurement_unit", - "rank": 112, + "rank": 111, "slot_group": "Environmental conditions and measurements" }, "alkalinity_measurement_method": { "name": "alkalinity_measurement_method", - "rank": 113, + "rank": 112, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_value": { "name": "conductivity_measurement_value", - "rank": 114, + "rank": 113, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_unit": { "name": "conductivity_measurement_unit", - "rank": 115, + "rank": 114, "slot_group": "Environmental conditions and measurements" }, "conductivity_measurement_method": { "name": "conductivity_measurement_method", - "rank": 116, + "rank": 115, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_value": { "name": "salinity_measurement_value", - "rank": 117, + "rank": 116, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_unit": { "name": "salinity_measurement_unit", - "rank": 118, + "rank": 117, "slot_group": "Environmental conditions and measurements" }, "salinity_measurement_method": { "name": "salinity_measurement_method", - "rank": 119, + "rank": 118, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_value": { "name": "total_nitrogen_tn_measurement_value", - "rank": 120, + "rank": 119, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_unit": { "name": "total_nitrogen_tn_measurement_unit", - "rank": 121, + "rank": 120, "slot_group": "Environmental conditions and measurements" }, "total_nitrogen_tn_measurement_method": { "name": "total_nitrogen_tn_measurement_method", - "rank": 122, + "rank": 121, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_value": { "name": "total_phosphorus_tp_measurement_value", - "rank": 123, + "rank": 122, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_unit": { "name": "total_phosphorus_tp_measurement_unit", - "rank": 124, + "rank": 123, "slot_group": "Environmental conditions and measurements" }, "total_phosphorus_tp_measurement_method": { "name": "total_phosphorus_tp_measurement_method", - "rank": 125, + "rank": 124, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_indicator_": { "name": "fecal_contamination_indicator_", - "rank": 126, + "rank": 125, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_value": { "name": "fecal_contamination_value", - "rank": 127, + "rank": 126, "slot_group": "Environmental conditions and measurements" }, "fecal_contamination_unit": { "name": "fecal_contamination_unit", - 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"rank": 155, + "rank": 154, "slot_group": "Sequence information" }, "sequencing_platform": { "name": "sequencing_platform", - "rank": 156, + "rank": 155, "slot_group": "Sequence information" }, "sequencing_instrument": { "name": "sequencing_instrument", - "rank": 157, + "rank": 156, "slot_group": "Sequence information" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 158, + "rank": 157, "slot_group": "Sequence information" }, "dna_fragment_length": { "name": "dna_fragment_length", - "rank": 159, + "rank": 158, "slot_group": "Sequence information" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 160, + "rank": 159, "slot_group": "Sequence information" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 161, + "rank": 160, "slot_group": "Sequence information" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 162, + "rank": 161, "slot_group": "Sequence information" }, "amplicon_size": { "name": "amplicon_size", - "rank": 163, + "rank": 162, "slot_group": "Sequence information" }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 164, + "rank": 163, "slot_group": "Sequence information" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 165, + "rank": 164, "slot_group": "Sequence information" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 166, + "rank": 165, "slot_group": "Sequence information" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - "rank": 167, + "rank": 166, "slot_group": "Sequence information" }, "fast5_filename": { "name": "fast5_filename", - "rank": 168, + "rank": 167, "slot_group": "Sequence information" }, "genome_sequence_file_name": { "name": "genome_sequence_file_name", - "rank": 169, + "rank": 168, "slot_group": "Sequence information" }, "assembly_filename": { "name": "assembly_filename", - "rank": 170, + "rank": 169, "slot_group": "Sequence information" }, "quality_control_method_name": { "name": "quality_control_method_name", - 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"rank": 178, + "rank": 177, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_software_version": { "name": "sequence_assembly_software_version", - "rank": 179, + "rank": 178, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "name": "consensus_sequence_software_name", - "rank": 180, + "rank": 179, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "name": "consensus_sequence_software_version", - "rank": 181, + "rank": 180, "slot_group": "Bioinformatics and QC metrics" }, "breadth_of_coverage_value": { "name": "breadth_of_coverage_value", - "rank": 182, + "rank": 181, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_value": { "name": "depth_of_coverage_value", - "rank": 183, + "rank": 182, "slot_group": "Bioinformatics and QC metrics" }, "depth_of_coverage_threshold": { "name": "depth_of_coverage_threshold", - "rank": 184, + "rank": 183, "slot_group": "Bioinformatics and QC metrics" }, "genome_completeness": { "name": "genome_completeness", - "rank": 185, + "rank": 184, "slot_group": "Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "name": "number_of_base_pairs_sequenced", - "rank": 186, + "rank": 185, "slot_group": "Bioinformatics and QC metrics" }, "number_of_total_reads": { "name": "number_of_total_reads", - "rank": 187, + "rank": 186, "slot_group": "Bioinformatics and QC metrics" }, "number_of_unique_reads": { "name": "number_of_unique_reads", - "rank": 188, + "rank": 187, "slot_group": "Bioinformatics and QC metrics" }, "minimum_posttrimming_read_length": { "name": "minimum_posttrimming_read_length", - "rank": 189, + "rank": 188, "slot_group": "Bioinformatics and QC metrics" }, "number_of_contigs": { "name": "number_of_contigs", - "rank": 190, + "rank": 189, "slot_group": "Bioinformatics and QC metrics" }, "percent_ns_across_total_genome_length": { "name": "percent_ns_across_total_genome_length", - "rank": 191, + "rank": 190, "slot_group": "Bioinformatics and QC metrics" }, "ns_per_100_kbp": { "name": "ns_per_100_kbp", - "rank": 192, + "rank": 191, "slot_group": "Bioinformatics and QC metrics" }, "n50": { "name": "n50", - "rank": 193, + "rank": 192, "slot_group": "Bioinformatics and QC metrics" }, "percent_read_contamination_": { "name": "percent_read_contamination_", - "rank": 194, + "rank": 193, "slot_group": "Bioinformatics and QC metrics" }, "sequence_assembly_length": { "name": "sequence_assembly_length", - "rank": 195, + "rank": 194, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 196, + "rank": 195, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 197, + "rank": 196, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 198, + "rank": 197, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 199, + "rank": 198, "slot_group": "Bioinformatics and QC metrics" }, "read_mapping_software_name": { "name": "read_mapping_software_name", - "rank": 200, + "rank": 199, "slot_group": "Taxonomic identification information" }, "read_mapping_software_version": { "name": "read_mapping_software_version", - "rank": 201, + "rank": 200, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_name": { "name": "taxonomic_reference_database_name", - "rank": 202, + "rank": 201, "slot_group": "Taxonomic identification information" }, "taxonomic_reference_database_version": { "name": "taxonomic_reference_database_version", - "rank": 203, + "rank": 202, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_report_filename": { "name": "taxonomic_analysis_report_filename", - "rank": 204, + "rank": 203, "slot_group": "Taxonomic identification information" }, "taxonomic_analysis_date": { "name": "taxonomic_analysis_date", - "rank": 205, + "rank": 204, "slot_group": "Taxonomic identification information" }, "read_mapping_criteria": { "name": "read_mapping_criteria", - "rank": 206, + "rank": 205, "slot_group": "Taxonomic identification information" }, "genetic_target_name": { "name": "genetic_target_name", - "rank": 207, + "rank": 206, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region": { "name": "genetic_target_region", - "rank": 208, + "rank": 207, "slot_group": "Pathogen diagnostic testing" }, "genetic_target_region_reference_genome": { "name": "genetic_target_region_reference_genome", - "rank": 209, + "rank": 208, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_target_presence": { "name": "diagnostic_target_presence", - "rank": 210, + "rank": 209, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_value": { "name": "diagnostic_measurement_value", - "rank": 211, + "rank": 210, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_unit": { "name": "diagnostic_measurement_unit", - "rank": 212, + "rank": 211, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_measurement_method": { "name": "diagnostic_measurement_method", - "rank": 213, + "rank": 212, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_value": { "name": "diagnostic_testing_threshold_value", - "rank": 214, + "rank": 213, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_threshold_units": { "name": "diagnostic_testing_threshold_units", - "rank": 215, + "rank": 214, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_testing_details": { "name": "diagnostic_testing_details", - "rank": 216, + "rank": 215, "slot_group": "Pathogen diagnostic testing" }, "prevalence_metrics": { "name": "prevalence_metrics", - "rank": 217, + "rank": 216, "slot_group": "Risk assessment information" }, "prevalence_metrics_details": { "name": "prevalence_metrics_details", - "rank": 218, + "rank": 217, "slot_group": "Risk assessment information" }, "stage_of_production": { "name": "stage_of_production", - "rank": 219, + "rank": 218, "slot_group": "Risk assessment information" }, "experimental_intervention": { "name": "experimental_intervention", - "rank": 220, + "rank": 219, "slot_group": "Risk assessment information" }, "experiment_intervention_details": { "name": "experiment_intervention_details", - "rank": 221, + "rank": 220, "slot_group": "Risk assessment information" } }, @@ -37598,7 +38382,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -38823,7 +39607,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "populated area type menu" + "range": "PopulatedAreaTypeMenu" }, { "range": "NullValueMenu" @@ -38896,39 +39680,6 @@ } ] }, - "precipitation_measurement_value": { - "name": "precipitation_measurement_value", - "description": "The amount of water which has fallen during a precipitation process.", - "title": "precipitation measurement value", - "comments": [ - "Provide the quantity of precipitation in the area leading up to the time of sample collection." - ], - "examples": [ - { - "value": "12" - } - ], - "from_schema": "https://example.com/hpai", - "rank": 65, - "slot_uri": "GENEPIO:0100911", - "alias": "precipitation_measurement_value", - "owner": "HPAIEnviro", - "domain_of": [ - "HPAI", - "HPAIWW", - "HPAIEnviro" - ], - "slot_group": "Environmental conditions and measurements", - "recommended": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "water_depth": { "name": "water_depth", "description": "The depth of some water.", @@ -38942,7 +39693,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 66, + "rank": 65, "slot_uri": "GENEPIO:0100440", "alias": "water_depth", "owner": "HPAIEnviro", @@ -38967,7 +39718,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 67, + "rank": 66, "slot_uri": "GENEPIO:0101025", "alias": "water_depth_units", "owner": "HPAIEnviro", @@ -38999,7 +39750,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 68, + "rank": 67, "slot_uri": "GENEPIO:0100697", "alias": "sediment_depth", "owner": "HPAIEnviro", @@ -39024,7 +39775,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 69, + "rank": 68, "slot_uri": "GENEPIO:0101026", "alias": "sediment_depth_units", "owner": "HPAIEnviro", @@ -39056,7 +39807,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 70, + "rank": 69, "slot_uri": "GENEPIO:0100441", "alias": "air_temperature", "owner": "HPAIEnviro", @@ -39081,7 +39832,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 71, + "rank": 70, "slot_uri": "GENEPIO:0101027", "alias": "air_temperature_units", "owner": "HPAIEnviro", @@ -39113,7 +39864,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 72, + "rank": 71, "slot_uri": "GENEPIO:0100698", "alias": "water_temperature", "owner": "HPAIEnviro", @@ -39138,7 +39889,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 73, + "rank": 72, "slot_uri": "GENEPIO:0101028", "alias": "water_temperature_units", "owner": "HPAIEnviro", @@ -39157,22 +39908,22 @@ } ] }, - "weather_type": { - "name": "weather_type", - "description": "The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc.", - "title": "weather_type", + "precipitation_measurement_value": { + "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", + "title": "precipitation measurement value", "comments": [ - "Provide the weather conditions at the time of sample collection." + "Provide the quantity of precipitation in the area leading up to the time of sample collection." ], "examples": [ { - "value": "Rain [ENVO:01001564]" + "value": "12" } ], "from_schema": "https://example.com/hpai", - "rank": 74, - "slot_uri": "GENEPIO:0100442", - "alias": "weather_type", + "rank": 73, + "slot_uri": "GENEPIO:0100911", + "alias": "precipitation_measurement_value", "owner": "HPAIEnviro", "domain_of": [ "HPAI", @@ -39180,10 +39931,10 @@ "HPAIEnviro" ], "slot_group": "Environmental conditions and measurements", - "multivalued": true, + "recommended": true, "any_of": [ { - "range": "WeatherTypeMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -39203,7 +39954,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 75, + "rank": 74, "slot_uri": "GENEPIO:0100912", "alias": "precipitation_measurement_unit", "owner": "HPAIEnviro", @@ -39236,7 +39987,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 76, + "rank": 75, "slot_uri": "GENEPIO:0100913", "alias": "precipitation_measurement_method", "owner": "HPAIEnviro", @@ -39261,7 +40012,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 77, + "rank": 76, "slot_uri": "GENEPIO:0100935", "alias": "ambient_temperature_measurement_value", "owner": "HPAIEnviro", @@ -39286,7 +40037,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 78, + "rank": 77, "slot_uri": "GENEPIO:0100936", "alias": "ambient_temperature_measurement_unit", "owner": "HPAIEnviro", @@ -39318,7 +40069,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 79, + "rank": 78, "slot_uri": "GENEPIO:0001736", "alias": "ph_measurement_value", "owner": "HPAIEnviro", @@ -39343,7 +40094,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 80, + "rank": 79, "slot_uri": "GENEPIO:0100781", "alias": "ph_measurement_method", "owner": "HPAIEnviro", @@ -39368,7 +40119,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 81, + "rank": 80, "slot_uri": "GENEPIO:0100905", "alias": "total_daily_flow_rate_measurement_value", "owner": "HPAIEnviro", @@ -39393,7 +40144,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 82, + "rank": 81, "slot_uri": "GENEPIO:0100906", "alias": "total_daily_flow_rate_measurement_unit", "owner": "HPAIEnviro", @@ -39425,7 +40176,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 83, + "rank": 82, "slot_uri": "GENEPIO:0100907", "alias": "total_daily_flow_rate_measurement_method", "owner": "HPAIEnviro", @@ -39450,7 +40201,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 84, + "rank": 83, "slot_uri": "GENEPIO:0100908", "alias": "instantaneous_flow_rate_measurement_value", "owner": "HPAIEnviro", @@ -39475,7 +40226,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 85, + "rank": 84, "slot_uri": "GENEPIO:0100909", "alias": "instantaneous_flow_rate_measurement_unit", "owner": "HPAIEnviro", @@ -39507,7 +40258,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 86, + "rank": 85, "slot_uri": "GENEPIO:0100910", "alias": "instantaneous_flow_rate_measurement_method", "owner": "HPAIEnviro", @@ -39532,7 +40283,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 87, + "rank": 86, "slot_uri": "GENEPIO:0100783", "alias": "turbidity_measurement_value", "owner": "HPAIEnviro", @@ -39558,7 +40309,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 88, + "rank": 87, "slot_uri": "GENEPIO:0100914", "alias": "turbidity_measurement_unit", "owner": "HPAIEnviro", @@ -39591,7 +40342,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 89, + "rank": 88, "slot_uri": "GENEPIO:0101013", "alias": "turbidity_measurement_method", "owner": "HPAIEnviro", @@ -39616,7 +40367,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 90, + "rank": 89, "slot_uri": "GENEPIO:0100915", "alias": "dissolved_oxygen_measurement_value", "owner": "HPAIEnviro", @@ -39641,7 +40392,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 91, + "rank": 90, "slot_uri": "GENEPIO:0100784", "alias": "dissolved_oxygen_measurement_unit", "owner": "HPAIEnviro", @@ -39673,7 +40424,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 92, + "rank": 91, "slot_uri": "GENEPIO:0100785", "alias": "dissolved_oxygen_measurement_method", "owner": "HPAIEnviro", @@ -39698,7 +40449,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 93, + "rank": 92, "slot_uri": "GENEPIO:0100917", "alias": "oxygen_reduction_potential_orp_measurement_value", "owner": "HPAIEnviro", @@ -39723,7 +40474,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 94, + "rank": 93, "slot_uri": "GENEPIO:0100786", "alias": "oxygen_reduction_potential_orp_measurement_unit", "owner": "HPAIEnviro", @@ -39755,7 +40506,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 95, + "rank": 94, "slot_uri": "GENEPIO:0100787", "alias": "oxygen_reduction_potential_orp_measurement_method", "owner": "HPAIEnviro", @@ -39780,7 +40531,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 96, + "rank": 95, "slot_uri": "GENEPIO:0100788", "alias": "chemical_oxygen_demand_cod_measurement_value", "owner": "HPAIEnviro", @@ -39805,7 +40556,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 97, + "rank": 96, "slot_uri": "GENEPIO:0100789", "alias": "chemical_oxygen_demand_cod_measurement_unit", "owner": "HPAIEnviro", @@ -39837,7 +40588,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 98, + "rank": 97, "slot_uri": "GENEPIO:0100790", "alias": "chemical_oxygen_demand_cod_measurement_method", "owner": "HPAIEnviro", @@ -39862,7 +40613,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 99, + "rank": 98, "slot_uri": "GENEPIO:0100791", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_value", "owner": "HPAIEnviro", @@ -39887,7 +40638,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 100, + "rank": 99, "slot_uri": "GENEPIO:0100792", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit", "owner": "HPAIEnviro", @@ -39919,7 +40670,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 101, + "rank": 100, "slot_uri": "GENEPIO:0100793", "alias": "carbonaceous_biochemical_oxygen_demand_cbod_measurement_method", "owner": "HPAIEnviro", @@ -39944,7 +40695,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 102, + "rank": 101, "slot_uri": "GENEPIO:0100794", "alias": "total_suspended_solids_tss_measurement_value", "owner": "HPAIEnviro", @@ -39969,7 +40720,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 103, + "rank": 102, "slot_uri": "GENEPIO:0100795", "alias": "total_suspended_solids_tss_measurement_unit", "owner": "HPAIEnviro", @@ -40001,7 +40752,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 104, + "rank": 103, "slot_uri": "GENEPIO:0100796", "alias": "total_suspended_solids_tss_measurement_method", "owner": "HPAIEnviro", @@ -40026,7 +40777,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 105, + "rank": 104, "slot_uri": "GENEPIO:0100797", "alias": "total_dissolved_solids_tds_measurement_value", "owner": "HPAIEnviro", @@ -40051,7 +40802,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 106, + "rank": 105, "slot_uri": "GENEPIO:0100798", "alias": "total_dissolved_solids_tds_measurement_unit", "owner": "HPAIEnviro", @@ -40083,7 +40834,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 107, + "rank": 106, "slot_uri": "GENEPIO:0100799", "alias": "total_dissolved_solids_tds_measurement_method", "owner": "HPAIEnviro", @@ -40108,7 +40859,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 108, + "rank": 107, "slot_uri": "GENEPIO:0100800", "alias": "total_solids_ts_measurement_value", "owner": "HPAIEnviro", @@ -40133,7 +40884,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 109, + "rank": 108, "slot_uri": "GENEPIO:0100801", "alias": "total_solids_ts_measurement_unit", "owner": "HPAIEnviro", @@ -40165,7 +40916,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 110, + "rank": 109, "slot_uri": "GENEPIO:0100802", "alias": "total_solids_ts_measurement_method", "owner": "HPAIEnviro", @@ -40190,7 +40941,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 111, + "rank": 110, "slot_uri": "GENEPIO:0100878", "alias": "alkalinity_measurement_value", "owner": "HPAIEnviro", @@ -40215,7 +40966,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 112, + "rank": 111, "slot_uri": "GENEPIO:0100879", "alias": "alkalinity_measurement_unit", "owner": "HPAIEnviro", @@ -40247,7 +40998,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 113, + "rank": 112, "slot_uri": "GENEPIO:0100880", "alias": "alkalinity_measurement_method", "owner": "HPAIEnviro", @@ -40272,7 +41023,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 114, + "rank": 113, "slot_uri": "GENEPIO:0100916", "alias": "conductivity_measurement_value", "owner": "HPAIEnviro", @@ -40297,7 +41048,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 115, + "rank": 114, "slot_uri": "GENEPIO:0100803", "alias": "conductivity_measurement_unit", "owner": "HPAIEnviro", @@ -40329,7 +41080,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 116, + "rank": 115, "slot_uri": "GENEPIO:0100804", "alias": "conductivity_measurement_method", "owner": "HPAIEnviro", @@ -40354,7 +41105,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 117, + "rank": 116, "slot_uri": "GENEPIO:0100805", "alias": "salinity_measurement_value", "owner": "HPAIEnviro", @@ -40379,7 +41130,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 118, + "rank": 117, "slot_uri": "GENEPIO:0100806", "alias": "salinity_measurement_unit", "owner": "HPAIEnviro", @@ -40411,7 +41162,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 119, + "rank": 118, "slot_uri": "GENEPIO:0100807", "alias": "salinity_measurement_method", "owner": "HPAIEnviro", @@ -40436,7 +41187,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 120, + "rank": 119, "slot_uri": "GENEPIO:0100808", "alias": "total_nitrogen_tn_measurement_value", "owner": "HPAIEnviro", @@ -40461,7 +41212,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 121, + "rank": 120, "slot_uri": "GENEPIO:0100809", "alias": "total_nitrogen_tn_measurement_unit", "owner": "HPAIEnviro", @@ -40493,7 +41244,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 122, + "rank": 121, "slot_uri": "GENEPIO:0100810", "alias": "total_nitrogen_tn_measurement_method", "owner": "HPAIEnviro", @@ -40518,7 +41269,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 123, + "rank": 122, "slot_uri": "GENEPIO:0100811", "alias": "total_phosphorus_tp_measurement_value", "owner": "HPAIEnviro", @@ -40543,7 +41294,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 124, + "rank": 123, "slot_uri": "GENEPIO:0100812", "alias": "total_phosphorus_tp_measurement_unit", "owner": "HPAIEnviro", @@ -40555,7 +41306,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTPMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -40575,7 +41326,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 125, + "rank": 124, "slot_uri": "GENEPIO:0100813", "alias": "total_phosphorus_tp_measurement_method", "owner": "HPAIEnviro", @@ -40600,7 +41351,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 126, + "rank": 125, "slot_uri": "GENEPIO:0100814", "alias": "fecal_contamination_indicator_", "owner": "HPAIEnviro", @@ -40633,7 +41384,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 127, + "rank": 126, "slot_uri": "GENEPIO:0100815", "alias": "fecal_contamination_value", "owner": "HPAIEnviro", @@ -40659,7 +41410,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 128, + "rank": 127, "slot_uri": "GENEPIO:0100816", "alias": "fecal_contamination_unit", "owner": "HPAIEnviro", @@ -40692,7 +41443,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 129, + "rank": 128, "slot_uri": "GENEPIO:0100817", "alias": "fecal_contamination_method", "owner": "HPAIEnviro", @@ -40717,7 +41468,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 130, + "rank": 129, "slot_uri": "GENEPIO:0100818", "alias": "fecal_coliform_count_value", "owner": "HPAIEnviro", @@ -40742,7 +41493,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 131, + "rank": 130, "slot_uri": "GENEPIO:0100819", "alias": "fecal_coliform_count_unit", "owner": "HPAIEnviro", @@ -40774,7 +41525,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 132, + "rank": 131, "slot_uri": "GENEPIO:0100820", "alias": "fecal_coliform_count_method", "owner": "HPAIEnviro", @@ -40799,7 +41550,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 133, + "rank": 132, "slot_uri": "GENEPIO:0100837", "alias": "urinary_contamination_indicator", "owner": "HPAIEnviro", @@ -40831,7 +41582,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 134, + "rank": 133, "slot_uri": "GENEPIO:0100838", "alias": "urinary_contamination_value", "owner": "HPAIEnviro", @@ -40856,7 +41607,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 135, + "rank": 134, "slot_uri": "GENEPIO:0100839", "alias": "urinary_contamination_unit", "owner": "HPAIEnviro", @@ -40888,7 +41639,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 136, + "rank": 135, "slot_uri": "GENEPIO:0100840", "alias": "urinary_contamination_method", "owner": "HPAIEnviro", @@ -40913,7 +41664,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 137, + "rank": 136, "slot_uri": "GENEPIO:0100821", "alias": "sample_temperature_value_at_collection", "owner": "HPAIEnviro", @@ -40938,7 +41689,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 138, + "rank": 137, "slot_uri": "GENEPIO:0100822", "alias": "sample_temperature_unit_at_collection", "owner": "HPAIEnviro", @@ -40970,7 +41721,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 139, + "rank": 138, "slot_uri": "GENEPIO:0100823", "alias": "sample_temperature_value_when_received", "owner": "HPAIEnviro", @@ -40995,7 +41746,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 140, + "rank": 139, "slot_uri": "GENEPIO:0100824", "alias": "sample_temperature_unit_when_received", "owner": "HPAIEnviro", @@ -41027,7 +41778,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 141, + "rank": 140, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "HPAIEnviro", @@ -41054,7 +41805,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 142, + "rank": 141, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "HPAIEnviro", @@ -41084,7 +41835,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 143, + "rank": 142, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "HPAIEnviro", @@ -41111,7 +41862,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 144, + "rank": 143, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing__", "owner": "HPAIEnviro", @@ -41147,7 +41898,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 145, + "rank": 144, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "HPAIEnviro", @@ -41178,7 +41929,7 @@ "GISAID:sequenced_by", "BIOSAMPLE_Enterics:sequenced_by" ], - "rank": 146, + "rank": 145, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "HPAIEnviro", @@ -41213,7 +41964,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 147, + "rank": 146, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "HPAIEnviro", @@ -41240,7 +41991,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 148, + "rank": 147, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "HPAIEnviro", @@ -41275,7 +42026,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 149, + "rank": 148, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "HPAIEnviro", @@ -41310,7 +42061,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 150, + "rank": 149, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "HPAIEnviro", @@ -41345,7 +42096,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 151, + "rank": 150, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "HPAIEnviro", @@ -41381,7 +42132,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 152, + "rank": 151, "slot_uri": "GENEPIO:0100939", "alias": "nucleic_acid_extraction_method", "owner": "HPAIEnviro", @@ -41392,7 +42143,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -41408,7 +42159,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 153, + "rank": 152, "slot_uri": "GENEPIO:0100772", "alias": "nucleic_acid_extraction_kit", "owner": "HPAIEnviro", @@ -41419,7 +42170,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -41430,7 +42181,7 @@ "Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample." ], "from_schema": "https://example.com/hpai", - "rank": 154, + "rank": 153, "slot_uri": "GENEPIO:0100923", "alias": "endogenous_control_details", "owner": "HPAIEnviro", @@ -41441,7 +42192,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -41458,7 +42209,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 155, + "rank": 154, "slot_uri": "GENEPIO:0100472", "alias": "sequencing_project_name", "owner": "HPAIEnviro", @@ -41485,7 +42236,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 156, + "rank": 155, "slot_uri": "GENEPIO:0100473", "alias": "sequencing_platform", "owner": "HPAIEnviro", @@ -41519,7 +42270,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 157, + "rank": 156, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "HPAIEnviro", @@ -41553,7 +42304,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 158, + "rank": 157, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "HPAIEnviro", @@ -41580,7 +42331,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 159, + "rank": 158, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "HPAIEnviro", @@ -41607,7 +42358,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 160, + "rank": 159, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "HPAIEnviro", @@ -41634,7 +42385,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 161, + "rank": 160, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "HPAIEnviro", @@ -41661,7 +42412,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 162, + "rank": 161, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "HPAIEnviro", @@ -41688,7 +42439,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 163, + "rank": 162, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "HPAIEnviro", @@ -41715,7 +42466,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 164, + "rank": 163, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "HPAIEnviro", @@ -41742,7 +42493,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 165, + "rank": 164, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "HPAIEnviro", @@ -41769,7 +42520,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 166, + "rank": 165, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "HPAIEnviro", @@ -41796,7 +42547,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 167, + "rank": 166, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "HPAIEnviro", @@ -41823,7 +42574,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 168, + "rank": 167, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "HPAIEnviro", @@ -41850,7 +42601,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 169, + "rank": 168, "slot_uri": "GENEPIO:0101715", "alias": "genome_sequence_file_name", "owner": "HPAIEnviro", @@ -41877,7 +42628,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 170, + "rank": 169, "slot_uri": "GENEPIO:0001461", "alias": "assembly_filename", "owner": "HPAIEnviro", @@ -41904,7 +42655,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 171, + "rank": 170, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "HPAIEnviro", @@ -41931,7 +42682,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 172, + "rank": 171, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "HPAIEnviro", @@ -41958,7 +42709,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 173, + "rank": 172, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "HPAIEnviro", @@ -41993,7 +42744,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 174, + "rank": 173, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "HPAIEnviro", @@ -42028,7 +42779,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 175, + "rank": 174, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "HPAIEnviro", @@ -42055,7 +42806,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 176, + "rank": 175, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "HPAIEnviro", @@ -42090,7 +42841,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 177, + "rank": 176, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "HPAIEnviro", @@ -42125,7 +42876,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 178, + "rank": 177, "slot_uri": "GENEPIO:0100825", "alias": "sequence_assembly_software_name", "owner": "HPAIEnviro", @@ -42159,7 +42910,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 179, + "rank": 178, "slot_uri": "GENEPIO:0100826", "alias": "sequence_assembly_software_version", "owner": "HPAIEnviro", @@ -42193,7 +42944,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 180, + "rank": 179, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "HPAIEnviro", @@ -42227,7 +42978,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 181, + "rank": 180, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "HPAIEnviro", @@ -42261,7 +43012,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 182, + "rank": 181, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "HPAIEnviro", @@ -42288,7 +43039,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 183, + "rank": 182, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "HPAIEnviro", @@ -42315,7 +43066,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 184, + "rank": 183, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "HPAIEnviro", @@ -42342,7 +43093,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 185, + "rank": 184, "slot_uri": "GENEPIO:0100844", "alias": "genome_completeness", "owner": "HPAIEnviro", @@ -42369,7 +43120,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 186, + "rank": 185, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "HPAIEnviro", @@ -42396,7 +43147,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 187, + "rank": 186, "slot_uri": "GENEPIO:0100827", "alias": "number_of_total_reads", "owner": "HPAIEnviro", @@ -42423,7 +43174,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 188, + "rank": 187, "slot_uri": "GENEPIO:0100828", "alias": "number_of_unique_reads", "owner": "HPAIEnviro", @@ -42450,7 +43201,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 189, + "rank": 188, "slot_uri": "GENEPIO:0100829", "alias": "minimum_posttrimming_read_length", "owner": "HPAIEnviro", @@ -42477,7 +43228,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 190, + "rank": 189, "slot_uri": "GENEPIO:0100937", "alias": "number_of_contigs", "owner": "HPAIEnviro", @@ -42504,7 +43255,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 191, + "rank": 190, "slot_uri": "GENEPIO:0100830", "alias": "percent_ns_across_total_genome_length", "owner": "HPAIEnviro", @@ -42531,7 +43282,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 192, + "rank": 191, "slot_uri": "GENEPIO:0001484", "alias": "ns_per_100_kbp", "owner": "HPAIEnviro", @@ -42558,7 +43309,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 193, + "rank": 192, "slot_uri": "GENEPIO:0100938", "alias": "n50", "owner": "HPAIEnviro", @@ -42585,7 +43336,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 194, + "rank": 193, "slot_uri": "GENEPIO:0100845", "alias": "percent_read_contamination_", "owner": "HPAIEnviro", @@ -42612,7 +43363,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 195, + "rank": 194, "slot_uri": "GENEPIO:0100846", "alias": "sequence_assembly_length", "owner": "HPAIEnviro", @@ -42639,7 +43390,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 196, + "rank": 195, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "HPAIEnviro", @@ -42666,7 +43417,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 197, + "rank": 196, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "HPAIEnviro", @@ -42693,7 +43444,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 198, + "rank": 197, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "HPAIEnviro", @@ -42720,7 +43471,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 199, + "rank": 198, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "HPAIEnviro", @@ -42747,7 +43498,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 200, + "rank": 199, "slot_uri": "GENEPIO:0100832", "alias": "read_mapping_software_name", "owner": "HPAIEnviro", @@ -42774,7 +43525,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 201, + "rank": 200, "slot_uri": "GENEPIO:0100833", "alias": "read_mapping_software_version", "owner": "HPAIEnviro", @@ -42801,7 +43552,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 202, + "rank": 201, "slot_uri": "GENEPIO:0100834", "alias": "taxonomic_reference_database_name", "owner": "HPAIEnviro", @@ -42828,7 +43579,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 203, + "rank": 202, "slot_uri": "GENEPIO:0100835", "alias": "taxonomic_reference_database_version", "owner": "HPAIEnviro", @@ -42855,7 +43606,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 204, + "rank": 203, "slot_uri": "GENEPIO:0101074", "alias": "taxonomic_analysis_report_filename", "owner": "HPAIEnviro", @@ -42882,7 +43633,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 205, + "rank": 204, "slot_uri": "GENEPIO:0101075", "alias": "taxonomic_analysis_date", "owner": "HPAIEnviro", @@ -42909,7 +43660,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 206, + "rank": 205, "slot_uri": "GENEPIO:0100836", "alias": "read_mapping_criteria", "owner": "HPAIEnviro", @@ -42936,7 +43687,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 207, + "rank": 206, "slot_uri": "GENEPIO:0101116", "alias": "genetic_target_name", "owner": "HPAIEnviro", @@ -42962,7 +43713,7 @@ "description": "The specific region or segment of a genetic sequence used for testing or analysis.", "title": "genetic target region", "from_schema": "https://example.com/hpai", - "rank": 208, + "rank": 207, "slot_uri": "GENEPIO:0101117", "alias": "genetic_target_region", "owner": "HPAIEnviro", @@ -42981,7 +43732,7 @@ "description": "The reference genome version used to determine the coordinates or identity of the genetic target region in testing or analysis.", "title": "genetic target region reference genome", "from_schema": "https://example.com/hpai", - "rank": 209, + "rank": 208, "slot_uri": "GENEPIO:0101118", "alias": "genetic_target_region_reference_genome", "owner": "HPAIEnviro", @@ -43008,7 +43759,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 210, + "rank": 209, "slot_uri": "GENEPIO:0100962", "alias": "diagnostic_target_presence", "owner": "HPAIEnviro", @@ -43042,7 +43793,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 211, + "rank": 210, "slot_uri": "GENEPIO:0100963", "alias": "diagnostic_measurement_value", "owner": "HPAIEnviro", @@ -43069,7 +43820,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 212, + "rank": 211, "slot_uri": "GENEPIO:0100964", "alias": "diagnostic_measurement_unit", "owner": "HPAIEnviro", @@ -43103,7 +43854,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 213, + "rank": 212, "slot_uri": "GENEPIO:0100965", "alias": "diagnostic_measurement_method", "owner": "HPAIEnviro", @@ -43129,7 +43880,7 @@ "description": "The numerical value which represents the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold value", "from_schema": "https://example.com/hpai", - "rank": 214, + "rank": 213, "slot_uri": "GENEPIO:0101104", "alias": "diagnostic_testing_threshold_value", "owner": "HPAIEnviro", @@ -43148,7 +43899,7 @@ "description": "The unit which are attributed to the threshold above/below which interpretation can be drawn on the diagnostic test", "title": "diagnostic testing threshold units", "from_schema": "https://example.com/hpai", - "rank": 215, + "rank": 214, "slot_uri": "GENEPIO:0101105", "alias": "diagnostic_testing_threshold_units", "owner": "HPAIEnviro", @@ -43167,7 +43918,7 @@ "description": "Describe any details of the diagnsotic testing.", "title": "diagnostic testing details", "from_schema": "https://example.com/hpai", - "rank": 216, + "rank": 215, "slot_uri": "GENEPIO:0101106", "alias": "diagnostic_testing_details", "owner": "HPAIEnviro", @@ -43194,7 +43945,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 217, + "rank": 216, "slot_uri": "GENEPIO:0100480", "alias": "prevalence_metrics", "owner": "HPAIEnviro", @@ -43222,7 +43973,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 218, + "rank": 217, "slot_uri": "GENEPIO:0100481", "alias": "prevalence_metrics_details", "owner": "HPAIEnviro", @@ -43250,7 +44001,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 219, + "rank": 218, "slot_uri": "GENEPIO:0100482", "alias": "stage_of_production", "owner": "HPAIEnviro", @@ -43265,7 +44016,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" @@ -43285,7 +44036,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 220, + "rank": 219, "slot_uri": "GENEPIO:0100483", "alias": "experimental_intervention", "owner": "HPAIEnviro", @@ -43321,7 +44072,7 @@ } ], "from_schema": "https://example.com/hpai", - "rank": 221, + "rank": 220, "slot_uri": "GENEPIO:0100484", "alias": "experiment_intervention_details", "owner": "HPAIEnviro", @@ -43613,27 +44364,27 @@ "host_common_name": { "name": "host_common_name", "rank": 53, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_scientific_name": { "name": "host_scientific_name", "rank": 54, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_ecotype": { "name": "host_ecotype", "rank": 55, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_breed": { "name": "host_breed", "rank": 56, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_food_production_name": { "name": "host_food_production_name", "rank": 57, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_age": { "name": "host_age", @@ -43648,12 +44399,12 @@ "host_age_bin": { "name": "host_age_bin", "rank": 60, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_disease": { "name": "host_disease", "rank": 61, - "slot_group": "Host information" + "slot_group": "Host Information" }, "host_health_state": { "name": "host_health_state", @@ -43833,17 +44584,17 @@ "nucleic_acid_extraction_method": { "name": "nucleic_acid_extraction_method", "rank": 97, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "nucleic_acid_extraction_kit": { "name": "nucleic_acid_extraction_kit", "rank": 98, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "endogenous_control_details": { "name": "endogenous_control_details", "rank": 99, - "slot_group": "Sample collection and processing" + "slot_group": "Sequence information" }, "sequencing_project_name": { "name": "sequencing_project_name", @@ -44852,7 +45603,7 @@ "HPAIHost" ], "slot_group": "Sample collection and processing", - "range": "InfluenzaSubsubtypeMenu", + "range": "InfluenzaSubtypeMenu", "required": true, "multivalued": true }, @@ -45798,7 +46549,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -45838,7 +46589,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "recommended": true, "any_of": [ { @@ -45873,7 +46624,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_breed": { @@ -45901,7 +46652,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, "host_food_production_name": { @@ -45928,7 +46679,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostFoodProductionNameMenu" @@ -46026,7 +46777,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostAgeBinMenu" @@ -46060,7 +46811,7 @@ "HPAI", "HPAIHost" ], - "slot_group": "Host information", + "slot_group": "Host Information", "any_of": [ { "range": "HostDiseaseMenu" @@ -47133,7 +47884,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "nucleic_acid_extraction_kit": { @@ -47160,7 +47911,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, "endogenous_control_details": { @@ -47182,7 +47933,7 @@ "HPAIEnviro", "HPAIHost" ], - "slot_group": "Sample collection and processing", + "slot_group": "Sequence information", "range": "WhitespaceMinimizedString", "recommended": true }, @@ -49006,7 +49757,7 @@ "recommended": true, "any_of": [ { - "range": "StageOfProductionMenu" + "range": "WhitespaceMinimizedString" }, { "range": "NullValueMenu" diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index 3bfe72a4..cac91b64 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -132,7 +132,6 @@ classes: - populated_area_type - sampling_weather_conditions - presampling_weather_conditions - - precipitation_measurement_value - water_depth - water_depth_units - sediment_depth @@ -141,7 +140,7 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - precipitation_measurement_value - precipitation_measurement_unit - precipitation_measurement_method - ambient_temperature_measurement_value @@ -490,19 +489,19 @@ classes: slot_group: Sample collection and processing host_common_name: rank: 67 - slot_group: Host information + slot_group: Host Information host_scientific_name: rank: 68 - slot_group: Host information + slot_group: Host Information host_ecotype: rank: 69 - slot_group: Host information + slot_group: Host Information host_breed: rank: 70 - slot_group: Host information + slot_group: Host Information host_food_production_name: rank: 71 - slot_group: Host information + slot_group: Host Information host_age: rank: 72 slot_group: Host Information @@ -511,10 +510,10 @@ classes: slot_group: Host Information host_age_bin: rank: 74 - slot_group: Host information + slot_group: Host Information host_disease: rank: 75 - slot_group: Host information + slot_group: Host Information host_health_state: rank: 76 slot_group: Host Information @@ -611,476 +610,473 @@ classes: presampling_weather_conditions: rank: 107 slot_group: Environmental conditions and measurements - precipitation_measurement_value: + water_depth: rank: 108 slot_group: Environmental conditions and measurements - water_depth: + water_depth_units: rank: 109 slot_group: Environmental conditions and measurements - water_depth_units: + sediment_depth: rank: 110 slot_group: Environmental conditions and measurements - sediment_depth: + sediment_depth_units: rank: 111 slot_group: Environmental conditions and measurements - sediment_depth_units: + air_temperature: rank: 112 slot_group: Environmental conditions and measurements - air_temperature: + air_temperature_units: rank: 113 slot_group: Environmental conditions and measurements - air_temperature_units: + water_temperature: rank: 114 slot_group: Environmental conditions and measurements - water_temperature: + water_temperature_units: rank: 115 slot_group: Environmental conditions and measurements - water_temperature_units: + precipitation_measurement_value: rank: 116 slot_group: Environmental conditions and measurements - weather_type: - rank: 117 - slot_group: Environmental conditions and measurements precipitation_measurement_unit: - rank: 118 + rank: 117 slot_group: Environmental conditions and measurements precipitation_measurement_method: - rank: 119 + rank: 118 slot_group: Environmental conditions and measurements ambient_temperature_measurement_value: - rank: 120 + rank: 119 slot_group: Environmental conditions and measurements ambient_temperature_measurement_unit: - rank: 121 + rank: 120 slot_group: Environmental conditions and measurements ph_measurement_value: - rank: 122 + rank: 121 slot_group: Environmental conditions and measurements ph_measurement_method: - rank: 123 + rank: 122 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_value: - rank: 124 + rank: 123 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_unit: - rank: 125 + rank: 124 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_method: - rank: 126 + rank: 125 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_value: - rank: 127 + rank: 126 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_unit: - rank: 128 + rank: 127 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_method: - rank: 129 + rank: 128 slot_group: Environmental conditions and measurements turbidity_measurement_value: - rank: 130 + rank: 129 slot_group: Environmental conditions and measurements turbidity_measurement_unit: - rank: 131 + rank: 130 slot_group: Environmental conditions and measurements turbidity_measurement_method: - rank: 132 + rank: 131 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_value: - rank: 133 + rank: 132 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_unit: - rank: 134 + rank: 133 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_method: - rank: 135 + rank: 134 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_value: - rank: 136 + rank: 135 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_unit: - rank: 137 + rank: 136 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_method: - rank: 138 + rank: 137 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_value: - rank: 139 + rank: 138 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_unit: - rank: 140 + rank: 139 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_method: - rank: 141 + rank: 140 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: - rank: 142 + rank: 141 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: - rank: 143 + rank: 142 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: - rank: 144 + rank: 143 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_value: - rank: 145 + rank: 144 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_unit: - rank: 146 + rank: 145 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_method: - rank: 147 + rank: 146 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_value: - rank: 148 + rank: 147 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_unit: - rank: 149 + rank: 148 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_method: - rank: 150 + rank: 149 slot_group: Environmental conditions and measurements total_solids_ts_measurement_value: - rank: 151 + rank: 150 slot_group: Environmental conditions and measurements total_solids_ts_measurement_unit: - rank: 152 + rank: 151 slot_group: Environmental conditions and measurements total_solids_ts_measurement_method: - rank: 153 + rank: 152 slot_group: Environmental conditions and measurements alkalinity_measurement_value: - rank: 154 + rank: 153 slot_group: Environmental conditions and measurements alkalinity_measurement_unit: - rank: 155 + rank: 154 slot_group: Environmental conditions and measurements alkalinity_measurement_method: - rank: 156 + rank: 155 slot_group: Environmental conditions and measurements conductivity_measurement_value: - rank: 157 + rank: 156 slot_group: Environmental conditions and measurements conductivity_measurement_unit: - rank: 158 + rank: 157 slot_group: Environmental conditions and measurements conductivity_measurement_method: - rank: 159 + rank: 158 slot_group: Environmental conditions and measurements salinity_measurement_value: - rank: 160 + rank: 159 slot_group: Environmental conditions and measurements salinity_measurement_unit: - rank: 161 + rank: 160 slot_group: Environmental conditions and measurements salinity_measurement_method: - rank: 162 + rank: 161 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_value: - rank: 163 + rank: 162 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_unit: - rank: 164 + rank: 163 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_method: - rank: 165 + rank: 164 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_value: - rank: 166 + rank: 165 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_unit: - rank: 167 + rank: 166 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_method: - rank: 168 + rank: 167 slot_group: Environmental conditions and measurements fecal_contamination_indicator_: - rank: 169 + rank: 168 slot_group: Environmental conditions and measurements fecal_contamination_value: - rank: 170 + rank: 169 slot_group: Environmental conditions and measurements fecal_contamination_unit: - rank: 171 + rank: 170 slot_group: Environmental conditions and measurements fecal_contamination_method: - rank: 172 + rank: 171 slot_group: Environmental conditions and measurements fecal_coliform_count_value: - rank: 173 + rank: 172 slot_group: Environmental conditions and measurements fecal_coliform_count_unit: - rank: 174 + rank: 173 slot_group: Environmental conditions and measurements fecal_coliform_count_method: - rank: 175 + rank: 174 slot_group: Environmental conditions and measurements urinary_contamination_indicator: - rank: 176 + rank: 175 slot_group: Environmental conditions and measurements urinary_contamination_value: - rank: 177 + rank: 176 slot_group: Environmental conditions and measurements urinary_contamination_unit: - rank: 178 + rank: 177 slot_group: Environmental conditions and measurements urinary_contamination_method: - rank: 179 + rank: 178 slot_group: Environmental conditions and measurements sample_temperature_value_at_collection: - rank: 180 + rank: 179 slot_group: Environmental conditions and measurements sample_temperature_unit_at_collection: - rank: 181 + rank: 180 slot_group: Environmental conditions and measurements sample_temperature_value_when_received: - rank: 182 + rank: 181 slot_group: Environmental conditions and measurements sample_temperature_unit_when_received: - rank: 183 + rank: 182 slot_group: Environmental conditions and measurements library_id: - rank: 184 + rank: 183 slot_group: Sequence information sequencing_assay_type: - rank: 185 + rank: 184 slot_group: Sequence information sequencing_date: - rank: 186 + rank: 185 slot_group: Sequence information purpose_of_sequencing__: - rank: 187 + rank: 186 slot_group: Sequence information purpose_of_sequencing_details: - rank: 188 + rank: 187 slot_group: Sequence information sequenced_by: - rank: 189 + rank: 188 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 190 + rank: 189 slot_group: Sequence information sequenced_by_contact_name: - rank: 191 + rank: 190 slot_group: Sequence information sequenced_by_contact_email: - rank: 192 + rank: 191 slot_group: Sequence information sequence_submitted_by: - rank: 193 + rank: 192 slot_group: Sequence information sequence_submitter_contact_email: - rank: 194 + rank: 193 slot_group: Sequence information nucleic_acid_extraction_method: - rank: 195 - slot_group: Sample collection and processing + rank: 194 + slot_group: Sequence information nucleic_acid_extraction_kit: - rank: 196 - slot_group: Sample collection and processing + rank: 195 + slot_group: Sequence information endogenous_control_details: - rank: 197 - slot_group: Sample collection and processing + rank: 196 + slot_group: Sequence information sequencing_project_name: - rank: 198 + rank: 197 slot_group: Sequence information sequencing_platform: - rank: 199 + rank: 198 slot_group: Sequence information sequencing_instrument: - rank: 200 + rank: 199 slot_group: Sequence information library_preparation_kit: - rank: 201 + rank: 200 slot_group: Sequence information dna_fragment_length: - rank: 202 + rank: 201 slot_group: Sequence information genomic_target_enrichment_method: - rank: 203 + rank: 202 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 204 + rank: 203 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 205 + rank: 204 slot_group: Sequence information amplicon_size: - rank: 206 + rank: 205 slot_group: Sequence information sequencing_flow_cell_version: - rank: 207 + rank: 206 slot_group: Sequence information sequencing_protocol: - rank: 208 + rank: 207 slot_group: Sequence information r1_fastq_filename: - rank: 209 + rank: 208 slot_group: Sequence information r2_fastq_filename: - rank: 210 + rank: 209 slot_group: Sequence information fast5_filename: - rank: 211 + rank: 210 slot_group: Sequence information genome_sequence_file_name: - rank: 212 + rank: 211 slot_group: Sequence information assembly_filename: - rank: 213 + rank: 212 slot_group: Sequence information quality_control_method_name: - rank: 214 + rank: 213 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 215 + rank: 214 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 216 + rank: 215 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 217 + rank: 216 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 218 + rank: 217 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 219 + rank: 218 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 220 + rank: 219 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 221 + rank: 220 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 222 + rank: 221 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 223 + rank: 222 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 224 + rank: 223 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 225 + rank: 224 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 226 + rank: 225 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 227 + rank: 226 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 228 + rank: 227 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 229 + rank: 228 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 230 + rank: 229 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 231 + rank: 230 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 232 + rank: 231 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 233 + rank: 232 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 234 + rank: 233 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 235 + rank: 234 slot_group: Bioinformatics and QC metrics n50: - rank: 236 + rank: 235 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 237 + rank: 236 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 238 + rank: 237 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 239 + rank: 238 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 240 + rank: 239 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 241 + rank: 240 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 242 + rank: 241 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 243 + rank: 242 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 244 + rank: 243 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 245 + rank: 244 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 246 + rank: 245 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 247 + rank: 246 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 248 + rank: 247 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 249 + rank: 248 slot_group: Taxonomic identification information genetic_target_name: - rank: 250 + rank: 249 slot_group: Pathogen diagnostic testing genetic_target_region: - rank: 251 + rank: 250 slot_group: Pathogen diagnostic testing genetic_target_region_reference_genome: - rank: 252 + rank: 251 slot_group: Pathogen diagnostic testing diagnostic_target_presence: - rank: 253 + rank: 252 slot_group: Pathogen diagnostic testing diagnostic_measurement_value: - rank: 254 + rank: 253 slot_group: Pathogen diagnostic testing diagnostic_measurement_unit: - rank: 255 + rank: 254 slot_group: Pathogen diagnostic testing diagnostic_measurement_method: - rank: 256 + rank: 255 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_value: - rank: 257 + rank: 256 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_units: - rank: 258 + rank: 257 slot_group: Pathogen diagnostic testing diagnostic_testing_details: - rank: 259 + rank: 258 slot_group: Pathogen diagnostic testing prevalence_metrics: - rank: 260 + rank: 259 slot_group: Risk assessment information prevalence_metrics_details: - rank: 261 + rank: 260 slot_group: Risk assessment information stage_of_production: - rank: 262 + rank: 261 slot_group: Risk assessment information experimental_intervention: - rank: 263 + rank: 262 slot_group: Risk assessment information experiment_intervention_details: - rank: 264 + rank: 263 slot_group: Risk assessment information HPAIFood: name: HPAIFood @@ -1432,13 +1428,13 @@ classes: slot_group: Sequence information nucleic_acid_extraction_method: rank: 68 - slot_group: Sample collection and processing + slot_group: Sequence information nucleic_acid_extraction_kit: rank: 69 - slot_group: Sample collection and processing + slot_group: Sequence information endogenous_control_details: rank: 70 - slot_group: Sample collection and processing + slot_group: Sequence information sequencing_project_name: rank: 71 slot_group: Sequence information @@ -1713,7 +1709,6 @@ classes: - populated_area_type - sampling_weather_conditions - presampling_weather_conditions - - precipitation_measurement_value - water_depth - water_depth_units - sediment_depth @@ -1722,7 +1717,7 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - precipitation_measurement_value - precipitation_measurement_unit - precipitation_measurement_method - ambient_temperature_measurement_value @@ -2063,476 +2058,473 @@ classes: presampling_weather_conditions: rank: 64 slot_group: Environmental conditions and measurements - precipitation_measurement_value: + water_depth: rank: 65 slot_group: Environmental conditions and measurements - water_depth: + water_depth_units: rank: 66 slot_group: Environmental conditions and measurements - water_depth_units: + sediment_depth: rank: 67 slot_group: Environmental conditions and measurements - sediment_depth: + sediment_depth_units: rank: 68 slot_group: Environmental conditions and measurements - sediment_depth_units: + air_temperature: rank: 69 slot_group: Environmental conditions and measurements - air_temperature: + air_temperature_units: rank: 70 slot_group: Environmental conditions and measurements - air_temperature_units: + water_temperature: rank: 71 slot_group: Environmental conditions and measurements - water_temperature: + water_temperature_units: rank: 72 slot_group: Environmental conditions and measurements - water_temperature_units: + precipitation_measurement_value: rank: 73 slot_group: Environmental conditions and measurements - weather_type: - rank: 74 - slot_group: Environmental conditions and measurements precipitation_measurement_unit: - rank: 75 + rank: 74 slot_group: Environmental conditions and measurements precipitation_measurement_method: - rank: 76 + rank: 75 slot_group: Environmental conditions and measurements ambient_temperature_measurement_value: - rank: 77 + rank: 76 slot_group: Environmental conditions and measurements ambient_temperature_measurement_unit: - rank: 78 + rank: 77 slot_group: Environmental conditions and measurements ph_measurement_value: - rank: 79 + rank: 78 slot_group: Environmental conditions and measurements ph_measurement_method: - rank: 80 + rank: 79 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_value: - rank: 81 + rank: 80 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_unit: - rank: 82 + rank: 81 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_method: - rank: 83 + rank: 82 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_value: - rank: 84 + rank: 83 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_unit: - rank: 85 + rank: 84 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_method: - rank: 86 + rank: 85 slot_group: Environmental conditions and measurements turbidity_measurement_value: - rank: 87 + rank: 86 slot_group: Environmental conditions and measurements turbidity_measurement_unit: - rank: 88 + rank: 87 slot_group: Environmental conditions and measurements turbidity_measurement_method: - rank: 89 + rank: 88 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_value: - rank: 90 + rank: 89 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_unit: - rank: 91 + rank: 90 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_method: - rank: 92 + rank: 91 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_value: - rank: 93 + rank: 92 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_unit: - rank: 94 + rank: 93 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_method: - rank: 95 + rank: 94 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_value: - rank: 96 + rank: 95 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_unit: - rank: 97 + rank: 96 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_method: - rank: 98 + rank: 97 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: - rank: 99 + rank: 98 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: - rank: 100 + rank: 99 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: - rank: 101 + rank: 100 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_value: - rank: 102 + rank: 101 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_unit: - rank: 103 + rank: 102 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_method: - rank: 104 + rank: 103 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_value: - rank: 105 + rank: 104 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_unit: - rank: 106 + rank: 105 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_method: - rank: 107 + rank: 106 slot_group: Environmental conditions and measurements total_solids_ts_measurement_value: - rank: 108 + rank: 107 slot_group: Environmental conditions and measurements total_solids_ts_measurement_unit: - rank: 109 + rank: 108 slot_group: Environmental conditions and measurements total_solids_ts_measurement_method: - rank: 110 + rank: 109 slot_group: Environmental conditions and measurements alkalinity_measurement_value: - rank: 111 + rank: 110 slot_group: Environmental conditions and measurements alkalinity_measurement_unit: - rank: 112 + rank: 111 slot_group: Environmental conditions and measurements alkalinity_measurement_method: - rank: 113 + rank: 112 slot_group: Environmental conditions and measurements conductivity_measurement_value: - rank: 114 + rank: 113 slot_group: Environmental conditions and measurements conductivity_measurement_unit: - rank: 115 + rank: 114 slot_group: Environmental conditions and measurements conductivity_measurement_method: - rank: 116 + rank: 115 slot_group: Environmental conditions and measurements salinity_measurement_value: - rank: 117 + rank: 116 slot_group: Environmental conditions and measurements salinity_measurement_unit: - rank: 118 + rank: 117 slot_group: Environmental conditions and measurements salinity_measurement_method: - rank: 119 + rank: 118 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_value: - rank: 120 + rank: 119 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_unit: - rank: 121 + rank: 120 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_method: - rank: 122 + rank: 121 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_value: - rank: 123 + rank: 122 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_unit: - rank: 124 + rank: 123 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_method: - rank: 125 + rank: 124 slot_group: Environmental conditions and measurements fecal_contamination_indicator_: - rank: 126 + rank: 125 slot_group: Environmental conditions and measurements fecal_contamination_value: - rank: 127 + rank: 126 slot_group: Environmental conditions and measurements fecal_contamination_unit: - rank: 128 + rank: 127 slot_group: Environmental conditions and measurements fecal_contamination_method: - rank: 129 + rank: 128 slot_group: Environmental conditions and measurements fecal_coliform_count_value: - rank: 130 + rank: 129 slot_group: Environmental conditions and measurements fecal_coliform_count_unit: - rank: 131 + rank: 130 slot_group: Environmental conditions and measurements fecal_coliform_count_method: - rank: 132 + rank: 131 slot_group: Environmental conditions and measurements urinary_contamination_indicator: - rank: 133 + rank: 132 slot_group: Environmental conditions and measurements urinary_contamination_value: - rank: 134 + rank: 133 slot_group: Environmental conditions and measurements urinary_contamination_unit: - rank: 135 + rank: 134 slot_group: Environmental conditions and measurements urinary_contamination_method: - rank: 136 + rank: 135 slot_group: Environmental conditions and measurements sample_temperature_value_at_collection: - rank: 137 + rank: 136 slot_group: Environmental conditions and measurements sample_temperature_unit_at_collection: - rank: 138 + rank: 137 slot_group: Environmental conditions and measurements sample_temperature_value_when_received: - rank: 139 + rank: 138 slot_group: Environmental conditions and measurements sample_temperature_unit_when_received: - rank: 140 + rank: 139 slot_group: Environmental conditions and measurements library_id: - rank: 141 + rank: 140 slot_group: Sequence information sequencing_assay_type: - rank: 142 + rank: 141 slot_group: Sequence information sequencing_date: - rank: 143 + rank: 142 slot_group: Sequence information purpose_of_sequencing__: - rank: 144 + rank: 143 slot_group: Sequence information purpose_of_sequencing_details: - rank: 145 + rank: 144 slot_group: Sequence information sequenced_by: - rank: 146 + rank: 145 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 147 + rank: 146 slot_group: Sequence information sequenced_by_contact_name: - rank: 148 + rank: 147 slot_group: Sequence information sequenced_by_contact_email: - rank: 149 + rank: 148 slot_group: Sequence information sequence_submitted_by: - rank: 150 + rank: 149 slot_group: Sequence information sequence_submitter_contact_email: - rank: 151 + rank: 150 slot_group: Sequence information nucleic_acid_extraction_method: - rank: 152 - slot_group: Sample collection and processing + rank: 151 + slot_group: Sequence information nucleic_acid_extraction_kit: - rank: 153 - slot_group: Sample collection and processing + rank: 152 + slot_group: Sequence information endogenous_control_details: - rank: 154 - slot_group: Sample collection and processing + rank: 153 + slot_group: Sequence information sequencing_project_name: - rank: 155 + rank: 154 slot_group: Sequence information sequencing_platform: - rank: 156 + rank: 155 slot_group: Sequence information sequencing_instrument: - rank: 157 + rank: 156 slot_group: Sequence information library_preparation_kit: - rank: 158 + rank: 157 slot_group: Sequence information dna_fragment_length: - rank: 159 + rank: 158 slot_group: Sequence information genomic_target_enrichment_method: - rank: 160 + rank: 159 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 161 + rank: 160 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 162 + rank: 161 slot_group: Sequence information amplicon_size: - rank: 163 + rank: 162 slot_group: Sequence information sequencing_flow_cell_version: - rank: 164 + rank: 163 slot_group: Sequence information sequencing_protocol: - rank: 165 + rank: 164 slot_group: Sequence information r1_fastq_filename: - rank: 166 + rank: 165 slot_group: Sequence information r2_fastq_filename: - rank: 167 + rank: 166 slot_group: Sequence information fast5_filename: - rank: 168 + rank: 167 slot_group: Sequence information genome_sequence_file_name: - rank: 169 + rank: 168 slot_group: Sequence information assembly_filename: - rank: 170 + rank: 169 slot_group: Sequence information quality_control_method_name: - rank: 171 + rank: 170 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 172 + rank: 171 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 173 + rank: 172 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 174 + rank: 173 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 175 + rank: 174 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 176 + rank: 175 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 177 + rank: 176 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 178 + rank: 177 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 179 + rank: 178 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 180 + rank: 179 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 181 + rank: 180 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 182 + rank: 181 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 183 + rank: 182 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 184 + rank: 183 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 185 + rank: 184 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 186 + rank: 185 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 187 + rank: 186 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 188 + rank: 187 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 189 + rank: 188 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 190 + rank: 189 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 191 + rank: 190 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 192 + rank: 191 slot_group: Bioinformatics and QC metrics n50: - rank: 193 + rank: 192 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 194 + rank: 193 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 195 + rank: 194 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 196 + rank: 195 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 197 + rank: 196 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 198 + rank: 197 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 199 + rank: 198 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 200 + rank: 199 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 201 + rank: 200 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 202 + rank: 201 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 203 + rank: 202 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 204 + rank: 203 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 205 + rank: 204 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 206 + rank: 205 slot_group: Taxonomic identification information genetic_target_name: - rank: 207 + rank: 206 slot_group: Pathogen diagnostic testing genetic_target_region: - rank: 208 + rank: 207 slot_group: Pathogen diagnostic testing genetic_target_region_reference_genome: - rank: 209 + rank: 208 slot_group: Pathogen diagnostic testing diagnostic_target_presence: - rank: 210 + rank: 209 slot_group: Pathogen diagnostic testing diagnostic_measurement_value: - rank: 211 + rank: 210 slot_group: Pathogen diagnostic testing diagnostic_measurement_unit: - rank: 212 + rank: 211 slot_group: Pathogen diagnostic testing diagnostic_measurement_method: - rank: 213 + rank: 212 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_value: - rank: 214 + rank: 213 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_units: - rank: 215 + rank: 214 slot_group: Pathogen diagnostic testing diagnostic_testing_details: - rank: 216 + rank: 215 slot_group: Pathogen diagnostic testing prevalence_metrics: - rank: 217 + rank: 216 slot_group: Risk assessment information prevalence_metrics_details: - rank: 218 + rank: 217 slot_group: Risk assessment information stage_of_production: - rank: 219 + rank: 218 slot_group: Risk assessment information experimental_intervention: - rank: 220 + rank: 219 slot_group: Risk assessment information experiment_intervention_details: - rank: 221 + rank: 220 slot_group: Risk assessment information HPAIEnviro: name: HPAIEnviro @@ -2607,7 +2599,6 @@ classes: - populated_area_type - sampling_weather_conditions - presampling_weather_conditions - - precipitation_measurement_value - water_depth - water_depth_units - sediment_depth @@ -2616,7 +2607,7 @@ classes: - air_temperature_units - water_temperature - water_temperature_units - - weather_type + - precipitation_measurement_value - precipitation_measurement_unit - precipitation_measurement_method - ambient_temperature_measurement_value @@ -2957,476 +2948,473 @@ classes: presampling_weather_conditions: rank: 64 slot_group: Environmental conditions and measurements - precipitation_measurement_value: + water_depth: rank: 65 slot_group: Environmental conditions and measurements - water_depth: + water_depth_units: rank: 66 slot_group: Environmental conditions and measurements - water_depth_units: + sediment_depth: rank: 67 slot_group: Environmental conditions and measurements - sediment_depth: + sediment_depth_units: rank: 68 slot_group: Environmental conditions and measurements - sediment_depth_units: + air_temperature: rank: 69 slot_group: Environmental conditions and measurements - air_temperature: + air_temperature_units: rank: 70 slot_group: Environmental conditions and measurements - air_temperature_units: + water_temperature: rank: 71 slot_group: Environmental conditions and measurements - water_temperature: + water_temperature_units: rank: 72 slot_group: Environmental conditions and measurements - water_temperature_units: + precipitation_measurement_value: rank: 73 slot_group: Environmental conditions and measurements - weather_type: - rank: 74 - slot_group: Environmental conditions and measurements precipitation_measurement_unit: - rank: 75 + rank: 74 slot_group: Environmental conditions and measurements precipitation_measurement_method: - rank: 76 + rank: 75 slot_group: Environmental conditions and measurements ambient_temperature_measurement_value: - rank: 77 + rank: 76 slot_group: Environmental conditions and measurements ambient_temperature_measurement_unit: - rank: 78 + rank: 77 slot_group: Environmental conditions and measurements ph_measurement_value: - rank: 79 + rank: 78 slot_group: Environmental conditions and measurements ph_measurement_method: - rank: 80 + rank: 79 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_value: - rank: 81 + rank: 80 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_unit: - rank: 82 + rank: 81 slot_group: Environmental conditions and measurements total_daily_flow_rate_measurement_method: - rank: 83 + rank: 82 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_value: - rank: 84 + rank: 83 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_unit: - rank: 85 + rank: 84 slot_group: Environmental conditions and measurements instantaneous_flow_rate_measurement_method: - rank: 86 + rank: 85 slot_group: Environmental conditions and measurements turbidity_measurement_value: - rank: 87 + rank: 86 slot_group: Environmental conditions and measurements turbidity_measurement_unit: - rank: 88 + rank: 87 slot_group: Environmental conditions and measurements turbidity_measurement_method: - rank: 89 + rank: 88 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_value: - rank: 90 + rank: 89 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_unit: - rank: 91 + rank: 90 slot_group: Environmental conditions and measurements dissolved_oxygen_measurement_method: - rank: 92 + rank: 91 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_value: - rank: 93 + rank: 92 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_unit: - rank: 94 + rank: 93 slot_group: Environmental conditions and measurements oxygen_reduction_potential_orp_measurement_method: - rank: 95 + rank: 94 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_value: - rank: 96 + rank: 95 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_unit: - rank: 97 + rank: 96 slot_group: Environmental conditions and measurements chemical_oxygen_demand_cod_measurement_method: - rank: 98 + rank: 97 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_value: - rank: 99 + rank: 98 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit: - rank: 100 + rank: 99 slot_group: Environmental conditions and measurements carbonaceous_biochemical_oxygen_demand_cbod_measurement_method: - rank: 101 + rank: 100 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_value: - rank: 102 + rank: 101 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_unit: - rank: 103 + rank: 102 slot_group: Environmental conditions and measurements total_suspended_solids_tss_measurement_method: - rank: 104 + rank: 103 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_value: - rank: 105 + rank: 104 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_unit: - rank: 106 + rank: 105 slot_group: Environmental conditions and measurements total_dissolved_solids_tds_measurement_method: - rank: 107 + rank: 106 slot_group: Environmental conditions and measurements total_solids_ts_measurement_value: - rank: 108 + rank: 107 slot_group: Environmental conditions and measurements total_solids_ts_measurement_unit: - rank: 109 + rank: 108 slot_group: Environmental conditions and measurements total_solids_ts_measurement_method: - rank: 110 + rank: 109 slot_group: Environmental conditions and measurements alkalinity_measurement_value: - rank: 111 + rank: 110 slot_group: Environmental conditions and measurements alkalinity_measurement_unit: - rank: 112 + rank: 111 slot_group: Environmental conditions and measurements alkalinity_measurement_method: - rank: 113 + rank: 112 slot_group: Environmental conditions and measurements conductivity_measurement_value: - rank: 114 + rank: 113 slot_group: Environmental conditions and measurements conductivity_measurement_unit: - rank: 115 + rank: 114 slot_group: Environmental conditions and measurements conductivity_measurement_method: - rank: 116 + rank: 115 slot_group: Environmental conditions and measurements salinity_measurement_value: - rank: 117 + rank: 116 slot_group: Environmental conditions and measurements salinity_measurement_unit: - rank: 118 + rank: 117 slot_group: Environmental conditions and measurements salinity_measurement_method: - rank: 119 + rank: 118 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_value: - rank: 120 + rank: 119 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_unit: - rank: 121 + rank: 120 slot_group: Environmental conditions and measurements total_nitrogen_tn_measurement_method: - rank: 122 + rank: 121 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_value: - rank: 123 + rank: 122 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_unit: - rank: 124 + rank: 123 slot_group: Environmental conditions and measurements total_phosphorus_tp_measurement_method: - rank: 125 + rank: 124 slot_group: Environmental conditions and measurements fecal_contamination_indicator_: - rank: 126 + rank: 125 slot_group: Environmental conditions and measurements fecal_contamination_value: - rank: 127 + rank: 126 slot_group: Environmental conditions and measurements fecal_contamination_unit: - rank: 128 + rank: 127 slot_group: Environmental conditions and measurements fecal_contamination_method: - rank: 129 + rank: 128 slot_group: Environmental conditions and measurements fecal_coliform_count_value: - rank: 130 + rank: 129 slot_group: Environmental conditions and measurements fecal_coliform_count_unit: - rank: 131 + rank: 130 slot_group: Environmental conditions and measurements fecal_coliform_count_method: - rank: 132 + rank: 131 slot_group: Environmental conditions and measurements urinary_contamination_indicator: - rank: 133 + rank: 132 slot_group: Environmental conditions and measurements urinary_contamination_value: - rank: 134 + rank: 133 slot_group: Environmental conditions and measurements urinary_contamination_unit: - rank: 135 + rank: 134 slot_group: Environmental conditions and measurements urinary_contamination_method: - rank: 136 + rank: 135 slot_group: Environmental conditions and measurements sample_temperature_value_at_collection: - rank: 137 + rank: 136 slot_group: Environmental conditions and measurements sample_temperature_unit_at_collection: - rank: 138 + rank: 137 slot_group: Environmental conditions and measurements sample_temperature_value_when_received: - rank: 139 + rank: 138 slot_group: Environmental conditions and measurements sample_temperature_unit_when_received: - rank: 140 + rank: 139 slot_group: Environmental conditions and measurements library_id: - rank: 141 + rank: 140 slot_group: Sequence information sequencing_assay_type: - rank: 142 + rank: 141 slot_group: Sequence information sequencing_date: - rank: 143 + rank: 142 slot_group: Sequence information purpose_of_sequencing__: - rank: 144 + rank: 143 slot_group: Sequence information purpose_of_sequencing_details: - rank: 145 + rank: 144 slot_group: Sequence information sequenced_by: - rank: 146 + rank: 145 slot_group: Sequence information sequenced_by_laboratory_name: - rank: 147 + rank: 146 slot_group: Sequence information sequenced_by_contact_name: - rank: 148 + rank: 147 slot_group: Sequence information sequenced_by_contact_email: - rank: 149 + rank: 148 slot_group: Sequence information sequence_submitted_by: - rank: 150 + rank: 149 slot_group: Sequence information sequence_submitter_contact_email: - rank: 151 + rank: 150 slot_group: Sequence information nucleic_acid_extraction_method: - rank: 152 - slot_group: Sample collection and processing + rank: 151 + slot_group: Sequence information nucleic_acid_extraction_kit: - rank: 153 - slot_group: Sample collection and processing + rank: 152 + slot_group: Sequence information endogenous_control_details: - rank: 154 - slot_group: Sample collection and processing + rank: 153 + slot_group: Sequence information sequencing_project_name: - rank: 155 + rank: 154 slot_group: Sequence information sequencing_platform: - rank: 156 + rank: 155 slot_group: Sequence information sequencing_instrument: - rank: 157 + rank: 156 slot_group: Sequence information library_preparation_kit: - rank: 158 + rank: 157 slot_group: Sequence information dna_fragment_length: - rank: 159 + rank: 158 slot_group: Sequence information genomic_target_enrichment_method: - rank: 160 + rank: 159 slot_group: Sequence information genomic_target_enrichment_method_details: - rank: 161 + rank: 160 slot_group: Sequence information amplicon_pcr_primer_scheme: - rank: 162 + rank: 161 slot_group: Sequence information amplicon_size: - rank: 163 + rank: 162 slot_group: Sequence information sequencing_flow_cell_version: - rank: 164 + rank: 163 slot_group: Sequence information sequencing_protocol: - rank: 165 + rank: 164 slot_group: Sequence information r1_fastq_filename: - rank: 166 + rank: 165 slot_group: Sequence information r2_fastq_filename: - rank: 167 + rank: 166 slot_group: Sequence information fast5_filename: - rank: 168 + rank: 167 slot_group: Sequence information genome_sequence_file_name: - rank: 169 + rank: 168 slot_group: Sequence information assembly_filename: - rank: 170 + rank: 169 slot_group: Sequence information quality_control_method_name: - rank: 171 + rank: 170 slot_group: Bioinformatics and QC metrics quality_control_method_version: - rank: 172 + rank: 171 slot_group: Bioinformatics and QC metrics quality_control_determination: - rank: 173 + rank: 172 slot_group: Bioinformatics and QC metrics quality_control_issues: - rank: 174 + rank: 173 slot_group: Bioinformatics and QC metrics quality_control_details: - rank: 175 + rank: 174 slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 176 + rank: 175 slot_group: Bioinformatics and QC metrics dehosting_method: - rank: 177 + rank: 176 slot_group: Bioinformatics and QC metrics sequence_assembly_software_name: - rank: 178 + rank: 177 slot_group: Bioinformatics and QC metrics sequence_assembly_software_version: - rank: 179 + rank: 178 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 180 + rank: 179 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 181 + rank: 180 slot_group: Bioinformatics and QC metrics breadth_of_coverage_value: - rank: 182 + rank: 181 slot_group: Bioinformatics and QC metrics depth_of_coverage_value: - rank: 183 + rank: 182 slot_group: Bioinformatics and QC metrics depth_of_coverage_threshold: - rank: 184 + rank: 183 slot_group: Bioinformatics and QC metrics genome_completeness: - rank: 185 + rank: 184 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 186 + rank: 185 slot_group: Bioinformatics and QC metrics number_of_total_reads: - rank: 187 + rank: 186 slot_group: Bioinformatics and QC metrics number_of_unique_reads: - rank: 188 + rank: 187 slot_group: Bioinformatics and QC metrics minimum_posttrimming_read_length: - rank: 189 + rank: 188 slot_group: Bioinformatics and QC metrics number_of_contigs: - rank: 190 + rank: 189 slot_group: Bioinformatics and QC metrics percent_ns_across_total_genome_length: - rank: 191 + rank: 190 slot_group: Bioinformatics and QC metrics ns_per_100_kbp: - rank: 192 + rank: 191 slot_group: Bioinformatics and QC metrics n50: - rank: 193 + rank: 192 slot_group: Bioinformatics and QC metrics percent_read_contamination_: - rank: 194 + rank: 193 slot_group: Bioinformatics and QC metrics sequence_assembly_length: - rank: 195 + rank: 194 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 196 + rank: 195 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 197 + rank: 196 slot_group: Bioinformatics and QC metrics deduplication_method: - rank: 198 + rank: 197 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 199 + rank: 198 slot_group: Bioinformatics and QC metrics read_mapping_software_name: - rank: 200 + rank: 199 slot_group: Taxonomic identification information read_mapping_software_version: - rank: 201 + rank: 200 slot_group: Taxonomic identification information taxonomic_reference_database_name: - rank: 202 + rank: 201 slot_group: Taxonomic identification information taxonomic_reference_database_version: - rank: 203 + rank: 202 slot_group: Taxonomic identification information taxonomic_analysis_report_filename: - rank: 204 + rank: 203 slot_group: Taxonomic identification information taxonomic_analysis_date: - rank: 205 + rank: 204 slot_group: Taxonomic identification information read_mapping_criteria: - rank: 206 + rank: 205 slot_group: Taxonomic identification information genetic_target_name: - rank: 207 + rank: 206 slot_group: Pathogen diagnostic testing genetic_target_region: - rank: 208 + rank: 207 slot_group: Pathogen diagnostic testing genetic_target_region_reference_genome: - rank: 209 + rank: 208 slot_group: Pathogen diagnostic testing diagnostic_target_presence: - rank: 210 + rank: 209 slot_group: Pathogen diagnostic testing diagnostic_measurement_value: - rank: 211 + rank: 210 slot_group: Pathogen diagnostic testing diagnostic_measurement_unit: - rank: 212 + rank: 211 slot_group: Pathogen diagnostic testing diagnostic_measurement_method: - rank: 213 + rank: 212 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_value: - rank: 214 + rank: 213 slot_group: Pathogen diagnostic testing diagnostic_testing_threshold_units: - rank: 215 + rank: 214 slot_group: Pathogen diagnostic testing diagnostic_testing_details: - rank: 216 + rank: 215 slot_group: Pathogen diagnostic testing prevalence_metrics: - rank: 217 + rank: 216 slot_group: Risk assessment information prevalence_metrics_details: - rank: 218 + rank: 217 slot_group: Risk assessment information stage_of_production: - rank: 219 + rank: 218 slot_group: Risk assessment information experimental_intervention: - rank: 220 + rank: 219 slot_group: Risk assessment information experiment_intervention_details: - rank: 221 + rank: 220 slot_group: Risk assessment information HPAIHost: name: HPAIHost @@ -3762,19 +3750,19 @@ classes: slot_group: Sample collection and processing host_common_name: rank: 53 - slot_group: Host information + slot_group: Host Information host_scientific_name: rank: 54 - slot_group: Host information + slot_group: Host Information host_ecotype: rank: 55 - slot_group: Host information + slot_group: Host Information host_breed: rank: 56 - slot_group: Host information + slot_group: Host Information host_food_production_name: rank: 57 - slot_group: Host information + slot_group: Host Information host_age: rank: 58 slot_group: Host Information @@ -3783,10 +3771,10 @@ classes: slot_group: Host Information host_age_bin: rank: 60 - slot_group: Host information + slot_group: Host Information host_disease: rank: 61 - slot_group: Host information + slot_group: Host Information host_health_state: rank: 62 slot_group: Host Information @@ -3894,13 +3882,13 @@ classes: slot_group: Sequence information nucleic_acid_extraction_method: rank: 97 - slot_group: Sample collection and processing + slot_group: Sequence information nucleic_acid_extraction_kit: rank: 98 - slot_group: Sample collection and processing + slot_group: Sequence information endogenous_control_details: rank: 99 - slot_group: Sample collection and processing + slot_group: Sequence information sequencing_project_name: rank: 100 slot_group: Sequence information @@ -4404,7 +4392,7 @@ slots: name: influenza_subtype title: influenza_subtype slot_uri: GENEPIO:0101108 - range: InfluenzaSubsubtypeMenu + range: InfluenzaSubtypeMenu multivalued: true required: true influenza_subtyping_scheme_name: @@ -5511,7 +5499,7 @@ slots: comments: Provide the populated area type from the pick list. slot_uri: GENEPIO:0100778 any_of: - - range: populated area type menu + - range: PopulatedAreaTypeMenu - range: NullValueMenu examples: - value: Urban area @@ -5540,19 +5528,6 @@ slots: multivalued: true examples: - value: Drizzle - precipitation_measurement_value: - name: precipitation_measurement_value - title: precipitation measurement value - description: The amount of water which has fallen during a precipitation process. - comments: Provide the quantity of precipitation in the area leading up to the - time of sample collection. - slot_uri: GENEPIO:0100911 - any_of: - - range: WhitespaceMinimizedString - - range: NullValueMenu - recommended: true - examples: - - value: '12' water_depth: name: water_depth title: water_depth @@ -5635,19 +5610,19 @@ slots: - range: NullValueMenu examples: - value: degree Celsius (C) [UO:0000027] - weather_type: - name: weather_type - title: weather_type - description: The state of the atmosphere at a place and time as regards heat, - dryness, sunshine, wind, rain, etc. - comments: Provide the weather conditions at the time of sample collection. - slot_uri: GENEPIO:0100442 + precipitation_measurement_value: + name: precipitation_measurement_value + title: precipitation measurement value + description: The amount of water which has fallen during a precipitation process. + comments: Provide the quantity of precipitation in the area leading up to the + time of sample collection. + slot_uri: GENEPIO:0100911 any_of: - - range: WeatherTypeMenu + - range: WhitespaceMinimizedString - range: NullValueMenu - multivalued: true + recommended: true examples: - - value: Rain [ENVO:01001564] + - value: '12' precipitation_measurement_unit: name: precipitation_measurement_unit title: precipitation measurement unit @@ -6154,7 +6129,7 @@ slots: comments: Provide the units of the measured TP. slot_uri: GENEPIO:0100812 any_of: - - range: TotalPhosphorusTPMeasurementUnitMenu + - range: TotalPhosphorpusTpMeasurementUnitMenu - range: NullValueMenu examples: - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) @@ -7209,7 +7184,7 @@ slots: comments: Provide the stage of food production as free text. slot_uri: GENEPIO:0100482 any_of: - - range: StageOfProductionMenu + - range: WhitespaceMinimizedString - range: NullValueMenu recommended: true examples: @@ -9534,9 +9509,9 @@ enums: Residual sample status unkown [GENEPIO:0101089]: text: Residual sample status unkown [GENEPIO:0101089] meaning: GENEPIO:0101089 - PurposeOfSampling: - name: PurposeOfSampling - title: purpose of sampling + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation [GENEPIO:0100001]: text: Cluster/Outbreak investigation [GENEPIO:0100001] @@ -9583,9 +9558,9 @@ enums: description: A sampling strategy in which individuals are sampled for surveillance investigations. meaning: GENEPIO:0100004 - PresamplingActivity: - name: PresamplingActivity - title: presampling activity + PresamplingActivityMenu: + name: PresamplingActivityMenu + title: presampling activity menu permissible_values: Addition of substances to food/water [GENEPIO:0100536]: text: Addition of substances to food/water [GENEPIO:0100536] @@ -9648,9 +9623,9 @@ enums: This includes any preparation intended for active immunological prophylaxis or treatment. meaning: NCIT:C15346 - SampleStorageDurationUnit: - name: SampleStorageDurationUnit - title: sample storage duration unit + SampleStorageDurationUnitMenu: + name: SampleStorageDurationUnitMenu + title: sample storage duration unit menu permissible_values: Second [UO:0000010]: text: Second [UO:0000010] @@ -9684,9 +9659,9 @@ enums: description: A time unit which is equal to 365 days, or 366 days during a leap year. meaning: UO:0000036 - SpecimenProcessing: - name: SpecimenProcessing - title: specimen processing + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Concentration [OBI:0600041]: text: Concentration [OBI:0600041] @@ -9707,9 +9682,9 @@ enums: text: Pooling specimens [OBI:0600016] description: Physical combination of several instances of like material. meaning: OBI:0600016 - ExperimentalSpecimenRoleType: - name: ExperimentalSpecimenRoleType - title: experimental specimen role type + ExperimentalSpecimenRoleTypeMenu: + name: ExperimentalSpecimenRoleTypeMenu + title: experimental specimen role type menu permissible_values: Positive experimental control [GENEPIO:0101018]: text: Positive experimental control [GENEPIO:0101018] @@ -10612,9 +10587,9 @@ enums: description: An age group that stratifies the age of a case to be greater than or equal to 100 years old. meaning: GENEPIO:0100059 - HostGender: - name: HostGender - title: host_gender + HostGenderMenu: + name: HostGenderMenu + title: host_gender menu permissible_values: Female [NCIT:C46110]: text: Female [NCIT:C46110] @@ -12198,18 +12173,32 @@ enums: permissible_values: <10 people: text: <10 people + description: An estimation of population size for a group smaller than 10 + people. 10 - 100 people: text: 10 - 100 people + description: An estimation of population size for a group smaller than 100 + people and larger than 10 people. 100 - 1,000 people: text: 100 - 1,000 people + description: An estimation of population size for a group smaller than 1,000 + people and larger than 100 people. 1,000 - 10,000 people: text: 1,000 - 10,000 people + description: An estimation of population size for a group smaller than 10,000 + people and larger than 1,000 people. 10,000 - 100,000 people: text: 10,000 - 100,000 people + description: An estimation of population size for a group smaller than 100,000 + people and larger than 10,000 people. 100,000 - 1,000,000 people: text: 100,000 - 1,000,000 people + description: An estimation of population size for a group smaller than 1,000,000 + people and larger than 100,000 people. 1,000,000+ people: text: 1,000,000+ people + description: An estimation of population size for a group larger than 1,000,000 + people. WaterCatchmentAreaHumanPopulationDensityUnitMenu: name: WaterCatchmentAreaHumanPopulationDensityUnitMenu title: water_catchment_area_human_population_density_unit menu @@ -12379,6 +12368,875 @@ enums: text: foot (ft) [UO:0010013] description: A non-SI unit of length which is approximately 0.3048 meters. meaning: UO:0010013 + WaterDepthUnitsMenu: + name: WaterDepthUnitsMenu + title: water_depth_units menu + permissible_values: + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m + meaning: UO:0000015 + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. + meaning: UO:0000008 + kilometer (km) [UO:0010066]: + text: kilometer (km) [UO:0010066] + description: A length unit which is equal to one thousand meters. + meaning: UO:0010066 + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. + meaning: UO:0010011 + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. + meaning: UO:0010013 + SedimentDepthUnitsMenu: + name: SedimentDepthUnitsMenu + title: sediment_depth_units menu + permissible_values: + centimeter (cm) [UO:0000015]: + text: centimeter (cm) [UO:0000015] + description: A length unit which is equal to one hundredth of a meter or 10^[-2] + m + meaning: UO:0000015 + meter (m) [UO:0000008]: + text: meter (m) [UO:0000008] + description: An SI unit of length defined as the length of the path travelled + by light in a vacuum in 1/299792458th of a second. + meaning: UO:0000008 + kilometer (km) [UO:0010066]: + text: kilometer (km) [UO:0010066] + description: A length unit which is equal to one thousand meters. + meaning: UO:0010066 + inch (in) [UO:0010011]: + text: inch (in) [UO:0010011] + description: A non-SI unit of length defined as one twelfth of a foot. + meaning: UO:0010011 + foot (ft) [UO:0010013]: + text: foot (ft) [UO:0010013] + description: A non-SI unit of length which is approximately 0.3048 meters. + meaning: UO:0010013 + AirTemperatureUnitsMenu: + name: AirTemperatureUnitsMenu + title: air_temperature_units menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + WaterTemperatureUnitsMenu: + name: WaterTemperatureUnitsMenu + title: water_temperature_units menu + permissible_values: + degree Fahrenheit (F) [UO:0000195]: + text: degree Fahrenheit (F) [UO:0000195] + description: A unit of temperature on a scale where water freezes at 32 degrees + and boils at 212 degrees under standard conditions. + meaning: UO:0000195 + degree Celsius (C) [UO:0000027]: + text: degree Celsius (C) [UO:0000027] + description: A unit of temperature on a scale where water freezes at 0 degrees + and boils at 100 degrees under standard conditions. + meaning: UO:0000027 + SequencingPlatformMenu: + name: SequencingPlatformMenu + title: sequencing_platform menu + permissible_values: + Illumina [GENEPIO:0001923]: + text: Illumina [GENEPIO:0001923] + description: A sequencing platform provided by the Illumina company. + meaning: GENEPIO:0001923 + Pacific Biosciences [GENEPIO:0001927]: + text: Pacific Biosciences [GENEPIO:0001927] + description: A sequencing platform provided by the Pacific Biosciences company. + meaning: GENEPIO:0001927 + Ion Torrent [GENEPIO:0002683]: + text: Ion Torrent [GENEPIO:0002683] + description: A sequencing platform provided by the Ion Torrent company. + meaning: GENEPIO:0002683 + Oxford Nanopore Technologies [GENEPIO:0100986]: + text: Oxford Nanopore Technologies [GENEPIO:0100986] + description: An sequencing platform that is developing and selling nanopore + sequencing products and is based in the UK. + meaning: GENEPIO:0100986 + BGI Genomics [GENEPIO:0004324]: + text: BGI Genomics [GENEPIO:0004324] + description: A sequencing platform provided by the BGI Genomics company. + meaning: GENEPIO:0004324 + MGI [GENEPIO:0004325]: + text: MGI [GENEPIO:0004325] + description: A sequencing platform provided by the MGI company. + meaning: GENEPIO:0004325 + Roche LS454 [GENEPIO:0001926]: + text: Roche LS454 [GENEPIO:0001926] + description: A sequencing platform provided by the 454 Life Sciences company. + meaning: GENEPIO:0001926 + SOLiD sequencing [GENEPIO:0002684]: + text: SOLiD sequencing [GENEPIO:0002684] + description: A sequencing platform provided by Life Technologies Corporation. + meaning: GENEPIO:0002684 + Complete Genomics [GENEPIO:0001924]: + text: Complete Genomics [GENEPIO:0001924] + description: An in-house sequencing platform provided by Complete Genomics. + meaning: GENEPIO:0001924 + Helicos [GENEPIO:0002682]: + text: Helicos [GENEPIO:0002682] + description: A sequencing platform brand provided by Helicos corporation (now + defunct). + meaning: GENEPIO:0002682 + Applied Biosystems [GENEPIO:0100985]: + text: Applied Biosystems [GENEPIO:0100985] + description: A sequencing platform provided by ThermoFisher. + meaning: GENEPIO:0100985 + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing_instrument menu + permissible_values: + Illumina [GENEPIO:0100105]: + text: Illumina [GENEPIO:0100105] + description: A DNA sequencer manufactured by the Illumina corporation. + meaning: GENEPIO:0100105 + Illumina Genome Analyzer [GENEPIO:0100106]: + text: Illumina Genome Analyzer [GENEPIO:0100106] + description: A DNA sequencer manufactured by Solexa as one of its first sequencer + lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data + in a single run. + meaning: GENEPIO:0100106 + is_a: Illumina [GENEPIO:0100105] + Illumina Genome Analyzer II [OBI:0000703]: + text: Illumina Genome Analyzer II [OBI:0000703] + description: A DNA sequencer manufactured by the Illumina (Solexa) corporation, + which supports sequencing of single or paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0000703 + is_a: Illumina [GENEPIO:0100105] + Illumina Genome Analyzer IIx [OBI:0002000]: + text: Illumina Genome Analyzer IIx [OBI:0002000] + description: An Illumina Genome Analyzer II which is manufactured by the Illumina + corporation. It supports sequencing of single, long or short insert paired + end clone libraries relying on sequencing by synthesis technology. The Genome + Analyzer IIx is the most widely adopted next-generation sequencing platform + and proven and published across the broadest range of research applications. + meaning: OBI:0002000 + is_a: Illumina [GENEPIO:0100105] + Illumina HiScanSQ [GENEPIO:0100109]: + text: Illumina HiScanSQ [GENEPIO:0100109] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing + and microarray-based analyses as well as an "SQ Module" to support microfluidics. + meaning: GENEPIO:0100109 + is_a: Illumina [GENEPIO:0100105] + Illumina HiSeq [GENEPIO:0100110]: + text: Illumina HiSeq [GENEPIO:0100110] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + meaning: GENEPIO:0100110 + is_a: Illumina [GENEPIO:0100105] + Illumina HiSeq X [GENEPIO:0100111]: + text: Illumina HiSeq X [GENEPIO:0100111] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that enables sufficient depth and coverage + to produce the first 30x human genome for $1000. + meaning: GENEPIO:0100111 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X Five [GENEPIO:0100112]: + text: Illumina HiSeq X Five [GENEPIO:0100112] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing + Systems. + meaning: GENEPIO:0100112 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq X Ten [GENEPIO:0100113]: + text: Illumina HiSeq X Ten [GENEPIO:0100113] + description: A DNA sequencer that consists of a set of 10 HiSeq X Sequencing + Systems. + meaning: GENEPIO:0100113 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 1000 [OBI:0002022]: + text: Illumina HiSeq 1000 [OBI:0002022] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35 Gb per day. It supports + sequencing of single, long or short insert paired end clone libraries relying + on sequencing by synthesis technology. + meaning: OBI:0002022 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 1500 [GENEPIO:0100115]: + text: Illumina HiSeq 1500 [GENEPIO:0100115] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with a single flow cell and a throughput of up to 35-50 Gb per day. + meaning: GENEPIO:0100115 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 2000 [OBI:0002001]: + text: Illumina HiSeq 2000 [OBI:0002001] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 55 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for multiple samples in a single run. + meaning: OBI:0002001 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 2500 [OBI:0002002]: + text: Illumina HiSeq 2500 [OBI:0002002] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and a throughput of up to 160 Gb per day. Built upon + sequencing by synthesis technology, the machine is optimized for generation + of data for batching multiple samples or rapid results on a few samples. + meaning: OBI:0002002 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 3000 [OBI:0002048]: + text: Illumina HiSeq 3000 [OBI:0002048] + description: A DNA sequencer manufactured by Illumina corporation, with a + single flow cell and a throughput of more than 200 Gb per day. + meaning: OBI:0002048 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina HiSeq 4000 [OBI:0002049]: + text: Illumina HiSeq 4000 [OBI:0002049] + description: A DNA sequencer manufactured by Illumina corporation, with two + flow cell and a throughput of more than 400 Gb per day. + meaning: OBI:0002049 + is_a: Illumina HiSeq [GENEPIO:0100110] + Illumina iSeq [GENEPIO:0100120]: + text: Illumina iSeq [GENEPIO:0100120] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight. + meaning: GENEPIO:0100120 + is_a: Illumina [GENEPIO:0100105] + Illumina iSeq 100 [GENEPIO:0100121]: + text: Illumina iSeq 100 [GENEPIO:0100121] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that is lightweight and has an output capacity + between 144MB-1.2GB. + meaning: GENEPIO:0100121 + is_a: Illumina iSeq [GENEPIO:0100120] + Illumina NovaSeq [GENEPIO:0100122]: + text: Illumina NovaSeq [GENEPIO:0100122] + description: A DNA sequencer manufactured by the Illumina corporation using + sequence-by-synthesis chemistry that has an output capacity of 6 Tb and + 20 billion reads in dual flow cell mode. + meaning: GENEPIO:0100122 + is_a: Illumina [GENEPIO:0100105] + Illumina NovaSeq 6000 [GENEPIO:0100123]: + text: Illumina NovaSeq 6000 [GENEPIO:0100123] + description: A DNA sequencer which is manufactured by the Illumina corporation, + with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). + The sequencer utilizes synthesis technology and patterned flow cells to + optimize throughput and even spacing of sequencing clusters. + meaning: GENEPIO:0100123 + is_a: Illumina NovaSeq [GENEPIO:0100122] + Illumina MiniSeq [GENEPIO:0100124]: + text: Illumina MiniSeq [GENEPIO:0100124] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. + meaning: GENEPIO:0100124 + is_a: Illumina [GENEPIO:0100105] + Illumina MiSeq [OBI:0002003]: + text: Illumina MiSeq [OBI:0002003] + description: A DNA sequencer which is manufactured by the Illumina corporation. + Built upon sequencing by synthesis technology, the machine provides an end-to-end + solution (cluster generation, amplification, sequencing, and data analysis) + in a single machine. + meaning: OBI:0002003 + is_a: Illumina [GENEPIO:0100105] + Illumina NextSeq [GENEPIO:0100126]: + text: Illumina NextSeq [GENEPIO:0100126] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 1.65-7.5 Gb. + meaning: GENEPIO:0100126 + is_a: Illumina [GENEPIO:0100105] + Illumina NextSeq 500 [OBI:0002021]: + text: Illumina NextSeq 500 [OBI:0002021] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. + meaning: OBI:0002021 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 550 [GENEPIO:0100128]: + text: Illumina NextSeq 550 [GENEPIO:0100128] + description: A DNA sequencer which is a desktop sequencer ideal for smaller-scale + studies manufactured by the Illumina corporation. It supports sequencing + of single, long or short insert paired end clone libraries relying on sequencing + by synthesis technology. The 550 is an upgrade on the 500 model. + meaning: GENEPIO:0100128 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 1000 [GENEPIO:0004432]: + text: Illumina NextSeq 1000 [GENEPIO:0004432] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 + and P2 flow cells. + meaning: GENEPIO:0004432 + is_a: Illumina NextSeq [GENEPIO:0100126] + Illumina NextSeq 2000 [GENEPIO:0100129]: + text: Illumina NextSeq 2000 [GENEPIO:0100129] + description: A DNA sequencer which is manufactured by the Illumina corporation + using sequence-by-synthesis chemistry that fits on a benchtop and has an + output capacity of 30-360 Gb. + meaning: GENEPIO:0100129 + is_a: Illumina NextSeq [GENEPIO:0100126] + PacBio [GENEPIO:0100130]: + text: PacBio [GENEPIO:0100130] + description: A DNA sequencer manufactured by the Pacific Biosciences corporation. + meaning: GENEPIO:0100130 + PacBio RS [GENEPIO:0100131]: + text: PacBio RS [GENEPIO:0100131] + description: "A DNA sequencer manufactured by the Pacific Biosciences corporation\ + \ which utilizes \u201CSMRT Cells\u201D for single-molecule real-time sequencing.\ + \ The RS was the first model made by the company." + meaning: GENEPIO:0100131 + is_a: PacBio [GENEPIO:0100130] + PacBio RS II [OBI:0002012]: + text: PacBio RS II [OBI:0002012] + description: A DNA sequencer which is manufactured by the Pacific Biosciences + corporation. Built upon single molecule real-time sequencing technology, + the machine is optimized for generation with long reads and high consensus + accuracy. + meaning: OBI:0002012 + is_a: PacBio [GENEPIO:0100130] + PacBio Sequel [GENEPIO:0100133]: + text: PacBio Sequel [GENEPIO:0100133] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation with long reads and high consensus + accuracy, and manufactured by the Pacific Biosciences corporation + meaning: GENEPIO:0100133 + is_a: PacBio [GENEPIO:0100130] + PacBio Sequel II [GENEPIO:0100134]: + text: PacBio Sequel II [GENEPIO:0100134] + description: A DNA sequencer built upon single molecule real-time sequencing + technology, optimized for generation of highly accurate ("HiFi") long reads, + and which is manufactured by the Pacific Biosciences corporation. + meaning: GENEPIO:0100134 + is_a: PacBio [GENEPIO:0100130] + Ion Torrent [GENEPIO:0100135]: + text: Ion Torrent [GENEPIO:0100135] + description: A DNA sequencer manufactured by the Ion Torrent corporation. + meaning: GENEPIO:0100135 + Ion Torrent PGM [GENEPIO:0100136]: + text: Ion Torrent PGM [GENEPIO:0100136] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of 300 + MB - 1GB. + meaning: GENEPIO:0100136 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent Proton [GENEPIO:0100137]: + text: Ion Torrent Proton [GENEPIO:0100137] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and has an output capacity of up to + 15 Gb. + meaning: GENEPIO:0100137 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent S5 XL [GENEPIO:0100138]: + text: Ion Torrent S5 XL [GENEPIO:0100138] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material while producing data faster than the S5 model. + meaning: GENEPIO:0100138 + is_a: Ion Torrent [GENEPIO:0100135] + Ion Torrent S5 [GENEPIO:0100139]: + text: Ion Torrent S5 [GENEPIO:0100139] + description: A DNA sequencer manufactured by the Ion Torrent corporation which + utilizes Ion semiconductor sequencing and requires only a small amount of + input material. + meaning: GENEPIO:0100139 + is_a: Ion Torrent [GENEPIO:0100135] + Oxford Nanopore [GENEPIO:0100140]: + text: Oxford Nanopore [GENEPIO:0100140] + description: A DNA sequencer manufactured by the Oxford Nanopore corporation. + meaning: GENEPIO:0100140 + Oxford Nanopore Flongle [GENEPIO:0004433]: + text: Oxford Nanopore Flongle [GENEPIO:0004433] + description: An adapter for MinION or GridION DNA sequencers manufactured + by the Oxford Nanopore corporation that enables sequencing on smaller, single-use + flow cells. + meaning: GENEPIO:0004433 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore GridION [GENEPIO:0100141]: + text: Oxford Nanopore GridION [GENEPIO:0100141] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, that can run and analyze up to five individual flow cells producing + up to 150 Gb of data per run. The sequencer produces real-time results and + utilizes nanopore technology with the option of running the flow cells concurrently + or individual + meaning: GENEPIO:0100141 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore MinION [GENEPIO:0100142]: + text: Oxford Nanopore MinION [GENEPIO:0100142] + description: A portable DNA sequencer which is manufactured by the Oxford + Nanopore Technologies corporation, that uses consumable flow cells producing + up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time + results and utilizes nanopore technology with up to 512 nanopore channels + in the sensor array. + meaning: GENEPIO:0100142 + is_a: Oxford Nanopore [GENEPIO:0100140] + Oxford Nanopore PromethION [GENEPIO:0100143]: + text: Oxford Nanopore PromethION [GENEPIO:0100143] + description: A DNA sequencer that is manufactured by the Oxford Nanopore Technologies + corporation, capable of running up to 48 flow cells and producing up to + 7.6 Tb of data per run. The sequencer produces real-time results and utilizes + Nanopore technology, with each flow cell allowing up to 3,000 nanopores + to be sequencing simultaneously. + meaning: GENEPIO:0100143 + is_a: Oxford Nanopore [GENEPIO:0100140] + BGI Genomics sequencing instrument [GENEPIO:0100144]: + text: BGI Genomics sequencing instrument [GENEPIO:0100144] + description: A DNA sequencer manufactured by the BGI Genomics corporation. + meaning: GENEPIO:0100144 + BGISEQ-500 [GENEPIO:0100145]: + text: BGISEQ-500 [GENEPIO:0100145] + description: A DNA sequencer manufactured by the BGI Genomics corporation + that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + meaning: GENEPIO:0100145 + is_a: BGI Genomics sequencing instrument [GENEPIO:0100144] + MGI sequencing instrument [GENEPIO:0100146]: + text: MGI sequencing instrument [GENEPIO:0100146] + description: A DNA sequencer manufactured by the MGI corporation. + meaning: GENEPIO:0100146 + MGISEQ-2000RS [GENEPIO:0100971]: + text: MGISEQ-2000RS [GENEPIO:0100971] + description: An MGI sequencing instrument model that utilises DNA nanoball + and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing + ad which is capable of medium to high throughput sequencing. + meaning: GENEPIO:0100971 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G99 [GENEPIO:0100972]: + text: MGI DNBSEQ-G99 [GENEPIO:0100972] + description: An MGI sequencing instrument model that utilises DNA nanoball + and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing + and which adopts triangular matrix signal spots on sequencing flow cell, + for low throughput at highspeeds. + meaning: GENEPIO:0100972 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G400 [GENEPIO:0100148]: + text: MGI DNBSEQ-G400 [GENEPIO:0100148] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB; 1440GB per run. + meaning: GENEPIO:0100148 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G400RS FAST [GENEPIO:0100149]: + text: MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] + description: A DNA sequencer manufactured by the MGI corporation with an output + capacity of 55GB; 330GB per run, which enables faster sequencing than the + DNBSEQ-G400. + meaning: GENEPIO:0100149 + is_a: MGI DNBSEQ-G400 [GENEPIO:0100148] + MGI DNBSEQ-T7 [GENEPIO:0100147]: + text: MGI DNBSEQ-T7 [GENEPIO:0100147] + description: A high throughput DNA sequencer manufactured by the MGI corporation + with an output capacity of 1; 6TB of data per day. + meaning: GENEPIO:0100147 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-E25 [GENEPIO:0100973]: + text: MGI DNBSEQ-E25 [GENEPIO:0100973] + description: An MGI sequencing instrument model that is a compact and lightweight + standalone system which can bu used inside or outside the lab. + meaning: GENEPIO:0100973 + is_a: MGI sequencing instrument [GENEPIO:0100146] + MGI DNBSEQ-G50 [GENEPIO:0100150]: + text: MGI DNBSEQ-G50 [GENEPIO:0100150] + description: "A DNA sequencer manufactured by the MGI corporation with an\ + \ output capacity of 10\uFF5E150 GB per run and enables different read lengths." + meaning: GENEPIO:0100150 + is_a: MGI sequencing instrument [GENEPIO:0100146] + 454 Genome Sequencer [GENEPIO:0001937]: + text: 454 Genome Sequencer [GENEPIO:0001937] + description: A DNA sequencer first manufactured by 454 Life Science Corporation + that conducts pyrosequencing. + meaning: GENEPIO:0001937 + 454 Genome Sequencer 20 [OBI:0000689]: + text: 454 Genome Sequencer 20 [OBI:0000689] + description: A DNA sequencer first manufactured by 454 Life Science Corporation + in 2005, and enables pyrosequencing to be performed. It comprises both optics + and fluidics subsystems, which are controlled by a computer subsystem. + meaning: OBI:0000689 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX [OBI:0000702]: + text: 454 Genome Sequencer FLX [OBI:0000702] + description: A DNA sequencer which was first manufactured by 454 Life Science + Corporation in 2008 and enables pyrosequencing to be performed. It comprises + both optics and fluidics subsystems, which are controlled by a computer + subsystem. It has the ability to sequence 400-600 million base pairs per + run with 400-500 base pair read lengths. + meaning: OBI:0000702 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX+ [GENEPIO:0100982]: + text: 454 Genome Sequencer FLX+ [GENEPIO:0100982] + description: A 454 Genome Sequencer that performs pyrosequencing and comprises + both optics and fluidics subsystems and can be used for longer reads when + used with the long-read Sequencing Kit XL+. + meaning: GENEPIO:0100982 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer FLX Titanium [GENEPIO:0001936]: + text: 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] + description: A 454 Genome Sequencer that performs pyrosequencing and has enhanced + capacity and generates longer reads. + meaning: GENEPIO:0001936 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + 454 Genome Sequencer Junior [GENEPIO:0001938]: + text: 454 Genome Sequencer Junior [GENEPIO:0001938] + description: A 454 Genome Sequencer that performs pyrosequencing and is more + compact. + meaning: GENEPIO:0001938 + is_a: 454 Genome Sequencer [GENEPIO:0001937] + SOLiD System [OBI:0000696]: + text: SOLiD System [OBI:0000696] + description: A DNA sequencer which is manufactured by Applied Biosystems and + which enable DNA sequencing by ligation. + meaning: OBI:0000696 + SOLiD 5500 [GENEPIO:0001929]: + text: SOLiD 5500 [GENEPIO:0001929] + description: A DNA sequencer which is manufactured by Applied Biosystems and + utillizes sequencing by ligation technology and faster run times than the + SOLiD 4 series. + meaning: GENEPIO:0001929 + is_a: SOLiD System [OBI:0000696] + SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930]: + text: SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] + description: A DNA sequencer which is manufactured by Applied Biosystems and + has two FlowChips for across 12 lanes and with a higher throughput than + the 5500 model. + meaning: GENEPIO:0001930 + is_a: SOLiD System [OBI:0000696] + SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984]: + text: SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology and with a higher throughput + than SOLiD 5500xl Genetic Analyzer. + meaning: GENEPIO:0100984 + is_a: SOLiD System [OBI:0000696] + SOLiD 3 Plus System [OBI:0002007]: + text: SOLiD 3 Plus System [OBI:0002007] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology, the machine generates + greater than 1 billion mappable reads per run. + meaning: OBI:0002007 + is_a: SOLiD System [OBI:0000696] + SOLiD 4 System [OBI:0002024]: + text: SOLiD 4 System [OBI:0002024] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology with 100 Gb mappable + throughput. + meaning: OBI:0002024 + is_a: SOLiD System [OBI:0000696] + SOLiD 4hq System [GENEPIO:0001928]: + text: SOLiD 4hq System [GENEPIO:0001928] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology with 300 Gb mappable + throughput. + meaning: GENEPIO:0001928 + is_a: SOLiD System [OBI:0000696] + SOLiD PI System [GENEPIO:0001931]: + text: SOLiD PI System [GENEPIO:0001931] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. Built upon SOLiD sequencing technology, the machine offers + 50Gb mappable throughput. + meaning: GENEPIO:0001931 + is_a: SOLiD System [OBI:0000696] + SOLiD System 2.0 [GENEPIO:0001932]: + text: SOLiD System 2.0 [GENEPIO:0001932] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. + meaning: GENEPIO:0001932 + is_a: SOLiD System [OBI:0000696] + SOLiD System 3.0 [GENEPIO:0001933]: + text: SOLiD System 3.0 [GENEPIO:0001933] + description: A DNA sequencer which is manufactured by the Applied Biosystems + corporation. + meaning: GENEPIO:0001933 + is_a: SOLiD System [OBI:0000696] + HeliScope Single Molecule Sequencer [OBI:0000717]: + text: HeliScope Single Molecule Sequencer [OBI:0000717] + description: A DNA sequencer manufacturer by Helicos Corporation to carry + out Single Molecule sequencing using reversible termination chemistry. + meaning: OBI:0000717 + Applied Biosystems sequencing instrument model [GENEPIO:0100974]: + text: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + description: A sequencing instrument model that is manufactured by Applied + Biosystems and which performs Sanger sequencing and fragment analysis by + capillary electrophoresis. + meaning: GENEPIO:0100974 + AB 310 Genetic Analyzer [GENEPIO:0100975]: + text: AB 310 Genetic Analyzer [GENEPIO:0100975] + description: An Applied Biosystems sequencing instrument model which utilises + a single capillary electrophoresis system to perform Sanger sequencing and + fragment analysis that is automated. + meaning: GENEPIO:0100975 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3130 Genetic Analyzer [GENEPIO:0100976]: + text: AB 3130 Genetic Analyzer [GENEPIO:0100976] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 4 capillaries. + meaning: GENEPIO:0100976 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3130xL Genetic Analyzer [GENEPIO:0100977]: + text: AB 3130xL Genetic Analyzer [GENEPIO:0100977] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 16 capillaries. + meaning: GENEPIO:0100977 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3500 Genetic Analyzer [GENEPIO:0100978]: + text: AB 3500 Genetic Analyzer [GENEPIO:0100978] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 8 capillaries, which can + run 96 well plates. + meaning: GENEPIO:0100978 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3500xL Genetic Analyzer [GENEPIO:0100979]: + text: AB 3500xL Genetic Analyzer [GENEPIO:0100979] + description: An Applied Biosystems sequencing instrument model which performs + capillary electrophoresis to sequence DNA and has 24 capillaries, which + can run 384 well plates. + meaning: GENEPIO:0100979 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3730 Genetic Analyzer [GENEPIO:0100980]: + text: AB 3730 Genetic Analyzer [GENEPIO:0100980] + description: An Applied Biosystems sequencing instrument model which utilises + an 48 capillary array electrophoresis system for sequencing. + meaning: GENEPIO:0100980 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + AB 3730xL Genetic Analyzer [GENEPIO:0100981]: + text: AB 3730xL Genetic Analyzer [GENEPIO:0100981] + description: An Applied Biosystems sequencing instrument model which utilises + an 96 capillary array electrophoresis system for sequencing. + meaning: GENEPIO:0100981 + is_a: Applied Biosystems sequencing instrument model [GENEPIO:0100974] + GenomicTargetEnrichmentMethodMenu: + name: GenomicTargetEnrichmentMethodMenu + title: genomic_target_enrichment_method menu + permissible_values: + Hybrid selection method (bait-capture) [GENEPIO:0001950]: + text: Hybrid selection method (bait-capture) [GENEPIO:0001950] + description: Selection by hybridization in array or solution. + meaning: GENEPIO:0001950 + rRNA depletion method [GENEPIO:0101020]: + text: rRNA depletion method [GENEPIO:0101020] + description: Removal of background RNA for the purposes of enriching the genomic + target. + meaning: GENEPIO:0101020 + QualityControlDeterminationMenu: + name: QualityControlDeterminationMenu + title: quality_control_determination menu + permissible_values: + No quality control issues identified [GENEPIO:0100562]: + text: No quality control issues identified [GENEPIO:0100562] + description: A statement confirming that quality control processes were carried + out and no quality issues were detected. + meaning: GENEPIO:0100562 + Sequence passed quality control [GENEPIO:0100563]: + text: Sequence passed quality control [GENEPIO:0100563] + description: A statement confirming that quality control processes were carried + out and that the sequence met the assessment criteria. + meaning: GENEPIO:0100563 + Sequence failed quality control [GENEPIO:0100564]: + text: Sequence failed quality control [GENEPIO:0100564] + description: A statement confirming that quality control processes were carried + out and that the sequence did not meet the assessment criteria. + meaning: GENEPIO:0100564 + Minor quality control issues identified [GENEPIO:0100565]: + text: Minor quality control issues identified [GENEPIO:0100565] + description: A statement confirming that quality control processes were carried + out and that the sequence did not meet the assessment criteria, however + the issues detected were minor. + meaning: GENEPIO:0100565 + Sequence flagged for potential quality control issues [GENEPIO:0100566]: + text: Sequence flagged for potential quality control issues [GENEPIO:0100566] + description: A statement confirming that quality control processes were carried + out however it is unclear whether the sequence meets the assessment criteria + and the assessment requires review. + meaning: GENEPIO:0100566 + Quality control not performed [GENEPIO:0100567]: + text: Quality control not performed [GENEPIO:0100567] + description: A statement confirming that quality control processes have not + been carried out. + meaning: GENEPIO:0100567 + QualityControlIssuesMenu: + name: QualityControlIssuesMenu + title: quality_control_issues menu + permissible_values: + Low quality sequence [GENEPIO:0100568]: + text: Low quality sequence [GENEPIO:0100568] + description: Sequence data that does not meet quality control thresholds. + meaning: GENEPIO:0100568 + Sequence contaminated [GENEPIO:0100569]: + text: Sequence contaminated [GENEPIO:0100569] + description: Sequence data that contains reads from unintended targets (e.g. + other organisms, other samples) due to contamination so that it does not + faithfully represent the genetic information from the biological source. + meaning: GENEPIO:0100569 + Low average genome coverage [GENEPIO:0100570]: + text: Low average genome coverage [GENEPIO:0100570] + description: Sequence data in which the entire length of the genome is not + sufficiently sequenced (low breadth of coverage), or particular positions + of the genome are not sequenced a prescribed number of times (low depth + of coverage). + meaning: GENEPIO:0100570 + Low percent genome captured [GENEPIO:0100571]: + text: Low percent genome captured [GENEPIO:0100571] + description: Sequence data in which the entire length of the genome is not + sufficiently sequenced (low breadth of coverage). + meaning: GENEPIO:0100571 + Read lengths shorter than expected [GENEPIO:0100572]: + text: Read lengths shorter than expected [GENEPIO:0100572] + description: Average sequence read lengths that are below the expected size + range given a particular sequencing instrument, reagents and conditions. + meaning: GENEPIO:0100572 + Sequence amplification artifacts [GENEPIO:0100573]: + text: Sequence amplification artifacts [GENEPIO:0100573] + description: Sequence data containing errors generated during the PCR amplification + process during library generation (e.g. mutations, altered read distribution, + amplicon dropouts). + meaning: GENEPIO:0100573 + Low signal to noise ratio [GENEPIO:0100574]: + text: Low signal to noise ratio [GENEPIO:0100574] + description: Sequence data containing more errors or undetermined bases (noise) + than sequence representing the biological source (signal). + meaning: GENEPIO:0100574 + Low coverage of characteristic mutations [GENEPIO:0100575]: + text: Low coverage of characteristic mutations [GENEPIO:0100575] + description: Sequence data that contains a lower than expected number of mutations + that are usually observed in the reference sequence. + meaning: GENEPIO:0100575 + DiagnosticTargetPresenceMenu: + name: DiagnosticTargetPresenceMenu + title: diagnostic target presence menu + permissible_values: + diagnostic target present [GENEPIO:0100987]: + text: diagnostic target present [GENEPIO:0100987] + description: A quality inhering in a bearer by virtue of the bearer's existence. + meaning: GENEPIO:0100987 + diagnostic target absent [GENEPIO:0100988]: + text: diagnostic target absent [GENEPIO:0100988] + description: Aquality denoting the lack of an entity. + meaning: GENEPIO:0100988 + DiagnosticMeasurementUnitMenu: + name: DiagnosticMeasurementUnitMenu + title: diagnostic measurement unit menu + permissible_values: + gene copies per liter (GC/L): + text: gene copies per liter (GC/L) + description: A unit that measures the number of copies of a given gene within + a liter of a biological material. + cycle threshold (Ct) [GENEPIO:0100657]: + text: cycle threshold (Ct) [GENEPIO:0100657] + description: A data field which describes the cycle threshold (Ct) value result + from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) + test. + meaning: GENEPIO:0100657 + colony forming units per milliliter (CFU/mL) [UO:0000213]: + text: colony forming units per milliliter (CFU/mL) [UO:0000213] + description: A unit of microbial density that describes the number of colony + forming units within a milliliter of material. + meaning: UO:0000213 + colony forming units per 100 milliliter (CFU/100 mL): + text: colony forming units per 100 milliliter (CFU/100 mL) + description: A unit of microbial density that describes the number of colony + forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS): + text: colony forming units per grams total solids (CFU/gTS) + description: A unit of microbial density that describes the number of colony + forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL): + text: most probable number per milliliter (MPN/mL) + description: A unit of microbial density that describes the most probable + number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL): + text: most probable number per 100 milliliter (MPN/100 mL) + description: A unit of microbial density that describes the most probable + number of microbes within 100 milliliters of material. + DiagnosticMeasurementMethodMenu: + name: DiagnosticMeasurementMethodMenu + title: diagnostic measurement method menu + permissible_values: + Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893]: + text: Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] + description: An assay, based on the PCR, that amplifies and simultaneously + quantifies a specific DNA molecule based on the use of complementary probes/primers. + It enables both detection and quantification (as absolute number of copies + or relative amount when normalized to DNA input or additional normalizing + genes) of one or more specific sequences in a DNA sample. + meaning: OBI:0000893 + Digital real time polymerase chain reaction (dPCR): + text: Digital real time polymerase chain reaction (dPCR) + description: A type of polymerase chain reaction technique in which the sample + is fractionated, within which individual PCR reactions occur in each fraction + Bacteria culture test: + text: Bacteria culture test + description: An assay to identify the presence of bacteria + ExperimentalInterventionMenu: + name: ExperimentalInterventionMenu + title: experimental_intervention menu + permissible_values: + Addition of substances to food/water [GENEPIO:0100536]: + text: Addition of substances to food/water [GENEPIO:0100536] + description: The addition of substances to food or water administered to an + individual or group of individuals. + meaning: GENEPIO:0100536 + Antimicrobial pre-treatment [GENEPIO:0100537]: + text: Antimicrobial pre-treatment [GENEPIO:0100537] + description: The administration of an antimicrobial agent to an individual + or its addition to a substance prior to some other event or activity. + meaning: GENEPIO:0100537 + Certified animal husbandry practices [GENEPIO:0100538]: + text: Certified animal husbandry practices [GENEPIO:0100538] + description: The implementation of animal husbandy practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100538 + Certified organic farming practices [GENEPIO:0100539]: + text: Certified organic farming practices [GENEPIO:0100539] + description: The implementation of organic farming practices that have been + certified by an authorized organization. + meaning: GENEPIO:0100539 + Change in storage conditions [GENEPIO:0100540]: + text: Change in storage conditions [GENEPIO:0100540] + description: A change in the storage conditions of a material or a substance. + meaning: GENEPIO:0100540 + Cleaning/disinfection [GENEPIO:0100541]: + text: Cleaning/disinfection [GENEPIO:0100541] + description: A process of removing unwanted substances, such as dirt, infectious + agents, and other impurities, from an object or environment. + meaning: GENEPIO:0100541 + Extended downtime between activities [GENEPIO:0100542]: + text: Extended downtime between activities [GENEPIO:0100542] + description: A prolonged period of inactivity between processes or events. + meaning: GENEPIO:0100542 + Fertilizer pre-treatment [GENEPIO:0100543]: + text: Fertilizer pre-treatment [GENEPIO:0100543] + description: The addition of fertilizer to a material or environment prior + to some other event or activity. + meaning: GENEPIO:0100543 + Logistic slaughter [GENEPIO:0100545]: + text: Logistic slaughter [GENEPIO:0100545] + description: The logistical planning of events and processes upstream of the + immediate slaughter of an animal (which may include controlling transport + climate; traffic conditions, number of pick-up farms, as well as time and + distance during transport; queuing at the abattoir etc) that optimize operations + and reduce stress on the animal. + meaning: GENEPIO:0100545 + Microbial pre-treatment [GENEPIO:0100546]: + text: Microbial pre-treatment [GENEPIO:0100546] + description: The deliberate addition of microbes or a mixture of microbes + to an individual or substance prior to some other event or activity. + meaning: GENEPIO:0100546 + Probiotic pre-treatment [GENEPIO:0100547]: + text: Probiotic pre-treatment [GENEPIO:0100547] + description: The addition of a probiotic substance to an individual or material + prior to some other event or activity. + meaning: GENEPIO:0100547 + Vaccination [NCIT:C15346]: + text: Vaccination [NCIT:C15346] + description: Administration of vaccines to stimulate the host's immune response. + This includes any preparation intended for active immunological prophylaxis + or treatment. + meaning: NCIT:C15346 AirPressureMeasurementUnitMenu: name: AirPressureMeasurementUnitMenu title: air_pressure_measurement_unit menu @@ -12414,46 +13272,96 @@ enums: permissible_values: cubic meter per second (m^3/s): text: cubic meter per second (m^3/s) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one second. cubic meter per minute (m^3/min): text: cubic meter per minute (m^3/min) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one minute. cubic meter per hour (m^3/h): text: cubic meter per hour (m^3/h) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one hour. liter per second (L/s): text: liter per second (L/s) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one second. liter per minute (L/min): text: liter per minute (L/min) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one minute. liter per hour (L/h): text: liter per hour (L/h) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one hour. liter per day (L/day): text: liter per day (L/day) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one day. million gallons per day (MGD): text: million gallons per day (MGD) + description: A volumetric flow rate unit which is the measure of the volume + of one million gallons of matter crosses a given surface during the period + of time equal to one day. InstantaneousFlowRateMeasurementUnitMenu: name: InstantaneousFlowRateMeasurementUnitMenu title: instantaneous_flow_rate_measurement_unit menu permissible_values: cubic meter per second (m^3/s): text: cubic meter per second (m^3/s) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one second. cubic meter per minute (m^3/min): text: cubic meter per minute (m^3/min) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one minute. cubic meter per hour (m^3/h): text: cubic meter per hour (m^3/h) + description: A volumetric flow rate unit which is the measure of the volume + of one cubic meter of matter crosses a given surface during the period of + time equal to one hour. liter per second (L/s): text: liter per second (L/s) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one second. liter per minute (L/min): text: liter per minute (L/min) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one minute. liter per hour (L/h): text: liter per hour (L/h) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one hour. liter per day (L/day): text: liter per day (L/day) + description: A volumetric flow rate unit which is the measure of the volume + of one liter of matter crosses a given surface during the period of time + equal to one day. million gallons per day (MGD): text: million gallons per day (MGD) + description: A volumetric flow rate unit which is the measure of the volume + of one million gallons of matter crosses a given surface during the period + of time equal to one day. TurbidityMeasurementUnitMenu: name: TurbidityMeasurementUnitMenu title: turbidity_measurement_unit menu permissible_values: nephelometric turbidity unit (NTU): text: nephelometric turbidity unit (NTU) + description: A measure of turbidity calculated by using a nephelometer to + compare how white light is scattered in a water sample. formazin nephelometric unit (FNU) [UO:0000318]: text: formazin nephelometric unit (FNU) [UO:0000318] description: A measure of turbidity calculated by comparing how infrared light @@ -12551,6 +13459,8 @@ enums: permissible_values: milliequivalent per liter (meq/L): text: milliequivalent per liter (meq/L) + description: A unit of ion concentration that represents chemical activity + per volume. milligram per liter (mg/L) [UO:0000273]: text: milligram per liter (mg/L) [UO:0000273] description: A non-SI unit of density that is equivalent to the SI metric @@ -12567,18 +13477,27 @@ enums: permissible_values: milliSiemen per centimeter (mS/cm): text: milliSiemen per centimeter (mS/cm) + description: A non-SI unit of electrical conductivity that is equivalent to + one tenth of a Siemen per meter (S/m). "microSiemen per centimeter (\u03BCS/cm)": text: "microSiemen per centimeter (\u03BCS/cm)" + description: A non-SI unit of electrical conductivity that is equivalent to + one ten thousandth of a Siemen per meter (S/m). Siemen per meter (S/m): text: Siemen per meter (S/m) + description: An SI unit of electrical conductivity that is equivalent to an + ampere per volt per meter (A/v/m). SalinityMeasurementUnitMenu: name: SalinityMeasurementUnitMenu title: salinity_measurement_unit menu permissible_values: practical salinity unit (PSU): text: practical salinity unit (PSU) + description: A unitless measure of salinity that is equivalent to per thousand. weight for weight (% w/w): text: weight for weight (% w/w) + description: A unitless comparison based on weight rather than volume, which + is equivalent to per hundred. parts per thousand [UO:0000168]: text: parts per thousand [UO:0000168] description: A dimensionless concentration notation which denotes the amount @@ -12606,12 +13525,16 @@ enums: meaning: UO:0000175 gram per total solids (g/gTS): text: gram per total solids (g/gTS) + description: A unitless comparison of the weight of a substance as a proportion + to the weight of total solids. TotalPhosphorpusTpMeasurementUnitMenu: name: TotalPhosphorpusTpMeasurementUnitMenu title: total_phosphorpus_(TP)_measurement_unit menu permissible_values: gram per total solids (g/gTS): text: gram per total solids (g/gTS) + description: A unitless comparison of the weight of a substance as a proportion + to the weight of total solids. orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998]: text: orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] description: A substance unit which describes the weight of orthophosphate @@ -12665,8 +13588,12 @@ enums: permissible_values: log10 gene copies per 100 milliliter (log10 GC/100 mL): text: log10 gene copies per 100 milliliter (log10 GC/100 mL) + description: A unit that expresses on a logarithmic scale the number of copies + of a given gene within one hundred milliliters of a biological material. gene copies per liter (GC/L): text: gene copies per liter (GC/L) + description: A unit that measures the number of copies of a given gene within + a liter of a biological material. PCR quantification cycle [UO:0010077]: text: PCR quantification cycle [UO:0010077] description: A count unit of how many Polymerase Chain Reaction (PCR) cycles @@ -12675,6 +13602,8 @@ enums: meaning: UO:0010077 log10 gene copies per nanogram total DNA: text: log10 gene copies per nanogram total DNA + description: A unit that expresses on a logarithmic scale the number of copies + within a nanogram of deoxyribonucleic acid genetic material. UrinaryContaminationIndicatorMenu: name: UrinaryContaminationIndicatorMenu title: urinary_contamination_indicator menu @@ -12704,12 +13633,20 @@ enums: meaning: UO:0000213 colony forming units per 100 milliliter (CFU/100 mL): text: colony forming units per 100 milliliter (CFU/100 mL) + description: A unit of microbial density that describes the number of colony + forming units within 100 milliliters of material. colony forming units per grams total solids (CFU/gTS): text: colony forming units per grams total solids (CFU/gTS) + description: A unit of microbial density that describes the number of colony + forming units within a gram of total solids in waste material. most probable number per milliliter (MPN/mL): text: most probable number per milliliter (MPN/mL) + description: A unit of microbial density that describes the most probable + number of microbes within one milliliter of material. most probable number per 100 milliliter (MPN/100 mL): text: most probable number per 100 milliliter (MPN/100 mL) + description: A unit of microbial density that describes the most probable + number of microbes within 100 milliliters of material. SampleTemperatureUnitAtCollectionMenu: name: SampleTemperatureUnitAtCollectionMenu title: sample_temperature_unit_(at collection) menu diff --git a/web/templates/hpai/schema_enums.tsv b/web/templates/hpai/schema_enums.tsv index f742904b..fc1d4d9d 100644 --- a/web/templates/hpai/schema_enums.tsv +++ b/web/templates/hpai/schema_enums.tsv @@ -427,7 +427,7 @@ residual_sample_status menu ResidualSampleStatusMenu GENEPIO:0101087 Residual sa GENEPIO:0101089 Residual sample status unkown [GENEPIO:0101089] -purpose of sampling PurposeOfSampling GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 Cluster/Outbreak investigation [GENEPIO:0100001] A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. GENEPIO:0100002 Diagnostic testing [GENEPIO:0100002] A sampling strategy in which individuals are sampled in the context of diagnostic testing. GENEPIO:0100548 Environmental testing [GENEPIO:0100548] A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena. GENEPIO:0100003 Research [GENEPIO:0100003] A sampling strategy in which samples are collected in order to perform research. @@ -436,7 +436,7 @@ purpose of sampling PurposeOfSampling GENEPIO:0100001 Cluster/Outbreak investiga GENEPIO:0100582 Survey study [GENEPIO:0100582] A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes. GENEPIO:0100004 Surveillance [GENEPIO:0100004] A sampling strategy in which individuals are sampled for surveillance investigations. -presampling activity PresamplingActivity GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. +presampling activity menu PresamplingActivityMenu GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. GENEPIO:0100537 Antimicrobial pre-treatment [GENEPIO:0100537] The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity. GENEPIO:0100538 Certified animal husbandry practices [GENEPIO:0100538] The implementation of animal husbandy practices that have been certified by an authorized organization. GENEPIO:0100894 Certified humane animal husbandry practices [GENEPIO:0100894] A certification organization in Washington DC that is dedicated to improving the lives of farm animals in food production from birth through slaughter. @@ -449,7 +449,7 @@ presampling activity PresamplingActivity GENEPIO:0100536 Addition of substances GENEPIO:0100547 Probiotic pre-treatment [GENEPIO:0100547] The addition of a probiotic substance to an individual or material prior to some other event or activity. NCIT:C15346 Vaccination [NCIT:C15346] Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. -sample storage duration unit SampleStorageDurationUnit UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. +sample storage duration unit menu SampleStorageDurationUnitMenu UO:0000010 Second [UO:0000010] A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. UO:0000031 Minute [UO:0000031] A time unit which is equal to 60 seconds. UO:0000032 Hour [UO:0000032] A time unit which is equal to 60 minutes. UO:0000033 Day [UO:0000033] A time unit which is equal to 24 hours. @@ -457,12 +457,12 @@ sample storage duration unit SampleStorageDurationUnit UO:0000010 Second [UO:000 UO:0000035 Month [UO:0000035] A time unit which is equal to approximately 4-4.5 weeks or 28-31 days. UO:0000036 Year [UO:0000036] A time unit which is equal to 365 days, or 366 days during a leap year. -specimen processing SpecimenProcessing OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. +specimen processing menu SpecimenProcessingMenu OBI:0600041 Concentration [OBI:0600041] A process used to increase the density of a material of interest by removing other materials in the entity containing the material of interest. OBI:0302886 Centrifugation [OBI:0302886] A process separating molecules by size or density using centrifugal forces generated by a spinning rotor. OBI:0302885 Filtration [OBI:0302885] A process which separates components suspended in a fluid based on granularity properties relying on a filter device. OBI:0600016 Pooling specimens [OBI:0600016] Physical combination of several instances of like material. -experimental specimen role type ExperimentalSpecimenRoleType GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. +experimental specimen role type menu ExperimentalSpecimenRoleTypeMenu GENEPIO:0101018 Positive experimental control [GENEPIO:0101018] A control specimen that is expected to yield a positive result, to establish a reference baseline for an experiment. GENEPIO:0101123 Validation strain [GENEPIO:0101123] GENEPIO:0101124 Proficiency test isolate [GENEPIO:0101124] GENEPIO:0101019 Negative experimental control [GENEPIO:0101019] A control specimen that is expected to yield a negative result, to establish a reference baseline for an experiment @@ -635,7 +635,7 @@ host_age_bin menu HostAgeBinMenu GENEPIO:0100684 First winter [GENEPIO:0100684] GENEPIO:0100058 90 - 99 [GENEPIO:0100058] An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). GENEPIO:0100059 100+ [GENEPIO:0100059] An age group that stratifies the age of a case to be greater than or equal to 100 years old. -host_gender HostGender NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. +host_gender menu HostGenderMenu NCIT:C46110 Female [NCIT:C46110] An individual who reports belonging to the cultural gender role distinction of female. NCIT:C46109 Male [NCIT:C46109] An individual who reports belonging to the cultural gender role distinction of male. GSSO:000132 Non-binary gender [GSSO:000132] Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. GSSO:004004 Transgender (assigned male at birth) [GSSO:004004] Having a feminine gender (identity) which is different from the sex one was assigned at birth. @@ -997,13 +997,13 @@ host_vaccination_status menu HostVaccinationStatusMenu GENEPIO:0100100 Fully Vac influenza_antiviral_treatment_administration menu InfluenzaAntiviralTreatmentAdministrationMenu GENEPIO:0101194 Influenza antiviral treatment administered [GENEPIO:0101194] GENEPIO:0101195 No influenza antiviral treatment administered [GENEPIO:0101195] -water_catchment_area_human_population_range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people - 10 - 100 people - 100 - 1,000 people - 1,000 - 10,000 people - 10,000 - 100,000 people - 100,000 - 1,000,000 people - 1,000,000+ people +water_catchment_area_human_population_range menu WaterCatchmentAreaHumanPopulationRangeMenu <10 people An estimation of population size for a group smaller than 10 people. + 10 - 100 people An estimation of population size for a group smaller than 100 people and larger than 10 people. + 100 - 1,000 people An estimation of population size for a group smaller than 1,000 people and larger than 100 people. + 1,000 - 10,000 people An estimation of population size for a group smaller than 10,000 people and larger than 1,000 people. + 10,000 - 100,000 people An estimation of population size for a group smaller than 100,000 people and larger than 10,000 people. + 100,000 - 1,000,000 people An estimation of population size for a group smaller than 1,000,000 people and larger than 100,000 people. + 1,000,000+ people An estimation of population size for a group larger than 1,000,000 people. water_catchment_area_human_population_density_unit menu WaterCatchmentAreaHumanPopulationDensityUnitMenu GENEPIO:0100989 persons per square mile [GENEPIO:0100989] A unit of population density that describes the average number of people in a square mile of a given area. GENEPIO:0100990 persons per square kilometer [GENEPIO:0100990] A unit of population density that describes the average number of people in a square kilometer of a given area. @@ -1038,6 +1038,161 @@ precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu UO:0000016 UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. +water_depth_units menu WaterDepthUnitsMenu UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010066 kilometer (km) [UO:0010066] A length unit which is equal to one thousand meters. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +sediment_depth_units menu SedimentDepthUnitsMenu UO:0000015 centimeter (cm) [UO:0000015] A length unit which is equal to one hundredth of a meter or 10^[-2] m + UO:0000008 meter (m) [UO:0000008] An SI unit of length defined as the length of the path travelled by light in a vacuum in 1/299792458th of a second. + UO:0010066 kilometer (km) [UO:0010066] A length unit which is equal to one thousand meters. + UO:0010011 inch (in) [UO:0010011] A non-SI unit of length defined as one twelfth of a foot. + UO:0010013 foot (ft) [UO:0010013] A non-SI unit of length which is approximately 0.3048 meters. + +air_temperature_units menu AirTemperatureUnitsMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +water_temperature_units menu WaterTemperatureUnitsMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. + UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. + +sequencing_platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. + GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. + GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. + GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. + GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. + GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. + GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. + GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. + GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. + GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). + GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. + + +sequencing_instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. + GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. + OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + GENEPIO:0100109 Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + GENEPIO:0100110 Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + GENEPIO:0100111 Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that enables sufficient depth and coverage to produce the first 30x human genome for $1000. + GENEPIO:0100112 Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + GENEPIO:0100113 Illumina HiSeq X Ten [GENEPIO:0100113] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + OBI:0002022 Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100115 Illumina HiSeq 1500 [GENEPIO:0100115] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. + OBI:0002001 Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + OBI:0002002 Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + OBI:0002048 Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + OBI:0002049 Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + GENEPIO:0100120 Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + GENEPIO:0100121 Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + GENEPIO:0100122 Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that has an output capacity of 6 Tb and 20 billion reads in dual flow cell mode. + GENEPIO:0100123 Illumina NovaSeq 6000 [GENEPIO:0100123] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + GENEPIO:0100124 Illumina MiniSeq [GENEPIO:0100124] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002003 Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + GENEPIO:0100126 Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + OBI:0002021 Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + GENEPIO:0100128 Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + GENEPIO:0004432 Illumina NextSeq 1000 [GENEPIO:0004432] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + GENEPIO:0100129 Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + GENEPIO:0100130 PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + GENEPIO:0100131 PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + OBI:0002012 PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + GENEPIO:0100133 PacBio Sequel [GENEPIO:0100133] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + GENEPIO:0100134 PacBio Sequel II [GENEPIO:0100134] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + GENEPIO:0100135 Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + GENEPIO:0100136 Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + GENEPIO:0100137 Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + GENEPIO:0100138 Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + GENEPIO:0100139 Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + GENEPIO:0100140 Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + GENEPIO:0004433 Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + GENEPIO:0100141 Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + GENEPIO:0100142 Oxford Nanopore MinION [GENEPIO:0100142] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + GENEPIO:0100143 Oxford Nanopore PromethION [GENEPIO:0100143] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + GENEPIO:0100144 BGI Genomics sequencing instrument [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + GENEPIO:0100145 BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + GENEPIO:0100146 MGI sequencing instrument [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + GENEPIO:0100971 MGISEQ-2000RS [GENEPIO:0100971] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing ad which is capable of medium to high throughput sequencing. + GENEPIO:0100972 MGI DNBSEQ-G99 [GENEPIO:0100972] An MGI sequencing instrument model that utilises DNA nanoball and (DNB) and probe-anchor synthesis (cPAS) for next generation sequencing and which adopts triangular matrix signal spots on sequencing flow cell, for low throughput at highspeeds. + GENEPIO:0100148 MGI DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. + GENEPIO:0100149 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 330GB per run, which enables faster sequencing than the DNBSEQ-G400. + GENEPIO:0100147 MGI DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. + GENEPIO:0100973 MGI DNBSEQ-E25 [GENEPIO:0100973] An MGI sequencing instrument model that is a compact and lightweight standalone system which can bu used inside or outside the lab. + GENEPIO:0100150 MGI DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + GENEPIO:0001937 454 Genome Sequencer [GENEPIO:0001937] A DNA sequencer first manufactured by 454 Life Science Corporation that conducts pyrosequencing. + OBI:0000689 454 Genome Sequencer 20 [OBI:0000689] A DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. + OBI:0000702 454 Genome Sequencer FLX [OBI:0000702] A DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + GENEPIO:0100982 454 Genome Sequencer FLX+ [GENEPIO:0100982] A 454 Genome Sequencer that performs pyrosequencing and comprises both optics and fluidics subsystems and can be used for longer reads when used with the long-read Sequencing Kit XL+. + GENEPIO:0001936 454 Genome Sequencer FLX Titanium [GENEPIO:0001936] A 454 Genome Sequencer that performs pyrosequencing and has enhanced capacity and generates longer reads. + GENEPIO:0001938 454 Genome Sequencer Junior [GENEPIO:0001938] A 454 Genome Sequencer that performs pyrosequencing and is more compact. + OBI:0000696 SOLiD System [OBI:0000696] A DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation. + GENEPIO:0001929 SOLiD 5500 [GENEPIO:0001929] A DNA sequencer which is manufactured by Applied Biosystems and utillizes sequencing by ligation technology and faster run times than the SOLiD 4 series. + GENEPIO:0001930 SOLiD 5500xl Genetic Analyzer [GENEPIO:0001930] A DNA sequencer which is manufactured by Applied Biosystems and has two FlowChips for across 12 lanes and with a higher throughput than the 5500 model. + GENEPIO:0100984 SOLiD 5500x-Wl Genetic Analyzer [GENEPIO:0100984] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology and with a higher throughput than SOLiD 5500xl Genetic Analyzer. + OBI:0002007 SOLiD 3 Plus System [OBI:0002007] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + OBI:0002024 SOLiD 4 System [OBI:0002024] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 100 Gb mappable throughput. + GENEPIO:0001928 SOLiD 4hq System [GENEPIO:0001928] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology with 300 Gb mappable throughput. + GENEPIO:0001931 SOLiD PI System [GENEPIO:0001931] A DNA sequencer which is manufactured by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine offers 50Gb mappable throughput. + GENEPIO:0001932 SOLiD System 2.0 [GENEPIO:0001932] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + GENEPIO:0001933 SOLiD System 3.0 [GENEPIO:0001933] A DNA sequencer which is manufactured by the Applied Biosystems corporation. + OBI:0000717 HeliScope Single Molecule Sequencer [OBI:0000717] A DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry. + GENEPIO:0100974 Applied Biosystems sequencing instrument model [GENEPIO:0100974] A sequencing instrument model that is manufactured by Applied Biosystems and which performs Sanger sequencing and fragment analysis by capillary electrophoresis. + GENEPIO:0100975 AB 310 Genetic Analyzer [GENEPIO:0100975] An Applied Biosystems sequencing instrument model which utilises a single capillary electrophoresis system to perform Sanger sequencing and fragment analysis that is automated. + GENEPIO:0100976 AB 3130 Genetic Analyzer [GENEPIO:0100976] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 4 capillaries. + GENEPIO:0100977 AB 3130xL Genetic Analyzer [GENEPIO:0100977] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 16 capillaries. + GENEPIO:0100978 AB 3500 Genetic Analyzer [GENEPIO:0100978] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 8 capillaries, which can run 96 well plates. + GENEPIO:0100979 AB 3500xL Genetic Analyzer [GENEPIO:0100979] An Applied Biosystems sequencing instrument model which performs capillary electrophoresis to sequence DNA and has 24 capillaries, which can run 384 well plates. + GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. + GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. + +genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybrid selection method (bait-capture) [GENEPIO:0001950] Selection by hybridization in array or solution. + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. + +quality_control_determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. + +quality_control_issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. + +diagnostic target presence menu DiagnosticTargetPresenceMenu GENEPIO:0100987 diagnostic target present [GENEPIO:0100987] A quality inhering in a bearer by virtue of the bearer's existence. + GENEPIO:0100988 diagnostic target absent [GENEPIO:0100988] Aquality denoting the lack of an entity. + +diagnostic measurement unit menu DiagnosticMeasurementUnitMenu gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. + GENEPIO:0100657 cycle threshold (Ct) [GENEPIO:0100657] A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. + UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. + +diagnostic measurement method menu DiagnosticMeasurementMethodMenu OBI:0000893 Quantitative real time polymerase chain reaction (qPCR) [OBI:0000893] An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + Digital real time polymerase chain reaction (dPCR) A type of polymerase chain reaction technique in which the sample is fractionated, within which individual PCR reactions occur in each fraction + Bacteria culture test An assay to identify the presence of bacteria + +experimental_intervention menu ExperimentalInterventionMenu GENEPIO:0100536 Addition of substances to food/water [GENEPIO:0100536] The addition of substances to food or water administered to an individual or group of individuals. + GENEPIO:0100537 Antimicrobial pre-treatment [GENEPIO:0100537] The administration of an antimicrobial agent to an individual or its addition to a substance prior to some other event or activity. + GENEPIO:0100538 Certified animal husbandry practices [GENEPIO:0100538] The implementation of animal husbandy practices that have been certified by an authorized organization. + GENEPIO:0100539 Certified organic farming practices [GENEPIO:0100539] The implementation of organic farming practices that have been certified by an authorized organization. + GENEPIO:0100540 Change in storage conditions [GENEPIO:0100540] A change in the storage conditions of a material or a substance. + GENEPIO:0100541 Cleaning/disinfection [GENEPIO:0100541] A process of removing unwanted substances, such as dirt, infectious agents, and other impurities, from an object or environment. + GENEPIO:0100542 Extended downtime between activities [GENEPIO:0100542] A prolonged period of inactivity between processes or events. + GENEPIO:0100543 Fertilizer pre-treatment [GENEPIO:0100543] The addition of fertilizer to a material or environment prior to some other event or activity. + GENEPIO:0100545 Logistic slaughter [GENEPIO:0100545] The logistical planning of events and processes upstream of the immediate slaughter of an animal (which may include controlling transport climate; traffic conditions, number of pick-up farms, as well as time and distance during transport; queuing at the abattoir etc) that optimize operations and reduce stress on the animal. + GENEPIO:0100546 Microbial pre-treatment [GENEPIO:0100546] The deliberate addition of microbes or a mixture of microbes to an individual or substance prior to some other event or activity. + GENEPIO:0100547 Probiotic pre-treatment [GENEPIO:0100547] The addition of a probiotic substance to an individual or material prior to some other event or activity. + NCIT:C15346 Vaccination [NCIT:C15346] Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment. + air_pressure_measurement_unit menu AirPressureMeasurementUnitMenu EFO:0005212 atmosphere (atm) [EFO:0005212] A non-SI unit of pressure defined as 101,325 pascals (Pa). bar UO:0000110 pascal [UO:0000110] An SI unit of pressure defined as one newton per square meter (N/m^2). @@ -1045,25 +1200,25 @@ air_pressure_measurement_unit menu AirPressureMeasurementUnitMenu EFO:0005212 at ambient_temperature_measurement_unit menu AmbientTemperatureMeasurementUnitMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. -total_daily_flow_rate_measurement_unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) - cubic meter per minute (m^3/min) - cubic meter per hour (m^3/h) - liter per second (L/s) - liter per minute (L/min) - liter per hour (L/h) - liter per day (L/day) - million gallons per day (MGD) - -instantaneous_flow_rate_measurement_unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) - cubic meter per minute (m^3/min) - cubic meter per hour (m^3/h) - liter per second (L/s) - liter per minute (L/min) - liter per hour (L/h) - liter per day (L/day) - million gallons per day (MGD) - -turbidity_measurement_unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) +total_daily_flow_rate_measurement_unit menu TotalDailyFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +instantaneous_flow_rate_measurement_unit menu InstantaneousFlowRateMeasurementUnitMenu cubic meter per second (m^3/s) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one second. + cubic meter per minute (m^3/min) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one minute. + cubic meter per hour (m^3/h) A volumetric flow rate unit which is the measure of the volume of one cubic meter of matter crosses a given surface during the period of time equal to one hour. + liter per second (L/s) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one second. + liter per minute (L/min) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one minute. + liter per hour (L/h) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one hour. + liter per day (L/day) A volumetric flow rate unit which is the measure of the volume of one liter of matter crosses a given surface during the period of time equal to one day. + million gallons per day (MGD) A volumetric flow rate unit which is the measure of the volume of one million gallons of matter crosses a given surface during the period of time equal to one day. + +turbidity_measurement_unit menu TurbidityMeasurementUnitMenu nephelometric turbidity unit (NTU) A measure of turbidity calculated by using a nephelometer to compare how white light is scattered in a water sample. UO:0000318 formazin nephelometric unit (FNU) [UO:0000318] A measure of turbidity calculated by comparing how infrared light is scattered in a water sample against the amount of infrared light scattered in a reference solution containing formazin. dissolved_oxygen_measurement_unit menu DissolvedOxygenMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. @@ -1085,24 +1240,24 @@ total_dissolved_solids_(TDS)_measurement_unit menu TotalDissolvedSolidsTdsMeasur total_solids_(TS)_measurement_unit menu TotalSolidsTsMeasurementUnitMenu UO:0000187 percent (%) [UO:0000187] A unitless measure that represents one in a hundred. UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. -alkalinity_measurement_unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) +alkalinity_measurement_unit menu AlkalinityMeasurementUnitMenu milliequivalent per liter (meq/L) A unit of ion concentration that represents chemical activity per volume. UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. UO:0000169 parts per million [UO:0000169] A unitless measure of density that represents one item out of a million. -conductivity_measurement_unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) - microSiemen per centimeter (μS/cm) - Siemen per meter (S/m) +conductivity_measurement_unit menu ConductivityMeasurementUnitMenu milliSiemen per centimeter (mS/cm) A non-SI unit of electrical conductivity that is equivalent to one tenth of a Siemen per meter (S/m). + microSiemen per centimeter (μS/cm) A non-SI unit of electrical conductivity that is equivalent to one ten thousandth of a Siemen per meter (S/m). + Siemen per meter (S/m) An SI unit of electrical conductivity that is equivalent to an ampere per volt per meter (A/v/m). -salinity_measurement_unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) - weight for weight (% w/w) +salinity_measurement_unit menu SalinityMeasurementUnitMenu practical salinity unit (PSU) A unitless measure of salinity that is equivalent to per thousand. + weight for weight (% w/w) A unitless comparison based on weight rather than volume, which is equivalent to per hundred. UO:0000168 parts per thousand [UO:0000168] A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1000 regardless of the units of measure as long as they are the same. UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. total_nitrogen_(TN)_measurement_unit menu TotalNitrogenTnMeasurementUnitMenu UO:0000273 milligram per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. UO:0000175 gram per liter (g/L) [UO:0000175] A non-SI unit of density that is a thousand kilograms per cubic meter. - gram per total solids (g/gTS) + gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. -total_phosphorpus_(TP)_measurement_unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) +total_phosphorpus_(TP)_measurement_unit menu TotalPhosphorpusTpMeasurementUnitMenu gram per total solids (g/gTS) A unitless comparison of the weight of a substance as a proportion to the weight of total solids. GENEPIO:0100998 orthophosphate as phosphorus per total solids (gPO4-P/gTS) [GENEPIO:0100998] A substance unit which describes the weight of orthophosphate as phosphorus (gPO4-P) within a sample to the weight of total solids. UO:0000273 milligrams per liter (mg/L) [UO:0000273] A non-SI unit of density that is equivalent to the SI metric kilogram per cubic meter. GENEPIO:0100999 milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) [GENEPIO:0100999] A density unit comparing the weight of orthophosphate as phosphorus (PO4-P) in milligrams within a standard liter volume. @@ -1114,20 +1269,20 @@ fecal contamination indicator menu FecalContaminationIndicatorMenu NCBITaxon:121 GENEPIO:0101002 F+ (male specific) coliphages A fecal indicator which is a bacteriophage that infects coliform bacteria and is used in water assessment. CHEBI:26756 Stercobilin Bile pigment found in fecal material. -fecal_contamination_unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) - gene copies per liter (GC/L) +fecal_contamination_unit menu FecalContaminationUnitMenu log10 gene copies per 100 milliliter (log10 GC/100 mL) A unit that expresses on a logarithmic scale the number of copies of a given gene within one hundred milliliters of a biological material. + gene copies per liter (GC/L) A unit that measures the number of copies of a given gene within a liter of a biological material. UO:0010077 PCR quantification cycle [UO:0010077] A count unit of how many Polymerase Chain Reaction (PCR) cycles it took to detect a real signal from a sample. Equivalent to the PCR cycle number at which a sample's reaction curve intersects the threshold line. - log10 gene copies per nanogram total DNA + log10 gene copies per nanogram total DNA A unit that expresses on a logarithmic scale the number of copies within a nanogram of deoxyribonucleic acid genetic material. urinary_contamination_indicator menu UrinaryContaminationIndicatorMenu CHEBI:36378 Urobilin [CHEBI:36378] A tetrapyrroledicarboxylic acid that causes the yellow color in urine. Also known as urochrome. urinary_contamination_unit menu UrinaryContaminationUnitMenu EFO:0004382 nanograms per liter (ng/L) [EFO:0004382] A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters. fecal_coliform_count_unit menu FecalColiformCountUnitMenu UO:0000213 colony forming units per milliliter (CFU/mL) [UO:0000213] A unit of microbial density that describes the number of colony forming units within a milliliter of material. - colony forming units per 100 milliliter (CFU/100 mL) - colony forming units per grams total solids (CFU/gTS) - most probable number per milliliter (MPN/mL) - most probable number per 100 milliliter (MPN/100 mL) + colony forming units per 100 milliliter (CFU/100 mL) A unit of microbial density that describes the number of colony forming units within 100 milliliters of material. + colony forming units per grams total solids (CFU/gTS) A unit of microbial density that describes the number of colony forming units within a gram of total solids in waste material. + most probable number per milliliter (MPN/mL) A unit of microbial density that describes the most probable number of microbes within one milliliter of material. + most probable number per 100 milliliter (MPN/100 mL) A unit of microbial density that describes the most probable number of microbes within 100 milliliters of material. sample_temperature_unit_(at collection) menu SampleTemperatureUnitAtCollectionMenu UO:0000195 degree Fahrenheit (F) [UO:0000195] A unit of temperature on a scale where water freezes at 32 degrees and boils at 212 degrees under standard conditions. UO:0000027 degree Celsius (C) [UO:0000027] A unit of temperature on a scale where water freezes at 0 degrees and boils at 100 degrees under standard conditions. diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv index 334908f3..1d311bf3 100644 --- a/web/templates/hpai/schema_slots.tsv +++ b/web/templates/hpai/schema_slots.tsv @@ -22,7 +22,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPI HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100309 geo_loc_latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100310 geo_loc_longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype InfluenzaSubsubtypeMenu TRUE TRUE +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101108 influenza_subtype influenza_subtype InfluenzaSubtypeMenu TRUE TRUE HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101109 influenza_subtyping_scheme_name influenza_subtyping_scheme_name InfluenzaSubtypingSchemeNameMenu HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101110 virus_identifier virus_identifier WhitespaceMinimizedString @@ -68,16 +68,16 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPI HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria HPAI;HPAIHost GENEPIO:0001268 Host information -HPAI;HPAIHost Host information GENEPIO:0001386 host_(common_name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host -HPAI;HPAIHost Host information GENEPIO:0001387 host_(scientific_name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host -HPAI;HPAIHost Host information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety -HPAI;HPAIHost Host information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed -HPAI;HPAIHost Host information GENEPIO:0100452 host_(food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host +HPAI;HPAIHost Host Information GENEPIO:0001386 host_(common_name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host +HPAI;HPAIHost Host Information GENEPIO:0001387 host_(scientific_name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host +HPAI;HPAIHost Host Information GENEPIO:0100450 host_(ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety +HPAI;HPAIHost Host Information GENEPIO:0100451 host_(breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed +HPAI;HPAIHost Host Information GENEPIO:0100452 host_(food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host HPAI;HPAIHost Host Information GENEPIO:0001392 host_age host_age decimal NullValueMenu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age HPAI;HPAIHost Host Information GENEPIO:0001393 host_age_unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] -HPAI;HPAIHost Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age - host_gender host_gender -HPAI;HPAIHost Host information GENEPIO:0001391 host_disease host_disease HostDiseaseMenu NullValueMenu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease +HPAI;HPAIHost Host Information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host Information host_gender host_gender +HPAI;HPAIHost Host Information GENEPIO:0001391 host_disease host_disease HostDiseaseMenu NullValueMenu The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease HPAI;HPAIHost Host Information GENEPIO:0001388 host_health_state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome @@ -115,10 +115,9 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100774 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100775 water_catchment_area_human_population_measurement_method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type populated area type menu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 @@ -127,7 +126,7 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100441 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100442 weather_type weather_type WeatherTypeMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 @@ -177,7 +176,7 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100808 HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTNMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorusTPMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorpusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator_ FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 @@ -206,9 +205,9 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100471 se HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001165 sequence_submitter_contact_email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100939 nucleic_acid_extraction_method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100772 nucleic_acid_extraction_kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] @@ -277,7 +276,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:010 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0100478 Risk assessment information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production WhitespaceMinimizedString NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed \ No newline at end of file diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 64044c3a..a9115c15 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -1573,6 +1573,11 @@ "meaning": "GENEPIO:0100031", "is_a": "Filtration" }, + "Finger Prick": { + "text": "Finger Prick", + "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.", + "meaning": "GENEPIO:0100036" + }, "Lavage": { "text": "Lavage", "description": "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid", @@ -1626,12 +1631,6 @@ "description": "The process of collecting specimen material using a swab collection device.", "meaning": "GENEPIO:0002117" }, - "Finger Prick": { - "text": "Finger Prick", - "description": "A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe.", - "meaning": "GENEPIO:0100036", - "is_a": "Swabbing" - }, "Thoracentesis (chest tap)": { "text": "Thoracentesis (chest tap)", "description": "The removal of excess fluid via needle puncture from the thoracic cavity.", @@ -14465,7 +14464,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionMenu" + "range": "PriorMpoxInfectionMenu" }, { "range": "NullValueMenu" @@ -14491,7 +14490,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentMenu" + "range": "PriorMpoxAntiviralTreatmentMenu" }, { "range": "NullValueMenu" @@ -17261,7 +17260,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionMenu" + "range": "PriorMpoxInfectionMenu" }, { "range": "NullValueMenu" @@ -17329,7 +17328,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentMenu" + "range": "PriorMpoxAntiviralTreatmentMenu" }, { "range": "NullValueMenu" @@ -20256,7 +20255,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionInternationalMenu" + "range": "PriorMpoxInfectionInternationalMenu" }, { "range": "NullValueMenu" @@ -20279,7 +20278,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu" + "range": "PriorMpoxAntiviralTreatmentInternationalMenu" }, { "range": "NullValueMenu" @@ -23066,7 +23065,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxInfectionInternationalMenu" + "range": "PriorMpoxInfectionInternationalMenu" }, { "range": "NullValueMenu" @@ -23131,7 +23130,7 @@ "slot_group": "Host reinfection information", "any_of": [ { - "range": "PriorMonkeypoxAntiviralTreatmentInternationalMenu" + "range": "PriorMpoxAntiviralTreatmentInternationalMenu" }, { "range": "NullValueMenu" diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 4d3a318e..f9d2e8e3 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -591,7 +591,7 @@ classes: examples: - value: Prior infection any_of: - - range: PriorMonkeypoxInfectionMenu + - range: PriorMpoxInfectionMenu - range: NullValueMenu exact_mappings: - NML_LIMS:prior%20Monkeypox%20infection @@ -604,7 +604,7 @@ classes: examples: - value: Prior antiviral treatment any_of: - - range: PriorMonkeypoxAntiviralTreatmentMenu + - range: PriorMpoxAntiviralTreatmentMenu - range: NullValueMenu exact_mappings: - NML_LIMS:prior%20Monkeypox%20antiviral%20treatment @@ -1476,7 +1476,7 @@ classes: examples: - value: Prior infection [GENEPIO:0100037] any_of: - - range: PriorMonkeypoxInfectionInternationalMenu + - range: PriorMpoxInfectionInternationalMenu - range: NullValueMenu prior_mpox_infection_date: rank: 70 @@ -1487,7 +1487,7 @@ classes: examples: - value: Prior antiviral treatment [GENEPIO:0100037] any_of: - - range: PriorMonkeypoxAntiviralTreatmentInternationalMenu + - range: PriorMpoxAntiviralTreatmentInternationalMenu - range: NullValueMenu prior_antiviral_treatment_during_prior_mpox_infection: rank: 72 @@ -5293,6 +5293,12 @@ enums: air via an air filtration device. meaning: GENEPIO:0100031 is_a: Filtration + Finger Prick: + text: Finger Prick + description: A collecting specimen from organism process in which a skin site + free of surface arterial flow is pierced with a sterile lancet, after a + capillary blood droplet is formed a sample is captured in a capillary tupe. + meaning: GENEPIO:0100036 Lavage: text: Lavage description: A protocol application to separate cells and/or cellular secretions @@ -5348,13 +5354,6 @@ enums: description: The process of collecting specimen material using a swab collection device. meaning: GENEPIO:0002117 - Finger Prick: - text: Finger Prick - description: A collecting specimen from organism process in which a skin site - free of surface arterial flow is pierced with a sterile lancet, after a - capillary blood droplet is formed a sample is captured in a capillary tupe. - meaning: GENEPIO:0100036 - is_a: Swabbing Thoracentesis (chest tap): text: Thoracentesis (chest tap) description: The removal of excess fluid via needle puncture from the thoracic diff --git a/web/templates/mpox/schema_enums.tsv b/web/templates/mpox/schema_enums.tsv index 06cb850b..794fcfed 100644 --- a/web/templates/mpox/schema_enums.tsv +++ b/web/templates/mpox/schema_enums.tsv @@ -241,6 +241,7 @@ collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis A pren OBI:0002651 Needle Biopsy A biopsy that uses a hollow needle to extract cells. OBI:0302885 Filtration Filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device GENEPIO:0100031 Air filtration A filtration process which removes solid particulates from the air via an air filtration device. + GENEPIO:0100036 Finger Prick A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. OBI:0600044 Lavage A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid GENEPIO:0100032 Bronchoalveolar lavage (BAL) The collection of bronchoalveolar lavage fluid (BAL) from the lungs. GENEPIO:0100033 Gastric Lavage The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. @@ -251,7 +252,6 @@ collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis A pren GENEPIO:0100034 Saline gargle (mouth rinse and gargle) A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device. GENEPIO:0100035 Scraping A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device. GENEPIO:0002117 Swabbing The process of collecting specimen material using a swab collection device. - GENEPIO:0100036 Finger Prick A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. NCIT:C15392 Thoracentesis (chest tap) The removal of excess fluid via needle puncture from the thoracic cavity. collection method international menu CollectionMethodInternationalMenu NCIT:C52009 Amniocentesis [NCIT:C52009] A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. Mpox_international diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 2cd58db4..738d420f 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -116,11 +116,11 @@ MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exp Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS Mpox;MpoxInternational Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information Mpox;MpoxInternational -Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMonkeypoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection Mpox -MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMonkeypoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] MpoxInternational +Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection Mpox +MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] MpoxInternational Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date Mpox;MpoxInternational -Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMonkeypoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment Mpox -MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMonkeypoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] MpoxInternational +Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment Mpox +MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] MpoxInternational Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection Mpox;MpoxInternational @@ -229,7 +229,6 @@ Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNam Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 Mpox Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 Mpox Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 Mpox - GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS Mpox;MpoxInternational Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS Mpox;MpoxInternational \ No newline at end of file diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index e6c15de8..1a4e3f05 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -304,27 +304,42 @@ "Not Applicable [GENEPIO:0001619]": { "text": "Not Applicable [GENEPIO:0001619]", "description": "A categorical choice recorded when a datum does not apply to a given context.", - "meaning": "GENEPIO:0001619" + "meaning": "GENEPIO:0001619", + "exact_mappings": [ + "NCBI_SRA:not%20applicable" + ] }, "Missing [GENEPIO:0001618]": { "text": "Missing [GENEPIO:0001618]", "description": "A categorical choice recorded when a datum is not included for an unknown reason.", - "meaning": "GENEPIO:0001618" + "meaning": "GENEPIO:0001618", + "exact_mappings": [ + "NCBI_SRA:missing" + ] }, "Not Collected [GENEPIO:0001620]": { "text": "Not Collected [GENEPIO:0001620]", "description": "A categorical choice recorded when a datum was not measured or collected.", - "meaning": "GENEPIO:0001620" + "meaning": "GENEPIO:0001620", + "exact_mappings": [ + "NCBI_SRA:not%20collected" + ] }, "Not Provided [GENEPIO:0001668]": { "text": "Not Provided [GENEPIO:0001668]", "description": "A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage.", - "meaning": "GENEPIO:0001668" + "meaning": "GENEPIO:0001668", + "exact_mappings": [ + "NCBI_SRA:not%20provided" + ] }, "Restricted Access [GENEPIO:0001810]": { "text": "Restricted Access [GENEPIO:0001810]", "description": "A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns.", - "meaning": "GENEPIO:0001810" + "meaning": "GENEPIO:0001810", + "exact_mappings": [ + "NCBI_SRA:restricted%20access" + ] } } }, @@ -2369,8 +2384,8 @@ } } }, - "environmental material menu": { - "name": "environmental material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", "title": "environmental material menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3475,57 +3490,90 @@ "Illumina [GENEPIO:0001923]": { "text": "Illumina [GENEPIO:0001923]", "description": "A sequencing platform provided by the Illumina company.", - "meaning": "GENEPIO:0001923" + "meaning": "GENEPIO:0001923", + "exact_mappings": [ + "NCBI_SRA:ILLUMINA" + ] }, "Pacific Biosciences [GENEPIO:0001927]": { "text": "Pacific Biosciences [GENEPIO:0001927]", "description": "A sequencing platform provided by the Pacific Biosciences company.", - "meaning": "GENEPIO:0001927" + "meaning": "GENEPIO:0001927", + "exact_mappings": [ + "NCBI_SRA:PACBIO_SMRT" + ] }, "Ion Torrent [GENEPIO:0002683]": { "text": "Ion Torrent [GENEPIO:0002683]", "description": "A sequencing platform provided by the Ion Torrent company.", - "meaning": "GENEPIO:0002683" + "meaning": "GENEPIO:0002683", + "exact_mappings": [ + "NCBI_SRA:ION_TORRENT" + ] }, "Oxford Nanopore Technologies [GENEPIO:0100986]": { "text": "Oxford Nanopore Technologies [GENEPIO:0100986]", "description": "An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK.", - "meaning": "GENEPIO:0100986" + "meaning": "GENEPIO:0100986", + "exact_mappings": [ + "NCBI_SRA:OXFORT_NANOPORE" + ] }, "BGI Genomics [GENEPIO:0004324]": { "text": "BGI Genomics [GENEPIO:0004324]", "description": "A sequencing platform provided by the BGI Genomics company.", - "meaning": "GENEPIO:0004324" + "meaning": "GENEPIO:0004324", + "exact_mappings": [ + "NCBI_SRA:BGISEQ" + ] }, "MGI [GENEPIO:0004325]": { "text": "MGI [GENEPIO:0004325]", "description": "A sequencing platform provided by the MGI company.", - "meaning": "GENEPIO:0004325" + "meaning": "GENEPIO:0004325", + "exact_mappings": [ + "NCBI_SRA:BGISEQ" + ] }, "Roche LS454 [GENEPIO:0001926]": { "text": "Roche LS454 [GENEPIO:0001926]", "description": "A sequencing platform provided by the 454 Life Sciences company.", - "meaning": "GENEPIO:0001926" + "meaning": "GENEPIO:0001926", + "exact_mappings": [ + "NCBI_SRA:_LS454" + ] }, "SOLiD sequencing [GENEPIO:0002684]": { "text": "SOLiD sequencing [GENEPIO:0002684]", "description": "A sequencing platform provided by Life Technologies Corporation.", - "meaning": "GENEPIO:0002684" + "meaning": "GENEPIO:0002684", + "exact_mappings": [ + "NCBI_SRA:ABI_SOLID" + ] }, "Complete Genomics [GENEPIO:0001924]": { "text": "Complete Genomics [GENEPIO:0001924]", "description": "An in-house sequencing platform provided by Complete Genomics.", - "meaning": "GENEPIO:0001924" + "meaning": "GENEPIO:0001924", + "exact_mappings": [ + "NCBI_SRA:COMPLETE_GENOMICS" + ] }, "Helicos [GENEPIO:0002682]": { "text": "Helicos [GENEPIO:0002682]", "description": "A sequencing platform brand provided by Helicos corporation (now defunct).", - "meaning": "GENEPIO:0002682" + "meaning": "GENEPIO:0002682", + "exact_mappings": [ + "NCBI_SRA:HELICOS" + ] }, "Applied Biosystems [GENEPIO:0100985]": { "text": "Applied Biosystems [GENEPIO:0100985]", "description": "A sequencing platform provided by ThermoFisher.", - "meaning": "GENEPIO:0100985" + "meaning": "GENEPIO:0100985", + "exact_mappings": [ + "NCBI_SRA:CAPILLARY" + ] } } }, @@ -3990,29 +4038,44 @@ "Amplicon sequencing assay [OBI:0002767]": { "text": "Amplicon sequencing assay [OBI:0002767]", "description": "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced.", - "meaning": "OBI:0002767" + "meaning": "OBI:0002767", + "exact_mappings": [ + "NCBI_SRA:AMPLICON" + ] }, "16S ribosomal gene sequencing assay [OBI:0002763]": { "text": "16S ribosomal gene sequencing assay [OBI:0002763]", "description": "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample.", "meaning": "OBI:0002763", - "is_a": "Amplicon sequencing assay [OBI:0002767]" + "is_a": "Amplicon sequencing assay [OBI:0002767]", + "exact_mappings": [ + "NCBI_SRA:AMPLICON" + ] }, "Whole genome sequencing assay [OBI:0002117]": { "text": "Whole genome sequencing assay [OBI:0002117]", "description": "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.", - "meaning": "OBI:0002117" + "meaning": "OBI:0002117", + "exact_mappings": [ + "NCBI_SRA:WGS" + ] }, "Whole metagenome sequencing assay [OBI:0002623]": { "text": "Whole metagenome sequencing assay [OBI:0002623]", "description": "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.", - "meaning": "OBI:0002623" + "meaning": "OBI:0002623", + "exact_mappings": [ + "NCBI_SRA:OTHER" + ] }, "Whole virome sequencing assay [OBI:0002768]": { "text": "Whole virome sequencing assay [OBI:0002768]", "description": "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample.", "meaning": "OBI:0002768", - "is_a": "Whole metagenome sequencing assay [OBI:0002623]" + "is_a": "Whole metagenome sequencing assay [OBI:0002623]", + "exact_mappings": [ + "NCBI_SRA:OTHER" + ] } } }, @@ -4024,112 +4087,178 @@ "artic-v1 [GENEPIO:0100847]": { "text": "artic-v1 [GENEPIO:0100847]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0.", - "meaning": "GENEPIO:0100847" + "meaning": "GENEPIO:0100847", + "exact_mappings": [ + "NCBI_SRA:artic-v1" + ] }, "artic-v2 [GENEPIO:0100848]": { "text": "artic-v2 [GENEPIO:0100848]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0.", - "meaning": "GENEPIO:0100848" + "meaning": "GENEPIO:0100848", + "exact_mappings": [ + "NCBI_SRA:artic-v2" + ] }, "artic-v3 [GENEPIO:0100849]": { "text": "artic-v3 [GENEPIO:0100849]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0.", - "meaning": "GENEPIO:0100849" + "meaning": "GENEPIO:0100849", + "exact_mappings": [ + "NCBI_SRA:artic-v3" + ] }, "artic-v4 [GENEPIO:0100850]": { "text": "artic-v4 [GENEPIO:0100850]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0.", - "meaning": "GENEPIO:0100850" + "meaning": "GENEPIO:0100850", + "exact_mappings": [ + "NCBI_SRA:artic-v4" + ] }, "artic-v4.1 [GENEPIO:0100851]": { "text": "artic-v4.1 [GENEPIO:0100851]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0.", - "meaning": "GENEPIO:0100851" + "meaning": "GENEPIO:0100851", + "exact_mappings": [ + "NCBI_SRA:artic-v4.1" + ] }, "artic-v5.0.0_400 [GENEPIO:0100852]": { "text": "artic-v5.0.0_400 [GENEPIO:0100852]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100852" + "meaning": "GENEPIO:0100852", + "exact_mappings": [ + "NCBI_SRA:artic-v5.0.0_400" + ] }, "artic-v5.1.0_400 [GENEPIO:0100853]": { "text": "artic-v5.1.0_400 [GENEPIO:0100853]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100853" + "meaning": "GENEPIO:0100853", + "exact_mappings": [ + "NCBI_SRA:artic-v5.1.0_400" + ] }, "artic-v5.2.0_1200 [GENEPIO:0100854]": { "text": "artic-v5.2.0_1200 [GENEPIO:0100854]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100854" + "meaning": "GENEPIO:0100854", + "exact_mappings": [ + "NCBI_SRA:artic-v5.2.0_1200" + ] }, "artic-v5.2.0_400 [GENEPIO:0100855]": { "text": "artic-v5.2.0_400 [GENEPIO:0100855]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100855" + "meaning": "GENEPIO:0100855", + "exact_mappings": [ + "NCBI_SRA:artic-v5.2.0_400" + ] }, "artic-v5.3.2_400 [GENEPIO:0100856]": { "text": "artic-v5.3.2_400 [GENEPIO:0100856]", "description": "An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length.", - "meaning": "GENEPIO:0100856" + "meaning": "GENEPIO:0100856", + "exact_mappings": [ + "NCBI_SRA:artic-v5.3.2_400" + ] }, "eden-v1 [GENEPIO:0100857]": { "text": "eden-v1 [GENEPIO:0100857]", "description": "An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length.", - "meaning": "GENEPIO:0100857" + "meaning": "GENEPIO:0100857", + "exact_mappings": [ + "NCBI_SRA:eden-v1" + ] }, "midnight-bccdc-v1 [GENEPIO:0100858]": { "text": "midnight-bccdc-v1 [GENEPIO:0100858]", "description": "An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100858" + "meaning": "GENEPIO:0100858", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v1" + ] }, "midnight-bccdc-v2 [GENEPIO:0100859]": { "text": "midnight-bccdc-v2 [GENEPIO:0100859]", "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100859" + "meaning": "GENEPIO:0100859", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v2" + ] }, "midnight-bccdc-v3 [GENEPIO:0100860]": { "text": "midnight-bccdc-v3 [GENEPIO:0100860]", "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100860" + "meaning": "GENEPIO:0100860", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v3" + ] }, "midnight-bccdc-v4 [GENEPIO:0100861]": { "text": "midnight-bccdc-v4 [GENEPIO:0100861]", "description": "An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100861" + "meaning": "GENEPIO:0100861", + "exact_mappings": [ + "NCBI_SRA:midnight-bccdc-v4" + ] }, "midnight-ont-v3 [GENEPIO:0100862]": { "text": "midnight-ont-v3 [GENEPIO:0100862]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100862" + "meaning": "GENEPIO:0100862", + "exact_mappings": [ + "NCBI_SRA:midnight-ont-v3" + ] }, "midnight-v1 [GENEPIO:0100863]": { "text": "midnight-v1 [GENEPIO:0100863]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100863" + "meaning": "GENEPIO:0100863", + "exact_mappings": [ + "NCBI_SRA:midnight-v1" + ] }, "midnight-v2 [GENEPIO:0100864]": { "text": "midnight-v2 [GENEPIO:0100864]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length.", - "meaning": "GENEPIO:0100864" + "meaning": "GENEPIO:0100864", + "exact_mappings": [ + "NCBI_SRA:midnight-v2" + ] }, "varskip-vsl1a [GENEPIO:0100865]": { "text": "varskip-vsl1a [GENEPIO:0100865]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long.", - "meaning": "GENEPIO:0100865" + "meaning": "GENEPIO:0100865", + "exact_mappings": [ + "NCBI_SRA:varskip-vsl1a" + ] }, "varskip-vss1a [GENEPIO:0100866]": { "text": "varskip-vss1a [GENEPIO:0100866]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short.", - "meaning": "GENEPIO:0100866" + "meaning": "GENEPIO:0100866", + "exact_mappings": [ + "NCBI_SRA:varskip-vss1a" + ] }, "varskip-vss2a [GENEPIO:0100867]": { "text": "varskip-vss2a [GENEPIO:0100867]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a.", - "meaning": "GENEPIO:0100867" + "meaning": "GENEPIO:0100867", + "exact_mappings": [ + "NCBI_SRA:varskip-vss2a" + ] }, "varskip-vss2b [GENEPIO:0100868]": { "text": "varskip-vss2b [GENEPIO:0100868]", "description": "An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b.", - "meaning": "GENEPIO:0100868" + "meaning": "GENEPIO:0100868", + "exact_mappings": [ + "NCBI_SRA:varskip-vss2b" + ] } } }, @@ -4141,12 +4270,18 @@ "Hybridization capture [GENEPIO:0001950]": { "text": "Hybridization capture [GENEPIO:0001950]", "description": "Selection by hybridization in array or solution.", - "meaning": "GENEPIO:0001950" + "meaning": "GENEPIO:0001950", + "exact_mappings": [ + "NCBI_SRA:Hybrid%20Selection" + ] }, "rRNA depletion method [GENEPIO:0101020]": { "text": "rRNA depletion method [GENEPIO:0101020]", "description": "Removal of background RNA for the purposes of enriching the genomic target.", - "meaning": "GENEPIO:0101020" + "meaning": "GENEPIO:0101020", + "exact_mappings": [ + "NCBI_SRA:Other" + ] } } }, @@ -4158,32 +4293,50 @@ "No quality control issues identified [GENEPIO:0100562]": { "text": "No quality control issues identified [GENEPIO:0100562]", "description": "A statement confirming that quality control processes were carried out and no quality issues were detected.", - "meaning": "GENEPIO:0100562" + "meaning": "GENEPIO:0100562", + "exact_mappings": [ + "NCBI_SRA:no%20quality%20control%20issues%20identified" + ] }, "Sequence passed quality control [GENEPIO:0100563]": { "text": "Sequence passed quality control [GENEPIO:0100563]", "description": "A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria.", - "meaning": "GENEPIO:0100563" + "meaning": "GENEPIO:0100563", + "exact_mappings": [ + "NCBI_SRA:Sequence%20passed%20quality%20control" + ] }, "Sequence failed quality control [GENEPIO:0100564]": { "text": "Sequence failed quality control [GENEPIO:0100564]", "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria.", - "meaning": "GENEPIO:0100564" + "meaning": "GENEPIO:0100564", + "exact_mappings": [ + "NCBI_SRA:Sequence%20failed%20quality%20control" + ] }, "Minor quality control issues identified [GENEPIO:0100565]": { "text": "Minor quality control issues identified [GENEPIO:0100565]", "description": "A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor.", - "meaning": "GENEPIO:0100565" + "meaning": "GENEPIO:0100565", + "exact_mappings": [ + "NCBI_SRA:minor%20quality%20control%20issues%20identified" + ] }, "Sequence flagged for potential quality control issues [GENEPIO:0100566]": { "text": "Sequence flagged for potential quality control issues [GENEPIO:0100566]", "description": "A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review.", - "meaning": "GENEPIO:0100566" + "meaning": "GENEPIO:0100566", + "exact_mappings": [ + "NCBI_SRA:sequence%20flagged%20for%20potential%20quality%20control%20issues" + ] }, "Quality control not performed [GENEPIO:0100567]": { "text": "Quality control not performed [GENEPIO:0100567]", "description": "A statement confirming that quality control processes have not been carried out.", - "meaning": "GENEPIO:0100567" + "meaning": "GENEPIO:0100567", + "exact_mappings": [ + "NCBI_SRA:not%20performed" + ] } } }, @@ -4195,42 +4348,66 @@ "Low quality sequence [GENEPIO:0100568]": { "text": "Low quality sequence [GENEPIO:0100568]", "description": "Sequence data that does not meet quality control thresholds.", - "meaning": "GENEPIO:0100568" + "meaning": "GENEPIO:0100568", + "exact_mappings": [ + "NCBI_SRA:low%20quality%20sequence" + ] }, "Sequence contaminated [GENEPIO:0100569]": { "text": "Sequence contaminated [GENEPIO:0100569]", "description": "Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source.", - "meaning": "GENEPIO:0100569" + "meaning": "GENEPIO:0100569", + "exact_mappings": [ + "NCBI_SRA:sequenced%20contaminated" + ] }, "Low average genome coverage [GENEPIO:0100570]": { "text": "Low average genome coverage [GENEPIO:0100570]", "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage).", - "meaning": "GENEPIO:0100570" + "meaning": "GENEPIO:0100570", + "exact_mappings": [ + "NCBI_SRA:low%20average%20genome%20coverage" + ] }, "Low percent genome captured [GENEPIO:0100571]": { "text": "Low percent genome captured [GENEPIO:0100571]", "description": "Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage).", - "meaning": "GENEPIO:0100571" + "meaning": "GENEPIO:0100571", + "exact_mappings": [ + "NCBI_SRA:low%20%25%20genome%20captured" + ] }, "Read lengths shorter than expected [GENEPIO:0100572]": { "text": "Read lengths shorter than expected [GENEPIO:0100572]", "description": "Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions.", - "meaning": "GENEPIO:0100572" + "meaning": "GENEPIO:0100572", + "exact_mappings": [ + "NCBI_SRA:read%20lengths%20shorter%20than%20expected" + ] }, "Sequence amplification artifacts [GENEPIO:0100573]": { "text": "Sequence amplification artifacts [GENEPIO:0100573]", "description": "Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts).", - "meaning": "GENEPIO:0100573" + "meaning": "GENEPIO:0100573", + "exact_mappings": [ + "NCBI_SRA:sequence%20amplification%20artifacts" + ] }, "Low signal to noise ratio [GENEPIO:0100574]": { "text": "Low signal to noise ratio [GENEPIO:0100574]", "description": "Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal).", - "meaning": "GENEPIO:0100574" + "meaning": "GENEPIO:0100574", + "exact_mappings": [ + "NCBI_SRA:low%20signal%20to%20noise%20ratio" + ] }, "Low coverage of characteristic mutations [GENEPIO:0100575]": { "text": "Low coverage of characteristic mutations [GENEPIO:0100575]", "description": "Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence.", - "meaning": "GENEPIO:0100575" + "meaning": "GENEPIO:0100575", + "exact_mappings": [ + "NCBI_SRA:low%20coverage%20of%20characteristic%20mutations" + ] } } }, @@ -7838,7 +8015,7 @@ ], "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -11349,7 +11526,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -11400,7 +11577,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -15008,7 +15185,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -17154,7 +17331,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -17349,7 +17526,7 @@ "slot_group": "Pathogen diagnostic testing", "any_of": [ { - "range": "GeneNameMenu" + "range": "GeneSymbolMenu" }, { "range": "NullValueMenu" @@ -22209,7 +22386,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" @@ -29850,7 +30027,7 @@ "slot_group": "Environmental conditions and measurements", "any_of": [ { - "range": "TotalPhosphorusTpMeasurementUnitMenu" + "range": "TotalPhosphorpusTpMeasurementUnitMenu" }, { "range": "NullValueMenu" diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index 277473ad..de8406e6 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -842,7 +842,7 @@ classes: examples: - value: E gene (orf4) any_of: - - range: GeneNameMenu + - range: GeneSymbolMenu - range: NullValueMenu diagnostic_target_presence_2: rank: 199 @@ -869,7 +869,7 @@ classes: examples: - value: E gene (orf4) any_of: - - range: GeneNameMenu + - range: GeneSymbolMenu - range: NullValueMenu diagnostic_target_presence_3: rank: 206 @@ -4389,7 +4389,7 @@ slots: comments: Provide the units of the measured TP. slot_uri: GENEPIO:0100812 any_of: - - range: TotalPhosphorusTpMeasurementUnitMenu + - range: TotalPhosphorpusTpMeasurementUnitMenu - range: NullValueMenu examples: - value: milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) @@ -5604,27 +5604,37 @@ enums: description: A categorical choice recorded when a datum does not apply to a given context. meaning: GENEPIO:0001619 + exact_mappings: + - NCBI_SRA:not%20applicable Missing [GENEPIO:0001618]: text: Missing [GENEPIO:0001618] description: A categorical choice recorded when a datum is not included for an unknown reason. meaning: GENEPIO:0001618 + exact_mappings: + - NCBI_SRA:missing Not Collected [GENEPIO:0001620]: text: Not Collected [GENEPIO:0001620] description: A categorical choice recorded when a datum was not measured or collected. meaning: GENEPIO:0001620 + exact_mappings: + - NCBI_SRA:not%20collected Not Provided [GENEPIO:0001668]: text: Not Provided [GENEPIO:0001668] description: A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. meaning: GENEPIO:0001668 + exact_mappings: + - NCBI_SRA:not%20provided Restricted Access [GENEPIO:0001810]: text: Restricted Access [GENEPIO:0001810] description: A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. meaning: GENEPIO:0001810 + exact_mappings: + - NCBI_SRA:restricted%20access GeoLocNameCountryMenu: name: GeoLocNameCountryMenu title: geo_loc_name (country) menu @@ -8673,8 +8683,8 @@ enums: thrust from a jet engine, propeller, or rocket engine. meaning: ENVO:03501349 is_a: Transportation vehicle [ENVO:01000604] - environmental material menu: - name: environmental material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu title: environmental material menu permissible_values: Bar screen [ENVO:03501474]: @@ -9687,48 +9697,70 @@ enums: text: Illumina [GENEPIO:0001923] description: A sequencing platform provided by the Illumina company. meaning: GENEPIO:0001923 + exact_mappings: + - NCBI_SRA:ILLUMINA Pacific Biosciences [GENEPIO:0001927]: text: Pacific Biosciences [GENEPIO:0001927] description: A sequencing platform provided by the Pacific Biosciences company. meaning: GENEPIO:0001927 + exact_mappings: + - NCBI_SRA:PACBIO_SMRT Ion Torrent [GENEPIO:0002683]: text: Ion Torrent [GENEPIO:0002683] description: A sequencing platform provided by the Ion Torrent company. meaning: GENEPIO:0002683 + exact_mappings: + - NCBI_SRA:ION_TORRENT Oxford Nanopore Technologies [GENEPIO:0100986]: text: Oxford Nanopore Technologies [GENEPIO:0100986] description: An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. meaning: GENEPIO:0100986 + exact_mappings: + - NCBI_SRA:OXFORT_NANOPORE BGI Genomics [GENEPIO:0004324]: text: BGI Genomics [GENEPIO:0004324] description: A sequencing platform provided by the BGI Genomics company. meaning: GENEPIO:0004324 + exact_mappings: + - NCBI_SRA:BGISEQ MGI [GENEPIO:0004325]: text: MGI [GENEPIO:0004325] description: A sequencing platform provided by the MGI company. meaning: GENEPIO:0004325 + exact_mappings: + - NCBI_SRA:BGISEQ Roche LS454 [GENEPIO:0001926]: text: Roche LS454 [GENEPIO:0001926] description: A sequencing platform provided by the 454 Life Sciences company. meaning: GENEPIO:0001926 + exact_mappings: + - NCBI_SRA:_LS454 SOLiD sequencing [GENEPIO:0002684]: text: SOLiD sequencing [GENEPIO:0002684] description: A sequencing platform provided by Life Technologies Corporation. meaning: GENEPIO:0002684 + exact_mappings: + - NCBI_SRA:ABI_SOLID Complete Genomics [GENEPIO:0001924]: text: Complete Genomics [GENEPIO:0001924] description: An in-house sequencing platform provided by Complete Genomics. meaning: GENEPIO:0001924 + exact_mappings: + - NCBI_SRA:COMPLETE_GENOMICS Helicos [GENEPIO:0002682]: text: Helicos [GENEPIO:0002682] description: A sequencing platform brand provided by Helicos corporation (now defunct). meaning: GENEPIO:0002682 + exact_mappings: + - NCBI_SRA:HELICOS Applied Biosystems [GENEPIO:0100985]: text: Applied Biosystems [GENEPIO:0100985] description: A sequencing platform provided by ThermoFisher. meaning: GENEPIO:0100985 + exact_mappings: + - NCBI_SRA:CAPILLARY SequencingInstrumentMenu: name: SequencingInstrumentMenu title: sequencing instrument menu @@ -10249,6 +10281,8 @@ enums: description: A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. meaning: OBI:0002767 + exact_mappings: + - NCBI_SRA:AMPLICON 16S ribosomal gene sequencing assay [OBI:0002763]: text: 16S ribosomal gene sequencing assay [OBI:0002763] description: An amplicon sequencing assay in which the amplicon is derived @@ -10257,24 +10291,32 @@ enums: sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. meaning: OBI:0002763 + exact_mappings: + - NCBI_SRA:AMPLICON is_a: Amplicon sequencing assay [OBI:0002767] Whole genome sequencing assay [OBI:0002117]: text: Whole genome sequencing assay [OBI:0002117] description: A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. meaning: OBI:0002117 + exact_mappings: + - NCBI_SRA:WGS Whole metagenome sequencing assay [OBI:0002623]: text: Whole metagenome sequencing assay [OBI:0002623] description: A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. meaning: OBI:0002623 + exact_mappings: + - NCBI_SRA:OTHER Whole virome sequencing assay [OBI:0002768]: text: Whole virome sequencing assay [OBI:0002768] description: A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. meaning: OBI:0002768 + exact_mappings: + - NCBI_SRA:OTHER is_a: Whole metagenome sequencing assay [OBI:0002623] AmpliconPcrPrimerSchemeMenu: name: AmpliconPcrPrimerSchemeMenu @@ -10285,62 +10327,84 @@ enums: description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. meaning: GENEPIO:0100847 + exact_mappings: + - NCBI_SRA:artic-v1 artic-v2 [GENEPIO:0100848]: text: artic-v2 [GENEPIO:0100848] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. meaning: GENEPIO:0100848 + exact_mappings: + - NCBI_SRA:artic-v2 artic-v3 [GENEPIO:0100849]: text: artic-v3 [GENEPIO:0100849] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. meaning: GENEPIO:0100849 + exact_mappings: + - NCBI_SRA:artic-v3 artic-v4 [GENEPIO:0100850]: text: artic-v4 [GENEPIO:0100850] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. meaning: GENEPIO:0100850 + exact_mappings: + - NCBI_SRA:artic-v4 artic-v4.1 [GENEPIO:0100851]: text: artic-v4.1 [GENEPIO:0100851] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. meaning: GENEPIO:0100851 + exact_mappings: + - NCBI_SRA:artic-v4.1 artic-v5.0.0_400 [GENEPIO:0100852]: text: artic-v5.0.0_400 [GENEPIO:0100852] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100852 + exact_mappings: + - NCBI_SRA:artic-v5.0.0_400 artic-v5.1.0_400 [GENEPIO:0100853]: text: artic-v5.1.0_400 [GENEPIO:0100853] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100853 + exact_mappings: + - NCBI_SRA:artic-v5.1.0_400 artic-v5.2.0_1200 [GENEPIO:0100854]: text: artic-v5.2.0_1200 [GENEPIO:0100854] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100854 + exact_mappings: + - NCBI_SRA:artic-v5.2.0_1200 artic-v5.2.0_400 [GENEPIO:0100855]: text: artic-v5.2.0_400 [GENEPIO:0100855] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100855 + exact_mappings: + - NCBI_SRA:artic-v5.2.0_400 artic-v5.3.2_400 [GENEPIO:0100856]: text: artic-v5.3.2_400 [GENEPIO:0100856] description: An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. meaning: GENEPIO:0100856 + exact_mappings: + - NCBI_SRA:artic-v5.3.2_400 eden-v1 [GENEPIO:0100857]: text: eden-v1 [GENEPIO:0100857] description: An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. meaning: GENEPIO:0100857 + exact_mappings: + - NCBI_SRA:eden-v1 midnight-bccdc-v1 [GENEPIO:0100858]: text: midnight-bccdc-v1 [GENEPIO:0100858] description: An amplicon strategy which is for SARS-CoV-2 and based on the @@ -10348,6 +10412,8 @@ enums: adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100858 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v1 midnight-bccdc-v2 [GENEPIO:0100859]: text: midnight-bccdc-v2 [GENEPIO:0100859] description: An amplicon strategy which targets SARS-CoV-2 and is based on @@ -10355,6 +10421,8 @@ enums: and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100859 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v2 midnight-bccdc-v3 [GENEPIO:0100860]: text: midnight-bccdc-v3 [GENEPIO:0100860] description: An amplicon strategy which targets SARS-CoV-2 and is based on @@ -10362,6 +10430,8 @@ enums: and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100860 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v3 midnight-bccdc-v4 [GENEPIO:0100861]: text: midnight-bccdc-v4 [GENEPIO:0100861] description: An amplicon strategy which targets SARS-CoV-2 and is based on @@ -10369,48 +10439,64 @@ enums: and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100861 + exact_mappings: + - NCBI_SRA:midnight-bccdc-v4 midnight-ont-v3 [GENEPIO:0100862]: text: midnight-ont-v3 [GENEPIO:0100862] description: An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100862 + exact_mappings: + - NCBI_SRA:midnight-ont-v3 midnight-v1 [GENEPIO:0100863]: text: midnight-v1 [GENEPIO:0100863] description: An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100863 + exact_mappings: + - NCBI_SRA:midnight-v1 midnight-v2 [GENEPIO:0100864]: text: midnight-v2 [GENEPIO:0100864] description: An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. meaning: GENEPIO:0100864 + exact_mappings: + - NCBI_SRA:midnight-v2 varskip-vsl1a [GENEPIO:0100865]: text: varskip-vsl1a [GENEPIO:0100865] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. meaning: GENEPIO:0100865 + exact_mappings: + - NCBI_SRA:varskip-vsl1a varskip-vss1a [GENEPIO:0100866]: text: varskip-vss1a [GENEPIO:0100866] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. meaning: GENEPIO:0100866 + exact_mappings: + - NCBI_SRA:varskip-vss1a varskip-vss2a [GENEPIO:0100867]: text: varskip-vss2a [GENEPIO:0100867] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. meaning: GENEPIO:0100867 + exact_mappings: + - NCBI_SRA:varskip-vss2a varskip-vss2b [GENEPIO:0100868]: text: varskip-vss2b [GENEPIO:0100868] description: An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. meaning: GENEPIO:0100868 + exact_mappings: + - NCBI_SRA:varskip-vss2b GenomicTargetEnrichmentMethodMenu: name: GenomicTargetEnrichmentMethodMenu title: genomic target enrichment method menu @@ -10419,11 +10505,15 @@ enums: text: Hybridization capture [GENEPIO:0001950] description: Selection by hybridization in array or solution. meaning: GENEPIO:0001950 + exact_mappings: + - NCBI_SRA:Hybrid%20Selection rRNA depletion method [GENEPIO:0101020]: text: rRNA depletion method [GENEPIO:0101020] description: Removal of background RNA for the purposes of enriching the genomic target. meaning: GENEPIO:0101020 + exact_mappings: + - NCBI_SRA:Other QualityControlDeterminationMenu: name: QualityControlDeterminationMenu title: quality control determination menu @@ -10433,33 +10523,45 @@ enums: description: A statement confirming that quality control processes were carried out and no quality issues were detected. meaning: GENEPIO:0100562 + exact_mappings: + - NCBI_SRA:no%20quality%20control%20issues%20identified Sequence passed quality control [GENEPIO:0100563]: text: Sequence passed quality control [GENEPIO:0100563] description: A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. meaning: GENEPIO:0100563 + exact_mappings: + - NCBI_SRA:Sequence%20passed%20quality%20control Sequence failed quality control [GENEPIO:0100564]: text: Sequence failed quality control [GENEPIO:0100564] description: A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. meaning: GENEPIO:0100564 + exact_mappings: + - NCBI_SRA:Sequence%20failed%20quality%20control Minor quality control issues identified [GENEPIO:0100565]: text: Minor quality control issues identified [GENEPIO:0100565] description: A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. meaning: GENEPIO:0100565 + exact_mappings: + - NCBI_SRA:minor%20quality%20control%20issues%20identified Sequence flagged for potential quality control issues [GENEPIO:0100566]: text: Sequence flagged for potential quality control issues [GENEPIO:0100566] description: A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. meaning: GENEPIO:0100566 + exact_mappings: + - NCBI_SRA:sequence%20flagged%20for%20potential%20quality%20control%20issues Quality control not performed [GENEPIO:0100567]: text: Quality control not performed [GENEPIO:0100567] description: A statement confirming that quality control processes have not been carried out. meaning: GENEPIO:0100567 + exact_mappings: + - NCBI_SRA:not%20performed QualityControlIssuesMenu: name: QualityControlIssuesMenu title: quality control issues menu @@ -10468,12 +10570,16 @@ enums: text: Low quality sequence [GENEPIO:0100568] description: Sequence data that does not meet quality control thresholds. meaning: GENEPIO:0100568 + exact_mappings: + - NCBI_SRA:low%20quality%20sequence Sequence contaminated [GENEPIO:0100569]: text: Sequence contaminated [GENEPIO:0100569] description: Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. meaning: GENEPIO:0100569 + exact_mappings: + - NCBI_SRA:sequenced%20contaminated Low average genome coverage [GENEPIO:0100570]: text: Low average genome coverage [GENEPIO:0100570] description: Sequence data in which the entire length of the genome is not @@ -10481,32 +10587,44 @@ enums: of the genome are not sequenced a prescribed number of times (low depth of coverage). meaning: GENEPIO:0100570 + exact_mappings: + - NCBI_SRA:low%20average%20genome%20coverage Low percent genome captured [GENEPIO:0100571]: text: Low percent genome captured [GENEPIO:0100571] description: Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). meaning: GENEPIO:0100571 + exact_mappings: + - NCBI_SRA:low%20%25%20genome%20captured Read lengths shorter than expected [GENEPIO:0100572]: text: Read lengths shorter than expected [GENEPIO:0100572] description: Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. meaning: GENEPIO:0100572 + exact_mappings: + - NCBI_SRA:read%20lengths%20shorter%20than%20expected Sequence amplification artifacts [GENEPIO:0100573]: text: Sequence amplification artifacts [GENEPIO:0100573] description: Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). meaning: GENEPIO:0100573 + exact_mappings: + - NCBI_SRA:sequence%20amplification%20artifacts Low signal to noise ratio [GENEPIO:0100574]: text: Low signal to noise ratio [GENEPIO:0100574] description: Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). meaning: GENEPIO:0100574 + exact_mappings: + - NCBI_SRA:low%20signal%20to%20noise%20ratio Low coverage of characteristic mutations [GENEPIO:0100575]: text: Low coverage of characteristic mutations [GENEPIO:0100575] description: Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. meaning: GENEPIO:0100575 + exact_mappings: + - NCBI_SRA:low%20coverage%20of%20characteristic%20mutations GeneSymbolMenu: name: GeneSymbolMenu title: gene symbol menu diff --git a/web/templates/wastewater/schema_enums.tsv b/web/templates/wastewater/schema_enums.tsv index 222799e6..6f123a56 100644 --- a/web/templates/wastewater/schema_enums.tsv +++ b/web/templates/wastewater/schema_enums.tsv @@ -1,10 +1,10 @@ -title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_NCBI_SRA EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. - GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. - GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. - GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. - GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. +null value menu NullValueMenu GENEPIO:0001619 Not Applicable [GENEPIO:0001619] A categorical choice recorded when a datum does not apply to a given context. not applicable + GENEPIO:0001618 Missing [GENEPIO:0001618] A categorical choice recorded when a datum is not included for an unknown reason. missing + GENEPIO:0001620 Not Collected [GENEPIO:0001620] A categorical choice recorded when a datum was not measured or collected. not collected + GENEPIO:0001668 Not Provided [GENEPIO:0001668] A categorical choice recorded when a datum was collected but is not currently provided in the information being shared. This value indicates the information may be shared at the later stage. not provided + GENEPIO:0001810 Restricted Access [GENEPIO:0001810] A categorical choice recorded when a given datum is available but not shared publicly because of information privacy concerns. restricted access geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan [GAZ:00006882] A landlocked country that is located approximately in the center of Asia. It is bordered by Pakistan in the south and east Iran in the west, Turkmenistan, Uzbekistan and Tajikistan in the north, and China in the far northeast. Afghanistan is administratively divided into thirty-four (34) provinces (welayats). Each province is then divided into many provincial districts, and each district normally covers a city or several townships. [ url:http://en.wikipedia.org/wiki/Afghanistan ] GAZ:00002953 Albania [GAZ:00002953] A country in South Eastern Europe. Albania is bordered by Greece to the south-east, Montenegro to the north, Kosovo to the northeast, and the Republic of Macedonia to the east. It has a coast on the Adriatic Sea to the west, and on the Ionian Sea to the southwest. From the Strait of Otranto, Albania is less than 100 km from Italy. Albania is divided into 12 administrative divisions called (Albanian: official qark/qarku, but often prefekture/prefektura Counties), 36 districts (Rrethe) and 351 municipalities (Bashkia) and communes (Komuna). [ url:http://en.wikipedia.org/wiki/Albania ] @@ -403,7 +403,7 @@ environmental site menu EnvironmentalSiteMenu ENVO:01001481 Correctional facilit ENVO:01000608 Boat [ENVO:01000608] A boat is a watercraft of any size which is able to float or plane on water. ENVO:03501349 Airplane [ENVO:03501349] An aircraft which 1) has fixed wings and 2) is propelled by a thrust from a jet engine, propeller, or rocket engine. -environmental material menu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater +environmental material menu EnvironmentalMaterialMenu ENVO:03501474 Bar screen [ENVO:03501474] A mechanical filter used to remove large objects, such as rags and plastics, from wastewater ENVO:00002042 Surface water [ENVO:00002042] Water that is found on the surface of an astronomical object. ENVO:00002001 Wastewater [ENVO:00002001] Water that has been adversely affected in quality by anthropogenic influence ENVO:03501456 Wastewater sediment [ENVO:03501456] A sediment which is removed from waste water during a waste water treatment process. @@ -612,17 +612,17 @@ purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surv GENEPIO:0100023 Viral passage experiment [GENEPIO:0100023] A research sampling strategy in which samples are selected in order to perform a viral passage experiment. GENEPIO:0100024 Protocol testing experiment [GENEPIO:0100024] A research sampling strategy in which samples are collected in order to test a method or protocol. -sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. - GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. - GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. - GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. - GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. - GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. - GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. - GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. - GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. - GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). - GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. +sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPIO:0001923] A sequencing platform provided by the Illumina company. ILLUMINA + GENEPIO:0001927 Pacific Biosciences [GENEPIO:0001927] A sequencing platform provided by the Pacific Biosciences company. PACBIO_SMRT + GENEPIO:0002683 Ion Torrent [GENEPIO:0002683] A sequencing platform provided by the Ion Torrent company. ION_TORRENT + GENEPIO:0100986 Oxford Nanopore Technologies [GENEPIO:0100986] An sequencing platform that is developing and selling nanopore sequencing products and is based in the UK. OXFORT_NANOPORE + GENEPIO:0004324 BGI Genomics [GENEPIO:0004324] A sequencing platform provided by the BGI Genomics company. BGISEQ + GENEPIO:0004325 MGI [GENEPIO:0004325] A sequencing platform provided by the MGI company. BGISEQ + GENEPIO:0001926 Roche LS454 [GENEPIO:0001926] A sequencing platform provided by the 454 Life Sciences company. _LS454 + GENEPIO:0002684 SOLiD sequencing [GENEPIO:0002684] A sequencing platform provided by Life Technologies Corporation. ABI_SOLID + GENEPIO:0001924 Complete Genomics [GENEPIO:0001924] An in-house sequencing platform provided by Complete Genomics. COMPLETE_GENOMICS + GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). HELICOS + GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. CAPILLARY sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. @@ -701,53 +701,53 @@ sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GE GENEPIO:0100980 AB 3730 Genetic Analyzer [GENEPIO:0100980] An Applied Biosystems sequencing instrument model which utilises an 48 capillary array electrophoresis system for sequencing. GENEPIO:0100981 AB 3730xL Genetic Analyzer [GENEPIO:0100981] An Applied Biosystems sequencing instrument model which utilises an 96 capillary array electrophoresis system for sequencing. -sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. - OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. - OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. - OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. - OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. - -amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. - GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. - GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. - GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. - GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. - GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. - GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. - GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. - GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. - GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. - GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. - GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. - GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. - GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. - GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. - -genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. - GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. - -quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. - GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. - GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. - GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. - GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. - GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. - -quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. - GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. - GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). - GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). - GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. - GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). - GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). - GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. +sequencing assay type menu SequencingAssayTypeMenu OBI:0002767 Amplicon sequencing assay [OBI:0002767] A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. AMPLICON + OBI:0002763 16S ribosomal gene sequencing assay [OBI:0002763] An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. AMPLICON + OBI:0002117 Whole genome sequencing assay [OBI:0002117] A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. WGS + OBI:0002623 Whole metagenome sequencing assay [OBI:0002623] A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. OTHER + OBI:0002768 Whole virome sequencing assay [OBI:0002768] A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. OTHER + +amplicon pcr primer scheme menu AmpliconPcrPrimerSchemeMenu GENEPIO:0100847 artic-v1 [GENEPIO:0100847] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 1.0.0. artic-v1 + GENEPIO:0100848 artic-v2 [GENEPIO:0100848] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 2.0.0. artic-v2 + GENEPIO:0100849 artic-v3 [GENEPIO:0100849] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 3.0.0. artic-v3 + GENEPIO:0100850 artic-v4 [GENEPIO:0100850] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.0.0. artic-v4 + GENEPIO:0100851 artic-v4.1 [GENEPIO:0100851] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 4.1.0. artic-v4.1 + GENEPIO:0100852 artic-v5.0.0_400 [GENEPIO:0100852] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.0.0 which produces amplicons approximately 400bp in length. artic-v5.0.0_400 + GENEPIO:0100853 artic-v5.1.0_400 [GENEPIO:0100853] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2with the attributes of version 5.1.0 which produces amplicons approximately 400bp in length. artic-v5.1.0_400 + GENEPIO:0100854 artic-v5.2.0_1200 [GENEPIO:0100854] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 1200bp in length. artic-v5.2.0_1200 + GENEPIO:0100855 artic-v5.2.0_400 [GENEPIO:0100855] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.2.0 which produces amplicons approximately 400bp in length. artic-v5.2.0_400 + GENEPIO:0100856 artic-v5.3.2_400 [GENEPIO:0100856] An amplicon strategy which was developed by the ARTIC consortium for SARS-CoV-2 with the attributes of version 5.3.2 which produces amplicons approximately 400bp in length. artic-v5.3.2_400 + GENEPIO:0100857 eden-v1 [GENEPIO:0100857] An amplicon strategy which was developed by John-Sebastian Eden with primers for SARS-CoV-2 and attributes of version 1.0.0 which produces amplicons approximately 2500bp in length. eden-v1 + GENEPIO:0100858 midnight-bccdc-v1 [GENEPIO:0100858] An amplicon strategy which is for SARS-CoV-2 and based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v1 + GENEPIO:0100859 midnight-bccdc-v2 [GENEPIO:0100859] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v2 + GENEPIO:0100860 midnight-bccdc-v3 [GENEPIO:0100860] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 3.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v3 + GENEPIO:0100861 midnight-bccdc-v4 [GENEPIO:0100861] An amplicon strategy which targets SARS-CoV-2 and is based on the original Midnight scheme developed by Oxford Nanopore Technologies, and adapted by the BCCDC Public Health Lab with the attributes of version 4.0.0 which produces amplicons approximately 1200bp in length. midnight-bccdc-v4 + GENEPIO:0100862 midnight-ont-v3 [GENEPIO:0100862] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-ont-v3 + GENEPIO:0100863 midnight-v1 [GENEPIO:0100863] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 1.0.0 which produces amplicons approximately 1200bp in length. midnight-v1 + GENEPIO:0100864 midnight-v2 [GENEPIO:0100864] An amplicon strategy which targets SARS-CoV-2 and was developed by Oxford Nanopore Technologies with the attributes of version 2.0.0 which produces amplicons approximately 1200bp in length. midnight-v2 + GENEPIO:0100865 varskip-vsl1a [GENEPIO:0100865] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a long. varskip-vsl1a + GENEPIO:0100866 varskip-vss1a [GENEPIO:0100866] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 1a short. varskip-vss1a + GENEPIO:0100867 varskip-vss2a [GENEPIO:0100867] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2a. varskip-vss2a + GENEPIO:0100868 varskip-vss2b [GENEPIO:0100868] An amplicon strategy which targets SARS-CoV-2 and was developed by New England BioLabs using PrimalSeq to reduce effects of variants with the attributes of version 2b. varskip-vss2b + +genomic target enrichment method menu GenomicTargetEnrichmentMethodMenu GENEPIO:0001950 Hybridization capture [GENEPIO:0001950] Selection by hybridization in array or solution. Hybrid Selection + GENEPIO:0101020 rRNA depletion method [GENEPIO:0101020] Removal of background RNA for the purposes of enriching the genomic target. Other + +quality control determination menu QualityControlDeterminationMenu GENEPIO:0100562 No quality control issues identified [GENEPIO:0100562] A statement confirming that quality control processes were carried out and no quality issues were detected. no quality control issues identified + GENEPIO:0100563 Sequence passed quality control [GENEPIO:0100563] A statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. Sequence passed quality control + GENEPIO:0100564 Sequence failed quality control [GENEPIO:0100564] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. Sequence failed quality control + GENEPIO:0100565 Minor quality control issues identified [GENEPIO:0100565] A statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. minor quality control issues identified + GENEPIO:0100566 Sequence flagged for potential quality control issues [GENEPIO:0100566] A statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. sequence flagged for potential quality control issues + GENEPIO:0100567 Quality control not performed [GENEPIO:0100567] A statement confirming that quality control processes have not been carried out. not performed + +quality control issues menu QualityControlIssuesMenu GENEPIO:0100568 Low quality sequence [GENEPIO:0100568] Sequence data that does not meet quality control thresholds. low quality sequence + GENEPIO:0100569 Sequence contaminated [GENEPIO:0100569] Sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. sequenced contaminated + GENEPIO:0100570 Low average genome coverage [GENEPIO:0100570] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). low average genome coverage + GENEPIO:0100571 Low percent genome captured [GENEPIO:0100571] Sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). low % genome captured + GENEPIO:0100572 Read lengths shorter than expected [GENEPIO:0100572] Average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. read lengths shorter than expected + GENEPIO:0100573 Sequence amplification artifacts [GENEPIO:0100573] Sequence data containing errors generated during the PCR amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). sequence amplification artifacts + GENEPIO:0100574 Low signal to noise ratio [GENEPIO:0100574] Sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). low signal to noise ratio + GENEPIO:0100575 Low coverage of characteristic mutations [GENEPIO:0100575] Sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. low coverage of characteristic mutations gene symbol menu GeneSymbolMenu GENEPIO:0100151 E gene (orf4) [GENEPIO:0100151] GENEPIO:0100152 M gene (orf5) [GENEPIO:0100152] diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index bddf02b9..299a4b05 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -1,263 +1,263 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ -WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml -WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 -WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 -WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. -WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection -WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet -WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 -WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 -WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly -WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf -WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information -WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 -WastewaterAMR GENEPIO:0100479 AMR detection information -WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier -WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 -WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) -WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 -WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc -WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 -WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 2 gene_symbol_2 GeneNameMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 3 gene_symbol_3 GeneNameMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) -WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors Authors -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance Additional Comments \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE_SARS-COV-2_WWS EXPORT_NCBI_SRA EXPORT_VirusSeq_Portal +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001122 Database Identifiers +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. ASDFG123 sample_name sample_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100752 specimen collector subsample ID specimen_collector_subsample_id WhitespaceMinimizedString The user-defined identifier assigned to a portion of the original sample. Store the ID for the subsample/aliquot. ASDFG123_12 specimen_processing_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100996 pooled sample ID pooled_sample_id WhitespaceMinimizedString The user-defined identifier assigned to a combined (pooled) set of samples. If the sample being analyzed is the result of pooling individual samples, rename the pooled sample with a new identifier. Store the pooled sample ID. 12345AYZ +WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100753 metagenome-assembled genome (MAG) ID metagenomeassembled_genome_mag_id WhitespaceMinimizedString The user-defined identifier assigned to a genome reconstructed from metagenomic data. Store the MAG ID. XYZ1234.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100918 specimen collector project ID specimen_collector_project_id WhitespaceMinimizedString The user-defined project name assigned to a sequencing project. If the sample was collected or analyzed under the umbrella of a specific project, include the name of that project here. project_name +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001136 BioProject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The INSDC (i.e., ENA, NCBI, or DDBJ) accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 bioproject_accession +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001139 BioSample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} {UPPER_CASE} The identifier assigned to a BioSample in INSDC (i.e., ENA, NCBI, or DDBJ) archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, ENA have the prefix SAMEA, DDBJ have SAMD SAMN14180202, SAMEA00000002, SAMD00000001 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. ERR123456, DRR123456, CRR123456 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100759 Enterobase accession enterobase_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in Enterobase archives. Store the barcode assigned to the submitted sequence. Enterobase barcodes start with different 3 letter codes depending on the organism. SAL_AA0019AA_ST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in GISAID (the Global Initiative on Sharing All Influenza Data) archives. Store the accession assigned to the submitted sequence. GISAID accessions start with EPI. EPI_ISL_402131 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100760 sampling site ID sampling_site_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific location from which samples are taken. Store the ID for the site from which a sample was taken. The "site" is user defined (e.g. it may be a building and its environs, a specific entity within an environment). Please use the same site ID for all samples from a given site, regardless of when these samples were taken. Any important changes in site location, should be represented with a new site ID. Site 12A collection_site_id +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Database identifiers GENEPIO:0100761 sampling event ID sampling_event_id WhitespaceMinimizedString TRUE The user-defined identifier assigned to a specific event during which one or more samples are taken, from one or more sites. Store the ID for the event during which a sample or samples were taken. For example, an event could be one person taking samples from multiple sites, or multiple people taking samples from one site. Event 120522.1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001150 Sample collection and processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100762 sample collection data steward name sample_collection_data_steward_name WhitespaceMinimizedString The name of the individual responsible for the data governance, (meta)data usage and distribution of the sample. Provide the name of the sample collection data steward. Joe Bloggs +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100428 sample collected by laboratory name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada collected_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100432 sample collector contact name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca WaterTester@facility.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001181 geo loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. If known, select a value from the pick list. Canada +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001185 geo loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100280 geo loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001189 geo loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100436 geo loc name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100309 geo loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100310 geo loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100919 watershed shapefile availability watershed_shapefile_availability WatershedShapefileAvailabilityMenu NullValueMenu The availability status of a shapefile descriping the catchment contributing to a watershed. Select a value from the picklist to describe whether or not a watershed shapefile would be available upon request. watershed shapefile available +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100920 watershed shapefile filename watershed_shapefile_filename WhitespaceMinimizedString The name of the watershed shapefile. Provide the shapefile filename corresponding to the watershed from which the sample was taken. If there are multiple files associated with the watershed, provide all names separated by commas. siteAD17.shp, siteAD17.kml +WastewaterSARS-CoV-2 Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism present in the sample. For SARS-CoV-2, use "Severe acute respiratory syndrome coronavirus 2" provided in the picklist. Severe acute respiratory syndrome coronavirus 2 ww_surv_target_1 +WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100766 sample collection time duration value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100767 sample collection time duration unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour ww_sample_duration +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100433 presampling activity presampling_activity PresamplingActivityMenu NullValueMenu TRUE The activities or variables upstream of sample collection that may affect the sample. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Agricultural activity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString NullValueMenu The details of the activities or variables that affected the sample collected. Briefly describe the presampling activities using free text. Agricultural waste from large farm contributes waste to the site sampled. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100768 sample volume measurement value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100769 sample volume measurement unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu NullValueMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. mL collection_volume +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100448 sample storage method sample_storage_method WhitespaceMinimizedString The process used to store the sample. Provide details of how the sample was stored from time of collection until time of processing. If there were issues with the cold chain storage, note those here. The sample was placed in a tube in a cooler bag during transportation (~3 hours) to the lab site. At this point the sample was placed in storage medium and put in a -10C freezer until it was processed and extracted 5 days later. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100449 sample storage medium sample_storage_medium WhitespaceMinimizedString The medium in which a sample is stored. Provide the name of the transport medium or storage medium used for this sample. If none was used, leave blank or write "None". Cary-Blair transport medium +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101014 sample storage duration value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101015 sample storage duration unit sample_storage_duration_unit SampleStorageDurationUnitMenu NullValueMenu The units of a measured sample storage duration. Provide the units from the pick list. Day +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Select processes from the picklist that were applied to this sample. Centrifugation specimen_processing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. specimen_processing_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101029 experimental protocol field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor of the environmental site sampled. Use the picklist provided in the template. If not applicable, choose a null value. Meat processing plant ww_sample_site +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101205 proximal environmental site proximal_environmental_site EnvironmentalSiteMenu TRUE An environmental location in the natural or built environment, that is proximal to a sampling location and which can impact a sample. Provide a descriptor of the environmental site close to the sampling site. Use the picklist provided in the template. If not applicable, choose a null value. Farm +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor of the environmental material sampled. Use the picklist provided in the template. If not applicable, choose a null value. Raw wastewater ww_sample_matrix +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100770 environmental material properties environmental_material_properties EnvironmentalMaterialPropertiesMenu NullValueMenu TRUE TRUE The properties, characteristics and qualities of a substance obtained from the natural or man-made environment. Provide the environmental material properties by selecting descriptors from the pick list. Stagnant +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100771 wastewater system type wastewater_system_type WastewaterSystemTypeMenu NullValueMenu TRUE The type or classification of a wastewater system e.g. sanitary sewer, combined sewer, latrine Provide the classification of the wastewater system by selecting from the provided pick list. Sanitary sewer +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. grab sampler. Provide a descriptor of the device used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic flow-proportional sampler +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample. Provide a descriptor of the collection method used for sampling. Use the picklist provided in the template. If not applicable, choose a null value. Automatic composite sampling ww_sample_type +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 extraction_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100923 endogenous control details endogenous_control_details WhitespaceMinimizedString TRUE The description of the endogenous controls included when extracting a sample. Provide the names of endogenous controls that were used as a reference during extraction. If relevant, include titers of these controls, as well as whether any controls were expected but not identified in the sample. ww_endog_control_1 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100924 extraction recovery efficiency measurement value extraction_recovery_efficiency_measurement_value WhitespaceMinimizedString The recovery efficiency of an extraction, calculated as the amount of a synthetic or endogenous compound identified in the sample relative to the amount expected. Provide value as a percent. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100925 extraction recovery efficiency measurement method extraction_recovery_efficiency_measurement_method WhitespaceMinimizedString The method by which recovery efficiency of an extraction was calculated. Provide a brief description of how extraction recovery efficiency was measured or estimated. +WastewaterPathogenAgnostic GENEPIO:0100453 Strain and isolation information +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100454 microbiological method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]. Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100458 progeny isolate ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isolated by isolated_by WhitespaceMinimizedString The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100773 water catchment area human population measurement value water_catchment_area_human_population_measurement_value integer NullValueMenu TRUE The numerical value of the human population measurement that contributes to the composition of water in a catchment area. Where known, provide the numerical value of population size, i.e. the number of people. 10,500 ww_population +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100774 water catchment area human population range water_catchment_area_human_population_range WaterCatchmentAreaHumanPopulationRangeMenu NullValueMenu The human population range of the water catchment that contributes effluent to a wastewater site. Where catchment population is not well known, provide an estimation of population size by selecting a value from the picklist. 1,000 - 10,000 people +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100775 water catchment area human population measurement method water_catchment_area_human_population_measurement_method WhitespaceMinimizedString The method by which a water catchment 's human population size was measured or estimated Provide a brief description of how catchment population size was measured or estimated. population of jurisdiction encompassing the wastewater service area ww_population_source +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100776 water catchment area human population density value water_catchment_area_human_population_density_value WhitespaceMinimizedString The numerical value describing the number of humans per geographical area in a water catchment. Provide the numerical value of the population density in the catchement area. 4 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100777 water catchment area human population density unit water_catchment_area_human_population_density_unit WaterCatchmentAreaHumanPopulationDensityUnitMenu NullValueMenu The unit describing the number of humans per geographical area in a water catchment. Provide the unit of the population density in the catchement area. persons per Km^2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100778 populated area type populated_area_type PopulatedAreaTypeMenu NullValueMenu A type of area that is populated by humans to different degrees. Provide the populated area type from the pick list. Urban area +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100779 sampling weather conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100780 presampling weather conditions presampling_weather_conditions PresamplingWeatherConditionsMenu NullValueMenu TRUE Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Drizzle +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100911 precipitation measurement value precipitation_measurement_value WhitespaceMinimizedString NullValueMenu TRUE The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100912 precipitation measurement unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu TRUE The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100913 precipitation measurement method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100935 ambient temperature measurement value ambient_temperature_measurement_value WhitespaceMinimizedString The numerical value of a measurement of the ambient temperature. Provide the numerical value of the measured temperature. 70 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100936 ambient temperature measurement unit ambient_temperature_measurement_unit AmbientTemperatureMeasurementUnitMenu NullValueMenu The units of a measurement of the ambient temperature. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0001736 pH measurement value ph_measurement_value WhitespaceMinimizedString The measured pH value indicating the acidity or basicity(alkalinity) of an aqueous solution. Provide the numerical value of the measured pH. 7.4 ww_ph +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100781 pH measurement method ph_measurement_method WhitespaceMinimizedString The process used to measure pH value. Provide the name of the procedure or technology used to measure pH. pH test strip (litmus test) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100905 total daily flow rate measurement value total_daily_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured fluid flow rate over the course of a day. Provide the numerical value of the measured flow rate. 10 ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100906 total daily flow rate measurement unit total_daily_flow_rate_measurement_unit TotalDailyFlowRateMeasurementUnitMenu NullValueMenu The units of a measured fluid flow rate over the course of a day. Provide the units of the measured flow rate by selecting a value from the pick list. million gallons per day (MGD) ww_flow +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100907 total daily flow rate measurement method total_daily_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure total daily fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100908 instantaneous flow rate measurement value instantaneous_flow_rate_measurement_value WhitespaceMinimizedString The numerical value of a measured instantaneous fluid flow rate. Provide the numerical value of the measured flow rate. 25 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100909 instantaneous flow rate measurement unit instantaneous_flow_rate_measurement_unit InstantaneousFlowRateMeasurementUnitMenu NullValueMenu The units of a measured instantaneous fluid flow rate. Provide the units of the measured flow rate by selecting a value from the pick list. cubic meter per hour (m^3/h) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100910 instantaneous flow rate measurement method instantaneous_flow_rate_measurement_method WhitespaceMinimizedString The process used to measure instantaneous fluid flow rate. Provide the name of the procedure or technology used to measure flow rate. Flow meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100783 turbidity measurement value turbidity_measurement_value WhitespaceMinimizedString TRUE The numerical value of a measurement of turbidity. Provide the numerical value of the measured turbidity. 0.02 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100914 turbidity measurement unit turbidity_measurement_unit TurbidityMeasurementUnitMenu NullValueMenu TRUE The units of a measurement of turbidity. Provide the units of the measured turbidity by selecting a value from the pick list. nephelometric turbidity unit (NTU) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0101013 turbidity measurement method turbidity_measurement_method WhitespaceMinimizedString The process used to measure turbidity. Provide the name of the procedure or technology used to measure turbidity. Nephelometric method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0000035 dissolved oxygen measurement value dissolved_oxygen_measurement_value WhitespaceMinimizedString The numerical value of a measurement of dissolved oxygen. Provide the numerical value of the measured dissolved oxygen. 5 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100784 dissolved oxygen measurement unit dissolved_oxygen_measurement_unit DissolvedOxygenMeasurementUnitMenu NullValueMenu The units of a measurement of dissolved oxygen. Provide the units of the measured dissolved oxygen by selecting a value from the pick list. part per million (ppm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100785 dissolved oxygen measurement method dissolved_oxygen_measurement_method WhitespaceMinimizedString The method used to measure dissolved oxygen. Provide the name of the procedure or technology used to measure dissolved oxygen. Dissolved oxygen meter in vertical direction +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements FIX:0000278 oxygen reduction potential (ORP) measurement value oxygen_reduction_potential_orp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of oxygen reduction potential (ORP). Provide the numerical value of the measured oxygen reduction potential. -50 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100786 oxygen reduction potential (ORP) measurement unit oxygen_reduction_potential_orp_measurement_unit OxygenReductionPotentialOrpMeasurementUnitMenu NullValueMenu The units of a measurement of oxygen reduction potential (ORP). Provide the units of the measured oxygen reduction potential by selecting a value from the pick list. milliVolt (mV) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100787 oxygen reduction potential (ORP) measurement method oxygen_reduction_potential_orp_measurement_method WhitespaceMinimizedString The method used to measure oxygen reduction potential (ORP). Provide the name of the procedure or technology used to measure oxygen reduction potential. ORP sensor +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100788 chemical oxygen demand (COD) measurement value chemical_oxygen_demand_cod_measurement_value WhitespaceMinimizedString The measured value from a chemical oxygen demand (COD) test. Provide the numerical value of the COD test result. 26 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100789 chemical oxygen demand (COD) measurement unit chemical_oxygen_demand_cod_measurement_unit ChemicalOxygenDemandCodMeasurementUnitMenu NullValueMenu The units associated with a value from a chemical oxygen demand (COD) test. Provide the units of the COD test result. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100790 chemical oxygen demand (COD) measurement method chemical_oxygen_demand_cod_measurement_method WhitespaceMinimizedString The method used to measure chemical oxygen demand (COD). Provide the name of the procedure or technology used to measure COD. Hach LCK test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100791 carbonaceous biochemical oxygen demand (CBOD) measurement value carbonaceous_biochemical_oxygen_demand_cbod_measurement_value WhitespaceMinimizedString The numerical value of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the numerical value of the measured CBOD. 20 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100792 carbonaceous biochemical oxygen demand (CBOD) measurement unit carbonaceous_biochemical_oxygen_demand_cbod_measurement_unit CarbonaceousBiochemicalOxygenDemandCbodMeasurementUnitMenu NullValueMenu The units of a measurement of carbonaceous biochemical oxygen demand (CBOD). Provide the units of the measured CBOD by selecting a value from the pick list. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100793 carbonaceous biochemical oxygen demand (CBOD) measurement method carbonaceous_biochemical_oxygen_demand_cbod_measurement_method WhitespaceMinimizedString The method used to measure carbonaceous biochemical oxygen demand (CBOD). Provide the name of the procedure or technology used to measure CBOD. CBOD measurement by optical probe +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100794 total suspended solids (TSS) measurement value total_suspended_solids_tss_measurement_value WhitespaceMinimizedString The numerical value from a total suspended solids (TSS) test. Provide the numerical value of the measured TSS. 8 ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100795 total suspended solids (TSS) measurement unit total_suspended_solids_tss_measurement_unit TotalSuspendedSolidsTssMeasurementUnitMenu NullValueMenu The units associated with a value from a total suspended solids (TSS) test. Provide the units of the measured TSS. percent (%) ww_total_suspended_solids +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100796 total suspended solids (TSS) measurement method total_suspended_solids_tss_measurement_method WhitespaceMinimizedString The method used to measure total suspended solids (TSS). Provide the name of the procedure or technology used to measure TSS. Vacuum filter through a 2-micron filter, then oven-dried and weighed sample +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100797 total dissolved solids (TDS) measurement value total_dissolved_solids_tds_measurement_value WhitespaceMinimizedString The numerical value from a total dissolved solids (TDS) test. Provide the numerical value of the measured TDS. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100798 total dissolved solids (TDS) measurement unit total_dissolved_solids_tds_measurement_unit TotalDissolvedSolidsTdsMeasurementUnitMenu NullValueMenu The units associated with a value from a total dissolved solids (TDS) test. Provide the units of the measured TDS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100799 total dissolved solids (TDS) measurement method total_dissolved_solids_tds_measurement_method WhitespaceMinimizedString The method used to measure total dissolved solids (TDS). Provide the name of the procedure or technology used to measure TDS. Subtract calculated TSS from calculated TS +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100800 total solids (TS) measurement value total_solids_ts_measurement_value WhitespaceMinimizedString The numerical value from a total solids (TS) test. Provide the numerical value of the measured TS. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100801 total solids (TS) measurement unit total_solids_ts_measurement_unit TotalSolidsTsMeasurementUnitMenu NullValueMenu The units associated with a value from a total solids (TS) test. Provide the units of the measured TS. percent (%) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100802 total solids (TS) measurement method total_solids_ts_measurement_method WhitespaceMinimizedString The method used to measure total solids (TS). Provide the name of the procedure or technology used to measure TS. Gravimetric method by oven drying, then weighing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100878 alkalinity measurement value alkalinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of alkalinity. Provide the numerical value of the measured alkalinity. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100879 alkalinity measurement unit alkalinity_measurement_unit AlkalinityMeasurementUnitMenu NullValueMenu The units of a measurement of alkalinity. Provide the units of the measured alkalinity. milligram per liter of calcium carbonate (mg/L CaCO3) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100880 alkalinity measurement method alkalinity_measurement_method WhitespaceMinimizedString The process used to measure alkalinity. Provide the name of the procedure or technology used to measure alkalinity. Titration method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100916 conductivity measurement value conductivity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of conductivity. Provide the numerical value of the measured conductivity. 1412 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100803 conductivity measurement unit conductivity_measurement_unit ConductivityMeasurementUnitMenu NullValueMenu The units of a measurement of conductivity. Provide the units of the measured conductivity. microSiemen per centimeter (μS/cm) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100804 conductivity measurement method conductivity_measurement_method WhitespaceMinimizedString The method used to measure conductivity. Provide the name of the procedure or technology used to measure conductivity. Conductivity electrode and meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100805 salinity measurement value salinity_measurement_value WhitespaceMinimizedString The numerical value of a measurement of salinity. Provide the numerical value of the measured salinity. 35 ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100806 salinity measurement unit salinity_measurement_unit SalinityMeasurementUnitMenu NullValueMenu The units of a measurement of salinity. Provide the units of the measured salinity. practical salinity unit (PSU) ww_sample_salinity +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100807 salinity measurement method salinity_measurement_method WhitespaceMinimizedString The method used to measure salinity. Provide the name of the procedure or technology used to measure salinity. conductivity meter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100808 total nitrogen (TN) measurement value total_nitrogen_tn_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total nitrogen (TN). Provide the numerical value of the measured TN. 120 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100809 total nitrogen (TN) measurement unit total_nitrogen_tn_measurement_unit TotalNitrogenTnMeasurementUnitMenu NullValueMenu The units of a measurement of total nitrogen (TN). Provide the units of the measured TN. milligram per liter (mg/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100810 total nitrogen (TN) measurement method total_nitrogen_tn_measurement_method WhitespaceMinimizedString The method used to measure total nitrogen (TN). Provide the name of the procedure or technology used to measure TN. Hach total nitrogen spectrophotometric test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100811 total phosphorus (TP) measurement value total_phosphorus_tp_measurement_value WhitespaceMinimizedString The numerical value of a measurement of total phosphorus (TP). Provide the numerical value of the measured TP. 2 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100812 total phosphorus (TP) measurement unit total_phosphorus_tp_measurement_unit TotalPhosphorpusTpMeasurementUnitMenu NullValueMenu The units of a measurement of total phosphorus (TP). Provide the units of the measured TP. milligrams orthophosphate as phosphorus per liter (mg PO4-P/L) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100813 total phosphorus (TP) measurement method total_phosphorus_tp_measurement_method WhitespaceMinimizedString The method used to measure total phosphorus (TP). Provide the name of the procedure or technology used to measure TP. Merck phosphate spectrophotometric test kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100814 fecal contamination indicator fecal_contamination_indicator FecalContaminationIndicatorMenu NullValueMenu TRUE A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to fecal contamination. If a fecal contamination indicator was measured, select it from the picklist. crAssphage +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100815 fecal contamination value fecal_contamination_value WhitespaceMinimizedString TRUE The numerical value of a measurement of fecal contamination. Provide the numerical value of the measured fecal contamination. 10 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100816 fecal contamination unit fecal_contamination_unit FecalContaminationUnitMenu NullValueMenu TRUE The units of a measurement of fecal contamination. Provide the units of the measured fecal contamination. cycle threshold (Ct) / quantification cycle (Cq) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100817 fecal contamination method fecal_contamination_method WhitespaceMinimizedString The method used to measure fecal contamination. Provide the name of the procedure or technology used to measure fecal contamination. quantitative PCR assay +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100818 fecal coliform count value fecal_coliform_count_value WhitespaceMinimizedString The numerical value of a measurement of fecal coliforms within a sample. Provide the numerical value of the measured fecal coliforms. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100819 fecal coliform count unit fecal_coliform_count_unit FecalColiformCountUnitMenu NullValueMenu The units of a measurement of fecal coliforms. Provide the units of the measured fecal coliforms. most probable number per milliliter (MPN/mL) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100820 fecal coliform count method fecal_coliform_count_method WhitespaceMinimizedString The method used to measure fecal coliforms. Provide the name of the procedure or technology used to measure fecal coliforms. MPN method via serial dilutions until lack of growth +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100837 urinary contamination indicator urinary_contamination_indicator UrinaryContaminationIndicatorMenu NullValueMenu A gene, virus, bacteria, or substance used to measure the sanitary quality of water in regards to urinary contamination. If a urinary contamination indicator was measured, select it from the picklist. urobilin +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100838 urinary contamination value urinary_contamination_value WhitespaceMinimizedString The numerical value of a measurement of urinary contamination. Provide the numerical value of the measured urinary contamination. 3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100839 urinary contamination unit urinary_contamination_unit UrinaryContaminationUnitMenu NullValueMenu The units of a measurement of urinary contamination. Provide the units of the measured urinary contamination. nanograms per liter +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100840 urinary contamination method urinary_contamination_method WhitespaceMinimizedString The method used to measure urinary contamination. Provide the name of the procedure or technology used to measure urinary contamination. Urobilin Concentration Test +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100821 sample temperature value (at collection) sample_temperature_value_at_collection WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample at collection. Provide the numerical value of the measured temperature. 20 ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100822 sample temperature unit (at collection) sample_temperature_unit_at_collection SampleTemperatureUnitAtCollectionMenu NullValueMenu The units of a measurement of temperature of a sample at the time of collection. Provide the units of the measured temperature. degree Celsius (C) ww_temperature +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100823 sample temperature value (when received) sample_temperature_value_when_received WhitespaceMinimizedString The numerical value of a measurement of temperature of a sample upon receipt. Provide the numerical value of the measured temperature. 22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Environmental conditions and measurements GENEPIO:0100824 sample temperature unit (when received) sample_temperature_unit_when_received SampleTemperatureUnitWhenReceivedMenu NullValueMenu The units of a measurement of temperature of a sample at the time upon receipt. Provide the units of the measured temperature. degree Celsius (C) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001441 Sequence Information +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance purpose_of_ww_sequencing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu NullValueMenu TRUE The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay library_strategy +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT library_preparation_kit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString TRUE The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method library_selection +WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme AmpliconPcrPrimerSchemeMenu NullValueMenu TRUE The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 amplicon_PCR_primer_scheme +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Sequence information GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 amplicon_size +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001457 Bioinformatics and QC metrics +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools quality_control_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 quality_control_method_version +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control quality_control_determination +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage quality_control_issues +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. quality_control_details +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version or a link to the github protocol e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 raw_sequence_data_processing_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper dehosting_method +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString NullValueMenu The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString NullValueMenu The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 +WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +WastewaterSARS-CoV-2 Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 assembly +WastewaterSARS-CoV-2;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf +WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0101082 Taxonomic identification information +WastewaterAMR Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterAMR Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +WastewaterAMR GENEPIO:0100479 AMR detection information +WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier +WastewaterAMR AMR detection information GENEPIO:0101077 AMR analysis software version amr_analysis_software_version WhitespaceMinimizedString TRUE The version number of the software used to perform an in silico antimicrobial resistance determinant idenrtification/analysis. Provide the version number of the software used for AMR analysis. 6.0.3 +WastewaterAMR AMR detection information GENEPIO:0101078 AMR reference database name amr_reference_database_name WhitespaceMinimizedString TRUE Thr name of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the reference database used for AMR analysis. Comprehensive Antibiotic Resistance Database (CARD) +WastewaterAMR AMR detection information GENEPIO:0101079 AMR reference database version amr_reference_database_version WhitespaceMinimizedString TRUE The version number of the reference database used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the version number of the reference database used for AMR analysis. 3.2.9 +WastewaterAMR AMR detection information GENEPIO:0101080 AMR analysis report filename amr_analysis_report_filename WhitespaceMinimizedString TRUE The filename of the report containing the results of an in silico antimicrobial resistance analysis. Provide the filename of the report containing the results of the AMR analysis. WWAMR_report_Feb1_2024.doc +WastewaterSARS-CoV-2 GENEPIO:0001498 Lineage/clade information +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001500 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. Multiple lineages/clades can be provided, separated by a semicolon. B.1.1.7 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Freyja +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 1.5.0 +WastewaterSARS-CoV-2 Lineage/clade information GENEPIO:0101081 lineage/clade analysis report filename lineage_clade_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a lineage/clade analysis. Provide the filename of the report containing the results of the lineage/clade analysis. aggregated-WWSC2-ABC-b_1234.tsv +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001506 Pathogen diagnostic testing +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102040 assay target details assay_target_details WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100962 diagnostic target presence 1 diagnostic_target_presence_1 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_1_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100963 diagnostic measurement value 1 diagnostic_measurement_value_1 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_1_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100964 diagnostic measurement unit 1 diagnostic_measurement_unit_1 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_1_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing GENEPIO:0100965 diagnostic measurement method 1 diagnostic_measurement_method_1 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR ww_surv_target_1_protocol +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 2 assay_target_name_2 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 2 gene_symbol_2 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) ww_surv_target_2_gene +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 2 gene_symbol_2 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A ww_surv_target_2_gene +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 2 diagnostic_target_presence_2 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present ww_surv_target_2_known_present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 2 diagnostic_measurement_value_2 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 ww_surv_target_2_conc +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 2 diagnostic_measurement_unit_2 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) ww_surv_target_2_conc_unit +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 2 diagnostic_measurement_method_2 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target name 3 assay_target_name_3 WhitespaceMinimizedString The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic RT-PCR test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +WastewaterSARS-CoV-2 Pathogen diagnostic testing gene symbol 3 gene_symbol_3 GeneSymbolMenu NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Select a gene name value from the pick list provided. E gene (orf4) +WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing gene symbol 3 gene_symbol_3 WhitespaceMinimizedString NullValueMenu The symbol of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic target presence 3 diagnostic_target_presence_3 DiagnosticTargetPresenceMenu NullValueMenu The binary value of the result from a diagnostic test. Select a value from the pick list provided, to describe whether a target was determined to be present or absent within a sample. diagnostic target present +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement value 3 diagnostic_measurement_value_3 WhitespaceMinimizedString The value of the result from a diagnostic test. Provide the numerical result of a diagnostic test (no need to include units). 1000 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement unit 3 diagnostic_measurement_unit_3 DiagnosticMeasurementUnitMenu NullValueMenu The unit of the result from a diagnostic test. Select a value from the pick list provided, to describe the units of the given diagnostic test. cycle threshold (Ct) +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Pathogen diagnostic testing diagnostic measurement method 3 diagnostic_measurement_method_3 DiagnosticMeasurementMethodMenu NullValueMenu The method by which a diagnostic result was determined. Select a value from the pick list provided to describe the method used for a given diagnostic test. qPCR +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic GENEPIO:0001516 Contributor acknowledgement +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001517 authors authors TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a semicolon. Tejinder Singh; Fei Hu; Joe Blogs Authors +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance \ No newline at end of file From 162c7996e0df2799aa858380b273329c1ce14052 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Tue, 22 Oct 2024 14:59:32 -0700 Subject: [PATCH 64/96] GRDI update --- web/templates/grdi/schema.json | 156 +- web/templates/grdi/schema.yaml | 120 +- web/templates/grdi/schema_enums.tsv | 3167 ++++++++++++++------------- web/templates/grdi/schema_slots.tsv | 1609 +++++++------- 4 files changed, 2525 insertions(+), 2527 deletions(-) diff --git a/web/templates/grdi/schema.json b/web/templates/grdi/schema.json index caa37dda..2f04fbbc 100644 --- a/web/templates/grdi/schema.json +++ b/web/templates/grdi/schema.json @@ -2,7 +2,7 @@ "name": "GRDI", "description": "", "id": "https://example.com/GRDI", - "version": "12.2.2", + "version": "13.3.3", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -298,7 +298,6 @@ "enums": { "NullValueMenu": { "name": "NullValueMenu", - "description": "", "title": "null value menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -311,7 +310,7 @@ "Missing [GENEPIO:0001618]": { "text": "Missing [GENEPIO:0001618]", "exact_mappings": [ - "NCBI_ANTIBIOGRAM:missing" + "NCBI_ANTIBIOGRAM:Missing" ] }, "Not Collected [GENEPIO:0001620]": { @@ -336,7 +335,6 @@ }, "SampleCollectedByMenu": { "name": "SampleCollectedByMenu", - "description": "", "title": "sample_collected_by menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -365,7 +363,6 @@ }, "PurposeOfSamplingMenu": { "name": "PurposeOfSamplingMenu", - "description": "", "title": "purpose_of_sampling menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -400,7 +397,6 @@ }, "PresamplingActivityMenu": { "name": "PresamplingActivityMenu", - "description": "", "title": "presampling_activity menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -483,7 +479,6 @@ }, "ExperimentalSpecimenRoleTypeMenu": { "name": "ExperimentalSpecimenRoleTypeMenu", - "description": "", "title": "experimental_specimen_role_type menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -503,7 +498,6 @@ }, "SpecimenProcessingMenu": { "name": "SpecimenProcessingMenu", - "description": "", "title": "specimen_processing menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -523,7 +517,6 @@ }, "GeoLocNameCountryMenu": { "name": "GeoLocNameCountryMenu", - "description": "", "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1344,7 +1337,6 @@ }, "GeoLocNameStateProvinceRegionMenu": { "name": "GeoLocNameStateProvinceRegionMenu", - "description": "", "title": "geo_loc_name (state/province/region) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1419,7 +1411,6 @@ }, "SampleCollectionDatePrecisionMenu": { "name": "SampleCollectionDatePrecisionMenu", - "description": "", "title": "sample_collection_date_precision menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1436,7 +1427,6 @@ }, "EnvironmentalSiteMenu": { "name": "EnvironmentalSiteMenu", - "description": "", "title": "environmental_site menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1703,7 +1693,6 @@ }, "WaterDepthUnitsMenu": { "name": "WaterDepthUnitsMenu", - "description": "", "title": "water_depth_units menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1726,7 +1715,6 @@ }, "SedimentDepthUnitsMenu": { "name": "SedimentDepthUnitsMenu", - "description": "", "title": "sediment_depth_units menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1749,7 +1737,6 @@ }, "AirTemperatureUnitsMenu": { "name": "AirTemperatureUnitsMenu", - "description": "", "title": "air_temperature_units menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1763,7 +1750,6 @@ }, "WaterTemperatureUnitsMenu": { "name": "WaterTemperatureUnitsMenu", - "description": "", "title": "water_temperature_units menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1777,7 +1763,6 @@ }, "PrecipitationMeasurementUnitMenu": { "name": "PrecipitationMeasurementUnitMenu", - "description": "", "title": "precipitation_measurement_unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1800,7 +1785,6 @@ }, "AvailableDataTypesMenu": { "name": "AvailableDataTypesMenu", - "description": "", "title": "available_data_types menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -1997,7 +1981,6 @@ }, "SamplingWeatherConditionsMenu": { "name": "SamplingWeatherConditionsMenu", - "description": "", "title": "sampling_weather_conditions menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2030,7 +2013,6 @@ }, "AnimalOrPlantPopulationMenu": { "name": "AnimalOrPlantPopulationMenu", - "description": "", "title": "animal_or_plant_population menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2102,7 +2084,6 @@ }, "EnvironmentalMaterialMenu": { "name": "EnvironmentalMaterialMenu", - "description": "", "title": "environmental_material menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2330,7 +2311,6 @@ }, "AnatomicalMaterialMenu": { "name": "AnatomicalMaterialMenu", - "description": "", "title": "anatomical_material menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2359,7 +2339,6 @@ }, "BodyProductMenu": { "name": "BodyProductMenu", - "description": "", "title": "body_product menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2411,7 +2390,6 @@ }, "AnatomicalPartMenu": { "name": "AnatomicalPartMenu", - "description": "", "title": "anatomical_part menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2744,7 +2722,6 @@ }, "AnatomicalRegionMenu": { "name": "AnatomicalRegionMenu", - "description": "", "title": "anatomical_region menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -2761,7 +2738,6 @@ }, "FoodProductMenu": { "name": "FoodProductMenu", - "description": "", "title": "food_product menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3673,7 +3649,6 @@ }, "FoodProductPropertiesMenu": { "name": "FoodProductPropertiesMenu", - "description": "", "title": "food_product_properties menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3754,7 +3729,6 @@ }, "LabelClaimMenu": { "name": "LabelClaimMenu", - "description": "", "title": "label_claim menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3780,7 +3754,6 @@ }, "AnimalSourceOfFoodMenu": { "name": "AnimalSourceOfFoodMenu", - "description": "", "title": "animal_source_of_food menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3830,7 +3803,6 @@ }, "FoodProductProductionStreamMenu": { "name": "FoodProductProductionStreamMenu", - "description": "", "title": "food_product_production_stream menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3863,7 +3835,6 @@ }, "CollectionDeviceMenu": { "name": "CollectionDeviceMenu", - "description": "", "title": "collection_device menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -3943,7 +3914,6 @@ }, "CollectionMethodMenu": { "name": "CollectionMethodMenu", - "description": "", "title": "collection_method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4003,7 +3973,6 @@ }, "SampleVolumeMeasurementUnitMenu": { "name": "SampleVolumeMeasurementUnitMenu", - "description": "", "title": "sample_volume_measurement_unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4020,7 +3989,6 @@ }, "ResidualSampleStatusMenu": { "name": "ResidualSampleStatusMenu", - "description": "", "title": "residual_sample_status menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4037,7 +4005,6 @@ }, "SampleStorageDurationUnitMenu": { "name": "SampleStorageDurationUnitMenu", - "description": "", "title": "sample_storage_duration_unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4066,7 +4033,6 @@ }, "NucelicAcidStorageDurationUnitMenu": { "name": "NucelicAcidStorageDurationUnitMenu", - "description": "", "title": "nucelic_acid_storage_duration_unit menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4095,7 +4061,6 @@ }, "FoodPackagingMenu": { "name": "FoodPackagingMenu", - "description": "", "title": "food_packaging menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4137,7 +4102,6 @@ }, "HostCommonNameMenu": { "name": "HostCommonNameMenu", - "description": "", "title": "host (common name) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4269,7 +4233,6 @@ }, "HostScientificNameMenu": { "name": "HostScientificNameMenu", - "description": "", "title": "host (scientific name) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4340,7 +4303,6 @@ }, "HostFoodProductionNameMenu": { "name": "HostFoodProductionNameMenu", - "description": "", "title": "host (food production name) menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4541,7 +4503,6 @@ }, "HostAgeBinMenu": { "name": "HostAgeBinMenu", - "description": "", "title": "host_age_bin menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4567,7 +4528,6 @@ }, "IsolatedByMenu": { "name": "IsolatedByMenu", - "description": "", "title": "isolated_by menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -4593,7 +4553,6 @@ }, "OrganismMenu": { "name": "OrganismMenu", - "description": "", "title": "organism menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5070,7 +5029,6 @@ }, "TaxonomicIdentificationProcessMenu": { "name": "TaxonomicIdentificationProcessMenu", - "description": "", "title": "taxonomic_identification_process menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5093,7 +5051,6 @@ }, "SequencedByMenu": { "name": "SequencedByMenu", - "description": "", "title": "sequenced_by menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5122,7 +5079,6 @@ }, "PurposeOfSequencingMenu": { "name": "PurposeOfSequencingMenu", - "description": "", "title": "purpose_of_sequencing menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5161,7 +5117,6 @@ }, "SequencingPlatformMenu": { "name": "SequencingPlatformMenu", - "description": "", "title": "sequencing_platform menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5187,7 +5142,6 @@ }, "SequencingInstrumentMenu": { "name": "SequencingInstrumentMenu", - "description": "A DNA sequencer manufactured by the Illumina corporation.", "title": "sequencing_instrument menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5429,7 +5383,6 @@ }, "SequencingAssayTypeMenu": { "name": "SequencingAssayTypeMenu", - "description": "", "title": "sequencing_assay_type menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5454,7 +5407,6 @@ }, "GenomicTargetEnrichmentMethodMenu": { "name": "GenomicTargetEnrichmentMethodMenu", - "description": "", "title": "genomic_target_enrichment_method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5468,7 +5420,6 @@ }, "SequenceSubmittedByMenu": { "name": "SequenceSubmittedByMenu", - "description": "", "title": "sequence_submitted_by menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5497,7 +5448,6 @@ }, "QualityControlDeterminationMenu": { "name": "QualityControlDeterminationMenu", - "description": "", "title": "quality_control_determination menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5523,7 +5473,6 @@ }, "QualityControlIssuesMenu": { "name": "QualityControlIssuesMenu", - "description": "", "title": "quality _control_issues menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5555,7 +5504,6 @@ }, "AttributePackageMenu": { "name": "AttributePackageMenu", - "description": "", "title": "attribute_package menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5569,7 +5517,6 @@ }, "ExperimentalInterventionMenu": { "name": "ExperimentalInterventionMenu", - "description": "", "title": "experimental_intervention menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5613,7 +5560,6 @@ }, "AmrTestingByMenu": { "name": "AmrTestingByMenu", - "description": "", "title": "AMR_testing_by menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5639,7 +5585,6 @@ }, "AntimicrobialPhenotypeMenu": { "name": "AntimicrobialPhenotypeMenu", - "description": "", "title": "antimicrobial_phenotype menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5691,7 +5636,6 @@ }, "AntimicrobialMeasurementUnitsMenu": { "name": "AntimicrobialMeasurementUnitsMenu", - "description": "", "title": "antimicrobial_measurement_units menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5714,7 +5658,6 @@ }, "AntimicrobialMeasurementSignMenu": { "name": "AntimicrobialMeasurementSignMenu", - "description": "", "title": "antimicrobial_measurement_sign menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5752,7 +5695,6 @@ }, "AntimicrobialLaboratoryTypingMethodMenu": { "name": "AntimicrobialLaboratoryTypingMethodMenu", - "description": "", "title": "antimicrobial_laboratory_typing_method menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5782,7 +5724,6 @@ }, "AntimicrobialLaboratoryTypingPlatformMenu": { "name": "AntimicrobialLaboratoryTypingPlatformMenu", - "description": "", "title": "antimicrobial_laboratory_typing_platform menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5820,7 +5761,6 @@ }, "AntimicrobialVendorNameMenu": { "name": "AntimicrobialVendorNameMenu", - "description": "", "title": "antimicrobial_vendor_name menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5858,7 +5798,6 @@ }, "AntimicrobialTestingStandardMenu": { "name": "AntimicrobialTestingStandardMenu", - "description": "", "title": "antimicrobial_testing_standard menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -5920,7 +5859,6 @@ }, "AntimicrobialResistanceTestDrugMenu": { "name": "AntimicrobialResistanceTestDrugMenu", - "description": "", "title": "Antimicrobial Resistance Test Drug Menu", "from_schema": "https://example.com/GRDI", "permissible_values": { @@ -6224,7 +6162,7 @@ "description": "An alternative sample_ID assigned to the sample by another organization.", "title": "alternative_sample_ID", "comments": [ - "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." + "\"Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.\"" ], "examples": [ { @@ -8029,6 +7967,11 @@ "comments": [ "Provide the weather conditions at the time of sample collection." ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100779", "domain_of": [ @@ -8046,7 +7989,16 @@ }, "presampling_weather_conditions": { "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", "title": "presampling_weather_conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100780", "domain_of": [ @@ -8063,7 +8015,16 @@ }, "precipitation_measurement_value": { "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", "title": "precipitation_measurement_value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100911", "domain_of": [ @@ -8080,7 +8041,16 @@ }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", "title": "precipitation_measurement_unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100912", "domain_of": [ @@ -8097,7 +8067,16 @@ }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", "title": "precipitation_measurement_method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample collection" + } + ], "from_schema": "https://example.com/GRDI", "slot_uri": "GENEPIO:0100913", "domain_of": [ @@ -8371,7 +8350,7 @@ "description": "An alternative isolate_ID assigned to the isolate by another organization.", "title": "alternative_isolate_ID", "comments": [ - "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons." + "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple alternative isolate IDs can be provided, separated by semi-colons." ], "examples": [ { @@ -28879,7 +28858,7 @@ "description": "An alternative sample_ID assigned to the sample by another organization.", "title": "alternative_sample_ID", "comments": [ - "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." + "\"Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.\"" ], "examples": [ { @@ -30972,6 +30951,11 @@ "comments": [ "Provide the weather conditions at the time of sample collection." ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 74, "slot_uri": "GENEPIO:0100779", @@ -30993,7 +30977,16 @@ }, "presampling_weather_conditions": { "name": "presampling_weather_conditions", + "description": "Weather conditions prior to collection that may affect the sample.", "title": "presampling_weather_conditions", + "comments": [ + "Provide the weather conditions prior to sample collection." + ], + "examples": [ + { + "value": "Rain [ENVO:01001564]" + } + ], "from_schema": "https://example.com/GRDI", "rank": 75, "slot_uri": "GENEPIO:0100780", @@ -31014,7 +31007,16 @@ }, "precipitation_measurement_value": { "name": "precipitation_measurement_value", + "description": "The amount of water which has fallen during a precipitation process.", "title": "precipitation_measurement_value", + "comments": [ + "Provide the quantity of precipitation in the area leading up to the time of sample collection." + ], + "examples": [ + { + "value": "12" + } + ], "from_schema": "https://example.com/GRDI", "rank": 76, "slot_uri": "GENEPIO:0100911", @@ -31035,7 +31037,16 @@ }, "precipitation_measurement_unit": { "name": "precipitation_measurement_unit", + "description": "The units of measurement for the amount of water which has fallen during a precipitation process.", "title": "precipitation_measurement_unit", + "comments": [ + "Provide the units of precipitation by selecting a value from the pick list." + ], + "examples": [ + { + "value": "inch" + } + ], "from_schema": "https://example.com/GRDI", "rank": 77, "slot_uri": "GENEPIO:0100912", @@ -31056,7 +31067,16 @@ }, "precipitation_measurement_method": { "name": "precipitation_measurement_method", + "description": "The process used to measure the amount of water which has fallen during a precipitation process.", "title": "precipitation_measurement_method", + "comments": [ + "Provide the name of the procedure or method used to measure precipitation." + ], + "examples": [ + { + "value": "Rain gauge over a 12 hour period prior to sample collection" + } + ], "from_schema": "https://example.com/GRDI", "rank": 78, "slot_uri": "GENEPIO:0100913", @@ -31374,7 +31394,7 @@ "description": "An alternative isolate_ID assigned to the isolate by another organization.", "title": "alternative_isolate_ID", "comments": [ - "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons." + "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following:\nPublic Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple alternative isolate IDs can be provided, separated by semi-colons." ], "examples": [ { diff --git a/web/templates/grdi/schema.yaml b/web/templates/grdi/schema.yaml index 96fd8cf0..902d809c 100644 --- a/web/templates/grdi/schema.yaml +++ b/web/templates/grdi/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/GRDI name: GRDI description: '' -version: 12.2.2 +version: 13.3.3 imports: - linkml:types prefixes: @@ -3183,17 +3183,17 @@ slots: name: alternative_sample_id title: alternative_sample_ID description: An alternative sample_ID assigned to the sample by another organization. - comments: "Alternative identifiers assigned to the sample should be tracked along\ - \ with original IDs to establish chain of custody. Alternative sample IDs should\ - \ be provided in the in a prescribed format which consists of the ID followed\ - \ by square brackets (no space in between the ID and bracket) containing the\ - \ short form of ID provider\u2019s agency name i.e. ID[short organization code].\ - \ Agency short forms include the following: Public Health Agency of Canada:\ - \ PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada:\ - \ AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada:\ - \ ECCC Health Canada: HC Multiple identifiers can be provided and separated\ - \ by semi-colons. If the information is unknown or cannot be provided, leave\ - \ blank or provide a null value." + comments: "\"Alternative identifiers assigned to the sample should be tracked\ + \ along with original IDs to establish chain of custody. Alternative sample\ + \ IDs should be provided in the in a prescribed format which consists of the\ + \ ID followed by square brackets (no space in between the ID and bracket) containing\ + \ the short form of ID provider\u2019s agency name i.e. ID[short organization\ + \ code]. Agency short forms include the following:\nPublic Health Agency of\ + \ Canada: PHAC\nCanadian Food Inspection Agency: CFIA\nAgriculture and Agri-Food\ + \ Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment and Climate Change\ + \ Canada: ECCC\nHealth Canada: HC \nMultiple identifiers can be provided and\ + \ separated by semi-colons. If the information is unknown or cannot be provided,\ + \ leave blank or provide a null value.\"" slot_uri: GENEPIO:0100427 range: WhitespaceMinimizedString required: true @@ -4191,32 +4191,54 @@ slots: - range: SamplingWeatherConditionsMenu - range: NullValueMenu multivalued: true + examples: + - value: Rain [ENVO:01001564] presampling_weather_conditions: name: presampling_weather_conditions title: presampling_weather_conditions + description: Weather conditions prior to collection that may affect the sample. + comments: Provide the weather conditions prior to sample collection. slot_uri: GENEPIO:0100780 any_of: - range: SamplingWeatherConditionsMenu - range: NullValueMenu + examples: + - value: Rain [ENVO:01001564] precipitation_measurement_value: name: precipitation_measurement_value title: precipitation_measurement_value + description: The amount of water which has fallen during a precipitation process. + comments: Provide the quantity of precipitation in the area leading up to the + time of sample collection. slot_uri: GENEPIO:0100911 any_of: - range: Whitespaceminimizedstring - range: NullValueMenu + examples: + - value: '12' precipitation_measurement_unit: name: precipitation_measurement_unit title: precipitation_measurement_unit + description: The units of measurement for the amount of water which has fallen + during a precipitation process. + comments: Provide the units of precipitation by selecting a value from the pick + list. slot_uri: GENEPIO:0100912 any_of: - range: PrecipitationMeasurementUnitMenu - range: NullValueMenu + examples: + - value: inch precipitation_measurement_method: name: precipitation_measurement_method title: precipitation_measurement_method + description: The process used to measure the amount of water which has fallen + during a precipitation process. + comments: Provide the name of the procedure or method used to measure precipitation. slot_uri: GENEPIO:0100913 range: WhitespaceMinimizedString + examples: + - value: Rain gauge over a 12 hour period prior to sample collection host_common_name: name: host_common_name title: host (common name) @@ -4372,11 +4394,11 @@ slots: comments: "Alternative isolate IDs should be provided in the in a prescribed format\ \ which consists of the ID followed by square brackets (no space in between\ \ the ID and bracket) containing the short form of ID provider\u2019s agency\ - \ name i.e. ID[short organization code]. Agency short forms include the following:\ - \ Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA\ - \ Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment\ - \ and Climate Change Canada: ECCC Health Canada: HC An example of a properly\ - \ formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple\ + \ name i.e. ID[short organization code]. Agency short forms include the following:\n\ + Public Health Agency of Canada: PHAC\nCanadian Food Inspection Agency: CFIA\n\ + Agriculture and Agri-Food Canada: AAFC\nFisheries and Oceans Canada: DFO\nEnvironment\ + \ and Climate Change Canada: ECCC\nHealth Canada: HC \nAn example of a properly\ + \ formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA]\nMultiple\ \ alternative isolate IDs can be provided, separated by semi-colons." slot_uri: GENEPIO:0100457 range: WhitespaceMinimizedString @@ -12696,7 +12718,6 @@ enums: NullValueMenu: name: NullValueMenu title: null value menu - description: '' permissible_values: Not Applicable [GENEPIO:0001619]: text: Not Applicable [GENEPIO:0001619] @@ -12705,7 +12726,7 @@ enums: Missing [GENEPIO:0001618]: text: Missing [GENEPIO:0001618] exact_mappings: - - NCBI_ANTIBIOGRAM:missing + - NCBI_ANTIBIOGRAM:Missing Not Collected [GENEPIO:0001620]: text: Not Collected [GENEPIO:0001620] exact_mappings: @@ -12721,7 +12742,6 @@ enums: SampleCollectedByMenu: name: SampleCollectedByMenu title: sample_collected_by menu - description: '' permissible_values: Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -12740,7 +12760,6 @@ enums: PurposeOfSamplingMenu: name: PurposeOfSamplingMenu title: purpose_of_sampling menu - description: '' permissible_values: Cluster/Outbreak investigation [GENEPIO:0100001]: text: Cluster/Outbreak investigation [GENEPIO:0100001] @@ -12764,7 +12783,6 @@ enums: PresamplingActivityMenu: name: PresamplingActivityMenu title: presampling_activity menu - description: '' permissible_values: Addition of substances to food/water [GENEPIO:0100536]: text: Addition of substances to food/water [GENEPIO:0100536] @@ -12828,7 +12846,6 @@ enums: ExperimentalSpecimenRoleTypeMenu: name: ExperimentalSpecimenRoleTypeMenu title: experimental_specimen_role_type menu - description: '' permissible_values: Positive experimental control [GENEPIO:0101018]: text: Positive experimental control [GENEPIO:0101018] @@ -12841,7 +12858,6 @@ enums: SpecimenProcessingMenu: name: SpecimenProcessingMenu title: specimen_processing menu - description: '' permissible_values: Biological replicate process [GENEPIO:0101022]: text: Biological replicate process [GENEPIO:0101022] @@ -12854,7 +12870,6 @@ enums: GeoLocNameCountryMenu: name: GeoLocNameCountryMenu title: geo_loc_name (country) menu - description: '' permissible_values: Afghanistan [GAZ:00006882]: text: Afghanistan [GAZ:00006882] @@ -13401,7 +13416,6 @@ enums: GeoLocNameStateProvinceRegionMenu: name: GeoLocNameStateProvinceRegionMenu title: geo_loc_name (state/province/region) menu - description: '' permissible_values: Atlantic region (Canada) [wikidata:Q246972]: text: Atlantic region (Canada) [wikidata:Q246972] @@ -13455,7 +13469,6 @@ enums: SampleCollectionDatePrecisionMenu: name: SampleCollectionDatePrecisionMenu title: sample_collection_date_precision menu - description: '' permissible_values: year [UO:0000036]: text: year [UO:0000036] @@ -13466,7 +13479,6 @@ enums: EnvironmentalSiteMenu: name: EnvironmentalSiteMenu title: environmental_site menu - description: '' permissible_values: Abattoir [ENVO:01000925]: text: Abattoir [ENVO:01000925] @@ -13658,7 +13670,6 @@ enums: WaterDepthUnitsMenu: name: WaterDepthUnitsMenu title: water_depth_units menu - description: '' permissible_values: centimeter (cm) [UO:0000015]: text: centimeter (cm) [UO:0000015] @@ -13673,7 +13684,6 @@ enums: SedimentDepthUnitsMenu: name: SedimentDepthUnitsMenu title: sediment_depth_units menu - description: '' permissible_values: centimeter (cm) [UO:0000015]: text: centimeter (cm) [UO:0000015] @@ -13688,7 +13698,6 @@ enums: AirTemperatureUnitsMenu: name: AirTemperatureUnitsMenu title: air_temperature_units menu - description: '' permissible_values: degree Fahrenheit (F) [UO:0000195]: text: degree Fahrenheit (F) [UO:0000195] @@ -13697,7 +13706,6 @@ enums: WaterTemperatureUnitsMenu: name: WaterTemperatureUnitsMenu title: water_temperature_units menu - description: '' permissible_values: degree Fahrenheit (F) [UO:0000195]: text: degree Fahrenheit (F) [UO:0000195] @@ -13706,7 +13714,6 @@ enums: PrecipitationMeasurementUnitMenu: name: PrecipitationMeasurementUnitMenu title: precipitation_measurement_unit menu - description: '' permissible_values: millimeter (mm) [UO:0000016]: text: millimeter (mm) [UO:0000016] @@ -13721,7 +13728,6 @@ enums: AvailableDataTypesMenu: name: AvailableDataTypesMenu title: available_data_types menu - description: '' permissible_values: Documentation [GENEPIO:0100702]: text: Documentation [GENEPIO:0100702] @@ -13866,7 +13872,6 @@ enums: SamplingWeatherConditionsMenu: name: SamplingWeatherConditionsMenu title: sampling_weather_conditions menu - description: '' permissible_values: Cloudy/Overcast [ENVO:03501418]: text: Cloudy/Overcast [ENVO:03501418] @@ -13888,7 +13893,6 @@ enums: AnimalOrPlantPopulationMenu: name: AnimalOrPlantPopulationMenu title: animal_or_plant_population menu - description: '' permissible_values: Algae [FOODON:03411301]: text: Algae [FOODON:03411301] @@ -13938,7 +13942,6 @@ enums: EnvironmentalMaterialMenu: name: EnvironmentalMaterialMenu title: environmental_material menu - description: '' permissible_values: Air [ENVO:00002005]: text: Air [ENVO:00002005] @@ -14100,7 +14103,6 @@ enums: AnatomicalMaterialMenu: name: AnatomicalMaterialMenu title: anatomical_material menu - description: '' permissible_values: Blood [UBERON:0000178]: text: Blood [UBERON:0000178] @@ -14120,7 +14122,6 @@ enums: BodyProductMenu: name: BodyProductMenu title: body_product menu - description: '' permissible_values: Digestive tract substance [GENEPIO:0100898]: text: Digestive tract substance [GENEPIO:0100898] @@ -14157,7 +14158,6 @@ enums: AnatomicalPartMenu: name: AnatomicalPartMenu title: anatomical_part menu - description: '' permissible_values: Carcass [UBERON:0008979]: text: Carcass [UBERON:0008979] @@ -14402,7 +14402,6 @@ enums: AnatomicalRegionMenu: name: AnatomicalRegionMenu title: anatomical_region menu - description: '' permissible_values: Dorso-lateral region [BSPO:0000080]: text: Dorso-lateral region [BSPO:0000080] @@ -14413,7 +14412,6 @@ enums: FoodProductMenu: name: FoodProductMenu title: food_product menu - description: '' permissible_values: Animal feed [ENVO:02000047]: text: Animal feed [ENVO:02000047] @@ -15092,7 +15090,6 @@ enums: FoodProductPropertiesMenu: name: FoodProductPropertiesMenu title: food_product_properties menu - description: '' permissible_values: Food (canned) [FOODON:00002418]: text: Food (canned) [FOODON:00002418] @@ -15148,7 +15145,6 @@ enums: LabelClaimMenu: name: LabelClaimMenu title: label_claim menu - description: '' permissible_values: Antibiotic free [FOODON:03601063]: text: Antibiotic free [FOODON:03601063] @@ -15165,7 +15161,6 @@ enums: AnimalSourceOfFoodMenu: name: AnimalSourceOfFoodMenu title: animal_source_of_food menu - description: '' permissible_values: Cow [NCBITaxon:9913]: text: Cow [NCBITaxon:9913] @@ -15200,7 +15195,6 @@ enums: FoodProductProductionStreamMenu: name: FoodProductProductionStreamMenu title: food_product_production_stream menu - description: '' permissible_values: Beef cattle production stream [FOODON:03000452]: text: Beef cattle production stream [FOODON:03000452] @@ -15222,7 +15216,6 @@ enums: CollectionDeviceMenu: name: CollectionDeviceMenu title: collection_device menu - description: '' permissible_values: Auger (earth auger) [AGRO:00000405]: text: Auger (earth auger) [AGRO:00000405] @@ -15278,7 +15271,6 @@ enums: CollectionMethodMenu: name: CollectionMethodMenu title: collection_method menu - description: '' permissible_values: Aspiration [HP:0002835]: text: Aspiration [HP:0002835] @@ -15319,7 +15311,6 @@ enums: SampleVolumeMeasurementUnitMenu: name: SampleVolumeMeasurementUnitMenu title: sample_volume_measurement_unit menu - description: '' permissible_values: microliter (uL) [UO:0000101]: text: microliter (uL) [UO:0000101] @@ -15330,7 +15321,6 @@ enums: ResidualSampleStatusMenu: name: ResidualSampleStatusMenu title: residual_sample_status menu - description: '' permissible_values: Residual sample remaining (some sample left) [GENEPIO:0101087]: text: Residual sample remaining (some sample left) [GENEPIO:0101087] @@ -15341,7 +15331,6 @@ enums: SampleStorageDurationUnitMenu: name: SampleStorageDurationUnitMenu title: sample_storage_duration_unit menu - description: '' permissible_values: Second [UO:0000010]: text: Second [UO:0000010] @@ -15360,7 +15349,6 @@ enums: NucelicAcidStorageDurationUnitMenu: name: NucelicAcidStorageDurationUnitMenu title: nucelic_acid_storage_duration_unit menu - description: '' permissible_values: Second [UO:0000010]: text: Second [UO:0000010] @@ -15379,7 +15367,6 @@ enums: FoodPackagingMenu: name: FoodPackagingMenu title: food_packaging menu - description: '' permissible_values: Bag, sack or pouch [FOODON:03490197]: text: Bag, sack or pouch [FOODON:03490197] @@ -15408,7 +15395,6 @@ enums: HostCommonNameMenu: name: HostCommonNameMenu title: host (common name) menu - description: '' permissible_values: Bird [NCBITaxon:8782]: text: Bird [NCBITaxon:8782] @@ -15505,7 +15491,6 @@ enums: HostScientificNameMenu: name: HostScientificNameMenu title: host (scientific name) menu - description: '' permissible_values: Anoplopoma fimbria [NCBITaxon:229290]: text: Anoplopoma fimbria [NCBITaxon:229290] @@ -15552,7 +15537,6 @@ enums: HostFoodProductionNameMenu: name: HostFoodProductionNameMenu title: host (food production name) menu - description: '' permissible_values: Cow (by age/production stage) (organizational term): text: Cow (by age/production stage) (organizational term) @@ -15700,7 +15684,6 @@ enums: HostAgeBinMenu: name: HostAgeBinMenu title: host_age_bin menu - description: '' permissible_values: First winter [GENEPIO:0100684]: text: First winter [GENEPIO:0100684] @@ -15717,7 +15700,6 @@ enums: IsolatedByMenu: name: IsolatedByMenu title: isolated_by menu - description: '' permissible_values: Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -15734,7 +15716,6 @@ enums: OrganismMenu: name: OrganismMenu title: organism menu - description: '' permissible_values: Acinetobacter [NCBITaxon:469]: text: Acinetobacter [NCBITaxon:469] @@ -16083,7 +16064,6 @@ enums: TaxonomicIdentificationProcessMenu: name: TaxonomicIdentificationProcessMenu title: taxonomic_identification_process menu - description: '' permissible_values: Whole genome sequencing assay [OBI:0002117]: text: Whole genome sequencing assay [OBI:0002117] @@ -16099,7 +16079,6 @@ enums: SequencedByMenu: name: SequencedByMenu title: sequenced_by menu - description: '' permissible_values: Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -16118,7 +16097,6 @@ enums: PurposeOfSequencingMenu: name: PurposeOfSequencingMenu title: purpose_of_sequencing menu - description: '' permissible_values: Cluster/Outbreak investigation [GENEPIO:0100001]: text: Cluster/Outbreak investigation [GENEPIO:0100001] @@ -16145,7 +16123,6 @@ enums: SequencingPlatformMenu: name: SequencingPlatformMenu title: sequencing_platform menu - description: '' permissible_values: Illumina [GENEPIO:0001923]: text: Illumina [GENEPIO:0001923] @@ -16162,7 +16139,6 @@ enums: SequencingInstrumentMenu: name: SequencingInstrumentMenu title: sequencing_instrument menu - description: A DNA sequencer manufactured by the Illumina corporation. permissible_values: Illumina [GENEPIO:0100105]: text: Illumina [GENEPIO:0100105] @@ -16446,7 +16422,6 @@ enums: SequencingAssayTypeMenu: name: SequencingAssayTypeMenu title: sequencing_assay_type menu - description: '' permissible_values: Amplicon sequencing assay [OBI:0002767]: text: Amplicon sequencing assay [OBI:0002767] @@ -16463,7 +16438,6 @@ enums: GenomicTargetEnrichmentMethodMenu: name: GenomicTargetEnrichmentMethodMenu title: genomic_target_enrichment_method menu - description: '' permissible_values: Hybrid selection method (bait-capture) [GENEPIO:0001950]: text: Hybrid selection method (bait-capture) [GENEPIO:0001950] @@ -16472,7 +16446,6 @@ enums: SequenceSubmittedByMenu: name: SequenceSubmittedByMenu title: sequence_submitted_by menu - description: '' permissible_values: Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -16491,7 +16464,6 @@ enums: QualityControlDeterminationMenu: name: QualityControlDeterminationMenu title: quality_control_determination menu - description: '' permissible_values: No quality control issues identified [GENEPIO:0100562]: text: No quality control issues identified [GENEPIO:0100562] @@ -16508,7 +16480,6 @@ enums: QualityControlIssuesMenu: name: QualityControlIssuesMenu title: quality _control_issues menu - description: '' permissible_values: Low quality sequence [GENEPIO:0100568]: text: Low quality sequence [GENEPIO:0100568] @@ -16529,7 +16500,6 @@ enums: AttributePackageMenu: name: AttributePackageMenu title: attribute_package menu - description: '' permissible_values: Pathogen.cl [GENEPIO:0001835]: text: Pathogen.cl [GENEPIO:0001835] @@ -16538,7 +16508,6 @@ enums: ExperimentalInterventionMenu: name: ExperimentalInterventionMenu title: experimental_intervention menu - description: '' permissible_values: Addition of substances to food/water [GENEPIO:0100536]: text: Addition of substances to food/water [GENEPIO:0100536] @@ -16567,7 +16536,6 @@ enums: AmrTestingByMenu: name: AmrTestingByMenu title: AMR_testing_by menu - description: '' permissible_values: Public Health Agency of Canada (PHAC) [GENEPIO:0100551]: text: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] @@ -16584,7 +16552,6 @@ enums: AntimicrobialPhenotypeMenu: name: AntimicrobialPhenotypeMenu title: antimicrobial_phenotype menu - description: '' permissible_values: Antibiotic resistance not defined [GENEPIO:0002040]: text: Antibiotic resistance not defined [GENEPIO:0002040] @@ -16619,7 +16586,6 @@ enums: AntimicrobialMeasurementUnitsMenu: name: AntimicrobialMeasurementUnitsMenu title: antimicrobial_measurement_units menu - description: '' permissible_values: milligram per litre (mg/L) [UO:0000273]: text: milligram per litre (mg/L) [UO:0000273] @@ -16634,7 +16600,6 @@ enums: AntimicrobialMeasurementSignMenu: name: AntimicrobialMeasurementSignMenu title: antimicrobial_measurement_sign menu - description: '' permissible_values: less than (<) [GENEPIO:0001002]: text: less than (<) [GENEPIO:0001002] @@ -16659,7 +16624,6 @@ enums: AntimicrobialLaboratoryTypingMethodMenu: name: AntimicrobialLaboratoryTypingMethodMenu title: antimicrobial_laboratory_typing_method menu - description: '' permissible_values: Agar diffusion [NCIT:85595]: text: Agar diffusion [NCIT:85595] @@ -16679,7 +16643,6 @@ enums: AntimicrobialLaboratoryTypingPlatformMenu: name: AntimicrobialLaboratoryTypingPlatformMenu title: antimicrobial_laboratory_typing_platform menu - description: '' permissible_values: BIOMIC Microbiology System [ARO:3007569]: text: BIOMIC Microbiology System [ARO:3007569] @@ -16704,7 +16667,6 @@ enums: AntimicrobialVendorNameMenu: name: AntimicrobialVendorNameMenu title: antimicrobial_vendor_name menu - description: '' permissible_values: Becton Dickinson [ARO:3004405]: text: Becton Dickinson [ARO:3004405] @@ -16729,7 +16691,6 @@ enums: AntimicrobialTestingStandardMenu: name: AntimicrobialTestingStandardMenu title: antimicrobial_testing_standard menu - description: '' permissible_values: British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365]: text: British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] @@ -16771,7 +16732,6 @@ enums: AntimicrobialResistanceTestDrugMenu: name: AntimicrobialResistanceTestDrugMenu title: Antimicrobial Resistance Test Drug Menu - description: '' permissible_values: amikacin: text: amikacin diff --git a/web/templates/grdi/schema_enums.tsv b/web/templates/grdi/schema_enums.tsv index ab2335ec..6b0edd75 100644 --- a/web/templates/grdi/schema_enums.tsv +++ b/web/templates/grdi/schema_enums.tsv @@ -1,1582 +1,1585 @@ -title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM Template - -null value menu NullValueMenu Not Applicable [GENEPIO:0001619] Not applicable - Missing [GENEPIO:0001618] missing - Not Collected [GENEPIO:0001620] Not collected - Not Provided [GENEPIO:0001668] Not provided - Restricted Access [GENEPIO:0001810] Restricted access - -sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - University of Manitoba (UM) [GENEPIO:0004434] - - -purpose_of_sampling menu PurposeOfSamplingMenu Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549] - Field experiment [GENEPIO:0100550] - Survey study [GENEPIO:0100582] - Surveillance [GENEPIO:0100004] - - -presampling_activity menu PresamplingActivityMenu Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538] - Certified humane animal husbandry practices [GENEPIO:0100894] - Certified organic farming practices [GENEPIO:0100539] - Conventional farming practices [GENEPIO:0100895] - Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543] - Genetic mutation [GENEPIO:0100544[ - Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346] - Wastewater treatment process [ENVO:06105300] A recycling process during which wastewater is treated. - Wastewater filtration [GENEPIO:0100881] A wastewater treatment process which removes solid particles from wastewater by means of filtration. - Wastewater grit removal [GENEPIO:0100882] A wastewater treatment process which removes sand, silt, and grit from wastewater. - Wastewater microbial treatment [GENEPIO:0100883] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. - Wastewater primary sedimentation [GENEPIO:0100884] A wastewater treatment process which removes solids and large particles from influent through gravitational force. - Wastewater secondary sedimentation [GENEPIO:0100885] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. - -experimental_specimen_role_type menu ExperimentalSpecimenRoleTypeMenu Positive experimental control [GENEPIO:0101018] - Negative experimental control [GENEPIO:0101019] - Technical replicate [EFO:0002090] - Biological replicate [EFO:0002091] - - -specimen_processing menu SpecimenProcessingMenu Biological replicate process [GENEPIO:0101022] - Samples pooled [OBI:0600016] - Technical replicate process [GENEPIO:0101021] - Isolated from single source [OBI:0002079] - - -geo_loc_name (country) menu GeoLocNameCountryMenu Afghanistan [GAZ:00006882] - Albania [GAZ:00002953] - Algeria [GAZ:00000563] - American Samoa [GAZ:00003957] - Andorra [GAZ:00002948] - Angola [GAZ:00001095] - Anguilla [GAZ:00009159] - Antarctica [GAZ:00000462] - Antigua and Barbuda [GAZ:00006883] - Argentina [GAZ:00002928] - Armenia [GAZ:00004094] - Aruba [GAZ:00004025] - Ashmore and Cartier Islands [GAZ:00005901] - Australia [GAZ:00000463] - Austria [GAZ:00002942] - Azerbaijan [GAZ:00004941] - Bahamas [GAZ:00002733] - Bahrain [GAZ:00005281] - Baker Island [GAZ:00007117] - Bangladesh [GAZ:00003750] - Barbados [GAZ:00001251] - Bassas da India [GAZ:00005810] - Belarus [GAZ:00006886] - Belgium [GAZ:00002938] - Belize [GAZ:00002934] - Benin [GAZ:00000904] - Bermuda [GAZ:00001264] - Bhutan [GAZ:00003920] - Bolivia [GAZ:00002511] - Borneo [GAZ:00025355] - Bosnia and Herzegovina [GAZ:00006887] - Botswana [GAZ:00001097] - Bouvet Island [GAZ:00001453] - Brazil [GAZ:00002828] - British Virgin Islands [GAZ:00003961] - Brunei [GAZ:00003901] - Bulgaria [GAZ:00002950] - Burkina Faso [GAZ:00000905] - Burundi [GAZ:00001090] - Cambodia [GAZ:00006888] - Cameroon [GAZ:00001093] - Canada [GAZ:00002560] - Cape Verde [GAZ:00001227] - Cayman Islands [GAZ:00003986] - Central African Republic [GAZ:00001089] - Chad [GAZ:00000586] - Chile [GAZ:00002825] - China [GAZ:00002845] - Christmas Island [GAZ:00005915] - Clipperton Island [GAZ:00005838] - Cocos Islands [GAZ:00009721] - Colombia [GAZ:00002929] - Comoros [GAZ:00005820] - Cook Islands [GAZ:00053798] - Coral Sea Islands [GAZ:00005917] - Costa Rica [GAZ:00002901] - Cote d'Ivoire [GAZ:00000906] - Croatia [GAZ:00002719] - Cuba [GAZ:00003762] - Curacao [GAZ:00012582] - Cyprus [GAZ:00004006] - Czech Republic [GAZ:00002954] - Democratic Republic of the Congo [GAZ:00001086] - Denmark [GAZ:00005852] - Djibouti [GAZ:00000582] - Dominica [GAZ:00006890] - Dominican Republic [GAZ:00003952] - Ecuador [GAZ:00002912] - Egypt [GAZ:00003934] - El Salvador [GAZ:00002935] - Equatorial Guinea [GAZ:00001091] - Eritrea [GAZ:00000581] - Estonia [GAZ:00002959] - Eswatini [GAZ:00001099] - Ethiopia [GAZ:00000567] - Europa Island [GAZ:00005811] - Falkland Islands (Islas Malvinas) [GAZ:00001412] - Faroe Islands [GAZ:00059206] - Fiji [GAZ:00006891] - Finland [GAZ:00002937] - France [GAZ:00003940] - French Guiana [GAZ:00002516] - French Polynesia [GAZ:00002918] - French Southern and Antarctic Lands [GAZ:00003753] - Gabon [GAZ:00001092] - Gambia [GAZ:00000907] - Gaza Strip [GAZ:00009571] - Georgia [GAZ:00004942] - Germany [GAZ:00002646] - Ghana [GAZ:00000908] - Gibraltar [GAZ:00003987] - Glorioso Islands [GAZ:00005808] - Greece [GAZ:00002945] - Greenland [GAZ:00001507] - Grenada [GAZ:02000573] - Guadeloupe [GAZ:00067142] - Guam [GAZ:00003706] - Guatemala [GAZ:00002936] - Guernsey [GAZ:00001550] - Guinea [GAZ:00000909] - Guinea-Bissau [GAZ:00000910] - Guyana [GAZ:00002522] - Haiti [GAZ:00003953] - Heard Island and McDonald Islands [GAZ:00009718] - Honduras [GAZ:00002894] - Hong Kong [GAZ:00003203] - Howland Island [GAZ:00007120] - Hungary [GAZ:00002952] - Iceland [GAZ:00000843] - India [GAZ:00002839] - Indonesia [GAZ:00003727] - Iran [GAZ:00004474] - Iraq [GAZ:00004483] - Ireland [GAZ:00002943] - Isle of Man [GAZ:00052477] - Israel [GAZ:00002476] - Italy [GAZ:00002650] - Jamaica [GAZ:00003781] - Jan Mayen [GAZ:00005853] - Japan [GAZ:00002747] - Jarvis Island [GAZ:00007118] - Jersey [GAZ:00001551] - Johnston Atoll [GAZ:00007114] - Jordan [GAZ:00002473] - Juan de Nova Island [GAZ:00005809] - Kazakhstan [GAZ:00004999] - Kenya [GAZ:00001101] - Kerguelen Archipelago [GAZ:00005682] - Kingman Reef [GAZ:00007116] - Kiribati [GAZ:00006894] - Kosovo [GAZ:00011337] - Kuwait [GAZ:00005285] - Kyrgyzstan [GAZ:00006893] - Laos [GAZ:00006889] - Latvia [GAZ:00002958] - Lebanon [GAZ:00002478] - Lesotho [GAZ:00001098] - Liberia [GAZ:00000911] - Libya [GAZ:00000566] - Liechtenstein [GAZ:00003858] - Line Islands [GAZ:00007144] - Lithuania [GAZ:00002960] - Luxembourg [GAZ:00002947] - Macau [GAZ:00003202] - Madagascar [GAZ:00001108] - Malawi [GAZ:00001105] - Malaysia [GAZ:00003902] - Maldives [GAZ:00006924] - Mali [GAZ:00000584] - Malta [GAZ:00004017] - Marshall Islands [GAZ:00007161] - Martinique [GAZ:00067143] - Mauritania [GAZ:00000583] - Mauritius [GAZ:00003745] - Mayotte [GAZ:00003943] - Mexico [GAZ:00002852] - Micronesia [GAZ:00005862] - Midway Islands [GAZ:00007112] - Moldova [GAZ:00003897] - Monaco [GAZ:00003857] - Mongolia [GAZ:00008744] - Montenegro [GAZ:00006898] - Montserrat [GAZ:00003988] - Morocco [GAZ:00000565] - Mozambique [GAZ:00001100] - Myanmar [GAZ:00006899] - Namibia [GAZ:00001096] - Nauru [GAZ:00006900] - Navassa Island [GAZ:00007119] - Nepal [GAZ:00004399] - Netherlands [GAZ:00002946] - New Caledonia [GAZ:00005206] - New Zealand [GAZ:00000469] - Nicaragua [GAZ:00002978] - Niger [GAZ:00000585] - Nigeria [GAZ:00000912] - Niue [GAZ:00006902] - Norfolk Island [GAZ:00005908] - North Korea [GAZ:00002801] - North Macedonia [GAZ:00006895] - North Sea [GAZ:00002284] - Northern Mariana Islands [GAZ:00003958] - Norway [GAZ:00002699] - Oman [GAZ:00005283] - Pakistan [GAZ:00005246] - Palau [GAZ:00006905] - Panama [GAZ:00002892] - Papua New Guinea [GAZ:00003922] - Paracel Islands [GAZ:00010832] - Paraguay [GAZ:00002933] - Peru [GAZ:00002932] - Philippines [GAZ:00004525] - Pitcairn Islands [GAZ:00005867] - Poland [GAZ:00002939] - Portugal [GAZ:00004126] - Puerto Rico [GAZ:00006935] - Qatar [GAZ:00005286] - Republic of the Congo [GAZ:00001088] - Reunion [GAZ:00003945] - Romania [GAZ:00002951] - Ross Sea [GAZ:00023304] - Russia [GAZ:00002721] - Rwanda [GAZ:00001087] - Saint Helena [GAZ:00000849] - Saint Kitts and Nevis [GAZ:00006906] - Saint Lucia [GAZ:00006909] - Saint Pierre and Miquelon [GAZ:00003942] - Saint Martin [GAZ:00005841] - Saint Vincent and the Grenadines [GAZ:02000565] - Samoa [GAZ:00006910] - San Marino [GAZ:00003102] - Sao Tome and Principe [GAZ:00006927] - Saudi Arabia [GAZ:00005279] - Senegal [GAZ:00000913] - Serbia [GAZ:00002957] - Seychelles [GAZ:00006922] - Sierra Leone [GAZ:00000914] - Singapore [GAZ:00003923] - Sint Maarten [GAZ:00012579] - Slovakia [GAZ:00002956] - Slovenia [GAZ:00002955] - Solomon Islands [GAZ:00005275] - Somalia [GAZ:00001104] - South Africa [GAZ:00001094] - South Georgia and the South Sandwich Islands [GAZ:00003990] - South Korea [GAZ:00002802] - South Sudan [GAZ:00233439] - Spain [GAZ:00003936] - Spratly Islands [GAZ:00010831] - Sri Lanka [GAZ:00003924] - State of Palestine [GAZ:00002475] - Sudan [GAZ:00000560] - Suriname [GAZ:00002525] - Svalbard [GAZ:00005396] - Swaziland [GAZ:00001099] - Sweden [GAZ:00002729] - Switzerland [GAZ:00002941] - Syria [GAZ:00002474] - Taiwan [GAZ:00005341] - Tajikistan [GAZ:00006912] - Tanzania [GAZ:00001103] - Thailand [GAZ:00003744] - Timor-Leste [GAZ:00006913] - Togo [GAZ:00000915] - Tokelau [GAZ:00260188] - Tonga [GAZ:00006916] - Trinidad and Tobago [GAZ:00003767] - Tromelin Island [GAZ:00005812] - Tunisia [GAZ:00000562] - Turkey [GAZ:00000558] - Turkmenistan [GAZ:00005018] - Turks and Caicos Islands [GAZ:00003955] - Tuvalu [GAZ:00009715] - United States of America [GAZ:00002459] - Uganda [GAZ:00001102] - Ukraine [GAZ:00002724] - United Arab Emirates [GAZ:00005282] - United Kingdom [GAZ:00002637] - Uruguay [GAZ:00002930] - Uzbekistan [GAZ:00004979] - Vanuatu [GAZ:00006918] - Venezuela [GAZ:00002931] - Viet Nam [GAZ:00003756] - Virgin Islands [GAZ:00003959] - Wake Island [GAZ:00007111] - Wallis and Futuna [GAZ:00007191] - West Bank [GAZ:00009572] - Western Sahara [GAZ:00000564] - Yemen [GAZ:00005284] - Zambia [GAZ:00001107] - Zimbabwe [GAZ:00001106] - - -geo_loc_name (state/province/region) menu GeoLocNameStateProvinceRegionMenu Atlantic region (Canada) [wikidata:Q246972] - New Brunswick [GAZ:00002570] - Newfoundland & Labrador [GAZ:00002567] - Nova Scotia [GAZ:00002565] - Prince Edward Island [GAZ:00002572] - Central region (Canada) [wikidata:Q1048064] - Ontario [GAZ:00002563] - Quebec [GAZ:00002569] - Northern region (Canada) [wikidata:Q764146] - Northwest Territories [GAZ:00002575] - Nunuvut [GAZ:00002574] - Yukon [GAZ:00002576] - Pacific region (Canada) [wikidata:Q122953299] - British Columbia [GAZ:00002562] - Prairie region (Canada) [wikidata:Q1364746] - Alberta [GAZ:00002566] - Manitoba [GAZ:00002571] - Saskatchewan [GAZ:00002564] - - -sample_collection_date_precision menu SampleCollectionDatePrecisionMenu year [UO:0000036] - month [UO:0000035] - day [UO:0000033] - - -environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] - Agricultural Field [ENVO:00000114] - Alluvial fan [ENVO:00000314] - Animal cage [ENVO:01000922] - Aquarium [ENVO:00002196] - Artificial wetland [ENVO:03501406] - Breeding ground [ENVO:03501441] - Building [ENVO:00000073] - Barn [ENVO:03501257] - Breeder barn [ENVO:03501383] - Broiler barn [ENVO:03501386] - Sheep barn [ENVO:03501385] - Biodome [ENVO:03501397] - Cottage [ENVO:03501393] - Dairy [ENVO:00003862] - Hospital [ENVO:00002173] - Laboratory facility [ENVO:01001406] - Pigsty [ENVO:03501413] - Building part (organizational term) - Air intake [ENVO:03501380] - Animal pen [ENVO:03501387] - Building floor [ENVO:01000486] - Building wall [ENVO:01000465] - Countertop [ENVO:03501404] - Shelf [ENVO:03501403] - Stall [EOL:0001903] - Window sill [ENVO:03501381] - Creek [ENVO:03501405] - Ditch [ENVO:00000037] A small, human-made channel which has been dug for draining or irrigating the land. - Drainage ditch [ENVO:00000140] A ditch that collects water from the surrounding land. - Irrigation ditch [ENVO:00000139] A ditch that supplies water to surrounding land. - Farm [ENVO:00000078] - Beef farm [ENVO:03501443] - Breeder farm [ENVO:03501384] - Dairy farm [ENVO:03501416] - Feedlot [ENVO:01000627] - Beef cattle feedlot [ENVO:03501444] - Fish farm [ENVO:00000294] - Research farm [ENVO:03501417] - Central Experimental Farm [GAZ:00004603] Central Experimental Farm - Freshwater environment [ENVO:01000306] - Hatchery [ENVO:01001873] - Poultry hatchery [ENVO:01001874] - Lake [ENVO:00000020] - Manure digester facility [ENVO:03501422] - Manure lagoon (Anaerobic lagoon) [ENVO:03501423] - Manure pit [ENVO:01001872] - Marine environment [ENVO:01000320] - Benthic zone [ENVO:03501440] - Pelagic zone [ENVO:00000208] - Park [ENVO:00000562] - Plumbing drain [ENVO:01000924 ] - Pond [ENVO:00000033] - Reservoir [ENVO:00000025] - Irrigation reservoir [ENVO:00000450] - Retail environment [ENVO:01001448] - Shop [ENVO:00002221] - Butcher shop [ENVO:03501396] - Pet store [ENVO:03501395] - Supermarket [ENVO:01000984] - River [ENVO:00000022] - Roost (bird) [ENVO:03501439] - Rural area [ENVO:01000772] - Slough [ENVO:03501438] - Stream [ENVO:00000023] - Trailer [ENVO:03501394] - Tributary [ENVO:00000495] - Truck [ENVO:01000602] - Urban area [ENVO:03501437] - Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. - Water surface [ENVO:01001191] - Woodland area [ENVO:00000109] - Zoo [ENVO:00010625] - - -water_depth_units menu WaterDepthUnitsMenu centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - kilometer (km) [UO:0010066] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - - -sediment_depth_units menu SedimentDepthUnitsMenu centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - kilometer (km) [UO:0010066] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - - -air_temperature_units menu AirTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] - degree Celsius (C) [UO:0000027] - - -water_temperature_units menu WaterTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] - degree Celsius (C) [UO:0000027] - -precipitation_measurement_unit menu PrecipitationMeasurementUnitMenu millimeter (mm) [UO:0000016] - centimeter (cm) [UO:0000015] - meter (m) [UO:0000008] - inch (in) [UO:0010011] - foot (ft) [UO:0010013] - -available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702] - Experimental parameters documentation [GENEPIO:0100703] - Feed history [GENEPIO:0100704] - Land use information [GENEPIO:0100705] - Therapeutic administration history [GENEPIO:0100706] - Chemical characterization [GENEPIO:0100707] - pH measurement [GENEPIO:0100708] - Dissolved oxygen measurement [GENEPIO:0100709] - Nitrate measurement [GENEPIO:0100710] - Nitrite measurement [GENEPIO:0100711] - Phosphorous measurement [GENEPIO:0100712] - Salinity measurement [GENEPIO:0100713] - Microbiological characterization [GENEPIO:0100714] - Microbiological identification [GENEPIO:0100715] - Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] - Microbiological identification (bioMérieux API) [GENEPIO:0100717] - Microbiological identification (Biolog) [GENEPIO:0100718] - Microbiological identification (FAME) [GENEPIO:0100719] - Microbiological identification (Sensititre) [GENEPIO:0100720] - Microbiological identification (ViTek) [GENEPIO:0100721] - Phage type [GENEPIO:0100722] - Serotype [GENEPIO:0100723] - Phenotypic microbiological characterization [GENEPIO:0100724] - AMR phenotypic testing [GENEPIO:0100725] - Biolog phenotype microarray [GENEPIO:0100726] - Microbiological quantification [GENEPIO:0100727] - Colony count [GENEPIO:0100728] - Total coliform count [GENEPIO:0100729] - Total fecal coliform count [GENEPIO:0100730] - Infectivity assay [GENEPIO:0100731] - ELISA toxin binding [GENEPIO:0100732] - Molecular characterization [GENEPIO:0100733] - 16S rRNA Sanger sequencing [GENEPIO:0100734] - Metagenomic sequencing [GENEPIO:0101024] - PCR marker detection [GENEPIO:0100735] - BOX PCR fingerprint [GENEPIO:0100736] - ERIC PCR fingerprint [GENEPIO:0100737] - Plasmid type [GENEPIO:0100738] - Ribotype [GENEPIO:0100739] - Molecular quantification [GENEPIO:0100740] - qPCR marker organism quantification [GENEPIO:0100741] - Physical characterization [GENEPIO:0100742] - Conductivity measurement [GENEPIO:0100743] - Mollusc shell measurement [GENEPIO:0100744] - Mollusc shell length [GENEPIO:0100745] - Matter compostion [GENEPIO:0100746] - Dry matter composition [GENEPIO:0100747] - Organic matter composition [GENEPIO:0100748] - Turbidity measurement [GENEPIO:0100749] - - -sampling_weather_conditions menu SamplingWeatherConditionsMenu Cloudy/Overcast [ENVO:03501418] - Partially cloudy [ENVO:03501419] - Drizzle [ENVO:03501420] - Fog [ENVO:01000844] - Rain [ENVO:01001564] - Snow [ENVO:01000406] - Storm [ENVO:01000876] - Sunny/Clear [ENVO:03501421] - - -animal_or_plant_population menu AnimalOrPlantPopulationMenu Algae [FOODON:03411301] - Algal bloom [ENVO:2000004] - Cattle [NCBITaxon:9913] - Beef cattle [FOODON:00004413] - Dairy cattle [FOODON:00002505] - Chicken [NCBITaxon:9031] - Crop [AGRO:00000325] - Fish [FOODON:03411222] - Pig [NCBITaxon:9823] - Poultry [FOODON:00004298] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Crustacean [FOODON:03411374] - Mollusc [FOODON:03412112] - Tropical fish [FOODON:00004283] - Turkey [NCBITaxon:9103] - Wildlife [FOODON:00004503] - Wild bird [FOODON:00004505] - Seabird [FOODON:00004504] - - - -environmental_material menu EnvironmentalMaterialMenu Air [ENVO:00002005] - Alluvium [ENVO:01001202] - Animal feeding equipment [AGRO:00000675] - Animal feeder [AGRO:00000679] - Animal drinker [AGRO:00000680] - Feed pan [AGRO:00000676] - Watering bowl [AGRO:00000677] - Animal transportation equipment [AGRO:00000671] - Dead haul trailer [GENEPIO:0100896] - Dead haul truck [AGRO:00000673] - Live haul trailer [GENEPIO:0100897] - Live haul truck [AGRO:00000674] - Belt [NCIT:C49844] - Biosolids [ENVO:00002059] - Boot [GSSO:012935] - Boot cover [OBI:0002806] - Broom [ENVO:03501431] - Bulk tank [ENVO:03501379] - Chick box [AGRO:00000678] - Chick pad [AGRO:00000672] - Cleaning equipment [ENVO:03501430] - Compost [ENVO:00002170] - Contaminated water [ENVO:00002186] - Fecal slurry [ENVO:03501436] - Fluid from meat rinse [GENEPIO:0004323] - Effluent [ENVO:03501407] - Influent [ENVO:03501442] - Surface runoff [ENVO:03501408] - Poultry plucking water [AGRO_00000693] - Wastewater [ENVO:00002001] - Weep fluid [AGRO_00000692] - Crate [ENVO:03501372] - Dumpster [ENVO:03501400] - Dust [ENVO:00002008] - Egg belt [AGRO:00000670] - Fan [NCIT:C49947] - Freezer [ENVO:03501415] - Freezer handle [ENVO:03501414] - Manure [ENVO:00003031] - Animal manure [AGRO:00000079] - Pig manure [AGRO:00000080] - Manure digester equipment [ENVO:03501424] - Nest [ENVO:03501432] - Bird's nest [ENVO:00005805] - Permafrost [ENVO:00000134] - Plucking belt [AGRO:00000669] - Poultry fluff [UBERON:0008291] - Poultry litter [AGRO:00000080] - Sediment [ENVO:00002007] - Soil [ENVO:00001998] - Agricultural soil [ENVO:00002259] - Forest soil [ENVO:00002261] - Straw [ENVO:00003869] - Canola straw [FOODON:00004430] - Oat straw [FOODON:03309878] - Barley straw [FOODON:00004559] - Sludge [ENVO:00002044] - Primary sludge [ENVO:00002057] - Secondary sludge [ENVO:00002058] - Water [CHEBI:15377] - Drinking water [ENVO:00003064] - Groundwater [ENVO:01001004] - Surface water [ENVO:00002042] - - -anatomical_material menu AnatomicalMaterialMenu Blood [UBERON:0000178] - Fluid [UBERON:0006314] - Fluid (cerebrospinal (CSF)) [UBERON:0001359] - Fluid (amniotic) [UBERON:0000173] - Saliva [UBERON:0001836] - Tissue [UBERON:0000479] - - -body_product menu BodyProductMenu Digestive tract substance [GENEPIO:0100898] - Caecal content [GENEPIO:0100899] - Intestinal content [GENEPIO:0100900] - Stomach content [GENEPIO:0100901] - Feces [UBERON:0001988] - Fecal composite [GENEPIO:0004512] - Feces (fresh) [GENEPIO:0004513] - Feces (environmental) [GENEPIO:0004514] - Meconium [UBERON:0007109] - Milk [UBERON:0001913] - Colostrum [UBERON:0001914] - Urine [UBERON:0001088] - - -anatomical_part menu AnatomicalPartMenu Carcass [UBERON:0008979] - Swine carcass [FOODON:03311719] - Digestive system [UBERON:0001007] - Caecum [UBERON:0001153] - Colon [UBERON:0001155] - Digestive gland [UBERON:0006925] - Foregut [UBERON:0001041] - Gall bladder [UBERON:0002110] - Gastrointestinal system mucosa [UBERON:0004786] - Gizzard [UBERON:0005052] - Hindgut [UBERON:0001046] - Intestine [UBERON:0000160] - Small intestine [UBERON:0002108] - Duodenum [UBERON:0002114] - Ileum [UBERON:0002116] - Jejunum [UBERON:0002115] - Stomach [UBERON:0000945] - Abomasum [UBERON:0007358] - Rumen [UBERON:0007365] - Excretory system (organizational term) - Anus [UBERON:0001245] - Anal gland [UBERON:0011253] - Cloaca [UBERON:0000162] - Liver [UBERON:0002107] - Kidney [UBERON:0002113] - Rectum [UBERON:0001052] - Spleen [UBERON:0002106] - Urinary bladder [UBERON:0001255] - Foot [UBERON:0002387] - Head [UBERON:0000033] - Brain [UBERON:0000955] - Ear [UBERON:0001690] - Eye [UBERON:0000970] - Mouth [UBERON:0000165] - Nose [UBERON:0000004] - Nasal turbinal [UBERON:0035612] - Nasopharynx (NP) [UBERON:0001728] - Pair of nares [UBERON:0002109] - Paranasal sinus [UBERON:0001825] - Snout [UBERON:0006333] - Lymphatic system [UBERON:0006558] - Lymph node [UBERON:0000029] - Mesenteric lymph node [UBERON:0002509] - Mantle (bird) [GENEPIO:0100927] - Neck [UBERON:0000974] - Esophagus [UBERON:0001043] - Trachea [UBERON:0003126] - Nerve [UBERON:0001021] - Spinal cord [UBERON:0002240] - Organs or organ parts [GENEPIO:0001117] - Organ [UBERON:0000062] - Muscle organ [UBERON:0001630] - Skin of body [UBERON:0002097] - Reproductive system [UBERON:0000990] - Embryo [UBERON:0000922] - Fetus [UBERON:0000323] - Ovary [UBERON:0000992] - Oviduct [UBERON:0000993] - Placenta [UBERON:0001987] - Testis [UBERON:0000473] - Udder [UBERON:0013216] - Uterus [UBERON:0000995] - Vagina [UBERON:0000996] - Yolk sac [UBERON:0001040] - Respiratory system [UBERON:0001004] - Air sac [UBERON:0009060] - Lung [UBERON:0002048] - Pleura [UBERON:0000977] - Respiratory system mucosa [UBERON:0004785] - Skeletal system [UBERON:0001434] - Skeletal joint [UBERON:0000982] - Bone element [UBERON:0001474] - Thoracic segment of trunk [UBERON:0000915] - Abdomen [UBERON:0000916] - Muscle of abdomen [UBERON:0002378] - Peritoneum [UBERON:0002358] - Vascular system [UBERON:0007798] - Blood vessel [UBERON:0001981] - Bursa of Fabricius [UBERON:0003903] - Gill [UBERON:0002535] - Heart [UBERON:0000948] - Lung [UBERON:0002048] - Pericardium [UBERON:0002407] - Vent (anatomical) [UBERON:2000298] - Bird vent [UBERON:0012464] - Fish vent [GENEPIO:0100902] - - -anatomical_region menu AnatomicalRegionMenu Dorso-lateral region [BSPO:0000080] - Exterior anatomical region [BSPO:0000034] - Interior anatomical region [BSPO:0000033] - - -food_product menu FoodProductMenu Animal feed [ENVO:02000047] - Blood meal [FOODON:00001564] - Bone meal [ENVO:02000054] - Brassica carinata meal [FOODON:00004310] - Canola meal [FOODON:00002694] - Compound feed premix [FOODON:00004323] - Compound feed premix (medicated) [FOODON:00004324] - Feather meal [FOODON:00003927] - Fish meal [FOODON:03301620] - Lay ration [FOODON:00004286] - Meat and bone meal [FOODON:00002738] - Meat meal [FOODON:00004282] - Pet food [FOODON:00002682] - Soybean meal [FOODON:03302757] - Animal feed ingredient [FOODON:00004322] - Dairy food product [FOODON:00001256] - Cheese block (whole or parts) [FOODON:03000287] - Cow skim milk (powdered) [FOODON:03310016] - Milk [UBERON:0001913] - Dietary supplement [FOODON:03401298] - Egg or egg component [FOODON:03420194] - Balut [FOODON:03302184] - Egg yolk [UBERON:0007378] - Poultry egg [FOODON:03000414] - Hen egg (whole) [FOODON:03316061] - Poultry egg (whole, shell on) [FOODON:03000415] - Food mixture [FOODON:00004130] - Food product analog (food subsitute) [FOODON:00001871] - Milk substitute [FOODON:03305408] - Meat (whole or parts) [FOODON:03317170] - Cutlet [FOODON:00003001] - Filet [FOODON:03530144] - Liver (whole, raw) [FOODON:03309772] - Meat trim [FOODON:03309475] - Rib (meat cut) [FOODON:03530023] - Rib chop [FOODON:00004290] - Shoulder (meat cut) [FOODON:03530043] - Grains, cereals, and bakery product (organizational term) - Bread loaf (whole or parts) [FOODON:03000288] - Breakfast cereal [FOODON:03311075] - Bulk grain [FOODON:03309390] - Oat grain [FOODON:00003429] - Legume food product [FOODON:00001264] - Chickpea (whole) [FOODON:03306811] - Hummus [FOODON:00003049] - Soybean (whole or parts) [FOODON:03000245] - Meat, poultry and fish (organizational term) - Beef (ground or minced) [FOODON:00001282] - Beef (ground or minced, boneless) [FOODON:0001282] - Beef (ground, extra lean) [FOODON:02000426] - Beef (ground, lean) [FOODON:02000425] - Beef (ground, medium) [FOODON:02000427] - Beef (ground, regular) [FOODON:02000428] - Beef (ground, sirloin) [FOODON:02000429] - Beef hamburger (dish) [FOODON:00002737] - Beef shoulder [FOODON:02000069] - Beef shoulder chop [FOODON:03000387] - Beef sirloin chop [FOODON:03000389] - Beef stew chunk [FOODON:00004288] - Beef tenderloin [FOODON:00003302] - Beef (pieces) [FOODON:02000412] - Brisket [FOODON:03530020] - Chicken breast [FOODON:00002703] - Chicken breast (back off) [FOODON:03000385] - Chicken breast (skinless) [FOODON:02020231] - Chicken breast (with skin) [FOODON:02020233] - Chicken breast (skinless, boneless) [FOODON:02020235] - Chicken breast cutlet [FOODON:00004308] - Chicken drumstick [FOODON:00002716] - Chicken drumstick (skinless) [FOODON:02020237] - Chicken drumstick(with skin) [FOODON:02020239] - Chicken meat [FOODON:00001040] - Chicken meat (ground) [FOODON:02020311] - Chicken meat (ground or minced, lean) [FOODON:03000392] - Chicken meat (ground or minced, extra lean) [FOODON:03000396] - Chicken meat (ground or minced, medium) [FOODON:03000400] - Chicken meat (ground or minced, regular) [FOODON:03000404] - Chicken meat (ground or minced, boneless) [FOODON:03000410] - Chicken nugget [FOODON:00002672] - Chicken thigh [FOODON:02020219] - Chicken thigh (skinless) [FOODON:00003331] - Chicken thigh (skinless, with bone) [FOODON:02020227] - Chicken thigh (skinless, boneless) [FOODON:02020228] - Chicken upper thigh [FOODON:03000381] - Chicken upper thigh (with skin) [FOODON:03000383] - Chicken thigh (with skin) [FOODON:00003330] - Chicken thigh (with skin, with bone) [FOODON_00003363] - Chicken wing [FOODON:00002674] - Fish food product [FOODON:00001248] - Fish steak [FOODON:00002986] - Ham food product [FOODON:00002502] - Head cheese [FOODON:03315658] - Lamb [FOODON:03411669] - Meat strip [FOODON:00004285] - Mutton [FOODON:00002912] - Pork chop [FOODON:00001049] - pork meat (ground) [FOODON:02021718] - Pork meat (ground or minced, boneless) [FOODON:03000413] - Pork meat (ground or minced, extra lean) [FOODON:03000399] - Pork meat (ground or minced, lean) [FOODON:03000395] - Pork meat (ground or minced, medium) [FOODON:03000403] - Pork meat (ground or minced, regular) [FOODON:03000407] - Pork meat (ground or minced, Sirloin) [FOODON:03000409] - Pork shoulder [FOODON:02000322] - Pork shoulder chop [FOODON:03000388] - Pork sirloin chop [FOODON:02000300] - Pork steak [FOODON:02021757] - Pork tenderloin [FOODON:02000306] - Poultry meat [FOODON:03315883] - Leg (poultry meat cut) [FOODON:03530159] - Poultry drumstick [FOODON:00003469] - Neck (poultry meat cut) [FOODON:03530294] - Thigh (poultry meat cut) [FOODON:03530160] - Wing (poultry meat cut) [FOODON:03530157] - Sausage (whole) [FOODON:03315904] - Pepperoni [FOODON:03311003] - Salami [FOODON:03312067] - Shellfish [FOODON:03411433] - Mussel [FOODON:03411223] - Oyster [FOODON:03411224] - Shrimp [FOODON:03301673] - Scallop [FOODON:02020805] - Squid [FOODON:03411205] - Turkey breast [FOODON:00002690] - Turkey breast (back off) [FOODON:03000386] - Turkey breast (skinless) [FOODON:02020495] - Turkey breast (skinless, boneless) [FOODON:02020499] - Turkey breast (with skin) [FOODON:02020497] - Turkey drumstick [FOODON:02020477] - Turkey drumstick (skinless) [FOODON:02020501] - Turkey drumstick (with skin) [FOODON:02020503] - Turkey meat [FOODON:00001286] - Turkey meat (ground) [FOODON:02020577] - Turkey meat (ground or minced, lean) [FOODON:03000393] - Turkey meat (ground or minced, extra lean) [FOODON:03000397] - Turkey meat (ground or minced, medium) [FOODON:03000401] - Turkey meat (ground or minced, regular) [FOODON:03000405] - Turkey meat (ground or minced, boneless) [FOODON:03000411] - Turkey thigh [FOODON:00003325] - Turkey thigh (skinless) [FOODON:00003329] - Turkey thigh (skinless, boneless) [FOODON:02020491] - Turkey thigh (with skin) [FOODON:00003328] - Turkey upper thigh [FOODON:03000382] - Turkey upper thigh (with skin) [FOODON:03000384] - Turkey wing [FOODON:02020478] - Veal [FOODON:00003083] - Formula fed veal [FOODON:000039111] - Grain-fed veal [FOODON:00004280] - Microbial food product [FOODON:00001145] - Yeast [FOODON:03411345] - Nuts and seed products - Almond (whole or parts) [FOODON:03000218] - Almond (whole) [FOODON:00003523] - Barley seed [FOODON:00003394] - Canola seed [FOODON:00004560] - Chia seed powder [FOODON:00003925] - Chia seed (whole or parts) [FOODON:03000241] - Flaxseed powder [FOODON:00004276] - Hazelnut [FOODON:00002933] - Nut (whole or part) [FOODON:03306632] - Peanut butter [FOODON:03306867] - Sesame seed [FOODON:03310306] - Tahini [FOODON:00003855] - Walnut (whole or parts) [FOODON:03316466] - Prepared food product [FOODON:00001180] - Condiment [FOODON:03315708] - Confectionery food product [FOODON:00001149] - Snack food [FOODON:03315013] - Produce [FOODON:03305145] - Apple (whole or parts) [FOODON:03310788] - Apple (whole) [FOODON:00002473] - Arugula greens bunch [FOODON:00003643] - Avocado [FOODON:00003600] - Cantaloupe (whole or parts) [FOODON:03000243] - Chilli pepper [FOODON:00003744] - Coconut (whole or parts) [FOODON:03309861] - Coconut meat [FOODON:00003856] - Corn cob (whole or parts) [FOODON:03310791] - Cucumber (whole or parts) [FOODON:03000229] - Fruit [PO:0009001] - Goji berry [FOODON:00004360] - Greens (raw) [FOODON:03310765] - Kale leaf (whole or parts) [FOODON:03000236] - Karela (bitter melon) [FOODON:00004367] - Lettuce head (whole or parts) [FOODON:03000239] - Mango (whole or parts) [FOODON:03000217] - Mushroom (fruitbody) [FOODON:00003528] - Papaya (whole or parts) [FOODON:03000228] - Pattypan squash (whole or parts) [FOODON:03000232] - Peach [FOODON:00002485] - Pepper (whole or parts) [FOODON:03000249] - Potato [FOODON:03315354] - Salad [FOODON:03316042] - Scallion (whole or parts) [FOODON:03000250] - Spinach (whole or parts) [FOODON:03000221] - Sprout [FOODON:03420183] - Germinated or sprouted seed [FOODON:03420102] - Alfalfa sprout [FOODON:00002670] - Bean sprout [FOODON:00002576] - Chia sprout [FOODON:03000180] - Mixed sprouts [FOODON:03000182] - Mung bean sprout [FOODON:03301446] - Tomato (whole or pieces) [FOODON:00002318] - Vegetable (whole or parts) [FOODON:03315308] - Spice or herb [FOODON:00001242] - Basil (whole or parts) [FOODON:03000233] - Black pepper (whole or parts) [FOODON:03000242] - Cardamom (whole or parts) [FOODON:03000246] - Chive leaf (whole or parts) [FOODON:03000240] - Coriander powder [FOODON:00004274] - Coriander seed (whole or parts) [FOODON:03000224] - Cumin powder [FOODON:00004275] - Cumin seed (whole) [FOODON:00003396] - Black cumin seed (whole or parts) [FOODON:03000247] - Curry leaf (whole or parts) [FOODON:03000225] - Curry powder [FOODON:03301842] - Dill spice [FOODON:00004307] - Fennel (whole or parts) [FOODON:03000244] - Garlic powder [FOODON:03301844] - Ginger root (whole or parts) [FOODON:03000220] - Mint leaf (whole or parts) [FOODON:03000238] - Oregano (whole or parts) [FOODON:03000226] - Paprika (ground) [FOODON:03301223] - Parsley leaf (whole or parts) [FOODON:03000231] - Pepper (ground) [FOODON:03301526] - Rasam powder [FOODON:00004277] - Sage [FOODON:03301560] - Turmeric (ground) [FOODON:03310841] - Spice [FOODON:03303380] - White peppercorn (whole or parts) [FOODON:03000251] - - -food_product_properties menu FoodProductPropertiesMenu Food (canned) [FOODON:00002418] - Food (cooked) [FOODON:00001181] - Food (cut) [FOODON:00004291] - Food (chopped) [FOODON:00002777] - Food (chunks) [FOODON:00004555] - Food (cubed) [FOODON:00004278] - Food (diced) [FOODON:00004549] - Food (grated) [FOODON:00004552] - Food (sliced) [FOODON:00002455] - Food (shredded) [FOODON:00004553] - Food (dried) [FOODON:03307539] - Food (fresh) [FOODON:00002457] - Food (frozen) [FOODON:03302148] - Food (pulped) [FOODON:00004554] - Food (raw) [FOODON:03311126] - Food (unseasoned) [FOODON:00004287] - Italian-style food product [FOODON:00004321] - Meat (boneless) [FOODON:00003467] - Meat (skinless) [FOODON:00003468] - Meat (with bone) [FOODON:02010116] - Meat (with skin) [FOODON:02010111] - Soft [PATO:0000387] - - - - -label_claim menu LabelClaimMenu Antibiotic free [FOODON:03601063] - Cage free [FOODON:03601064] - Hormone free [FOODON:03601062] - Organic food claim or use [FOODON:03510128] - Pasture raised [FOODON:03601065] - Ready-to-eat (RTE) [FOODON:03316636] - - -animal_source_of_food menu AnimalSourceOfFoodMenu Cow [NCBITaxon:9913] - Fish [FOODON:03411222] - Pig [NCBITaxon:9823] - Poultry or game bird [FOODON:03411563] - Chicken [NCBITaxon:9031] - Turkey [NCBITaxon:9103] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Mussel [FOODON:03411223] - Scallop [NCBITaxon:6566] - Shrimp [FOODON:03411237] - Squid [FOODON:03411205] - - -food_product_production_stream menu FoodProductProductionStreamMenu Beef cattle production stream [FOODON:03000452] - Broiler chicken production stream [FOODON:03000455] - Dairy cattle production stream [FOODON:03000453] - Egg production stream [FOODON:03000458] - Layer chicken production stream [FOODON:03000456] - Meat production stream [FOODON:03000460] - Veal meat production stream [FOODON:03000461] - Milk production stream [FOODON:03000459] - - -collection_device menu CollectionDeviceMenu Auger (earth auger) [AGRO:00000405] - Box corer [GENEPIO:0100928] - Container [OBI:0000967] - Bag [GSSO:008558] - Whirlpak sampling bag [GENEPIO:0002122] - Bottle [FOODON:03490214] - Vial [OBI:0000522] - Culture plate [GENEPIO:0004318] - Petri dish [NCIT:C96141] - Filter [GENEPIO:0100103] - PONAR grab sampler [GENEPIO:0100929] - Scoop [GENEPIO:0002125] - Soil sample probe [GENEPIO:0100930] - Spatula [NCIT:C149941] - Sponge [OBI:0002819] - Swab [GENEPIO:0100027] - Drag swab [OBI:0002822] - Surface wipe [OBI:0002824] - Tube [GENEPIO:0101196] - Vacuum device [GENEPIO:0002127] - Vacutainer [OBIB:0000032] - - -collection_method menu CollectionMethodMenu Aspiration [HP:0002835] - Biopsy [OBI:0002650] - Fecal grab [GENEPIO:0004326] - Filtration [OBI:0302885] - Air filtration [GENEPIO:0100031] - Water filtration [GENEPIO:0100931] - Lavage [OBI:0600044] - Bronchoalveolar lavage [GENEPIO:0100032] - Gastric lavage [GENEPIO:0100033] - Necropsy [MMO:0000344] - Phlebotomy [NCIT:C28221] - Rinsing for specimen collection [GENEPIO_0002116] - Scooping [GENEPIO:0100932] - Sediment collection [GENEPIO:0100933] - Soil coring [GENEPIO:0100934] - Weep fluid collection (pouring) [GENEPIO:0101003] - -sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu microliter (uL) [UO:0000101] - milliliter (mL) [UO:0000098] - liter (L) [UO:0000099] - -residual_sample_status menu ResidualSampleStatusMenu Residual sample remaining (some sample left) [GENEPIO:0101087] - No residual sample (sample all used) [GENEPIO:0101088] - Residual sample status unkown [GENEPIO:0101089] - -sample_storage_duration_unit menu SampleStorageDurationUnitMenu Second [UO:0000010] - Minute [UO:0000031] - Hour [UO:0000032] - Day [UO:0000033] - Week [UO:0000034] - Month [UO:0000035] - Year [UO:0000036] - -nucelic_acid_storage_duration_unit menu NucelicAcidStorageDurationUnitMenu Second [UO:0000010] - Minute [UO:0000031] - Hour [UO:0000032] - Day [UO:0000033] - Week [UO:0000034] - Month [UO:0000035] - Year [UO:0000036] - -food_packaging menu FoodPackagingMenu Bag, sack or pouch [FOODON:03490197] - Paper bag, sack or pouch [FOODON:03490120] - Plastic bag, sack or pouch [FOODON:03490166] - Plastic shrink wrap [FOODON:03490137] - Plastic wrapper [FOODON:03490128] - Bottle or jar [FOODON:03490203] - Can (container) [FOODON:03490204] - Paper container, treated [FOODON:03490330] - Paper container, untreated [FOODON:03490334] - Plastic tray or pan [FOODON:03490126] - - -host (common name) menu HostCommonNameMenu Bird [NCBITaxon:8782] - Chicken [NCBITaxon:9031] - Seabird [FOODON:00004504] - Cormorant [NCBITaxon:9206] - Double Crested Cormorant [NCBITaxon:56069] - Crane [NCBITaxon:9109] - Whooping Crane [NCBITaxon:9117] - Gull (Seagull) [NCBITaxon:8911] - Glaucous-winged Gull [NCBITaxon:119606] - Great Black-backed Gull [NCBITaxon:8912] - Herring Gull [NCBITaxon:35669] - Ring-billed Gull [NCBITaxon:126683] - Eider [NCBITaxon:50366] - Common Eider [NCBITaxon:76058] - Turkey [NCBITaxon:9103] - Fish [FOODON:03411222] - Rainbow Trout [NCBITaxon:8022] - Sablefish [NCBITaxon:229290] - Salmon [FOODON:00003473] - Atlantic Salmon [NCBITaxon:8030] - Chinook salmon [NCBITaxon:74940] - Coho Salmon [NCBITaxon:8019] - Mammal [FOODON:03411134] - Companion animal [FOODON:03000300] - Cow [NCBITaxon:9913] - Human [NCBITaxon:9606] - Pig [NCBITaxon:9823] - Sheep [NCBITaxon:9940] - Shellfish [FOODON:03411433] - Atlantic Lobster [NCBITaxon:6706] - Atlantic Oyster [NCBITaxon:6565] - Blue Mussel [NCBITaxon:6550] - - -host (scientific name) menu HostScientificNameMenu Anoplopoma fimbria [NCBITaxon:229290] - Bos taurus [NCBITaxon:9913] - Crassostrea virginica [NCBITaxon:6565] - Gallus gallus [NCBITaxon:9031] - Grus americana [NCBITaxon:9117] - Homarus americanus [NCBITaxon:6706] - Homo sapiens [NCBITaxon:9606] - Larus argentatus [NCBITaxon:35669] - Larus delawarensis [NCBITaxon:126683] - Larus glaucescens [NCBITaxon:119606] - Larus marinus [NCBITaxon:8912] - Meleagris gallopavo [NCBITaxon:9103] - Mytilus edulis [NCBITaxon:6550] - Oncorhynchus kisutch [NCBITaxon:8019] - Oncorhynchus mykiss [NCBITaxon:8022] - Oncorhynchus tshawytscha [NCBITaxon:74940] - Ovis aries [NCBITaxon:9940] - Phalacrocorax auritus [NCBITaxon:56069] - Salmo salar [NCBITaxon:8030] - Somateria mollissima [NCBITaxon:76058] - Sus scrofa domesticus [NCBITaxon:9825] - - -host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) - Calf [FOODON:03411349] - Dry cow [FOODON:00004411] - Feeder cow [FOODON:00004292] - Finisher cow [FOODON:00004293] - Milker cow [FOODON:03411201] - Stocker cow [FOODON:00004294] - Weanling cow [FOODON:00004295] - Cow (by sex/reproductive stage) (organizational term) - Bull [FOODON:00000015] - Cow [NCBITaxon:9913] - Freemartin [FOODON:00004296] - Heifer [FOODON:00002518] - Steer [FOODON:00002531] - Pig (by age/production stage) (organizational term) - Finisher pig [FOODON:00003371] - Grower pig [FOODON:00003370] - Nursing pig [FOODON:00004297 ] - Pig [NCBITaxon:9823] - Piglet [FOODON:00003952] - Weanling (weaner) pig [FOODON:00003373] - Pig (by sex/reproductive stage) (organizational term) - Barrow [FOODON:03411280] - Boar [FOODON:03412248] - Gilt [FOODON:00003369] - Sow [FOODON:00003333] - Poultry or game bird [FOODON:03411563] - Broiler or fryer chicken [FOODON:03411198] - Capon [FOODON:03411711] - Chick [FOODON:00004299] - Chicken [NCBITaxon:9031] - Egg [UBERON:0007379] - Hatchling [FOODON:00004300] - Hen [FOODON:00003282] - Layer chicken [FOODON:00004301] - Layer turkey [FOODON:00004302] - Poult [FOODON:00002962] - Pullet [FOODON:00004303] - Rooster [FOODON:03411714] - Tom (Gobbler) [FOODON:00004304 ] - Turkey [NCBITaxon:9103] - Sheep [NCBITaxon:9940] - Ram [FOODON:00004305] - Wether sheep [FOODON:00004306] - Ewe [FOODON:03412610] - Lamb [FOODON:03411669] - Fish [FOODON:03411222] - Fish egg [FOODON_00004319] - Fry (fish) [FOODON_00004318] - Juvenile fish [FOODON_00004317] - - -host_age_bin menu HostAgeBinMenu First winter [GENEPIO:0100684] - First summer [GENEPIO:0100685] - Second winter [GENEPIO:0100686] - Second summer [GENEPIO:0100687] - Third winter [GENEPIO:0100688] - Third summer [GENEPIO:0100689] - - -isolated_by menu IsolatedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - - -organism menu OrganismMenu Acinetobacter [NCBITaxon:469] - Acinetobacter baumannii [NCBITaxon:470] - Acinetobacter bereziniae [NCBITaxon:106648] - Acinetobacter ursingii [NCBITaxon:108980] - Aeromonas [NCBITaxon:642] - Aeromonas allosaccharophila [NCBITaxon:656] - Aeromonas hydrophila [NCBITaxon:644] - Aeromonas rivipollensis [NCBITaxon:948519] - Aeromonas salmonicida [NCBITaxon:645] - Campylobacter [NCBITaxon:194] - Campylobacter coli [NCBITaxon:195] - Campylobacter jejuni [NCBITaxon:197] - Campylobacter lari [NCBITaxon:201] - Citrobacter [NCBITaxon:544] - Citrobacter braakii [NCBITaxon:57706] - Citrobacter freundii [NCBITaxon:546] - Citrobacter gillenii [NCBITaxon:67828] - Clostridioides [NCBITaxon:1870884] - Clostridioides difficile [NCBITaxon:1496] - Clostridium [NCBITaxon:1485] - Clostridium perfringens [NCBITaxon:1502] - Clostridium sporogenes [NCBITaxon:1509] - Comamonas [NCBITaxon:283] - Comamonas aquatica [NCBITaxon:225991] - Enterobacter [NCBITaxon:547] - Enterobacter asburiae [NCBITaxon:61645] - Enterobacter cancerogenus [NCBITaxon:69218] - Enterobacter cloacae [NCBITaxon:550] - Enterobacter hormaechei [NCBITaxon:158836] - Enterobacter kobei [NCBITaxon:208224] - Enterobacter roggenkampii [NCBITaxon:1812935] - Enterobacter sp. [NCBITaxon:42895] - Lelliottia amnigena [NCBITaxon:61646] - Pluralibacter gergoviae [NCBITaxon:61647] - Enterococcus [NCBITaxon:1350] - Enterococcus asini [NCBITaxon:57732] - Enterococcus avium [NCBITaxon:33945] - Enterococcus caccae [NCBITaxon:317735] - Enterococcus canis [NCBITaxon:214095] - Enterococcus casseliflavus [NCBITaxon:37734] - Enterococcus cecorum [NCBITaxon:44008] - Enterococcus dispar [NCBITaxon:44009] - Enterococcus durans [NCBITaxon:53345] - Enterococcus faecium [NCBITaxon:1352] - Enterococcus faecalis [NCBITaxon:1351] - Enterococcus gallinarum [NCBITaxon:1353] - Enterococcus hirae [NCBITaxon:1354] - Enterococcus malodoratus [NCBITaxon:71451] - Enterococcus mundtii [NCBITaxon:53346] - Enterococcus ratti [NCBITaxon:150033] - Enterococcus saccharolyticus [NCBITaxon:41997] - Enterococcus thailandicus [NCBITaxon:417368] - Enterococcus villorum [NCBITaxon:112904] - Escherichia [NCBITaxon:561] - Escherichia coli [NCBITaxon:562] - Escherichia fergusonii [NCBITaxon:564] - Exiguobacterium [NCBITaxon:33986] - Exiguobacterium oxidotolerans [NCBITaxon:223958] - Exiguobacterium sp. [NCBITaxon:44751] - Klebsiella [NCBITaxon:570] - Klebsiella aerogenes [NCBITaxon:548] - Klebsiella michiganensis [NCBITaxon:1134687] - Klebsiella oxytoca [NCBITaxon:571] - Klebsiella pneumoniae [NCBITaxon:573] - Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] - Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] - Kluyvera [NCBITaxon:579] - Kluyvera intermedia [NCBITaxon:61648] - Kosakonia [NCBITaxon:1330547] - Kosakonia cowanii [NCBITaxon:208223] - Leclercia [NCBITaxon:83654] - Leclercia adecarboxylata [NCBITaxon:83655] - Listeria [NCBITaxon:1637] - Listeria monocytogenes [NCBITaxon:1639] - Ochrobactrum [NCBITaxon:528] - Ochrobactrum sp. [NCBITaxon:42190] - Pantoea [NCBITaxon:53335] - Pantoea ananatis [NCBITaxon:553] - Pantoea sp. [NCBITaxon:69393] - Photobacterium [NCBITaxon:657] - Photobacterium indicum[NCBITaxon:81447] - Photobacterium sp. [NCBITaxon:660] - Providencia [NCBITaxon:586] - Providencia rettgeri [NCBITaxon:587] - Pseudoalteromonas [NCBITaxon:53246] - Pseudoalteromonas tetraodonis [NCBITaxon:43659] - Pseudomonas [NCBITaxon:286] - Pseudomonas aeruginosa [NCBITaxon:287] - Pseudomonas fluorescens [NCBITaxon:294] - Pseudomonas soli [NCBITaxon:1306993] - Pseudomonas sp. [NCBITaxon:306] - Psychrobacter [NCBITaxon:497] - Psychrobacter faecalis [NCBITaxon:180588] - Psychrobacter nivimaris [NCBITaxon:281738] - Psychrobacter sp. [NCBITaxon:56811] - Rahnella [NCBITaxon:34037] - Rahnella aquatilis [NCBITaxon:34038] - Rahnella sp. [NCBITaxon:1873497] - Raoultella [NCBITaxon:160674] - Raoultella ornithinolytica [NCBITaxon:54291] - Raoultella planticola [NCBITaxon:575] - Salmonella enterica [NCBITaxon:28901] - Salmonella enterica subsp. enterica [NCBITaxon:59201] - Salmonella enterica subsp. arizonae [NCBITaxon:59203] - Serratia [NCBITaxon:613] - Shewanella [NCBITaxon:22] - Shewanella pealeana [NCBITaxon:70864] - Shewanella putrefaciens [NCBITaxon:24] - Shewanella oncorhynchi [NCBITaxon:2726434] - Shewanella sp. [NCBITaxon:50422] - Staphylococcus [NCBITaxon:1279] - Staphylococcus aureus [NCBITaxon:1280] - Streptococcus [NCBITaxon:1301] - Streptococcus alactolyticus [NCBITaxon:29389] - Streptococcus bovis [NCBITaxon:1335] - Streptococcus equinus [NCBITaxon:1335] - Streptococcus gallolyticus [NCBITaxon:315405] - Streptococcus infantarius [NCBITaxon:102684] - Streptococcus lutetiensis [NCBITaxon:150055] - Streptococcus macedonicus [NCBITaxon:59310] - Streptococcus pasteurianus [NCBITaxon:197614] - Streptococcus suis [NCBITaxon:1307] - Vibrio [NCBITaxon:662] - Vibrio cholerae [NCBITaxon:666] - Vibrio parahaemolyticus [NCBITaxon:670] - -taxonomic_identification_process menu TaxonomicIdentificationProcessMenu Whole genome sequencing assay [OBI:0002117] - 16S ribosomal gene sequencing assay [OBI:0002763] - PCR assay [OBI:0002740] - Comparative phenotypic assessment [OBI:0001546] - Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] - - -sequenced_by menu SequencedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - McGill University [GENEPIO:0101103] - - -purpose_of_sequencing menu PurposeOfSequencingMenu Cluster/Outbreak investigation [GENEPIO:0100001] - Diagnostic testing [GENEPIO:0100002] - Environmental testing [GENEPIO:0100548] - Research [GENEPIO:0100003] - Clinical trial [GENEPIO:0100549] - Field experiment [GENEPIO:0100550] - Protocol testing experiment [GENEPIO:0100024] - Survey study [GENEPIO:0100582] - Surveillance [GENEPIO:0100004] - - -sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] - Pacific Biosciences [GENEPIO:0001927] - Ion Torrent [GENEPIO:0002683] - Oxford Nanopore Technologies [OBI:0002755] - BGI Genomics [GENEPIO:0004324] - MGI [GENEPIO:0004325] - - -sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. - Illumina Genome Analyzer [OBI:0002128] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. - Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology - Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. - Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. - Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. - Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. - Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. - Illumina HiSeq X Ten [OBI:0002129] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Illumina HiSeq 1500 [OBI:0003386] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. - Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. - Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. - Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. - Illumina NovaSeq 6000 [OBI:0002630] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - Illumina MiniSeq [OBI:0003114] A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. - Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. - Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. - Illumina NextSeq 1000 [OBI:0003606] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. - Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. - PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. - PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. - PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - PacBio Sequel [OBI:0002632] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - PacBio Sequel II [OBI:0002633] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. - Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. - Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. - Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. - Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. - Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. - Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. - Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. - Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual - Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - BGISEQ [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. - BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". - DNBSEQ [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. - DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. - DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. - DNBSEQ-G400 FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. - DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. - - -sequencing_assay_type menu SequencingAssayTypeMenu Amplicon sequencing assay [OBI:0002767] - 16S ribosomal gene sequencing assay [OBI:0002763] - Whole genome sequencing assay [OBI:0002117] - Whole metagenome sequencing assay [OBI:0002623] - Whole virome sequencing assay [OBI:0002768] - -genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu Hybrid selection method (bait-capture) [GENEPIO:0001950] - rRNA depletion method [GENEPIO:0101020] - - -sequence_submitted_by menu SequenceSubmittedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - McGill University [GENEPIO:0101103] - -quality_control_determination menu QualityControlDeterminationMenu No quality control issues identified [GENEPIO:0100562] - Sequence passed quality control [GENEPIO:0100563] - Sequence failed quality control [GENEPIO:0100564] - Minor quality control issues identified [GENEPIO:0100565] - Sequence flagged for potential quality control issues [GENEPIO:0100566] - Quality control not performed [GENEPIO:0100567] - -quality _control_issues menu QualityControlIssuesMenu Low quality sequence [GENEPIO:0100568] - Sequence contaminated [GENEPIO:0100569] - Low average genome coverage [GENEPIO:0100570] - Low percent genome captured [GENEPIO:0100571] - Read lengths shorter than expected [GENEPIO:0100572] - Sequence amplification artifacts [GENEPIO:0100573] - Low signal to noise ratio [GENEPIO:0100574] - Low coverage of characteristic mutations [GENEPIO:0100575] - - -attribute_package menu AttributePackageMenu Pathogen.cl [GENEPIO:0001835] - Pathogen.env [GENEPIO:0100581] - - -experimental_intervention menu ExperimentalInterventionMenu Addition of substances to food/water [GENEPIO:0100536] - Antimicrobial pre-treatment [GENEPIO:0100537] - Certified animal husbandry practices [GENEPIO:0100538] - Certified organic farming practices [GENEPIO:0100539] - Change in storage conditions [GENEPIO:0100540] - Cleaning/disinfection [GENEPIO:0100541] - Extended downtime between activities [GENEPIO:0100542] - Fertilizer pre-treatment [GENEPIO:0100543] - Logistic slaughter [GENEPIO:0100545] - Microbial pre-treatment [GENEPIO:0100546] - Probiotic pre-treatment [GENEPIO:0100547] - Vaccination [NCIT:C15346] - - -AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] - Health Canada (HC) [GENEPIO:0100554] - Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] - - -antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] not defined - Intermediate antimicrobial phenotype [ARO:3004300] intermediate - Indeterminate antimicrobial phenotype [GENEPIO:0100585] indeterminate - Nonsusceptible antimicrobial phenotype [ARO:3004303] nonsusceptible - Resistant antimicrobial phenotype [ARO:3004301] resistant - Susceptible antimicrobial phenotype [ARO:3004302] susceptible - Susceptible dose dependent antimicrobial phenotype [ARO:3004304] susceptible-dose dependent - - -antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] mg/L - millimetre (mm) [UO:0000016] mm - microgram per millilitre (ug/mL) [UO:0000274] - - -antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] < - less than or equal to (<=) [GENEPIO:0001003] <= - equal to (==) [GENEPIO:0001004] == - greater than (>) [GENEPIO:0001006] > - greater than or equal to (>=) [GENEPIO:0001005] >= - - -antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion - Antimicrobial gradient (E-test) [NCIT:85596] - Agar dilution [ARO:3004411] agar dilution - Broth dilution [ARO:3004397] broth dilution - - -antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] BIOMIC - Microscan [ARO:3004400] Microscan - Phoenix [ARO:3004401] Phoenix - Sensititre [ARO:3004402] Sensititre - Vitek System [ARO:3004403] Vitek - - -antimicrobial_vendor_name menu AntimicrobialVendorNameMenu Becton Dickinson [ARO:3004405] Becton Dickinson - bioMérieux [ARO:3004406] Biomérieux - Omron [ARO:3004408] Omron - Siemens [ARO:3004407] Siemens - Trek [ARO:3004409] Trek - - -antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] BSAC - Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] CLSI - Deutsches Institut für Normung (DIN) [ARO:3004367] DIN - European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] EUCAST - National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] NARMS - National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] NCCLS - Société Française de Microbiologie (SFM) [ARO:3004369] SFM - Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] SIR - Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG - - -Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin amikacin - amoxicillin-clavulanic_acid amoxicillin-clavulanic acid - ampicillin ampicillin - azithromycin azithromycin - cefazolin cefazolin - cefepime cefepime - cefotaxime cefotaxime - cefotaxime-clavulanic_acid cefotaxime-clavulanic acid - cefoxitin cefoxitin - cefpodoxime cefpodoxime - ceftazidime ceftazidime - ceftazidime-clavulanic_acid ceftazidime-clavulanic acid - ceftiofur ceftiofur - ceftriaxone ceftriaxone - cephalothin cephalothin - chloramphenicol chloramphenicol - ciprofloxacin ciprofloxacin - clindamycin clindamycin - doxycycline doxycycline - enrofloxacin enrofloxacin - erythromycin erythromycin - florfenicol florfenicol - gentamicin gentamicin - imipenem imipenem - kanamycin kanamycin - levofloxacin levofloxacin - linezolid linezolid - meropenem meropenem - nalidixic_acid nalidixic acid - nitrofurantoin nitrofurantoin - norfloxacin norfloxacin - oxolinic-acid oxolinic-acid - oxytetracycline oxytetracycline - piperacillin piperacillin - piperacillin-tazobactam piperacillin-tazobactam - polymyxin-b polymyxin-b - quinupristin-dalfopristin quinupristin-dalfopristin - streptomycin streptomycin - sulfisoxazole sulfisoxazole - telithromycin telithromycin - tetracycline tetracycline - tigecycline tigecycline - trimethoprim-sulfamethoxazole trimethoprim-sulfamethoxazole \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM + +null value menu NullValueMenu Not Applicable [GENEPIO:0001619] Not applicable + Missing [GENEPIO:0001618] Missing + Not Collected [GENEPIO:0001620] Not collected + Not Provided [GENEPIO:0001668] Not provided + Restricted Access [GENEPIO:0001810] Restricted access + +sample_collected_by menu SampleCollectedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + University of Manitoba (UM) [GENEPIO:0004434] + + +purpose_of_sampling menu PurposeOfSamplingMenu Cluster/Outbreak investigation [GENEPIO:0100001] + Diagnostic testing [GENEPIO:0100002] + Environmental testing [GENEPIO:0100548] + Research [GENEPIO:0100003] + Clinical trial [GENEPIO:0100549] + Field experiment [GENEPIO:0100550] + Survey study [GENEPIO:0100582] + Surveillance [GENEPIO:0100004] + + +presampling_activity menu PresamplingActivityMenu Addition of substances to food/water [GENEPIO:0100536] + Antimicrobial pre-treatment [GENEPIO:0100537] + Certified animal husbandry practices [GENEPIO:0100538] + Certified humane animal husbandry practices [GENEPIO:0100894] + Certified organic farming practices [GENEPIO:0100539] + Conventional farming practices [GENEPIO:0100895] + Change in storage conditions [GENEPIO:0100540] + Cleaning/disinfection [GENEPIO:0100541] + Extended downtime between activities [GENEPIO:0100542] + Fertilizer pre-treatment [GENEPIO:0100543] + Genetic mutation [GENEPIO:0100544[ + Logistic slaughter [GENEPIO:0100545] + Microbial pre-treatment [GENEPIO:0100546] + Probiotic pre-treatment [GENEPIO:0100547] + Vaccination [NCIT:C15346] + Wastewater treatment process [ENVO:06105300] A recycling process during which wastewater is treated. + Wastewater filtration [GENEPIO:0100881] A wastewater treatment process which removes solid particles from wastewater by means of filtration. + Wastewater grit removal [GENEPIO:0100882] A wastewater treatment process which removes sand, silt, and grit from wastewater. + Wastewater microbial treatment [GENEPIO:0100883] A wastewater treatment process in which microbes are used to degrade the biological material in wastewater. + Wastewater primary sedimentation [GENEPIO:0100884] A wastewater treatment process which removes solids and large particles from influent through gravitational force. + Wastewater secondary sedimentation [GENEPIO:0100885] A wastewater treatment process which removes biomass produced in aeration from influent through gravitational force. + +experimental_specimen_role_type menu ExperimentalSpecimenRoleTypeMenu Positive experimental control [GENEPIO:0101018] + Negative experimental control [GENEPIO:0101019] + Technical replicate [EFO:0002090] + Biological replicate [EFO:0002091] + + +specimen_processing menu SpecimenProcessingMenu Biological replicate process [GENEPIO:0101022] + Samples pooled [OBI:0600016] + Technical replicate process [GENEPIO:0101021] + Isolated from single source [OBI:0002079] + + +geo_loc_name (country) menu GeoLocNameCountryMenu Afghanistan [GAZ:00006882] + Albania [GAZ:00002953] + Algeria [GAZ:00000563] + American Samoa [GAZ:00003957] + Andorra [GAZ:00002948] + Angola [GAZ:00001095] + Anguilla [GAZ:00009159] + Antarctica [GAZ:00000462] + Antigua and Barbuda [GAZ:00006883] + Argentina [GAZ:00002928] + Armenia [GAZ:00004094] + Aruba [GAZ:00004025] + Ashmore and Cartier Islands [GAZ:00005901] + Australia [GAZ:00000463] + Austria [GAZ:00002942] + Azerbaijan [GAZ:00004941] + Bahamas [GAZ:00002733] + Bahrain [GAZ:00005281] + Baker Island [GAZ:00007117] + Bangladesh [GAZ:00003750] + Barbados [GAZ:00001251] + Bassas da India [GAZ:00005810] + Belarus [GAZ:00006886] + Belgium [GAZ:00002938] + Belize [GAZ:00002934] + Benin [GAZ:00000904] + Bermuda [GAZ:00001264] + Bhutan [GAZ:00003920] + Bolivia [GAZ:00002511] + Borneo [GAZ:00025355] + Bosnia and Herzegovina [GAZ:00006887] + Botswana [GAZ:00001097] + Bouvet Island [GAZ:00001453] + Brazil [GAZ:00002828] + British Virgin Islands [GAZ:00003961] + Brunei [GAZ:00003901] + Bulgaria [GAZ:00002950] + Burkina Faso [GAZ:00000905] + Burundi [GAZ:00001090] + Cambodia [GAZ:00006888] + Cameroon [GAZ:00001093] + Canada [GAZ:00002560] + Cape Verde [GAZ:00001227] + Cayman Islands [GAZ:00003986] + Central African Republic [GAZ:00001089] + Chad [GAZ:00000586] + Chile [GAZ:00002825] + China [GAZ:00002845] + Christmas Island [GAZ:00005915] + Clipperton Island [GAZ:00005838] + Cocos Islands [GAZ:00009721] + Colombia [GAZ:00002929] + Comoros [GAZ:00005820] + Cook Islands [GAZ:00053798] + Coral Sea Islands [GAZ:00005917] + Costa Rica [GAZ:00002901] + Cote d'Ivoire [GAZ:00000906] + Croatia [GAZ:00002719] + Cuba [GAZ:00003762] + Curacao [GAZ:00012582] + Cyprus [GAZ:00004006] + Czech Republic [GAZ:00002954] + Democratic Republic of the Congo [GAZ:00001086] + Denmark [GAZ:00005852] + Djibouti [GAZ:00000582] + Dominica [GAZ:00006890] + Dominican Republic [GAZ:00003952] + Ecuador [GAZ:00002912] + Egypt [GAZ:00003934] + El Salvador [GAZ:00002935] + Equatorial Guinea [GAZ:00001091] + Eritrea [GAZ:00000581] + Estonia [GAZ:00002959] + Eswatini [GAZ:00001099] + Ethiopia [GAZ:00000567] + Europa Island [GAZ:00005811] + Falkland Islands (Islas Malvinas) [GAZ:00001412] + Faroe Islands [GAZ:00059206] + Fiji [GAZ:00006891] + Finland [GAZ:00002937] + France [GAZ:00003940] + French Guiana [GAZ:00002516] + French Polynesia [GAZ:00002918] + French Southern and Antarctic Lands [GAZ:00003753] + Gabon [GAZ:00001092] + Gambia [GAZ:00000907] + Gaza Strip [GAZ:00009571] + Georgia [GAZ:00004942] + Germany [GAZ:00002646] + Ghana [GAZ:00000908] + Gibraltar [GAZ:00003987] + Glorioso Islands [GAZ:00005808] + Greece [GAZ:00002945] + Greenland [GAZ:00001507] + Grenada [GAZ:02000573] + Guadeloupe [GAZ:00067142] + Guam [GAZ:00003706] + Guatemala [GAZ:00002936] + Guernsey [GAZ:00001550] + Guinea [GAZ:00000909] + Guinea-Bissau [GAZ:00000910] + Guyana [GAZ:00002522] + Haiti [GAZ:00003953] + Heard Island and McDonald Islands [GAZ:00009718] + Honduras [GAZ:00002894] + Hong Kong [GAZ:00003203] + Howland Island [GAZ:00007120] + Hungary [GAZ:00002952] + Iceland [GAZ:00000843] + India [GAZ:00002839] + Indonesia [GAZ:00003727] + Iran [GAZ:00004474] + Iraq [GAZ:00004483] + Ireland [GAZ:00002943] + Isle of Man [GAZ:00052477] + Israel [GAZ:00002476] + Italy [GAZ:00002650] + Jamaica [GAZ:00003781] + Jan Mayen [GAZ:00005853] + Japan [GAZ:00002747] + Jarvis Island [GAZ:00007118] + Jersey [GAZ:00001551] + Johnston Atoll [GAZ:00007114] + Jordan [GAZ:00002473] + Juan de Nova Island [GAZ:00005809] + Kazakhstan [GAZ:00004999] + Kenya [GAZ:00001101] + Kerguelen Archipelago [GAZ:00005682] + Kingman Reef [GAZ:00007116] + Kiribati [GAZ:00006894] + Kosovo [GAZ:00011337] + Kuwait [GAZ:00005285] + Kyrgyzstan [GAZ:00006893] + Laos [GAZ:00006889] + Latvia [GAZ:00002958] + Lebanon [GAZ:00002478] + Lesotho [GAZ:00001098] + Liberia [GAZ:00000911] + Libya [GAZ:00000566] + Liechtenstein [GAZ:00003858] + Line Islands [GAZ:00007144] + Lithuania [GAZ:00002960] + Luxembourg [GAZ:00002947] + Macau [GAZ:00003202] + Madagascar [GAZ:00001108] + Malawi [GAZ:00001105] + Malaysia [GAZ:00003902] + Maldives [GAZ:00006924] + Mali [GAZ:00000584] + Malta [GAZ:00004017] + Marshall Islands [GAZ:00007161] + Martinique [GAZ:00067143] + Mauritania [GAZ:00000583] + Mauritius [GAZ:00003745] + Mayotte [GAZ:00003943] + Mexico [GAZ:00002852] + Micronesia [GAZ:00005862] + Midway Islands [GAZ:00007112] + Moldova [GAZ:00003897] + Monaco [GAZ:00003857] + Mongolia [GAZ:00008744] + Montenegro [GAZ:00006898] + Montserrat [GAZ:00003988] + Morocco [GAZ:00000565] + Mozambique [GAZ:00001100] + Myanmar [GAZ:00006899] + Namibia [GAZ:00001096] + Nauru [GAZ:00006900] + Navassa Island [GAZ:00007119] + Nepal [GAZ:00004399] + Netherlands [GAZ:00002946] + New Caledonia [GAZ:00005206] + New Zealand [GAZ:00000469] + Nicaragua [GAZ:00002978] + Niger [GAZ:00000585] + Nigeria [GAZ:00000912] + Niue [GAZ:00006902] + Norfolk Island [GAZ:00005908] + North Korea [GAZ:00002801] + North Macedonia [GAZ:00006895] + North Sea [GAZ:00002284] + Northern Mariana Islands [GAZ:00003958] + Norway [GAZ:00002699] + Oman [GAZ:00005283] + Pakistan [GAZ:00005246] + Palau [GAZ:00006905] + Panama [GAZ:00002892] + Papua New Guinea [GAZ:00003922] + Paracel Islands [GAZ:00010832] + Paraguay [GAZ:00002933] + Peru [GAZ:00002932] + Philippines [GAZ:00004525] + Pitcairn Islands [GAZ:00005867] + Poland [GAZ:00002939] + Portugal [GAZ:00004126] + Puerto Rico [GAZ:00006935] + Qatar [GAZ:00005286] + Republic of the Congo [GAZ:00001088] + Reunion [GAZ:00003945] + Romania [GAZ:00002951] + Ross Sea [GAZ:00023304] + Russia [GAZ:00002721] + Rwanda [GAZ:00001087] + Saint Helena [GAZ:00000849] + Saint Kitts and Nevis [GAZ:00006906] + Saint Lucia [GAZ:00006909] + Saint Pierre and Miquelon [GAZ:00003942] + Saint Martin [GAZ:00005841] + Saint Vincent and the Grenadines [GAZ:02000565] + Samoa [GAZ:00006910] + San Marino [GAZ:00003102] + Sao Tome and Principe [GAZ:00006927] + Saudi Arabia [GAZ:00005279] + Senegal [GAZ:00000913] + Serbia [GAZ:00002957] + Seychelles [GAZ:00006922] + Sierra Leone [GAZ:00000914] + Singapore [GAZ:00003923] + Sint Maarten [GAZ:00012579] + Slovakia [GAZ:00002956] + Slovenia [GAZ:00002955] + Solomon Islands [GAZ:00005275] + Somalia [GAZ:00001104] + South Africa [GAZ:00001094] + South Georgia and the South Sandwich Islands [GAZ:00003990] + South Korea [GAZ:00002802] + South Sudan [GAZ:00233439] + Spain [GAZ:00003936] + Spratly Islands [GAZ:00010831] + Sri Lanka [GAZ:00003924] + State of Palestine [GAZ:00002475] + Sudan [GAZ:00000560] + Suriname [GAZ:00002525] + Svalbard [GAZ:00005396] + Swaziland [GAZ:00001099] + Sweden [GAZ:00002729] + Switzerland [GAZ:00002941] + Syria [GAZ:00002474] + Taiwan [GAZ:00005341] + Tajikistan [GAZ:00006912] + Tanzania [GAZ:00001103] + Thailand [GAZ:00003744] + Timor-Leste [GAZ:00006913] + Togo [GAZ:00000915] + Tokelau [GAZ:00260188] + Tonga [GAZ:00006916] + Trinidad and Tobago [GAZ:00003767] + Tromelin Island [GAZ:00005812] + Tunisia [GAZ:00000562] + Turkey [GAZ:00000558] + Turkmenistan [GAZ:00005018] + Turks and Caicos Islands [GAZ:00003955] + Tuvalu [GAZ:00009715] + United States of America [GAZ:00002459] + Uganda [GAZ:00001102] + Ukraine [GAZ:00002724] + United Arab Emirates [GAZ:00005282] + United Kingdom [GAZ:00002637] + Uruguay [GAZ:00002930] + Uzbekistan [GAZ:00004979] + Vanuatu [GAZ:00006918] + Venezuela [GAZ:00002931] + Viet Nam [GAZ:00003756] + Virgin Islands [GAZ:00003959] + Wake Island [GAZ:00007111] + Wallis and Futuna [GAZ:00007191] + West Bank [GAZ:00009572] + Western Sahara [GAZ:00000564] + Yemen [GAZ:00005284] + Zambia [GAZ:00001107] + Zimbabwe [GAZ:00001106] + + +geo_loc_name (state/province/region) menu GeoLocNameStateProvinceRegionMenu Atlantic region (Canada) [wikidata:Q246972] + New Brunswick [GAZ:00002570] + Newfoundland & Labrador [GAZ:00002567] + Nova Scotia [GAZ:00002565] + Prince Edward Island [GAZ:00002572] + Central region (Canada) [wikidata:Q1048064] + Ontario [GAZ:00002563] + Quebec [GAZ:00002569] + Northern region (Canada) [wikidata:Q764146] + Northwest Territories [GAZ:00002575] + Nunuvut [GAZ:00002574] + Yukon [GAZ:00002576] + Pacific region (Canada) [wikidata:Q122953299] + British Columbia [GAZ:00002562] + Prairie region (Canada) [wikidata:Q1364746] + Alberta [GAZ:00002566] + Manitoba [GAZ:00002571] + Saskatchewan [GAZ:00002564] + + +sample_collection_date_precision menu SampleCollectionDatePrecisionMenu year [UO:0000036] + month [UO:0000035] + day [UO:0000033] + + +environmental_site menu EnvironmentalSiteMenu Abattoir [ENVO:01000925] + Agricultural Field [ENVO:00000114] + Alluvial fan [ENVO:00000314] + Animal cage [ENVO:01000922] + Aquarium [ENVO:00002196] + Artificial wetland [ENVO:03501406] + Breeding ground [ENVO:03501441] + Building [ENVO:00000073] + Barn [ENVO:03501257] + Breeder barn [ENVO:03501383] + Broiler barn [ENVO:03501386] + Sheep barn [ENVO:03501385] + Biodome [ENVO:03501397] + Cottage [ENVO:03501393] + Dairy [ENVO:00003862] + Hospital [ENVO:00002173] + Laboratory facility [ENVO:01001406] + Pigsty [ENVO:03501413] + Building part (organizational term) + Air intake [ENVO:03501380] + Animal pen [ENVO:03501387] + Building floor [ENVO:01000486] + Building wall [ENVO:01000465] + Countertop [ENVO:03501404] + Shelf [ENVO:03501403] + Stall [EOL:0001903] + Window sill [ENVO:03501381] + Creek [ENVO:03501405] + Ditch [ENVO:00000037] A small, human-made channel which has been dug for draining or irrigating the land. + Drainage ditch [ENVO:00000140] A ditch that collects water from the surrounding land. + Irrigation ditch [ENVO:00000139] A ditch that supplies water to surrounding land. + Farm [ENVO:00000078] + Beef farm [ENVO:03501443] + Breeder farm [ENVO:03501384] + Dairy farm [ENVO:03501416] + Feedlot [ENVO:01000627] + Beef cattle feedlot [ENVO:03501444] + Fish farm [ENVO:00000294] + Research farm [ENVO:03501417] + Central Experimental Farm [GAZ:00004603] Central Experimental Farm + Freshwater environment [ENVO:01000306] + Hatchery [ENVO:01001873] + Poultry hatchery [ENVO:01001874] + Lake [ENVO:00000020] + Manure digester facility [ENVO:03501422] + Manure lagoon (Anaerobic lagoon) [ENVO:03501423] + Manure pit [ENVO:01001872] + Marine environment [ENVO:01000320] + Benthic zone [ENVO:03501440] + Pelagic zone [ENVO:00000208] + Park [ENVO:00000562] + Plumbing drain [ENVO:01000924 ] + Pond [ENVO:00000033] + Reservoir [ENVO:00000025] + Irrigation reservoir [ENVO:00000450] + Retail environment [ENVO:01001448] + Shop [ENVO:00002221] + Butcher shop [ENVO:03501396] + Pet store [ENVO:03501395] + Supermarket [ENVO:01000984] + River [ENVO:00000022] + Roost (bird) [ENVO:03501439] + Rural area [ENVO:01000772] + Slough [ENVO:03501438] + Stream [ENVO:00000023] + Trailer [ENVO:03501394] + Tributary [ENVO:00000495] + Truck [ENVO:01000602] + Urban area [ENVO:03501437] + Wastewater treatment plant [ENVO:00002272] A plant in which wastewater is treated. + Water surface [ENVO:01001191] + Woodland area [ENVO:00000109] + Zoo [ENVO:00010625] + + +water_depth_units menu WaterDepthUnitsMenu centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + kilometer (km) [UO:0010066] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + + +sediment_depth_units menu SedimentDepthUnitsMenu centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + kilometer (km) [UO:0010066] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + + +air_temperature_units menu AirTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] + degree Celsius (C) [UO:0000027] + + +water_temperature_units menu WaterTemperatureUnitsMenu degree Fahrenheit (F) [UO:0000195] + degree Celsius (C) [UO:0000027] + +"precipitation_measurement_unit menu +" "PrecipitationMeasurementUnitMenu +" millimeter (mm) [UO:0000016] + centimeter (cm) [UO:0000015] + meter (m) [UO:0000008] + inch (in) [UO:0010011] + foot (ft) [UO:0010013] + +available_data_types menu AvailableDataTypesMenu Documentation [GENEPIO:0100702] + Experimental parameters documentation [GENEPIO:0100703] + Feed history [GENEPIO:0100704] + Land use information [GENEPIO:0100705] + Therapeutic administration history [GENEPIO:0100706] + Chemical characterization [GENEPIO:0100707] + pH measurement [GENEPIO:0100708] + Dissolved oxygen measurement [GENEPIO:0100709] + Nitrate measurement [GENEPIO:0100710] + Nitrite measurement [GENEPIO:0100711] + Phosphorous measurement [GENEPIO:0100712] + Salinity measurement [GENEPIO:0100713] + Microbiological characterization [GENEPIO:0100714] + Microbiological identification [GENEPIO:0100715] + Microbiological identification (Beckson Dickson BBL Crystal) [GENEPIO:0100716] + Microbiological identification (bioMérieux API) [GENEPIO:0100717] + Microbiological identification (Biolog) [GENEPIO:0100718] + Microbiological identification (FAME) [GENEPIO:0100719] + Microbiological identification (Sensititre) [GENEPIO:0100720] + Microbiological identification (ViTek) [GENEPIO:0100721] + Phage type [GENEPIO:0100722] + Serotype [GENEPIO:0100723] + Phenotypic microbiological characterization [GENEPIO:0100724] + AMR phenotypic testing [GENEPIO:0100725] + Biolog phenotype microarray [GENEPIO:0100726] + Microbiological quantification [GENEPIO:0100727] + Colony count [GENEPIO:0100728] + Total coliform count [GENEPIO:0100729] + Total fecal coliform count [GENEPIO:0100730] + Infectivity assay [GENEPIO:0100731] + ELISA toxin binding [GENEPIO:0100732] + Molecular characterization [GENEPIO:0100733] + 16S rRNA Sanger sequencing [GENEPIO:0100734] + Metagenomic sequencing [GENEPIO:0101024] + PCR marker detection [GENEPIO:0100735] + BOX PCR fingerprint [GENEPIO:0100736] + ERIC PCR fingerprint [GENEPIO:0100737] + Plasmid type [GENEPIO:0100738] + Ribotype [GENEPIO:0100739] + Molecular quantification [GENEPIO:0100740] + qPCR marker organism quantification [GENEPIO:0100741] + Physical characterization [GENEPIO:0100742] + Conductivity measurement [GENEPIO:0100743] + Mollusc shell measurement [GENEPIO:0100744] + Mollusc shell length [GENEPIO:0100745] + Matter compostion [GENEPIO:0100746] + Dry matter composition [GENEPIO:0100747] + Organic matter composition [GENEPIO:0100748] + Turbidity measurement [GENEPIO:0100749] + + +sampling_weather_conditions menu SamplingWeatherConditionsMenu Cloudy/Overcast [ENVO:03501418] + Partially cloudy [ENVO:03501419] + Drizzle [ENVO:03501420] + Fog [ENVO:01000844] + Rain [ENVO:01001564] + Snow [ENVO:01000406] + Storm [ENVO:01000876] + Sunny/Clear [ENVO:03501421] + + +animal_or_plant_population menu AnimalOrPlantPopulationMenu Algae [FOODON:03411301] + Algal bloom [ENVO:2000004] + Cattle [NCBITaxon:9913] + Beef cattle [FOODON:00004413] + Dairy cattle [FOODON:00002505] + Chicken [NCBITaxon:9031] + Crop [AGRO:00000325] + Fish [FOODON:03411222] + Pig [NCBITaxon:9823] + Poultry [FOODON:00004298] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Crustacean [FOODON:03411374] + Mollusc [FOODON:03412112] + Tropical fish [FOODON:00004283] + Turkey [NCBITaxon:9103] + Wildlife [FOODON:00004503] + Wild bird [FOODON:00004505] + Seabird [FOODON:00004504] + + + +environmental_material menu EnvironmentalMaterialMenu Air [ENVO:00002005] + Alluvium [ENVO:01001202] + Animal feeding equipment [AGRO:00000675] + Animal feeder [AGRO:00000679] + Animal drinker [AGRO:00000680] + Feed pan [AGRO:00000676] + Watering bowl [AGRO:00000677] + Animal transportation equipment [AGRO:00000671] + Dead haul trailer [GENEPIO:0100896] + Dead haul truck [AGRO:00000673] + Live haul trailer [GENEPIO:0100897] + Live haul truck [AGRO:00000674] + Belt [NCIT:C49844] + Biosolids [ENVO:00002059] + Boot [GSSO:012935] + Boot cover [OBI:0002806] + Broom [ENVO:03501431] + Bulk tank [ENVO:03501379] + Chick box [AGRO:00000678] + Chick pad [AGRO:00000672] + Cleaning equipment [ENVO:03501430] + Compost [ENVO:00002170] + Contaminated water [ENVO:00002186] + Fecal slurry [ENVO:03501436] + Fluid from meat rinse [GENEPIO:0004323] + Effluent [ENVO:03501407] + Influent [ENVO:03501442] + Surface runoff [ENVO:03501408] + Poultry plucking water [AGRO_00000693] + Wastewater [ENVO:00002001] + Weep fluid [AGRO_00000692] + Crate [ENVO:03501372] + Dumpster [ENVO:03501400] + Dust [ENVO:00002008] + Egg belt [AGRO:00000670] + Fan [NCIT:C49947] + Freezer [ENVO:03501415] + Freezer handle [ENVO:03501414] + Manure [ENVO:00003031] + Animal manure [AGRO:00000079] + Pig manure [AGRO:00000080] + Manure digester equipment [ENVO:03501424] + Nest [ENVO:03501432] + Bird's nest [ENVO:00005805] + Permafrost [ENVO:00000134] + Plucking belt [AGRO:00000669] + Poultry fluff [UBERON:0008291] + Poultry litter [AGRO:00000080] + Sediment [ENVO:00002007] + Soil [ENVO:00001998] + Agricultural soil [ENVO:00002259] + Forest soil [ENVO:00002261] + Straw [ENVO:00003869] + Canola straw [FOODON:00004430] + Oat straw [FOODON:03309878] + Barley straw [FOODON:00004559] + Sludge [ENVO:00002044] + Primary sludge [ENVO:00002057] + Secondary sludge [ENVO:00002058] + Water [CHEBI:15377] + Drinking water [ENVO:00003064] + Groundwater [ENVO:01001004] + Surface water [ENVO:00002042] + + +anatomical_material menu AnatomicalMaterialMenu Blood [UBERON:0000178] + Fluid [UBERON:0006314] + Fluid (cerebrospinal (CSF)) [UBERON:0001359] + Fluid (amniotic) [UBERON:0000173] + Saliva [UBERON:0001836] + Tissue [UBERON:0000479] + + +body_product menu BodyProductMenu Digestive tract substance [GENEPIO:0100898] + Caecal content [GENEPIO:0100899] + Intestinal content [GENEPIO:0100900] + Stomach content [GENEPIO:0100901] + Feces [UBERON:0001988] + Fecal composite [GENEPIO:0004512] + Feces (fresh) [GENEPIO:0004513] + Feces (environmental) [GENEPIO:0004514] + Meconium [UBERON:0007109] + Milk [UBERON:0001913] + Colostrum [UBERON:0001914] + Urine [UBERON:0001088] + + +anatomical_part menu AnatomicalPartMenu Carcass [UBERON:0008979] + Swine carcass [FOODON:03311719] + Digestive system [UBERON:0001007] + Caecum [UBERON:0001153] + Colon [UBERON:0001155] + Digestive gland [UBERON:0006925] + Foregut [UBERON:0001041] + Gall bladder [UBERON:0002110] + Gastrointestinal system mucosa [UBERON:0004786] + Gizzard [UBERON:0005052] + Hindgut [UBERON:0001046] + Intestine [UBERON:0000160] + Small intestine [UBERON:0002108] + Duodenum [UBERON:0002114] + Ileum [UBERON:0002116] + Jejunum [UBERON:0002115] + Stomach [UBERON:0000945] + Abomasum [UBERON:0007358] + Rumen [UBERON:0007365] + Excretory system (organizational term) + Anus [UBERON:0001245] + Anal gland [UBERON:0011253] + Cloaca [UBERON:0000162] + Liver [UBERON:0002107] + Kidney [UBERON:0002113] + Rectum [UBERON:0001052] + Spleen [UBERON:0002106] + Urinary bladder [UBERON:0001255] + Foot [UBERON:0002387] + Head [UBERON:0000033] + Brain [UBERON:0000955] + Ear [UBERON:0001690] + Eye [UBERON:0000970] + Mouth [UBERON:0000165] + Nose [UBERON:0000004] + Nasal turbinal [UBERON:0035612] + Nasopharynx (NP) [UBERON:0001728] + Pair of nares [UBERON:0002109] + Paranasal sinus [UBERON:0001825] + Snout [UBERON:0006333] + Lymphatic system [UBERON:0006558] + Lymph node [UBERON:0000029] + Mesenteric lymph node [UBERON:0002509] + Mantle (bird) [GENEPIO:0100927] + Neck [UBERON:0000974] + Esophagus [UBERON:0001043] + Trachea [UBERON:0003126] + Nerve [UBERON:0001021] + Spinal cord [UBERON:0002240] + Organs or organ parts [GENEPIO:0001117] + Organ [UBERON:0000062] + Muscle organ [UBERON:0001630] + Skin of body [UBERON:0002097] + Reproductive system [UBERON:0000990] + Embryo [UBERON:0000922] + Fetus [UBERON:0000323] + Ovary [UBERON:0000992] + Oviduct [UBERON:0000993] + Placenta [UBERON:0001987] + Testis [UBERON:0000473] + Udder [UBERON:0013216] + Uterus [UBERON:0000995] + Vagina [UBERON:0000996] + Yolk sac [UBERON:0001040] + Respiratory system [UBERON:0001004] + Air sac [UBERON:0009060] + Lung [UBERON:0002048] + Pleura [UBERON:0000977] + Respiratory system mucosa [UBERON:0004785] + Skeletal system [UBERON:0001434] + Skeletal joint [UBERON:0000982] + Bone element [UBERON:0001474] + Thoracic segment of trunk [UBERON:0000915] + Abdomen [UBERON:0000916] + Muscle of abdomen [UBERON:0002378] + Peritoneum [UBERON:0002358] + Vascular system [UBERON:0007798] + Blood vessel [UBERON:0001981] + Bursa of Fabricius [UBERON:0003903] + Gill [UBERON:0002535] + Heart [UBERON:0000948] + Lung [UBERON:0002048] + Pericardium [UBERON:0002407] + Vent (anatomical) [UBERON:2000298] + Bird vent [UBERON:0012464] + Fish vent [GENEPIO:0100902] + + +anatomical_region menu AnatomicalRegionMenu Dorso-lateral region [BSPO:0000080] + Exterior anatomical region [BSPO:0000034] + Interior anatomical region [BSPO:0000033] + + +food_product menu FoodProductMenu Animal feed [ENVO:02000047] + Blood meal [FOODON:00001564] + Bone meal [ENVO:02000054] + Brassica carinata meal [FOODON:00004310] + Canola meal [FOODON:00002694] + Compound feed premix [FOODON:00004323] + Compound feed premix (medicated) [FOODON:00004324] + Feather meal [FOODON:00003927] + Fish meal [FOODON:03301620] + Lay ration [FOODON:00004286] + Meat and bone meal [FOODON:00002738] + Meat meal [FOODON:00004282] + Pet food [FOODON:00002682] + Soybean meal [FOODON:03302757] + Animal feed ingredient [FOODON:00004322] + Dairy food product [FOODON:00001256] + Cheese block (whole or parts) [FOODON:03000287] + Cow skim milk (powdered) [FOODON:03310016] + Milk [UBERON:0001913] + Dietary supplement [FOODON:03401298] + Egg or egg component [FOODON:03420194] + Balut [FOODON:03302184] + Egg yolk [UBERON:0007378] + Poultry egg [FOODON:03000414] + Hen egg (whole) [FOODON:03316061] + Poultry egg (whole, shell on) [FOODON:03000415] + Food mixture [FOODON:00004130] + Food product analog (food subsitute) [FOODON:00001871] + Milk substitute [FOODON:03305408] + Meat (whole or parts) [FOODON:03317170] + Cutlet [FOODON:00003001] + Filet [FOODON:03530144] + Liver (whole, raw) [FOODON:03309772] + Meat trim [FOODON:03309475] + Rib (meat cut) [FOODON:03530023] + Rib chop [FOODON:00004290] + Shoulder (meat cut) [FOODON:03530043] + Grains, cereals, and bakery product (organizational term) + Bread loaf (whole or parts) [FOODON:03000288] + Breakfast cereal [FOODON:03311075] + Bulk grain [FOODON:03309390] + Oat grain [FOODON:00003429] + Legume food product [FOODON:00001264] + Chickpea (whole) [FOODON:03306811] + Hummus [FOODON:00003049] + Soybean (whole or parts) [FOODON:03000245] + Meat, poultry and fish (organizational term) + Beef (ground or minced) [FOODON:00001282] + Beef (ground or minced, boneless) [FOODON:0001282] + Beef (ground, extra lean) [FOODON:02000426] + Beef (ground, lean) [FOODON:02000425] + Beef (ground, medium) [FOODON:02000427] + Beef (ground, regular) [FOODON:02000428] + Beef (ground, sirloin) [FOODON:02000429] + Beef hamburger (dish) [FOODON:00002737] + Beef shoulder [FOODON:02000069] + Beef shoulder chop [FOODON:03000387] + Beef sirloin chop [FOODON:03000389] + Beef stew chunk [FOODON:00004288] + Beef tenderloin [FOODON:00003302] + Beef (pieces) [FOODON:02000412] + Brisket [FOODON:03530020] + Chicken breast [FOODON:00002703] + Chicken breast (back off) [FOODON:03000385] + Chicken breast (skinless) [FOODON:02020231] + Chicken breast (with skin) [FOODON:02020233] + Chicken breast (skinless, boneless) [FOODON:02020235] + Chicken breast cutlet [FOODON:00004308] + Chicken drumstick [FOODON:00002716] + Chicken drumstick (skinless) [FOODON:02020237] + Chicken drumstick(with skin) [FOODON:02020239] + Chicken meat [FOODON:00001040] + Chicken meat (ground) [FOODON:02020311] + Chicken meat (ground or minced, lean) [FOODON:03000392] + Chicken meat (ground or minced, extra lean) [FOODON:03000396] + Chicken meat (ground or minced, medium) [FOODON:03000400] + Chicken meat (ground or minced, regular) [FOODON:03000404] + Chicken meat (ground or minced, boneless) [FOODON:03000410] + Chicken nugget [FOODON:00002672] + Chicken thigh [FOODON:02020219] + Chicken thigh (skinless) [FOODON:00003331] + Chicken thigh (skinless, with bone) [FOODON:02020227] + Chicken thigh (skinless, boneless) [FOODON:02020228] + Chicken upper thigh [FOODON:03000381] + Chicken upper thigh (with skin) [FOODON:03000383] + Chicken thigh (with skin) [FOODON:00003330] + Chicken thigh (with skin, with bone) [FOODON_00003363] + Chicken wing [FOODON:00002674] + Fish food product [FOODON:00001248] + Fish steak [FOODON:00002986] + Ham food product [FOODON:00002502] + Head cheese [FOODON:03315658] + Lamb [FOODON:03411669] + Meat strip [FOODON:00004285] + Mutton [FOODON:00002912] + Pork chop [FOODON:00001049] + pork meat (ground) [FOODON:02021718] + Pork meat (ground or minced, boneless) [FOODON:03000413] + Pork meat (ground or minced, extra lean) [FOODON:03000399] + Pork meat (ground or minced, lean) [FOODON:03000395] + Pork meat (ground or minced, medium) [FOODON:03000403] + Pork meat (ground or minced, regular) [FOODON:03000407] + Pork meat (ground or minced, Sirloin) [FOODON:03000409] + Pork shoulder [FOODON:02000322] + Pork shoulder chop [FOODON:03000388] + Pork sirloin chop [FOODON:02000300] + Pork steak [FOODON:02021757] + Pork tenderloin [FOODON:02000306] + Poultry meat [FOODON:03315883] + Leg (poultry meat cut) [FOODON:03530159] + Poultry drumstick [FOODON:00003469] + Neck (poultry meat cut) [FOODON:03530294] + Thigh (poultry meat cut) [FOODON:03530160] + Wing (poultry meat cut) [FOODON:03530157] + Sausage (whole) [FOODON:03315904] + Pepperoni [FOODON:03311003] + Salami [FOODON:03312067] + Shellfish [FOODON:03411433] + Mussel [FOODON:03411223] + Oyster [FOODON:03411224] + Shrimp [FOODON:03301673] + Scallop [FOODON:02020805] + Squid [FOODON:03411205] + Turkey breast [FOODON:00002690] + Turkey breast (back off) [FOODON:03000386] + Turkey breast (skinless) [FOODON:02020495] + Turkey breast (skinless, boneless) [FOODON:02020499] + Turkey breast (with skin) [FOODON:02020497] + Turkey drumstick [FOODON:02020477] + Turkey drumstick (skinless) [FOODON:02020501] + Turkey drumstick (with skin) [FOODON:02020503] + Turkey meat [FOODON:00001286] + Turkey meat (ground) [FOODON:02020577] + Turkey meat (ground or minced, lean) [FOODON:03000393] + Turkey meat (ground or minced, extra lean) [FOODON:03000397] + Turkey meat (ground or minced, medium) [FOODON:03000401] + Turkey meat (ground or minced, regular) [FOODON:03000405] + Turkey meat (ground or minced, boneless) [FOODON:03000411] + Turkey thigh [FOODON:00003325] + Turkey thigh (skinless) [FOODON:00003329] + Turkey thigh (skinless, boneless) [FOODON:02020491] + Turkey thigh (with skin) [FOODON:00003328] + Turkey upper thigh [FOODON:03000382] + Turkey upper thigh (with skin) [FOODON:03000384] + Turkey wing [FOODON:02020478] + Veal [FOODON:00003083] + Formula fed veal [FOODON:000039111] + Grain-fed veal [FOODON:00004280] + Microbial food product [FOODON:00001145] + Yeast [FOODON:03411345] + Nuts and seed products + Almond (whole or parts) [FOODON:03000218] + Almond (whole) [FOODON:00003523] + Barley seed [FOODON:00003394] + Canola seed [FOODON:00004560] + Chia seed powder [FOODON:00003925] + Chia seed (whole or parts) [FOODON:03000241] + Flaxseed powder [FOODON:00004276] + Hazelnut [FOODON:00002933] + Nut (whole or part) [FOODON:03306632] + Peanut butter [FOODON:03306867] + Sesame seed [FOODON:03310306] + Tahini [FOODON:00003855] + Walnut (whole or parts) [FOODON:03316466] + Prepared food product [FOODON:00001180] + Condiment [FOODON:03315708] + Confectionery food product [FOODON:00001149] + Snack food [FOODON:03315013] + Produce [FOODON:03305145] + Apple (whole or parts) [FOODON:03310788] + Apple (whole) [FOODON:00002473] + Arugula greens bunch [FOODON:00003643] + Avocado [FOODON:00003600] + Cantaloupe (whole or parts) [FOODON:03000243] + Chilli pepper [FOODON:00003744] + Coconut (whole or parts) [FOODON:03309861] + Coconut meat [FOODON:00003856] + Corn cob (whole or parts) [FOODON:03310791] + Cucumber (whole or parts) [FOODON:03000229] + Fruit [PO:0009001] + Goji berry [FOODON:00004360] + Greens (raw) [FOODON:03310765] + Kale leaf (whole or parts) [FOODON:03000236] + Karela (bitter melon) [FOODON:00004367] + Lettuce head (whole or parts) [FOODON:03000239] + Mango (whole or parts) [FOODON:03000217] + Mushroom (fruitbody) [FOODON:00003528] + Papaya (whole or parts) [FOODON:03000228] + Pattypan squash (whole or parts) [FOODON:03000232] + Peach [FOODON:00002485] + Pepper (whole or parts) [FOODON:03000249] + Potato [FOODON:03315354] + Salad [FOODON:03316042] + Scallion (whole or parts) [FOODON:03000250] + Spinach (whole or parts) [FOODON:03000221] + Sprout [FOODON:03420183] + Germinated or sprouted seed [FOODON:03420102] + Alfalfa sprout [FOODON:00002670] + Bean sprout [FOODON:00002576] + Chia sprout [FOODON:03000180] + Mixed sprouts [FOODON:03000182] + Mung bean sprout [FOODON:03301446] + Tomato (whole or pieces) [FOODON:00002318] + Vegetable (whole or parts) [FOODON:03315308] + Spice or herb [FOODON:00001242] + Basil (whole or parts) [FOODON:03000233] + Black pepper (whole or parts) [FOODON:03000242] + Cardamom (whole or parts) [FOODON:03000246] + Chive leaf (whole or parts) [FOODON:03000240] + Coriander powder [FOODON:00004274] + Coriander seed (whole or parts) [FOODON:03000224] + Cumin powder [FOODON:00004275] + Cumin seed (whole) [FOODON:00003396] + Black cumin seed (whole or parts) [FOODON:03000247] + Curry leaf (whole or parts) [FOODON:03000225] + Curry powder [FOODON:03301842] + Dill spice [FOODON:00004307] + Fennel (whole or parts) [FOODON:03000244] + Garlic powder [FOODON:03301844] + Ginger root (whole or parts) [FOODON:03000220] + Mint leaf (whole or parts) [FOODON:03000238] + Oregano (whole or parts) [FOODON:03000226] + Paprika (ground) [FOODON:03301223] + Parsley leaf (whole or parts) [FOODON:03000231] + Pepper (ground) [FOODON:03301526] + Rasam powder [FOODON:00004277] + Sage [FOODON:03301560] + Turmeric (ground) [FOODON:03310841] + Spice [FOODON:03303380] + White peppercorn (whole or parts) [FOODON:03000251] + + +food_product_properties menu FoodProductPropertiesMenu Food (canned) [FOODON:00002418] + Food (cooked) [FOODON:00001181] + Food (cut) [FOODON:00004291] + Food (chopped) [FOODON:00002777] + Food (chunks) [FOODON:00004555] + Food (cubed) [FOODON:00004278] + Food (diced) [FOODON:00004549] + Food (grated) [FOODON:00004552] + Food (sliced) [FOODON:00002455] + Food (shredded) [FOODON:00004553] + Food (dried) [FOODON:03307539] + Food (fresh) [FOODON:00002457] + Food (frozen) [FOODON:03302148] + Food (pulped) [FOODON:00004554] + Food (raw) [FOODON:03311126] + Food (unseasoned) [FOODON:00004287] + Italian-style food product [FOODON:00004321] + Meat (boneless) [FOODON:00003467] + Meat (skinless) [FOODON:00003468] + Meat (with bone) [FOODON:02010116] + Meat (with skin) [FOODON:02010111] + Soft [PATO:0000387] + + + + +label_claim menu LabelClaimMenu Antibiotic free [FOODON:03601063] + Cage free [FOODON:03601064] + Hormone free [FOODON:03601062] + Organic food claim or use [FOODON:03510128] + Pasture raised [FOODON:03601065] + Ready-to-eat (RTE) [FOODON:03316636] + + +animal_source_of_food menu AnimalSourceOfFoodMenu Cow [NCBITaxon:9913] + Fish [FOODON:03411222] + Pig [NCBITaxon:9823] + Poultry or game bird [FOODON:03411563] + Chicken [NCBITaxon:9031] + Turkey [NCBITaxon:9103] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Mussel [FOODON:03411223] + Scallop [NCBITaxon:6566] + Shrimp [FOODON:03411237] + Squid [FOODON:03411205] + + +food_product_production_stream menu FoodProductProductionStreamMenu Beef cattle production stream [FOODON:03000452] + Broiler chicken production stream [FOODON:03000455] + Dairy cattle production stream [FOODON:03000453] + Egg production stream [FOODON:03000458] + Layer chicken production stream [FOODON:03000456] + Meat production stream [FOODON:03000460] + Veal meat production stream [FOODON:03000461] + Milk production stream [FOODON:03000459] + + +collection_device menu CollectionDeviceMenu Auger (earth auger) [AGRO:00000405] + Box corer [GENEPIO:0100928] + Container [OBI:0000967] + Bag [GSSO:008558] + Whirlpak sampling bag [GENEPIO:0002122] + Bottle [FOODON:03490214] + Vial [OBI:0000522] + Culture plate [GENEPIO:0004318] + Petri dish [NCIT:C96141] + Filter [GENEPIO:0100103] + PONAR grab sampler [GENEPIO:0100929] + Scoop [GENEPIO:0002125] + Soil sample probe [GENEPIO:0100930] + Spatula [NCIT:C149941] + Sponge [OBI:0002819] + Swab [GENEPIO:0100027] + Drag swab [OBI:0002822] + Surface wipe [OBI:0002824] + Tube [GENEPIO:0101196] + Vacuum device [GENEPIO:0002127] + Vacutainer [OBIB:0000032] + + +collection_method menu CollectionMethodMenu Aspiration [HP:0002835] + Biopsy [OBI:0002650] + Fecal grab [GENEPIO:0004326] + Filtration [OBI:0302885] + Air filtration [GENEPIO:0100031] + Water filtration [GENEPIO:0100931] + Lavage [OBI:0600044] + Bronchoalveolar lavage [GENEPIO:0100032] + Gastric lavage [GENEPIO:0100033] + Necropsy [MMO:0000344] + Phlebotomy [NCIT:C28221] + Rinsing for specimen collection [GENEPIO_0002116] + Scooping [GENEPIO:0100932] + Sediment collection [GENEPIO:0100933] + Soil coring [GENEPIO:0100934] + Weep fluid collection (pouring) [GENEPIO:0101003] + +sample_volume_measurement_unit menu SampleVolumeMeasurementUnitMenu microliter (uL) [UO:0000101] + milliliter (mL) [UO:0000098] + liter (L) [UO:0000099] + +residual_sample_status menu ResidualSampleStatusMenu Residual sample remaining (some sample left) [GENEPIO:0101087] + No residual sample (sample all used) [GENEPIO:0101088] + Residual sample status unkown [GENEPIO:0101089] + +sample_storage_duration_unit menu SampleStorageDurationUnitMenu Second [UO:0000010] + Minute [UO:0000031] + Hour [UO:0000032] + Day [UO:0000033] + Week [UO:0000034] + Month [UO:0000035] + Year [UO:0000036] + +nucelic_acid_storage_duration_unit menu NucelicAcidStorageDurationUnitMenu Second [UO:0000010] + Minute [UO:0000031] + Hour [UO:0000032] + Day [UO:0000033] + Week [UO:0000034] + Month [UO:0000035] + Year [UO:0000036] + +food_packaging menu FoodPackagingMenu Bag, sack or pouch [FOODON:03490197] + Paper bag, sack or pouch [FOODON:03490120] + Plastic bag, sack or pouch [FOODON:03490166] + Plastic shrink wrap [FOODON:03490137] + Plastic wrapper [FOODON:03490128] + Bottle or jar [FOODON:03490203] + Can (container) [FOODON:03490204] + Paper container, treated [FOODON:03490330] + Paper container, untreated [FOODON:03490334] + Plastic tray or pan [FOODON:03490126] + + +host (common name) menu HostCommonNameMenu Bird [NCBITaxon:8782] + Chicken [NCBITaxon:9031] + Seabird [FOODON:00004504] + Cormorant [NCBITaxon:9206] + Double Crested Cormorant [NCBITaxon:56069] + Crane [NCBITaxon:9109] + Whooping Crane [NCBITaxon:9117] + Gull (Seagull) [NCBITaxon:8911] + Glaucous-winged Gull [NCBITaxon:119606] + Great Black-backed Gull [NCBITaxon:8912] + Herring Gull [NCBITaxon:35669] + Ring-billed Gull [NCBITaxon:126683] + Eider [NCBITaxon:50366] + Common Eider [NCBITaxon:76058] + Turkey [NCBITaxon:9103] + Fish [FOODON:03411222] + Rainbow Trout [NCBITaxon:8022] + Sablefish [NCBITaxon:229290] + Salmon [FOODON:00003473] + Atlantic Salmon [NCBITaxon:8030] + Chinook salmon [NCBITaxon:74940] + Coho Salmon [NCBITaxon:8019] + Mammal [FOODON:03411134] + Companion animal [FOODON:03000300] + Cow [NCBITaxon:9913] + Human [NCBITaxon:9606] + Pig [NCBITaxon:9823] + Sheep [NCBITaxon:9940] + Shellfish [FOODON:03411433] + Atlantic Lobster [NCBITaxon:6706] + Atlantic Oyster [NCBITaxon:6565] + Blue Mussel [NCBITaxon:6550] + + +host (scientific name) menu HostScientificNameMenu Anoplopoma fimbria [NCBITaxon:229290] + Bos taurus [NCBITaxon:9913] + Crassostrea virginica [NCBITaxon:6565] + Gallus gallus [NCBITaxon:9031] + Grus americana [NCBITaxon:9117] + Homarus americanus [NCBITaxon:6706] + Homo sapiens [NCBITaxon:9606] + Larus argentatus [NCBITaxon:35669] + Larus delawarensis [NCBITaxon:126683] + Larus glaucescens [NCBITaxon:119606] + Larus marinus [NCBITaxon:8912] + Meleagris gallopavo [NCBITaxon:9103] + Mytilus edulis [NCBITaxon:6550] + Oncorhynchus kisutch [NCBITaxon:8019] + Oncorhynchus mykiss [NCBITaxon:8022] + Oncorhynchus tshawytscha [NCBITaxon:74940] + Ovis aries [NCBITaxon:9940] + Phalacrocorax auritus [NCBITaxon:56069] + Salmo salar [NCBITaxon:8030] + Somateria mollissima [NCBITaxon:76058] + Sus scrofa domesticus [NCBITaxon:9825] + + +host (food production name) menu HostFoodProductionNameMenu Cow (by age/production stage) (organizational term) + Calf [FOODON:03411349] + Dry cow [FOODON:00004411] + Feeder cow [FOODON:00004292] + Finisher cow [FOODON:00004293] + Milker cow [FOODON:03411201] + Stocker cow [FOODON:00004294] + Weanling cow [FOODON:00004295] + Cow (by sex/reproductive stage) (organizational term) + Bull [FOODON:00000015] + Cow [NCBITaxon:9913] + Freemartin [FOODON:00004296] + Heifer [FOODON:00002518] + Steer [FOODON:00002531] + Pig (by age/production stage) (organizational term) + Finisher pig [FOODON:00003371] + Grower pig [FOODON:00003370] + Nursing pig [FOODON:00004297 ] + Pig [NCBITaxon:9823] + Piglet [FOODON:00003952] + Weanling (weaner) pig [FOODON:00003373] + Pig (by sex/reproductive stage) (organizational term) + Barrow [FOODON:03411280] + Boar [FOODON:03412248] + Gilt [FOODON:00003369] + Sow [FOODON:00003333] + Poultry or game bird [FOODON:03411563] + Broiler or fryer chicken [FOODON:03411198] + Capon [FOODON:03411711] + Chick [FOODON:00004299] + Chicken [NCBITaxon:9031] + Egg [UBERON:0007379] + Hatchling [FOODON:00004300] + Hen [FOODON:00003282] + Layer chicken [FOODON:00004301] + Layer turkey [FOODON:00004302] + Poult [FOODON:00002962] + Pullet [FOODON:00004303] + Rooster [FOODON:03411714] + Tom (Gobbler) [FOODON:00004304 ] + Turkey [NCBITaxon:9103] + Sheep [NCBITaxon:9940] + Ram [FOODON:00004305] + Wether sheep [FOODON:00004306] + Ewe [FOODON:03412610] + Lamb [FOODON:03411669] + Fish [FOODON:03411222] + Fish egg [FOODON_00004319] + Fry (fish) [FOODON_00004318] + Juvenile fish [FOODON_00004317] + + +host_age_bin menu HostAgeBinMenu First winter [GENEPIO:0100684] + First summer [GENEPIO:0100685] + Second winter [GENEPIO:0100686] + Second summer [GENEPIO:0100687] + Third winter [GENEPIO:0100688] + Third summer [GENEPIO:0100689] + + +isolated_by menu IsolatedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + + +organism menu OrganismMenu Acinetobacter [NCBITaxon:469] + Acinetobacter baumannii [NCBITaxon:470] + Acinetobacter bereziniae [NCBITaxon:106648] + Acinetobacter ursingii [NCBITaxon:108980] + Aeromonas [NCBITaxon:642] + Aeromonas allosaccharophila [NCBITaxon:656] + Aeromonas hydrophila [NCBITaxon:644] + Aeromonas rivipollensis [NCBITaxon:948519] + Aeromonas salmonicida [NCBITaxon:645] + Campylobacter [NCBITaxon:194] + Campylobacter coli [NCBITaxon:195] + Campylobacter jejuni [NCBITaxon:197] + Campylobacter lari [NCBITaxon:201] + Citrobacter [NCBITaxon:544] + Citrobacter braakii [NCBITaxon:57706] + Citrobacter freundii [NCBITaxon:546] + Citrobacter gillenii [NCBITaxon:67828] + Clostridioides [NCBITaxon:1870884] + Clostridioides difficile [NCBITaxon:1496] + Clostridium [NCBITaxon:1485] + Clostridium perfringens [NCBITaxon:1502] + Clostridium sporogenes [NCBITaxon:1509] + Comamonas [NCBITaxon:283] + Comamonas aquatica [NCBITaxon:225991] + Enterobacter [NCBITaxon:547] + Enterobacter asburiae [NCBITaxon:61645] + Enterobacter cancerogenus [NCBITaxon:69218] + Enterobacter cloacae [NCBITaxon:550] + Enterobacter hormaechei [NCBITaxon:158836] + Enterobacter kobei [NCBITaxon:208224] + Enterobacter roggenkampii [NCBITaxon:1812935] + Enterobacter sp. [NCBITaxon:42895] + Lelliottia amnigena [NCBITaxon:61646] + Pluralibacter gergoviae [NCBITaxon:61647] + Enterococcus [NCBITaxon:1350] + Enterococcus asini [NCBITaxon:57732] + Enterococcus avium [NCBITaxon:33945] + Enterococcus caccae [NCBITaxon:317735] + Enterococcus canis [NCBITaxon:214095] + Enterococcus casseliflavus [NCBITaxon:37734] + Enterococcus cecorum [NCBITaxon:44008] + Enterococcus dispar [NCBITaxon:44009] + Enterococcus durans [NCBITaxon:53345] + Enterococcus faecium [NCBITaxon:1352] + Enterococcus faecalis [NCBITaxon:1351] + Enterococcus gallinarum [NCBITaxon:1353] + Enterococcus hirae [NCBITaxon:1354] + Enterococcus malodoratus [NCBITaxon:71451] + Enterococcus mundtii [NCBITaxon:53346] + Enterococcus ratti [NCBITaxon:150033] + Enterococcus saccharolyticus [NCBITaxon:41997] + Enterococcus thailandicus [NCBITaxon:417368] + Enterococcus villorum [NCBITaxon:112904] + Escherichia [NCBITaxon:561] + Escherichia coli [NCBITaxon:562] + Escherichia fergusonii [NCBITaxon:564] + Exiguobacterium [NCBITaxon:33986] + Exiguobacterium oxidotolerans [NCBITaxon:223958] + Exiguobacterium sp. [NCBITaxon:44751] + Klebsiella [NCBITaxon:570] + Klebsiella aerogenes [NCBITaxon:548] + Klebsiella michiganensis [NCBITaxon:1134687] + Klebsiella oxytoca [NCBITaxon:571] + Klebsiella pneumoniae [NCBITaxon:573] + Klebsiella pneumoniae subsp. pneumoniae [NCBITaxon:72407] + Klebsiella pneumoniae subsp. ozaenae [NCBITaxon:574] + Kluyvera [NCBITaxon:579] + Kluyvera intermedia [NCBITaxon:61648] + Kosakonia [NCBITaxon:1330547] + Kosakonia cowanii [NCBITaxon:208223] + Leclercia [NCBITaxon:83654] + Leclercia adecarboxylata [NCBITaxon:83655] + Listeria [NCBITaxon:1637] + Listeria monocytogenes [NCBITaxon:1639] + Ochrobactrum [NCBITaxon:528] + Ochrobactrum sp. [NCBITaxon:42190] + Pantoea [NCBITaxon:53335] + Pantoea ananatis [NCBITaxon:553] + Pantoea sp. [NCBITaxon:69393] + Photobacterium [NCBITaxon:657] + Photobacterium indicum[NCBITaxon:81447] + Photobacterium sp. [NCBITaxon:660] + Providencia [NCBITaxon:586] + Providencia rettgeri [NCBITaxon:587] + Pseudoalteromonas [NCBITaxon:53246] + Pseudoalteromonas tetraodonis [NCBITaxon:43659] + Pseudomonas [NCBITaxon:286] + Pseudomonas aeruginosa [NCBITaxon:287] + Pseudomonas fluorescens [NCBITaxon:294] + Pseudomonas soli [NCBITaxon:1306993] + Pseudomonas sp. [NCBITaxon:306] + Psychrobacter [NCBITaxon:497] + Psychrobacter faecalis [NCBITaxon:180588] + Psychrobacter nivimaris [NCBITaxon:281738] + Psychrobacter sp. [NCBITaxon:56811] + Rahnella [NCBITaxon:34037] + Rahnella aquatilis [NCBITaxon:34038] + Rahnella sp. [NCBITaxon:1873497] + Raoultella [NCBITaxon:160674] + Raoultella ornithinolytica [NCBITaxon:54291] + Raoultella planticola [NCBITaxon:575] + Salmonella enterica [NCBITaxon:28901] + Salmonella enterica subsp. enterica [NCBITaxon:59201] + Salmonella enterica subsp. arizonae [NCBITaxon:59203] + Serratia [NCBITaxon:613] + Shewanella [NCBITaxon:22] + Shewanella pealeana [NCBITaxon:70864] + Shewanella putrefaciens [NCBITaxon:24] + Shewanella oncorhynchi [NCBITaxon:2726434] + Shewanella sp. [NCBITaxon:50422] + Staphylococcus [NCBITaxon:1279] + Staphylococcus aureus [NCBITaxon:1280] + Streptococcus [NCBITaxon:1301] + Streptococcus alactolyticus [NCBITaxon:29389] + Streptococcus bovis [NCBITaxon:1335] + Streptococcus equinus [NCBITaxon:1335] + Streptococcus gallolyticus [NCBITaxon:315405] + Streptococcus infantarius [NCBITaxon:102684] + Streptococcus lutetiensis [NCBITaxon:150055] + Streptococcus macedonicus [NCBITaxon:59310] + Streptococcus pasteurianus [NCBITaxon:197614] + Streptococcus suis [NCBITaxon:1307] + Vibrio [NCBITaxon:662] + Vibrio cholerae [NCBITaxon:666] + Vibrio parahaemolyticus [NCBITaxon:670] + +taxonomic_identification_process menu TaxonomicIdentificationProcessMenu Whole genome sequencing assay [OBI:0002117] + 16S ribosomal gene sequencing assay [OBI:0002763] + PCR assay [OBI:0002740] + Comparative phenotypic assessment [OBI:0001546] + Matrix Assisted Laser Desorption Ionization imaging mass spectrometry assay (MALDI) [OBI:0003099] + + +sequenced_by menu SequencedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + McGill University [GENEPIO:0101103] + + +purpose_of_sequencing menu PurposeOfSequencingMenu Cluster/Outbreak investigation [GENEPIO:0100001] + Diagnostic testing [GENEPIO:0100002] + Environmental testing [GENEPIO:0100548] + Research [GENEPIO:0100003] + Clinical trial [GENEPIO:0100549] + Field experiment [GENEPIO:0100550] + Protocol testing experiment [GENEPIO:0100024] + Survey study [GENEPIO:0100582] + Surveillance [GENEPIO:0100004] + + +sequencing_platform menu SequencingPlatformMenu Illumina [GENEPIO:0001923] + Pacific Biosciences [GENEPIO:0001927] + Ion Torrent [GENEPIO:0002683] + Oxford Nanopore Technologies [OBI:0002755] + BGI Genomics [GENEPIO:0004324] + MGI [GENEPIO:0004325] + + +sequencing_instrument menu SequencingInstrumentMenu Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. + Illumina Genome Analyzer [OBI:0002128] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + Illumina HiScanSQ [GENEPIO:0100109] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. + Illumina HiSeq [GENEPIO:0100110] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. + Illumina HiSeq X [GENEPIO:0100111] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. + Illumina HiSeq X Five [GENEPIO:0100112] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + Illumina HiSeq X Ten [OBI:0002129] A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + Illumina HiSeq 1000 [OBI:0002022] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Illumina HiSeq 1500 [OBI:0003386] A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + Illumina HiSeq 2000 [OBI:0002001] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + Illumina HiSeq 2500 [OBI:0002002] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + Illumina HiSeq 3000 [OBI:0002048] A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + Illumina HiSeq 4000 [OBI:0002049] A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + Illumina iSeq [GENEPIO:0100120] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. + Illumina iSeq 100 [GENEPIO:0100121] A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + Illumina NovaSeq [GENEPIO:0100122] A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. + Illumina NovaSeq 6000 [OBI:0002630] A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + Illumina MiniSeq [OBI:0003114] A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + Illumina MiSeq [OBI:0002003] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + Illumina NextSeq [GENEPIO:0100126] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + Illumina NextSeq 500 [OBI:0002021] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Illumina NextSeq 550 [GENEPIO:0100128] A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + Illumina NextSeq 1000 [OBI:0003606] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + Illumina NextSeq 2000 [GENEPIO:0100129] A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. + PacBio [GENEPIO:0100130] A DNA sequencer manufactured by the Pacific Biosciences corporation. + PacBio RS [GENEPIO:0100131] A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. + PacBio RS II [OBI:0002012] A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + PacBio Sequel [OBI:0002632] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + PacBio Sequel II [OBI:0002633] A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + Ion Torrent [GENEPIO:0100135] A DNA sequencer manufactured by the Ion Torrent corporation. + Ion Torrent PGM [GENEPIO:0100136] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + Ion Torrent Proton [GENEPIO:0100137] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + Ion Torrent S5 XL [GENEPIO:0100138] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + Ion Torrent S5 [GENEPIO:0100139] A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + Oxford Nanopore [GENEPIO:0100140] A DNA sequencer manufactured by the Oxford Nanopore corporation. + Oxford Nanopore Flongle [GENEPIO:0004433] An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. + Oxford Nanopore GridION [GENEPIO:0100141] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + Oxford Nanopore MinION [OBI:0002750] A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + Oxford Nanopore PromethION [OBI:0002752] A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + BGISEQ [GENEPIO:0100144] A DNA sequencer manufactured by the BGI Genomics corporation. + BGISEQ-500 [GENEPIO:0100145] A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". + DNBSEQ [GENEPIO:0100146] A DNA sequencer manufactured by the MGI corporation. + DNBSEQ-T7 [GENEPIO:0100147] A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. + DNBSEQ-G400 [GENEPIO:0100148] A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. + DNBSEQ-G400 FAST [GENEPIO:0100149] A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. + DNBSEQ-G50 [GENEPIO:0100150] A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + + +sequencing_assay_type menu SequencingAssayTypeMenu Amplicon sequencing assay [OBI:0002767] + 16S ribosomal gene sequencing assay [OBI:0002763] + Whole genome sequencing assay [OBI:0002117] + Whole metagenome sequencing assay [OBI:0002623] + Whole virome sequencing assay [OBI:0002768] + +genomic_target_enrichment_method menu GenomicTargetEnrichmentMethodMenu Hybrid selection method (bait-capture) [GENEPIO:0001950] + rRNA depletion method [GENEPIO:0101020] + + +sequence_submitted_by menu SequenceSubmittedByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + McGill University [GENEPIO:0101103] + +quality_control_determination menu QualityControlDeterminationMenu No quality control issues identified [GENEPIO:0100562] + Sequence passed quality control [GENEPIO:0100563] + Sequence failed quality control [GENEPIO:0100564] + Minor quality control issues identified [GENEPIO:0100565] + Sequence flagged for potential quality control issues [GENEPIO:0100566] + Quality control not performed [GENEPIO:0100567] + +quality _control_issues menu QualityControlIssuesMenu Low quality sequence [GENEPIO:0100568] + Sequence contaminated [GENEPIO:0100569] + Low average genome coverage [GENEPIO:0100570] + Low percent genome captured [GENEPIO:0100571] + Read lengths shorter than expected [GENEPIO:0100572] + Sequence amplification artifacts [GENEPIO:0100573] + Low signal to noise ratio [GENEPIO:0100574] + Low coverage of characteristic mutations [GENEPIO:0100575] + + +attribute_package menu AttributePackageMenu Pathogen.cl [GENEPIO:0001835] + Pathogen.env [GENEPIO:0100581] + + +experimental_intervention menu ExperimentalInterventionMenu Addition of substances to food/water [GENEPIO:0100536] + Antimicrobial pre-treatment [GENEPIO:0100537] + Certified animal husbandry practices [GENEPIO:0100538] + Certified organic farming practices [GENEPIO:0100539] + Change in storage conditions [GENEPIO:0100540] + Cleaning/disinfection [GENEPIO:0100541] + Extended downtime between activities [GENEPIO:0100542] + Fertilizer pre-treatment [GENEPIO:0100543] + Logistic slaughter [GENEPIO:0100545] + Microbial pre-treatment [GENEPIO:0100546] + Probiotic pre-treatment [GENEPIO:0100547] + Vaccination [NCIT:C15346] + + +AMR_testing_by menu AmrTestingByMenu Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Agriculture and Agri-Food Canada (AAFC) [GENEPIO:0100553] + Health Canada (HC) [GENEPIO:0100554] + Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Fisheries and Oceans Canada (DFO) [GENEPIO:0100556] + + +antimicrobial_phenotype menu AntimicrobialPhenotypeMenu Antibiotic resistance not defined [GENEPIO:0002040] not defined + Intermediate antimicrobial phenotype [ARO:3004300] intermediate + Indeterminate antimicrobial phenotype [GENEPIO:0100585] indeterminate + Nonsusceptible antimicrobial phenotype [ARO:3004303] nonsusceptible + Resistant antimicrobial phenotype [ARO:3004301] resistant + Susceptible antimicrobial phenotype [ARO:3004302] susceptible + Susceptible dose dependent antimicrobial phenotype [ARO:3004304] susceptible-dose dependent + + +antimicrobial_measurement_units menu AntimicrobialMeasurementUnitsMenu milligram per litre (mg/L) [UO:0000273] mg/L + millimetre (mm) [UO:0000016] mm + microgram per millilitre (ug/mL) [UO:0000274] + + +antimicrobial_measurement_sign menu AntimicrobialMeasurementSignMenu less than (<) [GENEPIO:0001002] < + less than or equal to (<=) [GENEPIO:0001003] <= + equal to (==) [GENEPIO:0001004] == + greater than (>) [GENEPIO:0001006] > + greater than or equal to (>=) [GENEPIO:0001005] >= + + +antimicrobial_laboratory_typing_method menu AntimicrobialLaboratoryTypingMethodMenu Agar diffusion [NCIT:85595] disk diffusion + Antimicrobial gradient (E-test) [NCIT:85596] + Agar dilution [ARO:3004411] agar dilution + Broth dilution [ARO:3004397] broth dilution + + +antimicrobial_laboratory_typing_platform menu AntimicrobialLaboratoryTypingPlatformMenu BIOMIC Microbiology System [ARO:3007569] BIOMIC + Microscan [ARO:3004400] Microscan + Phoenix [ARO:3004401] Phoenix + Sensititre [ARO:3004402] Sensititre + Vitek System [ARO:3004403] Vitek + + +antimicrobial_vendor_name menu AntimicrobialVendorNameMenu Becton Dickinson [ARO:3004405] Becton Dickinson + bioMérieux [ARO:3004406] Biomérieux + Omron [ARO:3004408] Omron + Siemens [ARO:3004407] Siemens + Trek [ARO:3004409] Trek + + +antimicrobial_testing_standard menu AntimicrobialTestingStandardMenu British Society for Antimicrobial Chemotherapy (BSAC) [ARO:3004365] BSAC + Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] CLSI + Deutsches Institut für Normung (DIN) [ARO:3004367] DIN + European Committee on Antimicrobial Susceptibility Testing (EUCAST) [ARO:3004368] EUCAST + National Antimicrobial Resistance Monitoring System (NARMS) [ARO:3007195] NARMS + National Committee for Clinical Laboratory Standards (NCCLS) [ARO:3007193] NCCLS + Société Française de Microbiologie (SFM) [ARO:3004369] SFM + Swedish Reference Group for Antibiotics (SIR) [ARO:3007397] SIR + Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) [ARO:3007398] WRG + + +Antimicrobial Resistance Test Drug Menu AntimicrobialResistanceTestDrugMenu amikacin amikacin + amoxicillin-clavulanic_acid amoxicillin-clavulanic acid + ampicillin ampicillin + azithromycin azithromycin + cefazolin cefazolin + cefepime cefepime + cefotaxime cefotaxime + cefotaxime-clavulanic_acid cefotaxime-clavulanic acid + cefoxitin cefoxitin + cefpodoxime cefpodoxime + ceftazidime ceftazidime + ceftazidime-clavulanic_acid ceftazidime-clavulanic acid + ceftiofur ceftiofur + ceftriaxone ceftriaxone + cephalothin cephalothin + chloramphenicol chloramphenicol + ciprofloxacin ciprofloxacin + clindamycin clindamycin + doxycycline doxycycline + enrofloxacin enrofloxacin + erythromycin erythromycin + florfenicol florfenicol + gentamicin gentamicin + imipenem imipenem + kanamycin kanamycin + levofloxacin levofloxacin + linezolid linezolid + meropenem meropenem + nalidixic_acid nalidixic acid + nitrofurantoin nitrofurantoin + norfloxacin norfloxacin + oxolinic-acid oxolinic-acid + oxytetracycline oxytetracycline + piperacillin piperacillin + piperacillin-tazobactam piperacillin-tazobactam + polymyxin-b polymyxin-b + quinupristin-dalfopristin quinupristin-dalfopristin + streptomycin streptomycin + sulfisoxazole sulfisoxazole + telithromycin telithromycin + tetracycline tetracycline + tigecycline tigecycline + trimethoprim-sulfamethoxazole trimethoprim-sulfamethoxazole + \ No newline at end of file diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index c8a3ddff..ee028ed4 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -1,797 +1,812 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM -GRDI GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession - Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. "Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value." ABCD1234[PHAC]; 12345rev[CFIA] - Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by - Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name - Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken - Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 - Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] - Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. - Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol - Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] - Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] - Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. - Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 - Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name - Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) - Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin - Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] - Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon - Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon - Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date Date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date - Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] - Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date Date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 - Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date Date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 - Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time Time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST - Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time Time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST - Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning - Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 - Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour - Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date Date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli - Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env - Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source - Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic - Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] - Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source - Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source - Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source - Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] - Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type - Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source - Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims - Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source - Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod - Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap - Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date Date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date - Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date Date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 - Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source - Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source - Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 - Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] - Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] - Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport - Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol - Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] - Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] - Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] - Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria - Environmental conditions and measurements - Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 - Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 - Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 - Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 - Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. - Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu - Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu - Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu - Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString - GENEPIO:0001268 Host information host_information - Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host - Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host - Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety - Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed - Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host - Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age - Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease - GENEPIO:0100453 Strain and isolation information strain_and_isolation_information - Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 - Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain - Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession - Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] Multiple alternative isolate IDs can be provided, separated by semi-colons. GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias - Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 - Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 - Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 - Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Strain and isolation information GENEPIO:0100465 isolation_date isolation_date Date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date - Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism - Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] - Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument - Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar - Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 - Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 - GENEPIO:0001441 Sequence information sequence_information - Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 - Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by - Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing - Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) - Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] - Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] - Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] - Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 - Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] - Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel - Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 - Sequence information GENEPIO:0001449 amplicon size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 - Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 - Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no - Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 - Sequence information GENEPIO:0101715 genome sequence filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools - Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control - Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage - Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper - Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet - Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 - Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 - Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 - Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 - Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 - Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 - Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 - Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 - Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 - Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 - Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 - Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ Integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 - Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length Integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 - Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf - GENEPIO:0101082 Taxonomic identification information - Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat - Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 - Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon - Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 - Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc - Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date Date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 - Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 - GENEPIO:0100477 Public repository information public_repository_information - Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca - Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 - Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] - Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession - Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID - Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 - Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 - GENEPIO:0100478 Risk assessment information risk_assessment_information - Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples - Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. - Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] - Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention - Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed - GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance - Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date Date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 - Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM +GRDI GENEPIO:0001150 Sample collection and processing + Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession + Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. """Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: +Public Health Agency of Canada: PHAC +Canadian Food Inspection Agency: CFIA +Agriculture and Agri-Food Canada: AAFC +Fisheries and Oceans Canada: DFO +Environment and Climate Change Canada: ECCC +Health Canada: HC +Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.""" ABCD1234[PHAC]; 12345rev[CFIA] + Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by + Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name + Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken + Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 + Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] + Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. + Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol + Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] + Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] + Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. + Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 + Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name + Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) + Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin + Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] + Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon + Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon + Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date Date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date + Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] + Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date Date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 + Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date Date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 + Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time Time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST + Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time Time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST + Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning + Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 + Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour + Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date Date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli + Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env + Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source + Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic + Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] + Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source + Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source + Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source + Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] + Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type + Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source + Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims + Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source + Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod + Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap + Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date Date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date + Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date Date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 + Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source + Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source + Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 + Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] + Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] + Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport + Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol + Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] + Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] + Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] + Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria + Environmental conditions and measurements + Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 + Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 + Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 + Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 + Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 + Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch + Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection + GENEPIO:0001268 Host information host_information + Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host + Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host + Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety + Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed + Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host + Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease + GENEPIO:0100453 Strain and isolation information strain_and_isolation_information + Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession + Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: +Public Health Agency of Canada: PHAC +Canadian Food Inspection Agency: CFIA +Agriculture and Agri-Food Canada: AAFC +Fisheries and Oceans Canada: DFO +Environment and Climate Change Canada: ECCC +Health Canada: HC +An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] +Multiple alternative isolate IDs can be provided, separated by semi-colons." GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias + Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 + Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 + Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 + Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Strain and isolation information GENEPIO:0100465 isolation_date isolation_date Date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date + Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism + Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] + Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument + Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar + Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 + Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 + GENEPIO:0001441 Sequence information sequence_information + Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 + Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by + Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing + Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) + Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] + Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] + Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] + Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 + Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] + Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel + Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 + Sequence information GENEPIO:0001449 amplicon size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 + Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 + Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no + Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz + Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz + Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 + Sequence information GENEPIO:0101715 genome sequence filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta + GENEPIO:0001457 Bioinformatics and QC metrics + Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools + Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 + Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control + Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage + Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper + Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet + Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 + Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 + Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 + Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 + Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 + Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 + Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 + Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 + Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 + Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 + Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 + Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ Integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 + Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length Integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 + Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf + GENEPIO:0101082 Taxonomic identification information + Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat + Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 + Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon + Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 + Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc + Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date Date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 + Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 + GENEPIO:0100477 Public repository information public_repository_information + Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca + Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 + Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] + Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession + Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID + Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 + Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 + GENEPIO:0100478 Risk assessment information risk_assessment_information + Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples + Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. + Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] + Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention + Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed + GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance + Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date Date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 + Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + GENEPIO:0001516 Contributor acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file From e9e46f7902fbb4d6addd9d2d9f1a23b087471193 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 24 Oct 2024 11:13:51 -0700 Subject: [PATCH 65/96] Version bump + new getFieldTitleMap function And moving getRowMap to phac_dexa export.js since it is only used there. --- lib/DataHarmonizer.js | 64 +++++++++++-------------------------------- package.json | 2 +- 2 files changed, 17 insertions(+), 49 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index 4c012c40..dc886500 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1608,11 +1608,24 @@ class DataHarmonizer { * @return {Dictionary} Dictionary of all fields. */ getFieldNameMap(fields) { - const titleMap = {}; + const map = {}; for (const [fieldIndex, field] of fields.entries()) { - titleMap[field.name] = fieldIndex; + map[field.name] = fieldIndex; } - return titleMap; + return map; + } + + /** + * Get a dictionary of source field TITLES pointing to column index + * @param {Object} fields A flat version of data.js. + * @return {Dictionary} Dictionary of all fields. + */ + getFieldTitleMap(fields) { + const map = {}; + for (const [fieldIndex, field] of fields.entries()) { + map[field.title] = fieldIndex; + } + return map; } /** @@ -1912,51 +1925,6 @@ class DataHarmonizer { return result; } - /** - * Get a dictionary of empty arrays for each ExportHeader field - * FUTURE: enable it to work with hierarchic vocabulary lists - * - * @param {Array} sourceRow array of values to be exported. - * @param {Array} sourceFields list of source fields to examine for mappings. - * @param {Array} RuleDB list of export fields modified by rules. - * @param {Array} fields list of export fields modified by rules. - * @param {Array} titleMap map of field names to column index. - * @param {String} prefix of export format to examine. - * @return {Array} fields Dictionary of all fields. - */ - - getRowMap(sourceRow, sourceFields, RuleDB, fields, titleMap, prefix) { - for (const title of sourceFields) { - const sourceIndex = titleMap[title]; - let value = sourceRow[sourceIndex]; // All text values. - // Sets source field to data value so that rules can reference it easily. - RuleDB[title] = value; - // Check to see if value is in vocabulary of given select field, and if it - // has a mapping for export to a GRDI target field above, then set target - // to value. - if (value && value.length > 0) { - const vocab_list = fields[sourceIndex]['schema:ItemList']; - if (value in vocab_list) { - const term = vocab_list[value]; - // Looking for term.exportField['GRDI'] for example: - if ('exportField' in term && prefix in term.exportField) { - for (let mapping of term.exportField[prefix]) { - // Here mapping involves a value substitution - if ('value' in mapping) { - value = mapping.value; - // Changed on a copy of data, not handsongrid table - sourceRow[sourceIndex] = value; - } - if ('field' in mapping && mapping['field'] in RuleDB) { - RuleDB[mapping['field']] = value; - } - } - } - } - } - } - } - /** * Return first and last items of a delimited string * @param {String} value A string of values separated by delimiter. diff --git a/package.json b/package.json index 0e0f29cb..3351ddd3 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "data-harmonizer", - "version": "1.7.1", + "version": "1.7.2", "description": "A standardized spreadsheet editor and validator that can be run offline and locally", "repository": "git@github.com:cidgoh/DataHarmonizer.git", "license": "MIT", From 4f0b5cfea2bfd69cb5d3791ae254e98fa13284cc Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 24 Oct 2024 11:22:14 -0700 Subject: [PATCH 66/96] phac_dexa export issue WIP --- .../exampleInput/small_samples_valid.tsv | 9 +++ web/templates/phac_dexa/export.js | 68 +++++++++++++++++-- 2 files changed, 71 insertions(+), 6 deletions(-) create mode 100644 web/templates/phac_dexa/exampleInput/small_samples_valid.tsv diff --git a/web/templates/phac_dexa/exampleInput/small_samples_valid.tsv b/web/templates/phac_dexa/exampleInput/small_samples_valid.tsv new file mode 100644 index 00000000..0107d077 --- /dev/null +++ b/web/templates/phac_dexa/exampleInput/small_samples_valid.tsv @@ -0,0 +1,9 @@ +SPECIMEN_ID ISOLATE_ID SAMPLE_ID SENTINEL_SITE LFZ_ADDITIONAL_SAMPLE_ID LFZ_ORIGIN_COUNTRY SUBJECT_CODE SUBJECT_DESCRIPTIONS SUBMITTINGORG_1 SUBMITTINGLAB_1 PROJECT_1 COUNTRY_1 PROVINCE_1 CENSUSDIVISION_1 REGION YEAR MONTH QTR DATECOLLECTED_1 DATERECEIVED_1 DATESHIPPED_1 ESTABLISHMENT_1 SPECIES STTYPE STYPE COMMODITY SPECIMENSOURCE_1 SPECIMENSUBSOURCE_1 SUBJECT_SUBTYPE FIELDSTAFF_1 IN_STORE_PROCESSING MAYCONTAINFROZENMEAT_1 NOOFCASHREGISTERS_1 PRICEPERKG_1 STORETYPE_SAMPLINGSITE_1 TEMPERATUREMAX_1 TEMPERATUREMIN_1 TEMPERATUREARRIVAL_1 VETID ROOMID PENID SAMPLING_TYPE BARN_ID DATE_PACKED FINAL_ID_GENUS FINAL_ID_SPECIES FINAL_ID_SUBSPECIES FINAL_ID_SEROTYPE FINAL_ID_ANTIGEN FINAL_ID_PHAGETYPE SA_Serotype_Method SEROTYPE_GR MIC_AMC MIC_AMK MIC_AMP MIC_AZM MIC_CEP MIC_CHL MIC_CIP MIC_CRO MIC_FOX MIC_GEN MIC_KAN MIC_MEM MIC_NAL MIC_SSS MIC_STR MIC_SXT MIC_TET MIC_TIO N_OF_RESISTANCE NBTESTED R_PATTERN AMR_PA2C RLEAST1 RLEAST2 RLEAST3 RLEAST4 RLEAST5 SIR_AMC SIR_AMK SIR_AMP SIR_AZM SIR_CEP SIR_CHL SIR_CIP SIR_CRO SIR_FOX SIR_GEN SIR_KAN SIR_MEM SIR_NAL SIR_SSS SIR_STR SIR_SXT SIR_TET SIR_TIO RAMC RAMK RAMP RAZM RCEP RCHL RCIP RCRO RFOX RGEN RKAN RMEM RNAL RSSS RSTR RSXT RTET RTIO A2C CAMC CAMK CAMP CAZM CCEP CCHL CCIP CCRO CFOX CGEN CKAN CMEM CNAL CSSS CSTR CSXT CTET CTIO STHY_TESTSRC_ID WINN_TESTSRC_ID GUEL_TESTSRC_ID RCIP_DANMAP EPIDATESTAMP_1 ACSSUT AKSSUT ACKSSUT MDR_A_SSUT EXCLUSION RAMINOGLY RBETALACTAM RQUINOLONES RFOLINHIBITOR MDR specimen_number EXTERNAL_AGENT FARM_FLAG AMIKACINGELET +29992 SA20132545 SA20132545 SA20132545 UofG - Food Microbiology 13-024322-1 Industrial Monitoring Canada ONTARIO ONTARIO 2013 5 2 09-May-13 09-May-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Schwarzengrund 4:d:1,7 PT Other serovars 0 SA20132545 23-May-13 Salmonella | +29993 SA20132546 SA20132546 SA20132546 UofG - Food Microbiology 13-025636-1 Industrial Monitoring Canada ONTARIO ONTARIO 2013 5 2 09-May-13 09-May-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Bredeney 4:l,v:1,7 PT Other serovars 0 SA20132546 23-May-13 Salmonella | +29994 SA20132547 SA20132547 SA20132547 UofG - Food Microbiology 13-027114-1 Industrial Monitoring Canada ONTARIO ONTARIO 2013 5 2 09-May-13 09-May-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Rubislaw 11:r:e,n,x PT Other serovars 0 SA20132547 23-May-13 Salmonella | +36372 SA20133878 SA20133878 SA20133878 UofG - Food Microbiology 13-045380-1 Industrial Monitoring Canada ONTARIO ONTARIO 2013 6 2 04-Jun-13 11-Jul-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Schwarzengrund 4:d:1,7 PT Other serovars 0 SA20133878 06-Aug-13 Salmonella | +36373 SA20133879 SA20133879 SA20133879 UofG - Food Microbiology 13-045380-3 Industrial Monitoring Canada ONTARIO ONTARIO 2013 6 2 06-Jun-13 11-Jul-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Schwarzengrund 4:d:1,7 PT Other serovars 0 SA20133879 06-Aug-13 Salmonella | +36374 SA20133880 SA20133880 SA20133880 UofG - Food Microbiology 13-048524-1 Industrial Monitoring Canada ONTARIO ONTARIO 2013 6 2 10-Jun-13 11-Jul-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Muenchen 6,8:d:1,2 PT Other serovars 0 SA20133880 06-Aug-13 Salmonella | +36375 SA20133881 SA20133881 SA20133881 UofG - Food Microbiology 13-048524-3 Industrial Monitoring Canada ONTARIO ONTARIO 2013 6 2 12-Jun-13 11-Jul-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Muenchen 6,8:d:1,2 PT Other serovars 0 SA20133881 06-Aug-13 Salmonella | +36376 SA20133882 SA20133882 SA20133882 UofG - Food Microbiology 13-048520-1 Industrial Monitoring Canada ONTARIO ONTARIO 2013 7 3 11-Jul-13 11-Jul-13 Chicken ANIMAL Avian Domestic/Farmed Carcass Swab 0 0 Salmonella enterica enterica (I) Muenchen 6,8:d:1,2 PT Other serovars 0 SA20133882 06-Aug-13 Salmonella | \ No newline at end of file diff --git a/web/templates/phac_dexa/export.js b/web/templates/phac_dexa/export.js index 22456a6e..fa7859e7 100644 --- a/web/templates/phac_dexa/export.js +++ b/web/templates/phac_dexa/export.js @@ -108,7 +108,7 @@ export default { ]; const sourceFields = dh.getFields(dh.table); - const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + const sourceFieldNameMap = dh.getFieldTitleMap(sourceFields); // Fills in the above mapping of export field to source fields (or just set // source fields manually above) @@ -117,7 +117,7 @@ export default { // Copy headers to 1st row of new export table const outputMatrix = [[...ExportHeaders.keys()]]; - let normalize = self.initLookup(self); + let normalize = self.initLookup(); const inputMatrix = dh.getTrimmedData(dh.hot); for (const inputRow of inputMatrix) { @@ -192,6 +192,55 @@ export default { return value.join(';'); }, + + /** + * Get a dictionary of empty arrays for each ExportHeader field + * FUTURE: enable it to work with hierarchic vocabulary lists + * + * @param {Array} sourceRow array of values to be exported. + * @param {Array} sourceFields list of source fields to examine for mappings. + * @param {Array} RuleDB list of export fields modified by rules. + * @param {Array} fields list of export fields modified by rules. + * @param {Array} titleMap map of field names to column index. + * @param {String} prefix of export format to examine. + * @return {Array} fields Dictionary of all fields. + */ + + getRowMap: function (sourceRow, ruleSourceFieldNames, RuleDB, fields, titleMap, prefix) { + for (const title of ruleSourceFieldNames) { + const sourceIndex = titleMap[title]; + let value = sourceRow[sourceIndex]; // All text values. + // Sets source field to data value so that rules can reference it easily. + RuleDB[title] = value; + // Check to see if value is in vocabulary of given select field, and if it + // has a mapping for export to a GRDI target field above, then set target + // to value. + if (value && value.length > 0) { + console.log("FIELDS", fields[sourceIndex], value); + const vocab_list = fields[sourceIndex]['flatVocabulary']; + if (vocab_list && vocab_list.includes(value)) { + const term = vocab_list[value]; + console.log("TERM", term); + // Looking for term.exportField['GRDI'] for example: + if ('exportField' in term && prefix in term.exportField) { + for (let mapping of term.exportField[prefix]) { + // Here mapping involves a value substitution + if ('value' in mapping) { + value = mapping.value; + // Changed on a copy of data, not handsongrid table + sourceRow[sourceIndex] = value; + } + if ('field' in mapping && mapping['field'] in RuleDB) { + RuleDB[mapping['field']] = value; + } + } + } + } + } + } + }, + + /** Rule-based target field value calculation based on given data row * @param {Object} dataRow. * @param {Object} sourceFields. @@ -238,7 +287,7 @@ export default { // This will set content of a target field based on data.js vocabulary // exportField {'field':[target column],'value':[replacement value]]} // mapping if any. - dh.getRowMap( + this.getRowMap( dataRow, ruleSourceFieldNames, RuleDB, @@ -247,6 +296,10 @@ export default { 'GRDI' ); + console.log("getRowMap"); + console.log(dataRow, ruleSourceFieldNames, RuleDB, sourceFields,sourceFieldNameMap); + + // So all rule field values can be referenced in lower case. for (let sourceField of Object.keys(RuleDB)) { if (RuleDB[sourceField]) RuleDB[sourceField] = RuleDB[sourceField].toLowerCase(); @@ -254,6 +307,7 @@ export default { // STTYPE: ANIMAL ENVIRONMENT FOOD HUMAN PRODUCT QA UNKNOWN switch (RuleDB.STTYPE) { + case 'animal': { // species-> host (common name); RuleDB['host (common name)'] = RuleDB.SPECIES; @@ -265,6 +319,7 @@ export default { ) { RuleDB.animal_or_plant_population = RuleDB.SPECIES; } + console.log("TESTING:RuleDB.STTYPE", RuleDB.STTYPE, RuleDB.SPECIES,RuleDB.collection_device,RuleDB.environmental_site, RuleDB.animal_or_plant_population); break; // prevents advancing to FOOD } @@ -345,9 +400,10 @@ export default { * * @return {Object} term normalize lookup table. */ - initLookup: function (self) { + initLookup: function () { let normalize = {}; - for (const line of self.LOOKUP.split('\n')) { + for (const line of this.LOOKUP.split('\n')) { + let [ontology_id, parent, label, normalization] = line .split('\t') .map(function (e) { @@ -810,5 +866,5 @@ FOODON_00002361 food_product white pepper FOODON_03411345 food_product yeast UBERON_0001040 anatomical_part yolk sac ENVO_00010625 environmental_site zoo pet/zoo; calgary zoo`, - }, + } }; From 4f10403381744567fc5e9ccc080924753c7f304f Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 24 Oct 2024 13:10:34 -0700 Subject: [PATCH 67/96] fixed export issue --- web/templates/phac_dexa/export.js | 58 +++++++++++++++++++------------ 1 file changed, 36 insertions(+), 22 deletions(-) diff --git a/web/templates/phac_dexa/export.js b/web/templates/phac_dexa/export.js index fa7859e7..c84cd583 100644 --- a/web/templates/phac_dexa/export.js +++ b/web/templates/phac_dexa/export.js @@ -1,5 +1,6 @@ // Adds existing functions/methods to DataHarminizer. export default { + // NOTE: FUTURE DEV: This has a mixture of sourceFieldNameMap AND sourceFieldTitleMap rules/lookups that should be just moved to sourceFieldNameMap. ALTERNATELY, a new LinkML based vision of converting from source to destination schema class. 'Dexa to GRDI': { fileType: 'xls', status: 'published', @@ -108,12 +109,15 @@ export default { ]; const sourceFields = dh.getFields(dh.table); - const sourceFieldNameMap = dh.getFieldTitleMap(sourceFields); + const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + const sourceFieldTitleMap = dh.getFieldTitleMap(sourceFields); // Fills in the above mapping of export field to source fields (or just set // source fields manually above) dh.getHeaderMap(ExportHeaders, sourceFields, 'GRDI'); + //console.log("Headers", ExportHeaders, sourceFields); + // Copy headers to 1st row of new export table const outputMatrix = [[...ExportHeaders.keys()]]; @@ -126,13 +130,15 @@ export default { dh, inputRow, sourceFields, - sourceFieldNameMap, + sourceFieldTitleMap, // TITLE Map normalize, preserveCapsFields ); + const outputRow = []; for (const headerName of ExportHeaders.keys()) { + // If Export Header field is in RuleDB, set output value from it, and // continue. // Sometimes fields have been set to 0 length. @@ -148,14 +154,19 @@ export default { continue; } + + // Otherwise apply source (many to one) to target field transform: const sources = ExportHeaders.get(headerName); + + //console.log("Header", headerName, headerName in RuleDB, inputRow, sources, sourceFields, sourceFieldNameMap) + let value = dh.getMappedField( headerName, inputRow, sources, sourceFields, - sourceFieldNameMap, + sourceFieldNameMap, // NAME Map ';', 'GRDI' ); @@ -206,7 +217,7 @@ export default { * @return {Array} fields Dictionary of all fields. */ - getRowMap: function (sourceRow, ruleSourceFieldNames, RuleDB, fields, titleMap, prefix) { + getRowMap: function (dh, sourceRow, ruleSourceFieldNames, RuleDB, fields, titleMap, prefix) { for (const title of ruleSourceFieldNames) { const sourceIndex = titleMap[title]; let value = sourceRow[sourceIndex]; // All text values. @@ -216,22 +227,26 @@ export default { // has a mapping for export to a GRDI target field above, then set target // to value. if (value && value.length > 0) { - console.log("FIELDS", fields[sourceIndex], value); - const vocab_list = fields[sourceIndex]['flatVocabulary']; + let field = fields[sourceIndex]; + const vocab_list = field['flatVocabulary']; if (vocab_list && vocab_list.includes(value)) { - const term = vocab_list[value]; - console.log("TERM", term); - // Looking for term.exportField['GRDI'] for example: - if ('exportField' in term && prefix in term.exportField) { - for (let mapping of term.exportField[prefix]) { - // Here mapping involves a value substitution - if ('value' in mapping) { - value = mapping.value; - // Changed on a copy of data, not handsongrid table - sourceRow[sourceIndex] = value; - } - if ('field' in mapping && mapping['field'] in RuleDB) { - RuleDB[mapping['field']] = value; + if ('sources' in field) { + // FUTURE REVISION: Currently ASSUMES first menu contains value (if multiple) menus. + const menu_name = field['sources'][0]; + const permissible_values = dh.schema.enums[menu_name]['permissible_values']; + const term = permissible_values[value]; + // Looking for 'GRDI' key in choice for example: + if ('exportField' in term && prefix in term.exportField) { + for (let mapping of term.exportField[prefix]) { + // Here mapping involves a value substitution + if ('value' in mapping) { + value = mapping.value; + // Changed on a copy of data, not handsongrid table + sourceRow[sourceIndex] = value; + } + if ('field' in mapping && mapping['field'] in RuleDB) { + RuleDB[mapping['field']] = value; + } } } } @@ -287,7 +302,7 @@ export default { // This will set content of a target field based on data.js vocabulary // exportField {'field':[target column],'value':[replacement value]]} // mapping if any. - this.getRowMap( + this.getRowMap(dh, dataRow, ruleSourceFieldNames, RuleDB, @@ -296,7 +311,6 @@ export default { 'GRDI' ); - console.log("getRowMap"); console.log(dataRow, ruleSourceFieldNames, RuleDB, sourceFields,sourceFieldNameMap); // So all rule field values can be referenced in lower case. @@ -319,7 +333,7 @@ export default { ) { RuleDB.animal_or_plant_population = RuleDB.SPECIES; } - console.log("TESTING:RuleDB.STTYPE", RuleDB.STTYPE, RuleDB.SPECIES,RuleDB.collection_device,RuleDB.environmental_site, RuleDB.animal_or_plant_population); + //console.log("TESTING:RuleDB", RuleDB); break; // prevents advancing to FOOD } From c7f201409a98e30606b78d2aca2656ad6031c535 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Thu, 24 Oct 2024 13:23:31 -0700 Subject: [PATCH 68/96] Updated descriptions --- web/templates/hpai/schema.json | 5 +++++ web/templates/hpai/schema.yaml | 11 ++++++----- web/templates/hpai/schema_core.yaml | 10 +++++----- 3 files changed, 16 insertions(+), 10 deletions(-) diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index 58fd8481..6098b9ff 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -15305,6 +15305,7 @@ "value": "1.0.0" } }, + "description": "Master specification (contains all fields/terms)", "title": "HPAI", "from_schema": "https://example.com/hpai", "is_a": "dh_interface", @@ -24357,6 +24358,7 @@ "value": "1.0.0" } }, + "description": "Food-specific template for HPAI surveillance", "title": "HPAI Food", "from_schema": "https://example.com/hpai", "is_a": "dh_interface", @@ -29115,6 +29117,7 @@ "value": "1.0.0" } }, + "description": "Wastewater-specific template for HPAI surveillance", "title": "HPAI Wastewater", "from_schema": "https://example.com/hpai", "is_a": "dh_interface", @@ -36606,6 +36609,7 @@ "value": "1.0.0" } }, + "description": "Environment-specific template for HPAI surveillance (wastewater template contains more specific fields)", "title": "HPAI Environmental", "from_schema": "https://example.com/hpai", "is_a": "dh_interface", @@ -44097,6 +44101,7 @@ "value": "1.0.0" } }, + "description": "Host-specific template for HPAI surveillance", "title": "HPAI Host", "from_schema": "https://example.com/hpai", "is_a": "dh_interface", diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index cac91b64..ef5dff03 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -19,7 +19,7 @@ classes: HPAI: name: HPAI title: HPAI - description: null + description: Master specification (contains all fields/terms) is_a: dh_interface see_also: null annotations: @@ -1081,7 +1081,7 @@ classes: HPAIFood: name: HPAIFood title: HPAI Food - description: null + description: Food-specific template for HPAI surveillance is_a: dh_interface see_also: null annotations: @@ -1639,7 +1639,7 @@ classes: HPAIWW: name: HPAIWW title: HPAI Wastewater - description: null + description: Wastewater-specific template for HPAI surveillance is_a: dh_interface see_also: null annotations: @@ -2529,7 +2529,8 @@ classes: HPAIEnviro: name: HPAIEnviro title: HPAI Environmental - description: null + description: Environment-specific template for HPAI surveillance (wastewater template + contains more specific fields) is_a: dh_interface see_also: null annotations: @@ -3419,7 +3420,7 @@ classes: HPAIHost: name: HPAIHost title: HPAI Host - description: null + description: Host-specific template for HPAI surveillance is_a: dh_interface see_also: null annotations: diff --git a/web/templates/hpai/schema_core.yaml b/web/templates/hpai/schema_core.yaml index d960a6e8..4ac22c7b 100644 --- a/web/templates/hpai/schema_core.yaml +++ b/web/templates/hpai/schema_core.yaml @@ -15,7 +15,7 @@ classes: 'HPAI': name: 'HPAI' title: 'HPAI' - description: + description: 'Master specification (contains all fields/terms)' is_a: dh_interface see_also: annotations: @@ -23,7 +23,7 @@ classes: 'HPAIFood': name: 'HPAIFood' title: 'HPAI Food' - description: + description: 'Food-specific template for HPAI surveillance' is_a: dh_interface see_also: annotations: @@ -31,7 +31,7 @@ classes: 'HPAIWW': name: 'HPAIWW' title: 'HPAI Wastewater' - description: + description: 'Wastewater-specific template for HPAI surveillance' is_a: dh_interface see_also: annotations: @@ -39,7 +39,7 @@ classes: 'HPAIEnviro': name: 'HPAIEnviro' title: 'HPAI Environmental' - description: + description: 'Environment-specific template for HPAI surveillance (wastewater template contains more specific fields)' is_a: dh_interface see_also: annotations: @@ -47,7 +47,7 @@ classes: 'HPAIHost': name: 'HPAIHost' title: 'HPAI Host' - description: + description: 'Host-specific template for HPAI surveillance' is_a: dh_interface see_also: annotations: From c9924d4a6b7e3de88a47bf7bed40cbc6cebd6b2a Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 25 Oct 2024 22:56:16 -0700 Subject: [PATCH 69/96] mpox GSAID export fix to address field --- web/templates/mpox/export.js | 47 ++++++++++++++--------------- web/templates/mpox/schema.json | 28 +++++------------ web/templates/mpox/schema.yaml | 11 +++---- web/templates/mpox/schema_slots.tsv | 8 ++--- 4 files changed, 39 insertions(+), 55 deletions(-) diff --git a/web/templates/mpox/export.js b/web/templates/mpox/export.js index 4dafaaf4..2f7d22ff 100644 --- a/web/templates/mpox/export.js +++ b/web/templates/mpox/export.js @@ -119,34 +119,33 @@ export default { // as below with 'Address', that a column name appears two or more times. const ExportHeaders = [ - ['Submitter', []], // submitter - ['FASTA filename', []], // fn - ['Virus name', []], // covv_virus_name + ['Submitter', []], // submitter + ['FASTA filename', []], // fn + ['Virus name', []], // pox_virus_name ['Passage details/history', []], // covv_passage - ['Collection date', []], // covv_collection_date - ['Location', []], // covv_location + ['Collection date', []], // pox_collection_date + ['Location', []], // pox_location ['Additional location information', []], // covv_add_location - ['Host', []], // covv_host + ['Host', []], // pox_host ['Additional host information', []], // covv_add_host_info - ['Sampling Strategy', []], // covv_sampling_strategy - ['Gender', []], // covv_gender - ['Patient age', []], // covv_patient_age - ['Patient status', []], // covv_patient_status - ['Specimen source', []], // covv_specimen - ['Outbreak', []], // covv_outbreak - ['Last vaccinated', []], // covv_last_vaccinated - ['Treatment', []], // covv_treatment - ['Sequencing technology', []], // covv_seq_technology - ['Assembly method', []], // covv_assembly_method - ['Depth of coverage', []], - ['Coverage', []], // covv_coverage - ['Originating lab', []], // covv_orig_lab - ['Address', []], // covv_orig_lab_addr - ['Sample ID given by the sample provider', []], // covv_provider_sample_id - ['Submitting lab', []], // covv_subm_lab + ['Sampling Strategy', []], // pox_sampling_strategy + ['Gender', []], // pox_gender + ['Patient age', []], // pox_patient_age + ['Patient status', []], // pox_patient_status + ['Specimen source', []], // pox_specimen + ['Outbreak', []], // pox_outbreak + ['Last vaccinated', []], // pox_last_vaccinated + ['Treatment', []], // pox_treatment + ['Sequencing technology', []], // pox_seq_technology + ['Assembly method', []], // pox_assembly_method + ['Depth of coverage', ['depth_of_coverage_value']], // pox_coverage + ['Originating lab', []], // pox_orig_lab + ['Address', ['sample_collector_contact_address']], // pox_orig_lab_addr + ['Sample ID given by the sample provider', []], // pox_provider_sample_id + ['Submitting lab', []], // pox_subm_lab // Custom rule: 2nd address points to sequence submitter. - ['Address', ['sequence submitter contact address']], // covv_subm_lab_addr - ['Sample ID given by the submitting laboratory', []], // covv_subm_sample_id + ['Address', ['sequence_submitter_contact_address']], // pox_subm_lab_addr + ['Sample ID given by the submitting laboratory', ['specimen_collector_sample_id']], // pox_subm_sample_id ['Authors', []], // covv_authors ]; diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index a9115c15..8e0e3c36 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -11647,9 +11647,6 @@ } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:sequenced%20by%20contact%20address" - ], "slot_uri": "GENEPIO:0100423", "domain_of": [ "Mpox", @@ -11714,7 +11711,6 @@ ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Address", "NML_LIMS:sequence%20submitter%20contact%20address" ], "slot_uri": "GENEPIO:0001167", @@ -13663,12 +13659,12 @@ "insdc_sequence_read_accession": { "name": "insdc_sequence_read_accession", "rank": 6, - "slot_group": "Database identifiers" + "slot_group": "Database Identifiers" }, "insdc_assembly_accession": { "name": "insdc_assembly_accession", "rank": 7, - "slot_group": "Database identifiers" + "slot_group": "Database Identifiers" }, "gisaid_accession": { "name": "gisaid_accession", @@ -15182,7 +15178,7 @@ "Mpox", "MpoxInternational" ], - "slot_group": "Database identifiers", + "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -15216,7 +15212,7 @@ "Mpox", "MpoxInternational" ], - "slot_group": "Database identifiers", + "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -17492,9 +17488,6 @@ } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:sequenced%20by%20contact%20address" - ], "rank": 74, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", @@ -17586,7 +17579,6 @@ ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Address", "NML_LIMS:sequence%20submitter%20contact%20address" ], "rank": 77, @@ -19481,12 +19473,12 @@ "insdc_sequence_read_accession": { "name": "insdc_sequence_read_accession", "rank": 5, - "slot_group": "Database identifiers" + "slot_group": "Database Identifiers" }, "insdc_assembly_accession": { "name": "insdc_assembly_accession", "rank": 6, - "slot_group": "Database identifiers" + "slot_group": "Database Identifiers" }, "gisaid_virus_name": { "name": "gisaid_virus_name", @@ -20924,7 +20916,7 @@ "Mpox", "MpoxInternational" ], - "slot_group": "Database identifiers", + "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -20958,7 +20950,7 @@ "Mpox", "MpoxInternational" ], - "slot_group": "Database identifiers", + "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "pattern": "{UPPER_CASE}", "structured_pattern": { @@ -23294,9 +23286,6 @@ } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:sequenced%20by%20contact%20address" - ], "rank": 77, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", @@ -23385,7 +23374,6 @@ ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Address", "NML_LIMS:sequence%20submitter%20contact%20address" ], "rank": 80, diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index f9d2e8e3..292ca16b 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -178,10 +178,10 @@ classes: slot_group: Database Identifiers insdc_sequence_read_accession: rank: 6 - slot_group: Database identifiers + slot_group: Database Identifiers insdc_assembly_accession: rank: 7 - slot_group: Database identifiers + slot_group: Database Identifiers gisaid_accession: rank: 8 slot_group: Database Identifiers @@ -1081,10 +1081,10 @@ classes: slot_group: Database Identifiers insdc_sequence_read_accession: rank: 5 - slot_group: Database identifiers + slot_group: Database Identifiers insdc_assembly_accession: rank: 6 - slot_group: Database identifiers + slot_group: Database Identifiers gisaid_virus_name: rank: 7 slot_group: Database Identifiers @@ -2871,8 +2871,6 @@ slots: range: WhitespaceMinimizedString examples: - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada - exact_mappings: - - NML_LIMS:sequenced%20by%20contact%20address sequence_submitted_by: name: sequence_submitted_by title: sequence submitted by @@ -2909,7 +2907,6 @@ slots: examples: - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada exact_mappings: - - GISAID:Address - NML_LIMS:sequence%20submitter%20contact%20address purpose_of_sequencing: name: purpose_of_sequencing diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 738d420f..dd39339b 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -5,8 +5,8 @@ Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_sp Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID Mpox;MpoxInternational Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession Mpox;MpoxInternational Mpox;MpoxInternational Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession Mpox;MpoxInternational -Mpox;MpoxInternational Database identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION Mpox;MpoxInternational -Mpox;MpoxInternational Database identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession Mpox;MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION Mpox;MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession Mpox;MpoxInternational MpoxInternational Database Identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name MpoxInternational Mpox;MpoxInternational Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession Mpox;MpoxInternational Mpox;MpoxInternational GENEPIO:0001150 Sample collection and processing sample_collection_and_processing Mpox;MpoxInternational @@ -131,11 +131,11 @@ MpoxInternational Sequencing GENEPIO:0100416 sequenced by sequenced_by Whitespac Mpox Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString NullValueMenu The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab Mpox MpoxInternational Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequenced by contact address Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Mpox;MpoxInternational Mpox Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by Mpox MpoxInternational Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address sequence submitter contact address Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequence submitter contact address Mpox;MpoxInternational Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Mpox MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details Mpox;MpoxInternational From dfb2020582c431f8ab292831b6160ab05ca4d1ff Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 25 Oct 2024 23:37:24 -0700 Subject: [PATCH 70/96] Fixing NML_LIMS export --- web/templates/mpox/export.js | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/web/templates/mpox/export.js b/web/templates/mpox/export.js index 2f7d22ff..282a1ecf 100644 --- a/web/templates/mpox/export.js +++ b/web/templates/mpox/export.js @@ -185,7 +185,8 @@ export default { if (field.fieldName === 'specimen processing') { // Specimen processing is a multi-select field const standardizedCellValArr = standardizedCellVal.split(';'); - if (!standardizedCellValArr.includes('virus passage')) continue; + if (!standardizedCellValArr.includes('virus passage')) + continue; // We only want to map "virus passage" mappedCellVal = 'Virus passage'; } @@ -204,6 +205,7 @@ export default { } // Add 'passage number ' prefix to number. + // APPEARS UNUSED Oct 25 2024 in Mpox specification if (field.fieldName === 'passage number') { mappedCellVal = 'passage number ' + mappedCellVal; } @@ -373,6 +375,7 @@ export default { const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + const sourceFieldTitleMap = dh.getFieldTitleMap(sourceFields); // Fills in the above mapping (or just set manually above) dh.getHeaderMap(ExportHeaders, sourceFields, 'NML_LIMS'); @@ -410,7 +413,7 @@ export default { // Note: if this field eventually gets null values, then must do // field.dataStatus check. const value = - inputRow[sourceFieldNameMap['signs and symptoms']] || ''; + inputRow[sourceFieldTitleMap['signs and symptoms']] || ''; outputRow.push(value ? 'Y' : 'N'); continue; } @@ -419,9 +422,9 @@ export default { // by looking at year or month in "sample collection date precision" if (headerName === 'HC_COLLECT_DATE') { let value = - inputRow[sourceFieldNameMap['sample collection date']] || ''; + inputRow[sourceFieldTitleMap['sample collection date']] || ''; const date_unit = - inputRow[sourceFieldNameMap['sample collection date precision']]; + inputRow[sourceFieldTitleMap['sample collection date precision']]; outputRow.push(dh.setDateChange(date_unit, value, '01')); continue; } @@ -437,7 +440,7 @@ export default { 'environmental material', 'environmental site', ]) { - const value = inputRow[sourceFieldNameMap[fieldName]]; + const value = inputRow[sourceFieldTitleMap[fieldName]]; // Ignore all null value types if (!value || null_values.has(value)) { From e11338235e21f955c1f21b92e2efb0998b094142 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 25 Oct 2024 23:42:20 -0700 Subject: [PATCH 71/96] notes --- web/templates/mpox/export.js | 1 + 1 file changed, 1 insertion(+) diff --git a/web/templates/mpox/export.js b/web/templates/mpox/export.js index 282a1ecf..137bec6e 100644 --- a/web/templates/mpox/export.js +++ b/web/templates/mpox/export.js @@ -182,6 +182,7 @@ export default { const field = sourceFields[sourceFieldIndex]; const standardizedCellVal = mappedCellVal.toLowerCase().trim(); + // NOT APPLICABLE TO GISAID? Oct 25, 2024 if (field.fieldName === 'specimen processing') { // Specimen processing is a multi-select field const standardizedCellValArr = standardizedCellVal.split(';'); From 1360a57ba340fc83355f3c2fa8f8fda12ee71bfc Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sat, 26 Oct 2024 09:28:32 -0700 Subject: [PATCH 72/96] fix to return schema.type of slot range when it is given in first any_of entry plus more docs. --- lib/Validator.js | 53 ++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 45 insertions(+), 8 deletions(-) diff --git a/lib/Validator.js b/lib/Validator.js index 2803f089..440a9144 100644 --- a/lib/Validator.js +++ b/lib/Validator.js @@ -45,14 +45,21 @@ class Validator { ); } - // LinkML does not yet have support for non-numeric minimum_value and maximum_value. In the - // meantime, DataHarmonizer has a convention of putting these values in todos with specific - // prefixes. + /* LinkML does not yet have support for non-numeric minimum_value and + maximum_value. In the meantime, DataHarmonizer has a convention of + putting these values in todos with specific prefixes. If a slot has + any todos, process them here. + + This has to be defined in runtime since variables like {today} exist + in todos array. + */ const processTodos = (slotDefinition, todos) => { if (!todos || !todos.length) { return; } - const slotType = this.#schema.types?.[slotDefinition.range]; + + const slotType = this.getSlotType(slotDefinition); + if (slotType?.uri === 'xsd:date') { for (const todo of todos) { if (todo.substring(0, 2) === '>=') { @@ -62,6 +69,7 @@ class Validator { } } } + for (const def of slotDefinition.any_of || []) { processTodos(def, todos); } @@ -75,13 +83,15 @@ class Validator { processTodos(def, todos); } }; + for (const slotDefinition of Object.values(this.#targetClassInducedSlots)) { processTodos(slotDefinition, slotDefinition.todos); } - // DataHarmonizer has a convention for using todos to specify that for a given row the value - // of one column is the min/max value of another column (e.g. ">={other slot name}"). Index - // info about that here. + /* DataHarmonizer has a convention for using todos to specify that for a + given row the value of one column is the min/max value of another column + (e.g. ">={other slot name}"). Index info about that here. + */ this.#dependantMinimumValuesMap = new Map(); this.#dependantMaximumValuesMap = new Map(); for (const slotDefinition of Object.values(this.#targetClassInducedSlots)) { @@ -130,6 +140,32 @@ class Validator { this.#valueValidatorMap = new Map(); } + + /* This returns a single primitve data type for a slot - a decimal, date, + string etc. or possibly an enumeration. Enumerations are handled + separately however (by const slotEnum = ...). Slots either use "range" + attribute, OR they use any_of or exactly_one_of etc. attribute expression + where an array of [range: x, range: y ...] is given. This call returns the + schema.types[] lookup for the FIRST range in the list in that case, which + may be undefined if that is a menu too. + */ + getSlotType(slotDefinition) { + + var slotType = this.#schema.types?.[slotDefinition.range]; + + if (slotType === undefined) { + const extended_range = ['any_of', 'all_of', 'exactly_one_of', 'none_of']; + for (let def of extended_range) { + if (def in slotDefinition) { + slotType = this.#schema.types?.[slotDefinition[def][0]['range']]; + break; + } + } + } + + return slotType + } + getValidatorForSlot(slot, options = {}) { const { cacheKey, inheritedRange } = options; if (typeof cacheKey === 'string' && this.#valueValidatorMap.has(cacheKey)) { @@ -147,7 +183,8 @@ class Validator { slotDefinition.range = inheritedRange; } - const slotType = this.#schema.types?.[slotDefinition.range]; + const slotType = this.getSlotType(slotDefinition); + const slotEnum = this.#schema.enums?.[slotDefinition.range]; const slotPermissibleValues = Object.values( slotEnum?.permissible_values ?? {} From 540450a2f51e6190e34cf5ea7431dfba879fc61d Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sat, 26 Oct 2024 09:33:31 -0700 Subject: [PATCH 73/96] underscored rename of {sample collection date} --- web/templates/ambr/schema.json | 2 +- web/templates/ambr/schema.yaml | 2 +- web/templates/ambr/schema_slots.tsv | 2 +- web/templates/canada_covid19/schema.json | 4 ++-- web/templates/canada_covid19/schema.yaml | 2 +- web/templates/canada_covid19/schema_slots.tsv | 2 +- web/templates/hpai/schema.json | 12 ++++++------ web/templates/hpai/schema.yaml | 2 +- web/templates/hpai/schema_slots.tsv | 2 +- web/templates/influenza/schema.json | 2 +- web/templates/influenza/schema.yaml | 2 +- web/templates/influenza/schema_slots.tsv | 2 +- web/templates/mpox/schema.json | 6 +++--- web/templates/mpox/schema.yaml | 2 +- web/templates/mpox/schema_slots.tsv | 4 ++-- web/templates/pathogen/schema.json | 4 ++-- web/templates/pathogen/schema.yaml | 2 +- web/templates/pathogen/schema_slots.tsv | 2 +- web/templates/wastewater/schema.json | 8 ++++---- web/templates/wastewater/schema.yaml | 2 +- web/templates/wastewater/schema_slots.tsv | 2 +- 21 files changed, 34 insertions(+), 34 deletions(-) diff --git a/web/templates/ambr/schema.json b/web/templates/ambr/schema.json index a32d287d..f5d8432d 100644 --- a/web/templates/ambr/schema.json +++ b/web/templates/ambr/schema.json @@ -3190,7 +3190,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." diff --git a/web/templates/ambr/schema.yaml b/web/templates/ambr/schema.yaml index 6dcc9b95..db263e95 100644 --- a/web/templates/ambr/schema.yaml +++ b/web/templates/ambr/schema.yaml @@ -944,7 +944,7 @@ slots: - range: date - range: null value menu todos: - - '>={sample collection date}' + - '>={sample_collection_date}' library ID: name: library ID title: library ID diff --git a/web/templates/ambr/schema_slots.tsv b/web/templates/ambr/schema_slots.tsv index 5bcf288e..05bee907 100644 --- a/web/templates/ambr/schema_slots.tsv +++ b/web/templates/ambr/schema_slots.tsv @@ -48,7 +48,7 @@ AMBR GENEPIO:0001122 Database Identifiers Sequencing GENEPIO:0100422 sequenced by contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. jjharris@ucalgary.ca Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Research Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. This information can provide details about why the sample source might contain antibiotic potentiators. Screening for antibiotic potentiators in Cystic fibrosis disease contexts. - Sequencing GENEPIO:0001447 sequencing date date null value menu {sample collection date} The date the sample was sequenced. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-06-22 + Sequencing GENEPIO:0001447 sequencing date date null value menu {sample_collection_date} The date the sample was sequenced. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-06-22 Sequencing GENEPIO:0001448 library ID WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Provide the name of the run. This value maps to information in the "Sequencing Batch #" field Alberta Microbiota Repository (AMBR) Master file. 1876515_SA01_Plate 02 library ID Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing GENEPIO:0001453 sequencing protocol name WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json index 44080e1b..d2bef2a3 100644 --- a/web/templates/canada_covid19/schema.json +++ b/web/templates/canada_covid19/schema.json @@ -8268,7 +8268,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -13326,7 +13326,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/canada_covid19/schema.yaml b/web/templates/canada_covid19/schema.yaml index 37aa58ce..597c7882 100644 --- a/web/templates/canada_covid19/schema.yaml +++ b/web/templates/canada_covid19/schema.yaml @@ -2183,7 +2183,7 @@ slots: - range: date - range: NullValueMenu todos: - - '>={sample collection date}' + - '>={sample_collection_date}' required: true examples: - value: '2020-06-22' diff --git a/web/templates/canada_covid19/schema_slots.tsv b/web/templates/canada_covid19/schema_slots.tsv index 72a06d58..58d9ea1e 100644 --- a/web/templates/canada_covid19/schema_slots.tsv +++ b/web/templates/canada_covid19/schema_slots.tsv @@ -105,7 +105,7 @@ CanCOGeNCovid19 GENEPIO:0001122 Database Identifiers GENEPIO:0001441 Sequencing Sequencing Séquençage GENEPIO:0001445 purpose of sequencing purpose_of_sequencing Objectif du séquençage purpose of sequencing menu PurposeOfSequencingMenu null value menu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Raison pour laquelle l’échantillon a été séquencé The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. La raison pour laquelle un échantillon a été initialement prélevé peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des renseignements sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. Le motif de prélèvement de l’échantillon doit être indiqué dans le champ « Objectif de l’échantillonnage ». Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Sequencing Séquençage GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details Détails de l’objectif du séquençage WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Description de la raison pour laquelle l’échantillon a été séquencé, fournissant des détails spécifiques Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été séquencé en utilisant du texte libre. La description peut inclure l’importance des séquences pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Les descriptions normalisées suggérées sont les suivantes : Dépistage de l’absence de détection du gène S (abandon du gène S), dépistage de variants associés aux visons, dépistage du variant B.1.1.7, dépistage du variant B.1.135, dépistage du variant P.1, dépistage en raison des antécédents de voyage, dépistage en raison d’un contact étroit avec une personne infectée, évaluation des mesures de contrôle de la santé publique, détermination des introductions et de la propagation précoces, enquête sur les expositions liées aux voyages aériens, enquête sur les travailleurs étrangers temporaires, enquête sur les régions éloignées, enquête sur les travailleurs de la santé, enquête sur les écoles et les universités, enquête sur la réinfection. Screened for S gene target failure (S dropout) Dépistage de l’absence de détection du gène S (abandon du gène S) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing Séquençage GENEPIO:0001447 sequencing date sequencing_date Date de séquençage date date null value menu NullValueMenu TRUE {sample collection date} The date the sample was sequenced. Date à laquelle l’échantillon a été séquencé ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-06-22 2020-06-22 PH_SEQUENCING_DATE + Sequencing Séquençage GENEPIO:0001447 sequencing date sequencing_date Date de séquençage date date null value menu NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. Date à laquelle l’échantillon a été séquencé ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-06-22 2020-06-22 PH_SEQUENCING_DATE Sequencing Séquençage GENEPIO:0001448 library ID library_id ID de la bibliothèque WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. Identifiant spécifié par l’utilisateur pour la bibliothèque faisant l’objet du séquençage The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. Le nom de la bibliothèque doit être unique et peut être un ID généré automatiquement à partir de votre système de gestion de l’information des laboratoires, ou une modification de l’ID de l’isolat. XYZ_123345 XYZ_123345 library ID Sequencing Séquençage GENEPIO:0001449 amplicon size amplicon_size Taille de l’amplicon WhitespaceMinimizedString WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Longueur de l’amplicon généré par l’amplification de la réaction de polymérisation en chaîne Provide the amplicon size, including the units. Fournissez la taille de l’amplicon, y compris les unités. 300bp 300 pb amplicon size Sequencing Séquençage GENEPIO:0001450 library preparation kit library_preparation_kit Trousse de préparation de la bibliothèque WhitespaceMinimizedString WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Nom de la trousse de préparation de la banque d’ADN utilisée pour générer la bibliothèque faisant l’objet du séquençage Provide the name of the library preparation kit used. Indiquez le nom de la trousse de préparation de la bibliothèque utilisée. Nextera XT Nextera XT PH_LIBRARY_PREP_KIT diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index 6098b9ff..2dc24af3 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -13343,7 +13343,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -22085,7 +22085,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -26844,7 +26844,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -34336,7 +34336,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -41828,7 +41828,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -47570,7 +47570,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index ef5dff03..1d6e8128 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -6338,7 +6338,7 @@ slots: slot_uri: GENEPIO:0001447 range: date todos: - - '>={sample collection date}' + - '>={sample_collection_date}' examples: - value: '2020-06-22' purpose_of_sequencing__: diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv index 1d311bf3..f72b69aa 100644 --- a/web/templates/hpai/schema_slots.tsv +++ b/web/templates/hpai/schema_slots.tsv @@ -196,7 +196,7 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100824 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001441 Sequence information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing__ PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001446 purpose_of_sequencing_details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by diff --git a/web/templates/influenza/schema.json b/web/templates/influenza/schema.json index 261f2f20..cd15558d 100644 --- a/web/templates/influenza/schema.json +++ b/web/templates/influenza/schema.json @@ -4782,7 +4782,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/influenza/schema.yaml b/web/templates/influenza/schema.yaml index a43dd8a9..1c67dbed 100644 --- a/web/templates/influenza/schema.yaml +++ b/web/templates/influenza/schema.yaml @@ -1372,7 +1372,7 @@ slots: - range: null value menu required: true todos: - - '>={sample collection date}' + - '>={sample_collection_date}' exact_mappings: - NML_LIMS:PH_SEQUENCING_DATE amplicon size: diff --git a/web/templates/influenza/schema_slots.tsv b/web/templates/influenza/schema_slots.tsv index 7c1e5eb1..17325427 100644 --- a/web/templates/influenza/schema_slots.tsv +++ b/web/templates/influenza/schema_slots.tsv @@ -65,7 +65,7 @@ Influenza GENEPIO:0001122 Database Identifiers GENEPIO:0001441 Sequencing Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Seasonal flu research project Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing GENEPIO:0001447 sequencing date date null value menu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2023-09-22 PH_SEQUENCING_DATE + Sequencing GENEPIO:0001447 sequencing date date null value menu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2023-09-22 PH_SEQUENCING_DATE Sequencing GENEPIO:0001449 amplicon size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size Sequencing GENEPIO:0001450 library preparation kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 8e0e3c36..0e9f56f7 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -11781,7 +11781,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -17702,7 +17702,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -23469,7 +23469,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 292ca16b..4bec6ea5 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -2957,7 +2957,7 @@ slots: - range: date - range: NullValueMenu todos: - - '>={sample collection date}' + - '>={sample_collection_date}' examples: - value: '2020-06-22' exact_mappings: diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index dd39339b..8f18dc44 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -139,8 +139,8 @@ Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact add Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Mpox MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details Mpox;MpoxInternational -Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE Mpox -MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE MpoxInternational +Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE Mpox +MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID Mpox;MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Mpox;MpoxInternational Mpox Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay Mpox diff --git a/web/templates/pathogen/schema.json b/web/templates/pathogen/schema.json index 883fd4a5..eda09d9e 100644 --- a/web/templates/pathogen/schema.json +++ b/web/templates/pathogen/schema.json @@ -4286,7 +4286,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -6317,7 +6317,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/pathogen/schema.yaml b/web/templates/pathogen/schema.yaml index 623b739e..58746195 100644 --- a/web/templates/pathogen/schema.yaml +++ b/web/templates/pathogen/schema.yaml @@ -1048,7 +1048,7 @@ slots: - range: date - range: NullValueMenu todos: - - '>={sample collection date}' + - '>={sample_collection_date}' recommended: true examples: - value: '2020-06-22' diff --git a/web/templates/pathogen/schema_slots.tsv b/web/templates/pathogen/schema_slots.tsv index 7e15d397..9e902a5e 100644 --- a/web/templates/pathogen/schema_slots.tsv +++ b/web/templates/pathogen/schema_slots.tsv @@ -44,7 +44,7 @@ PathogenAgnostic GENEPIO:0001122 Database Identifiers database_identifiers GENEPIO:0001441 Sequencing sequencing Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE + Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString TRUE The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index 1a4e3f05..a5469b3a 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -8651,7 +8651,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -15917,7 +15917,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -23118,7 +23118,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -30759,7 +30759,7 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample collection date}" + ">={sample_collection_date}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index de8406e6..77256b60 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -4709,7 +4709,7 @@ slots: slot_uri: GENEPIO:0001447 range: date todos: - - '>={sample collection date}' + - '>={sample_collection_date}' examples: - value: '2020-06-22' library_id: diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index 299a4b05..35295c93 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -168,7 +168,7 @@ WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence informati WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample collection date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model From a6eb92a8080e1522eb1ebd6bf7ecb21d25a439f9 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sat, 26 Oct 2024 10:08:58 -0700 Subject: [PATCH 74/96] note on one current issue --- lib/Validator.js | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/lib/Validator.js b/lib/Validator.js index 440a9144..36c29c73 100644 --- a/lib/Validator.js +++ b/lib/Validator.js @@ -190,6 +190,12 @@ class Validator { slotEnum?.permissible_values ?? {} ).map((pv) => pv.text); + // Issue: if any_of lists a NullValueList enumeration in 2nd range + // where first range is a date, we don't have a menu control but + // also a valid "Missing" etc isn't validated as ok. + // TEST CASE: + // if (slotDefinition.name == "sample_collection_date") + // console.log("any_of", DEBUG INFO) const anyOfValidators = (slotDefinition.any_of ?? []).map((subSlot) => this.getValidatorForSlot(subSlot, { inheritedRange: slotDefinition.range, From 0e6f9c41d91fbc0b6f8119c775b09237fbc8506d Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sun, 27 Oct 2024 10:42:14 -0700 Subject: [PATCH 75/96] version bump --- web/templates/ambr/schema.json | 2 +- web/templates/ambr/schema_core.yaml | 2 +- web/templates/influenza/schema.json | 2 +- web/templates/influenza/schema_core.yaml | 2 +- web/templates/pathogen/schema.json | 2 +- web/templates/pathogen/schema_core.yaml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/web/templates/ambr/schema.json b/web/templates/ambr/schema.json index f5d8432d..0e70d212 100644 --- a/web/templates/ambr/schema.json +++ b/web/templates/ambr/schema.json @@ -2,7 +2,7 @@ "name": "AMBR", "description": "", "id": "https://example.com/AMBR", - "version": "2.3.0", + "version": "2.3.1", "prefixes": { "linkml": { "prefix_prefix": "linkml", diff --git a/web/templates/ambr/schema_core.yaml b/web/templates/ambr/schema_core.yaml index ef0e6eca..3c2e205d 100644 --- a/web/templates/ambr/schema_core.yaml +++ b/web/templates/ambr/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/AMBR name: AMBR description: "" -version: 2.3.0 +version: 2.3.1 imports: - 'linkml:types' prefixes: diff --git a/web/templates/influenza/schema.json b/web/templates/influenza/schema.json index cd15558d..3c7187db 100644 --- a/web/templates/influenza/schema.json +++ b/web/templates/influenza/schema.json @@ -2,7 +2,7 @@ "name": "Influenza", "description": "Draft template for harmonizing human influenza virus genomic surveillance contextual data.", "id": "https://example.com/Influenza", - "version": "1.0.0", + "version": "1.0.1", "prefixes": { "linkml": { "prefix_prefix": "linkml", diff --git a/web/templates/influenza/schema_core.yaml b/web/templates/influenza/schema_core.yaml index d6c5a6bf..30eac49d 100644 --- a/web/templates/influenza/schema_core.yaml +++ b/web/templates/influenza/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/Influenza name: "Influenza" description: "Draft template for harmonizing human influenza virus genomic surveillance contextual data." -version: 1.0.0 +version: 1.0.1 imports: - 'linkml:types' prefixes: diff --git a/web/templates/pathogen/schema.json b/web/templates/pathogen/schema.json index eda09d9e..3f4181eb 100644 --- a/web/templates/pathogen/schema.json +++ b/web/templates/pathogen/schema.json @@ -2,7 +2,7 @@ "name": "PathogenAgnostic", "description": "", "id": "https://example.com/Pathogen_Agnostic", - "version": "1.0.0", + "version": "1.0.1", "prefixes": { "linkml": { "prefix_prefix": "linkml", diff --git a/web/templates/pathogen/schema_core.yaml b/web/templates/pathogen/schema_core.yaml index 53dac5dc..0b330b11 100644 --- a/web/templates/pathogen/schema_core.yaml +++ b/web/templates/pathogen/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/Pathogen_Agnostic name: PathogenAgnostic description: "" -version: 1.0.0 +version: 1.0.1 imports: - 'linkml:types' prefixes: From 6a8adab455a3abeb28c8426a03bd8be69e92f6ac Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Sun, 27 Oct 2024 12:27:23 -0700 Subject: [PATCH 76/96] cancogen viruseq export fixes --- web/templates/canada_covid19/export.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/web/templates/canada_covid19/export.js b/web/templates/canada_covid19/export.js index 18f5a076..ab8abe00 100644 --- a/web/templates/canada_covid19/export.js +++ b/web/templates/canada_covid19/export.js @@ -89,8 +89,8 @@ export default { const outputMatrix = [[...ExportHeaders.keys()]]; const numeric_datatypes = new Set([ - 'xs:nonNegativeInteger', - 'xs:decimal', + 'xsd:nonNegativeInteger', + 'xsd:decimal', ]); for (const inputRow of dh.getTrimmedData(dh.hot)) { @@ -113,7 +113,7 @@ export default { if (headerName == 'study_id') { // Autopopulate study_id based on studyMap - const lab = inputRow[sourceFieldNameMap['sequence submitted by']]; + const lab = inputRow[sourceFieldNameMap['sequence_submitted_by']]; if (lab && lab in studyMap) { value = studyMap[lab]; } From 5b539a3c263e01050e81e5959e151141a1db6982 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 08:27:27 -0700 Subject: [PATCH 77/96] Standard Naming for NullValueMenu enumeration --- lib/DataHarmonizer.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index dc886500..fb7f38b4 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1142,7 +1142,7 @@ class DataHarmonizer { // Note for autocomplete, indentation of items is controlled by // leading spaces and css white-space: pre. if ( - !field.sources.includes('null value menu') || + !field.sources.includes('NullValueMenu') || field.sources.length > 1 ) { col.trimDropdown = false; // Allow expansion of pulldown past field width @@ -1416,7 +1416,7 @@ class DataHarmonizer { let sources = []; for (const [, item] of Object.entries(field.sources)) { // List null value menu items directly - if (item === 'null value menu') { + if (item === 'NullValueMenu') { let null_values = Object.keys( self.schema.enums[item].permissible_values ); From 0e6fd3e7b7018c7fcc598a7f95ee5f02bca30d0d Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 08:28:02 -0700 Subject: [PATCH 78/96] fix CanCoGEN BioPortal and GISAID export --- web/templates/canada_covid19/export.js | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/web/templates/canada_covid19/export.js b/web/templates/canada_covid19/export.js index ab8abe00..69a6ed4e 100644 --- a/web/templates/canada_covid19/export.js +++ b/web/templates/canada_covid19/export.js @@ -263,6 +263,7 @@ export default { ':', 'BIOSAMPLE' ); + // Note: isolation_source may be populated with Null Value parts. outputRow.push(value); } outputMatrix.push(outputRow); @@ -292,7 +293,7 @@ export default { ['Submitter', []], // submitter ['FASTA filename', []], // fn ['Virus name', []], // covv_virus_name - ['Type', []], // covv_type + ['Type', []], // covv_type // Not in MPox GSAID. ['Passage details/history', []], // covv_passage ['Collection date', []], // covv_collection_date ['Location', []], // covv_location @@ -309,14 +310,14 @@ export default { ['Treatment', []], // covv_treatment ['Sequencing technology', []], // covv_seq_technology ['Assembly method', []], // covv_assembly_method - ['Coverage', []], // covv_coverage + ['Coverage', ['depth_of_coverage_value']], // covv_coverage ['Originating lab', []], // covv_orig_lab - ['Address', []], // covv_orig_lab_addr + ['Address', ['sample_collector_contact_address']], // covv_orig_lab_addr ['Sample ID given by the sample provider', []], // covv_provider_sample_id ['Submitting lab', []], // covv_subm_lab // Custom rule: 2nd address points to sequence submitter. - ['Address', ['sequence submitter contact address']], // covv_subm_lab_addr - ['Sample ID given by the submitting laboratory', []], // covv_subm_sample_id + ['Address', ['sequence_submitter_contact_address']], // covv_subm_lab_addr + ['Sample ID given by the submitting laboratory', ['specimen_collector_sample_id']], // covv_subm_sample_id ['Authors', []], // covv_authors ]; @@ -325,7 +326,7 @@ export default { 'submitter', 'fn', 'covv_virus_name', - 'covv_type', + 'covv_type', // Not in Mpox GSAID 'covv_passage', 'covv_collection_date', 'covv_location', @@ -354,6 +355,7 @@ export default { const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); + dh.getHeaderMap(ExportHeaders, sourceFields, 'GISAID'); // Create an export table with target format's headers and remaining rows of data @@ -382,7 +384,7 @@ export default { const field = sourceFields[sourceFieldIndex]; const standardizedCellVal = mappedCellVal.toLowerCase().trim(); - if (field.fieldName === 'specimen processing') { + if (field.name === 'specimen_processing') { // Specimen processing is a multi-select field const standardizedCellValArr = standardizedCellVal.split(';'); if (!standardizedCellValArr.includes('virus passage')) continue; @@ -390,6 +392,7 @@ export default { mappedCellVal = 'Virus passage'; } + console.log(field.name,field) // All null values should be converted to "Unknown" if (field.dataStatus) { const standardizedDataStatus = field.dataStatus.map((val) => @@ -404,7 +407,7 @@ export default { } // Add 'passage number ' prefix to number. - if (field.fieldName === 'passage number') { + if (field.name === 'passage_number') { mappedCellVal = 'passage number ' + mappedCellVal; } From 786bc1b74ba0eeecdc53b19398955d0ce47add7f Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 08:28:20 -0700 Subject: [PATCH 79/96] documentation tweak --- web/templates/mpox/export.js | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/web/templates/mpox/export.js b/web/templates/mpox/export.js index 137bec6e..a60ae661 100644 --- a/web/templates/mpox/export.js +++ b/web/templates/mpox/export.js @@ -150,7 +150,34 @@ export default { ]; // GISAID has new sampling_strategy field as of May 12, 2021 - const header_GISAID = ['submitter','fn','pox_virus_name','pox_passage','pox_collection_date','pox_location','pox_add_location','pox_host','pox_add_host_info','pox_sampling_strategy','pox_gender','pox_patient_age','pox_patient_status','pox_specimen','pox_outbreak','pox_last_vaccinated','pox_treatment','pox_seq_technology','pox_assembly_method','pox_coverage','pox_orig_lab','pox_orig_lab_addr','pox_provider_sample_id','pox_subm_lab','pox_subm_lab_addr','pox_subm_sample_id','pox_authors']; + const header_GISAID = [ + 'submitter', + 'fn', + 'pox_virus_name', + 'pox_passage', + 'pox_collection_date', + 'pox_location', + 'pox_add_location', + 'pox_host', + 'pox_add_host_info', + 'pox_sampling_strategy', + 'pox_gender', + 'pox_patient_age', + 'pox_patient_status', + 'pox_specimen', + 'pox_outbreak', + 'pox_last_vaccinated', + 'pox_treatment', + 'pox_seq_technology', + 'pox_assembly_method', + 'pox_coverage', + 'pox_orig_lab', + 'pox_orig_lab_addr', + 'pox_provider_sample_id', + 'pox_subm_lab', + 'pox_subm_lab_addr', + 'pox_subm_sample_id', + 'pox_authors']; const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); From 314fd986736a36dfd709cc188a1b562accbccf63 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 08:40:07 -0700 Subject: [PATCH 80/96] pathogen version bump --- web/templates/pathogen/schema.yaml | 2 +- web/templates/pathogen/schema_slots.tsv | 134 +++++++++++------------- 2 files changed, 61 insertions(+), 75 deletions(-) diff --git a/web/templates/pathogen/schema.yaml b/web/templates/pathogen/schema.yaml index 58746195..53f58e63 100644 --- a/web/templates/pathogen/schema.yaml +++ b/web/templates/pathogen/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/Pathogen_Agnostic name: PathogenAgnostic description: '' -version: 1.0.0 +version: 1.0.1 imports: - linkml:types prefixes: diff --git a/web/templates/pathogen/schema_slots.tsv b/web/templates/pathogen/schema_slots.tsv index 9e902a5e..737d0ddb 100644 --- a/web/templates/pathogen/schema_slots.tsv +++ b/web/templates/pathogen/schema_slots.tsv @@ -1,74 +1,60 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -PathogenAgnostic GENEPIO:0001122 Database Identifiers database_identifiers - Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID - Database Identifiers GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 - Database Identifiers GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY - Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID - Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID - Database Identifiers GENEPIO:0001131 IRIDA sample name irida_sample_name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name - Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession - Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession - Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers GENEPIO:0001142 SRA accession sra_accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers GENEPIO:0001145 GenBank accession genbank_accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession - Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession - GENEPIO:0001150 Sample collection and processing sample_collection_and_processing - Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by - Sample collection and processing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by - Sample collection and processing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by - Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date - Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) - Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 Pathogen HC_CURRENT_ID organism organism - Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name - Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling - Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details - Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NMLSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE - Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material - Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part - Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product - Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material - Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site - Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device - Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method - Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled Passage details/history specimen processing - Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. - GENEPIO:0001268 Host Information host_information - Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) - Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease - Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age - Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit - Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin - Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Male Gender Patient Sex VD_SEX host_sex host gender - GENEPIO:0001441 Sequencing sequencing - Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing - Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE - Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString TRUE The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT - Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument - GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method - Bioinformatics and QC metrics assembly software name assembly_software_name WhitespaceMinimizedString TRUE The name of software used to generate the assembled sequence. Provide the name of the software used to generate the assembled sequence. Shovill - Bioinformatics and QC metrics assembly software version assembly_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the assembled sequence. Provide the version of the software used to generate the assembled sequence. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol - GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS - - - - - - - - - - - - - - \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +PathogenAgnostic GENEPIO:0001122 Database Identifiers database_identifiers + Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID + Database Identifiers GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 + Database Identifiers GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY + Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID + Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID + Database Identifiers GENEPIO:0001131 IRIDA sample name irida_sample_name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name + Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession + Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession + Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION + Database Identifiers GENEPIO:0001142 SRA accession sra_accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION + Database Identifiers GENEPIO:0001145 GenBank accession genbank_accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession + Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession + GENEPIO:0001150 Sample collection and processing sample_collection_and_processing + Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by + Sample collection and processing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by + Sample collection and processing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by + Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date + Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) + Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Severe acute respiratory syndrome coronavirus 2 Pathogen HC_CURRENT_ID organism organism + Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name + Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling + Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details + Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NMLSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE + Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material + Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part + Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Feces Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product + Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Face mask Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material + Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Production Facility Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site + Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device + Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method + Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled Passage details/history specimen processing + Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. + GENEPIO:0001268 Host Information host_information + Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) + Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "COVID-19" from the pick list provided in the template. COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease + Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age + Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit + Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin + Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Male Gender Patient Sex VD_SEX host_sex host gender + GENEPIO:0001441 Sequencing sequencing + Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing + Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details + Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE + Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString TRUE The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT + Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument + GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method + Bioinformatics and QC metrics assembly software name assembly_software_name WhitespaceMinimizedString TRUE The name of software used to generate the assembled sequence. Provide the name of the software used to generate the assembled sequence. Shovill + Bioinformatics and QC metrics assembly software version assembly_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the assembled sequence. Provide the version of the software used to generate the assembled sequence. 1.2.3 + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS From 0c009d3f1010187a86ef82656227405dbe5cfffa Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 08:55:40 -0700 Subject: [PATCH 81/96] CanCoGEN deleting unused columns --- web/templates/canada_covid19/schema_slots.tsv | 324 +++++++++--------- 1 file changed, 162 insertions(+), 162 deletions(-) diff --git a/web/templates/canada_covid19/schema_slots.tsv b/web/templates/canada_covid19/schema_slots.tsv index 58d9ea1e..97413485 100644 --- a/web/templates/canada_covid19/schema_slots.tsv +++ b/web/templates/canada_covid19/schema_slots.tsv @@ -1,162 +1,162 @@ -class_name slot_group slot_group_fr slot_uri title name title_fr rangeOld range range_2_Old range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description description_fr comments comments_fr examples examples_fr EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -CanCOGeNCovid19 GENEPIO:0001122 Database Identifiers - Database Identifiers Identificateurs de base de données GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id ID du collecteur d’échantillons WhitespaceMinimizedString WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Nom défini par l’utilisateur pour l’échantillon Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de conserver la clé qui correspond aux identifiants d’origine et alternatifs aux fins de traçabilité et de suivi, au besoin. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n’importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire. prov_rona_99 prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID - Database Identifiers Identificateurs de base de données GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name Nom du fournisseur de services de laboratoire tiers WhitespaceMinimizedString WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Nom de la société ou du laboratoire tiers qui fournit les services Provide the full, unabbreviated name of the company or laboratory. Indiquez le nom complet et non abrégé de l’entreprise ou du laboratoire. Switch Health Switch Health HC_TEXT5 - Database Identifiers Identificateurs de base de données GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id ID de l’échantillon de laboratoire tiers WhitespaceMinimizedString WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Identifiant attribué à un échantillon par un prestataire de services tiers Store the sample identifier supplied by the third party services provider. Conservez l’identifiant de l’échantillon fourni par le prestataire de services tiers. SHK123456 SHK123456 PH_ID_NUMBER_PRIMARY - Database Identifiers Identificateurs de base de données GENEPIO:0100281 case ID case_id ID du dossier WhitespaceMinimizedString WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Identifiant utilisé pour désigner un cas de maladie détecté sur le plan épidémiologique Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. Fournissez l’identifiant du cas, lequel facilite grandement le lien entre les données de laboratoire et les données épidémiologiques. Il peut être considéré comme une information identifiable. Consultez l’intendant des données avant de le transmettre. ABCD1234 ABCD1234 PH_CASE_ID - Database Identifiers Identificateurs de base de données GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id ID principal de l’échantillon associé WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu The primary ID of a related specimen previously submitted to the repository. Identifiant principal d’un échantillon associé précédemment soumis au dépôt Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. Conservez l’identifiant primaire de l’échantillon correspondant précédemment soumis au Laboratoire national de microbiologie afin que les échantillons puissent être liés et suivis dans le système. SR20-12345 SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID - Database Identifiers Identificateurs de base de données GENEPIO:0001131 IRIDA sample name irida_sample_name Nom de l’échantillon IRIDA WhitespaceMinimizedString WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Identifiant attribué à un isolat séquencé dans IRIDA Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). Enregistrez le nom de l’échantillon IRIDA, lequel sera créé par la personne saisissant les données dans la plateforme connexe. Les échantillons IRIDA peuvent être liés à des métadonnées et à des données de séquence, ou simplement à des métadonnées. Il est recommandé que le nom de l’échantillon IRIDA soit identique ou contienne l’ID de l’échantillon du collecteur pour assurer une meilleure traçabilité. Il est également recommandé que le nom de l’échantillon IRIDA reflète l’accès à GISAID. Les noms d’échantillons IRIDA ne peuvent pas contenir de barres obliques. Celles-ci doivent être remplacées par des traits de soulignement. Consultez la documentation IRIDA pour en savoir plus sur les caractères spéciaux (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 prov_rona_99 IRIDA sample name - Database Identifiers Identificateurs de base de données GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession Numéro d’accès au bioprojet cadre umbrella bioproject accession menu UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Numéro d’accès à INSDC attribué au bioprojet cadre pour l’effort canadien de séquençage du SRAS-CoV-2 Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. Enregistrez le numéro d’accès au bioprojet cadre en le sélectionnant à partir de la liste déroulante du modèle. Ce numéro sera identique pour tous les soumissionnaires du RCanGéCO. Différentes provinces auront leurs propres bioprojets, mais ces derniers seront liés sous un seul bioprojet cadre. PRJNA623807 PRJNA623807 umbrella bioproject accession - Database Identifiers Identificateurs de base de données GENEPIO:0001136 bioproject accession bioproject_accession Numéro d’accès au bioprojet WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Numéro d’accès à INSDC du bioprojet auquel appartient un échantillon biologique Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. Enregistrez le numéro d’accès au bioprojet. Les bioprojets sont un outil d’organisation qui relie les données de séquence brutes, les assemblages et leurs métadonnées associées. Chaque province se verra attribuer un numéro d’accès différent au bioprojet par le Laboratoire national de microbiologie. Un numéro d’accès valide au bioprojet du NCBI contient le préfixe PRJN (p. ex., PRJNA12345); il est créé une fois au début d’un nouveau projet de séquençage. PRJNA608651 PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession - Database Identifiers Identificateurs de base de données GENEPIO:0001139 biosample accession biosample_accession Numéro d’accès à un échantillon biologique WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Identifiant attribué à un échantillon biologique dans les archives INSDC Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. Conservez le numéro d’accès renvoyé avec la soumission d’un échantillon biologique. Les échantillons biologiques de NCBI seront assortis du SAMN. SAMN14180202 SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers Identificateurs de base de données GENEPIO:0001142 SRA accession sra_accession Numéro d’accès à l’archive des séquences WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Identifiant de l’archive des séquences reliant les données de séquences brutes de lecture, les métadonnées méthodologiques et les mesures de contrôle de la qualité soumises à INSDC Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. Conservez le numéro d’accès attribué au « cycle » soumis. Les accès NCBI-SRA commencent par SRR. SRR11177792 SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers Identificateurs de base de données GENEPIO:0001145 GenBank accession genbank_accession Numéro d’accès à GenBank WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Identifiant GenBank attribué à la séquence dans les archives INSDC Store the accession returned from a GenBank submission (viral genome assembly). Conservez le numéro d’accès renvoyé avec la soumission de GenBank (assemblage du génome viral). MN908947.3 MN908947.3 GenBank Accession GenBank accession - Database Identifiers Identificateurs de base de données GENEPIO:0001147 GISAID accession gisaid_accession Numéro d’accès à la GISAID WhitespaceMinimizedString WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Numéro d’accès à la GISAID attribué à la séquence Store the accession returned from the GISAID submission. Conservez le numéro d’accès renvoyé avec la soumission de la GISAID. EPI_ISL_436489 EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession - GENEPIO:0001150 Sample collection and processing - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001153 sample collected by sample_collected_by Échantillon prélevé par sample collected by menu SampleCollectedByMenu null value menu NullValueMenu TRUE The name of the agency that collected the original sample. Nom de l’organisme ayant prélevé l’échantillon original The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). Le nom du collecteur d’échantillons doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions, par exemple Agence de la santé publique du Canada, Santé publique Ontario, Centre de contrôle des maladies de la Colombie-Britannique. BC Centre for Disease Control Centre de contrôle des maladies de la Colombie-Britannique Originating lab Lab Name CUSTOMER collected_by sample collected by - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001156 sample collector contact email sample_collector_contact_email Adresse courriel du collecteur d’échantillons WhitespaceMinimizedString WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca). RespLab@lab.ca RespLab@lab.ca sample collector contact email - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001158 sample collector contact address sample_collector_contact_address Adresse du collecteur d’échantillons WhitespaceMinimizedString WhitespaceMinimizedString The mailing address of the agency submitting the sample. Adresse postale de l’organisme soumettant l’échantillon The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays. 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada 655, rue Lab, Vancouver (Colombie-Britannique) V5N 2A2 Canada Address sample collector contact address - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001159 sequence submitted by sequence_submitted_by Séquence soumise par sequence submitted by menu SequenceSubmittedByMenu null value menu NullValueMenu TRUE The name of the agency that generated the sequence. Nom de l’organisme ayant généré la séquence The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Le nom de l’agence doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions. Si vous soumettez des échantillons plutôt que des données de séquençage, veuillez inscrire « Laboratoire national de microbiologie (LNM) ». Public Health Ontario (PHO) Santé publique Ontario (SPO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email Adresse courriel du soumissionnaire de séquence WhitespaceMinimizedString WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca). RespLab@lab.ca RespLab@lab.ca sequence submitter contact email - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address Adresse du soumissionnaire de séquence WhitespaceMinimizedString WhitespaceMinimizedString The mailing address of the agency submitting the sequence. Adresse postale de l’organisme soumettant l’échantillon The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays. 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada 123, rue Sunnybrooke, Toronto (Ontario) M4P 1L6 Canada Address sequence submitter contact address - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001174 sample collection date sample_collection_date Date de prélèvement de l’échantillon date date null value menu NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Date à laquelle l’échantillon a été prélevé Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". La date de prélèvement des échantillons est essentielle pour la surveillance et de nombreux types d’analyses. La granularité requise comprend l’année, le mois et le jour. Si cette date est considérée comme un renseignement identifiable, il est acceptable d’y ajouter une « gigue » en ajoutant ou en soustrayant un jour civil. La « date de réception » peut également servir de date de rechange. La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-16 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001177 sample collection date precision sample_collection_date_precision Précision de la date de prélèvement de l’échantillon sample collection date precision menu SampleCollectionDatePrecisionMenu null value menu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". Fournissez la précision de la granularité au « jour », au « mois » ou à « l’année » pour la date fournie dans le champ « Date de prélèvement de l’échantillon ». Cette date sera tronquée selon la précision spécifiée lors de l’exportation : « jour » pour « AAAA-MM-JJ », « mois » pour « AAAA-MM » ou « année » pour « AAAA ». year année Precision of date collected HC_TEXT2 - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001179 sample received date sample_received_date Date de réception de l’échantillon date date null value menu NullValueMenu The date on which the sample was received. Date à laquelle l’échantillon a été reçu ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-20 2020-03-20 sample received date - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country nom_lieu_géo (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu TRUE The country where the sample was collected. Pays d’origine de l’échantillon Provide the country name from the controlled vocabulary provided. Fournissez le nom du pays à partir du vocabulaire contrôlé fourni. Canada Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory nom_lieu_géo (état/province/territoire) geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu null value menu NullValueMenu TRUE The province/territory where the sample was collected. Province ou territoire où l’échantillon a été prélevé Provide the province/territory name from the controlled vocabulary provided. Fournissez le nom de la province ou du territoire à partir du vocabulaire contrôlé fourni. Saskatchewan Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001189 geo_loc_name (city) geo_loc_name_city nom_géo_loc (ville) WhitespaceMinimizedString WhitespaceMinimizedString The city where the sample was collected. Ville où l’échantillon a été prélevé Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Fournissez le nom de la ville. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. Medicine Hat Medicine Hat Patient City geo_loc_name (city) - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001191 organism organism Organisme organism menu OrganismMenu null value menu NullValueMenu TRUE Taxonomic name of the organism. Nom taxonomique de l’organisme Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Utilisez « coronavirus du syndrome respiratoire aigu sévère 2 ». Cette valeur est fournie dans le modèle. Severe acute respiratory syndrome coronavirus 2 Coronavirus du syndrome respiratoire aigu sévère 2 Pathogen HC_CURRENT_ID organism organism - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001195 isolate isolate Isolat WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE Identifier of the specific isolate. Identifiant de l’isolat spécifique Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. Fournissez le nom du virus de la GISAID, qui doit être écrit dans le format « hCov-19/CANADA/code ISO provincial à 2 chiffres-xxxxx/année ». hCov-19/CANADA/BC-prov_rona_99/2020 hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001198 purpose of sampling purpose_of_sampling Objectif de l’échantillonnage purpose of sampling menu PurposeOfSamplingMenu null value menu NullValueMenu TRUE The reason that the sample was collected. Motif de prélèvement de l’échantillon The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. La raison pour laquelle un échantillon a été prélevé peut fournir des renseignements sur les biais potentiels de la stratégie d’échantillonnage. Choisissez l’objectif de l’échantillonnage à partir de la liste déroulante du modèle. Il est très probable que l’échantillon ait été prélevé en vue d’un test diagnostique. La raison pour laquelle un échantillon a été prélevé à l’origine peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage, ce qui doit être indiqué dans le champ « Objectif du séquençage ». Diagnostic testing Tests diagnostiques Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details Détails de l’objectif de l’échantillonnage WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE The description of why the sample was collected, providing specific details. Détails précis concernant le motif de prélèvement de l’échantillon Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été prélevé en utilisant du texte libre. La description peut inclure l’importance de l’échantillon pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Si les détails ne sont pas disponibles, fournissez une valeur nulle. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. L’échantillon a été prélevé pour étudier la prévalence des variants associés à la transmission du vison à l’homme au Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type Type d’échantillon soumis au LNM NML submitted specimen type menu NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. Type d’échantillon soumis au Laboratoire national de microbiologie (LNM) aux fins d’analyse This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Ces renseignements sont requis pour le téléchargement à l’aide du système LaSER du RCRSP. Choisissez le type d’échantillon à partir de la liste de sélection fournie. Si les données de séquences sont soumises plutôt qu’un échantillon aux fins d’analyse, sélectionnez « Sans objet ». swab Écouvillon Specimen Type PH_SPECIMEN_TYPE - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type Type de relation de l’échantillon lié Related specimen relationship type menu RelatedSpecimenRelationshipTypeMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Relation entre l’échantillon actuel et celui précédemment soumis au dépôt Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Fournissez l’étiquette qui décrit comment l’échantillon précédent est lié à l’échantillon actuel soumis à partir de la liste de sélection fournie afin que les échantillons puissent être liés et suivis dans le système. Specimen sampling methods testing Test des méthodes de prélèvement des échantillons Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001211 anatomical material anatomical_material Matière anatomique anatomical material menu AnatomicalMaterialMenu null value menu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Substance obtenue à partir d’une partie anatomique d’un organisme (p. ex., tissu, sang) Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une matière anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Blood Sang Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001214 anatomical part anatomical_part Partie anatomique anatomical part menu AnatomicalPartMenu null value menu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Partie anatomique d’un organisme (p. ex., oropharynx) Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Nasopharynx (NP) Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001216 body product body_product Produit corporel body product menu BodyProductMenu null value menu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Substance excrétée ou sécrétée par un organisme (p. ex., selles, urine, sueur) Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Feces Selles Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001223 environmental material environmental_material Matériel environnemental environmental material menu EnvironmentalMaterialMenu null value menu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Substance obtenue à partir de l’environnement naturel ou artificiel (p. ex., sol, eau, eaux usées) Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une matière environnementale a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Face mask Masque Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001232 environmental site environmental_site Site environnemental environmental site menu EnvironmentalSiteMenu null value menu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Emplacement environnemental pouvant décrire un site dans l’environnement naturel ou artificiel (p. ex., surface de contact, boîte métallique, hôpital, marché traditionnel de produits frais, grotte de chauves-souris) Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Production Facility Installation de production Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001234 collection device collection_device Dispositif de prélèvement collection device menu CollectionDeviceMenu null value menu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Instrument ou contenant utilisé pour prélever l’échantillon (p. ex., écouvillon) Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Swab Écouvillon Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001241 collection method collection_method Méthode de prélèvement collection method menu CollectionMethodMenu null value menu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Processus utilisé pour prélever l’échantillon (p. ex., phlébotomie, autopsie) Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une méthode de prélèvement a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Bronchoalveolar lavage (BAL) Lavage bronchoalvéolaire (LBA) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001243 collection protocol collection_protocol Protocole de prélèvement WhitespaceMinimizedString WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Nom et version d’un protocole particulier utilisé pour l’échantillonnage Free text. Texte libre. BCRonaSamplingProtocol v. 1.2 CBRonaProtocoleÉchantillonnage v. 1.2 collection protocol - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001253 specimen processing specimen_processing Traitement des échantillons specimen processing menu SpecimenProcessingMenu null value menu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Tout traitement appliqué à l’échantillon pendant ou après sa réception Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Essentiel pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, ajoutez les renseignements dans les champs « Laboratoire hôte », « Nombre de transmissions » et « Méthode de transmission ». Si aucun des processus de la liste de sélection ne s’applique, inscrivez « Sans objet ». Virus passage Transmission du virus Passage details/history specimen processing - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0100311 specimen processing details specimen_processing_details Détails du traitement des échantillons WhitespaceMinimizedString WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Renseignements détaillés concernant le traitement appliqué à un échantillon pendant ou après sa réception Provide a free text description of any processing details applied to a sample. Fournissez une description en texte libre de tous les détails du traitement appliqués à un échantillon. 25 swabs were pooled and further prepared as a single sample during library prep. 25 écouvillons ont été regroupés et préparés en tant qu’échantillon unique lors de la préparation de la bibliothèque. - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001255 lab host lab_host Laboratoire hôte lab host menu LabHostMenu null value menu NullValueMenu TRUE Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Nom et description du laboratoire hôte utilisé pour propager l’organisme source ou le matériel à partir duquel l’échantillon a été obtenu Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Type de lignée cellulaire utilisée pour la propagation. Choisissez le nom de cette lignée à partir de la liste de sélection dans le modèle. Si le virus n’a pas été transmis, indiquez « Sans objet ». Vero E6 cell line Lignée cellulaire Vero E6 Passage details/history lab host lab_host - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001261 passage number passage_number Nombre de transmission integer integer null value menu NullValueMenu TRUE 0 Number of passages. Nombre de transmissions Provide number of known passages. If not passaged, put "not applicable" Indiquez le nombre de transmissions connues. Si le virus n’a pas été transmis, indiquez « Sans objet ». 3 3 Passage details/history passage number passage_history - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001264 passage method passage_method Méthode de transmission WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE Description of how organism was passaged. Description de la façon dont l’organisme a été transmis Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". Texte libre. Fournissez une brève description (<10 mots). Si le virus n’a pas été transmis, indiquez « Sans objet ». 0.25% trypsin + 0.02% EDTA 0,25 % de trypsine + 0,02 % d’EDTA Passage details/history passage method passage_method - Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001266 biomaterial extracted biomaterial_extracted Biomatériau extrait biomaterial extracted menu BiomaterialExtractedMenu null value menu NullValueMenu The biomaterial extracted from samples for the purpose of sequencing. Biomatériau extrait d’échantillons aux fins de séquençage Provide the biomaterial extracted from the picklist in the template. Fournissez le biomatériau extrait à partir de la liste de sélection dans le modèle. RNA (total) ARN (total) biomaterial extracted - GENEPIO:0001268 Host Information - Host Information Informations sur l'hôte GENEPIO:0001386 host (common name) host_common_name Hôte (nom commun) host (common name) menu HostCommonNameMenu null value menu NullValueMenu The commonly used name of the host. Nom couramment utilisé pour l’hôte Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Des exemples de noms communs sont « humain » et « chauve-souris ». Si l’échantillon était environnemental, inscrivez « Sans objet ». Human Humain Animal Type PH_ANIMAL_TYPE - Host Information Informations sur l'hôte GENEPIO:0001387 host (scientific name) host_scientific_name Hôte (nom scientifique) host (scientific name) menu HostScientificNameMenu null value menu NullValueMenu TRUE The taxonomic, or scientific name of the host. Nom taxonomique ou scientifique de l’hôte Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Un exemple de nom scientifique est « homo sapiens ». Si l’échantillon était environnemental, inscrivez « Sans objet ». Homo sapiens Homo sapiens Host host (scientific name) host host (scientific name) - Host Information Informations sur l'hôte GENEPIO:0001388 host health state host_health_state État de santé de l’hôte host health state menu HostHealthStateMenu null value menu NullValueMenu Health status of the host at the time of sample collection. État de santé de l’hôte au moment du prélèvement d’échantillons If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Symptomatic Symptomatique Patient status Host Health State PH_HOST_HEALTH host_health_state - Host Information Informations sur l'hôte GENEPIO:0001389 host health status details host_health_status_details Détails de l’état de santé de l’hôte host health status details menu HostHealthStatusDetailsMenu null value menu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. Plus de détails concernant l’état de santé ou de maladie de l’hôte au moment du prélèvement If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Hospitalized (ICU) Hospitalisé (USI) Host Health State Details PH_HOST_HEALTH_DETAILS - Host Information Informations sur l'hôte GENEPIO:0001390 host health outcome host_health_outcome Résultats sanitaires de l’hôte host health outcome menu HostHealthOutcomeMenu null value menu NullValueMenu Disease outcome in the host. Résultats de la maladie chez l’hôte If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Recovered Rétabli PH_HOST_HEALTH_OUTCOME host_disease_outcome - Host Information Informations sur l'hôte GENEPIO:0001391 host disease host_disease Maladie de l’hôte host disease menu HostDiseaseMenu null value menu NullValueMenu TRUE The name of the disease experienced by the host. Nom de la maladie vécue par l’hôte Select "COVID-19" from the pick list provided in the template. Sélectionnez « COVID-19 » à partir de la liste de sélection fournie dans le modèle. COVID-19 COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease - Host Information Informations sur l'hôte GENEPIO:0001392 host age host_age Âge de l’hôte decimal decimal null value menu NullValueMenu TRUE 0 130 Age of host at the time of sampling. Âge de l’hôte au moment du prélèvement d’échantillons Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". Entrez l’âge de l’hôte en années. S’il n’est pas disponible, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet ». 79 79 Patient age Patient Age PH_AGE host_age host age - Host Information Informations sur l'hôte GENEPIO:0001393 host age unit host_age_unit Catégorie d’âge de l’hôte host age unit menu HostAgeUnitMenu null value menu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Unité utilisée pour mesurer l’âge de l’hôte (mois ou année) Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. Indiquez si l’âge de l’hôte est en mois ou en années. L’âge indiqué en mois sera classé dans la tranche d’âge de 0 à 9 ans. year année Age Units PH_AGE_UNIT host age unit - Host Information Informations sur l'hôte GENEPIO:0001394 host age bin host_age_bin Groupe d’âge de l’hôte host age bin menu HostAgeBinMenu null value menu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Âge de l’hôte au moment du prélèvement d’échantillons (groupe d’âge) Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. Sélectionnez la tranche d’âge correspondante de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne la connaissez pas, fournissez une valeur nulle. 60 - 69 60 - 69 Host Age Category PH_AGE_GROUP host age bin - Host Information Informations sur l'hôte GENEPIO:0001395 host gender host_gender Genre de l’hôte host gender menu HostGenderMenu null value menu NullValueMenu TRUE The gender of the host at the time of sample collection. Genre de l’hôte au moment du prélèvement d’échantillons Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Sélectionnez le genre correspondant de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne le connaissez pas, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet ». Male Homme Gender Patient Sex VD_SEX host_sex host gender - Host Information Informations sur l'hôte GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country Résidence de l’hôte – Nom de géo_loc (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu The country of residence of the host. Pays de résidence de l’hôte Select the country name from pick list provided in the template. Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle. Canada Canada PH_HOST_COUNTRY - Host Information Informations sur l'hôte GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory Résidence de l’hôte – Nom de géo_loc (état/province/territoire) geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu null value menu NullValueMenu The state/province/territory of residence of the host. État, province ou territoire de résidence de l’hôte Select the province/territory name from pick list provided in the template. Sélectionnez le nom de la province ou du territoire à partir de la liste de sélection fournie dans le modèle. Quebec Québec PH_HOST_PROVINCE - Host Information Informations sur l'hôte GENEPIO:0001398 host subject ID host_subject_id ID du sujet de l’hôte WhitespaceMinimizedString WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Identifiant unique permettant de désigner chaque hôte (p. ex., 131) Provide the host identifier. Should be a unique, user-defined identifier. Fournissez l’identifiant de l’hôte. Il doit s’agir d’un identifiant unique défini par l’utilisateur. BCxy123 BCxy123 host subject ID host_subject_id - Host Information Informations sur l'hôte GENEPIO:0001399 symptom onset date symptom_onset_date Date d’apparition des symptômes date date null value menu NullValueMenu The date on which the symptoms began or were first noted. Date à laquelle les symptômes ont commencé ou ont été observés pour la première fois ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-16 2020-03-16 Symptoms Onset Date HC_ONSET_DATE - Host Information Informations sur l'hôte GENEPIO:0001400 signs and symptoms signs_and_symptoms Signes et symptômes signs and symptoms menu SignsAndSymptomsMenu null value menu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélant une maladie, qui est signalé par un patient ou un clinicien Select all of the symptoms experienced by the host from the pick list. Sélectionnez tous les symptômes ressentis par l’hôte à partir de la liste de sélection. Chills (sudden cold sensation); Cough; Fever Frissons (sensation soudaine de froid); toux; fièvre Symptoms HC_SYMPTOMS - Host Information Informations sur l'hôte GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors Conditions préexistantes et facteurs de risque pre-existing conditions and risk factors menu PreExistingConditionsAndRiskFactorsMenu null value menu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Conditions préexistantes et facteurs de risque du patient
  • Condition préexistante : Condition médicale qui existait avant l’infection actuelle
  • Facteur de risque : Variable associée à un risque accru de maladie ou d’infection  Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les conditions préexistantes et tous les facteurs de risque de l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Asthma; Pregnancy; Smoking Asthme; grossesse; tabagisme pre-existing conditions and risk factors - Host Information Informations sur l'hôte GENEPIO:0001402 complications complications Complications complications menu ComplicationsMenu null value menu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Complications médicales du patient qui seraient dues à une maladie de l’hôte Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les complications éprouvées par l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Acute Respiratory Failure; Coma; Septicemia Insuffisance respiratoire aiguë; coma; septicémie complications - GENEPIO:0001403 Host vaccination information - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001404 host vaccination status host_vaccination_status Statut de vaccination de l’hôte host vaccination status menu host vaccination status menu null value menu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Statut de vaccination de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné) Select the vaccination status of the host from the pick list. Sélectionnez le statut de vaccination de l’hôte à partir de la liste de sélection. Fully Vaccinated Entièrement vacciné PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received Nombre de doses du vaccin reçues integer integer The number of doses of the vaccine recived by the host. Nombre de doses du vaccin reçues par l’hôte Record how many doses of the vaccine the host has received. Enregistrez le nombre de doses du vaccin que l’hôte a reçues. 2 2 - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name Dose du vaccin 1 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Nom du vaccin administré comme première dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date Dose du vaccin 1 – Date du vaccin date date null value menu NullValueMenu The date the first dose of a vaccine was administered. Date à laquelle la première dose d’un vaccin a été administrée Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-03-01 2021-03-01 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100315 vaccination dose 2 vaccine name vaccination_dose_2_vaccine_name Dose du vaccin 2 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the second dose of a vaccine regimen. Nom du vaccin administré comme deuxième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100316 vaccination dose 2 vaccination date vaccination_dose_2_vaccination_date Dose du vaccin 2 – Date du vaccin date date null value menu NullValueMenu The date the second dose of a vaccine was administered. Date à laquelle la deuxième dose d’un vaccin a été administrée Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-09-01 2021-09-01 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100317 vaccination dose 3 vaccine name vaccination_dose_3_vaccine_name Dose du vaccin 3 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the third dose of a vaccine regimen. Nom du vaccin administré comme troisième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100318 vaccination dose 3 vaccination date vaccination_dose_3_vaccination_date Dose du vaccin 3 – Date du vaccin date date null value menu NullValueMenu The date the third dose of a vaccine was administered. Date à laquelle la troisième dose d’un vaccin a été administrée Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-12-30 2021-12-30 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100319 vaccination dose 4 vaccine name vaccination_dose_4_vaccine_name Dose du vaccin 4 – Nom du vaccin vaccine name menu VaccineNameMenu null value menu NullValueMenu The name of the vaccine administered as the fourth dose of a vaccine regimen. Nom du vaccin administré comme quatrième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100320 vaccination dose 4 vaccination date vaccination_dose_4_vaccination_date Dose du vaccin 4 – Date du vaccin date date null value menu NullValueMenu The date the fourth dose of a vaccine was administered. Date à laquelle la quatrième dose d’un vaccin a été administrée Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2022-01-15 2022-01-15 PH_VACCINATION_HISTORY - Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100321 vaccination history vaccination_history Antécédents de vaccination WhitespaceMinimizedString WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Description des vaccins reçus et dates d’administration d’une série de vaccins contre une maladie spécifique ou un ensemble de maladies Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Description en texte libre des dates et des vaccins administrés contre une maladie précise ou un ensemble de maladies. Il est également acceptable de concaténer les renseignements sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 PH_VACCINATION_HISTORY - GENEPIO:0001409 Host exposure information - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country Lieu de l’exposition – Nom de géo_loc (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Pays où l’hôte a probablement été exposé à l’agent causal de la maladie Select the country name from pick list provided in the template. Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle. Canada Canada PH_EXPOSURE_COUNTRY - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city Destination du dernier voyage (ville) WhitespaceMinimizedString WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Nom de la ville de destination du voyage le plus récent Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de la ville dans laquelle l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. New York City New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory Destination du dernier voyage (état/province/territoire) WhitespaceMinimizedString WhitespaceMinimizedString The name of the province that was the destination of most recent travel. Nom de la province de destination du voyage le plus récent Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de l’État, de la province ou du territoire où l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. California Californie Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country Destination du dernier voyage (pays) geo_loc_name (country) menu GeoLocNameCountryMenu null value menu NullValueMenu The name of the country that was the destination of most recent travel. Nom du pays de destination du voyage le plus récent Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom du pays dans lequel l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. United Kingdom Royaume-Uni Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date Date de départ de voyage la plus récente date date null value menu NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Date du départ le plus récent d’une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits Provide the travel departure date. Indiquez la date de départ du voyage. 2020-03-16 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001415 most recent travel return date most_recent_travel_return_date Date de retour de voyage la plus récente date date null value menu NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Date du retour le plus récent d’une personne à une résidence après un voyage au départ de cette résidence Provide the travel return date. Indiquez la date de retour du voyage. 2020-04-26 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100413 travel point of entry type travel_point_of_entry_type Type de point d’entrée du voyage travel point of entry type menu TravelPointOfEntryTypeMenu null value menu NullValueMenu TRUE The type of entry point a traveler arrives through. Type de point d’entrée par lequel un voyageur arrive Select the point of entry type. Sélectionnez le type de point d’entrée. Air Air PH_POINT_OF_ENTRY - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100414 border testing test day type border_testing_test_day_type Jour du dépistage à la frontière border testing test day type menu BorderTestingTestDayTypeMenu null value menu NullValueMenu TRUE The day a traveller was tested on or after arrival at their point of entry. Jour où un voyageur a été testé à son point d’entrée ou après cette date Select the test day. Sélectionnez le jour du test. day 1 Jour 1 PH_DAY - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001416 travel history travel_history Antécédents de voyage WhitespaceMinimizedString WhitespaceMinimizedString Travel history in last six months. Historique de voyage au cours des six derniers mois Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Précisez les pays (et les emplacements plus précis, si vous les connaissez) visités au cours des six derniers mois, ce qui peut comprendre plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Commencez par le voyage le plus récent. Canada, Vancouver; USA, Seattle; Italy, Milan Canada, Vancouver; États-Unis, Seattle; Italie, Milan PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100649 travel history availability travel_history_availability Disponibilité des antécédents de voyage travel history availability menu TravelHistoryAvailabilityMenu null value menu NullValueMenu The availability of different types of travel history in the last 6 months (e.g. international, domestic). Disponibilité de différents types d’historiques de voyages au cours des six derniers mois (p. ex., internationaux, nationaux) If travel history is available, but the details of travel cannot be provided, indicate this and the type of travel history availble by selecting a value from the picklist. The values in this field can be used to indicate a sample is associated with a travel when the "purpose of sequencing" is not travel-associated. Si les antécédents de voyage sont disponibles, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d’antécédents disponibles en sélectionnant une valeur à partir de la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu’un échantillon est associé à un voyage lorsque le « but du séquençage » n’est pas associé à un voyage. International travel history available Antécédents de voyage à l’étranger disponible PH_TRAVEL - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001417 exposure event exposure_event Événement d’exposition exposure event menu ExposureEventMenu null value menu NullValueMenu Event leading to exposure. Événement conduisant à une exposition Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez un événement conduisant à une exposition à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Convention Convention Additional location information Exposure Event PH_EXPOSURE - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001418 exposure contact level exposure_contact_level Niveau de contact de l’exposition exposure contact level menu ExposureContactLevelMenu null value menu NullValueMenu The exposure transmission contact type. Type de contact de transmission d’exposition Select direct or indirect exposure from the pick-list. Sélectionnez une exposition directe ou indirecte à partir de la liste de sélection. Direct Direct exposure contact level - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001419 host role host_role Rôle de l’hôte host role menu HostRoleMenu TRUE The role of the host in relation to the exposure setting. Rôle de l’hôte par rapport au paramètre d’exposition Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez les rôles personnels de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Patient Patient PH_HOST_ROLE - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001428 exposure setting exposure_setting Contexte de l’exposition exposure setting menu ExposureSettingMenu TRUE The setting leading to exposure. Contexte menant à l’exposition Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Sélectionnez les contextes menant à l’exposition de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Healthcare Setting Milieu de soins de santé PH_EXPOSURE - Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001431 exposure details exposure_details Détails de l’exposition WhitespaceMinimizedString WhitespaceMinimizedString Additional host exposure information. Renseignements supplémentaires sur l’exposition de l’hôte Free text description of the exposure. Description en texte libre de l’exposition. Host role - Other: Bus Driver Rôle d’hôte - Autre : Conducteur d’autobus PH_EXPOSURE_DETAILS - - - GENEPIO:0001434 Host reinfection information - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001435 prior SARS-CoV-2 infection prior_sarscov2_infection Infection antérieure par le SRAS-CoV-2 prior SARS-CoV-2 infection menu PriorSarsCov2InfectionMenu null value menu NullValueMenu Whether there was prior SARS-CoV-2 infection. Infection antérieure par le SRAS-CoV-2 ou non If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Si vous le savez, fournissez des renseignements indiquant si la personne a déjà eu une infection par le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection. Yes Oui prior SARS-CoV-2 infection - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001436 prior SARS-CoV-2 infection isolate prior_sarscov2_infection_isolate Isolat d’une infection antérieure par le SRAS-CoV-2 WhitespaceMinimizedString WhitespaceMinimizedString The identifier of the isolate found in the prior SARS-CoV-2 infection. Identifiant de l’isolat trouvé lors de l’infection antérieure par le SRAS-CoV-2 Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom de « l’isolat » pour qu’il soit conforme à la norme ICTV/INSDC dans le format suivant : « SRAS-CoV-2/hôte/pays/IDéchantillon/date ». SARS-CoV-2/human/USA/CA-CDPH-001/2020 SARS-CoV-2/human/USA/CA-CDPH-001/2020 prior SARS-CoV-2 infection isolate - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001437 prior SARS-CoV-2 infection date prior_sarscov2_infection_date Date d’une infection antérieure par le SRAS-CoV-2 date date The date of diagnosis of the prior SARS-CoV-2 infection. Date du diagnostic de l’infection antérieure par le SRAS-CoV-2 Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d’infection antérieure par le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-01-23 2021-01-23 prior SARS-CoV-2 infection date - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001438 prior SARS-CoV-2 antiviral treatment prior_sarscov2_antiviral_treatment Traitement antiviral contre une infection antérieure par le SRAS-CoV-2 prior SARS-CoV-2 antiviral treatment menu PriorSarsCov2AntiviralTreatmentMenu null value menu NullValueMenu Whether there was prior SARS-CoV-2 treatment with an antiviral agent. Traitement contre une infection antérieure par le SRAS-CoV-2 avec un agent antiviral ou non If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection. No prior antiviral treatment Aucun traitement antiviral antérieur prior SARS-CoV-2 antiviral treatment - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001439 prior SARS-CoV-2 antiviral treatment agent prior_sarscov2_antiviral_treatment_agent Agent du traitement antiviral contre une infection antérieure par le SRAS-CoV-2 WhitespaceMinimizedString WhitespaceMinimizedString The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SRAS-CoV-2 Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous, séparés par des virgules. Remdesivir Remdesivir prior SARS-CoV-2 antiviral treatment agent - Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001440 prior SARS-CoV-2 antiviral treatment date prior_sarscov2_antiviral_treatment_date Date du traitement antiviral contre une infection antérieure par le SRAS-CoV-2 date date The date treatment was first administered during the prior SARS-CoV-2 infection. Date à laquelle le traitement a été administré pour la première fois lors de l’infection antérieure par le SRAS-CoV-2 Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’agent de traitement antiviral a été administré pour la première fois lors de l’infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-01-28 2021-01-28 prior SARS-CoV-2 antiviral treatment date - - - GENEPIO:0001441 Sequencing - Sequencing Séquençage GENEPIO:0001445 purpose of sequencing purpose_of_sequencing Objectif du séquençage purpose of sequencing menu PurposeOfSequencingMenu null value menu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Raison pour laquelle l’échantillon a été séquencé The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. La raison pour laquelle un échantillon a été initialement prélevé peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des renseignements sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. Le motif de prélèvement de l’échantillon doit être indiqué dans le champ « Objectif de l’échantillonnage ». Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing - Sequencing Séquençage GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details Détails de l’objectif du séquençage WhitespaceMinimizedString WhitespaceMinimizedString null value menu NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Description de la raison pour laquelle l’échantillon a été séquencé, fournissant des détails spécifiques Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été séquencé en utilisant du texte libre. La description peut inclure l’importance des séquences pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Les descriptions normalisées suggérées sont les suivantes : Dépistage de l’absence de détection du gène S (abandon du gène S), dépistage de variants associés aux visons, dépistage du variant B.1.1.7, dépistage du variant B.1.135, dépistage du variant P.1, dépistage en raison des antécédents de voyage, dépistage en raison d’un contact étroit avec une personne infectée, évaluation des mesures de contrôle de la santé publique, détermination des introductions et de la propagation précoces, enquête sur les expositions liées aux voyages aériens, enquête sur les travailleurs étrangers temporaires, enquête sur les régions éloignées, enquête sur les travailleurs de la santé, enquête sur les écoles et les universités, enquête sur la réinfection. Screened for S gene target failure (S dropout) Dépistage de l’absence de détection du gène S (abandon du gène S) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing Séquençage GENEPIO:0001447 sequencing date sequencing_date Date de séquençage date date null value menu NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. Date à laquelle l’échantillon a été séquencé ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-06-22 2020-06-22 PH_SEQUENCING_DATE - Sequencing Séquençage GENEPIO:0001448 library ID library_id ID de la bibliothèque WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. Identifiant spécifié par l’utilisateur pour la bibliothèque faisant l’objet du séquençage The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. Le nom de la bibliothèque doit être unique et peut être un ID généré automatiquement à partir de votre système de gestion de l’information des laboratoires, ou une modification de l’ID de l’isolat. XYZ_123345 XYZ_123345 library ID - Sequencing Séquençage GENEPIO:0001449 amplicon size amplicon_size Taille de l’amplicon WhitespaceMinimizedString WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Longueur de l’amplicon généré par l’amplification de la réaction de polymérisation en chaîne Provide the amplicon size, including the units. Fournissez la taille de l’amplicon, y compris les unités. 300bp 300 pb amplicon size - Sequencing Séquençage GENEPIO:0001450 library preparation kit library_preparation_kit Trousse de préparation de la bibliothèque WhitespaceMinimizedString WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Nom de la trousse de préparation de la banque d’ADN utilisée pour générer la bibliothèque faisant l’objet du séquençage Provide the name of the library preparation kit used. Indiquez le nom de la trousse de préparation de la bibliothèque utilisée. Nextera XT Nextera XT PH_LIBRARY_PREP_KIT - Sequencing Séquençage GENEPIO:0001451 flow cell barcode flow_cell_barcode Code-barres de la cuve à circulation WhitespaceMinimizedString WhitespaceMinimizedString The barcode of the flow cell used for sequencing. Code-barres de la cuve à circulation utilisée aux fins de séquençage Provide the barcode of the flow cell used for sequencing the sample. Fournissez le code-barres de la cuve à circulation utilisée pour séquencer l’échantillon. FAB06069 FAB06069 flow cell barcode - Sequencing Séquençage GENEPIO:0001452 sequencing instrument sequencing_instrument Instrument de séquençage sequencing instrument menu SequencingInstrumentMenu null value menu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Modèle de l’instrument de séquençage utilisé Select a sequencing instrument from the picklist provided in the template. Sélectionnez l’instrument de séquençage à partir de la liste de sélection. Oxford Nanopore MinION Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument - Sequencing Séquençage GENEPIO:0001453 sequencing protocol name sequencing_protocol_name Nom du protocole de séquençage WhitespaceMinimizedString WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Nom et numéro de version du protocole de séquençage utilisé Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION Fournissez le nom et la version du protocole de séquençage (p. ex., 1D_DNA_MinION). https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name PH_SEQ_PROTOCOL_NAME - Sequencing Séquençage GENEPIO:0001454 sequencing protocol sequencing_protocol Protocole de séquençage WhitespaceMinimizedString WhitespaceMinimizedString The protocol used to generate the sequence. Protocole utilisé pour générer la séquence Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Voici le texte suggéré (insérez les renseignements manquants) : « Le séquençage viral a été effectué selon une stratégie d’amplicon en mosaïque en utilisant le schéma d’amorce <à remplir>. Le séquençage a été effectué à l’aide d’un instrument de séquençage <à remplir>. Les bibliothèques ont été préparées à l’aide de la trousse <à remplir>. » Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Les génomes ont été générés par séquençage d’amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l’aide des trousses de préparation de l’ADN Illumina et les données de séquence ont été produites à l’aide des trousses de séquençage Miseq Micro v2 (500 cycles). PH_TESTING_PROTOCOL sequencing protocol - Sequencing Séquençage GENEPIO:0001455 sequencing kit number sequencing_kit_number Numéro de la trousse de séquençage WhitespaceMinimizedString WhitespaceMinimizedString The manufacturer's kit number. Numéro de la trousse du fabricant Alphanumeric value. Valeur alphanumérique. AB456XYZ789 AB456XYZ789 sequencing kit number - Sequencing Séquençage GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme Schéma d’amorce pour la réaction de polymérisation en chaîne de l’amplicon WhitespaceMinimizedString WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Spécifications liées aux amorces (séquences d’amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer Provide the name and version of the primer scheme used to generate the amplicons for sequencing. Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons aux fins de séquençage. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon pcr primer scheme - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method Méthode de traitement des données de séquences brutes WhitespaceMinimizedString WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Nom et numéro de version du logiciel utilisé pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l’adaptateur, le filtrage, etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Fournissez le nom du logiciel, suivi de la version (p. ex., Trimmomatic v. 0.38, Porechop v. 0.2.03). Porechop 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001459 dehosting method dehosting_method Méthode de retrait de l’hôte WhitespaceMinimizedString WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Méthode utilisée pour supprimer les lectures de l’hôte de la séquence de l’agent pathogène Provide the name and version number of the software used to remove host reads. Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l’hôte. Nanostripper Nanostripper PH_DEHOSTING_METHOD dehosting method - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001460 consensus sequence name consensus_sequence_name Nom de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString The name of the consensus sequence. Nom de la séquence de consensus Provide the name and version number of the consensus sequence. Fournissez le nom et le numéro de version de la séquence de consensus. ncov123assembly3 ncov123assembly3 consensus sequence name - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001461 consensus sequence filename consensus_sequence_filename Nom du fichier de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString The name of the consensus sequence file. Nom du fichier de la séquence de consensus Provide the name and version number of the consensus sequence FASTA file. Fournissez le nom et le numéro de version du fichier FASTA de la séquence de consensus. ncov123assembly.fasta ncov123assembly.fasta consensus sequence filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001462 consensus sequence filepath consensus_sequence_filepath Chemin d’accès au fichier de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString The filepath of the consensus sequence file. Chemin d’accès au fichier de la séquence de consensus Provide the filepath of the consensus sequence FASTA file. Fournissez le chemin d’accès au fichier FASTA de la séquence de consensus. /User/Documents/RespLab/Data/ncov123assembly.fasta /User/Documents/RespLab/Data/ncov123assembly.fasta consensus sequence filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name Nom du logiciel de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Nom du logiciel utilisé pour générer la séquence de consensus Provide the name of the software used to generate the consensus sequence. Fournissez le nom du logiciel utilisé pour générer la séquence de consensus. iVar iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version Version du logiciel de la séquence de consensus WhitespaceMinimizedString WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Version du logiciel utilisé pour générer la séquence de consensus Provide the version of the software used to generate the consensus sequence. Fournir la version du logiciel utilisé pour générer la séquence de consensus. 1.3 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value Valeur de l’étendue de la couverture WhitespaceMinimizedString WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Pourcentage du génome de référence couvert par les données séquencées, jusqu’à une profondeur prescrite Provide value as a percent. Fournissez la valeur en pourcentage. 95% 95 % breadth of coverage value breadth of coverage value - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001474 depth of coverage value depth_of_coverage_value Valeur de l’ampleur de la couverture WhitespaceMinimizedString WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite Provide value as a fold of coverage. Fournissez la valeur sous forme de couverture amplifiée. 400x 400x Coverage depth of coverage value depth of coverage value - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold Seuil de l’ampleur de la couverture WhitespaceMinimizedString WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Seuil utilisé comme limite pour l’ampleur de la couverture Provide the threshold fold coverage. Fournissez la couverture amplifiée. 100x 100x depth of coverage threshold - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001476 r1 fastq filename r1_fastq_filename________ Nom de fichier R1 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Nom du fichier R1 FASTQ spécifié par l’utilisateur Provide the r1 FASTQ filename. Fournissez le nom du fichier R1 FASTQ. ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001477 r2 fastq filename r2_fastq_filename Nom de fichier R2 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Nom du fichier R2 FASTQ spécifié par l’utilisateur Provide the r2 FASTQ filename. Fournissez le nom du fichier R2 FASTQ. ABC123_S1_L001_R2_001.fastq.gz ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath Chemin d’accès au fichier R1 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Emplacement du fichier R1 FASTQ dans le système de l’utilisateur Provide the filepath for the r1 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R1 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath Chemin d’accès au fichier R2 FASTQ WhitespaceMinimizedString WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Emplacement du fichier R2 FASTQ dans le système de l’utilisateur Provide the filepath for the r2 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R2 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001480 fast5 filename fast5_filename Nom de fichier FAST5 WhitespaceMinimizedString WhitespaceMinimizedString The user-specified filename of the FAST5 file. Nom du fichier FAST5 spécifié par l’utilisateur Provide the FAST5 filename. Fournissez le nom du fichier FAST5. rona123assembly.fast5 rona123assembly.fast5 fast5 filename - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001481 fast5 filepath fast5_filepath Chemin d’accès au fichier FAST5 WhitespaceMinimizedString WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Emplacement du fichier FAST5 dans le système de l’utilisateur Provide the filepath for the FAST5 file. This information aids in data management. Fournissez le chemin d’accès au fichier FAST5. /User/Documents/RespLab/Data/rona123assembly.fast5 /User/Documents/RespLab/Data/rona123assembly.fast5 fast5 filepath - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Nombre de paires de bases séquencées integer integer 0 The number of total base pairs generated by the sequencing process. Nombre total de paires de bases générées par le processus de séquençage Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 387566 387 566 number of base pairs sequenced - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001483 consensus genome length consensus_genome_length Longueur consensuelle du génome integer integer 0 Size of the reconstructed genome described as the number of base pairs. Taille du génome reconstitué décrite comme étant le nombre de paires de bases Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 38677 38 677 consensus genome length - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp N par 100 kbp decimal decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Nombre de symboles N présents dans la séquence fasta de consensus, par 100 kbp de séquence Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 330 330 Ns per 100 kbp - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001485 reference genome accession reference_genome_accession Accès au génome de référence WhitespaceMinimizedString WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Identifiant persistant et unique d’une entrée dans une base de données génomique Provide the accession number of the reference genome. Fournissez le numéro d’accès au génome de référence. NC_045512.2 NC_045512.2 reference genome accession reference genome accession - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol Protocole bioinformatique WhitespaceMinimizedString WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Description de la stratégie bioinformatique globale utilisée Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes, générer des assemblages ou générer des séquences de consensus peuvent être fournis dans une PON, un protocole, un pipeline ou un flux de travail. Fournissez le nom et le numéro de version du protocole, ou un lien GitHub vers un pipeline ou un flux de travail. https://github.com/phac-nml/ncov2019-artic-nf https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol - GENEPIO:0001498 Lineage and Variant information - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001500 lineage/clade name lineage_clade_name Nom de la lignée ou du clade WhitespaceMinimizedString WhitespaceMinimizedString The name of the lineage or clade. Nom de la lignée ou du clade Provide the Pangolin or Nextstrain lineage/clade name. Fournissez le nom de la lignée ou du clade Pangolin ou Nextstrain. B.1.1.7 B.1.1.7 PH_LINEAGE_CLADE_NAME - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name Nom du logiciel d’analyse de la lignée ou du clade WhitespaceMinimizedString WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Nom du logiciel utilisé pour déterminer la lignée ou le clade Provide the name of the software used to determine the lineage/clade. Fournissez le nom du logiciel utilisé pour déterminer la lignée ou le clade. Pangolin Pangolin PH_LINEAGE_CLADE_SOFTWARE - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version Version du logiciel d’analyse de la lignée ou du clade WhitespaceMinimizedString WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Version du logiciel utilisé pour déterminer la lignée ou le clade Provide the version of the software used ot determine the lineage/clade. Fournissez la version du logiciel utilisé pour déterminer la lignée ou le clade. 2.1.10 2.1.10 PH_LINEAGE_CLADE_VERSION - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001503 variant designation variant_designation Désignation du variant variant designation menu VariantDesignationMenu null value menu NullValueMenu The variant classification of the lineage/clade i.e. variant, variant of concern. Classification des variants de la lignée ou du clade (c.-à-d. le variant, le variant préoccupant) If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Si la lignée ou le clade est considéré comme étant un variant préoccupant, sélectionnez l’option connexe à partir de la liste de sélection. Si la lignée ou le clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques), mais qu’il ne s’agit pas d’un variant préoccupant global, sélectionnez « Variante ». Si la lignée ou le clade ne contient pas de mutations préoccupantes, laissez ce champ vide. Variant of Concern Variant préoccupant PH_VARIANT_DESIGNATION - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001504 variant evidence variant_evidence Données probantes du variant variant evidence menu VariantEvidenceMenu null value menu NullValueMenu The evidence used to make the variant determination. Données probantes utilisées pour déterminer le variant Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. Indiquez si l’échantillon a fait l’objet d’un dépistage RT-qPCR ou par séquençage à partir de la liste de sélection. RT-qPCR RT-qPCR PH_VARIANT_EVIDENCE - Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001505 variant evidence details variant_evidence_details Détails liés aux données probantes du variant WhitespaceMinimizedString WhitespaceMinimizedString Details about the evidence used to make the variant determination. Détails sur les données probantes utilisées pour déterminer le variant Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Fournissez l’essai biologique et répertoriez l’ensemble des mutations définissant la lignée qui sont utilisées pour effectuer la détermination des variants. Si des mutations d’intérêt ou de préoccupation ont été observées en plus des mutations définissant la lignée, décrivez-les ici. Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). Mutations définissant la lignée : ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). PH_VARIANT_EVIDENCE_DETAILS - GENEPIO:0001506 Pathogen diagnostic testing - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001507 gene name 1 gene_name_1 Nom du gène 1 gene name menu GeneNameMenu null value menu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet du gène soumis au dépistage. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. E gene (orf4) Gène E (orf4) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 Protocole de diagnostic de polymérase en chaîne 1 WhitespaceMinimizedString WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. EGenePCRTest 2 EGenePCRTest 2 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 Valeur de diagnostic de polymérase en chaîne 1 decimal decimal null value menu NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the diagnostic RT-PCR test. Fournissez la valeur Ct de l’échantillon issu du test diagnostique RT-PCR. 21 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001510 gene name 2 gene_name_2 Nom du gène 2 gene name menu GeneNameMenu null value menu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. RdRp gene (nsp12) Gène RdRp (nsp12) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 Protocole de diagnostic de polymérase en chaîne 2 WhitespaceMinimizedString WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 Valeur de diagnostic de polymérase en chaîne 2 decimal decimal null value menu NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR. 36 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001513 gene name 3 gene_name_3 Nom du gène 3 gene name menu GeneNameMenu null value menu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. RdRp gene (nsp12) Gène RdRp (nsp12) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 Protocole de diagnostic de polymérase en chaîne 3 WhitespaceMinimizedString WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 - Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 Valeur de diagnostic de polymérase en chaîne 3 decimal decimal null value menu NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR. 30 30 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value - - - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001517 authors authors Auteurs WhitespaceMinimizedString WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Noms des personnes contribuant aux processus de prélèvement d’échantillons, de génération de séquences, d’analyse et de soumission de données Include the first and last names of all individuals that should be attributed, separated by a comma. Incluez le prénom et le nom de toutes les personnes qui doivent être affectées, séparés par une virgule. Tejinder Singh, Fei Hu, Joe Blogs Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS - Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance de DataHarmonizer Provenance Provenance The DataHarmonizer software and template version provenance. Provenance du logiciel DataHarmonizer et de la version du modèle The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. Les renseignements actuels sur la version du logiciel et du modèle seront automatiquement générés dans ce champ une fois que l’utilisateur aura utilisé la fonction « Valider ». Ces renseignements seront générés indépendamment du fait que la ligne soit valide ou non. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS - \ No newline at end of file +class_name slot_group slot_group_fr slot_uri title name title_fr range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description description_fr comments comments_fr examples examples_fr EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +CanCOGeNCovid19 GENEPIO:0001122 Database Identifiers + Database Identifiers Identificateurs de base de données GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id ID du collecteur d’échantillons WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Nom défini par l’utilisateur pour l’échantillon Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. Conservez l’ID de l’échantillon du collecteur. Si ce numéro est considéré comme une information identifiable, fournissez un autre identifiant. Assurez-vous de conserver la clé qui correspond aux identifiants d’origine et alternatifs aux fins de traçabilité et de suivi, au besoin. Chaque ID d’échantillon de collecteur provenant d’un seul demandeur doit être unique. Il peut avoir n’importe quel format, mais nous vous suggérons de le rendre concis, unique et cohérent au sein de votre laboratoire. prov_rona_99 prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID + Database Identifiers Identificateurs de base de données GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name Nom du fournisseur de services de laboratoire tiers WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Nom de la société ou du laboratoire tiers qui fournit les services Provide the full, unabbreviated name of the company or laboratory. Indiquez le nom complet et non abrégé de l’entreprise ou du laboratoire. Switch Health Switch Health HC_TEXT5 + Database Identifiers Identificateurs de base de données GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id ID de l’échantillon de laboratoire tiers WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Identifiant attribué à un échantillon par un prestataire de services tiers Store the sample identifier supplied by the third party services provider. Conservez l’identifiant de l’échantillon fourni par le prestataire de services tiers. SHK123456 SHK123456 PH_ID_NUMBER_PRIMARY + Database Identifiers Identificateurs de base de données GENEPIO:0100281 case ID case_id ID du dossier WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Identifiant utilisé pour désigner un cas de maladie détecté sur le plan épidémiologique Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. Fournissez l’identifiant du cas, lequel facilite grandement le lien entre les données de laboratoire et les données épidémiologiques. Il peut être considéré comme une information identifiable. Consultez l’intendant des données avant de le transmettre. ABCD1234 ABCD1234 PH_CASE_ID + Database Identifiers Identificateurs de base de données GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id ID principal de l’échantillon associé WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Identifiant principal d’un échantillon associé précédemment soumis au dépôt Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. Conservez l’identifiant primaire de l’échantillon correspondant précédemment soumis au Laboratoire national de microbiologie afin que les échantillons puissent être liés et suivis dans le système. SR20-12345 SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID + Database Identifiers Identificateurs de base de données GENEPIO:0001131 IRIDA sample name irida_sample_name Nom de l’échantillon IRIDA WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Identifiant attribué à un isolat séquencé dans IRIDA Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). Enregistrez le nom de l’échantillon IRIDA, lequel sera créé par la personne saisissant les données dans la plateforme connexe. Les échantillons IRIDA peuvent être liés à des métadonnées et à des données de séquence, ou simplement à des métadonnées. Il est recommandé que le nom de l’échantillon IRIDA soit identique ou contienne l’ID de l’échantillon du collecteur pour assurer une meilleure traçabilité. Il est également recommandé que le nom de l’échantillon IRIDA reflète l’accès à GISAID. Les noms d’échantillons IRIDA ne peuvent pas contenir de barres obliques. Celles-ci doivent être remplacées par des traits de soulignement. Consultez la documentation IRIDA pour en savoir plus sur les caractères spéciaux (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 prov_rona_99 IRIDA sample name + Database Identifiers Identificateurs de base de données GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession Numéro d’accès au bioprojet cadre UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject for the Canadian SARS-CoV-2 sequencing effort. Numéro d’accès à INSDC attribué au bioprojet cadre pour l’effort canadien de séquençage du SRAS-CoV-2 Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. Enregistrez le numéro d’accès au bioprojet cadre en le sélectionnant à partir de la liste déroulante du modèle. Ce numéro sera identique pour tous les soumissionnaires du RCanGéCO. Différentes provinces auront leurs propres bioprojets, mais ces derniers seront liés sous un seul bioprojet cadre. PRJNA623807 PRJNA623807 umbrella bioproject accession + Database Identifiers Identificateurs de base de données GENEPIO:0001136 bioproject accession bioproject_accession Numéro d’accès au bioprojet WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Numéro d’accès à INSDC du bioprojet auquel appartient un échantillon biologique Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. Enregistrez le numéro d’accès au bioprojet. Les bioprojets sont un outil d’organisation qui relie les données de séquence brutes, les assemblages et leurs métadonnées associées. Chaque province se verra attribuer un numéro d’accès différent au bioprojet par le Laboratoire national de microbiologie. Un numéro d’accès valide au bioprojet du NCBI contient le préfixe PRJN (p. ex., PRJNA12345); il est créé une fois au début d’un nouveau projet de séquençage. PRJNA608651 PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession + Database Identifiers Identificateurs de base de données GENEPIO:0001139 biosample accession biosample_accession Numéro d’accès à un échantillon biologique WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Identifiant attribué à un échantillon biologique dans les archives INSDC Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. Conservez le numéro d’accès renvoyé avec la soumission d’un échantillon biologique. Les échantillons biologiques de NCBI seront assortis du SAMN. SAMN14180202 SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION + Database Identifiers Identificateurs de base de données GENEPIO:0001142 SRA accession sra_accession Numéro d’accès à l’archive des séquences WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Identifiant de l’archive des séquences reliant les données de séquences brutes de lecture, les métadonnées méthodologiques et les mesures de contrôle de la qualité soumises à INSDC Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. Conservez le numéro d’accès attribué au « cycle » soumis. Les accès NCBI-SRA commencent par SRR. SRR11177792 SRR11177792 SRA Accession PH_SRA_ACCESSION + Database Identifiers Identificateurs de base de données GENEPIO:0001145 GenBank accession genbank_accession Numéro d’accès à GenBank WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Identifiant GenBank attribué à la séquence dans les archives INSDC Store the accession returned from a GenBank submission (viral genome assembly). Conservez le numéro d’accès renvoyé avec la soumission de GenBank (assemblage du génome viral). MN908947.3 MN908947.3 GenBank Accession GenBank accession + Database Identifiers Identificateurs de base de données GENEPIO:0001147 GISAID accession gisaid_accession Numéro d’accès à la GISAID WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Numéro d’accès à la GISAID attribué à la séquence Store the accession returned from the GISAID submission. Conservez le numéro d’accès renvoyé avec la soumission de la GISAID. EPI_ISL_436489 EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession + GENEPIO:0001150 Sample collection and processing + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001153 sample collected by sample_collected_by Échantillon prélevé par SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. Nom de l’organisme ayant prélevé l’échantillon original The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). Le nom du collecteur d’échantillons doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions, par exemple Agence de la santé publique du Canada, Santé publique Ontario, Centre de contrôle des maladies de la Colombie-Britannique. BC Centre for Disease Control Centre de contrôle des maladies de la Colombie-Britannique Originating lab Lab Name CUSTOMER collected_by sample collected by + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001156 sample collector contact email sample_collector_contact_email Adresse courriel du collecteur d’échantillons WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca). RespLab@lab.ca RespLab@lab.ca sample collector contact email + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001158 sample collector contact address sample_collector_contact_address Adresse du collecteur d’échantillons WhitespaceMinimizedString The mailing address of the agency submitting the sample. Adresse postale de l’organisme soumettant l’échantillon The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays. 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada 655, rue Lab, Vancouver (Colombie-Britannique) V5N 2A2 Canada Address sample collector contact address + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001159 sequence submitted by sequence_submitted_by Séquence soumise par SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. Nom de l’organisme ayant généré la séquence The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Le nom de l’agence doit être écrit au long (à quelques exceptions près) et être cohérent dans plusieurs soumissions. Si vous soumettez des échantillons plutôt que des données de séquençage, veuillez inscrire « Laboratoire national de microbiologie (LNM) ». Public Health Ontario (PHO) Santé publique Ontario (SPO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email Adresse courriel du soumissionnaire de séquence WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Adresse courriel de la personne-ressource responsable du suivi concernant l’échantillon The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca L’adresse courriel peut représenter une personne ou un laboratoire spécifique (p. ex., johnnyblogs@lab.ca, or RespLab@lab.ca). RespLab@lab.ca RespLab@lab.ca sequence submitter contact email + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address Adresse du soumissionnaire de séquence WhitespaceMinimizedString The mailing address of the agency submitting the sequence. Adresse postale de l’organisme soumettant l’échantillon The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country Le format de l’adresse postale doit être le suivant : Numéro et nom de la rue, ville, province/territoire, code postal et pays. 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada 123, rue Sunnybrooke, Toronto (Ontario) M4P 1L6 Canada Address sequence submitter contact address + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001174 sample collection date sample_collection_date Date de prélèvement de l’échantillon date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Date à laquelle l’échantillon a été prélevé Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". La date de prélèvement des échantillons est essentielle pour la surveillance et de nombreux types d’analyses. La granularité requise comprend l’année, le mois et le jour. Si cette date est considérée comme un renseignement identifiable, il est acceptable d’y ajouter une « gigue » en ajoutant ou en soustrayant un jour civil. La « date de réception » peut également servir de date de rechange. La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-16 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001177 sample collection date precision sample_collection_date_precision Précision de la date de prélèvement de l’échantillon SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Précision avec laquelle la « date de prélèvement de l’échantillon » a été fournie Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". Fournissez la précision de la granularité au « jour », au « mois » ou à « l’année » pour la date fournie dans le champ « Date de prélèvement de l’échantillon ». Cette date sera tronquée selon la précision spécifiée lors de l’exportation : « jour » pour « AAAA-MM-JJ », « mois » pour « AAAA-MM » ou « année » pour « AAAA ». year année Precision of date collected HC_TEXT2 + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001179 sample received date sample_received_date Date de réception de l’échantillon date NullValueMenu The date on which the sample was received. Date à laquelle l’échantillon a été reçu ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-20 2020-03-20 sample received date + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country nom_lieu_géo (pays) GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Pays d’origine de l’échantillon Provide the country name from the controlled vocabulary provided. Fournissez le nom du pays à partir du vocabulaire contrôlé fourni. Canada Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory nom_lieu_géo (état/province/territoire) GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The province/territory where the sample was collected. Province ou territoire où l’échantillon a été prélevé Provide the province/territory name from the controlled vocabulary provided. Fournissez le nom de la province ou du territoire à partir du vocabulaire contrôlé fourni. Saskatchewan Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001189 geo_loc_name (city) geo_loc_name_city nom_géo_loc (ville) WhitespaceMinimizedString The city where the sample was collected. Ville où l’échantillon a été prélevé Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Fournissez le nom de la ville. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. Medicine Hat Medicine Hat Patient City geo_loc_name (city) + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001191 organism organism Organisme OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Nom taxonomique de l’organisme Use "Severe acute respiratory syndrome coronavirus 2". This value is provided in the template. Utilisez « coronavirus du syndrome respiratoire aigu sévère 2 ». Cette valeur est fournie dans le modèle. Severe acute respiratory syndrome coronavirus 2 Coronavirus du syndrome respiratoire aigu sévère 2 Pathogen HC_CURRENT_ID organism organism + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001195 isolate isolate Isolat WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Identifiant de l’isolat spécifique Provide the GISAID virus name, which should be written in the format “hCov-19/CANADA/2 digit provincial ISO code-xxxxx/year”. Fournissez le nom du virus de la GISAID, qui doit être écrit dans le format « hCov-19/CANADA/code ISO provincial à 2 chiffres-xxxxx/année ». hCov-19/CANADA/BC-prov_rona_99/2020 hCov-19/CANADA/BC-prov_rona_99/2020 Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001198 purpose of sampling purpose_of_sampling Objectif de l’échantillonnage PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. Motif de prélèvement de l’échantillon The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. La raison pour laquelle un échantillon a été prélevé peut fournir des renseignements sur les biais potentiels de la stratégie d’échantillonnage. Choisissez l’objectif de l’échantillonnage à partir de la liste déroulante du modèle. Il est très probable que l’échantillon ait été prélevé en vue d’un test diagnostique. La raison pour laquelle un échantillon a été prélevé à l’origine peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage, ce qui doit être indiqué dans le champ « Objectif du séquençage ». Diagnostic testing Tests diagnostiques Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details Détails de l’objectif de l’échantillonnage WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Détails précis concernant le motif de prélèvement de l’échantillon Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été prélevé en utilisant du texte libre. La description peut inclure l’importance de l’échantillon pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Si les détails ne sont pas disponibles, fournissez une valeur nulle. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. L’échantillon a été prélevé pour étudier la prévalence des variants associés à la transmission du vison à l’homme au Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type Type d’échantillon soumis au LNM NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. Type d’échantillon soumis au Laboratoire national de microbiologie (LNM) aux fins d’analyse This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Ces renseignements sont requis pour le téléchargement à l’aide du système LaSER du RCRSP. Choisissez le type d’échantillon à partir de la liste de sélection fournie. Si les données de séquences sont soumises plutôt qu’un échantillon aux fins d’analyse, sélectionnez « Sans objet ». swab Écouvillon Specimen Type PH_SPECIMEN_TYPE + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type Type de relation de l’échantillon lié RelatedSpecimenRelationshipTypeMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Relation entre l’échantillon actuel et celui précédemment soumis au dépôt Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Fournissez l’étiquette qui décrit comment l’échantillon précédent est lié à l’échantillon actuel soumis à partir de la liste de sélection fournie afin que les échantillons puissent être liés et suivis dans le système. Specimen sampling methods testing Test des méthodes de prélèvement des échantillons Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001211 anatomical material anatomical_material Matière anatomique AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Substance obtenue à partir d’une partie anatomique d’un organisme (p. ex., tissu, sang) Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une matière anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Blood Sang Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001214 anatomical part anatomical_part Partie anatomique AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Partie anatomique d’un organisme (p. ex., oropharynx) Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une partie anatomique a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Nasopharynx (NP) Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001216 body product body_product Produit corporel BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Substance excrétée ou sécrétée par un organisme (p. ex., selles, urine, sueur) Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un produit corporel a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Feces Selles Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001223 environmental material environmental_material Matériel environnemental EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Substance obtenue à partir de l’environnement naturel ou artificiel (p. ex., sol, eau, eaux usées) Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une matière environnementale a été échantillonnée. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Face mask Masque Specimen source Environmental Material PH_ENVIRONMENTAL_MATERIAL isolation_source;environmental_material environmental material + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001232 environmental site environmental_site Site environnemental EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Emplacement environnemental pouvant décrire un site dans l’environnement naturel ou artificiel (p. ex., surface de contact, boîte métallique, hôpital, marché traditionnel de produits frais, grotte de chauves-souris) Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un site environnemental a été échantillonné. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Production Facility Installation de production Specimen source Environmental Site PH_ENVIRONMENTAL_SITE isolation_source;environmental_site environmental site + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001234 collection device collection_device Dispositif de prélèvement CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Instrument ou contenant utilisé pour prélever l’échantillon (p. ex., écouvillon) Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si un dispositif de prélèvement a été utilisé pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Swab Écouvillon Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001241 collection method collection_method Méthode de prélèvement CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Processus utilisé pour prélever l’échantillon (p. ex., phlébotomie, autopsie) Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Fournissez un descripteur si une méthode de prélèvement a été utilisée pour l’échantillonnage. Utilisez la liste de sélection fournie dans le modèle. Si un terme souhaité ne figure pas dans la liste de sélection, veuillez envoyer un courriel à l’adresse emma_griffiths@sfu.ca. Si ce n’est pas le cas, ne laissez pas le champ vide. Choisissez une valeur nulle. Bronchoalveolar lavage (BAL) Lavage bronchoalvéolaire (LBA) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001243 collection protocol collection_protocol Protocole de prélèvement WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Nom et version d’un protocole particulier utilisé pour l’échantillonnage Free text. Texte libre. BCRonaSamplingProtocol v. 1.2 CBRonaProtocoleÉchantillonnage v. 1.2 collection protocol + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001253 specimen processing specimen_processing Traitement des échantillons SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Tout traitement appliqué à l’échantillon pendant ou après sa réception Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Essentiel pour l’interprétation des données. Sélectionnez tous les processus applicables dans la liste de sélection. Si le virus a été transmis, ajoutez les renseignements dans les champs « Laboratoire hôte », « Nombre de transmissions » et « Méthode de transmission ». Si aucun des processus de la liste de sélection ne s’applique, inscrivez « Sans objet ». Virus passage Transmission du virus Passage details/history specimen processing + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0100311 specimen processing details specimen_processing_details Détails du traitement des échantillons WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Renseignements détaillés concernant le traitement appliqué à un échantillon pendant ou après sa réception Provide a free text description of any processing details applied to a sample. Fournissez une description en texte libre de tous les détails du traitement appliqués à un échantillon. 25 swabs were pooled and further prepared as a single sample during library prep. 25 écouvillons ont été regroupés et préparés en tant qu’échantillon unique lors de la préparation de la bibliothèque. + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001255 lab host lab_host Laboratoire hôte LabHostMenu NullValueMenu TRUE Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Nom et description du laboratoire hôte utilisé pour propager l’organisme source ou le matériel à partir duquel l’échantillon a été obtenu Type of cell line used for propagation. Provide the name of the cell line using the picklist in the template. If not passaged, put "not applicable". Type de lignée cellulaire utilisée pour la propagation. Choisissez le nom de cette lignée à partir de la liste de sélection dans le modèle. Si le virus n’a pas été transmis, indiquez « Sans objet ». Vero E6 cell line Lignée cellulaire Vero E6 Passage details/history lab host lab_host + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001261 passage number passage_number Nombre de transmission integer NullValueMenu TRUE 0 Number of passages. Nombre de transmissions Provide number of known passages. If not passaged, put "not applicable" Indiquez le nombre de transmissions connues. Si le virus n’a pas été transmis, indiquez « Sans objet ». 3 3 Passage details/history passage number passage_history + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001264 passage method passage_method Méthode de transmission WhitespaceMinimizedString NullValueMenu TRUE Description of how organism was passaged. Description de la façon dont l’organisme a été transmis Free text. Provide a very short description (<10 words). If not passaged, put "not applicable". Texte libre. Fournissez une brève description (<10 mots). Si le virus n’a pas été transmis, indiquez « Sans objet ». 0.25% trypsin + 0.02% EDTA 0,25 % de trypsine + 0,02 % d’EDTA Passage details/history passage method passage_method + Sample collection and processing Collecte et traitement des échantillons GENEPIO:0001266 biomaterial extracted biomaterial_extracted Biomatériau extrait BiomaterialExtractedMenu NullValueMenu The biomaterial extracted from samples for the purpose of sequencing. Biomatériau extrait d’échantillons aux fins de séquençage Provide the biomaterial extracted from the picklist in the template. Fournissez le biomatériau extrait à partir de la liste de sélection dans le modèle. RNA (total) ARN (total) biomaterial extracted + GENEPIO:0001268 Host Information + Host Information Informations sur l'hôte GENEPIO:0001386 host (common name) host_common_name Hôte (nom commun) HostCommonNameMenu NullValueMenu The commonly used name of the host. Nom couramment utilisé pour l’hôte Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Des exemples de noms communs sont « humain » et « chauve-souris ». Si l’échantillon était environnemental, inscrivez « Sans objet ». Human Humain Animal Type PH_ANIMAL_TYPE + Host Information Informations sur l'hôte GENEPIO:0001387 host (scientific name) host_scientific_name Hôte (nom scientifique) HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Nom taxonomique ou scientifique de l’hôte Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Le nom commun ou scientifique est requis s’il y avait un hôte. Les deux peuvent être fournis s’ils sont connus. Utilisez les termes figurant dans les listes de sélection du modèle. Un exemple de nom scientifique est « homo sapiens ». Si l’échantillon était environnemental, inscrivez « Sans objet ». Homo sapiens Homo sapiens Host host (scientific name) host host (scientific name) + Host Information Informations sur l'hôte GENEPIO:0001388 host health state host_health_state État de santé de l’hôte HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. État de santé de l’hôte au moment du prélèvement d’échantillons If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Symptomatic Symptomatique Patient status Host Health State PH_HOST_HEALTH host_health_state + Host Information Informations sur l'hôte GENEPIO:0001389 host health status details host_health_status_details Détails de l’état de santé de l’hôte HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. Plus de détails concernant l’état de santé ou de maladie de l’hôte au moment du prélèvement If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Hospitalized (ICU) Hospitalisé (USI) Host Health State Details PH_HOST_HEALTH_DETAILS + Host Information Informations sur l'hôte GENEPIO:0001390 host health outcome host_health_outcome Résultats sanitaires de l’hôte HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. Résultats de la maladie chez l’hôte If known, select a descriptor from the pick list provided in the template. Si vous le connaissez, sélectionnez un descripteur à partir de la liste de sélection fournie dans le modèle. Recovered Rétabli PH_HOST_HEALTH_OUTCOME host_disease_outcome + Host Information Informations sur l'hôte GENEPIO:0001391 host disease host_disease Maladie de l’hôte HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Nom de la maladie vécue par l’hôte Select "COVID-19" from the pick list provided in the template. Sélectionnez « COVID-19 » à partir de la liste de sélection fournie dans le modèle. COVID-19 COVID-19 Host Disease PH_HOST_DISEASE host_disease host disease + Host Information Informations sur l'hôte GENEPIO:0001392 host age host_age Âge de l’hôte decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. Âge de l’hôte au moment du prélèvement d’échantillons Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". Entrez l’âge de l’hôte en années. S’il n’est pas disponible, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet ». 79 79 Patient age Patient Age PH_AGE host_age host age + Host Information Informations sur l'hôte GENEPIO:0001393 host age unit host_age_unit Catégorie d’âge de l’hôte HostAgeUnitMenu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Unité utilisée pour mesurer l’âge de l’hôte (mois ou année) Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. Indiquez si l’âge de l’hôte est en mois ou en années. L’âge indiqué en mois sera classé dans la tranche d’âge de 0 à 9 ans. year année Age Units PH_AGE_UNIT host age unit + Host Information Informations sur l'hôte GENEPIO:0001394 host age bin host_age_bin Groupe d’âge de l’hôte HostAgeBinMenu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Âge de l’hôte au moment du prélèvement d’échantillons (groupe d’âge) Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. Sélectionnez la tranche d’âge correspondante de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne la connaissez pas, fournissez une valeur nulle. 60 - 69 60 - 69 Host Age Category PH_AGE_GROUP host age bin + Host Information Informations sur l'hôte GENEPIO:0001395 host gender host_gender Genre de l’hôte HostGenderMenu NullValueMenu TRUE The gender of the host at the time of sample collection. Genre de l’hôte au moment du prélèvement d’échantillons Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Sélectionnez le genre correspondant de l’hôte à partir de la liste de sélection fournie dans le modèle. Si vous ne le connaissez pas, fournissez une valeur nulle. S’il n’y a pas d’hôte, inscrivez « Sans objet ». Male Homme Gender Patient Sex VD_SEX host_sex host gender + Host Information Informations sur l'hôte GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country Résidence de l’hôte – Nom de géo_loc (pays) GeoLocNameCountryMenu NullValueMenu The country of residence of the host. Pays de résidence de l’hôte Select the country name from pick list provided in the template. Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle. Canada Canada PH_HOST_COUNTRY + Host Information Informations sur l'hôte GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory Résidence de l’hôte – Nom de géo_loc (état/province/territoire) GeoLocNameStateProvinceTerritoryMenu NullValueMenu The state/province/territory of residence of the host. État, province ou territoire de résidence de l’hôte Select the province/territory name from pick list provided in the template. Sélectionnez le nom de la province ou du territoire à partir de la liste de sélection fournie dans le modèle. Quebec Québec PH_HOST_PROVINCE + Host Information Informations sur l'hôte GENEPIO:0001398 host subject ID host_subject_id ID du sujet de l’hôte WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Identifiant unique permettant de désigner chaque hôte (p. ex., 131) Provide the host identifier. Should be a unique, user-defined identifier. Fournissez l’identifiant de l’hôte. Il doit s’agir d’un identifiant unique défini par l’utilisateur. BCxy123 BCxy123 host subject ID host_subject_id + Host Information Informations sur l'hôte GENEPIO:0001399 symptom onset date symptom_onset_date Date d’apparition des symptômes date NullValueMenu The date on which the symptoms began or were first noted. Date à laquelle les symptômes ont commencé ou ont été observés pour la première fois ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-03-16 2020-03-16 Symptoms Onset Date HC_ONSET_DATE + Host Information Informations sur l'hôte GENEPIO:0001400 signs and symptoms signs_and_symptoms Signes et symptômes SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient or clinician. Changement perçu dans la fonction ou la sensation (perte, perturbation ou apparence) révélant une maladie, qui est signalé par un patient ou un clinicien Select all of the symptoms experienced by the host from the pick list. Sélectionnez tous les symptômes ressentis par l’hôte à partir de la liste de sélection. Chills (sudden cold sensation); Cough; Fever Frissons (sensation soudaine de froid); toux; fièvre Symptoms HC_SYMPTOMS + Host Information Informations sur l'hôte GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors Conditions préexistantes et facteurs de risque PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Conditions préexistantes et facteurs de risque du patient
  • Condition préexistante : Condition médicale qui existait avant l’infection actuelle
  • Facteur de risque : Variable associée à un risque accru de maladie ou d’infection  Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les conditions préexistantes et tous les facteurs de risque de l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Asthma; Pregnancy; Smoking Asthme; grossesse; tabagisme pre-existing conditions and risk factors + Host Information Informations sur l'hôte GENEPIO:0001402 complications complications Complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Complications médicales du patient qui seraient dues à une maladie de l’hôte Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Sélectionnez toutes les complications éprouvées par l’hôte à partir de la liste de sélection. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Acute Respiratory Failure; Coma; Septicemia Insuffisance respiratoire aiguë; coma; septicémie complications + GENEPIO:0001403 Host vaccination information + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001404 host vaccination status host_vaccination_status Statut de vaccination de l’hôte host vaccination status menu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Statut de vaccination de l’hôte (entièrement vacciné, partiellement vacciné ou non vacciné) Select the vaccination status of the host from the pick list. Sélectionnez le statut de vaccination de l’hôte à partir de la liste de sélection. Fully Vaccinated Entièrement vacciné PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received Nombre de doses du vaccin reçues integer The number of doses of the vaccine recived by the host. Nombre de doses du vaccin reçues par l’hôte Record how many doses of the vaccine the host has received. Enregistrez le nombre de doses du vaccin que l’hôte a reçues. 2 2 + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name Dose du vaccin 1 – Nom du vaccin VaccineNameMenu NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Nom du vaccin administré comme première dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme première dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date Dose du vaccin 1 – Date du vaccin date NullValueMenu The date the first dose of a vaccine was administered. Date à laquelle la première dose d’un vaccin a été administrée Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la première dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-03-01 2021-03-01 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100315 vaccination dose 2 vaccine name vaccination_dose_2_vaccine_name Dose du vaccin 2 – Nom du vaccin VaccineNameMenu NullValueMenu The name of the vaccine administered as the second dose of a vaccine regimen. Nom du vaccin administré comme deuxième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme deuxième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100316 vaccination dose 2 vaccination date vaccination_dose_2_vaccination_date Dose du vaccin 2 – Date du vaccin date NullValueMenu The date the second dose of a vaccine was administered. Date à laquelle la deuxième dose d’un vaccin a été administrée Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la deuxième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-09-01 2021-09-01 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100317 vaccination dose 3 vaccine name vaccination_dose_3_vaccine_name Dose du vaccin 3 – Nom du vaccin VaccineNameMenu NullValueMenu The name of the vaccine administered as the third dose of a vaccine regimen. Nom du vaccin administré comme troisième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme troisième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100318 vaccination dose 3 vaccination date vaccination_dose_3_vaccination_date Dose du vaccin 3 – Date du vaccin date NullValueMenu The date the third dose of a vaccine was administered. Date à laquelle la troisième dose d’un vaccin a été administrée Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la troisième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-12-30 2021-12-30 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100319 vaccination dose 4 vaccine name vaccination_dose_4_vaccine_name Dose du vaccin 4 – Nom du vaccin VaccineNameMenu NullValueMenu The name of the vaccine administered as the fourth dose of a vaccine regimen. Nom du vaccin administré comme quatrième dose d’un schéma vaccinal Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list Fournissez le nom et le fabricant correspondant du vaccin contre la COVID-19 administré comme quatrième dose en sélectionnant une valeur à partir de la liste de sélection. Pfizer-BioNTech (Comirnaty) Pfizer-BioNTech (Comirnaty) PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100320 vaccination dose 4 vaccination date vaccination_dose_4_vaccination_date Dose du vaccin 4 – Date du vaccin date NullValueMenu The date the fourth dose of a vaccine was administered. Date à laquelle la quatrième dose d’un vaccin a été administrée Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle la quatrième dose du vaccin contre la COVID-19 a été administrée. La date doit être fournie selon le format standard ISO 8601 « AAAA-MM-DD ». 2022-01-15 2022-01-15 PH_VACCINATION_HISTORY + Host vaccination information Informations sur la vaccination de l'hôte GENEPIO:0100321 vaccination history vaccination_history Antécédents de vaccination WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Description des vaccins reçus et dates d’administration d’une série de vaccins contre une maladie spécifique ou un ensemble de maladies Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Description en texte libre des dates et des vaccins administrés contre une maladie précise ou un ensemble de maladies. Il est également acceptable de concaténer les renseignements sur les doses individuelles (nom du vaccin, date de vaccination) séparées par des points-virgules. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 PH_VACCINATION_HISTORY + GENEPIO:0001409 Host exposure information + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country Lieu de l’exposition – Nom de géo_loc (pays) GeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Pays où l’hôte a probablement été exposé à l’agent causal de la maladie Select the country name from pick list provided in the template. Sélectionnez le nom du pays à partir de la liste de sélection fournie dans le modèle. Canada Canada PH_EXPOSURE_COUNTRY + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city Destination du dernier voyage (ville) WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Nom de la ville de destination du voyage le plus récent Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de la ville dans laquelle l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. New York City New York City Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory Destination du dernier voyage (état/province/territoire) WhitespaceMinimizedString The name of the province that was the destination of most recent travel. Nom de la province de destination du voyage le plus récent Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom de l’État, de la province ou du territoire où l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. California Californie Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country Destination du dernier voyage (pays) GeoLocNameCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Nom du pays de destination du voyage le plus récent Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Indiquez le nom du pays dans lequel l’hôte s’est rendu. Utilisez ce service de recherche pour trouver le terme normalisé : https://www.ebi.ac.uk/ols/ontologies/gaz. United Kingdom Royaume-Uni Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date Date de départ de voyage la plus récente date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Date du départ le plus récent d’une personne de sa résidence principale (à ce moment-là) pour un voyage vers un ou plusieurs autres endroits Provide the travel departure date. Indiquez la date de départ du voyage. 2020-03-16 2020-03-16 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001415 most recent travel return date most_recent_travel_return_date Date de retour de voyage la plus récente date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Date du retour le plus récent d’une personne à une résidence après un voyage au départ de cette résidence Provide the travel return date. Indiquez la date de retour du voyage. 2020-04-26 2020-04-26 Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100413 travel point of entry type travel_point_of_entry_type Type de point d’entrée du voyage TravelPointOfEntryTypeMenu NullValueMenu TRUE The type of entry point a traveler arrives through. Type de point d’entrée par lequel un voyageur arrive Select the point of entry type. Sélectionnez le type de point d’entrée. Air Air PH_POINT_OF_ENTRY + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100414 border testing test day type border_testing_test_day_type Jour du dépistage à la frontière BorderTestingTestDayTypeMenu NullValueMenu TRUE The day a traveller was tested on or after arrival at their point of entry. Jour où un voyageur a été testé à son point d’entrée ou après cette date Select the test day. Sélectionnez le jour du test. day 1 Jour 1 PH_DAY + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001416 travel history travel_history Antécédents de voyage WhitespaceMinimizedString Travel history in last six months. Historique de voyage au cours des six derniers mois Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Précisez les pays (et les emplacements plus précis, si vous les connaissez) visités au cours des six derniers mois, ce qui peut comprendre plusieurs voyages. Séparez plusieurs événements de voyage par un point-virgule. Commencez par le voyage le plus récent. Canada, Vancouver; USA, Seattle; Italy, Milan Canada, Vancouver; États-Unis, Seattle; Italie, Milan PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0100649 travel history availability travel_history_availability Disponibilité des antécédents de voyage TravelHistoryAvailabilityMenu NullValueMenu The availability of different types of travel history in the last 6 months (e.g. international, domestic). Disponibilité de différents types d’historiques de voyages au cours des six derniers mois (p. ex., internationaux, nationaux) If travel history is available, but the details of travel cannot be provided, indicate this and the type of travel history availble by selecting a value from the picklist. The values in this field can be used to indicate a sample is associated with a travel when the "purpose of sequencing" is not travel-associated. Si les antécédents de voyage sont disponibles, mais que les détails du voyage ne peuvent pas être fournis, indiquez-le ainsi que le type d’antécédents disponibles en sélectionnant une valeur à partir de la liste de sélection. Les valeurs de ce champ peuvent être utilisées pour indiquer qu’un échantillon est associé à un voyage lorsque le « but du séquençage » n’est pas associé à un voyage. International travel history available Antécédents de voyage à l’étranger disponible PH_TRAVEL + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001417 exposure event exposure_event Événement d’exposition ExposureEventMenu NullValueMenu Event leading to exposure. Événement conduisant à une exposition Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez un événement conduisant à une exposition à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Convention Convention Additional location information Exposure Event PH_EXPOSURE + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001418 exposure contact level exposure_contact_level Niveau de contact de l’exposition ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Type de contact de transmission d’exposition Select direct or indirect exposure from the pick-list. Sélectionnez une exposition directe ou indirecte à partir de la liste de sélection. Direct Direct exposure contact level + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001419 host role host_role Rôle de l’hôte HostRoleMenu TRUE The role of the host in relation to the exposure setting. Rôle de l’hôte par rapport au paramètre d’exposition Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Sélectionnez les rôles personnels de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Patient Patient PH_HOST_ROLE + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001428 exposure setting exposure_setting Contexte de l’exposition ExposureSettingMenu TRUE The setting leading to exposure. Contexte menant à l’exposition Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Sélectionnez les contextes menant à l’exposition de l’hôte à partir de la liste de sélection fournie dans le modèle. S’il manque le terme souhaité, veuillez communiquer avec l’équipe de conservation des données. Healthcare Setting Milieu de soins de santé PH_EXPOSURE + Host exposure information Informations sur l'exposition de l'hôte GENEPIO:0001431 exposure details exposure_details Détails de l’exposition WhitespaceMinimizedString Additional host exposure information. Renseignements supplémentaires sur l’exposition de l’hôte Free text description of the exposure. Description en texte libre de l’exposition. Host role - Other: Bus Driver Rôle d’hôte - Autre : Conducteur d’autobus PH_EXPOSURE_DETAILS + + + GENEPIO:0001434 Host reinfection information + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001435 prior SARS-CoV-2 infection prior_sarscov2_infection Infection antérieure par le SRAS-CoV-2 PriorSarsCov2InfectionMenu NullValueMenu Whether there was prior SARS-CoV-2 infection. Infection antérieure par le SRAS-CoV-2 ou non If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Si vous le savez, fournissez des renseignements indiquant si la personne a déjà eu une infection par le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection. Yes Oui prior SARS-CoV-2 infection + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001436 prior SARS-CoV-2 infection isolate prior_sarscov2_infection_isolate Isolat d’une infection antérieure par le SRAS-CoV-2 WhitespaceMinimizedString The identifier of the isolate found in the prior SARS-CoV-2 infection. Identifiant de l’isolat trouvé lors de l’infection antérieure par le SRAS-CoV-2 Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". Indiquez le nom de l’isolat de l’infection antérieure la plus récente. Structurez le nom de « l’isolat » pour qu’il soit conforme à la norme ICTV/INSDC dans le format suivant : « SRAS-CoV-2/hôte/pays/IDéchantillon/date ». SARS-CoV-2/human/USA/CA-CDPH-001/2020 SARS-CoV-2/human/USA/CA-CDPH-001/2020 prior SARS-CoV-2 infection isolate + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001437 prior SARS-CoV-2 infection date prior_sarscov2_infection_date Date d’une infection antérieure par le SRAS-CoV-2 date The date of diagnosis of the prior SARS-CoV-2 infection. Date du diagnostic de l’infection antérieure par le SRAS-CoV-2 Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’infection antérieure la plus récente a été diagnostiquée. Fournissez la date d’infection antérieure par le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-01-23 2021-01-23 prior SARS-CoV-2 infection date + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001438 prior SARS-CoV-2 antiviral treatment prior_sarscov2_antiviral_treatment Traitement antiviral contre une infection antérieure par le SRAS-CoV-2 PriorSarsCov2AntiviralTreatmentMenu NullValueMenu Whether there was prior SARS-CoV-2 treatment with an antiviral agent. Traitement contre une infection antérieure par le SRAS-CoV-2 avec un agent antiviral ou non If known, provide information about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. Si vous le savez, indiquez si la personne a déjà reçu un traitement antiviral contre le SRAS-CoV-2. Sélectionnez une valeur à partir de la liste de sélection. No prior antiviral treatment Aucun traitement antiviral antérieur prior SARS-CoV-2 antiviral treatment + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001439 prior SARS-CoV-2 antiviral treatment agent prior_sarscov2_antiviral_treatment_agent Agent du traitement antiviral contre une infection antérieure par le SRAS-CoV-2 WhitespaceMinimizedString The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Nom de l’agent de traitement antiviral administré lors de l’infection antérieure par le SRAS-CoV-2 Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Indiquez le nom de l’agent de traitement antiviral administré lors de l’infection antérieure la plus récente. Si aucun traitement n’a été administré, inscrivez « Aucun traitement ». Si plusieurs agents antiviraux ont été administrés, énumérez-les tous, séparés par des virgules. Remdesivir Remdesivir prior SARS-CoV-2 antiviral treatment agent + Host reinfection information Informations sur la réinfection de l'hôte GENEPIO:0001440 prior SARS-CoV-2 antiviral treatment date prior_sarscov2_antiviral_treatment_date Date du traitement antiviral contre une infection antérieure par le SRAS-CoV-2 date The date treatment was first administered during the prior SARS-CoV-2 infection. Date à laquelle le traitement a été administré pour la première fois lors de l’infection antérieure par le SRAS-CoV-2 Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". Indiquez la date à laquelle l’agent de traitement antiviral a été administré pour la première fois lors de l’infection antérieure la plus récente. Fournissez la date du traitement antérieur contre le SRAS-CoV-2 selon le format standard ISO 8601 « AAAA-MM-DD ». 2021-01-28 2021-01-28 prior SARS-CoV-2 antiviral treatment date + + + GENEPIO:0001441 Sequencing + Sequencing Séquençage GENEPIO:0001445 purpose of sequencing purpose_of_sequencing Objectif du séquençage PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Raison pour laquelle l’échantillon a été séquencé The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. La raison pour laquelle un échantillon a été initialement prélevé peut différer de la raison pour laquelle il a été sélectionné aux fins de séquençage. La raison pour laquelle un échantillon a été séquencé peut fournir des renseignements sur les biais potentiels dans la stratégie de séquençage. Fournissez le but du séquençage à partir de la liste de sélection dans le modèle. Le motif de prélèvement de l’échantillon doit être indiqué dans le champ « Objectif de l’échantillonnage ». Baseline surveillance (random sampling) Surveillance de base (échantillonnage aléatoire) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing + Sequencing Séquençage GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details Détails de l’objectif du séquençage WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Description de la raison pour laquelle l’échantillon a été séquencé, fournissant des détails spécifiques Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Fournissez une description détaillée de la raison pour laquelle l’échantillon a été séquencé en utilisant du texte libre. La description peut inclure l’importance des séquences pour une enquête, une activité de surveillance ou une question de recherche particulière dans le domaine de la santé publique. Les descriptions normalisées suggérées sont les suivantes : Dépistage de l’absence de détection du gène S (abandon du gène S), dépistage de variants associés aux visons, dépistage du variant B.1.1.7, dépistage du variant B.1.135, dépistage du variant P.1, dépistage en raison des antécédents de voyage, dépistage en raison d’un contact étroit avec une personne infectée, évaluation des mesures de contrôle de la santé publique, détermination des introductions et de la propagation précoces, enquête sur les expositions liées aux voyages aériens, enquête sur les travailleurs étrangers temporaires, enquête sur les régions éloignées, enquête sur les travailleurs de la santé, enquête sur les écoles et les universités, enquête sur la réinfection. Screened for S gene target failure (S dropout) Dépistage de l’absence de détection du gène S (abandon du gène S) Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details + Sequencing Séquençage GENEPIO:0001447 sequencing date sequencing_date Date de séquençage date NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. Date à laquelle l’échantillon a été séquencé ISO 8601 standard "YYYY-MM-DD". La date doit être fournie selon le format standard ISO 8601 : « AAAA-MM-JJ ». 2020-06-22 2020-06-22 PH_SEQUENCING_DATE + Sequencing Séquençage GENEPIO:0001448 library ID library_id ID de la bibliothèque WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. Identifiant spécifié par l’utilisateur pour la bibliothèque faisant l’objet du séquençage The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. Le nom de la bibliothèque doit être unique et peut être un ID généré automatiquement à partir de votre système de gestion de l’information des laboratoires, ou une modification de l’ID de l’isolat. XYZ_123345 XYZ_123345 library ID + Sequencing Séquençage GENEPIO:0001449 amplicon size amplicon_size Taille de l’amplicon WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Longueur de l’amplicon généré par l’amplification de la réaction de polymérisation en chaîne Provide the amplicon size, including the units. Fournissez la taille de l’amplicon, y compris les unités. 300bp 300 pb amplicon size + Sequencing Séquençage GENEPIO:0001450 library preparation kit library_preparation_kit Trousse de préparation de la bibliothèque WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Nom de la trousse de préparation de la banque d’ADN utilisée pour générer la bibliothèque faisant l’objet du séquençage Provide the name of the library preparation kit used. Indiquez le nom de la trousse de préparation de la bibliothèque utilisée. Nextera XT Nextera XT PH_LIBRARY_PREP_KIT + Sequencing Séquençage GENEPIO:0001451 flow cell barcode flow_cell_barcode Code-barres de la cuve à circulation WhitespaceMinimizedString The barcode of the flow cell used for sequencing. Code-barres de la cuve à circulation utilisée aux fins de séquençage Provide the barcode of the flow cell used for sequencing the sample. Fournissez le code-barres de la cuve à circulation utilisée pour séquencer l’échantillon. FAB06069 FAB06069 flow cell barcode + Sequencing Séquençage GENEPIO:0001452 sequencing instrument sequencing_instrument Instrument de séquençage SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Modèle de l’instrument de séquençage utilisé Select a sequencing instrument from the picklist provided in the template. Sélectionnez l’instrument de séquençage à partir de la liste de sélection. Oxford Nanopore MinION Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument + Sequencing Séquençage GENEPIO:0001453 sequencing protocol name sequencing_protocol_name Nom du protocole de séquençage WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Nom et numéro de version du protocole de séquençage utilisé Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION Fournissez le nom et la version du protocole de séquençage (p. ex., 1D_DNA_MinION). https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Sequencing Protocol Name PH_SEQ_PROTOCOL_NAME + Sequencing Séquençage GENEPIO:0001454 sequencing protocol sequencing_protocol Protocole de séquençage WhitespaceMinimizedString The protocol used to generate the sequence. Protocole utilisé pour générer la séquence Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Fournissez une description en texte libre des méthodes et du matériel utilisés pour générer la séquence. Voici le texte suggéré (insérez les renseignements manquants) : « Le séquençage viral a été effectué selon une stratégie d’amplicon en mosaïque en utilisant le schéma d’amorce <à remplir>. Le séquençage a été effectué à l’aide d’un instrument de séquençage <à remplir>. Les bibliothèques ont été préparées à l’aide de la trousse <à remplir>. » Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. Les génomes ont été générés par séquençage d’amplicons de 1 200 pb avec des amorces de schéma Freed. Les bibliothèques ont été créées à l’aide des trousses de préparation de l’ADN Illumina et les données de séquence ont été produites à l’aide des trousses de séquençage Miseq Micro v2 (500 cycles). PH_TESTING_PROTOCOL sequencing protocol + Sequencing Séquençage GENEPIO:0001455 sequencing kit number sequencing_kit_number Numéro de la trousse de séquençage WhitespaceMinimizedString The manufacturer's kit number. Numéro de la trousse du fabricant Alphanumeric value. Valeur alphanumérique. AB456XYZ789 AB456XYZ789 sequencing kit number + Sequencing Séquençage GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme Schéma d’amorce pour la réaction de polymérisation en chaîne de l’amplicon WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Spécifications liées aux amorces (séquences d’amorces, positions de liaison, taille des fragments générés, etc.) utilisées pour générer les amplicons à séquencer Provide the name and version of the primer scheme used to generate the amplicons for sequencing. Fournissez le nom et la version du schéma d’amorce utilisé pour générer les amplicons aux fins de séquençage. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon pcr primer scheme + GENEPIO:0001457 Bioinformatics and QC metrics + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method Méthode de traitement des données de séquences brutes WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Nom et numéro de version du logiciel utilisé pour le traitement des données brutes, comme la suppression des codes-barres, le découpage de l’adaptateur, le filtrage, etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Fournissez le nom du logiciel, suivi de la version (p. ex., Trimmomatic v. 0.38, Porechop v. 0.2.03). Porechop 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001459 dehosting method dehosting_method Méthode de retrait de l’hôte WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Méthode utilisée pour supprimer les lectures de l’hôte de la séquence de l’agent pathogène Provide the name and version number of the software used to remove host reads. Fournissez le nom et le numéro de version du logiciel utilisé pour supprimer les lectures de l’hôte. Nanostripper Nanostripper PH_DEHOSTING_METHOD dehosting method + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001460 consensus sequence name consensus_sequence_name Nom de la séquence de consensus WhitespaceMinimizedString The name of the consensus sequence. Nom de la séquence de consensus Provide the name and version number of the consensus sequence. Fournissez le nom et le numéro de version de la séquence de consensus. ncov123assembly3 ncov123assembly3 consensus sequence name + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001461 consensus sequence filename consensus_sequence_filename Nom du fichier de la séquence de consensus WhitespaceMinimizedString The name of the consensus sequence file. Nom du fichier de la séquence de consensus Provide the name and version number of the consensus sequence FASTA file. Fournissez le nom et le numéro de version du fichier FASTA de la séquence de consensus. ncov123assembly.fasta ncov123assembly.fasta consensus sequence filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001462 consensus sequence filepath consensus_sequence_filepath Chemin d’accès au fichier de la séquence de consensus WhitespaceMinimizedString The filepath of the consensus sequence file. Chemin d’accès au fichier de la séquence de consensus Provide the filepath of the consensus sequence FASTA file. Fournissez le chemin d’accès au fichier FASTA de la séquence de consensus. /User/Documents/RespLab/Data/ncov123assembly.fasta /User/Documents/RespLab/Data/ncov123assembly.fasta consensus sequence filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name Nom du logiciel de la séquence de consensus WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Nom du logiciel utilisé pour générer la séquence de consensus Provide the name of the software used to generate the consensus sequence. Fournissez le nom du logiciel utilisé pour générer la séquence de consensus. iVar iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version Version du logiciel de la séquence de consensus WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Version du logiciel utilisé pour générer la séquence de consensus Provide the version of the software used to generate the consensus sequence. Fournir la version du logiciel utilisé pour générer la séquence de consensus. 1.3 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value Valeur de l’étendue de la couverture WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Pourcentage du génome de référence couvert par les données séquencées, jusqu’à une profondeur prescrite Provide value as a percent. Fournissez la valeur en pourcentage. 95% 95 % breadth of coverage value breadth of coverage value + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001474 depth of coverage value depth_of_coverage_value Valeur de l’ampleur de la couverture WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite Provide value as a fold of coverage. Fournissez la valeur sous forme de couverture amplifiée. 400x 400x Coverage depth of coverage value depth of coverage value + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold Seuil de l’ampleur de la couverture WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Seuil utilisé comme limite pour l’ampleur de la couverture Provide the threshold fold coverage. Fournissez la couverture amplifiée. 100x 100x depth of coverage threshold + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001476 r1 fastq filename r1_fastq_filename________ Nom de fichier R1 FASTQ WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Nom du fichier R1 FASTQ spécifié par l’utilisateur Provide the r1 FASTQ filename. Fournissez le nom du fichier R1 FASTQ. ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001477 r2 fastq filename r2_fastq_filename Nom de fichier R2 FASTQ WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Nom du fichier R2 FASTQ spécifié par l’utilisateur Provide the r2 FASTQ filename. Fournissez le nom du fichier R2 FASTQ. ABC123_S1_L001_R2_001.fastq.gz ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath Chemin d’accès au fichier R1 FASTQ WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Emplacement du fichier R1 FASTQ dans le système de l’utilisateur Provide the filepath for the r1 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R1 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath Chemin d’accès au fichier R2 FASTQ WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Emplacement du fichier R2 FASTQ dans le système de l’utilisateur Provide the filepath for the r2 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R2 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001480 fast5 filename fast5_filename Nom de fichier FAST5 WhitespaceMinimizedString The user-specified filename of the FAST5 file. Nom du fichier FAST5 spécifié par l’utilisateur Provide the FAST5 filename. Fournissez le nom du fichier FAST5. rona123assembly.fast5 rona123assembly.fast5 fast5 filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001481 fast5 filepath fast5_filepath Chemin d’accès au fichier FAST5 WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Emplacement du fichier FAST5 dans le système de l’utilisateur Provide the filepath for the FAST5 file. This information aids in data management. Fournissez le chemin d’accès au fichier FAST5. /User/Documents/RespLab/Data/rona123assembly.fast5 /User/Documents/RespLab/Data/rona123assembly.fast5 fast5 filepath + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Nombre de paires de bases séquencées integer 0 The number of total base pairs generated by the sequencing process. Nombre total de paires de bases générées par le processus de séquençage Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 387566 387 566 number of base pairs sequenced + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001483 consensus genome length consensus_genome_length Longueur consensuelle du génome integer 0 Size of the reconstructed genome described as the number of base pairs. Taille du génome reconstitué décrite comme étant le nombre de paires de bases Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 38677 38 677 consensus genome length + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp N par 100 kbp decimal 0 The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Nombre de symboles N présents dans la séquence fasta de consensus, par 100 kbp de séquence Provide a numerical value (no need to include units). Fournissez une valeur numérique (pas besoin d’inclure des unités). 330 330 Ns per 100 kbp + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001485 reference genome accession reference_genome_accession Accès au génome de référence WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Identifiant persistant et unique d’une entrée dans une base de données génomique Provide the accession number of the reference genome. Fournissez le numéro d’accès au génome de référence. NC_045512.2 NC_045512.2 reference genome accession reference genome accession + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol Protocole bioinformatique WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Description de la stratégie bioinformatique globale utilisée Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. Des détails supplémentaires concernant les méthodes utilisées pour traiter les données brutes, générer des assemblages ou générer des séquences de consensus peuvent être fournis dans une PON, un protocole, un pipeline ou un flux de travail. Fournissez le nom et le numéro de version du protocole, ou un lien GitHub vers un pipeline ou un flux de travail. https://github.com/phac-nml/ncov2019-artic-nf https://github.com/phac-nml/ncov2019-artic-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol + GENEPIO:0001498 Lineage and Variant information + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001500 lineage/clade name lineage_clade_name Nom de la lignée ou du clade WhitespaceMinimizedString The name of the lineage or clade. Nom de la lignée ou du clade Provide the Pangolin or Nextstrain lineage/clade name. Fournissez le nom de la lignée ou du clade Pangolin ou Nextstrain. B.1.1.7 B.1.1.7 PH_LINEAGE_CLADE_NAME + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001501 lineage/clade analysis software name lineage_clade_analysis_software_name Nom du logiciel d’analyse de la lignée ou du clade WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Nom du logiciel utilisé pour déterminer la lignée ou le clade Provide the name of the software used to determine the lineage/clade. Fournissez le nom du logiciel utilisé pour déterminer la lignée ou le clade. Pangolin Pangolin PH_LINEAGE_CLADE_SOFTWARE + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001502 lineage/clade analysis software version lineage_clade_analysis_software_version Version du logiciel d’analyse de la lignée ou du clade WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Version du logiciel utilisé pour déterminer la lignée ou le clade Provide the version of the software used ot determine the lineage/clade. Fournissez la version du logiciel utilisé pour déterminer la lignée ou le clade. 2.1.10 2.1.10 PH_LINEAGE_CLADE_VERSION + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001503 variant designation variant_designation Désignation du variant VariantDesignationMenu NullValueMenu The variant classification of the lineage/clade i.e. variant, variant of concern. Classification des variants de la lignée ou du clade (c.-à-d. le variant, le variant préoccupant) If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Si la lignée ou le clade est considéré comme étant un variant préoccupant, sélectionnez l’option connexe à partir de la liste de sélection. Si la lignée ou le clade contient des mutations préoccupantes (mutations qui augmentent la transmission, la gravité clinique ou d’autres facteurs épidémiologiques), mais qu’il ne s’agit pas d’un variant préoccupant global, sélectionnez « Variante ». Si la lignée ou le clade ne contient pas de mutations préoccupantes, laissez ce champ vide. Variant of Concern Variant préoccupant PH_VARIANT_DESIGNATION + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001504 variant evidence variant_evidence Données probantes du variant VariantEvidenceMenu NullValueMenu The evidence used to make the variant determination. Données probantes utilisées pour déterminer le variant Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. Indiquez si l’échantillon a fait l’objet d’un dépistage RT-qPCR ou par séquençage à partir de la liste de sélection. RT-qPCR RT-qPCR PH_VARIANT_EVIDENCE + Lineage and Variant information Informations sur les lignées et les variantes GENEPIO:0001505 variant evidence details variant_evidence_details Détails liés aux données probantes du variant WhitespaceMinimizedString Details about the evidence used to make the variant determination. Détails sur les données probantes utilisées pour déterminer le variant Provide the assay and list the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Fournissez l’essai biologique et répertoriez l’ensemble des mutations définissant la lignée qui sont utilisées pour effectuer la détermination des variants. Si des mutations d’intérêt ou de préoccupation ont été observées en plus des mutations définissant la lignée, décrivez-les ici. Lineage-defining mutations: ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). Mutations définissant la lignée : ORF1ab (K1655N), Spike (K417N, E484K, N501Y, D614G, A701V), N (T205I), E (P71L). PH_VARIANT_EVIDENCE_DETAILS + GENEPIO:0001506 Pathogen diagnostic testing + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001507 gene name 1 gene_name_1 Nom du gène 1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet du gène soumis au dépistage. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. E gene (orf4) Gène E (orf4) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 Protocole de diagnostic de polymérase en chaîne 1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. EGenePCRTest 2 EGenePCRTest 2 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 Valeur de diagnostic de polymérase en chaîne 1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the diagnostic RT-PCR test. Fournissez la valeur Ct de l’échantillon issu du test diagnostique RT-PCR. 21 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001510 gene name 2 gene_name_2 Nom du gène 2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. RdRp gene (nsp12) Gène RdRp (nsp12) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 Protocole de diagnostic de polymérase en chaîne 2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 Valeur de diagnostic de polymérase en chaîne 2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR. 36 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001513 gene name 3 gene_name_3 Nom du gène 3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Nom du gène utilisé dans le test diagnostique RT-PCR Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Indiquez le nom complet d’un autre gène utilisé dans le test RT-PCR. Le symbole du gène (forme abrégée du nom du gène) peut également être fourni. Il est possible de trouver les noms et les symboles de gènes normalisés dans Gene Ontology en utilisant ce service de recherche : https://bit.ly/2Sq1LbI. RdRp gene (nsp12) Gène RdRp (nsp12) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 Protocole de diagnostic de polymérase en chaîne 3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. Nom et numéro de version du protocole utilisé pour l’amplification des marqueurs diagnostiques The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. Le nom et le numéro de version du protocole utilisé pour réaliser un deuxième test diagnostique basé sur la réaction en chaîne de la polymérase. Ces renseignements peuvent être comparés aux données de séquence pour l’évaluation du rendement et le contrôle de la qualité. RdRpGenePCRTest 3 RdRpGenePCRTest 3 + Pathogen diagnostic testing Tests de diagnostic des agents pathogènes GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 Valeur de diagnostic de polymérase en chaîne 3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Valeur Ct obtenue à la suite d’un test de diagnostic RT-PCR du SRAS-CoV-2 Provide the CT value of the sample from the second diagnostic RT-PCR test. Fournissez la valeur Ct du deuxième échantillon issu du deuxième test diagnostique RT-PCR. 30 30 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value + + + GENEPIO:0001516 Contributor acknowledgement + Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001517 authors authors Auteurs WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Noms des personnes contribuant aux processus de prélèvement d’échantillons, de génération de séquences, d’analyse et de soumission de données Include the first and last names of all individuals that should be attributed, separated by a comma. Incluez le prénom et le nom de toutes les personnes qui doivent être affectées, séparés par une virgule. Tejinder Singh, Fei Hu, Joe Blogs Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS + Contributor acknowledgement Reconnaissance des contributeurs GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance de DataHarmonizer Provenance The DataHarmonizer software and template version provenance. Provenance du logiciel DataHarmonizer et de la version du modèle The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. Les renseignements actuels sur la version du logiciel et du modèle seront automatiquement générés dans ce champ une fois que l’utilisateur aura utilisé la fonction « Valider ». Ces renseignements seront générés indépendamment du fait que la ligne soit valide ou non. DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer v1.4.3, CanCOGeN Covid-19 v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS + \ No newline at end of file From 1f3ab17328f8ca4aec1fba8d136870d7e3b06042 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 08:59:20 -0700 Subject: [PATCH 82/96] Mpox accidental spaces in r1_fastq_filename and GISAID export tweak --- web/templates/mpox/schema.json | 30 ++++++++++++++--------------- web/templates/mpox/schema.yaml | 14 +++++++------- web/templates/mpox/schema_slots.tsv | 4 ++-- 3 files changed, 24 insertions(+), 24 deletions(-) diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 0e9f56f7..59d4d4b3 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -9759,7 +9759,7 @@ ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory", "CNPHI:Primary%20Specimen%20ID", "NML_LIMS:TEXT_ID", "BIOSAMPLE:sample_name", @@ -12390,8 +12390,8 @@ } ] }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", "comments": [ @@ -14825,8 +14825,8 @@ "rank": 107, "slot_group": "Bioinformatics and QC metrics" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "rank": 108, "slot_group": "Bioinformatics and QC metrics" }, @@ -15007,7 +15007,7 @@ ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory", "CNPHI:Primary%20Specimen%20ID", "NML_LIMS:TEXT_ID", "BIOSAMPLE:sample_name", @@ -18489,8 +18489,8 @@ } ] }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", "comments": [ @@ -18504,7 +18504,7 @@ "from_schema": "https://example.com/mpox", "rank": 108, "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename________", + "alias": "r1_fastq_filename", "owner": "Mpox", "domain_of": [ "Mpox", @@ -20540,8 +20540,8 @@ "rank": 110, "slot_group": "Bioinformatics and QC metrics" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "rank": 111, "slot_group": "Bioinformatics and QC metrics" }, @@ -20781,7 +20781,7 @@ ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory", "CNPHI:Primary%20Specimen%20ID", "NML_LIMS:TEXT_ID", "BIOSAMPLE:sample_name", @@ -24219,8 +24219,8 @@ } ] }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", "comments": [ @@ -24234,7 +24234,7 @@ "from_schema": "https://example.com/mpox", "rank": 111, "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename________", + "alias": "r1_fastq_filename", "owner": "MpoxInternational", "domain_of": [ "Mpox", diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 4bec6ea5..cfdec5e3 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -127,7 +127,7 @@ classes: - consensus_sequence_software_version - sequence_assembly_software_name - sequence_assembly_software_version - - r1_fastq_filename________ + - r1_fastq_filename - r2_fastq_filename - r1_fastq_filepath - r2_fastq_filepath @@ -802,7 +802,7 @@ classes: sequence_assembly_software_version: rank: 107 slot_group: Bioinformatics and QC metrics - r1_fastq_filename________: + r1_fastq_filename: rank: 108 slot_group: Bioinformatics and QC metrics r2_fastq_filename: @@ -1021,7 +1021,7 @@ classes: - consensus_sequence_software_version - sequence_assembly_software_name - sequence_assembly_software_version - - r1_fastq_filename________ + - r1_fastq_filename - r2_fastq_filename - r1_fastq_filepath - r2_fastq_filepath @@ -1637,7 +1637,7 @@ classes: sequence_assembly_software_version: rank: 110 slot_group: Bioinformatics and QC metrics - r1_fastq_filename________: + r1_fastq_filename: rank: 111 slot_group: Bioinformatics and QC metrics r2_fastq_filename: @@ -1790,7 +1790,7 @@ slots: examples: - value: prov_mpox_1234 exact_mappings: - - GISAID:Sample%20ID%20given%20by%20the%20sample%20provider + - GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory - CNPHI:Primary%20Specimen%20ID - NML_LIMS:TEXT_ID - BIOSAMPLE:sample_name @@ -3278,8 +3278,8 @@ slots: required: true examples: - value: 3.15.5 - r1_fastq_filename________: - name: r1_fastq_filename________ + r1_fastq_filename: + name: r1_fastq_filename title: r1 fastq filename description: The user-specified filename of the r1 FASTQ file. comments: Provide the r1 FASTQ filename. This information aids in data management. diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 8f18dc44..2670958a 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -1,6 +1,6 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal For RefGuide Matching Mpox;MpoxInternational GENEPIO:0001122 Database Identifiers database_identifiers Mpox;MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID Mpox;MpoxInternational +Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the submitting laboratory Primary Specimen ID TEXT_ID sample_name specimen collector sample ID Mpox;MpoxInternational Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID Mpox Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID Mpox;MpoxInternational Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession Mpox;MpoxInternational @@ -176,7 +176,7 @@ Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001463 consensus s Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version Mpox;MpoxInternational Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu TRUE The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet Mpox;MpoxInternational Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu TRUE The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename________ WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz Mpox;MpoxInternational Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz Mpox;MpoxInternational From b2af5013c68fc3afd0cccc30d151a0842090df45 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:02:50 -0700 Subject: [PATCH 83/96] pha4ge normalized names and updated exact_mappings --- web/templates/pha4ge/schema.json | 5698 ++++++++++++++++++------- web/templates/pha4ge/schema.yaml | 2948 ++++++------- web/templates/pha4ge/schema_enums.tsv | 2332 +++++----- web/templates/pha4ge/schema_slots.tsv | 318 +- 4 files changed, 6934 insertions(+), 4362 deletions(-) diff --git a/web/templates/pha4ge/schema.json b/web/templates/pha4ge/schema.json index 47bbc2ea..ac18e518 100644 --- a/web/templates/pha4ge/schema.json +++ b/web/templates/pha4ge/schema.json @@ -19,6 +19,10 @@ "shex": { "prefix_prefix": "shex", "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" } }, "default_prefix": "https://example.com/CanCOGeN_Covid-19/", @@ -26,6 +30,7 @@ "WhitespaceMinimizedString": { "name": "WhitespaceMinimizedString", "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/CanCOGeN_Covid-19", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -33,6 +38,7 @@ "Provenance": { "name": "Provenance", "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/CanCOGeN_Covid-19", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -40,18 +46,39 @@ "string": { "name": "string", "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "xsd:string" }, "integer": { "name": "integer", "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "xsd:integer" }, "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "xsd:boolean", "repr": "bool" @@ -59,18 +86,39 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:float" }, "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:double" }, "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "xsd:decimal" }, @@ -78,17 +126,27 @@ "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Time" ], "base": "XSDTime", - "uri": "xsd:dateTime", + "uri": "xsd:time", "repr": "str" }, "date": { "name": "date", "description": "a date (year, month and day) in an idealized calendar", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:Date" ], "base": "XSDDate", "uri": "xsd:date", @@ -97,6 +155,13 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "xsd:dateTime", "repr": "str" @@ -104,6 +169,10 @@ "date_or_datetime": { "name": "date_or_datetime", "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", "base": "str", "uri": "linkml:DateOrDatetime", "repr": "str" @@ -111,13 +180,44 @@ "uriorcurie": { "name": "uriorcurie", "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", "base": "URIorCURIE", "uri": "xsd:anyURI", "repr": "str" }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, "uri": { "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "xsd:anyURI", "repr": "str" @@ -125,6 +225,10 @@ "ncname": { "name": "ncname", "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", "base": "NCName", "uri": "xsd:string", "repr": "str" @@ -132,7 +236,13 @@ "objectidentifier": { "name": "objectidentifier", "description": "A URI or CURIE that represents an object in the model.", - "comments": ["Used for inheritence and type checking"], + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", "base": "ElementIdentifier", "uri": "shex:iri", "repr": "str" @@ -140,14 +250,55 @@ "nodeidentifier": { "name": "nodeidentifier", "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", "base": "NodeIdentifier", "uri": "shex:nonLiteral", "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/CanCOGeN_Covid-19", + "base": "str", + "uri": "xsd:string", + "repr": "str" } }, "enums": { - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "null value menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Not Applicable [GENEPIO:0001619]": { @@ -172,8 +323,9 @@ } } }, - "host age unit menu": { - "name": "host age unit menu", + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host age unit menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "month [UO:0000035]": { @@ -186,8 +338,9 @@ } } }, - "biomaterial extracted menu": { - "name": "biomaterial extracted menu", + "BiomaterialExtractedMenu": { + "name": "BiomaterialExtractedMenu", + "title": "biomaterial extracted menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "RNA (Total) [OBI:0000895]": { @@ -212,8 +365,9 @@ } } }, - "signs and symptoms menu": { - "name": "signs and symptoms menu", + "SignsAndSymptomsMenu": { + "name": "SignsAndSymptomsMenu", + "title": "signs and symptoms menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Abnormal lung auscultation [HP:0030829]": { @@ -597,55 +751,58 @@ } } }, - "host vaccination status menu": { - "name": "host vaccination status menu", + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "host vaccination status menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Fully Vaccinated [GENEPIO:0100100]": { "text": "Fully Vaccinated [GENEPIO:0100100]", "meaning": "GENEPIO:0100100", "exact_mappings": [ - "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination:Yes" + "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination%3AYes" ] }, "Partially Vaccinated [GENEPIO:0100101]": { "text": "Partially Vaccinated [GENEPIO:0100101]", "meaning": "GENEPIO:0100101", "exact_mappings": [ - "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination:Yes" + "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination%3AYes" ] }, "Not Vaccinated [GENEPIO:0100102]": { "text": "Not Vaccinated [GENEPIO:0100102]", "meaning": "GENEPIO:0100102", "exact_mappings": [ - "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination:No" + "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination%3ANo" ] } } }, - "prior SARS-CoV-2 antiviral treatment menu": { - "name": "prior SARS-CoV-2 antiviral treatment menu", + "PriorSarsCov2AntiviralTreatmentMenu": { + "name": "PriorSarsCov2AntiviralTreatmentMenu", + "title": "prior SARS-CoV-2 antiviral treatment menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Prior antiviral treatment [GENEPIO:0100037]": { "text": "Prior antiviral treatment [GENEPIO:0100037]", "meaning": "GENEPIO:0100237", "exact_mappings": [ - "NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment:Yes" + "NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment%3AYes" ] }, "No prior antiviral treatment [GENEPIO:0100233]": { "text": "No prior antiviral treatment [GENEPIO:0100233]", "meaning": "GENEPIO:0100233", "exact_mappings": [ - "NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment:No" + "NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment%3ANo" ] } } }, - "pre-existing conditions and risk factors menu": { - "name": "pre-existing conditions and risk factors menu", + "PreExistingConditionsAndRiskFactorsMenu": { + "name": "PreExistingConditionsAndRiskFactorsMenu", + "title": "pre-existing conditions and risk factors menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Age 60+ [VO:0004925]": { @@ -762,11 +919,6 @@ "text": "Chronic gastrointestinal disease [GENEPIO:0100076]", "meaning": "GENEPIO:0100076" }, - "Chronic lung disease [HP:0006528]": { - "text": "Chronic lung disease [HP:0006528]", - "meaning": "HP:0006528", - "is_a": "Lung disease [MONDO:0005275]" - }, "Corticosteroids [NCIT:C211]": { "text": "Corticosteroids [NCIT:C211]", "meaning": "NCIT:C211" @@ -939,15 +1091,10 @@ "meaning": "HP:0004469", "is_a": "Respiratory disorder [MONDO:0005087]" }, - "Chronic pulmonary disease [HP:0006528]": { - "text": "Chronic pulmonary disease [HP:0006528]", - "meaning": "HP:0006528", - "is_a": "Respiratory disorder [MONDO:0005087]" - }, "Chronic obstructive pulmonary disease [HP:0006510]": { "text": "Chronic obstructive pulmonary disease [HP:0006510]", "meaning": "HP:0006510", - "is_a": "Chronic pulmonary disease [HP:0006528]" + "is_a": "Respiratory disorder [MONDO:0005087]" }, "Emphysema [HP:0002097]": { "text": "Emphysema [HP:0002097]", @@ -959,6 +1106,11 @@ "meaning": "MONDO:0005275", "is_a": "Respiratory disorder [MONDO:0005087]" }, + "Chronic lung disease [HP:0006528]": { + "text": "Chronic lung disease [HP:0006528]", + "meaning": "HP:0006528", + "is_a": "Lung disease [MONDO:0005275]" + }, "Pulmonary fibrosis [HP:0002206]": { "text": "Pulmonary fibrosis [HP:0002206]", "meaning": "HP:0002206", @@ -1064,8 +1216,9 @@ } } }, - "variant designation menu": { - "name": "variant designation menu", + "VariantDesignationMenu": { + "name": "VariantDesignationMenu", + "title": "variant designation menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Variant of Interest (VOI) [GENEPIO:0100082]": { @@ -1082,8 +1235,9 @@ } } }, - "complications menu": { - "name": "complications menu", + "ComplicationsMenu": { + "name": "ComplicationsMenu", + "title": "complications menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Abnormal blood oxygen level [HP:0500165]": { @@ -1436,8 +1590,9 @@ } } }, - "sample collected in quarantine menu": { - "name": "sample collected in quarantine menu", + "SampleCollectedInQuarantineMenu": { + "name": "SampleCollectedInQuarantineMenu", + "title": "sample collected in quarantine menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Yes [NCIT:C49488]": { @@ -1450,8 +1605,9 @@ } } }, - "anatomical material menu": { - "name": "anatomical material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical material menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Blood [UBERON:0000178]": { @@ -1498,8 +1654,9 @@ } } }, - "anatomical part menu": { - "name": "anatomical part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical part menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Anus [UBERON:0001245]": { @@ -1619,8 +1776,9 @@ } } }, - "body product menu": { - "name": "body product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body product menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Breast Milk [UBERON:0001913]": { @@ -1658,8 +1816,9 @@ } } }, - "environmental material menu": { - "name": "environmental material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "environmental material menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air vent [ENVO:03501208]": { @@ -1797,8 +1956,9 @@ } } }, - "environmental site menu": { - "name": "environmental site menu", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental site menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Acute care facility [ENVO:03501135]": { @@ -1891,8 +2051,9 @@ } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Amniocentesis [NCIT:C52009]": { @@ -1989,8 +2150,9 @@ } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Air filter [ENVO:00003968]": { @@ -2063,8 +2225,9 @@ } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Homo sapiens [NCBITaxon:9606]": { @@ -2133,8 +2296,9 @@ } } }, - "host (common name) menu": { - "name": "host (common name) menu", + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Human [NCBITaxon:9606]": { @@ -2191,8 +2355,9 @@ } } }, - "host health state menu": { - "name": "host health state menu", + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "host health state menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Asymptomatic [NCIT:C3833]": { @@ -2217,8 +2382,9 @@ } } }, - "host health status details menu": { - "name": "host health status details menu", + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "host health status details menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Hospitalized [NCIT:C25179]": { @@ -2254,8 +2420,9 @@ } } }, - "host health outcome menu": { - "name": "host health outcome menu", + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "host health outcome menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Deceased [NCIT:C28554]": { @@ -2276,8 +2443,9 @@ } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]": { @@ -2294,8 +2462,9 @@ } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Cluster/Outbreak investigation [GENEPIO:0100001]": { @@ -2321,8 +2490,9 @@ } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose of sequencing menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Baseline surveillance (random sampling) [GENEPIO:0100005]": { @@ -2447,8 +2617,9 @@ } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Virus passage [GENEPIO:0100039]": { @@ -2469,8 +2640,9 @@ } } }, - "lab host menu": { - "name": "lab host menu", + "LabHostMenu": { + "name": "LabHostMenu", + "title": "lab host menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "293/ACE2 cell line [GENEPIO:0100041]": { @@ -2541,8 +2713,9 @@ } } }, - "host disease menu": { - "name": "host disease menu", + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host disease menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "COVID-19 [MONDO:0100096]": { @@ -2551,8 +2724,9 @@ } } }, - "host age bin menu": { - "name": "host age bin menu", + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host age bin menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "0 - 9 [GENEPIO:0100049]": { @@ -2601,8 +2775,9 @@ } } }, - "host gender menu": { - "name": "host gender menu", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host gender menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Female [NCIT:C46110]": { @@ -2631,8 +2806,9 @@ } } }, - "exposure event menu": { - "name": "exposure event menu", + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "exposure event menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Mass Gathering [GENEPIO:0100237]": { @@ -2712,8 +2888,9 @@ } } }, - "exposure contact level menu": { - "name": "exposure contact level menu", + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "exposure contact level menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Contact with infected individual": { @@ -2742,8 +2919,9 @@ } } }, - "host role menu": { - "name": "host role menu", + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "host role menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Attendee [GENEPIO:0100249]": { @@ -2918,8 +3096,9 @@ } } }, - "exposure setting menu": { - "name": "exposure setting menu", + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "exposure setting menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Human Exposure [ECTO:3000005]": { @@ -3243,8 +3422,9 @@ } } }, - "prior SARS-CoV-2 infection menu": { - "name": "prior SARS-CoV-2 infection menu", + "PriorSarsCov2InfectionMenu": { + "name": "PriorSarsCov2InfectionMenu", + "title": "prior SARS-CoV-2 infection menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Prior infection [GENEPIO:0100234]": { @@ -3257,22 +3437,25 @@ } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Illumina sequencing instrument [GENEPIO:0100105]": { "text": "Illumina sequencing instrument [GENEPIO:0100105]", "meaning": "GENEPIO:0100105", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina Genome Analyzer [GENEPIO:0100106]": { "text": "Illumina Genome Analyzer [GENEPIO:0100106]", "meaning": "GENEPIO:0100106", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina Genome Analyzer" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20Genome%20Analyzer" ] }, "Illumina Genome Analyzer II [GENEPIO:0100107]": { @@ -3280,8 +3463,8 @@ "meaning": "GENEPIO:0100107", "is_a": "Illumina Genome Analyzer [GENEPIO:0100106]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina Genome Analyzer II" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20Genome%20Analyzer%20II" ] }, "Illumina Genome Analyzer IIx [GENEPIO:0100108]": { @@ -3289,8 +3472,8 @@ "meaning": "GENEPIO:0100108", "is_a": "Illumina Genome Analyzer [GENEPIO:0100106]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina Genome Analyzer IIx" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20Genome%20Analyzer%20IIx" ] }, "Illumina HiScanSQ [GENEPIO:0100109]": { @@ -3298,29 +3481,33 @@ "meaning": "GENEPIO:0100109", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina HiScanSQ" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20HiScanSQ" ] }, "Illumina HiSeq [GENEPIO:0100110]": { "text": "Illumina HiSeq [GENEPIO:0100110]", "meaning": "GENEPIO:0100110", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina HiSeq X [GENEPIO:0100111]": { "text": "Illumina HiSeq X [GENEPIO:0100111]", "meaning": "GENEPIO:0100111", "is_a": "Illumina HiSeq [GENEPIO:0100110]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina HiSeq X Five [GENEPIO:0100112]": { "text": "Illumina HiSeq X Five [GENEPIO:0100112]", "meaning": "GENEPIO:0100112", "is_a": "Illumina HiSeq X [GENEPIO:0100111]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model: Illumina HiSeq X Five" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3A%20Illumina%20HiSeq%20X%20Five" ] }, "Illumina HiSeq X Ten [GENEPIO:0100113]": { @@ -3328,8 +3515,8 @@ "meaning": "GENEPIO:0100113", "is_a": "Illumina HiSeq X [GENEPIO:0100111]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina HiSeq X Ten" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20HiSeq%20X%20Ten" ] }, "Illumina HiSeq 1000 [GENEPIO:0100114]": { @@ -3337,23 +3524,25 @@ "meaning": "GENEPIO:0100114", "is_a": "Illumina HiSeq [GENEPIO:0100110]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina HiSeq 1000" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20HiSeq%201000" ] }, "Illumina HiSeq 1500 [GENEPIO:0100115]": { "text": "Illumina HiSeq 1500 [GENEPIO:0100115]", "meaning": "GENEPIO:0100115", "is_a": "Illumina HiSeq [GENEPIO:0100110]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina HiSeq 2000 [GENEPIO:0100116]": { "text": "Illumina HiSeq 2000 [GENEPIO:0100116]", "meaning": "GENEPIO:0100116", "is_a": "Illumina HiSeq [GENEPIO:0100110]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina HiSeq 2000" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20HiSeq%202000" ] }, "Illumina HiSeq 2500 [GENEPIO:0100117]": { @@ -3361,81 +3550,99 @@ "meaning": "GENEPIO:0100117", "is_a": "Illumina HiSeq [GENEPIO:0100110]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina HiSeq 2500" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20HiSeq%202500" ] }, "Illumina HiSeq 3000 [GENEPIO:0100118]": { "text": "Illumina HiSeq 3000 [GENEPIO:0100118]", "meaning": "GENEPIO:0100118", "is_a": "Illumina HiSeq [GENEPIO:0100110]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina HiSeq 4000 [GENEPIO:0100119]": { "text": "Illumina HiSeq 4000 [GENEPIO:0100119]", "meaning": "GENEPIO:0100119", "is_a": "Illumina HiSeq [GENEPIO:0100110]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina iSeq [GENEPIO:0100120]": { "text": "Illumina iSeq [GENEPIO:0100120]", "meaning": "GENEPIO:0100120", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina iSeq 100 [GENEPIO:0100121]": { "text": "Illumina iSeq 100 [GENEPIO:0100121]", "meaning": "GENEPIO:0100121", "is_a": "Illumina iSeq [GENEPIO:0100120]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina NovaSeq [GENEPIO:0100122]": { "text": "Illumina NovaSeq [GENEPIO:0100122]", "meaning": "GENEPIO:0100122", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina NovaSeq 6000 [GENEPIO:0100123]": { "text": "Illumina NovaSeq 6000 [GENEPIO:0100123]", "meaning": "GENEPIO:0100123", "is_a": "Illumina NovaSeq [GENEPIO:0100122]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina MiniSeq [GENEPIO:0100124]": { "text": "Illumina MiniSeq [GENEPIO:0100124]", "meaning": "GENEPIO:0100124", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina MiSeq [GENEPIO:0100125]": { "text": "Illumina MiSeq [GENEPIO:0100125]", "meaning": "GENEPIO:0100125", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina MiSeq" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20MiSeq" ] }, "Illumina NextSeq [GENEPIO:0100126]": { "text": "Illumina NextSeq [GENEPIO:0100126]", "meaning": "GENEPIO:0100126", "is_a": "Illumina sequencing instrument [GENEPIO:0100105]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina NextSeq 500 [GENEPIO:0100127]": { "text": "Illumina NextSeq 500 [GENEPIO:0100127]", "meaning": "GENEPIO:0100127", "is_a": "Illumina NextSeq [GENEPIO:0100126]", "exact_mappings": [ - "NCBI_SRA:platform:ILLUMINA", - "NCBI_SRA:instrument_model:Illumina NextSeq 500" + "NCBI_SRA:platform%3AILLUMINA", + "NCBI_SRA:instrument_model%3AIllumina%20NextSeq%20500" ] }, "Illumina NextSeq 550 [GENEPIO:0100128]": { "text": "Illumina NextSeq 550 [GENEPIO:0100128]", "meaning": "GENEPIO:0100128", "is_a": "Illumina NextSeq [GENEPIO:0100126]", - "exact_mappings": ["NCBI_SRA:platform:ILLUMINA"] + "exact_mappings": [ + "NCBI_SRA:platform%3AILLUMINA" + ] }, "Illumina NextSeq 2000 [GENEPIO:0100129]": { "text": "Illumina NextSeq 2000 [GENEPIO:0100129]", @@ -3445,15 +3652,17 @@ "Pacific Biosciences sequencing instrument [GENEPIO:0100130]": { "text": "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", "meaning": "GENEPIO:0100130", - "exact_mappings": ["NCBI_SRA:platform:PACBIO_SMRT"] + "exact_mappings": [ + "NCBI_SRA:platform%3APACBIO_SMRT" + ] }, "PacBio RS [GENEPIO:0100131]": { "text": "PacBio RS [GENEPIO:0100131]", "meaning": "GENEPIO:0100131", "is_a": "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", "exact_mappings": [ - "NCBI_SRA:platform:PACBIO_SMRT", - "NCBI_SRA:instrument_model:PacBio RS" + "NCBI_SRA:platform%3APACBIO_SMRT", + "NCBI_SRA:instrument_model%3APacBio%20RS" ] }, "PacBio RS II [GENEPIO:0100132]": { @@ -3461,34 +3670,40 @@ "meaning": "GENEPIO:0100132", "is_a": "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", "exact_mappings": [ - "NCBI_SRA:platform:PACBIO_SMRT", - "NCBI_SRA:instrument_model:PacBio RS II" + "NCBI_SRA:platform%3APACBIO_SMRT", + "NCBI_SRA:instrument_model%3APacBio%20RS%20II" ] }, "PacBio Sequel [GENEPIO:0100133]": { "text": "PacBio Sequel [GENEPIO:0100133]", "meaning": "GENEPIO:0100133", "is_a": "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "exact_mappings": ["NCBI_SRA:platform:PACBIO_SMRT"] + "exact_mappings": [ + "NCBI_SRA:platform%3APACBIO_SMRT" + ] }, "PacBio Sequel II [GENEPIO:0100134]": { "text": "PacBio Sequel II [GENEPIO:0100134]", "meaning": "GENEPIO:0100134", "is_a": "Pacific Biosciences sequencing instrument [GENEPIO:0100130]", - "exact_mappings": ["NCBI_SRA:platform:PACBIO_SMRT"] + "exact_mappings": [ + "NCBI_SRA:platform%3APACBIO_SMRT" + ] }, "Ion Torrent sequencing instrument [GENEPIO:0100135]": { "text": "Ion Torrent sequencing instrument [GENEPIO:0100135]", "meaning": "GENEPIO:0100135", - "exact_mappings": ["NCBI_SRA:platform:ION_TORRENT"] + "exact_mappings": [ + "NCBI_SRA:platform%3AION_TORRENT" + ] }, "Ion Torrent PGM [GENEPIO:0100136]": { "text": "Ion Torrent PGM [GENEPIO:0100136]", "meaning": "GENEPIO:0100136", "is_a": "Ion Torrent sequencing instrument [GENEPIO:0100135]", "exact_mappings": [ - "NCBI_SRA:platform:ION_TORRENT", - "NCBI_SRA:instrument_model:Ion Torrent PGM" + "NCBI_SRA:platform%3AION_TORRENT", + "NCBI_SRA:instrument_model%3AIon%20Torrent%20PGM" ] }, "Ion Torrent Proton [GENEPIO:0100137]": { @@ -3496,34 +3711,40 @@ "meaning": "GENEPIO:0100137", "is_a": "Ion Torrent sequencing instrument [GENEPIO:0100135]", "exact_mappings": [ - "NCBI_SRA:platform:ION_TORRENT", - "NCBI_SRA:instrument_model:Ion Torrent Proton" + "NCBI_SRA:platform%3AION_TORRENT", + "NCBI_SRA:instrument_model%3AIon%20Torrent%20Proton" ] }, "Ion Torrent S5 XL [GENEPIO:0100138]": { "text": "Ion Torrent S5 XL [GENEPIO:0100138]", "meaning": "GENEPIO:0100138", "is_a": "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "exact_mappings": ["NCBI_SRA:platform:ION_TORRENT"] + "exact_mappings": [ + "NCBI_SRA:platform%3AION_TORRENT" + ] }, "Ion Torrent S5 [GENEPIO:0100139]": { "text": "Ion Torrent S5 [GENEPIO:0100139]", "meaning": "GENEPIO:0100139", "is_a": "Ion Torrent sequencing instrument [GENEPIO:0100135]", - "exact_mappings": ["NCBI_SRA:platform:ION_TORRENT"] + "exact_mappings": [ + "NCBI_SRA:platform%3AION_TORRENT" + ] }, "Oxford Nanopore sequencing instrument [GENEPIO:0100140]": { "text": "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", "meaning": "GENEPIO:0100140", - "exact_mappings": ["NCBI_SRA:platform:OXFORD_NANOPORE"] + "exact_mappings": [ + "NCBI_SRA:platform%3AOXFORD_NANOPORE" + ] }, "Oxford Nanopore GridION [GENEPIO:0100141]": { "text": "Oxford Nanopore GridION [GENEPIO:0100141]", "meaning": "GENEPIO:0100141", "is_a": "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", "exact_mappings": [ - "NCBI_SRA:platform:OXFORD_NANOPORE", - "NCBI_SRA:instrument_model:GridION" + "NCBI_SRA:platform%3AOXFORD_NANOPORE", + "NCBI_SRA:instrument_model%3AGridION" ] }, "Oxford Nanopore MinION [GENEPIO:0100142]": { @@ -3531,15 +3752,17 @@ "meaning": "GENEPIO:0100142", "is_a": "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", "exact_mappings": [ - "NCBI_SRA:platform:OXFORD_NANOPORE", - "NCBI_SRA:instrument_model:MinION" + "NCBI_SRA:platform%3AOXFORD_NANOPORE", + "NCBI_SRA:instrument_model%3AMinION" ] }, "Oxford Nanopore PromethION [GENEPIO:0100143]": { "text": "Oxford Nanopore PromethION [GENEPIO:0100143]", "meaning": "GENEPIO:0100143", "is_a": "Oxford Nanopore sequencing instrument [GENEPIO:0100140]", - "exact_mappings": ["NCBI_SRA:platform:OXFORD_NANOPORE"] + "exact_mappings": [ + "NCBI_SRA:platform%3AOXFORD_NANOPORE" + ] }, "BGI Genomics sequencing instrument [GENEPIO:0100144]": { "text": "BGI Genomics sequencing instrument [GENEPIO:0100144]", @@ -3576,8 +3799,9 @@ } } }, - "gene name menu": { - "name": "gene name menu", + "GeneNameMenu": { + "name": "GeneNameMenu", + "title": "gene name menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "E gene (orf4) [GENEPIO:0100151]": { @@ -3731,8 +3955,9 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "Afghanistan [GAZ:00006882]": { @@ -4821,8 +5046,9 @@ } } }, - "library_strategy menu": { - "name": "library_strategy menu", + "LibraryStrategyMenu": { + "name": "LibraryStrategyMenu", + "title": "library_strategy menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "WGA": { @@ -4896,8 +5122,9 @@ } } }, - "library_source menu": { - "name": "library_source menu", + "LibrarySourceMenu": { + "name": "LibrarySourceMenu", + "title": "library_source menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "GENOMIC": { @@ -4923,8 +5150,9 @@ } } }, - "library_selection menu": { - "name": "library_selection menu", + "LibrarySelectionMenu": { + "name": "LibrarySelectionMenu", + "title": "library_selection menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "RANDOM": { @@ -5010,8 +5238,9 @@ } } }, - "library_layout menu": { - "name": "library_layout menu", + "LibraryLayoutMenu": { + "name": "LibraryLayoutMenu", + "title": "library_layout menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "single": { @@ -5022,8 +5251,9 @@ } } }, - "filetype menu": { - "name": "filetype menu", + "FiletypeMenu": { + "name": "FiletypeMenu", + "title": "filetype menu", "from_schema": "https://example.com/CanCOGeN_Covid-19", "permissible_values": { "bam": { @@ -5066,8 +5296,8 @@ } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -5080,19 +5310,22 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Sample ID given by the sample provider", - "GISAID:Sample ID given by the submitting laboratory", + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory", "NCBI_BIOSAMPLE:sample_name", "NCBI_SRA:sample_name", "NCBI_Genbank:sample_name", "NCBI_Genbank_source_modifiers:Sequence_ID" ], "slot_uri": "GENEPIO:0001123", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "required": true }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", "title": "umbrella bioproject accession", "comments": [ @@ -5105,6 +5338,9 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001133", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5112,8 +5348,8 @@ "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", "comments": [ @@ -5131,6 +5367,9 @@ "NCBI_Genbank_source_modifiers:BioProject" ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5138,8 +5377,8 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", "comments": [ @@ -5157,6 +5396,9 @@ "NCBI_Genbank_source_modifiers:BioSample" ], "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "recommended": true, "structured_pattern": { @@ -5165,8 +5407,8 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", "comments": [ @@ -5179,6 +5421,9 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001142", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5186,8 +5431,8 @@ "partial_match": false } }, - "GenBank/ENA/DDBJ accession": { - "name": "GenBank/ENA/DDBJ accession", + "genbank_ena_ddbj_accession": { + "name": "genbank_ena_ddbj_accession", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", "title": "GenBank/ENA/DDBJ accession", "comments": [ @@ -5200,6 +5445,9 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001145", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5207,19 +5455,26 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", - "comments": ["Store the accession returned from the GISAID submission."], + "comments": [ + "Store the accession returned from the GISAID submission." + ], "examples": [ { "value": "EPI_ISL_123456" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:gisaid_accession"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:gisaid_accession" + ], "slot_uri": "GENEPIO:0001147", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5227,8 +5482,8 @@ "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "description": "The user-defined GISAID virus name assigned to the sequence.", "title": "GISAID virus name", "comments": [ @@ -5241,10 +5496,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Virus name", + "GISAID:Virus%20name", "NCBI_BIOSAMPLE:gisaid_virus_name" ], "slot_uri": "GENEPIO:0100282", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5252,8 +5510,8 @@ "partial_match": false } }, - "host specimen voucher": { - "name": "host specimen voucher", + "host_specimen_voucher": { + "name": "host_specimen_voucher", "description": "Identifier for the physical specimen.", "title": "host specimen voucher", "comments": [ @@ -5265,8 +5523,13 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_specimen_voucher"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_specimen_voucher" + ], "slot_uri": "GENEPIO:0100283", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -5274,8 +5537,8 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the organization with which the sample collector is affiliated.", "title": "sample collected by", "comments": [ @@ -5288,22 +5551,25 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Originating lab", + "GISAID:Originating%20lab", "NCBI_BIOSAMPLE:collected_by" ], "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "comments": [ @@ -5316,10 +5582,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "comments": [ @@ -5331,12 +5600,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Address"], + "exact_mappings": [ + "GISAID:Address" + ], "slot_uri": "GENEPIO:0001158", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", "comments": [ @@ -5349,22 +5623,25 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Submitting lab", + "GISAID:Submitting%20lab", "NCBI_BIOSAMPLE:sequenced_by" ], "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", "comments": [ @@ -5376,12 +5653,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:sequence_submitter_contact_email"], + "exact_mappings": [ + "NCBI_SRA:sequence_submitter_contact_email" + ], "slot_uri": "GENEPIO:0001165", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "description": "The mailing address of the agency submitting the sequence.", "title": "sequence submitter contact address", "comments": [ @@ -5393,12 +5675,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Address"], + "exact_mappings": [ + "GISAID:Address" + ], "slot_uri": "GENEPIO:0001167", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", "comments": [ @@ -5411,23 +5698,26 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Collection date", + "GISAID:Collection%20date", "NCBI_BIOSAMPLE:collection_date", "NCBI_Genbank_source_modifiers:collection-date" ], "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", "comments": [ @@ -5440,17 +5730,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc name (country)": { - "name": "geo_loc name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo_loc name (country)", "comments": [ @@ -5468,18 +5761,21 @@ "NCBI_Genbank_source_modifiers:country" ], "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { - "range": "geo_loc name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc name (state/province/territory)": { - "name": "geo_loc name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The state/province/territory of origin of the sample.", "title": "geo_loc name (state/province/territory)", "comments": [ @@ -5491,20 +5787,25 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:geo_loc_name"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_name" + ], "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc name (county/region)": { - "name": "geo_loc name (county/region)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "description": "The county/region of origin of the sample.", "title": "geo_loc name (county/region)", "comments": [ @@ -5516,12 +5817,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:geo_loc_name"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_name" + ], "slot_uri": "GENEPIO:0100280", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc name (city)": { - "name": "geo_loc name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city of origin of the sample.", "title": "geo_loc name (city)", "comments": [ @@ -5533,12 +5839,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:geo_loc_name"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_name" + ], "slot_uri": "GENEPIO:0001189", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", "comments": [ @@ -5550,12 +5861,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:lat_lon"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:lat_lon" + ], "slot_uri": "GENEPIO:0100309", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", "comments": [ @@ -5567,8 +5883,13 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:lat_lon"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:lat_lon" + ], "slot_uri": "GENEPIO:0100310", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, "organism": { @@ -5584,15 +5905,20 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:organism"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:organism" + ], "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -5614,18 +5940,21 @@ "NCBI_Genbank_source_modifiers:isolate" ], "slot_uri": "GENEPIO:0001644", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "culture collection": { - "name": "culture collection", + "culture_collection": { + "name": "culture_collection", "description": "The name of the source collection and unique culture identifier.", "title": "culture collection", "comments": [ @@ -5638,33 +5967,43 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100284", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", - "comments": ["Select a value from the pick list in the template."], + "comments": [ + "Select a value from the pick list in the template." + ], "examples": [ { "value": "Diagnostic testing [GENEPIO:0100002]" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:purpose_of_sampling"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:purpose_of_sampling" + ], "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "PHA4GE" + ], "recommended": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "Further details pertaining to the reason the sample was collected.", "title": "purpose of sampling details", "comments": [ @@ -5677,10 +6016,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001200", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sample plan name": { - "name": "sample plan name", + "sample_plan_name": { + "name": "sample_plan_name", "description": "The name of the sample plan implemented for sample collection.", "title": "sample plan name", "comments": [ @@ -5693,10 +6035,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100285", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sample collected in quarantine": { - "name": "sample collected in quarantine", + "sample_collected_in_quarantine": { + "name": "sample_collected_in_quarantine", "description": "Whether the sample was collected from an individual in quarantine.", "title": "sample collected in quarantine", "comments": [ @@ -5709,17 +6054,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100277", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "sample collected in quarantine menu" + "range": "SampleCollectedInQuarantineMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", "comments": [ @@ -5732,24 +6080,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:host_anatomical_material", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001211", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "anatomical material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", "comments": [ @@ -5762,24 +6113,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:host_anatomical_part", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001214", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "anatomical part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", "comments": [ @@ -5792,24 +6146,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:host_body_product", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001216", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "body product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", "title": "environmental material", "comments": [ @@ -5822,24 +6179,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:environmental_material", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001223", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "environmental material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", "title": "environmental site", "comments": [ @@ -5852,24 +6212,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:environmental_site", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001232", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "environmental site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", "comments": [ @@ -5882,24 +6245,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:collection_device", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001234", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", "title": "collection method", "comments": [ @@ -5912,24 +6278,27 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Specimen source", + "GISAID:Specimen%20source", "NCBI_BIOSAMPLE:isolation_source", "NCBI_BIOSAMPLE:collection_method", "NCBI_Genbank_source_modifiers:isolation-source" ], "slot_uri": "GENEPIO:0001241", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "collection method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", "comments": [ @@ -5942,10 +6311,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001243", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -5958,19 +6330,22 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001253", - "multivalued": true, + "domain_of": [ + "PHA4GE" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "specimen processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -5983,10 +6358,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", "title": "lab host", "comments": [ @@ -5999,17 +6377,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001255", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "lab host menu" + "range": "LabHostMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "description": "Number of passages.", "title": "passage number", "comments": [ @@ -6021,13 +6402,18 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:passage_number"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:passage_number" + ], "slot_uri": "GENEPIO:0001261", + "domain_of": [ + "PHA4GE" + ], "range": "integer", "minimum_value": 0 }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "description": "Description of how organism was passaged.", "title": "passage method", "comments": [ @@ -6039,19 +6425,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:passage_method"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:passage_method" + ], "slot_uri": "GENEPIO:0001264", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "title": "biomaterial extracted", "comments": [ @@ -6064,17 +6455,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001266", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "biomaterial extracted menu" + "range": "BiomaterialExtractedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "data abstraction details": { - "name": "data abstraction details", + "data_abstraction_details": { + "name": "data_abstraction_details", "description": "A description of how any data elements were altered to preserve patient privacy.", "title": "data abstraction details", "comments": [ @@ -6087,10 +6481,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100278", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", "comments": [ @@ -6103,17 +6500,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", "comments": [ @@ -6131,21 +6531,26 @@ "NCBI_Genbank_source_modifiers:host" ], "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "description": "Health status of the host at the time of sample collection.", "title": "host health state", - "comments": ["If known, select a value from the pick list."], + "comments": [ + "If known, select a value from the pick list." + ], "examples": [ { "value": "Asymptomatic [NCIT:C3833]" @@ -6153,24 +6558,29 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Patient status", + "GISAID:Patient%20status", "NCBI_BIOSAMPLE:host_health_state" ], "slot_uri": "GENEPIO:0001388", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "host health state menu" + "range": "HostHealthStateMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "description": "Further details pertaining to the health or disease status of the host at time of collection.", "title": "host health status details", - "comments": ["If known, select a value from the pick list."], + "comments": [ + "If known, select a value from the pick list." + ], "examples": [ { "value": "Hospitalized (ICU) [GENEPIO:0100046]" @@ -6178,17 +6588,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "host health status details menu" + "range": "HostHealthStatusDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", "comments": [ @@ -6200,53 +6613,73 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_disease"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_disease" + ], "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { - "range": "host disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", - "comments": ["If known, select a value from the pick list."], + "comments": [ + "If known, select a value from the pick list." + ], "examples": [ { "value": "Recovered [NCIT:C49498]" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_disease_outcome"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_disease_outcome" + ], "slot_uri": "GENEPIO:0001390", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "host health outcome menu" + "range": "HostHealthOutcomeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", - "comments": ["If known, provide age. Age-binning is also acceptable."], + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], "examples": [ { "value": "79" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Patient age", "NCBI_BIOSAMPLE:host_age"], + "exact_mappings": [ + "GISAID:Patient%20age", + "NCBI_BIOSAMPLE:host_age" + ], "slot_uri": "GENEPIO:0001392", + "domain_of": [ + "PHA4GE" + ], "recommended": true, "maximum_value": 130, "any_of": [ @@ -6254,12 +6687,12 @@ "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The units used to measure the host's age.", "title": "host age unit", "comments": [ @@ -6272,18 +6705,21 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "PHA4GE" + ], "recommended": true, "any_of": [ { - "range": "host age unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "The age category of the host at the time of sampling.", "title": "host age bin", "comments": [ @@ -6296,44 +6732,57 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "PHA4GE" + ], "recommended": true, "any_of": [ { - "range": "host age bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", - "comments": ["If known, select a value from the pick list."], + "comments": [ + "If known, select a value from the pick list." + ], "examples": [ { "value": "Male [NCIT:C46109]" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Gender", "NCBI_BIOSAMPLE:host_sex"], - "slot_uri": "GENEPIO:0001395", + "exact_mappings": [ + "GISAID:Gender", + "NCBI_BIOSAMPLE:host_sex" + ], + "slot_uri": "GENEPIO:0001395", + "domain_of": [ + "PHA4GE" + ], "recommended": true, "any_of": [ { - "range": "host gender menu" + "range": "HostGenderMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "description": "The country where the host resides.", "title": "host residence geo_loc name (country)", - "comments": ["If known, select a value from the pick list."], + "comments": [ + "If known, select a value from the pick list." + ], "examples": [ { "value": "South Africa [GAZ:00001094]" @@ -6341,17 +6790,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001396", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "HostResidenceGeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host ethnicity": { - "name": "host ethnicity", + "host_ethnicity": { + "name": "host_ethnicity", "description": "The self-identified ethnicity(ies) of the host.", "title": "host ethnicity", "comments": [ @@ -6364,10 +6816,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100312", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to e.g. #131", "title": "host subject ID", "comments": [ @@ -6379,12 +6834,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_subject_id"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_subject_id" + ], "slot_uri": "GENEPIO:0001398", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", "comments": [ @@ -6397,10 +6857,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", "comments": [ @@ -6413,17 +6876,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001399", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", "title": "signs and symptoms", "comments": [ @@ -6436,18 +6902,21 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001400", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "signs and symptoms menu" + "range": "SignsAndSymptomsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", "title": "pre-existing conditions and risk factors", "comments": [ @@ -6460,13 +6929,16 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001401", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "pre-existing conditions and risk factors menu" + "range": "PreExistingConditionsAndRiskFactorsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -6484,18 +6956,21 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001402", + "domain_of": [ + "PHA4GE" + ], "multivalued": true, "any_of": [ { - "range": "complications menu" + "range": "ComplicationsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", "comments": [ @@ -6507,19 +6982,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination" + ], "slot_uri": "GENEPIO:0001404", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "host vaccination status menu" + "range": "HostVaccinationStatusMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "description": "The number of doses of the vaccine received by the host.", "title": "number of vaccine doses received", "comments": [ @@ -6532,11 +7012,14 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001406", + "domain_of": [ + "PHA4GE" + ], "range": "integer", "minimum_value": 0 }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", "title": "vaccination dose 1 vaccine name", "comments": [ @@ -6549,10 +7032,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100313", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", "comments": [ @@ -6565,10 +7051,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100314", + "domain_of": [ + "PHA4GE" + ], "range": "date" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", "title": "vaccination dose 2 vaccine name", "comments": [ @@ -6581,10 +7070,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100315", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination dose 2 vaccination date", "comments": [ @@ -6597,10 +7089,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100316", + "domain_of": [ + "PHA4GE" + ], "range": "date" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "description": "The name of the vaccine administered as the third dose of a vaccine regimen.", "title": "vaccination dose 3 vaccine name", "comments": [ @@ -6613,10 +7108,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100317", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "description": "The date the third dose of a vaccine was administered.", "title": "vaccination dose 3 vaccination date", "comments": [ @@ -6628,12 +7126,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:date_of_sars_cov_2_vaccination"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:date_of_sars_cov_2_vaccination" + ], "slot_uri": "GENEPIO:0100318", + "domain_of": [ + "PHA4GE" + ], "range": "date" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "description": "The name of the vaccine administered as the fourth dose of a vaccine regimen.", "title": "vaccination dose 4 vaccine name", "comments": [ @@ -6646,10 +7149,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100319", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "description": "The date the fourth dose of a vaccine was administered.", "title": "vaccination dose 4 vaccination date", "comments": [ @@ -6662,10 +7168,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0100320", + "domain_of": [ + "PHA4GE" + ], "range": "date" }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", "comments": [ @@ -6686,12 +7195,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Last vaccinated"], + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], "slot_uri": "GENEPIO:0100321", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "description": "The country where the host was likely exposed to the causative agent of the illness.", "title": "location of exposure geo_loc name (country)", "comments": [ @@ -6703,19 +7217,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:geo_loc_exposure"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_exposure" + ], "slot_uri": "GENEPIO:0001410", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "LocationOfExposureGeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "description": "The name of the city that was the destination of most recent travel.", "title": "destination of most recent travel (city)", "comments": [ @@ -6727,12 +7246,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_recent_travel_loc"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_loc" + ], "slot_uri": "GENEPIO:0001411", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "description": "The name of the province that was the destination of most recent travel.", "title": "destination of most recent travel (state/province/territory)", "comments": [ @@ -6744,12 +7268,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_recent_travel_loc"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_loc" + ], "slot_uri": "GENEPIO:0001412", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "description": "The name of the country that was the destination of most recent travel.", "title": "destination of most recent travel (country)", "comments": [ @@ -6761,19 +7290,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_recent_travel_loc"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_loc" + ], "slot_uri": "GENEPIO:0001413", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "DestinationOfMostRecentTravelCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", "title": "most recent travel departure date", "comments": [ @@ -6786,17 +7320,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001414", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", "title": "most recent travel return date", "comments": [ @@ -6808,19 +7345,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:host_recent_travel_return_date"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_return_date" + ], "slot_uri": "GENEPIO:0001415", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "description": "Travel history in last six months.", "title": "travel history", "comments": [ @@ -6839,13 +7381,18 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001416", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", - "comments": ["If known, select the exposure event from the pick list."], + "comments": [ + "If known, select the exposure event from the pick list." + ], "examples": [ { "value": "Mass Gathering [GENEPIO:0100237]" @@ -6853,24 +7400,29 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Additional location information", + "GISAID:Additional%20location%20information", "NCBI_BIOSAMPLE:exposure_event" ], "slot_uri": "GENEPIO:0001417", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", - "comments": ["Select direct or indirect exposure from the pick list."], + "comments": [ + "Select direct or indirect exposure from the pick list." + ], "examples": [ { "value": "Direct (human-to-human contact) [TRANS:0000001]" @@ -6878,17 +7430,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001418", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", "comments": [ @@ -6900,13 +7455,18 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Additional host information"], + "exact_mappings": [ + "GISAID:Additional%20host%20information" + ], "slot_uri": "GENEPIO:0001419", - "multivalued": true, - "range": "host role menu" + "domain_of": [ + "PHA4GE" + ], + "range": "HostRoleMenu", + "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", "comments": [ @@ -6918,16 +7478,23 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Additional host information"], + "exact_mappings": [ + "GISAID:Additional%20host%20information" + ], "slot_uri": "GENEPIO:0001428", - "multivalued": true, - "range": "exposure setting menu" + "domain_of": [ + "PHA4GE" + ], + "range": "ExposureSettingMenu", + "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", - "comments": ["Free text description of the exposure."], + "comments": [ + "Free text description of the exposure." + ], "examples": [ { "value": "Host role - Other: Bus Driver" @@ -6935,14 +7502,17 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001431", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "description": "Whether there was prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection", "comments": [ - "If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list." + "If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list." ], "examples": [ { @@ -6950,19 +7520,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:prior_sars_cov_2_infection"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:prior_sars_cov_2_infection" + ], "slot_uri": "GENEPIO:0001435", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "prior SARS-CoV-2 infection menu" + "range": "PriorSarsCov2InfectionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "description": "The identifier of the isolate found in the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection isolate", "comments": [ @@ -6974,12 +7549,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:virus_isolate_of_prior_infection"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:virus_isolate_of_prior_infection" + ], "slot_uri": "GENEPIO:0001436", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection date", "comments": [ @@ -6991,12 +7571,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:date_of_prior_sars_cov_2_infection"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:date_of_prior_sars_cov_2_infection" + ], "slot_uri": "GENEPIO:0001437", + "domain_of": [ + "PHA4GE" + ], "range": "date" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", "title": "prior SARS-CoV-2 antiviral treatment", "comments": [ @@ -7008,19 +7593,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treat"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treat" + ], "slot_uri": "GENEPIO:0001438", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "prior SARS-CoV-2 antiviral treatment menu" + "range": "PriorSarsCov2AntiviralTreatmentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment agent", "comments": [ @@ -7032,12 +7622,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:antiviral_treatment_agent"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:antiviral_treatment_agent" + ], "slot_uri": "GENEPIO:0001439", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "description": "The date treatment was first administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment date", "comments": [ @@ -7049,12 +7644,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:date_of_prior_antiviral_treat"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:date_of_prior_antiviral_treat" + ], "slot_uri": "GENEPIO:0001440", + "domain_of": [ + "PHA4GE" + ], "range": "date" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", "comments": [ @@ -7067,23 +7667,26 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Sampling Strategy", + "GISAID:Sampling%20Strategy", "NCBI_BIOSAMPLE:purpose_of_sequencing" ], "slot_uri": "GENEPIO:0001445", - "multivalued": true, + "domain_of": [ + "PHA4GE" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "purpose of sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "comments": [ @@ -7096,18 +7699,21 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "PHA4GE" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", "comments": [ @@ -7120,17 +7726,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", "comments": [ @@ -7142,31 +7751,45 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:library_ID"], + "exact_mappings": [ + "NCBI_SRA:library_ID" + ], "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", - "comments": ["Provide the amplicon size, including the units."], + "comments": [ + "Provide the amplicon size, including the units." + ], "examples": [ { "value": "300bp" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:amplicon_size"], + "exact_mappings": [ + "NCBI_SRA:amplicon_size" + ], "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", - "comments": ["Provide the name of the library preparation kit used."], + "comments": [ + "Provide the name of the library preparation kit used." + ], "examples": [ { "value": "Nextera XT" @@ -7174,10 +7797,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "description": "The barcode of the flow cell used for sequencing.", "title": "flow cell barcode", "comments": [ @@ -7190,13 +7816,18 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001451", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", - "comments": ["Select the sequencing instrument from the pick list."], + "comments": [ + "Select the sequencing instrument from the pick list." + ], "examples": [ { "value": "Oxford Nanopore MinION [GENEPIO:0100142]" @@ -7204,41 +7835,51 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Sequencing technology", + "GISAID:Sequencing%20technology", "NCBI_SRA:platform", "NCBI_SRA:instrument_model", "NCBI_Genbank:sequencing_technology" ], "slot_uri": "GENEPIO:0001452", - "multivalued": true, + "domain_of": [ + "PHA4GE" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "sequencing instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "description": "The name and version number of the sequencing protocol used.", "title": "sequencing protocol name", - "comments": ["Provide the name and version of the sequencing protocol."], + "comments": [ + "Provide the name and version of the sequencing protocol." + ], "examples": [ { "value": "1D_DNA_MinION, ARTIC Network Protocol V3" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:sequencing_protocol_name"], + "exact_mappings": [ + "NCBI_SRA:sequencing_protocol_name" + ], "slot_uri": "GENEPIO:0001453", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -7250,15 +7891,22 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:design_description"], + "exact_mappings": [ + "NCBI_SRA:design_description" + ], "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "description": "The manufacturer's kit number.", "title": "sequencing kit number", - "comments": ["Alphanumeric value."], + "comments": [ + "Alphanumeric value." + ], "examples": [ { "value": "AB456XYZ789" @@ -7266,10 +7914,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001455", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", "comments": [ @@ -7281,344 +7932,264 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:amplicon_pcr_primer_scheme"], + "exact_mappings": [ + "NCBI_SRA:amplicon_pcr_primer_scheme" + ], "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "#REF!", "title": "raw sequence data processing method", - "comments": [ - "Provide the name and version numbers of the software used to process the raw data." - ], - "examples": [ - { - "value": "Porechop 0.2.3" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:raw_sequence_data_processing_method"], + "exact_mappings": [ + "NCBI_SRA:raw_sequence_data_processing_method" + ], "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "dehosting method": { - "name": "dehosting method", - "description": "The method used to remove host reads from the pathogen sequence.", + "dehosting_method": { + "name": "dehosting_method", "title": "dehosting method", - "comments": [ - "Provide the name and version number of the software used to remove host reads." - ], - "examples": [ - { - "value": "Nanostripper 1.2.3" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:dehosting_method"], + "exact_mappings": [ + "NCBI_SRA:dehosting_method" + ], "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "The name of the consensus sequence.", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "title": "consensus sequence name", - "comments": [ - "Provide the name and version number of the consensus sequence." - ], - "examples": [ - { - "value": "ncov123assembly3" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001460", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "The name of the consensus sequence file.", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "title": "consensus sequence filename", - "comments": [ - "Provide the name and version number of the consensus sequence FASTA file." - ], - "examples": [ - { - "value": "ncov123assembly.fasta" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_Genbank:filename"], + "exact_mappings": [ + "NCBI_Genbank:filename" + ], "slot_uri": "GENEPIO:0001461", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "The filepath of the consesnsus sequence file.", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "description": "The filepath of the consensus sequence file.", "title": "consensus sequence filepath", - "comments": [ - "Provide the filepath of the consensus sequence FASTA file." - ], - "examples": [ - { - "value": "/User/Documents/RespLab/Data/ncov123assembly.fasta" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001462", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "The name of software used to generate the consensus sequence.", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "title": "consensus sequence software name", - "comments": [ - "Provide the name of the software used to generate the consensus sequence." - ], - "examples": [ - { - "value": "Ivar" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Assembly method", + "GISAID:Assembly%20method", "NCBI_Genbank:assembly_method" ], "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "The version of the software used to generate the consensus sequence.", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "title": "consensus sequence software version", - "comments": [ - "Provide the version of the software used to generate the consensus sequence." - ], - "examples": [ - { - "value": "1.3" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "exact_mappings": [ - "GISAID:Assembly method", + "GISAID:Assembly%20method", "NCBI_Genbank:assembly_method_version" ], "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "PHA4GE" + ], "range": "decimal", "required": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "title": "breadth of coverage value", - "comments": ["Provide value as a percent."], - "examples": [ - { - "value": "95%" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "title": "depth of coverage value", - "comments": ["Provide value as a fold of coverage."], - "examples": [ - { - "value": "400x" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Coverage", "NCBI_Genbank:genome_coverage"], + "exact_mappings": [ + "GISAID:Depth%20of%20coverage", + "NCBI_Genbank:genome_coverage" + ], "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "title": "depth of coverage threshold", - "comments": ["Provide the threshold fold coverage."], - "examples": [ - { - "value": "100x" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "The user-specified filename of the r1 FASTQ file.", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "title": "r1 fastq filename", - "comments": ["Provide the r1 FASTQ filename."], - "examples": [ - { - "value": "ABC123_S1_L001_R1_001.fastq.gz" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001476", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "The user-specified filename of the r2 FASTQ file.", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "title": "r2 fastq filename", - "comments": ["Provide the r2 FASTQ filename."], - "examples": [ - { - "value": "ABC123_S1_L001_R2_001.fastq.gz" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001477", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "The filepath of the r1 FASTQ file.", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "title": "r1 fastq filepath", - "comments": ["Provide the filepath of the r1 FASTQ file."], - "examples": [ - { - "value": "/User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001478", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "The filepath of the r2 FASTQ file.", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "title": "r2 fastq filepath", - "comments": ["Provide the filepath of the r2 FASTQ file."], - "examples": [ - { - "value": "/User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001479", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "fast5 filename": { - "name": "fast5 filename", - "description": "The user-specified filename of the FAST5 file.", + "fast5_filename": { + "name": "fast5_filename", "title": "fast5 filename", - "comments": ["Provide the FAST5 filename."], - "examples": [ - { - "value": "batch1a_sequences.fast5" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001480", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "The filepath of the FAST5 file.", + "fast5_filepath": { + "name": "fast5_filepath", "title": "fast5 filepath", - "comments": ["Provide the filepath of the FAST5 file."], - "examples": [ - { - "value": "/User/Documents/RespLab/Data/batch1a_sequences.fast5" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001481", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "The number of total base pairs generated by the sequencing process.", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "title": "number of base pairs sequenced", - "comments": ["Provide a numerical value (no need to include units)."], - "examples": [ - { - "value": "387566" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "PHA4GE" + ], "range": "integer", "minimum_value": 0 }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Size of the assembled genome described as the number of base pairs.", + "consensus_genome_length": { + "name": "consensus_genome_length", "title": "consensus genome length", - "comments": ["Provide a numerical value (no need to include units)."], - "examples": [ - { - "value": "38677" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "PHA4GE" + ], "range": "integer", "minimum_value": 0 }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", - "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "title": "Ns per 100 kbp", - "comments": ["Provide a numerical value (no need to include units)."], - "examples": [ - { - "value": "300" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001484", + "domain_of": [ + "PHA4GE" + ], "range": "decimal" }, - "reference genome accession": { - "name": "reference genome accession", - "description": "A persistent, unique identifier of a genome database entry.", + "reference_genome_accession": { + "name": "reference_genome_accession", "title": "reference genome accession", - "comments": ["Provide the accession number of the reference genome."], - "examples": [ - { - "value": "NC_045512.2" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_Genbank:reference_genome"], + "exact_mappings": [ + "NCBI_Genbank:reference_genome" + ], "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "The name and version number of the bioinformatics protocol used.", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "title": "bioinformatics protocol", - "comments": [ - "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol, or a link if deposited in a protocol repository." - ], - "examples": [ - { - "value": "https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members" - } - ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "description": "The name of the lineage or clade.", "title": "lineage/clade name", - "comments": ["Provide the Pangolin or Nextstrain lineage/clade name."], + "comments": [ + "Provide the Pangolin or Nextstrain lineage/clade name." + ], "examples": [ { "value": "B.1.1.7" @@ -7626,10 +8197,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001500", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "description": "The name of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software name", "comments": [ @@ -7642,10 +8216,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001501", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "description": "The version of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software version", "comments": [ @@ -7658,10 +8235,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001502", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", "title": "variant designation", "comments": [ @@ -7674,17 +8254,20 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001503", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "variant designation menu" + "range": "VariantDesignationMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "description": "The evidence used to make the variant determination.", "title": "variant evidence details", "comments": [ @@ -7696,11 +8279,14 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "slot_uri": "GENEPIO:0001504", + "slot_uri": "GENEPIO:0001505", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 1", "comments": [ @@ -7712,19 +8298,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_1"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_1" + ], "slot_uri": "GENEPIO:0001507", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 1", "comments": [ @@ -7737,10 +8328,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001508", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "description": "The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", "comments": [ @@ -7752,12 +8346,17 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_1"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_1" + ], "slot_uri": "GENEPIO:0001509", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 2", "comments": [ @@ -7769,19 +8368,24 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_2"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_2" + ], "slot_uri": "GENEPIO:0001510", + "domain_of": [ + "PHA4GE" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 2", "comments": [ @@ -7794,10 +8398,13 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001511", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", "comments": [ @@ -7809,23 +8416,35 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_2"], + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_2" + ], "slot_uri": "GENEPIO:0001512", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, "title": { "name": "title", "description": "Short description that will identify the dataset on public pages.", "title": "title", - "comments": ["Format: {methodology} of {organism}: {sample info}"], + "comments": [ + "Format: {methodology} of {organism}: {sample info}" + ], "examples": [ { "value": "Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:title"], + "exact_mappings": [ + "NCBI_SRA:title" + ], "slot_uri": "GENEPIO:0100323", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, "library_strategy": { @@ -7836,9 +8455,14 @@ "Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select \"AMPLICON\"." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:library_strategy"], + "exact_mappings": [ + "NCBI_SRA:library_strategy" + ], "slot_uri": "GENEPIO:0100324", - "range": "library_strategy menu" + "domain_of": [ + "PHA4GE" + ], + "range": "LibraryStrategyMenu" }, "library_source": { "name": "library_source", @@ -7848,9 +8472,14 @@ "Provide the library source by selecting a value from the pick list. For amplicon sequencing select \"Viral RNA\"." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:library_source"], + "exact_mappings": [ + "NCBI_SRA:library_source" + ], "slot_uri": "GENEPIO:0100325", - "range": "library_source menu" + "domain_of": [ + "PHA4GE" + ], + "range": "LibrarySourceMenu" }, "library_selection": { "name": "library_selection", @@ -7860,9 +8489,14 @@ "Provide the library selection by selecting a value from the pick list. For amplicon sequencing select \"PCR\"." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:library_selection"], + "exact_mappings": [ + "NCBI_SRA:library_selection" + ], "slot_uri": "GENEPIO:0100326", - "range": "library_selection menu" + "domain_of": [ + "PHA4GE" + ], + "range": "LibrarySelectionMenu" }, "library_layout": { "name": "library_layout", @@ -7872,9 +8506,14 @@ "Provide the library layout by selecting a value from the pick list. For Illumina instruments, select \"PAIRED\". For Oxford Nanopore instruments, select \"SINGLE\"." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:library_layout"], + "exact_mappings": [ + "NCBI_SRA:library_layout" + ], "slot_uri": "GENEPIO:0100327", - "range": "library_layout menu" + "domain_of": [ + "PHA4GE" + ], + "range": "LibraryLayoutMenu" }, "filetype": { "name": "filetype", @@ -7884,9 +8523,14 @@ "Provide the filetype by selecting a value from the pick list." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:filetype"], + "exact_mappings": [ + "NCBI_SRA:filetype" + ], "slot_uri": "GENEPIO:0100328", - "range": "filetype menu" + "domain_of": [ + "PHA4GE" + ], + "range": "FiletypeMenu" }, "filename": { "name": "filename", @@ -7896,8 +8540,13 @@ "Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is \"paired\", provide the second filename under \"Filename 2\"." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:filename"], + "exact_mappings": [ + "NCBI_SRA:filename" + ], "slot_uri": "GENEPIO:0100329", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, "filename2": { @@ -7908,8 +8557,13 @@ "Provide the appropriate filename recorded in the Bioinformatics and QC metrics section." ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["NCBI_SRA:filename2"], + "exact_mappings": [ + "NCBI_SRA:filename2" + ], "slot_uri": "GENEPIO:0100330", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString" }, "authors": { @@ -7925,25 +8579,33 @@ } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", - "exact_mappings": ["GISAID:Authors"], + "exact_mappings": [ + "GISAID:Authors" + ], "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "PHA4GE" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software version provenance.", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", "comments": [ - "The current software version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." ], "examples": [ { - "value": "DataHarmonizer provenance: v0.13.21" + "value": "DataHarmonizer v1.4.3, PHA4GE v1.0.0" } ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "PHA4GE" + ], "range": "Provenance" } }, @@ -7962,118 +8624,118 @@ ], "is_a": "dh_interface", "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 1, "slot_group": "Database Identifiers" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "rank": 2, "slot_group": "Database Identifiers" }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "rank": 3, "slot_group": "Database Identifiers" }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "rank": 4, "slot_group": "Database Identifiers" }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "rank": 5, "slot_group": "Database Identifiers" }, - "GenBank/ENA/DDBJ accession": { - "name": "GenBank/ENA/DDBJ accession", + "genbank_ena_ddbj_accession": { + "name": "genbank_ena_ddbj_accession", "rank": 6, "slot_group": "Database Identifiers" }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "rank": 7, "slot_group": "Database Identifiers" }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "rank": 8, "slot_group": "Database Identifiers" }, - "host specimen voucher": { - "name": "host specimen voucher", + "host_specimen_voucher": { + "name": "host_specimen_voucher", "rank": 9, "slot_group": "Database Identifiers" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 10, "slot_group": "Sample collection and processing" }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "rank": 11, "slot_group": "Sample collection and processing" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "rank": 12, "slot_group": "Sample collection and processing" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 13, "slot_group": "Sample collection and processing" }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "rank": 14, "slot_group": "Sample collection and processing" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "rank": 15, "slot_group": "Sample collection and processing" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "rank": 16, "slot_group": "Sample collection and processing" }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc name (country)": { - "name": "geo_loc name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 18, "slot_group": "Sample collection and processing" }, - "geo_loc name (state/province/territory)": { - "name": "geo_loc name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 19, "slot_group": "Sample collection and processing" }, - "geo_loc name (county/region)": { - "name": "geo_loc name (county/region)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "rank": 20, "slot_group": "Sample collection and processing" }, - "geo_loc name (city)": { - "name": "geo_loc name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "rank": 21, "slot_group": "Sample collection and processing" }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "rank": 22, "slot_group": "Sample collection and processing" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "rank": 23, "slot_group": "Sample collection and processing" }, @@ -8087,188 +8749,188 @@ "rank": 25, "slot_group": "Sample collection and processing" }, - "culture collection": { - "name": "culture collection", + "culture_collection": { + "name": "culture_collection", "rank": 26, "slot_group": "Sample collection and processing" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "rank": 27, "slot_group": "Sample collection and processing" }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "rank": 28, "slot_group": "Sample collection and processing" }, - "sample plan name": { - "name": "sample plan name", + "sample_plan_name": { + "name": "sample_plan_name", "rank": 29, "slot_group": "Sample collection and processing" }, - "sample collected in quarantine": { - "name": "sample collected in quarantine", + "sample_collected_in_quarantine": { + "name": "sample_collected_in_quarantine", "rank": 30, "slot_group": "Sample collection and processing" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "rank": 31, "slot_group": "Sample collection and processing" }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "rank": 32, "slot_group": "Sample collection and processing" }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "rank": 33, "slot_group": "Sample collection and processing" }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "rank": 34, "slot_group": "Sample collection and processing" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "rank": 35, "slot_group": "Sample collection and processing" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 36, "slot_group": "Sample collection and processing" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 37, "slot_group": "Sample collection and processing" }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "rank": 38, "slot_group": "Sample collection and processing" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "rank": 39, "slot_group": "Sample collection and processing" }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "rank": 40, "slot_group": "Sample collection and processing" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "rank": 41, "slot_group": "Sample collection and processing" }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "rank": 42, "slot_group": "Sample collection and processing" }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "rank": 43, "slot_group": "Sample collection and processing" }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "rank": 44, "slot_group": "Sample collection and processing" }, - "data abstraction details": { - "name": "data abstraction details", + "data_abstraction_details": { + "name": "data_abstraction_details", "rank": 45, "slot_group": "Sample collection and processing" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "rank": 46, "slot_group": "Host Information" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 47, "slot_group": "Host Information" }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "rank": 48, "slot_group": "Host Information" }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "rank": 49, "slot_group": "Host Information" }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "rank": 50, "slot_group": "Host Information" }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "rank": 51, "slot_group": "Host Information" }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "rank": 52, "slot_group": "Host Information" }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "rank": 53, "slot_group": "Host Information" }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "rank": 54, "slot_group": "Host Information" }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "rank": 55, "slot_group": "Host Information" }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "rank": 56, "slot_group": "Host Information" }, - "host ethnicity": { - "name": "host ethnicity", + "host_ethnicity": { + "name": "host_ethnicity", "rank": 57, "slot_group": "Host Information" }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "rank": 58, "slot_group": "Host Information" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "rank": 59, "slot_group": "Host Information" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "rank": 60, "slot_group": "Host Information" }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "rank": 61, "slot_group": "Host Information" }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "rank": 62, "slot_group": "Host Information" }, @@ -8277,368 +8939,368 @@ "rank": 63, "slot_group": "Host Information" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "rank": 64, "slot_group": "Host vaccination information" }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "rank": 65, "slot_group": "Host vaccination information" }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "rank": 66, "slot_group": "Host vaccination information" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "rank": 67, "slot_group": "Host vaccination information" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "rank": 68, "slot_group": "Host vaccination information" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "rank": 69, "slot_group": "Host vaccination information" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "rank": 70, "slot_group": "Host vaccination information" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "rank": 71, "slot_group": "Host vaccination information" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "rank": 72, "slot_group": "Host vaccination information" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "rank": 73, "slot_group": "Host vaccination information" }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "rank": 74, "slot_group": "Host vaccination information" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "rank": 75, "slot_group": "Host exposure information" }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "rank": 76, "slot_group": "Host exposure information" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "rank": 77, "slot_group": "Host exposure information" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "rank": 78, "slot_group": "Host exposure information" }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "rank": 79, "slot_group": "Host exposure information" }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "rank": 80, "slot_group": "Host exposure information" }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "rank": 81, "slot_group": "Host exposure information" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "rank": 82, "slot_group": "Host exposure information" }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "rank": 83, "slot_group": "Host exposure information" }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "rank": 84, "slot_group": "Host exposure information" }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "rank": 85, "slot_group": "Host exposure information" }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "rank": 86, "slot_group": "Host exposure information" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "rank": 87, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "rank": 88, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "rank": 89, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "rank": 90, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "rank": 91, "slot_group": "Host reinfection information" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "rank": 92, "slot_group": "Host reinfection information" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 93, "slot_group": "Sequencing" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 94, "slot_group": "Sequencing" }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "rank": 95, "slot_group": "Sequencing" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "rank": 96, "slot_group": "Sequencing" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "rank": 97, "slot_group": "Sequencing" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 98, "slot_group": "Sequencing" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "rank": 99, "slot_group": "Sequencing" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 100, "slot_group": "Sequencing" }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "rank": 101, "slot_group": "Sequencing" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 102, "slot_group": "Sequencing" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "rank": 103, "slot_group": "Sequencing" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 104, "slot_group": "Sequencing" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 105, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "rank": 106, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence name": { - "name": "consensus sequence name", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "rank": 107, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence filename": { - "name": "consensus sequence filename", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "rank": 108, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", "rank": 109, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 110, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 111, "slot_group": "Bioinformatics and QC metrics" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 112, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 113, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 114, "slot_group": "Bioinformatics and QC metrics" }, - "r1 fastq filename": { - "name": "r1 fastq filename", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "rank": 115, "slot_group": "Bioinformatics and QC metrics" }, - "r2 fastq filename": { - "name": "r2 fastq filename", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "rank": 116, "slot_group": "Bioinformatics and QC metrics" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "rank": 117, "slot_group": "Bioinformatics and QC metrics" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "rank": 118, "slot_group": "Bioinformatics and QC metrics" }, - "fast5 filename": { - "name": "fast5 filename", + "fast5_filename": { + "name": "fast5_filename", "rank": 119, "slot_group": "Bioinformatics and QC metrics" }, - "fast5 filepath": { - "name": "fast5 filepath", + "fast5_filepath": { + "name": "fast5_filepath", "rank": 120, "slot_group": "Bioinformatics and QC metrics" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 121, "slot_group": "Bioinformatics and QC metrics" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "rank": 122, "slot_group": "Bioinformatics and QC metrics" }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "rank": 123, "slot_group": "Bioinformatics and QC metrics" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 124, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 125, "slot_group": "Bioinformatics and QC metrics" }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "rank": 126, "slot_group": "Lineage and Variant information" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "rank": 127, "slot_group": "Lineage and Variant information" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "rank": 128, "slot_group": "Lineage and Variant information" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "rank": 129, "slot_group": "Lineage and Variant information" }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "rank": 130, "slot_group": "Lineage and Variant information" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "rank": 131, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "rank": 132, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "rank": 133, "slot_group": "Pathogen diagnostic testing" }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "rank": 134, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "rank": 135, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "rank": 136, "slot_group": "Pathogen diagnostic testing" }, @@ -8687,35 +9349,65 @@ "rank": 145, "slot_group": "Contributor acknowledgement" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 146, "slot_group": "Contributor acknowledgement" } }, "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", + "comments": [ + "Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory", + "NCBI_BIOSAMPLE:sample_name", + "NCBI_SRA:sample_name", + "NCBI_Genbank:sample_name", + "NCBI_Genbank_source_modifiers:Sequence_ID" + ], "rank": 1, "slot_uri": "GENEPIO:0001123", - "alias": "specimen_collector_sample_ID", + "alias": "specimen_collector_sample_id", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC umbrella accession number of the BioProject to which the BioSample belongs.", "title": "umbrella bioproject accession", + "comments": [ + "Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects." + ], + "examples": [ + { + "value": "PRJNA623807" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 2, "slot_uri": "GENEPIO:0001133", "alias": "umbrella_bioproject_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8724,15 +9416,31 @@ "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", + "comments": [ + "Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects." + ], + "examples": [ + { + "value": "PRJNA12345" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:bioproject_accession", + "NCBI_SRA:bioproject_accession", + "NCBI_Genbank_source_modifiers:BioProject" + ], "rank": 3, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8741,15 +9449,31 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:biosample_accession", + "NCBI_Genbank:biosample_accession", + "NCBI_Genbank_source_modifiers:BioSample" + ], "rank": 4, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "recommended": true, @@ -8759,15 +9483,26 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", + "comments": [ + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 5, "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "alias": "sra_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8776,15 +9511,26 @@ "partial_match": false } }, - "GenBank/ENA/DDBJ accession": { - "name": "GenBank/ENA/DDBJ accession", + "genbank_ena_ddbj_accession": { + "name": "genbank_ena_ddbj_accession", "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.", "title": "GenBank/ENA/DDBJ accession", + "comments": [ + "Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly)." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 6, "slot_uri": "GENEPIO:0001145", - "alias": "GenBank/ENA/DDBJ_accession", + "alias": "genbank_ena_ddbj_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8793,15 +9539,29 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", + "comments": [ + "Store the accession returned from the GISAID submission." + ], + "examples": [ + { + "value": "EPI_ISL_123456" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:gisaid_accession" + ], "rank": 7, "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "alias": "gisaid_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8810,15 +9570,30 @@ "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "description": "The user-defined GISAID virus name assigned to the sequence.", "title": "GISAID virus name", + "comments": [ + "GISAID virus names should be in the format \"hCoV-19/Country/Identifier/year\"." + ], + "examples": [ + { + "value": "hCoV-19/Canada/prov_rona_99/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Virus%20name", + "NCBI_BIOSAMPLE:gisaid_virus_name" + ], "rank": 8, "slot_uri": "GENEPIO:0100282", - "alias": "GISAID_virus_name", + "alias": "gisaid_virus_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8827,15 +9602,29 @@ "partial_match": false } }, - "host specimen voucher": { - "name": "host specimen voucher", + "host_specimen_voucher": { + "name": "host_specimen_voucher", "description": "Identifier for the physical specimen.", "title": "host specimen voucher", + "comments": [ + "Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher=\"[:[:]]\"): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier" + ], + "examples": [ + { + "value": "URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_specimen_voucher" + ], "rank": 9, "slot_uri": "GENEPIO:0100283", "alias": "host_specimen_voucher", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "structured_pattern": { @@ -8844,170 +9633,414 @@ "partial_match": false } }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the organization with which the sample collector is affiliated.", "title": "sample collected by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Public Health Agency of Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Originating%20lab", + "NCBI_BIOSAMPLE:collected_by" + ], "rank": 10, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "johnnyblogs@lab.ca" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 11, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code" + ], + "examples": [ + { + "value": "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Address" + ], "rank": 12, "slot_uri": "GENEPIO:0001158", "alias": "sample_collector_contact_address", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions." + ], + "examples": [ + { + "value": "Centers for Disease Control and Prevention" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "NCBI_BIOSAMPLE:sequenced_by" + ], "rank": 13, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitter contact email": { - "name": "sequence submitter contact email", + "sequence_submitter_contact_email": { + "name": "sequence_submitter_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequence submitter contact email", + "comments": [ + "The email address can represent a specific individual or laboratory." + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:sequence_submitter_contact_email" + ], "rank": 14, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sequence submitter contact address": { - "name": "sequence submitter contact address", + "sequence_submitter_contact_address": { + "name": "sequence_submitter_contact_address", "description": "The mailing address of the agency submitting the sequence.", "title": "sequence submitter contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code" + ], + "examples": [ + { + "value": "123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Address" + ], "rank": 15, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", + "comments": [ + "Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add \"jitter\" to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-19" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Collection%20date", + "NCBI_BIOSAMPLE:collection_date", + "NCBI_Genbank_source_modifiers:collection-date" + ], "rank": 16, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "comments": [ + "The date the sample was received by a lab that was not the point of collection. ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 17, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc name (country)": { - "name": "geo_loc name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country of origin of the sample.", "title": "geo_loc name (country)", + "comments": [ + "Provide the country name from the pick list in the template" + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Location", + "NCBI_BIOSAMPLE:geo_loc_name", + "NCBI_Genbank_source_modifiers:country" + ], "rank": 18, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "alias": "geo_loc_name_country", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc name (state/province/territory)": { - "name": "geo_loc name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The state/province/territory of origin of the sample.", "title": "geo_loc name (state/province/territory)", + "comments": [ + "Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Western Cape" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_name" + ], "rank": 19, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "alias": "geo_loc_name_state_province_territory", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc name (county/region)": { - "name": "geo_loc name (county/region)", + "geo_loc_name_county_region": { + "name": "geo_loc_name_county_region", "description": "The county/region of origin of the sample.", "title": "geo_loc name (county/region)", + "comments": [ + "Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Derbyshire" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_name" + ], "rank": 20, "slot_uri": "GENEPIO:0100280", - "alias": "geo_loc_name_(county/region)", + "alias": "geo_loc_name_county_region", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc name (city)": { - "name": "geo_loc name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city of origin of the sample.", "title": "geo_loc name (city)", + "comments": [ + "Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Vancouver" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_name" + ], "rank": 21, "slot_uri": "GENEPIO:0001189", - "alias": "geo_loc_name_(city)", + "alias": "geo_loc_name_city", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc latitude": { - "name": "geo_loc latitude", + "geo_loc_latitude": { + "name": "geo_loc_latitude", "description": "The latitude coordinates of the geographical location of sample collection.", "title": "geo_loc latitude", + "comments": [ + "Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format \"d[d.dddd] N|S\"." + ], + "examples": [ + { + "value": "38.98 N" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:lat_lon" + ], "rank": 22, "slot_uri": "GENEPIO:0100309", "alias": "geo_loc_latitude", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc longitude": { - "name": "geo_loc longitude", + "geo_loc_longitude": { + "name": "geo_loc_longitude", "description": "The longitude coordinates of the geographical location of sample collection.", "title": "geo_loc longitude", + "comments": [ + "Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format \"d[dd.dddd] W|E\"." + ], + "examples": [ + { + "value": "77.11 W" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:lat_lon" + ], "rank": 23, "slot_uri": "GENEPIO:0100310", "alias": "geo_loc_longitude", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, @@ -9015,1348 +10048,2984 @@ "name": "organism", "description": "Taxonomic name of the organism.", "title": "organism", + "comments": [ + "Select \"Severe acute respiratory syndrome coronavirus 2\" if sequencing SARS-CoV-2. If another Coronaviridae is being sequenced, provide the taxonomic name from NCBITaxon. Search for taxonomy terms at https://www.ebi.ac.uk/ols/ontologies/ncbitaxon." + ], + "examples": [ + { + "value": "Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:organism" + ], "rank": 24, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "OrganismMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "isolate": { "name": "isolate", "description": "Identifier of the specific isolate.", "title": "isolate", + "comments": [ + "This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the \"isolate\" name is propagated throughtout different databases. As such, structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"SARS-CoV-2/host/country/sampleID/date\"." + ], + "examples": [ + { + "value": "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:isolate", + "NCBI_Genbank_source_modifiers:isolate" + ], "rank": 25, "slot_uri": "GENEPIO:0001644", "alias": "isolate", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "culture collection": { - "name": "culture collection", + "culture_collection": { + "name": "culture_collection", "description": "The name of the source collection and unique culture identifier.", "title": "culture collection", + "comments": [ + "Format: \":[:]\". For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier." + ], + "examples": [ + { + "value": "/culture_collection=\"ATCC:26370\"" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 26, "slot_uri": "GENEPIO:0100284", "alias": "culture_collection", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "Select a value from the pick list in the template." + ], + "examples": [ + { + "value": "Diagnostic testing [GENEPIO:0100002]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:purpose_of_sampling" + ], "rank": 27, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "Further details pertaining to the reason the sample was collected.", "title": "purpose of sampling details", + "comments": [ + "Provide a free text description of the sampling strategy or samples collected." + ], + "examples": [ + { + "value": "Screening of bat specimens in museum collections." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 28, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample plan name": { - "name": "sample plan name", + "sample_plan_name": { + "name": "sample_plan_name", "description": "The name of the sample plan implemented for sample collection.", "title": "sample plan name", + "comments": [ + "Provide the name and version of the sample plan outlining the sample strategy." + ], + "examples": [ + { + "value": "CanCOGeN Sampling Strategy 1.0" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 29, "slot_uri": "GENEPIO:0100285", "alias": "sample_plan_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collected in quarantine": { - "name": "sample collected in quarantine", + "sample_collected_in_quarantine": { + "name": "sample_collected_in_quarantine", "description": "Whether the sample was collected from an individual in quarantine.", "title": "sample collected in quarantine", + "comments": [ + "Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template." + ], + "examples": [ + { + "value": "Yes [NCIT:C49488]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 30, "slot_uri": "GENEPIO:0100277", "alias": "sample_collected_in_quarantine", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "SampleCollectedInQuarantineMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Blood [UBERON:0000178]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:host_anatomical_material", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 31, "slot_uri": "GENEPIO:0001211", - "multivalued": true, "alias": "anatomical_material", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Nasopharynx (NP) [UBERON:0001728]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:host_anatomical_part", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 32, "slot_uri": "GENEPIO:0001214", - "multivalued": true, "alias": "anatomical_part", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Feces [UBERON:0001988]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:host_body_product", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 33, "slot_uri": "GENEPIO:0001216", - "multivalued": true, "alias": "body_product", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.", "title": "environmental material", + "comments": [ + "Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Face mask [OBI:0002787]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:environmental_material", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 34, "slot_uri": "GENEPIO:0001223", - "multivalued": true, "alias": "environmental_material", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.", "title": "environmental site", + "comments": [ + "Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Hospital [ENVO:00002173]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:environmental_site", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 35, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", + "comments": [ + "Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Swab [GENEPIO:0100027]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:collection_device", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 36, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotomy, necropsy.", "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank." + ], + "examples": [ + { + "value": "Bronchoalveolar lavage (BAL) [GENEPIO:0100032]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Specimen%20source", + "NCBI_BIOSAMPLE:isolation_source", + "NCBI_BIOSAMPLE:collection_method", + "NCBI_Genbank_source_modifiers:isolation-source" + ], "rank": 37, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", + "comments": [ + "Provide the name and version of the protocol used to collect the samples." + ], + "examples": [ + { + "value": "SC2SamplingProtocol 1.2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 38, "slot_uri": "GENEPIO:0001243", "alias": "collection_protocol", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." + ], + "examples": [ + { + "value": "Virus passage [GENEPIO:0100039]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 39, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample." + ], + "examples": [ + { + "value": "25 swabs were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 40, "slot_uri": "GENEPIO:0100311", "alias": "specimen_processing_details", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "lab host": { - "name": "lab host", + "lab_host": { + "name": "lab_host", "description": "Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.", "title": "lab host", + "comments": [ + "Type of cell line used for propagation. Select a value form the pick list. If not passaged, put \"not applicable\"." + ], + "examples": [ + { + "value": "Vero E6 cell line [BTO:0004755]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 41, "slot_uri": "GENEPIO:0001255", "alias": "lab_host", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "LabHostMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "passage number": { - "name": "passage number", + "passage_number": { + "name": "passage_number", "description": "Number of passages.", "title": "passage number", + "comments": [ + "Provide number of known passages. If not passaged, put \"not applicable\"" + ], + "examples": [ + { + "value": "3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:passage_number" + ], "rank": 42, "slot_uri": "GENEPIO:0001261", "alias": "passage_number", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "integer", "minimum_value": 0 }, - "passage method": { - "name": "passage method", + "passage_method": { + "name": "passage_method", "description": "Description of how organism was passaged.", "title": "passage method", + "comments": [ + "Free text. Provide a short description. If not passaged, put \"not applicable\"." + ], + "examples": [ + { + "value": "AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:passage_method" + ], "rank": 43, "slot_uri": "GENEPIO:0001264", "alias": "passage_method", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "title": "biomaterial extracted", + "comments": [ + "Provide the biomaterial extracted from the pick list in the template." + ], + "examples": [ + { + "value": "RNA (Total) [OBI:0000895]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 44, "slot_uri": "GENEPIO:0001266", "alias": "biomaterial_extracted", "owner": "PHA4GE", - "slot_group": "Sample collection and processing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "BiomaterialExtractedMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "data abstraction details": { - "name": "data abstraction details", + "data_abstraction_details": { + "name": "data_abstraction_details", "description": "A description of how any data elements were altered to preserve patient privacy.", "title": "data abstraction details", + "comments": [ + "If applicable, provide a description of how each data element was abstracted." + ], + "examples": [ + { + "value": "Jitter added to publicly shared collection dates to prevent re-identifiability." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 45, "slot_uri": "GENEPIO:0100278", "alias": "data_abstraction_details", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put \"not applicable\"." + ], + "examples": [ + { + "value": "Human [NCBITaxon:9606]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 46, "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", + "alias": "host_common_name", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostCommonNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put \"not applicable\"." + ], + "examples": [ + { + "value": "Homo sapiens [NCBITaxon:9606]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Host", + "NCBI_BIOSAMPLE:host", + "NCBI_Genbank_source_modifiers:host" + ], "rank": 47, "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", + "alias": "host_scientific_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "description": "Health status of the host at the time of sample collection.", "title": "host health state", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Asymptomatic [NCIT:C3833]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Patient%20status", + "NCBI_BIOSAMPLE:host_health_state" + ], "rank": 48, "slot_uri": "GENEPIO:0001388", "alias": "host_health_state", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStateMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "description": "Further details pertaining to the health or disease status of the host at time of collection.", "title": "host health status details", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Hospitalized (ICU) [GENEPIO:0100046]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 49, "slot_uri": "GENEPIO:0001389", "alias": "host_health_status_details", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStatusDetailsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", + "comments": [ + "This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. \"COVID-19\" should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”." + ], + "examples": [ + { + "value": "COVID-19 [MONDO:0100096]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_disease" + ], "rank": 50, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Recovered [NCIT:C49498]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_disease_outcome" + ], "rank": 51, "slot_uri": "GENEPIO:0001390", "alias": "host_health_outcome", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthOutcomeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", + "comments": [ + "If known, provide age. Age-binning is also acceptable." + ], + "examples": [ + { + "value": "79" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Patient%20age", + "NCBI_BIOSAMPLE:host_age" + ], "rank": 52, "slot_uri": "GENEPIO:0001392", "alias": "host_age", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", "recommended": true, - "maximum_value": 130 + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The units used to measure the host's age.", "title": "host age unit", + "comments": [ + "If known, provide the age units used to measure the host's age from the pick list." + ], + "examples": [ + { + "value": "year [UO:0000036]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 53, "slot_uri": "GENEPIO:0001393", "alias": "host_age_unit", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "HostAgeUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "The age category of the host at the time of sampling.", "title": "host age bin", + "comments": [ + "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative." + ], + "examples": [ + { + "value": "50 - 59 [GENEPIO:0100054]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 54, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "Male [NCIT:C46109]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Gender", + "NCBI_BIOSAMPLE:host_sex" + ], "rank": 55, "slot_uri": "GENEPIO:0001395", "alias": "host_gender", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", - "recommended": true + "recommended": true, + "any_of": [ + { + "range": "HostGenderMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host residence geo_loc name (country)": { - "name": "host residence geo_loc name (country)", + "host_residence_geo_loc_name_country": { + "name": "host_residence_geo_loc_name_country", "description": "The country where the host resides.", "title": "host residence geo_loc name (country)", + "comments": [ + "If known, select a value from the pick list." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 56, "slot_uri": "GENEPIO:0001396", - "alias": "host_residence_geo_loc_name_(country)", + "alias": "host_residence_geo_loc_name_country", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostResidenceGeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host ethnicity": { - "name": "host ethnicity", + "host_ethnicity": { + "name": "host_ethnicity", "description": "The self-identified ethnicity(ies) of the host.", "title": "host ethnicity", + "comments": [ + "If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative." + ], + "examples": [ + { + "value": "Indigenous, European" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 57, "slot_uri": "GENEPIO:0100312", "alias": "host_ethnicity", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to e.g. #131", "title": "host subject ID", + "comments": [ + "Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward." + ], + "examples": [ + { + "value": "BCxy123" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_subject_id" + ], "rank": 58, "slot_uri": "GENEPIO:0001398", - "alias": "host_subject_ID", + "alias": "host_subject_id", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 59, "slot_uri": "GENEPIO:0100281", - "alias": "case_ID", + "alias": "case_id", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "symptom onset date": { - "name": "symptom onset date", + "symptom_onset_date": { + "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom onset date", + "comments": [ + "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 60, "slot_uri": "GENEPIO:0001399", "alias": "symptom_onset_date", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "signs and symptoms": { - "name": "signs and symptoms", + "signs_and_symptoms": { + "name": "signs_and_symptoms", "description": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.", "title": "signs and symptoms", + "comments": [ + "Select all of the symptoms experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 61, "slot_uri": "GENEPIO:0001400", - "multivalued": true, "alias": "signs_and_symptoms", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "SignsAndSymptomsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "pre-existing conditions and risk factors": { - "name": "pre-existing conditions and risk factors", + "preexisting_conditions_and_risk_factors": { + "name": "preexisting_conditions_and_risk_factors", "description": "Patient pre-existing conditions and risk factors.\nPre-existing condition: A medical condition that existed prior to the current infection.\nRisk Factor: A variable associated with an increased risk of disease or infection.", "title": "pre-existing conditions and risk factors", + "comments": [ + "Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Asthma [HP:0002099]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 62, "slot_uri": "GENEPIO:0001401", - "multivalued": true, - "alias": "pre_existing_conditions_and_risk_factors", + "alias": "preexisting_conditions_and_risk_factors", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "PreExistingConditionsAndRiskFactorsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "complications": { "name": "complications", "description": "Patient medical complications that are believed to have occurred as a result of host disease.", "title": "complications", + "comments": [ + "Select all of the complications experienced by the host from the pick list." + ], + "examples": [ + { + "value": "Acute respiratory failure [MONDO:0001208]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 63, "slot_uri": "GENEPIO:0001402", - "multivalued": true, "alias": "complications", "owner": "PHA4GE", - "slot_group": "Host Information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host Information", + "multivalued": true, + "any_of": [ + { + "range": "ComplicationsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated [GENEPIO:0100100]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination" + ], "rank": 64, "slot_uri": "GENEPIO:0001404", "alias": "host_vaccination_status", "owner": "PHA4GE", - "slot_group": "Host vaccination information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "HostVaccinationStatusMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "number of vaccine doses received": { - "name": "number of vaccine doses received", + "number_of_vaccine_doses_received": { + "name": "number_of_vaccine_doses_received", "description": "The number of doses of the vaccine received by the host.", "title": "number of vaccine doses received", + "comments": [ + "Record how many doses of the vaccine the host has received." + ], + "examples": [ + { + "value": "2" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 65, "slot_uri": "GENEPIO:0001406", "alias": "number_of_vaccine_doses_received", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "integer", "minimum_value": 0 }, - "vaccination dose 1 vaccine name": { - "name": "vaccination dose 1 vaccine name", + "vaccination_dose_1_vaccine_name": { + "name": "vaccination_dose_1_vaccine_name", "description": "The name of the vaccine administered as the first dose of a vaccine regimen.", "title": "vaccination dose 1 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 66, "slot_uri": "GENEPIO:0100313", "alias": "vaccination_dose_1_vaccine_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "vaccination dose 1 vaccination date": { - "name": "vaccination dose 1 vaccination date", + "vaccination_dose_1_vaccination_date": { + "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination dose 1 vaccination date", + "comments": [ + "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-03-01" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 67, "slot_uri": "GENEPIO:0100314", "alias": "vaccination_dose_1_vaccination_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "date" }, - "vaccination dose 2 vaccine name": { - "name": "vaccination dose 2 vaccine name", + "vaccination_dose_2_vaccine_name": { + "name": "vaccination_dose_2_vaccine_name", "description": "The name of the vaccine administered as the second dose of a vaccine regimen.", "title": "vaccination dose 2 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 68, "slot_uri": "GENEPIO:0100315", "alias": "vaccination_dose_2_vaccine_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "vaccination dose 2 vaccination date": { - "name": "vaccination dose 2 vaccination date", + "vaccination_dose_2_vaccination_date": { + "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination dose 2 vaccination date", + "comments": [ + "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-09-01" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 69, "slot_uri": "GENEPIO:0100316", "alias": "vaccination_dose_2_vaccination_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "date" }, - "vaccination dose 3 vaccine name": { - "name": "vaccination dose 3 vaccine name", + "vaccination_dose_3_vaccine_name": { + "name": "vaccination_dose_3_vaccine_name", "description": "The name of the vaccine administered as the third dose of a vaccine regimen.", "title": "vaccination dose 3 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 70, "slot_uri": "GENEPIO:0100317", "alias": "vaccination_dose_3_vaccine_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "vaccination dose 3 vaccination date": { - "name": "vaccination dose 3 vaccination date", + "vaccination_dose_3_vaccination_date": { + "name": "vaccination_dose_3_vaccination_date", "description": "The date the third dose of a vaccine was administered.", "title": "vaccination dose 3 vaccination date", + "comments": [ + "Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-12-30" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:date_of_sars_cov_2_vaccination" + ], "rank": 71, "slot_uri": "GENEPIO:0100318", "alias": "vaccination_dose_3_vaccination_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "date" }, - "vaccination dose 4 vaccine name": { - "name": "vaccination dose 4 vaccine name", + "vaccination_dose_4_vaccine_name": { + "name": "vaccination_dose_4_vaccine_name", "description": "The name of the vaccine administered as the fourth dose of a vaccine regimen.", "title": "vaccination dose 4 vaccine name", + "comments": [ + "Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list" + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 72, "slot_uri": "GENEPIO:0100319", "alias": "vaccination_dose_4_vaccine_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "vaccination dose 4 vaccination date": { - "name": "vaccination dose 4 vaccination date", + "vaccination_dose_4_vaccination_date": { + "name": "vaccination_dose_4_vaccination_date", "description": "The date the fourth dose of a vaccine was administered.", "title": "vaccination dose 4 vaccination date", + "comments": [ + "Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2022-01-15" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 73, "slot_uri": "GENEPIO:0100320", "alias": "vaccination_dose_4_vaccination_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "date" }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], + "examples": [ + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2021-03-01" + }, + { + "value": "Pfizer-BioNTech (Comirnaty)" + }, + { + "value": "2022-01-15" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Last%20vaccinated" + ], "rank": 74, "slot_uri": "GENEPIO:0100321", "alias": "vaccination_history", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "location of exposure geo_loc name (country)": { - "name": "location of exposure geo_loc name (country)", + "location_of_exposure_geo_loc_name_country": { + "name": "location_of_exposure_geo_loc_name_country", "description": "The country where the host was likely exposed to the causative agent of the illness.", "title": "location of exposure geo_loc name (country)", + "comments": [ + "This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list." + ], + "examples": [ + { + "value": "South Africa [GAZ:00001094]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:geo_loc_exposure" + ], "rank": 75, "slot_uri": "GENEPIO:0001410", - "alias": "location_of_exposure_geo_loc_name_(country)", + "alias": "location_of_exposure_geo_loc_name_country", "owner": "PHA4GE", - "slot_group": "Host exposure information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "LocationOfExposureGeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "destination of most recent travel (city)": { - "name": "destination of most recent travel (city)", + "destination_of_most_recent_travel_city": { + "name": "destination_of_most_recent_travel_city", "description": "The name of the city that was the destination of most recent travel.", "title": "destination of most recent travel (city)", + "comments": [ + "Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "New York City" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_loc" + ], "rank": 76, "slot_uri": "GENEPIO:0001411", - "alias": "destination_of_most_recent_travel_(city)", + "alias": "destination_of_most_recent_travel_city", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (state/province/territory)": { - "name": "destination of most recent travel (state/province/territory)", + "destination_of_most_recent_travel_state_province_territory": { + "name": "destination_of_most_recent_travel_state_province_territory", "description": "The name of the province that was the destination of most recent travel.", "title": "destination of most recent travel (state/province/territory)", + "comments": [ + "Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "California" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_loc" + ], "rank": 77, "slot_uri": "GENEPIO:0001412", - "alias": "destination_of_most_recent_travel_(state/province/territory)", + "alias": "destination_of_most_recent_travel_state_province_territory", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "destination of most recent travel (country)": { - "name": "destination of most recent travel (country)", + "destination_of_most_recent_travel_country": { + "name": "destination_of_most_recent_travel_country", "description": "The name of the country that was the destination of most recent travel.", "title": "destination of most recent travel (country)", + "comments": [ + "Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "United Kingdom [GAZ:00002637]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_loc" + ], "rank": 78, "slot_uri": "GENEPIO:0001413", - "alias": "destination_of_most_recent_travel_(country)", + "alias": "destination_of_most_recent_travel_country", "owner": "PHA4GE", - "slot_group": "Host exposure information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "DestinationOfMostRecentTravelCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "most recent travel departure date": { - "name": "most recent travel departure date", + "most_recent_travel_departure_date": { + "name": "most_recent_travel_departure_date", "description": "The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.", "title": "most recent travel departure date", + "comments": [ + "Provide the travel departure date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 79, "slot_uri": "GENEPIO:0001414", "alias": "most_recent_travel_departure_date", "owner": "PHA4GE", - "slot_group": "Host exposure information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "most recent travel return date": { - "name": "most recent travel return date", + "most_recent_travel_return_date": { + "name": "most_recent_travel_return_date", "description": "The date of a person's most recent return to some residence from a journey originating at that residence.", "title": "most recent travel return date", + "comments": [ + "Provide the travel return date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-04-26" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:host_recent_travel_return_date" + ], "rank": 80, "slot_uri": "GENEPIO:0001415", "alias": "most_recent_travel_return_date", "owner": "PHA4GE", - "slot_group": "Host exposure information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "travel history": { - "name": "travel history", + "travel_history": { + "name": "travel_history", "description": "Travel history in last six months.", "title": "travel history", + "comments": [ + "Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text." + ], + "examples": [ + { + "value": "Canada, Vancouver" + }, + { + "value": "USA, Seattle" + }, + { + "value": "Italy, Milan" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 81, "slot_uri": "GENEPIO:0001416", "alias": "travel_history", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", + "comments": [ + "If known, select the exposure event from the pick list." + ], + "examples": [ + { + "value": "Mass Gathering [GENEPIO:0100237]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "NCBI_BIOSAMPLE:exposure_event" + ], "rank": 82, "slot_uri": "GENEPIO:0001417", "alias": "exposure_event", "owner": "PHA4GE", - "slot_group": "Host exposure information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureEventMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick list." + ], + "examples": [ + { + "value": "Direct (human-to-human contact) [TRANS:0000001]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 83, "slot_uri": "GENEPIO:0001418", "alias": "exposure_contact_level", "owner": "PHA4GE", - "slot_group": "Host exposure information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureContactLevelMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Patient [OMRSE:00000030]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Additional%20host%20information" + ], "rank": 84, "slot_uri": "GENEPIO:0001419", - "multivalued": true, "alias": "host_role", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host exposure information", - "range": "host role menu" + "range": "HostRoleMenu", + "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting [GENEPIO:0100201]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Additional%20host%20information" + ], "rank": 85, "slot_uri": "GENEPIO:0001428", - "multivalued": true, "alias": "exposure_setting", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host exposure information", - "range": "exposure setting menu" + "range": "ExposureSettingMenu", + "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Host role - Other: Bus Driver" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 86, "slot_uri": "GENEPIO:0001431", "alias": "exposure_details", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection": { - "name": "prior SARS-CoV-2 infection", + "prior_sarscov2_infection": { + "name": "prior_sarscov2_infection", "description": "Whether there was prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection", + "comments": [ + "If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list." + ], + "examples": [ + { + "value": "Prior infection [GENEPIO:0100234]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:prior_sars_cov_2_infection" + ], "rank": 87, "slot_uri": "GENEPIO:0001435", - "alias": "prior_SARS_CoV_2_infection", + "alias": "prior_sarscov2_infection", "owner": "PHA4GE", - "slot_group": "Host reinfection information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorSarsCov2InfectionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "prior SARS-CoV-2 infection isolate": { - "name": "prior SARS-CoV-2 infection isolate", + "prior_sarscov2_infection_isolate": { + "name": "prior_sarscov2_infection_isolate", "description": "The identifier of the isolate found in the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection isolate", + "comments": [ + "Provide the isolate name of the most recent prior infection. Structure the \"isolate\" name to be ICTV/INSDC compliant in the following format: \"SARS-CoV-2/host/country/sampleID/date\"." + ], + "examples": [ + { + "value": "SARS-CoV-2/human/USA/CA-CDPH-001/2020" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:virus_isolate_of_prior_infection" + ], "rank": 88, "slot_uri": "GENEPIO:0001436", - "alias": "prior_SARS_CoV_2_infection_isolate", + "alias": "prior_sarscov2_infection_isolate", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host reinfection information", "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 infection date": { - "name": "prior SARS-CoV-2 infection date", + "prior_sarscov2_infection_date": { + "name": "prior_sarscov2_infection_date", "description": "The date of diagnosis of the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 infection date", + "comments": [ + "Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-01-23" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:date_of_prior_sars_cov_2_infection" + ], "rank": 89, "slot_uri": "GENEPIO:0001437", - "alias": "prior_SARS_CoV_2_infection_date", + "alias": "prior_sarscov2_infection_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host reinfection information", "range": "date" }, - "prior SARS-CoV-2 antiviral treatment": { - "name": "prior SARS-CoV-2 antiviral treatment", + "prior_sarscov2_antiviral_treatment": { + "name": "prior_sarscov2_antiviral_treatment", "description": "Whether there was prior SARS-CoV-2 treatment with an antiviral agent.", "title": "prior SARS-CoV-2 antiviral treatment", + "comments": [ + "If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list." + ], + "examples": [ + { + "value": "Prior antiviral treatment [GENEPIO:0100037]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treat" + ], "rank": 90, "slot_uri": "GENEPIO:0001438", - "alias": "prior_SARS_CoV_2_antiviral_treatment", + "alias": "prior_sarscov2_antiviral_treatment", "owner": "PHA4GE", - "slot_group": "Host reinfection information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Host reinfection information", + "any_of": [ + { + "range": "PriorSarsCov2AntiviralTreatmentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "prior SARS-CoV-2 antiviral treatment agent": { - "name": "prior SARS-CoV-2 antiviral treatment agent", + "prior_sarscov2_antiviral_treatment_agent": { + "name": "prior_sarscov2_antiviral_treatment_agent", "description": "The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment agent", + "comments": [ + "Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put \"No treatment\". If multiple antiviral agents were administered, list them all separated by commas." + ], + "examples": [ + { + "value": "Remdesivir" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:antiviral_treatment_agent" + ], "rank": 91, "slot_uri": "GENEPIO:0001439", - "alias": "prior_SARS_CoV_2_antiviral_treatment_agent", + "alias": "prior_sarscov2_antiviral_treatment_agent", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host reinfection information", "range": "WhitespaceMinimizedString" }, - "prior SARS-CoV-2 antiviral treatment date": { - "name": "prior SARS-CoV-2 antiviral treatment date", + "prior_sarscov2_antiviral_treatment_date": { + "name": "prior_sarscov2_antiviral_treatment_date", "description": "The date treatment was first administered during the prior SARS-CoV-2 infection.", "title": "prior SARS-CoV-2 antiviral treatment date", + "comments": [ + "Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-01-28" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:date_of_prior_antiviral_treat" + ], "rank": 92, "slot_uri": "GENEPIO:0001440", - "alias": "prior_SARS_CoV_2_antiviral_treatment_date", + "alias": "prior_sarscov2_antiviral_treatment_date", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Host reinfection information", "range": "date" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Sampling%20Strategy", + "NCBI_BIOSAMPLE:purpose_of_sequencing" + ], "rank": 93, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection." + ], + "examples": [ + { + "value": "Screened for S gene target failure (S dropout)" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 94, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "comments": [ + "Provide the sequencing date in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2021-04-26" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 95, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "PHA4GE", - "slot_group": "Sequencing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Sequencing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", + "comments": [ + "The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID." + ], + "examples": [ + { + "value": "XYZ_123345" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:library_ID" + ], "rank": 96, "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", + "alias": "library_id", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", + "comments": [ + "Provide the amplicon size, including the units." + ], + "examples": [ + { + "value": "300bp" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:amplicon_size" + ], "rank": 97, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 98, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "flow cell barcode": { - "name": "flow cell barcode", + "flow_cell_barcode": { + "name": "flow_cell_barcode", "description": "The barcode of the flow cell used for sequencing.", "title": "flow cell barcode", + "comments": [ + "Provide the barcode of the flow cell used for sequencing the sample." + ], + "examples": [ + { + "value": "FAB06069" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 99, "slot_uri": "GENEPIO:0001451", "alias": "flow_cell_barcode", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Select the sequencing instrument from the pick list." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION [GENEPIO:0100142]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Sequencing%20technology", + "NCBI_SRA:platform", + "NCBI_SRA:instrument_model", + "NCBI_Genbank:sequencing_technology" + ], "rank": 100, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "description": "The name and version number of the sequencing protocol used.", "title": "sequencing protocol name", + "comments": [ + "Provide the name and version of the sequencing protocol." + ], + "examples": [ + { + "value": "1D_DNA_MinION, ARTIC Network Protocol V3" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:sequencing_protocol_name" + ], "rank": 101, "slot_uri": "GENEPIO:0001453", "alias": "sequencing_protocol_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString", "recommended": true }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", + "comments": [ + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + ], + "examples": [ + { + "value": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:design_description" + ], "rank": 102, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing kit number": { - "name": "sequencing kit number", + "sequencing_kit_number": { + "name": "sequencing_kit_number", "description": "The manufacturer's kit number.", "title": "sequencing kit number", + "comments": [ + "Alphanumeric value." + ], + "examples": [ + { + "value": "AB456XYZ789" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 103, "slot_uri": "GENEPIO:0001455", "alias": "sequencing_kit_number", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], + "examples": [ + { + "value": "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:amplicon_pcr_primer_scheme" + ], "rank": 104, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", - "description": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", + "description": "#REF!", "title": "raw sequence data processing method", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:raw_sequence_data_processing_method" + ], "rank": 105, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "dehosting method": { - "name": "dehosting method", - "description": "The method used to remove host reads from the pathogen sequence.", + "dehosting_method": { + "name": "dehosting_method", "title": "dehosting method", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:dehosting_method" + ], "rank": 106, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "recommended": true }, - "consensus sequence name": { - "name": "consensus sequence name", - "description": "The name of the consensus sequence.", + "consensus_sequence_name": { + "name": "consensus_sequence_name", "title": "consensus sequence name", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 107, "slot_uri": "GENEPIO:0001460", "alias": "consensus_sequence_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence filename": { - "name": "consensus sequence filename", - "description": "The name of the consensus sequence file.", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "title": "consensus sequence filename", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_Genbank:filename" + ], "rank": 108, "slot_uri": "GENEPIO:0001461", "alias": "consensus_sequence_filename", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence filepath": { - "name": "consensus sequence filepath", - "description": "The filepath of the consesnsus sequence file.", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "description": "The filepath of the consensus sequence file.", "title": "consensus sequence filepath", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 109, "slot_uri": "GENEPIO:0001462", "alias": "consensus_sequence_filepath", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "consensus sequence software name": { - "name": "consensus sequence software name", - "description": "The name of software used to generate the consensus sequence.", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "title": "consensus sequence software name", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Assembly%20method", + "NCBI_Genbank:assembly_method" + ], "rank": 110, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", - "description": "The version of the software used to generate the consensus sequence.", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "title": "consensus sequence software version", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Assembly%20method", + "NCBI_Genbank:assembly_method_version" + ], "rank": 111, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "decimal", "required": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", - "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "title": "breadth of coverage value", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 112, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "title": "depth of coverage value", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Depth%20of%20coverage", + "NCBI_Genbank:genome_coverage" + ], "rank": 113, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "title": "depth of coverage threshold", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 114, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r1 fastq filename": { - "name": "r1 fastq filename", - "description": "The user-specified filename of the r1 FASTQ file.", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "title": "r1 fastq filename", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 115, "slot_uri": "GENEPIO:0001476", "alias": "r1_fastq_filename", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r2 fastq filename": { - "name": "r2 fastq filename", - "description": "The user-specified filename of the r2 FASTQ file.", + "r2_fastq_filename": { + "name": "r2_fastq_filename", "title": "r2 fastq filename", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 116, "slot_uri": "GENEPIO:0001477", "alias": "r2_fastq_filename", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r1 fastq filepath": { - "name": "r1 fastq filepath", - "description": "The filepath of the r1 FASTQ file.", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", "title": "r1 fastq filepath", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 117, "slot_uri": "GENEPIO:0001478", "alias": "r1_fastq_filepath", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r2 fastq filepath": { - "name": "r2 fastq filepath", - "description": "The filepath of the r2 FASTQ file.", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", "title": "r2 fastq filepath", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 118, "slot_uri": "GENEPIO:0001479", "alias": "r2_fastq_filepath", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "fast5 filename": { - "name": "fast5 filename", - "description": "The user-specified filename of the FAST5 file.", + "fast5_filename": { + "name": "fast5_filename", "title": "fast5 filename", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 119, "slot_uri": "GENEPIO:0001480", "alias": "fast5_filename", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "fast5 filepath": { - "name": "fast5 filepath", - "description": "The filepath of the FAST5 file.", + "fast5_filepath": { + "name": "fast5_filepath", "title": "fast5 filepath", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 120, "slot_uri": "GENEPIO:0001481", "alias": "fast5_filepath", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", - "description": "The number of total base pairs generated by the sequencing process.", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "title": "number of base pairs sequenced", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 121, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "integer", "minimum_value": 0 }, - "consensus genome length": { - "name": "consensus genome length", - "description": "Size of the assembled genome described as the number of base pairs.", + "consensus_genome_length": { + "name": "consensus_genome_length", "title": "consensus genome length", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 122, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "integer", "minimum_value": 0 }, - "Ns per 100 kbp": { - "name": "Ns per 100 kbp", - "description": "The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence.", + "ns_per_100_kbp": { + "name": "ns_per_100_kbp", "title": "Ns per 100 kbp", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 123, "slot_uri": "GENEPIO:0001484", - "alias": "Ns_per_100_kbp", + "alias": "ns_per_100_kbp", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "decimal" }, - "reference genome accession": { - "name": "reference genome accession", - "description": "A persistent, unique identifier of a genome database entry.", + "reference_genome_accession": { + "name": "reference_genome_accession", "title": "reference genome accession", "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_Genbank:reference_genome" + ], "rank": 124, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", - "description": "The name and version number of the bioinformatics protocol used.", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "title": "bioinformatics protocol", "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 125, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "lineage/clade name": { - "name": "lineage/clade name", + "lineage_clade_name": { + "name": "lineage_clade_name", "description": "The name of the lineage or clade.", "title": "lineage/clade name", + "comments": [ + "Provide the Pangolin or Nextstrain lineage/clade name." + ], + "examples": [ + { + "value": "B.1.1.7" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 126, "slot_uri": "GENEPIO:0001500", - "alias": "lineage/clade_name", + "alias": "lineage_clade_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software name": { - "name": "lineage/clade analysis software name", + "lineage_clade_analysis_software_name": { + "name": "lineage_clade_analysis_software_name", "description": "The name of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software name", + "comments": [ + "Provide the name of the software used to determine the lineage/clade." + ], + "examples": [ + { + "value": "Pangolin" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 127, "slot_uri": "GENEPIO:0001501", - "alias": "lineage/clade_analysis_software_name", + "alias": "lineage_clade_analysis_software_name", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "lineage/clade analysis software version": { - "name": "lineage/clade analysis software version", + "lineage_clade_analysis_software_version": { + "name": "lineage_clade_analysis_software_version", "description": "The version of the software used to determine the lineage/clade.", "title": "lineage/clade analysis software version", + "comments": [ + "Provide the version of the software used ot determine the lineage/clade." + ], + "examples": [ + { + "value": "2.1.10" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 128, "slot_uri": "GENEPIO:0001502", - "alias": "lineage/clade_analysis_software_version", + "alias": "lineage_clade_analysis_software_version", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "variant designation": { - "name": "variant designation", + "variant_designation": { + "name": "variant_designation", "description": "The variant classification of the lineage/clade i.e. variant, variant of concern.", "title": "variant designation", + "comments": [ + "If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank." + ], + "examples": [ + { + "value": "Variant of Concern (VOC) [GENEPIO:0100083]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 129, "slot_uri": "GENEPIO:0001503", "alias": "variant_designation", "owner": "PHA4GE", - "slot_group": "Lineage and Variant information" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Lineage and Variant information", + "any_of": [ + { + "range": "VariantDesignationMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "variant evidence details": { - "name": "variant evidence details", + "variant_evidence_details": { + "name": "variant_evidence_details", "description": "The evidence used to make the variant determination.", "title": "variant evidence details", + "comments": [ + "List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here." + ], + "examples": [ + { + "value": "RT-qPCR TaqPath assay: S gene target failure" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 130, - "slot_uri": "GENEPIO:0001504", + "slot_uri": "GENEPIO:0001505", "alias": "variant_evidence_details", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Lineage and Variant information", "range": "WhitespaceMinimizedString" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 1", + "comments": [ + "Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "E gene (orf4) [GENEPIO:0100151]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_1" + ], "rank": 131, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", "owner": "PHA4GE", - "slot_group": "Pathogen diagnostic testing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr protocol 1": { - "name": "diagnostic pcr protocol 1", + "diagnostic_pcr_protocol_1": { + "name": "diagnostic_pcr_protocol_1", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 1", + "comments": [ + "The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "PCREGene 2.0" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 132, "slot_uri": "GENEPIO:0001508", "alias": "diagnostic_pcr_protocol_1", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "description": "The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", + "comments": [ + "Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "21" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_1" + ], "rank": 133, "slot_uri": "GENEPIO:0001509", - "alias": "diagnostic_pcr_Ct_value_1", + "alias": "diagnostic_pcr_ct_value_1", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 2", + "comments": [ + "Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], + "examples": [ + { + "value": "RdRp gene (nsp12) [GENEPIO:0100168]" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_2" + ], "rank": 134, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", "owner": "PHA4GE", - "slot_group": "Pathogen diagnostic testing" + "domain_of": [ + "PHA4GE" + ], + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr protocol 2": { - "name": "diagnostic pcr protocol 2", + "diagnostic_pcr_protocol_2": { + "name": "diagnostic_pcr_protocol_2", "description": "The name and version number of the protocol used for diagnostic marker amplification.", "title": "diagnostic pcr protocol 2", + "comments": [ + "The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control." + ], + "examples": [ + { + "value": "PCRRdRpGene 3.0" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 135, "slot_uri": "GENEPIO:0001511", "alias": "diagnostic_pcr_protocol_2", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", + "comments": [ + "Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "36" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_2" + ], "rank": 136, "slot_uri": "GENEPIO:0001512", - "alias": "diagnostic_pcr_Ct_value_2", + "alias": "diagnostic_pcr_ct_value_2", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Pathogen diagnostic testing", "range": "WhitespaceMinimizedString" }, @@ -10364,11 +13033,25 @@ "name": "title", "description": "Short description that will identify the dataset on public pages.", "title": "title", + "comments": [ + "Format: {methodology} of {organism}: {sample info}" + ], + "examples": [ + { + "value": "Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:title" + ], "rank": 137, "slot_uri": "GENEPIO:0100323", "alias": "title", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", "range": "WhitespaceMinimizedString" }, @@ -10376,71 +13059,125 @@ "name": "library_strategy", "description": "See NCBI SRA template for details.", "title": "library_strategy", + "comments": [ + "Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select \"AMPLICON\"." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:library_strategy" + ], "rank": 138, "slot_uri": "GENEPIO:0100324", "alias": "library_strategy", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", - "range": "library_strategy menu" + "range": "LibraryStrategyMenu" }, "library_source": { "name": "library_source", "description": "See NCBI SRA template for details.", "title": "library_source", + "comments": [ + "Provide the library source by selecting a value from the pick list. For amplicon sequencing select \"Viral RNA\"." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:library_source" + ], "rank": 139, "slot_uri": "GENEPIO:0100325", "alias": "library_source", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", - "range": "library_source menu" + "range": "LibrarySourceMenu" }, "library_selection": { "name": "library_selection", "description": "See NCBI SRA template for details.", "title": "library_selection", + "comments": [ + "Provide the library selection by selecting a value from the pick list. For amplicon sequencing select \"PCR\"." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:library_selection" + ], "rank": 140, "slot_uri": "GENEPIO:0100326", "alias": "library_selection", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", - "range": "library_selection menu" + "range": "LibrarySelectionMenu" }, "library_layout": { "name": "library_layout", "description": "See NCBI SRA template for details.", "title": "library_layout", + "comments": [ + "Provide the library layout by selecting a value from the pick list. For Illumina instruments, select \"PAIRED\". For Oxford Nanopore instruments, select \"SINGLE\"." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:library_layout" + ], "rank": 141, "slot_uri": "GENEPIO:0100327", "alias": "library_layout", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", - "range": "library_layout menu" + "range": "LibraryLayoutMenu" }, "filetype": { "name": "filetype", "description": "See NCBI SRA template for details.", "title": "filetype", + "comments": [ + "Provide the filetype by selecting a value from the pick list." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:filetype" + ], "rank": 142, "slot_uri": "GENEPIO:0100328", "alias": "filetype", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", - "range": "filetype menu" + "range": "FiletypeMenu" }, "filename": { "name": "filename", "description": "See NCBI SRA template for details.", "title": "filename", + "comments": [ + "Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is \"paired\", provide the second filename under \"Filename 2\"." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:filename" + ], "rank": 143, "slot_uri": "GENEPIO:0100329", "alias": "filename", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", "range": "WhitespaceMinimizedString" }, @@ -10448,11 +13185,20 @@ "name": "filename2", "description": "See NCBI SRA template for details.", "title": "filename2", + "comments": [ + "Provide the appropriate filename recorded in the Bioinformatics and QC metrics section." + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "NCBI_SRA:filename2" + ], "rank": 144, "slot_uri": "GENEPIO:0100330", "alias": "filename2", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "NCBI SRA information", "range": "WhitespaceMinimizedString" }, @@ -10460,31 +13206,55 @@ "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Johnny Blogs" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", + "exact_mappings": [ + "GISAID:Authors" + ], "rank": 145, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Contributor acknowledgement", "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", - "description": "The DataHarmonizer software version provenance.", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", + "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, PHA4GE v1.0.0" + } + ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 146, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "alias": "dataharmonizer_provenance", "owner": "PHA4GE", + "domain_of": [ + "PHA4GE" + ], "slot_group": "Contributor acknowledgement", "range": "Provenance" } } } }, - "source_file": "schema.yaml", "settings": { "Title_Case": { "setting_key": "Title_Case", @@ -10500,4 +13270,4 @@ } }, "@type": "SchemaDefinition" -} +} \ No newline at end of file diff --git a/web/templates/pha4ge/schema.yaml b/web/templates/pha4ge/schema.yaml index c3978a04..1e63da20 100644 --- a/web/templates/pha4ge/schema.yaml +++ b/web/templates/pha4ge/schema.yaml @@ -3,7 +3,7 @@ name: PHA4GE description: '' version: 1.0.0 imports: - - linkml:types +- linkml:types prefixes: linkml: https://w3id.org/linkml/ GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ @@ -18,220 +18,220 @@ classes: is_a: dh_interface see_also: templates/pha4ge/SOP.pdf slots: - - specimen collector sample ID - - umbrella bioproject accession - - bioproject accession - - biosample accession - - SRA accession - - GenBank/ENA/DDBJ accession - - GISAID accession - - GISAID virus name - - host specimen voucher - - sample collected by - - sample collector contact email - - sample collector contact address - - sequence submitted by - - sequence submitter contact email - - sequence submitter contact address - - sample collection date - - sample received date - - geo_loc name (country) - - geo_loc name (state/province/territory) - - geo_loc name (county/region) - - geo_loc name (city) - - geo_loc latitude - - geo_loc longitude - - organism - - isolate - - culture collection - - purpose of sampling - - purpose of sampling details - - sample plan name - - sample collected in quarantine - - anatomical material - - anatomical part - - body product - - environmental material - - environmental site - - collection device - - collection method - - collection protocol - - specimen processing - - specimen processing details - - lab host - - passage number - - passage method - - biomaterial extracted - - data abstraction details - - host (common name) - - host (scientific name) - - host health state - - host health status details - - host disease - - host health outcome - - host age - - host age unit - - host age bin - - host gender - - host residence geo_loc name (country) - - host ethnicity - - host subject ID - - case ID - - symptom onset date - - signs and symptoms - - pre-existing conditions and risk factors - - complications - - host vaccination status - - number of vaccine doses received - - vaccination dose 1 vaccine name - - vaccination dose 1 vaccination date - - vaccination dose 2 vaccine name - - vaccination dose 2 vaccination date - - vaccination dose 3 vaccine name - - vaccination dose 3 vaccination date - - vaccination dose 4 vaccine name - - vaccination dose 4 vaccination date - - vaccination history - - location of exposure geo_loc name (country) - - destination of most recent travel (city) - - destination of most recent travel (state/province/territory) - - destination of most recent travel (country) - - most recent travel departure date - - most recent travel return date - - travel history - - exposure event - - exposure contact level - - host role - - exposure setting - - exposure details - - prior SARS-CoV-2 infection - - prior SARS-CoV-2 infection isolate - - prior SARS-CoV-2 infection date - - prior SARS-CoV-2 antiviral treatment - - prior SARS-CoV-2 antiviral treatment agent - - prior SARS-CoV-2 antiviral treatment date - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library ID - - amplicon size - - library preparation kit - - flow cell barcode - - sequencing instrument - - sequencing protocol name - - sequencing protocol - - sequencing kit number - - amplicon pcr primer scheme - - raw sequence data processing method - - dehosting method - - consensus sequence name - - consensus sequence filename - - consensus sequence filepath - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - r1 fastq filename - - r2 fastq filename - - r1 fastq filepath - - r2 fastq filepath - - fast5 filename - - fast5 filepath - - number of base pairs sequenced - - consensus genome length - - Ns per 100 kbp - - reference genome accession - - bioinformatics protocol - - lineage/clade name - - lineage/clade analysis software name - - lineage/clade analysis software version - - variant designation - - variant evidence details - - gene name 1 - - diagnostic pcr protocol 1 - - diagnostic pcr Ct value 1 - - gene name 2 - - diagnostic pcr protocol 2 - - diagnostic pcr Ct value 2 - - title - - library_strategy - - library_source - - library_selection - - library_layout - - filetype - - filename - - filename2 - - authors - - DataHarmonizer provenance + - specimen_collector_sample_id + - umbrella_bioproject_accession + - bioproject_accession + - biosample_accession + - sra_accession + - genbank_ena_ddbj_accession + - gisaid_accession + - gisaid_virus_name + - host_specimen_voucher + - sample_collected_by + - sample_collector_contact_email + - sample_collector_contact_address + - sequence_submitted_by + - sequence_submitter_contact_email + - sequence_submitter_contact_address + - sample_collection_date + - sample_received_date + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_county_region + - geo_loc_name_city + - geo_loc_latitude + - geo_loc_longitude + - organism + - isolate + - culture_collection + - purpose_of_sampling + - purpose_of_sampling_details + - sample_plan_name + - sample_collected_in_quarantine + - anatomical_material + - anatomical_part + - body_product + - environmental_material + - environmental_site + - collection_device + - collection_method + - collection_protocol + - specimen_processing + - specimen_processing_details + - lab_host + - passage_number + - passage_method + - biomaterial_extracted + - data_abstraction_details + - host_common_name + - host_scientific_name + - host_health_state + - host_health_status_details + - host_disease + - host_health_outcome + - host_age + - host_age_unit + - host_age_bin + - host_gender + - host_residence_geo_loc_name_country + - host_ethnicity + - host_subject_id + - case_id + - symptom_onset_date + - signs_and_symptoms + - preexisting_conditions_and_risk_factors + - complications + - host_vaccination_status + - number_of_vaccine_doses_received + - vaccination_dose_1_vaccine_name + - vaccination_dose_1_vaccination_date + - vaccination_dose_2_vaccine_name + - vaccination_dose_2_vaccination_date + - vaccination_dose_3_vaccine_name + - vaccination_dose_3_vaccination_date + - vaccination_dose_4_vaccine_name + - vaccination_dose_4_vaccination_date + - vaccination_history + - location_of_exposure_geo_loc_name_country + - destination_of_most_recent_travel_city + - destination_of_most_recent_travel_state_province_territory + - destination_of_most_recent_travel_country + - most_recent_travel_departure_date + - most_recent_travel_return_date + - travel_history + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - prior_sarscov2_infection + - prior_sarscov2_infection_isolate + - prior_sarscov2_infection_date + - prior_sarscov2_antiviral_treatment + - prior_sarscov2_antiviral_treatment_agent + - prior_sarscov2_antiviral_treatment_date + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_id + - amplicon_size + - library_preparation_kit + - flow_cell_barcode + - sequencing_instrument + - sequencing_protocol_name + - sequencing_protocol + - sequencing_kit_number + - amplicon_pcr_primer_scheme + - raw_sequence_data_processing_method + - dehosting_method + - consensus_sequence_name + - consensus_sequence_filename + - consensus_sequence_filepath + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - r1_fastq_filename + - r2_fastq_filename + - r1_fastq_filepath + - r2_fastq_filepath + - fast5_filename + - fast5_filepath + - number_of_base_pairs_sequenced + - consensus_genome_length + - ns_per_100_kbp + - reference_genome_accession + - bioinformatics_protocol + - lineage_clade_name + - lineage_clade_analysis_software_name + - lineage_clade_analysis_software_version + - variant_designation + - variant_evidence_details + - gene_name_1 + - diagnostic_pcr_protocol_1 + - diagnostic_pcr_ct_value_1 + - gene_name_2 + - diagnostic_pcr_protocol_2 + - diagnostic_pcr_ct_value_2 + - title + - library_strategy + - library_source + - library_selection + - library_layout + - filetype + - filename + - filename2 + - authors + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database Identifiers - umbrella bioproject accession: + umbrella_bioproject_accession: rank: 2 slot_group: Database Identifiers - bioproject accession: + bioproject_accession: rank: 3 slot_group: Database Identifiers - biosample accession: + biosample_accession: rank: 4 slot_group: Database Identifiers - SRA accession: + sra_accession: rank: 5 slot_group: Database Identifiers - GenBank/ENA/DDBJ accession: + genbank_ena_ddbj_accession: rank: 6 slot_group: Database Identifiers - GISAID accession: + gisaid_accession: rank: 7 slot_group: Database Identifiers - GISAID virus name: + gisaid_virus_name: rank: 8 slot_group: Database Identifiers - host specimen voucher: + host_specimen_voucher: rank: 9 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 10 slot_group: Sample collection and processing - sample collector contact email: + sample_collector_contact_email: rank: 11 slot_group: Sample collection and processing - sample collector contact address: + sample_collector_contact_address: rank: 12 slot_group: Sample collection and processing - sequence submitted by: + sequence_submitted_by: rank: 13 slot_group: Sample collection and processing - sequence submitter contact email: + sequence_submitter_contact_email: rank: 14 slot_group: Sample collection and processing - sequence submitter contact address: + sequence_submitter_contact_address: rank: 15 slot_group: Sample collection and processing - sample collection date: + sample_collection_date: rank: 16 slot_group: Sample collection and processing - sample received date: + sample_received_date: rank: 17 slot_group: Sample collection and processing - geo_loc name (country): + geo_loc_name_country: rank: 18 slot_group: Sample collection and processing - geo_loc name (state/province/territory): + geo_loc_name_state_province_territory: rank: 19 slot_group: Sample collection and processing - geo_loc name (county/region): + geo_loc_name_county_region: rank: 20 slot_group: Sample collection and processing - geo_loc name (city): + geo_loc_name_city: rank: 21 slot_group: Sample collection and processing - geo_loc latitude: + geo_loc_latitude: rank: 22 slot_group: Sample collection and processing - geo_loc longitude: + geo_loc_longitude: rank: 23 slot_group: Sample collection and processing organism: @@ -240,337 +240,337 @@ classes: isolate: rank: 25 slot_group: Sample collection and processing - culture collection: + culture_collection: rank: 26 slot_group: Sample collection and processing - purpose of sampling: + purpose_of_sampling: rank: 27 slot_group: Sample collection and processing - purpose of sampling details: + purpose_of_sampling_details: rank: 28 slot_group: Sample collection and processing - sample plan name: + sample_plan_name: rank: 29 slot_group: Sample collection and processing - sample collected in quarantine: + sample_collected_in_quarantine: rank: 30 slot_group: Sample collection and processing - anatomical material: + anatomical_material: rank: 31 slot_group: Sample collection and processing - anatomical part: + anatomical_part: rank: 32 slot_group: Sample collection and processing - body product: + body_product: rank: 33 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 34 slot_group: Sample collection and processing - environmental site: + environmental_site: rank: 35 slot_group: Sample collection and processing - collection device: + collection_device: rank: 36 slot_group: Sample collection and processing - collection method: + collection_method: rank: 37 slot_group: Sample collection and processing - collection protocol: + collection_protocol: rank: 38 slot_group: Sample collection and processing - specimen processing: + specimen_processing: rank: 39 slot_group: Sample collection and processing - specimen processing details: + specimen_processing_details: rank: 40 slot_group: Sample collection and processing - lab host: + lab_host: rank: 41 slot_group: Sample collection and processing - passage number: + passage_number: rank: 42 slot_group: Sample collection and processing - passage method: + passage_method: rank: 43 slot_group: Sample collection and processing - biomaterial extracted: + biomaterial_extracted: rank: 44 slot_group: Sample collection and processing - data abstraction details: + data_abstraction_details: rank: 45 slot_group: Sample collection and processing - host (common name): + host_common_name: rank: 46 slot_group: Host Information - host (scientific name): + host_scientific_name: rank: 47 slot_group: Host Information - host health state: + host_health_state: rank: 48 slot_group: Host Information - host health status details: + host_health_status_details: rank: 49 slot_group: Host Information - host disease: + host_disease: rank: 50 slot_group: Host Information - host health outcome: + host_health_outcome: rank: 51 slot_group: Host Information - host age: + host_age: rank: 52 slot_group: Host Information - host age unit: + host_age_unit: rank: 53 slot_group: Host Information - host age bin: + host_age_bin: rank: 54 slot_group: Host Information - host gender: + host_gender: rank: 55 slot_group: Host Information - host residence geo_loc name (country): + host_residence_geo_loc_name_country: rank: 56 slot_group: Host Information - host ethnicity: + host_ethnicity: rank: 57 slot_group: Host Information - host subject ID: + host_subject_id: rank: 58 slot_group: Host Information - case ID: + case_id: rank: 59 slot_group: Host Information - symptom onset date: + symptom_onset_date: rank: 60 slot_group: Host Information - signs and symptoms: + signs_and_symptoms: rank: 61 slot_group: Host Information - pre-existing conditions and risk factors: + preexisting_conditions_and_risk_factors: rank: 62 slot_group: Host Information complications: rank: 63 slot_group: Host Information - host vaccination status: + host_vaccination_status: rank: 64 slot_group: Host vaccination information - number of vaccine doses received: + number_of_vaccine_doses_received: rank: 65 slot_group: Host vaccination information - vaccination dose 1 vaccine name: + vaccination_dose_1_vaccine_name: rank: 66 slot_group: Host vaccination information - vaccination dose 1 vaccination date: + vaccination_dose_1_vaccination_date: rank: 67 slot_group: Host vaccination information - vaccination dose 2 vaccine name: + vaccination_dose_2_vaccine_name: rank: 68 slot_group: Host vaccination information - vaccination dose 2 vaccination date: + vaccination_dose_2_vaccination_date: rank: 69 slot_group: Host vaccination information - vaccination dose 3 vaccine name: + vaccination_dose_3_vaccine_name: rank: 70 slot_group: Host vaccination information - vaccination dose 3 vaccination date: + vaccination_dose_3_vaccination_date: rank: 71 slot_group: Host vaccination information - vaccination dose 4 vaccine name: + vaccination_dose_4_vaccine_name: rank: 72 slot_group: Host vaccination information - vaccination dose 4 vaccination date: + vaccination_dose_4_vaccination_date: rank: 73 slot_group: Host vaccination information - vaccination history: + vaccination_history: rank: 74 slot_group: Host vaccination information - location of exposure geo_loc name (country): + location_of_exposure_geo_loc_name_country: rank: 75 slot_group: Host exposure information - destination of most recent travel (city): + destination_of_most_recent_travel_city: rank: 76 slot_group: Host exposure information - destination of most recent travel (state/province/territory): + destination_of_most_recent_travel_state_province_territory: rank: 77 slot_group: Host exposure information - destination of most recent travel (country): + destination_of_most_recent_travel_country: rank: 78 slot_group: Host exposure information - most recent travel departure date: + most_recent_travel_departure_date: rank: 79 slot_group: Host exposure information - most recent travel return date: + most_recent_travel_return_date: rank: 80 slot_group: Host exposure information - travel history: + travel_history: rank: 81 slot_group: Host exposure information - exposure event: + exposure_event: rank: 82 slot_group: Host exposure information - exposure contact level: + exposure_contact_level: rank: 83 slot_group: Host exposure information - host role: + host_role: rank: 84 slot_group: Host exposure information - exposure setting: + exposure_setting: rank: 85 slot_group: Host exposure information - exposure details: + exposure_details: rank: 86 slot_group: Host exposure information - prior SARS-CoV-2 infection: + prior_sarscov2_infection: rank: 87 slot_group: Host reinfection information - prior SARS-CoV-2 infection isolate: + prior_sarscov2_infection_isolate: rank: 88 slot_group: Host reinfection information - prior SARS-CoV-2 infection date: + prior_sarscov2_infection_date: rank: 89 slot_group: Host reinfection information - prior SARS-CoV-2 antiviral treatment: + prior_sarscov2_antiviral_treatment: rank: 90 slot_group: Host reinfection information - prior SARS-CoV-2 antiviral treatment agent: + prior_sarscov2_antiviral_treatment_agent: rank: 91 slot_group: Host reinfection information - prior SARS-CoV-2 antiviral treatment date: + prior_sarscov2_antiviral_treatment_date: rank: 92 slot_group: Host reinfection information - purpose of sequencing: + purpose_of_sequencing: rank: 93 slot_group: Sequencing - purpose of sequencing details: + purpose_of_sequencing_details: rank: 94 slot_group: Sequencing - sequencing date: + sequencing_date: rank: 95 slot_group: Sequencing - library ID: + library_id: rank: 96 slot_group: Sequencing - amplicon size: + amplicon_size: rank: 97 slot_group: Sequencing - library preparation kit: + library_preparation_kit: rank: 98 slot_group: Sequencing - flow cell barcode: + flow_cell_barcode: rank: 99 slot_group: Sequencing - sequencing instrument: + sequencing_instrument: rank: 100 slot_group: Sequencing - sequencing protocol name: + sequencing_protocol_name: rank: 101 slot_group: Sequencing - sequencing protocol: + sequencing_protocol: rank: 102 slot_group: Sequencing - sequencing kit number: + sequencing_kit_number: rank: 103 slot_group: Sequencing - amplicon pcr primer scheme: + amplicon_pcr_primer_scheme: rank: 104 slot_group: Sequencing - raw sequence data processing method: + raw_sequence_data_processing_method: rank: 105 slot_group: Bioinformatics and QC metrics - dehosting method: + dehosting_method: rank: 106 slot_group: Bioinformatics and QC metrics - consensus sequence name: + consensus_sequence_name: rank: 107 slot_group: Bioinformatics and QC metrics - consensus sequence filename: + consensus_sequence_filename: rank: 108 slot_group: Bioinformatics and QC metrics - consensus sequence filepath: + consensus_sequence_filepath: rank: 109 slot_group: Bioinformatics and QC metrics - consensus sequence software name: + consensus_sequence_software_name: rank: 110 slot_group: Bioinformatics and QC metrics - consensus sequence software version: + consensus_sequence_software_version: rank: 111 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + breadth_of_coverage_value: rank: 112 slot_group: Bioinformatics and QC metrics - depth of coverage value: + depth_of_coverage_value: rank: 113 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + depth_of_coverage_threshold: rank: 114 slot_group: Bioinformatics and QC metrics - r1 fastq filename: + r1_fastq_filename: rank: 115 slot_group: Bioinformatics and QC metrics - r2 fastq filename: + r2_fastq_filename: rank: 116 slot_group: Bioinformatics and QC metrics - r1 fastq filepath: + r1_fastq_filepath: rank: 117 slot_group: Bioinformatics and QC metrics - r2 fastq filepath: + r2_fastq_filepath: rank: 118 slot_group: Bioinformatics and QC metrics - fast5 filename: + fast5_filename: rank: 119 slot_group: Bioinformatics and QC metrics - fast5 filepath: + fast5_filepath: rank: 120 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + number_of_base_pairs_sequenced: rank: 121 slot_group: Bioinformatics and QC metrics - consensus genome length: + consensus_genome_length: rank: 122 slot_group: Bioinformatics and QC metrics - Ns per 100 kbp: + ns_per_100_kbp: rank: 123 slot_group: Bioinformatics and QC metrics - reference genome accession: + reference_genome_accession: rank: 124 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + bioinformatics_protocol: rank: 125 slot_group: Bioinformatics and QC metrics - lineage/clade name: + lineage_clade_name: rank: 126 slot_group: Lineage and Variant information - lineage/clade analysis software name: + lineage_clade_analysis_software_name: rank: 127 slot_group: Lineage and Variant information - lineage/clade analysis software version: + lineage_clade_analysis_software_version: rank: 128 slot_group: Lineage and Variant information - variant designation: + variant_designation: rank: 129 slot_group: Lineage and Variant information - variant evidence details: + variant_evidence_details: rank: 130 slot_group: Lineage and Variant information - gene name 1: + gene_name_1: rank: 131 slot_group: Pathogen diagnostic testing - diagnostic pcr protocol 1: + diagnostic_pcr_protocol_1: rank: 132 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 1: + diagnostic_pcr_ct_value_1: rank: 133 slot_group: Pathogen diagnostic testing - gene name 2: + gene_name_2: rank: 134 slot_group: Pathogen diagnostic testing - diagnostic pcr protocol 2: + diagnostic_pcr_protocol_2: rank: 135 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 2: + diagnostic_pcr_ct_value_2: rank: 136 slot_group: Pathogen diagnostic testing title: @@ -600,81 +600,73 @@ classes: authors: rank: 145 slot_group: Contributor acknowledgement - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 146 slot_group: Contributor acknowledgement slots: - specimen collector sample ID: - name: specimen collector sample ID + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. - comments: - Every Sample ID from a single submitter must be unique. It can have + comments: Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. - examples: - - value: prov_rona_99 slot_uri: GENEPIO:0001123 range: WhitespaceMinimizedString required: true + examples: + - value: prov_rona_99 exact_mappings: - - GISAID:Sample ID given by the sample provider - - GISAID:Sample ID given by the submitting laboratory - - NCBI_BIOSAMPLE:sample_name - - NCBI_SRA:sample_name - - NCBI_Genbank:sample_name - - NCBI_Genbank_source_modifiers:Sequence_ID - umbrella bioproject accession: - name: umbrella bioproject accession + - GISAID:Sample%20ID%20given%20by%20the%20sample%20provider + - GISAID:Sample%20ID%20given%20by%20the%20submitting%20laboratory + - NCBI_BIOSAMPLE:sample_name + - NCBI_SRA:sample_name + - NCBI_Genbank:sample_name + - NCBI_Genbank_source_modifiers:Sequence_ID + umbrella_bioproject_accession: + name: umbrella_bioproject_accession title: umbrella bioproject accession - description: - The INSDC umbrella accession number of the BioProject to which the + description: The INSDC umbrella accession number of the BioProject to which the BioSample belongs. - comments: - Required if submission is linked to an umbrella BioProject. An umbrella + comments: Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects. - examples: - - value: PRJNA623807 slot_uri: GENEPIO:0001133 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true - bioproject accession: - name: bioproject accession + examples: + - value: PRJNA623807 + bioproject_accession: + name: bioproject_accession title: bioproject accession - description: - The INSDC accession number of the BioProject(s) to which the BioSample + description: The INSDC accession number of the BioProject(s) to which the BioSample belongs. - comments: - Required if submission is linked to a BioProject. BioProjects are an + comments: Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. - examples: - - value: PRJNA12345 slot_uri: GENEPIO:0001136 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: PRJNA12345 exact_mappings: - - NCBI_BIOSAMPLE:bioproject_accession - - NCBI_SRA:bioproject_accession - - NCBI_Genbank_source_modifiers:BioProject - biosample accession: - name: biosample accession + - NCBI_BIOSAMPLE:bioproject_accession + - NCBI_SRA:bioproject_accession + - NCBI_Genbank_source_modifiers:BioProject + biosample_accession: + name: biosample_accession title: biosample accession description: The identifier assigned to a BioSample in INSDC archives. - comments: - Store the accession returned from the BioSample submission. NCBI BioSamples + comments: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. - examples: - - value: SAMN14180202 slot_uri: GENEPIO:0001139 range: WhitespaceMinimizedString recommended: true @@ -682,82 +674,79 @@ slots: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: SAMN14180202 exact_mappings: - - NCBI_SRA:biosample_accession - - NCBI_Genbank:biosample_accession - - NCBI_Genbank_source_modifiers:BioSample - SRA accession: - name: SRA accession + - NCBI_SRA:biosample_accession + - NCBI_Genbank:biosample_accession + - NCBI_Genbank_source_modifiers:BioSample + sra_accession: + name: sra_accession title: SRA accession - description: - The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) + description: The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. - comments: - Store the accession assigned to the submitted "run". NCBI-SRA accessions + comments: Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. - examples: - - value: SRR11177792 slot_uri: GENEPIO:0001142 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true - GenBank/ENA/DDBJ accession: - name: GenBank/ENA/DDBJ accession + examples: + - value: SRR11177792 + genbank_ena_ddbj_accession: + name: genbank_ena_ddbj_accession title: GenBank/ENA/DDBJ accession - description: - The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC + description: The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. - comments: - Store the accession returned from a GenBank/ENA/DDBJ submission (viral + comments: Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly). - examples: - - value: MN908947.3 slot_uri: GENEPIO:0001145 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true - GISAID accession: - name: GISAID accession + examples: + - value: MN908947.3 + gisaid_accession: + name: gisaid_accession title: GISAID accession description: The GISAID accession number assigned to the sequence. comments: Store the accession returned from the GISAID submission. - examples: - - value: EPI_ISL_123456 slot_uri: GENEPIO:0001147 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: EPI_ISL_123456 exact_mappings: - - NCBI_BIOSAMPLE:gisaid_accession - GISAID virus name: - name: GISAID virus name + - NCBI_BIOSAMPLE:gisaid_accession + gisaid_virus_name: + name: gisaid_virus_name title: GISAID virus name description: The user-defined GISAID virus name assigned to the sequence. comments: GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". - examples: - - value: hCoV-19/Canada/prov_rona_99/2020 slot_uri: GENEPIO:0100282 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: hCoV-19/Canada/prov_rona_99/2020 exact_mappings: - - GISAID:Virus name - - NCBI_BIOSAMPLE:gisaid_virus_name - host specimen voucher: - name: host specimen voucher + - GISAID:Virus%20name + - NCBI_BIOSAMPLE:gisaid_virus_name + host_specimen_voucher: + name: host_specimen_voucher title: host specimen voucher description: Identifier for the physical specimen. - comments: - 'Include a URI (Uniform Resource Identifier) in the form of a URL providing + comments: 'Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided @@ -765,108 +754,100 @@ slots: is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher="[:[:]]"): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier' - examples: - - value: - 'URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, - INSDC triplet example: UAM:Mamm:52179' slot_uri: GENEPIO:0100283 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: 'URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, + INSDC triplet example: UAM:Mamm:52179' exact_mappings: - - NCBI_BIOSAMPLE:host_specimen_voucher - sample collected by: - name: sample collected by + - NCBI_BIOSAMPLE:host_specimen_voucher + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the organization with which the sample collector is affiliated. - comments: - The name of the agency should be written out in full, (with minor exceptions) + comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. - examples: - - value: Public Health Agency of Canada slot_uri: GENEPIO:0001153 any_of: - - range: WhitespaceMinimizedString - - range: null value menu + - range: WhitespaceMinimizedString + - range: NullValueMenu required: true + examples: + - value: Public Health Agency of Canada exact_mappings: - - GISAID:Originating lab - - NCBI_BIOSAMPLE:collected_by - sample collector contact email: - name: sample collector contact email + - GISAID:Originating%20lab + - NCBI_BIOSAMPLE:collected_by + sample_collector_contact_email: + name: sample_collector_contact_email title: sample collector contact email - description: - The email address of the contact responsible for follow-up regarding + description: The email address of the contact responsible for follow-up regarding the sample. comments: The email address can represent a specific individual or laboratory. - examples: - - value: johnnyblogs@lab.ca slot_uri: GENEPIO:0001156 range: WhitespaceMinimizedString - sample collector contact address: - name: sample collector contact address + examples: + - value: johnnyblogs@lab.ca + sample_collector_contact_address: + name: sample_collector_contact_address title: sample collector contact address description: The mailing address of the agency submitting the sample. - comments: - 'The mailing address should be in the format: Street number and name, + comments: 'The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code' - examples: - - value: 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada slot_uri: GENEPIO:0001158 range: WhitespaceMinimizedString + examples: + - value: 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada exact_mappings: - - GISAID:Address - sequence submitted by: - name: sequence submitted by + - GISAID:Address + sequence_submitted_by: + name: sequence_submitted_by title: sequence submitted by description: The name of the agency that generated the sequence. - comments: - The name of the agency should be written out in full, (with minor exceptions) + comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. - examples: - - value: Centers for Disease Control and Prevention slot_uri: GENEPIO:0001159 any_of: - - range: WhitespaceMinimizedString - - range: null value menu + - range: WhitespaceMinimizedString + - range: NullValueMenu required: true + examples: + - value: Centers for Disease Control and Prevention exact_mappings: - - GISAID:Submitting lab - - NCBI_BIOSAMPLE:sequenced_by - sequence submitter contact email: - name: sequence submitter contact email + - GISAID:Submitting%20lab + - NCBI_BIOSAMPLE:sequenced_by + sequence_submitter_contact_email: + name: sequence_submitter_contact_email title: sequence submitter contact email - description: - The email address of the contact responsible for follow-up regarding + description: The email address of the contact responsible for follow-up regarding the sequence. comments: The email address can represent a specific individual or laboratory. - examples: - - value: RespLab@lab.ca slot_uri: GENEPIO:0001165 range: WhitespaceMinimizedString + examples: + - value: RespLab@lab.ca exact_mappings: - - NCBI_SRA:sequence_submitter_contact_email - sequence submitter contact address: - name: sequence submitter contact address + - NCBI_SRA:sequence_submitter_contact_email + sequence_submitter_contact_address: + name: sequence_submitter_contact_address title: sequence submitter contact address description: The mailing address of the agency submitting the sequence. - comments: - 'The mailing address should be in the format: Street number and name, + comments: 'The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code' - examples: - - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada slot_uri: GENEPIO:0001167 range: WhitespaceMinimizedString + examples: + - value: 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada exact_mappings: - - GISAID:Address - sample collection date: - name: sample collection date + - GISAID:Address + sample_collection_date: + name: sample_collection_date title: sample collection date description: The date on which the sample was collected. - comments: - "Record the collection date accurately in the template. Required granularity\ + comments: "Record the collection date accurately in the template. Required granularity\ \ includes year, month and day. Before sharing this data, ensure this date is\ \ not considered identifiable information. If this date is considered identifiable,\ \ it is acceptable to add \"jitter\" to the collection date by adding or subtracting\ @@ -874,714 +855,669 @@ slots: \ Alternatively, \u201Dreceived date\u201D may be used as a substitute in the\ \ data you share. The date should be provided in ISO 8601 standard format \"\ YYYY-MM-DD\"." - examples: - - value: '2020-03-19' slot_uri: GENEPIO:0001174 any_of: - - range: date - - range: null value menu + - range: date + - range: NullValueMenu required: true + examples: + - value: '2020-03-19' exact_mappings: - - GISAID:Collection date - - NCBI_BIOSAMPLE:collection_date - - NCBI_Genbank_source_modifiers:collection-date - sample received date: - name: sample received date + - GISAID:Collection%20date + - NCBI_BIOSAMPLE:collection_date + - NCBI_Genbank_source_modifiers:collection-date + sample_received_date: + name: sample_received_date title: sample received date description: The date on which the sample was received. - comments: - The date the sample was received by a lab that was not the point of + comments: The date the sample was received by a lab that was not the point of collection. ISO 8601 standard "YYYY-MM-DD". - examples: - - value: '2020-03-20' slot_uri: GENEPIO:0001179 any_of: - - range: date - - range: null value menu - geo_loc name (country): - name: geo_loc name (country) + - range: date + - range: NullValueMenu + examples: + - value: '2020-03-20' + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc name (country) description: The country of origin of the sample. comments: Provide the country name from the pick list in the template - examples: - - value: South Africa [GAZ:00001094] slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true + examples: + - value: South Africa [GAZ:00001094] exact_mappings: - - GISAID:Location - - NCBI_BIOSAMPLE:geo_loc_name - - NCBI_Genbank_source_modifiers:country - geo_loc name (state/province/territory): - name: geo_loc name (state/province/territory) + - GISAID:Location + - NCBI_BIOSAMPLE:geo_loc_name + - NCBI_Genbank_source_modifiers:country + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo_loc name (state/province/territory) description: The state/province/territory of origin of the sample. - comments: - 'Provide the state/province/territory name from the GAZ geography ontology. + comments: 'Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: Western Cape slot_uri: GENEPIO:0001185 any_of: - - range: WhitespaceMinimizedString - - range: null value menu + - range: WhitespaceMinimizedString + - range: NullValueMenu required: true + examples: + - value: Western Cape exact_mappings: - - NCBI_BIOSAMPLE:geo_loc_name - geo_loc name (county/region): - name: geo_loc name (county/region) + - NCBI_BIOSAMPLE:geo_loc_name + geo_loc_name_county_region: + name: geo_loc_name_county_region title: geo_loc name (county/region) description: The county/region of origin of the sample. - comments: - 'Provide the county/region name from the GAZ geography ontology. Search + comments: 'Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: Derbyshire slot_uri: GENEPIO:0100280 range: WhitespaceMinimizedString + examples: + - value: Derbyshire exact_mappings: - - NCBI_BIOSAMPLE:geo_loc_name - geo_loc name (city): - name: geo_loc name (city) + - NCBI_BIOSAMPLE:geo_loc_name + geo_loc_name_city: + name: geo_loc_name_city title: geo_loc name (city) description: The city of origin of the sample. - comments: - 'Provide the city name from the GAZ geography ontology. Search for geography + comments: 'Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: Vancouver slot_uri: GENEPIO:0001189 range: WhitespaceMinimizedString + examples: + - value: Vancouver exact_mappings: - - NCBI_BIOSAMPLE:geo_loc_name - geo_loc latitude: - name: geo_loc latitude + - NCBI_BIOSAMPLE:geo_loc_name + geo_loc_latitude: + name: geo_loc_latitude title: geo_loc latitude description: The latitude coordinates of the geographical location of sample collection. - comments: - Provide latitude coordinates if available. Do not use the centre of + comments: Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". - examples: - - value: 38.98 N slot_uri: GENEPIO:0100309 range: WhitespaceMinimizedString + examples: + - value: 38.98 N exact_mappings: - - NCBI_BIOSAMPLE:lat_lon - geo_loc longitude: - name: geo_loc longitude + - NCBI_BIOSAMPLE:lat_lon + geo_loc_longitude: + name: geo_loc_longitude title: geo_loc longitude - description: - The longitude coordinates of the geographical location of sample + description: The longitude coordinates of the geographical location of sample collection. - comments: - Provide longitude coordinates if available. Do not use the centre of + comments: Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". - examples: - - value: 77.11 W slot_uri: GENEPIO:0100310 range: WhitespaceMinimizedString + examples: + - value: 77.11 W exact_mappings: - - NCBI_BIOSAMPLE:lat_lon + - NCBI_BIOSAMPLE:lat_lon organism: name: organism title: organism description: Taxonomic name of the organism. - comments: - Select "Severe acute respiratory syndrome coronavirus 2" if sequencing + comments: Select "Severe acute respiratory syndrome coronavirus 2" if sequencing SARS-CoV-2. If another Coronaviridae is being sequenced, provide the taxonomic name from NCBITaxon. Search for taxonomy terms at https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. - examples: - - value: Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] slot_uri: GENEPIO:0001191 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu required: true + examples: + - value: Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] exact_mappings: - - NCBI_BIOSAMPLE:organism + - NCBI_BIOSAMPLE:organism isolate: name: isolate title: isolate description: Identifier of the specific isolate. - comments: - 'This identifier should be an unique, indexed, alpha-numeric ID within + comments: 'This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date".' - examples: - - value: SARS-CoV-2/human/USA/CA-CDPH-001/2020 slot_uri: GENEPIO:0001644 any_of: - - range: WhitespaceMinimizedString - - range: null value menu + - range: WhitespaceMinimizedString + - range: NullValueMenu required: true + examples: + - value: SARS-CoV-2/human/USA/CA-CDPH-001/2020 exact_mappings: - - NCBI_BIOSAMPLE:isolate - - NCBI_Genbank_source_modifiers:isolate - culture collection: - name: culture collection + - NCBI_BIOSAMPLE:isolate + - NCBI_Genbank_source_modifiers:isolate + culture_collection: + name: culture_collection title: culture collection description: The name of the source collection and unique culture identifier. - comments: - 'Format: ":[:]". For + comments: 'Format: ":[:]". For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier.' - examples: - - value: /culture_collection="ATCC:26370" slot_uri: GENEPIO:0100284 range: WhitespaceMinimizedString - purpose of sampling: - name: purpose of sampling + examples: + - value: /culture_collection="ATCC:26370" + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: Select a value from the pick list in the template. - examples: - - value: Diagnostic testing [GENEPIO:0100002] slot_uri: GENEPIO:0001198 any_of: - - range: purpose of sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu recommended: true + examples: + - value: Diagnostic testing [GENEPIO:0100002] exact_mappings: - - NCBI_BIOSAMPLE:purpose_of_sampling - purpose of sampling details: - name: purpose of sampling details + - NCBI_BIOSAMPLE:purpose_of_sampling + purpose_of_sampling_details: + name: purpose_of_sampling_details title: purpose of sampling details description: Further details pertaining to the reason the sample was collected. - comments: - Provide a free text description of the sampling strategy or samples + comments: Provide a free text description of the sampling strategy or samples collected. - examples: - - value: Screening of bat specimens in museum collections. slot_uri: GENEPIO:0001200 range: WhitespaceMinimizedString - sample plan name: - name: sample plan name + examples: + - value: Screening of bat specimens in museum collections. + sample_plan_name: + name: sample_plan_name title: sample plan name description: The name of the sample plan implemented for sample collection. - comments: - Provide the name and version of the sample plan outlining the sample + comments: Provide the name and version of the sample plan outlining the sample strategy. - examples: - - value: CanCOGeN Sampling Strategy 1.0 slot_uri: GENEPIO:0100285 range: WhitespaceMinimizedString - sample collected in quarantine: - name: sample collected in quarantine + examples: + - value: CanCOGeN Sampling Strategy 1.0 + sample_collected_in_quarantine: + name: sample_collected_in_quarantine title: sample collected in quarantine description: Whether the sample was collected from an individual in quarantine. - comments: - Whether a sample was collected under quarantine conditions (e.g. self-quarantining, + comments: Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. - examples: - - value: Yes [NCIT:C49488] slot_uri: GENEPIO:0100277 any_of: - - range: sample collected in quarantine menu - - range: null value menu - anatomical material: - name: anatomical material + - range: SampleCollectedInQuarantineMenu + - range: NullValueMenu + examples: + - value: Yes [NCIT:C49488] + anatomical_material: + name: anatomical_material title: anatomical material - description: - A substance obtained from an anatomical part of an organism e.g. + description: A substance obtained from an anatomical part of an organism e.g. tissue, blood. - comments: - 'Provide a descriptor if an anatomical material was sampled. Use the + comments: 'Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.' - examples: - - value: Blood [UBERON:0000178] slot_uri: GENEPIO:0001211 any_of: - - range: anatomical material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true + examples: + - value: Blood [UBERON:0000178] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:host_anatomical_material - - NCBI_Genbank_source_modifiers:isolation-source - anatomical part: - name: anatomical part + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:host_anatomical_material + - NCBI_Genbank_source_modifiers:isolation-source + anatomical_part: + name: anatomical_part title: anatomical part description: An anatomical part of an organism e.g. oropharynx. - comments: - 'Provide a descriptor if an anatomical part was sampled. Use the pick + comments: 'Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.' - examples: - - value: Nasopharynx (NP) [UBERON:0001728] slot_uri: GENEPIO:0001214 any_of: - - range: anatomical part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true + examples: + - value: Nasopharynx (NP) [UBERON:0001728] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:host_anatomical_part - - NCBI_Genbank_source_modifiers:isolation-source - body product: - name: body product + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:host_anatomical_part + - NCBI_Genbank_source_modifiers:isolation-source + body_product: + name: body_product title: body product - description: - A substance excreted/secreted from an organism e.g. feces, urine, + description: A substance excreted/secreted from an organism e.g. feces, urine, sweat. - comments: - 'Provide a descriptor if a body product was sampled. Use the pick list + comments: 'Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.' - examples: - - value: Feces [UBERON:0001988] slot_uri: GENEPIO:0001216 any_of: - - range: body product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true + examples: + - value: Feces [UBERON:0001988] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:host_body_product - - NCBI_Genbank_source_modifiers:isolation-source - environmental material: - name: environmental material + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:host_body_product + - NCBI_Genbank_source_modifiers:isolation-source + environmental_material: + name: environmental_material title: environmental material - description: - A substance obtained from the natural or man-made environment e.g. + description: A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. - comments: - 'Provide a descriptor if an environmental material was sampled. Use + comments: 'Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.' - examples: - - value: Face mask [OBI:0002787] slot_uri: GENEPIO:0001223 any_of: - - range: environmental material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true + examples: + - value: Face mask [OBI:0002787] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:environmental_material - - NCBI_Genbank_source_modifiers:isolation-source - environmental site: - name: environmental site + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:environmental_material + - NCBI_Genbank_source_modifiers:isolation-source + environmental_site: + name: environmental_site title: environmental site - description: - An environmental location may describe a site in the natural or built + description: An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. - comments: - 'Provide a descriptor if an environmental site was sampled. Use the + comments: 'Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.' - examples: - - value: Hospital [ENVO:00002173] slot_uri: GENEPIO:0001232 any_of: - - range: environmental site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true + examples: + - value: Hospital [ENVO:00002173] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:environmental_site - - NCBI_Genbank_source_modifiers:isolation-source - collection device: - name: collection device + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:environmental_site + - NCBI_Genbank_source_modifiers:isolation-source + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. swab. - comments: - 'Provide a descriptor if a collection device was used for sampling. + comments: 'Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.' - examples: - - value: Swab [GENEPIO:0100027] slot_uri: GENEPIO:0001234 any_of: - - range: collection device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu multivalued: true + examples: + - value: Swab [GENEPIO:0100027] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:collection_device - - NCBI_Genbank_source_modifiers:isolation-source - collection method: - name: collection method + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:collection_device + - NCBI_Genbank_source_modifiers:isolation-source + collection_method: + name: collection_method title: collection method description: The process used to collect the sample e.g. phlebotomy, necropsy. - comments: - 'Provide a descriptor if a collection method was used for sampling. + comments: 'Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.' - examples: - - value: Bronchoalveolar lavage (BAL) [GENEPIO:0100032] slot_uri: GENEPIO:0001241 any_of: - - range: collection method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu multivalued: true + examples: + - value: Bronchoalveolar lavage (BAL) [GENEPIO:0100032] exact_mappings: - - GISAID:Specimen source - - NCBI_BIOSAMPLE:isolation_source - - NCBI_BIOSAMPLE:collection_method - - NCBI_Genbank_source_modifiers:isolation-source - collection protocol: - name: collection protocol + - GISAID:Specimen%20source + - NCBI_BIOSAMPLE:isolation_source + - NCBI_BIOSAMPLE:collection_method + - NCBI_Genbank_source_modifiers:isolation-source + collection_protocol: + name: collection_protocol title: collection protocol description: The name and version of a particular protocol used for sampling. comments: Provide the name and version of the protocol used to collect the samples. - examples: - - value: SC2SamplingProtocol 1.2 slot_uri: GENEPIO:0001243 range: WhitespaceMinimizedString - specimen processing: - name: specimen processing + examples: + - value: SC2SamplingProtocol 1.2 + specimen_processing: + name: specimen_processing title: specimen processing - description: - Any processing applied to the sample during or after receiving the + description: Any processing applied to the sample during or after receiving the sample. - comments: - Critical for interpreting data. Select all the applicable processes + comments: Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". - examples: - - value: Virus passage [GENEPIO:0100039] slot_uri: GENEPIO:0001253 any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true recommended: true - specimen processing details: - name: specimen processing details + examples: + - value: Virus passage [GENEPIO:0100039] + specimen_processing_details: + name: specimen_processing_details title: specimen processing details - description: - Detailed information regarding the processing applied to a sample + description: Detailed information regarding the processing applied to a sample during or after receiving the sample. - comments: - Provide a free text description of any processing details applied to + comments: Provide a free text description of any processing details applied to a sample. - examples: - - value: - 25 swabs were pooled and further prepared as a single sample during library - prep. slot_uri: GENEPIO:0100311 range: WhitespaceMinimizedString - lab host: - name: lab host + examples: + - value: 25 swabs were pooled and further prepared as a single sample during library + prep. + lab_host: + name: lab_host title: lab host - description: - Name and description of the laboratory host used to propagate the + description: Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. - comments: - Type of cell line used for propagation. Select a value form the pick + comments: Type of cell line used for propagation. Select a value form the pick list. If not passaged, put "not applicable". - examples: - - value: Vero E6 cell line [BTO:0004755] slot_uri: GENEPIO:0001255 any_of: - - range: lab host menu - - range: null value menu - passage number: - name: passage number + - range: LabHostMenu + - range: NullValueMenu + examples: + - value: Vero E6 cell line [BTO:0004755] + passage_number: + name: passage_number title: passage number description: Number of passages. comments: Provide number of known passages. If not passaged, put "not applicable" - examples: - - value: '3' slot_uri: GENEPIO:0001261 range: integer - minimum_value: '0' + minimum_value: 0 + examples: + - value: '3' exact_mappings: - - NCBI_BIOSAMPLE:passage_number - passage method: - name: passage method + - NCBI_BIOSAMPLE:passage_number + passage_method: + name: passage_method title: passage method description: Description of how organism was passaged. comments: Free text. Provide a short description. If not passaged, put "not applicable". - examples: - - value: - AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in - Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the - SP-2/reference lab strain. slot_uri: GENEPIO:0001264 any_of: - - range: WhitespaceMinimizedString - - range: null value menu + - range: WhitespaceMinimizedString + - range: NullValueMenu + examples: + - value: AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in + Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the + SP-2/reference lab strain. exact_mappings: - - NCBI_BIOSAMPLE:passage_method - biomaterial extracted: - name: biomaterial extracted + - NCBI_BIOSAMPLE:passage_method + biomaterial_extracted: + name: biomaterial_extracted title: biomaterial extracted description: The biomaterial extracted from samples for the purpose of sequencing. comments: Provide the biomaterial extracted from the pick list in the template. - examples: - - value: RNA (Total) [OBI:0000895] slot_uri: GENEPIO:0001266 any_of: - - range: biomaterial extracted menu - - range: null value menu - data abstraction details: - name: data abstraction details + - range: BiomaterialExtractedMenu + - range: NullValueMenu + examples: + - value: RNA (Total) [OBI:0000895] + data_abstraction_details: + name: data_abstraction_details title: data abstraction details - description: - A description of how any data elements were altered to preserve patient + description: A description of how any data elements were altered to preserve patient privacy. comments: If applicable, provide a description of how each data element was abstracted. - examples: - - value: Jitter added to publicly shared collection dates to prevent re-identifiability. slot_uri: GENEPIO:0100278 range: WhitespaceMinimizedString - host (common name): - name: host (common name) + examples: + - value: Jitter added to publicly shared collection dates to prevent re-identifiability. + host_common_name: + name: host_common_name title: host (common name) description: The commonly used name of the host. - comments: - Common name or scientific name are required if there was a host. Common + comments: Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put "not applicable". - examples: - - value: Human [NCBITaxon:9606] slot_uri: GENEPIO:0001386 any_of: - - range: host (common name) menu - - range: null value menu - host (scientific name): - name: host (scientific name) + - range: HostCommonNameMenu + - range: NullValueMenu + examples: + - value: Human [NCBITaxon:9606] + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. - comments: - Common name or scientific name are required if there was a host. Scientific + comments: Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put "not applicable". - examples: - - value: Homo sapiens [NCBITaxon:9606] slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu + - range: HostScientificNameMenu + - range: NullValueMenu required: true + examples: + - value: Homo sapiens [NCBITaxon:9606] exact_mappings: - - GISAID:Host - - NCBI_BIOSAMPLE:host - - NCBI_Genbank_source_modifiers:host - host health state: - name: host health state + - GISAID:Host + - NCBI_BIOSAMPLE:host + - NCBI_Genbank_source_modifiers:host + host_health_state: + name: host_health_state title: host health state description: Health status of the host at the time of sample collection. comments: If known, select a value from the pick list. - examples: - - value: Asymptomatic [NCIT:C3833] slot_uri: GENEPIO:0001388 any_of: - - range: host health state menu - - range: null value menu + - range: HostHealthStateMenu + - range: NullValueMenu + examples: + - value: Asymptomatic [NCIT:C3833] exact_mappings: - - GISAID:Patient status - - NCBI_BIOSAMPLE:host_health_state - host health status details: - name: host health status details + - GISAID:Patient%20status + - NCBI_BIOSAMPLE:host_health_state + host_health_status_details: + name: host_health_status_details title: host health status details - description: - Further details pertaining to the health or disease status of the + description: Further details pertaining to the health or disease status of the host at time of collection. comments: If known, select a value from the pick list. - examples: - - value: Hospitalized (ICU) [GENEPIO:0100046] slot_uri: GENEPIO:0001389 any_of: - - range: host health status details menu - - range: null value menu - host disease: - name: host disease + - range: HostHealthStatusDetailsMenu + - range: NullValueMenu + examples: + - value: Hospitalized (ICU) [GENEPIO:0100046] + host_disease: + name: host_disease title: host disease description: The name of the disease experienced by the host. - comments: - "This field is only required if there was a host. If the host was a\ + comments: "This field is only required if there was a host. If the host was a\ \ human select COVID-19 from the pick list. If the host was asymptomatic, this\ \ can be recorded under \u201Chost health state details\u201D. \"COVID-19\"\ \ should still be provided if patient is asymptomatic. If the host is not human,\ \ and the disease state is not known or the host appears healthy, put \u201C\ not applicable\u201D." - examples: - - value: COVID-19 [MONDO:0100096] slot_uri: GENEPIO:0001391 any_of: - - range: host disease menu - - range: null value menu + - range: HostDiseaseMenu + - range: NullValueMenu required: true + examples: + - value: COVID-19 [MONDO:0100096] exact_mappings: - - NCBI_BIOSAMPLE:host_disease - host health outcome: - name: host health outcome + - NCBI_BIOSAMPLE:host_disease + host_health_outcome: + name: host_health_outcome title: host health outcome description: Disease outcome in the host. comments: If known, select a value from the pick list. - examples: - - value: Recovered [NCIT:C49498] slot_uri: GENEPIO:0001390 any_of: - - range: host health outcome menu - - range: null value menu + - range: HostHealthOutcomeMenu + - range: NullValueMenu + examples: + - value: Recovered [NCIT:C49498] exact_mappings: - - NCBI_BIOSAMPLE:host_disease_outcome - host age: - name: host age + - NCBI_BIOSAMPLE:host_disease_outcome + host_age: + name: host_age title: host age description: Age of host at the time of sampling. comments: If known, provide age. Age-binning is also acceptable. - examples: - - value: '79' slot_uri: GENEPIO:0001392 any_of: - - range: decimal - - range: null value menu + - range: decimal + - range: NullValueMenu + maximum_value: 130 recommended: true - maximum_value: '130' + examples: + - value: '79' exact_mappings: - - GISAID:Patient age - - NCBI_BIOSAMPLE:host_age - host age unit: - name: host age unit + - GISAID:Patient%20age + - NCBI_BIOSAMPLE:host_age + host_age_unit: + name: host_age_unit title: host age unit description: The units used to measure the host's age. - comments: - If known, provide the age units used to measure the host's age from + comments: If known, provide the age units used to measure the host's age from the pick list. - examples: - - value: year [UO:0000036] slot_uri: GENEPIO:0001393 any_of: - - range: host age unit menu - - range: null value menu + - range: HostAgeUnitMenu + - range: NullValueMenu recommended: true - host age bin: - name: host age bin + examples: + - value: year [UO:0000036] + host_age_bin: + name: host_age_bin title: host age bin description: The age category of the host at the time of sampling. - comments: - Age bins in 10 year intervals have been provided. If a host's age cannot + comments: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. - examples: - - value: 50 - 59 [GENEPIO:0100054] slot_uri: GENEPIO:0001394 any_of: - - range: host age bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu recommended: true - host gender: - name: host gender + examples: + - value: 50 - 59 [GENEPIO:0100054] + host_gender: + name: host_gender title: host gender description: The gender of the host at the time of sample collection. comments: If known, select a value from the pick list. - examples: - - value: Male [NCIT:C46109] slot_uri: GENEPIO:0001395 any_of: - - range: host gender menu - - range: null value menu + - range: HostGenderMenu + - range: NullValueMenu recommended: true + examples: + - value: Male [NCIT:C46109] exact_mappings: - - GISAID:Gender - - NCBI_BIOSAMPLE:host_sex - host residence geo_loc name (country): - name: host residence geo_loc name (country) + - GISAID:Gender + - NCBI_BIOSAMPLE:host_sex + host_residence_geo_loc_name_country: + name: host_residence_geo_loc_name_country title: host residence geo_loc name (country) description: The country where the host resides. comments: If known, select a value from the pick list. - examples: - - value: South Africa [GAZ:00001094] slot_uri: GENEPIO:0001396 any_of: - - range: geo_loc_name (country) menu - - range: null value menu - host ethnicity: - name: host ethnicity + - range: HostResidenceGeoLocNameCountryMenu + - range: NullValueMenu + examples: + - value: South Africa [GAZ:00001094] + host_ethnicity: + name: host_ethnicity title: host ethnicity description: The self-identified ethnicity(ies) of the host. - comments: - If known, provide the self-identified ethnicity or ethnicities of the + comments: If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. - examples: - - value: Indigenous, European slot_uri: GENEPIO:0100312 range: WhitespaceMinimizedString - host subject ID: - name: host subject ID + examples: + - value: Indigenous, European + host_subject_id: + name: host_subject_id title: host subject ID description: 'A unique identifier by which each host can be referred to e.g. #131' - comments: - Should be a unique, user-defined identifier. This ID can help link laboratory + comments: Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. - examples: - - value: BCxy123 slot_uri: GENEPIO:0001398 range: WhitespaceMinimizedString + examples: + - value: BCxy123 exact_mappings: - - NCBI_BIOSAMPLE:host_subject_id - case ID: - name: case ID + - NCBI_BIOSAMPLE:host_subject_id + case_id: + name: case_id title: case ID - description: - The identifier used to specify an epidemiologically detected case + description: The identifier used to specify an epidemiologically detected case of disease. - comments: - Provide the case identifer. The case ID greatly facilitates linkage + comments: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. - examples: - - value: ABCD1234 slot_uri: GENEPIO:0100281 range: WhitespaceMinimizedString - symptom onset date: - name: symptom onset date + examples: + - value: ABCD1234 + symptom_onset_date: + name: symptom_onset_date title: symptom onset date description: The date on which the symptoms began or were first noted. - comments: - If known, provide the symptom onset date in ISO 8601 standard format + comments: If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2020-03-16' slot_uri: GENEPIO:0001399 any_of: - - range: date - - range: null value menu - signs and symptoms: - name: signs and symptoms + - range: date + - range: NullValueMenu + examples: + - value: '2020-03-16' + signs_and_symptoms: + name: signs_and_symptoms title: signs and symptoms - description: - A perceived change in function or sensation, (loss, disturbance or + description: A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. comments: Select all of the symptoms experienced by the host from the pick list. - examples: - - value: Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] slot_uri: GENEPIO:0001400 any_of: - - range: signs and symptoms menu - - range: null value menu + - range: SignsAndSymptomsMenu + - range: NullValueMenu multivalued: true - pre-existing conditions and risk factors: - name: pre-existing conditions and risk factors + examples: + - value: Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] + preexisting_conditions_and_risk_factors: + name: preexisting_conditions_and_risk_factors title: pre-existing conditions and risk factors description: 'Patient pre-existing conditions and risk factors. @@ -1589,457 +1525,417 @@ slots: infection. Risk Factor: A variable associated with an increased risk of disease or infection.' - comments: - Select all of the pre-existing conditions and risk factors experienced + comments: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. - examples: - - value: Asthma [HP:0002099] slot_uri: GENEPIO:0001401 any_of: - - range: pre-existing conditions and risk factors menu - - range: null value menu + - range: PreExistingConditionsAndRiskFactorsMenu + - range: NullValueMenu multivalued: true + examples: + - value: Asthma [HP:0002099] complications: name: complications title: complications - description: - Patient medical complications that are believed to have occurred + description: Patient medical complications that are believed to have occurred as a result of host disease. - comments: - Select all of the complications experienced by the host from the pick + comments: Select all of the complications experienced by the host from the pick list. - examples: - - value: Acute respiratory failure [MONDO:0001208] slot_uri: GENEPIO:0001402 any_of: - - range: complications menu - - range: null value menu + - range: ComplicationsMenu + - range: NullValueMenu multivalued: true - host vaccination status: - name: host vaccination status + examples: + - value: Acute respiratory failure [MONDO:0001208] + host_vaccination_status: + name: host_vaccination_status title: host vaccination status - description: - The vaccination status of the host (fully vaccinated, partially vaccinated, + description: The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). comments: Select the vaccination status of the host from the pick list. - examples: - - value: Fully Vaccinated [GENEPIO:0100100] slot_uri: GENEPIO:0001404 any_of: - - range: host vaccination status menu - - range: null value menu + - range: HostVaccinationStatusMenu + - range: NullValueMenu + examples: + - value: Fully Vaccinated [GENEPIO:0100100] exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination - number of vaccine doses received: - name: number of vaccine doses received + - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination + number_of_vaccine_doses_received: + name: number_of_vaccine_doses_received title: number of vaccine doses received description: The number of doses of the vaccine received by the host. comments: Record how many doses of the vaccine the host has received. - examples: - - value: '2' slot_uri: GENEPIO:0001406 range: integer - minimum_value: '0' - vaccination dose 1 vaccine name: - name: vaccination dose 1 vaccine name + minimum_value: 0 + examples: + - value: '2' + vaccination_dose_1_vaccine_name: + name: vaccination_dose_1_vaccine_name title: vaccination dose 1 vaccine name - description: - The name of the vaccine administered as the first dose of a vaccine + description: The name of the vaccine administered as the first dose of a vaccine regimen. - comments: - Provide the name and the corresponding manufacturer of the COVID-19 + comments: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list - examples: - - value: Pfizer-BioNTech (Comirnaty) slot_uri: GENEPIO:0100313 range: WhitespaceMinimizedString - vaccination dose 1 vaccination date: - name: vaccination dose 1 vaccination date + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_1_vaccination_date: + name: vaccination_dose_1_vaccination_date title: vaccination dose 1 vaccination date description: The date the first dose of a vaccine was administered. - comments: - Provide the date the first dose of COVID-19 vaccine was administered. + comments: Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2021-03-01' slot_uri: GENEPIO:0100314 range: date - vaccination dose 2 vaccine name: - name: vaccination dose 2 vaccine name + examples: + - value: '2021-03-01' + vaccination_dose_2_vaccine_name: + name: vaccination_dose_2_vaccine_name title: vaccination dose 2 vaccine name - description: - The name of the vaccine administered as the second dose of a vaccine + description: The name of the vaccine administered as the second dose of a vaccine regimen. - comments: - Provide the name and the corresponding manufacturer of the COVID-19 + comments: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list - examples: - - value: Pfizer-BioNTech (Comirnaty) slot_uri: GENEPIO:0100315 range: WhitespaceMinimizedString - vaccination dose 2 vaccination date: - name: vaccination dose 2 vaccination date + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_2_vaccination_date: + name: vaccination_dose_2_vaccination_date title: vaccination dose 2 vaccination date description: The date the second dose of a vaccine was administered. - comments: - Provide the date the second dose of COVID-19 vaccine was administered. + comments: Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2021-09-01' slot_uri: GENEPIO:0100316 range: date - vaccination dose 3 vaccine name: - name: vaccination dose 3 vaccine name + examples: + - value: '2021-09-01' + vaccination_dose_3_vaccine_name: + name: vaccination_dose_3_vaccine_name title: vaccination dose 3 vaccine name - description: - The name of the vaccine administered as the third dose of a vaccine + description: The name of the vaccine administered as the third dose of a vaccine regimen. - comments: - Provide the name and the corresponding manufacturer of the COVID-19 + comments: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list - examples: - - value: Pfizer-BioNTech (Comirnaty) slot_uri: GENEPIO:0100317 range: WhitespaceMinimizedString - vaccination dose 3 vaccination date: - name: vaccination dose 3 vaccination date + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_3_vaccination_date: + name: vaccination_dose_3_vaccination_date title: vaccination dose 3 vaccination date description: The date the third dose of a vaccine was administered. - comments: - Provide the date the third dose of COVID-19 vaccine was administered. + comments: Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2021-12-30' slot_uri: GENEPIO:0100318 range: date + examples: + - value: '2021-12-30' exact_mappings: - - NCBI_BIOSAMPLE:date_of_sars_cov_2_vaccination - vaccination dose 4 vaccine name: - name: vaccination dose 4 vaccine name + - NCBI_BIOSAMPLE:date_of_sars_cov_2_vaccination + vaccination_dose_4_vaccine_name: + name: vaccination_dose_4_vaccine_name title: vaccination dose 4 vaccine name - description: - The name of the vaccine administered as the fourth dose of a vaccine + description: The name of the vaccine administered as the fourth dose of a vaccine regimen. - comments: - Provide the name and the corresponding manufacturer of the COVID-19 + comments: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list - examples: - - value: Pfizer-BioNTech (Comirnaty) slot_uri: GENEPIO:0100319 range: WhitespaceMinimizedString - vaccination dose 4 vaccination date: - name: vaccination dose 4 vaccination date + examples: + - value: Pfizer-BioNTech (Comirnaty) + vaccination_dose_4_vaccination_date: + name: vaccination_dose_4_vaccination_date title: vaccination dose 4 vaccination date description: The date the fourth dose of a vaccine was administered. - comments: - Provide the date the fourth dose of COVID-19 vaccine was administered. + comments: Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2022-01-15' slot_uri: GENEPIO:0100320 range: date - vaccination history: - name: vaccination history + examples: + - value: '2022-01-15' + vaccination_history: + name: vaccination_history title: vaccination history - description: - A description of the vaccines received and the administration dates + description: A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. - comments: - Free text description of the dates and vaccines administered against + comments: Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. - examples: - - value: Pfizer-BioNTech (Comirnaty) - - value: '2021-03-01' - - value: Pfizer-BioNTech (Comirnaty) - - value: '2022-01-15' slot_uri: GENEPIO:0100321 range: WhitespaceMinimizedString + examples: + - value: Pfizer-BioNTech (Comirnaty) + - value: '2021-03-01' + - value: Pfizer-BioNTech (Comirnaty) + - value: '2022-01-15' exact_mappings: - - GISAID:Last vaccinated - location of exposure geo_loc name (country): - name: location of exposure geo_loc name (country) + - GISAID:Last%20vaccinated + location_of_exposure_geo_loc_name_country: + name: location_of_exposure_geo_loc_name_country title: location of exposure geo_loc name (country) - description: - The country where the host was likely exposed to the causative agent + description: The country where the host was likely exposed to the causative agent of the illness. - comments: - This location pertains to the country the host was believed to be exposed, + comments: This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list. - examples: - - value: South Africa [GAZ:00001094] slot_uri: GENEPIO:0001410 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: LocationOfExposureGeoLocNameCountryMenu + - range: NullValueMenu + examples: + - value: South Africa [GAZ:00001094] exact_mappings: - - NCBI_BIOSAMPLE:geo_loc_exposure - destination of most recent travel (city): - name: destination of most recent travel (city) + - NCBI_BIOSAMPLE:geo_loc_exposure + destination_of_most_recent_travel_city: + name: destination_of_most_recent_travel_city title: destination of most recent travel (city) description: The name of the city that was the destination of most recent travel. - comments: - 'Provide the name of the city that the host travelled to. Use this look-up + comments: 'Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: New York City slot_uri: GENEPIO:0001411 range: WhitespaceMinimizedString + examples: + - value: New York City exact_mappings: - - NCBI_BIOSAMPLE:host_recent_travel_loc - destination of most recent travel (state/province/territory): - name: destination of most recent travel (state/province/territory) + - NCBI_BIOSAMPLE:host_recent_travel_loc + destination_of_most_recent_travel_state_province_territory: + name: destination_of_most_recent_travel_state_province_territory title: destination of most recent travel (state/province/territory) - description: - The name of the province that was the destination of most recent + description: The name of the province that was the destination of most recent travel. - comments: - 'Provide the name of the state/province/territory that the host travelled + comments: 'Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: California slot_uri: GENEPIO:0001412 range: WhitespaceMinimizedString + examples: + - value: California exact_mappings: - - NCBI_BIOSAMPLE:host_recent_travel_loc - destination of most recent travel (country): - name: destination of most recent travel (country) + - NCBI_BIOSAMPLE:host_recent_travel_loc + destination_of_most_recent_travel_country: + name: destination_of_most_recent_travel_country title: destination of most recent travel (country) description: The name of the country that was the destination of most recent travel. - comments: - 'Provide the name of the country that the host travelled to. Use this + comments: 'Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: United Kingdom [GAZ:00002637] slot_uri: GENEPIO:0001413 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: DestinationOfMostRecentTravelCountryMenu + - range: NullValueMenu + examples: + - value: United Kingdom [GAZ:00002637] exact_mappings: - - NCBI_BIOSAMPLE:host_recent_travel_loc - most recent travel departure date: - name: most recent travel departure date + - NCBI_BIOSAMPLE:host_recent_travel_loc + most_recent_travel_departure_date: + name: most_recent_travel_departure_date title: most recent travel departure date - description: - The date of a person's most recent departure from their primary residence + description: The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. comments: Provide the travel departure date in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2020-03-16' slot_uri: GENEPIO:0001414 any_of: - - range: date - - range: null value menu - most recent travel return date: - name: most recent travel return date + - range: date + - range: NullValueMenu + examples: + - value: '2020-03-16' + most_recent_travel_return_date: + name: most_recent_travel_return_date title: most recent travel return date - description: - The date of a person's most recent return to some residence from + description: The date of a person's most recent return to some residence from a journey originating at that residence. comments: Provide the travel return date in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2020-04-26' slot_uri: GENEPIO:0001415 any_of: - - range: date - - range: null value menu + - range: date + - range: NullValueMenu + examples: + - value: '2020-04-26' exact_mappings: - - NCBI_BIOSAMPLE:host_recent_travel_return_date - travel history: - name: travel history + - NCBI_BIOSAMPLE:host_recent_travel_return_date + travel_history: + name: travel_history title: travel history description: Travel history in last six months. - comments: - Specify the countries (and more granular locations if known) travelled + comments: Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. - examples: - - value: Canada, Vancouver - - value: USA, Seattle - - value: Italy, Milan slot_uri: GENEPIO:0001416 range: WhitespaceMinimizedString - exposure event: - name: exposure event + examples: + - value: Canada, Vancouver + - value: USA, Seattle + - value: Italy, Milan + exposure_event: + name: exposure_event title: exposure event description: Event leading to exposure. comments: If known, select the exposure event from the pick list. - examples: - - value: Mass Gathering [GENEPIO:0100237] slot_uri: GENEPIO:0001417 any_of: - - range: exposure event menu - - range: null value menu + - range: ExposureEventMenu + - range: NullValueMenu + examples: + - value: Mass Gathering [GENEPIO:0100237] exact_mappings: - - GISAID:Additional location information - - NCBI_BIOSAMPLE:exposure_event - exposure contact level: - name: exposure contact level + - GISAID:Additional%20location%20information + - NCBI_BIOSAMPLE:exposure_event + exposure_contact_level: + name: exposure_contact_level title: exposure contact level description: The exposure transmission contact type. comments: Select direct or indirect exposure from the pick list. - examples: - - value: Direct (human-to-human contact) [TRANS:0000001] slot_uri: GENEPIO:0001418 any_of: - - range: exposure contact level menu - - range: null value menu - host role: - name: host role + - range: ExposureContactLevelMenu + - range: NullValueMenu + examples: + - value: Direct (human-to-human contact) [TRANS:0000001] + host_role: + name: host_role title: host role description: The role of the host in relation to the exposure setting. - comments: - Select the host's personal role(s) from the pick list provided in the + comments: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. - examples: - - value: Patient [OMRSE:00000030] slot_uri: GENEPIO:0001419 - range: host role menu + range: HostRoleMenu multivalued: true + examples: + - value: Patient [OMRSE:00000030] exact_mappings: - - GISAID:Additional host information - exposure setting: - name: exposure setting + - GISAID:Additional%20host%20information + exposure_setting: + name: exposure_setting title: exposure setting description: The setting leading to exposure. - comments: - Select the host exposure setting(s) from the pick list provided in the + comments: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. - examples: - - value: Healthcare Setting [GENEPIO:0100201] slot_uri: GENEPIO:0001428 - range: exposure setting menu + range: ExposureSettingMenu multivalued: true + examples: + - value: Healthcare Setting [GENEPIO:0100201] exact_mappings: - - GISAID:Additional host information - exposure details: - name: exposure details + - GISAID:Additional%20host%20information + exposure_details: + name: exposure_details title: exposure details description: Additional host exposure information. comments: Free text description of the exposure. - examples: - - value: 'Host role - Other: Bus Driver' slot_uri: GENEPIO:0001431 range: WhitespaceMinimizedString - prior SARS-CoV-2 infection: - name: prior SARS-CoV-2 infection + examples: + - value: 'Host role - Other: Bus Driver' + prior_sarscov2_infection: + name: prior_sarscov2_infection title: prior SARS-CoV-2 infection description: Whether there was prior SARS-CoV-2 infection. - comments: - If known, provide infromation about whether the individual had a previous + comments: If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. - examples: - - value: Prior infection [GENEPIO:0100234] slot_uri: GENEPIO:0001435 any_of: - - range: prior SARS-CoV-2 infection menu - - range: null value menu + - range: PriorSarsCov2InfectionMenu + - range: NullValueMenu + examples: + - value: Prior infection [GENEPIO:0100234] exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_infection - prior SARS-CoV-2 infection isolate: - name: prior SARS-CoV-2 infection isolate + - NCBI_BIOSAMPLE:prior_sars_cov_2_infection + prior_sarscov2_infection_isolate: + name: prior_sarscov2_infection_isolate title: prior SARS-CoV-2 infection isolate description: The identifier of the isolate found in the prior SARS-CoV-2 infection. - comments: - 'Provide the isolate name of the most recent prior infection. Structure + comments: 'Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date".' - examples: - - value: SARS-CoV-2/human/USA/CA-CDPH-001/2020 slot_uri: GENEPIO:0001436 range: WhitespaceMinimizedString + examples: + - value: SARS-CoV-2/human/USA/CA-CDPH-001/2020 exact_mappings: - - NCBI_BIOSAMPLE:virus_isolate_of_prior_infection - prior SARS-CoV-2 infection date: - name: prior SARS-CoV-2 infection date + - NCBI_BIOSAMPLE:virus_isolate_of_prior_infection + prior_sarscov2_infection_date: + name: prior_sarscov2_infection_date title: prior SARS-CoV-2 infection date description: The date of diagnosis of the prior SARS-CoV-2 infection. - comments: - Provide the date that the most recent prior infection was diagnosed. + comments: Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2021-01-23' slot_uri: GENEPIO:0001437 range: date + examples: + - value: '2021-01-23' exact_mappings: - - NCBI_BIOSAMPLE:date_of_prior_sars_cov_2_infection - prior SARS-CoV-2 antiviral treatment: - name: prior SARS-CoV-2 antiviral treatment + - NCBI_BIOSAMPLE:date_of_prior_sars_cov_2_infection + prior_sarscov2_antiviral_treatment: + name: prior_sarscov2_antiviral_treatment title: prior SARS-CoV-2 antiviral treatment description: Whether there was prior SARS-CoV-2 treatment with an antiviral agent. - comments: - If known, provide infromation about whether the individual had a previous + comments: If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. - examples: - - value: Prior antiviral treatment [GENEPIO:0100037] slot_uri: GENEPIO:0001438 any_of: - - range: prior SARS-CoV-2 antiviral treatment menu - - range: null value menu + - range: PriorSarsCov2AntiviralTreatmentMenu + - range: NullValueMenu + examples: + - value: Prior antiviral treatment [GENEPIO:0100037] exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treat - prior SARS-CoV-2 antiviral treatment agent: - name: prior SARS-CoV-2 antiviral treatment agent + - NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treat + prior_sarscov2_antiviral_treatment_agent: + name: prior_sarscov2_antiviral_treatment_agent title: prior SARS-CoV-2 antiviral treatment agent - description: - The name of the antiviral treatment agent administered during the + description: The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. - comments: - Provide the name of the antiviral treatment agent administered during + comments: Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. - examples: - - value: Remdesivir slot_uri: GENEPIO:0001439 range: WhitespaceMinimizedString + examples: + - value: Remdesivir exact_mappings: - - NCBI_BIOSAMPLE:antiviral_treatment_agent - prior SARS-CoV-2 antiviral treatment date: - name: prior SARS-CoV-2 antiviral treatment date + - NCBI_BIOSAMPLE:antiviral_treatment_agent + prior_sarscov2_antiviral_treatment_date: + name: prior_sarscov2_antiviral_treatment_date title: prior SARS-CoV-2 antiviral treatment date - description: - The date treatment was first administered during the prior SARS-CoV-2 + description: The date treatment was first administered during the prior SARS-CoV-2 infection. - comments: - Provide the date that the antiviral treatment agent was first administered + comments: Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2021-01-28' slot_uri: GENEPIO:0001440 range: date + examples: + - value: '2021-01-28' exact_mappings: - - NCBI_BIOSAMPLE:date_of_prior_antiviral_treat - purpose of sequencing: - name: purpose of sequencing + - NCBI_BIOSAMPLE:date_of_prior_antiviral_treat + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. - comments: - The reason why a sample was originally collected may differ from the + comments: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. - examples: - - value: Baseline surveillance (random sampling) [GENEPIO:0100005] slot_uri: GENEPIO:0001445 any_of: - - range: purpose of sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Baseline surveillance (random sampling) [GENEPIO:0100005] exact_mappings: - - GISAID:Sampling Strategy - - NCBI_BIOSAMPLE:purpose_of_sequencing - purpose of sequencing details: - name: purpose of sequencing details + - GISAID:Sampling%20Strategy + - NCBI_BIOSAMPLE:purpose_of_sequencing + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details - description: - The description of why the sample was sequenced providing specific + description: The description of why the sample was sequenced providing specific details. - comments: - 'Provide an expanded description of why the sample was sequenced using + comments: 'Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure @@ -2050,641 +1946,514 @@ slots: airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection.' - examples: - - value: Screened for S gene target failure (S dropout) slot_uri: GENEPIO:0001446 any_of: - - range: WhitespaceMinimizedString - - range: null value menu + - range: WhitespaceMinimizedString + - range: NullValueMenu required: true - sequencing date: - name: sequencing date + examples: + - value: Screened for S gene target failure (S dropout) + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: Provide the sequencing date in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2021-04-26' slot_uri: GENEPIO:0001447 any_of: - - range: date - - range: null value menu - library ID: - name: library ID + - range: date + - range: NullValueMenu + examples: + - value: '2021-04-26' + library_id: + name: library_id title: library ID description: The user-specified identifier for the library prepared for sequencing. - comments: - The library name should be unique, and can be an autogenerated ID from + comments: The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. - examples: - - value: XYZ_123345 slot_uri: GENEPIO:0001448 range: WhitespaceMinimizedString recommended: true + examples: + - value: XYZ_123345 exact_mappings: - - NCBI_SRA:library_ID - amplicon size: - name: amplicon size + - NCBI_SRA:library_ID + amplicon_size: + name: amplicon_size title: amplicon size description: The length of the amplicon generated by PCR amplification. comments: Provide the amplicon size, including the units. - examples: - - value: 300bp slot_uri: GENEPIO:0001449 range: WhitespaceMinimizedString + examples: + - value: 300bp exact_mappings: - - NCBI_SRA:amplicon_size - library preparation kit: - name: library preparation kit + - NCBI_SRA:amplicon_size + library_preparation_kit: + name: library_preparation_kit title: library preparation kit - description: - The name of the DNA library preparation kit used to generate the + description: The name of the DNA library preparation kit used to generate the library being sequenced. comments: Provide the name of the library preparation kit used. - examples: - - value: Nextera XT slot_uri: GENEPIO:0001450 range: WhitespaceMinimizedString - flow cell barcode: - name: flow cell barcode + examples: + - value: Nextera XT + flow_cell_barcode: + name: flow_cell_barcode title: flow cell barcode description: The barcode of the flow cell used for sequencing. comments: Provide the barcode of the flow cell used for sequencing the sample. - examples: - - value: FAB06069 slot_uri: GENEPIO:0001451 range: WhitespaceMinimizedString - sequencing instrument: - name: sequencing instrument + examples: + - value: FAB06069 + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Select the sequencing instrument from the pick list. - examples: - - value: Oxford Nanopore MinION [GENEPIO:0100142] slot_uri: GENEPIO:0001452 any_of: - - range: sequencing instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Oxford Nanopore MinION [GENEPIO:0100142] exact_mappings: - - GISAID:Sequencing technology - - NCBI_SRA:platform - - NCBI_SRA:instrument_model - - NCBI_Genbank:sequencing_technology - sequencing protocol name: - name: sequencing protocol name + - GISAID:Sequencing%20technology + - NCBI_SRA:platform + - NCBI_SRA:instrument_model + - NCBI_Genbank:sequencing_technology + sequencing_protocol_name: + name: sequencing_protocol_name title: sequencing protocol name description: The name and version number of the sequencing protocol used. comments: Provide the name and version of the sequencing protocol. - examples: - - value: 1D_DNA_MinION, ARTIC Network Protocol V3 slot_uri: GENEPIO:0001453 range: WhitespaceMinimizedString recommended: true + examples: + - value: 1D_DNA_MinION, ARTIC Network Protocol V3 exact_mappings: - - NCBI_SRA:sequencing_protocol_name - sequencing protocol: - name: sequencing protocol + - NCBI_SRA:sequencing_protocol_name + sequencing_protocol: + name: sequencing_protocol title: sequencing protocol description: The protocol used to generate the sequence. - comments: - 'Provide a free text description of the methods and materials used to + comments: 'Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. "' - examples: - - value: - Genomes were generated through amplicon sequencing of 1200 bp amplicons - with Freed schema primers. Libraries were created using Illumina DNA Prep - kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing - kits. slot_uri: GENEPIO:0001454 range: WhitespaceMinimizedString + examples: + - value: Genomes were generated through amplicon sequencing of 1200 bp amplicons + with Freed schema primers. Libraries were created using Illumina DNA Prep + kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing + kits. exact_mappings: - - NCBI_SRA:design_description - sequencing kit number: - name: sequencing kit number + - NCBI_SRA:design_description + sequencing_kit_number: + name: sequencing_kit_number title: sequencing kit number description: The manufacturer's kit number. comments: Alphanumeric value. - examples: - - value: AB456XYZ789 slot_uri: GENEPIO:0001455 range: WhitespaceMinimizedString - amplicon pcr primer scheme: - name: amplicon pcr primer scheme + examples: + - value: AB456XYZ789 + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme title: amplicon pcr primer scheme - description: - The specifications of the primers (primer sequences, binding positions, + description: The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. - comments: - Provide the name and version of the primer scheme used to generate the + comments: Provide the name and version of the primer scheme used to generate the amplicons for sequencing. - examples: - - value: https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv slot_uri: GENEPIO:0001456 range: WhitespaceMinimizedString + examples: + - value: https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv exact_mappings: - - NCBI_SRA:amplicon_pcr_primer_scheme - raw sequence data processing method: - name: raw sequence data processing method + - NCBI_SRA:amplicon_pcr_primer_scheme + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method - description: - The method used for raw data processing such as removing barcodes, - adapter trimming, filtering etc. - comments: - Provide the name and version numbers of the software used to process - the raw data. - examples: - - value: Porechop 0.2.3 + description: '#REF!' slot_uri: GENEPIO:0001458 range: WhitespaceMinimizedString recommended: true exact_mappings: - - NCBI_SRA:raw_sequence_data_processing_method - dehosting method: - name: dehosting method + - NCBI_SRA:raw_sequence_data_processing_method + dehosting_method: + name: dehosting_method title: dehosting method - description: The method used to remove host reads from the pathogen sequence. - comments: - Provide the name and version number of the software used to remove host - reads. - examples: - - value: Nanostripper 1.2.3 slot_uri: GENEPIO:0001459 range: WhitespaceMinimizedString recommended: true exact_mappings: - - NCBI_SRA:dehosting_method - consensus sequence name: - name: consensus sequence name + - NCBI_SRA:dehosting_method + consensus_sequence_name: + name: consensus_sequence_name title: consensus sequence name - description: The name of the consensus sequence. - comments: Provide the name and version number of the consensus sequence. - examples: - - value: ncov123assembly3 slot_uri: GENEPIO:0001460 range: WhitespaceMinimizedString - consensus sequence filename: - name: consensus sequence filename + consensus_sequence_filename: + name: consensus_sequence_filename title: consensus sequence filename - description: The name of the consensus sequence file. - comments: - Provide the name and version number of the consensus sequence FASTA - file. - examples: - - value: ncov123assembly.fasta slot_uri: GENEPIO:0001461 range: WhitespaceMinimizedString exact_mappings: - - NCBI_Genbank:filename - consensus sequence filepath: - name: consensus sequence filepath + - NCBI_Genbank:filename + consensus_sequence_filepath: + name: consensus_sequence_filepath title: consensus sequence filepath - description: The filepath of the consesnsus sequence file. - comments: Provide the filepath of the consensus sequence FASTA file. - examples: - - value: /User/Documents/RespLab/Data/ncov123assembly.fasta + description: The filepath of the consensus sequence file. slot_uri: GENEPIO:0001462 range: WhitespaceMinimizedString - consensus sequence software name: - name: consensus sequence software name + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name - description: The name of software used to generate the consensus sequence. - comments: Provide the name of the software used to generate the consensus sequence. - examples: - - value: Ivar slot_uri: GENEPIO:0001463 range: WhitespaceMinimizedString required: true exact_mappings: - - GISAID:Assembly method - - NCBI_Genbank:assembly_method - consensus sequence software version: - name: consensus sequence software version + - GISAID:Assembly%20method + - NCBI_Genbank:assembly_method + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version - description: The version of the software used to generate the consensus sequence. - comments: Provide the version of the software used to generate the consensus sequence. - examples: - - value: '1.3' slot_uri: GENEPIO:0001469 range: decimal required: true exact_mappings: - - GISAID:Assembly method - - NCBI_Genbank:assembly_method_version - breadth of coverage value: - name: breadth of coverage value + - GISAID:Assembly%20method + - NCBI_Genbank:assembly_method_version + breadth_of_coverage_value: + name: breadth_of_coverage_value title: breadth of coverage value - description: - The percentage of the reference genome covered by the sequenced data, - to a prescribed depth. - comments: Provide value as a percent. - examples: - - value: 95% slot_uri: GENEPIO:0001472 range: WhitespaceMinimizedString - depth of coverage value: - name: depth of coverage value + depth_of_coverage_value: + name: depth_of_coverage_value title: depth of coverage value - description: - The average number of reads representing a given nucleotide in the - reconstructed sequence. - comments: Provide value as a fold of coverage. - examples: - - value: 400x slot_uri: GENEPIO:0001474 range: WhitespaceMinimizedString exact_mappings: - - GISAID:Coverage - - NCBI_Genbank:genome_coverage - depth of coverage threshold: - name: depth of coverage threshold + - GISAID:Depth%20of%20coverage + - NCBI_Genbank:genome_coverage + depth_of_coverage_threshold: + name: depth_of_coverage_threshold title: depth of coverage threshold - description: The threshold used as a cut-off for the depth of coverage. - comments: Provide the threshold fold coverage. - examples: - - value: 100x slot_uri: GENEPIO:0001475 range: WhitespaceMinimizedString - r1 fastq filename: - name: r1 fastq filename + r1_fastq_filename: + name: r1_fastq_filename title: r1 fastq filename - description: The user-specified filename of the r1 FASTQ file. - comments: Provide the r1 FASTQ filename. - examples: - - value: ABC123_S1_L001_R1_001.fastq.gz slot_uri: GENEPIO:0001476 range: WhitespaceMinimizedString - r2 fastq filename: - name: r2 fastq filename + r2_fastq_filename: + name: r2_fastq_filename title: r2 fastq filename - description: The user-specified filename of the r2 FASTQ file. - comments: Provide the r2 FASTQ filename. - examples: - - value: ABC123_S1_L001_R2_001.fastq.gz slot_uri: GENEPIO:0001477 range: WhitespaceMinimizedString - r1 fastq filepath: - name: r1 fastq filepath + r1_fastq_filepath: + name: r1_fastq_filepath title: r1 fastq filepath - description: The filepath of the r1 FASTQ file. - comments: Provide the filepath of the r1 FASTQ file. - examples: - - value: /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz slot_uri: GENEPIO:0001478 range: WhitespaceMinimizedString - r2 fastq filepath: - name: r2 fastq filepath + r2_fastq_filepath: + name: r2_fastq_filepath title: r2 fastq filepath - description: The filepath of the r2 FASTQ file. - comments: Provide the filepath of the r2 FASTQ file. - examples: - - value: /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz slot_uri: GENEPIO:0001479 range: WhitespaceMinimizedString - fast5 filename: - name: fast5 filename + fast5_filename: + name: fast5_filename title: fast5 filename - description: The user-specified filename of the FAST5 file. - comments: Provide the FAST5 filename. - examples: - - value: batch1a_sequences.fast5 slot_uri: GENEPIO:0001480 range: WhitespaceMinimizedString - fast5 filepath: - name: fast5 filepath + fast5_filepath: + name: fast5_filepath title: fast5 filepath - description: The filepath of the FAST5 file. - comments: Provide the filepath of the FAST5 file. - examples: - - value: /User/Documents/RespLab/Data/batch1a_sequences.fast5 slot_uri: GENEPIO:0001481 range: WhitespaceMinimizedString - number of base pairs sequenced: - name: number of base pairs sequenced + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced title: number of base pairs sequenced - description: The number of total base pairs generated by the sequencing process. - comments: Provide a numerical value (no need to include units). - examples: - - value: '387566' slot_uri: GENEPIO:0001482 range: integer - minimum_value: '0' - consensus genome length: - name: consensus genome length + minimum_value: 0 + consensus_genome_length: + name: consensus_genome_length title: consensus genome length - description: Size of the assembled genome described as the number of base pairs. - comments: Provide a numerical value (no need to include units). - examples: - - value: '38677' slot_uri: GENEPIO:0001483 range: integer - minimum_value: '0' - Ns per 100 kbp: - name: Ns per 100 kbp + minimum_value: 0 + ns_per_100_kbp: + name: ns_per_100_kbp title: Ns per 100 kbp - description: - The number of N symbols present in the consensus fasta sequence, - per 100kbp of sequence. - comments: Provide a numerical value (no need to include units). - examples: - - value: '300' slot_uri: GENEPIO:0001484 range: decimal - reference genome accession: - name: reference genome accession + reference_genome_accession: + name: reference_genome_accession title: reference genome accession - description: A persistent, unique identifier of a genome database entry. - comments: Provide the accession number of the reference genome. - examples: - - value: NC_045512.2 slot_uri: GENEPIO:0001485 range: WhitespaceMinimizedString exact_mappings: - - NCBI_Genbank:reference_genome - bioinformatics protocol: - name: bioinformatics protocol + - NCBI_Genbank:reference_genome + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol - description: The name and version number of the bioinformatics protocol used. - comments: - Further details regarding the methods used to process raw data, and/or - generate assemblies, and/or generate consensus sequences can be provided in - an SOP or protocol. Provide the name and version number of the protocol, or - a link if deposited in a protocol repository. - examples: - - value: https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members slot_uri: GENEPIO:0001489 range: WhitespaceMinimizedString - lineage/clade name: - name: lineage/clade name + lineage_clade_name: + name: lineage_clade_name title: lineage/clade name description: The name of the lineage or clade. comments: Provide the Pangolin or Nextstrain lineage/clade name. - examples: - - value: B.1.1.7 slot_uri: GENEPIO:0001500 range: WhitespaceMinimizedString - lineage/clade analysis software name: - name: lineage/clade analysis software name + examples: + - value: B.1.1.7 + lineage_clade_analysis_software_name: + name: lineage_clade_analysis_software_name title: lineage/clade analysis software name description: The name of the software used to determine the lineage/clade. comments: Provide the name of the software used to determine the lineage/clade. - examples: - - value: Pangolin slot_uri: GENEPIO:0001501 range: WhitespaceMinimizedString - lineage/clade analysis software version: - name: lineage/clade analysis software version + examples: + - value: Pangolin + lineage_clade_analysis_software_version: + name: lineage_clade_analysis_software_version title: lineage/clade analysis software version description: The version of the software used to determine the lineage/clade. comments: Provide the version of the software used ot determine the lineage/clade. - examples: - - value: 2.1.10 slot_uri: GENEPIO:0001502 range: WhitespaceMinimizedString - variant designation: - name: variant designation + examples: + - value: 2.1.10 + variant_designation: + name: variant_designation title: variant designation - description: - The variant classification of the lineage/clade i.e. variant, variant + description: The variant classification of the lineage/clade i.e. variant, variant of concern. - comments: - If the lineage/clade is considered a Variant of Concern, select Variant + comments: If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. - examples: - - value: Variant of Concern (VOC) [GENEPIO:0100083] slot_uri: GENEPIO:0001503 any_of: - - range: variant designation menu - - range: null value menu - variant evidence details: - name: variant evidence details + - range: VariantDesignationMenu + - range: NullValueMenu + examples: + - value: Variant of Concern (VOC) [GENEPIO:0100083] + variant_evidence_details: + name: variant_evidence_details title: variant evidence details description: The evidence used to make the variant determination. - comments: - List the set of lineage-defining mutations used to make the variant + comments: List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. - examples: - - value: 'RT-qPCR TaqPath assay: S gene target failure' - slot_uri: GENEPIO:0001504 + slot_uri: GENEPIO:0001505 range: WhitespaceMinimizedString - gene name 1: - name: gene name 1 + examples: + - value: 'RT-qPCR TaqPath assay: S gene target failure' + gene_name_1: + name: gene_name_1 title: gene name 1 description: The name of the gene used in the diagnostic RT-PCR test. - comments: - 'Select a gene from the pick list. If the gene of interest is not in + comments: 'Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' - examples: - - value: E gene (orf4) [GENEPIO:0100151] slot_uri: GENEPIO:0001507 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu + examples: + - value: E gene (orf4) [GENEPIO:0100151] exact_mappings: - - NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_1 - diagnostic pcr protocol 1: - name: diagnostic pcr protocol 1 + - NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_1 + diagnostic_pcr_protocol_1: + name: diagnostic_pcr_protocol_1 title: diagnostic pcr protocol 1 - description: - The name and version number of the protocol used for diagnostic marker + description: The name and version number of the protocol used for diagnostic marker amplification. - comments: - The name and version number of the protocol used for carrying out a + comments: The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. - examples: - - value: PCREGene 2.0 slot_uri: GENEPIO:0001508 range: WhitespaceMinimizedString - diagnostic pcr Ct value 1: - name: diagnostic pcr Ct value 1 + examples: + - value: PCREGene 2.0 + diagnostic_pcr_ct_value_1: + name: diagnostic_pcr_ct_value_1 title: diagnostic pcr Ct value 1 - description: - The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 + description: The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test. - comments: - Provide the cycle threshold (Ct) value of the sample from the diagnostic + comments: Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test. - examples: - - value: '21' slot_uri: GENEPIO:0001509 range: WhitespaceMinimizedString + examples: + - value: '21' exact_mappings: - - NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_1 - gene name 2: - name: gene name 2 + - NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_1 + gene_name_2: + name: gene_name_2 title: gene name 2 description: The name of the gene used in the diagnostic RT-PCR test. - comments: - 'Select a gene from the pick list. If the gene of interest is not in + comments: 'Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' - examples: - - value: RdRp gene (nsp12) [GENEPIO:0100168] slot_uri: GENEPIO:0001510 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu + examples: + - value: RdRp gene (nsp12) [GENEPIO:0100168] exact_mappings: - - NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_2 - diagnostic pcr protocol 2: - name: diagnostic pcr protocol 2 + - NCBI_BIOSAMPLE:sars_cov_2_diag_gene_name_2 + diagnostic_pcr_protocol_2: + name: diagnostic_pcr_protocol_2 title: diagnostic pcr protocol 2 - description: - The name and version number of the protocol used for diagnostic marker + description: The name and version number of the protocol used for diagnostic marker amplification. - comments: - The name and version number of the protocol used for carrying out a + comments: The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. - examples: - - value: PCRRdRpGene 3.0 slot_uri: GENEPIO:0001511 range: WhitespaceMinimizedString - diagnostic pcr Ct value 2: - name: diagnostic pcr Ct value 2 + examples: + - value: PCRRdRpGene 3.0 + diagnostic_pcr_ct_value_2: + name: diagnostic_pcr_ct_value_2 title: diagnostic pcr Ct value 2 - description: - The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 + description: The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test. - comments: - Provide the cycle threshold (Ct) value of the sample from the second + comments: Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test. - examples: - - value: '36' slot_uri: GENEPIO:0001512 range: WhitespaceMinimizedString + examples: + - value: '36' exact_mappings: - - NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_2 + - NCBI_BIOSAMPLE:sars_cov_2_diag_pcr_ct_value_2 title: name: title title: title description: Short description that will identify the dataset on public pages. comments: 'Format: {methodology} of {organism}: {sample info}' - examples: - - value: 'Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab' slot_uri: GENEPIO:0100323 range: WhitespaceMinimizedString + examples: + - value: 'Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab' exact_mappings: - - NCBI_SRA:title + - NCBI_SRA:title library_strategy: name: library_strategy title: library_strategy description: See NCBI SRA template for details. - comments: - Provide the library strategy by selecting a value from the pick list. + comments: Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select "AMPLICON". slot_uri: GENEPIO:0100324 - range: library_strategy menu + range: LibraryStrategyMenu exact_mappings: - - NCBI_SRA:library_strategy + - NCBI_SRA:library_strategy library_source: name: library_source title: library_source description: See NCBI SRA template for details. - comments: - Provide the library source by selecting a value from the pick list. + comments: Provide the library source by selecting a value from the pick list. For amplicon sequencing select "Viral RNA". slot_uri: GENEPIO:0100325 - range: library_source menu + range: LibrarySourceMenu exact_mappings: - - NCBI_SRA:library_source + - NCBI_SRA:library_source library_selection: name: library_selection title: library_selection description: See NCBI SRA template for details. - comments: - Provide the library selection by selecting a value from the pick list. + comments: Provide the library selection by selecting a value from the pick list. For amplicon sequencing select "PCR". slot_uri: GENEPIO:0100326 - range: library_selection menu + range: LibrarySelectionMenu exact_mappings: - - NCBI_SRA:library_selection + - NCBI_SRA:library_selection library_layout: name: library_layout title: library_layout description: See NCBI SRA template for details. - comments: - Provide the library layout by selecting a value from the pick list. + comments: Provide the library layout by selecting a value from the pick list. For Illumina instruments, select "PAIRED". For Oxford Nanopore instruments, select "SINGLE". slot_uri: GENEPIO:0100327 - range: library_layout menu + range: LibraryLayoutMenu exact_mappings: - - NCBI_SRA:library_layout + - NCBI_SRA:library_layout filetype: name: filetype title: filetype description: See NCBI SRA template for details. comments: Provide the filetype by selecting a value from the pick list. slot_uri: GENEPIO:0100328 - range: filetype menu + range: FiletypeMenu exact_mappings: - - NCBI_SRA:filetype + - NCBI_SRA:filetype filename: name: filename title: filename description: See NCBI SRA template for details. - comments: - Provide the appropriate filename recorded in the Bioinformatics and + comments: Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is "paired", provide the second filename under "Filename 2". slot_uri: GENEPIO:0100329 range: WhitespaceMinimizedString exact_mappings: - - NCBI_SRA:filename + - NCBI_SRA:filename filename2: name: filename2 title: filename2 description: See NCBI SRA template for details. - comments: - Provide the appropriate filename recorded in the Bioinformatics and + comments: Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. slot_uri: GENEPIO:0100330 range: WhitespaceMinimizedString exact_mappings: - - NCBI_SRA:filename2 + - NCBI_SRA:filename2 authors: name: authors title: authors - description: - Names of individuals contributing to the processes of sample collection, + description: Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. - comments: - Include the first and last names of all individuals that should be attributed, + comments: Include the first and last names of all individuals that should be attributed, separated by a comma. - examples: - - value: Tejinder Singh, Fei Hu, Johnny Blogs slot_uri: GENEPIO:0001517 range: WhitespaceMinimizedString recommended: true + examples: + - value: Tejinder Singh, Fei Hu, Johnny Blogs exact_mappings: - - GISAID:Authors - DataHarmonizer provenance: - name: DataHarmonizer provenance + - GISAID:Authors + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance - description: The DataHarmonizer software version provenance. - comments: - The current software version information will be automatically generated - in this field after the user utilizes the "validate" function. This information - will be generated regardless as to whether the row is valid of not. - examples: - - value: 'DataHarmonizer provenance: v0.13.21' + description: The DataHarmonizer software and template version provenance. + comments: The current software and template version information will be automatically + generated in this field after the user utilizes the "validate" function. This + information will be generated regardless as to whether the row is valid of not. slot_uri: GENEPIO:0001518 range: Provenance + examples: + - value: DataHarmonizer v1.4.3, PHA4GE v1.0.0 enums: - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu + title: null value menu permissible_values: Not Applicable [GENEPIO:0001619]: text: Not Applicable [GENEPIO:0001619] @@ -2701,8 +2470,9 @@ enums: Restricted Access [GENEPIO:0001810]: text: Restricted Access [GENEPIO:0001810] meaning: GENEPIO:0001810 - host age unit menu: - name: host age unit menu + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host age unit menu permissible_values: month [UO:0000035]: text: month [UO:0000035] @@ -2710,8 +2480,9 @@ enums: year [UO:0000036]: text: year [UO:0000036] meaning: UO:0000036 - biomaterial extracted menu: - name: biomaterial extracted menu + BiomaterialExtractedMenu: + name: BiomaterialExtractedMenu + title: biomaterial extracted menu permissible_values: RNA (Total) [OBI:0000895]: text: RNA (Total) [OBI:0000895] @@ -2728,8 +2499,9 @@ enums: mRNA (cDNA) [OBI:0002754]: text: mRNA (cDNA) [OBI:0002754] meaning: OBI:0002754 - signs and symptoms menu: - name: signs and symptoms menu + SignsAndSymptomsMenu: + name: SignsAndSymptomsMenu + title: signs and symptoms menu permissible_values: Abnormal lung auscultation [HP:0030829]: text: Abnormal lung auscultation [HP:0030829] @@ -3023,39 +2795,42 @@ enums: Vomiting (throwing up) [HP:0002013]: text: Vomiting (throwing up) [HP:0002013] meaning: HP:0002013 - host vaccination status menu: - name: host vaccination status menu + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu + title: host vaccination status menu permissible_values: Fully Vaccinated [GENEPIO:0100100]: text: Fully Vaccinated [GENEPIO:0100100] meaning: GENEPIO:0100100 exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination:Yes + - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination%3AYes Partially Vaccinated [GENEPIO:0100101]: text: Partially Vaccinated [GENEPIO:0100101] meaning: GENEPIO:0100101 exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination:Yes + - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination%3AYes Not Vaccinated [GENEPIO:0100102]: text: Not Vaccinated [GENEPIO:0100102] meaning: GENEPIO:0100102 exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination:No - prior SARS-CoV-2 antiviral treatment menu: - name: prior SARS-CoV-2 antiviral treatment menu + - NCBI_BIOSAMPLE:prior_sars_cov_2_vaccination%3ANo + PriorSarsCov2AntiviralTreatmentMenu: + name: PriorSarsCov2AntiviralTreatmentMenu + title: prior SARS-CoV-2 antiviral treatment menu permissible_values: Prior antiviral treatment [GENEPIO:0100037]: text: Prior antiviral treatment [GENEPIO:0100037] meaning: GENEPIO:0100237 exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment:Yes + - NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment%3AYes No prior antiviral treatment [GENEPIO:0100233]: text: No prior antiviral treatment [GENEPIO:0100233] meaning: GENEPIO:0100233 exact_mappings: - - NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment:No - pre-existing conditions and risk factors menu: - name: pre-existing conditions and risk factors menu + - NCBI_BIOSAMPLE:prior_sars_cov_2_antiviral_treatment%3ANo + PreExistingConditionsAndRiskFactorsMenu: + name: PreExistingConditionsAndRiskFactorsMenu + title: pre-existing conditions and risk factors menu permissible_values: Age 60+ [VO:0004925]: text: Age 60+ [VO:0004925] @@ -3146,10 +2921,6 @@ enums: Chronic gastrointestinal disease [GENEPIO:0100076]: text: Chronic gastrointestinal disease [GENEPIO:0100076] meaning: GENEPIO:0100076 - Chronic lung disease [HP:0006528]: - text: Chronic lung disease [HP:0006528] - meaning: HP:0006528 - is_a: Lung disease [MONDO:0005275] Corticosteroids [NCIT:C211]: text: Corticosteroids [NCIT:C211] meaning: NCIT:C211 @@ -3284,14 +3055,10 @@ enums: text: Chronic bronchitis [HP:0004469] meaning: HP:0004469 is_a: Respiratory disorder [MONDO:0005087] - Chronic pulmonary disease [HP:0006528]: - text: Chronic pulmonary disease [HP:0006528] - meaning: HP:0006528 - is_a: Respiratory disorder [MONDO:0005087] Chronic obstructive pulmonary disease [HP:0006510]: text: Chronic obstructive pulmonary disease [HP:0006510] meaning: HP:0006510 - is_a: Chronic pulmonary disease [HP:0006528] + is_a: Respiratory disorder [MONDO:0005087] Emphysema [HP:0002097]: text: Emphysema [HP:0002097] meaning: HP:0002097 @@ -3300,6 +3067,10 @@ enums: text: Lung disease [MONDO:0005275] meaning: MONDO:0005275 is_a: Respiratory disorder [MONDO:0005087] + Chronic lung disease [HP:0006528]: + text: Chronic lung disease [HP:0006528] + meaning: HP:0006528 + is_a: Lung disease [MONDO:0005275] Pulmonary fibrosis [HP:0002206]: text: Pulmonary fibrosis [HP:0002206] meaning: HP:0002206 @@ -3381,8 +3152,9 @@ enums: text: Liver transplant [GENEPIO:0100081] meaning: GENEPIO:0100081 is_a: Transplant [NCIT:C159659] - variant designation menu: - name: variant designation menu + VariantDesignationMenu: + name: VariantDesignationMenu + title: variant designation menu permissible_values: Variant of Interest (VOI) [GENEPIO:0100082]: text: Variant of Interest (VOI) [GENEPIO:0100082] @@ -3393,8 +3165,9 @@ enums: Variant Under Monitoring (VUM) [GENEPIO:0100279]: text: Variant Under Monitoring (VUM) [GENEPIO:0100279] meaning: GENEPIO:0100279 - complications menu: - name: complications menu + ComplicationsMenu: + name: ComplicationsMenu + title: complications menu permissible_values: Abnormal blood oxygen level [HP:0500165]: text: Abnormal blood oxygen level [HP:0500165] @@ -3665,8 +3438,9 @@ enums: Vasculitis [HP:0002633]: text: Vasculitis [HP:0002633] meaning: HP:0002633 - sample collected in quarantine menu: - name: sample collected in quarantine menu + SampleCollectedInQuarantineMenu: + name: SampleCollectedInQuarantineMenu + title: sample collected in quarantine menu permissible_values: Yes [NCIT:C49488]: text: Yes [NCIT:C49488] @@ -3674,8 +3448,9 @@ enums: No [NCIT:C49487]: text: No [NCIT:C49487] meaning: NCIT:C49487 - anatomical material menu: - name: anatomical material menu + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical material menu permissible_values: Blood [UBERON:0000178]: text: Blood [UBERON:0000178] @@ -3710,8 +3485,9 @@ enums: Tissue [UBERON:0000479]: text: Tissue [UBERON:0000479] meaning: UBERON:0000479 - anatomical part menu: - name: anatomical part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical part menu permissible_values: Anus [UBERON:0001245]: text: Anus [UBERON:0001245] @@ -3803,8 +3579,9 @@ enums: text: Oropharynx (OP) [UBERON:0001729] meaning: UBERON:0001729 is_a: Upper respiratory tract [UBERON:0001557] - body product menu: - name: body product menu + BodyProductMenu: + name: BodyProductMenu + title: body product menu permissible_values: Breast Milk [UBERON:0001913]: text: Breast Milk [UBERON:0001913] @@ -3831,8 +3608,9 @@ enums: Urine [UBERON:0001088]: text: Urine [UBERON:0001088] meaning: UBERON:0001088 - environmental material menu: - name: environmental material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu + title: environmental material menu permissible_values: Air vent [ENVO:03501208]: text: Air vent [ENVO:03501208] @@ -3934,8 +3712,9 @@ enums: Wood [ENVO:00002040]: text: Wood [ENVO:00002040] meaning: ENVO:00002040 - environmental site menu: - name: environmental site menu + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental site menu permissible_values: Acute care facility [ENVO:03501135]: text: Acute care facility [ENVO:03501135] @@ -4003,8 +3782,9 @@ enums: Wet market [ENVO:03501198]: text: Wet market [ENVO:03501198] meaning: ENVO:03501198 - collection method menu: - name: collection method menu + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: Amniocentesis [NCIT:C52009]: text: Amniocentesis [NCIT:C52009] @@ -4077,8 +3857,9 @@ enums: Washout Tear Collection [GENEPIO:0100038]: text: Washout Tear Collection [GENEPIO:0100038] meaning: GENEPIO:0100038 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: Air filter [ENVO:00003968]: text: Air filter [ENVO:00003968] @@ -4131,8 +3912,9 @@ enums: Virus Transport Medium [OBI:0002866]: text: Virus Transport Medium [OBI:0002866] meaning: OBI:0002866 - host (scientific name) menu: - name: host (scientific name) menu + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu permissible_values: Homo sapiens [NCBITaxon:9606]: text: Homo sapiens [NCBITaxon:9606] @@ -4182,8 +3964,9 @@ enums: Viverridae [NCBITaxon:9673]: text: Viverridae [NCBITaxon:9673] meaning: NCBITaxon:9673 - host (common name) menu: - name: host (common name) menu + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu permissible_values: Human [NCBITaxon:9606]: text: Human [NCBITaxon:9606] @@ -4224,8 +4007,9 @@ enums: Tiger [NCBITaxon:9694]: text: Tiger [NCBITaxon:9694] meaning: NCBITaxon:9694 - host health state menu: - name: host health state menu + HostHealthStateMenu: + name: HostHealthStateMenu + title: host health state menu permissible_values: Asymptomatic [NCIT:C3833]: text: Asymptomatic [NCIT:C3833] @@ -4242,8 +4026,9 @@ enums: Symptomatic [NCIT:C25269]: text: Symptomatic [NCIT:C25269] meaning: NCIT:C25269 - host health status details menu: - name: host health status details menu + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu + title: host health status details menu permissible_values: Hospitalized [NCIT:C25179]: text: Hospitalized [NCIT:C25179] @@ -4269,8 +4054,9 @@ enums: Self-quarantining [NCIT:C173768]: text: Self-quarantining [NCIT:C173768] meaning: NCIT:C173768 - host health outcome menu: - name: host health outcome menu + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu + title: host health outcome menu permissible_values: Deceased [NCIT:C28554]: text: Deceased [NCIT:C28554] @@ -4284,8 +4070,9 @@ enums: Stable [NCIT:C30103]: text: Stable [NCIT:C30103] meaning: NCIT:C30103 - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu + title: organism menu permissible_values: Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049]: text: Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] @@ -4296,8 +4083,9 @@ enums: RmYN02 [GENEPIO:0100000]: text: RmYN02 [GENEPIO:0100000] meaning: GENEPIO:0100000 - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation [GENEPIO:0100001]: text: Cluster/Outbreak investigation [GENEPIO:0100001] @@ -4315,8 +4103,9 @@ enums: Surveillance [GENEPIO:0100004]: text: Surveillance [GENEPIO:0100004] meaning: GENEPIO:0100004 - purpose of sequencing menu: - name: purpose of sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose of sequencing menu permissible_values: Baseline surveillance (random sampling) [GENEPIO:0100005]: text: Baseline surveillance (random sampling) [GENEPIO:0100005] @@ -4373,8 +4162,7 @@ enums: meaning: GENEPIO:0100014 is_a: Travel-associated surveillance [GENEPIO:0100012] Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015]: - text: - Surveillance of international border crossing by air travel or ground + text: Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015] meaning: GENEPIO:0100015 is_a: International travel surveillance [GENEPIO:0100014] @@ -4415,8 +4203,9 @@ enums: Retrospective sequencing [GENEPIO:0100356]: text: Retrospective sequencing [GENEPIO:0100356] meaning: GENEPIO:0100356 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Virus passage [GENEPIO:0100039]: text: Virus passage [GENEPIO:0100039] @@ -4430,8 +4219,9 @@ enums: Technical replicate [EFO:0002090]: text: Technical replicate [EFO:0002090] meaning: EFO:0002090 - lab host menu: - name: lab host menu + LabHostMenu: + name: LabHostMenu + title: lab host menu permissible_values: 293/ACE2 cell line [GENEPIO:0100041]: text: 293/ACE2 cell line [GENEPIO:0100041] @@ -4483,14 +4273,16 @@ enums: text: VeroE6/TMPRSS2 cell line [GENEPIO:0100044] meaning: GENEPIO:0100044 is_a: Vero E6 cell line [BTO:0004755] - host disease menu: - name: host disease menu + HostDiseaseMenu: + name: HostDiseaseMenu + title: host disease menu permissible_values: COVID-19 [MONDO:0100096]: text: COVID-19 [MONDO:0100096] meaning: MONDO:0100096 - host age bin menu: - name: host age bin menu + HostAgeBinMenu: + name: HostAgeBinMenu + title: host age bin menu permissible_values: 0 - 9 [GENEPIO:0100049]: text: 0 - 9 [GENEPIO:0100049] @@ -4525,8 +4317,9 @@ enums: 100+ [GENEPIO:0100059]: text: 100+ [GENEPIO:0100059] meaning: GENEPIO:0100059 - host gender menu: - name: host gender menu + HostGenderMenu: + name: HostGenderMenu + title: host gender menu permissible_values: Female [NCIT:C46110]: text: Female [NCIT:C46110] @@ -4546,8 +4339,9 @@ enums: Undeclared [NCIT:C110959]: text: Undeclared [NCIT:C110959] meaning: NCIT:C110959 - exposure event menu: - name: exposure event menu + ExposureEventMenu: + name: ExposureEventMenu + title: exposure event menu permissible_values: Mass Gathering [GENEPIO:0100237]: text: Mass Gathering [GENEPIO:0100237] @@ -4608,8 +4402,9 @@ enums: is_a: Social Gathering [PCO:0000033] Other exposure event: text: Other exposure event - exposure contact level menu: - name: exposure contact level menu + ExposureContactLevelMenu: + name: ExposureContactLevelMenu + title: exposure contact level menu permissible_values: Contact with infected individual: text: Contact with infected individual @@ -4630,8 +4425,9 @@ enums: text: Casual contact [GENEPIO:0100248] meaning: GENEPIO:0100248 is_a: Indirect contact [GENEPIO:0100246] - host role menu: - name: host role menu + HostRoleMenu: + name: HostRoleMenu + title: host role menu permissible_values: Attendee [GENEPIO:0100249]: text: Attendee [GENEPIO:0100249] @@ -4767,8 +4563,9 @@ enums: is_a: Social role [OMRSE:00000001] Other Host Role: text: Other Host Role - exposure setting menu: - name: exposure setting menu + ExposureSettingMenu: + name: ExposureSettingMenu + title: exposure setting menu permissible_values: Human Exposure [ECTO:3000005]: text: Human Exposure [ECTO:3000005] @@ -5024,8 +4821,9 @@ enums: No prior antiviral treatment [GENEPIO:0100233]: text: No prior antiviral treatment [GENEPIO:0100233] meaning: GENEPIO:0100233 - prior SARS-CoV-2 infection menu: - name: prior SARS-CoV-2 infection menu + PriorSarsCov2InfectionMenu: + name: PriorSarsCov2InfectionMenu + title: prior SARS-CoV-2 infection menu permissible_values: Prior infection [GENEPIO:0100234]: text: Prior infection [GENEPIO:0100234] @@ -5033,162 +4831,163 @@ enums: No prior infection [GENEPIO:0100236]: text: No prior infection [GENEPIO:0100236] meaning: GENEPIO:0100236 - sequencing instrument menu: - name: sequencing instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: Illumina sequencing instrument [GENEPIO:0100105]: text: Illumina sequencing instrument [GENEPIO:0100105] meaning: GENEPIO:0100105 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA Illumina Genome Analyzer [GENEPIO:0100106]: text: Illumina Genome Analyzer [GENEPIO:0100106] meaning: GENEPIO:0100106 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina Genome Analyzer + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20Genome%20Analyzer is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina Genome Analyzer II [GENEPIO:0100107]: text: Illumina Genome Analyzer II [GENEPIO:0100107] meaning: GENEPIO:0100107 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina Genome Analyzer II + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20Genome%20Analyzer%20II is_a: Illumina Genome Analyzer [GENEPIO:0100106] Illumina Genome Analyzer IIx [GENEPIO:0100108]: text: Illumina Genome Analyzer IIx [GENEPIO:0100108] meaning: GENEPIO:0100108 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina Genome Analyzer IIx + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20Genome%20Analyzer%20IIx is_a: Illumina Genome Analyzer [GENEPIO:0100106] Illumina HiScanSQ [GENEPIO:0100109]: text: Illumina HiScanSQ [GENEPIO:0100109] meaning: GENEPIO:0100109 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina HiScanSQ + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20HiScanSQ is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina HiSeq [GENEPIO:0100110]: text: Illumina HiSeq [GENEPIO:0100110] meaning: GENEPIO:0100110 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina HiSeq X [GENEPIO:0100111]: text: Illumina HiSeq X [GENEPIO:0100111] meaning: GENEPIO:0100111 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq X Five [GENEPIO:0100112]: text: Illumina HiSeq X Five [GENEPIO:0100112] meaning: GENEPIO:0100112 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - 'NCBI_SRA:instrument_model: Illumina HiSeq X Five' + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3A%20Illumina%20HiSeq%20X%20Five is_a: Illumina HiSeq X [GENEPIO:0100111] Illumina HiSeq X Ten [GENEPIO:0100113]: text: Illumina HiSeq X Ten [GENEPIO:0100113] meaning: GENEPIO:0100113 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina HiSeq X Ten + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20HiSeq%20X%20Ten is_a: Illumina HiSeq X [GENEPIO:0100111] Illumina HiSeq 1000 [GENEPIO:0100114]: text: Illumina HiSeq 1000 [GENEPIO:0100114] meaning: GENEPIO:0100114 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina HiSeq 1000 + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20HiSeq%201000 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 1500 [GENEPIO:0100115]: text: Illumina HiSeq 1500 [GENEPIO:0100115] meaning: GENEPIO:0100115 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 2000 [GENEPIO:0100116]: text: Illumina HiSeq 2000 [GENEPIO:0100116] meaning: GENEPIO:0100116 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina HiSeq 2000 + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20HiSeq%202000 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 2500 [GENEPIO:0100117]: text: Illumina HiSeq 2500 [GENEPIO:0100117] meaning: GENEPIO:0100117 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina HiSeq 2500 + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20HiSeq%202500 is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 3000 [GENEPIO:0100118]: text: Illumina HiSeq 3000 [GENEPIO:0100118] meaning: GENEPIO:0100118 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina HiSeq [GENEPIO:0100110] Illumina HiSeq 4000 [GENEPIO:0100119]: text: Illumina HiSeq 4000 [GENEPIO:0100119] meaning: GENEPIO:0100119 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina HiSeq [GENEPIO:0100110] Illumina iSeq [GENEPIO:0100120]: text: Illumina iSeq [GENEPIO:0100120] meaning: GENEPIO:0100120 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina iSeq 100 [GENEPIO:0100121]: text: Illumina iSeq 100 [GENEPIO:0100121] meaning: GENEPIO:0100121 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina iSeq [GENEPIO:0100120] Illumina NovaSeq [GENEPIO:0100122]: text: Illumina NovaSeq [GENEPIO:0100122] meaning: GENEPIO:0100122 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina NovaSeq 6000 [GENEPIO:0100123]: text: Illumina NovaSeq 6000 [GENEPIO:0100123] meaning: GENEPIO:0100123 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina NovaSeq [GENEPIO:0100122] Illumina MiniSeq [GENEPIO:0100124]: text: Illumina MiniSeq [GENEPIO:0100124] meaning: GENEPIO:0100124 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina MiSeq [GENEPIO:0100125]: text: Illumina MiSeq [GENEPIO:0100125] meaning: GENEPIO:0100125 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina MiSeq + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20MiSeq is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina NextSeq [GENEPIO:0100126]: text: Illumina NextSeq [GENEPIO:0100126] meaning: GENEPIO:0100126 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina sequencing instrument [GENEPIO:0100105] Illumina NextSeq 500 [GENEPIO:0100127]: text: Illumina NextSeq 500 [GENEPIO:0100127] meaning: GENEPIO:0100127 exact_mappings: - - NCBI_SRA:platform:ILLUMINA - - NCBI_SRA:instrument_model:Illumina NextSeq 500 + - NCBI_SRA:platform%3AILLUMINA + - NCBI_SRA:instrument_model%3AIllumina%20NextSeq%20500 is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 550 [GENEPIO:0100128]: text: Illumina NextSeq 550 [GENEPIO:0100128] meaning: GENEPIO:0100128 exact_mappings: - - NCBI_SRA:platform:ILLUMINA + - NCBI_SRA:platform%3AILLUMINA is_a: Illumina NextSeq [GENEPIO:0100126] Illumina NextSeq 2000 [GENEPIO:0100129]: text: Illumina NextSeq 2000 [GENEPIO:0100129] @@ -5198,88 +4997,88 @@ enums: text: Pacific Biosciences sequencing instrument [GENEPIO:0100130] meaning: GENEPIO:0100130 exact_mappings: - - NCBI_SRA:platform:PACBIO_SMRT + - NCBI_SRA:platform%3APACBIO_SMRT PacBio RS [GENEPIO:0100131]: text: PacBio RS [GENEPIO:0100131] meaning: GENEPIO:0100131 exact_mappings: - - NCBI_SRA:platform:PACBIO_SMRT - - NCBI_SRA:instrument_model:PacBio RS + - NCBI_SRA:platform%3APACBIO_SMRT + - NCBI_SRA:instrument_model%3APacBio%20RS is_a: Pacific Biosciences sequencing instrument [GENEPIO:0100130] PacBio RS II [GENEPIO:0100132]: text: PacBio RS II [GENEPIO:0100132] meaning: GENEPIO:0100132 exact_mappings: - - NCBI_SRA:platform:PACBIO_SMRT - - NCBI_SRA:instrument_model:PacBio RS II + - NCBI_SRA:platform%3APACBIO_SMRT + - NCBI_SRA:instrument_model%3APacBio%20RS%20II is_a: Pacific Biosciences sequencing instrument [GENEPIO:0100130] PacBio Sequel [GENEPIO:0100133]: text: PacBio Sequel [GENEPIO:0100133] meaning: GENEPIO:0100133 exact_mappings: - - NCBI_SRA:platform:PACBIO_SMRT + - NCBI_SRA:platform%3APACBIO_SMRT is_a: Pacific Biosciences sequencing instrument [GENEPIO:0100130] PacBio Sequel II [GENEPIO:0100134]: text: PacBio Sequel II [GENEPIO:0100134] meaning: GENEPIO:0100134 exact_mappings: - - NCBI_SRA:platform:PACBIO_SMRT + - NCBI_SRA:platform%3APACBIO_SMRT is_a: Pacific Biosciences sequencing instrument [GENEPIO:0100130] Ion Torrent sequencing instrument [GENEPIO:0100135]: text: Ion Torrent sequencing instrument [GENEPIO:0100135] meaning: GENEPIO:0100135 exact_mappings: - - NCBI_SRA:platform:ION_TORRENT + - NCBI_SRA:platform%3AION_TORRENT Ion Torrent PGM [GENEPIO:0100136]: text: Ion Torrent PGM [GENEPIO:0100136] meaning: GENEPIO:0100136 exact_mappings: - - NCBI_SRA:platform:ION_TORRENT - - NCBI_SRA:instrument_model:Ion Torrent PGM + - NCBI_SRA:platform%3AION_TORRENT + - NCBI_SRA:instrument_model%3AIon%20Torrent%20PGM is_a: Ion Torrent sequencing instrument [GENEPIO:0100135] Ion Torrent Proton [GENEPIO:0100137]: text: Ion Torrent Proton [GENEPIO:0100137] meaning: GENEPIO:0100137 exact_mappings: - - NCBI_SRA:platform:ION_TORRENT - - NCBI_SRA:instrument_model:Ion Torrent Proton + - NCBI_SRA:platform%3AION_TORRENT + - NCBI_SRA:instrument_model%3AIon%20Torrent%20Proton is_a: Ion Torrent sequencing instrument [GENEPIO:0100135] Ion Torrent S5 XL [GENEPIO:0100138]: text: Ion Torrent S5 XL [GENEPIO:0100138] meaning: GENEPIO:0100138 exact_mappings: - - NCBI_SRA:platform:ION_TORRENT + - NCBI_SRA:platform%3AION_TORRENT is_a: Ion Torrent sequencing instrument [GENEPIO:0100135] Ion Torrent S5 [GENEPIO:0100139]: text: Ion Torrent S5 [GENEPIO:0100139] meaning: GENEPIO:0100139 exact_mappings: - - NCBI_SRA:platform:ION_TORRENT + - NCBI_SRA:platform%3AION_TORRENT is_a: Ion Torrent sequencing instrument [GENEPIO:0100135] Oxford Nanopore sequencing instrument [GENEPIO:0100140]: text: Oxford Nanopore sequencing instrument [GENEPIO:0100140] meaning: GENEPIO:0100140 exact_mappings: - - NCBI_SRA:platform:OXFORD_NANOPORE + - NCBI_SRA:platform%3AOXFORD_NANOPORE Oxford Nanopore GridION [GENEPIO:0100141]: text: Oxford Nanopore GridION [GENEPIO:0100141] meaning: GENEPIO:0100141 exact_mappings: - - NCBI_SRA:platform:OXFORD_NANOPORE - - NCBI_SRA:instrument_model:GridION + - NCBI_SRA:platform%3AOXFORD_NANOPORE + - NCBI_SRA:instrument_model%3AGridION is_a: Oxford Nanopore sequencing instrument [GENEPIO:0100140] Oxford Nanopore MinION [GENEPIO:0100142]: text: Oxford Nanopore MinION [GENEPIO:0100142] meaning: GENEPIO:0100142 exact_mappings: - - NCBI_SRA:platform:OXFORD_NANOPORE - - NCBI_SRA:instrument_model:MinION + - NCBI_SRA:platform%3AOXFORD_NANOPORE + - NCBI_SRA:instrument_model%3AMinION is_a: Oxford Nanopore sequencing instrument [GENEPIO:0100140] Oxford Nanopore PromethION [GENEPIO:0100143]: text: Oxford Nanopore PromethION [GENEPIO:0100143] meaning: GENEPIO:0100143 exact_mappings: - - NCBI_SRA:platform:OXFORD_NANOPORE + - NCBI_SRA:platform%3AOXFORD_NANOPORE is_a: Oxford Nanopore sequencing instrument [GENEPIO:0100140] BGI Genomics sequencing instrument [GENEPIO:0100144]: text: BGI Genomics sequencing instrument [GENEPIO:0100144] @@ -5307,8 +5106,9 @@ enums: text: MGI DNBSEQ-G50 [GENEPIO:0100150] meaning: GENEPIO:0100150 is_a: MGI sequencing instrument [GENEPIO:0100146] - gene name menu: - name: gene name menu + GeneNameMenu: + name: GeneNameMenu + title: gene name menu permissible_values: E gene (orf4) [GENEPIO:0100151]: text: E gene (orf4) [GENEPIO:0100151] @@ -5426,8 +5226,9 @@ enums: SARS-COV-2 5' UTR [GENEPIO:0100183]: text: SARS-COV-2 5' UTR [GENEPIO:0100183] meaning: GENEPIO:0100183 - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: Afghanistan [GAZ:00006882]: text: Afghanistan [GAZ:00006882] @@ -6242,8 +6043,9 @@ enums: Zimbabwe [GAZ:00001106]: text: Zimbabwe [GAZ:00001106] meaning: GAZ:00001106 - library_strategy menu: - name: library_strategy menu + LibraryStrategyMenu: + name: LibraryStrategyMenu + title: library_strategy menu permissible_values: WGA: text: WGA @@ -6291,8 +6093,9 @@ enums: text: MBD-Seq OTHER: text: OTHER - library_source menu: - name: library_source menu + LibrarySourceMenu: + name: LibrarySourceMenu + title: library_source menu permissible_values: GENOMIC: text: GENOMIC @@ -6308,8 +6111,9 @@ enums: text: VIRAL RNA OTHER: text: OTHER - library_selection menu: - name: library_selection menu + LibrarySelectionMenu: + name: LibrarySelectionMenu + title: library_selection menu permissible_values: RANDOM: text: RANDOM @@ -6365,15 +6169,17 @@ enums: text: other unspecified: text: unspecified - library_layout menu: - name: library_layout menu + LibraryLayoutMenu: + name: LibraryLayoutMenu + title: library_layout menu permissible_values: single: text: single paired: text: paired - filetype menu: - name: filetype menu + FiletypeMenu: + name: FiletypeMenu + title: filetype menu permissible_values: bam: text: bam @@ -6403,8 +6209,7 @@ types: WhitespaceMinimizedString: name: WhitespaceMinimizedString typeof: string - description: - 'A string that has all whitespace trimmed off of beginning and end, + description: 'A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).' base: str @@ -6412,8 +6217,7 @@ types: Provenance: name: Provenance typeof: string - description: - A field containing a DataHarmonizer versioning marker. It is issued + description: A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data. base: str uri: xsd:token diff --git a/web/templates/pha4ge/schema_enums.tsv b/web/templates/pha4ge/schema_enums.tsv index 185fad8b..ea59caf8 100644 --- a/web/templates/pha4ge/schema_enums.tsv +++ b/web/templates/pha4ge/schema_enums.tsv @@ -1,1167 +1,1165 @@ -title meaning in_subset menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE EXPORT_NCBI_SRA EXPORT_NCBI_Genbank EXPORT_NCBI_Genbank_source_modifiers - -null value menu GENEPIO:0001619 Covid-19 Not Applicable [GENEPIO:0001619] - GENEPIO:0001620 Covid-19 Not Collected [GENEPIO:0001620] - GENEPIO:0001668 Covid-19 Not Provided [GENEPIO:0001668] - GENEPIO:0001618 Covid-19 Missing [GENEPIO:0001618] - GENEPIO:0001810 Covid-19 Restricted Access [GENEPIO:0001810] - - -host age unit menu UO:0000035 Covid-19 month [UO:0000035] - UO:0000036 Covid-19 year [UO:0000036] - - -biomaterial extracted menu OBI:0000895 Covid-19 RNA (Total) [OBI:0000895] - OBI:0000869 Covid-19 RNA (Poly-A) [OBI:0000869] - OBI:0002627 Covid-19 RNA (Ribo-Depleted) [OBI:0002627] - GENEPIO:0100104 Covid-19 mRNA (messenger RNA) [GENEPIO:0100104] - OBI:0002754 Covid-19 mRNA (cDNA) [OBI:0002754] - - -signs and symptoms menu HP:0030829 Covid-19 Abnormal lung auscultation [HP:0030829] - HP:0000223 Covid-19 Abnormality of taste sensation [HP:0000223] - HP:0041051 Covid-19 Ageusia (complete loss of taste) [HP:0041051] - HP:0031249 Covid-19 Parageusia (distorted sense of taste) [HP:0031249] - HP:0000224 Covid-19 Hypogeusia (reduced sense of taste) [HP:0000224] - HP:0004408 Covid-19 Abnormality of the sense of smell [HP:0004408] - HP:0000458 Covid-19 Anosmia (lost sense of smell) [HP:0000458] - HP:0004409 Covid-19 Hyposmia (reduced sense of smell) [HP:0004409] - HP:0033677 Covid-19 Acute Respiratory Distress Syndrome [HP:0033677] - HP:0011446 Covid-19 Altered mental status [HP:0011446] - HP:0100543 Covid-19 Cognitive impairment [HP:0100543] - HP:0001259 Covid-19 Coma [HP:0001259] - HP:0001289 Covid-19 Confusion [HP:0001289] - HP:0031258 Covid-19 Delirium (sudden severe confusion) [HP:0031258] - GENEPIO:0100061 Covid-19 Inability to arouse (inability to stay awake) [GENEPIO:0100061] - HP:0000737 Covid-19 Irritability [HP:0000737] - HP:0002371 Covid-19 Loss of speech [HP:0002371] - HP:0011675 Covid-19 Arrhythmia [HP:0011675] - HP:0025406 Covid-19 Asthenia (generalized weakness) [HP:0025406] - HP:0031352 Covid-19 Chest tightness or pressure [HP:0031352] - HP:0025145 Covid-19 Rigors (fever shakes) [HP:0025145] - HP:0025143 Covid-19 Chills (sudden cold sensation) [HP:0025143] - HP:0030953 Covid-19 Conjunctival injection [HP:0030953] - HP:0000509 Covid-19 Conjunctivitis (pink eye) [HP:0000509] - MP:0001867 Covid-19 Coryza (rhinitis) [MP:0001867] - HP:0012735 Covid-19 Cough [HP:0012735] - HP:0031246 Covid-19 Nonproductive cough (dry cough) [HP:0031246] - HP:0031245 Covid-19 Productive cough (wet cough) [HP:0031245] - HP:0000961 Covid-19 Cyanosis (blueish skin discolouration) [HP:0000961] - HP:0001063 Covid-19 Acrocyanosis [HP:0001063] - HP:0032556 Covid-19 Circumoral cyanosis (bluish around mouth) [HP:0032556] - GENEPIO:0100062 Covid-19 Cyanotic face (bluish face) [GENEPIO:0100062] - GENEPIO:0100063 Covid-19 Central Cyanosis [GENEPIO:0100063] - GENEPIO:0100064 Covid-19 Cyanotic lips (bluish lips) [GENEPIO:0100064] - GENEPIO:0100065 Covid-19 Peripheral Cyanosis [GENEPIO:0100065] - HP:0002094 Covid-19 Dyspnea (breathing difficulty) [HP:0002094] - HP:0002014 Covid-19 Diarrhea (watery stool) [HP:0002014] - MP:0031127 Covid-19 Dry gangrene [MP:0031127] - HP:0002383 Covid-19 Encephalitis (brain inflammation) [HP:0002383] - HP:0001298 Covid-19 Encephalopathy [HP:0001298] - HP:0012378 Covid-19 Fatigue (tiredness) [HP:0012378] - HP:0001945 Covid-19 Fever [HP:0001945] - GENEPIO:0100066 Covid-19 Fever (>=38°C) [GENEPIO:0100066] - HP:0000206 Covid-19 Glossitis (inflammation of the tongue) [HP:0000206] - GENEPIO:0100067 Covid-19 Ground Glass Opacities (GGO) [GENEPIO:0100067] - HP:0002315 Covid-19 Headache [HP:0002315] - HP:0002105 Covid-19 Hemoptysis (coughing up blood) [HP:0002105] - HP:0012417 Covid-19 Hypocapnia [HP:0012417] - HP:0002615 Covid-19 Hypotension (low blood pressure) [HP:0002615] - HP:0012418 Covid-19 Hypoxemia (low blood oxygen) [HP:0012418] - GENEPIO:0100068 Covid-19 Silent hypoxemia [GENEPIO:0100068] - HP:0011029 Covid-19 Internal hemorrhage (internal bleeding) [HP:0011029] - NCIT:C121416 Covid-19 Loss of Fine Movements [NCIT:C121416] - HP:0004396 Covid-19 Low appetite [HP:0004396] - HP:0033834 Covid-19 Malaise (general discomfort/unease) [HP:0033834] - HP:0031179 Covid-19 Meningismus/nuchal rigidity [HP:0031179] - HP:0001324 Covid-19 Muscle weakness [HP:0001324] - HP:0001742 Covid-19 Nasal obstruction (stuffy nose) [HP:0001742] - HP:0002018 Covid-19 Nausea [HP:0002018] - HP:0000421 Covid-19 Nose bleed [HP:0000421] - GENEPIO:0100069 Covid-19 Otitis [GENEPIO:0100069] - HP:0012531 Covid-19 Pain [HP:0012531] - HP:0002027 Covid-19 Abdominal pain [HP:0002027] - HP:0002829 Covid-19 Arthralgia (painful joints) [HP:0002829] - HP:0100749 Covid-19 Chest pain [HP:0100749] - HP:0033771 Covid-19 Pleuritic chest pain [HP:0033771] - HP:0003326 Covid-19 Myalgia (muscle pain) [HP:0003326] - HP:0025439 Covid-19 Pharyngitis (sore throat) [HP:0025439] - GENEPIO:0100070 Covid-19 Pharyngeal exudate [GENEPIO:0100070] - HP:0002202 Covid-19 Pleural effusion [HP:0002202] - HP:0002090 Covid-19 Pneumonia [HP:0002090] - HP:0033696 Covid-19 Pseudo-chilblains [HP:0033696] - GENEPIO:0100072 Covid-19 Pseudo-chilblains on fingers (covid fingers) [GENEPIO:0100072] - GENEPIO:0100073 Covid-19 Pseudo-chilblains on toes (covid toes) [GENEPIO:0100073] - HP:0000988 Covid-19 Rash [HP:0000988] - HP:0031417 Covid-19 Rhinorrhea (runny nose) [HP:0031417] - HP:0001250 Covid-19 Seizure [HP:0001250] - HP:0020219 Covid-19 Motor seizure [HP:0020219] - HP:0025144 Covid-19 Shivering (involuntary muscle twitching) [HP:0025144] - HP:0001350 Covid-19 Slurred speech [HP:0001350] - HP:0025095 Covid-19 Sneezing [HP:0025095] - HP:0033709 Covid-19 Sputum Production [HP:0033709] - HP:0001297 Covid-19 Stroke [HP:0001297] - HP:0002716 Covid-19 Swollen Lymph Nodes [HP:0002716] - HP:0002789 Covid-19 Tachypnea (accelerated respiratory rate) [HP:0002789] - HP:0002321 Covid-19 Vertigo (dizziness) [HP:0002321] - HP:0002013 Covid-19 Vomiting (throwing up) [HP:0002013] - - -host vaccination status menu GENEPIO:0100100 Covid-19 Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination:Yes - GENEPIO:0100101 Covid-19 Partially Vaccinated [GENEPIO:0100101] prior_sars_cov_2_vaccination:Yes - GENEPIO:0100102 Covid-19 Not Vaccinated [GENEPIO:0100102] prior_sars_cov_2_vaccination:No - - -prior SARS-CoV-2 antiviral treatment menu GENEPIO:0100237 Covid-19 Prior antiviral treatment [GENEPIO:0100037] prior_sars_cov_2_antiviral_treatment:Yes - GENEPIO:0100233 Covid-19 No prior antiviral treatment [GENEPIO:0100233] prior_sars_cov_2_antiviral_treatment:No - - -pre-existing conditions and risk factors menu VO:0004925 Covid-19 Age 60+ [VO:0004925] - HP:0001903 Covid-19 Anemia [HP:0001903] - HP:0002039 Covid-19 Anorexia [HP:0002039] - NCIT:C92743 Covid-19 Birthing labor [NCIT:C92743] - NCIT:C80693 Covid-19 Bone marrow failure [NCIT:C80693] - MONDO:0004992 Covid-19 Cancer [MONDO:0004992] - MONDO:0007254 Covid-19 Breast cancer [MONDO:0007254] - MONDO:0005575 Covid-19 Colorectal cancer [MONDO:0005575] - DOID:2531 Covid-19 Hematologic malignancy (cancer of the blood) [DOID:2531] - MONDO:0008903 Covid-19 Lung cancer [MONDO:0008903] - MONDO:0024880 Covid-19 Metastatic disease [MONDO:0024880] - NCIT:C16212 Covid-19 Cancer treatment [NCIT:C16212] - NCIT:C157740 Covid-19 Cancer surgery [NCIT:C157740] - NCIT:C15632 Covid-19 Chemotherapy [NCIT:C15632] - NCIT:C15360 Covid-19 Adjuvant chemotherapy [NCIT:C15360] - NCIT:C3079 Covid-19 Cardiac disorder [NCIT:C3079] - HP:0011675 Covid-19 Arrhythmia [HP:0011675] - MONDO:0005267 Covid-19 Cardiac disease [MONDO:0005267] - HP:0001638 Covid-19 Cardiomyopathy [HP:0001638] - GENEPIO:0100074 Covid-19 Cardiac injury [GENEPIO:0100074] - HP:0000822 Covid-19 Hypertension (high blood pressure) [HP:0000822] - HP:0002615 Covid-19 Hypotension (low blood pressure) [HP:0002615] - HP:0011410 Covid-19 Cesarean section [HP:0011410] - GENEPIO:0100075 Covid-19 Chronic cough [GENEPIO:0100075] - GENEPIO:0100076 Covid-19 Chronic gastrointestinal disease [GENEPIO:0100076] - HP:0006528 Covid-19 Chronic lung disease [HP:0006528] - NCIT:C211 Covid-19 Corticosteroids [NCIT:C211] - HP:0000819 Covid-19 Diabetes mellitus (diabetes) [HP:0000819] - HP:0100651 Covid-19 Type I diabetes mellitus (T1D) [HP:0100651] - HP:0005978 Covid-19 Type II diabetes mellitus (T2D) [HP:0005978] - HP:0000964 Covid-19 Eczema [HP:0000964] - HP:0003111 Covid-19 Electrolyte disturbance [HP:0003111] - HP:0002901 Covid-19 Hypocalcemia [HP:0002901] - HP:0002900 Covid-19 Hypokalemia [HP:0002900] - HP:0002917 Covid-19 Hypomagnesemia [HP:0002917] - HP:0002383 Covid-19 Encephalitis (brain inflammation) [HP:0002383] - MONDO:0005027 Covid-19 Epilepsy [MONDO:0005027] - NCIT:C15248 Covid-19 Hemodialysis [NCIT:C15248] - MONDO:0044348 Covid-19 Hemoglobinopathy [MONDO:0044348] - MONDO:0005109 Covid-19 Human immunodeficiency virus (HIV) [MONDO:0005109] - MONDO:0012268 Covid-19 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] - NCIT:C16118 Covid-19 HIV and antiretroviral therapy (ART) [NCIT:C16118] - NCIT:C14139 Covid-19 Immunocompromised [NCIT:C14139] - MONDO:0004670 Covid-19 Lupus [MONDO:0004670] - MONDO:0005265 Covid-19 Inflammatory bowel disease (IBD) [MONDO:0005265] - HP:0002583 Covid-19 Colitis [HP:0002583] - HP:0100279 Covid-19 Ulcerative colitis [HP:0100279] - HP:0100280 Covid-19 Crohn's disease [HP:0100280] - NCIT:C3149 Covid-19 Renal disorder [NCIT:C3149] - MONDO:0005240 Covid-19 Renal disease [MONDO:0005240] - HP:0012622 Covid-19 Chronic renal disease [HP:0012622] - HP:0000083 Covid-19 Renal failure [HP:0000083] - MONDO:0005154 Covid-19 Liver disease [MONDO:0005154] - NCIT:C113609 Covid-19 Chronic liver disease [NCIT:C113609] - HP:0001397 Covid-19 Fatty liver disease (FLD) [HP:0001397] - HP:0003326 Covid-19 Myalgia (muscle pain) [HP:0003326] - MONDO:0005404 Covid-19 Myalgic encephalomyelitis (ME) [MONDO:0005404] - MONDO:0005071 Covid-19 Neurological disorder [MONDO:0005071] - MONDO:0019056 Covid-19 Neuromuscular disorder [MONDO:0019056] - HP:0001513 Covid-19 Obesity [HP:0001513] - MONDO:0005139 Covid-19 Severe obesity [MONDO:0005139] - MONDO:0005087 Covid-19 Respiratory disorder [MONDO:0005087] - HP:0002099 Covid-19 Asthma [HP:0002099] - HP:0004469 Covid-19 Chronic bronchitis [HP:0004469] - HP:0006528 Covid-19 Chronic pulmonary disease [HP:0006528] - HP:0006510 Covid-19 Chronic obstructive pulmonary disease [HP:0006510] - HP:0002097 Covid-19 Emphysema [HP:0002097] - MONDO:0005275 Covid-19 Lung disease [MONDO:0005275] - HP:0006528 Covid-19 Chronic lung disease [HP:0006528] - HP:0002206 Covid-19 Pulmonary fibrosis [HP:0002206] - HP:0002090 Covid-19 Pneumonia [HP:0002090] - HP:0002878 Covid-19 Respiratory failure [HP:0002878] - HP:0033677 Covid-19 Adult respiratory distress syndrome [HP:0033677] - MONDO:0009971 Covid-19 Newborn respiratory distress syndrome [MONDO:0009971] - MONDO:0018076 Covid-19 Tuberculosis [MONDO:0018076] - GENEPIO:0100077 Covid-19 Postpartum (≤6 weeks) [GENEPIO:0100077] - NCIT:C25742 Covid-19 Pregnancy [NCIT:C25742] - MONDO:0005554 Covid-19 Rheumatic disease [MONDO:0005554] - MONDO:0011382 Covid-19 Sickle cell disease [MONDO:0011382] - NBO:0001845 Covid-19 Substance use [NBO:0001845] - MONDO:0002046 Covid-19 Alcohol abuse [MONDO:0002046] - GENEPIO:0100078 Covid-19 Drug abuse [GENEPIO:0100078] - GENEPIO:0100079 Covid-19 Injection drug abuse [GENEPIO:0100079] - NBO:0015005 Covid-19 Smoking [NBO:0015005] - NCIT:C173621 Covid-19 Vaping [NCIT:C173621] - HP:0002789 Covid-19 Tachypnea (accelerated respiratory rate) [HP:0002789] - NCIT:C159659 Covid-19 Transplant [NCIT:C159659] - GENEPIO:0100080 Covid-19 Cardiac transplant [NCIT:C131759] - NCIT:C131759 Covid-19 Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080] - NCIT:C157332 Covid-19 Kidney transplant [NCIT:C157332] - GENEPIO:0100081 Covid-19 Liver transplant [GENEPIO:0100081] - - -variant designation menu GENEPIO:0100082 Covid-19 Variant of Interest (VOI) [GENEPIO:0100082] - GENEPIO:0100083 Covid-19 Variant of Concern (VOC) [GENEPIO:0100083] - GENEPIO:0100279 Covid-19 Variant Under Monitoring (VUM) [GENEPIO:0100279] - - -complications menu HP:0500165 Covid-19 Abnormal blood oxygen level [HP:0500165] - HP:0001919 Covid-19 Acute kidney injury [HP:0001919] - MONDO:0015796 Covid-19 Acute lung injury [MONDO:0015796] - GENEPIO:0100092 Covid-19 Ventilation induced lung injury (VILI) [GENEPIO:0100092] - MONDO:0001208 Covid-19 Acute respiratory failure [MONDO:0001208] - HP:0011675 Covid-19 Arrhythmia (complication) [HP:0011675] - HP:0001649 Covid-19 Tachycardia [HP:0001649] - HP:0031677 Covid-19 Polymorphic ventricular tachycardia (VT) [HP:0031677] - GENEPIO:0100084 Covid-19 Tachyarrhythmia [GENEPIO:0100084] - GENEPIO:0100087 Covid-19 Cardiac injury [GENEPIO:0100074] - HP:0001695 Covid-19 Cardiac arrest [HP:0001695] - HP:0030149 Covid-19 Cardiogenic shock [HP:0030149] - HP:0001977 Covid-19 Blood clot [HP:0001977] - HP:0004420 Covid-19 Arterial clot [HP:0004420] - HP:0002625 Covid-19 Deep vein thrombosis (DVT) [HP:0002625] - HP:0002204 Covid-19 Pulmonary embolism (PE) [HP:0002204] - HP:0001638 Covid-19 Cardiomyopathy [HP:0001638] - MONDO:0024619 Covid-19 Central nervous system invasion [MONDO:0024619] - HP:0001297 Covid-19 Stroke (complication) [HP:0001297] - MONDO:0003346 Covid-19 Central Nervous System Vasculitis [MONDO:0003346] - HP:0002140 Covid-19 Acute ischemic stroke [HP:0002140] - HP:0001259 Covid-19 Coma [HP:0001259] - HP:0011097 Covid-19 Convulsions [HP:0011097] - NCIT:C171562 Covid-19 COVID-19 associated coagulopathy (CAC) [NCIT:C171562] - MONDO:0009061 Covid-19 Cystic fibrosis [MONDO:0009061] - MONDO:0600008 Covid-19 Cytokine release syndrome [MONDO:0600008] - MPATH:108 Covid-19 Disseminated intravascular coagulation (DIC) [MPATH:108] - HP:0001298 Covid-19 Encephalopathy [HP:0001298] - GENEPIO:0100088 Covid-19 Fulminant myocarditis [GENEPIO:0100088] - MONDO:0016218 Covid-19 Guillain-Barré syndrome [MONDO:0016218] - HP:0011029 Covid-19 Internal hemorrhage (complication; internal bleeding) [HP:0011029] - MONDO:0013792 Covid-19 Intracerebral haemorrhage [MONDO:0013792] - MONDO:0012727 Covid-19 Kawasaki disease [MONDO:0012727] - GENEPIO:0100089 Covid-19 Complete Kawasaki disease [GENEPIO:0100089] - GENEPIO:0100090 Covid-19 Incomplete Kawasaki disease [GENEPIO:0100090] - HP:0001410 Covid-19 Liver dysfunction [HP:0001410] - GENEPIO:0100091 Covid-19 Acute liver injury [GENEPIO:0100091] - MONDO:0100233 Covid-19 Long COVID-19 [MONDO:0100233] - HP:0001287 Covid-19 Meningitis [HP:0001287] - HP:0002076 Covid-19 Migraine [HP:0002076] - HP:0005268 Covid-19 Miscarriage [HP:0005268] - MONDO:0100163 Covid-19 Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163] - MONDO:0100319 Covid-19 Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319] - GENEPIO:0100093 Covid-19 Muscle injury [GENEPIO:0100093] - MONDO:0005404 Covid-19 Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404] - MONDO:0005068 Covid-19 Myocardial infarction (heart attack) [MONDO:0005068] - MONDO:0004781 Covid-19 Acute myocardial infarction [MONDO:0004781] - MONDO:0041656 Covid-19 ST-segment elevation myocardial infarction [MONDO:0041656] - HP:0001700 Covid-19 Myocardial injury [HP:0001700] - NCIT:C168498 Covid-19 Neonatal complications [NCIT:C168498] - GENEPIO:0100085 Covid-19 Noncardiogenic pulmonary edema [GENEPIO:0100085] - HP:0033677 Covid-19 Acute respiratory distress syndrome (ARDS) [HP:0033677] - NCIT:C171551 Covid-19 COVID-19 associated ARDS (CARDS) [NCIT:C171551] - GENEPIO:0100086 Covid-19 Neurogenic pulmonary edema (NPE) [GENEPIO:0100086] - GENEPIO:0100094 Covid-19 Organ failure [GENEPIO:0100094] - HP:0001635 Covid-19 Heart failure [HP:0001635] - MONDO:0100192 Covid-19 Liver failure [MONDO:0100192] - HP:0003470 Covid-19 Paralysis [HP:0003470] - HP:0002107 Covid-19 Pneumothorax (collapsed lung) [HP:0002107] - HP:0002108 Covid-19 Spontaneous pneumothorax [HP:0002108] - MONDO:0002075 Covid-19 Spontaneous tension pneymothorax [MONDO:0002075] - HP:0002090 Covid-19 Pneumonia (complication) [HP:0002090] - NCIT:C171550 Covid-19 COVID-19 pneumonia [NCIT:C171550] - HP:0001197 Covid-19 Pregancy complications [HP:0001197] - HP:0003201 Covid-19 Rhabdomyolysis [HP:0003201] - IDO:0000567 Covid-19 Secondary infection [IDO:0000567] - GENEPIO:0100095 Covid-19 Secondary staph infection [GENEPIO:0100095] - GENEPIO:0100096 Covid-19 Secondary strep infection [GENEPIO:0100096] - HP:0001250 Covid-19 Seizure (complication) [HP:0001250] - HP:0020219 Covid-19 Motor seizure [HP:0020219] - HP:0100806 Covid-19 Sepsis/Septicemia [HP:0100806] - IDO:0000636 Covid-19 Sepsis (systemic inflammatory response to infection) [IDO:0000636] - NCIT:C3364 Covid-19 Septicemia (bloodstream infection) [NCIT:C3364] - HP:0031273 Covid-19 Shock [HP:0031273] - GENEPIO:0100097 Covid-19 Hyperinflammatory shock [GENEPIO:0100097] - GENEPIO:0100098 Covid-19 Refractory cardiogenic shock [GENEPIO:0100098] - GENEPIO:0100099 Covid-19 Refractory cardiogenic plus vasoplegic shock [GENEPIO:0100099] - NCIT:C35018 Covid-19 Septic shock [NCIT:C35018] - HP:0002633 Covid-19 Vasculitis [HP:0002633] - - -sample collected in quarantine menu NCIT:C49488 Covid-19 Yes [NCIT:C49488] - NCIT:C49487 Covid-19 No [NCIT:C49487] - - -anatomical material menu UBERON:0000178 Covid-19 Blood [UBERON:0000178] - UBERON:0006314 Covid-19 Fluid [UBERON:0006314] - UBERON:0001359 Covid-19 Fluid (cerebrospinal (CSF)) [UBERON:0001359] - UBERON:0002409 Covid-19 Fluid (pericardial) [UBERON:0002409] - UBERON:0001087 Covid-19 Fluid (pleural) [UBERON:0001087] - UBERON:0036243 Covid-19 Fluid (vaginal) [UBERON:0036243] - UBERON:0000173 Covid-19 Fluid (amniotic) [UBERON:0000173] - UBERON:0001836 Covid-19 Saliva [UBERON:0001836] - UBERON:0000479 Covid-19 Tissue [UBERON:0000479] - - -anatomical part menu UBERON:0001245 Covid-19 Anus [UBERON:0001245] - UBERON:0006956 Covid-19 Buccal mucosa [UBERON:0006956] - UBERON:0002114 Covid-19 Duodenum [UBERON:0002114] - UBERON:0000970 Covid-19 Eye [UBERON:0000970] - UBERON:0000160 Covid-19 Intestine [UBERON:0000160] - UBERON:0001558 Covid-19 Lower respiratory tract [UBERON:0001558] - UBERON:0002185 Covid-19 Bronchus [UBERON:0002185] - UBERON:0002048 Covid-19 Lung [UBERON:0002048] - UBERON:0002186 Covid-19 Bronchiole [UBERON:0002186] - UBERON:0002169 Covid-19 Alveolar sac [UBERON:0002169] - UBERON:0009778 Covid-19 Pleural sac [UBERON:0009778] - UBERON:0002402 Covid-19 Pleural cavity [UBERON:0002402] - UBERON:0003126 Covid-19 Trachea [UBERON:0003126] - UBERON:0001052 Covid-19 Rectum [UBERON:0001052] - UBERON:0001003 Covid-19 Skin [UBERON:0001003] - UBERON:0000945 Covid-19 Stomach [UBERON:0000945] - UBERON:0001557 Covid-19 Upper respiratory tract [UBERON:0001557] - UBERON:2001427 Covid-19 Anterior Nares [UBERON:2001427] - UBERON:0001043 Covid-19 Esophagus [UBERON:0001043] - UBERON:0002453 Covid-19 Ethmoid sinus [UBERON:0002453] - UBERON:0001707 Covid-19 Nasal Cavity [UBERON:0001707] - UBERON:0005921 Covid-19 Middle Nasal Turbinate [UBERON:0005921] - UBERON:0005922 Covid-19 Inferior Nasal Turbinate [UBERON:0005922] - UBERON:0001728 Covid-19 Nasopharynx (NP) [UBERON:0001728] - UBERON:0001729 Covid-19 Oropharynx (OP) [UBERON:0001729] - - -body product menu UBERON:0001913 Covid-19 Breast Milk [UBERON:0001913] - UBERON:0001988 Covid-19 Feces [UBERON:0001988] - UBERON:0006530 Covid-19 Fluid (seminal) [UBERON:0006530] - UBERON:0000912 Covid-19 Mucus [UBERON:0000912] - UBERON:0007311 Covid-19 Sputum [UBERON:0007311] - UBERON:0001089 Covid-19 Sweat [UBERON:0001089] - UBERON:0001827 Covid-19 Tear [UBERON:0001827] - UBERON:0001088 Covid-19 Urine [UBERON:0001088] - - -environmental material menu ENVO:03501208 Covid-19 Air vent [ENVO:03501208] - ENVO:00003896 Covid-19 Banknote [ENVO:00003896] - ENVO:03501209 Covid-19 Bed rail [ENVO:03501209] - ENVO:01000486 Covid-19 Building floor [ENVO:01000486] - ENVO:02000058 Covid-19 Cloth [ENVO:02000058] - ENVO:03501210 Covid-19 Control panel [ENVO:03501210] - ENVO:03501220 Covid-19 Door [ENVO:03501220] - ENVO:03501211 Covid-19 Door handle [ENVO:03501211] - OBI:0002787 Covid-19 Face mask [OBI:0002787] - OBI:0002791 Covid-19 Face shield [OBI:0002791] - FOODON:00002403 Covid-19 Food [FOODON:00002403] - FOODON:03490100 Covid-19 Food packaging [FOODON:03490100] - ENVO:01000481 Covid-19 Glass [ENVO:01000481] - ENVO:03501212 Covid-19 Handrail [ENVO:03501212] - OBI:0002796 Covid-19 Hospital gown [OBI:0002796] - ENVO:03501213 Covid-19 Light switch [ENVO:03501213] - ENVO:03501214 Covid-19 Locker [ENVO:03501214] - OBI:0002790 Covid-19 N95 mask [OBI:0002790] - ENVO:03501215 Covid-19 Nurse call button [ENVO:03501215] - ENVO:03501256 Covid-19 Paper [ENVO:03501256] - ENVO:01000060 Covid-19 Particulate matter [ENVO:01000060] - ENVO:01000404 Covid-19 Plastic [ENVO:01000404] - GENEPIO:0100025 Covid-19 PPE gown [GENEPIO:0100025] - ENVO:00002018 Covid-19 Sewage [ENVO:00002018] - ENVO:01000990 Covid-19 Sink [ENVO:01000990] - ENVO:00001998 Covid-19 Soil [ENVO:00001998] - ENVO:03501216 Covid-19 Stainless steel [ENVO:03501216] - ENVO:03501217 Covid-19 Tissue paper [ENVO:03501217] - ENVO:03501218 Covid-19 Toilet bowl [ENVO:03501218] - ENVO:00002006 Covid-19 Water [ENVO:00002006] - ENVO:00002001 Covid-19 Wastewater [ENVO:00002001] - ENVO:03501219 Covid-19 Window [ENVO:03501219] - ENVO:00002040 Covid-19 Wood [ENVO:00002040] - - -environmental site menu ENVO:03501135 Covid-19 Acute care facility [ENVO:03501135] - ENVO:00003040 Covid-19 Animal house [ENVO:00003040] - ENVO:01000422 Covid-19 Bathroom [ENVO:01000422] - ENVO:03501136 Covid-19 Clinical assessment centre [ENVO:03501136] - ENVO:03501127 Covid-19 Conference venue [ENVO:03501127] - ENVO:03501121 Covid-19 Corridor [ENVO:03501121] - ENVO:01000927 Covid-19 Daycare [ENVO:01000927] - ENVO:03501145 Covid-19 Emergency room (ER) [ENVO:03501145] - ENVO:03501186 Covid-19 Family practice clinic [ENVO:03501186] - ENVO:03501196 Covid-19 Group home [ENVO:03501196] - ENVO:03501133 Covid-19 Homeless shelter [ENVO:03501133] - ENVO:00002173 Covid-19 Hospital [ENVO:00002173] - ENVO:03501152 Covid-19 Intensive Care Unit (ICU) [ENVO:03501152] - ENVO:03501194 Covid-19 Long Term Care Facility [ENVO:03501194] - ENVO:03501180 Covid-19 Patient room [ENVO:03501180] - ENVO:03501204 Covid-19 Prison [ENVO:03501204] - ENVO:01000536 Covid-19 Production Facility [ENVO:01000536] - ENVO:03501130 Covid-19 School [ENVO:03501130] - ENVO:00003043 Covid-19 Sewage Plant [ENVO:00003043] - ENVO:03501109 Covid-19 Subway train [ENVO:03501109] - ENVO:00000467 Covid-19 University campus [ENVO:00000467] - ENVO:03501198 Covid-19 Wet market [ENVO:03501198] - - -collection method menu NCIT:C52009 Covid-19 Amniocentesis [NCIT:C52009] - NCIT:C15631 Covid-19 Aspiration [NCIT:C15631] - GENEPIO:0100028 Covid-19 Suprapubic Aspiration [GENEPIO:0100028] - GENEPIO:0100029 Covid-19 Tracheal Aspiration [GENEPIO:0100029] - GENEPIO:0100030 Covid-19 Vacuum Aspiration [GENEPIO:0100030] - OBI:0002650 Covid-19 Biopsy [OBI:0002650] - OBI:0002651 Covid-19 Needle Biopsy [OBI:0002651] - OBI:0302885 Covid-19 Filtration [OBI:0302885] - GENEPIO:0100031 Covid-19 Air filtration [GENEPIO:0100031] - OBI:0600044 Covid-19 Lavage (medical wash) [OBI:0600044] - GENEPIO:0100032 Covid-19 Bronchoalveolar lavage (BAL) [GENEPIO:0100032] - GENEPIO:0100033 Covid-19 Gastric Lavage [GENEPIO:0100033] - NCIT:C15327 Covid-19 Lumbar Puncture [NCIT:C15327] - MMO:0000344 Covid-19 Necropsy [MMO:0000344] - NCIT:C28221 Covid-19 Phlebotomy [NCIT:C28221] - GENEPIO:0002116 Covid-19 Rinsing (wash) [GENEPIO:0002116] - GENEPIO:0100034 Covid-19 Saline gargle (mouth rinse and gargle) [GENEPIO:0100034] - GENEPIO:0100035 Covid-19 Scraping [GENEPIO:0100035] - GENEPIO:0002117 Covid-19 Swabbing [GENEPIO:0002117] - GENEPIO:0100036 Covid-19 Finger Prick [GENEPIO:0100036] - GENEPIO:0100038 Covid-19 Washout Tear Collection [GENEPIO:0100038] - - -collection device menu ENVO:00003968 Covid-19 Air filter [ENVO:00003968] - OBI:0002859 Covid-19 Blood Collection Tube [OBI:0002859] - OBI:0002826 Covid-19 Bronchoscope [OBI:0002826] - OBI:0002088 Covid-19 Collection Container [OBI:0002088] - GENEPIO:0100026 Covid-19 Collection Cup [GENEPIO:0100026] - OBI:0002825 Covid-19 Fibrobronchoscope Brush [OBI:0002825] - GENEPIO:0100103 Covid-19 Filter [GENEPIO:0100103] - OBI:0002827 Covid-19 Fine Needle [OBI:0002827] - OBI:0002858 Covid-19 Microcapillary tube [OBI:0002858] - OBI:0001128 Covid-19 Micropipette [OBI:0001128] - OBI:0000436 Covid-19 Needle [OBI:0000436] - OBI:0002860 Covid-19 Serum Collection Tube [OBI:0002860] - OBI:0002861 Covid-19 Sputum Collection Tube [OBI:0002861] - OBI:0002831 Covid-19 Suction Catheter [OBI:0002831] - GENEPIO:0100027 Covid-19 Swab [GENEPIO:0100027] - OBI:0002862 Covid-19 Urine Collection Tube [OBI:0002862] - OBI:0002866 Covid-19 Virus Transport Medium [OBI:0002866] - - -host (scientific name) menu NCBITaxon:9913 Covid-19 Homo sapiens [NCBITaxon:9606] - NCBITaxon:9615 Covid-19 Bos taurus [NCBITaxon:9913] - NCBITaxon:9397 Covid-19 Canis lupus familiaris [NCBITaxon:9615] - NCBITaxon:8930 Covid-19 Chiroptera [NCBITaxon:9397] - NCBITaxon:9685 Covid-19 Columbidae [NCBITaxon:8930] - NCBITaxon:9031 Covid-19 Felis catus [NCBITaxon:9685] - NCBITaxon:9606 Covid-19 Gallus gallus [NCBITaxon:9031] - NCBITaxon:9973 Covid-19 Manis [NCBITaxon:9973] - NCBITaxon:9974 Covid-19 Manis javanica [NCBITaxon:9974] - NCBITaxon:452646 Covid-19 Neovison vison [NCBITaxon:452646] - NCBITaxon:9689 Covid-19 Panthera leo [NCBITaxon:9689] - NCBITaxon:9694 Covid-19 Panthera tigris [NCBITaxon:9694] - NCBITaxon:58055 Covid-19 Rhinolophidae [NCBITaxon:58055] - NCBITaxon:59477 Covid-19 Rhinolophus affinis [NCBITaxon:59477] - NCBITaxon:9825 Covid-19 Sus scrofa domesticus [NCBITaxon:9825] - NCBITaxon:9673 Covid-19 Viverridae [NCBITaxon:9673] - - -host (common name) menu NCBITaxon:9605 Covid-19 Human [NCBITaxon:9606] - NCBITaxon:9397 Covid-19 Bat [NCBITaxon:9397] - NCBITaxon:9685 Covid-19 Cat [NCBITaxon:9685] - NCBITaxon:9031 Covid-19 Chicken [NCBITaxon:9031] - NCBITaxon:9673 Covid-19 Civets [NCBITaxon:9673] - NCBITaxon:9913 Covid-19 Cow [NCBITaxon:9913] - NCBITaxon:9615 Covid-19 Dog [NCBITaxon:9615] - NCBITaxon:9689 Covid-19 Lion [NCBITaxon:9689] - NCBITaxon:452646 Covid-19 Mink [NCBITaxon:452646] - NCBITaxon:9973 Covid-19 Pangolin [NCBITaxon:9973] - NCBITaxon:9825 Covid-19 Pig [NCBITaxon:9825] - NCBITaxon:8930 Covid-19 Pigeon [NCBITaxon:8930] - NCBITaxon:9694 Covid-19 Tiger [NCBITaxon:9694] - - -host health state menu NCIT:C3833 Covid-19 Asymptomatic [NCIT:C3833] - NCIT:C28554 Covid-19 Deceased [NCIT:C28554] - NCIT:C115935 Covid-19 Healthy [NCIT:C115935] - NCIT:C49498 Covid-19 Recovered [NCIT:C49498] - NCIT:C25269 Covid-19 Symptomatic [NCIT:C25269] - - -host health status details menu NCIT:C25179 Covid-19 Hospitalized [NCIT:C25179] - GENEPIO:0100045 Covid-19 Hospitalized (Non-ICU) [GENEPIO:0100045] - GENEPIO:0100046 Covid-19 Hospitalized (ICU) [GENEPIO:0100046] - NCIT:C70909 Covid-19 Mechanical Ventilation [NCIT:C70909] - GENEPIO:0100047 Covid-19 Medically Isolated [GENEPIO:0100047] - GENEPIO:0100048 Covid-19 Medically Isolated (Negative Pressure) [GENEPIO:0100048] - NCIT:C173768 Covid-19 Self-quarantining [NCIT:C173768] - - -host health outcome menu NCIT:C28554 Covid-19 Deceased [NCIT:C28554] - NCIT:C25254 Covid-19 Deteriorating [NCIT:C25254] - NCIT:C49498 Covid-19 Recovered [NCIT:C49498] - NCIT:C30103 Covid-19 Stable [NCIT:C30103] - - -organism menu NCBITaxon:2697049 Covid-19 Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] - NCBITaxon:2709072 Covid-19 RaTG13 [NCBITaxon:2709072] - GENEPIO:0100000 Covid-19 RmYN02 [GENEPIO:0100000] - - -purpose of sampling menu GENEPIO:0100001 Covid-19 Cluster/Outbreak investigation [GENEPIO:0100001] - GENEPIO:0100002 Covid-19 Diagnostic testing [GENEPIO:0100002] - GENEPIO:0100003 Covid-19 Research [GENEPIO:0100003] - GENEPIO:0100024 Covid-19 Protocol testing [GENEPIO:0100024] - GENEPIO:0100004 Covid-19 Surveillance [GENEPIO:0100004] - - -purpose of sequencing menu GENEPIO:0100005 Covid-19 Baseline surveillance (random sampling) [GENEPIO:0100005] - GENEPIO:0100006 Covid-19 Targeted surveillance (non-random sampling) [GENEPIO:0100006] - GENEPIO:0100007 Covid-19 Priority surveillance project [GENEPIO:0100007] - GENEPIO:0100008 Covid-19 Screening for Variants of Concern (VoC) [GENEPIO:0100008] - GENEPIO:0100273 Covid-19 Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273] - GENEPIO:0100274 Covid-19 Sample has epidemiological link to Omicron Variant [GENEPIO:0100274] - GENEPIO:0100009 Covid-19 Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] - GENEPIO:0100010 Covid-19 Re-infection surveillance [GENEPIO:0100010] - GENEPIO:0100011 Covid-19 Vaccine escape surveillance [GENEPIO:0100011] - GENEPIO:0100012 Covid-19 Travel-associated surveillance [GENEPIO:0100012] - GENEPIO:0100013 Covid-19 Domestic travel surveillance [GENEPIO:0100013] - GENEPIO:0100275 Covid-19 Interstate/ interprovincial travel surveillance [GENEPIO:0100275] - GENEPIO:0100276 Covid-19 Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276] - GENEPIO:0100014 Covid-19 International travel surveillance [GENEPIO:0100014] - GENEPIO:0100015 Covid-19 Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015] - GENEPIO:0100016 Covid-19 Surveillance of international border crossing by air travel [GENEPIO:0100016] - GENEPIO:0100017 Covid-19 Surveillance of international border crossing by ground transport [GENEPIO:0100017] - GENEPIO:0100018 Covid-19 Surveillance from international worker testing [GENEPIO:0100018] - GENEPIO:0100019 Covid-19 Cluster/Outbreak investigation [GENEPIO:0100019] - GENEPIO:0100020 Covid-19 Multi-jurisdictional outbreak investigation [GENEPIO:0100020] - GENEPIO:0100021 Covid-19 Intra-jurisdictional outbreak investigation [GENEPIO:0100021] - GENEPIO:0100022 Covid-19 Research [GENEPIO:0100022] - GENEPIO:0100023 Covid-19 Viral passage experiment [GENEPIO:0100023] - GENEPIO:0100024 Covid-19 Protocol testing experiment [GENEPIO:0100024] - GENEPIO:0100356 Retrospective sequencing [GENEPIO:0100356] - - -specimen processing menu GENEPIO:0100039 Covid-19 Virus passage [GENEPIO:0100039] - GENEPIO:0100040 Covid-19 RNA re-extraction (post RT-PCR) [GENEPIO:0100040] - OBI:0600016 Covid-19 Specimens pooled [OBI:0600016] - EFO:0002090 Covid-19 Technical replicate [EFO:0002090] - - -lab host menu GENEPIO:0100041 Covid-19 293/ACE2 cell line [GENEPIO:0100041] - BTO:0000195 Covid-19 Caco2 cell line [BTO:0000195] - BTO:0002750 Covid-19 Calu3 cell line [BTO:0002750] - GENEPIO:0100042 Covid-19 EFK3B cell line [GENEPIO:0100042] - BTO:0002181 Covid-19 HEK293T cell line [BTO:0002181] - GENEPIO:0100043 Covid-19 HRCE cell line [GENEPIO:0100043] - BTO:0001950 Covid-19 Huh7 cell line [BTO:0001950] - CLO:0007330 Covid-19 LLCMk2 cell line [CLO:0007330] - BTO:0000836 Covid-19 MDBK cell line [BTO:0000836] - BTO:0002924 Covid-19 NHBE cell line [BTO:0002924] - BTO:0001865 Covid-19 PK-15 cell line [BTO:0001865] - BTO:0002909 Covid-19 RK-13 cell line [BTO:0002909] - BTO:0002035 Covid-19 U251 cell line [BTO:0002035] - BTO:0001444 Covid-19 Vero cell line [BTO:0001444] - BTO:0004755 Covid-19 Vero E6 cell line [BTO:0004755] - GENEPIO:0100044 Covid-19 VeroE6/TMPRSS2 cell line [GENEPIO:0100044] - - -host disease menu MONDO:0100096 Covid-19 COVID-19 [MONDO:0100096] - - -host age bin menu GENEPIO:0100049 Covid-19 0 - 9 [GENEPIO:0100049] - GENEPIO:0100050 Covid-19 10 - 19 [GENEPIO:0100050] - GENEPIO:0100051 Covid-19 20 - 29 [GENEPIO:0100051] - GENEPIO:0100052 Covid-19 30 - 39 [GENEPIO:0100052] - GENEPIO:0100053 Covid-19 40 - 49 [GENEPIO:0100053] - GENEPIO:0100054 Covid-19 50 - 59 [GENEPIO:0100054] - GENEPIO:0100055 Covid-19 60 - 69 [GENEPIO:0100055] - GENEPIO:0100056 Covid-19 70 - 79 [GENEPIO:0100056] - GENEPIO:0100057 Covid-19 80 - 89 [GENEPIO:0100057] - GENEPIO:0100058 Covid-19 90 - 99 [GENEPIO:0100058] - GENEPIO:0100059 Covid-19 100+ [GENEPIO:0100059] - - -host gender menu NCIT:C46110 Covid-19 Female [NCIT:C46110] - NCIT:C46109 Covid-19 Male [NCIT:C46109] - GSSO:000132 Covid-19 Non-binary gender [GSSO:000132] - GSSO:004004 Covid-19 Transgender (assigned male at birth) [GSSO:004004] - GSSO:004005 Covid-19 Transgender (assigned female at birth) [GSSO:004005] - NCIT:C110959 Covid-19 Undeclared [NCIT:C110959] - - -exposure event menu GENEPIO:0100237 Covid-19 Mass Gathering [GENEPIO:0100237] - GENEPIO:0100238 Covid-19 Convention [GENEPIO:0100238] - GENEPIO:0100239 Covid-19 Convocation [GENEPIO:0100239] - GENEPIO:0100240 Covid-19 Agricultural Event [GENEPIO:0100240] - GENEPIO:0100241 Covid-19 Religious Gathering [GENEPIO:0100241] - GENEPIO:0100242 Covid-19 Mass [GENEPIO:0100242] - PCO:0000033 Covid-19 Social Gathering [PCO:0000033] - PCO:0000039 Covid-19 Baby Shower [PCO:0000039] - PCO:0000034 Covid-19 Community Event [PCO:0000034] - GENEPIO:0100243 Covid-19 Family Gathering [GENEPIO:0100243] - GENEPIO:0100244 Covid-19 Family Reunion [GENEPIO:0100244] - GENEPIO:0100245 Covid-19 Funeral [GENEPIO:0100245] - PCO:0000035 Covid-19 Party [PCO:0000035] - PCO:0000037 Covid-19 Potluck [PCO:0000037] - PCO:0000038 Covid-19 Wedding [PCO:0000038] - Other exposure event - - -exposure contact level menu GENEPIO:0100357 Covid-19 Contact with infected individual - TRANS:0000001 Covid-19 Direct (human-to-human contact) [TRANS:0000001] - GENEPIO:0100246 Covid-19 Indirect contact [GENEPIO:0100246] - GENEPIO:0100247 Covid-19 Close contact (face-to-face contact) [GENEPIO:0100247] - GENEPIO:0100248 Covid-19 Casual contact [GENEPIO:0100248] - - -host role menu GENEPIO:0100249 Covid-19 Attendee [GENEPIO:0100249] - OMRSE:00000058 Covid-19 Student [OMRSE:00000058] - OMRSE:00000030 Covid-19 Patient [OMRSE:00000030] - NCIT:C25182 Covid-19 Inpatient [NCIT:C25182] - NCIT:C28293 Covid-19 Outpatient [NCIT:C28293] - GENEPIO:0100250 Covid-19 Passenger [GENEPIO:0100250] - GENEPIO:0100251 Covid-19 Resident [GENEPIO:0100251] - GENEPIO:0100252 Covid-19 Visitor [GENEPIO:0100252] - GENEPIO:0100253 Covid-19 Volunteer [GENEPIO:0100253] - GENEPIO:0100254 Covid-19 Work [GENEPIO:0100254] - GENEPIO:0100255 Covid-19 Administrator [GENEPIO:0100255] - GENEPIO:0100256 Covid-19 First Responder [GENEPIO:0100256] - GENEPIO:0100257 Covid-19 Firefighter [GENEPIO:0100257] - GENEPIO:0100258 Covid-19 Paramedic [GENEPIO:0100258] - GENEPIO:0100259 Covid-19 Police Officer [GENEPIO:0100259] - GENEPIO:0100260 Covid-19 Housekeeper [GENEPIO:0100260] - GENEPIO:0100261 Covid-19 Kitchen Worker [GENEPIO:0100261] - GENEPIO:0100334 Covid-19 Healthcare Worker [GENEPIO:0100334] - GENEPIO:0100420 Covid-19 Community Healthcare Worker [GENEPIO:0100420] - GENEPIO:0100262 Covid-19 Laboratory Worker [GENEPIO:0100262] - OMRSE:00000014 Covid-19 Nurse [OMRSE:00000014] - GENEPIO:0100263 Covid-19 Personal Care Aid [GENEPIO:0100263] - GENEPIO:0100264 Covid-19 Pharmacist [GENEPIO:0100264] - OMRSE:00000013 Covid-19 Physician [OMRSE:00000013] - GENEPIO:0100354 Covid-19 Rotational Worker [GENEPIO:0100354] - GENEPIO:0100355 Covid-19 Seasonal Worker [GENEPIO:0100355] - GENEPIO:0100265 Covid-19 Veterinarian [GENEPIO:0100265] - OMRSE:00000001 Covid-19 Social role [OMRSE:00000001] - GENEPIO:0100266 Covid-19 Acquaintance of case [GENEPIO:0100266] - GENEPIO:0100267 Covid-19 Relative of case [GENEPIO:0100267] - GENEPIO:0100268 Covid-19 Child of case [GENEPIO:0100268] - GENEPIO:0100269 Covid-19 Parent of case [GENEPIO:0100269] - GENEPIO:0100270 Covid-19 Father of case [GENEPIO:0100270] - GENEPIO:0100271 Covid-19 Mother of case [GENEPIO:0100271] - GENEPIO:0100272 Covid-19 Spouse of case [GENEPIO:0100272] - Other Host Role - - -exposure setting menu ECTO:3000005 Covid-19 Human Exposure [ECTO:3000005] - GENEPIO:0100184 Covid-19 Contact with Known COVID-19 Case [GENEPIO:0100184] - GENEPIO:0100185 Covid-19 Contact with Patient [GENEPIO:0100185] - GENEPIO:0100186 Covid-19 Contact with Probable COVID-19 Case [GENEPIO:0100186] - GENEPIO:0100187 Covid-19 Contact with Person with Acute Respiratory Illness [GENEPIO:0100187] - GENEPIO:0100188 Covid-19 Contact with Person with Fever and/or Cough [GENEPIO:0100188] - GENEPIO:0100189 Covid-19 Contact with Person who Recently Travelled [GENEPIO:0100189] - GENEPIO:0100190 Covid-19 Occupational, Residency or Patronage Exposure [GENEPIO:0100190] - ECTO:1000033 Covid-19 Abbatoir [ECTO:1000033] - GENEPIO:0100191 Covid-19 Animal Rescue [GENEPIO:0100191] - GENEPIO:0100192 Covid-19 Childcare [GENEPIO:0100192] - GENEPIO:0100193 Covid-19 Daycare [GENEPIO:0100193] - GENEPIO:0100194 Covid-19 Nursery [GENEPIO:0100194] - GENEPIO:0100195 Covid-19 Community Service Centre [GENEPIO:0100195] - GENEPIO:0100196 Covid-19 Correctional Facility [GENEPIO:0100196] - GENEPIO:0100197 Covid-19 Dormitory [GENEPIO:0100197] - ECTO:1000034 Covid-19 Farm [ECTO:1000034] - GENEPIO:0100198 Covid-19 First Nations Reserve [GENEPIO:0100198] - GENEPIO:0100199 Covid-19 Funeral Home [GENEPIO:0100199] - GENEPIO:0100200 Covid-19 Group Home [GENEPIO:0100200] - GENEPIO:0100201 Covid-19 Healthcare Setting [GENEPIO:0100201] - GENEPIO:0100202 Covid-19 Ambulance [GENEPIO:0100202] - GENEPIO:0100203 Covid-19 Acute Care Facility [GENEPIO:0100203] - GENEPIO:0100204 Covid-19 Clinic [GENEPIO:0100204] - GENEPIO:0100415 Covid-19 Community Healthcare (At-Home) Setting [GENEPIO:0100415] - GENEPIO:0100205 Covid-19 Community Health Centre [GENEPIO:0100205] - ECTO:1000035 Covid-19 Hospital [ECTO:1000035] - GENEPIO:0100206 Covid-19 Emergency Department [GENEPIO:0100206] - GENEPIO:0100207 Covid-19 ICU [GENEPIO:0100207] - GENEPIO:0100208 Covid-19 Ward [GENEPIO:0100208] - ECTO:1000036 Covid-19 Laboratory [ECTO:1000036] - GENEPIO:0100209 Covid-19 Long-Term Care Facility [GENEPIO:0100209] - GENEPIO:0100210 Covid-19 Pharmacy [GENEPIO:0100210] - GENEPIO:0100211 Covid-19 Physician's Office [GENEPIO:0100211] - GENEPIO:0100212 Covid-19 Household [GENEPIO:0100212] - GENEPIO:0100213 Covid-19 Insecure Housing (Homeless) [GENEPIO:0100213] - GENEPIO:0100214 Covid-19 Occupational Exposure [GENEPIO:0100214] - GENEPIO:0100215 Covid-19 Worksite [GENEPIO:0100215] - ECTO:1000037 Covid-19 Office [ECTO:1000037] - GENEPIO:0100216 Covid-19 Outdoors [GENEPIO:0100216] - ECTO:5000009 Covid-19 Camp/camping [ECTO:5000009] - GENEPIO:0100217 Covid-19 Hiking Trail [GENEPIO:0100217] - ECTO:6000030 Covid-19 Hunting Ground [ECTO:6000030] - GENEPIO:0100218 Covid-19 Ski Resort [GENEPIO:0100218] - ECTO:5000008 Covid-19 Petting zoo [ECTO:5000008] - GENEPIO:0100220 Covid-19 Place of Worship [GENEPIO:0100220] - GENEPIO:0100221 Covid-19 Church [GENEPIO:0100221] - GENEPIO:0100222 Covid-19 Mosque [GENEPIO:0100222] - GENEPIO:0100223 Covid-19 Temple [GENEPIO:0100223] - ECTO:1000040 Covid-19 Restaurant [ECTO:1000040] - ECTO:1000041 Covid-19 Retail Store [ECTO:1000041] - GENEPIO:0100224 Covid-19 School [GENEPIO:0100224] - GENEPIO:0100225 Covid-19 Temporary Residence [GENEPIO:0100225] - GENEPIO:0100226 Covid-19 Homeless Shelter [GENEPIO:0100226] - GENEPIO:0100227 Covid-19 Hotel [GENEPIO:0100227] - GENEPIO:0100228 Covid-19 Veterinary Care Clinic [GENEPIO:0100228] - GENEPIO:0100229 Covid-19 Travel Exposure [GENEPIO:0100229] - GENEPIO:0100230 Covid-19 Travelled on a Cruise Ship [GENEPIO:0100230] - GENEPIO:0100231 Covid-19 Travelled on a Plane [GENEPIO:0100231] - GENEPIO:0100232 Covid-19 Travelled on Ground Transport [GENEPIO:0100232] - GENEPIO:0001118 Covid-19 Travelled outside Province/Territory [GENEPIO:0001118] - GENEPIO:0001119 Covid-19 Travelled outside Canada [GENEPIO:0001119] - GENEPIO:0100235 Covid-19 Other Exposure Setting [GENEPIO:0100235] - - -prior SARS-CoV-2 antiviral treatment menu GENEPIO:0100037 Covid-19 Prior antiviral treatment [GENEPIO:0100037] - GENEPIO:0100233 Covid-19 No prior antiviral treatment [GENEPIO:0100233] - - -prior SARS-CoV-2 infection menu GENEPIO:0100234 Covid-19 Prior infection [GENEPIO:0100234] - GENEPIO:0100236 Covid-19 No prior infection [GENEPIO:0100236] - - -sequencing instrument menu GENEPIO:0100105 Covid-19 Illumina sequencing instrument [GENEPIO:0100105] platform:ILLUMINA - GENEPIO:0100106 Covid-19 Illumina Genome Analyzer [GENEPIO:0100106] platform:ILLUMINA;instrument_model:Illumina Genome Analyzer - GENEPIO:0100107 Covid-19 Illumina Genome Analyzer II [GENEPIO:0100107] platform:ILLUMINA;instrument_model:Illumina Genome Analyzer II - GENEPIO:0100108 Covid-19 Illumina Genome Analyzer IIx [GENEPIO:0100108] platform:ILLUMINA;instrument_model:Illumina Genome Analyzer IIx - GENEPIO:0100109 Covid-19 Illumina HiScanSQ [GENEPIO:0100109] platform:ILLUMINA;instrument_model:Illumina HiScanSQ - GENEPIO:0100110 Covid-19 Illumina HiSeq [GENEPIO:0100110] platform:ILLUMINA - GENEPIO:0100111 Covid-19 Illumina HiSeq X [GENEPIO:0100111] platform:ILLUMINA - GENEPIO:0100112 Covid-19 Illumina HiSeq X Five [GENEPIO:0100112] platform:ILLUMINA;instrument_model: Illumina HiSeq X Five - GENEPIO:0100113 Covid-19 Illumina HiSeq X Ten [GENEPIO:0100113] platform:ILLUMINA;instrument_model:Illumina HiSeq X Ten - GENEPIO:0100114 Covid-19 Illumina HiSeq 1000 [GENEPIO:0100114] platform:ILLUMINA;instrument_model:Illumina HiSeq 1000 - GENEPIO:0100115 Covid-19 Illumina HiSeq 1500 [GENEPIO:0100115] platform:ILLUMINA - GENEPIO:0100116 Covid-19 Illumina HiSeq 2000 [GENEPIO:0100116] platform:ILLUMINA;instrument_model:Illumina HiSeq 2000 - GENEPIO:0100117 Covid-19 Illumina HiSeq 2500 [GENEPIO:0100117] platform:ILLUMINA;instrument_model:Illumina HiSeq 2500 - GENEPIO:0100118 Covid-19 Illumina HiSeq 3000 [GENEPIO:0100118] platform:ILLUMINA - GENEPIO:0100119 Covid-19 Illumina HiSeq 4000 [GENEPIO:0100119] platform:ILLUMINA - GENEPIO:0100120 Covid-19 Illumina iSeq [GENEPIO:0100120] platform:ILLUMINA - GENEPIO:0100121 Covid-19 Illumina iSeq 100 [GENEPIO:0100121] platform:ILLUMINA - GENEPIO:0100122 Covid-19 Illumina NovaSeq [GENEPIO:0100122] platform:ILLUMINA - GENEPIO:0100123 Covid-19 Illumina NovaSeq 6000 [GENEPIO:0100123] platform:ILLUMINA - GENEPIO:0100124 Covid-19 Illumina MiniSeq [GENEPIO:0100124] platform:ILLUMINA - GENEPIO:0100125 Covid-19 Illumina MiSeq [GENEPIO:0100125] platform:ILLUMINA;instrument_model:Illumina MiSeq - GENEPIO:0100126 Covid-19 Illumina NextSeq [GENEPIO:0100126] platform:ILLUMINA - GENEPIO:0100127 Covid-19 Illumina NextSeq 500 [GENEPIO:0100127] platform:ILLUMINA;instrument_model:Illumina NextSeq 500 - GENEPIO:0100128 Covid-19 Illumina NextSeq 550 [GENEPIO:0100128] platform:ILLUMINA - GENEPIO:0100129 Covid-19 Illumina NextSeq 2000 [GENEPIO:0100129] - GENEPIO:0100130 Covid-19 Pacific Biosciences sequencing instrument [GENEPIO:0100130] platform:PACBIO_SMRT - GENEPIO:0100131 Covid-19 PacBio RS [GENEPIO:0100131] platform:PACBIO_SMRT;instrument_model:PacBio RS - GENEPIO:0100132 Covid-19 PacBio RS II [GENEPIO:0100132] platform:PACBIO_SMRT;instrument_model:PacBio RS II - GENEPIO:0100133 Covid-19 PacBio Sequel [GENEPIO:0100133] platform:PACBIO_SMRT - GENEPIO:0100134 Covid-19 PacBio Sequel II [GENEPIO:0100134] platform:PACBIO_SMRT - GENEPIO:0100135 Covid-19 Ion Torrent sequencing instrument [GENEPIO:0100135] platform:ION_TORRENT - GENEPIO:0100136 Covid-19 Ion Torrent PGM [GENEPIO:0100136] platform:ION_TORRENT;instrument_model:Ion Torrent PGM - GENEPIO:0100137 Covid-19 Ion Torrent Proton [GENEPIO:0100137] platform:ION_TORRENT;instrument_model:Ion Torrent Proton - GENEPIO:0100138 Covid-19 Ion Torrent S5 XL [GENEPIO:0100138] platform:ION_TORRENT - GENEPIO:0100139 Covid-19 Ion Torrent S5 [GENEPIO:0100139] platform:ION_TORRENT - GENEPIO:0100140 Covid-19 Oxford Nanopore sequencing instrument [GENEPIO:0100140] platform:OXFORD_NANOPORE - GENEPIO:0100141 Covid-19 Oxford Nanopore GridION [GENEPIO:0100141] platform:OXFORD_NANOPORE;instrument_model:GridION - GENEPIO:0100142 Covid-19 Oxford Nanopore MinION [GENEPIO:0100142] platform:OXFORD_NANOPORE;instrument_model:MinION - GENEPIO:0100143 Covid-19 Oxford Nanopore PromethION [GENEPIO:0100143] platform:OXFORD_NANOPORE - GENEPIO:0100144 Covid-19 BGI Genomics sequencing instrument [GENEPIO:0100144] - GENEPIO:0100145 Covid-19 BGI Genomics BGISEQ-500 [GENEPIO:0100145] - GENEPIO:0100146 Covid-19 MGI sequencing instrument [GENEPIO:0100146] - GENEPIO:0100147 Covid-19 MGI DNBSEQ-T7 [GENEPIO:0100147] - GENEPIO:0100148 Covid-19 MGI DNBSEQ-G400 [GENEPIO:0100148] - GENEPIO:0100149 Covid-19 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] - GENEPIO:0100150 Covid-19 MGI DNBSEQ-G50 [GENEPIO:0100150] - - -gene name menu GENEPIO:0100151 Covid-19 E gene (orf4) [GENEPIO:0100151] - GENEPIO:0100152 Covid-19 M gene (orf5) [GENEPIO:0100152] - GENEPIO:0100153 Covid-19 N gene (orf9) [GENEPIO:0100153] - GENEPIO:0100154 Covid-19 Spike gene (orf2) [GENEPIO:0100154] - GENEPIO:0100155 Covid-19 orf1ab (rep) [GENEPIO:0100155] - GENEPIO:0100156 Covid-19 orf1a (pp1a) [GENEPIO:0100156] - GENEPIO:0100157 Covid-19 nsp11 [GENEPIO:0100157] - GENEPIO:0100158 Covid-19 nsp1 [GENEPIO:0100158] - GENEPIO:0100159 Covid-19 nsp2 [GENEPIO:0100159] - GENEPIO:0100160 Covid-19 nsp3 [GENEPIO:0100160] - GENEPIO:0100161 Covid-19 nsp4 [GENEPIO:0100161] - GENEPIO:0100162 Covid-19 nsp5 [GENEPIO:0100162] - GENEPIO:0100163 Covid-19 nsp6 [GENEPIO:0100163] - GENEPIO:0100164 Covid-19 nsp7 [GENEPIO:0100164] - GENEPIO:0100165 Covid-19 nsp8 [GENEPIO:0100165] - GENEPIO:0100166 Covid-19 nsp9 [GENEPIO:0100166] - GENEPIO:0100167 Covid-19 nsp10 [GENEPIO:0100167] - GENEPIO:0100168 Covid-19 RdRp gene (nsp12) [GENEPIO:0100168] - GENEPIO:0100169 Covid-19 hel gene (nsp13) [GENEPIO:0100169] - GENEPIO:0100170 Covid-19 exoN gene (nsp14) [GENEPIO:0100170] - GENEPIO:0100171 Covid-19 nsp15 [GENEPIO:0100171] - GENEPIO:0100172 Covid-19 nsp16 [GENEPIO:0100172] - GENEPIO:0100173 Covid-19 orf3a [GENEPIO:0100173] - GENEPIO:0100174 Covid-19 orf3b [GENEPIO:0100174] - GENEPIO:0100175 Covid-19 orf6 (ns6) [GENEPIO:0100175] - GENEPIO:0100176 Covid-19 orf7a [GENEPIO:0100176] - GENEPIO:0100177 Covid-19 orf7b (ns7b) [GENEPIO:0100177] - GENEPIO:0100178 Covid-19 orf8 (ns8) [GENEPIO:0100178] - GENEPIO:0100179 Covid-19 orf9b [GENEPIO:0100179] - GENEPIO:0100180 Covid-19 orf9c [GENEPIO:0100180] - GENEPIO:0100181 Covid-19 orf10 [GENEPIO:0100181] - GENEPIO:0100182 Covid-19 orf14 [GENEPIO:0100182] - GENEPIO:0100183 Covid-19 SARS-COV-2 5' UTR [GENEPIO:0100183] - - -geo_loc_name (country) menu GAZ:00006882 Covid-19 Afghanistan [GAZ:00006882] - GAZ:00002953 Covid-19 Albania [GAZ:00002953] - GAZ:00000563 Covid-19 Algeria [GAZ:00000563] - GAZ:00003957 Covid-19 American Samoa [GAZ:00003957] - GAZ:00002948 Covid-19 Andorra [GAZ:00002948] - GAZ:00001095 Covid-19 Angola [GAZ:00001095] - GAZ:00009159 Covid-19 Anguilla [GAZ:00009159] - GAZ:00000462 Covid-19 Antarctica [GAZ:00000462] - GAZ:00006883 Covid-19 Antigua and Barbuda [GAZ:00006883] - GAZ:00002928 Covid-19 Argentina [GAZ:00002928] - GAZ:00004094 Covid-19 Armenia [GAZ:00004094] - GAZ:00004025 Covid-19 Aruba [GAZ:00004025] - GAZ:00005901 Covid-19 Ashmore and Cartier Islands [GAZ:00005901] - GAZ:00000463 Covid-19 Australia [GAZ:00000463] - GAZ:00002942 Covid-19 Austria [GAZ:00002942] - GAZ:00004941 Covid-19 Azerbaijan [GAZ:00004941] - GAZ:00002733 Covid-19 Bahamas [GAZ:00002733] - GAZ:00005281 Covid-19 Bahrain [GAZ:00005281] - GAZ:00007117 Covid-19 Baker Island [GAZ:00007117] - GAZ:00003750 Covid-19 Bangladesh [GAZ:00003750] - GAZ:00001251 Covid-19 Barbados [GAZ:00001251] - GAZ:00005810 Covid-19 Bassas da India [GAZ:00005810] - GAZ:00006886 Covid-19 Belarus [GAZ:00006886] - GAZ:00002938 Covid-19 Belgium [GAZ:00002938] - GAZ:00002934 Covid-19 Belize [GAZ:00002934] - GAZ:00000904 Covid-19 Benin [GAZ:00000904] - GAZ:00001264 Covid-19 Bermuda [GAZ:00001264] - GAZ:00003920 Covid-19 Bhutan [GAZ:00003920] - GAZ:00002511 Covid-19 Bolivia [GAZ:00002511] - GAZ:00025355 Covid-19 Borneo [GAZ:00025355] - GAZ:00006887 Covid-19 Bosnia and Herzegovina [GAZ:00006887] - GAZ:00001097 Covid-19 Botswana [GAZ:00001097] - GAZ:00001453 Covid-19 Bouvet Island [GAZ:00001453] - GAZ:00002828 Covid-19 Brazil [GAZ:00002828] - GAZ:00003961 Covid-19 British Virgin Islands [GAZ:00003961] - GAZ:00003901 Covid-19 Brunei [GAZ:00003901] - GAZ:00002950 Covid-19 Bulgaria [GAZ:00002950] - GAZ:00000905 Covid-19 Burkina Faso [GAZ:00000905] - GAZ:00001090 Covid-19 Burundi [GAZ:00001090] - GAZ:00006888 Covid-19 Cambodia [GAZ:00006888] - GAZ:00001093 Covid-19 Cameroon [GAZ:00001093] - GAZ:00002560 Covid-19 Canada [GAZ:00002560] - GAZ:00001227 Covid-19 Cape Verde [GAZ:00001227] - GAZ:00003986 Covid-19 Cayman Islands [GAZ:00003986] - GAZ:00001089 Covid-19 Central African Republic [GAZ:00001089] - GAZ:00000586 Covid-19 Chad [GAZ:00000586] - GAZ:00002825 Covid-19 Chile [GAZ:00002825] - GAZ:00002845 Covid-19 China [GAZ:00002845] - GAZ:00005915 Covid-19 Christmas Island [GAZ:00005915] - GAZ:00005838 Covid-19 Clipperton Island [GAZ:00005838] - GAZ:00009721 Covid-19 Cocos Islands [GAZ:00009721] - GAZ:00002929 Covid-19 Colombia [GAZ:00002929] - GAZ:00005820 Covid-19 Comoros [GAZ:00005820] - GAZ:00053798 Covid-19 Cook Islands [GAZ:00053798] - GAZ:00005917 Covid-19 Coral Sea Islands [GAZ:00005917] - GAZ:00002901 Covid-19 Costa Rica [GAZ:00002901] - GAZ:00000906 Covid-19 Cote d'Ivoire [GAZ:00000906] - GAZ:00002719 Covid-19 Croatia [GAZ:00002719] - GAZ:00003762 Covid-19 Cuba [GAZ:00003762] - GAZ:00012582 Covid-19 Curacao [GAZ:00012582] - GAZ:00004006 Covid-19 Cyprus [GAZ:00004006] - GAZ:00002954 Covid-19 Czech Republic [GAZ:00002954] - GAZ:00001086 Covid-19 Democratic Republic of the Congo [GAZ:00001086] - GAZ:00005852 Covid-19 Denmark [GAZ:00005852] - GAZ:00000582 Covid-19 Djibouti [GAZ:00000582] - GAZ:00006890 Covid-19 Dominica [GAZ:00006890] - GAZ:00003952 Covid-19 Dominican Republic [GAZ:00003952] - GAZ:00002912 Covid-19 Ecuador [GAZ:00002912] - GAZ:00003934 Covid-19 Egypt [GAZ:00003934] - GAZ:00002935 Covid-19 El Salvador [GAZ:00002935] - GAZ:00001091 Covid-19 Equatorial Guinea [GAZ:00001091] - GAZ:00000581 Covid-19 Eritrea [GAZ:00000581] - GAZ:00002959 Covid-19 Estonia [GAZ:00002959] - GAZ:00001099 Covid-19 Eswatini [GAZ:00001099] - GAZ:00000567 Covid-19 Ethiopia [GAZ:00000567] - GAZ:00005811 Covid-19 Europa Island [GAZ:00005811] - GAZ:00001412 Covid-19 Falkland Islands (Islas Malvinas) [GAZ:00001412] - GAZ:00059206 Covid-19 Faroe Islands [GAZ:00059206] - GAZ:00006891 Covid-19 Fiji [GAZ:00006891] - GAZ:00002937 Covid-19 Finland [GAZ:00002937] - GAZ:00003940 Covid-19 France [GAZ:00003940] - GAZ:00002516 Covid-19 French Guiana [GAZ:00002516] - GAZ:00002918 Covid-19 French Polynesia [GAZ:00002918] - GAZ:00003753 Covid-19 French Southern and Antarctic Lands [GAZ:00003753] - GAZ:00001092 Covid-19 Gabon [GAZ:00001092] - GAZ:00000907 Covid-19 Gambia [GAZ:00000907] - GAZ:00009571 Covid-19 Gaza Strip [GAZ:00009571] - GAZ:00004942 Covid-19 Georgia [GAZ:00004942] - GAZ:00002646 Covid-19 Germany [GAZ:00002646] - GAZ:00000908 Covid-19 Ghana [GAZ:00000908] - GAZ:00003987 Covid-19 Gibraltar [GAZ:00003987] - GAZ:00005808 Covid-19 Glorioso Islands [GAZ:00005808] - GAZ:00002945 Covid-19 Greece [GAZ:00002945] - GAZ:00001507 Covid-19 Greenland [GAZ:00001507] - GAZ:02000573 Covid-19 Grenada [GAZ:02000573] - GAZ:00067142 Covid-19 Guadeloupe [GAZ:00067142] - GAZ:00003706 Covid-19 Guam [GAZ:00003706] - GAZ:00002936 Covid-19 Guatemala [GAZ:00002936] - GAZ:00001550 Covid-19 Guernsey [GAZ:00001550] - GAZ:00000909 Covid-19 Guinea [GAZ:00000909] - GAZ:00000910 Covid-19 Guinea-Bissau [GAZ:00000910] - GAZ:00002522 Covid-19 Guyana [GAZ:00002522] - GAZ:00003953 Covid-19 Haiti [GAZ:00003953] - GAZ:00009718 Covid-19 Heard Island and McDonald Islands [GAZ:00009718] - GAZ:00002894 Covid-19 Honduras [GAZ:00002894] - GAZ:00003203 Covid-19 Hong Kong [GAZ:00003203] - GAZ:00007120 Covid-19 Howland Island [GAZ:00007120] - GAZ:00002952 Covid-19 Hungary [GAZ:00002952] - GAZ:00000843 Covid-19 Iceland [GAZ:00000843] - GAZ:00002839 Covid-19 India [GAZ:00002839] - GAZ:00003727 Covid-19 Indonesia [GAZ:00003727] - GAZ:00004474 Covid-19 Iran [GAZ:00004474] - GAZ:00004483 Covid-19 Iraq [GAZ:00004483] - GAZ:00002943 Covid-19 Ireland [GAZ:00002943] - GAZ:00052477 Covid-19 Isle of Man [GAZ:00052477] - GAZ:00002476 Covid-19 Israel [GAZ:00002476] - GAZ:00002650 Covid-19 Italy [GAZ:00002650] - GAZ:00003781 Covid-19 Jamaica [GAZ:00003781] - GAZ:00005853 Covid-19 Jan Mayen [GAZ:00005853] - GAZ:00002747 Covid-19 Japan [GAZ:00002747] - GAZ:00007118 Covid-19 Jarvis Island [GAZ:00007118] - GAZ:00001551 Covid-19 Jersey [GAZ:00001551] - GAZ:00007114 Covid-19 Johnston Atoll [GAZ:00007114] - GAZ:00002473 Covid-19 Jordan [GAZ:00002473] - GAZ:00005809 Covid-19 Juan de Nova Island [GAZ:00005809] - GAZ:00004999 Covid-19 Kazakhstan [GAZ:00004999] - GAZ:00001101 Covid-19 Kenya [GAZ:00001101] - GAZ:00005682 Covid-19 Kerguelen Archipelago [GAZ:00005682] - GAZ:00007116 Covid-19 Kingman Reef [GAZ:00007116] - GAZ:00006894 Covid-19 Kiribati [GAZ:00006894] - GAZ:00011337 Covid-19 Kosovo [GAZ:00011337] - GAZ:00005285 Covid-19 Kuwait [GAZ:00005285] - GAZ:00006893 Covid-19 Kyrgyzstan [GAZ:00006893] - GAZ:00006889 Covid-19 Laos [GAZ:00006889] - GAZ:00002958 Covid-19 Latvia [GAZ:00002958] - GAZ:00002478 Covid-19 Lebanon [GAZ:00002478] - GAZ:00001098 Covid-19 Lesotho [GAZ:00001098] - GAZ:00000911 Covid-19 Liberia [GAZ:00000911] - GAZ:00000566 Covid-19 Libya [GAZ:00000566] - GAZ:00003858 Covid-19 Liechtenstein [GAZ:00003858] - GAZ:00007144 Covid-19 Line Islands [GAZ:00007144] - GAZ:00002960 Covid-19 Lithuania [GAZ:00002960] - GAZ:00002947 Covid-19 Luxembourg [GAZ:00002947] - GAZ:00003202 Covid-19 Macau [GAZ:00003202] - GAZ:00001108 Covid-19 Madagascar [GAZ:00001108] - GAZ:00001105 Covid-19 Malawi [GAZ:00001105] - GAZ:00003902 Covid-19 Malaysia [GAZ:00003902] - GAZ:00006924 Covid-19 Maldives [GAZ:00006924] - GAZ:00000584 Covid-19 Mali [GAZ:00000584] - GAZ:00004017 Covid-19 Malta [GAZ:00004017] - GAZ:00007161 Covid-19 Marshall Islands [GAZ:00007161] - GAZ:00067143 Covid-19 Martinique [GAZ:00067143] - GAZ:00000583 Covid-19 Mauritania [GAZ:00000583] - GAZ:00003745 Covid-19 Mauritius [GAZ:00003745] - GAZ:00003943 Covid-19 Mayotte [GAZ:00003943] - GAZ:00002852 Covid-19 Mexico [GAZ:00002852] - GAZ:00005862 Covid-19 Micronesia [GAZ:00005862] - GAZ:00007112 Covid-19 Midway Islands [GAZ:00007112] - GAZ:00003897 Covid-19 Moldova [GAZ:00003897] - GAZ:00003857 Covid-19 Monaco [GAZ:00003857] - GAZ:00008744 Covid-19 Mongolia [GAZ:00008744] - GAZ:00006898 Covid-19 Montenegro [GAZ:00006898] - GAZ:00003988 Covid-19 Montserrat [GAZ:00003988] - GAZ:00000565 Covid-19 Morocco [GAZ:00000565] - GAZ:00001100 Covid-19 Mozambique [GAZ:00001100] - GAZ:00006899 Covid-19 Myanmar [GAZ:00006899] - GAZ:00001096 Covid-19 Namibia [GAZ:00001096] - GAZ:00006900 Covid-19 Nauru [GAZ:00006900] - GAZ:00007119 Covid-19 Navassa Island [GAZ:00007119] - GAZ:00004399 Covid-19 Nepal [GAZ:00004399] - GAZ:00002946 Covid-19 Netherlands [GAZ:00002946] - GAZ:00005206 Covid-19 New Caledonia [GAZ:00005206] - GAZ:00000469 Covid-19 New Zealand [GAZ:00000469] - GAZ:00002978 Covid-19 Nicaragua [GAZ:00002978] - GAZ:00000585 Covid-19 Niger [GAZ:00000585] - GAZ:00000912 Covid-19 Nigeria [GAZ:00000912] - GAZ:00006902 Covid-19 Niue [GAZ:00006902] - GAZ:00005908 Covid-19 Norfolk Island [GAZ:00005908] - GAZ:00002801 Covid-19 North Korea [GAZ:00002801] - GAZ:00006895 Covid-19 North Macedonia [GAZ:00006895] - GAZ:00002284 Covid-19 North Sea [GAZ:00002284] - GAZ:00003958 Covid-19 Northern Mariana Islands [GAZ:00003958] - GAZ:00002699 Covid-19 Norway [GAZ:00002699] - GAZ:00005283 Covid-19 Oman [GAZ:00005283] - GAZ:00005246 Covid-19 Pakistan [GAZ:00005246] - GAZ:00006905 Covid-19 Palau [GAZ:00006905] - GAZ:00002892 Covid-19 Panama [GAZ:00002892] - GAZ:00003922 Covid-19 Papua New Guinea [GAZ:00003922] - GAZ:00010832 Covid-19 Paracel Islands [GAZ:00010832] - GAZ:00002933 Covid-19 Paraguay [GAZ:00002933] - GAZ:00002932 Covid-19 Peru [GAZ:00002932] - GAZ:00004525 Covid-19 Philippines [GAZ:00004525] - GAZ:00005867 Covid-19 Pitcairn Islands [GAZ:00005867] - GAZ:00002939 Covid-19 Poland [GAZ:00002939] - GAZ:00004126 Covid-19 Portugal [GAZ:00004126] - GAZ:00006935 Covid-19 Puerto Rico [GAZ:00006935] - GAZ:00005286 Covid-19 Qatar [GAZ:00005286] - GAZ:00001088 Covid-19 Republic of the Congo [GAZ:00001088] - GAZ:00003945 Covid-19 Reunion [GAZ:00003945] - GAZ:00002951 Covid-19 Romania [GAZ:00002951] - GAZ:00023304 Covid-19 Ross Sea [GAZ:00023304] - GAZ:00002721 Covid-19 Russia [GAZ:00002721] - GAZ:00001087 Covid-19 Rwanda [GAZ:00001087] - GAZ:00000849 Covid-19 Saint Helena [GAZ:00000849] - GAZ:00006906 Covid-19 Saint Kitts and Nevis [GAZ:00006906] - GAZ:00006909 Covid-19 Saint Lucia [GAZ:00006909] - GAZ:00003942 Covid-19 Saint Pierre and Miquelon [GAZ:00003942] - GAZ:00005841 Covid-19 Saint Martin [GAZ:00005841] - GAZ:02000565 Covid-19 Saint Vincent and the Grenadines [GAZ:02000565] - GAZ:00006910 Covid-19 Samoa [GAZ:00006910] - GAZ:00003102 Covid-19 San Marino [GAZ:00003102] - GAZ:00006927 Covid-19 Sao Tome and Principe [GAZ:00006927] - GAZ:00005279 Covid-19 Saudi Arabia [GAZ:00005279] - GAZ:00000913 Covid-19 Senegal [GAZ:00000913] - GAZ:00002957 Covid-19 Serbia [GAZ:00002957] - GAZ:00006922 Covid-19 Seychelles [GAZ:00006922] - GAZ:00000914 Covid-19 Sierra Leone [GAZ:00000914] - GAZ:00003923 Covid-19 Singapore [GAZ:00003923] - GAZ:00012579 Covid-19 Sint Maarten [GAZ:00012579] - GAZ:00002956 Covid-19 Slovakia [GAZ:00002956] - GAZ:00002955 Covid-19 Slovenia [GAZ:00002955] - GAZ:00005275 Covid-19 Solomon Islands [GAZ:00005275] - GAZ:00001104 Covid-19 Somalia [GAZ:00001104] - GAZ:00001094 Covid-19 South Africa [GAZ:00001094] - GAZ:00003990 Covid-19 South Georgia and the South Sandwich Islands [GAZ:00003990] - GAZ:00002802 Covid-19 South Korea [GAZ:00002802] - GAZ:00233439 Covid-19 South Sudan [GAZ:00233439] - GAZ:00003936 Covid-19 Spain [GAZ:00003936] - GAZ:00010831 Covid-19 Spratly Islands [GAZ:00010831] - GAZ:00003924 Covid-19 Sri Lanka [GAZ:00003924] - GAZ:00002475 Covid-19 State of Palestine [GAZ:00002475] - GAZ:00000560 Covid-19 Sudan [GAZ:00000560] - GAZ:00002525 Covid-19 Suriname [GAZ:00002525] - GAZ:00005396 Covid-19 Svalbard [GAZ:00005396] - GAZ:00001099 Covid-19 Swaziland [GAZ:00001099] - GAZ:00002729 Covid-19 Sweden [GAZ:00002729] - GAZ:00002941 Covid-19 Switzerland [GAZ:00002941] - GAZ:00002474 Covid-19 Syria [GAZ:00002474] - GAZ:00005341 Covid-19 Taiwan [GAZ:00005341] - GAZ:00006912 Covid-19 Tajikistan [GAZ:00006912] - GAZ:00001103 Covid-19 Tanzania [GAZ:00001103] - GAZ:00003744 Covid-19 Thailand [GAZ:00003744] - GAZ:00006913 Covid-19 Timor-Leste [GAZ:00006913] - GAZ:00000915 Covid-19 Togo [GAZ:00000915] - GAZ:00260188 Covid-19 Tokelau [GAZ:00260188] - GAZ:00006916 Covid-19 Tonga [GAZ:00006916] - GAZ:00003767 Covid-19 Trinidad and Tobago [GAZ:00003767] - GAZ:00005812 Covid-19 Tromelin Island [GAZ:00005812] - GAZ:00000562 Covid-19 Tunisia [GAZ:00000562] - GAZ:00000558 Covid-19 Turkey [GAZ:00000558] - GAZ:00005018 Covid-19 Turkmenistan [GAZ:00005018] - GAZ:00003955 Covid-19 Turks and Caicos Islands [GAZ:00003955] - GAZ:00009715 Covid-19 Tuvalu [GAZ:00009715] - GAZ:00002459 Covid-19 United States of America [GAZ:00002459] - GAZ:00001102 Covid-19 Uganda [GAZ:00001102] - GAZ:00002724 Covid-19 Ukraine [GAZ:00002724] - GAZ:00005282 Covid-19 United Arab Emirates [GAZ:00005282] - GAZ:00002637 Covid-19 United Kingdom [GAZ:00002637] - GAZ:00002930 Covid-19 Uruguay [GAZ:00002930] - GAZ:00004979 Covid-19 Uzbekistan [GAZ:00004979] - GAZ:00006918 Covid-19 Vanuatu [GAZ:00006918] - GAZ:00002931 Covid-19 Venezuela [GAZ:00002931] - GAZ:00003756 Covid-19 Viet Nam [GAZ:00003756] - GAZ:00003959 Covid-19 Virgin Islands [GAZ:00003959] - GAZ:00007111 Covid-19 Wake Island [GAZ:00007111] - GAZ:00007191 Covid-19 Wallis and Futuna [GAZ:00007191] - GAZ:00009572 Covid-19 West Bank [GAZ:00009572] - GAZ:00000564 Covid-19 Western Sahara [GAZ:00000564] - GAZ:00005284 Covid-19 Yemen [GAZ:00005284] - GAZ:00001107 Covid-19 Zambia [GAZ:00001107] - GAZ:00001106 Covid-19 Zimbabwe [GAZ:00001106] - - -library_strategy menu WGA - WGS - WXS - RNA-Seq - miRNA-Seq - WCS - CLONE - POOLCLONE - AMPLICON - CLONEEND - FINISHING - ChIP-Seq - MNase-Seq - DNase-Hypersensitivity - Bisulfite-Seq - Tn-Seq - EST - FL-cDNA - CTS - MRE-Seq - MeDIP-Seq - MBD-Seq - OTHER - - -library_source menu GENOMIC - TRANSCRIPTOMIC - METAGENOMIC - METATRANSCRIPTOMIC - SYNTHETIC - VIRAL RNA - OTHER - - -library_selection menu RANDOM - PCR - RANDOM PCR - RT-PCR - HMPR - MF - CF-S - CF-M - CF-H - CF-T - MDA - MSLL - cDNA - ChIP - MNase - DNAse - Hybrid Selection - Reduced Representation - Restriction Digest - 5-methylcytidine antibody - MBD2 protein methyl-CpG binding domain - CAGE - RACE - size fractionation - Padlock probes capture method - other - unspecified - - -library_layout menu single - paired - - -filetype menu bam - sra - kar - srf - sff - fastq - tab - 454_native - Helicos_native - SOLiD_native - PacBio_HDF5 - CompleteGenomics_native - - - - \ No newline at end of file +title name meaning in_subset menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE EXPORT_NCBI_SRA EXPORT_NCBI_Genbank EXPORT_NCBI_Genbank_source_modifiers + +null value menu NullValueMenu GENEPIO:0001619 Covid-19 Not Applicable [GENEPIO:0001619] + GENEPIO:0001620 Covid-19 Not Collected [GENEPIO:0001620] + GENEPIO:0001668 Covid-19 Not Provided [GENEPIO:0001668] + GENEPIO:0001618 Covid-19 Missing [GENEPIO:0001618] + GENEPIO:0001810 Covid-19 Restricted Access [GENEPIO:0001810] + + +host age unit menu HostAgeUnitMenu UO:0000035 Covid-19 month [UO:0000035] + UO:0000036 Covid-19 year [UO:0000036] + + +biomaterial extracted menu BiomaterialExtractedMenu OBI:0000895 Covid-19 RNA (Total) [OBI:0000895] + OBI:0000869 Covid-19 RNA (Poly-A) [OBI:0000869] + OBI:0002627 Covid-19 RNA (Ribo-Depleted) [OBI:0002627] + GENEPIO:0100104 Covid-19 mRNA (messenger RNA) [GENEPIO:0100104] + OBI:0002754 Covid-19 mRNA (cDNA) [OBI:0002754] + + +signs and symptoms menu SignsAndSymptomsMenu HP:0030829 Covid-19 Abnormal lung auscultation [HP:0030829] + HP:0000223 Covid-19 Abnormality of taste sensation [HP:0000223] + HP:0041051 Covid-19 Ageusia (complete loss of taste) [HP:0041051] + HP:0031249 Covid-19 Parageusia (distorted sense of taste) [HP:0031249] + HP:0000224 Covid-19 Hypogeusia (reduced sense of taste) [HP:0000224] + HP:0004408 Covid-19 Abnormality of the sense of smell [HP:0004408] + HP:0000458 Covid-19 Anosmia (lost sense of smell) [HP:0000458] + HP:0004409 Covid-19 Hyposmia (reduced sense of smell) [HP:0004409] + HP:0033677 Covid-19 Acute Respiratory Distress Syndrome [HP:0033677] + HP:0011446 Covid-19 Altered mental status [HP:0011446] + HP:0100543 Covid-19 Cognitive impairment [HP:0100543] + HP:0001259 Covid-19 Coma [HP:0001259] + HP:0001289 Covid-19 Confusion [HP:0001289] + HP:0031258 Covid-19 Delirium (sudden severe confusion) [HP:0031258] + GENEPIO:0100061 Covid-19 Inability to arouse (inability to stay awake) [GENEPIO:0100061] + HP:0000737 Covid-19 Irritability [HP:0000737] + HP:0002371 Covid-19 Loss of speech [HP:0002371] + HP:0011675 Covid-19 Arrhythmia [HP:0011675] + HP:0025406 Covid-19 Asthenia (generalized weakness) [HP:0025406] + HP:0031352 Covid-19 Chest tightness or pressure [HP:0031352] + HP:0025145 Covid-19 Rigors (fever shakes) [HP:0025145] + HP:0025143 Covid-19 Chills (sudden cold sensation) [HP:0025143] + HP:0030953 Covid-19 Conjunctival injection [HP:0030953] + HP:0000509 Covid-19 Conjunctivitis (pink eye) [HP:0000509] + MP:0001867 Covid-19 Coryza (rhinitis) [MP:0001867] + HP:0012735 Covid-19 Cough [HP:0012735] + HP:0031246 Covid-19 Nonproductive cough (dry cough) [HP:0031246] + HP:0031245 Covid-19 Productive cough (wet cough) [HP:0031245] + HP:0000961 Covid-19 Cyanosis (blueish skin discolouration) [HP:0000961] + HP:0001063 Covid-19 Acrocyanosis [HP:0001063] + HP:0032556 Covid-19 Circumoral cyanosis (bluish around mouth) [HP:0032556] + GENEPIO:0100062 Covid-19 Cyanotic face (bluish face) [GENEPIO:0100062] + GENEPIO:0100063 Covid-19 Central Cyanosis [GENEPIO:0100063] + GENEPIO:0100064 Covid-19 Cyanotic lips (bluish lips) [GENEPIO:0100064] + GENEPIO:0100065 Covid-19 Peripheral Cyanosis [GENEPIO:0100065] + HP:0002094 Covid-19 Dyspnea (breathing difficulty) [HP:0002094] + HP:0002014 Covid-19 Diarrhea (watery stool) [HP:0002014] + MP:0031127 Covid-19 Dry gangrene [MP:0031127] + HP:0002383 Covid-19 Encephalitis (brain inflammation) [HP:0002383] + HP:0001298 Covid-19 Encephalopathy [HP:0001298] + HP:0012378 Covid-19 Fatigue (tiredness) [HP:0012378] + HP:0001945 Covid-19 Fever [HP:0001945] + GENEPIO:0100066 Covid-19 Fever (>=38°C) [GENEPIO:0100066] + HP:0000206 Covid-19 Glossitis (inflammation of the tongue) [HP:0000206] + GENEPIO:0100067 Covid-19 Ground Glass Opacities (GGO) [GENEPIO:0100067] + HP:0002315 Covid-19 Headache [HP:0002315] + HP:0002105 Covid-19 Hemoptysis (coughing up blood) [HP:0002105] + HP:0012417 Covid-19 Hypocapnia [HP:0012417] + HP:0002615 Covid-19 Hypotension (low blood pressure) [HP:0002615] + HP:0012418 Covid-19 Hypoxemia (low blood oxygen) [HP:0012418] + GENEPIO:0100068 Covid-19 Silent hypoxemia [GENEPIO:0100068] + HP:0011029 Covid-19 Internal hemorrhage (internal bleeding) [HP:0011029] + NCIT:C121416 Covid-19 Loss of Fine Movements [NCIT:C121416] + HP:0004396 Covid-19 Low appetite [HP:0004396] + HP:0033834 Covid-19 Malaise (general discomfort/unease) [HP:0033834] + HP:0031179 Covid-19 Meningismus/nuchal rigidity [HP:0031179] + HP:0001324 Covid-19 Muscle weakness [HP:0001324] + HP:0001742 Covid-19 Nasal obstruction (stuffy nose) [HP:0001742] + HP:0002018 Covid-19 Nausea [HP:0002018] + HP:0000421 Covid-19 Nose bleed [HP:0000421] + GENEPIO:0100069 Covid-19 Otitis [GENEPIO:0100069] + HP:0012531 Covid-19 Pain [HP:0012531] + HP:0002027 Covid-19 Abdominal pain [HP:0002027] + HP:0002829 Covid-19 Arthralgia (painful joints) [HP:0002829] + HP:0100749 Covid-19 Chest pain [HP:0100749] + HP:0033771 Covid-19 Pleuritic chest pain [HP:0033771] + HP:0003326 Covid-19 Myalgia (muscle pain) [HP:0003326] + HP:0025439 Covid-19 Pharyngitis (sore throat) [HP:0025439] + GENEPIO:0100070 Covid-19 Pharyngeal exudate [GENEPIO:0100070] + HP:0002202 Covid-19 Pleural effusion [HP:0002202] + HP:0002090 Covid-19 Pneumonia [HP:0002090] + HP:0033696 Covid-19 Pseudo-chilblains [HP:0033696] + GENEPIO:0100072 Covid-19 Pseudo-chilblains on fingers (covid fingers) [GENEPIO:0100072] + GENEPIO:0100073 Covid-19 Pseudo-chilblains on toes (covid toes) [GENEPIO:0100073] + HP:0000988 Covid-19 Rash [HP:0000988] + HP:0031417 Covid-19 Rhinorrhea (runny nose) [HP:0031417] + HP:0001250 Covid-19 Seizure [HP:0001250] + HP:0020219 Covid-19 Motor seizure [HP:0020219] + HP:0025144 Covid-19 Shivering (involuntary muscle twitching) [HP:0025144] + HP:0001350 Covid-19 Slurred speech [HP:0001350] + HP:0025095 Covid-19 Sneezing [HP:0025095] + HP:0033709 Covid-19 Sputum Production [HP:0033709] + HP:0001297 Covid-19 Stroke [HP:0001297] + HP:0002716 Covid-19 Swollen Lymph Nodes [HP:0002716] + HP:0002789 Covid-19 Tachypnea (accelerated respiratory rate) [HP:0002789] + HP:0002321 Covid-19 Vertigo (dizziness) [HP:0002321] + HP:0002013 Covid-19 Vomiting (throwing up) [HP:0002013] + + +host vaccination status menu HostVaccinationStatusMenu GENEPIO:0100100 Covid-19 Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination:Yes + GENEPIO:0100101 Covid-19 Partially Vaccinated [GENEPIO:0100101] prior_sars_cov_2_vaccination:Yes + GENEPIO:0100102 Covid-19 Not Vaccinated [GENEPIO:0100102] prior_sars_cov_2_vaccination:No + + +prior SARS-CoV-2 antiviral treatment menu PriorSarsCov2AntiviralTreatmentMenu GENEPIO:0100237 Covid-19 Prior antiviral treatment [GENEPIO:0100037] prior_sars_cov_2_antiviral_treatment:Yes + GENEPIO:0100233 Covid-19 No prior antiviral treatment [GENEPIO:0100233] prior_sars_cov_2_antiviral_treatment:No + + +pre-existing conditions and risk factors menu PreExistingConditionsAndRiskFactorsMenu VO:0004925 Covid-19 Age 60+ [VO:0004925] + HP:0001903 Covid-19 Anemia [HP:0001903] + HP:0002039 Covid-19 Anorexia [HP:0002039] + NCIT:C92743 Covid-19 Birthing labor [NCIT:C92743] + NCIT:C80693 Covid-19 Bone marrow failure [NCIT:C80693] + MONDO:0004992 Covid-19 Cancer [MONDO:0004992] + MONDO:0007254 Covid-19 Breast cancer [MONDO:0007254] + MONDO:0005575 Covid-19 Colorectal cancer [MONDO:0005575] + DOID:2531 Covid-19 Hematologic malignancy (cancer of the blood) [DOID:2531] + MONDO:0008903 Covid-19 Lung cancer [MONDO:0008903] + MONDO:0024880 Covid-19 Metastatic disease [MONDO:0024880] + NCIT:C16212 Covid-19 Cancer treatment [NCIT:C16212] + NCIT:C157740 Covid-19 Cancer surgery [NCIT:C157740] + NCIT:C15632 Covid-19 Chemotherapy [NCIT:C15632] + NCIT:C15360 Covid-19 Adjuvant chemotherapy [NCIT:C15360] + NCIT:C3079 Covid-19 Cardiac disorder [NCIT:C3079] + HP:0011675 Covid-19 Arrhythmia [HP:0011675] + MONDO:0005267 Covid-19 Cardiac disease [MONDO:0005267] + HP:0001638 Covid-19 Cardiomyopathy [HP:0001638] + GENEPIO:0100074 Covid-19 Cardiac injury [GENEPIO:0100074] + HP:0000822 Covid-19 Hypertension (high blood pressure) [HP:0000822] + HP:0002615 Covid-19 Hypotension (low blood pressure) [HP:0002615] + HP:0011410 Covid-19 Cesarean section [HP:0011410] + GENEPIO:0100075 Covid-19 Chronic cough [GENEPIO:0100075] + GENEPIO:0100076 Covid-19 Chronic gastrointestinal disease [GENEPIO:0100076] + NCIT:C211 Covid-19 Corticosteroids [NCIT:C211] + HP:0000819 Covid-19 Diabetes mellitus (diabetes) [HP:0000819] + HP:0100651 Covid-19 Type I diabetes mellitus (T1D) [HP:0100651] + HP:0005978 Covid-19 Type II diabetes mellitus (T2D) [HP:0005978] + HP:0000964 Covid-19 Eczema [HP:0000964] + HP:0003111 Covid-19 Electrolyte disturbance [HP:0003111] + HP:0002901 Covid-19 Hypocalcemia [HP:0002901] + HP:0002900 Covid-19 Hypokalemia [HP:0002900] + HP:0002917 Covid-19 Hypomagnesemia [HP:0002917] + HP:0002383 Covid-19 Encephalitis (brain inflammation) [HP:0002383] + MONDO:0005027 Covid-19 Epilepsy [MONDO:0005027] + NCIT:C15248 Covid-19 Hemodialysis [NCIT:C15248] + MONDO:0044348 Covid-19 Hemoglobinopathy [MONDO:0044348] + MONDO:0005109 Covid-19 Human immunodeficiency virus (HIV) [MONDO:0005109] + MONDO:0012268 Covid-19 Acquired immunodeficiency syndrome (AIDS) [MONDO:0012268] + NCIT:C16118 Covid-19 HIV and antiretroviral therapy (ART) [NCIT:C16118] + NCIT:C14139 Covid-19 Immunocompromised [NCIT:C14139] + MONDO:0004670 Covid-19 Lupus [MONDO:0004670] + MONDO:0005265 Covid-19 Inflammatory bowel disease (IBD) [MONDO:0005265] + HP:0002583 Covid-19 Colitis [HP:0002583] + HP:0100279 Covid-19 Ulcerative colitis [HP:0100279] + HP:0100280 Covid-19 Crohn's disease [HP:0100280] + NCIT:C3149 Covid-19 Renal disorder [NCIT:C3149] + MONDO:0005240 Covid-19 Renal disease [MONDO:0005240] + HP:0012622 Covid-19 Chronic renal disease [HP:0012622] + HP:0000083 Covid-19 Renal failure [HP:0000083] + MONDO:0005154 Covid-19 Liver disease [MONDO:0005154] + NCIT:C113609 Covid-19 Chronic liver disease [NCIT:C113609] + HP:0001397 Covid-19 Fatty liver disease (FLD) [HP:0001397] + HP:0003326 Covid-19 Myalgia (muscle pain) [HP:0003326] + MONDO:0005404 Covid-19 Myalgic encephalomyelitis (ME) [MONDO:0005404] + MONDO:0005071 Covid-19 Neurological disorder [MONDO:0005071] + MONDO:0019056 Covid-19 Neuromuscular disorder [MONDO:0019056] + HP:0001513 Covid-19 Obesity [HP:0001513] + MONDO:0005139 Covid-19 Severe obesity [MONDO:0005139] + MONDO:0005087 Covid-19 Respiratory disorder [MONDO:0005087] + HP:0002099 Covid-19 Asthma [HP:0002099] + HP:0004469 Covid-19 Chronic bronchitis [HP:0004469] + HP:0006510 Covid-19 Chronic obstructive pulmonary disease [HP:0006510] + HP:0002097 Covid-19 Emphysema [HP:0002097] + MONDO:0005275 Covid-19 Lung disease [MONDO:0005275] + HP:0006528 Covid-19 Chronic lung disease [HP:0006528] + HP:0002206 Covid-19 Pulmonary fibrosis [HP:0002206] + HP:0002090 Covid-19 Pneumonia [HP:0002090] + HP:0002878 Covid-19 Respiratory failure [HP:0002878] + HP:0033677 Covid-19 Adult respiratory distress syndrome [HP:0033677] + MONDO:0009971 Covid-19 Newborn respiratory distress syndrome [MONDO:0009971] + MONDO:0018076 Covid-19 Tuberculosis [MONDO:0018076] + GENEPIO:0100077 Covid-19 Postpartum (≤6 weeks) [GENEPIO:0100077] + NCIT:C25742 Covid-19 Pregnancy [NCIT:C25742] + MONDO:0005554 Covid-19 Rheumatic disease [MONDO:0005554] + MONDO:0011382 Covid-19 Sickle cell disease [MONDO:0011382] + NBO:0001845 Covid-19 Substance use [NBO:0001845] + MONDO:0002046 Covid-19 Alcohol abuse [MONDO:0002046] + GENEPIO:0100078 Covid-19 Drug abuse [GENEPIO:0100078] + GENEPIO:0100079 Covid-19 Injection drug abuse [GENEPIO:0100079] + NBO:0015005 Covid-19 Smoking [NBO:0015005] + NCIT:C173621 Covid-19 Vaping [NCIT:C173621] + HP:0002789 Covid-19 Tachypnea (accelerated respiratory rate) [HP:0002789] + NCIT:C159659 Covid-19 Transplant [NCIT:C159659] + GENEPIO:0100080 Covid-19 Cardiac transplant [NCIT:C131759] + NCIT:C131759 Covid-19 Hematopoietic stem cell transplant (bone marrow transplant) [GENEPIO:0100080] + NCIT:C157332 Covid-19 Kidney transplant [NCIT:C157332] + GENEPIO:0100081 Covid-19 Liver transplant [GENEPIO:0100081] + + +variant designation menu VariantDesignationMenu GENEPIO:0100082 Covid-19 Variant of Interest (VOI) [GENEPIO:0100082] + GENEPIO:0100083 Covid-19 Variant of Concern (VOC) [GENEPIO:0100083] + GENEPIO:0100279 Covid-19 Variant Under Monitoring (VUM) [GENEPIO:0100279] + + +complications menu ComplicationsMenu HP:0500165 Covid-19 Abnormal blood oxygen level [HP:0500165] + HP:0001919 Covid-19 Acute kidney injury [HP:0001919] + MONDO:0015796 Covid-19 Acute lung injury [MONDO:0015796] + GENEPIO:0100092 Covid-19 Ventilation induced lung injury (VILI) [GENEPIO:0100092] + MONDO:0001208 Covid-19 Acute respiratory failure [MONDO:0001208] + HP:0011675 Covid-19 Arrhythmia (complication) [HP:0011675] + HP:0001649 Covid-19 Tachycardia [HP:0001649] + HP:0031677 Covid-19 Polymorphic ventricular tachycardia (VT) [HP:0031677] + GENEPIO:0100084 Covid-19 Tachyarrhythmia [GENEPIO:0100084] + GENEPIO:0100087 Covid-19 Cardiac injury [GENEPIO:0100074] + HP:0001695 Covid-19 Cardiac arrest [HP:0001695] + HP:0030149 Covid-19 Cardiogenic shock [HP:0030149] + HP:0001977 Covid-19 Blood clot [HP:0001977] + HP:0004420 Covid-19 Arterial clot [HP:0004420] + HP:0002625 Covid-19 Deep vein thrombosis (DVT) [HP:0002625] + HP:0002204 Covid-19 Pulmonary embolism (PE) [HP:0002204] + HP:0001638 Covid-19 Cardiomyopathy [HP:0001638] + MONDO:0024619 Covid-19 Central nervous system invasion [MONDO:0024619] + HP:0001297 Covid-19 Stroke (complication) [HP:0001297] + MONDO:0003346 Covid-19 Central Nervous System Vasculitis [MONDO:0003346] + HP:0002140 Covid-19 Acute ischemic stroke [HP:0002140] + HP:0001259 Covid-19 Coma [HP:0001259] + HP:0011097 Covid-19 Convulsions [HP:0011097] + NCIT:C171562 Covid-19 COVID-19 associated coagulopathy (CAC) [NCIT:C171562] + MONDO:0009061 Covid-19 Cystic fibrosis [MONDO:0009061] + MONDO:0600008 Covid-19 Cytokine release syndrome [MONDO:0600008] + MPATH:108 Covid-19 Disseminated intravascular coagulation (DIC) [MPATH:108] + HP:0001298 Covid-19 Encephalopathy [HP:0001298] + GENEPIO:0100088 Covid-19 Fulminant myocarditis [GENEPIO:0100088] + MONDO:0016218 Covid-19 Guillain-Barré syndrome [MONDO:0016218] + HP:0011029 Covid-19 Internal hemorrhage (complication; internal bleeding) [HP:0011029] + MONDO:0013792 Covid-19 Intracerebral haemorrhage [MONDO:0013792] + MONDO:0012727 Covid-19 Kawasaki disease [MONDO:0012727] + GENEPIO:0100089 Covid-19 Complete Kawasaki disease [GENEPIO:0100089] + GENEPIO:0100090 Covid-19 Incomplete Kawasaki disease [GENEPIO:0100090] + HP:0001410 Covid-19 Liver dysfunction [HP:0001410] + GENEPIO:0100091 Covid-19 Acute liver injury [GENEPIO:0100091] + MONDO:0100233 Covid-19 Long COVID-19 [MONDO:0100233] + HP:0001287 Covid-19 Meningitis [HP:0001287] + HP:0002076 Covid-19 Migraine [HP:0002076] + HP:0005268 Covid-19 Miscarriage [HP:0005268] + MONDO:0100163 Covid-19 Multisystem inflammatory syndrome in children (MIS-C) [MONDO:0100163] + MONDO:0100319 Covid-19 Multisystem inflammatory syndrome in adults (MIS-A) [MONDO:0100319] + GENEPIO:0100093 Covid-19 Muscle injury [GENEPIO:0100093] + MONDO:0005404 Covid-19 Myalgic encephalomyelitis (chronic fatigue syndrome) [MONDO:0005404] + MONDO:0005068 Covid-19 Myocardial infarction (heart attack) [MONDO:0005068] + MONDO:0004781 Covid-19 Acute myocardial infarction [MONDO:0004781] + MONDO:0041656 Covid-19 ST-segment elevation myocardial infarction [MONDO:0041656] + HP:0001700 Covid-19 Myocardial injury [HP:0001700] + NCIT:C168498 Covid-19 Neonatal complications [NCIT:C168498] + GENEPIO:0100085 Covid-19 Noncardiogenic pulmonary edema [GENEPIO:0100085] + HP:0033677 Covid-19 Acute respiratory distress syndrome (ARDS) [HP:0033677] + NCIT:C171551 Covid-19 COVID-19 associated ARDS (CARDS) [NCIT:C171551] + GENEPIO:0100086 Covid-19 Neurogenic pulmonary edema (NPE) [GENEPIO:0100086] + GENEPIO:0100094 Covid-19 Organ failure [GENEPIO:0100094] + HP:0001635 Covid-19 Heart failure [HP:0001635] + MONDO:0100192 Covid-19 Liver failure [MONDO:0100192] + HP:0003470 Covid-19 Paralysis [HP:0003470] + HP:0002107 Covid-19 Pneumothorax (collapsed lung) [HP:0002107] + HP:0002108 Covid-19 Spontaneous pneumothorax [HP:0002108] + MONDO:0002075 Covid-19 Spontaneous tension pneymothorax [MONDO:0002075] + HP:0002090 Covid-19 Pneumonia (complication) [HP:0002090] + NCIT:C171550 Covid-19 COVID-19 pneumonia [NCIT:C171550] + HP:0001197 Covid-19 Pregancy complications [HP:0001197] + HP:0003201 Covid-19 Rhabdomyolysis [HP:0003201] + IDO:0000567 Covid-19 Secondary infection [IDO:0000567] + GENEPIO:0100095 Covid-19 Secondary staph infection [GENEPIO:0100095] + GENEPIO:0100096 Covid-19 Secondary strep infection [GENEPIO:0100096] + HP:0001250 Covid-19 Seizure (complication) [HP:0001250] + HP:0020219 Covid-19 Motor seizure [HP:0020219] + HP:0100806 Covid-19 Sepsis/Septicemia [HP:0100806] + IDO:0000636 Covid-19 Sepsis (systemic inflammatory response to infection) [IDO:0000636] + NCIT:C3364 Covid-19 Septicemia (bloodstream infection) [NCIT:C3364] + HP:0031273 Covid-19 Shock [HP:0031273] + GENEPIO:0100097 Covid-19 Hyperinflammatory shock [GENEPIO:0100097] + GENEPIO:0100098 Covid-19 Refractory cardiogenic shock [GENEPIO:0100098] + GENEPIO:0100099 Covid-19 Refractory cardiogenic plus vasoplegic shock [GENEPIO:0100099] + NCIT:C35018 Covid-19 Septic shock [NCIT:C35018] + HP:0002633 Covid-19 Vasculitis [HP:0002633] + + +sample collected in quarantine menu SampleCollectedInQuarantineMenu NCIT:C49488 Covid-19 Yes [NCIT:C49488] + NCIT:C49487 Covid-19 No [NCIT:C49487] + + +anatomical material menu AnatomicalMaterialMenu UBERON:0000178 Covid-19 Blood [UBERON:0000178] + UBERON:0006314 Covid-19 Fluid [UBERON:0006314] + UBERON:0001359 Covid-19 Fluid (cerebrospinal (CSF)) [UBERON:0001359] + UBERON:0002409 Covid-19 Fluid (pericardial) [UBERON:0002409] + UBERON:0001087 Covid-19 Fluid (pleural) [UBERON:0001087] + UBERON:0036243 Covid-19 Fluid (vaginal) [UBERON:0036243] + UBERON:0000173 Covid-19 Fluid (amniotic) [UBERON:0000173] + UBERON:0001836 Covid-19 Saliva [UBERON:0001836] + UBERON:0000479 Covid-19 Tissue [UBERON:0000479] + + +anatomical part menu AnatomicalPartMenu UBERON:0001245 Covid-19 Anus [UBERON:0001245] + UBERON:0006956 Covid-19 Buccal mucosa [UBERON:0006956] + UBERON:0002114 Covid-19 Duodenum [UBERON:0002114] + UBERON:0000970 Covid-19 Eye [UBERON:0000970] + UBERON:0000160 Covid-19 Intestine [UBERON:0000160] + UBERON:0001558 Covid-19 Lower respiratory tract [UBERON:0001558] + UBERON:0002185 Covid-19 Bronchus [UBERON:0002185] + UBERON:0002048 Covid-19 Lung [UBERON:0002048] + UBERON:0002186 Covid-19 Bronchiole [UBERON:0002186] + UBERON:0002169 Covid-19 Alveolar sac [UBERON:0002169] + UBERON:0009778 Covid-19 Pleural sac [UBERON:0009778] + UBERON:0002402 Covid-19 Pleural cavity [UBERON:0002402] + UBERON:0003126 Covid-19 Trachea [UBERON:0003126] + UBERON:0001052 Covid-19 Rectum [UBERON:0001052] + UBERON:0001003 Covid-19 Skin [UBERON:0001003] + UBERON:0000945 Covid-19 Stomach [UBERON:0000945] + UBERON:0001557 Covid-19 Upper respiratory tract [UBERON:0001557] + UBERON:2001427 Covid-19 Anterior Nares [UBERON:2001427] + UBERON:0001043 Covid-19 Esophagus [UBERON:0001043] + UBERON:0002453 Covid-19 Ethmoid sinus [UBERON:0002453] + UBERON:0001707 Covid-19 Nasal Cavity [UBERON:0001707] + UBERON:0005921 Covid-19 Middle Nasal Turbinate [UBERON:0005921] + UBERON:0005922 Covid-19 Inferior Nasal Turbinate [UBERON:0005922] + UBERON:0001728 Covid-19 Nasopharynx (NP) [UBERON:0001728] + UBERON:0001729 Covid-19 Oropharynx (OP) [UBERON:0001729] + + +body product menu BodyProductMenu UBERON:0001913 Covid-19 Breast Milk [UBERON:0001913] + UBERON:0001988 Covid-19 Feces [UBERON:0001988] + UBERON:0006530 Covid-19 Fluid (seminal) [UBERON:0006530] + UBERON:0000912 Covid-19 Mucus [UBERON:0000912] + UBERON:0007311 Covid-19 Sputum [UBERON:0007311] + UBERON:0001089 Covid-19 Sweat [UBERON:0001089] + UBERON:0001827 Covid-19 Tear [UBERON:0001827] + UBERON:0001088 Covid-19 Urine [UBERON:0001088] + + +environmental material menu EnvironmentalMaterialMenu ENVO:03501208 Covid-19 Air vent [ENVO:03501208] + ENVO:00003896 Covid-19 Banknote [ENVO:00003896] + ENVO:03501209 Covid-19 Bed rail [ENVO:03501209] + ENVO:01000486 Covid-19 Building floor [ENVO:01000486] + ENVO:02000058 Covid-19 Cloth [ENVO:02000058] + ENVO:03501210 Covid-19 Control panel [ENVO:03501210] + ENVO:03501220 Covid-19 Door [ENVO:03501220] + ENVO:03501211 Covid-19 Door handle [ENVO:03501211] + OBI:0002787 Covid-19 Face mask [OBI:0002787] + OBI:0002791 Covid-19 Face shield [OBI:0002791] + FOODON:00002403 Covid-19 Food [FOODON:00002403] + FOODON:03490100 Covid-19 Food packaging [FOODON:03490100] + ENVO:01000481 Covid-19 Glass [ENVO:01000481] + ENVO:03501212 Covid-19 Handrail [ENVO:03501212] + OBI:0002796 Covid-19 Hospital gown [OBI:0002796] + ENVO:03501213 Covid-19 Light switch [ENVO:03501213] + ENVO:03501214 Covid-19 Locker [ENVO:03501214] + OBI:0002790 Covid-19 N95 mask [OBI:0002790] + ENVO:03501215 Covid-19 Nurse call button [ENVO:03501215] + ENVO:03501256 Covid-19 Paper [ENVO:03501256] + ENVO:01000060 Covid-19 Particulate matter [ENVO:01000060] + ENVO:01000404 Covid-19 Plastic [ENVO:01000404] + GENEPIO:0100025 Covid-19 PPE gown [GENEPIO:0100025] + ENVO:00002018 Covid-19 Sewage [ENVO:00002018] + ENVO:01000990 Covid-19 Sink [ENVO:01000990] + ENVO:00001998 Covid-19 Soil [ENVO:00001998] + ENVO:03501216 Covid-19 Stainless steel [ENVO:03501216] + ENVO:03501217 Covid-19 Tissue paper [ENVO:03501217] + ENVO:03501218 Covid-19 Toilet bowl [ENVO:03501218] + ENVO:00002006 Covid-19 Water [ENVO:00002006] + ENVO:00002001 Covid-19 Wastewater [ENVO:00002001] + ENVO:03501219 Covid-19 Window [ENVO:03501219] + ENVO:00002040 Covid-19 Wood [ENVO:00002040] + + +environmental site menu EnvironmentalSiteMenu ENVO:03501135 Covid-19 Acute care facility [ENVO:03501135] + ENVO:00003040 Covid-19 Animal house [ENVO:00003040] + ENVO:01000422 Covid-19 Bathroom [ENVO:01000422] + ENVO:03501136 Covid-19 Clinical assessment centre [ENVO:03501136] + ENVO:03501127 Covid-19 Conference venue [ENVO:03501127] + ENVO:03501121 Covid-19 Corridor [ENVO:03501121] + ENVO:01000927 Covid-19 Daycare [ENVO:01000927] + ENVO:03501145 Covid-19 Emergency room (ER) [ENVO:03501145] + ENVO:03501186 Covid-19 Family practice clinic [ENVO:03501186] + ENVO:03501196 Covid-19 Group home [ENVO:03501196] + ENVO:03501133 Covid-19 Homeless shelter [ENVO:03501133] + ENVO:00002173 Covid-19 Hospital [ENVO:00002173] + ENVO:03501152 Covid-19 Intensive Care Unit (ICU) [ENVO:03501152] + ENVO:03501194 Covid-19 Long Term Care Facility [ENVO:03501194] + ENVO:03501180 Covid-19 Patient room [ENVO:03501180] + ENVO:03501204 Covid-19 Prison [ENVO:03501204] + ENVO:01000536 Covid-19 Production Facility [ENVO:01000536] + ENVO:03501130 Covid-19 School [ENVO:03501130] + ENVO:00003043 Covid-19 Sewage Plant [ENVO:00003043] + ENVO:03501109 Covid-19 Subway train [ENVO:03501109] + ENVO:00000467 Covid-19 University campus [ENVO:00000467] + ENVO:03501198 Covid-19 Wet market [ENVO:03501198] + + +collection method menu CollectionMethodMenu NCIT:C52009 Covid-19 Amniocentesis [NCIT:C52009] + NCIT:C15631 Covid-19 Aspiration [NCIT:C15631] + GENEPIO:0100028 Covid-19 Suprapubic Aspiration [GENEPIO:0100028] + GENEPIO:0100029 Covid-19 Tracheal Aspiration [GENEPIO:0100029] + GENEPIO:0100030 Covid-19 Vacuum Aspiration [GENEPIO:0100030] + OBI:0002650 Covid-19 Biopsy [OBI:0002650] + OBI:0002651 Covid-19 Needle Biopsy [OBI:0002651] + OBI:0302885 Covid-19 Filtration [OBI:0302885] + GENEPIO:0100031 Covid-19 Air filtration [GENEPIO:0100031] + OBI:0600044 Covid-19 Lavage (medical wash) [OBI:0600044] + GENEPIO:0100032 Covid-19 Bronchoalveolar lavage (BAL) [GENEPIO:0100032] + GENEPIO:0100033 Covid-19 Gastric Lavage [GENEPIO:0100033] + NCIT:C15327 Covid-19 Lumbar Puncture [NCIT:C15327] + MMO:0000344 Covid-19 Necropsy [MMO:0000344] + NCIT:C28221 Covid-19 Phlebotomy [NCIT:C28221] + GENEPIO:0002116 Covid-19 Rinsing (wash) [GENEPIO:0002116] + GENEPIO:0100034 Covid-19 Saline gargle (mouth rinse and gargle) [GENEPIO:0100034] + GENEPIO:0100035 Covid-19 Scraping [GENEPIO:0100035] + GENEPIO:0002117 Covid-19 Swabbing [GENEPIO:0002117] + GENEPIO:0100036 Covid-19 Finger Prick [GENEPIO:0100036] + GENEPIO:0100038 Covid-19 Washout Tear Collection [GENEPIO:0100038] + + +collection device menu CollectionDeviceMenu ENVO:00003968 Covid-19 Air filter [ENVO:00003968] + OBI:0002859 Covid-19 Blood Collection Tube [OBI:0002859] + OBI:0002826 Covid-19 Bronchoscope [OBI:0002826] + OBI:0002088 Covid-19 Collection Container [OBI:0002088] + GENEPIO:0100026 Covid-19 Collection Cup [GENEPIO:0100026] + OBI:0002825 Covid-19 Fibrobronchoscope Brush [OBI:0002825] + GENEPIO:0100103 Covid-19 Filter [GENEPIO:0100103] + OBI:0002827 Covid-19 Fine Needle [OBI:0002827] + OBI:0002858 Covid-19 Microcapillary tube [OBI:0002858] + OBI:0001128 Covid-19 Micropipette [OBI:0001128] + OBI:0000436 Covid-19 Needle [OBI:0000436] + OBI:0002860 Covid-19 Serum Collection Tube [OBI:0002860] + OBI:0002861 Covid-19 Sputum Collection Tube [OBI:0002861] + OBI:0002831 Covid-19 Suction Catheter [OBI:0002831] + GENEPIO:0100027 Covid-19 Swab [GENEPIO:0100027] + OBI:0002862 Covid-19 Urine Collection Tube [OBI:0002862] + OBI:0002866 Covid-19 Virus Transport Medium [OBI:0002866] + + +host (scientific name) menu HostScientificNameMenu NCBITaxon:9913 Covid-19 Homo sapiens [NCBITaxon:9606] + NCBITaxon:9615 Covid-19 Bos taurus [NCBITaxon:9913] + NCBITaxon:9397 Covid-19 Canis lupus familiaris [NCBITaxon:9615] + NCBITaxon:8930 Covid-19 Chiroptera [NCBITaxon:9397] + NCBITaxon:9685 Covid-19 Columbidae [NCBITaxon:8930] + NCBITaxon:9031 Covid-19 Felis catus [NCBITaxon:9685] + NCBITaxon:9606 Covid-19 Gallus gallus [NCBITaxon:9031] + NCBITaxon:9973 Covid-19 Manis [NCBITaxon:9973] + NCBITaxon:9974 Covid-19 Manis javanica [NCBITaxon:9974] + NCBITaxon:452646 Covid-19 Neovison vison [NCBITaxon:452646] + NCBITaxon:9689 Covid-19 Panthera leo [NCBITaxon:9689] + NCBITaxon:9694 Covid-19 Panthera tigris [NCBITaxon:9694] + NCBITaxon:58055 Covid-19 Rhinolophidae [NCBITaxon:58055] + NCBITaxon:59477 Covid-19 Rhinolophus affinis [NCBITaxon:59477] + NCBITaxon:9825 Covid-19 Sus scrofa domesticus [NCBITaxon:9825] + NCBITaxon:9673 Covid-19 Viverridae [NCBITaxon:9673] + + +host (common name) menu HostCommonNameMenu NCBITaxon:9605 Covid-19 Human [NCBITaxon:9606] + NCBITaxon:9397 Covid-19 Bat [NCBITaxon:9397] + NCBITaxon:9685 Covid-19 Cat [NCBITaxon:9685] + NCBITaxon:9031 Covid-19 Chicken [NCBITaxon:9031] + NCBITaxon:9673 Covid-19 Civets [NCBITaxon:9673] + NCBITaxon:9913 Covid-19 Cow [NCBITaxon:9913] + NCBITaxon:9615 Covid-19 Dog [NCBITaxon:9615] + NCBITaxon:9689 Covid-19 Lion [NCBITaxon:9689] + NCBITaxon:452646 Covid-19 Mink [NCBITaxon:452646] + NCBITaxon:9973 Covid-19 Pangolin [NCBITaxon:9973] + NCBITaxon:9825 Covid-19 Pig [NCBITaxon:9825] + NCBITaxon:8930 Covid-19 Pigeon [NCBITaxon:8930] + NCBITaxon:9694 Covid-19 Tiger [NCBITaxon:9694] + + +host health state menu HostHealthStateMenu NCIT:C3833 Covid-19 Asymptomatic [NCIT:C3833] + NCIT:C28554 Covid-19 Deceased [NCIT:C28554] + NCIT:C115935 Covid-19 Healthy [NCIT:C115935] + NCIT:C49498 Covid-19 Recovered [NCIT:C49498] + NCIT:C25269 Covid-19 Symptomatic [NCIT:C25269] + + +host health status details menu HostHealthStatusDetailsMenu NCIT:C25179 Covid-19 Hospitalized [NCIT:C25179] + GENEPIO:0100045 Covid-19 Hospitalized (Non-ICU) [GENEPIO:0100045] + GENEPIO:0100046 Covid-19 Hospitalized (ICU) [GENEPIO:0100046] + NCIT:C70909 Covid-19 Mechanical Ventilation [NCIT:C70909] + GENEPIO:0100047 Covid-19 Medically Isolated [GENEPIO:0100047] + GENEPIO:0100048 Covid-19 Medically Isolated (Negative Pressure) [GENEPIO:0100048] + NCIT:C173768 Covid-19 Self-quarantining [NCIT:C173768] + + +host health outcome menu HostHealthOutcomeMenu NCIT:C28554 Covid-19 Deceased [NCIT:C28554] + NCIT:C25254 Covid-19 Deteriorating [NCIT:C25254] + NCIT:C49498 Covid-19 Recovered [NCIT:C49498] + NCIT:C30103 Covid-19 Stable [NCIT:C30103] + + +organism menu OrganismMenu NCBITaxon:2697049 Covid-19 Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] + NCBITaxon:2709072 Covid-19 RaTG13 [NCBITaxon:2709072] + GENEPIO:0100000 Covid-19 RmYN02 [GENEPIO:0100000] + + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 Covid-19 Cluster/Outbreak investigation [GENEPIO:0100001] + GENEPIO:0100002 Covid-19 Diagnostic testing [GENEPIO:0100002] + GENEPIO:0100003 Covid-19 Research [GENEPIO:0100003] + GENEPIO:0100024 Covid-19 Protocol testing [GENEPIO:0100024] + GENEPIO:0100004 Covid-19 Surveillance [GENEPIO:0100004] + + +purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Covid-19 Baseline surveillance (random sampling) [GENEPIO:0100005] + GENEPIO:0100006 Covid-19 Targeted surveillance (non-random sampling) [GENEPIO:0100006] + GENEPIO:0100007 Covid-19 Priority surveillance project [GENEPIO:0100007] + GENEPIO:0100008 Covid-19 Screening for Variants of Concern (VoC) [GENEPIO:0100008] + GENEPIO:0100273 Covid-19 Sample has epidemiological link to Variant of Concern (VoC) [GENEPIO:0100273] + GENEPIO:0100274 Covid-19 Sample has epidemiological link to Omicron Variant [GENEPIO:0100274] + GENEPIO:0100009 Covid-19 Longitudinal surveillance (repeat sampling of individuals) [GENEPIO:0100009] + GENEPIO:0100010 Covid-19 Re-infection surveillance [GENEPIO:0100010] + GENEPIO:0100011 Covid-19 Vaccine escape surveillance [GENEPIO:0100011] + GENEPIO:0100012 Covid-19 Travel-associated surveillance [GENEPIO:0100012] + GENEPIO:0100013 Covid-19 Domestic travel surveillance [GENEPIO:0100013] + GENEPIO:0100275 Covid-19 Interstate/ interprovincial travel surveillance [GENEPIO:0100275] + GENEPIO:0100276 Covid-19 Intra-state/ intra-provincial travel surveillance [GENEPIO:0100276] + GENEPIO:0100014 Covid-19 International travel surveillance [GENEPIO:0100014] + GENEPIO:0100015 Covid-19 Surveillance of international border crossing by air travel or ground transport [GENEPIO:0100015] + GENEPIO:0100016 Covid-19 Surveillance of international border crossing by air travel [GENEPIO:0100016] + GENEPIO:0100017 Covid-19 Surveillance of international border crossing by ground transport [GENEPIO:0100017] + GENEPIO:0100018 Covid-19 Surveillance from international worker testing [GENEPIO:0100018] + GENEPIO:0100019 Covid-19 Cluster/Outbreak investigation [GENEPIO:0100019] + GENEPIO:0100020 Covid-19 Multi-jurisdictional outbreak investigation [GENEPIO:0100020] + GENEPIO:0100021 Covid-19 Intra-jurisdictional outbreak investigation [GENEPIO:0100021] + GENEPIO:0100022 Covid-19 Research [GENEPIO:0100022] + GENEPIO:0100023 Covid-19 Viral passage experiment [GENEPIO:0100023] + GENEPIO:0100024 Covid-19 Protocol testing experiment [GENEPIO:0100024] + GENEPIO:0100356 Retrospective sequencing [GENEPIO:0100356] + + +specimen processing menu SpecimenProcessingMenu GENEPIO:0100039 Covid-19 Virus passage [GENEPIO:0100039] + GENEPIO:0100040 Covid-19 RNA re-extraction (post RT-PCR) [GENEPIO:0100040] + OBI:0600016 Covid-19 Specimens pooled [OBI:0600016] + EFO:0002090 Covid-19 Technical replicate [EFO:0002090] + + +lab host menu LabHostMenu GENEPIO:0100041 Covid-19 293/ACE2 cell line [GENEPIO:0100041] + BTO:0000195 Covid-19 Caco2 cell line [BTO:0000195] + BTO:0002750 Covid-19 Calu3 cell line [BTO:0002750] + GENEPIO:0100042 Covid-19 EFK3B cell line [GENEPIO:0100042] + BTO:0002181 Covid-19 HEK293T cell line [BTO:0002181] + GENEPIO:0100043 Covid-19 HRCE cell line [GENEPIO:0100043] + BTO:0001950 Covid-19 Huh7 cell line [BTO:0001950] + CLO:0007330 Covid-19 LLCMk2 cell line [CLO:0007330] + BTO:0000836 Covid-19 MDBK cell line [BTO:0000836] + BTO:0002924 Covid-19 NHBE cell line [BTO:0002924] + BTO:0001865 Covid-19 PK-15 cell line [BTO:0001865] + BTO:0002909 Covid-19 RK-13 cell line [BTO:0002909] + BTO:0002035 Covid-19 U251 cell line [BTO:0002035] + BTO:0001444 Covid-19 Vero cell line [BTO:0001444] + BTO:0004755 Covid-19 Vero E6 cell line [BTO:0004755] + GENEPIO:0100044 Covid-19 VeroE6/TMPRSS2 cell line [GENEPIO:0100044] + + +host disease menu HostDiseaseMenu MONDO:0100096 Covid-19 COVID-19 [MONDO:0100096] + + +host age bin menu HostAgeBinMenu GENEPIO:0100049 Covid-19 0 - 9 [GENEPIO:0100049] + GENEPIO:0100050 Covid-19 10 - 19 [GENEPIO:0100050] + GENEPIO:0100051 Covid-19 20 - 29 [GENEPIO:0100051] + GENEPIO:0100052 Covid-19 30 - 39 [GENEPIO:0100052] + GENEPIO:0100053 Covid-19 40 - 49 [GENEPIO:0100053] + GENEPIO:0100054 Covid-19 50 - 59 [GENEPIO:0100054] + GENEPIO:0100055 Covid-19 60 - 69 [GENEPIO:0100055] + GENEPIO:0100056 Covid-19 70 - 79 [GENEPIO:0100056] + GENEPIO:0100057 Covid-19 80 - 89 [GENEPIO:0100057] + GENEPIO:0100058 Covid-19 90 - 99 [GENEPIO:0100058] + GENEPIO:0100059 Covid-19 100+ [GENEPIO:0100059] + + +host gender menu HostGenderMenu NCIT:C46110 Covid-19 Female [NCIT:C46110] + NCIT:C46109 Covid-19 Male [NCIT:C46109] + GSSO:000132 Covid-19 Non-binary gender [GSSO:000132] + GSSO:004004 Covid-19 Transgender (assigned male at birth) [GSSO:004004] + GSSO:004005 Covid-19 Transgender (assigned female at birth) [GSSO:004005] + NCIT:C110959 Covid-19 Undeclared [NCIT:C110959] + + +exposure event menu ExposureEventMenu GENEPIO:0100237 Covid-19 Mass Gathering [GENEPIO:0100237] + GENEPIO:0100238 Covid-19 Convention [GENEPIO:0100238] + GENEPIO:0100239 Covid-19 Convocation [GENEPIO:0100239] + GENEPIO:0100240 Covid-19 Agricultural Event [GENEPIO:0100240] + GENEPIO:0100241 Covid-19 Religious Gathering [GENEPIO:0100241] + GENEPIO:0100242 Covid-19 Mass [GENEPIO:0100242] + PCO:0000033 Covid-19 Social Gathering [PCO:0000033] + PCO:0000039 Covid-19 Baby Shower [PCO:0000039] + PCO:0000034 Covid-19 Community Event [PCO:0000034] + GENEPIO:0100243 Covid-19 Family Gathering [GENEPIO:0100243] + GENEPIO:0100244 Covid-19 Family Reunion [GENEPIO:0100244] + GENEPIO:0100245 Covid-19 Funeral [GENEPIO:0100245] + PCO:0000035 Covid-19 Party [PCO:0000035] + PCO:0000037 Covid-19 Potluck [PCO:0000037] + PCO:0000038 Covid-19 Wedding [PCO:0000038] + Other exposure event + + +exposure contact level menu ExposureContactLevelMenu GENEPIO:0100357 Covid-19 Contact with infected individual + TRANS:0000001 Covid-19 Direct (human-to-human contact) [TRANS:0000001] + GENEPIO:0100246 Covid-19 Indirect contact [GENEPIO:0100246] + GENEPIO:0100247 Covid-19 Close contact (face-to-face contact) [GENEPIO:0100247] + GENEPIO:0100248 Covid-19 Casual contact [GENEPIO:0100248] + + +host role menu HostRoleMenu GENEPIO:0100249 Covid-19 Attendee [GENEPIO:0100249] + OMRSE:00000058 Covid-19 Student [OMRSE:00000058] + OMRSE:00000030 Covid-19 Patient [OMRSE:00000030] + NCIT:C25182 Covid-19 Inpatient [NCIT:C25182] + NCIT:C28293 Covid-19 Outpatient [NCIT:C28293] + GENEPIO:0100250 Covid-19 Passenger [GENEPIO:0100250] + GENEPIO:0100251 Covid-19 Resident [GENEPIO:0100251] + GENEPIO:0100252 Covid-19 Visitor [GENEPIO:0100252] + GENEPIO:0100253 Covid-19 Volunteer [GENEPIO:0100253] + GENEPIO:0100254 Covid-19 Work [GENEPIO:0100254] + GENEPIO:0100255 Covid-19 Administrator [GENEPIO:0100255] + GENEPIO:0100256 Covid-19 First Responder [GENEPIO:0100256] + GENEPIO:0100257 Covid-19 Firefighter [GENEPIO:0100257] + GENEPIO:0100258 Covid-19 Paramedic [GENEPIO:0100258] + GENEPIO:0100259 Covid-19 Police Officer [GENEPIO:0100259] + GENEPIO:0100260 Covid-19 Housekeeper [GENEPIO:0100260] + GENEPIO:0100261 Covid-19 Kitchen Worker [GENEPIO:0100261] + GENEPIO:0100334 Covid-19 Healthcare Worker [GENEPIO:0100334] + GENEPIO:0100420 Covid-19 Community Healthcare Worker [GENEPIO:0100420] + GENEPIO:0100262 Covid-19 Laboratory Worker [GENEPIO:0100262] + OMRSE:00000014 Covid-19 Nurse [OMRSE:00000014] + GENEPIO:0100263 Covid-19 Personal Care Aid [GENEPIO:0100263] + GENEPIO:0100264 Covid-19 Pharmacist [GENEPIO:0100264] + OMRSE:00000013 Covid-19 Physician [OMRSE:00000013] + GENEPIO:0100354 Covid-19 Rotational Worker [GENEPIO:0100354] + GENEPIO:0100355 Covid-19 Seasonal Worker [GENEPIO:0100355] + GENEPIO:0100265 Covid-19 Veterinarian [GENEPIO:0100265] + OMRSE:00000001 Covid-19 Social role [OMRSE:00000001] + GENEPIO:0100266 Covid-19 Acquaintance of case [GENEPIO:0100266] + GENEPIO:0100267 Covid-19 Relative of case [GENEPIO:0100267] + GENEPIO:0100268 Covid-19 Child of case [GENEPIO:0100268] + GENEPIO:0100269 Covid-19 Parent of case [GENEPIO:0100269] + GENEPIO:0100270 Covid-19 Father of case [GENEPIO:0100270] + GENEPIO:0100271 Covid-19 Mother of case [GENEPIO:0100271] + GENEPIO:0100272 Covid-19 Spouse of case [GENEPIO:0100272] + Other Host Role + + +exposure setting menu ExposureSettingMenu ECTO:3000005 Covid-19 Human Exposure [ECTO:3000005] + GENEPIO:0100184 Covid-19 Contact with Known COVID-19 Case [GENEPIO:0100184] + GENEPIO:0100185 Covid-19 Contact with Patient [GENEPIO:0100185] + GENEPIO:0100186 Covid-19 Contact with Probable COVID-19 Case [GENEPIO:0100186] + GENEPIO:0100187 Covid-19 Contact with Person with Acute Respiratory Illness [GENEPIO:0100187] + GENEPIO:0100188 Covid-19 Contact with Person with Fever and/or Cough [GENEPIO:0100188] + GENEPIO:0100189 Covid-19 Contact with Person who Recently Travelled [GENEPIO:0100189] + GENEPIO:0100190 Covid-19 Occupational, Residency or Patronage Exposure [GENEPIO:0100190] + ECTO:1000033 Covid-19 Abbatoir [ECTO:1000033] + GENEPIO:0100191 Covid-19 Animal Rescue [GENEPIO:0100191] + GENEPIO:0100192 Covid-19 Childcare [GENEPIO:0100192] + GENEPIO:0100193 Covid-19 Daycare [GENEPIO:0100193] + GENEPIO:0100194 Covid-19 Nursery [GENEPIO:0100194] + GENEPIO:0100195 Covid-19 Community Service Centre [GENEPIO:0100195] + GENEPIO:0100196 Covid-19 Correctional Facility [GENEPIO:0100196] + GENEPIO:0100197 Covid-19 Dormitory [GENEPIO:0100197] + ECTO:1000034 Covid-19 Farm [ECTO:1000034] + GENEPIO:0100198 Covid-19 First Nations Reserve [GENEPIO:0100198] + GENEPIO:0100199 Covid-19 Funeral Home [GENEPIO:0100199] + GENEPIO:0100200 Covid-19 Group Home [GENEPIO:0100200] + GENEPIO:0100201 Covid-19 Healthcare Setting [GENEPIO:0100201] + GENEPIO:0100202 Covid-19 Ambulance [GENEPIO:0100202] + GENEPIO:0100203 Covid-19 Acute Care Facility [GENEPIO:0100203] + GENEPIO:0100204 Covid-19 Clinic [GENEPIO:0100204] + GENEPIO:0100415 Covid-19 Community Healthcare (At-Home) Setting [GENEPIO:0100415] + GENEPIO:0100205 Covid-19 Community Health Centre [GENEPIO:0100205] + ECTO:1000035 Covid-19 Hospital [ECTO:1000035] + GENEPIO:0100206 Covid-19 Emergency Department [GENEPIO:0100206] + GENEPIO:0100207 Covid-19 ICU [GENEPIO:0100207] + GENEPIO:0100208 Covid-19 Ward [GENEPIO:0100208] + ECTO:1000036 Covid-19 Laboratory [ECTO:1000036] + GENEPIO:0100209 Covid-19 Long-Term Care Facility [GENEPIO:0100209] + GENEPIO:0100210 Covid-19 Pharmacy [GENEPIO:0100210] + GENEPIO:0100211 Covid-19 Physician's Office [GENEPIO:0100211] + GENEPIO:0100212 Covid-19 Household [GENEPIO:0100212] + GENEPIO:0100213 Covid-19 Insecure Housing (Homeless) [GENEPIO:0100213] + GENEPIO:0100214 Covid-19 Occupational Exposure [GENEPIO:0100214] + GENEPIO:0100215 Covid-19 Worksite [GENEPIO:0100215] + ECTO:1000037 Covid-19 Office [ECTO:1000037] + GENEPIO:0100216 Covid-19 Outdoors [GENEPIO:0100216] + ECTO:5000009 Covid-19 Camp/camping [ECTO:5000009] + GENEPIO:0100217 Covid-19 Hiking Trail [GENEPIO:0100217] + ECTO:6000030 Covid-19 Hunting Ground [ECTO:6000030] + GENEPIO:0100218 Covid-19 Ski Resort [GENEPIO:0100218] + ECTO:5000008 Covid-19 Petting zoo [ECTO:5000008] + GENEPIO:0100220 Covid-19 Place of Worship [GENEPIO:0100220] + GENEPIO:0100221 Covid-19 Church [GENEPIO:0100221] + GENEPIO:0100222 Covid-19 Mosque [GENEPIO:0100222] + GENEPIO:0100223 Covid-19 Temple [GENEPIO:0100223] + ECTO:1000040 Covid-19 Restaurant [ECTO:1000040] + ECTO:1000041 Covid-19 Retail Store [ECTO:1000041] + GENEPIO:0100224 Covid-19 School [GENEPIO:0100224] + GENEPIO:0100225 Covid-19 Temporary Residence [GENEPIO:0100225] + GENEPIO:0100226 Covid-19 Homeless Shelter [GENEPIO:0100226] + GENEPIO:0100227 Covid-19 Hotel [GENEPIO:0100227] + GENEPIO:0100228 Covid-19 Veterinary Care Clinic [GENEPIO:0100228] + GENEPIO:0100229 Covid-19 Travel Exposure [GENEPIO:0100229] + GENEPIO:0100230 Covid-19 Travelled on a Cruise Ship [GENEPIO:0100230] + GENEPIO:0100231 Covid-19 Travelled on a Plane [GENEPIO:0100231] + GENEPIO:0100232 Covid-19 Travelled on Ground Transport [GENEPIO:0100232] + GENEPIO:0001118 Covid-19 Travelled outside Province/Territory [GENEPIO:0001118] + GENEPIO:0001119 Covid-19 Travelled outside Canada [GENEPIO:0001119] + GENEPIO:0100235 Covid-19 Other Exposure Setting [GENEPIO:0100235] + + +prior SARS-CoV-2 antiviral treatment menu PriorSarsCov2AntiviralTreatmentMenu GENEPIO:0100037 Covid-19 Prior antiviral treatment [GENEPIO:0100037] + GENEPIO:0100233 Covid-19 No prior antiviral treatment [GENEPIO:0100233] + + +prior SARS-CoV-2 infection menu PriorSarsCov2InfectionMenu GENEPIO:0100234 Covid-19 Prior infection [GENEPIO:0100234] + GENEPIO:0100236 Covid-19 No prior infection [GENEPIO:0100236] + + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Covid-19 Illumina sequencing instrument [GENEPIO:0100105] platform:ILLUMINA + GENEPIO:0100106 Covid-19 Illumina Genome Analyzer [GENEPIO:0100106] platform:ILLUMINA;instrument_model:Illumina Genome Analyzer + GENEPIO:0100107 Covid-19 Illumina Genome Analyzer II [GENEPIO:0100107] platform:ILLUMINA;instrument_model:Illumina Genome Analyzer II + GENEPIO:0100108 Covid-19 Illumina Genome Analyzer IIx [GENEPIO:0100108] platform:ILLUMINA;instrument_model:Illumina Genome Analyzer IIx + GENEPIO:0100109 Covid-19 Illumina HiScanSQ [GENEPIO:0100109] platform:ILLUMINA;instrument_model:Illumina HiScanSQ + GENEPIO:0100110 Covid-19 Illumina HiSeq [GENEPIO:0100110] platform:ILLUMINA + GENEPIO:0100111 Covid-19 Illumina HiSeq X [GENEPIO:0100111] platform:ILLUMINA + GENEPIO:0100112 Covid-19 Illumina HiSeq X Five [GENEPIO:0100112] platform:ILLUMINA;instrument_model: Illumina HiSeq X Five + GENEPIO:0100113 Covid-19 Illumina HiSeq X Ten [GENEPIO:0100113] platform:ILLUMINA;instrument_model:Illumina HiSeq X Ten + GENEPIO:0100114 Covid-19 Illumina HiSeq 1000 [GENEPIO:0100114] platform:ILLUMINA;instrument_model:Illumina HiSeq 1000 + GENEPIO:0100115 Covid-19 Illumina HiSeq 1500 [GENEPIO:0100115] platform:ILLUMINA + GENEPIO:0100116 Covid-19 Illumina HiSeq 2000 [GENEPIO:0100116] platform:ILLUMINA;instrument_model:Illumina HiSeq 2000 + GENEPIO:0100117 Covid-19 Illumina HiSeq 2500 [GENEPIO:0100117] platform:ILLUMINA;instrument_model:Illumina HiSeq 2500 + GENEPIO:0100118 Covid-19 Illumina HiSeq 3000 [GENEPIO:0100118] platform:ILLUMINA + GENEPIO:0100119 Covid-19 Illumina HiSeq 4000 [GENEPIO:0100119] platform:ILLUMINA + GENEPIO:0100120 Covid-19 Illumina iSeq [GENEPIO:0100120] platform:ILLUMINA + GENEPIO:0100121 Covid-19 Illumina iSeq 100 [GENEPIO:0100121] platform:ILLUMINA + GENEPIO:0100122 Covid-19 Illumina NovaSeq [GENEPIO:0100122] platform:ILLUMINA + GENEPIO:0100123 Covid-19 Illumina NovaSeq 6000 [GENEPIO:0100123] platform:ILLUMINA + GENEPIO:0100124 Covid-19 Illumina MiniSeq [GENEPIO:0100124] platform:ILLUMINA + GENEPIO:0100125 Covid-19 Illumina MiSeq [GENEPIO:0100125] platform:ILLUMINA;instrument_model:Illumina MiSeq + GENEPIO:0100126 Covid-19 Illumina NextSeq [GENEPIO:0100126] platform:ILLUMINA + GENEPIO:0100127 Covid-19 Illumina NextSeq 500 [GENEPIO:0100127] platform:ILLUMINA;instrument_model:Illumina NextSeq 500 + GENEPIO:0100128 Covid-19 Illumina NextSeq 550 [GENEPIO:0100128] platform:ILLUMINA + GENEPIO:0100129 Covid-19 Illumina NextSeq 2000 [GENEPIO:0100129] + GENEPIO:0100130 Covid-19 Pacific Biosciences sequencing instrument [GENEPIO:0100130] platform:PACBIO_SMRT + GENEPIO:0100131 Covid-19 PacBio RS [GENEPIO:0100131] platform:PACBIO_SMRT;instrument_model:PacBio RS + GENEPIO:0100132 Covid-19 PacBio RS II [GENEPIO:0100132] platform:PACBIO_SMRT;instrument_model:PacBio RS II + GENEPIO:0100133 Covid-19 PacBio Sequel [GENEPIO:0100133] platform:PACBIO_SMRT + GENEPIO:0100134 Covid-19 PacBio Sequel II [GENEPIO:0100134] platform:PACBIO_SMRT + GENEPIO:0100135 Covid-19 Ion Torrent sequencing instrument [GENEPIO:0100135] platform:ION_TORRENT + GENEPIO:0100136 Covid-19 Ion Torrent PGM [GENEPIO:0100136] platform:ION_TORRENT;instrument_model:Ion Torrent PGM + GENEPIO:0100137 Covid-19 Ion Torrent Proton [GENEPIO:0100137] platform:ION_TORRENT;instrument_model:Ion Torrent Proton + GENEPIO:0100138 Covid-19 Ion Torrent S5 XL [GENEPIO:0100138] platform:ION_TORRENT + GENEPIO:0100139 Covid-19 Ion Torrent S5 [GENEPIO:0100139] platform:ION_TORRENT + GENEPIO:0100140 Covid-19 Oxford Nanopore sequencing instrument [GENEPIO:0100140] platform:OXFORD_NANOPORE + GENEPIO:0100141 Covid-19 Oxford Nanopore GridION [GENEPIO:0100141] platform:OXFORD_NANOPORE;instrument_model:GridION + GENEPIO:0100142 Covid-19 Oxford Nanopore MinION [GENEPIO:0100142] platform:OXFORD_NANOPORE;instrument_model:MinION + GENEPIO:0100143 Covid-19 Oxford Nanopore PromethION [GENEPIO:0100143] platform:OXFORD_NANOPORE + GENEPIO:0100144 Covid-19 BGI Genomics sequencing instrument [GENEPIO:0100144] + GENEPIO:0100145 Covid-19 BGI Genomics BGISEQ-500 [GENEPIO:0100145] + GENEPIO:0100146 Covid-19 MGI sequencing instrument [GENEPIO:0100146] + GENEPIO:0100147 Covid-19 MGI DNBSEQ-T7 [GENEPIO:0100147] + GENEPIO:0100148 Covid-19 MGI DNBSEQ-G400 [GENEPIO:0100148] + GENEPIO:0100149 Covid-19 MGI DNBSEQ-G400RS FAST [GENEPIO:0100149] + GENEPIO:0100150 Covid-19 MGI DNBSEQ-G50 [GENEPIO:0100150] + + +gene name menu GeneNameMenu GENEPIO:0100151 Covid-19 E gene (orf4) [GENEPIO:0100151] + GENEPIO:0100152 Covid-19 M gene (orf5) [GENEPIO:0100152] + GENEPIO:0100153 Covid-19 N gene (orf9) [GENEPIO:0100153] + GENEPIO:0100154 Covid-19 Spike gene (orf2) [GENEPIO:0100154] + GENEPIO:0100155 Covid-19 orf1ab (rep) [GENEPIO:0100155] + GENEPIO:0100156 Covid-19 orf1a (pp1a) [GENEPIO:0100156] + GENEPIO:0100157 Covid-19 nsp11 [GENEPIO:0100157] + GENEPIO:0100158 Covid-19 nsp1 [GENEPIO:0100158] + GENEPIO:0100159 Covid-19 nsp2 [GENEPIO:0100159] + GENEPIO:0100160 Covid-19 nsp3 [GENEPIO:0100160] + GENEPIO:0100161 Covid-19 nsp4 [GENEPIO:0100161] + GENEPIO:0100162 Covid-19 nsp5 [GENEPIO:0100162] + GENEPIO:0100163 Covid-19 nsp6 [GENEPIO:0100163] + GENEPIO:0100164 Covid-19 nsp7 [GENEPIO:0100164] + GENEPIO:0100165 Covid-19 nsp8 [GENEPIO:0100165] + GENEPIO:0100166 Covid-19 nsp9 [GENEPIO:0100166] + GENEPIO:0100167 Covid-19 nsp10 [GENEPIO:0100167] + GENEPIO:0100168 Covid-19 RdRp gene (nsp12) [GENEPIO:0100168] + GENEPIO:0100169 Covid-19 hel gene (nsp13) [GENEPIO:0100169] + GENEPIO:0100170 Covid-19 exoN gene (nsp14) [GENEPIO:0100170] + GENEPIO:0100171 Covid-19 nsp15 [GENEPIO:0100171] + GENEPIO:0100172 Covid-19 nsp16 [GENEPIO:0100172] + GENEPIO:0100173 Covid-19 orf3a [GENEPIO:0100173] + GENEPIO:0100174 Covid-19 orf3b [GENEPIO:0100174] + GENEPIO:0100175 Covid-19 orf6 (ns6) [GENEPIO:0100175] + GENEPIO:0100176 Covid-19 orf7a [GENEPIO:0100176] + GENEPIO:0100177 Covid-19 orf7b (ns7b) [GENEPIO:0100177] + GENEPIO:0100178 Covid-19 orf8 (ns8) [GENEPIO:0100178] + GENEPIO:0100179 Covid-19 orf9b [GENEPIO:0100179] + GENEPIO:0100180 Covid-19 orf9c [GENEPIO:0100180] + GENEPIO:0100181 Covid-19 orf10 [GENEPIO:0100181] + GENEPIO:0100182 Covid-19 orf14 [GENEPIO:0100182] + GENEPIO:0100183 Covid-19 SARS-COV-2 5' UTR [GENEPIO:0100183] + + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Covid-19 Afghanistan [GAZ:00006882] + GAZ:00002953 Covid-19 Albania [GAZ:00002953] + GAZ:00000563 Covid-19 Algeria [GAZ:00000563] + GAZ:00003957 Covid-19 American Samoa [GAZ:00003957] + GAZ:00002948 Covid-19 Andorra [GAZ:00002948] + GAZ:00001095 Covid-19 Angola [GAZ:00001095] + GAZ:00009159 Covid-19 Anguilla [GAZ:00009159] + GAZ:00000462 Covid-19 Antarctica [GAZ:00000462] + GAZ:00006883 Covid-19 Antigua and Barbuda [GAZ:00006883] + GAZ:00002928 Covid-19 Argentina [GAZ:00002928] + GAZ:00004094 Covid-19 Armenia [GAZ:00004094] + GAZ:00004025 Covid-19 Aruba [GAZ:00004025] + GAZ:00005901 Covid-19 Ashmore and Cartier Islands [GAZ:00005901] + GAZ:00000463 Covid-19 Australia [GAZ:00000463] + GAZ:00002942 Covid-19 Austria [GAZ:00002942] + GAZ:00004941 Covid-19 Azerbaijan [GAZ:00004941] + GAZ:00002733 Covid-19 Bahamas [GAZ:00002733] + GAZ:00005281 Covid-19 Bahrain [GAZ:00005281] + GAZ:00007117 Covid-19 Baker Island [GAZ:00007117] + GAZ:00003750 Covid-19 Bangladesh [GAZ:00003750] + GAZ:00001251 Covid-19 Barbados [GAZ:00001251] + GAZ:00005810 Covid-19 Bassas da India [GAZ:00005810] + GAZ:00006886 Covid-19 Belarus [GAZ:00006886] + GAZ:00002938 Covid-19 Belgium [GAZ:00002938] + GAZ:00002934 Covid-19 Belize [GAZ:00002934] + GAZ:00000904 Covid-19 Benin [GAZ:00000904] + GAZ:00001264 Covid-19 Bermuda [GAZ:00001264] + GAZ:00003920 Covid-19 Bhutan [GAZ:00003920] + GAZ:00002511 Covid-19 Bolivia [GAZ:00002511] + GAZ:00025355 Covid-19 Borneo [GAZ:00025355] + GAZ:00006887 Covid-19 Bosnia and Herzegovina [GAZ:00006887] + GAZ:00001097 Covid-19 Botswana [GAZ:00001097] + GAZ:00001453 Covid-19 Bouvet Island [GAZ:00001453] + GAZ:00002828 Covid-19 Brazil [GAZ:00002828] + GAZ:00003961 Covid-19 British Virgin Islands [GAZ:00003961] + GAZ:00003901 Covid-19 Brunei [GAZ:00003901] + GAZ:00002950 Covid-19 Bulgaria [GAZ:00002950] + GAZ:00000905 Covid-19 Burkina Faso [GAZ:00000905] + GAZ:00001090 Covid-19 Burundi [GAZ:00001090] + GAZ:00006888 Covid-19 Cambodia [GAZ:00006888] + GAZ:00001093 Covid-19 Cameroon [GAZ:00001093] + GAZ:00002560 Covid-19 Canada [GAZ:00002560] + GAZ:00001227 Covid-19 Cape Verde [GAZ:00001227] + GAZ:00003986 Covid-19 Cayman Islands [GAZ:00003986] + GAZ:00001089 Covid-19 Central African Republic [GAZ:00001089] + GAZ:00000586 Covid-19 Chad [GAZ:00000586] + GAZ:00002825 Covid-19 Chile [GAZ:00002825] + GAZ:00002845 Covid-19 China [GAZ:00002845] + GAZ:00005915 Covid-19 Christmas Island [GAZ:00005915] + GAZ:00005838 Covid-19 Clipperton Island [GAZ:00005838] + GAZ:00009721 Covid-19 Cocos Islands [GAZ:00009721] + GAZ:00002929 Covid-19 Colombia [GAZ:00002929] + GAZ:00005820 Covid-19 Comoros [GAZ:00005820] + GAZ:00053798 Covid-19 Cook Islands [GAZ:00053798] + GAZ:00005917 Covid-19 Coral Sea Islands [GAZ:00005917] + GAZ:00002901 Covid-19 Costa Rica [GAZ:00002901] + GAZ:00000906 Covid-19 Cote d'Ivoire [GAZ:00000906] + GAZ:00002719 Covid-19 Croatia [GAZ:00002719] + GAZ:00003762 Covid-19 Cuba [GAZ:00003762] + GAZ:00012582 Covid-19 Curacao [GAZ:00012582] + GAZ:00004006 Covid-19 Cyprus [GAZ:00004006] + GAZ:00002954 Covid-19 Czech Republic [GAZ:00002954] + GAZ:00001086 Covid-19 Democratic Republic of the Congo [GAZ:00001086] + GAZ:00005852 Covid-19 Denmark [GAZ:00005852] + GAZ:00000582 Covid-19 Djibouti [GAZ:00000582] + GAZ:00006890 Covid-19 Dominica [GAZ:00006890] + GAZ:00003952 Covid-19 Dominican Republic [GAZ:00003952] + GAZ:00002912 Covid-19 Ecuador [GAZ:00002912] + GAZ:00003934 Covid-19 Egypt [GAZ:00003934] + GAZ:00002935 Covid-19 El Salvador [GAZ:00002935] + GAZ:00001091 Covid-19 Equatorial Guinea [GAZ:00001091] + GAZ:00000581 Covid-19 Eritrea [GAZ:00000581] + GAZ:00002959 Covid-19 Estonia [GAZ:00002959] + GAZ:00001099 Covid-19 Eswatini [GAZ:00001099] + GAZ:00000567 Covid-19 Ethiopia [GAZ:00000567] + GAZ:00005811 Covid-19 Europa Island [GAZ:00005811] + GAZ:00001412 Covid-19 Falkland Islands (Islas Malvinas) [GAZ:00001412] + GAZ:00059206 Covid-19 Faroe Islands [GAZ:00059206] + GAZ:00006891 Covid-19 Fiji [GAZ:00006891] + GAZ:00002937 Covid-19 Finland [GAZ:00002937] + GAZ:00003940 Covid-19 France [GAZ:00003940] + GAZ:00002516 Covid-19 French Guiana [GAZ:00002516] + GAZ:00002918 Covid-19 French Polynesia [GAZ:00002918] + GAZ:00003753 Covid-19 French Southern and Antarctic Lands [GAZ:00003753] + GAZ:00001092 Covid-19 Gabon [GAZ:00001092] + GAZ:00000907 Covid-19 Gambia [GAZ:00000907] + GAZ:00009571 Covid-19 Gaza Strip [GAZ:00009571] + GAZ:00004942 Covid-19 Georgia [GAZ:00004942] + GAZ:00002646 Covid-19 Germany [GAZ:00002646] + GAZ:00000908 Covid-19 Ghana [GAZ:00000908] + GAZ:00003987 Covid-19 Gibraltar [GAZ:00003987] + GAZ:00005808 Covid-19 Glorioso Islands [GAZ:00005808] + GAZ:00002945 Covid-19 Greece [GAZ:00002945] + GAZ:00001507 Covid-19 Greenland [GAZ:00001507] + GAZ:02000573 Covid-19 Grenada [GAZ:02000573] + GAZ:00067142 Covid-19 Guadeloupe [GAZ:00067142] + GAZ:00003706 Covid-19 Guam [GAZ:00003706] + GAZ:00002936 Covid-19 Guatemala [GAZ:00002936] + GAZ:00001550 Covid-19 Guernsey [GAZ:00001550] + GAZ:00000909 Covid-19 Guinea [GAZ:00000909] + GAZ:00000910 Covid-19 Guinea-Bissau [GAZ:00000910] + GAZ:00002522 Covid-19 Guyana [GAZ:00002522] + GAZ:00003953 Covid-19 Haiti [GAZ:00003953] + GAZ:00009718 Covid-19 Heard Island and McDonald Islands [GAZ:00009718] + GAZ:00002894 Covid-19 Honduras [GAZ:00002894] + GAZ:00003203 Covid-19 Hong Kong [GAZ:00003203] + GAZ:00007120 Covid-19 Howland Island [GAZ:00007120] + GAZ:00002952 Covid-19 Hungary [GAZ:00002952] + GAZ:00000843 Covid-19 Iceland [GAZ:00000843] + GAZ:00002839 Covid-19 India [GAZ:00002839] + GAZ:00003727 Covid-19 Indonesia [GAZ:00003727] + GAZ:00004474 Covid-19 Iran [GAZ:00004474] + GAZ:00004483 Covid-19 Iraq [GAZ:00004483] + GAZ:00002943 Covid-19 Ireland [GAZ:00002943] + GAZ:00052477 Covid-19 Isle of Man [GAZ:00052477] + GAZ:00002476 Covid-19 Israel [GAZ:00002476] + GAZ:00002650 Covid-19 Italy [GAZ:00002650] + GAZ:00003781 Covid-19 Jamaica [GAZ:00003781] + GAZ:00005853 Covid-19 Jan Mayen [GAZ:00005853] + GAZ:00002747 Covid-19 Japan [GAZ:00002747] + GAZ:00007118 Covid-19 Jarvis Island [GAZ:00007118] + GAZ:00001551 Covid-19 Jersey [GAZ:00001551] + GAZ:00007114 Covid-19 Johnston Atoll [GAZ:00007114] + GAZ:00002473 Covid-19 Jordan [GAZ:00002473] + GAZ:00005809 Covid-19 Juan de Nova Island [GAZ:00005809] + GAZ:00004999 Covid-19 Kazakhstan [GAZ:00004999] + GAZ:00001101 Covid-19 Kenya [GAZ:00001101] + GAZ:00005682 Covid-19 Kerguelen Archipelago [GAZ:00005682] + GAZ:00007116 Covid-19 Kingman Reef [GAZ:00007116] + GAZ:00006894 Covid-19 Kiribati [GAZ:00006894] + GAZ:00011337 Covid-19 Kosovo [GAZ:00011337] + GAZ:00005285 Covid-19 Kuwait [GAZ:00005285] + GAZ:00006893 Covid-19 Kyrgyzstan [GAZ:00006893] + GAZ:00006889 Covid-19 Laos [GAZ:00006889] + GAZ:00002958 Covid-19 Latvia [GAZ:00002958] + GAZ:00002478 Covid-19 Lebanon [GAZ:00002478] + GAZ:00001098 Covid-19 Lesotho [GAZ:00001098] + GAZ:00000911 Covid-19 Liberia [GAZ:00000911] + GAZ:00000566 Covid-19 Libya [GAZ:00000566] + GAZ:00003858 Covid-19 Liechtenstein [GAZ:00003858] + GAZ:00007144 Covid-19 Line Islands [GAZ:00007144] + GAZ:00002960 Covid-19 Lithuania [GAZ:00002960] + GAZ:00002947 Covid-19 Luxembourg [GAZ:00002947] + GAZ:00003202 Covid-19 Macau [GAZ:00003202] + GAZ:00001108 Covid-19 Madagascar [GAZ:00001108] + GAZ:00001105 Covid-19 Malawi [GAZ:00001105] + GAZ:00003902 Covid-19 Malaysia [GAZ:00003902] + GAZ:00006924 Covid-19 Maldives [GAZ:00006924] + GAZ:00000584 Covid-19 Mali [GAZ:00000584] + GAZ:00004017 Covid-19 Malta [GAZ:00004017] + GAZ:00007161 Covid-19 Marshall Islands [GAZ:00007161] + GAZ:00067143 Covid-19 Martinique [GAZ:00067143] + GAZ:00000583 Covid-19 Mauritania [GAZ:00000583] + GAZ:00003745 Covid-19 Mauritius [GAZ:00003745] + GAZ:00003943 Covid-19 Mayotte [GAZ:00003943] + GAZ:00002852 Covid-19 Mexico [GAZ:00002852] + GAZ:00005862 Covid-19 Micronesia [GAZ:00005862] + GAZ:00007112 Covid-19 Midway Islands [GAZ:00007112] + GAZ:00003897 Covid-19 Moldova [GAZ:00003897] + GAZ:00003857 Covid-19 Monaco [GAZ:00003857] + GAZ:00008744 Covid-19 Mongolia [GAZ:00008744] + GAZ:00006898 Covid-19 Montenegro [GAZ:00006898] + GAZ:00003988 Covid-19 Montserrat [GAZ:00003988] + GAZ:00000565 Covid-19 Morocco [GAZ:00000565] + GAZ:00001100 Covid-19 Mozambique [GAZ:00001100] + GAZ:00006899 Covid-19 Myanmar [GAZ:00006899] + GAZ:00001096 Covid-19 Namibia [GAZ:00001096] + GAZ:00006900 Covid-19 Nauru [GAZ:00006900] + GAZ:00007119 Covid-19 Navassa Island [GAZ:00007119] + GAZ:00004399 Covid-19 Nepal [GAZ:00004399] + GAZ:00002946 Covid-19 Netherlands [GAZ:00002946] + GAZ:00005206 Covid-19 New Caledonia [GAZ:00005206] + GAZ:00000469 Covid-19 New Zealand [GAZ:00000469] + GAZ:00002978 Covid-19 Nicaragua [GAZ:00002978] + GAZ:00000585 Covid-19 Niger [GAZ:00000585] + GAZ:00000912 Covid-19 Nigeria [GAZ:00000912] + GAZ:00006902 Covid-19 Niue [GAZ:00006902] + GAZ:00005908 Covid-19 Norfolk Island [GAZ:00005908] + GAZ:00002801 Covid-19 North Korea [GAZ:00002801] + GAZ:00006895 Covid-19 North Macedonia [GAZ:00006895] + GAZ:00002284 Covid-19 North Sea [GAZ:00002284] + GAZ:00003958 Covid-19 Northern Mariana Islands [GAZ:00003958] + GAZ:00002699 Covid-19 Norway [GAZ:00002699] + GAZ:00005283 Covid-19 Oman [GAZ:00005283] + GAZ:00005246 Covid-19 Pakistan [GAZ:00005246] + GAZ:00006905 Covid-19 Palau [GAZ:00006905] + GAZ:00002892 Covid-19 Panama [GAZ:00002892] + GAZ:00003922 Covid-19 Papua New Guinea [GAZ:00003922] + GAZ:00010832 Covid-19 Paracel Islands [GAZ:00010832] + GAZ:00002933 Covid-19 Paraguay [GAZ:00002933] + GAZ:00002932 Covid-19 Peru [GAZ:00002932] + GAZ:00004525 Covid-19 Philippines [GAZ:00004525] + GAZ:00005867 Covid-19 Pitcairn Islands [GAZ:00005867] + GAZ:00002939 Covid-19 Poland [GAZ:00002939] + GAZ:00004126 Covid-19 Portugal [GAZ:00004126] + GAZ:00006935 Covid-19 Puerto Rico [GAZ:00006935] + GAZ:00005286 Covid-19 Qatar [GAZ:00005286] + GAZ:00001088 Covid-19 Republic of the Congo [GAZ:00001088] + GAZ:00003945 Covid-19 Reunion [GAZ:00003945] + GAZ:00002951 Covid-19 Romania [GAZ:00002951] + GAZ:00023304 Covid-19 Ross Sea [GAZ:00023304] + GAZ:00002721 Covid-19 Russia [GAZ:00002721] + GAZ:00001087 Covid-19 Rwanda [GAZ:00001087] + GAZ:00000849 Covid-19 Saint Helena [GAZ:00000849] + GAZ:00006906 Covid-19 Saint Kitts and Nevis [GAZ:00006906] + GAZ:00006909 Covid-19 Saint Lucia [GAZ:00006909] + GAZ:00003942 Covid-19 Saint Pierre and Miquelon [GAZ:00003942] + GAZ:00005841 Covid-19 Saint Martin [GAZ:00005841] + GAZ:02000565 Covid-19 Saint Vincent and the Grenadines [GAZ:02000565] + GAZ:00006910 Covid-19 Samoa [GAZ:00006910] + GAZ:00003102 Covid-19 San Marino [GAZ:00003102] + GAZ:00006927 Covid-19 Sao Tome and Principe [GAZ:00006927] + GAZ:00005279 Covid-19 Saudi Arabia [GAZ:00005279] + GAZ:00000913 Covid-19 Senegal [GAZ:00000913] + GAZ:00002957 Covid-19 Serbia [GAZ:00002957] + GAZ:00006922 Covid-19 Seychelles [GAZ:00006922] + GAZ:00000914 Covid-19 Sierra Leone [GAZ:00000914] + GAZ:00003923 Covid-19 Singapore [GAZ:00003923] + GAZ:00012579 Covid-19 Sint Maarten [GAZ:00012579] + GAZ:00002956 Covid-19 Slovakia [GAZ:00002956] + GAZ:00002955 Covid-19 Slovenia [GAZ:00002955] + GAZ:00005275 Covid-19 Solomon Islands [GAZ:00005275] + GAZ:00001104 Covid-19 Somalia [GAZ:00001104] + GAZ:00001094 Covid-19 South Africa [GAZ:00001094] + GAZ:00003990 Covid-19 South Georgia and the South Sandwich Islands [GAZ:00003990] + GAZ:00002802 Covid-19 South Korea [GAZ:00002802] + GAZ:00233439 Covid-19 South Sudan [GAZ:00233439] + GAZ:00003936 Covid-19 Spain [GAZ:00003936] + GAZ:00010831 Covid-19 Spratly Islands [GAZ:00010831] + GAZ:00003924 Covid-19 Sri Lanka [GAZ:00003924] + GAZ:00002475 Covid-19 State of Palestine [GAZ:00002475] + GAZ:00000560 Covid-19 Sudan [GAZ:00000560] + GAZ:00002525 Covid-19 Suriname [GAZ:00002525] + GAZ:00005396 Covid-19 Svalbard [GAZ:00005396] + GAZ:00001099 Covid-19 Swaziland [GAZ:00001099] + GAZ:00002729 Covid-19 Sweden [GAZ:00002729] + GAZ:00002941 Covid-19 Switzerland [GAZ:00002941] + GAZ:00002474 Covid-19 Syria [GAZ:00002474] + GAZ:00005341 Covid-19 Taiwan [GAZ:00005341] + GAZ:00006912 Covid-19 Tajikistan [GAZ:00006912] + GAZ:00001103 Covid-19 Tanzania [GAZ:00001103] + GAZ:00003744 Covid-19 Thailand [GAZ:00003744] + GAZ:00006913 Covid-19 Timor-Leste [GAZ:00006913] + GAZ:00000915 Covid-19 Togo [GAZ:00000915] + GAZ:00260188 Covid-19 Tokelau [GAZ:00260188] + GAZ:00006916 Covid-19 Tonga [GAZ:00006916] + GAZ:00003767 Covid-19 Trinidad and Tobago [GAZ:00003767] + GAZ:00005812 Covid-19 Tromelin Island [GAZ:00005812] + GAZ:00000562 Covid-19 Tunisia [GAZ:00000562] + GAZ:00000558 Covid-19 Turkey [GAZ:00000558] + GAZ:00005018 Covid-19 Turkmenistan [GAZ:00005018] + GAZ:00003955 Covid-19 Turks and Caicos Islands [GAZ:00003955] + GAZ:00009715 Covid-19 Tuvalu [GAZ:00009715] + GAZ:00002459 Covid-19 United States of America [GAZ:00002459] + GAZ:00001102 Covid-19 Uganda [GAZ:00001102] + GAZ:00002724 Covid-19 Ukraine [GAZ:00002724] + GAZ:00005282 Covid-19 United Arab Emirates [GAZ:00005282] + GAZ:00002637 Covid-19 United Kingdom [GAZ:00002637] + GAZ:00002930 Covid-19 Uruguay [GAZ:00002930] + GAZ:00004979 Covid-19 Uzbekistan [GAZ:00004979] + GAZ:00006918 Covid-19 Vanuatu [GAZ:00006918] + GAZ:00002931 Covid-19 Venezuela [GAZ:00002931] + GAZ:00003756 Covid-19 Viet Nam [GAZ:00003756] + GAZ:00003959 Covid-19 Virgin Islands [GAZ:00003959] + GAZ:00007111 Covid-19 Wake Island [GAZ:00007111] + GAZ:00007191 Covid-19 Wallis and Futuna [GAZ:00007191] + GAZ:00009572 Covid-19 West Bank [GAZ:00009572] + GAZ:00000564 Covid-19 Western Sahara [GAZ:00000564] + GAZ:00005284 Covid-19 Yemen [GAZ:00005284] + GAZ:00001107 Covid-19 Zambia [GAZ:00001107] + GAZ:00001106 Covid-19 Zimbabwe [GAZ:00001106] + + +library_strategy menu LibraryStrategyMenu WGA + WGS + WXS + RNA-Seq + miRNA-Seq + WCS + CLONE + POOLCLONE + AMPLICON + CLONEEND + FINISHING + ChIP-Seq + MNase-Seq + DNase-Hypersensitivity + Bisulfite-Seq + Tn-Seq + EST + FL-cDNA + CTS + MRE-Seq + MeDIP-Seq + MBD-Seq + OTHER + + +library_source menu LibrarySourceMenu GENOMIC + TRANSCRIPTOMIC + METAGENOMIC + METATRANSCRIPTOMIC + SYNTHETIC + VIRAL RNA + OTHER + + +library_selection menu LibrarySelectionMenu RANDOM + PCR + RANDOM PCR + RT-PCR + HMPR + MF + CF-S + CF-M + CF-H + CF-T + MDA + MSLL + cDNA + ChIP + MNase + DNAse + Hybrid Selection + Reduced Representation + Restriction Digest + 5-methylcytidine antibody + MBD2 protein methyl-CpG binding domain + CAGE + RACE + size fractionation + Padlock probes capture method + other + unspecified + + +library_layout menu LibraryLayoutMenu single + paired + + +filetype menu FiletypeMenu bam + sra + kar + srf + sff + fastq + tab + 454_native + Helicos_native + SOLiD_native + PacBio_HDF5 + CompleteGenomics_native + + + + \ No newline at end of file diff --git a/web/templates/pha4ge/schema_slots.tsv b/web/templates/pha4ge/schema_slots.tsv index 3c09f5e8..6ac6df30 100644 --- a/web/templates/pha4ge/schema_slots.tsv +++ b/web/templates/pha4ge/schema_slots.tsv @@ -1,170 +1,170 @@ class_name slot_group slot_uri in_subset meaning (LinkML) title name range range_2 identifier required recommended multivalued minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_NCBI_BIOSAMPLE EXPORT_NCBI_SRA EXPORT_NCBI_Genbank EXPORT_NCBI_Genbank_source_modifiers -PHA4GE GENEPIO:0001122 Covid-19 Database Identifiers - Database Identifiers GENEPIO:0001123 Covid-19 specimen collector sample ID WhitespaceMinimizedString TRUE The user-defined name for the sample. Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. prov_rona_99 Sample ID given by the sample provider;Sample ID given by the submitting laboratory sample_name sample_name sample_name Sequence_ID - Database Identifiers GENEPIO:0001133 Covid-19 umbrella bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC umbrella accession number of the BioProject to which the BioSample belongs. Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects. PRJNA623807 - Database Identifiers GENEPIO:0001136 Covid-19 GENEPIO:0001836 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession BioProject - Database Identifiers GENEPIO:0001139 Covid-19 GENEPIO:0001836 biosample accession WhitespaceMinimizedString TRUE {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 biosample_accession biosample_accession BioSample - Database Identifiers GENEPIO:0001142 Covid-19 GENEPIO:0000147 SRA accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 - Database Identifiers GENEPIO:0001145 Covid-19 OBI:0001614 GenBank/ENA/DDBJ accession WhitespaceMinimizedString {UPPER_CASE} The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly). MN908947.3 - Database Identifiers GENEPIO:0001147 Covid-19 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_123456 gisaid_accession - Database Identifiers GENEPIO:0100282 Covid-19 GISAID virus name WhitespaceMinimizedString {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 Virus name gisaid_virus_name - Database Identifiers GENEPIO:0100283 Covid-19 host specimen voucher WhitespaceMinimizedString {UPPER_CASE} Identifier for the physical specimen. Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher="[:[:]]"): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 host_specimen_voucher - GENEPIO:0001268 Covid-19 Sample collection and processing - Sample collection and processing GENEPIO:0001153 Covid-19 sample collected by WhitespaceMinimizedString null value menu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada Originating lab collected_by - Sample collection and processing GENEPIO:0001156 Covid-19 sample collector contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or laboratory. johnnyblogs@lab.ca - Sample collection and processing GENEPIO:0001158 Covid-19 sample collector contact address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address - Sample collection and processing GENEPIO:0001159 Covid-19 sequence submitted by WhitespaceMinimizedString null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Centers for Disease Control and Prevention Submitting lab sequenced_by - Sample collection and processing GENEPIO:0001165 Covid-19 sequence submitter contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email - Sample collection and processing GENEPIO:0001167 Covid-19 sequence submitter contact address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address - Sample collection and processing GENEPIO:0001174 Covid-19 sample collection date date null value menu TRUE The date on which the sample was collected. Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add "jitter" to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-19 Collection date collection_date collection-date - Sample collection and processing GENEPIO:0001179 Covid-19 sample received date date null value menu The date on which the sample was received. The date the sample was received by a lab that was not the point of collection. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 - Sample collection and processing GENEPIO:0001181 Covid-19 geo_loc name (country) geo_loc name (country) menu null value menu TRUE The country of origin of the sample. Provide the country name from the pick list in the template South Africa [GAZ:00001094] Location geo_loc_name country - Sample collection and processing GENEPIO:0001185 Covid-19 geo_loc name (state/province/territory) WhitespaceMinimizedString null value menu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Western Cape geo_loc_name - Sample collection and processing GENEPIO:0100280 Covid-19 geo_loc name (county/region) WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire geo_loc_name - Sample collection and processing GENEPIO:0001189 Covid-19 geo_loc name (city) WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver geo_loc_name - Sample collection and processing GENEPIO:0100309 Covid-19 OBI:0001620 geo_loc latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon - Sample collection and processing GENEPIO:0100310 Covid-19 OBI:0001621 geo_loc longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon - Sample collection and processing GENEPIO:0001191 Covid-19 organism organism menu null value menu TRUE Taxonomic name of the organism. Select "Severe acute respiratory syndrome coronavirus 2" if sequencing SARS-CoV-2. If another Coronaviridae is being sequenced, provide the taxonomic name from NCBITaxon. Search for taxonomy terms at https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] organism - Sample collection and processing GENEPIO:0001644 Covid-19 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 isolate isolate - Sample collection and processing GENEPIO:0100284 Covid-19 culture collection WhitespaceMinimizedString The name of the source collection and unique culture identifier. Format: ":[:]". For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. /culture_collection="ATCC:26370" - Sample collection and processing GENEPIO:0001198 Covid-19 purpose of sampling purpose of sampling menu null value menu TRUE The reason that the sample was collected. Select a value from the pick list in the template. Diagnostic testing [GENEPIO:0100002] purpose_of_sampling - Sample collection and processing GENEPIO:0001200 Covid-19 purpose of sampling details WhitespaceMinimizedString Further details pertaining to the reason the sample was collected. Provide a free text description of the sampling strategy or samples collected. Screening of bat specimens in museum collections. - Sample collection and processing GENEPIO:0100285 Covid-19 sample plan name WhitespaceMinimizedString The name of the sample plan implemented for sample collection. Provide the name and version of the sample plan outlining the sample strategy. CanCOGeN Sampling Strategy 1.0 - Sample collection and processing GENEPIO:0100277 Covid-19 sample collected in quarantine sample collected in quarantine menu null value menu Whether the sample was collected from an individual in quarantine. Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. Yes [NCIT:C49488] - Sample collection and processing GENEPIO:0001211 Covid-19 anatomical material anatomical material menu null value menu TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. Blood [UBERON:0000178] Specimen source isolation_source;host_anatomical_material isolation-source - Sample collection and processing GENEPIO:0001214 Covid-19 anatomical part anatomical part menu null value menu TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. Nasopharynx (NP) [UBERON:0001728] Specimen source isolation_source;host_anatomical_part isolation-source - Sample collection and processing GENEPIO:0001216 Covid-19 body product body product menu null value menu TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. Feces [UBERON:0001988] Specimen source isolation_source;host_body_product isolation-source - Sample collection and processing GENEPIO:0001223 Covid-19 environmental material environmental material menu null value menu TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. Face mask [OBI:0002787] Specimen source isolation_source;environmental_material isolation-source - Sample collection and processing GENEPIO:0001232 Covid-19 environmental site environmental site menu null value menu TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. Hospital [ENVO:00002173] Specimen source isolation_source;environmental_site isolation-source - Sample collection and processing GENEPIO:0001234 Covid-19 collection device collection device menu null value menu TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. Swab [GENEPIO:0100027] Specimen source isolation_source;collection_device isolation-source - Sample collection and processing GENEPIO:0001241 Covid-19 collection method collection method menu null value menu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. Bronchoalveolar lavage (BAL) [GENEPIO:0100032] Specimen source isolation_source;collection_method isolation-source - Sample collection and processing GENEPIO:0001243 Covid-19 collection protocol WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Provide the name and version of the protocol used to collect the samples. SC2SamplingProtocol 1.2 - Sample collection and processing GENEPIO:0001253 Covid-19 specimen processing specimen processing menu null value menu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage [GENEPIO:0100039] - Sample collection and processing GENEPIO:0100311 Covid-19 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. - Sample collection and processing GENEPIO:0001255 Covid-19 lab host lab host menu null value menu Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Select a value form the pick list. If not passaged, put "not applicable". Vero E6 cell line [BTO:0004755] - Sample collection and processing GENEPIO:0001261 Covid-19 passage number integer 0 Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 passage_number - Sample collection and processing GENEPIO:0001264 Covid-19 passage method WhitespaceMinimizedString null value menu Description of how organism was passaged. Free text. Provide a short description. If not passaged, put "not applicable". AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. passage_method - Sample collection and processing GENEPIO:0001266 Covid-19 biomaterial extracted biomaterial extracted menu null value menu The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the pick list in the template. RNA (Total) [OBI:0000895] - Sample collection and processing GENEPIO:0100278 Covid-19 data abstraction details WhitespaceMinimizedString A description of how any data elements were altered to preserve patient privacy. If applicable, provide a description of how each data element was abstracted. Jitter added to publicly shared collection dates to prevent re-identifiability. - GENEPIO:0001268 Covid-19 Host Information - Host Information GENEPIO:0001386 Covid-19 host (common name) host (common name) menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put "not applicable". Human [NCBITaxon:9606] - Host Information GENEPIO:0001387 Covid-19 host (scientific name) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put "not applicable". Homo sapiens [NCBITaxon:9606] Host host host - Host Information GENEPIO:0001388 Covid-19 host health state host health state menu null value menu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state - Host Information GENEPIO:0001389 Covid-19 host health status details host health status details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] - Host Information GENEPIO:0001391 Covid-19 host disease host disease menu null value menu TRUE The name of the disease experienced by the host. This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. "COVID-19" should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”. COVID-19 [MONDO:0100096] host_disease - Host Information GENEPIO:0001390 Covid-19 host health outcome host health outcome menu null value menu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome - Host Information GENEPIO:0001392 Covid-19 host age decimal null value menu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age - Host Information GENEPIO:0001393 Covid-19 host age unit host age unit menu null value menu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] - Host Information GENEPIO:0001394 Covid-19 host age bin host age bin menu null value menu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] - Host Information GENEPIO:0001395 Covid-19 host gender host gender menu null value menu TRUE The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex - Host Information GENEPIO:0001396 Covid-19 host residence geo_loc name (country) geo_loc_name (country) menu null value menu The country where the host resides. If known, select a value from the pick list. South Africa [GAZ:00001094] - Host Information GENEPIO:0100312 GECKO:0000061 host ethnicity WhitespaceMinimizedString The self-identified ethnicity(ies) of the host. If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. Indigenous, European - Host Information GENEPIO:0001398 Covid-19 host subject ID WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. BCxy123 host_subject_id - Host Information GENEPIO:0100281 Covid-19 case ID WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 - Host Information GENEPIO:0001399 Covid-19 symptom onset date date null value menu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 - Host Information GENEPIO:0001400 Covid-19 signs and symptoms signs and symptoms menu null value menu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] - Host Information GENEPIO:0001401 Covid-19 pre-existing conditions and risk factors pre-existing conditions and risk factors menu null value menu TRUE "Patient pre-existing conditions and risk factors. +PHA4GE GENEPIO:0001122 Covid-19 Database Identifiers database_identifiers + Database Identifiers GENEPIO:0001123 Covid-19 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE The user-defined name for the sample. Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. prov_rona_99 Sample ID given by the sample provider;Sample ID given by the submitting laboratory sample_name sample_name sample_name Sequence_ID + Database Identifiers GENEPIO:0001133 Covid-19 umbrella bioproject accession umbrella_bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC umbrella accession number of the BioProject to which the BioSample belongs. Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects. PRJNA623807 + Database Identifiers GENEPIO:0001136 Covid-19 GENEPIO:0001836 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession BioProject + Database Identifiers GENEPIO:0001139 Covid-19 GENEPIO:0001836 biosample accession biosample_accession WhitespaceMinimizedString TRUE {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 biosample_accession biosample_accession BioSample + Database Identifiers GENEPIO:0001142 Covid-19 GENEPIO:0000147 SRA accession sra_accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 + Database Identifiers GENEPIO:0001145 Covid-19 OBI:0001614 GenBank/ENA/DDBJ accession genbank_ena_ddbj_accession WhitespaceMinimizedString {UPPER_CASE} The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly). MN908947.3 + Database Identifiers GENEPIO:0001147 Covid-19 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_123456 gisaid_accession + Database Identifiers GENEPIO:0100282 Covid-19 GISAID virus name gisaid_virus_name WhitespaceMinimizedString {UPPER_CASE} The user-defined GISAID virus name assigned to the sequence. GISAID virus names should be in the format "hCoV-19/Country/Identifier/year". hCoV-19/Canada/prov_rona_99/2020 Virus name gisaid_virus_name + Database Identifiers GENEPIO:0100283 Covid-19 host specimen voucher host_specimen_voucher WhitespaceMinimizedString {UPPER_CASE} Identifier for the physical specimen. Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher="[:[:]]"): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 host_specimen_voucher + GENEPIO:0001268 Covid-19 Sample collection and processing sample_collection_and_processing + Sample collection and processing GENEPIO:0001153 Covid-19 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the organization with which the sample collector is affiliated. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Agency of Canada Originating lab collected_by + Sample collection and processing GENEPIO:0001156 Covid-19 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or laboratory. johnnyblogs@lab.ca + Sample collection and processing GENEPIO:0001158 Covid-19 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address + Sample collection and processing GENEPIO:0001159 Covid-19 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Centers for Disease Control and Prevention Submitting lab sequenced_by + Sample collection and processing GENEPIO:0001165 Covid-19 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email + Sample collection and processing GENEPIO:0001167 Covid-19 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Address + Sample collection and processing GENEPIO:0001174 Covid-19 sample collection date sample_collection_date date NullValueMenu TRUE The date on which the sample was collected. Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add "jitter" to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-19 Collection date collection_date collection-date + Sample collection and processing GENEPIO:0001179 Covid-19 sample received date sample_received_date date NullValueMenu The date on which the sample was received. The date the sample was received by a lab that was not the point of collection. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 + Sample collection and processing GENEPIO:0001181 Covid-19 geo_loc name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the country name from the pick list in the template South Africa [GAZ:00001094] Location geo_loc_name country + Sample collection and processing GENEPIO:0001185 Covid-19 geo_loc name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Western Cape geo_loc_name + Sample collection and processing GENEPIO:0100280 Covid-19 geo_loc name (county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire geo_loc_name + Sample collection and processing GENEPIO:0001189 Covid-19 geo_loc name (city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver geo_loc_name + Sample collection and processing GENEPIO:0100309 Covid-19 OBI:0001620 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon + Sample collection and processing GENEPIO:0100310 Covid-19 OBI:0001621 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon + Sample collection and processing GENEPIO:0001191 Covid-19 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Select "Severe acute respiratory syndrome coronavirus 2" if sequencing SARS-CoV-2. If another Coronaviridae is being sequenced, provide the taxonomic name from NCBITaxon. Search for taxonomy terms at https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] organism + Sample collection and processing GENEPIO:0001644 Covid-19 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 isolate isolate + Sample collection and processing GENEPIO:0100284 Covid-19 culture collection culture_collection WhitespaceMinimizedString The name of the source collection and unique culture identifier. Format: ":[:]". For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. /culture_collection="ATCC:26370" + Sample collection and processing GENEPIO:0001198 Covid-19 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. Select a value from the pick list in the template. Diagnostic testing [GENEPIO:0100002] purpose_of_sampling + Sample collection and processing GENEPIO:0001200 Covid-19 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString Further details pertaining to the reason the sample was collected. Provide a free text description of the sampling strategy or samples collected. Screening of bat specimens in museum collections. + Sample collection and processing GENEPIO:0100285 Covid-19 sample plan name sample_plan_name WhitespaceMinimizedString The name of the sample plan implemented for sample collection. Provide the name and version of the sample plan outlining the sample strategy. CanCOGeN Sampling Strategy 1.0 + Sample collection and processing GENEPIO:0100277 Covid-19 sample collected in quarantine sample_collected_in_quarantine SampleCollectedInQuarantineMenu NullValueMenu Whether the sample was collected from an individual in quarantine. Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. Yes [NCIT:C49488] + Sample collection and processing GENEPIO:0001211 Covid-19 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. Blood [UBERON:0000178] Specimen source isolation_source;host_anatomical_material isolation-source + Sample collection and processing GENEPIO:0001214 Covid-19 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. Nasopharynx (NP) [UBERON:0001728] Specimen source isolation_source;host_anatomical_part isolation-source + Sample collection and processing GENEPIO:0001216 Covid-19 body product body_product BodyProductMenu NullValueMenu TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. Feces [UBERON:0001988] Specimen source isolation_source;host_body_product isolation-source + Sample collection and processing GENEPIO:0001223 Covid-19 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. Face mask [OBI:0002787] Specimen source isolation_source;environmental_material isolation-source + Sample collection and processing GENEPIO:0001232 Covid-19 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. Hospital [ENVO:00002173] Specimen source isolation_source;environmental_site isolation-source + Sample collection and processing GENEPIO:0001234 Covid-19 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. Swab [GENEPIO:0100027] Specimen source isolation_source;collection_device isolation-source + Sample collection and processing GENEPIO:0001241 Covid-19 collection method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. Bronchoalveolar lavage (BAL) [GENEPIO:0100032] Specimen source isolation_source;collection_method isolation-source + Sample collection and processing GENEPIO:0001243 Covid-19 collection protocol collection_protocol WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Provide the name and version of the protocol used to collect the samples. SC2SamplingProtocol 1.2 + Sample collection and processing GENEPIO:0001253 Covid-19 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage [GENEPIO:0100039] + Sample collection and processing GENEPIO:0100311 Covid-19 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. + Sample collection and processing GENEPIO:0001255 Covid-19 lab host lab_host LabHostMenu NullValueMenu Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. Type of cell line used for propagation. Select a value form the pick list. If not passaged, put "not applicable". Vero E6 cell line [BTO:0004755] + Sample collection and processing GENEPIO:0001261 Covid-19 passage number passage_number integer 0 Number of passages. Provide number of known passages. If not passaged, put "not applicable" 3 passage_number + Sample collection and processing GENEPIO:0001264 Covid-19 passage method passage_method WhitespaceMinimizedString NullValueMenu Description of how organism was passaged. Free text. Provide a short description. If not passaged, put "not applicable". AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. passage_method + Sample collection and processing GENEPIO:0001266 Covid-19 biomaterial extracted biomaterial_extracted BiomaterialExtractedMenu NullValueMenu The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the pick list in the template. RNA (Total) [OBI:0000895] + Sample collection and processing GENEPIO:0100278 Covid-19 data abstraction details data_abstraction_details WhitespaceMinimizedString A description of how any data elements were altered to preserve patient privacy. If applicable, provide a description of how each data element was abstracted. Jitter added to publicly shared collection dates to prevent re-identifiability. + GENEPIO:0001268 Covid-19 Host Information host_information + Host Information GENEPIO:0001386 Covid-19 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put "not applicable". Human [NCBITaxon:9606] + Host Information GENEPIO:0001387 Covid-19 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put "not applicable". Homo sapiens [NCBITaxon:9606] Host host host + Host Information GENEPIO:0001388 Covid-19 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state + Host Information GENEPIO:0001389 Covid-19 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a value from the pick list. Hospitalized (ICU) [GENEPIO:0100046] + Host Information GENEPIO:0001391 Covid-19 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. "COVID-19" should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”. COVID-19 [MONDO:0100096] host_disease + Host Information GENEPIO:0001390 Covid-19 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome + Host Information GENEPIO:0001392 Covid-19 host age host_age decimal NullValueMenu TRUE 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age + Host Information GENEPIO:0001393 Covid-19 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] + Host Information GENEPIO:0001394 Covid-19 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] + Host Information GENEPIO:0001395 Covid-19 host gender host_gender HostGenderMenu NullValueMenu TRUE The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex + Host Information GENEPIO:0001396 Covid-19 host residence geo_loc name (country) host_residence_geo_loc_name_country HostResidenceGeoLocNameCountryMenu NullValueMenu The country where the host resides. If known, select a value from the pick list. South Africa [GAZ:00001094] + Host Information GENEPIO:0100312 GECKO:0000061 host ethnicity host_ethnicity WhitespaceMinimizedString The self-identified ethnicity(ies) of the host. If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. Indigenous, European + Host Information GENEPIO:0001398 Covid-19 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. BCxy123 host_subject_id + Host Information GENEPIO:0100281 Covid-19 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 + Host Information GENEPIO:0001399 Covid-19 symptom onset date symptom_onset_date date NullValueMenu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 + Host Information GENEPIO:0001400 Covid-19 signs and symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] + Host Information GENEPIO:0001401 Covid-19 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE "Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. Risk Factor: A variable associated with an increased risk of disease or infection." Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. Asthma [HP:0002099] - Host Information GENEPIO:0001402 Covid-19 complications complications menu null value menu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. Acute respiratory failure [MONDO:0001208] - GENEPIO:0001403 Covid-19 Host vaccination information - Host vaccination information GENEPIO:0001404 Covid-19 host vaccination status host vaccination status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination - Host vaccination information GENEPIO:0001406 Covid-19 number of vaccine doses received integer 0 The number of doses of the vaccine received by the host. Record how many doses of the vaccine the host has received. 2 - Host vaccination information GENEPIO:0100313 Covid-19 vaccination dose 1 vaccine name WhitespaceMinimizedString The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) - Host vaccination information GENEPIO:0100314 Covid-19 vaccination dose 1 vaccination date date The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 - Host vaccination information GENEPIO:0100315 Covid-19 vaccination dose 2 vaccine name WhitespaceMinimizedString The name of the vaccine administered as the second dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) - Host vaccination information GENEPIO:0100316 Covid-19 vaccination dose 2 vaccination date date The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 - Host vaccination information GENEPIO:0100317 Covid-19 vaccination dose 3 vaccine name WhitespaceMinimizedString The name of the vaccine administered as the third dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) - Host vaccination information GENEPIO:0100318 Covid-19 vaccination dose 3 vaccination date date The date the third dose of a vaccine was administered. Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-12-30 date_of_sars_cov_2_vaccination - Host vaccination information GENEPIO:0100319 Covid-19 vaccination dose 4 vaccine name WhitespaceMinimizedString The name of the vaccine administered as the fourth dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) - Host vaccination information GENEPIO:0100320 Covid-19 vaccination dose 4 vaccination date date The date the fourth dose of a vaccine was administered. Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-01-15 - Host vaccination information GENEPIO:0100321 Covid-19 vaccination history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated - GENEPIO:0001409 Covid-19 Host exposure information - Host exposure information GENEPIO:0001410 Covid-19 location of exposure geo_loc name (country) geo_loc_name (country) menu null value menu The country where the host was likely exposed to the causative agent of the illness. This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list. South Africa [GAZ:00001094] geo_loc_exposure - Host exposure information GENEPIO:0001411 Covid-19 destination of most recent travel (city) WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City host_recent_travel_loc - Host exposure information GENEPIO:0001412 Covid-19 destination of most recent travel (state/province/territory) WhitespaceMinimizedString The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California host_recent_travel_loc - Host exposure information GENEPIO:0001413 Covid-19 destination of most recent travel (country) geo_loc_name (country) menu null value menu The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom [GAZ:00002637] host_recent_travel_loc - Host exposure information GENEPIO:0001414 Covid-19 most recent travel departure date date null value menu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 - Host exposure information GENEPIO:0001415 Covid-19 most recent travel return date date null value menu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date in ISO 8601 standard format "YYYY-MM-DD". 2020-04-26 host_recent_travel_return_date - Host exposure information GENEPIO:0001416 Covid-19 travel history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. Canada, Vancouver; USA, Seattle; Italy, Milan - Host exposure information GENEPIO:0001417 Covid-19 exposure event exposure event menu null value menu Event leading to exposure. If known, select the exposure event from the pick list. Mass Gathering [GENEPIO:0100237] Additional location information exposure_event - Host exposure information GENEPIO:0001418 Covid-19 exposure contact level exposure contact level menu null value menu The exposure transmission contact type. Select direct or indirect exposure from the pick list. Direct (human-to-human contact) [TRANS:0000001] - Host exposure information GENEPIO:0001419 Covid-19 host role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Patient [OMRSE:00000030] Additional host information - Host exposure information GENEPIO:0001428 Covid-19 exposure setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting [GENEPIO:0100201] Additional host information - Host exposure information GENEPIO:0001431 Covid-19 exposure details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver + Host Information GENEPIO:0001402 Covid-19 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. Acute respiratory failure [MONDO:0001208] + GENEPIO:0001403 Covid-19 Host vaccination information host_vaccination_information + Host vaccination information GENEPIO:0001404 Covid-19 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination + Host vaccination information GENEPIO:0001406 Covid-19 number of vaccine doses received number_of_vaccine_doses_received integer 0 The number of doses of the vaccine received by the host. Record how many doses of the vaccine the host has received. 2 + Host vaccination information GENEPIO:0100313 Covid-19 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) + Host vaccination information GENEPIO:0100314 Covid-19 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date date The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 + Host vaccination information GENEPIO:0100315 Covid-19 vaccination dose 2 vaccine name vaccination_dose_2_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the second dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) + Host vaccination information GENEPIO:0100316 Covid-19 vaccination dose 2 vaccination date vaccination_dose_2_vaccination_date date The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 + Host vaccination information GENEPIO:0100317 Covid-19 vaccination dose 3 vaccine name vaccination_dose_3_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the third dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) + Host vaccination information GENEPIO:0100318 Covid-19 vaccination dose 3 vaccination date vaccination_dose_3_vaccination_date date The date the third dose of a vaccine was administered. Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-12-30 date_of_sars_cov_2_vaccination + Host vaccination information GENEPIO:0100319 Covid-19 vaccination dose 4 vaccine name vaccination_dose_4_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the fourth dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) + Host vaccination information GENEPIO:0100320 Covid-19 vaccination dose 4 vaccination date vaccination_dose_4_vaccination_date date The date the fourth dose of a vaccine was administered. Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-01-15 + Host vaccination information GENEPIO:0100321 Covid-19 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated + GENEPIO:0001409 Covid-19 Host exposure information host_exposure_information + Host exposure information GENEPIO:0001410 Covid-19 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country LocationOfExposureGeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list. South Africa [GAZ:00001094] geo_loc_exposure + Host exposure information GENEPIO:0001411 Covid-19 destination of most recent travel (city) destination_of_most_recent_travel_city WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City host_recent_travel_loc + Host exposure information GENEPIO:0001412 Covid-19 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory WhitespaceMinimizedString The name of the province that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California host_recent_travel_loc + Host exposure information GENEPIO:0001413 Covid-19 destination of most recent travel (country) destination_of_most_recent_travel_country DestinationOfMostRecentTravelCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz United Kingdom [GAZ:00002637] host_recent_travel_loc + Host exposure information GENEPIO:0001414 Covid-19 most recent travel departure date most_recent_travel_departure_date date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 + Host exposure information GENEPIO:0001415 Covid-19 most recent travel return date most_recent_travel_return_date date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date in ISO 8601 standard format "YYYY-MM-DD". 2020-04-26 host_recent_travel_return_date + Host exposure information GENEPIO:0001416 Covid-19 travel history travel_history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. Canada, Vancouver; USA, Seattle; Italy, Milan + Host exposure information GENEPIO:0001417 Covid-19 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. If known, select the exposure event from the pick list. Mass Gathering [GENEPIO:0100237] Additional location information exposure_event + Host exposure information GENEPIO:0001418 Covid-19 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select direct or indirect exposure from the pick list. Direct (human-to-human contact) [TRANS:0000001] + Host exposure information GENEPIO:0001419 Covid-19 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Patient [OMRSE:00000030] Additional host information + Host exposure information GENEPIO:0001428 Covid-19 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting [GENEPIO:0100201] Additional host information + Host exposure information GENEPIO:0001431 Covid-19 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Host role - Other: Bus Driver - GENEPIO:0001434 Covid-19 Host reinfection information - Host reinfection information GENEPIO:0001435 Covid-19 prior SARS-CoV-2 infection prior SARS-CoV-2 infection menu null value menu Whether there was prior SARS-CoV-2 infection. If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Prior infection [GENEPIO:0100234] prior_sars_cov_2_infection - Host reinfection information GENEPIO:0001436 Covid-19 prior SARS-CoV-2 infection isolate WhitespaceMinimizedString The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 virus_isolate_of_prior_infection - Host reinfection information GENEPIO:0001437 Covid-19 prior SARS-CoV-2 infection date date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 date_of_prior_sars_cov_2_infection - Host reinfection information GENEPIO:0001438 Covid-19 prior SARS-CoV-2 antiviral treatment prior SARS-CoV-2 antiviral treatment menu null value menu Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] prior_sars_cov_2_antiviral_treat - Host reinfection information GENEPIO:0001439 Covid-19 prior SARS-CoV-2 antiviral treatment agent WhitespaceMinimizedString The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir antiviral_treatment_agent - Host reinfection information GENEPIO:0001440 Covid-19 prior SARS-CoV-2 antiviral treatment date date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 date_of_prior_antiviral_treat + GENEPIO:0001434 Covid-19 Host reinfection information host_reinfection_information + Host reinfection information GENEPIO:0001435 Covid-19 prior SARS-CoV-2 infection prior_sarscov2_infection PriorSarsCov2InfectionMenu NullValueMenu Whether there was prior SARS-CoV-2 infection. If known, provide information about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. Prior infection [GENEPIO:0100234] prior_sars_cov_2_infection + Host reinfection information GENEPIO:0001436 Covid-19 prior SARS-CoV-2 infection isolate prior_sarscov2_infection_isolate WhitespaceMinimizedString The identifier of the isolate found in the prior SARS-CoV-2 infection. Provide the isolate name of the most recent prior infection. Structure the "isolate" name to be ICTV/INSDC compliant in the following format: "SARS-CoV-2/host/country/sampleID/date". SARS-CoV-2/human/USA/CA-CDPH-001/2020 virus_isolate_of_prior_infection + Host reinfection information GENEPIO:0001437 Covid-19 prior SARS-CoV-2 infection date prior_sarscov2_infection_date date The date of diagnosis of the prior SARS-CoV-2 infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-23 date_of_prior_sars_cov_2_infection + Host reinfection information GENEPIO:0001438 Covid-19 prior SARS-CoV-2 antiviral treatment prior_sarscov2_antiviral_treatment PriorSarsCov2AntiviralTreatmentMenu NullValueMenu Whether there was prior SARS-CoV-2 treatment with an antiviral agent. If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] prior_sars_cov_2_antiviral_treat + Host reinfection information GENEPIO:0001439 Covid-19 prior SARS-CoV-2 antiviral treatment agent prior_sarscov2_antiviral_treatment_agent WhitespaceMinimizedString The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection. Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put "No treatment". If multiple antiviral agents were administered, list them all separated by commas. Remdesivir antiviral_treatment_agent + Host reinfection information GENEPIO:0001440 Covid-19 prior SARS-CoV-2 antiviral treatment date prior_sarscov2_antiviral_treatment_date date The date treatment was first administered during the prior SARS-CoV-2 infection. Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format "YYYY-MM-DD". 2021-01-28 date_of_prior_antiviral_treat - GENEPIO:0001441 Covid-19 Sequencing - Sequencing GENEPIO:0001445 Covid-19 purpose of sequencing purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy purpose_of_sequencing - Sequencing GENEPIO:0001446 Covid-19 purpose of sequencing details WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) - Sequencing GENEPIO:0001447 Covid-19 sequencing date date null value menu The date the sample was sequenced. Provide the sequencing date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-26 - Sequencing GENEPIO:0001448 Covid-19 library ID WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID - Sequencing GENEPIO:0001449 Covid-19 amplicon size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon_size - Sequencing GENEPIO:0001450 Covid-19 library preparation kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequencing GENEPIO:0001451 Covid-19 flow cell barcode WhitespaceMinimizedString The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 - Sequencing GENEPIO:0001452 Covid-19 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select the sequencing instrument from the pick list. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology platform;instrument_model sequencing_technology - Sequencing GENEPIO:0001453 Covid-19 sequencing protocol name WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol. 1D_DNA_MinION, ARTIC Network Protocol V3 sequencing_protocol_name - Sequencing GENEPIO:0001454 Covid-19 sequencing protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. design_description - Sequencing GENEPIO:0001455 Covid-19 sequencing kit number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 - Sequencing GENEPIO:0001456 Covid-19 amplicon pcr primer scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon_pcr_primer_scheme + GENEPIO:0001441 Covid-19 Sequencing sequencing + Sequencing GENEPIO:0001445 Covid-19 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy purpose_of_sequencing + Sequencing GENEPIO:0001446 Covid-19 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) + Sequencing GENEPIO:0001447 Covid-19 sequencing date sequencing_date date NullValueMenu The date the sample was sequenced. Provide the sequencing date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-26 + Sequencing GENEPIO:0001448 Covid-19 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID + Sequencing GENEPIO:0001449 Covid-19 amplicon size amplicon_size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon_size + Sequencing GENEPIO:0001450 Covid-19 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequencing GENEPIO:0001451 Covid-19 flow cell barcode flow_cell_barcode WhitespaceMinimizedString The barcode of the flow cell used for sequencing. Provide the barcode of the flow cell used for sequencing the sample. FAB06069 + Sequencing GENEPIO:0001452 Covid-19 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select the sequencing instrument from the pick list. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology platform;instrument_model sequencing_technology + Sequencing GENEPIO:0001453 Covid-19 sequencing protocol name sequencing_protocol_name WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol. 1D_DNA_MinION, ARTIC Network Protocol V3 sequencing_protocol_name + Sequencing GENEPIO:0001454 Covid-19 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. design_description + Sequencing GENEPIO:0001455 Covid-19 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 + Sequencing GENEPIO:0001456 Covid-19 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv amplicon_pcr_primer_scheme - GENEPIO:0001457 Covid-19 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0001458 Covid-19 raw sequence data processing method WhitespaceMinimizedString TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the name and version numbers of the software used to process the raw data. Porechop 0.2.3 raw_sequence_data_processing_method - Bioinformatics and QC metrics GENEPIO:0001459 Covid-19 dehosting method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper 1.2.3 dehosting_method - Bioinformatics and QC metrics GENEPIO:0001460 Covid-19 consensus sequence name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. ncov123assembly3 - Bioinformatics and QC metrics GENEPIO:0001461 Covid-19 consensus sequence filename WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. ncov123assembly.fasta filename - Bioinformatics and QC metrics GENEPIO:0001462 Covid-19 consensus sequence filepath WhitespaceMinimizedString The filepath of the consesnsus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/RespLab/Data/ncov123assembly.fasta - Bioinformatics and QC metrics GENEPIO:0001463 Covid-19 consensus sequence software name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. Ivar Assembly method assembly_method - Bioinformatics and QC metrics GENEPIO:0001469 Covid-19 consensus sequence software version decimal TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method assembly_method_version - Bioinformatics and QC metrics GENEPIO:0001472 Covid-19 breadth of coverage value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% - Bioinformatics and QC metrics GENEPIO:0001474 Covid-19 depth of coverage value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage genome_coverage - Bioinformatics and QC metrics GENEPIO:0001475 Covid-19 depth of coverage threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x - Bioinformatics and QC metrics GENEPIO:0001476 Covid-19 r1 fastq filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Bioinformatics and QC metrics GENEPIO:0001477 Covid-19 r2 fastq filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Bioinformatics and QC metrics GENEPIO:0001478 Covid-19 r1 fastq filepath WhitespaceMinimizedString The filepath of the r1 FASTQ file. Provide the filepath of the r1 FASTQ file. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz - Bioinformatics and QC metrics GENEPIO:0001479 Covid-19 r2 fastq filepath WhitespaceMinimizedString The filepath of the r2 FASTQ file. Provide the filepath of the r2 FASTQ file. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz - Bioinformatics and QC metrics GENEPIO:0001480 Covid-19 fast5 filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 - Bioinformatics and QC metrics GENEPIO:0001481 Covid-19 fast5 filepath WhitespaceMinimizedString The filepath of the FAST5 file. Provide the filepath of the FAST5 file. /User/Documents/RespLab/Data/batch1a_sequences.fast5 - Bioinformatics and QC metrics GENEPIO:0001482 Covid-19 number of base pairs sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics GENEPIO:0001483 Covid-19 consensus genome length integer 0 Size of the assembled genome described as the number of base pairs. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics GENEPIO:0001484 Covid-19 Ns per 100 kbp decimal The number of N symbols present in the consensus fasta sequence, per 100kbp of sequence. Provide a numerical value (no need to include units). 300 - Bioinformatics and QC metrics GENEPIO:0001485 Covid-19 reference genome accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 reference_genome - Bioinformatics and QC metrics GENEPIO:0001489 Covid-19 bioinformatics protocol WhitespaceMinimizedString The name and version number of the bioinformatics protocol used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol, or a link if deposited in a protocol repository. https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members - GENEPIO:0001498 Covid-19 Lineage and Variant information - Lineage and Variant information GENEPIO:0001500 Covid-19 lineage/clade name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 - Lineage and Variant information GENEPIO:0001501 Covid-19 lineage/clade analysis software name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin - Lineage and Variant information GENEPIO:0001502 Covid-19 lineage/clade analysis software version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 - Lineage and Variant information GENEPIO:0001503 Covid-19 variant designation variant designation menu null value menu The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern (VOC) [GENEPIO:0100083] - Lineage and Variant information GENEPIO:0001504 Covid-19 variant evidence details WhitespaceMinimizedString The evidence used to make the variant determination. List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. RT-qPCR TaqPath assay: S gene target failure - GENEPIO:0001506 Covid-19 Pathogen diagnostic testing - Pathogen diagnostic testing GENEPIO:0001507 Covid-19 gene name 1 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI E gene (orf4) [GENEPIO:0100151] sars_cov_2_diag_gene_name_1 - Pathogen diagnostic testing GENEPIO:0001508 Covid-19 diagnostic pcr protocol 1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. PCREGene 2.0 - Pathogen diagnostic testing GENEPIO:0001509 Covid-19 diagnostic pcr Ct value 1 WhitespaceMinimizedString The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test. 21 sars_cov_2_diag_pcr_ct_value_1 - Pathogen diagnostic testing GENEPIO:0001510 Covid-19 gene name 2 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI RdRp gene (nsp12) [GENEPIO:0100168] sars_cov_2_diag_gene_name_2 - Pathogen diagnostic testing GENEPIO:0001511 Covid-19 diagnostic pcr protocol 2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. PCRRdRpGene 3.0 - Pathogen diagnostic testing GENEPIO:0001512 Covid-19 diagnostic pcr Ct value 2 WhitespaceMinimizedString The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test. 36 sars_cov_2_diag_pcr_ct_value_2 - Covid-19 - GENEPIO:0100322 Covid-19 NCBI SRA information - NCBI SRA information GENEPIO:0100323 Covid-19 title WhitespaceMinimizedString Short description that will identify the dataset on public pages. Format: {methodology} of {organism}: {sample info} Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab title - NCBI SRA information GENEPIO:0100324 Covid-19 library_strategy library_strategy menu See NCBI SRA template for details. Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select "AMPLICON". library_strategy - NCBI SRA information GENEPIO:0100325 Covid-19 library_source library_source menu See NCBI SRA template for details. Provide the library source by selecting a value from the pick list. For amplicon sequencing select "Viral RNA". library_source - NCBI SRA information GENEPIO:0100326 Covid-19 library_selection library_selection menu See NCBI SRA template for details. Provide the library selection by selecting a value from the pick list. For amplicon sequencing select "PCR". library_selection - NCBI SRA information GENEPIO:0100327 Covid-19 library_layout library_layout menu See NCBI SRA template for details. Provide the library layout by selecting a value from the pick list. For Illumina instruments, select "PAIRED". For Oxford Nanopore instruments, select "SINGLE". library_layout - NCBI SRA information GENEPIO:0100328 Covid-19 filetype filetype menu See NCBI SRA template for details. Provide the filetype by selecting a value from the pick list. filetype - NCBI SRA information GENEPIO:0100329 Covid-19 filename WhitespaceMinimizedString See NCBI SRA template for details. Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is "paired", provide the second filename under "Filename 2". filename - NCBI SRA information GENEPIO:0100330 Covid-19 filename2 WhitespaceMinimizedString See NCBI SRA template for details. Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. filename2 + GENEPIO:0001457 Covid-19 Bioinformatics and QC metrics bioinformatics_and_qc_metrics + Bioinformatics and QC metrics GENEPIO:0001458 Covid-19 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE #REF! raw_sequence_data_processing_method + Bioinformatics and QC metrics GENEPIO:0001459 Covid-19 dehosting method dehosting_method WhitespaceMinimizedString TRUE dehosting_method + Bioinformatics and QC metrics GENEPIO:0001460 Covid-19 consensus sequence name consensus_sequence_name WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001461 Covid-19 consensus sequence filename consensus_sequence_filename WhitespaceMinimizedString filename + Bioinformatics and QC metrics GENEPIO:0001462 Covid-19 consensus sequence filepath consensus_sequence_filepath WhitespaceMinimizedString The filepath of the consensus sequence file. + Bioinformatics and QC metrics GENEPIO:0001463 Covid-19 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE Assembly method assembly_method + Bioinformatics and QC metrics GENEPIO:0001469 Covid-19 consensus sequence software version consensus_sequence_software_version decimal TRUE Assembly method assembly_method_version + Bioinformatics and QC metrics GENEPIO:0001472 Covid-19 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001474 Covid-19 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString Depth of coverage genome_coverage + Bioinformatics and QC metrics GENEPIO:0001475 Covid-19 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001476 Covid-19 r1 fastq filename r1_fastq_filename WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001477 Covid-19 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001478 Covid-19 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001479 Covid-19 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001480 Covid-19 fast5 filename fast5_filename WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001481 Covid-19 fast5 filepath fast5_filepath WhitespaceMinimizedString + Bioinformatics and QC metrics GENEPIO:0001482 Covid-19 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 + Bioinformatics and QC metrics GENEPIO:0001483 Covid-19 consensus genome length consensus_genome_length integer 0 + Bioinformatics and QC metrics GENEPIO:0001484 Covid-19 Ns per 100 kbp ns_per_100_kbp decimal + Bioinformatics and QC metrics GENEPIO:0001485 Covid-19 reference genome accession reference_genome_accession WhitespaceMinimizedString reference_genome + Bioinformatics and QC metrics GENEPIO:0001489 Covid-19 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString + GENEPIO:0001498 Covid-19 Lineage and Variant information lineage_and_variant_information + Lineage and Variant information GENEPIO:0001500 Covid-19 lineage/clade name lineage_clade_name WhitespaceMinimizedString The name of the lineage or clade. Provide the Pangolin or Nextstrain lineage/clade name. B.1.1.7 + Lineage and Variant information GENEPIO:0001501 Covid-19 lineage/clade analysis software name lineage_clade_analysis_software_name WhitespaceMinimizedString The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin + Lineage and Variant information GENEPIO:0001502 Covid-19 lineage/clade analysis software version lineage_clade_analysis_software_version WhitespaceMinimizedString The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 + Lineage and Variant information GENEPIO:0001503 Covid-19 variant designation variant_designation VariantDesignationMenu NullValueMenu The variant classification of the lineage/clade i.e. variant, variant of concern. If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. Variant of Concern (VOC) [GENEPIO:0100083] + Lineage and Variant information GENEPIO:0001505 Covid-19 variant evidence details variant_evidence_details WhitespaceMinimizedString The evidence used to make the variant determination. List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. RT-qPCR TaqPath assay: S gene target failure + GENEPIO:0001506 Covid-19 Pathogen diagnostic testing pathogen_diagnostic_testing + Pathogen diagnostic testing GENEPIO:0001507 Covid-19 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI E gene (orf4) [GENEPIO:0100151] sars_cov_2_diag_gene_name_1 + Pathogen diagnostic testing GENEPIO:0001508 Covid-19 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. PCREGene 2.0 + Pathogen diagnostic testing GENEPIO:0001509 Covid-19 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 WhitespaceMinimizedString The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the cycle threshold (Ct) value of the sample from the diagnostic RT-PCR test. 21 sars_cov_2_diag_pcr_ct_value_1 + Pathogen diagnostic testing GENEPIO:0001510 Covid-19 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select a gene from the pick list. If the gene of interest is not in the list, provide the full name of the gene or the gene symbol (short form of gene name). Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI RdRp gene (nsp12) [GENEPIO:0100168] sars_cov_2_diag_gene_name_2 + Pathogen diagnostic testing GENEPIO:0001511 Covid-19 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. PCRRdRpGene 3.0 + Pathogen diagnostic testing GENEPIO:0001512 Covid-19 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 WhitespaceMinimizedString The cycle threshold (Ct) value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the cycle threshold (Ct) value of the sample from the second diagnostic RT-PCR test. 36 sars_cov_2_diag_pcr_ct_value_2 - GENEPIO:0001516 Covid-19 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 Covid-19 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Johnny Blogs Authors - Contributor acknowledgement GENEPIO:0001518 Covid-19 DataHarmonizer provenance Provenance The DataHarmonizer software version provenance. The current software version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer provenance: v0.13.21 + GENEPIO:0100322 Covid-19 NCBI SRA information ncbi_sra_information + NCBI SRA information GENEPIO:0100323 Covid-19 title title WhitespaceMinimizedString Short description that will identify the dataset on public pages. Format: {methodology} of {organism}: {sample info} Genomic sequencing of SARS-CoV-2: Nasopharynx (NP), Swab title + NCBI SRA information GENEPIO:0100324 Covid-19 library_strategy library_strategy LibraryStrategyMenu See NCBI SRA template for details. Provide the library strategy by selecting a value from the pick list. For amplicon sequencing select "AMPLICON". library_strategy + NCBI SRA information GENEPIO:0100325 Covid-19 library_source library_source LibrarySourceMenu See NCBI SRA template for details. Provide the library source by selecting a value from the pick list. For amplicon sequencing select "Viral RNA". library_source + NCBI SRA information GENEPIO:0100326 Covid-19 library_selection library_selection LibrarySelectionMenu See NCBI SRA template for details. Provide the library selection by selecting a value from the pick list. For amplicon sequencing select "PCR". library_selection + NCBI SRA information GENEPIO:0100327 Covid-19 library_layout library_layout LibraryLayoutMenu See NCBI SRA template for details. Provide the library layout by selecting a value from the pick list. For Illumina instruments, select "PAIRED". For Oxford Nanopore instruments, select "SINGLE". library_layout + NCBI SRA information GENEPIO:0100328 Covid-19 filetype filetype FiletypeMenu See NCBI SRA template for details. Provide the filetype by selecting a value from the pick list. filetype + NCBI SRA information GENEPIO:0100329 Covid-19 filename filename WhitespaceMinimizedString See NCBI SRA template for details. Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. If sequence data is "paired", provide the second filename under "Filename 2". filename + NCBI SRA information GENEPIO:0100330 Covid-19 filename2 filename2 WhitespaceMinimizedString See NCBI SRA template for details. Provide the appropriate filename recorded in the Bioinformatics and QC metrics section. filename2 + + GENEPIO:0001516 Covid-19 Contributor acknowledgement contributor_acknowledgement + Contributor acknowledgement GENEPIO:0001517 Covid-19 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Johnny Blogs Authors + Contributor acknowledgement GENEPIO:0001518 Covid-19 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, PHA4GE v1.0.0 \ No newline at end of file From 3cfcf9c7a692ec0966a33a4500409251203e126f Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:14:37 -0700 Subject: [PATCH 84/96] gisaid update --- web/templates/gisaid/schema.json | 710 ++++++++++++++++++-------- web/templates/gisaid/schema.yaml | 254 +++++---- web/templates/gisaid/schema_enums.tsv | 7 +- web/templates/gisaid/schema_slots.tsv | 56 +- 4 files changed, 666 insertions(+), 361 deletions(-) diff --git a/web/templates/gisaid/schema.json b/web/templates/gisaid/schema.json index bb8bb997..1b8dd179 100644 --- a/web/templates/gisaid/schema.json +++ b/web/templates/gisaid/schema.json @@ -19,6 +19,10 @@ "shex": { "prefix_prefix": "shex", "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" } }, "default_prefix": "https://example.com/GISAID/", @@ -26,6 +30,7 @@ "WhitespaceMinimizedString": { "name": "WhitespaceMinimizedString", "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/GISAID", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -33,6 +38,7 @@ "Provenance": { "name": "Provenance", "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/GISAID", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -40,18 +46,39 @@ "string": { "name": "string", "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "xsd:string" }, "integer": { "name": "integer", "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "xsd:integer" }, "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "xsd:boolean", "repr": "bool" @@ -59,18 +86,39 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:float" }, "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/GISAID", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:double" }, "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/GISAID", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "xsd:decimal" }, @@ -78,17 +126,27 @@ "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:Time" ], "base": "XSDTime", - "uri": "xsd:dateTime", + "uri": "xsd:time", "repr": "str" }, "date": { "name": "date", "description": "a date (year, month and day) in an idealized calendar", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:Date" ], "base": "XSDDate", "uri": "xsd:date", @@ -97,6 +155,13 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/GISAID", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "xsd:dateTime", "repr": "str" @@ -104,6 +169,10 @@ "date_or_datetime": { "name": "date_or_datetime", "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/GISAID", "base": "str", "uri": "linkml:DateOrDatetime", "repr": "str" @@ -111,13 +180,44 @@ "uriorcurie": { "name": "uriorcurie", "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/GISAID", "base": "URIorCURIE", "uri": "xsd:anyURI", "repr": "str" }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://example.com/GISAID", + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, "uri": { "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://example.com/GISAID", + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "xsd:anyURI", "repr": "str" @@ -125,6 +225,10 @@ "ncname": { "name": "ncname", "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/GISAID", "base": "NCName", "uri": "xsd:string", "repr": "str" @@ -132,7 +236,13 @@ "objectidentifier": { "name": "objectidentifier", "description": "A URI or CURIE that represents an object in the model.", - "comments": ["Used for inheritence and type checking"], + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://example.com/GISAID", "base": "ElementIdentifier", "uri": "shex:iri", "repr": "str" @@ -140,14 +250,55 @@ "nodeidentifier": { "name": "nodeidentifier", "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/GISAID", "base": "NodeIdentifier", "uri": "shex:nonLiteral", "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/GISAID", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/GISAID", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/GISAID", + "base": "str", + "uri": "xsd:string", + "repr": "str" } }, "enums": { - "Type menu": { - "name": "Type menu", + "TypeMenu": { + "name": "TypeMenu", + "title": "Type menu", "from_schema": "https://example.com/GISAID", "permissible_values": { "betacoronavirus": { @@ -157,205 +308,286 @@ } }, "slots": { - "Submitter": { - "name": "Submitter", + "submitter": { + "name": "submitter", "description": "enter your GISAID-Username", "title": "Submitter", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "FASTA filename": { - "name": "FASTA filename", + "fasta_filename": { + "name": "fasta_filename", "description": "the filename that contains the sequence without path (e.g. all_sequences.fasta not c:\\users\\meier\\docs\\all_sequences.fasta)", "title": "FASTA filename", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Virus name": { - "name": "Virus name", + "virus_name": { + "name": "virus_name", "description": "e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta)", "title": "Virus name", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Type": { - "name": "Type", + "type": { + "name": "type", "description": "default must remain \"betacoronavirus\"", "title": "Type", "from_schema": "https://example.com/GISAID", - "range": "Type menu", + "domain_of": [ + "GISAID" + ], + "range": "TypeMenu", "required": true }, - "Passage details/history": { - "name": "Passage details/history", + "passage_details_history": { + "name": "passage_details_history", "description": "e.g. Original, Vero", "title": "Passage details/history", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Collection date": { - "name": "Collection date", + "collection_date": { + "name": "collection_date", "description": "Date in the format YYYY or YYYY-MM or YYYY-MM-DD", "title": "Collection date", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Location": { - "name": "Location", + "location": { + "name": "location", "description": "e.g. Europe / Germany / Bavaria / Munich", "title": "Location", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Additional location information": { - "name": "Additional location information", + "additional_location_information": { + "name": "additional_location_information", "description": "e.g. Cruise Ship, Convention, Live animal market", "title": "Additional location information", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Host": { - "name": "Host", + "host": { + "name": "host", "description": "e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc", "title": "Host", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Additional host information": { - "name": "Additional host information", + "additional_host_information": { + "name": "additional_host_information", "description": "e.g. Patient infected while traveling in ….", "title": "Additional host information", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Sampling Strategy": { - "name": "Sampling Strategy", + "sampling_strategy": { + "name": "sampling_strategy", "description": "e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout", "title": "Sampling Strategy", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Gender": { - "name": "Gender", + "gender": { + "name": "gender", "description": "Male, Female, or unknown", "title": "Gender", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Patient age": { - "name": "Patient age", + "patient_age": { + "name": "patient_age", "description": "e.g. 65 or 7 months, or unknown", "title": "Patient age", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Patient status": { - "name": "Patient status", + "patient_status": { + "name": "patient_status", "description": "e.g. Hospitalized, Released, Live, Deceased, or unknown", "title": "Patient status", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Specimen source": { - "name": "Specimen source", + "specimen_source": { + "name": "specimen_source", "description": "e.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other", "title": "Specimen source", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Outbreak": { - "name": "Outbreak", + "outbreak": { + "name": "outbreak", "description": "Date, Location e.g. type of gathering, Family cluster, etc.", "title": "Outbreak", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Last vaccinated": { - "name": "Last vaccinated", + "last_vaccinated": { + "name": "last_vaccinated", "description": "provide details if applicable", "title": "Last vaccinated", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Treatment": { - "name": "Treatment", + "treatment": { + "name": "treatment", "description": "Include drug name, dosage", "title": "Treatment", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Sequencing technology": { - "name": "Sequencing technology", + "sequencing_technology": { + "name": "sequencing_technology", "description": "e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc.", "title": "Sequencing technology", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Assembly method": { - "name": "Assembly method", + "assembly_method": { + "name": "assembly_method", "description": "e.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc.", "title": "Assembly method", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Coverage": { - "name": "Coverage", + "coverage": { + "name": "coverage", "description": "e.g. 70x, 1,000x, 10,000x (average)", "title": "Coverage", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Originating lab": { - "name": "Originating lab", + "originating_lab": { + "name": "originating_lab", "description": "Where the clinical specimen or virus isolate was first obtained", "title": "Originating lab", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Address": { - "name": "Address", + "address": { + "name": "address", "title": "Address", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Sample ID given by the sample provider": { - "name": "Sample ID given by the sample provider", + "sample_id_given_by_the_sample_provider": { + "name": "sample_id_given_by_the_sample_provider", "title": "Sample ID given by the sample provider", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Submitting lab": { - "name": "Submitting lab", + "submitting_lab": { + "name": "submitting_lab", "description": "Where sequence data have been generated and submitted to GISAID", "title": "Submitting lab", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString", "required": true }, - "Sample ID given by the submitting laboratory": { - "name": "Sample ID given by the submitting laboratory", + "sample_id_given_by_the_submitting_laboratory": { + "name": "sample_id_given_by_the_submitting_laboratory", "title": "Sample ID given by the submitting laboratory", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" }, - "Authors": { - "name": "Authors", + "authors": { + "name": "authors", "description": "a comma separated list of Authors with complete First followed by Last Name", "title": "Authors", "from_schema": "https://example.com/GISAID", + "domain_of": [ + "GISAID" + ], "range": "WhitespaceMinimizedString" } }, @@ -371,456 +603,536 @@ "from_schema": "https://example.com/GISAID", "is_a": "dh_interface", "slot_usage": { - "Submitter": { - "name": "Submitter", + "submitter": { + "name": "submitter", "rank": 1, "slot_group": "GISAID Submission Form" }, - "FASTA filename": { - "name": "FASTA filename", + "fasta_filename": { + "name": "fasta_filename", "rank": 2, "slot_group": "GISAID Submission Form" }, - "Virus name": { - "name": "Virus name", + "virus_name": { + "name": "virus_name", "rank": 3, "slot_group": "GISAID Submission Form" }, - "Type": { - "name": "Type", + "type": { + "name": "type", "rank": 4, "slot_group": "GISAID Submission Form" }, - "Passage details/history": { - "name": "Passage details/history", + "passage_details_history": { + "name": "passage_details_history", "rank": 5, "slot_group": "GISAID Submission Form" }, - "Collection date": { - "name": "Collection date", + "collection_date": { + "name": "collection_date", "rank": 6, "slot_group": "GISAID Submission Form" }, - "Location": { - "name": "Location", + "location": { + "name": "location", "rank": 7, "slot_group": "GISAID Submission Form" }, - "Additional location information": { - "name": "Additional location information", + "additional_location_information": { + "name": "additional_location_information", "rank": 8, "slot_group": "GISAID Submission Form" }, - "Host": { - "name": "Host", + "host": { + "name": "host", "rank": 9, "slot_group": "GISAID Submission Form" }, - "Additional host information": { - "name": "Additional host information", + "additional_host_information": { + "name": "additional_host_information", "rank": 10, "slot_group": "GISAID Submission Form" }, - "Sampling Strategy": { - "name": "Sampling Strategy", + "sampling_strategy": { + "name": "sampling_strategy", "rank": 11, "slot_group": "GISAID Submission Form" }, - "Gender": { - "name": "Gender", + "gender": { + "name": "gender", "rank": 12, "slot_group": "GISAID Submission Form" }, - "Patient age": { - "name": "Patient age", + "patient_age": { + "name": "patient_age", "rank": 13, "slot_group": "GISAID Submission Form" }, - "Patient status": { - "name": "Patient status", + "patient_status": { + "name": "patient_status", "rank": 14, "slot_group": "GISAID Submission Form" }, - "Specimen source": { - "name": "Specimen source", + "specimen_source": { + "name": "specimen_source", "rank": 15, "slot_group": "GISAID Submission Form" }, - "Outbreak": { - "name": "Outbreak", + "outbreak": { + "name": "outbreak", "rank": 16, "slot_group": "GISAID Submission Form" }, - "Last vaccinated": { - "name": "Last vaccinated", + "last_vaccinated": { + "name": "last_vaccinated", "rank": 17, "slot_group": "GISAID Submission Form" }, - "Treatment": { - "name": "Treatment", + "treatment": { + "name": "treatment", "rank": 18, "slot_group": "GISAID Submission Form" }, - "Sequencing technology": { - "name": "Sequencing technology", + "sequencing_technology": { + "name": "sequencing_technology", "rank": 19, "slot_group": "GISAID Submission Form" }, - "Assembly method": { - "name": "Assembly method", + "assembly_method": { + "name": "assembly_method", "rank": 20, "slot_group": "GISAID Submission Form" }, - "Coverage": { - "name": "Coverage", + "coverage": { + "name": "coverage", "rank": 21, "slot_group": "GISAID Submission Form" }, - "Originating lab": { - "name": "Originating lab", + "originating_lab": { + "name": "originating_lab", "rank": 22, "slot_group": "GISAID Submission Form" }, - "Address": { - "name": "Address", + "address": { + "name": "address", "rank": 26, "slot_group": "GISAID Submission Form" }, - "Sample ID given by the sample provider": { - "name": "Sample ID given by the sample provider", + "sample_id_given_by_the_sample_provider": { + "name": "sample_id_given_by_the_sample_provider", "rank": 24, "slot_group": "GISAID Submission Form" }, - "Submitting lab": { - "name": "Submitting lab", + "submitting_lab": { + "name": "submitting_lab", "rank": 25, "slot_group": "GISAID Submission Form" }, - "Sample ID given by the submitting laboratory": { - "name": "Sample ID given by the submitting laboratory", + "sample_id_given_by_the_submitting_laboratory": { + "name": "sample_id_given_by_the_submitting_laboratory", "rank": 27, "slot_group": "GISAID Submission Form" }, - "Authors": { - "name": "Authors", + "authors": { + "name": "authors", "rank": 28, "slot_group": "GISAID Submission Form" } }, "attributes": { - "Submitter": { - "name": "Submitter", + "submitter": { + "name": "submitter", "description": "enter your GISAID-Username", "title": "Submitter", "from_schema": "https://example.com/GISAID", "rank": 1, - "alias": "Submitter", + "alias": "submitter", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "FASTA filename": { - "name": "FASTA filename", + "fasta_filename": { + "name": "fasta_filename", "description": "the filename that contains the sequence without path (e.g. all_sequences.fasta not c:\\users\\meier\\docs\\all_sequences.fasta)", "title": "FASTA filename", "from_schema": "https://example.com/GISAID", "rank": 2, - "alias": "FASTA_filename", + "alias": "fasta_filename", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Virus name": { - "name": "Virus name", + "virus_name": { + "name": "virus_name", "description": "e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta)", "title": "Virus name", "from_schema": "https://example.com/GISAID", "rank": 3, - "alias": "Virus_name", + "alias": "virus_name", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Type": { - "name": "Type", + "type": { + "name": "type", "description": "default must remain \"betacoronavirus\"", "title": "Type", "from_schema": "https://example.com/GISAID", "rank": 4, - "alias": "Type", + "alias": "type", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", - "range": "Type menu", + "range": "TypeMenu", "required": true }, - "Passage details/history": { - "name": "Passage details/history", + "passage_details_history": { + "name": "passage_details_history", "description": "e.g. Original, Vero", "title": "Passage details/history", "from_schema": "https://example.com/GISAID", "rank": 5, - "alias": "Passage_details/history", + "alias": "passage_details_history", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Collection date": { - "name": "Collection date", + "collection_date": { + "name": "collection_date", "description": "Date in the format YYYY or YYYY-MM or YYYY-MM-DD", "title": "Collection date", "from_schema": "https://example.com/GISAID", "rank": 6, - "alias": "Collection_date", + "alias": "collection_date", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Location": { - "name": "Location", + "location": { + "name": "location", "description": "e.g. Europe / Germany / Bavaria / Munich", "title": "Location", "from_schema": "https://example.com/GISAID", "rank": 7, - "alias": "Location", + "alias": "location", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Additional location information": { - "name": "Additional location information", + "additional_location_information": { + "name": "additional_location_information", "description": "e.g. Cruise Ship, Convention, Live animal market", "title": "Additional location information", "from_schema": "https://example.com/GISAID", "rank": 8, - "alias": "Additional_location_information", + "alias": "additional_location_information", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Host": { - "name": "Host", + "host": { + "name": "host", "description": "e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc", "title": "Host", "from_schema": "https://example.com/GISAID", "rank": 9, - "alias": "Host", + "alias": "host", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Additional host information": { - "name": "Additional host information", + "additional_host_information": { + "name": "additional_host_information", "description": "e.g. Patient infected while traveling in ….", "title": "Additional host information", "from_schema": "https://example.com/GISAID", "rank": 10, - "alias": "Additional_host_information", + "alias": "additional_host_information", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Sampling Strategy": { - "name": "Sampling Strategy", + "sampling_strategy": { + "name": "sampling_strategy", "description": "e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout", "title": "Sampling Strategy", "from_schema": "https://example.com/GISAID", "rank": 11, - "alias": "Sampling_Strategy", + "alias": "sampling_strategy", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Gender": { - "name": "Gender", + "gender": { + "name": "gender", "description": "Male, Female, or unknown", "title": "Gender", "from_schema": "https://example.com/GISAID", "rank": 12, - "alias": "Gender", + "alias": "gender", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Patient age": { - "name": "Patient age", + "patient_age": { + "name": "patient_age", "description": "e.g. 65 or 7 months, or unknown", "title": "Patient age", "from_schema": "https://example.com/GISAID", "rank": 13, - "alias": "Patient_age", + "alias": "patient_age", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Patient status": { - "name": "Patient status", + "patient_status": { + "name": "patient_status", "description": "e.g. Hospitalized, Released, Live, Deceased, or unknown", "title": "Patient status", "from_schema": "https://example.com/GISAID", "rank": 14, - "alias": "Patient_status", + "alias": "patient_status", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Specimen source": { - "name": "Specimen source", + "specimen_source": { + "name": "specimen_source", "description": "e.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other", "title": "Specimen source", "from_schema": "https://example.com/GISAID", "rank": 15, - "alias": "Specimen_source", + "alias": "specimen_source", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Outbreak": { - "name": "Outbreak", + "outbreak": { + "name": "outbreak", "description": "Date, Location e.g. type of gathering, Family cluster, etc.", "title": "Outbreak", "from_schema": "https://example.com/GISAID", "rank": 16, - "alias": "Outbreak", + "alias": "outbreak", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Last vaccinated": { - "name": "Last vaccinated", + "last_vaccinated": { + "name": "last_vaccinated", "description": "provide details if applicable", "title": "Last vaccinated", "from_schema": "https://example.com/GISAID", "rank": 17, - "alias": "Last_vaccinated", + "alias": "last_vaccinated", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Treatment": { - "name": "Treatment", + "treatment": { + "name": "treatment", "description": "Include drug name, dosage", "title": "Treatment", "from_schema": "https://example.com/GISAID", "rank": 18, - "alias": "Treatment", + "alias": "treatment", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Sequencing technology": { - "name": "Sequencing technology", + "sequencing_technology": { + "name": "sequencing_technology", "description": "e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc.", "title": "Sequencing technology", "from_schema": "https://example.com/GISAID", "rank": 19, - "alias": "Sequencing_technology", + "alias": "sequencing_technology", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Assembly method": { - "name": "Assembly method", + "assembly_method": { + "name": "assembly_method", "description": "e.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc.", "title": "Assembly method", "from_schema": "https://example.com/GISAID", "rank": 20, - "alias": "Assembly_method", + "alias": "assembly_method", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Coverage": { - "name": "Coverage", + "coverage": { + "name": "coverage", "description": "e.g. 70x, 1,000x, 10,000x (average)", "title": "Coverage", "from_schema": "https://example.com/GISAID", "rank": 21, - "alias": "Coverage", + "alias": "coverage", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Originating lab": { - "name": "Originating lab", + "originating_lab": { + "name": "originating_lab", "description": "Where the clinical specimen or virus isolate was first obtained", "title": "Originating lab", "from_schema": "https://example.com/GISAID", "rank": 22, - "alias": "Originating_lab", + "alias": "originating_lab", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Address": { - "name": "Address", + "address": { + "name": "address", "title": "Address", "from_schema": "https://example.com/GISAID", "rank": 26, - "alias": "Address", + "alias": "address", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Sample ID given by the sample provider": { - "name": "Sample ID given by the sample provider", + "sample_id_given_by_the_sample_provider": { + "name": "sample_id_given_by_the_sample_provider", "title": "Sample ID given by the sample provider", "from_schema": "https://example.com/GISAID", "rank": 24, - "alias": "Sample_ID_given_by_the_sample_provider", + "alias": "sample_id_given_by_the_sample_provider", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Submitting lab": { - "name": "Submitting lab", + "submitting_lab": { + "name": "submitting_lab", "description": "Where sequence data have been generated and submitted to GISAID", "title": "Submitting lab", "from_schema": "https://example.com/GISAID", "rank": 25, - "alias": "Submitting_lab", + "alias": "submitting_lab", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString", "required": true }, - "Sample ID given by the submitting laboratory": { - "name": "Sample ID given by the submitting laboratory", + "sample_id_given_by_the_submitting_laboratory": { + "name": "sample_id_given_by_the_submitting_laboratory", "title": "Sample ID given by the submitting laboratory", "from_schema": "https://example.com/GISAID", "rank": 27, - "alias": "Sample_ID_given_by_the_submitting_laboratory", + "alias": "sample_id_given_by_the_submitting_laboratory", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" }, - "Authors": { - "name": "Authors", + "authors": { + "name": "authors", "description": "a comma separated list of Authors with complete First followed by Last Name", "title": "Authors", "from_schema": "https://example.com/GISAID", "rank": 28, - "alias": "Authors", + "alias": "authors", "owner": "GISAID", + "domain_of": [ + "GISAID" + ], "slot_group": "GISAID Submission Form", "range": "WhitespaceMinimizedString" } } } }, - "source_file": "schema.yaml", "settings": { "Title_Case": { "setting_key": "Title_Case", @@ -836,4 +1148,4 @@ } }, "@type": "SchemaDefinition" -} +} \ No newline at end of file diff --git a/web/templates/gisaid/schema.yaml b/web/templates/gisaid/schema.yaml index 8b8eec7d..7a509078 100644 --- a/web/templates/gisaid/schema.yaml +++ b/web/templates/gisaid/schema.yaml @@ -3,7 +3,7 @@ name: GISAID description: '' version: 1.0.0 imports: - - linkml:types +- linkml:types prefixes: linkml: https://w3id.org/linkml/ GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_ @@ -17,282 +17,276 @@ classes: description: Specification for GISAID virus biosample data gathering is_a: dh_interface slots: - - Submitter - - FASTA filename - - Virus name - - Type - - Passage details/history - - Collection date - - Location - - Additional location information - - Host - - Additional host information - - Sampling Strategy - - Gender - - Patient age - - Patient status - - Specimen source - - Outbreak - - Last vaccinated - - Treatment - - Sequencing technology - - Assembly method - - Coverage - - Originating lab - - Address - - Sample ID given by the sample provider - - Submitting lab - - Address - - Sample ID given by the submitting laboratory - - Authors + - submitter + - fasta_filename + - virus_name + - type + - passage_details_history + - collection_date + - location + - additional_location_information + - host + - additional_host_information + - sampling_strategy + - gender + - patient_age + - patient_status + - specimen_source + - outbreak + - last_vaccinated + - treatment + - sequencing_technology + - assembly_method + - coverage + - originating_lab + - address + - sample_id_given_by_the_sample_provider + - submitting_lab + - address + - sample_id_given_by_the_submitting_laboratory + - authors slot_usage: - Submitter: + submitter: rank: 1 slot_group: GISAID Submission Form - FASTA filename: + fasta_filename: rank: 2 slot_group: GISAID Submission Form - Virus name: + virus_name: rank: 3 slot_group: GISAID Submission Form - Type: + type: rank: 4 slot_group: GISAID Submission Form - Passage details/history: + passage_details_history: rank: 5 slot_group: GISAID Submission Form - Collection date: + collection_date: rank: 6 slot_group: GISAID Submission Form - Location: + location: rank: 7 slot_group: GISAID Submission Form - Additional location information: + additional_location_information: rank: 8 slot_group: GISAID Submission Form - Host: + host: rank: 9 slot_group: GISAID Submission Form - Additional host information: + additional_host_information: rank: 10 slot_group: GISAID Submission Form - Sampling Strategy: + sampling_strategy: rank: 11 slot_group: GISAID Submission Form - Gender: + gender: rank: 12 slot_group: GISAID Submission Form - Patient age: + patient_age: rank: 13 slot_group: GISAID Submission Form - Patient status: + patient_status: rank: 14 slot_group: GISAID Submission Form - Specimen source: + specimen_source: rank: 15 slot_group: GISAID Submission Form - Outbreak: + outbreak: rank: 16 slot_group: GISAID Submission Form - Last vaccinated: + last_vaccinated: rank: 17 slot_group: GISAID Submission Form - Treatment: + treatment: rank: 18 slot_group: GISAID Submission Form - Sequencing technology: + sequencing_technology: rank: 19 slot_group: GISAID Submission Form - Assembly method: + assembly_method: rank: 20 slot_group: GISAID Submission Form - Coverage: + coverage: rank: 21 slot_group: GISAID Submission Form - Originating lab: + originating_lab: rank: 22 slot_group: GISAID Submission Form - Address: + address: rank: 26 slot_group: GISAID Submission Form - Sample ID given by the sample provider: + sample_id_given_by_the_sample_provider: rank: 24 slot_group: GISAID Submission Form - Submitting lab: + submitting_lab: rank: 25 slot_group: GISAID Submission Form - Sample ID given by the submitting laboratory: + sample_id_given_by_the_submitting_laboratory: rank: 27 slot_group: GISAID Submission Form - Authors: + authors: rank: 28 slot_group: GISAID Submission Form slots: - Submitter: - name: Submitter + submitter: + name: submitter title: Submitter description: enter your GISAID-Username range: WhitespaceMinimizedString required: true - FASTA filename: - name: FASTA filename + fasta_filename: + name: fasta_filename title: FASTA filename - description: - the filename that contains the sequence without path (e.g. all_sequences.fasta + description: the filename that contains the sequence without path (e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta) range: WhitespaceMinimizedString required: true - Virus name: - name: Virus name + virus_name: + name: virus_name title: Virus name - description: - e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header + description: e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta) range: WhitespaceMinimizedString required: true - Type: - name: Type + type: + name: type title: Type description: default must remain "betacoronavirus" - range: Type menu + range: TypeMenu required: true - Passage details/history: - name: Passage details/history + passage_details_history: + name: passage_details_history title: Passage details/history description: e.g. Original, Vero range: WhitespaceMinimizedString required: true - Collection date: - name: Collection date + collection_date: + name: collection_date title: Collection date description: Date in the format YYYY or YYYY-MM or YYYY-MM-DD range: WhitespaceMinimizedString required: true - Location: - name: Location + location: + name: location title: Location description: e.g. Europe / Germany / Bavaria / Munich range: WhitespaceMinimizedString required: true - Additional location information: - name: Additional location information + additional_location_information: + name: additional_location_information title: Additional location information description: e.g. Cruise Ship, Convention, Live animal market range: WhitespaceMinimizedString - Host: - name: Host + host: + name: host title: Host - description: - e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, + description: e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc range: WhitespaceMinimizedString required: true - Additional host information: - name: Additional host information + additional_host_information: + name: additional_host_information title: Additional host information description: "e.g. Patient infected while traveling in \u2026." range: WhitespaceMinimizedString - Sampling Strategy: - name: Sampling Strategy + sampling_strategy: + name: sampling_strategy title: Sampling Strategy - description: - e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel + description: e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout range: WhitespaceMinimizedString - Gender: - name: Gender + gender: + name: gender title: Gender description: Male, Female, or unknown range: WhitespaceMinimizedString required: true - Patient age: - name: Patient age + patient_age: + name: patient_age title: Patient age description: e.g. 65 or 7 months, or unknown range: WhitespaceMinimizedString required: true - Patient status: - name: Patient status + patient_status: + name: patient_status title: Patient status description: e.g. Hospitalized, Released, Live, Deceased, or unknown range: WhitespaceMinimizedString required: true - Specimen source: - name: Specimen source + specimen_source: + name: specimen_source title: Specimen source - description: - e.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal + description: e.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other range: WhitespaceMinimizedString - Outbreak: - name: Outbreak + outbreak: + name: outbreak title: Outbreak description: Date, Location e.g. type of gathering, Family cluster, etc. range: WhitespaceMinimizedString - Last vaccinated: - name: Last vaccinated + last_vaccinated: + name: last_vaccinated title: Last vaccinated description: provide details if applicable range: WhitespaceMinimizedString - Treatment: - name: Treatment + treatment: + name: treatment title: Treatment description: Include drug name, dosage range: WhitespaceMinimizedString - Sequencing technology: - name: Sequencing technology + sequencing_technology: + name: sequencing_technology title: Sequencing technology description: e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc. range: WhitespaceMinimizedString required: true - Assembly method: - name: Assembly method + assembly_method: + name: assembly_method title: Assembly method - description: - e.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, + description: e.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc. range: WhitespaceMinimizedString - Coverage: - name: Coverage + coverage: + name: coverage title: Coverage description: e.g. 70x, 1,000x, 10,000x (average) range: WhitespaceMinimizedString - Originating lab: - name: Originating lab + originating_lab: + name: originating_lab title: Originating lab description: Where the clinical specimen or virus isolate was first obtained range: WhitespaceMinimizedString required: true - Address: - name: Address + address: + name: address title: Address range: WhitespaceMinimizedString required: true - Sample ID given by the sample provider: - name: Sample ID given by the sample provider + sample_id_given_by_the_sample_provider: + name: sample_id_given_by_the_sample_provider title: Sample ID given by the sample provider range: WhitespaceMinimizedString - Submitting lab: - name: Submitting lab + submitting_lab: + name: submitting_lab title: Submitting lab description: Where sequence data have been generated and submitted to GISAID range: WhitespaceMinimizedString required: true - Sample ID given by the submitting laboratory: - name: Sample ID given by the submitting laboratory + sample_id_given_by_the_submitting_laboratory: + name: sample_id_given_by_the_submitting_laboratory title: Sample ID given by the submitting laboratory range: WhitespaceMinimizedString - Authors: - name: Authors + authors: + name: authors title: Authors - description: - a comma separated list of Authors with complete First followed by + description: a comma separated list of Authors with complete First followed by Last Name range: WhitespaceMinimizedString enums: - Type menu: - name: Type menu + TypeMenu: + name: TypeMenu + title: Type menu permissible_values: betacoronavirus: text: betacoronavirus @@ -300,8 +294,7 @@ types: WhitespaceMinimizedString: name: WhitespaceMinimizedString typeof: string - description: - 'A string that has all whitespace trimmed off of beginning and end, + description: 'A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).' base: str @@ -309,8 +302,7 @@ types: Provenance: name: Provenance typeof: string - description: - A field containing a DataHarmonizer versioning marker. It is issued + description: A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data. base: str uri: xsd:token diff --git a/web/templates/gisaid/schema_enums.tsv b/web/templates/gisaid/schema_enums.tsv index 69d6b621..99564dfc 100644 --- a/web/templates/gisaid/schema_enums.tsv +++ b/web/templates/gisaid/schema_enums.tsv @@ -1,3 +1,4 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description - -Type menu betacoronavirus \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description + +Type menu TypeMenu betacoronavirus + \ No newline at end of file diff --git a/web/templates/gisaid/schema_slots.tsv b/web/templates/gisaid/schema_slots.tsv index 63d64e4d..3d5a8c8f 100644 --- a/web/templates/gisaid/schema_slots.tsv +++ b/web/templates/gisaid/schema_slots.tsv @@ -1,32 +1,32 @@ class_name slot_group slot_uri title name range range_2 identifier required recommended multivalued minimum_value maximum_value pattern structured_pattern description comments examples -GISAID GISAID Submission Form Submitter WhitespaceMinimizedString TRUE enter your GISAID-Username - GISAID Submission Form FASTA filename WhitespaceMinimizedString TRUE the filename that contains the sequence without path (e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta) - GISAID Submission Form Virus name WhitespaceMinimizedString TRUE e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta) - GISAID Submission Form Type Type menu TRUE default must remain "betacoronavirus" - GISAID Submission Form Passage details/history WhitespaceMinimizedString TRUE e.g. Original, Vero - GISAID Submission Form Collection date WhitespaceMinimizedString TRUE Date in the format YYYY or YYYY-MM or YYYY-MM-DD - GISAID Submission Form Location WhitespaceMinimizedString TRUE e.g. Europe / Germany / Bavaria / Munich - GISAID Submission Form Additional location information WhitespaceMinimizedString e.g. Cruise Ship, Convention, Live animal market - GISAID Submission Form Host WhitespaceMinimizedString TRUE e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc - GISAID Submission Form Additional host information WhitespaceMinimizedString e.g. Patient infected while traveling in …. - GISAID Submission Form Sampling Strategy WhitespaceMinimizedString e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout - GISAID Submission Form Gender WhitespaceMinimizedString TRUE Male, Female, or unknown - GISAID Submission Form Patient age WhitespaceMinimizedString TRUE e.g. 65 or 7 months, or unknown - GISAID Submission Form Patient status WhitespaceMinimizedString TRUE e.g. Hospitalized, Released, Live, Deceased, or unknown - GISAID Submission Form Specimen source WhitespaceMinimizedString e.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other - GISAID Submission Form Outbreak WhitespaceMinimizedString Date, Location e.g. type of gathering, Family cluster, etc. - GISAID Submission Form Last vaccinated WhitespaceMinimizedString provide details if applicable - GISAID Submission Form Treatment WhitespaceMinimizedString Include drug name, dosage - GISAID Submission Form Sequencing technology WhitespaceMinimizedString TRUE e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc. - GISAID Submission Form Assembly method WhitespaceMinimizedString e.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc. - GISAID Submission Form Coverage WhitespaceMinimizedString e.g. 70x, 1,000x, 10,000x (average) - GISAID Submission Form Originating lab WhitespaceMinimizedString TRUE Where the clinical specimen or virus isolate was first obtained - GISAID Submission Form Address WhitespaceMinimizedString TRUE - GISAID Submission Form Sample ID given by the sample provider WhitespaceMinimizedString - GISAID Submission Form Submitting lab WhitespaceMinimizedString TRUE Where sequence data have been generated and submitted to GISAID - GISAID Submission Form Address WhitespaceMinimizedString TRUE - GISAID Submission Form Sample ID given by the submitting laboratory WhitespaceMinimizedString - GISAID Submission Form Authors WhitespaceMinimizedString a comma separated list of Authors with complete First followed by Last Name +GISAID GISAID Submission Form Submitter submitter WhitespaceMinimizedString TRUE enter your GISAID-Username + GISAID Submission Form FASTA filename fasta_filename WhitespaceMinimizedString TRUE the filename that contains the sequence without path (e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta) + GISAID Submission Form Virus name virus_name WhitespaceMinimizedString TRUE e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta) + GISAID Submission Form Type type TypeMenu TRUE default must remain "betacoronavirus" + GISAID Submission Form Passage details/history passage_details_history WhitespaceMinimizedString TRUE e.g. Original, Vero + GISAID Submission Form Collection date collection_date WhitespaceMinimizedString TRUE Date in the format YYYY or YYYY-MM or YYYY-MM-DD + GISAID Submission Form Location location WhitespaceMinimizedString TRUE e.g. Europe / Germany / Bavaria / Munich + GISAID Submission Form Additional location information additional_location_information WhitespaceMinimizedString e.g. Cruise Ship, Convention, Live animal market + GISAID Submission Form Host host WhitespaceMinimizedString TRUE e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc + GISAID Submission Form Additional host information additional_host_information WhitespaceMinimizedString e.g. Patient infected while traveling in …. + GISAID Submission Form Sampling Strategy sampling_strategy WhitespaceMinimizedString e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout + GISAID Submission Form Gender gender WhitespaceMinimizedString TRUE Male, Female, or unknown + GISAID Submission Form Patient age patient_age WhitespaceMinimizedString TRUE e.g. 65 or 7 months, or unknown + GISAID Submission Form Patient status patient_status WhitespaceMinimizedString TRUE e.g. Hospitalized, Released, Live, Deceased, or unknown + GISAID Submission Form Specimen source specimen_source WhitespaceMinimizedString e.g. Sputum, Alveolar lavage fluid, Oro-pharyngeal swab, Blood, Tracheal swab, Urine, Stool, Cloakal swab, Organ, Feces, Other + GISAID Submission Form Outbreak outbreak WhitespaceMinimizedString Date, Location e.g. type of gathering, Family cluster, etc. + GISAID Submission Form Last vaccinated last_vaccinated WhitespaceMinimizedString provide details if applicable + GISAID Submission Form Treatment treatment WhitespaceMinimizedString Include drug name, dosage + GISAID Submission Form Sequencing technology sequencing_technology WhitespaceMinimizedString TRUE e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc. + GISAID Submission Form Assembly method assembly_method WhitespaceMinimizedString e.g. CLC Genomics Workbench 12, Geneious 10.2.4, SPAdes/MEGAHIT v1.2.9, UGENE v. 33, etc. + GISAID Submission Form Coverage coverage WhitespaceMinimizedString e.g. 70x, 1,000x, 10,000x (average) + GISAID Submission Form Originating lab originating_lab WhitespaceMinimizedString TRUE Where the clinical specimen or virus isolate was first obtained + GISAID Submission Form Address address WhitespaceMinimizedString TRUE + GISAID Submission Form Sample ID given by the sample provider sample_id_given_by_the_sample_provider WhitespaceMinimizedString + GISAID Submission Form Submitting lab submitting_lab WhitespaceMinimizedString TRUE Where sequence data have been generated and submitted to GISAID + GISAID Submission Form Address address WhitespaceMinimizedString TRUE + GISAID Submission Form Sample ID given by the submitting laboratory sample_id_given_by_the_submitting_laboratory WhitespaceMinimizedString + GISAID Submission Form Authors authors WhitespaceMinimizedString a comma separated list of Authors with complete First followed by Last Name \ No newline at end of file From 2b6110138d951ab149b68b1d4477da41c3be57b5 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:16:07 -0700 Subject: [PATCH 85/96] grdi drop empty columns --- web/templates/grdi/schema_slots.tsv | 1594 +++++++++++++-------------- 1 file changed, 797 insertions(+), 797 deletions(-) diff --git a/web/templates/grdi/schema_slots.tsv b/web/templates/grdi/schema_slots.tsv index ee028ed4..50bd1f7c 100644 --- a/web/templates/grdi/schema_slots.tsv +++ b/web/templates/grdi/schema_slots.tsv @@ -1,6 +1,6 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM -GRDI GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_BIOSAMPLE EXPORT_NCBI_BIOSAMPLE_Enterics EXPORT_NCBI_ANTIBIOGRAM EXPORT_ENA_ANTIBIOGRAM +GRDI GENEPIO:0001150 Sample collection and processing + Sample collection and processing GENEPIO:0001123 sample_collector_sample_ID sample_collector_sample_id WhitespaceMinimizedString NullValueMenu TRUE TRUE The user-defined name for the sample. The sample_ID should represent the identifier assigned to the sample at time of collection, for which all the descriptive information applies. If the original sample_ID is unknown or cannot be provided, leave blank or provide a null value. ABCD123 sample_name sample_name sample_name/biosample_accession Sample collection and processing GENEPIO:0100427 alternative_sample_ID alternative_sample_id WhitespaceMinimizedString TRUE An alternative sample_ID assigned to the sample by another organization. """Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. Alternative sample IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA @@ -8,96 +8,96 @@ Agriculture and Agri-Food Canada: AAFC Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC -Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.""" ABCD1234[PHAC]; 12345rev[CFIA] - Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by - Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name - Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken - Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 - Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] - Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. - Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol - Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] - Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] - Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. - Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 - Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name - Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) - Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin - Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] - Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon - Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon - Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date Date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date - Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] - Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date Date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 - Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date Date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 - Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time Time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST - Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time Time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST - Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning - Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 - Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour - Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date Date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli - Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env - Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source - Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic - Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] - Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source - Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source - Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source - Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] - Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type - Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source - Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims - Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source - Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod - Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap - Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date Date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date - Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date Date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 - Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source - Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source - Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 - Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] - Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] - Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport - Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol - Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] - Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 - Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] - Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] - Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria - Environmental conditions and measurements - Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 - Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 - Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] - Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 - Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 - Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] - Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] - Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Rain [ENVO:01001564] - Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 - Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch - Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection - GENEPIO:0001268 Host information host_information - Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host - Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host - Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety - Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed - Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host - Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age - Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease - GENEPIO:0100453 Strain and isolation information strain_and_isolation_information - Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 - Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain - Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession +Multiple identifiers can be provided and separated by semi-colons. If the information is unknown or cannot be provided, leave blank or provide a null value.""" ABCD1234[PHAC]; 12345rev[CFIA] + Sample collection and processing GENEPIO:0001153 sample_collected_by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency, organization or institution with which the sample collector is affiliated. Provide the name of the agency, organization or institution that collected the sample in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] collected_by collected_by + Sample collection and processing GENEPIO:0100428 sample_collected_by_laboratory_name sample_collected_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the sample collector. Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sample collection and processing GENEPIO:0100429 sample_collection_project_name sample_collection_project_name WhitespaceMinimizedString The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Watershed Project (HA-120) project_name + Sample collection and processing GENEPIO:0100430 sample_plan_name sample_plan_name WhitespaceMinimizedString TRUE The name of the study design for a surveillance project. Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. National Microbiological Baseline Study in Broiler Chicken + Sample collection and processing GENEPIO:0100431 sample_plan_ID sample_plan_id WhitespaceMinimizedString TRUE The identifier of the study design for a surveillance project. Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. 2001_M205 + Sample collection and processing GENEPIO:0100432 sample_collector_contact_name sample_collector_contact_name WhitespaceMinimizedString The name or job title of the contact responsible for follow-up regarding the sample. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sample collection and processing GENEPIO:0001156 sample_collector_contact_email sample_collector_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sample. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Sample collection and processing GENEPIO:0001198 purpose_of_sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Surveillance [GENEPIO:0100004] purpose_of_sampling purpose_of_sampling + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The experimental activities or variables that affected the sample collected. If there was experimental activity that would affect the sample prior to collection (this is different than sample processing), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Antimicrobial pre-treatment [GENEPIO:0100537] + Sample collection and processing GENEPIO:0100434 presampling_activity_details presampling_activity_details WhitespaceMinimizedString The details of the experimental activities or variables that affected the sample collected. Briefly describe the experimental details using free text. Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. + Sample collection and processing GENEPIO:0101029 experimental_protocol_field experimental_protocol_field WhitespaceMinimizedString The name of the overarching experimental methodology that was used to process the biomaterial. Provide the name of the methodology used in your study. If available, provide a link to the protocol. OneHealth2024_protocol + Sample collection and processing GENEPIO:0100921 experimental_specimen_role_type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] + Sample collection and processing GENEPIO:0100435 specimen_processing specimen_processing SpecimenProcessingMenu NullValueMenu The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Samples pooled [OBI:0600016] + Sample collection and processing GENEPIO:0100311 specimen_processing_details specimen_processing_details WhitespaceMinimizedString The details of the processing applied to the sample during or after receiving the sample. Briefly describe the processes applied to the sample. 25 samples were pooled and further prepared as a single sample during library prep. + Sample collection and processing GENEPIO:0100939 nucleic acid extraction method nucleic_acid_extraction_method WhitespaceMinimizedString The process used to extract genomic material from a sample. Briefly describe the extraction method used. Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and Salmonella (4S)" method v4 found at https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-36wgq581ygk5/v4 + Sample collection and processing GENEPIO:0100772 nucleic acid extraction kit nucleic_acid_extraction_kit WhitespaceMinimizedString The kit used to extract genomic material from a sample Provide the name of the genomic extraction kit used. QIAamp PowerFecal Pro DNA Kit + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country of origin of the sample. Provide the name of the country where the sample was collected. Use the controlled vocabulary provided in the template pick list. If the information is unknown or cannot be provided, provide a null value. Canada [GAZ:00002560] geo_loc_name;geo_loc_name (country) geo_loc_name + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/region) geo_loc_name_state_province_region GeoLocNameStateProvinceRegionMenu NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the name of the province/state/region where the sample was collected. If the information is unknown or cannot be provided, provide a null value. British Columbia [GAZ:00002562] geo_loc_name;geo_loc_name (state/province/region) geo_loc_name + Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River geo_loc_name;geo_loc_name (site) + Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin + Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] + Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. If known, provide the degrees latitude. Do NOT simply provide latitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 38.98 N lat_lon + Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. If known, provide the degrees longitude. Do NOT simply provide longitude of the institution if this is not where the sample was collected, nor the centre of the city/region where the sample was collected as this falsely implicates an existing geographical location and creates data inaccuracies. If the information is unknown or cannot be provided, leave blank or provide a null value. 77.11 W lat_lon + Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date Date TRUE The date on which the sample was collected. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 sample collection date collection_date + Sample collection and processing GENEPIO:0001177 sample_collection_date_precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". day [UO:0000033] + Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date Date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 + Sample collection and processing GENEPIO:0100763 sample_processing_date sample_processing_date Date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 + Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time Time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST + Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time Time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST + Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning + Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 1900-01-03 + Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour + Sample collection and processing GENEPIO:0001179 sample_received_date sample_received_date Date The date on which the sample was received. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Sample collection and processing GENEPIO:0100439 original_sample_description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. RTE Prosciutto from deli + Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env + Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source + Sample collection and processing GENEPIO:0101197 environmental_material_constituent environmental_material_constituent WhitespaceMinimizedString The material constituents that comprise an environmental material e.g. lead, plastic, paper. If applicable, describe the material constituents for the environmental material. Multiple values can be provided, separated by a semi-colon. lead; plastic + Sample collection and processing GENEPIO:0100443 animal_or_plant_population animal_or_plant_population AnimalOrPlantPopulationMenu NullValueMenu TRUE TRUE The type of animal or plant population inhabiting an area. This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. Turkey [NCBITaxon:9103] + Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source + Sample collection and processing GENEPIO:0001216 body_product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. A body product is a substance produced by the body but meant to be excreted/secreted (i.e. not part of the body). If applicable, select the standardized term and ontology ID for the body product from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feces [UBERON:0001988]; Urine [UBERON:0001088] isolation_source;body_product host_body_product;isolation_source + Sample collection and processing GENEPIO:0001214 anatomical_part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. An anatomical part is a structure or location in the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Snout [UBERON:0006333] isolation_source;anatomical_part isolation_source + Sample collection and processing GENEPIO:0100700 anatomical_region anatomical_region AnatomicalRegionMenu NullValueMenu TRUE TRUE A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. Dorso-lateral region [BSPO:0000080] + Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type + Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source + Sample collection and processing FOODON:03602001 label_claim label_claim LabelClaimMenu NullValueMenu TRUE The claim made by the label that relates to food processing, allergen information etc. Provide any characteristic of the food product, as described on the label only. Antibiotic free [FOODON:03601063] label_claims + Sample collection and processing GENEPIO:0100446 animal_source_of_food animal_source_of_food AnimalSourceOfFoodMenu NullValueMenu TRUE TRUE The animal from which the food product was derived. Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. Chicken [NCBITaxon:9031] food_source + Sample collection and processing GENEPIO:0100699 food_product_production_stream food_product_production_stream FoodProductProductionStreamMenu NullValueMenu A production pathway incorporating the processes, material entities (e.g. equipment, animals, locations), and conditions that participate in the generation of a food commodity. Provide the name of the agricultural production stream from the picklist. Beef cattle production stream [FOODON:03000452] food_prod + Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap + Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date Date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date + Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date Date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 + Sample collection and processing GENEPIO:0001234 collection_device collection_device CollectionDeviceMenu NullValueMenu TRUE The instrument or container used to collect the sample e.g. swab. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Drag swab [OBI:0002822] isolation_source;collection_device samp_collect_device;isolation_source + Sample collection and processing GENEPIO:0001241 collection_method collection_method CollectionMethodMenu NullValueMenu TRUE The process used to collect the sample e.g. phlebotomy, necropsy. If applicable, provide the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Rinsing for specimen collection [GENEPIO_0002116] isolation_source;collection_method isolation_source + Sample collection and processing GENEPIO:0100768 sample_volume_measurement_value sample_volume_measurement_value WhitespaceMinimizedString The numerical value of the volume measurement of the sample collected. Provide the numerical value of volume. 5 + Sample collection and processing GENEPIO:0100769 sample_volume_measurement_unit sample_volume_measurement_unit SampleVolumeMeasurementUnitMenu The units of the volume measurement of the sample collected. Provide the units from the pick list. milliliter (mL) [UO:0000098] + Sample collection and processing GENEPIO:0101090 residual_sample_status residual_sample_status ResidualSampleStatusMenu The status of the residual sample (whether any sample remains after its original use). Residual samples are samples that remain after the sample material was used for its original purpose. Select a residual sample status from the picklist. If sample still exists, select "Residual sample remaining (some sample left)". No residual sample (sample all used) [GENEPIO:0101088] + Sample collection and processing GENEPIO:0100448 sample_storage_method sample_storage_method WhitespaceMinimizedString A specification of the way that a specimen is or was stored. Provide a description of how the sample was stored. packed on ice during transport + Sample collection and processing GENEPIO:0100449 sample_storage_medium sample_storage_medium WhitespaceMinimizedString The material or matrix in which a sample is stored. Provide a description of the medium in which the sample was stored. PBS + 20% glycerol + Sample collection and processing GENEPIO:0101014 sample_storage_duration_value sample_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which a sample is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101015 sample_storage_duration_unit sample_storage_duration_unit SampleStorageDurationUnitMenu The units of a measured sample storage duration. Provide the units from the pick list. Day [UO:0000033] + Sample collection and processing GENEPIO:0101085 nucleic_acid_storage_duration_value nucleic_acid_storage_duration_value WhitespaceMinimizedString The numerical value of the time measurement during which the extracted nucleic acid is in storage. Provide the numerical value of time. 5 + Sample collection and processing GENEPIO:0101086 nucleic_acid_storage_duration_unit nucleic_acid_storage_duration_unit NucleicAcidStorageDurationUnitMenu The units of a measured extracted nucleic acid storage duration. Provide the units from the pick list. Year [UO:0000036] + Sample collection and processing GENEPIO:0100690 available_data_types available_data_types AvailableDataTypesMenu NullValueMenu TRUE The type of data that is available, that may or may not require permission to access. This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. Total coliform count [GENEPIO:0100729] + Sample collection and processing GENEPIO:0101023 available_data_type_details available_data_type_details WhitespaceMinimizedString Detailed information regarding other available data types. Use this field to provide free text details describing other available data types that may provide context for interpreting genomic sequence data. Pooled metagenomes containing extended spectrum beta-lactamase (ESBL) bacteria + Environmental conditions and measurements + Environmental conditions and measurements GENEPIO:0100440 water_depth water_depth WhitespaceMinimizedString The depth of some water. Provide the numerical depth only of water only (without units). 5 + Environmental conditions and measurements GENEPIO:0101025 water_depth_units water_depth_units WaterDepthUnitsMenu NullValueMenu The units of measurement for water depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100697 sediment_depth sediment_depth WhitespaceMinimizedString The depth of some sediment. Provide the numerical depth only of the sediment (without units). 2 + Environmental conditions and measurements GENEPIO:0101026 sediment_depth_units sediment_depth_units SedimentDepthUnitsMenu NullValueMenu The units of measurement for sediment depth. Provide the units of measurement for which the depth was recorded. meter (m) [UO:0000008] + Environmental conditions and measurements GENEPIO:0100441 air_temperature air_temperature WhitespaceMinimizedString The temperature of some air. Provide the numerical value for the temperature of the air (without units). 25 + Environmental conditions and measurements GENEPIO:0101027 air_temperature_units air_temperature_units AirTemperatureUnitsMenu NullValueMenu The units of measurement for air temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100698 water_temperature water_temperature WhitespaceMinimizedString The temperature of some water. Provide the numerical value for the temperature of the water (without units). 4 + Environmental conditions and measurements GENEPIO:0101028 water_temperature_units water_temperature_units WaterTemperatureUnitsMenu NullValueMenu The units of measurement for water temperature. Provide the units of measurement for which the temperature was recorded. degree Celsius (C) [UO:0000027] + Environmental conditions and measurements GENEPIO:0100779 sampling_weather_conditions sampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu TRUE The state of the atmosphere at a place and time as regards heat, dryness, sunshine, wind, rain, etc. Provide the weather conditions at the time of sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0100780 presampling_weather_conditions presampling_weather_conditions SamplingWeatherConditionsMenu NullValueMenu Weather conditions prior to collection that may affect the sample. Provide the weather conditions prior to sample collection. Rain [ENVO:01001564] + Environmental conditions and measurements GENEPIO:0100911 precipitation_measurement_value precipitation_measurement_value Whitespaceminimizedstring NullValueMenu The amount of water which has fallen during a precipitation process. Provide the quantity of precipitation in the area leading up to the time of sample collection. 12 + Environmental conditions and measurements GENEPIO:0100912 precipitation_measurement_unit precipitation_measurement_unit PrecipitationMeasurementUnitMenu NullValueMenu The units of measurement for the amount of water which has fallen during a precipitation process. Provide the units of precipitation by selecting a value from the pick list. inch + Environmental conditions and measurements GENEPIO:0100913 precipitation_measurement_method precipitation_measurement_method WhitespaceMinimizedString The process used to measure the amount of water which has fallen during a precipitation process. Provide the name of the procedure or method used to measure precipitation. Rain gauge over a 12 hour period prior to sample collection + GENEPIO:0001268 Host information host_information + Host information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, provide the common name. Cow [NCBITaxon:9913]; Chicken [NCBITaxon:9913], Human [NCBITaxon:9606] host + Host information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. If the sample is directly from a host, either a common or scientific name must be provided (although both can be included, if known). If known, select the scientific name from the picklist provided. Bos taurus [NCBITaxon:9913]; Homo sapiens [NCBITaxon:9103] host isolation_source;host + Host information GENEPIO:0100450 host (ecotype) host_ecotype WhitespaceMinimizedString The biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler. Provide the name of the ecotype of the host organism. Sea ecotype host_variety + Host information GENEPIO:0100451 host (breed) host_breed WhitespaceMinimizedString A breed is a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. Provide the name of the breed of the host organism. Holstein host_disease host_animal_breed + Host information GENEPIO:0100452 host (food production name) host_food_production_name HostFoodProductionNameMenu NullValueMenu The name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. Select the host's food production name from the pick list. Calf [FOODON:03411349] host + Host information GENEPIO:0001394 host_age_bin host_age_bin HostAgeBinMenu NullValueMenu Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value or leave blank. host_age + Host information GENEPIO:0001391 host_disease host_disease WhitespaceMinimizedString The name of the disease experienced by the host. This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”. mastitis, gastroenteritis host_disease + GENEPIO:0100453 Strain and isolation information strain_and_isolation_information + Strain and isolation information GENEPIO:0100454 microbiological_method microbiological_method WhitespaceMinimizedString TRUE The laboratory method used to grow, prepare, and/or isolate the microbial isolate. Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. MFHPB-30 + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString The strain identifier. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. K12 strain + Strain and isolation information GENEPIO:0100456 isolate_ID isolate_id WhitespaceMinimizedString NullValueMenu TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the isolate_ID created by the lab that first isolated the isolate (i.e. the original isolate ID). If the information is unknown or cannot be provided, leave blank or provide a null value. If only an alternate isolate ID is known (e.g. the ID from your lab, if your lab did not isolate the isolate from the original sample), make asure to include it in the alternative_isolate_ID field. SA20131043 strain sample_name/biosample_accession Strain and isolation information GENEPIO:0100457 alternative_isolate_ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. "Alternative isolate IDs should be provided in the in a prescribed format which consists of the ID followed by square brackets (no space in between the ID and bracket) containing the short form of ID provider’s agency name i.e. ID[short organization code]. Agency short forms include the following: Public Health Agency of Canada: PHAC Canadian Food Inspection Agency: CFIA @@ -106,707 +106,707 @@ Fisheries and Oceans Canada: DFO Environment and Climate Change Canada: ECCC Health Canada: HC An example of a properly formatted alternative_isolate_identifier would be e.g. XYZ4567[CFIA] -Multiple alternative isolate IDs can be provided, separated by semi-colons." GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias - Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 - Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 - Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 - Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Strain and isolation information GENEPIO:0100465 isolation_date isolation_date Date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date - Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 - Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism - Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] - Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument - Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar - Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 - Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 - GENEPIO:0001441 Sequence information sequence_information - Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 - Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by - Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca - Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing - Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) - Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] - Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] - Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] - Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT - Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 - Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] - Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel - Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 - Sequence information GENEPIO:0001449 amplicon size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 - Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 - Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no - Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz - Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz - Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 - Sequence information GENEPIO:0101715 genome sequence filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools - Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 - Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control - Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage - Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper - Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet - Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 - Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 - Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 - Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 - Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 - Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 - Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 - Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 - Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 - Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 - Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 - Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 - Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ Integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 - Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 - Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length Integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 - Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 - Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf - GENEPIO:0101082 Taxonomic identification information - Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat - Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 - Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon - Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 - Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc - Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date Date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 - Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 - GENEPIO:0100477 Public repository information public_repository_information - Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] - Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca - Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 - Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] - Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession - Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID - Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 - Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 - GENEPIO:0100478 Risk assessment information risk_assessment_information - Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples - Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. - Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] - Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention - Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed - GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance - Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] - Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab - Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager - Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca - Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date Date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 - Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units - Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform - Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF - Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 - Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. - Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 - Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 - Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file +Multiple alternative isolate IDs can be provided, separated by semi-colons." GHIF3456[PHAC]; QWICK222[CFIA] isolate_name_alias + Strain and isolation information GENEPIO:0100458 progeny_isolate_ID progeny_isolate_id WhitespaceMinimizedString The identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. SUB_ON_1526 + Strain and isolation information GENEPIO:0100459 IRIDA_isolate_ID irida_isolate_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the isolate in the IRIDA platform. Provide the "sample ID" used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. GRDI_LL_12345 + Strain and isolation information GENEPIO:0100460 IRIDA_project_ID irida_project_id WhitespaceMinimizedString NullValueMenu TRUE The identifier of the Project in the iRIDA platform. Provide the IRIDA "project ID". 666 + Strain and isolation information GENEPIO:0100461 isolated_by isolated_by IsolatedByMenu The name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] + Strain and isolation information GENEPIO:0100462 isolated_by_laboratory_name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Strain and isolation information GENEPIO:0100463 isolated_by_contact_name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Strain and isolation information GENEPIO:0100464 isolated_by_contact_email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Strain and isolation information GENEPIO:0100465 isolation_date isolation_date Date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 cult_isol_date + Strain and isolation information GENEPIO:0100466 isolate_received_date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 + Strain and isolation information GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. Note: If taxonomic identification was performed using metagenomic approaches, multiple organisms may be included. There is no need to list organisms detected as the result of noise in the data (only a few reads present). Only include organism names that you are confident are present. Also include the taxonomic mapping software and reference database(s) used. Salmonella enterica subsp. enterica [NCBITaxon:59201] organism organism + Strain and isolation information GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. PCR assay [OBI:0002740] + Strain and isolation information GENEPIO:0100584 taxonomic_identification_process_details taxonomic_identification_process_details WhitespaceMinimizedString The details of the process used to determine the taxonomic identification of an organism. Briefly describe the taxonomic identififcation method details using free text. Biolog instrument + Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg serovar + Strain and isolation information GENEPIO:0100468 serotyping_method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 + Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 + GENEPIO:0001441 Sequence information sequence_information + Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 + Sequence information GENEPIO:0100416 sequenced_by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by + Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Sequence information GENEPIO:0100471 sequenced_by_contact_name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Sequence information GENEPIO:0100422 sequenced_by_contact_email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca + Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. Provide the reason for sequencing by selecting a value from the following pick list: Diagnostic testing, Surveillance, Monitoring, Clinical trial, Field experiment, Environmental testing. If the information is unknown or cannot be provided, leave blank or provide a null value. Research [GENEPIO:0100003] purpose_of_sequencing + Sequence information GENEPIO:0100472 sequencing_project_name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR-GRDI (PA-1356) + Sequence information GENEPIO:0100473 sequencing_platform sequencing_platform SequencingPlatformMenu NullValueMenu The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] + Sequence information GENEPIO:0001452 sequencing_instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] + Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] + Sequence information GENEPIO:0001450 library_preparation_kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT + Sequence information GENEPIO:0100843 DNA fragment length dna_fragment_length Integer The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 + Sequence information GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method Hybrid selection method (bait-capture) [GENEPIO:0001950] + Sequence information GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. Note: If bait-capture methods were used for enrichment, provide the panel name and version number (or a URL providing that information). enrichment was done using Twist's respiratory virus research panel: https://www.twistbioscience.com/products/ngs/fixed-panels/respiratory-virus-research-panel + Sequence information GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. artic v3 + Sequence information GENEPIO:0001449 amplicon size amplicon_size Integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300 + Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 + Sequence information GENEPIO:0001454 sequencing_protocol sequencing_protocol WhitespaceMinimizedString The protocol or method used for sequencing. Provide the name and version of the procedure or protocol used for sequencing. You can also provide a link to a protocol online. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w?version_warning=no + Sequence information GENEPIO:0001476 r1_fastq_filename r1_fastq_filename WhitespaceMinimizedString The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. ABC123_S1_L001_R1_001.fastq.gz + Sequence information GENEPIO:0001477 r2_fastq_filename r2_fastq_filename WhitespaceMinimizedString The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. ABC123_S1_L001_R2_001.fastq.gz + Sequence information GENEPIO:0001480 fast5_filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. batch1a_sequences.fast5 + Sequence information GENEPIO:0101715 genome sequence filename genome_sequence_filename WhitespaceMinimizedString The user-defined filename of the FASTA file. Provide the FASTA filename. pathogenassembly123.fasta + GENEPIO:0001457 Bioinformatics and QC metrics + Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools + Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 + Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control + Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage + Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString NullValueMenu TRUE The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Raw data processing can have a significant impact on data quality and how it can be used. Provide the names and version numbers of software used for trimming adaptors, quality filtering, etc (e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3), or a link to a GitHub protocol. Porechop 0.2.3 + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString NullValueMenu TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper + Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet + Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString NullValueMenu The name of the software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString NullValueMenu The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 + Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95 + Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400 + Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100 + Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 + Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced Integer The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 387566 + Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 + Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 + Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 + Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 + Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 + Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 + Bioinformatics and QC metrics GENEPIO:0100845 percent read contamination percent_read_contamination_ Integer The percent of the total number of reads identified as contamination (not belonging to the target organism) in a sequence dataset. Provide the percent contamination value (no need to include units). 2 + Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 + Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length Integer The length of the genome defined by the most common nucleotides at each position. Provide a numerical value (no need to include units). 38677 + Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_045512.2 + Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/ncov2019-artic-nf + GENEPIO:0101082 Taxonomic identification information + Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat + Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 + Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon + Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 + Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc + Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date Date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 + Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 + GENEPIO:0100477 Public repository information public_repository_information + Public repository information GENEPIO:0001159 sequence_submitted_by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Environment and Climate Change Canada (ECCC) [GENEPIO:0100555] + Public repository information GENEPIO:0100474 sequence_submitted_by_contact_name sequence_submitted_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Public repository information GENEPIO:0001165 sequence_submitted_by_contact_email sequence_submitted_by_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca + Public repository information GENEPIO:0100475 publication_ID publication_id WhitespaceMinimizedString The identifier for a publication. If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. PMID: 33205991 + Public repository information GENEPIO:0100476 attribute_package attribute_package AttributePackageMenu NullValueMenu The attribute package used to structure metadata in an INSDC BioSample. If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. Pathogen.env [GENEPIO:0100581] + Public repository information GENEPIO:0001136 bioproject_accession bioproject_accession WhitespaceMinimizedString The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 bioproject_accession bioproject_accession + Public repository information GENEPIO:0001139 biosample_accession biosample_accession WhitespaceMinimizedString The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, whileEMBL- EBI BioSamples will have the prefix SAMEA. SAMN14180202 bioSample_ID + Public repository information GENEPIO:0001142 SRA_accession sra_accession WhitespaceMinimizedString The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRR11177792 + Public repository information GENEPIO:0001145 GenBank_accession genbank_accession WhitespaceMinimizedString The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank/ENA/DDBJ submission. MN908947.3 + GENEPIO:0100478 Risk assessment information risk_assessment_information + Risk assessment information GENEPIO:0100480 prevalence_metrics prevalence_metrics WhitespaceMinimizedString TRUE Metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are " Number of total samples collected", "Number of positive samples", "Average count of hazard organism", "Average count of indicator organism". You do not need to provide the actual values, just indicate that the information is available. Number of total samples collected, Number of positive samples + Risk assessment information GENEPIO:0100481 prevalence_metrics_details prevalence_metrics_details WhitespaceMinimizedString TRUE The details pertaining to the prevalence metrics from a surveillance project. If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. + Risk assessment information GENEPIO:0100482 stage_of_production stage_of_production StageOfProductionMenu NullValueMenu TRUE The stage of food production. Provide the stage of food production as free text. Abattoir [ENVO:01000925] + Risk assessment information GENEPIO:0100483 experimental_intervention experimental_intervention ExperimentalInterventionMenu NullValueMenu TRUE TRUE The category of the experimental intervention applied in the food production system. In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. Vaccination [NCIT:C15346] upstream_intervention + Risk assessment information GENEPIO:0100484 experiment_intervention_details experiment_intervention_details WhitespaceMinimizedString TRUE The details of the experimental intervention applied in the food production system. If an experimental intervention was applied in the survey, provide details in this field as free text. 2% cranberry solution mixed in feed + GENEPIO:0100479 Antimicrobial resistance antimicrobial_resistance + Antimicrobial resistance GENEPIO:0100511 AMR_testing_by amr_testing_by AmrTestingByMenu NullValueMenu TRUE The name of the organization that performed the antimicrobial resistance testing. Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] + Antimicrobial resistance GENEPIO:0100512 AMR_testing_by_laboratory_name amr_testing_by_laboratory_name WhitespaceMinimizedString The name of the lab within the organization that performed the antimicrobial resistance testing. Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab + Antimicrobial resistance GENEPIO:0100513 AMR_testing_by_contact_name amr_testing_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager + Antimicrobial resistance GENEPIO:0100514 AMR_testing_by_contact_email amr_testing_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email of the individual or the individual's role in the organization that performed the antimicrobial resistance testing. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. johnnyblogs@lab.ca + Antimicrobial resistance GENEPIO:0100515 AMR_testing_date amr_testing_date Date The date the antimicrobial resistance testing was performed. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2022-04-03 + Antimicrobial resistance amikacin_resistance_phenotype amikacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amikacin_measurement amikacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amikacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amikacin_measurement_units amikacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amikacin_measurement_sign amikacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amikacin_laboratory_typing_method amikacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amikacin_laboratory_typing_platform amikacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amikacin_laboratory_typing_platform_version amikacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amikacin_vendor_name amikacin_vendor_name AntimicrobialVendorName NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amikacin_testing_standard amikacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance amikacin_testing_standard_version amikacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amikacin_testing_standard_details amikacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amikacin_susceptible_breakpoint amikacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amikacin_intermediate_breakpoint amikacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amikacin_resistant_breakpoint amikacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistance_phenotype amoxicillinclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement amoxicillinclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of amoxicillin-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_units amoxicillinclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance amoxicillin-clavulanic_acid_measurement_sign amoxicillinclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_method amoxicillinclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform amoxicillinclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance amoxicillin-clavulanic_acid_laboratory_typing_platform_version amoxicillinclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance amoxicillin-clavulanic_acid_vendor_name amoxicillinclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard amoxicillinclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_version amoxicillinclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance amoxicillin-clavulanic_acid_testing_standard_details amoxicillinclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance amoxicillin-clavulanic_acid_susceptible_breakpoint amoxicillinclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance amoxicillin-clavulanic_acid_intermediate_breakpoint amoxicillinclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance amoxicillin-clavulanic_acid_resistant_breakpoint amoxicillinclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ampicillin_resistance_phenotype ampicillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ampicillin_measurement ampicillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ampicillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ampicillin_measurement_units ampicillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ampicillin_measurement_sign ampicillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ampicillin_laboratory_typing_method ampicillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ampicillin_laboratory_typing_platform ampicillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ampicillin_laboratory_typing_platform_version ampicillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ampicillin_vendor_name ampicillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ampicillin_testing_standard ampicillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ampicillin_testing_standard_version ampicillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ampicillin_testing_standard_details ampicillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ampicillin_susceptible_breakpoint ampicillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ampicillin_intermediate_breakpoint ampicillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ampicillin_resistant_breakpoint ampicillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance azithromycin_resistance_phenotype azithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance azithromycin_measurement azithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of azithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance azithromycin_measurement_units azithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance azithromycin_measurement_sign azithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance azithromycin_laboratory_typing_method azithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance azithromycin_laboratory_typing_platform azithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance azithromycin_laboratory_typing_platform_version azithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance azithromycin_vendor_name azithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance azithromycin_testing_standard azithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance azithromycin_testing_standard_version azithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance azithromycin_testing_standard_details azithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance azithromycin_susceptible_breakpoint azithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance azithromycin_intermediate_breakpoint azithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance azithromycin_resistant_breakpoint azithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefazolin_resistance_phenotype cefazolin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefazolin_measurement cefazolin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefazolin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefazolin_measurement_units cefazolin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefazolin_measurement_sign cefazolin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefazolin_laboratory_typing_method cefazolin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefazolin_laboratory_typing_platform cefazolin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefazolin_laboratory_typing_platform_version cefazolin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefazolin_vendor_name cefazolin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefazolin_testing_standard cefazolin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefazolin_testing_standard_version cefazolin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefazolin_testing_standard_details cefazolin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefazolin_susceptible_breakpoint cefazolin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefazolin_intermediate_breakpoint cefazolin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefazolin_resistant_breakpoint cefazolin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefepime_resistance_phenotype cefepime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefepime_measurement cefepime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefepime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefepime_measurement_units cefepime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefepime_measurement_sign cefepime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefepime_laboratory_typing_method cefepime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefepime_laboratory_typing_platform cefepime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefepime_laboratory_typing_platform_version cefepime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefepime_vendor_name cefepime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefepime_testing_standard cefepime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefepime_testing_standard_version cefepime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefepime_testing_standard_details cefepime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefepime_susceptible_breakpoint cefepime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefepime_intermediate_breakpoint cefepime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefepime_resistant_breakpoint cefepime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime_resistance_phenotype cefotaxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime_measurement cefotaxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime_measurement_units cefotaxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime_measurement_sign cefotaxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime_laboratory_typing_method cefotaxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime_laboratory_typing_platform cefotaxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime_laboratory_typing_platform_version cefotaxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime_vendor_name cefotaxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime_testing_standard cefotaxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefotaxime_testing_standard_version cefotaxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime_testing_standard_details cefotaxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime_susceptible_breakpoint cefotaxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime_intermediate_breakpoint cefotaxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime_resistant_breakpoint cefotaxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistance_phenotype cefotaximeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement cefotaximeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefotaxime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_units cefotaximeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefotaxime-clavulanic_acid_measurement_sign cefotaximeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_method cefotaximeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform cefotaximeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefotaxime-clavulanic_acid_laboratory_typing_platform_version cefotaximeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefotaxime-clavulanic_acid_vendor_name cefotaximeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard cefotaximeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_version cefotaximeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefotaxime-clavulanic_acid_testing_standard_details cefotaximeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefotaxime-clavulanic_acid_susceptible_breakpoint cefotaximeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefotaxime-clavulanic_acid_intermediate_breakpoint cefotaximeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefotaxime-clavulanic_acid_resistant_breakpoint cefotaximeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefoxitin_resistance_phenotype cefoxitin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefoxitin_measurement cefoxitin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefoxitin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefoxitin_measurement_units cefoxitin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefoxitin_measurement_sign cefoxitin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefoxitin_laboratory_typing_method cefoxitin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefoxitin_laboratory_typing_platform cefoxitin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefoxitin_laboratory_typing_platform_version cefoxitin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefoxitin_vendor_name cefoxitin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefoxitin_testing_standard cefoxitin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefoxitin_testing_standard_version cefoxitin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefoxitin_testing_standard_details cefoxitin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefoxitin_susceptible_breakpoint cefoxitin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefoxitin_intermediate_breakpoint cefoxitin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefoxitin_resistant_breakpoint cefoxitin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cefpodoxime_resistance_phenotype cefpodoxime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cefpodoxime_measurement cefpodoxime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cefpodoxime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cefpodoxime_measurement_units cefpodoxime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cefpodoxime_measurement_sign cefpodoxime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cefpodoxime_laboratory_typing_method cefpodoxime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cefpodoxime_laboratory_typing_platform cefpodoxime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cefpodoxime_laboratory_typing_platform_version cefpodoxime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cefpodoxime_vendor_name cefpodoxime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cefpodoxime_testing_standard cefpodoxime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cefpodoxime_testing_standard_version cefpodoxime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cefpodoxime_testing_standard_details cefpodoxime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cefpodoxime_susceptible_breakpoint cefpodoxime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cefpodoxime_intermediate_breakpoint cefpodoxime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cefpodoxime_resistant_breakpoint cefpodoxime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime_resistance_phenotype ceftazidime_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime_measurement ceftazidime_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime_measurement_units ceftazidime_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime_measurement_sign ceftazidime_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime_laboratory_typing_method ceftazidime_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime_laboratory_typing_platform ceftazidime_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime_laboratory_typing_platform_version ceftazidime_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime_vendor_name ceftazidime_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime_testing_standard ceftazidime_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftazidime_testing_standard_version ceftazidime_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime_testing_standard_details ceftazidime_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime_susceptible_breakpoint ceftazidime_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime_intermediate_breakpoint ceftazidime_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime_resistant_breakpoint ceftazidime_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistance_phenotype ceftazidimeclavulanic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement ceftazidimeclavulanic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftazidime-clavulanic acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_units ceftazidimeclavulanic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftazidime-clavulanic_acid_measurement_sign ceftazidimeclavulanic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_method ceftazidimeclavulanic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform ceftazidimeclavulanic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftazidime-clavulanic_acid_laboratory_typing_platform_version ceftazidimeclavulanic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftazidime-clavulanic_acid_vendor_name ceftazidimeclavulanic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard ceftazidimeclavulanic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_version ceftazidimeclavulanic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftazidime-clavulanic_acid_testing_standard_details ceftazidimeclavulanic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftazidime-clavulanic_acid_susceptible_breakpoint ceftazidimeclavulanic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftazidime-clavulanic_acid_intermediate_breakpoint ceftazidimeclavulanic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftazidime-clavulanic_acid_resistant_breakpoint ceftazidimeclavulanic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftiofur_resistance_phenotype ceftiofur_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftiofur_measurement ceftiofur_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftiofur resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftiofur_measurement_units ceftiofur_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftiofur_measurement_sign ceftiofur_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftiofur_laboratory_typing_method ceftiofur_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftiofur_laboratory_typing_platform ceftiofur_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftiofur_laboratory_typing_platform_version ceftiofur_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftiofur_vendor_name ceftiofur_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftiofur_testing_standard ceftiofur_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftiofur_testing_standard_version ceftiofur_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftiofur_testing_standard_details ceftiofur_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftiofur_susceptible_breakpoint ceftiofur_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftiofur_intermediate_breakpoint ceftiofur_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftiofur_resistant_breakpoint ceftiofur_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ceftriaxone_resistance_phenotype ceftriaxone_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ceftriaxone_measurement ceftriaxone_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ceftriaxone resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ceftriaxone_measurement_units ceftriaxone_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ceftriaxone_measurement_sign ceftriaxone_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ceftriaxone_laboratory_typing_method ceftriaxone_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ceftriaxone_laboratory_typing_platform ceftriaxone_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ceftriaxone_laboratory_typing_platform_version ceftriaxone_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ceftriaxone_vendor_name ceftriaxone_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ceftriaxone_testing_standard ceftriaxone_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ceftriaxone_testing_standard_version ceftriaxone_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ceftriaxone_testing_standard_details ceftriaxone_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ceftriaxone_susceptible_breakpoint ceftriaxone_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ceftriaxone_intermediate_breakpoint ceftriaxone_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ceftriaxone_resistant_breakpoint ceftriaxone_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance cephalothin_resistance_phenotype cephalothin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance cephalothin_measurement cephalothin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of cephalothin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance cephalothin_measurement_units cephalothin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance cephalothin_measurement_sign cephalothin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance cephalothin_laboratory_typing_method cephalothin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance cephalothin_laboratory_typing_platform cephalothin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance cephalothin_laboratory_typing_platform_version cephalothin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance cephalothin_vendor_name cephalothin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance cephalothin_testing_standard cephalothin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance cephalothin_testing_standard_version cephalothin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance cephalothin_testing_standard_details cephalothin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance cephalothin_susceptible_breakpoint cephalothin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance cephalothin_intermediate_breakpoint cephalothin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance cephalothin_resistant_breakpoint cephalothin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance chloramphenicol_resistance_phenotype chloramphenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance chloramphenicol_measurement chloramphenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of chloramphenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance chloramphenicol_measurement_units chloramphenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance chloramphenicol_measurement_sign chloramphenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance chloramphenicol_laboratory_typing_method chloramphenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance chloramphenicol_laboratory_typing_platform chloramphenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance chloramphenicol_laboratory_typing_platform_version chloramphenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance chloramphenicol_vendor_name chloramphenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance chloramphenicol_testing_standard chloramphenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance chloramphenicol_testing_standard_version chloramphenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance chloramphenicol_testing_standard_details chloramphenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance chloramphenicol_susceptible_breakpoint chloramphenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance chloramphenicol_intermediate_breakpoint chloramphenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance chloramphenicol_resistant_breakpoint chloramphenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance ciprofloxacin_resistance_phenotype ciprofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance ciprofloxacin_measurement ciprofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of ciprofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance ciprofloxacin_measurement_units ciprofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance ciprofloxacin_measurement_sign ciprofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance ciprofloxacin_laboratory_typing_method ciprofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform ciprofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance ciprofloxacin_laboratory_typing_platform_version ciprofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance ciprofloxacin_vendor_name ciprofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance ciprofloxacin_testing_standard ciprofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance ciprofloxacin_testing_standard_version ciprofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance ciprofloxacin_testing_standard_details ciprofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance ciprofloxacin_susceptible_breakpoint ciprofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance ciprofloxacin_intermediate_breakpoint ciprofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance ciprofloxacin_resistant_breakpoint ciprofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance clindamycin_resistance_phenotype clindamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance clindamycin_measurement clindamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of clindamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance clindamycin_measurement_units clindamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance clindamycin_measurement_sign clindamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance clindamycin_laboratory_typing_method clindamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance clindamycin_laboratory_typing_platform clindamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance clindamycin_laboratory_typing_platform_version clindamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance clindamycin_vendor_name clindamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance clindamycin_testing_standard clindamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance clindamycin_testing_standard_version clindamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance clindamycin_testing_standard_details clindamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance clindamycin_susceptible_breakpoint clindamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance clindamycin_intermediate_breakpoint clindamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance clindamycin_resistant_breakpoint clindamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance doxycycline_resistance_phenotype doxycycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance doxycycline_measurement doxycycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of doxycycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance doxycycline_measurement_units doxycycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance doxycycline_measurement_sign doxycycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance doxycycline_laboratory_typing_method doxycycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance doxycycline_laboratory_typing_platform doxycycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance doxycycline_laboratory_typing_platform_version doxycycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance doxycycline_vendor_name doxycycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance doxycycline_testing_standard doxycycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance doxycycline_testing_standard_version doxycycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance doxycycline_testing_standard_details doxycycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance doxycycline_susceptible_breakpoint doxycycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance doxycycline_intermediate_breakpoint doxycycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance doxycycline_resistant_breakpoint doxycycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance enrofloxacin_resistance_phenotype enrofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance enrofloxacin_measurement enrofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of enrofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance enrofloxacin_measurement_units enrofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance enrofloxacin_measurement_sign enrofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance enrofloxacin_laboratory_typing_method enrofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance enrofloxacin_laboratory_typing_platform enrofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance enrofloxacin_laboratory_typing_platform_version enrofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance enrofloxacin_vendor_name enrofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance enrofloxacin_testing_standard enrofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance enrofloxacin_testing_standard_version enrofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance enrofloxacin_testing_standard_details enrofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance enrofloxacin_susceptible_breakpoint enrofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance enrofloxacin_intermediate_breakpoint enrofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance enrofloxacin_resistant_breakpoint enrofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance erythromycin_resistance_phenotype erythromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance erythromycin_measurement erythromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of erythromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance erythromycin_measurement_units erythromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance erythromycin_measurement_sign erythromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance erythromycin_laboratory_typing_method erythromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance erythromycin_laboratory_typing_platform erythromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance erythromycin_laboratory_typing_platform_version erythromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance erythromycin_vendor_name erythromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance erythromycin_testing_standard erythromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance erythromycin_testing_standard_version erythromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance erythromycin_testing_standard_details erythromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance erythromycin_susceptible_breakpoint erythromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance erythromycin_intermediate_breakpoint erythromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance erythromycin_resistant_breakpoint erythromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance florfenicol_resistance_phenotype florfenicol_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance florfenicol_measurement florfenicol_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of florfenicol resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance florfenicol_measurement_units florfenicol_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance florfenicol_measurement_sign florfenicol_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance florfenicol_laboratory_typing_method florfenicol_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance florfenicol_laboratory_typing_platform florfenicol_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance florfenicol_laboratory_typing_platform_version florfenicol_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance florfenicol_vendor_name florfenicol_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance florfenicol_testing_standard florfenicol_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance florfenicol_testing_standard_version florfenicol_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance florfenicol_testing_standard_details florfenicol_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance florfenicol_susceptible_breakpoint florfenicol_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance florfenicol_intermediate_breakpoint florfenicol_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance florfenicol_resistant_breakpoint florfenicol_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance gentamicin_resistance_phenotype gentamicin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance gentamicin_measurement gentamicin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of gentamicin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance gentamicin_measurement_units gentamicin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance gentamicin_measurement_sign gentamicin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance gentamicin_laboratory_typing_method gentamicin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance gentamicin_laboratory_typing_platform gentamicin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance gentamicin_laboratory_typing_platform_version gentamicin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance gentamicin_vendor_name gentamicin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance gentamicin_testing_standard gentamicin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance gentamicin_testing_standard_version gentamicin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance gentamicin_testing_standard_details gentamicin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance gentamicin_susceptible_breakpoint gentamicin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance gentamicin_intermediate_breakpoint gentamicin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance gentamicin_resistant_breakpoint gentamicin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance imipenem_resistance_phenotype imipenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance imipenem_measurement imipenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of imipenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance imipenem_measurement_units imipenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance imipenem_measurement_sign imipenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance imipenem_laboratory_typing_method imipenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance imipenem_laboratory_typing_platform imipenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance imipenem_laboratory_typing_platform_version imipenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance imipenem_vendor_name imipenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance imipenem_testing_standard imipenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance imipenem_testing_standard_version imipenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance imipenem_testing_standard_details imipenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance imipenem_susceptible_breakpoint imipenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance imipenem_intermediate_breakpoint imipenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance imipenem_resistant_breakpoint imipenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance kanamycin_resistance_phenotype kanamycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance kanamycin_measurement kanamycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of kanamycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance kanamycin_measurement_units kanamycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance kanamycin_measurement_sign kanamycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance kanamycin_laboratory_typing_method kanamycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance kanamycin_laboratory_typing_platform kanamycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance kanamycin_laboratory_typing_platform_version kanamycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance kanamycin_vendor_name kanamycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance kanamycin_testing_standard kanamycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance kanamycin_testing_standard_version kanamycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance kanamycin_testing_standard_details kanamycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance kanamycin_susceptible_breakpoint kanamycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance kanamycin_intermediate_breakpoint kanamycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance kanamycin_resistant_breakpoint kanamycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance levofloxacin_resistance_phenotype levofloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance levofloxacin_measurement levofloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of levofloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance levofloxacin_measurement_units levofloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance levofloxacin_measurement_sign levofloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance levofloxacin_laboratory_typing_method levofloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance levofloxacin_laboratory_typing_platform levofloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance levofloxacin_laboratory_typing_platform_version levofloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance levofloxacin_vendor_name levofloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance levofloxacin_testing_standard levofloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance levofloxacin_testing_standard_version levofloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance levofloxacin_testing_standard_details levofloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance levofloxacin_susceptible_breakpoint levofloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance levofloxacin_intermediate_breakpoint levofloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance levofloxacin_resistant_breakpoint levofloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance linezolid_resistance_phenotype linezolid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance linezolid_measurement linezolid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of linezolid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance linezolid_measurement_units linezolid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance linezolid_measurement_sign linezolid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance linezolid_laboratory_typing_method linezolid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance linezolid_laboratory_typing_platform linezolid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance linezolid_laboratory_typing_platform_version linezolid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance linezolid_vendor_name linezolid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance linezolid_testing_standard linezolid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance linezolid_testing_standard_version linezolid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance linezolid_testing_standard_details linezolid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance linezolid_susceptible_breakpoint linezolid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance linezolid_intermediate_breakpoint linezolid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance linezolid_resistant_breakpoint linezolid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance meropenem_resistance_phenotype meropenem_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance meropenem_measurement meropenem_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of meropenem resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance meropenem_measurement_units meropenem_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance meropenem_measurement_sign meropenem_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance meropenem_laboratory_typing_method meropenem_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance meropenem_laboratory_typing_platform meropenem_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance meropenem_laboratory_typing_platform_version meropenem_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance meropenem_vendor_name meropenem_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance meropenem_testing_standard meropenem_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance meropenem_testing_standard_version meropenem_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance meropenem_testing_standard_details meropenem_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance meropenem_susceptible_breakpoint meropenem_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance meropenem_intermediate_breakpoint meropenem_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance meropenem_resistant_breakpoint meropenem_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nalidixic_acid_resistance_phenotype nalidixic_acid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nalidixic_acid_measurement nalidixic_acid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nalidixic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nalidixic_acid_measurement_units nalidixic_acid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nalidixic_acid_measurement_sign nalidixic_acid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nalidixic_acid_laboratory_typing_method nalidixic_acid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform nalidixic_acid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nalidixic_acid_laboratory_typing_platform_version nalidixic_acid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nalidixic_acid_vendor_name nalidixic_acid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nalidixic_acid_testing_standard nalidixic_acid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance nalidixic_acid_testing_standard_version nalidixic_acid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nalidixic_acid_testing_standard_details nalidixic_acid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nalidixic_acid_susceptible_breakpoint nalidixic_acid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nalidixic_acid_intermediate_breakpoint nalidixic_acid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nalidixic_acid_resistant_breakpoint nalidixic_acid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance nitrofurantoin_resistance_phenotype nitrofurantoin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance nitrofurantoin_measurement nitrofurantoin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of nitrofurantoin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance nitrofurantoin_measurement_units nitrofurantoin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance nitrofurantoin_measurement_sign nitrofurantoin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance nitrofurantoin_laboratory_typing_method nitrofurantoin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform nitrofurantoin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance nitrofurantoin_laboratory_typing_platform_version nitrofurantoin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance nitrofurantoin_vendor_name nitrofurantoin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance nitrofurantoin_testing_standard nitrofurantoin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance nitrofurantoin_testing_standard_version nitrofurantoin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance nitrofurantoin_testing_standard_details nitrofurantoin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance nitrofurantoin_susceptible_breakpoint nitrofurantoin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance nitrofurantoin_intermediate_breakpoint nitrofurantoin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance nitrofurantoin_resistant_breakpoint nitrofurantoin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance norfloxacin_resistance_phenotype norfloxacin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance norfloxacin_measurement norfloxacin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of norfloxacin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance norfloxacin_measurement_units norfloxacin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance norfloxacin_measurement_sign norfloxacin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance norfloxacin_laboratory_typing_method norfloxacin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance norfloxacin_laboratory_typing_platform norfloxacin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance norfloxacin_laboratory_typing_platform_version norfloxacin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance norfloxacin_vendor_name norfloxacin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance norfloxacin_testing_standard norfloxacin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance norfloxacin_testing_standard_version norfloxacin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance norfloxacin_testing_standard_details norfloxacin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance norfloxacin_susceptible_breakpoint norfloxacin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance norfloxacin_intermediate_breakpoint norfloxacin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance norfloxacin_resistant_breakpoint norfloxacin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxolinic-acid_resistance_phenotype oxolinicacid_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxolinic-acid_measurement oxolinicacid_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxolinic-acid resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxolinic-acid_measurement_units oxolinicacid_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxolinic-acid_measurement_sign oxolinicacid_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxolinic-acid_laboratory_typing_method oxolinicacid_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform oxolinicacid_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxolinic-acid_laboratory_typing_platform_version oxolinicacid_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxolinic-acid_vendor_name oxolinicacid_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxolinic-acid_testing_standard oxolinicacid_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance oxolinic-acid_testing_standard_version oxolinicacid_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxolinic-acid_testing_standard_details oxolinicacid_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxolinic-acid_susceptible_breakpoint oxolinicacid_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxolinic-acid_intermediate_breakpoint oxolinicacid_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxolinic-acid_resistant_breakpoint oxolinicacid_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance oxytetracycline_resistance_phenotype oxytetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance oxytetracycline_measurement oxytetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of oxytetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance oxytetracycline_measurement_units oxytetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance oxytetracycline_measurement_sign oxytetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance oxytetracycline_laboratory_typing_method oxytetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance oxytetracycline_laboratory_typing_platform oxytetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance oxytetracycline_laboratory_typing_platform_version oxytetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance oxytetracycline_vendor_name oxytetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance oxytetracycline_testing_standard oxytetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance oxytetracycline_testing_standard_version oxytetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance oxytetracycline_testing_standard_details oxytetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance oxytetracycline_susceptible_breakpoint oxytetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance oxytetracycline_intermediate_breakpoint oxytetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance oxytetracycline_resistant_breakpoint oxytetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin_resistance_phenotype piperacillin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin_measurement piperacillin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin_measurement_units piperacillin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin_measurement_sign piperacillin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin_laboratory_typing_method piperacillin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin_laboratory_typing_platform piperacillin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin_laboratory_typing_platform_version piperacillin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin_vendor_name piperacillin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin_testing_standard piperacillin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance piperacillin_testing_standard_version piperacillin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin_testing_standard_details piperacillin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin_susceptible_breakpoint piperacillin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin_intermediate_breakpoint piperacillin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin_resistant_breakpoint piperacillin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance piperacillin-tazobactam_resistance_phenotype piperacillintazobactam_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance piperacillin-tazobactam_measurement piperacillintazobactam_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of piperacillin-tazobactam resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance piperacillin-tazobactam_measurement_units piperacillintazobactam_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance piperacillin-tazobactam_measurement_sign piperacillintazobactam_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_method piperacillintazobactam_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform piperacillintazobactam_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance piperacillin-tazobactam_laboratory_typing_platform_version piperacillintazobactam_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance piperacillin-tazobactam_vendor_name piperacillintazobactam_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance piperacillin-tazobactam_testing_standard piperacillintazobactam_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance piperacillin-tazobactam_testing_standard_version piperacillintazobactam_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance piperacillin-tazobactam_testing_standard_details piperacillintazobactam_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance piperacillin-tazobactam_susceptible_breakpoint piperacillintazobactam_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance piperacillin-tazobactam_intermediate_breakpoint piperacillintazobactam_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance piperacillin-tazobactam_resistant_breakpoint piperacillintazobactam_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance polymyxin-b_resistance_phenotype polymyxinb_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance polymyxin-b_measurement polymyxinb_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of polymyxin B resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance polymyxin-b_measurement_units polymyxinb_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance polymyxin-b_measurement_sign polymyxinb_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance polymyxin-b_laboratory_typing_method polymyxinb_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance polymyxin-b_laboratory_typing_platform polymyxinb_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance polymyxin-b_laboratory_typing_platform_version polymyxinb_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance polymyxin-b_vendor_name polymyxinb_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance polymyxin-b_testing_standard polymyxinb_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance polymyxin-b_testing_standard_version polymyxinb_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance polymyxin-b_testing_standard_details polymyxinb_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance polymyxin-b_susceptible_breakpoint polymyxinb_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance polymyxin-b_intermediate_breakpoint polymyxinb_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance polymyxin-b_resistant_breakpoint polymyxinb_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance quinupristin-dalfopristin_resistance_phenotype quinupristindalfopristin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance quinupristin-dalfopristin_measurement quinupristindalfopristin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of quinupristin-dalfopristin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance quinupristin-dalfopristin_measurement_units quinupristindalfopristin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance quinupristin-dalfopristin_measurement_sign quinupristindalfopristin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_method quinupristindalfopristin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform quinupristindalfopristin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance quinupristin-dalfopristin_laboratory_typing_platform_version quinupristindalfopristin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance quinupristin-dalfopristin_vendor_name quinupristindalfopristin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance quinupristin-dalfopristin_testing_standard quinupristindalfopristin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_version quinupristindalfopristin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance quinupristin-dalfopristin_testing_standard_details quinupristindalfopristin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance quinupristin-dalfopristin_susceptible_breakpoint quinupristindalfopristin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance quinupristin-dalfopristin_intermediate_breakpoint quinupristindalfopristin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance quinupristin-dalfopristin_resistant_breakpoint quinupristindalfopristin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance streptomycin_resistance_phenotype streptomycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance streptomycin_measurement streptomycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of streptomycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance streptomycin_measurement_units streptomycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance streptomycin_measurement_sign streptomycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance streptomycin_laboratory_typing_method streptomycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance streptomycin_laboratory_typing_platform streptomycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance streptomycin_laboratory_typing_platform_version streptomycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance streptomycin_vendor_name streptomycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance streptomycin_testing_standard streptomycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance streptomycin_testing_standard_version streptomycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance streptomycin_testing_standard_details streptomycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance streptomycin_susceptible_breakpoint streptomycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance streptomycin_intermediate_breakpoint streptomycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance streptomycin_resistant_breakpoint streptomycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance sulfisoxazole_resistance_phenotype sulfisoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance sulfisoxazole_measurement sulfisoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of sulfisoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance sulfisoxazole_measurement_units sulfisoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance sulfisoxazole_measurement_sign sulfisoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance sulfisoxazole_laboratory_typing_method sulfisoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform sulfisoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance sulfisoxazole_laboratory_typing_platform_version sulfisoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance sulfisoxazole_vendor_name sulfisoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance sulfisoxazole_testing_standard sulfisoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance sulfisoxazole_testing_standard_version sulfisoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance sulfisoxazole_testing_standard_details sulfisoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance sulfisoxazole_susceptible_breakpoint sulfisoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance sulfisoxazole_intermediate_breakpoint sulfisoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance sulfisoxazole_resistant_breakpoint sulfisoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance telithromycin_resistance_phenotype telithromycin_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance telithromycin_measurement telithromycin_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of telithromycin resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance telithromycin_measurement_units telithromycin_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance telithromycin_measurement_sign telithromycin_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance telithromycin_laboratory_typing_method telithromycin_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance telithromycin_laboratory_typing_platform telithromycin_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance telithromycin_laboratory_typing_platform_version telithromycin_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance telithromycin_vendor_name telithromycin_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance telithromycin_testing_standard telithromycin_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance telithromycin_testing_standard_version telithromycin_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance telithromycin_testing_standard_details telithromycin_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance telithromycin_susceptible_breakpoint telithromycin_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance telithromycin_intermediate_breakpoint telithromycin_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance telithromycin_resistant_breakpoint telithromycin_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tetracycline_resistance_phenotype tetracycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tetracycline_measurement tetracycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tetracycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tetracycline_measurement_units tetracycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tetracycline_measurement_sign tetracycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tetracycline_laboratory_typing_method tetracycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tetracycline_laboratory_typing_platform tetracycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tetracycline_laboratory_typing_platform_version tetracycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tetracycline_vendor_name tetracycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tetracycline_testing_standard tetracycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance tetracycline_testing_standard_version tetracycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tetracycline_testing_standard_details tetracycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tetracycline_susceptible_breakpoint tetracycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tetracycline_intermediate_breakpoint tetracycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tetracycline_resistant_breakpoint tetracycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance tigecycline_resistance_phenotype tigecycline_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance tigecycline_measurement tigecycline_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of tigecycline resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance tigecycline_measurement_units tigecycline_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance tigecycline_measurement_sign tigecycline_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance tigecycline_laboratory_typing_method tigecycline_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance tigecycline_laboratory_typing_platform tigecycline_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance tigecycline_laboratory_typing_platform_version tigecycline_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance tigecycline_vendor_name tigecycline_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance tigecycline_testing_standard tigecycline_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance tigecycline_testing_standard_version tigecycline_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance tigecycline_testing_standard_details tigecycline_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance tigecycline_susceptible_breakpoint tigecycline_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance tigecycline_intermediate_breakpoint tigecycline_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance tigecycline_resistant_breakpoint tigecycline_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistance_phenotype trimethoprimsulfamethoxazole_resistance_phenotype AntimicrobialPhenotypeMenu NullValueMenu TRUE The antimicrobial resistance phenotype, as determined by the antibiotic susceptibility measurement and testing standard for this antibiotic Select a phenotype from the pick list provided. Susceptible antimicrobial phenotype [ARO:3004302] resistance_phenotype + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement trimethoprimsulfamethoxazole_measurement WhitespaceMinimizedString NullValueMenu TRUE The measured value of trimethoprim-sulfamethoxazole resistance. This field should only contain a number (either an integer or a number with decimals). 4 measurement + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_units trimethoprimsulfamethoxazole_measurement_units AntimicrobialMeasurementUnitsMenu NullValueMenu TRUE The units of the antimicrobial resistance measurement. Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. ug/mL [UO:0000274] measurement_units + Antimicrobial resistance trimethoprim-sulfamethoxazole_measurement_sign trimethoprimsulfamethoxazole_measurement_sign AntimicrobialMeasurementSignMenu NullValueMenu TRUE The qualifier associated with the antimicrobial resistance measurement Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. greater than (>) [GENEPIO:0001006] measurement_sign + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_method trimethoprimsulfamethoxazole_laboratory_typing_method AntimicrobialLaboratoryTypingMethodMenu NullValueMenu The general method used for antimicrobial susceptibility testing. Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. Broth dilution [ARO:3004397] laboratory_typing_method + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform trimethoprimsulfamethoxazole_laboratory_typing_platform AntimicrobialLaboratoryTypingPlatformMenu NullValueMenu The brand/platform used for antimicrobial susceptibility testing. Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. Sensitire [ARO:3004402] laboratory_typing_platform + Antimicrobial resistance trimethoprim-sulfamethoxazole_laboratory_typing_platform_version trimethoprimsulfamethoxazole_laboratory_typing_platform_version WhitespaceMinimizedString The specific name and version of the plate, panel, or other platform used for antimicrobial susceptibility testing. Include any additional information about the antimicrobial susceptibility test such as the drug panel details. CMV3AGNF + Antimicrobial resistance trimethoprim-sulfamethoxazole_vendor_name trimethoprimsulfamethoxazole_vendor_name AntimicrobialVendorNameMenu NullValueMenu The name of the vendor of the testing platform used. Provide the full name of the company (avoid abbreviations). Sensititre vendor + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard trimethoprimsulfamethoxazole_testing_standard AntimicrobialTestingStandardMenu NullValueMenu TRUE The testing standard used for determination of resistance phenotype Select a testing standard from the pick list provided. Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] testing_standard + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_version trimethoprimsulfamethoxazole_testing_standard_version WhitespaceMinimizedString The version number associated with the testing standard used for determination of antimicrobial resistance phenotype. If applicable, include a version number for the testing standard used. If applicable, include a version number for the testing standard used. M100 + Antimicrobial resistance trimethoprim-sulfamethoxazole_testing_standard_details trimethoprimsulfamethoxazole_testing_standard_details WhitespaceMinimizedString Additional details associated with the testing standard used for determination of antimicrobial resistance phenotype This information may include the year or location where the testing standard was published. If not applicable, leave blank. 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. + Antimicrobial resistance trimethoprim-sulfamethoxazole_susceptible_breakpoint trimethoprimsulfamethoxazole_susceptible_breakpoint WhitespaceMinimizedString The maximum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “sensitive” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. 8 + Antimicrobial resistance trimethoprim-sulfamethoxazole_intermediate_breakpoint trimethoprimsulfamethoxazole_intermediate_breakpoint WhitespaceMinimizedString The intermediate measurement(s), in the units specified in the “AMR_measurement_units” field, where a sample would be considered to have an “intermediate” phenotype for this antimicrobial. 16 + Antimicrobial resistance trimethoprim-sulfamethoxazole_resistant_breakpoint trimethoprimsulfamethoxazole_resistant_breakpoint WhitespaceMinimizedString The minimum measurement, in the units specified in the “antibiotic_measurement_units” field, for a sample to be considered “resistant” to this antimicrobial. This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. 32 + GENEPIO:0001516 Contributor acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, GRDI v1.0.0 \ No newline at end of file From ebc885c41a05e467b551a170456a948577169cb2 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:19:20 -0700 Subject: [PATCH 86/96] AMBR update, normalizing names --- web/templates/ambr/schema.json | 2524 ++++++++++++++++++++------- web/templates/ambr/schema.yaml | 980 ++++++----- web/templates/ambr/schema_enums.tsv | 1044 +++++------ web/templates/ambr/schema_slots.tsv | 140 +- 4 files changed, 3021 insertions(+), 1667 deletions(-) diff --git a/web/templates/ambr/schema.json b/web/templates/ambr/schema.json index 0e70d212..2da20332 100644 --- a/web/templates/ambr/schema.json +++ b/web/templates/ambr/schema.json @@ -30,6 +30,7 @@ "WhitespaceMinimizedString": { "name": "WhitespaceMinimizedString", "description": "A string that has all whitespace trimmed off of beginning and end, and all internal whitespace segments reduced to single spaces. Whitespace includes #x9 (tab), #xA (linefeed), and #xD (carriage return).", + "from_schema": "https://example.com/AMBR", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -37,6 +38,7 @@ "Provenance": { "name": "Provenance", "description": "A field containing a DataHarmonizer versioning marker. It is issued by DataHarmonizer when validation is applied to a given row of data.", + "from_schema": "https://example.com/AMBR", "typeof": "string", "base": "str", "uri": "xsd:token" @@ -44,6 +46,10 @@ "string": { "name": "string", "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:Text" ], @@ -53,6 +59,10 @@ "integer": { "name": "integer", "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:Integer" ], @@ -62,6 +72,10 @@ "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:Boolean" ], @@ -72,6 +86,10 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:Float" ], @@ -81,6 +99,10 @@ "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], + "from_schema": "https://example.com/AMBR", "close_mappings": [ "schema:Float" ], @@ -90,6 +112,10 @@ "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], + "from_schema": "https://example.com/AMBR", "broad_mappings": [ "schema:Number" ], @@ -100,21 +126,25 @@ "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:Time" ], "base": "XSDTime", - "uri": "xsd:dateTime", + "uri": "xsd:time", "repr": "str" }, "date": { "name": "date", "description": "a date (year, month and day) in an idealized calendar", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:Date" ], @@ -125,6 +155,10 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], + "from_schema": "https://example.com/AMBR", "exact_mappings": [ "schema:DateTime" ], @@ -135,6 +169,10 @@ "date_or_datetime": { "name": "date_or_datetime", "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], + "from_schema": "https://example.com/AMBR", "base": "str", "uri": "linkml:DateOrDatetime", "repr": "str" @@ -142,6 +180,10 @@ "uriorcurie": { "name": "uriorcurie", "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], + "from_schema": "https://example.com/AMBR", "base": "URIorCURIE", "uri": "xsd:anyURI", "repr": "str" @@ -150,10 +192,14 @@ "name": "curie", "conforms_to": "https://www.w3.org/TR/curie/", "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], "comments": [ "in RDF serializations this MUST be expanded to a URI", "in non-RDF serializations MAY be serialized as the compact representation" ], + "from_schema": "https://example.com/AMBR", "base": "Curie", "uri": "xsd:string", "repr": "str" @@ -162,9 +208,13 @@ "name": "uri", "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], "comments": [ "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" ], + "from_schema": "https://example.com/AMBR", "close_mappings": [ "schema:URL" ], @@ -175,6 +225,10 @@ "ncname": { "name": "ncname", "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], + "from_schema": "https://example.com/AMBR", "base": "NCName", "uri": "xsd:string", "repr": "str" @@ -182,9 +236,13 @@ "objectidentifier": { "name": "objectidentifier", "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], "comments": [ - "Used for inheritence and type checking" + "Used for inheritance and type checking" ], + "from_schema": "https://example.com/AMBR", "base": "ElementIdentifier", "uri": "shex:iri", "repr": "str" @@ -192,14 +250,55 @@ "nodeidentifier": { "name": "nodeidentifier", "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], + "from_schema": "https://example.com/AMBR", "base": "NodeIdentifier", "uri": "shex:nonLiteral", "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/AMBR", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/AMBR", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/AMBR", + "base": "str", + "uri": "xsd:string", + "repr": "str" } }, "enums": { - "null value menu": { - "name": "null value menu", + "NullValueMenu": { + "name": "NullValueMenu", + "title": "null value menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Not Applicable": { @@ -224,8 +323,9 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Afghanistan": { @@ -1314,8 +1414,9 @@ } } }, - "geo_loc_name (site) menu": { - "name": "geo_loc_name (site) menu", + "GeoLocNameSiteMenu": { + "name": "GeoLocNameSiteMenu", + "title": "geo_loc_name (site) menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Banff National Park": { @@ -1346,8 +1447,9 @@ } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Cluster/Outbreak investigation": { @@ -1373,8 +1475,9 @@ } } }, - "anatomical material menu": { - "name": "anatomical material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical material menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Skin": { @@ -1396,8 +1499,9 @@ } } }, - "anatomical part menu": { - "name": "anatomical part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical part menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Animal body or body part": { @@ -1448,8 +1552,9 @@ } } }, - "body product menu": { - "name": "body product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body product menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Feces": { @@ -1458,8 +1563,9 @@ } } }, - "environmental material menu": { - "name": "environmental material menu", + "EnvironmentalMaterialMenu": { + "name": "EnvironmentalMaterialMenu", + "title": "environmental material menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Algal film": { @@ -1563,8 +1669,9 @@ } } }, - "environmental site menu": { - "name": "environmental site menu", + "EnvironmentalSiteMenu": { + "name": "EnvironmentalSiteMenu", + "title": "environmental site menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Bird bath": { @@ -1620,8 +1727,9 @@ } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Filter": { @@ -1638,8 +1746,9 @@ } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Biopsy": { @@ -1648,8 +1757,9 @@ } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Biological replicate": { @@ -1658,8 +1768,9 @@ } } }, - "incubation temperature unit menu": { - "name": "incubation temperature unit menu", + "IncubationTemperatureUnitMenu": { + "name": "IncubationTemperatureUnitMenu", + "title": "incubation temperature unit menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Degree Celsius": { @@ -1672,8 +1783,9 @@ } } }, - "isolation medium menu": { - "name": "isolation medium menu", + "IsolationMediumMenu": { + "name": "IsolationMediumMenu", + "title": "isolation medium menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "1/10 869": { @@ -1821,8 +1933,9 @@ } } }, - "taxonomic identification method menu": { - "name": "taxonomic identification method menu", + "TaxonomicIdentificationMethodMenu": { + "name": "TaxonomicIdentificationMethodMenu", + "title": "taxonomic identification method menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Whole genome sequencing assay": { @@ -1843,8 +1956,9 @@ } } }, - "taxonomic identification method details menu": { - "name": "taxonomic identification method details menu", + "TaxonomicIdentificationMethodDetailsMenu": { + "name": "TaxonomicIdentificationMethodDetailsMenu", + "title": "taxonomic identification method details menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database": { @@ -1861,8 +1975,9 @@ } } }, - "cellular respiration type menu": { - "name": "cellular respiration type menu", + "CellularRespirationTypeMenu": { + "name": "CellularRespirationTypeMenu", + "title": "cellular respiration type menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Aerobic respiration": { @@ -1875,8 +1990,9 @@ } } }, - "host (common name) menu": { - "name": "host (common name) menu", + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Horse": { @@ -1922,8 +2038,9 @@ } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Equus caballus": { @@ -1934,8 +2051,9 @@ } } }, - "host disease menu": { - "name": "host disease menu", + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host disease menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Colitis": { @@ -1963,8 +2081,9 @@ } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "Illumina": { @@ -2193,8 +2312,9 @@ } } }, - "amplicon pcr primer list menu": { - "name": "amplicon pcr primer list menu", + "AmpliconPcrPrimerListMenu": { + "name": "AmpliconPcrPrimerListMenu", + "title": "amplicon pcr primer list menu", "from_schema": "https://example.com/AMBR", "permissible_values": { "27F": { @@ -2237,8 +2357,8 @@ } }, "slots": { - "isolate ID": { - "name": "isolate ID", + "isolate_id": { + "name": "isolate_id", "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", "title": "isolate ID", "comments": [ @@ -2251,11 +2371,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100456", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "required": true }, - "alternative isolate ID": { - "name": "alternative isolate ID", + "alternative_isolate_id": { + "name": "alternative_isolate_id", "description": "An alternative isolate ID assigned to the isolate by another organization.", "title": "alternative isolate ID", "comments": [ @@ -2268,11 +2391,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100457", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -2286,10 +2412,14 @@ "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001123", "identifier": true, - "range": "WhitespaceMinimizedString" + "domain_of": [ + "AMBR" + ], + "range": "WhitespaceMinimizedString", + "required": true }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", "comments": [ @@ -2302,18 +2432,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "AMBR" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection project name": { - "name": "sample collection project name", + "sample_collection_project_name": { + "name": "sample_collection_project_name", "description": "The name of the project/initiative/program for which the sample was collected.", "title": "sample collection project name", "comments": [ @@ -2326,11 +2459,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100429", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "comments": [ @@ -2343,11 +2479,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", "comments": [ @@ -2360,10 +2499,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001158", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", "todos": [ @@ -2380,18 +2522,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "AMBR" + ], "recommended": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", "comments": [ @@ -2404,17 +2549,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001179", + "domain_of": [ + "AMBR" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", "comments": [ @@ -2427,18 +2575,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "AMBR" + ], "recommended": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", "comments": [ @@ -2451,18 +2602,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "AMBR" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city where the sample was collected.", "title": "geo_loc_name (city)", "comments": [ @@ -2475,10 +2629,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001189", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name (site)", "comments": [ @@ -2491,7 +2648,10 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100436", - "range": "geo_loc_name (site) menu" + "domain_of": [ + "AMBR" + ], + "range": "GeoLocNameSiteMenu" }, "organism": { "name": "organism", @@ -2507,18 +2667,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", "comments": [ @@ -2531,18 +2694,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "AMBR" + ], "recommended": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "comments": [ @@ -2555,18 +2721,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001200", + "domain_of": [ + "AMBR" + ], "recommended": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "original sample description": { - "name": "original sample description", + "original_sample_description": { + "name": "original_sample_description", "description": "The original sample description provided by the sample collector.", "title": "original sample description", "comments": [ @@ -2579,10 +2748,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100439", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", "comments": [ @@ -2595,19 +2767,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001211", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "anatomical material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", "comments": [ @@ -2620,19 +2795,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001214", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "anatomical part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", "comments": [ @@ -2645,19 +2823,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001216", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "body product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", "comments": [ @@ -2670,19 +2851,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001223", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "environmental material menu" + "range": "EnvironmentalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", "comments": [ @@ -2695,19 +2879,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001232", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "environmental site menu" + "range": "EnvironmentalSiteMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", "comments": [ @@ -2720,19 +2907,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001234", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", "comments": [ @@ -2745,19 +2935,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001241", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "collection method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", "comments": [ @@ -2770,10 +2963,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001243", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -2786,19 +2982,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001253", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "specimen processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -2811,6 +3010,9 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, "strain": { @@ -2827,18 +3029,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100455", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "taxonomic identification method": { - "name": "taxonomic identification method", + "taxonomic_identification_method": { + "name": "taxonomic_identification_method", "description": "The type of planned process by which an organismal entity is associated with a taxon or taxa.", "title": "taxonomic identification method", "comments": [ @@ -2851,18 +3056,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100583", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { - "range": "taxonomic identification method menu" + "range": "TaxonomicIdentificationMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "taxonomic identification method details": { - "name": "taxonomic identification method details", + "taxonomic_identification_method_details": { + "name": "taxonomic_identification_method_details", "description": "The details of the process used to determine the taxonomic identification of an organism.", "title": "taxonomic identification method details", "comments": [ @@ -2875,18 +3083,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100584", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { - "range": "taxonomic identification method details menu" + "range": "TaxonomicIdentificationMethodDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "incubation temperature value": { - "name": "incubation temperature value", + "incubation_temperature_value": { + "name": "incubation_temperature_value", "description": "An environmental datum specifying the temperature at which an organism or organisms were incubated for the purposes of growth on or in a particular medium.", "title": "incubation temperature value", "comments": [ @@ -2899,18 +3110,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100617", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "incubation temperature unit": { - "name": "incubation temperature unit", + "incubation_temperature_unit": { + "name": "incubation_temperature_unit", "description": "An environmental datum specifying the temperature unit at which an organism or organisms were incubated for the purposes of growth on or in a particular medium.", "title": "incubation temperature unit", "comments": [ @@ -2923,18 +3137,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100618", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { - "range": "incubation temperature unit menu" + "range": "IncubationTemperatureUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "isolation medium": { - "name": "isolation medium", + "isolation_medium": { + "name": "isolation_medium", "description": "An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment.", "title": "isolation medium", "comments": [ @@ -2947,18 +3164,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0002107", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { - "range": "isolation medium menu" + "range": "IsolationMediumMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "isolate storage location": { - "name": "isolate storage location", + "isolate_storage_location": { + "name": "isolate_storage_location", "description": "An isolate datum specifying the location of where an isolate is stored e.g. in a particular freezer, on a particular shelf", "title": "isolate storage location", "comments": [ @@ -2971,11 +3191,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100619", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "required": true }, - "cellular respiration type": { - "name": "cellular respiration type", + "cellular_respiration_type": { + "name": "cellular_respiration_type", "description": "An isolate datum specifying the type of cellular respiration process used by the organism.", "title": "cellular respiration type", "comments": [ @@ -2988,18 +3211,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100620", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { - "range": "cellular respiration type menu" + "range": "CellularRespirationTypeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", "comments": [ @@ -3012,18 +3238,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", "comments": [ @@ -3036,17 +3265,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "AMBR" + ], "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", "comments": [ @@ -3059,17 +3291,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "AMBR" + ], "any_of": [ { - "range": "host disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", "title": "sequenced by", "comments": [ @@ -3082,17 +3317,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "AMBR" + ], "any_of": [ { - "range": "sequenced_by menu" + "range": "SequencedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequenced by laboratory name": { - "name": "sequenced by laboratory name", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", "title": "sequenced by laboratory name", "comments": [ @@ -3105,10 +3343,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100470", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact name", "comments": [ @@ -3121,10 +3362,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100471", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", "comments": [ @@ -3137,10 +3381,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100422", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", "comments": [ @@ -3153,17 +3400,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001445", + "domain_of": [ + "AMBR" + ], "any_of": [ { - "range": "purpose of sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "comments": [ @@ -3176,22 +3426,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "AMBR" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", - "todos": [ - ">={sample_collection_date}" - ], "comments": [ "The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -3202,17 +3452,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "AMBR" + ], "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", "comments": [ @@ -3225,10 +3478,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001448", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", "comments": [ @@ -3241,19 +3497,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001452", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "sequencing instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "description": "The name and version number of the sequencing protocol used.", "title": "sequencing protocol name", "comments": [ @@ -3266,11 +3525,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001453", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon pcr primer list": { - "name": "amplicon pcr primer list", + "amplicon_pcr_primer_list": { + "name": "amplicon_pcr_primer_list", "description": "An information content entity specifying a list of primers used for amplicon sequencing.", "title": "amplicon pcr primer list", "comments": [ @@ -3286,19 +3548,22 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100623", - "multivalued": true, + "domain_of": [ + "AMBR" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "amplicon pcr primer list menu" + "range": "AmpliconPcrPrimerListMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "input file name": { - "name": "input file name", + "input_file_name": { + "name": "input_file_name", "description": "The name of the file containing the sequence data to be analysed.", "title": "input file name", "comments": [ @@ -3311,10 +3576,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "OBI:0002874", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "reference accession": { - "name": "reference accession", + "reference_accession": { + "name": "reference_accession", "description": "An identifier that specifies an individual sequence record in a public sequence repository.", "title": "reference accession", "comments": [ @@ -3327,18 +3595,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "OBI:0002885", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "comments": [ @@ -3351,10 +3622,13 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, - "reference database name": { - "name": "reference database name", + "reference_database_name": { + "name": "reference_database_name", "description": "An identifier of a biological or bioinformatics database.", "title": "reference database name", "comments": [ @@ -3367,18 +3641,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "OBI:0002883", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "reference database version": { - "name": "reference database version", + "reference_database_version": { + "name": "reference_database_version", "description": "The version of the database containing the reference sequences used for analysis.", "title": "reference database version", "comments": [ @@ -3391,18 +3668,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "OBI:0002884", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "coverage (percentage)": { - "name": "coverage (percentage)", + "coverage_percentage": { + "name": "coverage_percentage", "description": "The percentage of the reference sequence covered by the sequence of interest.", "title": "coverage (percentage)", "comments": [ @@ -3415,18 +3695,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "OBI:0002880", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence identity percentage": { - "name": "sequence identity percentage", + "sequence_identity_percentage": { + "name": "sequence_identity_percentage", "description": "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.", "title": "sequence identity percentage", "comments": [ @@ -3439,18 +3722,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "OBI:0002882", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence identity (variance ratio)": { - "name": "sequence identity (variance ratio)", + "sequence_identity_variance_ratio": { + "name": "sequence_identity_variance_ratio", "description": "The ratio of the reference sequence not covered by the sequence of interest.", "title": "sequence identity (variance ratio)", "comments": [ @@ -3463,17 +3749,20 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100624", + "domain_of": [ + "AMBR" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "top-hit taxon determination": { - "name": "top-hit taxon determination", + "tophit_taxon_determination": { + "name": "tophit_taxon_determination", "description": "The taxon derived from the top hit in search results produced from a sequence similarity comparison.", "title": "top-hit taxon determination", "comments": [ @@ -3486,18 +3775,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100625", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "top-hit strain determination": { - "name": "top-hit strain determination", + "tophit_strain_determination": { + "name": "tophit_strain_determination", "description": "The strain designation derived from the top hit in search results produced from a sequence similarity comparison.", "title": "top-hit strain determination", "comments": [ @@ -3510,18 +3802,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100648", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "trimmed ribosomal gene sequence": { - "name": "trimmed ribosomal gene sequence", + "trimmed_ribosomal_gene_sequence": { + "name": "trimmed_ribosomal_gene_sequence", "description": "The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed to produce a trimmed ribosomal RNA sequence.", "title": "trimmed ribosomal gene sequence", "comments": [ @@ -3534,18 +3829,21 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100626", + "domain_of": [ + "AMBR" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "bioinformatics analysis details": { - "name": "bioinformatics analysis details", + "bioinformatics_analysis_details": { + "name": "bioinformatics_analysis_details", "description": "Any notes regarding the bioinformatics analysis.", "title": "bioinformatics analysis details", "comments": [ @@ -3558,6 +3856,9 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100627", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString" }, "authors": { @@ -3574,11 +3875,14 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "AMBR" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", "comments": [ @@ -3591,6 +3895,9 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "AMBR" + ], "range": "Provenance" } }, @@ -3606,68 +3913,68 @@ "from_schema": "https://example.com/AMBR", "is_a": "dh_interface", "slot_usage": { - "isolate ID": { - "name": "isolate ID", + "isolate_id": { + "name": "isolate_id", "rank": 1, "slot_group": "Database Identifiers" }, - "alternative isolate ID": { - "name": "alternative isolate ID", + "alternative_isolate_id": { + "name": "alternative_isolate_id", "rank": 2, "slot_group": "Database Identifiers" }, - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 3, "slot_group": "Database Identifiers" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 4, "slot_group": "Sample collection and processing" }, - "sample collection project name": { - "name": "sample collection project name", + "sample_collection_project_name": { + "name": "sample_collection_project_name", "rank": 5, "slot_group": "Sample collection and processing" }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "rank": 6, "slot_group": "Sample collection and processing" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "rank": 7, "slot_group": "Sample collection and processing" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "rank": 8, "slot_group": "Sample collection and processing" }, - "sample received date": { - "name": "sample received date", + "sample_received_date": { + "name": "sample_received_date", "rank": 9, "slot_group": "Sample collection and processing" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 10, "slot_group": "Sample collection and processing" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 11, "slot_group": "Sample collection and processing" }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "geo_loc_name_city": { + "name": "geo_loc_name_city", "rank": 12, "slot_group": "Sample collection and processing" }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 13, "slot_group": "Sample collection and processing" }, @@ -3676,68 +3983,68 @@ "rank": 14, "slot_group": "Sample collection and processing" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "rank": 15, "slot_group": "Sample collection and processing" }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "rank": 16, "slot_group": "Sample collection and processing" }, - "original sample description": { - "name": "original sample description", + "original_sample_description": { + "name": "original_sample_description", "rank": 17, "slot_group": "Sample collection and processing" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "rank": 18, "slot_group": "Sample collection and processing" }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "rank": 19, "slot_group": "Sample collection and processing" }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "rank": 20, "slot_group": "Sample collection and processing" }, - "environmental material": { - "name": "environmental material", + "environmental_material": { + "name": "environmental_material", "rank": 21, "slot_group": "Sample collection and processing" }, - "environmental site": { - "name": "environmental site", + "environmental_site": { + "name": "environmental_site", "rank": 22, "slot_group": "Sample collection and processing" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 23, "slot_group": "Sample collection and processing" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 24, "slot_group": "Sample collection and processing" }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "rank": 25, "slot_group": "Sample collection and processing" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "rank": 26, "slot_group": "Sample collection and processing" }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "rank": 27, "slot_group": "Sample collection and processing" }, @@ -3746,168 +4053,168 @@ "rank": 28, "slot_group": "Strain and isolation information" }, - "taxonomic identification method": { - "name": "taxonomic identification method", + "taxonomic_identification_method": { + "name": "taxonomic_identification_method", "rank": 29, "slot_group": "Strain and isolation information" }, - "taxonomic identification method details": { - "name": "taxonomic identification method details", + "taxonomic_identification_method_details": { + "name": "taxonomic_identification_method_details", "rank": 30, "slot_group": "Strain and isolation information" }, - "incubation temperature value": { - "name": "incubation temperature value", + "incubation_temperature_value": { + "name": "incubation_temperature_value", "rank": 31, "slot_group": "Strain and isolation information" }, - "incubation temperature unit": { - "name": "incubation temperature unit", + "incubation_temperature_unit": { + "name": "incubation_temperature_unit", "rank": 32, "slot_group": "Strain and isolation information" }, - "isolation medium": { - "name": "isolation medium", + "isolation_medium": { + "name": "isolation_medium", "rank": 33, "slot_group": "Strain and isolation information" }, - "isolate storage location": { - "name": "isolate storage location", + "isolate_storage_location": { + "name": "isolate_storage_location", "rank": 34, "slot_group": "Strain and isolation information" }, - "cellular respiration type": { - "name": "cellular respiration type", + "cellular_respiration_type": { + "name": "cellular_respiration_type", "rank": 35, "slot_group": "Strain and isolation information" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "rank": 36, "slot_group": "Host Information" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 37, "slot_group": "Host Information" }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "rank": 38, "slot_group": "Host Information" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "rank": 39, "slot_group": "Sequencing" }, - "sequenced by laboratory name": { - "name": "sequenced by laboratory name", + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", "rank": 40, "slot_group": "Sequencing" }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "rank": 41, "slot_group": "Sequencing" }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "rank": 42, "slot_group": "Sequencing" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 43, "slot_group": "Sequencing" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 44, "slot_group": "Sequencing" }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "rank": 45, "slot_group": "Sequencing" }, - "library ID": { - "name": "library ID", + "library_id": { + "name": "library_id", "rank": 46, "slot_group": "Sequencing" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 47, "slot_group": "Sequencing" }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "rank": 48, "slot_group": "Sequencing" }, - "amplicon pcr primer list": { - "name": "amplicon pcr primer list", + "amplicon_pcr_primer_list": { + "name": "amplicon_pcr_primer_list", "rank": 49, "slot_group": "Sequencing" }, - "input file name": { - "name": "input file name", + "input_file_name": { + "name": "input_file_name", "rank": 50, "slot_group": "Bioinformatics and QC metrics" }, - "reference accession": { - "name": "reference accession", + "reference_accession": { + "name": "reference_accession", "rank": 51, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 52, "slot_group": "Bioinformatics and QC metrics" }, - "reference database name": { - "name": "reference database name", + "reference_database_name": { + "name": "reference_database_name", "rank": 53, "slot_group": "Bioinformatics and QC metrics" }, - "reference database version": { - "name": "reference database version", + "reference_database_version": { + "name": "reference_database_version", "rank": 54, "slot_group": "Bioinformatics and QC metrics" }, - "coverage (percentage)": { - "name": "coverage (percentage)", + "coverage_percentage": { + "name": "coverage_percentage", "rank": 55, "slot_group": "Bioinformatics and QC metrics" }, - "sequence identity percentage": { - "name": "sequence identity percentage", + "sequence_identity_percentage": { + "name": "sequence_identity_percentage", "rank": 56, "slot_group": "Bioinformatics and QC metrics" }, - "sequence identity (variance ratio)": { - "name": "sequence identity (variance ratio)", + "sequence_identity_variance_ratio": { + "name": "sequence_identity_variance_ratio", "rank": 57, "slot_group": "Bioinformatics and QC metrics" }, - "top-hit taxon determination": { - "name": "top-hit taxon determination", + "tophit_taxon_determination": { + "name": "tophit_taxon_determination", "rank": 58, "slot_group": "Bioinformatics and QC metrics" }, - "top-hit strain determination": { - "name": "top-hit strain determination", + "tophit_strain_determination": { + "name": "tophit_strain_determination", "rank": 59, "slot_group": "Bioinformatics and QC metrics" }, - "trimmed ribosomal gene sequence": { - "name": "trimmed ribosomal gene sequence", + "trimmed_ribosomal_gene_sequence": { + "name": "trimmed_ribosomal_gene_sequence", "rank": 60, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics analysis details": { - "name": "bioinformatics analysis details", + "bioinformatics_analysis_details": { + "name": "bioinformatics_analysis_details", "rank": 61, "slot_group": "Bioinformatics and QC metrics" }, @@ -3916,346 +4223,775 @@ "rank": 62, "slot_group": "Contributor acknowledgement" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 63, "slot_group": "Contributor acknowledgement" } }, "attributes": { - "isolate ID": { - "name": "isolate ID", + "isolate_id": { + "name": "isolate_id", "description": "The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate.", "title": "isolate ID", + "comments": [ + "Provide the identifier created by the lab for the organism after isolation. This value maps to the \"Strain ID#\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "SA01" + } + ], "from_schema": "https://example.com/AMBR", "rank": 1, "slot_uri": "GENEPIO:0100456", - "alias": "isolate_ID", + "alias": "isolate_id", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "required": true }, - "alternative isolate ID": { - "name": "alternative isolate ID", + "alternative_isolate_id": { + "name": "alternative_isolate_id", "description": "An alternative isolate ID assigned to the isolate by another organization.", "title": "alternative isolate ID", + "comments": [ + "Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the \"Label ID\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "3411301" + } + ], "from_schema": "https://example.com/AMBR", "rank": 2, "slot_uri": "GENEPIO:0100457", - "alias": "alternative_isolate_ID", + "alias": "alternative_isolate_id", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString", "recommended": true }, - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", + "comments": [ + "Provide the sample ID provided by the original sample collector. This value is different from the \"isolate_ID\" as it represents the original material sampled rather than the organism that was isolated from the sampled material. This identifier may or may not be available." + ], + "examples": [ + { + "value": "Lake_Louise_Water23" + } + ], "from_schema": "https://example.com/AMBR", "rank": 3, "slot_uri": "GENEPIO:0001123", "identifier": true, - "alias": "specimen_collector_sample_ID", + "alias": "specimen_collector_sample_id", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", + "comments": [ + "The name of the institution of the original sample collector should be written out in full, (no abbreviations, with minor exceptions) and be consistent across multiple submissions e.g. University of Calgary, Alberta Health Services. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)." + ], + "examples": [ + { + "value": "University of Calgary" + } + ], "from_schema": "https://example.com/AMBR", "rank": 4, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "sample collection project name": { - "name": "sample collection project name", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_collection_project_name": { + "name": "sample_collection_project_name", "description": "The name of the project/initiative/program for which the sample was collected.", "title": "sample collection project name", + "comments": [ + "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Children's Hospital biofilm study (A3-701-01)" + } + ], "from_schema": "https://example.com/AMBR", "rank": 5, "slot_uri": "GENEPIO:0100429", "alias": "sample_collection_project_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString", "recommended": true }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/AMBR", "rank": 6, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sample collector contact address": { - "name": "sample collector contact address", + "sample_collector_contact_address": { + "name": "sample_collector_contact_address", "description": "The mailing address of the agency submitting the sample.", "title": "sample collector contact address", + "comments": [ + "The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country" + ], + "examples": [ + { + "value": "655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada" + } + ], "from_schema": "https://example.com/AMBR", "rank": 7, "slot_uri": "GENEPIO:0001158", "alias": "sample_collector_contact_address", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/AMBR", "rank": 8, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "sample received date": { - "name": "sample received date", + "recommended": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sample_received_date": { + "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "comments": [ + "The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-20" + } + ], "from_schema": "https://example.com/AMBR", "rank": 9, "slot_uri": "GENEPIO:0001179", "alias": "sample_received_date", "owner": "AMBR", - "slot_group": "Sample collection and processing" - }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "domain_of": [ + "AMBR" + ], + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", + "comments": [ + "Provide the country name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/AMBR", "rank": 10, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "alias": "geo_loc_name_country", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "recommended": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], "from_schema": "https://example.com/AMBR", "rank": 11, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "alias": "geo_loc_name_state_province_territory", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "geo_loc_name (city)": { - "name": "geo_loc_name (city)", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "geo_loc_name_city": { + "name": "geo_loc_name_city", "description": "The city where the sample was collected.", "title": "geo_loc_name (city)", + "comments": [ + "Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz" + ], + "examples": [ + { + "value": "Medicine Hat" + } + ], "from_schema": "https://example.com/AMBR", "rank": 12, "slot_uri": "GENEPIO:0001189", - "alias": "geo_loc_name_(city)", + "alias": "geo_loc_name_city", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name (site)": { - "name": "geo_loc_name (site)", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name (site)", + "comments": [ + "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing)." + ], + "examples": [ + { + "value": "Lake Louise" + } + ], "from_schema": "https://example.com/AMBR", "rank": 13, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_(site)", + "alias": "geo_loc_name_site", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "range": "geo_loc_name (site) menu" + "range": "GeoLocNameSiteMenu" }, "organism": { "name": "organism", "description": "Taxonomic name of the organism.", "title": "organism", + "comments": [ + "Provide the confirmed taxonomic name of the species. This value maps to the \"Recommended identification\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Staphylococcus aureus" + } + ], "from_schema": "https://example.com/AMBR", "rank": 14, "slot_uri": "GENEPIO:0001191", "alias": "organism", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "purpose of sampling": { - "name": "purpose of sampling", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field. Motivation for sampling may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Targeted surveillance" + } + ], "from_schema": "https://example.com/AMBR", "rank": 15, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "recommended": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", + "comments": [ + "Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular investigation/surveillance activity/research question. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "ProvLab/IPC routine monitoring" + } + ], "from_schema": "https://example.com/AMBR", "rank": 16, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "original sample description": { - "name": "original sample description", + "recommended": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "original_sample_description": { + "name": "original_sample_description", "description": "The original sample description provided by the sample collector.", "title": "original sample description", + "comments": [ + "Provide the sample description provided by the original sample collector or the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file. The original description is useful as it may provide further details, or can be used to clarify higher level classifications." + ], + "examples": [ + { + "value": "ACH coupons-water study, isolates 2010, 2011 see appendix 3 (Alberta Childrens Hospital)" + } + ], "from_schema": "https://example.com/AMBR", "rank": 17, "slot_uri": "GENEPIO:0100439", "alias": "original_sample_description", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Wound tissue (injury)" + } + ], "from_schema": "https://example.com/AMBR", "rank": 18, "slot_uri": "GENEPIO:0001211", - "multivalued": true, "alias": "anatomical_material", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "anatomical part": { - "name": "anatomical part", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Nasal cavity" + } + ], "from_schema": "https://example.com/AMBR", "rank": 19, "slot_uri": "GENEPIO:0001214", - "multivalued": true, "alias": "anatomical_part", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "body product": { - "name": "body product", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Feces" + } + ], "from_schema": "https://example.com/AMBR", "rank": 20, "slot_uri": "GENEPIO:0001216", - "multivalued": true, "alias": "body_product", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "environmental material": { - "name": "environmental material", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "environmental_material": { + "name": "environmental_material", "description": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage.", "title": "environmental material", + "comments": [ + "Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Bandage" + } + ], "from_schema": "https://example.com/AMBR", "rank": 21, "slot_uri": "GENEPIO:0001223", - "multivalued": true, "alias": "environmental_material", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "environmental site": { - "name": "environmental site", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "environmental_site": { + "name": "environmental_site", "description": "An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave.", "title": "environmental site", + "comments": [ + "Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Hospital" + } + ], "from_schema": "https://example.com/AMBR", "rank": 22, "slot_uri": "GENEPIO:0001232", - "multivalued": true, "alias": "environmental_site", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "collection device": { - "name": "collection device", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "EnvironmentalSiteMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", + "comments": [ + "Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Swab" + } + ], "from_schema": "https://example.com/AMBR", "rank": 23, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "collection method": { - "name": "collection method", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Biopsy" + } + ], "from_schema": "https://example.com/AMBR", "rank": 24, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "required": true - }, - "collection protocol": { - "name": "collection protocol", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", + "comments": [ + "Free text. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Collection_protocol_Children's Hospital biofilm study (A3-701-01)" + } + ], "from_schema": "https://example.com/AMBR", "rank": 25, "slot_uri": "GENEPIO:0001243", "alias": "collection_protocol", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "If multiple PCR products were generated from the isolate using different primer sets, indicate that the sequence records represents the same isolate by selecting \"Biological replicate\" in the \"specimen processing\" field. Every different sequence experiment should have its own record (i.e. if different amplicons have the same sequence but were generated using different primer sets, these should be stored as separate entries/lines in the spreadsheet). Information about replicates may be available in the \"Top-hit taxon (taxa)\" or \"Trimmed Ribosomal Sequence\" fields if there are multiple values for the same \"Strain ID#\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Biological replicate" + } + ], "from_schema": "https://example.com/AMBR", "rank": 26, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", - "recommended": true - }, - "specimen processing details": { - "name": "specimen processing details", + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample. Information about replicates may be available in the \"Top-hit taxon (taxa)\" or \"Trimmed Ribosomal Sequence\" fields if there are multiple values for the same \"Strain ID#\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Multiple amplicons generated for isolate SA32 using different primer sets" + } + ], "from_schema": "https://example.com/AMBR", "rank": 27, "slot_uri": "GENEPIO:0100311", "alias": "specimen_processing_details", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, @@ -4263,404 +4999,981 @@ "name": "strain", "description": "The strain identifier.", "title": "strain", + "comments": [ + "Provide the strain of the isolate. This value maps to the \"Strain\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "CL10" + } + ], "from_schema": "https://example.com/AMBR", "rank": 28, "slot_uri": "GENEPIO:0100455", "alias": "strain", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "taxonomic identification method": { - "name": "taxonomic identification method", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "taxonomic_identification_method": { + "name": "taxonomic_identification_method", "description": "The type of planned process by which an organismal entity is associated with a taxon or taxa.", "title": "taxonomic identification method", + "comments": [ + "Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. For the AMBR Project, the \"16S ribosomal gene sequencing assay\" value will be the most appropriate. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "16S ribosomal gene sequencing assay" + } + ], "from_schema": "https://example.com/AMBR", "rank": 29, "slot_uri": "GENEPIO:0100583", "alias": "taxonomic_identification_method", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "taxonomic identification method details": { - "name": "taxonomic identification method details", + "required": true, + "any_of": [ + { + "range": "TaxonomicIdentificationMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "taxonomic_identification_method_details": { + "name": "taxonomic_identification_method_details", "description": "The details of the process used to determine the taxonomic identification of an organism.", "title": "taxonomic identification method details", + "comments": [ + "Provide the criteria used for 16S sequencing taxonomic determination by selection a value from the pick list. These criteria are specific to the AMBR project and so do not correspond with standardized criteria in any ontology. The pick list is strictly for providing consistency in records rather than implementing community data standards. If another method was used for the taxonomic determination, leave blank. This value maps to the information stored in the \"ID Category*\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database" + } + ], "from_schema": "https://example.com/AMBR", "rank": 30, "slot_uri": "GENEPIO:0100584", "alias": "taxonomic_identification_method_details", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "incubation temperature value": { - "name": "incubation temperature value", + "required": true, + "any_of": [ + { + "range": "TaxonomicIdentificationMethodDetailsMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "incubation_temperature_value": { + "name": "incubation_temperature_value", "description": "An environmental datum specifying the temperature at which an organism or organisms were incubated for the purposes of growth on or in a particular medium.", "title": "incubation temperature value", + "comments": [ + "Provide the temperature at which the isolate was isolated. This value maps to the information stored in the \"Incubation temperature\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "37" + } + ], "from_schema": "https://example.com/AMBR", "rank": 31, "slot_uri": "GENEPIO:0100617", "alias": "incubation_temperature_value", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "incubation temperature unit": { - "name": "incubation temperature unit", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "incubation_temperature_unit": { + "name": "incubation_temperature_unit", "description": "An environmental datum specifying the temperature unit at which an organism or organisms were incubated for the purposes of growth on or in a particular medium.", "title": "incubation temperature unit", + "comments": [ + "Select the temperature unit from the pick list. This value maps to the information stored in the \"Incubation temperature\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Degree Celsius" + } + ], "from_schema": "https://example.com/AMBR", "rank": 32, "slot_uri": "GENEPIO:0100618", "alias": "incubation_temperature_unit", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "isolation medium": { - "name": "isolation medium", + "required": true, + "any_of": [ + { + "range": "IncubationTemperatureUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "isolation_medium": { + "name": "isolation_medium", "description": "An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment.", "title": "isolation medium", + "comments": [ + "Select the isolation medium from the pick list. This value maps to the information stored in the \"Incubation media\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Brain heart infusion (BHI)" + } + ], "from_schema": "https://example.com/AMBR", "rank": 33, "slot_uri": "GENEPIO:0002107", "alias": "isolation_medium", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "isolate storage location": { - "name": "isolate storage location", + "required": true, + "any_of": [ + { + "range": "IsolationMediumMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "isolate_storage_location": { + "name": "isolate_storage_location", "description": "An isolate datum specifying the location of where an isolate is stored e.g. in a particular freezer, on a particular shelf", "title": "isolate storage location", + "comments": [ + "Enter the freezer storage location of the isolate as the \"freezer number-shelf number-box number-unit number\" e.g. FR1-R3-B1-S01. This value maps to the information stored in the \"Spot code\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "FR1-R3-B1-S01" + } + ], "from_schema": "https://example.com/AMBR", "rank": 34, "slot_uri": "GENEPIO:0100619", "alias": "isolate_storage_location", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", "range": "WhitespaceMinimizedString", "required": true }, - "cellular respiration type": { - "name": "cellular respiration type", + "cellular_respiration_type": { + "name": "cellular_respiration_type", "description": "An isolate datum specifying the type of cellular respiration process used by the organism.", "title": "cellular respiration type", + "comments": [ + "Select the respiration type from the pick list. This value maps to the information stored in the \"Aerobic/Anaerobic\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Aerobic respiration" + } + ], "from_schema": "https://example.com/AMBR", "rank": 35, "slot_uri": "GENEPIO:0100620", "alias": "cellular_respiration_type", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Strain and isolation information", - "required": true - }, - "host (common name)": { - "name": "host (common name)", + "required": true, + "any_of": [ + { + "range": "CellularRespirationTypeMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", + "comments": [ + "Common name is required if there was a host. Both common anime and scientific name can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Examples of common names are “Human” and “Canola plant”. Examples of scientific names are “Homo sapiens” and “Equus caballus”. If the sample was environmental, select \"Not Applicable\". Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Human" + } + ], "from_schema": "https://example.com/AMBR", "rank": 36, "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", + "alias": "host_common_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Host Information", - "required": true - }, - "host (scientific name)": { - "name": "host (scientific name)", + "required": true, + "any_of": [ + { + "range": "HostCommonNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Common name e.g. Human, Canola plant. If the sample was environmental, select \"Not Applicable\". Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Homo sapiens" + } + ], "from_schema": "https://example.com/AMBR", "rank": 37, "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", + "alias": "host_scientific_name", "owner": "AMBR", - "slot_group": "Host Information" - }, - "host disease": { - "name": "host disease", + "domain_of": [ + "AMBR" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", + "comments": [ + "If the sample was obtained from a host with a known disease, provide the name of the disease by seleting a value from the picklist. Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Cystic fibrosis" + } + ], "from_schema": "https://example.com/AMBR", "rank": 38, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", "owner": "AMBR", - "slot_group": "Host Information" - }, - "sequenced by": { - "name": "sequenced by", + "domain_of": [ + "AMBR" + ], + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.", "title": "sequenced by", + "comments": [ + "Provide the name of the organization that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the \"University of Calgary\"." + ], + "examples": [ + { + "value": "University of Calgary" + } + ], "from_schema": "https://example.com/AMBR", "rank": 39, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "AMBR", - "slot_group": "Sequencing" - }, - "sequenced by laboratory name": { - "name": "sequenced by laboratory name", + "domain_of": [ + "AMBR" + ], + "slot_group": "Sequencing", + "any_of": [ + { + "range": "SequencedByMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the \"Harrison Lab\"." + ], + "examples": [ + { + "value": "Harrison Lab" + } + ], "from_schema": "https://example.com/AMBR", "rank": 40, "slot_uri": "GENEPIO:0100470", "alias": "sequenced_by_laboratory_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequenced by contact name": { - "name": "sequenced by contact name", + "sequenced_by_contact_name": { + "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact name", + "comments": [ + "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Joe Harrison" + } + ], "from_schema": "https://example.com/AMBR", "rank": 41, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequenced by contact email": { - "name": "sequenced by contact email", + "sequenced_by_contact_email": { + "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", "title": "sequenced by contact email", + "comments": [ + "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "jjharris@ucalgary.ca" + } + ], "from_schema": "https://example.com/AMBR", "rank": 42, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Research" + } + ], "from_schema": "https://example.com/AMBR", "rank": 43, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing", "owner": "AMBR", - "slot_group": "Sequencing" - }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "domain_of": [ + "AMBR" + ], + "slot_group": "Sequencing", + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. This information can provide details about why the sample source might contain antibiotic potentiators." + ], + "examples": [ + { + "value": "Screening for antibiotic potentiators in Cystic fibrosis disease contexts." + } + ], "from_schema": "https://example.com/AMBR", "rank": 44, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "AMBR", - "slot_group": "Sequencing" - }, - "sequencing date": { - "name": "sequencing date", + "domain_of": [ + "AMBR" + ], + "slot_group": "Sequencing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "comments": [ + "The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-06-22" + } + ], "from_schema": "https://example.com/AMBR", "rank": 45, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "AMBR", - "slot_group": "Sequencing" - }, - "library ID": { - "name": "library ID", + "domain_of": [ + "AMBR" + ], + "slot_group": "Sequencing", + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] + }, + "library_id": { + "name": "library_id", "description": "The user-specified identifier for the library prepared for sequencing.", "title": "library ID", + "comments": [ + "Provide the name of the run. This value maps to information in the \"Sequencing Batch #\" field Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "1876515_SA01_Plate 02" + } + ], "from_schema": "https://example.com/AMBR", "rank": 46, "slot_uri": "GENEPIO:0001448", - "alias": "library_ID", + "alias": "library_id", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], "from_schema": "https://example.com/AMBR", "rank": 47, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", - "required": true - }, - "sequencing protocol name": { - "name": "sequencing protocol name", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequencing_protocol_name": { + "name": "sequencing_protocol_name", "description": "The name and version number of the sequencing protocol used.", "title": "sequencing protocol name", + "comments": [ + "Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION" + ], + "examples": [ + { + "value": "https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann" + } + ], "from_schema": "https://example.com/AMBR", "rank": 48, "slot_uri": "GENEPIO:0001453", "alias": "sequencing_protocol_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", "range": "WhitespaceMinimizedString", "recommended": true }, - "amplicon pcr primer list": { - "name": "amplicon pcr primer list", + "amplicon_pcr_primer_list": { + "name": "amplicon_pcr_primer_list", "description": "An information content entity specifying a list of primers used for amplicon sequencing.", "title": "amplicon pcr primer list", + "comments": [ + "Select the primers used to generate the ribosomal 16S or 23S amplicon for sequencing from the pick list. This value maps to the information in the \"Primers Used for sequencing\" field Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "27F" + }, + { + "value": "1492R" + } + ], "from_schema": "https://example.com/AMBR", "rank": 49, "slot_uri": "GENEPIO:0100623", - "multivalued": true, "alias": "amplicon_pcr_primer_list", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Sequencing", - "required": true - }, - "input file name": { - "name": "input file name", + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AmpliconPcrPrimerListMenu" + }, + { + "range": "NullValueMenu" + } + ] + }, + "input_file_name": { + "name": "input_file_name", "description": "The name of the file containing the sequence data to be analysed.", "title": "input file name", + "comments": [ + "Enter the file name of the target gene sequence to be analyzed." + ], + "examples": [ + { + "value": "ambr_staph_ABC_123.fasta" + } + ], "from_schema": "https://example.com/AMBR", "rank": 50, "slot_uri": "OBI:0002874", "alias": "input_file_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "reference accession": { - "name": "reference accession", + "reference_accession": { + "name": "reference_accession", "description": "An identifier that specifies an individual sequence record in a public sequence repository.", "title": "reference accession", + "comments": [ + "Enter the EZBioCloud gene accession that most closely matches the sequence being analyzed. This value maps to the information in the \"Accession No(s).\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "FR821777" + } + ], "from_schema": "https://example.com/AMBR", "rank": 51, "slot_uri": "OBI:0002885", "alias": "reference_accession", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Provide the name of the protocol used to perform the species identification (i.e. the name of the protocol to perform the EZBioCloud search)." + ], + "examples": [ + { + "value": "EZBioCloud_searchprotocol_2023.txt" + } + ], "from_schema": "https://example.com/AMBR", "rank": 52, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "reference database name": { - "name": "reference database name", + "reference_database_name": { + "name": "reference_database_name", "description": "An identifier of a biological or bioinformatics database.", "title": "reference database name", + "comments": [ + "Select the reference database name from the pick list. For the AMBR Project, the reference database will be EZBioCloud." + ], + "examples": [ + { + "value": "EZBioCloud" + } + ], "from_schema": "https://example.com/AMBR", "rank": 53, "slot_uri": "OBI:0002883", "alias": "reference_database_name", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "reference database version": { - "name": "reference database version", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "reference_database_version": { + "name": "reference_database_version", "description": "The version of the database containing the reference sequences used for analysis.", "title": "reference database version", + "comments": [ + "Enter the sequence search date as the version of EZBioCloud used. Record the date in ISO 8601 format i.e. YYYY_MM_DD. This value maps to the information in the \"Search date\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "2021-05-23" + } + ], "from_schema": "https://example.com/AMBR", "rank": 54, "slot_uri": "OBI:0002884", "alias": "reference_database_version", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "coverage (percentage)": { - "name": "coverage (percentage)", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "coverage_percentage": { + "name": "coverage_percentage", "description": "The percentage of the reference sequence covered by the sequence of interest.", "title": "coverage (percentage)", + "comments": [ + "Enter the completeness value. Do not include any symbols e.g. %. This value maps to \"Completeness (%)\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "98.2" + } + ], "from_schema": "https://example.com/AMBR", "rank": 55, "slot_uri": "OBI:0002880", - "alias": "coverage_(percentage)", + "alias": "coverage_percentage", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "sequence identity percentage": { - "name": "sequence identity percentage", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequence_identity_percentage": { + "name": "sequence_identity_percentage", "description": "Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences.", "title": "sequence identity percentage", + "comments": [ + "Enter the identity value. Do not include any symbols e.g. %. This value maps to \"Similarity (%)\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "99" + } + ], "from_schema": "https://example.com/AMBR", "rank": 56, "slot_uri": "OBI:0002882", "alias": "sequence_identity_percentage", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "sequence identity (variance ratio)": { - "name": "sequence identity (variance ratio)", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "sequence_identity_variance_ratio": { + "name": "sequence_identity_variance_ratio", "description": "The ratio of the reference sequence not covered by the sequence of interest.", "title": "sequence identity (variance ratio)", + "comments": [ + "Enter the number of different positions in the target sequence compared to the reference sequence length, expressed as a ratio. This value maps to \"Variation ratio\" in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "1/420" + } + ], "from_schema": "https://example.com/AMBR", "rank": 57, "slot_uri": "GENEPIO:0100624", - "alias": "sequence_identity_(variance_ratio)", + "alias": "sequence_identity_variance_ratio", "owner": "AMBR", - "slot_group": "Bioinformatics and QC metrics" - }, - "top-hit taxon determination": { - "name": "top-hit taxon determination", + "domain_of": [ + "AMBR" + ], + "slot_group": "Bioinformatics and QC metrics", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "tophit_taxon_determination": { + "name": "tophit_taxon_determination", "description": "The taxon derived from the top hit in search results produced from a sequence similarity comparison.", "title": "top-hit taxon determination", + "comments": [ + "Enter the EZBioCloud taxon best-hit. This value maps to the information in the \"Top-hit taxon (taxa)\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Staphylococcus argenteus" + } + ], "from_schema": "https://example.com/AMBR", "rank": 58, "slot_uri": "GENEPIO:0100625", - "alias": "top_hit_taxon_determination", + "alias": "tophit_taxon_determination", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "top-hit strain determination": { - "name": "top-hit strain determination", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "tophit_strain_determination": { + "name": "tophit_strain_determination", "description": "The strain designation derived from the top hit in search results produced from a sequence similarity comparison.", "title": "top-hit strain determination", + "comments": [ + "Enter the EZBioCloud strain best-hit. This value maps to the information in the \"Top-hit strain(s)\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "MSHR1132(T)" + } + ], "from_schema": "https://example.com/AMBR", "rank": 59, "slot_uri": "GENEPIO:0100648", - "alias": "top_hit_strain_determination", + "alias": "tophit_strain_determination", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "trimmed ribosomal gene sequence": { - "name": "trimmed ribosomal gene sequence", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "trimmed_ribosomal_gene_sequence": { + "name": "trimmed_ribosomal_gene_sequence", "description": "The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed to produce a trimmed ribosomal RNA sequence.", "title": "trimmed ribosomal gene sequence", + "comments": [ + "Enter the sequence of the trimmed ribosomal gene sequence. This value maps to the sequence in the \"Trimmed Ribosomal Sequence\" field in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "TGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGSGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCTAGCCGTCGAAG" + } + ], "from_schema": "https://example.com/AMBR", "rank": 60, "slot_uri": "GENEPIO:0100626", "alias": "trimmed_ribosomal_gene_sequence", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", - "required": true - }, - "bioinformatics analysis details": { - "name": "bioinformatics analysis details", + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, + "bioinformatics_analysis_details": { + "name": "bioinformatics_analysis_details", "description": "Any notes regarding the bioinformatics analysis.", "title": "bioinformatics analysis details", + "comments": [ + "Enter any notes regarding the analysis as free text. This value maps to the \"Comment\" field in the information in the Alberta Microbiota Repository (AMBR) Master file." + ], + "examples": [ + { + "value": "Pure-June 09-2022,Tube replaced by Rahgavi" + } + ], "from_schema": "https://example.com/AMBR", "rank": 61, "slot_uri": "GENEPIO:0100627", "alias": "bioinformatics_analysis_details", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, @@ -4668,31 +5981,52 @@ "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Rahgavi Poopalaraj, Shirin Afroj, Joe Harrison" + } + ], "from_schema": "https://example.com/AMBR", "rank": 62, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Contributor acknowledgement", "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v1.4.3, AMBR v1.0.0" + } + ], "from_schema": "https://example.com/AMBR", "rank": 63, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "alias": "dataharmonizer_provenance", "owner": "AMBR", + "domain_of": [ + "AMBR" + ], "slot_group": "Contributor acknowledgement", "range": "Provenance" } } } }, - "source_file": "schema.yaml", "settings": { "Title_Case": { "setting_key": "Title_Case", diff --git a/web/templates/ambr/schema.yaml b/web/templates/ambr/schema.yaml index db263e95..c6b4e1c5 100644 --- a/web/templates/ambr/schema.yaml +++ b/web/templates/ambr/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/AMBR name: AMBR description: '' -version: 2.3.0 +version: 2.3.1 imports: - linkml:types prefixes: @@ -21,301 +21,301 @@ classes: associated with the isolate repository from this work. is_a: dh_interface slots: - - isolate ID - - alternative isolate ID - - specimen collector sample ID - - sample collected by - - sample collection project name - - sample collector contact email - - sample collector contact address - - sample collection date - - sample received date - - geo_loc_name (country) - - geo_loc_name (state/province/territory) - - geo_loc_name (city) - - geo_loc_name (site) + - isolate_id + - alternative_isolate_id + - specimen_collector_sample_id + - sample_collected_by + - sample_collection_project_name + - sample_collector_contact_email + - sample_collector_contact_address + - sample_collection_date + - sample_received_date + - geo_loc_name_country + - geo_loc_name_state_province_territory + - geo_loc_name_city + - geo_loc_name_site - organism - - purpose of sampling - - purpose of sampling details - - original sample description - - anatomical material - - anatomical part - - body product - - environmental material - - environmental site - - collection device - - collection method - - collection protocol - - specimen processing - - specimen processing details + - purpose_of_sampling + - purpose_of_sampling_details + - original_sample_description + - anatomical_material + - anatomical_part + - body_product + - environmental_material + - environmental_site + - collection_device + - collection_method + - collection_protocol + - specimen_processing + - specimen_processing_details - strain - - taxonomic identification method - - taxonomic identification method details - - incubation temperature value - - incubation temperature unit - - isolation medium - - isolate storage location - - cellular respiration type - - host (common name) - - host (scientific name) - - host disease - - sequenced by - - sequenced by laboratory name - - sequenced by contact name - - sequenced by contact email - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - library ID - - sequencing instrument - - sequencing protocol name - - amplicon pcr primer list - - input file name - - reference accession - - bioinformatics protocol - - reference database name - - reference database version - - coverage (percentage) - - sequence identity percentage - - sequence identity (variance ratio) - - top-hit taxon determination - - top-hit strain determination - - trimmed ribosomal gene sequence - - bioinformatics analysis details + - taxonomic_identification_method + - taxonomic_identification_method_details + - incubation_temperature_value + - incubation_temperature_unit + - isolation_medium + - isolate_storage_location + - cellular_respiration_type + - host_common_name + - host_scientific_name + - host_disease + - sequenced_by + - sequenced_by_laboratory_name + - sequenced_by_contact_name + - sequenced_by_contact_email + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - library_id + - sequencing_instrument + - sequencing_protocol_name + - amplicon_pcr_primer_list + - input_file_name + - reference_accession + - bioinformatics_protocol + - reference_database_name + - reference_database_version + - coverage_percentage + - sequence_identity_percentage + - sequence_identity_variance_ratio + - tophit_taxon_determination + - tophit_strain_determination + - trimmed_ribosomal_gene_sequence + - bioinformatics_analysis_details - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - isolate ID: + isolate_id: rank: 1 slot_group: Database Identifiers - alternative isolate ID: + alternative_isolate_id: rank: 2 slot_group: Database Identifiers - specimen collector sample ID: + specimen_collector_sample_id: rank: 3 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 4 slot_group: Sample collection and processing - sample collection project name: + sample_collection_project_name: rank: 5 slot_group: Sample collection and processing - sample collector contact email: + sample_collector_contact_email: rank: 6 slot_group: Sample collection and processing - sample collector contact address: + sample_collector_contact_address: rank: 7 slot_group: Sample collection and processing - sample collection date: + sample_collection_date: rank: 8 slot_group: Sample collection and processing - sample received date: + sample_received_date: rank: 9 slot_group: Sample collection and processing - geo_loc_name (country): + geo_loc_name_country: rank: 10 slot_group: Sample collection and processing - geo_loc_name (state/province/territory): + geo_loc_name_state_province_territory: rank: 11 slot_group: Sample collection and processing - geo_loc_name (city): + geo_loc_name_city: rank: 12 slot_group: Sample collection and processing - geo_loc_name (site): + geo_loc_name_site: rank: 13 slot_group: Sample collection and processing organism: rank: 14 slot_group: Sample collection and processing - purpose of sampling: + purpose_of_sampling: rank: 15 slot_group: Sample collection and processing - purpose of sampling details: + purpose_of_sampling_details: rank: 16 slot_group: Sample collection and processing - original sample description: + original_sample_description: rank: 17 slot_group: Sample collection and processing - anatomical material: + anatomical_material: rank: 18 slot_group: Sample collection and processing - anatomical part: + anatomical_part: rank: 19 slot_group: Sample collection and processing - body product: + body_product: rank: 20 slot_group: Sample collection and processing - environmental material: + environmental_material: rank: 21 slot_group: Sample collection and processing - environmental site: + environmental_site: rank: 22 slot_group: Sample collection and processing - collection device: + collection_device: rank: 23 slot_group: Sample collection and processing - collection method: + collection_method: rank: 24 slot_group: Sample collection and processing - collection protocol: + collection_protocol: rank: 25 slot_group: Sample collection and processing - specimen processing: + specimen_processing: rank: 26 slot_group: Sample collection and processing - specimen processing details: + specimen_processing_details: rank: 27 slot_group: Sample collection and processing strain: rank: 28 slot_group: Strain and isolation information - taxonomic identification method: + taxonomic_identification_method: rank: 29 slot_group: Strain and isolation information - taxonomic identification method details: + taxonomic_identification_method_details: rank: 30 slot_group: Strain and isolation information - incubation temperature value: + incubation_temperature_value: rank: 31 slot_group: Strain and isolation information - incubation temperature unit: + incubation_temperature_unit: rank: 32 slot_group: Strain and isolation information - isolation medium: + isolation_medium: rank: 33 slot_group: Strain and isolation information - isolate storage location: + isolate_storage_location: rank: 34 slot_group: Strain and isolation information - cellular respiration type: + cellular_respiration_type: rank: 35 slot_group: Strain and isolation information - host (common name): + host_common_name: rank: 36 slot_group: Host Information - host (scientific name): + host_scientific_name: rank: 37 slot_group: Host Information - host disease: + host_disease: rank: 38 slot_group: Host Information - sequenced by: + sequenced_by: rank: 39 slot_group: Sequencing - sequenced by laboratory name: + sequenced_by_laboratory_name: rank: 40 slot_group: Sequencing - sequenced by contact name: + sequenced_by_contact_name: rank: 41 slot_group: Sequencing - sequenced by contact email: + sequenced_by_contact_email: rank: 42 slot_group: Sequencing - purpose of sequencing: + purpose_of_sequencing: rank: 43 slot_group: Sequencing - purpose of sequencing details: + purpose_of_sequencing_details: rank: 44 slot_group: Sequencing - sequencing date: + sequencing_date: rank: 45 slot_group: Sequencing - library ID: + library_id: rank: 46 slot_group: Sequencing - sequencing instrument: + sequencing_instrument: rank: 47 slot_group: Sequencing - sequencing protocol name: + sequencing_protocol_name: rank: 48 slot_group: Sequencing - amplicon pcr primer list: + amplicon_pcr_primer_list: rank: 49 slot_group: Sequencing - input file name: + input_file_name: rank: 50 slot_group: Bioinformatics and QC metrics - reference accession: + reference_accession: rank: 51 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + bioinformatics_protocol: rank: 52 slot_group: Bioinformatics and QC metrics - reference database name: + reference_database_name: rank: 53 slot_group: Bioinformatics and QC metrics - reference database version: + reference_database_version: rank: 54 slot_group: Bioinformatics and QC metrics - coverage (percentage): + coverage_percentage: rank: 55 slot_group: Bioinformatics and QC metrics - sequence identity percentage: + sequence_identity_percentage: rank: 56 slot_group: Bioinformatics and QC metrics - sequence identity (variance ratio): + sequence_identity_variance_ratio: rank: 57 slot_group: Bioinformatics and QC metrics - top-hit taxon determination: + tophit_taxon_determination: rank: 58 slot_group: Bioinformatics and QC metrics - top-hit strain determination: + tophit_strain_determination: rank: 59 slot_group: Bioinformatics and QC metrics - trimmed ribosomal gene sequence: + trimmed_ribosomal_gene_sequence: rank: 60 slot_group: Bioinformatics and QC metrics - bioinformatics analysis details: + bioinformatics_analysis_details: rank: 61 slot_group: Bioinformatics and QC metrics authors: rank: 62 slot_group: Contributor acknowledgement - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 63 slot_group: Contributor acknowledgement slots: - isolate ID: - name: isolate ID + isolate_id: + name: isolate_id title: isolate ID description: The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. comments: Provide the identifier created by the lab for the organism after isolation. This value maps to the "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: SA01 slot_uri: GENEPIO:0100456 range: WhitespaceMinimizedString required: true - alternative isolate ID: - name: alternative isolate ID + examples: + - value: SA01 + alternative_isolate_id: + name: alternative_isolate_id title: alternative isolate ID description: An alternative isolate ID assigned to the isolate by another organization. comments: Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the "Label ID" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: '3411301' slot_uri: GENEPIO:0100457 range: WhitespaceMinimizedString recommended: true - specimen collector sample ID: - name: specimen collector sample ID + examples: + - value: '3411301' + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. comments: Provide the sample ID provided by the original sample collector. This value is different from the "isolate_ID" as it represents the original material sampled rather than the organism that was isolated from the sampled material. This identifier may or may not be available. - examples: - - value: Lake_Louise_Water23 slot_uri: GENEPIO:0001123 - range: WhitespaceMinimizedString identifier: true - sample collected by: - name: sample collected by + range: WhitespaceMinimizedString + examples: + - value: Lake_Louise_Water23 + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the agency that collected the original sample. comments: The name of the institution of the original sample collector should @@ -323,118 +323,118 @@ slots: across multiple submissions e.g. University of Calgary, Alberta Health Services. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). - examples: - - value: University of Calgary slot_uri: GENEPIO:0001153 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true - sample collection project name: - name: sample collection project name + examples: + - value: University of Calgary + sample_collection_project_name: + name: sample_collection_project_name title: sample collection project name description: The name of the project/initiative/program for which the sample was collected. comments: Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. - examples: - - value: Children's Hospital biofilm study (A3-701-01) slot_uri: GENEPIO:0100429 range: WhitespaceMinimizedString recommended: true - sample collector contact email: - name: sample collector contact email + examples: + - value: Children's Hospital biofilm study (A3-701-01) + sample_collector_contact_email: + name: sample_collector_contact_email title: sample collector contact email description: The email address of the contact responsible for follow-up regarding the sample. comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca - examples: - - value: RespLab@lab.ca slot_uri: GENEPIO:0001156 range: WhitespaceMinimizedString pattern: ^\S+@\S+\.\S+$ - sample collector contact address: - name: sample collector contact address + examples: + - value: RespLab@lab.ca + sample_collector_contact_address: + name: sample_collector_contact_address title: sample collector contact address description: The mailing address of the agency submitting the sample. comments: 'The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country' - examples: - - value: 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada slot_uri: GENEPIO:0001158 range: WhitespaceMinimizedString - sample collection date: - name: sample collection date + examples: + - value: 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada + sample_collection_date: + name: sample_collection_date title: sample collection date description: The date on which the sample was collected. comments: The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2020-03-16' slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu - recommended: true + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} - sample received date: - name: sample received date + recommended: true + examples: + - value: '2020-03-16' + sample_received_date: + name: sample_received_date title: sample received date description: The date on which the sample was received. comments: The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2020-03-20' slot_uri: GENEPIO:0001179 any_of: - range: date - - range: null value menu - geo_loc_name (country): - name: geo_loc_name (country) + - range: NullValueMenu + examples: + - value: '2020-03-20' + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc_name (country) description: The country where the sample was collected. comments: Provide the country name from the controlled vocabulary provided. - examples: - - value: Canada slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu recommended: true - geo_loc_name (state/province/territory): - name: geo_loc_name (state/province/territory) + examples: + - value: Canada + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo_loc_name (state/province/territory) description: The province/territory where the sample was collected. comments: Provide the province/territory name from the controlled vocabulary provided. - examples: - - value: Saskatchewan slot_uri: GENEPIO:0001185 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true - geo_loc_name (city): - name: geo_loc_name (city) + examples: + - value: Saskatchewan + geo_loc_name_city: + name: geo_loc_name_city title: geo_loc_name (city) description: The city where the sample was collected. comments: 'Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz' - examples: - - value: Medicine Hat slot_uri: GENEPIO:0001189 range: WhitespaceMinimizedString - geo_loc_name (site): - name: geo_loc_name (site) + examples: + - value: Medicine Hat + geo_loc_name_site: + name: geo_loc_name_site title: geo_loc_name (site) description: The name of a specific geographical location e.g. Credit River (rather than river). comments: Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). + slot_uri: GENEPIO:0100436 + range: GeoLocNameSiteMenu examples: - value: Lake Louise - slot_uri: GENEPIO:0100436 - range: geo_loc_name (site) menu organism: name: organism title: organism @@ -442,15 +442,15 @@ slots: comments: Provide the confirmed taxonomic name of the species. This value maps to the "Recommended identification" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Staphylococcus aureus slot_uri: GENEPIO:0001191 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - purpose of sampling: - name: purpose of sampling + examples: + - value: Staphylococcus aureus + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: The reason a sample was collected may provide information about potential @@ -460,15 +460,15 @@ slots: in the "purpose of sequencing" field. Motivation for sampling may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Targeted surveillance slot_uri: GENEPIO:0001198 any_of: - - range: purpose of sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu recommended: true - purpose of sampling details: - name: purpose of sampling details + examples: + - value: Targeted surveillance + purpose_of_sampling_details: + name: purpose_of_sampling_details title: purpose of sampling details description: The description of why the sample was collected, providing specific details. @@ -477,28 +477,28 @@ slots: investigation/surveillance activity/research question. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: ProvLab/IPC routine monitoring slot_uri: GENEPIO:0001200 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu recommended: true - original sample description: - name: original sample description + examples: + - value: ProvLab/IPC routine monitoring + original_sample_description: + name: original_sample_description title: original sample description description: The original sample description provided by the sample collector. comments: Provide the sample description provided by the original sample collector or the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. + slot_uri: GENEPIO:0100439 + range: WhitespaceMinimizedString examples: - value: ACH coupons-water study, isolates 2010, 2011 see appendix 3 (Alberta Childrens Hospital) - slot_uri: GENEPIO:0100439 - range: WhitespaceMinimizedString - anatomical material: - name: anatomical material + anatomical_material: + name: anatomical_material title: anatomical material description: A substance obtained from an anatomical part of an organism e.g. tissue, blood. @@ -508,16 +508,16 @@ slots: a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Wound tissue (injury) slot_uri: GENEPIO:0001211 any_of: - - range: anatomical material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true required: true - anatomical part: - name: anatomical part + examples: + - value: Wound tissue (injury) + anatomical_part: + name: anatomical_part title: anatomical part description: An anatomical part of an organism e.g. oropharynx. comments: Provide a descriptor if an anatomical part was sampled. Use the picklist @@ -525,16 +525,16 @@ slots: emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Nasal cavity slot_uri: GENEPIO:0001214 any_of: - - range: anatomical part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true required: true - body product: - name: body product + examples: + - value: Nasal cavity + body_product: + name: body_product title: body product description: A substance excreted/secreted from an organism e.g. feces, urine, sweat. @@ -543,16 +543,16 @@ slots: emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Feces slot_uri: GENEPIO:0001216 any_of: - - range: body product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true required: true - environmental material: - name: environmental material + examples: + - value: Feces + environmental_material: + name: environmental_material title: environmental material description: A substance obtained from the natural or man-made environment e.g. soil, water, sewage. @@ -562,16 +562,16 @@ slots: a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Bandage slot_uri: GENEPIO:0001223 any_of: - - range: environmental material menu - - range: null value menu + - range: EnvironmentalMaterialMenu + - range: NullValueMenu multivalued: true required: true - environmental site: - name: environmental site + examples: + - value: Bandage + environmental_site: + name: environmental_site title: environmental site description: An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. @@ -580,16 +580,16 @@ slots: emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Hospital slot_uri: GENEPIO:0001232 any_of: - - range: environmental site menu - - range: null value menu + - range: EnvironmentalSiteMenu + - range: NullValueMenu multivalued: true required: true - collection device: - name: collection device + examples: + - value: Hospital + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. swab. comments: Provide a descriptor if a device was used for sampling. Use the picklist @@ -597,16 +597,16 @@ slots: emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Swab slot_uri: GENEPIO:0001234 any_of: - - range: collection device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu multivalued: true required: true - collection method: - name: collection method + examples: + - value: Swab + collection_method: + name: collection_method title: collection method description: The process used to collect the sample e.g. phlebotamy, necropsy. comments: Provide a descriptor if a collection method was used for sampling. Use @@ -615,27 +615,27 @@ slots: Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Biopsy slot_uri: GENEPIO:0001241 any_of: - - range: collection method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu multivalued: true required: true - collection protocol: - name: collection protocol + examples: + - value: Biopsy + collection_protocol: + name: collection_protocol title: collection protocol description: The name and version of a particular protocol used for sampling. comments: Free text. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Collection_protocol_Children's Hospital biofilm study (A3-701-01) slot_uri: GENEPIO:0001243 range: WhitespaceMinimizedString - specimen processing: - name: specimen processing + examples: + - value: Collection_protocol_Children's Hospital biofilm study (A3-701-01) + specimen_processing: + name: specimen_processing title: specimen processing description: Any processing applied to the sample during or after receiving the sample. @@ -648,16 +648,16 @@ slots: about replicates may be available in the "Top-hit taxon (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Biological replicate slot_uri: GENEPIO:0001253 any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true recommended: true - specimen processing details: - name: specimen processing details + examples: + - value: Biological replicate + specimen_processing_details: + name: specimen_processing_details title: specimen processing details description: Detailed information regarding the processing applied to a sample during or after receiving the sample. @@ -666,26 +666,26 @@ slots: (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString examples: - value: Multiple amplicons generated for isolate SA32 using different primer sets - slot_uri: GENEPIO:0100311 - range: WhitespaceMinimizedString strain: name: strain title: strain description: The strain identifier. comments: Provide the strain of the isolate. This value maps to the "Strain" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: CL10 slot_uri: GENEPIO:0100455 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - taxonomic identification method: - name: taxonomic identification method + examples: + - value: CL10 + taxonomic_identification_method: + name: taxonomic_identification_method title: taxonomic identification method description: The type of planned process by which an organismal entity is associated with a taxon or taxa. @@ -694,15 +694,15 @@ slots: the "16S ribosomal gene sequencing assay" value will be the most appropriate. If the information is unknown or cannot be provided, leave blank or provide a null value. - examples: - - value: 16S ribosomal gene sequencing assay slot_uri: GENEPIO:0100583 any_of: - - range: taxonomic identification method menu - - range: null value menu + - range: TaxonomicIdentificationMethodMenu + - range: NullValueMenu required: true - taxonomic identification method details: - name: taxonomic identification method details + examples: + - value: 16S ribosomal gene sequencing assay + taxonomic_identification_method_details: + name: taxonomic_identification_method_details title: taxonomic identification method details description: The details of the process used to determine the taxonomic identification of an organism. @@ -713,16 +713,16 @@ slots: community data standards. If another method was used for the taxonomic determination, leave blank. This value maps to the information stored in the "ID Category*" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: 'Species-level ID: >99.3% identity and unambiguous match to one type - (T) sequence in a curated database' slot_uri: GENEPIO:0100584 any_of: - - range: taxonomic identification method details menu - - range: null value menu + - range: TaxonomicIdentificationMethodDetailsMenu + - range: NullValueMenu required: true - incubation temperature value: - name: incubation temperature value + examples: + - value: 'Species-level ID: >99.3% identity and unambiguous match to one type + (T) sequence in a curated database' + incubation_temperature_value: + name: incubation_temperature_value title: incubation temperature value description: An environmental datum specifying the temperature at which an organism or organisms were incubated for the purposes of growth on or in a particular @@ -730,15 +730,15 @@ slots: comments: Provide the temperature at which the isolate was isolated. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: '37' slot_uri: GENEPIO:0100617 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - incubation temperature unit: - name: incubation temperature unit + examples: + - value: '37' + incubation_temperature_unit: + name: incubation_temperature_unit title: incubation temperature unit description: An environmental datum specifying the temperature unit at which an organism or organisms were incubated for the purposes of growth on or in a particular @@ -746,15 +746,15 @@ slots: comments: Select the temperature unit from the pick list. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Degree Celsius slot_uri: GENEPIO:0100618 any_of: - - range: incubation temperature unit menu - - range: null value menu + - range: IncubationTemperatureUnitMenu + - range: NullValueMenu required: true - isolation medium: - name: isolation medium + examples: + - value: Degree Celsius + isolation_medium: + name: isolation_medium title: isolation medium description: An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the @@ -762,15 +762,15 @@ slots: comments: Select the isolation medium from the pick list. This value maps to the information stored in the "Incubation media" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Brain heart infusion (BHI) slot_uri: GENEPIO:0002107 any_of: - - range: isolation medium menu - - range: null value menu + - range: IsolationMediumMenu + - range: NullValueMenu required: true - isolate storage location: - name: isolate storage location + examples: + - value: Brain heart infusion (BHI) + isolate_storage_location: + name: isolate_storage_location title: isolate storage location description: An isolate datum specifying the location of where an isolate is stored e.g. in a particular freezer, on a particular shelf @@ -778,28 +778,28 @@ slots: number-box number-unit number" e.g. FR1-R3-B1-S01. This value maps to the information stored in the "Spot code" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: FR1-R3-B1-S01 slot_uri: GENEPIO:0100619 range: WhitespaceMinimizedString required: true - cellular respiration type: - name: cellular respiration type + examples: + - value: FR1-R3-B1-S01 + cellular_respiration_type: + name: cellular_respiration_type title: cellular respiration type description: An isolate datum specifying the type of cellular respiration process used by the organism. comments: Select the respiration type from the pick list. This value maps to the information stored in the "Aerobic/Anaerobic" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Aerobic respiration slot_uri: GENEPIO:0100620 any_of: - - range: cellular respiration type menu - - range: null value menu + - range: CellularRespirationTypeMenu + - range: NullValueMenu required: true - host (common name): - name: host (common name) + examples: + - value: Aerobic respiration + host_common_name: + name: host_common_name title: host (common name) description: The commonly used name of the host. comments: "Common name is required if there was a host. Both common anime and\ @@ -810,15 +810,15 @@ slots: . If the sample was environmental, select \"Not Applicable\". Information for\ \ populating this field may be available in the \"Source of Isolation\" field\ \ in the Alberta Microbiota Repository (AMBR) Master file." - examples: - - value: Human slot_uri: GENEPIO:0001386 any_of: - - range: host (common name) menu - - range: null value menu + - range: HostCommonNameMenu + - range: NullValueMenu required: true - host (scientific name): - name: host (scientific name) + examples: + - value: Human + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. comments: Common name or scientific name are required if there was a host. Both @@ -827,28 +827,28 @@ slots: plant. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Homo sapiens slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu - host disease: - name: host disease + - range: HostScientificNameMenu + - range: NullValueMenu + examples: + - value: Homo sapiens + host_disease: + name: host_disease title: host disease description: The name of the disease experienced by the host. comments: If the sample was obtained from a host with a known disease, provide the name of the disease by seleting a value from the picklist. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Cystic fibrosis slot_uri: GENEPIO:0001391 any_of: - - range: host disease menu - - range: null value menu - sequenced by: - name: sequenced by + - range: HostDiseaseMenu + - range: NullValueMenu + examples: + - value: Cystic fibrosis + sequenced_by: + name: sequenced_by title: sequenced by description: The name of the agency, organization or institution responsible for sequencing the isolate's genome. @@ -856,14 +856,14 @@ slots: full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "University of Calgary". - examples: - - value: University of Calgary slot_uri: GENEPIO:0100416 any_of: - - range: sequenced_by menu - - range: null value menu - sequenced by laboratory name: - name: sequenced by laboratory name + - range: SequencedByMenu + - range: NullValueMenu + examples: + - value: University of Calgary + sequenced_by_laboratory_name: + name: sequenced_by_laboratory_name title: sequenced by laboratory name description: The specific laboratory affiliation of the responsible for sequencing the isolate's genome. @@ -871,12 +871,12 @@ slots: sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "Harrison Lab". - examples: - - value: Harrison Lab slot_uri: GENEPIO:0100470 range: WhitespaceMinimizedString - sequenced by contact name: - name: sequenced by contact name + examples: + - value: Harrison Lab + sequenced_by_contact_name: + name: sequenced_by_contact_name title: sequenced by contact name description: The name or title of the contact responsible for follow-up regarding the sequence. @@ -885,12 +885,12 @@ slots: job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. - examples: - - value: Joe Harrison slot_uri: GENEPIO:0100471 range: WhitespaceMinimizedString - sequenced by contact email: - name: sequenced by contact email + examples: + - value: Joe Harrison + sequenced_by_contact_email: + name: sequenced_by_contact_email title: sequenced by contact email description: The email address of the contact responsible for follow-up regarding the sequence. @@ -899,12 +899,12 @@ slots: an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. - examples: - - value: jjharris@ucalgary.ca slot_uri: GENEPIO:0100422 range: WhitespaceMinimizedString - purpose of sequencing: - name: purpose of sequencing + examples: + - value: jjharris@ucalgary.ca + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the @@ -912,74 +912,72 @@ slots: may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. - examples: - - value: Research slot_uri: GENEPIO:0001445 any_of: - - range: purpose of sequencing menu - - range: null value menu - purpose of sequencing details: - name: purpose of sequencing details + - range: PurposeOfSequencingMenu + - range: NullValueMenu + examples: + - value: Research + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details description: The description of why the sample was sequenced providing specific details. comments: Provide an expanded description of why the sample was sequenced using free text. This information can provide details about why the sample source might contain antibiotic potentiators. - examples: - - value: Screening for antibiotic potentiators in Cystic fibrosis disease contexts. slot_uri: GENEPIO:0001446 any_of: - range: WhitespaceMinimizedString - - range: null value menu - sequencing date: - name: sequencing date + - range: NullValueMenu + examples: + - value: Screening for antibiotic potentiators in Cystic fibrosis disease contexts. + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: The date should be provided in ISO 8601 standard format "YYYY-MM-DD". - examples: - - value: '2020-06-22' slot_uri: GENEPIO:0001447 any_of: - range: date - - range: null value menu - todos: - - '>={sample_collection_date}' - library ID: - name: library ID + - range: NullValueMenu + examples: + - value: '2020-06-22' + library_id: + name: library_id title: library ID description: The user-specified identifier for the library prepared for sequencing. comments: 'Provide the name of the run. This value maps to information in the "Sequencing Batch #" field Alberta Microbiota Repository (AMBR) Master file.' - examples: - - value: 1876515_SA01_Plate 02 slot_uri: GENEPIO:0001448 range: WhitespaceMinimizedString - sequencing instrument: - name: sequencing instrument + examples: + - value: 1876515_SA01_Plate 02 + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Select a sequencing instrument from the picklist provided in the template. - examples: - - value: Oxford Nanopore MinION slot_uri: GENEPIO:0001452 any_of: - - range: sequencing instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu multivalued: true required: true - sequencing protocol name: - name: sequencing protocol name + examples: + - value: Oxford Nanopore MinION + sequencing_protocol_name: + name: sequencing_protocol_name title: sequencing protocol name description: The name and version number of the sequencing protocol used. comments: Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION - examples: - - value: https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann slot_uri: GENEPIO:0001453 range: WhitespaceMinimizedString recommended: true - amplicon pcr primer list: - name: amplicon pcr primer list + examples: + - value: https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann + amplicon_pcr_primer_list: + name: amplicon_pcr_primer_list title: amplicon pcr primer list description: An information content entity specifying a list of primers used for amplicon sequencing. @@ -987,64 +985,64 @@ slots: for sequencing from the pick list. This value maps to the information in the "Primers Used for sequencing" field Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: 27F - - value: 1492R slot_uri: GENEPIO:0100623 any_of: - - range: amplicon pcr primer list menu - - range: null value menu + - range: AmpliconPcrPrimerListMenu + - range: NullValueMenu multivalued: true required: true - input file name: - name: input file name + examples: + - value: 27F + - value: 1492R + input_file_name: + name: input_file_name title: input file name description: The name of the file containing the sequence data to be analysed. comments: Enter the file name of the target gene sequence to be analyzed. - examples: - - value: ambr_staph_ABC_123.fasta slot_uri: OBI:0002874 range: WhitespaceMinimizedString - reference accession: - name: reference accession + examples: + - value: ambr_staph_ABC_123.fasta + reference_accession: + name: reference_accession title: reference accession description: An identifier that specifies an individual sequence record in a public sequence repository. comments: Enter the EZBioCloud gene accession that most closely matches the sequence being analyzed. This value maps to the information in the "Accession No(s)." field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: FR821777 slot_uri: OBI:0002885 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - bioinformatics protocol: - name: bioinformatics protocol + examples: + - value: FR821777 + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Provide the name of the protocol used to perform the species identification (i.e. the name of the protocol to perform the EZBioCloud search). - examples: - - value: EZBioCloud_searchprotocol_2023.txt slot_uri: GENEPIO:0001489 range: WhitespaceMinimizedString - reference database name: - name: reference database name + examples: + - value: EZBioCloud_searchprotocol_2023.txt + reference_database_name: + name: reference_database_name title: reference database name description: An identifier of a biological or bioinformatics database. comments: Select the reference database name from the pick list. For the AMBR Project, the reference database will be EZBioCloud. - examples: - - value: EZBioCloud slot_uri: OBI:0002883 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - reference database version: - name: reference database version + examples: + - value: EZBioCloud + reference_database_version: + name: reference_database_version title: reference database version description: The version of the database containing the reference sequences used for analysis. @@ -1052,113 +1050,113 @@ slots: the date in ISO 8601 format i.e. YYYY_MM_DD. This value maps to the information in the "Search date" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: '2021-05-23' slot_uri: OBI:0002884 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - coverage (percentage): - name: coverage (percentage) + examples: + - value: '2021-05-23' + coverage_percentage: + name: coverage_percentage title: coverage (percentage) description: The percentage of the reference sequence covered by the sequence of interest. comments: Enter the completeness value. Do not include any symbols e.g. %. This value maps to "Completeness (%)" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: '98.2' slot_uri: OBI:0002880 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - sequence identity percentage: - name: sequence identity percentage + examples: + - value: '98.2' + sequence_identity_percentage: + name: sequence_identity_percentage title: sequence identity percentage description: Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. comments: Enter the identity value. Do not include any symbols e.g. %. This value maps to "Similarity (%)" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: '99' slot_uri: OBI:0002882 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - sequence identity (variance ratio): - name: sequence identity (variance ratio) + examples: + - value: '99' + sequence_identity_variance_ratio: + name: sequence_identity_variance_ratio title: sequence identity (variance ratio) description: The ratio of the reference sequence not covered by the sequence of interest. comments: Enter the number of different positions in the target sequence compared to the reference sequence length, expressed as a ratio. This value maps to "Variation ratio" in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: 1/420 slot_uri: GENEPIO:0100624 any_of: - range: WhitespaceMinimizedString - - range: null value menu - top-hit taxon determination: - name: top-hit taxon determination + - range: NullValueMenu + examples: + - value: 1/420 + tophit_taxon_determination: + name: tophit_taxon_determination title: top-hit taxon determination description: The taxon derived from the top hit in search results produced from a sequence similarity comparison. comments: Enter the EZBioCloud taxon best-hit. This value maps to the information in the "Top-hit taxon (taxa)" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Staphylococcus argenteus slot_uri: GENEPIO:0100625 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - top-hit strain determination: - name: top-hit strain determination + examples: + - value: Staphylococcus argenteus + tophit_strain_determination: + name: tophit_strain_determination title: top-hit strain determination description: The strain designation derived from the top hit in search results produced from a sequence similarity comparison. comments: Enter the EZBioCloud strain best-hit. This value maps to the information in the "Top-hit strain(s)" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: MSHR1132(T) slot_uri: GENEPIO:0100648 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - trimmed ribosomal gene sequence: - name: trimmed ribosomal gene sequence + examples: + - value: MSHR1132(T) + trimmed_ribosomal_gene_sequence: + name: trimmed_ribosomal_gene_sequence title: trimmed ribosomal gene sequence description: The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed to produce a trimmed ribosomal RNA sequence. comments: Enter the sequence of the trimmed ribosomal gene sequence. This value maps to the sequence in the "Trimmed Ribosomal Sequence" field in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: TGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGSGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCTAGCCGTCGAAG slot_uri: GENEPIO:0100626 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true - bioinformatics analysis details: - name: bioinformatics analysis details + examples: + - value: TGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGSGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCTAGCCGTCGAAG + bioinformatics_analysis_details: + name: bioinformatics_analysis_details title: bioinformatics analysis details description: Any notes regarding the bioinformatics analysis. comments: Enter any notes regarding the analysis as free text. This value maps to the "Comment" field in the information in the Alberta Microbiota Repository (AMBR) Master file. - examples: - - value: Pure-June 09-2022,Tube replaced by Rahgavi slot_uri: GENEPIO:0100627 range: WhitespaceMinimizedString + examples: + - value: Pure-June 09-2022,Tube replaced by Rahgavi authors: name: authors title: authors @@ -1166,25 +1164,26 @@ slots: sequence generation, analysis, and data submission. comments: Include the first and last names of all individuals that should be attributed, separated by a comma. - examples: - - value: Rahgavi Poopalaraj, Shirin Afroj, Joe Harrison slot_uri: GENEPIO:0001517 range: WhitespaceMinimizedString recommended: true - DataHarmonizer provenance: - name: DataHarmonizer provenance + examples: + - value: Rahgavi Poopalaraj, Shirin Afroj, Joe Harrison + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance description: The DataHarmonizer software and template version provenance. comments: The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. - examples: - - value: DataHarmonizer v1.4.3, AMBR v1.0.0 slot_uri: GENEPIO:0001518 range: Provenance + examples: + - value: DataHarmonizer v1.4.3, AMBR v1.0.0 enums: - null value menu: - name: null value menu + NullValueMenu: + name: NullValueMenu + title: null value menu permissible_values: Not Applicable: text: Not Applicable @@ -1201,8 +1200,9 @@ enums: Restricted Access: text: Restricted Access meaning: GENEPIO:0001810 - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: Afghanistan: text: Afghanistan @@ -2017,8 +2017,9 @@ enums: Zimbabwe: text: Zimbabwe meaning: GAZ:00001106 - geo_loc_name (site) menu: - name: geo_loc_name (site) menu + GeoLocNameSiteMenu: + name: GeoLocNameSiteMenu + title: geo_loc_name (site) menu permissible_values: Banff National Park: text: Banff National Park @@ -2039,8 +2040,9 @@ enums: Sylvan Lake: text: Sylvan Lake meaning: GAZ:00084188 - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation: text: Cluster/Outbreak investigation @@ -2058,8 +2060,9 @@ enums: Surveillance: text: Surveillance meaning: GENEPIO:0100004 - anatomical material menu: - name: anatomical material menu + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical material menu permissible_values: Skin: text: Skin @@ -2074,8 +2077,9 @@ enums: text: Wound tissue (injury) meaning: NCIT:C3671 is_a: Tissue - anatomical part menu: - name: anatomical part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical part menu permissible_values: Animal body or body part: text: Animal body or body part @@ -2112,14 +2116,16 @@ enums: Vagina: text: Vagina meaning: UBERON:0000996 - body product menu: - name: body product menu + BodyProductMenu: + name: BodyProductMenu + title: body product menu permissible_values: Feces: text: Feces meaning: UBERON:0001988 - environmental material menu: - name: environmental material menu + EnvironmentalMaterialMenu: + name: EnvironmentalMaterialMenu + title: environmental material menu permissible_values: Algal film: text: Algal film @@ -2194,8 +2200,9 @@ enums: is_a: Tap water Water outlet: text: Water outlet - environmental site menu: - name: environmental site menu + EnvironmentalSiteMenu: + name: EnvironmentalSiteMenu + title: environmental site menu permissible_values: Bird bath: text: Bird bath @@ -2234,8 +2241,9 @@ enums: Waterfall: text: Waterfall meaning: ENVO:00000040 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: Filter: text: Filter @@ -2246,20 +2254,23 @@ enums: Swab: text: Swab meaning: GENEPIO:0100027 - collection method menu: - name: collection method menu + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: Biopsy: text: Biopsy meaning: OBI:0002650 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Biological replicate: text: Biological replicate meaning: EFO:0002091 - incubation temperature unit menu: - name: incubation temperature unit menu + IncubationTemperatureUnitMenu: + name: IncubationTemperatureUnitMenu + title: incubation temperature unit menu permissible_values: Degree Celsius: text: Degree Celsius @@ -2267,8 +2278,9 @@ enums: Degree Farenheit: text: Degree Farenheit meaning: UO:0000195 - isolation medium menu: - name: isolation medium menu + IsolationMediumMenu: + name: IsolationMediumMenu + title: isolation medium menu permissible_values: 1/10 869: text: 1/10 869 @@ -2372,8 +2384,9 @@ enums: text: Supplement B Supplement 2.0: text: Supplement 2.0 - taxonomic identification method menu: - name: taxonomic identification method menu + TaxonomicIdentificationMethodMenu: + name: TaxonomicIdentificationMethodMenu + title: taxonomic identification method menu permissible_values: Whole genome sequencing assay: text: Whole genome sequencing assay @@ -2387,8 +2400,9 @@ enums: Comparative phenotypic assessment: text: Comparative phenotypic assessment meaning: OBI:0001546 - taxonomic identification method details menu: - name: taxonomic identification method details menu + TaxonomicIdentificationMethodDetailsMenu: + name: TaxonomicIdentificationMethodDetailsMenu + title: taxonomic identification method details menu permissible_values: 'Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database': text: 'Species-level ID: >99.3% identity and unambiguous match to one type @@ -2401,8 +2415,9 @@ enums: identity with a sequence that has not been typed*' Need to do whole genome sequencing to confirm their identity: text: Need to do whole genome sequencing to confirm their identity - cellular respiration type menu: - name: cellular respiration type menu + CellularRespirationTypeMenu: + name: CellularRespirationTypeMenu + title: cellular respiration type menu permissible_values: Aerobic respiration: text: Aerobic respiration @@ -2410,8 +2425,9 @@ enums: Anaerobic respiration: text: Anaerobic respiration meaning: GO:0009061 - host (common name) menu: - name: host (common name) menu + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu permissible_values: Horse: text: Horse @@ -2444,15 +2460,17 @@ enums: Snail: text: Snail meaning: FOODON:03412114 - host (scientific name) menu: - name: host (scientific name) menu + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu permissible_values: Equus caballus: text: Equus caballus Homo sapiens: text: Homo sapiens - host disease menu: - name: host disease menu + HostDiseaseMenu: + name: HostDiseaseMenu + title: host disease menu permissible_values: Colitis: text: Colitis @@ -2470,8 +2488,9 @@ enums: is_a: Pyelonephritis Urinary tract infection: text: Urinary tract infection - sequencing instrument menu: - name: sequencing instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: Illumina: text: Illumina @@ -2651,8 +2670,9 @@ enums: text: MGI DNBSEQ-G50 meaning: GENEPIO:0100150 is_a: MGI - amplicon pcr primer list menu: - name: amplicon pcr primer list menu + AmpliconPcrPrimerListMenu: + name: AmpliconPcrPrimerListMenu + title: amplicon pcr primer list menu permissible_values: 27F: text: 27F diff --git a/web/templates/ambr/schema_enums.tsv b/web/templates/ambr/schema_enums.tsv index 9d3a37bc..4ea5b6ac 100644 --- a/web/templates/ambr/schema_enums.tsv +++ b/web/templates/ambr/schema_enums.tsv @@ -1,522 +1,522 @@ -title meaning in_subset menu_1 menu_2 menu_3 menu_4 menu_5 description - -null value menu GENEPIO:0001619 Covid-19 Not Applicable - GENEPIO:0001620 Covid-19 Not Collected - GENEPIO:0001668 Covid-19 Not Provided - GENEPIO:0001618 Covid-19 Missing - GENEPIO:0001810 Covid-19 Restricted Access - - -geo_loc_name (country) menu GAZ:00006882 AMBR Afghanistan - GAZ:00002953 AMBR Albania - GAZ:00000563 AMBR Algeria - GAZ:00003957 AMBR American Samoa - GAZ:00002948 AMBR Andorra - GAZ:00001095 AMBR Angola - GAZ:00009159 AMBR Anguilla - GAZ:00000462 AMBR Antarctica - GAZ:00006883 AMBR Antigua and Barbuda - GAZ:00002928 AMBR Argentina - GAZ:00004094 AMBR Armenia - GAZ:00004025 AMBR Aruba - GAZ:00005901 AMBR Ashmore and Cartier Islands - GAZ:00000463 AMBR Australia - GAZ:00002942 AMBR Austria - GAZ:00004941 AMBR Azerbaijan - GAZ:00002733 AMBR Bahamas - GAZ:00005281 AMBR Bahrain - GAZ:00007117 AMBR Baker Island - GAZ:00003750 AMBR Bangladesh - GAZ:00001251 AMBR Barbados - GAZ:00005810 AMBR Bassas da India - GAZ:00006886 AMBR Belarus - GAZ:00002938 AMBR Belgium - GAZ:00002934 AMBR Belize - GAZ:00000904 AMBR Benin - GAZ:00001264 AMBR Bermuda - GAZ:00003920 AMBR Bhutan - GAZ:00002511 AMBR Bolivia - GAZ:00025355 AMBR Borneo - GAZ:00006887 AMBR Bosnia and Herzegovina - GAZ:00001097 AMBR Botswana - GAZ:00001453 AMBR Bouvet Island - GAZ:00002828 AMBR Brazil - GAZ:00003961 AMBR British Virgin Islands - GAZ:00003901 AMBR Brunei - GAZ:00002950 AMBR Bulgaria - GAZ:00000905 AMBR Burkina Faso - GAZ:00001090 AMBR Burundi - GAZ:00006888 AMBR Cambodia - GAZ:00001093 AMBR Cameroon - GAZ:00002560 AMBR Canada - GAZ:00001227 AMBR Cape Verde - GAZ:00003986 AMBR Cayman Islands - GAZ:00001089 AMBR Central African Republic - GAZ:00000586 AMBR Chad - GAZ:00002825 AMBR Chile - GAZ:00002845 AMBR China - GAZ:00005915 AMBR Christmas Island - GAZ:00005838 AMBR Clipperton Island - GAZ:00009721 AMBR Cocos Islands - GAZ:00002929 AMBR Colombia - GAZ:00005820 AMBR Comoros - GAZ:00053798 AMBR Cook Islands - GAZ:00005917 AMBR Coral Sea Islands - GAZ:00002901 AMBR Costa Rica - GAZ:00000906 AMBR Cote d'Ivoire - GAZ:00002719 AMBR Croatia - GAZ:00003762 AMBR Cuba - GAZ:00012582 AMBR Curacao - GAZ:00004006 AMBR Cyprus - GAZ:00002954 AMBR Czech Republic - GAZ:00001086 AMBR Democratic Republic of the Congo - GAZ:00005852 AMBR Denmark - GAZ:00000582 AMBR Djibouti - GAZ:00006890 AMBR Dominica - GAZ:00003952 AMBR Dominican Republic - GAZ:00002912 AMBR Ecuador - GAZ:00003934 AMBR Egypt - GAZ:00002935 AMBR El Salvador - GAZ:00001091 AMBR Equatorial Guinea - GAZ:00000581 AMBR Eritrea - GAZ:00002959 AMBR Estonia - GAZ:00001099 AMBR Eswatini - GAZ:00000567 AMBR Ethiopia - GAZ:00005811 AMBR Europa Island - GAZ:00001412 AMBR Falkland Islands (Islas Malvinas) - GAZ:00059206 AMBR Faroe Islands - GAZ:00006891 AMBR Fiji - GAZ:00002937 AMBR Finland - GAZ:00003940 AMBR France - GAZ:00002516 AMBR French Guiana - GAZ:00002918 AMBR French Polynesia - GAZ:00003753 AMBR French Southern and Antarctic Lands - GAZ:00001092 AMBR Gabon - GAZ:00000907 AMBR Gambia - GAZ:00009571 AMBR Gaza Strip - GAZ:00004942 AMBR Georgia - GAZ:00002646 AMBR Germany - GAZ:00000908 AMBR Ghana - GAZ:00003987 AMBR Gibraltar - GAZ:00005808 AMBR Glorioso Islands - GAZ:00002945 AMBR Greece - GAZ:00001507 AMBR Greenland - GAZ:02000573 AMBR Grenada - GAZ:00067142 AMBR Guadeloupe - GAZ:00003706 AMBR Guam - GAZ:00002936 AMBR Guatemala - GAZ:00001550 AMBR Guernsey - GAZ:00000909 AMBR Guinea - GAZ:00000910 AMBR Guinea-Bissau - GAZ:00002522 AMBR Guyana - GAZ:00003953 AMBR Haiti - GAZ:00009718 AMBR Heard Island and McDonald Islands - GAZ:00002894 AMBR Honduras - GAZ:00003203 AMBR Hong Kong - GAZ:00007120 AMBR Howland Island - GAZ:00002952 AMBR Hungary - GAZ:00000843 AMBR Iceland - GAZ:00002839 AMBR India - GAZ:00003727 AMBR Indonesia - GAZ:00004474 AMBR Iran - GAZ:00004483 AMBR Iraq - GAZ:00002943 AMBR Ireland - GAZ:00052477 AMBR Isle of Man - GAZ:00002476 AMBR Israel - GAZ:00002650 AMBR Italy - GAZ:00003781 AMBR Jamaica - GAZ:00005853 AMBR Jan Mayen - GAZ:00002747 AMBR Japan - GAZ:00007118 AMBR Jarvis Island - GAZ:00001551 AMBR Jersey - GAZ:00007114 AMBR Johnston Atoll - GAZ:00002473 AMBR Jordan - GAZ:00005809 AMBR Juan de Nova Island - GAZ:00004999 AMBR Kazakhstan - GAZ:00001101 AMBR Kenya - GAZ:00005682 AMBR Kerguelen Archipelago - GAZ:00007116 AMBR Kingman Reef - GAZ:00006894 AMBR Kiribati - GAZ:00011337 AMBR Kosovo - GAZ:00005285 AMBR Kuwait - GAZ:00006893 AMBR Kyrgyzstan - GAZ:00006889 AMBR Laos - GAZ:00002958 AMBR Latvia - GAZ:00002478 AMBR Lebanon - GAZ:00001098 AMBR Lesotho - GAZ:00000911 AMBR Liberia - GAZ:00000566 AMBR Libya - GAZ:00003858 AMBR Liechtenstein - GAZ:00007144 AMBR Line Islands - GAZ:00002960 AMBR Lithuania - GAZ:00002947 AMBR Luxembourg - GAZ:00003202 AMBR Macau - GAZ:00001108 AMBR Madagascar - GAZ:00001105 AMBR Malawi - GAZ:00003902 AMBR Malaysia - GAZ:00006924 AMBR Maldives - GAZ:00000584 AMBR Mali - GAZ:00004017 AMBR Malta - GAZ:00007161 AMBR Marshall Islands - GAZ:00067143 AMBR Martinique - GAZ:00000583 AMBR Mauritania - GAZ:00003745 AMBR Mauritius - GAZ:00003943 AMBR Mayotte - GAZ:00002852 AMBR Mexico - GAZ:00005862 AMBR Micronesia - GAZ:00007112 AMBR Midway Islands - GAZ:00003897 AMBR Moldova - GAZ:00003857 AMBR Monaco - GAZ:00008744 AMBR Mongolia - GAZ:00006898 AMBR Montenegro - GAZ:00003988 AMBR Montserrat - GAZ:00000565 AMBR Morocco - GAZ:00001100 AMBR Mozambique - GAZ:00006899 AMBR Myanmar - GAZ:00001096 AMBR Namibia - GAZ:00006900 AMBR Nauru - GAZ:00007119 AMBR Navassa Island - GAZ:00004399 AMBR Nepal - GAZ:00002946 AMBR Netherlands - GAZ:00005206 AMBR New Caledonia - GAZ:00000469 AMBR New Zealand - GAZ:00002978 AMBR Nicaragua - GAZ:00000585 AMBR Niger - GAZ:00000912 AMBR Nigeria - GAZ:00006902 AMBR Niue - GAZ:00005908 AMBR Norfolk Island - GAZ:00002801 AMBR North Korea - GAZ:00006895 AMBR North Macedonia - GAZ:00002284 AMBR North Sea - GAZ:00003958 AMBR Northern Mariana Islands - GAZ:00002699 AMBR Norway - GAZ:00005283 AMBR Oman - GAZ:00005246 AMBR Pakistan - GAZ:00006905 AMBR Palau - GAZ:00002892 AMBR Panama - GAZ:00003922 AMBR Papua New Guinea - GAZ:00010832 AMBR Paracel Islands - GAZ:00002933 AMBR Paraguay - GAZ:00002932 AMBR Peru - GAZ:00004525 AMBR Philippines - GAZ:00005867 AMBR Pitcairn Islands - GAZ:00002939 AMBR Poland - GAZ:00004126 AMBR Portugal - GAZ:00006935 AMBR Puerto Rico - GAZ:00005286 AMBR Qatar - GAZ:00001088 AMBR Republic of the Congo - GAZ:00003945 AMBR Reunion - GAZ:00002951 AMBR Romania - GAZ:00023304 AMBR Ross Sea - GAZ:00002721 AMBR Russia - GAZ:00001087 AMBR Rwanda - GAZ:00000849 AMBR Saint Helena - GAZ:00006906 AMBR Saint Kitts and Nevis - GAZ:00006909 AMBR Saint Lucia - GAZ:00003942 AMBR Saint Pierre and Miquelon - GAZ:00005841 AMBR Saint Martin - GAZ:02000565 AMBR Saint Vincent and the Grenadines - GAZ:00006910 AMBR Samoa - GAZ:00003102 AMBR San Marino - GAZ:00006927 AMBR Sao Tome and Principe - GAZ:00005279 AMBR Saudi Arabia - GAZ:00000913 AMBR Senegal - GAZ:00002957 AMBR Serbia - GAZ:00006922 AMBR Seychelles - GAZ:00000914 AMBR Sierra Leone - GAZ:00003923 AMBR Singapore - GAZ:00012579 AMBR Sint Maarten - GAZ:00002956 AMBR Slovakia - GAZ:00002955 AMBR Slovenia - GAZ:00005275 AMBR Solomon Islands - GAZ:00001104 AMBR Somalia - GAZ:00001094 AMBR South Africa - GAZ:00003990 AMBR South Georgia and the South Sandwich Islands - GAZ:00002802 AMBR South Korea - GAZ:00233439 AMBR South Sudan - GAZ:00003936 AMBR Spain - GAZ:00010831 AMBR Spratly Islands - GAZ:00003924 AMBR Sri Lanka - GAZ:00002475 AMBR State of Palestine - GAZ:00000560 AMBR Sudan - GAZ:00002525 AMBR Suriname - GAZ:00005396 AMBR Svalbard - GAZ:00001099 AMBR Swaziland - GAZ:00002729 AMBR Sweden - GAZ:00002941 AMBR Switzerland - GAZ:00002474 AMBR Syria - GAZ:00005341 AMBR Taiwan - GAZ:00006912 AMBR Tajikistan - GAZ:00001103 AMBR Tanzania - GAZ:00003744 AMBR Thailand - GAZ:00006913 AMBR Timor-Leste - GAZ:00000915 AMBR Togo - GAZ:00260188 AMBR Tokelau - GAZ:00006916 AMBR Tonga - GAZ:00003767 AMBR Trinidad and Tobago - GAZ:00005812 AMBR Tromelin Island - GAZ:00000562 AMBR Tunisia - GAZ:00000558 AMBR Turkey - GAZ:00005018 AMBR Turkmenistan - GAZ:00003955 AMBR Turks and Caicos Islands - GAZ:00009715 AMBR Tuvalu - GAZ:00002459 AMBR United States of America - GAZ:00001102 AMBR Uganda - GAZ:00002724 AMBR Ukraine - GAZ:00005282 AMBR United Arab Emirates - GAZ:00002637 AMBR United Kingdom - GAZ:00002930 AMBR Uruguay - GAZ:00004979 AMBR Uzbekistan - GAZ:00006918 AMBR Vanuatu - GAZ:00002931 AMBR Venezuela - GAZ:00003756 AMBR Viet Nam - GAZ:00003959 AMBR Virgin Islands - GAZ:00007111 AMBR Wake Island - GAZ:00007191 AMBR Wallis and Futuna - GAZ:00009572 AMBR West Bank - GAZ:00000564 AMBR Western Sahara - GAZ:00005284 AMBR Yemen - GAZ:00001107 AMBR Zambia - GAZ:00001106 AMBR Zimbabwe - - -geo_loc_name (site) menu GAZ:00055489 AMBR Banff National Park - GAZ:00055538 AMBR Clayoquot Sound - AMBR Grassi Lakes - GAZ:00284745 AMBR Horseshoe Canyon - AMBR Ink Pots - GAZ:00084160 AMBR Lake Louise - GAZ:00084188 AMBR Sylvan Lake - - -purpose of sampling menu GENEPIO:0100001 AMBR Cluster/Outbreak investigation - GENEPIO:0100002 AMBR Diagnostic testing - GENEPIO:0100003 AMBR Research - GENEPIO:0100582 Survey study - GENEPIO:0100004 AMBR Surveillance - - - -anatomical material menu UBERON:0002097 AMBR Skin - UBERON:0000479 AMBR Tissue - AMBR Pierced tissue - NCIT:C3671 AMBR Wound tissue (injury) - - -anatomical part menu FOODON:03420127 AMBR Animal body or body part - FOODON:00003521 AMBR Berry - UBERON:0001155 AMBR Colon - UBERON:0001156 AMBR Ascending colon - UBERON:0001690 AMBR Ear - PO:0009046 AMBR Flower - PO:0009032 AMBR Flower petal - PO:0025034 AMBR Leaf - UBERON:0001707 AMBR Nasal cavity - UBERON:0000167 AMBR Oral cavity - UBERON:0000996 AMBR Vagina - - -body product menu UBERON:0001988 AMBR Feces - - -environmental material menu ENVO:01001189 AMBR Algal film - AMBR Bandage - AMBR Cerebral spinal fluid (CSF) shunt - CHEBI:33290 AMBR Food - AMBR Gauze - ENVO:01000018 AMBR Gravel - AMBR Moss - ENVO:00005774 AMBR Peat - ENVO:01000581 AMBR Phone - AMBR Phone screen - AMBR Pipe (metal) - AMBR Prosthetic limb - AMBR Prosthetic hip - ENVO:00001995 AMBR Rock - ENVO:01000017 AMBR Sand - AMBR Black sand - AMBR Copper sand - ENVO:00002044 AMBR Sludge - ENVO:00001998 AMBR Soil - ENVO:01000406 AMBR Snow - ENVO:00002006 AMBR Water - AMBR Surface runoff - ENVO:00005738 AMBR Surface water foam - AMBR Tap water - ENVO:00003064 AMBR Drinking water - AMBR Water outlet - - -environmental site menu AMBR Bird bath - AMBR Deep water area - AMBR Fish tank - AMBR Fountain - AMBR Fountain pond - AMBR Hoodoo - ENVO:00002173 AMBR Hospital - ENVO:01001406 AMBR Laboratory - ENVO:00000020 AMBR Lake - ENVO:00000033 AMBR Pond - ENVO:00000486 AMBR Shoreline - ENVO:00000023 AMBR Stream - ENVO:03600021 AMBR Tailing pond - ENVO:00000040 AMBR Waterfall - - -collection device menu GENEPIO:0100103 AMBR Filter - AMBR Filter cage - GENEPIO:0100027 AMBR Swab - - -collection method menu OBI:0002650 AMBR Biopsy - - -specimen processing menu EFO:0002091 Biological replicate - - -incubation temperature unit menu UO:0000027 AMBR Degree Celsius - UO:0000195 AMBR Degree Farenheit - - -isolation medium menu AMBR 1/10 869 - AMBR Anaerobic agar (AA) - MICRO:0000605 AMBR Bile esculin agar (BEA) - MICRO:0000566 AMBR Brain heart infusion (BHI) - AMBR Brain heart infusion III + Supplement Set A (BHI-A) - AMBR Brain heart infusion II + Supplement Set B (BHI-B) - AMBR Brain heart infusion IV + Supplement Set A & B (BHI-AB) - AMBR Supplemented BHI (sBHI 2.0) - AMBR Brewer’s anaerobic agar (BAA) - MICRO:0000086 AMBR Brucella blood agar + 5% sheep’s blood - MICRO:0000591 AMBR Chocolate blood agar - MICRO:0000535 AMBR Columbia blood agar + 5% sheep’s blood (CBA) - AMBR Cooked meat medium from dehydrated meat extracts (Meat) - AMBR Cooke rose bengal agar (CRB) - AMBR Desoxycholate (DOC) - AMBR Fastidious anaerobic agar (FAA) - MICRO:0001182 AMBR Kligler iron agar (KIA) - AMBR Lysogeny broth agar (LB) - AMBR M9 minimal medium (M9) - AMBR M9 minimal media + insulin (M9 + insulin) - AMBR M9 minimal media + mucin (M9 + mucin) - AMBR M9 minimal media + starch (M9 + starch) - AMBR M17 minimal medium (M17) - MICRO:0000558 AMBR MacConkey agar (MCA) - AMBR Marine broth agar (MBA) - AMBR Medium 10 agar (M10) - AMBR Medium DAMS5.8 simple - AMBR No salt lysogeny broth agar (NSLB) - AMBR No salt lysogeny broth agar + 5-15% sucrose (NSLB + 5-15% sucrose) - MICRO:0000553 AMBR Nutrient agar - MICRO:0000622 AMBR Phenylethyl alcohol agar + 5% sheep’s blood (PEA) - MICRO:0000549 AMBR Plate count medium (PC) - MICRO:0000550 AMBR Pseudomonas isolation medium (PIA) - MICRO:0000543 AMBR Reasoner's 2A agar (R2A) - AMBR Reinforced Clostridial agar (RCA) - AMBR Staphylococcus isolation medium (SIA) - AMBR Tryptic soy agar + Supplement A & B + yeast (TSY) - AMBR Sheep’s blood (5%) - AMBR Supplement A - AMBR Supplement B - AMBR Supplement 2.0 - - -taxonomic identification method menu OBI:0002117 AMBR Whole genome sequencing assay - OBI:0002763 AMBR 16S ribosomal gene sequencing assay - OBI:0002740 AMBR PCR assay - OBI:0001546 AMBR Comparative phenotypic assessment - - -taxonomic identification method details menu AMBR Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database - AMBR Genus-level ID: >99.0% identity but ambiguous match to >1 type (T) sequence in databases - AMBR Genus-level ID: >98.7% identity to a type (T) sequence AND/OR >99.0% identity with a sequence that has not been typed* - AMBR Need to do whole genome sequencing to confirm their identity - - -cellular respiration type menu GO:0009060 AMBR Aerobic respiration - GO:0009061 AMBR Anaerobic respiration - - -host (common name) menu NCBITaxon:9796 AMBR Horse - NCBITaxon:9606 AMBR Human - NCBITaxon:47299 AMBR Plant - AMBR Bush - AMBR Canola plant - NCBITaxon:4028 AMBR Gerranium plant - AMBR Tree - AMBR Poplar tree - AMBR Willow tree - FOODON:03412114 AMBR Snail - - -host (scientific name) menu AMBR Equus caballus - AMBR Homo sapiens - - -host disease menu AMBR Colitis - AMBR Acute colitis - AMBR Cystic fibrosis - AMBR Gastroenteritis - AMBR Pyelonephritis - AMBR Acute pyelonephritis - AMBR Urinary tract infection - - -sequencing instrument menu GENEPIO:0100105 AMBR Illumina - GENEPIO:0100106 AMBR Illumina Genome Analyzer - GENEPIO:0100107 AMBR Illumina Genome Analyzer II - GENEPIO:0100108 AMBR Illumina Genome Analyzer IIx - GENEPIO:0100109 AMBR Illumina HiScanSQ - GENEPIO:0100110 AMBR Illumina HiSeq - GENEPIO:0100111 AMBR Illumina HiSeq X - GENEPIO:0100112 AMBR Illumina HiSeq X Five - GENEPIO:0100113 AMBR Illumina HiSeq X Ten - GENEPIO:0100114 AMBR Illumina HiSeq 1000 - GENEPIO:0100115 AMBR Illumina HiSeq 1500 - GENEPIO:0100116 AMBR Illumina HiSeq 2000 - GENEPIO:0100117 AMBR Illumina HiSeq 2500 - GENEPIO:0100118 AMBR Illumina HiSeq 3000 - GENEPIO:0100119 AMBR Illumina HiSeq 4000 - GENEPIO:0100120 AMBR Illumina iSeq - GENEPIO:0100121 AMBR Illumina iSeq 100 - GENEPIO:0100122 AMBR Illumina NovaSeq - GENEPIO:0100123 AMBR Illumina NovaSeq 6000 - GENEPIO:0100124 AMBR Illumina MiniSeq - GENEPIO:0100125 AMBR Illumina MiSeq - GENEPIO:0100126 AMBR Illumina NextSeq - GENEPIO:0100127 AMBR Illumina NextSeq 500 - GENEPIO:0100128 AMBR Illumina NextSeq 550 - GENEPIO:0100129 AMBR Illumina NextSeq 2000 - GENEPIO:0100130 AMBR Pacific Biosciences - GENEPIO:0100131 AMBR PacBio RS - GENEPIO:0100132 AMBR PacBio RS II - GENEPIO:0100133 AMBR PacBio Sequel - GENEPIO:0100134 AMBR PacBio Sequel II - GENEPIO:0100135 AMBR Ion Torrent - GENEPIO:0100136 AMBR Ion Torrent PGM - GENEPIO:0100137 AMBR Ion Torrent Proton - GENEPIO:0100138 AMBR Ion Torrent S5 XL - GENEPIO:0100139 AMBR Ion Torrent S5 - GENEPIO:0100140 AMBR Oxford Nanopore - GENEPIO:0100141 AMBR Oxford Nanopore GridION - GENEPIO:0100142 AMBR Oxford Nanopore MinION - GENEPIO:0100143 AMBR Oxford Nanopore PromethION - GENEPIO:0100144 AMBR BGI Genomics - GENEPIO:0100145 AMBR BGI Genomics BGISEQ-500 - GENEPIO:0100146 AMBR MGI - GENEPIO:0100147 AMBR MGI DNBSEQ-T7 - GENEPIO:0100148 AMBR MGI DNBSEQ-G400 - GENEPIO:0100149 AMBR MGI DNBSEQ-G400 FAST - GENEPIO:0100150 AMBR MGI DNBSEQ-G50 - - - -amplicon pcr primer list menu GENEPIO:0100640 AMBR 27F - GENEPIO:0100645 AMBR 357F - GENEPIO:0100642 AMBR 543R - GENEPIO:0100643 AMBR 926R - GENEPIO:0100644 AMBR 1492R - GENEPIO:0100668 AMBR ITS1F - GENEPIO:0100646 AMBR ITS3F - GENEPIO:0100647 AMBR ITS4F - GENEPIO:0100669 AMBR ITS4R \ No newline at end of file +title name meaning in_subset menu_1 menu_2 menu_3 menu_4 menu_5 description + +null value menu NullValueMenu GENEPIO:0001619 Covid-19 Not Applicable + GENEPIO:0001620 Covid-19 Not Collected + GENEPIO:0001668 Covid-19 Not Provided + GENEPIO:0001618 Covid-19 Missing + GENEPIO:0001810 Covid-19 Restricted Access + + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 AMBR Afghanistan + GAZ:00002953 AMBR Albania + GAZ:00000563 AMBR Algeria + GAZ:00003957 AMBR American Samoa + GAZ:00002948 AMBR Andorra + GAZ:00001095 AMBR Angola + GAZ:00009159 AMBR Anguilla + GAZ:00000462 AMBR Antarctica + GAZ:00006883 AMBR Antigua and Barbuda + GAZ:00002928 AMBR Argentina + GAZ:00004094 AMBR Armenia + GAZ:00004025 AMBR Aruba + GAZ:00005901 AMBR Ashmore and Cartier Islands + GAZ:00000463 AMBR Australia + GAZ:00002942 AMBR Austria + GAZ:00004941 AMBR Azerbaijan + GAZ:00002733 AMBR Bahamas + GAZ:00005281 AMBR Bahrain + GAZ:00007117 AMBR Baker Island + GAZ:00003750 AMBR Bangladesh + GAZ:00001251 AMBR Barbados + GAZ:00005810 AMBR Bassas da India + GAZ:00006886 AMBR Belarus + GAZ:00002938 AMBR Belgium + GAZ:00002934 AMBR Belize + GAZ:00000904 AMBR Benin + GAZ:00001264 AMBR Bermuda + GAZ:00003920 AMBR Bhutan + GAZ:00002511 AMBR Bolivia + GAZ:00025355 AMBR Borneo + GAZ:00006887 AMBR Bosnia and Herzegovina + GAZ:00001097 AMBR Botswana + GAZ:00001453 AMBR Bouvet Island + GAZ:00002828 AMBR Brazil + GAZ:00003961 AMBR British Virgin Islands + GAZ:00003901 AMBR Brunei + GAZ:00002950 AMBR Bulgaria + GAZ:00000905 AMBR Burkina Faso + GAZ:00001090 AMBR Burundi + GAZ:00006888 AMBR Cambodia + GAZ:00001093 AMBR Cameroon + GAZ:00002560 AMBR Canada + GAZ:00001227 AMBR Cape Verde + GAZ:00003986 AMBR Cayman Islands + GAZ:00001089 AMBR Central African Republic + GAZ:00000586 AMBR Chad + GAZ:00002825 AMBR Chile + GAZ:00002845 AMBR China + GAZ:00005915 AMBR Christmas Island + GAZ:00005838 AMBR Clipperton Island + GAZ:00009721 AMBR Cocos Islands + GAZ:00002929 AMBR Colombia + GAZ:00005820 AMBR Comoros + GAZ:00053798 AMBR Cook Islands + GAZ:00005917 AMBR Coral Sea Islands + GAZ:00002901 AMBR Costa Rica + GAZ:00000906 AMBR Cote d'Ivoire + GAZ:00002719 AMBR Croatia + GAZ:00003762 AMBR Cuba + GAZ:00012582 AMBR Curacao + GAZ:00004006 AMBR Cyprus + GAZ:00002954 AMBR Czech Republic + GAZ:00001086 AMBR Democratic Republic of the Congo + GAZ:00005852 AMBR Denmark + GAZ:00000582 AMBR Djibouti + GAZ:00006890 AMBR Dominica + GAZ:00003952 AMBR Dominican Republic + GAZ:00002912 AMBR Ecuador + GAZ:00003934 AMBR Egypt + GAZ:00002935 AMBR El Salvador + GAZ:00001091 AMBR Equatorial Guinea + GAZ:00000581 AMBR Eritrea + GAZ:00002959 AMBR Estonia + GAZ:00001099 AMBR Eswatini + GAZ:00000567 AMBR Ethiopia + GAZ:00005811 AMBR Europa Island + GAZ:00001412 AMBR Falkland Islands (Islas Malvinas) + GAZ:00059206 AMBR Faroe Islands + GAZ:00006891 AMBR Fiji + GAZ:00002937 AMBR Finland + GAZ:00003940 AMBR France + GAZ:00002516 AMBR French Guiana + GAZ:00002918 AMBR French Polynesia + GAZ:00003753 AMBR French Southern and Antarctic Lands + GAZ:00001092 AMBR Gabon + GAZ:00000907 AMBR Gambia + GAZ:00009571 AMBR Gaza Strip + GAZ:00004942 AMBR Georgia + GAZ:00002646 AMBR Germany + GAZ:00000908 AMBR Ghana + GAZ:00003987 AMBR Gibraltar + GAZ:00005808 AMBR Glorioso Islands + GAZ:00002945 AMBR Greece + GAZ:00001507 AMBR Greenland + GAZ:02000573 AMBR Grenada + GAZ:00067142 AMBR Guadeloupe + GAZ:00003706 AMBR Guam + GAZ:00002936 AMBR Guatemala + GAZ:00001550 AMBR Guernsey + GAZ:00000909 AMBR Guinea + GAZ:00000910 AMBR Guinea-Bissau + GAZ:00002522 AMBR Guyana + GAZ:00003953 AMBR Haiti + GAZ:00009718 AMBR Heard Island and McDonald Islands + GAZ:00002894 AMBR Honduras + GAZ:00003203 AMBR Hong Kong + GAZ:00007120 AMBR Howland Island + GAZ:00002952 AMBR Hungary + GAZ:00000843 AMBR Iceland + GAZ:00002839 AMBR India + GAZ:00003727 AMBR Indonesia + GAZ:00004474 AMBR Iran + GAZ:00004483 AMBR Iraq + GAZ:00002943 AMBR Ireland + GAZ:00052477 AMBR Isle of Man + GAZ:00002476 AMBR Israel + GAZ:00002650 AMBR Italy + GAZ:00003781 AMBR Jamaica + GAZ:00005853 AMBR Jan Mayen + GAZ:00002747 AMBR Japan + GAZ:00007118 AMBR Jarvis Island + GAZ:00001551 AMBR Jersey + GAZ:00007114 AMBR Johnston Atoll + GAZ:00002473 AMBR Jordan + GAZ:00005809 AMBR Juan de Nova Island + GAZ:00004999 AMBR Kazakhstan + GAZ:00001101 AMBR Kenya + GAZ:00005682 AMBR Kerguelen Archipelago + GAZ:00007116 AMBR Kingman Reef + GAZ:00006894 AMBR Kiribati + GAZ:00011337 AMBR Kosovo + GAZ:00005285 AMBR Kuwait + GAZ:00006893 AMBR Kyrgyzstan + GAZ:00006889 AMBR Laos + GAZ:00002958 AMBR Latvia + GAZ:00002478 AMBR Lebanon + GAZ:00001098 AMBR Lesotho + GAZ:00000911 AMBR Liberia + GAZ:00000566 AMBR Libya + GAZ:00003858 AMBR Liechtenstein + GAZ:00007144 AMBR Line Islands + GAZ:00002960 AMBR Lithuania + GAZ:00002947 AMBR Luxembourg + GAZ:00003202 AMBR Macau + GAZ:00001108 AMBR Madagascar + GAZ:00001105 AMBR Malawi + GAZ:00003902 AMBR Malaysia + GAZ:00006924 AMBR Maldives + GAZ:00000584 AMBR Mali + GAZ:00004017 AMBR Malta + GAZ:00007161 AMBR Marshall Islands + GAZ:00067143 AMBR Martinique + GAZ:00000583 AMBR Mauritania + GAZ:00003745 AMBR Mauritius + GAZ:00003943 AMBR Mayotte + GAZ:00002852 AMBR Mexico + GAZ:00005862 AMBR Micronesia + GAZ:00007112 AMBR Midway Islands + GAZ:00003897 AMBR Moldova + GAZ:00003857 AMBR Monaco + GAZ:00008744 AMBR Mongolia + GAZ:00006898 AMBR Montenegro + GAZ:00003988 AMBR Montserrat + GAZ:00000565 AMBR Morocco + GAZ:00001100 AMBR Mozambique + GAZ:00006899 AMBR Myanmar + GAZ:00001096 AMBR Namibia + GAZ:00006900 AMBR Nauru + GAZ:00007119 AMBR Navassa Island + GAZ:00004399 AMBR Nepal + GAZ:00002946 AMBR Netherlands + GAZ:00005206 AMBR New Caledonia + GAZ:00000469 AMBR New Zealand + GAZ:00002978 AMBR Nicaragua + GAZ:00000585 AMBR Niger + GAZ:00000912 AMBR Nigeria + GAZ:00006902 AMBR Niue + GAZ:00005908 AMBR Norfolk Island + GAZ:00002801 AMBR North Korea + GAZ:00006895 AMBR North Macedonia + GAZ:00002284 AMBR North Sea + GAZ:00003958 AMBR Northern Mariana Islands + GAZ:00002699 AMBR Norway + GAZ:00005283 AMBR Oman + GAZ:00005246 AMBR Pakistan + GAZ:00006905 AMBR Palau + GAZ:00002892 AMBR Panama + GAZ:00003922 AMBR Papua New Guinea + GAZ:00010832 AMBR Paracel Islands + GAZ:00002933 AMBR Paraguay + GAZ:00002932 AMBR Peru + GAZ:00004525 AMBR Philippines + GAZ:00005867 AMBR Pitcairn Islands + GAZ:00002939 AMBR Poland + GAZ:00004126 AMBR Portugal + GAZ:00006935 AMBR Puerto Rico + GAZ:00005286 AMBR Qatar + GAZ:00001088 AMBR Republic of the Congo + GAZ:00003945 AMBR Reunion + GAZ:00002951 AMBR Romania + GAZ:00023304 AMBR Ross Sea + GAZ:00002721 AMBR Russia + GAZ:00001087 AMBR Rwanda + GAZ:00000849 AMBR Saint Helena + GAZ:00006906 AMBR Saint Kitts and Nevis + GAZ:00006909 AMBR Saint Lucia + GAZ:00003942 AMBR Saint Pierre and Miquelon + GAZ:00005841 AMBR Saint Martin + GAZ:02000565 AMBR Saint Vincent and the Grenadines + GAZ:00006910 AMBR Samoa + GAZ:00003102 AMBR San Marino + GAZ:00006927 AMBR Sao Tome and Principe + GAZ:00005279 AMBR Saudi Arabia + GAZ:00000913 AMBR Senegal + GAZ:00002957 AMBR Serbia + GAZ:00006922 AMBR Seychelles + GAZ:00000914 AMBR Sierra Leone + GAZ:00003923 AMBR Singapore + GAZ:00012579 AMBR Sint Maarten + GAZ:00002956 AMBR Slovakia + GAZ:00002955 AMBR Slovenia + GAZ:00005275 AMBR Solomon Islands + GAZ:00001104 AMBR Somalia + GAZ:00001094 AMBR South Africa + GAZ:00003990 AMBR South Georgia and the South Sandwich Islands + GAZ:00002802 AMBR South Korea + GAZ:00233439 AMBR South Sudan + GAZ:00003936 AMBR Spain + GAZ:00010831 AMBR Spratly Islands + GAZ:00003924 AMBR Sri Lanka + GAZ:00002475 AMBR State of Palestine + GAZ:00000560 AMBR Sudan + GAZ:00002525 AMBR Suriname + GAZ:00005396 AMBR Svalbard + GAZ:00001099 AMBR Swaziland + GAZ:00002729 AMBR Sweden + GAZ:00002941 AMBR Switzerland + GAZ:00002474 AMBR Syria + GAZ:00005341 AMBR Taiwan + GAZ:00006912 AMBR Tajikistan + GAZ:00001103 AMBR Tanzania + GAZ:00003744 AMBR Thailand + GAZ:00006913 AMBR Timor-Leste + GAZ:00000915 AMBR Togo + GAZ:00260188 AMBR Tokelau + GAZ:00006916 AMBR Tonga + GAZ:00003767 AMBR Trinidad and Tobago + GAZ:00005812 AMBR Tromelin Island + GAZ:00000562 AMBR Tunisia + GAZ:00000558 AMBR Turkey + GAZ:00005018 AMBR Turkmenistan + GAZ:00003955 AMBR Turks and Caicos Islands + GAZ:00009715 AMBR Tuvalu + GAZ:00002459 AMBR United States of America + GAZ:00001102 AMBR Uganda + GAZ:00002724 AMBR Ukraine + GAZ:00005282 AMBR United Arab Emirates + GAZ:00002637 AMBR United Kingdom + GAZ:00002930 AMBR Uruguay + GAZ:00004979 AMBR Uzbekistan + GAZ:00006918 AMBR Vanuatu + GAZ:00002931 AMBR Venezuela + GAZ:00003756 AMBR Viet Nam + GAZ:00003959 AMBR Virgin Islands + GAZ:00007111 AMBR Wake Island + GAZ:00007191 AMBR Wallis and Futuna + GAZ:00009572 AMBR West Bank + GAZ:00000564 AMBR Western Sahara + GAZ:00005284 AMBR Yemen + GAZ:00001107 AMBR Zambia + GAZ:00001106 AMBR Zimbabwe + + +geo_loc_name (site) menu GeoLocNameSiteMenu GAZ:00055489 AMBR Banff National Park + GAZ:00055538 AMBR Clayoquot Sound + AMBR Grassi Lakes + GAZ:00284745 AMBR Horseshoe Canyon + AMBR Ink Pots + GAZ:00084160 AMBR Lake Louise + GAZ:00084188 AMBR Sylvan Lake + + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 AMBR Cluster/Outbreak investigation + GENEPIO:0100002 AMBR Diagnostic testing + GENEPIO:0100003 AMBR Research + GENEPIO:0100582 Survey study + GENEPIO:0100004 AMBR Surveillance + + + +anatomical material menu AnatomicalMaterialMenu UBERON:0002097 AMBR Skin + UBERON:0000479 AMBR Tissue + AMBR Pierced tissue + NCIT:C3671 AMBR Wound tissue (injury) + + +anatomical part menu AnatomicalPartMenu FOODON:03420127 AMBR Animal body or body part + FOODON:00003521 AMBR Berry + UBERON:0001155 AMBR Colon + UBERON:0001156 AMBR Ascending colon + UBERON:0001690 AMBR Ear + PO:0009046 AMBR Flower + PO:0009032 AMBR Flower petal + PO:0025034 AMBR Leaf + UBERON:0001707 AMBR Nasal cavity + UBERON:0000167 AMBR Oral cavity + UBERON:0000996 AMBR Vagina + + +body product menu BodyProductMenu UBERON:0001988 AMBR Feces + + +environmental material menu EnvironmentalMaterialMenu ENVO:01001189 AMBR Algal film + AMBR Bandage + AMBR Cerebral spinal fluid (CSF) shunt + CHEBI:33290 AMBR Food + AMBR Gauze + ENVO:01000018 AMBR Gravel + AMBR Moss + ENVO:00005774 AMBR Peat + ENVO:01000581 AMBR Phone + AMBR Phone screen + AMBR Pipe (metal) + AMBR Prosthetic limb + AMBR Prosthetic hip + ENVO:00001995 AMBR Rock + ENVO:01000017 AMBR Sand + AMBR Black sand + AMBR Copper sand + ENVO:00002044 AMBR Sludge + ENVO:00001998 AMBR Soil + ENVO:01000406 AMBR Snow + ENVO:00002006 AMBR Water + AMBR Surface runoff + ENVO:00005738 AMBR Surface water foam + AMBR Tap water + ENVO:00003064 AMBR Drinking water + AMBR Water outlet + + +environmental site menu EnvironmentalSiteMenu AMBR Bird bath + AMBR Deep water area + AMBR Fish tank + AMBR Fountain + AMBR Fountain pond + AMBR Hoodoo + ENVO:00002173 AMBR Hospital + ENVO:01001406 AMBR Laboratory + ENVO:00000020 AMBR Lake + ENVO:00000033 AMBR Pond + ENVO:00000486 AMBR Shoreline + ENVO:00000023 AMBR Stream + ENVO:03600021 AMBR Tailing pond + ENVO:00000040 AMBR Waterfall + + +collection device menu CollectionDeviceMenu GENEPIO:0100103 AMBR Filter + AMBR Filter cage + GENEPIO:0100027 AMBR Swab + + +collection method menu CollectionMethodMenu OBI:0002650 AMBR Biopsy + + +specimen processing menu SpecimenProcessingMenu EFO:0002091 Biological replicate + + +incubation temperature unit menu IncubationTemperatureUnitMenu UO:0000027 AMBR Degree Celsius + UO:0000195 AMBR Degree Farenheit + + +isolation medium menu IsolationMediumMenu AMBR 1/10 869 + AMBR Anaerobic agar (AA) + MICRO:0000605 AMBR Bile esculin agar (BEA) + MICRO:0000566 AMBR Brain heart infusion (BHI) + AMBR Brain heart infusion III + Supplement Set A (BHI-A) + AMBR Brain heart infusion II + Supplement Set B (BHI-B) + AMBR Brain heart infusion IV + Supplement Set A & B (BHI-AB) + AMBR Supplemented BHI (sBHI 2.0) + AMBR Brewer’s anaerobic agar (BAA) + MICRO:0000086 AMBR Brucella blood agar + 5% sheep’s blood + MICRO:0000591 AMBR Chocolate blood agar + MICRO:0000535 AMBR Columbia blood agar + 5% sheep’s blood (CBA) + AMBR Cooked meat medium from dehydrated meat extracts (Meat) + AMBR Cooke rose bengal agar (CRB) + AMBR Desoxycholate (DOC) + AMBR Fastidious anaerobic agar (FAA) + MICRO:0001182 AMBR Kligler iron agar (KIA) + AMBR Lysogeny broth agar (LB) + AMBR M9 minimal medium (M9) + AMBR M9 minimal media + insulin (M9 + insulin) + AMBR M9 minimal media + mucin (M9 + mucin) + AMBR M9 minimal media + starch (M9 + starch) + AMBR M17 minimal medium (M17) + MICRO:0000558 AMBR MacConkey agar (MCA) + AMBR Marine broth agar (MBA) + AMBR Medium 10 agar (M10) + AMBR Medium DAMS5.8 simple + AMBR No salt lysogeny broth agar (NSLB) + AMBR No salt lysogeny broth agar + 5-15% sucrose (NSLB + 5-15% sucrose) + MICRO:0000553 AMBR Nutrient agar + MICRO:0000622 AMBR Phenylethyl alcohol agar + 5% sheep’s blood (PEA) + MICRO:0000549 AMBR Plate count medium (PC) + MICRO:0000550 AMBR Pseudomonas isolation medium (PIA) + MICRO:0000543 AMBR Reasoner's 2A agar (R2A) + AMBR Reinforced Clostridial agar (RCA) + AMBR Staphylococcus isolation medium (SIA) + AMBR Tryptic soy agar + Supplement A & B + yeast (TSY) + AMBR Sheep’s blood (5%) + AMBR Supplement A + AMBR Supplement B + AMBR Supplement 2.0 + + +taxonomic identification method menu TaxonomicIdentificationMethodMenu OBI:0002117 AMBR Whole genome sequencing assay + OBI:0002763 AMBR 16S ribosomal gene sequencing assay + OBI:0002740 AMBR PCR assay + OBI:0001546 AMBR Comparative phenotypic assessment + + +taxonomic identification method details menu TaxonomicIdentificationMethodDetailsMenu AMBR Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database + AMBR Genus-level ID: >99.0% identity but ambiguous match to >1 type (T) sequence in databases + AMBR Genus-level ID: >98.7% identity to a type (T) sequence AND/OR >99.0% identity with a sequence that has not been typed* + AMBR Need to do whole genome sequencing to confirm their identity + + +cellular respiration type menu CellularRespirationTypeMenu GO:0009060 AMBR Aerobic respiration + GO:0009061 AMBR Anaerobic respiration + + +host (common name) menu HostCommonNameMenu NCBITaxon:9796 AMBR Horse + NCBITaxon:9606 AMBR Human + NCBITaxon:47299 AMBR Plant + AMBR Bush + AMBR Canola plant + NCBITaxon:4028 AMBR Gerranium plant + AMBR Tree + AMBR Poplar tree + AMBR Willow tree + FOODON:03412114 AMBR Snail + + +host (scientific name) menu HostScientificNameMenu AMBR Equus caballus + AMBR Homo sapiens + + +host disease menu HostDiseaseMenu AMBR Colitis + AMBR Acute colitis + AMBR Cystic fibrosis + AMBR Gastroenteritis + AMBR Pyelonephritis + AMBR Acute pyelonephritis + AMBR Urinary tract infection + + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 AMBR Illumina + GENEPIO:0100106 AMBR Illumina Genome Analyzer + GENEPIO:0100107 AMBR Illumina Genome Analyzer II + GENEPIO:0100108 AMBR Illumina Genome Analyzer IIx + GENEPIO:0100109 AMBR Illumina HiScanSQ + GENEPIO:0100110 AMBR Illumina HiSeq + GENEPIO:0100111 AMBR Illumina HiSeq X + GENEPIO:0100112 AMBR Illumina HiSeq X Five + GENEPIO:0100113 AMBR Illumina HiSeq X Ten + GENEPIO:0100114 AMBR Illumina HiSeq 1000 + GENEPIO:0100115 AMBR Illumina HiSeq 1500 + GENEPIO:0100116 AMBR Illumina HiSeq 2000 + GENEPIO:0100117 AMBR Illumina HiSeq 2500 + GENEPIO:0100118 AMBR Illumina HiSeq 3000 + GENEPIO:0100119 AMBR Illumina HiSeq 4000 + GENEPIO:0100120 AMBR Illumina iSeq + GENEPIO:0100121 AMBR Illumina iSeq 100 + GENEPIO:0100122 AMBR Illumina NovaSeq + GENEPIO:0100123 AMBR Illumina NovaSeq 6000 + GENEPIO:0100124 AMBR Illumina MiniSeq + GENEPIO:0100125 AMBR Illumina MiSeq + GENEPIO:0100126 AMBR Illumina NextSeq + GENEPIO:0100127 AMBR Illumina NextSeq 500 + GENEPIO:0100128 AMBR Illumina NextSeq 550 + GENEPIO:0100129 AMBR Illumina NextSeq 2000 + GENEPIO:0100130 AMBR Pacific Biosciences + GENEPIO:0100131 AMBR PacBio RS + GENEPIO:0100132 AMBR PacBio RS II + GENEPIO:0100133 AMBR PacBio Sequel + GENEPIO:0100134 AMBR PacBio Sequel II + GENEPIO:0100135 AMBR Ion Torrent + GENEPIO:0100136 AMBR Ion Torrent PGM + GENEPIO:0100137 AMBR Ion Torrent Proton + GENEPIO:0100138 AMBR Ion Torrent S5 XL + GENEPIO:0100139 AMBR Ion Torrent S5 + GENEPIO:0100140 AMBR Oxford Nanopore + GENEPIO:0100141 AMBR Oxford Nanopore GridION + GENEPIO:0100142 AMBR Oxford Nanopore MinION + GENEPIO:0100143 AMBR Oxford Nanopore PromethION + GENEPIO:0100144 AMBR BGI Genomics + GENEPIO:0100145 AMBR BGI Genomics BGISEQ-500 + GENEPIO:0100146 AMBR MGI + GENEPIO:0100147 AMBR MGI DNBSEQ-T7 + GENEPIO:0100148 AMBR MGI DNBSEQ-G400 + GENEPIO:0100149 AMBR MGI DNBSEQ-G400 FAST + GENEPIO:0100150 AMBR MGI DNBSEQ-G50 + + + +amplicon pcr primer list menu AmpliconPcrPrimerListMenu GENEPIO:0100640 AMBR 27F + GENEPIO:0100645 AMBR 357F + GENEPIO:0100642 AMBR 543R + GENEPIO:0100643 AMBR 926R + GENEPIO:0100644 AMBR 1492R + GENEPIO:0100668 AMBR ITS1F + GENEPIO:0100646 AMBR ITS3F + GENEPIO:0100647 AMBR ITS4F + GENEPIO:0100669 AMBR ITS4R \ No newline at end of file diff --git a/web/templates/ambr/schema_slots.tsv b/web/templates/ambr/schema_slots.tsv index 05bee907..d3e067e6 100644 --- a/web/templates/ambr/schema_slots.tsv +++ b/web/templates/ambr/schema_slots.tsv @@ -1,71 +1,71 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples -AMBR GENEPIO:0001122 Database Identifiers - Database Identifiers GENEPIO:0100456 isolate ID WhitespaceMinimizedString TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the identifier created by the lab for the organism after isolation. This value maps to the "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. SA01 - Database Identifiers GENEPIO:0100457 alternative isolate ID WhitespaceMinimizedString TRUE An alternative isolate ID assigned to the isolate by another organization. Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the "Label ID" in the Alberta Microbiota Repository (AMBR) Master file. 3411301 - Database Identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE The user-defined name for the sample. Provide the sample ID provided by the original sample collector. This value is different from the "isolate_ID" as it represents the original material sampled rather than the organism that was isolated from the sampled material. This identifier may or may not be available. Lake_Louise_Water23 - GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001153 sample collected by WhitespaceMinimizedString null value menu TRUE The name of the agency that collected the original sample. The name of the institution of the original sample collector should be written out in full, (no abbreviations, with minor exceptions) and be consistent across multiple submissions e.g. University of Calgary, Alberta Health Services. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). University of Calgary - Sample collection and processing GENEPIO:0100429 sample collection project name WhitespaceMinimizedString TRUE The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Children's Hospital biofilm study (A3-701-01) - Sample collection and processing GENEPIO:0001156 sample collector contact email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca - Sample collection and processing GENEPIO:0001158 sample collector contact address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada - Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 - Sample collection and processing GENEPIO:0001179 sample received date date null value menu The date on which the sample was received. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-20 - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) WhitespaceMinimizedString null value menu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan - Sample collection and processing GENEPIO:0001189 geo_loc_name (city) WhitespaceMinimizedString The city where the sample was collected. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Medicine Hat - Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name (site) menu The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Lake Louise - Sample collection and processing GENEPIO:0001191 organism WhitespaceMinimizedString null value menu TRUE Taxonomic name of the organism. Provide the confirmed taxonomic name of the species. This value maps to the "Recommended identification" in the Alberta Microbiota Repository (AMBR) Master file. Staphylococcus aureus - Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling menu null value menu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Motivation for sampling may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Targeted surveillance - Sample collection and processing GENEPIO:0001200 purpose of sampling details WhitespaceMinimizedString null value menu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular investigation/surveillance activity/research question. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. ProvLab/IPC routine monitoring - Sample collection and processing GENEPIO:0100439 original sample description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector or the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. ACH coupons-water study, isolates 2010, 2011 see appendix 3 (Alberta Childrens Hospital) - Sample collection and processing GENEPIO:0001211 anatomical material anatomical material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Wound tissue (injury) - Sample collection and processing GENEPIO:0001214 anatomical part anatomical part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Nasal cavity - Sample collection and processing GENEPIO:0001216 body product body product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Feces - Sample collection and processing GENEPIO:0001223 environmental material environmental material menu null value menu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Bandage - Sample collection and processing GENEPIO:0001232 environmental site environmental site menu null value menu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Hospital - Sample collection and processing GENEPIO:0001234 collection device collection device menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Swab - Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Biopsy - Sample collection and processing GENEPIO:0001243 collection protocol WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Free text. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Collection_protocol_Children's Hospital biofilm study (A3-701-01) - Sample collection and processing GENEPIO:0001253 specimen processing specimen processing menu null value menu TRUE TRUE Any processing applied to the sample during or after receiving the sample. If multiple PCR products were generated from the isolate using different primer sets, indicate that the sequence records represents the same isolate by selecting "Biological replicate" in the "specimen processing" field. Every different sequence experiment should have its own record (i.e. if different amplicons have the same sequence but were generated using different primer sets, these should be stored as separate entries/lines in the spreadsheet). Information about replicates may be available in the "Top-hit taxon (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. Biological replicate - Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. Information about replicates may be available in the "Top-hit taxon (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. Multiple amplicons generated for isolate SA32 using different primer sets - GENEPIO:0100453 Strain and isolation information - Strain and isolation information GENEPIO:0100455 strain WhitespaceMinimizedString null value menu TRUE The strain identifier. Provide the strain of the isolate. This value maps to the "Strain" in the Alberta Microbiota Repository (AMBR) Master file. CL10 - Strain and isolation information GENEPIO:0100583 taxonomic identification method taxonomic identification method menu null value menu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. For the AMBR Project, the "16S ribosomal gene sequencing assay" value will be the most appropriate. If the information is unknown or cannot be provided, leave blank or provide a null value. 16S ribosomal gene sequencing assay - Strain and isolation information GENEPIO:0100584 taxonomic identification method details taxonomic identification method details menu null value menu TRUE The details of the process used to determine the taxonomic identification of an organism. Provide the criteria used for 16S sequencing taxonomic determination by selection a value from the pick list. These criteria are specific to the AMBR project and so do not correspond with standardized criteria in any ontology. The pick list is strictly for providing consistency in records rather than implementing community data standards. If another method was used for the taxonomic determination, leave blank. This value maps to the information stored in the "ID Category*" field in the Alberta Microbiota Repository (AMBR) Master file. Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database - Strain and isolation information GENEPIO:0100617 incubation temperature value WhitespaceMinimizedString null value menu TRUE An environmental datum specifying the temperature at which an organism or organisms were incubated for the purposes of growth on or in a particular medium. Provide the temperature at which the isolate was isolated. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. 37 - Strain and isolation information GENEPIO:0100618 incubation temperature unit incubation temperature unit menu null value menu TRUE An environmental datum specifying the temperature unit at which an organism or organisms were incubated for the purposes of growth on or in a particular medium. Select the temperature unit from the pick list. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. Degree Celsius - Strain and isolation information GENEPIO:0002107 isolation medium isolation medium menu null value menu TRUE An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. Select the isolation medium from the pick list. This value maps to the information stored in the "Incubation media" field in the Alberta Microbiota Repository (AMBR) Master file. Brain heart infusion (BHI) - Strain and isolation information GENEPIO:0100619 isolate storage location WhitespaceMinimizedString TRUE An isolate datum specifying the location of where an isolate is stored e.g. in a particular freezer, on a particular shelf Enter the freezer storage location of the isolate as the "freezer number-shelf number-box number-unit number" e.g. FR1-R3-B1-S01. This value maps to the information stored in the "Spot code" in the Alberta Microbiota Repository (AMBR) Master file. FR1-R3-B1-S01 - Strain and isolation information GENEPIO:0100620 cellular respiration type cellular respiration type menu null value menu TRUE An isolate datum specifying the type of cellular respiration process used by the organism. Select the respiration type from the pick list. This value maps to the information stored in the "Aerobic/Anaerobic" field in the Alberta Microbiota Repository (AMBR) Master file. Aerobic respiration - GENEPIO:0001268 Host Information - Host Information GENEPIO:0001386 host (common name) host (common name) menu null value menu TRUE The commonly used name of the host. Common name is required if there was a host. Both common anime and scientific name can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Examples of common names are “Human” and “Canola plant”. Examples of scientific names are “Homo sapiens” and “Equus caballus”. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Human - Host Information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Common name e.g. Human, Canola plant. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Homo sapiens - Host Information GENEPIO:0001391 host disease host disease menu null value menu The name of the disease experienced by the host. If the sample was obtained from a host with a known disease, provide the name of the disease by seleting a value from the picklist. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Cystic fibrosis - GENEPIO:0001441 Sequencing - Sequencing GENEPIO:0100416 sequenced by sequenced_by menu null value menu The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the organization that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "University of Calgary". University of Calgary - Sequencing GENEPIO:0100470 sequenced by laboratory name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "Harrison Lab". Harrison Lab - Sequencing GENEPIO:0100471 sequenced by contact name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Harrison - Sequencing GENEPIO:0100422 sequenced by contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. jjharris@ucalgary.ca - Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Research - Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. This information can provide details about why the sample source might contain antibiotic potentiators. Screening for antibiotic potentiators in Cystic fibrosis disease contexts. - Sequencing GENEPIO:0001447 sequencing date date null value menu {sample_collection_date} The date the sample was sequenced. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-06-22 - Sequencing GENEPIO:0001448 library ID WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Provide the name of the run. This value maps to information in the "Sequencing Batch #" field Alberta Microbiota Repository (AMBR) Master file. 1876515_SA01_Plate 02 library ID - Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION - Sequencing GENEPIO:0001453 sequencing protocol name WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann - Sequencing GENEPIO:0100623 amplicon pcr primer list amplicon pcr primer list menu null value menu TRUE TRUE An information content entity specifying a list of primers used for amplicon sequencing. Select the primers used to generate the ribosomal 16S or 23S amplicon for sequencing from the pick list. This value maps to the information in the "Primers Used for sequencing" field Alberta Microbiota Repository (AMBR) Master file. 27F;1492R - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics OBI:0002874 input file name WhitespaceMinimizedString The name of the file containing the sequence data to be analysed. Enter the file name of the target gene sequence to be analyzed. ambr_staph_ABC_123.fasta - Bioinformatics and QC metrics OBI:0002885 reference accession WhitespaceMinimizedString null value menu TRUE An identifier that specifies an individual sequence record in a public sequence repository. Enter the EZBioCloud gene accession that most closely matches the sequence being analyzed. This value maps to the information in the "Accession No(s)." field in the Alberta Microbiota Repository (AMBR) Master file. FR821777 - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Provide the name of the protocol used to perform the species identification (i.e. the name of the protocol to perform the EZBioCloud search). EZBioCloud_searchprotocol_2023.txt - Bioinformatics and QC metrics OBI:0002883 reference database name WhitespaceMinimizedString null value menu TRUE An identifier of a biological or bioinformatics database. Select the reference database name from the pick list. For the AMBR Project, the reference database will be EZBioCloud. EZBioCloud - Bioinformatics and QC metrics OBI:0002884 reference database version WhitespaceMinimizedString null value menu TRUE The version of the database containing the reference sequences used for analysis. Enter the sequence search date as the version of EZBioCloud used. Record the date in ISO 8601 format i.e. YYYY_MM_DD. This value maps to the information in the "Search date" field in the Alberta Microbiota Repository (AMBR) Master file. 2021-05-23 - Bioinformatics and QC metrics OBI:0002880 coverage (percentage) WhitespaceMinimizedString null value menu TRUE The percentage of the reference sequence covered by the sequence of interest. Enter the completeness value. Do not include any symbols e.g. %. This value maps to "Completeness (%)" in the Alberta Microbiota Repository (AMBR) Master file. 98.2 - Bioinformatics and QC metrics OBI:0002882 sequence identity percentage WhitespaceMinimizedString null value menu TRUE Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. Enter the identity value. Do not include any symbols e.g. %. This value maps to "Similarity (%)" in the Alberta Microbiota Repository (AMBR) Master file. 99 - Bioinformatics and QC metrics GENEPIO:0100624 sequence identity (variance ratio) WhitespaceMinimizedString null value menu The ratio of the reference sequence not covered by the sequence of interest. Enter the number of different positions in the target sequence compared to the reference sequence length, expressed as a ratio. This value maps to "Variation ratio" in the Alberta Microbiota Repository (AMBR) Master file. 1/420 - Bioinformatics and QC metrics GENEPIO:0100625 top-hit taxon determination WhitespaceMinimizedString null value menu TRUE The taxon derived from the top hit in search results produced from a sequence similarity comparison. Enter the EZBioCloud taxon best-hit. This value maps to the information in the "Top-hit taxon (taxa)" field in the Alberta Microbiota Repository (AMBR) Master file. Staphylococcus argenteus - Bioinformatics and QC metrics GENEPIO:0100648 top-hit strain determination WhitespaceMinimizedString null value menu TRUE The strain designation derived from the top hit in search results produced from a sequence similarity comparison. Enter the EZBioCloud strain best-hit. This value maps to the information in the "Top-hit strain(s)" field in the Alberta Microbiota Repository (AMBR) Master file. MSHR1132(T) - Bioinformatics and QC metrics GENEPIO:0100626 trimmed ribosomal gene sequence WhitespaceMinimizedString null value menu TRUE The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed to produce a trimmed ribosomal RNA sequence. Enter the sequence of the trimmed ribosomal gene sequence. This value maps to the sequence in the "Trimmed Ribosomal Sequence" field in the Alberta Microbiota Repository (AMBR) Master file. TGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGSGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCTAGCCGTCGAAG - Bioinformatics and QC metrics GENEPIO:0100627 bioinformatics analysis details WhitespaceMinimizedString Any notes regarding the bioinformatics analysis. Enter any notes regarding the analysis as free text. This value maps to the "Comment" field in the information in the Alberta Microbiota Repository (AMBR) Master file. Pure-June 09-2022,Tube replaced by Rahgavi - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Rahgavi Poopalaraj, Shirin Afroj, Joe Harrison - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, AMBR v1.0.0 \ No newline at end of file +AMBR GENEPIO:0001122 Database Identifiers database_identifiers + Database Identifiers GENEPIO:0100456 isolate ID isolate_id WhitespaceMinimizedString TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the identifier created by the lab for the organism after isolation. This value maps to the "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. SA01 + Database Identifiers GENEPIO:0100457 alternative isolate ID alternative_isolate_id WhitespaceMinimizedString TRUE An alternative isolate ID assigned to the isolate by another organization. Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the "Label ID" in the Alberta Microbiota Repository (AMBR) Master file. 3411301 + Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE The user-defined name for the sample. Provide the sample ID provided by the original sample collector. This value is different from the "isolate_ID" as it represents the original material sampled rather than the organism that was isolated from the sampled material. This identifier may or may not be available. Lake_Louise_Water23 + GENEPIO:0001150 Sample collection and processing sample_collection_and_processing + Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that collected the original sample. The name of the institution of the original sample collector should be written out in full, (no abbreviations, with minor exceptions) and be consistent across multiple submissions e.g. University of Calgary, Alberta Health Services. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). University of Calgary + Sample collection and processing GENEPIO:0100429 sample collection project name sample_collection_project_name WhitespaceMinimizedString TRUE The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Children's Hospital biofilm study (A3-701-01) + Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca + Sample collection and processing GENEPIO:0001158 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada + Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 + Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-20 + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan + Sample collection and processing GENEPIO:0001189 geo_loc_name (city) geo_loc_name_city WhitespaceMinimizedString The city where the sample was collected. Provide the city name. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz Medicine Hat + Sample collection and processing GENEPIO:0100436 geo_loc_name (site) geo_loc_name_site GeoLocNameSiteMenu The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Lake Louise + Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE Taxonomic name of the organism. Provide the confirmed taxonomic name of the species. This value maps to the "Recommended identification" in the Alberta Microbiota Repository (AMBR) Master file. Staphylococcus aureus + Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Motivation for sampling may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Targeted surveillance + Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular investigation/surveillance activity/research question. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. ProvLab/IPC routine monitoring + Sample collection and processing GENEPIO:0100439 original sample description original_sample_description WhitespaceMinimizedString The original sample description provided by the sample collector. Provide the sample description provided by the original sample collector or the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. ACH coupons-water study, isolates 2010, 2011 see appendix 3 (Alberta Childrens Hospital) + Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Wound tissue (injury) + Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Nasal cavity + Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Feces + Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Bandage + Sample collection and processing GENEPIO:0001232 environmental site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. contact surface, metal can, hospital, wet market, bat cave. Provide a descriptor if an environmental site was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Hospital + Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Swab + Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Biopsy + Sample collection and processing GENEPIO:0001243 collection protocol collection_protocol WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Free text. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Collection_protocol_Children's Hospital biofilm study (A3-701-01) + Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. If multiple PCR products were generated from the isolate using different primer sets, indicate that the sequence records represents the same isolate by selecting "Biological replicate" in the "specimen processing" field. Every different sequence experiment should have its own record (i.e. if different amplicons have the same sequence but were generated using different primer sets, these should be stored as separate entries/lines in the spreadsheet). Information about replicates may be available in the "Top-hit taxon (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. Biological replicate + Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. Information about replicates may be available in the "Top-hit taxon (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. Multiple amplicons generated for isolate SA32 using different primer sets + GENEPIO:0100453 Strain and isolation information strain_and_isolation_information + Strain and isolation information GENEPIO:0100455 strain strain WhitespaceMinimizedString NullValueMenu TRUE The strain identifier. Provide the strain of the isolate. This value maps to the "Strain" in the Alberta Microbiota Repository (AMBR) Master file. CL10 + Strain and isolation information GENEPIO:0100583 taxonomic identification method taxonomic_identification_method TaxonomicIdentificationMethodMenu NullValueMenu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. For the AMBR Project, the "16S ribosomal gene sequencing assay" value will be the most appropriate. If the information is unknown or cannot be provided, leave blank or provide a null value. 16S ribosomal gene sequencing assay + Strain and isolation information GENEPIO:0100584 taxonomic identification method details taxonomic_identification_method_details TaxonomicIdentificationMethodDetailsMenu NullValueMenu TRUE The details of the process used to determine the taxonomic identification of an organism. Provide the criteria used for 16S sequencing taxonomic determination by selection a value from the pick list. These criteria are specific to the AMBR project and so do not correspond with standardized criteria in any ontology. The pick list is strictly for providing consistency in records rather than implementing community data standards. If another method was used for the taxonomic determination, leave blank. This value maps to the information stored in the "ID Category*" field in the Alberta Microbiota Repository (AMBR) Master file. Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database + Strain and isolation information GENEPIO:0100617 incubation temperature value incubation_temperature_value WhitespaceMinimizedString NullValueMenu TRUE An environmental datum specifying the temperature at which an organism or organisms were incubated for the purposes of growth on or in a particular medium. Provide the temperature at which the isolate was isolated. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. 37 + Strain and isolation information GENEPIO:0100618 incubation temperature unit incubation_temperature_unit IncubationTemperatureUnitMenu NullValueMenu TRUE An environmental datum specifying the temperature unit at which an organism or organisms were incubated for the purposes of growth on or in a particular medium. Select the temperature unit from the pick list. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. Degree Celsius + Strain and isolation information GENEPIO:0002107 isolation medium isolation_medium IsolationMediumMenu NullValueMenu TRUE An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. Select the isolation medium from the pick list. This value maps to the information stored in the "Incubation media" field in the Alberta Microbiota Repository (AMBR) Master file. Brain heart infusion (BHI) + Strain and isolation information GENEPIO:0100619 isolate storage location isolate_storage_location WhitespaceMinimizedString TRUE An isolate datum specifying the location of where an isolate is stored e.g. in a particular freezer, on a particular shelf Enter the freezer storage location of the isolate as the "freezer number-shelf number-box number-unit number" e.g. FR1-R3-B1-S01. This value maps to the information stored in the "Spot code" in the Alberta Microbiota Repository (AMBR) Master file. FR1-R3-B1-S01 + Strain and isolation information GENEPIO:0100620 cellular respiration type cellular_respiration_type CellularRespirationTypeMenu NullValueMenu TRUE An isolate datum specifying the type of cellular respiration process used by the organism. Select the respiration type from the pick list. This value maps to the information stored in the "Aerobic/Anaerobic" field in the Alberta Microbiota Repository (AMBR) Master file. Aerobic respiration + GENEPIO:0001268 Host Information host_information + Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu TRUE The commonly used name of the host. Common name is required if there was a host. Both common anime and scientific name can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Examples of common names are “Human” and “Canola plant”. Examples of scientific names are “Homo sapiens” and “Equus caballus”. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Human + Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Common name e.g. Human, Canola plant. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Homo sapiens + Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu The name of the disease experienced by the host. If the sample was obtained from a host with a known disease, provide the name of the disease by seleting a value from the picklist. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Cystic fibrosis + GENEPIO:0001441 Sequencing sequencing_ + Sequencing GENEPIO:0100416 sequenced by sequenced_by SequencedByMenu NullValueMenu The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the organization that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "University of Calgary". University of Calgary + Sequencing GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "Harrison Lab". Harrison Lab + Sequencing GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Harrison + Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. jjharris@ucalgary.ca + Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Research + Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. This information can provide details about why the sample source might contain antibiotic potentiators. Screening for antibiotic potentiators in Cystic fibrosis disease contexts. + Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu The date the sample was sequenced. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-06-22 + Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Provide the name of the run. This value maps to information in the "Sequencing Batch #" field Alberta Microbiota Repository (AMBR) Master file. 1876515_SA01_Plate 02 library ID + Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION + Sequencing GENEPIO:0001453 sequencing protocol name sequencing_protocol_name WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann + Sequencing GENEPIO:0100623 amplicon pcr primer list amplicon_pcr_primer_list AmpliconPcrPrimerListMenu NullValueMenu TRUE TRUE An information content entity specifying a list of primers used for amplicon sequencing. Select the primers used to generate the ribosomal 16S or 23S amplicon for sequencing from the pick list. This value maps to the information in the "Primers Used for sequencing" field Alberta Microbiota Repository (AMBR) Master file. 27F;1492R + GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics + Bioinformatics and QC metrics OBI:0002874 input file name input_file_name WhitespaceMinimizedString The name of the file containing the sequence data to be analysed. Enter the file name of the target gene sequence to be analyzed. ambr_staph_ABC_123.fasta + Bioinformatics and QC metrics OBI:0002885 reference accession reference_accession WhitespaceMinimizedString NullValueMenu TRUE An identifier that specifies an individual sequence record in a public sequence repository. Enter the EZBioCloud gene accession that most closely matches the sequence being analyzed. This value maps to the information in the "Accession No(s)." field in the Alberta Microbiota Repository (AMBR) Master file. FR821777 + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Provide the name of the protocol used to perform the species identification (i.e. the name of the protocol to perform the EZBioCloud search). EZBioCloud_searchprotocol_2023.txt + Bioinformatics and QC metrics OBI:0002883 reference database name reference_database_name WhitespaceMinimizedString NullValueMenu TRUE An identifier of a biological or bioinformatics database. Select the reference database name from the pick list. For the AMBR Project, the reference database will be EZBioCloud. EZBioCloud + Bioinformatics and QC metrics OBI:0002884 reference database version reference_database_version WhitespaceMinimizedString NullValueMenu TRUE The version of the database containing the reference sequences used for analysis. Enter the sequence search date as the version of EZBioCloud used. Record the date in ISO 8601 format i.e. YYYY_MM_DD. This value maps to the information in the "Search date" field in the Alberta Microbiota Repository (AMBR) Master file. 2021-05-23 + Bioinformatics and QC metrics OBI:0002880 coverage (percentage) coverage_percentage WhitespaceMinimizedString NullValueMenu TRUE The percentage of the reference sequence covered by the sequence of interest. Enter the completeness value. Do not include any symbols e.g. %. This value maps to "Completeness (%)" in the Alberta Microbiota Repository (AMBR) Master file. 98.2 + Bioinformatics and QC metrics OBI:0002882 sequence identity percentage sequence_identity_percentage WhitespaceMinimizedString NullValueMenu TRUE Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. Enter the identity value. Do not include any symbols e.g. %. This value maps to "Similarity (%)" in the Alberta Microbiota Repository (AMBR) Master file. 99 + Bioinformatics and QC metrics GENEPIO:0100624 sequence identity (variance ratio) sequence_identity_variance_ratio WhitespaceMinimizedString NullValueMenu The ratio of the reference sequence not covered by the sequence of interest. Enter the number of different positions in the target sequence compared to the reference sequence length, expressed as a ratio. This value maps to "Variation ratio" in the Alberta Microbiota Repository (AMBR) Master file. 1/420 + Bioinformatics and QC metrics GENEPIO:0100625 top-hit taxon determination tophit_taxon_determination WhitespaceMinimizedString NullValueMenu TRUE The taxon derived from the top hit in search results produced from a sequence similarity comparison. Enter the EZBioCloud taxon best-hit. This value maps to the information in the "Top-hit taxon (taxa)" field in the Alberta Microbiota Repository (AMBR) Master file. Staphylococcus argenteus + Bioinformatics and QC metrics GENEPIO:0100648 top-hit strain determination tophit_strain_determination WhitespaceMinimizedString NullValueMenu TRUE The strain designation derived from the top hit in search results produced from a sequence similarity comparison. Enter the EZBioCloud strain best-hit. This value maps to the information in the "Top-hit strain(s)" field in the Alberta Microbiota Repository (AMBR) Master file. MSHR1132(T) + Bioinformatics and QC metrics GENEPIO:0100626 trimmed ribosomal gene sequence trimmed_ribosomal_gene_sequence WhitespaceMinimizedString NullValueMenu TRUE The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed to produce a trimmed ribosomal RNA sequence. Enter the sequence of the trimmed ribosomal gene sequence. This value maps to the sequence in the "Trimmed Ribosomal Sequence" field in the Alberta Microbiota Repository (AMBR) Master file. TGCAAGTCGAGCGAACGGACGAGAAGCTTGCTTCTCTGATGTTAGCGGCGGACGSGTGAGTAACACGTGGATAACCTACCTATAAGACTGGGATAACTTCGGGAAACCGGAGCTAATACCGGATAATATTTTGAACCGCATGGTTCAAAAGTGAAAGACGGTCTTGCTGTCACTTATAGATGGATCCGCGCTGCATTAGCTAGTTGGTAAGGTAACGGCTTACCAAGGCAACGATGCATAGCCGACCTGAGAGGGTGATCGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCAAATCTTGACATCCTTTGACAACTCTAGAGATAGAGCCTTCCCCTTCGGGGGACAAAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTAAGCTTAGTTGCCATCATTAAGTTGGGCACTCTAAGTTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCTACACACGTGCTACAATGGACAATACAAAGGGCAGCGAAACCGCGAGGTCAAGCAAATCCCATAAAGTTGTTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGCCGGTGGAGTAACCTTTTAGGAGCTAGCCGTCGAAG + Bioinformatics and QC metrics GENEPIO:0100627 bioinformatics analysis details bioinformatics_analysis_details WhitespaceMinimizedString Any notes regarding the bioinformatics analysis. Enter any notes regarding the analysis as free text. This value maps to the "Comment" field in the information in the Alberta Microbiota Repository (AMBR) Master file. Pure-June 09-2022,Tube replaced by Rahgavi + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Rahgavi Poopalaraj, Shirin Afroj, Joe Harrison + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, AMBR v1.0.0 \ No newline at end of file From ddd8a58317a54dd95239d642611ac639022a983c Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:22:48 -0700 Subject: [PATCH 87/96] Influenza update, normalizing names --- web/templates/influenza/schema.json | 3416 ++++++++++++++++------ web/templates/influenza/schema.yaml | 1547 +++++----- web/templates/influenza/schema_enums.tsv | 1530 +++++----- web/templates/influenza/schema_slots.tsv | 182 +- 4 files changed, 4206 insertions(+), 2469 deletions(-) diff --git a/web/templates/influenza/schema.json b/web/templates/influenza/schema.json index 3c7187db..e826e028 100644 --- a/web/templates/influenza/schema.json +++ b/web/templates/influenza/schema.json @@ -46,6 +46,9 @@ "string": { "name": "string", "description": "A character string", + "notes": [ + "In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"string\"." + ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ "schema:Text" @@ -56,6 +59,9 @@ "integer": { "name": "integer", "description": "An integer", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"integer\"." + ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ "schema:Integer" @@ -66,6 +72,9 @@ "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"boolean\"." + ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ "schema:Boolean" @@ -77,6 +86,9 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"float\"." + ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ "schema:Float" @@ -87,6 +99,9 @@ "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"double\"." + ], "from_schema": "https://example.com/Influenza", "close_mappings": [ "schema:Float" @@ -97,6 +112,9 @@ "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"decimal\"." + ], "from_schema": "https://example.com/Influenza", "broad_mappings": [ "schema:Number" @@ -108,21 +126,23 @@ "name": "time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"time\"." ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ "schema:Time" ], "base": "XSDTime", - "uri": "xsd:dateTime", + "uri": "xsd:time", "repr": "str" }, "date": { "name": "date", "description": "a date (year, month and day) in an idealized calendar", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners don't work with straight date or time", + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date\"." ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ @@ -135,6 +155,9 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"datetime\"." + ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ "schema:DateTime" @@ -146,6 +169,9 @@ "date_or_datetime": { "name": "date_or_datetime", "description": "Either a date or a datetime", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"date_or_datetime\"." + ], "from_schema": "https://example.com/Influenza", "base": "str", "uri": "linkml:DateOrDatetime", @@ -154,6 +180,9 @@ "uriorcurie": { "name": "uriorcurie", "description": "a URI or a CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uriorcurie\"." + ], "from_schema": "https://example.com/Influenza", "base": "URIorCURIE", "uri": "xsd:anyURI", @@ -163,6 +192,9 @@ "name": "curie", "conforms_to": "https://www.w3.org/TR/curie/", "description": "a compact URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"curie\"." + ], "comments": [ "in RDF serializations this MUST be expanded to a URI", "in non-RDF serializations MAY be serialized as the compact representation" @@ -176,6 +208,9 @@ "name": "uri", "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"uri\"." + ], "comments": [ "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" ], @@ -190,6 +225,9 @@ "ncname": { "name": "ncname", "description": "Prefix part of CURIE", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"ncname\"." + ], "from_schema": "https://example.com/Influenza", "base": "NCName", "uri": "xsd:string", @@ -198,8 +236,11 @@ "objectidentifier": { "name": "objectidentifier", "description": "A URI or CURIE that represents an object in the model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"objectidentifier\"." + ], "comments": [ - "Used for inheritence and type checking" + "Used for inheritance and type checking" ], "from_schema": "https://example.com/Influenza", "base": "ElementIdentifier", @@ -209,19 +250,60 @@ "nodeidentifier": { "name": "nodeidentifier", "description": "A URI, CURIE or BNODE that represents a node in a model.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"nodeidentifier\"." + ], "from_schema": "https://example.com/Influenza", "base": "NodeIdentifier", "uri": "shex:nonLiteral", "repr": "str" + }, + "jsonpointer": { + "name": "jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpointer\"." + ], + "from_schema": "https://example.com/Influenza", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "jsonpath": { + "name": "jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"jsonpath\"." + ], + "from_schema": "https://example.com/Influenza", + "base": "str", + "uri": "xsd:string", + "repr": "str" + }, + "sparqlpath": { + "name": "sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "notes": [ + "If you are authoring schemas in LinkML YAML, the type is referenced with the lower case \"sparqlpath\"." + ], + "from_schema": "https://example.com/Influenza", + "base": "str", + "uri": "xsd:string", + "repr": "str" } }, "enums": { - "umbrella bioproject accession menu": { - "name": "umbrella bioproject accession menu", + "UmbrellaBioprojectAccessionMenu": { + "name": "UmbrellaBioprojectAccessionMenu", + "title": "umbrella bioproject accession menu", "from_schema": "https://example.com/Influenza" }, "null value menu": { "name": "null value menu", + "title": "null value menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Not Applicable": { @@ -246,8 +328,9 @@ } } }, - "geo_loc_name (state/province/territory) menu": { - "name": "geo_loc_name (state/province/territory) menu", + "GeoLocNameStateProvinceTerritoryMenu": { + "name": "GeoLocNameStateProvinceTerritoryMenu", + "title": "geo_loc_name (state/province/territory) menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Alberta": { @@ -304,8 +387,9 @@ } } }, - "host age unit menu": { - "name": "host age unit menu", + "HostAgeUnitMenu": { + "name": "HostAgeUnitMenu", + "title": "host age unit menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "month": { @@ -318,8 +402,9 @@ } } }, - "sample collection date precision menu": { - "name": "sample collection date precision menu", + "SampleCollectionDatePrecisionMenu": { + "name": "SampleCollectionDatePrecisionMenu", + "title": "sample collection date precision menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "year": { @@ -336,8 +421,9 @@ } } }, - "biomaterial extracted menu": { - "name": "biomaterial extracted menu", + "BiomaterialExtractedMenu": { + "name": "BiomaterialExtractedMenu", + "title": "biomaterial extracted menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "RNA (total)": { @@ -362,8 +448,9 @@ } } }, - "host vaccination status menu": { - "name": "host vaccination status menu", + "HostVaccinationStatusMenu": { + "name": "HostVaccinationStatusMenu", + "title": "host vaccination status menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Fully Vaccinated": { @@ -380,8 +467,9 @@ } } }, - "NML submitted specimen type menu": { - "name": "NML submitted specimen type menu", + "NmlSubmittedSpecimenTypeMenu": { + "name": "NmlSubmittedSpecimenTypeMenu", + "title": "NML submitted specimen type menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Swab": { @@ -406,8 +494,9 @@ } } }, - "Related specimen relationship type menu": { - "name": "Related specimen relationship type menu", + "RelatedSpecimenRelationshipTypeMenu": { + "name": "RelatedSpecimenRelationshipTypeMenu", + "title": "Related specimen relationship type menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Acute": { @@ -439,16 +528,19 @@ } } }, - "presampling activity menu": { - "name": "presampling activity menu", + "PresamplingActivityMenu": { + "name": "PresamplingActivityMenu", + "title": "presampling activity menu", "from_schema": "https://example.com/Influenza" }, - "vaccine name menu": { - "name": "vaccine name menu", + "VaccineNameMenu": { + "name": "VaccineNameMenu", + "title": "vaccine name menu", "from_schema": "https://example.com/Influenza" }, - "anatomical material menu": { - "name": "anatomical material menu", + "AnatomicalMaterialMenu": { + "name": "AnatomicalMaterialMenu", + "title": "anatomical material menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Blood": { @@ -480,8 +572,9 @@ } } }, - "anatomical part menu": { - "name": "anatomical part menu", + "AnatomicalPartMenu": { + "name": "AnatomicalPartMenu", + "title": "anatomical part menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Eye": { @@ -578,8 +671,9 @@ } } }, - "body product menu": { - "name": "body product menu", + "BodyProductMenu": { + "name": "BodyProductMenu", + "title": "body product menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Feces": { @@ -604,8 +698,9 @@ } } }, - "collection method menu": { - "name": "collection method menu", + "CollectionMethodMenu": { + "name": "CollectionMethodMenu", + "title": "collection method menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Amniocentesis": { @@ -668,8 +763,9 @@ } } }, - "collection device menu": { - "name": "collection device menu", + "CollectionDeviceMenu": { + "name": "CollectionDeviceMenu", + "title": "collection device menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Air filter": { @@ -722,8 +818,9 @@ } } }, - "host (scientific name) menu": { - "name": "host (scientific name) menu", + "HostScientificNameMenu": { + "name": "HostScientificNameMenu", + "title": "host (scientific name) menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Homo sapiens": { @@ -732,8 +829,9 @@ } } }, - "host (common name) menu": { - "name": "host (common name) menu", + "HostCommonNameMenu": { + "name": "HostCommonNameMenu", + "title": "host (common name) menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Human": { @@ -742,8 +840,9 @@ } } }, - "host health state menu": { - "name": "host health state menu", + "HostHealthStateMenu": { + "name": "HostHealthStateMenu", + "title": "host health state menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Asymptomatic": { @@ -768,8 +867,9 @@ } } }, - "host health status details menu": { - "name": "host health status details menu", + "HostHealthStatusDetailsMenu": { + "name": "HostHealthStatusDetailsMenu", + "title": "host health status details menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Hospitalized": { @@ -805,8 +905,9 @@ } } }, - "host health outcome menu": { - "name": "host health outcome menu", + "HostHealthOutcomeMenu": { + "name": "HostHealthOutcomeMenu", + "title": "host health outcome menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Deceased": { @@ -827,8 +928,9 @@ } } }, - "host disease menu": { - "name": "host disease menu", + "HostDiseaseMenu": { + "name": "HostDiseaseMenu", + "title": "host disease menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Influenza": { @@ -837,8 +939,9 @@ } } }, - "organism menu": { - "name": "organism menu", + "OrganismMenu": { + "name": "OrganismMenu", + "title": "organism menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Influenza A virus (H1N1)": { @@ -881,8 +984,9 @@ } } }, - "purpose of sampling menu": { - "name": "purpose of sampling menu", + "PurposeOfSamplingMenu": { + "name": "PurposeOfSamplingMenu", + "title": "purpose of sampling menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Cluster/Outbreak investigation": { @@ -903,8 +1007,9 @@ } } }, - "purpose of sequencing menu": { - "name": "purpose of sequencing menu", + "PurposeOfSequencingMenu": { + "name": "PurposeOfSequencingMenu", + "title": "purpose of sequencing menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Baseline surveillance (random sampling)": { @@ -969,8 +1074,9 @@ } } }, - "specimen processing menu": { - "name": "specimen processing menu", + "SpecimenProcessingMenu": { + "name": "SpecimenProcessingMenu", + "title": "specimen processing menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Virus passage": { @@ -1007,8 +1113,9 @@ } } }, - "host age bin menu": { - "name": "host age bin menu", + "HostAgeBinMenu": { + "name": "HostAgeBinMenu", + "title": "host age bin menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "0 - 9": { @@ -1051,20 +1158,21 @@ "text": "90 - 99", "meaning": "GENEPIO:0100058", "exact_mappings": [ - "VirusSeq_Portal:90+" + "VirusSeq_Portal:90%2B" ] }, "100+": { "text": "100+", "meaning": "GENEPIO:0100059", "exact_mappings": [ - "VirusSeq_Portal:90+" + "VirusSeq_Portal:90%2B" ] } } }, - "host gender menu": { - "name": "host gender menu", + "HostGenderMenu": { + "name": "HostGenderMenu", + "title": "host gender menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Female": { @@ -1093,8 +1201,9 @@ } } }, - "exposure event menu": { - "name": "exposure event menu", + "ExposureEventMenu": { + "name": "ExposureEventMenu", + "title": "exposure event menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Mass Gathering": { @@ -1189,8 +1298,9 @@ } } }, - "exposure contact level menu": { - "name": "exposure contact level menu", + "ExposureContactLevelMenu": { + "name": "ExposureContactLevelMenu", + "title": "exposure contact level menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Contact with infected individual": { @@ -1219,8 +1329,9 @@ } } }, - "host role menu": { - "name": "host role menu", + "HostRoleMenu": { + "name": "HostRoleMenu", + "title": "host role menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Attendee": { @@ -1415,8 +1526,9 @@ } } }, - "exposure setting menu": { - "name": "exposure setting menu", + "ExposureSettingMenu": { + "name": "ExposureSettingMenu", + "title": "exposure setting menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Human Exposure": { @@ -1722,8 +1834,9 @@ } } }, - "sequencing instrument menu": { - "name": "sequencing instrument menu", + "SequencingInstrumentMenu": { + "name": "SequencingInstrumentMenu", + "title": "sequencing instrument menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Illumina": { @@ -1952,38 +2065,40 @@ } } }, - "gene name menu": { - "name": "gene name menu", + "GeneNameMenu": { + "name": "GeneNameMenu", + "title": "gene name menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Matrix (M) gene": { "text": "Matrix (M) gene", "exact_mappings": [ - "BIOSAMPLE:E (orf4)" + "BIOSAMPLE:E%20%28orf4%29" ] }, "Haemagglutinin (HA) gene": { "text": "Haemagglutinin (HA) gene", "exact_mappings": [ - "BIOSAMPLE:M (orf5)" + "BIOSAMPLE:M%20%28orf5%29" ] }, "Influenza B- Matrix (M), NP, NS, HA gene": { "text": "Influenza B- Matrix (M), NP, NS, HA gene", "exact_mappings": [ - "BIOSAMPLE:N (orf9)" + "BIOSAMPLE:N%20%28orf9%29" ] }, "In of couple journals genes like PB2, PB1, PA": { "text": "In of couple journals genes like PB2, PB1, PA", "exact_mappings": [ - "BIOSAMPLE:S (orf2)" + "BIOSAMPLE:S%20%28orf2%29" ] } } }, - "sequence submitted by menu": { - "name": "sequence submitted by menu", + "SequenceSubmittedByMenu": { + "name": "SequenceSubmittedByMenu", + "title": "sequence submitted by menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -2065,8 +2180,9 @@ } } }, - "sample collected by menu": { - "name": "sample collected by menu", + "SampleCollectedByMenu": { + "name": "SampleCollectedByMenu", + "title": "sample collected by menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Alberta Precision Labs (APL)": { @@ -2172,8 +2288,9 @@ } } }, - "geo_loc_name (country) menu": { - "name": "geo_loc_name (country) menu", + "GeoLocNameCountryMenu": { + "name": "GeoLocNameCountryMenu", + "title": "geo_loc_name (country) menu", "from_schema": "https://example.com/Influenza", "permissible_values": { "Afghanistan": { @@ -3264,8 +3381,8 @@ } }, "slots": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", "comments": [ @@ -3278,19 +3395,22 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Sample ID given by the sample provider", - "CNPHI:Primary Specimen ID", + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", "NML_LIMS:TEXT_ID", "BIOSAMPLE:sample_name", - "VirusSeq_Portal:specimen collector sample ID" + "VirusSeq_Portal:specimen%20collector%20sample%20ID" ], "slot_uri": "GENEPIO:0001123", "identifier": true, + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "description": "The name of the third party company or laboratory that provided services.", "title": "third party lab service provider name", "comments": [ @@ -3306,10 +3426,13 @@ "NML_LIMS:HC_TEXT5" ], "slot_uri": "GENEPIO:0001202", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "description": "The identifier assigned to a sample by a third party service provider.", "title": "third party lab sample ID", "comments": [ @@ -3325,10 +3448,13 @@ "NML_LIMS:PH_ID_NUMBER_PRIMARY" ], "slot_uri": "GENEPIO:0001149", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", "comments": [ @@ -3344,11 +3470,14 @@ "NML_LIMS:PH_CASE_ID" ], "slot_uri": "GENEPIO:0100281", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", "comments": [ @@ -3361,22 +3490,25 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Related Specimen ID", - "CNPHI:Related Specimen Relationship Type", + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", "NML_LIMS:PH_RELATED_PRIMARY_ID" ], "slot_uri": "GENEPIO:0001128", + "domain_of": [ + "Influenza" + ], "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "description": "The identifier assigned to a sequenced isolate in IRIDA.", "title": "IRIDA sample name", "comments": [ @@ -3389,13 +3521,16 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:IRIDA sample name" + "NML_LIMS:IRIDA%20sample%20name" ], "slot_uri": "GENEPIO:0001131", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC accession number assigned to the umbrella BioProject.", "title": "umbrella bioproject accession", "comments": [ @@ -3408,18 +3543,21 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:umbrella bioproject accession" + "NML_LIMS:umbrella%20bioproject%20accession" ], "slot_uri": "GENEPIO:0001133", - "range": "umbrella bioproject accession menu", + "domain_of": [ + "Influenza" + ], + "range": "UmbrellaBioprojectAccessionMenu", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", "comments": [ @@ -3432,11 +3570,14 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:BioProject Accession", + "CNPHI:BioProject%20Accession", "NML_LIMS:PH_BIOPROJECT_ACCESSION", "BIOSAMPLE:bioproject_accession" ], "slot_uri": "GENEPIO:0001136", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3444,8 +3585,8 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", "comments": [ @@ -3458,10 +3599,13 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:BioSample Accession", + "CNPHI:BioSample%20Accession", "NML_LIMS:PH_BIOSAMPLE_ACCESSION" ], "slot_uri": "GENEPIO:0001139", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3469,8 +3613,8 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", "comments": [ @@ -3483,10 +3627,13 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:SRA Accession", + "CNPHI:SRA%20Accession", "NML_LIMS:PH_SRA_ACCESSION" ], "slot_uri": "GENEPIO:0001142", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3494,8 +3641,8 @@ "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", "comments": [ @@ -3508,10 +3655,13 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:GenBank Accession", - "NML_LIMS:GenBank accession" + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" ], "slot_uri": "GENEPIO:0001145", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3519,8 +3669,8 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", "comments": [ @@ -3533,12 +3683,15 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:GISAID Accession (if known)", - "NML_LIMS:SUBMISSIONS - GISAID Accession ID", + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID", "BIOSAMPLE:GISAID_accession", - "VirusSeq_Portal:GISAID accession" + "VirusSeq_Portal:GISAID%20accession" ], "slot_uri": "GENEPIO:0001147", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "structured_pattern": { "syntax": "{UPPER_CASE}", @@ -3546,8 +3699,8 @@ "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "description": "The user-defined name of the virus, specified in the organism-specific format prescribed by the GISAID database.", "title": "GISAID virus name", "comments": [ @@ -3559,11 +3712,14 @@ } ], "from_schema": "https://example.com/Influenza", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", "comments": [ @@ -3576,25 +3732,28 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Originating lab", - "CNPHI:Lab Name", + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", "NML_LIMS:CUSTOMER", "BIOSAMPLE:collected_by", - "VirusSeq_Portal:sample collected by" + "VirusSeq_Portal:sample%20collected%20by" ], "slot_uri": "GENEPIO:0001153", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "sample collected by menu" + "range": "SampleCollectedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", "comments": [ @@ -3607,14 +3766,17 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:sample collector contact email" + "NML_LIMS:sample%20collector%20contact%20email" ], "slot_uri": "GENEPIO:0001156", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency that generated the sequence.", "title": "sequenced by", "comments": [ @@ -3631,18 +3793,21 @@ "BIOSAMPLE:sequenced_by" ], "slot_uri": "GENEPIO:0100416", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "SequencedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", "comments": [ @@ -3655,25 +3820,28 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Submitting lab", - "CNPHI:Sequencing Centre", + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by", - "VirusSeq_Portal:sequence submitted by" + "VirusSeq_Portal:sequence%20submitted%20by" ], "slot_uri": "GENEPIO:0001159", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "sequence submitted by menu" + "range": "SequenceSubmittedByMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", "todos": [ @@ -3690,25 +3858,28 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Collection date", - "CNPHI:Patient Sample Collected Date", + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", "NML_LIMS:HC_COLLECT_DATE", - "BIOSAMPLE:sample collection date", - "VirusSeq_Portal:sample collection date" + "BIOSAMPLE:sample%20collection%20date", + "VirusSeq_Portal:sample%20collection%20date" ], "slot_uri": "GENEPIO:0001174", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", "comments": [ @@ -3721,22 +3892,25 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Precision of date collected", + "CNPHI:Precision%20of%20date%20collected", "NML_LIMS:HC_TEXT2" ], "slot_uri": "GENEPIO:0001177", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "sample collection date precision menu" + "range": "SampleCollectionDatePrecisionMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", "comments": [ @@ -3750,24 +3924,27 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "GISAID:Location", - "CNPHI:Patient Country", + "CNPHI:Patient%20Country", "NML_LIMS:HC_COUNTRY", "BIOSAMPLE:geo_loc_name", - "VirusSeq_Portal:geo_loc_name (country)" + "VirusSeq_Portal:geo_loc_name%20%28country%29" ], "slot_uri": "GENEPIO:0001181", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (country) menu" + "range": "GeoLocNameCountryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", "comments": [ @@ -3780,19 +3957,22 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Patient Province", + "CNPHI:Patient%20Province", "NML_LIMS:HC_PROVINCE", "BIOSAMPLE:geo_loc_name", - "VirusSeq_Portal:geo_loc_name (state/province/territory)" + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" ], "slot_uri": "GENEPIO:0001185", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "geo_loc_name (state/province/territory) menu" + "range": "GeoLocNameStateProvinceTerritoryMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -3816,13 +3996,16 @@ "VirusSeq_Portal:organism" ], "slot_uri": "GENEPIO:0001191", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "organism menu" + "range": "OrganismMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -3832,27 +4015,30 @@ "title": "isolate", "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Virus name", - "CNPHI:GISAID Virus Name", - "NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS", + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS", "BIOSAMPLE:isolate", "BIOSAMPLE:GISAID_virus_name", "VirusSeq_Portal:isolate", - "VirusSeq_Portal:fasta header name" + "VirusSeq_Portal:fasta%20header%20name" ], "slot_uri": "GENEPIO:0001195", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", "comments": [ @@ -3865,24 +4051,27 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Reason for Sampling", + "CNPHI:Reason%20for%20Sampling", "NML_LIMS:HC_SAMPLE_CATEGORY", "BIOSAMPLE:purpose_of_sampling", - "VirusSeq_Portal:purpose of sampling" + "VirusSeq_Portal:purpose%20of%20sampling" ], "slot_uri": "GENEPIO:0001198", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "purpose of sampling menu" + "range": "PurposeOfSamplingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", "comments": [ @@ -3895,24 +4084,27 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Details on the Reason for Sampling", + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", "NML_LIMS:PH_SAMPLING_DETAILS", "BIOSAMPLE:description", - "VirusSeq_Portal:purpose of sampling details" + "VirusSeq_Portal:purpose%20of%20sampling%20details" ], "slot_uri": "GENEPIO:0001200", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", "comments": [ @@ -3925,15 +4117,18 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Specimen Type", + "CNPHI:Specimen%20Type", "NML_LIMS:PH_SPECIMEN_TYPE" ], "slot_uri": "GENEPIO:0001204", - "range": "NML submitted specimen type menu", + "domain_of": [ + "Influenza" + ], + "range": "NmlSubmittedSpecimenTypeMenu", "required": true }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", "title": "Related specimen relationship type", "comments": [ @@ -3946,12 +4141,15 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Related Specimen ID", - "CNPHI:Related Specimen Relationship Type", + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", "NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE" ], "slot_uri": "GENEPIO:0001209", - "range": "Related specimen relationship type menu" + "domain_of": [ + "Influenza" + ], + "range": "RelatedSpecimenRelationshipTypeMenu" }, "presampling_activity": { "name": "presampling_activity", @@ -3967,17 +4165,20 @@ ], "from_schema": "https://example.com/Influenza", "slot_uri": "GENEPIO:0100433", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "presampling_activity menu" + "range": "PresamplingActivityMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "presampling activity details": { - "name": "presampling activity details", + "presampling_activity_details": { + "name": "presampling_activity_details", "description": "The details of the activities or variables that may affect the sample collected.", "title": "presampling activity details", "comments": [ @@ -3990,10 +4191,13 @@ ], "from_schema": "https://example.com/Influenza", "slot_uri": "GENEPIO:0100434", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", "comments": [ @@ -4006,27 +4210,30 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Anatomical Material", + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", "NML_LIMS:PH_ISOLATION_SITE_DESC", "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_material", - "VirusSeq_Portal:anatomical material" + "VirusSeq_Portal:anatomical%20material" ], "slot_uri": "GENEPIO:0001211", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "anatomical material menu" + "range": "AnatomicalMaterialMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", "comments": [ @@ -4039,27 +4246,30 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Anatomical Site", + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", "NML_LIMS:PH_ISOLATION_SITE", "BIOSAMPLE:isolation_source", "BIOSAMPLE:anatomical_part", - "VirusSeq_Portal:anatomical part" + "VirusSeq_Portal:anatomical%20part" ], "slot_uri": "GENEPIO:0001214", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "anatomical part menu" + "range": "AnatomicalPartMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", "comments": [ @@ -4072,27 +4282,30 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Body Product", + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", "BIOSAMPLE:isolation_source", "BIOSAMPLE:body_product", - "VirusSeq_Portal:body product" + "VirusSeq_Portal:body%20product" ], "slot_uri": "GENEPIO:0001216", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "body product menu" + "range": "BodyProductMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", "comments": [ @@ -4105,27 +4318,30 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Specimen Collection Matrix", + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_device", - "VirusSeq_Portal:collection device" + "VirusSeq_Portal:collection%20device" ], "slot_uri": "GENEPIO:0001234", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "collection device menu" + "range": "CollectionDeviceMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", "comments": [ @@ -4138,27 +4354,30 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Specimen source", - "CNPHI:Collection Method", + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", "NML_LIMS:COLLECTION_METHOD", "BIOSAMPLE:isolation_source", "BIOSAMPLE:collection_method", - "VirusSeq_Portal:collection method" + "VirusSeq_Portal:collection%20method" ], "slot_uri": "GENEPIO:0001241", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "collection method menu" + "range": "CollectionMethodMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", "comments": [ @@ -4171,13 +4390,16 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:collection protocol" + "NML_LIMS:collection%20protocol" ], "slot_uri": "GENEPIO:0001243", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", "comments": [ @@ -4190,23 +4412,26 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Passage details/history", - "NML_LIMS:specimen processing" + "GISAID:Passage%20details/history", + "NML_LIMS:specimen%20processing" ], "slot_uri": "GENEPIO:0001253", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "recommended": true, + "multivalued": true, "any_of": [ { - "range": "specimen processing menu" + "range": "SpecimenProcessingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", "comments": [ @@ -4219,10 +4444,13 @@ ], "from_schema": "https://example.com/Influenza", "slot_uri": "GENEPIO:0100311", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "title": "biomaterial extracted", "comments": [ @@ -4235,20 +4463,23 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:biomaterial extracted" + "NML_LIMS:biomaterial%20extracted" ], "slot_uri": "GENEPIO:0001266", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "biomaterial extracted menu" + "range": "BiomaterialExtractedMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", "comments": [ @@ -4261,21 +4492,24 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Animal Type", + "CNPHI:Animal%20Type", "NML_LIMS:PH_ANIMAL_TYPE" ], "slot_uri": "GENEPIO:0001386", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "host (common name) menu" + "range": "HostCommonNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", "comments": [ @@ -4289,23 +4523,26 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "GISAID:Host", - "NML_LIMS:host (scientific name)", + "NML_LIMS:host%20%28scientific%20name%29", "BIOSAMPLE:host", - "VirusSeq_Portal:host (scientific name)" + "VirusSeq_Portal:host%20%28scientific%20name%29" ], "slot_uri": "GENEPIO:0001387", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "host (scientific name) menu" + "range": "HostScientificNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "description": "Health status of the host at the time of sample collection.", "title": "host health state", "comments": [ @@ -4318,23 +4555,26 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Patient status", - "CNPHI:Host Health State", + "GISAID:Patient%20status", + "CNPHI:Host%20Health%20State", "NML_LIMS:PH_HOST_HEALTH", "BIOSAMPLE:host_health_state" ], "slot_uri": "GENEPIO:0001388", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "host health state menu" + "range": "HostHealthStateMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "description": "Further details pertaining to the health or disease status of the host at time of collection.", "title": "host health status details", "comments": [ @@ -4347,21 +4587,24 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Host Health State Details", + "CNPHI:Host%20Health%20State%20Details", "NML_LIMS:PH_HOST_HEALTH_DETAILS" ], "slot_uri": "GENEPIO:0001389", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "host health status details menu" + "range": "HostHealthStatusDetailsMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", "comments": [ @@ -4378,17 +4621,20 @@ "BIOSAMPLE:host_disease_outcome" ], "slot_uri": "GENEPIO:0001390", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "host health outcome menu" + "range": "HostHealthOutcomeMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", "comments": [ @@ -4401,24 +4647,27 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Host Disease", + "CNPHI:Host%20Disease", "NML_LIMS:PH_HOST_DISEASE", "BIOSAMPLE:host_disease", - "VirusSeq_Portal:host disease" + "VirusSeq_Portal:host%20disease" ], "slot_uri": "GENEPIO:0001391", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "host disease menu" + "range": "HostDiseaseMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", "comments": [ @@ -4431,13 +4680,16 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Patient age", - "CNPHI:Patient Age", + "GISAID:Patient%20age", + "CNPHI:Patient%20Age", "NML_LIMS:PH_AGE", "BIOSAMPLE:host_age", - "VirusSeq_Portal:host age" + "VirusSeq_Portal:host%20age" ], "slot_uri": "GENEPIO:0001392", + "domain_of": [ + "Influenza" + ], "required": true, "minimum_value": 0, "maximum_value": 130, @@ -4446,12 +4698,12 @@ "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The unit used to measure the host age, in either months or years.", "title": "host age unit", "comments": [ @@ -4464,23 +4716,26 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Age Units", + "CNPHI:Age%20Units", "NML_LIMS:PH_AGE_UNIT", - "VirusSeq_Portal:host age unit" + "VirusSeq_Portal:host%20age%20unit" ], "slot_uri": "GENEPIO:0001393", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "host age unit menu" + "range": "HostAgeUnitMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host age bin", "comments": [ @@ -4493,23 +4748,26 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Host Age Category", + "CNPHI:Host%20Age%20Category", "NML_LIMS:PH_AGE_GROUP", - "VirusSeq_Portal:host age bin" + "VirusSeq_Portal:host%20age%20bin" ], "slot_uri": "GENEPIO:0001394", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { - "range": "host age bin menu" + "range": "HostAgeBinMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", "comments": [ @@ -4523,12 +4781,15 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "GISAID:Gender", - "CNPHI:Patient Sex", + "CNPHI:Patient%20Sex", "NML_LIMS:VD_SEX", "BIOSAMPLE:host_sex", - "VirusSeq_Portal:host gender" + "VirusSeq_Portal:host%20gender" ], "slot_uri": "GENEPIO:0001395", + "domain_of": [ + "Influenza" + ], "required": true, "structured_pattern": { "syntax": "{Title_Case}", @@ -4537,15 +4798,15 @@ }, "any_of": [ { - "range": "host gender menu" + "range": "HostGenderMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to e.g. #131", "title": "host subject ID", "comments": [ @@ -4558,14 +4819,17 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:host subject ID", + "NML_LIMS:host%20subject%20ID", "BIOSAMPLE:host_subject_id" ], "slot_uri": "GENEPIO:0001398", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", "comments": [ @@ -4581,17 +4845,20 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0001404", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "host vaccination status menu" + "range": "HostVaccinationStatusMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", "comments": [ @@ -4602,10 +4869,13 @@ "NML_LIMS:PH_VACCINATION_HISTORY" ], "slot_uri": "GENEPIO:0100321", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", "comments": [ @@ -4618,22 +4888,25 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Additional location information", - "CNPHI:Exposure Event", + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", "NML_LIMS:PH_EXPOSURE" ], "slot_uri": "GENEPIO:0001417", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "exposure event menu" + "range": "ExposureEventMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", "comments": [ @@ -4646,20 +4919,23 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:exposure contact level" + "NML_LIMS:exposure%20contact%20level" ], "slot_uri": "GENEPIO:0001418", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "exposure contact level menu" + "range": "ExposureContactLevelMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", "comments": [ @@ -4675,11 +4951,14 @@ "NML_LIMS:PH_HOST_ROLE" ], "slot_uri": "GENEPIO:0001419", - "multivalued": true, - "range": "host role menu" + "domain_of": [ + "Influenza" + ], + "range": "HostRoleMenu", + "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", "comments": [ @@ -4695,11 +4974,14 @@ "NML_LIMS:PH_EXPOSURE" ], "slot_uri": "GENEPIO:0001428", - "multivalued": true, - "range": "exposure setting menu" + "domain_of": [ + "Influenza" + ], + "range": "ExposureSettingMenu", + "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", "comments": [ @@ -4715,10 +4997,13 @@ "NML_LIMS:PH_EXPOSURE_DETAILS" ], "slot_uri": "GENEPIO:0001431", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", "comments": [ @@ -4731,25 +5016,28 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Reason for Sequencing", + "CNPHI:Reason%20for%20Sequencing", "NML_LIMS:PH_REASON_FOR_SEQUENCING", "BIOSAMPLE:purpose_of_sequencing", - "VirusSeq_Portal:purpose of sequencing" + "VirusSeq_Portal:purpose%20of%20sequencing" ], "slot_uri": "GENEPIO:0001445", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "purpose of sequencing menu" + "range": "PurposeOfSequencingMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", "comments": [ @@ -4762,28 +5050,28 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Details on the Reason for Sequencing", + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", - "VirusSeq_Portal:purpose of sequencing details" + "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], "slot_uri": "GENEPIO:0001446", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { "range": "WhitespaceMinimizedString" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", - "todos": [ - ">={sample_collection_date}" - ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." ], @@ -4797,18 +5085,21 @@ "NML_LIMS:PH_SEQUENCING_DATE" ], "slot_uri": "GENEPIO:0001447", + "domain_of": [ + "Influenza" + ], "required": true, "any_of": [ { "range": "date" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", "comments": [ @@ -4821,13 +5112,16 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:amplicon size" + "NML_LIMS:amplicon%20size" ], "slot_uri": "GENEPIO:0001449", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", "comments": [ @@ -4843,10 +5137,13 @@ "NML_LIMS:PH_LIBRARY_PREP_KIT" ], "slot_uri": "GENEPIO:0001450", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", "comments": [ @@ -4859,25 +5156,28 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Sequencing technology", - "CNPHI:Sequencing Instrument", + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", "NML_LIMS:PH_INSTRUMENT_CGN", - "VirusSeq_Portal:sequencing instrument" + "VirusSeq_Portal:sequencing%20instrument" ], "slot_uri": "GENEPIO:0001452", - "multivalued": true, + "domain_of": [ + "Influenza" + ], "required": true, + "multivalued": true, "any_of": [ { - "range": "sequencing instrument menu" + "range": "SequencingInstrumentMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol__": { + "name": "sequencing_protocol__", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -4891,13 +5191,16 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "NML_LIMS:PH_TESTING_PROTOCOL", - "VirusSeq_Portal:sequencing protocol" + "VirusSeq_Portal:sequencing%20protocol" ], "slot_uri": "GENEPIO:0001454", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", "comments": [ @@ -4905,13 +5208,16 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:amplicon pcr primer scheme" + "NML_LIMS:amplicon%20pcr%20primer%20scheme" ], "slot_uri": "GENEPIO:0001456", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", "comments": [ @@ -4925,14 +5231,17 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "NML_LIMS:PH_RAW_SEQUENCE_METHOD", - "VirusSeq_Portal:raw sequence data processing method" + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" ], "slot_uri": "GENEPIO:0001458", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", "comments": [ @@ -4946,14 +5255,17 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "NML_LIMS:PH_DEHOSTING_METHOD", - "VirusSeq_Portal:dehosting method" + "VirusSeq_Portal:dehosting%20method" ], "slot_uri": "GENEPIO:0001459", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", "comments": [ @@ -4966,17 +5278,20 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:Assembly method", - "CNPHI:consensus sequence", + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", "NML_LIMS:PH_CONSENSUS_SEQUENCE", - "VirusSeq_Portal:consensus sequence software name" + "VirusSeq_Portal:consensus%20sequence%20software%20name" ], "slot_uri": "GENEPIO:0001463", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", "comments": [ @@ -4989,16 +5304,19 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:consensus sequence", + "CNPHI:consensus%20sequence", "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", - "VirusSeq_Portal:consensus sequence software version" + "VirusSeq_Portal:consensus%20sequence%20software%20version" ], "slot_uri": "GENEPIO:0001469", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", "comments": [ @@ -5011,14 +5329,17 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:breadth of coverage value", - "VirusSeq_Portal:breadth of coverage value" + "NML_LIMS:breadth%20of%20coverage%20value", + "VirusSeq_Portal:breadth%20of%20coverage%20value" ], "slot_uri": "GENEPIO:0001472", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", "comments": [ @@ -5032,14 +5353,17 @@ "from_schema": "https://example.com/Influenza", "exact_mappings": [ "GISAID:Coverage", - "NML_LIMS:depth of coverage value", - "VirusSeq_Portal:depth of coverage value" + "NML_LIMS:depth%20of%20coverage%20value", + "VirusSeq_Portal:depth%20of%20coverage%20value" ], "slot_uri": "GENEPIO:0001474", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", "comments": [ @@ -5052,13 +5376,16 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:depth of coverage threshold" + "NML_LIMS:depth%20of%20coverage%20threshold" ], "slot_uri": "GENEPIO:0001475", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", "comments": [ @@ -5066,14 +5393,17 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:number of base pairs sequenced" + "NML_LIMS:number%20of%20base%20pairs%20sequenced" ], "slot_uri": "GENEPIO:0001482", + "domain_of": [ + "Influenza" + ], "range": "integer", "minimum_value": 0 }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "Size of the reconstructed genome described as the number of base pairs.", "title": "consensus genome length", "comments": [ @@ -5081,14 +5411,17 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:consensus genome length" + "NML_LIMS:consensus%20genome%20length" ], "slot_uri": "GENEPIO:0001483", + "domain_of": [ + "Influenza" + ], "range": "integer", "minimum_value": 0 }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", "comments": [ @@ -5096,14 +5429,17 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "NML_LIMS:reference genome accession", - "VirusSeq_Portal:reference genome accession" + "NML_LIMS:reference%20genome%20accession", + "VirusSeq_Portal:reference%20genome%20accession" ], "slot_uri": "GENEPIO:0001485", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", "comments": [ @@ -5111,16 +5447,19 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Bioinformatics Protocol", + "CNPHI:Bioinformatics%20Protocol", "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", - "VirusSeq_Portal:bioinformatics protocol" + "VirusSeq_Portal:bioinformatics%20protocol" ], "slot_uri": "GENEPIO:0001489", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "required": true }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 1", "comments": [ @@ -5128,23 +5467,26 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Gene Target 1", - "NML_LIMS:SUBMITTED_RESLT - Gene Target #1", + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", "BIOSAMPLE:gene_name_1", - "VirusSeq_Portal:gene name" + "VirusSeq_Portal:gene%20name" ], "slot_uri": "GENEPIO:0001507", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", "comments": [ @@ -5157,23 +5499,26 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Gene Target 1 CT Value", - "NML_LIMS:SUBMITTED_RESLT - Gene Target #1 CT Value", + "CNPHI:Gene%20Target%201%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", "BIOSAMPLE:diagnostic_PCR_CT_value_1", - "VirusSeq_Portal:diagnostic pcr Ct value" + "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" ], "slot_uri": "GENEPIO:0001509", + "domain_of": [ + "Influenza" + ], "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 2", "comments": [ @@ -5181,22 +5526,25 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Gene Target 2", - "NML_LIMS:SUBMITTED_RESLT - Gene Target #2", + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", "BIOSAMPLE:gene_name_2" ], "slot_uri": "GENEPIO:0001510", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", "comments": [ @@ -5209,22 +5557,25 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Gene Target 2 CT Value", - "NML_LIMS:SUBMITTED_RESLT - Gene Target #2 CT Value", + "CNPHI:Gene%20Target%202%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", "BIOSAMPLE:diagnostic_PCR_CT_value_2" ], "slot_uri": "GENEPIO:0001512", + "domain_of": [ + "Influenza" + ], "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 3", "comments": [ @@ -5232,21 +5583,24 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Gene Target 3", - "NML_LIMS:SUBMITTED_RESLT - Gene Target #3" + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233" ], "slot_uri": "GENEPIO:0001513", + "domain_of": [ + "Influenza" + ], "any_of": [ { - "range": "gene name menu" + "range": "GeneNameMenu" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", "comments": [ @@ -5259,16 +5613,19 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "CNPHI:Gene Target 3 CT Value", - "NML_LIMS:SUBMITTED_RESLT - Gene Target #3 CT Value" + "CNPHI:Gene%20Target%203%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value" ], "slot_uri": "GENEPIO:0001515", + "domain_of": [ + "Influenza" + ], "any_of": [ { "range": "decimal" }, { - "range": "null value menu" + "range": "NullValueMenu" } ] }, @@ -5291,11 +5648,14 @@ "NML_LIMS:PH_CANCOGEN_AUTHORS" ], "slot_uri": "GENEPIO:0001517", + "domain_of": [ + "Influenza" + ], "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", "comments": [ @@ -5308,11 +5668,14 @@ ], "from_schema": "https://example.com/Influenza", "exact_mappings": [ - "GISAID:DataHarmonizer provenance", - "CNPHI:Additional Comments", + "GISAID:DataHarmonizer%20provenance", + "CNPHI:Additional%20Comments", "NML_LIMS:HC_COMMENTS" ], "slot_uri": "GENEPIO:0001518", + "domain_of": [ + "Influenza" + ], "range": "Provenance" } }, @@ -5328,108 +5691,108 @@ "from_schema": "https://example.com/Influenza", "is_a": "dh_interface", "slot_usage": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "rank": 1, "slot_group": "Database Identifiers" }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "rank": 2, "slot_group": "Database Identifiers" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "rank": 3, "slot_group": "Database Identifiers" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "rank": 4, "slot_group": "Database Identifiers" }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "rank": 5, "slot_group": "Database Identifiers" }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "rank": 6, "slot_group": "Database Identifiers" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "rank": 7, "slot_group": "Database Identifiers" }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "rank": 8, "slot_group": "Database Identifiers" }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "rank": 9, "slot_group": "Database Identifiers" }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "rank": 10, "slot_group": "Database Identifiers" }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "rank": 11, "slot_group": "Database Identifiers" }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "rank": 12, "slot_group": "Database Identifiers" }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "rank": 13, "slot_group": "Database Identifiers" }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "rank": 14, "slot_group": "Sample collection and processing" }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "rank": 15, "slot_group": "Sample collection and processing" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "rank": 16, "slot_group": "Sample collection and processing" }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "rank": 17, "slot_group": "Sample collection and processing" }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "rank": 18, "slot_group": "Sample collection and processing" }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "rank": 19, "slot_group": "Sample collection and processing" }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "rank": 20, "slot_group": "Sample collection and processing" }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "rank": 21, "slot_group": "Sample collection and processing" }, @@ -5443,23 +5806,23 @@ "rank": 23, "slot_group": "Sample collection and processing" }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "rank": 24, "slot_group": "Sample collection and processing" }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "rank": 25, "slot_group": "Sample collection and processing" }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "rank": 26, "slot_group": "Sample collection and processing" }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "rank": 27, "slot_group": "Sample collection and processing" }, @@ -5468,268 +5831,268 @@ "rank": 28, "slot_group": "Sample collection and processing" }, - "presampling activity details": { - "name": "presampling activity details", + "presampling_activity_details": { + "name": "presampling_activity_details", "rank": 29, "slot_group": "Sample collection and processing" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "rank": 30, "slot_group": "Sample collection and processing" }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "rank": 31, "slot_group": "Sample collection and processing" }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "rank": 32, "slot_group": "Sample collection and processing" }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "rank": 33, "slot_group": "Sample collection and processing" }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "rank": 34, "slot_group": "Sample collection and processing" }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "rank": 35, "slot_group": "Sample collection and processing" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "rank": 36, "slot_group": "Sample collection and processing" }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "rank": 37, "slot_group": "Sample collection and processing" }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "rank": 38, "slot_group": "Sample collection and processing" }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "rank": 39, "slot_group": "Host Information" }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "rank": 40, "slot_group": "Host Information" }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "rank": 41, "slot_group": "Host Information" }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "rank": 42, "slot_group": "Host Information" }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "rank": 43, "slot_group": "Host Information" }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "rank": 44, "slot_group": "Host Information" }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "rank": 45, "slot_group": "Host Information" }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "rank": 46, "slot_group": "Host Information" }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "rank": 47, "slot_group": "Host Information" }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "rank": 48, "slot_group": "Host Information" }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "rank": 49, "slot_group": "Host Information" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "rank": 50, "slot_group": "Host vaccination information" }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "rank": 51, "slot_group": "Host vaccination information" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "rank": 52, "slot_group": "Host exposure information" }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "rank": 53, "slot_group": "Host exposure information" }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "rank": 54, "slot_group": "Host exposure information" }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "rank": 55, "slot_group": "Host exposure information" }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "rank": 56, "slot_group": "Host exposure information" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 57, "slot_group": "Sequencing" }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "rank": 58, "slot_group": "Sequencing" }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "rank": 59, "slot_group": "Sequencing" }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "rank": 60, "slot_group": "Sequencing" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "rank": 61, "slot_group": "Sequencing" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "rank": 62, "slot_group": "Sequencing" }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol__": { + "name": "sequencing_protocol__", "rank": 63, "slot_group": "Sequencing" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "rank": 64, "slot_group": "Sequencing" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "rank": 65, "slot_group": "Bioinformatics and QC metrics" }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "rank": 66, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "rank": 67, "slot_group": "Bioinformatics and QC metrics" }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "rank": 68, "slot_group": "Bioinformatics and QC metrics" }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "rank": 69, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "rank": 70, "slot_group": "Bioinformatics and QC metrics" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "rank": 71, "slot_group": "Bioinformatics and QC metrics" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "rank": 72, "slot_group": "Bioinformatics and QC metrics" }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "rank": 73, "slot_group": "Bioinformatics and QC metrics" }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "rank": 74, "slot_group": "Bioinformatics and QC metrics" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "rank": 75, "slot_group": "Bioinformatics and QC metrics" }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "rank": 76, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "rank": 77, "slot_group": "Pathogen diagnostic testing" }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "rank": 78, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "rank": 79, "slot_group": "Pathogen diagnostic testing" }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "rank": 80, "slot_group": "Pathogen diagnostic testing" }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "rank": 81, "slot_group": "Pathogen diagnostic testing" }, @@ -5738,22 +6101,37 @@ "rank": 82, "slot_group": "Contributor acknowledgement" }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "rank": 83, "slot_group": "Contributor acknowledgement" } }, "attributes": { - "specimen collector sample ID": { - "name": "specimen collector sample ID", + "specimen_collector_sample_id": { + "name": "specimen_collector_sample_id", "description": "The user-defined name for the sample.", "title": "specimen collector sample ID", + "comments": [ + "Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Sample%20ID%20given%20by%20the%20sample%20provider", + "CNPHI:Primary%20Specimen%20ID", + "NML_LIMS:TEXT_ID", + "BIOSAMPLE:sample_name", + "VirusSeq_Portal:specimen%20collector%20sample%20ID" + ], "rank": 1, "slot_uri": "GENEPIO:0001123", "identifier": true, - "alias": "specimen_collector_sample_ID", + "alias": "specimen_collector_sample_id", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5762,11 +6140,22 @@ "range": "WhitespaceMinimizedString", "required": true }, - "third party lab service provider name": { - "name": "third party lab service provider name", + "third_party_lab_service_provider_name": { + "name": "third_party_lab_service_provider_name", "description": "The name of the third party company or laboratory that provided services.", "title": "third party lab service provider name", + "comments": [ + "Provide the full, unabbreviated name of the company or laboratory." + ], + "examples": [ + { + "value": "Switch Health" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:HC_TEXT5" + ], "rank": 2, "slot_uri": "GENEPIO:0001202", "alias": "third_party_lab_service_provider_name", @@ -5777,14 +6166,25 @@ "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "third party lab sample ID": { - "name": "third party lab sample ID", + "third_party_lab_sample_id": { + "name": "third_party_lab_sample_id", "description": "The identifier assigned to a sample by a third party service provider.", "title": "third party lab sample ID", + "comments": [ + "Store the sample identifier supplied by the third party services provider." + ], + "examples": [ + { + "value": "SHK123456" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_ID_NUMBER_PRIMARY" + ], "rank": 3, "slot_uri": "GENEPIO:0001149", - "alias": "third_party_lab_sample_ID", + "alias": "third_party_lab_sample_id", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5792,14 +6192,25 @@ "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "case ID": { - "name": "case ID", + "case_id": { + "name": "case_id", "description": "The identifier used to specify an epidemiologically detected case of disease.", "title": "case ID", + "comments": [ + "Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing." + ], + "examples": [ + { + "value": "ABCD1234" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_CASE_ID" + ], "rank": 4, "slot_uri": "GENEPIO:0100281", - "alias": "case_ID", + "alias": "case_id", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5808,28 +6219,60 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "Related specimen primary ID": { - "name": "Related specimen primary ID", + "related_specimen_primary_id": { + "name": "related_specimen_primary_id", "description": "The primary ID of a related specimen previously submitted to the repository.", "title": "Related specimen primary ID", + "comments": [ + "Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system." + ], + "examples": [ + { + "value": "SR20-12345" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_PRIMARY_ID" + ], "rank": 5, "slot_uri": "GENEPIO:0001128", - "alias": "Related_specimen_primary_ID", + "alias": "related_specimen_primary_id", "owner": "Influenza", "domain_of": [ "Influenza" ], - "slot_group": "Database Identifiers" + "slot_group": "Database Identifiers", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "IRIDA sample name": { - "name": "IRIDA sample name", + "irida_sample_name": { + "name": "irida_sample_name", "description": "The identifier assigned to a sequenced isolate in IRIDA.", "title": "IRIDA sample name", + "comments": [ + "Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample)." + ], + "examples": [ + { + "value": "prov_rona_99" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:IRIDA%20sample%20name" + ], "rank": 6, "slot_uri": "GENEPIO:0001131", - "alias": "IRIDA_sample_name", + "alias": "irida_sample_name", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5837,11 +6280,22 @@ "slot_group": "Database Identifiers", "range": "WhitespaceMinimizedString" }, - "umbrella bioproject accession": { - "name": "umbrella bioproject accession", + "umbrella_bioproject_accession": { + "name": "umbrella_bioproject_accession", "description": "The INSDC accession number assigned to the umbrella BioProject.", "title": "umbrella bioproject accession", + "comments": [ + "Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject." + ], + "examples": [ + { + "value": "PRJNA623807" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:umbrella%20bioproject%20accession" + ], "rank": 7, "slot_uri": "GENEPIO:0001133", "alias": "umbrella_bioproject_accession", @@ -5850,18 +6304,31 @@ "Influenza" ], "slot_group": "Database Identifiers", - "range": "umbrella bioproject accession menu", + "range": "UmbrellaBioprojectAccessionMenu", "structured_pattern": { "syntax": "{UPPER_CASE}", "interpolated": true, "partial_match": false } }, - "bioproject accession": { - "name": "bioproject accession", + "bioproject_accession": { + "name": "bioproject_accession", "description": "The INSDC accession number of the BioProject(s) to which the BioSample belongs.", "title": "bioproject accession", + "comments": [ + "Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project." + ], + "examples": [ + { + "value": "PRJNA608651" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:BioProject%20Accession", + "NML_LIMS:PH_BIOPROJECT_ACCESSION", + "BIOSAMPLE:bioproject_accession" + ], "rank": 8, "slot_uri": "GENEPIO:0001136", "alias": "bioproject_accession", @@ -5877,11 +6344,23 @@ "partial_match": false } }, - "biosample accession": { - "name": "biosample accession", + "biosample_accession": { + "name": "biosample_accession", "description": "The identifier assigned to a BioSample in INSDC archives.", "title": "biosample accession", + "comments": [ + "Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN." + ], + "examples": [ + { + "value": "SAMN14180202" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:BioSample%20Accession", + "NML_LIMS:PH_BIOSAMPLE_ACCESSION" + ], "rank": 9, "slot_uri": "GENEPIO:0001139", "alias": "biosample_accession", @@ -5897,14 +6376,26 @@ "partial_match": false } }, - "SRA accession": { - "name": "SRA accession", + "sra_accession": { + "name": "sra_accession", "description": "The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.", "title": "SRA accession", + "comments": [ + "Store the accession assigned to the submitted \"run\". NCBI-SRA accessions start with SRR." + ], + "examples": [ + { + "value": "SRR11177792" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:SRA%20Accession", + "NML_LIMS:PH_SRA_ACCESSION" + ], "rank": 10, "slot_uri": "GENEPIO:0001142", - "alias": "SRA_accession", + "alias": "sra_accession", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5917,14 +6408,26 @@ "partial_match": false } }, - "GenBank accession": { - "name": "GenBank accession", + "genbank_accession": { + "name": "genbank_accession", "description": "The GenBank identifier assigned to the sequence in the INSDC archives.", "title": "GenBank accession", + "comments": [ + "Store the accession returned from a GenBank submission (viral genome assembly)." + ], + "examples": [ + { + "value": "MN908947.3" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:GenBank%20Accession", + "NML_LIMS:GenBank%20accession" + ], "rank": 11, "slot_uri": "GENEPIO:0001145", - "alias": "GenBank_accession", + "alias": "genbank_accession", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5937,14 +6440,28 @@ "partial_match": false } }, - "GISAID accession": { - "name": "GISAID accession", + "gisaid_accession": { + "name": "gisaid_accession", "description": "The GISAID accession number assigned to the sequence.", "title": "GISAID accession", + "comments": [ + "Store the accession returned from the GISAID submission." + ], + "examples": [ + { + "value": "EPI_ISL_436489" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:GISAID%20Accession%20%28if%20known%29", + "NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID", + "BIOSAMPLE:GISAID_accession", + "VirusSeq_Portal:GISAID%20accession" + ], "rank": 12, "slot_uri": "GENEPIO:0001147", - "alias": "GISAID_accession", + "alias": "gisaid_accession", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5957,13 +6474,21 @@ "partial_match": false } }, - "GISAID virus name": { - "name": "GISAID virus name", + "gisaid_virus_name": { + "name": "gisaid_virus_name", "description": "The user-defined name of the virus, specified in the organism-specific format prescribed by the GISAID database.", "title": "GISAID virus name", + "comments": [ + "Provide the GISAID virus name, which should be written in the format: A/Province/Country/SampleID/year" + ], + "examples": [ + { + "value": "A/Ontario/Canada/ABCD1234/2023" + } + ], "from_schema": "https://example.com/Influenza", "rank": 13, - "alias": "GISAID_virus_name", + "alias": "gisaid_virus_name", "owner": "Influenza", "domain_of": [ "Influenza" @@ -5972,11 +6497,26 @@ "range": "WhitespaceMinimizedString", "required": true }, - "sample collected by": { - "name": "sample collected by", + "sample_collected_by": { + "name": "sample_collected_by", "description": "The name of the agency that collected the original sample.", "title": "sample collected by", + "comments": [ + "The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other)." + ], + "examples": [ + { + "value": "BC Centre for Disease Control" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Originating%20lab", + "CNPHI:Lab%20Name", + "NML_LIMS:CUSTOMER", + "BIOSAMPLE:collected_by", + "VirusSeq_Portal:sample%20collected%20by" + ], "rank": 14, "slot_uri": "GENEPIO:0001153", "alias": "sample_collected_by", @@ -5985,13 +6525,32 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SampleCollectedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collector contact email": { - "name": "sample collector contact email", + "sample_collector_contact_email": { + "name": "sample_collector_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sample.", "title": "sample collector contact email", + "comments": [ + "The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca" + ], + "examples": [ + { + "value": "RespLab@lab.ca" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:sample%20collector%20contact%20email" + ], "rank": 15, "slot_uri": "GENEPIO:0001156", "alias": "sample_collector_contact_email", @@ -6003,11 +6562,23 @@ "range": "WhitespaceMinimizedString", "pattern": "^\\S+@\\S+\\.\\S+$" }, - "sequenced by": { - "name": "sequenced by", + "sequenced_by": { + "name": "sequenced_by", "description": "The name of the agency that generated the sequence.", "title": "sequenced by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by" + ], "rank": 16, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", @@ -6016,13 +6587,36 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SequencedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequence submitted by": { - "name": "sequence submitted by", + "sequence_submitted_by": { + "name": "sequence_submitted_by", "description": "The name of the agency that generated the sequence.", "title": "sequence submitted by", + "comments": [ + "The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the \"National Microbiology Laboratory (NML)\"." + ], + "examples": [ + { + "value": "Public Health Ontario (PHO)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Submitting%20lab", + "CNPHI:Sequencing%20Centre", + "NML_LIMS:PH_SEQUENCING_CENTRE", + "BIOSAMPLE:sequenced_by", + "VirusSeq_Portal:sequence%20submitted%20by" + ], "rank": 17, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", @@ -6031,13 +6625,40 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SequenceSubmittedByMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date": { - "name": "sample collection date", + "sample_collection_date": { + "name": "sample_collection_date", "description": "The date on which the sample was collected.", "title": "sample collection date", + "todos": [ + ">=2019-10-01", + "<={today}" + ], + "comments": [ + "Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add \"jitter\" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2020-03-16" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Collection%20date", + "CNPHI:Patient%20Sample%20Collected%20Date", + "NML_LIMS:HC_COLLECT_DATE", + "BIOSAMPLE:sample%20collection%20date", + "VirusSeq_Portal:sample%20collection%20date" + ], "rank": 18, "slot_uri": "GENEPIO:0001174", "alias": "sample_collection_date", @@ -6046,13 +6667,33 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "sample collection date precision": { - "name": "sample collection date precision", + "sample_collection_date_precision": { + "name": "sample_collection_date_precision", "description": "The precision to which the \"sample collection date\" was provided.", "title": "sample collection date precision", + "comments": [ + "Provide the precision of granularity to the \"day\", \"month\", or \"year\" for the date provided in the \"sample collection date\" field. The \"sample collection date\" will be truncated to the precision specified upon export; \"day\" for \"YYYY-MM-DD\", \"month\" for \"YYYY-MM\", or \"year\" for \"YYYY\"." + ], + "examples": [ + { + "value": "year" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Precision%20of%20date%20collected", + "NML_LIMS:HC_TEXT2" + ], "rank": 19, "slot_uri": "GENEPIO:0001177", "alias": "sample_collection_date_precision", @@ -6061,43 +6702,110 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "SampleCollectionDatePrecisionMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (country)": { - "name": "geo_loc_name (country)", + "geo_loc_name_country": { + "name": "geo_loc_name_country", "description": "The country where the sample was collected.", "title": "geo_loc_name (country)", + "comments": [ + "Provide the country name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Canada" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Location", + "CNPHI:Patient%20Country", + "NML_LIMS:HC_COUNTRY", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28country%29" + ], "rank": 20, "slot_uri": "GENEPIO:0001181", - "alias": "geo_loc_name_(country)", + "alias": "geo_loc_name_country", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameCountryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "geo_loc_name (state/province/territory)": { - "name": "geo_loc_name (state/province/territory)", + "geo_loc_name_state_province_territory": { + "name": "geo_loc_name_state_province_territory", "description": "The province/territory where the sample was collected.", "title": "geo_loc_name (state/province/territory)", + "comments": [ + "Provide the province/territory name from the controlled vocabulary provided." + ], + "examples": [ + { + "value": "Saskatchewan" + } + ], "from_schema": "https://example.com/Influenza", - "rank": 21, + "exact_mappings": [ + "CNPHI:Patient%20Province", + "NML_LIMS:HC_PROVINCE", + "BIOSAMPLE:geo_loc_name", + "VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29" + ], + "rank": 21, "slot_uri": "GENEPIO:0001185", - "alias": "geo_loc_name_(state/province/territory)", + "alias": "geo_loc_name_state_province_territory", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "GeoLocNameStateProvinceTerritoryMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "organism": { "name": "organism", "description": "Taxonomic name of the organism.", "title": "organism", + "comments": [ + "Select the type of influenza virus from the picklist provided." + ], + "examples": [ + { + "value": "Influenza virus A virus (H1N1)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Pathogen", + "NML_LIMS:HC_CURRENT_ID", + "BIOSAMPLE:organism", + "VirusSeq_Portal:organism" + ], "rank": 22, "slot_uri": "GENEPIO:0001191", "alias": "organism", @@ -6106,13 +6814,30 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "OrganismMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "isolate": { "name": "isolate", "description": "Identifier of the specific isolate.", "title": "isolate", "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Virus%20name", + "CNPHI:GISAID%20Virus%20Name", + "NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS", + "BIOSAMPLE:isolate", + "BIOSAMPLE:GISAID_virus_name", + "VirusSeq_Portal:isolate", + "VirusSeq_Portal:fasta%20header%20name" + ], "rank": 23, "slot_uri": "GENEPIO:0001195", "alias": "isolate", @@ -6121,13 +6846,35 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling": { - "name": "purpose of sampling", + "purpose_of_sampling": { + "name": "purpose_of_sampling", "description": "The reason that the sample was collected.", "title": "purpose of sampling", + "comments": [ + "The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the \"purpose of sequencing\" field." + ], + "examples": [ + { + "value": "Diagnostic testing" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sampling", + "NML_LIMS:HC_SAMPLE_CATEGORY", + "BIOSAMPLE:purpose_of_sampling", + "VirusSeq_Portal:purpose%20of%20sampling" + ], "rank": 24, "slot_uri": "GENEPIO:0001198", "alias": "purpose_of_sampling", @@ -6136,13 +6883,35 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "PurposeOfSamplingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sampling details": { - "name": "purpose of sampling details", + "purpose_of_sampling_details": { + "name": "purpose_of_sampling_details", "description": "The description of why the sample was collected, providing specific details.", "title": "purpose of sampling details", + "comments": [ + "Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value." + ], + "examples": [ + { + "value": "The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada." + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sampling", + "NML_LIMS:PH_SAMPLING_DETAILS", + "BIOSAMPLE:description", + "VirusSeq_Portal:purpose%20of%20sampling%20details" + ], "rank": 25, "slot_uri": "GENEPIO:0001200", "alias": "purpose_of_sampling_details", @@ -6151,43 +6920,84 @@ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "NML submitted specimen type": { - "name": "NML submitted specimen type", + "nml_submitted_specimen_type": { + "name": "nml_submitted_specimen_type", "description": "The type of specimen submitted to the National Microbiology Laboratory (NML) for testing.", "title": "NML submitted specimen type", + "comments": [ + "This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”." + ], + "examples": [ + { + "value": "swab" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Specimen%20Type", + "NML_LIMS:PH_SPECIMEN_TYPE" + ], "rank": 26, "slot_uri": "GENEPIO:0001204", - "alias": "NML_submitted_specimen_type", + "alias": "nml_submitted_specimen_type", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "range": "NML submitted specimen type menu", + "range": "NmlSubmittedSpecimenTypeMenu", "required": true }, - "Related specimen relationship type": { - "name": "Related specimen relationship type", + "related_specimen_relationship_type": { + "name": "related_specimen_relationship_type", "description": "The relationship of the current specimen to the specimen/sample previously submitted to the repository.", "title": "Related specimen relationship type", + "comments": [ + "Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system." + ], + "examples": [ + { + "value": "Reinfection testing" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Related%20Specimen%20ID", + "CNPHI:Related%20Specimen%20Relationship%20Type", + "NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE" + ], "rank": 27, "slot_uri": "GENEPIO:0001209", - "alias": "Related_specimen_relationship_type", + "alias": "related_specimen_relationship_type", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "range": "Related specimen relationship type menu" + "range": "RelatedSpecimenRelationshipTypeMenu" }, "presampling_activity": { "name": "presampling_activity", "description": "The upstream activities or variables that may affect the sample collected.", "title": "presampling_activity", + "comments": [ + "If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Vaccination" + } + ], "from_schema": "https://example.com/Influenza", "rank": 28, "slot_uri": "GENEPIO:0100433", @@ -6196,12 +7006,28 @@ "domain_of": [ "Influenza" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "PresamplingActivityMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "presampling activity details": { - "name": "presampling activity details", + "presampling_activity_details": { + "name": "presampling_activity_details", "description": "The details of the activities or variables that may affect the sample collected.", "title": "presampling activity details", + "comments": [ + "Briefly describe the presampling details using free text." + ], + "examples": [ + { + "value": "Patient was previously infected. Sample taken during convalescence." + } + ], "from_schema": "https://example.com/Influenza", "rank": 29, "slot_uri": "GENEPIO:0100434", @@ -6213,91 +7039,222 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "anatomical material": { - "name": "anatomical material", + "anatomical_material": { + "name": "anatomical_material", "description": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.", "title": "anatomical material", + "comments": [ + "Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Blood" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Material", + "NML_LIMS:PH_ISOLATION_SITE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_material", + "VirusSeq_Portal:anatomical%20material" + ], "rank": 30, "slot_uri": "GENEPIO:0001211", - "multivalued": true, "alias": "anatomical_material", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalMaterialMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "anatomical part": { - "name": "anatomical part", + "anatomical_part": { + "name": "anatomical_part", "description": "An anatomical part of an organism e.g. oropharynx.", "title": "anatomical part", + "comments": [ + "Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Nasopharynx (NP)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Anatomical%20Site", + "NML_LIMS:PH_ISOLATION_SITE", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:anatomical_part", + "VirusSeq_Portal:anatomical%20part" + ], "rank": 31, "slot_uri": "GENEPIO:0001214", - "multivalued": true, "alias": "anatomical_part", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "AnatomicalPartMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "body product": { - "name": "body product", + "body_product": { + "name": "body_product", "description": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.", "title": "body product", + "comments": [ + "Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Urine" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Body%20Product", + "NML_LIMS:PH_SPECIMEN_SOURCE_DESC", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:body_product", + "VirusSeq_Portal:body%20product" + ], "rank": 32, "slot_uri": "GENEPIO:0001216", - "multivalued": true, "alias": "body_product", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "BodyProductMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection device": { - "name": "collection device", + "collection_device": { + "name": "collection_device", "description": "The instrument or container used to collect the sample e.g. swab.", "title": "collection device", + "comments": [ + "Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Swab" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Specimen%20Collection%20Matrix", + "NML_LIMS:PH_SPECIMEN_TYPE_ORIG", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_device", + "VirusSeq_Portal:collection%20device" + ], "rank": 33, "slot_uri": "GENEPIO:0001234", - "multivalued": true, "alias": "collection_device", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionDeviceMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection method": { - "name": "collection method", + "collection_method": { + "name": "collection_method", "description": "The process used to collect the sample e.g. phlebotamy, necropsy.", "title": "collection method", + "comments": [ + "Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value." + ], + "examples": [ + { + "value": "Bronchoalveolar lavage (BAL)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Specimen%20source", + "CNPHI:Collection%20Method", + "NML_LIMS:COLLECTION_METHOD", + "BIOSAMPLE:isolation_source", + "BIOSAMPLE:collection_method", + "VirusSeq_Portal:collection%20method" + ], "rank": 34, "slot_uri": "GENEPIO:0001241", - "multivalued": true, "alias": "collection_method", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "CollectionMethodMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "collection protocol": { - "name": "collection protocol", + "collection_protocol": { + "name": "collection_protocol", "description": "The name and version of a particular protocol used for sampling.", "title": "collection protocol", + "comments": [ + "Free text." + ], + "examples": [ + { + "value": "FluSamplingProtocol v. 1.2" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:collection%20protocol" + ], "rank": 35, "slot_uri": "GENEPIO:0001243", "alias": "collection_protocol", @@ -6308,26 +7265,54 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "specimen processing": { - "name": "specimen processing", + "specimen_processing": { + "name": "specimen_processing", "description": "Any processing applied to the sample during or after receiving the sample.", "title": "specimen processing", + "comments": [ + "Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in \"lab host\", \"passage number\", and \"passage method\" fields. If none of the processes in the pick list apply, put \"not applicable\"." + ], + "examples": [ + { + "value": "Virus passage" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Passage%20details/history", + "NML_LIMS:specimen%20processing" + ], "rank": 36, "slot_uri": "GENEPIO:0001253", - "multivalued": true, "alias": "specimen_processing", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sample collection and processing", - "recommended": true + "recommended": true, + "multivalued": true, + "any_of": [ + { + "range": "SpecimenProcessingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "specimen processing details": { - "name": "specimen processing details", + "specimen_processing_details": { + "name": "specimen_processing_details", "description": "Detailed information regarding the processing applied to a sample during or after receiving the sample.", "title": "specimen processing details", + "comments": [ + "Provide a free text description of any processing details applied to a sample." + ], + "examples": [ + { + "value": "25 swabs were pooled and further prepared as a single sample during library prep." + } + ], "from_schema": "https://example.com/Influenza", "rank": 37, "slot_uri": "GENEPIO:0100311", @@ -6339,11 +7324,22 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "biomaterial extracted": { - "name": "biomaterial extracted", + "biomaterial_extracted": { + "name": "biomaterial_extracted", "description": "The biomaterial extracted from samples for the purpose of sequencing.", "title": "biomaterial extracted", + "comments": [ + "Provide the biomaterial extracted from the picklist in the template." + ], + "examples": [ + { + "value": "RNA (total)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:biomaterial%20extracted" + ], "rank": 38, "slot_uri": "GENEPIO:0001266", "alias": "biomaterial_extracted", @@ -6351,42 +7347,106 @@ "domain_of": [ "Influenza" ], - "slot_group": "Sample collection and processing" + "slot_group": "Sample collection and processing", + "any_of": [ + { + "range": "BiomaterialExtractedMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host (common name)": { - "name": "host (common name)", + "host_common_name": { + "name": "host_common_name", "description": "The commonly used name of the host.", "title": "host (common name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put \"not applicable." + ], + "examples": [ + { + "value": "Human" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Animal%20Type", + "NML_LIMS:PH_ANIMAL_TYPE" + ], "rank": 39, "slot_uri": "GENEPIO:0001386", - "alias": "host_(common_name)", + "alias": "host_common_name", "owner": "Influenza", "domain_of": [ "Influenza" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostCommonNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host (scientific name)": { - "name": "host (scientific name)", + "host_scientific_name": { + "name": "host_scientific_name", "description": "The taxonomic, or scientific name of the host.", "title": "host (scientific name)", + "comments": [ + "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put \"not applicable" + ], + "examples": [ + { + "value": "Homo sapiens" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Host", + "NML_LIMS:host%20%28scientific%20name%29", + "BIOSAMPLE:host", + "VirusSeq_Portal:host%20%28scientific%20name%29" + ], "rank": 40, "slot_uri": "GENEPIO:0001387", - "alias": "host_(scientific_name)", + "alias": "host_scientific_name", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostScientificNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health state": { - "name": "host health state", + "host_health_state": { + "name": "host_health_state", "description": "Health status of the host at the time of sample collection.", "title": "host health state", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Symptomatic" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Patient%20status", + "CNPHI:Host%20Health%20State", + "NML_LIMS:PH_HOST_HEALTH", + "BIOSAMPLE:host_health_state" + ], "rank": 41, "slot_uri": "GENEPIO:0001388", "alias": "host_health_state", @@ -6394,13 +7454,33 @@ "domain_of": [ "Influenza" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStateMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health status details": { - "name": "host health status details", + "host_health_status_details": { + "name": "host_health_status_details", "description": "Further details pertaining to the health or disease status of the host at time of collection.", "title": "host health status details", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Hospitalized (ICU)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Host%20Health%20State%20Details", + "NML_LIMS:PH_HOST_HEALTH_DETAILS" + ], "rank": 42, "slot_uri": "GENEPIO:0001389", "alias": "host_health_status_details", @@ -6408,13 +7488,33 @@ "domain_of": [ "Influenza" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthStatusDetailsMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host health outcome": { - "name": "host health outcome", + "host_health_outcome": { + "name": "host_health_outcome", "description": "Disease outcome in the host.", "title": "host health outcome", + "comments": [ + "If known, select a descriptor from the pick list provided in the template." + ], + "examples": [ + { + "value": "Recovered" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_HOST_HEALTH_OUTCOME", + "BIOSAMPLE:host_disease_outcome" + ], "rank": 43, "slot_uri": "GENEPIO:0001390", "alias": "host_health_outcome", @@ -6422,13 +7522,35 @@ "domain_of": [ "Influenza" ], - "slot_group": "Host Information" + "slot_group": "Host Information", + "any_of": [ + { + "range": "HostHealthOutcomeMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host disease": { - "name": "host disease", + "host_disease": { + "name": "host_disease", "description": "The name of the disease experienced by the host.", "title": "host disease", + "comments": [ + "Select \"Influenza\" from the pick list provided in the template." + ], + "examples": [ + { + "value": "Influenza" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Host%20Disease", + "NML_LIMS:PH_HOST_DISEASE", + "BIOSAMPLE:host_disease", + "VirusSeq_Portal:host%20disease" + ], "rank": 44, "slot_uri": "GENEPIO:0001391", "alias": "host_disease", @@ -6437,13 +7559,36 @@ "Influenza" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostDiseaseMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age": { - "name": "host age", + "host_age": { + "name": "host_age", "description": "Age of host at the time of sampling.", "title": "host age", + "comments": [ + "Enter the age of the host in years. If not available, provide a null value. If there is not host, put \"Not Applicable\"." + ], + "examples": [ + { + "value": "79" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Patient%20age", + "CNPHI:Patient%20Age", + "NML_LIMS:PH_AGE", + "BIOSAMPLE:host_age", + "VirusSeq_Portal:host%20age" + ], "rank": 45, "slot_uri": "GENEPIO:0001392", "alias": "host_age", @@ -6454,13 +7599,34 @@ "slot_group": "Host Information", "required": true, "minimum_value": 0, - "maximum_value": 130 + "maximum_value": 130, + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age unit": { - "name": "host age unit", + "host_age_unit": { + "name": "host_age_unit", "description": "The unit used to measure the host age, in either months or years.", "title": "host age unit", + "comments": [ + "Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin." + ], + "examples": [ + { + "value": "years" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Age%20Units", + "NML_LIMS:PH_AGE_UNIT", + "VirusSeq_Portal:host%20age%20unit" + ], "rank": 46, "slot_uri": "GENEPIO:0001393", "alias": "host_age_unit", @@ -6469,13 +7635,34 @@ "Influenza" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostAgeUnitMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host age bin": { - "name": "host age bin", + "host_age_bin": { + "name": "host_age_bin", "description": "Age of host at the time of sampling, expressed as an age group.", "title": "host age bin", + "comments": [ + "Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value." + ], + "examples": [ + { + "value": "60 - 69" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Host%20Age%20Category", + "NML_LIMS:PH_AGE_GROUP", + "VirusSeq_Portal:host%20age%20bin" + ], "rank": 47, "slot_uri": "GENEPIO:0001394", "alias": "host_age_bin", @@ -6484,13 +7671,36 @@ "Influenza" ], "slot_group": "Host Information", - "required": true + "required": true, + "any_of": [ + { + "range": "HostAgeBinMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host gender": { - "name": "host gender", + "host_gender": { + "name": "host_gender", "description": "The gender of the host at the time of sample collection.", "title": "host gender", + "comments": [ + "Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put \"Not Applicable\"." + ], + "examples": [ + { + "value": "Male" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Gender", + "CNPHI:Patient%20Sex", + "NML_LIMS:VD_SEX", + "BIOSAMPLE:host_sex", + "VirusSeq_Portal:host%20gender" + ], "rank": 48, "slot_uri": "GENEPIO:0001395", "alias": "host_gender", @@ -6504,16 +7714,36 @@ "syntax": "{Title_Case}", "interpolated": true, "partial_match": false - } + }, + "any_of": [ + { + "range": "HostGenderMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host subject ID": { - "name": "host subject ID", + "host_subject_id": { + "name": "host_subject_id", "description": "A unique identifier by which each host can be referred to e.g. #131", "title": "host subject ID", + "comments": [ + "Provide the host identifier. Should be a unique, user-defined identifier." + ], + "examples": [ + { + "value": "BCxy123" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:host%20subject%20ID", + "BIOSAMPLE:host_subject_id" + ], "rank": 49, "slot_uri": "GENEPIO:0001398", - "alias": "host_subject_ID", + "alias": "host_subject_id", "owner": "Influenza", "domain_of": [ "Influenza" @@ -6521,11 +7751,22 @@ "slot_group": "Host Information", "range": "WhitespaceMinimizedString" }, - "host vaccination status": { - "name": "host vaccination status", + "host_vaccination_status": { + "name": "host_vaccination_status", "description": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).", "title": "host vaccination status", + "comments": [ + "Select the vaccination status of the host from the pick list." + ], + "examples": [ + { + "value": "Fully Vaccinated" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 50, "slot_uri": "GENEPIO:0001404", "alias": "host_vaccination_status", @@ -6533,13 +7774,27 @@ "domain_of": [ "Influenza" ], - "slot_group": "Host vaccination information" + "slot_group": "Host vaccination information", + "any_of": [ + { + "range": "HostVaccinationStatusMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "vaccination history": { - "name": "vaccination history", + "vaccination_history": { + "name": "vaccination_history", "description": "A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases.", "title": "vaccination history", + "comments": [ + "Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons." + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_VACCINATION_HISTORY" + ], "rank": 51, "slot_uri": "GENEPIO:0100321", "alias": "vaccination_history", @@ -6550,11 +7805,24 @@ "slot_group": "Host vaccination information", "range": "WhitespaceMinimizedString" }, - "exposure event": { - "name": "exposure event", + "exposure_event": { + "name": "exposure_event", "description": "Event leading to exposure.", "title": "exposure event", + "comments": [ + "Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Social Gathering" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Additional%20location%20information", + "CNPHI:Exposure%20Event", + "NML_LIMS:PH_EXPOSURE" + ], "rank": 52, "slot_uri": "GENEPIO:0001417", "alias": "exposure_event", @@ -6562,13 +7830,32 @@ "domain_of": [ "Influenza" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureEventMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "exposure contact level": { - "name": "exposure contact level", + "exposure_contact_level": { + "name": "exposure_contact_level", "description": "The exposure transmission contact type.", "title": "exposure contact level", + "comments": [ + "Select direct or indirect exposure from the pick-list." + ], + "examples": [ + { + "value": "Direct" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:exposure%20contact%20level" + ], "rank": 53, "slot_uri": "GENEPIO:0001418", "alias": "exposure_contact_level", @@ -6576,45 +7863,86 @@ "domain_of": [ "Influenza" ], - "slot_group": "Host exposure information" + "slot_group": "Host exposure information", + "any_of": [ + { + "range": "ExposureContactLevelMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "host role": { - "name": "host role", + "host_role": { + "name": "host_role", "description": "The role of the host in relation to the exposure setting.", "title": "host role", + "comments": [ + "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Inpatient" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_HOST_ROLE" + ], "rank": 54, "slot_uri": "GENEPIO:0001419", - "multivalued": true, "alias": "host_role", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Host exposure information", - "range": "host role menu" + "range": "HostRoleMenu", + "multivalued": true }, - "exposure setting": { - "name": "exposure setting", + "exposure_setting": { + "name": "exposure_setting", "description": "The setting leading to exposure.", "title": "exposure setting", + "comments": [ + "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team." + ], + "examples": [ + { + "value": "Healthcare Setting" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE" + ], "rank": 55, "slot_uri": "GENEPIO:0001428", - "multivalued": true, "alias": "exposure_setting", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Host exposure information", - "range": "exposure setting menu" + "range": "ExposureSettingMenu", + "multivalued": true }, - "exposure details": { - "name": "exposure details", + "exposure_details": { + "name": "exposure_details", "description": "Additional host exposure information.", "title": "exposure details", + "comments": [ + "Free text description of the exposure." + ], + "examples": [ + { + "value": "Case infected family at home" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_EXPOSURE_DETAILS" + ], "rank": 56, "slot_uri": "GENEPIO:0001431", "alias": "exposure_details", @@ -6625,27 +7953,62 @@ "slot_group": "Host exposure information", "range": "WhitespaceMinimizedString" }, - "purpose of sequencing": { - "name": "purpose of sequencing", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose of sequencing", + "comments": [ + "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field." + ], + "examples": [ + { + "value": "Baseline surveillance (random sampling)" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING", + "BIOSAMPLE:purpose_of_sequencing", + "VirusSeq_Portal:purpose%20of%20sequencing" + ], "rank": 57, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "PurposeOfSequencingMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "purpose of sequencing details": { - "name": "purpose of sequencing details", + "purpose_of_sequencing_details": { + "name": "purpose_of_sequencing_details", "description": "The description of why the sample was sequenced providing specific details.", "title": "purpose of sequencing details", + "comments": [ + "Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection." + ], + "examples": [ + { + "value": "Seasonal flu research project" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Details%20on%20the%20Reason%20for%20Sequencing", + "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", + "VirusSeq_Portal:purpose%20of%20sequencing%20details" + ], "rank": 58, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", @@ -6654,13 +8017,32 @@ "Influenza" ], "slot_group": "Sequencing", - "required": true + "required": true, + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing date": { - "name": "sequencing date", + "sequencing_date": { + "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "comments": [ + "ISO 8601 standard \"YYYY-MM-DD\"." + ], + "examples": [ + { + "value": "2023-09-22" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_SEQUENCING_DATE" + ], "rank": 59, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", @@ -6669,13 +8051,32 @@ "Influenza" ], "slot_group": "Sequencing", - "required": true + "required": true, + "any_of": [ + { + "range": "date" + }, + { + "range": "NullValueMenu" + } + ] }, - "amplicon size": { - "name": "amplicon size", + "amplicon_size": { + "name": "amplicon_size", "description": "The length of the amplicon generated by PCR amplification.", "title": "amplicon size", + "comments": [ + "Provide the amplicon size, including the units." + ], + "examples": [ + { + "value": "300bp" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:amplicon%20size" + ], "rank": 60, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", @@ -6686,11 +8087,22 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "library preparation kit": { - "name": "library preparation kit", + "library_preparation_kit": { + "name": "library_preparation_kit", "description": "The name of the DNA library preparation kit used to generate the library being sequenced.", "title": "library preparation kit", + "comments": [ + "Provide the name of the library preparation kit used." + ], + "examples": [ + { + "value": "Nextera XT" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_LIBRARY_PREP_KIT" + ], "rank": 61, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", @@ -6701,30 +8113,64 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing instrument": { - "name": "sequencing instrument", + "sequencing_instrument": { + "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", "title": "sequencing instrument", + "comments": [ + "Select a sequencing instrument from the picklist provided in the template." + ], + "examples": [ + { + "value": "Oxford Nanopore MinION" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Sequencing%20technology", + "CNPHI:Sequencing%20Instrument", + "NML_LIMS:PH_INSTRUMENT_CGN", + "VirusSeq_Portal:sequencing%20instrument" + ], "rank": 62, "slot_uri": "GENEPIO:0001452", - "multivalued": true, "alias": "sequencing_instrument", "owner": "Influenza", "domain_of": [ "Influenza" ], "slot_group": "Sequencing", - "required": true + "required": true, + "multivalued": true, + "any_of": [ + { + "range": "SequencingInstrumentMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "sequencing protocol": { - "name": "sequencing protocol", + "sequencing_protocol__": { + "name": "sequencing_protocol__", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", + "comments": [ + "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. \"" + ], + "examples": [ + { + "value": "Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits." + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_TESTING_PROTOCOL", + "VirusSeq_Portal:sequencing%20protocol" + ], "rank": 63, "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol", + "alias": "sequencing_protocol__", "owner": "Influenza", "domain_of": [ "Influenza" @@ -6732,11 +8178,17 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "amplicon pcr primer scheme": { - "name": "amplicon pcr primer scheme", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", "title": "amplicon pcr primer scheme", + "comments": [ + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:amplicon%20pcr%20primer%20scheme" + ], "rank": 64, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", @@ -6747,11 +8199,23 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "raw sequence data processing method": { - "name": "raw sequence data processing method", + "raw_sequence_data_processing_method": { + "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", "title": "raw sequence data processing method", + "comments": [ + "Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3" + ], + "examples": [ + { + "value": "Porechop 0.2.3" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_RAW_SEQUENCE_METHOD", + "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" + ], "rank": 65, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", @@ -6763,11 +8227,23 @@ "range": "WhitespaceMinimizedString", "required": true }, - "dehosting method": { - "name": "dehosting method", + "dehosting_method": { + "name": "dehosting_method", "description": "The method used to remove host reads from the pathogen sequence.", "title": "dehosting method", + "comments": [ + "Provide the name and version number of the software used to remove host reads." + ], + "examples": [ + { + "value": "Nanostripper" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:PH_DEHOSTING_METHOD", + "VirusSeq_Portal:dehosting%20method" + ], "rank": 66, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", @@ -6779,11 +8255,25 @@ "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software name": { - "name": "consensus sequence software name", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", "description": "The name of software used to generate the consensus sequence.", "title": "consensus sequence software name", + "comments": [ + "Provide the name of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "iVar" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" + ], "rank": 67, "slot_uri": "GENEPIO:0001463", "alias": "consensus_sequence_software_name", @@ -6795,11 +8285,24 @@ "range": "WhitespaceMinimizedString", "required": true }, - "consensus sequence software version": { - "name": "consensus sequence software version", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", "description": "The version of the software used to generate the consensus sequence.", "title": "consensus sequence software version", + "comments": [ + "Provide the version of the software used to generate the consensus sequence." + ], + "examples": [ + { + "value": "1.3" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" + ], "rank": 68, "slot_uri": "GENEPIO:0001469", "alias": "consensus_sequence_software_version", @@ -6811,11 +8314,23 @@ "range": "WhitespaceMinimizedString", "required": true }, - "breadth of coverage value": { - "name": "breadth of coverage value", + "breadth_of_coverage_value": { + "name": "breadth_of_coverage_value", "description": "The percentage of the reference genome covered by the sequenced data, to a prescribed depth.", "title": "breadth of coverage value", + "comments": [ + "Provide value as a percent." + ], + "examples": [ + { + "value": "95%" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:breadth%20of%20coverage%20value", + "VirusSeq_Portal:breadth%20of%20coverage%20value" + ], "rank": 69, "slot_uri": "GENEPIO:0001472", "alias": "breadth_of_coverage_value", @@ -6826,11 +8341,24 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage value": { - "name": "depth of coverage value", + "depth_of_coverage_value": { + "name": "depth_of_coverage_value", "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", "title": "depth of coverage value", + "comments": [ + "Provide value as a fold of coverage." + ], + "examples": [ + { + "value": "400x" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Coverage", + "NML_LIMS:depth%20of%20coverage%20value", + "VirusSeq_Portal:depth%20of%20coverage%20value" + ], "rank": 70, "slot_uri": "GENEPIO:0001474", "alias": "depth_of_coverage_value", @@ -6841,11 +8369,22 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "depth of coverage threshold": { - "name": "depth of coverage threshold", + "depth_of_coverage_threshold": { + "name": "depth_of_coverage_threshold", "description": "The threshold used as a cut-off for the depth of coverage.", "title": "depth of coverage threshold", + "comments": [ + "Provide the threshold fold coverage." + ], + "examples": [ + { + "value": "100x" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:depth%20of%20coverage%20threshold" + ], "rank": 71, "slot_uri": "GENEPIO:0001475", "alias": "depth_of_coverage_threshold", @@ -6856,11 +8395,17 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "number of base pairs sequenced": { - "name": "number of base pairs sequenced", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", "description": "The number of total base pairs generated by the sequencing process.", "title": "number of base pairs sequenced", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:number%20of%20base%20pairs%20sequenced" + ], "rank": 72, "slot_uri": "GENEPIO:0001482", "alias": "number_of_base_pairs_sequenced", @@ -6872,11 +8417,17 @@ "range": "integer", "minimum_value": 0 }, - "consensus genome length": { - "name": "consensus genome length", + "consensus_genome_length": { + "name": "consensus_genome_length", "description": "Size of the reconstructed genome described as the number of base pairs.", "title": "consensus genome length", + "comments": [ + "Provide a numerical value (no need to include units)." + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:consensus%20genome%20length" + ], "rank": 73, "slot_uri": "GENEPIO:0001483", "alias": "consensus_genome_length", @@ -6888,11 +8439,18 @@ "range": "integer", "minimum_value": 0 }, - "reference genome accession": { - "name": "reference genome accession", + "reference_genome_accession": { + "name": "reference_genome_accession", "description": "A persistent, unique identifier of a genome database entry.", "title": "reference genome accession", + "comments": [ + "Provide the accession number of the reference genome." + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "NML_LIMS:reference%20genome%20accession", + "VirusSeq_Portal:reference%20genome%20accession" + ], "rank": 74, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", @@ -6903,11 +8461,19 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "bioinformatics protocol": { - "name": "bioinformatics protocol", + "bioinformatics_protocol": { + "name": "bioinformatics_protocol", "description": "A description of the overall bioinformatics strategy used.", "title": "bioinformatics protocol", + "comments": [ + "Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow." + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Bioinformatics%20Protocol", + "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", + "VirusSeq_Portal:bioinformatics%20protocol" + ], "rank": 75, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", @@ -6919,11 +8485,20 @@ "range": "WhitespaceMinimizedString", "required": true }, - "gene name 1": { - "name": "gene name 1", + "gene_name_1": { + "name": "gene_name_1", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 1", + "comments": [ + "Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Gene%20Target%201", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231", + "BIOSAMPLE:gene_name_1", + "VirusSeq_Portal:gene%20name" + ], "rank": 76, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", @@ -6931,27 +8506,65 @@ "domain_of": [ "Influenza" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr Ct value 1": { - "name": "diagnostic pcr Ct value 1", + "diagnostic_pcr_ct_value_1": { + "name": "diagnostic_pcr_ct_value_1", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 1", + "comments": [ + "Provide the CT value of the sample from the diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "21" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Gene%20Target%201%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_1", + "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" + ], "rank": 77, "slot_uri": "GENEPIO:0001509", - "alias": "diagnostic_pcr_Ct_value_1", + "alias": "diagnostic_pcr_ct_value_1", "owner": "Influenza", "domain_of": [ "Influenza" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "gene name 2": { - "name": "gene name 2", + "gene_name_2": { + "name": "gene_name_2", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 2", + "comments": [ + "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Gene%20Target%202", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", + "BIOSAMPLE:gene_name_2" + ], "rank": 78, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", @@ -6959,27 +8572,63 @@ "domain_of": [ "Influenza" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr Ct value 2": { - "name": "diagnostic pcr Ct value 2", + "diagnostic_pcr_ct_value_2": { + "name": "diagnostic_pcr_ct_value_2", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 2", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "36" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Gene%20Target%202%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", + "BIOSAMPLE:diagnostic_PCR_CT_value_2" + ], "rank": 79, "slot_uri": "GENEPIO:0001512", - "alias": "diagnostic_pcr_Ct_value_2", + "alias": "diagnostic_pcr_ct_value_2", "owner": "Influenza", "domain_of": [ "Influenza" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, - "gene name 3": { - "name": "gene name 3", + "gene_name_3": { + "name": "gene_name_3", "description": "The name of the gene used in the diagnostic RT-PCR test.", "title": "gene name 3", + "comments": [ + "Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI" + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Gene%20Target%203", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233" + ], "rank": 80, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", @@ -6987,27 +8636,68 @@ "domain_of": [ "Influenza" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "GeneNameMenu" + }, + { + "range": "NullValueMenu" + } + ] }, - "diagnostic pcr Ct value 3": { - "name": "diagnostic pcr Ct value 3", + "diagnostic_pcr_ct_value_3": { + "name": "diagnostic_pcr_ct_value_3", "description": "The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.", "title": "diagnostic pcr Ct value 3", + "comments": [ + "Provide the CT value of the sample from the second diagnostic RT-PCR test." + ], + "examples": [ + { + "value": "30" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "CNPHI:Gene%20Target%203%20CT%20Value", + "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value" + ], "rank": 81, "slot_uri": "GENEPIO:0001515", - "alias": "diagnostic_pcr_Ct_value_3", + "alias": "diagnostic_pcr_ct_value_3", "owner": "Influenza", "domain_of": [ "Influenza" ], - "slot_group": "Pathogen diagnostic testing" + "slot_group": "Pathogen diagnostic testing", + "any_of": [ + { + "range": "decimal" + }, + { + "range": "NullValueMenu" + } + ] }, "authors": { "name": "authors", "description": "Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.", "title": "authors", + "comments": [ + "Include the first and last names of all individuals that should be attributed, separated by a comma." + ], + "examples": [ + { + "value": "Tejinder Singh, Fei Hu, Joe Blogs" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:Authors", + "CNPHI:Authors", + "NML_LIMS:PH_CANCOGEN_AUTHORS" + ], "rank": 82, "slot_uri": "GENEPIO:0001517", "alias": "authors", @@ -7019,14 +8709,27 @@ "range": "WhitespaceMinimizedString", "recommended": true }, - "DataHarmonizer provenance": { - "name": "DataHarmonizer provenance", + "dataharmonizer_provenance": { + "name": "dataharmonizer_provenance", "description": "The DataHarmonizer software and template version provenance.", "title": "DataHarmonizer provenance", + "comments": [ + "The current software and template version information will be automatically generated in this field after the user utilizes the \"validate\" function. This information will be generated regardless as to whether the row is valid of not." + ], + "examples": [ + { + "value": "DataHarmonizer v3.3.3, Influenza v1.0.0" + } + ], "from_schema": "https://example.com/Influenza", + "exact_mappings": [ + "GISAID:DataHarmonizer%20provenance", + "CNPHI:Additional%20Comments", + "NML_LIMS:HC_COMMENTS" + ], "rank": 83, "slot_uri": "GENEPIO:0001518", - "alias": "DataHarmonizer_provenance", + "alias": "dataharmonizer_provenance", "owner": "Influenza", "domain_of": [ "Influenza" @@ -7037,7 +8740,6 @@ } } }, - "source_file": "schema.yaml", "settings": { "Title_Case": { "setting_key": "Title_Case", diff --git a/web/templates/influenza/schema.yaml b/web/templates/influenza/schema.yaml index 1c67dbed..26a3dc1f 100644 --- a/web/templates/influenza/schema.yaml +++ b/web/templates/influenza/schema.yaml @@ -2,7 +2,7 @@ id: https://example.com/Influenza name: Influenza description: Draft template for harmonizing human influenza virus genomic surveillance contextual data. -version: 1.0.0 +version: 1.0.1 imports: - linkml:types prefixes: @@ -19,151 +19,151 @@ classes: contextual data. is_a: dh_interface slots: - - specimen collector sample ID - - third party lab service provider name - - third party lab sample ID - - case ID - - Related specimen primary ID - - IRIDA sample name - - umbrella bioproject accession - - bioproject accession - - biosample accession - - SRA accession - - GenBank accession - - GISAID accession - - GISAID virus name - - sample collected by - - sample collector contact email - - sequenced by - - sequence submitted by - - sample collection date - - sample collection date precision - - geo_loc_name (country) - - geo_loc_name (state/province/territory) + - specimen_collector_sample_id + - third_party_lab_service_provider_name + - third_party_lab_sample_id + - case_id + - related_specimen_primary_id + - irida_sample_name + - umbrella_bioproject_accession + - bioproject_accession + - biosample_accession + - sra_accession + - genbank_accession + - gisaid_accession + - gisaid_virus_name + - sample_collected_by + - sample_collector_contact_email + - sequenced_by + - sequence_submitted_by + - sample_collection_date + - sample_collection_date_precision + - geo_loc_name_country + - geo_loc_name_state_province_territory - organism - isolate - - purpose of sampling - - purpose of sampling details - - NML submitted specimen type - - Related specimen relationship type + - purpose_of_sampling + - purpose_of_sampling_details + - nml_submitted_specimen_type + - related_specimen_relationship_type - presampling_activity - - presampling activity details - - anatomical material - - anatomical part - - body product - - collection device - - collection method - - collection protocol - - specimen processing - - specimen processing details - - biomaterial extracted - - host (common name) - - host (scientific name) - - host health state - - host health status details - - host health outcome - - host disease - - host age - - host age unit - - host age bin - - host gender - - host subject ID - - host vaccination status - - vaccination history - - exposure event - - exposure contact level - - host role - - exposure setting - - exposure details - - purpose of sequencing - - purpose of sequencing details - - sequencing date - - amplicon size - - library preparation kit - - sequencing instrument - - sequencing protocol - - amplicon pcr primer scheme - - raw sequence data processing method - - dehosting method - - consensus sequence software name - - consensus sequence software version - - breadth of coverage value - - depth of coverage value - - depth of coverage threshold - - number of base pairs sequenced - - consensus genome length - - reference genome accession - - bioinformatics protocol - - gene name 1 - - diagnostic pcr Ct value 1 - - gene name 2 - - diagnostic pcr Ct value 2 - - gene name 3 - - diagnostic pcr Ct value 3 + - presampling_activity_details + - anatomical_material + - anatomical_part + - body_product + - collection_device + - collection_method + - collection_protocol + - specimen_processing + - specimen_processing_details + - biomaterial_extracted + - host_common_name + - host_scientific_name + - host_health_state + - host_health_status_details + - host_health_outcome + - host_disease + - host_age + - host_age_unit + - host_age_bin + - host_gender + - host_subject_id + - host_vaccination_status + - vaccination_history + - exposure_event + - exposure_contact_level + - host_role + - exposure_setting + - exposure_details + - purpose_of_sequencing + - purpose_of_sequencing_details + - sequencing_date + - amplicon_size + - library_preparation_kit + - sequencing_instrument + - sequencing_protocol__ + - amplicon_pcr_primer_scheme + - raw_sequence_data_processing_method + - dehosting_method + - consensus_sequence_software_name + - consensus_sequence_software_version + - breadth_of_coverage_value + - depth_of_coverage_value + - depth_of_coverage_threshold + - number_of_base_pairs_sequenced + - consensus_genome_length + - reference_genome_accession + - bioinformatics_protocol + - gene_name_1 + - diagnostic_pcr_ct_value_1 + - gene_name_2 + - diagnostic_pcr_ct_value_2 + - gene_name_3 + - diagnostic_pcr_ct_value_3 - authors - - DataHarmonizer provenance + - dataharmonizer_provenance slot_usage: - specimen collector sample ID: + specimen_collector_sample_id: rank: 1 slot_group: Database Identifiers - third party lab service provider name: + third_party_lab_service_provider_name: rank: 2 slot_group: Database Identifiers - third party lab sample ID: + third_party_lab_sample_id: rank: 3 slot_group: Database Identifiers - case ID: + case_id: rank: 4 slot_group: Database Identifiers - Related specimen primary ID: + related_specimen_primary_id: rank: 5 slot_group: Database Identifiers - IRIDA sample name: + irida_sample_name: rank: 6 slot_group: Database Identifiers - umbrella bioproject accession: + umbrella_bioproject_accession: rank: 7 slot_group: Database Identifiers - bioproject accession: + bioproject_accession: rank: 8 slot_group: Database Identifiers - biosample accession: + biosample_accession: rank: 9 slot_group: Database Identifiers - SRA accession: + sra_accession: rank: 10 slot_group: Database Identifiers - GenBank accession: + genbank_accession: rank: 11 slot_group: Database Identifiers - GISAID accession: + gisaid_accession: rank: 12 slot_group: Database Identifiers - GISAID virus name: + gisaid_virus_name: rank: 13 slot_group: Database Identifiers - sample collected by: + sample_collected_by: rank: 14 slot_group: Sample collection and processing - sample collector contact email: + sample_collector_contact_email: rank: 15 slot_group: Sample collection and processing - sequenced by: + sequenced_by: rank: 16 slot_group: Sample collection and processing - sequence submitted by: + sequence_submitted_by: rank: 17 slot_group: Sample collection and processing - sample collection date: + sample_collection_date: rank: 18 slot_group: Sample collection and processing - sample collection date precision: + sample_collection_date_precision: rank: 19 slot_group: Sample collection and processing - geo_loc_name (country): + geo_loc_name_country: rank: 20 slot_group: Sample collection and processing - geo_loc_name (state/province/territory): + geo_loc_name_state_province_territory: rank: 21 slot_group: Sample collection and processing organism: @@ -172,189 +172,189 @@ classes: isolate: rank: 23 slot_group: Sample collection and processing - purpose of sampling: + purpose_of_sampling: rank: 24 slot_group: Sample collection and processing - purpose of sampling details: + purpose_of_sampling_details: rank: 25 slot_group: Sample collection and processing - NML submitted specimen type: + nml_submitted_specimen_type: rank: 26 slot_group: Sample collection and processing - Related specimen relationship type: + related_specimen_relationship_type: rank: 27 slot_group: Sample collection and processing presampling_activity: rank: 28 slot_group: Sample collection and processing - presampling activity details: + presampling_activity_details: rank: 29 slot_group: Sample collection and processing - anatomical material: + anatomical_material: rank: 30 slot_group: Sample collection and processing - anatomical part: + anatomical_part: rank: 31 slot_group: Sample collection and processing - body product: + body_product: rank: 32 slot_group: Sample collection and processing - collection device: + collection_device: rank: 33 slot_group: Sample collection and processing - collection method: + collection_method: rank: 34 slot_group: Sample collection and processing - collection protocol: + collection_protocol: rank: 35 slot_group: Sample collection and processing - specimen processing: + specimen_processing: rank: 36 slot_group: Sample collection and processing - specimen processing details: + specimen_processing_details: rank: 37 slot_group: Sample collection and processing - biomaterial extracted: + biomaterial_extracted: rank: 38 slot_group: Sample collection and processing - host (common name): + host_common_name: rank: 39 slot_group: Host Information - host (scientific name): + host_scientific_name: rank: 40 slot_group: Host Information - host health state: + host_health_state: rank: 41 slot_group: Host Information - host health status details: + host_health_status_details: rank: 42 slot_group: Host Information - host health outcome: + host_health_outcome: rank: 43 slot_group: Host Information - host disease: + host_disease: rank: 44 slot_group: Host Information - host age: + host_age: rank: 45 slot_group: Host Information - host age unit: + host_age_unit: rank: 46 slot_group: Host Information - host age bin: + host_age_bin: rank: 47 slot_group: Host Information - host gender: + host_gender: rank: 48 slot_group: Host Information - host subject ID: + host_subject_id: rank: 49 slot_group: Host Information - host vaccination status: + host_vaccination_status: rank: 50 slot_group: Host vaccination information - vaccination history: + vaccination_history: rank: 51 slot_group: Host vaccination information - exposure event: + exposure_event: rank: 52 slot_group: Host exposure information - exposure contact level: + exposure_contact_level: rank: 53 slot_group: Host exposure information - host role: + host_role: rank: 54 slot_group: Host exposure information - exposure setting: + exposure_setting: rank: 55 slot_group: Host exposure information - exposure details: + exposure_details: rank: 56 slot_group: Host exposure information - purpose of sequencing: + purpose_of_sequencing: rank: 57 slot_group: Sequencing - purpose of sequencing details: + purpose_of_sequencing_details: rank: 58 slot_group: Sequencing - sequencing date: + sequencing_date: rank: 59 slot_group: Sequencing - amplicon size: + amplicon_size: rank: 60 slot_group: Sequencing - library preparation kit: + library_preparation_kit: rank: 61 slot_group: Sequencing - sequencing instrument: + sequencing_instrument: rank: 62 slot_group: Sequencing - sequencing protocol: + sequencing_protocol__: rank: 63 slot_group: Sequencing - amplicon pcr primer scheme: + amplicon_pcr_primer_scheme: rank: 64 slot_group: Sequencing - raw sequence data processing method: + raw_sequence_data_processing_method: rank: 65 slot_group: Bioinformatics and QC metrics - dehosting method: + dehosting_method: rank: 66 slot_group: Bioinformatics and QC metrics - consensus sequence software name: + consensus_sequence_software_name: rank: 67 slot_group: Bioinformatics and QC metrics - consensus sequence software version: + consensus_sequence_software_version: rank: 68 slot_group: Bioinformatics and QC metrics - breadth of coverage value: + breadth_of_coverage_value: rank: 69 slot_group: Bioinformatics and QC metrics - depth of coverage value: + depth_of_coverage_value: rank: 70 slot_group: Bioinformatics and QC metrics - depth of coverage threshold: + depth_of_coverage_threshold: rank: 71 slot_group: Bioinformatics and QC metrics - number of base pairs sequenced: + number_of_base_pairs_sequenced: rank: 72 slot_group: Bioinformatics and QC metrics - consensus genome length: + consensus_genome_length: rank: 73 slot_group: Bioinformatics and QC metrics - reference genome accession: + reference_genome_accession: rank: 74 slot_group: Bioinformatics and QC metrics - bioinformatics protocol: + bioinformatics_protocol: rank: 75 slot_group: Bioinformatics and QC metrics - gene name 1: + gene_name_1: rank: 76 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 1: + diagnostic_pcr_ct_value_1: rank: 77 slot_group: Pathogen diagnostic testing - gene name 2: + gene_name_2: rank: 78 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 2: + diagnostic_pcr_ct_value_2: rank: 79 slot_group: Pathogen diagnostic testing - gene name 3: + gene_name_3: rank: 80 slot_group: Pathogen diagnostic testing - diagnostic pcr Ct value 3: + diagnostic_pcr_ct_value_3: rank: 81 slot_group: Pathogen diagnostic testing authors: rank: 82 slot_group: Contributor acknowledgement - DataHarmonizer provenance: + dataharmonizer_provenance: rank: 83 slot_group: Contributor acknowledgement slots: - specimen collector sample ID: - name: specimen collector sample ID + specimen_collector_sample_id: + name: specimen_collector_sample_id title: specimen collector sample ID description: The user-defined name for the sample. comments: Store the collector sample ID. If this number is considered identifiable @@ -363,75 +363,75 @@ slots: Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. - examples: - - value: prov_rona_99 slot_uri: GENEPIO:0001123 - range: WhitespaceMinimizedString identifier: true + range: WhitespaceMinimizedString required: true + examples: + - value: prov_rona_99 exact_mappings: - - GISAID:Sample ID given by the sample provider - - CNPHI:Primary Specimen ID + - GISAID:Sample%20ID%20given%20by%20the%20sample%20provider + - CNPHI:Primary%20Specimen%20ID - NML_LIMS:TEXT_ID - BIOSAMPLE:sample_name - - VirusSeq_Portal:specimen collector sample ID - third party lab service provider name: - name: third party lab service provider name + - VirusSeq_Portal:specimen%20collector%20sample%20ID + third_party_lab_service_provider_name: + name: third_party_lab_service_provider_name title: third party lab service provider name description: The name of the third party company or laboratory that provided services. comments: Provide the full, unabbreviated name of the company or laboratory. - examples: - - value: Switch Health slot_uri: GENEPIO:0001202 range: WhitespaceMinimizedString + examples: + - value: Switch Health exact_mappings: - NML_LIMS:HC_TEXT5 - third party lab sample ID: - name: third party lab sample ID + third_party_lab_sample_id: + name: third_party_lab_sample_id title: third party lab sample ID description: The identifier assigned to a sample by a third party service provider. comments: Store the sample identifier supplied by the third party services provider. - examples: - - value: SHK123456 slot_uri: GENEPIO:0001149 range: WhitespaceMinimizedString + examples: + - value: SHK123456 exact_mappings: - NML_LIMS:PH_ID_NUMBER_PRIMARY - case ID: - name: case ID + case_id: + name: case_id title: case ID description: The identifier used to specify an epidemiologically detected case of disease. comments: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. - examples: - - value: ABCD1234 slot_uri: GENEPIO:0100281 range: WhitespaceMinimizedString recommended: true + examples: + - value: ABCD1234 exact_mappings: - NML_LIMS:PH_CASE_ID - Related specimen primary ID: - name: Related specimen primary ID + related_specimen_primary_id: + name: related_specimen_primary_id title: Related specimen primary ID description: The primary ID of a related specimen previously submitted to the repository. comments: Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. - examples: - - value: SR20-12345 slot_uri: GENEPIO:0001128 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu + examples: + - value: SR20-12345 exact_mappings: - - CNPHI:Related Specimen ID - - CNPHI:Related Specimen Relationship Type + - CNPHI:Related%20Specimen%20ID + - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_PRIMARY_ID - IRIDA sample name: - name: IRIDA sample name + irida_sample_name: + name: irida_sample_name title: IRIDA sample name description: The identifier assigned to a sequenced isolate in IRIDA. comments: Store the IRIDA sample name. The IRIDA sample name will be created by @@ -442,32 +442,32 @@ slots: mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). - examples: - - value: prov_rona_99 slot_uri: GENEPIO:0001131 range: WhitespaceMinimizedString + examples: + - value: prov_rona_99 exact_mappings: - - NML_LIMS:IRIDA sample name - umbrella bioproject accession: - name: umbrella bioproject accession + - NML_LIMS:IRIDA%20sample%20name + umbrella_bioproject_accession: + name: umbrella_bioproject_accession title: umbrella bioproject accession description: The INSDC accession number assigned to the umbrella BioProject. comments: Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. - examples: - - value: PRJNA623807 slot_uri: GENEPIO:0001133 - range: umbrella bioproject accession menu + range: UmbrellaBioprojectAccessionMenu structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: PRJNA623807 exact_mappings: - - NML_LIMS:umbrella bioproject accession - bioproject accession: - name: bioproject accession + - NML_LIMS:umbrella%20bioproject%20accession + bioproject_accession: + name: bioproject_accession title: bioproject accession description: The INSDC accession number of the BioProject(s) to which the BioSample belongs. @@ -477,101 +477,101 @@ slots: by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. - examples: - - value: PRJNA608651 slot_uri: GENEPIO:0001136 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: PRJNA608651 exact_mappings: - - CNPHI:BioProject Accession + - CNPHI:BioProject%20Accession - NML_LIMS:PH_BIOPROJECT_ACCESSION - BIOSAMPLE:bioproject_accession - biosample accession: - name: biosample accession + biosample_accession: + name: biosample_accession title: biosample accession description: The identifier assigned to a BioSample in INSDC archives. comments: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. - examples: - - value: SAMN14180202 slot_uri: GENEPIO:0001139 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: SAMN14180202 exact_mappings: - - CNPHI:BioSample Accession + - CNPHI:BioSample%20Accession - NML_LIMS:PH_BIOSAMPLE_ACCESSION - SRA accession: - name: SRA accession + sra_accession: + name: sra_accession title: SRA accession description: The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. comments: Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. - examples: - - value: SRR11177792 slot_uri: GENEPIO:0001142 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: SRR11177792 exact_mappings: - - CNPHI:SRA Accession + - CNPHI:SRA%20Accession - NML_LIMS:PH_SRA_ACCESSION - GenBank accession: - name: GenBank accession + genbank_accession: + name: genbank_accession title: GenBank accession description: The GenBank identifier assigned to the sequence in the INSDC archives. comments: Store the accession returned from a GenBank submission (viral genome assembly). - examples: - - value: MN908947.3 slot_uri: GENEPIO:0001145 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: MN908947.3 exact_mappings: - - CNPHI:GenBank Accession - - NML_LIMS:GenBank accession - GISAID accession: - name: GISAID accession + - CNPHI:GenBank%20Accession + - NML_LIMS:GenBank%20accession + gisaid_accession: + name: gisaid_accession title: GISAID accession description: The GISAID accession number assigned to the sequence. comments: Store the accession returned from the GISAID submission. - examples: - - value: EPI_ISL_436489 slot_uri: GENEPIO:0001147 range: WhitespaceMinimizedString structured_pattern: syntax: '{UPPER_CASE}' partial_match: false interpolated: true + examples: + - value: EPI_ISL_436489 exact_mappings: - - CNPHI:GISAID Accession (if known) - - NML_LIMS:SUBMISSIONS - GISAID Accession ID + - CNPHI:GISAID%20Accession%20%28if%20known%29 + - NML_LIMS:SUBMISSIONS%20-%20GISAID%20Accession%20ID - BIOSAMPLE:GISAID_accession - - VirusSeq_Portal:GISAID accession - GISAID virus name: - name: GISAID virus name + - VirusSeq_Portal:GISAID%20accession + gisaid_virus_name: + name: gisaid_virus_name title: GISAID virus name description: The user-defined name of the virus, specified in the organism-specific format prescribed by the GISAID database. comments: 'Provide the GISAID virus name, which should be written in the format: A/Province/Country/SampleID/year' - examples: - - value: A/Ontario/Canada/ABCD1234/2023 range: WhitespaceMinimizedString required: true - sample collected by: - name: sample collected by + examples: + - value: A/Ontario/Canada/ABCD1234/2023 + sample_collected_by: + name: sample_collected_by title: sample collected by description: The name of the agency that collected the original sample. comments: The name of the sample collector should be written out in full, (with @@ -579,72 +579,72 @@ slots: Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). - examples: - - value: BC Centre for Disease Control slot_uri: GENEPIO:0001153 any_of: - - range: sample collected by menu - - range: null value menu + - range: SampleCollectedByMenu + - range: NullValueMenu required: true + examples: + - value: BC Centre for Disease Control exact_mappings: - - GISAID:Originating lab - - CNPHI:Lab Name + - GISAID:Originating%20lab + - CNPHI:Lab%20Name - NML_LIMS:CUSTOMER - BIOSAMPLE:collected_by - - VirusSeq_Portal:sample collected by - sample collector contact email: - name: sample collector contact email + - VirusSeq_Portal:sample%20collected%20by + sample_collector_contact_email: + name: sample_collector_contact_email title: sample collector contact email description: The email address of the contact responsible for follow-up regarding the sample. comments: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca - examples: - - value: RespLab@lab.ca slot_uri: GENEPIO:0001156 range: WhitespaceMinimizedString pattern: ^\S+@\S+\.\S+$ + examples: + - value: RespLab@lab.ca exact_mappings: - - NML_LIMS:sample collector contact email - sequenced by: - name: sequenced by + - NML_LIMS:sample%20collector%20contact%20email + sequenced_by: + name: sequenced_by title: sequenced by description: The name of the agency that generated the sequence. comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". - examples: - - value: Public Health Ontario (PHO) slot_uri: GENEPIO:0100416 any_of: - - range: sequence submitted by menu - - range: null value menu + - range: SequencedByMenu + - range: NullValueMenu required: true + examples: + - value: Public Health Ontario (PHO) exact_mappings: - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by - sequence submitted by: - name: sequence submitted by + sequence_submitted_by: + name: sequence_submitted_by title: sequence submitted by description: The name of the agency that generated the sequence. comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". - examples: - - value: Public Health Ontario (PHO) slot_uri: GENEPIO:0001159 any_of: - - range: sequence submitted by menu - - range: null value menu + - range: SequenceSubmittedByMenu + - range: NullValueMenu required: true + examples: + - value: Public Health Ontario (PHO) exact_mappings: - - GISAID:Submitting lab - - CNPHI:Sequencing Centre + - GISAID:Submitting%20lab + - CNPHI:Sequencing%20Centre - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by - - VirusSeq_Portal:sequence submitted by - sample collection date: - name: sample collection date + - VirusSeq_Portal:sequence%20submitted%20by + sample_collection_date: + name: sample_collection_date title: sample collection date description: The date on which the sample was collected. comments: "Sample collection date is critical for surveillance and many types\ @@ -653,87 +653,87 @@ slots: \ by adding or subtracting a calendar day (acceptable by GISAID). Alternatively,\ \ \u201Dreceived date\u201D may be used as a substitute. The date should be\ \ provided in ISO 8601 standard format \"YYYY-MM-DD\"." - examples: - - value: '2020-03-16' slot_uri: GENEPIO:0001174 any_of: - range: date - - range: null value menu - required: true + - range: NullValueMenu todos: - '>=2019-10-01' - <={today} + required: true + examples: + - value: '2020-03-16' exact_mappings: - - GISAID:Collection date - - CNPHI:Patient Sample Collected Date + - GISAID:Collection%20date + - CNPHI:Patient%20Sample%20Collected%20Date - NML_LIMS:HC_COLLECT_DATE - - BIOSAMPLE:sample collection date - - VirusSeq_Portal:sample collection date - sample collection date precision: - name: sample collection date precision + - BIOSAMPLE:sample%20collection%20date + - VirusSeq_Portal:sample%20collection%20date + sample_collection_date_precision: + name: sample_collection_date_precision title: sample collection date precision description: The precision to which the "sample collection date" was provided. comments: Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". - examples: - - value: year slot_uri: GENEPIO:0001177 any_of: - - range: sample collection date precision menu - - range: null value menu + - range: SampleCollectionDatePrecisionMenu + - range: NullValueMenu required: true + examples: + - value: year exact_mappings: - - CNPHI:Precision of date collected + - CNPHI:Precision%20of%20date%20collected - NML_LIMS:HC_TEXT2 - geo_loc_name (country): - name: geo_loc_name (country) + geo_loc_name_country: + name: geo_loc_name_country title: geo_loc_name (country) description: The country where the sample was collected. comments: Provide the country name from the controlled vocabulary provided. - examples: - - value: Canada slot_uri: GENEPIO:0001181 any_of: - - range: geo_loc_name (country) menu - - range: null value menu + - range: GeoLocNameCountryMenu + - range: NullValueMenu required: true + examples: + - value: Canada exact_mappings: - GISAID:Location - - CNPHI:Patient Country + - CNPHI:Patient%20Country - NML_LIMS:HC_COUNTRY - BIOSAMPLE:geo_loc_name - - VirusSeq_Portal:geo_loc_name (country) - geo_loc_name (state/province/territory): - name: geo_loc_name (state/province/territory) + - VirusSeq_Portal:geo_loc_name%20%28country%29 + geo_loc_name_state_province_territory: + name: geo_loc_name_state_province_territory title: geo_loc_name (state/province/territory) description: The province/territory where the sample was collected. comments: Provide the province/territory name from the controlled vocabulary provided. - examples: - - value: Saskatchewan slot_uri: GENEPIO:0001185 any_of: - - range: geo_loc_name (state/province/territory) menu - - range: null value menu + - range: GeoLocNameStateProvinceTerritoryMenu + - range: NullValueMenu required: true + examples: + - value: Saskatchewan exact_mappings: - - CNPHI:Patient Province + - CNPHI:Patient%20Province - NML_LIMS:HC_PROVINCE - BIOSAMPLE:geo_loc_name - - VirusSeq_Portal:geo_loc_name (state/province/territory) + - VirusSeq_Portal:geo_loc_name%20%28state/province/territory%29 organism: name: organism title: organism description: Taxonomic name of the organism. comments: Select the type of influenza virus from the picklist provided. - examples: - - value: Influenza virus A virus (H1N1) slot_uri: GENEPIO:0001191 any_of: - - range: organism menu - - range: null value menu + - range: OrganismMenu + - range: NullValueMenu required: true + examples: + - value: Influenza virus A virus (H1N1) exact_mappings: - CNPHI:Pathogen - NML_LIMS:HC_CURRENT_ID @@ -746,18 +746,18 @@ slots: slot_uri: GENEPIO:0001195 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true exact_mappings: - - GISAID:Virus name - - CNPHI:GISAID Virus Name - - NML_LIMS:RESULT - CANCOGEN_SUBMISSIONS + - GISAID:Virus%20name + - CNPHI:GISAID%20Virus%20Name + - NML_LIMS:RESULT%20-%20CANCOGEN_SUBMISSIONS - BIOSAMPLE:isolate - BIOSAMPLE:GISAID_virus_name - VirusSeq_Portal:isolate - - VirusSeq_Portal:fasta header name - purpose of sampling: - name: purpose of sampling + - VirusSeq_Portal:fasta%20header%20name + purpose_of_sampling: + name: purpose_of_sampling title: purpose of sampling description: The reason that the sample was collected. comments: The reason a sample was collected may provide information about potential @@ -766,20 +766,20 @@ slots: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. - examples: - - value: Diagnostic testing slot_uri: GENEPIO:0001198 any_of: - - range: purpose of sampling menu - - range: null value menu + - range: PurposeOfSamplingMenu + - range: NullValueMenu required: true + examples: + - value: Diagnostic testing exact_mappings: - - CNPHI:Reason for Sampling + - CNPHI:Reason%20for%20Sampling - NML_LIMS:HC_SAMPLE_CATEGORY - BIOSAMPLE:purpose_of_sampling - - VirusSeq_Portal:purpose of sampling - purpose of sampling details: - name: purpose of sampling details + - VirusSeq_Portal:purpose%20of%20sampling + purpose_of_sampling_details: + name: purpose_of_sampling_details title: purpose of sampling details description: The description of why the sample was collected, providing specific details. @@ -787,21 +787,21 @@ slots: free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. - examples: - - value: The sample was collected to investigate the prevalence of variants associated - with mink-to-human transmission in Canada. slot_uri: GENEPIO:0001200 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true + examples: + - value: The sample was collected to investigate the prevalence of variants associated + with mink-to-human transmission in Canada. exact_mappings: - - CNPHI:Details on the Reason for Sampling + - CNPHI:Details%20on%20the%20Reason%20for%20Sampling - NML_LIMS:PH_SAMPLING_DETAILS - BIOSAMPLE:description - - VirusSeq_Portal:purpose of sampling details - NML submitted specimen type: - name: NML submitted specimen type + - VirusSeq_Portal:purpose%20of%20sampling%20details + nml_submitted_specimen_type: + name: nml_submitted_specimen_type title: NML submitted specimen type description: The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. @@ -809,29 +809,29 @@ slots: \ Select the specimen type from the pick list provided. If sequence data is\ \ being submitted rather than a specimen for testing, select \u201CNot Applicable\u201D\ ." - examples: - - value: swab slot_uri: GENEPIO:0001204 - range: NML submitted specimen type menu + range: NmlSubmittedSpecimenTypeMenu required: true + examples: + - value: swab exact_mappings: - - CNPHI:Specimen Type + - CNPHI:Specimen%20Type - NML_LIMS:PH_SPECIMEN_TYPE - Related specimen relationship type: - name: Related specimen relationship type + related_specimen_relationship_type: + name: related_specimen_relationship_type title: Related specimen relationship type description: The relationship of the current specimen to the specimen/sample previously submitted to the repository. comments: Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. + slot_uri: GENEPIO:0001209 + range: RelatedSpecimenRelationshipTypeMenu examples: - value: Reinfection testing - slot_uri: GENEPIO:0001209 - range: Related specimen relationship type menu exact_mappings: - - CNPHI:Related Specimen ID - - CNPHI:Related Specimen Relationship Type + - CNPHI:Related%20Specimen%20ID + - CNPHI:Related%20Specimen%20Relationship%20Type - NML_LIMS:PH_RELATED_RELATIONSHIP_TYPE presampling_activity: name: presampling_activity @@ -841,24 +841,24 @@ slots: (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. - examples: - - value: Vaccination slot_uri: GENEPIO:0100433 any_of: - - range: presampling_activity menu - - range: null value menu - presampling activity details: - name: presampling activity details + - range: PresamplingActivityMenu + - range: NullValueMenu + examples: + - value: Vaccination + presampling_activity_details: + name: presampling_activity_details title: presampling activity details description: The details of the activities or variables that may affect the sample collected. comments: Briefly describe the presampling details using free text. - examples: - - value: Patient was previously infected. Sample taken during convalescence. slot_uri: GENEPIO:0100434 range: WhitespaceMinimizedString - anatomical material: - name: anatomical material + examples: + - value: Patient was previously infected. Sample taken during convalescence. + anatomical_material: + name: anatomical_material title: anatomical material description: A substance obtained from an anatomical part of an organism e.g. tissue, blood. @@ -866,46 +866,46 @@ slots: picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Blood slot_uri: GENEPIO:0001211 any_of: - - range: anatomical material menu - - range: null value menu + - range: AnatomicalMaterialMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Blood exact_mappings: - - GISAID:Specimen source - - CNPHI:Anatomical Material + - GISAID:Specimen%20source + - CNPHI:Anatomical%20Material - NML_LIMS:PH_ISOLATION_SITE_DESC - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_material - - VirusSeq_Portal:anatomical material - anatomical part: - name: anatomical part + - VirusSeq_Portal:anatomical%20material + anatomical_part: + name: anatomical_part title: anatomical part description: An anatomical part of an organism e.g. oropharynx. comments: Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Nasopharynx (NP) slot_uri: GENEPIO:0001214 any_of: - - range: anatomical part menu - - range: null value menu + - range: AnatomicalPartMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Nasopharynx (NP) exact_mappings: - - GISAID:Specimen source - - CNPHI:Anatomical Site + - GISAID:Specimen%20source + - CNPHI:Anatomical%20Site - NML_LIMS:PH_ISOLATION_SITE - BIOSAMPLE:isolation_source - BIOSAMPLE:anatomical_part - - VirusSeq_Portal:anatomical part - body product: - name: body product + - VirusSeq_Portal:anatomical%20part + body_product: + name: body_product title: body product description: A substance excreted/secreted from an organism e.g. feces, urine, sweat. @@ -913,80 +913,80 @@ slots: provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Urine slot_uri: GENEPIO:0001216 any_of: - - range: body product menu - - range: null value menu + - range: BodyProductMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Urine exact_mappings: - - GISAID:Specimen source - - CNPHI:Body Product + - GISAID:Specimen%20source + - CNPHI:Body%20Product - NML_LIMS:PH_SPECIMEN_SOURCE_DESC - BIOSAMPLE:isolation_source - BIOSAMPLE:body_product - - VirusSeq_Portal:body product - collection device: - name: collection device + - VirusSeq_Portal:body%20product + collection_device: + name: collection_device title: collection device description: The instrument or container used to collect the sample e.g. swab. comments: Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Swab slot_uri: GENEPIO:0001234 any_of: - - range: collection device menu - - range: null value menu + - range: CollectionDeviceMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Swab exact_mappings: - - GISAID:Specimen source - - CNPHI:Specimen Collection Matrix + - GISAID:Specimen%20source + - CNPHI:Specimen%20Collection%20Matrix - NML_LIMS:PH_SPECIMEN_TYPE_ORIG - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_device - - VirusSeq_Portal:collection device - collection method: - name: collection method + - VirusSeq_Portal:collection%20device + collection_method: + name: collection_method title: collection method description: The process used to collect the sample e.g. phlebotamy, necropsy. comments: Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. - examples: - - value: Bronchoalveolar lavage (BAL) slot_uri: GENEPIO:0001241 any_of: - - range: collection method menu - - range: null value menu + - range: CollectionMethodMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Bronchoalveolar lavage (BAL) exact_mappings: - - GISAID:Specimen source - - CNPHI:Collection Method + - GISAID:Specimen%20source + - CNPHI:Collection%20Method - NML_LIMS:COLLECTION_METHOD - BIOSAMPLE:isolation_source - BIOSAMPLE:collection_method - - VirusSeq_Portal:collection method - collection protocol: - name: collection protocol + - VirusSeq_Portal:collection%20method + collection_protocol: + name: collection_protocol title: collection protocol description: The name and version of a particular protocol used for sampling. comments: Free text. - examples: - - value: FluSamplingProtocol v. 1.2 slot_uri: GENEPIO:0001243 range: WhitespaceMinimizedString + examples: + - value: FluSamplingProtocol v. 1.2 exact_mappings: - - NML_LIMS:collection protocol - specimen processing: - name: specimen processing + - NML_LIMS:collection%20protocol + specimen_processing: + name: specimen_processing title: specimen processing description: Any processing applied to the sample during or after receiving the sample. @@ -994,246 +994,246 @@ slots: from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". - examples: - - value: Virus passage slot_uri: GENEPIO:0001253 any_of: - - range: specimen processing menu - - range: null value menu + - range: SpecimenProcessingMenu + - range: NullValueMenu multivalued: true recommended: true + examples: + - value: Virus passage exact_mappings: - - GISAID:Passage details/history - - NML_LIMS:specimen processing - specimen processing details: - name: specimen processing details + - GISAID:Passage%20details/history + - NML_LIMS:specimen%20processing + specimen_processing_details: + name: specimen_processing_details title: specimen processing details description: Detailed information regarding the processing applied to a sample during or after receiving the sample. comments: Provide a free text description of any processing details applied to a sample. + slot_uri: GENEPIO:0100311 + range: WhitespaceMinimizedString examples: - value: 25 swabs were pooled and further prepared as a single sample during library prep. - slot_uri: GENEPIO:0100311 - range: WhitespaceMinimizedString - biomaterial extracted: - name: biomaterial extracted + biomaterial_extracted: + name: biomaterial_extracted title: biomaterial extracted description: The biomaterial extracted from samples for the purpose of sequencing. comments: Provide the biomaterial extracted from the picklist in the template. - examples: - - value: RNA (total) slot_uri: GENEPIO:0001266 any_of: - - range: biomaterial extracted menu - - range: null value menu + - range: BiomaterialExtractedMenu + - range: NullValueMenu + examples: + - value: RNA (total) exact_mappings: - - NML_LIMS:biomaterial extracted - host (common name): - name: host (common name) + - NML_LIMS:biomaterial%20extracted + host_common_name: + name: host_common_name title: host (common name) description: The commonly used name of the host. comments: Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. - examples: - - value: Human slot_uri: GENEPIO:0001386 any_of: - - range: host (common name) menu - - range: null value menu + - range: HostCommonNameMenu + - range: NullValueMenu + examples: + - value: Human exact_mappings: - - CNPHI:Animal Type + - CNPHI:Animal%20Type - NML_LIMS:PH_ANIMAL_TYPE - host (scientific name): - name: host (scientific name) + host_scientific_name: + name: host_scientific_name title: host (scientific name) description: The taxonomic, or scientific name of the host. comments: Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable - examples: - - value: Homo sapiens slot_uri: GENEPIO:0001387 any_of: - - range: host (scientific name) menu - - range: null value menu + - range: HostScientificNameMenu + - range: NullValueMenu required: true + examples: + - value: Homo sapiens exact_mappings: - GISAID:Host - - NML_LIMS:host (scientific name) + - NML_LIMS:host%20%28scientific%20name%29 - BIOSAMPLE:host - - VirusSeq_Portal:host (scientific name) - host health state: - name: host health state + - VirusSeq_Portal:host%20%28scientific%20name%29 + host_health_state: + name: host_health_state title: host health state description: Health status of the host at the time of sample collection. comments: If known, select a descriptor from the pick list provided in the template. - examples: - - value: Symptomatic slot_uri: GENEPIO:0001388 any_of: - - range: host health state menu - - range: null value menu + - range: HostHealthStateMenu + - range: NullValueMenu + examples: + - value: Symptomatic exact_mappings: - - GISAID:Patient status - - CNPHI:Host Health State + - GISAID:Patient%20status + - CNPHI:Host%20Health%20State - NML_LIMS:PH_HOST_HEALTH - BIOSAMPLE:host_health_state - host health status details: - name: host health status details + host_health_status_details: + name: host_health_status_details title: host health status details description: Further details pertaining to the health or disease status of the host at time of collection. comments: If known, select a descriptor from the pick list provided in the template. - examples: - - value: Hospitalized (ICU) slot_uri: GENEPIO:0001389 any_of: - - range: host health status details menu - - range: null value menu + - range: HostHealthStatusDetailsMenu + - range: NullValueMenu + examples: + - value: Hospitalized (ICU) exact_mappings: - - CNPHI:Host Health State Details + - CNPHI:Host%20Health%20State%20Details - NML_LIMS:PH_HOST_HEALTH_DETAILS - host health outcome: - name: host health outcome + host_health_outcome: + name: host_health_outcome title: host health outcome description: Disease outcome in the host. comments: If known, select a descriptor from the pick list provided in the template. - examples: - - value: Recovered slot_uri: GENEPIO:0001390 any_of: - - range: host health outcome menu - - range: null value menu + - range: HostHealthOutcomeMenu + - range: NullValueMenu + examples: + - value: Recovered exact_mappings: - NML_LIMS:PH_HOST_HEALTH_OUTCOME - BIOSAMPLE:host_disease_outcome - host disease: - name: host disease + host_disease: + name: host_disease title: host disease description: The name of the disease experienced by the host. comments: Select "Influenza" from the pick list provided in the template. - examples: - - value: Influenza slot_uri: GENEPIO:0001391 any_of: - - range: host disease menu - - range: null value menu + - range: HostDiseaseMenu + - range: NullValueMenu required: true + examples: + - value: Influenza exact_mappings: - - CNPHI:Host Disease + - CNPHI:Host%20Disease - NML_LIMS:PH_HOST_DISEASE - BIOSAMPLE:host_disease - - VirusSeq_Portal:host disease - host age: - name: host age + - VirusSeq_Portal:host%20disease + host_age: + name: host_age title: host age description: Age of host at the time of sampling. comments: Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". - examples: - - value: '79' slot_uri: GENEPIO:0001392 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu + minimum_value: 0 + maximum_value: 130 required: true - minimum_value: '0' - maximum_value: '130' + examples: + - value: '79' exact_mappings: - - GISAID:Patient age - - CNPHI:Patient Age + - GISAID:Patient%20age + - CNPHI:Patient%20Age - NML_LIMS:PH_AGE - BIOSAMPLE:host_age - - VirusSeq_Portal:host age - host age unit: - name: host age unit + - VirusSeq_Portal:host%20age + host_age_unit: + name: host_age_unit title: host age unit description: The unit used to measure the host age, in either months or years. comments: Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. - examples: - - value: years slot_uri: GENEPIO:0001393 any_of: - - range: host age unit menu - - range: null value menu + - range: HostAgeUnitMenu + - range: NullValueMenu required: true + examples: + - value: years exact_mappings: - - CNPHI:Age Units + - CNPHI:Age%20Units - NML_LIMS:PH_AGE_UNIT - - VirusSeq_Portal:host age unit - host age bin: - name: host age bin + - VirusSeq_Portal:host%20age%20unit + host_age_bin: + name: host_age_bin title: host age bin description: Age of host at the time of sampling, expressed as an age group. comments: Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. - examples: - - value: 60 - 69 slot_uri: GENEPIO:0001394 any_of: - - range: host age bin menu - - range: null value menu + - range: HostAgeBinMenu + - range: NullValueMenu required: true + examples: + - value: 60 - 69 exact_mappings: - - CNPHI:Host Age Category + - CNPHI:Host%20Age%20Category - NML_LIMS:PH_AGE_GROUP - - VirusSeq_Portal:host age bin - host gender: - name: host gender + - VirusSeq_Portal:host%20age%20bin + host_gender: + name: host_gender title: host gender description: The gender of the host at the time of sample collection. comments: Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". - examples: - - value: Male slot_uri: GENEPIO:0001395 any_of: - - range: host gender menu - - range: null value menu + - range: HostGenderMenu + - range: NullValueMenu required: true structured_pattern: syntax: '{Title_Case}' partial_match: false interpolated: true + examples: + - value: Male exact_mappings: - GISAID:Gender - - CNPHI:Patient Sex + - CNPHI:Patient%20Sex - NML_LIMS:VD_SEX - BIOSAMPLE:host_sex - - VirusSeq_Portal:host gender - host subject ID: - name: host subject ID + - VirusSeq_Portal:host%20gender + host_subject_id: + name: host_subject_id title: host subject ID description: 'A unique identifier by which each host can be referred to e.g. #131' comments: Provide the host identifier. Should be a unique, user-defined identifier. - examples: - - value: BCxy123 slot_uri: GENEPIO:0001398 range: WhitespaceMinimizedString + examples: + - value: BCxy123 exact_mappings: - - NML_LIMS:host subject ID + - NML_LIMS:host%20subject%20ID - BIOSAMPLE:host_subject_id - host vaccination status: - name: host vaccination status + host_vaccination_status: + name: host_vaccination_status title: host vaccination status description: The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). comments: Select the vaccination status of the host from the pick list. - examples: - - value: Fully Vaccinated slot_uri: GENEPIO:0001404 any_of: - - range: host vaccination status menu - - range: null value menu + - range: HostVaccinationStatusMenu + - range: NullValueMenu + examples: + - value: Fully Vaccinated exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - vaccination history: - name: vaccination history + vaccination_history: + name: vaccination_history title: vaccination history description: A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. @@ -1244,74 +1244,74 @@ slots: range: WhitespaceMinimizedString exact_mappings: - NML_LIMS:PH_VACCINATION_HISTORY - exposure event: - name: exposure event + exposure_event: + name: exposure_event title: exposure event description: Event leading to exposure. comments: Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. - examples: - - value: Social Gathering slot_uri: GENEPIO:0001417 any_of: - - range: exposure event menu - - range: null value menu + - range: ExposureEventMenu + - range: NullValueMenu + examples: + - value: Social Gathering exact_mappings: - - GISAID:Additional location information - - CNPHI:Exposure Event + - GISAID:Additional%20location%20information + - CNPHI:Exposure%20Event - NML_LIMS:PH_EXPOSURE - exposure contact level: - name: exposure contact level + exposure_contact_level: + name: exposure_contact_level title: exposure contact level description: The exposure transmission contact type. comments: Select direct or indirect exposure from the pick-list. - examples: - - value: Direct slot_uri: GENEPIO:0001418 any_of: - - range: exposure contact level menu - - range: null value menu + - range: ExposureContactLevelMenu + - range: NullValueMenu + examples: + - value: Direct exact_mappings: - - NML_LIMS:exposure contact level - host role: - name: host role + - NML_LIMS:exposure%20contact%20level + host_role: + name: host_role title: host role description: The role of the host in relation to the exposure setting. comments: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. - examples: - - value: Inpatient slot_uri: GENEPIO:0001419 - range: host role menu + range: HostRoleMenu multivalued: true + examples: + - value: Inpatient exact_mappings: - NML_LIMS:PH_HOST_ROLE - exposure setting: - name: exposure setting + exposure_setting: + name: exposure_setting title: exposure setting description: The setting leading to exposure. comments: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. - examples: - - value: Healthcare Setting slot_uri: GENEPIO:0001428 - range: exposure setting menu + range: ExposureSettingMenu multivalued: true + examples: + - value: Healthcare Setting exact_mappings: - NML_LIMS:PH_EXPOSURE - exposure details: - name: exposure details + exposure_details: + name: exposure_details title: exposure details description: Additional host exposure information. comments: Free text description of the exposure. - examples: - - value: Case infected family at home slot_uri: GENEPIO:0001431 range: WhitespaceMinimizedString + examples: + - value: Case infected family at home exact_mappings: - NML_LIMS:PH_EXPOSURE_DETAILS - purpose of sequencing: - name: purpose of sequencing + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose of sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the @@ -1319,21 +1319,21 @@ slots: may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. - examples: - - value: Baseline surveillance (random sampling) slot_uri: GENEPIO:0001445 any_of: - - range: purpose of sequencing menu - - range: null value menu + - range: PurposeOfSequencingMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Baseline surveillance (random sampling) exact_mappings: - - CNPHI:Reason for Sequencing + - CNPHI:Reason%20for%20Sequencing - NML_LIMS:PH_REASON_FOR_SEQUENCING - BIOSAMPLE:purpose_of_sequencing - - VirusSeq_Portal:purpose of sequencing - purpose of sequencing details: - name: purpose of sequencing details + - VirusSeq_Portal:purpose%20of%20sequencing + purpose_of_sequencing_details: + name: purpose_of_sequencing_details title: purpose of sequencing details description: The description of why the sample was sequenced providing specific details. @@ -1348,76 +1348,74 @@ slots: airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection.' - examples: - - value: Seasonal flu research project slot_uri: GENEPIO:0001446 any_of: - range: WhitespaceMinimizedString - - range: null value menu + - range: NullValueMenu required: true + examples: + - value: Seasonal flu research project exact_mappings: - - CNPHI:Details on the Reason for Sequencing + - CNPHI:Details%20on%20the%20Reason%20for%20Sequencing - NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS - - VirusSeq_Portal:purpose of sequencing details - sequencing date: - name: sequencing date + - VirusSeq_Portal:purpose%20of%20sequencing%20details + sequencing_date: + name: sequencing_date title: sequencing date description: The date the sample was sequenced. comments: ISO 8601 standard "YYYY-MM-DD". - examples: - - value: '2023-09-22' slot_uri: GENEPIO:0001447 any_of: - range: date - - range: null value menu + - range: NullValueMenu required: true - todos: - - '>={sample_collection_date}' + examples: + - value: '2023-09-22' exact_mappings: - NML_LIMS:PH_SEQUENCING_DATE - amplicon size: - name: amplicon size + amplicon_size: + name: amplicon_size title: amplicon size description: The length of the amplicon generated by PCR amplification. comments: Provide the amplicon size, including the units. - examples: - - value: 300bp slot_uri: GENEPIO:0001449 range: WhitespaceMinimizedString + examples: + - value: 300bp exact_mappings: - - NML_LIMS:amplicon size - library preparation kit: - name: library preparation kit + - NML_LIMS:amplicon%20size + library_preparation_kit: + name: library_preparation_kit title: library preparation kit description: The name of the DNA library preparation kit used to generate the library being sequenced. comments: Provide the name of the library preparation kit used. - examples: - - value: Nextera XT slot_uri: GENEPIO:0001450 range: WhitespaceMinimizedString + examples: + - value: Nextera XT exact_mappings: - NML_LIMS:PH_LIBRARY_PREP_KIT - sequencing instrument: - name: sequencing instrument + sequencing_instrument: + name: sequencing_instrument title: sequencing instrument description: The model of the sequencing instrument used. comments: Select a sequencing instrument from the picklist provided in the template. - examples: - - value: Oxford Nanopore MinION slot_uri: GENEPIO:0001452 any_of: - - range: sequencing instrument menu - - range: null value menu + - range: SequencingInstrumentMenu + - range: NullValueMenu multivalued: true required: true + examples: + - value: Oxford Nanopore MinION exact_mappings: - - GISAID:Sequencing technology - - CNPHI:Sequencing Instrument + - GISAID:Sequencing%20technology + - CNPHI:Sequencing%20Instrument - NML_LIMS:PH_INSTRUMENT_CGN - - VirusSeq_Portal:sequencing instrument - sequencing protocol: - name: sequencing protocol + - VirusSeq_Portal:sequencing%20instrument + sequencing_protocol__: + name: sequencing_protocol__ title: sequencing protocol description: The protocol used to generate the sequence. comments: 'Provide a free text description of the methods and materials used to @@ -1425,18 +1423,18 @@ slots: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. "' + slot_uri: GENEPIO:0001454 + range: WhitespaceMinimizedString examples: - value: Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. - slot_uri: GENEPIO:0001454 - range: WhitespaceMinimizedString exact_mappings: - NML_LIMS:PH_TESTING_PROTOCOL - - VirusSeq_Portal:sequencing protocol - amplicon pcr primer scheme: - name: amplicon pcr primer scheme + - VirusSeq_Portal:sequencing%20protocol + amplicon_pcr_primer_scheme: + name: amplicon_pcr_primer_scheme title: amplicon pcr primer scheme description: The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. @@ -1445,136 +1443,136 @@ slots: slot_uri: GENEPIO:0001456 range: WhitespaceMinimizedString exact_mappings: - - NML_LIMS:amplicon pcr primer scheme - raw sequence data processing method: - name: raw sequence data processing method + - NML_LIMS:amplicon%20pcr%20primer%20scheme + raw_sequence_data_processing_method: + name: raw_sequence_data_processing_method title: raw sequence data processing method description: The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. comments: Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 - examples: - - value: Porechop 0.2.3 slot_uri: GENEPIO:0001458 range: WhitespaceMinimizedString required: true + examples: + - value: Porechop 0.2.3 exact_mappings: - NML_LIMS:PH_RAW_SEQUENCE_METHOD - - VirusSeq_Portal:raw sequence data processing method - dehosting method: - name: dehosting method + - VirusSeq_Portal:raw%20sequence%20data%20processing%20method + dehosting_method: + name: dehosting_method title: dehosting method description: The method used to remove host reads from the pathogen sequence. comments: Provide the name and version number of the software used to remove host reads. - examples: - - value: Nanostripper slot_uri: GENEPIO:0001459 range: WhitespaceMinimizedString required: true + examples: + - value: Nanostripper exact_mappings: - NML_LIMS:PH_DEHOSTING_METHOD - - VirusSeq_Portal:dehosting method - consensus sequence software name: - name: consensus sequence software name + - VirusSeq_Portal:dehosting%20method + consensus_sequence_software_name: + name: consensus_sequence_software_name title: consensus sequence software name description: The name of software used to generate the consensus sequence. comments: Provide the name of the software used to generate the consensus sequence. - examples: - - value: iVar slot_uri: GENEPIO:0001463 range: WhitespaceMinimizedString required: true + examples: + - value: iVar exact_mappings: - - GISAID:Assembly method - - CNPHI:consensus sequence + - GISAID:Assembly%20method + - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE - - VirusSeq_Portal:consensus sequence software name - consensus sequence software version: - name: consensus sequence software version + - VirusSeq_Portal:consensus%20sequence%20software%20name + consensus_sequence_software_version: + name: consensus_sequence_software_version title: consensus sequence software version description: The version of the software used to generate the consensus sequence. comments: Provide the version of the software used to generate the consensus sequence. - examples: - - value: '1.3' slot_uri: GENEPIO:0001469 range: WhitespaceMinimizedString required: true + examples: + - value: '1.3' exact_mappings: - - CNPHI:consensus sequence + - CNPHI:consensus%20sequence - NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION - - VirusSeq_Portal:consensus sequence software version - breadth of coverage value: - name: breadth of coverage value + - VirusSeq_Portal:consensus%20sequence%20software%20version + breadth_of_coverage_value: + name: breadth_of_coverage_value title: breadth of coverage value description: The percentage of the reference genome covered by the sequenced data, to a prescribed depth. comments: Provide value as a percent. - examples: - - value: 95% slot_uri: GENEPIO:0001472 range: WhitespaceMinimizedString + examples: + - value: 95% exact_mappings: - - NML_LIMS:breadth of coverage value - - VirusSeq_Portal:breadth of coverage value - depth of coverage value: - name: depth of coverage value + - NML_LIMS:breadth%20of%20coverage%20value + - VirusSeq_Portal:breadth%20of%20coverage%20value + depth_of_coverage_value: + name: depth_of_coverage_value title: depth of coverage value description: The average number of reads representing a given nucleotide in the reconstructed sequence. comments: Provide value as a fold of coverage. - examples: - - value: 400x slot_uri: GENEPIO:0001474 range: WhitespaceMinimizedString + examples: + - value: 400x exact_mappings: - GISAID:Coverage - - NML_LIMS:depth of coverage value - - VirusSeq_Portal:depth of coverage value - depth of coverage threshold: - name: depth of coverage threshold + - NML_LIMS:depth%20of%20coverage%20value + - VirusSeq_Portal:depth%20of%20coverage%20value + depth_of_coverage_threshold: + name: depth_of_coverage_threshold title: depth of coverage threshold description: The threshold used as a cut-off for the depth of coverage. comments: Provide the threshold fold coverage. - examples: - - value: 100x slot_uri: GENEPIO:0001475 range: WhitespaceMinimizedString + examples: + - value: 100x exact_mappings: - - NML_LIMS:depth of coverage threshold - number of base pairs sequenced: - name: number of base pairs sequenced + - NML_LIMS:depth%20of%20coverage%20threshold + number_of_base_pairs_sequenced: + name: number_of_base_pairs_sequenced title: number of base pairs sequenced description: The number of total base pairs generated by the sequencing process. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001482 range: integer - minimum_value: '0' + minimum_value: 0 exact_mappings: - - NML_LIMS:number of base pairs sequenced - consensus genome length: - name: consensus genome length + - NML_LIMS:number%20of%20base%20pairs%20sequenced + consensus_genome_length: + name: consensus_genome_length title: consensus genome length description: Size of the reconstructed genome described as the number of base pairs. comments: Provide a numerical value (no need to include units). slot_uri: GENEPIO:0001483 range: integer - minimum_value: '0' + minimum_value: 0 exact_mappings: - - NML_LIMS:consensus genome length - reference genome accession: - name: reference genome accession + - NML_LIMS:consensus%20genome%20length + reference_genome_accession: + name: reference_genome_accession title: reference genome accession description: A persistent, unique identifier of a genome database entry. comments: Provide the accession number of the reference genome. slot_uri: GENEPIO:0001485 range: WhitespaceMinimizedString exact_mappings: - - NML_LIMS:reference genome accession - - VirusSeq_Portal:reference genome accession - bioinformatics protocol: - name: bioinformatics protocol + - NML_LIMS:reference%20genome%20accession + - VirusSeq_Portal:reference%20genome%20accession + bioinformatics_protocol: + name: bioinformatics_protocol title: bioinformatics protocol description: A description of the overall bioinformatics strategy used. comments: Further details regarding the methods used to process raw data, and/or @@ -1585,11 +1583,11 @@ slots: range: WhitespaceMinimizedString required: true exact_mappings: - - CNPHI:Bioinformatics Protocol + - CNPHI:Bioinformatics%20Protocol - NML_LIMS:PH_BIOINFORMATICS_PROTOCOL - - VirusSeq_Portal:bioinformatics protocol - gene name 1: - name: gene name 1 + - VirusSeq_Portal:bioinformatics%20protocol + gene_name_1: + name: gene_name_1 title: gene name 1 description: The name of the gene used in the diagnostic RT-PCR test. comments: 'Provide the full name of the gene used in the test. The gene symbol @@ -1597,31 +1595,31 @@ slots: symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' slot_uri: GENEPIO:0001507 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu exact_mappings: - - CNPHI:Gene Target 1 - - 'NML_LIMS:SUBMITTED_RESLT - Gene Target #1' + - CNPHI:Gene%20Target%201 + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231 - BIOSAMPLE:gene_name_1 - - VirusSeq_Portal:gene name - diagnostic pcr Ct value 1: - name: diagnostic pcr Ct value 1 + - VirusSeq_Portal:gene%20name + diagnostic_pcr_ct_value_1: + name: diagnostic_pcr_ct_value_1 title: diagnostic pcr Ct value 1 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the diagnostic RT-PCR test. - examples: - - value: '21' slot_uri: GENEPIO:0001509 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu + examples: + - value: '21' exact_mappings: - - CNPHI:Gene Target 1 CT Value - - 'NML_LIMS:SUBMITTED_RESLT - Gene Target #1 CT Value' + - CNPHI:Gene%20Target%201%20CT%20Value + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%231%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_1 - - VirusSeq_Portal:diagnostic pcr Ct value - gene name 2: - name: gene name 2 + - VirusSeq_Portal:diagnostic%20pcr%20Ct%20value + gene_name_2: + name: gene_name_2 title: gene name 2 description: The name of the gene used in the diagnostic RT-PCR test. comments: 'Provide the full name of another gene used in an RT-PCR test. The gene @@ -1629,30 +1627,30 @@ slots: and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' slot_uri: GENEPIO:0001510 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu exact_mappings: - - CNPHI:Gene Target 2 - - 'NML_LIMS:SUBMITTED_RESLT - Gene Target #2' + - CNPHI:Gene%20Target%202 + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232 - BIOSAMPLE:gene_name_2 - diagnostic pcr Ct value 2: - name: diagnostic pcr Ct value 2 + diagnostic_pcr_ct_value_2: + name: diagnostic_pcr_ct_value_2 title: diagnostic pcr Ct value 2 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR test. - examples: - - value: '36' slot_uri: GENEPIO:0001512 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu + examples: + - value: '36' exact_mappings: - - CNPHI:Gene Target 2 CT Value - - 'NML_LIMS:SUBMITTED_RESLT - Gene Target #2 CT Value' + - CNPHI:Gene%20Target%202%20CT%20Value + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value - BIOSAMPLE:diagnostic_PCR_CT_value_2 - gene name 3: - name: gene name 3 + gene_name_3: + name: gene_name_3 title: gene name 3 description: The name of the gene used in the diagnostic RT-PCR test. comments: 'Provide the full name of another gene used in an RT-PCR test. The gene @@ -1660,26 +1658,26 @@ slots: and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI' slot_uri: GENEPIO:0001513 any_of: - - range: gene name menu - - range: null value menu + - range: GeneNameMenu + - range: NullValueMenu exact_mappings: - - CNPHI:Gene Target 3 - - 'NML_LIMS:SUBMITTED_RESLT - Gene Target #3' - diagnostic pcr Ct value 3: - name: diagnostic pcr Ct value 3 + - CNPHI:Gene%20Target%203 + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233 + diagnostic_pcr_ct_value_3: + name: diagnostic_pcr_ct_value_3 title: diagnostic pcr Ct value 3 description: The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. comments: Provide the CT value of the sample from the second diagnostic RT-PCR test. - examples: - - value: '30' slot_uri: GENEPIO:0001515 any_of: - range: decimal - - range: null value menu + - range: NullValueMenu + examples: + - value: '30' exact_mappings: - - CNPHI:Gene Target 3 CT Value - - 'NML_LIMS:SUBMITTED_RESLT - Gene Target #3 CT Value' + - CNPHI:Gene%20Target%203%20CT%20Value + - NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value authors: name: authors title: authors @@ -1687,36 +1685,38 @@ slots: sequence generation, analysis, and data submission. comments: Include the first and last names of all individuals that should be attributed, separated by a comma. - examples: - - value: Tejinder Singh, Fei Hu, Joe Blogs slot_uri: GENEPIO:0001517 range: WhitespaceMinimizedString recommended: true + examples: + - value: Tejinder Singh, Fei Hu, Joe Blogs exact_mappings: - GISAID:Authors - CNPHI:Authors - NML_LIMS:PH_CANCOGEN_AUTHORS - DataHarmonizer provenance: - name: DataHarmonizer provenance + dataharmonizer_provenance: + name: dataharmonizer_provenance title: DataHarmonizer provenance description: The DataHarmonizer software and template version provenance. comments: The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. - examples: - - value: DataHarmonizer v3.3.3, Influenza v1.0.0 slot_uri: GENEPIO:0001518 range: Provenance + examples: + - value: DataHarmonizer v3.3.3, Influenza v1.0.0 exact_mappings: - - GISAID:DataHarmonizer provenance - - CNPHI:Additional Comments + - GISAID:DataHarmonizer%20provenance + - CNPHI:Additional%20Comments - NML_LIMS:HC_COMMENTS enums: - umbrella bioproject accession menu: - name: umbrella bioproject accession menu + UmbrellaBioprojectAccessionMenu: + name: UmbrellaBioprojectAccessionMenu + title: umbrella bioproject accession menu permissible_values: {} null value menu: name: null value menu + title: null value menu permissible_values: Not Applicable: text: Not Applicable @@ -1733,8 +1733,9 @@ enums: Restricted Access: text: Restricted Access meaning: GENEPIO:0001810 - geo_loc_name (state/province/territory) menu: - name: geo_loc_name (state/province/territory) menu + GeoLocNameStateProvinceTerritoryMenu: + name: GeoLocNameStateProvinceTerritoryMenu + title: geo_loc_name (state/province/territory) menu permissible_values: Alberta: text: Alberta @@ -1775,8 +1776,9 @@ enums: Yukon: text: Yukon meaning: GAZ:00002576 - host age unit menu: - name: host age unit menu + HostAgeUnitMenu: + name: HostAgeUnitMenu + title: host age unit menu permissible_values: month: text: month @@ -1784,8 +1786,9 @@ enums: year: text: year meaning: UO:0000036 - sample collection date precision menu: - name: sample collection date precision menu + SampleCollectionDatePrecisionMenu: + name: SampleCollectionDatePrecisionMenu + title: sample collection date precision menu permissible_values: year: text: year @@ -1796,8 +1799,9 @@ enums: day: text: day meaning: UO:0000033 - biomaterial extracted menu: - name: biomaterial extracted menu + BiomaterialExtractedMenu: + name: BiomaterialExtractedMenu + title: biomaterial extracted menu permissible_values: RNA (total): text: RNA (total) @@ -1814,8 +1818,9 @@ enums: mRNA (cDNA): text: mRNA (cDNA) meaning: OBI:0002754 - host vaccination status menu: - name: host vaccination status menu + HostVaccinationStatusMenu: + name: HostVaccinationStatusMenu + title: host vaccination status menu permissible_values: Fully Vaccinated: text: Fully Vaccinated @@ -1826,8 +1831,9 @@ enums: Not Vaccinated: text: Not Vaccinated meaning: GENEPIO:0100102 - NML submitted specimen type menu: - name: NML submitted specimen type menu + NmlSubmittedSpecimenTypeMenu: + name: NmlSubmittedSpecimenTypeMenu + title: NML submitted specimen type menu permissible_values: Swab: text: Swab @@ -1844,8 +1850,9 @@ enums: Not Applicable: text: Not Applicable meaning: GENEPIO:0001619 - Related specimen relationship type menu: - name: Related specimen relationship type menu + RelatedSpecimenRelationshipTypeMenu: + name: RelatedSpecimenRelationshipTypeMenu + title: Related specimen relationship type menu permissible_values: Acute: text: Acute @@ -1866,14 +1873,17 @@ enums: text: Sequencing/bioinformatics methods development/validation Specimen sampling methods testing: text: Specimen sampling methods testing - presampling activity menu: - name: presampling activity menu + PresamplingActivityMenu: + name: PresamplingActivityMenu + title: presampling activity menu permissible_values: {} - vaccine name menu: - name: vaccine name menu + VaccineNameMenu: + name: VaccineNameMenu + title: vaccine name menu permissible_values: {} - anatomical material menu: - name: anatomical material menu + AnatomicalMaterialMenu: + name: AnatomicalMaterialMenu + title: anatomical material menu permissible_values: Blood: text: Blood @@ -1896,8 +1906,9 @@ enums: Tissue: text: Tissue meaning: UBERON:0000479 - anatomical part menu: - name: anatomical part menu + AnatomicalPartMenu: + name: AnatomicalPartMenu + title: anatomical part menu permissible_values: Eye: text: Eye @@ -1972,8 +1983,9 @@ enums: text: Throat meaning: UBERON:0000341 is_a: Upper respiratory tract - body product menu: - name: body product menu + BodyProductMenu: + name: BodyProductMenu + title: body product menu permissible_values: Feces: text: Feces @@ -1990,8 +2002,9 @@ enums: Urine: text: Urine meaning: UBERON:0001088 - collection method menu: - name: collection method menu + CollectionMethodMenu: + name: CollectionMethodMenu + title: collection method menu permissible_values: Amniocentesis: text: Amniocentesis @@ -2038,8 +2051,9 @@ enums: Swabbing: text: Swabbing meaning: GENEPIO:0002117 - collection device menu: - name: collection device menu + CollectionDeviceMenu: + name: CollectionDeviceMenu + title: collection device menu permissible_values: Air filter: text: Air filter @@ -2077,20 +2091,23 @@ enums: Virus Transport Medium: text: Virus Transport Medium meaning: OBI:0002866 - host (scientific name) menu: - name: host (scientific name) menu + HostScientificNameMenu: + name: HostScientificNameMenu + title: host (scientific name) menu permissible_values: Homo sapiens: text: Homo sapiens meaning: NCBITaxon:9606 - host (common name) menu: - name: host (common name) menu + HostCommonNameMenu: + name: HostCommonNameMenu + title: host (common name) menu permissible_values: Human: text: Human meaning: NCBITaxon:9606 - host health state menu: - name: host health state menu + HostHealthStateMenu: + name: HostHealthStateMenu + title: host health state menu permissible_values: Asymptomatic: text: Asymptomatic @@ -2107,8 +2124,9 @@ enums: Symptomatic: text: Symptomatic meaning: NCIT:C25269 - host health status details menu: - name: host health status details menu + HostHealthStatusDetailsMenu: + name: HostHealthStatusDetailsMenu + title: host health status details menu permissible_values: Hospitalized: text: Hospitalized @@ -2134,8 +2152,9 @@ enums: Self-quarantining: text: Self-quarantining meaning: NCIT:C173768 - host health outcome menu: - name: host health outcome menu + HostHealthOutcomeMenu: + name: HostHealthOutcomeMenu + title: host health outcome menu permissible_values: Deceased: text: Deceased @@ -2149,14 +2168,16 @@ enums: Stable: text: Stable meaning: NCIT:C30103 - host disease menu: - name: host disease menu + HostDiseaseMenu: + name: HostDiseaseMenu + title: host disease menu permissible_values: Influenza: text: Influenza meaning: MONDO:0005812 - organism menu: - name: organism menu + OrganismMenu: + name: OrganismMenu + title: organism menu permissible_values: Influenza A virus (H1N1): text: Influenza A virus (H1N1) @@ -2186,8 +2207,9 @@ enums: Influenza B virus (Victoria/87): text: Influenza B virus (Victoria/87) meaning: NCBITaxon:11548 - purpose of sampling menu: - name: purpose of sampling menu + PurposeOfSamplingMenu: + name: PurposeOfSamplingMenu + title: purpose of sampling menu permissible_values: Cluster/Outbreak investigation: text: Cluster/Outbreak investigation @@ -2201,8 +2223,9 @@ enums: Surveillance: text: Surveillance meaning: GENEPIO:0100004 - purpose of sequencing menu: - name: purpose of sequencing menu + PurposeOfSequencingMenu: + name: PurposeOfSequencingMenu + title: purpose of sequencing menu permissible_values: Baseline surveillance (random sampling): text: Baseline surveillance (random sampling) @@ -2251,8 +2274,9 @@ enums: Retrospective sequencing: text: Retrospective sequencing meaning: GENEPIO:0100356 - specimen processing menu: - name: specimen processing menu + SpecimenProcessingMenu: + name: SpecimenProcessingMenu + title: specimen processing menu permissible_values: Virus passage: text: Virus passage @@ -2278,8 +2302,9 @@ enums: mRNA (cDNA): text: mRNA (cDNA) meaning: OBI:0002754 - host age bin menu: - name: host age bin menu + HostAgeBinMenu: + name: HostAgeBinMenu + title: host age bin menu permissible_values: 0 - 9: text: 0 - 9 @@ -2312,14 +2337,15 @@ enums: text: 90 - 99 meaning: GENEPIO:0100058 exact_mappings: - - VirusSeq_Portal:90+ + - VirusSeq_Portal:90%2B 100+: text: 100+ meaning: GENEPIO:0100059 exact_mappings: - - VirusSeq_Portal:90+ - host gender menu: - name: host gender menu + - VirusSeq_Portal:90%2B + HostGenderMenu: + name: HostGenderMenu + title: host gender menu permissible_values: Female: text: Female @@ -2339,8 +2365,9 @@ enums: Undeclared: text: Undeclared meaning: NCIT:C110959 - exposure event menu: - name: exposure event menu + ExposureEventMenu: + name: ExposureEventMenu + title: exposure event menu permissible_values: Mass Gathering: text: Mass Gathering @@ -2413,8 +2440,9 @@ enums: is_a: Social Gathering Other exposure event: text: Other exposure event - exposure contact level menu: - name: exposure contact level menu + ExposureContactLevelMenu: + name: ExposureContactLevelMenu + title: exposure contact level menu permissible_values: Contact with infected individual: text: Contact with infected individual @@ -2435,8 +2463,9 @@ enums: text: Casual contact meaning: GENEPIO:0100248 is_a: Indirect contact - host role menu: - name: host role menu + HostRoleMenu: + name: HostRoleMenu + title: host role menu permissible_values: Attendee: text: Attendee @@ -2587,8 +2616,9 @@ enums: is_a: Social role Other Host Role: text: Other Host Role - exposure setting menu: - name: exposure setting menu + ExposureSettingMenu: + name: ExposureSettingMenu + title: exposure setting menu permissible_values: Human Exposure: text: Human Exposure @@ -2830,8 +2860,9 @@ enums: Other Exposure Setting: text: Other Exposure Setting meaning: GENEPIO:0100235 - sequencing instrument menu: - name: sequencing instrument menu + SequencingInstrumentMenu: + name: SequencingInstrumentMenu + title: sequencing instrument menu permissible_values: Illumina: text: Illumina @@ -3011,27 +3042,29 @@ enums: text: MGI DNBSEQ-G50 meaning: GENEPIO:0100150 is_a: MGI - gene name menu: - name: gene name menu + GeneNameMenu: + name: GeneNameMenu + title: gene name menu permissible_values: Matrix (M) gene: text: Matrix (M) gene exact_mappings: - - BIOSAMPLE:E (orf4) + - BIOSAMPLE:E%20%28orf4%29 Haemagglutinin (HA) gene: text: Haemagglutinin (HA) gene exact_mappings: - - BIOSAMPLE:M (orf5) + - BIOSAMPLE:M%20%28orf5%29 Influenza B- Matrix (M), NP, NS, HA gene: text: Influenza B- Matrix (M), NP, NS, HA gene exact_mappings: - - BIOSAMPLE:N (orf9) + - BIOSAMPLE:N%20%28orf9%29 In of couple journals genes like PB2, PB1, PA: text: In of couple journals genes like PB2, PB1, PA exact_mappings: - - BIOSAMPLE:S (orf2) - sequence submitted by menu: - name: sequence submitted by menu + - BIOSAMPLE:S%20%28orf2%29 + SequenceSubmittedByMenu: + name: SequenceSubmittedByMenu + title: sequence submitted by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -3085,8 +3118,9 @@ enums: text: Sunnybrook Health Sciences Centre Thunder Bay Regional Health Sciences Centre: text: Thunder Bay Regional Health Sciences Centre - sample collected by menu: - name: sample collected by menu + SampleCollectedByMenu: + name: SampleCollectedByMenu + title: sample collected by menu permissible_values: Alberta Precision Labs (APL): text: Alberta Precision Labs (APL) @@ -3156,8 +3190,9 @@ enums: text: Unity Health Toronto William Osler Health System: text: William Osler Health System - geo_loc_name (country) menu: - name: geo_loc_name (country) menu + GeoLocNameCountryMenu: + name: GeoLocNameCountryMenu + title: geo_loc_name (country) menu permissible_values: Afghanistan: text: Afghanistan diff --git a/web/templates/influenza/schema_enums.tsv b/web/templates/influenza/schema_enums.tsv index 344c4b6a..be8143f2 100644 --- a/web/templates/influenza/schema_enums.tsv +++ b/web/templates/influenza/schema_enums.tsv @@ -1,765 +1,765 @@ -title meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal - -umbrella bioproject accession menu - -null value menu GENEPIO:0001619 Not Applicable - GENEPIO:0001618 Missing - GENEPIO:0001620 Not Collected - GENEPIO:0001668 Not Provided - GENEPIO:0001810 Restricted Access - -geo_loc_name (state/province/territory) menu GAZ:00002566 Alberta - GAZ:00002562 British Columbia - GAZ:00002571 Manitoba - GAZ:00002570 New Brunswick - GAZ:00002567 Newfoundland and Labrador - GAZ:00002575 Northwest Territories - GAZ:00002565 Nova Scotia - GAZ:00002574 Nunavut - GAZ:00002563 Ontario - GAZ:00002572 Prince Edward Island - GAZ:00002569 Quebec - GAZ:00002564 Saskatchewan - GAZ:00002576 Yukon - - -host age unit menu UO:0000035 month - UO:0000036 year - - -sample collection date precision menu UO:0000036 year - UO:0000035 month - UO:0000033 day - - -biomaterial extracted menu OBI:0000895 RNA (total) - OBI:0000869 RNA (poly-A) - OBI:0002627 RNA (ribo-depleted) - GENEPIO:0100104 mRNA (messenger RNA) - OBI:0002754 mRNA (cDNA) - - -host vaccination status menu GENEPIO:0100100 Fully Vaccinated - GENEPIO:0100101 Partially Vaccinated - GENEPIO:0100102 Not Vaccinated - - -NML submitted specimen type menu OBI:0002600 Swab - OBI:0000880 RNA - OBI:0002754 mRNA (cDNA) - OBI:0001010 Nucleic acid - GENEPIO:0001619 Not Applicable - - -Related specimen relationship type menu HP:0011009 Acute - Convalescent - Familial - EFO:0009642 Follow-up - Reinfection testing - Previously Submitted - Sequencing/bioinformatics methods development/validation - Specimen sampling methods testing - -presampling activity menu Post-infection convalescence - Vaccination - - - -vaccine name menu - - - - - - -anatomical material menu UBERON:0000178 Blood - UBERON:0001977 Blood serum - UBERON:0006314 Fluid - UBERON:0001359 Fluid (cerebrospinal (CSF)) - UBERON:0001836 Saliva - UBERON:0000479 Tissue - - -anatomical part menu UBERON:0000970 Eye - UBERON:0001558 Lower respiratory tract - UBERON:0002185 Bronchus - UBERON:0002048 Lung - UBERON:0002186 Bronchiole - UBERON:0002169 Alveolar sac - UBERON:0009778 Pleural sac - UBERON:0002402 Pleural cavity - UBERON:0003126 Trachea - UBERON:0001557 Upper respiratory tract - UBERON:2001427 Anterior Nares - UBERON:0001043 Esophagus - UBERON:0002453 Ethmoid sinus - UBERON:0001707 Nasal Cavity - UBERON:0005921 Middle Nasal Turbinate - UBERON:0005922 Inferior Nasal Turbinate - UBERON:0001728 Nasopharynx (NP) - UBERON:0001729 Oropharynx (OP) - UBERON:0000341 Throat - - -body product menu UBERON:0001988 Feces - Intestinal content - UBERON:0007311 Sputum - UBERON:0001089 Sweat - UBERON:0001088 Urine - - - -collection method menu NCIT:C52009 Amniocentesis - NCIT:C15631 Aspiration - GENEPIO:0100029 Tracheal aspiration - GENEPIO:0100030 Vacuum Aspiration - OBI:0002650 Biopsy - OBI:0302885 Filtration - GENEPIO:0100031 Air filtration - OBI:0600044 Lavage - GENEPIO:0100032 Bronchoalveolar lavage (BAL) - GENEPIO:0100033 Gastric Lavage - GENEPIO:0002116 Rinsing - GENEPIO:0100034 Saline gargle (mouth rinse and gargle) - GENEPIO:0002117 Swabbing - - -collection device menu ENVO:00003968 Air filter - OBI:0002826 Bronchoscope - OBI:0002088 Collection Container - GENEPIO:0100026 Collection Cup - OBI:0002825 Fibrobronchoscope Brush - GENEPIO:0100103 Filter - OBI:0002858 Microcapillary tube - OBI:0001128 Micropipette - OBI:0000436 Needle - OBI:0002861 Sputum Collection Tube - GENEPIO:0100027 Swab - OBI:0002866 Virus Transport Medium - - -host (scientific name) menu NCBITaxon:9606 Homo sapiens - - -host (common name) menu NCBITaxon:9606 Human - - - -host health state menu NCIT:C3833 Asymptomatic - NCIT:C28554 Deceased - NCIT:C115935 Healthy - NCIT:C49498 Recovered - NCIT:C25269 Symptomatic - - -host health status details menu NCIT:C25179 Hospitalized - GENEPIO:0100045 Hospitalized (Non-ICU) - GENEPIO:0100046 Hospitalized (ICU) - NCIT:C70909 Mechanical Ventilation - GENEPIO:0100047 Medically Isolated - GENEPIO:0100048 Medically Isolated (Negative Pressure) - NCIT:C173768 Self-quarantining - - -host health outcome menu NCIT:C28554 Deceased - NCIT:C25254 Deteriorating - NCIT:C49498 Recovered - NCIT:C30103 Stable - - -host disease menu MONDO:0005812 Influenza - - - -organism menu NCBITaxon:1323429 Influenza A virus (H1N1) - NCBITaxon:41857 Influenza A virus (H3N2) - NCBITaxon:102793 Influenza A virus (H5N1) - NCBITaxon:333278 Influenza A virus (H7N9) - NCBITaxon:102796 Influenza A virus (H9N2) - Influenza A virus (H7Nx) - Influenza A virus (H5Nx) - NCBITaxon:286285 Influenza A virus (H10N8) - NCBITaxon:11550 Influenza B virus (Yamagata 1/73) - NCBITaxon:11548 Influenza B virus (Victoria/87) - - - -purpose of sampling menu GENEPIO:0100001 Cluster/Outbreak investigation - GENEPIO:0100002 Diagnostic testing - GENEPIO:0100003 Research - GENEPIO:0100004 Surveillance - - -purpose of sequencing menu GENEPIO:0100005 Baseline surveillance (random sampling) - GENEPIO:0100006 Targeted surveillance (non-random sampling) - GENEPIO:0100007 Priority surveillance project - GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) - GENEPIO:0100010 Re-infection surveillance - GENEPIO:0100011 Vaccine escape surveillance - GENEPIO:0100019 Cluster/Outbreak investigation - GENEPIO:0100020 Multi-jurisdictional outbreak investigation - GENEPIO:0100021 Intra-jurisdictional outbreak investigation - GENEPIO:0100022 Research - GENEPIO:0100023 Viral passage experiment - GENEPIO:0100024 Protocol testing experiment - GENEPIO:0100356 Retrospective sequencing - - -specimen processing menu GENEPIO:0100039 Virus passage - GENEPIO:0100040 RNA re-extraction (post RT-PCR) - OBI:0600016 Specimens pooled - - -biomaterial extracted menu OBI:0000895 RNA (total) - OBI:0000869 RNA (poly-A) - OBI:0002627 RNA (ribo-depleted) - GENEPIO:0100104 mRNA (messenger RNA) - OBI:0002754 mRNA (cDNA) - - - -host age bin menu GENEPIO:0100049 0 - 9 - GENEPIO:0100050 10 - 19 - GENEPIO:0100051 20 - 29 - GENEPIO:0100052 30 - 39 - GENEPIO:0100053 40 - 49 - GENEPIO:0100054 50 - 59 - GENEPIO:0100055 60 - 69 - GENEPIO:0100056 70 - 79 - GENEPIO:0100057 80 - 89 - GENEPIO:0100058 90 - 99 90+ - GENEPIO:0100059 100+ 90+ - - -host gender menu NCIT:C46110 Female - NCIT:C46109 Male - GSSO:000132 Non-binary gender - GSSO:004004 Transgender (assigned male at birth) - GSSO:004005 Transgender (assigned female at birth) - NCIT:C110959 Undeclared - - -exposure event menu GENEPIO:0100237 Mass Gathering - GENEPIO:0100240 Agricultural Event - GENEPIO:0100238 Convention - GENEPIO:0100239 Convocation - GENEPIO:0100417 Recreational Event - GENEPIO:0100418 Concert - GENEPIO:0100419 Sporting Event - GENEPIO:0100241 Religious Gathering - GENEPIO:0100242 Mass - PCO:0000033 Social Gathering - PCO:0000039 Baby Shower - PCO:0000034 Community Event - GENEPIO:0100243 Family Gathering - GENEPIO:0100244 Family Reunion - GENEPIO:0100245 Funeral - PCO:0000035 Party - PCO:0000037 Potluck - PCO:0000038 Wedding - Other exposure event - - -exposure contact level menu GENEPIO:0100357 Contact with infected individual - TRANS:0000001 Direct contact (direct human-to-human contact) - GENEPIO:0100246 Indirect contact - GENEPIO:0100247 Close contact (face-to-face, no direct contact) - GENEPIO:0100248 Casual contact - - -host role menu GENEPIO:0100249 Attendee - OMRSE:00000058 Student - OMRSE:00000030 Patient - NCIT:C25182 Inpatient - NCIT:C28293 Outpatient - GENEPIO:0100250 Passenger - GENEPIO:0100251 Resident - GENEPIO:0100252 Visitor - GENEPIO:0100253 Volunteer - GENEPIO:0100254 Work - GENEPIO:0100255 Administrator - Child Care/Education Worker - Essential Worker - GENEPIO:0100256 First Responder - GENEPIO:0100257 Firefighter - GENEPIO:0100258 Paramedic - GENEPIO:0100259 Police Officer - GENEPIO:0100334 Healthcare Worker - GENEPIO:0100420 Community Healthcare Worker - GENEPIO:0100262 Laboratory Worker - OMRSE:00000014 Nurse - GENEPIO:0100263 Personal Care Aid - GENEPIO:0100264 Pharmacist - OMRSE:00000013 Physician - GENEPIO:0100260 Housekeeper - International worker - GENEPIO:0100261 Kitchen Worker - GENEPIO:0100354 Rotational Worker - GENEPIO:0100355 Seasonal Worker - Transport Worker - Transport Truck Driver - GENEPIO:0100265 Veterinarian - OMRSE:00000001 Social role - GENEPIO:0100266 Acquaintance of case - GENEPIO:0100267 Relative of case - GENEPIO:0100268 Child of case - GENEPIO:0100269 Parent of case - GENEPIO:0100270 Father of case - GENEPIO:0100271 Mother of case - GENEPIO:0100272 Spouse of case - Other Host Role - - -exposure setting menu ECTO:3000005 Human Exposure - GENEPIO:0100185 Contact with Patient - GENEPIO:0100187 Contact with Person with Acute Respiratory Illness - GENEPIO:0100188 Contact with Person with Fever and/or Cough - GENEPIO:0100189 Contact with Person who Recently Travelled - GENEPIO:0100190 Occupational, Residency or Patronage Exposure - ECTO:1000033 Abbatoir - GENEPIO:0100191 Animal Rescue - GENEPIO:0100192 Childcare - GENEPIO:0100193 Daycare - GENEPIO:0100194 Nursery - GENEPIO:0100195 Community Service Centre - GENEPIO:0100196 Correctional Facility - GENEPIO:0100197 Dormitory - ECTO:1000034 Farm - GENEPIO:0100198 First Nations Reserve - GENEPIO:0100199 Funeral Home - GENEPIO:0100200 Group Home - GENEPIO:0100201 Healthcare Setting - GENEPIO:0100202 Ambulance - GENEPIO:0100203 Acute Care Facility - GENEPIO:0100204 Clinic - GENEPIO:0100415 Community Healthcare (At-Home) Setting - GENEPIO:0100205 Community Health Centre - ECTO:1000035 Hospital - GENEPIO:0100206 Emergency Department - GENEPIO:0100207 ICU - GENEPIO:0100208 Ward - ECTO:1000036 Laboratory - GENEPIO:0100209 Long-Term Care Facility - GENEPIO:0100210 Pharmacy - GENEPIO:0100211 Physician's Office - GENEPIO:0100212 Household - GENEPIO:0100213 Insecure Housing (Homeless) - GENEPIO:0100214 Occupational Exposure - GENEPIO:0100215 Worksite - ECTO:1000037 Office - GENEPIO:0100216 Outdoors - ECTO:5000009 Camp/camping - GENEPIO:0100217 Hiking Trail - ECTO:6000030 Hunting Ground - GENEPIO:0100218 Ski Resort - ECTO:5000008 Petting zoo - GENEPIO:0100220 Place of Worship - GENEPIO:0100221 Church - GENEPIO:0100222 Mosque - GENEPIO:0100223 Temple - ECTO:1000040 Restaurant - ECTO:1000041 Retail Store - GENEPIO:0100224 School - GENEPIO:0100225 Temporary Residence - GENEPIO:0100226 Homeless Shelter - GENEPIO:0100227 Hotel - GENEPIO:0100228 Veterinary Care Clinic - GENEPIO:0100229 Travel Exposure - GENEPIO:0100230 Travelled on a Cruise Ship - GENEPIO:0100231 Travelled on a Plane - GENEPIO:0100232 Travelled on Ground Transport - GENEPIO:0001118 Travelled outside Province/Territory - GENEPIO:0001119 Travelled outside Canada - GENEPIO:0100235 Other Exposure Setting - - -sequencing instrument menu GENEPIO:0100105 Illumina - GENEPIO:0100106 Illumina Genome Analyzer - GENEPIO:0100107 Illumina Genome Analyzer II - GENEPIO:0100108 Illumina Genome Analyzer IIx - GENEPIO:0100109 Illumina HiScanSQ - GENEPIO:0100110 Illumina HiSeq - GENEPIO:0100111 Illumina HiSeq X - GENEPIO:0100112 Illumina HiSeq X Five - GENEPIO:0100113 Illumina HiSeq X Ten - GENEPIO:0100114 Illumina HiSeq 1000 - GENEPIO:0100115 Illumina HiSeq 1500 - GENEPIO:0100116 Illumina HiSeq 2000 - GENEPIO:0100117 Illumina HiSeq 2500 - GENEPIO:0100118 Illumina HiSeq 3000 - GENEPIO:0100119 Illumina HiSeq 4000 - GENEPIO:0100120 Illumina iSeq - GENEPIO:0100121 Illumina iSeq 100 - GENEPIO:0100122 Illumina NovaSeq - GENEPIO:0100123 Illumina NovaSeq 6000 - GENEPIO:0100124 Illumina MiniSeq - GENEPIO:0100125 Illumina MiSeq - GENEPIO:0100126 Illumina NextSeq - GENEPIO:0100127 Illumina NextSeq 500 - GENEPIO:0100128 Illumina NextSeq 550 - GENEPIO:0100129 Illumina NextSeq 2000 - GENEPIO:0100130 Pacific Biosciences - GENEPIO:0100131 PacBio RS - GENEPIO:0100132 PacBio RS II - GENEPIO:0100133 PacBio Sequel - GENEPIO:0100134 PacBio Sequel II - GENEPIO:0100135 Ion Torrent - GENEPIO:0100136 Ion Torrent PGM - GENEPIO:0100137 Ion Torrent Proton - GENEPIO:0100138 Ion Torrent S5 XL - GENEPIO:0100139 Ion Torrent S5 - GENEPIO:0100140 Oxford Nanopore - GENEPIO:0100141 Oxford Nanopore GridION - GENEPIO:0100142 Oxford Nanopore MinION - GENEPIO:0100143 Oxford Nanopore PromethION - GENEPIO:0100144 BGI Genomics - GENEPIO:0100145 BGI Genomics BGISEQ-500 - GENEPIO:0100146 MGI - GENEPIO:0100147 MGI DNBSEQ-T7 - GENEPIO:0100148 MGI DNBSEQ-G400 - GENEPIO:0100149 MGI DNBSEQ-G400 FAST - GENEPIO:0100150 MGI DNBSEQ-G50 - - -gene name menu Matrix (M) gene E (orf4) - Haemagglutinin (HA) gene M (orf5) - Influenza B- Matrix (M), NP, NS, HA gene N (orf9) - In of couple journals genes like PB2, PB1, PA S (orf2) - orf1ab (rep) - - -sequence submitted by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Canadore College - The Centre for Applied Genomics (TCAG) - Dynacare - Dynacare (Brampton) - Dynacare (Manitoba) - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Manitoba Cadham Provincial Laboratory - McGill University - McMaster University - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Sunnybrook Health Sciences Centre - Thunder Bay Regional Health Sciences Centre - - - sample collected by menu Alberta Precision Labs (APL) - Alberta ProvLab North (APLN) - Alberta ProvLab South (APLS) - BCCDC Public Health Laboratory - Dynacare - Dynacare (Manitoba) - Dynacare (Brampton) - Eastern Ontario Regional Laboratory Association - Hamilton Health Sciences - The Hospital for Sick Children (SickKids) - Laboratoire de santé publique du Québec (LSPQ) - Lake of the Woods District Hospital - Ontario - LifeLabs - LifeLabs (Ontario) - Manitoba Cadham Provincial Laboratory - McMaster University - Mount Sinai Hospital - National Microbiology Laboratory (NML) - New Brunswick - Vitalité Health Network - Newfoundland and Labrador - Eastern Health - Nova Scotia Health Authority - Nunavut - Ontario Institute for Cancer Research (OICR) - Prince Edward Island - Health PEI - Public Health Ontario (PHO) - Queen's University / Kingston Health Sciences Centre - Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) - Shared Hospital Laboratory - St. John's Rehab at Sunnybrook Hospital - Switch Health - Sunnybrook Health Sciences Centre - Unity Health Toronto - William Osler Health System - - -geo_loc_name (country) menu GAZ:00006882 Afghanistan - GAZ:00002953 Albania - GAZ:00000563 Algeria - GAZ:00003957 American Samoa - GAZ:00002948 Andorra - GAZ:00001095 Angola - GAZ:00009159 Anguilla - GAZ:00000462 Antarctica - GAZ:00006883 Antigua and Barbuda - GAZ:00002928 Argentina - GAZ:00004094 Armenia - GAZ:00004025 Aruba - GAZ:00005901 Ashmore and Cartier Islands - GAZ:00000463 Australia - GAZ:00002942 Austria - GAZ:00004941 Azerbaijan - GAZ:00002733 Bahamas - GAZ:00005281 Bahrain - GAZ:00007117 Baker Island - GAZ:00003750 Bangladesh - GAZ:00001251 Barbados - GAZ:00005810 Bassas da India - GAZ:00006886 Belarus - GAZ:00002938 Belgium - GAZ:00002934 Belize - GAZ:00000904 Benin - GAZ:00001264 Bermuda - GAZ:00003920 Bhutan - GAZ:00002511 Bolivia - GAZ:00025355 Borneo - GAZ:00006887 Bosnia and Herzegovina - GAZ:00001097 Botswana - GAZ:00001453 Bouvet Island - GAZ:00002828 Brazil - GAZ:00003961 British Virgin Islands - GAZ:00003901 Brunei - GAZ:00002950 Bulgaria - GAZ:00000905 Burkina Faso - GAZ:00001090 Burundi - GAZ:00006888 Cambodia - GAZ:00001093 Cameroon - GAZ:00002560 Canada - GAZ:00001227 Cape Verde - GAZ:00003986 Cayman Islands - GAZ:00001089 Central African Republic - GAZ:00000586 Chad - GAZ:00002825 Chile - GAZ:00002845 China - GAZ:00005915 Christmas Island - GAZ:00005838 Clipperton Island - GAZ:00009721 Cocos Islands - GAZ:00002929 Colombia - GAZ:00005820 Comoros - GAZ:00053798 Cook Islands - GAZ:00005917 Coral Sea Islands - GAZ:00002901 Costa Rica - GAZ:00000906 Cote d'Ivoire - GAZ:00002719 Croatia - GAZ:00003762 Cuba - GAZ:00012582 Curacao - GAZ:00004006 Cyprus - GAZ:00002954 Czech Republic - GAZ:00001086 Democratic Republic of the Congo - GAZ:00005852 Denmark - GAZ:00000582 Djibouti - GAZ:00006890 Dominica - GAZ:00003952 Dominican Republic - GAZ:00002912 Ecuador - GAZ:00003934 Egypt - GAZ:00002935 El Salvador - GAZ:00001091 Equatorial Guinea - GAZ:00000581 Eritrea - GAZ:00002959 Estonia - GAZ:00001099 Eswatini - GAZ:00000567 Ethiopia - GAZ:00005811 Europa Island - GAZ:00001412 Falkland Islands (Islas Malvinas) - GAZ:00059206 Faroe Islands - GAZ:00006891 Fiji - GAZ:00002937 Finland - GAZ:00003940 France - GAZ:00002516 French Guiana - GAZ:00002918 French Polynesia - GAZ:00003753 French Southern and Antarctic Lands - GAZ:00001092 Gabon - GAZ:00000907 Gambia - GAZ:00009571 Gaza Strip - GAZ:00004942 Georgia - GAZ:00002646 Germany - GAZ:00000908 Ghana - GAZ:00003987 Gibraltar - GAZ:00005808 Glorioso Islands - GAZ:00002945 Greece - GAZ:00001507 Greenland - GAZ:02000573 Grenada - GAZ:00067142 Guadeloupe - GAZ:00003706 Guam - GAZ:00002936 Guatemala - GAZ:00001550 Guernsey - GAZ:00000909 Guinea - GAZ:00000910 Guinea-Bissau - GAZ:00002522 Guyana - GAZ:00003953 Haiti - GAZ:00009718 Heard Island and McDonald Islands - GAZ:00002894 Honduras - GAZ:00003203 Hong Kong - GAZ:00007120 Howland Island - GAZ:00002952 Hungary - GAZ:00000843 Iceland - GAZ:00002839 India - GAZ:00003727 Indonesia - GAZ:00004474 Iran - GAZ:00004483 Iraq - GAZ:00002943 Ireland - GAZ:00052477 Isle of Man - GAZ:00002476 Israel - GAZ:00002650 Italy - GAZ:00003781 Jamaica - GAZ:00005853 Jan Mayen - GAZ:00002747 Japan - GAZ:00007118 Jarvis Island - GAZ:00001551 Jersey - GAZ:00007114 Johnston Atoll - GAZ:00002473 Jordan - GAZ:00005809 Juan de Nova Island - GAZ:00004999 Kazakhstan - GAZ:00001101 Kenya - GAZ:00005682 Kerguelen Archipelago - GAZ:00007116 Kingman Reef - GAZ:00006894 Kiribati - GAZ:00011337 Kosovo - GAZ:00005285 Kuwait - GAZ:00006893 Kyrgyzstan - GAZ:00006889 Laos - GAZ:00002958 Latvia - GAZ:00002478 Lebanon - GAZ:00001098 Lesotho - GAZ:00000911 Liberia - GAZ:00000566 Libya - GAZ:00003858 Liechtenstein - GAZ:00007144 Line Islands - GAZ:00002960 Lithuania - GAZ:00002947 Luxembourg - GAZ:00003202 Macau - GAZ:00001108 Madagascar - GAZ:00001105 Malawi - GAZ:00003902 Malaysia - GAZ:00006924 Maldives - GAZ:00000584 Mali - GAZ:00004017 Malta - GAZ:00007161 Marshall Islands - GAZ:00067143 Martinique - GAZ:00000583 Mauritania - GAZ:00003745 Mauritius - GAZ:00003943 Mayotte - GAZ:00002852 Mexico - GAZ:00005862 Micronesia - GAZ:00007112 Midway Islands - GAZ:00003897 Moldova - GAZ:00003857 Monaco - GAZ:00008744 Mongolia - GAZ:00006898 Montenegro - GAZ:00003988 Montserrat - GAZ:00000565 Morocco - GAZ:00001100 Mozambique - GAZ:00006899 Myanmar - GAZ:00001096 Namibia - GAZ:00006900 Nauru - GAZ:00007119 Navassa Island - GAZ:00004399 Nepal - GAZ:00002946 Netherlands - GAZ:00005206 New Caledonia - GAZ:00000469 New Zealand - GAZ:00002978 Nicaragua - GAZ:00000585 Niger - GAZ:00000912 Nigeria - GAZ:00006902 Niue - GAZ:00005908 Norfolk Island - GAZ:00002801 North Korea - GAZ:00006895 North Macedonia - GAZ:00002284 North Sea - GAZ:00003958 Northern Mariana Islands - GAZ:00002699 Norway - GAZ:00005283 Oman - GAZ:00005246 Pakistan - GAZ:00006905 Palau - GAZ:00002892 Panama - GAZ:00003922 Papua New Guinea - GAZ:00010832 Paracel Islands - GAZ:00002933 Paraguay - GAZ:00002932 Peru - GAZ:00004525 Philippines - GAZ:00005867 Pitcairn Islands - GAZ:00002939 Poland - GAZ:00004126 Portugal - GAZ:00006935 Puerto Rico - GAZ:00005286 Qatar - GAZ:00001088 Republic of the Congo - GAZ:00003945 Reunion - GAZ:00002951 Romania - GAZ:00023304 Ross Sea - GAZ:00002721 Russia - GAZ:00001087 Rwanda - GAZ:00000849 Saint Helena - GAZ:00006906 Saint Kitts and Nevis - GAZ:00006909 Saint Lucia - GAZ:00003942 Saint Pierre and Miquelon - GAZ:00005841 Saint Martin - GAZ:02000565 Saint Vincent and the Grenadines - GAZ:00006910 Samoa - GAZ:00003102 San Marino - GAZ:00006927 Sao Tome and Principe - GAZ:00005279 Saudi Arabia - GAZ:00000913 Senegal - GAZ:00002957 Serbia - GAZ:00006922 Seychelles - GAZ:00000914 Sierra Leone - GAZ:00003923 Singapore - GAZ:00012579 Sint Maarten - GAZ:00002956 Slovakia - GAZ:00002955 Slovenia - GAZ:00005275 Solomon Islands - GAZ:00001104 Somalia - GAZ:00001094 South Africa - GAZ:00003990 South Georgia and the South Sandwich Islands - GAZ:00002802 South Korea - GAZ:00233439 South Sudan - GAZ:00000591 Spain - GAZ:00010831 Spratly Islands - GAZ:00003924 Sri Lanka - GAZ:00002475 State of Palestine - GAZ:00000560 Sudan - GAZ:00002525 Suriname - GAZ:00005396 Svalbard - GAZ:00001099 Swaziland - GAZ:00002729 Sweden - GAZ:00002941 Switzerland - GAZ:00002474 Syria - GAZ:00005341 Taiwan - GAZ:00006912 Tajikistan - GAZ:00001103 Tanzania - GAZ:00003744 Thailand - GAZ:00006913 Timor-Leste - GAZ:00000915 Togo - GAZ:00260188 Tokelau - GAZ:00006916 Tonga - GAZ:00003767 Trinidad and Tobago - GAZ:00005812 Tromelin Island - GAZ:00000562 Tunisia - GAZ:00000558 Turkey - GAZ:00005018 Turkmenistan - GAZ:00003955 Turks and Caicos Islands - GAZ:00009715 Tuvalu - GAZ:00002459 United States of America - GAZ:00001102 Uganda - GAZ:00002724 Ukraine - GAZ:00005282 United Arab Emirates - GAZ:00002637 United Kingdom - GAZ:00002930 Uruguay - GAZ:00004979 Uzbekistan - GAZ:00006918 Vanuatu - GAZ:00002931 Venezuela - GAZ:00003756 Viet Nam - GAZ:00003959 Virgin Islands - GAZ:00007111 Wake Island - GAZ:00007191 Wallis and Futuna - GAZ:00009572 West Bank - GAZ:00000564 Western Sahara - GAZ:00005284 Yemen - GAZ:00001107 Zambia - GAZ:00001106 Zimbabwe - - \ No newline at end of file +title name meaning menu_1 menu_2 menu_3 menu_4 menu_5 description EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal + +umbrella bioproject accession menu UmbrellaBioprojectAccessionMenu + +null value menu GENEPIO:0001619 Not Applicable + GENEPIO:0001618 Missing + GENEPIO:0001620 Not Collected + GENEPIO:0001668 Not Provided + GENEPIO:0001810 Restricted Access + +geo_loc_name (state/province/territory) menu GeoLocNameStateProvinceTerritoryMenu GAZ:00002566 Alberta + GAZ:00002562 British Columbia + GAZ:00002571 Manitoba + GAZ:00002570 New Brunswick + GAZ:00002567 Newfoundland and Labrador + GAZ:00002575 Northwest Territories + GAZ:00002565 Nova Scotia + GAZ:00002574 Nunavut + GAZ:00002563 Ontario + GAZ:00002572 Prince Edward Island + GAZ:00002569 Quebec + GAZ:00002564 Saskatchewan + GAZ:00002576 Yukon + + +host age unit menu HostAgeUnitMenu UO:0000035 month + UO:0000036 year + + +sample collection date precision menu SampleCollectionDatePrecisionMenu UO:0000036 year + UO:0000035 month + UO:0000033 day + + +biomaterial extracted menu BiomaterialExtractedMenu OBI:0000895 RNA (total) + OBI:0000869 RNA (poly-A) + OBI:0002627 RNA (ribo-depleted) + GENEPIO:0100104 mRNA (messenger RNA) + OBI:0002754 mRNA (cDNA) + + +host vaccination status menu HostVaccinationStatusMenu GENEPIO:0100100 Fully Vaccinated + GENEPIO:0100101 Partially Vaccinated + GENEPIO:0100102 Not Vaccinated + + +NML submitted specimen type menu NmlSubmittedSpecimenTypeMenu OBI:0002600 Swab + OBI:0000880 RNA + OBI:0002754 mRNA (cDNA) + OBI:0001010 Nucleic acid + GENEPIO:0001619 Not Applicable + + +Related specimen relationship type menu RelatedSpecimenRelationshipTypeMenu HP:0011009 Acute + Convalescent + Familial + EFO:0009642 Follow-up + Reinfection testing + Previously Submitted + Sequencing/bioinformatics methods development/validation + Specimen sampling methods testing + +presampling activity menu PresamplingActivityMenu Post-infection convalescence + Vaccination + + + +vaccine name menu VaccineNameMenu + + + + + + +anatomical material menu AnatomicalMaterialMenu UBERON:0000178 Blood + UBERON:0001977 Blood serum + UBERON:0006314 Fluid + UBERON:0001359 Fluid (cerebrospinal (CSF)) + UBERON:0001836 Saliva + UBERON:0000479 Tissue + + +anatomical part menu AnatomicalPartMenu UBERON:0000970 Eye + UBERON:0001558 Lower respiratory tract + UBERON:0002185 Bronchus + UBERON:0002048 Lung + UBERON:0002186 Bronchiole + UBERON:0002169 Alveolar sac + UBERON:0009778 Pleural sac + UBERON:0002402 Pleural cavity + UBERON:0003126 Trachea + UBERON:0001557 Upper respiratory tract + UBERON:2001427 Anterior Nares + UBERON:0001043 Esophagus + UBERON:0002453 Ethmoid sinus + UBERON:0001707 Nasal Cavity + UBERON:0005921 Middle Nasal Turbinate + UBERON:0005922 Inferior Nasal Turbinate + UBERON:0001728 Nasopharynx (NP) + UBERON:0001729 Oropharynx (OP) + UBERON:0000341 Throat + + +body product menu BodyProductMenu UBERON:0001988 Feces + Intestinal content + UBERON:0007311 Sputum + UBERON:0001089 Sweat + UBERON:0001088 Urine + + + +collection method menu CollectionMethodMenu NCIT:C52009 Amniocentesis + NCIT:C15631 Aspiration + GENEPIO:0100029 Tracheal aspiration + GENEPIO:0100030 Vacuum Aspiration + OBI:0002650 Biopsy + OBI:0302885 Filtration + GENEPIO:0100031 Air filtration + OBI:0600044 Lavage + GENEPIO:0100032 Bronchoalveolar lavage (BAL) + GENEPIO:0100033 Gastric Lavage + GENEPIO:0002116 Rinsing + GENEPIO:0100034 Saline gargle (mouth rinse and gargle) + GENEPIO:0002117 Swabbing + + +collection device menu CollectionDeviceMenu ENVO:00003968 Air filter + OBI:0002826 Bronchoscope + OBI:0002088 Collection Container + GENEPIO:0100026 Collection Cup + OBI:0002825 Fibrobronchoscope Brush + GENEPIO:0100103 Filter + OBI:0002858 Microcapillary tube + OBI:0001128 Micropipette + OBI:0000436 Needle + OBI:0002861 Sputum Collection Tube + GENEPIO:0100027 Swab + OBI:0002866 Virus Transport Medium + + +host (scientific name) menu HostScientificNameMenu NCBITaxon:9606 Homo sapiens + + +host (common name) menu HostCommonNameMenu NCBITaxon:9606 Human + + + +host health state menu HostHealthStateMenu NCIT:C3833 Asymptomatic + NCIT:C28554 Deceased + NCIT:C115935 Healthy + NCIT:C49498 Recovered + NCIT:C25269 Symptomatic + + +host health status details menu HostHealthStatusDetailsMenu NCIT:C25179 Hospitalized + GENEPIO:0100045 Hospitalized (Non-ICU) + GENEPIO:0100046 Hospitalized (ICU) + NCIT:C70909 Mechanical Ventilation + GENEPIO:0100047 Medically Isolated + GENEPIO:0100048 Medically Isolated (Negative Pressure) + NCIT:C173768 Self-quarantining + + +host health outcome menu HostHealthOutcomeMenu NCIT:C28554 Deceased + NCIT:C25254 Deteriorating + NCIT:C49498 Recovered + NCIT:C30103 Stable + + +host disease menu HostDiseaseMenu MONDO:0005812 Influenza + + + +organism menu OrganismMenu NCBITaxon:1323429 Influenza A virus (H1N1) + NCBITaxon:41857 Influenza A virus (H3N2) + NCBITaxon:102793 Influenza A virus (H5N1) + NCBITaxon:333278 Influenza A virus (H7N9) + NCBITaxon:102796 Influenza A virus (H9N2) + Influenza A virus (H7Nx) + Influenza A virus (H5Nx) + NCBITaxon:286285 Influenza A virus (H10N8) + NCBITaxon:11550 Influenza B virus (Yamagata 1/73) + NCBITaxon:11548 Influenza B virus (Victoria/87) + + + +purpose of sampling menu PurposeOfSamplingMenu GENEPIO:0100001 Cluster/Outbreak investigation + GENEPIO:0100002 Diagnostic testing + GENEPIO:0100003 Research + GENEPIO:0100004 Surveillance + + +purpose of sequencing menu PurposeOfSequencingMenu GENEPIO:0100005 Baseline surveillance (random sampling) + GENEPIO:0100006 Targeted surveillance (non-random sampling) + GENEPIO:0100007 Priority surveillance project + GENEPIO:0100009 Longitudinal surveillance (repeat sampling of individuals) + GENEPIO:0100010 Re-infection surveillance + GENEPIO:0100011 Vaccine escape surveillance + GENEPIO:0100019 Cluster/Outbreak investigation + GENEPIO:0100020 Multi-jurisdictional outbreak investigation + GENEPIO:0100021 Intra-jurisdictional outbreak investigation + GENEPIO:0100022 Research + GENEPIO:0100023 Viral passage experiment + GENEPIO:0100024 Protocol testing experiment + GENEPIO:0100356 Retrospective sequencing + + +specimen processing menu SpecimenProcessingMenu GENEPIO:0100039 Virus passage + GENEPIO:0100040 RNA re-extraction (post RT-PCR) + OBI:0600016 Specimens pooled + + +biomaterial extracted menu BiomaterialExtractedMenu OBI:0000895 RNA (total) + OBI:0000869 RNA (poly-A) + OBI:0002627 RNA (ribo-depleted) + GENEPIO:0100104 mRNA (messenger RNA) + OBI:0002754 mRNA (cDNA) + + + +host age bin menu HostAgeBinMenu GENEPIO:0100049 0 - 9 + GENEPIO:0100050 10 - 19 + GENEPIO:0100051 20 - 29 + GENEPIO:0100052 30 - 39 + GENEPIO:0100053 40 - 49 + GENEPIO:0100054 50 - 59 + GENEPIO:0100055 60 - 69 + GENEPIO:0100056 70 - 79 + GENEPIO:0100057 80 - 89 + GENEPIO:0100058 90 - 99 90+ + GENEPIO:0100059 100+ 90+ + + +host gender menu HostGenderMenu NCIT:C46110 Female + NCIT:C46109 Male + GSSO:000132 Non-binary gender + GSSO:004004 Transgender (assigned male at birth) + GSSO:004005 Transgender (assigned female at birth) + NCIT:C110959 Undeclared + + +exposure event menu ExposureEventMenu GENEPIO:0100237 Mass Gathering + GENEPIO:0100240 Agricultural Event + GENEPIO:0100238 Convention + GENEPIO:0100239 Convocation + GENEPIO:0100417 Recreational Event + GENEPIO:0100418 Concert + GENEPIO:0100419 Sporting Event + GENEPIO:0100241 Religious Gathering + GENEPIO:0100242 Mass + PCO:0000033 Social Gathering + PCO:0000039 Baby Shower + PCO:0000034 Community Event + GENEPIO:0100243 Family Gathering + GENEPIO:0100244 Family Reunion + GENEPIO:0100245 Funeral + PCO:0000035 Party + PCO:0000037 Potluck + PCO:0000038 Wedding + Other exposure event + + +exposure contact level menu ExposureContactLevelMenu GENEPIO:0100357 Contact with infected individual + TRANS:0000001 Direct contact (direct human-to-human contact) + GENEPIO:0100246 Indirect contact + GENEPIO:0100247 Close contact (face-to-face, no direct contact) + GENEPIO:0100248 Casual contact + + +host role menu HostRoleMenu GENEPIO:0100249 Attendee + OMRSE:00000058 Student + OMRSE:00000030 Patient + NCIT:C25182 Inpatient + NCIT:C28293 Outpatient + GENEPIO:0100250 Passenger + GENEPIO:0100251 Resident + GENEPIO:0100252 Visitor + GENEPIO:0100253 Volunteer + GENEPIO:0100254 Work + GENEPIO:0100255 Administrator + Child Care/Education Worker + Essential Worker + GENEPIO:0100256 First Responder + GENEPIO:0100257 Firefighter + GENEPIO:0100258 Paramedic + GENEPIO:0100259 Police Officer + GENEPIO:0100334 Healthcare Worker + GENEPIO:0100420 Community Healthcare Worker + GENEPIO:0100262 Laboratory Worker + OMRSE:00000014 Nurse + GENEPIO:0100263 Personal Care Aid + GENEPIO:0100264 Pharmacist + OMRSE:00000013 Physician + GENEPIO:0100260 Housekeeper + International worker + GENEPIO:0100261 Kitchen Worker + GENEPIO:0100354 Rotational Worker + GENEPIO:0100355 Seasonal Worker + Transport Worker + Transport Truck Driver + GENEPIO:0100265 Veterinarian + OMRSE:00000001 Social role + GENEPIO:0100266 Acquaintance of case + GENEPIO:0100267 Relative of case + GENEPIO:0100268 Child of case + GENEPIO:0100269 Parent of case + GENEPIO:0100270 Father of case + GENEPIO:0100271 Mother of case + GENEPIO:0100272 Spouse of case + Other Host Role + + +exposure setting menu ExposureSettingMenu ECTO:3000005 Human Exposure + GENEPIO:0100185 Contact with Patient + GENEPIO:0100187 Contact with Person with Acute Respiratory Illness + GENEPIO:0100188 Contact with Person with Fever and/or Cough + GENEPIO:0100189 Contact with Person who Recently Travelled + GENEPIO:0100190 Occupational, Residency or Patronage Exposure + ECTO:1000033 Abbatoir + GENEPIO:0100191 Animal Rescue + GENEPIO:0100192 Childcare + GENEPIO:0100193 Daycare + GENEPIO:0100194 Nursery + GENEPIO:0100195 Community Service Centre + GENEPIO:0100196 Correctional Facility + GENEPIO:0100197 Dormitory + ECTO:1000034 Farm + GENEPIO:0100198 First Nations Reserve + GENEPIO:0100199 Funeral Home + GENEPIO:0100200 Group Home + GENEPIO:0100201 Healthcare Setting + GENEPIO:0100202 Ambulance + GENEPIO:0100203 Acute Care Facility + GENEPIO:0100204 Clinic + GENEPIO:0100415 Community Healthcare (At-Home) Setting + GENEPIO:0100205 Community Health Centre + ECTO:1000035 Hospital + GENEPIO:0100206 Emergency Department + GENEPIO:0100207 ICU + GENEPIO:0100208 Ward + ECTO:1000036 Laboratory + GENEPIO:0100209 Long-Term Care Facility + GENEPIO:0100210 Pharmacy + GENEPIO:0100211 Physician's Office + GENEPIO:0100212 Household + GENEPIO:0100213 Insecure Housing (Homeless) + GENEPIO:0100214 Occupational Exposure + GENEPIO:0100215 Worksite + ECTO:1000037 Office + GENEPIO:0100216 Outdoors + ECTO:5000009 Camp/camping + GENEPIO:0100217 Hiking Trail + ECTO:6000030 Hunting Ground + GENEPIO:0100218 Ski Resort + ECTO:5000008 Petting zoo + GENEPIO:0100220 Place of Worship + GENEPIO:0100221 Church + GENEPIO:0100222 Mosque + GENEPIO:0100223 Temple + ECTO:1000040 Restaurant + ECTO:1000041 Retail Store + GENEPIO:0100224 School + GENEPIO:0100225 Temporary Residence + GENEPIO:0100226 Homeless Shelter + GENEPIO:0100227 Hotel + GENEPIO:0100228 Veterinary Care Clinic + GENEPIO:0100229 Travel Exposure + GENEPIO:0100230 Travelled on a Cruise Ship + GENEPIO:0100231 Travelled on a Plane + GENEPIO:0100232 Travelled on Ground Transport + GENEPIO:0001118 Travelled outside Province/Territory + GENEPIO:0001119 Travelled outside Canada + GENEPIO:0100235 Other Exposure Setting + + +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina + GENEPIO:0100106 Illumina Genome Analyzer + GENEPIO:0100107 Illumina Genome Analyzer II + GENEPIO:0100108 Illumina Genome Analyzer IIx + GENEPIO:0100109 Illumina HiScanSQ + GENEPIO:0100110 Illumina HiSeq + GENEPIO:0100111 Illumina HiSeq X + GENEPIO:0100112 Illumina HiSeq X Five + GENEPIO:0100113 Illumina HiSeq X Ten + GENEPIO:0100114 Illumina HiSeq 1000 + GENEPIO:0100115 Illumina HiSeq 1500 + GENEPIO:0100116 Illumina HiSeq 2000 + GENEPIO:0100117 Illumina HiSeq 2500 + GENEPIO:0100118 Illumina HiSeq 3000 + GENEPIO:0100119 Illumina HiSeq 4000 + GENEPIO:0100120 Illumina iSeq + GENEPIO:0100121 Illumina iSeq 100 + GENEPIO:0100122 Illumina NovaSeq + GENEPIO:0100123 Illumina NovaSeq 6000 + GENEPIO:0100124 Illumina MiniSeq + GENEPIO:0100125 Illumina MiSeq + GENEPIO:0100126 Illumina NextSeq + GENEPIO:0100127 Illumina NextSeq 500 + GENEPIO:0100128 Illumina NextSeq 550 + GENEPIO:0100129 Illumina NextSeq 2000 + GENEPIO:0100130 Pacific Biosciences + GENEPIO:0100131 PacBio RS + GENEPIO:0100132 PacBio RS II + GENEPIO:0100133 PacBio Sequel + GENEPIO:0100134 PacBio Sequel II + GENEPIO:0100135 Ion Torrent + GENEPIO:0100136 Ion Torrent PGM + GENEPIO:0100137 Ion Torrent Proton + GENEPIO:0100138 Ion Torrent S5 XL + GENEPIO:0100139 Ion Torrent S5 + GENEPIO:0100140 Oxford Nanopore + GENEPIO:0100141 Oxford Nanopore GridION + GENEPIO:0100142 Oxford Nanopore MinION + GENEPIO:0100143 Oxford Nanopore PromethION + GENEPIO:0100144 BGI Genomics + GENEPIO:0100145 BGI Genomics BGISEQ-500 + GENEPIO:0100146 MGI + GENEPIO:0100147 MGI DNBSEQ-T7 + GENEPIO:0100148 MGI DNBSEQ-G400 + GENEPIO:0100149 MGI DNBSEQ-G400 FAST + GENEPIO:0100150 MGI DNBSEQ-G50 + + +gene name menu GeneNameMenu Matrix (M) gene E (orf4) + Haemagglutinin (HA) gene M (orf5) + Influenza B- Matrix (M), NP, NS, HA gene N (orf9) + In of couple journals genes like PB2, PB1, PA S (orf2) + orf1ab (rep) + + +sequence submitted by menu SequenceSubmittedByMenu Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Canadore College + The Centre for Applied Genomics (TCAG) + Dynacare + Dynacare (Brampton) + Dynacare (Manitoba) + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Manitoba Cadham Provincial Laboratory + McGill University + McMaster University + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Sunnybrook Health Sciences Centre + Thunder Bay Regional Health Sciences Centre + + + sample collected by menu SampleCollectedByMenu Alberta Precision Labs (APL) + Alberta ProvLab North (APLN) + Alberta ProvLab South (APLS) + BCCDC Public Health Laboratory + Dynacare + Dynacare (Manitoba) + Dynacare (Brampton) + Eastern Ontario Regional Laboratory Association + Hamilton Health Sciences + The Hospital for Sick Children (SickKids) + Laboratoire de santé publique du Québec (LSPQ) + Lake of the Woods District Hospital - Ontario + LifeLabs + LifeLabs (Ontario) + Manitoba Cadham Provincial Laboratory + McMaster University + Mount Sinai Hospital + National Microbiology Laboratory (NML) + New Brunswick - Vitalité Health Network + Newfoundland and Labrador - Eastern Health + Nova Scotia Health Authority + Nunavut + Ontario Institute for Cancer Research (OICR) + Prince Edward Island - Health PEI + Public Health Ontario (PHO) + Queen's University / Kingston Health Sciences Centre + Saskatchewan - Roy Romanow Provincial Laboratory (RRPL) + Shared Hospital Laboratory + St. John's Rehab at Sunnybrook Hospital + Switch Health + Sunnybrook Health Sciences Centre + Unity Health Toronto + William Osler Health System + + +geo_loc_name (country) menu GeoLocNameCountryMenu GAZ:00006882 Afghanistan + GAZ:00002953 Albania + GAZ:00000563 Algeria + GAZ:00003957 American Samoa + GAZ:00002948 Andorra + GAZ:00001095 Angola + GAZ:00009159 Anguilla + GAZ:00000462 Antarctica + GAZ:00006883 Antigua and Barbuda + GAZ:00002928 Argentina + GAZ:00004094 Armenia + GAZ:00004025 Aruba + GAZ:00005901 Ashmore and Cartier Islands + GAZ:00000463 Australia + GAZ:00002942 Austria + GAZ:00004941 Azerbaijan + GAZ:00002733 Bahamas + GAZ:00005281 Bahrain + GAZ:00007117 Baker Island + GAZ:00003750 Bangladesh + GAZ:00001251 Barbados + GAZ:00005810 Bassas da India + GAZ:00006886 Belarus + GAZ:00002938 Belgium + GAZ:00002934 Belize + GAZ:00000904 Benin + GAZ:00001264 Bermuda + GAZ:00003920 Bhutan + GAZ:00002511 Bolivia + GAZ:00025355 Borneo + GAZ:00006887 Bosnia and Herzegovina + GAZ:00001097 Botswana + GAZ:00001453 Bouvet Island + GAZ:00002828 Brazil + GAZ:00003961 British Virgin Islands + GAZ:00003901 Brunei + GAZ:00002950 Bulgaria + GAZ:00000905 Burkina Faso + GAZ:00001090 Burundi + GAZ:00006888 Cambodia + GAZ:00001093 Cameroon + GAZ:00002560 Canada + GAZ:00001227 Cape Verde + GAZ:00003986 Cayman Islands + GAZ:00001089 Central African Republic + GAZ:00000586 Chad + GAZ:00002825 Chile + GAZ:00002845 China + GAZ:00005915 Christmas Island + GAZ:00005838 Clipperton Island + GAZ:00009721 Cocos Islands + GAZ:00002929 Colombia + GAZ:00005820 Comoros + GAZ:00053798 Cook Islands + GAZ:00005917 Coral Sea Islands + GAZ:00002901 Costa Rica + GAZ:00000906 Cote d'Ivoire + GAZ:00002719 Croatia + GAZ:00003762 Cuba + GAZ:00012582 Curacao + GAZ:00004006 Cyprus + GAZ:00002954 Czech Republic + GAZ:00001086 Democratic Republic of the Congo + GAZ:00005852 Denmark + GAZ:00000582 Djibouti + GAZ:00006890 Dominica + GAZ:00003952 Dominican Republic + GAZ:00002912 Ecuador + GAZ:00003934 Egypt + GAZ:00002935 El Salvador + GAZ:00001091 Equatorial Guinea + GAZ:00000581 Eritrea + GAZ:00002959 Estonia + GAZ:00001099 Eswatini + GAZ:00000567 Ethiopia + GAZ:00005811 Europa Island + GAZ:00001412 Falkland Islands (Islas Malvinas) + GAZ:00059206 Faroe Islands + GAZ:00006891 Fiji + GAZ:00002937 Finland + GAZ:00003940 France + GAZ:00002516 French Guiana + GAZ:00002918 French Polynesia + GAZ:00003753 French Southern and Antarctic Lands + GAZ:00001092 Gabon + GAZ:00000907 Gambia + GAZ:00009571 Gaza Strip + GAZ:00004942 Georgia + GAZ:00002646 Germany + GAZ:00000908 Ghana + GAZ:00003987 Gibraltar + GAZ:00005808 Glorioso Islands + GAZ:00002945 Greece + GAZ:00001507 Greenland + GAZ:02000573 Grenada + GAZ:00067142 Guadeloupe + GAZ:00003706 Guam + GAZ:00002936 Guatemala + GAZ:00001550 Guernsey + GAZ:00000909 Guinea + GAZ:00000910 Guinea-Bissau + GAZ:00002522 Guyana + GAZ:00003953 Haiti + GAZ:00009718 Heard Island and McDonald Islands + GAZ:00002894 Honduras + GAZ:00003203 Hong Kong + GAZ:00007120 Howland Island + GAZ:00002952 Hungary + GAZ:00000843 Iceland + GAZ:00002839 India + GAZ:00003727 Indonesia + GAZ:00004474 Iran + GAZ:00004483 Iraq + GAZ:00002943 Ireland + GAZ:00052477 Isle of Man + GAZ:00002476 Israel + GAZ:00002650 Italy + GAZ:00003781 Jamaica + GAZ:00005853 Jan Mayen + GAZ:00002747 Japan + GAZ:00007118 Jarvis Island + GAZ:00001551 Jersey + GAZ:00007114 Johnston Atoll + GAZ:00002473 Jordan + GAZ:00005809 Juan de Nova Island + GAZ:00004999 Kazakhstan + GAZ:00001101 Kenya + GAZ:00005682 Kerguelen Archipelago + GAZ:00007116 Kingman Reef + GAZ:00006894 Kiribati + GAZ:00011337 Kosovo + GAZ:00005285 Kuwait + GAZ:00006893 Kyrgyzstan + GAZ:00006889 Laos + GAZ:00002958 Latvia + GAZ:00002478 Lebanon + GAZ:00001098 Lesotho + GAZ:00000911 Liberia + GAZ:00000566 Libya + GAZ:00003858 Liechtenstein + GAZ:00007144 Line Islands + GAZ:00002960 Lithuania + GAZ:00002947 Luxembourg + GAZ:00003202 Macau + GAZ:00001108 Madagascar + GAZ:00001105 Malawi + GAZ:00003902 Malaysia + GAZ:00006924 Maldives + GAZ:00000584 Mali + GAZ:00004017 Malta + GAZ:00007161 Marshall Islands + GAZ:00067143 Martinique + GAZ:00000583 Mauritania + GAZ:00003745 Mauritius + GAZ:00003943 Mayotte + GAZ:00002852 Mexico + GAZ:00005862 Micronesia + GAZ:00007112 Midway Islands + GAZ:00003897 Moldova + GAZ:00003857 Monaco + GAZ:00008744 Mongolia + GAZ:00006898 Montenegro + GAZ:00003988 Montserrat + GAZ:00000565 Morocco + GAZ:00001100 Mozambique + GAZ:00006899 Myanmar + GAZ:00001096 Namibia + GAZ:00006900 Nauru + GAZ:00007119 Navassa Island + GAZ:00004399 Nepal + GAZ:00002946 Netherlands + GAZ:00005206 New Caledonia + GAZ:00000469 New Zealand + GAZ:00002978 Nicaragua + GAZ:00000585 Niger + GAZ:00000912 Nigeria + GAZ:00006902 Niue + GAZ:00005908 Norfolk Island + GAZ:00002801 North Korea + GAZ:00006895 North Macedonia + GAZ:00002284 North Sea + GAZ:00003958 Northern Mariana Islands + GAZ:00002699 Norway + GAZ:00005283 Oman + GAZ:00005246 Pakistan + GAZ:00006905 Palau + GAZ:00002892 Panama + GAZ:00003922 Papua New Guinea + GAZ:00010832 Paracel Islands + GAZ:00002933 Paraguay + GAZ:00002932 Peru + GAZ:00004525 Philippines + GAZ:00005867 Pitcairn Islands + GAZ:00002939 Poland + GAZ:00004126 Portugal + GAZ:00006935 Puerto Rico + GAZ:00005286 Qatar + GAZ:00001088 Republic of the Congo + GAZ:00003945 Reunion + GAZ:00002951 Romania + GAZ:00023304 Ross Sea + GAZ:00002721 Russia + GAZ:00001087 Rwanda + GAZ:00000849 Saint Helena + GAZ:00006906 Saint Kitts and Nevis + GAZ:00006909 Saint Lucia + GAZ:00003942 Saint Pierre and Miquelon + GAZ:00005841 Saint Martin + GAZ:02000565 Saint Vincent and the Grenadines + GAZ:00006910 Samoa + GAZ:00003102 San Marino + GAZ:00006927 Sao Tome and Principe + GAZ:00005279 Saudi Arabia + GAZ:00000913 Senegal + GAZ:00002957 Serbia + GAZ:00006922 Seychelles + GAZ:00000914 Sierra Leone + GAZ:00003923 Singapore + GAZ:00012579 Sint Maarten + GAZ:00002956 Slovakia + GAZ:00002955 Slovenia + GAZ:00005275 Solomon Islands + GAZ:00001104 Somalia + GAZ:00001094 South Africa + GAZ:00003990 South Georgia and the South Sandwich Islands + GAZ:00002802 South Korea + GAZ:00233439 South Sudan + GAZ:00000591 Spain + GAZ:00010831 Spratly Islands + GAZ:00003924 Sri Lanka + GAZ:00002475 State of Palestine + GAZ:00000560 Sudan + GAZ:00002525 Suriname + GAZ:00005396 Svalbard + GAZ:00001099 Swaziland + GAZ:00002729 Sweden + GAZ:00002941 Switzerland + GAZ:00002474 Syria + GAZ:00005341 Taiwan + GAZ:00006912 Tajikistan + GAZ:00001103 Tanzania + GAZ:00003744 Thailand + GAZ:00006913 Timor-Leste + GAZ:00000915 Togo + GAZ:00260188 Tokelau + GAZ:00006916 Tonga + GAZ:00003767 Trinidad and Tobago + GAZ:00005812 Tromelin Island + GAZ:00000562 Tunisia + GAZ:00000558 Turkey + GAZ:00005018 Turkmenistan + GAZ:00003955 Turks and Caicos Islands + GAZ:00009715 Tuvalu + GAZ:00002459 United States of America + GAZ:00001102 Uganda + GAZ:00002724 Ukraine + GAZ:00005282 United Arab Emirates + GAZ:00002637 United Kingdom + GAZ:00002930 Uruguay + GAZ:00004979 Uzbekistan + GAZ:00006918 Vanuatu + GAZ:00002931 Venezuela + GAZ:00003756 Viet Nam + GAZ:00003959 Virgin Islands + GAZ:00007111 Wake Island + GAZ:00007191 Wallis and Futuna + GAZ:00009572 West Bank + GAZ:00000564 Western Sahara + GAZ:00005284 Yemen + GAZ:00001107 Zambia + GAZ:00001106 Zimbabwe + + \ No newline at end of file diff --git a/web/templates/influenza/schema_slots.tsv b/web/templates/influenza/schema_slots.tsv index 17325427..8c7b6bf9 100644 --- a/web/templates/influenza/schema_slots.tsv +++ b/web/templates/influenza/schema_slots.tsv @@ -1,97 +1,97 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal Influenza GENEPIO:0001122 Database Identifiers - Database Identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID - Database Identifiers GENEPIO:0001202 third party lab service provider name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 - Database Identifiers GENEPIO:0001149 third party lab sample ID WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY - Database Identifiers GENEPIO:0100281 case ID WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID - Database Identifiers GENEPIO:0001128 Related specimen primary ID WhitespaceMinimizedString null value menu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID - Database Identifiers GENEPIO:0001131 IRIDA sample name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name - Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella bioproject accession menu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession - Database Identifiers GENEPIO:0001136 bioproject accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession - Database Identifiers GENEPIO:0001139 biosample accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION - Database Identifiers GENEPIO:0001142 SRA accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION - Database Identifiers GENEPIO:0001145 GenBank accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession - Database Identifiers GENEPIO:0001147 GISAID accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession - Database Identifiers GISAID virus name WhitespaceMinimizedString TRUE The user-defined name of the virus, specified in the organism-specific format prescribed by the GISAID database. Provide the GISAID virus name, which should be written in the format: A/Province/Country/SampleID/year A/Ontario/Canada/ABCD1234/2023 - GENEPIO:0001150 Sample collection and processing - Sample collection and processing GENEPIO:0001153 sample collected by sample collected by menu null value menu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by - Sample collection and processing GENEPIO:0001156 sample collector contact email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email - Sample collection and processing GENEPIO:0100416 sequenced by sequence submitted by menu null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by - Sample collection and processing GENEPIO:0001159 sequence submitted by sequence submitted by menu null value menu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by - Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date - Sample collection and processing GENEPIO:0001177 sample collection date precision sample collection date precision menu null value menu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 - Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name (country) menu null value menu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) - Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name (state/province/territory) menu null value menu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) - Sample collection and processing GENEPIO:0001191 organism organism menu null value menu TRUE Taxonomic name of the organism. Select the type of influenza virus from the picklist provided. Influenza virus A virus (H1N1) Pathogen HC_CURRENT_ID organism organism - Sample collection and processing GENEPIO:0001195 isolate WhitespaceMinimizedString null value menu TRUE Identifier of the specific isolate. Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name - Sample collection and processing GENEPIO:0001198 purpose of sampling purpose of sampling menu null value menu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling - Sample collection and processing GENEPIO:0001200 purpose of sampling details WhitespaceMinimizedString null value menu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details - Sample collection and processing GENEPIO:0001204 NML submitted specimen type NML submitted specimen type menu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE - Sample collection and processing GENEPIO:0001209 Related specimen relationship type Related specimen relationship type menu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Reinfection testing Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE - Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity menu null value menu The upstream activities or variables that may affect the sample collected. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Vaccination - Sample collection and processing GENEPIO:0100434 presampling activity details WhitespaceMinimizedString The details of the activities or variables that may affect the sample collected. Briefly describe the presampling details using free text. Patient was previously infected. Sample taken during convalescence. - Sample collection and processing GENEPIO:0001211 anatomical material anatomical material menu null value menu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material - Sample collection and processing GENEPIO:0001214 anatomical part anatomical part menu null value menu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part - Sample collection and processing GENEPIO:0001216 body product body product menu null value menu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Urine Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product - Sample collection and processing GENEPIO:0001234 collection device collection device menu null value menu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device - Sample collection and processing GENEPIO:0001241 collection method collection method menu null value menu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method - Sample collection and processing GENEPIO:0001243 collection protocol WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Free text. FluSamplingProtocol v. 1.2 collection protocol - Sample collection and processing GENEPIO:0001253 specimen processing specimen processing menu null value menu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history specimen processing - Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. - Sample collection and processing GENEPIO:0001266 biomaterial extracted biomaterial extracted menu null value menu The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) biomaterial extracted - GENEPIO:0001268 Host Information - Host Information GENEPIO:0001386 host (common name) host (common name) menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human Animal Type PH_ANIMAL_TYPE - Host Information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) - Host Information GENEPIO:0001388 host health state host health state menu null value menu Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Symptomatic Patient status Host Health State PH_HOST_HEALTH host_health_state - Host Information GENEPIO:0001389 host health status details host health status details menu null value menu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS - Host Information GENEPIO:0001390 host health outcome host health outcome menu null value menu Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered PH_HOST_HEALTH_OUTCOME host_disease_outcome - Host Information GENEPIO:0001391 host disease host disease menu null value menu TRUE The name of the disease experienced by the host. Select "Influenza" from the pick list provided in the template. Influenza Host Disease PH_HOST_DISEASE host_disease host disease - Host Information GENEPIO:0001392 host age decimal null value menu TRUE 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age - Host Information GENEPIO:0001393 host age unit host age unit menu null value menu TRUE The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit - Host Information GENEPIO:0001394 host age bin host age bin menu null value menu TRUE Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin - Host Information GENEPIO:0001395 host gender host gender menu null value menu TRUE {Title_Case} The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Male Gender Patient Sex VD_SEX host_sex host gender - Host Information GENEPIO:0001398 host subject ID WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host subject ID host_subject_id - GENEPIO:0001403 Host vaccination information - Host vaccination information GENEPIO:0001404 host vaccination status host vaccination status menu null value menu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated PH_VACCINATION_HISTORY - Host vaccination information GENEPIO:0100321 vaccination history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. PH_VACCINATION_HISTORY - GENEPIO:0001409 Host exposure information - Host exposure information GENEPIO:0001417 exposure event exposure event menu null value menu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Social Gathering Additional location information Exposure Event PH_EXPOSURE - Host exposure information GENEPIO:0001418 exposure contact level exposure contact level menu null value menu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct exposure contact level - Host exposure information GENEPIO:0001419 host role host role menu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Inpatient PH_HOST_ROLE - Host exposure information GENEPIO:0001428 exposure setting exposure setting menu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting PH_EXPOSURE - Host exposure information GENEPIO:0001431 exposure details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Case infected family at home PH_EXPOSURE_DETAILS + Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_rona_99 Sample ID given by the sample provider Primary Specimen ID TEXT_ID sample_name specimen collector sample ID + Database Identifiers GENEPIO:0001202 third party lab service provider name third_party_lab_service_provider_name WhitespaceMinimizedString The name of the third party company or laboratory that provided services. Provide the full, unabbreviated name of the company or laboratory. Switch Health HC_TEXT5 + Database Identifiers GENEPIO:0001149 third party lab sample ID third_party_lab_sample_id WhitespaceMinimizedString The identifier assigned to a sample by a third party service provider. Store the sample identifier supplied by the third party services provider. SHK123456 PH_ID_NUMBER_PRIMARY + Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString TRUE The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID + Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID + Database Identifiers GENEPIO:0001131 IRIDA sample name irida_sample_name WhitespaceMinimizedString The identifier assigned to a sequenced isolate in IRIDA. Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). prov_rona_99 IRIDA sample name + Database Identifiers GENEPIO:0001133 umbrella bioproject accession umbrella_bioproject_accession UmbrellaBioprojectAccessionMenu {UPPER_CASE} The INSDC accession number assigned to the umbrella BioProject. Store the umbrella BioProject accession by selecting it from the picklist in the template. The umbrella BioProject accession will be identical for all CanCOGen submitters. Different provinces will have their own BioProjects, however these BioProjects will be linked under one umbrella BioProject. PRJNA623807 umbrella bioproject accession + Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Store the BioProject accession number. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. Each province will be assigned a different bioproject accession number by the National Microbiology Lab. A valid NCBI BioProject accession has prefix PRJN e.g., PRJNA12345, and is created once at the beginning of a new sequencing project. PRJNA608651 BioProject Accession PH_BIOPROJECT_ACCESSION bioproject_accession + Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN. SAMN14180202 BioSample Accession PH_BIOSAMPLE_ACCESSION + Database Identifiers GENEPIO:0001142 SRA accession sra_accession WhitespaceMinimizedString {UPPER_CASE} The Sequence Read Archive (SRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC. Store the accession assigned to the submitted "run". NCBI-SRA accessions start with SRR. SRR11177792 SRA Accession PH_SRA_ACCESSION + Database Identifiers GENEPIO:0001145 GenBank accession genbank_accession WhitespaceMinimizedString {UPPER_CASE} The GenBank identifier assigned to the sequence in the INSDC archives. Store the accession returned from a GenBank submission (viral genome assembly). MN908947.3 GenBank Accession GenBank accession + Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession ID GISAID_accession GISAID accession + Database Identifiers GISAID virus name gisaid_virus_name WhitespaceMinimizedString TRUE The user-defined name of the virus, specified in the organism-specific format prescribed by the GISAID database. Provide the GISAID virus name, which should be written in the format: A/Province/Country/SampleID/year A/Ontario/Canada/ABCD1234/2023 + GENEPIO:0001150 Sample collection and processing sample_collection_and_processing + Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by + Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email + Sample collection and processing GENEPIO:0100416 sequenced by sequenced_by SequencedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by + Sample collection and processing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCING_CENTRE sequenced_by sequence submitted by + Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE sample collection date sample collection date + Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 + Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) + Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) + Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Select the type of influenza virus from the picklist provided. Influenza virus A virus (H1N1) Pathogen HC_CURRENT_ID organism organism + Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Virus name GISAID Virus Name RESULT - CANCOGEN_SUBMISSIONS isolate;GISAID_virus_name isolate;fasta header name + Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Diagnostic testing. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling + Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details + Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. swab Specimen Type PH_SPECIMEN_TYPE + Sample collection and processing GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type RelatedSpecimenRelationshipTypeMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Reinfection testing Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE + Sample collection and processing GENEPIO:0100433 presampling_activity presampling_activity PresamplingActivityMenu NullValueMenu The upstream activities or variables that may affect the sample collected. If there was an activity that would affect the sample prior to collection (this is different than sample processing), provide the activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Vaccination + Sample collection and processing GENEPIO:0100434 presampling activity details presampling_activity_details WhitespaceMinimizedString The details of the activities or variables that may affect the sample collected. Briefly describe the presampling details using free text. Patient was previously infected. Sample taken during convalescence. + Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Blood Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material + Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Nasopharynx (NP) Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part + Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Urine Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product + Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device + Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bronchoalveolar lavage (BAL) Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method + Sample collection and processing GENEPIO:0001243 collection protocol collection_protocol WhitespaceMinimizedString The name and version of a particular protocol used for sampling. Free text. FluSamplingProtocol v. 1.2 collection protocol + Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Virus passage Passage details/history specimen processing + Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 25 swabs were pooled and further prepared as a single sample during library prep. + Sample collection and processing GENEPIO:0001266 biomaterial extracted biomaterial_extracted BiomaterialExtractedMenu NullValueMenu The biomaterial extracted from samples for the purpose of sequencing. Provide the biomaterial extracted from the picklist in the template. RNA (total) biomaterial extracted + GENEPIO:0001268 Host Information host_information + Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human, bat. If the sample was environmental, put "not applicable. Human Animal Type PH_ANIMAL_TYPE + Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) + Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a descriptor from the pick list provided in the template. Symptomatic Patient status Host Health State PH_HOST_HEALTH host_health_state + Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized (ICU) Host Health State Details PH_HOST_HEALTH_DETAILS + Host Information GENEPIO:0001390 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a descriptor from the pick list provided in the template. Recovered PH_HOST_HEALTH_OUTCOME host_disease_outcome + Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Influenza" from the pick list provided in the template. Influenza Host Disease PH_HOST_DISEASE host_disease host disease + Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. Enter the age of the host in years. If not available, provide a null value. If there is not host, put "Not Applicable". 79 Patient age Patient Age PH_AGE host_age host age + Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The unit used to measure the host age, in either months or years. Indicate whether the host age is in months or years. Age indicated in months will be binned to the 0 - 9 year age bin. years Age Units PH_AGE_UNIT host age unit + Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE Age of host at the time of sampling, expressed as an age group. Select the corresponding host age bin from the pick list provided in the template. If not available, provide a null value. 60 - 69 Host Age Category PH_AGE_GROUP host age bin + Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. Select the corresponding host gender from the pick list provided in the template. If not available, provide a null value. If there is no host, put "Not Applicable". Male Gender Patient Sex VD_SEX host_sex host gender + Host Information GENEPIO:0001398 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Provide the host identifier. Should be a unique, user-defined identifier. BCxy123 host subject ID host_subject_id + GENEPIO:0001403 Host vaccination information host_vaccination_information + Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated PH_VACCINATION_HISTORY + Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. PH_VACCINATION_HISTORY + GENEPIO:0001409 Host exposure information host_exposure_information + Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the curation team. Social Gathering Additional location information Exposure Event PH_EXPOSURE + Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select direct or indirect exposure from the pick-list. Direct exposure contact level + Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. Inpatient PH_HOST_ROLE + Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. Healthcare Setting PH_EXPOSURE + Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Case infected family at home PH_EXPOSURE_DETAILS - GENEPIO:0001441 Sequencing - Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing - Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Seasonal flu research project Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details - Sequencing GENEPIO:0001447 sequencing date date null value menu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2023-09-22 PH_SEQUENCING_DATE - Sequencing GENEPIO:0001449 amplicon size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size - Sequencing GENEPIO:0001450 library preparation kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT - Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument - Sequencing GENEPIO:0001454 sequencing protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol - Sequencing GENEPIO:0001456 amplicon pcr primer scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. amplicon pcr primer scheme - GENEPIO:0001457 Bioinformatics and QC metrics - Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method - Bioinformatics and QC metrics GENEPIO:0001459 dehosting method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method - Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name - Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version - Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% breadth of coverage value breadth of coverage value - Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage depth of coverage value depth of coverage value - Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold - Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). number of base pairs sequenced - Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). consensus genome length - Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. reference genome accession reference genome accession - Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol - GENEPIO:0001506 Pathogen diagnostic testing - Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name - Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value - Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 - Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 - Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene name menu null value menu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Gene Target 3 SUBMITTED_RESLT - Gene Target #3 - Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 decimal null value menu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value + GENEPIO:0001441 Sequencing sequencing + Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing + Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Seasonal flu research project Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details + Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2023-09-22 PH_SEQUENCING_DATE + Sequencing GENEPIO:0001449 amplicon size amplicon_size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size + Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT + Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument + Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol__ WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol + Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. amplicon pcr primer scheme + GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics + Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method + Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method + Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name + Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version + Bioinformatics and QC metrics GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Provide value as a percent. 95% breadth of coverage value breadth of coverage value + Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Coverage depth of coverage value depth of coverage value + Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold + Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). number of base pairs sequenced + Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). consensus genome length + Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. reference genome accession reference genome accession + Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol + GENEPIO:0001506 Pathogen diagnostic testing pathogen_diagnostic_testing + Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of the gene used in the test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name + Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value + Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 + Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 + Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene_name_3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI Gene Target 3 SUBMITTED_RESLT - Gene Target #3 + Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value - GENEPIO:0001516 Contributor acknowledgement - Contributor acknowledgement GENEPIO:0001517 authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS - Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS \ No newline at end of file + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement + Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_CANCOGEN_AUTHORS + Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v3.3.3, Influenza v1.0.0 DataHarmonizer provenance Additional Comments HC_COMMENTS \ No newline at end of file From 47318b6cc74eeb9f216b5fa03ef7c9edc461c3e4 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:24:54 -0700 Subject: [PATCH 88/96] Wastewater enumeration tweak --- web/templates/wastewater/schema.json | 5 ++++- web/templates/wastewater/schema.yaml | 2 ++ web/templates/wastewater/schema_enums.tsv | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index a5469b3a..e27046cb 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -3585,7 +3585,10 @@ "Illumina [GENEPIO:0100105]": { "text": "Illumina [GENEPIO:0100105]", "description": "A DNA sequencer manufactured by the Illumina corporation.", - "meaning": "GENEPIO:0100105" + "meaning": "GENEPIO:0100105", + "exact_mappings": [ + "NCBI_SRA:ILLUMINA" + ] }, "Illumina Genome Analyzer [GENEPIO:0100106]": { "text": "Illumina Genome Analyzer [GENEPIO:0100106]", diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index 77256b60..0564e807 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -9769,6 +9769,8 @@ enums: text: Illumina [GENEPIO:0100105] description: A DNA sequencer manufactured by the Illumina corporation. meaning: GENEPIO:0100105 + exact_mappings: + - NCBI_SRA:ILLUMINA Illumina Genome Analyzer [GENEPIO:0100106]: text: Illumina Genome Analyzer [GENEPIO:0100106] description: A DNA sequencer manufactured by Solexa as one of its first sequencer diff --git a/web/templates/wastewater/schema_enums.tsv b/web/templates/wastewater/schema_enums.tsv index 6f123a56..81259962 100644 --- a/web/templates/wastewater/schema_enums.tsv +++ b/web/templates/wastewater/schema_enums.tsv @@ -624,7 +624,7 @@ sequencing platform menu SequencingPlatformMenu GENEPIO:0001923 Illumina [GENEPI GENEPIO:0002682 Helicos [GENEPIO:0002682] A sequencing platform brand provided by Helicos corporation (now defunct). HELICOS GENEPIO:0100985 Applied Biosystems [GENEPIO:0100985] A sequencing platform provided by ThermoFisher. CAPILLARY -sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. +sequencing instrument menu SequencingInstrumentMenu GENEPIO:0100105 Illumina [GENEPIO:0100105] A DNA sequencer manufactured by the Illumina corporation. ILLUMINA GENEPIO:0100106 Illumina Genome Analyzer [GENEPIO:0100106] A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. OBI:0000703 Illumina Genome Analyzer II [OBI:0000703] A DNA sequencer manufactured by the Illumina (Solexa) corporation, which supports sequencing of single or paired end clone libraries relying on sequencing by synthesis technology. OBI:0002000 Illumina Genome Analyzer IIx [OBI:0002000] An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. From 8e47d608b131b92e4a9f07b3666409052f77d243 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 09:43:36 -0700 Subject: [PATCH 89/96] Mpox documentation alignment to match CanCoGEN --- web/templates/mpox/export.js | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/web/templates/mpox/export.js b/web/templates/mpox/export.js index a60ae661..e3f7cf3a 100644 --- a/web/templates/mpox/export.js +++ b/web/templates/mpox/export.js @@ -288,27 +288,24 @@ export default { ['PH_CASE_ID', []], ['PH_RELATED_PRIMARY_ID', []], - ['CUSTOMER', []], - ['PH_SEQUENCING_CENTRE', []], - ['PH_SEQUENCE_SUBMITTER', []], + ['CUSTOMER', []], + ['PH_SEQUENCING_CENTRE', []], + ['PH_SEQUENCE_SUBMITTER', []], ['HC_COLLECT_DATE', []], ['HC_TEXT2', []], - ['HC_COUNTRY', []], ['HC_PROVINCE', []], - ['HC_CURRENT_ID', []], - ['SUBMISSIONS - BioProject Accession', []], ['SUBMISSIONS - BioSample Accession', []], ['SUBMISSIONS - SRA Accession', []], ['SUBMISSIONS - GenBank Accession', []], ['SUBMISSIONS - GISAID Virus Name', []], ['SUBMISSIONS - GISAID Accession', []], - + ['HC_SAMPLE_CATEGORY', []], ['PH_SAMPLING_DETAILS', []], ['PH_SPECIMEN_TYPE', []], @@ -321,7 +318,6 @@ export default { //['PH_ENVIRONMENTAL_SITE', []], ['PH_SPECIMEN_TYPE_ORIG', []], ['COLLECTION_METHOD', []], - ['PH_ANIMAL_TYPE', []], ['PH_HOST_HEALTH', []], ['PH_HOST_HEALTH_DETAILS', []], @@ -345,10 +341,10 @@ export default { ['PH_EXPOSURE_DETAILS', []], ['PH_HOST_ROLE', []], ['PH_REASON_FOR_SEQUENCING', []], - ['PH_REASON_FOR_SEQUENCING_DETAILS', []], ['PH_SEQUENCING_DATE', []], ['PH_LIBRARY_PREP_KIT', []], + ['PH_SEQUENCING_INSTRUMENT', []], ['PH_TESTING_PROTOCOL', []], //['PH_SEQ_PROTOCOL_NAME', []], @@ -357,7 +353,6 @@ export default { ['PH_CONSENSUS_SEQUENCE', []], // from 'Consensus Sequence Method Name' or 'consensus sequence software name' ['PH_CONSENSUS_SEQUENCE_VERSION', []], // From 'Consensus Sequence Method Version Name' or 'consensus sequence software version' - ['PH_BIOINFORMATICS_PROTOCOL', []], //['PH_LINEAGE_CLADE_NAME', []], //['PH_LINEAGE_CLADE_SOFTWARE',[]], @@ -429,6 +424,7 @@ export default { for (const inputRow of dh.getTrimmedData(dh.hot)) { const outputRow = []; + for (const [headerName, sources] of ExportHeaders) { if (headerName === 'HC_CURRENT_ID') { // Assign constant value. @@ -474,13 +470,15 @@ export default { if (!value || null_values.has(value)) { continue; } + // value = value.toLowerCase(); //Only in CanCoGEN if ( fieldName === 'host (scientific name)' || fieldName === 'host (common name)' ) { if (value === 'Homo sapiens' || value === 'Human') cellValue = 'Human'; - else cellValue = 'ANIMAL'; + else + cellValue = 'ANIMAL'; break; } if ( From 4b96d7d438f6ecad71b40e008161086d3d2469ac Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 10:11:21 -0700 Subject: [PATCH 90/96] CanCoGEN Adapt NML_LIMS export plus documentation column alignment --- web/templates/canada_covid19/export.js | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/web/templates/canada_covid19/export.js b/web/templates/canada_covid19/export.js index 69a6ed4e..248e6a5a 100644 --- a/web/templates/canada_covid19/export.js +++ b/web/templates/canada_covid19/export.js @@ -463,11 +463,18 @@ export default { ['SUBMISSIONS - GISAID Accession ID', []], ['CUSTOMER', []], ['PH_SEQUENCING_CENTRE', []], + ['HC_COLLECT_DATE', []], ['HC_TEXT2', []], ['HC_COUNTRY', []], ['HC_PROVINCE', []], ['HC_CURRENT_ID', []], + + + + + + ['RESULT - CANCOGEN_SUBMISSIONS', []], ['HC_SAMPLE_CATEGORY', []], ['PH_SAMPLING_DETAILS', []], @@ -504,12 +511,11 @@ export default { ['PH_EXPOSURE_DETAILS', []], ['PH_HOST_ROLE', []], ['PH_REASON_FOR_SEQUENCING', []], - ['PH_REASON_FOR_SEQUENCING_DETAILS', []], ['PH_SEQUENCING_DATE', []], ['PH_LIBRARY_PREP_KIT', []], - ['PH_INSTRUMENT_CGN', []], + ['PH_TESTING_PROTOCOL', []], ['PH_SEQ_PROTOCOL_NAME', []], ['PH_RAW_SEQUENCE_METHOD', []], @@ -530,6 +536,10 @@ export default { ['SUBMITTED_RESLT - Gene Target #2 CT Value', []], ['SUBMITTED_RESLT - Gene Target #3', []], ['SUBMITTED_RESLT - Gene Target #3 CT Value', []], + + + + ['PH_CANCOGEN_AUTHORS', []], ['HC_COMMENTS', []], @@ -539,7 +549,8 @@ export default { const sourceFields = dh.getFields(dh.table); const sourceFieldNameMap = dh.getFieldNameMap(sourceFields); - + const sourceFieldTitleMap = dh.getFieldTitleMap(sourceFields); + // Fills in the above mapping (or just set manually above) dh.getHeaderMap(ExportHeaders, sourceFields, 'NML_LIMS'); @@ -577,7 +588,7 @@ export default { // Note: if this field eventually gets null values, then must do // field.dataStatus check. const value = - inputRow[sourceFieldNameMap['signs and symptoms']] || ''; + inputRow[sourceFieldTitleMap['signs and symptoms']] || ''; outputRow.push(value ? 'Y' : 'N'); continue; } @@ -586,9 +597,9 @@ export default { // by looking at year or month in "sample collection date precision" if (headerName === 'HC_COLLECT_DATE') { let value = - inputRow[sourceFieldNameMap['sample collection date']] || ''; + inputRow[sourceFieldTitleMap['sample collection date']] || ''; const date_unit = - inputRow[sourceFieldNameMap['sample collection date precision']]; + inputRow[sourceFieldTitleMap['sample collection date precision']]; outputRow.push(dh.setDateChange(date_unit, value, '01')); continue; } @@ -604,7 +615,7 @@ export default { 'environmental material', 'environmental site', ]) { - let value = inputRow[sourceFieldNameMap[fieldName]]; + let value = inputRow[sourceFieldTitleMap[fieldName]]; // Ignore all null value types if (!value || null_values.has(value)) { From 7e610d23da4f9b75b58faae48965d99dd00848e2 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 10:31:05 -0700 Subject: [PATCH 91/96] template fix for multiple space to underscore in names --- .../canada_covid19/locales/fr/schema.json | 14 +- .../canada_covid19/locales/fr/schema.yaml | 8 +- web/templates/canada_covid19/schema.json | 14 +- web/templates/canada_covid19/schema.yaml | 8 +- web/templates/canada_covid19/schema_slots.tsv | 2 +- web/templates/hpai/schema.json | 132 +++++++++--------- web/templates/hpai/schema.yaml | 60 ++++---- web/templates/hpai/schema_slots.tsv | 6 +- web/templates/influenza/schema.json | 14 +- web/templates/influenza/schema.yaml | 8 +- web/templates/influenza/schema_slots.tsv | 2 +- web/templates/mpox/schema.json | 24 ++-- web/templates/mpox/schema.yaml | 12 +- web/templates/mpox/schema_slots.tsv | 2 +- 14 files changed, 153 insertions(+), 153 deletions(-) diff --git a/web/templates/canada_covid19/locales/fr/schema.json b/web/templates/canada_covid19/locales/fr/schema.json index 1d2a66ed..fcaec4f5 100644 --- a/web/templates/canada_covid19/locales/fr/schema.json +++ b/web/templates/canada_covid19/locales/fr/schema.json @@ -5981,8 +5981,8 @@ ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "Nom du fichier R1 FASTQ spécifié par l’utilisateur", "title": "Nom de fichier R1 FASTQ", "comments": [ @@ -7077,8 +7077,8 @@ "rank": 115, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "rank": 116, "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, @@ -9667,8 +9667,8 @@ ], "slot_group": "Bioinformatique et mesures de contrôle de la qualité" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "Nom du fichier R1 FASTQ spécifié par l’utilisateur", "title": "Nom de fichier R1 FASTQ", "comments": [ @@ -9681,7 +9681,7 @@ ], "from_schema": "https://example.com/CanCOGeN_Covid-19", "rank": 116, - "alias": "r1_fastq_filename________", + "alias": "r1_fastq_filename", "owner": "CanCOGeNCovid19", "domain_of": [ "CanCOGeNCovid19" diff --git a/web/templates/canada_covid19/locales/fr/schema.yaml b/web/templates/canada_covid19/locales/fr/schema.yaml index 03f8f725..737fc4d8 100644 --- a/web/templates/canada_covid19/locales/fr/schema.yaml +++ b/web/templates/canada_covid19/locales/fr/schema.yaml @@ -136,7 +136,7 @@ classes: - breadth_of_coverage_value - depth_of_coverage_value - depth_of_coverage_threshold - - r1_fastq_filename________ + - r1_fastq_filename - r2_fastq_filename - r1_fastq_filepath - r2_fastq_filepath @@ -510,7 +510,7 @@ classes: depth_of_coverage_threshold: rank: 115 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" - r1_fastq_filename________: + r1_fastq_filename: rank: 116 slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" r2_fastq_filename: @@ -1896,8 +1896,8 @@ slots: comments: "Fournissez la couverture amplifi\xE9e." examples: - value: 100x - r1_fastq_filename________: - name: r1_fastq_filename________ + r1_fastq_filename: + name: r1_fastq_filename title: "Nom de fichier\_R1\_FASTQ" description: "Nom du fichier\_R1\_FASTQ sp\xE9cifi\xE9 par l\u2019utilisateur" slot_group: "Bioinformatique et mesures de contr\xF4le de la qualit\xE9" diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json index d2bef2a3..dc97f0a4 100644 --- a/web/templates/canada_covid19/schema.json +++ b/web/templates/canada_covid19/schema.json @@ -8744,8 +8744,8 @@ ], "range": "WhitespaceMinimizedString" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", "comments": [ @@ -10025,8 +10025,8 @@ "rank": 115, "slot_group": "Bioinformatics and QC metrics" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "rank": 116, "slot_group": "Bioinformatics and QC metrics" }, @@ -13882,8 +13882,8 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "r1_fastq_filename________": { - "name": "r1_fastq_filename________", + "r1_fastq_filename": { + "name": "r1_fastq_filename", "description": "The user-specified filename of the r1 FASTQ file.", "title": "r1 fastq filename", "comments": [ @@ -13900,7 +13900,7 @@ ], "rank": 116, "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename________", + "alias": "r1_fastq_filename", "owner": "CanCOGeNCovid19", "domain_of": [ "CanCOGeNCovid19" diff --git a/web/templates/canada_covid19/schema.yaml b/web/templates/canada_covid19/schema.yaml index 597c7882..3d0a017c 100644 --- a/web/templates/canada_covid19/schema.yaml +++ b/web/templates/canada_covid19/schema.yaml @@ -138,7 +138,7 @@ classes: - breadth_of_coverage_value - depth_of_coverage_value - depth_of_coverage_threshold - - r1_fastq_filename________ + - r1_fastq_filename - r2_fastq_filename - r1_fastq_filepath - r2_fastq_filepath @@ -512,7 +512,7 @@ classes: depth_of_coverage_threshold: rank: 115 slot_group: Bioinformatics and QC metrics - r1_fastq_filename________: + r1_fastq_filename: rank: 116 slot_group: Bioinformatics and QC metrics r2_fastq_filename: @@ -2440,8 +2440,8 @@ slots: - value: 100x exact_mappings: - NML_LIMS:depth%20of%20coverage%20threshold - r1_fastq_filename________: - name: r1_fastq_filename________ + r1_fastq_filename: + name: r1_fastq_filename title: r1 fastq filename description: The user-specified filename of the r1 FASTQ file. comments: Provide the r1 FASTQ filename. diff --git a/web/templates/canada_covid19/schema_slots.tsv b/web/templates/canada_covid19/schema_slots.tsv index 97413485..4d659c2e 100644 --- a/web/templates/canada_covid19/schema_slots.tsv +++ b/web/templates/canada_covid19/schema_slots.tsv @@ -126,7 +126,7 @@ CanCOGeNCovid19 GENEPIO:0001122 Database Identifiers Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001472 breadth of coverage value breadth_of_coverage_value Valeur de l’étendue de la couverture WhitespaceMinimizedString The percentage of the reference genome covered by the sequenced data, to a prescribed depth. Pourcentage du génome de référence couvert par les données séquencées, jusqu’à une profondeur prescrite Provide value as a percent. Fournissez la valeur en pourcentage. 95% 95 % breadth of coverage value breadth of coverage value Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001474 depth of coverage value depth_of_coverage_value Valeur de l’ampleur de la couverture WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Nombre moyen de lectures représentant un nucléotide donné dans la séquence reconstruite Provide value as a fold of coverage. Fournissez la valeur sous forme de couverture amplifiée. 400x 400x Coverage depth of coverage value depth of coverage value Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold Seuil de l’ampleur de la couverture WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Seuil utilisé comme limite pour l’ampleur de la couverture Provide the threshold fold coverage. Fournissez la couverture amplifiée. 100x 100x depth of coverage threshold - Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001476 r1 fastq filename r1_fastq_filename________ Nom de fichier R1 FASTQ WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Nom du fichier R1 FASTQ spécifié par l’utilisateur Provide the r1 FASTQ filename. Fournissez le nom du fichier R1 FASTQ. ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename + Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001476 r1 fastq filename r1_fastq_filename Nom de fichier R1 FASTQ WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Nom du fichier R1 FASTQ spécifié par l’utilisateur Provide the r1 FASTQ filename. Fournissez le nom du fichier R1 FASTQ. ABC123_S1_L001_R1_001.fastq.gz ABC123_S1_L001_R1_001.fastq.gz r1 fastq filename Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001477 r2 fastq filename r2_fastq_filename Nom de fichier R2 FASTQ WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Nom du fichier R2 FASTQ spécifié par l’utilisateur Provide the r2 FASTQ filename. Fournissez le nom du fichier R2 FASTQ. ABC123_S1_L001_R2_001.fastq.gz ABC123_S1_L001_R2_001.fastq.gz r2 fastq filename Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath Chemin d’accès au fichier R1 FASTQ WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Emplacement du fichier R1 FASTQ dans le système de l’utilisateur Provide the filepath for the r1 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R1 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz r1 fastq filepath Bioinformatics and QC metrics Bioinformatique et mesures de contrôle de la qualité GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath Chemin d’accès au fichier R2 FASTQ WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Emplacement du fichier R2 FASTQ dans le système de l’utilisateur Provide the filepath for the r2 FASTQ file. This information aids in data management. Fournissez le chemin d’accès au fichier R2 FASTQ. /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz r2 fastq filepath diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index 2dc24af3..20f6fc3b 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -9081,8 +9081,8 @@ ], "range": "WhitespaceMinimizedString" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name_(site)", "comments": [ @@ -11267,8 +11267,8 @@ } ] }, - "influenza_antiviral_agent__": { - "name": "influenza_antiviral_agent__", + "influenza_antiviral_agent": { + "name": "influenza_antiviral_agent", "description": "A substance that destroys or inhibits replication of viruses.", "title": "influenza_antiviral_agent", "from_schema": "https://example.com/hpai", @@ -13364,8 +13364,8 @@ ], "range": "date" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", "comments": [ @@ -15395,8 +15395,8 @@ "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 18, "slot_group": "Sample collection and processing" }, @@ -15795,8 +15795,8 @@ "rank": 97, "slot_group": "Host treatment information" }, - "influenza_antiviral_agent__": { - "name": "influenza_antiviral_agent__", + "influenza_antiviral_agent": { + "name": "influenza_antiviral_agent", "rank": 98, "slot_group": "Host treatment information" }, @@ -16235,8 +16235,8 @@ "rank": 185, "slot_group": "Sequence information" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 186, "slot_group": "Sequence information" }, @@ -17155,8 +17155,8 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name_(site)", "comments": [ @@ -17170,7 +17170,7 @@ "from_schema": "https://example.com/hpai", "rank": 18, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_site__", + "alias": "geo_loc_name_site", "owner": "HPAI", "domain_of": [ "HPAI", @@ -19661,14 +19661,14 @@ } ] }, - "influenza_antiviral_agent__": { - "name": "influenza_antiviral_agent__", + "influenza_antiviral_agent": { + "name": "influenza_antiviral_agent", "description": "A substance that destroys or inhibits replication of viruses.", "title": "influenza_antiviral_agent", "from_schema": "https://example.com/hpai", "rank": 98, "slot_uri": "GENEPIO:0101114", - "alias": "influenza_antiviral_agent__", + "alias": "influenza_antiviral_agent", "owner": "HPAI", "domain_of": [ "HPAI", @@ -22110,8 +22110,8 @@ "slot_group": "Sequence information", "range": "date" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", "comments": [ @@ -22125,7 +22125,7 @@ "from_schema": "https://example.com/hpai", "rank": 186, "slot_uri": "GENEPIO:0001445", - "alias": "purpose_of_sequencing__", + "alias": "purpose_of_sequencing", "owner": "HPAI", "domain_of": [ "HPAI", @@ -24448,8 +24448,8 @@ "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 18, "slot_group": "Sample collection and processing" }, @@ -24658,8 +24658,8 @@ "rank": 59, "slot_group": "Sequence information" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 60, "slot_group": "Sequence information" }, @@ -25578,8 +25578,8 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name_(site)", "comments": [ @@ -25593,7 +25593,7 @@ "from_schema": "https://example.com/hpai", "rank": 18, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_site__", + "alias": "geo_loc_name_site", "owner": "HPAIFood", "domain_of": [ "HPAI", @@ -26869,8 +26869,8 @@ "slot_group": "Sequence information", "range": "date" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", "comments": [ @@ -26884,7 +26884,7 @@ "from_schema": "https://example.com/hpai", "rank": 60, "slot_uri": "GENEPIO:0001445", - "alias": "purpose_of_sequencing__", + "alias": "purpose_of_sequencing", "owner": "HPAIFood", "domain_of": [ "HPAI", @@ -29207,8 +29207,8 @@ "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 18, "slot_group": "Sample collection and processing" }, @@ -29832,8 +29832,8 @@ "rank": 142, "slot_group": "Sequence information" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 143, "slot_group": "Sequence information" }, @@ -30752,8 +30752,8 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name_(site)", "comments": [ @@ -30767,7 +30767,7 @@ "from_schema": "https://example.com/hpai", "rank": 18, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_site__", + "alias": "geo_loc_name_site", "owner": "HPAIWW", "domain_of": [ "HPAI", @@ -34361,8 +34361,8 @@ "slot_group": "Sequence information", "range": "date" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", "comments": [ @@ -34376,7 +34376,7 @@ "from_schema": "https://example.com/hpai", "rank": 143, "slot_uri": "GENEPIO:0001445", - "alias": "purpose_of_sequencing__", + "alias": "purpose_of_sequencing", "owner": "HPAIWW", "domain_of": [ "HPAI", @@ -36699,8 +36699,8 @@ "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 18, "slot_group": "Sample collection and processing" }, @@ -37324,8 +37324,8 @@ "rank": 142, "slot_group": "Sequence information" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 143, "slot_group": "Sequence information" }, @@ -38244,8 +38244,8 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name_(site)", "comments": [ @@ -38259,7 +38259,7 @@ "from_schema": "https://example.com/hpai", "rank": 18, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_site__", + "alias": "geo_loc_name_site", "owner": "HPAIEnviro", "domain_of": [ "HPAI", @@ -41853,8 +41853,8 @@ "slot_group": "Sequence information", "range": "date" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", "comments": [ @@ -41868,7 +41868,7 @@ "from_schema": "https://example.com/hpai", "rank": 143, "slot_uri": "GENEPIO:0001445", - "alias": "purpose_of_sequencing__", + "alias": "purpose_of_sequencing", "owner": "HPAIEnviro", "domain_of": [ "HPAI", @@ -44191,8 +44191,8 @@ "rank": 17, "slot_group": "Sample collection and processing" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "rank": 18, "slot_group": "Sample collection and processing" }, @@ -44521,8 +44521,8 @@ "rank": 83, "slot_group": "Host treatment information" }, - "influenza_antiviral_agent__": { - "name": "influenza_antiviral_agent__", + "influenza_antiviral_agent": { + "name": "influenza_antiviral_agent", "rank": 84, "slot_group": "Host treatment information" }, @@ -44546,8 +44546,8 @@ "rank": 88, "slot_group": "Sequence information" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "rank": 89, "slot_group": "Sequence information" }, @@ -45466,8 +45466,8 @@ "slot_group": "Sample collection and processing", "range": "WhitespaceMinimizedString" }, - "geo_loc_name_site__": { - "name": "geo_loc_name_site__", + "geo_loc_name_site": { + "name": "geo_loc_name_site", "description": "The name of a specific geographical location e.g. Credit River (rather than river).", "title": "geo_loc_name_(site)", "comments": [ @@ -45481,7 +45481,7 @@ "from_schema": "https://example.com/hpai", "rank": 18, "slot_uri": "GENEPIO:0100436", - "alias": "geo_loc_name_site__", + "alias": "geo_loc_name_site", "owner": "HPAIHost", "domain_of": [ "HPAI", @@ -47476,14 +47476,14 @@ } ] }, - "influenza_antiviral_agent__": { - "name": "influenza_antiviral_agent__", + "influenza_antiviral_agent": { + "name": "influenza_antiviral_agent", "description": "A substance that destroys or inhibits replication of viruses.", "title": "influenza_antiviral_agent", "from_schema": "https://example.com/hpai", "rank": 84, "slot_uri": "GENEPIO:0101114", - "alias": "influenza_antiviral_agent__", + "alias": "influenza_antiviral_agent", "owner": "HPAIHost", "domain_of": [ "HPAI", @@ -47595,8 +47595,8 @@ "slot_group": "Sequence information", "range": "date" }, - "purpose_of_sequencing__": { - "name": "purpose_of_sequencing__", + "purpose_of_sequencing": { + "name": "purpose_of_sequencing", "description": "The reason that the sample was sequenced.", "title": "purpose_of_sequencing", "comments": [ @@ -47610,7 +47610,7 @@ "from_schema": "https://example.com/hpai", "rank": 89, "slot_uri": "GENEPIO:0001445", - "alias": "purpose_of_sequencing__", + "alias": "purpose_of_sequencing", "owner": "HPAIHost", "domain_of": [ "HPAI", diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index 1d6e8128..59e0002b 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -42,7 +42,7 @@ classes: - geo_loc_name_state_province_territory - geo_loc_name_county_region - geo_loc_name_city - - geo_loc_name_site__ + - geo_loc_name_site - geo_loc_latitude - geo_loc_longitude - organism @@ -122,7 +122,7 @@ classes: - vaccination_dose_2_vaccination_date - vaccination_history - influenza_antiviral_treatment_administration - - influenza_antiviral_agent__ + - influenza_antiviral_agent - influenza_antiviral_treatment_date - water_catchment_area_human_population_measurement_value - water_catchment_area_human_population_range @@ -210,7 +210,7 @@ classes: - library_id - sequencing_assay_type - sequencing_date - - purpose_of_sequencing__ + - purpose_of_sequencing - purpose_of_sequencing_details - sequenced_by - sequenced_by_laboratory_name @@ -340,7 +340,7 @@ classes: geo_loc_name_city: rank: 17 slot_group: Sample collection and processing - geo_loc_name_site__: + geo_loc_name_site: rank: 18 slot_group: Sample collection and processing geo_loc_latitude: @@ -580,7 +580,7 @@ classes: influenza_antiviral_treatment_administration: rank: 97 slot_group: Host treatment information - influenza_antiviral_agent__: + influenza_antiviral_agent: rank: 98 slot_group: Host treatment information influenza_antiviral_treatment_date: @@ -844,7 +844,7 @@ classes: sequencing_date: rank: 185 slot_group: Sequence information - purpose_of_sequencing__: + purpose_of_sequencing: rank: 186 slot_group: Sequence information purpose_of_sequencing_details: @@ -1104,7 +1104,7 @@ classes: - geo_loc_name_state_province_territory - geo_loc_name_county_region - geo_loc_name_city - - geo_loc_name_site__ + - geo_loc_name_site - geo_loc_latitude - geo_loc_longitude - organism @@ -1146,7 +1146,7 @@ classes: - library_id - sequencing_assay_type - sequencing_date - - purpose_of_sequencing__ + - purpose_of_sequencing - purpose_of_sequencing_details - sequenced_by - sequenced_by_laboratory_name @@ -1276,7 +1276,7 @@ classes: geo_loc_name_city: rank: 17 slot_group: Sample collection and processing - geo_loc_name_site__: + geo_loc_name_site: rank: 18 slot_group: Sample collection and processing geo_loc_latitude: @@ -1402,7 +1402,7 @@ classes: sequencing_date: rank: 59 slot_group: Sequence information - purpose_of_sequencing__: + purpose_of_sequencing: rank: 60 slot_group: Sequence information purpose_of_sequencing_details: @@ -1662,7 +1662,7 @@ classes: - geo_loc_name_state_province_territory - geo_loc_name_county_region - geo_loc_name_city - - geo_loc_name_site__ + - geo_loc_name_site - geo_loc_latitude - geo_loc_longitude - organism @@ -1787,7 +1787,7 @@ classes: - library_id - sequencing_assay_type - sequencing_date - - purpose_of_sequencing__ + - purpose_of_sequencing - purpose_of_sequencing_details - sequenced_by - sequenced_by_laboratory_name @@ -1917,7 +1917,7 @@ classes: geo_loc_name_city: rank: 17 slot_group: Sample collection and processing - geo_loc_name_site__: + geo_loc_name_site: rank: 18 slot_group: Sample collection and processing geo_loc_latitude: @@ -2292,7 +2292,7 @@ classes: sequencing_date: rank: 142 slot_group: Sequence information - purpose_of_sequencing__: + purpose_of_sequencing: rank: 143 slot_group: Sequence information purpose_of_sequencing_details: @@ -2553,7 +2553,7 @@ classes: - geo_loc_name_state_province_territory - geo_loc_name_county_region - geo_loc_name_city - - geo_loc_name_site__ + - geo_loc_name_site - geo_loc_latitude - geo_loc_longitude - organism @@ -2678,7 +2678,7 @@ classes: - library_id - sequencing_assay_type - sequencing_date - - purpose_of_sequencing__ + - purpose_of_sequencing - purpose_of_sequencing_details - sequenced_by - sequenced_by_laboratory_name @@ -2808,7 +2808,7 @@ classes: geo_loc_name_city: rank: 17 slot_group: Sample collection and processing - geo_loc_name_site__: + geo_loc_name_site: rank: 18 slot_group: Sample collection and processing geo_loc_latitude: @@ -3183,7 +3183,7 @@ classes: sequencing_date: rank: 142 slot_group: Sequence information - purpose_of_sequencing__: + purpose_of_sequencing: rank: 143 slot_group: Sequence information purpose_of_sequencing_details: @@ -3443,7 +3443,7 @@ classes: - geo_loc_name_state_province_territory - geo_loc_name_county_region - geo_loc_name_city - - geo_loc_name_site__ + - geo_loc_name_site - geo_loc_latitude - geo_loc_longitude - organism @@ -3509,12 +3509,12 @@ classes: - vaccination_dose_2_vaccination_date - vaccination_history - influenza_antiviral_treatment_administration - - influenza_antiviral_agent__ + - influenza_antiviral_agent - influenza_antiviral_treatment_date - library_id - sequencing_assay_type - sequencing_date - - purpose_of_sequencing__ + - purpose_of_sequencing - purpose_of_sequencing_details - sequenced_by - sequenced_by_laboratory_name @@ -3644,7 +3644,7 @@ classes: geo_loc_name_city: rank: 17 slot_group: Sample collection and processing - geo_loc_name_site__: + geo_loc_name_site: rank: 18 slot_group: Sample collection and processing geo_loc_latitude: @@ -3842,7 +3842,7 @@ classes: influenza_antiviral_treatment_administration: rank: 83 slot_group: Host treatment information - influenza_antiviral_agent__: + influenza_antiviral_agent: rank: 84 slot_group: Host treatment information influenza_antiviral_treatment_date: @@ -3857,7 +3857,7 @@ classes: sequencing_date: rank: 88 slot_group: Sequence information - purpose_of_sequencing__: + purpose_of_sequencing: rank: 89 slot_group: Sequence information purpose_of_sequencing_details: @@ -4332,8 +4332,8 @@ slots: range: WhitespaceMinimizedString examples: - value: Vancouver - geo_loc_name_site__: - name: geo_loc_name_site__ + geo_loc_name_site: + name: geo_loc_name_site title: geo_loc_name_(site) description: The name of a specific geographical location e.g. Credit River (rather than river). @@ -5416,8 +5416,8 @@ slots: - range: NullValueMenu examples: - value: Influenza antiviral treatment administered [GENEPIO:0101194] - influenza_antiviral_agent__: - name: influenza_antiviral_agent__ + influenza_antiviral_agent: + name: influenza_antiviral_agent title: influenza_antiviral_agent description: A substance that destroys or inhibits replication of viruses. slot_uri: GENEPIO:0101114 @@ -6341,8 +6341,8 @@ slots: - '>={sample_collection_date}' examples: - value: '2020-06-22' - purpose_of_sequencing__: - name: purpose_of_sequencing__ + purpose_of_sequencing: + name: purpose_of_sequencing title: purpose_of_sequencing description: The reason that the sample was sequenced. comments: The reason why a sample was originally collected may differ from the diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv index f72b69aa..718860f4 100644 --- a/web/templates/hpai/schema_slots.tsv +++ b/web/templates/hpai/schema_slots.tsv @@ -18,7 +18,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPI HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001185 geo_loc_name_(state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory of origin of the sample. Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/ga Western Cape geo_loc_name HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100280 geo_loc_name_(county/region) geo_loc_name_county_region WhitespaceMinimizedString The county/region of origin of the sample. Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Derbyshire HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001189 geo_loc_name_(city) geo_loc_name_city WhitespaceMinimizedString The city of origin of the sample. Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz Vancouver -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100436 geo_loc_name_(site) geo_loc_name_site__ WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100436 geo_loc_name_(site) geo_loc_name_site WhitespaceMinimizedString The name of a specific geographical location e.g. Credit River (rather than river). Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). Credit River HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100309 geo_loc_latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100310 geo_loc_longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae organism @@ -105,7 +105,7 @@ HPAI;HPAIHost Host vaccination information GENEPIO:0100316 vaccination_dose_2_va HPAI;HPAIHost Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated HPAI;HPAIHost Host treatment information HPAI;HPAIHost Host treatment information GENEPIO:0101113 influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration InfluenzaAntiviralTreatmentAdministrationMenu NullValueMenu An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen. Influenza antiviral treatment administered [GENEPIO:0101194] -HPAI;HPAIHost Host treatment information GENEPIO:0101114 influenza_antiviral_agent influenza_antiviral_agent__ WhitespaceMinimizedString A substance that destroys or inhibits replication of viruses. +HPAI;HPAIHost Host treatment information GENEPIO:0101114 influenza_antiviral_agent influenza_antiviral_agent WhitespaceMinimizedString A substance that destroys or inhibits replication of viruses. HPAI;HPAIHost Host treatment information GENEPIO:0101115 influenza_antiviral_treatment_date influenza_antiviral_treatment_date date The date on which the influenza antiviral agent was administered to a patient as part of treatment "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given. " @@ -197,7 +197,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001441 Sequence information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing__ PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001446 purpose_of_sequencing_details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100470 sequenced_by_laboratory_name sequenced_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab diff --git a/web/templates/influenza/schema.json b/web/templates/influenza/schema.json index e826e028..fce721ab 100644 --- a/web/templates/influenza/schema.json +++ b/web/templates/influenza/schema.json @@ -5176,8 +5176,8 @@ } ] }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -6001,8 +6001,8 @@ "rank": 62, "slot_group": "Sequencing" }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 63, "slot_group": "Sequencing" }, @@ -8151,8 +8151,8 @@ } ] }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -8170,7 +8170,7 @@ ], "rank": 63, "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol__", + "alias": "sequencing_protocol", "owner": "Influenza", "domain_of": [ "Influenza" diff --git a/web/templates/influenza/schema.yaml b/web/templates/influenza/schema.yaml index 26a3dc1f..141f2e25 100644 --- a/web/templates/influenza/schema.yaml +++ b/web/templates/influenza/schema.yaml @@ -81,7 +81,7 @@ classes: - amplicon_size - library_preparation_kit - sequencing_instrument - - sequencing_protocol__ + - sequencing_protocol - amplicon_pcr_primer_scheme - raw_sequence_data_processing_method - dehosting_method @@ -289,7 +289,7 @@ classes: sequencing_instrument: rank: 62 slot_group: Sequencing - sequencing_protocol__: + sequencing_protocol: rank: 63 slot_group: Sequencing amplicon_pcr_primer_scheme: @@ -1414,8 +1414,8 @@ slots: - CNPHI:Sequencing%20Instrument - NML_LIMS:PH_INSTRUMENT_CGN - VirusSeq_Portal:sequencing%20instrument - sequencing_protocol__: - name: sequencing_protocol__ + sequencing_protocol: + name: sequencing_protocol title: sequencing protocol description: The protocol used to generate the sequence. comments: 'Provide a free text description of the methods and materials used to diff --git a/web/templates/influenza/schema_slots.tsv b/web/templates/influenza/schema_slots.tsv index 8c7b6bf9..25022e04 100644 --- a/web/templates/influenza/schema_slots.tsv +++ b/web/templates/influenza/schema_slots.tsv @@ -69,7 +69,7 @@ Influenza GENEPIO:0001122 Database Identifiers Sequencing GENEPIO:0001449 amplicon size amplicon_size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon size Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_INSTRUMENT_CGN sequencing instrument - Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol__ WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol + Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a tiling amplicon strategy using the primer scheme. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Genomes were generated through amplicon sequencing of 300 bp amplicons with ARTIC schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. amplicon pcr primer scheme GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 59d4d4b3..44244e35 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -11912,8 +11912,8 @@ ], "range": "WhitespaceMinimizedString" }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -14669,8 +14669,8 @@ "rank": 85, "slot_group": "Sequence information" }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 86, "slot_group": "Sequencing" }, @@ -17877,8 +17877,8 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -17896,7 +17896,7 @@ ], "rank": 86, "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol__", + "alias": "sequencing_protocol", "owner": "Mpox", "domain_of": [ "Mpox", @@ -20420,8 +20420,8 @@ "rank": 88, "slot_group": "Sequence information" }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "rank": 89, "slot_group": "Sequencing" }, @@ -23643,8 +23643,8 @@ "slot_group": "Sequence information", "range": "WhitespaceMinimizedString" }, - "sequencing_protocol__": { - "name": "sequencing_protocol__", + "sequencing_protocol": { + "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", "title": "sequencing protocol", "comments": [ @@ -23662,7 +23662,7 @@ ], "rank": 89, "slot_uri": "GENEPIO:0001454", - "alias": "sequencing_protocol__", + "alias": "sequencing_protocol", "owner": "MpoxInternational", "domain_of": [ "Mpox", diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index cfdec5e3..0303a728 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -105,7 +105,7 @@ classes: - sequencing_assay_type - sequencing_instrument - sequencing_flow_cell_version - - sequencing_protocol__ + - sequencing_protocol - sequencing_kit_number - dna_fragment_length - genomic_target_enrichment_method @@ -710,7 +710,7 @@ classes: sequencing_flow_cell_version: rank: 85 slot_group: Sequence information - sequencing_protocol__: + sequencing_protocol: rank: 86 slot_group: Sequencing sequencing_kit_number: @@ -999,7 +999,7 @@ classes: - sequencing_assay_type - sequencing_instrument - sequencing_flow_cell_version - - sequencing_protocol__ + - sequencing_protocol - sequencing_kit_number - dna_fragment_length - genomic_target_enrichment_method @@ -1566,7 +1566,7 @@ classes: sequencing_flow_cell_version: rank: 88 slot_group: Sequence information - sequencing_protocol__: + sequencing_protocol: rank: 89 slot_group: Sequencing sequencing_kit_number: @@ -3022,8 +3022,8 @@ slots: range: WhitespaceMinimizedString examples: - value: R.9.4.1 - sequencing_protocol__: - name: sequencing_protocol__ + sequencing_protocol: + name: sequencing_protocol title: sequencing protocol description: The protocol used to generate the sequence. comments: 'Provide a free text description of the methods and materials used to diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 2670958a..516ca6ca 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -148,7 +148,7 @@ MpoxInternational Sequence information GENEPIO:0100997 sequencing assay type seq Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument Mpox MpoxInternational Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentInternationalMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument MpoxInternational Mpox;MpoxInternational Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol__ WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol Mpox;MpoxInternational +Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol Mpox;MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0001455 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number Mpox;MpoxInternational Mpox;MpoxInternational Sequencing GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 Mpox;MpoxInternational Mpox Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method Mpox From 092d67355bf464537eb24ab6f7b350f9e203c9fd Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 15:00:29 -0700 Subject: [PATCH 92/96] adding {today} test to a number of template fields --- web/templates/hpai/schema.json | 160 +++++++- web/templates/hpai/schema.yaml | 24 ++ web/templates/hpai/schema_slots.tsv | 24 +- web/templates/mpox/schema.json | 18 +- web/templates/mpox/schema.yaml | 3 + web/templates/mpox/schema_slots.tsv | 468 +++++++++++----------- web/templates/pha4ge/schema.json | 6 + web/templates/pha4ge/schema.yaml | 2 + web/templates/pha4ge/schema_slots.tsv | 2 +- web/templates/wastewater/schema.json | 85 +++- web/templates/wastewater/schema.yaml | 16 + web/templates/wastewater/schema_slots.tsv | 16 +- 12 files changed, 556 insertions(+), 268 deletions(-) diff --git a/web/templates/hpai/schema.json b/web/templates/hpai/schema.json index 20f6fc3b..ffe1ea94 100644 --- a/web/templates/hpai/schema.json +++ b/web/templates/hpai/schema.json @@ -9267,6 +9267,9 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -9301,6 +9304,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample_collection_end_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -9474,6 +9481,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -9504,6 +9514,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -9703,6 +9716,9 @@ "name": "food_quality_date", "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", "title": "food_quality_date", + "todos": [ + "<={today}" + ], "comments": [ "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." ], @@ -9726,6 +9742,9 @@ "name": "food_packaging_date", "description": "A food product's packaging date as marked by a food manufacturer or retailer.", "title": "food_packaging_date", + "todos": [ + "<={today}" + ], "comments": [ "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." ], @@ -10840,6 +10859,9 @@ "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom_onset_date", + "todos": [ + "<={today}" + ], "comments": [ "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -11155,6 +11177,9 @@ "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination_dose_1_vaccination_date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -11195,6 +11220,9 @@ "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination_dose_2_vaccination_date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -11283,6 +11311,9 @@ "name": "influenza_antiviral_treatment_date", "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", "title": "influenza_antiviral_treatment_date", + "todos": [ + "<={today}" + ], "comments": [ "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." ], @@ -13343,7 +13374,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -14895,6 +14927,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -17377,6 +17412,9 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -17415,6 +17453,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample_collection_end_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -17612,6 +17654,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -17646,6 +17691,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -17869,6 +17917,9 @@ "name": "food_quality_date", "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", "title": "food_quality_date", + "todos": [ + "<={today}" + ], "comments": [ "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." ], @@ -17896,6 +17947,9 @@ "name": "food_packaging_date", "description": "A food product's packaging date as marked by a food manufacturer or retailer.", "title": "food_packaging_date", + "todos": [ + "<={today}" + ], "comments": [ "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." ], @@ -19166,6 +19220,9 @@ "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom_onset_date", + "todos": [ + "<={today}" + ], "comments": [ "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -19529,6 +19586,9 @@ "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination_dose_1_vaccination_date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -19577,6 +19637,9 @@ "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination_dose_2_vaccination_date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -19681,6 +19744,9 @@ "name": "influenza_antiviral_treatment_date", "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", "title": "influenza_antiviral_treatment_date", + "todos": [ + "<={today}" + ], "comments": [ "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." ], @@ -22085,7 +22151,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -23885,6 +23952,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -25800,6 +25870,9 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -25838,6 +25911,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -25872,6 +25948,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -26064,6 +26143,9 @@ "name": "food_quality_date", "description": "A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula.", "title": "food_quality_date", + "todos": [ + "<={today}" + ], "comments": [ "This date is typically labeled on a food product as \"best if used by\", best by\", \"use by\", or \"freeze by\" e.g. 5/24/2020. If the date is known, leave blank or provide a null value." ], @@ -26091,6 +26173,9 @@ "name": "food_packaging_date", "description": "A food product's packaging date as marked by a food manufacturer or retailer.", "title": "food_packaging_date", + "todos": [ + "<={today}" + ], "comments": [ "The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value." ], @@ -26844,7 +26929,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -28644,6 +28730,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -30974,6 +31063,9 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -31012,6 +31104,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample_collection_end_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -31209,6 +31305,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -31243,6 +31342,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -34336,7 +34438,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -36136,6 +36239,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -38466,6 +38572,9 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -38504,6 +38613,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample_collection_end_date", + "todos": [ + ">={sample_collection_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -38701,6 +38814,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -38735,6 +38851,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -41828,7 +41947,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -43628,6 +43748,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -45688,6 +45811,9 @@ "name": "sample_collection_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample_collection_date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -45726,6 +45852,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -45760,6 +45889,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -46981,6 +47113,9 @@ "name": "symptom_onset_date", "description": "The date on which the symptoms began or were first noted.", "title": "symptom_onset_date", + "todos": [ + "<={today}" + ], "comments": [ "If known, provide the symptom onset date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -47344,6 +47479,9 @@ "name": "vaccination_dose_1_vaccination_date", "description": "The date the first dose of a vaccine was administered.", "title": "vaccination_dose_1_vaccination_date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -47392,6 +47530,9 @@ "name": "vaccination_dose_2_vaccination_date", "description": "The date the second dose of a vaccine was administered.", "title": "vaccination_dose_2_vaccination_date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -47496,6 +47637,9 @@ "name": "influenza_antiviral_treatment_date", "description": "The date on which the influenza antiviral agent was administered to a patient as part of treatment", "title": "influenza_antiviral_treatment_date", + "todos": [ + "<={today}" + ], "comments": [ "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given." ], @@ -47570,7 +47714,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing_date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -49370,6 +49515,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], diff --git a/web/templates/hpai/schema.yaml b/web/templates/hpai/schema.yaml index 59e0002b..2fdee1e5 100644 --- a/web/templates/hpai/schema.yaml +++ b/web/templates/hpai/schema.yaml @@ -4429,6 +4429,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} required: true examples: - value: '2020-03-16' @@ -4444,6 +4446,9 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - '>={sample_collection_date}' + - <={today} recommended: true examples: - value: '2020-03-18' @@ -4517,6 +4522,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2020-03-28' sample_processing_date: @@ -4530,6 +4537,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2020-03-16' host_origin_geo_loc_name_country: @@ -4633,6 +4642,8 @@ slots: blank or provide a null value. slot_uri: GENEPIO:0100615 range: date + todos: + - <={today} examples: - value: '2020-05-25' exact_mappings: @@ -4647,6 +4658,8 @@ slots: provide a null value. slot_uri: GENEPIO:0100616 range: date + todos: + - <={today} examples: - value: '2020-05-25' environmental_site: @@ -5208,6 +5221,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2020-03-16' signs_and_symptoms: @@ -5365,6 +5380,8 @@ slots: The date should be provided in ISO 8601 standard format "YYYY-MM-DD". slot_uri: GENEPIO:0100314 range: date + todos: + - <={today} examples: - value: '2021-03-01' vaccination_dose_2_vaccine_name: @@ -5386,6 +5403,8 @@ slots: The date should be provided in ISO 8601 standard format "YYYY-MM-DD". slot_uri: GENEPIO:0100316 range: date + todos: + - <={today} examples: - value: '2021-09-01' vaccination_history: @@ -5432,6 +5451,8 @@ slots: the first administration date if multiple doses were given. slot_uri: GENEPIO:0101115 range: date + todos: + - <={today} water_catchment_area_human_population_measurement_value: name: water_catchment_area_human_population_measurement_value title: water_catchment_area_human_population_measurement_value @@ -6339,6 +6360,7 @@ slots: range: date todos: - '>={sample_collection_date}' + - <={today} examples: - value: '2020-06-22' purpose_of_sequencing: @@ -7044,6 +7066,8 @@ slots: analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". slot_uri: GENEPIO:0101075 range: date + todos: + - <={today} examples: - value: '2024-02-01' read_mapping_criteria: diff --git a/web/templates/hpai/schema_slots.tsv b/web/templates/hpai/schema_slots.tsv index 718860f4..165635ea 100644 --- a/web/templates/hpai/schema_slots.tsv +++ b/web/templates/hpai/schema_slots.tsv @@ -27,22 +27,22 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPI HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100583 taxonomic_identification_process taxonomic_identification_process TaxonomicIdentificationProcessMenu HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101110 virus_identifier virus_identifier WhitespaceMinimizedString HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0101111 WHO/OIE/FAO_H5_clade who_oie_fao_h5_clade WhitespaceMinimizedString -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 collection_date -HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001174 sample_collection_date sample_collection_date date NullValueMenu TRUE {today} The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 collection_date +HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101071 sample_collection_end_date sample_collection_end_date date NullValueMenu TRUE {sample_collection_date} {today} The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101072 sample_collection_start_time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0101073 sample_collection_end_time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100765 sample_collection_time_of_day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100766 sample_collection_time_duration_value sample_collection_time_duration_value WhitespaceMinimizedString NullValueMenu TRUE The amount of time over which the sample was collected. Provide the numerical value of time. 4 HPAI;HPAIWW;HPAIEnviro Sample collection and processing GENEPIO:0100767 sample_collection_time_duration_unit sample_collection_time_duration_unit SampleCollectionDurationUnitMenu NullValueMenu TRUE The units of the time duration measurement of sample collection. Provide the units from the pick list. Hour -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu {today} The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu {today} The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 HPAI;HPAIHost Sample collection and processing GENEPIO:0100438 host_origin_geo_loc_name (country) host_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of the host. If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. South Africa [GAZ:00001094] HPAI;HPAIFood Sample collection and processing GENEPIO:0100437 food_product_origin_geo_loc_name (country) food_product_origin_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of origin of a food product. If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. United States of America [GAZ:00002459] food_origin HPAI;HPAIFood Sample collection and processing GENEPIO:0100444 food_product food_product FoodProductMenu NullValueMenu TRUE TRUE A material consumed and digested for nutritional value or enjoyment. This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] isolation_source;food_product isolation_source;food_product_type HPAI;HPAIFood Sample collection and processing GENEPIO:0100445 food_product_properties food_product_properties FoodProductPropertiesMenu NullValueMenu TRUE TRUE Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] isolation_source;food_product_properties isolation_source HPAI;HPAIFood Sample collection and processing GENEPIO:0100447 food_packaging food_packaging FoodPackagingMenu NullValueMenu TRUE TRUE The type of packaging used to contain a food product. If known, provide information regarding how the food product was packaged. Plastic tray or pan [FOODON:03490126] isolation_source;food_packaging food_contain_wrap -HPAI;HPAIFood Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date -HPAI;HPAIFood Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 +HPAI;HPAIFood Sample collection and processing GENEPIO:0100615 food_quality_date food_quality_date date {today} A date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. This date is typically labeled on a food product as "best if used by", best by", "use by", or "freeze by" e.g. 5/24/2020. If the date is known, leave blank or provide a null value. 2020-05-25 food_quality_date +HPAI;HPAIFood Sample collection and processing GENEPIO:0100616 food_packaging_date food_packaging_date date {today} A food product's packaging date as marked by a food manufacturer or retailer. The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. 2020-05-25 HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001232 environmental_site environmental_site EnvironmentalSiteMenu NullValueMenu TRUE TRUE An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave. If applicable, select the standardized term and ontology ID for the environmental site from the picklist provided. Multiple values can be provided, separated by a semi-colon. Poultry hatchery [ENVO:01001874] isolation_source;environmental_site isolation_source;animal_env HPAI;HPAIWW;HPAIEnviro;HPAIFood Sample collection and processing GENEPIO:0001223 environmental_material environmental_material EnvironmentalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask. If applicable, select the standardized term and ontology ID for the environmental material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Soil [ENVO:00001998]; Water [CHEBI:15377]; Wastewater [ENVO:00002001]; Broom [ENVO:03501377] isolation_source;environmental_material isolation_source HPAI;HPAIHost Sample collection and processing GENEPIO:0001211 anatomical_material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. An anatomical material is a substance taken from the body. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. Tissue [UBERON:0000479]; Blood [UBERON:0000178] isolation_source;anatomical_material host_tissue_sampled;isolation_source @@ -83,7 +83,7 @@ HPAI;HPAIHost Host Information GENEPIO:0001389 host_health_status_details host_h HPAI;HPAIHost Host Information GENEPIO:0001390 host_health_outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_disease_outcome HPAI;HPAIHost Host Information GENEPIO:0001398 host_subject_ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to e.g. #131 Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. BCxy123 host_subject_id HPAI;HPAIHost Host Information GENEPIO:0100281 case_ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 -HPAI;HPAIHost Host Information GENEPIO:0001399 symptom_onset_date symptom_onset_date date NullValueMenu The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +HPAI;HPAIHost Host Information GENEPIO:0001399 symptom_onset_date symptom_onset_date date NullValueMenu {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 HPAI;HPAIHost Host Information GENEPIO:0001400 signs_and_symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] HPAI;HPAIHost Host Information GENEPIO:0001401 pre-existing_conditions_and_risk_factors preexisting_conditions_and_risk_factors PreexistingConditionsAndRiskFactorsMenu NullValueMenu TRUE "Patient pre-existing conditions and risk factors. Pre-existing condition: A medical condition that existed prior to the current infection. @@ -99,14 +99,14 @@ HPAI;HPAIHost GENEPIO:0001403 Host vaccination information HPAI;HPAIHost Host vaccination information GENEPIO:0001404 host_vaccination_status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Fully Vaccinated [GENEPIO:0100100] prior_sars_cov_2_vaccination HPAI;HPAIHost Host vaccination information GENEPIO:0001406 number_of_vaccine_doses_received number_of_vaccine_doses_received integer 0 The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 2 HPAI;HPAIHost Host vaccination information GENEPIO:0100313 vaccination_dose_1_vaccine_name vaccination_dose_1_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) -HPAI;HPAIHost Host vaccination information GENEPIO:0100314 vaccination_dose_1_vaccination_date vaccination_dose_1_vaccination_date date The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 +HPAI;HPAIHost Host vaccination information GENEPIO:0100314 vaccination_dose_1_vaccination_date vaccination_dose_1_vaccination_date date {today} The date the first dose of a vaccine was administered. Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-03-01 HPAI;HPAIHost Host vaccination information GENEPIO:0100315 vaccination_dose_2_vaccine_name vaccination_dose_2_vaccine_name WhitespaceMinimizedString The name of the vaccine administered as the second dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list Pfizer-BioNTech (Comirnaty) -HPAI;HPAIHost Host vaccination information GENEPIO:0100316 vaccination_dose_2_vaccination_date vaccination_dose_2_vaccination_date date The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 +HPAI;HPAIHost Host vaccination information GENEPIO:0100316 vaccination_dose_2_vaccination_date vaccination_dose_2_vaccination_date date {today} The date the second dose of a vaccine was administered. Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2021-09-01 HPAI;HPAIHost Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 Last vaccinated HPAI;HPAIHost Host treatment information HPAI;HPAIHost Host treatment information GENEPIO:0101113 influenza_antiviral_treatment_administration influenza_antiviral_treatment_administration InfluenzaAntiviralTreatmentAdministrationMenu NullValueMenu An action of giving or applying an influenza antiviral agent to a patient as part of a treatment regimen. Influenza antiviral treatment administered [GENEPIO:0101194] HPAI;HPAIHost Host treatment information GENEPIO:0101114 influenza_antiviral_agent influenza_antiviral_agent WhitespaceMinimizedString A substance that destroys or inhibits replication of viruses. -HPAI;HPAIHost Host treatment information GENEPIO:0101115 influenza_antiviral_treatment_date influenza_antiviral_treatment_date date The date on which the influenza antiviral agent was administered to a patient as part of treatment "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given. +HPAI;HPAIHost Host treatment information GENEPIO:0101115 influenza_antiviral_treatment_date influenza_antiviral_treatment_date date {today} The date on which the influenza antiviral agent was administered to a patient as part of treatment "This field records the exact date when the antiviral treatment was administered. The date should be provided in a standard format (e.g., YYYY-MM-DD) and reflect the first administration date if multiple doses were given. " HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements @@ -196,7 +196,7 @@ HPAI;HPAIWW;HPAIEnviro Environmental conditions and measurements GENEPIO:0100824 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001441 Sequence information HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001448 library_ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Every "library ID" from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. LS_2010_NP_123446 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100997 sequencing_assay_type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001447 sequencing_date sequencing_date date {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001445 purpose_of_sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Travel-associated surveillance HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0001446 purpose_of_sequencing_details purpose_of_sequencing_details WhitespaceMinimizedString The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating remote regions, Investigating health care workers, Investigating schools/universities. Investigating schools/universities HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Sequence information GENEPIO:0100416 sequenced_by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency, organization or institution responsible for sequencing the isolate's genome. Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Public Health Agency of Canada (PHAC) [GENEPIO:0100551] sequenced_by sequenced_by @@ -260,7 +260,7 @@ HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GE HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc -HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date {today} The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost GENEPIO:0001506 Pathogen diagnostic testing HPAI;HPAIFood;HPAIWW;HPAIEnviro;HPAIHost Pathogen diagnostic testing GENEPIO:0101116 genetic target name genetic_target_name WhitespaceMinimizedString NullValueMenu The name of the genetic marker used for testing. Provide the full name of the gene used in the test. Standardized gene names can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI gyrase A diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 44244e35..0a38f110 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -11458,6 +11458,9 @@ "name": "prior_mpox_infection_date", "description": "The date of diagnosis of the prior Mpox infection.", "title": "prior Mpox infection date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -11781,7 +11784,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -17267,6 +17271,9 @@ "name": "prior_mpox_infection_date", "description": "The date of diagnosis of the prior Mpox infection.", "title": "prior Mpox infection date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -17702,7 +17709,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -23068,6 +23076,9 @@ "name": "prior_mpox_infection_date", "description": "The date of diagnosis of the prior Mpox infection.", "title": "prior Mpox infection date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -23469,7 +23480,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 0303a728..80e6d704 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -2773,6 +2773,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2022-06-20' exact_mappings: @@ -2958,6 +2960,7 @@ slots: - range: NullValueMenu todos: - '>={sample_collection_date}' + - <={today} examples: - value: '2020-06-22' exact_mappings: diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 516ca6ca..5a7791dd 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -1,234 +1,234 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal For RefGuide Matching -Mpox;MpoxInternational GENEPIO:0001122 Database Identifiers database_identifiers Mpox;MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the submitting laboratory Primary Specimen ID TEXT_ID sample_name specimen collector sample ID Mpox;MpoxInternational -Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID Mpox -Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID Mpox;MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession Mpox;MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession Mpox;MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION Mpox;MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession Mpox;MpoxInternational -MpoxInternational Database Identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name MpoxInternational -Mpox;MpoxInternational Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession Mpox;MpoxInternational -Mpox;MpoxInternational GENEPIO:0001150 Sample collection and processing sample_collection_and_processing Mpox;MpoxInternational -Mpox Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by Mpox -MpoxInternational Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by MpoxInternational -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email Mpox;MpoxInternational -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001158 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address Mpox;MpoxInternational -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date Mpox;MpoxInternational -Mpox Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 Mpox -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date Mpox;MpoxInternational -Mpox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) Mpox -MpoxInternational Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) MpoxInternational -Mpox Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) Mpox -MpoxInternational Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the state/province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) MpoxInternational -MpoxInternational Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon MpoxInternational -MpoxInternational Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon MpoxInternational -Mpox Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus Pathogen HC_CURRENT_ID organism organism Mpox -MpoxInternational Sample collection and processing GENEPIO:0001191 organism organism OrganismInternationalMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism MpoxInternational -Mpox Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name Mpox -MpoxInternational Sample collection and processing GENEPIO:0001644 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate MpoxInternational -Mpox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling Mpox -MpoxInternational Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingInternationalMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling MpoxInternational -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Symptomology and history suggested Monkeypox diagnosis. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details Mpox;MpoxInternational -Mpox Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Nucleic Acid Specimen Type PH_SPECIMEN_TYPE Mpox -Mpox Sample collection and processing GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type RelatedSpecimenRelationshipTypeMenu NullValueMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Previously Submitted Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE Mpox -Mpox Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material Mpox -MpoxInternational Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) [NCIT:C78582] Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material MpoxInternational -Mpox Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part Mpox -MpoxInternational Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartInternationalMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part MpoxInternational -Mpox Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product Mpox -MpoxInternational Sample collection and processing GENEPIO:0001216 body product body_product BodyProductInternationalMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product MpoxInternational -MpoxInternational Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material MpoxInternational -Mpox Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device Mpox -MpoxInternational Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceInternationalMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device MpoxInternational -Mpox Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method Mpox -MpoxInternational Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodInternationalMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method MpoxInternational -Mpox Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing Mpox -MpoxInternational Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingInternationalMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] MpoxInternational -Mpox;MpoxInternational Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details Mpox;MpoxInternational -Mpox Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control Mpox -MpoxInternational Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeInternationalMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] MpoxInternational -Mpox;MpoxInternational Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control Mpox;MpoxInternational -Mpox;MpoxInternational GENEPIO:0001498 Lineage and Variant information -MpoxInternational Lineage and Variant information GENEPIO:0001500 lineage/clade name LineageCladeNameINternationalMenu NullValueMenu The name of the lineage or clade. Provide the lineage/clade name. B.1.1.7 PH_LINEAGE_CLADE_NAME -MpoxInternational Lineage and Variant information GENEPIO:0001501 lineage/clade analysis software name WhitespaceMinimizedString NullValueMenu The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin PH_LINEAGE_CLADE_SOFTWARE -MpoxInternational Lineage and Variant information GENEPIO:0001502 lineage/clade analysis software version WhitespaceMinimizedString NullValueMenu The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION -Mpox;MpoxInternational GENEPIO:0001268 Host Information host_information Mpox;MpoxInternational -Mpox Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE Mpox -MpoxInternational Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameInternationalMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human MpoxInternational -Mpox Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) Mpox -MpoxInternational Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameInternationalMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) MpoxInternational -Mpox Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state Mpox -MpoxInternational Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateInternationalMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state MpoxInternational -Mpox Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS Mpox -MpoxInternational Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsInternationalMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] MpoxInternational -Mpox Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome Mpox -MpoxInternational Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeInternationalMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome MpoxInternational -Mpox Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox Host Disease PH_HOST_DISEASE host_disease host disease Mpox -MpoxInternational Host Information GENEPIO:0001391 host disease host_disease HostDiseaseInternationalMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease MpoxInternational -MpoxInternational Host Information GENEPIO:0001398 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id MpoxInternational -Mpox Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age Mpox -MpoxInternational Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age MpoxInternational -Mpox Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit Mpox -MpoxInternational Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitInternationalMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit MpoxInternational -Mpox Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin Mpox -MpoxInternational Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinInternationalMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin MpoxInternational -Mpox Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex Mpox -MpoxInternational Host Information GENEPIO:0001395 host gender host_gender HostGenderInternationalMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex MpoxInternational -Mpox Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY Mpox -MpoxInternational Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] MpoxInternational -Mpox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE Mpox -Mpox;MpoxInternational Host Information GENEPIO:0001399 symptom onset date symptom_onset_date date NullValueMenu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE Mpox;MpoxInternational -Mpox Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS Mpox -MpoxInternational Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsInternationalMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] MpoxInternational -Mpox Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors Mpox -MpoxInternational Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsInternationalMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors MpoxInternational -Mpox Host Information GENEPIO:0001402 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications Mpox -MpoxInternational Host Information GENEPIO:0001402 complications complications ComplicationsInternationalMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] MpoxInternational -Mpox;MpoxInternational Host Information GENEPIO:0100580 antiviral therapy antiviral_therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy Mpox;MpoxInternational -Mpox;MpoxInternational GENEPIO:0001403 Host vaccination information host_vaccination_information Mpox;MpoxInternational -Mpox Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY Mpox -MpoxInternational Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusInternationalMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY MpoxInternational -Mpox;MpoxInternational Host vaccination information GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received Mpox;MpoxInternational -Mpox;MpoxInternational Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name WhitespaceMinimizedString NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY Mpox;MpoxInternational -Mpox;MpoxInternational Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date date NullValueMenu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY Mpox;MpoxInternational -Mpox;MpoxInternational Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY Mpox;MpoxInternational - -Mpox;MpoxInternational GENEPIO:0001409 Host exposure information host_exposure_information Mpox;MpoxInternational -Mpox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY Mpox -MpoxInternational Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] MpoxInternational -Mpox;MpoxInternational Host exposure information GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL Mpox;MpoxInternational -Mpox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL Mpox -MpoxInternational Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California MpoxInternational -Mpox Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL Mpox -MpoxInternational Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryInternationalMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] MpoxInternational -Mpox;MpoxInternational Host exposure information GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL Mpox;MpoxInternational -Mpox;MpoxInternational Host exposure information GENEPIO:0001415 most recent travel return date most_recent_travel_return_date date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL Mpox;MpoxInternational -Mpox;MpoxInternational Host exposure information GENEPIO:0001416 travel history travel_history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL Mpox;MpoxInternational -Mpox Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE Mpox -MpoxInternational Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventInternationalMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE MpoxInternational -Mpox Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level Mpox -MpoxInternational Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelInternationalMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level MpoxInternational -Mpox Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE Mpox -MpoxInternational Host exposure information GENEPIO:0001419 host role host_role HostRoleInternationalMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE MpoxInternational -Mpox Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE Mpox -MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingInternationalMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE MpoxInternational -Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS Mpox;MpoxInternational - -Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information Mpox;MpoxInternational -Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection Mpox -MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] MpoxInternational -Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date Mpox;MpoxInternational -Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment Mpox -MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] MpoxInternational -Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection Mpox;MpoxInternational - - -Mpox;MpoxInternational GENEPIO:0001441 Sequencing sequencing Mpox;MpoxInternational -Mpox;MpoxInternational Sequence information GENEPIO:0100472 sequencing project name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. MPOX-1356 Mpox;MpoxInternational -Mpox Sequencing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by Mpox -MpoxInternational Sequencing GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Ontario (PHO) sequenced_by MpoxInternational -Mpox Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString NullValueMenu The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab Mpox -MpoxInternational Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada Mpox;MpoxInternational -Mpox Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by Mpox -MpoxInternational Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequence submitter contact address Mpox;MpoxInternational -Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing Mpox -MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details Mpox;MpoxInternational -Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE Mpox -MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT Mpox;MpoxInternational -Mpox Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay Mpox -MpoxInternational Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeInternationalMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] MpoxInternational -Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument Mpox -MpoxInternational Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentInternationalMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument MpoxInternational -Mpox;MpoxInternational Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001455 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 Mpox;MpoxInternational -Mpox Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method Mpox -MpoxInternational Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodInternationalMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. Mpox;MpoxInternational -Mpox;MpoxInternational Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme Mpox;MpoxInternational - Sequencing GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300bp -Mpox;MpoxInternational GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 Mpox;MpoxInternational -Mpox Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control Mpox -MpoxInternational Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationInternationalMenu MpoxInternational -Mpox Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage Mpox -MpoxInternational Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesInternationalMenu MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. Mpox;MpoxInternational -Mpox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method Mpox -MpoxInternational Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method MpoxInternational -Mpox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method Mpox -MpoxInternational Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name consensus_sequence_name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta consensus sequence filename Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu TRUE The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu TRUE The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath fast5_filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 Mpox;MpoxInternational -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession Mpox;MpoxInternational -Mpox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol Mpox -MpoxInternational Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol MpoxInternational -MpoxInternational GENEPIO:0101082 Taxonomic identification information -MpoxInternational Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -MpoxInternational Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -MpoxInternational Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon -MpoxInternational Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 -MpoxInternational Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. MPXV_report123.doc -MpoxInternational Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 -MpoxInternational Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 -Mpox;MpoxInternational GENEPIO:0001506 Pathogen diagnostic testing pathogen_diagnostic_testing Mpox;MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. MPX (orf B6R) MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0102045 assay target details 1 assay_target_details_1 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -Mpox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name Mpox -MpoxInternational Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg190 gene (MPOX) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. B6R (Li et al., 2006) -Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value Mpox;MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OVP (orf 17L) -MpoxInternational Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -Mpox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 Mpox -MpoxInternational Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg002 gene (MPOX) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G). -Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 Mpox;MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OPHA (orf B2R) -MpoxInternational Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -Mpox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene_name_3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 Mpox -MpoxInternational Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg188 gene (MPOX) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 MpoxInternational -MpoxInternational Pathogen diagnostic testing GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R_G (Li et al., 2010) assay -Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3 Mpox;MpoxInternational -Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4 Mpox -Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 Mpox -Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 Mpox -Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 Mpox - GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement -Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS Mpox;MpoxInternational -Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS Mpox;MpoxInternational \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +Mpox;MpoxInternational GENEPIO:0001122 Database Identifiers database_identifiers +Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the submitting laboratory Primary Specimen ID TEXT_ID sample_name specimen collector sample ID +Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID +Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID +Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession +Mpox;MpoxInternational Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession +Mpox;MpoxInternational Database Identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION +Mpox;MpoxInternational Database Identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession +MpoxInternational Database Identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name +Mpox;MpoxInternational Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession +Mpox;MpoxInternational GENEPIO:0001150 Sample collection and processing sample_collection_and_processing +Mpox Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by +MpoxInternational Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001158 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date +Mpox Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date +Mpox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) +MpoxInternational Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) +Mpox Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) +MpoxInternational Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the state/province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) +MpoxInternational Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon +MpoxInternational Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon +Mpox Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus Pathogen HC_CURRENT_ID organism organism +MpoxInternational Sample collection and processing GENEPIO:0001191 organism organism OrganismInternationalMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism +Mpox Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name +MpoxInternational Sample collection and processing GENEPIO:0001644 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate +Mpox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling +MpoxInternational Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingInternationalMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Symptomology and history suggested Monkeypox diagnosis. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details +Mpox Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Nucleic Acid Specimen Type PH_SPECIMEN_TYPE +Mpox Sample collection and processing GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type RelatedSpecimenRelationshipTypeMenu NullValueMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Previously Submitted Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE +Mpox Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material +MpoxInternational Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) [NCIT:C78582] Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material +Mpox Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part +MpoxInternational Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartInternationalMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part +Mpox Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product +MpoxInternational Sample collection and processing GENEPIO:0001216 body product body_product BodyProductInternationalMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product +MpoxInternational Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material +Mpox Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device +MpoxInternational Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceInternationalMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device +Mpox Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method +MpoxInternational Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodInternationalMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method +Mpox Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing +MpoxInternational Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingInternationalMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] +Mpox;MpoxInternational Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details +Mpox Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +MpoxInternational Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeInternationalMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] +Mpox;MpoxInternational Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control +Mpox;MpoxInternational GENEPIO:0001498 Lineage and Variant information +MpoxInternational Lineage and Variant information GENEPIO:0001500 lineage/clade name LineageCladeNameINternationalMenu NullValueMenu The name of the lineage or clade. Provide the lineage/clade name. B.1.1.7 PH_LINEAGE_CLADE_NAME +MpoxInternational Lineage and Variant information GENEPIO:0001501 lineage/clade analysis software name WhitespaceMinimizedString NullValueMenu The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin PH_LINEAGE_CLADE_SOFTWARE +MpoxInternational Lineage and Variant information GENEPIO:0001502 lineage/clade analysis software version WhitespaceMinimizedString NullValueMenu The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION +Mpox;MpoxInternational GENEPIO:0001268 Host Information host_information +Mpox Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE +MpoxInternational Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameInternationalMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human +Mpox Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) +MpoxInternational Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameInternationalMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) +Mpox Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state +MpoxInternational Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateInternationalMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state +Mpox Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS +MpoxInternational Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsInternationalMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] +Mpox Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome +MpoxInternational Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeInternationalMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome +Mpox Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox Host Disease PH_HOST_DISEASE host_disease host disease +MpoxInternational Host Information GENEPIO:0001391 host disease host_disease HostDiseaseInternationalMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease +MpoxInternational Host Information GENEPIO:0001398 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id +Mpox Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age +MpoxInternational Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +Mpox Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit +MpoxInternational Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitInternationalMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit +Mpox Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin +MpoxInternational Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinInternationalMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin +Mpox Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex +MpoxInternational Host Information GENEPIO:0001395 host gender host_gender HostGenderInternationalMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex +Mpox Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY +MpoxInternational Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] +Mpox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE +Mpox;MpoxInternational Host Information GENEPIO:0001399 symptom onset date symptom_onset_date date NullValueMenu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE +Mpox Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS +MpoxInternational Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsInternationalMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] +Mpox Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors +MpoxInternational Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsInternationalMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors +Mpox Host Information GENEPIO:0001402 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications +MpoxInternational Host Information GENEPIO:0001402 complications complications ComplicationsInternationalMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] +Mpox;MpoxInternational Host Information GENEPIO:0100580 antiviral therapy antiviral_therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy +Mpox;MpoxInternational GENEPIO:0001403 Host vaccination information host_vaccination_information +Mpox Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY +MpoxInternational Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusInternationalMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY +Mpox;MpoxInternational Host vaccination information GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received +Mpox;MpoxInternational Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name WhitespaceMinimizedString NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY +Mpox;MpoxInternational Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date date NullValueMenu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY +Mpox;MpoxInternational Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY + +Mpox;MpoxInternational GENEPIO:0001409 Host exposure information host_exposure_information +Mpox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY +MpoxInternational Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] +Mpox;MpoxInternational Host exposure information GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL +Mpox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL +MpoxInternational Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California +Mpox Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL +MpoxInternational Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryInternationalMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] +Mpox;MpoxInternational Host exposure information GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL +Mpox;MpoxInternational Host exposure information GENEPIO:0001415 most recent travel return date most_recent_travel_return_date date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL +Mpox;MpoxInternational Host exposure information GENEPIO:0001416 travel history travel_history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL +Mpox Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE +MpoxInternational Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventInternationalMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE +Mpox Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level +MpoxInternational Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelInternationalMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level +Mpox Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE +MpoxInternational Host exposure information GENEPIO:0001419 host role host_role HostRoleInternationalMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE +Mpox Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE +MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingInternationalMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE +Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS + +Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information +Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection +MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] +Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu {today} The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date +Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment +MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] +Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection + + +Mpox;MpoxInternational GENEPIO:0001441 Sequencing sequencing +Mpox;MpoxInternational Sequence information GENEPIO:0100472 sequencing project name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. MPOX-1356 +Mpox Sequencing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by +MpoxInternational Sequencing GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Ontario (PHO) sequenced_by +Mpox Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString NullValueMenu The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +MpoxInternational Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +Mpox;MpoxInternational Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email +Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada +Mpox Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by +MpoxInternational Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by +Mpox;MpoxInternational Sequencing GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email +Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequence submitter contact address +Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing +MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing +Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details +Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE +MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE +Mpox;MpoxInternational Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID +Mpox;MpoxInternational Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT +Mpox Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay +MpoxInternational Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeInternationalMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] +Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument +MpoxInternational Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentInternationalMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument +Mpox;MpoxInternational Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 +Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol +Mpox;MpoxInternational Sequencing GENEPIO:0001455 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number +Mpox;MpoxInternational Sequencing GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +Mpox Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method +MpoxInternational Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodInternationalMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method +Mpox;MpoxInternational Sequencing GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. +Mpox;MpoxInternational Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme + Sequencing GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300bp +Mpox;MpoxInternational GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 +Mpox Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationInternationalMenu +Mpox Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesInternationalMenu +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. +Mpox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method +Mpox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name consensus_sequence_name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta consensus sequence filename +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu TRUE The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu TRUE The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath fast5_filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession +Mpox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol +MpoxInternational GENEPIO:0101082 Taxonomic identification information +MpoxInternational Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +MpoxInternational Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +MpoxInternational Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +MpoxInternational Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +MpoxInternational Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. MPXV_report123.doc +MpoxInternational Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +MpoxInternational Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +Mpox;MpoxInternational GENEPIO:0001506 Pathogen diagnostic testing pathogen_diagnostic_testing +MpoxInternational Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. MPX (orf B6R) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102045 assay target details 1 assay_target_details_1 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name +MpoxInternational Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg190 gene (MPOX) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name +MpoxInternational Pathogen diagnostic testing GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. B6R (Li et al., 2006) +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value +MpoxInternational Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OVP (orf 17L) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 +MpoxInternational Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg002 gene (MPOX) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 +MpoxInternational Pathogen diagnostic testing GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G). +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 +MpoxInternational Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OPHA (orf B2R) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene_name_3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 +MpoxInternational Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg188 gene (MPOX) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 +MpoxInternational Pathogen diagnostic testing GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R_G (Li et al., 2010) assay +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3 +Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4 +Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 +Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 +Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement +Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS +Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS \ No newline at end of file diff --git a/web/templates/pha4ge/schema.json b/web/templates/pha4ge/schema.json index ac18e518..a43cb454 100644 --- a/web/templates/pha4ge/schema.json +++ b/web/templates/pha4ge/schema.json @@ -7716,6 +7716,9 @@ "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sequencing date in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -12152,6 +12155,9 @@ "name": "sequencing_date", "description": "The date the sample was sequenced.", "title": "sequencing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sequencing date in ISO 8601 standard format \"YYYY-MM-DD\"." ], diff --git a/web/templates/pha4ge/schema.yaml b/web/templates/pha4ge/schema.yaml index 1e63da20..56383b1d 100644 --- a/web/templates/pha4ge/schema.yaml +++ b/web/templates/pha4ge/schema.yaml @@ -1962,6 +1962,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2021-04-26' library_id: diff --git a/web/templates/pha4ge/schema_slots.tsv b/web/templates/pha4ge/schema_slots.tsv index 6ac6df30..16f95fa5 100644 --- a/web/templates/pha4ge/schema_slots.tsv +++ b/web/templates/pha4ge/schema_slots.tsv @@ -106,7 +106,7 @@ Risk Factor: A variable associated with an increased risk of disease or infectio GENEPIO:0001441 Covid-19 Sequencing sequencing Sequencing GENEPIO:0001445 Covid-19 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy purpose_of_sequencing Sequencing GENEPIO:0001446 Covid-19 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. Screened for S gene target failure (S dropout) - Sequencing GENEPIO:0001447 Covid-19 sequencing date sequencing_date date NullValueMenu The date the sample was sequenced. Provide the sequencing date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-26 + Sequencing GENEPIO:0001447 Covid-19 sequencing date sequencing_date date NullValueMenu {today} The date the sample was sequenced. Provide the sequencing date in ISO 8601 standard format "YYYY-MM-DD". 2021-04-26 Sequencing GENEPIO:0001448 Covid-19 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID Sequencing GENEPIO:0001449 Covid-19 amplicon size amplicon_size WhitespaceMinimizedString The length of the amplicon generated by PCR amplification. Provide the amplicon size, including the units. 300bp amplicon_size Sequencing GENEPIO:0001450 Covid-19 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT diff --git a/web/templates/wastewater/schema.json b/web/templates/wastewater/schema.json index e27046cb..1cfb152a 100644 --- a/web/templates/wastewater/schema.json +++ b/web/templates/wastewater/schema.json @@ -5411,6 +5411,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -5439,6 +5442,9 @@ "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample collection start date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -5468,6 +5474,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", + "todos": [ + ">={sample_collection_start_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -5497,6 +5507,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -6491,6 +6504,9 @@ "name": "isolation_date", "description": "The date on which the isolate was isolated from a sample.", "title": "isolation date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], @@ -6510,6 +6526,9 @@ "name": "isolate_received_date", "description": "The date on which the isolate was received by the laboratory.", "title": "isolate received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], @@ -8654,7 +8673,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -9802,6 +9822,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -12491,6 +12514,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -12523,6 +12549,9 @@ "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample collection start date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -12556,6 +12585,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", + "todos": [ + ">={sample_collection_start_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -12589,6 +12622,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -15920,7 +15956,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -19692,6 +19729,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -19724,6 +19764,9 @@ "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample collection start date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -19757,6 +19800,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", + "todos": [ + ">={sample_collection_start_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -19790,6 +19837,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -23121,7 +23171,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -24101,6 +24152,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -26995,6 +27049,9 @@ "name": "sample_received_date", "description": "The date on which the sample was received.", "title": "sample received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample received date in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], @@ -27027,6 +27084,9 @@ "name": "sample_collection_start_date", "description": "The date on which the sample was collected, or sampling began for a continuous sample.", "title": "sample collection start date", + "todos": [ + "<={today}" + ], "comments": [ "If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\"." ], @@ -27060,6 +27120,10 @@ "name": "sample_collection_end_date", "description": "The date on which sample collection ended for a continuous sample.", "title": "sample collection end date", + "todos": [ + ">={sample_collection_start_date}", + "<={today}" + ], "comments": [ "Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD" ], @@ -27093,6 +27157,9 @@ "name": "sample_processing_date", "description": "The date on which the sample was processed.", "title": "sample processing date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the sample processed date in ISO 8601 format, i.e. \"YYYY-MM-DD\". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates." ], @@ -28247,6 +28314,9 @@ "name": "isolation_date", "description": "The date on which the isolate was isolated from a sample.", "title": "isolation date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], @@ -28270,6 +28340,9 @@ "name": "isolate_received_date", "description": "The date on which the isolate was received by the laboratory.", "title": "isolate received date", + "todos": [ + "<={today}" + ], "comments": [ "Provide the date according to the ISO 8601 standard \"YYYY-MM-DD\", \"YYYY-MM\" or \"YYYY\"." ], @@ -30762,7 +30835,8 @@ "description": "The date the sample was sequenced.", "title": "sequencing date", "todos": [ - ">={sample_collection_date}" + ">={sample_collection_date}", + "<={today}" ], "comments": [ "ISO 8601 standard \"YYYY-MM-DD\"." @@ -31998,6 +32072,9 @@ "name": "taxonomic_analysis_date", "description": "The date a taxonomic analysis was performed.", "title": "taxonomic analysis date", + "todos": [ + "<={today}" + ], "comments": [ "Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. \"YYYY-MM-DD\"." ], diff --git a/web/templates/wastewater/schema.yaml b/web/templates/wastewater/schema.yaml index 0564e807..8340c557 100644 --- a/web/templates/wastewater/schema.yaml +++ b/web/templates/wastewater/schema.yaml @@ -3157,6 +3157,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2020-03-28' sample_collection_start_date: @@ -3172,6 +3174,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} required: true examples: - value: '2020-03-16' @@ -3185,6 +3189,9 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - '>={sample_collection_start_date}' + - <={today} recommended: true examples: - value: '2020-03-18' @@ -3199,6 +3206,8 @@ slots: any_of: - range: date - range: NullValueMenu + todos: + - <={today} examples: - value: '2020-03-16' sample_collection_start_time: @@ -3711,6 +3720,8 @@ slots: or "YYYY". slot_uri: GENEPIO:0100465 range: date + todos: + - <={today} examples: - value: '2020-10-30' isolate_received_date: @@ -3721,6 +3732,8 @@ slots: or "YYYY". slot_uri: GENEPIO:0100466 range: WhitespaceMinimizedString + todos: + - <={today} examples: - value: '2020-11-15' serovar: @@ -4710,6 +4723,7 @@ slots: range: date todos: - '>={sample_collection_date}' + - <={today} examples: - value: '2020-06-22' library_id: @@ -5277,6 +5291,8 @@ slots: analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". slot_uri: GENEPIO:0101075 range: date + todos: + - <={today} examples: - value: '2024-02-01' read_mapping_criteria: diff --git a/web/templates/wastewater/schema_slots.tsv b/web/templates/wastewater/schema_slots.tsv index 35295c93..a119eccb 100644 --- a/web/templates/wastewater/schema_slots.tsv +++ b/web/templates/wastewater/schema_slots.tsv @@ -34,10 +34,10 @@ WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001191 orga WastewaterAMR Sample collection and processing GENEPIO:0001191 organism organism WhitespaceMinimizedString NullValueMenu TRUE TRUE Taxonomic name of the organism. Provide the official nomenclature for the organism(s) present in the sample if AMR profiles are assigned to organisms. Multiple organisms can be entered, separated by semicolons. Avoid abbreviations. Search for taxonomic names here: ncbi.nlm.nih.gov/taxonomy. Vibrio cholerae ww_surv_target_1 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE TRUE The reason that the sample was collected. The reason a sample was collected may provide information about potential biases in sampling strategy. Provide the purpose of sampling from the picklist in the template. Most likely, the sample was collected for Public health surveillance. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Public health surveillance purpose_of_ww_sampling WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100877 scale of sampling scale_of_sampling ScaleOfSamplingMenu NullValueMenu TRUE The range of locations or entities sampled expressed in general terms. Provide the scale of wastewater sampling by selecting a value from the picklist. Community-level surveillance purpose_of_ww_sampling -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu {today} The date on which the sample was received. Provide the sample received date in ISO 8601 format, i.e. "YYYY-MM-DD". 2020-03-28 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0001174 sample collection start date sample_collection_start_date date NullValueMenu TRUE {today} The date on which the sample was collected, or sampling began for a continuous sample. If your sample is a continuous sample please use this field to capture your start date. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101071 sample collection end date sample_collection_end_date date NullValueMenu TRUE {sample_collection_start_date} {today} The date on which sample collection ended for a continuous sample. Provide the date that sample collection ended in ISO 8601 format i.e. YYYY-MM-DD 2020-03-18 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100763 sample processing date sample_processing_date date NullValueMenu {today} The date on which the sample was processed. Provide the sample processed date in ISO 8601 format, i.e. "YYYY-MM-DD". The sample may be collected and processed (e.g. filtered, extraction) on the same day, or on different dates. 2020-03-16 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101072 sample collection start time sample_collection_start_time time NullValueMenu TRUE The time at which sample collection began. Provide this time in ISO 8601 24hr format, in your local time. 17:15 PST WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0101073 sample collection end time sample_collection_end_time time NullValueMenu TRUE The time at which sample collection ended. Provide this time in ISO 8601 24hr format, in your local time. 19:15 PST WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sample collection and processing GENEPIO:0100765 sample collection time of day sample_collection_time_of_day SampleCollectionTimeOfDayMenu NullValueMenu The descriptive time of day during which the sample was collected. If known, select a value from the pick list. The time of sample processing matters especially for grab samples, as fecal concentration in wastewater fluctuates over the course of the day. Morning @@ -78,8 +78,8 @@ WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100461 isol WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100462 isolated by laboratory name isolated_by_laboratory_name WhitespaceMinimizedString The specific laboratory affiliation of the individual who performed the isolation procedure. Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100463 isolated by contact name isolated_by_contact_name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the isolate. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Enterics Lab Manager WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100464 isolated by contact email isolated_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the isolate. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 -WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100465 isolation date isolation_date date {today} The date on which the isolate was isolated from a sample. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-10-30 +WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100466 isolate received date isolate_received_date WhitespaceMinimizedString {today} The date on which the isolate was received by the laboratory. Provide the date according to the ISO 8601 standard "YYYY-MM-DD", "YYYY-MM" or "YYYY". 2020-11-15 WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100467 serovar serovar WhitespaceMinimizedString TRUE The serovar of the organism. Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. Heidelberg WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100468 serotyping method serotyping_method WhitespaceMinimizedString TRUE The method used to determine the serovar. If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. SISTR 1.0.1 WastewaterPathogenAgnostic Strain and isolation information GENEPIO:0100469 phagetype phagetype WhitespaceMinimizedString The phagetype of the organism. Provide if known. If unknown, put “missing”. 47 @@ -168,7 +168,7 @@ WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence informati WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100471 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString NullValueMenu TRUE The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. enterics@lab.ca WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. For Canadian institutions submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) sequenced_by WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString NullValueMenu TRUE ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or laboratory. RespLab@lab.ca sequence_submitter_contact_email -WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample_collection_date} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 +WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001447 sequencing date sequencing_date date {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001448 library ID library_id WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library_ID WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0100473 sequencing platform sequencing_platform SequencingPlatformMenu NullValueMenu TRUE The platform technology used to perform the sequencing. Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina [GENEPIO:0001923] platform WastewaterSARS-CoV-2;WastewaterAMR;WastewaterPathogenAgnostic Sequence information GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Provide the model sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. Illumina HiSeq 2500 [GENEPIO:0100117] instrument_model @@ -220,7 +220,7 @@ WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100833 WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. WWtax_report_Feb1_2024.doc -WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date {today} The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 WastewaterAMR;WastewaterPathogenAgnostic Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 WastewaterAMR GENEPIO:0100479 AMR detection information WastewaterAMR AMR detection information GENEPIO:0101076 AMR analysis software name amr_analysis_software_name WhitespaceMinimizedString TRUE The name of the software used to perform an in silico antimicrobial resistance determinant identification/analysis. Provide the name of the software used for AMR analysis. Resistance Gene Identifier From bd1dd2897f86f0d21153b7c769465877b766a207 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 15:01:01 -0700 Subject: [PATCH 93/96] Bug fix: ensure slot['todos'] created before adding min value --- script/tabular_to_schema.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/script/tabular_to_schema.py b/script/tabular_to_schema.py index ef589801..a7e2d170 100644 --- a/script/tabular_to_schema.py +++ b/script/tabular_to_schema.py @@ -158,6 +158,8 @@ def set_min_max(slot, slot_minimum_value, slot_maximum_value): elif isDecimal(slot_minimum_value): slot['minimum_value'] = float(slot_minimum_value); else: + if not 'todos' in slot: + slot['todos'] = []; slot['todos'] = ['>=' + slot_minimum_value]; if slot_maximum_value > '': if isInteger(slot_maximum_value): @@ -165,10 +167,9 @@ def set_min_max(slot, slot_minimum_value, slot_maximum_value): elif isDecimal(slot_maximum_value): slot['maximum_value'] = float(slot_maximum_value); else: - if slot['todos']: - slot['todos'].append('<=' + slot_maximum_value); - else: - slot['todos'] = ['<=' + slot_maximum_value]; + if not 'todos' in slot: + slot['todos'] = []; + slot['todos'].append('<=' + slot_maximum_value); def isDecimal(x): try: From ca45d1eab2804731c2bc1056c58fc905463b7195 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 16:27:45 -0700 Subject: [PATCH 94/96] version bump for gisaid and pha4ge --- web/templates/gisaid/schema.json | 2 +- web/templates/gisaid/schema.yaml | 2 +- web/templates/gisaid/schema_core.yaml | 2 +- web/templates/pha4ge/schema.json | 2 +- web/templates/pha4ge/schema.yaml | 2 +- web/templates/pha4ge/schema_core.yaml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/web/templates/gisaid/schema.json b/web/templates/gisaid/schema.json index 1b8dd179..3fa6b018 100644 --- a/web/templates/gisaid/schema.json +++ b/web/templates/gisaid/schema.json @@ -2,7 +2,7 @@ "name": "GISAID", "description": "", "id": "https://example.com/GISAID", - "version": "1.0.0", + "version": "1.0.2", "prefixes": { "linkml": { "prefix_prefix": "linkml", diff --git a/web/templates/gisaid/schema.yaml b/web/templates/gisaid/schema.yaml index 7a509078..c0522914 100644 --- a/web/templates/gisaid/schema.yaml +++ b/web/templates/gisaid/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/GISAID name: GISAID description: '' -version: 1.0.0 +version: 1.0.2 imports: - linkml:types prefixes: diff --git a/web/templates/gisaid/schema_core.yaml b/web/templates/gisaid/schema_core.yaml index 77060484..9345e5ef 100644 --- a/web/templates/gisaid/schema_core.yaml +++ b/web/templates/gisaid/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/GISAID name: "GISAID" description: "" -version: 1.0.0 +version: 1.0.2 imports: - 'linkml:types' prefixes: diff --git a/web/templates/pha4ge/schema.json b/web/templates/pha4ge/schema.json index a43cb454..1e59b4bd 100644 --- a/web/templates/pha4ge/schema.json +++ b/web/templates/pha4ge/schema.json @@ -2,7 +2,7 @@ "name": "PHA4GE", "description": "", "id": "https://example.com/CanCOGeN_Covid-19", - "version": "1.0.0", + "version": "1.0.2", "prefixes": { "linkml": { "prefix_prefix": "linkml", diff --git a/web/templates/pha4ge/schema.yaml b/web/templates/pha4ge/schema.yaml index 56383b1d..e478b5f0 100644 --- a/web/templates/pha4ge/schema.yaml +++ b/web/templates/pha4ge/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/CanCOGeN_Covid-19 name: PHA4GE description: '' -version: 1.0.0 +version: 1.0.2 imports: - linkml:types prefixes: diff --git a/web/templates/pha4ge/schema_core.yaml b/web/templates/pha4ge/schema_core.yaml index 60cd3a8b..fcc09883 100644 --- a/web/templates/pha4ge/schema_core.yaml +++ b/web/templates/pha4ge/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/CanCOGeN_Covid-19 name: PHA4GE description: "" -version: 1.0.0 +version: 1.0.2 imports: - 'linkml:types' prefixes: From 538da5710c31fc3d992cb89ebb0b76befe98f2be Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Mon, 28 Oct 2024 23:12:58 -0700 Subject: [PATCH 95/96] Mpox update --- web/templates/mpox/schema.json | 1694 +++++++-------------------- web/templates/mpox/schema.yaml | 340 ++---- web/templates/mpox/schema_slots.tsv | 466 ++++---- 3 files changed, 760 insertions(+), 1740 deletions(-) diff --git a/web/templates/mpox/schema.json b/web/templates/mpox/schema.json index 0a38f110..52409f0d 100644 --- a/web/templates/mpox/schema.json +++ b/web/templates/mpox/schema.json @@ -11539,7 +11539,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100472", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -11576,7 +11575,7 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100470", "domain_of": [ - "Mpox" + "MpoxInternational" ], "any_of": [ { @@ -11867,12 +11866,17 @@ "comments": [ "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." ], + "examples": [ + { + "value": "whole genome sequencing assay [OBI:0002117]" + } + ], "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100997", "domain_of": [ - "Mpox", "MpoxInternational" - ] + ], + "range": "SequencingAssayTypeInternationalMenu" }, "sequencing_instrument": { "name": "sequencing_instrument", @@ -11911,7 +11915,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0101102", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -11978,7 +11981,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100843", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -11998,11 +12000,18 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100966", "domain_of": [ - "Mpox", "MpoxInternational" ], "recommended": true, - "multivalued": true + "multivalued": true, + "any_of": [ + { + "range": "GenomicTargetEnrichmentMethodInternationalMenu" + }, + { + "range": "NullValueMenu" + } + ] }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", @@ -12019,7 +12028,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100967", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12082,7 +12090,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100557", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12102,7 +12109,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100558", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12113,9 +12119,9 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100559", "domain_of": [ - "Mpox", "MpoxInternational" - ] + ], + "range": "QualityControlDeterminationInternationalMenu" }, "quality_control_issues": { "name": "quality_control_issues", @@ -12123,9 +12129,9 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100560", "domain_of": [ - "Mpox", "MpoxInternational" - ] + ], + "range": "QualityControlIssuesInternationalMenu" }, "quality_control_details": { "name": "quality_control_details", @@ -12142,7 +12148,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100561", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12210,7 +12215,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100831", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12233,8 +12237,51 @@ ], "slot_uri": "GENEPIO:0001460", "domain_of": [ - "Mpox", - "MpoxInternational" + "Mpox" + ], + "range": "WhitespaceMinimizedString" + }, + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", + "description": "The name of the consensus sequence file.", + "title": "consensus sequence filename", + "comments": [ + "Provide the name and version number of the consensus sequence FASTA file." + ], + "examples": [ + { + "value": "mpox123assembly.fasta" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filename" + ], + "slot_uri": "GENEPIO:0001461", + "domain_of": [ + "Mpox" + ], + "range": "WhitespaceMinimizedString" + }, + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "description": "The filepath of the consensus sequence file.", + "title": "consensus sequence filepath", + "comments": [ + "Provide the filepath of the consensus sequence FASTA file." + ], + "examples": [ + { + "value": "/User/Documents/STILab/Data/mpox123assembly.fasta" + } + ], + "from_schema": "https://example.com/mpox", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filepath" + ], + "slot_uri": "GENEPIO:0001462", + "domain_of": [ + "Mpox" ], "range": "WhitespaceMinimizedString" }, @@ -12256,7 +12303,6 @@ ], "slot_uri": "GENEPIO:0101715", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12279,7 +12325,6 @@ ], "slot_uri": "GENEPIO:0101716", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12353,7 +12398,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100825", "domain_of": [ - "Mpox", "MpoxInternational" ], "required": true, @@ -12381,7 +12425,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100826", "domain_of": [ - "Mpox", "MpoxInternational" ], "required": true, @@ -12531,7 +12574,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100827", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12551,7 +12593,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100828", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12571,7 +12612,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100829", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12596,7 +12636,6 @@ ], "slot_uri": "GENEPIO:0001474", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12619,7 +12658,6 @@ ], "slot_uri": "GENEPIO:0001475", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12687,7 +12725,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100846", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12707,7 +12744,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100937", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12727,7 +12763,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100844", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "WhitespaceMinimizedString" @@ -12747,7 +12782,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100938", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12767,7 +12801,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0100830", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -12787,7 +12820,6 @@ "from_schema": "https://example.com/mpox", "slot_uri": "GENEPIO:0001484", "domain_of": [ - "Mpox", "MpoxInternational" ], "range": "Integer" @@ -14502,11 +14534,6 @@ "rank": 69, "slot_group": "Host reinfection information" }, - "sequencing_project_name": { - "name": "sequencing_project_name", - "rank": 70, - "slot_group": "Sequence information" - }, "sequenced_by": { "name": "sequenced_by", "comments": [ @@ -14516,7 +14543,7 @@ "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by" ], - "rank": 71, + "rank": 70, "slot_group": "Sequencing", "any_of": [ { @@ -14527,19 +14554,14 @@ } ] }, - "sequenced_by_laboratory_name": { - "name": "sequenced_by_laboratory_name", - "rank": 72, - "slot_group": "Sequence information" - }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", - "rank": 73, + "rank": 71, "slot_group": "Sequencing" }, "sequenced_by_contact_address": { "name": "sequenced_by_contact_address", - "rank": 74, + "rank": 72, "slot_group": "Sequencing" }, "sequence_submitted_by": { @@ -14551,7 +14573,7 @@ "BIOSAMPLE:sequence_submitted_by", "VirusSeq_Portal:sequence%20submitted%20by" ], - "rank": 75, + "rank": 73, "slot_group": "Sequencing", "any_of": [ { @@ -14564,12 +14586,12 @@ }, "sequence_submitter_contact_email": { "name": "sequence_submitter_contact_email", - "rank": 76, + "rank": 74, "slot_group": "Sequencing" }, "sequence_submitter_contact_address": { "name": "sequence_submitter_contact_address", - "rank": 77, + "rank": 75, "slot_group": "Sequencing" }, "purpose_of_sequencing": { @@ -14607,7 +14629,7 @@ "description": "In all other cases use" } ], - "rank": 78, + "rank": 76, "slot_group": "Sequencing", "any_of": [ { @@ -14620,36 +14642,25 @@ }, "purpose_of_sequencing_details": { "name": "purpose_of_sequencing_details", - "rank": 79, + "rank": 77, "slot_group": "Sequencing" }, "sequencing_date": { "name": "sequencing_date", - "rank": 80, + "rank": 78, "slot_group": "Sequencing", "required": true }, "library_id": { "name": "library_id", - "rank": 81, + "rank": 79, "slot_group": "Sequencing" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 82, + "rank": 80, "slot_group": "Sequencing" }, - "sequencing_assay_type": { - "name": "sequencing_assay_type", - "examples": [ - { - "value": "whole genome sequencing assay" - } - ], - "rank": 83, - "slot_group": "Sequence information", - "range": "SequencingAssayTypeMenu" - }, "sequencing_instrument": { "name": "sequencing_instrument", "examples": [ @@ -14657,7 +14668,7 @@ "value": "Oxford Nanopore MinION" } ], - "rank": 84, + "rank": 81, "slot_group": "Sequencing", "any_of": [ { @@ -14668,331 +14679,172 @@ } ] }, - "sequencing_flow_cell_version": { - "name": "sequencing_flow_cell_version", - "rank": 85, - "slot_group": "Sequence information" - }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 86, + "rank": 82, "slot_group": "Sequencing" }, "sequencing_kit_number": { "name": "sequencing_kit_number", - "rank": 87, - "slot_group": "Sequencing" - }, - "dna_fragment_length": { - "name": "dna_fragment_length", - "rank": 88, - "slot_group": "Sequencing" - }, - "genomic_target_enrichment_method": { - "name": "genomic_target_enrichment_method", - "rank": 89, - "slot_group": "Sequencing", - "any_of": [ - { - "range": "GenomicTargetEnrichmentMethodMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "genomic_target_enrichment_method_details": { - "name": "genomic_target_enrichment_method_details", - "rank": 90, + "rank": 83, "slot_group": "Sequencing" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 91, + "rank": 84, "slot_group": "Sequencing" }, "amplicon_size": { "name": "amplicon_size", - "rank": 92, + "rank": 85, "slot_group": "Sequencing" }, - "quality_control_method_name": { - "name": "quality_control_method_name", - "rank": 93, - "slot_group": "Bioinformatics and QC metrics" - }, - "quality_control_method_version": { - "name": "quality_control_method_version", - "rank": 94, - "slot_group": "Bioinformatics and QC metrics" - }, - "quality_control_determination": { - "name": "quality_control_determination", - "description": "The determination of a quality control assessment.", - "comments": [ - "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." - ], - "examples": [ - { - "value": "sequence failed quality control" - } - ], - "rank": 95, - "slot_group": "Bioinformatics and QC metrics", - "multivalued": true, - "any_of": [ - { - "range": "QualityControlDeterminationMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "quality_control_issues": { - "name": "quality_control_issues", - "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", - "comments": [ - "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." - ], - "examples": [ - { - "value": "low average genome coverage" - } - ], - "rank": 96, - "slot_group": "Bioinformatics and QC metrics", - "multivalued": true, - "any_of": [ - { - "range": "QualityControlIssuesMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "quality_control_details": { - "name": "quality_control_details", - "rank": 97, - "slot_group": "Bioinformatics and QC metrics" - }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", - "rank": 98, + "rank": 86, "slot_group": "Bioinformatics and QC metrics", "required": true }, "dehosting_method": { "name": "dehosting_method", - "rank": 99, + "rank": 87, "slot_group": "Bioinformatics and QC metrics", "required": true }, - "deduplication_method": { - "name": "deduplication_method", - "rank": 100, - "slot_group": "Bioinformatics and QC metrics" - }, "consensus_sequence_name": { "name": "consensus_sequence_name", - "rank": 101, + "rank": 88, "slot_group": "Bioinformatics and QC metrics" }, - "genome_sequence_file_name": { - "name": "genome_sequence_file_name", - "rank": 102, + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", + "rank": 89, "slot_group": "Bioinformatics and QC metrics" }, - "genome_sequence_file_path": { - "name": "genome_sequence_file_path", - "rank": 103, + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "rank": 90, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_name": { "name": "consensus_sequence_software_name", - "rank": 104, + "rank": 91, "slot_group": "Bioinformatics and QC metrics" }, "consensus_sequence_software_version": { "name": "consensus_sequence_software_version", - "rank": 105, - "slot_group": "Bioinformatics and QC metrics" - }, - "sequence_assembly_software_name": { - "name": "sequence_assembly_software_name", - "rank": 106, - "slot_group": "Bioinformatics and QC metrics" - }, - "sequence_assembly_software_version": { - "name": "sequence_assembly_software_version", - "rank": 107, + "rank": 92, "slot_group": "Bioinformatics and QC metrics" }, "r1_fastq_filename": { "name": "r1_fastq_filename", - "rank": 108, + "rank": 93, "slot_group": "Bioinformatics and QC metrics" }, "r2_fastq_filename": { "name": "r2_fastq_filename", - "rank": 109, + "rank": 94, "slot_group": "Bioinformatics and QC metrics" }, "r1_fastq_filepath": { "name": "r1_fastq_filepath", - "rank": 110, + "rank": 95, "slot_group": "Bioinformatics and QC metrics" }, "r2_fastq_filepath": { "name": "r2_fastq_filepath", - "rank": 111, + "rank": 96, "slot_group": "Bioinformatics and QC metrics" }, "fast5_filename": { "name": "fast5_filename", - "rank": 112, + "rank": 97, "slot_group": "Bioinformatics and QC metrics" }, "fast5_filepath": { "name": "fast5_filepath", - "rank": 113, - "slot_group": "Bioinformatics and QC metrics" - }, - "number_of_total_reads": { - "name": "number_of_total_reads", - "rank": 114, - "slot_group": "Bioinformatics and QC metrics" - }, - "number_of_unique_reads": { - "name": "number_of_unique_reads", - "rank": 115, - "slot_group": "Bioinformatics and QC metrics" - }, - "minimum_posttrimming_read_length": { - "name": "minimum_posttrimming_read_length", - "rank": 116, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth_of_coverage_value": { - "name": "depth_of_coverage_value", - "rank": 117, - "slot_group": "Bioinformatics and QC metrics" - }, - "depth_of_coverage_threshold": { - "name": "depth_of_coverage_threshold", - "rank": 118, + "rank": 98, "slot_group": "Bioinformatics and QC metrics" }, "number_of_base_pairs_sequenced": { "name": "number_of_base_pairs_sequenced", - "rank": 119, + "rank": 99, "slot_group": "Bioinformatics and QC metrics" }, "consensus_genome_length": { "name": "consensus_genome_length", - "rank": 120, - "slot_group": "Bioinformatics and QC metrics" - }, - "sequence_assembly_length": { - "name": "sequence_assembly_length", - "rank": 121, - "slot_group": "Bioinformatics and QC metrics" - }, - "number_of_contigs": { - "name": "number_of_contigs", - "rank": 122, - "slot_group": "Bioinformatics and QC metrics" - }, - "genome_completeness": { - "name": "genome_completeness", - "rank": 123, - "slot_group": "Bioinformatics and QC metrics" - }, - "n50": { - "name": "n50", - "rank": 124, - "slot_group": "Bioinformatics and QC metrics" - }, - "percent_ns_across_total_genome_length": { - "name": "percent_ns_across_total_genome_length", - "rank": 125, - "slot_group": "Bioinformatics and QC metrics" - }, - "ns_per_100_kbp": { - "name": "ns_per_100_kbp", - "rank": 126, + "rank": 100, "slot_group": "Bioinformatics and QC metrics" }, "reference_genome_accession": { "name": "reference_genome_accession", - "rank": 127, + "rank": 101, "slot_group": "Bioinformatics and QC metrics" }, "bioinformatics_protocol": { "name": "bioinformatics_protocol", - "rank": 128, + "rank": 102, "slot_group": "Bioinformatics and QC metrics", "required": true }, "gene_name_1": { "name": "gene_name_1", - "rank": 129, + "rank": 103, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_pcr_ct_value_1": { "name": "diagnostic_pcr_ct_value_1", - "rank": 130, + "rank": 104, "slot_group": "Pathogen diagnostic testing" }, "gene_name_2": { "name": "gene_name_2", - "rank": 131, + "rank": 105, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_pcr_ct_value_2": { "name": "diagnostic_pcr_ct_value_2", - "rank": 132, + "rank": 106, "slot_group": "Pathogen diagnostic testing" }, "gene_name_3": { "name": "gene_name_3", - "rank": 133, + "rank": 107, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_pcr_ct_value_3": { "name": "diagnostic_pcr_ct_value_3", - "rank": 134, + "rank": 108, "slot_group": "Pathogen diagnostic testing" }, "gene_name_4": { "name": "gene_name_4", - "rank": 135, + "rank": 109, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_pcr_ct_value_4": { "name": "diagnostic_pcr_ct_value_4", - "rank": 136, + "rank": 110, "slot_group": "Pathogen diagnostic testing" }, "gene_name_5": { "name": "gene_name_5", - "rank": 137, + "rank": 111, "slot_group": "Pathogen diagnostic testing" }, "diagnostic_pcr_ct_value_5": { "name": "diagnostic_pcr_ct_value_5", - "rank": 138, + "rank": 112, "slot_group": "Pathogen diagnostic testing" }, "authors": { "name": "authors", - "rank": 139, + "rank": 113, "slot_group": "Contributor acknowledgement" }, "dataharmonizer_provenance": { "name": "dataharmonizer_provenance", - "rank": 140, + "rank": 114, "slot_group": "Contributor acknowledgement" } }, @@ -17365,30 +17217,6 @@ "slot_group": "Host reinfection information", "range": "WhitespaceMinimizedString" }, - "sequencing_project_name": { - "name": "sequencing_project_name", - "description": "The name of the project/initiative/program for which sequencing was performed.", - "title": "sequencing project name", - "comments": [ - "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." - ], - "examples": [ - { - "value": "MPOX-1356" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 70, - "slot_uri": "GENEPIO:0100472", - "alias": "sequencing_project_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, "sequenced_by": { "name": "sequenced_by", "description": "The name of the agency that generated the sequence.", @@ -17406,7 +17234,7 @@ "NML_LIMS:PH_SEQUENCING_CENTRE", "BIOSAMPLE:sequenced_by" ], - "rank": 71, + "rank": 70, "slot_uri": "GENEPIO:0100416", "alias": "sequenced_by", "owner": "Mpox", @@ -17425,36 +17253,6 @@ } ] }, - "sequenced_by_laboratory_name": { - "name": "sequenced_by_laboratory_name", - "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", - "title": "sequenced by laboratory name", - "comments": [ - "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." - ], - "examples": [ - { - "value": "Topp Lab" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 72, - "slot_uri": "GENEPIO:0100470", - "alias": "sequenced_by_laboratory_name", - "owner": "Mpox", - "domain_of": [ - "Mpox" - ], - "slot_group": "Sequence information", - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", "description": "The email address of the contact responsible for follow-up regarding the sequence.", @@ -17471,7 +17269,7 @@ "exact_mappings": [ "NML_LIMS:sequenced%20by%20contact%20email" ], - "rank": 73, + "rank": 71, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "Mpox", @@ -17495,7 +17293,7 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 74, + "rank": 72, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", "owner": "Mpox", @@ -17526,7 +17324,7 @@ "BIOSAMPLE:sequence_submitted_by", "VirusSeq_Portal:sequence%20submitted%20by" ], - "rank": 75, + "rank": 73, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "Mpox", @@ -17561,7 +17359,7 @@ "exact_mappings": [ "NML_LIMS:sequence%20submitter%20contact%20email" ], - "rank": 76, + "rank": 74, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "Mpox", @@ -17588,7 +17386,7 @@ "exact_mappings": [ "NML_LIMS:sequence%20submitter%20contact%20address" ], - "rank": 77, + "rank": 75, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", "owner": "Mpox", @@ -17647,7 +17445,7 @@ "BIOSAMPLE:purpose_of_sequencing", "VirusSeq_Portal:purpose%20of%20sequencing" ], - "rank": 78, + "rank": 76, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing", "owner": "Mpox", @@ -17685,7 +17483,7 @@ "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], - "rank": 79, + "rank": 77, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "Mpox", @@ -17724,7 +17522,7 @@ "exact_mappings": [ "NML_LIMS:PH_SEQUENCING_DATE" ], - "rank": 80, + "rank": 78, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "Mpox", @@ -17759,7 +17557,7 @@ "exact_mappings": [ "NML_LIMS:library%20ID" ], - "rank": 81, + "rank": 79, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "Mpox", @@ -17787,7 +17585,7 @@ "exact_mappings": [ "NML_LIMS:PH_LIBRARY_PREP_KIT" ], - "rank": 82, + "rank": 80, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "Mpox", @@ -17798,30 +17596,6 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "sequencing_assay_type": { - "name": "sequencing_assay_type", - "description": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.", - "title": "sequencing assay type", - "comments": [ - "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value." - ], - "examples": [ - { - "value": "whole genome sequencing assay" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 83, - "slot_uri": "GENEPIO:0100997", - "alias": "sequencing_assay_type", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Sequence information", - "range": "SequencingAssayTypeMenu" - }, "sequencing_instrument": { "name": "sequencing_instrument", "description": "The model of the sequencing instrument used.", @@ -17841,7 +17615,7 @@ "NML_LIMS:PH_SEQUENCING_INSTRUMENT", "VirusSeq_Portal:sequencing%20instrument" ], - "rank": 84, + "rank": 81, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "Mpox", @@ -17861,30 +17635,6 @@ } ] }, - "sequencing_flow_cell_version": { - "name": "sequencing_flow_cell_version", - "description": "The version number of the flow cell used for generating sequence data.", - "title": "sequencing flow cell version", - "comments": [ - "Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include \"version\" or \"v\" in the version number." - ], - "examples": [ - { - "value": "R.9.4.1" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 85, - "slot_uri": "GENEPIO:0101102", - "alias": "sequencing_flow_cell_version", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Sequence information", - "range": "WhitespaceMinimizedString" - }, "sequencing_protocol": { "name": "sequencing_protocol", "description": "The protocol used to generate the sequence.", @@ -17902,7 +17652,7 @@ "NML_LIMS:PH_TESTING_PROTOCOL", "VirusSeq_Portal:sequencing%20protocol" ], - "rank": 86, + "rank": 82, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "Mpox", @@ -17929,7 +17679,7 @@ "exact_mappings": [ "NML_LIMS:sequencing%20kit%20number" ], - "rank": 87, + "rank": 83, "slot_uri": "GENEPIO:0001455", "alias": "sequencing_kit_number", "owner": "Mpox", @@ -17940,22 +17690,25 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "dna_fragment_length": { - "name": "dna_fragment_length", - "description": "The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation.", - "title": "DNA fragment length", + "amplicon_pcr_primer_scheme": { + "name": "amplicon_pcr_primer_scheme", + "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", + "title": "amplicon pcr primer scheme", "comments": [ - "Provide the fragment length in base pairs (do not include the units)." + "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." ], "examples": [ { - "value": "400" + "value": "MPXV Sunrise 3.1" } ], "from_schema": "https://example.com/mpox", - "rank": 88, - "slot_uri": "GENEPIO:0100843", - "alias": "dna_fragment_length", + "exact_mappings": [ + "NML_LIMS:amplicon%20pcr%20primer%20scheme" + ], + "rank": 84, + "slot_uri": "GENEPIO:0001456", + "alias": "amplicon_pcr_primer_scheme", "owner": "Mpox", "domain_of": [ "Mpox", @@ -17964,106 +17717,22 @@ "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, - "genomic_target_enrichment_method": { - "name": "genomic_target_enrichment_method", - "description": "The molecular technique used to selectively capture and amplify specific regions of interest from a genome.", - "title": "genomic target enrichment method", + "amplicon_size": { + "name": "amplicon_size", + "description": "The length of the amplicon generated by PCR amplification.", + "title": "amplicon size", "comments": [ - "Provide the name of the enrichment method" + "Provide the amplicon size expressed in base pairs." ], "examples": [ { - "value": "hybrid selection method" + "value": "300bp" } ], "from_schema": "https://example.com/mpox", - "rank": 89, - "slot_uri": "GENEPIO:0100966", - "alias": "genomic_target_enrichment_method", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Sequencing", - "recommended": true, - "multivalued": true, - "any_of": [ - { - "range": "GenomicTargetEnrichmentMethodMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "genomic_target_enrichment_method_details": { - "name": "genomic_target_enrichment_method_details", - "description": "Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome.", - "title": "genomic target enrichment method details", - "comments": [ - "Provide details that are applicable to the method you used." - ], - "examples": [ - { - "value": "enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit." - } - ], - "from_schema": "https://example.com/mpox", - "rank": 90, - "slot_uri": "GENEPIO:0100967", - "alias": "genomic_target_enrichment_method_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" - }, - "amplicon_pcr_primer_scheme": { - "name": "amplicon_pcr_primer_scheme", - "description": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.", - "title": "amplicon pcr primer scheme", - "comments": [ - "Provide the name and version of the primer scheme used to generate the amplicons for sequencing." - ], - "examples": [ - { - "value": "MPXV Sunrise 3.1" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:amplicon%20pcr%20primer%20scheme" - ], - "rank": 91, - "slot_uri": "GENEPIO:0001456", - "alias": "amplicon_pcr_primer_scheme", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Sequencing", - "range": "WhitespaceMinimizedString" - }, - "amplicon_size": { - "name": "amplicon_size", - "description": "The length of the amplicon generated by PCR amplification.", - "title": "amplicon size", - "comments": [ - "Provide the amplicon size expressed in base pairs." - ], - "examples": [ - { - "value": "300bp" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 92, - "slot_uri": "GENEPIO:0001449", - "alias": "amplicon_size", + "rank": 85, + "slot_uri": "GENEPIO:0001449", + "alias": "amplicon_size", "owner": "Mpox", "domain_of": [ "Mpox", @@ -18072,142 +17741,6 @@ "slot_group": "Sequencing", "range": "integer" }, - "quality_control_method_name": { - "name": "quality_control_method_name", - "description": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.", - "title": "quality control method name", - "comments": [ - "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided." - ], - "examples": [ - { - "value": "ncov-tools" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 93, - "slot_uri": "GENEPIO:0100557", - "alias": "quality_control_method_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "quality_control_method_version": { - "name": "quality_control_method_version", - "description": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.", - "title": "quality control method version", - "comments": [ - "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon." - ], - "examples": [ - { - "value": "1.2.3" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 94, - "slot_uri": "GENEPIO:0100558", - "alias": "quality_control_method_version", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "quality_control_determination": { - "name": "quality_control_determination", - "description": "The determination of a quality control assessment.", - "title": "quality control determination", - "comments": [ - "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." - ], - "examples": [ - { - "value": "sequence failed quality control" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 95, - "slot_uri": "GENEPIO:0100559", - "alias": "quality_control_determination", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "multivalued": true, - "any_of": [ - { - "range": "QualityControlDeterminationMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "quality_control_issues": { - "name": "quality_control_issues", - "description": "The reason contributing to, or causing, a low quality determination in a quality control assessment.", - "title": "quality control issues", - "comments": [ - "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form." - ], - "examples": [ - { - "value": "low average genome coverage" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 96, - "slot_uri": "GENEPIO:0100560", - "alias": "quality_control_issues", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "multivalued": true, - "any_of": [ - { - "range": "QualityControlIssuesMenu" - }, - { - "range": "NullValueMenu" - } - ] - }, - "quality_control_details": { - "name": "quality_control_details", - "description": "The details surrounding a low quality determination in a quality control assessment.", - "title": "quality control details", - "comments": [ - "Provide notes or details regarding QC results using free text." - ], - "examples": [ - { - "value": "CT value of 39. Low viral load. Low DNA concentration after amplification." - } - ], - "from_schema": "https://example.com/mpox", - "rank": 97, - "slot_uri": "GENEPIO:0100561", - "alias": "quality_control_details", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", "description": "The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc.", @@ -18225,7 +17758,7 @@ "NML_LIMS:PH_RAW_SEQUENCE_METHOD", "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" ], - "rank": 98, + "rank": 86, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "Mpox", @@ -18254,7 +17787,7 @@ "NML_LIMS:PH_DEHOSTING_METHOD", "VirusSeq_Portal:dehosting%20method" ], - "rank": 99, + "rank": 87, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "Mpox", @@ -18266,30 +17799,6 @@ "range": "WhitespaceMinimizedString", "required": true }, - "deduplication_method": { - "name": "deduplication_method", - "description": "The method used to remove duplicated reads in a sequence read dataset.", - "title": "deduplication method", - "comments": [ - "Provide the deduplication software name followed by the version, or a link to a tool or method." - ], - "examples": [ - { - "value": "DeDup 0.12.8" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 100, - "slot_uri": "GENEPIO:0100831", - "alias": "deduplication_method", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, "consensus_sequence_name": { "name": "consensus_sequence_name", "description": "The name of the consensus sequence.", @@ -18306,591 +17815,244 @@ "exact_mappings": [ "NML_LIMS:consensus%20sequence%20name" ], - "rank": 101, + "rank": 88, "slot_uri": "GENEPIO:0001460", "alias": "consensus_sequence_name", "owner": "Mpox", "domain_of": [ - "Mpox", - "MpoxInternational" + "Mpox" ], "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "genome_sequence_file_name": { - "name": "genome_sequence_file_name", + "consensus_sequence_filename": { + "name": "consensus_sequence_filename", "description": "The name of the consensus sequence file.", - "title": "genome sequence file name", + "title": "consensus sequence filename", "comments": [ - "Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file." + "Provide the name and version number of the consensus sequence FASTA file." ], "examples": [ { - "value": "mpxvassembly.fasta" + "value": "mpox123assembly.fasta" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ "NML_LIMS:consensus%20sequence%20filename" ], - "rank": 102, - "slot_uri": "GENEPIO:0101715", - "alias": "genome_sequence_file_name", + "rank": 89, + "slot_uri": "GENEPIO:0001461", + "alias": "consensus_sequence_filename", "owner": "Mpox", "domain_of": [ - "Mpox", - "MpoxInternational" + "Mpox" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "genome_sequence_file_path": { - "name": "genome_sequence_file_path", - "description": "The filepath of the consensus sequence file.", - "title": "genome sequence file path", - "comments": [ - "Provide the filepath of the genome sequence FASTA file." - ], - "examples": [ - { - "value": "/User/Documents/ViralLab/Data/mpxvassembly.fasta" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:consensus%20sequence%20filepath" - ], - "rank": 103, - "slot_uri": "GENEPIO:0101716", - "alias": "genome_sequence_file_path", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "consensus_sequence_software_name": { - "name": "consensus_sequence_software_name", - "description": "The name of software used to generate the consensus sequence.", - "title": "consensus sequence software name", - "comments": [ - "Provide the name of the software used to generate the consensus sequence." - ], - "examples": [ - { - "value": "iVar" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Assembly%20method", - "CNPHI:consensus%20sequence", - "NML_LIMS:PH_CONSENSUS_SEQUENCE", - "VirusSeq_Portal:consensus%20sequence%20software%20name" - ], - "rank": 104, - "slot_uri": "GENEPIO:0001463", - "alias": "consensus_sequence_software_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "required": true - }, - "consensus_sequence_software_version": { - "name": "consensus_sequence_software_version", - "description": "The version of the software used to generate the consensus sequence.", - "title": "consensus sequence software version", - "comments": [ - "Provide the version of the software used to generate the consensus sequence." - ], - "examples": [ - { - "value": "1.3" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "GISAID:Assembly%20method", - "CNPHI:consensus%20sequence", - "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", - "VirusSeq_Portal:consensus%20sequence%20software%20version" - ], - "rank": 105, - "slot_uri": "GENEPIO:0001469", - "alias": "consensus_sequence_software_version", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "required": true - }, - "sequence_assembly_software_name": { - "name": "sequence_assembly_software_name", - "description": "The name of the software used to assemble a sequence.", - "title": "sequence assembly software name", - "comments": [ - "Provide the name of the software used to assemble the sequence." - ], - "examples": [ - { - "value": "SPAdes Genome Assembler, Canu, wtdbg2, velvet" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 106, - "slot_uri": "GENEPIO:0100825", - "alias": "sequence_assembly_software_name", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, - "sequence_assembly_software_version": { - "name": "sequence_assembly_software_version", - "description": "The version of the software used to assemble a sequence.", - "title": "sequence assembly software version", - "comments": [ - "Provide the version of the software used to assemble the sequence." - ], - "examples": [ - { - "value": "3.15.5" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 107, - "slot_uri": "GENEPIO:0100826", - "alias": "sequence_assembly_software_version", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "required": true, - "any_of": [ - { - "range": "WhitespaceMinimizedString" - }, - { - "range": "NullValueMenu" - } - ] - }, - "r1_fastq_filename": { - "name": "r1_fastq_filename", - "description": "The user-specified filename of the r1 FASTQ file.", - "title": "r1 fastq filename", - "comments": [ - "Provide the r1 FASTQ filename. This information aids in data management." - ], - "examples": [ - { - "value": "ABC123_S1_L001_R1_001.fastq.gz" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 108, - "slot_uri": "GENEPIO:0001476", - "alias": "r1_fastq_filename", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "r2_fastq_filename": { - "name": "r2_fastq_filename", - "description": "The user-specified filename of the r2 FASTQ file.", - "title": "r2 fastq filename", - "comments": [ - "Provide the r2 FASTQ filename. This information aids in data management." - ], - "examples": [ - { - "value": "ABC123_S1_L001_R2_001.fastq.gz" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 109, - "slot_uri": "GENEPIO:0001477", - "alias": "r2_fastq_filename", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString", - "recommended": true - }, - "r1_fastq_filepath": { - "name": "r1_fastq_filepath", - "description": "The location of the r1 FASTQ file within a user's file system.", - "title": "r1 fastq filepath", - "comments": [ - "Provide the filepath for the r1 FASTQ file. This information aids in data management." - ], - "examples": [ - { - "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 110, - "slot_uri": "GENEPIO:0001478", - "alias": "r1_fastq_filepath", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "r2_fastq_filepath": { - "name": "r2_fastq_filepath", - "description": "The location of the r2 FASTQ file within a user's file system.", - "title": "r2 fastq filepath", - "comments": [ - "Provide the filepath for the r2 FASTQ file. This information aids in data management." - ], - "examples": [ - { - "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 111, - "slot_uri": "GENEPIO:0001479", - "alias": "r2_fastq_filepath", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "fast5_filename": { - "name": "fast5_filename", - "description": "The user-specified filename of the FAST5 file.", - "title": "fast5 filename", - "comments": [ - "Provide the FAST5 filename. This information aids in data management." - ], - "examples": [ - { - "value": "mpxv123seq.fast5" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 112, - "slot_uri": "GENEPIO:0001480", - "alias": "fast5_filename", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "fast5_filepath": { - "name": "fast5_filepath", - "description": "The location of the FAST5 file within a user's file system.", - "title": "fast5 filepath", - "comments": [ - "Provide the filepath for the FAST5 file. This information aids in data management." - ], - "examples": [ - { - "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 113, - "slot_uri": "GENEPIO:0001481", - "alias": "fast5_filepath", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "number_of_total_reads": { - "name": "number_of_total_reads", - "description": "The total number of non-unique reads generated by the sequencing process.", - "title": "number of total reads", - "comments": [ - "Provide a numerical value (no need to include units)." - ], - "examples": [ - { - "value": "423867" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 114, - "slot_uri": "GENEPIO:0100827", - "alias": "number_of_total_reads", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" - }, - "number_of_unique_reads": { - "name": "number_of_unique_reads", - "description": "The number of unique reads generated by the sequencing process.", - "title": "number of unique reads", - "comments": [ - "Provide a numerical value (no need to include units)." - ], - "examples": [ - { - "value": "248236" - } - ], - "from_schema": "https://example.com/mpox", - "rank": 115, - "slot_uri": "GENEPIO:0100828", - "alias": "number_of_unique_reads", - "owner": "Mpox", - "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "WhitespaceMinimizedString" }, - "minimum_posttrimming_read_length": { - "name": "minimum_posttrimming_read_length", - "description": "The threshold used as a cut-off for the minimum length of a read after trimming.", - "title": "minimum post-trimming read length", + "consensus_sequence_filepath": { + "name": "consensus_sequence_filepath", + "description": "The filepath of the consensus sequence file.", + "title": "consensus sequence filepath", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the filepath of the consensus sequence FASTA file." ], "examples": [ { - "value": "150" + "value": "/User/Documents/STILab/Data/mpox123assembly.fasta" } ], "from_schema": "https://example.com/mpox", - "rank": 116, - "slot_uri": "GENEPIO:0100829", - "alias": "minimum_posttrimming_read_length", + "exact_mappings": [ + "NML_LIMS:consensus%20sequence%20filepath" + ], + "rank": 90, + "slot_uri": "GENEPIO:0001462", + "alias": "consensus_sequence_filepath", "owner": "Mpox", "domain_of": [ - "Mpox", - "MpoxInternational" + "Mpox" ], "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "WhitespaceMinimizedString" }, - "depth_of_coverage_value": { - "name": "depth_of_coverage_value", - "description": "The average number of reads representing a given nucleotide in the reconstructed sequence.", - "title": "depth of coverage value", + "consensus_sequence_software_name": { + "name": "consensus_sequence_software_name", + "description": "The name of software used to generate the consensus sequence.", + "title": "consensus sequence software name", "comments": [ - "Provide value as a fold of coverage." + "Provide the name of the software used to generate the consensus sequence." ], "examples": [ { - "value": "400x" + "value": "iVar" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "GISAID:Depth%20of%20coverage", - "NML_LIMS:depth%20of%20coverage%20value", - "VirusSeq_Portal:depth%20of%20coverage%20value" + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE", + "VirusSeq_Portal:consensus%20sequence%20software%20name" ], - "rank": 117, - "slot_uri": "GENEPIO:0001474", - "alias": "depth_of_coverage_value", + "rank": 91, + "slot_uri": "GENEPIO:0001463", + "alias": "consensus_sequence_software_name", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "WhitespaceMinimizedString", + "required": true }, - "depth_of_coverage_threshold": { - "name": "depth_of_coverage_threshold", - "description": "The threshold used as a cut-off for the depth of coverage.", - "title": "depth of coverage threshold", + "consensus_sequence_software_version": { + "name": "consensus_sequence_software_version", + "description": "The version of the software used to generate the consensus sequence.", + "title": "consensus sequence software version", "comments": [ - "Provide the threshold fold coverage." + "Provide the version of the software used to generate the consensus sequence." ], "examples": [ { - "value": "100x" + "value": "1.3" } ], "from_schema": "https://example.com/mpox", "exact_mappings": [ - "NML_LIMS:depth%20of%20coverage%20threshold" + "GISAID:Assembly%20method", + "CNPHI:consensus%20sequence", + "NML_LIMS:PH_CONSENSUS_SEQUENCE_VERSION", + "VirusSeq_Portal:consensus%20sequence%20software%20version" ], - "rank": 118, - "slot_uri": "GENEPIO:0001475", - "alias": "depth_of_coverage_threshold", + "rank": 92, + "slot_uri": "GENEPIO:0001469", + "alias": "consensus_sequence_software_version", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" + "range": "WhitespaceMinimizedString", + "required": true }, - "number_of_base_pairs_sequenced": { - "name": "number_of_base_pairs_sequenced", - "description": "The number of total base pairs generated by the sequencing process.", - "title": "number of base pairs sequenced", + "r1_fastq_filename": { + "name": "r1_fastq_filename", + "description": "The user-specified filename of the r1 FASTQ file.", + "title": "r1 fastq filename", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the r1 FASTQ filename. This information aids in data management." ], "examples": [ { - "value": "2639019" + "value": "ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:number%20of%20base%20pairs%20sequenced" - ], - "rank": 119, - "slot_uri": "GENEPIO:0001482", - "alias": "number_of_base_pairs_sequenced", + "rank": 93, + "slot_uri": "GENEPIO:0001476", + "alias": "r1_fastq_filename", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer", - "minimum_value": 0 + "range": "WhitespaceMinimizedString", + "recommended": true }, - "consensus_genome_length": { - "name": "consensus_genome_length", - "description": "Size of the reconstructed genome described as the number of base pairs.", - "title": "consensus genome length", + "r2_fastq_filename": { + "name": "r2_fastq_filename", + "description": "The user-specified filename of the r2 FASTQ file.", + "title": "r2 fastq filename", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the r2 FASTQ filename. This information aids in data management." ], "examples": [ { - "value": "197063" + "value": "ABC123_S1_L001_R2_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:consensus%20genome%20length" - ], - "rank": 120, - "slot_uri": "GENEPIO:0001483", - "alias": "consensus_genome_length", + "rank": 94, + "slot_uri": "GENEPIO:0001477", + "alias": "r2_fastq_filename", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "integer", - "minimum_value": 0 + "range": "WhitespaceMinimizedString", + "recommended": true }, - "sequence_assembly_length": { - "name": "sequence_assembly_length", - "description": "The length of the genome generated by assembling reads using a scaffold or by reference-based mapping.", - "title": "sequence assembly length", + "r1_fastq_filepath": { + "name": "r1_fastq_filepath", + "description": "The location of the r1 FASTQ file within a user's file system.", + "title": "r1 fastq filepath", "comments": [ - "Provide a numerical value (no need to include units)." + "Provide the filepath for the r1 FASTQ file. This information aids in data management." ], "examples": [ { - "value": "34272" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "rank": 121, - "slot_uri": "GENEPIO:0100846", - "alias": "sequence_assembly_length", + "rank": 95, + "slot_uri": "GENEPIO:0001478", + "alias": "r1_fastq_filepath", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "WhitespaceMinimizedString" }, - "number_of_contigs": { - "name": "number_of_contigs", - "description": "The number of contigs (contiguous sequences) in a sequence assembly.", - "title": "number of contigs", + "r2_fastq_filepath": { + "name": "r2_fastq_filepath", + "description": "The location of the r2 FASTQ file within a user's file system.", + "title": "r2 fastq filepath", "comments": [ - "Provide a numerical value." + "Provide the filepath for the r2 FASTQ file. This information aids in data management." ], "examples": [ { - "value": "10" + "value": "/User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz" } ], "from_schema": "https://example.com/mpox", - "rank": 122, - "slot_uri": "GENEPIO:0100937", - "alias": "number_of_contigs", + "rank": 96, + "slot_uri": "GENEPIO:0001479", + "alias": "r2_fastq_filepath", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "WhitespaceMinimizedString" }, - "genome_completeness": { - "name": "genome_completeness", - "description": "The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data.", - "title": "genome completeness", + "fast5_filename": { + "name": "fast5_filename", + "description": "The user-specified filename of the FAST5 file.", + "title": "fast5 filename", "comments": [ - "Provide the genome completeness as a percent (no need to include units)." + "Provide the FAST5 filename. This information aids in data management." ], "examples": [ { - "value": "85" + "value": "mpxv123seq.fast5" } ], "from_schema": "https://example.com/mpox", - "rank": 123, - "slot_uri": "GENEPIO:0100844", - "alias": "genome_completeness", + "rank": 97, + "slot_uri": "GENEPIO:0001480", + "alias": "fast5_filename", "owner": "Mpox", "domain_of": [ "Mpox", @@ -18899,77 +18061,85 @@ "slot_group": "Bioinformatics and QC metrics", "range": "WhitespaceMinimizedString" }, - "n50": { - "name": "n50", - "description": "The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences.", - "title": "N50", + "fast5_filepath": { + "name": "fast5_filepath", + "description": "The location of the FAST5 file within a user's file system.", + "title": "fast5 filepath", "comments": [ - "Provide the N50 value in Mb." + "Provide the filepath for the FAST5 file. This information aids in data management." ], "examples": [ { - "value": "150" + "value": "/User/Documents/RespLab/Data/mpxv123seq.fast5" } ], "from_schema": "https://example.com/mpox", - "rank": 124, - "slot_uri": "GENEPIO:0100938", - "alias": "n50", + "rank": 98, + "slot_uri": "GENEPIO:0001481", + "alias": "fast5_filepath", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "WhitespaceMinimizedString" }, - "percent_ns_across_total_genome_length": { - "name": "percent_ns_across_total_genome_length", - "description": "The percentage of the assembly that consists of ambiguous bases (Ns).", - "title": "percent Ns across total genome length", + "number_of_base_pairs_sequenced": { + "name": "number_of_base_pairs_sequenced", + "description": "The number of total base pairs generated by the sequencing process.", + "title": "number of base pairs sequenced", "comments": [ "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "2" + "value": "2639019" } ], "from_schema": "https://example.com/mpox", - "rank": 125, - "slot_uri": "GENEPIO:0100830", - "alias": "percent_ns_across_total_genome_length", + "exact_mappings": [ + "NML_LIMS:number%20of%20base%20pairs%20sequenced" + ], + "rank": 99, + "slot_uri": "GENEPIO:0001482", + "alias": "number_of_base_pairs_sequenced", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "integer", + "minimum_value": 0 }, - "ns_per_100_kbp": { - "name": "ns_per_100_kbp", - "description": "The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp).", - "title": "Ns per 100 kbp", + "consensus_genome_length": { + "name": "consensus_genome_length", + "description": "Size of the reconstructed genome described as the number of base pairs.", + "title": "consensus genome length", "comments": [ "Provide a numerical value (no need to include units)." ], "examples": [ { - "value": "342" + "value": "197063" } ], "from_schema": "https://example.com/mpox", - "rank": 126, - "slot_uri": "GENEPIO:0001484", - "alias": "ns_per_100_kbp", + "exact_mappings": [ + "NML_LIMS:consensus%20genome%20length" + ], + "rank": 100, + "slot_uri": "GENEPIO:0001483", + "alias": "consensus_genome_length", "owner": "Mpox", "domain_of": [ "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", - "range": "Integer" + "range": "integer", + "minimum_value": 0 }, "reference_genome_accession": { "name": "reference_genome_accession", @@ -18987,7 +18157,7 @@ "exact_mappings": [ "NML_LIMS:reference%20genome%20accession" ], - "rank": 127, + "rank": 101, "slot_uri": "GENEPIO:0001485", "alias": "reference_genome_accession", "owner": "Mpox", @@ -19016,7 +18186,7 @@ "NML_LIMS:PH_BIOINFORMATICS_PROTOCOL", "VirusSeq_Portal:bioinformatics%20protocol" ], - "rank": 128, + "rank": 102, "slot_uri": "GENEPIO:0001489", "alias": "bioinformatics_protocol", "owner": "Mpox", @@ -19047,7 +18217,7 @@ "BIOSAMPLE:gene_name_1", "VirusSeq_Portal:gene%20name" ], - "rank": 129, + "rank": 103, "slot_uri": "GENEPIO:0001507", "alias": "gene_name_1", "owner": "Mpox", @@ -19083,7 +18253,7 @@ "BIOSAMPLE:diagnostic_PCR_CT_value_1", "VirusSeq_Portal:diagnostic%20pcr%20Ct%20value" ], - "rank": 130, + "rank": 104, "slot_uri": "GENEPIO:0001509", "alias": "diagnostic_pcr_ct_value_1", "owner": "Mpox", @@ -19119,7 +18289,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232", "BIOSAMPLE:gene_name_2" ], - "rank": 131, + "rank": 105, "slot_uri": "GENEPIO:0001510", "alias": "gene_name_2", "owner": "Mpox", @@ -19154,7 +18324,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%232%20CT%20Value", "BIOSAMPLE:diagnostic_PCR_CT_value_2" ], - "rank": 132, + "rank": 106, "slot_uri": "GENEPIO:0001512", "alias": "diagnostic_pcr_ct_value_2", "owner": "Mpox", @@ -19190,7 +18360,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233", "BIOSAMPLE:gene_name_3" ], - "rank": 133, + "rank": 107, "slot_uri": "GENEPIO:0001513", "alias": "gene_name_3", "owner": "Mpox", @@ -19225,7 +18395,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%233%20CT%20Value", "BIOSAMPLE:diagnostic_PCR_CT_value_3" ], - "rank": 134, + "rank": 108, "slot_uri": "GENEPIO:0001515", "alias": "diagnostic_pcr_ct_value_3", "owner": "Mpox", @@ -19261,7 +18431,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234", "BIOSAMPLE:gene_name_4" ], - "rank": 135, + "rank": 109, "slot_uri": "GENEPIO:0100576", "alias": "gene_name_4", "owner": "Mpox", @@ -19296,7 +18466,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%234%20CT%20Value", "BIOSAMPLE:diagnostic_PCR_CT_value_4" ], - "rank": 136, + "rank": 110, "slot_uri": "GENEPIO:0100577", "alias": "diagnostic_pcr_ct_value_4", "owner": "Mpox", @@ -19331,7 +18501,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235", "BIOSAMPLE:gene_name_5" ], - "rank": 137, + "rank": 111, "slot_uri": "GENEPIO:0100578", "alias": "gene_name_5", "owner": "Mpox", @@ -19366,7 +18536,7 @@ "NML_LIMS:SUBMITTED_RESLT%20-%20Gene%20Target%20%235%20CT%20Value", "BIOSAMPLE:diagnostic_PCR_CT_value_5" ], - "rank": 138, + "rank": 112, "slot_uri": "GENEPIO:0100579", "alias": "diagnostic_pcr_ct_value_5", "owner": "Mpox", @@ -19401,7 +18571,7 @@ "CNPHI:Authors", "NML_LIMS:PH_SEQUENCING_AUTHORS" ], - "rank": 139, + "rank": 113, "slot_uri": "GENEPIO:0001517", "alias": "authors", "owner": "Mpox", @@ -19430,7 +18600,7 @@ "CNPHI:Additional%20Comments", "NML_LIMS:HC_COMMENTS" ], - "rank": 140, + "rank": 114, "slot_uri": "GENEPIO:0001518", "alias": "dataharmonizer_provenance", "owner": "Mpox", @@ -20293,7 +19463,7 @@ "sequencing_project_name": { "name": "sequencing_project_name", "rank": 73, - "slot_group": "Sequence information" + "slot_group": "Sequencing" }, "sequenced_by": { "name": "sequenced_by", @@ -20314,19 +19484,24 @@ } ] }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "rank": 75, + "slot_group": "Sequencing" + }, "sequenced_by_contact_name": { "name": "sequenced_by_contact_name", - "rank": 75, - "slot_group": "Sequence information" + "rank": 76, + "slot_group": "Sequencing" }, "sequenced_by_contact_email": { "name": "sequenced_by_contact_email", - "rank": 76, + "rank": 77, "slot_group": "Sequencing" }, "sequenced_by_contact_address": { "name": "sequenced_by_contact_address", - "rank": 77, + "rank": 78, "slot_group": "Sequencing" }, "sequence_submitted_by": { @@ -20335,7 +19510,7 @@ "GISAID:Submitting%20lab", "BIOSAMPLE:sequence_submitted_by" ], - "rank": 78, + "rank": 79, "slot_group": "Sequencing", "any_of": [ { @@ -20348,12 +19523,12 @@ }, "sequence_submitter_contact_email": { "name": "sequence_submitter_contact_email", - "rank": 79, + "rank": 80, "slot_group": "Sequencing" }, "sequence_submitter_contact_address": { "name": "sequence_submitter_contact_address", - "rank": 80, + "rank": 81, "slot_group": "Sequencing" }, "purpose_of_sequencing": { @@ -20363,7 +19538,7 @@ "value": "Baseline surveillance (random sampling) [GENEPIO:0100005]" } ], - "rank": 81, + "rank": 82, "slot_group": "Sequencing", "any_of": [ { @@ -20376,34 +19551,28 @@ }, "purpose_of_sequencing_details": { "name": "purpose_of_sequencing_details", - "rank": 82, + "rank": 83, "slot_group": "Sequencing" }, "sequencing_date": { "name": "sequencing_date", - "rank": 83, + "rank": 84, "slot_group": "Sequencing" }, "library_id": { "name": "library_id", - "rank": 84, + "rank": 85, "slot_group": "Sequencing" }, "library_preparation_kit": { "name": "library_preparation_kit", - "rank": 85, + "rank": 86, "slot_group": "Sequencing" }, "sequencing_assay_type": { "name": "sequencing_assay_type", - "examples": [ - { - "value": "whole genome sequencing assay [OBI:0002117]" - } - ], - "rank": 86, - "slot_group": "Sequence information", - "range": "SequencingAssayTypeInternationalMenu" + "rank": 87, + "slot_group": "Sequencing" }, "sequencing_instrument": { "name": "sequencing_instrument", @@ -20412,7 +19581,7 @@ "value": "Oxford Nanopore MinION [GENEPIO:0100142]" } ], - "rank": 87, + "rank": 88, "slot_group": "Sequencing", "any_of": [ { @@ -20425,96 +19594,81 @@ }, "sequencing_flow_cell_version": { "name": "sequencing_flow_cell_version", - "rank": 88, - "slot_group": "Sequence information" + "rank": 89, + "slot_group": "Sequencing" }, "sequencing_protocol": { "name": "sequencing_protocol", - "rank": 89, + "rank": 90, "slot_group": "Sequencing" }, "sequencing_kit_number": { "name": "sequencing_kit_number", - "rank": 90, + "rank": 91, "slot_group": "Sequencing" }, "dna_fragment_length": { "name": "dna_fragment_length", - "rank": 91, + "rank": 92, "slot_group": "Sequencing" }, "genomic_target_enrichment_method": { "name": "genomic_target_enrichment_method", - "rank": 92, - "slot_group": "Sequencing", - "any_of": [ - { - "range": "GenomicTargetEnrichmentMethodInternationalMenu" - }, - { - "range": "NullValueMenu" - } - ] + "rank": 93, + "slot_group": "Sequencing" }, "genomic_target_enrichment_method_details": { "name": "genomic_target_enrichment_method_details", - "rank": 93, + "rank": 94, "slot_group": "Sequencing" }, "amplicon_pcr_primer_scheme": { "name": "amplicon_pcr_primer_scheme", - "rank": 94, + "rank": 95, "slot_group": "Sequencing" }, "amplicon_size": { "name": "amplicon_size", - "rank": 95, + "rank": 96, "slot_group": "Sequencing" }, "quality_control_method_name": { "name": "quality_control_method_name", - "rank": 96, + "rank": 97, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_method_version": { "name": "quality_control_method_version", - "rank": 97, + "rank": 98, "slot_group": "Bioinformatics and QC metrics" }, "quality_control_determination": { "name": "quality_control_determination", - "rank": 98, - "slot_group": "Bioinformatics and QC metrics", - "range": "QualityControlDeterminationInternationalMenu" + "rank": 99, + "slot_group": "Bioinformatics and QC metrics" }, "quality_control_issues": { "name": "quality_control_issues", - "rank": 99, - "slot_group": "Bioinformatics and QC metrics", - "range": "QualityControlIssuesInternationalMenu" + "rank": 100, + "slot_group": "Bioinformatics and QC metrics" }, "quality_control_details": { "name": "quality_control_details", - "rank": 100, + "rank": 101, "slot_group": "Bioinformatics and QC metrics" }, "raw_sequence_data_processing_method": { "name": "raw_sequence_data_processing_method", - "rank": 101, + "rank": 102, "slot_group": "Bioinformatics and QC metrics" }, "dehosting_method": { "name": "dehosting_method", - "rank": 102, + "rank": 103, "slot_group": "Bioinformatics and QC metrics" }, "deduplication_method": { "name": "deduplication_method", - "rank": 103, - "slot_group": "Bioinformatics and QC metrics" - }, - "consensus_sequence_name": { - "name": "consensus_sequence_name", "rank": 104, "slot_group": "Bioinformatics and QC metrics" }, @@ -23185,10 +22339,9 @@ "alias": "sequencing_project_name", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], - "slot_group": "Sequence information", + "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, "sequenced_by": { @@ -23226,6 +22379,36 @@ } ] }, + "sequenced_by_laboratory_name": { + "name": "sequenced_by_laboratory_name", + "description": "The specific laboratory affiliation of the responsible for sequencing the isolate's genome.", + "title": "sequenced by laboratory name", + "comments": [ + "Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value." + ], + "examples": [ + { + "value": "Topp Lab" + } + ], + "from_schema": "https://example.com/mpox", + "rank": 75, + "slot_uri": "GENEPIO:0100470", + "alias": "sequenced_by_laboratory_name", + "owner": "MpoxInternational", + "domain_of": [ + "MpoxInternational" + ], + "slot_group": "Sequencing", + "any_of": [ + { + "range": "WhitespaceMinimizedString" + }, + { + "range": "NullValueMenu" + } + ] + }, "sequenced_by_contact_name": { "name": "sequenced_by_contact_name", "description": "The name or title of the contact responsible for follow-up regarding the sequence.", @@ -23239,14 +22422,14 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 75, + "rank": 76, "slot_uri": "GENEPIO:0100471", "alias": "sequenced_by_contact_name", "owner": "MpoxInternational", "domain_of": [ "MpoxInternational" ], - "slot_group": "Sequence information", + "slot_group": "Sequencing", "required": true, "any_of": [ { @@ -23273,7 +22456,7 @@ "exact_mappings": [ "NML_LIMS:sequenced%20by%20contact%20email" ], - "rank": 76, + "rank": 77, "slot_uri": "GENEPIO:0100422", "alias": "sequenced_by_contact_email", "owner": "MpoxInternational", @@ -23297,7 +22480,7 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 77, + "rank": 78, "slot_uri": "GENEPIO:0100423", "alias": "sequenced_by_contact_address", "owner": "MpoxInternational", @@ -23325,7 +22508,7 @@ "GISAID:Submitting%20lab", "BIOSAMPLE:sequence_submitted_by" ], - "rank": 78, + "rank": 79, "slot_uri": "GENEPIO:0001159", "alias": "sequence_submitted_by", "owner": "MpoxInternational", @@ -23360,7 +22543,7 @@ "exact_mappings": [ "NML_LIMS:sequence%20submitter%20contact%20email" ], - "rank": 79, + "rank": 80, "slot_uri": "GENEPIO:0001165", "alias": "sequence_submitter_contact_email", "owner": "MpoxInternational", @@ -23387,7 +22570,7 @@ "exact_mappings": [ "NML_LIMS:sequence%20submitter%20contact%20address" ], - "rank": 80, + "rank": 81, "slot_uri": "GENEPIO:0001167", "alias": "sequence_submitter_contact_address", "owner": "MpoxInternational", @@ -23418,7 +22601,7 @@ "BIOSAMPLE:purpose_of_sequencing", "VirusSeq_Portal:purpose%20of%20sequencing" ], - "rank": 81, + "rank": 82, "slot_uri": "GENEPIO:0001445", "alias": "purpose_of_sequencing", "owner": "MpoxInternational", @@ -23456,7 +22639,7 @@ "NML_LIMS:PH_REASON_FOR_SEQUENCING_DETAILS", "VirusSeq_Portal:purpose%20of%20sequencing%20details" ], - "rank": 82, + "rank": 83, "slot_uri": "GENEPIO:0001446", "alias": "purpose_of_sequencing_details", "owner": "MpoxInternational", @@ -23495,7 +22678,7 @@ "exact_mappings": [ "NML_LIMS:PH_SEQUENCING_DATE" ], - "rank": 83, + "rank": 84, "slot_uri": "GENEPIO:0001447", "alias": "sequencing_date", "owner": "MpoxInternational", @@ -23529,7 +22712,7 @@ "exact_mappings": [ "NML_LIMS:library%20ID" ], - "rank": 84, + "rank": 85, "slot_uri": "GENEPIO:0001448", "alias": "library_id", "owner": "MpoxInternational", @@ -23557,7 +22740,7 @@ "exact_mappings": [ "NML_LIMS:PH_LIBRARY_PREP_KIT" ], - "rank": 85, + "rank": 86, "slot_uri": "GENEPIO:0001450", "alias": "library_preparation_kit", "owner": "MpoxInternational", @@ -23581,15 +22764,14 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 86, + "rank": 87, "slot_uri": "GENEPIO:0100997", "alias": "sequencing_assay_type", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], - "slot_group": "Sequence information", + "slot_group": "Sequencing", "range": "SequencingAssayTypeInternationalMenu" }, "sequencing_instrument": { @@ -23611,7 +22793,7 @@ "NML_LIMS:PH_SEQUENCING_INSTRUMENT", "VirusSeq_Portal:sequencing%20instrument" ], - "rank": 87, + "rank": 88, "slot_uri": "GENEPIO:0001452", "alias": "sequencing_instrument", "owner": "MpoxInternational", @@ -23644,15 +22826,14 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 88, + "rank": 89, "slot_uri": "GENEPIO:0101102", "alias": "sequencing_flow_cell_version", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], - "slot_group": "Sequence information", + "slot_group": "Sequencing", "range": "WhitespaceMinimizedString" }, "sequencing_protocol": { @@ -23672,7 +22853,7 @@ "NML_LIMS:PH_TESTING_PROTOCOL", "VirusSeq_Portal:sequencing%20protocol" ], - "rank": 89, + "rank": 90, "slot_uri": "GENEPIO:0001454", "alias": "sequencing_protocol", "owner": "MpoxInternational", @@ -23699,7 +22880,7 @@ "exact_mappings": [ "NML_LIMS:sequencing%20kit%20number" ], - "rank": 90, + "rank": 91, "slot_uri": "GENEPIO:0001455", "alias": "sequencing_kit_number", "owner": "MpoxInternational", @@ -23723,12 +22904,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 91, + "rank": 92, "slot_uri": "GENEPIO:0100843", "alias": "dna_fragment_length", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Sequencing", @@ -23747,12 +22927,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 92, + "rank": 93, "slot_uri": "GENEPIO:0100966", "alias": "genomic_target_enrichment_method", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Sequencing", @@ -23780,12 +22959,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 93, + "rank": 94, "slot_uri": "GENEPIO:0100967", "alias": "genomic_target_enrichment_method_details", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Sequencing", @@ -23807,7 +22985,7 @@ "exact_mappings": [ "NML_LIMS:amplicon%20pcr%20primer%20scheme" ], - "rank": 94, + "rank": 95, "slot_uri": "GENEPIO:0001456", "alias": "amplicon_pcr_primer_scheme", "owner": "MpoxInternational", @@ -23831,7 +23009,7 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 95, + "rank": 96, "slot_uri": "GENEPIO:0001449", "alias": "amplicon_size", "owner": "MpoxInternational", @@ -23855,12 +23033,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 96, + "rank": 97, "slot_uri": "GENEPIO:0100557", "alias": "quality_control_method_name", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -23879,12 +23056,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 97, + "rank": 98, "slot_uri": "GENEPIO:0100558", "alias": "quality_control_method_version", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -23894,12 +23070,11 @@ "name": "quality_control_determination", "title": "quality control determination", "from_schema": "https://example.com/mpox", - "rank": 98, + "rank": 99, "slot_uri": "GENEPIO:0100559", "alias": "quality_control_determination", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -23909,12 +23084,11 @@ "name": "quality_control_issues", "title": "quality control issues", "from_schema": "https://example.com/mpox", - "rank": 99, + "rank": 100, "slot_uri": "GENEPIO:0100560", "alias": "quality_control_issues", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -23933,12 +23107,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 100, + "rank": 101, "slot_uri": "GENEPIO:0100561", "alias": "quality_control_details", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -23961,7 +23134,7 @@ "NML_LIMS:PH_RAW_SEQUENCE_METHOD", "VirusSeq_Portal:raw%20sequence%20data%20processing%20method" ], - "rank": 101, + "rank": 102, "slot_uri": "GENEPIO:0001458", "alias": "raw_sequence_data_processing_method", "owner": "MpoxInternational", @@ -23989,7 +23162,7 @@ "NML_LIMS:PH_DEHOSTING_METHOD", "VirusSeq_Portal:dehosting%20method" ], - "rank": 102, + "rank": 103, "slot_uri": "GENEPIO:0001459", "alias": "dehosting_method", "owner": "MpoxInternational", @@ -24013,39 +23186,11 @@ } ], "from_schema": "https://example.com/mpox", - "rank": 103, + "rank": 104, "slot_uri": "GENEPIO:0100831", "alias": "deduplication_method", "owner": "MpoxInternational", "domain_of": [ - "Mpox", - "MpoxInternational" - ], - "slot_group": "Bioinformatics and QC metrics", - "range": "WhitespaceMinimizedString" - }, - "consensus_sequence_name": { - "name": "consensus_sequence_name", - "description": "The name of the consensus sequence.", - "title": "consensus sequence name", - "comments": [ - "Provide the name and version number of the consensus sequence." - ], - "examples": [ - { - "value": "mpxvassembly3" - } - ], - "from_schema": "https://example.com/mpox", - "exact_mappings": [ - "NML_LIMS:consensus%20sequence%20name" - ], - "rank": 104, - "slot_uri": "GENEPIO:0001460", - "alias": "consensus_sequence_name", - "owner": "MpoxInternational", - "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24072,7 +23217,6 @@ "alias": "genome_sequence_file_name", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24099,7 +23243,6 @@ "alias": "genome_sequence_file_path", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24185,7 +23328,6 @@ "alias": "sequence_assembly_software_name", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24217,7 +23359,6 @@ "alias": "sequence_assembly_software_version", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24395,7 +23536,6 @@ "alias": "number_of_total_reads", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24419,7 +23559,6 @@ "alias": "number_of_unique_reads", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24443,7 +23582,6 @@ "alias": "minimum_posttrimming_read_length", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24472,7 +23610,6 @@ "alias": "depth_of_coverage_value", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24499,7 +23636,6 @@ "alias": "depth_of_coverage_threshold", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24579,7 +23715,6 @@ "alias": "sequence_assembly_length", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24603,7 +23738,6 @@ "alias": "number_of_contigs", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24627,7 +23761,6 @@ "alias": "genome_completeness", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24651,7 +23784,6 @@ "alias": "n50", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24675,7 +23807,6 @@ "alias": "percent_ns_across_total_genome_length", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", @@ -24699,7 +23830,6 @@ "alias": "ns_per_100_kbp", "owner": "MpoxInternational", "domain_of": [ - "Mpox", "MpoxInternational" ], "slot_group": "Bioinformatics and QC metrics", diff --git a/web/templates/mpox/schema.yaml b/web/templates/mpox/schema.yaml index 80e6d704..da3f8554 100644 --- a/web/templates/mpox/schema.yaml +++ b/web/templates/mpox/schema.yaml @@ -89,9 +89,7 @@ classes: - prior_mpox_infection_date - prior_mpox_antiviral_treatment - prior_antiviral_treatment_during_prior_mpox_infection - - sequencing_project_name - sequenced_by - - sequenced_by_laboratory_name - sequenced_by_contact_email - sequenced_by_contact_address - sequence_submitted_by @@ -102,50 +100,26 @@ classes: - sequencing_date - library_id - library_preparation_kit - - sequencing_assay_type - sequencing_instrument - - sequencing_flow_cell_version - sequencing_protocol - sequencing_kit_number - - dna_fragment_length - - genomic_target_enrichment_method - - genomic_target_enrichment_method_details - amplicon_pcr_primer_scheme - amplicon_size - - quality_control_method_name - - quality_control_method_version - - quality_control_determination - - quality_control_issues - - quality_control_details - raw_sequence_data_processing_method - dehosting_method - - deduplication_method - consensus_sequence_name - - genome_sequence_file_name - - genome_sequence_file_path + - consensus_sequence_filename + - consensus_sequence_filepath - consensus_sequence_software_name - consensus_sequence_software_version - - sequence_assembly_software_name - - sequence_assembly_software_version - r1_fastq_filename - r2_fastq_filename - r1_fastq_filepath - r2_fastq_filepath - fast5_filename - fast5_filepath - - number_of_total_reads - - number_of_unique_reads - - minimum_posttrimming_read_length - - depth_of_coverage_value - - depth_of_coverage_threshold - number_of_base_pairs_sequenced - consensus_genome_length - - sequence_assembly_length - - number_of_contigs - - genome_completeness - - n50 - - percent_ns_across_total_genome_length - - ns_per_100_kbp - reference_genome_accession - bioinformatics_protocol - gene_name_1 @@ -611,11 +585,8 @@ classes: prior_antiviral_treatment_during_prior_mpox_infection: rank: 69 slot_group: Host reinfection information - sequencing_project_name: - rank: 70 - slot_group: Sequence information sequenced_by: - rank: 71 + rank: 70 slot_group: Sequencing comments: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting @@ -627,17 +598,14 @@ classes: exact_mappings: - NML_LIMS:PH_SEQUENCING_CENTRE - BIOSAMPLE:sequenced_by - sequenced_by_laboratory_name: - rank: 72 - slot_group: Sequence information sequenced_by_contact_email: - rank: 73 + rank: 71 slot_group: Sequencing sequenced_by_contact_address: - rank: 74 + rank: 72 slot_group: Sequencing sequence_submitted_by: - rank: 75 + rank: 73 slot_group: Sequencing any_of: - range: SequenceSubmittedByMenu @@ -649,13 +617,13 @@ classes: - BIOSAMPLE:sequence_submitted_by - VirusSeq_Portal:sequence%20submitted%20by sequence_submitter_contact_email: - rank: 76 + rank: 74 slot_group: Sequencing sequence_submitter_contact_address: - rank: 77 + rank: 75 slot_group: Sequencing purpose_of_sequencing: - rank: 78 + rank: 76 slot_group: Sequencing examples: - description: Select "Targeted surveillance (non-random sampling)" if the @@ -681,226 +649,127 @@ classes: - range: PurposeOfSequencingMenu - range: NullValueMenu purpose_of_sequencing_details: - rank: 79 + rank: 77 slot_group: Sequencing sequencing_date: - rank: 80 + rank: 78 slot_group: Sequencing required: true library_id: - rank: 81 + rank: 79 slot_group: Sequencing library_preparation_kit: - rank: 82 + rank: 80 slot_group: Sequencing - sequencing_assay_type: - rank: 83 - slot_group: Sequence information - range: SequencingAssayTypeMenu - examples: - - value: whole genome sequencing assay sequencing_instrument: - rank: 84 + rank: 81 slot_group: Sequencing examples: - value: Oxford Nanopore MinION any_of: - range: SequencingInstrumentMenu - range: NullValueMenu - sequencing_flow_cell_version: - rank: 85 - slot_group: Sequence information sequencing_protocol: - rank: 86 + rank: 82 slot_group: Sequencing sequencing_kit_number: - rank: 87 - slot_group: Sequencing - dna_fragment_length: - rank: 88 - slot_group: Sequencing - genomic_target_enrichment_method: - rank: 89 - slot_group: Sequencing - any_of: - - range: GenomicTargetEnrichmentMethodMenu - - range: NullValueMenu - genomic_target_enrichment_method_details: - rank: 90 + rank: 83 slot_group: Sequencing amplicon_pcr_primer_scheme: - rank: 91 + rank: 84 slot_group: Sequencing amplicon_size: - rank: 92 + rank: 85 slot_group: Sequencing - quality_control_method_name: - rank: 93 - slot_group: Bioinformatics and QC metrics - quality_control_method_version: - rank: 94 - slot_group: Bioinformatics and QC metrics - quality_control_determination: - rank: 95 - slot_group: Bioinformatics and QC metrics - multivalued: true - description: The determination of a quality control assessment. - comments: Select a value from the pick list provided. If a desired value is - missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker - using the New Term Request form. - examples: - - value: sequence failed quality control - any_of: - - range: QualityControlDeterminationMenu - - range: NullValueMenu - quality_control_issues: - rank: 96 - slot_group: Bioinformatics and QC metrics - multivalued: true - description: The reason contributing to, or causing, a low quality determination - in a quality control assessment. - comments: Select a value from the pick list provided. If a desired value is - missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker - using the New Term Request form. - examples: - - value: low average genome coverage - any_of: - - range: QualityControlIssuesMenu - - range: NullValueMenu - quality_control_details: - rank: 97 - slot_group: Bioinformatics and QC metrics raw_sequence_data_processing_method: - rank: 98 + rank: 86 slot_group: Bioinformatics and QC metrics required: true dehosting_method: - rank: 99 + rank: 87 slot_group: Bioinformatics and QC metrics required: true - deduplication_method: - rank: 100 - slot_group: Bioinformatics and QC metrics consensus_sequence_name: - rank: 101 + rank: 88 slot_group: Bioinformatics and QC metrics - genome_sequence_file_name: - rank: 102 + consensus_sequence_filename: + rank: 89 slot_group: Bioinformatics and QC metrics - genome_sequence_file_path: - rank: 103 + consensus_sequence_filepath: + rank: 90 slot_group: Bioinformatics and QC metrics consensus_sequence_software_name: - rank: 104 + rank: 91 slot_group: Bioinformatics and QC metrics consensus_sequence_software_version: - rank: 105 - slot_group: Bioinformatics and QC metrics - sequence_assembly_software_name: - rank: 106 - slot_group: Bioinformatics and QC metrics - sequence_assembly_software_version: - rank: 107 + rank: 92 slot_group: Bioinformatics and QC metrics r1_fastq_filename: - rank: 108 + rank: 93 slot_group: Bioinformatics and QC metrics r2_fastq_filename: - rank: 109 + rank: 94 slot_group: Bioinformatics and QC metrics r1_fastq_filepath: - rank: 110 + rank: 95 slot_group: Bioinformatics and QC metrics r2_fastq_filepath: - rank: 111 + rank: 96 slot_group: Bioinformatics and QC metrics fast5_filename: - rank: 112 + rank: 97 slot_group: Bioinformatics and QC metrics fast5_filepath: - rank: 113 - slot_group: Bioinformatics and QC metrics - number_of_total_reads: - rank: 114 - slot_group: Bioinformatics and QC metrics - number_of_unique_reads: - rank: 115 - slot_group: Bioinformatics and QC metrics - minimum_posttrimming_read_length: - rank: 116 - slot_group: Bioinformatics and QC metrics - depth_of_coverage_value: - rank: 117 - slot_group: Bioinformatics and QC metrics - depth_of_coverage_threshold: - rank: 118 + rank: 98 slot_group: Bioinformatics and QC metrics number_of_base_pairs_sequenced: - rank: 119 + rank: 99 slot_group: Bioinformatics and QC metrics consensus_genome_length: - rank: 120 - slot_group: Bioinformatics and QC metrics - sequence_assembly_length: - rank: 121 - slot_group: Bioinformatics and QC metrics - number_of_contigs: - rank: 122 - slot_group: Bioinformatics and QC metrics - genome_completeness: - rank: 123 - slot_group: Bioinformatics and QC metrics - n50: - rank: 124 - slot_group: Bioinformatics and QC metrics - percent_ns_across_total_genome_length: - rank: 125 - slot_group: Bioinformatics and QC metrics - ns_per_100_kbp: - rank: 126 + rank: 100 slot_group: Bioinformatics and QC metrics reference_genome_accession: - rank: 127 + rank: 101 slot_group: Bioinformatics and QC metrics bioinformatics_protocol: - rank: 128 + rank: 102 slot_group: Bioinformatics and QC metrics required: true gene_name_1: - rank: 129 + rank: 103 slot_group: Pathogen diagnostic testing diagnostic_pcr_ct_value_1: - rank: 130 + rank: 104 slot_group: Pathogen diagnostic testing gene_name_2: - rank: 131 + rank: 105 slot_group: Pathogen diagnostic testing diagnostic_pcr_ct_value_2: - rank: 132 + rank: 106 slot_group: Pathogen diagnostic testing gene_name_3: - rank: 133 + rank: 107 slot_group: Pathogen diagnostic testing diagnostic_pcr_ct_value_3: - rank: 134 + rank: 108 slot_group: Pathogen diagnostic testing gene_name_4: - rank: 135 + rank: 109 slot_group: Pathogen diagnostic testing diagnostic_pcr_ct_value_4: - rank: 136 + rank: 110 slot_group: Pathogen diagnostic testing gene_name_5: - rank: 137 + rank: 111 slot_group: Pathogen diagnostic testing diagnostic_pcr_ct_value_5: - rank: 138 + rank: 112 slot_group: Pathogen diagnostic testing authors: - rank: 139 + rank: 113 slot_group: Contributor acknowledgement dataharmonizer_provenance: - rank: 140 + rank: 114 slot_group: Contributor acknowledgement MpoxInternational: name: MpoxInternational @@ -985,6 +854,7 @@ classes: - prior_antiviral_treatment_during_prior_mpox_infection - sequencing_project_name - sequenced_by + - sequenced_by_laboratory_name - sequenced_by_contact_name - sequenced_by_contact_email - sequenced_by_contact_address @@ -1014,7 +884,6 @@ classes: - raw_sequence_data_processing_method - dehosting_method - deduplication_method - - consensus_sequence_name - genome_sequence_file_name - genome_sequence_file_path - consensus_sequence_software_name @@ -1494,7 +1363,7 @@ classes: slot_group: Host reinfection information sequencing_project_name: rank: 73 - slot_group: Sequence information + slot_group: Sequencing sequenced_by: rank: 74 slot_group: Sequencing @@ -1505,18 +1374,21 @@ classes: - range: NullValueMenu exact_mappings: - BIOSAMPLE:sequenced_by - sequenced_by_contact_name: + sequenced_by_laboratory_name: rank: 75 - slot_group: Sequence information - sequenced_by_contact_email: + slot_group: Sequencing + sequenced_by_contact_name: rank: 76 slot_group: Sequencing - sequenced_by_contact_address: + sequenced_by_contact_email: rank: 77 slot_group: Sequencing - sequence_submitted_by: + sequenced_by_contact_address: rank: 78 slot_group: Sequencing + sequence_submitted_by: + rank: 79 + slot_group: Sequencing any_of: - range: WhitespaceMinimizedString - range: NullValueMenu @@ -1524,13 +1396,13 @@ classes: - GISAID:Submitting%20lab - BIOSAMPLE:sequence_submitted_by sequence_submitter_contact_email: - rank: 79 + rank: 80 slot_group: Sequencing sequence_submitter_contact_address: - rank: 80 + rank: 81 slot_group: Sequencing purpose_of_sequencing: - rank: 81 + rank: 82 slot_group: Sequencing examples: - value: Baseline surveillance (random sampling) [GENEPIO:0100005] @@ -1538,85 +1410,74 @@ classes: - range: PurposeOfSequencingInternationalMenu - range: NullValueMenu purpose_of_sequencing_details: - rank: 82 + rank: 83 slot_group: Sequencing sequencing_date: - rank: 83 + rank: 84 slot_group: Sequencing library_id: - rank: 84 + rank: 85 slot_group: Sequencing library_preparation_kit: - rank: 85 + rank: 86 slot_group: Sequencing sequencing_assay_type: - rank: 86 - slot_group: Sequence information - range: SequencingAssayTypeInternationalMenu - examples: - - value: whole genome sequencing assay [OBI:0002117] - sequencing_instrument: rank: 87 slot_group: Sequencing + sequencing_instrument: + rank: 88 + slot_group: Sequencing examples: - value: Oxford Nanopore MinION [GENEPIO:0100142] any_of: - range: SequencingInstrumentInternationalMenu - range: NullValueMenu sequencing_flow_cell_version: - rank: 88 - slot_group: Sequence information - sequencing_protocol: rank: 89 slot_group: Sequencing - sequencing_kit_number: + sequencing_protocol: rank: 90 slot_group: Sequencing - dna_fragment_length: + sequencing_kit_number: rank: 91 slot_group: Sequencing - genomic_target_enrichment_method: + dna_fragment_length: rank: 92 slot_group: Sequencing - any_of: - - range: GenomicTargetEnrichmentMethodInternationalMenu - - range: NullValueMenu - genomic_target_enrichment_method_details: + genomic_target_enrichment_method: rank: 93 slot_group: Sequencing - amplicon_pcr_primer_scheme: + genomic_target_enrichment_method_details: rank: 94 slot_group: Sequencing - amplicon_size: + amplicon_pcr_primer_scheme: rank: 95 slot_group: Sequencing - quality_control_method_name: + amplicon_size: rank: 96 - slot_group: Bioinformatics and QC metrics - quality_control_method_version: + slot_group: Sequencing + quality_control_method_name: rank: 97 slot_group: Bioinformatics and QC metrics - quality_control_determination: + quality_control_method_version: rank: 98 slot_group: Bioinformatics and QC metrics - range: QualityControlDeterminationInternationalMenu - quality_control_issues: + quality_control_determination: rank: 99 slot_group: Bioinformatics and QC metrics - range: QualityControlIssuesInternationalMenu - quality_control_details: + quality_control_issues: rank: 100 slot_group: Bioinformatics and QC metrics - raw_sequence_data_processing_method: + quality_control_details: rank: 101 slot_group: Bioinformatics and QC metrics - dehosting_method: + raw_sequence_data_processing_method: rank: 102 slot_group: Bioinformatics and QC metrics - deduplication_method: + dehosting_method: rank: 103 slot_group: Bioinformatics and QC metrics - consensus_sequence_name: + deduplication_method: rank: 104 slot_group: Bioinformatics and QC metrics genome_sequence_file_name: @@ -2999,6 +2860,9 @@ slots: used in your study. If unsure refer to the protocol documentation, or provide a null value.' slot_uri: GENEPIO:0100997 + range: SequencingAssayTypeInternationalMenu + examples: + - value: whole genome sequencing assay [OBI:0002117] sequencing_instrument: name: sequencing_instrument title: sequencing instrument @@ -3071,6 +2935,9 @@ slots: regions of interest from a genome. comments: Provide the name of the enrichment method slot_uri: GENEPIO:0100966 + any_of: + - range: GenomicTargetEnrichmentMethodInternationalMenu + - range: NullValueMenu multivalued: true recommended: true examples: @@ -3141,10 +3008,12 @@ slots: name: quality_control_determination title: quality control determination slot_uri: GENEPIO:0100559 + range: QualityControlDeterminationInternationalMenu quality_control_issues: name: quality_control_issues title: quality control issues slot_uri: GENEPIO:0100560 + range: QualityControlIssuesInternationalMenu quality_control_details: name: quality_control_details title: quality control details @@ -3203,6 +3072,29 @@ slots: - value: mpxvassembly3 exact_mappings: - NML_LIMS:consensus%20sequence%20name + consensus_sequence_filename: + name: consensus_sequence_filename + title: consensus sequence filename + description: The name of the consensus sequence file. + comments: Provide the name and version number of the consensus sequence FASTA + file. + slot_uri: GENEPIO:0001461 + range: WhitespaceMinimizedString + examples: + - value: mpox123assembly.fasta + exact_mappings: + - NML_LIMS:consensus%20sequence%20filename + consensus_sequence_filepath: + name: consensus_sequence_filepath + title: consensus sequence filepath + description: The filepath of the consensus sequence file. + comments: Provide the filepath of the consensus sequence FASTA file. + slot_uri: GENEPIO:0001462 + range: WhitespaceMinimizedString + examples: + - value: /User/Documents/STILab/Data/mpox123assembly.fasta + exact_mappings: + - NML_LIMS:consensus%20sequence%20filepath genome_sequence_file_name: name: genome_sequence_file_name title: genome sequence file name diff --git a/web/templates/mpox/schema_slots.tsv b/web/templates/mpox/schema_slots.tsv index 5a7791dd..237705a1 100644 --- a/web/templates/mpox/schema_slots.tsv +++ b/web/templates/mpox/schema_slots.tsv @@ -1,234 +1,232 @@ -class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal -Mpox;MpoxInternational GENEPIO:0001122 Database Identifiers database_identifiers -Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the submitting laboratory Primary Specimen ID TEXT_ID sample_name specimen collector sample ID -Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID -Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID -Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession -Mpox;MpoxInternational Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession -Mpox;MpoxInternational Database Identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION -Mpox;MpoxInternational Database Identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession -MpoxInternational Database Identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name -Mpox;MpoxInternational Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession -Mpox;MpoxInternational GENEPIO:0001150 Sample collection and processing sample_collection_and_processing -Mpox Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by -MpoxInternational Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001158 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date -Mpox Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date -Mpox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) -MpoxInternational Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) -Mpox Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) -MpoxInternational Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the state/province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) -MpoxInternational Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon -MpoxInternational Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon -Mpox Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus Pathogen HC_CURRENT_ID organism organism -MpoxInternational Sample collection and processing GENEPIO:0001191 organism organism OrganismInternationalMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism -Mpox Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name -MpoxInternational Sample collection and processing GENEPIO:0001644 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate -Mpox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling -MpoxInternational Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingInternationalMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling -Mpox;MpoxInternational Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Symptomology and history suggested Monkeypox diagnosis. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details -Mpox Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Nucleic Acid Specimen Type PH_SPECIMEN_TYPE -Mpox Sample collection and processing GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type RelatedSpecimenRelationshipTypeMenu NullValueMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Previously Submitted Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE -Mpox Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material -MpoxInternational Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) [NCIT:C78582] Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material -Mpox Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part -MpoxInternational Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartInternationalMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part -Mpox Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product -MpoxInternational Sample collection and processing GENEPIO:0001216 body product body_product BodyProductInternationalMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product -MpoxInternational Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material -Mpox Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device -MpoxInternational Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceInternationalMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device -Mpox Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method -MpoxInternational Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodInternationalMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method -Mpox Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing -MpoxInternational Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingInternationalMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] -Mpox;MpoxInternational Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details -Mpox Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control -MpoxInternational Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeInternationalMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] -Mpox;MpoxInternational Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control -Mpox;MpoxInternational GENEPIO:0001498 Lineage and Variant information -MpoxInternational Lineage and Variant information GENEPIO:0001500 lineage/clade name LineageCladeNameINternationalMenu NullValueMenu The name of the lineage or clade. Provide the lineage/clade name. B.1.1.7 PH_LINEAGE_CLADE_NAME -MpoxInternational Lineage and Variant information GENEPIO:0001501 lineage/clade analysis software name WhitespaceMinimizedString NullValueMenu The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin PH_LINEAGE_CLADE_SOFTWARE -MpoxInternational Lineage and Variant information GENEPIO:0001502 lineage/clade analysis software version WhitespaceMinimizedString NullValueMenu The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION -Mpox;MpoxInternational GENEPIO:0001268 Host Information host_information -Mpox Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE -MpoxInternational Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameInternationalMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human -Mpox Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) -MpoxInternational Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameInternationalMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) -Mpox Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state -MpoxInternational Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateInternationalMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state -Mpox Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS -MpoxInternational Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsInternationalMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] -Mpox Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome -MpoxInternational Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeInternationalMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome -Mpox Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox Host Disease PH_HOST_DISEASE host_disease host disease -MpoxInternational Host Information GENEPIO:0001391 host disease host_disease HostDiseaseInternationalMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease -MpoxInternational Host Information GENEPIO:0001398 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id -Mpox Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age -MpoxInternational Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age -Mpox Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit -MpoxInternational Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitInternationalMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit -Mpox Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin -MpoxInternational Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinInternationalMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin -Mpox Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex -MpoxInternational Host Information GENEPIO:0001395 host gender host_gender HostGenderInternationalMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex -Mpox Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY -MpoxInternational Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] -Mpox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE -Mpox;MpoxInternational Host Information GENEPIO:0001399 symptom onset date symptom_onset_date date NullValueMenu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE -Mpox Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS -MpoxInternational Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsInternationalMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] -Mpox Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors -MpoxInternational Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsInternationalMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors -Mpox Host Information GENEPIO:0001402 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications -MpoxInternational Host Information GENEPIO:0001402 complications complications ComplicationsInternationalMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] -Mpox;MpoxInternational Host Information GENEPIO:0100580 antiviral therapy antiviral_therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy -Mpox;MpoxInternational GENEPIO:0001403 Host vaccination information host_vaccination_information -Mpox Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY -MpoxInternational Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusInternationalMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY -Mpox;MpoxInternational Host vaccination information GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received -Mpox;MpoxInternational Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name WhitespaceMinimizedString NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY -Mpox;MpoxInternational Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date date NullValueMenu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY -Mpox;MpoxInternational Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY - -Mpox;MpoxInternational GENEPIO:0001409 Host exposure information host_exposure_information -Mpox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY -MpoxInternational Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] -Mpox;MpoxInternational Host exposure information GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL -Mpox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL -MpoxInternational Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California -Mpox Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL -MpoxInternational Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryInternationalMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] -Mpox;MpoxInternational Host exposure information GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL -Mpox;MpoxInternational Host exposure information GENEPIO:0001415 most recent travel return date most_recent_travel_return_date date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL -Mpox;MpoxInternational Host exposure information GENEPIO:0001416 travel history travel_history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL -Mpox Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE -MpoxInternational Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventInternationalMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE -Mpox Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level -MpoxInternational Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelInternationalMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level -Mpox Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE -MpoxInternational Host exposure information GENEPIO:0001419 host role host_role HostRoleInternationalMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE -Mpox Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE -MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingInternationalMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE -Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS - -Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information -Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection -MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] -Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu {today} The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date -Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment -MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] -Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection - - -Mpox;MpoxInternational GENEPIO:0001441 Sequencing sequencing -Mpox;MpoxInternational Sequence information GENEPIO:0100472 sequencing project name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. MPOX-1356 -Mpox Sequencing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by -MpoxInternational Sequencing GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Ontario (PHO) sequenced_by -Mpox Sequence information GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString NullValueMenu The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab -MpoxInternational Sequence information GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager -Mpox;MpoxInternational Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email -Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada -Mpox Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by -MpoxInternational Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by -Mpox;MpoxInternational Sequencing GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email -Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequence submitter contact address -Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing -MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing -Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details -Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE -MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE -Mpox;MpoxInternational Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID -Mpox;MpoxInternational Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT -Mpox Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay -MpoxInternational Sequence information GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeInternationalMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] -Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument -MpoxInternational Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentInternationalMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument -Mpox;MpoxInternational Sequence information GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 -Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol -Mpox;MpoxInternational Sequencing GENEPIO:0001455 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number -Mpox;MpoxInternational Sequencing GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 -Mpox Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method -MpoxInternational Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodInternationalMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method -Mpox;MpoxInternational Sequencing GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. -Mpox;MpoxInternational Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme - Sequencing GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300bp -Mpox;MpoxInternational GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 -Mpox Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationMenu NullValueMenu TRUE The determination of a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. sequence failed quality control -MpoxInternational Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationInternationalMenu -Mpox Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesMenu NullValueMenu TRUE The reason contributing to, or causing, a low quality determination in a quality control assessment. Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form. low average genome coverage -MpoxInternational Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesInternationalMenu -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. -Mpox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method -MpoxInternational Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method -Mpox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method -MpoxInternational Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name consensus_sequence_name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta consensus sequence filename -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu TRUE The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu TRUE The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath fast5_filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 -Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession -Mpox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol -MpoxInternational Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol -MpoxInternational GENEPIO:0101082 Taxonomic identification information -MpoxInternational Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat -MpoxInternational Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 -MpoxInternational Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon -MpoxInternational Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 -MpoxInternational Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. MPXV_report123.doc -MpoxInternational Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 -MpoxInternational Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 -Mpox;MpoxInternational GENEPIO:0001506 Pathogen diagnostic testing pathogen_diagnostic_testing -MpoxInternational Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. MPX (orf B6R) -MpoxInternational Pathogen diagnostic testing GENEPIO:0102045 assay target details 1 assay_target_details_1 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -Mpox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name -MpoxInternational Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg190 gene (MPOX) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name -MpoxInternational Pathogen diagnostic testing GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. B6R (Li et al., 2006) -Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value -MpoxInternational Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OVP (orf 17L) -MpoxInternational Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -Mpox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 -MpoxInternational Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg002 gene (MPOX) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 -MpoxInternational Pathogen diagnostic testing GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G). -Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 -MpoxInternational Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OPHA (orf B2R) -MpoxInternational Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. -Mpox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene_name_3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 -MpoxInternational Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg188 gene (MPOX) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 -MpoxInternational Pathogen diagnostic testing GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R_G (Li et al., 2010) assay -Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3 -Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4 -Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 -Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 -Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 - GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement -Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS -Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS \ No newline at end of file +class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples EXPORT_GISAID EXPORT_CNPHI EXPORT_NML_LIMS EXPORT_BIOSAMPLE EXPORT_VirusSeq_Portal +Mpox;MpoxInternational GENEPIO:0001122 Database Identifiers database_identifiers +Mpox;MpoxInternational Database Identifiers GENEPIO:0001123 specimen collector sample ID specimen_collector_sample_id WhitespaceMinimizedString TRUE TRUE The user-defined name for the sample. Store the collector sample ID. If this number is considered identifiable information, provide an alternative ID. Be sure to store the key that maps between the original and alternative IDs for traceability and follow up if necessary. Every collector sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab. prov_mpox_1234 Sample ID given by the submitting laboratory Primary Specimen ID TEXT_ID sample_name specimen collector sample ID +Mpox Database Identifiers GENEPIO:0001128 Related specimen primary ID related_specimen_primary_id WhitespaceMinimizedString NullValueMenu The primary ID of a related specimen previously submitted to the repository. Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. SR20-12345 Related Specimen ID;Related Specimen Relationship Type PH_RELATED_PRIMARY_ID host_subject_ID +Mpox;MpoxInternational Database Identifiers GENEPIO:0100281 case ID case_id WhitespaceMinimizedString The identifier used to specify an epidemiologically detected case of disease. Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. ABCD1234 PH_CASE_ID +Mpox;MpoxInternational Database Identifiers GENEPIO:0001136 bioproject accession bioproject_accession WhitespaceMinimizedString {UPPER_CASE} The INSDC accession number of the BioProject(s) to which the BioSample belongs. Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA12345 SUBMISSIONS - BioProject Accession +Mpox;MpoxInternational Database Identifiers GENEPIO:0001139 biosample accession biosample_accession WhitespaceMinimizedString {UPPER_CASE} The identifier assigned to a BioSample in INSDC archives. Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. SAMN14180202 SUBMISSIONS - BioSample Accession +Mpox;MpoxInternational Database Identifiers GENEPIO:0101203 INSDC sequence read accession insdc_sequence_read_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The identifier assigned to a sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the accession assigned to the submitted sequence. European Nucleotide Archive (ENA) sequence accessions start with ERR, NCBI-SRA accessions start with SRR, DNA Data Bank of Japan (DDBJ) accessions start with DRR and Genome Sequence Archive (GSA) accessions start with CRR. SRR123456, ERR123456, DRR123456, CRR123456 SRA Accession PH_SRA_ACCESSION +Mpox;MpoxInternational Database Identifiers GENEPIO:0101204 INSDC assembly accession insdc_assembly_accession WhitespaceMinimizedString {UPPER_CASE} {UPPER_CASE} The versioned identifier assigned to an assembly or consensus sequence in one of the International Nucleotide Sequence Database Collaboration (INSDC) repositories. Store the versioned accession assigned to the submitted sequence e.g. the GenBank accession version. LZ986655.1 GenBank Accession GenBank accession +MpoxInternational Database Identifiers GENEPIO:0100282 GISAID virus name gisaid_virus_name WhitespaceMinimizedString Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID_virus_name +Mpox;MpoxInternational Database Identifiers GENEPIO:0001147 GISAID accession gisaid_accession WhitespaceMinimizedString {UPPER_CASE} The GISAID accession number assigned to the sequence. Store the accession returned from the GISAID submission. EPI_ISL_436489 GISAID Accession (if known) SUBMISSIONS - GISAID Accession GISAID_accession GISAID accession +Mpox;MpoxInternational GENEPIO:0001150 Sample collection and processing sample_collection_and_processing +Mpox Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by SampleCollectedByMenu NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab Lab Name CUSTOMER collected_by sample collected by +MpoxInternational Sample collection and processing GENEPIO:0001153 sample collected by sample_collected_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that collected the original sample. The name of the sample collector should be written out in full, (with minor exceptions) and be consistent across multple submissions e.g. Public Health Agency of Canada, Public Health Ontario, BC Centre for Disease Control. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). BC Centre for Disease Control Originating lab collected_by +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001156 sample collector contact email sample_collector_contact_email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sample collector contact email +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001158 sample collector contact address sample_collector_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Address sample collector contact address +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001174 sample collection date sample_collection_date date NullValueMenu TRUE 2019-10-01 {today} The date on which the sample was collected. Sample collection date is critical for surveillance and many types of analyses. Required granularity includes year, month and day. If this date is considered identifiable information, it is acceptable to add "jitter" by adding or subtracting a calendar day (acceptable by GISAID). Alternatively, ”received date” may be used as a substitute. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 Collection date Patient Sample Collected Date HC_COLLECT_DATE collection_date sample collection date +Mpox Sample collection and processing GENEPIO:0001177 sample collection date precision sample_collection_date_precision SampleCollectionDatePrecisionMenu NullValueMenu TRUE The precision to which the "sample collection date" was provided. Provide the precision of granularity to the "day", "month", or "year" for the date provided in the "sample collection date" field. The "sample collection date" will be truncated to the precision specified upon export; "day" for "YYYY-MM-DD", "month" for "YYYY-MM", or "year" for "YYYY". year Precision of date collected HC_TEXT2 +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001179 sample received date sample_received_date date NullValueMenu 2019-10-01 {today} The date on which the sample was received. ISO 8601 standard "YYYY-MM-DD". 2020-03-20 sample received date +Mpox Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. Canada Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) +MpoxInternational Sample collection and processing GENEPIO:0001181 geo_loc_name (country) geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu TRUE The country where the sample was collected. Provide the country name from the controlled vocabulary provided. United States of America [GAZ:00002459] Location Patient Country HC_COUNTRY geo_loc_name geo_loc_name (country) +Mpox Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) +MpoxInternational Sample collection and processing GENEPIO:0001185 geo_loc_name (state/province/territory) geo_loc_name_state_province_territory WhitespaceMinimizedString NullValueMenu TRUE The state/province/territory where the sample was collected. Provide the state/province/territory name from the controlled vocabulary provided. Saskatchewan Patient Province HC_PROVINCE geo_loc_name geo_loc_name (state/province/territory) +MpoxInternational Sample collection and processing GENEPIO:0100309 geo_loc latitude geo_loc_latitude WhitespaceMinimizedString The latitude coordinates of the geographical location of sample collection. Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format "d[d.dddd] N|S". 38.98 N lat_lon +MpoxInternational Sample collection and processing GENEPIO:0100310 geo_loc longitude geo_loc_longitude WhitespaceMinimizedString The longitude coordinates of the geographical location of sample collection. Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format "d[dd.dddd] W|E". 77.11 W lat_lon +Mpox Sample collection and processing GENEPIO:0001191 organism organism OrganismMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus Pathogen HC_CURRENT_ID organism organism +MpoxInternational Sample collection and processing GENEPIO:0001191 organism organism OrganismInternationalMenu NullValueMenu TRUE Taxonomic name of the organism. Use "Mpox virus". This value is provided in the template. Note: the Mpox virus was formerly referred to as the "Monkeypox virus" but the international nomenclature has changed (2022). Mpox virus [NCBITaxon:10244] Pathogen HC_CURRENT_ID organism organism +Mpox Sample collection and processing GENEPIO:0001195 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. Provide the GISAID EpiPox virus name, which should be written in the format “hMpxV/Canada/2 digit provincial ISO code-xxxxx/year”. If the province code cannot be shared for privacy reasons, put "UN" for "Unknown". hMpxV/Canada/UN-NML-12345/2022 Virus name GISAID Virus Name SUBMISSIONS - GISAID Virus Name isolate;GISAID_virus_name isolate;fasta header name +MpoxInternational Sample collection and processing GENEPIO:0001644 isolate isolate WhitespaceMinimizedString NullValueMenu TRUE Identifier of the specific isolate. This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the "isolate" name is propagated throughtout different databases. As such, structure the "isolate" name to be ICTV/INSDC compliant in the following format: "MpxV/host/country/sampleID/date". MpxV/human/USA/CA-CDPH-001/2020 isolate +Mpox Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling +MpoxInternational Sample collection and processing GENEPIO:0001198 purpose of sampling purpose_of_sampling PurposeOfSamplingInternationalMenu NullValueMenu TRUE The reason that the sample was collected. As all samples are taken for diagnostic purposes, "Diagnostic Testing" should be chosen from the picklist at this time. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing, which should be indicated in the "purpose of sequencing" field. Diagnostic testing [GENEPIO:0100002] Reason for Sampling HC_SAMPLE_CATEGORY purpose_of_sampling purpose of sampling +Mpox;MpoxInternational Sample collection and processing GENEPIO:0001200 purpose of sampling details purpose_of_sampling_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was collected, providing specific details. Provide an expanded description of why the sample was collected using free text. The description may include the importance of the sample for a particular public health investigation/surveillance activity/research question. If details are not available, provide a null value. Symptomology and history suggested Monkeypox diagnosis. Details on the Reason for Sampling PH_SAMPLING_DETAILS description purpose of sampling details +Mpox Sample collection and processing GENEPIO:0001204 NML submitted specimen type nml_submitted_specimen_type NmlSubmittedSpecimenTypeMenu TRUE The type of specimen submitted to the National Microbiology Laboratory (NML) for testing. This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. Nucleic Acid Specimen Type PH_SPECIMEN_TYPE +Mpox Sample collection and processing GENEPIO:0001209 Related specimen relationship type related_specimen_relationship_type RelatedSpecimenRelationshipTypeMenu NullValueMenu The relationship of the current specimen to the specimen/sample previously submitted to the repository. Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Previously Submitted Related Specimen ID;Related Specimen Relationship Type PH_RELATED_RELATIONSHIP_TYPE +Mpox Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material +MpoxInternational Sample collection and processing GENEPIO:0001211 anatomical material anatomical_material AnatomicalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from an anatomical part of an organism e.g. tissue, blood. Provide a descriptor if an anatomical material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Lesion (Pustule) [NCIT:C78582] Specimen source Anatomical Material PH_ISOLATION_SITE_DESC isolation_source;anatomical_material anatomical material +Mpox Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part +MpoxInternational Sample collection and processing GENEPIO:0001214 anatomical part anatomical_part AnatomicalPartInternationalMenu NullValueMenu TRUE TRUE An anatomical part of an organism e.g. oropharynx. Provide a descriptor if an anatomical part was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Genital area [BTO:0003358] Specimen source Anatomical Site PH_ISOLATION_SITE isolation_source;anatomical_part anatomical part +Mpox Sample collection and processing GENEPIO:0001216 body product body_product BodyProductMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product +MpoxInternational Sample collection and processing GENEPIO:0001216 body product body_product BodyProductInternationalMenu NullValueMenu TRUE TRUE A substance excreted/secreted from an organism e.g. feces, urine, sweat. Provide a descriptor if a body product was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Pus [UBERON:0000177] Specimen source Body Product PH_SPECIMEN_SOURCE_DESC isolation_source;body_product body product +MpoxInternational Sample collection and processing GENEPIO:0001223 environmental material environmental_material EnvironmentalMaterialInternationalMenu NullValueMenu TRUE TRUE A substance obtained from the natural or man-made environment e.g. soil, water, sewage. Provide a descriptor if an environmental material was sampled. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Bed linen Specimen source isolation_source;environmental_material +Mpox Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device +MpoxInternational Sample collection and processing GENEPIO:0001234 collection device collection_device CollectionDeviceInternationalMenu NullValueMenu TRUE TRUE The instrument or container used to collect the sample e.g. swab. Provide a descriptor if a device was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Swab [GENEPIO:0100027] Specimen source Specimen Collection Matrix PH_SPECIMEN_TYPE_ORIG isolation_source;collection_device collection device +Mpox Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method +MpoxInternational Sample collection and processing GENEPIO:0001241 collection method collection_method CollectionMethodInternationalMenu NullValueMenu TRUE TRUE The process used to collect the sample e.g. phlebotamy, necropsy. Provide a descriptor if a collection method was used for sampling. Use the picklist provided in the template. If a desired term is missing from the picklist, contact emma_griffiths@sfu.ca. If not applicable, do not leave blank. Choose a null value. Biopsy [OBI:0002650] Specimen source Collection Method COLLECTION_METHOD isolation_source;collection_method collection method +Mpox Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled specimen processing +MpoxInternational Sample collection and processing GENEPIO:0001253 specimen processing specimen_processing SpecimenProcessingInternationalMenu NullValueMenu TRUE Any processing applied to the sample during or after receiving the sample. Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in "lab host", "passage number", and "passage method" fields. If none of the processes in the pick list apply, put "not applicable". Specimens pooled [OBI:0600016] +Mpox;MpoxInternational Sample collection and processing GENEPIO:0100311 specimen processing details specimen_processing_details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. 5 swabs from different body sites were pooled and further prepared as a single sample during library prep. specimen processing details +Mpox Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control +MpoxInternational Sample collection and processing GENEPIO:0100921 experimental specimen role type experimental_specimen_role_type ExperimentalSpecimenRoleTypeInternationalMenu NullValueMenu TRUE The type of role that the sample represents in the experiment. Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". Positive experimental control [GENEPIO:0101018] +Mpox;MpoxInternational Sample collection and processing GENEPIO:0100922 experimental control details experimental_control_details WhitespaceMinimizedString The details regarding the experimental control contained in the sample. Provide details regarding the nature of the reference strain used as a control, or what is was used to monitor. Human coronavirus 229E (HCoV-229E) spiked in sample as process control +Mpox;MpoxInternational GENEPIO:0001498 Lineage and Variant information +MpoxInternational Lineage and Variant information GENEPIO:0001500 lineage/clade name LineageCladeNameINternationalMenu NullValueMenu The name of the lineage or clade. Provide the lineage/clade name. B.1.1.7 PH_LINEAGE_CLADE_NAME +MpoxInternational Lineage and Variant information GENEPIO:0001501 lineage/clade analysis software name WhitespaceMinimizedString NullValueMenu The name of the software used to determine the lineage/clade. Provide the name of the software used to determine the lineage/clade. Pangolin PH_LINEAGE_CLADE_SOFTWARE +MpoxInternational Lineage and Variant information GENEPIO:0001502 lineage/clade analysis software version WhitespaceMinimizedString NullValueMenu The version of the software used to determine the lineage/clade. Provide the version of the software used ot determine the lineage/clade. 2.1.10 PH_LINEAGE_CLADE_VERSION +Mpox;MpoxInternational GENEPIO:0001268 Host Information host_information +Mpox Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human PH_ANIMAL_TYPE +MpoxInternational Host Information GENEPIO:0001386 host (common name) host_common_name HostCommonNameInternationalMenu NullValueMenu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Common name e.g. human. Human +Mpox Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens Host host (scientific name) host host (scientific name) +MpoxInternational Host Information GENEPIO:0001387 host (scientific name) host_scientific_name HostScientificNameInternationalMenu NullValueMenu TRUE The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Scientific name e.g. Homo sapiens, If the sample was environmental, put "not applicable Homo sapiens [NCBITaxon:9606] Host host (scientific name) host host (scientific name) +Mpox Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic Patient status PH_HOST_HEALTH host_health_state +MpoxInternational Host Information GENEPIO:0001388 host health state host_health_state HostHealthStateInternationalMenu NullValueMenu Health status of the host at the time of sample collection. If known, select a value from the pick list. Asymptomatic [NCIT:C3833] Patient status host_health_state +Mpox Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized PH_HOST_HEALTH_DETAILS +MpoxInternational Host Information GENEPIO:0001389 host health status details host_health_status_details HostHealthStatusDetailsInternationalMenu NullValueMenu Further details pertaining to the health or disease status of the host at time of collection. If known, select a descriptor from the pick list provided in the template. Hospitalized [NCIT:C25179] +Mpox Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered PH_HOST_HEALTH_OUTCOME host_health_outcome +MpoxInternational Host Information GENEPIO:0001389 host health outcome host_health_outcome HostHealthOutcomeInternationalMenu NullValueMenu Disease outcome in the host. If known, select a value from the pick list. Recovered [NCIT:C49498] host_health_outcome +Mpox Host Information GENEPIO:0001391 host disease host_disease HostDiseaseMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox Host Disease PH_HOST_DISEASE host_disease host disease +MpoxInternational Host Information GENEPIO:0001391 host disease host_disease HostDiseaseInternationalMenu NullValueMenu TRUE The name of the disease experienced by the host. Select "Mpox" from the pick list provided in the template. Note: the Mpox disease was formerly referred to as "Monkeypox" but the international nomenclature has changed (2022). Mpox [MONDO:0002594] Host Disease PH_HOST_DISEASE host_disease host disease +MpoxInternational Host Information GENEPIO:0001398 host subject ID host_subject_id WhitespaceMinimizedString A unique identifier by which each host can be referred to. This identifier can be used to link samples from the same individual. Caution: consult the data steward before sharing as this value may be considered identifiable information. 12345B-222 host_subject_id +Mpox Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age PH_AGE host_age +MpoxInternational Host Information GENEPIO:0001392 host age host_age decimal NullValueMenu TRUE 0 130 Age of host at the time of sampling. If known, provide age. Age-binning is also acceptable. 79 Patient age host_age +Mpox Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year PH_AGE_UNIT host_age_unit +MpoxInternational Host Information GENEPIO:0001393 host age unit host_age_unit HostAgeUnitInternationalMenu NullValueMenu TRUE The units used to measure the host's age. If known, provide the age units used to measure the host's age from the pick list. year [UO:0000036] host_age_unit +Mpox Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 PH_AGE_GROUP host_age_bin +MpoxInternational Host Information GENEPIO:0001394 host age bin host_age_bin HostAgeBinInternationalMenu NullValueMenu TRUE The age category of the host at the time of sampling. Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. 50 - 59 [GENEPIO:0100054] host_age_bin +Mpox Host Information GENEPIO:0001395 host gender host_gender HostGenderMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male Gender VD_SEX host_sex +MpoxInternational Host Information GENEPIO:0001395 host gender host_gender HostGenderInternationalMenu NullValueMenu TRUE {Title_Case} The gender of the host at the time of sample collection. If known, select a value from the pick list. Male [NCIT:C46109] Gender host_sex +Mpox Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada PH_HOST_COUNTRY +MpoxInternational Host Information GENEPIO:0001396 host residence geo_loc name (country) host_residence_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country of residence of the host. Select the country name from pick list provided in the template. Canada [GAZ:00002560] +Mpox Host Information GENEPIO:0001397 host residence geo_loc name (state/province/territory) host_residence_geo_loc_name_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The state/province/territory of residence of the host. Select the province/territory name from pick list provided in the template. Quebec PH_HOST_PROVINCE +Mpox;MpoxInternational Host Information GENEPIO:0001399 symptom onset date symptom_onset_date date NullValueMenu 2019-10-01 {today} The date on which the symptoms began or were first noted. If known, provide the symptom onset date in ISO 8601 standard format "YYYY-MM-DD". 2022-05-25 HC_ONSET_DATE +Mpox Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule), Swollen Lymph Nodes, Myalgia (muscle pain) HC_SYMPTOMS +MpoxInternational Host Information GENEPIO:0001400 signs and symptoms signs_and_symptoms SignsAndSymptomsInternationalMenu NullValueMenu TRUE A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient. Select all of the symptoms experienced by the host from the pick list. Lesion (Pustule) [NCIT:C78582], Swollen Lymph Nodes [HP:0002716], Myalgia (muscle pain) [HP:0003326] +Mpox Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors +MpoxInternational Host Information GENEPIO:0001401 pre-existing conditions and risk factors preexisting_conditions_and_risk_factors PreExistingConditionsAndRiskFactorsInternationalMenu NullValueMenu TRUE Patient pre-existing conditions and risk factors.
  • Pre-existing condition: A medical condition that existed prior to the current infection.
  • Risk Factor: A variable associated with an increased risk of disease or infection. Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors +Mpox Host Information GENEPIO:0001402 complications complications ComplicationsMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) complications +MpoxInternational Host Information GENEPIO:0001402 complications complications ComplicationsInternationalMenu NullValueMenu TRUE Patient medical complications that are believed to have occurred as a result of host disease. Select all of the complications experienced by the host from the pick list. If the desired term is missing, contact the curation team. Delayed wound healing (lesion healing) [MP:0002908] +Mpox;MpoxInternational Host Information GENEPIO:0100580 antiviral therapy antiviral_therapy WhitespaceMinimizedString Treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection antiviral therapy +Mpox;MpoxInternational GENEPIO:0001403 Host vaccination information host_vaccination_information +Mpox Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated PH_VACCINATION_HISTORY +MpoxInternational Host vaccination information GENEPIO:0001404 host vaccination status host_vaccination_status HostVaccinationStatusInternationalMenu NullValueMenu The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). Select the vaccination status of the host from the pick list. Not Vaccinated [GENEPIO:0100102] PH_VACCINATION_HISTORY +Mpox;MpoxInternational Host vaccination information GENEPIO:0001406 number of vaccine doses received number_of_vaccine_doses_received integer The number of doses of the vaccine recived by the host. Record how many doses of the vaccine the host has received. 1 number of vaccine doses received +Mpox;MpoxInternational Host vaccination information GENEPIO:0100313 vaccination dose 1 vaccine name vaccination_dose_1_vaccine_name WhitespaceMinimizedString NullValueMenu The name of the vaccine administered as the first dose of a vaccine regimen. Provide the name and the corresponding manufacturer of the Smallpox vaccine administered as the first dose. IMVAMUNE (Bavarian Nordic) PH_VACCINATION_HISTORY +Mpox;MpoxInternational Host vaccination information GENEPIO:0100314 vaccination dose 1 vaccination date vaccination_dose_1_vaccination_date date NullValueMenu 2019-10-01 {today} The date the first dose of a vaccine was administered. Provide the date the first dose of Smallpox vaccine was administered. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2022-06-01 PH_VACCINATION_HISTORY +Mpox;MpoxInternational Host vaccination information GENEPIO:0100321 vaccination history vaccination_history WhitespaceMinimizedString A description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. IMVAMUNE (Bavarian Nordic); 2022-06-01 PH_VACCINATION_HISTORY + +Mpox;MpoxInternational GENEPIO:0001409 Host exposure information host_exposure_information +Mpox Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada PH_EXPOSURE_COUNTRY +MpoxInternational Host exposure information GENEPIO:0001410 location of exposure geo_loc name (country) location_of_exposure_geo_loc_name_country GeoLocNameCountryInternationalMenu NullValueMenu The country where the host was likely exposed to the causative agent of the illness. Select the country name from the pick list provided in the template. Canada [GAZ:00002560] +Mpox;MpoxInternational Host exposure information GENEPIO:0001411 destination of most recent travel (city) destination_of_most_recent_travel_city WhitespaceMinimizedString The name of the city that was the destination of most recent travel. Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz New York City PH_TRAVEL +Mpox Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory GeoLocNameStateProvinceTerritoryMenu NullValueMenu The name of the state/province/territory that was the destination of most recent travel. Select the province name from the pick list provided in the template. PH_TRAVEL +MpoxInternational Host exposure information GENEPIO:0001412 destination of most recent travel (state/province/territory) destination_of_most_recent_travel_state_province_territory WhitespaceMinimizedString The name of the state/province/territory that was the destination of most recent travel. Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz California +Mpox Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. Canada PH_TRAVEL +MpoxInternational Host exposure information GENEPIO:0001413 destination of most recent travel (country) destination_of_most_recent_travel_country GeoLocNameCountryInternationalMenu NullValueMenu The name of the country that was the destination of most recent travel. Select the country name from the pick list provided in the template. United Kingdom [GAZ:00002637] +Mpox;MpoxInternational Host exposure information GENEPIO:0001414 most recent travel departure date most_recent_travel_departure_date date NullValueMenu The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations. Provide the travel departure date. 2020-03-16 PH_TRAVEL +Mpox;MpoxInternational Host exposure information GENEPIO:0001415 most recent travel return date most_recent_travel_return_date date NullValueMenu The date of a person's most recent return to some residence from a journey originating at that residence. Provide the travel return date. 2020-04-26 PH_TRAVEL +Mpox;MpoxInternational Host exposure information GENEPIO:0001416 travel history travel_history WhitespaceMinimizedString Travel history in last six months. Specify the countries (and more granular locations if known, separated by a comma) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semi-colon. List most recent travel first. Canada, Vancouver; USA, Seattle; Italy, Milan PH_TRAVEL +Mpox Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party Additional location information Exposure Event PH_EXPOSURE +MpoxInternational Host exposure information GENEPIO:0001417 exposure event exposure_event ExposureEventInternationalMenu NullValueMenu Event leading to exposure. Select an exposure event from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Party [PCO:0000035] Additional location information Exposure Event PH_EXPOSURE +Mpox Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual exposure contact level +MpoxInternational Host exposure information GENEPIO:0001418 exposure contact level exposure_contact_level ExposureContactLevelInternationalMenu NullValueMenu The exposure transmission contact type. Select exposure contact level from the pick-list. Contact with infected individual [GENEPIO:0100357] exposure contact level +Mpox Host exposure information GENEPIO:0001419 host role host_role HostRoleMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case PH_HOST_ROLE +MpoxInternational Host exposure information GENEPIO:0001419 host role host_role HostRoleInternationalMenu TRUE The role of the host in relation to the exposure setting. Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the DataHarmonizer curation team. Acquaintance of case [GENEPIO:0100266] PH_HOST_ROLE +Mpox Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting PH_EXPOSURE +MpoxInternational Host exposure information GENEPIO:0001428 exposure setting exposure_setting ExposureSettingInternationalMenu TRUE The setting leading to exposure. Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the DataHarmonizer curation team. Healthcare Setting [GENEPIO:0100201] PH_EXPOSURE +Mpox;MpoxInternational Host exposure information GENEPIO:0001431 exposure details exposure_details WhitespaceMinimizedString Additional host exposure information. Free text description of the exposure. Large party, many contacts PH_EXPOSURE_DETAILS + +Mpox;MpoxInternational GENEPIO:0001434 Host reinfection information host_reinfection_information +Mpox Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection prior Monkeypox infection +MpoxInternational Host reinfection information GENEPIO:0100532 prior Mpox infection prior_mpox_infection PriorMpoxInfectionInternationalMenu NullValueMenu The absence or presence of a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox infection. Select a value from the pick list. Prior infection [GENEPIO:0100037] +Mpox;MpoxInternational Host reinfection information GENEPIO:0100533 prior Mpox infection date prior_mpox_infection_date date NullValueMenu {today} The date of diagnosis of the prior Mpox infection. Provide the date that the most recent prior infection was diagnosed. Provide the prior Mpox infection date in ISO 8601 standard format "YYYY-MM-DD". 2022-06-20 prior Monkeypox infection date +Mpox Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment prior Monkeypox antiviral treatment +MpoxInternational Host reinfection information GENEPIO:0100534 prior Mpox antiviral treatment prior_mpox_antiviral_treatment PriorMpoxAntiviralTreatmentInternationalMenu NullValueMenu The absence or presence of antiviral treatment for a prior Mpox infection. If known, provide information about whether the individual had a previous Mpox antiviral treatment. Select a value from the pick list. Prior antiviral treatment [GENEPIO:0100037] +Mpox;MpoxInternational Host reinfection information GENEPIO:0100535 prior antiviral treatment during prior Mpox infection prior_antiviral_treatment_during_prior_mpox_infection WhitespaceMinimizedString Antiviral treatment for any infection during the prior Mpox infection period. Provide a description of any antiviral treatment administered for viral infections (not including Mpox treatment) during the prior Mpox infection period. This field is meant to capture concurrent treatment information. AZT was administered for HIV infection during the prior Mpox infection. prior antiviral treatment during Monkeypox infection + + +Mpox;MpoxInternational GENEPIO:0001441 Sequencing sequencing +MpoxInternational Sequencing GENEPIO:0100472 sequencing project name sequencing_project_name WhitespaceMinimizedString The name of the project/initiative/program for which sequencing was performed. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. MPOX-1356 +Mpox Sequencing GENEPIO:0100416 sequenced by sequenced_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) PH_SEQUENCING_CENTRE sequenced_by +MpoxInternational Sequencing GENEPIO:0100416 sequenced by sequenced_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that generated the sequence. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. Public Health Ontario (PHO) sequenced_by +MpoxInternational Sequencing GENEPIO:0100470 sequenced by laboratory name sequenced_by_laboratory_name WhitespaceMinimizedString NullValueMenu The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. Topp Lab +MpoxInternational Sequencing GENEPIO:0100471 sequenced by contact name sequenced_by_contact_name WhitespaceMinimizedString NullValueMenu TRUE The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Bloggs, Enterics Lab Manager +Mpox;MpoxInternational Sequencing GENEPIO:0100422 sequenced by contact email sequenced_by_contact_email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequenced by contact email +Mpox;MpoxInternational Sequencing GENEPIO:0100423 sequenced by contact address sequenced_by_contact_address WhitespaceMinimizedString The mailing address of the agency submitting the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada +Mpox Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by SequenceSubmittedByMenu NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab Sequencing Centre PH_SEQUENCE_SUBMITTER sequence_submitted_by sequence submitted by +MpoxInternational Sequencing GENEPIO:0001159 sequence submitted by sequence_submitted_by WhitespaceMinimizedString NullValueMenu TRUE The name of the agency that submitted the sequence to a database. The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the "National Microbiology Laboratory (NML)". Public Health Ontario (PHO) Submitting lab sequence_submitted_by +Mpox;MpoxInternational Sequencing GENEPIO:0001165 sequence submitter contact email sequence_submitter_contact_email WhitespaceMinimizedString The email address of the agency responsible for submission of the sequence. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca sequence submitter contact email +Mpox;MpoxInternational Sequencing GENEPIO:0001167 sequence submitter contact address sequence_submitter_contact_address WhitespaceMinimizedString The mailing address of the agency responsible for submission of the sequence. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada sequence submitter contact address +Mpox Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Select "Targeted surveillance (non-random sampling)" if the specimen fits any of the following criteria: Specimens attributed to individuals with no known intimate contacts to positive cases;Specimens attributed to youth/minors <18 yrs.;Specimens attributed to vulnerable persons living in transient shelters or congregant settings;Specimens attributed to individuals self-identifying as “female”;For specimens with a recent international and/or domestic travel history, please select the most appropriate tag from the following three options: Domestic travel surveillance;International travel surveillance;Travel-associated surveillance;For specimens targeted for sequencing as part of an outbreak investigation, please select: Cluster/Outbreak investigation; In all other cases use: Baseline surveillance (random sampling). Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing +MpoxInternational Sequencing GENEPIO:0001445 purpose of sequencing purpose_of_sequencing PurposeOfSequencingInternationalMenu NullValueMenu TRUE TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Baseline surveillance (random sampling) [GENEPIO:0100005] Sampling Strategy Reason for Sequencing PH_REASON_FOR_SEQUENCING purpose_of_sequencing purpose of sequencing +Mpox;MpoxInternational Sequencing GENEPIO:0001446 purpose of sequencing details purpose_of_sequencing_details WhitespaceMinimizedString NullValueMenu TRUE The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriotions include: Screened due to travel history, Screened due to close contact with infected individual. Outbreak in MSM community Details on the Reason for Sequencing PH_REASON_FOR_SEQUENCING_DETAILS purpose of sequencing details +Mpox Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu TRUE {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE +MpoxInternational Sequencing GENEPIO:0001447 sequencing date sequencing_date date NullValueMenu {sample_collection_date} {today} The date the sample was sequenced. ISO 8601 standard "YYYY-MM-DD". 2020-06-22 PH_SEQUENCING_DATE +Mpox;MpoxInternational Sequencing GENEPIO:0001448 library ID library_id WhitespaceMinimizedString TRUE The user-specified identifier for the library prepared for sequencing. The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. XYZ_123345 library ID +Mpox;MpoxInternational Sequencing GENEPIO:0001450 library preparation kit library_preparation_kit WhitespaceMinimizedString The name of the DNA library preparation kit used to generate the library being sequenced. Provide the name of the library preparation kit used. Nextera XT PH_LIBRARY_PREP_KIT +MpoxInternational Sequencing GENEPIO:0100997 sequencing assay type sequencing_assay_type SequencingAssayTypeInternationalMenu The overarching sequencing methodology that was used to determine the sequence of a biomaterial. Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value. whole genome sequencing assay [OBI:0002117] +Mpox Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument +MpoxInternational Sequencing GENEPIO:0001452 sequencing instrument sequencing_instrument SequencingInstrumentInternationalMenu NullValueMenu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION [GENEPIO:0100142] Sequencing technology Sequencing Instrument PH_SEQUENCING_INSTRUMENT sequencing instrument +MpoxInternational Sequencing GENEPIO:0101102 sequencing flow cell version sequencing_flow_cell_version WhitespaceMinimizedString The version number of the flow cell used for generating sequence data. Flow cells can vary in terms of design, chemistry, capacity, etc. The version of the flow cell used to generate sequence data can affect sequence quantity and quality. Record the version of the flow cell used to generate sequence data. Do not include "version" or "v" in the version number. R.9.4.1 +Mpox;MpoxInternational Sequencing GENEPIO:0001454 sequencing protocol sequencing_protocol WhitespaceMinimizedString The protocol used to generate the sequence. Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: "Viral sequencing was performed following a metagenomic shotgun sequencing approach. Sequencing was performed using a sequencing instrument. Libraries were prepared using library kit. " Viral sequencing was performed following a metagenomic shotgun sequencing approach. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. PH_TESTING_PROTOCOL sequencing protocol +Mpox;MpoxInternational Sequencing GENEPIO:0001455 sequencing kit number sequencing_kit_number WhitespaceMinimizedString The manufacturer's kit number. Alphanumeric value. AB456XYZ789 sequencing kit number +MpoxInternational Sequencing GENEPIO:0100843 DNA fragment length dna_fragment_length WhitespaceMinimizedString The length of the DNA fragment generated by mechanical shearing or enzymatic digestion for the purposes of library preparation. Provide the fragment length in base pairs (do not include the units). 400 +MpoxInternational Sequencing GENEPIO:0100966 genomic target enrichment method genomic_target_enrichment_method GenomicTargetEnrichmentMethodInternationalMenu NullValueMenu TRUE TRUE The molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide the name of the enrichment method hybrid selection method +MpoxInternational Sequencing GENEPIO:0100967 genomic target enrichment method details genomic_target_enrichment_method_details WhitespaceMinimizedString Details that provide additional context to the molecular technique used to selectively capture and amplify specific regions of interest from a genome. Provide details that are applicable to the method you used. enrichment was done using Illumina Target Enrichment methodology with the Illumina DNA Prep with enrichment kit. +Mpox;MpoxInternational Sequencing GENEPIO:0001456 amplicon pcr primer scheme amplicon_pcr_primer_scheme WhitespaceMinimizedString The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced. Provide the name and version of the primer scheme used to generate the amplicons for sequencing. MPXV Sunrise 3.1 amplicon pcr primer scheme +Mpox;MpoxInternational Sequencing GENEPIO:0001449 amplicon size amplicon_size integer The length of the amplicon generated by PCR amplification. Provide the amplicon size expressed in base pairs. 300bp +Mpox;MpoxInternational GENEPIO:0001457 Bioinformatics and QC metrics bioinformatics_and_qc_metrics +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100557 quality control method name quality_control_method_name WhitespaceMinimizedString The name of the method used to assess whether a sequence passed a predetermined quality control threshold. Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided. ncov-tools +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100558 quality control method version quality_control_method_version WhitespaceMinimizedString The version number of the method used to assess whether a sequence passed a predetermined quality control threshold. Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon. 1.2.3 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100559 quality control determination quality_control_determination QualityControlDeterminationInternationalMenu +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100560 quality control issues quality_control_issues QualityControlIssuesInternationalMenu +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100561 quality control details quality_control_details WhitespaceMinimizedString The details surrounding a low quality determination in a quality control assessment. Provide notes or details regarding QC results using free text. CT value of 39. Low viral load. Low DNA concentration after amplification. +Mpox Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString TRUE The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001458 raw sequence data processing method raw_sequence_data_processing_method WhitespaceMinimizedString The names of the software and version number used for raw data processing such as removing barcodes, adapter trimming, filtering etc. Provide the software name followed by the version e.g. Trimmomatic v. 0.38, Porechop v. 0.2.3 Porechop 0.2.3 PH_RAW_SEQUENCE_METHOD raw sequence data processing method +Mpox Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString TRUE The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001459 dehosting method dehosting_method WhitespaceMinimizedString The method used to remove host reads from the pathogen sequence. Provide the name and version number of the software used to remove host reads. Nanostripper PH_DEHOSTING_METHOD dehosting method +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100831 deduplication method deduplication_method WhitespaceMinimizedString The method used to remove duplicated reads in a sequence read dataset. Provide the deduplication software name followed by the version, or a link to a tool or method. DeDup 0.12.8 +Mpox Bioinformatics and QC metrics GENEPIO:0001460 consensus sequence name consensus_sequence_name WhitespaceMinimizedString The name of the consensus sequence. Provide the name and version number of the consensus sequence. mpxvassembly3 consensus sequence name +Mpox Bioinformatics and QC metrics GENEPIO:0001461 consensus sequence filename consensus_sequence_filename WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number of the consensus sequence FASTA file. mpox123assembly.fasta consensus sequence filename +Mpox Bioinformatics and QC metrics GENEPIO:0001462 consensus sequence filepath consensus_sequence_filepath WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the consensus sequence FASTA file. /User/Documents/STILab/Data/mpox123assembly.fasta consensus sequence filepath +MpoxInternational Bioinformatics and QC metrics GENEPIO:0101715 genome sequence file name genome_sequence_file_name WhitespaceMinimizedString The name of the consensus sequence file. Provide the name and version number, with the file extension, of the processed genome sequence file e.g. a consensus sequence FASTA file or a genome assembly file. mpxvassembly.fasta consensus sequence filename +MpoxInternational Bioinformatics and QC metrics GENEPIO:0101716 genome sequence file path genome_sequence_file_path WhitespaceMinimizedString The filepath of the consensus sequence file. Provide the filepath of the genome sequence FASTA file. /User/Documents/ViralLab/Data/mpxvassembly.fasta consensus sequence filepath +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001463 consensus sequence software name consensus_sequence_software_name WhitespaceMinimizedString TRUE The name of software used to generate the consensus sequence. Provide the name of the software used to generate the consensus sequence. iVar Assembly method consensus sequence PH_CONSENSUS_SEQUENCE consensus sequence software name +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001469 consensus sequence software version consensus_sequence_software_version WhitespaceMinimizedString TRUE The version of the software used to generate the consensus sequence. Provide the version of the software used to generate the consensus sequence. 1.3 Assembly method consensus sequence PH_CONSENSUS_SEQUENCE_VERSION consensus sequence software version +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100825 sequence assembly software name sequence_assembly_software_name WhitespaceMinimizedString NullValueMenu TRUE The name of the software used to assemble a sequence. Provide the name of the software used to assemble the sequence. SPAdes Genome Assembler, Canu, wtdbg2, velvet +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100826 sequence assembly software version sequence_assembly_software_version WhitespaceMinimizedString NullValueMenu TRUE The version of the software used to assemble a sequence. Provide the version of the software used to assemble the sequence. 3.15.5 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001476 r1 fastq filename r1_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r1 FASTQ file. Provide the r1 FASTQ filename. This information aids in data management. ABC123_S1_L001_R1_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001477 r2 fastq filename r2_fastq_filename WhitespaceMinimizedString TRUE The user-specified filename of the r2 FASTQ file. Provide the r2 FASTQ filename. This information aids in data management. ABC123_S1_L001_R2_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001478 r1 fastq filepath r1_fastq_filepath WhitespaceMinimizedString The location of the r1 FASTQ file within a user's file system. Provide the filepath for the r1 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R1_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001479 r2 fastq filepath r2_fastq_filepath WhitespaceMinimizedString The location of the r2 FASTQ file within a user's file system. Provide the filepath for the r2 FASTQ file. This information aids in data management. /User/Documents/ViralLab/Data/ABC123_S1_L001_R2_001.fastq.gz +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001480 fast5 filename fast5_filename WhitespaceMinimizedString The user-specified filename of the FAST5 file. Provide the FAST5 filename. This information aids in data management. mpxv123seq.fast5 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001481 fast5 filepath fast5_filepath WhitespaceMinimizedString The location of the FAST5 file within a user's file system. Provide the filepath for the FAST5 file. This information aids in data management. /User/Documents/RespLab/Data/mpxv123seq.fast5 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100827 number of total reads number_of_total_reads Integer The total number of non-unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 423867 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100828 number of unique reads number_of_unique_reads Integer The number of unique reads generated by the sequencing process. Provide a numerical value (no need to include units). 248236 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100829 minimum post-trimming read length minimum_posttrimming_read_length Integer The threshold used as a cut-off for the minimum length of a read after trimming. Provide a numerical value (no need to include units). 150 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001474 depth of coverage value depth_of_coverage_value WhitespaceMinimizedString The average number of reads representing a given nucleotide in the reconstructed sequence. Provide value as a fold of coverage. 400x Depth of coverage depth of coverage value depth of coverage value +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001475 depth of coverage threshold depth_of_coverage_threshold WhitespaceMinimizedString The threshold used as a cut-off for the depth of coverage. Provide the threshold fold coverage. 100x depth of coverage threshold +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001482 number of base pairs sequenced number_of_base_pairs_sequenced integer 0 The number of total base pairs generated by the sequencing process. Provide a numerical value (no need to include units). 2639019 number of base pairs sequenced +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001483 consensus genome length consensus_genome_length integer 0 Size of the reconstructed genome described as the number of base pairs. Provide a numerical value (no need to include units). 197063 consensus genome length +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100846 sequence assembly length sequence_assembly_length Integer The length of the genome generated by assembling reads using a scaffold or by reference-based mapping. Provide a numerical value (no need to include units). 34272 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100937 number of contigs number_of_contigs Integer The number of contigs (contiguous sequences) in a sequence assembly. Provide a numerical value. 10 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100844 genome completeness genome_completeness WhitespaceMinimizedString The percentage of expected genes identified in the genome being sequenced. Missing genes indicate missing genomic regions (incompleteness) in the data. Provide the genome completeness as a percent (no need to include units). 85 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100938 N50 n50 Integer The length of the shortest read that, together with other reads, represents at least 50% of the nucleotides in a set of sequences. Provide the N50 value in Mb. 150 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0100830 percent Ns across total genome length percent_ns_across_total_genome_length Integer The percentage of the assembly that consists of ambiguous bases (Ns). Provide a numerical value (no need to include units). 2 +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001484 Ns per 100 kbp ns_per_100_kbp Integer The number of ambiguous bases (Ns) normalized per 100 kilobasepairs (kbp). Provide a numerical value (no need to include units). 342 +Mpox;MpoxInternational Bioinformatics and QC metrics GENEPIO:0001485 reference genome accession reference_genome_accession WhitespaceMinimizedString A persistent, unique identifier of a genome database entry. Provide the accession number of the reference genome. NC_063383.1 reference genome accession +Mpox Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString TRUE A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol +MpoxInternational Bioinformatics and QC metrics GENEPIO:0001489 bioinformatics protocol bioinformatics_protocol WhitespaceMinimizedString A description of the overall bioinformatics strategy used. Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can. This information can be provided in an SOP or protocol or pipeline/workflow. Provide the name and version number of the protocol, or a GitHub link to a pipeline or workflow. https://github.com/phac-nml/monkeypox-nf Bioinformatics Protocol PH_BIOINFORMATICS_PROTOCOL bioinformatics protocol +MpoxInternational GENEPIO:0101082 Taxonomic identification information +MpoxInternational Taxonomic identification information GENEPIO:0100832 read mapping software name read_mapping_software_name WhitespaceMinimizedString TRUE The name of the software used to map sequence reads to a reference genome or set of reference genes. Provide the name of the read mapping software. Bowtie2, BWA-MEM, TopHat +MpoxInternational Taxonomic identification information GENEPIO:0100833 read mapping software version read_mapping_software_version WhitespaceMinimizedString TRUE The version of the software used to map sequence reads to a reference genome or set of reference genes. Provide the version number of the read mapping software. 2.5.1 +MpoxInternational Taxonomic identification information GENEPIO:0100834 taxonomic reference database name taxonomic_reference_database_name WhitespaceMinimizedString TRUE The name of the taxonomic reference database used to identify the organism. Provide the name of the taxonomic reference database. NCBITaxon +MpoxInternational Taxonomic identification information GENEPIO:0100835 taxonomic reference database version taxonomic_reference_database_version WhitespaceMinimizedString TRUE The version of the taxonomic reference database used to identify the organism. Provide the version number of the taxonomic reference database. 1.3 +MpoxInternational Taxonomic identification information GENEPIO:0101074 taxonomic analysis report filename taxonomic_analysis_report_filename WhitespaceMinimizedString The filename of the report containing the results of a taxonomic analysis. Provide the filename of the report containing the results of the taxonomic analysis. MPXV_report123.doc +MpoxInternational Taxonomic identification information GENEPIO:0101075 taxonomic analysis date taxonomic_analysis_date date The date a taxonomic analysis was performed. Providing the date that an analyis was performed can help provide context for tool and reference database versions. Provide the date that the taxonomic analysis was performed in ISO 8601 format, i.e. "YYYY-MM-DD". 2024-02-01 +MpoxInternational Taxonomic identification information GENEPIO:0100836 read mapping criteria read_mapping_criteria WhitespaceMinimizedString A description of the criteria used to map reads to a reference sequence. Provide a description of the read mapping criteria. Phred score >20 +Mpox;MpoxInternational GENEPIO:0001506 Pathogen diagnostic testing pathogen_diagnostic_testing +MpoxInternational Pathogen diagnostic testing GENEPIO:0101206 assay target name 1 assay_target_name_1 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. MPX (orf B6R) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102045 assay target details 1 assay_target_details_1 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001507 gene name 1 gene_name_1 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. MPX (orf B6R) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name +MpoxInternational Pathogen diagnostic testing GENEPIO:0102041 gene symbol 1 gene_symbol_1 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg190 gene (MPOX) Gene Target 1 SUBMITTED_RESLT - Gene Target #1 gene_name_1 gene name +MpoxInternational Pathogen diagnostic testing GENEPIO:0001508 diagnostic pcr protocol 1 diagnostic_pcr_protocol_1 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. B6R (Li et al., 2006) +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001509 diagnostic pcr Ct value 1 diagnostic_pcr_ct_value_1 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the diagnostic RT-PCR test. 21 Gene Target 1 CT Value SUBMITTED_RESLT - Gene Target #1 CT Value diagnostic_PCR_CT_value_1 diagnostic pcr Ct value +MpoxInternational Pathogen diagnostic testing GENEPIO:0102038 assay target name 2 assay_target_name_2 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OVP (orf 17L) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102046 assay target details 2 assay_target_details_2 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001510 gene name 2 gene_name_2 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OVP (orf 17L) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 +MpoxInternational Pathogen diagnostic testing GENEPIO:0102042 gene symbol 2 gene_symbol_2 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg002 gene (MPOX) Gene Target 2 SUBMITTED_RESLT - Gene Target #2 gene_name_2 +MpoxInternational Pathogen diagnostic testing GENEPIO:0001511 diagnostic pcr protocol 2 diagnostic_pcr_protocol_2 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R (Li et al., 2010) assays (includes G2R_WA, C3L, and G2R_G). +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001512 diagnostic pcr Ct value 2 diagnostic_pcr_ct_value_2 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 36 Gene Target 2 CT Value SUBMITTED_RESLT - Gene Target #2 CT Value diagnostic_PCR_CT_value_2 +MpoxInternational Pathogen diagnostic testing GENEPIO:0102039 assay target name 3 assay_target_name_3 WhitespaceMinimizedString NullValueMenu The name of the assay target used in the diagnostic RT-PCR test. The specific genomic region, sequence, or variant targeted by the assay in a diagnostic test. This may include parts of a gene, non-coding regions, or other genetic elements that serve as a marker for detecting the presence of a pathogen or other relevant entities. OPHA (orf B2R) +MpoxInternational Pathogen diagnostic testing GENEPIO:0102047 assay target details 3 assay_target_details_3 WhitespaceMinimizedString Describe any details of the assay target. Provide details that are applicable to the assay used for the diagnostic test. +Mpox Pathogen diagnostic testing GENEPIO:0001513 gene name 3 gene_name_3 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. OPHA (orf B2R) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 +MpoxInternational Pathogen diagnostic testing GENEPIO:0102043 gene symbol 3 gene_symbol_3 GeneSymbolInternationalMenu NullValueMenu The gene symbol used in the diagnostic RT-PCR test. Select the abbreviated representation or standardized symbol of the gene used in the diagnostic test from the pick list. The assay target or specific primer region should be added to assay target name. opg188 gene (MPOX) Gene Target 3 SUBMITTED_RESLT - Gene Target #3 gene_name_3 +MpoxInternational Pathogen diagnostic testing GENEPIO:0001514 diagnostic pcr protocol 3 diagnostic_pcr_protocol_3 WhitespaceMinimizedString The name and version number of the protocol used for diagnostic marker amplification. The name and version number of the protocol used for carrying out a diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control. G2R_G (Li et al., 2010) assay +Mpox;MpoxInternational Pathogen diagnostic testing GENEPIO:0001515 diagnostic pcr Ct value 3 diagnostic_pcr_ct_value_3 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 19 Gene Target 3 CT Value SUBMITTED_RESLT - Gene Target #3 CT Value diagnostic_PCR_CT_value_3 +Mpox Pathogen diagnostic testing GENEPIO:0100576 gene name 4 gene_name_4 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. G2R_G (TNFR) Gene Target 4 SUBMITTED_RESLT - Gene Target #4 gene_name_4 +Mpox Pathogen diagnostic testing GENEPIO:0100577 diagnostic pcr Ct value 4 diagnostic_pcr_ct_value_4 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 27 Gene Target 4 CT Value SUBMITTED_RESLT - Gene Target #4 CT Value diagnostic_PCR_CT_value_4 +Mpox Pathogen diagnostic testing GENEPIO:0100578 gene name 5 gene_name_5 GeneNameMenu NullValueMenu The name of the gene used in the diagnostic RT-PCR test. Select the name of the gene used for the diagnostic PCR from the standardized pick list. RNAse P Gene Target 5 SUBMITTED_RESLT - Gene Target #5 gene_name_5 +Mpox Pathogen diagnostic testing GENEPIO:0100579 diagnostic pcr Ct value 5 diagnostic_pcr_ct_value_5 decimal NullValueMenu The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test. Provide the CT value of the sample from the second diagnostic RT-PCR test. 30 Gene Target 5 CT Value SUBMITTED_RESLT - Gene Target #5 CT Value diagnostic_PCR_CT_value_5 + GENEPIO:0001516 Contributor acknowledgement contributor_acknowledgement +Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001517 authors authors WhitespaceMinimizedString TRUE Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. Include the first and last names of all individuals that should be attributed, separated by a comma. Tejinder Singh, Fei Hu, Joe Blogs Authors Authors PH_SEQUENCING_AUTHORS +Mpox;MpoxInternational Contributor acknowledgement GENEPIO:0001518 DataHarmonizer provenance dataharmonizer_provenance Provenance The DataHarmonizer software and template version provenance. The current software and template version information will be automatically generated in this field after the user utilizes the "validate" function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer v1.4.3, Mpox v3.3.1 Additional Comments HC_COMMENTS \ No newline at end of file From 1a4766035eada500eefb39429cacaaad7a156a55 Mon Sep 17 00:00:00 2001 From: Damion Dooley Date: Fri, 1 Nov 2024 17:14:45 -0700 Subject: [PATCH 96/96] Fix to issue of mapping not working in multiselect case --- lib/DataHarmonizer.js | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/lib/DataHarmonizer.js b/lib/DataHarmonizer.js index fb7f38b4..020d9511 100644 --- a/lib/DataHarmonizer.js +++ b/lib/DataHarmonizer.js @@ -1757,21 +1757,21 @@ class DataHarmonizer { // if sources exist, fetch transformed Value if (field.sources) { - mappedCell.push( - self.getTransformedField(headerName, mappedCellVal, field, prefix) - ); - } else if (field.multivalued === true) { - // ISSUE: relying on semicolon delimiter in input - - for (let cellVal of mappedCellVal.split(';')) { - mappedCell.push( - self.getTransformedField(headerName, cellVal.trim(), field, prefix) - ); + if (field.multivalued === true) { //Map list of semicolon-delimited choices + // ISSUE: relying on semicolon delimiter in input + for (let cellVal of mappedCellVal.split(';')) { + mappedCell.push( self.getTransformedField(headerName, cellVal.trim(), field, prefix)); + } } - } else { + else { // Map single choice + mappedCell.push(self.getTransformedField(headerName, mappedCellVal, field, prefix)); + } + } + else { // No mapping. mappedCell.push(mappedCellVal); } } + return mappedCell.join(delimiter); }